Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 27
Found at i:3617575 original size:29 final size:29
Alignment explanation
Indices: 3617522--3617604 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
3617512 ATCTCAGCTT
* * * *
3617522 GGTCGCCGGGACTGCTTGGCTACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
* ***
3617551 GGTCGCTGGGAGTGCATGGTGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
3617580 GGTCGCTGGGAGTGCATGGCGACCT
1 GGTCGCTGGGAGTGCATGGCGACCT
3617605 GTGTTGGAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.14, C:0.24, G:0.39, T:0.23
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCATGGCGACCTACAA
Found at i:3623338 original size:39 final size:39
Alignment explanation
Indices: 3623284--3623363 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
3623274 AGTTGAGTTG
3623284 TTAAGAGCAGGAGCAACATTGAAAGCTATCACTTGCTCC
1 TTAAGAGCAGGAGCAACATTGAAAGCTATCACTTGCTCC
*
3623323 TTAAGAGGAGGAGCAACATTGAAAGCTATCACTTGCTCC
1 TTAAGAGCAGGAGCAACATTGAAAGCTATCACTTGCTCC
3623362 TT
1 TT
3623364 TCCTCACAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (39 bp):
TTAAGAGCAGGAGCAACATTGAAAGCTATCACTTGCTCC
Found at i:3626222 original size:32 final size:32
Alignment explanation
Indices: 3626179--3626250 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
3626169 AATTTACAAG
3626179 GCATCAATGAGTAATAGAATAGCAACCTGCAA
1 GCATCAATGAGTAATAGAATAGCAACCTGCAA
*
3626211 GCATGAATGAGTAATAGAATAGCAACCTGCAA
1 GCATCAATGAGTAATAGAATAGCAACCTGCAA
3626243 GCATCAAT
1 GCATCAAT
3626251 ATACCTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (32 bp):
GCATCAATGAGTAATAGAATAGCAACCTGCAA
Found at i:3626307 original size:22 final size:23
Alignment explanation
Indices: 3626259--3626307 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
3626249 ATATACCTTC
**
3626259 AACAAGCATCATTGCATCAATTC
1 AACAAGCATCATTGCATCAATAA
*
3626282 AACAAGCATC-TTGCATTAATAA
1 AACAAGCATCATTGCATCAATAA
3626304 AACA
1 AACA
3626308 TACAATCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.24
Consensus pattern (23 bp):
AACAAGCATCATTGCATCAATAA
Found at i:3628838 original size:20 final size:21
Alignment explanation
Indices: 3628797--3628838 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3628787 AAGATAATTA
*
3628797 ACATTACTATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
3628819 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
3628839 TTATTTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:3628905 original size:18 final size:18
Alignment explanation
Indices: 3628882--3629075 Score: 181
Period size: 18 Copynumber: 11.2 Consensus size: 18
3628872 TAGTACACTA
*
3628882 ATATAGTTTACATATACT
1 ATATAGTTTATATATACT
3628900 ATATAGTTTATATATACT
1 ATATAGTTTATATATACT
* *
3628918 A-AT-G--AACTATATAAT
1 ATATAGTTTA-TATATACT
3628933 ATATAGTTTATATATACT
1 ATATAGTTTATATATACT
** *
3628951 A-AT-GAAATATATATAAT
1 ATATAG-TTTATATATACT
* * *
3628968 GTATAGTTTATATGTACC
1 ATATAGTTTATATATACT
*
3628986 ATATAGTTTATATATATT
1 ATATAGTTTATATATACT
3629004 ATATAGTTTATATATACT
1 ATATAGTTTATATATACT
***
3629022 A-ATAAACTATATA-A-T
1 ATATAGTTTATATATACT
*
3629037 ATATAGTTTATATATATT
1 ATATAGTTTATATATACT
3629055 ATATAGTTTATATATACT
1 ATATAGTTTATATATACT
3629073 ATA
1 ATA
3629076 GTATAAATTA
Statistics
Matches: 139, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
14 1 0.01
15 10 0.07
16 14 0.10
17 24 0.17
18 88 0.63
19 2 0.01
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (18 bp):
ATATAGTTTATATATACT
Found at i:3628930 original size:17 final size:17
Alignment explanation
Indices: 3628908--3628965 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
3628898 CTATATAGTT
*
3628908 TATATATACTAATGAAC
1 TATATATACTAATGAAA
**
3628925 TATATA-A-TATAT-AGT
1 TATATATACTA-ATGAAA
3628940 TTATATATACTAATGAAA
1 T-ATATATACTAATGAAA
3628958 TATATATA
1 TATATATA
3628966 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 16 0.50
18 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAA
Found at i:3628936 original size:33 final size:33
Alignment explanation
Indices: 3628893--3629052 Score: 187
Period size: 33 Copynumber: 4.7 Consensus size: 33
3628883 TATAGTTTAC
*
3628893 ATATACTATATAGTTTATATATACTAATGAACT
1 ATATAATATATAGTTTATATATACTAATGAACT
*
3628926 ATATAATATATAGTTTATATATACTAATGAAATAT
1 ATATAATATATAGTTTATATATACTAATG-AA-CT
* * **
3628961 ATATAATGTATAGTTTATATGTACCATATAGTTTA-T
1 ATATAATATATAGTTTATATATA-C-TA-A-TGAACT
* *
3628997 ATATATTATATAGTTTATATATACTAATAAACT
1 ATATAATATATAGTTTATATATACTAATGAACT
3629030 ATATAATATATAGTTTATATATA
1 ATATAATATATAGTTTATATATA
3629053 TTATATAGTT
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
32 2 0.02
33 52 0.48
34 4 0.04
35 23 0.21
36 22 0.20
37 2 0.02
38 2 0.02
39 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (33 bp):
ATATAATATATAGTTTATATATACTAATGAACT
Found at i:3628942 original size:51 final size:51
Alignment explanation
Indices: 3628882--3629073 Score: 221
Period size: 51 Copynumber: 3.7 Consensus size: 51
3628872 TAGTACACTA
*
3628882 ATATAGTTTACATATACTATATAGTTTATATATACTAATGAACTATATAAT
1 ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAAT
** * **
3628933 ATATAGTTTATATATACTA-AT-G-AAATATATA-TAATGTATAGTTTATATGTACC
1 ATATAGTTTATATATACTATATAGTTTATATATACTAATG-A-A--CTATA--TAAT
* *
3628986 ATATAGTTTATATATATTATATAGTTTATATATACTAATAAACTATATAAT
1 ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAAT
*
3629037 ATATAGTTTATATATATTATATAGTTTATATATACTA
1 ATATAGTTTATATATACTATATAGTTTATATATACTA
3629074 TAGTATAAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
47 5 0.04
48 8 0.07
49 2 0.02
50 2 0.02
51 61 0.52
53 24 0.20
54 2 0.02
55 2 0.02
56 8 0.07
57 4 0.03
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (51 bp):
ATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATATAAT
Found at i:3629001 original size:2 final size:2
Alignment explanation
Indices: 3628994--3629276 Score: 68
Period size: 2 Copynumber: 135.0 Consensus size: 2
3628984 CCATATAGTT
* *
3628994 TA TA TA TA T- TA TA TA GTT TA TA TA TA CTA -A TA AA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA -TA TA TA
* *
3629035 -A TA TA TA GTT TA TA TA TA T- TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* * *
3629076 GTA TA AA T- TA T- TT TA TA TA GTA TA TA AA TA TCA -A CTA TA GTA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA
* * * * * *
3629118 TA TA GTT TA TA TGG TT TT TA TA TA TA GT- TCA TA TG TA AA T- TA
1 TA TA -TA TA TA T-A TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA
* *
3629160 TA CTA TA TA GTA TA TA TA GTT TA TA TA TA GTA TA TA AA TA TA -A
1 TA -TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* ** * *
3629203 AA TA TA GTA TA TA TA TA TA GG TCA TA TG TA AA CTA TA TA GTA TA
1 TA TA TA -TA TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA -TA TA
*
3629247 TA AA TA TCA -A CTA TA T- TA TA TA TA TA TA TA
1 TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA
3629277 GGTCATATGC
Statistics
Matches: 207, Mismatches: 37, Indels: 74
0.65 0.12 0.23
Matches are distributed among these distances:
1 12 0.06
2 160 0.77
3 35 0.17
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3629042 original size:69 final size:71
Alignment explanation
Indices: 3628893--3629075 Score: 225
Period size: 69 Copynumber: 2.6 Consensus size: 71
3628883 TATAGTTTAC
* **
3628893 ATATACTATATAGTTTATATATA-C-TA-A-TGAACTATATAATATATAGTTTATATATACTAAT
1 ATATAATATATAGTTTATATATACCATATAGTTTA-TATATAATATATAGTTTATATATACTAAT
3628954 GAAATAT
65 GAAATAT
* * *
3628961 ATATAATGTATAGTTTATATGTACCATATAGTTTATATATATTATATAGTTTATATATACTAAT-
1 ATATAATATATAGTTTATATATACCATATAGTTTATATATAATATATAGTTTATATATACTAATG
*
3629025 AAA-CT
66 AAATAT
** *
3629030 ATATAATATATAGTTTATATATATTATATAGTTTATATATACTATA
1 ATATAATATATAGTTTATATATACCATATAGTTTATATATAATATA
3629076 GTATAAATTA
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
68 20 0.20
69 43 0.43
70 5 0.05
71 29 0.29
72 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (71 bp):
ATATAATATATAGTTTATATATACCATATAGTTTATATATAATATATAGTTTATATATACTAATG
AAATAT
Found at i:3629075 original size:9 final size:9
Alignment explanation
Indices: 3628993--3629080 Score: 62
Period size: 9 Copynumber: 10.0 Consensus size: 9
3628983 ACCATATAGT
3628993 TTATATATA
1 TTATATATA
3629002 TTATATAGT-
1 TTATATA-TA
3629011 TTATATATA
1 TTATATATA
* *
3629020 CTA-ATAAA
1 TTATATATA
*
3629028 CTATATA-A
1 TTATATATA
3629036 -TATATAGT-
1 TTATATA-TA
3629044 TTATATATA
1 TTATATATA
3629053 TTATATAGT-
1 TTATATA-TA
3629062 TTATATATA
1 TTATATATA
*
3629071 CTATAGTATA
1 TTATA-TATA
3629081 AATTATTTTA
Statistics
Matches: 66, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
7 6 0.09
8 11 0.17
9 43 0.65
10 6 0.09
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (9 bp):
TTATATATA
Found at i:3629120 original size:104 final size:102
Alignment explanation
Indices: 3628900--3629121 Score: 229
Period size: 104 Copynumber: 2.1 Consensus size: 102
3628890 TACATATACT
*
3628900 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAATATATAT
1 ATATAG-TTATATATACTAATAAACTATATAATATATAGTTTATATATACTAATGAAATATATAT
** * * *
3628965 AATGTATAGTTTATATGTACCATATAGTTTATATATATT
65 AATGTATAAATTATATGTA-CATATAGTATATAAATATA
* **
3629004 ATATAGTTTATATATACTAATAAACTATATAATATATAGTTTATATATATTATAT-AGTTTATAT
1 ATATAG-TTATATATACTAATAAACTATATAATATATAGTTTATATATACTA-ATGA-AATATAT
*
3629068 ATACTATAGTATAAATTAT-T-T-TATATAGTATATAAATATCA
63 ATA--AT-GTATAAATTATATGTACATATAGTATATAAATAT-A
3629109 ACTATAG-TATATA
1 A-TATAGTTATATA
3629122 GTTTATATGG
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
104 72 0.71
105 11 0.11
106 6 0.06
107 3 0.03
108 9 0.09
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (102 bp):
ATATAGTTATATATACTAATAAACTATATAATATATAGTTTATATATACTAATGAAATATATATA
ATGTATAAATTATATGTACATATAGTATATAAATATA
Found at i:3629241 original size:33 final size:33
Alignment explanation
Indices: 3629204--3629327 Score: 126
Period size: 33 Copynumber: 4.1 Consensus size: 33
3629194 TAAATATAAA
3629204 ATATAGTATATATATATAGGTCATATGTAAACT
1 ATATAGTATATATATATAGGTCATATGTAAACT
*
3629237 ATATAGTATATA-A-ATA--TCA-A-CT--A-T
1 ATATAGTATATATATATAGGTCATATGTAAACT
*
3629261 AT-TA-TATATATATATAGGTCATATGCAAACT
1 ATATAGTATATATATATAGGTCATATGTAAACT
* * *
3629292 ATATAGTTTTTATATATAGTTCATATGTAAACT
1 ATATAGTATATATATATAGGTCATATGTAAACT
3629325 ATA
1 ATA
3629328 GTTCATATGT
Statistics
Matches: 73, Mismatches: 7, Indels: 22
0.72 0.07 0.22
Matches are distributed among these distances:
22 6 0.08
23 3 0.04
24 6 0.08
25 1 0.01
26 3 0.04
27 2 0.03
28 1 0.01
29 3 0.04
30 1 0.01
31 6 0.08
32 3 0.04
33 38 0.52
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (33 bp):
ATATAGTATATATATATAGGTCATATGTAAACT
Found at i:3629241 original size:53 final size:55
Alignment explanation
Indices: 3629183--3629298 Score: 184
Period size: 55 Copynumber: 2.1 Consensus size: 55
3629173 ATATAGTTTA
*
3629183 TATATAGTATATAAATAT-AA-AATA-TAGTATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATCAACAATATTA-TATATATATATAGGTCATATGCAAAC
*
3629236 TATATAGTATATAAATATCAACTATATTATATATATATATAGGTCATATGCAAAC
1 TATATAGTATATAAATATCAACAATATTATATATATATATAGGTCATATGCAAAC
3629291 TATATAGT
1 TATATAGT
3629299 TTTTATATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
53 18 0.31
54 2 0.03
55 36 0.62
56 2 0.03
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.39
Consensus pattern (55 bp):
TATATAGTATATAAATATCAACAATATTATATATATATATAGGTCATATGCAAAC
Found at i:3629248 original size:9 final size:9
Alignment explanation
Indices: 3628986--3629221 Score: 52
Period size: 9 Copynumber: 27.1 Consensus size: 9
3628976 TATATGTACC
*
3628986 ATATAGTTT
1 ATATAGTAT
3628995 ATATA-TATT
1 ATATAGTA-T
*
3629004 ATATAGTTT
1 ATATAGTAT
3629013 ATATA-TACT
1 ATATAGTA-T
*
3629022 A-ATA-AACT
1 ATATAGTA-T
3629030 ATATA--AT
1 ATATAGTAT
*
3629037 ATATAGTTT
1 ATATAGTAT
3629046 ATATA-TATT
1 ATATAGTA-T
3629055 ATATAGT-T
1 ATATAGTAT
3629063 -TATA-TAT
1 ATATAGTAT
3629070 ACTATAGTAT
1 A-TATAGTAT
* * *
3629080 AAATTATTTT
1 ATA-TAGTAT
3629090 ATATAGTAT
1 ATATAGTAT
*
3629099 ATA-AATAT
1 ATATAGTAT
3629107 CA-ACTA-TAGT
1 -ATA-TAGTA-T
*
3629117 ATATAGTTT
1 ATATAGTAT
*
3629126 ATATGGT-T
1 ATATAGTAT
3629134 -T-T--TAT
1 ATATAGTAT
3629139 ATATAGT-T
1 ATATAGTAT
*
3629147 CATAT-GTAA
1 -ATATAGTAT
3629156 AT-TA-TACT
1 ATATAGTA-T
3629164 ATATAGTAT
1 ATATAGTAT
3629173 ATATAGTTTAT
1 ATATAG--TAT
3629184 ATATAGTAT
1 ATATAGTAT
*
3629193 ATAAATA-TAAA
1 AT--ATAGT-AT
3629204 ATATAGTAT
1 ATATAGTAT
3629213 ATATA-TAT
1 ATATAGTAT
3629221 A
1 A
3629222 GGTCATATGT
Statistics
Matches: 172, Mismatches: 19, Indels: 73
0.65 0.07 0.28
Matches are distributed among these distances:
4 1 0.01
5 1 0.01
6 3 0.02
7 16 0.09
8 29 0.17
9 87 0.51
10 20 0.12
11 15 0.09
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (9 bp):
ATATAGTAT
Found at i:3629329 original size:18 final size:18
Alignment explanation
Indices: 3629306--3629458 Score: 112
Period size: 18 Copynumber: 7.9 Consensus size: 18
3629296 AGTTTTTATA
3629306 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
3629324 TATAGTTCATATGTAAATATCAAC
1 TATAGTTCATATG----TA--AAC
*
3629348 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
*
3629366 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
* *
3629384 TATATAGTTTATATGTAAAG
1 --TATAGTTCATATGTAAAC
*
3629404 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
* *
3629422 TATATAGTTTATATTTAAAC
1 --TATAGTTCATATGTAAAC
*
3629442 TATAGTTCATATATAAA
1 TATAGTTCATATGTAAA
3629459 TATTAACTTT
Statistics
Matches: 112, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.02
18 60 0.54
20 31 0.28
21 2 0.02
22 2 0.02
24 15 0.13
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:3629399 original size:38 final size:38
Alignment explanation
Indices: 3629304--3629458 Score: 197
Period size: 38 Copynumber: 4.0 Consensus size: 38
3629294 ATAGTTTTTA
* *
3629304 TATATAGTTCATATGTAAACTATAGTTCATATGTAAATATC
1 TATATAGTTTATATGTAAACTATAGTTCATATAT-AA-A-C
*
3629345 AACTATAGTTTATATGTAAACTATAGTT-AGTATATAAAC
1 TA-TATAGTTTATATGTAAACTATAGTTCA-TATATAAAC
*
3629384 TATATAGTTTATATGTAAAGTATAGTT-AGTATATAAAC
1 TATATAGTTTATATGTAAACTATAGTTCA-TATATAAAC
*
3629422 TATATAGTTTATATTTAAACTATAGTTCATATATAAA
1 TATATAGTTTATATGTAAACTATAGTTCATATATAAA
3629459 TATTAACTTT
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
38 68 0.65
39 3 0.03
40 1 0.01
41 4 0.04
42 28 0.27
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (38 bp):
TATATAGTTTATATGTAAACTATAGTTCATATATAAAC
Found at i:3629532 original size:33 final size:32
Alignment explanation
Indices: 3629451--3629549 Score: 96
Period size: 33 Copynumber: 3.1 Consensus size: 32
3629441 CTATAGTTCA
* *
3629451 TATATAAATATTAACTTTAG-TATATATATAG
1 TATATAAATATAAACTATAGTTATATATATAG
* * * *
3629482 T-T-CACATGTAAATTATAGTTCATATATATAG
1 TATATAAATATAAACTATAGTT-ATATATATAG
*
3629513 TATATAAATATAAACTATAGTTTATATAAATAG
1 TATATAAATATAAACTATAG-TTATATATATAG
3629546 TATA
1 TATA
3629550 AATTATAGTA
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
29 10 0.19
30 2 0.04
31 12 0.23
32 1 0.02
33 25 0.48
34 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (32 bp):
TATATAAATATAAACTATAGTTATATATATAG
Found at i:3629663 original size:22 final size:22
Alignment explanation
Indices: 3629632--3629686 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3629622 CTATAAACCC
*
3629632 TAAACCATATA-TACTATA-TACA
1 TAAACTATATAGT-CTATATTA-A
*
3629654 TAAACTATATAGTTTATATTAA
1 TAAACTATATAGTCTATATTAA
3629676 TAAACTATATA
1 TAAACTATATA
3629687 ATTTATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAACTATATAGTCTATATTAA
Found at i:3629819 original size:20 final size:20
Alignment explanation
Indices: 3629790--3629881 Score: 56
Period size: 20 Copynumber: 4.8 Consensus size: 20
3629780 TATATAGTTC
*
3629790 AATATTTATAGTTTATACAT
1 AATATATATAGTTTATACAT
3629810 AATATATATA---TAT--A-
1 AATATATATAGTTTATACAT
* *
3629824 AA-CTATATAGTTTATATATAT
1 AATATATATAG-TT-TATACAT
* *
3629845 AATACATATACTTTATACAT
1 AATATATATAGTTTATACAT
3629865 AA-ACTATATAGTTTATA
1 AATA-TATATAGTTTATA
3629882 TTATATATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
13 6 0.11
14 2 0.04
15 1 0.02
17 3 0.06
18 3 0.06
19 1 0.02
20 29 0.54
21 4 0.07
22 5 0.09
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATATATAGTTTATACAT
Found at i:3629839 original size:22 final size:22
Alignment explanation
Indices: 3629814--3629888 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
3629804 ATACATAATA
3629814 TATATATATAAACTATATAGTT
1 TATATATATAAACTATATAGTT
*
3629836 TATATATATAATAC-ATATA-CT
1 TATATATATAA-ACTATATAGTT
*
3629857 T-TATACATAAACTATATAGTT
1 TATATATATAAACTATATAGTT
3629878 TATATTATATA
1 TATA-TATATA
3629889 TATATTAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 4 0.09
22 18 0.41
23 7 0.16
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (22 bp):
TATATATATAAACTATATAGTT
Found at i:3629872 original size:89 final size:88
Alignment explanation
Indices: 3629704--3629877 Score: 199
Period size: 89 Copynumber: 2.0 Consensus size: 88
3629694 CAATATATAT
* * * *
3629704 TATTTATAATTATACATAATATATAAATATAAATTGTATAGTTTATATATAATTCATATATAAAC
1 TATTTATAATTATACATAATATATAAATATAAACTATATAGTTTATATATAATTAATACATAAAC
* * **
3629769 TATGTAGTTTCTATATAGTTCAA
66 TATATAATAACTATATAGTTCAA
* * *
3629792 TATTTATAGTTTATACATAATATATATATATAAACTATATAGTTTATATAT-A-TAATACATATA
1 TATTTATA-ATTATACATAATATATAAATATAAACTATATAGTTTATATATAATTAATACATAAA
*
3629855 CTTTATACATAAACTATATAGTT
65 CTATATA-AT-AACTATATAGTT
3629878 TATATTATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
87 13 0.18
88 10 0.14
89 48 0.68
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (88 bp):
TATTTATAATTATACATAATATATAAATATAAACTATATAGTTTATATATAATTAATACATAAAC
TATATAATAACTATATAGTTCAA
Found at i:3629892 original size:20 final size:20
Alignment explanation
Indices: 3629827--3629898 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
3629817 ATATATAAAC
3629827 TATATAGTTTATATATATAATA
1 TATATAGTTTATAT-TAT-ATA
* * * *
3629849 CATATACTTTATA-CATAAA
1 TATATAGTTTATATTATATA
3629868 CTATATAGTTTATATTATATA
1 -TATATAGTTTATATTATATA
3629889 TATATTAGTT
1 TATA-TAGTT
3629899 GTTTTAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 2 0.05
20 17 0.44
21 9 0.23
22 11 0.28
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (20 bp):
TATATAGTTTATATTATATA
Found at i:3630509 original size:434 final size:432
Alignment explanation
Indices: 3629976--3630896 Score: 1573
Period size: 435 Copynumber: 2.1 Consensus size: 432
3629966 TGATCCCTTT
* * **
3629976 TGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCACT
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAA
* *
3630041 TTTTATTTGCATCTGAAATTGACTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAAC
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
*
3630106 -TTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAATATCACAATTTAAAATTATTT
131 TTTTTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACATCACAATTTAAAATTATTT
*
3630170 CGATTTGAT-CCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATT
195 CGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATT
3630234 TGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTT-ATTAC
260 TGTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATT-C
*
3630298 TATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC-ATTTTTGTATTAATTTC
324 TATTTTTAAATTGGCCCATAACTTTTTAAATGGCTATAATTTAGTACTATTTTTGTATTAATTTC
*
3630362 AACAC-CACAATTTAAAATTACTTTTTTCGATTTGATCCCTCATCAATC
389 AAC-CTCACAATTTAAAATTA---GTTT-GATTTGATCCCTCATCAATC
3630410 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAA
*
3630475 TTTTATTTGCATCTTAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
3630540 TTTTTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTC
131 TTTTTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTC
3630605 GATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTT
196 GATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTT
* *
3630670 GTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGATCTATACTTATTACTTAATTCTA
261 GTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATTCTA
* * * *
3630735 TTTTTTAATTGGCCCATATCTTTTTAAATGGCTATAATTTAGTACTTTTTTTTTATTAATTTCAA
326 TTTTTAAATTGGCCCATAACTTTTTAAATGGCTATAATTTAGTACTATTTTTGTATTAATTTCAA
*
3630800 CCTCACAATTTAAAATTAGTTTGATTTGATCCCTCATCAATG
391 CCTCACAATTTAAAATTAGTTTGATTTGATCCCTCATCAATC
*
3630842 TATGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTA
3630897 ATTATTAAAT
Statistics
Matches: 463, Mismatches: 19, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
432 73 0.16
433 3 0.01
434 170 0.37
435 181 0.39
436 36 0.08
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (432 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
TTTTTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTC
GATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTT
GTTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTAATTCTA
TTTTTAAATTGGCCCATAACTTTTTAAATGGCTATAATTTAGTACTATTTTTGTATTAATTTCAA
CCTCACAATTTAAAATTAGTTTGATTTGATCCCTCATCAATC
Found at i:3630711 original size:215 final size:217
Alignment explanation
Indices: 3629976--3630896 Score: 1532
Period size: 215 Copynumber: 4.3 Consensus size: 217
3629966 TGATCCCTTT
* **
3629976 TGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCACT
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* *
3630041 TTTTATTTGCATCTGAAATTGACTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAAC
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
*
3630106 -TTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAATATCACAATTTAAAATTA-TT
131 TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTT
3630169 TCGATTTGAT-CCTCATCAATG
196 TCGATTTGATCCCTCATCAATG
3630190 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
3630255 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTA-TTACTATTTTTAAATTGGCCCATAA
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTA-TATTTTTAAATTGGCCCATAA
* *
3630319 CTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACACCACAATTTAAAATTACT
130 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTA--
*
3630384 TTTTTCGATTTGATCCCTCATCAATC
193 -TTTTCGATTTGATCCCTCATCAATG
*
3630410 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
*
3630475 TTTTATTTGCATCTTAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
3630540 TTTTTAAATGGGTATAATTTAGTAC-TTTTTGTATTAATTTCAACATCACAATTTAAAATTA-TT
131 TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTT
3630603 TCGATTTGATCCCTCATCAATG
196 TCGATTTGATCCCTCATCAATG
*
3630625 TGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
* * * * * *
3630690 TTTTATTTGCATCTGAAATTGATCTATACTTATTACTTAATTCTATTTTTTAATTGGCCCATATC
66 TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
* * * *
3630755 TTTTTAAATGGCTATAATTTAGTACTTTTTTTTTATTAATTTCAACCTCACAATTTAAAATTAGT
131 TTTTTAAATGGGTATAATTTAGTAC-TTTTTTGTATTAATTTCAACATCACAATTTAAAATTATT
3630820 TT-GATTTGATCCCTCATCAATG
195 TTCGATTTGATCCCTCATCAATG
* *
3630842 TATGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
3630897 ATTATTAAAT
Statistics
Matches: 668, Mismatches: 28, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
213 2 0.00
214 122 0.18
215 226 0.34
217 106 0.16
218 3 0.00
219 47 0.07
220 159 0.24
221 3 0.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (217 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAAC
TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTT
TCGATTTGATCCCTCATCAATG
Found at i:3631045 original size:435 final size:427
Alignment explanation
Indices: 3629978--3631046 Score: 1072
Period size: 435 Copynumber: 2.5 Consensus size: 427
3629968 ATCCCTTTTG
* * * * **
3629978 TGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCACTTT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAATCATCCAAATT
* *
3630043 TTATTTGCATCTGAAATTG-ACTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAAC-
66 TTATTTGCA-CTAAAATTGAAC-CATACTTATTACTTATTTATATTTTTAAATT---CCATAACA
** ** * * ****** * * * * * * ***
3630106 TTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAATATCACAATTTAAAATTATTTC
126 TTACAAATGGCAATAAATTAGGA-AAGACGGAAATAATTTCAACA-CAAAAATAAAAATTAACCC
*
3630171 GATTTGATCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
189 GATTTGATCCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTG
3630236 TTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTACTAT
254 TTCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTACTAT
*
3630301 TTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACATTTTTGTATTAATTTCAACA
319 TTTTAAATTGGCCCATAACTTTTTAAATGGCTATAATTTAGTACATTTTTGTATTAATTTCAACA
* *
3630366 CCACAATTTAAAATTACTTTTTTCGATTTGATCCCTCATCAATCTG
384 CCACAATTTAAAATTA--TGTTTCGATTTGATCCCTCATCAATCTA
* *
3630412 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAGTCCTCCAAATT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAATCATCCAAATT
* * *
3630477 TTATTTGCATCTTAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTT
66 TTATTTGCA-CTAAAATTGAACCATACTTATTACTTATTTATATTTTTAAATT---CCATAACAT
** ** * * ****** * * * * * ***
3630542 TTTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGA
127 TACAAATGGCAATAAATTAGGAAAGACGGAAATAATTTCAACA-CAAAAATAAAAATTAACCCGA
3630607 TTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGT
191 TTTGAT-CCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGT
* *
3630672 TCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGATCTATACTTATTACTTAATT-CTAT
255 TCAATTTAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTT-ATTACTAT
* * * *
3630736 TTTTTAATTGGCCCATATCTTTTTAAATGGCTATAATTTAGTACTTTTTTTTTATTAATTTCAAC
319 TTTTAAATTGGCCCATAACTTTTTAAATGGCTATAATTTAGTAC-ATTTTTGTATTAATTTCAAC
*
3630801 -CTCACAATTTAAAATTA-GTTT-GATTTGATCCCTCATCAATGTA
383 AC-CACAATTTAAAATTATGTTTCGATTTGATCCCTCATCAATCTA
* *
3630844 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAATTAT-TAAATT
1 TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAATCATCCAAATT
*
3630908 TGTATTTTTCA-TAAAATTGAACCATGA-TTATT--TATATTCTTAGTAATTTACTCTAAA-T-C
66 T-TA-TTTGCACTAAAATTGAACCAT-ACTTATTACT-TA-T-TTA-T-ATTT--T-TAAATTCC
* *
3630967 ATATACAATTACAAATTGCAATTCAACATTCGCGAAAGACGGAAATAA-TT-AATC-CAAAAATA
120 ATA-AC-ATTACAAATGGCAA-T-AA-ATTAG-GAAAGACGGAAATAATTTCAA-CACAAAAATA
3631029 AAAATTAACCCGATTTGA
178 AAAATTAACCCGATTTGA
3631047 ACTCAATCTG
Statistics
Matches: 561, Mismatches: 50, Indels: 47
0.85 0.08 0.07
Matches are distributed among these distances:
429 1 0.00
430 2 0.00
431 24 0.04
432 85 0.15
433 11 0.02
434 178 0.32
435 202 0.36
436 42 0.07
437 10 0.02
438 6 0.01
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (427 bp):
TGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTTATATTTGTTCAATTTAATCATCCAAATT
TTATTTGCACTAAAATTGAACCATACTTATTACTTATTTATATTTTTAAATTCCATAACATTACA
AATGGCAATAAATTAGGAAAGACGGAAATAATTTCAACACAAAAATAAAAATTAACCCGATTTGA
TCCTCATCAATGTGTGTTGTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATT
TAGTCCTCCAAATTTTATTTGCATCTGAAATTGACCCATACTTATTACTTATTACTATTTTTAAA
TTGGCCCATAACTTTTTAAATGGCTATAATTTAGTACATTTTTGTATTAATTTCAACACCACAAT
TTAAAATTATGTTTCGATTTGATCCCTCATCAATCTA
Found at i:3633173 original size:47 final size:49
Alignment explanation
Indices: 3633097--3633216 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 49
3633087 CACGTAGGGG
**
3633097 TATAGCGCGGATCAGGTACCGCGCTATACCTTTA-CTG-CATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACCTGACATAATTTTA
*
3633144 TATAGCGCGGGGCAGGTACTGCGAC-ATACCTTTACTCCTGACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACCTTTA--CCTGACATAATTTTA
3633195 TATAGCGCGGGGCAGGTACCGC
1 TATAGCGCGGGGCAGGTACCGC
3633217 ATTTTGTATA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
47 29 0.45
48 1 0.02
50 3 0.05
51 31 0.48
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (49 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACCTGACATAATTTTA
Found at i:3635120 original size:105 final size:108
Alignment explanation
Indices: 3634925--3635131 Score: 294
Period size: 105 Copynumber: 1.9 Consensus size: 108
3634915 ATTAAAAAAA
* * * **
3634925 TAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTAA
1 TAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAAAATTAATAATAA-TT--ATTAA
* *
3634990 ATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATATT
63 ATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATATT
*
3635036 TAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAAAATTACTAATAA-T-TTAAATT
1 TAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAAAATTAATAATAATTATTAAATT
3635098 AAAACGTTAAAATATTACCGTATCAGCAAAGTGT
66 AAAACGTTAAAATATTACCGTATCAGCAAAGTGT
3635132 AAAGATATAT
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
105 39 0.44
108 1 0.01
110 16 0.18
111 32 0.36
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (108 bp):
TAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAAAATTAATAATAATTATTAAATT
AAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATATT
Found at i:3638758 original size:2 final size:2
Alignment explanation
Indices: 3638747--3639084 Score: 209
Period size: 2 Copynumber: 176.0 Consensus size: 2
3638737 TTTTCATCTA
3638747 AT AT -T AT AT AT AT -T AT AT AGT AT A- AGT AT A- AGT AT A- AGT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT A-T
3638786 AT A- AGT AT AT AT -T AT AT -T AT AT AGT AT AT AT -T AT AT -T AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
3638825 AT -T AT AT -T AT AA AGT A- AT AT -T AT -T TT AT AGT AGT AT -T
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T A-T AT AT
*
3638862 AT -T AT AT AT -T AT AT AT AGT AC AT AGT AGT AT -T AT -T AT AGT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T A-T AT AT AT AT AT A-T
*
3638902 AGT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3638945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
*
3638987 -T AT AT AT -T AT AT AT -T AT AC AT AT ACT -T AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
3639025 AGT AGT AT AGT -T AT AT -T AT AT AT TT AT -T AT TT AT -T A- AT
1 A-T A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3639063 AT AT AT AT TT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
3639085 TATTATTAAT
Statistics
Matches: 273, Mismatches: 17, Indels: 92
0.71 0.04 0.24
Matches are distributed among these distances:
1 32 0.12
2 208 0.76
3 33 0.12
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3639238 original size:39 final size:39
Alignment explanation
Indices: 3639163--3639239 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
3639153 GAAGCCTAAC
* * *
3639163 CGAAGCAAGCCTGACCCAGTAAGCTCGATAAGGCCCAAT
1 CGAAGCAAGCCTGACCCAGAAAGCCCGATAACGCCCAAT
3639202 CGAAGCAAGCCTGACCCAGAAAGCCC-AGTAACGCCCAA
1 CGAAGCAAGCCTGACCCAGAAAGCCCGA-TAACGCCCAA
3639240 GCTCGTCTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.35, C:0.34, G:0.22, T:0.09
Consensus pattern (39 bp):
CGAAGCAAGCCTGACCCAGAAAGCCCGATAACGCCCAAT
Found at i:3639735 original size:12 final size:12
Alignment explanation
Indices: 3639718--3639742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3639708 AATACCCATC
3639718 GGAAAAATCAAG
1 GGAAAAATCAAG
3639730 GGAAAAATCAAG
1 GGAAAAATCAAG
3639742 G
1 G
3639743 CAAGCATCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (12 bp):
GGAAAAATCAAG
Found at i:3639935 original size:13 final size:13
Alignment explanation
Indices: 3639917--3639941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3639907 TTTAGATTCT
3639917 CGGCAGCCGGAGG
1 CGGCAGCCGGAGG
3639930 CGGCAGCCGGAG
1 CGGCAGCCGGAG
3639942 TGGTGGAGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.52, T:0.00
Consensus pattern (13 bp):
CGGCAGCCGGAGG
Found at i:3641364 original size:42 final size:42
Alignment explanation
Indices: 3641310--3641506 Score: 131
Period size: 40 Copynumber: 4.8 Consensus size: 42
3641300 AGTTAACATA
* * **
3641310 TAGCGACGTTTTTACAACAAACGCCGCAATAGGGTGGTTTAT
1 TAGCGACATTTTTACAACAAACGCCGCAATAGAGTGGTAAAT
* * * *
3641352 TA-CGGCGTTTTT-TAACAAACGCCACAATAGAGTGGTAAAT
1 TAGCGACATTTTTACAACAAACGCCGCAATAGAGTGGTAAAT
* *
3641392 TAGCGACATTTATACCACAAACGCCGCAATAGA---GTAACAT
1 TAGCGACATTTTTACAACAAACGCCGCAATAGAGTGGTAA-AT
* * * *
3641432 ATAGTGGC-GTTTTAGCCA-AAACGCCGCAATAGA-TCGGTAAAT
1 -TAGCGACATTTTTA-CAACAAACGCCGCAATAGAGT-GGTAAAT
** * * *
3641474 TAGCGGTATTTATACCACAAACGCCACAATAGA
1 TAGCGACATTTTTACAACAAACGCCGCAATAGA
3641507 TTACACATAT
Statistics
Matches: 124, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
39 4 0.03
40 46 0.37
41 32 0.26
42 38 0.31
43 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (42 bp):
TAGCGACATTTTTACAACAAACGCCGCAATAGAGTGGTAAAT
Found at i:3641441 original size:82 final size:83
Alignment explanation
Indices: 3641361--3641522 Score: 233
Period size: 82 Copynumber: 2.0 Consensus size: 83
3641351 TTACGGCGTT
*
3641361 TTTTA-AC-AAACGCCACAATAGAGT-GGTAAATTAGCGACATTTATACCACAAACGCCGCAATA
1 TTTTAGACAAAACGCCACAATAGA-TCGGTAAATTAGCGACATTTATACCACAAACGCCACAATA
3641423 GAGTA-ACATATAGTGGCG
65 GAGTACACATATAGTGGCG
* * **
3641441 TTTTAGCCAAAACGCCGCAATAGATCGGTAAATTAGCGGTATTTATACCACAAACGCCACAATAG
1 TTTTAGACAAAACGCCACAATAGATCGGTAAATTAGCGACATTTATACCACAAACGCCACAATAG
*
3641506 ATTACACATATAGTGGC
66 AGTACACATATAGTGGC
3641523 ATTTATTCTT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
80 5 0.07
81 2 0.03
82 53 0.74
83 12 0.17
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (83 bp):
TTTTAGACAAAACGCCACAATAGATCGGTAAATTAGCGACATTTATACCACAAACGCCACAATAG
AGTACACATATAGTGGCG
Found at i:3641527 original size:42 final size:41
Alignment explanation
Indices: 3641398--3641609 Score: 152
Period size: 42 Copynumber: 5.1 Consensus size: 41
3641388 AAATTAGCGA
*
3641398 CATTTATACCACAAACGCCGCAATAGAGTAACATATAGTGG
1 CATTTATACCACAAACGCCGCAATAGATTAACATATAGTGG
* *
3641439 CGTTT-TAGCCA-AAACGCCGCAATAGATCGGTAA-AT-TAGCGG
1 CATTTATA-CCACAAACGCCGCAATAGAT---TAACATATAGTGG
* *
3641480 TATTTATACCACAAACGCCACAATAGATTACACATATAGTGG
1 CATTTATACCACAAACGCCGCAATAGATTA-ACATATAGTGG
* * * *
3641522 CATTTATTCTTA-AAACGCCGCAATAG-TGATAATAAATAGTGG
1 CATTTATAC-CACAAACGCCGCAATAGAT--TAACATATAGTGG
* * * * *
3641564 CGTTTTTA-GACAAACGCCGCAAAAGTGTTAATCA-ATAGTGG
1 CATTTATACCACAAACGCCGCAATAG-ATTAA-CATATAGTGG
3641605 CATTT
1 CATTT
3641610 TTAGAAAAAC
Statistics
Matches: 135, Mismatches: 20, Indels: 32
0.72 0.11 0.17
Matches are distributed among these distances:
39 2 0.01
40 19 0.14
41 48 0.36
42 59 0.44
43 7 0.05
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (41 bp):
CATTTATACCACAAACGCCGCAATAGATTAACATATAGTGG
Found at i:3641601 original size:41 final size:41
Alignment explanation
Indices: 3641534--3641692 Score: 214
Period size: 41 Copynumber: 3.9 Consensus size: 41
3641524 TTTATTCTTA
* *
3641534 AAACGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGAC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
* * *
3641575 AAACGCCGCAAAAGTGTTAATCAATAGTGGCATTTTTAGAA
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
* *
3641616 AAACGCTGCAATAGTTTTAATCAATAGTGGCGTTTTTTA-AC
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCG-TTTTTAGAC
* *
3641657 AAACGCCACAATAGTG-TAATCAATAATGGCGTTTTT
1 AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
3641693 TTATAAACGC
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 5 0.05
40 14 0.14
41 78 0.76
42 6 0.06
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (41 bp):
AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAC
Found at i:3641643 original size:82 final size:81
Alignment explanation
Indices: 3641490--3641707 Score: 235
Period size: 82 Copynumber: 2.7 Consensus size: 81
3641480 TATTTATACC
* * * *
3641490 ACAAACGCCACAATAGAT-TACA-CATATAGTGGCATTTATTCTTAAAACGCCGCAATAGTGATA
1 ACAAACGCCACAAAAG-TGTA-ATCA-ATAGTGGCATTT-TTATAAAAACGCTGCAATAGTGATA
3641553 ATAAATAGTGGCG-TTTTTA
62 ATAAATAGTGGCGTTTTTTA
* * **
3641572 GACAAACGCCGCAAAAGTGTTAATCAATAGTGGCATTTTTAGAAAAACGCTGCAATAGTTTTAAT
1 -ACAAACGCCACAAAAGTG-TAATCAATAGTGGCATTTTTATAAAAACGCTGCAATAGTGATAAT
*
3641637 CAATAGTGGCGTTTTTTA
64 AAATAGTGGCGTTTTTTA
* * * * *
3641655 ACAAACGCCACAATAGTGTAATCAATAATGGCGTTTTTTTATAAACGCTGCAA
1 ACAAACGCCACAAAAGTGTAATCAATAGTGGCATTTTTATAAAAACGCTGCAA
3641708 AATGTTAAAT
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
81 30 0.26
82 48 0.42
83 33 0.29
84 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (81 bp):
ACAAACGCCACAAAAGTGTAATCAATAGTGGCATTTTTATAAAAACGCTGCAATAGTGATAATAA
ATAGTGGCGTTTTTTA
Found at i:3652238 original size:21 final size:21
Alignment explanation
Indices: 3652220--3652296 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3652210 ATGAAGCAAG
3652220 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
3652241 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
3652262 GGAAGCAGAGAAAGAAGCAGT
1 GGAAGCAGAGAGAGCAGCAGC
* *
3652283 GGCAGCACAGAGAG
1 GGAAGCAGAGAGAG
3652297 AGGTAGCGGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.39, C:0.18, G:0.40, T:0.03
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:3652908 original size:43 final size:43
Alignment explanation
Indices: 3652672--3652969 Score: 219
Period size: 43 Copynumber: 6.9 Consensus size: 43
3652662 GTTTGTGATA
* ** * *
3652672 AAAACGCCGCAAAAGCTCAAGACATATTGCGGCGTTT-TC-GAC
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTG-C
* * * * * *
3652714 TAAAATGCCGCTAAATCTCAAGACATATTATGCGGCGTTTGT-AGG
1 -AAAACGCCGCTAAATATCAACACCTA-T-TGCGGCGTTTGTCTGC
* ** *
3652759 AAAACGCCGCTAAATATCAACATCT-TCTGCGGCGTTTGTAGGA
1 AAAACGCCGCTAAATATCAACACCTAT-TGCGGCGTTTGTCTGC
* * * * * * **
3652802 AAAACGCCGGTAAAAATAAACATCTACTACGGCGTTTGTGAAG-
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-CTGC
* *
3652845 AAAACGCCGCTAAACATCAACGCCTATTGCGGCGTTTGTCTGC
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGC
* * * * *
3652888 CAAATGCCGTTAAATGTCAACACCTATTGCGGCGTTTTTCTGC
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGC
* *
3652931 AAAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT
3652970 TGAAACAAAC
Statistics
Matches: 206, Mismatches: 41, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
42 14 0.07
43 157 0.76
44 23 0.11
45 10 0.05
46 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (43 bp):
AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTGC
Found at i:3652921 original size:86 final size:85
Alignment explanation
Indices: 3652657--3652969 Score: 242
Period size: 86 Copynumber: 3.6 Consensus size: 85
3652647 CATACATTTA
* * *
3652657 GCGGCGTTTGTGATA-AAAACGCCGCAAAAGC-TCAAGACATATTGCGGCGTTT-TCGACTAAAA
1 GCGGCGTTTGTGA-AGAAAACGCCGCTAAA-CATCAACACCTATTGCGGCGTTTGTCG-C-AAAA
* * *
3652719 TGCCGCTAAATCTCAAGACATATTAT
62 TGCCGCTAAATATCAACACCTA-T-T
* * * * * *
3652745 GCGGCGTTTGT-AGGAAAACGCCGCTAAATATCAACATCT-TCTGCGGCGTTTGTAGGAAAAACG
1 GCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTAT-TGCGGCGTTTGT-CGCAAAATG
* * * * *
3652808 CCGGTAAAAATAAACATCTACT
64 CCGCTAAATATCAACACCTATT
* * *
3652830 ACGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACGCCTATTGCGGCGTTTGTCTGCCAAATGC
1 GCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTC-GCAAAATGC
* *
3652895 CGTTAAATGTCAACACCTATT
65 CGCTAAATATCAACACCTATT
*** * * *
3652916 GCGGCGTTT-TTCTGCAAAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 GCGGCGTTTGTGAAG-AAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGT
3652970 TGAAACAAAC
Statistics
Matches: 176, Mismatches: 40, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
85 13 0.07
86 101 0.57
87 49 0.28
88 12 0.07
89 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (85 bp):
GCGGCGTTTGTGAAGAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCGCAAAATGCC
GCTAAATATCAACACCTATT
Found at i:3653218 original size:22 final size:22
Alignment explanation
Indices: 3653192--3653237 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3653182 ATAAAAATGT
*
3653192 TATAATTTAAATATTTATTTTA
1 TATAATTTAAACATTTATTTTA
3653214 TATAATTTAAACATTTATTTTA
1 TATAATTTAAACATTTATTTTA
3653236 TA
1 TA
3653238 ATTATATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAATTTAAACATTTATTTTA
Found at i:3653434 original size:28 final size:28
Alignment explanation
Indices: 3653376--3653435 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
3653366 TTTAGAAGTG
* **
3653376 TAATAAAAAGATTTTAAACATTTAATTT
1 TAATAAAAAGATTTTAAACATATAAAAT
*
3653404 TAATAAAAA-ATCTTTAAACGTATAAAAT
1 TAATAAAAAGAT-TTTAAACATATAAAAT
3653432 TAAT
1 TAAT
3653436 TTAAGATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (28 bp):
TAATAAAAAGATTTTAAACATATAAAAT
Found at i:3659460 original size:7 final size:7
Alignment explanation
Indices: 3659448--3659520 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
3659438 GATTACACCT
3659448 TAAATCC
1 TAAATCC
3659455 TAAATCC
1 TAAATCC
*
3659462 TAAACCC
1 TAAATCC
3659469 TAAAT-C
1 TAAATCC
3659475 TAAA-CTC
1 TAAATC-C
*
3659482 TAGA-CC
1 TAAATCC
3659488 ATAAA-CC
1 -TAAATCC
3659495 ATAAA-CC
1 -TAAATCC
3659502 ATAAATCC
1 -TAAATCC
3659510 TAAATCC
1 TAAATCC
3659517 TAAA
1 TAAA
3659521 CTATAAACCC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.10
7 50 0.86
8 2 0.03
ACGTcount: A:0.48, C:0.27, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAATCC
Found at i:3659470 original size:14 final size:13
Alignment explanation
Indices: 3659448--3659570 Score: 84
Period size: 14 Copynumber: 8.9 Consensus size: 13
3659438 GATTACACCT
*
3659448 TAAATCCTAAATCC
1 TAAACCCTAAA-CC
*
3659462 TAAACCCTAAATC
1 TAAACCCTAAACC
* *
3659475 TAAACTCTAGACC
1 TAAACCCTAAACC
*
3659488 ATAAACCATAAACC
1 -TAAACCCTAAACC
*
3659502 ATAAATCCTAAATCC
1 -TAAACCCTAAA-CC
**
3659517 TAAACTATAAACCC
1 TAAACCCTAAA-CC
3659531 TAAACCCTAAACC
1 TAAACCCTAAACC
**
3659544 ATAAACAATAAACCC
1 -TAAACCCTAAA-CC
*
3659559 TAAGCCCTAAAC
1 TAAACCCTAAAC
3659571 TCTTTATCTA
Statistics
Matches: 84, Mismatches: 21, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
13 14 0.17
14 66 0.79
15 4 0.05
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (13 bp):
TAAACCCTAAACC
Found at i:3659473 original size:21 final size:20
Alignment explanation
Indices: 3659448--3659549 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 20
3659438 GATTACACCT
3659448 TAAATCCTAAATCCTAAACCC
1 TAAATCCTAAA-CCTAAACCC
* *
3659469 TAAAT-CTAAACTCTAGACCA
1 TAAATCCTAAAC-CTAAACCC
*
3659489 TAAA-CCATAAACCATAAATCC
1 TAAATCC-TAAACC-TAAACCC
*
3659510 TAAATCCTAAACTATAAACCC
1 TAAATCCTAAAC-CTAAACCC
*
3659531 TAAACCCTAAACCATAAAC
1 TAAATCCTAAACC-TAAAC
3659550 AATAAACCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 17 0.26
21 45 0.69
22 2 0.03
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (20 bp):
TAAATCCTAAACCTAAACCC
Found at i:3659527 original size:7 final size:7
Alignment explanation
Indices: 3659485--3659557 Score: 78
Period size: 7 Copynumber: 10.4 Consensus size: 7
3659475 TAAACTCTAG
3659485 ACCATAA
1 ACCATAA
3659492 ACCATAA
1 ACCATAA
3659499 ACCATAA
1 ACCATAA
3659506 ATCC-TAA
1 A-CCATAA
3659513 ATCC-TAA
1 A-CCATAA
*
3659520 ACTATAA
1 ACCATAA
*
3659527 ACCCTAA
1 ACCATAA
*
3659534 ACCCTAA
1 ACCATAA
3659541 ACCATAA
1 ACCATAA
*
3659548 ACAATAA
1 ACCATAA
3659555 ACC
1 ACC
3659558 CTAAGCCCTA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
6 1 0.02
7 55 0.95
8 2 0.03
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (7 bp):
ACCATAA
Found at i:3659569 original size:21 final size:21
Alignment explanation
Indices: 3659488--3659570 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3659478 ACTCTAGACC
*
3659488 ATAAACCATAAACCATAAATC-
1 ATAAACCCTAAACCATAAA-CA
* * * *
3659509 CTAAATCCTAAACTATAAACC
1 ATAAACCCTAAACCATAAACA
*
3659530 CTAAACCCTAAACCATAAACA
1 ATAAACCCTAAACCATAAACA
* *
3659551 ATAAACCCTAAGCCCTAAAC
1 ATAAACCCTAAACCATAAAC
3659571 TCTTTATCTA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (21 bp):
ATAAACCCTAAACCATAAACA
Found at i:3661152 original size:11 final size:11
Alignment explanation
Indices: 3661136--3661174 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3661126 AATAAAACCT
3661136 ATTGAGTTTGA
1 ATTGAGTTTGA
*
3661147 ATTGAGCTTGA
1 ATTGAGTTTGA
*
3661158 ATCGAGTTTGA
1 ATTGAGTTTGA
3661169 ATTGAG
1 ATTGAG
3661175 CTTTAATCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.38
Consensus pattern (11 bp):
ATTGAGTTTGA
Found at i:3661167 original size:22 final size:22
Alignment explanation
Indices: 3661139--3661185 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3661129 AAAACCTATT
3661139 GAGTTTGAATTGAGCTTGAATC
1 GAGTTTGAATTGAGCTTGAATC
*
3661161 GAGTTTGAATTGAGCTTTAATC
1 GAGTTTGAATTGAGCTTGAATC
3661183 GAG
1 GAG
3661186 CTCGAGTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.36
Consensus pattern (22 bp):
GAGTTTGAATTGAGCTTGAATC
Found at i:3668285 original size:18 final size:18
Alignment explanation
Indices: 3668259--3668297 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3668249 TTTTTATTTC
* *
3668259 TTCAACTCTCTGGCATCT
1 TTCAACTCTCCGACATCT
*
3668277 TTCAGCTCTCCGACATCT
1 TTCAACTCTCCGACATCT
3668295 TTC
1 TTC
3668298 TTGTTGGACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.36, G:0.10, T:0.38
Consensus pattern (18 bp):
TTCAACTCTCCGACATCT
Found at i:3669308 original size:40 final size:39
Alignment explanation
Indices: 3669264--3669348 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 39
3669254 AAAATTAAAT
* *
3669264 AAATAAATACACAAATAATACAAGAATAATAAAAGATTGA
1 AAATAAATAAACAAATAATACAAGAATAAT-AAAGATTAA
* * *
3669304 AAATAAATAAATAAATAATTCAAGAATAATAATGATTAA
1 AAATAAATAAACAAATAATACAAGAATAATAAAGATTAA
3669343 AAATAA
1 AAATAA
3669349 TTATGATGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 13 0.32
40 27 0.68
ACGTcount: A:0.66, C:0.05, G:0.06, T:0.24
Consensus pattern (39 bp):
AAATAAATAAACAAATAATACAAGAATAATAAAGATTAA
Found at i:3670532 original size:341 final size:341
Alignment explanation
Indices: 3669909--3670593 Score: 1219
Period size: 341 Copynumber: 2.0 Consensus size: 341
3669899 CATACTTAAC
* *
3669909 ATGAAGAAGAAAGAAAATAAATTAAAGAAGATGAAGAAGAAAAATAATATTTATTAAAATCTCAA
1 ATGAAGAAGAAAGAAAAGAAAATAAAGAAGATGAAGAAGAAAAATAATATTTATTAAAATCTCAA
* * *
3669974 AGCTAATTAAAGCCAAGAAAACAATACATTTATCAAGCTTCACTCTTGGGCGATTACACCAAAAA
66 AGCTAATTAAAGCCAAGAAAACAATACATTTATCAAGCATCACCCCTGGGCGATTACACCAAAAA
* * *
3670039 ATCACCCTTTATAACTTTAATTACCTGTCAGACATCATTTCATCTTTATTTATTGATTTAACACC
131 ATCACCCTTTAAAACTTTAATTACCTATCAGACATCATTTCATCTTTATTTATTGATCTAACACC
*
3670104 CTTTTGCAGGAAGTCACGTCTCATTCACCGCGCCTTACGCTGATGTGGCACCATGTGGGGGTAAG
196 CTTTTGCAGGAAGTCACGTCTCATTCACCGCGCCTTACGCTGATGTGGCACCACGTGGGGGTAAG
*
3670169 GCGCGGCCCATGCACGCGCCTGGTGAAACGTGTAAAAAATTAGATGTTAGTTTAGTAAATATTTT
261 GCGCGGCCCATGCACGCGCCTGGTGAAACGTGTAAAAAATTAGACGTTAGTTTAGTAAATATTTT
*
3670234 TAAAATTGTGTCTAAT
326 TAAAATGGTGTCTAAT
3670250 ATGAAGAAGAAAGAAAAGAAAATAAAGAAGATGAAGAAGAAAAATAATATTTATTAAAATCTCAA
1 ATGAAGAAGAAAGAAAAGAAAATAAAGAAGATGAAGAAGAAAAATAATATTTATTAAAATCTCAA
*
3670315 AGCTAATTAAAGCCAAGAAAACAATACATTTATCAAGCATCACCCCTGGGCGATTACACCGAAAA
66 AGCTAATTAAAGCCAAGAAAACAATACATTTATCAAGCATCACCCCTGGGCGATTACACCAAAAA
*
3670380 ATCATCCTTTAAAACTTTAATTACCTATCAGACATCATTTCATCTTTATTTATTGATCTAACACC
131 ATCACCCTTTAAAACTTTAATTACCTATCAGACATCATTTCATCTTTATTTATTGATCTAACACC
* *
3670445 C-TTTGCAGGAAGTCACGTCTCATTCACCGCGTCTTACGCTGATGTGGCGCCACGTGGGGGTAAG
196 CTTTTGCAGGAAGTCACGTCTCATTCACCGCGCCTTACGCTGATGTGGCACCACGTGGGGGTAAG
3670509 GCGCGGCCCATGCACCGCGCCTGGTGAAACGTGTAAAAAATTAGACGTTAGTTTAGTAAATATTT
261 GCGCGGCCCATGCA-CGCGCCTGGTGAAACGTGTAAAAAATTAGACGTTAGTTTAGTAAATATTT
3670574 TTAAAATGGTGTCTAAT
325 TTAAAATGGTGTCTAAT
3670591 ATG
1 ATG
3670594 TAATTAATTT
Statistics
Matches: 328, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
340 74 0.23
341 254 0.77
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (341 bp):
ATGAAGAAGAAAGAAAAGAAAATAAAGAAGATGAAGAAGAAAAATAATATTTATTAAAATCTCAA
AGCTAATTAAAGCCAAGAAAACAATACATTTATCAAGCATCACCCCTGGGCGATTACACCAAAAA
ATCACCCTTTAAAACTTTAATTACCTATCAGACATCATTTCATCTTTATTTATTGATCTAACACC
CTTTTGCAGGAAGTCACGTCTCATTCACCGCGCCTTACGCTGATGTGGCACCACGTGGGGGTAAG
GCGCGGCCCATGCACGCGCCTGGTGAAACGTGTAAAAAATTAGACGTTAGTTTAGTAAATATTTT
TAAAATGGTGTCTAAT
Found at i:3671353 original size:333 final size:329
Alignment explanation
Indices: 3670724--3671723 Score: 1611
Period size: 333 Copynumber: 3.0 Consensus size: 329
3670714 AACTCTATAA
*
3670724 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAAGGTAAG
1 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAG
* *
3670789 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTACAAAATGATGAT
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCATTATTTCTTTTACAAAATGATGAT
3670854 GATGATGATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAATTTATTG
131 GATGATGATAAATATTTTATAATTTAAAAAATTATAAATTT-ATATATTTTTGAAAAATTTATTG
3670919 ACTTTTAAAATTAATTGTTTAAAATATAATAAATATTAAAATAAACTTTTAATTACAATTGAGGG
195 ACTTTTAAAATTAATTGTTTAAAA-AT-AT-AATATTAAAATAAACTTTTAATTACAATTGA-GG
* *
3670984 ATCAAATGAATTATTATTCATTAATTGTTA-TTTTAACAACAGTTAATAATGTTTATTTATTTTT
256 ATCAAATGAATTATTATTCATTAATTATTATTTTTAACAACAGTTAATAATGTTTATTCATTTTT
3671048 AATAAAATT
321 AATAAAATT
* *
3671057 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGTAAAACTTTGAGGGTAAA
1 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAG
3671122 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCATTATTTCTTTTACAAAATGATGAT
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCATTATTTCTTTTACAAAATGATGAT
3671187 GATGATGATAATAAATATTTTATAATTTAAAAAATTATAAACTTTATATATTTTTGAAAAATTTA
131 GATGATG---ATAAATATTTTATAATTTAAAAAATTATAAA-TTTATATATTTTTGAAAAATTTA
* *
3671252 TTGACTTTTAAAATTAATTGTTTAAAAATAT-TTATTAAAATAAAATTTTAATTACAATTGATGG
192 TTGACTTTTAAAATTAATTGTTTAAAAATATAATATTAAAATAAACTTTTAATTACAATTGA-GG
3671316 ATCAAATGAATTATTATTCATTAATTATTATTTTTAACAACAGTTAATAATGTTTATTCATTTTT
256 ATCAAATGAATTATTATTCATTAATTATTATTTTTAACAACAGTTAATAATGTTTATTCATTTTT
3671381 AATAAAATT
321 AATAAAATT
* *
3671390 ATTTTGATTTATGCATGAAATTACACAATACATATAATCTAGTTTAGGAAAACTTTGAGGGTAAG
1 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAG
3671455 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCATTATTTCTTTTAC-AAA--ATGAT
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCATTATTTCTTTTACAAAATGATGAT
*
3671517 GATGATGATAAATATTTTATAATTTAAAAAATTATAAATTTTATATATTTTTAAAAAATTTATTG
131 GATGATGATAAATATTTTATAATTTAAAAAATTATAAA-TTTATATATTTTTGAAAAATTTATTG
3671582 ACTTTT--AATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTGAGA
195 ACTTTTAAAATTAATTGTTTAAAAATAT----AATATTAAAATAAACTTTTAATTACAATTGAG-
* * * * *
3671645 TATCAAATGAATTATTATTTATTTATTATT-TTTTAATAACATAACAGTTAATAATATTTACTCA
255 GATCAAATGAATTATTATTCATTAATTATTATTTT--TAAC--AACAGTTAATAATGTTTATTCA
3671709 TTTTTAATAAAATT
316 TTTTTAATAAAATT
3671723 A
1 A
3671724 GAATTTAATA
Statistics
Matches: 629, Mismatches: 23, Indels: 30
0.92 0.03 0.04
Matches are distributed among these distances:
325 20 0.03
327 62 0.10
329 5 0.01
330 67 0.11
331 4 0.01
332 62 0.10
333 324 0.52
334 2 0.00
335 2 0.00
336 78 0.12
337 3 0.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (329 bp):
ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAG
TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCATTATTTCTTTTACAAAATGATGAT
GATGATGATAAATATTTTATAATTTAAAAAATTATAAATTTATATATTTTTGAAAAATTTATTGA
CTTTTAAAATTAATTGTTTAAAAATATAATATTAAAATAAACTTTTAATTACAATTGAGGATCAA
ATGAATTATTATTCATTAATTATTATTTTTAACAACAGTTAATAATGTTTATTCATTTTTAATAA
AATT
Found at i:3671554 original size:26 final size:27
Alignment explanation
Indices: 3671524--3671576 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3671514 GATGATGATG
3671524 ATAAATATTT-TATA-ATTTAAAAAATT
1 ATAAAT-TTTATATATATTTAAAAAATT
*
3671550 ATAAATTTTATATATTTTTAAAAAATT
1 ATAAATTTTATATATATTTAAAAAATT
3671577 TATTGACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 10 0.42
27 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAATTTTATATATATTTAAAAAATT
Found at i:3672926 original size:31 final size:30
Alignment explanation
Indices: 3672855--3672927 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
3672845 TGCTGATGAA
* **
3672855 AATGAAGAAGCTGGGCTTGCTGACAATTGG
1 AATGAAGAAGCTGGGCTTGCTAACAACGGG
*
3672885 AACGAAGAAGCTGGGCTTGCTTAACAACGGG
1 AATGAAGAAGCTGGGCTTGC-TAACAACGGG
3672916 AATGAAGAAGCT
1 AATGAAGAAGCT
3672928 AGGTTTTCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.19
Consensus pattern (30 bp):
AATGAAGAAGCTGGGCTTGCTAACAACGGG
Found at i:3672976 original size:30 final size:30
Alignment explanation
Indices: 3672940--3672997 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3672930 GTTTTCTGAC
3672940 CTTGCTGACAACGTGG-ATGAAGAAGCTAAG
1 CTTGCTGACAACG-GGAATGAAGAAGCTAAG
* *
3672970 CTTGCTGACAATGGGAATGAAGATGCTA
1 CTTGCTGACAACGGGAATGAAGAAGCTA
3672998 TACCGAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (30 bp):
CTTGCTGACAACGGGAATGAAGAAGCTAAG
Found at i:3680424 original size:21 final size:21
Alignment explanation
Indices: 3680400--3680442 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3680390 GCTGTGGCCA
*
3680400 GCCA-ACATTAGAGTGAGACAT
1 GCCATACA-TAGAGGGAGACAT
*
3680421 GCCATTCATAGAGGGAGACAT
1 GCCATACATAGAGGGAGACAT
3680442 G
1 G
3680443 GGTGGAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.19
Consensus pattern (21 bp):
GCCATACATAGAGGGAGACAT
Found at i:3681794 original size:20 final size:20
Alignment explanation
Indices: 3681771--3681811 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3681761 ACATATAATC
3681771 CAATATTGC-ATAAAATATTA
1 CAATATT-CAATAAAATATTA
*
3681791 CAATATTCAATAAGATATTA
1 CAATATTCAATAAAATATTA
3681811 C
1 C
3681812 TGGATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (20 bp):
CAATATTCAATAAAATATTA
Found at i:3684737 original size:13 final size:13
Alignment explanation
Indices: 3684719--3684744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3684709 AACAACAGAC
3684719 AGTATCGATACTT
1 AGTATCGATACTT
3684732 AGTATCGATACTT
1 AGTATCGATACTT
3684745 CTCTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
AGTATCGATACTT
Found at i:3693945 original size:24 final size:25
Alignment explanation
Indices: 3693913--3693959 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3693903 CTATTCTTTC
3693913 GCTTCAATCAAGC-TCGAATTTTAA
1 GCTTCAATCAAGCTTCGAATTTTAA
* *
3693937 GCTTCAATCGAGCTTCTAATTTT
1 GCTTCAATCAAGCTTCGAATTTT
3693960 TTTTTTGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (25 bp):
GCTTCAATCAAGCTTCGAATTTTAA
Found at i:3694262 original size:18 final size:18
Alignment explanation
Indices: 3694220--3694254 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3694210 CCGGTTCGAA
3694220 CGGTTCAGCGGTTCTGGC
1 CGGTTCAGCGGTTCTGGC
3694238 CGGTTCAGCGGTTCTGG
1 CGGTTCAGCGGTTCTGG
3694255 TTGGTTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.26, G:0.40, T:0.29
Consensus pattern (18 bp):
CGGTTCAGCGGTTCTGGC
Found at i:3697831 original size:26 final size:26
Alignment explanation
Indices: 3697803--3697852 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3697793 TTGTGTGTTT
*
3697803 TTTTTAAA-AAAATATATAATTTTAA
1 TTTTTAAATAAAATATATAAATTTAA
*
3697828 TTTTTAAATAAAATATTTAAATTTA
1 TTTTTAAATAAAATATATAAATTTA
3697853 TCATATGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTTAAATAAAATATATAAATTTAA
Found at i:3702150 original size:2 final size:2
Alignment explanation
Indices: 3702143--3702167 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3702133 ATGATCAGTT
3702143 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3702168 TGATAAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3705408 original size:22 final size:22
Alignment explanation
Indices: 3705380--3705421 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3705370 TTGATTATTT
3705380 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
3705402 TATTATATTATTATAAATAT
1 TATTATAATATTAAAAATAT
3705422 TTTTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:3705741 original size:42 final size:42
Alignment explanation
Indices: 3705647--3705730 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
3705637 TTCCTTCAGC
* * * *
3705647 CAAACACTGGAAAACATTTTTATAAAAATGAATTACGTGAAA
1 CAAACACGGGAAAACATTTTTAGAAAAACGAATTACATGAAA
* *
3705689 CAAACACGGGAAAATATTTTTCGAAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTTTTAGAAAAACGAATTACATGAAA
3705731 TAAGTACGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (42 bp):
CAAACACGGGAAAACATTTTTAGAAAAACGAATTACATGAAA
Found at i:3713341 original size:29 final size:29
Alignment explanation
Indices: 3713295--3713353 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
3713285 GTATAAAGAT
3713295 TAATCAAACTATCAATTTTTTTAAAAAAAA
1 TAATCAAACTATCAA-TTTTTTAAAAAAAA
* * *
3713325 TAATC-AAGTATCGATTTTTTAAAATAAA
1 TAATCAAACTATCAATTTTTTAAAAAAAA
3713353 T
1 T
3713354 TAAGTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 14 0.54
29 7 0.27
30 5 0.19
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.39
Consensus pattern (29 bp):
TAATCAAACTATCAATTTTTTAAAAAAAA
Found at i:3723087 original size:31 final size:31
Alignment explanation
Indices: 3723049--3723112 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3723039 ATGCTAAACC
3723049 TTCTATAGTGGCAGTAGATTGTTCTTATCAT
1 TTCTATAGTGGCAGTAGATTGTTCTTATCAT
3723080 TTCTATAGTGGCAGTAGATTGTTCTTATCAT
1 TTCTATAGTGGCAGTAGATTGTTCTTATCAT
3723111 TT
1 TT
3723113 GTAGGACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (31 bp):
TTCTATAGTGGCAGTAGATTGTTCTTATCAT
Found at i:3734295 original size:14 final size:15
Alignment explanation
Indices: 3734264--3734296 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3734254 ATACCATGTT
3734264 GAAAACAGACTGTGTA
1 GAAAACAGAC-GTGTA
3734280 GAAAACAGAC-TGTA
1 GAAAACAGACGTGTA
3734294 GAA
1 GAA
3734297 TACTTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.15
Consensus pattern (15 bp):
GAAAACAGACGTGTA
Found at i:3745630 original size:3 final size:3
Alignment explanation
Indices: 3745622--3745654 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3745612 TTTTCCCTGA
*
3745622 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3745655 TTGTAATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3762146 original size:173 final size:164
Alignment explanation
Indices: 3761839--3762161 Score: 565
Period size: 173 Copynumber: 1.9 Consensus size: 164
3761829 CCGTTATATG
3761839 TAAAGTTTGTTTAATGTATCGACCTTTGTGTTCAATGAAAGTTGTTAAGATGGTCACTGGAATGA
1 TAAAGTTTGTTTAATGTATCGACCTTTGTGTTCAATGAAAGTTGTTAAGATGGTCACTGGAATGA
3761904 CACCTTTGTATTTGCATTTGGCATTTGCATTAATGTATTTATTAAGCATTTTACATGCATTAATT
66 CACCTTTGTATTTGCATTTGGCATTTGCATTAATGTATTTATTAAGCATTTTACATGCATTAATT
3761969 ATAAAAACATAGAAATAATTGAAGTTGTCAGTAA
131 ATAAAAACATAGAAATAATTGAAGTTGTCAGTAA
3762003 TAAAGTTTGTTTAATGTATCGAGACCTTTGTGTTCAATGAAAGTTGTTTTAAGATGGTCACTCTG
1 TAAAGTTTGTTTAATGTATC--GACCTTTGTGTTCAATGAAAGTTG--TTAAGATGGTCA--CTG
3762068 GAATGACACCTTTTGTATTTGCATTTGGCATTTGCATTACATGTATTTATTTAAGCATTTTACAT
60 GAATGACACC-TTTGTATTTGCATTTGGCATTTGCATTA-ATGTATTTA-TTAAGCATTTTACAT
3762133 GCATTAATTATAAAAACATAGAAATAATT
122 GCATTAATTATAAAAACATAGAAATAATT
3762162 TATGGAAGGT
Statistics
Matches: 150, Mismatches: 0, Indels: 9
0.94 0.00 0.06
Matches are distributed among these distances:
164 20 0.13
166 24 0.16
168 12 0.08
170 13 0.09
171 28 0.19
172 9 0.06
173 44 0.29
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (164 bp):
TAAAGTTTGTTTAATGTATCGACCTTTGTGTTCAATGAAAGTTGTTAAGATGGTCACTGGAATGA
CACCTTTGTATTTGCATTTGGCATTTGCATTAATGTATTTATTAAGCATTTTACATGCATTAATT
ATAAAAACATAGAAATAATTGAAGTTGTCAGTAA
Found at i:3766433 original size:42 final size:42
Alignment explanation
Indices: 3766371--3766460 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
3766361 ACTTAGTAAG
* *
3766371 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATAATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATAATGATTAAA
* *
3766413 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATAATGATTAAA
3766455 TCCTTC
1 TCCTTC
3766461 GGGTAATTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATAATGATTAAA
Found at i:3766521 original size:80 final size:80
Alignment explanation
Indices: 3766422--3766593 Score: 326
Period size: 80 Copynumber: 2.1 Consensus size: 80
3766412 ATCCTTCAGG
3766422 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
3766487 AGTAGTGAAGCAAAC
66 AGTAGTGAAGCAAAC
*
3766502 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
*
3766567 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAC
3766582 CCATCAGTAAGT
1 CCATCAGTAAGT
3766594 GCCATCAGTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 90 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
AGTAGTGAAGCAAAC
Found at i:3766600 original size:13 final size:13
Alignment explanation
Indices: 3766582--3766606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3766572 TGAAGCAAAT
3766582 CCATCAGTAAGTG
1 CCATCAGTAAGTG
3766595 CCATCAGTAAGT
1 CCATCAGTAAGT
3766607 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:3766664 original size:42 final size:41
Alignment explanation
Indices: 3766594--3766674 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
3766584 ATCAGTAAGT
* *
3766594 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAG
1 GCCATCAGTAAGTCGTTCGAGCAAGATGAT-AAATCCTTCAG
*
3766636 GCCATCAGTAAGTCGTTCGGGCAAGATGATAAATCCTTC
1 GCCATCAGTAAGTCGTTCGAGCAAGATGATAAATCCTTC
3766675 GTGTCATCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 9 0.25
42 27 0.75
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
GCCATCAGTAAGTCGTTCGAGCAAGATGATAAATCCTTCAG
Found at i:3766689 original size:41 final size:42
Alignment explanation
Indices: 3766594--3766696 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
3766584 ATCAGTAAGT
* * *
3766594 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAG
1 GCCATCAGTAAGTCCTTCGGGCAAGATGATGAAATCCTTCAG
*
3766636 GCCATCAGTAAGTCGTTCGGGCAAGATGAT-AAATCCTTC-G
1 GCCATCAGTAAGTCCTTCGGGCAAGATGATGAAATCCTTCAG
*
3766676 TGTCATCCA-TAAGTCCTTCGG
1 -GCCAT-CAGTAAGTCCTTCGG
3766697 ATAGGATGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 24 0.44
42 29 0.54
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
GCCATCAGTAAGTCCTTCGGGCAAGATGATGAAATCCTTCAG
Found at i:3767201 original size:53 final size:53
Alignment explanation
Indices: 3767115--3767427 Score: 403
Period size: 53 Copynumber: 5.9 Consensus size: 53
3767105 AGAATTACAC
*
3767115 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* ** *
3767168 CAGACGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACTTGTGGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
3767221 CAGAAGATTGTTCGAGTTATACCCCCTGAAGCAAGAGGTAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * * *
3767274 AAAAAGATTGTTCGAGTTCTACTCCTTGAAGCAAAAAGGAGCGAACCCGTAGA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
3767327 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGTGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* ** * * *
3767380 AAGAAGATAT-TTTTAGTTCTATTCCTTGAAGCAAGAGGGAGGGAACCC
1 CAGAAGAT-TGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
3767428 ACTGGTTGAA
Statistics
Matches: 225, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 224 1.00
54 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:3770060 original size:21 final size:21
Alignment explanation
Indices: 3769966--3770061 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
3769956 CACACTCCTT
*
3769966 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATTCCA
*
3769987 AAGGACCA-A-ATATATGTCTCG
1 AAGGACCACATATATAT-TC-CA
* * *
3770008 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATATTCCA
** *
3770029 AAGGATTACATATATATCTCGA
1 AAGGACCACATATATAT-TCCA
3770051 AA-GACCACATA
1 AAGGACCACATA
3770062 GAACCCTCGA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
19 6 0.11
20 3 0.05
21 34 0.61
22 8 0.14
23 5 0.09
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (21 bp):
AAGGACCACATATATATTCCA
Found at i:3771568 original size:20 final size:20
Alignment explanation
Indices: 3771543--3771594 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3771533 TTTTCATGGG
3771543 GTATCGATACC-TGAAAGGT-A
1 GTATCGATACCAT--AAGGTAA
3771563 GTATCGATACCATAAGGTAA
1 GTATCGATACCATAAGGTAA
3771583 GTATCGATACCA
1 GTATCGATACCA
3771595 ATTTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.17
20 24 0.80
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (20 bp):
GTATCGATACCATAAGGTAA
Found at i:3772517 original size:30 final size:30
Alignment explanation
Indices: 3772481--3772537 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3772471 AAGGGTTACC
* *
3772481 TATGTCCTTCGGGGCATATGGATAGGTACA
1 TATGTCCTTCGGGACATATAGATAGGTACA
3772511 TATGTCCTTCGGGACATATAGATAGGT
1 TATGTCCTTCGGGACATATAGATAGGT
3772538 CTTTCGGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (30 bp):
TATGTCCTTCGGGACATATAGATAGGTACA
Found at i:3773083 original size:2 final size:2
Alignment explanation
Indices: 3773041--3773068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3773031 AAGTATAAGA
3773041 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
3773069 TAGATAAGTT
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:3775218 original size:15 final size:16
Alignment explanation
Indices: 3775198--3775229 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3775188 GACGTCATCT
3775198 AAAATATTA-AAAAAA
1 AAAATATTATAAAAAA
3775213 AAAATATTATAAAAAA
1 AAAATATTATAAAAAA
3775229 A
1 A
3775230 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATATTATAAAAAA
Found at i:3775243 original size:19 final size:19
Alignment explanation
Indices: 3775206--3775244 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3775196 CTAAAATATT
*
3775206 AAAAAAAAAAATATTATAA
1 AAAAAAAAAAATATAATAA
3775225 AAAAATAAAAAATA-AATAA
1 AAAAA-AAAAAATATAATAA
3775244 A
1 A
3775245 TTTATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAAAAAAATATAATAA
Found at i:3775315 original size:291 final size:294
Alignment explanation
Indices: 3774738--3775325 Score: 1065
Period size: 294 Copynumber: 2.0 Consensus size: 294
3774728 AATAGAATTA
3774738 TAAATATCAAATATCAAAGTTATATATATAAAGTTAAAAAGATTCAAAAAAATAATAATAATTTC
1 TAAATATCAAATATCAAAGTTATATATATAAAGTTAAAAAGATTCAAAAAAATAATAATAATTTC
3774803 GTATGTCATACCGCGAATCGACCAACAATGTCAATCCTAATCCGTATATCTCGTGCAGTGGCACA
66 GTATGTCATACCGCGAATCGACCAACAATGTCAATCCTAATCCGTATATCTCGTGCAGTGGCACA
* *
3774868 TGCGAAGTTCTTCTCAGAGATTTTATGACGTCATCTAAAATATTTAAAAATAAAAAATTATTATA
131 TGCCAAGTTCGTCTCAGAGATTTTATGACGTCATCTAAAATATTTAAAAATAAAAAATTATTATA
*
3774933 AACAAATAAAAAATAAATAAATTTATGAAATTAAAAAAGTTAAATAAATGAAGTTAAACAATTAC
196 AAAAAATAAAAAATAAATAAATTTATGAAATTAAAAAAGTTAAATAAATGAAGTTAAACAATTAC
*
3774998 CTTCCAGTCAGCGGAAACTTGACAGAGGCATCTG
261 CTTCCAGTCAGCGGAAACTCGACAGAGGCATCTG
*
3775032 TAAATATCAAATATCAAAGTTATATATATAAAGTTAAAAAGATTCAAAATAATAATAATAATTTC
1 TAAATATCAAATATCAAAGTTATATATATAAAGTTAAAAAGATTCAAAAAAATAATAATAATTTC
* * * * *
3775097 GTATGTCATACCGTGAATCGACCAACAATGTCGATCCTCATCCGTATGTCTCGTGCAGTGGCACC
66 GTATGTCATACCGCGAATCGACCAACAATGTCAATCCTAATCCGTATATCTCGTGCAGTGGCACA
3775162 TGCCAAGTTCGTCTCAGAGATTTTATGACGTCATCTAAAATA-TTAAAAA-AAAAAA-TATTATA
131 TGCCAAGTTCGTCTCAGAGATTTTATGACGTCATCTAAAATATTTAAAAATAAAAAATTATTATA
3775224 AAAAAATAAAAAATAAATAAATTTATGAAATTAAAAAAGTTAAATAAATGAAGTTAAACAATTAC
196 AAAAAATAAAAAATAAATAAATTTATGAAATTAAAAAAGTTAAATAAATGAAGTTAAACAATTAC
3775289 CTTCCAGTCAGCGGAAACTCGACAGAGGCATCTG
261 CTTCCAGTCAGCGGAAACTCGACAGAGGCATCTG
3775323 TAA
1 TAA
3775326 TTGGCATAAA
Statistics
Matches: 284, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
291 107 0.38
292 6 0.02
293 7 0.02
294 164 0.58
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (294 bp):
TAAATATCAAATATCAAAGTTATATATATAAAGTTAAAAAGATTCAAAAAAATAATAATAATTTC
GTATGTCATACCGCGAATCGACCAACAATGTCAATCCTAATCCGTATATCTCGTGCAGTGGCACA
TGCCAAGTTCGTCTCAGAGATTTTATGACGTCATCTAAAATATTTAAAAATAAAAAATTATTATA
AAAAAATAAAAAATAAATAAATTTATGAAATTAAAAAAGTTAAATAAATGAAGTTAAACAATTAC
CTTCCAGTCAGCGGAAACTCGACAGAGGCATCTG
Found at i:3791038 original size:21 final size:20
Alignment explanation
Indices: 3791014--3791053 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3791004 TTTGGTCATC
*
3791014 TAATTTTTAAAATTTATAATA
1 TAATTATTAAAATTT-TAATA
*
3791035 TAATTATTAAACTTTTAAT
1 TAATTATTAAAATTTTAAT
3791054 TCGTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTATTAAAATTTTAATA
Found at i:3803446 original size:21 final size:19
Alignment explanation
Indices: 3803404--3803449 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
3803394 CGGAGGAGAA
3803404 GAGGAAGAAAACGGAAGAG
1 GAGGAAGAAAACGGAAGAG
3803423 GAGGAAGAACGAA-GGAATGAG
1 GAGGAAGAA--AACGGAA-GAG
3803444 GAGGAA
1 GAGGAA
3803450 TTGGGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
21 11 0.46
ACGTcount: A:0.50, C:0.04, G:0.43, T:0.02
Consensus pattern (19 bp):
GAGGAAGAAAACGGAAGAG
Found at i:3803869 original size:33 final size:33
Alignment explanation
Indices: 3803827--3803890 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
3803817 AATCTATAAC
3803827 AGAAGATAAGGTAGAAACACATGATAGCTACTA
1 AGAAGATAAGGTAGAAACACATGATAGCTACTA
*
3803860 AGAAGATAAGGTAGAAACACATTATAGCTAC
1 AGAAGATAAGGTAGAAACACATGATAGCTAC
3803891 CTCATAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.19
Consensus pattern (33 bp):
AGAAGATAAGGTAGAAACACATGATAGCTACTA
Found at i:3809553 original size:24 final size:25
Alignment explanation
Indices: 3809526--3809579 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 25
3809516 CATATAAGTA
3809526 TGAATGCTATTATAATAATT-AAAT
1 TGAATGCTATTATAATAATTAAAAT
3809550 TGAATGCTATTATAATAATTAAAAT
1 TGAATGCTATTATAATAATTAAAAT
3809575 TGAAT
1 TGAAT
3809580 ACCAATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (25 bp):
TGAATGCTATTATAATAATTAAAAT
Found at i:3809590 original size:25 final size:24
Alignment explanation
Indices: 3809536--3809590 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
3809526 TGAATGCTAT
* * *
3809536 TATAATAATTAAATTGAATGCTAT
1 TATAATAATTAAATTGAATACCAA
3809560 TATAATAATTAAAATTGAATACCAA
1 TATAATAATT-AAATTGAATACCAA
*
3809585 TCTAAT
1 TATAAT
3809591 GTGAATGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (24 bp):
TATAATAATTAAATTGAATACCAA
Found at i:3831265 original size:39 final size:39
Alignment explanation
Indices: 3831222--3831333 Score: 199
Period size: 39 Copynumber: 2.9 Consensus size: 39
3831212 ATTTCCATAG
3831222 CTTTGTTGGCTCAAATCAGCATTGTACATGTTTATGTTC
1 CTTTGTTGGCTCAAATCAGCATTGTACATGTTTATGTTC
*
3831261 CTTTGTTGGCTCAAATCAGCATTGTGCATGTTTATGTTC
1 CTTTGTTGGCTCAAATCAGCATTGTACATGTTTATGTTC
3831300 CTTTGTTGGCTCAAATCAGCATTGTA-ATTGTTTA
1 CTTTGTTGGCTCAAATCAGCATTGTACA-TGTTTA
3831334 CATTCCTTAC
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
38 1 0.01
39 69 0.99
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.44
Consensus pattern (39 bp):
CTTTGTTGGCTCAAATCAGCATTGTACATGTTTATGTTC
Found at i:3832637 original size:2 final size:2
Alignment explanation
Indices: 3832630--3832657 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3832620 GTCAATATTA
3832630 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
3832658 TGATTAAGCT
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:3836807 original size:29 final size:29
Alignment explanation
Indices: 3836766--3836860 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 29
3836756 GTTTTATTCA
3836766 AAATAAACACTTAATACCCTTTTACGTCC
1 AAATAAACACTTAATACCCTTTTACGTCC
* * *
3836795 AAATAAGCCCTTAA-ACTGTGCCGTTTTA--TTC
1 AAATAAACACTTAATAC----CC-TTTTACGTCC
3836826 AAATAAACACTTAATACCCTTTTACGTCC
1 AAATAAACACTTAATACCCTTTTACGTCC
3836855 AAATAA
1 AAATAA
3836861 TTAACTAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
27 5 0.10
28 4 0.08
29 20 0.38
31 14 0.27
32 4 0.08
33 5 0.10
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (29 bp):
AAATAAACACTTAATACCCTTTTACGTCC
Found at i:3836857 original size:60 final size:61
Alignment explanation
Indices: 3836735--3836860 Score: 236
Period size: 60 Copynumber: 2.1 Consensus size: 61
3836725 CTATTACACT
*
3836735 AATAAGCCCTTAAACTGTGTCGTTTTATTCAAAATAAACACTTAATACCCTTTTACGTCCA
1 AATAAGCCCTTAAACTGTGCCGTTTTATTCAAAATAAACACTTAATACCCTTTTACGTCCA
3836796 AATAAGCCCTTAAACTGTGCCGTTTTATTC-AAATAAACACTTAATACCCTTTTACGTCCA
1 AATAAGCCCTTAAACTGTGCCGTTTTATTCAAAATAAACACTTAATACCCTTTTACGTCCA
3836856 AATAA
1 AATAA
3836861 TTAACTAGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 35 0.55
61 29 0.45
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (61 bp):
AATAAGCCCTTAAACTGTGCCGTTTTATTCAAAATAAACACTTAATACCCTTTTACGTCCA
Found at i:3839631 original size:16 final size:18
Alignment explanation
Indices: 3839591--3839633 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
3839581 CTAAAAAATT
3839591 TAAT-TTTTTATTTGCTTA
1 TAATATTTTTATTT-CTTA
3839609 TAATATTTTTATTT-TTA
1 TAATATTTTTATTTCTTA
3839626 -AATATTTT
1 TAATATTTT
3839634 AGATGATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 4 0.17
19 9 0.38
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TAATATTTTTATTTCTTA
Found at i:3840849 original size:14 final size:14
Alignment explanation
Indices: 3840830--3840857 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3840820 CATCGAATTT
3840830 TTTTATTTTATAAA
1 TTTTATTTTATAAA
3840844 TTTTATTTTATAAA
1 TTTTATTTTATAAA
3840858 AAATATATGT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTTTATAAA
Found at i:3842242 original size:22 final size:22
Alignment explanation
Indices: 3842202--3842243 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3842192 AAGAAAAATT
* **
3842202 AATGTTTAATTATTGAAGATCA
1 AATGTGTAATTATACAAGATCA
3842224 AATGTGTAATTATACAAGAT
1 AATGTGTAATTATACAAGAT
3842244 ACCGATCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (22 bp):
AATGTGTAATTATACAAGATCA
Found at i:3843171 original size:3 final size:3
Alignment explanation
Indices: 3843156--3843185 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3843146 TTTTAATTTG
*
3843156 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3843186 TAATAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3851037 original size:29 final size:29
Alignment explanation
Indices: 3851005--3851126 Score: 104
Period size: 29 Copynumber: 4.2 Consensus size: 29
3850995 AATTATTGTT
* *
3851005 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGATATTATGGGAAATATTTCGAAAA
* * *
3851034 AGGTGATATTTTGGGAATTATTTTGAAAAA
1 AGGTGATATTATGGGAAATATTTCG-AAAA
* * *
3851064 AAGTGACATTATGAGAAATATTTCGAAAA
1 AGGTGATATTATGGGAAATATTTCGAAAA
* * * *
3851093 A-GTAACA-TATTGGGAATTATTTCGTAAA
1 AGGTGATATTA-TGGGAAATATTTCGAAAA
3851121 AGGTGA
1 AGGTGA
3851127 CACTCTGAGA
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
27 2 0.03
28 21 0.28
29 30 0.40
30 22 0.29
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (29 bp):
AGGTGATATTATGGGAAATATTTCGAAAA
Found at i:3851100 original size:28 final size:28
Alignment explanation
Indices: 3851061--3851122 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3851051 TTATTTTGAA
*
3851061 AAAAAGTGACAT-TATGAGAAATATTTCG
1 AAAAAGTAACATAT-TGAGAAATATTTCG
* *
3851089 AAAAAGTAACATATTGGGAATTATTTCG
1 AAAAAGTAACATATTGAGAAATATTTCG
*
3851117 TAAAAG
1 AAAAAG
3851123 GTGACACTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (28 bp):
AAAAAGTAACATATTGAGAAATATTTCG
Found at i:3851113 original size:58 final size:57
Alignment explanation
Indices: 3851019--3851168 Score: 165
Period size: 58 Copynumber: 2.6 Consensus size: 57
3851009 GATATTCTGG
* * * *
3851019 GAAATATTTCGATAAAGGTGATATTTTGGGAATTATTTTGAAAAAAAGTGACATTATGA
1 GAAATATTTCGA-AAAAGTGACATTTTGGGAATTATTTCG-AAAAAAGTGACACTATGA
* * * * *
3851078 GAAATATTTCGAAAAAGTAACATATTGGGAATTATTTCGTAAAAGGTGACACTCTGA
1 GAAATATTTCGAAAAAGTGACATTTTGGGAATTATTTCGAAAAAAGTGACACTATGA
* **
3851135 GAATTATTTTAAAAAAAGTGACATTTTGGGAATT
1 GAAATA-TTTCGAAAAAGTGACATTTTGGGAATT
3851169 TTCAAATGTT
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
57 19 0.25
58 45 0.59
59 12 0.16
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (57 bp):
GAAATATTTCGAAAAAGTGACATTTTGGGAATTATTTCGAAAAAAGTGACACTATGA
Found at i:3851167 original size:29 final size:29
Alignment explanation
Indices: 3851036--3851168 Score: 115
Period size: 29 Copynumber: 4.6 Consensus size: 29
3851026 TTCGATAAAG
*
3851036 GTGATATTTTGGGAATTATTTTGAAAAAAA
1 GTGACATTTTGGGAATTATTTT-AAAAAAA
* * * **
3851066 GTGACATTATGAGAAATA-TTTCGAAAAA
1 GTGACATTTTGGGAATTATTTTAAAAAAA
* * *** *
3851094 GTAACATATTGGGAATTATTTCGTAAAAG
1 GTGACATTTTGGGAATTATTTTAAAAAAA
* * *
3851123 GTGACACTCTGAGAATTATTTTAAAAAAA
1 GTGACATTTTGGGAATTATTTTAAAAAAA
3851152 GTGACATTTTGGGAATT
1 GTGACATTTTGGGAATT
3851169 TTCAAATGTT
Statistics
Matches: 75, Mismatches: 27, Indels: 3
0.71 0.26 0.03
Matches are distributed among these distances:
28 18 0.24
29 43 0.57
30 14 0.19
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.35
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTAAAAAAA
Found at i:3857584 original size:29 final size:29
Alignment explanation
Indices: 3857552--3857687 Score: 111
Period size: 29 Copynumber: 4.8 Consensus size: 29
3857542 AATTGTTGTT
* *
3857552 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATTCTGGGAATTATTTCGATAA
* * *
3857581 AGGTGAAATTTTGGGAATTATTTTGA-AA
1 AGGTGACATTCTGGGAATTATTTCGATAA
* * * *
3857609 A-GTGACATTATGAGAAATATTT-GAAAA
1 AGGTGACATTCTGGGAATTATTTCGATAA
* *
3857636 AGGTAATATAT-TGGGAATTATTTCG-TAAA
1 AGGTGACAT-TCTGGGAATTATTTCGAT-AA
*
3857665 AGGTGACACTCTGGGAATTATTT
1 AGGTGACATTCTGGGAATTATTT
3857688 TTAAAAAAAG
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
26 2 0.02
27 20 0.24
28 19 0.22
29 44 0.52
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (29 bp):
AGGTGACATTCTGGGAATTATTTCGATAA
Found at i:3857636 original size:27 final size:27
Alignment explanation
Indices: 3857566--3857637 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
3857556 GATATTCTGG
* * *
3857566 GAAATATTTCGATAAAGGTGAAATTTTGG
1 GAAATATTT-GA-AAAAGTGAAATTATGA
* *
3857595 GAATTATTTTG-AAAAGTGACATTATGA
1 GAAATA-TTTGAAAAAGTGAAATTATGA
3857622 GAAATATTTGAAAAAG
1 GAAATATTTGAAAAAG
3857638 GTAATATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 4 0.11
27 22 0.63
29 6 0.17
30 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (27 bp):
GAAATATTTGAAAAAGTGAAATTATGA
Found at i:3857651 original size:55 final size:58
Alignment explanation
Indices: 3857552--3857672 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 58
3857542 AATTGTTGTT
* * * * * *
3857552 AGGTGATATTCTGGGAAATATTTCGATAAAGGTGAAATTTTGGGAATTATTTTG-AAA
1 AGGTGACATTATGAGAAATATTTCGAAAAAGGTGAAATATTGGGAATTATTTCGTAAA
3857609 A-GTGACATTATGAGAAATATTT-GAAAAAGGT-AATATATTGGGAATTATTTCGTAAA
1 AGGTGACATTATGAGAAATATTTCGAAAAAGGTGAA-ATATTGGGAATTATTTCGTAAA
3857665 AGGTGACA
1 AGGTGACA
3857673 CTCTGGGAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
54 2 0.04
55 24 0.44
56 22 0.40
57 7 0.13
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (58 bp):
AGGTGACATTATGAGAAATATTTCGAAAAAGGTGAAATATTGGGAATTATTTCGTAAA
Found at i:3863703 original size:3 final size:3
Alignment explanation
Indices: 3863695--3863745 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3863685 TCTCTTAAGA
3863695 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3863743 AAT
1 AAT
3863746 GATGATGATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3863750 original size:3 final size:3
Alignment explanation
Indices: 3863744--3863785 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3863734 AATAATAATA
3863744 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3863786 TGAGATTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:3866709 original size:106 final size:106
Alignment explanation
Indices: 3866383--3867318 Score: 1201
Period size: 106 Copynumber: 9.0 Consensus size: 106
3866373 AGCATTGTTC
* * * **
3866383 TGAGTCCAATATCCTCCGTCT-TGAAGTTGAAATTGGCTTTGGAACCGGGAAATTGTTTGTTGAC
1 TGAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * *
3866447 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
3866489 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * * *
3866548 ATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGCCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
3866589 TGGGTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3866654 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3866695 TGAGTCCAATATCCTACGATGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3866760 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
3866801 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3866866 ATCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3866907 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTTTTTGTTAACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3866972 ACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3867013 GGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
3867078 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
3867119 CGAGACCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * * * *
3867184 ATCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCA
66 ACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
*
3867225 TGAGTCCAATATCCTTCGC--T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3867278 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3867319 GGAGAGAAAC
Statistics
Matches: 737, Mismatches: 84, Indels: 30
0.87 0.10 0.04
Matches are distributed among these distances:
94 55 0.07
95 2 0.00
96 1 0.00
99 2 0.00
100 83 0.11
101 4 0.01
102 5 0.01
104 4 0.01
105 6 0.01
106 575 0.78
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:3867374 original size:36 final size:36
Alignment explanation
Indices: 3867327--3867460 Score: 135
Period size: 37 Copynumber: 3.7 Consensus size: 36
3867317 CTGGAGAGAA
*
3867327 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAG
1 ACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAG
* * * *
3867363 ACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAA
1 ACTGTCTCAAGCGAGACAAAATTTGTTTC-AAGGAAG
* * * *
3867400 ACTATCTCAAGCGAGATAAAATCTTGTTTTAAATG-AG
1 ACTGTCTCAAGCGAGACAAAAT-TTG-TTTCAAGGAAG
* *
3867437 ATTGTCTCAAGCGTGACAAAATTT
1 ACTGTCTCAAGCGAGACAAAATTT
3867461 ATATTGGAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
36 30 0.38
37 42 0.52
38 5 0.06
39 3 0.04
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
ACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAG
Found at i:3868211 original size:22 final size:22
Alignment explanation
Indices: 3868185--3868261 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
3868175 TTGTGTTTGG
3868185 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* * *
3868207 TCAAATGTTTGGTATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
3868229 TCAAAGGTTTGTCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3868251 TCAAAGGTTTG
1 TCAAAGGTTTG
3868262 ATGGGGTAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3868881 original size:19 final size:18
Alignment explanation
Indices: 3868855--3868902 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
3868845 TTTTTGTCCC
3868855 TTTTTCTTTTTGATTTTG
1 TTTTTCTTTTTGATTTTG
**
3868873 TTCTTTCTTTTTTCTTTTG
1 TT-TTTCTTTTTGATTTTG
*
3868892 TTTCTCTTTTT
1 TTTTTCTTTTT
3868903 TCTTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTTGATTTTG
Found at i:3868908 original size:17 final size:18
Alignment explanation
Indices: 3868868--3868911 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
3868858 TTCTTTTTGA
*
3868868 TTTTGTTCTTTCTTTTTTC
1 TTTTGTT-TCTCTTTTTTC
3868887 TTTTGTTTCTCTTTTTTC
1 TTTTGTTTCTCTTTTTTC
3868905 -TTTGTTT
1 TTTTGTTT
3868912 TTGATTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTGTTTCTCTTTTTTC
Found at i:3870809 original size:5 final size:5
Alignment explanation
Indices: 3870799--3870826 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3870789 GAAAATGATG
3870799 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
3870827 GATGAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3872254 original size:2 final size:2
Alignment explanation
Indices: 3872247--3872279 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3872237 AAAATAGGAA
3872247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3872280 ATAACACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3872729 original size:37 final size:37
Alignment explanation
Indices: 3872688--3872785 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
3872678 GTGCTTGTGG
* * * *
3872688 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
* *
3872725 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
*
3872762 ATCATATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
3872786 CTAATAGGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:3874167 original size:22 final size:22
Alignment explanation
Indices: 3874139--3874197 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
3874129 AATCCAACAG
3874139 TTTGTAACTCATGCAATAAAGC
1 TTTGTAACTCATGCAATAAAGC
* *
3874161 TTTGTAACT-ATTGTATTAAAGC
1 TTTGTAACTCA-TGCAATAAAGC
*
3874183 TTTGTAACTCTTGCA
1 TTTGTAACTCATGCA
3874198 TTCATTCTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (22 bp):
TTTGTAACTCATGCAATAAAGC
Found at i:3874868 original size:2 final size:2
Alignment explanation
Indices: 3874861--3874902 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
3874851 GATGTGTAAG
3874861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
3874903 TTGACCATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 36 0.95
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3877628 original size:26 final size:22
Alignment explanation
Indices: 3877569--3877617 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3877559 ATAAATACTC
3877569 TCAATCATTTGATAATGAATGT
1 TCAATCATTTGATAATGAATGT
3877591 TCAATCATTTGATAATGAATGT
1 TCAATCATTTGATAATGAATGT
3877613 TCAAT
1 TCAAT
3877618 TATCTCGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
TCAATCATTTGATAATGAATGT
Found at i:3883812 original size:22 final size:22
Alignment explanation
Indices: 3883784--3883827 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3883774 ATATTATATT
3883784 TTTTTTAAAAAATAAACACATA
1 TTTTTTAAAAAATAAACACATA
3883806 TTTTTTAAAAAATAAACACATA
1 TTTTTTAAAAAATAAACACATA
3883828 AATGTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTTTTAAAAAATAAACACATA
Found at i:3883835 original size:22 final size:22
Alignment explanation
Indices: 3883788--3883835 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3883778 TATATTTTTT
** *
3883788 TTAAAAAATAAACACATATTTT
1 TTAAAAAATAAACACATAAATG
3883810 TTAAAAAATAAACACATAAATG
1 TTAAAAAATAAACACATAAATG
3883832 TTAA
1 TTAA
3883836 TATTTAAAAA
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:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAAAAATAAACACATAAATG
Found at i:3887973 original size:2 final size:2
Alignment explanation
Indices: 3887966--3888020 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3887956 CTTCAAGGAC
3887966 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
3888008 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3888021 CTCGTACACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.