Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 6 of 66
Found at i:2015241 original size:38 final size:38
Alignment explanation
Indices: 2015190--2015273 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 38
2015180 GGCCGGCGAT
2015190 AGGAAGAGATCGGTAGAGGGAGAGCCCGATTTGGGCAA
1 AGGAAGAGATCGGTAGAGGGAGAGCCCGATTTGGGCAA
* *
2015228 AGGAAGAGATCGGTGGAGGGAGAGCTCGATTTGGGCAA
1 AGGAAGAGATCGGTAGAGGGAGAGCCCGATTTGGGCAA
*
2015266 AGGGAGAG
1 AGGAAGAG
2015274 CAGATCTAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.31, C:0.11, G:0.45, T:0.13
Consensus pattern (38 bp):
AGGAAGAGATCGGTAGAGGGAGAGCCCGATTTGGGCAA
Found at i:2015263 original size:137 final size:137
Alignment explanation
Indices: 2015017--2015361 Score: 539
Period size: 137 Copynumber: 2.5 Consensus size: 137
2015007 AGGCAATTGA
* * * * * *
2015017 CAGAGGGAGGTCTGACGTGGGCTAGAGGTCAGCGATAGAAAGAGATCGGTAGAGGGAGAGCTCGA
1 CAGAGGGAGGTCTGGCGTGGGCTAGTGGCCGGCGATAGGAAGAGATCGGTAGAGGGAGAGCCCGA
2015082 TTTGGGCAAAGGAAGAGATCGGTGGAGGGAGAGCCCGATTTGGGCAAAGGGAGAGCAAATCTAAG
66 TTTGGGCAAAGGAAGAGATCGGTGGAGGGAGAGCCCGATTTGGGCAAAGGGAGAGCAAATCTAAG
2015147 C-AGTCGG
131 CGA-TCGG
2015154 CAGAGGGAGGTCTGGCGTGGGCTAGTGGCCGGCGATAGGAAGAGATCGGTAGAGGGAGAGCCCGA
1 CAGAGGGAGGTCTGGCGTGGGCTAGTGGCCGGCGATAGGAAGAGATCGGTAGAGGGAGAGCCCGA
* * *
2015219 TTTGGGCAAAGGAAGAGATCGGTGGAGGGAGAGCTCGATTTGGGCAAAGGGAGAGCAGATCTAGG
66 TTTGGGCAAAGGAAGAGATCGGTGGAGGGAGAGCCCGATTTGGGCAAAGGGAGAGCAAATCTAAG
2015284 CGATCGG
131 CGATCGG
* * * * * *
2015291 CAGAGGGAGGTCCGGCGTGGGCTATTGGCTGGAGGTGGGAAGAGATCGGTAGAGGGAGAGCCCGA
1 CAGAGGGAGGTCTGGCGTGGGCTAGTGGCCGGCGATAGGAAGAGATCGGTAGAGGGAGAGCCCGA
2015356 TTTGGG
66 TTTGGG
2015362 GTTGGCTGGC
Statistics
Matches: 192, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
137 191 0.99
138 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.45, T:0.15
Consensus pattern (137 bp):
CAGAGGGAGGTCTGGCGTGGGCTAGTGGCCGGCGATAGGAAGAGATCGGTAGAGGGAGAGCCCGA
TTTGGGCAAAGGAAGAGATCGGTGGAGGGAGAGCCCGATTTGGGCAAAGGGAGAGCAAATCTAAG
CGATCGG
Found at i:2016392 original size:15 final size:16
Alignment explanation
Indices: 2016372--2016401 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2016362 ATGATAAGAT
2016372 AAATAATT-ATTAATA
1 AAATAATTGATTAATA
2016387 AAATAATTGATTAAT
1 AAATAATTGATTAAT
2016402 TTAATACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AAATAATTGATTAATA
Found at i:2016567 original size:14 final size:14
Alignment explanation
Indices: 2016548--2016574 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2016538 TTTTAAATAA
2016548 ATAAAAAAATAAAT
1 ATAAAAAAATAAAT
2016562 ATAAAAAAATAAA
1 ATAAAAAAATAAA
2016575 AAAATGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
ATAAAAAAATAAAT
Found at i:2020083 original size:15 final size:15
Alignment explanation
Indices: 2020042--2020088 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2020032 AAAAATTATT
*
2020042 ATATAATAAATTAGTCA
1 ATATAATAAA-TA-TAA
2020059 ATAT-ATAAATATAA
1 ATATAATAAATATAA
2020073 ATATAATAAATATAA
1 ATATAATAAATATAA
2020088 A
1 A
2020089 AGAACAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 13 0.46
16 5 0.18
17 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
ATATAATAAATATAA
Found at i:2022023 original size:25 final size:25
Alignment explanation
Indices: 2021976--2022023 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2021966 ATAAAAATAT
*
2021976 TTTTTATTATATATATAATTATTTA
1 TTTTTATTATATATATAAATATTTA
* * *
2022001 TTTTTATTTTATTTTTAAATATT
1 TTTTTATTATATATATAAATATT
2022024 AATAATTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTATTATATATATAAATATTTA
Found at i:2022032 original size:32 final size:32
Alignment explanation
Indices: 2021973--2022033 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2021963 AAGATAAAAA
* *
2021973 TATTTTTTATTATATATATAATTATTTATTTT
1 TATTTTTTATTAAATATATAATAATTTATTTT
*
2022005 TATTTTATTTTTAAATAT-TAATAATTTAT
1 TATTTT-TTATTAAATATATAATAATTTAT
2022034 AATTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 16 0.64
33 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TATTTTTTATTAAATATATAATAATTTATTTT
Found at i:2022098 original size:16 final size:16
Alignment explanation
Indices: 2022070--2022181 Score: 72
Period size: 16 Copynumber: 6.9 Consensus size: 16
2022060 TTATTTTTTA
2022070 TTTAATATCATTAAAAT
1 TTTAATAT-ATTAAAAT
2022087 TTTAATATATTAATAA-
1 TTTAATATATTAA-AAT
* *
2022103 TTTAATA-AGTAAAAC
1 TTTAATATATTAAAAT
* *
2022118 ATTAATATTTTAAAAT
1 TTTAATATATTAAAAT
*
2022134 ATTT-ATAT-TATAATAT
1 -TTTAATATAT-TAAAAT
*
2022150 TTTAATCATATTAATAT
1 TTTAAT-ATATTAAAAT
*
2022167 TAATAATAT-TTAAAA
1 T-TTAATATATTAAAA
2022182 AATATATAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.03
15 14 0.18
16 33 0.43
17 23 0.30
18 5 0.06
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (16 bp):
TTTAATATATTAAAAT
Found at i:2022099 original size:8 final size:8
Alignment explanation
Indices: 2022071--2022205 Score: 56
Period size: 8 Copynumber: 17.5 Consensus size: 8
2022061 TATTTTTTAT
2022071 TTAATATCA
1 TTAATAT-A
* *
2022080 TTAAAATT
1 TTAATATA
2022088 TTAATATA
1 TTAATATA
2022096 TTAATA-A
1 TTAATATA
2022103 TTTAATA-A
1 -TTAATATA
* * *
2022111 GTAAAACA
1 TTAATATA
*
2022119 TTAATATT
1 TTAATATA
*
2022127 TTAAAATA
1 TTAATATA
*
2022135 TTTATAT-
1 TTAATATA
*
2022142 TATAATATT
1 T-TAATATA
2022151 TTAATCATA
1 TTAAT-ATA
2022160 TTAATATTA
1 TTAATA-TA
*
2022169 ATAATAT-
1 TTAATATA
2022176 TTAA-A-A
1 TTAATATA
2022182 --AATATA
1 TTAATATA
2022188 -TAA-ATA
1 TTAATATA
*
2022194 TTAATATT
1 TTAATATA
2022202 TTAA
1 TTAA
2022206 AATTTATAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
4 2 0.02
5 1 0.01
6 5 0.05
7 14 0.15
8 52 0.55
9 21 0.22
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (8 bp):
TTAATATA
Found at i:2022099 original size:55 final size:56
Alignment explanation
Indices: 2022001--2022110 Score: 140
Period size: 56 Copynumber: 2.0 Consensus size: 56
2021991 TAATTATTTA
*
2022001 TTTTTATTTTATTTTTAAATATTAATAATTTATAATTTAATTAA-AATATTAATAAT
1 TTTTTATTTTATTTTTAAATATTAATAATTTATAATATAATTAATAAT-TTAATAAT
2022057 TTTTTATTTT-TTATTTAATATCATTAA-AATTT-TAATAT-ATTAATAATTTAATAA
1 TTTTTATTTTATT-TTTAA-AT-ATTAATAATTTATAATATAATTAATAATTTAATAA
2022111 GTAAAACATT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
55 14 0.29
56 23 0.47
57 7 0.14
58 5 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (56 bp):
TTTTTATTTTATTTTTAAATATTAATAATTTATAATATAATTAATAATTTAATAAT
Found at i:2022166 original size:25 final size:25
Alignment explanation
Indices: 2022120--2022208 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
2022110 AGTAAAACAT
*
2022120 TAATATTTTAAAATATTTATATT-A
1 TAATATTTTAAAATATTAATATTAA
*
2022144 TAATATTTTAATCATATTAATATTAA
1 TAATATTTTAA-AATATTAATATTAA
* *
2022170 TAATATTTAAAAAATATATAA-A-TAT
1 TAATATTT-TAAAATAT-TAATATTAA
2022195 TAATATTTTAAAAT
1 TAATATTTTAAAAT
2022209 TTATAAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
24 16 0.29
25 20 0.36
26 14 0.25
27 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (25 bp):
TAATATTTTAAAATATTAATATTAA
Found at i:2024394 original size:17 final size:20
Alignment explanation
Indices: 2024372--2024411 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
2024362 TAGGATCTAA
2024372 AAAAATAT-T-TAA-TTATT
1 AAAAATATCTCTAATTTATT
2024389 AAAAATATCTCTAATTTATT
1 AAAAATATCTCTAATTTATT
2024409 AAA
1 AAA
2024412 TGGGTATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 3 0.15
20 8 0.40
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAATATCTCTAATTTATT
Found at i:2036783 original size:2 final size:2
Alignment explanation
Indices: 2036771--2036804 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2036761 GCACAAGCAA
*
2036771 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2036805 CACAAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2038239 original size:12 final size:12
Alignment explanation
Indices: 2038174--2038240 Score: 62
Period size: 12 Copynumber: 5.2 Consensus size: 12
2038164 TAAAACTAAT
2038174 TTTTTATATATA
1 TTTTTATATATA
* *
2038186 TTAATATATATAAA
1 TT--TTTATATATA
2038200 TTTTTATATATA
1 TTTTTATATATA
*
2038212 TTAATATATATAATA
1 TT--TTTATAT-ATA
2038227 TTTTTATATATA
1 TTTTTATATATA
2038239 TT
1 TT
2038241 AAAAATCATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 17 0.39
13 6 0.14
14 16 0.36
15 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTTTATATATA
Found at i:2038253 original size:27 final size:27
Alignment explanation
Indices: 2038170--2038242 Score: 132
Period size: 26 Copynumber: 2.8 Consensus size: 27
2038160 AAAATAAAAC
2038170 TAAT-TTTTTATATATATTAATATATA
1 TAATATTTTTATATATATTAATATATA
2038196 TAA-ATTTTTATATATATTAATATATA
1 TAATATTTTTATATATATTAATATATA
2038222 TAATATTTTTATATATATTAA
1 TAATATTTTTATATATATTAA
2038243 AAATCATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
26 28 0.62
27 17 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TAATATTTTTATATATATTAATATATA
Found at i:2042750 original size:164 final size:166
Alignment explanation
Indices: 2042523--2042836 Score: 499
Period size: 165 Copynumber: 1.9 Consensus size: 166
2042513 TATGGAGATC
* *
2042523 CTCTTGATGATCAACATTTTGACCTGTGTTTAGCTTTCTTTGATTCTGAGTTTTAGTTTGTTTTT
1 CTCTTAATGATCAACATTTTGACCTGTGTTTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTT
* * * ** * *
2042588 TCAAAA-TTAAATTTTGAGTTTGAAGATGGTCTTGTAAATTTACAGAATGGTAAACAAGGGG-GT
66 CCAAAACGTAAATCTTGAGTTTGAAGATGGTCTTGTAAACATAAAGAATGATAAACAAGGGGTGT
2042651 GGGGGTTGCTTCCCTTGTTCTCTCATTAAAGTTTATT
131 GGGGG-TGCTTCCCTTGTTCTCTCATTAAAGTTTATT
2042688 CTCTTAATGATCAACATTTTGACCTGTG-TTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTT
1 CTCTTAATGATCAACATTTTGACCTGTGTTTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTT
*
2042752 CCAAAACGTAAATCTTGAGTTTTAAGATGGTCTTGTAAACATAAAGAATGATAAACAAGGGGTGT
66 CCAAAACGTAAATCTTGAGTTTGAAGATGGTCTTGTAAACATAAAGAATGATAAACAAGGGGTGT
*
2042817 GGGGGTGCTTCCTTTGTTCT
131 GGGGGTGCTTCCCTTGTTCT
2042837 TTCAGCTTTA
Statistics
Matches: 136, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
164 40 0.29
165 89 0.65
166 7 0.05
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (166 bp):
CTCTTAATGATCAACATTTTGACCTGTGTTTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTT
CCAAAACGTAAATCTTGAGTTTGAAGATGGTCTTGTAAACATAAAGAATGATAAACAAGGGGTGT
GGGGGTGCTTCCCTTGTTCTCTCATTAAAGTTTATT
Found at i:2053581 original size:90 final size:90
Alignment explanation
Indices: 2053406--2053574 Score: 218
Period size: 90 Copynumber: 1.9 Consensus size: 90
2053396 TCAAGTTTTT
*
2053406 GTATTATTTTATTTTCATCATCTTCAAACTTTAAAAGGATTTCAATGATTAGATTTTGATTTCTA
1 GTATTATTTTATTTTCATCATCTTCAAACTTTAAAAGGATTTCAATGATTAGATTTTAATTTCTA
* *
2053471 ATTTTAGCAAATCAGATAAGTGTTG
66 ATTGTAACAAATCAGATAAGTGTTG
* * *
2053496 GTATTATTTTATTTTCAAT-ATC-TCGAATCTTTAAAAGGATTTCAATGGTT-GGTCTTTAATTT
1 GTATTATTTTATTTTC-ATCATCTTC-AAACTTTAAAAGGATTTCAATGATTAGAT-TTTAATTT
* *
2053558 TTGATTGTAACAAATCA
63 CTAATTGTAACAAATCA
2053575 CGTAAGTAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
89 4 0.06
90 62 0.91
91 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (90 bp):
GTATTATTTTATTTTCATCATCTTCAAACTTTAAAAGGATTTCAATGATTAGATTTTAATTTCTA
ATTGTAACAAATCAGATAAGTGTTG
Found at i:2056941 original size:29 final size:29
Alignment explanation
Indices: 2056899--2056980 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
2056889 AAAAAGTGGA
* *
2056899 TAACCCACCAAGAAGTGCATGGATGCTTG
1 TAACCCACCAAGAAATGCATGGATACTTG
*
2056928 TAACCCACCAAGAAATGGATGGATACTTG
1 TAACCCACCAAGAAATGCATGGATACTTG
* * *
2056957 TCACCCA-CAAAAAATGAATGGATA
1 TAACCCACCAAGAAATGCATGGATA
2056981 TTTTTAATCC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 15 0.32
29 32 0.68
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (29 bp):
TAACCCACCAAGAAATGCATGGATACTTG
Found at i:2060219 original size:2 final size:2
Alignment explanation
Indices: 2060212--2060242 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2060202 GAGCATGTAA
2060212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2060243 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2066665 original size:3 final size:3
Alignment explanation
Indices: 2066657--2066682 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2066647 TAAATGGAAT
2066657 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2066683 TGGGGGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2069027 original size:22 final size:21
Alignment explanation
Indices: 2068999--2069042 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
2068989 GTTAGTATAA
*
2068999 AATAATAATTAATATTTTAATT
1 AATAATAATTAAT-TATTAATT
2069021 AATAATAATTAATTATTAATT
1 AATAATAATTAATTATTAATT
2069042 A
1 A
2069043 TAAGCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAATAATTAATTATTAATT
Found at i:2069228 original size:15 final size:16
Alignment explanation
Indices: 2069208--2069241 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2069198 AGGAGACTTC
2069208 ACAATT-GAGAAAGGA
1 ACAATTAGAGAAAGGA
*
2069223 ACAATTAGAGACAGGA
1 ACAATTAGAGAAAGGA
2069239 ACA
1 ACA
2069242 TTGGTACACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (16 bp):
ACAATTAGAGAAAGGA
Found at i:2071759 original size:4 final size:4
Alignment explanation
Indices: 2071750--2071779 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2071740 CGATCAAAAG
2071750 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
2071780 GACGGGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2075607 original size:28 final size:25
Alignment explanation
Indices: 2075554--2075623 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
2075544 CTTGCAGACA
*
2075554 GTGAGAAGAAGGAGAATAAGGTAAG
1 GTGAGAAGAAGGAGAAAAAGGTAAG
2075579 GTGAGAAGAAGGAGAAAAAGGT-AG
1 GTGAGAAGAAGGAGAAAAAGGTAAG
* *
2075603 G-AAGGAAGAAGGAGAAGAAGG
1 GTGA-GAAGAAGGAGAAAAAGG
2075624 CAAGAAGGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.02
24 19 0.46
25 21 0.51
ACGTcount: A:0.50, C:0.00, G:0.43, T:0.07
Consensus pattern (25 bp):
GTGAGAAGAAGGAGAAAAAGGTAAG
Found at i:2075615 original size:24 final size:24
Alignment explanation
Indices: 2075558--2075636 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
2075548 CAGACAGTGA
* *
2075558 GAAGAAGGAGAATAAGGTAAGG-TG
1 GAAGAAGGAGAAAAAGGT-AGGAAG
2075582 AGAAGAAGGAGAAAAAGGTAGGAAG
1 -GAAGAAGGAGAAAAAGGTAGGAAG
* * *
2075607 GAAGAAGGAGAAGAAGGCAAGAAG
1 GAAGAAGGAGAAAAAGGTAGGAAG
2075631 GAAGAA
1 GAAGAA
2075637 AGTGAATAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
24 30 0.62
25 18 0.38
ACGTcount: A:0.53, C:0.01, G:0.41, T:0.05
Consensus pattern (24 bp):
GAAGAAGGAGAAAAAGGTAGGAAG
Found at i:2075647 original size:24 final size:24
Alignment explanation
Indices: 2075583--2075648 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
2075573 GGTAAGGTGA
* * * *
2075583 GAAGAAGGAGAAAAAGGTAGGAAG
1 GAAGAAAGAGAAGAAGGCAAGAAG
*
2075607 GAAGAAGGAGAAGAAGGCAAGAAG
1 GAAGAAAGAGAAGAAGGCAAGAAG
* *
2075631 GAAGAAAGTGAATAAGGC
1 GAAGAAAGAGAAGAAGGC
2075649 TGAAAGGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.03, G:0.39, T:0.05
Consensus pattern (24 bp):
GAAGAAAGAGAAGAAGGCAAGAAG
Found at i:2077056 original size:15 final size:16
Alignment explanation
Indices: 2077029--2077065 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2077019 ATTTTGGGGA
2077029 AAGAAAGGAAAAA-AG
1 AAGAAAGGAAAAAGAG
2077044 TAAGAAA-GAAAAAGAG
1 -AAGAAAGGAAAAAGAG
2077060 AAGAAA
1 AAGAAA
2077066 CGAAGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (16 bp):
AAGAAAGGAAAAAGAG
Found at i:2078765 original size:29 final size:30
Alignment explanation
Indices: 2078713--2078776 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
2078703 AATTAAATAC
* * *
2078713 TTATATTTTTATTTTGAACCAAATGAGTCT
1 TTATATTTTTATTTAGAACCAAATAACTCT
**
2078743 TTATATTTTT-TTTAGAGTCAAATAACTCT
1 TTATATTTTTATTTAGAACCAAATAACTCT
2078772 TTATA
1 TTATA
2078777 ACTAATGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (30 bp):
TTATATTTTTATTTAGAACCAAATAACTCT
Found at i:2080735 original size:22 final size:21
Alignment explanation
Indices: 2080707--2080754 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2080697 TGTCGGAGTA
2080707 TTTTCAAAATAAAAAAATTATT
1 TTTTCAAAAT-AAAAAATTATT
* *
2080729 TTTTC-AAATGAAAAGTTATT
1 TTTTCAAAATAAAAAATTATT
2080749 TTTTCA
1 TTTTCA
2080755 TATTGTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 14 0.61
21 4 0.17
22 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
TTTTCAAAATAAAAAATTATT
Found at i:2084276 original size:39 final size:38
Alignment explanation
Indices: 2084201--2084276 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
2084191 GACAACTACA
* *
2084201 CAAGACAGGAGAAATACAAAATAACAATACCAAAAATC
1 CAAGACAGAAGAAATACAAAATAACAATAACAAAAATC
* *
2084239 CAAGACAGAAGTAAATA-ATAAATAACACTAACGAAAAT
1 CAAGACAGAAG-AAATACA-AAATAACAATAACAAAAAT
2084277 AAAAGGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 11 0.34
39 21 0.66
ACGTcount: A:0.61, C:0.16, G:0.11, T:0.13
Consensus pattern (38 bp):
CAAGACAGAAGAAATACAAAATAACAATAACAAAAATC
Found at i:2090299 original size:18 final size:18
Alignment explanation
Indices: 2090278--2090314 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2090268 TCCTTCCTTC
2090278 AACGCTTCTTATAAGAAG
1 AACGCTTCTTATAAGAAG
2090296 AACGCTTCTTATAAGAAG
1 AACGCTTCTTATAAGAAG
2090314 A
1 A
2090315 GGGGCAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (18 bp):
AACGCTTCTTATAAGAAG
Found at i:2091644 original size:50 final size:50
Alignment explanation
Indices: 2091569--2091669 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
2091559 TATCCGCCGG
*
2091569 TGTATCACAATATTACTTAACTTCTATATGATTTCTTTACAACAAAATGA
1 TGTATCACAATATTACTTAACTTCTATAAGATTTCTTTACAACAAAATGA
2091619 TGTATCACAATATTACTTAACTTCTATAAGATTTCTTTACAACAAAATGA
1 TGTATCACAATATTACTTAACTTCTATAAGATTTCTTTACAACAAAATGA
2091669 T
1 T
2091670 ATAGAAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.40
Consensus pattern (50 bp):
TGTATCACAATATTACTTAACTTCTATAAGATTTCTTTACAACAAAATGA
Found at i:2095700 original size:55 final size:55
Alignment explanation
Indices: 2095618--2095803 Score: 196
Period size: 55 Copynumber: 3.4 Consensus size: 55
2095608 ATTAGAGTTA
* * * *
2095618 TTTTT-GCGTGTCATGGCTTTTCGTGGCGTGTTGTGGGTTAACTAGTTTTTTGGG
1 TTTTTAGCGTGTCACGGCTGTTCCTGGCGTGTAGTGGGTTAACTAGTTTTTTGGG
* * * * *
2095672 TTATTAGCGTGTCACGGCTGTTCCTGGCGTGTCGTGGGTTAA-TTGAATTTATGGG
1 TTTTTAGCGTGTCACGGCTGTTCCTGGCGTGTAGTGGGTTAACTAG-TTTTTTGGG
* * ** * * *
2095727 TTTTTGGAGTGTCACAACTATTCTTGGCGTGTAGTGGGTTAACTGGTTTTTTGGG
1 TTTTTAGCGTGTCACGGCTGTTCCTGGCGTGTAGTGGGTTAACTAGTTTTTTGGG
*
2095782 TTTTTAGCATGTCACGGCTGTT
1 TTTTTAGCGTGTCACGGCTGTT
2095804 GGTGTAACGA
Statistics
Matches: 104, Mismatches: 25, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
54 6 0.06
55 96 0.92
56 2 0.02
ACGTcount: A:0.12, C:0.13, G:0.31, T:0.44
Consensus pattern (55 bp):
TTTTTAGCGTGTCACGGCTGTTCCTGGCGTGTAGTGGGTTAACTAGTTTTTTGGG
Found at i:2095908 original size:31 final size:31
Alignment explanation
Indices: 2095873--2095954 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
2095863 CATGATACTG
*
2095873 ATGCATGGCATGTCACGACATTTGAC-TTGAT
1 ATGCATGGCATGTCACAACATTTGACGTT-AT
* *
2095904 ATGCATGGCGTGTTACAACATTTGACGTTAT
1 ATGCATGGCATGTCACAACATTTGACGTTAT
* *
2095935 ATGCATGGCGTGTAACAACA
1 ATGCATGGCATGTCACAACA
2095955 CGACAAACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 44 0.96
32 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (31 bp):
ATGCATGGCATGTCACAACATTTGACGTTAT
Found at i:2099122 original size:31 final size:31
Alignment explanation
Indices: 2099080--2099221 Score: 194
Period size: 31 Copynumber: 4.6 Consensus size: 31
2099070 GGTGCTAAAG
**
2099080 GTTATGACACGCCATGCATAACAAGTTAAAC
1 GTTATGACACGCCATGCATAACAAGCAAAAC
* * *
2099111 TTTGTGACACGCCATGCATAACAAGCAAAAG
1 GTTATGACACGCCATGCATAACAAGCAAAAC
**
2099142 GTTATGACACGCCATGCATAACAAGTTAAAC
1 GTTATGACACGCCATGCATAACAAGCAAAAC
* * *
2099173 GTTGTGACATGCCATGCATAACAAGCAAAAG
1 GTTATGACACGCCATGCATAACAAGCAAAAC
2099204 GTTATGACACGCCATGCA
1 GTTATGACACGCCATGCA
2099222 GTATCGTGGG
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 94 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (31 bp):
GTTATGACACGCCATGCATAACAAGCAAAAC
Found at i:2099152 original size:62 final size:62
Alignment explanation
Indices: 2099076--2099221 Score: 274
Period size: 62 Copynumber: 2.4 Consensus size: 62
2099066 TTTAGGTGCT
*
2099076 AAAGGTTATGACACGCCATGCATAACAAGTTAAACTTTGTGACACGCCATGCATAACAAGCA
1 AAAGGTTATGACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAAGCA
*
2099138 AAAGGTTATGACACGCCATGCATAACAAGTTAAACGTTGTGACATGCCATGCATAACAAGCA
1 AAAGGTTATGACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAAGCA
2099200 AAAGGTTATGACACGCCATGCA
1 AAAGGTTATGACACGCCATGCA
2099222 GTATCGTGGG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (62 bp):
AAAGGTTATGACACGCCATGCATAACAAGTTAAACGTTGTGACACGCCATGCATAACAAGCA
Found at i:2099638 original size:52 final size:52
Alignment explanation
Indices: 2099581--2099690 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
2099571 ATCAAATTGT
* * * *
2099581 TTGTGTATAGGCA-AAAAAATTAATTTTGTATAAAAT-AATTGTATAAAGTATA
1 TTGTGTATA--CAGAAAAAATGAATTCTGTATAAAATAAATTGTATAAAATAAA
* * *
2099633 TTGTGTATACAGAAAGAATGAATTCTGTTTACAATAAATTGTATAAAATAAA
1 TTGTGTATACAGAAAAAATGAATTCTGTATAAAATAAATTGTATAAAATAAA
2099685 TTGTGT
1 TTGTGT
2099691 TTACCATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
50 2 0.04
51 18 0.37
52 29 0.59
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (52 bp):
TTGTGTATACAGAAAAAATGAATTCTGTATAAAATAAATTGTATAAAATAAA
Found at i:2099694 original size:30 final size:32
Alignment explanation
Indices: 2099653--2099721 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
2099643 AGAAAGAATG
*
2099653 AATTCTGTTTACAATAAA-T-TGTATAAAATA
1 AATTGTGTTTACAATAAATTGTGTATAAAATA
* *
2099683 AATTGTGTTTACCATAAATTTGTGTATAAAATT
1 AATTGTGTTTACAATAAA-TTGTGTATAAAATA
2099716 AATTGT
1 AATTGT
2099722 ATTAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 16 0.48
32 1 0.03
33 16 0.48
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (32 bp):
AATTGTGTTTACAATAAATTGTGTATAAAATA
Found at i:2099721 original size:16 final size:16
Alignment explanation
Indices: 2099672--2099721 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2099662 TACAATAAAT
2099672 TGTATAAAATAAATTG
1 TGTATAAAATAAATTG
* **
2099688 TGTTTACCATAAATTTG
1 TGTATAAAATAAA-TTG
*
2099705 TGTATAAAATTAATTG
1 TGTATAAAATAAATTG
2099721 T
1 T
2099722 ATTAAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (16 bp):
TGTATAAAATAAATTG
Found at i:2100622 original size:19 final size:20
Alignment explanation
Indices: 2100595--2100641 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2100585 AGGAGACAAG
*
2100595 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
* *
2100614 ATAATATTTTTATTAATTAA
1 ATAATATTTTTATGAATAAA
2100634 ATAATATT
1 ATAATATT
2100642 AAAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:2101453 original size:34 final size:34
Alignment explanation
Indices: 2101412--2101508 Score: 115
Period size: 34 Copynumber: 2.9 Consensus size: 34
2101402 GAAGGAAAAG
** *
2101412 AGAGCCATTTAAAGGCTGGTTTTGGAGGCTGAAA
1 AGAGCCATTTTTATGCTGGTTTTGGAGGCTGAAA
* * *
2101446 AGAGCCATTTTTTTGCTGGTTTTGGAGGTTGGAA
1 AGAGCCATTTTTATGCTGGTTTTGGAGGCTGAAA
*
2101480 AGTA-CCATTTTTCTGCTGGTTTTGGAGGC
1 AG-AGCCATTTTTATGCTGGTTTTGGAGGC
2101509 CAAAAAGTGC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
34 53 0.98
35 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (34 bp):
AGAGCCATTTTTATGCTGGTTTTGGAGGCTGAAA
Found at i:2101516 original size:34 final size:35
Alignment explanation
Indices: 2101426--2101508 Score: 125
Period size: 34 Copynumber: 2.4 Consensus size: 35
2101416 CCATTTAAAG
*
2101426 GCTGGTTTTGGAGGCTGAAAAG-AGCCATTTTTTT
1 GCTGGTTTTGGAGGCTGAAAAGTAGCCATTTTTCT
* *
2101460 GCTGGTTTTGGAGGTTGGAAAGTA-CCATTTTTCT
1 GCTGGTTTTGGAGGCTGAAAAGTAGCCATTTTTCT
2101494 GCTGGTTTTGGAGGC
1 GCTGGTTTTGGAGGC
2101509 CAAAAAGTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 43 0.98
35 1 0.02
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.39
Consensus pattern (35 bp):
GCTGGTTTTGGAGGCTGAAAAGTAGCCATTTTTCT
Found at i:2101845 original size:5 final size:5
Alignment explanation
Indices: 2101823--2101874 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
2101813 GGACGGTGGG
*
2101823 AAAG- AAAG- AAAG- AAAGA AAAGA AAAGA AAAGA AAAGA AAATA ACAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA
2101871 AAAG
1 AAAG
2101875 TGAGCATGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
4 12 0.27
5 28 0.64
6 4 0.09
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:2101952 original size:25 final size:25
Alignment explanation
Indices: 2101897--2101954 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
2101887 AACAAGCAAG
* *
2101897 AAAAATGGCCATGGTCCAATAAAGG
1 AAAAATGGACATGGTCCAATAAAGA
*
2101922 AAAAATGGACATGGTCCAAT-TAGA
1 AAAAATGGACATGGTCCAATAAAGA
2101946 AAGAAATGG
1 AA-AAATGG
2101955 GAGAAGTCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.17
Consensus pattern (25 bp):
AAAAATGGACATGGTCCAATAAAGA
Found at i:2104863 original size:62 final size:62
Alignment explanation
Indices: 2104797--2105042 Score: 273
Period size: 62 Copynumber: 4.0 Consensus size: 62
2104787 CCTAAAATAC
* * * * **
2104797 TGTGACACGCCATGCATGACAAACAAAATGTTGTGACACGCCATCCATAACAAAAAAATTAT
1 TGTGACACGCAATGCATAACAAGCAAAACGTTGTGACACGCCATCCATAACAAGCAAATTAT
* * *
2104859 TGTGACACACAATGCATAACAAGTAAAACGTTGTGACACGCCATCCATAACAAGCAAATTGT
1 TGTGACACGCAATGCATAACAAGCAAAACGTTGTGACACGCCATCCATAACAAGCAAATTAT
** * *
2104921 TGTGACACGTC-ATGCATAACAAGTTAAACGTTGTGACACACCATCCATAACAAGCAAA-CACT
1 TGTGACACG-CAATGCATAACAAGCAAAACGTTGTGACACGCCATCCATAACAAGCAAATTA-T
* * * * *
2104983 TGTGACACGCTAATG-ATAGCAAGCAAAATGTTCTGACACGCCATGCATATCAAGTCAAAT
1 TGTGACACGC-AATGCATAACAAGCAAAACGTTGTGACACGCCATCCATAACAAG-CAAAT
2105043 GTTGTCACAC
Statistics
Matches: 156, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
61 1 0.01
62 147 0.94
63 8 0.05
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (62 bp):
TGTGACACGCAATGCATAACAAGCAAAACGTTGTGACACGCCATCCATAACAAGCAAATTAT
Found at i:2104894 original size:93 final size:92
Alignment explanation
Indices: 2104797--2105036 Score: 270
Period size: 93 Copynumber: 2.6 Consensus size: 92
2104787 CCTAAAATAC
* * *
2104797 TGTGACACGCCATGCATGACAAACAAAATGTTGTGACACGCCATCCATAACAA-AAAAATTATTG
1 TGTGACACGCCATGCAT-ACAAGCAAAATGTTGTGACACGCCATGCATAACAAGAAAAA-CATTG
* *
2104861 TGACACACAATGCATAACAAGTAAA-ACGT
64 TGACACACAATCCATAACAAGCAAACAC-T
* * * ** *
2104890 TGTGACACGCCATCCATAACAAGCAAATTGTTGTGACACGTCATGCATAACAAGTTAAACGTTGT
1 TGTGACACGCCATGCAT-ACAAGCAAAATGTTGTGACACGCCATGCATAACAAGAAAAACATTGT
*
2104955 GACACACCATCCATAACAAGCAAACACT
65 GACACACAATCCATAACAAGCAAACACT
* * *
2104983 TGTGACACGCTAATG-ATAGCAAGCAAAATGTTCTGACACGCCATGCATATCAAG
1 TGTGACACGC-CATGCATA-CAAGCAAAATGTTGTGACACGCCATGCATAACAAG
2105037 TCAAATGTTG
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
92 1 0.01
93 116 0.94
94 7 0.06
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (92 bp):
TGTGACACGCCATGCATACAAGCAAAATGTTGTGACACGCCATGCATAACAAGAAAAACATTGTG
ACACACAATCCATAACAAGCAAACACT
Found at i:2105053 original size:31 final size:31
Alignment explanation
Indices: 2104699--2105054 Score: 233
Period size: 31 Copynumber: 11.5 Consensus size: 31
2104689 ATAAACAGTA
* * * *
2104699 AAATGTTGTGATACGCCGTGCATATCAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTC
* * ** * *
2104730 AAATGTTGTCATA-AACATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTC
* * ** *
2104760 AAATATTGTGACACGCCATGCACATAC-CCTA
1 AAATGTTGTGACACGCCATGCATA-ACAAGTC
** * *
2104791 AAATACTGTGACACGCCATGCATGACAA-AC
1 AAATGTTGTGACACGCCATGCATAACAAGTC
* **
2104821 AAAATGTTGTGACACGCCATCCATAACAA-AA
1 -AAATGTTGTGACACGCCATGCATAACAAGTC
* * * *
2104852 AAATTATTGTGACACACAATGCATAACAAGTA
1 AAA-TGTTGTGACACGCCATGCATAACAAGTC
* *
2104884 AAACGTTGTGACACGCCATCCATAACAAG-C
1 AAATGTTGTGACACGCCATGCATAACAAGTC
* *
2104914 AAATTGTTGTGACACGTCATGCATAACAAGTT
1 AAA-TGTTGTGACACGCCATGCATAACAAGTC
* * *
2104946 AAACGTTGTGACACACCATCCATAACAAG-C
1 AAATGTTGTGACACGCCATGCATAACAAGTC
** * *
2104976 AAACACTTGTGACACGCTAATG-ATAGCAAG-C
1 AAA-TGTTGTGACACGC-CATGCATAACAAGTC
* *
2105007 AAAATGTTCTGACACGCCATGCATATCAAGTC
1 -AAATGTTGTGACACGCCATGCATAACAAGTC
*
2105039 AAATGTTGTCACACGC
1 AAATGTTGTGACACGC
2105055 TAAACAGTTG
Statistics
Matches: 254, Mismatches: 58, Indels: 26
0.75 0.17 0.08
Matches are distributed among these distances:
30 37 0.15
31 203 0.80
32 14 0.06
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTC
Found at i:2105069 original size:11 final size:11
Alignment explanation
Indices: 2105053--2105081 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2105043 GTTGTCACAC
2105053 GCTAAACAGTT
1 GCTAAACAGTT
2105064 GCTAAACAGTT
1 GCTAAACAGTT
2105075 GCTAAAC
1 GCTAAAC
2105082 GTAAACCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (11 bp):
GCTAAACAGTT
Found at i:2107631 original size:31 final size:31
Alignment explanation
Indices: 2107263--2107627 Score: 426
Period size: 31 Copynumber: 11.8 Consensus size: 31
2107253 AATAAGGAAC
* * * * *
2107263 AAAA-GTTATGACACGTCATTCATAGCAAGC
1 AAAATGTTGTGACACGCCATGCATAACAAGT
*
2107293 AAAATGTTGTGACATGCCATGCATAACAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* *
2107324 TAAATGTTGTGACACGCCATGCATAACAACT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
*
2107355 TAAATGTTGTGACACGCCATGCATAACAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* * *
2107386 TAAACGTTGTGACACGCCATGCATAACAGGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* * *
2107417 CAAATGTTGTGACATGCCATGCATATCAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* * * *
2107448 AAAATGCTGTCACACACCATGCATAGCAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* * *
2107479 AAATTGTTGTGACACGTCATGCATATCAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* * * *
2107510 AAAATGCTGTCATACGCCATGCATATCAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* *
2107541 AAAATGCTGTCACACGCCATGCATAACAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* *
2107572 AAAATGCTGTGACACGCCATGCATATCAAGT
1 AAAATGTTGTGACACGCCATGCATAACAAGT
* * *
2107603 CAAATGCTATGACACGCCATGCATA
1 AAAATGTTGTGACACGCCATGCATA
2107628 TCAAAGCAAA
Statistics
Matches: 294, Mismatches: 40, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
30 4 0.01
31 290 0.99
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (31 bp):
AAAATGTTGTGACACGCCATGCATAACAAGT
Found at i:2108221 original size:53 final size:53
Alignment explanation
Indices: 2108145--2108256 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 53
2108135 CTCTATTCAA
* * * *
2108145 ACCATGATGTGTCAGCTGCTCAAGCACTGACGTGTCACACACTCTAAGCCATG
1 ACCATGATGTGTCAACTGCTCAAGCAATGACGTATCACACACTCTAAACCATG
* ** *
2108198 ACCATGGTGTGTCAACTTTTCAAGCAATGTCGTATCACACACTCTAAACCATG
1 ACCATGATGTGTCAACTGCTCAAGCAATGACGTATCACACACTCTAAACCATG
2108251 ACCATG
1 ACCATG
2108257 CCGTGTCACC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (53 bp):
ACCATGATGTGTCAACTGCTCAAGCAATGACGTATCACACACTCTAAACCATG
Found at i:2108337 original size:47 final size:47
Alignment explanation
Indices: 2108252--2108883 Score: 647
Period size: 47 Copynumber: 13.4 Consensus size: 47
2108242 TAAACCATGA
* * * *
2108252 CCATGCCGTGTCACCAACTCTGAACTCTGACGTGTCACAGCTTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * *
2108299 CCAAGGCATGTCACCAACTCTTAACTCTGGCGTTTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * * * *
2108346 CCATGGCGTCTCACTAACTCTGAACACTAGCGTGTAACAAATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * *
2108393 CAATGCCGTGTCACCAACTCTTAACTCTGGCATGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
** * * * *
2108440 TTATGGCATCTCACCAACT-TTGAACGCTGACGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTT-AACTCTGGCGTGTCACAGATTCCCT
* * * *
2108487 CAATGGCGTGTCACCAACTCTGAACTCTAGCGTGTCACAGCTTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * *
2108534 CCATGGCGTGTCACAAACTCTTAACTCTGACATGTCACACATTCCAT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * *
2108581 CCATGGCGTTTCACCAACTCTGAACGCTGGCTTGTCATAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * *
2108628 CCATGCCGTGTCACTAACTTTTAACTCTGGCGTCTCACAAATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * *
2108675 CCATGGCGTCTCACCAACTCTGAACAT-TGACGTGTCATAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAAC-TCTGGCGTGTCACAGATTCCCT
* * * *
2108722 CCATGCCGTGTCACCAACTCCTAACTCTGGCGTGTCATAGATTCTCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * *** *
2108769 CCATGGCATCTCACCAACTCTGAACACTAATGTGCCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * *
2108816 TCATGGCGTGTCGCCAACTCTTAACTCTAGCGTCTCACAAATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* *
2108863 CCATGACGTCTCACCAACTCT
1 CCATGGCGTGTCACCAACTCT
2108884 GACCGGTACC
Statistics
Matches: 467, Mismatches: 114, Indels: 8
0.79 0.19 0.01
Matches are distributed among these distances:
46 3 0.01
47 462 0.99
48 2 0.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.28
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
Found at i:2111282 original size:2 final size:2
Alignment explanation
Indices: 2111275--2111327 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2111265 NATATGGCGA
2111275 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
2111317 AT AT AT AT AT A
1 AT AT AT AT AT A
2111328 AACACACTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2112584 original size:16 final size:16
Alignment explanation
Indices: 2112563--2112597 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2112553 ATTTAGGAAA
*
2112563 AATATTTAAATTAATT
1 AATATTTAAATAAATT
*
2112579 AATATTTTAATAAATT
1 AATATTTAAATAAATT
2112595 AAT
1 AAT
2112598 CAAATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATTTAAATAAATT
Found at i:2116355 original size:18 final size:18
Alignment explanation
Indices: 2116329--2116364 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2116319 GTTGAACATA
*
2116329 ACGAAGAAGATGATGAAG
1 ACGAAGAAGATAATGAAG
*
2116347 ACGAGGAAGATAATGAAG
1 ACGAAGAAGATAATGAAG
2116365 CTGAAGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.33, T:0.11
Consensus pattern (18 bp):
ACGAAGAAGATAATGAAG
Found at i:2127347 original size:31 final size:31
Alignment explanation
Indices: 2127309--2127449 Score: 185
Period size: 31 Copynumber: 4.5 Consensus size: 31
2127299 GTTAACCCAT
*
2127309 AATGTTGTAACACGCCATACATATAATATAA
1 AATGTTGTAACACGCCATACATATAATGTAA
*
2127340 AATGTTGTAACACGCCATGCATATAATGTAA
1 AATGTTGTAACACGCCATACATATAATGTAA
* * *
2127371 AATGTTGTAATACGCTATACATATAACGTAA
1 AATGTTGTAACACGCCATACATATAATGTAA
* *
2127402 AATGTTGTAACACGCCATGCATATCAA-GTCA
1 AATGTTGTAACACGCCATACATAT-AATGTAA
* *
2127433 AATGTCGTTACACGCCA
1 AATGTTGTAACACGCCA
2127450 ATACTGACAC
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 95 0.98
32 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (31 bp):
AATGTTGTAACACGCCATACATATAATGTAA
Found at i:2128089 original size:23 final size:23
Alignment explanation
Indices: 2128057--2128100 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2128047 TTGTTCTTTT
2128057 TTCAAACCATGTCGTGTCACATG
1 TTCAAACCATGTCGTGTCACATG
*
2128080 TTCAAGCCATGTCGTGTCACA
1 TTCAAACCATGTCGTGTCACA
2128101 CACTCTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (23 bp):
TTCAAACCATGTCGTGTCACATG
Found at i:2128190 original size:23 final size:23
Alignment explanation
Indices: 2128160--2128238 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
2128150 TGAACCCTAC
2128160 CGTGTCACAGATTCCCTCCATGG
1 CGTGTCACAGATTCCCTCCATGG
* * ***
2128183 CGTGTCACAAACTCTGAACGC-TGG
1 CGTGTCACAGATTC-CCTC-CATGG
*
2128207 CGTGTCACAGATTCTCTCCATGG
1 CGTGTCACAGATTCCCTCCATGG
*
2128230 TGTGTCACA
1 CGTGTCACA
2128239 AACTTTGAAC
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 1 0.02
23 24 0.57
24 16 0.38
25 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (23 bp):
CGTGTCACAGATTCCCTCCATGG
Found at i:2128194 original size:47 final size:47
Alignment explanation
Indices: 2128086--2128592 Score: 538
Period size: 47 Copynumber: 10.9 Consensus size: 47
2128076 CATGTTCAAG
* * * * * * *
2128086 CCATGTCGTGTCACACACTCTAAACCCTACCATGTCATAGA-T--CT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* * * * * *
2128130 CCATGGAGTCTGACAAACTTTGAACCCTACCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* *
2128177 CCATGGCGTGTCACAAACTCTGAACGCTGGCGTGTCACAGATTCTCT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* * * *
2128224 CCATGGTGTGTCACAAACTTTGAACGCTGACATGTCACAGATTCCCT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* * * *
2128271 CCATGGTGTGTCACAAACTCTAAACGCTGACGTGTCACTGATTCCCT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* * *
2128318 CCATGCCGTGTCACAAACTCTGAACGCTAG-CGTGTCATAGATTCCAT
1 CCATGGCGTGTCACAAACTCTGAACGCT-GCCGTGTCACAGATTCCCT
* * *
2128365 CCATGGCATGTCACAAACTTTGAAC-CTTGCCATGTCACAGATTCCCT
1 CCATGGCGTGTCACAAACTCTGAACGC-TGCCGTGTCACAGATTCCCT
* * * * *
2128412 CCATGGTGTGTCATAAACTCTAAACGCTGGCATGTCACAGATTCCCT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* * * *
2128459 CCATGCCGTATCACAAACTCTAAACGCTGCCGTGTCACAGATTCCTT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* * * * * *
2128506 CCATGGGGTGTCACAAACTCTGAACCCTGTCGTATCACAAATTCTCT
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
* * *
2128553 CCATGGCGTGTCACAAACTCTAAACCCTGCCATGTCACAG
1 CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAG
2128593 TTGTGTCACA
Statistics
Matches: 389, Mismatches: 67, Indels: 11
0.83 0.14 0.02
Matches are distributed among these distances:
44 32 0.08
45 1 0.00
46 2 0.01
47 352 0.90
48 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (47 bp):
CCATGGCGTGTCACAAACTCTGAACGCTGCCGTGTCACAGATTCCCT
Found at i:2128320 original size:141 final size:140
Alignment explanation
Indices: 2128160--2128592 Score: 598
Period size: 141 Copynumber: 3.1 Consensus size: 140
2128150 TGAACCCTAC
*
2128160 CGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCTGGCGTGTCACAGATTCTC-T
1 CGTGTCACAGATTCCCTCCATGCCGTGTCACAAACTCTGAACGCTGGCGTGTCACAGATTC-CAT
*
2128224 CCATGGTGTGTCACAAACTTTGAACGCTGACATGTCACAGATTCCCTCCATGGTGTGTCACAAAC
65 CCATGGCGTGTCACAAACTTTGAAC-CTGACATGTCACAGATTCCCTCCATGGTGTGTCACAAAC
2128289 TCTAAACGCTGA
129 TCTAAACGCTGA
* * *
2128301 CGTGTCACTGATTCCCTCCATGCCGTGTCACAAACTCTGAACGCTAGCGTGTCATAGATTCCATC
1 CGTGTCACAGATTCCCTCCATGCCGTGTCACAAACTCTGAACGCTGGCGTGTCACAGATTCCATC
* * *
2128366 CATGGCATGTCACAAACTTTGAACCTTGCCATGTCACAGATTCCCTCCATGGTGTGTCATAAACT
66 CATGGCGTGTCACAAACTTTGAACC-TGACATGTCACAGATTCCCTCCATGGTGTGTCACAAACT
*
2128431 CTAAACGCTGG
130 CTAAACGCTGA
* * * * *
2128442 CATGTCACAGATTCCCTCCATGCCGTATCACAAACTCTAAACGCTGCCGTGTCACAGATTCCTTC
1 CGTGTCACAGATTCCCTCCATGCCGTGTCACAAACTCTGAACGCTGGCGTGTCACAGATTCCATC
* * * * * * * *
2128507 CATGGGGTGTCACAAACTCTGAACCCTGTCGTATCACAAATTCTCTCCATGGCGTGTCACAAACT
66 CATGGCGTGTCACAAACTTTGAA-CCTGACATGTCACAGATTCCCTCCATGGTGTGTCACAAACT
* *
2128572 CTAAACCCTGC
130 CTAAACGCTGA
*
2128583 CATGTCACAG
1 CGTGTCACAG
2128593 TTGTGTCACA
Statistics
Matches: 260, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
140 2 0.01
141 256 0.98
142 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (140 bp):
CGTGTCACAGATTCCCTCCATGCCGTGTCACAAACTCTGAACGCTGGCGTGTCACAGATTCCATC
CATGGCGTGTCACAAACTTTGAACCTGACATGTCACAGATTCCCTCCATGGTGTGTCACAAACTC
TAAACGCTGA
Found at i:2128569 original size:23 final size:23
Alignment explanation
Indices: 2128489--2128569 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
2128479 TAAACGCTGC
*
2128489 CGTGTCACAGATTC-CTTCCATGG
1 CGTGTCACAAATTCTC-TCCATGG
* * ** * *
2128512 GGTGTCACAAACTCTGAACCCTGT
1 CGTGTCACAAATTCT-CTCCATGG
*
2128536 CGTATCACAAATTCTCTCCATGG
1 CGTGTCACAAATTCTCTCCATGG
2128559 CGTGTCACAAA
1 CGTGTCACAAA
2128570 CTCTAAACCC
Statistics
Matches: 41, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
23 25 0.61
24 16 0.39
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (23 bp):
CGTGTCACAAATTCTCTCCATGG
Found at i:2128625 original size:23 final size:23
Alignment explanation
Indices: 2128595--2128638 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2128585 TGTCACAGTT
*
2128595 GTGTCACACATTCCCACCATGTC
1 GTGTCACACATTCCCAACATGTC
2128618 GTGTCACACATTCCCAACATG
1 GTGTCACACATTCCCAACATG
2128639 CCATTTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (23 bp):
GTGTCACACATTCCCAACATGTC
Found at i:2128647 original size:23 final size:23
Alignment explanation
Indices: 2128596--2128648 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2128586 GTCACAGTTG
* * *
2128596 TGTCACACATTCCCACCATGTCG
1 TGTCACACATTCCCAACATGCCA
2128619 TGTCACACATTCCCAACATGCCA
1 TGTCACACATTCCCAACATGCCA
*
2128642 TTTCACA
1 TGTCACA
2128649 AACTCTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.38, G:0.09, T:0.26
Consensus pattern (23 bp):
TGTCACACATTCCCAACATGCCA
Found at i:2152316 original size:17 final size:17
Alignment explanation
Indices: 2152278--2152317 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2152268 CAATACATTG
*
2152278 TGTGTTGAATCATTCCG
1 TGTGTTGAATCATTCCA
*
2152295 CGTGTTGAATCATTCCA
1 TGTGTTGAATCATTCCA
2152312 TGTGTT
1 TGTGTT
2152318 TGCAGTCTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (17 bp):
TGTGTTGAATCATTCCA
Found at i:2156882 original size:32 final size:32
Alignment explanation
Indices: 2156844--2156921 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
2156834 TAGGTTATTA
2156844 ATGTGGCAATGTCACAGCTCCTTGACATGCTG
1 ATGTGGCAATGTCACAGCTCCTTGACATGCTG
*
2156876 ATGTGGCAATGTCACGGCTCCTTGACATGCTG
1 ATGTGGCAATGTCACAGCTCCTTGACATGCTG
2156908 ATGTGGCAATGTCA
1 ATGTGGCAATGTCA
2156922 TACACCTTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (32 bp):
ATGTGGCAATGTCACAGCTCCTTGACATGCTG
Found at i:2164591 original size:179 final size:179
Alignment explanation
Indices: 2164291--2164648 Score: 707
Period size: 179 Copynumber: 2.0 Consensus size: 179
2164281 AAAAGCACAT
2164291 CTGGTTATTGTTTTTCACTTGGCAGTACAGTTTTTAGCTGGAATTCAAAAAAGCAGGAGGTGGTG
1 CTGGTTATTGTTTTTCACTTGGCAGTACAGTTTTTAGCTGGAATTCAAAAAAGCAGGAGGTGGTG
*
2164356 GCTCAATCTTTAGCAGAAGCAGAATATATTGCTGCTGCAGCTGTTACAAATCATGTGATTTGGTT
66 GCTCAATCTTCAGCAGAAGCAGAATATATTGCTGCTGCAGCTGTTACAAATCATGTGATTTGGTT
2164421 GAGAAAAGTCTTTCATGATTTGGGGTATAACTATGAGAAGGGTACACTG
131 GAGAAAAGTCTTTCATGATTTGGGGTATAACTATGAGAAGGGTACACTG
2164470 CTGGTTATTGTTTTTCACTTGGCAGTACAGTTTTTAGCTGGAATTCAAAAAAGCAGGAGGTGGTG
1 CTGGTTATTGTTTTTCACTTGGCAGTACAGTTTTTAGCTGGAATTCAAAAAAGCAGGAGGTGGTG
2164535 GCTCAATCTTCAGCAGAAGCAGAATATATTGCTGCTGCAGCTGTTACAAATCATGTGATTTGGTT
66 GCTCAATCTTCAGCAGAAGCAGAATATATTGCTGCTGCAGCTGTTACAAATCATGTGATTTGGTT
2164600 GAGAAAAGTCTTTCATGATTTGGGGTATAACTATGAGAAGGGTACACTG
131 GAGAAAAGTCTTTCATGATTTGGGGTATAACTATGAGAAGGGTACACTG
2164649 TTATTCATTG
Statistics
Matches: 178, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 178 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.33
Consensus pattern (179 bp):
CTGGTTATTGTTTTTCACTTGGCAGTACAGTTTTTAGCTGGAATTCAAAAAAGCAGGAGGTGGTG
GCTCAATCTTCAGCAGAAGCAGAATATATTGCTGCTGCAGCTGTTACAAATCATGTGATTTGGTT
GAGAAAAGTCTTTCATGATTTGGGGTATAACTATGAGAAGGGTACACTG
Found at i:2171341 original size:10 final size:10
Alignment explanation
Indices: 2171315--2171353 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
2171305 TATATAAAAT
2171315 TAAAAATTATA
1 TAAAAATTA-A
2171326 TAAAAATTAA
1 TAAAAATTAA
*
2171336 TTAAAATT-A
1 TAAAAATTAA
2171345 TAAAAATTA
1 TAAAAATTA
2171354 TTTATTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:2173432 original size:21 final size:21
Alignment explanation
Indices: 2173395--2173434 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2173385 TTTTTCTTTA
*
2173395 TCAAATCGAATTGGATTGAGT
1 TCAAATCGAATTAGATTGAGT
2173416 TCAAATGCGAA-TAGATTGA
1 TCAAAT-CGAATTAGATTGA
2173435 TCATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (21 bp):
TCAAATCGAATTAGATTGAGT
Found at i:2176297 original size:21 final size:21
Alignment explanation
Indices: 2176273--2176315 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2176263 CAACATAAAA
2176273 TTAGAGACAGCATAATAGAAT
1 TTAGAGACAGCATAATAGAAT
2176294 TTAGAGACAGCATAATAGAAT
1 TTAGAGACAGCATAATAGAAT
2176315 T
1 T
2176316 AGATAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (21 bp):
TTAGAGACAGCATAATAGAAT
Found at i:2179992 original size:18 final size:18
Alignment explanation
Indices: 2179969--2180009 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2179959 ACCTTTTGAA
* * *
2179969 CAAATATAGTTGTTCGAG
1 CAAATATAATTATTCGAC
2179987 CAAATATAATTATTCGAC
1 CAAATATAATTATTCGAC
2180005 CAAAT
1 CAAAT
2180010 CAGGGAGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (18 bp):
CAAATATAATTATTCGAC
Found at i:2181665 original size:18 final size:18
Alignment explanation
Indices: 2181634--2181678 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2181624 GTGACCGCTT
2181634 TTTCTTT-TCT-ACTTCAC
1 TTTCTTTCTCTGACTT-AC
*
2181651 TTT-TTTCTCTGACTTTC
1 TTTCTTTCTCTGACTTAC
2181668 TTTCTTTCTCT
1 TTTCTTTCTCT
2181679 CTCTCTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.12
17 10 0.42
18 11 0.46
ACGTcount: A:0.07, C:0.27, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTCTTTCTCTGACTTAC
Found at i:2193383 original size:71 final size:71
Alignment explanation
Indices: 2193263--2193398 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 71
2193253 GGCAGGGTTT
* * * * * *
2193263 AGAGTTTGTGAAACGTCATGTTGGGAATGTGTGACACGGCACCGCTCAGAGTTGGTGAGACGCCA
1 AGAGTTGGTGAAACGTCATGGTGAGAATCTGTGACACGCCAACGCTCAGAGTTGGTGAGACGCCA
2193328 GAGTTA
66 GAGTTA
* *
2193334 AGAGTTGGTGACACGTCATGGTGAGAATCTGTGACACGCCAACGTTCAGAGTTGGTGAGACGCCA
1 AGAGTTGGTGAAACGTCATGGTGAGAATCTGTGACACGCCAACGCTCAGAGTTGGTGAGACGCCA
2193399 TGGAGGGAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (71 bp):
AGAGTTGGTGAAACGTCATGGTGAGAATCTGTGACACGCCAACGCTCAGAGTTGGTGAGACGCCA
GAGTTA
Found at i:2193385 original size:47 final size:47
Alignment explanation
Indices: 2193317--2193683 Score: 434
Period size: 47 Copynumber: 7.8 Consensus size: 47
2193307 CTCAGAGTTG
* * * *
2193317 GTGAGACGCCAGAGTTAAGAGTTGGTGACACGTCATGGTGAGAATCT
1 GTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
* *
2193364 GTGACACGCCA-ACGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCT
1 GTGACACGCCAGA-GTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
* *
2193411 GTGACACGCCAGAGTTAAGAGTTGGTGACACGACATAGAGGGAATCT
1 GTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
* * * *
2193458 GTGACACGCCA-ACGTTTAGAGTTTGTGAGACGCTATGGAGGGAATCT
1 GTGACACGCCAGA-GTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
* * *
2193505 GTGACACGTCAAAGTTAAGAGTTGGTGACACGCTATGGAGGGAATCT
1 GTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
* * * * * *
2193552 GTGACATGCCGGCA-TTCAGAGTTCGTGAGAGGCCATGGAGGGAATCT
1 GTGACACGCCAG-AGTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
* * *
2193599 GTGACATGCCAGAGTTTAGAGTTGGTGACACGCCATGGAGGGAAGCT
1 GTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
* * * *
2193646 GTGATACTCTAGAGTTAAGAGTTGGTGACACACCATGG
1 GTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGG
2193684 TCATGGTTTA
Statistics
Matches: 273, Mismatches: 41, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
46 3 0.01
47 267 0.98
48 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.22
Consensus pattern (47 bp):
GTGACACGCCAGAGTTAAGAGTTGGTGACACGCCATGGAGGGAATCT
Found at i:2193396 original size:24 final size:23
Alignment explanation
Indices: 2193308--2193442 Score: 76
Period size: 24 Copynumber: 5.7 Consensus size: 23
2193298 ACGGCACCGC
*
2193308 TCAGAGTTGGTGAGACGCCAGAGT
1 TCAGAGTTGGTGACACGCCA-AGT
* * * *
2193332 TAAGAGTTGGTGACACGTCATGG
1 TCAGAGTTGGTGACACGCCAAGT
* *
2193355 TGAGAATCT-GTGACACGCCAACGT
1 TCAGAGT-TGGTGACACGCCAA-GT
* * *
2193379 TCAGAGTTGGTGAGACGCCATGG
1 TCAGAGTTGGTGACACGCCAAGT
*** *
2193402 AGGGAATCT-GTGACACGCCAGAGT
1 TCAGAGT-TGGTGACACGCCA-AGT
*
2193426 TAAGAGTTGGTGACACG
1 TCAGAGTTGGTGACACG
2193443 ACATAGAGGG
Statistics
Matches: 79, Mismatches: 26, Indels: 12
0.68 0.22 0.10
Matches are distributed among these distances:
23 32 0.41
24 47 0.59
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (23 bp):
TCAGAGTTGGTGACACGCCAAGT
Found at i:2193419 original size:23 final size:22
Alignment explanation
Indices: 2193388--2193468 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 22
2193378 TTCAGAGTTG
*
2193388 GTGAGACGCCATGGAGGGAATCT
1 GTGACACGCCAT-GAGGGAATCT
* *
2193411 GTGACACGCCA-GAGTTAAGAGT-T
1 GTGACACGCCATGAG---GGAATCT
*
2193434 GGTGACACGACATAGAGGGAATCT
1 -GTGACACGCCAT-GAGGGAATCT
2193458 GTGACACGCCA
1 GTGACACGCCA
2193469 ACGTTTAGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 14
0.68 0.11 0.22
Matches are distributed among these distances:
21 3 0.07
23 24 0.55
24 14 0.32
26 3 0.07
ACGTcount: A:0.30, C:0.20, G:0.33, T:0.17
Consensus pattern (22 bp):
GTGACACGCCATGAGGGAATCT
Found at i:2193769 original size:53 final size:53
Alignment explanation
Indices: 2193671--2193790 Score: 159
Period size: 53 Copynumber: 2.3 Consensus size: 53
2193661 TAAGAGTTGG
* *
2193671 TGACACACCATGGTCATGGTTTAAAGTGTGTGACACGGCATTGCTTGAAAAGT
1 TGACACACCATGGTCATGGTTTAAAGTGTGTGACACGACAGTGCTTGAAAAGT
* * * ** *
2193724 TGACACGCCATGGTCATGGTTTAGAGTGTGTGACACGATAGTGCTTGAGCAGC
1 TGACACACCATGGTCATGGTTTAAAGTGTGTGACACGACAGTGCTTGAAAAGT
*
2193777 TGACACATCATGGT
1 TGACACACCATGGT
2193791 TTGAAATAGA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (53 bp):
TGACACACCATGGTCATGGTTTAAAGTGTGTGACACGACAGTGCTTGAAAAGT
Found at i:2194321 original size:31 final size:31
Alignment explanation
Indices: 2194287--2194621 Score: 433
Period size: 31 Copynumber: 10.8 Consensus size: 31
2194277 TTTGATTTGA
* * *
2194287 TATGCATGGCATGTGACAACATTTTACTTGA
1 TATGCATGGCGTGTCACAACATTTTACTTGT
2194318 TATGCATGGCGTGTCACAACATTTTACTTGT
1 TATGCATGGCGTGTCACAACATTTTACTTGT
* *
2194349 TATGCATGGCGTGTGACAGCATTTTACTT-T
1 TATGCATGGCGTGTCACAACATTTTACTTGT
*
2194379 ATATGCATGGCGTGTAACAACATTTTACTTGT
1 -TATGCATGGCGTGTCACAACATTTTACTTGT
* * *
2194411 TATGCATGGCGTGTGACAGCATTTTA-TTTT
1 TATGCATGGCGTGTCACAACATTTTACTTGT
* **
2194441 ATATGCATGGCGTGTGACAGTATTTTACTTGT
1 -TATGCATGGCGTGTCACAACATTTTACTTGT
* *
2194473 TATGCATGGCGTGTCACAACGTTTAACTTGT
1 TATGCATGGCGTGTCACAACATTTTACTTGT
**
2194504 TATGCATGATGTGTCACAACATTTTACTTGT
1 TATGCATGGCGTGTCACAACATTTTACTTGT
* *
2194535 TATTCATGACGTGTCACAACATTTTACTTGT
1 TATGCATGGCGTGTCACAACATTTTACTTGT
* * * *
2194566 TATGCATGGTGTGTCACAATATTTTGCTTGC
1 TATGCATGGCGTGTCACAACATTTTACTTGT
2194597 TATGCATGGCGTGTCACAAC-TTTTA
1 TATGCATGGCGTGTCACAACATTTTA
2194622 TTCCTTATTG
Statistics
Matches: 268, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.03
31 256 0.96
32 4 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (31 bp):
TATGCATGGCGTGTCACAACATTTTACTTGT
Found at i:2201861 original size:12 final size:12
Alignment explanation
Indices: 2201822--2201853 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
2201812 AACAATCATT
2201822 TAAAAAATTATA
1 TAAAAAATTATA
2201834 TAAAAAATTATA
1 TAAAAAATTATA
2201846 TAAAAAAT
1 TAAAAAAT
2201854 AAGATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAAAATTATA
Found at i:2204867 original size:15 final size:16
Alignment explanation
Indices: 2204837--2204882 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
2204827 ATTGTTATTT
2204837 AAAATAATATACATAA
1 AAAATAATATACATAA
2204853 AAAATAATATA-AT-A
1 AAAATAATATACATAA
*
2204867 AAAATAA-ATATATAA
1 AAAATAATATACATAA
2204882 A
1 A
2204883 TAAGGCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.11
14 10 0.36
15 4 0.14
16 11 0.39
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAATATACATAA
Found at i:2204869 original size:14 final size:15
Alignment explanation
Indices: 2204837--2204882 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
2204827 ATTGTTATTT
2204837 AAAATAATATACATAA
1 AAAATAATATACAT-A
2204853 AAAATAATATA-ATA
1 AAAATAATATACATA
*
2204867 AAAATAA-ATATATA
1 AAAATAATATACATA
2204881 AA
1 AA
2204883 TAAGGCAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.10
14 13 0.45
15 2 0.07
16 11 0.38
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATAATATACATA
Found at i:2204885 original size:21 final size:20
Alignment explanation
Indices: 2204838--2204885 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
2204828 TTGTTATTTA
* *
2204838 AAATAATATACATAAAAAAT
1 AAATAATAAAAATAAAAAAT
*
2204858 AATATAATAAAAATAAATATAT
1 AA-ATAATAAAAATAAA-AAAT
2204880 AAATAA
1 AAATAA
2204886 GGCAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 16 0.70
22 5 0.22
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAATAAAAATAAAAAAT
Found at i:2208647 original size:22 final size:22
Alignment explanation
Indices: 2208620--2208661 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2208610 TAAGGTCAAT
2208620 TAATAAAATTAT-TAAAAAATAA
1 TAAT-AAATTATATAAAAAATAA
*
2208642 TAATAAATTATATAATAAAT
1 TAATAAATTATATAAAAAAT
2208662 TGATAGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATAAATTATATAAAAAATAA
Found at i:2209240 original size:132 final size:131
Alignment explanation
Indices: 2209100--2209346 Score: 415
Period size: 132 Copynumber: 1.9 Consensus size: 131
2209090 ATATATTTTT
*
2209100 TTTACTTAATTAACTTATTACGTTAACTCTCATACATTTACGTTAA-ATTTTAAAATTTAGTTAT
1 TTTACTTAATTAACTTATTACGTTAACTCTCATACATTTACATTAAGA-TTTAAAATTTAGTTAT
* *
2209164 TCCACTTTTAAATGTTTTTACGTAAATTATTACAGTTTTACGTCAAGGCTTTTCCATGTCAACTT
65 TCCACCTTTAAATGTTTTTACGTAAATTATTACAATTTTACGTCAAGGCTTTTCCATGTCAACTT
2209229 TG
130 TG
2209231 NTTTACTTAATTAACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTAT
1 -TTTACTTAATTAACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTAT
* * *
2209296 TCCACCTTTATATGTTTTTACGTCAATTGTTACAATTTTACGTCAAGGCTT
65 TCCACCTTTAAATGTTTTTACGTAAATTATTACAATTTTACGTCAAGGCTT
2209347 ATCTATATCA
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
132 107 0.99
133 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.46
Consensus pattern (131 bp):
TTTACTTAATTAACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTATT
CCACCTTTAAATGTTTTTACGTAAATTATTACAATTTTACGTCAAGGCTTTTCCATGTCAACTTT
G
Found at i:2210289 original size:499 final size:498
Alignment explanation
Indices: 2209232--2210549 Score: 1756
Period size: 499 Copynumber: 2.6 Consensus size: 498
2209222 TCAACTTTGN
*
2209232 TTTACTTAATTAACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTATT
* * * *
2209297 CCACCTTTATATGTTTTTACGTCAATTGTTACAATTTTACGTCAAGGCTTATCTATATCAATTTT
66 CCACCTTTATAAGTTTTTACGTCAAATGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
* *
2209362 GAATTATAATTATATTTCTTATTATTATTTTTTATTTAAAAATTAAAATTTG-TATATCGTTAAA
131 GAATTATAATTATTTTTATTATTATTA-TTTTTATTTAAAAATTAAAA-TTGATATATCGTTAAA
* * *
2209426 CACTTTTAACTCGATAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTTACTT
194 CACTTTTAATTAGAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGA-TTTTTTTACTT
* * * *
2209491 AATTGACTTGTTACGTTAACTTTTACACATTTACGTTAAGATTTAAAATTTAATTATTGCACATT
258 AATTGACTTGTTACGTTAACTCTCACATATTTACTTTAAGATTTAAAATTTAATTATTGCACATT
* * * ** * *
2209556 TGTAAGTTTTTACGTCAATTGTTACAGTTTTACGTCAAGGTTTACCAATGTCAATTTTGAACTAT
323 TATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAAATTTACCAATATCAAATTTGAACTAT
* * *
2209621 AATTATTTTTATTATTATTTTTTATTTAAAAATTAAAATTTATATATCGTTAAATACTTTCAGTA
388 AATTATTTTTATTATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTCAATA
** *
2209686 TGAGAATATGAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
453 CAAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
* * * *
2209732 TTTACTTAATTGACTTGTTACGTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTATT
* * *
2209797 CCACCTTTATAAGTTTTTACGTCAAATCTTACAGTTTTACGTCAAGACTTTTCTATGTCAATTTT
66 CCACCTTTATAAGTTTTTACGTCAAATGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
* * * *
2209862 AAACTATAATTATTTTTATCT-TTATTATTTTTATTTAAAAATTAAAATTGATATATCATTAAAT
131 GAATTATAATTATTTTTAT-TATTATTATTTTTATTTAAAAATTAAAATTGATATATCGTTAAAC
* * * *
2209926 ACTTTTATTTTGAGAATATAAATTTAAAT-GTT-TTTTT-ACTAGAATTAGATTTTTTTACTTAA
195 ACTTTTAATTAGAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAA
** * * *
2209988 TTGACTTGTTATATTAAGTCACACATATTTACTTTAAGATTTAAAATTTAATTATT-CTA-TTTT
260 TTGACTTGTTACGTTAACTCTCACATATTTACTTTAAGATTTAAAATTTAATTATTGC-ACATTT
***
2210051 AATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAAATTT-TTTATATCAAATTTGAACTAT
324 -ATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAAAATTTACCAATATCAAATTTGAACTAT
*
2210115 AATTATTTTTATCCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTTA
388 AATTATTTTTA---TTATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTCA
* * * *
2210180 ATCCAAGAGTATAAATTTAAATGTTTGTTTTTCACTAAAATTAGATTTTTT
450 ATACAAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGA--TTTT
*
2210231 TTTACTTAATTGACTTATTACGTTAACTCTCATACATTTACATTCAGATTTAAAATTTAGTTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTATT
* * * * * * *
2210296 CTACTTTTATAAATTTTTATGTCAAATGTTACAATGTTACGTCAATACTTATCTGTGTCAATTTT
66 CCACCTTTATAAGTTTTTACGTCAAATGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
*
2210361 GAATTACAATTATTTTTATTTTTATTATTATTATTTATTTAAAAATTAAAATAT-ATATATCGTT
131 GAATTATAATTATTTTTA---TTATTATTATT-TTTATTTAAAAATTAAAAT-TGATATATCGTT
** * * * *
2210425 AAACACTTTTGGTTAGAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGATTTTTCTCC
191 AAACACTTTTAATTAGAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTAC
* * *
2210490 TTAATTGACTTATTACGTTAACTCTCACATATTTA-TGTTAAGATTTTAAATTTAGTTATT
256 TTAATTGACTTGTTACGTTAACTCTCACATATTTACT-TTAAGATTTAAAATTTAATTATT
2210550 TTACCTTTAC
Statistics
Matches: 710, Mismatches: 89, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
494 31 0.04
495 99 0.14
496 11 0.02
497 90 0.13
498 5 0.01
499 190 0.27
500 139 0.20
501 2 0.00
502 9 0.01
503 57 0.08
504 3 0.00
505 6 0.01
506 68 0.10
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (498 bp):
TTTACTTAATTGACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTATT
CCACCTTTATAAGTTTTTACGTCAAATGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
GAATTATAATTATTTTTATTATTATTATTTTTATTTAAAAATTAAAATTGATATATCGTTAAACA
CTTTTAATTAGAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTTTTACTTAAT
TGACTTGTTACGTTAACTCTCACATATTTACTTTAAGATTTAAAATTTAATTATTGCACATTTAT
AAGTTTTTACGTCAATTCTTACAATTTTACGTCAAAATTTACCAATATCAAATTTGAACTATAAT
TATTTTTATTATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAACACTTTCAATACAA
GAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
Found at i:2210397 original size:252 final size:250
Alignment explanation
Indices: 2209232--2210568 Score: 1634
Period size: 252 Copynumber: 5.3 Consensus size: 250
2209222 TCAACTTTGN
* * *
2209232 TTTACTTAATTAACTTATTACGTTAACTCTCATACATTTACATTAAGATTTAAAATTTAGTTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
* * * *
2209297 CCACCTTTATATGTTTTTACGTCAATTGTTACAATTTTACGTCAAGGCTTATCTATATCAATTTT
66 CTACCTTTATAAGTTTTTACGTCAATTGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
* * * *
2209362 GAATTATAATTATATTTCTTATTATTATTTTTTATTTAAAAATTAAAATTTGTATATCGTTAAAC
131 GAACTATAATTATTTTTATTATTATTA-TTTTTATTTAAAAATTAAAATTTATATATCGTTAAAC
* *
2209427 ACTTTTAA-CTCGATAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTTT
195 ACTTTTAATCT-AAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGA-TTTT
* * * *
2209484 TTTACTTAATTGACTTGTTACGTTAACTTTTACACATTTACGTTAAGATTTAAAATTTAATTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
* * * ** * *
2209549 GC-ACATTTGTAAGTTTTTACGTCAATTGTTACAGTTTTACGTCAAGGTTTACCAATGTCAATTT
66 -CTACCTTTATAAGTTTTTACGTCAATTGTTACAATTTTACGTCAAGACTTATCTATGTCAATTT
*
2209613 TGAACTATAATTATTTTTATTATTA-T-TTTTTATTTAAAAATTAAAATTTATATATCGTTAAAT
130 TGAACTATAATTATTTTTATTATTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAAC
* * * * *
2209676 ACTTTCAGTATGAGAATATGAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
195 ACTTTTAATCTAAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
* *
2209732 TTTACTTAATTGACTTGTTACGTTAATTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
* * * * *
2209797 CCACCTTTATAAGTTTTTACGTCAAATCTTACAGTTTTACGTCAAGACTTTTCTATGTCAATTTT
66 CTACCTTTATAAGTTTTTACGTCAATTGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
* * * *
2209862 AAACTATAATTATTTTTATCT-TTATTATTTTTATTTAAAAATTAAAATTGATATATCATTAAAT
131 GAACTATAATTATTTTTAT-TATTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAAC
* * * * *
2209926 ACTTTTATTTTGAGAATATAAATTTAAAT-GTT-TTTTT-ACTAGAATTAGATTTT
195 ACTTTTAATCTAAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
* ** * * * * *
2209979 TTTACTTAATTGACTTGTTATATTAAGTCACACATATTTACTTTAAGATTTAAAATTTAATTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
* * * * * * *
2210044 CTA-TTTTAATAAGTTTTTACGTCAATTCTTACAATTTTACGTCAA-AATTTTTTATATCAAATT
66 CTACCTTT-ATAAGTTTTTACGTCAATTGTTACAATTTTACGTCAAGACTTATCTATGTCAATTT
** *
2210107 TGAACTATAATTATTTTTATCCTTATTATTTTTTATTTAAAAATTAAAATTTATATATCATTAAA
130 TGAACTATAATTATTTTTATTATTATTA-TTTTTATTTAAAAATTAAAATTTATATATCGTTAAA
* * * *
2210172 CACTTTTAATCCAAGAGTATAAATTTAAATGTTTGTTTTTCACTAAAATTAGATTTTTT
194 CACTTTTAATCTAAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGA--TTTT
* * *
2210231 TTTACTTAATTGACTTATTACGTTAACTCTCATACATTTACATTCAGATTTAAAATTTAGTTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
* * * * * * *
2210296 CTACTTTTATAAATTTTTATGTCAAATGTTACAATGTTACGTCAATACTTATCTGTGTCAATTTT
66 CTACCTTTATAAGTTTTTACGTCAATTGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
* * *
2210361 GAATTACAATTATTTTTATTTTTATTATTATTATTTATTTAAAAATTAAAATATATATATCGTTA
131 GAACTATAATTATTTTTA---TTATTATTATT-TTTATTTAAAAATTAAAATTTATATATCGTTA
** * *
2210426 AACACTTTTGGT-TAGAGAATATAAATTTAAATATTTGTTTTTCATTAAAATTAGATTTT
192 AACACTTTTAATCTA-AGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
* * * * *
2210485 TCTCCTTAATTGACTTATTACGTTAACTCTCACATATTTATGTTAAGATTTTAAATTTAGTTATT
1 TTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
* **
2210550 TTACCTTTACGAGTTTTTA
66 CTACCTTTATAAGTTTTTA
2210569 TGTTAGTTCT
Statistics
Matches: 945, Mismatches: 119, Indels: 40
0.86 0.11 0.04
Matches are distributed among these distances:
246 42 0.04
247 170 0.18
248 147 0.16
249 89 0.09
250 72 0.08
251 1 0.00
252 228 0.24
253 34 0.04
254 75 0.08
255 3 0.00
256 84 0.09
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (250 bp):
TTTACTTAATTGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTAAAATTTAGTTATT
CTACCTTTATAAGTTTTTACGTCAATTGTTACAATTTTACGTCAAGACTTATCTATGTCAATTTT
GAACTATAATTATTTTTATTATTATTATTTTTATTTAAAAATTAAAATTTATATATCGTTAAACA
CTTTTAATCTAAGAATATAAATTTAAATATTTATTTTTCACTAAAATTAGATTTT
Found at i:2212317 original size:66 final size:66
Alignment explanation
Indices: 2212119--2212319 Score: 176
Period size: 66 Copynumber: 3.0 Consensus size: 66
2212109 TTATTAAGTG
* * *
2212119 TAATCATATTAATAAAGTTTATTATAAGTTATAGTAATGCTTATGTATAAATTATATATATATAT
1 TAATCATATTAATAAAGTATATTATAAGTTATAGTAATGCTTATTTATAAATTAAATATATATAT
2212184 A
66 A
* ** * * * * * * * * *
2212185 TAAT-ATATTACTTTATTATATGTAT-A-TAAAATTAATGATAAAAATTATATATTAAA-ATGTT
1 TAATCATATTAATAAAGTATAT-TATAAGTTATAGTAATGCT--TATTTATAAATTAAATAT-AT
*
2212246 TTATA
62 ATATA
* *
2212251 TAATCATATAAATAAAGTATATTATAAGTTATAGTAATGCTTATTTATAAATTAAATATATGTAT
1 TAATCATATTAATAAAGTATATTATAAGTTATAGTAATGCTTATTTATAAATTAAATATATATAT
2212316 A
66 A
2212317 TAA
1 TAA
2212320 AATATATGAC
Statistics
Matches: 97, Mismatches: 30, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
64 9 0.09
65 15 0.15
66 49 0.51
67 15 0.15
68 9 0.09
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (66 bp):
TAATCATATTAATAAAGTATATTATAAGTTATAGTAATGCTTATTTATAAATTAAATATATATAT
A
Found at i:2219174 original size:13 final size:13
Alignment explanation
Indices: 2219156--2219181 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2219146 TTAATTAAAA
2219156 TTATTATCTAATT
1 TTATTATCTAATT
2219169 TTATTATCTAATT
1 TTATTATCTAATT
2219182 ATACTACAAT
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:0.08, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATCTAATT
Found at i:2219249 original size:11 final size:11
Alignment explanation
Indices: 2219222--2219259 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2219212 TAATATTGTT
2219222 AATT-AATTAA
1 AATTAAATTAA
2219232 AATTAAATTATA
1 AATTAAATTA-A
*
2219244 AATAAAATTAA
1 AATTAAATTAA
2219255 AATTA
1 AATTA
2219260 GTTTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTAAATTAA
Found at i:2227799 original size:2 final size:2
Alignment explanation
Indices: 2227792--2227830 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2227782 CTCATTGAAG
2227792 AT AT AT 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 AT AT AT A
2227831 CAATAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2232039 original size:2 final size:2
Alignment explanation
Indices: 2232032--2232061 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2232022 AGATGGATAG
2232032 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
2232062 GTGAGTGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2238971 original size:36 final size:35
Alignment explanation
Indices: 2238928--2239020 Score: 100
Period size: 34 Copynumber: 2.6 Consensus size: 35
2238918 ACTTATTTCA
* * **
2238928 AATAATAGGAAAACAAACTATTTCGTAATGTAAAAT
1 AATAATAGGAAAA-AAATTATTTCCTAAAATAAAAT
*
2238964 AATAATA-GAAAAAAATTAATTCCTAAAATAAAAT
1 AATAATAGGAAAAAAATTATTTCCTAAAATAAAAT
2238998 AATAAT-GAGAAAATAAATTATTT
1 AATAATAG-GAAAA-AAATTATTT
2239021 TTTACTACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
34 23 0.48
35 10 0.21
36 15 0.31
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (35 bp):
AATAATAGGAAAAAAATTATTTCCTAAAATAAAAT
Found at i:2239115 original size:25 final size:25
Alignment explanation
Indices: 2239087--2239173 Score: 131
Period size: 25 Copynumber: 3.5 Consensus size: 25
2239077 AATAAACGTG
*
2239087 ATTATAGGAATTAGAAATCACTATA
1 ATTATAGGGATTAGAAATCACTATA
2239112 ATTATAGGGATTAGAAATCACTATA
1 ATTATAGGGATTAGAAATCACTATA
*
2239137 ATTATAGGGATTAGGAATCA-TCATA
1 ATTATAGGGATTAGAAATCACT-ATA
*
2239162 ATTATACGGATT
1 ATTATAGGGATT
2239174 TTATTTTCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
24 1 0.02
25 57 0.98
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (25 bp):
ATTATAGGGATTAGAAATCACTATA
Found at i:2243704 original size:25 final size:25
Alignment explanation
Indices: 2243645--2243706 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
2243635 AATAAACGTG
*
2243645 ATTATAGGAATTAGAAATCACCATA
1 ATTATAGGGATTAGAAATCACCATA
* * * *
2243670 ATTATTGGGATTGGGAATCATCATA
1 ATTATAGGGATTAGAAATCACCATA
2243695 ATTATAGGGATT
1 ATTATAGGGATT
2243707 TTATTTTCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (25 bp):
ATTATAGGGATTAGAAATCACCATA
Found at i:2243893 original size:35 final size:38
Alignment explanation
Indices: 2243802--2243900 Score: 150
Period size: 39 Copynumber: 2.7 Consensus size: 38
2243792 CTCTTCCTAA
*
2243802 ATAACAAATGGAAAACAAACTATTTCCTAATACAAAATT
1 ATAATAAATGGAAAACAAACTATTTCCTAATACAAAA-T
*
2243841 ATAATAAATGGAAAACAAACTATTTCCTAATA-TAAA-
1 ATAATAAATGGAAAACAAACTATTTCCTAATACAAAAT
2243877 ATAAT-AATGGAAAACAAACTATTT
1 ATAATAAATGGAAAACAAACTATTT
2243901 TCATTATTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
35 19 0.33
36 5 0.09
38 3 0.05
39 31 0.53
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (38 bp):
ATAATAAATGGAAAACAAACTATTTCCTAATACAAAAT
Found at i:2244039 original size:39 final size:38
Alignment explanation
Indices: 2243898--2244252 Score: 389
Period size: 39 Copynumber: 9.5 Consensus size: 38
2243888 AAACAAACTA
2243898 TTTT-CATTATTATAATTTTGTATTAGGAAATAGTTTG
1 TTTTCCATTATTATAATTTTGTATTAGGAAATAGTTTG
* * *
2243935 TTTTCCATTA-T-T-GTTTTATATTAGGAAATGGTTTG
1 TTTTCCATTATTATAATTTTGTATTAGGAAATAGTTTG
* * *
2243970 ATTTACCATTA-T-T-ATTTTATATTAGG-AATAGTTTA
1 -TTTTCCATTATTATAATTTTGTATTAGGAAATAGTTTG
2244005 TTTTCCATTTATTATAATTTTGT-TTCAGGAAATAGTTTG
1 TTTTCCA-TTATTATAATTTTGTATT-AGGAAATAGTTTG
*
2244044 TTTTCCATTTATTATAATTTTGTATT-GGAAAATAATTTG
1 TTTTCCA-TTATTATAATTTTGTATTAGG-AAATAGTTTG
* *
2244083 TTATCCCATTATTGTAATTTTGTATTAGGAAATAGTTTG
1 TT-TTCCATTATTATAATTTTGTATTAGGAAATAGTTTG
* * *
2244122 TTTTCCATCA-T-T-ATTTTATATCAGGAAATAGTTTG
1 TTTTCCATTATTATAATTTTGTATTAGGAAATAGTTTG
*
2244157 TTTTCCCATTATTATAATTTTGTATTAGAAAATAGTTTG
1 TTTT-CCATTATTATAATTTTGTATTAGGAAATAGTTTG
* * *
2244196 TTTT-C-TCATTATCATTCTGTATTAGGAAATAGTTTG
1 TTTTCCATTATTATAATTTTGTATTAGGAAATAGTTTG
2244232 TTTTTCCATTATTATAATTTT
1 -TTTTCCATTATTATAATTTT
2244253 AAAGTTGTGA
Statistics
Matches: 270, Mismatches: 29, Indels: 36
0.81 0.09 0.11
Matches are distributed among these distances:
34 6 0.02
35 55 0.20
36 58 0.21
37 15 0.06
38 24 0.09
39 104 0.39
40 8 0.03
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (38 bp):
TTTTCCATTATTATAATTTTGTATTAGGAAATAGTTTG
Found at i:2244043 original size:74 final size:73
Alignment explanation
Indices: 2243906--2244252 Score: 400
Period size: 74 Copynumber: 4.7 Consensus size: 73
2243896 TATTTTCATT
* * * *
2243906 ATTATAATTTTGTATTAGGAAATAGTTTGTTTTCCATTA-T-T-GTTTTATATTAGGAAATGGTT
1 ATTATTATTTTGTATTAGGAAATAGTTTGTTTTCCATTATTATAATTTTGTATTAGGAAATAGTT
*
2243968 TGATTTACC
66 TG-TTTTCC
* *
2243977 ATTATTATTTTATATTAGG-AATAGTTTATTTTCCATTTATTATAATTTTGT-TTCAGGAAATAG
1 ATTATTATTTTGTATTAGGAAATAGTTTGTTTTCCA-TTATTATAATTTTGTATT-AGGAAATAG
2244040 TTTGTTTTCC
64 TTTGTTTTCC
* * *
2244050 ATTTATTATAATTTTGTATT-GGAAAATAATTTGTTATCCCATTATTGTAATTTTGTATTAGGAA
1 A-TTA-T-T-ATTTTGTATTAGG-AAATAGTTTGTT-TTCCATTATTATAATTTTGTATTAGGAA
2244114 ATAGTTTGTTTTCC
60 ATAGTTTGTTTTCC
* * * *
2244128 ATCATTATTTTATATCAGGAAATAGTTTGTTTTCCCATTATTATAATTTTGTATTAGAAAATAGT
1 ATTATTATTTTGTATTAGGAAATAGTTTGTTTT-CCATTATTATAATTTTGTATTAGGAAATAGT
2244193 TTGTTTTCTC
65 TTGTTTTC-C
* *
2244203 ATTATCATTCTGTATTAGGAAATAGTTTGTTTTTCCATTATTATAATTTT
1 ATTATTATTTTGTATTAGGAAATAGTTTG-TTTTCCATTATTATAATTTT
2244253 AAAGTTGTGA
Statistics
Matches: 235, Mismatches: 24, Indels: 30
0.81 0.08 0.10
Matches are distributed among these distances:
70 15 0.06
71 20 0.09
72 1 0.00
73 10 0.04
74 76 0.32
75 45 0.19
76 8 0.03
77 11 0.05
78 43 0.18
79 6 0.03
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (73 bp):
ATTATTATTTTGTATTAGGAAATAGTTTGTTTTCCATTATTATAATTTTGTATTAGGAAATAGTT
TGTTTTCC
Found at i:2244146 original size:113 final size:110
Alignment explanation
Indices: 2243906--2244246 Score: 354
Period size: 113 Copynumber: 3.1 Consensus size: 110
2243896 TATTTTCATT
* * * * * * **
2243906 ATTATAATTTTGTATTAGGAAATAGTTTGTTTT-CCATTA-T-T-GTTTTATATTAGGAAATGGT
1 ATTATTATTTTATATCAGGAAATAGTTTGTTTTCCCATTATTATAATTTTGTATTAGAAAATAAT
* * * *
2243967 TTGATT-TACCATTATTATTTTATATTAGG-AATAGTTTATTTTCC
66 TTG-TTATCCCATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
* * *
2244011 ATTTATTATAATTTTGTTTCAGGAAATAGTTTGTTTT-CCATTTATTATAATTTTGTATTGGAAA
1 A-TTA-T-T-ATTTTATATCAGGAAATAGTTTGTTTTCCCA-TTATTATAATTTTGTATTAGAAA
2244075 ATAATTTGTTATCCCATTATTGTAATTTTGTATTAGGAAATAGTTTGTTTTCC
61 ATAATTTGTTATCCCATTA---TAATTTTGTATTAGGAAATAGTTTGTTTTCC
* *
2244128 ATCATTATTTTATATCAGGAAATAGTTTGTTTTCCCATTATTATAATTTTGTATTAGAAAATAGT
1 ATTATTATTTTATATCAGGAAATAGTTTGTTTTCCCATTATTATAATTTTGTATTAGAAAATAAT
* * * *
2244193 TTGTTTTCTCATTATCATTCTGTATTAGGAAATAGTTTGTTTTTCC
66 TTGTTATCCCATTATAATTTTGTATTAGGAAATAGTTTG-TTTTCC
2244239 ATTATTAT
1 ATTATTAT
2244247 AATTTTAAAG
Statistics
Matches: 198, Mismatches: 23, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
105 1 0.01
106 3 0.02
107 1 0.01
109 28 0.14
110 26 0.13
111 14 0.07
112 3 0.02
113 87 0.44
114 4 0.02
115 1 0.01
116 15 0.08
117 15 0.08
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.52
Consensus pattern (110 bp):
ATTATTATTTTATATCAGGAAATAGTTTGTTTTCCCATTATTATAATTTTGTATTAGAAAATAAT
TTGTTATCCCATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
Found at i:2244377 original size:49 final size:50
Alignment explanation
Indices: 2244248--2244417 Score: 236
Period size: 50 Copynumber: 3.4 Consensus size: 50
2244238 CATTATTATA
* * *
2244248 ATTTTAAAGTTGTGAAGCCTTGGATTAGGAGTTATTTATCTTTTCAAATC
1 ATTTTAAAGTCGTAAAGCCTCGGATTAGGAGTTATTTATCTTTTCAAATC
* *
2244298 ATTTTAAATTCGTAAAGTCTCGGATTAGGAGTTATTTATCCTTTT-AAATC
1 ATTTTAAAGTCGTAAAGCCTCGGATTAGGAGTTATTTAT-CTTTTCAAATC
* *
2244348 A-TTTAAAGTCGTAAAGCCTCGGATGAGGAGTTATTTATCTTTTCAAATT
1 ATTTTAAAGTCGTAAAGCCTCGGATTAGGAGTTATTTATCTTTTCAAATC
* *
2244397 ATTTTAAAATTGTAAAGCCTC
1 ATTTTAAAGTCGTAAAGCCTC
2244418 ATATGAAGAA
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
48 5 0.05
49 39 0.37
50 57 0.54
51 5 0.05
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42
Consensus pattern (50 bp):
ATTTTAAAGTCGTAAAGCCTCGGATTAGGAGTTATTTATCTTTTCAAATC
Found at i:2244434 original size:99 final size:99
Alignment explanation
Indices: 2244250--2244435 Score: 248
Period size: 99 Copynumber: 1.9 Consensus size: 99
2244240 TTATTATAAT
* * * *
2244250 TTTAAAGTTGTGAAGCCTTGGATTAGGAGTTATTTATCTTTTCAAATCATTTTAAATTCGTAAAG
1 TTTAAAGTCGTAAAGCCTCGGATGAGGAGTTATTTATCTTTTCAAATCATTTTAAATTCGTAAAG
* * * * * *
2244315 TCTCGGATTAGGAGTTATTTATCCTTTTAAATCA
66 CCTCAGATGAAGAATCATTTATCCTTTTAAATCA
*
2244349 TTTAAAGTCGTAAAGCCTCGGATGAGGAGTTATTTATCTTTTCAAATTATTTTAAAATT-GTAAA
1 TTTAAAGTCGTAAAGCCTCGGATGAGGAGTTATTTATCTTTTCAAATCATTTT-AAATTCGTAAA
*
2244413 GCCTCATATGAAGAATCATTTAT
65 GCCTCAGATGAAGAATCATTTAT
2244436 TATTTAAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
99 69 0.93
100 5 0.07
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (99 bp):
TTTAAAGTCGTAAAGCCTCGGATGAGGAGTTATTTATCTTTTCAAATCATTTTAAATTCGTAAAG
CCTCAGATGAAGAATCATTTATCCTTTTAAATCA
Found at i:2244545 original size:87 final size:86
Alignment explanation
Indices: 2244374--2244622 Score: 270
Period size: 87 Copynumber: 2.8 Consensus size: 86
2244364 CCTCGGATGA
* * *
2244374 GGAGTTATTTATCTTTTCAAATTATTTTAAAATTGTAAAGCCTCATATGAAGAATCATTTATTAT
1 GGAGTTATTTATCTTTTCAAATTATTTTAAAGTTGTAAAGCCTCA-ATGAAGAGTCATTTATCAT
* * ****
2244439 TTAAAATTGTAGGGTCTCAAAT
65 TTAAAGTGGTACAACCTCAAAT
* * *
2244461 -GATTTATTTATCTTTTCAAATTATTTTCAAAGTTGTGAAGTCTCTAATGAAGAGTCATTTATCA
1 GGAGTTATTTATCTTTTCAAATTATTTT-AAAGTTGTAAAGCCTC-AATGAAGAGTCATTTATCA
2244525 TTTAAAGTGGTACAACCTCAAAT
64 TTTAAAGTGGTACAACCTCAAAT
* *
2244548 GAGGAGTTATTCATTTTTTTCAAATTATCTTTAAAGTTGTAAAGCCTCGAAT-AAGGAGTCATTT
1 --GGAGTTATTTA-TCTTTTCAAATTAT-TTTAAAGTTGTAAAGCCTC-AATGAA-GAGTCATTT
2244612 ATC-TTTAAAGT
60 ATCATTTAAAGT
2244623 TGTAAAGCCA
Statistics
Matches: 136, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
86 26 0.19
87 46 0.34
88 1 0.01
90 18 0.13
91 42 0.31
92 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (86 bp):
GGAGTTATTTATCTTTTCAAATTATTTTAAAGTTGTAAAGCCTCAATGAAGAGTCATTTATCATT
TAAAGTGGTACAACCTCAAAT
Found at i:2244640 original size:38 final size:38
Alignment explanation
Indices: 2244572--2244651 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
2244562 TTTTTTCAAA
* *
2244572 TTATCTTTAAAGTTGTAAAGCCTCGAATAAGGAGTCAT
1 TTATCTTTAAAGTTGTAAAGCCTCGAATAAGAAGCCAT
*
2244610 TTATCTTTAAAGTTGTAAAGCCAT-GGATAAGAAGCCAT
1 TTATCTTTAAAGTTGTAAAGCC-TCGAATAAGAAGCCAT
2244648 TTAT
1 TTAT
2244652 TTTTTCCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (38 bp):
TTATCTTTAAAGTTGTAAAGCCTCGAATAAGAAGCCAT
Found at i:2246419 original size:23 final size:23
Alignment explanation
Indices: 2246393--2246438 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2246383 GCTTGAAAGG
*
2246393 TAGAG-AGTTAGAATATTTATGCT
1 TAGAGAAG-TAGAATACTTATGCT
*
2246416 TAGAGAAGTAGACTACTTATGCT
1 TAGAGAAGTAGAATACTTATGCT
2246439 ACTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (23 bp):
TAGAGAAGTAGAATACTTATGCT
Found at i:2246973 original size:30 final size:29
Alignment explanation
Indices: 2246933--2246992 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
2246923 TTTTCCATTA
* *
2246933 GAAAAACATTTCCGATAGAAAATTTCGTT
1 GAAAAACATTTCAGATAAAAAATTTCGTT
*
2246962 GAAAAAGCATTTCAGATAAAAAATTTTGTT
1 GAAAAA-CATTTCAGATAAAAAATTTCGTT
2246992 G
1 G
2246993 GAAATTTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (29 bp):
GAAAAACATTTCAGATAAAAAATTTCGTT
Found at i:2252758 original size:45 final size:45
Alignment explanation
Indices: 2252702--2252789 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
2252692 AAGCCAAGAA
* *
2252702 GTCAGAAAACAATGGAGAAGGAGCAGGAGGAGAACGGCAATAGAT
1 GTCAAAAAACAATGGAGAAGGAGCAAGAGGAGAACGGCAATAGAT
*
2252747 GTCAAAAAACAATGGTGAAGGAGCAAGAGGAGAACGGCAATAG
1 GTCAAAAAACAATGGAGAAGGAGCAAGAGGAGAACGGCAATAG
2252790 CAGCAGCTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.45, C:0.11, G:0.34, T:0.09
Consensus pattern (45 bp):
GTCAAAAAACAATGGAGAAGGAGCAAGAGGAGAACGGCAATAGAT
Found at i:2261137 original size:2 final size:2
Alignment explanation
Indices: 2261132--2261157 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2261122 AAAAAAAATA
2261132 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
2261158 TTGTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2263933 original size:120 final size:120
Alignment explanation
Indices: 2263720--2263947 Score: 348
Period size: 120 Copynumber: 1.9 Consensus size: 120
2263710 GGGGTATCAA
* * * ** *
2263720 ACACAAATGTCCAGATGAAATGTAATTGACCTCCTCAGTATTATTAAGTGTTATGGTAATCTCAA
1 ACACAAATATCCAGAAGAAATGTAATCGACCTCCTCAGTATTATTAAGTCATATGGCAATCTCAA
* *
2263785 ATCTCTGTCTCATTGACCTTTCCATGTTTTTTTTGGTTAGTTTTGGGGAACAAAC
66 ATCTCTGCCCCATTGACCTTTCCATGTTTTTTTTGGTTAGTTTTGGGGAACAAAC
* * *
2263840 ACACAAATATCTAGAAGAAATGTAATCGACCTCCTTAGTGTTATTAAGTCATATGGCAATCTCAA
1 ACACAAATATCCAGAAGAAATGTAATCGACCTCCTCAGTATTATTAAGTCATATGGCAATCTCAA
*
2263905 ATCTCTGCCCCATTGACCTTTTCATGTTTTTTTTGGTTAGTTT
66 ATCTCTGCCCCATTGACCTTTCCATGTTTTTTTTGGTTAGTTT
2263948 CAGGTTTTCT
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 96 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (120 bp):
ACACAAATATCCAGAAGAAATGTAATCGACCTCCTCAGTATTATTAAGTCATATGGCAATCTCAA
ATCTCTGCCCCATTGACCTTTCCATGTTTTTTTTGGTTAGTTTTGGGGAACAAAC
Found at i:2279561 original size:89 final size:89
Alignment explanation
Indices: 2279462--2279689 Score: 257
Period size: 89 Copynumber: 2.6 Consensus size: 89
2279452 AGTTCTTATC
* * *
2279462 TTAAGAAGAGAAAAGCAAAGAAAATACTATACCTATAAAATATTGGTATCAT-TCTGCAAATGGG
1 TTAACAAGAGAAAAGAAAAGAAAATACTATACCTATAAAACATTGGTATCATCTC-GCAAA-GGG
* *
2279526 -TACAATTAA-TCTGAAATTTCATGCA
64 ATACAATTAATTC-AAAAGTTCATGCA
* * * * *
2279551 TTGACAAGAGAAAGGAAAAGAAAATACTATACCAATCAAACATTGGTATCATCTCGTAAAGGGAT
1 TTAACAAGAGAAAAGAAAAGAAAATACTATACCTATAAAACATTGGTATCATCTCGCAAAGGGAT
* *
2279616 ACAATTAATTCAAAAGTTCTTGTA
66 ACAATTAATTCAAAAGTTCATGCA
* *
2279640 TTAAGAAGAG-AAAGAAAAAGAAAACACTATACCTATAAAAACATTGGTAT
1 TTAACAAGAGAAAAG-AAAAGAAAATACTATACCTAT-AAAACATTGGTAT
2279690 AATTGCACCA
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
88 6 0.05
89 94 0.81
90 16 0.14
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (89 bp):
TTAACAAGAGAAAAGAAAAGAAAATACTATACCTATAAAACATTGGTATCATCTCGCAAAGGGAT
ACAATTAATTCAAAAGTTCATGCA
Found at i:2283548 original size:16 final size:18
Alignment explanation
Indices: 2283515--2283551 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2283505 ATTTTATATT
2283515 AATATTTTAATAATTTAA
1 AATATTTTAATAATTTAA
2283533 AATATTTTAA-AA-TTAA
1 AATATTTTAATAATTTAA
2283549 AAT
1 AAT
2283552 TAAATACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTTTAATAATTTAA
Found at i:2284248 original size:18 final size:19
Alignment explanation
Indices: 2284213--2284250 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2284203 TTTTTATTCC
2284213 AAAAATATGCTCATTTATT
1 AAAAATATGCTCATTTATT
2284232 AAAAATAAT-CTCA-TTATT
1 AAAAAT-ATGCTCATTTATT
2284250 A
1 A
2284251 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 10 0.56
20 2 0.11
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAAATATGCTCATTTATT
Found at i:2285873 original size:16 final size:17
Alignment explanation
Indices: 2285852--2285883 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2285842 CCTGTTATAA
2285852 AAATAA-TTAAAATTTT
1 AAATAATTTAAAATTTT
2285868 AAATAATTTAAAATTT
1 AAATAATTTAAAATTT
2285884 CTTTTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAATTTAAAATTTT
Found at i:2307098 original size:8 final size:8
Alignment explanation
Indices: 2307085--2307124 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
2307075 GACTGTGCAT
2307085 AGAGGGAG
1 AGAGGGAG
2307093 AGAGGGAG
1 AGAGGGAG
2307101 AGAGTGGAG
1 AGAG-GGAG
*
2307110 -GAGGGGG
1 AGAGGGAG
2307117 AGAGGGAG
1 AGAGGGAG
2307125 GAGCAGAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 3 0.11
8 21 0.75
9 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.65, T:0.03
Consensus pattern (8 bp):
AGAGGGAG
Found at i:2308509 original size:173 final size:173
Alignment explanation
Indices: 2308217--2308557 Score: 524
Period size: 173 Copynumber: 2.0 Consensus size: 173
2308207 CACTCTGTCT
* * *
2308217 GGCTGTTTAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTTTAAGTATATATG
1 GGCTGTTCAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTATAAGTATATATA
* *
2308282 CAACTTAAAGAGGGATTTCCTCATTATTGATTTGTTTACTTATATCTTTAACTTTTTCATATTGT
66 CAACTTAAAGAGGGATTTCCTCATTATCGATTTGTTTACTTATATCTTTAAC-TTTTCATATTAT
* *
2308347 ATTGAT-TTCAATATTCTGTTCTATTATGCTCAATTCCTGTTTCG
130 AGTGATCTT-AATATTCTGTTCAATTATGCTCAATTCCTGTTTCG
* * * *
2308391 GGCTGTTCAAATTATTTGGTTTCCTATTGGTTATCCTATGTGATTCCTTGTTAT-AGTGTATATA
1 GGCTGTTCAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTATAAGTATATATA
* * *
2308455 CAATTTAAAGAGGGATTTCCTCTTTATCGATTTGTTTAGTTATATCTTTAACTTTTCATATTATA
66 CAACTTAAAGAGGGATTTCCTCATTATCGATTTGTTTACTTATATCTTTAACTTTTCATATTATA
2308520 GTGATCTTAATATTCTGTTCAATTATGCTCAATTCCTG
131 GTGATCTTAATATTCTGTTCAATTATGCTCAATTCCTG
2308558 ACAAATCGTT
Statistics
Matches: 152, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
172 45 0.30
173 58 0.38
174 49 0.32
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.48
Consensus pattern (173 bp):
GGCTGTTCAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTATAAGTATATATA
CAACTTAAAGAGGGATTTCCTCATTATCGATTTGTTTACTTATATCTTTAACTTTTCATATTATA
GTGATCTTAATATTCTGTTCAATTATGCTCAATTCCTGTTTCG
Found at i:2316299 original size:16 final size:15
Alignment explanation
Indices: 2316279--2316315 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2316269 TTATTCAAGC
2316279 TTTTATTATTTTGAT
1 TTTTATTATTTTGAT
*
2316294 TCTTTATTATTTTTAT
1 T-TTTATTATTTTGAT
2316310 TTTTAT
1 TTTTAT
2316316 AATGTTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTATTATTTTGAT
Found at i:2320751 original size:20 final size:20
Alignment explanation
Indices: 2320726--2320771 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2320716 TTTTGACCCC
2320726 ATTTGACTTATT-AGAGTATA
1 ATTTGACTTATTGA-AGTATA
*
2320746 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
2320766 ATTTGA
1 ATTTGA
2320772 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:2320847 original size:28 final size:27
Alignment explanation
Indices: 2320816--2320868 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2320806 TTTGAAGTAT
*
2320816 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
2320844 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
2320869 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:2320874 original size:28 final size:28
Alignment explanation
Indices: 2320816--2320874 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2320806 TTTGAAGTAT
* *
2320816 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
2320844 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
2320872 AGG
1 AGG
2320875 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:2340058 original size:18 final size:18
Alignment explanation
Indices: 2340035--2340072 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
2340025 GTTTGAATTG
2340035 TTATTACTTTATTA-TTAT
1 TTATTAC-TTATTATTTAT
2340053 TTATTACTTATTATTTAT
1 TTATTACTTATTATTTAT
2340071 TT
1 TT
2340073 TTATCAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTACTTATTATTTAT
Found at i:2340087 original size:13 final size:13
Alignment explanation
Indices: 2340071--2340100 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2340061 TATTATTTAT
2340071 TTTTATCAAGTAA
1 TTTTATCAAGTAA
2340084 TTTTATCAAGTAA
1 TTTTATCAAGTAA
2340097 TTTT
1 TTTT
2340101 TTGTATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (13 bp):
TTTTATCAAGTAA
Found at i:2340453 original size:20 final size:20
Alignment explanation
Indices: 2340421--2340458 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2340411 ATTTTATTAT
2340421 TATTGTTTTTGTTATCTACC
1 TATTGTTTTTGTTATCTACC
*
2340441 TATT-TTTTATGTTTTCTA
1 TATTGTTTT-TGTTATCTA
2340459 TTTTAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.66
Consensus pattern (20 bp):
TATTGTTTTTGTTATCTACC
Found at i:2340974 original size:44 final size:44
Alignment explanation
Indices: 2340895--2340998 Score: 174
Period size: 44 Copynumber: 2.4 Consensus size: 44
2340885 ATTTCCCCTC
* *
2340895 CTCACGCCGGCAAACT-CCCCTTGGCCGTCAACCTGCAGGAGAT
1 CTCACGCCGGCGAACTCCCCCTTGGCCGTCAACCTGCAGGAAAT
*
2340938 CTCACGCCGGCGAACTCCCCCTTGGCTGTCAACCTGCAGGAAAT
1 CTCACGCCGGCGAACTCCCCCTTGGCCGTCAACCTGCAGGAAAT
2340982 CTCACGCCGGCGAACTC
1 CTCACGCCGGCGAACTC
2340999 TTAAGGTCGG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 15 0.26
44 42 0.74
ACGTcount: A:0.20, C:0.40, G:0.23, T:0.16
Consensus pattern (44 bp):
CTCACGCCGGCGAACTCCCCCTTGGCCGTCAACCTGCAGGAAAT
Found at i:2341219 original size:129 final size:127
Alignment explanation
Indices: 2341004--2341254 Score: 412
Period size: 129 Copynumber: 2.0 Consensus size: 127
2340994 AACTCTTAAG
* *
2341004 GTCGGCTTCCCCAACCGGTGACGTCGCAGCTGTCCCGGATGGGCTCTTCCTTCCAGCGGCAGATC
1 GTCGGCTTCCCCAACCGGTGACATCGCAGCTGTCCCGGATCGGCTCTTCCTTCCAGCGGCAGATC
* *
2341069 TGACGGTGTCGATGGTCTGGTTCCTTCTCCGCCGGCGAGCTCCTTCTTGCGGCGTGGGTCAA
66 TGACGGCGTCGATGGTCTGGTTCCTTCTCCGCCGGCGAGCTCCTCCTTGCGGCGTGGGTCAA
* **
2341131 GTCGGCTTTCCCCCAACCGGTGGCATCGCAGCTGTCTTGGATCGGCTCTTCCTTCCAGCGGCAGA
1 GTCGGC-TT-CCCCAACCGGTGACATCGCAGCTGTCCCGGATCGGCTCTTCCTTCCAGCGGCAGA
*
2341196 TCTGGCGGCGTCGATGGTCTGGTTCCTTCTCCGCCGGCGAGCTCCTCCTTGCGGCGTGG
64 TCTGACGGCGTCGATGGTCTGGTTCCTTCTCCGCCGGCGAGCTCCTCCTTGCGGCGTGG
2341255 ATCCTCACTG
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
127 6 0.05
128 2 0.02
129 106 0.93
ACGTcount: A:0.09, C:0.34, G:0.31, T:0.25
Consensus pattern (127 bp):
GTCGGCTTCCCCAACCGGTGACATCGCAGCTGTCCCGGATCGGCTCTTCCTTCCAGCGGCAGATC
TGACGGCGTCGATGGTCTGGTTCCTTCTCCGCCGGCGAGCTCCTCCTTGCGGCGTGGGTCAA
Done.