Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold355
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: 482196
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.32
Warning! 38188 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:239625 original size:51 final size:51
Alignment explanation
Indices: 239569--239672 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
239559 TTATCTCAAC
* ** *
239569 TTTAAGGTGATAATTTGGTATAAAAATTTATTGTGACAAGTCACTTTTCCA
1 TTTAAGGTGATAAATTGGTATAAAAATTTAACGTGACAAGTCACTTCTCCA
*
239620 TTTAAGGTGATAAATTGGTATAAAAATTTAACGTGACAATTCACTTCTCCA
1 TTTAAGGTGATAAATTGGTATAAAAATTTAACGTGACAAGTCACTTCTCCA
239671 TT
1 TT
239673 AAATTTAGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (51 bp):
TTTAAGGTGATAAATTGGTATAAAAATTTAACGTGACAAGTCACTTCTCCA
Found at i:240201 original size:14 final size:14
Alignment explanation
Indices: 240164--240201 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
240154 TTTTTGTGTA
240164 ATAAATAATACAAC
1 ATAAATAATACAAC
*
240178 ATAAAAAATA-AAC
1 ATAAATAATACAAC
240191 ATAATATAATA
1 ATAA-ATAATA
240202 TATTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAATAATACAAC
Found at i:249501 original size:19 final size:18
Alignment explanation
Indices: 249477--249527 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
249467 TTCTTCAATA
*
249477 TTTATAATTTTATAATTTT
1 TTTATAATTTTATAA-ATT
249496 TTTATAATTTTCATAAATT
1 TTTATAATTTT-ATAAATT
*
249515 TTTATAGTTTTAT
1 TTTATAATTTTAT
249528 TATTAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 23 0.79
20 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATAATTTTATAAATT
Found at i:249584 original size:26 final size:26
Alignment explanation
Indices: 249555--249636 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
249545 TAATATATTT
249555 ATGATTTTTAAATAATCAAGCACAGA
1 ATGATTTTTAAATAATCAAGCACAGA
** * ** ***
249581 ATGA-ACTTAGAATATATTAATTATTTA
1 ATGATTTTTA-AATA-ATCAAGCACAGA
249608 -TGATTTTTAAATAATCAAGCACAGA
1 ATGATTTTTAAATAATCAAGCACAGA
249633 ATGA
1 ATGA
249637 ACTTAGACTA
Statistics
Matches: 36, Mismatches: 16, Indels: 8
0.60 0.27 0.13
Matches are distributed among these distances:
25 9 0.25
26 18 0.50
27 9 0.25
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (26 bp):
ATGATTTTTAAATAATCAAGCACAGA
Found at i:249612 original size:52 final size:53
Alignment explanation
Indices: 249538--249643 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
249528 TATTAATATT
249538 AATATATTAATATATTTATGATTTTTAAATAATCAAGCACAGAATGAACTTAG
1 AATATATTAATATATTTATGATTTTTAAATAATCAAGCACAGAATGAACTTAG
249591 AATATATTAAT-TATTTATGATTTTTAAATAATCAAGCACAGAATGAACTTAG
1 AATATATTAATATATTTATGATTTTTAAATAATCAAGCACAGAATGAACTTAG
249643 A
1 A
249644 CTAATAATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 42 0.79
53 11 0.21
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (53 bp):
AATATATTAATATATTTATGATTTTTAAATAATCAAGCACAGAATGAACTTAG
Found at i:253679 original size:20 final size:20
Alignment explanation
Indices: 253644--253706 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
253634 CTAAATATTT
253644 TATAGTTAAAAT-TTATTAAA
1 TATA-TTAAAATATTATTAAA
*
253664 TAT-TTATAAATATTATTCATA
1 TATATTA-AAATATTATT-AAA
253685 TATATTAAATATATT-TTAAA
1 TATATTAAA-ATATTATTAAA
253705 TA
1 TA
253707 CTATATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 12 0.33
21 9 0.25
22 8 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATTAAAATATTATTAAA
Found at i:253723 original size:12 final size:11
Alignment explanation
Indices: 253644--253716 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
253634 CTAAATATTT
253644 TATAGTTAAA-A
1 TATA-TTAAATA
*
253655 TTTATTAAATA
1 TATATTAAATA
*
253666 TTTA-TAAATA
1 TATATTAAATA
*
253676 T-TATT-CATA
1 TATATTAAATA
253685 TATATTAAATA
1 TATATTAAATA
*
253696 TATTTTAAATA
1 TATATTAAATA
253707 CTATATTAAA
1 -TATATTAAA
253717 AATTATACAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
9 6 0.12
10 17 0.33
11 21 0.40
12 8 0.15
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (11 bp):
TATATTAAATA
Found at i:256129 original size:31 final size:31
Alignment explanation
Indices: 256091--256159 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
256081 CTAATATGGA
* *
256091 TAAATTTGTTAA-AAGTTTTTATGAACTTTTT
1 TAAATTTGCTAATAACTTTTTATGAA-TTTTT
* *
256122 TAAATTTGCTAATTACTTTTTATTAATTTTT
1 TAAATTTGCTAATAACTTTTTATGAATTTTT
256153 TAAATTT
1 TAAATTT
256160 TTATGAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (31 bp):
TAAATTTGCTAATAACTTTTTATGAATTTTT
Found at i:259404 original size:20 final size:21
Alignment explanation
Indices: 259367--259405 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
259357 CCATGTGTAC
* *
259367 TTGATTTTTTTATATTTATAT
1 TTGAATTTTTAATATTTATAT
259388 TTGAATTTTTAAT-TTTAT
1 TTGAATTTTTAATATTTAT
259406 GAATATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
TTGAATTTTTAATATTTATAT
Found at i:259598 original size:13 final size:15
Alignment explanation
Indices: 259574--259611 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
259564 AACTAATAAT
*
259574 AAATTTAATTTA-AA
1 AAATATAATTTACAA
259588 AAATA-AATTTACAA
1 AAATATAATTTACAA
259602 AAATATAATT
1 AAATATAATT
259612 ATCCTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 6 0.29
14 11 0.52
15 4 0.19
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATAATTTACAA
Found at i:262247 original size:21 final size:21
Alignment explanation
Indices: 262223--262263 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
262213 GAGCTTCTGT
262223 TTAACTCAT-ATGAGTTTCCGA
1 TTAAC-CATAATGAGTTTCCGA
*
262244 TTAACCTTAATGAGTTTCCG
1 TTAACCATAATGAGTTTCCG
262264 TTCATCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (21 bp):
TTAACCATAATGAGTTTCCGA
Found at i:262726 original size:9 final size:9
Alignment explanation
Indices: 262703--262746 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
262693 CAATAAATTA
*
262703 TCAATTGAT
1 TCAATTTAT
*
262712 TAAATTT-T
1 TCAATTTAT
262720 TACAATTTAT
1 T-CAATTTAT
262730 TCAATTTAT
1 TCAATTTAT
262739 TCAATTTA
1 TCAATTTA
262747 GTTCCTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 2 0.07
9 26 0.87
10 2 0.07
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (9 bp):
TCAATTTAT
Found at i:270133 original size:16 final size:16
Alignment explanation
Indices: 270112--270145 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
270102 TACTATTTAC
270112 AAAATAATATTATATT
1 AAAATAATATTATATT
* *
270128 AAAATATTTTTATATT
1 AAAATAATATTATATT
270144 AA
1 AA
270146 TATTTATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATAATATTATATT
Found at i:281258 original size:29 final size:30
Alignment explanation
Indices: 281217--281275 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
281207 GAATTGGACC
* *
281217 AAATCAAAATTTCATATATAAAATTACACA
1 AAATCAAAATTTCACATAGAAAATTACACA
*
281247 AAATC-AAATTTCACATAGAGAATTACACA
1 AAATCAAAATTTCACATAGAAAATTACACA
281276 TTAAACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATCAAAATTTCACATAGAAAATTACACA
Found at i:283498 original size:5 final size:5
Alignment explanation
Indices: 283490--283546 Score: 60
Period size: 5 Copynumber: 10.6 Consensus size: 5
283480 ACTTTTTATT
*
283490 TTTCA TTTCA TTTCA TTTTTA TTTCCA TTTCA TTTCA TTTACA TTTCTA
1 TTTCA TTTCA TTTCA -TTTCA TTT-CA TTTCA TTTCA TTT-CA TTTC-A
*
283539 TTCCA TTT
1 TTTCA TTT
283547 AAATAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 27 0.61
6 17 0.39
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:283518 original size:22 final size:23
Alignment explanation
Indices: 283482--283529 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
283472 TCCTTTCAAC
*
283482 TTTTTATTTTTCATTTCATTTCA
1 TTTTTATTTTCCATTTCATTTCA
283505 TTTTTA-TTTCCATTTCATTTCA
1 TTTTTATTTTCCATTTCATTTCA
283527 TTT
1 TTT
283530 ACATTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTTATTTTCCATTTCATTTCA
Found at i:283523 original size:27 final size:27
Alignment explanation
Indices: 283490--283546 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
283480 ACTTTTTATT
*
283490 TTTCATTTCATTT-CATTTTTATTTCCA
1 TTTCATTTCATTTACATTTCTA-TTCCA
283517 TTTCATTTCATTTACATTTCTATTCCA
1 TTTCATTTCATTTACATTTCTATTCCA
283544 TTT
1 TTT
283547 AAATAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTCATTTCATTTACATTTCTATTCCA
Found at i:283524 original size:11 final size:10
Alignment explanation
Indices: 283490--283546 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 10
283480 ACTTTTTATT
283490 TTTCATTTCA
1 TTTCATTTCA
*
283500 TTTCATTTTTA
1 TTTCA-TTTCA
283511 TTTCCATTTCA
1 TTT-CATTTCA
283522 TTTCATTTACA
1 TTTCATTT-CA
*
283533 TTTCTATTCCA
1 TTTC-ATTTCA
283544 TTT
1 TTT
283547 AAATAATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 10 0.25
11 25 0.62
12 5 0.12
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTCATTTCA
Found at i:283535 original size:22 final size:22
Alignment explanation
Indices: 283493--283546 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
283483 TTTTATTTTT
**
283493 CATTTCATTTCATTTTTATTTC
1 CATTTCATTTCATTTACATTTC
283515 CATTTCATTTCATTTACATTTC
1 CATTTCATTTCATTTACATTTC
* *
283537 TATTCCATTT
1 CATTTCATTT
283547 AAATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.59
Consensus pattern (22 bp):
CATTTCATTTCATTTACATTTC
Found at i:283616 original size:18 final size:17
Alignment explanation
Indices: 283553--283627 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 17
283543 ATTTAAATAA
* *
283553 TTTTTTTCCATTTAAAT
1 TTTTTTTTCATTTCAAT
283570 TTAATTATTTCTCATTTCAAT
1 TT--TT-TTT-TCATTTCAAT
*
283591 TTTTTTTTCATTTCAGT
1 TTTTTTTTCATTTCAAT
283608 TTTTGTTTTCATTTCAAT
1 TTTT-TTTTCATTTCAAT
283626 TT
1 TT
283628 ATAATTTACT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
17 15 0.31
18 17 0.35
19 4 0.08
20 3 0.06
21 10 0.20
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTTTTTTCATTTCAAT
Found at i:284118 original size:5 final size:5
Alignment explanation
Indices: 284095--284170 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
284085 TTTTTTTTTT
* * * *
284095 TTTCAA TTTTA TTTCCA TTTCA TTTCA TTTC- TTCCA TTTCA TTCCA TTTGTA
1 TTTC-A TTTCA TTT-CA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTT-CA
*
284147 TTTCCA TTTAA TTTCA TTTCA TTT
1 TTT-CA TTTCA TTTCA TTTCA TTT
284171 AAATTATCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
4 3 0.05
5 38 0.68
6 15 0.27
ACGTcount: A:0.20, C:0.20, G:0.01, T:0.59
Consensus pattern (5 bp):
TTTCA
Found at i:284190 original size:21 final size:21
Alignment explanation
Indices: 284166--284354 Score: 89
Period size: 21 Copynumber: 8.2 Consensus size: 21
284156 AATTTCATTT
*
284166 CATTTAAATTATCTTTTTTTC
1 CATTTAAATTATATTTTTTTC
284187 CATTTAAATT-TAATTTTTTTC
1 CATTTAAATTAT-ATTTTTTTC
* *
284208 TCATTTTATTTAAATTATTTTTTTC
1 -CATTTAAATT--A-TATTTTTTTC
284233 CATTTAAATT-TAATTTTTTTCTC
1 CATTTAAATTAT-A-TTTTTT-TC
* * *
284256 ATTTCATTTAAATTATCTTTCTTCC
1 ----CATTTAAATTATATTTTTTTC
*
284281 CATTTTAATT-TAATTTTTTTCTC
1 CATTTAAATTAT-A-TTTTTT-TC
*
284304 ATTTCATTTAAATTATCTTTTTTTTC
1 ----CATTTAAATTAT-ATTTTTTTC
*
284330 CATTTAAATT-TATTTTTTCC
1 CATTTAAATTATATTTTTTTC
284350 CATTT
1 CATTT
284355 CACTTAAATT
Statistics
Matches: 129, Mismatches: 17, Indels: 45
0.68 0.09 0.24
Matches are distributed among these distances:
20 15 0.12
21 29 0.22
22 29 0.22
23 3 0.02
24 8 0.06
25 10 0.08
26 8 0.06
27 25 0.19
28 2 0.02
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.62
Consensus pattern (21 bp):
CATTTAAATTATATTTTTTTC
Found at i:284212 original size:94 final size:89
Alignment explanation
Indices: 284158--284423 Score: 327
Period size: 94 Copynumber: 2.8 Consensus size: 89
284148 TTCCATTTAA
* *
284158 TTTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTCTCATTTTATTTAAAT
1 TTTCATTTCATTTAAATTATCTTTCTTTCCATTT-AATTTAATTTTTTTCTCATTTCATTT-AAT
284223 T-ATTTTTTTCCATTTAAATTTAATTTTT
64 TCATTTTTTTCCATTTAAATTT-A--TTT
*
284251 TTCTCATTTCATTTAAATTATCTTTCTTCCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAA
1 TT-TCATTTCATTTAAATTATCTTTCTTTCCA-TTTAATTTAATTTTTTTCTCATTTCATTT-AA
*
284316 TTATCTTTTTTTTCCATTTAAATTTATTT
63 -T-TCATTTTTTTCCATTTAAATTTATTT
* *
284345 TTTCCCATTTCACTTAAATTATCTTTCTTTCCATTCTAATTTAATTTTTTTCTCATTTCATCTAA
1 TTT--CATTTCATTTAAATTATCTTTCTTTCCATT-TAATTTAATTTTTTTCTCATTTCAT-TTA
*
284410 ATTTCATTCTTTTC
62 A-TTCATTTTTTTC
284424 TTTTCATTTA
Statistics
Matches: 155, Mismatches: 9, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
93 3 0.02
94 71 0.46
95 59 0.38
96 3 0.02
97 19 0.12
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (89 bp):
TTTCATTTCATTTAAATTATCTTTCTTTCCATTTAATTTAATTTTTTTCTCATTTCATTTAATTC
ATTTTTTTCCATTTAAATTTATTT
Found at i:284213 original size:48 final size:48
Alignment explanation
Indices: 284160--284453 Score: 386
Period size: 48 Copynumber: 6.1 Consensus size: 48
284150 CCATTTAATT
284160 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
*
284208 TCATTTTATTTAAATTA--TTTTTTTCCATTTAAATTTAATTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
* * *
284254 TCATTTCATTTAAATTATCTTTCTTCCCATTTTAATTTAATTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
284302 TCATTTCATTTAAATTATCTTTTTTTTCCATTTAAATTT-A-TTTTTTC
1 TCATTTCATTTAAATTATC-TTTTTTTCCATTTAAATTTAATTTTTTTC
* * *
284349 CCATTTCACTTAAATTATCTTTCTTTCCATTCT-AATTTAATTTTTTTC
1 TCATTTCATTTAAATTATCTTTTTTTCCATT-TAAATTTAATTTTTTTC
* * *
284397 TCATTTCATCTAAATTTCATTCTTTTCTTTTCATTTAAA-TTAACTTTCTTTC
1 TCATTTCATTTAAA-TT-A-TCTTTT-TTTCCATTTAAATTTAA-TTTTTTTC
284449 -CATTT
1 TCATTT
284454 TAATTTACGT
Statistics
Matches: 217, Mismatches: 17, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
46 61 0.28
47 26 0.12
48 80 0.37
49 18 0.08
50 1 0.00
51 15 0.07
52 16 0.07
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (48 bp):
TCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTC
Found at i:284362 original size:95 final size:97
Alignment explanation
Indices: 284161--284453 Score: 404
Period size: 95 Copynumber: 3.1 Consensus size: 97
284151 CATTTAATTT
* * *
284161 CATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAATTTTTTTCTCATTTTATTTAAATTA-
1 CATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTAT
*
284225 --TTTTTTTCCATTTAAATTTAATTTTTTTCT
66 CTTTTTTTTCCATTTAAATTTAATTTTTTTCC
*
284255 CATTTCATTTAAATTATCTTTCTTCCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTAT
1 CATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTAT
284320 CTTTTTTTTCCATTTAAATTT-A-TTTTTTCC
66 CTTTTTTTTCCATTTAAATTTAATTTTTTTCC
* * *
284350 CATTTCACTTAAATTATCTTTCTTTCCATTCTAATTTAATTTTTTTCTCATTTCATCTAAATTTC
1 CATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAA-TT-
*
284415 ATTCTTTTCTTTT-CATTTAAA-TTAACTTTCTTT-C
64 A-TCTTTT-TTTTCCATTTAAATTTAA-TTTTTTTCC
284449 CATTT
1 CATTT
284454 TAATTTACGT
Statistics
Matches: 179, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
94 60 0.34
95 64 0.36
96 3 0.02
97 22 0.12
98 15 0.08
99 10 0.06
100 5 0.03
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (97 bp):
CATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTAT
CTTTTTTTTCCATTTAAATTTAATTTTTTTCC
Found at i:284412 original size:22 final size:22
Alignment explanation
Indices: 284160--284437 Score: 138
Period size: 22 Copynumber: 11.7 Consensus size: 22
284150 CCATTTAATT
*
284160 TCATTTCATTTAAATTATCTTTTTT
1 TCATTTCATTTAAA-T-T-TTTTTC
*
284185 TCCATTTAAATTT-AATTTTTTTC
1 T-CATTT-CATTTAAATTTTTTTC
* *
284208 TCATTTTATTTAAATTATTTTTT
1 TCATTTCATTTAAATT-TTTTTC
*
284231 TCCATTTAAATTT-AATTTTTTTC
1 T-CATTT-CATTTAAATTTTTTTC
284254 TCATTTCATTTAAATTATCTTTCTTC
1 TCATTTCATTTAAA-T-T-TTT-TTC
* *
284280 CCATTTTAATTT-AATTTTTTTC
1 TCA-TTTCATTTAAATTTTTTTC
284302 TCATTTCATTTAAATTATCTTTT-
1 TCATTTCATTTAAATT-T-TTTTC
284325 T--TTTCCATTTAAATTTATTTTTTC
1 TCATTT-CATTTAAA--T-TTTTTTC
* * *
284349 CCATTTCACTTAAATTATCTTTCTT
1 TCATTTCATTTAAATT-T-TTT-TC
*
284374 TCCATTCTAATTT-AATTTTTTTC
1 T-CATT-TCATTTAAATTTTTTTC
* *
284397 TCATTTCATCTAAATTTCATTCTTT
1 TCATTTCATTTAAATTT--TT-TTC
*
284422 TCTTTTCATTTAAATT
1 TCATTTCATTTAAATT
284438 AACTTTCTTT
Statistics
Matches: 199, Mismatches: 23, Indels: 62
0.70 0.08 0.22
Matches are distributed among these distances:
21 22 0.11
22 43 0.22
23 32 0.16
24 26 0.13
25 36 0.18
26 25 0.13
27 15 0.08
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (22 bp):
TCATTTCATTTAAATTTTTTTC
Found at i:284429 original size:73 final size:72
Alignment explanation
Indices: 284187--284460 Score: 217
Period size: 73 Copynumber: 3.8 Consensus size: 72
284177 TCTTTTTTTC
* * * *
284187 CATTTAAATTTAATTTTTTTCTCATTTTATTTAAATTAT-TTT-TTTCCATTTAAATTTAATTTT
1 CATTTAAATTTCATTCTTTTCT--TTTCAATTAAATTATCTTTCTTTCCATTT-AATTTAATTTT
284250 TTTCTCATTT
63 TTTCTCATTT
* ** * * * * *
284260 CATTTAAATTATCTTTCTTCCCATTTT-AATTTAATT-TTTTTCTCATTTCATTTAAATT-ATCT
1 CATTTAAATT-TCATTCTTTTC-TTTTCAATTAAATTATCTTTCT--TTCCATTTAATTTAATTT
*
284322 TTTT-T--TTC
62 TTTTCTCATTT
* *
284330 CATTTAAATTT-ATT-TTTTCCCATTTCACTTAAATTATCTTTCTTTCCATTCTAATTTAATTTT
1 CATTTAAATTTCATTCTTTT--CTTTTCAATTAAATTATCTTTCTTTCCATT-TAATTTAATTTT
284393 TTTCTCATTT
63 TTTCTCATTT
* * *
284403 CATCTAAATTTCATTCTTTTCTTTTCATTTAAATTAACTTTCTTTCCATTTTAATTTA
1 CATTTAAATTTCATTCTTTTCTTTTCAATTAAATTATCTTTCTTTCCA-TTTAATTTA
284461 CGTTTATTAC
Statistics
Matches: 157, Mismatches: 26, Indels: 36
0.72 0.12 0.16
Matches are distributed among these distances:
67 2 0.01
68 11 0.07
69 14 0.09
70 25 0.16
71 2 0.01
72 11 0.07
73 65 0.41
74 15 0.10
75 12 0.08
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (72 bp):
CATTTAAATTTCATTCTTTTCTTTTCAATTAAATTATCTTTCTTTCCATTTAATTTAATTTTTTT
CTCATTT
Found at i:284448 original size:25 final size:25
Alignment explanation
Indices: 284366--284448 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
284356 ACTTAAATTA
* *
284366 TCTTTCTTTCCATTCTAATTTAA-TT
1 TCTTTCTTTTCATT-TAAATTAACTT
* * * *
284391 TTTTTCTCATTTCATCTAAATT-TCAT
1 TCTTTCT--TTTCATTTAAATTAACTT
284417 TCTTTTCTTTTCATTTAAATTAACTT
1 TC-TTTCTTTTCATTTAAATTAACTT
284443 TCTTTC
1 TCTTTC
284449 CATTTTAATT
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
25 22 0.51
26 11 0.26
27 10 0.23
ACGTcount: A:0.20, C:0.19, G:0.00, T:0.60
Consensus pattern (25 bp):
TCTTTCTTTTCATTTAAATTAACTT
Found at i:287568 original size:16 final size:16
Alignment explanation
Indices: 287547--287578 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
287537 AAATTTGGAA
287547 GTCAAATATTTTTTTT
1 GTCAAATATTTTTTTT
287563 GTCAAATATTTTTTTT
1 GTCAAATATTTTTTTT
287579 AAATGACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
GTCAAATATTTTTTTT
Found at i:287811 original size:122 final size:123
Alignment explanation
Indices: 287571--287814 Score: 300
Period size: 122 Copynumber: 2.0 Consensus size: 123
287561 TTGTCAAATA
*
287571 TTTTTTTTAAATGACACTGGTGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAATGCATTAGGAG
1 TTTTTTTTAAATGACACTGGTGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAATACATTAGGAG
* * * ** * *
287636 CCGAAAATTGTACTTGATGCTGGTTATCTACTGGCTATCACCCAAAATATTTTTTTTC
66 CCAAAAATTGTACCTGATGCCGGCCATCTACTGGCCAGCACCCAAAATATTTTTTTTC
* *
287694 TTTTTTTTAAAT-ACACTGGTGCCGGCCATCAGTGTCCCAAAGTAAAAAAAAAATTTACCTT-GG
1 TTTTTTTTAAATGACACTGGTGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAA--TACATTAGG
* * *
287757 GGACCAAAAATAT-TACCTGGTGCCGGCCATCTATTGGCCAGCA-CCAAAAT-TTTTTTTT
64 AG-CCAAAAAT-TGTACCTGATGCCGGCCATCTACTGGCCAGCACCCAAAATATTTTTTTT
287815 ATTAAATATA
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
122 48 0.46
123 22 0.21
124 33 0.32
125 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (123 bp):
TTTTTTTTAAATGACACTGGTGCCGACCATCAGTGTCCCAAAGTAAAAAAAAAATACATTAGGAG
CCAAAAATTGTACCTGATGCCGGCCATCTACTGGCCAGCACCCAAAATATTTTTTTTC
Found at i:288015 original size:107 final size:106
Alignment explanation
Indices: 287826--288128 Score: 374
Period size: 107 Copynumber: 2.8 Consensus size: 106
287816 TTAAATATAT
*
287826 TTGGTGCC-AGCCATTACATGGCCAGCACCTAAATTTTTTTTTAAATATACTGGTGTCAAGCATC
1 TTGGTGCCGA-CCATTACATGGCCAGCACC-AAATTTTTTTTTAAATAT-CTGGTG-CCAGCATC
* * *
287890 AGTGTTCCAAAATTAAAAAAATACATTGGGAGCCGGAAATTGTAC
62 AGTGTTCCAAAATAAAAAAAATACATTGAGAGCCGAAAATTGTAC
* *
287935 TTGGTGCCGACCATTACATGGCCATCACCAAATTTTATTTTAAATATCTGGTGCCAGCCATCAGT
1 TTGGTGCCGACCATTACATGGCCAGCACCAAATTTTTTTTTAAATATCTGGTGCCAG-CATCAGT
* *
288000 GTTTCAAAATAAAAAAAATGCATTGAGAGCCGAAAATTGTAC
65 GTTCCAAAATAAAAAAAATACATTGAGAGCCGAAAATTGTAC
* * * *
288042 CTGGTGCCGGCCATTACATGGCCAGCACCCAATTTTTTTTTTTTAAATACACTGGTGCCAGTCAT
1 TTGGTGCCGACCATTACATGGCCAGCA-CCAA--ATTTTTTTTTAAATA-TCTGGTGCCAG-CAT
* * *
288107 CAATGTCCCAAAGTAAAAAAAA
61 CAGTGTTCCAAAATAAAAAAAA
288129 AATGTGGCTT
Statistics
Matches: 169, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
106 3 0.02
107 74 0.44
108 21 0.12
109 26 0.15
110 14 0.08
111 31 0.18
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (106 bp):
TTGGTGCCGACCATTACATGGCCAGCACCAAATTTTTTTTTAAATATCTGGTGCCAGCATCAGTG
TTCCAAAATAAAAAAAATACATTGAGAGCCGAAAATTGTAC
Found at i:294775 original size:22 final size:21
Alignment explanation
Indices: 294735--294788 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
294725 ATACTTTTAA
*
294735 TTTTAA-AATTACATTATATT
1 TTTTAATAATTAAATTATATT
294755 TTTTAATAAGTTAAATTATATT
1 TTTTAATAA-TTAAATTATATT
*
294777 TTTTTATAATTA
1 TTTTAATAATTA
294789 GATCCTTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 6 0.20
21 5 0.17
22 19 0.63
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAATAATTAAATTATATT
Found at i:295674 original size:16 final size:17
Alignment explanation
Indices: 295644--295676 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
295634 ATTACTATAA
295644 TTAAAAAATATAATATT
1 TTAAAAAATATAATATT
295661 TTAAAAAATA-AATATT
1 TTAAAAAATATAATATT
295677 AAATGTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAATATAATATT
Found at i:296086 original size:44 final size:46
Alignment explanation
Indices: 296021--296108 Score: 105
Period size: 44 Copynumber: 2.0 Consensus size: 46
296011 TAAAATATAT
*
296021 TTTATTCAAATTTTCTTAAA-TTA-TTGAA-TGTATTTCATTTTACC
1 TTTATTCAAATTTTCTTAAATTTATTTGAATTGAATTTC-TTTTACC
296065 TTTATTC-AATTTT-TTAAAAATTTATTTGAATTGAATTTCTTTTA
1 TTTATTCAAATTTTCTT--AAATTTATTTGAATTGAATTTCTTTTA
296109 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
42 2 0.05
43 6 0.16
44 10 0.26
45 3 0.08
46 10 0.26
47 7 0.18
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.57
Consensus pattern (46 bp):
TTTATTCAAATTTTCTTAAATTTATTTGAATTGAATTTCTTTTACC
Found at i:298220 original size:32 final size:34
Alignment explanation
Indices: 298177--298268 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 34
298167 ATCCCAATTT
* *
298177 TAAATAATTTCAAAGAAAT-A-TATAAAAATACA
1 TAAATATTTTCAAAGAAATAATTATAAAAATAAA
*
298209 TAAATATTTTCAAATATAGATAATTATAAAAATAAA
1 TAAATATTTTCAAAGA-A-ATAATTATAAAAATAAA
* *
298245 AAAATATTGTTCACAGAAAATAAT
1 TAAATATT-TTCAAAG-AAATAAT
298269 AATATATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
32 14 0.29
33 1 0.02
34 2 0.04
35 1 0.02
36 23 0.48
37 6 0.12
38 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (34 bp):
TAAATATTTTCAAAGAAATAATTATAAAAATAAA
Found at i:302191 original size:17 final size:16
Alignment explanation
Indices: 302162--302196 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
302152 GTGAAGCAAT
302162 AAAGAAAAAAAGAAGA
1 AAAGAAAAAAAGAAGA
302178 AAAGAAAAAGAAGAAGA
1 AAAGAAAAA-AAGAAGA
302195 AA
1 AA
302197 GGAATAGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAGAAGA
Found at i:304420 original size:25 final size:25
Alignment explanation
Indices: 304392--304445 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
304382 CTTAAAATAC
*
304392 TATT-AATTGATAAATTAATTTTATT
1 TATTAAATTGA-AAATTAAATTTATT
*
304417 TATTAAATTTAAAATTAAATTTATT
1 TATTAAATTGAAAATTAAATTTATT
304442 TATT
1 TATT
304446 TTTAGTGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TATTAAATTGAAAATTAAATTTATT
Found at i:309368 original size:15 final size:15
Alignment explanation
Indices: 309344--309373 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
309334 TCATCAGTCA
309344 AAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAT
*
309359 AAAAATAAAAAAAAT
1 AAAAAAAAAAAAAAT
309374 CCATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAAAAAAAAAT
Found at i:309886 original size:17 final size:18
Alignment explanation
Indices: 309831--309891 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
309821 TTAAGATTAC
*
309831 TATATAAAAATT-TTCAA
1 TATATAAAAATTATTAAA
* *
309848 TAAATAAAAATGTATAAAA
1 TATATAAAAAT-TATTAAA
309867 TATAT-AAAATTATTAAA
1 TATATAAAAATTATTAAA
309884 TAT-TAAAA
1 TATATAAAA
309892 TAAAATAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 1 0.03
17 22 0.61
18 6 0.17
19 7 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TATATAAAAATTATTAAA
Found at i:311511 original size:15 final size:15
Alignment explanation
Indices: 311487--311516 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
311477 TCATCAGTCA
311487 AAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAT
*
311502 AAAAATAAAAAAAAT
1 AAAAAAAAAAAAAAT
311517 CCATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAAAAAAAAAAT
Found at i:312029 original size:17 final size:18
Alignment explanation
Indices: 311974--312034 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
311964 TTAAGATTAC
*
311974 TATATAAAAATT-TTCAA
1 TATATAAAAATTATTAAA
* *
311991 TAAATAAAAATGTATAAAA
1 TATATAAAAAT-TATTAAA
312010 TATAT-AAAATTATTAAA
1 TATATAAAAATTATTAAA
312027 TAT-TAAAA
1 TATATAAAA
312035 TAAAATAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 1 0.03
17 22 0.61
18 6 0.17
19 7 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TATATAAAAATTATTAAA
Found at i:314820 original size:6 final size:6
Alignment explanation
Indices: 314795--314833 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
314785 TATTCAACGA
* *
314795 ATTTAT ATTCAAT ATATAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATT-TAT ATTTAT ATTTAT ATTTAT ATTTAT AT
314834 AACATGTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTTAT
Found at i:317894 original size:82 final size:81
Alignment explanation
Indices: 317738--317900 Score: 202
Period size: 82 Copynumber: 2.0 Consensus size: 81
317728 AATCAATTCA
* * *
317738 ACTTCATTCAATAGTGGAAGGCCTTGAACCATTGAGATTAACACTTTCATCCTTGGATTATATCT
1 ACTTCATTCAATAGTGGAAGACCTTGAACCATTAAGATTAACACTTTCATCCTTGGA-TATATCC
**
317803 TGGAATTGGGAACAACT
65 TACAATTGGGAACAACT
** * *
317820 ACTTCATTCAATAGTGGAAGACCTTGAGTCATTAAGATTGACACTTCTCATCCTTGGA-AGTTTC
1 ACTTCATTCAATAGTGGAAGACCTTGAACCATTAAGATTAACACTT-TCATCCTTGGATA-TATC
*
317884 CTACATTTGGGAACAAC
64 CTACAATTGGGAACAAC
317901 GCTAGATCTT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.01
82 57 0.83
83 11 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (81 bp):
ACTTCATTCAATAGTGGAAGACCTTGAACCATTAAGATTAACACTTTCATCCTTGGATATATCCT
ACAATTGGGAACAACT
Found at i:322879 original size:19 final size:19
Alignment explanation
Indices: 322855--322910 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
322845 AGGATTGCAC
322855 TTTGGTGCCTTTGTTACAG
1 TTTGGTGCCTTTGTTACAG
* * *
322874 TTTGGTGTCTTTGTTTGCAT
1 TTTGGTGCCTTTG-TTACAG
*
322894 TTTGGTGCCTCTGTTAC
1 TTTGGTGCCTTTGTTAC
322911 GCATCTACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.07, C:0.16, G:0.25, T:0.52
Consensus pattern (19 bp):
TTTGGTGCCTTTGTTACAG
Found at i:324751 original size:64 final size:63
Alignment explanation
Indices: 324632--324752 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 63
324622 CTGTGGGGTT
* * *
324632 TCACACGGCCTGACACACGCCTGTGTCTCTGGCCCATGTGGTCTCCAAATTACAAACAGTGAG
1 TCACACGGCCTGACACACGCCTGTGTCTCTGACCCATGTGGACTCCAAATCACAAACAGTGAG
* * **
324695 TCACACGGCCTGGACACATG-CTCGTGTCTCTGACCCGTGTGGACTGTAAATCACAAAC
1 TCACACGGCCT-GACACACGCCT-GTGTCTCTGACCCATGTGGACTCCAAATCACAAAC
324753 TGTAACACCC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 13 0.27
64 36 0.73
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (63 bp):
TCACACGGCCTGACACACGCCTGTGTCTCTGACCCATGTGGACTCCAAATCACAAACAGTGAG
Found at i:326154 original size:64 final size:64
Alignment explanation
Indices: 325916--326153 Score: 422
Period size: 64 Copynumber: 3.7 Consensus size: 64
325906 GCACACGCCC
*
325916 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGCCCCCTACTT
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTT
*
325980 GTGCCTCCCTATTTATCAAGTTAGTGAGTCCCATGGCCTGGGCACAAGCCTGTGTCCCCTACTT
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTT
* * * *
326044 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACACGGCCTGGGCACACGCTTGTGTCCCCTACCT
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTT
326108 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACA
1 GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACA
326154 CACCCGTGTG
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 166 1.00
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCCTCCCTATTTATCAAGTTAGTGAGTCACATGGCCTGGGCACAAGCCTGTGTCCCCTACTT
Found at i:330649 original size:49 final size:49
Alignment explanation
Indices: 330592--330691 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
330582 ATTTGAGAAT
330592 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
1 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
330641 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
1 GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
330690 GA
1 GA
330692 ACGTAGTCAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (49 bp):
GAGTAAAACCTATATCAGTTAAGGTAGAATATAGTACAAAGTAAATAAA
Found at i:334714 original size:21 final size:21
Alignment explanation
Indices: 334656--334706 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
334646 GCAAATTGTT
334656 GATTTTCAAAAGAAAATAGAG
1 GATTTTCAAAAGAAAATAGAG
*
334677 GATTTTCAAAAGAAAATAGTG
1 GATTTTCAAAAGAAAATAGAG
334698 GATTTTCAA
1 GATTTTCAA
334707 CATAAAATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (21 bp):
GATTTTCAAAAGAAAATAGAG
Found at i:338181 original size:5 final size:6
Alignment explanation
Indices: 338159--338198 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
338149 GACAATTACC
*
338159 AAAAAA AAAAGAG AAAAAG AAAAAG AAAAAGG AAAAAG AA
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAA-G AAAAAG AA
338199 TGAGAGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:338181 original size:13 final size:12
Alignment explanation
Indices: 338159--338198 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
338149 GACAATTACC
*
338159 AAAAAAAAAAGAG
1 AAAAAGAAAA-AG
338172 AAAAAGAAAAAG
1 AAAAAGAAAAAG
338184 AAAAAGGAAAAAG
1 AAAAA-GAAAAAG
338197 AA
1 AA
338199 TGAGAGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:338187 original size:19 final size:19
Alignment explanation
Indices: 338159--338198 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
338149 GACAATTACC
338159 AAAAAAAAAAGAGAAAAAGA
1 AAAAAAAAAAG-GAAAAAGA
*
338179 AAAAGAAAAAGGAAAAAGA
1 AAAAAAAAAAGGAAAAAGA
338198 A
1 A
338199 TGAGAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGGAAAAAGA
Found at i:338784 original size:64 final size:64
Alignment explanation
Indices: 338573--338784 Score: 289
Period size: 64 Copynumber: 3.3 Consensus size: 64
338563 TGGGGTGTTA
* * *
338573 CACAAACAGCGAGTCACATGACCTGGACACACACCCGTGTCTTTGGCCCTTGTGGTTTCTAAAT
1 CACAAACAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGTGGTTTCTAAAT
* * * * * * *
338637 CACAAACAGTGAGTCAGACAAGCTGGACACACACCCATATGTCTGGCCCGTGTGGTTTCTAAAT
1 CACAAACAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGTGGTTTCTAAAT
* * * *
338701 CACAAATAGTGAGTCACACGACCTGGACACACAACCGTGTCTCTAGCCCTTGTGTTTTCTAAAT
1 CACAAACAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGTGGTTTCTAAAT
*
338765 CACAAATAGTGAGTCACACG
1 CACAAACAGTGAGTCACACG
338785 GCCTACCACA
Statistics
Matches: 127, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 127 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (64 bp):
CACAAACAGTGAGTCACACGACCTGGACACACACCCGTGTCTCTGGCCCTTGTGGTTTCTAAAT
Found at i:341032 original size:15 final size:16
Alignment explanation
Indices: 341007--341044 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
340997 TGTTATTATT
341007 ATAATAAAGTAA-TAAA
1 ATAA-AAAGTAAGTAAA
*
341023 GTAAAAAGTAAGTAAA
1 ATAAAAAGTAAGTAAA
341039 ATAAAA
1 ATAAAA
341045 GAAAAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (16 bp):
ATAAAAAGTAAGTAAA
Found at i:341510 original size:21 final size:21
Alignment explanation
Indices: 341484--341525 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
341474 ATAGAGTGTG
341484 AATTGAATTAAGAAAGTAAGT
1 AATTGAATTAAGAAAGTAAGT
*
341505 AATTGAATTAGGAAAGTAAGT
1 AATTGAATTAAGAAAGTAAGT
341526 GAACTTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (21 bp):
AATTGAATTAAGAAAGTAAGT
Found at i:341959 original size:79 final size:79
Alignment explanation
Indices: 341824--341974 Score: 266
Period size: 79 Copynumber: 1.9 Consensus size: 79
341814 ATTATTACTA
*
341824 TTATTAAGATGAGTGAGAATTAAATTGAATAGTTGATATGAATTAAAATTTAAATTGTTTGTTGA
1 TTATTAAGATGAGTGAGAATTAAATTGAATAGTTGATATGAATTAAAATTTAAATTGTTTGTTAA
341889 TTGAAAGCATGAAG
66 TTGAAAGCATGAAG
* * *
341903 TTATTAAGATGAGTGGGAATTAAATTGAATAGTTGATATGAATTAATATTTGAATTGTTTGTTAA
1 TTATTAAGATGAGTGAGAATTAAATTGAATAGTTGATATGAATTAAAATTTAAATTGTTTGTTAA
341968 TTGAAAG
66 TTGAAAG
341975 TGGGAAGTGG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.39, C:0.01, G:0.21, T:0.40
Consensus pattern (79 bp):
TTATTAAGATGAGTGAGAATTAAATTGAATAGTTGATATGAATTAAAATTTAAATTGTTTGTTAA
TTGAAAGCATGAAG
Found at i:349158 original size:2 final size:2
Alignment explanation
Indices: 349151--349177 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
349141 AATGTTTGCA
349151 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
349178 AGAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:349905 original size:162 final size:162
Alignment explanation
Indices: 349660--350011 Score: 605
Period size: 162 Copynumber: 2.2 Consensus size: 162
349650 TGCAATTGGG
349660 AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
1 AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
* * *
349725 AATTTCAATTTGTTGCATTCTCTGACTTGTAATTTCCTTAGGCATTGGAAGCTTATGGTTGATAC
66 AATTTCAACTTATTGCATTCTCTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
* *
349790 TTGTGAGTCTTGGATTATTTCTTCCATTCCAA
131 TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
* * * *
349822 AGCACCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGTGAAGAGA
1 AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
* *
349887 AATTTCAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
66 AATTTCAACTTATTGCATTCTCTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
349952 TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
131 TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
349984 AACAACTCTCTATCTTCAGAGTTTGCAA
1 AACAACTCTCTATCTTCAGAGTTTGCAA
350012 ATTGGGCGCA
Statistics
Matches: 177, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 177 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (162 bp):
AACAACTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGA
AATTTCAACTTATTGCATTCTCTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATAC
TTGCGAGTCTTGAATTATTTCTTCCATTCCAA
Found at i:350822 original size:21 final size:22
Alignment explanation
Indices: 350788--350836 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
350778 CTATTCAAAC
* *
350788 AACAAATTATTAAA-AAAAAAA
1 AACAAATAAATAAATAAAAAAA
* *
350809 AACAAATAAATAAATAATATAA
1 AACAAATAAATAAATAAAAAAA
350831 AACAAA
1 AACAAA
350837 AGGAAAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (22 bp):
AACAAATAAATAAATAAAAAAA
Found at i:354789 original size:19 final size:19
Alignment explanation
Indices: 354767--354811 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
354757 AATTACAAAA
*
354767 AAAAATT-AAAATAATTTTT
1 AAAAATTGAAAAT-ATTTAT
354786 AAAAATTGAAAATATTTAT
1 AAAAATTGAAAATATTTAT
354805 AAAAATT
1 AAAAATT
354812 CTAACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAATTGAAAATATTTAT
Found at i:356211 original size:16 final size:16
Alignment explanation
Indices: 356177--356226 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
356167 AAAACTAAAG
* *
356177 TTTTTAAAACATTTA-
1 TTTTTAAAATATTCAT
*
356192 TTTTTATAATATTCAT
1 TTTTTAAAATATTCAT
*
356208 TTTTTAAAATTTTCAT
1 TTTTTAAAATATTCAT
356224 TTT
1 TTT
356227 AAATTATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTAAAATATTCAT
Found at i:358317 original size:42 final size:42
Alignment explanation
Indices: 358212--358366 Score: 150
Period size: 43 Copynumber: 3.6 Consensus size: 42
358202 ATGTGATTTT
* * *
358212 GTGTAAGACCACGTCTGGGACGTTGGCTTCG-ATTTGAGATTTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGTATTT--GA-TTAC
* *
358256 GTGTAAGACCATGTTTGGGACATTGACATCGTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTAC
* * * *
358298 GTGTAAGACCTTGTCTGGGATAGTGGCATTGTTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATTAC
* ** *
358341 ATGTAAGACCACATCTGGGACGTTGG
1 GTGTAAGACCATGTCTGGGACATTGG
358367 TATTGTACGA
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 29 0.32
43 32 0.35
44 26 0.29
45 4 0.04
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTAC
Found at i:358348 original size:43 final size:42
Alignment explanation
Indices: 358212--358361 Score: 133
Period size: 42 Copynumber: 3.5 Consensus size: 42
358202 ATGTGATTTT
* * *
358212 GTGTAAGACCACGTCTGGGAC-GTTGGCTTCG-ATTTGAGATTTAC
1 GTGTAAGACCATGTCTGGGACAG-TGACATCGTATTT--GA-TTAC
* *
358256 GTGTAAGACCATGTTTGGGACATTGACATCGTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAGTGACATCGTATTTGATTAC
* * * *
358298 GTGTAAGACCTTGTCTGGGATAGTGGCATTGTTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAGTGACATCG-TATTTGATTAC
* **
358341 ATGTAAGACCACATCTGGGAC
1 GTGTAAGACCATGTCTGGGAC
358362 GTTGGTATTG
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 29 0.33
43 29 0.33
44 25 0.29
45 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACAGTGACATCGTATTTGATTAC
Found at i:359731 original size:2 final size:2
Alignment explanation
Indices: 359724--359754 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
359714 TAAGCTTGAT
359724 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 T
359755 TAAATATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:361243 original size:15 final size:15
Alignment explanation
Indices: 361223--361281 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
361213 AATAAAAAGG
361223 AAATAATAAGT-AAAT
1 AAATAATAA-TAAAAT
361238 AAATAA-AATAAAAT
1 AAATAATAATAAAAT
361252 AAAATAA-AATAAAAT
1 -AAATAATAATAAAAT
*
361267 AAAAAATAAATAAAA
1 AAATAAT-AATAAAA
361282 ATAATAACAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.28
15 20 0.51
16 7 0.18
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAATAATAAAAT
Found at i:361248 original size:5 final size:5
Alignment explanation
Indices: 361234--361281 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
361224 AATAATAAGT
*
361234 AAAT- AAATA AAATA AAATA AAATA AAATA AAATA AAAAA TAAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAA
361282 ATAATAACAC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
4 4 0.10
5 32 0.80
6 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:361272 original size:27 final size:27
Alignment explanation
Indices: 361242--361298 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
361232 GTAAATAAAT
361242 AAAATAAAATAAAATAAAATAA-A-ATAA
1 AAAAT-AAATAAAA-AAAATAACACATAA
*
361269 AAAATAAATAAAAATAATAACACATAA
1 AAAATAAATAAAAAAAATAACACATAA
361296 AAA
1 AAA
361299 TGAATAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 6 0.22
26 9 0.33
27 12 0.44
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (27 bp):
AAAATAAATAAAAAAAATAACACATAA
Found at i:361277 original size:11 final size:11
Alignment explanation
Indices: 361187--361282 Score: 56
Period size: 11 Copynumber: 9.1 Consensus size: 11
361177 AAAAATGCAC
361187 AATAAATAAAA
1 AATAAATAAAA
* * *
361198 AACAAATCAAT
1 AATAAATAAAA
**
361209 TTTAAATAAAA
1 AATAAATAAAA
** *
361220 AGGAAATAATA
1 AATAAATAAAA
*
361231 AGTAAAT-AAA
1 AATAAATAAAA
*
361241 TA-AAATAAAA
1 AATAAATAAAA
*
361251 TA-AAATAAAA
1 AATAAATAAAA
*
361261 TA-AAATAAAA
1 AATAAATAAAA
361271 AATAAATAAAA
1 AATAAATAAAA
361282 A
1 A
361283 TAATAACACA
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
9 4 0.06
10 26 0.39
11 36 0.55
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:361282 original size:10 final size:10
Alignment explanation
Indices: 361211--361285 Score: 57
Period size: 11 Copynumber: 7.3 Consensus size: 10
361201 AAATCAATTT
361211 TAAATAAAAA
1 TAAATAAAAA
* *
361221 GGAAATAATAAG
1 -TAAATAA-AAA
*
361233 TAAATAAATA
1 TAAATAAAAA
361243 -AAAT-AAAA
1 TAAATAAAAA
361251 TAAA-ATAAAA
1 TAAATA-AAAA
361261 TAAAATAAAAAA
1 T-AAAT-AAAAA
361273 TAAATAAAAA
1 TAAATAAAAA
361283 TAA
1 TAA
361286 TAACACATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
8 3 0.06
9 7 0.14
10 14 0.27
11 19 0.37
12 7 0.14
13 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:361287 original size:20 final size:19
Alignment explanation
Indices: 361223--361288 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
361213 AATAAAAAGG
* *
361223 AAATAATAAGTAAATAAATA
1 AAATAAAAAATAAATAAA-A
*
361243 AAATAAAATA-AAATAAAATA
1 AAATAAAAAATAAAT-AAA-A
361263 AAATAAAAAATAAATAAAA
1 AAATAAAAAATAAATAAAA
361282 ATAATAA
1 A-AATAA
361289 CACATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.15
20 29 0.74
21 4 0.10
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
AAATAAAAAATAAATAAAA
Found at i:361296 original size:20 final size:17
Alignment explanation
Indices: 361234--361288 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 17
361224 AATAATAAGT
361234 AAATAAATAAAATAAAATA
1 AAATAAAT-AAA-AAAATA
*
361253 AAATAAAATAAAATAA-A
1 AAAT-AAATAAAAAAATA
361270 AAATAAATAAAAATAATA
1 AAATAAATAAAAA-AATA
361288 A
1 A
361289 CACATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 5 0.16
19 7 0.23
20 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAAATAAAAAAATA
Found at i:361950 original size:3 final size:3
Alignment explanation
Indices: 361942--362024 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
361932 AAAAAGGTAA
*
361942 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
361990 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
362025 AGTTTTGATT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:362407 original size:89 final size:89
Alignment explanation
Indices: 362229--362711 Score: 416
Period size: 89 Copynumber: 5.4 Consensus size: 89
362219 TTTGTAGTTC
* ** * * * *
362229 TAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTT-ATAGCTTTAATCTGCTCCACCG-AACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* * *
362292 TCAGAGAGATAAGATTTATGTTTT
66 TCAGGGAGATAAGATTTGTGTCTT
* * * *
362316 TAATCTGCTCTACTACAACTTCAGAAAGATAAGATTTGCTATCTTCAAACTGCTCTACTGCAACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
*
362381 TCAGGGAGATAAGATTTGTGGCTT
66 TCAGGGAGATAAGATTTGTGTCTT
* * * *
362405 TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTTAATCTACTCCACTGCAACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* *
362470 TCAAGGAGATAAGATTTGCTATCTT
66 TCAGGGAGATAAGATTTG-TGTCTT
* ** * * * ** * *
362495 CAATCTGCTCCACTGTGACTTTAGGAAGATAAGATTTTCTATCTTCAATCTTTTCTACTGCGACT
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* * * *
362560 TCGGGGAGATAAGGTTTGCTATCAT
66 TCAGGGAGATAAGATTTG-TGTCTT
* ** * ** * * * **
362585 CAATCTGCTCCACTGTGACTTTAGGGAGATAAGATTTG-TGGT-TTTAATCTGCTCAACTATAAC
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCT-ATCTTCAATCTGCTCCACTGCAAC
* * *
362648 TTCAGAGAGATAGGATTTGTGGCTT
65 TTCAGGGAGATAAGATTTGTGTCTT
* * * ** *
362673 TAATCTACTCCACCGCAACTTTAGGGAGATAATATTTGC
1 TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGC
362712 CATAATAACT
Statistics
Matches: 327, Mismatches: 64, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
87 32 0.10
88 51 0.16
89 130 0.40
90 114 0.35
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (89 bp):
TAATCTGCTCCACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
TCAGGGAGATAAGATTTGTGTCTT
Found at i:362710 original size:44 final size:44
Alignment explanation
Indices: 362229--362710 Score: 437
Period size: 45 Copynumber: 10.9 Consensus size: 44
362219 TTTGTAGTTC
* * *
362229 TAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAGCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* * * * *
362273 TAATCTGCTCCACCG-AACTTCAGAGAGATAAGATTTATGTTTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* * **
362316 TAATCTGCTCTACTACAACTTCAGAAAGATAAGATTTGCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* * * **
362361 CAAACTGCTCTACTGCAACTTCAGGGAGATAAGATTTGTGGCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* *
362405 TAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* *
362450 TAATCTACTCCACTGCAACTTCAAGGAGATAAGATTTGCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* ** * * *
362495 CAATCTGCTCCACTGTGACTTTAGGAAGATAAGATTTTCTATCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTATCTT
* ** * * * * *
362540 CAATCTTTTCTACTGCGACTTCGGGGAGATAAGGTTTGCTATCAT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTT
* ** * *
362585 CAATCTGCTCCACTGTGACTTTAGGGAGATAAGATTTGTGGT-TT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ATCTT
* ** * * **
362629 TAATCTGCTCAACTATAACTTCAGAGAGATAGGATTTGTGGCTT
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
* * * *
362673 TAATCTACTCCACCGCAACTTTAGGGAGATAATATTTG
1 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
362711 CCATAATAAC
Statistics
Matches: 358, Mismatches: 73, Indels: 14
0.80 0.16 0.03
Matches are distributed among these distances:
43 37 0.10
44 140 0.39
45 178 0.50
46 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (44 bp):
TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTT
Found at i:364280 original size:13 final size:13
Alignment explanation
Indices: 364262--364286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
364252 TAATTTATAT
364262 GTGTGAAAATTTC
1 GTGTGAAAATTTC
364275 GTGTGAAAATTT
1 GTGTGAAAATTT
364287 TACCATTTAA
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:368331 original size:16 final size:15
Alignment explanation
Indices: 368306--368335 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
368296 TTAATTTCAT
368306 TCATTTCACAATTTC
1 TCATTTCACAATTTC
368321 TCATATTCACAATTT
1 TCAT-TTCACAATTT
368336 AAAATCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATTTCACAATTTC
Found at i:371675 original size:23 final size:23
Alignment explanation
Indices: 371645--371688 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
371635 NNNNNNNNNN
371645 GTAGCCGAAGCTACCACTGATAC
1 GTAGCCGAAGCTACCACTGATAC
371668 GTAGCCGAAGCTACCACTGAT
1 GTAGCCGAAGCTACCACTGAT
371689 CAATAACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (23 bp):
GTAGCCGAAGCTACCACTGATAC
Found at i:371940 original size:18 final size:17
Alignment explanation
Indices: 371914--371952 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
371904 ATTTTCCTTC
371914 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
371931 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
371949 CACA
1 CACA
371953 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:376218 original size:43 final size:43
Alignment explanation
Indices: 376153--376281 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 43
376143 TACTTCACAT
* *
376153 TGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGA
1 TGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATCGA
*
376196 TGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACA-AAAGTCGA
1 TGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACATA-TCGA
* *
376239 TGCCAACATCCCAGACGTGGTCTTACACGAAAACACATATCGA
1 TGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATCGA
376282 AAATCCTATG
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
42 5 0.07
43 64 0.86
44 5 0.07
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (43 bp):
TGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATCGA
Found at i:380126 original size:21 final size:20
Alignment explanation
Indices: 380090--380128 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
380080 AATTTGAAAA
*
380090 TTAAATAAAAATAGATAATT
1 TTAAAAAAAAATAGATAATT
380110 TTAAAAAAAAGATAGATAA
1 TTAAAAAAAA-ATAGATAA
380129 GTGAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (20 bp):
TTAAAAAAAAATAGATAATT
Found at i:380804 original size:29 final size:29
Alignment explanation
Indices: 380770--380826 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
380760 CTAGTCTTCG
380770 AAGGTACAAGAGTGAGGAATCATCATTCA
1 AAGGTACAAGAGTGAGGAATCATCATTCA
*
380799 AAGGTACAAGAGTGAGGAATCTTCATTC
1 AAGGTACAAGAGTGAGGAATCATCATTC
380827 TGTATAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
AAGGTACAAGAGTGAGGAATCATCATTCA
Found at i:384455 original size:162 final size:162
Alignment explanation
Indices: 384217--384725 Score: 883
Period size: 162 Copynumber: 3.1 Consensus size: 162
384207 TTGGGAACAG
* *
384217 CTCTCTATCCTTAGAGTTTGCAATTGCCCGAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
* * * *
384282 TAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTAGATACTTGTA
66 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
384347 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
* * *
384379 CTCTCTATCTTTAGAGTTTGTAATTTCCCAAGACTATTAGCAACACACATTGAGAAGAGAAATTT
1 CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
* *
384444 CAATTTATTGCATTTTGTGACTTGTAATTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
*
384509 AGTCTTGGATTATTTCTTCCATTCCAAAGCAG
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
*
384541 CTCTCTATCTTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
384606 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
*
384671 AGTATTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
*
384703 CTCTCTATCCTCAGAGTTTGCAA
1 CTCTCTATCCTTAGAGTTTGCAA
384726 ATTGGGCGCA
Statistics
Matches: 327, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 327 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (162 bp):
CTCTCTATCCTTAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
Found at i:395088 original size:28 final size:28
Alignment explanation
Indices: 395054--395110 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
395044 GAGCAAAAGT
395054 ATGTAAAACTTAATACAAAAAGAAAGGA
1 ATGTAAAACTTAATACAAAAAGAAAGGA
*
395082 ATGTAAAACTTAATACAAAAGGAAAGGA
1 ATGTAAAACTTAATACAAAAAGAAAGGA
395110 A
1 A
395111 CTTGAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.60, C:0.07, G:0.16, T:0.18
Consensus pattern (28 bp):
ATGTAAAACTTAATACAAAAAGAAAGGA
Found at i:395482 original size:15 final size:14
Alignment explanation
Indices: 395453--395496 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
395443 AAAATATCTA
* *
395453 CTTTTCTTCAGTTT
1 CTTTTCTTAATTTT
395467 CTTTTTCTTAATTTT
1 C-TTTTCTTAATTTT
*
395482 CATTTCTTAATTTT
1 CTTTTCTTAATTTT
395496 C
1 C
395497 AGTTGATCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.14, C:0.18, G:0.02, T:0.66
Consensus pattern (14 bp):
CTTTTCTTAATTTT
Found at i:395487 original size:14 final size:14
Alignment explanation
Indices: 395470--395497 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
395460 TCAGTTTCTT
395470 TTTCTTAATTTTCA
1 TTTCTTAATTTTCA
395484 TTTCTTAATTTTCA
1 TTTCTTAATTTTCA
395498 GTTGATCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTCTTAATTTTCA
Found at i:399580 original size:30 final size:30
Alignment explanation
Indices: 399508--399620 Score: 140
Period size: 30 Copynumber: 3.8 Consensus size: 30
399498 TTTGGCCTGT
* * *
399508 GCCCTATACAGTAGCA-A-TGTGTGGCCATA
1 GCCCAATACAGTAACAGAGTGTG-GGCCTTA
*
399537 GCCCAATATAGTAACAGAGTGTGGGCCTTA
1 GCCCAATACAGTAACAGAGTGTGGGCCTTA
*
399567 GCCTAATACAGTAACAGAGTGTGGGCCTTA
1 GCCCAATACAGTAACAGAGTGTGGGCCTTA
* *
399597 TCCCAATACAGTAATAGAGTGTGG
1 GCCCAATACAGTAACAGAGTGTGG
399621 TGCAAGTATA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.18
30 56 0.77
31 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (30 bp):
GCCCAATACAGTAACAGAGTGTGGGCCTTA
Found at i:399855 original size:32 final size:32
Alignment explanation
Indices: 399800--400002 Score: 291
Period size: 32 Copynumber: 6.4 Consensus size: 32
399790 GAATGACTAC
* * * *
399800 AAGCCATAAGT-ACAGTAATATGATTGGTACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
399831 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
399863 CAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
399895 CAGCCATCAGTAACGGTAATATGATCGGTACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
399927 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
399959 AAGCCATCAATAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
399991 AAGCCATCAGTA
1 AAGCCATCAGTA
400003 GCATCGCAGC
Statistics
Matches: 156, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
31 10 0.06
32 146 0.94
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:400061 original size:27 final size:26
Alignment explanation
Indices: 400030--400090 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
400020 CCAACAATAG
400030 TAACAGTATATGTGGCCA-AGCCACCAA
1 TAACAGTAT-TGTGG-CAGAGCCACCAA
*
400057 TAACAGTGATTGTGGCAGAGCCACCAG
1 TAACAGT-ATTGTGGCAGAGCCACCAA
400084 T-ACAGTA
1 TAACAGTA
400091 CTTCCTCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 1 0.03
26 7 0.23
27 21 0.68
28 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (26 bp):
TAACAGTATTGTGGCAGAGCCACCAA
Found at i:400189 original size:24 final size:24
Alignment explanation
Indices: 400153--400230 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 24
400143 TACATGCTCA
* *
400153 AAATCAGTCATACAAATCACAGAC
1 AAATCAATTATACAAATCACAGAC
*
400177 AAATCAATTATACTAATCACAGAC
1 AAATCAATTATACAAATCACAGAC
*
400201 AAATCAACTATTA-AAATCACAGAC
1 AAATCAATTA-TACAAATCACAGAC
400225 AAATCA
1 AAATCA
400231 GTCATTTACA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.53, C:0.22, G:0.05, T:0.21
Consensus pattern (24 bp):
AAATCAATTATACAAATCACAGAC
Found at i:400243 original size:24 final size:24
Alignment explanation
Indices: 400166--400263 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 24
400156 TCAGTCATAC
* *
400166 AAATCACAGACAAATCAATTATACT
1 AAATCACAGACAAATCAATCAT-TT
*
400191 -AATCACAGACAAATCAA-CTATTA
1 AAATCACAGACAAATCAATC-ATTT
*
400214 AAATCACAGACAAATCAGTCATTT
1 AAATCACAGACAAATCAATCATTT
* *
400238 ACATCAC-GAAAAAATCAATCATTT
1 AAATCACAG-ACAAATCAATCATTT
400262 AA
1 AA
400264 CCTCGAGGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
23 1 0.02
24 58 0.97
25 1 0.02
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.23
Consensus pattern (24 bp):
AAATCACAGACAAATCAATCATTT
Found at i:400403 original size:27 final size:27
Alignment explanation
Indices: 400335--400478 Score: 166
Period size: 27 Copynumber: 5.4 Consensus size: 27
400325 AGGTACTATA
*
400335 GTCATTTTA-CCTACAGGGGCATCACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * **
400361 GTCATTTTACTTTACAGGGGTATTTTG
1 GTCATTTTACCCTACAGGGGCATTACG
*
400388 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
400415 GTCATTATACCCTACAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* *
400442 ATCATTTTACCCTACA-GGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
*
400468 ATCATTTTACC
1 GTCATTTTACC
400479 AATATTGGGG
Statistics
Matches: 98, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 28 0.29
27 70 0.71
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:403942 original size:22 final size:22
Alignment explanation
Indices: 403917--403960 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
403907 TATTCTGAAT
403917 TATCGATATTCTATTTGACTAA
1 TATCGATATTCTATTTGACTAA
403939 TATCGATATTCTATTTGACTAA
1 TATCGATATTCTATTTGACTAA
403961 GTAAATGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
TATCGATATTCTATTTGACTAA
Found at i:406814 original size:18 final size:17
Alignment explanation
Indices: 406771--406817 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
406761 TAATAAAAAA
*
406771 AACGTTTTGAATTGAAT
1 AACGTTTTGAAATGAAT
*
406788 AACGATTTGTAAATGAAT
1 AACGTTTTG-AAATGAAT
*
406806 AATGTTTTGAAA
1 AACGTTTTGAAA
406818 ACGAACGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (17 bp):
AACGTTTTGAAATGAAT
Found at i:409027 original size:38 final size:39
Alignment explanation
Indices: 408948--409027 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
408938 AGTCCCTTTA
* **
408948 TATTTTTTTATATATTAATTAATTTTCATTTTTATTTTG
1 TATTTTTTCATATATTAATTAATTTTCATTTAAATTTTG
408987 TATTTTTCTCATAT-TTAATT-ATTTT-ATTTAAATTTATG
1 TATTTTT-TCATATATTAATTAATTTTCATTTAAATTT-TG
409025 TAT
1 TAT
409028 GTATGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 8 0.22
38 10 0.28
39 13 0.36
40 5 0.14
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (39 bp):
TATTTTTTCATATATTAATTAATTTTCATTTAAATTTTG
Found at i:409123 original size:22 final size:22
Alignment explanation
Indices: 409065--409127 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
409055 TGTATACGCA
* *
409065 TATTTTTTTTAATGTAATGTAAT
1 TATTTTTTATAAT-TTATGTAAT
*
409088 TATTTTTTAT--TTTATGTGAT
1 TATTTTTTATAATTTATGTAAT
409108 TATTTTTTATAATTTATGTA
1 TATTTTTTATAATTTATGTA
409128 TGTATACTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 7 0.21
23 9 0.26
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (22 bp):
TATTTTTTATAATTTATGTAAT
Found at i:409198 original size:6 final size:6
Alignment explanation
Indices: 409187--409211 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
409177 TTAATTATTT
409187 TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA T
409212 ATATGGATAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:409404 original size:20 final size:21
Alignment explanation
Indices: 409381--409423 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
409371 TTATGTGCTG
* *
409381 TTTATTTTTTTTATTT-TTTA
1 TTTATTTCTTTCATTTGTTTA
409401 TTTATTTCTTTCATTTGTTTA
1 TTTATTTCTTTCATTTGTTTA
409422 TT
1 TT
409424 GACTTATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATTTCTTTCATTTGTTTA
Found at i:414710 original size:22 final size:22
Alignment explanation
Indices: 414653--414714 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
414643 TGCATACGCA
*
414653 TATTTTTT-TAATGTAATGTAAT
1 TATTTTTTATAAT-TTATGTAAT
*
414675 TATTTTTTAT--TTTATGTGAT
1 TATTTTTTATAATTTATGTAAT
414695 TATTTTTTATAATTTATGTA
1 TATTTTTTATAATTTATGTA
414715 TGTATACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 15 0.44
23 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (22 bp):
TATTTTTTATAATTTATGTAAT
Found at i:414791 original size:12 final size:12
Alignment explanation
Indices: 414776--414818 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
414766 TTAATTATTT
*
414776 TTTATATTTATA
1 TTTATATATATA
414788 TTTATATATATA
1 TTTATATATATA
**
414800 TGGATATATATA
1 TTTATATATATA
*
414812 TATATAT
1 TTTATAT
414819 TTTTAAAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (12 bp):
TTTATATATATA
Found at i:414861 original size:15 final size:14
Alignment explanation
Indices: 414840--414873 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
414830 CGAATGCATG
414840 TTTTTTTTACTTTA
1 TTTTTTTTACTTTA
*
414854 TATTTTTTTCCTTTA
1 T-TTTTTTTACTTTA
414869 TTTTT
1 TTTTT
414874 GTAAATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTACTTTA
Found at i:414997 original size:20 final size:21
Alignment explanation
Indices: 414974--415016 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
414964 TTATGTGCTG
* *
414974 TTTATTTTTTTTATTT-TTTA
1 TTTATTTCTTTCATTTGTTTA
414994 TTTATTTCTTTCATTTGTTTA
1 TTTATTTCTTTCATTTGTTTA
415015 TT
1 TT
415017 GACTTATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATTTCTTTCATTTGTTTA
Found at i:416749 original size:14 final size:15
Alignment explanation
Indices: 416723--416755 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
416713 TCCCAAGCTG
416723 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
416738 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
416752 GGAA
1 GGAA
416756 AACATTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:418239 original size:44 final size:43
Alignment explanation
Indices: 418101--418680 Score: 192
Period size: 44 Copynumber: 13.2 Consensus size: 43
418091 AGATAGCAGA
* * *
418101 TCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCAAAGACACCAG
1 TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA-CAG
* ** * * ** * * *
418145 TCTTGCCTCCCTG-GGTTACAGTGGCGCAGGTTC-AAAATAGCAG
1 TCTTGCCTTCCTGTACTGACAGCGAAGCA-GATCGAAGACA-CAG
*
418188 ATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACTAG
1 -TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC-AG
* * * * * * *
418233 TTTTGCCTCCCTAGT--TTACAGTGGAGTAGA-CTGAAGATAGCAG
1 TCTTGCCTTCCT-GTACTGACAGCGAAGCAGATC-GAAGACA-CAG
*
418276 ATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACCAG
1 -TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA-CAG
* * * * *
418321 TCTTGCCTCCCTAGGT--TG-CAGTGGAGTAGA-CTGAAGATAGCAG
1 TCTTGCCTTCCT--GTACTGACAGCGAAGCAGATC-GAAGACA-CAG
* * **
418364 ATCTTACCTTCCTATACAAACAGCGAAGCAGATC-AAGGACACCAG
1 -TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-GACA-CAG
* * * * * * *
418409 CCTTGCCTCCCTAGGT--TG-CAGCGGAGCAGGTTGAAAATAGCAG
1 TCTTGCCTTCCT--GTACTGACAGCGAAGCAGATCGAAGACA-CAG
*
418452 ATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACACCAG
1 -TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA-CAG
* * * *
418497 TCTTGCCTCCCTAGGT--TG-CAGTGTAGCAGA-CTGAAGATAGCAG
1 TCTTGCCTTCCT--GTACTGACAGCGAAGCAGATC-GAAGACA-CAG
* * * *
418540 ATCTTGCCTTCCTGTAC-CAGCAGCAAAGCAGATCAAATACACCAG
1 -TCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACA-CAG
* * *** * * * * *
418585 CCTTGCCTCCCTGGGTTG-CAGC-AGAGCAGGTTGAAAATAGTAG
1 TCTTGCCTTCCTGTACTGACAGCGA-AGCAGATCGAAGACA-CAG
* *
418628 ATCTTGGCTTCCTGTACTGACAGCGAAGCAGATCGAAGACGCCAG
1 -TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGAC-ACAG
418673 TCTTGCCT
1 TCTTGCCT
418681 CCCTAGGTTG
Statistics
Matches: 373, Mismatches: 120, Indels: 86
0.64 0.21 0.15
Matches are distributed among these distances:
42 9 0.02
43 102 0.27
44 152 0.41
45 101 0.27
46 9 0.02
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.23
Consensus pattern (43 bp):
TCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACAG
Found at i:418242 original size:88 final size:88
Alignment explanation
Indices: 418088--418852 Score: 908
Period size: 88 Copynumber: 8.7 Consensus size: 88
418078 AACAGATCAT
* * * *
418088 TGAAGATAGCAGATCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCAAAGACACCAGTCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * * **
418153 CCCTGGGTTACAGTGGCGCAGGT
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * *
418176 TCAAAATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACTAGTTTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * *
418241 CCCTAGTTTACAGTGGAGTAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* *
418264 TGAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
418329 CCCTAGGTTGCAGTGGAGTAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * ** *
418352 TGAAGATAGCAGATCTTACCTTCCTATACAAACAGCGAAGCAGATC-AAGGACACCAGCCTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-GACACCAGTCTTGCC
* **
418416 TCCCTAGGTTGCAGCGGAGCAGGT
65 TCCCTAGGTTGCAGTGGAGCAGAC
*
418440 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACACCAGTCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
418505 CCCTAGGTTGCAGTGTAGCAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * * * *
418528 TGAAGATAGCAGATCTTGCCTTCCTGTAC-CAGCAGCAAAGCAGATCAAATACACCAGCCTTGCC
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACACCAGTCTTGCC
* ** **
418592 TCCCTGGGTTGCAGCAGAGCAGGT
65 TCCCTAGGTTGCAGTGGAGCAGAC
* * *
418616 TGAAAATAGTAGATCTTGGCTTCCTGTACTGACAGCGAAGCAGATCGAAGACGCCAGTCTTGCCT
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
418681 CCCTAGGTTGCAGTGGAGTAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * * * * * * * *
418704 TGAAGATAGTAGATCTTGCCTTCTTGTACCGGCAGTGAAGCAGATCGAA-AAATCCGGCCTTGTC
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA-CCAGTCTTGCC
* * **
418768 TCCCT-GAGTAGCAGTGGAGTAGGT
65 TCCCTAG-GTTGCAGTGGAGCAGAC
* * *
418792 TGAAAATAGCAGATCTTGCCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACATCAGTCTT
1 TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTT
418853 ATTGCCTTGA
Statistics
Matches: 577, Mismatches: 93, Indels: 14
0.84 0.14 0.02
Matches are distributed among these distances:
87 5 0.01
88 567 0.98
89 5 0.01
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (88 bp):
TGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
CCCTAGGTTGCAGTGGAGCAGAC
Found at i:418827 original size:45 final size:45
Alignment explanation
Indices: 418690--418828 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 45
418680 TCCCTAGGTT
* * * * *
418690 GCAGTGGAGTAGACTGAAGATAGTAGATCTTGCCTTCTTGTACCG
1 GCAGTGGAGTAGATTGAAAATAGCAGATCTTGCCTTCCTGTACTG
* * * * * ** * * * *
418735 GCAGTGAAGCAGATCGAAAA-ATCCGGCCTTGTCTCCCTG-AGTA
1 GCAGTGGAGTAGATTGAAAATAGCAGATCTTGCCTTCCTGTACTG
*
418778 GCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTG
1 GCAGTGGAGTAGATTGAAAATAGCAGATCTTGCCTTCCTGTACTG
418823 GCAGTG
1 GCAGTG
418829 AAGCAGATCG
Statistics
Matches: 64, Mismatches: 28, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
43 17 0.27
44 24 0.38
45 23 0.36
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (45 bp):
GCAGTGGAGTAGATTGAAAATAGCAGATCTTGCCTTCCTGTACTG
Found at i:419080 original size:44 final size:44
Alignment explanation
Indices: 419032--419135 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
419022 CTCTTTGGCA
* *
419032 TTGCAGTGGAGCAGATTAAAGCCAATAG-TCCTATCTCCCTGAAG
1 TTGCAGTGGAGCAGATTAAA-ACAACAGATCCTATCTCCCTGAAG
* * * *
419076 TTGCAGTGGAGCGGATTAAAACTACAGATCTTATCTCTCTGAAG
1 TTGCAGTGGAGCAGATTAAAACAACAGATCCTATCTCCCTGAAG
* *
419120 TTGCAGTAGAGTAGAT
1 TTGCAGTGGAGCAGAT
419136 CACATCGGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 4 0.08
44 46 0.92
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TTGCAGTGGAGCAGATTAAAACAACAGATCCTATCTCCCTGAAG
Found at i:419742 original size:19 final size:20
Alignment explanation
Indices: 419700--419751 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
419690 TTCAAGGAAG
419700 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
419721 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
419740 TGCAATCTTAGA
1 TGCAATCTTAGA
419752 AAGATGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:419761 original size:23 final size:24
Alignment explanation
Indices: 419709--419775 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
419699 GTGCAATCTT
419709 AGATATGATATATGCAATCTT----
1 AGATATGAT-TATGCAATCTTAGAA
419730 AGATATGA-TATGCAATCTTAGAA
1 AGATATGATTATGCAATCTTAGAA
* * *
419753 AGATGTGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
419776 GATTTAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 11 0.29
21 8 0.21
23 7 0.18
24 12 0.32
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (24 bp):
AGATATGATTATGCAATCTTAGAA
Found at i:420071 original size:21 final size:20
Alignment explanation
Indices: 420047--420132 Score: 84
Period size: 21 Copynumber: 4.2 Consensus size: 20
420037 TAGTCTTTTT
*
420047 TTAATTTATTATTTATTTTTA
1 TTAATTTATTA-TTATTATTA
* *
420068 TTAAATTTGATT-TTCTTGTTA
1 TT-AATTT-ATTATTATTATTA
*
420089 TTAAGTTATTATTATTATTA
1 TTAATTTATTATTATTATTA
*
420109 TTATTGTTATTATTATTATTA
1 TTAAT-TTATTATTATTATTA
420130 TTA
1 TTA
420133 TTACNNNNNN
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 3 0.06
20 14 0.26
21 29 0.54
22 5 0.09
23 3 0.06
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (20 bp):
TTAATTTATTATTATTATTA
Found at i:420102 original size:3 final size:3
Alignment explanation
Indices: 420094--420135 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
420084 TGTTATTAAG
*
420094 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
420136 CNNNNNNNNN
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:423113 original size:20 final size:20
Alignment explanation
Indices: 423088--423153 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
423078 TTAAGATATA
423088 AATAAACAAACATAAATAAT
1 AATAAACAAACATAAATAAT
*
423108 AATAAACAAATTATAAATAAAT
1 AATAAACAAA-CATAAAT-AAT
*
423130 AA-AAGA-AACACATAAACAAT
1 AATAA-ACAA-ACATAAATAAT
423150 AATA
1 AATA
423154 GTATTAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 15 0.39
21 16 0.42
22 7 0.18
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.20
Consensus pattern (20 bp):
AATAAACAAACATAAATAAT
Found at i:423734 original size:25 final size:23
Alignment explanation
Indices: 423683--423733 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
423673 CCTATCGGTT
423683 AAAACTAGTTATTTTTCCTTTTAA
1 AAAACTAGTTATTTTT-CTTTTAA
423707 AAAATCTAGTTATTTTT-TTTTAA
1 AAAA-CTAGTTATTTTTCTTTTAA
423730 AAAA
1 AAAA
423734 AGTAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 10 0.38
24 4 0.15
25 12 0.46
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (23 bp):
AAAACTAGTTATTTTTCTTTTAA
Found at i:424932 original size:9 final size:10
Alignment explanation
Indices: 424917--424951 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
424907 CCCCAAATTA
*
424917 TTTTTTTTTC
1 TTTTTTCTTC
424927 TTTTTTCTT-
1 TTTTTTCTTC
424936 TTTTTTCTTC
1 TTTTTTCTTC
424946 TTTTTT
1 TTTTTT
424952 TTTATTATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:424937 original size:12 final size:11
Alignment explanation
Indices: 424917--424954 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
424907 CCCCAAATTA
*
424917 TTTTTT-TTTC
1 TTTTTTCTTTT
424927 TTTTTTCTTTT
1 TTTTTTCTTTT
424938 TTTTCTTCTTTT
1 TTTT-TTCTTTT
424950 TTTTT
1 TTTTT
424955 ATTATGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 6 0.24
11 8 0.32
12 11 0.44
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:424939 original size:16 final size:16
Alignment explanation
Indices: 424917--424954 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
424907 CCCCAAATTA
424917 TTTTTTTTTCTT-TTT
1 TTTTTTTTTCTTCTTT
424932 TCTTTTTTTTCTTCTTT
1 T-TTTTTTTTCTTCTTT
424949 TTTTTT
1 TTTTTT
424955 ATTATGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTTTTTCTTCTTT
Found at i:427958 original size:52 final size:50
Alignment explanation
Indices: 427881--428016 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 50
427871 TTGCATGTTC
427881 GATTGAAAAATTTGTTCAATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
1 GATTGAAAAA-TTGTT--ATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
*
427934 GATTGAAGAATATTTGTT-TCCTTAAGCGAAATAGTTTTATGGGTTGCGTTGT
1 GATTGAA-AA-A-TTGTTATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
427986 GATTGAAAAATTGTTCAATCCTTAAGCTAAA
1 GATTGAAAAATTGTT--ATCCTTAAGCTAAA
428017 ACTCTTTGTA
Statistics
Matches: 76, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
49 5 0.07
50 1 0.01
51 2 0.03
52 52 0.68
53 7 0.09
54 2 0.03
55 7 0.09
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.40
Consensus pattern (50 bp):
GATTGAAAAATTGTTATCCTTAAGCTAAATAGTTTTATGGGTTGCGTTGT
Found at i:429713 original size:18 final size:18
Alignment explanation
Indices: 429690--429724 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
429680 ATTGGTTAAA
*
429690 ATAAAAATATTTAAATTC
1 ATAAAAATAATTAAATTC
*
429708 ATAAAACTAATTAAATT
1 ATAAAAATAATTAAATT
429725 ATATATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAAAATAATTAAATTC
Found at i:431853 original size:49 final size:49
Alignment explanation
Indices: 431796--431899 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
431786 TCATGTGTTA
* * * *
431796 TAATTTTATACAGTGTTGAGCTTTTGATTCATGATATTTAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
431845 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
431894 TAATTT
1 TAATTT
431900 GTTTTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:433231 original size:15 final size:16
Alignment explanation
Indices: 433203--433232 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
433193 TAAATTCATA
433203 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
433219 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
433233 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:433252 original size:18 final size:17
Alignment explanation
Indices: 433224--433258 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
433214 ATTATTAAGA
*
433224 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
433241 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
433259 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:433288 original size:59 final size:61
Alignment explanation
Indices: 433209--433391 Score: 173
Period size: 59 Copynumber: 3.0 Consensus size: 61
433199 CATATAAGAA
*
433209 TATTTATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAT
1 TATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAT
** * * * * ** * * *
433270 TATTTCAA-ATT-A-TCTTTTA-TAGTATCATATATTATGATTTGAGTAAATTTATATAAGAA-
1 TATTT-AATATTAAGAATTTTATTA-AATTATATATTTTAATTAAAATATATTTA-ATAATAAT
433329 TA-TTAATTATTAAGAATTTTATTAAATTA-ATATTTTAATTAAAATATATTTAATAATAAT
1 TATTTAA-TATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAT
433389 TAT
1 TAT
433392 GTTTAAATAT
Statistics
Matches: 89, Mismatches: 23, Indels: 20
0.67 0.17 0.15
Matches are distributed among these distances:
57 2 0.02
58 4 0.04
59 37 0.42
60 27 0.30
61 16 0.18
62 3 0.03
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (61 bp):
TATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAT
Done.