Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold28
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: 2815568
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.30
Warning! 166732 characters in sequence are not A, C, G, or T
File 4 of 16
Found at i:472124 original size:35 final size:33
Alignment explanation
Indices: 472061--472125 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
472051 ATATATTTTA
* * *
472061 TTATATTATAATCATATTTAATATATTTTATAT
1 TTATATTATAATAATATTAAATAAATTTTATAT
472094 TTATATTAATAATTAATATTAAATAAATTTTA
1 TTATATT-ATAA-TAATATTAAATAAATTTTA
472126 AAAAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 7 0.26
34 4 0.15
35 16 0.59
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (33 bp):
TTATATTATAATAATATTAAATAAATTTTATAT
Found at i:479046 original size:17 final size:17
Alignment explanation
Indices: 479020--479052 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
479010 AAGAGGTTAT
479020 AATTTAAATA-TAAAAA
1 AATTTAAATATTAAAAA
479036 AATTATAAATATTAAAA
1 AATT-TAAATATTAAAA
479053 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAATATTAAAAA
Found at i:480241 original size:3 final size:3
Alignment explanation
Indices: 480233--480262 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
480223 GTAATATCGT
480233 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
480263 AATGTATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:482519 original size:18 final size:17
Alignment explanation
Indices: 482473--482522 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
482463 GGTTAGTTCG
482473 ATTTAAATT-ATTATTT
1 ATTTAAATTAATTATTT
* *
482489 ATTATAAAATAATTTTTT
1 ATT-TAAATTAATTATTT
482507 ATTTAAATTTAATTAT
1 ATTTAAA-TTAATTAT
482523 AAAAAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.11
17 9 0.33
18 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAATTAATTATTT
Found at i:482950 original size:18 final size:15
Alignment explanation
Indices: 482912--482964 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
482902 TTTTATAATT
*
482912 TTTATATTATTTATA
1 TTTATTTTATTTATA
482927 TTTATTTTATTTGATCA
1 TTTATTTTATTT-AT-A
*
482944 TTATATTTTATTTTTA
1 TT-TATTTTATTTATA
482960 TTTAT
1 TTTAT
482965 ATAAATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 14 0.42
16 5 0.15
17 4 0.12
18 10 0.30
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTATTTTATTTATA
Found at i:484262 original size:20 final size:21
Alignment explanation
Indices: 484230--484279 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
484220 TAGATTTTAT
*
484230 TTTCAGCTAAAATAAAATATA
1 TTTCAGTTAAAATAAAATATA
*
484251 TTT-AGTTAAAATAATATATA
1 TTTCAGTTAAAATAAAATATA
484271 TTTCAGTTA
1 TTTCAGTTA
484280 TATTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (21 bp):
TTTCAGTTAAAATAAAATATA
Found at i:485227 original size:38 final size:38
Alignment explanation
Indices: 485167--485296 Score: 118
Period size: 38 Copynumber: 3.4 Consensus size: 38
485157 ACCGGATAAG
* *
485167 AATAATAGTTTTTGTATT-GAACCGTGTCACTGGTTTAA
1 AATAATAATTTTTGT-TTCGAACCGTGCCACTGGTTTAA
* * *
485205 AATAATAATTTTTATTTCGAACCATGCCACTGGTTTAG
1 AATAATAATTTTTGTTTCGAACCGTGCCACTGGTTTAA
* * * * * * *
485243 AACAGTGATTTTTGTTTCTAACCGTGCTACCGATTTAA
1 AATAATAATTTTTGTTTCGAACCGTGCCACTGGTTTAA
* *
485281 AATAGTGATTTTTGTT
1 AATAATAATTTTTGTT
485297 CATAGCTTGT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
37 2 0.03
38 73 0.97
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (38 bp):
AATAATAATTTTTGTTTCGAACCGTGCCACTGGTTTAA
Found at i:486500 original size:13 final size:13
Alignment explanation
Indices: 486482--486506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486472 CTGCCAGTTT
486482 ATGTATCGATACA
1 ATGTATCGATACA
486495 ATGTATCGATAC
1 ATGTATCGATAC
486507 TAAGCAAAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:496280 original size:20 final size:19
Alignment explanation
Indices: 496251--496332 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 19
496241 TTTCTATTTA
*
496251 TTTTTTTAGATTTTTTAAT
1 TTTTTTTAGAATTTTTAAT
*
496270 TTTTCTTTAGAATTTTTAGAA
1 TTTT-TTTAGAATTTTTA-AT
* *
496291 TTTATTTA-ATTTTTTAA-
1 TTTTTTTAGAATTTTTAAT
** *
496308 -AGTTTTAGAATTTTTTAT
1 TTTTTTTAGAATTTTTAAT
496326 TTTTTTT
1 TTTTTTT
496333 TGAAATATTC
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
16 4 0.09
17 7 0.15
18 1 0.02
19 15 0.32
20 16 0.34
21 4 0.09
ACGTcount: A:0.24, C:0.01, G:0.06, T:0.68
Consensus pattern (19 bp):
TTTTTTTAGAATTTTTAAT
Found at i:496332 original size:27 final size:28
Alignment explanation
Indices: 496254--496332 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 28
496244 CTATTTATTT
*
496254 TTTTAG-ATTTTTTAATTTTTCTTTAGAAT
1 TTTTAGAATTTTTT-ATTTTT-TTTAGAAG
*
496283 TTTTAGAATTTATTTA-ATTTTTTA-AAG
1 TTTTAGAATTT-TTTATTTTTTTTAGAAG
496310 TTTTAGAATTTTTTATTTTTTTT
1 TTTTAGAATTTTTTATTTTTTTT
496333 TGAAATATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.09
27 19 0.43
28 4 0.09
29 9 0.20
30 5 0.11
31 3 0.07
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.67
Consensus pattern (28 bp):
TTTTAGAATTTTTTATTTTTTTTAGAAG
Found at i:499520 original size:21 final size:21
Alignment explanation
Indices: 499496--499540 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
499486 TTAGCATTAA
* * *
499496 TTTTCATATAGGTTACAAACC
1 TTTTAATATAGGTCAAAAACC
*
499517 TTTTAATGTAGGTCAAAAACC
1 TTTTAATATAGGTCAAAAACC
499538 TTT
1 TTT
499541 AATTTCATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (21 bp):
TTTTAATATAGGTCAAAAACC
Found at i:503981 original size:13 final size:13
Alignment explanation
Indices: 503963--504078 Score: 70
Period size: 13 Copynumber: 7.5 Consensus size: 13
503953 AGCTTCGTAG
503963 CGATACATTGTAT
1 CGATACATTGTAT
503976 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
503995 CGATACATTGTAT
1 CGATACATTGTAT
504008 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
504027 CGATACATTGTAT
1 CGATACATTGTAT
504040 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
504059 CGATACATTGTAT
1 CGATACATTGTAT
504072 CGATACA
1 CGATACA
504079 ACACTTATGT
Statistics
Matches: 85, Mismatches: 0, Indels: 36
0.70 0.00 0.30
Matches are distributed among these distances:
13 33 0.39
14 2 0.02
15 2 0.02
16 18 0.21
17 2 0.02
18 2 0.02
19 26 0.31
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:503995 original size:19 final size:19
Alignment explanation
Indices: 503971--504097 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
503961 AGCGATACAT
503971 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
503990 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
504003 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
504022 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
504035 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
504054 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
504067 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
504086 TGTATTGATACA
1 TGTATCGATACA
504098 GTTACTTGTT
Statistics
Matches: 89, Mismatches: 1, Indels: 36
0.71 0.01 0.29
Matches are distributed among these distances:
13 27 0.30
14 3 0.03
16 18 0.20
18 3 0.03
19 38 0.43
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:504004 original size:32 final size:32
Alignment explanation
Indices: 503963--504097 Score: 261
Period size: 32 Copynumber: 4.2 Consensus size: 32
503953 AGCTTCGTAG
503963 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
503995 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
504027 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
504059 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
504091 TGATACA
1 CGATACA
504098 GTTACTTGTT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 102 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:504187 original size:21 final size:21
Alignment explanation
Indices: 504157--504275 Score: 220
Period size: 21 Copynumber: 5.7 Consensus size: 21
504147 GTTGGGACCT
504157 TGTATCGATACATTCTAGCAA
1 TGTATCGATACATTCTAGCAA
*
504178 TGTATTGATACATTCTAGCAA
1 TGTATCGATACATTCTAGCAA
504199 TGTATCGATACATTCTAGCAA
1 TGTATCGATACATTCTAGCAA
*
504220 TGTATTGATACATTCTAGCAA
1 TGTATCGATACATTCTAGCAA
504241 TGTATCGATACATTCTAGCAA
1 TGTATCGATACATTCTAGCAA
504262 TGTATCGATACATT
1 TGTATCGATACATT
504276 TAGACAAAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 94 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGCAA
Found at i:513612 original size:20 final size:20
Alignment explanation
Indices: 513587--513655 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 20
513577 ATGTAGTCAT
513587 TAATAAAATAAAATTAATTA
1 TAATAAAATAAAATTAATTA
513607 TAATAAAAT--AATTAATT-
1 TAATAAAATAAAATTAATTA
*
513624 TAATCATAAATTAAAA-TAAATA
1 TAAT-A-AAA-TAAAATTAATTA
513646 -AATAAAATAA
1 TAATAAAATAA
513656 GTAATTTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
17 4 0.10
18 12 0.29
19 6 0.14
20 11 0.26
21 7 0.17
22 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATAAAATAAAATTAATTA
Found at i:513632 original size:23 final size:23
Alignment explanation
Indices: 513565--513642 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
513555 ATTTTATTTG
* * *
513565 AATAGAATAATT-ATGTAGTCATT
1 AATAAAATAATTAATTTAATCA-T
*
513588 AATAAAATAA--AA-TTAATTAT
1 AATAAAATAATTAATTTAATCAT
513608 AATAAAATAATTAATTTAATCAT
1 AATAAAATAATTAATTTAATCAT
513631 AAATTAAAATAA
1 -AA-TAAAATAA
513643 ATAAATAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
20 11 0.25
21 4 0.09
22 3 0.07
23 16 0.36
24 2 0.05
25 8 0.18
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (23 bp):
AATAAAATAATTAATTTAATCAT
Found at i:516497 original size:21 final size:21
Alignment explanation
Indices: 516473--516531 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
516463 TAATATTCTT
**
516473 GAAAAGAAATTAAATGAATTA
1 GAAAAGAAAACAAATGAATTA
516494 GAAAAGAAAACAAATGAATTA
1 GAAAAGAAAACAAATGAATTA
** *
516515 GAGGAGAAAAGAAATGA
1 GAAAAGAAAACAAATGA
516532 GTTACAAGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.63, C:0.02, G:0.20, T:0.15
Consensus pattern (21 bp):
GAAAAGAAAACAAATGAATTA
Found at i:519948 original size:13 final size:13
Alignment explanation
Indices: 519930--519954 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
519920 ATTTTGCTTA
519930 GTATCGATACATT
1 GTATCGATACATT
519943 GTATCGATACAT
1 GTATCGATACAT
519955 AAAACTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:520004 original size:10 final size:10
Alignment explanation
Indices: 519989--520013 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
519979 TTTTTCATTG
519989 TTCATCACTA
1 TTCATCACTA
519999 TTCATCACTA
1 TTCATCACTA
520009 TTCAT
1 TTCAT
520014 GTATCGATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (10 bp):
TTCATCACTA
Found at i:520069 original size:52 final size:52
Alignment explanation
Indices: 519991--520097 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
519981 TTTCATTGTT
* *
519991 CATCACTATTCATCACTATTCATGTATCGATACATTGTGAATAGTATCAATA
1 CATCACTATTCATCACTATTCATGTATCGATACATTATAAATAGTATCAATA
* *
520043 CATCACTATTTATCACTATTCATGTATCGATACATTATAAATAGTATCGATA
1 CATCACTATTCATCACTATTCATGTATCGATACATTATAAATAGTATCAATA
520095 CAT
1 CAT
520098 TGAGTCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (52 bp):
CATCACTATTCATCACTATTCATGTATCGATACATTATAAATAGTATCAATA
Found at i:524277 original size:27 final size:27
Alignment explanation
Indices: 524242--524307 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
524232 CAACTTATCA
* * * *
524242 ATTTGTTTATTGTTATTAAATTTATATT
1 ATTT-TTTATTATAATTAAATTTAAAAT
*
524270 ATTTTTTATTATAATTATATTTAAAAT
1 ATTTTTTATTATAATTAAATTTAAAAT
*
524297 ATTTTATATTA
1 ATTTTTTATTA
524308 ATATAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
ATTTTTTATTATAATTAAATTTAAAAT
Found at i:524749 original size:27 final size:28
Alignment explanation
Indices: 524718--524773 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
524708 ATATTTGCAG
* *
524718 ATAACACTTGA-TAAATAACTCAAAAAT
1 ATAACACTTAATTAAATAACTAAAAAAT
* *
524745 ATAACTCTTAATTAAATAATTAAAAAAT
1 ATAACACTTAATTAAATAACTAAAAAAT
524773 A
1 A
524774 ATTTTATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (28 bp):
ATAACACTTAATTAAATAACTAAAAAAT
Found at i:526666 original size:2 final size:2
Alignment explanation
Indices: 526628--526653 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
526618 TATATGCAGT
526628 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
526654 GATTACCATA
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:527162 original size:28 final size:29
Alignment explanation
Indices: 527130--527195 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
527120 GATCGAATAT
*
527130 AATTATATATTT-AATATAATATT-TAAAA
1 AATTATATATTTAAATA-AATATTGAAAAA
527158 AATTATATATTTAAATAAATATTGAAAAA
1 AATTATATATTTAAATAAATATTGAAAAA
527187 AATTATATA
1 AATTATATA
527196 AATCATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
AATTATATATTTAAATAAATATTGAAAAA
Found at i:527164 original size:17 final size:17
Alignment explanation
Indices: 527125--527177 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
527115 TATTAGATCG
527125 AATATAATTATATATTT-
1 AATA-AATTATATATTTA
527142 AAT--A-TA-ATATTTA
1 AATAAATTATATATTTA
527155 AA-AAATTATATATTTA
1 AATAAATTATATATTTA
527171 AATAAAT
1 AATAAAT
527178 ATTGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
12 6 0.20
13 4 0.13
14 2 0.07
15 2 0.07
16 9 0.30
17 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAAATTATATATTTA
Found at i:527757 original size:2 final size:2
Alignment explanation
Indices: 527721--527746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
527711 TTTCTTGATC
527721 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
527747 TATCCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:532834 original size:2 final size:2
Alignment explanation
Indices: 532829--532855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
532819 TTTTTTATTT
532829 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 T
532856 TACATGATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:533195 original size:19 final size:19
Alignment explanation
Indices: 533168--533219 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
533158 TAATTTGTTT
*
533168 TATTAATATATTTATTTTA
1 TATTTATATATTTATTTTA
*
533187 TATTTATATATTT-TTATA
1 TATTTATATATTTATTTTA
533205 TA-TTATA-A-TTATTTT
1 TATTTATATATTTATTTT
533220 TAAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 2 0.07
16 4 0.14
17 5 0.17
18 6 0.21
19 12 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTATATATTTATTTTA
Found at i:533220 original size:19 final size:19
Alignment explanation
Indices: 533165--533221 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 19
533155 ATTTAATTTG
* *
533165 TTTTAT-TAATATATTTA-
1 TTTTATATATTATAATTAT
533182 TTTTATAT-TTAT-A-TAT
1 TTTTATATATTATAATTAT
533198 TTTTATATATTATAATTAT
1 TTTTATATATTATAATTAT
533217 TTTTA
1 TTTTA
533222 AAATAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 2 0.06
16 8 0.24
17 13 0.39
18 2 0.06
19 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATATATTATAATTAT
Found at i:533232 original size:27 final size:27
Alignment explanation
Indices: 533217--533293 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
533207 TTATAATTAT
533217 TTTTAAAATAAAATATATTTATATAAA
1 TTTTAAAATAAAATATATTTATATAAA
*
533244 TTTTAAAATATTAATA-ATTTTATATATAA
1 TTTTAAAATA-AAATATA-TTTATATA-AA
* *
533273 TTTT-TAATAAATTGATATTTA
1 TTTTAAAATAAAAT-ATATTTA
533294 AAGTTCTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
27 13 0.32
28 21 0.51
29 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTTAAAATAAAATATATTTATATAAA
Found at i:533246 original size:28 final size:30
Alignment explanation
Indices: 533207--533279 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 30
533197 TTTTTATATA
*
533207 TTATA-ATTATTTTTAAAATA-AAAT-ATAT
1 TTATATATAATTTTTAAAATATAAATAAT-T
*
533235 TTATATA-AA-TTTTAAAATATTAATAATT
1 TTATATATAATTTTTAAAATATAAATAATT
533263 TTATATATAATTTTTAA
1 TTATATATAATTTTTAA
533280 TAAATTGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 10 0.26
28 17 0.45
29 5 0.13
30 6 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATATATAATTTTTAAAATATAAATAATT
Found at i:533367 original size:27 final size:27
Alignment explanation
Indices: 533310--533369 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
533300 TTTTAAATAA
533310 AAAT-ATTTTTATATAATTTAATAATT
1 AAATAATTTTTATATAATTTAATAATT
*
533336 TAATAATTTTTATATTATATTT-AT-ATT
1 AAATAATTTTTATA-TA-ATTTAATAATT
533363 AAATAAT
1 AAATAAT
533370 AATATCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 3 0.10
27 18 0.62
28 4 0.14
29 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AAATAATTTTTATATAATTTAATAATT
Found at i:536909 original size:85 final size:85
Alignment explanation
Indices: 536810--536979 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
536800 AAAGAGCTCA
536810 GTGATGGATGATGATACGTTGAAATAGAAATAAAAAAGTTGTATAACAAGTCAGGAATCTTCAAG
1 GTGATGGATGATGATACGTTGAAATAGAAATAAAAAAGTTGTATAACAAGTCAGGAATCTTCAAG
536875 TTTGTTAGCTTTATTAGCTT
66 TTTGTTAGCTTTATTAGCTT
536895 GTGATGGATGATGATACGTTGAAATAGAAATAAAAAAGTTGTATAACAAGTCAGGAATCTTCAAG
1 GTGATGGATGATGATACGTTGAAATAGAAATAAAAAAGTTGTATAACAAGTCAGGAATCTTCAAG
536960 TTTGTTAGCTTTATTAGCTT
66 TTTGTTAGCTTTATTAGCTT
536980 TGAAGTAATC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.34
Consensus pattern (85 bp):
GTGATGGATGATGATACGTTGAAATAGAAATAAAAAAGTTGTATAACAAGTCAGGAATCTTCAAG
TTTGTTAGCTTTATTAGCTT
Found at i:541954 original size:21 final size:21
Alignment explanation
Indices: 541929--541983 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
541919 CACATGGTCC
541929 TGTATCGATACATTTCAAGCA
1 TGTATCGATACATTTCAAGCA
* ***
541950 TGTATCGATATA-TTCACTTA
1 TGTATCGATACATTTCAAGCA
541970 TGTATCGATACATT
1 TGTATCGATACATT
541984 GCCTTATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTCAAGCA
Found at i:541989 original size:20 final size:20
Alignment explanation
Indices: 541929--542002 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
541919 CACATGGTCC
***
541929 TGTATCGATACATTTCAAGCA
1 TGTATCGATACA-TTCACTTA
*
541950 TGTATCGATATATTCACTTA
1 TGTATCGATACATTCACTTA
541970 TGTATCGATACATTGC-CTTA
1 TGTATCGATACATT-CACTTA
*
541990 TTATATCGATACA
1 -TGTATCGATACA
542003 AATTGTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 22 0.49
21 23 0.51
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:547220 original size:28 final size:27
Alignment explanation
Indices: 547189--547255 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
547179 ATCGGGATTA
** *
547189 GAGTATCCCCTCGGAAATAACGGGGTTG
1 GAGTATCCCCGAGG-AATAACGAGGTTG
* *
547217 GAGTATCCCCGATGATTAACGAGGTTG
1 GAGTATCCCCGAGGAATAACGAGGTTG
547244 GAGTATCCCCGA
1 GAGTATCCCCGA
547256 TTGTGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22
Consensus pattern (27 bp):
GAGTATCCCCGAGGAATAACGAGGTTG
Found at i:547304 original size:53 final size:51
Alignment explanation
Indices: 547240--547362 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
547230 GATTAACGAG
* * *
547240 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAATATCCCCGATTGTAG-AAAATTAGTG--TTTTGAAAATAAAATCGGA
*
547293 GTTGGAATATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAATATCCCCGATTGTAGAAAATTAGTGTTTTGAAAATAAAATCGGA
*
547344 GATGGAATATCCCCGATTG
1 GTTGGAATATCCCCGATTG
547363 CGGAGAATTG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
51 35 0.56
53 27 0.43
54 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAATATCCCCGATTGTAGAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:549728 original size:13 final size:13
Alignment explanation
Indices: 549710--549735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
549700 CAAAGAATAG
549710 ATGTATCGATACA
1 ATGTATCGATACA
549723 ATGTATCGATACA
1 ATGTATCGATACA
549736 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:549734 original size:34 final size:33
Alignment explanation
Indices: 549691--549755 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
549681 TCTGGGTAAA
*
549691 GTATCGATACAAAGAATAGATGTATCGATACAAT
1 GTATCGATACAAAGAA-AAATGTATCGATACAAT
*
549725 GTATCGATACACAGAAAAATGTATCGATACA
1 GTATCGATACAAAGAAAAATGTATCGATACA
549756 TTCCCTTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (33 bp):
GTATCGATACAAAGAAAAATGTATCGATACAAT
Found at i:549801 original size:19 final size:18
Alignment explanation
Indices: 549776--549840 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
549766 AGTAGCTAAT
549776 TATGTATCGATACAATAC
1 TATGTATCGATACAATAC
549794 TCATGTATCGATAC---A-
1 T-ATGTATCGATACAATAC
549809 T-TGTATCGATACAATAC
1 TATGTATCGATACAATAC
549826 TTATGTATCGATACA
1 -TATGTATCGATACA
549841 TTGTATCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
16 2 0.05
18 2 0.05
19 24 0.60
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (18 bp):
TATGTATCGATACAATAC
Found at i:549815 original size:13 final size:13
Alignment explanation
Indices: 549797--549853 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
549787 ACAATACTCA
549797 TGTATCGATACAT
1 TGTATCGATACAT
549810 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
549828 ATGTATCGATACAT
1 -TGTATCGATACAT
*
549842 TGTATCAATACA
1 TGTATCGATACA
549854 ACATTTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.30
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:549819 original size:32 final size:32
Alignment explanation
Indices: 549778--549872 Score: 154
Period size: 32 Copynumber: 3.0 Consensus size: 32
549768 TAGCTAATTA
*
549778 TGTATCGATACAATACTCATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
549810 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
* * *
549842 TGTATCAATACAACATTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
549873 AATCGCTGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:549936 original size:21 final size:22
Alignment explanation
Indices: 549910--549967 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
549900 GTTGGGACCT
* *
549910 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
549931 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
549952 TGTATCGATACATTTG
1 TGTATCGATACATTTG
549968 GATAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:550793 original size:55 final size:55
Alignment explanation
Indices: 550709--551323 Score: 672
Period size: 55 Copynumber: 10.9 Consensus size: 55
550699 ATAAAGTGTA
* * * * * *
550709 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
550764 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
550819 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
550874 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
550929 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
550984 TCCTGCTCTTTGAAGACTGGAAGATGCCACCAACTTGTGTGGGCTTTGAAAGGAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
551039 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGC-TTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* **
551099 TCCTGTTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGACG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* *
551158 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * *
551217 TCCCGCTTTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* *
551277 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGGGGGCTTT
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT
551324 TAAAAGGAAA
Statistics
Matches: 502, Mismatches: 37, Indels: 37
0.87 0.06 0.06
Matches are distributed among these distances:
54 14 0.03
55 270 0.54
56 12 0.02
59 98 0.20
60 100 0.20
61 2 0.00
64 6 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:562693 original size:4 final size:4
Alignment explanation
Indices: 562686--562710 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
562676 AAACAGATAT
562686 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
562711 CACCTCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:568180 original size:20 final size:20
Alignment explanation
Indices: 568148--568201 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
568138 GTATTGATAC
* **
568148 AATGTATCAATACATGACTA
1 AATGTATCGATACATGAAAA
* *
568168 AATGTATTGATACTTGAAAA
1 AATGTATCGATACATGAAAA
568188 AATGTATCGATACA
1 AATGTATCGATACA
568202 AGTCATTGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:568289 original size:33 final size:32
Alignment explanation
Indices: 568233--568300 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
568223 GTAGCTAAAT
*
568233 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
568265 TTGTATCGATAGATCACAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
568298 TTG
1 TTG
568301 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:570947 original size:58 final size:57
Alignment explanation
Indices: 570902--571362 Score: 286
Period size: 58 Copynumber: 8.0 Consensus size: 57
570892 CTCTCAACTT
* *
570902 CATGAAATTGCATTGAAGTCCCTAAATTATGGAAAATGATCTAAATGACATCAAAATA
1 CATGAAATTGCATTAAAGTCCCTAAATCATGGAAAATGA-CTAAATGACATCAAAATA
* * * *
570960 CATGAAATTGCACTAAAGTCTCTAGATCATAGAAAATGACCTAAATGACATCAAAATA
1 CATGAAATTGCATTAAAGTCCCTAAATCATGGAAAATGA-CTAAATGACATCAAAATA
* * * * *
571018 CATGAAATTGCATCAAAGTCCCTAAATCATGGAAAATTACCTAATTGATATCAAAATG
1 CATGAAATTGCATTAAAGTCCCTAAATCATGGAAAATGA-CTAAATGACATCAAAATA
* * * * * *
571076 CATGAAATTGCATCAAAGTCCTTAAGT-A--AAAAATGAACTAAGTGACATCAAAAAA
1 CATGAAATTGCATTAAAGTCCCTAAATCATGGAAAATG-ACTAAATGACATCAAAATA
* * * * * * * * ** *
571131 CATAAAATTTGTATGAAAGTCCTTAGATCTTAGAAAATGACCTAAATAACCCCAACATA
1 CATGAAA-TTGCATTAAAGTCCCTAAATCATGGAAAATGA-CTAAATGACATCAAAATA
* * ** * * * **
571190 TATAAAATTGCA-TAAGAGTCATTAGATCATGGAAAATGGCCTAAATGGCCCCAATAA-A
1 CATGAAATTGCATTAA-AGTCCCTAAATCATGGAAAAT-GACTAAATGACATCAA-AATA
* * * * * ** * * *
571248 CATGGGATTTGCATCAAGGTCCCTAGATC-TTAAAAATGACCAAAATGACATTAAAATG
1 CAT-GAAATTGCATTAAAGTCCCTAAATCATGGAAAATGA-CTAAATGACATCAAAATA
* * * * * * *
571306 CATGAAATTGCATCAAAATCTCTAAGTCATGAAAAATGACCTAGATGACATGAAAAT
1 CATGAAATTGCATTAAAGTCCCTAAATCATGGAAAATGA-CTAAATGACATCAAAAT
571363 GATATAAAAG
Statistics
Matches: 314, Mismatches: 75, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
55 25 0.08
56 17 0.05
57 24 0.08
58 205 0.65
59 41 0.13
60 2 0.01
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (57 bp):
CATGAAATTGCATTAAAGTCCCTAAATCATGGAAAATGACTAAATGACATCAAAATA
Found at i:572746 original size:20 final size:20
Alignment explanation
Indices: 572721--572786 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
572711 CATTCGAAGA
572721 TGTATTCATACAATATGCAT
1 TGTATTCATACAATATGCAT
* * *
572741 TGTATTGATAC-ATATGTAA
1 TGTATTCATACAATATGCAT
572760 T-TATATCAATACAATATGCAAT
1 TGTAT-TC-ATACAATATGC-AT
572782 TGTAT
1 TGTAT
572787 CGATACAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.09
19 8 0.23
20 14 0.40
21 5 0.14
22 2 0.06
23 3 0.09
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (20 bp):
TGTATTCATACAATATGCAT
Found at i:572777 original size:21 final size:21
Alignment explanation
Indices: 572728--572794 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
572718 AGATGTATTC
* **
572728 ATACAATATGC-ATTGTATTG
1 ATACAATATGCAATTATATCA
*
572748 ATAC-ATATGTAATTATATCA
1 ATACAATATGCAATTATATCA
* *
572768 ATACAATATGCAATTGTATCG
1 ATACAATATGCAATTATATCA
572789 ATACAA
1 ATACAA
572795 CTATACTCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 5 0.13
20 14 0.37
21 19 0.50
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ATACAATATGCAATTATATCA
Found at i:573425 original size:64 final size:64
Alignment explanation
Indices: 573365--573507 Score: 189
Period size: 64 Copynumber: 2.2 Consensus size: 64
573355 AAAAAGACAA
* * * * *
573365 AGGTTTAAATTTTGACTTTTTCGAAAAGAGACAAGTTTGACTCCTAATC-TATTTAGAAAGATAT
1 AGGTTTGAATTTTGACTTGTTCAAAAAAAGAAAAGTTTGACTCCTAA-CATATTTAGAAAGATAT
* * **
573429 AGGTTTGACTTTTGACTTGTTCAAAAAAAGAAAAGTTTGATTTTTAACATATTTAGAAAGATAT
1 AGGTTTGAATTTTGACTTGTTCAAAAAAAGAAAAGTTTGACTCCTAACATATTTAGAAAGATAT
573493 AGGTTTGAATTTTGA
1 AGGTTTGAATTTTGA
573508 TGATGGAGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 1 0.01
64 67 0.99
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (64 bp):
AGGTTTGAATTTTGACTTGTTCAAAAAAAGAAAAGTTTGACTCCTAACATATTTAGAAAGATAT
Found at i:573499 original size:32 final size:32
Alignment explanation
Indices: 573414--573505 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 32
573404 ACTCCTAATC
* * *
573414 TATTTAGAAAGATATAGGTTTGACTTTTGACT
1 TATTTAGAAAGATATAGGTTTGAATTTTAACA
* * * * * * * *
573446 TGTTCAAAAAAAGAAAAGTTTGATTTTTAACA
1 TATTTAGAAAGATATAGGTTTGAATTTTAACA
573478 TATTTAGAAAGATATAGGTTTGAATTTT
1 TATTTAGAAAGATATAGGTTTGAATTTT
573506 GATGATGGAG
Statistics
Matches: 42, Mismatches: 18, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.41
Consensus pattern (32 bp):
TATTTAGAAAGATATAGGTTTGAATTTTAACA
Found at i:574686 original size:578 final size:579
Alignment explanation
Indices: 573565--574726 Score: 1871
Period size: 578 Copynumber: 2.0 Consensus size: 579
573555 ATCTTTTGGA
*
573565 AGGAATTGGAGGTCCAATGATTAGGACAAAGACTAAATGCATGGAGCAAGCTTTGGAAGGTTTAA
1 AGGAATTGGAGGTCCAATG---AGGACAAAGACTAAATGCATGGAGCAAGCTTTGCAAGGTTTAA
* * *
573630 CCATGGAAATGCAAGCAAATGAGGCTATTCAAGATGAACCAGATGCATTGCCAAGATTGATCACT
63 CCATGGAAATGCAAGCAAATAAGGCTATTCAAGATGAACCAGATGCATCGCCAAGATTAATCACT
* * *
573695 TTATTATATTATGATGAGGATGAAAAACATTGAAGAATAAAGCTTGGAGCCCAATTTGTATGTCC
128 TTATTATATTATGATGACGATGAAAAACATTGAAGAATAAAGCTTAGAGCCCAATTCGTATGTCC
* *** *
573760 AAGAAGAGTGAAGCCTAATTTGTATGTATTCATGGCTTGGAGCCTAATTCACATGTCCAAGAAGA
193 AAGAAGAGTGAAGCCCAATTCCCATGTATTCATGGCTTAGAGCCTAATTCACATGTCCAAGAAGA
* * *
573825 GTGGAGCCCAATTCACATATATTTATGGGCCTATTGTTTAGGATTTCAAATTATAATTTTTTTAT
258 GTGGAGCCCAATTCACATATATTTATGGGCCTACTATTTAGGATTTCAAATTATAATGTTTTTAT
*
573890 TATGAATAAGAATTTGATTATAATAAGGAGTAGACTTTTCCTTACTGGACAAGAGAGTCCTTGTT
323 TATGAATAAGAATTTGATTATAATAAAGAGTAGACTTTTCCTTACTGGACAAGAGAGTCCTTGTT
*
573955 TAGTTAGGACTCTACAAATTTTAAAATTTTAAGTTGTTTAGATCAGATTAGGATAAGGAATAGAT
388 TAGTTAGGACTCTACAAATTTTAAAATTTTAAGTTGTTTAGATCAGATTAGGATAAGGAATAGAC
*
574020 TTTGAATAGACTTTTACTTATTAGATAGAAGAGTCCTTATTTAGTGAGGACTCTACAGATTCTAG
453 TTTGAATAGACTTTTACTTATTAGAAAGAAGAGTCCTTATTTAGTGAGGACTCTACAGATTCTAG
* *
574085 GCCTATAAAAAGATGTCTCATTCATGTAATTTAGCAGATTTGAATAGAGAAAAATATTTTGAG
518 GCCTATAAAAAGATGTCTCATTCATGTAATTTAACAGATTTGAATA-AAAAAAATATTTTGAG
*
574148 AGGAATTGGAGGTCCAATG-GG-CAAAGACTAAATGCATGGAGCAAGCTTTGCAAGGTTTAATCA
1 AGGAATTGGAGGTCCAATGAGGACAAAGACTAAATGCATGGAGCAAGCTTTGCAAGGTTTAACCA
* *
574211 TGGAAATGCAAGCAGAA-AAGGCTGTTCAAGATGAACTAGATGCATCGCCAAGATTAATCACTTT
66 TGGAAATGCAAGCA-AATAAGGCTATTCAAGATGAACCAGATGCATCGCCAAGATTAATCACTTT
574275 ATTATATTATGATGACGATGAAAAACATTGAAGAATAAAGCTTAGAGCCCAATTCGTATGTCCAA
130 ATTATATTATGATGACGATGAAAAACATTGAAGAATAAAGCTTAGAGCCCAATTCGTATGTCCAA
574340 GAAGAGTGAAGCCCAATTCCCATGTATTCATGGCTTAGAGCCTAATTCACATGTCCAAGAAGAGT
195 GAAGAGTGAAGCCCAATTCCCATGTATTCATGGCTTAGAGCCTAATTCACATGTCCAAGAAGAGT
** * * *
574405 GGAGCCCAATTTGCATATATTTATGGGCCTACTATTTAGGATTTTAGATTATGATGTTTTTATTA
260 GGAGCCCAATTCACATATATTTATGGGCCTACTATTTAGGATTTCAAATTATAATGTTTTTATTA
* * * * *
574470 TGAATAAGAATTTGATTATGATAAAGAGTAGACTTTTCCTTATTGGATAGGATAGTCCTTGTTTA
325 TGAATAAGAATTTGATTATAATAAAGAGTAGACTTTTCCTTACTGGACAAGAGAGTCCTTGTTTA
** *
574535 GTTAGGACTCTACAAATTTTAGTATTTTAAGTTGTTTAGATCATATTAGGATAAGGAATAGACTT
390 GTTAGGACTCTACAAATTTTAAAATTTTAAGTTGTTTAGATCAGATTAGGATAAGGAATAGACTT
* * * * * *
574600 TGAATAGGCTTTTACTTATTGGAAAGAAGAGTCCTTGTTTAGTTAGGACTTTATAGATTCTAGGC
455 TGAATAGACTTTTACTTATTAGAAAGAAGAGTCCTTATTTAGTGAGGACTCTACAGATTCTAGGC
*
574665 TTATAAAAAGATGTCTCATTCATGTAATTTAACAGATTTGAATAAAAAAAATATTTTGAG
520 CTATAAAAAGATGTCTCATTCATGTAATTTAACAGATTTGAATAAAAAAAATATTTTGAG
574725 AG
1 AG
574727 TTTCTTCACT
Statistics
Matches: 535, Mismatches: 43, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
577 17 0.03
578 495 0.93
579 4 0.01
583 19 0.04
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (579 bp):
AGGAATTGGAGGTCCAATGAGGACAAAGACTAAATGCATGGAGCAAGCTTTGCAAGGTTTAACCA
TGGAAATGCAAGCAAATAAGGCTATTCAAGATGAACCAGATGCATCGCCAAGATTAATCACTTTA
TTATATTATGATGACGATGAAAAACATTGAAGAATAAAGCTTAGAGCCCAATTCGTATGTCCAAG
AAGAGTGAAGCCCAATTCCCATGTATTCATGGCTTAGAGCCTAATTCACATGTCCAAGAAGAGTG
GAGCCCAATTCACATATATTTATGGGCCTACTATTTAGGATTTCAAATTATAATGTTTTTATTAT
GAATAAGAATTTGATTATAATAAAGAGTAGACTTTTCCTTACTGGACAAGAGAGTCCTTGTTTAG
TTAGGACTCTACAAATTTTAAAATTTTAAGTTGTTTAGATCAGATTAGGATAAGGAATAGACTTT
GAATAGACTTTTACTTATTAGAAAGAAGAGTCCTTATTTAGTGAGGACTCTACAGATTCTAGGCC
TATAAAAAGATGTCTCATTCATGTAATTTAACAGATTTGAATAAAAAAAATATTTTGAG
Found at i:575016 original size:64 final size:64
Alignment explanation
Indices: 574947--575093 Score: 156
Period size: 64 Copynumber: 2.3 Consensus size: 64
574937 GTTCGCATTA
** * * * * *
574947 TTTGACTTGCTTA-AAAGGAAATAAATTT-AGCTTTTTACTTGA-TTAGAAAGATATAGGTTGAA
1 TTTGACTTGCTTAGAAA-GAAATAAATTTGA-CTTTCAACCT-ATTTAGAAAGACACAGGCTCAA
575009 AT
63 AT
* *
575011 TTTGACTTGCCTAGAAAGATATAAATTTGACTTTCAACCTATTTAGAAAGACACAGGCTCAAAT
1 TTTGACTTGCTTAGAAAGAAATAAATTTGACTTTCAACCTATTTAGAAAGACACAGGCTCAAAT
*
575075 TTTGACTTGCTTGGAAAGA
1 TTTGACTTGCTTAGAAAGA
575094 GACAAGTTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 64 0.93
65 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (64 bp):
TTTGACTTGCTTAGAAAGAAATAAATTTGACTTTCAACCTATTTAGAAAGACACAGGCTCAAAT
Found at i:575114 original size:64 final size:61
Alignment explanation
Indices: 575046--575227 Score: 150
Period size: 62 Copynumber: 2.9 Consensus size: 61
575036 TTTGACTTTC
*
575046 AACCTATTTAGAAAGACACAGGCTCAAATTTTGACTTGCTT-GGAAAGAGACAAGTTTAACTCCT
1 AACCTATTTAGAAAGACACAGG-TCAAATTTTGACTT-CTTCGAAAAGAGACAAG-TT-ACTCCT
* * * * * * ** * **
575110 AACCTATTAAAAAAAATATAAGTTTAGTTTTGGACTTCTTCGAAAAGAGACAAGTTACTTTT
1 AACCTATTTAGAAAGACACAGGTCAAATTTT-GACTTCTTCGAAAAGAGACAAGTTACTCCT
* * * * *
575172 GACCTATTTAGAAAGACACAGGTTCAAATTTTGATTTATTCAAAAAGAGAAAAGTT
1 AACCTATTTAGAAAGACACAGG-TCAAATTTTGACTTCTTCGAAAAGAGACAAGTT
575228 TGACATTTAA
Statistics
Matches: 89, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
62 39 0.44
63 17 0.19
64 33 0.37
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (61 bp):
AACCTATTTAGAAAGACACAGGTCAAATTTTGACTTCTTCGAAAAGAGACAAGTTACTCCT
Found at i:575323 original size:32 final size:32
Alignment explanation
Indices: 575152--575389 Score: 92
Period size: 32 Copynumber: 7.5 Consensus size: 32
575142 GACTTCTTCG
* * *
575152 AAAAGAGACAAG-TT-ACTTTTGACCTATTTA
1 AAAAGAAACAAGTTTGAATTTTGACCTATTCA
* * * ** **
575182 GAAAGACACAGGTTCAAATTTTGATTTATTCA
1 AAAAGAAACAAGTTTGAATTTTGACCTATTCA
* * *
575214 AAAAGAGAA-AAGTTTGACA-TTTAACTTGTTCA
1 AAAAGA-AACAAGTTTGA-ATTTTGACCTATTCA
* * ** * * **
575246 AAAAGATACTAGTTAAAATTTTGATCTTTTTT
1 AAAAGAAACAAGTTTGAATTTTGACCTATTCA
* *
575278 GAAGGATAA-AAGTTTGAATTTTGACCTATTCA
1 AAAAGA-AACAAGTTTGAATTTTGACCTATTCA
* * * *
575310 AAAAGAAACAAGTTTCAATTTTGACTTGTTCG
1 AAAAGAAACAAGTTTGAATTTTGACCTATTCA
* * * * *
575342 AAAAGAGACAAATGTG-ATTCCTAACCTATTCA
1 AAAAGAAACAAGTTTGAATT-TTGACCTATTCA
* *
575374 TAAAGATACAAGTTTG
1 AAAAGAAACAAGTTTG
575390 GCTATAGTAA
Statistics
Matches: 144, Mismatches: 55, Indels: 16
0.67 0.26 0.07
Matches are distributed among these distances:
30 9 0.06
31 8 0.06
32 124 0.86
33 3 0.02
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (32 bp):
AAAAGAAACAAGTTTGAATTTTGACCTATTCA
Found at i:577249 original size:165 final size:165
Alignment explanation
Indices: 577077--577470 Score: 402
Period size: 166 Copynumber: 2.4 Consensus size: 165
577067 CTGGGTTTTT
* *
577077 AATTTTTAAAATTTATCAAATATTATTATTTAATTCATATTAAATCAATTTTTAAAAATTCATTC
1 AATTTTTAAAATTTATCTAATATTGTTATTTAATTCA-ATTAAATCAATTTTTAAAAATTCATTC
* * *
577142 ATTCCCATGAGTTTTGA-ATTTTTTCTTG-AAAT-TCCCTTTTCTCCAAAAAATCGAGTTTTTTA
65 ATTCCCATGAGTTTGGATATTTTTTCTTGAAAATCTCCTTTTTC-CCAAAAAA-CGAGTTTTCTA
* *
577204 CTCAATAAATGTTTTTGGAGAGATTTTCTTTGGTTTAA
128 CTCAATAAATATTTTTGGAGAGATTTTCTTTGGTGTAA
* * * ** * * * * * *
577242 AATTTTTATAATTTATCTAATAATGTCATAGAATTCCCATTAAATTAGTTTTGAACAATTAATTC
1 AATTTTTAAAATTTATCTAATATTGTTATTTAATT-CAATTAAATCAATTTTTAAAAATTCATTC
* ** * * * *
577307 CTTTTCATGAGTTTGGATTTTTTTTCTTTAAAATCTCCTTTTTCCCGAAAAACGAGTTTTCTATT
65 ATTCCCATGAGTTTGGATATTTTTTCTTGAAAATCTCCTTTTTCCCAAAAAACGAGTTTTCTACT
* * *
577372 CTATAAATATTTTTGGGGGGATTTTCTTTGGTGTAA
130 CAATAAATATTTTTGGAGAGATTTTCTTTGGTGTAA
* **
577408 AATTTTTAAAAATGTATCTAATATTGTT-TTTGAACTTCAATTATTTC-ATTTTTGAAAAATTCA
1 AATTTTT-AAAATTTATCTAATATTGTTATTT-AA-TTCAATTAAATCAATTTTT-AAAAATTCA
577471 ATTTATTTTC
Statistics
Matches: 179, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
165 63 0.35
166 64 0.36
167 42 0.23
168 10 0.06
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (165 bp):
AATTTTTAAAATTTATCTAATATTGTTATTTAATTCAATTAAATCAATTTTTAAAAATTCATTCA
TTCCCATGAGTTTGGATATTTTTTCTTGAAAATCTCCTTTTTCCCAAAAAACGAGTTTTCTACTC
AATAAATATTTTTGGAGAGATTTTCTTTGGTGTAA
Found at i:578960 original size:15 final size:15
Alignment explanation
Indices: 578923--578958 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
578913 TCCATTAAGA
578923 TACGAAATGATATTT
1 TACGAAATGATATTT
578938 TACGAAATGATATTT
1 TACGAAATGATATTT
578953 T-CGAAA
1 TACGAAA
578959 ATAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (15 bp):
TACGAAATGATATTT
Found at i:580488 original size:50 final size:50
Alignment explanation
Indices: 580418--580528 Score: 120
Period size: 52 Copynumber: 2.2 Consensus size: 50
580408 AATGGGGATA
*
580418 GGAGTATCCCTGATGGTG-AAAATC-GATGT-TATGGAAATAAAACCGGGGTT
1 GGAGTATCCCTGATGATGAAAAATCAG-TGTGT-TGGAAATAAAA-CGGGGTT
* * *
580468 GGAGTATCCTTGATTATGAAAAAATCAGTGTGTTGGAAATAAAACTGGGTT
1 GGAGTATCCCTGATGATG-AAAAATCAGTGTGTTGGAAATAAAACGGGGTT
*
580519 AGAGTATCCC
1 GGAGTATCCC
580529 CTTAGAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
50 15 0.29
51 14 0.27
52 20 0.39
53 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (50 bp):
GGAGTATCCCTGATGATGAAAAATCAGTGTGTTGGAAATAAAACGGGGTT
Found at i:580567 original size:79 final size:80
Alignment explanation
Indices: 580464--580954 Score: 428
Period size: 79 Copynumber: 6.2 Consensus size: 80
580454 ATAAAACCGG
** * * * *
580464 GGTTGGAGTATCCTTGATTATGAAAAAATCAGTGTGTTGGAAATAAAACTGGG-TTAGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGGAAATAAAACTGGGATTGGAGTATCC
*
580528 CCTTAGAAATAACGA
66 CCTCAGAAATAACGA
* * * *
580543 GATTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGAAAATGAAACCGAGG-TTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGGAAATAAAACTG-GGATTGGAGTATC
* * *
580607 CGCTCAGAAATAATGG
65 CCCTCAGAAATAACGA
* * * *
580623 GGTTGGAGTATCCTCGATGGTG-AAAAATCGGTGTTTTAGAAATAAAACTGGGTTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGGAAATAAAACTGGGATTGGAGTATCC
*
580687 CCT-TGAAAATAAC-A
66 CCTCAG-AAATAACGA
*
580701 GGGTTGGAGTATCCCCGATTGTGAAAAAAATCGATGTTTTGGAAATAAAA-TCGGGATTGGAGTA
1 -GGTTGGAGTATCCCCGATTGTG-AAAAAATCGGTGTTTTGGAAATAAAACT-GGGATTGGAGTA
*
580765 TCCCCTCAGAAATAACGG
63 TCCCCTCAGAAATAACGA
* * * * * * *
580783 GGTTGGAGTATCCCCGATGGTG-GAAAATTGGTGTTTTAGAAACAAAA-TCGGGGTAGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGGAAATAAAACT-GGGATTGGAGTATC
* * *
580846 CCTTCAAAAATAA-TA
65 CCCTCAGAAATAACGA
* * * * ** * ** * *
580861 GGGTTGGACTATCTCCGATTATGAAAAAATTGACGCTTTATAAATAAAGCATGGG-TTAGAGTAT
1 -GGTTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGGAAATAAAAC-TGGGATTGGAGTAT
*
580925 CCCCTC-GAAAATAACGG
64 CCCCTCAG-AAATAACGA
*
580942 GGTTGGGGTATCC
1 GGTTGGAGTATCC
580955 TTGAAGGTGG
Statistics
Matches: 333, Mismatches: 64, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
78 3 0.01
79 168 0.50
80 89 0.27
81 71 0.21
82 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (80 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGGAAATAAAACTGGGATTGGAGTATCC
CCTCAGAAATAACGA
Found at i:580795 original size:160 final size:156
Alignment explanation
Indices: 580461--580988 Score: 589
Period size: 159 Copynumber: 3.3 Consensus size: 156
580451 GAAATAAAAC
* ** * * * *
580461 CGGGGTTGGAGTATCCTTGATTATGAAAAAATCAGTGTGTTGGAAATAAAACTGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCTCGATGGTG-AAAAATCGGTGTTTTAGAAATAAAACTGGGTTGGAGTAT
* * *
580526 CCCCTTAGAAATAAC-GAGATTGGAGTATCCCCGATTGTGAAAAAATCGGTGTTTTGAAAATGAA
65 CCCCTTA-AAATAACAG-GGTTGGAGTATCCCCGATTGTGAAAAAATCGATGTTTTGAAAATAAA
* *
580590 ACCGAGGTTGGAGTATCCGCTCAGAAATAA
128 ATCG-GGTTGGAGTATCCCCTCAGAAATAA
*
580620 TGGGGTTGGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAACTGGGTTTGGAGTAT
1 CGGGGTTGGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAACTGGG-TTGGAGTAT
*
580685 CCCCTTGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAAAATCGATGTTTTGGAAATAAA
65 CCCCTT-AAAATAACAGGGTTGGAGTATCCCCGATTGTG-AAAAAATCGATGTTTTGAAAATAAA
580750 ATCGGGATTGGAGTATCCCCTCAGAAATAA
128 ATCGGG-TTGGAGTATCCCCTCAGAAATAA
* * * * * *
580780 CGGGGTTGGAGTATCCCCGATGGTGGAAAATTGGTGTTTTAGAAACAAAATCGGGGTAGGAGTAT
1 CGGGGTTGGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAA-CTGGGTTGGAGTAT
* * * * * * *
580845 -CCCTTCAAAAATAATAGGGTTGGACTATCTCCGATTATGAAAAAATTGACGCTTT-ATAAATAA
65 CCCCTT--AAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAAATCGATGTTTTGA-AAATAA
*
580908 AGCAT-GGGTTAGAGTATCCCCTC-GAAAATAA
127 A--ATCGGGTTGGAGTATCCCCTCAG-AAATAA
* * * * *
580939 CGGGGTTGGGGTATCCTTGAAGGTGGAAAATCGGTATTTTAGAAATAAAA
1 CGGGGTTGGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAA
580989 ACATGAATGA
Statistics
Matches: 320, Mismatches: 38, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
158 28 0.09
159 153 0.48
160 133 0.42
161 6 0.02
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.27
Consensus pattern (156 bp):
CGGGGTTGGAGTATCCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAACTGGGTTGGAGTATC
CCCTTAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAAATCGATGTTTTGAAAATAAAATC
GGGTTGGAGTATCCCCTCAGAAATAA
Found at i:583393 original size:20 final size:20
Alignment explanation
Indices: 583367--583420 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
583357 TAAAACCCAT
*
583367 AATGTATTGATACAATGAAG
1 AATGTATCGATACAATGAAG
*
583387 GATGTATCGATACAATGAAG
1 AATGTATCGATACAATGAAG
*
583407 AATGTATCAATACA
1 AATGTATCGATACA
583421 TTTGGGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATGAAG
Found at i:583433 original size:70 final size:70
Alignment explanation
Indices: 583318--583469 Score: 225
Period size: 70 Copynumber: 2.2 Consensus size: 70
583308 AAATGCTGGA
* * *
583318 ATGTATCGATACATTAAGAAATGTATCTATACATCTAGGTAAAACCCATAATGTATTGATACAAT
1 ATGTATCGATACATGAAGAAATGTATCAATACATCTAGGTAAAACCCATAATGTATCGATACAAT
583383 GAAGG
66 GAAGG
* * * *
583388 ATGTATCGATACAATGAAG-AATGTATCAATACATTTGGGTCAAACCCATAATGTATCGATATAA
1 ATGTATCGATAC-ATGAAGAAATGTATCAATACATCTAGGTAAAACCCATAATGTATCGATACAA
583452 TGAAGG
65 TGAAGG
583458 ATGTATCGATAC
1 ATGTATCGATAC
583470 GAATTATCGA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
70 69 0.93
71 5 0.07
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (70 bp):
ATGTATCGATACATGAAGAAATGTATCAATACATCTAGGTAAAACCCATAATGTATCGATACAAT
GAAGG
Found at i:594952 original size:20 final size:20
Alignment explanation
Indices: 594927--594983 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
594917 TTTTACTAGT
594927 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
*
594947 TTCATGTATCGATACAA-TG
1 TTCATGTATCGATACAATTC
**
594966 AACATGTATCGATACAAT
1 TTCATGTATCGATACAAT
594984 AAACATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:594973 original size:19 final size:19
Alignment explanation
Indices: 594929--595000 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
594919 TTACTAGTTT
***
594929 CATGTATCGATACAATTCTT
1 CATGTATCGATACAA-TAAA
*
594949 CATGTATCGATACAATGAA
1 CATGTATCGATACAATAAA
594968 CATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
594987 CATGTATCGATACA
1 CATGTATCGATACA
595001 TTGTATCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
19 33 0.69
20 15 0.31
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:648362 original size:20 final size:20
Alignment explanation
Indices: 648339--648411 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
648329 AAAGTACCTA
648339 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* *
648359 AATGCATCGATACA-TTCT-
1 AATGTATCGATACATTTTTC
* * *
648377 GATGTATCAATACATTCTTC
1 AATGTATCGATACATTTTTC
648397 AATGTATCGATACAT
1 AATGTATCGATACAT
648412 CTAGTTAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
18 11 0.26
19 5 0.12
20 26 0.62
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:654037 original size:15 final size:16
Alignment explanation
Indices: 654011--654041 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
654001 AGCTTTTCTT
654011 TAAATAAAAAAATGGA
1 TAAATAAAAAAATGGA
654027 TAAAT-AAAAAATGGA
1 TAAATAAAAAAATGGA
654042 ATCAGTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (16 bp):
TAAATAAAAAAATGGA
Found at i:658151 original size:2 final size:2
Alignment explanation
Indices: 658144--658179 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
658134 TTTAGGCCTC
658144 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
658180 GCAGGTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:667713 original size:74 final size:76
Alignment explanation
Indices: 667566--667742 Score: 236
Period size: 74 Copynumber: 2.3 Consensus size: 76
667556 GTAAATGGCA
* *
667566 CCACCAACTTGTGTGGGCTTTGAAGAAGAAAAAAAAAAGGCATCTTGCTCTTTCAAGACTAGAAA
1 CCACCAGCTTGTGTGGGATTTGAAG-AGAAAAAAAAAAGGCATCTTGCTCTTTCAAGACTAGAAA
*
667631 AGATAAATGATG
65 AGAAAAATGATG
* * * *
667643 CCACTAGCTTGTGTGGGTTTTGAAGA-AAAAGAAAAA-GCGTCTTGCTCTTT-AAGGA-TAGAAA
1 CCACCAGCTTGTGTGGGATTTGAAGAGAAAAAAAAAAGGCATCTTGCTCTTTCAA-GACTAG-AA
667704 AAGAAAAATGATG
64 AAGAAAAATGATG
667717 CCACCAGCTTGTGTGGGATTTGAAGA
1 CCACCAGCTTGTGTGGGATTTGAAGA
667743 CTTTTTAAGG
Statistics
Matches: 90, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
73 5 0.06
74 53 0.59
75 9 0.10
76 1 0.01
77 22 0.24
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (76 bp):
CCACCAGCTTGTGTGGGATTTGAAGAGAAAAAAAAAAGGCATCTTGCTCTTTCAAGACTAGAAAA
GAAAAATGATG
Found at i:667780 original size:56 final size:56
Alignment explanation
Indices: 667690--667798 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 56
667680 CGTCTTGCTC
667690 TTTAAGGATAGAAAAAGAAAAATGATGCCACCAGCTTGTGTGGGA-TTTGAAGACTT
1 TTTAAGGATAGAAAAAGAAAAATGATGCCACCAGCTTGTGT-GGACTTTGAAGACTT
* * *
667746 TTTAAGGACTAG-AAAAGATAAATGATGGCGCCAGCTTGTGTGGACTTTGAAGA
1 TTTAAGGA-TAGAAAAAGAAAAATGATGCCACCAGCTTGTGTGGACTTTGAAGA
667799 AAAAAAAGGC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
55 3 0.06
56 42 0.88
57 3 0.06
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (56 bp):
TTTAAGGATAGAAAAAGAAAAATGATGCCACCAGCTTGTGTGGACTTTGAAGACTT
Found at i:667914 original size:73 final size:70
Alignment explanation
Indices: 667742--667914 Score: 170
Period size: 71 Copynumber: 2.4 Consensus size: 70
667732 GGATTTGAAG
* * ** **
667742 ACTTTTTAAGGACTAGAAAAGATAAATGATGGCGCCAGCTTGTGTGGACTTTGAAGAAAAAAAAG
1 ACTTTTTAAGGACTAAAAAAGATAAATGATGCCAACAGC-TGCATGGACTTTGAAGAAAAAAAAG
667807 GCATCC
65 GCATCC
* * * * *
667813 AGC-TCTTGAGAACTGAAAAAGATAAATGATGCCAACAG-TGCATGGGCTTTGAAGAAAACAGAA
1 A-CTTTTTAAGGACTAAAAAAGATAAATGATGCCAACAGCTGCATGGACTTTGAAG-AAA-A-AA
*
667876 AATGCATCC
62 AAGGCATCC
667885 TACTTTTTAAGGACTAAAAAAGATAAATGA
1 -ACTTTTTAAGGACTAAAAAAGATAAATGA
667915 GTTCAAATAC
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
69 13 0.16
70 3 0.04
71 29 0.36
72 12 0.15
73 23 0.29
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (70 bp):
ACTTTTTAAGGACTAAAAAAGATAAATGATGCCAACAGCTGCATGGACTTTGAAGAAAAAAAAGG
CATCC
Found at i:680029 original size:22 final size:23
Alignment explanation
Indices: 679995--680039 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
679985 GTCGAAAAAA
679995 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
680017 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
680040 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:680431 original size:11 final size:11
Alignment explanation
Indices: 680393--680433 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
680383 AAATTTAGGT
680393 AAAAAAGAAAG
1 AAAAAAGAAAG
*
680404 AAAGAAGATGAAG
1 AAAAAAGA--AAG
680417 AAAAAAGAAAG
1 AAAAAAGAAAG
680428 AAAAAA
1 AAAAAA
680434 AATATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:688267 original size:30 final size:31
Alignment explanation
Indices: 688227--688284 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
688217 GTACTGTGAC
*
688227 CTTTTCAAAGTCCACGACTCAGTGGCATTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCATTTT
*
688258 CTTTT-AAAGTCCACAACTCCGTGGCAT
1 CTTTTCAAAGTCCACAACTCAGTGGCAT
688285 CCTTTTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.33
Consensus pattern (31 bp):
CTTTTCAAAGTCCACAACTCAGTGGCATTTT
Found at i:688319 original size:46 final size:46
Alignment explanation
Indices: 688252--688345 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
688242 GACTCAGTGG
* *
688252 CATTTTCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGTTCA
1 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
688298 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
1 CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
688344 CA
1 CA
688346 ACTCCGTGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (46 bp):
CATTTTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
Found at i:688343 original size:27 final size:27
Alignment explanation
Indices: 688304--688604 Score: 494
Period size: 27 Copynumber: 11.0 Consensus size: 27
688294 TTCACATTTT
688304 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
688332 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
688359 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
688386 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
688414 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
688441 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
688469 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
688496 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
688523 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
688550 CTTTTAAGTCCACAACTCCGTGGCGTC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
688577 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
688604 C
1 C
688605 ATTTCAAAGC
Statistics
Matches: 255, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
27 200 0.78
28 55 0.22
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:688502 original size:164 final size:164
Alignment explanation
Indices: 688311--688619 Score: 548
Period size: 164 Copynumber: 1.9 Consensus size: 164
688301 TTTCTTTTAA
688311 AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
1 AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
* *
688376 CCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACC
66 CCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATC-CTTTTAAATCCACAACTCTGTGGCACC
* *
688441 C-TTTTAAAGTCCACAACTCCGTGGCACCCTTTTT
130 CATTTCAAAGCCCACAACTCCGTGGCACCCTTTTT
*
688475 AGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
1 AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
*
688540 CCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCGTCCTTTTAAATCCACAACTCTGTGGCACCC
66 CCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCCACAACTCTGTGGCACCC
688605 ATTTCAAAGCCCACA
131 ATTTCAAAGCCCACA
688620 CAAGTCGGTG
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
163 27 0.20
164 111 0.80
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (164 bp):
AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
CCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCCACAACTCTGTGGCACCC
ATTTCAAAGCCCACAACTCCGTGGCACCCTTTTT
Found at i:688619 original size:137 final size:137
Alignment explanation
Indices: 688304--688604 Score: 516
Period size: 137 Copynumber: 2.2 Consensus size: 137
688294 TTCACATTTT
688304 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* * *
688369 CACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTG
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCG
688434 TGGCACC
131 TGGCACC
* *
688441 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTC
1 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
688506 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCG
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCG
**
688570 TGGCGTC
131 TGGCACC
*
688577 CTTTTAAA-TCCACAACTCTGTGGCACCC
1 CTTTTAAAGTCCACAACTCCGTGGCACCC
688605 ATTTCAAAGC
Statistics
Matches: 156, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
135 19 0.12
136 33 0.21
137 104 0.67
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (137 bp):
CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCG
TGGCACC
Found at i:688645 original size:32 final size:32
Alignment explanation
Indices: 688587--689381 Score: 1432
Period size: 32 Copynumber: 24.8 Consensus size: 32
688577 CTTTTAAATC
* *
688587 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
688618 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688650 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688682 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688714 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688746 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688778 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688810 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688842 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688874 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688906 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
688938 CACAAGTCGGTGGCAACCCATTTCACAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
688970 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
689002 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
689034 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
689066 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
689098 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
689130 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
689162 CACAAGTCGGTGGCAACCCATTTCAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
689195 CACAGGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
689227 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
689259 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
689291 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
689323 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
689355 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
689382 TCACCATTTT
Statistics
Matches: 745, Mismatches: 16, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
31 12 0.02
32 703 0.94
33 30 0.04
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:690256 original size:22 final size:23
Alignment explanation
Indices: 690222--690266 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
690212 TCGAAAAAAA
690222 AAAAAAAAAAAAG-GGGCTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
** *
690244 AAAAAAACCAAAGTGGGTTTTCC
1 AAAAAAAAAAAAGTGGGCTTTCC
690267 GATTGAGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAAAAAAAAGTGGGCTTTCC
Found at i:690659 original size:11 final size:11
Alignment explanation
Indices: 690621--690661 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
690611 AAATTTAGGT
690621 AAAAAAGAAAG
1 AAAAAAGAAAG
*
690632 AAAGAAGATGAAG
1 AAAAAAGA--AAG
690645 AAAAAAGAAAG
1 AAAAAAGAAAG
690656 AAAAAA
1 AAAAAA
690662 ATATGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:702455 original size:12 final size:13
Alignment explanation
Indices: 702436--702461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
702426 TCCGTATTTC
702436 GAAAAAAATTCAA
1 GAAAAAAATTCAA
702449 GAAAAAAATTCAA
1 GAAAAAAATTCAA
702462 AATTTATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
GAAAAAAATTCAA
Found at i:704910 original size:17 final size:18
Alignment explanation
Indices: 704874--704935 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 18
704864 TAGCCAAACT
704874 TGTATCGATACACAAAGTA
1 TGTATCGATA-ACAAAGTA
704893 TGTATCGAT-AC--A--A
1 TGTATCGATAACAAAGTA
*
704906 TGTATCGATACACAAAATA
1 TGTATCGATA-ACAAAGTA
704925 TTGTATCGATA
1 -TGTATCGATA
704936 CATTGGCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.28
15 3 0.08
17 3 0.08
19 10 0.28
20 10 0.28
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (18 bp):
TGTATCGATAACAAAGTA
Found at i:704915 original size:32 final size:33
Alignment explanation
Indices: 704874--704937 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
704864 TAGCCAAACT
*
704874 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAATATTGTATCGATACAA
704906 TGTATCGATACACAAAATATTGTATCGATACA
1 TGTATCGATACACAAAATATTGTATCGATACA
704938 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAATATTGTATCGATACAA
Found at i:708992 original size:15 final size:15
Alignment explanation
Indices: 708972--709002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
708962 TAAAAATGTC
*
708972 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
708987 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
709002 C
1 C
709003 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:711099 original size:13 final size:13
Alignment explanation
Indices: 711081--711119 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
711071 ACATTTTTCT
711081 TTGTATCGATACA
1 TTGTATCGATACA
711094 TTGTATCGATACA
1 TTGTATCGATACA
*
711107 CTGTATCGATACA
1 TTGTATCGATACA
711120 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:711274 original size:20 final size:20
Alignment explanation
Indices: 711231--711276 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
711221 AAATCTTTTG
711231 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
711252 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
711272 CAAAA
1 CAAAA
711277 CCAGTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:713709 original size:32 final size:33
Alignment explanation
Indices: 713664--713727 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
713654 TAGCCAAACT
* **
713664 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGAAACACAAAAAATTGTATCGATACAA
713696 TGTATCGAAACACAAAAAATTGTATCGATACA
1 TGTATCGAAACACAAAAAATTGTATCGATACA
713728 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGAAACACAAAAAATTGTATCGATACAA
Found at i:715878 original size:13 final size:12
Alignment explanation
Indices: 715854--715897 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
715844 TATTTATTTC
*
715854 TTTTTCTTTCTT
1 TTTTTCTCTCTT
715866 TTCTTTCTCTCTT
1 TT-TTTCTCTCTT
715879 TTTATTCTCTCTCT
1 TTT-TTCTCTCT-T
715893 TTTTT
1 TTTTT
715898 AGTTGAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 3 0.11
13 21 0.75
14 4 0.14
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTCTCTCTT
Found at i:716533 original size:19 final size:19
Alignment explanation
Indices: 716505--716541 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
716495 AAATTCAGTT
716505 TTTCAAAAAAATG-GAAAA
1 TTTCAAAAAAATGAGAAAA
716523 TTTCAAAAAAAATGAGAAA
1 TTTC-AAAAAAATGAGAAA
716542 CTTATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (19 bp):
TTTCAAAAAAATGAGAAAA
Found at i:720822 original size:26 final size:25
Alignment explanation
Indices: 720786--720834 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
720776 TTGTTAGCTA
720786 TGTTTTGACTCAACATTGATTTCATT
1 TGTTTTGACTCAACATT-ATTTCATT
*
720812 TGTTTTGACTCAATATTATTTCA
1 TGTTTTGACTCAACATTATTTCA
720835 ATATGATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.51
Consensus pattern (25 bp):
TGTTTTGACTCAACATTATTTCATT
Found at i:724287 original size:52 final size:52
Alignment explanation
Indices: 724209--724313 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
724199 TCACTGTTTG
* * *
724209 TCACTATTTATCACTGTTCATGTATCGATCCATTGTGAATAATATCGATACA
1 TCACTATTCATCACTGTTCATGTATCGATACATTATGAATAATATCGATACA
*
724261 TCACTATTCATCACTGTTCATGTATCGATACATTATGAATAGTATCGATACA
1 TCACTATTCATCACTGTTCATGTATCGATACATTATGAATAATATCGATACA
724313 T
1 T
724314 TGAGTCCAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (52 bp):
TCACTATTCATCACTGTTCATGTATCGATACATTATGAATAATATCGATACA
Found at i:726438 original size:21 final size:21
Alignment explanation
Indices: 726396--726455 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
726386 GAATTAGAGG
726396 AGAAAATGAATGAGTTAGAAA
1 AGAAAATGAATGAGTTAGAAA
726417 AGAAAA-GAAATGAGTT-GCAAA
1 AGAAAATG-AATGAGTTAG-AAA
726438 ATGAAAATG-ATGAGTTAG
1 A-GAAAATGAATGAGTTAG
726456 CTAATAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.06
21 25 0.74
22 6 0.18
23 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.25, T:0.20
Consensus pattern (21 bp):
AGAAAATGAATGAGTTAGAAA
Found at i:727473 original size:13 final size:13
Alignment explanation
Indices: 727455--727480 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
727445 ACATTTTGGG
727455 ATGTATCGATACA
1 ATGTATCGATACA
727468 ATGTATCGATACA
1 ATGTATCGATACA
727481 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:727475 original size:33 final size:32
Alignment explanation
Indices: 727433--727498 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
727423 CGTTACAAGC
*
727433 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
727466 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
727498 C
1 C
727499 GAATTTGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:727569 original size:20 final size:20
Alignment explanation
Indices: 727522--727574 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
727512 GCCAATGACC
*
727522 TGTATCGATACATGCTTTTCA
1 TGTATCGATACAT-CTTGTCA
*
727543 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTT-GTCA
727563 TGTATCGATACA
1 TGTATCGATACA
727575 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 14 0.50
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATCTTGTCA
Found at i:727580 original size:13 final size:13
Alignment explanation
Indices: 727562--727586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
727552 ACATTTGGTC
727562 ATGTATCGATACA
1 ATGTATCGATACA
727575 ATGTATCGATAC
1 ATGTATCGATAC
727587 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:728170 original size:22 final size:23
Alignment explanation
Indices: 728143--728187 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
728133 TTTTCTTTTC
728143 TCTCCCCCTTAATCAAA-AAATT
1 TCTCCCCCTTAATCAAATAAATT
728165 TCTCCCCCTTAATCAAATAAATT
1 TCTCCCCCTTAATCAAATAAATT
728188 AACAATTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (23 bp):
TCTCCCCCTTAATCAAATAAATT
Found at i:729902 original size:20 final size:21
Alignment explanation
Indices: 729873--729913 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
729863 TATTTTTATT
729873 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
729892 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
729914 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:730271 original size:8 final size:8
Alignment explanation
Indices: 730258--730283 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
730248 AACATCATTC
730258 ATCACAAA
1 ATCACAAA
730266 ATCACAAA
1 ATCACAAA
730274 ATCACAAA
1 ATCACAAA
730282 AT
1 AT
730284 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:736238 original size:13 final size:13
Alignment explanation
Indices: 736220--736245 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
736210 ACATTTTAGG
736220 ATGTATCGATACA
1 ATGTATCGATACA
736233 ATGTATCGATACA
1 ATGTATCGATACA
736246 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:736240 original size:33 final size:32
Alignment explanation
Indices: 736198--736263 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
736188 CGTTACAAGC
*
736198 CAATGTATCGATACATTTTAG-GATGTATCGATA
1 CAATGTATCGATACATATT-GTG-TGTATCGATA
736231 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGTGTGTATCGATA
736263 C
1 C
736264 GAATTTGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (32 bp):
CAATGTATCGATACATATTGTGTGTATCGATA
Found at i:736334 original size:20 final size:21
Alignment explanation
Indices: 736287--736339 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
736277 GCCAATGACC
**
736287 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
736308 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
736328 TGTATCGATACA
1 TGTATCGATACA
736340 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:737363 original size:13 final size:13
Alignment explanation
Indices: 737345--737369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
737335 ATTACTCACA
737345 TGTATCGATACAT
1 TGTATCGATACAT
737358 TGTATCGATACA
1 TGTATCGATACA
737370 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:737481 original size:51 final size:52
Alignment explanation
Indices: 737378--737553 Score: 318
Period size: 52 Copynumber: 3.4 Consensus size: 52
737368 CACTGATCTT
737378 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
737430 TGTATCGATACATGCAGGCAAATTTG-CCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
737481 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
737533 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
737554 CTTTTCATAT
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 51 0.43
52 69 0.57
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:740983 original size:23 final size:24
Alignment explanation
Indices: 740957--741003 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
740947 TTATTGAAAA
740957 TTTGT-TTTCAATTG-ATTTGTGTT
1 TTTGTGTTT-AATTGAATTTGTGTT
*
740980 TTTGTGTTTAGTTGAATTTGTGTT
1 TTTGTGTTTAATTGAATTTGTGTT
741004 CAATCCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.13, C:0.02, G:0.21, T:0.64
Consensus pattern (24 bp):
TTTGTGTTTAATTGAATTTGTGTT
Found at i:741609 original size:13 final size:13
Alignment explanation
Indices: 741591--741616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
741581 ACAATCAAAT
741591 TTATATCGATATA
1 TTATATCGATATA
741604 TTATATCGATATA
1 TTATATCGATATA
741617 ATTTTAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTATATCGATATA
Found at i:743365 original size:20 final size:20
Alignment explanation
Indices: 743340--743380 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
743330 ATCTCATTTT
*
743340 TCACTGTTCATCACTATTCA
1 TCACTGATCATCACTATTCA
*
743360 TCACTGATCATCACTGTTCA
1 TCACTGATCATCACTATTCA
743380 T
1 T
743381 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.39
Consensus pattern (20 bp):
TCACTGATCATCACTATTCA
Found at i:743495 original size:20 final size:21
Alignment explanation
Indices: 743449--743495 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
743439 AATTTCAAAT
*
743449 GCATGTATCGATACATTATGA
1 GCATGTATCGATACATTAAGA
743470 --ATTGTATCGATACA-TAAGA
1 GCA-TGTATCGATACATTAAGA
743489 GCATGTA
1 GCATGTA
743496 AGTGCGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
GCATGTATCGATACATTAAGA
Found at i:744261 original size:20 final size:20
Alignment explanation
Indices: 744176--744303 Score: 96
Period size: 20 Copynumber: 6.3 Consensus size: 20
744166 GAGCTAACAA
*
744176 ATACATTAAAAAATGTATCG
1 ATACATTTAAAAATGTATCG
* * *
744196 ATACAATGAGAAATGTATCG
1 ATACATTTAAAAATGTATCG
* * * *
744216 ATATAATTT-CATATATATCG
1 ATA-CATTTAAAAATGTATCG
744236 ATACATTTAAAAATGTATCG
1 ATACATTTAAAAATGTATCG
***
744256 ATACATTTTAGGCATGTATCG
1 ATACA-TTTAAAAATGTATCG
* ***
744277 ATACATTCACTTATGTATCG
1 ATACATTTAAAAATGTATCG
744297 ATACATT
1 ATACATT
744304 GCCTTATTAT
Statistics
Matches: 85, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
19 4 0.05
20 62 0.73
21 19 0.22
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (20 bp):
ATACATTTAAAAATGTATCG
Found at i:744309 original size:20 final size:20
Alignment explanation
Indices: 744269--744322 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
744259 CATTTTAGGC
744269 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
744289 ATGTATCGATACATTGC-CTT
1 ATGTATCGATACATT-CACTT
*
744309 ATTATATCGATACA
1 A-TGTATCGATACA
744323 AATTGTTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:745042 original size:53 final size:53
Alignment explanation
Indices: 744957--745226 Score: 197
Period size: 53 Copynumber: 5.1 Consensus size: 53
744947 TAGACTAAAA
* * * ** *
744957 GATGGTAAGAGTGCCAAATGTGTTGATTCAAGGCCAACGCCATTGGGCTTAAG
1 GATGATAAGAATGCCAAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAG
* * * *
745010 GATGATAAGAATGCTAAATGTGCTGATTCAAGGCCAGCAACACTGGACTTAAA
1 GATGATAAGAATGCCAAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAG
* * * * * * * *
745063 GATGA-AGAGGATGTCGAATATGCTGATTCAAGACTAGCACCATTGGACTT-AG
1 GATGATA-AGAATGCCAAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAG
* * * *
745115 AGATAATAAGAATGCCAAATGTGTTGATTCAAGGCTAACGACATTGGACTTAAG
1 -GATGATAAGAATGCCAAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAG
* * * * * * * * *
745169 GGT-AAAGAGAATGCCGAATATGCTGACTT-AAGGCTAGCGATATTGGACTTAAA
1 GATGATA-AGAATGCCAAATGTGCTGA-TTCAAGGCCAACAACATTGGACTTAAG
745222 GATGA
1 GATGA
745227 AGAAAGTGCT
Statistics
Matches: 171, Mismatches: 39, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
52 4 0.02
53 161 0.94
54 6 0.04
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (53 bp):
GATGATAAGAATGCCAAATGTGCTGATTCAAGGCCAACAACATTGGACTTAAG
Found at i:745143 original size:106 final size:106
Alignment explanation
Indices: 744996--745220 Score: 267
Period size: 106 Copynumber: 2.1 Consensus size: 106
744986 AAGGCCAACG
* * * *
744996 CCATTGGGCTTAAGGATGATAAGAATGCTAAATGTGCTGATTCAAGGCCAGCAACACTGGACTTA
1 CCATTGGACTTAA-GATAATAAGAATGCCAAATGTGCTGATTCAAGGCCAACAACACTGGACTTA
* * *
745061 AAGATGAAGAGGATGTCGAATATGCTGA-TTCAAGACTAGC-A
65 AAGATAAAGAGAATGCCGAATATGCTGACTT-AAGACTAGCGA
* * * *
745102 CCATTGGACTTAGAGATAATAAGAATGCCAAATGTGTTGATTCAAGGCTAACGACATTGGACTTA
1 CCATTGGACTTA-AGATAATAAGAATGCCAAATGTGCTGATTCAAGGCCAACAACACTGGACTTA
* * *
745167 AGGGTAAAGAGAATGCCGAATATGCTGACTTAAGGCTAGCGA
65 AAGATAAAGAGAATGCCGAATATGCTGACTTAAGACTAGCGA
*
745209 -TATTGGACTTAA
1 CCATTGGACTTAA
745221 AGATGAAGAA
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
105 1 0.01
106 96 0.95
107 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (106 bp):
CCATTGGACTTAAGATAATAAGAATGCCAAATGTGCTGATTCAAGGCCAACAACACTGGACTTAA
AGATAAAGAGAATGCCGAATATGCTGACTTAAGACTAGCGA
Found at i:745435 original size:32 final size:32
Alignment explanation
Indices: 745399--745651 Score: 249
Period size: 32 Copynumber: 7.7 Consensus size: 32
745389 GAAGGAGATA
*
745399 CCACCAACTTGTGTGGGCTTTTAAGAAGGCTG
1 CCACCAACTTGTGTGGGCTTTTAAGAAGGTTG
* *
745431 CCACCAACTTGTGTGGGCTTTTGAGAGGGTTG
1 CCACCAACTTGTGTGGGCTTTTAAGAAGGTTG
* *
745463 CCACCAACTGGTGTGGGCTTTTGAGAAGGTTG
1 CCACCAACTTGTGTGGGCTTTTAAGAAGGTTG
* ** * * * * *
745495 CCATCGGCATGTGCGAGCTTTGAAAAAGGTTG
1 CCACCAACTTGTGTGGGCTTTTAAGAAGGTTG
* * *
745527 CCACCGACTTTTGTGGGCTTTTGAAAGAAAGGAATG
1 CCACCAACTTGTGTGGGCTTTT--AAG-AAGG-TTG
*
745563 CCACTAAC-T-TGTGGGCTTTTGGAAGGAAAGGTTG
1 CCACCAACTTGTGTGGGCTTTT--AA-G-AAGGTTG
*
745597 CCACCAACTTGTGTGGACTTTTGAAGAAGGTTG
1 CCACCAACTTGTGTGGGCTTTT-AAGAAGGTTG
745630 CCACCAACTTGTGTGGGCTTTT
1 CCACCAACTTGTGTGGGCTTTT
745652 GAAAAATGTT
Statistics
Matches: 183, Mismatches: 31, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
32 96 0.52
33 28 0.15
34 26 0.14
35 15 0.08
36 18 0.10
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (32 bp):
CCACCAACTTGTGTGGGCTTTTAAGAAGGTTG
Found at i:745479 original size:64 final size:66
Alignment explanation
Indices: 745399--745654 Score: 281
Period size: 64 Copynumber: 3.9 Consensus size: 66
745389 GAAGGAGATA
* *
745399 CCACCAACTTGTGTGGGCTTTT-AAGAAGGCTGCCACCAACTTGTGTGGGCTTTTG-AGAGGGTT
1 CCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTT
745462 G
66 G
* * ** * * * *
745463 CCACCAACTGGTGTGGGCTTTTG-AGAAGGTTGCCATCGGCATGTGCGAGC-TTTGAAAAAGGTT
1 CCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTT
745526 G
66 G
* * * *
745527 CCACCGACTTTTGTGGGCTTTTGAAAGAAAGGAATGCCACTAAC-T-TGTGGGCTTTTGGAAGGA
1 CCACCAACTTGTGTGGGCTTTTG-AAG-AAGG-TTGCCACCAACTTGTGTGGGCTTTT-GAA-G-
745590 AAGGTTG
60 AAGGTTG
*
745597 CCACCAACTTGTGTGGACTTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTTGAA
1 CCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTTGAA
745655 AAATGTTTCT
Statistics
Matches: 154, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
63 4 0.03
64 68 0.44
66 7 0.05
67 17 0.11
68 17 0.11
69 14 0.09
70 27 0.18
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (66 bp):
CCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTT
G
Found at i:747245 original size:41 final size:37
Alignment explanation
Indices: 747148--747234 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
747138 CATCCGAATA
*
747148 CTTTTCTTTTTTTT-TCTTTTGATTGATTTCTTTCTTT
1 CTTTT-TTTTTTTTGTTTTTTGATTGATTTCTTTCTTT
*
747185 CTTTTTTTTTTTTGTTTTTTGATTGATTTTTTTCTTT
1 CTTTTTTTTTTTTGTTTTTTGATTGATTTCTTTCTTT
*
747222 CTTTCTTTTTTTT
1 CTTTTTTTTTTTT
747235 CATGATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 8 0.17
37 38 0.83
ACGTcount: A:0.05, C:0.10, G:0.06, T:0.79
Consensus pattern (37 bp):
CTTTTTTTTTTTTGTTTTTTGATTGATTTCTTTCTTT
Found at i:751087 original size:20 final size:21
Alignment explanation
Indices: 751046--751100 Score: 103
Period size: 20 Copynumber: 2.7 Consensus size: 21
751036 ACATGTTGCA
751046 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
751067 ATGTATCGATACATG-AAAAG
1 ATGTATCGATACATGAAAAAG
751087 ATGTATCGATACAT
1 ATGTATCGATACAT
751101 TTCTTGGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:751157 original size:13 final size:13
Alignment explanation
Indices: 751139--751164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
751129 TACAGCAAGT
751139 ATGTATCGATACA
1 ATGTATCGATACA
751152 ATGTATCGATACA
1 ATGTATCGATACA
751165 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:753416 original size:21 final size:21
Alignment explanation
Indices: 753383--753427 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
753373 TTGCAAGTTG
*
753383 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
753405 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
753425 AAA
1 AAA
753428 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Done.