Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 309 of 318
Found at i:96309210 original size:20 final size:19
Alignment explanation
Indices: 96309154--96309227 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
96309144 CAACCCAATC
96309154 TTTCTTTTTATTTTTATT-T
1 TTTC-TTTTATTTTTATTAT
* *
96309173 ATT-TATT-TTTTTATTTAT
1 TTTCTTTTATTTTTA-TTAT
96309191 TTTCTTTTATTATTTATTAT
1 TTTCTTTTATT-TTTATTAT
96309211 TTTCTTTTATTTTTATT
1 TTTCTTTTATTTTTATT
96309228 TTATTTTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
16 6 0.13
17 5 0.11
18 3 0.07
19 11 0.24
20 17 0.37
21 4 0.09
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCTTTTATTTTTATTAT
Found at i:96309211 original size:36 final size:36
Alignment explanation
Indices: 96309154--96309235 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 36
96309144 CAACCCAATC
96309154 TTTCTTTTTATTTTTATTTATTTAT-TTTT-TTATTTAT
1 TTTC-TTTTATTTTTATTTATTT-TCTTTTATT-TTTAT
96309191 TTTCTTTTATTATTTA-TTATTTTCTTTTATTTTTAT
1 TTTCTTTTATT-TTTATTTATTTTCTTTTATTTTTAT
*
96309227 TTTATTTTA
1 TTTCTTTTA
96309236 GTTAAATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
35 1 0.02
36 30 0.73
37 10 0.24
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (36 bp):
TTTCTTTTATTTTTATTTATTTTCTTTTATTTTTAT
Found at i:96310360 original size:118 final size:118
Alignment explanation
Indices: 96310152--96310382 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
96310142 TGTTTTCCAT
* *
96310152 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
96310217 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
96310270 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
96310335 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
96310383 ACCGGAAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:96312399 original size:10 final size:10
Alignment explanation
Indices: 96312384--96312433 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
96312374 TAGATTTAAC
96312384 ATTTATCTTT
1 ATTTATCTTT
96312394 ATTTATCTTT
1 ATTTATCTTT
*
96312404 AATTATCTTT
1 ATTTATCTTT
96312414 ATTTAT-TTGT
1 ATTTATCTT-T
*
96312424 ATTCATCTTT
1 ATTTATCTTT
96312434 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:96313199 original size:29 final size:29
Alignment explanation
Indices: 96313157--96313214 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
96313147 TGAAATTTCA
*
96313157 ATCAAAAATTTTAATTCTGTTTTTATTTT
1 ATCAAAAATTTTAATTCTATTTTTATTTT
* *
96313186 ATCAAAACTTTTAATTCTATTTTTCTTTT
1 ATCAAAAATTTTAATTCTATTTTTATTTT
96313215 TTCTTTTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (29 bp):
ATCAAAAATTTTAATTCTATTTTTATTTT
Found at i:96315379 original size:10 final size:10
Alignment explanation
Indices: 96315351--96315400 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
96315341 GGTCTCTCTC
96315351 TCAACAATAAT
1 TCAA-AATAAT
96315362 TACAAAATAAT
1 T-CAAAATAAT
96315373 TCAAAATAATTT
1 TCAAAATAA--T
96315385 TC-AAA-AAT
1 TCAAAATAAT
96315393 TCAAAATA
1 TCAAAATA
96315401 CTTTTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
8 3 0.09
9 3 0.09
10 11 0.32
11 11 0.32
12 6 0.18
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (10 bp):
TCAAAATAAT
Found at i:96315382 original size:21 final size:20
Alignment explanation
Indices: 96315351--96315438 Score: 65
Period size: 20 Copynumber: 4.3 Consensus size: 20
96315341 GGTCTCTCTC
96315351 TCAACAATAA-TTACAAAATAAT
1 TCAA-AATAATTTAC-AAA-AAT
*
96315373 TCAAAATAATTTTCAAAAAT
1 TCAAAATAATTTACAAAAAT
* **
96315393 TCAAAATACTTT-TTAAAAT
1 TCAAAATAATTTACAAAAAT
* *
96315412 TCAAAAT-AGTTATAAAAAT
1 TCAAAATAATTTACAAAAAT
96315431 TCCAAAAT
1 T-CAAAAT
96315439 TTTTATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
18 2 0.04
19 19 0.34
20 20 0.36
21 8 0.14
22 7 0.12
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.33
Consensus pattern (20 bp):
TCAAAATAATTTACAAAAAT
Found at i:96315412 original size:19 final size:19
Alignment explanation
Indices: 96315370--96315438 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
96315360 ATTACAAAAT
96315370 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
* *
96315390 AATTCAAAATACTTTTTAA
1 AATTCAAAATAATTTTAAA
* *
96315409 AATTCAAAATAGTTATAAA
1 AATTCAAAATAATTTTAAA
96315428 AATTCCAAAAT
1 AATT-CAAAAT
96315439 TTTTATTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 22 0.51
20 21 0.49
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:96315444 original size:20 final size:19
Alignment explanation
Indices: 96315387--96315444 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
96315377 AATAATTTTC
96315387 AAAAATTCAAAATACTTTT-T
1 AAAAATTCAAAAT--TTTTAT
**
96315407 -AAAATTCAAAATAGTTAT
1 AAAAATTCAAAATTTTTAT
96315425 AAAAATTCCAAAATTTTTAT
1 AAAAATT-CAAAATTTTTAT
96315445 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 2 0.06
18 1 0.03
19 18 0.58
20 10 0.32
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATTTTTAT
Found at i:96315487 original size:28 final size:26
Alignment explanation
Indices: 96315448--96315509 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
96315438 TTTTTATTTT
*
96315448 TTAAAAATTATAAAAATTTCAAAAAAAA
1 TTAAAAA-TATAAAAAGTT-AAAAAAAA
*
96315476 TTAATAAATATATAAAGTTAAAAAAAA
1 TTAA-AAATATAAAAAGTTAAAAAAAA
*
96315503 GTAAAAA
1 TTAAAAA
96315510 ATCACTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 3 0.10
27 11 0.37
28 13 0.43
29 3 0.10
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (26 bp):
TTAAAAATATAAAAAGTTAAAAAAAA
Found at i:96318613 original size:20 final size:18
Alignment explanation
Indices: 96318579--96318615 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
96318569 GCAACTCATA
96318579 ATTTCAACTATTTTACAC
1 ATTTCAACTATTTTACAC
96318597 ATTTACAACTCATTTTACA
1 ATTT-CAACT-ATTTTACA
96318616 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCAACTATTTTACAC
Found at i:96322806 original size:27 final size:28
Alignment explanation
Indices: 96322765--96322833 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
96322755 TTTGTAATAT
*
96322765 ATATTGTCAAATGAGCATA-GTCTAGGCG
1 ATATTG-CCAATGAGCATAGGTCTAGGCG
* *
96322793 ATATTGCCAATGAGGATAGGTGTAGGCG
1 ATATTGCCAATGAGCATAGGTCTAGGCG
*
96322821 ATATTGGCAATGA
1 ATATTGCCAATGA
96322834 ATGCATTGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 10 0.28
28 26 0.72
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.28
Consensus pattern (28 bp):
ATATTGCCAATGAGCATAGGTCTAGGCG
Found at i:96328630 original size:21 final size:21
Alignment explanation
Indices: 96328604--96328645 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
96328594 GTTACTCTTG
96328604 TAATTTAGTTCATTTTGAACT
1 TAATTTAGTTCATTTTGAACT
96328625 TAATTTAGTTCATTTTGAACT
1 TAATTTAGTTCATTTTGAACT
96328646 ATGTTTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (21 bp):
TAATTTAGTTCATTTTGAACT
Found at i:96334038 original size:61 final size:62
Alignment explanation
Indices: 96333896--96334038 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 62
96333886 TCAAGCTCTA
* *
96333896 CTGGGCCTAAGCCCTATT-CAGAAATCAGAGTTAACTAGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCCT-AGCCCTATTACAGAAATCAGAGATAACTAGGCCTTAGCCCATATCAATATCAAT
* * * *
96333958 CTGGGCCATAGCCC-CTTACAG-TATCAGAGCAT-ACTAGGCC-TAGCCCATATCAGTATCATT
1 CTGGGCC-TAGCCCTATTACAGAAATCAGAG-ATAACTAGGCCTTAGCCCATATCAATATCAAT
96334018 CTGGGCCGTAGCCCTATTACA
1 CTGGGCC-TAGCCCTATTACA
96334039 AGTCGAGATA
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
60 30 0.43
61 22 0.32
62 16 0.23
63 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (62 bp):
CTGGGCCTAGCCCTATTACAGAAATCAGAGATAACTAGGCCTTAGCCCATATCAATATCAAT
Found at i:96334114 original size:19 final size:20
Alignment explanation
Indices: 96334060--96334115 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
96334050 ATTGGGCATT
*
96334060 GCCCATATTAACACAGTTGG
1 GCCCATATTAAAACAGTTGG
*
96334080 GCCCAT-TTCAATACAGTT-G
1 GCCCATATT-AAAACAGTTGG
*
96334099 GCCCATAATAAAACAGT
1 GCCCATATTAAAACAGT
96334116 CTCATATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (20 bp):
GCCCATATTAAAACAGTTGG
Found at i:96334506 original size:18 final size:18
Alignment explanation
Indices: 96334472--96334520 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
96334462 GGGTGTGCAC
96334472 AATTCGGTTAAAACCGAAAA
1 AATTCGGTT--AACCGAAAA
***
96334492 AATTCGGTTAACCGACCC
1 AATTCGGTTAACCGAAAA
96334510 AATTCGGTTAA
1 AATTCGGTTAA
96334521 TCAGTCGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 17 0.65
20 9 0.35
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (18 bp):
AATTCGGTTAACCGAAAA
Found at i:96334630 original size:18 final size:18
Alignment explanation
Indices: 96334609--96334652 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
96334599 GAAACATGTC
96334609 GGTTAACCGAATTTTTTT
1 GGTTAACCGAATTTTTTT
96334627 GGTTAACCGAATTTTTTT
1 GGTTAACCGAATTTTTTT
96334645 GGTTAACC
1 GGTTAACC
96334653 AAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (18 bp):
GGTTAACCGAATTTTTTT
Found at i:96336617 original size:18 final size:20
Alignment explanation
Indices: 96336584--96336628 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
96336574 CAGTATAAAA
96336584 ATATGTTTAATATTATTA-AT
1 ATAT-TTTAATATTATTACAT
96336604 ATATTTTAAT-TTATTACAT
1 ATATTTTAATATTATTACAT
96336623 A-ATTTT
1 ATATTTT
96336629 TTTTCTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.46
19 9 0.38
20 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
ATATTTTAATATTATTACAT
Found at i:96339104 original size:37 final size:37
Alignment explanation
Indices: 96339054--96339156 Score: 152
Period size: 37 Copynumber: 2.8 Consensus size: 37
96339044 TGTTAATTTC
* * *
96339054 AAGACTTAAGTAATGTTTTTAAATATTTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAAATATGTAGTAATTCA
*
96339091 AAGACTTATGTAATGTTTTTAATTATGTAGTAATTCA
1 AAGACTTATGTAATGTTTTTAAATATGTAGTAATTCA
* *
96339128 AAGACTTATGTAATATTTTTAATTATGTA
1 AAGACTTATGTAATGTTTTTAAATATGTA
96339157 CTGTAGTGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAAATATGTAGTAATTCA
Found at i:96339153 original size:17 final size:17
Alignment explanation
Indices: 96339096--96339156 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
96339086 ATTCAAAGAC
*
96339096 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
* ***
96339113 TTATGTAGTAATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
96339132 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
96339150 TTATGTA
1 TTATGTA
96339157 CTGTAGTGAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 5 0.16
20 8 0.25
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:96339254 original size:9 final size:9
Alignment explanation
Indices: 96339169--96339253 Score: 98
Period size: 9 Copynumber: 9.4 Consensus size: 9
96339159 GTAGTGATTC
*
96339169 AATTCGGTC
1 AATTCGGTT
*
96339178 AATTCGGTC
1 AATTCGGTT
*
96339187 AATTCGGTC
1 AATTCGGTT
*
96339196 AAATCGGTT
1 AATTCGGTT
*
96339205 AATTTGGTT
1 AATTCGGTT
96339214 AATTCGGTT
1 AATTCGGTT
96339223 AATTCGGTT
1 AATTCGGTT
* *
96339232 AATCCGGGT
1 AATTCGGTT
*
96339241 AATTTGGTT
1 AATTCGGTT
96339250 AATT
1 AATT
96339254 TTTAACCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:96346055 original size:94 final size:94
Alignment explanation
Indices: 96345894--96346157 Score: 429
Period size: 94 Copynumber: 2.7 Consensus size: 94
96345884 TTTGAGTACT
96345894 TCTGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACA
96345959 AATGATAAGTGGTAGCTTAGCTACTCTTA
66 AATGATAAGTGGTAGCTTAGCTACTCTTA
96345988 TCTGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACA
96346053 AATGATAAGTGGTAGCTTAGCTACTCTTA
66 AATGATAAGTGGTAGCTTAGCTACTCTTA
* * *
96346082 TCTGATCAGTGACAAGTGATAAGTGTTAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 TCTGATCAGTGACAAGTG---A----TAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
*
96346147 AGTGATAAATG
59 AGTGACAAATG
96346158 TGATCAGTGT
Statistics
Matches: 159, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
94 112 0.70
97 1 0.01
101 46 0.29
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (94 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACA
AATGATAAGTGGTAGCTTAGCTACTCTTA
Found at i:96346154 original size:51 final size:50
Alignment explanation
Indices: 96345995--96346151 Score: 242
Period size: 51 Copynumber: 3.1 Consensus size: 50
96345985 TTATCTGATC
* *
96345995 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
96346046 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
* *
96346096 AGTGATAAGTGTTAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
96346147 AGTGA
1 AGTGA
96346152 TAAATGTGAT
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 45 0.46
51 52 0.54
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:96349784 original size:33 final size:34
Alignment explanation
Indices: 96349742--96349810 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
96349732 AAAACACCAA
96349742 AGAACGTAACAGAAGTGCGGAG-TTCTTGGGATT
1 AGAACGTAACAGAAGTGCGGAGTTTCTTGGGATT
96349775 AGAACGTAACAGAAGTGCGGAGTTTCTTGGGATT
1 AGAACGTAACAGAAGTGCGGAGTTTCTTGGGATT
96349809 AG
1 AG
96349811 CGGGATACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (34 bp):
AGAACGTAACAGAAGTGCGGAGTTTCTTGGGATT
Found at i:96353932 original size:101 final size:101
Alignment explanation
Indices: 96353802--96354065 Score: 483
Period size: 101 Copynumber: 2.6 Consensus size: 101
96353792 ACTTTTGATC
*
96353802 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAATGATA
1 AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAATGATA
96353867 AGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
66 AGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
96353903 AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAATGATA
1 AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAATGATA
96353968 AGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
66 AGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
* * * *
96354004 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATAAATG
1 AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAATG
96354066 TGATCAGTGT
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 158 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (101 bp):
AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACAAATGATA
AGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
Found at i:96353950 original size:51 final size:51
Alignment explanation
Indices: 96353802--96354059 Score: 403
Period size: 51 Copynumber: 5.1 Consensus size: 51
96353792 ACTTTTGATC
* *
96353802 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGTGACA
* *
96353853 AGTGACAAATGATAAGTGGTAG-CTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGTGACA
* * *
96353903 AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGTGACA
* *
96353954 AGTGACAAATGATAAGTGGTAG-CTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGTGACA
* *
96354004 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGTGACA
96354055 AGTGA
1 AGTGA
96354060 TAAATGTGAT
Statistics
Matches: 187, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
50 90 0.48
51 97 0.52
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAGTGACA
Found at i:96358186 original size:21 final size:21
Alignment explanation
Indices: 96358160--96358201 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
96358150 GTTACTCTTG
96358160 TAATTTAGTTCATTTTGAACT
1 TAATTTAGTTCATTTTGAACT
96358181 TAATTTAGTTCATTTTGAACT
1 TAATTTAGTTCATTTTGAACT
96358202 ATGTTTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (21 bp):
TAATTTAGTTCATTTTGAACT
Found at i:96376048 original size:10 final size:10
Alignment explanation
Indices: 96376028--96376058 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
96376018 ATTTGGTTCC
96376028 TTCTCTTTTTT
1 TTCT-TTTTTT
96376039 TTCTTTTTTT
1 TTCTTTTTTT
96376049 TTCTTTTTTT
1 TTCTTTTTTT
96376059 GGCCTTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:96379460 original size:38 final size:40
Alignment explanation
Indices: 96379406--96379618 Score: 223
Period size: 46 Copynumber: 4.9 Consensus size: 40
96379396 TCTGATATGA
96379406 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
96379446 -A-GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
96379484 ATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 ------AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG
**
96379535 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTG
1 -AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
96379576 ATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 A-ATG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
96379619 ATGACAGAAA
Statistics
Matches: 150, Mismatches: 4, Indels: 32
0.81 0.02 0.17
Matches are distributed among these distances:
38 37 0.25
39 1 0.01
40 1 0.01
41 5 0.03
44 2 0.01
45 1 0.01
46 101 0.67
51 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (40 bp):
AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:96379514 original size:46 final size:46
Alignment explanation
Indices: 96379447--96379662 Score: 306
Period size: 46 Copynumber: 4.7 Consensus size: 46
96379437 GGCAACCTGA
96379447 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
96379493 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
** *
96379539 GTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
96379585 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
96379631 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
96379663 TCATGTCAAA
Statistics
Matches: 154, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 154 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:96379641 original size:138 final size:130
Alignment explanation
Indices: 96379397--96379662 Score: 370
Period size: 138 Copynumber: 2.0 Consensus size: 130
96379387 AGTGTGCTCT
*
96379397 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
* * * * * *
96379462 TGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
**
96379527 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
*
96379592 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACT
58 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACC
96379657 ATGGCA
123 ATGGCA
96379663 TCATGTCAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
130 47 0.40
132 1 0.01
133 1 0.01
136 2 0.02
138 67 0.57
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Found at i:96385774 original size:19 final size:19
Alignment explanation
Indices: 96385750--96385787 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
96385740 AAATTCGAAA
96385750 TTGGGAACTTTTATCTGTC
1 TTGGGAACTTTTATCTGTC
96385769 TTGGGAACTTTTATCTGTC
1 TTGGGAACTTTTATCTGTC
96385788 ACACAGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (19 bp):
TTGGGAACTTTTATCTGTC
Found at i:96387173 original size:18 final size:17
Alignment explanation
Indices: 96387152--96387193 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
96387142 TTTTTTTTTT
96387152 TTTTTTTACTTGTTTTAC
1 TTTTTTTACTT-TTTTAC
*
96387170 TTTTTTAACTTTTTTAC
1 TTTTTTTACTTTTTTAC
96387187 TTTTTTT
1 TTTTTTT
96387194 CTTATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTTACTTTTTTAC
Found at i:96387175 original size:8 final size:8
Alignment explanation
Indices: 96387153--96387192 Score: 62
Period size: 9 Copynumber: 4.8 Consensus size: 8
96387143 TTTTTTTTTT
96387153 TTTTTTAC
1 TTTTTTAC
96387161 TTGTTTTAC
1 TT-TTTTAC
96387170 TTTTTTAAC
1 TTTTTT-AC
96387179 TTTTTTAC
1 TTTTTTAC
96387187 TTTTTT
1 TTTTTT
96387193 TCTTATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 14 0.47
9 16 0.53
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (8 bp):
TTTTTTAC
Found at i:96387277 original size:36 final size:36
Alignment explanation
Indices: 96387207--96387278 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
96387197 ATATTTTGTC
*
96387207 TCTTAGATTTTTTTCTTTTTTAAGCTTTATATTATTT
1 TCTTAGATTTTTTTCTTATTTAA-CTTTATATTATTT
96387244 TCTTA-ATTTATTTTACTTATTTAA-TTTATATTATT
1 TCTTAGATTT-TTTT-CTTATTTAACTTTATATTATT
96387279 AATTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 15 0.47
37 9 0.28
38 8 0.25
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.67
Consensus pattern (36 bp):
TCTTAGATTTTTTTCTTATTTAACTTTATATTATTT
Found at i:96387283 original size:18 final size:17
Alignment explanation
Indices: 96387232--96387279 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
96387222 TTTTTTAAGC
*
96387232 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
*
96387250 TTTATTTTACTTATTTAA
1 TTTATATTA-TTATTTAA
96387268 TTTATATTATTA
1 TTTATATTATTA
96387280 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:96387323 original size:21 final size:21
Alignment explanation
Indices: 96387295--96387348 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
96387285 AAAAAAATTG
96387295 TAATATATATTTAAAATGTTTTA
1 TAATAT-TATTTAAAAT-TTTTA
*
96387318 TAATATTTTTTAAAATTTTTA
1 TAATATTATTTAAAATTTTTA
*
96387339 -ATTATTATTT
1 TAATATTATTT
96387349 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.29
21 5 0.18
22 9 0.32
23 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TAATATTATTTAAAATTTTTA
Found at i:96387329 original size:22 final size:23
Alignment explanation
Indices: 96387295--96387361 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
96387285 AAAAAAATTG
*
96387295 TAATATATATTTAAAATGTTTT-A-
1 TAATAT-TTTTTAAAAT-TTTTAAT
96387318 TAATATTTTTTAAAATTTTTAAT
1 TAATATTTTTTAAAATTTTTAAT
* *
96387341 TATTATTTTTAAAAATATTTT
1 TAATATTTTTTAAAAT-TTTT
96387362 TTAACTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 4 0.11
22 10 0.26
23 20 0.53
24 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (23 bp):
TAATATTTTTTAAAATTTTTAAT
Found at i:96387518 original size:18 final size:17
Alignment explanation
Indices: 96387483--96387533 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
96387473 TTTTGAAGTC
96387483 TATTTTTTTTCTTATTT
1 TATTTTTTTTCTTATTT
96387500 TATTTTGTTTATC-TATTT
1 TATTTT-TTT-TCTTATTT
*
96387518 TATTTATTTTTATTAT
1 TATTT-TTTTTCTTAT
96387534 ACATTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 7 0.24
18 19 0.66
19 3 0.10
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTTTTTCTTATTT
Found at i:96387629 original size:13 final size:13
Alignment explanation
Indices: 96387611--96387648 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
96387601 TTTTTAAGTT
96387611 TTATATTATTTTC
1 TTATATTATTTTC
*
96387624 TTATATTATTTTG
1 TTATATTATTTTC
96387637 TT-TATTAGTTTT
1 TTATATTA-TTTT
96387649 ATAATATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 5 0.22
13 18 0.78
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (13 bp):
TTATATTATTTTC
Found at i:96387902 original size:21 final size:23
Alignment explanation
Indices: 96387869--96387920 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
96387859 TTTTAAATGT
96387869 ATATTACTCAAAT-TAATTTTTGAA
1 ATATTA-T-AAATATAATTTTTGAA
* *
96387893 A-ATTATAAATATTATTTTTTAA
1 ATATTATAAATATAATTTTTGAA
96387915 ATATTA
1 ATATTA
96387921 ACCATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 4 0.17
22 11 0.46
23 8 0.33
24 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTATAAATATAATTTTTGAA
Found at i:96388134 original size:10 final size:9
Alignment explanation
Indices: 96388116--96388204 Score: 63
Period size: 10 Copynumber: 9.4 Consensus size: 9
96388106 TAAAATTTAA
96388116 AAAATATTT
1 AAAATATTT
96388125 AAAATCATTT
1 AAAAT-ATTT
*
96388135 AAAATATTAA
1 AAAATATT-T
96388145 AAAATATTT
1 AAAATATTT
*
96388154 TAAATCATTT
1 AAAAT-ATTT
* *
96388164 TAAATGTTTT
1 AAAAT-ATTT
* *
96388174 ATAATATTA
1 AAAATATTT
96388183 AAAATATATT
1 AAAATAT-TT
*
96388193 -TAATATTT
1 AAAATATTT
96388201 AAAA
1 AAAA
96388205 AATAATTTGA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 2 0.03
9 27 0.44
10 33 0.53
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:96388140 original size:19 final size:18
Alignment explanation
Indices: 96388116--96388204 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 18
96388106 TAAAATTTAA
96388116 AAAATATTTAAAATCATTT
1 AAAATATTTAAAAT-ATTT
*
96388135 AAAATATTAAAAAATATTT
1 AAAATATT-TAAAATATTT
* * *
96388154 TAAATCATTTTAAATGTTTT
1 AAAAT-ATTTAAAAT-ATTT
* *
96388174 ATAATATTAAAAATATATT
1 AAAATATTTAAAATAT-TT
*
96388193 -TAATATTTAAAA
1 AAAATATTTAAAA
96388205 AATAATTTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
18 12 0.22
19 29 0.53
20 14 0.25
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAAATATTT
Found at i:96388144 original size:29 final size:28
Alignment explanation
Indices: 96388106--96388218 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 28
96388096 AAATTCTATG
96388106 TAAAATTTAAAAAATATTTAAAATCATT
1 TAAAATTTAAAAAATATTTAAAATCATT
*
96388134 TAAAATATTAAAAAATATTTTAAATCATT
1 TAAAAT-TTAAAAAATATTTAAAATCATT
* ** * * *
96388163 TTAAATGTTTTATAATATTAAAAATATATT
1 TAAAAT-TTAAAAAATATTTAAAAT-CATT
*
96388193 TAATATTTAAAAAATAATTTGAAAAT
1 TAAAATTTAAAAAAT-ATTT-AAAAT
96388219 ATATTTTTAA
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 6 0.09
29 45 0.68
30 10 0.15
31 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAAATTTAAAAAATATTTAAAATCATT
Found at i:96388221 original size:31 final size:34
Alignment explanation
Indices: 96388174--96388263 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 34
96388164 TAAATGTTTT
96388174 ATAATATTAAAAATATA-TTTAATATTTA-AAAA
1 ATAATATTAAAAATATATTTTAATATTTATAAAA
*
96388206 ATAAT-TTGAAAATATATTTTTAATATTTATAAAA
1 ATAATATTAAAAATATA-TTTTAATATTTATAAAA
* *
96388240 ACATATATTATAAAACAT-TTTTAA
1 ATA-ATATTA-AAAATATATTTTAA
96388264 AAAATATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
31 10 0.21
32 5 0.10
33 11 0.23
34 6 0.12
35 8 0.17
36 2 0.04
37 6 0.12
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (34 bp):
ATAATATTAAAAATATATTTTAATATTTATAAAA
Found at i:96391821 original size:30 final size:30
Alignment explanation
Indices: 96391701--96391823 Score: 156
Period size: 30 Copynumber: 4.1 Consensus size: 30
96391691 GGTCAAATGG
* * *
96391701 ACTCGAACCGCCTATATCCGAGTGATATGA
1 ACTCGAACCACCTATGTCCGGGTGATATGA
* * *
96391731 ACTCGAACCACCAATGTCTGGGTGATATAA
1 ACTCGAACCACCTATGTCCGGGTGATATGA
* *
96391761 ACTCGAACCACCCATGTCCGGATGATATGA
1 ACTCGAACCACCTATGTCCGGGTGATATGA
* *
96391791 ACTCGAACCACCTATGTCCGGGTTACATGA
1 ACTCGAACCACCTATGTCCGGGTGATATGA
96391821 ACT
1 ACT
96391824 GTTCTGGGAC
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (30 bp):
ACTCGAACCACCTATGTCCGGGTGATATGA
Found at i:96394753 original size:20 final size:21
Alignment explanation
Indices: 96394730--96394783 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
96394720 TACATATTTC
*
96394730 TAATGTTAAAAAAT-TAAAAA
1 TAATATTAAAAAATGTAAAAA
* *
96394750 TAATATTTAAAATTGTAAAAA
1 TAATATTAAAAAATGTAAAAA
*
96394771 T-ATATTATAAAAT
1 TAATATTAAAAAAT
96394784 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
TAATATTAAAAAATGTAAAAA
Found at i:96394783 original size:21 final size:21
Alignment explanation
Indices: 96394744--96394783 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
96394734 GTTAAAAAAT
96394744 TAAAAATAATATTTAAAATTG
1 TAAAAATAATATTTAAAATTG
96394765 TAAAAAT-ATATTATAAAAT
1 TAAAAATAATATT-TAAAAT
96394784 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAAAATAATATTTAAAATTG
Found at i:96394800 original size:23 final size:22
Alignment explanation
Indices: 96394768--96394827 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
96394758 AAAATTGTAA
96394768 AAATAT-ATTATAAAATATTTT
1 AAATATAATTATAAAATATTTT
* *
96394789 AAATATACATTACAAAAT-TTTA
1 AAATATA-ATTATAAAATATTTT
*
96394811 AAAT-TAATAATAAAATA
1 AAATATAATTATAAAATA
96394828 AATAAACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 8 0.25
21 8 0.25
22 7 0.22
23 9 0.28
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATAATTATAAAATATTTT
Found at i:96394963 original size:27 final size:25
Alignment explanation
Indices: 96394910--96394970 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
96394900 AAAAATATAT
* * *
96394910 TTAAAATATTATGATTTTTATATTA
1 TTAAAAAATTATAATTTTTAAATTA
96394935 TTAAAAAATTATAATTTTTTAAATGTA
1 TTAAAAAATTATAA-TTTTTAAAT-TA
*
96394962 TTTAAAAAT
1 TTAAAAAAT
96394971 GTATTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 12 0.40
26 8 0.27
27 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (25 bp):
TTAAAAAATTATAATTTTTAAATTA
Found at i:96394972 original size:12 final size:12
Alignment explanation
Indices: 96394955--96394980 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
96394945 ATAATTTTTT
96394955 AAATGTATTTAA
1 AAATGTATTTAA
96394967 AAATGTATTTAA
1 AAATGTATTTAA
96394979 AA
1 AA
96394981 TTTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
AAATGTATTTAA
Found at i:96395029 original size:2 final size:2
Alignment explanation
Indices: 96395022--96395060 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
96395012 AAATTTACAA
96395022 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT -T A- 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
96395061 TTCAAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:96395482 original size:21 final size:23
Alignment explanation
Indices: 96395460--96395535 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 23
96395450 TATAAAGTTA
96395460 AAAATATTTTAAAAATA-ATT--
1 AAAATATTTTAAAAATATATTAC
* *
96395480 -AAA-ATTTTAAAAAAATATTAT
1 AAAATATTTTAAAAATATATTAC
* * *
96395501 AAAACATTGTAAATATATATTAC
1 AAAATATTTTAAAAATATATTAC
96395524 AAAAT-TTTTAAA
1 AAAATATTTTAAA
96395536 TTAATAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 11 0.25
19 6 0.14
22 9 0.20
23 18 0.41
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (23 bp):
AAAATATTTTAAAAATATATTAC
Found at i:96395554 original size:18 final size:17
Alignment explanation
Indices: 96395531--96395583 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
96395521 TACAAAATTT
96395531 TTAAATTAATAATATAAA
1 TTAAA-TAATAATATAAA
* *
96395549 TTAAATAAGCAAAATAAA
1 TTAAATAA-TAATATAAA
96395567 TTAAA-AATAATTATAAA
1 TTAAATAATAA-TATAAA
96395584 AAAAAAATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 2 0.07
17 10 0.34
18 17 0.59
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
TTAAATAATAATATAAA
Found at i:96396819 original size:228 final size:235
Alignment explanation
Indices: 96396414--96396884 Score: 848
Period size: 228 Copynumber: 2.0 Consensus size: 235
96396404 TATTAGTGAA
*
96396414 CTTTTATTCCGTTAACGTTTGTAAATCTGACCTGATTTTGGGGTAGGTCCATTAATTTTGATCCT
1 CTTTTATTCCGTTAACGTTTGTAAATCTGACCTGATTTTGGAG-AGGTCCATTAATTTTGATCCT
96396479 CTACTTTTCACTTTAATTTTATGCAAGTTAGGAACCTTTTAATGAACGTATTTTCAATACGATTT
65 CTAC-TTTCACTTTAATTTTATGCAAGTTAGGAACCTTTTAATGAACGTATTTTCAATACGATTT
96396544 GTTTAAAAAAAAATTTTGATCTTACACTATAATATTGTTACAACATTTAATCTCACATTTATTAT
129 GTTTAAAAAAAAATTTTGATCTTACACTATAATATTGTTACAACATTTAATCTCACATTTATTAT
96396609 TA-TTTTTACATTAACAGCAAATGTATCACCTATACAAAGTG
194 TATTTTTTACATTAACAGCAAATGTATCACCTATACAAAGTG
96396650 CTTTTATTCCGTTAACGTTTGTAAATCTGACCTGA-TTT-GAG-GGTCCATTAA-TTTGAT-CTC
1 CTTTTATTCCGTTAACGTTTGTAAATCTGACCTGATTTTGGAGAGGTCCATTAATTTTGATCCTC
*
96396710 TAC-TTCACTTTAATTTTATGCAAGTTAGGACCCTTTTAATGAACGTATTTTCAATACGATTTGT
66 TACTTTCACTTTAATTTTATGCAAGTTAGGAACCTTTTAATGAACGTATTTTCAATACGATTTGT
96396774 TTAAAAAAAAATTTTGATCTTACACTATAATATTGTTACAACATTTAATCTCACATTTATTATTA
131 TTAAAAAAAAATTTTGATCTTACACTATAATATTGTTACAACATTTAATCTCACATTTATTATTA
96396839 TTTTTTACATTAACAGCAAATGTATCACCTATACAAAGTG
196 TTTTTTACATTAACAGCAAATGTATCACCTATACAAAGTG
*
96396879 CCTTTA
1 CTTTTA
96396885 GTCCTACTTT
Statistics
Matches: 231, Mismatches: 3, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
228 125 0.54
229 44 0.19
230 6 0.03
231 6 0.03
232 10 0.04
234 2 0.01
235 3 0.01
236 35 0.15
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (235 bp):
CTTTTATTCCGTTAACGTTTGTAAATCTGACCTGATTTTGGAGAGGTCCATTAATTTTGATCCTC
TACTTTCACTTTAATTTTATGCAAGTTAGGAACCTTTTAATGAACGTATTTTCAATACGATTTGT
TTAAAAAAAAATTTTGATCTTACACTATAATATTGTTACAACATTTAATCTCACATTTATTATTA
TTTTTTACATTAACAGCAAATGTATCACCTATACAAAGTG
Found at i:96399013 original size:19 final size:18
Alignment explanation
Indices: 96398976--96399024 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
96398966 TAAAAGATAT
*
96398976 TTTTAAAAATTGTTATAAA
1 TTTTAAAAA-TATTATAAA
96398995 TTTTAAAAATATTATTAAA
1 TTTTAAAAATATTA-TAAA
*
96399014 ATTTATAAAAT
1 TTTTA-AAAAT
96399025 CATTTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 17 0.65
20 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTTAAAAATATTATAAA
Found at i:96399024 original size:20 final size:20
Alignment explanation
Indices: 96398976--96399024 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
96398966 TAAAAGATAT
*
96398976 TTTTAAAA-ATTGTTATAAA
1 TTTTAAAATATTATTATAAA
96398995 TTTTAAAAATATTATTA-AAA
1 TTTT-AAAATATTATTATAAA
96399015 TTTATAAAAT
1 TTT-TAAAAT
96399025 CATTTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 15 0.58
21 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTTAAAATATTATTATAAA
Found at i:96401887 original size:4 final size:4
Alignment explanation
Indices: 96401864--96401914 Score: 57
Period size: 4 Copynumber: 12.5 Consensus size: 4
96401854 TAAAAGCGGC
* * * *
96401864 TGTA TTTA TGTA TATA TGTA TGTA TGTA TGTA TGTG TGTG TGTA TTGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -TGTA
96401913 TG
1 TG
96401915 CTGAGATGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
4 36 0.90
5 4 0.10
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (4 bp):
TGTA
Found at i:96402054 original size:4 final size:4
Alignment explanation
Indices: 96402037--96402083 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
96402027 TAAAAGCTGC
* ** *
96402037 TGTA TGTT TGTA TGTA TGTA TCCA TGTA TGTA TGTA TATA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
96402084 GTATGTGTGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.23, C:0.04, G:0.21, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:96402193 original size:50 final size:50
Alignment explanation
Indices: 96402139--96402238 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
96402129 TGTTGGACTG
96402139 TGATATATTGCCATATGGTTGATGTGTTTATAAATCTGCAGGCTTGGTTT
1 TGATATATTGCCATATGGTTGATGTGTTTATAAATCTGCAGGCTTGGTTT
96402189 TGATATATTGCCATATGGTTGATGTGTTTATAAATCTGCAGGCTTGGTTT
1 TGATATATTGCCATATGGTTGATGTGTTTATAAATCTGCAGGCTTGGTTT
96402239 AGGGAACTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (50 bp):
TGATATATTGCCATATGGTTGATGTGTTTATAAATCTGCAGGCTTGGTTT
Found at i:96407997 original size:39 final size:39
Alignment explanation
Indices: 96407954--96408028 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
96407944 AATTTTACTT
*
96407954 CTTTTTGCATTGACAATAATATTCATACCAATTGAGTTA
1 CTTTTTGCATCGACAATAATATTCATACCAATTGAGTTA
96407993 CTTTTTGCATCGACAATAATATTCATACCAATTGAG
1 CTTTTTGCATCGACAATAATATTCATACCAATTGAG
96408029 CTAAAACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (39 bp):
CTTTTTGCATCGACAATAATATTCATACCAATTGAGTTA
Found at i:96408861 original size:29 final size:28
Alignment explanation
Indices: 96408822--96408876 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
96408812 TTTTTATAGA
96408822 TTTAGAATTTAATTATTATACTTTTACT
1 TTTAGAATTTAATTATTATACTTTTACT
* * *
96408850 TTTAGGAATTTAGTTTTTTTACTTTTA
1 TTTA-GAATTTAATTATTATACTTTTA
96408877 AAATTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.60
Consensus pattern (28 bp):
TTTAGAATTTAATTATTATACTTTTACT
Found at i:96409350 original size:42 final size:42
Alignment explanation
Indices: 96409261--96409504 Score: 133
Period size: 42 Copynumber: 5.8 Consensus size: 42
96409251 CAGGCAATAT
* * * *
96409261 GAAGCAATTATACTAGCACACAT-AGTGC--CATTGGATAAATC
1 GAAGCAATCATACT-G-ACACATAAGTGCATCATCGAATAAACC
* **
96409302 GAAGCAATCATACTGATACATAAGTGCATCATCGAATTTACC
1 GAAGCAATCATACTGACACATAAGTGCATCATCGAATAAACC
* * * * * *
96409344 GAAGCAAAT-AAACTGACACACGAGGTGCATAATTGGATAAACC
1 GAAGC-AATCATACTGACACA-TAAGTGCATCATCGAATAAACC
* * * * *
96409387 GAAGTAATCATGCTGACACATAAGTGCATAATTGGAAGT--ACT
1 GAAGCAATCATACTGACACATAAGTGCATCA-TCGAA-TAAACC
* * * * * * *
96409429 GAAGTAAAT-ATATTGACACACGAGGTGCGTCATTGAATAAACT
1 GAAG-CAATCATACTGACACA-TAAGTGCATCATCGAATAAACC
*
96409472 GAAGCAATCATACTGATACATAAGTGCATCATC
1 GAAGCAATCATACTGACACATAAGTGCATCATC
96409505 AGATAGATTG
Statistics
Matches: 151, Mismatches: 39, Indels: 25
0.70 0.18 0.12
Matches are distributed among these distances:
39 5 0.03
40 6 0.04
41 14 0.09
42 65 0.43
43 60 0.40
44 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (42 bp):
GAAGCAATCATACTGACACATAAGTGCATCATCGAATAAACC
Found at i:96409388 original size:43 final size:43
Alignment explanation
Indices: 96409341--96409487 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
96409331 CATCGAATTT
*
96409341 ACCGAAGCAAATAAACTGACACACGAGGTGCATAATTGGATAA
1 ACCGAAGCAAATATACTGACACACGAGGTGCATAATTGGATAA
* * * * *
96409384 ACCGAAG-TAATCATGCTGACACA-TAAGTGCATAATTGGA-AGT
1 ACCGAAGCAAAT-ATACTGACACACGAGGTGCATAATTGGATA-A
* * * * * *
96409426 ACTGAAGTAAATATATTGACACACGAGGTGCGTCATTGAATAA
1 ACCGAAGCAAATATACTGACACACGAGGTGCATAATTGGATAA
*
96409469 ACTGAAGC-AATCATACTGA
1 ACCGAAGCAAAT-ATACTGA
96409488 TACATAAGTG
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
41 1 0.01
42 35 0.44
43 43 0.54
44 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (43 bp):
ACCGAAGCAAATATACTGACACACGAGGTGCATAATTGGATAA
Found at i:96409408 original size:85 final size:84
Alignment explanation
Indices: 96409290--96409504 Score: 277
Period size: 85 Copynumber: 2.5 Consensus size: 84
96409280 ACATAGTGCC
* *
96409290 ATTGGATAAATCGAAGCAATCATACTGATACATAAGTGCATCATCGAATTTACCGAAGCAAATAA
1 ATTGGATAAACCGAAGCAATCATACTGATACATAAGTGCATCATCGAA-GTACCGAAGCAAATAA
96409355 ACTGACACACGAGGTGCATA
65 ACTGACACACGAGGTGCATA
* * * * * * * *
96409375 ATTGGATAAACCGAAGTAATCATGCTGACACATAAGTGCATAATTGGAAGTACTGAAGTAAATAT
1 ATTGGATAAACCGAAGCAATCATACTGATACATAAGTGCATCA-TCGAAGTACCGAAGCAAATAA
* * *
96409440 ATTGACACACGAGGTGCGTC
65 ACTGACACACGAGGTGCATA
* *
96409460 ATTGAATAAACTGAAGCAATCATACTGATACATAAGTGCATCATC
1 ATTGGATAAACCGAAGCAATCATACTGATACATAAGTGCATCATC
96409505 AGATAGATTG
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
84 1 0.01
85 104 0.95
86 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (84 bp):
ATTGGATAAACCGAAGCAATCATACTGATACATAAGTGCATCATCGAAGTACCGAAGCAAATAAA
CTGACACACGAGGTGCATA
Found at i:96409615 original size:7 final size:7
Alignment explanation
Indices: 96409603--96409639 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
96409593 ATTCATCGTG
96409603 AATTCGC
1 AATTCGC
96409610 AATTCGC
1 AATTCGC
96409617 AATTCGC
1 AATTCGC
96409624 AATTCGC
1 AATTCGC
96409631 AATTC-C
1 AATTCGC
96409637 AAT
1 AAT
96409640 ACAACATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (7 bp):
AATTCGC
Found at i:96417481 original size:15 final size:15
Alignment explanation
Indices: 96417463--96417514 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
96417453 AGAGGAAGAG
*
96417463 GAGGAAGTGGAAGTT
1 GAGGAAGTGGAAGTA
* * *
96417478 GAGGAAGAGGTAGAA
1 GAGGAAGTGGAAGTA
96417493 GAGGAAGTGGAAGTA
1 GAGGAAGTGGAAGTA
*
96417508 GAAGAAG
1 GAGGAAG
96417515 AAGAGGACGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12
Consensus pattern (15 bp):
GAGGAAGTGGAAGTA
Found at i:96417486 original size:24 final size:24
Alignment explanation
Indices: 96417454--96417500 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
96417444 TGAAGAAATA
*
96417454 GAGGAAGAGG-AGGAAGTGGAAGTT
1 GAGGAAGAGGTA-GAAGAGGAAGTT
96417478 GAGGAAGAGGTAGAAGAGGAAGT
1 GAGGAAGAGGTAGAAGAGGAAGT
96417501 GGAAGTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (24 bp):
GAGGAAGAGGTAGAAGAGGAAGTT
Found at i:96417497 original size:30 final size:30
Alignment explanation
Indices: 96417453--96417515 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
96417443 ATGAAGAAAT
* * *
96417453 AGAGGAAGAGGAGGAAGTGGAAGTTGAGGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
*
96417483 AGAGGTAGAAGAGGAAGTGGAAGTAGAAGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
96417513 AGA
1 AGA
96417516 AGAGGACGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10
Consensus pattern (30 bp):
AGAGGAAGAAGAGGAAGTGGAAGTAGAAGA
Found at i:96426863 original size:166 final size:166
Alignment explanation
Indices: 96426589--96427087 Score: 944
Period size: 166 Copynumber: 3.0 Consensus size: 166
96426579 TCCTATTTAA
* *
96426589 GAACGGTATTTTTGTCATATAGCCTAAAACAAAATTAGCAAATAACACATGCATCATAATTAAAA
1 GAACGGTATTTTTGTCGTATAGCCTAAAACAAAATTAGCAAATAACACATGCACCATAATTAAAA
96426654 CGATTTTCTTTAAAACCTTTCTTTGAAAAGATTGATCTCTGTAAATTTGGCTATCTCAAATAACG
66 CGATTTTCTTTAAAACCTTTCTTTGAAAAGATTGATCTCTGTAAATTTGGCTATCTCAAATAACG
96426719 GAAAACATTGATCAAACAGTGAAAACTAAGATATTG
131 GAAAACATTGATCAAACAGTGAAAACTAAGATATTG
*
96426755 GAACGGTATTTTTGTCGTATAGCCTAAAACAAAATTAGCAAATAACACATGCACCATAATTGAAA
1 GAACGGTATTTTTGTCGTATAGCCTAAAACAAAATTAGCAAATAACACATGCACCATAATTAAAA
*
96426820 CAATTTTCTTTAAAACCTTTCTTTGAAAAGATTGATCTCTGTAAATTTGGCTATCTCAAATAACG
66 CGATTTTCTTTAAAACCTTTCTTTGAAAAGATTGATCTCTGTAAATTTGGCTATCTCAAATAACG
96426885 GAAAACATTGATCAAACAGTGAAAACTAAGATATTG
131 GAAAACATTGATCAAACAGTGAAAACTAAGATATTG
*
96426921 GAACGGTATTTTTGTCGTATAGCCTAAAACAAAAGTAGCAAATAACACATGCACCATAATTAAAA
1 GAACGGTATTTTTGTCGTATAGCCTAAAACAAAATTAGCAAATAACACATGCACCATAATTAAAA
96426986 CGATTTTCTTTAAAACCTTTCTTTGAAAAGATTGATCTCTGTAAATTTGGCTATCTCAAATAACG
66 CGATTTTCTTTAAAACCTTTCTTTGAAAAGATTGATCTCTGTAAATTTGGCTATCTCAAATAACG
*
96427051 GAAAACATTGATCAAAAAGTGAAAACTAAGATATTG
131 GAAAACATTGATCAAACAGTGAAAACTAAGATATTG
96427087 G
1 G
96427088 TTAGAAGAAT
Statistics
Matches: 325, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
166 325 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (166 bp):
GAACGGTATTTTTGTCGTATAGCCTAAAACAAAATTAGCAAATAACACATGCACCATAATTAAAA
CGATTTTCTTTAAAACCTTTCTTTGAAAAGATTGATCTCTGTAAATTTGGCTATCTCAAATAACG
GAAAACATTGATCAAACAGTGAAAACTAAGATATTG
Found at i:96429416 original size:27 final size:27
Alignment explanation
Indices: 96429378--96429431 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
96429368 ACCTTTATGC
96429378 CTAGTCATTTTATTGGGAACATAATGG
1 CTAGTCATTTTATTGGGAACATAATGG
96429405 CTAGTCATTTTATTGGGAACATAATGG
1 CTAGTCATTTTATTGGGAACATAATGG
96429432 ATAACAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (27 bp):
CTAGTCATTTTATTGGGAACATAATGG
Found at i:96431806 original size:30 final size:30
Alignment explanation
Indices: 96431770--96431838 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
96431760 GCGGTTTTAG
*
96431770 TATTTTGGCTATAACTTGATATACAAACAT
1 TATTTTGGCCATAACTTGATATACAAACAT
96431800 TATTTTGGCCATAACTTGATATACAAACAT
1 TATTTTGGCCATAACTTGATATACAAACAT
96431830 TCATTTTGG
1 T-ATTTTGG
96431839 ACCCACAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 30 0.81
31 7 0.19
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (30 bp):
TATTTTGGCCATAACTTGATATACAAACAT
Found at i:96433644 original size:107 final size:108
Alignment explanation
Indices: 96433521--96433736 Score: 398
Period size: 107 Copynumber: 2.0 Consensus size: 108
96433511 TAAACAAAAA
96433521 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
96433586 AATTATATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
66 AATTATATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
* *
96433628 ATTAGTTTAACAAAACAATGATATGTTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
*
96433693 AATTGTATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTATATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
96433736 A
1 A
96433737 CGTGTTTTTT
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 92 0.88
108 13 0.12
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (108 bp):
ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCAAACAA
AATTATATTAAAATTTTTGTTAATTACTCTGATAAAATTTTTG
Found at i:96434413 original size:14 final size:14
Alignment explanation
Indices: 96434378--96434421 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
96434368 GTTAGTTAAA
96434378 AAAAATTTAA-TAT
1 AAAAATTTAATTAT
96434391 AAAAA--TAATTAT
1 AAAAATTTAATTAT
*
96434403 AAAAATTTAATAAT
1 AAAAATTTAATTAT
96434417 AAAAA
1 AAAAA
96434422 ATAGATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
13 5 0.19
14 11 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAAATTTAATTAT
Found at i:96435422 original size:20 final size:20
Alignment explanation
Indices: 96435383--96435434 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
96435373 GTTCATTCGG
* * *
96435383 GGGAAGGAAAAAAGGGAAATT
1 GGGAA-GAAGAAAGGAAAATC
96435404 GGGAAGAAGAAAGGAAAATC
1 GGGAAGAAGAAAGGAAAATC
*
96435424 GGGAAAAAGAA
1 GGGAAGAAGAA
96435435 GAAGAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.37, T:0.06
Consensus pattern (20 bp):
GGGAAGAAGAAAGGAAAATC
Found at i:96435821 original size:2 final size:2
Alignment explanation
Indices: 96435814--96435841 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96435804 ATGGTTTGAT
96435814 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
96435842 AAAGTATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96436279 original size:80 final size:78
Alignment explanation
Indices: 96436107--96436312 Score: 314
Period size: 80 Copynumber: 2.7 Consensus size: 78
96436097 GGAAAATTTA
* *
96436107 TGATAATTATAATTATTAATT-AAAATTTTGATATAAAAAAGAA---GTGATAAATCATAAAACA
1 TGATAATTATAATTATTAATTAAAAAATTTGATATAAAAAAGAAGTTGTGCTAAATCATAAAACA
*
96436168 TCGGAAAACATTG
66 TCGGAAAAAATTG
*
96436181 TGATAATTATAATTATTAATTAAAAAATTTGATATAAAAAAGAAGTTGTGCTAAATCATAAAATA
1 TGATAATTATAATTATTAATTAAAAAATTTGATATAAAAAAGAAGTTGTGCTAAATCATAAAACA
96436246 TCGGGAAAAAAATTG
66 TC-GG-AAAAAATTG
96436261 TGATAATTATAATTATTAATTAAAAACA-TTGATATAAAAAAGAAGTTGTGCT
1 TGATAATTATAATTATTAATTAAAAA-ATTTGATATAAAAAAGAAGTTGTGCT
96436313 CTTTTTATTG
Statistics
Matches: 121, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
74 21 0.17
75 21 0.17
78 18 0.15
79 2 0.02
80 58 0.48
81 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (78 bp):
TGATAATTATAATTATTAATTAAAAAATTTGATATAAAAAAGAAGTTGTGCTAAATCATAAAACA
TCGGAAAAAATTG
Found at i:96436879 original size:2 final size:2
Alignment explanation
Indices: 96436872--96436896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
96436862 TTGAAAACTG
96436872 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 A
96436897 GGCACAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96438178 original size:22 final size:22
Alignment explanation
Indices: 96438153--96438200 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
96438143 AATACTTATA
96438153 TTATTTTTAATTTAATAATTTT
1 TTATTTTTAATTTAATAATTTT
* * *
96438175 TTATTTTTTATTTATTATTTTT
1 TTATTTTTAATTTAATAATTTT
96438197 TTAT
1 TTAT
96438201 AATCATAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TTATTTTTAATTTAATAATTTT
Found at i:96442454 original size:2 final size:2
Alignment explanation
Indices: 96442447--96442474 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96442437 TATTTCAAGG
96442447 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
96442475 GGATAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96444509 original size:36 final size:35
Alignment explanation
Indices: 96444442--96444510 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
96444432 AAAATAGTAA
** *
96444442 CAAAATTAACAATAAAATAAGTGTTATATAATATC
1 CAAAATTAACAATAAAATAAGTGCAACATAATATC
96444477 CAAAGATTAACAATAAAAT-AGTAGCAACATAATA
1 CAAA-ATTAACAATAAAATAAGT-GCAACATAATA
96444511 GTAAAATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 7 0.24
36 22 0.76
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (35 bp):
CAAAATTAACAATAAAATAAGTGCAACATAATATC
Found at i:96445682 original size:31 final size:31
Alignment explanation
Indices: 96445647--96445742 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
96445637 TAATATCATC
*
96445647 ATTAAATTATTTAAAAATTTTTATTTAAATT
1 ATTAAACTATTTAAAAATTTTTATTTAAATT
* * * *
96445678 ATTAAACTATTT-GAAGTTTTTCATCTAAATC
1 ATTAAACTATTTAAAAATTTTT-ATTTAAATT
* * * *
96445709 AGTAAACTGTTCAAAAATTTTTATTTAATTT
1 ATTAAACTATTTAAAAATTTTTATTTAAATT
96445740 ATT
1 ATT
96445743 GGGCTATTAA
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
30 7 0.14
31 35 0.71
32 7 0.14
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (31 bp):
ATTAAACTATTTAAAAATTTTTATTTAAATT
Found at i:96449358 original size:9 final size:9
Alignment explanation
Indices: 96449340--96449383 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
96449330 TTCTCAACAA
*
96449340 AAAAAATTT
1 AAAAATTTT
96449349 AAAAATTTT
1 AAAAATTTT
96449358 AAAAATTTT
1 AAAAATTTT
96449367 AAAAAAATTTT
1 --AAAAATTTT
96449378 AAAAAT
1 AAAAAT
96449384 ATATAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 23 0.72
11 9 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAAATTTT
Found at i:96449372 original size:11 final size:11
Alignment explanation
Indices: 96449349--96449382 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
96449339 AAAAAAATTT
96449349 AAAAATTTT--
1 AAAAATTTTAA
96449358 AAAAATTTTAA
1 AAAAATTTTAA
96449369 AAAAATTTTAA
1 AAAAATTTTAA
96449380 AAA
1 AAA
96449383 TATATAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:96449372 original size:20 final size:20
Alignment explanation
Indices: 96449349--96449406 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
96449339 AAAAAAATTT
96449349 AAAAATTTTAAAAATTTTAA
1 AAAAATTTTAAAAATTTTAA
*
96449369 AAAAATTTTAAAAATATATAA
1 AAAAATTTTAAAAAT-TTTAA
* * *
96449390 AGAAAGTTAAAAAATTT
1 AAAAATTTTAAAAATTT
96449407 CTAGAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAATTTTAAAAATTTTAA
Found at i:96455183 original size:3 final size:3
Alignment explanation
Indices: 96455177--96455201 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
96455167 TACGAGTAGT
96455177 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
96455202 AAGCTTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:96455604 original size:23 final size:23
Alignment explanation
Indices: 96455574--96455617 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
96455564 AAGTTTTTTT
*
96455574 TTTAATTTAGGTC-TTAAAAAAAA
1 TTTAATTT-GGCCATTAAAAAAAA
96455597 TTTAATTTGGCCATTAAAAAA
1 TTTAATTTGGCCATTAAAAAA
96455618 TTGATTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (23 bp):
TTTAATTTGGCCATTAAAAAAAA
Found at i:96455751 original size:20 final size:22
Alignment explanation
Indices: 96455728--96455767 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
96455718 TTTATTTAAA
*
96455728 TTTTAAGTT-TTT-TAAACAAG
1 TTTTAAATTATTTATAAACAAG
96455748 TTTTAAATTATTTATAAACA
1 TTTTAAATTATTTATAAACA
96455768 TGATACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTAAATTATTTATAAACAAG
Found at i:96456799 original size:15 final size:15
Alignment explanation
Indices: 96456779--96456808 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
96456769 AATAATAATT
96456779 ATAATAGTAAAAATA
1 ATAATAGTAAAAATA
*
96456794 ATAATAGTAATAATA
1 ATAATAGTAAAAATA
96456809 GCTAAGTAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
ATAATAGTAAAAATA
Found at i:96456894 original size:3 final size:3
Alignment explanation
Indices: 96456888--96457163 Score: 78
Period size: 3 Copynumber: 92.7 Consensus size: 3
96456878 AAAAAAGTAT
* * * *
96456888 TAA TAA TAG TAA TAA -ATA TAA TAG TAA TAAA TAGA AAA TAA TAG TACA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TA-A TAA TAA TAA TA-A
* *
96456936 TTAA TAA TAA TAA TAA TATA TAA -AA AAA TAGGA -AA TAA TAA T-A TGA
1 -TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA--A TAA TAA TAA TAA TAA
** * * * *
96456982 TAA -AA -AA TAA T-A TGT TAA TAA AAA TAA CAA -AG TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
96457026 AAA TAA AAA TAA AAA TAA TAG TAA TAA T-G TAT TAA TAA GAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
96457073 TAA TGA -AA TGAGA TTA TAA TAA TAA T-A TAA -AA AAA TAGA -CA TAA
1 TAA TAA TAA T-A-A TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * * *
96457117 -AA GAAA TAG TAA TAA TAG TAA TAA TAA TAG TAA TAA T-A TAAA TAA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
96457162 TA
1 TA
96457164 TATGTATGAA
Statistics
Matches: 197, Mismatches: 49, Indels: 54
0.66 0.16 0.18
Matches are distributed among these distances:
2 24 0.12
3 151 0.77
4 17 0.09
5 5 0.03
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:96456932 original size:35 final size:36
Alignment explanation
Indices: 96456889--96456991 Score: 99
Period size: 35 Copynumber: 3.0 Consensus size: 36
96456879 AAAAAGTATT
*
96456889 AATAATAGTA-ATAAAT-ATAATAGTAATAAATAGAA
1 AATAATAGTACATAAATAATAATAATAATAAATA-AA
* *
96456924 AATAATAGTACATTAATAATAATAATAATATATAAA
1 AATAATAGTACATAAATAATAATAATAATAAATAAA
* * * *
96456960 AA-AATAGGAAAT-AATAAT-ATGATAAAAAATAA
1 AATAATAGTACATAAATAATAATAATAATAAATAA
96456992 TATGTTAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 11 0.19
34 6 0.10
35 18 0.31
36 9 0.16
37 14 0.24
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (36 bp):
AATAATAGTACATAAATAATAATAATAATAAATAAA
Found at i:96456975 original size:34 final size:33
Alignment explanation
Indices: 96456901--96456978 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
96456891 TAATAGTAAT
* * *
96456901 AAAT-ATAATAGTAATAAATAGAAAATAATAGT
1 AAATAATAATAATAATAAATAGAAAAAAATAGG
* *
96456933 ACATTAATAATAATAATAATATATAAAAAAATAGG
1 A-AATAATAATAATAATAA-ATAGAAAAAAATAGG
96456968 AAATAATAATA
1 AAATAATAATA
96456979 TGATAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
32 1 0.03
33 2 0.05
34 21 0.57
35 13 0.35
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.28
Consensus pattern (33 bp):
AAATAATAATAATAATAAATAGAAAAAAATAGG
Found at i:96457051 original size:27 final size:29
Alignment explanation
Indices: 96456998--96457052 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 29
96456988 ATAATATGTT
96456998 AATAAAAATAACAAAGTAATAGTAATAAA
1 AATAAAAATAACAAAGTAATAGTAATAAA
96457027 AATAAAAATAA-AAA-TAATAGTAATAA
1 AATAAAAATAACAAAGTAATAGTAATAA
96457053 TGTATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 12 0.46
28 3 0.12
29 11 0.42
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (29 bp):
AATAAAAATAACAAAGTAATAGTAATAAA
Found at i:96457235 original size:18 final size:18
Alignment explanation
Indices: 96457209--96457243 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96457199 GTATATATAT
*
96457209 AATAATAATAATAATGGA
1 AATAATAATAAAAATGGA
*
96457227 AATAGTAATAAAAATGG
1 AATAATAATAAAAATGG
96457244 CATGAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
AATAATAATAAAAATGGA
Found at i:96460977 original size:19 final size:18
Alignment explanation
Indices: 96460922--96460970 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 18
96460912 TATTTTAGAT
*
96460922 TTTTTAAAATTTTTATATA
1 TTTTTAGAATTTTTA-ATA
96460941 TTCTTTAGAATTTTTAATA
1 TT-TTTAGAATTTTTAATA
96460960 TTTTTA-AATTT
1 TTTTTAGAATTT
96460971 CTGTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 7 0.25
20 12 0.43
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTTAGAATTTTTAATA
Found at i:96461849 original size:69 final size:69
Alignment explanation
Indices: 96461757--96461892 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 69
96461747 TGGTCCGAAA
* * * * * *
96461757 TTAAATTCGAATTTTAATAAAAGATCTGATTCCGATTTTAATTGGACTCGATTTGAATATAATTT
1 TTAAATCCAAATTTTAATAAAAGATCTGATTCCGACTTTAATTCGACCCGATCTGAATATAATTT
96461822 AAAT
66 AAAT
* * *
96461826 TTAAATCCAAATTTTAATAAAAGATTTGATTTCGACTTTAATTCGTCCCGATCTGAATATAATTT
1 TTAAATCCAAATTTTAATAAAAGATCTGATTCCGACTTTAATTCGACCCGATCTGAATATAATTT
96461891 AA
66 AA
96461893 TTGTTTTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (69 bp):
TTAAATCCAAATTTTAATAAAAGATCTGATTCCGACTTTAATTCGACCCGATCTGAATATAATTT
AAAT
Found at i:96469313 original size:7 final size:7
Alignment explanation
Indices: 96469303--96469327 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
96469293 CTAGGATTTG
96469303 AGTTTAA
1 AGTTTAA
96469310 AGTTTAA
1 AGTTTAA
96469317 AGTTTAA
1 AGTTTAA
96469324 AGTT
1 AGTT
96469328 ATAGTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (7 bp):
AGTTTAA
Found at i:96470183 original size:3 final size:3
Alignment explanation
Indices: 96470175--96470208 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
96470165 TAAATGGAGT
* *
96470175 TGA TGA TGA TGA TGA TGA TGA TGG TGA CGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
96470209 AGTTGCAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:96470741 original size:27 final size:27
Alignment explanation
Indices: 96470710--96470763 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
96470700 AATACTAATC
96470710 TTCAAAA-ATTTAAAATAATTTTTAAAA
1 TTCAAAATATTT-AAATAATTTTTAAAA
* *
96470737 TTCAAAATATTTATATATTTTTTAAAA
1 TTCAAAATATTTAAATAATTTTTAAAA
96470764 AAAATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (27 bp):
TTCAAAATATTTAAATAATTTTTAAAA
Found at i:96470775 original size:11 final size:12
Alignment explanation
Indices: 96470761--96470790 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
96470751 ATATTTTTTA
96470761 AAAAAAAT-TAT
1 AAAAAAATCTAT
96470772 AAAAAAATCTAT
1 AAAAAAATCTAT
96470784 AAAAAAA
1 AAAAAAA
96470791 GTTAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAAATCTAT
Found at i:96470776 original size:12 final size:13
Alignment explanation
Indices: 96470759--96470790 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
96470749 ATATATTTTT
96470759 TAAAAAAAAT-TA
1 TAAAAAAAATCTA
96470771 T-AAAAAAATCTA
1 TAAAAAAAATCTA
96470783 TAAAAAAA
1 TAAAAAAA
96470791 GTTAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.44
12 4 0.22
13 6 0.33
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAAAAAAATCTA
Found at i:96471229 original size:3 final size:3
Alignment explanation
Indices: 96471221--96471254 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
96471211 ACCTATAACC
96471221 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
96471255 GAAATTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:96486058 original size:18 final size:16
Alignment explanation
Indices: 96486026--96486059 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
96486016 GGATTTCTTG
96486026 TTGTGTTAAATATATA
1 TTGTGTTAAATATATA
96486042 TTGTGTTAAATATATA
1 TTGTGTTAAATATATA
96486058 TT
1 TT
96486060 ATCTTAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TTGTGTTAAATATATA
Found at i:96486066 original size:16 final size:16
Alignment explanation
Indices: 96486031--96486066 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
96486021 TCTTGTTGTG
* *
96486031 TTAAATATATATTGTG
1 TTAAATATATATTATC
96486047 TTAAATATATATTATC
1 TTAAATATATATTATC
96486063 TTAA
1 TTAA
96486067 GCAAATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAATATATATTATC
Found at i:96489560 original size:10 final size:10
Alignment explanation
Indices: 96489545--96489574 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
96489535 TGAGTGACTG
96489545 TTTTATAATT
1 TTTTATAATT
*
96489555 TTTTATAGTT
1 TTTTATAATT
96489565 TTTTATAATT
1 TTTTATAATT
96489575 GAATGACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:96489789 original size:16 final size:16
Alignment explanation
Indices: 96489776--96489809 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
96489766 AAAAAAATCT
96489776 ATAAAATTATAAATTA
1 ATAAAATTATAAATTA
*
96489792 ATATAATTATAAAATTA
1 ATAAAATTAT-AAATTA
96489809 A
1 A
96489810 ATTTTGACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAATTATAAATTA
Found at i:96492430 original size:17 final size:18
Alignment explanation
Indices: 96492402--96492441 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
96492392 TTGATTTGAT
96492402 TAAATAAAATAAAATTTA
1 TAAATAAAATAAAATTTA
*
96492420 TAAAT-AAATAAATTTTA
1 TAAATAAAATAAAATTTA
*
96492437 AAAAT
1 TAAAT
96492442 TAGTACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATAAAATAAAATTTA
Found at i:96492579 original size:2 final size:2
Alignment explanation
Indices: 96492574--96492605 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
96492564 CTCAAGTTTA
96492574 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
96492606 TTAGTGTACA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96495335 original size:29 final size:30
Alignment explanation
Indices: 96495280--96495337 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
96495270 TCTTAAAATT
*
96495280 ATACATGAATTTTGATTTGTTGTGTAATTTG
1 ATACATGAATTTTGATTTG-TATGTAATTTG
96495311 ATACATGAATTTTGATTTG-ATGTAATT
1 ATACATGAATTTTGATTTGTATGTAATT
96495338 GCACACATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
31 19 0.73
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.50
Consensus pattern (30 bp):
ATACATGAATTTTGATTTGTATGTAATTTG
Found at i:96495345 original size:29 final size:30
Alignment explanation
Indices: 96495282--96495358 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
96495272 TTAAAATTAT
* *
96495282 ACATGAATTTTGATTTGTTGTGTAATTTGAT
1 ACATGAATTTTGATTTG-TATGTAATTTGAC
96495313 ACATGAATTTTGATTTG-ATGTAA-TTGCAC
1 ACATGAATTTTGATTTGTATGTAATTTG-AC
*
96495342 ACATGAAACTTTGATTT
1 ACATG-AATTTTGATTT
96495359 TTGATTCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.07
29 11 0.27
30 10 0.24
31 17 0.41
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (30 bp):
ACATGAATTTTGATTTGTATGTAATTTGAC
Found at i:96495406 original size:31 final size:32
Alignment explanation
Indices: 96495347--96495406 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
96495337 TGCACACATG
* * *
96495347 AAACTTTGATTTTTGATTCAAATGTACACGTC
1 AAACTTTGAATTTTAATTCAAATATACACGTC
*
96495379 AAACTTT-AATTTTAATTCAATTATACAC
1 AAACTTTGAATTTTAATTCAAATATACAC
96495407 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (32 bp):
AAACTTTGAATTTTAATTCAAATATACACGTC
Found at i:96495884 original size:18 final size:20
Alignment explanation
Indices: 96495852--96495890 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
96495842 ATAAAATTCT
*
96495852 ATTTTTTAAAGAAAT-ATAA
1 ATTTGTTAAAGAAATCATAA
96495871 ATTTGTTAAA-AAATCATAA
1 ATTTGTTAAAGAAATCATAA
96495890 A
1 A
96495891 AATTATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTTGTTAAAGAAATCATAA
Found at i:96496225 original size:15 final size:15
Alignment explanation
Indices: 96496205--96496233 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
96496195 GATTCAAATT
96496205 TAAATATAAAATATA
1 TAAATATAAAATATA
96496220 TAAATATAAAATAT
1 TAAATATAAAATAT
96496234 TTTATTATTT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAATATAAAATATA
Found at i:96506607 original size:32 final size:32
Alignment explanation
Indices: 96506562--96506641 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
96506552 CGATTTAATC
96506562 TTAATAAAAAAAATCATTAATAAATTATAAAAT
1 TTAA-AAAAAAAATCATTAATAAATTATAAAAT
96506595 TTAAAAAAAAAATCATTAATAAATTATAAAAT
1 TTAAAAAAAAAATCATTAATAAATTATAAAAT
96506627 TTAAAAAAAAAATCA
1 TTAAAAAAAAAATCA
96506642 ATTCACCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 43 0.91
33 4 0.09
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (32 bp):
TTAAAAAAAAAATCATTAATAAATTATAAAAT
Found at i:96506687 original size:24 final size:24
Alignment explanation
Indices: 96506655--96506703 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
96506645 CACCAATTCG
96506655 TTCTATCCAACTGCTATATTTTAT
1 TTCTATCCAACTGCTATATTTTAT
96506679 TTCTATCCAACTGCTATATTTTAT
1 TTCTATCCAACTGCTATATTTTAT
96506703 T
1 T
96506704 ATATTATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (24 bp):
TTCTATCCAACTGCTATATTTTAT
Found at i:96507354 original size:31 final size:31
Alignment explanation
Indices: 96507316--96507388 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
96507306 ATTTACAGTC
96507316 GGTACC-AATTCAAACTAAAAAGCCAAGTTTA
1 GGTACCAAATTCAAACT-AAAAGCCAAGTTTA
* * *
96507347 GGTACCAAATTGAACCTTAAAGCCAAGTTTA
1 GGTACCAAATTCAAACTAAAAGCCAAGTTTA
* *
96507378 AGTACCTAATT
1 GGTACCAAATT
96507389 GGAACCAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 28 0.78
32 8 0.22
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (31 bp):
GGTACCAAATTCAAACTAAAAGCCAAGTTTA
Found at i:96507389 original size:31 final size:32
Alignment explanation
Indices: 96507334--96507394 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
96507324 TTCAAACTAA
*
96507334 AAAGCCAAGTTTAGGTACCAAATT-GAACCTT
1 AAAGCCAAGTTTAAGTACCAAATTGGAACCTT
*
96507365 AAAGCCAAGTTTAAGTACCTAATTGGAACC
1 AAAGCCAAGTTTAAGTACCAAATTGGAACC
96507395 AAAAAAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (32 bp):
AAAGCCAAGTTTAAGTACCAAATTGGAACCTT
Found at i:96510281 original size:32 final size:31
Alignment explanation
Indices: 96510219--96510286 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 31
96510209 TTATTTAAAC
* * * *
96510219 TATTCGCATTTTTTATTTCTTTATTGATAAT
1 TATTTGCATTTTTAATTTCTTTAATAATAAT
96510250 TATTTGCATTGTTTAATTTCTTTAATAATAAT
1 TATTTGCATT-TTTAATTTCTTTAATAATAAT
*
96510282 GATTT
1 TATTT
96510287 TTAAAAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (31 bp):
TATTTGCATTTTTAATTTCTTTAATAATAAT
Found at i:96512730 original size:14 final size:14
Alignment explanation
Indices: 96512705--96512739 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
96512695 AGGGTCCGTT
96512705 TGTTTATATGTAAAA
1 TGTTT-TATGTAAAA
96512720 TGTTTTATGTAAAA
1 TGTTTTATGTAAAA
96512734 TGTTTT
1 TGTTTT
96512740 CTATATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (14 bp):
TGTTTTATGTAAAA
Found at i:96513085 original size:24 final size:23
Alignment explanation
Indices: 96513026--96513088 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
96513016 ATTTAATCAT
96513026 ATAATAAATTATTAATATAATTTA
1 ATAATAAATT-TTAATATAATTTA
* * * *
96513050 TTAAAAATATTTTAATTTTATTTTA
1 ATAATAA-ATTTTAA-TATAATTTA
96513075 ATAATAAATTTTAA
1 ATAATAAATTTTAA
96513089 AAATAATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATAAATTTTAATATAATTTA
Done.