Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 33 of 39
Found at i:6333649 original size:15 final size:15
Alignment explanation
Indices: 6333631--6333659 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6333621 GACCACTACA
6333631 TCCCGAAGGACTATG
1 TCCCGAAGGACTATG
6333646 TCCCGAAGGACTAT
1 TCCCGAAGGACTAT
6333660 TATACCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (15 bp):
TCCCGAAGGACTATG
Found at i:6333802 original size:28 final size:28
Alignment explanation
Indices: 6333743--6333810 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
6333733 TTTCATATGT
**
6333743 TCATGTGCTCATGTCATTTCTCTTGTGA
1 TCATGTGCTCATGTCATTTCTCTCATGA
6333771 TCATGTAGCTCATGTCATTTACT-TCATG-
1 TCATGT-GCTCATGTCATTT-CTCTCATGA
*
6333799 TCATGTTCTCAT
1 TCATGTGCTCAT
6333811 ATCACATATC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 5 0.14
28 12 0.34
29 16 0.46
30 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.46
Consensus pattern (28 bp):
TCATGTGCTCATGTCATTTCTCTCATGA
Found at i:6334254 original size:64 final size:63
Alignment explanation
Indices: 6334185--6334341 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
6334175 TAGTGAATGT
* * *
6334185 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATAG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCAATGTTTTTATT-TTAA-AA
6334248 G
63 G
* * *
6334249 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCAATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCAATGTTTTTATTTTAAAAG
* * *
6334312 AGTACATCGATGCACTACCTGTGCGTCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
6334342 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 4 0.05
64 64 0.83
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCAATGTTTTTATTTTAAAAG
Found at i:6341523 original size:19 final size:18
Alignment explanation
Indices: 6341504--6341552 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
6341494 GTTATTTTTA
6341504 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
6341522 AAATAAAATAAAAATAATT
1 AAATAAAA-AATAAGAATT
6341541 AAATAAATAAAT
1 AAATAAA-AAAT
6341553 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:6341547 original size:23 final size:22
Alignment explanation
Indices: 6341502--6341556 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
6341492 AAGTTATTTT
*
6341502 TAAAATAAAAAATAAGAATTAAA
1 TAAAAT-AAAAATAAGAAATAAA
*
6341525 TAAAATAAAAATAATTAAATAAA
1 TAAAATAAAAATAA-GAAATAAA
*
6341548 TAAATTAAA
1 TAAAATAAA
6341557 GAGATTGAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (22 bp):
TAAAATAAAAATAAGAAATAAA
Found at i:6342170 original size:19 final size:21
Alignment explanation
Indices: 6342128--6342171 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
6342118 AAAAACAAGC
*
6342128 TAAAACATCTTATATACTAAT
1 TAAAACATCTTATAAACTAAT
*
6342149 TAAAACA-CTTA-AAACTATT
1 TAAAACATCTTATAAACTAAT
6342168 TAAA
1 TAAA
6342172 CTAAAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 4 0.19
21 7 0.33
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAACATCTTATAAACTAAT
Found at i:6344338 original size:5 final size:5
Alignment explanation
Indices: 6344330--6344365 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
6344320 TAAGCATCTG
6344330 ATAAA ATAAA ATAAA ATAAA A-AAA ATGAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA A
6344366 CGAAATGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.69
6 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:6349990 original size:19 final size:18
Alignment explanation
Indices: 6349971--6350019 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
6349961 GTTGCTTTTA
6349971 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
6349989 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
6350008 AAATAAATAAAT
1 AAATAAA-AAAT
6350020 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:6351318 original size:17 final size:17
Alignment explanation
Indices: 6351296--6351346 Score: 102
Period size: 17 Copynumber: 3.0 Consensus size: 17
6351286 ATCAATTGAG
6351296 GACATTTTCTCACATGT
1 GACATTTTCTCACATGT
6351313 GACATTTTCTCACATGT
1 GACATTTTCTCACATGT
6351330 GACATTTTCTCACATGT
1 GACATTTTCTCACATGT
6351347 CACTATATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (17 bp):
GACATTTTCTCACATGT
Found at i:6366310 original size:22 final size:23
Alignment explanation
Indices: 6366276--6366319 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
6366266 AGGGTTTCAT
6366276 AGGTCATTCGGGACATA-CTCAC
1 AGGTCATTCGGGACATATCTCAC
* *
6366298 AGGTCCTTTGGGACATATCTCA
1 AGGTCATTCGGGACATATCTCA
6366320 TATGCCACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (23 bp):
AGGTCATTCGGGACATATCTCAC
Found at i:6366876 original size:21 final size:21
Alignment explanation
Indices: 6366850--6366897 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
6366840 TGGCCAATAT
*
6366850 CACTGTAGCAGTGCATCGATA
1 CACTGTAGCAATGCATCGATA
* *
6366871 CACTGTAGCAATGTATCGGTA
1 CACTGTAGCAATGCATCGATA
6366892 CACTGT
1 CACTGT
6366898 TCATTATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
CACTGTAGCAATGCATCGATA
Found at i:6367296 original size:2 final size:2
Alignment explanation
Indices: 6367289--6367373 Score: 147
Period size: 2 Copynumber: 43.5 Consensus size: 2
6367279 TCTTATAAAG
6367289 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
*
6367331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6367371 AT A
1 AT A
6367374 AATTAAAGAG
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 2 0.03
2 77 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6368166 original size:14 final size:14
Alignment explanation
Indices: 6368147--6368196 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
6368137 GTAAAATTAA
6368147 AATTATATATATAT
1 AATTATATATATAT
* *
6368161 AATTATATAAAAAT
1 AATTATATATATAT
* *
6368175 ACTTAAATAT-TAT
1 AATTATATATATAT
6368188 -ATTATATAT
1 AATTATATAT
6368197 TTGATCAATA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
12 7 0.25
13 2 0.07
14 19 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTATATATATAT
Found at i:6368382 original size:7 final size:7
Alignment explanation
Indices: 6368370--6368426 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
6368360 GGATTATCGA
6368370 TATTTAT
1 TATTTAT
6368377 TATTTAT
1 TATTTAT
6368384 TATTT-T
1 TATTTAT
6368390 TA--TAT
1 TATTTAT
6368395 TATATTA-
1 TAT-TTAT
6368402 TATTTAT
1 TATTTAT
*
6368409 TTTTTA-
1 TATTTAT
6368415 TATTTAT
1 TATTTAT
6368422 T-TTTA
1 TATTTA
6368427 GTTTTCAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 15 0.36
7 21 0.50
8 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:6368400 original size:16 final size:15
Alignment explanation
Indices: 6368369--6368426 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
6368359 TGGATTATCG
6368369 ATATTTATTATTTATT
1 ATATTTA-TATTTATT
*
6368385 ATTTTTATATTATATT
1 ATATTTATATT-TATT
6368401 ATATTTAT-TTT-TT
1 ATATTTATATTTATT
*
6368414 ATATTTATTTTTA
1 ATATTTATATTTA
6368427 GTTTTCAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 10 0.27
14 4 0.11
15 6 0.16
16 17 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATATTTATATTTATT
Found at i:6368423 original size:13 final size:13
Alignment explanation
Indices: 6368376--6368425 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
6368366 TCGATATTTA
* *
6368376 TTATTTATTATTT
1 TTATTTTTTATAT
6368389 TTATATTATATTATAT
1 TTAT-TT-T-TTATAT
6368405 TTATTTTTTATAT
1 TTATTTTTTATAT
6368418 TTATTTTT
1 TTATTTTT
6368426 AGTTTTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 18 0.56
14 3 0.09
15 2 0.06
16 9 0.28
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTTTATAT
Found at i:6368431 original size:18 final size:17
Alignment explanation
Indices: 6368383--6368431 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
6368373 TTATTATTTA
*
6368383 TTATTTTTATATTATAT
1 TTATTTTTATTTTATAT
6368400 TATATTTATT-TTTTATAT
1 T-TATTT-TTATTTTATAT
6368418 TTATTTTTAGTTTT
1 TTATTTTTA-TTTT
6368432 CAATAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 2 0.07
17 6 0.22
18 17 0.63
19 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TTATTTTTATTTTATAT
Found at i:6368491 original size:16 final size:16
Alignment explanation
Indices: 6368472--6368503 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6368462 CTTTTTTCGG
6368472 TTTGTTTGATTTTTTT
1 TTTGTTTGATTTTTTT
*
6368488 TTTGTTTTATTTTTTT
1 TTTGTTTGATTTTTTT
6368504 CTCGTGGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTGTTTGATTTTTTT
Found at i:6393880 original size:20 final size:19
Alignment explanation
Indices: 6393852--6393890 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6393842 AAACTTGCTT
*
6393852 TCTCTTTTTGATATTTTTTA
1 TCTCATTTT-ATATTTTTTA
*
6393872 TCTCATTTTATTTTTTTTA
1 TCTCATTTTATATTTTTTA
6393891 AATAATTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (19 bp):
TCTCATTTTATATTTTTTA
Found at i:6395392 original size:17 final size:17
Alignment explanation
Indices: 6395370--6395407 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
6395360 GCAAGTGTAA
6395370 GTGTTAGATGTGAGTAT
1 GTGTTAGATGTGAGTAT
6395387 GTGTTAGATGTGAGTAT
1 GTGTTAGATGTGAGTAT
6395404 GTGT
1 GTGT
6395408 CCAATACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (17 bp):
GTGTTAGATGTGAGTAT
Found at i:6397749 original size:35 final size:35
Alignment explanation
Indices: 6397710--6397779 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
6397700 ATTAAGGTTG
*
6397710 GTTTAAATAATTCTTTTCATAAAATGCATTTTGAT
1 GTTTAAATAATTCTTTTAATAAAATGCATTTTGAT
6397745 GTTTAAATAATTCTTTTAATAAAATGCATTTTGAT
1 GTTTAAATAATTCTTTTAATAAAATGCATTTTGAT
6397780 TATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (35 bp):
GTTTAAATAATTCTTTTAATAAAATGCATTTTGAT
Found at i:6402891 original size:22 final size:22
Alignment explanation
Indices: 6402853--6402895 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6402843 GACTATCTGT
6402853 AAGATAAAGCAGAATTATCTAG
1 AAGATAAAGCAGAATTATCTAG
*
6402875 AAGATAAATCATG-ATTATCTA
1 AAGATAAAGCA-GAATTATCTA
6402896 TGTATTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (22 bp):
AAGATAAAGCAGAATTATCTAG
Found at i:6409030 original size:8 final size:8
Alignment explanation
Indices: 6409017--6409043 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6409007 TCTGATAGAA
6409017 AAACAGGT
1 AAACAGGT
6409025 AAACAGGT
1 AAACAGGT
6409033 AAACAGGT
1 AAACAGGT
6409041 AAA
1 AAA
6409044 GAGATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.11, G:0.22, T:0.11
Consensus pattern (8 bp):
AAACAGGT
Found at i:6417367 original size:14 final size:14
Alignment explanation
Indices: 6417350--6417377 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6417340 ATGATAACAA
6417350 AATTATATAACTAT
1 AATTATATAACTAT
6417364 AATTATATAACTAT
1 AATTATATAACTAT
6417378 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:6420422 original size:37 final size:39
Alignment explanation
Indices: 6420369--6420444 Score: 129
Period size: 37 Copynumber: 2.0 Consensus size: 39
6420359 GTTCTAAACT
*
6420369 TAAATAATGTCTATATAATTACAATTA-AAAT-TAATTA
1 TAAATAATGTCAATATAATTACAATTAGAAATATAATTA
6420406 TAAATAATGTCAATATAATTACAATTAGAAATATAATTA
1 TAAATAATGTCAATATAATTACAATTAGAAATATAATTA
6420445 AGTAGATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 26 0.72
38 4 0.11
39 6 0.17
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (39 bp):
TAAATAATGTCAATATAATTACAATTAGAAATATAATTA
Found at i:6421811 original size:16 final size:15
Alignment explanation
Indices: 6421786--6421824 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6421776 AAGCTCAAAT
6421786 TACAAATATTAAATAA
1 TACAAATATTAAA-AA
*
6421802 TACAAGTATTAAAAA
1 TACAAATATTAAAAA
*
6421817 TAAAAATA
1 TACAAATA
6421825 ACCCATAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (15 bp):
TACAAATATTAAAAA
Found at i:6423413 original size:12 final size:12
Alignment explanation
Indices: 6423382--6423425 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
6423372 AATTAGTAAT
6423382 AATAATAATA-A
1 AATAATAATATA
6423393 ATATAAATAATATA
1 A-AT-AATAATATA
6423407 AATAATAATATA
1 AATAATAATATA
6423419 AATAATA
1 AATAATA
6423426 TAAATAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.03
12 18 0.60
13 9 0.30
14 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATAATATA
Found at i:6423416 original size:21 final size:22
Alignment explanation
Indices: 6423385--6423432 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
6423375 TAGTAATAAT
6423385 AATAATAAATATAAATAATATA
1 AATAATAAATATAAATAATATA
6423407 AATAAT-AATATAAATAATATA
1 AATAATAAATATAAATAATATA
6423428 AATAA
1 AATAA
6423433 ATGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATAAATATAAATAATATA
Found at i:6423416 original size:25 final size:25
Alignment explanation
Indices: 6423386--6423434 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6423376 AGTAATAATA
6423386 ATAATA-AATATAA-ATAATATAAATA
1 ATAATATAA-ATAATATAA-ATAAATA
6423411 ATAATATAAATAATATAAATAAAT
1 ATAATATAAATAATATAAATAAAT
6423435 GAAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATATAAATAATATAAATAAATA
Found at i:6423426 original size:9 final size:9
Alignment explanation
Indices: 6423379--6423432 Score: 56
Period size: 9 Copynumber: 5.6 Consensus size: 9
6423369 TGTAATTAGT
6423379 AATAATA-A
1 AATAATATA
6423387 TAATAAATATA
1 -AAT-AATATA
6423398 AATAATATAAA
1 AATAATAT--A
6423409 TAATAATATA
1 -AATAATATA
6423419 AATAATATA
1 AATAATATA
6423428 AATAA
1 AATAA
6423433 ATGAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 22 0.55
10 8 0.20
11 2 0.05
12 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATATA
Found at i:6424262 original size:30 final size:30
Alignment explanation
Indices: 6424228--6424298 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
6424218 GGGAAACGTT
* *
6424228 CTCAAAGATCGATGTTTCGAGAGAAACAAA
1 CTCAAAGATCGATGTTTCAAGAAAAACAAA
** *
6424258 CTCAAAGATGTCTTTGTTTCAAGAAAAACATA
1 CTCAAAGA--TCGATGTTTCAAGAAAAACAAA
6424290 CTCAAAGAT
1 CTCAAAGAT
6424299 TTTGTTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 9 0.26
32 25 0.74
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.25
Consensus pattern (30 bp):
CTCAAAGATCGATGTTTCAAGAAAAACAAA
Found at i:6424883 original size:64 final size:61
Alignment explanation
Indices: 6424773--6424891 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 61
6424763 GTGTTTCAAA
*
6424773 AGAAATTATCTCGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCCAC
1 AGAAATTATCTCGAGACAAAAATTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCCAC
* * *
6424834 AGAAATTGTCTCAAGAGACAAAAAATTTGTTTTC-AGAGAAACATACTCAAAGATTTTT
1 AGAAATTATCTC--GAGAC-AAAAATTTG-TTTCAAAAGAAACAAACTCAAAGATTTTT
6424892 GTTCTTATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 11 0.22
63 5 0.10
64 30 0.60
65 4 0.08
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (61 bp):
AGAAATTATCTCGAGACAAAAATTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCCAC
Found at i:6425669 original size:36 final size:36
Alignment explanation
Indices: 6425628--6425768 Score: 144
Period size: 35 Copynumber: 3.9 Consensus size: 36
6425618 AAAGGAAAAA
* * *
6425628 TGTCTCTAGCGAGACGAAATTTATTTTTCAAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGAAAT
*
6425664 TGTCTCAAACGAGACAAAATTTGTTTTT--AGAAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTCAAG-AAAT
* *
6425699 TGTCTCAAGCGAGACAAAATTTGTTTTACAAAAGAAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTC--AAGAAAT
* * * *
6425737 TGTCTCTAGCGAGACGACATTT-TGTTTCAAGA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGA
6425769 GAAACAACAT
Statistics
Matches: 88, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
34 2 0.02
35 34 0.39
36 24 0.27
37 4 0.05
38 22 0.25
39 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGAAAT
Found at i:6426428 original size:4 final size:4
Alignment explanation
Indices: 6426075--6426416 Score: 643
Period size: 4 Copynumber: 86.0 Consensus size: 4
6426065 TTTATGTGTC
6426075 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
6426123 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
6426169 ATGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
6426217 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
6426265 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
6426313 ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
6426361 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
6426409 ATGT ATGT
1 ATGT ATGT
6426417 GTTGATGTAT
Statistics
Matches: 331, Mismatches: 5, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
2 2 0.01
4 329 0.99
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:6426565 original size:21 final size:22
Alignment explanation
Indices: 6426539--6426581 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
6426529 GACCTGAGAC
*
6426539 AATTTA-TTTTCTTGCCCCAAA
1 AATTTACTTCTCTTGCCCCAAA
6426560 AATTTAGCTTCTCTTGCCCCAA
1 AATTTA-CTTCTCTTGCCCCAA
6426582 CTTCGATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTTACTTCTCTTGCCCCAAA
Found at i:6427425 original size:15 final size:15
Alignment explanation
Indices: 6427407--6427436 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6427397 TAATTGAACC
6427407 AAGGATCAATTTACT
1 AAGGATCAATTTACT
6427422 AAGGATCAATTTACT
1 AAGGATCAATTTACT
6427437 CGGATGCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
AAGGATCAATTTACT
Found at i:6427665 original size:16 final size:15
Alignment explanation
Indices: 6427634--6427691 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
6427624 TGTTCTTTGC
6427634 TCTTTTCTTTGTTTT
1 TCTTTTCTTTGTTTT
6427649 TGCTTTTCTTT-TCTTT
1 T-CTTTTCTTTGT-TTT
*
6427665 TCTTTT-TTCT-TTAT
1 TCTTTTCTT-TGTTTT
6427679 T-TTTTCTTTGTTT
1 TCTTTTCTTTGTTT
6427692 CTTTTCTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 5 0.14
14 9 0.25
15 9 0.25
16 13 0.36
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (15 bp):
TCTTTTCTTTGTTTT
Found at i:6427681 original size:26 final size:26
Alignment explanation
Indices: 6427634--6427702 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
6427624 TGTTCTTTGC
**
6427634 TCTTTTCTTTGTTT-TTGCTTTTCTT-T
1 TCTTTTCTTT-TTTCTTTATTTT-TTCT
6427660 TCTTTTCTTTTTTCTTTATTTTTTCT
1 TCTTTTCTTTTTTCTTTATTTTTTCT
*
6427686 T-TGTTTCTTTTCTCTTT
1 TCT-TTTCTTTTTTCTTT
6427703 GATATGATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 6 0.16
26 31 0.84
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (26 bp):
TCTTTTCTTTTTTCTTTATTTTTTCT
Found at i:6428314 original size:20 final size:20
Alignment explanation
Indices: 6428291--6428331 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6428281 GGATAAATGC
6428291 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
*
6428311 AATGTTTCATGGTCTCAAAG
1 AATGTTTCAAGGTCTCAAAG
6428331 A
1 A
6428332 GAAAGAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (20 bp):
AATGTTTCAAGGTCTCAAAG
Found at i:6429001 original size:21 final size:20
Alignment explanation
Indices: 6428977--6429016 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
6428967 GAATGATGAA
*
6428977 ATGCAGATACGAAATGCAAAG
1 ATGCAAATAC-AAATGCAAAG
*
6428998 ATGCAAATACAGATGCAAA
1 ATGCAAATACAAATGCAAA
6429017 AATGTTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (20 bp):
ATGCAAATACAAATGCAAAG
Found at i:6430271 original size:52 final size:52
Alignment explanation
Indices: 6430209--6430311 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
6430199 AAATTGGACA
6430209 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
6430261 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
6430312 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:6434861 original size:52 final size:52
Alignment explanation
Indices: 6434799--6434901 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
6434789 AAATTGGACA
6434799 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
6434851 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
6434902 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:6436627 original size:16 final size:15
Alignment explanation
Indices: 6436606--6436644 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
6436596 AAGCTCAAAT
6436606 TACAAATATTAAATAA
1 TACAAATATTAAA-AA
6436622 TACAAATATTAAAAA
1 TACAAATATTAAAAA
*
6436637 TAAAAATA
1 TACAAATA
6436645 ACCCATAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
TACAAATATTAAAAA
Found at i:6438208 original size:3 final size:3
Alignment explanation
Indices: 6438200--6438243 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
6438190 TTGTAATTAG
6438200 TAA TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA TAAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TA
6438244 TAAATAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 27 0.71
4 7 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6438217 original size:14 final size:14
Alignment explanation
Indices: 6438200--6438246 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
6438190 TTGTAATTAG
6438200 TAATAATAATAATA
1 TAATAATAATAATA
6438214 TAATAATAAT-ATAA
1 TAATAATAATAAT-A
6438228 TAATAAATAAATAATA
1 TAAT-AAT-AATAATA
6438244 TAA
1 TAA
6438247 ATAAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.07
14 15 0.52
15 3 0.10
16 7 0.24
17 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:6438218 original size:11 final size:11
Alignment explanation
Indices: 6438202--6438246 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
6438192 GTAATTAGTA
6438202 ATAATAATAAT
1 ATAATAATAAT
6438213 ATAATAATAAT
1 ATAATAATAAT
6438224 ATAATAATAA-
1 ATAATAATAAT
6438234 AT-A-AATAAT
1 ATAATAATAAT
6438243 ATAA
1 ATAA
6438247 ATAAATGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 5 0.16
9 3 0.09
10 3 0.09
11 21 0.66
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:6438860 original size:16 final size:16
Alignment explanation
Indices: 6438839--6438893 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
6438829 CATTTAATAA
*
6438839 ATAAACGAACACAAAC
1 ATAAACGAACACGAAC
6438855 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
6438871 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
6438887 ATAAACG
1 ATAAACG
6438894 TTGGAGACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:6440433 original size:24 final size:24
Alignment explanation
Indices: 6440406--6440460 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
6440396 TATTAGGTTA
* *
6440406 AACATAAATGAATGCACATAAACG
1 AACATAAATAAACGCACATAAACG
* *
6440430 AACATAACTAAACGCATATAAACG
1 AACATAAATAAACGCACATAAACG
6440454 AACATAA
1 AACATAA
6440461 CCGAACGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.16
Consensus pattern (24 bp):
AACATAAATAAACGCACATAAACG
Found at i:6442146 original size:18 final size:18
Alignment explanation
Indices: 6442123--6442170 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
6442113 CGATGAACAA
6442123 TATCGATACTGATGTGGG
1 TATCGATACTGATGTGGG
6442141 TATCGATACTGATGTGGG
1 TATCGATACTGATGTGGG
6442159 TATCGATACTGA
1 TATCGATACTGA
6442171 GAGAAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (18 bp):
TATCGATACTGATGTGGG
Found at i:6442722 original size:46 final size:46
Alignment explanation
Indices: 6442672--6442823 Score: 189
Period size: 46 Copynumber: 3.3 Consensus size: 46
6442662 GAACTGCTCT
*
6442672 ATAACAGTGCATTATAGGCATGAAAGGATGCCATAAATGAAAATGC
1 ATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGC
* * *
6442718 ATAACGGTGCATTATCGACATGAAAGGATGTCATAAATGAAAATGC
1 ATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGC
* * ** * * *
6442764 ATAACGGTGCTTTATCGGTTTGAAATGATGCCACAAATAAAAATGC
1 ATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGC
6442810 ATAA-AGGTGCATTA
1 ATAACA-GTGCATTA
6442824 ACGACTTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (46 bp):
ATAACAGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGC
Found at i:6448635 original size:17 final size:15
Alignment explanation
Indices: 6448598--6448635 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
6448588 CTCCTTTCTT
6448598 TAATATTAATAAATA
1 TAATATTAATAAATA
6448613 -AATATTAATAAGAATA
1 TAATATTAAT-A-AATA
6448629 TAATATT
1 TAATATT
6448636 TTTCTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 4 0.20
17 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TAATATTAATAAATA
Found at i:6448668 original size:2 final size:2
Alignment explanation
Indices: 6448661--6448713 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
6448651 AAAAATGAAG
6448661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6448703 TA TA TA TA TA T
1 TA TA TA TA TA T
6448714 CAGGATATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6448825 original size:24 final size:23
Alignment explanation
Indices: 6448802--6448866 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
6448792 TAAATAATAT
*
6448802 TATTTAATTAAATATATTTTATA
1 TATTAAATTAAATATATTTTATA
** *
6448825 TGCTAAAATAAATA-ATATTTATA
1 TATTAAATTAAATATAT-TTTATA
6448848 GTATTAAATTAAATATATT
1 -TATTAAATTAAATATATT
6448867 GAAATTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
22 2 0.06
23 16 0.50
24 12 0.38
25 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (23 bp):
TATTAAATTAAATATATTTTATA
Found at i:6448837 original size:23 final size:23
Alignment explanation
Indices: 6448810--6448866 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
6448800 ATTATTTAAT
6448810 TAAATATATTT-TA-TATGCTAAAA
1 TAAATATATTTATAGTAT--TAAAA
*
6448833 TAAATAATATTTATAGTATTAAAT
1 TAAAT-ATATTTATAGTATTAAAA
6448857 TAAATATATT
1 TAAATATATT
6448867 GAAATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 10 0.33
24 15 0.50
25 2 0.07
26 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TAAATATATTTATAGTATTAAAA
Found at i:6449775 original size:21 final size:22
Alignment explanation
Indices: 6449751--6449797 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
6449741 CGTTTCCGTT
6449751 TCTT-GTTGCTCCCGT-TCCTTC
1 TCTTGGTTGCT-CCGTGTCCTTC
*
6449772 TCTTGGTTGCTCCGTGTCTTTC
1 TCTTGGTTGCTCCGTGTCCTTC
6449794 TCTT
1 TCTT
6449798 TGCAGGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.00, C:0.32, G:0.17, T:0.51
Consensus pattern (22 bp):
TCTTGGTTGCTCCGTGTCCTTC
Found at i:6450273 original size:3 final size:3
Alignment explanation
Indices: 6450265--6450339 Score: 116
Period size: 3 Copynumber: 25.0 Consensus size: 3
6450255 ATTTATAATT
* *
6450265 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAT TAT TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
6450310 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6450340 AAGTAAAATG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 63 0.93
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:6450323 original size:39 final size:40
Alignment explanation
Indices: 6450243--6450334 Score: 127
Period size: 39 Copynumber: 2.3 Consensus size: 40
6450233 GTTGGGCTTG
*
6450243 TAAT-ATATAATTATTTATAATTTAATAATAATAATAATAA
1 TAATAATATAATTATTAATAA-TTAATAATAATAATAATAA
6450283 TAATAATAT-ATTATTAATAA-TAATAAATAATAATAATAA
1 TAATAATATAATTATTAATAATTAAT-AATAATAATAATAA
6450322 TAATAATAATAAT
1 TAATAAT-ATAAT
6450335 AATAAAAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
38 4 0.09
39 21 0.45
40 16 0.34
41 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (40 bp):
TAATAATATAATTATTAATAATTAATAATAATAATAATAA
Found at i:6450507 original size:20 final size:20
Alignment explanation
Indices: 6450479--6450533 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
6450469 AAAACATTCT
*
6450479 GCCCAGAGGTCTTAT-GAATG
1 GCCCTGAGGTCTTATAG-ATG
6450499 GCCCTGAGGTCTTATAGATG
1 GCCCTGAGGTCTTATAGATG
6450519 GCCCTGAGGTCTTAT
1 GCCCTGAGGTCTTAT
6450534 CATCTTGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (20 bp):
GCCCTGAGGTCTTATAGATG
Found at i:6450832 original size:74 final size:75
Alignment explanation
Indices: 6450664--6450834 Score: 263
Period size: 74 Copynumber: 2.3 Consensus size: 75
6450654 GAGGTCTTAT
* * *
6450664 CATCTTGCACTGTAGGTTTTACAGATGACCCGGAGGCTTTAAATATCAAAAAAATCTCCCGAAGG
1 CATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATC-AAAAAAGCTCCCGAAGG
6450729 CTTTTTGAAAA
65 CTTTTTGAAAA
* * * *
6450740 CATCCTGCACTGTTGGTCTTACATATGACCCAGAGGCTTTAAATATC-AAAAAGCTTCCGAAGGC
1 CATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAAGCTCCCGAAGGC
6450804 TTTTTGAAAA
66 TTTTTGAAAA
6450814 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTGTAGGTCTTA
6450835 TGGATGGCCC
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 44 0.51
76 42 0.49
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (75 bp):
CATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAAGCTCCCGAAGGC
TTTTTGAAAA
Found at i:6450875 original size:22 final size:23
Alignment explanation
Indices: 6450814--6450876 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 23
6450804 TTTTTGAAAA
6450814 CATCTTGCACTGTAGGTCTTATG
1 CATCTTGCACTGTAGGTCTTATG
* * *
6450837 GA--TGGCCCTG-AGGTCTTAT-
1 CATCTTGCACTGTAGGTCTTATG
6450856 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTGTAGGTCTTA
6450877 CAGATGACCC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.03
20 9 0.29
21 12 0.39
22 8 0.26
23 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (23 bp):
CATCTTGCACTGTAGGTCTTATG
Found at i:6450949 original size:116 final size:116
Alignment explanation
Indices: 6450740--6451072 Score: 549
Period size: 116 Copynumber: 2.9 Consensus size: 116
6450730 TTTTTGAAAA
* * * *
6450740 CATCCTGCACTGTTGGTCTTACATATGACCCAGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
1 CATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
*
6450805 TTTTGAAAACATCTTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAT
66 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAT
*
6450856 CATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
*
6450921 TTTTGAAAACATCCTGCACTATAGGTCTTATGGATGGCCCTGAGGTCTTAT
66 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAT
* * * *
6450972 CATCTTGCACTGTAAGTCTTATAGATGACCCGAAGGTTTTAAATATCAAAAAGCTTCCGAAGGCT
1 CATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
* *
6451037 TTTTGAAAACATCCTGTATTGTAGGTCTTATGGATG
66 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATG
6451073 TGGGAAATAG
Statistics
Matches: 202, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
116 202 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (116 bp):
CATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAT
Found at i:6452214 original size:54 final size:54
Alignment explanation
Indices: 6452108--6452215 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
6452098 ATAATAACTG
* * **
6452108 GTTCATAAAACATTTGACAACATATTCATCATTTCTTGTGGCTTCTGTCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTACCCAGAT
* * *
6452162 GTTCGTAAAGCATTTGACAACGCATTCATCCA-TTCCTGTGGCTTCTACCCAGAT
1 GTTCATAAAACATTTGACAACACATTCAT-CATTTCCTGTGGCTTCTACCCAGAT
6452216 TTCTCAATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
54 44 0.96
55 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (54 bp):
GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTACCCAGAT
Found at i:6453211 original size:41 final size:39
Alignment explanation
Indices: 6453166--6453278 Score: 99
Period size: 41 Copynumber: 2.8 Consensus size: 39
6453156 TTATTTTTGT
*
6453166 TTGAATTAGGCATTCAAAATGCCCCAACATTCTAT-TTCTC
1 TTGAATT-GGCCTTCAAAATGCCCCAACATTCTATCTT-TC
* * * *
6453206 ATTGAAATGGGCCTTCAAGATGTCCC-ACA-TGTATCTTTC
1 -TTG-AATTGGCCTTCAAAATGCCCCAACATTCTATCTTTC
6453245 -TGAATTGTGCCTTCAAAAATGCCCCAACATTCTA
1 TTGAATTG-GCCTTC-AAAATGCCCCAACATTCTA
6453279 AATTGTAAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
36 4 0.07
37 8 0.14
38 8 0.14
39 9 0.16
40 8 0.14
41 17 0.30
42 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (39 bp):
TTGAATTGGCCTTCAAAATGCCCCAACATTCTATCTTTC
Found at i:6454784 original size:72 final size:72
Alignment explanation
Indices: 6454654--6454788 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
6454644 TATAATAGGT
6454654 TAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTCTAGAGGGACAACTCAAGCAT
1 TAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTCTAGAGGGACAACTCAAGCAT
6454719 AACAGAC
66 AACAGAC
* * * * *
6454726 TAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCAGTTGCTTTAGGGGGATAACTCAAGC
1 TAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTCTAGAGGGACAACTCAAGC
6454789 TTTATTGTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAGTCGGGGCGATTAACCAATTGCTCTAGAGGGACAACTCAAGCAT
AACAGAC
Found at i:6460480 original size:15 final size:15
Alignment explanation
Indices: 6460460--6460490 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6460450 TATACAGAGA
6460460 TTTTTTCGCAGGGAT
1 TTTTTTCGCAGGGAT
*
6460475 TTTTTTTGCAGGGAT
1 TTTTTTCGCAGGGAT
6460490 T
1 T
6460491 ACTGCCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.26, T:0.52
Consensus pattern (15 bp):
TTTTTTCGCAGGGAT
Found at i:6461217 original size:23 final size:23
Alignment explanation
Indices: 6461145--6461217 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
6461135 TAATATTTAA
*
6461145 AAATAAATAA-ATAT-TATTATTT
1 AAATAAATAATATTTATATTA-TT
* * ** *
6461167 AATTAAATATATTTTTATATGCTA
1 AAATAAATA-ATATTTATATTATT
6461191 AAATAAATAATATTTATATTATT
1 AAATAAATAATATTTATATTATT
6461214 AAAT
1 AAAT
6461218 TAAACATATT
Statistics
Matches: 37, Mismatches: 11, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
22 8 0.22
23 15 0.41
24 11 0.30
25 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (23 bp):
AAATAAATAATATTTATATTATT
Found at i:6461226 original size:23 final size:23
Alignment explanation
Indices: 6461159--6461227 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
6461149 AAATAAATAT
* * *
6461159 TATTATTTAATTAAATATATTTT
1 TATTATTAAATTAAAAATATTTA
*
6461182 TA-TATGCTAAAATAAATAATATTTA
1 TATTAT--TAAATTAAA-AATATTTA
*
6461207 TATTATTAAATTAAACATATT
1 TATTATTAAATTAAAAATATT
6461228 GAAATTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
22 3 0.08
23 7 0.19
24 15 0.42
25 8 0.22
26 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (23 bp):
TATTATTAAATTAAAAATATTTA
Found at i:6462542 original size:17 final size:17
Alignment explanation
Indices: 6462522--6462571 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
6462512 GTAATTATTT
* *
6462522 ATAATTTAATAATAATA
1 ATAATATAATAATAAAA
*
6462539 ATAATATATTAATAAAA
1 ATAATATAATAATAAAA
6462556 ATAA-A-AATAAGTAAAA
1 ATAATATAATAA-TAAAA
6462572 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 4 0.14
16 6 0.21
17 18 0.64
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
ATAATATAATAATAAAA
Found at i:6462552 original size:20 final size:20
Alignment explanation
Indices: 6462527--6462564 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6462517 TATTTATAAT
* *
6462527 TTAATAATAATAATAATATA
1 TTAATAAAAATAAAAATATA
6462547 TTAATAAAAATAAAAATA
1 TTAATAAAAATAAAAATA
6462565 AGTAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAATAAAAATAAAAATATA
Found at i:6464176 original size:22 final size:21
Alignment explanation
Indices: 6464134--6464176 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
6464124 TTTTATTGAA
* **
6464134 TTTTATTTAAAATATCTAATT
1 TTTTATTTAAAAAATAAAATT
6464155 TTTTATATTAAAAAATAAAATT
1 TTTTAT-TTAAAAAATAAAATT
6464177 CTGAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATTTAAAAAATAAAATT
Found at i:6464516 original size:181 final size:182
Alignment explanation
Indices: 6464254--6464661 Score: 651
Period size: 181 Copynumber: 2.3 Consensus size: 182
6464244 TATTTATTTA
* *
6464254 TTATATTGTTATGGATCGATACATTTTTATAAAGTAT-GGCACTTTATTAAAGCTATAACTTCTT
1 TTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAAAGCTATAACTTATT
* * * * *
6464318 TTCTTTTAAATTTCAAAATTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTA
66 CTCTTTTAAATTTCAAAAGTGTCGATACTTATAATAAAATATCGACACTATCAACACATCCGGTA
*
6464383 GC-TCTTTACCGGTTTTGTCATTTCGAGATCGGTTTTGTCATATTTTTACATG
131 GCGT-TTTACCGGTTTTGTCATTTAGAGATCGGTTTTGTCATATTTTTACATG
*
6464435 TTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAACGCTATAACTTATT
1 TTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAAAGCTATAACTTATT
*
6464500 CTCTTTTAAA-TTCAAAAGTGTCGATACTTATAATAAAATATCGACACTATCAACACATTCGGTA
66 CTCTTTTAAATTTCAAAAGTGTCGATACTTATAATAAAATATCGACACTATCAACACATCCGGTA
* * *
6464564 GCGTTTTACCTGTTTTGTCATTTATAGATCGGTTTTGTCATTTTTTTACATG
131 GCGTTTTACCGGTTTTGTCATTTAGAGATCGGTTTTGTCATATTTTTACATG
* *
6464616 TTATATTGTTATGGATCGATAAATTTTTATAAAATATCGACACTTT
1 TTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
6464662 CAATATATTC
Statistics
Matches: 210, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
181 176 0.84
182 34 0.16
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (182 bp):
TTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTAAAGCTATAACTTATT
CTCTTTTAAATTTCAAAAGTGTCGATACTTATAATAAAATATCGACACTATCAACACATCCGGTA
GCGTTTTACCGGTTTTGTCATTTAGAGATCGGTTTTGTCATATTTTTACATG
Found at i:6464945 original size:113 final size:112
Alignment explanation
Indices: 6464532--6464995 Score: 669
Period size: 112 Copynumber: 4.1 Consensus size: 112
6464522 GATACTTATA
* * * * * * *
6464532 ATAAAATATCGACACTATCAACACATTCGGTAGCGTTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
6464597 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATAAATTTTT
66 TTTATCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
* * * * *
6464644 ATAAAATATCGACACTTTCAATATATTCGATATCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
6464709 TTTATCA-TTTTTTACCTGTTATATTGTTATGAATCAATACATTTTT
66 TTTATCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
* * *
6464755 ATAAAGTATCGACACTTTTAAATATATCCGGTACCGCTTTACCTATTTTGTCATTTATAGACCGG
1 ATAAAGTATCGACAC-TTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
*
6464820 TTTTATCATTTTTTTATCTGTTATATTGTTATGGATCAATATATTTTT
65 TTTTATCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
* *
6464868 ATAAAGTATCGACCCTTTCAATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
6464933 TTTGTCATTTTTTTTACCTGTTATATTGTTGTGGATCAATATATTTTT
66 TTTATCA-TTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
6464981 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
6464996 AAACCGACAA
Statistics
Matches: 317, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
111 49 0.15
112 166 0.52
113 102 0.32
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTATCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
Found at i:6468863 original size:29 final size:29
Alignment explanation
Indices: 6468799--6468856 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
6468789 ATATCTGAAA
*
6468799 AAAATTAATTAAATACAATATTAAACAATT
1 AAAA-TAATTAAATACAATACTAAACAATT
6468829 AAAATAATTAAATA-AAGTACTAAA-AATT
1 AAAATAATTAAATACAA-TACTAAACAATT
6468857 CTAAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATAATTAAATACAATACTAAACAATT
Found at i:6474252 original size:20 final size:20
Alignment explanation
Indices: 6474229--6474279 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
6474219 CACGGAATGT
6474229 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
6474249 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
6474269 AAGATTACCAG
1 AAGATTACCAG
6474280 GGAATAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:6484055 original size:21 final size:21
Alignment explanation
Indices: 6484016--6484056 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6484006 TACTTTGTTC
*
6484016 ATTTTGTTATAGTTCTAAAAT
1 ATTTTGTTATAGTTATAAAAT
6484037 ATTTTGTT-TAGTGTATAAAA
1 ATTTTGTTATAGT-TATAAAA
6484057 GGTTGTGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
ATTTTGTTATAGTTATAAAAT
Found at i:6485627 original size:12 final size:12
Alignment explanation
Indices: 6485610--6485640 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
6485600 TTAAATATAT
6485610 ATACCCGGCCCG
1 ATACCCGGCCCG
6485622 ATACCCGGCCCG
1 ATACCCGGCCCG
6485634 ATACCCG
1 ATACCCG
6485641 TTTAAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.10
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:6486427 original size:23 final size:23
Alignment explanation
Indices: 6486395--6486444 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6486385 TGATATATTT
*
6486395 ATTTAACATTCGCAAACATGATC
1 ATTTAACATTAGCAAACATGATC
* * *
6486418 ATTTAGCATTAGTAAACATGTTC
1 ATTTAACATTAGCAAACATGATC
6486441 ATTT
1 ATTT
6486445 GCAAGCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
ATTTAACATTAGCAAACATGATC
Found at i:6487059 original size:28 final size:28
Alignment explanation
Indices: 6487001--6487061 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
6486991 AAATATTTAG
** **
6487001 TTTTTAATAATACAATTAGGTATGTGTT
1 TTTTTAATAATACAATTAGGTACCTAAT
* *
6487029 TTTTTAATAATATAATTAGGTCCCTAAT
1 TTTTTAATAATACAATTAGGTACCTAAT
6487057 TTTTT
1 TTTTT
6487062 TGGATGAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (28 bp):
TTTTTAATAATACAATTAGGTACCTAAT
Found at i:6488013 original size:8 final size:7
Alignment explanation
Indices: 6487996--6488038 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
6487986 TATAATAATT
*
6487996 AAAATTA
1 AAAAATA
6488003 AAAAATA
1 AAAAATA
6488010 AAAAATA
1 AAAAATA
* *
6488017 TAATATAA
1 AAAAAT-A
6488025 AAAAATA
1 AAAAATA
6488032 AAAAATA
1 AAAAATA
6488039 CAGACAATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 25 0.83
8 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAAATA
Found at i:6488271 original size:18 final size:18
Alignment explanation
Indices: 6488225--6488278 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
6488215 ATGATAATTA
*
6488225 AAAAATAAGA-AAAAAAT
1 AAAAATAAAATAAAAAAT
* *
6488242 AAAAATATAATATAAAAT
1 AAAAATAAAATAAAAAAT
6488260 AATAAA-AAAATAAAAAAT
1 AA-AAATAAAATAAAAAAT
6488278 A
1 A
6488279 CAAACAATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 8 0.27
18 19 0.63
19 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:6488432 original size:39 final size:40
Alignment explanation
Indices: 6488377--6488457 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
6488367 TTAGGACAAA
6488377 ATCCTAAAAAAATATATTAATTAATAACGTATCAAAATAT
1 ATCCTAAAAAAATATATTAATTAATAACGTATCAAAATAT
6488417 ATCCT-AAAAAATATATTAATTAATAACGTATCAAAATAT
1 ATCCTAAAAAAATATATTAATTAATAACGTATCAAAATAT
6488456 AT
1 AT
6488458 ATACAATCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 36 0.88
40 5 0.12
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (40 bp):
ATCCTAAAAAAATATATTAATTAATAACGTATCAAAATAT
Found at i:6494789 original size:40 final size:40
Alignment explanation
Indices: 6494735--6494820 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
6494725 TGTTGAGACA
*
6494735 TACCC-ATATGAAGTTGGCGAGAGACCTTCAACACCCCCT
1 TACCCTATATGAAGTTGGCGAAAGACCTTCAACACCCCCT
*
6494774 TACCCTATATGAAGTTGGTGAAAGACCTTCAACACCCCCT
1 TACCCTATATGAAGTTGGCGAAAGACCTTCAACACCCCCT
6494814 TACCCTA
1 TACCCTA
6494821 CCATGCCAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 5 0.11
40 39 0.89
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (40 bp):
TACCCTATATGAAGTTGGCGAAAGACCTTCAACACCCCCT
Found at i:6495747 original size:2 final size:2
Alignment explanation
Indices: 6495736--6496156 Score: 140
Period size: 2 Copynumber: 213.0 Consensus size: 2
6495726 TTGAAATAAT
* * *
6495736 TA TA -A TA TA TA TA TA TA TA TA AA CTA AA TA TA TA CA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
6495777 TA AA CTA TA TGA TT TA TA T- TA -A TA AA CTA TA TA -A TT TA TA
1 TA TA -TA TA T-A TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
6495817 TA GTA TA TA TA -A TT TA GA -A T- TA TA CA TA GTA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
6495858 TA TA TA -A CTA TA TA GTG TA TA TA T- TG TT TA TA AA TA TA GTT
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * **
6495899 TA TA TT TA TA TA CA -A TA TA TA AA CTA TA TA GC T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
6495940 TA TA CTA TA TA TA -A T- TA TA AA T- TA TA TA TA CTA TG TA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
6495981 T- TA TA TA -A TT TA T- TA -A TA TA AA T- TA TA TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
6496019 TA GTT TA TA CT- TA TA TA T- TA CTA TG TA TA AA CTA TA TA GTT TA
1 TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA
* * *
6496062 TA TA T- TG TA TA TA AA TA TA TA GTT TA TA TA TA -A TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
6496102 T- TA TA TA GTT TA TA TA TA AA CTA TA TA GTA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
6496144 -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
6496157 GTTTAGAGTT
Statistics
Matches: 307, Mismatches: 63, Indels: 98
0.66 0.13 0.21
Matches are distributed among these distances:
1 27 0.09
2 251 0.82
3 29 0.09
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:6495748 original size:9 final size:9
Alignment explanation
Indices: 6495736--6496156 Score: 111
Period size: 9 Copynumber: 46.4 Consensus size: 9
6495726 TTGAAATAAT
6495736 TATAATATA
1 TATAATATA
6495745 TAT-ATATA
1 TATAATATA
*
6495753 TATAA-A-C
1 TATAATATA
6495760 TA-AATATA
1 TATAATATA
*
6495768 TACAATATA
1 TATAATATA
6495777 TA-AACTATA
1 TATAA-TATA
*
6495786 TGAT-TTATA
1 T-ATAATATA
6495795 T-TAATAAACTA
1 TATAAT--A-TA
*
6495806 TATAATTTA
1 TATAATATA
*
6495815 TATAGTATA
1 TATAATATA
6495824 TATAAT-T-
1 TATAATATA
*
6495831 TAGAATTATA
1 TATAA-TATA
* *
6495841 CATAGTATA
1 TATAATATA
6495850 TATATATATA
1 TATA-ATATA
6495860 TATAACTATA
1 TATAA-TATA
*
6495870 TAGT-GTATA
1 TA-TAATATA
** *
6495879 TATTGTTTA
1 TATAATATA
6495888 TA-AATATA
1 TATAATATA
* *
6495896 GTTTATATTTA
1 -TATA-ATATA
6495907 TATACA-ATA
1 TATA-ATATA
6495916 TATAAACTATA
1 TAT-AA-TATA
6495927 TAGCTTATATATA
1 TA---TA-ATATA
*
6495940 TATACTATA
1 TATAATATA
6495949 TATAAT-TA
1 TATAATATA
6495957 TA-AATTATA
1 TATAA-TATA
* *
6495966 TATACTATG
1 TATAATATA
6495975 TATAA-ATTA
1 TATAATA-TA
*
6495984 TATAATTTA
1 TATAATATA
6495993 T-TAATATA
1 TATAATATA
*
6496001 -A-ATTATA
1 TATAATATA
6496008 TATAA-ACTA
1 TATAATA-TA
* *
6496017 TATAGTTTA
1 TATAATATA
*
6496026 TACTTATATA
1 TA-TAATATA
* *
6496036 T-TACTATG
1 TATAATATA
6496044 TATAA-ACTA
1 TATAATA-TA
* *
6496053 TATAGTTTA
1 TATAATATA
* *
6496062 TATATTGTA
1 TATAATATA
6496071 TATAA-ATA
1 TATAATATA
*
6496079 TATAGTTTATA
1 TATA--ATATA
6496090 TATAATATA
1 TATAATATA
*
6496099 T-TATTATA
1 TATAATATA
*
6496107 TAGT-TTATA
1 TA-TAATATA
6496116 TATAA-ACTA
1 TATAATA-TA
*
6496125 TATAGTATA
1 TATAATATA
6496134 TAT-ATATA
1 TATAATATA
6496142 TAATATATATA
1 T-ATA-ATATA
6496153 TATA
1 TATA
6496157 GTTTAGAGTT
Statistics
Matches: 302, Mismatches: 56, Indels: 107
0.65 0.12 0.23
Matches are distributed among these distances:
6 2 0.01
7 15 0.05
8 60 0.20
9 149 0.49
10 37 0.12
11 26 0.09
12 4 0.01
13 7 0.02
14 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (9 bp):
TATAATATA
Found at i:6495958 original size:15 final size:13
Alignment explanation
Indices: 6495736--6496156 Score: 99
Period size: 13 Copynumber: 34.8 Consensus size: 13
6495726 TTGAAATAAT
6495736 TATA-ATATATA-
1 TATATATATATAC
*
6495747 TATATATATAAAC
1 TATATATATATAC
6495760 TA-A-ATATATAC
1 TATATATATATAC
*
6495771 -A-ATATATAAAC
1 TATATATATATAC
6495782 TATATGAT-T-TA-
1 TATAT-ATATATAC
*
6495793 TAT-TA-ATAAAC
1 TATATATATATAC
*
6495804 TATATA-ATTTA-
1 TATATATATATAC
*
6495815 TATAGTATATATAA
1 TATA-TATATATAC
* *
6495829 TTTAGA-ATTATAC
1 TATATATA-TATAC
6495842 -ATAGTATATATA-
1 TATA-TATATATAC
6495854 TATATATATA-AC
1 TATATATATATAC
*
6495866 TATATAGTGTATA-
1 TATATA-TATATAC
* *
6495879 TAT-TGTTTATA-
1 TATATATATATAC
* *
6495890 AATATAGTTTATA-
1 TATATA-TATATAC
* *
6495903 TTTATATACAATA-
1 TATATATA-TATAC
*
6495916 TATAAACTATATAGC
1 TATATA-TATATA-C
6495931 TTATATATATATAC
1 -TATATATATATAC
6495945 TATATATA-ATTA-
1 TATATATATA-TAC
*
6495957 TAAATTATATATAC
1 TATA-TATATATAC
* *
6495971 TATGTATA-A-AT
1 TATATATATATAC
*
6495982 TATATA-ATTTA-
1 TATATATATATAC
*
6495993 T-TA-ATATA-AA
1 TATATATATATAC
*
6496003 T-TATATATAAAC
1 TATATATATATAC
*
6496015 TATATAGTTTATAC
1 TATATA-TATATAC
6496029 T-TATATAT-TAC
1 TATATATATATAC
*
6496040 TATGTATA-A-AC
1 TATATATATATAC
*
6496051 TATATAGTTTATA-
1 TATATA-TATATAC
*
6496064 TAT-TGTATATA-
1 TATATATATATAC
* *
6496075 AATATATAGTTTA-
1 TATATATA-TATAC
6496088 TATATA-ATATA-
1 TATATATATATAC
*
6496099 T-TAT-TATATAG
1 TATATATATATAC
* *
6496110 TTTATATATAAAC
1 TATATATATATAC
6496123 TATATAGTATATA-
1 TATATA-TATATAC
6496136 TATATATA-ATA-
1 TATATATATATAC
6496147 TATATATATA
1 TATATATATA
6496157 GTTTAGAGTT
Statistics
Matches: 307, Mismatches: 51, Indels: 103
0.67 0.11 0.22
Matches are distributed among these distances:
9 4 0.01
10 20 0.07
11 82 0.27
12 61 0.20
13 104 0.34
14 25 0.08
15 6 0.02
16 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (13 bp):
TATATATATATAC
Found at i:6496065 original size:11 final size:11
Alignment explanation
Indices: 6496051--6496199 Score: 56
Period size: 11 Copynumber: 12.7 Consensus size: 11
6496041 ATGTATAAAC
6496051 TATATAGTTTA
1 TATATAGTTTA
*
6496062 TATATTGTATATAAA
1 TATATAGT-T-T--A
6496077 TATATAGTTTA
1 TATATAGTTTA
*
6496088 TATATAATATATTA
1 TATAT-A-GT-TTA
6496102 TTATATAGTTTA
1 -TATATAGTTTA
* *
6496114 TATATAAACTATA
1 TATAT--AGTTTA
*
6496127 TAGTATA-TATA
1 TA-TATAGTTTA
*
6496138 TATATAATATATA
1 TATATAGT-T-TA
6496151 TATATAGTTTA
1 TATATAGTTTA
* *
6496162 GAGT-TAATTTA
1 TA-TATAGTTTA
6496173 TATA-A--TTA
1 TATATAGTTTA
6496181 TATATAGTTTA
1 TATATAGTTTA
*
6496192 TACATAGT
1 TATATAGT
6496200 AGTATATAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
8 7 0.07
9 1 0.01
10 6 0.06
11 45 0.42
12 8 0.07
13 19 0.18
14 8 0.07
15 13 0.12
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:6496175 original size:48 final size:49
Alignment explanation
Indices: 6496086--6496186 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 49
6496076 ATATATAGTT
* *
6496086 TATATATAATATATTATTATATAGTTTATATATAAACTATATAGTATATA
1 TATATATAATATATTATTATATAGTTTAGATATAAACTATATAAT-TATA
**
6496136 TATATATAATATA-TA-TATATAGTTTAGAGT-TAATTTATATAATTATA
1 TATATATAATATATTATTATATAGTTTAGA-TATAAACTATATAATTATA
6496183 TATA
1 TATA
6496187 GTTTATACAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
47 8 0.17
48 22 0.48
49 3 0.07
50 13 0.28
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.49
Consensus pattern (49 bp):
TATATATAATATATTATTATATAGTTTAGATATAAACTATATAATTATA
Found at i:6496216 original size:11 final size:11
Alignment explanation
Indices: 6496202--6496321 Score: 62
Period size: 11 Copynumber: 11.4 Consensus size: 11
6496192 TACATAGTAG
6496202 TATATAAACTA
1 TATATAAACTA
6496213 TATATAAACTATA
1 TATATAAAC--TA
6496226 TATATAAACTA
1 TATATAAACTA
*
6496237 -A-ATAAATTA
1 TATATAAACTA
**
6496246 TATAGTTTAC-A
1 TATA-TAAACTA
*
6496257 TATGA-ATTA-TA
1 TAT-ATA-AACTA
6496268 TATATAAAC--
1 TATATAAACTA
6496277 TA-ATAAAC--
1 TATATAAACTA
*
6496285 TATATAAATTA
1 TATATAAACTA
*
6496296 TATATGAACTA
1 TATATAAACTA
*
6496307 TATATAAACTG
1 TATATAAACTA
6496318 TATA
1 TATA
6496322 GTTTATATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
8 8 0.09
9 14 0.16
10 4 0.05
11 45 0.53
12 3 0.04
13 11 0.13
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (11 bp):
TATATAAACTA
Found at i:6496227 original size:13 final size:13
Alignment explanation
Indices: 6496202--6496312 Score: 59
Period size: 13 Copynumber: 8.3 Consensus size: 13
6496192 TACATAGTAG
6496202 TATATAAAC--TA
1 TATATAAACTATA
6496213 TATATAAACTATA
1 TATATAAACTATA
6496226 TATATAAACTAAATA
1 TATATAAACT--ATA
* * * *
6496241 AATTATATAGTTTA
1 TA-TATAAACTATA
* * *
6496255 CATATGAATTATA
1 TATATAAACTATA
6496268 TATATAAACTAATAAA
1 TATATAAACT-AT--A
6496284 CTATATAAA-T-TA
1 -TATATAAACTATA
*
6496296 TATATGAACTATA
1 TATATAAACTATA
6496309 TATA
1 TATA
6496313 AACTGTATAG
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
11 16 0.21
12 2 0.03
13 32 0.42
14 6 0.08
15 4 0.05
16 8 0.11
17 8 0.11
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (13 bp):
TATATAAACTATA
Found at i:6496232 original size:24 final size:22
Alignment explanation
Indices: 6496202--6496290 Score: 78
Period size: 21 Copynumber: 4.1 Consensus size: 22
6496192 TACATAGTAG
6496202 TATATAAACTATATATAAACTATA
1 TATATAAACTA-A-ATAAACTATA
6496226 TATATAAACTAAATAAA-T-TA
1 TATATAAACTAAATAAACTATA
** * * *
6496246 TATAGTTTAC-ATATGAATTATA
1 TATA-TAAACTAAATAAACTATA
6496268 TATATAAACT-AATAAACTATA
1 TATATAAACTAAATAAACTATA
6496289 TA
1 TA
6496291 AATTATATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
20 11 0.21
21 18 0.35
22 11 0.21
23 1 0.02
24 11 0.21
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
TATATAAACTAAATAAACTATA
Found at i:6496297 original size:9 final size:9
Alignment explanation
Indices: 6496268--6496310 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
6496258 ATGAATTATA
6496268 TATATAAAC
1 TATATAAAC
6496277 TA-ATAAAC
1 TATATAAAC
*
6496285 TATATAAAT
1 TATATAAAC
6496294 TATATATGAAC
1 TATATA--AAC
6496305 TATATA
1 TATATA
6496311 TAAACTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 8 0.28
9 13 0.45
11 8 0.28
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (9 bp):
TATATAAAC
Found at i:6496328 original size:31 final size:32
Alignment explanation
Indices: 6496279--6496358 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 32
6496269 ATATAAACTA
6496279 ATAAACTATATAAATTATA-TATGA-ACTATAT
1 ATAAACTATATAAATTATATTAT-ATACTATAT
* **
6496310 ATAAACTGTATAGTTTATATTTATATACTATAT
1 ATAAACTATATAAATTATA-TTATATACTATAT
6496343 AT-AA-T-TATAAATTATA
1 ATAAACTATATAAATTATA
6496359 ATACTATTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
30 9 0.22
31 17 0.41
32 3 0.07
33 12 0.29
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (32 bp):
ATAAACTATATAAATTATATTATATACTATAT
Found at i:6496785 original size:17 final size:17
Alignment explanation
Indices: 6496765--6496813 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
6496755 AAAAGTTAGT
6496765 AAAAAAGAAAATAAACA
1 AAAAAAGAAAATAAACA
*
6496782 AAAATAA-AAAATAAAGA
1 AAAA-AAGAAAATAAACA
*
6496799 AAGAAAGAAAATAAA
1 AAAAAAGAAAATAAA
6496814 ATGAATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.82, C:0.02, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAAAGAAAATAAACA
Found at i:6496859 original size:5 final size:5
Alignment explanation
Indices: 6496849--6496891 Score: 68
Period size: 5 Copynumber: 8.2 Consensus size: 5
6496839 GTTAATTAAA
6496849 AAAAT AAAAT AAAAAT AAGAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT A
6496892 TTTAAACTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 26 0.72
6 10 0.28
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:6498014 original size:24 final size:25
Alignment explanation
Indices: 6497982--6498039 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
6497972 GATCCTGTAA
*
6497982 ATAAAATAAT-AA-ATAAATTAGTAT
1 ATAATATAATCAACATAAATTA-TAT
*
6498006 ATAATATAATCAATCATATATTATAT
1 ATAATATAATCAA-CATAAATTATAT
6498032 ATAATATA
1 ATAATATA
6498040 TTTTATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 2 0.07
26 11 0.38
27 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATATAATCAACATAAATTATAT
Found at i:6498653 original size:30 final size:30
Alignment explanation
Indices: 6498617--6498673 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6498607 GAAAAACAAA
* *
6498617 TTCAAAGATTT-TGTTTTAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
6498647 TTCAAAGTTTATGTTTCAAGAGAAACT
1 TTCAAAGTTTATGTTTCAAGAGAAACT
6498674 ATCTCAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:6498708 original size:36 final size:36
Alignment explanation
Indices: 6498658--6498743 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
6498648 TCAAAGTTTA
* * *
6498658 TGTTTCAAGAGAAACTATCTCAAGGGAGA-CAAAATT
1 TGTTTCAAGGGAAACT-TCTCAAGAGAGATAAAAATT
6498694 TGTTTCAAGGGAAACTTCTCAAGAGAGATAAAAATT
1 TGTTTCAAGGGAAACTTCTCAAGAGAGATAAAAATT
**
6498730 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
6498744 TGTTTTCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 11 0.25
36 33 0.75
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTTCTCAAGAGAGATAAAAATT
Found at i:6498940 original size:204 final size:205
Alignment explanation
Indices: 6498634--6499137 Score: 752
Period size: 205 Copynumber: 2.5 Consensus size: 205
6498624 ATTTTGTTTT
* *
6498634 AAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTTGT-
1 AAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAA-GGAGACAAAATTTTCTA
*
6498697 TTCAAGGGAAACT-TCTCAAGAGAGATAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
64 TTCGAGGGAAACTATCTCAAGAGAGATAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
* *
6498761 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGATTAAAATGAAATTATCTCAAGAGAGAC
129 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGATTAAAAGGAAACTATCTCAAGAGAGAC
6498825 AAAATTCATTTC
194 AAAATTCATTTC
* *
6498837 ATGGGAAATGTTTTCAATGTTTATGTTTCAAGAG-AACTGTCTCAAGAGAGACAAAATTTTCTAC
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAG-GAGACAAAATTTTCTA-
*
6498901 TTCGAGGGAAACTATCTCAAGAGAGA-CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
64 TTCGAGGGAAACTATCTCAAGAGAGATAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
* * *
6498965 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
129 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGATTAAAAGGAAACTATCTCAAGAGAGAC
6499030 AAAATTCATTTC
194 AAAATTCATTTC
* * * *
6499042 AAGGGAAATGTTTTTAATGTTTATGTTCCAGGAGAAACTATCTCAAGGTAGACAAAATTTCCTAT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGG-AGACAAAATTTTCTA-
*
6499107 TTCGAAGGAAACTATCTCAAGCA-AGATAAAA
64 TTCGAGGGAAACTATCTCAAG-AGAGATAAAA
6499138 TCTTGTTTTA
Statistics
Matches: 271, Mismatches: 20, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
200 1 0.00
201 19 0.07
202 29 0.11
203 7 0.03
204 81 0.30
205 82 0.30
206 48 0.18
207 4 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (205 bp):
AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGAGACAAAATTTTCTATT
CGAGGGAAACTATCTCAAGAGAGATAAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGATTAAAAGGAAACTATCTCAAGAGAGACAA
AATTCATTTC
Found at i:6499014 original size:37 final size:36
Alignment explanation
Indices: 6498963--6499049 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
6498953 TCAATGTTTA
* * *
6498963 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
6499000 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
6499036 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
6499050 TGTTTTTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 14 0.31
37 31 0.69
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:6499043 original size:102 final size:102
Alignment explanation
Indices: 6498634--6499127 Score: 728
Period size: 102 Copynumber: 4.8 Consensus size: 102
6498624 ATTTTGTTTT
* *
6498634 AAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTTGTT
1 AAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT
*
6498698 TCAAGGGAAACT-TCTCAAGAGAGATAAAAATTCATTTC
65 TCAAGGGAAACTATCTCAAGAGAGA-CAAAATTCATTTC
*
6498736 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGATT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTT
* ** *
6498800 AAAATGAAATTATCTCAAGAGAGACAAAATTCATTTC
66 CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTC
* * *
6498837 ATGGGAAATGTTTTCAATGTTTATGTTTCAAGAG-AACTGTCTCAAGAGAGACAAAATTTTCTAC
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGT--
*
6498901 TTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTC
64 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTC
6498940 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTT
6499005 CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTC
66 CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTC
* * * * * *
6499042 AAGGGAAATGTTTTTAATGTTTATGTTCCAGGAGAAACTATCTCAAGGTAGACAAAATTTCCTAT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT--TGT
6499107 TTCGAA-GGAAACTATCTCAAG
64 TTC-AAGGGAAACTATCTCAAG
6499128 CAAGATAAAA
Statistics
Matches: 357, Mismatches: 27, Indels: 14
0.90 0.07 0.04
Matches are distributed among these distances:
100 21 0.06
101 108 0.30
102 113 0.32
103 67 0.19
104 46 0.13
105 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (102 bp):
AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTT
CAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTC
Found at i:6499175 original size:36 final size:36
Alignment explanation
Indices: 6499135--6499272 Score: 109
Period size: 36 Copynumber: 3.8 Consensus size: 36
6499125 AAGCAAGATA
* * **
6499135 AAATCTTGTTTTAAGAAAAACAATCTTGAGGGAAAT
1 AAATCTTCTTTCAAGAAAAACAATCTCAAGGGAAAT
* * * * * *
6499171 AAATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGAC
1 AAATCTTCTTTCAAGAAAAACAATCTCAAGGGAAAT
** *
6499207 AAAGTCTGT-TTT-AAGAATGACAATCACAAGGGAAAT
1 AAA-TCT-TCTTTCAAGAAAAACAATCTCAAGGGAAAT
* *
6499243 AAATCTTCTTTCAAGTAAAACAGTCTCAAG
1 AAATCTTCTTTCAAGAAAAACAATCTCAAG
6499273 TGAGACAAAT
Statistics
Matches: 74, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
34 1 0.01
35 6 0.08
36 61 0.82
37 5 0.07
38 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (36 bp):
AAATCTTCTTTCAAGAAAAACAATCTCAAGGGAAAT
Found at i:6500450 original size:83 final size:87
Alignment explanation
Indices: 6500357--6500583 Score: 284
Period size: 95 Copynumber: 2.6 Consensus size: 87
6500347 GGCTAGCTGA
*
6500357 ATCCATAAAGCCGAGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAA-TAT-GTA-AAT-ACC
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
* *
6500418 TTGATCAGGTTAGCTGAATCTT
66 TTGATCAGGCTAGCTGAATATT
6500440 ATCCATAAAGCCGGGGTGTTTAACCAATTGC-CTTAGAGGGACAACTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A-T-TATAGT
*
6500504 ATAATCACCTTTATCAGGCTAGCTGAATATT
57 ATAATCACCTTGATCAGGCTAGCTGAATATT
* *
6500535 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAA
1 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAA
6500584 GCTTTATTGT
Statistics
Matches: 124, Mismatches: 6, Indels: 22
0.82 0.04 0.14
Matches are distributed among these distances:
82 1 0.01
83 44 0.35
84 1 0.01
89 2 0.02
92 3 0.02
93 3 0.02
94 4 0.03
95 66 0.53
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (87 bp):
ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
TTGATCAGGCTAGCTGAATATT
Found at i:6500578 original size:95 final size:95
Alignment explanation
Indices: 6500415--6500595 Score: 317
Period size: 95 Copynumber: 1.9 Consensus size: 95
6500405 ATATGTAAAT
* * *
6500415 ACCTTGATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGTGTTTAACCAATTGCCTTAGAGGG
1 ACCTTGATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
6500480 ACAACTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
* *
6500510 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGG
1 ACCTTGATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
6500575 ACAACTCAAGCTTTATTGTAT
66 ACAACTCAAGCTTTATTGTAT
6500596 GTAAATAATA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (95 bp):
ACCTTGATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:6504702 original size:17 final size:17
Alignment explanation
Indices: 6504682--6504730 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
6504672 AAAAGTTACT
6504682 AAAAAAGAAAATAAACA
1 AAAAAAGAAAATAAACA
* *
6504699 AAAATAA-TAAATAAAGA
1 AAAA-AAGAAAATAAACA
*
6504716 AAGAAAGAAAATAAA
1 AAAAAAGAAAATAAA
6504731 ATGAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (17 bp):
AAAAAAGAAAATAAACA
Found at i:6504775 original size:5 final size:5
Alignment explanation
Indices: 6504765--6504813 Score: 62
Period size: 5 Copynumber: 9.2 Consensus size: 5
6504755 GGTTAATTAA
*
6504765 AAAAT AAAAT AAAAAT AAGAAT AAACT AAAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT -AAAAT AA-AAT AAAAT -AAAAT AAAAT AAAAT AAAAT
6504813 A
1 A
6504814 TTTAAACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 25 0.64
6 14 0.36
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:6504780 original size:11 final size:11
Alignment explanation
Indices: 6504765--6504813 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
6504755 GGTTAATTAA
6504765 AAAAT-AAAAT
1 AAAATAAAAAT
*
6504775 AAAAATAAGAAT
1 -AAAATAAAAAT
*
6504787 AAACTAAAAAT
1 AAAATAAAAAT
6504798 AAAAT-AAAAT
1 AAAATAAAAAT
6504808 AAAATA
1 AAAATA
6504814 TTTAAACTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 10 0.31
11 18 0.56
12 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:6504789 original size:17 final size:16
Alignment explanation
Indices: 6504765--6504811 Score: 76
Period size: 17 Copynumber: 2.9 Consensus size: 16
6504755 GGTTAATTAA
6504765 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
*
6504781 AAGAATAAACTAAAAAT
1 AA-AATAAAATAAAAAT
6504798 AAAATAAAATAAAA
1 AAAATAAAATAAAA
6504812 TATTTAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:6505953 original size:24 final size:25
Alignment explanation
Indices: 6505921--6505978 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
6505911 AATCCTGTAA
*
6505921 ATAAAATAAT-AA-ATAAATTAGTAT
1 ATAATATAATCAACATAAATTA-TAT
*
6505945 ATAATATAATCAATCATATATTATAT
1 ATAATATAATCAA-CATAAATTATAT
6505971 ATAATATA
1 ATAATATA
6505979 TTTTATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.31
25 2 0.07
26 11 0.38
27 7 0.24
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATATAATCAACATAAATTATAT
Found at i:6506058 original size:22 final size:21
Alignment explanation
Indices: 6506026--6506124 Score: 69
Period size: 22 Copynumber: 4.7 Consensus size: 21
6506016 TACAACTATG
*
6506026 TATAAATTATATAGTTTACTAA
1 TATAAACTATATA-TTTACTAA
6506048 TATAAACTATATA--TACTATA
1 TATAAACTATATATTTACTA-A
* * * *
6506068 TGTAAACTATATATATAAATTA
1 TATAAACTATATAT-TTACTAA
* *
6506090 TATATACTACATAGTTTAC-AA
1 TATAAACTATATA-TTTACTAA
*
6506111 TATGAACTATATAT
1 TATAAACTATATAT
6506125 AAAAACTATA
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
19 5 0.09
20 14 0.24
21 11 0.19
22 25 0.43
23 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.41
Consensus pattern (21 bp):
TATAAACTATATATTTACTAA
Found at i:6506086 original size:13 final size:13
Alignment explanation
Indices: 6506064--6506179 Score: 63
Period size: 13 Copynumber: 8.6 Consensus size: 13
6506054 CTATATATAC
*
6506064 TATATGTAAACTA
1 TATATATAAACTA
*
6506077 TATATATAAATTA
1 TATATATAAACTA
* *
6506090 TATATACTACATAGTT
1 TATATA-TA-A-ACTA
* *
6506106 TACAATATGAACTA
1 TA-TATATAAACTA
*
6506120 TATATAAAAACTA
1 TATATATAAACTA
*
6506133 TATATATAAATTA
1 TATATATAAACTA
* ***
6506146 TACACTATAGTTTA
1 TATA-TATAAACTA
*
6506160 TATATATATA-TA
1 TATATATAAACTA
6506172 TATATATA
1 TATATATA
6506180 GTATACATTA
Statistics
Matches: 79, Mismatches: 19, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
12 10 0.13
13 43 0.54
14 16 0.20
15 2 0.03
16 5 0.06
17 3 0.04
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:6506091 original size:11 final size:11
Alignment explanation
Indices: 6506019--6506138 Score: 54
Period size: 11 Copynumber: 11.0 Consensus size: 11
6506009 TGTGTGCTAC
*
6506019 AACTATGTATA
1 AACTATATATA
* *
6506030 AATTATATAGTT
1 AACTATATA-TA
*
6506042 TACTA-ATATA
1 AACTATATATA
6506052 AACTATATAT-
1 AACTATATATA
*
6506062 -ACTATATGTA
1 AACTATATATA
6506072 AACTATATATA
1 AACTATATATA
*
6506083 TAAAT-TATATA
1 -AACTATATATA
* * *
6506094 TACTACATAGTT
1 AACTATATA-TA
* *
6506106 TAC-A-ATATG
1 AACTATATATA
6506115 AACTATATATAAA
1 AACTATATAT--A
6506128 AACTATATATA
1 AACTATATATA
6506139 TAAATTATAC
Statistics
Matches: 81, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
9 11 0.14
10 11 0.14
11 38 0.47
12 11 0.14
13 10 0.12
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.39
Consensus pattern (11 bp):
AACTATATATA
Found at i:6506178 original size:56 final size:58
Alignment explanation
Indices: 6506035--6506179 Score: 131
Period size: 56 Copynumber: 2.5 Consensus size: 58
6506025 GTATAAATTA
* ** *
6506035 TATAGTTTACTAATATAAACTATATATACTATATGTAAACTATATATATAAATTATATATAC
1 TATAGTTTA-T-ATATATA-TATATATA-TATATAAAAACTATATATATAAATTATATACAC
* * *
6506097 TACATAGTTTACA-ATAT-GA-A-CTATATATAAAAACTATATATATAAA-T-TATACAC
1 T--ATAGTTTATATATATATATATATATATATAAAAACTATATATATAAATTATATACAC
6506151 TATAGTTTATATATATATATATATATATA
1 TATAGTTTATATATATATATATATATATA
6506180 GTATACATTA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
52 9 0.13
53 4 0.06
54 8 0.12
55 2 0.03
56 27 0.40
57 2 0.03
58 1 0.01
59 1 0.01
61 3 0.04
62 2 0.03
64 8 0.12
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (58 bp):
TATAGTTTATATATATATATATATATATATAAAAACTATATATATAAATTATATACAC
Found at i:6506179 original size:54 final size:56
Alignment explanation
Indices: 6506055--6506179 Score: 134
Period size: 56 Copynumber: 2.2 Consensus size: 56
6506045 TAATATAAAC
** *
6506055 TATATATACTATATGTAAACTATATATATAAATTATATATACTACATAGTTTACAATA
1 TATATATA-TATATAAAAACTATATATATAAATTATATACACTA-ATAGTTTACAATA
* *
6506113 TGA-A-CTATATATAAAAACTATATATATAAA-T-TATACACT-ATAGTTTATATATA
1 T-ATATATATATATAAAAACTATATATATAAATTATATACACTAATAGTTTACA-ATA
6506166 TATATATATATATA
1 TATATATATATATA
6506180 GTATACATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
52 10 0.18
53 5 0.09
54 15 0.26
55 1 0.02
56 21 0.37
57 2 0.04
58 2 0.04
59 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (56 bp):
TATATATATATATAAAAACTATATATATAAATTATATACACTAATAGTTTACAATA
Found at i:6506210 original size:37 final size:37
Alignment explanation
Indices: 6506131--6506210 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
6506121 ATATAAAAAC
* *
6506131 TATATATATAAATTATACACTATAGTTTATATATATA
1 TATATATATAAAGTATACACTATACTTTATATATATA
* *
6506168 TATATATATATAGTATACATTATAC-TTATA-AGTATA
1 TATATATATAAAGTATACACTATACTTTATATA-TATA
6506204 TA-ATATA
1 TATATATA
6506211 CATTATAAGC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.16
36 11 0.29
37 21 0.55
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
TATATATATAAAGTATACACTATACTTTATATATATA
Found at i:6506250 original size:2 final size:2
Alignment explanation
Indices: 6506245--6506424 Score: 89
Period size: 2 Copynumber: 93.0 Consensus size: 2
6506235 ACACACACAC
6506245 AT AT AT AT AT A- AT A- AT AT AT A- AT AT AT A- 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
* * * * *
6506283 AT AT AT AC AT AG AT AA AT -T AA AT A- AGT AT A- AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * * *
6506323 AA AGT AT AA AGT AT -T AA AGT AT A- AT AT -T AGT GT AT GT AT AT
1 AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* * *
6506364 AT AT AA AGT AT AA AGT AT AA AT -T AT A- AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6506406 AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
6506425 GCGTAGGACT
Statistics
Matches: 133, Mismatches: 25, Indels: 40
0.67 0.13 0.20
Matches are distributed among these distances:
1 13 0.10
2 113 0.85
3 7 0.05
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.41
Consensus pattern (2 bp):
AT
Found at i:6506943 original size:44 final size:42
Alignment explanation
Indices: 6506865--6506947 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
6506855 CAGTTCTTCA
* *
6506865 TTATTTTTTTGGATCCAAAATAACATAAAAATCGTTCATTTC
1 TTATTTTTTTAGATCCAAAATAAAATAAAAATCGTTCATTTC
* **
6506907 TTATTTTTTTAGATCTAAACCATAAAATAAGTATCGTTCAT
1 TTATTTTTTTAGATCCAAA--ATAAAATAAAAATCGTTCAT
6506948 CCGGAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 17 0.50
44 17 0.50
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (42 bp):
TTATTTTTTTAGATCCAAAATAAAATAAAAATCGTTCATTTC
Found at i:6507535 original size:20 final size:20
Alignment explanation
Indices: 6507496--6507536 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6507486 TATTTTTTAA
*
6507496 TTTTATATTCTTTTTTGTAT
1 TTTTATATTCTTTTTGGTAT
6507516 TTTTAT-TTCTTTTCTGGTAT
1 TTTTATATTCTTTT-TGGTAT
6507536 T
1 T
6507537 CATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTATATTCTTTTTGGTAT
Found at i:6507731 original size:31 final size:31
Alignment explanation
Indices: 6507692--6507767 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
6507682 TATTTGATAA
6507692 TTGTTTTTATTTTTTATATG-TTTTTTATTT
1 TTGTTTTTATTTTTTATATGTTTTTTTATTT
**
6507722 TGTGTTTTTAAATTTTATATGTTTTTTTATTT
1 T-TGTTTTTATTTTTTATATGTTTTTTTATTT
6507754 TT-TATTTTATTTTT
1 TTGT-TTTTATTTTT
6507768 GTTTTCTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 2 0.05
31 26 0.67
32 11 0.28
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (31 bp):
TTGTTTTTATTTTTTATATGTTTTTTTATTT
Found at i:6507766 original size:17 final size:17
Alignment explanation
Indices: 6507678--6507754 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
6507668 TTTATTATTA
*
6507678 TTTTTATTTGATAATTGTT
1 TTTTTATTTTAT-A-TGTT
6507697 TTTATT-TTTTATATG-T
1 TTT-TTATTTTATATGTT
*
6507713 TTTTTA-TTT-TGTGTT
1 TTTTTATTTTATATGTT
**
6507728 TTTAAATTTTATATGTT
1 TTTTTATTTTATATGTT
6507745 TTTTTATTTT
1 TTTTTATTTT
6507755 TTATTTTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.07
15 10 0.22
16 7 0.15
17 15 0.33
18 1 0.02
19 8 0.17
20 2 0.04
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTTATTTTATATGTT
Found at i:6507853 original size:31 final size:31
Alignment explanation
Indices: 6507758--6507858 Score: 98
Period size: 31 Copynumber: 3.2 Consensus size: 31
6507748 TTATTTTTTA
*
6507758 TTTTATTTTTGTTTTCTATATACATTATATGTT
1 TTTTATTTTTGTTTTCTAT-T-TATTATATGTT
* * * *
6507791 TTATGTTTTATGTTTTTTATTT-TTATTTGTT
1 TTTTATTTT-TGTTTTCTATTTATTATATGTT
*
6507822 TTTTATTTTCTGTTTTCTATTTATT-TCTGTT
1 TTTTATTTT-TGTTTTCTATTTATTATATGTT
6507853 TTTTAT
1 TTTTAT
6507859 AAGTTCAATC
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 37 0.66
32 2 0.04
33 8 0.14
34 9 0.16
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73
Consensus pattern (31 bp):
TTTTATTTTTGTTTTCTATTTATTATATGTT
Done.