Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 9 of 20
Found at i:1378817 original size:6 final size:6
Alignment explanation
Indices: 1378808--1378841 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1378798 TGCCTCCTCG
*
1378808 TTTCCC TTT-CC TTTCAC TTTCCC TTTCCC TTTCC
1 TTTCCC TTTCCC TTTCCC TTTCCC TTTCCC TTTCC
1378842 TAGCTCCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (6 bp):
TTTCCC
Found at i:1378924 original size:42 final size:42
Alignment explanation
Indices: 1378877--1378957 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 42
1378867 AACTTTGAGA
1378877 GGTCTTCCTACCCATGTTTAAGA-AGA-TGGGAGAGAAGACACT
1 GGTCTTCCTACCCATGTTTAA-ATAGACT-GGAGAGAAGACACT
1378919 GGTCTTCCTACCCATGTTTAAATAGACTGGAGAGAAGAC
1 GGTCTTCCTACCCATGTTTAAATAGACTGGAGAGAAGAC
1378958 GCCTTCTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
41 1 0.03
42 35 0.95
43 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (42 bp):
GGTCTTCCTACCCATGTTTAAATAGACTGGAGAGAAGACACT
Found at i:1379031 original size:21 final size:19
Alignment explanation
Indices: 1379005--1379044 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
1378995 TGTTATATTT
1379005 TTATATTTTATTATATTATAA
1 TTATATTTT-TTAT-TTATAA
1379026 TTATATTTTTTATTTATAA
1 TTATATTTTTTATTTATAA
1379045 AAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATATTTTTTATTTATAA
Found at i:1379103 original size:19 final size:18
Alignment explanation
Indices: 1379079--1379123 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
1379069 TTTAAAAATC
1379079 TATATATTTAATCATATTA
1 TATATATTTAATCAT-TTA
* *
1379098 TATATATTTAATTATTTT
1 TATATATTTAATCATTTA
1379116 TATATATT
1 TATATATT
1379124 ATTTTAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATATTTAATCATTTA
Found at i:1379689 original size:2 final size:2
Alignment explanation
Indices: 1379682--1379715 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1379672 GGGTGAAGTG
1379682 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
1379716 GTATGTATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1380501 original size:21 final size:21
Alignment explanation
Indices: 1380477--1380519 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1380467 ATTATATCAG
1380477 TTTATTTTTAAAAAAAAATTA
1 TTTATTTTTAAAAAAAAATTA
**
1380498 TTTATTTTTTTAAAAAAATTA
1 TTTATTTTTAAAAAAAAATTA
1380519 T
1 T
1380520 CCGCTTTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATTTTTAAAAAAAAATTA
Found at i:1381227 original size:20 final size:20
Alignment explanation
Indices: 1381199--1381236 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1381189 AATTTTTTAC
* *
1381199 ATATTTTATTTTTTAAAAAT
1 ATATATTATTTTATAAAAAT
1381219 ATATATTATTTTATAAAA
1 ATATATTATTTTATAAAA
1381237 TTTAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTATTTTATAAAAAT
Found at i:1384139 original size:21 final size:21
Alignment explanation
Indices: 1384110--1384149 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1384100 GAGGAATTAT
*
1384110 GTATGTATATACATATATAAA
1 GTATATATATACATATATAAA
*
1384131 GTATATATATATATATATA
1 GTATATATATACATATATA
1384150 TATGTTGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
GTATATATATACATATATAAA
Found at i:1384720 original size:6 final size:6
Alignment explanation
Indices: 1384709--1384743 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1384699 TCATACCAAG
* *
1384709 CTTTTT CTTTTT CTTTTT TTTTTT CTTTTT ATTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
1384744 AATCCTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (6 bp):
CTTTTT
Found at i:1385336 original size:28 final size:29
Alignment explanation
Indices: 1385305--1385359 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1385295 TAACTTAAAC
1385305 TTAATTAATTTT-TAATTAAGTAATTTTA
1 TTAATTAATTTTATAATTAAGTAATTTTA
* * *
1385333 TTAATTGATTTTATATTTAATTAATTT
1 TTAATTAATTTTATAATTAAGTAATTT
1385360 GTGATATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (29 bp):
TTAATTAATTTTATAATTAAGTAATTTTA
Found at i:1385523 original size:33 final size:31
Alignment explanation
Indices: 1385485--1385558 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
1385475 TTTTTAAAAT
*
1385485 TTTAAAATAATTTTCATCCCCGATAATATTAAA
1 TTTAAAATAATATTCAT-CCC-ATAATATTAAA
* * *
1385518 TTTAAAATACTATTCATCTCATATTATTAAA
1 TTTAAAATAATATTCATCCCATAATATTAAA
*
1385549 TTTAATATAA
1 TTTAAAATAA
1385559 AAAAATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 18 0.51
32 2 0.06
33 15 0.43
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (31 bp):
TTTAAAATAATATTCATCCCATAATATTAAA
Found at i:1386104 original size:23 final size:23
Alignment explanation
Indices: 1386074--1386148 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
1386064 ATTTAAATTA
*
1386074 TTATTTAATTAATAAAAAATATT
1 TTATTTAATTAATATAAAATATT
1386097 TTATTTAAATTTAATTATAAAATATAT
1 TTATTT-AA-TTAA-TATAAAATAT-T
**
1386124 TTAAAT-ATTAATATAAAATAATT
1 TTATTTAATTAATATAAAAT-ATT
1386147 TT
1 TT
1386149 TAATATATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
23 17 0.39
24 8 0.18
25 5 0.11
26 9 0.20
27 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTTAATTAATATAAAATATT
Found at i:1386189 original size:30 final size:32
Alignment explanation
Indices: 1386145--1386208 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
1386135 TATAAAATAA
* *
1386145 TTTTTAATATATTTAA-AAGCTAAAATTAATTT
1 TTTTTAATATATTTAACAA-ATAAAATTAAATT
1386177 TTTTTAA-A-ATTTAACAAATAAAATTAAATT
1 TTTTTAATATATTTAACAAATAAAATTAAATT
1386207 TT
1 TT
1386209 AAATTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 19 0.66
31 3 0.10
32 7 0.24
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (32 bp):
TTTTTAATATATTTAACAAATAAAATTAAATT
Found at i:1392123 original size:2 final size:2
Alignment explanation
Indices: 1392116--1392150 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1392106 AACGTTCTCT
* *
1392116 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1392151 CAAATCCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1393394 original size:17 final size:16
Alignment explanation
Indices: 1393371--1393419 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1393361 AAGTATTATA
1393371 TATTTATATAAAATTT
1 TATTTATATAAAATTT
1393387 TAATTTAT-TAATAA-TT
1 T-ATTTATATAA-AATTT
1393403 TATATTATAT-AAATTT
1 TAT-TTATATAAAATTT
1393419 T
1 T
1393420 GATATAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 4 0.14
16 15 0.54
17 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTATATAAAATTT
Found at i:1393417 original size:26 final size:28
Alignment explanation
Indices: 1393388--1393446 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
1393378 ATAAAATTTT
*
1393388 AATTTATTA-ATAATT-TATATTATATA
1 AATTTATGATATAATTATATATTATATA
1393414 AATTT-TGATATAATTATATATTATATA
1 AATTTATGATATAATTATATATTATATA
*
1393441 ATTTTA
1 AATTTA
1393447 AAATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 11 0.39
27 15 0.54
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
AATTTATGATATAATTATATATTATATA
Found at i:1393438 original size:32 final size:30
Alignment explanation
Indices: 1393365--1393439 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 30
1393355 TGTTTAAAGT
*
1393365 ATTATATATT-TA-TATAAAATTTTAATTT
1 ATTATATATTATATTATAAAATTTTAATTA
*
1393393 ATTA-ATAATTTATATTATATAAATTTTGATATA
1 ATTATAT-A-TTATATTATA-AAATTTTAAT-TA
1393426 ATTATATATTATAT
1 ATTATATATTATAT
1393440 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 2 0.05
28 5 0.13
29 2 0.05
30 2 0.05
31 4 0.11
32 15 0.39
33 6 0.16
34 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
ATTATATATTATATTATAAAATTTTAATTA
Found at i:1393441 original size:15 final size:15
Alignment explanation
Indices: 1393392--1393443 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
1393382 AATTTTAATT
1393392 TATTA-ATAATT-TA
1 TATTATATAATTATA
1393405 TATTATATAA--AT-
1 TATTATATAATTATA
1393417 T-TTGATATAATTATA
1 TATT-ATATAATTATA
1393432 TATTATATAATT
1 TATTATATAATT
1393444 TTAAAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
11 2 0.06
12 7 0.22
13 6 0.19
14 6 0.19
15 9 0.28
16 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTATATAATTATA
Found at i:1393460 original size:27 final size:26
Alignment explanation
Indices: 1393401--1393492 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 26
1393391 TTATTAATAA
* *
1393401 TTTATATTATATAAATTTT-GATATAAT
1 TTTATATTATAT-AATTTTAAAT-TATT
*
1393428 TATATATTATATAATTTTAAAATTATT
1 TTTATATTATATAATTTT-AAATTATT
1393455 TTTATATTATATTATATTTT-AATTATT
1 TTTATATTATA-TA-ATTTTAAATTATT
*
1393482 AATTATATTAT
1 -TTTATATTAT
1393493 GAAAAAAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
26 6 0.11
27 31 0.56
28 13 0.24
29 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (26 bp):
TTTATATTATATAATTTTAAATTATT
Found at i:1393468 original size:16 final size:16
Alignment explanation
Indices: 1393449--1393490 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
1393439 TAATTTTAAA
1393449 ATTAT-TTTTATATTAT
1 ATTATATTTTA-ATTAT
1393465 ATTATATTTTAATTATT
1 ATTATATTTTAATTA-T
1393482 AATTATATT
1 -ATTATATT
1393491 ATGAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.39
17 6 0.26
18 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATATTTTAATTAT
Found at i:1393474 original size:18 final size:18
Alignment explanation
Indices: 1393448--1393490 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1393438 ATAATTTTAA
1393448 AATTAT-TTTT-A-TATT
1 AATTATATTTTAATTATT
1393463 ATATTATATTTTAATTATT
1 A-ATTATATTTTAATTATT
1393482 AATTATATT
1 AATTATATT
1393491 ATGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 5 0.21
17 4 0.17
18 9 0.38
19 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTATATTTTAATTATT
Found at i:1395349 original size:13 final size:14
Alignment explanation
Indices: 1395323--1395356 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1395313 TTTATTAATG
1395323 TATAAAAGTTATTT
1 TATAAAAGTTATTT
*
1395337 TTTAAAA-TTATTT
1 TATAAAAGTTATTT
1395350 TATAAAA
1 TATAAAA
1395357 ATAGTGATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TATAAAAGTTATTT
Found at i:1395418 original size:28 final size:29
Alignment explanation
Indices: 1395373--1395430 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 29
1395363 ATAGTTTTAT
1395373 TAAATATATTACAGATAATAAATAAAATTA
1 TAAATATATTACAGATAAT-AATAAAATTA
* *
1395403 TAAATAT-TTA-ATATAATAATAATATTA
1 TAAATATATTACAGATAATAATAAAATTA
1395430 T
1 T
1395431 TATAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 6 0.23
29 3 0.12
30 7 0.27
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAATATATTACAGATAATAATAAAATTA
Found at i:1395813 original size:2 final size:2
Alignment explanation
Indices: 1395808--1395846 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1395798 TCTCTCTCTC
* *
1395808 TA TA TA TA TA TA TA TA TA TC TA TA TA TC TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1395847 TCATGGATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1401444 original size:16 final size:16
Alignment explanation
Indices: 1401423--1401468 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1401413 ATTAATAAGA
*
1401423 TAATAAAT-AATATTTT
1 TAATAAATCAAT-TATT
1401439 TAAT-AATCAATTATT
1 TAATAAATCAATTATT
*
1401454 TAATAAATTAATTAT
1 TAATAAATCAATTAT
1401469 ATATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATAAATCAATTATT
Found at i:1401893 original size:16 final size:18
Alignment explanation
Indices: 1401865--1401905 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1401855 ATTTAATATA
*
1401865 AATATAAATATTTA-TTTT
1 AATATATAT-TTTATTTTT
1401883 AATATATATTTTATTTTT
1 AATATATATTTTATTTTT
1401901 AATAT
1 AATAT
1401906 TTAATTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AATATATATTTTATTTTT
Found at i:1401913 original size:13 final size:13
Alignment explanation
Indices: 1401871--1401932 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 13
1401861 TATAAATATA
1401871 AATATTTATTTTAAT
1 AATATTTATTTT--T
1401886 ATATATTTTATTTTT
1 A-ATA-TTTATTTTT
*
1401901 AATATTTAATTTT
1 AATATTTATTTTT
*
1401914 ACTAATTTATTTTT
1 AAT-ATTTATTTTT
1401928 AATAT
1 AATAT
1401933 AAATATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 12 0.30
14 14 0.35
15 3 0.08
16 3 0.08
17 8 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
AATATTTATTTTT
Found at i:1401952 original size:28 final size:30
Alignment explanation
Indices: 1401844--1402006 Score: 95
Period size: 31 Copynumber: 5.3 Consensus size: 30
1401834 AATAACATGT
* *
1401844 TATAATTTTTA-ATTTAATATAAATATAAA
1 TATAATTTTTATATTTATTATTAATATAAA
* * * * *
1401873 TATTTATTTTAATATATATT-TTATTTTTAATA
1 TA-TAATTTTTATATTTATTATTA-ATATAA-A
* *
1401905 TTTAA-TTTTACTAATTTATTTTTAATATAAA
1 TATAATTTTTA-T-ATTTATTATTAATATAAA
* *
1401936 TATAATTTTT-TA-TTATTATTCAT-TCTAA
1 TATAATTTTTATATTTATTATTAATAT-AAA
1401964 TATAATTTTACTTATATTTAATTATTAATATAAA
1 TATAA-TTT--TTATATTT-ATTATTAATATAAA
1401998 TATAATTTT
1 TATAATTTT
1402007 AATAAATTTT
Statistics
Matches: 99, Mismatches: 19, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
27 1 0.01
28 16 0.16
29 6 0.06
30 14 0.14
31 20 0.20
32 18 0.18
33 8 0.08
34 15 0.15
35 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
TATAATTTTTATATTTATTATTAATATAAA
Found at i:1405769 original size:11 final size:11
Alignment explanation
Indices: 1405753--1405777 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1405743 ACACTTTGTC
1405753 TTTTTTTTTTA
1 TTTTTTTTTTA
1405764 TTTTTTTTTTA
1 TTTTTTTTTTA
1405775 TTT
1 TTT
1405778 AGTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:1406026 original size:2 final size:2
Alignment explanation
Indices: 1406019--1406059 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1406009 CTCATTTTCT
1406019 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1406060 CCCTGGGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1407218 original size:13 final size:13
Alignment explanation
Indices: 1407200--1407226 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1407190 AAATCTGTTC
1407200 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
1407213 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
1407226 T
1 T
1407227 GAAGTTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:1407688 original size:11 final size:12
Alignment explanation
Indices: 1407668--1407727 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
1407658 TAATGTTAAT
1407668 ATAATATAAAAA
1 ATAATATAAAAA
*
1407680 ATAAT-TAAAAT
1 ATAATATAAAAA
*
1407691 ATGATATAAAAA
1 ATAATATAAAAA
1407703 TATGAATATATTAAAA
1 -AT-AATATA--AAAA
*
1407719 ATTATATAA
1 ATAATATAA
1407728 CTTTATAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 9 0.24
12 11 0.29
13 2 0.05
14 10 0.26
15 2 0.05
16 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:1408391 original size:23 final size:22
Alignment explanation
Indices: 1408352--1408400 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1408342 TGTTATTAAT
*
1408352 TTTAAAATATAACATATAATAAA
1 TTTAAAATATAAAATATAA-AAA
*
1408375 TTTAAAAGT-TAAAATATTAAAA
1 TTTAAAA-TATAAAATATAAAAA
1408397 TTTA
1 TTTA
1408401 TAATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 15 0.65
24 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TTTAAAATATAAAATATAAAAA
Found at i:1409200 original size:2 final size:2
Alignment explanation
Indices: 1409193--1409220 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1409183 AGCAGTTCTT
1409193 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1409221 CTTTGCCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1417157 original size:2 final size:2
Alignment explanation
Indices: 1417152--1417187 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1417142 CCCCCCCCAA
*
1417152 AC AC AC AC AC AC AC AC AC AC AC AC GC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1417188 CAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1419079 original size:19 final size:19
Alignment explanation
Indices: 1419055--1419103 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1419045 TTAAAATATA
1419055 ATATAAATATAATAAAAAT
1 ATATAAATATAATAAAAAT
* **
1419074 ATATAAATATATTAAATTT
1 ATATAAATATAATAAAAAT
1419093 ATAT-AATATAA
1 ATATAAATATAA
1419104 ATTATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAATATAATAAAAAT
Found at i:1419097 original size:32 final size:31
Alignment explanation
Indices: 1419061--1419149 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
1419051 TATAATATAA
1419061 ATATAATAAAAATATATAAATATATTAAATTT
1 ATATAATAAAAATATAT-AATATATTAAATTT
*
1419093 ATATAATATAAAT-TATTAATATATTAAAATTT
1 ATATAATAAAAATATA-TAATATATT-AAATTT
*
1419125 AT-T-AT-AAAATATATAATATTTTAAA
1 ATATAATAAAAATATATAATATATTAAA
1419150 ATAAAATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
28 3 0.06
29 12 0.24
30 4 0.08
31 11 0.22
32 21 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATAATAAAAATATATAATATATTAAATTT
Found at i:1419102 original size:18 final size:18
Alignment explanation
Indices: 1419073--1419136 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 18
1419063 ATAATAAAAA
1419073 TATATAAATATATTAAATT
1 TATAT-AATATATTAAATT
1419092 TATAT-A-ATA-TAAA-T
1 TATATAATATATTAAATT
1419106 TAT-TAATATATTAAAATT
1 TATATAATATATT-AAATT
*
1419124 TATTATAAAATAT
1 TA-TATAATATAT
1419137 ATAATATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 7 0.19
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
20 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATAATATATTAAATT
Found at i:1419121 original size:50 final size:47
Alignment explanation
Indices: 1419045--1419180 Score: 134
Period size: 50 Copynumber: 2.8 Consensus size: 47
1419035 AAAAAATTAA
*
1419045 TTAAAATATAA-TATAAATATAATAAAAATATAT-AAATATATTAA-ATT
1 TTAAAATAAAATTAT-AATAT-ATAAAAATATATAAAATATA-TAATATT
* *
1419092 TATATAATATAAATTATTAATATATTAAAATTTATTATAAAATATATAATATT
1 T-TAAAATA-AAATTA-TAATATA-TAAAA-ATA-TATAAAATATATAATATT
*
1419145 TTAAAATAAAATTATAATACATAAAAATATATAAAA
1 TTAAAATAAAATTATAATATATAAAAATATATAAAA
1419181 AATCAAATCT
Statistics
Matches: 74, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
47 8 0.11
48 8 0.11
49 8 0.11
50 18 0.24
51 9 0.12
52 12 0.16
53 11 0.15
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (47 bp):
TTAAAATAAAATTATAATATATAAAAATATATAAAATATATAATATT
Found at i:1419171 original size:21 final size:22
Alignment explanation
Indices: 1419128--1419173 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1419118 AAAATTTATT
** *
1419128 ATAAAATATATAATATTTTAAA
1 ATAAAATATATAATACATAAAA
1419150 ATAAAAT-TATAATACATAAAA
1 ATAAAATATATAATACATAAAA
1419171 ATA
1 ATA
1419174 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAAATATATAATACATAAAA
Found at i:1425985 original size:2 final size:2
Alignment explanation
Indices: 1425978--1426015 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1425968 AGGGAAATAC
*
1425978 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA TA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1426016 AAAACCTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:1426903 original size:2 final size:2
Alignment explanation
Indices: 1426898--1426932 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1426888 CTACCATAGA
*
1426898 AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1426933 CACCTGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1429070 original size:1 final size:1
Alignment explanation
Indices: 1429064--1429088 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1429054 TTAGCATTTG
1429064 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1429089 AATTTTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1433567 original size:1 final size:1
Alignment explanation
Indices: 1433561--1433591 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
1433551 ATCGAAGAAG
1433561 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1433592 TTCTTCTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1436420 original size:18 final size:18
Alignment explanation
Indices: 1436397--1436431 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1436387 AAAAAATGTA
1436397 AATAAAA-TATATATATTT
1 AATAAAATTA-ATATATTT
1436415 AATAAAATTAATATATT
1 AATAAAATTAATATATT
1436432 AAATGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAAATTAATATATTT
Found at i:1436697 original size:15 final size:15
Alignment explanation
Indices: 1436677--1436705 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1436667 AAATAATTCA
1436677 TTATATTTTTAATTT
1 TTATATTTTTAATTT
1436692 TTATATTTTTAATT
1 TTATATTTTTAATT
1436706 ATTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATATTTTTAATTT
Found at i:1437210 original size:21 final size:23
Alignment explanation
Indices: 1437184--1437227 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1437174 ATCATATTCA
*
1437184 TATTTTTT-T-TATTTTGTGTTT
1 TATTTTTTCTCTATGTTGTGTTT
1437205 TATTTTTTCTCTATGTTGTGTTT
1 TATTTTTTCTCTATGTTGTGTTT
1437228 ATGCCGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 1 0.05
23 11 0.55
ACGTcount: A:0.09, C:0.05, G:0.11, T:0.75
Consensus pattern (23 bp):
TATTTTTTCTCTATGTTGTGTTT
Found at i:1437703 original size:16 final size:17
Alignment explanation
Indices: 1437676--1437716 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1437666 ATTTTTAAAT
1437676 AAAA-TTTA-TTAATT-
1 AAAATTTTATTTAATTA
*
1437690 ATAATTTTATTTAATTA
1 AAAATTTTATTTAATTA
1437707 AAAATTTTAT
1 AAAATTTTAT
1437717 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 4 0.18
16 6 0.27
17 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAATTTTATTTAATTA
Found at i:1438153 original size:35 final size:34
Alignment explanation
Indices: 1438070--1438150 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 34
1438060 ACTATGTGTC
1438070 AAATATAAAAATATATATAAAATAAAATAAATTAT
1 AAATATAAAAATATATATAAAATAAAAT-AATTAT
* * * *
1438105 CAATATGTAAAATATATATAAAAATATAAT-ATTTT
1 AAATAT-AAAAATATATAT-AAAATAAAATAATTAT
1438140 AAATATAAAAA
1 AAATATAAAAA
1438151 ATAATACGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
34 4 0.11
35 14 0.37
36 11 0.29
37 9 0.24
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (34 bp):
AAATATAAAAATATATATAAAATAAAATAATTAT
Found at i:1438357 original size:22 final size:21
Alignment explanation
Indices: 1438322--1438373 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1438312 AGACACGATA
*
1438322 TAATTATAACATAAATAAAAAG
1 TAATTAAAACAT-AATAAAAAG
*
1438344 TAATTAAAATATAATAAAAAG
1 TAATTAAAACATAATAAAAAG
1438365 TAATATAAA
1 TAAT-TAAA
1438374 TATGATACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
TAATTAAAACATAATAAAAAG
Found at i:1438374 original size:21 final size:21
Alignment explanation
Indices: 1438326--1438376 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
1438316 ACGATATAAT
1438326 TATAACATA-AATAAAAAGTAA
1 TATAA-ATATAATAAAAAGTAA
1438347 T-TAAAATATAATAAAAAGTAA
1 TAT-AAATATAATAAAAAGTAA
1438368 TATAAATAT
1 TATAAATAT
1438377 GATACTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.15
21 22 0.81
22 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
TATAAATATAATAAAAAGTAA
Found at i:1438710 original size:16 final size:16
Alignment explanation
Indices: 1438685--1438730 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1438675 AATACAAACA
*
1438685 TTTATATTTTTTTCTT
1 TTTATTTTTTTTTCTT
*
1438701 TTTATTTTTTCTTCTT
1 TTTATTTTTTTTTCTT
1438717 TCTT-TTTTTTTTTC
1 T-TTATTTTTTTTTC
1438731 ATCTTTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 24 0.92
17 2 0.08
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTTTTTCTT
Found at i:1438727 original size:19 final size:20
Alignment explanation
Indices: 1438695--1438736 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1438685 TTTATATTTT
*
1438695 TTTCTTTTTATTTTTTCTTC
1 TTTCTTTTTATTTTTTCATC
1438715 TTTCTTTTT-TTTTTTCATC
1 TTTCTTTTTATTTTTTCATC
1438734 TTT
1 TTT
1438737 TCTCTTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTCTTTTTATTTTTTCATC
Found at i:1438737 original size:27 final size:27
Alignment explanation
Indices: 1438691--1438744 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1438681 AACATTTATA
* *
1438691 TTTTTTTCTTTTTATTTTTTCTTCTTTC
1 TTTTTTTCTTTTCATCTTTTC-TCTTTC
1438719 TTTTTTT-TTTTCATCTTTTCTCTTTC
1 TTTTTTTCTTTTCATCTTTTCTCTTTC
1438745 CTAAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 11 0.46
28 7 0.29
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTTTCTTTTCATCTTTTCTCTTTC
Found at i:1438738 original size:20 final size:21
Alignment explanation
Indices: 1438694--1438739 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1438684 ATTTATATTT
*
1438694 TTTTCTTTTTATTTTTTCTTC
1 TTTTCTTTTTATTTTTTCATC
1438715 -TTTCTTTTT-TTTTTTCATC
1 TTTTCTTTTTATTTTTTCATC
1438734 TTTTCT
1 TTTTCT
1438740 CTTTCCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTATTTTTTCATC
Found at i:1438803 original size:25 final size:25
Alignment explanation
Indices: 1438769--1438840 Score: 117
Period size: 25 Copynumber: 2.9 Consensus size: 25
1438759 AAAGATAGAT
* *
1438769 ACGTATCATCACTATAGCCATGAAC
1 ACGTGTCATCACTATAGACATGAAC
*
1438794 ACGTGTCATCATTATAGACATGAAC
1 ACGTGTCATCACTATAGACATGAAC
1438819 ACGTGTCATCACTATAGACATG
1 ACGTGTCATCACTATAGACATG
1438841 CTTGTAGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (25 bp):
ACGTGTCATCACTATAGACATGAAC
Found at i:1439625 original size:81 final size:82
Alignment explanation
Indices: 1439470--1439632 Score: 247
Period size: 82 Copynumber: 2.0 Consensus size: 82
1439460 ATACGGTTGA
*** * * *
1439470 CTTTTTTGTTCGTCATCTTTTCTGGGTGACACTGGCTTTTTTTTTCTTGCTAAACTATGATCTTT
1 CTTTTTTGTTCGTCATCTTTTCTAAATGACACTAGCTTTTGTTCTCTTGCTAAACTATGATCTTT
1439535 GTTGCTTTATTAGCTCT
66 GTTGCTTTATTAGCTCT
*
1439552 CTTTTTTGTTCGTCATCTTTTTTAAATGACACTAGCTTTTGTTCT-TTGCTAAACTATGATCTTT
1 CTTTTTTGTTCGTCATCTTTTCTAAATGACACTAGCTTTTGTTCTCTTGCTAAACTATGATCTTT
*
1439616 GTTGTTTTATTAGCTCT
66 GTTGCTTTATTAGCTCT
1439633 TATATTATGT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 35 0.48
82 38 0.52
ACGTcount: A:0.15, C:0.17, G:0.14, T:0.54
Consensus pattern (82 bp):
CTTTTTTGTTCGTCATCTTTTCTAAATGACACTAGCTTTTGTTCTCTTGCTAAACTATGATCTTT
GTTGCTTTATTAGCTCT
Found at i:1444642 original size:17 final size:17
Alignment explanation
Indices: 1444622--1444655 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1444612 CAAATGTTTC
1444622 TTCATAATCAATGCCAT
1 TTCATAATCAATGCCAT
1444639 TTCATAATCAATGCCAT
1 TTCATAATCAATGCCAT
1444656 AAGTTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (17 bp):
TTCATAATCAATGCCAT
Found at i:1449986 original size:911 final size:910
Alignment explanation
Indices: 1448110--1450830 Score: 3610
Period size: 911 Copynumber: 3.0 Consensus size: 910
1448100 AAGATGATAG
* * * *
1448110 GACTCCGTCAACCAGTTGAACTTAAAGAATCAAGAGTCGATGATGAAAGAAAAAATTGATGCTTC
1 GACTACGTCAACCAGTTGAACTTAGAGAATCAAGAGTCAATGATGAAAGAAAAAATTGATGCCTC
* * *
1448175 AAGCTTTAGAAAATTTGATATTAAAAGCTACGAACTTAACCATTAACACAAGTGCTAGAACCAGC
66 AAGCTTTAGAAAATCTGAGATTAAAAGCTACGAACTTAACCATTAACAC-AGTGCTGGAACCAGC
* * *
1448240 TTACACAGAAAGTTTCTCAGAAAGCTACAGAAGATAAAACCTCCAATAGAAAATGCAGACTCTAT
130 TTACATAGAAAG-TTCTCAGAAAGCTACAGAAGATAAAACCACCAATAGAAAATGCAGCCTCTAT
*
1448305 TGATGCAGTGGAGGGCTTAAGATGGATACTCCAAGAAACACAAGTATACAAGTCAGTTTTCTCCA
194 TGATGCAGTGGAGGGCTTAAGATGGATACTCCAAGGAACACAAGTA-ACAAGTCAGTTTTCT-C-
*
1448370 TATGTTTTGGAAGCATGTCCTGGTTTTCAGCTGTTT-GCTTAATGATATTGCGAAGGGTCTAGAA
256 TATGTTTTGGAAGCATGTCCTGGTTTTCAGCTGTTTAGCTTAATGATATTGCTAAGGGTCTAGAA
* * *
1448434 GCTTCTAGAGAGGTTTTCAATTGGGTTGTCCAGAAGGTTAATAATAAAGACGGTGAATAATAAAG
321 GCTTCTAGAGAGGGTTTCAATTGGGTTGTCAAGAAGG-T--GAAT----AC--TG------AAA-
*
1448499 ACCAAGAAGAGTGGTCACCAGAAGGATTTGAACAAAGAATGGAAGAGTTTGATCATAGGGGGATA
370 ACCAAGAAGAGTGGTCACCAGAAGGATTTGAACAAAGAATGGAAGAGTTTGATCATAAGGGGATA
* ** * ** * * *
1448564 AGCACCTCAACTGCAAATTCATGATCATAAAACATTGAAACTAAAAGAAGGTTCATGACAA-A-A
435 AGCACCTCAAGTGCTGATTCATGATCATGAAACATTGAAACTGTAGGAGGGTTCATGACAATACG
* *
1448627 T-G-TGG-A-T--G--C-------A--ACT-C-AG-C-A-CATGGCCACCCAGTAATGAACAGAT
500 TGGATGGAACTCAGCACAGTGGGTATCACTGCTGGACTATCATGGCCACTCAGTAATGAACAGAT
*
1448670 -TAACAATGAAAAGCTCATTAGAGAGATACTAAGAATAAGGTTTGGAGCCCAAAAATGGTCTAGA
565 CT-ACAATGAAAAGCTCATTAGAGAGATACTAAGAATAGGGTTTGGAGCCCAAAAATGGTC-AGA
* * * * *
1448734 TGGATGGA-ATAGATATTATTATCAACAAAAGAAAATATAACAGAAGTAGTGACTCATCTTATTG
628 TGGA-AGATA-AGTTATTATTAGCAACAAAAGAAAATATAACAAAAGTAGTGACTCACCTTATTG
*
1448798 TTGGTGAAGCAGCCAATGACATAAGAAACAGAGCTAGAGTGAAATGGATGGAACAAAGAGTGCTC
691 TTGGTGAAGCAGCTAATGACATAAGAAACAGAGCTAGAGTGAAATGGATGGAACAAAGAGTGCTC
* *
1448863 TTCAAGAAGGTGATCACCCCACACAGTTTT-GAAGTATTTATTAGATTGATTGAGATTGAACAAC
756 TTCAAGAAGGTGATCACCCCACACA-TTTTCGAAGTCTTTATTAGATTGAATGAGATTGAACAAC
*
1448927 CCTCAAGTAGAGCAATTATGTACTAAGGGAAGAC-AAA-AATAATTTCAAGCACAAAGCTCTTAG
820 CCTCAAGTAGAGCAATTATGTACTAAGGGAAGACTAAAGAATAAGTTCAAGCACAAAGCTC-TAG
*
1448990 ATCAAATTATAAGATAAATACTGATAA
884 ATCAAATTATAAGATAAATACTGAGAA
* *
1449017 GACTACATCAACCAGTTGAACTTCAGAGAATCAAGAATCAATGATGAAAGAAAAAATTGATGCCT
1 GACTACGTCAACCAGTTGAACTT-AGAGAATCAAGAGTCAATGATGAAAGAAAAAATTGATGCCT
* * *
1449082 CAAGCTTTAGAAAATGTGAGATTAAAAGCTACGAATTTAACCATTAACAC-GTGCTGGAACCACC
65 CAAGCTTTAGAAAATCTGAGATTAAAAGCTACGAACTTAACCATTAACACAGTGCTGGAACCAGC
* * *
1449146 TTACGTAGAAAGGTTC-CTAGAAAGCTACAGAAGATAAAACCACAAAGAGAAAATGCAGCCTCTA
130 TTACATAGAAA-GTTCTC-AGAAAGCTACAGAAGATAAAACCACCAATAGAAAATGCAGCCTCTA
* *
1449210 TTGATGCAGTGGAAGGCATAAGATGGATACTCCAAGGAACACAAGTACACAAGTCAGTTTTCTCT
193 TTGATGCAGTGGAGGGCTTAAGATGGATACTCCAAGGAACACAAGTA-ACAAGTCAGTTTTCTCT
*
1449275 GTGTTTTGGAAGCATGTCCTGGTTTTCAGCTGTTTAGCTTAATGATATTGCTAAGGGTCTAGAAG
257 ATGTTTTGGAAGCATGTCCTGGTTTTCAGCTGTTTAGCTTAATGATATTGCTAAGGGTCTAGAAG
* * * *
1449340 CTTCTAGTGAGGGTTTCAA-TCGGTCTGTCAAGAAGGTGAATACTGAAAACCAAGAAGAGCGATC
322 CTTCTAGAGAGGGTTTCAATTGGGT-TGTCAAGAAGGTGAATACTGAAAACCAAGAAGAGTGGTC
* * * *
1449404 ACCAGAAGGATTTGAGCAAAGAATGGAACAGTTTGATCATAAGGGGATGAGCACCTCATGTGCTG
386 ACCAGAAGGATTTGAACAAAGAATGGAAGAGTTTGATCATAAGGGGATAAGCACCTCAAGTGCTG
*
1449469 ATTCATGATGATGGAAACATTGAAACTGTAGGAGGGTTCATGACAATACGTGGATGGAACTCAGC
451 ATTCATGATCAT-GAAACATTGAAACTGTAGGAGGGTTCATGACAATACGTGGATGGAACTCAGC
1449534 ACAGTGGAGTATCACTGCTGGACTATCATGGCCACTCAGTAATGAACAGATCTACAATGAAAAGC
515 ACAGTGG-GTATCACTGCTGGACTATCATGGCCACTCAGTAATGAACAGATCTACAATGAAAAGC
*
1449599 TCATTAAAGAGATACTAAGAATAGGGTTTGGAGCCCAAAAATGGTC-GATGGAAGATAAGTTATT
579 TCATTAGAGAGATACTAAGAATAGGGTTTGGAGCCCAAAAATGGTCAGATGGAAGATAAGTTATT
* * * * **
1449663 ATTAGCAACAAAACAAAGTATAACAAAAATAGTGACTCACCTTACTCCTGGTGAAGCAGCTAATG
644 ATTAGCAACAAAAGAAAATATAACAAAAGTAGTGACTCACCTTATTGTTGGTGAAGCAGCTAATG
*
1449728 ACATAAGAAACAGAGCTAG-GTGAAGTGGATGGAACAAAGAGTGCTCTTCAAGAAGGTGATCACC
709 ACATAAGAAACAGAGCTAGAGTGAAATGGATGGAACAAAGAGTGCTCTTCAAGAAGGTGATCACC
* * *
1449792 CCACACATTTTCGAAGTCCTTATTAGATTGAATGACG-TTGAACGACCCTCGAGTAGAGCAATTA
774 CCACACATTTTCGAAGTCTTTATTAGATTGAATGA-GATTGAACAACCCTCAAGTAGAGCAATTA
*
1449856 TGTACTAAAGGAAGACTAAAGAATAAGTTCAAGCACAAAGCTCTAGATCAAATTATAAGATAAAT
838 TGTACTAAGGGAAGACTAAAGAATAAGTTCAAGCACAAAGCTCTAGATCAAATTATAAGATAAAT
1449921 ACTGAGAA
903 ACTGAGAA
* * * * *
1449929 GACTGCGTCAACCAGTTGAAATTAGATAAACAAGAGTCAATGATGAAAGAAAAAATTGATCCCTC
1 GACTACGTCAACCAGTTGAACTTAGAGAATCAAGAGTCAATGATGAAAGAAAAAATTGATGCCTC
* *
1449994 AAGCTTTAAAAAATCTGAGATTAAAAGCTACGAAGTTAACCATTAACACGAGTGCTGGAACCAGC
66 AAGCTTTAGAAAATCTGAGATTAAAAGCTACGAACTTAACCATTAACAC-AGTGCTGGAACCAGC
* *
1450059 TTACATAGAAAAGTTCTCAGAAAGCTACA-ATAGATAAAACGACCAATAGAAAATGCAACCTCTA
130 TTACATAG-AAAGTTCTCAGAAAGCTACAGA-AGATAAAACCACCAATAGAAAATGCAGCCTCTA
* *
1450123 TTGATGCAATGGAGGGCTTAAGATGGATTACTCCAA-GAA-AC-A-CAACAAGTCAGTTTTCTCT
193 TTGATGCAGTGGAGGGCTTAAGATGGA-TACTCCAAGGAACACAAGTAACAAGTCAGTTTTCTCT
* * *
1450184 AAATGTTTTGGAAGCATGTCCTAGTTTTCAGCTGTTTAGCTTAACGATATTGCTAAGCGTCTAGA
257 --ATGTTTTGGAAGCATGTCCTGGTTTTCAGCTGTTTAGCTTAATGATATTGCTAAGGGTCTAGA
* * *
1450249 AGCTTCTAAAGAGGGTTTCAATTGGGTTGTCAAGAAGGTGAATAATGAAGACCAA-AATGAGTGG
320 AGCTTCTAGAGAGGGTTTCAATTGGGTTGTCAAGAAGGTGAATACTGAAAACCAAGAA-GAGTGG
* * * *
1450313 TCACCAGAAGGATTTGACCAAAGAATGGAAGGGATTGATCATAAGGGGATAAGCACCTAAAGTGC
384 TCACCAGAAGGATTTGAACAAAGAATGGAAGAGTTTGATCATAAGGGGATAAGCACCTCAAGTGC
* *
1450378 TGATTCATGATCATGAAGCATTGGAACTGTAGGAGGGTT-ATGACAATACGTGGATGGAACTCAG
449 TGATTCATGATCATGAAACATTGAAACTGTAGGAGGGTTCATGACAATACGTGGATGGAACTCAG
* * *
1450442 CACAGTAGGGTATCATTGCTGGACTGCAAGTCATGGCCAGTCAGTAATGAACAGATCTGCAATGA
514 CACAGT-GGGTATCACTGCTGGACT---A-TCATGGCCACTCAGTAATGAACAGATCTACAATGA
* *
1450507 AAAGCTCATTAGAGAGATACTAAGAGTAGGGTTTGGAGCCCAAAAATGGTCTAGATGGATGGAAA
574 AAAGCTCATTAGAGAGATACTAAGAATAGGGTTTGGAGCCCAAAAATGGTC---A--GATGGAAG
* * * *
1450572 ATAAGTTATTATTAGCAGCAAAAGAAAACATAACAAAAGTAAATG-CTCACCTTATTGTTAGTGA
634 ATAAGTTATTATTAGCAACAAAAGAAAATATAACAAAAGT-AGTGACTCACCTTATTGTTGGTGA
* *
1450636 AGCAGCTAATAACATAAGAAACAGAGCTAGAGTGAAATCGATGGAACAAAGAGTGCTCTTCAAGA
698 AGCAGCTAATGACATAAGAAACAGAGCTAGAGTGAAATGGATGGAACAAAGAGTGCTCTTCAAGA
* * *** *
1450701 ACGTGACCACCCCACACAGACTC--A-TCTTTATTAGATTGACTGAGATTGAACAACCCTCAAGT
763 AGGTGATCACCCCACACATTTTCGAAGTCTTTATTAGATTGAATGAGATTGAACAACCCTCAAGT
* * *
1450763 AGAGCAATTATGTACTGAGGGAAGACTAAAGAATAAGTTCAAACACAAAGCTCCAAGATCAAATT
828 AGAGCAATTATGTACTAAGGGAAGACTAAAGAATAAGTTCAAGCACAAAGCT-CTAGATCAAATT
1450828 ATA
892 ATA
1450831 TAGTAATACC
Statistics
Matches: 1609, Mismatches: 143, Indels: 113
0.86 0.08 0.06
Matches are distributed among these distances:
889 82 0.05
890 31 0.02
891 1 0.00
892 1 0.00
893 1 0.00
894 3 0.00
895 1 0.00
896 3 0.00
898 3 0.00
900 1 0.00
902 3 0.00
904 40 0.02
905 57 0.04
906 125 0.08
907 22 0.01
908 85 0.05
909 63 0.04
910 35 0.02
911 376 0.23
912 144 0.09
913 202 0.13
914 13 0.01
915 80 0.05
916 2 0.00
917 81 0.05
918 15 0.01
919 86 0.05
920 53 0.03
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (910 bp):
GACTACGTCAACCAGTTGAACTTAGAGAATCAAGAGTCAATGATGAAAGAAAAAATTGATGCCTC
AAGCTTTAGAAAATCTGAGATTAAAAGCTACGAACTTAACCATTAACACAGTGCTGGAACCAGCT
TACATAGAAAGTTCTCAGAAAGCTACAGAAGATAAAACCACCAATAGAAAATGCAGCCTCTATTG
ATGCAGTGGAGGGCTTAAGATGGATACTCCAAGGAACACAAGTAACAAGTCAGTTTTCTCTATGT
TTTGGAAGCATGTCCTGGTTTTCAGCTGTTTAGCTTAATGATATTGCTAAGGGTCTAGAAGCTTC
TAGAGAGGGTTTCAATTGGGTTGTCAAGAAGGTGAATACTGAAAACCAAGAAGAGTGGTCACCAG
AAGGATTTGAACAAAGAATGGAAGAGTTTGATCATAAGGGGATAAGCACCTCAAGTGCTGATTCA
TGATCATGAAACATTGAAACTGTAGGAGGGTTCATGACAATACGTGGATGGAACTCAGCACAGTG
GGTATCACTGCTGGACTATCATGGCCACTCAGTAATGAACAGATCTACAATGAAAAGCTCATTAG
AGAGATACTAAGAATAGGGTTTGGAGCCCAAAAATGGTCAGATGGAAGATAAGTTATTATTAGCA
ACAAAAGAAAATATAACAAAAGTAGTGACTCACCTTATTGTTGGTGAAGCAGCTAATGACATAAG
AAACAGAGCTAGAGTGAAATGGATGGAACAAAGAGTGCTCTTCAAGAAGGTGATCACCCCACACA
TTTTCGAAGTCTTTATTAGATTGAATGAGATTGAACAACCCTCAAGTAGAGCAATTATGTACTAA
GGGAAGACTAAAGAATAAGTTCAAGCACAAAGCTCTAGATCAAATTATAAGATAAATACTGAGAA
Found at i:1453608 original size:13 final size:13
Alignment explanation
Indices: 1453590--1453629 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
1453580 GAAAGTTGAT
1453590 TGGAAAAAATAAA
1 TGGAAAAAATAAA
1453603 TGGAAAAAA-AAA
1 TGGAAAAAATAAA
*
1453615 TTGAAAAAAGTAAA
1 TGGAAAAAA-TAAA
1453629 T
1 T
1453630 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 11 0.46
13 9 0.38
14 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (13 bp):
TGGAAAAAATAAA
Found at i:1453620 original size:25 final size:25
Alignment explanation
Indices: 1453592--1453641 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1453582 AAGTTGATTG
1453592 GAAAAAA-TAAATGGAAAAAAAAATT
1 GAAAAAAGTAAAT-GAAAAAAAAATT
*
1453617 GAAAAAAGTAAATTAAAAAAAAATT
1 GAAAAAAGTAAATGAAAAAAAAATT
1453642 ATGCAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (25 bp):
GAAAAAAGTAAATGAAAAAAAAATT
Found at i:1456560 original size:18 final size:18
Alignment explanation
Indices: 1456539--1456575 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1456529 GCAAAAAGTT
1456539 TGTCTAAACTTAAAATTG
1 TGTCTAAACTTAAAATTG
1456557 TGTCTAAACTTAAAATTG
1 TGTCTAAACTTAAAATTG
1456575 T
1 T
1456576 CCGCTGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TGTCTAAACTTAAAATTG
Found at i:1456576 original size:16 final size:17
Alignment explanation
Indices: 1456532--1456573 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
1456522 TGAACTCGCA
1456532 AAAAGTTTGTCTAAACTT
1 AAAA-TTTGTCTAAACTT
1456550 AAAATTGTGTCTAAACTT
1 AAAATT-TGTCTAAACTT
1456568 AAAATT
1 AAAATT
1456574 GTCCGCTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (17 bp):
AAAATTTGTCTAAACTT
Found at i:1463875 original size:18 final size:18
Alignment explanation
Indices: 1463848--1463885 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1463838 ATTCTAGAAC
1463848 AAGGACGCCATGAGGAAT
1 AAGGACGCCATGAGGAAT
*
1463866 AAGGATGCCATGAGGAAT
1 AAGGACGCCATGAGGAAT
1463884 AA
1 AA
1463886 CAATTGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.32, T:0.13
Consensus pattern (18 bp):
AAGGACGCCATGAGGAAT
Found at i:1464349 original size:15 final size:15
Alignment explanation
Indices: 1464329--1464359 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1464319 AAAATGAAAG
1464329 TAATGTACTTCAAAT
1 TAATGTACTTCAAAT
1464344 TAATGTACTTCAAAT
1 TAATGTACTTCAAAT
1464359 T
1 T
1464360 TATTCAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
TAATGTACTTCAAAT
Found at i:1465719 original size:179 final size:179
Alignment explanation
Indices: 1465419--1465780 Score: 706
Period size: 179 Copynumber: 2.0 Consensus size: 179
1465409 ATCTACGCGA
1465419 AGCCTTAAATTAGGAACATAAACACCAAGAATACCAAATGAAACCTGCATCAGATAAATGAGAAC
1 AGCCTTAAATTAGGAACATAAACACCAAGAATACCAAATGAAACCTGCATCAGATAAATGAGAAC
*
1465484 AATAAAATGTGACTGACATGCTATATCAAACAAGTTTATAAAAAAAGCAAACCTTAATAACTACG
66 AATAAAATGTGACTGACATGCTATATAAAACAAGTTTATAAAAAAAGCAAACCTTAATAACTACG
1465549 TAAAAGTTTTTCCAAAGATTTTTCCCTTCTTCTAGGAGACAGTCATTTC
131 TAAAAGTTTTTCCAAAGATTTTTCCCTTCTTCTAGGAGACAGTCATTTC
1465598 AGCCTTAAATTAGGAACATAAACACCAAGAATACCAAATGAAACCTGCATCAGATAAATGAGAAC
1 AGCCTTAAATTAGGAACATAAACACCAAGAATACCAAATGAAACCTGCATCAGATAAATGAGAAC
*
1465663 AATAAAATGTGACTGACATGCTATATAAAACAAGTTTATAAAAAAATCAAACCTTAATAACTACG
66 AATAAAATGTGACTGACATGCTATATAAAACAAGTTTATAAAAAAAGCAAACCTTAATAACTACG
1465728 TAAAAGTTTTTCCAAAGATTTTTCCCTTCTTCTAGGAGACAGTCATTTC
131 TAAAAGTTTTTCCAAAGATTTTTCCCTTCTTCTAGGAGACAGTCATTTC
1465777 AGCC
1 AGCC
1465781 AGAAATTTGC
Statistics
Matches: 181, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 181 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (179 bp):
AGCCTTAAATTAGGAACATAAACACCAAGAATACCAAATGAAACCTGCATCAGATAAATGAGAAC
AATAAAATGTGACTGACATGCTATATAAAACAAGTTTATAAAAAAAGCAAACCTTAATAACTACG
TAAAAGTTTTTCCAAAGATTTTTCCCTTCTTCTAGGAGACAGTCATTTC
Found at i:1470523 original size:30 final size:30
Alignment explanation
Indices: 1470487--1470548 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1470477 AAAATAATTA
*
1470487 AGGAAATAAAAAAAGGAATGTTATTATATC
1 AGGAAATAAAAAAAGGAACGTTATTATATC
*
1470517 AGGAAATAAAAAAAGGAACGTTATTATGTC
1 AGGAAATAAAAAAAGGAACGTTATTATATC
1470547 AG
1 AG
1470549 CATCCTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (30 bp):
AGGAAATAAAAAAAGGAACGTTATTATATC
Found at i:1477311 original size:16 final size:16
Alignment explanation
Indices: 1477285--1477323 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1477275 AAAAAAAAAC
* *
1477285 ATTTTCGTCCTTTCCA
1 ATTTTCTTCCTCTCCA
*
1477301 TTTTTCTTCCTCTCCA
1 ATTTTCTTCCTCTCCA
1477317 ATTTTCT
1 ATTTTCT
1477324 ATTCAACCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.10, C:0.31, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTTTCTTCCTCTCCA
Found at i:1479235 original size:19 final size:18
Alignment explanation
Indices: 1479211--1479256 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1479201 TGCAAATTCC
*
1479211 CAGATTCTCTTAATTCTAG
1 CAGATT-TCCTAATTCTAG
* *
1479230 CAGATTTCCTAATTTTTG
1 CAGATTTCCTAATTCTAG
1479248 CAGATTTCC
1 CAGATTTCC
1479257 AGATCTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (18 bp):
CAGATTTCCTAATTCTAG
Found at i:1481319 original size:23 final size:23
Alignment explanation
Indices: 1481289--1481333 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1481279 CCTTCAAGGG
1481289 TTCAAAATATCACAGGGGCAAAT
1 TTCAAAATATCACAGGGGCAAAT
*
1481312 TTCAAAATATTACAGGGGCAAA
1 TTCAAAATATCACAGGGGCAAA
1481334 ATGATTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (23 bp):
TTCAAAATATCACAGGGGCAAAT
Found at i:1485296 original size:16 final size:16
Alignment explanation
Indices: 1485261--1485308 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
1485251 AAGAAAACTA
* *
1485261 TTCTCTCCATTCTG-T
1 TTCTCTCCAATCAGTT
1485276 TTCTCTCCAATCAGTT
1 TTCTCTCCAATCAGTT
1485292 TTCTCTCCAATCAGTT
1 TTCTCTCCAATCAGTT
1485308 T
1 T
1485309 CATCTATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.15, C:0.31, G:0.06, T:0.48
Consensus pattern (16 bp):
TTCTCTCCAATCAGTT
Found at i:1485309 original size:15 final size:15
Alignment explanation
Indices: 1485261--1485309 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
1485251 AAGAAAACTA
* *
1485261 TTCTCTCCATTCTGT
1 TTCTCTCCAATCAGT
1485276 TTCTCTCCAATCAGTT
1 TTCTCTCCAATCAG-T
1485292 TTCTCTCCAATCAGT
1 TTCTCTCCAATCAGT
1485307 TTC
1 TTC
1485310 ATCTATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 16 0.52
16 15 0.48
ACGTcount: A:0.14, C:0.33, G:0.06, T:0.47
Consensus pattern (15 bp):
TTCTCTCCAATCAGT
Found at i:1486499 original size:39 final size:41
Alignment explanation
Indices: 1486456--1486536 Score: 139
Period size: 39 Copynumber: 2.0 Consensus size: 41
1486446 TGATTTTTAA
1486456 GAAAGTTGATTGG-AAAATAAATGGAG-AAAAAATTGAAAC
1 GAAAGTTGATTGGAAAAATAAATGGAGAAAAAAATTGAAAC
1486495 GAAAGTTGATTGGAAAAAATAAATGGAGAAAAAAATTGAAAC
1 GAAAGTTGATTGG-AAAAATAAATGGAGAAAAAAATTGAAAC
1486537 AAGTAAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 13 0.33
41 13 0.33
42 13 0.33
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (41 bp):
GAAAGTTGATTGGAAAAATAAATGGAGAAAAAAATTGAAAC
Found at i:1486706 original size:16 final size:16
Alignment explanation
Indices: 1486685--1486717 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1486675 AAACATATTA
1486685 CCCATTGCAATTTCAG
1 CCCATTGCAATTTCAG
1486701 CCCATTGCAATTTCAG
1 CCCATTGCAATTTCAG
1486717 C
1 C
1486718 ATTCAGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.30
Consensus pattern (16 bp):
CCCATTGCAATTTCAG
Found at i:1493807 original size:102 final size:103
Alignment explanation
Indices: 1493598--1493807 Score: 277
Period size: 102 Copynumber: 2.1 Consensus size: 103
1493588 CTCATTATTG
* * * *
1493598 TAGTATCTTATACACTCGATTTCATGGAATTAATTTAAATTCATACACGAAATTATAAAATATAT
1 TAGTGTCTTATACACTAGATTTCATGAAATTAATCTAAATTCATACACGAAATTATAAAATATAT
* ** * *
1493663 ATATATAACATATATATTTTAAATTTACTCATTTTTGA
66 ATATATAACATATATATTTTAAATTTACTAACATGTAA
1493701 -AGTGTCTTATACACTAGATTTCATGAAATTAATCTAAATTCATACACGAAA-TA-AAAA-ATAT
1 TAGTGTCTTATACACTAGATTTCATGAAATTAATCTAAATTCATACACGAAATTATAAAATATAT
1493762 ATATATAA-ATATATATTTTAAATTTACTAAAAACATGTAA
66 ATATATAACATATATATTTTAAATTTACT---AACATGTAA
1493802 TAGTGT
1 TAGTGT
1493808 ATGAAGTCGT
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
98 20 0.21
99 12 0.13
100 4 0.04
101 6 0.06
102 52 0.55
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.40
Consensus pattern (103 bp):
TAGTGTCTTATACACTAGATTTCATGAAATTAATCTAAATTCATACACGAAATTATAAAATATAT
ATATATAACATATATATTTTAAATTTACTAACATGTAA
Found at i:1501494 original size:17 final size:17
Alignment explanation
Indices: 1501472--1501504 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1501462 TATAGATTGA
*
1501472 AAAAAAAAAAATAAAGG
1 AAAAAAAAAAAGAAAGG
1501489 AAAAAAAAAAAGAAAG
1 AAAAAAAAAAAGAAAG
1501505 AACGTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAGG
Found at i:1507983 original size:76 final size:76
Alignment explanation
Indices: 1507896--1508051 Score: 303
Period size: 76 Copynumber: 2.1 Consensus size: 76
1507886 CCACATAAGA
1507896 TAAATGAGAACAATTAAATGTGCCTGACATGCTATATAAAACAAGTTTATAATAAAAGCAAACCT
1 TAAATGAGAACAATTAAATGTGCCTGACATGCTATATAAAACAAGTTTATAATAAAAGCAAACCT
1507961 TAAAAAATACG
66 TAAAAAATACG
1507972 TAAATGAGAACAATTAAATGTGCCTGACATGCTATATAAAACAAGTTTATAATAAAAGCAAACCT
1 TAAATGAGAACAATTAAATGTGCCTGACATGCTATATAAAACAAGTTTATAATAAAAGCAAACCT
*
1508037 TAAAAACTACG
66 TAAAAAATACG
1508048 TAAA
1 TAAA
1508052 AGGTTTTCCA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (76 bp):
TAAATGAGAACAATTAAATGTGCCTGACATGCTATATAAAACAAGTTTATAATAAAAGCAAACCT
TAAAAAATACG
Found at i:1512893 original size:6 final size:7
Alignment explanation
Indices: 1512874--1512904 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1512864 TTATCGCATG
1512874 TATTTTT
1 TATTTTT
1512881 TATTTTT
1 TATTTTT
1512888 TATTTTT
1 TATTTTT
1512895 TATTTTT
1 TATTTTT
1512902 TAT
1 TAT
1512905 ATATATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:1513740 original size:2 final size:2
Alignment explanation
Indices: 1513733--1513770 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1513723 TGAAGAGCGT
* *
1513733 AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AC AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1513771 GGAAAGCCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1515985 original size:13 final size:15
Alignment explanation
Indices: 1515956--1515990 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1515946 TGGGTTCAGT
1515956 TTAAAAAAATAATTA
1 TTAAAAAAATAATTA
1515971 TTAAAAAAAT-A-TA
1 TTAAAAAAATAATTA
1515984 TTAAAAA
1 TTAAAAA
1515991 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 1 0.05
15 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAAAATAATTA
Found at i:1516017 original size:25 final size:25
Alignment explanation
Indices: 1515989--1516072 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 25
1515979 ATATATTAAA
1515989 AATTAAATTTTATGTATATAAATTT
1 AATTAAATTTTATGTATATAAATTT
* * *
1516014 AATTAAAAATTAAT-T-T-TTAA---
1 AATT-AAATTTTATGTATATAAATTT
*
1516034 AATTAATTTTTATGTATATAAATTT
1 AATTAAATTTTATGTATATAAATTT
1516059 ACA-TAAATTTTATG
1 A-ATTAAATTTTATG
1516073 CAAATTTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
19 6 0.14
20 5 0.12
21 1 0.02
22 3 0.07
23 3 0.07
24 1 0.02
25 16 0.37
26 8 0.19
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (25 bp):
AATTAAATTTTATGTATATAAATTT
Found at i:1516022 original size:45 final size:44
Alignment explanation
Indices: 1515970--1516059 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
1515960 AAAAATAATT
1515970 ATTAAAAA-AATATATTAAAAATTAAATTTTATGTATATAAATTTA
1 ATTAAAAATAAT-T-TTAAAAATTAAATTTTATGTATATAAATTTA
* *
1516015 ATTAAAAATTAATTTTTAAAATTAATTTTTATGTATATAAATTTA
1 ATTAAAAA-TAATTTTAAAAATTAAATTTTATGTATATAAATTTA
1516060 CATAAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 37 0.90
46 1 0.02
47 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (44 bp):
ATTAAAAATAATTTTAAAAATTAAATTTTATGTATATAAATTTA
Found at i:1516043 original size:12 final size:13
Alignment explanation
Indices: 1516019--1516045 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1516009 AATTTAATTA
1516019 AAAATTAATTTTT
1 AAAATTAATTTTT
1516032 AAAATTAATTTTT
1 AAAATTAATTTTT
1516045 A
1 A
1516046 TGTATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTAATTTTT
Found at i:1520071 original size:54 final size:55
Alignment explanation
Indices: 1519988--1520093 Score: 196
Period size: 54 Copynumber: 1.9 Consensus size: 55
1519978 GCACAATGGT
*
1519988 AATAAAGTTAGTTTTGTTTTCGTGTGTTCATTTTGGGAACCTATTTGTGACATTA
1 AATAAAGTTAGTTTTGTTTTCGTGTGTTCATTTTGGGAACCTAATTGTGACATTA
1520043 AATAAAGTTAG-TTTGTTTTCGTGTGTTCATTTTGGGAACCTAATTGTGACA
1 AATAAAGTTAGTTTTGTTTTCGTGTGTTCATTTTGGGAACCTAATTGTGACA
1520094 CTTATTTGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 39 0.78
55 11 0.22
ACGTcount: A:0.25, C:0.09, G:0.21, T:0.45
Consensus pattern (55 bp):
AATAAAGTTAGTTTTGTTTTCGTGTGTTCATTTTGGGAACCTAATTGTGACATTA
Found at i:1535579 original size:27 final size:28
Alignment explanation
Indices: 1535539--1535591 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1535529 TATTAGTTAA
*
1535539 AAATATGTTATTTA-TAAATTAAATTTT
1 AAATATATTATTTATTAAATTAAATTTT
* *
1535566 AAATATATTTTTTATTAATTTAAATT
1 AAATATATTATTTATTAAATTAAATT
1535592 GATTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
AAATATATTATTTATTAAATTAAATTTT
Found at i:1535634 original size:14 final size:13
Alignment explanation
Indices: 1535607--1535648 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1535597 AAATTATTTA
1535607 ATAATTA-AAAAT
1 ATAATTATAAAAT
**
1535619 ATTTTTATATAAAT
1 ATAATTATA-AAAT
1535633 ATAATTATAAAAT
1 ATAATTATAAAAT
1535646 ATA
1 ATA
1535649 TAAATTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 5 0.21
13 8 0.33
14 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATTATAAAAT
Found at i:1535666 original size:22 final size:21
Alignment explanation
Indices: 1535624--1535698 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
1535614 AAAATATTTT
1535624 TATATAAATATAATTATAAAA
1 TATATAAATATAATTATAAAA
1535645 TATATAAATTATAA-TATAAAA
1 TATATAAA-TATAATTATAAAA
***
1535666 -ATAATTTTTATTAATTAT-AAA
1 TAT-ATAAATA-TAATTATAAAA
1535687 TA-ATAAATATAA
1 TATATAAATATAA
1535699 ATAATTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 3 0.07
20 8 0.19
21 23 0.53
22 9 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATATAAATATAATTATAAAA
Found at i:1535667 original size:49 final size:46
Alignment explanation
Indices: 1535607--1535700 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 46
1535597 AAATTATTTA
1535607 ATAATTAAAAAT-ATTTTTATATAAATATAATTATAA-AATATATAAATT
1 ATAATTAAAAATAATTTTTAT-TAAATATAA--ATAATAA-ATATAAATT
*
1535655 ATAATATAAAAATAATTTTTATTAATTATAAATAATAAATATAAAT
1 ATAAT-TAAAAATAATTTTTATTAAATATAAATAATAAATATAAAT
1535701 AATTTAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
47 12 0.29
48 7 0.17
49 15 0.36
50 8 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (46 bp):
ATAATTAAAAATAATTTTTATTAAATATAAATAATAAATATAAATT
Found at i:1535669 original size:27 final size:27
Alignment explanation
Indices: 1535630--1535711 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
1535620 TTTTTATATA
**
1535630 AATATAATTATAAAATATATAAATTAT
1 AATATAAAAATAAAATATATAAATTAT
** * *
1535657 AATATAAAAATAATTTTTATTAATTAT
1 AATATAAAAATAAAATATATAAATTAT
*
1535684 AA-ATAATAAATATAAATAATTTAAATTA
1 AATATAA-AAATA-AAAT-ATATAAATTA
1535712 ATCTAAATAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
26 4 0.10
27 28 0.68
28 2 0.05
29 7 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATAAAAATAAAATATATAAATTAT
Found at i:1540991 original size:24 final size:21
Alignment explanation
Indices: 1540950--1540992 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
1540940 TTATGAGATT
1540950 CTTAATCTATCTTTTAACTCC
1 CTTAATCTATCTTTTAACTCC
1540971 CTTAATTCTTATCTATTTAACT
1 CTTAA-TC-TATCT-TTTAACT
1540993 TATTTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 5 0.26
24 7 0.37
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (21 bp):
CTTAATCTATCTTTTAACTCC
Found at i:1541163 original size:9 final size:9
Alignment explanation
Indices: 1541144--1541176 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1541134 ATTAGTGGGA
1541144 CTTTCTTTTT
1 CTTT-TTTTT
1541154 CTTTTTTTT
1 CTTTTTTTT
1541163 CTTTTTTTT
1 CTTTTTTTT
1541172 -TTTTT
1 CTTTTT
1541177 AAATTGGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.22
9 14 0.61
10 4 0.17
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:1541165 original size:15 final size:14
Alignment explanation
Indices: 1541145--1541176 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1541135 TTAGTGGGAC
1541145 TTTCTTTTTCTTTTT
1 TTTCTTTTT-TTTTT
1541160 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
1541174 TTT
1 TTT
1541177 AAATTGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:1545436 original size:21 final size:22
Alignment explanation
Indices: 1545412--1545513 Score: 104
Period size: 21 Copynumber: 4.7 Consensus size: 22
1545402 GTTATCAAAT
*
1545412 TTATTAAAATTATAT-TAATAG
1 TTATTAAAATTATATGTAAAAG
*
1545433 TTATAAAAAAATTATATGT-AAAG
1 TTAT--TAAAATTATATGTAAAAG
* * *
1545456 TTATAAAAAATTAT-TGCAAAAA
1 TTAT-TAAAATTATATGTAAAAG
1545478 TTATTAAAATTATAT-TAAAAG
1 TTATTAAAATTATATGTAAAAG
1545499 TTATTAAAATTATAT
1 TTATTAAAATTATAT
1545514 CTAATTTACC
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
21 33 0.48
22 18 0.26
23 17 0.25
24 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (22 bp):
TTATTAAAATTATATGTAAAAG
Found at i:1545488 original size:9 final size:10
Alignment explanation
Indices: 1545398--1545511 Score: 52
Period size: 10 Copynumber: 10.9 Consensus size: 10
1545388 CAATTATATC
1545398 AAAAGTTA-T
1 AAAAGTTATT
* *
1545407 CAAATTTATT
1 AAAAGTTATT
*
1545417 AAAATTATATT
1 AAAAGT-TATT
* *
1545428 AATAGTTATAA
1 AAAAGTTAT-T
*
1545439 AAAAATTATAT
1 AAAAGTTAT-T
* *
1545450 GTAAAGTTATA
1 -AAAAGTTATT
*
1545461 AAAAATTATT
1 AAAAGTTATT
*
1545471 GCAAAAATTATT
1 --AAAAGTTATT
*
1545483 AAAATTATATT
1 AAAAGT-TATT
1545494 AAAAGTTATT
1 AAAAGTTATT
1545504 AAAA-TTAT
1 AAAAGTTAT
1545512 ATCTAATTTA
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
9 10 0.12
10 29 0.36
11 25 0.31
12 17 0.21
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (10 bp):
AAAAGTTATT
Found at i:1545765 original size:21 final size:21
Alignment explanation
Indices: 1545664--1545918 Score: 87
Period size: 21 Copynumber: 12.7 Consensus size: 21
1545654 ATTAAAAGAA
*
1545664 TAAAATTATATTAAATATTAT
1 TAAAATTATATTAAAGATTAT
* * *
1545685 CAAAATCATA--AAGGATTAT
1 TAAAATTATATTAAAGATTAT
* *
1545704 CAAAATTAT-TTCAAGAATTAT
1 TAAAATTATATTAAAG-ATTAT
** * *
1545725 CGAAATGATATCCAAA-ATTAT
1 TAAAATTATAT-TAAAGATTAT
1545746 TAAAATTATATTAAAGATTAT
1 TAAAATTATATTAAAGATTAT
*
1545767 T--AACTATCA--AAAG-TTA-
1 TAAAATTAT-ATTAAAGATTAT
* * * * *
1545783 AAAAACTACTA-CAAAGGTTAC
1 TAAAATTA-TATTAAAGATTAT
* *
1545804 TAAAATTAAATCTAAAG-TTTT
1 TAAAATTATAT-TAAAGATTAT
*
1545825 TAAAATTATATTAAAGATTCT
1 TAAAATTATATTAAAGATTAT
* *
1545846 T--AA--ATATTAAAGGTTAC
1 TAAAATTATATTAAAGATTAT
* *
1545863 AAAAATTAT-TACAAATGA-TAT
1 TAAAATTATAT-TAAA-GATTAT
* *
1545884 TAAAATTATATAAAAAATTAT
1 TAAAATTATATTAAAGATTAT
*
1545905 CAAAATTATATTAA
1 TAAAATTATATTAA
1545919 CGGTTATCAA
Statistics
Matches: 173, Mismatches: 37, Indels: 48
0.67 0.14 0.19
Matches are distributed among these distances:
17 14 0.08
18 10 0.06
19 29 0.17
20 17 0.10
21 94 0.54
22 7 0.04
23 2 0.01
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (21 bp):
TAAAATTATATTAAAGATTAT
Found at i:1545910 original size:80 final size:79
Alignment explanation
Indices: 1545738--1545918 Score: 218
Period size: 80 Copynumber: 2.3 Consensus size: 79
1545728 AATGATATCC
* *
1545738 AAAATTATTAAAATTATATTAAAGATTATTAACTATCAAAAGTTAAAAAACTACTACAAAGGTTA
1 AAAATTATTAAAATTATATTAAAGATTATTAAATATCAAAAGTTAAAAAACTACTACAAAGGATA
**
1545803 CTAAAATTAAATCT
66 CTAAAATTAAATAA
* * * * * * * *
1545817 AAAGTTTTTAAAATTATATTAAAGATTCTTAAATATTAAAGGTTACAAAAATTATTACAAATGAT
1 AAAATTATTAAAATTATATTAAAGATTATTAAATATCAAAAGTTA-AAAAACTACTACAAAGGAT
* *
1545882 ATTAAAATTATATAA
65 ACTAAAATTAAATAA
*
1545897 AAAATTATCAAAATTATATTAA
1 AAAATTATTAAAATTATATTAA
1545919 CGGTTATCAA
Statistics
Matches: 84, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
79 39 0.46
80 45 0.54
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (79 bp):
AAAATTATTAAAATTATATTAAAGATTATTAAATATCAAAAGTTAAAAAACTACTACAAAGGATA
CTAAAATTAAATAA
Found at i:1546119 original size:21 final size:20
Alignment explanation
Indices: 1546095--1546148 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1546085 TGTATCCATG
1546095 ATTATCAAAAT-TAGTTCAAAA
1 ATTATCAAAATATA-TT-AAAA
1546116 ATTATCAAAATCATATTAAAA
1 ATTATCAAAAT-ATATTAAAA
*
1546137 ATTATTAAAATA
1 ATTATCAAAATA
1546149 AAATAATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.83
22 2 0.07
23 2 0.07
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTATCAAAATATATTAAAA
Found at i:1550078 original size:2 final size:2
Alignment explanation
Indices: 1550071--1550099 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1550061 TTTAAGAGGT
1550071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1550100 TTACAGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1554811 original size:12 final size:12
Alignment explanation
Indices: 1554794--1554818 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1554784 GGAATTTGAG
1554794 TCTATCTTTATA
1 TCTATCTTTATA
1554806 TCTATCTTTATA
1 TCTATCTTTATA
1554818 T
1 T
1554819 ATGTAGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TCTATCTTTATA
Found at i:1554910 original size:6 final size:6
Alignment explanation
Indices: 1554901--1554925 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1554891 GTGGGGGTGG
1554901 AGGGAA AGGGAA AGGGAA AGGGAA A
1 AGGGAA AGGGAA AGGGAA AGGGAA A
1554926 AGGCAGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:1555328 original size:2 final size:2
Alignment explanation
Indices: 1555317--1555366 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
1555307 AGGCTTATCA
* * *
1555317 AT AT -T AT AT AT AT AT AT AT AT AT AT AT CT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1555358 AT AG AT AT A
1 AT AT AT AT A
1555367 GACGTAGATG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1558230 original size:14 final size:14
Alignment explanation
Indices: 1558211--1558237 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1558201 TTCTCACATG
1558211 ATATATATACATAC
1 ATATATATACATAC
1558225 ATATATATACATA
1 ATATATATACATA
1558238 TCTTTTCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:1558516 original size:2 final size:2
Alignment explanation
Indices: 1558509--1558537 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1558499 ACAGCTAGGG
1558509 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 A
1558538 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1558542 original size:2 final size:2
Alignment explanation
Indices: 1558537--1558572 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1558527 ATATATATAT
1558537 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1558573 CATGATAAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1560945 original size:17 final size:19
Alignment explanation
Indices: 1560924--1560965 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 19
1560914 TTTTTATATT
1560924 TTTATTATATTTA-AAATA
1 TTTATTATATTTATAAATA
1560942 -TTA-TATATTTATAAATA
1 TTTATTATATTTATAAATA
1560959 TTTATTA
1 TTTATTA
1560966 AGCATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.38
17 8 0.38
18 3 0.14
19 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATTATATTTATAAATA
Found at i:1562047 original size:23 final size:23
Alignment explanation
Indices: 1562014--1562082 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
1562004 TTATATTTAA
*
1562014 TAATTAAAAAAATTATTTAAATT
1 TAATTATAAAAATTATTTAAATT
*
1562037 TAATTAT-AAAA-TATATAAATTT
1 TAATTATAAAAATTATTTAAA-TT
* *
1562059 TAA-TATAAAATATAATTTTAATT
1 TAATTATAAAA-ATTATTTAAATT
1562082 T
1 T
1562083 CTTATTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 10 0.27
22 12 0.32
23 10 0.27
24 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTATAAAAATTATTTAAATT
Found at i:1562057 original size:21 final size:21
Alignment explanation
Indices: 1562022--1562072 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1562012 AATAATTAAA
*
1562022 AAAATTATTTAAA-TTTAATTAT
1 AAAA-TATATAAATTTTAA-TAT
1562044 AAAATATATAAATTTTAATAT
1 AAAATATATAAATTTTAATAT
1562065 AAAATATA
1 AAAATATA
1562073 ATTTTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATATATAAATTTTAATAT
Found at i:1562322 original size:34 final size:34
Alignment explanation
Indices: 1562284--1562375 Score: 120
Period size: 32 Copynumber: 2.8 Consensus size: 34
1562274 AATAATTAAA
*
1562284 ATATAATATAATATAAATATATATTTTAAAATTT
1 ATATAATATAATATAAATATATATATTAAAATTT
1562318 ATATAATATTAAT-T-AATA-ATATATTAAAATTT
1 ATATAATA-TAATATAAATATATATATTAAAATTT
*
1562350 ATATAA-ATATTATAAATATAATATAT
1 ATATAATATAATATAAATAT-ATATAT
1562376 AAATAAGAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
30 3 0.06
31 2 0.04
32 23 0.45
33 4 0.08
34 15 0.29
35 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATAATATAATATAAATATATATATTAAAATTT
Found at i:1563102 original size:21 final size:21
Alignment explanation
Indices: 1563042--1563108 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
1563032 TTTAAAACAT
* * *
1563042 TTTTTATATATTAATATATAAA
1 TTTTAATAAATTAATA-ATATA
*
1563064 TTTTAATAAATTAATAATTTA
1 TTTTAATAAATTAATAATATA
*
1563085 TTTTATATAAATT-TTAATATA
1 TTTTA-ATAAATTAATAATATA
1563106 TTT
1 TTT
1563109 ATGTGTTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 17 0.45
22 21 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAATAAATTAATAATATA
Found at i:1563156 original size:28 final size:28
Alignment explanation
Indices: 1563117--1563182 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
1563107 TTATGTGTTA
*
1563117 ATATTAATATTACTTCTTAAAT-ATATTAT
1 ATATT-ATATTACTTCTTAAATCATAAT-T
* * *
1563146 ATATTATATTATTTTTTATATCATAATT
1 ATATTATATTACTTCTTAAATCATAATT
1563174 ATATTATAT
1 ATATTATAT
1563183 AATCATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 23 0.72
29 9 0.28
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTATATTACTTCTTAAATCATAATT
Found at i:1565952 original size:3 final size:3
Alignment explanation
Indices: 1565944--1565970 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1565934 TCCTTTGTAA
1565944 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1565971 GGCATGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1577025 original size:27 final size:27
Alignment explanation
Indices: 1576973--1577028 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1576963 AGCTTAAGTT
**
1576973 TTGTTTTGCAACAATCGTTTGTGACTG
1 TTGTTTTGCAACAATCGTTTCAGACTG
*
1577000 TTGTTTTGCAACAAT-TTCTTCAGACTG
1 TTGTTTTGCAACAATCGT-TTCAGACTG
1577027 TT
1 TT
1577029 TACCACTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (27 bp):
TTGTTTTGCAACAATCGTTTCAGACTG
Found at i:1580236 original size:3 final size:3
Alignment explanation
Indices: 1580228--1580259 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1580218 TTGCAAAAAC
1580228 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1580260 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1580264 original size:4 final size:4
Alignment explanation
Indices: 1580255--1580280 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1580245 TAATAATAAT
1580255 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
1580281 AGAAATAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1581055 original size:11 final size:11
Alignment explanation
Indices: 1581020--1581064 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1581010 ATATTAAATA
1581020 TTTTTATATTT
1 TTTTTATATTT
* *
1581031 TATTTAAATATT
1 TTTTTATAT-TT
1581043 TTTTTATATTT
1 TTTTTATATTT
*
1581054 TTTTCATATTT
1 TTTTTATATTT
1581065 AAACATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:1581064 original size:21 final size:23
Alignment explanation
Indices: 1581013--1581054 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1581003 TAATTAAATA
1581013 TTAAATA--TTTTTATATTTTAT
1 TTAAATATTTTTTTATATTTTAT
1581034 TTAAATATTTTTTTATATTTT
1 TTAAATATTTTTTTATATTTT
1581055 TTTCATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTAAATATTTTTTTATATTTTAT
Found at i:1581075 original size:29 final size:29
Alignment explanation
Indices: 1581022--1581106 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
1581012 ATTAAATATT
*
1581022 TTTATATTT-TATTTAAATATTTTTTTATA
1 TTTA-ATTTATATTTAAATATATTTTTATA
* *
1581051 TTT-TTTTCATATTTAAACATATTTTTATA
1 TTTAATTT-ATATTTAAATATATTTTTATA
*
1581080 TTTAATTTATATTTAAATAAATTTTTA
1 TTTAATTTATATTTAAATATATTTTTA
1581107 AAAATAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.06
29 41 0.87
30 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTAATTTATATTTAAATATATTTTTATA
Found at i:1581244 original size:20 final size:20
Alignment explanation
Indices: 1581194--1581259 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1581184 TTTAAAATTT
*
1581194 AAATTATTAT-TTAATAATAA
1 AAATAATTATATTAAT-ATAA
*
1581214 AAA-ATATTAT-TT-ATTTAA
1 AAATA-ATTATATTAATATAA
*
1581232 AATTAATTATATTAATATAA
1 AAATAATTATATTAATATAA
1581252 AAATAATT
1 AAATAATT
1581260 TAATTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 10 0.27
19 5 0.14
20 22 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATTATATTAATATAA
Found at i:1581306 original size:29 final size:29
Alignment explanation
Indices: 1581247--1581316 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
1581237 ATTATATTAA
* * *
1581247 TATAAAAATAATTTAATTTTTTATTAATT
1 TATAAAAAAAATTTAAGTTTTTATGAATT
*
1581276 TATAAATAAAAATTTAAGTTTTT-TGACTT
1 TATAAA-AAAAATTTAAGTTTTTATGAATT
*
1581305 TA-ACAAAAAATT
1 TATAAAAAAAATT
1581317 AAAAAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 7 0.20
28 2 0.06
29 12 0.34
30 14 0.40
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (29 bp):
TATAAAAAAAATTTAAGTTTTTATGAATT
Found at i:1581385 original size:24 final size:24
Alignment explanation
Indices: 1581344--1581394 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1581334 TGATAAATAA
* **
1581344 ATATTTTTATTTGTATTAAAAAAT
1 ATATTTATATTTAAATTAAAAAAT
* *
1581368 ATATTTATATTTAAATTATAAATT
1 ATATTTATATTTAAATTAAAAAAT
1581392 ATA
1 ATA
1581395 ATTTTTTTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATTTATATTTAAATTAAAAAAT
Done.