Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006874.1 Hibiscus syriacus cultivar Beakdansim tig00017506_pilon, whole genome shotgun sequence
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: 250946
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:10812 original size:31 final size:31
Alignment explanation
Indices: 10770--10868 Score: 144
Period size: 31 Copynumber: 3.2 Consensus size: 31
10760 TAATAAATCA
*
10770 ATCACTGACGTTATCGATTTGTAACAAAATG
1 ATCACTAACGTTATCGATTTGTAACAAAATG
10801 ATCACTAACGTTATCGATTTGTAACAAAATG
1 ATCACTAACGTTATCGATTTGTAACAAAATG
* * * * *
10832 GTCATTAATGTTATTGATTTGTAACAAAATC
1 ATCACTAACGTTATCGATTTGTAACAAAATG
10863 ATCACT
1 ATCACT
10869 CTACTGTCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (31 bp):
ATCACTAACGTTATCGATTTGTAACAAAATG
Found at i:13097 original size:38 final size:38
Alignment explanation
Indices: 13026--13100 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
13016 AGAAGAGAGT
* *
13026 GAGTCATAACTTATTTTTAAACTATGTTTTGTATATTC
1 GAGTCATAACTTATTTTTAAACTATGGTCTGTATATTC
13064 GAGTCATAACTTATTTTTAAA-TGATGGTCTGTATATT
1 GAGTCATAACTTATTTTTAAACT-ATGGTCTGTATATT
13101 TTGATTTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.48
Consensus pattern (38 bp):
GAGTCATAACTTATTTTTAAACTATGGTCTGTATATTC
Found at i:16022 original size:20 final size:20
Alignment explanation
Indices: 15994--16032 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15984 CCTATAATCC
* *
15994 AACTCTAATCATACATTATT
1 AACTATAATAATACATTATT
*
16014 AACTATAATAATCCATTAT
1 AACTATAATAATACATTAT
16033 ATACAAATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (20 bp):
AACTATAATAATACATTATT
Found at i:16470 original size:2 final size:2
Alignment explanation
Indices: 16460--16491 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16450 CAAAAAAAAT
16460 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16492 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:22943 original size:23 final size:21
Alignment explanation
Indices: 22916--22958 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
22906 ATATAAAAAA
22916 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
22937 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
22958 T
1 T
22959 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:24395 original size:53 final size:52
Alignment explanation
Indices: 24293--24397 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 52
24283 ATAAAGAAAA
* * *
24293 AAGTGTTATGAGCAAAGAGCAGCGGATAATCATAAGGTAACATTAGATAGAG
1 AAGTGTTATGAACAAAGAGCAGCGGATAATCATAAGGTAAAACTAGATAGAG
* *
24345 AAGTGTTCTGAACAAAAGAGCAGCAGG-TAATCATGAA-GTAAAACTCGATAGAG
1 AAGTGTTATGAAC-AAAGAGCAGC-GGATAATCAT-AAGGTAAAACTAGATAGAG
24398 CACCTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
52 11 0.24
53 30 0.67
54 4 0.09
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (52 bp):
AAGTGTTATGAACAAAGAGCAGCGGATAATCATAAGGTAAAACTAGATAGAG
Found at i:27412 original size:15 final size:15
Alignment explanation
Indices: 27392--27473 Score: 86
Period size: 14 Copynumber: 5.8 Consensus size: 15
27382 CATTTTACTT
27392 AAATTATTATTATTA
1 AAATTATTATTATTA
*
27407 AAATTA--A-AATTA
1 AAATTATTATTATTA
27419 AAATTATTATTATTA
1 AAATTATTATTATTA
27434 TAAA-TATTATTATT-
1 -AAATTATTATTATTA
*
27448 ATATTATTATTATT-
1 AAATTATTATTATTA
*
27462 ATATTATTATTA
1 AAATTATTATTA
27474 AATAATTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
12 10 0.17
13 3 0.05
14 23 0.39
15 20 0.34
16 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:27417 original size:21 final size:22
Alignment explanation
Indices: 27391--27475 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 22
27381 TCATTTTACT
27391 TAAATTATTATTATTAAAATTA
1 TAAATTATTATTATTAAAATTA
** **
27413 -AAATTAAAATTATTATTATTA
1 TAAATTATTATTATTAAAATTA
*
27434 TAAA-TATTATTATTATATTATTA
1 TAAATTATTATTATTA-A-AATTA
* *
27457 TTATTATATTATTATTAAA
1 TAAAT-TATTATTATTAAA
27476 TAATTATTAC
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
21 26 0.54
22 3 0.06
23 7 0.15
24 1 0.02
25 11 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATTATTATTATTAAAATTA
Found at i:27473 original size:11 final size:11
Alignment explanation
Indices: 27421--27471 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
27411 TAAAATTAAA
27421 ATTATTATTATT
1 ATTA-TATTATT
*
27433 ATAAATATTATT
1 AT-TATATTATT
27445 ATTATATTATT
1 ATTATATTATT
27456 ATTAT-TATATT
1 ATTATAT-TATT
27467 ATTAT
1 ATTAT
27472 TAAATAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 1 0.03
11 22 0.63
12 11 0.31
13 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATATTATT
Found at i:27484 original size:3 final size:3
Alignment explanation
Indices: 27421--27473 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
27411 TAAAATTAAA
* *
27421 ATT ATT ATT ATT ATA AAT ATT ATT ATT A-T ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27467 ATT ATT A
1 ATT ATT A
27474 AATAATTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:28197 original size:13 final size:13
Alignment explanation
Indices: 28179--28207 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28169 ACCACCGTTA
28179 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
28192 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
28205 CGG
1 CGG
28208 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:28797 original size:19 final size:19
Alignment explanation
Indices: 28759--28796 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28749 TATAATTTAG
28759 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
28778 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
28796 T
1 T
28797 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:28914 original size:13 final size:13
Alignment explanation
Indices: 28896--28934 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
28886 GTAATTAAAT
28896 TTTTAAATATTTA
1 TTTTAAATATTTA
*
28909 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
28923 TTTT-AATATTTA
1 TTTTAAATATTTA
28935 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:29574 original size:20 final size:21
Alignment explanation
Indices: 29551--29602 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
29541 AGAAATTAAA
29551 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
29571 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
29593 -ATT-ATTTATT
1 AATTCATTTATT
29603 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:36718 original size:83 final size:83
Alignment explanation
Indices: 36579--36833 Score: 474
Period size: 83 Copynumber: 3.1 Consensus size: 83
36569 GTAATTGGGA
36579 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
36644 TTTAGAAGATGAATGTGC
66 TTTAGAAGATGAATGTGC
36662 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
36727 TTTAGAAGATGAATGTGC
66 TTTAGAAGATGAATGTGC
* *
36745 TCATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTATACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
* *
36810 TTTAAAAGATGAATTTGC
66 TTTAGAAGATGAATGTGC
36828 TCATAG
1 TCATAG
36834 GAGAAATAAG
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 168 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (83 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
TTTAGAAGATGAATGTGC
Found at i:39612 original size:22 final size:22
Alignment explanation
Indices: 39544--39623 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
39534 TACATCTGCA
* *
39544 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
39566 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
39588 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
39610 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
39624 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:40441 original size:76 final size:76
Alignment explanation
Indices: 40292--41313 Score: 1864
Period size: 76 Copynumber: 13.4 Consensus size: 76
40282 CTATTTCTCA
*
40292 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
40357 AAAGCCTTCGGGT
64 AAAGCCTTCGGGT
40370 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
40435 ATCCTTCGGGT
66 AGCCTTCGGGT
*
40446 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGTAGCTTTTTGATGTTTTC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
40511 AAAGCCTTCGGGT
64 AAAGCCTTCGGGT
*
40524 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40589 AGCCTTCGGGT
66 AGCCTTCGGGT
*
40600 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
40665 ATCCTTCGGGT
66 AGCCTTCGGGT
* *
40676 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40741 AGCCTTCGGGT
66 AGCCTTCGGGT
*
40752 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40817 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
40828 CATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40893 AGCCTTCGGGT
66 AGCCTTCGGGT
40904 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40969 AGCCTTCGGGT
66 AGCCTTCGGGT
*
40980 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41045 AGCCTTCGGGT
66 AGCCTTCGGGT
41056 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41121 AGCCTTCGGGT
66 AGCCTTCGGGT
*
41132 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
41197 AGCCTTCGGGT
66 AGCCTTCGGGT
41208 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
41273 ATCCTTCGGGT
66 AGCCTTCGGGT
* *
41284 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTT
41314 TTAAGACCTC
Statistics
Matches: 918, Mismatches: 24, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
76 813 0.89
78 105 0.11
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:41548 original size:14 final size:13
Alignment explanation
Indices: 41463--41551 Score: 80
Period size: 14 Copynumber: 7.0 Consensus size: 13
41453 TTCATTTTAC
41463 TTAAATTATTATTA
1 TTAAA-TATTATTA
**
41477 TTAAA-ATTAAAA
1 TTAAATATTATTA
*
41489 TT-ATTATTATTA
1 TTAAATATTATTA
41501 -TAAATATTATTA
1 TTAAATATTATTA
41513 TT--ATATTATTA
1 TTAAATATTATTA
*
41524 TTATTATATTATTA
1 TTA-AATATTATTA
41538 TTAAATAATTATTA
1 TTAAAT-ATTATTA
41552 CAAACCCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 13 0.21
12 21 0.34
13 3 0.05
14 24 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATATTATTA
Found at i:41551 original size:3 final size:3
Alignment explanation
Indices: 41467--41540 Score: 80
Period size: 3 Copynumber: 25.3 Consensus size: 3
41457 TTTTACTTAA
** ** * *
41467 ATT ATT ATT ATT AAA ATT AAA ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41515 A-T ATT ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
41541 AATAATTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:41989 original size:13 final size:13
Alignment explanation
Indices: 41971--41995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41961 GCAGAGAACG
41971 ACAAAAAAAAAAA
1 ACAAAAAAAAAAA
41984 ACAAAAAAAAAA
1 ACAAAAAAAAAA
41996 CAAAGCAAGA
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
ACAAAAAAAAAAA
Found at i:41991 original size:11 final size:11
Alignment explanation
Indices: 41975--41999 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41965 AGAACGACAA
41975 AAAAAAAAAAC
1 AAAAAAAAAAC
41986 AAAAAAAAAAC
1 AAAAAAAAAAC
41997 AAA
1 AAA
42000 GCAAGAGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:42264 original size:13 final size:13
Alignment explanation
Indices: 42246--42274 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42236 ACCACCGTTA
42246 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
42259 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
42272 CGG
1 CGG
42275 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:42864 original size:19 final size:19
Alignment explanation
Indices: 42826--42863 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
42816 TATAATTTAG
42826 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
42845 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
42863 T
1 T
42864 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:42978 original size:13 final size:13
Alignment explanation
Indices: 42960--42998 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
42950 GTAATTAAAT
42960 TTTTAAATATTTA
1 TTTTAAATATTTA
*
42973 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
42987 TTTT-AATATTTA
1 TTTTAAATATTTA
42999 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:46296 original size:3 final size:3
Alignment explanation
Indices: 46288--46341 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
46278 ATGGACTATA
*
46288 AAG AAG AAG AAG AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
46336 AAG AAG
1 AAG AAG
46342 TAATAATGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:50018 original size:2 final size:2
Alignment explanation
Indices: 50011--50042 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50001 TGTTAGGTCC
50011 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
50043 TAGGGAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:60312 original size:29 final size:30
Alignment explanation
Indices: 60279--60342 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
60269 ATTTTGTTAG
*
60279 AATTTTTA-GGAATTT-AGGAGTTTTTTTGA
1 AATTTTTATGAAATTTAAGG-GTTTTTTTGA
*
60308 AA-TTTTATGAAATTTAAGGGTTTTTTTGG
1 AATTTTTATGAAATTTAAGGGTTTTTTTGA
60337 AATTTT
1 AATTTT
60343 AATAACTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.17
29 19 0.63
30 6 0.20
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (30 bp):
AATTTTTATGAAATTTAAGGGTTTTTTTGA
Found at i:62479 original size:69 final size:66
Alignment explanation
Indices: 62333--62670 Score: 269
Period size: 66 Copynumber: 5.0 Consensus size: 66
62323 TGCAGCAGCA
* * * * * *
62333 GCAGCAACAACAACTAGTTCAAGATTTTAGTTATACATTGCAGCAACCCCATTTTGATCATCAGT
1 GCAGCAACAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGATCAACAGT
62398 T
66 T
* * *
62399 GCAGCAGCAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCTCAATTTGATCAACGGT
1 GCAGCAACAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGATCAACAGT
62464 T
66 T
* * *
62465 GCAACAGCAACAACAACGT-GTTCCGGATTGT-GATTATAT-CTTTCAGCAACCCCAATTTGATC
1 G---CAGCAACAACAAC-TAGTTCAGGATTCTAG-TTATATAC-TGCAGCAACCCCAATTTGATC
*
62527 TACAGTT
60 AACAGTT
* * * * * * *
62534 GCAG---CAGCAACTAGTTCCGGATTCTGGTTATATATTGCAGCAACTCCAATTTGAACAACAGC
1 GCAGCAACAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGATCAACAGT
*
62596 A
66 T
* * * *
62597 GCAGCAGAGATAACATCAACAACTTCAGGATTCT-GTTTATATATTGTC-GCAACCCCAATTTGA
1 GCAGC------AACAACAACTAGTTCAGGATTCTAG-TTATATACTG-CAGCAACCCCAATTTGA
62660 TCAACAGTT
58 TCAACAGTT
62669 GC
1 GC
62671 GACAACCATC
Statistics
Matches: 219, Mismatches: 33, Indels: 34
0.77 0.12 0.12
Matches are distributed among these distances:
62 1 0.00
63 49 0.22
64 1 0.00
66 61 0.28
68 2 0.01
69 53 0.24
70 1 0.00
71 1 0.00
72 49 0.22
73 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (66 bp):
GCAGCAACAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCCCAATTTGATCAACAGT
T
Found at i:62649 original size:135 final size:132
Alignment explanation
Indices: 62325--62670 Score: 340
Period size: 135 Copynumber: 2.6 Consensus size: 132
62315 TCAACAGTTG
* * * * * * * *
62325 CAGCAGCAGCAGCAACAACAACTAGTTCAAGATT-TTAGTTATACATTGCAGCAACCCCATTTTG
1 CAGCAGCAACAGCAACAACAACAACTTCAGGATTCTGA-TTATATATTTCAGCAACCCCAATTTG
62389 ATCATCAGTTGCAGCAGCAACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCTCAATTT
65 ATCA-CAGTTGCAGCAG--ACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCTCAATTT
*
62454 GATCAA
127 GAACAA
* ** *** * * *
62460 CGGTTGCAACAGCAACAACAACGTGTTCCGGATTGTGATTATATCTTTCAGCAACCCCAATTTGA
1 CAGCAGCAACAGCAACAACAACAACTTCAGGATTCTGATTATATATTTCAGCAACCCCAATTTGA
* * *
62525 TCTACAGTTGCAGCAG-CAACTAGTTCCGGATTCTGGTTATATATTGCAGCAA-CTCCAATTTGA
66 TC-ACAGTTGCAGCAGACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCT-CAATTTGA
62588 ACAA
129 ACAA
* * * *
62592 CAGCAGCAGCAGAGATAACATCAACAACTTCAGGATTCTGTTTATATATTGTC-GCAACCCCAAT
1 CAGCAGCA--ACAG-CAACAACAACAACTTCAGGATTCTGATTATATATT-TCAGCAACCCCAAT
62656 TTGATCAACAGTTGC
62 TTGATC-ACAGTTGC
62671 GACAACCATC
Statistics
Matches: 173, Mismatches: 31, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
131 2 0.01
132 49 0.28
134 3 0.02
135 114 0.66
136 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (132 bp):
CAGCAGCAACAGCAACAACAACAACTTCAGGATTCTGATTATATATTTCAGCAACCCCAATTTGA
TCACAGTTGCAGCAGACAACTAGTTCAGGATTCTAGTTATATACTGCAGCAACCTCAATTTGAAC
AA
Found at i:65357 original size:3 final size:3
Alignment explanation
Indices: 65349--65397 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
65339 AAATATTAAA
65349 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
65397 T
1 T
65398 TTTCTAGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:69694 original size:2 final size:2
Alignment explanation
Indices: 69689--69719 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69679 TTAAAAAATA
69689 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69720 ACTTGACAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73941 original size:19 final size:19
Alignment explanation
Indices: 73917--73953 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73907 ATGATCAACA
*
73917 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
73936 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
73954 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:76443 original size:109 final size:109
Alignment explanation
Indices: 76248--76447 Score: 348
Period size: 109 Copynumber: 1.8 Consensus size: 109
76238 TTCAAAATTA
76248 TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCACTTTTGCATTAAATAGGAACTAGGACA
1 TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCACTTTTGCATTAAATAGGAACTAGGACA
**
76313 CAACACAAAGGATTTTGCGATAGGGAAGACAGGTAGGACTCAAT
66 CAACACAAAGGATTTCACGATAGGGAAGACAGGTAGGACTCAAT
*
76357 TCACCATAAGACTTAGATAGTTAGATTTAGCACAAG-AGCTTTTGCATTAAATAGGAACTAGGAC
1 TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCA-CTTTTGCATTAAATAGGAACTAGGAC
*
76421 ACAACACAAAGGGTTTCACGATAGGGA
65 ACAACACAAAGGATTTCACGATAGGGA
76448 CACAACACAA
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
108 1 0.01
109 85 0.99
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (109 bp):
TCACCATAAGACTAAGATAGTTAGATTTAGCACAAGCACTTTTGCATTAAATAGGAACTAGGACA
CAACACAAAGGATTTCACGATAGGGAAGACAGGTAGGACTCAAT
Found at i:81254 original size:60 final size:60
Alignment explanation
Indices: 81188--81312 Score: 142
Period size: 60 Copynumber: 2.1 Consensus size: 60
81178 TAAAGTACAC
* *
81188 AAATGGTCCCCTGACTATAGAGTATTATTTTATTAAGTCTCTCAACAATTAAAAGTTAAA
1 AAATGGTCACCTGACTATAGAATATTATTTTATTAAGTCTCTCAACAATTAAAAGTTAAA
* ** * * * * * * *
81248 AAATGGTTATTTGGCTATAGAATGTTGTTTTATTGAGTCTCTCGACTATTAAAAGTTACA
1 AAATGGTCACCTGACTATAGAATATTATTTTATTAAGTCTCTCAACAATTAAAAGTTAAA
81308 AAATG
1 AAATG
81313 ATCTCTCGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (60 bp):
AAATGGTCACCTGACTATAGAATATTATTTTATTAAGTCTCTCAACAATTAAAAGTTAAA
Found at i:91657 original size:16 final size:16
Alignment explanation
Indices: 91619--91657 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
91609 AGCAACCTTA
91619 GGGACTCGGTCGATTG
1 GGGACTCGGTCGATTG
*
91635 GGTACTCGG-CGATTCG
1 GGGACTCGGTCGATT-G
91651 GGGACTC
1 GGGACTC
91658 ATCGAAGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.13, C:0.23, G:0.41, T:0.23
Consensus pattern (16 bp):
GGGACTCGGTCGATTG
Found at i:96050 original size:20 final size:20
Alignment explanation
Indices: 95956--96148 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
95946 GATGTTCCAG
* ** *
95956 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
95976 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
95996 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
96016 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
96036 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
96056 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
96076 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
96096 AATCGTAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
96117 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
96137 AATCGCAACGCG
1 AATCGCAACGCG
96149 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 130 0.87
21 18 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:96567 original size:33 final size:33
Alignment explanation
Indices: 96528--96598 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
96518 TTCACTTAGA
96528 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
96561 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
96594 TTTCA
1 TTTCA
96599 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:96704 original size:21 final size:20
Alignment explanation
Indices: 96678--96784 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
96668 TGCAGAAGAG
96678 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
96699 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
96719 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
96741 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
96755 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
96774 TCGCAACGAGA
1 TCGCAACGAGA
96785 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:96758 original size:14 final size:14
Alignment explanation
Indices: 96739--96795 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
96729 GAAAAATGAA
96739 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
96753 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
96772 AATCGCAACGAGAG
1 AATCGCAACGAGAG
96786 AATCGCAACG
1 AATCGCAACG
96796 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:96770 original size:33 final size:33
Alignment explanation
Indices: 96732--96811 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
96722 GCAACGAGAA
96732 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
96765 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
96798 AAACCAAAATCGCA
1 AAATGAAAATCGCA
96812 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:99773 original size:3 final size:3
Alignment explanation
Indices: 99755--99844 Score: 98
Period size: 3 Copynumber: 30.7 Consensus size: 3
99745 CAAATAGTTG
* *
99755 TAA TAAA TAT TAA TAA TAA TAA TGAA TAA TAA TAA TAA TAA TCA T-A
1 TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* *
99801 TAA T-A TAA TAA TAA TAA TAA TTA TAA TTA TAA T-A TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
99845 TTTATATCCC
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
2 8 0.11
3 60 0.81
4 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:99777 original size:19 final size:19
Alignment explanation
Indices: 99755--99834 Score: 81
Period size: 19 Copynumber: 4.1 Consensus size: 19
99745 CAAATAGTTG
99755 TAATAAATATTAATAATAA
1 TAATAAATATTAATAATAA
* *
99774 TAATGAATAATAATAATAA
1 TAATAAATATTAATAATAA
*
99793 TAATCATATAATATAATAATAA
1 TAAT-AAAT-AT-TAATAATAA
* *
99815 TAATAATTA-TAATTATAA
1 TAATAAATATTAATAATAA
99833 TA
1 TA
99835 TAATATAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
18 10 0.20
19 21 0.42
20 3 0.06
21 3 0.06
22 13 0.26
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
TAATAAATATTAATAATAA
Found at i:99788 original size:25 final size:24
Alignment explanation
Indices: 99755--99844 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 24
99745 CAAATAGTTG
*
99755 TAATAAATATTAATAATAATAATGAA
1 TAAT-AATAATAATAATAATAAT-AA
*
99781 TAATAATAATAATAATCAT-ATAA
1 TAATAATAATAATAATAATAATAA
*
99804 T-ATAATAATAATAATAATTATAA
1 TAATAATAATAATAATAATAATAA
*
99827 TTATAAT-ATAAT-ATAATA
1 TAATAATAATAATAATAATA
99845 TTTATATCCC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
22 21 0.36
23 13 0.22
24 7 0.12
25 13 0.22
26 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (24 bp):
TAATAATAATAATAATAATAATAA
Found at i:99850 original size:25 final size:26
Alignment explanation
Indices: 99755--99846 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 26
99745 CAAATAGTTG
* *
99755 TAATAAATATTAATAATAATAAT-GAA
1 TAAT-AATATTAATAATTATAATATAA
*
99781 TAATAATAATAATAATCATATAATATAA
1 TAATAATATTAATAAT--TATAATATAA
*
99809 TAATAATAATAATTATAATTATAATATAA
1 TAATAAT-AT--TAATAATTATAATATAA
99838 T-ATAATATT
1 TAATAATATT
99847 TATATCCCGG
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 12 0.22
26 4 0.07
27 7 0.13
28 14 0.25
29 12 0.22
31 6 0.11
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (26 bp):
TAATAATATTAATAATTATAATATAA
Found at i:100165 original size:52 final size:52
Alignment explanation
Indices: 100102--100654 Score: 944
Period size: 52 Copynumber: 10.6 Consensus size: 52
100092 TCGCTCTCTA
* *
100102 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
100154 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
100206 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* *
100258 TTTCTTCATGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * * *
100310 TTTCTTCAGGGACTAGAACTCAAAAAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
100362 TTTCTTCAAGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
100414 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
100466 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
100518 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
100570 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
100622 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
100655 CCAACGATCG
Statistics
Matches: 472, Mismatches: 29, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 472 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
Found at i:100263 original size:24 final size:24
Alignment explanation
Indices: 100236--100316 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
100226 CGAACAATAA
*
100236 TCTTCCTACGAGACTGCCCAATTT
1 TCTTCCTACGAGACTGACCAATTT
* * * **
100260 TCTTCATGGACTAGAACTCGAACAATAA
1 TCTTCCT--ACGAG-ACT-GACCAATTT
*
100288 TCTTCCTACGAGACTGTCCAATTT
1 TCTTCCTACGAGACTGACCAATTT
100312 TCTTC
1 TCTTC
100317 AGGGACTAGA
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
24 16 0.39
25 3 0.07
26 8 0.20
27 3 0.07
28 11 0.27
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.33
Consensus pattern (24 bp):
TCTTCCTACGAGACTGACCAATTT
Found at i:100709 original size:55 final size:55
Alignment explanation
Indices: 100650--100929 Score: 465
Period size: 55 Copynumber: 5.1 Consensus size: 55
100640 CTCGAACAAT
* *
100650 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
100705 AATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
100760 AATCTTCAACCATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
100813 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
100868 AATCTTCAACGATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
100923 AATCTTC
1 AATCTTC
100930 TTTTGCTTCA
Statistics
Matches: 209, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
53 48 0.23
54 4 0.02
55 157 0.75
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
AATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:100854 original size:108 final size:110
Alignment explanation
Indices: 100650--100929 Score: 483
Period size: 108 Copynumber: 2.6 Consensus size: 110
100640 CTCGAACAAT
*
100650 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
100715 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* * *
100760 AATCTTCAACCATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
100823 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
*
100868 AATCTTCAACGATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
100930 TTTTGCTTCA
Statistics
Matches: 159, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
108 100 0.63
109 4 0.03
110 55 0.35
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (110 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:102250 original size:8 final size:8
Alignment explanation
Indices: 102207--102331 Score: 64
Period size: 8 Copynumber: 15.6 Consensus size: 8
102197 TTGAACCCCC
102207 TTTTTATT
1 TTTTTATT
*
102215 TTTTTGGTT
1 TTTTT-ATT
*
102224 TTTTT-TC
1 TTTTTATT
* *
102231 TTCTT-CT
1 TTTTTATT
102238 TTTTTATT
1 TTTTTATT
102246 TTTTTATT
1 TTTTTATT
*
102254 TTTTCCATT
1 TTTT-TATT
*
102263 TTTCTATT
1 TTTTTATT
*
102271 TTTCTA--
1 TTTTTATT
*
102277 -TTTCATT
1 TTTTTATT
102284 TTTTTCATT
1 TTTTT-ATT
*
102293 TTTTCATTT
1 TTTTTA-TT
102302 TTTTTCATT
1 TTTTT-ATT
102311 TTTTTCA-T
1 TTTTT-ATT
*
102319 TTTTCATT
1 TTTTTATT
102327 TTTTT
1 TTTTT
102332 TATCTTTAAG
Statistics
Matches: 90, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
5 3 0.03
7 10 0.11
8 41 0.46
9 35 0.39
10 1 0.01
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTATT
Found at i:102256 original size:9 final size:9
Alignment explanation
Indices: 102207--102334 Score: 59
Period size: 9 Copynumber: 13.8 Consensus size: 9
102197 TTGAACCCCC
102207 TTTTTATTT
1 TTTTTATTT
*
102216 TTTTGGTTTTT
1 TTTT--TATTT
*
102227 TTTCTTCTTCT
1 TTT-TTATT-T
102238 TTTTTA-TT
1 TTTTTATTT
102246 TTTTTATTT
1 TTTTTATTT
**
102255 TTTCCATTT
1 TTTTTATTT
102264 TTCTATT-TTT
1 TT-T-TTATTT
*
102274 CTATTTCATTT
1 -T-TTTTATTT
*
102285 TTTTCA-TT
1 TTTTTATTT
*
102293 TTTTCATTT
1 TTTTTATTT
102302 TTTTTCATTT
1 TTTTT-ATTT
*
102312 TTTTCA--T
1 TTTTTATTT
*
102319 TTTTCATTT
1 TTTTTATTT
102328 TTTTTAT
1 TTTTTAT
102335 CTTTAAGCAA
Statistics
Matches: 94, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
7 7 0.07
8 15 0.16
9 35 0.37
10 19 0.20
11 16 0.17
12 2 0.02
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTTATTT
Found at i:102265 original size:38 final size:38
Alignment explanation
Indices: 102223--102305 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
102213 TTTTTTTGGT
* * *
102223 TTTTTTTCTTCTTCTTTTTTATTTTTTT-ATTTTTTCCA
1 TTTTTTTATTCTTCTATTTCATTTTTTTCATTTTTT-CA
* *
102261 TTTTTCTATTTTTCTATTTCATTTTTTTCATTTTTTCA
1 TTTTTTTATTCTTCTATTTCATTTTTTTCATTTTTTCA
102299 TTTTTTT
1 TTTTTTT
102306 TCATTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 31 0.82
39 7 0.18
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (38 bp):
TTTTTTTATTCTTCTATTTCATTTTTTTCATTTTTTCA
Found at i:102315 original size:27 final size:25
Alignment explanation
Indices: 102237--102331 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 25
102227 TTTCTTCTTC
* *
102237 TTTTTTATTTTTTT-ATTTTTTCCA
1 TTTTTCATTTTTTTCATTTTTTTCA
102261 TTTTTCTATTTTTCTATTTCATTTTTTTCA
1 TTTTTC-A--TTT-T-TTTCATTTTTTTCA
102291 TTTTTTCATTTTTTTTCATTTTTTTCA
1 -TTTTTCA-TTTTTTTCATTTTTTTCA
102318 TTTTTCATTTTTTT
1 TTTTTCATTTTTTT
102332 TATCTTTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
24 5 0.08
25 8 0.13
26 7 0.11
27 17 0.27
28 2 0.03
29 7 0.11
30 10 0.16
31 6 0.10
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTCATTTTTTTCATTTTTTTCA
Found at i:103841 original size:14 final size:14
Alignment explanation
Indices: 103824--103853 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
103814 GAAATCAAGT
103824 TTTGAAATTAGAAA
1 TTTGAAATTAGAAA
103838 TTTGAAATTAGAAA
1 TTTGAAATTAGAAA
103852 TT
1 TT
103854 ACTCCCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (14 bp):
TTTGAAATTAGAAA
Found at i:106140 original size:21 final size:21
Alignment explanation
Indices: 106114--106153 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
106104 CAGAACCCCA
*
106114 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
106135 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
106154 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:113083 original size:3 final size:3
Alignment explanation
Indices: 113069--113100 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
113059 GTACCAAGGC
113069 CTT CTAT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT C
113101 AATACTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:114523 original size:2 final size:2
Alignment explanation
Indices: 114516--114553 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
114506 CCGGAAGAGA
114516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
114554 GGGAGAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120808 original size:3 final size:3
Alignment explanation
Indices: 120790--120853 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
120780 CAAATAGTTG
* *
120790 TAA TAAA TAT TAA TAA TAA TAA TGAA TAA TAA TAA TAA TAA TCA T-A
1 TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
120836 TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
120854 TATTATTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:120812 original size:19 final size:19
Alignment explanation
Indices: 120790--120876 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
120780 CAAATAGTTG
120790 TAATAAATATTAATAATAA
1 TAATAAATATTAATAATAA
* *
120809 TAATGAATAATAATAATAA
1 TAATAAATATTAATAATAA
* *
120828 TAAT-CATATAATATAATAA
1 TAATAAATATTA-ATAATAA
* * *
120847 TAATAATTATT-ATTATTA
1 TAATAAATATTAATAATAA
120865 TAATATAATATT
1 TAATA-AATATT
120877 TATATCTCGG
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
18 14 0.26
19 37 0.69
20 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (19 bp):
TAATAAATATTAATAATAA
Found at i:122296 original size:93 final size:93
Alignment explanation
Indices: 122137--122359 Score: 401
Period size: 93 Copynumber: 2.4 Consensus size: 93
122127 TAGATTGCTT
*
122137 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
122202 TTTGTCTTTGTTTTATCTTTTGGTTAAA
66 TTTGTCTTTGTTTTATCTTTTAGTTAAA
122230 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
* *
122295 TTTGTCTTTGTTTTGTCTTTTAGTTGAA
66 TTTGTCTTTGTTTTATCTTTTAGTTAAA
*
122323 AGTAAATTTGTTTGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
122360 AATACCCTGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 125 1.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTATCTTTTAGTTAAA
Found at i:122510 original size:33 final size:33
Alignment explanation
Indices: 122457--122580 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
122447 TAGTTTACTT
* *
122457 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGAGAGAA
* **
122491 TCGTAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGAGAGAA
* *
122524 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGAGAGAA
122557 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
122581 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGAGAGAA
Found at i:122517 original size:19 final size:18
Alignment explanation
Indices: 122489--122580 Score: 56
Period size: 19 Copynumber: 5.4 Consensus size: 18
122479 GCAACGAGAG
*
122489 AATCGTAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
122508 AATCGCAA--CG--AGAG
1 AATCGCAACGCGAAAGAA
*
122522 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
122541 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
122555 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
122574 AATCGCA
1 AATCGCA
122581 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 21 0.36
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 26 0.44
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:122527 original size:14 final size:14
Alignment explanation
Indices: 122475--122531 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
122465 CGAAACTTAA
122475 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
122489 AATCGTAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
122508 AATCGCAACGAGAG
1 AATCGCAACGAGAG
122522 AATCGCAACG
1 AATCGCAACG
122532 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:122557 original size:14 final size:14
Alignment explanation
Indices: 122506--122564 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
122496 ACGCGAAATG
*
122506 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
122520 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
122539 AAAATCGCAACGAC
1 AAAATCGCAACGAC
122553 AAAATCGCAACG
1 AAAATCGCAACG
122565 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 9 0.24
ACGTcount: A:0.47, C:0.27, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:122598 original size:19 final size:19
Alignment explanation
Indices: 122576--122748 Score: 132
Period size: 19 Copynumber: 9.6 Consensus size: 19
122566 GAAACCAAAA
*
122576 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
122595 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
122609 TCTCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
122628 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
122644 T--CGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
**
122661 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
122680 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
122699 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
122718 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
122738 TCGTGTTGCGA
1 TCGCGTTGCGA
122749 AAGTAAACTA
Statistics
Matches: 123, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
14 15 0.12
16 7 0.06
17 8 0.07
19 81 0.66
20 12 0.10
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:122621 original size:33 final size:33
Alignment explanation
Indices: 122579--122673 Score: 145
Period size: 33 Copynumber: 2.9 Consensus size: 33
122569 ACCAAAATCG
*
122579 CATTGCGATTTTCATTTCGCGTTGTGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
122612 CATTGCGATTTTCATTTCGCATTGCGATTCTGT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
122645 CGTTGCGATTTTTATTTCGCGTTGCGATT
1 CATTGCGATTTTCATTTCGCGTTGCGATT
122674 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:122706 original size:38 final size:38
Alignment explanation
Indices: 122576--122748 Score: 132
Period size: 33 Copynumber: 4.8 Consensus size: 38
122566 GAAACCAAAA
* * *
122576 TCGCATTGCGATTTTCATTTCGCGTTGTGATTCTC---
1 TCGCGTTGCGATTTTGATTTCGCGTTGCGATTCTCATT
* * * *
122611 T--CATTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTGATTTCGCGTTGCGATTCTCATT
* * **
122644 T--CGTTGCGATTTTTATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTGATTTCGCGTTGCGATTCTCATT
* *
122680 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTGATTTCGCGTTGCGATTCTCATT
* *
122718 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTGA-TTTCGCGTTGCGA
122749 AAGTAAACTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 50 0.44
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTGATTTCGCGTTGCGATTCTCATT
Found at i:124692 original size:14 final size:14
Alignment explanation
Indices: 124673--124708 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
124663 ATTGTTTAAT
124673 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
124687 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
124701 TGATTTGT
1 TGATTTGT
124709 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:124891 original size:20 final size:20
Alignment explanation
Indices: 124815--124942 Score: 177
Period size: 20 Copynumber: 6.9 Consensus size: 20
124805 AAAAATGACT
124815 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
124834 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
*
124853 ATCGCAA--C-G--A-GAGA
1 ATCGCAATGCGGAAATGAAA
124867 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGGAAATGAAA
124887 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGGAAATGAAA
124907 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGGAAATGAAA
124927 ATCGCAA--CGGAAATGA
1 ATCGCAATGCGGAAATGA
124943 TTTTCATTTC
Statistics
Matches: 101, Mismatches: 2, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 1 0.01
17 3 0.03
18 9 0.09
19 27 0.27
20 50 0.50
ACGTcount: A:0.45, C:0.16, G:0.24, T:0.14
Consensus pattern (20 bp):
ATCGCAATGCGGAAATGAAA
Found at i:124965 original size:19 final size:18
Alignment explanation
Indices: 124941--124996 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
124931 CAACGGAAAT
124941 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCG-ATTGC
*
124960 GATTTTCA--T-G-TTGG
1 GATTTTCATTTCGATTGC
124974 GATTTTCATTTCGTATTGC
1 GATTTTCATTTCG-ATTGC
124993 GATT
1 GATT
124997 CTCTCGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 11 0.37
16 2 0.07
17 2 0.07
19 15 0.50
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (18 bp):
GATTTTCATTTCGATTGC
Found at i:125018 original size:33 final size:33
Alignment explanation
Indices: 124948--125029 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
124938 AATGATTTTC
* * * * *
124948 ATTTCGCATTGCGATTTTCATGTTGGGATTTTC
1 ATTTCGTATTGCGATTCTCATGTTGCGATTGTA
124981 ATTTCGTATTGCGATTCTC-TCGTTGCGATTGTA
1 ATTTCGTATTGCGATTCTCAT-GTTGCGATTGTA
*
125014 ATTTCCGTGTTGCGAT
1 ATTT-CGTATTGCGAT
125030 AGTCAAATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 30 0.73
34 10 0.24
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (33 bp):
ATTTCGTATTGCGATTCTCATGTTGCGATTGTA
Found at i:127311 original size:12 final size:12
Alignment explanation
Indices: 127294--127320 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
127284 TCTTCGGGGA
127294 CTTTTTCTTCTT
1 CTTTTTCTTCTT
127306 CTTTTTCTTCTT
1 CTTTTTCTTCTT
127318 CTT
1 CTT
127321 CAGGATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:127530 original size:24 final size:24
Alignment explanation
Indices: 127496--127542 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
127486 CTGAAACATC
127496 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
127520 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
127543 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:128263 original size:20 final size:20
Alignment explanation
Indices: 128235--128463 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
128225 AAATTTCAGT
* * *
128235 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
128255 GTTGCGATTTACGAATTATC
1 GTTGCGATTTACGGATTCGC
* *
128275 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
128295 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
128315 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
128335 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
128355 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
128375 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
128395 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
128415 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
128435 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
128455 GTTGCGATT
1 GTTGCGATT
128464 CTTGAAAATC
Statistics
Matches: 179, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 178 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:128516 original size:21 final size:20
Alignment explanation
Indices: 128431--128528 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
128421 ATTTATGTGT
* *
128431 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
128451 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
128472 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
128493 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
128514 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
128529 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:128524 original size:42 final size:43
Alignment explanation
Indices: 128431--128529 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
128421 ATTTATGTGT
* *
128431 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
128472 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
128514 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
128530 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:129938 original size:32 final size:32
Alignment explanation
Indices: 129902--129962 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
129892 CAATGAAATG
* *
129902 TAATGA-TAATTTTGTAATAATTTAATAAAAGT
1 TAATGACT-ATTTTATAACAATTTAATAAAAGT
*
129934 TAATGACTATTTTATAGCAATTTAATAAA
1 TAATGACTATTTTATAACAATTTAATAAA
129963 GTAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (32 bp):
TAATGACTATTTTATAACAATTTAATAAAAGT
Found at i:132542 original size:2 final size:2
Alignment explanation
Indices: 132535--132606 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
132525 AACAAGGAGA
132535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132607 GAATCTTAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:137836 original size:13 final size:13
Alignment explanation
Indices: 137818--137842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
137808 TATTCGTACA
137818 AAAATAATATTTT
1 AAAATAATATTTT
137831 AAAATAATATTT
1 AAAATAATATTT
137843 AATCAGTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATAATATTTT
Found at i:138408 original size:3 final size:3
Alignment explanation
Indices: 138400--138451 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
138390 AACATAAGTT
138400 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
138448 TTA T
1 TTA T
138452 GTTAGCAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:140214 original size:20 final size:20
Alignment explanation
Indices: 140189--140232 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
140179 AAACAGTACT
140189 ATCGCAACGCGAATAGGAAA
1 ATCGCAACGCGAATAGGAAA
* *
140209 ATCGCAACGTGAATAGTAAA
1 ATCGCAACGCGAATAGGAAA
140229 ATCG
1 ATCG
140233 TAACATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAATAGGAAA
Found at i:140571 original size:20 final size:20
Alignment explanation
Indices: 140548--140601 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
140538 AGTTTGAAAA
*
140548 TCGCGTTGCGATTTCCCTAT
1 TCGCGTTGTGATTTCCCTAT
*
140568 TCGCGTTGTAATTTCCCTAT
1 TCGCGTTGTGATTTCCCTAT
140588 TCGCGTTGTGATTT
1 TCGCGTTGTGATTT
140602 TGGAACCTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (20 bp):
TCGCGTTGTGATTTCCCTAT
Found at i:142589 original size:224 final size:225
Alignment explanation
Indices: 142279--142741 Score: 743
Period size: 224 Copynumber: 2.1 Consensus size: 225
142269 TTGTCGATTT
* *
142279 GTGTCGATACTTTATAAAAAATTTATTGATCCATAACAATATAACAGGTAAAAAATAGACAAAAC
1 GTGTCGATACTTTATAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATAGACAAAAC
* *
142344 CGGTTTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATATTTTATAA
66 CGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
*
142409 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAA
131 AAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATAACAAAACCGGTCTATAAATGACAA
*
142474 AACAGGTAAAACGCTACCT-AATATATTGAAA
195 AACAGATAAAACGCTA-CTGAATATATTGAAA
142505 GTGTCGATACTTTAT-AAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAT-GACAAAAC
1 GTGTCGATACTTTATAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATAGACAAAAC
* *
142568 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTTGATACTTTATAA
66 CGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
* * *
142633 AAATGTATCGATCCATAACAATATAACATGTAAAAAAATAACAAAATCGGTTTATAAATGACAAA
131 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAA
* * * * *
142698 ACATATAAAGCGCTACTGGATATGTTGATA
196 ACAGATAAAACGCTACTGAATATATTGAAA
142728 GTGTCGATACTTTA
1 GTGTCGATACTTTA
142742 ATATAAGTAT
Statistics
Matches: 220, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
222 2 0.01
223 66 0.30
224 99 0.45
225 38 0.17
226 15 0.07
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (225 bp):
GTGTCGATACTTTATAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATAGACAAAAC
CGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAACCGGTCTATAAATGACAAA
ACAGATAAAACGCTACTGAATATATTGAAA
Found at i:142619 original size:111 final size:112
Alignment explanation
Indices: 142279--142741 Score: 723
Period size: 113 Copynumber: 4.1 Consensus size: 112
142269 TTGTCGATTT
* *
142279 GTGTCGATACTTTATAAAAAATTTATTGATCCATAACAATATAACAGGT-AAAAAATAGACAAAA
1 GTGTCGATACTTTAT-AAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAT-GACAAAA
*
142343 CCGGTTTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
64 CCGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
*
142392 GTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
**
142457 CGGTCTATAAATGACAAAACAGGTAAAACGCTACCTAATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
142505 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
142569 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
* * * *
142616 GTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATAACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* ** * * * *
142681 GGTTTATAAATGACAAAACATATAAAGCGCTACTGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
142728 GTGTCGATACTTTA
1 GTGTCGATACTTTA
142742 ATATAAGTAT
Statistics
Matches: 326, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
111 106 0.33
112 99 0.30
113 114 0.35
114 7 0.02
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
Found at i:142920 original size:182 final size:181
Alignment explanation
Indices: 142613--143062 Score: 623
Period size: 182 Copynumber: 2.5 Consensus size: 181
142603 GGATATATTG
* * * *
142613 AAAGTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATAACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * * * *
142678 ATCGGTTTATAAATGACAAAACATATAAAGCGCTACTGGATATGTTGATAGTGTCGATACTTTAA
66 ATCGGTCT-GAAATGACAAAACATATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAA
* * *
142743 TATAAGTATCAACACTTTTGGAATTTAAAAGAGAAGAAGTTACAAAGCTAAT
130 TATAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTACAAAGCCAAT
* *
142795 AAAGTGTCGATACTTTATAAAATTGTATCGATCTATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * * *
142860 ACCGGTCTCGAAATGACAAAAC-TGGTATAGAGTTACCGGATATGTTGAAAGTGTCGATACTTTA
66 ATCGGTCT-GAAATGACAAAACAT-ATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTA
* ** * **
142924 TTATAAGTATTGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGTGCCAAT
129 ATATAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTACAAAGCCAAT
* *
142977 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
143042 ATCGGTCTGGAATGACAAAAC
66 ATCGGTCTGAAATGACAAAAC
143063 CAGTAGTAAA
Statistics
Matches: 236, Mismatches: 31, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
181 13 0.06
182 223 0.94
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (181 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ATCGGTCTGAAATGACAAAACATATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAAT
ATAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTACAAAGCCAAT
Found at i:143536 original size:23 final size:23
Alignment explanation
Indices: 143501--143548 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
143491 AAATAGCTCA
* *
143501 ATATAAGCACTACCTATTACATT
1 ATATAAACACTACCTAATACATT
* *
143524 ATATAAACGCTACCTAATATATT
1 ATATAAACACTACCTAATACATT
143547 AT
1 AT
143549 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACACTACCTAATACATT
Found at i:145646 original size:24 final size:24
Alignment explanation
Indices: 145625--145671 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
145615 GAGTAAAACT
145625 CGATTCTATTCAGGAAAAAAAAAA
1 CGATTCTATTCAGGAAAAAAAAAA
145649 CGATTCTATTCAGGAAAAAAAAA
1 CGATTCTATTCAGGAAAAAAAAA
145672 GATTCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (24 bp):
CGATTCTATTCAGGAAAAAAAAAA
Found at i:145669 original size:22 final size:23
Alignment explanation
Indices: 145625--145681 Score: 89
Period size: 24 Copynumber: 2.5 Consensus size: 23
145615 GAGTAAAACT
145625 CGATTCTATTCAGGAAAAAAAAAA
1 CGATTCTATTCAGG-AAAAAAAAA
145649 CGATTCTATTCAGGAAAAAAAAA
1 CGATTCTATTCAGGAAAAAAAAA
*
145672 -GATTCAATTC
1 CGATTCTATTC
145682 GACTCGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 9 0.28
23 9 0.28
24 14 0.44
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (23 bp):
CGATTCTATTCAGGAAAAAAAAA
Found at i:151169 original size:442 final size:442
Alignment explanation
Indices: 150345--151225 Score: 1582
Period size: 442 Copynumber: 2.0 Consensus size: 442
150335 TGACTAAGTC
*
150345 AATTTTTTTACTTGACTAGACATGTAATTTTATAAGTTCAATTCAAAAAAAAGTTAGAGTTATAA
1 AATTTTTTTACTTGACTAGACATGCAATTTTATAAGTTCAATTCAAAAAAAAGTTAGAGTTATAA
* *
150410 AATAAGACTCAAATAAATCGAATTTTTTAAGGCTTAAATATAAATTAGGTTCCCAATCTATATCG
66 AATAAGACTCAAATAAATCGAATTTTTTAAGGCTTAAATACAAATTAAGTTCCCAATCTATATCG
150475 TTTTTCACGAATAGGTACCTAAAATATTTTTTTACTCATCTCAGTGTCTAACATTACAAACATTA
131 TTTTTCACGAATAGGTACCTAAAATATTTTTTTACTCATCTCAGTGTCTAACATTACAAACATTA
150540 CCATTTTAGGTGCACACGCAGTCAACAGTGCTAATTTATTCTGTTAAGTGATGCATGTCACAATT
196 CCATTTTAGGTGCACACGCAGTCAACAGTGCTAATTTATTCTGTTAAGTGATGCATGTCACAATT
*
150605 TGATGAATTTGAAAAAAAAATATTAAAATAGTATTATATTTATATATAAATTTTTCTTAAATTAT
261 TGATGAATTTGAAAAAAAAATATTAAAATAGTATTATATTTATATATAAATTTCTCTTAAATTAT
* *
150670 AAAAAACCCTAAAATCCCCAAAGTCTAACATTAACCCCTCGCTGCTACTCTTTCCGGCCACTACT
326 AAAAAACCCTAAAATCCCCAAAGTCTAACATTAACCCCTCGCTGCTACCCTTTCCGGCCACGACT
* *
150735 ATCGCCGTTGACGTAGTCCCTACCATCCTCTTAGTCATACGTCATCGTATCA
391 ATCACCGTTGACGTAGTCCCTACCATCCTCTTAGTCATACATCATCGTATCA
*
150787 AATTTTTTTACTTGACTAGACGTGCAATTTTATAAGTTCAATTCAAAAAAAAGTTAGAGTTATAA
1 AATTTTTTTACTTGACTAGACATGCAATTTTATAAGTTCAATTCAAAAAAAAGTTAGAGTTATAA
* * * *
150852 AATAGGACTCAACTAAATCGAATTTTTTAAGGCTTAAATACAAATTAAGTTCTCAATTTATATCG
66 AATAAGACTCAAATAAATCGAATTTTTTAAGGCTTAAATACAAATTAAGTTCCCAATCTATATCG
* * *
150917 TTTTTTACGAATAGGTGCCTAAAATATTTTTTTACTCATTTCAGTGTCTAACATTACAAACATTA
131 TTTTTCACGAATAGGTACCTAAAATATTTTTTTACTCATCTCAGTGTCTAACATTACAAACATTA
*
150982 TCATTTTAGGTGCACACGCAGTCAACAGTGCTAATTTATTCTGTTAAGTGATGCATGTCACAATT
196 CCATTTTAGGTGCACACGCAGTCAACAGTGCTAATTTATTCTGTTAAGTGATGCATGTCACAATT
*
151047 TGATGAATTTGAAAGAAAAATATTAAAATAGTATTATATTTATATATAAATTTCTCTTAAATTAT
261 TGATGAATTTGAAAAAAAAATATTAAAATAGTATTATATTTATATATAAATTTCTCTTAAATTAT
*
151112 AAAAAGCCCTAAAATCCCCAAAGTCTAACATTAACCCCTCGCTGCTACCCTTTCCGGCCACGACT
326 AAAAAACCCTAAAATCCCCAAAGTCTAACATTAACCCCTCGCTGCTACCCTTTCCGGCCACGACT
*
151177 ATCACCGTTGACGTAGTCCCTACCATGCTCTTAGTCATACATCATCGTA
391 ATCACCGTTGACGTAGTCCCTACCATCCTCTTAGTCATACATCATCGTA
151226 GTTGTCATCG
Statistics
Matches: 419, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
442 419 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (442 bp):
AATTTTTTTACTTGACTAGACATGCAATTTTATAAGTTCAATTCAAAAAAAAGTTAGAGTTATAA
AATAAGACTCAAATAAATCGAATTTTTTAAGGCTTAAATACAAATTAAGTTCCCAATCTATATCG
TTTTTCACGAATAGGTACCTAAAATATTTTTTTACTCATCTCAGTGTCTAACATTACAAACATTA
CCATTTTAGGTGCACACGCAGTCAACAGTGCTAATTTATTCTGTTAAGTGATGCATGTCACAATT
TGATGAATTTGAAAAAAAAATATTAAAATAGTATTATATTTATATATAAATTTCTCTTAAATTAT
AAAAAACCCTAAAATCCCCAAAGTCTAACATTAACCCCTCGCTGCTACCCTTTCCGGCCACGACT
ATCACCGTTGACGTAGTCCCTACCATCCTCTTAGTCATACATCATCGTATCA
Found at i:151641 original size:29 final size:29
Alignment explanation
Indices: 151599--151667 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
151589 AATGTTTGTA
151599 ACTTTAGGCACCGGGATGAGTCAAAAAAT
1 ACTTTAGGCACCGGGATGAGTCAAAAAAT
151628 ACTTTAGGCACCGGGATGAGTCAAAAAAT
1 ACTTTAGGCACCGGGATGAGTCAAAAAAT
*
151657 ATTTTAGGCAC
1 ACTTTAGGCAC
151668 ATATTCATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (29 bp):
ACTTTAGGCACCGGGATGAGTCAAAAAAT
Found at i:159223 original size:40 final size:39
Alignment explanation
Indices: 159178--159267 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 39
159168 GTAAGGTATA
*
159178 ATTATTTTTATAATTTATTTTTTTATTC-ATTAACATTT-TT
1 ATTATTTTTATAA-TTAATTTTTTATTCGATT-A-ATTTATT
* *
159218 ATTA-TTTGAGTAATTAATTTTTTATTCGATTAGTTTATT
1 ATTATTTTTA-TAATTAATTTTTTATTCGATTAATTTATT
159257 ATTATTTTTAT
1 ATTATTTTTAT
159268 TTGATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
38 3 0.07
39 25 0.60
40 14 0.33
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.64
Consensus pattern (39 bp):
ATTATTTTTATAATTAATTTTTTATTCGATTAATTTATT
Found at i:161632 original size:26 final size:26
Alignment explanation
Indices: 161596--161645 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
161586 CAATGACACA
*
161596 TCGATATATCTAATAAAATTGTAATC
1 TCGATAGATCTAATAAAATTGTAATC
161622 TCGATAGATCTAATAAAATTGTAA
1 TCGATAGATCTAATAAAATTGTAA
161646 CCTTTTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (26 bp):
TCGATAGATCTAATAAAATTGTAATC
Found at i:164427 original size:16 final size:16
Alignment explanation
Indices: 164406--164437 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
164396 TTTGTTTGAC
164406 GGAAAATAGATTTCGA
1 GGAAAATAGATTTCGA
164422 GGAAAATAGATTTCGA
1 GGAAAATAGATTTCGA
164438 AAAATTAACA
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:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
GGAAAATAGATTTCGA
Found at i:164862 original size:25 final size:27
Alignment explanation
Indices: 164829--164891 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
164819 AATATATTAT
* **
164829 TAATTATATTAATT-ACTTATT-AAAA
1 TAATAATATTAATTAAAATATTAAAAA
164854 TAATAATATT-ATTAAAATATTAAAAA
1 TAATAATATTAATTAAAATATTAAAAA
*
164880 TAAAAATATTAA
1 TAATAATATTAA
164892 AATAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 3 0.10
25 14 0.45
26 13 0.42
27 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (27 bp):
TAATAATATTAATTAAAATATTAAAAA
Found at i:164867 original size:17 final size:17
Alignment explanation
Indices: 164816--164872 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
164806 TTAAAACAAG
164816 AATAAT-ATATTATTAA
1 AATAATAATATTATTAA
* *
164832 TTATATTAATTACTTATTAA
1 -AATAATAA-TA-TTATTAA
164852 AATAATAATATTATTAA
1 AATAATAATATTATTAA
164869 AATA
1 AATA
164873 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 15 0.45
18 3 0.09
19 8 0.24
20 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAATAATATTATTAA
Found at i:164872 original size:14 final size:14
Alignment explanation
Indices: 164846--164904 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
164836 ATTAATTACT
164846 TATTAAAATAATAA
1 TATTAAAATAATAA
*
164860 TATT--ATTAA-AA
1 TATTAAAATAATAA
*
164871 TATTAAAAATAAAAA
1 TATT-AAAATAATAA
*
164886 TATTAAAATAAAAA
1 TATTAAAATAATAA
164900 TATTA
1 TATTA
164905 TATTATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 6 0.15
12 4 0.10
14 23 0.59
15 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:164876 original size:8 final size:8
Alignment explanation
Indices: 164846--164904 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
164836 ATTAATTACT
164846 TATTAAAA
1 TATTAAAA
* *
164854 TAATAATAT
1 TATTAA-AA
164863 TATTAAAA
1 TATTAAAA
164871 TATTAAAA
1 TATTAAAA
*
164879 -ATAAAAA
1 TATTAAAA
164886 TATTAAAA
1 TATTAAAA
164894 TA--AAAA
1 TATTAAAA
164900 TATTA
1 TATTA
164905 TATTATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
6 6 0.15
7 6 0.15
8 23 0.56
9 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TATTAAAA
Found at i:164887 original size:15 final size:15
Alignment explanation
Indices: 164867--164904 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
164857 TAATATTATT
164867 AAAATATTAAAAATA
1 AAAATATTAAAAATA
164882 AAAATATT-AAAATA
1 AAAATATTAAAAATA
164896 AAAATATTA
1 AAAATATTA
164905 TATTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATTAAAAATA
Found at i:184618 original size:21 final size:22
Alignment explanation
Indices: 184589--184635 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
184579 ATTCTGACTA
184589 TCGCATTGCGA-TTTCCTAAAT
1 TCGCATTGCGATTTTCCTAAAT
*
184610 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
184631 TCGCA
1 TCGCA
184636 ACGAGATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:185551 original size:24 final size:24
Alignment explanation
Indices: 185492--185551 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
185482 TAGTCAGTAT
185492 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * * *
185516 -CCAGACTATGATCTTGGTTAATAC
1 TCGA-AATTTGATCTTGGTCAATAC
*
185540 TCGAATTTTGAT
1 TCGAAATTTGAT
185552 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
23 2 0.07
24 23 0.85
25 2 0.07
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:188125 original size:33 final size:33
Alignment explanation
Indices: 188083--188209 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
188073 GGAAATTACT
188083 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
188116 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
188149 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
188182 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCACAACG
188210 CGAATTTAGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:188406 original size:14 final size:13
Alignment explanation
Indices: 188387--188425 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
188377 CATCAATTAA
188387 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
188401 ACAAATCATATTTT
1 ACAAATCA-ATTTT
*
188415 ATAAATCAATT
1 ACAAATCAATT
188426 AAACCATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 19 0.83
15 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:195129 original size:21 final size:21
Alignment explanation
Indices: 195103--195142 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
195093 CCCCCTTTGA
*
195103 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
195124 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
195143 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:201434 original size:20 final size:19
Alignment explanation
Indices: 201388--201425 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
201378 TCTTTTGGTT
201388 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
201407 GAGAATGAAAATCGCAACG
1 GA-AATGAAAATCGCAACG
201426 CGGAAATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.50, C:0.16, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:202206 original size:21 final size:21
Alignment explanation
Indices: 202164--202206 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
202154 TTTCTGGGCT
* *
202164 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
202185 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
202206 A
1 A
202207 ACGAATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:207674 original size:19 final size:19
Alignment explanation
Indices: 207655--207724 Score: 104
Period size: 19 Copynumber: 3.7 Consensus size: 19
207645 CGAACAAGAG
* *
207655 AATCACAACGCGAAATGAG
1 AATCGCAACGCGAAATGAA
*
207674 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
207693 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
207712 AATCGCAATGCGA
1 AATCGCAACGCGA
207725 TTTTGGTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:207770 original size:21 final size:20
Alignment explanation
Indices: 207751--207822 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
207741 CGATTCTCTC
207751 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
* ** *
207771 CATTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
207792 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
207812 GTTGCGATTTT
1 GTTGCGATTTT
207823 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:208374 original size:20 final size:21
Alignment explanation
Indices: 208351--208441 Score: 107
Period size: 20 Copynumber: 4.5 Consensus size: 21
208341 ATGGCGCTAT
*
208351 GTAAATCGCAATGCGA-TTAC
1 GTAAATCGCATTGCGATTTAC
208371 GTAAATCGCATTGCGATTTAC
1 GTAAATCGCATTGCGATTTAC
* *
208392 GT-ATTCGTATTGCGATTTAC
1 GTAAATCGCATTGCGATTTAC
* *
208412 GT-ATTCGCATTGCGATTTAG
1 GTAAATCGCATTGCGATTTAC
*
208432 GAAAATCGCA
1 GTAAATCGCA
208442 ACGCGATAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 50 0.81
21 12 0.19
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (21 bp):
GTAAATCGCATTGCGATTTAC
Found at i:209796 original size:18 final size:18
Alignment explanation
Indices: 209775--209814 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
209765 TTTCTTGTAA
209775 TTTTAGAAAGAATAATTTT
1 TTTTAGAAA-AATAATTTT
* *
209794 TTTTATAAATATAATTTT
1 TTTTAGAAAAATAATTTT
209812 TTT
1 TTT
209815 ATTATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTTAGAAAAATAATTTT
Found at i:225272 original size:18 final size:18
Alignment explanation
Indices: 225251--225285 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
225241 CAATGAAGAA
225251 GAGGAAGAAGATGAAAGT
1 GAGGAAGAAGATGAAAGT
*
225269 GAGGAGGAAGATGAAAG
1 GAGGAAGAAGATGAAAG
225286 CTTAGGTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.43, T:0.09
Consensus pattern (18 bp):
GAGGAAGAAGATGAAAGT
Found at i:233762 original size:75 final size:75
Alignment explanation
Indices: 233639--233790 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
233629 AAATTCATAT
233639 ACAACAAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTC
1 ACAACAAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTC
233704 TCAAACAAGG
66 TCAAACAAGG
233714 ACAACAAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTC
1 ACAACAAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTC
233779 TCAAACAAGG
66 TCAAACAAGG
233789 AC
1 AC
233791 CTCTCGGTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (75 bp):
ACAACAAAATGTACTAAAGATGTTGTACAATTTTATTCACAGATTATGTCACTAGCATGATTCTC
TCAAACAAGG
Found at i:234241 original size:20 final size:19
Alignment explanation
Indices: 234213--234251 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
234203 AGCCAAACAT
234213 AGAAATTCTCAAACAGTAAA
1 AGAAATTCTCAAACA-TAAA
* *
234233 AGAACTTCTGAAACATAAA
1 AGAAATTCTCAAACATAAA
234252 TGCAGTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (19 bp):
AGAAATTCTCAAACATAAA
Found at i:237884 original size:19 final size:19
Alignment explanation
Indices: 237860--237904 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
237850 TCCAAGGGCT
237860 ATTCGTAATCTTAGGACTG
1 ATTCGTAATCTTAGGACTG
237879 ATTCGTAATCTTAGGACTG
1 ATTCGTAATCTTAGGACTG
237898 ATTCGTA
1 ATTCGTA
237905 GATCCGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (19 bp):
ATTCGTAATCTTAGGACTG
Found at i:246975 original size:22 final size:22
Alignment explanation
Indices: 246944--246992 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
246934 TTGAAAATCG
* *
246944 CGTTGCGATAGTTTACAGTTGT
1 CGTTGAGATAGTCTACAGTTGT
246966 CGTTGAGATAGTCTACAGTTGT
1 CGTTGAGATAGTCTACAGTTGT
246988 CGTTG
1 CGTTG
246993 CGATTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (22 bp):
CGTTGAGATAGTCTACAGTTGT
Found at i:247118 original size:15 final size:15
Alignment explanation
Indices: 247098--247128 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
247088 ATTACCACGA
247098 ACACGACCCGACCCG
1 ACACGACCCGACCCG
247113 ACACGACCCGACCCG
1 ACACGACCCGACCCG
247128 A
1 A
247129 GACGGACAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.52, G:0.19, T:0.00
Consensus pattern (15 bp):
ACACGACCCGACCCG
Found at i:247297 original size:20 final size:20
Alignment explanation
Indices: 247269--247332 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
247259 ACTGTAGACT
* *
247269 ATCGTAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * **
247289 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
247310 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
247330 ATC
1 ATC
247333 ATAACGCGAT
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:247315 original size:21 final size:21
Alignment explanation
Indices: 247289--247362 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
247279 GAAATGGAAA
247289 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * **
247310 ATCGCAACGCGA-AATGAAAA
1 ATCGCAACGCGATTTTCAACT
**
247330 ATCATAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
247351 ATTGCAACGCGA
1 ATCGCAACGCGA
247363 AATGCAACGC
Statistics
Matches: 37, Mismatches: 15, Indels: 2
0.69 0.28 0.04
Matches are distributed among these distances:
20 13 0.35
21 24 0.65
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:247323 original size:41 final size:41
Alignment explanation
Indices: 247266--247366 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
247256 CCAACTGTAG
* * *
247266 ACTATCGTAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCACAACGCGATTTTCA
*
247307 ACTATCGCAACGCGAAATGAAAAATCATAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCACAACGCGATTTTCA
*
247348 ACTATTGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
247367 CAACGCTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCACAACGCGATTTTCA
Found at i:247413 original size:19 final size:19
Alignment explanation
Indices: 247389--247434 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
247379 ACGATAGTAA
247389 AGATCGCAATGCGAATTAG
1 AGATCGCAATGCGAATTAG
247408 AGATCGCAATGCGAATTAG
1 AGATCGCAATGCGAATTAG
247427 AGATCGCA
1 AGATCGCA
247435 TTACGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (19 bp):
AGATCGCAATGCGAATTAG
Done.