Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold449
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: 551709
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 3
Found at i:403226 original size:29 final size:29
Alignment explanation
Indices: 403194--403254 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
403184 ATGAGATAAA
*
403194 AAATTTA-AAATTTATATAATAAAAAAATT
1 AAATTTATAAAATT-TATAATAAAAAAATT
403223 AAATTTATAAAATTTATAATAAAAAAATT
1 AAATTTATAAAATTTATAATAAAAAAATT
403252 AAA
1 AAA
403255 ATCTTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAATTTATAAAATTTATAATAAAAAAATT
Found at i:403533 original size:9 final size:9
Alignment explanation
Indices: 403519--403543 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
403509 TATTATAATT
403519 ATATTAAAA
1 ATATTAAAA
403528 ATATTAAAA
1 ATATTAAAA
403537 ATATTAA
1 ATATTAA
403544 TATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATTAAAA
Found at i:403581 original size:20 final size:20
Alignment explanation
Indices: 403558--403624 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
403548 AATAATTTAT
*
403558 TTTATATATTTTTTTAATTA
1 TTTATATAATTTTTTAATTA
* *
403578 TTTATATAATTATTTAA-AA
1 TTTATATAATTTTTTAATTA
* *
403597 TTTTTATAATATTTTAATTA
1 TTTATATAATTTTTTAATTA
*
403617 TTTTTATA
1 TTTATATA
403625 TTATATTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 15 0.38
20 24 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATATAATTTTTTAATTA
Found at i:403627 original size:11 final size:11
Alignment explanation
Indices: 403554--403639 Score: 62
Period size: 11 Copynumber: 8.4 Consensus size: 11
403544 TATAAATAAT
403554 TTATTTTATATA
1 TTATTTT-TATA
403566 TT-TTTTTA-A
1 TTATTTTTATA
403575 TTA--TTTATA
1 TTATTTTTATA
*
403584 TAATTATTTA-A
1 TTATT-TTTATA
*
403595 -AATTTTTATA
1 TTATTTTTATA
*
403605 ATA-TTTTA-A
1 TTATTTTTATA
403614 TTATTTTTATA
1 TTATTTTTATA
*
403625 TTATATTTATA
1 TTATTTTTATA
403636 TTAT
1 TTAT
403640 ATAATTATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
8 4 0.07
9 13 0.21
10 17 0.28
11 21 0.34
12 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:403640 original size:11 final size:11
Alignment explanation
Indices: 403599--403657 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
403589 ATTTAAAATT
*
403599 TTTATAATAT-
1 TTTATATTATA
*
403609 TTTA-ATTATT
1 TTTATATTATA
403619 TTTATATTATA
1 TTTATATTATA
403630 TTTATATTATA
1 TTTATATTATA
*
403641 TAATTATATTAAA
1 T--TTATATTATA
403654 TTTA
1 TTTA
403658 AAATTATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
9 4 0.10
10 8 0.19
11 20 0.48
13 10 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTATATTATA
Found at i:403667 original size:15 final size:15
Alignment explanation
Indices: 403647--403678 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
403637 TATATAATTA
*
403647 TATTAAATTTAAAAT
1 TATTAAATTAAAAAT
403662 TATTAAATTAAAAAT
1 TATTAAATTAAAAAT
403677 TA
1 TA
403679 ATATTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTAAATTAAAAAT
Found at i:403701 original size:26 final size:26
Alignment explanation
Indices: 403659--403723 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
403649 TTAAATTTAA
* *
403659 AATTAT-TAAATTAAAAATTAA-TATT
1 AATTATATAATTTTAAAA-TAATTATT
403684 AAATTATAT-ATTTTAAAATAATTATT
1 -AATTATATAATTTTAAAATAATTATT
*
403710 ATTTATATAATTTT
1 AATTATATAATTTT
403724 TAATTTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 10 0.30
26 22 0.67
27 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTATATAATTTTAAAATAATTATT
Found at i:403921 original size:17 final size:17
Alignment explanation
Indices: 403895--403953 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
403885 CCTTTTTTTT
*
403895 TTTTAATTTTCTTATTC
1 TTTTATTTTTCTTATTC
*
403912 TTTTATTTTTCTTATAC
1 TTTTATTTTTCTTATTC
*
403929 CTTTATTCTTT-TT-TTC
1 TTTTATT-TTTCTTATTC
403945 TTTTTATTT
1 -TTTTATTT
403954 ATAAATAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.09
17 29 0.83
18 3 0.09
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTCTTATTC
Found at i:404145 original size:18 final size:18
Alignment explanation
Indices: 404122--404175 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
404112 ATAATTTATA
404122 TTATAAATTAAAATAATT
1 TTATAAATTAAAATAATT
404140 TTATAAGTATT-AAATAATT
1 TTATAA--ATTAAAATAATT
*
404159 TATAAAAATATAAAATA
1 T-TATAAAT-TAAAATA
404176 TTTATTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 8 0.27
19 10 0.33
20 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TTATAAATTAAAATAATT
Found at i:404219 original size:26 final size:25
Alignment explanation
Indices: 404184--404241 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
404174 TATTTATTTA
404184 TATTAATTTTCTAATTTTT-TC-TTTT
1 TATTAATTTTCT--TTTTTATCTTTTT
404209 TATTATATTTTCTTTTTTATCTTTTT
1 TATTA-ATTTTCTTTTTTATCTTTTT
404235 TATTAAT
1 TATTAAT
404242 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.17
25 9 0.30
26 16 0.53
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (25 bp):
TATTAATTTTCTTTTTTATCTTTTT
Found at i:404671 original size:28 final size:29
Alignment explanation
Indices: 404636--404694 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
404626 CTAATATCAA
404636 ATTTTAAAA-TAAAAAAATTAAT-TAAAAT
1 ATTTTAAAATTAAAAAAA-TAATATAAAAT
*
404664 ATTTTAAAATTTAAAAAATAATATAAAAT
1 ATTTTAAAATTAAAAAAATAATATAAAAT
404693 AT
1 AT
404695 ATTATTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
ATTTTAAAATTAAAAAAATAATATAAAAT
Found at i:406340 original size:14 final size:15
Alignment explanation
Indices: 406291--406332 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
406281 ATGCATATTG
*
406291 TAATAAGTAT-AAAA
1 TAATAAATATAAAAA
406305 TAATAAATATAAAAA
1 TAATAAATATAAAAA
406320 TAATAAA-ATAAAA
1 TAATAAATATAAAA
406333 CAAATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
TAATAAATATAAAAA
Found at i:406347 original size:25 final size:23
Alignment explanation
Indices: 406299--406352 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
406289 TGTAATAAGT
*
406299 ATAAAATAATAAATATAAAAATA
1 ATAAAATAATAAAAATAAAAATA
406322 ATAAAATAA-AACAAATAAACAGATA
1 ATAAAATAATAA-AAATAAA-A-ATA
406347 ATAAAA
1 ATAAAA
406353 GTGATCATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 15 0.56
24 1 0.04
25 9 0.33
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (23 bp):
ATAAAATAATAAAAATAAAAATA
Found at i:407131 original size:6 final size:6
Alignment explanation
Indices: 407120--407167 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
407110 AATTTTGTTC
*
407120 TTTATT TTTATT CTCTTTTT ATTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT -T-TTATT -TTTATT TTTATT TTTATT TTTATT TTT
407168 CTCATTATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 27 0.73
7 5 0.14
8 5 0.14
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:407140 original size:11 final size:10
Alignment explanation
Indices: 407120--407165 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
407110 AATTTTGTTC
407120 TTTATTTTTA
1 TTTATTTTTA
*
407130 TTCTCTTTTTA
1 TT-TATTTTTA
407141 TTTATTTTTA
1 TTTATTTTTA
407151 TTTTTATTTTTA
1 --TTTATTTTTA
407163 TTT
1 TTT
407166 TTCTCATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 12 0.39
11 9 0.29
12 10 0.32
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:409454 original size:5 final size:5
Alignment explanation
Indices: 409446--409486 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
409436 TTTCCTTTTA
*
409446 TTCTT TTCTT TTCTT CTCTT TTCTT TTCTT TTCTT TTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT T
409487 CTGTTAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:411415 original size:15 final size:18
Alignment explanation
Indices: 411391--411437 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
411381 TATTTTATTT
*
411391 TTATTTTTTATT-TAAAA
1 TTATTTTTAATTATAAAA
411408 -TATTTTTAATTATAAAA
1 TTATTTTTAATTATAAAA
411425 TTA-TTTTAATTAT
1 TTATTTTTAATTAT
411438 TATCAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 15 0.56
18 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTTAATTATAAAA
Found at i:411880 original size:21 final size:21
Alignment explanation
Indices: 411838--411883 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
411828 TTTATATATA
*
411838 TATTTATTCTTTATTCTTTTT
1 TATTTATTCTTTATTCTATTT
*
411859 TATTTTTTCTTTA-TCTAATTT
1 TATTTATTCTTTATTCT-ATTT
411880 TATT
1 TATT
411884 ATCATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTTATTCTTTATTCTATTT
Found at i:412228 original size:28 final size:32
Alignment explanation
Indices: 412196--412265 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 32
412186 AATCAAATTT
412196 AAAATAAATAAATA-TTTTTA-AAT-A-TTAA
1 AAAATAAATAAATATTTTTTATAATAATTTAA
*
412224 AAAATAAATATATATTTTTTATAATAATTTAA
1 AAAATAAATAAATATTTTTTATAATAATTTAA
*
412256 GAAATAAATA
1 AAAATAAATA
412266 TTTTTTTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 13 0.36
29 6 0.17
30 3 0.08
31 1 0.03
32 13 0.36
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
AAAATAAATAAATATTTTTTATAATAATTTAA
Found at i:412261 original size:32 final size:29
Alignment explanation
Indices: 412196--412273 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 29
412186 AATCAAATTT
*
412196 AAAATAAATAAATA-TTTTTAAATATTAA
1 AAAATAAATATATATTTTTTAAATATTAA
412224 AAAATAAATATATATTTTTTATAATAATTTAA
1 AAAATAAATATATATTTTTTA-AAT-A-TTAA
*
412256 GAAATAAATAT-T-TTTTTT
1 AAAATAAATATATATTTTTT
412274 CTTGCTAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
28 13 0.30
29 6 0.14
30 9 0.20
31 2 0.05
32 14 0.32
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
AAAATAAATATATATTTTTTAAATATTAA
Found at i:412842 original size:17 final size:17
Alignment explanation
Indices: 412807--412840 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
412797 AAGATTTATC
412807 ATTATTTAAAATTAAAA
1 ATTATTTAAAATTAAAA
*
412824 ATTA-TTAAATTTAAAA
1 ATTATTTAAAATTAAAA
412840 A
1 A
412841 ATAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATTTAAAATTAAAA
Found at i:412946 original size:2 final size:2
Alignment explanation
Indices: 412941--412985 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
412931 CTTTTTTAAT
*
412941 TA TA TA -A TA TA TA CTA TA TG TA T- 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 TA
412981 TA TA T
1 TA TA T
412986 TTTTATAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 32 0.86
3 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:412992 original size:17 final size:17
Alignment explanation
Indices: 412941--412985 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
412931 CTTTTTTAAT
*
412941 TATATAATATATACTATA
1 TATATTATATATA-TATA
*
412959 TGTATTATATATATATA
1 TATATTATATATATATA
412976 TATATTATAT
1 TATATTATAT
412986 TTTTATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATTATATATATATA
Found at i:414359 original size:18 final size:18
Alignment explanation
Indices: 414336--414373 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
414326 TAATTTAATC
414336 ATAAATTAAAAT-AAATAA
1 ATAAA-TAAAATAAAATAA
*
414354 ATAAATATAATAAAATAA
1 ATAAATAAAATAAAATAA
414372 AT
1 AT
414374 TTGACGTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATAAAATAAAATAA
Found at i:417151 original size:16 final size:17
Alignment explanation
Indices: 417122--417153 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
417112 AATTCAAAAA
417122 TTAAAAAATGAAAAATT
1 TTAAAAAATGAAAAATT
417139 TTAAAAAAT-AAAAAT
1 TTAAAAAATGAAAAAT
417154 AAAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
TTAAAAAATGAAAAATT
Found at i:417377 original size:2 final size:2
Alignment explanation
Indices: 417364--417399 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
417354 GAAATATGGA
*
417364 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
417400 TGAGGCGTGG
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:418686 original size:14 final size:14
Alignment explanation
Indices: 418656--418699 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
418646 TTATTATTTT
* *
418656 TTTATTTAAATTTA
1 TTTATTTAAAATAA
418670 TTTATTTAAAATAA
1 TTTATTTAAAATAA
*
418684 TTTATATATAAATAA
1 TTTATTTA-AAATAA
418699 T
1 T
418700 CAATCAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATTTAAAATAA
Found at i:419259 original size:2 final size:2
Alignment explanation
Indices: 419252--419298 Score: 53
Period size: 2 Copynumber: 23.5 Consensus size: 2
419242 TTTATTTCAA
*
419252 AT AT AT AT AT AT AT AT A- AT CAT TT AT -T CAT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT AT AT AT AT
419294 AT AT A
1 AT AT A
419299 ATGAATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 2 0.05
2 34 0.87
3 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:419288 original size:30 final size:31
Alignment explanation
Indices: 419242--419300 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
419232 ATTATTTTAT
419242 TTTATTTCAAATATATATATATATATAATCA
1 TTTATTTCAAATATATATATATATATAATCA
*
419273 TTTA-TTCATATATATATATATATATAAT
1 TTTATTTCAAATATATATATATATATAAT
419301 GAATTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTATTTCAAATATATATATATATATAATCA
Found at i:419982 original size:17 final size:17
Alignment explanation
Indices: 419957--419990 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
419947 TTTTTATATG
*
419957 TAAATAATAAATTAATT
1 TAAAAAATAAATTAATT
*
419974 TAAAAAATAACTTAATT
1 TAAAAAATAAATTAATT
419991 CGAAAAACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAATAAATTAATT
Found at i:421560 original size:79 final size:80
Alignment explanation
Indices: 421426--421582 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 80
421416 CAGGATTTAA
* *
421426 TTTATGTTATTTTAGGATATCCAATTTATATTAACATCTACTATGAGTTCAATAATTATTTTTGT
1 TTTATGTTATTTTAGGATATCCAATTTATATTAACATCTACCATGAGTTCAATAATTATTTTTAT
421491 TAAA-AATTTTATAT
66 TAAAGAATTTTATAT
* **
421505 TTTATGTTGTTTTAGGATATCCAATTTATATTAACATCTACCATGAGTTTGATAATTATTTTTAT
1 TTTATGTTATTTTAGGATATCCAATTTATATTAACATCTACCATGAGTTCAATAATTATTTTTAT
421570 TAAAGAATTTTAT
66 TAAAGAATTTTAT
421583 TTATCAATTT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
79 64 0.89
80 8 0.11
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (80 bp):
TTTATGTTATTTTAGGATATCCAATTTATATTAACATCTACCATGAGTTCAATAATTATTTTTAT
TAAAGAATTTTATAT
Found at i:422565 original size:16 final size:17
Alignment explanation
Indices: 422523--422565 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
422513 TTTAATATTT
*
422523 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
*
422540 ATAAAA-TTATAATT-C
1 ATAAAATTTATAATTAA
422555 ATAAAATTTAT
1 ATAAAATTTAT
422566 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:422674 original size:24 final size:26
Alignment explanation
Indices: 422647--422710 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
422637 AAATTGAGAC
*
422647 ATAATACAAACATAATAT-CA-AAAA
1 ATAATATAAACATAATATACATAAAA
* *
422671 ATAATTTAAATATAATATAACATAAAA
1 ATAATATAAACATAATAT-ACATAAAA
422698 ATAATATAAACAT
1 ATAATATAAACAT
422711 GACATAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 15 0.47
26 2 0.06
27 15 0.47
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (26 bp):
ATAATATAAACATAATATACATAAAA
Found at i:422717 original size:27 final size:24
Alignment explanation
Indices: 422647--422710 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 24
422637 AAATTGAGAC
* *
422647 ATAATACAAACATAATATCAAAAA
1 ATAATATAAACATAATAACAAAAA
* *
422671 ATAATTTAAATATAATATAACATAAAA
1 ATAATATAAACAT-A-ATAACA-AAAA
422698 ATAATATAAACAT
1 ATAATATAAACAT
422711 GACATAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 10 0.32
25 1 0.03
26 5 0.16
27 15 0.48
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAATATAAACATAATAACAAAAA
Found at i:424659 original size:8 final size:8
Alignment explanation
Indices: 424646--424696 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
424636 AATACAAATA
424646 TTTTTCTC
1 TTTTTCTC
424654 TTTTTCT-
1 TTTTTCTC
424661 TTTTT-TC
1 TTTTTCTC
424668 TGTTTTCTTC
1 T-TTTTC-TC
*
424678 TTTTTTTC
1 TTTTTCTC
*
424686 TTTTTTTC
1 TTTTTCTC
424694 TTT
1 TTT
424697 CTTTCTTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
6 1 0.03
7 6 0.16
8 24 0.63
9 4 0.11
10 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTCTC
Found at i:424679 original size:24 final size:24
Alignment explanation
Indices: 424647--424718 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 24
424637 ATACAAATAT
424647 TTTTC-TCTTTTTCTTTTTTTCTG
1 TTTTCTTCTTTTTCTTTTTTTCTG
*
424670 TTTTCTTCTTTTTTTCTTTTTTTCTT
1 TTTTCTTC--TTTTTCTTTTTTTCTG
* *
424696 TCTTTCTT-TCTTTCTTTCTTTCT
1 T-TTTCTTCTTTTTCTTTTTTTCT
424719 CTCCTGTTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 5 0.12
24 15 0.36
26 16 0.38
27 6 0.14
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (24 bp):
TTTTCTTCTTTTTCTTTTTTTCTG
Found at i:424684 original size:19 final size:16
Alignment explanation
Indices: 424646--424718 Score: 92
Period size: 16 Copynumber: 4.4 Consensus size: 16
424636 AATACAAATA
*
424646 TTTTTCTCTTTTTCTT
1 TTTTTCTTTTTTTCTT
424662 TTTTTCTGTTTTCTTCTT
1 TTTTTCT-TTTT-TTCTT
424680 TTTTTCTTTTTTTCTT
1 TTTTTCTTTTTTTCTT
* *
424696 TCTTTCTTTCTTTCTT
1 TTTTTCTTTTTTTCTT
*
424712 TCTTTCT
1 TTTTTCT
424719 CTCCTGTTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
16 33 0.63
17 7 0.13
18 12 0.23
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTTTTCTT
Found at i:424699 original size:4 final size:4
Alignment explanation
Indices: 424656--424718 Score: 76
Period size: 4 Copynumber: 16.2 Consensus size: 4
424646 TTTTTCTCTT
* * * *
424656 TTTC TTTT TTTC TGT- TTTC -TTC TTTT TTTC TTTT TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
424702 TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC T
424719 CTCCTGTTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 5 0.10
4 44 0.90
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:426802 original size:52 final size:52
Alignment explanation
Indices: 426732--426852 Score: 145
Period size: 52 Copynumber: 2.3 Consensus size: 52
426722 TTTGAAAAGA
* * * *
426732 AAATGTATTGATACA-TTTTTTATTGTAATGATATATTTTGAGTTTTTGACCC
1 AAATGTATCGATACATTTTTTTATTGTAATAATACATTTTG-GGTTTTGACCC
* * * * *
426784 AATTGTATCGATATATTTTTTTATTGTATTAATGCATTTTGGGTTTTGACTC
1 AAATGTATCGATACATTTTTTTATTGTAATAATACATTTTGGGTTTTGACCC
426836 AAATGTATCGATACATT
1 AAATGTATCGATACATT
426853 CTTCAATGCA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
52 36 0.63
53 21 0.37
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTTTATTGTAATAATACATTTTGGGTTTTGACCC
Found at i:428934 original size:170 final size:163
Alignment explanation
Indices: 428642--428972 Score: 459
Period size: 170 Copynumber: 2.0 Consensus size: 163
428632 AATAATCTAT
*
428642 TTAAAAAGATTGATCTATACATTCACGTATATATTGATTTAAAATTCACATTAACTTATTCAATA
1 TTAAAAAGATTGATCTACACATTCACGTATATATTGATTTAAAATTCACATTAACTTATTCAATA
* *
428707 AAAAAGAAATTTTTTTTGAATGATGCTGCTAAATAGTATAATATACATGTCAAATTCTGCTTGCC
66 AAAAAAAAATTTTTTTTGAATAATGCTGCTAAATAGTATAATATACATGTCAAATTCTGCTTGCC
428772 AATAAGC-CTTTTATTTTTTTTTAAAGTTTTGC
131 AATAAGCTCTTTTATTTTTTTTTAAAGTTTTGC
* * * *
428804 TTAAAAA-ATTGATCTACACATTGACGTGTATATTGTTTTAAAATTCATATTAACTTATTCAATG
1 TTAAAAAGATTGATCTACACATTCACGTATATATTGATTTAAAATTCACATTAACTTATTCAAT-
* *
428868 AAAAATAAATATTTTATTTTATTTTTGAATAATGCTGCTAATTAGTATAATATACATGTTAAATT
65 AAAAA-AAA-A----A-TTT-TTTTTGAATAATGCTGCTAAATAGTATAATATACATGTCAAATT
* * *
428933 CTGCTTGCCAATAAGCTTTTTTTTTTTTTTTTTAAGTTTT
122 CTGCTTGCCAATAAGCTCTTTTATTTTTTTTTAAAGTTTT
428973 ACGTTTACCT
Statistics
Matches: 147, Mismatches: 12, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
161 51 0.35
162 12 0.08
163 2 0.01
164 1 0.01
168 1 0.01
169 3 0.02
170 57 0.39
171 20 0.14
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.45
Consensus pattern (163 bp):
TTAAAAAGATTGATCTACACATTCACGTATATATTGATTTAAAATTCACATTAACTTATTCAATA
AAAAAAAAATTTTTTTTGAATAATGCTGCTAAATAGTATAATATACATGTCAAATTCTGCTTGCC
AATAAGCTCTTTTATTTTTTTTTAAAGTTTTGC
Found at i:432647 original size:18 final size:18
Alignment explanation
Indices: 432610--432648 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
432600 GATTCTTCCC
*
432610 TCTCTTTCTCTTTAATTT
1 TCTCTTTCTCTTTAACTT
*
432628 TCTCTTTCTCTTTCACTT
1 TCTCTTTCTCTTTAACTT
432646 TCT
1 TCT
432649 GTTTAGGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (18 bp):
TCTCTTTCTCTTTAACTT
Found at i:433938 original size:19 final size:20
Alignment explanation
Indices: 433916--433957 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
433906 AAAAAAAGTT
433916 AAAA-ATAGAAATTTTTTAA
1 AAAATATAGAAATTTTTTAA
** *
433935 AAAATATTTAATTTTTTTAA
1 AAAATATAGAAATTTTTTAA
433955 AAA
1 AAA
433958 GTAGAAGCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATATAGAAATTTTTTAA
Found at i:433995 original size:2 final size:2
Alignment explanation
Indices: 433988--434023 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
433978 ATTGAAAATA
433988 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
434024 GAGGGGAAAC
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:434526 original size:9 final size:9
Alignment explanation
Indices: 434512--434551 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
434502 TTTTATTTTT
434512 TATTTTTAA
1 TATTTTTAA
434521 TATTTTTAA
1 TATTTTTAA
*
434530 AATTTTTAA
1 TATTTTTAA
434539 -A-TTTTAA
1 TATTTTTAA
434546 T-TTTTT
1 TATTTTT
434552 CTTTTTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
7 6 0.21
8 5 0.18
9 17 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTTTTAA
Found at i:434944 original size:20 final size:21
Alignment explanation
Indices: 434921--434959 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
434911 TTTTTCAAAA
434921 ATAT-ACTTTTTTTTCTTTAT
1 ATATGACTTTTTTTTCTTTAT
**
434941 ATATGTTTTTTTTTTCTTT
1 ATATGACTTTTTTTTCTTT
434960 CGCTAATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (21 bp):
ATATGACTTTTTTTTCTTTAT
Found at i:435287 original size:15 final size:15
Alignment explanation
Indices: 435267--435302 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
435257 AAATATTAAT
435267 TTAATATAAAATAAA
1 TTAATATAAAATAAA
**
435282 TTAATATAACGTAAA
1 TTAATATAAAATAAA
435297 TTAATA
1 TTAATA
435303 ATTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (15 bp):
TTAATATAAAATAAA
Found at i:435363 original size:26 final size:24
Alignment explanation
Indices: 435307--435364 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 24
435297 TTAATAATTT
435307 ATTTTAATTTTATAATTTTAAATA
1 ATTTTAATTTTATAATTTTAAATA
435331 ATCTTTTAATTTTAT-ATATTTAACATTA
1 A--TTTTAATTTTATAAT-TTTAA-A-TA
435359 ATTTTA
1 ATTTTA
435365 TTAATCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
24 1 0.03
25 2 0.07
26 22 0.76
27 1 0.03
28 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTAATTTTATAATTTTAAATA
Found at i:436096 original size:2 final size:2
Alignment explanation
Indices: 436091--436142 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
436081 AAGAGAGAAA
* *
436091 AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT -T AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
436133 AT GT AT AT AT
1 AT AT AT AT AT
436143 TAAAGTGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:437242 original size:30 final size:29
Alignment explanation
Indices: 437208--437292 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
437198 AAATGAAAAA
* * *
437208 TTATTTAACTATAAATCAAAATATATGAAT
1 TTATTTAAAT-TAAATAAAAATATATAAAT
*
437238 TTATTTAAATTTAATAAAAATATATAAAT
1 TTATTTAAATTAAATAAAAATATATAAAT
* *
437267 TTATCTAAATAAAATAATAAAGTATA
1 TTATTTAAATTAAATAA-AAA-TATA
437293 GAGATGCTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 30 0.65
30 12 0.26
31 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (29 bp):
TTATTTAAATTAAATAAAAATATATAAAT
Found at i:446428 original size:15 final size:15
Alignment explanation
Indices: 446410--446461 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
446400 ATTATAAAAT
*
446410 TTTAAGAAATTATAA
1 TTTAAAAAATTATAA
*
446425 TTTAAAAAATATTAAAA
1 TTT-AAAAA-ATTATAA
**
446442 TTTAATTAATTATAA
1 TTTAAAAAATTATAA
446457 TTTAA
1 TTTAA
446462 TTTATAAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 14 0.47
16 7 0.23
17 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TTTAAAAAATTATAA
Found at i:446443 original size:17 final size:16
Alignment explanation
Indices: 446404--446446 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
446394 AATTAAATTA
* *
446404 TAAAATTTTAAGAAAT
1 TAAAATTTAAAAAAAT
*
446420 TATAATTTAAAAAATAT
1 TAAAATTTAAAAAA-AT
446437 TAAAATTTAA
1 TAAAATTTAA
446447 TTAATTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAAATTTAAAAAAAT
Found at i:448774 original size:16 final size:17
Alignment explanation
Indices: 448743--448775 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
448733 AACAAAAACT
*
448743 TTAACAATATTTAATTA
1 TTAAAAATATTTAATTA
448760 TTAAAAATA-TTAATTA
1 TTAAAAATATTTAATTA
448776 ATAATATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAAAATATTTAATTA
Found at i:450120 original size:15 final size:13
Alignment explanation
Indices: 450089--450137 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
450079 AAAAATTATT
450089 TTTATATTATTAAA
1 TTTATATT-TTAAA
450103 TTTAATATTTTAATA
1 TTT-ATATTTTAA-A
450118 TTTATATTTTTAAA
1 TTTATA-TTTTAAA
*
450132 ATTATA
1 TTTATA
450138 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 16 0.52
15 15 0.48
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATATTTTAAA
Found at i:451002 original size:3 final size:3
Alignment explanation
Indices: 450994--451034 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
450984 CGGTTTATTT
*
450994 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
451035 TTTTTAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:451305 original size:16 final size:16
Alignment explanation
Indices: 451261--451307 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
451251 TTTAATAAAA
451261 TAAAAAA-TAAATT-T
1 TAAAAAATTAAATTAT
451275 TAAAAAAATT--A-TAT
1 T-AAAAAATTAAATTAT
451289 TAAAAAATTAAATTAT
1 TAAAAAATTAAATTAT
451305 TAA
1 TAA
451308 TTATTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 7 0.26
16 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAAAATTAAATTAT
Found at i:451348 original size:66 final size:61
Alignment explanation
Indices: 451236--451359 Score: 144
Period size: 66 Copynumber: 1.9 Consensus size: 61
451226 GAAATCAATA
451236 TATTAATTATTAATTTTTAATAAAATAAAAAATAAATTTTAAAAAAATTATATTAAAAAATTAAA
1 TATTAATTATTAATTTTTAATAAAATAAAAAAT--ATTTTAAAAAAA--A-ATTAAAAAATTAAA
451301 T
61 T
*
451302 TATTAATTATTAATTTTTTAAT-AAATAAAAAGT-TTTTAAATTAAAAAAATTAAAAAAT
1 TATTAATTATTAA-TTTTTAATAAAATAAAAAATATTTT-AA--AAAAAAATTAAAAAAT
451360 AAGAGTCATA
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
63 14 0.26
64 3 0.06
66 28 0.53
67 8 0.15
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (61 bp):
TATTAATTATTAATTTTTAATAAAATAAAAAATATTTTAAAAAAAAATTAAAAAATTAAAT
Found at i:451921 original size:74 final size:70
Alignment explanation
Indices: 451715--451924 Score: 206
Period size: 74 Copynumber: 2.9 Consensus size: 70
451705 AAATGTATTG
* *
451715 TTTATTTCTATTTGTATAAGTTTAAATTTGTTTTTATTTGATTATATGAGTTTAAA-TTTTAGGG
1 TTTATTTTTATTTGTAAAAGTTTAAATTTGTTTTTATTTGATTATATGAGTTTAAATTTTTAGGG
451779 TATAA
66 TATAA
* * * * * * *
451784 TTTGTTTTAATTTGTAAAATTTTAAATGTGTTTTTTAGATATGATTAGATGAGTTTGAATTTTTG
1 TTTATTTTTATTTGTAAAAGTTTAAATTTG-TTTTT--ATTTGATTATATGAGTTTAAATTTTT-
* *
451849 ATGGTGTAA
62 AGGGTATAA
* * * * *
451858 TTTATTTTTATTTGTAGAAGTGTAGGATTTGTTTTCTATTTTGATTATATAAATTTAAATTTTTA
1 TTTATTTTTATTTGTAAAAGTTTA-AATTTGTTTT-TA-TTTGATTATATGAGTTTAAATTTTTA
451923 GG
63 GG
451925 TGTGGTGATC
Statistics
Matches: 109, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
69 24 0.22
70 5 0.05
72 18 0.17
73 7 0.06
74 50 0.46
75 5 0.05
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (70 bp):
TTTATTTTTATTTGTAAAAGTTTAAATTTGTTTTTATTTGATTATATGAGTTTAAATTTTTAGGG
TATAA
Found at i:452023 original size:4 final size:4
Alignment explanation
Indices: 451991--452064 Score: 63
Period size: 4 Copynumber: 20.0 Consensus size: 4
451981 AGGGAAGGAG
*
451991 GAAA G-AA G-AA GAAAA GAAG GAAA -AAA GAAA GAAA GAAA G-AA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* *
452036 -AAT GAAG GAAA G-AA GAAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
452065 AAAAAGATGG
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
3 20 0.34
4 35 0.60
5 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:452024 original size:11 final size:10
Alignment explanation
Indices: 451992--452071 Score: 76
Period size: 11 Copynumber: 7.8 Consensus size: 10
451982 GGGAAGGAGG
451992 AAAGAAGAAGA
1 AAAGAAGAA-A
452003 AAAGAAGGAAA
1 AAAGAA-GAAA
452014 AAAGAAAGAAA
1 AAAG-AAGAAA
452025 GAAAGAAGAAA
1 -AAAGAAGAAA
* *
452036 AATGAAG--G
1 AAAGAAGAAA
452044 AAAGAAGAAA
1 AAAGAAGAAA
452054 AAAGAAAGAAA
1 AAAG-AAGAAA
452065 AAA-AAGA
1 AAAGAAGA
452072 TGGGTGGCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
8 6 0.10
9 4 0.07
10 10 0.17
11 30 0.51
12 9 0.15
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:452628 original size:137 final size:137
Alignment explanation
Indices: 452439--452995 Score: 700
Period size: 137 Copynumber: 4.1 Consensus size: 137
452429 AATATGTTTC
* * *
452439 ATATGTCAAAAATAAAAAGATTTAATTTGACGTGGTTTTGGGTTATATTTTTTGTTTAATATGAG
1 ATATGTCAAAAATAAAAAGACTTAGTTTGACGTGGTTTTGGGTTATATTTTTTGTTTAATATGAA
* * * * * **
452504 GTACTCATTTAGGTACCTTTTAATATTGTTTGAGGTTTTTGATATTATTAATTTTTTATAACATG
66 ATGCTCATTTAGATA-CTTTTAATGTTGTTTGAGATTTTTGATATTATTAATTTTTTATGGCATG
* *
452569 GTTTTTTA
130 CTTATTTA
* * *
452577 ATATGTCAAAAATAAAAAGACTTAGCTTGCCGT-GTTTTGGGTTATAGTTTTTGTTTAATATGAA
1 ATATGTCAAAAATAAAAAGACTTAGTTTGACGTGGTTTTGGGTTATATTTTTTGTTTAATATGAA
* * * *
452641 ATGCTTATTTAAATACCTTTTGATGTTGTTTGAGATTTTTGATATTATTAA-TTTTTATGGTATG
66 ATGCTCATTTAGATA-CTTTTAATGTTGTTTGAGATTTTTGATATTATTAATTTTTTATGGCATG
452705 CTTATTTA
130 CTTATTTA
* * *
452713 ATATGTCAAAAATAAAAAGACTTAGTTTGACGAGATTTTCGGTTATATTTTTTGGTTTAATATGA
1 ATATGTCAAAAATAAAAAGACTTAGTTTGACGTGGTTTTGGGTTATATTTTTT-GTTTAATATGA
* * *
452778 AATGCTCGTTTAGATACTTCTTGATGTTGTTTGAGATTTTTTGATATTATTAATTTTTGTATTGC
65 AATGCTCATTTAGATACTT-TTAATGTTGTTTGAGA-TTTTTGATATTATTAATTTTT-TATGGC
* *
452843 ATACTTGTTTA
127 ATGCTTATTTA
* * *
452854 GTATGTCAAAAATAAAAAGACTTAGTTTAATGTGGTTTTGGGTTATATTTTTTGTTTAATAT-AA
1 ATATGTCAAAAATAAAAAGACTTAGTTTGACGTGGTTTTGGGTTATATTTTTTGTTTAATATGAA
* *
452918 GATGCTCATTTA-A-A---TTAATGTTATTTAAGATTTTTGATATTATT-ATTTTTTATGGCATG
66 -ATGCTCATTTAGATACTTTTAATGTTGTTTGAGATTTTTGATATTATTAATTTTTTATGGCATG
452977 CTTATTTA
130 CTTATTTA
452985 ATATGTCAAAA
1 ATATGTCAAAA
452996 TATATTTAAT
Statistics
Matches: 366, Mismatches: 46, Indels: 21
0.85 0.11 0.05
Matches are distributed among these distances:
131 24 0.07
132 6 0.02
133 14 0.04
134 13 0.04
136 46 0.13
137 91 0.25
138 70 0.19
139 19 0.05
140 23 0.06
141 60 0.16
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.49
Consensus pattern (137 bp):
ATATGTCAAAAATAAAAAGACTTAGTTTGACGTGGTTTTGGGTTATATTTTTTGTTTAATATGAA
ATGCTCATTTAGATACTTTTAATGTTGTTTGAGATTTTTGATATTATTAATTTTTTATGGCATGC
TTATTTA
Found at i:452987 original size:272 final size:271
Alignment explanation
Indices: 452439--452995 Score: 728
Period size: 272 Copynumber: 2.0 Consensus size: 271
452429 AATATGTTTC
* * * * *
452439 ATATGTCAAAAATAAAAAGATTTAATTTGACGTGGTTTTGGGTTATATTTTTTGTTTAATATGAG
1 ATATGTCAAAAATAAAAAGACTTAATTTGACGAGATTTTCGGTTATATTTTTTGTTTAATATGAA
* * *
452504 GTACTCATTTAGGTACCTTTTAATATTGTTTGAGGTTTTTGATATTATTAATTTTTTATAACATG
66 ATACTCATTTAGATACCTTTTAATATTGTTTGAGGTTTTTGATATTATTAATTTTTTATAACATA
* * **
452569 GTTTTTTAATATGTCAAAAATAAAAAGACTTAGCTTGCCGTGTTTTGGGTTATAGTTTTTGTTTA
131 CTTGTTTAATATGTCAAAAATAAAAAGACTTAGCTTAACGTGTTTTGGGTTATAGTTTTTGTTTA
* * * *
452634 ATATGAAATGCTTATTTAAATACCTTTTGATGTTGTTTGAGATTTTTGATATTATTAATTTTTAT
196 ATATGAAATGCTCATTTAAATA-C--TTAATGTTATTTAAGATTTTTGATATTATTAATTTTTAT
*
452699 GGTATGCTTATTTA
258 GGCATGCTTATTTA
*
452713 ATATGTCAAAAATAAAAAGACTTAGTTTGACGAGATTTTCGGTTATATTTTTTGGTTTAATATGA
1 ATATGTCAAAAATAAAAAGACTTAATTTGACGAGATTTTCGGTTATATTTTTT-GTTTAATATGA
* * * * * **
452778 AATGCTCGTTTAGATA-CTTCTTGATGTTGTTTGAGATTTTTTGATATTATTAATTTTTGTATTG
65 AATACTCATTTAGATACCTT-TTAATATTGTTTGAG-GTTTTTGATATTATTAATTTTT-TATAA
* * * *
452842 CATACTTGTTTAGTATGTCAAAAATAAAAAGACTTAGTTTAATGTGGTTTTGGGTTATATTTTTT
127 CATACTTGTTTAATATGTCAAAAATAAAAAGACTTAGCTTAACGT-GTTTTGGGTTATAGTTTTT
*
452907 GTTTAATAT-AAGATGCTCATTT-AA-A-TTAATGTTATTTAAGATTTTTGATATTATTATTTTT
191 GTTTAATATGAA-ATGCTCATTTAAATACTTAATGTTATTTAAGATTTTTGATATTATTAATTTT
452968 TATGGCATGCTTATTTA
255 TATGGCATGCTTATTTA
452985 ATATGTCAAAA
1 ATATGTCAAAA
452996 TATATTTAAT
Statistics
Matches: 247, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
272 59 0.24
274 51 0.21
275 35 0.14
276 22 0.09
277 44 0.18
278 36 0.15
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.49
Consensus pattern (271 bp):
ATATGTCAAAAATAAAAAGACTTAATTTGACGAGATTTTCGGTTATATTTTTTGTTTAATATGAA
ATACTCATTTAGATACCTTTTAATATTGTTTGAGGTTTTTGATATTATTAATTTTTTATAACATA
CTTGTTTAATATGTCAAAAATAAAAAGACTTAGCTTAACGTGTTTTGGGTTATAGTTTTTGTTTA
ATATGAAATGCTCATTTAAATACTTAATGTTATTTAAGATTTTTGATATTATTAATTTTTATGGC
ATGCTTATTTA
Found at i:455661 original size:18 final size:19
Alignment explanation
Indices: 455631--455677 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
455621 AAAAATATTT
*
455631 TATTTTTCT-TTTAA-AAA
1 TATTTTTATATTTAACAAA
*
455648 TATTTTTATATTTAACCAA
1 TATTTTTATATTTAACAAA
455667 TCATTTTTATA
1 T-ATTTTTATA
455678 AAATTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 5 0.20
19 3 0.12
20 9 0.36
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTTATATTTAACAAA
Found at i:455907 original size:12 final size:13
Alignment explanation
Indices: 455890--455945 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
455880 TATCCACATA
455890 AAAATA-ATAATT
1 AAAATACATAATT
* *
455902 AAAATACAAAATA
1 AAAATACATAATT
*
455915 AAAATATATAA-T
1 AAAATACATAATT
455927 ATAAATA-ATAATT
1 A-AAATACATAATT
455940 AAAATA
1 AAAATA
455946 TAACATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 16 0.44
13 20 0.56
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATACATAATT
Found at i:460798 original size:79 final size:77
Alignment explanation
Indices: 460667--460970 Score: 283
Period size: 79 Copynumber: 3.9 Consensus size: 77
460657 ACAATGGGGC
* ** *
460667 TAGAGTATCCCCGATTATGAAAAATC-AGTGTTCTCGAAATAAAATCGGGGTTGGAGTATCTCCT
1 TAGAGTATCCCCGATTATGAAAAATCGA-TGTTTTAAAAATAAAACCGGGGTTGGAGTATC-CCT
460731 C-AGAAATAACAGGGT
64 CGA-AAATAAC-GGGT
* * * *
460746 TAGAGTATCCCTGATTAT-AGAGAATCGGTGTTTTAAAAATAAAATCGGGGTTGGAGTATCCCTT
1 TAGAGTATCCCCGATTATGA-AAAATCGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCC-T
*
460810 CGAAAATAATGGGGT
64 CGAAAATAA-CGGGT
* * * * * ** * *
460825 TGGAGTATCCCCGATTGTGGAAAATCGATGCTTTAGAAATAAGGCCAGGGGTTTGAGTATCCGCG
1 TAGAGTATCCCCGATTATGAAAAATCGATGTTTTAAAAATAAAACC-GGGGTTGGAGTATCC-CT
*
460890 CGAAAATAACGGTAT
64 CGAAAATAACGG-GT
* * *
460905 TGGAGTATCCCTC-ATTATGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCTC
1 TAGAGTATCCC-CGATTATGAAAAATCGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCTC
460969 GA
65 GA
460971 GATGAAAAAT
Statistics
Matches: 183, Mismatches: 32, Indels: 21
0.78 0.14 0.09
Matches are distributed among these distances:
78 7 0.04
79 113 0.62
80 61 0.33
81 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (77 bp):
TAGAGTATCCCCGATTATGAAAAATCGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCTCG
AAAATAACGGGT
Found at i:468046 original size:12 final size:12
Alignment explanation
Indices: 468025--468057 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
468015 AAAGAGCAAG
*
468025 AATGAGAATAAA
1 AATGATAATAAA
468037 AATGATAATAAA
1 AATGATAATAAA
468049 AATGATAAT
1 AATGATAAT
468058 GATCAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (12 bp):
AATGATAATAAA
Found at i:468651 original size:113 final size:112
Alignment explanation
Indices: 468445--468653 Score: 249
Period size: 113 Copynumber: 1.9 Consensus size: 112
468435 TACATCATAT
* * * * * * * * * *
468445 GAATGTATCGATACATCTGTTGGCATTAGCTAAAGAAGTGCTAAAACCCTCATTTGTATCGATAT
1 GAATGTATCGATAAATCTATTAGCAATAGCTAAAAAAATCCTAAAACCCTAATTTATATCGATAC
* * *
468510 ATGTCGAAATATATCGATGCAATGCACAATGTACTGATACATTATGA
66 ATATCGAAATATATCGATACAATACACAATGTACTGATACATTATGA
* *
468557 GAATGTATCGATAAATCTAATTAGCAATAGCTAAAAAAATCCTGAAACCCTAATTTATATTGATA
1 GAATGTATCGATAAATCT-ATTAGCAATAGCTAAAAAAATCCTAAAACCCTAATTTATATCGATA
*
468622 CATAT-GAAAATGTATCGATACAATACACAATG
65 CATATCG-AAATATATCGATACAATACACAATG
468654 CATCGATACC
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
112 18 0.23
113 61 0.77
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (112 bp):
GAATGTATCGATAAATCTATTAGCAATAGCTAAAAAAATCCTAAAACCCTAATTTATATCGATAC
ATATCGAAATATATCGATACAATACACAATGTACTGATACATTATGA
Found at i:469922 original size:62 final size:62
Alignment explanation
Indices: 469689--470161 Score: 521
Period size: 61 Copynumber: 8.0 Consensus size: 62
469679 ACTGTAGACT
* *
469689 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAACGAAAAGGCGTCTTGCTCTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
* **
469751 CTAG-AAAGTGCCACCAACTTGTGTGGGTTTTAAAAGGAAAAGATGTCCTGCTCTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
* ** *
469812 CTAG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGATGTCCTGCCCTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
* ** *
469873 CTAGAAAAGTGCCACCAAATTGTGTAAGCTTTAAAAGGAAAAGGCGTCCTGCTTTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
* * * *
469935 CTA-AAAGGTGCCACCAACTTATATGGGCTTT--------AAGGCGTCTTGCTCTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
* *
469988 CTAGAAAAGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
* * * * * *
470050 CT-G-AAGGTGCCATCAGCTTGTGTGGGCTTT-----G-AAATGCGTCCTGTTTTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
* *
470104 CT-GAAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCATCCTGCTCTTTGAGGA
1 CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
470159 CTA
1 CTA
470162 AAGGGTGAAA
Statistics
Matches: 355, Mismatches: 44, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
53 23 0.06
54 48 0.14
55 46 0.13
60 23 0.06
61 137 0.39
62 78 0.22
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (62 bp):
CTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGA
Found at i:469931 original size:123 final size:121
Alignment explanation
Indices: 469697--470165 Score: 555
Period size: 115 Copynumber: 4.0 Consensus size: 121
469687 CTCTAGAAAA
469697 GTGCCACCAACTTGTGTGGGCTTTAAAACGAAAAGGCGTCTTGCTCTTTGAGGACTAG-AAAGTG
1 GTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAA-GCGTCTTGCTCTTTGAGGACTAGAAAAGTG
* **
469761 CCACCAACTTGTGTGGGTTTTAAAAGGAAAAGATGTCCTGCTCTTTGAGGACTAGAAG
64 CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAG
* * *
469819 GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGATGTCCTGCCCTTTGAGGACTAGAAAAGTG
1 GTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAG-CGTCTTGCTCTTTGAGGACTAGAAAAGTG
* ** * *
469884 CCACCAAATTGTGTAAGCTTTAAAAGGAAAAGGCGTCCTGCTTTTTGAGGACTAAAAG
64 CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAG
* *
469942 GTGCCACCAACTTATATGGGCTTT--AAG----GCGTCTTGCTCTTTGAGGACTAGAAAAGTGCC
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCGTCTTGCTCTTTGAGGACTAGAAAAGTGCC
* *
470001 ACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-GAAG
66 ACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAG
* * * * * * *
470056 GTGCCATCAGCTTGTGTGGGCTTT----GAAATGCGTCCTGTTTTTTGAGGACT-GAAAAATGCC
1 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCGTCTTGCTCTTTGAGGACTAGAAAAGTGCC
*
470116 ACCAACTTGTGTGGGCTTT-----G-AAAGGCATCCTGCTCTTTGAGGACTA-AAG
66 ACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAG
470165 G
1 G
470166 GTGAAAGGAG
Statistics
Matches: 307, Mismatches: 33, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
109 29 0.09
110 1 0.00
112 1 0.00
114 23 0.07
115 100 0.33
116 19 0.06
120 1 0.00
121 3 0.01
122 52 0.17
123 78 0.25
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (121 bp):
GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCGTCTTGCTCTTTGAGGACTAGAAAAGTGCC
ACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAG
Found at i:470015 original size:54 final size:55
Alignment explanation
Indices: 469912--470161 Score: 249
Period size: 54 Copynumber: 4.5 Consensus size: 55
469902 TTTAAAAGGA
* * *
469912 AAAGGCGTCCTGCTTTTTGAGGACTA-AAAGGTGCCACCAACTTATATGGGCTTT
1 AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTT
*
469966 -AAGGCGTCTTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTT
1 AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTT
* * * * *
470020 AAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-G-AAGGTGCCATCAGCTTGTGTGGGCTTT
1 -------AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTT
* * * * *
470080 GAAATGCGTCCTGTTTTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTT
1 -AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTT
*
470135 GAAAGGCATCCTGCTCTTTGAGGACTA
1 -AAAGGCGTCCTGCTCTTTGAGGACTA
470162 AAGGGTGAAA
Statistics
Matches: 162, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
53 23 0.14
54 48 0.30
55 45 0.28
60 23 0.14
61 1 0.01
62 22 0.14
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (55 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTATGGGCTTT
Found at i:470257 original size:94 final size:94
Alignment explanation
Indices: 470112--470328 Score: 371
Period size: 94 Copynumber: 2.3 Consensus size: 94
470102 GACTGAAAAA
* *
470112 TGCCACCAACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGAAAGGAGA
*
470177 GAGCATCATACTCTTTGAGGACTAGGAAG
66 GAGCATCATACTCTTTGAGAACTAGGAAG
*
470206 TGCCAGCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGAAAGGAGA
1 TGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGAAAGGAGA
* * *
470271 GAGCATCCTGCTCTTTGAGAACTGGGAAG
66 GAGCATCATACTCTTTGAGAACTAGGAAG
470300 TGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAAAGG
470329 AGAAGGCGTC
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 115 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (94 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGAAAGGAGA
GAGCATCATACTCTTTGAGAACTAGGAAG
Found at i:471348 original size:1 final size:1
Alignment explanation
Indices: 471342--471404 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
471332 CTTTTCTCTC
* * * * * * *
471342 TTTTTTTTTTCTTTGTTTTGTTTTTTTTTTATTTTTTTTGTTTTTTGTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
471405 AAAAAAGAAG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:471365 original size:19 final size:20
Alignment explanation
Indices: 471342--471404 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
471332 CTTTTCTCTC
*
471342 TTTTTTTTTTCTTTGTTTTG
1 TTTTTTTTTTATTTGTTTTG
*
471362 TTTTTTTTTTATTTTTTTTG
1 TTTTTTTTTTATTTGTTTTG
*
471382 TTTTTTGTTTT-TTTATTTT-
1 TTTTTT-TTTTATTTGTTTTG
471401 TTTT
1 TTTT
471405 AAAAAAGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.10
20 31 0.79
21 4 0.10
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (20 bp):
TTTTTTTTTTATTTGTTTTG
Found at i:471369 original size:24 final size:25
Alignment explanation
Indices: 471342--471403 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 25
471332 CTTTTCTCTC
471342 TTTTTTTTTTCTTTG-TTTTGTTTT
1 TTTTTTTTTTCTTTGTTTTTGTTTT
*
471366 TTTTTTATTTTTTTTGTTTTTTGTTTT
1 TTTTTT-TTTTCTTTG-TTTTTGTTTT
471393 TTTATTTTTTT
1 TTT-TTTTTTT
471404 TAAAAAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 6 0.18
25 8 0.24
27 16 0.48
28 3 0.09
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (25 bp):
TTTTTTTTTTCTTTGTTTTTGTTTT
Found at i:471393 original size:16 final size:15
Alignment explanation
Indices: 471342--471403 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 15
471332 CTTTTCTCTC
*
471342 TTTTTTTTTTCTTTG
1 TTTTTTTTTTTTTTG
*
471357 TTTTGTTTTTTTTTTA
1 TTTT-TTTTTTTTTTG
471373 TTTTTTTTGTTTTTTG
1 TTTTTTTT-TTTTTTG
471389 TTTTTTTATTTTTTT
1 TTTTTTT-TTTTTTT
471404 TAAAAAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.20
16 32 0.78
17 1 0.02
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:471404 original size:24 final size:25
Alignment explanation
Indices: 471342--471404 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
471332 CTTTTCTCTC
* *
471342 TTTTTT-TTTTCTTTGTTTTGTTTT
1 TTTTTTATTTTTTTTGTTTTGTTGT
471366 TTTTTTATTTTTTTTGTTTT-TTGT
1 TTTTTTATTTTTTTTGTTTTGTTGT
471390 TTTTTTATTTTTTTT
1 TTTTTTATTTTTTTT
471405 AAAAAAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.03, C:0.02, G:0.06, T:0.89
Consensus pattern (25 bp):
TTTTTTATTTTTTTTGTTTTGTTGT
Found at i:477111 original size:52 final size:52
Alignment explanation
Indices: 477022--477150 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
477012 CGAAATATGA
* *
477022 AAATTTACCTGTATGTATCGATACATGTAATAGTGTATCGATACATCTAGGC
1 AAATTTACCTGCATGTATCGATACATGTAATAATGTATCGATACATCTAGGC
* * *
477074 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATGTAATAATGTATCGATACATCTAGGC
477126 AAATTTACCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
477151 ATGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATGTAATAATGTATCGATACATCTAGGC
Found at i:477163 original size:52 final size:51
Alignment explanation
Indices: 477022--477170 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 51
477012 CGAAATATGA
*
477022 AAATTTACCTGTATGTATCGATAC-ATGTAATAGTGTATCGATACATCTAGGC
1 AAATTTACCTGCATGTATCGATACAATG--ATAGTGTATCGATACATCTAGGC
* * * *
477074 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-ATGATAGTGTATCGATACATCTAGGC
477126 AAATTTACCTGCATGTATCGATACAATGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACAATGAT-AGTGTATCGATACA
477171 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 3 0.03
52 82 0.95
54 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACAATGATAGTGTATCGATACATCTAGGC
Found at i:477177 original size:13 final size:13
Alignment explanation
Indices: 477159--477183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
477149 CAATGATCAG
477159 TGTATCGATACAA
1 TGTATCGATACAA
477172 TGTATCGATACA
1 TGTATCGATACA
477184 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:485177 original size:4 final size:4
Alignment explanation
Indices: 485170--485200 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
485160 CAAAAAAAAC
485170 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
485201 CACCTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:487334 original size:51 final size:51
Alignment explanation
Indices: 487269--487411 Score: 150
Period size: 51 Copynumber: 2.8 Consensus size: 51
487259 CAACGGGGCA
* * *
487269 GGAGTAT-CTCGATTATGAAAAATC-AGTGTTCTAGAAATAAAATCGGGGTT
1 GGAGTATCCCCGATTATGAAAAATCGA-TGTTCTAAAAATAAAATCAGGGTT
* * *
487319 GGAGTTTCCCTGATTAT-AGAAAATCGATGTTTTAAAAATAAAATCAGGGTT
1 GGAGTATCCCCGATTATGA-AAAATCGATGTTCTAAAAATAAAATCAGGGTT
* * *
487370 GGAGTATCCCCGATTGTGAAAAATTGATGCTT-TACAAATAAA
1 GGAGTATCCCCGATTATGAAAAATCGATG-TTCTAAAAATAAA
487412 GCTGGGGTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
50 7 0.09
51 66 0.86
52 4 0.05
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (51 bp):
GGAGTATCCCCGATTATGAAAAATCGATGTTCTAAAAATAAAATCAGGGTT
Found at i:487534 original size:78 final size:79
Alignment explanation
Indices: 487368--487568 Score: 244
Period size: 78 Copynumber: 2.6 Consensus size: 79
487358 AAAATCAGGG
* * * * *
487368 TTGGAGTATCCCCGATTGTGAAAAATTGATGCTTTACAAATAAAGCTGGGGTTTGAATATCCCCA
1 TTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAGCTCGGGTTGGAATATCCCCA
*
487433 TGAAAATAACGGGG
66 TGAAAATAACGGGA
* * * *
487447 TTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGC-CGGGTTGGAATATCCTC-
1 TTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAGCTCGGGTTGGAATATCCCCA
*
487510 TAGGAAATAACGGGA
66 T-GAAAATAACGGGA
** * *
487525 TTGGAGTATCCCTAATTATGAAAAATTAATGTTTTGGAAATAAA
1 TTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAA
487569 ATAGAGGTTG
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 62 0.60
79 40 0.39
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (79 bp):
TTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTAGAAATAAAGCTCGGGTTGGAATATCCCCA
TGAAAATAACGGGA
Found at i:491257 original size:78 final size:77
Alignment explanation
Indices: 491143--491513 Score: 354
Period size: 79 Copynumber: 4.7 Consensus size: 77
491133 GGGGCAGGAC
* * * * *
491143 TATCCCGATTATGAAAAATCGATGTTCTGAAAATAAAATCGTGGTTGGAGTATCCCTTCAGAAAT
1 TATCCCTATTATGAAAAATCGATGTTTTAAAAATAAAACCG-GGTTGGAGTATCCCCTCAGAAAT
491208 AACAGGGTTGGAG
65 AACAGGGTTGGAG
* * *
491221 TATCCCTATTTATAAAAAATCGGT-TTTTAAAAATAAAATCAGGGTTGGAGTATCCCCTC-GAAA
1 TATCCCTA-TTATGAAAAATCGATGTTTTAAAAATAAAA-CCGGGTTGGAGTATCCCCTCAG-AA
*
491284 ATAACGGGGTTGGAG
63 ATAACAGGGTTGGAG
* * * * ** * * *
491299 TATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAGGCTGGGGTTTGAGTATCCCCGT-AAAA
1 TAT-CCCTATTATGAAAAATCGATGTTTTAAAAATAAAAC-CGGGTTGGAGTATCCCC-TCAGAA
491363 ATAACAGGGTTGGAG
63 ATAACAGGGTTGGAG
* * * * * * * * *
491378 TATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAAGGTTGGAATATCCCCTCGGAAA
1 TATCCCT-ATTATGAAAAATCGATGTTTTAAAAATAAAACC-GGGTTGGAGTATCCCCTCAGAAA
491443 TAAC-GGGATTGGAG
64 TAACAGGG-TTGGAG
* *
491457 TATCCCTAATTATGAAAAATTGATGTTTTGAAAATAAAACCGGGTTGGAGTATCCCC
1 TATCCCT-ATTATGAAAAATCGATGTTTTAAAAATAAAACCGGGTTGGAGTATCCCC
491514 GAGATGAAAA
Statistics
Matches: 237, Mismatches: 44, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
77 1 0.00
78 88 0.37
79 147 0.62
80 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (77 bp):
TATCCCTATTATGAAAAATCGATGTTTTAAAAATAAAACCGGGTTGGAGTATCCCCTCAGAAATA
ACAGGGTTGGAG
Found at i:491492 original size:158 final size:157
Alignment explanation
Indices: 491150--491512 Score: 421
Period size: 158 Copynumber: 2.3 Consensus size: 157
491140 GACTATCCCG
* * * *
491150 ATTATGAAAAATCGATGTTCTGAAAATAAAATCGTGGTTGGAGTATCCCTTCAGAAATAACAGGG
1 ATTATGAAAAATCGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCGTCAAAAATAACAGGG
** * * *
491215 TTGGAGTATCCCTATTTATAAAAAATCGGTTTTTAAAAATAAAATCAGGGTTGGAGTATCCCCTC
66 TTGGAGTATCCCTATTTATAAAAAATCAATTTTTAAAAATAAAACCAAGGTTGGAATATCCCCTC
* *
491280 GAAAATAACGGGGTTGGAGTATCCCCG
131 GAAAATAACGGGATTGGAGTATCCCCA
* * ** *
491307 ATTGTGAAAAATCGATGCTTT-AGAAAT-AAGGCTGGGGTTTGAGTATCCCCGT-AAAAATAACA
1 ATTATGAAAAATCGATGTTTTGA-AAATAAAATC-GGGGTTGGAGTAT-CCCGTCAAAAATAACA
* * * * *
491369 GGGTTGGAGTATCCCTGA-TTGTGAGAAATCAATATTTTAGAAATAAAGCCAAGGTTGGAATATC
63 GGGTTGGAGTATCCCT-ATTTATAAAAAATCAAT-TTTTAAAAATAAAACCAAGGTTGGAATATC
* *
491433 CCCTCGGAAATAACGGGATTGGAGTATCCCTA
126 CCCTCGAAAATAACGGGATTGGAGTATCCCCA
* *
491465 ATTATGAAAAATTGATGTTTTGAAAATAAAA-CCGGGTTGGAGTATCCC
1 ATTATGAAAAATCGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCC
491513 CGAGATGAAA
Statistics
Matches: 170, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
156 7 0.04
157 79 0.46
158 81 0.48
159 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (157 bp):
ATTATGAAAAATCGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCGTCAAAAATAACAGGG
TTGGAGTATCCCTATTTATAAAAAATCAATTTTTAAAAATAAAACCAAGGTTGGAATATCCCCTC
GAAAATAACGGGATTGGAGTATCCCCA
Found at i:495822 original size:12 final size:12
Alignment explanation
Indices: 495801--495835 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
495791 AAAGAGCAAG
*
495801 AATGAGAATAAA
1 AATGACAATAAA
*
495813 AATGATAATAAA
1 AATGACAATAAA
495825 AATGACAATAA
1 AATGACAATAA
495836 TCAACTCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (12 bp):
AATGACAATAAA
Found at i:497462 original size:19 final size:20
Alignment explanation
Indices: 497438--497492 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
497428 GTATCGATAT
**
497438 ATTGTATCGATACATGTTC-
1 ATTGTATCGATACATGCACA
* *
497457 ATTGTATTGATATATGCACA
1 ATTGTATCGATACATGCACA
497477 ATTGTATCGATACATG
1 ATTGTATCGATACATG
497493 AAACTAGCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (20 bp):
ATTGTATCGATACATGCACA
Found at i:497469 original size:32 final size:33
Alignment explanation
Indices: 497409--497471 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
497399 TATCCAGATC
*
497409 TATCGATACATTATGCTTTGTATCGATATATTG
1 TATCGATACATTATGCATTGTATCGATATATTG
*
497442 TATCGATACATGT-T-CATTGTATTGATATAT
1 TATCGATACAT-TATGCATTGTATCGATATAT
497472 GCACAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (33 bp):
TATCGATACATTATGCATTGTATCGATATATTG
Found at i:497559 original size:33 final size:32
Alignment explanation
Indices: 497522--497586 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
497512 TACCACTGTT
497522 TGTATCAATACAT-AGCACATTATATCGATACAA
1 TGTATCAATACATGA-CA-ATTATATCGATACAA
*
497555 TGTATCGATACATGACGAATTATATCGATACA
1 TGTATCAATACATGAC-AATTATATCGATACA
497587 TTGTCCTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (32 bp):
TGTATCAATACATGACAATTATATCGATACAA
Found at i:499167 original size:15 final size:15
Alignment explanation
Indices: 499147--499179 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
499137 AACCATCAAA
499147 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
499162 GATGATGATGATAAT
1 GATGATGAAGATAAT
499177 GAT
1 GAT
499180 AAAGTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:503743 original size:13 final size:13
Alignment explanation
Indices: 503725--503764 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
503715 ACAATATTCT
503725 TTGTATCGATACA
1 TTGTATCGATACA
*
503738 TTGTATCGATATA
1 TTGTATCGATACA
*
503751 ATGTATCGATACA
1 TTGTATCGATACA
503764 T
1 T
503765 GAGTTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:506351 original size:20 final size:19
Alignment explanation
Indices: 506326--506379 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
506316 CTACCACTGT
506326 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
*
506346 TTGTATTGATACATGATGAA
1 TTGTATCGATACATGA-GAA
506366 TTGTATCGATACAT
1 TTGTATCGATACAT
506380 TGTCCTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:515062 original size:52 final size:51
Alignment explanation
Indices: 515000--515128 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 51
514990 CACTAATCTT
515000 TGTATCGATACATGCAGTCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAG-CAAATTTGCCCAGATGTATCGATACACTATGAAA
* ** *
515052 TGTATTGATACACACAGGCAAATTTGCCCAGATGTATCTATACACTATGAAA
1 TGTATCGATACATGCA-GCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
515104 TGTATCAATACATGCAAGCAAATTT
1 TGTATCGATACATGC-AGCAAATTT
515129 TCATATTTTG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 65 0.97
53 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:522385 original size:15 final size:15
Alignment explanation
Indices: 522365--522404 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
522355 TAAAAATGTC
**
522365 CAAAATGAGGAAGCT
1 CAAAATGAAAAAGCT
522380 CAAAATGAAAAAGCT
1 CAAAATGAAAAAGCT
*
522395 CCAAATGAAA
1 CAAAATGAAA
522405 TTGATGAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.55, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
CAAAATGAAAAAGCT
Found at i:524495 original size:13 final size:13
Alignment explanation
Indices: 524477--524501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524467 CATTTTTCTT
524477 TGTATCGATACAA
1 TGTATCGATACAA
524490 TGTATCGATACA
1 TGTATCGATACA
524502 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:526121 original size:23 final size:21
Alignment explanation
Indices: 526079--526122 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
526069 GTTTAATGTT
**
526079 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
526100 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
526123 ATCTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:526330 original size:18 final size:18
Alignment explanation
Indices: 526307--526342 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
526297 GGGGGAGAAA
526307 GTACGAATTTGTTAAAAT
1 GTACGAATTTGTTAAAAT
526325 GTACGAATTTGTTAAAAT
1 GTACGAATTTGTTAAAAT
526343 TATTTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
GTACGAATTTGTTAAAAT
Found at i:527020 original size:13 final size:13
Alignment explanation
Indices: 527002--527027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
526992 TACACAAAGT
527002 ATGTATCGATACA
1 ATGTATCGATACA
527015 ATGTATCGATACA
1 ATGTATCGATACA
527028 CAAATAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:527025 original size:32 final size:33
Alignment explanation
Indices: 526984--527047 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
526974 TAGCCAAACT
526984 TGTATCGATACACAAAGT-A-TGTATCGATACAA
1 TGTATCGATACACAAA-TAATTGTATCGATACAA
527016 TGTATCGATACACAAATAATTGTATCGATACA
1 TGTATCGATACACAAATAATTGTATCGATACA
527048 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 1 0.03
32 17 0.57
33 12 0.40
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAATAATTGTATCGATACAA
Found at i:527110 original size:61 final size:66
Alignment explanation
Indices: 527015--527181 Score: 238
Period size: 71 Copynumber: 2.5 Consensus size: 66
527005 TATCGATACA
527015 ATGTATCGATACA-CAAATAATTGTATCGATACATTGGC-T-T-G-T-AACGACTATATTTTCAA
1 ATGTATCGATACATCAAA-AATTGTATCGATACATTGGCTTGTAGCTAAACGACTATATTTTCAA
527074 AT
65 AT
527076 ATGTATCGATACATCAAAAATTGTATCGATACATTGGCTTGTAACGGCTAGAAACGACTATATTT
1 ATGTATCGATACATCAAAAATTGTATCGATACATTGGCTTGT-A--GCT--AAACGACTATATTT
527141 TCAAAT
61 TCAAAT
527147 ATGTATCGATACATCAAAAATTGTATCGATACATT
1 ATGTATCGATACATCAAAAATTGTATCGATACATT
527182 CACACGGGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 12
0.89 0.00 0.11
Matches are distributed among these distances:
61 33 0.35
62 5 0.05
63 1 0.01
67 1 0.01
68 1 0.01
71 54 0.57
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (66 bp):
ATGTATCGATACATCAAAAATTGTATCGATACATTGGCTTGTAGCTAAACGACTATATTTTCAAA
T
Found at i:528823 original size:19 final size:21
Alignment explanation
Indices: 528799--528847 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
528789 ACCCTCATTT
528799 TATCGATACAAATA-AAAA-A
1 TATCGATACAAATACAAAATA
*
528818 TATCGATAC-AATACAAAATG
1 TATCGATACAAATACAAAATA
528838 TATCGATACA
1 TATCGATACA
528848 TCCCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 9 0.35
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.24
Consensus pattern (21 bp):
TATCGATACAAATACAAAATA
Found at i:528838 original size:111 final size:110
Alignment explanation
Indices: 528613--528849 Score: 255
Period size: 111 Copynumber: 2.1 Consensus size: 110
528603 TTTAGGATTG
* * * *
528613 AATGTATCGATACATCATATAAATGTATTGATATATCTGTTGGTAGTAGCTAAAGAAGTGCTAAA
1 AATGTATCGATACATCATATAAATGTATCGATACATCTGTTGGTAGTAGCTAAAGAAATCCTAAA
** * ** * * *
528678 ACCCTCATTTGTATCAAAACATGTCAATGTACTGACATAATGCAC
66 ACCCTCATTTGTATCAAAACAAATAAAAATACTGACACAATACAA
* * *
528723 AATGTATTGATACATTATATGAATGTATCGATACATCTGATTGGCTA-TAGCTAAAGAAATCCTA
1 AATGTATCGATACATCATATAAATGTATCGATACATCTG-TTGG-TAGTAGCTAAAGAAATCCTA
* * *
528787 AAACCCTCATTT-TATCGATACAAATAAAAAATA-TCGATACAATACAA
64 AAACCCTCATTTGTATCAAAACAAAT-AAAAATACT-GACACAATACAA
528834 AATGTATCGATACATC
1 AATGTATCGATACATC
528850 CCAAAATATA
Statistics
Matches: 103, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
110 44 0.43
111 57 0.55
112 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (110 bp):
AATGTATCGATACATCATATAAATGTATCGATACATCTGTTGGTAGTAGCTAAAGAAATCCTAAA
ACCCTCATTTGTATCAAAACAAATAAAAATACTGACACAATACAA
Found at i:528854 original size:20 final size:20
Alignment explanation
Indices: 528799--528861 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
528789 ACCCTCATTT
528799 TATCGATACAAATA-AAAA-A
1 TATCGATAC-AATACAAAATA
*
528818 TATCGATACAATACAAAATG
1 TATCGATACAATACAAAATA
*
528838 TATCGATAC-ATCCCAAAATA
1 TATCGATACAAT-ACAAAATA
528858 TATC
1 TATC
528862 AATAATCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 4 0.11
19 15 0.39
20 19 0.50
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.25
Consensus pattern (20 bp):
TATCGATACAATACAAAATA
Found at i:529423 original size:11 final size:11
Alignment explanation
Indices: 529407--529465 Score: 82
Period size: 11 Copynumber: 5.4 Consensus size: 11
529397 TTATTACTTT
529407 TTATTTATAAA
1 TTATTTATAAA
* *
529418 TTATTTTTAAT
1 TTATTTATAAA
529429 TTATTTATAAA
1 TTATTTATAAA
* *
529440 TTATTTTTAAT
1 TTATTTATAAA
529451 TTATTTATAAA
1 TTATTTATAAA
529462 TTAT
1 TTAT
529466 ACAAATTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:529425 original size:18 final size:18
Alignment explanation
Indices: 529399--529454 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 18
529389 TGCATGTATT
*
529399 ATTACTTTTTATTTATAA
1 ATTATTTTTTATTTATAA
529417 ATTATTTTTAATTTATTTATAA
1 ATTA--TTT--TTTATTTATAA
*
529439 ATTATTTTTAATTTAT
1 ATTATTTTTTATTTAT
529455 TTATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 12 0.38
20 5 0.16
22 15 0.47
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTATTTTTTATTTATAA
Found at i:529434 original size:22 final size:22
Alignment explanation
Indices: 529406--529465 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
529396 ATTATTACTT
529406 TTTATTTATAAATTATTTTTAA
1 TTTATTTATAAATTATTTTTAA
529428 TTTATTTATAAATTATTTTTAA
1 TTTATTTATAAATTATTTTTAA
529450 TTTATTTATAAATTAT
1 TTTATTTATAAATTAT
529466 ACAAATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATTTATAAATTATTTTTAA
Found at i:529731 original size:10 final size:10
Alignment explanation
Indices: 529716--529740 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
529706 TGTGCATGTA
529716 TTATTACTTT
1 TTATTACTTT
529726 TTATTACTTT
1 TTATTACTTT
529736 TTATT
1 TTATT
529741 TATAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTACTTT
Found at i:529869 original size:307 final size:314
Alignment explanation
Indices: 529284--529972 Score: 1034
Period size: 307 Copynumber: 2.2 Consensus size: 314
529274 TTTACATATA
* *
529284 TTATTTTTCGGTAACAACTTAAATACGAGCTTTCCTTTACCTGTAAAATGACCAAGAAAAAATTT
1 TTATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATTT
*
529349 ATTGTACATATATTATTTTTATTAAAATTAATTAATATTATGCATGTATTATTACTTTTTATTTA
66 ATTGTACATATATTATTCTTATTAAAATTAATTAATATTATGCATGTATTATTAC---TTATTTA
* *
529414 TAAATTATTTTTAATTTATTTATAAATTATTTTTAATTTATTTATAAATTATACAAATTTATTTT
128 T-AATTA-TCTT-ATTTATTTATAAATTATATTTAATTTATTTATAAATTATACAAATTTATTTT
*
529479 TATTAAAATTAATTAATATTGTACATGTATTATTTTTATAGTTGATAGAACTTAAATTTATGTTA
190 TATTAAAATTAATTAATATTGTACATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTA
* **
529544 GCCAATAATATTTTACTTTTCTT-ATAACGACTCATTTCGGATTTACAGATGCACACATT
255 GCCAACAATAAATTACTTTTCTTGATAACGACTCATTTCGGATTTACAGATGCACACATT
* * *
529603 TTATTTTTCGGTAACGATTTAAATACGAGCTTTCTTTTATCTATAAAATGACCAAGAAAAAATTT
1 TTATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATTT
*
529668 ATTGTACATATATTATTCTTATTAAAATTAATTAATATTGTGCATGTATTATTAC-T-TTT-T-A
66 ATTGTACATATATTATTCTTATTAAAATTAATTAATATTATGCATGTATTATTACTTATTTATAA
*
529729 TTA-CTT-TTTATTTATAAATTATATTTAATTTATTTGTAAATTATACAAATTTAATTTTT-TTA
131 TTATCTTATTTATTTATAAATTATATTTAATTTATTTATAAATTATACAAATTT-ATTTTTATTA
* *
529791 AAATTAATTAATATTGTATATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCCGA
195 AAATTAATTAATATTGTACATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCCAA
* * * *
529856 CAATAAATTACTTTTTTTGATAACGACTTATTTCGGATTTATAGGTGCACACATT
260 CAATAAATTACTTTTCTTGATAACGACTCATTTCGGATTTACAGATGCACACATT
* * * * *
529911 TCATTTTTCAGTAATGACTTAAATACGAGCTTTCCTTTATCTGTAAAATAACTAAGAAAAAA
1 TTATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAA
529973 ATTTCCTCAA
Statistics
Matches: 340, Mismatches: 28, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
307 123 0.36
308 93 0.27
309 2 0.01
311 4 0.01
313 1 0.00
314 3 0.01
315 1 0.00
319 113 0.33
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (314 bp):
TTATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAGAAAAAATTT
ATTGTACATATATTATTCTTATTAAAATTAATTAATATTATGCATGTATTATTACTTATTTATAA
TTATCTTATTTATTTATAAATTATATTTAATTTATTTATAAATTATACAAATTTATTTTTATTAA
AATTAATTAATATTGTACATGTATTATTTTTATAATTGATAGAACTTAAATTTATGTTAGCCAAC
AATAAATTACTTTTCTTGATAACGACTCATTTCGGATTTACAGATGCACACATT
Found at i:530357 original size:40 final size:40
Alignment explanation
Indices: 530302--530378 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
530292 TAATCTATAA
530302 ATATTGTCAATATATTCCATGTAATCTATATGGACATTTT
1 ATATTGTCAATATATTCCATGTAATCTATATGGACATTTT
530342 ATATTGTCAATATATTCCATGTAATCTATATGGACAT
1 ATATTGTCAATATATTCCATGTAATCTATATGGACAT
530379 GAGCACAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (40 bp):
ATATTGTCAATATATTCCATGTAATCTATATGGACATTTT
Found at i:531590 original size:183 final size:183
Alignment explanation
Indices: 531256--531737 Score: 514
Period size: 183 Copynumber: 2.6 Consensus size: 183
531246 ACTATGATAA
* * * * * ** *
531256 TTACAATCAATTAACTTTTCAGTTTT-TGTATCAAAAGGAATTTAATTCTCAAATATAATTTATG
1 TTACAATCAATCAACTTTTC-TTTTTATATATAAAAAAGAATTCGATTCTCAAATATAATTCATG
* * ** * * * * *
531320 CATTAGTCTAATCTTTGCAGCGTGA-TTCTTATAATCAACCAA-CTTT-TTTTTTTTACCA-AAA
65 CATTAGTCTAATCCTTACAGTATGACAT-TTACAATCAATCAATCTTTCTTTTTTATA-TATAAA
* * *
531381 GAAATCCGATTCTCATGTACAATTCATACATTAGTTTAATCCTTGCAATCTAATAT
128 GAAATCCAATTCTCATGTACAATTCATACATTAGTCTAATCCTTGCAATCTAACAT
* *
531437 TTATAATCAATC-AGTCTTTCTTGTTTATATATAAAAAAGAA-TCTGATTCTCAAATATAATTCA
1 TTACAATCAATCAACT-TTTCTT-TTTATATATAAAAAAGAATTC-GATTCTCAAATATAATTCA
* *
531500 TGCA-TAGTCTAATCCTTACAGTATGACATTTACAATCAATTAGTCTTTCTTTTTTATATATAAA
63 TGCATTAGTCTAATCCTTACAGTATGACATTTACAATCAATCAATCTTTCTTTTTTATATATAAA
* * * * *
531564 GAAATCCAATTCTCA-GATATAATTCATGCATTAGTCTAATCCTTGTAGTCTGACAT
128 GAAATCCAATTCTCATG-TACAATTCATACATTAGTCTAATCCTTGCAATCTAACAT
* * *
531620 TTACAATCAATCAACTTTTCTTTTTTTATATAAAAAAGAATTCGATTCTCAGATATAATTCATGT
1 TTACAATCAATCAACTTTTCTTTTTATATATAAAAAAGAATTCGATTCTCAAATATAATTCATGC
* * * *
531685 ATTAGTCTAATCTTTACAGTTTGGCATTTACAATCAATCAATTTTTCTTTTTT
66 ATTAGTCTAATCCTTACAGTATGACATTTACAATCAATCAATCTTTCTTTTTT
531738 TCCATAAAAA
Statistics
Matches: 249, Mismatches: 40, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
180 3 0.01
181 46 0.18
182 77 0.31
183 121 0.49
184 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (183 bp):
TTACAATCAATCAACTTTTCTTTTTATATATAAAAAAGAATTCGATTCTCAAATATAATTCATGC
ATTAGTCTAATCCTTACAGTATGACATTTACAATCAATCAATCTTTCTTTTTTATATATAAAGAA
ATCCAATTCTCATGTACAATTCATACATTAGTCTAATCCTTGCAATCTAACAT
Found at i:531738 original size:92 final size:92
Alignment explanation
Indices: 531256--531748 Score: 407
Period size: 92 Copynumber: 5.4 Consensus size: 92
531246 ACTATGATAA
* ** * * * ** * *
531256 TTACAATCAATTAA-CTTTTCAGTTTTTGTATCAAAAGGAATTTAATTCTCAAATATAATTTATG
1 TTACAATCAATCAATC-TTTCTTTTTTTATATAAAAAAGAATTCGATTCTCAGATATAATTCATG
* * ** *
531320 CATTAGTCTAATCTTTGCAGCGTGA-TT
65 CATTAGTCTAATCCTTACAGTATGACAT
* * ** * *
531347 CTTATAATCAACCAA-CTTT-TTTTTTT-TA-CCAAAAGAAATCCGATTCTCATG-TACAATTCA
1 -TTACAATCAATCAATCTTTCTTTTTTTATATAAAAAAG-AATTCGATTCTCA-GATATAATTCA
* * * * * * *
531407 TACATTAGTTTAATCCTTGCAATCTAATAT
63 TGCATTAGTCTAATCCTTACAGTATGACAT
* * * *
531437 TTATAATCAATCAGTCTTTCTTGTTTATATATAAAAAAGAA-TCTGATTCTCAAATATAATTCAT
1 TTACAATCAATCAATCTTTCTT-TTTTTATATAAAAAAGAATTC-GATTCTCAGATATAATTCAT
531501 GCA-TAGTCTAATCCTTACAGTATGACAT
64 GCATTAGTCTAATCCTTACAGTATGACAT
* * * * *
531529 TTACAATCAATTAGTCTTTC-TTTTTTATAT-ATAAAGAAATCCAATTCTCAGATATAATTCATG
1 TTACAATCAATCAATCTTTCTTTTTTTATATAAAAAAG-AATTCGATTCTCAGATATAATTCATG
** *
531592 CATTAGTCTAATCCTTGTAGTCTGACAT
65 CATTAGTCTAATCCTTACAGTATGACAT
531620 TTACAATCAATCAA-CTTTTCTTTTTTTATATAAAAAAGAATTCGATTCTCAGATATAATTCATG
1 TTACAATCAATCAATC-TTTCTTTTTTTATATAAAAAAGAATTCGATTCTCAGATATAATTCATG
* * * *
531684 TATTAGTCTAATCTTTACAGTTTGGCAT
65 CATTAGTCTAATCCTTACAGTATGACAT
* **
531712 TTACAATCAATCAATTTTTCTTTTTTTCCATAAAAAA
1 TTACAATCAATCAATCTTTCTTTTTTTATATAAAAAA
531749 TTCGATTCTA
Statistics
Matches: 324, Mismatches: 60, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
88 5 0.02
89 56 0.17
90 42 0.13
91 45 0.14
92 143 0.44
93 28 0.09
94 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (92 bp):
TTACAATCAATCAATCTTTCTTTTTTTATATAAAAAAGAATTCGATTCTCAGATATAATTCATGC
ATTAGTCTAATCCTTACAGTATGACAT
Found at i:531800 original size:143 final size:143
Alignment explanation
Indices: 531616--531900 Score: 491
Period size: 143 Copynumber: 2.0 Consensus size: 143
531606 TTGTAGTCTG
* *
531616 ACATTTACAATCAATCAACTTTTCTTTTTTTATATAAAAAAGAATTCGATTCTCAGATATAATTC
1 ACATTTACAAACAATCAACTTTTCTTTTTTTATATAAAAAAGAATCCGATTCTCAGATATAATTC
* * * *
531681 ATGTATTAGTCTAATCTTTACAGTTTGGCATTTACAATCAATCAATTTTTCTTTTTTTCC-ATAA
66 ATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAATCAACTTTTC-TTTTTTCCAATAA
531745 AAAATTCGATTCTA
130 AAAATTCGATTCTA
*
531759 ACATTTACAAACAATCAACTTTTCTTTTTTTATATAAAAAAGAATCCGATTCTCATATATAATTC
1 ACATTTACAAACAATCAACTTTTCTTTTTTTATATAAAAAAGAATCCGATTCTCAGATATAATTC
531824 ATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTCCAATAAA
66 ATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTCCAATAAA
531889 AAATTCGATTCT
131 AAATTCGATTCT
531901 CAGATATAAT
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
142 8 0.06
143 126 0.94
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (143 bp):
ACATTTACAAACAATCAACTTTTCTTTTTTTATATAAAAAAGAATCCGATTCTCAGATATAATTC
ATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTCCAATAAA
AAATTCGATTCTA
Found at i:531931 original size:89 final size:88
Alignment explanation
Indices: 531755--531998 Score: 310
Period size: 89 Copynumber: 2.7 Consensus size: 88
531745 AAAATTCGAT
* * * *
531755 TCTAACATTTACAAACAATCAACTTTTCTTTTTTTATATAAAAAAGAATCCGATTCTCATATATA
1 TCTAACATTTACAATCAATCAACTTTTCTTTTTTCA-AT--AAAA-AATTCGATTCTCAAATATA
531820 ATTCATGCATTAGTCTAATCTTTACAG
62 ATTCATGCATTAGTCTAATCTTTACAG
* *
531847 TCTGACATTTACAATCAATCAACTTTTCTTTTTTCCAATAAAAAATTCGATTCTCAGATATAATT
1 TCTAACATTTACAATCAATCAACTTTTCTTTTTT-CAATAAAAAATTCGATTCTCAAATATAATT
**
531912 CATGCATTAGTCTAATCTTTGTAG
65 CATGCATTAGTCTAATCTTTACAG
* * * * *
531936 TTTAACATTTACAATCAATCAACCTTTC-TTTTTCTATAAAAAAGTTTGATTCTTAAATATAAT
1 TCTAACATTTACAATCAATCAACTTTTCTTTTTTCAATAAAAAA-TTCGATTCTCAAATATAAT
531999 CACATTTATT
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
87 9 0.07
88 21 0.15
89 67 0.49
90 4 0.03
92 34 0.25
93 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (88 bp):
TCTAACATTTACAATCAATCAACTTTTCTTTTTTCAATAAAAAATTCGATTCTCAAATATAATTC
ATGCATTAGTCTAATCTTTACAG
Found at i:532113 original size:24 final size:24
Alignment explanation
Indices: 532085--532134 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
532075 AGTCTGATAT
* *
532085 AAATAATTTTTTATAATTTAATAA
1 AAATAAATTTATATAATTTAATAA
532109 AAATAAATTTATATAATTTAATAA
1 AAATAAATTTATATAATTTAATAA
532133 AA
1 AA
532135 TACTACATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
AAATAAATTTATATAATTTAATAA
Found at i:537276 original size:20 final size:20
Alignment explanation
Indices: 537251--537300 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
537241 GTTAGAAGTA
*
537251 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
537271 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
537291 ATGTATCGAT
1 ATGTATCGAT
537301 GCAAACAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:537358 original size:20 final size:19
Alignment explanation
Indices: 537332--537405 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
537322 ACTGCTAGTT
537332 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-TGA
537351 TCCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
* *
537371 TTATGTATCGATACAAAGCA
1 TCATGTATCGATACAATG-A
*
537391 TAATGTATCGATACA
1 TCATGTATCGATACA
537406 TCTGGGTGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.37
20 31 0.63
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:538090 original size:166 final size:165
Alignment explanation
Indices: 537918--538276 Score: 438
Period size: 165 Copynumber: 2.2 Consensus size: 165
537908 ATTAATTACC
* ** * *
537918 TTTATTTCAAAACAGAATCCATGCATTAGTTTTAT-TTTTCAAATTCCAATCCATATATTAGTCT
1 TTTATTTAAAAACAGAATCCATGCATTAGTCCTATCTTTT-AAACTCCAATCCATACATTAGTCT
* *
537982 ATTCTTTGCAGTCTGACATTTACGATCCATACATTAGTCTTATTAACTT-TTTTCA-AGACAGAA
65 ATT-TTTGCAGTCTGACATTTACAATCCATACATTAGTCTTATCAACTTCTTTT-ATA-ACA-AA
* *
538045 AA-AATTTGATTTCCATTAAAAATCTTTGCATTTATCATA
126 AAGAATTTAATTTCCATTAAAAATCTGTGCATTTATCATA
* * * *
538084 TTTATTTAAAAACAGAATCTATGCATTAGTCCTATCTTTTAAACTCTAATCCATGCATTAGTTTA
1 TTTATTTAAAAACAGAATCCATGCATTAGTCCTATCTTTTAAACTCCAATCCATACATTAGTCTA
* * * * *
538149 TTTTTGTAGTTTGACATTTACAATTCATGCATTAGTCTTATCAACTTCTTTTATATCAAAAAGAA
66 TTTTTGCAGTCTGACATTTACAATCCATACATTAGTCTTATCAACTTCTTTTATAACAAAAAGAA
**
538214 TTTAATTTTTATTAAAAATCTGTGCATTTATCATA
131 TTTAATTTCCATTAAAAATCTGTGCATTTATCATA
* * *
538249 TCTACTTAAAAACAGAATTCATGCATTA
1 TTTATTTAAAAACAGAATCCATGCATTA
538277 ATCTCATCTT
Statistics
Matches: 165, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
164 4 0.02
165 99 0.60
166 58 0.35
167 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.43
Consensus pattern (165 bp):
TTTATTTAAAAACAGAATCCATGCATTAGTCCTATCTTTTAAACTCCAATCCATACATTAGTCTA
TTTTTGCAGTCTGACATTTACAATCCATACATTAGTCTTATCAACTTCTTTTATAACAAAAAGAA
TTTAATTTCCATTAAAAATCTGTGCATTTATCATA
Found at i:541524 original size:22 final size:22
Alignment explanation
Indices: 541499--541542 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
541489 TATAATTATG
541499 ATTTTGATAAGTT-ATAAAATAT
1 ATTTTGATAA-TTAATAAAATAT
*
541521 ATTTTTATAATTAATAAAATAT
1 ATTTTGATAATTAATAAAATAT
541543 TAAATGTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTTGATAATTAATAAAATAT
Found at i:544772 original size:13 final size:13
Alignment explanation
Indices: 544754--544779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
544744 ACACCAAAGT
544754 ATGTATCGATACA
1 ATGTATCGATACA
544767 ATGTATCGATACA
1 ATGTATCGATACA
544780 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:544777 original size:33 final size:33
Alignment explanation
Indices: 544735--544799 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
544725 TAGCCAAACT
* *
544735 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
544768 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
544800 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:548313 original size:15 final size:15
Alignment explanation
Indices: 548293--548322 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
548283 CTAAATTGAG
548293 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
548308 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
548323 ATCGATGAAC
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:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Done.