Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 14 of 26
Found at i:2340861 original size:3 final size:3
Alignment explanation
Indices: 2340846--2340884 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2340836 TACACTCTTA
*
2340846 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2340885 TTGGATTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2341737 original size:3 final size:3
Alignment explanation
Indices: 2341729--2341759 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2341719 GATAATGATA
*
2341729 AAG AAG AAG AAG ATG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2341760 TAATCATGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:2345506 original size:2 final size:2
Alignment explanation
Indices: 2345499--2345523 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2345489 TTCTACCCAC
2345499 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2345524 TTCAACAACC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2346924 original size:18 final size:18
Alignment explanation
Indices: 2346901--2346937 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2346891 TATAACTTAA
2346901 CATATAAGGACTGAGATT
1 CATATAAGGACTGAGATT
*
2346919 CATATAGGGACTGAGATT
1 CATATAAGGACTGAGATT
2346937 C
1 C
2346938 TAACAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (18 bp):
CATATAAGGACTGAGATT
Found at i:2348459 original size:2 final size:2
Alignment explanation
Indices: 2348452--2348488 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2348442 TCGTTTTTCA
2348452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2348489 GCAAAATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2354292 original size:5 final size:6
Alignment explanation
Indices: 2354268--2354299 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
2354258 TCCACTACAT
2354268 AGAAATA AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAA-A AGAAAA AGAAAA AGAAAA AGAAAA A
2354300 TGTTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:2355067 original size:2 final size:2
Alignment explanation
Indices: 2355060--2355089 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2355050 AAATTAGAAG
*
2355060 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2355090 GATAGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2355337 original size:16 final size:16
Alignment explanation
Indices: 2355318--2355366 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
2355308 AATTAAAAAA
*
2355318 ATATAAAAATAAATTT
1 ATATATAAATAAATTT
*
2355334 ATATATAAATAAAATT
1 ATATATAAATAAATTT
*
2355350 ATTTATAAATCAAATTT
1 ATATATAAAT-AAATTT
2355367 TTTATCTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATAAATAAATTT
Found at i:2355370 original size:16 final size:15
Alignment explanation
Indices: 2355324--2355371 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
2355314 AAAAATATAA
*
2355324 AAATAAATTTATATAT
1 AAATAAATTT-TTTAT
*
2355340 AAATAAAATTATTTAT
1 AAAT-AAATTTTTTAT
2355356 AAATCAAATTTTTTAT
1 AAAT-AAATTTTTTAT
2355372 CTGAACTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATAAATTTTTTAT
Found at i:2357651 original size:2 final size:2
Alignment explanation
Indices: 2357644--2357670 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2357634 TGAGGAATAC
2357644 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 A
2357671 ATTATTAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2362575 original size:14 final size:16
Alignment explanation
Indices: 2362544--2362578 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
2362534 ATTTATTTAT
2362544 ATTTAACATATCTAAA
1 ATTTAACATATCTAAA
2362560 ATTTAA-ATAT-TAAA
1 ATTTAACATATCTAAA
2362574 ATTTA
1 ATTTA
2362579 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 4 0.21
16 6 0.32
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTAACATATCTAAA
Found at i:2362777 original size:21 final size:20
Alignment explanation
Indices: 2362732--2362774 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2362722 GTGTCTCATT
2362732 TAATTTTTTTATTTTTTAAA
1 TAATTTTTTTATTTTTTAAA
2362752 TAATTTTTTTATTTTTTAAA
1 TAATTTTTTTATTTTTTAAA
2362772 TAA
1 TAA
2362775 ATTCTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TAATTTTTTTATTTTTTAAA
Found at i:2363890 original size:25 final size:26
Alignment explanation
Indices: 2363832--2363890 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
2363822 CGATTTAAAA
2363832 ATTTAT-A-TTATTATTTAAAATAAT
1 ATTTATAATTTATTATTTAAAATAAT
* * *
2363856 ATTAAAAATTTATT-TTTATAATAAT
1 ATTTATAATTTATTATTTAAAATAAT
2363881 ATTTATAATT
1 ATTTATAATT
2363891 AAATTTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 19 0.68
26 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTATAATTTATTATTTAAAATAAT
Found at i:2363928 original size:39 final size:44
Alignment explanation
Indices: 2363856--2363953 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 44
2363846 TTAAAATAAT
* *
2363856 ATTAAAAATTTATTTTTATAATAATATTTATAA-TTAAATTTAA
1 ATTAAAAATTTATTATTATAATAATATTAATAATTTAAATTTAA
2363899 ATTAAAAATTT-TTATTAT-ATAA-A-TAATAATTTAAA-TTAA
1 ATTAAAAATTTATTATTATAATAATATTAATAATTTAAATTTAA
* *
2363938 TTTAATAAAATTATTA
1 ATTAA-AAATTTATTA
2363954 AAATATTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
39 13 0.27
40 11 0.23
41 7 0.15
42 6 0.12
43 11 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (44 bp):
ATTAAAAATTTATTATTATAATAATATTAATAATTTAAATTTAA
Found at i:2363936 original size:45 final size:42
Alignment explanation
Indices: 2363856--2363942 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 42
2363846 TTAAAATAAT
2363856 ATTAAAAATTTATTTTTATAATAATATTTATAATTAAATTTAA
1 ATTAAAAATTTATTTTTATAATAATATTTATAATT-AATTTAA
2363899 ATTAAAAATTT-TTATTATATAAATAATAATTTA-AATTAATTTAA
1 ATTAAAAATTTATT-TT-TAT-AATAAT-ATTTATAATTAATTTAA
2363943 TAAAATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
42 2 0.05
43 13 0.32
44 10 0.25
45 10 0.25
46 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
ATTAAAAATTTATTTTTATAATAATATTTATAATTAATTTAA
Found at i:2364336 original size:21 final size:21
Alignment explanation
Indices: 2364306--2364362 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
2364296 TTTTATTAAA
*
2364306 TTATAATTATAT-TTAAAATAT
1 TTATATTTATATATTAAAA-AT
* *
2364327 TTTTATTTATATATTAATAAT
1 TTATATTTATATATTAAAAAT
2364348 TTATATTATATATAT
1 TTATATT-TATATAT
2364363 ATATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATTTATATATTAAAAAT
Found at i:2364354 original size:13 final size:14
Alignment explanation
Indices: 2364336--2364383 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
2364326 TTTTTATTTA
2364336 TATATTAATA-ATT
1 TATATTAATATATT
*
2364349 TATATTATATATATA
1 TATATTA-ATATATT
*
2364364 TATTTTAA-ATATT
1 TATATTAATATATT
2364377 TATATTA
1 TATATTA
2364384 TATTTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 17 0.59
14 4 0.14
15 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATTAATATATT
Found at i:2364356 original size:20 final size:20
Alignment explanation
Indices: 2364292--2364360 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
2364282 ATCGTATTAA
* * *
2364292 TATATTTTATTAAATTATAAT
1 TATATATTAATAATTTAT-AT
* *
2364313 TATAT-TTAAAATATTTTTATT
1 TATATATTAATA-ATTTATA-T
2364334 TATATATTAATAATTTATAT
1 TATATATTAATAATTTATAT
2364354 TATATAT
1 TATATAT
2364361 ATATATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 13 0.33
21 21 0.54
22 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATATTAATAATTTATAT
Found at i:2364370 original size:20 final size:19
Alignment explanation
Indices: 2364327--2364388 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
2364317 TTTAAAATAT
2364327 TTTTAT-TTATATATTAATA
1 TTTTATATTATATATT-ATA
*
2364346 ATTTATATTATATATATATA
1 TTTTATATTATATAT-TATA
2364366 TTTTAAATATT-TATATTATA
1 TTTT--ATATTATATATTATA
2364386 TTT
1 TTT
2364389 AATAATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 5 0.14
20 21 0.57
21 6 0.16
22 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATATTATATATTATA
Found at i:2365526 original size:14 final size:14
Alignment explanation
Indices: 2365507--2365538 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2365497 TGGATAACGT
*
2365507 ATTTAATTTTATAA
1 ATTTAATTTTAAAA
2365521 ATTTAATTTTAAAA
1 ATTTAATTTTAAAA
2365535 ATTT
1 ATTT
2365539 TTAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAATTTTAAAA
Found at i:2365639 original size:28 final size:27
Alignment explanation
Indices: 2365571--2365639 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
2365561 TTAATTTAAA
2365571 TTATTATTTATTTAATAAAAAATTTAT
1 TTATTATTTATTTAATAAAAAATTTAT
**
2365598 TTATATATAAATTTAATTAAAAATATTT-T
1 TTAT-TATTTATTTAA-TAAAAA-ATTTAT
*
2365627 TTATTTTTTATTT
1 TTATTATTTATTT
2365640 TTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 4 0.12
28 15 0.44
29 11 0.32
30 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATTATTTATTTAATAAAAAATTTAT
Found at i:2366217 original size:23 final size:22
Alignment explanation
Indices: 2366162--2366222 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
2366152 TAAAAAATTA
*
2366162 AAATAATTTTTATTTTAATATTT
1 AAAT-ATTTTTATATTAATATTT
*
2366185 TAATATTTTTATAATTAAT-TTT
1 AAATATTTTTAT-ATTAATATTT
2366207 AAATATTTTT-TATTAA
1 AAATATTTTTATATTAA
2366223 ATAATAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.15
21 1 0.03
22 20 0.59
23 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATATTTTTATATTAATATTT
Found at i:2366513 original size:29 final size:29
Alignment explanation
Indices: 2366480--2366561 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
2366470 TAAATAATAA
* * *
2366480 AAAATTTAAATTTTATCAAATTTAATTTT
1 AAAATTTAAATTTAATTAAATTTAAATTT
* *
2366509 AAAATTTAAGTTTAATTTAAA-ATAAATTT
1 AAAATTTAAATTTAA-TTAAATTTAAATTT
*
2366538 AAAATTTATATTTAATTAAATTTA
1 AAAATTTAAATTTAATTAAATTTA
2366562 TTTATTTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 5 0.12
29 34 0.79
30 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
AAAATTTAAATTTAATTAAATTTAAATTT
Found at i:2366515 original size:13 final size:13
Alignment explanation
Indices: 2366480--2366523 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2366470 TAAATAATAA
2366480 AAAATTTAAATTTT
1 AAAATTT-AATTTT
2366494 ATCAAATTTAATTTT
1 A--AAATTTAATTTT
*
2366509 AAAATTTAAGTTT
1 AAAATTTAATTTT
2366522 AA
1 AA
2366524 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 13 0.48
14 1 0.04
15 7 0.26
16 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (13 bp):
AAAATTTAATTTT
Found at i:2366545 original size:23 final size:23
Alignment explanation
Indices: 2366510--2366561 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2366500 TTTAATTTTA
*
2366510 AAATTT-AAGTTTA-ATTTAAAAT
1 AAATTTAAAATTTATATTT-AAAT
*
2366532 AAATTTAAAATTTATATTTAATT
1 AAATTTAAAATTTATATTTAAAT
2366555 AAATTTA
1 AAATTTA
2366562 TTTATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATTTAAAATTTATATTTAAAT
Found at i:2367625 original size:3 final size:3
Alignment explanation
Indices: 2367617--2367645 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2367607 TTTGTGGGTT
2367617 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2367646 TATTATTATT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2367650 original size:3 final size:3
Alignment explanation
Indices: 2367644--2367676 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2367634 AATAATAATA
*
2367644 ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2367677 GAAATGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:2368041 original size:8 final size:8
Alignment explanation
Indices: 2368028--2368056 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2368018 ACCTTTTCTC
2368028 AAAAAAA-
1 AAAAAAAG
2368035 AAAAAAAG
1 AAAAAAAG
2368043 AAAAAAAG
1 AAAAAAAG
2368051 AAAAAA
1 AAAAAA
2368057 TGGTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2372103 original size:2 final size:2
Alignment explanation
Indices: 2372096--2372138 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2372086 TTGGAATCTT
* *
2372096 CA CA CA CA CT CA GA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2372138 C
1 C
2372139 GTGTATACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.49, G:0.02, T:0.02
Consensus pattern (2 bp):
CA
Found at i:2372152 original size:2 final size:2
Alignment explanation
Indices: 2372142--2372177 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2372132 CACACACGTG
* *
2372142 TA TA CA TA TA TA TA TA TA TA TA CA 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
2372178 CACTTCCGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2372878 original size:42 final size:42
Alignment explanation
Indices: 2372819--2372902 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
2372809 GAGAAGACCA
*
2372819 AAGGAATAAGCAATTTGAGCTATATTGATTCAAGGATAGAAC
1 AAGGAATAAGCAATTTGAGCTATATAGATTCAAGGATAGAAC
2372861 AAGGAATAAGCAATTTGAGCTATATAGATTCAAGGATAGAAC
1 AAGGAATAAGCAATTTGAGCTATATAGATTCAAGGATAGAAC
2372903 GTATCGAAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (42 bp):
AAGGAATAAGCAATTTGAGCTATATAGATTCAAGGATAGAAC
Found at i:2377963 original size:16 final size:16
Alignment explanation
Indices: 2377944--2377977 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2377934 TAAATAAACT
*
2377944 TATTTATATATAAATA
1 TATTCATATATAAATA
*
2377960 TATTCATGTATAAATA
1 TATTCATATATAAATA
2377976 TA
1 TA
2377978 AATATAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TATTCATATATAAATA
Found at i:2380312 original size:3 final size:3
Alignment explanation
Indices: 2380304--2380329 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2380294 TACCACCCTT
2380304 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2380330 TTGACAGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2382979 original size:19 final size:18
Alignment explanation
Indices: 2382925--2382975 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2382915 TGTAAGATCA
*
2382925 ATTTA-ATTTAAATTATT
1 ATTTATATTTAAATTAAT
*
2382942 ATTTATATTATAAAGTAAT
1 ATTTATATT-TAAATTAAT
*
2382961 ATTTTTATTTAAATT
1 ATTTATATTTAAATT
2382976 TAATTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 15 0.54
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTTATATTTAAATTAAT
Found at i:2385551 original size:21 final size:20
Alignment explanation
Indices: 2385530--2385569 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2385520 GTGTTTGTTC
*
2385530 CCTTTTTTTATT-TGTATTTT
1 CCTTTATTTATTGTG-ATTTT
2385550 CCTTTATTTATTGTGATTTT
1 CCTTTATTTATTGTGATTTT
2385570 GTTTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.70
Consensus pattern (20 bp):
CCTTTATTTATTGTGATTTT
Found at i:2386178 original size:18 final size:19
Alignment explanation
Indices: 2386143--2386183 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2386133 GATATAATTT
**
2386143 TTTAAAAATATTTTATATA
1 TTTAAAAATATTAAATATA
2386162 TTTAAAAA-ATTAAATATA
1 TTTAAAAATATTAAATATA
2386180 TTTA
1 TTTA
2386184 TATTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAAATATTAAATATA
Found at i:2390567 original size:21 final size:23
Alignment explanation
Indices: 2390511--2390571 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
2390501 AAAATTAGTT
*
2390511 ATTGAAAAAATAAATATAAAAAAAA
1 ATTGAAAAAA-ATA-ATAAAAAAAA
*
2390536 ATTGATTAAAAATAATAAAAAAAA
1 ATTGA-AAAAAATAATAAAAAAAA
2390560 A-T-AAAAAAATAA
1 ATTGAAAAAAATAA
2390572 AAACAAGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 8 0.25
22 1 0.03
23 1 0.03
24 11 0.34
25 7 0.22
26 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (23 bp):
ATTGAAAAAAATAATAAAAAAAA
Found at i:2390646 original size:26 final size:26
Alignment explanation
Indices: 2390581--2390655 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
2390571 AAAACAAGGA
2390581 AGGAATCAGGAGAGAGTGGGGAT-GG
1 AGGAATCAGGAGAGAGTGGGGATGGG
*
2390606 AGGGAT--GG-G-GA-TGGGGATGGG
1 AGGAATCAGGAGAGAGTGGGGATGGG
*
2390627 AGGAATCAGGAGAGAGTGGGGAAGGG
1 AGGAATCAGGAGAGAGTGGGGATGGG
2390653 AGG
1 AGG
2390656 GAGGGGGATG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
20 7 0.17
21 9 0.22
22 1 0.02
23 4 0.10
24 1 0.02
25 7 0.17
26 12 0.29
ACGTcount: A:0.29, C:0.03, G:0.57, T:0.11
Consensus pattern (26 bp):
AGGAATCAGGAGAGAGTGGGGATGGG
Found at i:2390648 original size:46 final size:47
Alignment explanation
Indices: 2390581--2390674 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
2390571 AAAACAAGGA
* *
2390581 AGGAATCAGGAGAGAGTGGGG-ATGGAGGGATGGGGATGGGGATGGG
1 AGGAATCAGGAGAGAGTGGGGAAGGGAGGGAGGGGGATGGGGATGGG
2390627 AGGAATCAGGAGAGAGTGGGGAAGGGAGGGAGGGGGATGGGGATGGG
1 AGGAATCAGGAGAGAGTGGGGAAGGGAGGGAGGGGGATGGGGATGGG
2390674 A
1 A
2390675 AGGGAGAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 21 0.47
47 24 0.53
ACGTcount: A:0.28, C:0.02, G:0.60, T:0.11
Consensus pattern (47 bp):
AGGAATCAGGAGAGAGTGGGGAAGGGAGGGAGGGGGATGGGGATGGG
Found at i:2391207 original size:2 final size:2
Alignment explanation
Indices: 2391200--2391240 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
2391190 ATATAACCTG
*
2391200 TA TA TA TA TA TA TA -A TA T- TA GCA 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
2391241 ATGTGATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2392423 original size:2 final size:2
Alignment explanation
Indices: 2392416--2392440 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2392406 TTTAATGTTG
2392416 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 A
2392441 AAATAAATGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2393007 original size:32 final size:32
Alignment explanation
Indices: 2392949--2393009 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2392939 CCATTAATAT
* *
2392949 ATGTATATATTTCTCTCATAATTTTTTAAAAA
1 ATGTATAAATTTCTATCATAATTTTTTAAAAA
*
2392981 ATGTATAAATTT-TATCATTATATTTTTAA
1 ATGTATAAATTTCTATCATAAT-TTTTTAA
2393010 TTTCATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (32 bp):
ATGTATAAATTTCTATCATAATTTTTTAAAAA
Found at i:2393929 original size:18 final size:19
Alignment explanation
Indices: 2393906--2393956 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
2393896 TTAGTTGATC
*
2393906 TTTTATATATTTATCATT-
1 TTTTATATATTTATAATTA
2393924 TTTTATA-ATTTTATAATTA
1 TTTTATATA-TTTATAATTA
2393943 TATTT-TATATTTAT
1 T-TTTATATATTTAT
2393957 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 15 0.54
19 8 0.29
20 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATATATTTATAATTA
Found at i:2393945 original size:30 final size:27
Alignment explanation
Indices: 2393906--2393973 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 27
2393896 TTAGTTGATC
2393906 TTTTA-TATATTTATCATTT-TTTATAAT
1 TTTTATTATATTTAT-ATTTATTT-TAAT
2393933 TTTATAATTATATTTTATATTTATTTTAAT
1 TTT-T-ATTATA-TTTATATTTATTTTAAT
2393963 TTTTATTATAT
1 TTTTATTATAT
2393974 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
27 4 0.11
28 7 0.19
29 2 0.06
30 15 0.42
31 8 0.22
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTATTATATTTATATTTATTTTAAT
Found at i:2393950 original size:21 final size:21
Alignment explanation
Indices: 2393924--2393996 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
2393914 ATTTATCATT
2393924 TTTTATAATTTTATAATTATA
1 TTTTATAATTTTATAATTATA
* * *
2393945 TTTTATATTTATTTTAATTTTTA
1 TTTTATAATT-TTATAA-TTATA
*
2393968 TTATATAAATTTTA-AATTATA
1 TTTTAT-AATTTTATAATTATA
2393989 TATTTATA
1 T-TTTATA
2393997 TTATATATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
21 15 0.38
22 11 0.28
23 11 0.28
24 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATAATTTTATAATTATA
Found at i:2393969 original size:12 final size:11
Alignment explanation
Indices: 2393931--2393998 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
2393921 ATTTTTTATA
2393931 ATTTTATAATTAT
1 ATTTTAT-ATT-T
2393944 ATTTTATATTT
1 ATTTTATATTT
2393955 ATTTTA-ATTT
1 ATTTTATATTT
**
2393965 -TTATTATATAA
1 ATT-TTATATTT
*
2393976 ATTTTAAATTAT
1 ATTTTATATT-T
2393988 ATATTTATATT
1 AT-TTTATATT
2393999 ATATATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 2 0.05
10 7 0.16
11 14 0.32
12 7 0.16
13 14 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTTATATTT
Found at i:2394003 original size:13 final size:13
Alignment explanation
Indices: 2393925--2394005 Score: 60
Period size: 13 Copynumber: 6.2 Consensus size: 13
2393915 TTTATCATTT
*
2393925 TTTATAATTTTATA
1 TTTAT-ATTATATA
* *
2393939 ATTATATTTTATA
1 TTTATATTATATA
2393952 TTTAT-TT-TA-A
1 TTTATATTATATA
*
2393962 TTTTTATTATATAAA
1 TTTATATTATAT--A
*
2393977 TTTTAAATTATATA
1 -TTTATATTATATA
2393991 TTTATATTATATA
1 TTTATATTATATA
2394004 TT
1 TT
2394006 AAACATTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
10 5 0.09
11 4 0.07
12 4 0.07
13 26 0.47
14 5 0.09
15 1 0.02
16 10 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATATTATATA
Found at i:2394320 original size:19 final size:19
Alignment explanation
Indices: 2394292--2394328 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2394282 TTAAAATTTT
* *
2394292 TATTATTAATTTTTATAAA
1 TATTAATAATTATTATAAA
2394311 TATTAATAATTATTATAA
1 TATTAATAATTATTATAA
2394329 TTAATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTAATAATTATTATAAA
Found at i:2394348 original size:25 final size:27
Alignment explanation
Indices: 2394314--2394368 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
2394304 TTATAAATAT
2394314 TAATAATTATTATA-AT-TAATTAAAA
1 TAATAATTATTATATATATAATTAAAA
* *
2394339 TAATATTTATTATATTTATAATTAAAA
1 TAATAATTATTATATATATAATTAAAA
2394366 TAA
1 TAA
2394369 ATATAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 13 0.50
26 1 0.04
27 12 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATAATTATTATATATATAATTAAAA
Found at i:2394801 original size:18 final size:18
Alignment explanation
Indices: 2394780--2394822 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2394770 AATTTTTTAT
2394780 ATATTTTA-TAATATATAA
1 ATATTTTATTAA-ATATAA
2394798 ATATTTTATTAAATATAA
1 ATATTTTATTAAATATAA
2394816 ATATTTT
1 ATATTTT
2394823 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTTATTAAATATAA
Found at i:2394833 original size:18 final size:18
Alignment explanation
Indices: 2394780--2394829 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2394770 AATTTTTTAT
* *
2394780 ATATTTTATAATATATAA
1 ATATTTTATAAAAAATAA
* *
2394798 ATATTTTATTAAATATAA
1 ATATTTTATAAAAAATAA
2394816 ATATTTT-TAAAAAA
1 ATATTTTATAAAAAA
2394830 ATAATAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATTTTATAAAAAATAA
Found at i:2398318 original size:2 final size:2
Alignment explanation
Indices: 2398311--2398362 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
2398301 TTTTAACATC
* *
2398311 TA TA TA TA -A CA TA TA TA TA TA TA TA TA -A TA TA GCA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
2398351 TA TA TA TA TA TA
1 TA TA TA TA TA TA
2398363 AATCTGCCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2398322 original size:13 final size:13
Alignment explanation
Indices: 2398304--2398356 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
2398294 TACTTGATTT
*
2398304 TAACATCTATATA
1 TAACATATATATA
2398317 TAACATATATATA
1 TAACATATATATA
*
2398330 T-ATATATA-ATA
1 TAACATATATATA
*
2398341 TAGCATATTATATA
1 TAACATA-TATATA
2398355 TA
1 TA
2398357 TATATAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 4 0.12
12 9 0.27
13 15 0.45
14 5 0.15
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (13 bp):
TAACATATATATA
Found at i:2398335 original size:19 final size:21
Alignment explanation
Indices: 2398311--2398358 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
2398301 TTTTAACATC
*
2398311 TATATATAACATA-TATA-TA
1 TATATATAACATAGCATATTA
*
2398330 TATATATAATATAGCATATTA
1 TATATATAACATAGCATATTA
2398351 TATATATA
1 TATATATA
2398359 TATAAATCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.48
20 3 0.12
21 10 0.40
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATATAACATAGCATATTA
Found at i:2398465 original size:3 final size:3
Alignment explanation
Indices: 2398457--2398493 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2398447 TATTAATTAG
2398457 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2398494 AGGCTTGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2399132 original size:19 final size:18
Alignment explanation
Indices: 2399110--2399153 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
2399100 GAGAGAAGGT
2399110 TTTTATTATAATTTTTTAA
1 TTTTATTATAATTTTTT-A
*
2399129 TTTTATTTTTAATTTTTTA
1 TTTTA-TTATAATTTTTTA
2399148 TTTTAT
1 TTTTAT
2399154 AGTGTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 11 0.48
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTATAATTTTTTA
Found at i:2399546 original size:13 final size:13
Alignment explanation
Indices: 2399528--2399552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2399518 AAAATACATA
2399528 TTAAATATAAATT
1 TTAAATATAAATT
2399541 TTAAATATAAAT
1 TTAAATATAAAT
2399553 ATATATAAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATATAAATT
Found at i:2399962 original size:6 final size:6
Alignment explanation
Indices: 2399942--2399983 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
2399932 GTTAGATTTT
2399942 TTTTAA -TTTAGA TTTTAA TTTTAA TTTTTAA TTTT-A TTTTAA
1 TTTTAA TTTTA-A TTTTAA TTTTAA -TTTTAA TTTTAA TTTTAA
2399984 AATGATGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 9 0.28
6 13 0.41
7 10 0.31
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:2399964 original size:13 final size:13
Alignment explanation
Indices: 2399941--2399981 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2399931 CGTTAGATTT
2399941 TTTTTAA-TTTAGA
1 TTTTTAATTTTA-A
2399954 -TTTTAATTTTAA
1 TTTTTAATTTTAA
2399966 TTTTTAATTTT-A
1 TTTTTAATTTTAA
2399978 TTTT
1 TTTT
2399982 AAAATGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTTAATTTTAA
Found at i:2399965 original size:18 final size:16
Alignment explanation
Indices: 2399933--2399968 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
2399923 CCATGACTCG
2399933 TTAGATTTTTTTTAAT
1 TTAGATTTTTTTTAAT
2399949 TTAGATTTTAATTTTAAT
1 TTAGATTTT--TTTTAAT
2399967 TT
1 TT
2399969 TTAATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TTAGATTTTTTTTAAT
Found at i:2399980 original size:18 final size:17
Alignment explanation
Indices: 2399933--2399983 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
2399923 CCATGACTCG
2399933 TTAGATTTT-TTTTAAT
1 TTAGATTTTATTTTAAT
2399949 TTAGATTTTAATTTTAATTT
1 TTAGATTTT-ATTTTAA--T
2399969 TTA-ATTTTATTTTAA
1 TTAGATTTTATTTTAA
2399984 AATGATGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.29
18 13 0.42
19 5 0.16
20 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTAGATTTTATTTTAAT
Found at i:2400095 original size:18 final size:19
Alignment explanation
Indices: 2400058--2400097 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2400048 AAAAATTATT
2400058 ATTTTATTAATTAATTTTAA
1 ATTTTATT-ATTAATTTTAA
*
2400078 ATTTTATT-TTATTTTTAA
1 ATTTTATTATTAATTTTAA
2400096 AT
1 AT
2400098 CACATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTATTATTAATTTTAA
Found at i:2400578 original size:17 final size:17
Alignment explanation
Indices: 2400555--2400596 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2400545 AATTATTAGT
2400555 TAATTAAATTTAATTTAA
1 TAATTAAATTTAA-TTAA
* *
2400573 -AATTAATTTTTATTAA
1 TAATTAAATTTAATTAA
2400589 TAATTAAA
1 TAATTAAA
2400597 AATTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAAATTTAATTAA
Found at i:2402363 original size:30 final size:30
Alignment explanation
Indices: 2402313--2402369 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2402303 TTAAATCAAG
* *
2402313 TTTAAGTTAATATAAAAATTTATTTTATTT
1 TTTAAATTAATATAAAAATTTAATTTATTT
2402343 TTTAAATTAA-ATAAATAATTTAATTTA
1 TTTAAATTAATATAAA-AATTTAATTTA
2402370 ATACAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TTTAAATTAATATAAAAATTTAATTTATTT
Found at i:2405917 original size:25 final size:25
Alignment explanation
Indices: 2405889--2405945 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
2405879 TAATATAGTA
* *
2405889 TAAAATATGATA-AAAATATATTTTT
1 TAAAATATGATATAAAATA-AATTAT
*
2405914 TAAAAT-TTATATAAAATAAATTAT
1 TAAAATATGATATAAAATAAATTAT
2405938 TAAAATAT
1 TAAAATAT
2405946 TTAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TAAAATATGATATAAAATAAATTAT
Found at i:2405980 original size:19 final size:19
Alignment explanation
Indices: 2405972--2406020 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
2405962 TATATGATAT
2405972 TATAAATATAAATATAATA
1 TATAAATATAAATATAATA
*
2405991 TATAAATA-ACATATACATAA
1 TATAAATATAAATATA-AT-A
2406011 TATAAATATA
1 TATAAATATA
2406021 TAGATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 6 0.23
19 10 0.38
20 9 0.35
21 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TATAAATATAAATATAATA
Found at i:2405995 original size:13 final size:13
Alignment explanation
Indices: 2405972--2406022 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
2405962 TATATGATAT
2405972 TATAA-ATATAAA
1 TATAATATATAAA
2405984 TATAATATATAAA
1 TATAATATATAAA
*
2405997 TA-ACATATACATAA
1 TATA-ATATATA-AA
2406011 TATAAATATATA
1 TAT-AATATATA
2406023 GATTATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
12 6 0.19
13 15 0.47
14 4 0.12
15 6 0.19
16 1 0.03
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (13 bp):
TATAATATATAAA
Found at i:2407277 original size:2 final size:2
Alignment explanation
Indices: 2407270--2407303 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2407260 TAAGGTGAAC
* *
2407270 AT AT AT AT AT AT AT AT AT AT AT AT TT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2407304 TTATTTGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2414003 original size:31 final size:30
Alignment explanation
Indices: 2413967--2414051 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
2413957 TTACATAATA
2413967 TTAAATTTAATTAGAATATAAAAAATT-AAT
1 TTAAATTTAATTA-AATATAAAAAATTAAAT
*
2413997 TATAAATTTAATTACATA-AATAAAATTAAAAT
1 T-TAAATTTAATTAAATATAA-AAAATT-AAAT
*
2414029 TT-ATTTTAATTAAAATATAAAAA
1 TTAAATTTAATT-AAATATAAAAA
2414052 TTATTTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
29 2 0.04
30 18 0.39
31 20 0.43
32 6 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAATTTAATTAAATATAAAAAATTAAAT
Found at i:2414067 original size:30 final size:30
Alignment explanation
Indices: 2413970--2414067 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
2413960 CATAATATTA
* * *
2413970 AATTTAATTAGAATATAAAAAATTAATTATA
1 AATTTAATTAAAATAT-AAAAATTAATTTTT
**
2414001 AATTTAATTACATAA-AT-AAAATTAAAATTT
1 AATTTAATTA-A-AATATAAAAATTAATTTTT
* *
2414031 ATTTTAATTAAAATATAAAAATTATTTTTT
1 AATTTAATTAAAATATAAAAATTAATTTTT
2414061 AATTTAA
1 AATTTAA
2414068 ATTTATTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 2 0.04
29 3 0.06
30 34 0.64
31 10 0.19
32 2 0.04
33 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
AATTTAATTAAAATATAAAAATTAATTTTT
Found at i:2417688 original size:10 final size:9
Alignment explanation
Indices: 2417674--2417709 Score: 56
Period size: 10 Copynumber: 4.0 Consensus size: 9
2417664 TTAGACTTAT
2417674 TTAAAAAAA
1 TTAAAAAAA
2417683 TATAAAAAAA
1 T-TAAAAAAA
2417693 TT-AAAAAA
1 TTAAAAAAA
2417701 TTAAAAAAA
1 TTAAAAAAA
2417710 GGAGAGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.32
9 8 0.32
10 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:2418086 original size:540 final size:543
Alignment explanation
Indices: 2417066--2418149 Score: 1397
Period size: 545 Copynumber: 2.0 Consensus size: 543
2417056 ATTAATTAAG
* * *
2417066 TCATCTTTAATTTAGATTTATTGGATCCAAATTAATTGGGTTTAATTCATTTTAATTTAGATTTA
1 TCATCTTTAATTTAGATTTATTGGATCCAAATTAATTGGGCTAAATTCATTTTAATTTAGACTTA
* * * ** * *
2417131 TTTGAAAAAATACAAAAAAAAAAATTTTTAAAAGGGAGAGAATGAGTGGTCTGGGTTCAAAACTC
66 TTTAAAAAAATAAAAAAAAAAAAAATTAAAAAAAGGAGAGAATAAGTGGTCTGGGTTCAAAACTC
* * * * * *
2417196 AGGCCGCCTTTGTGAAAAAGGGTCATTATGATTCATGCATCAAAGTTAAGCTTTGGTCATAAATT
131 AGGCCACCTTTGTAAAAAAAGGTCATTATGACTCATGCACCAAAGTTAAGATTTGGTCATAAATT
* * *
2417261 AACAAAAGAATGTCAAAAAGAAAAAAAAAAAAAACGAATGGTTTGGGTTTCGAACCCAGGCCATC
196 AACAAAAAAATGTCAAAAAGAAAAAAAAAAAAAACGAA-GG-TTGAG--TCGAACCCAGGCCACC
* * * *
2417326 TAGATGGATAATAAAGGTCCTTATGACCAACAGGTCAAAGCTTTACTTTGGTAATAAAATGGCAA
257 TAAATGGATAATAAAAGTCCTTATGACCAACAGGCCAAAGCCTTACTTTGGTAATAAAATGGCAA
*
2417391 AAACAAAGAAAAAGTTATGAAAAAATAAAAAAATCGAAAAAAATAATAAAAACAAGACAACTTCG
322 AAACAAAGAAAAAGTTATGAAAAAATAAAAAAATCAAAAAAAATAATAAAAACAAGACAACTTCG
* ** * * * *
2417456 GTAGAGAGACTTGGTGGTCGATAAAGTGGCTGAAAATGGGGAAGAATGAAAAAAGCAAAACGAAA
387 ATAGAGAGACTTGGTCCTCGACAAAGTGCCTGAAAATGAGAAAGAATGAAAAAAGCAAAACGAAA
** * * * *
2417521 ATATATGATAAAATGGGGAGGTGACGAGTGAAAAAAAAGAAAATAAA-AAGAAAGA-A-AAAAGA
452 ATATATGATAAAATGGGGAGGTGACGAGCAAAAAAAAAAAAAAGAAAGAAAAAAGAGAGAAAAAA
2417583 -GGGTGGAGAAGC-TTAAAAAAATAAA
517 TGGGTGGAGAAGCTTTAAAAAAATAAA
* * *
2417608 TCATCTTTAATTTGGATTTATTGGATCCAAATTGATTTGGCTAAATTCATTTTAATTTAGACTTA
1 TCATCTTTAATTTAGATTTATTGGATCCAAATTAATTGGGCTAAATTCATTTTAATTTAGACTTA
* ***
2417673 TTTAAAAAAATATAAAAAAATTAAAAAATTAAAAAAAGGAGAGAATAAGTGG-CTTAGGTTTTGA
66 TTTAAAAAAATA-AAAAAAA--AAAAAATTAAAAAAAGGAGAGAATAAGTGGTC-TGGGTTCAAA
* * *
2417737 A-TCCATGCCACTTTTGTAAAAAAAGGTTATTATGAC-CTATGCACCAAAGTTAAGATTTGGTCA
127 ACT-CAGGCCACCTTTGTAAAAAAAGGTCATTATGACTC-ATGCACCAAAGTTAAGATTTGGTCA
* *
2417800 TATATTAATAAAAAAATGTCAAAAAGAAAAAAAAAAGAAAAACG-A-G-T-AG-CGAAACCCAGG
190 TAAATTAACAAAAAAATGTCAAAAAG-AAAAAAAAA-AAAAACGAAGGTTGAGTCG-AACCCAGG
** * * *
2417860 CCACCTAAATGGATAATAAAAGTTTTTATGACTAATAGGCCAAAGCCTTACTTTGGTTATAAAAT
252 CCACCTAAATGGATAATAAAAGTCCTTATGACCAACAGGCCAAAGCCTTACTTTGGTAATAAAAT
* * *
2417925 -G-ACAAACAAAGAAAAAGTTATGAAAAAAATAGAAAAATCAAAAAAAAATAATAAAAACAAGGC
317 GGCAAAAACAAAGAAAAAGTTATG-AAAAAATAAAAAAATC-AAAAAAAATAATAAAAACAAGAC
*
2417988 AACTTTCGATGGAGAGACTTGGTCCTCGACAAAGTGCCTGAAAATGAGAAAGAATGAAAAAAGCA
380 AAC-TTCGATAGAGAGACTTGGTCCTCGACAAAGTGCCTGAAAATGAGAAAGAATGAAAAAAGCA
2418053 AAACGAAAATATATGATAAAATGGGGAGGTGACGAGCAAAAAAAAAAAAAAGAAAGAAAAAAGAG
444 AAACGAAAATATATGATAAAATGGGGAGGTGACGAGCAAAAAAAAAAAAAAGAAAGAAAAAAGAG
2418118 AGAAAAAATGGGTGGAGAAGCTTTAAAAAAAT
509 AGAAAAAATGGGTGGAGAAGCTTTAAAAAAAT
2418150 CAAAAAAATA
Statistics
Matches: 467, Mismatches: 58, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
537 20 0.04
538 18 0.04
539 87 0.19
540 104 0.22
541 8 0.02
542 72 0.15
543 11 0.02
544 16 0.03
545 114 0.24
546 10 0.02
547 7 0.01
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (543 bp):
TCATCTTTAATTTAGATTTATTGGATCCAAATTAATTGGGCTAAATTCATTTTAATTTAGACTTA
TTTAAAAAAATAAAAAAAAAAAAAATTAAAAAAAGGAGAGAATAAGTGGTCTGGGTTCAAAACTC
AGGCCACCTTTGTAAAAAAAGGTCATTATGACTCATGCACCAAAGTTAAGATTTGGTCATAAATT
AACAAAAAAATGTCAAAAAGAAAAAAAAAAAAAACGAAGGTTGAGTCGAACCCAGGCCACCTAAA
TGGATAATAAAAGTCCTTATGACCAACAGGCCAAAGCCTTACTTTGGTAATAAAATGGCAAAAAC
AAAGAAAAAGTTATGAAAAAATAAAAAAATCAAAAAAAATAATAAAAACAAGACAACTTCGATAG
AGAGACTTGGTCCTCGACAAAGTGCCTGAAAATGAGAAAGAATGAAAAAAGCAAAACGAAAATAT
ATGATAAAATGGGGAGGTGACGAGCAAAAAAAAAAAAAAGAAAGAAAAAAGAGAGAAAAAATGGG
TGGAGAAGCTTTAAAAAAATAAA
Found at i:2418156 original size:9 final size:9
Alignment explanation
Indices: 2418142--2418170 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2418132 GAGAAGCTTT
2418142 AAAAAAATC
1 AAAAAAATC
2418151 AAAAAAAT-
1 AAAAAAATC
2418159 AAAAAAATC
1 AAAAAAATC
2418168 AAA
1 AAA
2418171 GTGTGTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:2418560 original size:24 final size:24
Alignment explanation
Indices: 2418533--2418580 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2418523 GTTATGGGTG
2418533 AAAAAGAAGAAGGTTCAAACTTCT
1 AAAAAGAAGAAGGTTCAAACTTCT
2418557 AAAAAGAAGAAGGTTCAAACTTCT
1 AAAAAGAAGAAGGTTCAAACTTCT
2418581 CTTACAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (24 bp):
AAAAAGAAGAAGGTTCAAACTTCT
Found at i:2418775 original size:259 final size:259
Alignment explanation
Indices: 2418307--2418781 Score: 596
Period size: 259 Copynumber: 1.8 Consensus size: 259
2418297 TTAGAGATAT
* * * * *
2418307 AAGGTTTAAACTTCTCTCATATATCTAGAAAAATCTAAAAAGAATTAGAAAAATCCGACTCCGGA
1 AAGGTTCAAACTTCTCTCACAGATCTAGAAAAATCTAAAAAGAACTAAAAAAATCCGACTCCGGA
* * * * *
2418372 TTTGGAAAGAGGAGGTCAAAAAGAGTTTAGAGGTAAAATTTGGGAGCCAACGGCCGCTGGTGAGC
66 TTTGGAAAGAGGAGGTCAAAAAGAGTTTAAAGGTAAAATTTGGGAGCCAACGGCCACCGATAAGC
* * * *
2418437 GACGACTGATGGTGGTTGTCGACGATCAGCATAGTGGTCAGTCCCGTTTCTGAGTTGCTTTTTCT
131 GACGACTGACGATGGTTGCCGACGATCAGCATAGTGGTCAGTCCCGTTTCTGAGTTGATTTTTCT
** *
2418502 GTTATCATTTGGTTATAGGTGGTTATGGGTGAAAAAGAAGAAGGTTCAAACTTCTAAAAAGAAG
196 GCCATCACTTGGTTATAGGTGGTTATGGGTGAAAAAGAAGAAGGTTCAAACTTCTAAAAAGAAG
* * * * *
2418566 AAGGTTCAAACTTCTCTTACAGATGTAGGAAAATCTAAAAAGAACTAAAAAAATTCGACTCTGGA
1 AAGGTTCAAACTTCTCTCACAGATCTAGAAAAATCTAAAAAGAACTAAAAAAATCCGACTCCGGA
* *
2418631 TTTGGAAAGAGGAGGTCGAAAAGAGTTTAAAGGTAAAATTTGGGAGCCAACGGTCACCGATAAGC
66 TTTGGAAAGAGGAGGTCAAAAAGAGTTTAAAGGTAAAATTTGGGAGCCAACGGCCACCGATAAGC
* * * * * * * *
2418696 -AGTGATTGACGATGGTTGCCTG-TGATCAGCATGGTGGTCGGTTCGGTTTCTGGGTT-ATTTTT
131 GA-CGACTGACGATGGTTGCC-GACGATCAGCATAGTGGTCAGTCCCGTTTCTGAGTTGATTTTT
* *
2418758 CCTGCCATCGCTTGGTTATGGGTG
194 -CTGCCATCACTTGGTTATAGGTG
2418782 AGAAAGAAGG
Statistics
Matches: 179, Mismatches: 34, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
258 6 0.03
259 172 0.96
260 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (259 bp):
AAGGTTCAAACTTCTCTCACAGATCTAGAAAAATCTAAAAAGAACTAAAAAAATCCGACTCCGGA
TTTGGAAAGAGGAGGTCAAAAAGAGTTTAAAGGTAAAATTTGGGAGCCAACGGCCACCGATAAGC
GACGACTGACGATGGTTGCCGACGATCAGCATAGTGGTCAGTCCCGTTTCTGAGTTGATTTTTCT
GCCATCACTTGGTTATAGGTGGTTATGGGTGAAAAAGAAGAAGGTTCAAACTTCTAAAAAGAAG
Found at i:2418907 original size:17 final size:17
Alignment explanation
Indices: 2418885--2418917 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2418875 ATTAATCACT
2418885 GCACCATACTCATTTTA
1 GCACCATACTCATTTTA
2418902 GCACCATACTCATTTT
1 GCACCATACTCATTTT
2418918 TCAAGTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.06, T:0.36
Consensus pattern (17 bp):
GCACCATACTCATTTTA
Found at i:2419438 original size:23 final size:21
Alignment explanation
Indices: 2419377--2419438 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
2419367 ATTTTTACCC
2419377 AAAAAAATAA-AAAAGTATAA
1 AAAAAAATAATAAAAGTATAA
**
2419397 ATAAAAAATTTTAAAAAGTATAA
1 A-AAAAAATAAT-AAAAGTATAA
2419420 AAAAATAATAATAATAAGT
1 AAAAA-AATAATAA-AAGT
2419439 GTTCTTCAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.03
21 7 0.21
22 6 0.18
23 19 0.58
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAAAAATAATAAAAGTATAA
Found at i:2421199 original size:152 final size:152
Alignment explanation
Indices: 2420923--2421226 Score: 599
Period size: 152 Copynumber: 2.0 Consensus size: 152
2420913 ATCGAGAAAG
2420923 AGTAAGAATCAATCTCCTCGCTGATTCAACAATCGCTAACGATTTCGATAGGTGTTTGGTCACAC
1 AGTAAGAATCAATCTCCTCGCTGATTCAACAATCGCTAACGATTTCGATAGGTGTTTGGTCACAC
2420988 CTAGCCAAAATGATCGGTGACGACTCTAAATCTTCGATCATTTCGCGGTGACCGTTGAAGATCAG
66 CTAGCCAAAATGATCGGTGACGACTCTAAATCTTCGATCATTTCGCGGTGACCGTTGAAGATCAG
2421053 TTAGACGGGCGATTCGACTAAT
131 TTAGACGGGCGATTCGACTAAT
*
2421075 AGTAAGAATCAATCTCCTCGCTGATTCAACAATTGCTAACGATTTCGATAGGTGTTTGGTCACAC
1 AGTAAGAATCAATCTCCTCGCTGATTCAACAATCGCTAACGATTTCGATAGGTGTTTGGTCACAC
2421140 CTAGCCAAAATGATCGGTGACGACTCTAAATCTTCGATCATTTCGCGGTGACCGTTGAAGATCAG
66 CTAGCCAAAATGATCGGTGACGACTCTAAATCTTCGATCATTTCGCGGTGACCGTTGAAGATCAG
2421205 TTAGACGGGCGATTCGACTAAT
131 TTAGACGGGCGATTCGACTAAT
2421227 GATCTTCCCC
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 151 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (152 bp):
AGTAAGAATCAATCTCCTCGCTGATTCAACAATCGCTAACGATTTCGATAGGTGTTTGGTCACAC
CTAGCCAAAATGATCGGTGACGACTCTAAATCTTCGATCATTTCGCGGTGACCGTTGAAGATCAG
TTAGACGGGCGATTCGACTAAT
Found at i:2422496 original size:2 final size:2
Alignment explanation
Indices: 2422491--2422528 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2422481 TTTTGTCTCA
2422491 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
2422529 TTGTAAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2431400 original size:21 final size:20
Alignment explanation
Indices: 2431346--2431401 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
2431336 CTTATTAAAC
*
2431346 ATAAATATA-TTTAATTTTT
1 ATAAATATATTTTAATTTAT
* *
2431365 AAAAATTTATATTTAATTTAT
1 ATAAATATAT-TTTAATTTAT
2431386 ATTAAATATATTTTAA
1 A-TAAATATATTTTAA
2431402 ATATAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 7 0.24
21 15 0.52
22 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAAATATATTTTAATTTAT
Found at i:2431673 original size:23 final size:21
Alignment explanation
Indices: 2431642--2431685 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
2431632 AATATTAGAT
2431642 TATTATTTATATATTAATATTTA
1 TATTATTTATA-ATTAA-ATTTA
*
2431665 TATTTTTTATAATTAAATTTA
1 TATTATTTATAATTAAATTTA
2431686 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATTTATAATTAAATTTA
Found at i:2431675 original size:21 final size:23
Alignment explanation
Indices: 2431642--2431685 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
2431632 AATATTAGAT
2431642 TATTATTTATAT-ATTAATATTTA
1 TATTATTTATATAATTAA-ATTTA
2431665 TATT-TTT-TATAATTAAATTTA
1 TATTATTTATATAATTAAATTTA
2431686 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.40
22 8 0.40
23 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATTTATATAATTAAATTTA
Found at i:2436367 original size:20 final size:21
Alignment explanation
Indices: 2436344--2436404 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
2436334 AAGTGATTTT
*
2436344 TAAAATATTAATTTTATAT-A
1 TAAAATAATAATTTTATATAA
*
2436364 T-AAATAAATAATTTAATATAA
1 TAAAAT-AATAATTTTATATAA
*
2436385 TAAAAATAATATTTTTATAT
1 T-AAAATAATAATTTTATAT
2436405 TTACAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
21 2 0.06
22 11 0.33
23 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATAATAATTTTATATAA
Found at i:2436378 original size:19 final size:19
Alignment explanation
Indices: 2436356--2436394 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2436346 AAATATTAAT
*
2436356 TTTATATATAA-ATAAATAA
1 TTTA-ATATAATAAAAATAA
2436375 TTTAATATAATAAAAATAA
1 TTTAATATAATAAAAATAA
2436394 T
1 T
2436395 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAATATAATAAAAATAA
Found at i:2436959 original size:2 final size:2
Alignment explanation
Indices: 2436947--2436982 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2436937 TAATCGCACC
* *
2436947 CT CT TT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2436983 ATTTTTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2438897 original size:18 final size:18
Alignment explanation
Indices: 2438874--2438909 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2438864 ATTCAAGCCG
2438874 ATATTCCAAAAATTCTTA
1 ATATTCCAAAAATTCTTA
2438892 ATATTCCAAAAATTCTTA
1 ATATTCCAAAAATTCTTA
2438910 CATAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTCCAAAAATTCTTA
Found at i:2440963 original size:2 final size:2
Alignment explanation
Indices: 2440952--2440985 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
2440942 TAATCGCACC
2440952 CT CT -T CT CT CT CT CT GCT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT
2440986 ATTTTTGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2440978 original size:17 final size:16
Alignment explanation
Indices: 2440952--2440983 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2440942 TAATCGCACC
2440952 CTCTTCTCTCTCTCTG
1 CTCTTCTCTCTCTCTG
2440968 CTCTCTCTCTCTCTCT
1 CTCT-TCTCTCTCTCT
2440984 CTATTTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (16 bp):
CTCTTCTCTCTCTCTG
Found at i:2461284 original size:143 final size:142
Alignment explanation
Indices: 2461047--2461305 Score: 383
Period size: 143 Copynumber: 1.8 Consensus size: 142
2461037 CCACTGAGAT
* * * * *
2461047 CTGAATTCGGGTCACTGGATTCAGAGTAAAATACTCAGTACCTTCAGTTTTGTTTCGAGTACGTA
1 CTGAATTCGGATAACTGGATTCAGAGTAAAATACTCAGTACCTTCAATTTTGTTTCAAGTACGAA
* *
2461112 TGCTTATTGATATCAATAGATTTTGATATATTATTTTTAATTTAATAATTTTTTACGAGAAAAAG
66 TACTTATTGATATCAATAGATTTTAATATATTATTTTTAATTTAAT-ATTTTTTACGAGAAAAAG
2461177 AGCTCATTAAGAC
130 AGCTCATTAAGAC
* * * *
2461190 CTGAATTCGGATAACTGGATTCAGAGTAAAATAGTCAGTACTTTTAATTTTGTTTTAAGTACGAA
1 CTGAATTCGGATAACTGGATTCAGAGTAAAATACTCAGTACCTTCAATTTTGTTTCAAGTACGAA
* * *
2461255 TATTTATTGATATCGATATATTTTAATATATTATTTTTAATTTAATATTTT
66 TACTTATTGATATCAATAGATTTTAATATATTATTTTTAATTTAATATTTT
2461306 GTATAATATT
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
142 5 0.05
143 97 0.95
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (142 bp):
CTGAATTCGGATAACTGGATTCAGAGTAAAATACTCAGTACCTTCAATTTTGTTTCAAGTACGAA
TACTTATTGATATCAATAGATTTTAATATATTATTTTTAATTTAATATTTTTTACGAGAAAAAGA
GCTCATTAAGAC
Found at i:2461891 original size:24 final size:23
Alignment explanation
Indices: 2461864--2461913 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
2461854 TATGTTAAAA
2461864 ATATTAAATA-AATTATTAATTATT
1 ATATTAAATATAA-TATT-ATTATT
*
2461888 ATATTAAATATAATATTATTTTT
1 ATATTAAATATAATATTATTATT
2461911 ATA
1 ATA
2461914 AATAATGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 14 0.58
25 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTAAATATAATATTATTATT
Found at i:2461892 original size:12 final size:12
Alignment explanation
Indices: 2461863--2461905 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
2461853 ATATGTTAAA
2461863 AATATTAAATA-
1 AATATTAAATAT
*
2461874 AATTATTAATTAT
1 AA-TATTAAATAT
*
2461887 TATATTAAATAT
1 AATATTAAATAT
2461899 AATATTA
1 AATATTA
2461906 TTTTTATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 2 0.08
12 23 0.88
13 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATTAAATAT
Found at i:2462262 original size:18 final size:18
Alignment explanation
Indices: 2462231--2462284 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
2462221 TTTATGATTG
* * *
2462231 AATTTTAATTTATTTATA
1 AATTTAAATATATTTAAA
*
2462249 ACTTTAAATATATTTAAA
1 AATTTAAATATATTTAAA
2462267 AATTTAAATATAATTTAA
1 AATTTAAATAT-ATTTAA
2462285 TATCAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTAAATATATTTAAA
Found at i:2463739 original size:18 final size:18
Alignment explanation
Indices: 2463716--2463754 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2463706 AAATTTTTAA
2463716 TTAAAA-AATTTAAATATT
1 TTAAAATAATTT-AATATT
*
2463734 TTAAAATAATTTTATATT
1 TTAAAATAATTTAATATT
2463752 TTA
1 TTA
2463755 TTTAAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAATAATTTAATATT
Found at i:2464076 original size:16 final size:16
Alignment explanation
Indices: 2464055--2464085 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2464045 CATAAAATAA
2464055 TTATTTTATTATAATT
1 TTATTTTATTATAATT
*
2464071 TTATTTTATTTTAAT
1 TTATTTTATTATAAT
2464086 AAATTATATA
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTATTATAATT
Found at i:2464907 original size:25 final size:23
Alignment explanation
Indices: 2464862--2464907 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2464852 TGATATTATA
*
2464862 AATATTATTAATTAATATTTAAT
1 AATATTATTAAATAATATTTAAT
2464885 AATATTAATTAAAATAATATTTA
1 AATATT-ATT-AAATAATATTTA
2464908 TAAAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTATTAAATAATATTTAAT
Found at i:2466073 original size:12 final size:13
Alignment explanation
Indices: 2466055--2466093 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
2466045 AATAGTGTAT
*
2466055 TTAAAAAATATAA
1 TTAAAAAATAAAA
2466068 -TAAAAAATAAAA
1 TTAAAAAATAAAA
2466080 TTAAAATAATAAAA
1 TTAAAA-AATAAAA
2466094 ATTTAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.48
13 5 0.22
14 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TTAAAAAATAAAA
Found at i:2467319 original size:18 final size:18
Alignment explanation
Indices: 2467266--2467321 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
2467256 AAAAATTAAA
*
2467266 AAATATTAAATTTTATAT
1 AAATATTAAAATTTATAT
2467284 -AATA-T-AAA-TTAT-T
1 AAATATTAAAATTTATAT
2467297 AAAATATTAAAATTTATAT
1 -AAATATTAAAATTTATAT
2467316 AAATAT
1 AAATAT
2467322 AAATTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
13 1 0.03
14 4 0.13
15 6 0.19
16 2 0.06
17 7 0.23
18 10 0.32
19 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATTAAAATTTATAT
Found at i:2467321 original size:33 final size:32
Alignment explanation
Indices: 2467248--2467329 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 32
2467238 TAAAAAAATA
* * *
2467248 ATATAATAAAAAATTA-AAAAATATTAAATTTT
1 ATATAAT-ATAAATTATTAAAATATTAAAATTT
2467280 ATATAATATAAATTATTAAAATATTAAAATTT
1 ATATAATATAAATTATTAAAATATTAAAATTT
2467312 ATATAAATATAAATTATT
1 ATAT-AATATAAATTATT
2467330 TTATCTCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 7 0.16
32 25 0.56
33 13 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAATATAAATTATTAAAATATTAAAATTT
Found at i:2467324 original size:17 final size:17
Alignment explanation
Indices: 2467266--2467324 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
2467256 AAAAATTAAA
*
2467266 AAATATTAAATTT-TAT
1 AAATATAAAATTTATAT
2467282 ATAATAT-AAA-TTAT-T
1 A-AATATAAAATTTATAT
2467297 AAAATATTAAAATTTATAT
1 -AAATA-TAAAATTTATAT
2467316 AAATATAAA
1 AAATATAAA
2467325 TTATTTTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
15 7 0.19
16 7 0.19
17 12 0.33
18 9 0.25
19 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATAAAATTTATAT
Found at i:2468977 original size:19 final size:19
Alignment explanation
Indices: 2468923--2468970 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2468913 TGTTAAATAT
2468923 ATTATA-TT-AATCATATTA
1 ATTATATTTAAAT-ATATTA
*
2468941 ATTATATTTAAATATATTG
1 ATTATATTTAAATATATTA
2468960 ATTCATATTTA
1 ATT-ATATTTA
2468971 TTATATTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 6 0.23
19 10 0.38
20 10 0.38
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTATATTTAAATATATTA
Found at i:2472952 original size:16 final size:17
Alignment explanation
Indices: 2472931--2472963 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2472921 TTTGATATAA
2472931 ATATA-TTTAAATTTTT
1 ATATATTTTAAATTTTT
2472947 ATATATTTTAAATTTTT
1 ATATATTTTAAATTTTT
2472964 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATATTTTAAATTTTT
Found at i:2472975 original size:24 final size:25
Alignment explanation
Indices: 2472947--2473002 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
2472937 TTAAATTTTT
2472947 ATATATTTTAAATTT-T-TTTAAAA
1 ATATATTTTAAATTTATATTTAAAA
* *
2472970 ATTATATTTTATATTTATATTTAAAT
1 A-TATATTTTAAATTTATATTTAAAA
2472996 ATATATT
1 ATATATT
2473003 AAATATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 13 0.46
25 7 0.25
26 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATATATTTTAAATTTATATTTAAAA
Found at i:2473407 original size:20 final size:19
Alignment explanation
Indices: 2473354--2473408 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
2473344 TTTTTAAGAT
2473354 ATAAAA-AATTAAAA-ATA
1 ATAAAATAATTAAAATATA
* * * *
2473371 ATTATATAAATATAATATAA
1 ATAAAATAATTAAAATAT-A
2473391 ATAAAATAATTAAAATAT
1 ATAAAATAATTAAAATAT
2473409 TATATGAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 2 0.07
20 15 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAAATAATTAAAATATA
Found at i:2473435 original size:24 final size:24
Alignment explanation
Indices: 2473385--2473504 Score: 75
Period size: 24 Copynumber: 4.7 Consensus size: 24
2473375 TATAAATATA
*
2473385 ATATAA-ATAAAATAATTAAAATATT
1 ATATAATATAAAAT-ATTAATAT-TT
* *
2473410 ATATGAATA-AATATCTTAATATTT
1 ATAT-AATATAAAATATTAATATTT
2473434 ATATAATATAAAATATTAATATATT
1 ATATAATATAAAATATTAATAT-TT
* *
2473459 AAAATTAATAT-AAATATAAAATTATTTAT
1 -ATA-TAATATAAAATAT-TAA-TA-TT-T
2473488 ATATAATATAAATATAT
1 ATATAATATAAA-ATAT
2473505 AAATTACCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
23 4 0.05
24 17 0.23
25 12 0.16
26 14 0.19
27 15 0.20
28 7 0.09
29 6 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (24 bp):
ATATAATATAAAATATTAATATTT
Found at i:2473456 original size:20 final size:19
Alignment explanation
Indices: 2473365--2473504 Score: 82
Period size: 18 Copynumber: 7.4 Consensus size: 19
2473355 TAAAAAATTA
2473365 AAAATAATTATATA-AATAT
1 AAAAT-ATTATATATAATAT
* * *
2473384 AATATA-AATAAAATAAT-T
1 AAAATATTAT-ATATAATAT
2473402 AAAATATTATATGAATAAATAT
1 AAAATATTATAT--AT-AATAT
**
2473424 CTTAATATT-TATATAATAT
1 -AAAATATTATATATAATAT
2473443 AAAATATTA-ATAT-AT-T
1 AAAATATTATATATAATAT
*
2473459 AAAAT-TAATATA-AATAT
1 AAAATATTATATATAATAT
2473476 AAAATTATTTATATATAATAT
1 AAAA-TA-TTATATATAATAT
2473497 AAATATAT
1 AAA-ATAT
2473505 AAATTACCAT
Statistics
Matches: 92, Mismatches: 12, Indels: 33
0.67 0.09 0.24
Matches are distributed among these distances:
15 2 0.02
16 11 0.12
17 9 0.10
18 21 0.23
19 14 0.15
20 11 0.12
21 13 0.14
22 5 0.05
23 6 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (19 bp):
AAAATATTATATATAATAT
Found at i:2473470 original size:32 final size:34
Alignment explanation
Indices: 2473419--2473491 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 34
2473409 TATATGAATA
* * *
2473419 AATATCTTAATATTTATAT-AATATAAAA-TATT
1 AATATATTAAAATTAATATAAATATAAAATTATT
2473451 AATATATTAAAATTAATATAAATATAAAATTATT
1 AATATATTAAAATTAATATAAATATAAAATTATT
*
2473485 TATATAT
1 AATATAT
2473492 AATATAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 16 0.46
33 9 0.26
34 10 0.29
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (34 bp):
AATATATTAAAATTAATATAAATATAAAATTATT
Found at i:2473494 original size:27 final size:28
Alignment explanation
Indices: 2473433--2473510 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
2473423 TCTTAATATT
*
2473433 TATATAATATAAA-ATATTAATATATTAA
1 TATATAATATAAATATATAAAT-TATTAA
* *
2473461 AAT-TAATATAAATATA-AAATTATTTA
1 TATATAATATAAATATATAAATTATTAA
2473487 TATATAATATAAATATATAAATTA
1 TATATAATATAAATATATAAATTA
2473511 CCATATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
26 7 0.16
27 25 0.58
28 11 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TATATAATATAAATATATAAATTATTAA
Found at i:2473516 original size:27 final size:27
Alignment explanation
Indices: 2473464--2473516 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2473454 ATATTAAAAT
**
2473464 TAATATAAATATAAAATTATTTATATA
1 TAATATAAATATAAAATTATCCATATA
2473491 TAATATAAATATATAAATTA-CCATAT
1 TAATATAAATATA-AAATTATCCATAT
2473517 TTAAATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATATAAATATAAAATTATCCATATA
Found at i:2475334 original size:15 final size:15
Alignment explanation
Indices: 2475286--2475338 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
2475276 TTACTTCGAT
2475286 TTTAATATAA--ATA
1 TTTAATATAATTATA
* *
2475299 TTAAATATAAATATATT
1 TTTAATAT-AAT-TATA
2475316 TTTAATATAATTATA
1 TTTAATATAATTATA
2475331 TTTAATAT
1 TTTAATAT
2475339 TTTTTAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 7 0.22
14 2 0.06
15 11 0.34
16 3 0.09
17 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAATATAATTATA
Found at i:2477672 original size:14 final size:14
Alignment explanation
Indices: 2477632--2477673 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2477622 TTCATTAGAT
* *
2477632 TTATAATTTATACA
1 TTATTATTTATATA
2477646 TTATTATTTATATA
1 TTATTATTTATATA
*
2477660 TTATTCTTTATATA
1 TTATTATTTATATA
2477674 AAAATTCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATTTATATA
Found at i:2478101 original size:22 final size:21
Alignment explanation
Indices: 2478019--2478102 Score: 66
Period size: 21 Copynumber: 3.9 Consensus size: 21
2478009 TTTCATTTAT
* *
2478019 TAAAATAA-AATATAATTATAA
1 TAAAATAATTATATAA-TAAAA
* *
2478040 TAAAATAATTATTTTATAAAAA
1 TAAAATAATTATATAAT-AAAA
2478062 TAAAATAAAGTTA-A-AATAAAA
1 TAAAAT-AA-TTATATAATAAAA
2478083 TAAAATAATTACTATAATAA
1 TAAAATAATTA-TATAATAA
2478103 TAATTTAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.06
20 2 0.04
21 20 0.40
22 20 0.40
23 2 0.04
24 3 0.06
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (21 bp):
TAAAATAATTATATAATAAAA
Found at i:2479179 original size:18 final size:17
Alignment explanation
Indices: 2479148--2479209 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
2479138 TTATTATATA
2479148 ATATTTA-A-AAAATTAT
1 ATATTTATATAAAATT-T
2479164 ATATTTATATAAAATTT
1 ATATTTATATAAAATTT
*
2479181 -TA-ATATATTAAAAATTT
1 ATATTTATA-T-AAAATTT
2479198 ATA-TTATATAAA
1 ATATTTATATAAA
2479210 TTTTTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 4 0.10
16 13 0.33
17 10 0.26
18 12 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTTATATAAAATTT
Found at i:2479196 original size:17 final size:16
Alignment explanation
Indices: 2479169--2479221 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
2479159 ATTATATATT
2479169 TATA-TAAAATTTTAA
1 TATATTAAAATTTTAA
*
2479184 TATATTAAAAATTT-A
1 TATATTAAAATTTTAA
*
2479199 TATTATATAAATTTTTAA
1 TA-TAT-TAAAATTTTAA
2479217 TATAT
1 TATAT
2479222 ATTATTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.23
16 11 0.35
17 10 0.32
18 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTAAAATTTTAA
Found at i:2479201 original size:15 final size:15
Alignment explanation
Indices: 2479169--2479222 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
2479159 ATTATATATT
*
2479169 TATATAAAATTTTAA
1 TATATAAAAATTTAA
2479184 TATATTAAAAATTTATA
1 TATA-TAAAAATTTA-A
**
2479201 TTATATAAATTTTTAA
1 -TATATAAAAATTTAA
2479217 TATATA
1 TATATA
2479223 TTATTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.30
16 10 0.30
17 9 0.27
18 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATAAAAATTTAA
Found at i:2479215 original size:33 final size:36
Alignment explanation
Indices: 2479146--2479221 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 36
2479136 TTTTATTATA
2479146 TAATAT-TTAAAAAATTATATATTTATATAAAATTT
1 TAATATATTAAAAAATTATATATTTATATAAAATTT
*
2479181 TAATATATT-AAAAATT-TATA-TTATATAAATTTT
1 TAATATATTAAAAAATTATATATTTATATAAAATTT
2479214 TAATATAT
1 TAATATAT
2479222 ATTATTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
33 20 0.51
34 4 0.10
35 13 0.33
36 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
TAATATATTAAAAAATTATATATTTATATAAAATTT
Found at i:2479222 original size:17 final size:17
Alignment explanation
Indices: 2479146--2479223 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
2479136 TTTTATTATA
* * *
2479146 TAATATTTAAAAAATTA
1 TAATATATATAAAATTT
*
2479163 TATATTTATATAAAATTT
1 TA-ATATATATAAAATTT
*
2479181 TAATATAT-TAAAAATT
1 TAATATATATAAAATTT
*
2479197 T-ATATTATATAAATTTT
1 TAATA-TATATAAAATTT
2479214 TAATATATAT
1 TAATATATAT
2479224 TATTTTATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
15 3 0.06
16 11 0.22
17 19 0.39
18 16 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATATATAAAATTT
Found at i:2479254 original size:23 final size:24
Alignment explanation
Indices: 2479197--2479260 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
2479187 ATTAAAAATT
*
2479197 TATATTATA-TA-AATTTTTAATA
1 TATATTATATTATTATTTTTAATA
*
2479219 TATATTATTTTATTATTTTT-ATCA
1 TATATTATATTATTATTTTTAAT-A
2479243 TATATTA-ATTATTATTTT
1 TATATTATATTATTATTTT
2479261 ATTTACTGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.22
23 14 0.39
24 14 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTATATTATTATTTTTAATA
Found at i:2479257 original size:26 final size:24
Alignment explanation
Indices: 2479209--2479260 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2479199 TATTATATAA
2479209 ATTTTTAATATATATTATTTTATT
1 ATTTTTAATATATATTATTTTATT
*
2479233 ATTTTT-ATCATATATTA-ATTATT
1 ATTTTTAAT-ATATATTATTTTATT
2479256 ATTTT
1 ATTTT
2479261 ATTTACTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTTAATATATATTATTTTATT
Found at i:2488523 original size:4 final size:4
Alignment explanation
Indices: 2488514--2488549 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
2488504 TTTATCAACG
2488514 AATT AATT AATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT
2488550 CATGATAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:2489853 original size:2 final size:2
Alignment explanation
Indices: 2489846--2489888 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2489836 AGGCCTCCAT
2489846 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2489888 A
1 A
2489889 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Done.