Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 13 of 56
Found at i:2494336 original size:21 final size:22
Alignment explanation
Indices: 2494298--2494352 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
2494288 ATTAACATTA
*
2494298 TAATTAAATTAAAAAATATTTT
1 TAATTAAATTAAAAAATAATTT
* *
2494320 TAATTATA-TAAATAATAATTT
1 TAATTAAATTAAAAAATAATTT
*
2494341 AAATTAAATTAA
1 TAATTAAATTAA
2494353 TTTAAATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATTAAATTAAAAAATAATTT
Found at i:2494715 original size:15 final size:15
Alignment explanation
Indices: 2494697--2494728 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2494687 AGCATGAAGC
*
2494697 TATTTATTATATATA
1 TATTTATAATATATA
2494712 TATTTATAATATATA
1 TATTTATAATATATA
2494727 TA
1 TA
2494729 AGTTATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTATAATATATA
Found at i:2494786 original size:21 final size:21
Alignment explanation
Indices: 2494740--2494790 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2494730 GTTATTTATG
* *
2494740 ATTTTTATGTAATATTTTTAT
1 ATTTTTATTTAATATTTTTAA
*
2494761 TTTTTTATTT-ATAATTTTTAA
1 ATTTTTATTTAAT-ATTTTTAA
2494782 A-TTTTATTT
1 ATTTTTATTT
2494791 TCAACATATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTTATTTAATATTTTTAA
Found at i:2494909 original size:13 final size:14
Alignment explanation
Indices: 2494880--2494909 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2494870 TTTTATTAAA
2494880 TAAATATTTATATT
1 TAAATATTTATATT
2494894 TAAATATTTA-ATT
1 TAAATATTTATATT
2494907 TAA
1 TAA
2494910 TGATTGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATATTTATATT
Found at i:2494986 original size:13 final size:13
Alignment explanation
Indices: 2494970--2494998 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2494960 TTTTAAATTT
2494970 AAAAATTA-ATCA
1 AAAAATTATATCA
2494982 AAAAATTATATCA
1 AAAAATTATATCA
2494995 AAAA
1 AAAA
2494999 TTAATTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTATATCA
Found at i:2494987 original size:12 final size:11
Alignment explanation
Indices: 2494970--2495003 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
2494960 TTTTAAATTT
2494970 AAAAATTAATC
1 AAAAATTAATC
2494981 AAAAAATTATATC
1 -AAAAATTA-ATC
2494994 AAAAATTAAT
1 AAAAATTAAT
2495004 TTATCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 16 0.76
13 3 0.14
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAAATTAATC
Found at i:2495354 original size:27 final size:30
Alignment explanation
Indices: 2495304--2495371 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 30
2495294 TATATCTAAA
2495304 ATACAATAATAGTGCTCTGGACAAAAA-AAAT
1 ATACAATAATAGTGC-CT-GACAAAAAGAAAT
2495335 ATACAATAATAGTG-CT-ACAAAAAGAAAT
1 ATACAATAATAGTGCCTGACAAAAAGAAAT
*
2495363 -TATAATAAT
1 ATACAATAAT
2495372 TAATCAAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 15 0.43
28 4 0.11
29 2 0.06
31 14 0.40
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (30 bp):
ATACAATAATAGTGCCTGACAAAAAGAAAT
Found at i:2498568 original size:12 final size:12
Alignment explanation
Indices: 2498551--2498577 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2498541 AAACGTTACC
2498551 TCTTTTTTTTTT
1 TCTTTTTTTTTT
2498563 TCTTTTTTTTTT
1 TCTTTTTTTTTT
2498575 TCT
1 TCT
2498578 CTGGTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:2504314 original size:13 final size:14
Alignment explanation
Indices: 2504260--2504318 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
2504250 AATTTGTGTA
*
2504260 AATATATTATTTTT
1 AATATAATATTTTT
*
2504274 AATTATAAATAAATTTT
1 AA-TAT-AAT-ATTTTT
2504291 AATATAATATTTTT
1 AATATAATATTTTT
*
2504305 AATA-ATTATTTTT
1 AATATAATATTTTT
2504318 A
1 A
2504319 TTTTTACCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 9 0.24
14 11 0.29
15 6 0.16
16 5 0.13
17 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATAATATTTTT
Found at i:2506460 original size:2 final size:2
Alignment explanation
Indices: 2506453--2506479 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2506443 TGAGATTCTT
2506453 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2506480 TTTTTTTTCC
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2507350 original size:33 final size:33
Alignment explanation
Indices: 2507311--2507377 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2507301 TGCCCCCATG
2507311 GGATCAATAGAATCATGTTCATTAGGCTAATGA
1 GGATCAATAGAATCATGTTCATTAGGCTAATGA
2507344 GGATCAATAGAATCATGTTCATTAGGCTAATGA
1 GGATCAATAGAATCATGTTCATTAGGCTAATGA
2507377 G
1 G
2507378 AACACAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (33 bp):
GGATCAATAGAATCATGTTCATTAGGCTAATGA
Found at i:2510698 original size:21 final size:22
Alignment explanation
Indices: 2510669--2510709 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2510659 TTTATGAAAA
2510669 AATTATAATTAAT-ATATAATAC
1 AATTATAA-TAATAATATAATAC
2510691 AATT-TAATAATAATATAAT
1 AATTATAATAATAATATAAT
2510710 CAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTATAATAATAATATAATAC
Found at i:2511134 original size:22 final size:22
Alignment explanation
Indices: 2511103--2511153 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2511093 TTAAAGTGAC
2511103 TTAAAATT-AAAATTATAACAAT
1 TTAAAATTAAAAATTATAA-AAT
* *
2511125 TTAAACTTAAAAATTTTAAAAT
1 TTAAAATTAAAAATTATAAAAT
2511147 TTAAAAT
1 TTAAAAT
2511154 GACTCAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAATTAAAAATTATAAAAT
Found at i:2513565 original size:34 final size:32
Alignment explanation
Indices: 2513520--2513596 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
2513510 AAAAATATAA
* *
2513520 ATATAAAATAAATACATAAATAATTTTAAAATTT
1 ATATAATATAAAT-CATAAA-AATATTAAAATTT
* * *
2513554 ATATAATATAAATTATTAAAATATTAAATTTT
1 ATATAATATAAATCATAAAAATATTAAAATTT
2513586 ATATAAATATA
1 ATAT-AATATA
2513597 TGACATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 15 0.41
33 10 0.27
34 12 0.32
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAATATAAATCATAAAAATATTAAAATTT
Found at i:2513593 original size:18 final size:18
Alignment explanation
Indices: 2513545--2513595 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 18
2513535 ATAAATAATT
*
2513545 TTAAAATTTATAT-AATA
1 TTAAATTTTATATAAATA
*
2513562 -TAAATTAT-TA-AAATA
1 TTAAATTTTATATAAATA
2513577 TTAAATTTTATATAAATA
1 TTAAATTTTATATAAATA
2513595 T
1 T
2513596 ATGACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
17 2 0.07
18 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTTTATATAAATA
Found at i:2513852 original size:3 final size:3
Alignment explanation
Indices: 2513846--2513870 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2513836 TATTTTTTTA
2513846 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
2513871 TGTTTTCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2517967 original size:27 final size:28
Alignment explanation
Indices: 2517927--2517985 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
2517917 TTTTTATGAG
*
2517927 TTAATATTTAATAAATTTAGATTTAAAT
1 TTAATATATAATAAATTTAGATTTAAAT
* **
2517955 TTAATATAT-ATAATTTTTTATTTAAAT
1 TTAATATATAATAAATTTAGATTTAAAT
2517982 TTAA
1 TTAA
2517986 ACTTTAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTAATATATAATAAATTTAGATTTAAAT
Found at i:2518838 original size:16 final size:16
Alignment explanation
Indices: 2518813--2518853 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2518803 AGAATCACAA
2518813 AAAAATTTAAAAAAATT
1 AAAAA-TTAAAAAAATT
*
2518830 AAAAATTAAAAATATT
1 AAAAATTAAAAAAATT
*
2518846 AAATATTA
1 AAAAATTA
2518854 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTAAAAAAATT
Found at i:2519849 original size:15 final size:16
Alignment explanation
Indices: 2519808--2519864 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
2519798 TTCATATTAA
2519808 ATTTAAATTTTATATT
1 ATTTAAATTTTATATT
* *
2519824 AATAAATATTTTAT-TT
1 ATTTAA-ATTTTATATT
* *
2519840 ATTTAAATTTAATATA
1 ATTTAAATTTTATATT
2519856 ATTTAAATT
1 ATTTAAATT
2519865 ATAAAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.18
16 20 0.61
17 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATTTTATATT
Found at i:2519958 original size:32 final size:32
Alignment explanation
Indices: 2519916--2519993 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
2519906 TTATTATTGA
*
2519916 AATTCTTATATAAATTATACACATAT-AAAATT
1 AATTCATATATAAATT-TACACATATAAAAATT
* *
2519948 GATTCATATATAAATTTATACATATAAAAATT
1 AATTCATATATAAATTTACACATATAAAAATT
*
2519980 AATTCGTATATAAA
1 AATTCATATATAAA
2519994 AAGATTGATC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 8 0.20
32 32 0.80
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.40
Consensus pattern (32 bp):
AATTCATATATAAATTTACACATATAAAAATT
Found at i:2519962 original size:16 final size:15
Alignment explanation
Indices: 2519917--2519993 Score: 64
Period size: 16 Copynumber: 4.9 Consensus size: 15
2519907 TATTATTGAA
*
2519917 ATTCTTATATAAATT
1 ATTCATATATAAATT
* *
2519932 ATACACATATAAAATT
1 ATTCATATAT-AAATT
2519948 GATTCATATATAAATTT
1 -ATTCATATATAAA-TT
* *
2519965 ATACATATAAAAATT
1 ATTCATATATAAATT
*
2519980 AATTCGTATATAAA
1 -ATTCATATATAAA
2519994 AAGATTGATC
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
15 9 0.19
16 29 0.60
17 10 0.21
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (15 bp):
ATTCATATATAAATT
Found at i:2520123 original size:19 final size:19
Alignment explanation
Indices: 2520050--2520124 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
2520040 TTAAATTAAA
*
2520050 TTTAAATAAAAATTAATATAT
1 TTTAAAT-AAAATT-ATATTT
* ** *
2520071 TTAAAATTTAATTAAATTT
1 TTTAAATAAAATTATATTT
2520090 TTTAAATAAAATTATATTT
1 TTTAAATAAAATTATATTT
*
2520109 TTT-ATTAAAATT-TATT
1 TTTAAATAAAATTATATT
2520125 CTCAAATTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
17 4 0.09
18 8 0.18
19 22 0.50
20 4 0.09
21 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAATAAAATTATATTT
Found at i:2525079 original size:10 final size:10
Alignment explanation
Indices: 2525064--2525128 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
2525054 AATATTAATA
*
2525064 TTATTTATAT
1 TTATTTAAAT
2525074 TTATTTAAAAT
1 TTATTT-AAAT
* *
2525085 TGATTT-GA-
1 TTATTTAAAT
2525093 TTATTTTAAATT
1 TTA-TTTAAA-T
2525105 TTATTTAAAT
1 TTATTTAAAT
*
2525115 TTATTTATAT
1 TTATTTAAAT
2525125 TTAT
1 TTAT
2525129 AAATAATTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
8 2 0.05
9 4 0.09
10 21 0.48
11 14 0.32
12 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
TTATTTAAAT
Found at i:2525297 original size:18 final size:17
Alignment explanation
Indices: 2525269--2525318 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
2525259 ATTAAAGCTC
2525269 AATTTATTTTTTAAACA
1 AATTTATTTTTTAAACA
***
2525286 AATTTAATTTTTTATTTA
1 AATTT-ATTTTTTAAACA
2525304 AATTTATTTTTTAAA
1 AATTTATTTTTTAAA
2525319 ATTTTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTATTTTTTAAACA
Found at i:2525329 original size:27 final size:27
Alignment explanation
Indices: 2525291--2525346 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2525281 AAACAAATTT
* *
2525291 AATTTTTTATTTAAATTTATTTTTTAA
1 AATTTTATATTTAAATTTAATTTTTAA
**
2525318 AATTTTATATTTTTATTTAATTTTTAA
1 AATTTTATATTTAAATTTAATTTTTAA
2525345 AA
1 AA
2525347 ATATCAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
AATTTTATATTTAAATTTAATTTTTAA
Found at i:2527501 original size:16 final size:17
Alignment explanation
Indices: 2527482--2527528 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
2527472 TTATATGATG
2527482 ATAT-TAAAATAAATTA
1 ATATATAAAATAAATTA
*
2527498 ATATATAATATAAATTA
1 ATATATAAAATAAATTA
* *
2527515 A-ATCTAAGATAAAT
1 ATATATAAAATAAAT
2527529 AAAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
ATATATAAAATAAATTA
Found at i:2527529 original size:22 final size:22
Alignment explanation
Indices: 2527486--2527533 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
2527476 ATGATGATAT
*
2527486 TAAAATAAATTAATATATAATA
1 TAAAATAAATTAAGATATAATA
*
2527508 TAAATTAAATCTAAGATA-AATA
1 TAAAATAAAT-TAAGATATAATA
2527530 -AAAA
1 TAAAA
2527534 GAAAGAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.14
22 13 0.59
23 6 0.27
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATTAAGATATAATA
Found at i:2527666 original size:17 final size:15
Alignment explanation
Indices: 2527639--2527709 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
2527629 TAAAAATTTA
2527639 TATATTTATATAAATT
1 TATA-TTATATAAATT
2527655 T-TATTATTATATAATT
1 TATATTA-TATA-AATT
2527671 TATATTATATAAAATT
1 TATATTATAT-AAATT
** *
2527687 TA-AAAATATATATT
1 TATATTATATAAATT
2527701 TATA-TATAT
1 TATATTATAT
2527710 TTATTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
14 13 0.28
15 12 0.26
16 15 0.33
17 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:2527709 original size:14 final size:14
Alignment explanation
Indices: 2527637--2527715 Score: 58
Period size: 14 Copynumber: 5.6 Consensus size: 14
2527627 TTTAAAAATT
2527637 TATATATTTATATA
1 TATATATTTATATA
2527651 -A-AT-TTTAT-TA
1 TATATATTTATATA
2527661 TTATATAATTTATATTA
1 -TATAT-ATTTATA-TA
* * *
2527678 TATAAAATTTAAAAA
1 TAT-ATATTTATATA
2527693 TATATATTTATATA
1 TATATATTTATATA
*
2527707 TATTTATTT
1 TATATATTT
2527716 TATTTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
10 2 0.04
11 5 0.10
12 3 0.06
13 3 0.06
14 16 0.32
15 9 0.18
16 9 0.18
17 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATATTTATATA
Found at i:2527732 original size:52 final size:57
Alignment explanation
Indices: 2527627--2527732 Score: 150
Period size: 56 Copynumber: 1.9 Consensus size: 57
2527617 ATATTATTGT
2527627 TTTAAAAATTTATATATTTATATAAATTTTATTATTATATAATTTATATTATATAAAA
1 TTTAAAAA-TTATATATTTATATAAATTTTATTATTATATAATTTATATTATATAAAA
* *
2527685 TTTAAAAA-TATATATTTATATATA-TTTATT-TTAT-T-TTTTATATTATAT
1 TTTAAAAATTATATATTTATATAAATTTTATTATTATATAATTTATATTATAT
2527733 TTTATTACGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 12 0.26
53 1 0.02
54 4 0.09
55 6 0.13
56 15 0.33
58 8 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (57 bp):
TTTAAAAATTATATATTTATATAAATTTTATTATTATATAATTTATATTATATAAAA
Found at i:2528989 original size:23 final size:23
Alignment explanation
Indices: 2528962--2529012 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2528952 TTCATATTTT
*
2528962 TATATAATTTTTGATATTATA-AA
1 TATATAAATTTT-ATATTATATAA
*
2528985 TATATAAATTTTATATTTTATAA
1 TATATAAATTTTATATTATATAA
2529008 TATAT
1 TATAT
2529013 TCATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TATATAAATTTTATATTATATAA
Found at i:2532357 original size:20 final size:20
Alignment explanation
Indices: 2532334--2532371 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2532324 ATAAAAATAA
2532334 AATT-ATTTAAATATATTTTT
1 AATTAATTT-AATATATTTTT
*
2532354 AATTAATTTTATATATTT
1 AATTAATTTAATATATTT
2532372 ATTATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTAATTTAATATATTTTT
Found at i:2532381 original size:20 final size:20
Alignment explanation
Indices: 2532344--2532381 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2532334 AATTATTTAA
*
2532344 ATATATTTTTAATTAATTTT
1 ATATATTTTTAATAAATTTT
2532364 ATATATTTATT-ATAAATT
1 ATATATTT-TTAATAAATT
2532382 AAAATTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTTTTAATAAATTTT
Found at i:2533703 original size:29 final size:33
Alignment explanation
Indices: 2533635--2533703 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
2533625 TAATATATTA
* *
2533635 ATTAATATTTATAATTTATATTATAATAAAAAT
1 ATTAATATTTATAATATAGATTATAATAAAAAT
2533668 ATATAATA-TTATAATATAGA-TATAA-AAAAAT
1 AT-TAATATTTATAATATAGATTATAATAAAAAT
2533699 -TTAAT
1 ATTAAT
2533704 TAATCATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 4 0.12
30 1 0.03
31 6 0.18
32 5 0.15
33 12 0.36
34 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
ATTAATATTTATAATATAGATTATAATAAAAAT
Found at i:2533880 original size:4 final size:4
Alignment explanation
Indices: 2533871--2533899 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2533861 AAACTAAATT
2533871 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
2533900 TATTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:2534330 original size:27 final size:28
Alignment explanation
Indices: 2534265--2534331 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
2534255 TTTGATGATG
* * *
2534265 TATATTTAGATTTAAATATTAATAAATAT
1 TATATTT-TATTTAAATATTAATAAAAAA
* *
2534294 TA-AATATATTTAAA-ATTAATAAAAAA
1 TATATTTTATTTAAATATTAATAAAAAA
2534320 TATATTTTATTT
1 TATATTTTATTT
2534332 TTTAATTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
26 12 0.40
27 14 0.47
28 2 0.07
29 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TATATTTTATTTAAATATTAATAAAAAA
Found at i:2534531 original size:32 final size:29
Alignment explanation
Indices: 2534462--2534532 Score: 70
Period size: 32 Copynumber: 2.3 Consensus size: 29
2534452 TTTGAGTAAT
* **
2534462 ATTTAATTTTAATATATTTATTAAATTAA
1 ATTTAATTTTAATATATTTAATAAACGAA
**
2534491 ATAAAATTTTAATTATTAATTTAATAAACGAA
1 ATTTAATTTTAA-TA-T-ATTTAATAAACGAA
2534523 ATTTAATTTT
1 ATTTAATTTT
2534533 TTTATCAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 10 0.31
30 2 0.06
31 1 0.03
32 19 0.59
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
ATTTAATTTTAATATATTTAATAAACGAA
Found at i:2534734 original size:2 final size:2
Alignment explanation
Indices: 2534694--2534719 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2534684 TTTTGACAAG
2534694 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
2534720 CACACACAAA
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:2534868 original size:27 final size:26
Alignment explanation
Indices: 2534809--2534871 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
2534799 TCGTTAACTT
* * *
2534809 TATATTTTTTAATTTTTATTATTTTA
1 TATATATTTTAAATTTTATTAATTTA
2534835 TATATATTTTAAATTTT-TTAATTTA
1 TATATATTTTAAATTTTATTAATTTA
2534860 TAATAATATTTT
1 T-AT-ATATTTT
2534872 TTACAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.25
26 17 0.53
27 7 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TATATATTTTAAATTTTATTAATTTA
Found at i:2537857 original size:21 final size:22
Alignment explanation
Indices: 2537832--2537879 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
2537822 TGACTTTACA
2537832 TTTTAATATTTATAA-TAT-ATT
1 TTTTAATATTTA-AATTATAATT
*
2537853 TTTTAATTTTTAAATTATAATT
1 TTTTAATATTTAAATTATAATT
2537875 TTTTA
1 TTTTA
2537880 TGTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 14 0.58
22 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTAATATTTAAATTATAATT
Found at i:2538233 original size:13 final size:13
Alignment explanation
Indices: 2538215--2538241 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2538205 TGATTTGTGG
2538215 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
2538228 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
2538241 T
1 T
2538242 AATAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:2538286 original size:18 final size:16
Alignment explanation
Indices: 2538255--2538293 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
2538245 AAAAAATATA
2538255 TTTTTTAAAATTTTAT
1 TTTTTTAAAATTTTAT
*
2538271 TTTTTTAATAACTTTTCT
1 TTTTTTAA-AA-TTTTAT
2538289 TTTTT
1 TTTTT
2538294 CTTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTAAAATTTTAT
Found at i:2538291 original size:23 final size:22
Alignment explanation
Indices: 2538265--2538320 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
2538255 TTTTTTAAAA
*
2538265 TTTTATTTTTTTAAT-AACTTT
1 TTTTATTTTTTTAATAAACTAT
*
2538286 TCTTTTTTCTTTTTAATAAACTAT
1 T-TTTATT-TTTTTAATAAACTAT
2538310 TTTTATTTTTT
1 TTTTATTTTTT
2538321 CTTTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
23 13 0.45
24 6 0.21
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTTTTTTAATAAACTAT
Found at i:2538822 original size:26 final size:25
Alignment explanation
Indices: 2538793--2538857 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
2538783 ACTAAATAAA
2538793 ATATATTTTTATTTAAATTTAATCTT
1 ATATATTTTTATTTAAATTTAAT-TT
* *
2538819 ATATATGTATA-TTAAATTTAATTT
1 ATATATTTTTATTTAAATTTAATTT
*
2538843 A-AAATTATTTATTTA
1 ATATATT-TTTATTTA
2538858 TTTCTTCGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 3 0.09
24 6 0.19
25 14 0.44
26 9 0.28
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATATTTTTATTTAAATTTAATTT
Found at i:2548141 original size:15 final size:15
Alignment explanation
Indices: 2548117--2548174 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
2548107 TGAAATTAAT
*
2548117 TTTATTTTTATATTA
1 TTTATATTTATATTA
*
2548132 TTTATATTTATTTTA
1 TTTATATTTATATTA
* *
2548147 TTTTTTATTTATATAA
1 -TTTATATTTATATTA
* *
2548163 ATTATATATATA
1 TTTATATTTATA
2548175 AATTAAAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATATTTATATTA
Found at i:2548172 original size:13 final size:13
Alignment explanation
Indices: 2548151--2548194 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2548141 ATTTTATTTT
*
2548151 TTATTTATATAAA
1 TTATATATATAAA
2548164 TTATATATATAAA
1 TTATATATATAAA
* *
2548177 TTAAAAATATATAA
1 TTATATATATA-AA
2548191 TTAT
1 TTAT
2548195 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATATATATAAA
Found at i:2548312 original size:21 final size:20
Alignment explanation
Indices: 2548288--2548338 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2548278 ATGTATATAT
*
2548288 ATAATTATATTATTAAATTTA
1 ATAATTATATTATTAAA-ATA
2548309 ATAATTA-ATTTATTAAAATA
1 ATAATTATA-TTATTAAAATA
*
2548329 TTAATTATAT
1 ATAATTATAT
2548339 AAAAATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATTATATTATTAAAATA
Found at i:2548331 original size:16 final size:17
Alignment explanation
Indices: 2548312--2548344 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2548302 AAATTTAATA
*
2548312 ATTAATT-TATTAAAAT
1 ATTAATTATATAAAAAT
2548328 ATTAATTATATAAAAAT
1 ATTAATTATATAAAAAT
2548345 TATGATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAATTATATAAAAAT
Found at i:2548398 original size:17 final size:17
Alignment explanation
Indices: 2548296--2548414 Score: 54
Period size: 15 Copynumber: 6.9 Consensus size: 17
2548286 ATATAATTAT
*
2548296 ATTATTA-AATTTAATA
1 ATTATTATAAATTAATA
* *
2548312 ATTAATTTATTAAAATATTA
1 ATT-A-TTA-TAAATTAATA
*
2548332 ATTATATAAAAATTATGATA
1 ATTAT-TATAAATTA--ATA
2548352 A-TA-TATAAAATTAAATTA
1 ATTATTAT-AAATT-AA-TA
*
2548370 ATT-TT-TACATTAATA
1 ATTATTATAAATTAATA
2548385 ATTATTATAAATTAAT-
1 ATTATTATAAATTAATA
*
2548401 -TTTTTATAAATTAA
1 ATTATTATAAATTAA
2548415 ATTTTATATA
Statistics
Matches: 79, Mismatches: 10, Indels: 29
0.67 0.08 0.25
Matches are distributed among these distances:
15 18 0.23
16 7 0.09
17 16 0.20
18 18 0.23
19 8 0.10
20 12 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (17 bp):
ATTATTATAAATTAATA
Found at i:2548419 original size:16 final size:15
Alignment explanation
Indices: 2548363--2548424 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
2548353 TATATAAAAT
*
2548363 TAAATTAATTTTTACA
1 TAAATTAATTTTT-TA
* *
2548379 TTAA-TAA-TTATTA
1 TAAATTAATTTTTTA
2548392 TAAATTAATTTTTTA
1 TAAATTAATTTTTTA
*
2548407 TAAATTAAATTTTATA
1 TAAATT-AATTTTTTA
2548423 TA
1 TA
2548425 TCATAAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.11
14 6 0.16
15 14 0.38
16 13 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATTAATTTTTTA
Found at i:2555955 original size:2 final size:2
Alignment explanation
Indices: 2555948--2555986 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2555938 TCTTCTCCTT
2555948 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 T
2555987 TGTGATCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2556234 original size:17 final size:18
Alignment explanation
Indices: 2556204--2556237 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2556194 AATTTTCTCA
2556204 TTTTATATTATTTAAATT
1 TTTTATATTATTTAAATT
*
2556222 TTTTAT-TTTTTTAAAT
1 TTTTATATTATTTAAAT
2556238 ATTCATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATATTATTTAAATT
Found at i:2557894 original size:92 final size:90
Alignment explanation
Indices: 2557766--2557935 Score: 261
Period size: 92 Copynumber: 1.9 Consensus size: 90
2557756 ACATACATAC
*
2557766 ATATATATATATACCAACTTGCTCATCCTTTGGCTTAAAATTCTCTAGATTTGTTTTCTTTTGAA
1 ATATATATATATACCAACTTGCTCATCCTTTAGCTTAAAATTCTCTAGATTTGTTTTCTTTTGAA
2557831 ACCTG-AATTATCATTATATATATAT
66 A-CTGAAATTATCATTATATATATAT
* * *
2557856 ATATATATATATAACCAGCTTGCTGATCCTTTTAGCTTAAAATTTTCTAGATTTGTTTTCTTTTG
1 ATATATATATAT-ACCAACTTGCTCATCC-TTTAGCTTAAAATTCTCTAGATTTGTTTTCTTTTG
*
2557921 GAACTGAAATTATCA
64 AAACTGAAATTATCA
2557936 ATAGATTAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
90 12 0.17
91 17 0.24
92 43 0.60
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (90 bp):
ATATATATATATACCAACTTGCTCATCCTTTAGCTTAAAATTCTCTAGATTTGTTTTCTTTTGAA
ACTGAAATTATCATTATATATATAT
Found at i:2561040 original size:23 final size:22
Alignment explanation
Indices: 2560992--2561040 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
2560982 TTTATTTTAT
* * *
2560992 TTTATTTTTTAATATAAATTTT
1 TTTATTTTTTAAAATAAATATA
*
2561014 TTTATTTTTATAAAATTAATATA
1 TTTATTTTT-TAAAATAAATATA
2561037 TTTA
1 TTTA
2561041 ATAATAAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTTTTTAAAATAAATATA
Found at i:2561340 original size:23 final size:21
Alignment explanation
Indices: 2561291--2561343 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
2561281 TTTCTAGCAG
2561291 TTATATATAAATATAATAAAAA
1 TTATAT-TAAATATAATAAAAA
2561313 -T-TATTAAATATAAATAAAAA
1 TTATATTAAATAT-AATAAAAA
2561333 TTTATATTAAA
1 -TTATATTAAA
2561344 ATACATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.26
20 11 0.41
21 1 0.04
22 1 0.04
23 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATATTAAATATAATAAAAA
Found at i:2561389 original size:21 final size:21
Alignment explanation
Indices: 2561347--2561397 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2561337 TATTAAAATA
*
2561347 CATATTATATTATCTATCTTAT
1 CATATT-TATTATATATCTTAT
* *
2561369 CATATTTATTATATTTTTTAT
1 CATATTTATTATATATCTTAT
*
2561390 AATATTTA
1 CATATTTA
2561398 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (21 bp):
CATATTTATTATATATCTTAT
Found at i:2564164 original size:18 final size:18
Alignment explanation
Indices: 2564123--2564171 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2564113 AATATTATTT
* * *
2564123 TTAAATTTTTTTTAAATA
1 TTAAATTATTTTAAAAAA
2564141 TATAAATTATTTTAAAAAA
1 T-TAAATTATTTTAAAAAA
2564160 TTAAATATATTT
1 TTAAAT-TATTT
2564172 ATTTTCAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATTATTTTAAAAAA
Found at i:2565031 original size:25 final size:23
Alignment explanation
Indices: 2564986--2565036 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
2564976 ATATTTTAAA
* *
2564986 AAATATATTTTATATTTATATTT
1 AAATATATTTTAAATTAATATTT
2565009 AAATATATTTTAAATCTAAATATTT
1 AAATATATTTTAAAT-T-AATATTT
2565034 AAA
1 AAA
2565037 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.58
24 1 0.04
25 9 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATATTTTAAATTAATATTT
Found at i:2565738 original size:22 final size:23
Alignment explanation
Indices: 2565696--2565749 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
2565686 TAACATTTAA
2565696 ATTTTAATATTTATAATTTTTTTT
1 ATTTTAA-ATTTATAATTTTTTTT
2565720 ATTTTAAA-TTATGAA-TTTTTTT
1 ATTTTAAATTTAT-AATTTTTTTT
*
2565742 ATGTTAAA
1 ATTTTAAA
2565750 AAAAGTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 18 0.64
23 3 0.11
24 7 0.25
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (23 bp):
ATTTTAAATTTATAATTTTTTTT
Found at i:2565739 original size:24 final size:24
Alignment explanation
Indices: 2565696--2565741 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
2565686 TAACATTTAA
2565696 ATTTTAATATTTATAATTTTTTTT
1 ATTTTAATATTTATAATTTTTTTT
2565720 ATTTTAA-A-TTATGAATTTTTTT
1 ATTTTAATATTTAT-AATTTTTTT
2565742 ATGTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 10 0.48
24 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
ATTTTAATATTTATAATTTTTTTT
Found at i:2566757 original size:21 final size:21
Alignment explanation
Indices: 2566733--2566781 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
2566723 TGATATAATT
2566733 TTAAAATTTTAA-TTTTAATGA
1 TTAAAA-TTTAATTTTTAATGA
2566754 TTAAAATTTAATTTTTAATGA
1 TTAAAATTTAATTTTTAATGA
2566775 TATAAAA
1 T-TAAAA
2566782 AAATTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.19
21 16 0.62
22 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTAAAATTTAATTTTTAATGA
Found at i:2570769 original size:97 final size:96
Alignment explanation
Indices: 2570603--2570797 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 96
2570593 CAAAGATTGA
*
2570603 AACCCAAACTAGGTGCCTTTACTGTATGTATATGTGCATACAGAGATGATGACAAGAAATTTAGA
1 AACCCAAACTAGGTGCCTTTACTGTATGTATATGTGCATACAGAGATGATGACAAGAAATTTAAA
*
2570668 GAGCAGTTCTGTAGAAAAATAAGTAGAGATAT
66 GAGCAGTTCTGTAG-AAAATAAGTAGAGACAT
*
2570700 AACCCAAACTAGGTGCCTTTACTGTATGTATATGTGCATAGAGAGATGATGACAAGAAATTTAAA
1 AACCCAAACTAGGTGCCTTTACTGTATGTATATGTGCATACAGAGATGATGACAAGAAATTTAAA
2570765 GAGCAGTTCTGTAGAAAATAAGTAGAGACAT
66 GAGCAGTTCTGTAGAAAATAAGTAGAGACAT
2570796 AA
1 AA
2570798 ATTTAACATC
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 18 0.19
97 77 0.81
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (96 bp):
AACCCAAACTAGGTGCCTTTACTGTATGTATATGTGCATACAGAGATGATGACAAGAAATTTAAA
GAGCAGTTCTGTAGAAAATAAGTAGAGACAT
Found at i:2573141 original size:15 final size:16
Alignment explanation
Indices: 2573109--2573146 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
2573099 TTCGTAATGA
*
2573109 ATATTAAATATAAAAT
1 ATATTTAATATAAAAT
2573125 ATATTTAATAT-AAAT
1 ATATTTAATATAAAAT
2573140 ATATTTA
1 ATATTTA
2573147 TTTTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTTAATATAAAAT
Found at i:2574386 original size:14 final size:15
Alignment explanation
Indices: 2574367--2574395 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2574357 ACACAACCTC
2574367 TTTTCTCT-TTTATT
1 TTTTCTCTGTTTATT
2574381 TTTTCTCTGTTTATT
1 TTTTCTCTGTTTATT
2574396 ACCAAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTCTCTGTTTATT
Found at i:2577088 original size:34 final size:34
Alignment explanation
Indices: 2577051--2577177 Score: 182
Period size: 34 Copynumber: 3.7 Consensus size: 34
2577041 AATATAAAAT
* * *
2577051 ACCTAACACACTTAATATTCTCACCAAATACATT
1 ACCTAACACACCTAACATTCTCACCAAATACATC
*
2577085 ACCTAACACACCTAACATTCTCACCAAATAAATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
** *
2577119 ACCTAACACATTTAACATTATCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
*
2577153 ACCTAATACACCTAACATTCTCACC
1 ACCTAACACACCTAACATTCTCACC
2577178 GAACACACTT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 81 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:2577125 original size:68 final size:67
Alignment explanation
Indices: 2577047--2577177 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 67
2577037 AATAAATATA
* * *
2577047 AAATACCTAACACACTTAATATTCTCACCAAATACATTACCTAACACACCTAACATTCTCACCAA
1 AAATACCTAACACACTTAACATTATCACCAAATACATCACCTAACACACCTAACATTCTCACCAA
2577112 AT
66 AT
* *
2577114 AAATCACCTAACACATTTAACATTATCACCAAATACATCACCTAATACACCTAACATTCTCACC
1 AAAT-ACCTAACACACTTAACATTATCACCAAATACATCACCTAACACACCTAACATTCTCACC
2577178 GAACACACTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
67 4 0.07
68 54 0.93
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (67 bp):
AAATACCTAACACACTTAACATTATCACCAAATACATCACCTAACACACCTAACATTCTCACCAA
AT
Found at i:2577605 original size:43 final size:42
Alignment explanation
Indices: 2577544--2577628 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 42
2577534 AGATTAATTA
*
2577544 ATCAACGATTTCACTTTCAGTCAAAATGTGATTAATTGAAAAT
1 ATCAACGATTTCACTTTCAGTCAAAATATGA-TAATTGAAAAT
2577587 ATCAACGATTTCACTTTCAGTCAAAATATGATAATTGAAAAT
1 ATCAACGATTTCACTTTCAGTCAAAATATGATAATTGAAAAT
2577629 TCCCACCTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 11 0.27
43 30 0.73
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (42 bp):
ATCAACGATTTCACTTTCAGTCAAAATATGATAATTGAAAAT
Found at i:2579430 original size:15 final size:15
Alignment explanation
Indices: 2579405--2579459 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
2579395 TTCAAAATCG
2579405 AATTA-TTTAAGTTC
1 AATTATTTTAAGTTC
*
2579419 AATTATTTTAAGCTC
1 AATTATTTTAAGTTC
*
2579434 ATATTATTTTAAGTTA
1 A-ATTATTTTAAGTTC
2579450 AATTTATTTT
1 AA-TTATTTT
2579460 GGTTTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.14
15 10 0.29
16 20 0.57
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (15 bp):
AATTATTTTAAGTTC
Found at i:2580176 original size:22 final size:21
Alignment explanation
Indices: 2580151--2580191 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2580141 ATAAAAAAAA
*
2580151 CATACTTTTAATATAAAAATTT
1 CATAATTTT-ATATAAAAATTT
*
2580173 CATAATTTTATTTAAAAAT
1 CATAATTTTATATAAAAAT
2580192 ATTTATCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
CATAATTTTATATAAAAATTT
Found at i:2580366 original size:64 final size:64
Alignment explanation
Indices: 2580260--2580389 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
2580250 GGGACATCAC
2580260 ACTACACCAAATCTAGGGATTAGGGGTACATATAATACGAATAAATACAGTTCAGCCTACTCCT
1 ACTACACCAAATCTAGGGATTAGGGGTACATATAATACGAATAAATACAGTTCAGCCTACTCCT
*
2580324 ACTACACCAAATCTAGGGATTAGGGGTACATATAATATGAATAAATACAGTTCAGCCTACTCCT
1 ACTACACCAAATCTAGGGATTAGGGGTACATATAATACGAATAAATACAGTTCAGCCTACTCCT
2580388 AC
1 AC
2580390 CTAGGAGCCC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (64 bp):
ACTACACCAAATCTAGGGATTAGGGGTACATATAATACGAATAAATACAGTTCAGCCTACTCCT
Found at i:2584428 original size:12 final size:12
Alignment explanation
Indices: 2584411--2584442 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2584401 ATATAGATGG
2584411 TCCAAGCAGGGT
1 TCCAAGCAGGGT
2584423 TCCAAGCAGGGT
1 TCCAAGCAGGGT
*
2584435 TTCAAGCA
1 TCCAAGCA
2584443 CAAAGAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (12 bp):
TCCAAGCAGGGT
Found at i:2590456 original size:16 final size:15
Alignment explanation
Indices: 2590435--2590464 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2590425 TGCTAGGTAG
2590435 GAAAGAAAAATAAGAA
1 GAAAGAAAAA-AAGAA
2590451 GAAAGAAAAAAAGA
1 GAAAGAAAAAAAGA
2590465 TTTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (15 bp):
GAAAGAAAAAAAGAA
Found at i:2594349 original size:22 final size:21
Alignment explanation
Indices: 2594323--2594384 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
2594313 TTGAAAAAAT
* *
2594323 ATATATGAATTAATTATGATTC
1 ATATATGAATTAATTAAG-TAC
*
2594345 ATATATAAATTTAATTAAGTAC
1 ATATATGAA-TTAATTAAGTAC
*
2594367 ATGTATGAATT-ATTAAGT
1 ATATATGAATTAATTAAGT
2594385 TCATCTACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.21
21 2 0.06
22 17 0.50
23 8 0.24
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (21 bp):
ATATATGAATTAATTAAGTAC
Found at i:2595541 original size:2 final size:2
Alignment explanation
Indices: 2595529--2595566 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2595519 AAAGATATTA
*
2595529 AT AT TT 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
2595567 GCATGTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2595969 original size:16 final size:16
Alignment explanation
Indices: 2595940--2596000 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
2595930 TAAAAAGTGA
2595940 AAAACAAAATAAAAAG
1 AAAACAAAATAAAAAG
*
2595956 AAAACTAAAA-AAAAAT
1 AAAAC-AAAATAAAAAG
****
2595972 AAATGTTAATAAAAAG
1 AAAACAAAATAAAAAG
2595988 AAAACAAAATAAA
1 AAAACAAAATAAA
2596001 GTACACCTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
15 2 0.06
16 27 0.82
17 4 0.12
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAACAAAATAAAAAG
Found at i:2597777 original size:2 final size:2
Alignment explanation
Indices: 2597770--2597826 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2597760 GTTAGTGTTT
2597770 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2597812 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2597827 GTAGTAGATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2598077 original size:63 final size:63
Alignment explanation
Indices: 2597969--2598087 Score: 175
Period size: 63 Copynumber: 1.9 Consensus size: 63
2597959 TGATATATAT
* * * *
2597969 ATATATATTGAATCTTAACATAATTTAAGCCACATGCTTGCACATGATCATTCAAATGCATAA
1 ATATATATCGAATCCTAAAATAATTTAAGCCACATGCATGCACATGATCATTCAAATGCATAA
* * *
2598032 ATATTTATCGAATCCTAAAATAATTTAAGCCACGTGCATGTACATGATCATTCAAA
1 ATATATATCGAATCCTAAAATAATTTAAGCCACATGCATGCACATGATCATTCAAA
2598088 CCTCTATAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (63 bp):
ATATATATCGAATCCTAAAATAATTTAAGCCACATGCATGCACATGATCATTCAAATGCATAA
Found at i:2602041 original size:34 final size:34
Alignment explanation
Indices: 2602002--2602095 Score: 154
Period size: 34 Copynumber: 2.7 Consensus size: 34
2601992 TTAAAGGGCT
2602002 TTTGTATTCTTTATTGTTATTCTTTAAAAGCTTA
1 TTTGTATTCTTTATTGTTATTCTTTAAAAGCTTA
2602036 TTTGTATTCTTTATTGTTATTCTTTAAAAGCTTA
1 TTTGTATTCTTTATTGTTATTCTTTAAAAGCTTA
*
2602070 TTTGTATTCCTTT-GTGCTTATTCTTT
1 TTTGTATT-CTTTATTG-TTATTCTTT
2602096 CATAAACACC
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
34 44 0.77
35 13 0.23
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.61
Consensus pattern (34 bp):
TTTGTATTCTTTATTGTTATTCTTTAAAAGCTTA
Found at i:2602403 original size:32 final size:32
Alignment explanation
Indices: 2602362--2602423 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
2602352 ATGTTTGGAT
2602362 CGAACCTCTATAAACACTTGTGTCAAGCTTAC
1 CGAACCTCTATAAACACTTGTGTCAAGCTTAC
2602394 CGAACCTCTATAAACACTTGTGTCAAGCTT
1 CGAACCTCTATAAACACTTGTGTCAAGCTT
2602424 TCTCTTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (32 bp):
CGAACCTCTATAAACACTTGTGTCAAGCTTAC
Found at i:2607680 original size:63 final size:63
Alignment explanation
Indices: 2607577--2607703 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
2607567 GAGACAAGTA
2607577 AGCATTACACTTCTAGATTTTAACTTAGCAAATCAAGTAGCTTTAAGTTCATCTAAGTCAGCC
1 AGCATTACACTTCTAGATTTTAACTTAGCAAATCAAGTAGCTTTAAGTTCATCTAAGTCAGCC
** * * **
2607640 AGCATTACGGTTCTAGATTTTAGCTTAGCAAATCACGTAGCTTTAAGTTTGTCTAAGTCAGCC
1 AGCATTACACTTCTAGATTTTAACTTAGCAAATCAAGTAGCTTTAAGTTCATCTAAGTCAGCC
2607703 A
1 A
2607704 TTAAGCACTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (63 bp):
AGCATTACACTTCTAGATTTTAACTTAGCAAATCAAGTAGCTTTAAGTTCATCTAAGTCAGCC
Found at i:2612897 original size:8 final size:8
Alignment explanation
Indices: 2612886--2612918 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
2612876 CATTTTGGTT
2612886 TTTTTATC
1 TTTTTATC
2612894 TTTTTATC
1 TTTTTATC
*
2612902 TTTTTTTC
1 TTTTTATC
2612910 TTTTT-TC
1 TTTTTATC
2612917 TT
1 TT
2612919 CTTCTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTATC
Found at i:2614810 original size:12 final size:12
Alignment explanation
Indices: 2614770--2614812 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
2614760 CTTCAATTAT
*
2614770 CTTGCCCTCCAC
1 CTTGGCCTCCAC
*
2614782 CTTGACCTCCAC
1 CTTGGCCTCCAC
2614794 CTTGGCCTCCAC
1 CTTGGCCTCCAC
2614806 CTTGGCC
1 CTTGGCC
2614813 CCCTGTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.51, G:0.14, T:0.26
Consensus pattern (12 bp):
CTTGGCCTCCAC
Found at i:2615398 original size:2 final size:2
Alignment explanation
Indices: 2615338--2615380 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2615328 ATTGATATTG
2615338 AT AT -T 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
2615379 AT
1 AT
2615381 CCATTGCGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2617867 original size:20 final size:19
Alignment explanation
Indices: 2617839--2617889 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
2617829 TTAAAATAAA
2617839 ATAAA-TATTAATTAAATAT
1 ATAAATTATTAATTAAA-AT
*
2617858 ATAAATTATTTATTTAAAAT
1 ATAAATTA-TTAATTAAAAT
2617878 A-ATAATTATTAA
1 ATA-AATTATTAA
2617890 ATAATTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.33
20 10 0.37
21 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATTATTAATTAAAAT
Found at i:2619620 original size:92 final size:92
Alignment explanation
Indices: 2619444--2619621 Score: 197
Period size: 92 Copynumber: 1.9 Consensus size: 92
2619434 AAATTAAACC
* *
2619444 AATGCATGAATTATATTTGAGAATAGGATTTCTTCTGATAGAAAGAAAGAAAAGTTGAATGATTG
1 AATGCATGAATTATATTTGAGAATAGGATTCCTTCTGATAGAAAGAAAGAAAAGTTGAATGATTA
* * *
2619509 TAAATATTATACTGTAAGGATTAGACT
66 TAAATATCACAATGTAAGGATTAGACT
*
2619536 AATGCAT-AGATTATATTTGAGAATCA-GATTCCTTTTGATA-AAA-AAAGAAAAAAGTT-AATT
1 AATGCATGA-ATTATATTTGAGAAT-AGGATTCCTTCTGATAGAAAGAAAG--AAAAGTTGAA-T
*
2619596 GATTATAAATGTCACAAT-TAAAGGAT
61 GATTATAAATATCACAATGT-AAGGAT
2619622 GATACAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
90 4 0.05
91 7 0.10
92 61 0.84
93 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (92 bp):
AATGCATGAATTATATTTGAGAATAGGATTCCTTCTGATAGAAAGAAAGAAAAGTTGAATGATTA
TAAATATCACAATGTAAGGATTAGACT
Found at i:2620838 original size:73 final size:73
Alignment explanation
Indices: 2620526--2621021 Score: 527
Period size: 74 Copynumber: 6.8 Consensus size: 73
2620516 CTCTAAATAA
* * * * * *
2620526 AAATTTAAACTTCTA-AAAGTAAAGATAAATAATACCGTAAAAATTTAAACCCATATAATCA-AC
1 AAATTTAAACTTCTACAAA-TAAAAATAAATTATACCATAAAAATTTAAACTCGTATAATAATAC
2620589 CC-AAAAAT
65 CCAAAAAAT
* * *
2620597 AAATTTAAACTTTTACAAATAAAAATAAATTATATCATAAAAAATTTAAACTTGTATAATAATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCAT-AAAAATTTAAACTCGTATAATAATAC
* *
2620662 CCTAAAAAC
65 CCAAAAAAT
* * * * * *
2620671 ACATTTAAACTTATAAAAATAAAAATAAATTATACCATCAAAAATTTAAATTCATATAATCATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCAT-AAAAATTTAAACTCGTATAATAATAC
2620736 CCAAAAAAT
65 CCAAAAAAT
* * * * *
2620745 ATATTTAAACTTCTATAAATAAAAATAAATTATACCATCAAAACTTAAACTCGTATAATAATATC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAATTTAAACTCGTATAATAATACC
*
2620810 AAAAAAAT
66 CAAAAAAT
* ** * * * * *
2620818 AAATTTAAACTTTTACAAATAATGATAAATAATACCTTAAAAATTTAAACACGAATAATAA-AAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAATTTAAACTCGTATAATAATACC
*
2620882 TAAAAAAT
66 CAAAAAAT
* ** * *
2620890 AAATTTAAACTTCTACAAATAAAAATAAATTACACTTTAAAAATTTTAAACTCATATAATCATAC
1 AAATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAA-TTTAAACTCGTATAATAATAC
*
2620955 CTAAAAAAT
65 CCAAAAAAT
* * * *
2620964 ACATTTAAACTTCTACAAATCAAAATAAATTATATTC-T-AAAATTTAAACTCGCATAAT
1 AAATTTAAACTTCTACAAATAAAAATAAATTATA-CCATAAAAATTTAAACTCGTATAAT
2621022 CAAATAAAAA
Statistics
Matches: 356, Mismatches: 62, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
71 29 0.08
72 82 0.23
73 100 0.28
74 145 0.41
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (73 bp):
AAATTTAAACTTCTACAAATAAAAATAAATTATACCATAAAAATTTAAACTCGTATAATAATACC
CAAAAAAT
Found at i:2620947 original size:219 final size:217
Alignment explanation
Indices: 2620528--2621052 Score: 605
Period size: 219 Copynumber: 2.4 Consensus size: 217
2620518 CTAAATAAAA
* * * * * * **
2620528 ATTTAAACTTCTAAAAGTAAAGATAAATAATACCGTAAAAATTTAAACCCATATAATCAACCCAA
1 ATTTAAACTTCTAAAA-TAAAAATAAATTATACCATCAAAATTTAAACTCGTATAAT-AAATCAA
* ** *
2620593 AAATAAATTTAAACTTTTACAAATAAAAATAAATTATATCATAAAAAATTTAAACTTGTATAATA
64 AAATAAATTTAAACTTTTACAAATAAAAATAAATAATATCATAAAAAATTTAAACACGAATAATA
* * * *
2620658 ATACCCTAAAAACACATTTAAACTTATAAAAATAAAAATAAATTATACCATCAAAAATTTAAATT
129 ATACACTAAAAACAAATTTAAACTTATAAAAATAAAAATAAATTACACCATCAAAAATTTAAACT
*
2620723 CATATAATCATACCCAAAAAATAT
194 CATATAATCATACCCAAAAAATAC
*
2620747 ATTTAAACTTCTATAAATAAAAATAAATTATACCATCAAAACTTAAACTCGTATAATAATATCAA
1 ATTTAAACTTCTA-AAATAAAAATAAATTATACCATCAAAATTTAAACTCGTATAATAA-ATC--
** * *
2620812 AAAAATAAATTTAAACTTTTACAAATAATGATAAATAATA-CCTTAAAAATTTAAACACGAATAA
62 AAAAATAAATTTAAACTTTTACAAATAAAAATAAATAATATCATAAAAAATTTAAACACGAATAA
* * * * *
2620876 TAA-A-ACTAAAAAATAAATTTAAACTTCTACAAATAAAAATAAATTACA-CTTTAAAAATTTTA
127 TAATACACT-AAAAACAAATTTAAACTTATAAAAATAAAAATAAATTACACCATCAAAAA-TTTA
*
2620938 AACTCATATAATCATACCTAAAAAATAC
190 AACTCATATAATCATACCCAAAAAATAC
* * *
2620966 ATTTAAACTTCTACAAATCAAAATAAATTATA--TTCTAAAATTTAAACTCGCATAATCAAAT-A
1 ATTTAAACTTCTA-AAATAAAAATAAATTATACCATC-AAAATTTAAACTCGTATAAT-AAATCA
* *
2621028 AAAATAAACTTAAACTTTTATAAAT
63 AAAATAAATTTAAACTTTTACAAAT
2621053 TCGTATAATC
Statistics
Matches: 263, Mismatches: 35, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
215 24 0.09
217 2 0.01
218 31 0.12
219 144 0.55
220 25 0.10
221 37 0.14
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (217 bp):
ATTTAAACTTCTAAAATAAAAATAAATTATACCATCAAAATTTAAACTCGTATAATAAATCAAAA
ATAAATTTAAACTTTTACAAATAAAAATAAATAATATCATAAAAAATTTAAACACGAATAATAAT
ACACTAAAAACAAATTTAAACTTATAAAAATAAAAATAAATTACACCATCAAAAATTTAAACTCA
TATAATCATACCCAAAAAATAC
Found at i:2621196 original size:25 final size:23
Alignment explanation
Indices: 2621132--2621200 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 23
2621122 CTAATCTTAT
* *
2621132 AAATAAAAATAAATTACACATTA
1 AAATAAAAATAAATTAAACTTTA
2621155 AAAT-AAAATAAATTTAAACTTCTA
1 AAATAAAAATAAA-TTAAACTT-TA
*
2621179 CAATTAAAAATAAATTAAACTT
1 -AAATAAAAATAAATTAAACTT
2621201 GTATAATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 8 0.21
23 10 0.26
24 2 0.05
25 11 0.28
26 8 0.21
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATAAAAATAAATTAAACTTTA
Found at i:2621474 original size:15 final size:15
Alignment explanation
Indices: 2621454--2621487 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2621444 GGCACTTATT
*
2621454 TTTAAATTTTTTTAA
1 TTTAAAATTTTTTAA
*
2621469 TTTAAAATTTTTTAT
1 TTTAAAATTTTTTAA
2621484 TTTA
1 TTTA
2621488 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTAAAATTTTTTAA
Found at i:2623964 original size:3 final size:3
Alignment explanation
Indices: 2623958--2623996 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2623948 TATAATACTT
2623958 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2623997 AGGTTTTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2625372 original size:31 final size:32
Alignment explanation
Indices: 2625347--2625430 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 32
2625337 TATTTTATTT
*
2625347 TATTTTTAAATATA-ATTATTGTATTTTAAAG
1 TATTATTAAATATATATTATTGTATTTTAAAG
* * *
2625378 TATTATTAAATATATTTTTTTGTATTTTAATG
1 TATTATTAAATATATATTATTGTATTTTAAAG
* * *
2625410 GATTATCAAATATAAATTATT
1 TATTATTAAATATATATTATT
2625431 TCATTATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 13 0.30
32 30 0.70
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (32 bp):
TATTATTAAATATATATTATTGTATTTTAAAG
Found at i:2625385 original size:21 final size:21
Alignment explanation
Indices: 2625335--2625385 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2625325 GAAAAATAAT
*
2625335 AATATT-TTATTTTATTTTTA
1 AATATTATTATTGTATTTTTA
*
2625355 AATATAATTATTGTA-TTTTA
1 AATATTATTATTGTATTTTTA
2625375 AAGTATTATTA
1 AA-TATTATTA
2625386 AATATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
AATATTATTATTGTATTTTTA
Found at i:2625486 original size:35 final size:35
Alignment explanation
Indices: 2625442--2625555 Score: 86
Period size: 35 Copynumber: 3.2 Consensus size: 35
2625432 CATTATTATA
2625442 TAATAATAATAATTAAATATTATTTATAAATATTTT
1 TAAT-ATAATAATTAAATATTATTTATAAATATTTT
*** * * * *
2625478 TAATATAATAGGAAAATCTTATTCATAAGATGTATTA
1 TAATATAATAATTAAATATTATTTATAA-ATAT-TTT
* * *
2625515 AAATATAATATTTAAATATTA-TTAAACAATATTTT
1 TAATATAATAATTAAATATTATTTATA-AATATTTT
*
2625550 TGATAT
1 TAATAT
2625556 TAAATTAGAG
Statistics
Matches: 57, Mismatches: 18, Indels: 7
0.70 0.22 0.09
Matches are distributed among these distances:
35 25 0.44
36 13 0.23
37 19 0.33
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (35 bp):
TAATATAATAATTAAATATTATTTATAAATATTTT
Found at i:2625594 original size:76 final size:75
Alignment explanation
Indices: 2625447--2625639 Score: 279
Period size: 76 Copynumber: 2.6 Consensus size: 75
2625437 TTATATAATA
* * *
2625447 ATAATAATTAAATATTATTTATAAATATTTTTAATA-T-AA-TAG-GAAAATCTTATTCATAAGA
1 ATAATATTTAAATATTA-TTAAAAATATTTTTGATATTAAATTAGAGAAAATCTTATTCATAAGA
*
2625508 TGTATTAAAAT
65 TGTATAAAAAT
*
2625519 ATAATATTTAAATATTATTAAACAATATTTTTGATATTAAATTAGAGTAAATCTTATTCATAAGA
1 ATAATATTTAAATATTATTAAA-AATATTTTTGATATTAAATTAGAGAAAATCTTATTCATAAGA
2625584 TGTATAAAAAT
65 TGTATAAAAAT
2625595 ATAATATTTAAATATTATTAAATAATA-TTTTGATATTAAATTAGA
1 ATAATATTTAAATATTATTAAA-AATATTTTTGATATTAAATTAGA
2625640 ATTATTAAAT
Statistics
Matches: 110, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
71 4 0.04
72 28 0.25
73 1 0.01
74 2 0.02
75 21 0.19
76 54 0.49
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (75 bp):
ATAATATTTAAATATTATTAAAAATATTTTTGATATTAAATTAGAGAAAATCTTATTCATAAGAT
GTATAAAAAT
Found at i:2625672 original size:23 final size:24
Alignment explanation
Indices: 2625644--2625696 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2625634 ATTAGAATTA
2625644 TTAAATAATT-AT-TAGATAAACTT
1 TTAAATAATTCATAT-GATAAACTT
* *
2625667 TTAAATATTTCATATTATAAACTT
1 TTAAATAATTCATATGATAAACTT
2625691 TTAAAT
1 TTAAAT
2625697 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 9 0.35
24 16 0.62
25 1 0.04
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (24 bp):
TTAAATAATTCATATGATAAACTT
Found at i:2627846 original size:24 final size:24
Alignment explanation
Indices: 2627797--2627846 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2627787 TTAAAGACAT
* *
2627797 TATTTTTATTTTATTATATAATAA
1 TATTTTTATTTAATTATATAAAAA
2627821 TATTTTTATTTAATGTAT-TAAAAA
1 TATTTTTATTTAAT-TATATAAAAA
2627845 TA
1 TA
2627847 ATAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TATTTTTATTTAATTATATAAAAA
Found at i:2628424 original size:24 final size:24
Alignment explanation
Indices: 2628397--2628452 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2628387 ACATCAATGC
2628397 ATTAAATATAAATTTATATTTAAT
1 ATTAAATATAAATTTATATTTAAT
* * *
2628421 ATTATATATTAATTTATATTTTAT
1 ATTAAATATAAATTTATATTTAAT
*
2628445 AATAAATA
1 ATTAAATA
2628453 CTTTTTACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTAAATATAAATTTATATTTAAT
Found at i:2628427 original size:12 final size:11
Alignment explanation
Indices: 2628407--2628441 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
2628397 ATTAAATATA
2628407 AATTTATATTT
1 AATTTATATTT
2628418 AATATTATATATT
1 AAT-TTATAT-TT
2628431 AATTTATATTT
1 AATTTATATTT
2628442 TATAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 12 0.55
13 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTATATTT
Found at i:2628809 original size:27 final size:28
Alignment explanation
Indices: 2628760--2628814 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2628750 TTTTTTAAAA
*
2628760 TTTTTAAAAAAAATCATGTAATAATTAT
1 TTTTTAAAAAAAATAATGTAATAATTAT
* *
2628788 TTTTTAAAAAAATTAATG-AATATTTAT
1 TTTTTAAAAAAAATAATGTAATAATTAT
2628815 AAATATTCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (28 bp):
TTTTTAAAAAAAATAATGTAATAATTAT
Found at i:2629372 original size:24 final size:24
Alignment explanation
Indices: 2629331--2629376 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2629321 CAATTGATTT
*
2629331 ATTATTTATATAAATAAAAAATAA
1 ATTATTGATATAAATAAAAAATAA
2629355 ATTATTGA-ATAAATTAAAAAAT
1 ATTATTGATATAAA-TAAAAAAT
2629377 TAGACGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTATTGATATAAATAAAAAATAA
Found at i:2631209 original size:21 final size:23
Alignment explanation
Indices: 2631166--2631212 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2631156 TGTAAATGGT
2631166 AAAAATGAAAATGATCAAAAACG
1 AAAAATGAAAATGATCAAAAACG
*
2631189 AAAAATGAAAGT-ATC-AAAACG
1 AAAAATGAAAATGATCAAAAACG
2631210 AAA
1 AAA
2631213 CCTATTGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 11 0.48
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (23 bp):
AAAAATGAAAATGATCAAAAACG
Found at i:2637911 original size:21 final size:21
Alignment explanation
Indices: 2637876--2637984 Score: 62
Period size: 21 Copynumber: 5.2 Consensus size: 21
2637866 TGTTTTTGTC
* *
2637876 ATTTTGATAAGTTTCAATATGA
1 ATTTTGGTAATTTTCAATAT-A
*
2637898 A-TTTGGTAATTTTCAATGTA
1 ATTTTGGTAATTTTCAATATA
* ** * *
2637918 ATTTTAGTAATTTTTTACATT
1 ATTTTGGTAATTTTCAATATA
** *
2637939 ATTTTAATAATTTTTAATATA
1 ATTTTGGTAATTTTCAATATA
* *
2637960 A--TTGATTAATTTTTAATATA
1 ATTTTG-GTAATTTTCAATATA
2637980 ATTTT
1 ATTTT
2637985 AATAGTATTT
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.03
20 17 0.25
21 46 0.68
22 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTTTGGTAATTTTCAATATA
Found at i:2638154 original size:27 final size:27
Alignment explanation
Indices: 2638124--2638179 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2638114 ACCTTTTTTT
* *
2638124 TTTTTTTGGGTACTTTTTTCACATCAA
1 TTTTTTTCGGTACTTTTTTAACATCAA
* *
2638151 TTTTTTTCGGTATTTTTTTAACTTCAA
1 TTTTTTTCGGTACTTTTTTAACATCAA
2638178 TT
1 TT
2638180 CCAACACTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (27 bp):
TTTTTTTCGGTACTTTTTTAACATCAA
Found at i:2638452 original size:2 final size:2
Alignment explanation
Indices: 2638442--2638477 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
2638432 TCTCACACAA
2638442 AT AT GAT 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 A
2638478 CATACATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2641799 original size:104 final size:104
Alignment explanation
Indices: 2641614--2641818 Score: 311
Period size: 104 Copynumber: 2.0 Consensus size: 104
2641604 ATATATCAAG
*
2641614 CATAAAAAATAGAAGGATTATTACTAATCTACTTTATTAGTAATAGAAATGTAAACATAGTTAAT
1 CATAAAAAATAGAAGGATTATTACTAATCTACTTTATTAGTAATAGAAATGTAAACATAATTAAT
* * *
2641679 GAAAGAAAAACTTTGGCTAATCACTTTCTAATTAAAGAA
66 AAAAGAAAAACGTTGGCAAATCACTTTCTAATTAAAGAA
* * * * ** *
2641718 CATAAAGAATAGAAGGATTATTGCTAATCTTCTTTATTAGTTATAGAGGTTTAAACATAATTAAT
1 CATAAAAAATAGAAGGATTATTACTAATCTACTTTATTAGTAATAGAAATGTAAACATAATTAAT
2641783 AAAAGAAAAACGTTGGCAAATCACTTTCTAATTAAA
66 AAAAGAAAAACGTTGGCAAATCACTTTCTAATTAAA
2641819 ATTAACAACA
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 90 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (104 bp):
CATAAAAAATAGAAGGATTATTACTAATCTACTTTATTAGTAATAGAAATGTAAACATAATTAAT
AAAAGAAAAACGTTGGCAAATCACTTTCTAATTAAAGAA
Found at i:2643094 original size:9 final size:9
Alignment explanation
Indices: 2643077--2643157 Score: 53
Period size: 9 Copynumber: 9.2 Consensus size: 9
2643067 ATTTAAAATT
2643077 TAATATATA
1 TAATATATA
*
2643086 TAATCTATA
1 TAATATATA
*
2643095 TAA-ATAAA
1 TAATATATA
*
2643103 TAATAAAATA
1 TAAT-ATATA
2643113 TAAT-TAT-
1 TAATATATA
* *
2643120 TAAAATAAA
1 TAATATATA
2643129 TAA-ATATAA
1 TAATATAT-A
* *
2643138 TTATATAAA
1 TAATATATA
2643147 TAATATATA
1 TAATATATA
2643156 TA
1 TA
2643158 TAAATAATTT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
7 3 0.06
8 13 0.25
9 27 0.51
10 10 0.19
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (9 bp):
TAATATATA
Found at i:2643133 original size:22 final size:22
Alignment explanation
Indices: 2643078--2643160 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 22
2643068 TTTAAAATTT
*
2643078 AATATATATAATCTATATAAATAAA
1 AATAAATATAAT-TATATAAAT--A
2643103 TAATAAAATATAATTAT-TAAAATA
1 -AAT-AAATATAATTATAT-AAATA
2643127 AATAAATATAATTATATAAATA
1 AATAAATATAATTATATAAATA
*
2643149 ATATATATATAA
1 A-ATAAATATAA
2643161 ATAATTTAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
22 18 0.35
23 13 0.25
24 1 0.02
25 1 0.02
26 10 0.20
27 8 0.16
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
AATAAATATAATTATATAAATA
Found at i:2643570 original size:22 final size:20
Alignment explanation
Indices: 2643544--2643617 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
2643534 AATATACCGT
2643544 AATATTGTTATATAATAATTAA
1 AATATT-TTATAT-ATAATTAA
* *
2643566 TATATTATTAT-TATATTTAA
1 AATATT-TTATATATAATTAA
*
2643586 AATATTTTATAT-TTA-TATA
1 AATATTTTATATATAATTA-A
2643605 AAT-TTTTATATAT
1 AATATTTTATATAT
2643618 TAATAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 10 0.23
19 10 0.23
20 13 0.30
21 1 0.02
22 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
AATATTTTATATATAATTAA
Found at i:2643580 original size:11 final size:11
Alignment explanation
Indices: 2643561--2643664 Score: 50
Period size: 11 Copynumber: 10.4 Consensus size: 11
2643551 TTATATAATA
2643561 ATTAATATATT
1 ATTAATATATT
*
2643572 ATTATTATA-T
1 ATTAATATATT
*
2643582 -TTAAAATATT
1 ATTAATATATT
2643592 -TT-ATAT-TT
1 ATTAATATATT
2643600 ATATAA-AT-TT
1 AT-TAATATATT
2643610 -TT-ATATATT
1 ATTAATATATT
* *
2643619 AATAATTTA-T
1 ATTAATATATT
*
2643629 ATT-ATATAAT
1 ATTAATATATT
* *
2643639 ATTTATATAGT
1 ATTAATATATT
*
2643650 ATTTATATATT
1 ATTAATATATT
2643661 ATTA
1 ATTA
2643665 TGTTTTAATT
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
7 1 0.01
8 5 0.07
9 17 0.24
10 17 0.24
11 32 0.44
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (11 bp):
ATTAATATATT
Found at i:2643597 original size:16 final size:16
Alignment explanation
Indices: 2643571--2643646 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
2643561 ATTAATATAT
2643571 TATTATTATATTTAAAA
1 TATT-TTATATTTAAAA
2643588 TATTTTATATTTATATAA
1 TATTTTATATTTA-A-AA
2643606 -ATTTTTATATATT--AA
1 TA-TTTTATAT-TTAAAA
* *
2643621 TAATTTATATTATATAA
1 TATTTTATATT-TAAAA
2643638 TA-TTTATAT
1 TATTTTATAT
2643647 AGTATTTATA
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
14 1 0.02
15 10 0.20
16 17 0.34
17 10 0.20
18 10 0.20
19 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTATATTTAAAA
Found at i:2643613 original size:18 final size:18
Alignment explanation
Indices: 2643585--2643658 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 18
2643575 ATTATATTTA
2643585 AAATATTTTATATTTATAT
1 AAAT-TTTTATATTTATAT
2643604 AAATTTTTATATATTA-AT
1 AAATTTTTATAT-TTATAT
2643622 -AA--TTTATA-TTATAT
1 AAATTTTTATATTTATAT
2643636 AATATTTATATAGTATTTATAT
1 AA-ATTT-T-TA-TATTTATAT
2643658 A
1 A
2643659 TTATTATGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.07
14 2 0.04
15 7 0.16
16 1 0.02
17 2 0.04
18 11 0.24
19 8 0.18
20 2 0.04
21 2 0.04
22 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (18 bp):
AAATTTTTATATTTATAT
Found at i:2643628 original size:33 final size:31
Alignment explanation
Indices: 2643586--2643647 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
2643576 TTATATTTAA
* *
2643586 AATATTTTATATTTATATAAATTTTTATATATT
1 AATAATTTATA-TTATAT-AATATTTATATATT
2643619 AATAATTTATATTATATAATATTTATATA
1 AATAATTTATATTATATAATATTTATATA
2643648 GTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 11 0.41
32 6 0.22
33 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
AATAATTTATATTATATAATATTTATATATT
Found at i:2643676 original size:21 final size:21
Alignment explanation
Indices: 2643610--2643720 Score: 74
Period size: 20 Copynumber: 5.4 Consensus size: 21
2643600 ATATAAATTT
*
2643610 TTATATATTA--ATAATTTATA
1 TTATATATTATTATATTTTA-A
* ** *
2643630 TTATATAATATTTATATAGTAT
1 TTATATATTA-TTATATTTTAA
*
2643652 TTATATATTATTATGTTTTAA
1 TTATATATTATTATATTTTAA
2643673 TTATAT-TT-TTATATTTT-A
1 TTATATATTATTATATTTTAA
*
2643691 TT-TATATAATTATA-TTTATA
1 TTATATATTATTATATTTTA-A
2643711 TTATTATATT
1 TTA-TATATT
2643721 TAAATTAAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
17 3 0.04
18 7 0.10
19 13 0.19
20 14 0.20
21 13 0.19
22 14 0.20
23 5 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATATATTATTATATTTTAA
Found at i:2643677 original size:19 final size:19
Alignment explanation
Indices: 2643655--2643740 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
2643645 ATAGTATTTA
*
2643655 TATATTATTATGTTTTAAT
1 TATATTATTATATTTTAAT
*
2643674 TATATTTTTATATTTT-AT
1 TATATTATTATATTTTAAT
* *
2643692 T-TA-TA-TA-ATTATATT
1 TATATTATTATATTTTAAT
*
2643707 TATATTATTATATTTAAAT
1 TATATTATTATATTTTAAT
2643726 TAAATATTATTATAT
1 T--ATATTATTATAT
2643741 GATTATGTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.08
15 4 0.08
16 3 0.06
17 4 0.08
18 5 0.10
19 20 0.38
21 12 0.23
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (19 bp):
TATATTATTATATTTTAAT
Found at i:2643679 original size:27 final size:27
Alignment explanation
Indices: 2643649--2643748 Score: 91
Period size: 27 Copynumber: 3.7 Consensus size: 27
2643639 ATTTATATAG
2643649 TATTTATATATTATTATGTTTTAATTA
1 TATTTATATATTATTATGTTTTAATTA
*
2643676 TATTTTTATATT-TTAT-TTATATAATTA
1 TATTTATATATTATTATGTT-T-TAATTA
* *
2643703 TA-TT-TATATTATTATATTTAAATTA
1 TATTTATATATTATTATGTTTTAATTA
* *
2643728 AATATTATTATATGATTATGT
1 TAT-TTA-TATATTATTATGT
2643749 ATTTTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
25 14 0.23
26 12 0.20
27 23 0.38
29 11 0.18
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (27 bp):
TATTTATATATTATTATGTTTTAATTA
Found at i:2643703 original size:8 final size:7
Alignment explanation
Indices: 2643552--2643740 Score: 75
Period size: 7 Copynumber: 27.7 Consensus size: 7
2643542 GTAATATTGT
*
2643552 TATATAA
1 TATATTA
2643559 TA-ATTAA
1 TATATT-A
2643566 TATATTA
1 TATATTA
2643573 T-TATTA
1 TATATTA
2643579 TAT-TTAA
1 TATATT-A
* *
2643586 AATATTT
1 TATATTA
2643593 TATATT-
1 TATATTA
2643599 TATA-TA
1 TATATTA
* *
2643605 AATTTTTA
1 TA-TATTA
2643613 TATATTA
1 TATATTA
2643620 -ATAATT-
1 TAT-ATTA
2643626 TATATTA
1 TATATTA
*
2643633 TATAATA
1 TATATTA
*
2643640 TTTA-TA
1 TATATTA
2643646 TAGTATTTA
1 TA-TA-TTA
2643655 TATATTA
1 TATATTA
* *
2643662 TTATGTTT
1 -TATATTA
2643670 TA-ATTA
1 TATATTA
*
2643676 TAT-TTT
1 TATATTA
*
2643682 TATATTT
1 TATATTA
2643689 TAT-TTA
1 TATATTA
2643695 TATAATTA
1 TAT-ATTA
2643703 TAT-TTA
1 TATATTA
2643709 TATTATTA
1 TA-TATTA
2643717 TAT-TTA
1 TATATTA
2643723 -A-ATTA
1 TATATTA
*
2643728 AATATTA
1 TATATTA
2643735 TTATAT
1 -TATAT
2643741 GATTATGTAT
Statistics
Matches: 139, Mismatches: 18, Indels: 49
0.67 0.09 0.24
Matches are distributed among these distances:
5 5 0.04
6 46 0.33
7 54 0.39
8 30 0.22
9 4 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:2643708 original size:14 final size:13
Alignment explanation
Indices: 2643565--2643722 Score: 101
Period size: 14 Copynumber: 11.5 Consensus size: 13
2643555 ATAATAATTA
2643565 ATATATTAT-TATT
1 ATAT-TTATATATT
*
2643578 ATATTTAAAATATTTT
1 ATATTT---ATATATT
*
2643594 ATATTTATATA-A
1 ATATTTATATATT
*
2643606 ATTTTTATATATT
1 ATATTTATATATT
2643619 AATAATTTATATTATAT
1 -AT-ATTTATA-TAT-T
2643636 AATATTTATATA--
1 -ATATTTATATATT
*
2643648 GTATTTATATATT
1 ATATTTATATATT
*
2643661 ATTATGTTTTA-ATT
1 A-TAT-TTATATATT
*
2643675 ATATTTTTATATT
1 ATATTTATATATT
*
2643688 TTATTTATATAATT
1 ATATTTATAT-ATT
2643702 ATATTTATATTATT
1 ATATTTATA-TATT
2643716 ATATTTA
1 ATATTTA
2643723 AATTAAATAT
Statistics
Matches: 117, Mismatches: 12, Indels: 31
0.73 0.08 0.19
Matches are distributed among these distances:
11 10 0.09
12 17 0.15
13 22 0.19
14 30 0.26
15 15 0.13
16 19 0.16
17 4 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (13 bp):
ATATTTATATATT
Found at i:2643740 original size:81 final size:81
Alignment explanation
Indices: 2643592--2643748 Score: 180
Period size: 81 Copynumber: 1.9 Consensus size: 81
2643582 TTAAAATATT
* *
2643592 TTATATTTATATAAATTTTTATATATTAATAATTTATATTATATAATATTTATATAGTATTTATA
1 TTATATTTATATAAATTTTTATATATTAATAATTTATATTATATAATATTTAAATAATATTTATA
*
2643657 TATTATTATGTTTTAA
66 TATGATTATGTTTTAA
* **
2643673 TTATATTTTTATATTTTATTTATATAATT-AT-ATTTATATTAT-T-ATATTTAAATTAA-ATAT
1 TTATATTTATATAAATT-TTTATAT-ATTAATAATTTATATTATATAATATTTAAA-TAATAT-T
2643733 TATTATATGATTATGT
62 TA-TATATGATTATGT
2643749 ATTTTTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
79 10 0.15
80 6 0.09
81 37 0.57
82 9 0.14
83 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (81 bp):
TTATATTTATATAAATTTTTATATATTAATAATTTATATTATATAATATTTAAATAATATTTATA
TATGATTATGTTTTAA
Found at i:2643814 original size:15 final size:15
Alignment explanation
Indices: 2643794--2643824 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2643784 TCCCTCAGCT
*
2643794 AAAAAAAATAGAAAA
1 AAAAAAAAAAGAAAA
2643809 AAAAAAAAAAGAAAA
1 AAAAAAAAAAGAAAA
2643824 A
1 A
2643825 GGAAATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:2644125 original size:17 final size:18
Alignment explanation
Indices: 2644105--2644142 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2644095 TTTATATTTG
2644105 ATTTCA-GTTTAAAAAAT
1 ATTTCATGTTTAAAAAAT
* *
2644122 ATTTTATGTTTAAAATAT
1 ATTTCATGTTTAAAAAAT
2644140 ATT
1 ATT
2644143 AAGATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTCATGTTTAAAAAAT
Done.