Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 9 of 74
Found at i:2403306 original size:22 final size:20
Alignment explanation
Indices: 2403284--2403323 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2403274 TATTTATATA
2403284 AATTTCATATAAAATTTTAAT
1 AATTT-ATATAAAATTTTAAT
* *
2403305 AATTTGTATATAATTTTAA
1 AATTTATATAAAATTTTAA
2403324 ATTATGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTTATATAAAATTTTAAT
Found at i:2403875 original size:24 final size:24
Alignment explanation
Indices: 2403848--2403896 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2403838 TTTTTAAAAA
*
2403848 TTTTAAATTAGATTATTTTTATAT
1 TTTTAAATTAGAATATTTTTATAT
* * *
2403872 TTTTTATTTATAATATTTTTATAT
1 TTTTAAATTAGAATATTTTTATAT
2403896 T
1 T
2403897 ATATAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAATTAGAATATTTTTATAT
Found at i:2403887 original size:16 final size:18
Alignment explanation
Indices: 2403868--2403903 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
2403858 GATTATTTTT
2403868 ATATTTTT-TATT-TATA
1 ATATTTTTATATTATATA
2403884 ATATTTTTATATTATATA
1 ATATTTTTATATTATATA
2403902 AT
1 AT
2403904 TATATCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTATATTATATA
Found at i:2403906 original size:24 final size:25
Alignment explanation
Indices: 2403861--2403916 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2403851 TAAATTAGAT
* * *
2403861 TATTTTTATATTTTTTATTTATA-A
1 TATTTTTATATTATATAATTATACA
2403885 TATTTTTATATTATATAATTATATCA
1 TATTTTTATATTATATAATTATA-CA
2403911 TATTTT
1 TATTTT
2403917 AAATTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 20 0.74
26 7 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
TATTTTTATATTATATAATTATACA
Found at i:2424576 original size:22 final size:22
Alignment explanation
Indices: 2424538--2424590 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2424528 TTTTATGAAT
* *
2424538 TTAA-TTTGATTTATTAATTTA
1 TTAATTTTAATTTATTAATATA
*
2424559 TTAATTTTAATTTTTTAATATA
1 TTAATTTTAATTTATTAATATA
2424581 TT-ATTTTAAT
1 TTAATTTTAAT
2424591 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TTAATTTTAATTTATTAATATA
Found at i:2425449 original size:22 final size:23
Alignment explanation
Indices: 2425422--2425464 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2425412 TAATTCATTG
2425422 ATTAATT-ATCAAAT-TAATTTTA
1 ATTAATTAAT-AAATATAATTTTA
2425444 ATTAATTAATAAATATAATTT
1 ATTAATTAATAAATATAATTT
2425465 AAGAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTAATTAATAAATATAATTTTA
Found at i:2425542 original size:16 final size:16
Alignment explanation
Indices: 2425517--2425551 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2425507 TTAATTGAAT
*
2425517 TAATTAAAATATAATA
1 TAATTAAAATATAAGA
*
2425533 TAATTTAAATATAAGA
1 TAATTAAAATATAAGA
2425549 TAA
1 TAA
2425552 AATGTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TAATTAAAATATAAGA
Found at i:2428077 original size:24 final size:23
Alignment explanation
Indices: 2428042--2428088 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2428032 TATTATAAAA
* *
2428042 AATTATTTTTTAATTATTTATAT
1 AATTATTATTTAAATATTTATAT
2428065 AATTATATATTTAAATATTTATAT
1 AATTAT-TATTTAAATATTTATAT
2428089 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AATTATTATTTAAATATTTATAT
Found at i:2428174 original size:26 final size:26
Alignment explanation
Indices: 2428119--2428174 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
2428109 ATTTTGAATC
* **
2428119 AAATTAAATATAATTTATATAATATC
1 AAATTAAATATAATTTAAATAATAAA
*
2428145 AAATTAAAT-TAAATTTAAATATTAAA
1 AAATTAAATAT-AATTTAAATAATAAA
2428171 AAAT
1 AAAT
2428175 AAAAAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATTAAATATAATTTAAATAATAAA
Found at i:2428217 original size:16 final size:16
Alignment explanation
Indices: 2428177--2428224 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
2428167 TAAAAAATAA
*
2428177 AAAAATTAAATTAAAT
1 AAAAATCAAATTAAAT
* * *
2428193 TAAATTCAAATTTAAT
1 AAAAATCAAATTAAAT
*
2428209 AAAAATCAAATCAAAT
1 AAAAATCAAATTAAAT
2428225 CGAATTTGAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATCAAATTAAAT
Found at i:2439372 original size:12 final size:13
Alignment explanation
Indices: 2439355--2439383 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2439345 AATATTAATG
2439355 AATTTTTTA-TAT
1 AATTTTTTATTAT
2439367 AATTTTTTATTAT
1 AATTTTTTATTAT
2439380 AATT
1 AATT
2439384 GGATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
AATTTTTTATTAT
Found at i:2446573 original size:18 final size:18
Alignment explanation
Indices: 2446550--2446586 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2446540 TTTAGAACAC
2446550 TCATGTATTATGATATAT
1 TCATGTATTATGATATAT
2446568 TCATGTATTATGATATAT
1 TCATGTATTATGATATAT
2446586 T
1 T
2446587 TACTATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TCATGTATTATGATATAT
Found at i:2447422 original size:14 final size:15
Alignment explanation
Indices: 2447394--2447438 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
2447384 ATTATCTAAA
2447394 TAAAATATATATAAT
1 TAAAATATATATAAT
2447409 TAAAATAT-TATAAT
1 TAAAATATATATAAT
2447423 TATATAAGTATATATA
1 TA-A-AA-TATATATA
2447439 TTTTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.31
15 9 0.35
16 2 0.08
17 3 0.12
18 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
TAAAATATATATAAT
Found at i:2454572 original size:3 final size:3
Alignment explanation
Indices: 2454564--2454592 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2454554 ATTTCAAGTA
2454564 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2454593 ATTTATTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2468087 original size:11 final size:11
Alignment explanation
Indices: 2468071--2468096 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2468061 TTTAAATCTC
2468071 ATATTTATTAG
1 ATATTTATTAG
2468082 ATATTTATTAG
1 ATATTTATTAG
2468093 ATAT
1 ATAT
2468097 CGATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
ATATTTATTAG
Found at i:2469263 original size:2 final size:2
Alignment explanation
Indices: 2469256--2469280 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2469246 AAAAAGGTCC
2469256 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2469281 ATGCGATGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2479097 original size:2 final size:2
Alignment explanation
Indices: 2479084--2479123 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2479074 AGAAATGGGA
* *
2479084 AT AT AA AT AT AT AT AT AT AT TT 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 AT AT
2479124 CACAAGAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 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:2484514 original size:19 final size:19
Alignment explanation
Indices: 2484490--2484535 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2484480 TCACACATTA
* * *
2484490 TTTTTATTTTTTATTATAT
1 TTTTTATATTTAATAATAT
*
2484509 TTTTTATATTTAATAATTT
1 TTTTTATATTTAATAATAT
2484528 TTTTTATA
1 TTTTTATA
2484536 AAACTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATATTTAATAATAT
Found at i:2485106 original size:9 final size:10
Alignment explanation
Indices: 2485092--2485135 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
2485082 TTGGAGCTTT
2485092 TTTTTTTA-A
1 TTTTTTTATA
2485101 TTTTTTTATA
1 TTTTTTTATA
2485111 TTTTTTTCA-A
1 TTTTTTT-ATA
2485121 -TTTTTTATA
1 TTTTTTTATA
2485130 TTTTTT
1 TTTTTT
2485136 ATTTGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.03
9 15 0.48
10 14 0.45
11 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:2485116 original size:19 final size:19
Alignment explanation
Indices: 2485091--2485135 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
2485081 ATTGGAGCTT
*
2485091 TTTTTTTTAATTTTTTTATA
1 TTTTTTTCAA-TTTTTTATA
2485111 TTTTTTTCAATTTTTTATA
1 TTTTTTTCAATTTTTTATA
2485130 TTTTTT
1 TTTTTT
2485136 ATTTGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTCAATTTTTTATA
Found at i:2485257 original size:17 final size:17
Alignment explanation
Indices: 2485227--2485261 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2485217 ATTTTTAATT
*
2485227 AAATAAAATTAATAAAA
1 AAATAAAATGAATAAAA
*
2485244 AAATACAATGAATAAAA
1 AAATAAAATGAATAAAA
2485261 A
1 A
2485262 TGGCAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAAATGAATAAAA
Found at i:2487748 original size:28 final size:29
Alignment explanation
Indices: 2487698--2487760 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
2487688 TAATAAAATA
2487698 TTTAATATAATATTTAAATTTAAAAATTT
1 TTTAATATAATATTTAAATTTAAAAATTT
* *
2487727 TTTAATGTAATATTTGAA-TTAAAAATTT
1 TTTAATATAATATTTAAATTTAAAAATTT
*
2487755 ATTAAT
1 TTTAAT
2487761 TATTATACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTAATATAATATTTAAATTTAAAAATTT
Found at i:2493703 original size:15 final size:15
Alignment explanation
Indices: 2493656--2493701 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
2493646 ATTAAGTTAA
* * *
2493656 AAATAATTTTTTAAT
1 AAATAAATTTATATT
2493671 AAA-AAATTTATATT
1 AAATAAATTTATATT
2493685 AAATAAATTTA-ATT
1 AAATAAATTTATATT
2493699 AAA
1 AAA
2493702 ATTGTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATAAATTTATATT
Found at i:2494333 original size:6 final size:6
Alignment explanation
Indices: 2494313--2494345 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2494303 TAAAACGGAA
2494313 AGAAAG A-AAAG -GAAAG AGAAAG AGAAAG AGAAA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGAAAG AGAAA
2494346 CGTGTTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 8 0.32
6 17 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:2498451 original size:16 final size:17
Alignment explanation
Indices: 2498425--2498459 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2498415 TTTATAAAAA
2498425 AAAATTCAATAAAAATT
1 AAAATTCAATAAAAATT
*
2498442 AAAATT-AATAATAATT
1 AAAATTCAATAAAAATT
2498458 AA
1 AA
2498460 TATATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTCAATAAAAATT
Found at i:2498641 original size:21 final size:21
Alignment explanation
Indices: 2498591--2498641 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2498581 AATATTCATC
* * *
2498591 AAATTTAAATAATTTTTTTTT
1 AAATTTTATTAATTTTTTCTT
* *
2498612 ATATATTATTAATTTTTTCTT
1 AAATTTTATTAATTTTTTCTT
2498633 AAATTTTAT
1 AAATTTTAT
2498642 CGATCATTTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
AAATTTTATTAATTTTTTCTT
Found at i:2506537 original size:12 final size:12
Alignment explanation
Indices: 2506522--2506551 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2506512 GTAAAAAGGC
2506522 AGAAAAAAAGAA
1 AGAAAAAAAGAA
*
2506534 AGAAAGAAAGAA
1 AGAAAAAAAGAA
2506546 AGAAAA
1 AGAAAA
2506552 GAACAAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:2507195 original size:3 final size:3
Alignment explanation
Indices: 2507187--2507221 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2507177 ACAATCTCCT
2507187 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2507222 CATAATCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2509063 original size:2 final size:2
Alignment explanation
Indices: 2509056--2509095 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2509046 TCAGCAAGTT
2509056 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
2509096 GAGTAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2531942 original size:20 final size:19
Alignment explanation
Indices: 2531897--2531949 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
2531887 AACGATACAG
2531897 TTATTATATTAATAAAATAA
1 TTATT-TATTAATAAAATAA
*
2531917 TAATTTATT-ATATAAATATA
1 TTATTTATTAATA-AAATA-A
*
2531937 TTATTTATAAATA
1 TTATTTATTAATA
2531950 TTATATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 3 0.11
19 9 0.33
20 12 0.44
21 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATTTATTAATAAAATAA
Found at i:2531969 original size:15 final size:15
Alignment explanation
Indices: 2531901--2531973 Score: 67
Period size: 15 Copynumber: 4.5 Consensus size: 15
2531891 ATACAGTTAT
2531901 TATATTAATAAAATAA
1 TATATTAAT-AAATAA
2531917 TAATTTATTATATAAAT-A
1 T-A--TATTA-ATAAATAA
* *
2531935 TATTATTTATAAATAT
1 TA-TATTAATAAATAA
2531951 TATATTAATAAATAA
1 TATATTAATAAATAA
2531966 TATATTAA
1 TATATTAA
2531974 CAATATTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
15 25 0.52
16 8 0.17
17 2 0.04
18 2 0.04
19 9 0.19
20 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATTAATAAATAA
Found at i:2531969 original size:24 final size:24
Alignment explanation
Indices: 2531898--2531969 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
2531888 ACGATACAGT
**
2531898 TATTATATTAATAAAATAATA-ATT
1 TATTATATTAAT-AAATAATATAAA
* * *
2531922 TATTATATAAATATATTATTTATAAA
1 TATTATATTAATA-AATA-ATATAAA
2531948 TATTATATTAATAAATAATATA
1 TATTATATTAATAAATAATATA
2531970 TTAACAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
23 1 0.03
24 18 0.49
25 5 0.14
26 13 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTATATTAATAAATAATATAAA
Found at i:2531987 original size:50 final size:50
Alignment explanation
Indices: 2531898--2531996 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
2531888 ACGATACAGT
* ** *
2531898 TATTATATTAATAAAATAATAATTTATTATATAAATATATTATTTATAAA
1 TATTATATTAATAAAATAATAATTAACAATATAAATATATTATTAATAAA
* *
2531948 TATTATATTAAT-AAATAATATATTAACAATATTATTATATTATTAATAA
1 TATTATATTAATAAAATAATA-ATTAACAATATAAATATATTATTAATAA
2531997 CAAATTGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 8 0.19
50 34 0.81
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (50 bp):
TATTATATTAATAAAATAATAATTAACAATATAAATATATTATTAATAAA
Found at i:2533069 original size:33 final size:33
Alignment explanation
Indices: 2533028--2533098 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
2533018 TATTATATAT
*
2533028 AATT-TTAATGTAAAACATAATATAAATACATA
1 AATTATTAATATAAAACATAATATAAATACATA
*** *
2533060 AATTATTAATATTTTACATAATATAAATATATA
1 AATTATTAATATAAAACATAATATAAATACATA
2533093 AATTAT
1 AATTAT
2533099 CATATTTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (33 bp):
AATTATTAATATAAAACATAATATAAATACATA
Found at i:2565110 original size:21 final size:20
Alignment explanation
Indices: 2565076--2565114 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2565066 GGGAGAGAAA
**
2565076 AAAGAATGTTTAAGTGTTAAC
1 AAAGAATGAATAAG-GTTAAC
2565097 AAAGAATGAATAAGGTTA
1 AAAGAATGAATAAGGTTA
2565115 CTATGTACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.28
Consensus pattern (20 bp):
AAAGAATGAATAAGGTTAAC
Found at i:2573873 original size:16 final size:16
Alignment explanation
Indices: 2573854--2573884 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2573844 ATATATATAT
2573854 ATACACACACACATAC
1 ATACACACACACATAC
*
2573870 ATACACACACGCATA
1 ATACACACACACATA
2573885 GATGTATCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.35, G:0.03, T:0.13
Consensus pattern (16 bp):
ATACACACACACATAC
Found at i:2594178 original size:27 final size:27
Alignment explanation
Indices: 2594140--2594195 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
2594130 CTTTCATACA
2594140 GCCGACCCCTGAGTTATGGGTTATAAG
1 GCCGACCCCTGAGTTATGGGTTATAAG
2594167 GCCGACCCCTGAGTTATGGGTTATAAG
1 GCCGACCCCTGAGTTATGGGTTATAAG
2594194 GC
1 GC
2594196 TTAGTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.25
Consensus pattern (27 bp):
GCCGACCCCTGAGTTATGGGTTATAAG
Found at i:2595137 original size:2 final size:2
Alignment explanation
Indices: 2595132--2595157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2595122 ATACAATTAT
2595132 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
2595158 ACTTTTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2595479 original size:2 final size:2
Alignment explanation
Indices: 2595472--2595519 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2595462 GAATTGTTAA
2595472 AT AT AT 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 AT AT AT
2595514 AT AT AT
1 AT AT AT
2595520 CCTCTGTGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2598830 original size:3 final size:3
Alignment explanation
Indices: 2598779--2598813 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2598769 TTTTAAATCT
2598779 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2598814 TATTTCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2607739 original size:2 final size:2
Alignment explanation
Indices: 2607732--2607761 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2607722 TCCTCATGAG
2607732 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
2607762 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2608469 original size:25 final size:24
Alignment explanation
Indices: 2608423--2608469 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2608413 TTTTATTTAT
* **
2608423 TTAAAAACAAATAAAATTAAAAAA
1 TTAAAAAAAAATAAAAGGAAAAAA
2608447 TTAAAAATAAAATAAAAGGAAAA
1 TTAAAAA-AAAATAAAAGGAAAA
2608470 GAAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (24 bp):
TTAAAAAAAAATAAAAGGAAAAAA
Found at i:2612887 original size:33 final size:34
Alignment explanation
Indices: 2612844--2612954 Score: 127
Period size: 34 Copynumber: 3.3 Consensus size: 34
2612834 TTTGGAGTTT
2612844 TATAACTTTTTGAAAATAAATTTATGAAAAATCA
1 TATAACTTTTTGAAAATAAATTTATGAAAAATCA
* * * *
2612878 TATAATTTTTTGAAAATTAATTTCT-AAAAATTA
1 TATAACTTTTTGAAAATAAATTTATGAAAAATCA
* * *
2612911 TA-AACCTTTTTAAAAATGAATTTTTGAAAAATCA
1 TATAA-CTTTTTGAAAATAAATTTATGAAAAATCA
*
2612945 TATGACTTTT
1 TATAACTTTT
2612955 CAAAAATCTA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 2 0.03
33 25 0.39
34 36 0.56
35 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (34 bp):
TATAACTTTTTGAAAATAAATTTATGAAAAATCA
Found at i:2613106 original size:68 final size:68
Alignment explanation
Indices: 2613034--2613162 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 68
2613024 TCATCTCCTG
* *
2613034 AAAA-TGAATTTTCAAAAAAGTCATTTGATTTTTTGAAAATTTATTTCTGAAAAAGTTTATATTA
1 AAAATTGAATTTTCAAAAAA-TCATATAATTTTTTGAAAATTTATTTCTGAAAAAGTTTATATTA
2613098 TTTC
65 TTTC
** * * * * *
2613102 AAAATTTTATTTTCGATAAATTATATAATTTTTTTAAAATTTATTTTTGAAAAAGTTTATA
1 AAAATTGAATTTTCAAAAAATCATATAATTTTTTGAAAATTTATTTCTGAAAAAGTTTATA
2613163 ACTTTTTATA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 40 0.78
69 11 0.22
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (68 bp):
AAAATTGAATTTTCAAAAAATCATATAATTTTTTGAAAATTTATTTCTGAAAAAGTTTATATTAT
TTC
Found at i:2613163 original size:34 final size:34
Alignment explanation
Indices: 2613061--2613182 Score: 124
Period size: 34 Copynumber: 3.6 Consensus size: 34
2613051 AAGTCATTTG
* *
2613061 ATTTTTTGAAAATTTATTTCTGAAAAAGTTTAT-
1 ATTTTTTTAAAATTTATTTTTGAAAAAGTTTATA
* * * *
2613094 ATTATTTCAAAATTTTATTTTCGATAAA-TTATATA
1 ATTTTTTTAAAA-TTTATTTTTGAAAAAGTT-TATA
2613129 ATTTTTTTAAAATTTATTTTTGAAAAAGTTTATA
1 ATTTTTTTAAAATTTATTTTTGAAAAAGTTTATA
* *
2613163 A-CTTTTTATAAATCTATTTT
1 ATTTTTTTA-AAATTTATTTT
2613183 CAGAAACTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
33 18 0.25
34 43 0.59
35 12 0.16
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (34 bp):
ATTTTTTTAAAATTTATTTTTGAAAAAGTTTATA
Found at i:2614176 original size:52 final size:51
Alignment explanation
Indices: 2614020--2614176 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 51
2614010 TATAACCATA
* * * *
2614020 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCACT-TTCTCTTAGAATTCTTCTCTTGTAAGT
* * **
2614072 CAAACTTGCCTATTAAGAATCACTTTCCTTTTAAAATTCTTCTCTTACAAGT
1 CAAACTTGCCTATTAAGAATCACTTT-CTCTTAGAATTCTTCTCTTGTAAGT
* * * *
2614124 CAAACTTACCTATTAAGAATCTTCTTTCTCTTGGAATTCTTCTTTTGTAAGT
1 CAAACTTGCCTATTAAGAATC-ACTTTCTCTTAGAATTCTTCTCTTGTAAGT
2614176 C
1 C
2614177 TTTTTGTCCA
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
51 1 0.01
52 82 0.94
53 4 0.05
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCACTTTCTCTTAGAATTCTTCTCTTGTAAGT
Found at i:2615132 original size:52 final size:52
Alignment explanation
Indices: 2615037--2615193 Score: 181
Period size: 52 Copynumber: 3.0 Consensus size: 52
2615027 TATAATCATA
* * *
2615037 CAAACTTGCCCATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCACTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * * *
2615089 CAAACTTGCCTATTAAGAATCACTTTCCTTTTATAATTTTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCACTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * **
2615141 CAAACTTACCTATTAAGAATC-CTCTTTCTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCACTC-TCCTCTTAGAATTCTTCTCCTGCAAGT
2615193 C
1 C
2615194 TTCTTGTCCG
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCACTCTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:2615249 original size:11 final size:11
Alignment explanation
Indices: 2615218--2615249 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2615208 GCAATATCTG
*
2615218 ACAAATCTCAA
1 ACAAATCTCTA
2615229 ACAAATCTCTA
1 ACAAATCTCTA
2615240 ACAAATCTCT
1 ACAAATCTCT
2615250 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:2619105 original size:16 final size:16
Alignment explanation
Indices: 2619084--2619122 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2619074 CTTGGAAGTT
*
2619084 GGAATCACATCTGGGG
1 GGAATCACATCTAGGG
*
2619100 GGAATCATATCTAGGG
1 GGAATCACATCTAGGG
*
2619116 GAAATCA
1 GGAATCA
2619123 AATAAACCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (16 bp):
GGAATCACATCTAGGG
Found at i:2623027 original size:30 final size:29
Alignment explanation
Indices: 2622974--2623034 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
2622964 ATAAGTTTTG
* *
2622974 ATATTTTTATTATATTCAAATAAATCCTT
1 ATATTTTGATTACATTCAAATAAATCCTT
*
2623003 ATATTTTGATTTACATTTAAATAAATCCTT
1 ATATTTTGA-TTACATTCAAATAAATCCTT
2623033 AT
1 AT
2623035 TTCACATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATTTTGATTACATTCAAATAAATCCTT
Found at i:2623091 original size:30 final size:30
Alignment explanation
Indices: 2623057--2623195 Score: 145
Period size: 30 Copynumber: 4.6 Consensus size: 30
2623047 AACAATTTAT
* * *
2623057 ATTAAAAACTTATGTAAAAATAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
*
2623087 ATTAAAAATTTTATTTAAATACAAATTAAAA
1 ATTAAAAA-TTTATTTAAATATAAATTAAAA
* * *
2623118 ATTAAAAGTTTATTTAAGTGTAAATTAAAA
1 ATTAAAAATTTATTTAAATATAAATTAAAA
* *
2623148 ATTAAAAATTTATTTAAGTA-AAGTTATAAA
1 ATTAAAAATTTATTTAAATATAAATTA-AAA
* *
2623178 ATTTAAAACTTTTTTTAA
1 A-TTAAAAATTTATTTAA
2623196 TTATTTTAGC
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
29 5 0.05
30 49 0.53
31 39 0.42
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (30 bp):
ATTAAAAATTTATTTAAATATAAATTAAAA
Found at i:2623123 original size:61 final size:60
Alignment explanation
Indices: 2623057--2623188 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 60
2623047 AACAATTTAT
2623057 ATTAAAAACTTATGTAAAAATAAATTAAAAATTAAAAATTTTATTTAAATACAAATTA-AAA
1 ATTAAAAACTTATGTAAAAATAAATTAAAAATTAAAAA-TTTATTTAAATA-AAATTATAAA
** * *** * *
2623118 ATTAAAAGTTTATTTAAGTGTAAATTAAAAATTAAAAATTTATTTAAGTAAAGTTATAAA
1 ATTAAAAACTTATGTAAAAATAAATTAAAAATTAAAAATTTATTTAAATAAAATTATAAA
*
2623178 ATTTAAAACTT
1 ATTAAAAACTT
2623189 TTTTTAATTA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 5 0.08
60 22 0.37
61 32 0.54
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (60 bp):
ATTAAAAACTTATGTAAAAATAAATTAAAAATTAAAAATTTATTTAAATAAAATTATAAA
Found at i:2623195 original size:61 final size:61
Alignment explanation
Indices: 2623077--2623195 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
2623067 TATGTAAAAA
*
2623077 TAAATTAAAAATTAAAAATTTTATTTAAATACAAATTAAAAATTAAAAGTTTATTTAAGTG
1 TAAATTAAAAATTAAAAATTTTATTTAAATACAAATTAAAAATTAAAACTTTATTTAAGTG
* * *
2623138 TAAATTAAAAATTAAAAA-TTTATTTAAGTA-AAGTTATAAAATTTAAAACTTTTTTTAA
1 TAAATTAAAAATTAAAAATTTTATTTAAATACAAATTA-AAAA-TTAAAACTTTATTTAA
2623196 TTATTTTAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
59 5 0.10
60 15 0.29
61 32 0.62
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (61 bp):
TAAATTAAAAATTAAAAATTTTATTTAAATACAAATTAAAAATTAAAACTTTATTTAAGTG
Found at i:2624324 original size:36 final size:35
Alignment explanation
Indices: 2624281--2624357 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
2624271 TAATCATTAA
*
2624281 ATAAAAAT-ATATGTATAA-ATTTAAATTTTAAATTT
1 ATAAAAATCAT-TGTATAATA-TTAAAATTTAAATTT
**
2624316 ATGAAAAATCATTGTATTGTATTAAAATTTAAATTT
1 AT-AAAAATCATTGTATAATATTAAAATTTAAATTT
2624352 ATAAAA
1 ATAAAA
2624358 GAAAGCTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 6 0.17
36 27 0.75
37 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (35 bp):
ATAAAAATCATTGTATAATATTAAAATTTAAATTT
Found at i:2628957 original size:12 final size:12
Alignment explanation
Indices: 2628926--2628963 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
2628916 TGAAAAATTT
2628926 TTTTAA-AAAAA
1 TTTTAATAAAAA
2628937 TGGTTTAATAAAAA
1 T--TTTAATAAAAA
2628951 TTTTAATAAAAA
1 TTTTAATAAAAA
2628963 T
1 T
2628964 CTAAATAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.04
12 12 0.50
13 5 0.21
14 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (12 bp):
TTTTAATAAAAA
Found at i:2629206 original size:13 final size:13
Alignment explanation
Indices: 2629188--2629212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2629178 TAATCTATCA
2629188 AATTTAATTTTTG
1 AATTTAATTTTTG
2629201 AATTTAATTTTT
1 AATTTAATTTTT
2629213 ATTAATAGTT
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
AATTTAATTTTTG
Found at i:2629493 original size:18 final size:19
Alignment explanation
Indices: 2629472--2629511 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2629462 ATTTTTAAAT
2629472 AAAAAAAAAGA-AAAAGAA
1 AAAAAAAAAGACAAAAGAA
* *
2629490 AAAAAGAAAGACAAACGAA
1 AAAAAAAAAGACAAAAGAA
2629509 AAA
1 AAA
2629512 TCCAAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGACAAAAGAA
Found at i:2630655 original size:17 final size:16
Alignment explanation
Indices: 2630628--2630664 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
2630618 TTTTAATAAT
2630628 AATAAATAATAATTAA
1 AATAAATAATAATTAA
2630644 AATAAGATAATAATTAA
1 AATAA-ATAATAATTAA
2630661 AATA
1 AATA
2630665 TATATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AATAAATAATAATTAA
Found at i:2631154 original size:58 final size:59
Alignment explanation
Indices: 2631085--2631205 Score: 210
Period size: 59 Copynumber: 2.1 Consensus size: 59
2631075 GATTAATAAA
*
2631085 TAAAAAGTATAATAATAAA-TTGAGATCTTAAA-ATAAACAGTGACACCTAAACTCTGTC
1 TAAAAAGTATAATAATAAATTTG-GATCTTAAATATAAACAGTGACACCTAAACTCTGCC
2631143 TAAAAAGTATAATAATAAATTTGGATCTTAAATATAAACAGTGACACCTAAACTCTGCC
1 TAAAAAGTATAATAATAAATTTGGATCTTAAATATAAACAGTGACACCTAAACTCTGCC
2631202 TAAA
1 TAAA
2631206 TGTTGGAGAG
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
58 28 0.47
59 32 0.53
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (59 bp):
TAAAAAGTATAATAATAAATTTGGATCTTAAATATAAACAGTGACACCTAAACTCTGCC
Found at i:2634841 original size:29 final size:28
Alignment explanation
Indices: 2634809--2634880 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
2634799 CAATAAAATA
*
2634809 TTTAATAAAATAATTAAATTTTAAAATTT
1 TTTAATAAAATAATTAAATTAT-AAATTT
* *
2634838 TTTAATATAATATTTAAATTATAAATTT
1 TTTAATAAAATAATTAAATTATAAATTT
* *
2634866 ATTAATTAAAGTAAT
1 TTTAA-TAAAATAAT
2634881 ATGTATCTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TTTAATAAAATAATTAAATTATAAATTT
Found at i:2634976 original size:20 final size:21
Alignment explanation
Indices: 2634953--2634991 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2634943 TAATTATCAG
*
2634953 ATTAATAATTTA-AAAATTAT
1 ATTAAAAATTTATAAAATTAT
2634973 ATTAAAAATTTATAAAATT
1 ATTAAAAATTTATAAAATT
2634992 TAAACATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAAAAATTTATAAAATTAT
Found at i:2635717 original size:38 final size:38
Alignment explanation
Indices: 2635662--2635761 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 38
2635652 TCTATGTATG
** *
2635662 AATAAATTTTATTATATTTATAATTTATTTATTAAA-TT
1 AATAAATTTTAAAATATTTATAA-TAATTTATTAAATTT
2635700 AATAAATTTTAAAATATTATTTATAATAATTTATTAAATTT
1 AATAAATTTT-AAA-A-TATTTATAATAATTTATTAAATTT
** *
2635741 AATAAATAATAAAATAATTAT
1 AATAAATTTTAAAATATTTAT
2635762 TCATCAAACT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
38 16 0.31
39 2 0.04
40 15 0.29
41 19 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
AATAAATTTTAAAATATTTATAATAATTTATTAAATTT
Found at i:2635743 original size:41 final size:42
Alignment explanation
Indices: 2635676--2635762 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
2635666 AATTTTATTA
* **
2635676 TATTTATAATTTATTTATTAAATTAATAAATTTTAAAAT-AT
1 TATTTATAATTAATTTATTAAATTAATAAATAATAAAATAAT
2635717 TATTTATAA-TAATTTATTAAATTTAATAAATAATAAAATAAT
1 TATTTATAATTAATTTATTAAA-TTAATAAATAATAAAATAAT
2635759 TATT
1 TATT
2635763 CATCAAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
40 11 0.27
41 24 0.59
42 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (42 bp):
TATTTATAATTAATTTATTAAATTAATAAATAATAAAATAAT
Found at i:2635957 original size:24 final size:24
Alignment explanation
Indices: 2635923--2635969 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2635913 GAATTGAAAA
* *
2635923 TAATTATAAAAGTTATAATAATTG
1 TAATTAAAAAAATTATAATAATTG
*
2635947 TAATTAAAAAAATTATTATAATT
1 TAATTAAAAAAATTATAATAATT
2635970 ATTTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TAATTAAAAAAATTATAATAATTG
Found at i:2646436 original size:2 final size:2
Alignment explanation
Indices: 2646431--2646464 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2646421 ACACACACAC
2646431 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
2646465 CAGTCACTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2654263 original size:4 final size:4
Alignment explanation
Indices: 2654254--2654286 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
2654244 ACTCACTATA
*
2654254 TATG TATG TATG TATG TATG TATG TATC TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG T
2654287 GTATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2655661 original size:18 final size:20
Alignment explanation
Indices: 2655620--2655661 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2655610 AAGATTCGTT
* *
2655620 ATAATATTCTTTTTTTAACT
1 ATAATATTCTTTTTGTAACA
2655640 ATAATATTC-TTTTGTAA-A
1 ATAATATTCTTTTTGTAACA
2655658 ATAA
1 ATAA
2655662 CATATAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAATATTCTTTTTGTAACA
Found at i:2662049 original size:17 final size:18
Alignment explanation
Indices: 2662017--2662050 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2662007 CTCAAAGCCA
2662017 TATTTTCTTCTTTCTTAC
1 TATTTTCTTCTTTCTTAC
*
2662035 TATTTTGTT-TTTCTTA
1 TATTTTCTTCTTTCTTA
2662051 AATCTACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.71
Consensus pattern (18 bp):
TATTTTCTTCTTTCTTAC
Found at i:2678120 original size:17 final size:17
Alignment explanation
Indices: 2678082--2678121 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2678072 ATTTTTATTT
* *
2678082 TATAAAAATTTAAAAAA
1 TATATAAATTAAAAAAA
2678099 TATATAAATTAAAAAAA
1 TATATAAATTAAAAAAA
2678116 TATATA
1 TATATA
2678122 TTTTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATATAAATTAAAAAAA
Found at i:2678144 original size:11 final size:12
Alignment explanation
Indices: 2678120--2678157 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
2678110 AAAAAATATA
2678120 TATTTTTTGATT
1 TATTTTTTGATT
*
2678132 TATTTTTT-TTT
1 TATTTTTTGATT
2678143 TATTTTTTGCATT
1 TATTTTTTG-ATT
2678156 TA
1 TA
2678158 AAATTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 8 0.36
13 4 0.18
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (12 bp):
TATTTTTTGATT
Found at i:2678254 original size:18 final size:20
Alignment explanation
Indices: 2678220--2678256 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2678210 GATCAAAATT
2678220 AAATCAAATATTATAATTTC
1 AAATCAAATATTATAATTTC
2678240 AAATCAAAT-TT-TAATTT
1 AAATCAAATATTATAATTT
2678257 TTTCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATCAAATATTATAATTTC
Found at i:2686665 original size:18 final size:19
Alignment explanation
Indices: 2686642--2686683 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
2686632 ATAATTTGAT
2686642 TTTAATTGAA-TTAATTTA
1 TTTAATTGAATTTAATTTA
2686660 TTTAA-TGAATTTAATTTA
1 TTTAATTGAATTTAATTTA
*
2686678 ATTAAT
1 TTTAAT
2686684 CGATCGATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTAATTGAATTTAATTTA
Found at i:2687067 original size:20 final size:20
Alignment explanation
Indices: 2686995--2687067 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
2686985 TTGATTAATT
2686995 TTTAAAATTAAA-AATTTAA
1 TTTAAAATTAAATAATTTAA
*
2687014 TTTAATTAATAAAAATAATTTAA
1 TTTAA--AAT-TAAATAATTTAA
**
2687037 TTTAATTTTAAATAATTTAA
1 TTTAAAATTAAATAATTTAA
2687057 TTTAAAATTAA
1 TTTAAAATTAA
2687068 TTAAACCAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 5 0.11
20 20 0.45
21 4 0.09
22 3 0.07
23 12 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAATTAAATAATTTAA
Found at i:2687071 original size:15 final size:16
Alignment explanation
Indices: 2687033--2687069 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2687023 TAAAAATAAT
*
2687033 TTAATTTAATTTTAAA
1 TTAATTTAATTTAAAA
2687049 -TAATTTAATTTAAAA
1 TTAATTTAATTTAAAA
2687064 TTAATT
1 TTAATT
2687070 AAACCAACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATTTAATTTAAAA
Found at i:2688182 original size:22 final size:23
Alignment explanation
Indices: 2688157--2688199 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2688147 AATTGATTAG
2688157 TTGATTATC-AAATTAATTTTAA
1 TTGATTATCAAAATTAATTTTAA
*
2688179 TTGATTATCAAAATTTATTTT
1 TTGATTATCAAAATTAATTTT
2688200 GAAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (23 bp):
TTGATTATCAAAATTAATTTTAA
Found at i:2688418 original size:12 final size:12
Alignment explanation
Indices: 2688401--2688426 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2688391 TAACAAATAA
2688401 AAAATATAATTT
1 AAAATATAATTT
2688413 AAAATATAATTT
1 AAAATATAATTT
2688425 AA
1 AA
2688427 TTTAACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATATAATTT
Found at i:2708295 original size:133 final size:133
Alignment explanation
Indices: 2708057--2708323 Score: 498
Period size: 133 Copynumber: 2.0 Consensus size: 133
2708047 GGCATTTTAT
*
2708057 CATCAATTTTTGCCTACTTTTTCTTCTGCTTCGATTTGGGCCTTGACTTCAACTTGGGTCTCTTT
1 CATCAATTTTTGCCTACCTTTTCTTCTGCTTCGATTTGGGCCTTGACTTCAACTTGGGTCTCTTT
2708122 TCTCTCTCGCTAACAACACTATTTTGACCTGACCTCTTCACTTTCTCACTTGATTTTACCCTCAA
66 TCTCTCTCGCTAACAACACTATTTTGACCTGACCTCTTCACTTTCTCACTTGATTTTACCCTCAA
2708187 CTC
131 CTC
* *
2708190 CATCAATTTTTGCCTTCCTTTTCTTCTGCTTCGATTTGGGCCTTGACTTCGACTTGGGTCTCTTT
1 CATCAATTTTTGCCTACCTTTTCTTCTGCTTCGATTTGGGCCTTGACTTCAACTTGGGTCTCTTT
*
2708255 TCTCTCTCGCTAACAACACTATTTTGAGCTGACCTCTTCACTTTCTCACTTGATTTTACCCTCAA
66 TCTCTCTCGCTAACAACACTATTTTGACCTGACCTCTTCACTTTCTCACTTGATTTTACCCTCAA
2708320 CTC
131 CTC
2708323 C
1 C
2708324 CATTTTCCTA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 130 1.00
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (133 bp):
CATCAATTTTTGCCTACCTTTTCTTCTGCTTCGATTTGGGCCTTGACTTCAACTTGGGTCTCTTT
TCTCTCTCGCTAACAACACTATTTTGACCTGACCTCTTCACTTTCTCACTTGATTTTACCCTCAA
CTC
Found at i:2713442 original size:46 final size:46
Alignment explanation
Indices: 2713392--2713482 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
2713382 TACACTGAAT
*
2713392 AAAAAAGAGGTCTCGCAAAATTCTGTATACTGAAGAAAAAGAAAAA
1 AAAAAAGAGGTCTCGCAAAATTCTGTACACTGAAGAAAAAGAAAAA
* * **
2713438 AAAAAGGAGGTCTTGTTAAATTCTGTACACTGAAGAAAAAGAAAA
1 AAAAAAGAGGTCTCGCAAAATTCTGTACACTGAAGAAAAAGAAAA
2713483 GAGAAGAGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.20
Consensus pattern (46 bp):
AAAAAAGAGGTCTCGCAAAATTCTGTACACTGAAGAAAAAGAAAAA
Found at i:2717541 original size:24 final size:24
Alignment explanation
Indices: 2717500--2717547 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2717490 TGATGTGGAT
** * *
2717500 TTTACAAATGCATGTTGCTTATAA
1 TTTACAAATAAATATTGCATATAA
2717524 TTTACAAATAAATATTGCATATAA
1 TTTACAAATAAATATTGCATATAA
2717548 GCAAATGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (24 bp):
TTTACAAATAAATATTGCATATAA
Found at i:2720469 original size:2 final size:2
Alignment explanation
Indices: 2720464--2720489 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2720454 CGCACACATA
2720464 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2720490 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2720494 original size:2 final size:2
Alignment explanation
Indices: 2720489--2720520 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2720479 TCTCTCTCTC
2720489 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
2720521 GCCTGATTTA
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):
TA
Found at i:2721625 original size:71 final size:72
Alignment explanation
Indices: 2721508--2721649 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 72
2721498 AGCGGAGTCG
* *
2721508 CTCATAATTTCTTTTTGTTTTTGCCTCAGAGTGATAGTCCACCATCGTTCATTGCCTAAAACATA
1 CTCATAACTTCTTTTTGTTTTTGCCTCAGAGTGATAGTCCACCATCGTTCATTGCCAAAAACATA
2721573 TACATTA
66 TACATTA
* *
2721580 CTCATAACTTCTTTTTG-TTTTGCCTCAGATTGATAGTCCTCCATCGTTCATTGCCAAAAACATA
1 CTCATAACTTCTTTTTGTTTTTGCCTCAGAGTGATAGTCCACCATCGTTCATTGCCAAAAACATA
2721644 TACATT
66 TACATT
2721650 GCACTAGCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 50 0.76
72 16 0.24
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (72 bp):
CTCATAACTTCTTTTTGTTTTTGCCTCAGAGTGATAGTCCACCATCGTTCATTGCCAAAAACATA
TACATTA
Found at i:2721718 original size:94 final size:94
Alignment explanation
Indices: 2721590--2721774 Score: 309
Period size: 94 Copynumber: 2.0 Consensus size: 94
2721580 CTCATAACTT
* * * *
2721590 CTTTTTGTTTTGCCTCAGATTGATAGTCCTCCATCGTTCATTGCCAAAAACATATACATTGCACT
1 CTTTTTGTCTTGCCTCAGATTGACAGTCCCCCATCGTTCATTGCCAAAAACATATACATTACACT
2721655 AGCAAAATCG-AACTCCTGCTTTTTTAATG
66 AGCAAAATCGAAAC-CCTGCTTTTTTAATG
*
2721684 CTTTTTGTCTTGCCTCAGATTGACAGTCCCCCATCGTTCATTGCCTAAAACATATACATTACACT
1 CTTTTTGTCTTGCCTCAGATTGACAGTCCCCCATCGTTCATTGCCAAAAACATATACATTACACT
2721749 AGCAAAATCGAAACCCTGCTTTTTTA
66 AGCAAAATCGAAACCCTGCTTTTTTA
2721775 TAAATGCCAA
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
94 82 0.96
95 3 0.04
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (94 bp):
CTTTTTGTCTTGCCTCAGATTGACAGTCCCCCATCGTTCATTGCCAAAAACATATACATTACACT
AGCAAAATCGAAACCCTGCTTTTTTAATG
Found at i:2725357 original size:32 final size:32
Alignment explanation
Indices: 2725320--2725388 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
2725310 ATGACACTAT
* *
2725320 CACATCAGCAATCATGTATCAAATGGCACGAC
1 CACATCAACAATCACGTATCAAATGGCACGAC
* * **
2725352 CACATCAACAATTACGTATCATATGGCATTAC
1 CACATCAACAATCACGTATCAAATGGCACGAC
2725384 CACAT
1 CACAT
2725389 TATTTAACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.23
Consensus pattern (32 bp):
CACATCAACAATCACGTATCAAATGGCACGAC
Found at i:2727033 original size:25 final size:25
Alignment explanation
Indices: 2726986--2727033 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2726976 CACATTCAAT
*
2726986 AAAGCATCATCTTTGTGGCAAAAAA
1 AAAGCATCATCTTTGTGGAAAAAAA
* *
2727011 AAAGCGTCATCTTTGTTGAAAAA
1 AAAGCATCATCTTTGTGGAAAAA
2727034 TCTTATAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (25 bp):
AAAGCATCATCTTTGTGGAAAAAAA
Found at i:2744408 original size:6 final size:6
Alignment explanation
Indices: 2744399--2744435 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
2744389 GAACGTGAGA
*
2744399 GACAAC GACAAC GACAAC GACAAA GACAAAC GACAAC
1 GACAAC GACAAC GACAAC GACAAC GAC-AAC GACAAC
2744436 AATTCCCGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.54, C:0.30, G:0.16, T:0.00
Consensus pattern (6 bp):
GACAAC
Found at i:2744432 original size:19 final size:18
Alignment explanation
Indices: 2744399--2744435 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2744389 GAACGTGAGA
*
2744399 GACAACGACAACGACAAC
1 GACAAAGACAACGACAAC
2744417 GACAAAGACAAACGACAAC
1 GACAAAGAC-AACGACAAC
2744436 AATTCCCGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.54, C:0.30, G:0.16, T:0.00
Consensus pattern (18 bp):
GACAAAGACAACGACAAC
Found at i:2757674 original size:6 final size:6
Alignment explanation
Indices: 2757664--2757699 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
2757654 CCTCGTGACT
*
2757664 CTGATT CTGATC CTGATC CTGATC CTGATC CTGATC
1 CTGATC CTGATC CTGATC CTGATC CTGATC CTGATC
2757700 ATGACCATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.36
Consensus pattern (6 bp):
CTGATC
Found at i:2758175 original size:13 final size:13
Alignment explanation
Indices: 2758139--2758175 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2758129 TTTTAAGTAA
2758139 AAAAAATT-AAA-
1 AAAAAATTAAAAT
*
2758150 GAAAAATTAAAAT
1 AAAAAATTAAAAT
2758163 AAAAAATTAAAAT
1 AAAAAATTAAAAT
2758176 TAATAGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 7 0.32
12 3 0.14
13 12 0.55
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAAAATTAAAAT
Found at i:2758424 original size:22 final size:22
Alignment explanation
Indices: 2758396--2758439 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2758386 ATTTATCAAT
*
2758396 TTAAATT-TTTATTAAAATTTTA
1 TTAAATTATTT-TTAAAAATTTA
2758418 TTAAATTATTTTTAAAAATTTA
1 TTAAATTATTTTTAAAAATTTA
2758440 CAAATTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAATTATTTTTAAAAATTTA
Found at i:2767950 original size:2 final size:2
Alignment explanation
Indices: 2767945--2767970 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2767935 AGTACTTCAA
2767945 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
2767971 TGTGCTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2769225 original size:2 final size:2
Alignment explanation
Indices: 2769218--2769243 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2769208 CAAGCAAATT
2769218 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
2769244 ATCACACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2771923 original size:12 final size:12
Alignment explanation
Indices: 2771889--2771931 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
2771879 GAACGATAAG
*
2771889 AAAAGGGAAGAA
1 AAAAGGAAAGAA
*
2771901 AAAAGCAGAAAAAA
1 AAAAG--GAAAGAA
2771915 AAAAGGAAAGAA
1 AAAAGGAAAGAA
2771927 AAAAG
1 AAAAG
2771932 AAACCTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAGAA
Found at i:2774597 original size:19 final size:19
Alignment explanation
Indices: 2774554--2774615 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
2774544 CCTTTTCTTA
* *
2774554 TATTTTTTGTTTGTCTTCT-
1 TATTTTTTGTTT-TTTTTTG
2774573 TA-TTTTTGTTTTTTTTTG
1 TATTTTTTGTTTTTTTTTG
* *
2774591 TATTTTTTGTATTATTATTG
1 TATTTTTTGT-TTTTTTTTG
2774611 TATTT
1 TATTT
2774616 AATAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.11
18 11 0.31
19 9 0.25
20 12 0.33
ACGTcount: A:0.11, C:0.03, G:0.10, T:0.76
Consensus pattern (19 bp):
TATTTTTTGTTTTTTTTTG
Found at i:2774912 original size:51 final size:51
Alignment explanation
Indices: 2774814--2774981 Score: 184
Period size: 49 Copynumber: 3.3 Consensus size: 51
2774804 CTTCTTACTC
* *
2774814 GAGGCTCAATAACTTTTAAAAATT-TAAAATCTGAAAAA-GGCTTATCTCAACA
1 GAGGCTCAATAAC-TTTAAAAATTCT--AATCTGAAAAATGGCTCATCTCAGCA
* * *
2774866 GAGGCTCAATAACTTTAAAAATTCTCATCTGAAAAATGACTCATCTCAGTA
1 GAGGCTCAATAACTTTAAAAATTCTAATCTGAAAAATGGCTCATCTCAGCA
* * * *
2774917 GAAGCTCAACAACTTT-AAAA-TCTTATCTTG-AAAATGGCTCTTCTCAGCA
1 GAGGCTCAATAACTTTAAAAATTCTAATC-TGAAAAATGGCTCATCTCAGCA
2774966 GAGGCTCAATAACTTT
1 GAGGCTCAATAACTTT
2774982 GAATTAAATC
Statistics
Matches: 100, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 36 0.36
50 16 0.16
51 34 0.34
52 14 0.14
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (51 bp):
GAGGCTCAATAACTTTAAAAATTCTAATCTGAAAAATGGCTCATCTCAGCA
Found at i:2774973 original size:49 final size:50
Alignment explanation
Indices: 2774814--2774981 Score: 173
Period size: 51 Copynumber: 3.3 Consensus size: 50
2774804 CTTCTTACTC
* * *
2774814 GAGGCTCAATAACTTTTAAAAATT-TAAAATCTGAAAAAGGCT-TATCTCAACA
1 GAGGCTCAATAAC-TTTAAAAATTCT--CATCTGAAAATGGCTCT-TCTCAGCA
* * *
2774866 GAGGCTCAATAACTTTAAAAATTCTCATCTGAAAAATGACTCATCTCAGTA
1 GAGGCTCAATAACTTTAAAAATTCTCATCTG-AAAATGGCTCTTCTCAGCA
* * *
2774917 GAAGCTCAACAACTTT-AAAA-TCTTATCTTGAAAATGGCTCTTCTCAGCA
1 GAGGCTCAATAACTTTAAAAATTCTCATC-TGAAAATGGCTCTTCTCAGCA
2774966 GAGGCTCAATAACTTT
1 GAGGCTCAATAACTTT
2774982 GAATTAAATC
Statistics
Matches: 98, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
49 36 0.37
50 11 0.11
51 37 0.38
52 14 0.14
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (50 bp):
GAGGCTCAATAACTTTAAAAATTCTCATCTGAAAATGGCTCTTCTCAGCA
Found at i:2775313 original size:147 final size:147
Alignment explanation
Indices: 2775036--2775402 Score: 429
Period size: 147 Copynumber: 2.5 Consensus size: 147
2775026 GATAAATAAT
* ** * *
2775036 CTCGGATATCACCACCAAAAAGATGCAAATGATTTCGGCTATTACCACCGAAGGAAACTCAAATA
1 CTCGAATATCACCACCAAAAAGATGCAAATGATTTCGAATATCACCACCGAAGAAAACTCAAATA
* *
2775101 TCACCATTGAGAAAATACAATTCAAGCTTTAATACTCGGATATCACCACCGAAAAAATGTCAATG
66 TCACCATCGAGAAAATACAATTCAAGCTTCAATACTCGGATATCACCACCGAAAAAATGTCAATG
*
2775166 CAAATTCAAATTTTAAA
131 CAAATTCAAACTTTAAA
* * * * *
2775183 CTCGAATATCACCACCGAGAAGATGCAAAT-ATTTTTGAATATCACCACTGAAGAAAACTCGAAT
1 CTCGAATATCACCACCAAAAAGATGCAAATGA-TTTCGAATATCACCACCGAAGAAAACTCAAAT
* ** * * * *
2775247 ATCACTATCGAGAAAATGTAATTCAAGCTTCAATACTTGGATATCACCACTGAGAGAATG-CAAA
65 ATCACCATCGAGAAAATACAATTCAAGCTTCAATACTCGGATATCACCACCGAAAAAATGTC-AA
2775311 TGCAAATTCAAACTTTAAA
129 TGCAAATTCAAACTTTAAA
* * ** *
2775330 CTC-ATATATCACCACAAAAAATATGCAAATG-TCTTC-AGATATCGTCATCGAAGAAAACTCAA
1 CTCGA-ATATCACCACCAAAAAGATGCAAATGAT-TTCGA-ATATCACCACCGAAGAAAACTCAA
2775392 ATATCACCATC
63 ATATCACCATC
2775403 AAGAGAATGC
Statistics
Matches: 183, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
146 5 0.03
147 178 0.97
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (147 bp):
CTCGAATATCACCACCAAAAAGATGCAAATGATTTCGAATATCACCACCGAAGAAAACTCAAATA
TCACCATCGAGAAAATACAATTCAAGCTTCAATACTCGGATATCACCACCGAAAAAATGTCAATG
CAAATTCAAACTTTAAA
Found at i:2775339 original size:48 final size:48
Alignment explanation
Indices: 2775287--2775465 Score: 120
Period size: 48 Copynumber: 3.6 Consensus size: 48
2775277 CAATACTTGG
*
2775287 ATATCACCACTGAGAGA-ATGCAAATGCAAATTCAAACTTTAAACTCA
1 ATATCACCACTAAGAGATATGCAAATGCAAATTCAAACTTTAAACTCA
* * **
2775334 TATATCACCAC-AAAAAATATGCAAATGTCTTCAGATATCGTCATCGAA--GAAAACTCAA
1 -ATATCACCACTAAGAGATATGCAAATG----CA-A-AT--TCA---AACTTTAAACTC-A
2775392 ATATCACCA-TCAAGAGA-ATGCAAATGCAAATTCAAACTTTAAACTCGA
1 ATATCACCACT-AAGAGATATGCAAATGCAAATTCAAACTTTAAACTC-A
*
2775440 ATATCACCACTGAGA-ATATGCAAATG
1 ATATCACCACTAAGAGATATGCAAATG
2775466 ACTTTGGATA
Statistics
Matches: 101, Mismatches: 11, Indels: 38
0.67 0.07 0.25
Matches are distributed among these distances:
46 2 0.02
47 4 0.04
48 47 0.47
49 4 0.04
51 2 0.02
52 3 0.03
53 3 0.03
54 2 0.02
56 3 0.03
57 24 0.24
58 5 0.05
59 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (48 bp):
ATATCACCACTAAGAGATATGCAAATGCAAATTCAAACTTTAAACTCA
Found at i:2775493 original size:105 final size:105
Alignment explanation
Indices: 2775299--2775547 Score: 280
Period size: 105 Copynumber: 2.4 Consensus size: 105
2775289 ATCACCACTG
*
2775299 AGAGAATGCAAATGCAAATTCAAACTTTAAACTCATATATCACCACAAAAAATATGCAAATGTCT
1 AGAGAATGCAAATGCAAATTCAAACTTTAAACTCATATATCACCACAAAAAATATGCAAATGACT
* * *
2775364 TCAGATATCGTCATCGAAGAAAACTCAAATATCACCATCA
66 TCAGATATCGCCACCAAAGAAAACTCAAATATCACCATCA
** *
2775404 AGAGAATGCAAATGCAAATTCAAACTTTAAACTCGA-ATATCACCACTGAGAATATGCAAATGAC
1 AGAGAATGCAAATGCAAATTCAAACTTTAAACTC-ATATATCACCACAAAAAATATGCAAATGAC
** * * ** *
2775468 TTTGGATATTGCCACCAAAGGAAACTTGAATATTACCAT-A
65 TTCAGATATCGCCACCAAAGAAAACTCAAATATCACCATCA
* *
2775508 A-A-AA---AAATGC-AATTCAAGCTTTAATACTCAGATATCACCA
1 AGAGAATGCAAATGCAAATTCAAACTTTAA-ACTCATATATCACCA
2775548 TTGAAAAAAT
Statistics
Matches: 126, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
98 14 0.11
99 19 0.15
102 2 0.02
103 1 0.01
104 2 0.02
105 87 0.69
106 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (105 bp):
AGAGAATGCAAATGCAAATTCAAACTTTAAACTCATATATCACCACAAAAAATATGCAAATGACT
TCAGATATCGCCACCAAAGAAAACTCAAATATCACCATCA
Found at i:2775786 original size:105 final size:105
Alignment explanation
Indices: 2775670--2775954 Score: 376
Period size: 105 Copynumber: 2.7 Consensus size: 105
2775660 TAATACTTGG
* **
2775670 ATATCACCACCGAGAAGATACAAAT-ATCTTCGGATATCGTCATTAAAGGAAACTCGAATATCAC
1 ATATCACCACCGAGAAGATACAAATGA-CTTCAGATATCGTCACCAAAGGAAACTCGAATATCAC
* * *
2775734 CATCGAAAAAATACAAATGTAAATTTAAATTTTAAACTCAA
65 CATCGAAAAAATACAAATGCAAATTCAAACTTTAAACTCAA
* *
2775775 ATATCACCACCGAGAAGATACAAATGACTTCAGATATCGTCACCGAAGGAAACTCGAATATCATC
1 ATATCACCACCGAGAAGATACAAATGACTTCAGATATCGTCACCAAAGGAAACTCGAATATCACC
* * * *
2775840 ATCGAGAGAATGCAAATGCAAATTCAAACTTTAAACTCAG
66 ATCGAAAAAATACAAATGCAAATTCAAACTTTAAACTCAA
* * * ***
2775880 ATATCACCATCAAGAAGATGCAAATGACTTCAGATATTACCACCAAAGGAAACTCGAATATCACC
1 ATATCACCACCGAGAAGATACAAATGACTTCAGATATCGTCACCAAAGGAAACTCGAATATCACC
*
2775945 AT-AAAAAAAT
66 ATCGAAAAAAT
2775955 GTAATTCAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
104 5 0.03
105 150 0.96
106 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (105 bp):
ATATCACCACCGAGAAGATACAAATGACTTCAGATATCGTCACCAAAGGAAACTCGAATATCACC
ATCGAAAAAATACAAATGCAAATTCAAACTTTAAACTCAA
Found at i:2776012 original size:42 final size:42
Alignment explanation
Indices: 2775931--2776256 Score: 206
Period size: 42 Copynumber: 7.5 Consensus size: 42
2775921 ACCAAAGGAA
* * *
2775931 ACTCGAATATCACCA-TAAAAAAATGT-AATTCAAACTTTAAT
1 ACTCGGATATCACCACCAAGAAAATGTAAATTCAAA-TTTAAT
*
2775972 ACTCGGATATCACCACCAAGAAAATGTAAATGCAAATTTAAAATTT
1 ACTCGGATATCACCACCAAGAAAATGTAAATTCAAATTT--AA--T
* ** * *
2776018 AAACTCAGATA-CACCA--TTGAGAATATACAATTCAAATCTTAAT
1 --ACTCGGATATCACCACCAAGAAAATGTA-AATTCAAAT-TTAAT
* ** *
2776061 ACTCGGATATCACCATCGAA-AAAATGT-AATTCAAATCTCGAC
1 ACTCGGATATCACCA-CCAAGAAAATGTAAATTCAAAT-TTAAT
* *
2776103 ACTCGGATATCACCACCGAGAAGA--TACAATTCAAATCTTAAT
1 ACTCGGATATCACCACCAAGAAAATGTA-AATTCAAAT-TTAAT
*
2776145 ACTCGGATATCACCACCAAGAAAATG-AAATTCAAGCTTTAAT
1 ACTCGGATATCACCACCAAGAAAATGTAAATTCAA-ATTTAAT
** * *
2776187 ACTCGGATATCATTACTGAAAGAATGTAAATGCAAATTCAAACTTTAA-
1 ACTCGGATATCACCAC--CAAG-A---AAATGTAAATTCAAA-TTTAAT
2776235 ACTCGGATATCACCACCAAGAA
1 ACTCGGATATCACCACCAAGAA
2776257 GATACAAATG
Statistics
Matches: 223, Mismatches: 34, Indels: 55
0.71 0.11 0.18
Matches are distributed among these distances:
40 1 0.00
41 24 0.11
42 108 0.48
43 10 0.04
44 10 0.04
45 11 0.05
46 12 0.05
47 7 0.03
48 27 0.12
49 13 0.06
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.25
Consensus pattern (42 bp):
ACTCGGATATCACCACCAAGAAAATGTAAATTCAAATTTAAT
Found at i:2776191 original size:84 final size:83
Alignment explanation
Indices: 2775957--2776198 Score: 265
Period size: 84 Copynumber: 2.8 Consensus size: 83
2775947 AAAAAAATGT
*
2775957 AATTCAAA-CTTTAATACTCGGATATCACCACCAAGAAAATGTAAATGCAAATTTAAAATTTAAA
1 AATTCAAATC-TTAATACTCGGATATCACCACCAAGAAAATG-AAATTCAAATTT--AA--T--A
* ** *
2776021 CTCAGATA-CACCATTGAGAATATAC
58 CTCGGATATCACCACCGAGAAGATAC
* * ** *
2776046 AATTCAAATCTTAATACTCGGATATCACCATCGAA-AAAATGTAATTCAAATCTCGACACTCGGA
1 AATTCAAATCTTAATACTCGGATATCACCA-CCAAGAAAATGAAATTCAAAT-TTAATACTCGGA
2776110 TATCACCACCGAGAAGATAC
64 TATCACCACCGAGAAGATAC
*
2776130 AATTCAAATCTTAATACTCGGATATCACCACCAAGAAAATGAAATTCAAGCTTTAATACTCGGAT
1 AATTCAAATCTTAATACTCGGATATCACCACCAAGAAAATGAAATTCAA-ATTTAATACTCGGAT
2776195 ATCA
65 ATCA
2776199 TTACTGAAAG
Statistics
Matches: 131, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
83 11 0.08
84 71 0.54
85 1 0.01
87 1 0.01
88 8 0.06
89 35 0.27
90 4 0.03
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (83 bp):
AATTCAAATCTTAATACTCGGATATCACCACCAAGAAAATGAAATTCAAATTTAATACTCGGATA
TCACCACCGAGAAGATAC
Found at i:2776380 original size:104 final size:105
Alignment explanation
Indices: 2776187--2776408 Score: 297
Period size: 104 Copynumber: 2.1 Consensus size: 105
2776177 AAGCTTTAAT
* * * *
2776187 ACTCGGATATCATTACTGAAAGAATGTAAATGCAAATTCAAACTTTAAACTCGGATATCACCACC
1 ACTCGAATATCACTACTGAAAGAATGCAAATGCAAATTCAAACTTTAAACTCGAATATCACCACC
* **
2776252 AAGAAGATACAAATGACTTTGGATATCGTCATCGAAGAAA
66 AAGAAGATACAAATGACTTCGGATATCACCATCGAAGAAA
*
2776292 ACTCGAATATCACTA-TCGAAAGAATGCAAATGCAAATTCAAA-TTTAAACTCGAATATCATCAC
1 ACTCGAATATCACTACT-GAAAGAATGCAAATGCAAATTCAAACTTTAAACTCGAATATCACCAC
* * *
2776355 CGAA-AAGATGCAAATGACTTCGGATATTACCATCGAAGGAA
65 C-AAGAAGATACAAATGACTTCGGATATCACCATCGAAGAAA
*
2776396 ACTCAAATATCAC
1 ACTCGAATATCAC
2776409 CATTAAGAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
104 64 0.62
105 39 0.38
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (105 bp):
ACTCGAATATCACTACTGAAAGAATGCAAATGCAAATTCAAACTTTAAACTCGAATATCACCACC
AAGAAGATACAAATGACTTCGGATATCACCATCGAAGAAA
Found at i:2776460 original size:42 final size:41
Alignment explanation
Indices: 2776396--2776670 Score: 201
Period size: 42 Copynumber: 6.4 Consensus size: 41
2776386 ATCGAAGGAA
* ** *
2776396 ACTCAAATATCACCATTAAGAAAATGTAATTCAAGCTTTAAT
1 ACTCGAATATCACCATCGAGAAAATGTAATTCAA-ATTTAAT
*
2776438 ACTCGAATATCACCATCGAGAAAATACAAATACAAATTCAAAATTTAA-
1 ACTCGAATATCACCATCGAGAAAAT----GT---AATTC-AAATTTAAT
* *
2776486 ACTCGAATATCACCATCGAGAAGATGCCAATTCAAATATTAAT
1 ACTCGAATATCACCATCGAGAAAATG-TAATTCAAAT-TTAAT
* * * ** *
2776529 ACTCGAATATCATCATTGAAAAAATGTAATTCAAACTTCGAC
1 ACTCGAATATCACCATCGAGAAAATGTAATTCAAA-TTTAAT
* * * *
2776571 ACTCGGATATCACCACCAAGAAGATGTAATTCAAATCTTAAT
1 ACTCGAATATCACCATCGAGAAAATGTAATTCAAAT-TTAAT
* * * ***
2776613 ACTCGAATATCACTATCGAAAAAATGTAAATGACTTTTTTAAT
1 ACTCGAATATCACCATCGAGAAAATGT-AAT-TCAAATTTAAT
2776656 ACTCGAATATCACCA
1 ACTCGAATATCACCA
2776671 CCTAGTGATT
Statistics
Matches: 181, Mismatches: 37, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
41 5 0.03
42 92 0.51
43 45 0.25
44 2 0.01
46 1 0.01
48 24 0.13
49 10 0.06
50 2 0.01
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (41 bp):
ACTCGAATATCACCATCGAGAAAATGTAATTCAAATTTAAT
Found at i:2776613 original size:84 final size:85
Alignment explanation
Indices: 2776486--2776641 Score: 235
Period size: 84 Copynumber: 1.8 Consensus size: 85
2776476 CAAAATTTAA
* * *
2776486 ACTCGAATATCACCATCGAGAAGATGCCAATTCAAATATTAATACTCGAATATCA-TCATTGAAA
1 ACTCGAATATCACCACCAAGAAGATGCCAATTCAAATATTAATACTCGAATATCACT-ATCGAAA
2776550 AAATGTAATTCAAACTTCGAC
65 AAATGTAATTCAAACTTCGAC
* * *
2776571 ACTCGGATATCACCACCAAGAAGATG-TAATTCAAATCTTAATACTCGAATATCACTATCGAAAA
1 ACTCGAATATCACCACCAAGAAGATGCCAATTCAAATATTAATACTCGAATATCACTATCGAAAA
2776635 AATGTAA
66 AATGTAA
2776642 ATGACTTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
84 40 0.62
85 24 0.38
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (85 bp):
ACTCGAATATCACCACCAAGAAGATGCCAATTCAAATATTAATACTCGAATATCACTATCGAAAA
AATGTAATTCAAACTTCGAC
Found at i:2777095 original size:35 final size:35
Alignment explanation
Indices: 2777053--2777139 Score: 122
Period size: 35 Copynumber: 2.5 Consensus size: 35
2777043 ATAAGGATGC
2777053 AAATACAAATATCTTTTCCTAAAATGATGCACT-TG
1 AAATACAAATATCTTTTCCTAAAATGATGCA-TATG
* *
2777088 AAATACAAATGTCTTTTCTTAAAATGATGCATATG
1 AAATACAAATATCTTTTCCTAAAATGATGCATATG
* *
2777123 AAATGCAAATATGTTTT
1 AAATACAAATATCTTTT
2777140 AAAAAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 1 0.02
35 45 0.98
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (35 bp):
AAATACAAATATCTTTTCCTAAAATGATGCATATG
Found at i:2777312 original size:19 final size:20
Alignment explanation
Indices: 2777288--2777333 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2777278 TTCAAAGTTC
2777288 TCTTTCAT-TCAATCCCAAA
1 TCTTTCATCTCAATCCCAAA
*
2777307 TCTTTCATCTCAATTCCAAA
1 TCTTTCATCTCAATCCCAAA
2777327 TCCTTTC
1 T-CTTTC
2777334 TTTGCTGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.33
20 11 0.46
21 5 0.21
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (20 bp):
TCTTTCATCTCAATCCCAAA
Found at i:2783516 original size:7 final size:7
Alignment explanation
Indices: 2783489--2783529 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
2783479 TAATATTTAA
2783489 AAAAAAT
1 AAAAAAT
2783496 CAAAAAATT
1 -AAAAAA-T
*
2783505 CAAAAAT
1 AAAAAAT
2783512 AAAAAAT
1 AAAAAAT
2783519 AAAAAAT
1 AAAAAAT
2783526 AAAA
1 AAAA
2783530 TTTTTTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 18 0.60
8 11 0.37
9 1 0.03
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:2799255 original size:13 final size:13
Alignment explanation
Indices: 2799239--2799279 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2799229 TTTAAATTTT
*
2799239 TTATTTTTATATA
1 TTATTTTAATATA
2799252 TTATTTTAATATA
1 TTATTTTAATATA
**
2799265 AAATTTTAATATA
1 TTATTTTAATATA
2799278 TT
1 TT
2799280 TAAGTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTTTAATATA
Found at i:2801989 original size:25 final size:24
Alignment explanation
Indices: 2801961--2802028 Score: 57
Period size: 25 Copynumber: 2.7 Consensus size: 24
2801951 TAATATGTTG
2801961 ATATGATATAAAAAATATAAATATA
1 ATAT-ATATAAAAAATATAAATATA
* * *
2801986 ATATAATTTAAATCATATATAAATTTA
1 ATAT-ATATAAA--AAATATAAATATA
*
2802013 ATA-AAATAAAAAATAT
1 ATATATATAAAAAATAT
2802029 TTTATATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
23 5 0.15
25 15 0.44
27 14 0.41
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (24 bp):
ATATATATAAAAAATATAAATATA
Found at i:2802702 original size:16 final size:17
Alignment explanation
Indices: 2802650--2802703 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
2802640 GCCCATTAAA
*
2802650 AAATATTTTAAAATTTT
1 AAATATTTTAATATTTT
**
2802667 AAA-ATTTTTTTATTTT
1 AAATATTTTAATATTTT
2802683 -AATA-TTTAATATTTT
1 AAATATTTTAATATTTT
2802698 AAATAT
1 AAATAT
2802704 ATATTAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.38
16 15 0.52
17 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATATTTTAATATTTT
Found at i:2803060 original size:28 final size:27
Alignment explanation
Indices: 2803029--2803087 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
2803019 AATACGATGG
*
2803029 ATTAAATTTAAATATCAA-TTTTATTAAA
1 ATTAAA-TT-AATATAAATTTTTATTAAA
2803057 ATTAAATTAATATAAATTTTTTATTAAA
1 ATTAAATTAATATAAA-TTTTTATTAAA
2803085 ATT
1 ATT
2803088 TTTTTAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.25
27 2 0.07
28 19 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTAAATTAATATAAATTTTTATTAAA
Found at i:2806560 original size:11 final size:11
Alignment explanation
Indices: 2806532--2806561 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2806522 TTTTTACAAT
*
2806532 AAAATGGACTG
1 AAAATGTACTG
2806543 AAAATGTACTG
1 AAAATGTACTG
2806554 AAAATGTA
1 AAAATGTA
2806562 AGGGAAGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (11 bp):
AAAATGTACTG
Found at i:2814128 original size:119 final size:116
Alignment explanation
Indices: 2813990--2814295 Score: 327
Period size: 119 Copynumber: 2.6 Consensus size: 116
2813980 ATTTTAGAAA
2813990 TTTTATTTTT-AAGAAAAATTTATACTTTCAACTTTTCCT-AAAAATATTTTTAAAAAATTTT-T
1 TTTTATTTTTAAAG-AAAATTTATACTTTCAACTTTTCCTCAAAAATATTTTTAAAAAATTTTAT
* *
2814052 GTTATCAATGAAAATTGATACTTTTAACTTTTCCTTTAAAAA-ATATTTTTCTTCAAG
65 -TTA--AA-AAAAATTGATACTTTTAACTTTTCCTTTAAAAATATATATTT-TT-AAG
**
2814109 TTTTATTTTTAAAGAAAA-TTAGTACTTTCAACTTTTCCTCAAGAAATGCATTTTTTTAAAATTT
1 TTTTATTTTTAAAGAAAATTTA-TACTTTCAACTTTTCCTCAA-AAAT--ATTTTTAAAAAATTT
* *
2814173 TATTTAAAAAAAATTGATACTTTTAACTTTTTCTTTAAAAATATATATTTTTAAT
62 TATTTAAAAAAAATTGATACTTTTAACTTTTCCTTTAAAAATATATATTTTTAAG
* * * * * **
2814228 TTTTATGTTCAAAGAAAATTGATA-TATTCAACTTTTCTTGAAAAACTATTTTTTTCAAAATTTT
1 TTTTATTTTTAAAGAAAATTTATACT-TTCAACTTTTCCTCAAAAA-TA-TTTTTAAAAAATTTT
2814292 ATTT
63 ATTT
2814296 TAAAGAGATC
Statistics
Matches: 163, Mismatches: 12, Indels: 25
0.81 0.06 0.12
Matches are distributed among these distances:
117 1 0.01
118 25 0.15
119 66 0.40
120 40 0.25
121 13 0.08
123 17 0.10
124 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (116 bp):
TTTTATTTTTAAAGAAAATTTATACTTTCAACTTTTCCTCAAAAATATTTTTAAAAAATTTTATT
TAAAAAAAATTGATACTTTTAACTTTTCCTTTAAAAATATATATTTTTAAG
Found at i:2814250 original size:60 final size:59
Alignment explanation
Indices: 2813981--2814301 Score: 255
Period size: 59 Copynumber: 5.4 Consensus size: 59
2813971 AAAATTTTTA
** * *
2813981 TTTTAGAAATTTTATTTTTAAGAAAAATTTATACTTTCAACTTTTC-CT-AAAA-ATATTT
1 TTTTA-AAATTTTATTTCAAAG-AAAATTGATACTTTCAACTTTTCTTTAAAAATATATTT
** * * *
2814039 TTAAAAAATTTTTGTTATCAATGAAAATTGATACTTTTAACTTTTCCTTTAAAAA-ATATTT
1 TTTTAAAA-TTTTATT-TCAAAGAAAATTGATACTTTCAACTTTT-CTTTAAAAATATATTT
* * * * * **
2814100 TTCTTCAAGTTTTATTTTTAAAGAAAATT-AGTACTTTCAACTTTTCCTCAAGAAATGCATTT
1 TT-TTAAAATTTTA-TTTCAAAGAAAATTGA-TACTTTCAACTTTTCTTTAA-AAATATATTT
* * *
2814162 TTTTAAAATTTTATTT-AAAAAAAATTGATACTTTTAACTTTTTCTTTAAAAATATATAT
1 TTTTAAAATTTTATTTCAAAGAAAATTGATACTTTCAAC-TTTTCTTTAAAAATATATTT
* *
2814221 TTTT-AATTTTTATGTTCAAAGAAAATTGATA-TATTCAACTTTTCTTGAAAAACTAT-TTT
1 TTTTAAAATTTTAT-TTCAAAGAAAATTGATACT-TTCAACTTTTCTTTAAAAA-TATATTT
* *
2814280 TTTCAAAATTTTATTTTAAAGA
1 TTTTAAAATTTTATTTCAAAGA
2814302 GATCATTGAA
Statistics
Matches: 208, Mismatches: 38, Indels: 33
0.75 0.14 0.12
Matches are distributed among these distances:
57 3 0.01
58 37 0.18
59 60 0.29
60 47 0.23
61 51 0.25
62 10 0.05
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.49
Consensus pattern (59 bp):
TTTTAAAATTTTATTTCAAAGAAAATTGATACTTTCAACTTTTCTTTAAAAATATATTT
Found at i:2814354 original size:21 final size:21
Alignment explanation
Indices: 2814330--2814389 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2814320 GATGTTTAAT
*
2814330 TAAATAGATAAAAAAAATCAA
1 TAAATAGATAAAAAAAATAAA
* * *
2814351 TAAATAAATAATAAAACTAAA
1 TAAATAGATAAAAAAAATAAA
* *
2814372 TGAAAAAGAAAAAAAAAA
1 T-AAATAGATAAAAAAAA
2814390 AACCTTTGGC
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (21 bp):
TAAATAGATAAAAAAAATAAA
Found at i:2814664 original size:14 final size:15
Alignment explanation
Indices: 2814626--2814674 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
2814616 TAATTCTTTT
*
2814626 TTTCTCTCTCTCTCTC
1 TTTC-CTCTCCCTCTC
* *
2814642 TCTCTTCTCCCT-TC
1 TTTCCTCTCCCTCTC
2814656 TTTCCTCTCCCTCTC
1 TTTCCTCTCCCTCTC
2814671 TTTC
1 TTTC
2814675 TACCTGGATG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 12 0.44
15 12 0.44
16 3 0.11
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTCCTCTCCCTCTC
Found at i:2815201 original size:22 final size:21
Alignment explanation
Indices: 2815151--2815201 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2815141 TTTTATTAAT
* *
2815151 AAAATAAATAATAAAAATTTA
1 AAAAAAAATAATAAAAATGTA
*
2815172 AAATAAAAATAATAATAATAGTA
1 AAA-AAAAATAATAAAAAT-GTA
2815195 AAAAAAA
1 AAAAAAA
2815202 CAAACAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 17 0.68
23 5 0.20
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAAAATAATAAAAATGTA
Found at i:2815847 original size:15 final size:15
Alignment explanation
Indices: 2815824--2815906 Score: 89
Period size: 15 Copynumber: 5.6 Consensus size: 15
2815814 AAAAATAAAT
* *
2815824 AATATTATATTTATA
1 AATAATATATTAATA
2815839 AATAATATATTAATA
1 AATAATATATTAATA
* *
2815854 AATAATATACTATTA
1 AATAATATATTAATA
*
2815869 ATATAATATACTAATA
1 A-ATAATATATTAATA
*
2815885 AAT-AT-TAATAATA
1 AATAATATATTAATA
2815898 AATAATATA
1 AATAATATA
2815907 AAGAATAACA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
13 10 0.17
14 4 0.07
15 31 0.53
16 14 0.24
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:2815854 original size:33 final size:31
Alignment explanation
Indices: 2815817--2815888 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
2815807 TTATAATAAA
*
2815817 AATAAATAATATTA-TATTTATAAATAATATATT
1 AATAAATAATA-TACTA-TTA-AAATAATATACT
*
2815850 AATAAATAATATACTATTAATATAATATACT
1 AATAAATAATATACTATTAAAATAATATACT
2815881 AATAAATA
1 AATAAATA
2815889 TTAATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 18 0.50
32 5 0.14
33 13 0.36
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
AATAAATAATATACTATTAAAATAATATACT
Done.