Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 16 of 167
Found at i:4872917 original size:34 final size:36
Alignment explanation
Indices: 4872872--4872957 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 36
4872862 GGACAGACAA
*
4872872 ATAAAAAATTAATAATATACGAAAC-ATA-TAATA-T
1 ATAAAACATTAATAATATAC-AAACGATAGTAATAGT
* * *
4872906 TTAAAACATTAACAATATACATACGATAGTAATAGT
1 ATAAAACATTAATAATATACAAACGATAGTAATAGT
*
4872942 ATAAAACAATAATAAT
1 ATAAAACATTAATAAT
4872958 GCATATGGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
33 3 0.07
34 20 0.48
35 5 0.12
36 14 0.33
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (36 bp):
ATAAAACATTAATAATATACAAACGATAGTAATAGT
Found at i:4873208 original size:26 final size:27
Alignment explanation
Indices: 4873179--4873238 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
4873169 TATGGCGTTG
*
4873179 AAAAATACATACATAACATAGTAT-TA
1 AAAAATACATACATAACATAATATGTA
* * *
4873205 AAAAACATATACATAAGATAATATGTA
1 AAAAATACATACATAACATAATATGTA
4873232 AAAAATA
1 AAAAATA
4873239 TAATATAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (27 bp):
AAAAATACATACATAACATAATATGTA
Found at i:4873539 original size:27 final size:25
Alignment explanation
Indices: 4873470--4873547 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 25
4873460 CACAATATAT
4873470 ATATACACATAATATAGTTATTAAGA
1 ATATACACATAATATAG-TATTAAGA
* *
4873496 AAATACATATAATATATAGTATTAAGA
1 ATATACACAT-A-ATATAGTATTAAGA
*
4873523 ATATACACAATACATATGGTATTAA
1 ATATACAC-ATA-ATATAGTATTAA
4873548 AAAATATAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 8 0.19
27 27 0.63
28 8 0.19
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (25 bp):
ATATACACATAATATAGTATTAAGA
Found at i:4873559 original size:15 final size:15
Alignment explanation
Indices: 4873536--4873566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4873526 TACACAATAC
*
4873536 ATATGGTATTAAAAA
1 ATATAGTATTAAAAA
4873551 ATATAGTATTAAAAA
1 ATATAGTATTAAAAA
4873566 A
1 A
4873567 ACATAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
ATATAGTATTAAAAA
Found at i:4874239 original size:14 final size:11
Alignment explanation
Indices: 4874217--4874277 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
4874207 CTAATGATGC
4874217 TAAAATATATGCA
1 TAAAATATAT--A
4874230 TAATAATATATA
1 TAA-AATATATA
4874242 TAAAATATATA
1 TAAAATATATA
* *
4874253 CACAATATAGT-
1 TAAAATATA-TA
4874264 TACAAATATATA
1 TA-AAATATATA
4874276 TA
1 TA
4874278 TATAATCGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 17 0.43
12 13 0.32
13 3 0.08
14 7 0.17
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (11 bp):
TAAAATATATA
Found at i:4875137 original size:27 final size:27
Alignment explanation
Indices: 4875088--4875163 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
4875078 ATGTACATAA
4875088 AAAGAGAGAAA-AAAATAAA-AAATAAACG
1 AAAGA-AGAAAGAAAA-AAAGAAAT-AACG
**
4875116 AAA-AAGAAAGAAAAAAAGAAATTTCG
1 AAAGAAGAAAGAAAAAAAGAAATAACG
4875142 AAAGAAGAAAGAAAAAAAGAAA
1 AAAGAAGAAAGAAAAAAAGAAA
4875164 ATGATGTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 13 0.30
27 27 0.63
28 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.07
Consensus pattern (27 bp):
AAAGAAGAAAGAAAAAAAGAAATAACG
Found at i:4875662 original size:27 final size:25
Alignment explanation
Indices: 4875631--4875690 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
4875621 TGTGGGTTTA
*
4875631 TTTTGGGTTGTTTGTTTGGAAATTGGG
1 TTTTGGGTTG-TTGGTTGGAAA-TGGG
*
4875658 TTTTGGGTTGTTGGTTGTAAATGGG
1 TTTTGGGTTGTTGGTTGGAAATGGG
*
4875683 GTTTGGGT
1 TTTTGGGT
4875691 AATTTGGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 11 0.37
26 9 0.30
27 10 0.33
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (25 bp):
TTTTGGGTTGTTGGTTGGAAATGGG
Found at i:4875686 original size:26 final size:27
Alignment explanation
Indices: 4875631--4875690 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
4875621 TGTGGGTTTA
* *
4875631 TTTTGGGTTGTTTGTTTGGAAATTGGG
1 TTTTGGGTTGTTTGGTTGGAAATGGGG
*
4875658 TTTTGGGTTG-TTGGTTGTAAATGGGG
1 TTTTGGGTTGTTTGGTTGGAAATGGGG
4875684 -TTTGGGT
1 TTTTGGGT
4875691 AATTTGGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 7 0.23
26 13 0.43
27 10 0.33
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (27 bp):
TTTTGGGTTGTTTGGTTGGAAATGGGG
Found at i:4878246 original size:27 final size:27
Alignment explanation
Indices: 4878197--4878272 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
4878187 ATGTACATAA
4878197 AAAGAGAGAAA-AAAATAAA-AAATAAACG
1 AAAGA-AGAAAGAAAA-AAAGAAAT-AACG
**
4878225 AAA-AAGAAAGAAAAAAAGAAATTTCG
1 AAAGAAGAAAGAAAAAAAGAAATAACG
4878251 AAAGAAGAAAGAAAAAAAGAAA
1 AAAGAAGAAAGAAAAAAAGAAA
4878273 ATGATGTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 13 0.30
27 27 0.63
28 3 0.07
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.07
Consensus pattern (27 bp):
AAAGAAGAAAGAAAAAAAGAAATAACG
Found at i:4878771 original size:27 final size:25
Alignment explanation
Indices: 4878740--4878799 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
4878730 TGTGGGTTTA
*
4878740 TTTTGGGTTGTTTGTTTGGAAATTGGG
1 TTTTGGGTTG-TTGGTTGGAAA-TGGG
*
4878767 TTTTGGGTTGTTGGTTGTAAATGGG
1 TTTTGGGTTGTTGGTTGGAAATGGG
*
4878792 GTTTGGGT
1 TTTTGGGT
4878800 AATTTGGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 11 0.37
26 9 0.30
27 10 0.33
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (25 bp):
TTTTGGGTTGTTGGTTGGAAATGGG
Found at i:4878795 original size:26 final size:27
Alignment explanation
Indices: 4878740--4878799 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
4878730 TGTGGGTTTA
* *
4878740 TTTTGGGTTGTTTGTTTGGAAATTGGG
1 TTTTGGGTTGTTTGGTTGGAAATGGGG
*
4878767 TTTTGGGTTG-TTGGTTGTAAATGGGG
1 TTTTGGGTTGTTTGGTTGGAAATGGGG
4878793 -TTTGGGT
1 TTTTGGGT
4878800 AATTTGGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 7 0.23
26 13 0.43
27 10 0.33
ACGTcount: A:0.10, C:0.00, G:0.40, T:0.50
Consensus pattern (27 bp):
TTTTGGGTTGTTTGGTTGGAAATGGGG
Found at i:4886038 original size:73 final size:73
Alignment explanation
Indices: 4885939--4886085 Score: 267
Period size: 73 Copynumber: 2.0 Consensus size: 73
4885929 AAAAATTATT
* *
4885939 TAAATTTATTTCTTTAAGAAGTCCACTCTCATTTCGATTGTCTCCAGTTATCCAAAAAATACTGT
1 TAAATTTATTTCTTTAAGAAGTCCACTCTCATTTCGATTGTCTCCAGTAATCCAAAAAATACAGT
4886004 TCTATCAC
66 TCTATCAC
*
4886012 TAAATTTATTTCTTTAAGAAGTCCACTCTCATTTCGATTGTCTCCAGTAATCCACAAAATACAGT
1 TAAATTTATTTCTTTAAGAAGTCCACTCTCATTTCGATTGTCTCCAGTAATCCAAAAAATACAGT
4886077 TCTATCAC
66 TCTATCAC
4886085 T
1 T
4886086 CCCATTTTCA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (73 bp):
TAAATTTATTTCTTTAAGAAGTCCACTCTCATTTCGATTGTCTCCAGTAATCCAAAAAATACAGT
TCTATCAC
Found at i:4887197 original size:13 final size:13
Alignment explanation
Indices: 4887181--4887207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4887171 GGGAAAGTTG
4887181 GGAAGGAATTAAA
1 GGAAGGAATTAAA
4887194 GGAAGGAATTAAA
1 GGAAGGAATTAAA
4887207 G
1 G
4887208 TGAGTGTGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (13 bp):
GGAAGGAATTAAA
Found at i:4891628 original size:15 final size:16
Alignment explanation
Indices: 4891608--4891640 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4891598 TTTATATTAG
4891608 TATTG-TATTTATAAT
1 TATTGATATTTATAAT
4891623 TATTGTATATTTATAAT
1 TATTG-ATATTTATAAT
4891640 T
1 T
4891641 GTAATCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TATTGATATTTATAAT
Found at i:4892100 original size:7 final size:7
Alignment explanation
Indices: 4892088--4892114 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4892078 CATTCCATTG
4892088 TTTTTTC
1 TTTTTTC
4892095 TTTTTTC
1 TTTTTTC
4892102 TTTTTTC
1 TTTTTTC
4892109 TTTTTT
1 TTTTTT
4892115 TTTACAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:4902493 original size:10 final size:10
Alignment explanation
Indices: 4902480--4902517 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
4902470 TGGAATATGG
*
4902480 ATAAATAAAA
1 ATAAATAAAT
4902490 ATAAATAAAT
1 ATAAATAAAT
4902500 A-AAATAGAAT
1 ATAAATA-AAT
4902510 ATAAATAA
1 ATAAATAA
4902518 GATAAAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 5 0.20
10 15 0.60
11 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:4902499 original size:14 final size:16
Alignment explanation
Indices: 4902480--4902517 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
4902470 TGGAATATGG
*
4902480 ATAAATAAAA-ATAA-
1 ATAAATAAAATAGAAT
4902494 ATAAATAAAATAGAAT
1 ATAAATAAAATAGAAT
4902510 ATAAATAA
1 ATAAATAA
4902518 GATAAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 3 0.14
16 8 0.38
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
ATAAATAAAATAGAAT
Found at i:4910486 original size:12 final size:12
Alignment explanation
Indices: 4910469--4910499 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4910459 AGAATTGAGG
4910469 TAAATAAGTGAA
1 TAAATAAGTGAA
*
4910481 TAAATAAGTGAG
1 TAAATAAGTGAA
4910493 TAAATAA
1 TAAATAA
4910500 CTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (12 bp):
TAAATAAGTGAA
Found at i:4911252 original size:33 final size:33
Alignment explanation
Indices: 4911173--4911351 Score: 145
Period size: 33 Copynumber: 5.5 Consensus size: 33
4911163 GTGGACTTTA
* *
4911173 TCTGTGTTTACTGTCCCAACGGACTATCTCTAT
1 TCTGTGTTTACTGTCCTAACAGACTATCTCTAT
* * * * *
4911206 TATATGTTAACTGTCCTAACAGACTATCTTTGT
1 TCTGTGTTTACTGTCCTAACAGACTATCTCTAT
***
4911239 TCTGTGTTTACTGTCCTAGTGGACTA--TCTAT
1 TCTGTGTTTACTGTCCTAACAGACTATCTCTAT
* * * *
4911270 TCTGCGTTTATTGTCCCAAC-GAACTATCTTTAT
1 TCTGTGTTTACTGTCCTAACAG-ACTATCTCTAT
* * *
4911303 TATGTGTTTATTGT-CTCAACAGATTATCTCT-T
1 TCTGTGTTTACTGTCCT-AACAGACTATCTCTAT
4911335 T-TGTGTTTACTGTCCTA
1 TCTGTGTTTACTGTCCTA
4911352 GCGAACTATT
Statistics
Matches: 113, Mismatches: 27, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
30 1 0.01
31 34 0.30
32 5 0.04
33 72 0.64
34 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.45
Consensus pattern (33 bp):
TCTGTGTTTACTGTCCTAACAGACTATCTCTAT
Found at i:4911324 original size:97 final size:92
Alignment explanation
Indices: 4911150--4911352 Score: 264
Period size: 97 Copynumber: 2.2 Consensus size: 92
4911140 ACTTACCGGG
* *
4911150 GTTTACTGTCCTAGTGGACTTTATCTGTGTTTACTGTCCCAACGGACTATCTCTATTATATGTTA
1 GTTTACTGTCCTAGTGGACTTTATCTGCGTTTACTGTCCCAACGAACTATCTCTATTATATGTTA
*
4911215 ACTGTCCTAACAGACTATCTTTGTTCTGT
66 ACTGTCCTAACAGACTATCTCT-TT-TGT
* * *
4911244 GTTTACTGTCCTAGTGGACTATCTATTCTGCGTTTATTGTCCCAACGAACTATCTTTATTATGTG
1 GTTTACTGTCCTAGTGGACT-T-TA-TCTGCGTTTACTGTCCCAACGAACTATCTCTATTATATG
* * *
4911309 TTTATTGT-CTCAACAGATTATCTCTTTTGT
63 TTAACTGTCCT-AACAGACTATCTCTTTTGT
4911339 GTTTACTGTCCTAG
1 GTTTACTGTCCTAG
4911353 CGAACTATTT
Statistics
Matches: 96, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
94 20 0.21
95 18 0.19
96 6 0.06
97 52 0.54
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (92 bp):
GTTTACTGTCCTAGTGGACTTTATCTGCGTTTACTGTCCCAACGAACTATCTCTATTATATGTTA
ACTGTCCTAACAGACTATCTCTTTTGT
Found at i:4915907 original size:32 final size:32
Alignment explanation
Indices: 4915862--4915930 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
4915852 GATCTACACA
4915862 GGCAATGTCAATCTGGGCGTGTGGGCCACATG
1 GGCAATGTCAATCTGGGCGTGTGGGCCACATG
*
4915894 GGCAATG-CTAATCTGGGTGTGTGGGCCACATG
1 GGCAATGTC-AATCTGGGCGTGTGGGCCACATG
4915926 GGCAA
1 GGCAA
4915931 ACCACACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 1 0.03
32 34 0.97
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (32 bp):
GGCAATGTCAATCTGGGCGTGTGGGCCACATG
Found at i:4916773 original size:11 final size:11
Alignment explanation
Indices: 4916757--4916803 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
4916747 CCACGTTAGC
4916757 AAATTATTTTA
1 AAATTATTTTA
*
4916768 AAATTATTGTA
1 AAATTATTTTA
*
4916779 AAA-AATTATTA
1 AAATTATT-TTA
*
4916790 AAATGATTTTA
1 AAATTATTTTA
4916801 AAA
1 AAA
4916804 CCATCATCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 3 0.10
11 24 0.80
12 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:4938040 original size:19 final size:19
Alignment explanation
Indices: 4937976--4938032 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
4937966 TATCTAAACA
4937976 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
4937995 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
4938014 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
4938033 TCCAAAAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:4938991 original size:17 final size:17
Alignment explanation
Indices: 4938957--4938991 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4938947 TCTGAATCCA
*
4938957 AAATAACATAATAAAAT
1 AAATAACATAACAAAAT
*
4938974 AAATAACATAACACAAT
1 AAATAACATAACAAAAT
4938991 A
1 A
4938992 TTTACCATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (17 bp):
AAATAACATAACAAAAT
Found at i:4942429 original size:22 final size:22
Alignment explanation
Indices: 4942404--4942446 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4942394 TAATAAAAAG
4942404 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* *
4942426 AATATTTACAGAATATTCCTA
1 AATATCTACAAAATATTCCTA
4942447 CACTCCCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:4946158 original size:22 final size:22
Alignment explanation
Indices: 4946133--4946175 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4946123 TAATAAAAAG
4946133 AATATCTACAAAATATTCCTAA
1 AATATCTACAAAATATTCCTAA
* *
4946155 AATATTTACAGAATATTCCTA
1 AATATCTACAAAATATTCCTA
4946176 CAAAGATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATCTACAAAATATTCCTAA
Found at i:4947685 original size:23 final size:23
Alignment explanation
Indices: 4947655--4947701 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4947645 CCCTTGGAAA
4947655 TAAATAGTCTCTCTAATTTTAAT
1 TAAATAGTCTCTCTAATTTTAAT
4947678 TAAATAGTCTCTCTAATTTTAAT
1 TAAATAGTCTCTCTAATTTTAAT
4947701 T
1 T
4947702 TCAAACGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (23 bp):
TAAATAGTCTCTCTAATTTTAAT
Found at i:4948754 original size:15 final size:15
Alignment explanation
Indices: 4948734--4948764 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4948724 ATTGAGAAAT
4948734 TTTTAAAAGTTCAAA
1 TTTTAAAAGTTCAAA
*
4948749 TTTTAAAAGTTGAAA
1 TTTTAAAAGTTCAAA
4948764 T
1 T
4948765 GTGGAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (15 bp):
TTTTAAAAGTTCAAA
Found at i:4949216 original size:22 final size:22
Alignment explanation
Indices: 4949177--4949229 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
4949167 AAATTTTGAG
*
4949177 AAATTATAAGTATTAAATTAAA-
1 AAATTATAAGTA-TAAAATAAAT
4949199 AAATTATTAAGTA-AAAATAAAT
1 AAATTA-TAAGTATAAAATAAAT
4949221 AAATATATA
1 AAAT-TATA
4949230 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 7 0.26
22 12 0.44
23 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
AAATTATAAGTATAAAATAAAT
Found at i:4949230 original size:2 final size:2
Alignment explanation
Indices: 4949223--4949254 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4949213 AAATAAATAA
*
4949223 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4949255 TGAGAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4950880 original size:25 final size:25
Alignment explanation
Indices: 4950846--4950897 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4950836 GTGAAGCGGT
4950846 GAAGTCTTTAGCTTACGCTTTCACC
1 GAAGTCTTTAGCTTACGCTTTCACC
4950871 GAAGTCTTTAGCTTACGCTTTCACC
1 GAAGTCTTTAGCTTACGCTTTCACC
4950896 GA
1 GA
4950898 GCCAGCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (25 bp):
GAAGTCTTTAGCTTACGCTTTCACC
Found at i:4962071 original size:2 final size:2
Alignment explanation
Indices: 4962064--4962096 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4962054 TGTAAAAGAT
*
4962064 GA GA GA GA GA GA GA GA GA GA GA GA GC GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4962097 CTGAGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4963720 original size:31 final size:31
Alignment explanation
Indices: 4963685--4963744 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
4963675 TCTTGCACTA
4963685 AATCCAACCAAAAACAGCAAATATAGCATTG
1 AATCCAACCAAAAACAGCAAATATAGCATTG
* *
4963716 AATCCAACCAAATACAGCAAATGTAGCAT
1 AATCCAACCAAAAACAGCAAATATAGCAT
4963745 AAAAAAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.17
Consensus pattern (31 bp):
AATCCAACCAAAAACAGCAAATATAGCATTG
Found at i:4964466 original size:13 final size:14
Alignment explanation
Indices: 4964440--4964468 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4964430 ACTACCGACG
4964440 AATTAAACCATTAT
1 AATTAAACCATTAT
4964454 AATTAAA-CATTAT
1 AATTAAACCATTAT
4964467 AA
1 AA
4964469 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:4977880 original size:56 final size:56
Alignment explanation
Indices: 4977813--4977988 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
4977803 TATTAGTTTA
*
4977813 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
4977869 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
4977925 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
4977981 TTGCCCAT
1 TTGCCCAT
4977989 CATCCCTTGT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:4980952 original size:9 final size:9
Alignment explanation
Indices: 4980938--4981058 Score: 63
Period size: 9 Copynumber: 13.4 Consensus size: 9
4980928 TAAGTATAAT
4980938 TAAGTTATG
1 TAAGTTATG
4980947 TAAGTTATG
1 TAAGTTATG
* * *
4980956 ATATGATATA
1 -TAAGTTATG
*
4980966 T-ATTTATG
1 TAAGTTATG
4980974 T-A-TTATG
1 TAAGTTATG
4980981 TAAGTTATG
1 TAAGTTATG
* *
4980990 CAAATTATG
1 TAAGTTATG
*
4980999 TAAGATATGATA
1 TAAG-T-T-ATG
*
4981011 TATATTTATG
1 TA-AGTTATG
4981021 T-A-TTATG
1 TAAGTTATG
*
4981028 TAAGTTTTG
1 TAAGTTATG
*
4981037 TAAATTATG
1 TAAGTTATG
*
4981046 TAAATTATG
1 TAAGTTATG
4981055 TAAG
1 TAAG
4981059 ATATAATATA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
7 12 0.14
8 8 0.09
9 47 0.55
10 10 0.12
11 2 0.02
12 5 0.06
13 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:4980987 original size:43 final size:43
Alignment explanation
Indices: 4980938--4981045 Score: 153
Period size: 47 Copynumber: 2.4 Consensus size: 43
4980928 TAAGTATAAT
*
4980938 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATG
1 TAAGTTATGTAAATTATGATATGATATATATTTATGTATTATG
*
4980981 TAAGTTATGCAAATTATGTAAGATATGATATATATTTATGTATTATG
1 TAAGTTATGTAAATTA--T--GATATGATATATATTTATGTATTATG
*
4981028 TAAGTTTTGTAAATTATG
1 TAAGTTATGTAAATTATG
4981046 TAAATTATGT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
43 15 0.26
45 2 0.04
47 40 0.70
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (43 bp):
TAAGTTATGTAAATTATGATATGATATATATTTATGTATTATG
Found at i:4981015 original size:47 final size:47
Alignment explanation
Indices: 4980955--4981048 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
4980945 TGTAAGTTAT
4980955 GATATGATATATATTTATGTATTATGTAAGTTATGCAAATTATGTAA
1 GATATGATATATATTTATGTATTATGTAAGTTATGCAAATTATGTAA
* *
4981002 GATATGATATATATTTATGTATTATGTAAGTTTTGTAAATTATGTAA
1 GATATGATATATATTTATGTATTATGTAAGTTATGCAAATTATGTAA
4981049 ATTATGTAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.47
Consensus pattern (47 bp):
GATATGATATATATTTATGTATTATGTAAGTTATGCAAATTATGTAA
Found at i:4981448 original size:105 final size:105
Alignment explanation
Indices: 4981330--4981794 Score: 738
Period size: 105 Copynumber: 4.4 Consensus size: 105
4981320 CAATATTTAA
* *
4981330 AAATATAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGATAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
* * *
4981395 ATTAAATTAAAATAAAATACAATATTTACAATAAACCTTT
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTT
*
4981435 AAATATAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
*
4981500 ATTAAATTAAAATAAATAAAATAAAATATTTAAAATAAATCTTT
66 ATTAAATT---A-AAATAAAATAAAATATTTAAAATAAAACTTT
* *
4981544 AAATACAATTTAATTTAATGAGGTAATTTAAAAATAAAATAAAAGTAGATAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
*
4981609 ATTAAATTAAATTAAAATAAAATATTTAAAATAAAACTTT
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTT
* * * *
4981649 AAATGCAATTTACTTTAATTAGCTAATTTAAAAATAAAATAAAAGTACACAAAATA-TTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
4981713 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTT
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTT
*
4981753 AATTACAATTTAATTTAATTAGGTAA-TT-AAAATAAAATAAAA
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
4981795 CTTTAGCGGC
Statistics
Matches: 336, Mismatches: 20, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
102 14 0.04
103 2 0.01
104 69 0.21
105 151 0.45
106 1 0.00
108 1 0.00
109 98 0.29
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (105 bp):
AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTT
Found at i:4981705 original size:214 final size:209
Alignment explanation
Indices: 4981330--4981794 Score: 754
Period size: 214 Copynumber: 2.2 Consensus size: 209
4981320 CAATATTTAA
*
4981330 AAATATAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGATAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGATAAAATATTTTTCGTG
* * * * *
4981395 ATTAAATTAAAATAAAATACAATATTTACAATAAACCTTTAAATATAATTTAATTTAATTAGGTA
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGCTA
*
4981460 ATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAATTAAAATAAATAAAATAAA
131 ATTTAAAAATAAAATAAAAGTACACAAAATA-TTTTCGTGATTAAATT---A-AAATAAAATAAA
*
4981525 ATATTTAAAATAAATCTTT
191 ATATTTAAAATAAAACTTT
*
4981544 AAATACAATTTAATTTAATGAGGTAATTTAAAAATAAAATAAAAGTAGATAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGATAAAATATTTTTCGTG
* * *
4981609 ATTAAATTAAATTAAAATAAAATATTTAAAATAAAACTTTAAATGCAATTTACTTTAATTAGCTA
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGCTA
4981674 ATTTAAAAATAAAATAAAAGTACACAAAATATTTTCGTGATTAAATTAAAATAAAATAAAATATT
131 ATTTAAAAATAAAATAAAAGTACACAAAATATTTTCGTGATTAAATTAAAATAAAATAAAATATT
4981739 TAAAATAAAACTTT
196 TAAAATAAAACTTT
*
4981753 AATTACAATTTAATTTAATTAGGTAA-TT-AAAATAAAATAAAA
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
4981795 CTTTAGCGGC
Statistics
Matches: 237, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
207 14 0.06
208 2 0.01
209 54 0.23
210 1 0.00
213 16 0.07
214 150 0.63
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (209 bp):
AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGATAAAATATTTTTCGTG
ATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGCTA
ATTTAAAAATAAAATAAAAGTACACAAAATATTTTCGTGATTAAATTAAAATAAAATAAAATATT
TAAAATAAAACTTT
Found at i:4985356 original size:75 final size:74
Alignment explanation
Indices: 4985178--4985340 Score: 202
Period size: 74 Copynumber: 2.2 Consensus size: 74
4985168 TAATACTCGA
* * * * * *
4985178 TCTTTGGCGGCATTTTTAAAAGGCACCGCTAAAGCCACTAAAAGCTCAATAAAAAAGACGGCGTT
1 TCTTTTGCGGCGTTTCTAAAAAGCGCCGCTAAAGCCAATAAAAGCTCAATAAAAAAGACGGCGTT
*
4985243 TTGCAAAAT
66 GTGCAAAAT
* * *
4985252 TCTTTTGCGGCGTTTCTAAAAAGCGCCGCTAAAGCCAATAAAGGCTTAATAGAAAATGACGGCGT
1 TCTTTTGCGGCGTTTCTAAAAAGCGCCGCTAAAGCCAATAAAAGCTCAATA-AAAAAGACGGCGT
**
4985317 TGTGTTAAAT
65 TGTGCAAAAT
4985327 T-TTTTGCGGCGTTT
1 TCTTTTGCGGCGTTT
4985341 TTTGTAAAGC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
74 56 0.74
75 20 0.26
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (74 bp):
TCTTTTGCGGCGTTTCTAAAAAGCGCCGCTAAAGCCAATAAAAGCTCAATAAAAAAGACGGCGTT
GTGCAAAAT
Found at i:4986873 original size:29 final size:29
Alignment explanation
Indices: 4986840--4986898 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4986830 AACCACCATA
*
4986840 TTCAATTTTTAGAGGATAAGACAAGAGAG
1 TTCAATTTTTAGAGGATAAGACAAAAGAG
4986869 TTCAATTTTTAGAGGATAAGACAAAAGAG
1 TTCAATTTTTAGAGGATAAGACAAAAGAG
4986898 T
1 T
4986899 GCTGATAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (29 bp):
TTCAATTTTTAGAGGATAAGACAAAAGAG
Found at i:4987043 original size:12 final size:13
Alignment explanation
Indices: 4987021--4987057 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
4987011 GATATGTTTG
4987021 TATTAATTTTTTA
1 TATTAATTTTTTA
4987034 TATT-ATTTTTTA
1 TATTAATTTTTTA
*
4987046 TATAAATTTTTT
1 TATTAATTTTTT
4987058 TAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTAATTTTTTA
Found at i:4987249 original size:11 final size:11
Alignment explanation
Indices: 4987235--4987287 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
4987225 ATACAATAAC
4987235 AACAAAATAGT
1 AACAAAATAGT
* *
4987246 AACAACATAAT
1 AACAAAATAGT
***
4987257 AGTGAAATAGT
1 AACAAAATAGT
4987268 AACAAAATAGT
1 AACAAAATAGT
*
4987279 AAAAAAATA
1 AACAAAATA
4987288 ACAGCTTTTT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.64, C:0.08, G:0.09, T:0.19
Consensus pattern (11 bp):
AACAAAATAGT
Found at i:4987286 original size:22 final size:22
Alignment explanation
Indices: 4987229--4987287 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
4987219 AGAGTTATAC
* *
4987229 AATAACAACAAAATAGTAACAA
1 AATAATAAAAAAATAGTAACAA
* ***
4987251 CATAATAGTGAAATAGTAACAA
1 AATAATAAAAAAATAGTAACAA
*
4987273 AATAGTAAAAAAATA
1 AATAATAAAAAAATA
4987288 ACAGCTTTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.19
Consensus pattern (22 bp):
AATAATAAAAAAATAGTAACAA
Found at i:4988518 original size:15 final size:16
Alignment explanation
Indices: 4988498--4988527 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4988488 TTATTTTGAT
4988498 TTTTTAAAAA-AATTA
1 TTTTTAAAAATAATTA
4988513 TTTTTAAAAATAATT
1 TTTTTAAAAATAATT
4988528 TAAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTAAAAATAATTA
Found at i:4988534 original size:13 final size:13
Alignment explanation
Indices: 4988500--4988538 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4988490 ATTTTGATTT
*
4988500 TTTAAAAAAATTA
1 TTTAAAAAAATAA
**
4988513 TTTTTAAAAATAA
1 TTTAAAAAAATAA
4988526 TTTAAAAAAATAA
1 TTTAAAAAAATAA
4988539 AAAATCTAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAAAAATAA
Found at i:4989450 original size:25 final size:25
Alignment explanation
Indices: 4989417--4989465 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
4989407 TAGTTGATTT
* *
4989417 TTTTTTTTTTTTG-CTTCAATCAAG
1 TTTTTATTTTATGACTTCAATCAAG
4989441 TTTTTATTTTATGACTTCAATCAAG
1 TTTTTATTTTATGACTTCAATCAAG
4989466 CATGGACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.57
Consensus pattern (25 bp):
TTTTTATTTTATGACTTCAATCAAG
Found at i:4990514 original size:21 final size:23
Alignment explanation
Indices: 4990471--4990516 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
4990461 GACTCGAAAG
*
4990471 TTTGATAAAATTTTTGAAGTTTT
1 TTTGATAAAATTTTTGAAATTTT
4990494 TTTG-TAAAATTTTT-AAATTTT
1 TTTGATAAAATTTTTGAAATTTT
4990515 TT
1 TT
4990517 ACATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (23 bp):
TTTGATAAAATTTTTGAAATTTT
Found at i:4993596 original size:46 final size:46
Alignment explanation
Indices: 4993543--4993716 Score: 258
Period size: 46 Copynumber: 3.8 Consensus size: 46
4993533 TTCTGAAATA
*
4993543 AAATGTGTAAGACCATGGTTGAAAGATACCTTGGCAACATGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
*
4993589 AAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* * **
4993635 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCATGACAAA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
* * * *
4993681 AAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
4993717 TAATGTCGAA
Statistics
Matches: 117, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 117 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATG
Found at i:4994722 original size:15 final size:16
Alignment explanation
Indices: 4994702--4994734 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4994692 ATATATATTT
4994702 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
4994717 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
4994734 T
1 T
4994735 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:4994807 original size:21 final size:22
Alignment explanation
Indices: 4994781--4994867 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
4994771 GTTTTAAGAA
*
4994781 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
4994802 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
4994824 GTT-TTTAAATATTTGATTTATTAT
1 -TTGTTTTAATATTT-ATTT-TTAT
*
4994848 AT-TTTTAA-A-TT-TTTTTAT
1 TTGTTTTAATATTTATTTTTAT
4994866 TT
1 TT
4994868 AATGAAATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
18 5 0.09
19 3 0.05
21 12 0.22
22 20 0.36
23 11 0.20
24 4 0.07
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:4994852 original size:24 final size:22
Alignment explanation
Indices: 4994795--4994857 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
4994785 TTTAGTATTA
*
4994795 TTTTTAT-TTGTTTTAATATTTG
1 TTTTTATATT-TTTAAATATTTG
*
4994817 TTTTTATGTTTTTAAATATTTG
1 TTTTTATATTTTTAAATATTTG
4994839 ATTTATTATATTTTTAAAT
1 -TTT-TTATATTTTTAAAT
4994858 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
22 18 0.50
23 5 0.14
24 13 0.36
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.68
Consensus pattern (22 bp):
TTTTTATATTTTTAAATATTTG
Found at i:4998238 original size:10 final size:9
Alignment explanation
Indices: 4998220--4998268 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
4998210 AACATATTAG
4998220 AAAATTATA
1 AAAATTATA
4998229 AAAATATATA
1 AAAAT-TATA
4998239 GAAAATTATA
1 -AAAATTATA
4998249 AAAA-TATA
1 AAAATTATA
*
4998257 AACACTTATA
1 AA-AATTATA
4998267 AA
1 AA
4998269 GGTATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
8 6 0.17
9 10 0.29
10 14 0.40
11 5 0.14
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:4998268 original size:18 final size:20
Alignment explanation
Indices: 4998213--4998256 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
4998203 TTTTTAGAAC
4998213 ATAT-TAGAAAATTATAAAA
1 ATATATAGAAAATTATAAAA
4998232 ATATATAGAAAATTATAAAA
1 ATATATAGAAAATTATAAAA
4998252 ATATA
1 ATATA
4998257 AACACTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
ATATATAGAAAATTATAAAA
Found at i:4998379 original size:19 final size:18
Alignment explanation
Indices: 4998352--4998412 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
4998342 AAAATAGAAC
*
4998352 TTATAAAAAAGATATAAAA
1 TTATTAAAAAGATA-AAAA
*
4998371 TTATTAAAAATATAAAAA
1 TTATTAAAAAGATAAAAA
* *
4998389 CTAATAAAAAATGTATAAAAA
1 -TTATTAAAAA-G-ATAAAAA
4998410 TTA
1 TTA
4998413 AAATTTAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.12
19 20 0.61
20 2 0.06
21 7 0.21
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (18 bp):
TTATTAAAAAGATAAAAA
Found at i:4998908 original size:17 final size:17
Alignment explanation
Indices: 4998841--4998919 Score: 63
Period size: 17 Copynumber: 4.5 Consensus size: 17
4998831 TAAGGGGATT
*
4998841 TTTCTGATTTTTTATAAAA
1 TTTCT-ATTTTTT-TATAA
4998860 TTT-TA-TTTTTTATAA
1 TTTCTATTTTTTTATAA
*
4998875 CTTTTCTACTATTTTTATAA
1 --TTTCTA-TTTTTTTATAA
*
4998895 TTTCTATTTTTTTATGA
1 TTTCTATTTTTTTATAA
*
4998912 TTTTTATT
1 TTTCTATT
4998920 GTTGTTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.08
16 5 0.10
17 20 0.40
18 9 0.18
19 3 0.06
20 9 0.18
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTCTATTTTTTTATAA
Found at i:5029806 original size:71 final size:74
Alignment explanation
Indices: 5029648--5029831 Score: 230
Period size: 71 Copynumber: 2.5 Consensus size: 74
5029638 AAAATAAATA
* * * *
5029648 ATTAAATCTCAAAATTTAACACATTGGATAGATAAAAACGAGTAATATGGGGGGTTTGATGGATT
1 ATTAAATCTCAAAATTTAACACAATAGATAGATCAAAAC-AGTAATATGGGAGGTTTGATGGATT
*
5029713 TAACCGCTCC
65 TAACCGCTAC
* * * *
5029723 ATAAAATTTCAAAATTTAACACAATAGATAGATCAAAAC-G-AATAT-TGAGGTTTGGTGGATTT
1 ATTAAATCTCAAAATTTAACACAATAGATAGATCAAAACAGTAATATGGGAGGTTTGATGGATTT
* *
5029785 AACTGGTAC
66 AACCGCTAC
*
5029794 ATTAAATCTCAAAATTTAACACAATAGATAAATCAAAA
1 ATTAAATCTCAAAATTTAACACAATAGATAGATCAAAA
5029832 TGAGTACTAT
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
71 55 0.58
72 5 0.05
73 1 0.01
75 34 0.36
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (74 bp):
ATTAAATCTCAAAATTTAACACAATAGATAGATCAAAACAGTAATATGGGAGGTTTGATGGATTT
AACCGCTAC
Found at i:5029875 original size:54 final size:54
Alignment explanation
Indices: 5029793--5029896 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
5029783 TTAACTGGTA
* * *
5029793 CATTAAATCTCAAAATTTAACACAATAGATAAATCAAAATGAGTACTATAGCTT
1 CATTAAATCTCAAAATTTAACACAATAGATAAACCAAAACGAGTAATATAGCTT
* *
5029847 CATTAAATCTCAATATTTAACACAATAGATAGACCAAAACGAGTAATATA
1 CATTAAATCTCAAAATTTAACACAATAGATAAACCAAAACGAGTAATATA
5029897 TGGGTTTGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (54 bp):
CATTAAATCTCAAAATTTAACACAATAGATAAACCAAAACGAGTAATATAGCTT
Found at i:5030039 original size:127 final size:127
Alignment explanation
Indices: 5029720--5030054 Score: 383
Period size: 127 Copynumber: 2.6 Consensus size: 127
5029710 ATTTAACCGC
* * * *
5029720 TCCATAAAATTTCAAAATTTAACACAATAGATAGATCAAAACGAAT-AT-TGAGGTTTGGTGGAT
1 TCCATTAAATATCAATATTTAACACAATAGATAGATCAAAACGAGTAATATGAGGTTTGGTGGAT
* * * * * * *
5029783 TTAACTGGTACATTAAATCTCAAAATTTAACACAATAGATAAATCAAAATGAGTACTATAGC
66 TTAATTGCTCCATTAAATCTCAAAATTTAACAAAATAGATAAATCAAAACGAGTAATATAGA
* * *
5029845 TTCATTAAATCTCAATATTTAACACAATAGATAGACCAAAACGAGTAATAT-ATGGGTTTGGTGG
1 TCCATTAAATATCAATATTTAACACAATAGATAGATCAAAACGAGTAATATGA--GGTTTGGTGG
*
5029909 ATTTAATTGCTCCATTAAATCTCAAATTTTAACAAAATAGATAAATC-AAACGAGTAATAT-GAA
64 ATTTAATTGCTCCATTAAATCTCAAAATTTAACAAAATAGATAAATCAAAACGAGTAATATAG-A
* * * * * * * *
5029972 TCCATTAAATATTAGTATTTAACACAATAAATATATCAAAATGAGTAATATGAGAATTTGATAGA
1 TCCATTAAATATCAATATTTAACACAATAGATAGATCAAAACGAGTAATATGAG-GTTTGGTGGA
*
5030037 TTTAATCGCTCCATTAAA
65 TTTAATTGCTCCATTAAA
5030055 ATTTGATTTG
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
125 40 0.23
126 5 0.03
127 79 0.45
128 53 0.30
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (127 bp):
TCCATTAAATATCAATATTTAACACAATAGATAGATCAAAACGAGTAATATGAGGTTTGGTGGAT
TTAATTGCTCCATTAAATCTCAAAATTTAACAAAATAGATAAATCAAAACGAGTAATATAGA
Found at i:5031710 original size:20 final size:17
Alignment explanation
Indices: 5031669--5031703 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5031659 TTTTAAAATG
5031669 TAAATTTAGTAACATGA
1 TAAATTTAGTAACATGA
5031686 TAAATTTAGTAACATGA
1 TAAATTTAGTAACATGA
5031703 T
1 T
5031704 GAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (17 bp):
TAAATTTAGTAACATGA
Found at i:5034519 original size:80 final size:81
Alignment explanation
Indices: 5034412--5034571 Score: 279
Period size: 80 Copynumber: 2.0 Consensus size: 81
5034402 ACACACGCCC
*
5034412 GTGTGCTCGACCGTGTGGGGGAAAATTAGGCTTGGTTTAAGCCATATTTCTCATCCACATCAAGC
1 GTGTGCTCGACCGTGTGGGGGAAAATTAGGCTTGGTTTAAGCCACATTTCTCATCCACATCAAGC
5034477 ATACCTAAGCCACAAT
66 ATACCTAAGCCACAAT
*
5034493 GTGT-CTCGACCGTGTAGGGGG-TAATTAGGCTTGGTTTAAGCCACATTTCTCATCCACATCAAG
1 GTGTGCTCGACCGTGT-GGGGGAAAATTAGGCTTGGTTTAAGCCACATTTCTCATCCACATCAAG
5034556 CATACCTAAGCCACAA
65 CATACCTAAGCCACAA
5034572 CATTTAATAC
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
80 67 0.88
81 9 0.12
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (81 bp):
GTGTGCTCGACCGTGTGGGGGAAAATTAGGCTTGGTTTAAGCCACATTTCTCATCCACATCAAGC
ATACCTAAGCCACAAT
Found at i:5035544 original size:43 final size:42
Alignment explanation
Indices: 5035497--5035603 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 42
5035487 TATCCCAGAT
* *
5035497 ATGGTTTTACATGCTATCACACATTGATGCCAATGTCCCAAAC
1 ATGGTTTTACATG-TATCACACAATGATACCAATGTCCCAAAC
* * * *
5035540 ATGGTTTTACACGATATCATATAATGATACCAATGTCCCAGAC
1 ATGGTTTTACATG-TATCACACAATGATACCAATGTCCCAAAC
*
5035583 ATGGTCTTACATGTAATCACA
1 ATGGTTTTACATGT-ATCACA
5035604 TCTCTGTAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 52 0.98
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (42 bp):
ATGGTTTTACATGTATCACACAATGATACCAATGTCCCAAAC
Found at i:5038104 original size:11 final size:10
Alignment explanation
Indices: 5038088--5038158 Score: 52
Period size: 11 Copynumber: 6.6 Consensus size: 10
5038078 GTCTTTCCCC
5038088 TTTTCTTTCCT
1 TTTTCTTT-CT
5038099 TTTTCTTTCT
1 TTTTCTTTCT
*
5038109 TTTTCCCTTCT
1 TTTT-CTTTCT
* *
5038120 GTTTCGTTTAT
1 TTTTC-TTTCT
5038131 TCTTTCTTTCT
1 T-TTTCTTTCT
*
5038142 TTTCTATTTCT
1 TTT-TCTTTCT
*
5038153 ATTTCT
1 TTTTCT
5038159 ATTTCTTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
10 11 0.23
11 32 0.68
12 4 0.09
ACGTcount: A:0.04, C:0.23, G:0.03, T:0.70
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:5038113 original size:29 final size:29
Alignment explanation
Indices: 5038085--5038139 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
5038075 TTGGTCTTTC
*
5038085 CCCTTTTCTTTCCTTT-TTCTTTCTTTTT
1 CCCTTCTCTTTCCTTTATTCTTTCTTTTT
* *
5038113 CCCTTCTGTTTCGTTTATTCTTTCTTT
1 CCCTTCTCTTTCCTTTATTCTTTCTTT
5038140 CTTTTCTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (29 bp):
CCCTTCTCTTTCCTTTATTCTTTCTTTTT
Found at i:5038159 original size:12 final size:11
Alignment explanation
Indices: 5038137--5038167 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
5038127 TTATTCTTTC
5038137 TTTCTTTTCTA
1 TTTCTTTTCTA
5038148 TTTCTATTTCTA
1 TTTCT-TTTCTA
5038160 TTTCTTTT
1 TTTCTTTT
5038168 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTCTTTTCTA
Found at i:5038456 original size:13 final size:14
Alignment explanation
Indices: 5038438--5038466 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5038428 AACTAACTTC
5038438 ATAAATATTT-CTA
1 ATAAATATTTACTA
5038451 ATAAATATTTACTA
1 ATAAATATTTACTA
5038465 AT
1 AT
5038467 CTAATTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAAATATTTACTA
Found at i:5039940 original size:15 final size:15
Alignment explanation
Indices: 5039895--5039941 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5039885 TGTAATTTCT
*
5039895 TTTTTAAATGTG-T-
1 TTTTTAAATTTGATA
* *
5039908 TTTTTAAATTTAAAA
1 TTTTTAAATTTGATA
5039923 TTTTTAAATTTGATA
1 TTTTTAAATTTGATA
5039938 TTTT
1 TTTT
5039942 ATTTTGGTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.37
15 17 0.63
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTTAAATTTGATA
Found at i:5043727 original size:8 final size:8
Alignment explanation
Indices: 5043685--5043709 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5043675 ATATAGACTA
5043685 AATAAAAT
1 AATAAAAT
5043693 AATAAAAT
1 AATAAAAT
5043701 AATAAAAT
1 AATAAAAT
5043709 A
1 A
5043710 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:5043733 original size:29 final size:31
Alignment explanation
Indices: 5043682--5043760 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 31
5043672 TATATATAGA
*
5043682 CTAAATAAAATAATAAAATAATAA-AA-TAT
1 CTAATTAAAATAATAAAATAATAATAATTAT
* *
5043711 CTTATTAAAAT-ATTAAATAAATAATAATTAT
1 CTAATTAAAATAATAAAAT-AATAATAATTAT
5043742 CTAATT-AAATAATAAAATA
1 CTAATTAAAATAATAAAATA
5043761 TCACCAACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
28 6 0.15
29 14 0.34
30 7 0.17
31 14 0.34
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (31 bp):
CTAATTAAAATAATAAAATAATAATAATTAT
Found at i:5051600 original size:50 final size:50
Alignment explanation
Indices: 5051476--5051724 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
5051466 GATAATAACA
* * ** * *
5051476 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
5051527 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
5051577 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
5051627 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
5051682 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
5051725 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:5051654 original size:100 final size:104
Alignment explanation
Indices: 5051475--5051724 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
5051465 TGATAATAAC
**
5051475 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
5051540 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
5051577 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
5051640 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
5051682 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5051725 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:5051840 original size:13 final size:13
Alignment explanation
Indices: 5051819--5051850 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5051809 GCTTGGATCA
*
5051819 TCATCAAATAAAT
1 TCATAAAATAAAT
5051832 TCATAAAATAAAT
1 TCATAAAATAAAT
5051845 TCATAA
1 TCATAA
5051851 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5052097 original size:30 final size:30
Alignment explanation
Indices: 5052062--5052119 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5052052 CCTCGACTCT
*
5052062 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
5052092 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
5052120 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:5067280 original size:24 final size:25
Alignment explanation
Indices: 5067253--5067301 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5067243 GCTTTTTTAT
*
5067253 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
5067277 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
5067302 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:5067294 original size:25 final size:23
Alignment explanation
Indices: 5067265--5067329 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 23
5067255 AATAAAAAAC
*
5067265 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
5067290 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
5067311 -TTAAAACA-AAAAACAAATA
1 TTTAAAACATAAAAACAAATA
5067330 AAAAATAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 1 0.03
23 5 0.13
24 3 0.08
25 11 0.29
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:5067324 original size:19 final size:20
Alignment explanation
Indices: 5067291--5067329 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
5067281 TCAAATACAT
5067291 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
5067311 TTAAAACA-AAAAACAAATA
1 TTAAAACATAAAAACAAATA
5067330 AAAAATAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:5069139 original size:3 final size:3
Alignment explanation
Indices: 5069131--5069176 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
5069121 TTGAATTATT
*
5069131 TCA TCA TCA TCA TCA TCA CCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
5069177 TATTATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:5069304 original size:26 final size:25
Alignment explanation
Indices: 5069275--5069330 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
5069265 TTATTTTCTT
5069275 TATTTTATTACTATTAACATTAGTAC
1 TATTTTATTACTATT-ACATTAGTAC
* *
5069301 TATTTTTATTACTATTACTTTATTAC
1 TA-TTTTATTACTATTACATTAGTAC
5069327 TATT
1 TATT
5069331 ACTACTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 12 0.44
27 13 0.48
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (25 bp):
TATTTTATTACTATTACATTAGTAC
Found at i:5069307 original size:41 final size:41
Alignment explanation
Indices: 5069252--5069331 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
5069242 CATCATTATT
* * *
5069252 ATTATTACAATTTTTATTTTCT-TTATTTTATTACTATTAAC
1 ATTAGTACAATTTTTA-TTACTATTACTTTATTACTATTAAC
*
5069293 ATTAGTACTATTTTTATTACTATTACTTTATTACTATTA
1 ATTAGTACAATTTTTATTACTATTACTTTATTACTATTA
5069332 CTACTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.59
Consensus pattern (41 bp):
ATTAGTACAATTTTTATTACTATTACTTTATTACTATTAAC
Found at i:5069368 original size:20 final size:20
Alignment explanation
Indices: 5069343--5069382 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5069333 TACTAATATC
*
5069343 ACTATTATCATTTTTTTATT
1 ACTATTATCATTTTATTATT
*
5069363 ACTATTATTATTTTATTATT
1 ACTATTATCATTTTATTATT
5069383 TTTTTTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
ACTATTATCATTTTATTATT
Found at i:5069405 original size:27 final size:27
Alignment explanation
Indices: 5069345--5069408 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
5069335 CTAATATCAC
* *
5069345 TATTATCATTTTTTTATTACTATTATTA
1 TATTATTA-TTTTTTATTACTATTAATA
*
5069373 TTTTATTATTTTTT-TTACTATCTAATA
1 TATTATTATTTTTTATTACTAT-TAATA
5069400 TATTATTAT
1 TATTATTAT
5069409 ACCTTTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 7 0.23
27 18 0.58
28 6 0.19
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTATTATTTTTTATTACTATTAATA
Found at i:5072270 original size:44 final size:44
Alignment explanation
Indices: 5072207--5072298 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
5072197 TTTGGTTAGT
5072207 ATACATGGGGAATAACTACAAAAAGAAAGTTCGCGAAATATCAA
1 ATACATGGGGAATAACTACAAAAAGAAAGTTCGCGAAATATCAA
*
5072251 ATACATGGGGAATAACTACAAAAAGAAAGTTCGCGAGATATCAA
1 ATACATGGGGAATAACTACAAAAAGAAAGTTCGCGAAATATCAA
5072295 ATAC
1 ATAC
5072299 CTGGAACCAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (44 bp):
ATACATGGGGAATAACTACAAAAAGAAAGTTCGCGAAATATCAA
Found at i:5081593 original size:87 final size:87
Alignment explanation
Indices: 5081337--5081979 Score: 941
Period size: 87 Copynumber: 7.4 Consensus size: 87
5081327 GCATTCGTAA
* * * * * * ** *
5081337 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAAATCTTGTCTCCCTAAACAATA
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCT-GAATTTACAGATCTTATCACCCTAAGTAGTA
** ** *
5081402 GTGG-AGTAGATCGAAGACGAAGG
65 G-GGAAACAGATCGAAGGTGATGG
*
5081425 GCCTT-AACTCCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCACCCTAAGTAGT
1 GCCTTAAAC-CCCTAAGCAGTAGGGTAACAGGCTG-AATTTACAGATCTTATCACCCTAAGTAGT
5081489 AGGGAAACAGATCGAAGGTGATGG
64 AGGGAAACAGATCGAAGGTGATGG
5081513 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
* *
5081578 GGAAACAGATTGAAGGTGATAG
66 GGAAACAGATCGAAGGTGATGG
* *
5081600 ACCTTAAACCCCCTAAGTAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTA
1 GCCTTAAA-CCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTA
*
5081665 GGGAAACAGATCGAAGGTAATGG
65 GGGAAACAGATCGAAGGTGATGG
* * *
5081688 GCCTTAAACCCCTAAGCAGTAGGATAACAGGCTGAATTTACGGATCTTATCACCCTAAGCAGTAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
* * *
5081753 GCAAACAGATCAAAAGTGATGG
66 GGAAACAGATCGAAGGTGATGG
5081775 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
5081840 GGAAACAGATCGAAGGTGATGG
66 GGAAACAGATCGAAGGTGATGG
*
5081862 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATTTTATCACCCTAAGTAGTA-
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
* *
5081926 GGAGAACAGATCAAAGATGATGG
66 GGA-AACAGATCGAAGGTGATGG
*
5081949 GCCTTAAACCCCTAAGCAGTAGGTTAACAGG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAGG
5081980 TTGGAAATCA
Statistics
Matches: 509, Mismatches: 40, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
86 3 0.01
87 323 0.63
88 180 0.35
89 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (87 bp):
GCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
GGAAACAGATCGAAGGTGATGG
Found at i:5081934 original size:43 final size:43
Alignment explanation
Indices: 5081434--5081927 Score: 293
Period size: 44 Copynumber: 11.3 Consensus size: 43
5081424 GGCCTTAACT
*
5081434 CCCTAAGCAGTAGGGTAACAGGCTGAAAATTACAGATCTTATCA
1 CCCTAAGCAGTAGGGTAACAGGCTG-AATTTACAGATCTTATCA
* * * * * ** ** *
5081478 CCCTAAGTAGTAGGGAAACA-GATCGAAGGTGATGGGCCTTA-AA
1 CCCTAAGCAGTAGGGTAACAGGCT-GAA-TTTACAGATCTTATCA
5081521 CCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
1 -CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
* * ** * * * * * *
5081565 CCCTAAGTAGTAGGGAAACAGATTGAAGGTGATAGACCTTAAACC
1 CCCTAAGCAGTAGGGTAACAGGCTGAA-TTTACAGATCTT-ATCA
*
5081610 CCCTAAGTAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
* * * ** ** *
5081653 CCCTAAGTAGTAGGGAAACA-GATCGAAGGTA-ATGGGCCTTA-AA
1 CCCTAAGCAGTAGGGTAACAGGCT-GAATTTACA--GATCTTATCA
* *
5081696 CCCCTAAGCAGTAGGATAACAGGCTGAATTTACGGATCTTATCA
1 -CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
** * ** * * ** ** *
5081740 CCCTAAGCAGTAGGCAAACAGATCAAAAGTGATGGGCCTTA-AA
1 CCCTAAGCAGTAGGGTAACAG-GCTGAATTTACAGATCTTATCA
5081783 CCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
1 -CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
* * * * * ** ** *
5081827 CCCTAAGTAGTAGGGAAACA-GATCGAAGGTGATGGGCCTTA-AA
1 CCCTAAGCAGTAGGGTAACAGGCT-GAA-TTTACAGATCTTATCA
*
5081870 CCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATTTTATCA
1 -CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
*
5081914 CCCTAAGTAGTAGG
1 CCCTAAGCAGTAGG
5081928 AGAACAGATC
Statistics
Matches: 327, Mismatches: 101, Indels: 45
0.69 0.21 0.10
Matches are distributed among these distances:
42 5 0.02
43 138 0.42
44 152 0.46
45 32 0.10
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCA
Found at i:5081978 original size:44 final size:43
Alignment explanation
Indices: 5081478--5081978 Score: 187
Period size: 44 Copynumber: 11.5 Consensus size: 43
5081468 GATCTTATCA
* * *
5081478 CCCTAAGTAGTAGGGAAACAGATCGAAGGTGATGGGCCTTAAAC
1 CCCTAAGCAGTAGGGTAACAGATCGAA-ATGATGGGCCTTAAAC
* * * ** ** *
5081522 CCCTAAGCAGTAGGGTAACAG-GCTGAATTTACAGATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGATC-GAAATGATGGGCCTTAAAC
* * * * * *
5081564 ACCCTAAGTAGTAGGGAAACAGATTGAAGGTGATAGACCTTAAACC
1 -CCCTAAGCAGTAGGGTAACAGATCGAA-ATGATGGGCCTTAAA-C
* * * * ** ** *
5081610 CCCTAAGTAGTAGGGTAACAG-GCTGAATTTACAGATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGATC-GAAATGATGGGCCTTAAAC
* * * *
5081652 ACCCTAAGTAGTAGGGAAACAGATCGAAGGTAATGGGCCTTAAAC
1 -CCCTAAGCAGTAGGGTAACAGATCGAA-ATGATGGGCCTTAAAC
* * * * * ** *
5081697 CCCTAAGCAGTAGGATAACAG-GCTGAATTTACGGATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGATC-GAAATGATGGGCCTTAAAC
** *
5081739 ACCCTAAGCAGTAGGCAAACAGATCAAAAGTGATGGGCCTTAAAC
1 -CCCTAAGCAGTAGGGTAACAGATCGAAA-TGATGGGCCTTAAAC
* * * ** ** *
5081784 CCCTAAGCAGTAGGGTAACAG-GCTGAATTTACAGATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGATC-GAAATGATGGGCCTTAAAC
* * *
5081826 ACCCTAAGTAGTAGGGAAACAGATCGAAGGTGATGGGCCTTAAAC
1 -CCCTAAGCAGTAGGGTAACAGATCGAA-ATGATGGGCCTTAAAC
* * * ** ** * *
5081871 CCCTAAGCAGTAGGGTAACAG-GCTGAATTTA-CAGATTTTATC
1 CCCTAAGCAGTAGGGTAACAGATC-GAAATGATGGGCCTTAAAC
* *
5081913 ACCCTAAGTAGTAGGAG-AACAGATCAAAGATGATGGGCCTTAAAC
1 -CCCTAAGCAGTAGG-GTAACAGATCGAA-ATGATGGGCCTTAAAC
*
5081958 CCCTAAGCAGTAGGTTAACAG
1 CCCTAAGCAGTAGGGTAACAG
5081979 GTTGGAAATC
Statistics
Matches: 328, Mismatches: 101, Indels: 56
0.68 0.21 0.12
Matches are distributed among these distances:
42 12 0.04
43 134 0.41
44 146 0.45
45 35 0.11
46 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGATCGAAATGATGGGCCTTAAAC
Found at i:5082063 original size:262 final size:259
Alignment explanation
Indices: 5081338--5082000 Score: 870
Period size: 262 Copynumber: 2.5 Consensus size: 259
5081328 CATTCGTAAG
* * * * * ** *
5081338 CCTT-AACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAAATCTTGTCTCCCTAAACAATA
1 CCTTAAACCCCCTAAGCAGTAGGGTAACAGGCT-GAATTTACAGATCTTATCACCCTAAGTAGTA
** * * *
5081402 GTGG-AGTAGATCGAAGACGAA-GGGCCTT-AACTCCCTAAGCAGTAGGGTAACAGGCTGAAAAT
65 G-GGAAACAGATCAAAGA-TAATGGGCCTTAAAC-CCCTAAGCAGTAGGATAACAGGCTG-AAAT
* * * * * *
5081464 TACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAAGGTGATGGGCCTTAAACCCCTAAG
126 CAAAGATCTTATCACCCTAAGCAGTAGGCAAACAGATCAAAAGTGAT--G-CTTAAACCCCTAAG
*
5081529 CAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATTGAAGG
188 CAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAAGG
5081594 TGATAGA
253 TGATAGA
*
5081601 CCTTAAACCCCCTAAGTAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
1 CCTTAAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
* * * * **
5081666 GGAAACAGATCGAAGGTAATGGGCCTTAAACCCCTAAGCAGTAGGATAACAGGCTGAATTTACGG
66 GGAAACAGATCAAAGATAATGGGCCTTAAACCCCTAAGCAGTAGGATAACAGGCTGAAATCAAAG
5081731 ATCTTATCACCCTAAGCAGTAGGCAAACAGATCAAAAGTGATGGGCCTTAAACCCCTAAGCAGTA
131 ATCTTATCACCCTAAGCAGTAGGCAAACAGATCAAAAGTGAT--G-CTTAAACCCCTAAGCAGTA
*
5081796 GGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAAGGTGATG
193 GGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAAGGTGATA
*
5081861 GG
258 GA
*
5081863 CCTTAAA-CCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATTTTATCACCCTAAGTAGTA-
1 CCTTAAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
* * *
5081926 GGAGAACAGATCAAAGATGATGGGCCTTAAACCCCTAAGCAGTAGGTTAACAGGTTGGAAATCAA
66 GGA-AACAGATCAAAGATAATGGGCCTTAAACCCCTAAGCAGTAGGATAACAGGCT-GAAATCAA
5081991 AGATCTTATC
129 AGATCTTATC
5082001 TCTCTGAGTA
Statistics
Matches: 360, Mismatches: 34, Indels: 13
0.88 0.08 0.03
Matches are distributed among these distances:
260 3 0.01
261 101 0.28
262 157 0.44
263 69 0.19
264 30 0.08
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (259 bp):
CCTTAAACCCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAG
GGAAACAGATCAAAGATAATGGGCCTTAAACCCCTAAGCAGTAGGATAACAGGCTGAAATCAAAG
ATCTTATCACCCTAAGCAGTAGGCAAACAGATCAAAAGTGATGCTTAAACCCCTAAGCAGTAGGG
TAACAGGCTGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAAGGTGATAGA
Found at i:5083748 original size:18 final size:17
Alignment explanation
Indices: 5083725--5083767 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
5083715 AAATACTATT
*
5083725 ATTATTTCTACTATTGTC
1 ATTATTTCTACTATTG-A
* *
5083743 ATTATTACTATTATTGA
1 ATTATTTCTACTATTGA
5083760 ATTATTTC
1 ATTATTTC
5083768 ATCATCATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (17 bp):
ATTATTTCTACTATTGA
Found at i:5083891 original size:3 final size:3
Alignment explanation
Indices: 5083854--5084156 Score: 78
Period size: 3 Copynumber: 103.3 Consensus size: 3
5083844 TTTCATATCG
* * *
5083854 TTA TCA TTA -TA TTA -TA TATA TTA TGTA TATA TTA TTA TT- TGCA TCA
1 TTA TTA TTA TTA TTA TTA T-TA TTA T-TA T-TA TTA TTA TTA T-TA TTA
** * * *
5083900 TTA TTA TTA TTA CAA TTT TTA TT- TTCT TTA TT- TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
** * * * * * * * *
5083944 ACA TTA GTA CTA TTT TTA TTA CTA TTA CT- TTA TTA CTA TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * * * *
5083991 ACA TCA CTA TTA TCA TT- TTT TTA TTA TTA TTT TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
5084037 TTT TTT TTA CTA TCTA ATA -TA TTA TTA -TA CCTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA --TTA TTA TTA TTA TTA
* * * * *
5084083 -TA TT- TTC TT- TT- TTA TTA CTA TTA CTA TT- TTA TTT TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
5084126 CTA CTA TTA TTA TTA TCA ATA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5084157 CACTATCGTT
Statistics
Matches: 217, Mismatches: 62, Indels: 42
0.68 0.19 0.13
Matches are distributed among these distances:
2 28 0.13
3 173 0.80
4 14 0.06
5 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5083960 original size:41 final size:41
Alignment explanation
Indices: 5083905--5083984 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
5083895 CATCATTATT
* * *
5083905 ATTATTACAATTTTTATTTTCT-TTATTTTATTACTATTAAC
1 ATTAGTACAATTTTTA-TTACTATTACTTTATTACTATTAAC
*
5083946 ATTAGTACTATTTTTATTACTATTACTTTATTACTATTA
1 ATTAGTACAATTTTTATTACTATTACTTTATTACTATTA
5083985 CTACTAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.59
Consensus pattern (41 bp):
ATTAGTACAATTTTTATTACTATTACTTTATTACTATTAAC
Found at i:5084017 original size:14 final size:15
Alignment explanation
Indices: 5083998--5084030 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5083988 CTAACATCAC
5083998 TATTATCATTTTT-T
1 TATTATCATTTTTAT
*
5084012 TATTATTATTTTTAT
1 TATTATCATTTTTAT
5084027 TATT
1 TATT
5084031 TTATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTATCATTTTTAT
Found at i:5084119 original size:23 final size:23
Alignment explanation
Indices: 5084012--5084139 Score: 77
Period size: 23 Copynumber: 5.4 Consensus size: 23
5084002 ATCATTTTTT
*
5084012 TATTATTATTTTTATTATT-TTAT
1 TATT-TTATTTTTATTATTATTAC
* *
5084035 TA-TTT-TTTTTACTATCTAATA-
1 TATTTTATTTTTATTAT-TATTAC
5084056 TATTATTATACCTTATTATTATTATTA-
1 TATT-TTAT---TT-TTATTATTATTAC
* *
5084083 TATTTTCTTTTTTATTACTATTAC
1 TATTTT-ATTTTTATTATTATTAC
* *
5084107 TATTTTATTTTTATTTTTACTAC
1 TATTTTATTTTTATTATTATTAC
5084130 TATTATTATT
1 TATT-TTATT
5084140 ATCAATATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 23
0.72 0.09 0.20
Matches are distributed among these distances:
20 9 0.11
21 5 0.06
22 4 0.05
23 32 0.39
24 14 0.17
26 2 0.02
27 11 0.13
28 6 0.07
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTTATTTTTATTATTATTAC
Found at i:5084123 original size:29 final size:29
Alignment explanation
Indices: 5084072--5084141 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5084062 TATACCTTAT
*
5084072 TATTATTATTATATTTTCTTTTTTATTAC
1 TATTATTATTATATTTTCTTTTTTACTAC
* *
5084101 TATTACTATTTTATTTT-TATTTTTACTAC
1 TATTATTATTATATTTTCT-TTTTTACTAC
5084130 TATTATTATTAT
1 TATTATTATTAT
5084142 CAATATTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (29 bp):
TATTATTATTATATTTTCTTTTTTACTAC
Found at i:5084312 original size:18 final size:18
Alignment explanation
Indices: 5084289--5084323 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5084279 CTTGCTTTTT
*
5084289 TCATATTTTTATTATTGC
1 TCATATTATTATTATTGC
*
5084307 TCATATTATTGTTATTG
1 TCATATTATTATTATTG
5084324 ATATTGTCGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (18 bp):
TCATATTATTATTATTGC
Found at i:5088368 original size:17 final size:16
Alignment explanation
Indices: 5088327--5088377 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
5088317 AATATTTATT
5088327 TAAAATTAATTATAAA
1 TAAAATTAATTATAAA
5088343 -AATATATTAATTATAAA
1 TAA-A-ATTAATTATAAA
5088360 CTAAAATTATATTA-AAA
1 -TAAAATTA-ATTATAAA
5088377 T
1 T
5088378 TAAGTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 19 0.63
18 5 0.17
19 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATTAATTATAAA
Found at i:5088386 original size:22 final size:22
Alignment explanation
Indices: 5088322--5088386 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
5088312 AGTAAAATAT
*
5088322 TTAT-TTAAAATTAATTATAAAA
1 TTATATTAAAATTAAAT-TAAAA
* * *
5088344 ATATATT-AATTATAAACTAAAA
1 TTATATTAAAAT-TAAATTAAAA
*
5088366 TTATATTAAAATTAAGTTAAA
1 TTATATTAAAATTAAATTAAA
5088387 TCAGGTCGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TTATATTAAAATTAAATTAAAA
Found at i:5088786 original size:22 final size:22
Alignment explanation
Indices: 5088761--5088804 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5088751 TAGTCTTATA
5088761 ATAATTTATTAATATAATAAAT
1 ATAATTTATTAATATAATAAAT
* *
5088783 ATAATTTATTATTTTAATAAAT
1 ATAATTTATTAATATAATAAAT
5088805 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTTATTAATATAATAAAT
Found at i:5088815 original size:20 final size:22
Alignment explanation
Indices: 5088761--5088816 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
5088751 TAGTCTTATA
* * *
5088761 ATAATTTATTAATATAATAAAT
1 ATAATTTAATATTTTAATAAAT
*
5088783 ATAATTTATTATTTTAATAAAT
1 ATAATTTAATATTTTAATAAAT
5088805 -T-ATTTAATATTT
1 ATAATTTAATATTT
5088817 CAATTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 10 0.32
21 1 0.03
22 20 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTTAATATTTTAATAAAT
Found at i:5088856 original size:15 final size:16
Alignment explanation
Indices: 5088829--5088859 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5088819 ATTTTATTTT
5088829 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
5088845 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
5088860 GAACATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:5088918 original size:15 final size:15
Alignment explanation
Indices: 5088898--5088954 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
5088888 ATTCAATATT
5088898 AATATTTTAATAATA
1 AATATTTTAATAATA
*
5088913 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
5088932 AATATATTAATAATA
1 AATATTTTAATAATA
*
5088947 AATGTTTT
1 AATATTTT
5088955 GTAGTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:5089429 original size:14 final size:14
Alignment explanation
Indices: 5089410--5089447 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5089400 CCAGAAAAGT
5089410 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
5089424 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
5089438 AAGTCATTTT
1 AAATCATTTT
5089448 TAGTGAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:5090886 original size:14 final size:14
Alignment explanation
Indices: 5090867--5090896 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5090857 AAACCCTTTC
5090867 AATAATAATAGTTT
1 AATAATAATAGTTT
*
5090881 AATAATAATGGTTT
1 AATAATAATAGTTT
5090895 AA
1 AA
5090897 GAGTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (14 bp):
AATAATAATAGTTT
Found at i:5093097 original size:18 final size:19
Alignment explanation
Indices: 5093076--5093118 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
5093066 TAATAAGTAT
*
5093076 TAATTTTTTTATAA-TTTA
1 TAATTTTTTAATAATTTTA
5093094 TAATTTTTTAATAATTTTA
1 TAATTTTTTAATAATTTTA
5093113 TAATTT
1 TAATTT
5093119 ATACTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATTTTTTAATAATTTTA
Found at i:5093170 original size:20 final size:19
Alignment explanation
Indices: 5093086--5093202 Score: 57
Period size: 18 Copynumber: 6.3 Consensus size: 19
5093076 TAATTTTTTT
5093086 ATAATTTATAAT-TTTT-TA
1 ATAATTT-TAATATTTTGTA
* *
5093104 ATAATTTT-ATAATTTATA
1 ATAATTTTAATATTTTGTA
* *
5093122 CTAATTATTAA-ATTTGGTA
1 ATAATT-TTAATATTTTGTA
*** *
5093141 GCCATGTTAATATTTTGTA
1 ATAATTTTAATATTTTGTA
*
5093160 ATAATTATTAATATATT-T-
1 ATAATT-TTAATATTTTGTA
*
5093178 ATAATTTTTATAGTTTTGTA
1 ATAATTTTAATA-TTTTGTA
*
5093198 CTAAT
1 ATAAT
5093203 CAAAATGAAT
Statistics
Matches: 72, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
16 2 0.03
17 9 0.12
18 27 0.38
19 20 0.28
20 14 0.19
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (19 bp):
ATAATTTTAATATTTTGTA
Found at i:5093188 original size:21 final size:20
Alignment explanation
Indices: 5093065--5093182 Score: 56
Period size: 18 Copynumber: 6.2 Consensus size: 20
5093055 ATTTTTAAGA
*
5093065 ATAATAAGTATTAAT-TTTT
1 ATAATAATTATTAATATTTT
*
5093084 -TTATAATT-TATAAT-TTTT
1 ATAATAATTAT-TAATATTTT
*
5093102 -TAATAATT-TT-ATAATTT
1 ATAATAATTATTAATATTTT
* *
5093119 ATACTAATTATTAA-ATTTG
1 ATAATAATTATTAATATTTT
* *** *
5093138 GTAGCCA-TGTTAATATTTT
1 ATAATAATTATTAATATTTT
*
5093157 GTAATAATTATTAATATATTT
1 ATAATAATTATTAATAT-TTT
5093178 ATAAT
1 ATAAT
5093183 TTTTATAGTT
Statistics
Matches: 73, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
16 2 0.03
17 5 0.07
18 34 0.47
19 16 0.22
20 9 0.12
21 7 0.10
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
ATAATAATTATTAATATTTT
Found at i:5097996 original size:8 final size:7
Alignment explanation
Indices: 5097981--5098044 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
5097971 GTTAAATCTG
5097981 AATTTAA
1 AATTTAA
5097988 AATTTTAA
1 AA-TTTAA
* *
5097996 AAATAAA
1 AATTTAA
*
5098003 AATTCTTA
1 AATT-TAA
*
5098011 AATATAAA
1 AAT-TTAA
5098019 AATTTAA
1 AATTTAA
5098026 AATTTAA
1 AATTTAA
5098033 AATTTAA
1 AATTTAA
5098040 AATTT
1 AATTT
5098045 TTGAAGAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 30 0.65
8 15 0.33
9 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
AATTTAA
Found at i:5098058 original size:38 final size:38
Alignment explanation
Indices: 5097981--5098057 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 38
5097971 GTTAAATCTG
*
5097981 AATTTAAAATTTTAAAAATAAAAATTCTTAAATATAAA
1 AATTTAAAATTTTAAAAATAAAAATTCTTAAAGATAAA
* * * * *
5098019 AATTTAAAA-TTTAAAATTTAAAATTTTTGAAGAGAAA
1 AATTTAAAATTTTAAAAATAAAAATTCTTAAAGATAAA
5098056 AA
1 AA
5098058 AACTTATAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.36
Consensus pattern (38 bp):
AATTTAAAATTTTAAAAATAAAAATTCTTAAAGATAAA
Found at i:5099601 original size:13 final size:13
Alignment explanation
Indices: 5099583--5099620 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5099573 TTAATAAAAA
*
5099583 ATATATTTAATAT
1 ATATATTAAATAT
5099596 ATATATTAAATAT
1 ATATATTAAATAT
*
5099609 ATTTA-TAAATAT
1 ATATATTAAATAT
5099621 CAAATGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATATTAAATAT
Found at i:5101745 original size:31 final size:32
Alignment explanation
Indices: 5101700--5101766 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
5101690 TTTTTGCAAT
*
5101700 TATACATATTAAATTTTGATTTTGATTCAAATG
1 TATACATA-TAAATTTTAATTTTGATTCAAATG
*
5101733 TATACATA-AAATTTTAATTTTGATTTAAATG
1 TATACATATAAATTTTAATTTTGATTCAAATG
5101764 TAT
1 TAT
5101767 GAATTTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 24 0.75
33 8 0.25
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (32 bp):
TATACATATAAATTTTAATTTTGATTCAAATG
Found at i:5102194 original size:20 final size:20
Alignment explanation
Indices: 5102158--5102207 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5102148 TTTTAATTAT
*
5102158 TATATTTTA-ATACTTAAAA
1 TATAATTTATATACTTAAAA
* *
5102177 TATAATTTATATATTTAAAT
1 TATAATTTATATACTTAAAA
*
5102197 TAAAATTTATA
1 TATAATTTATA
5102208 AATAGTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATTTATATACTTAAAA
Found at i:5119680 original size:8 final size:8
Alignment explanation
Indices: 5119667--5119691 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5119657 GGTGTTCGGC
5119667 GCAAGTGG
1 GCAAGTGG
5119675 GCAAGTGG
1 GCAAGTGG
5119683 GCAAGTGG
1 GCAAGTGG
5119691 G
1 G
5119692 GGGTAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:5123411 original size:102 final size:100
Alignment explanation
Indices: 5123235--5123422 Score: 252
Period size: 99 Copynumber: 1.9 Consensus size: 100
5123225 TTTCTTTAAT
* * * *
5123235 TTTGGGACACTGATGGCCGGCACCAGTGTCAATTAAAAAAAATTGGGTGTTGGCCAGAAGATGAC
1 TTTGGGACACTGATGGCAGGCACAAATGTCAATTAAAAAAAATTGGGTGCTGGCCAGAAGATGAC
*
5123300 CGGCACCAAGTAC-ATTTTTTGCAATTTTTTTTAC
66 CGACACCAAGTACAATTTTTTGCAATTTTTTTTAC
* *
5123334 TTTGGGACACTGATGGCAGGCAGAAATGTCAATTAAAAAAATATTTTGGGTGCTGGCCAGTAGAT
1 TTTGGGACACTGATGGCAGGCACAAATGTCAATTAAAAAAA-A--TTGGGTGCTGGCCAGAAGAT
***
5123399 GGTTGACACCAAGTACAATTTTTT
63 GACCGACACCAAGTACAATTTTTT
5123423 AGGTTCCAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
99 37 0.49
100 1 0.01
102 30 0.40
103 7 0.09
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (100 bp):
TTTGGGACACTGATGGCAGGCACAAATGTCAATTAAAAAAAATTGGGTGCTGGCCAGAAGATGAC
CGACACCAAGTACAATTTTTTGCAATTTTTTTTAC
Found at i:5123703 original size:12 final size:12
Alignment explanation
Indices: 5123688--5123713 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5123678 TCCATTTGAG
5123688 TTTTTGTTTGCT
1 TTTTTGTTTGCT
5123700 TTTTTGTTTGCT
1 TTTTTGTTTGCT
5123712 TT
1 TT
5123714 ATTAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTTTGTTTGCT
Found at i:5126650 original size:44 final size:44
Alignment explanation
Indices: 5126600--5126751 Score: 241
Period size: 44 Copynumber: 3.5 Consensus size: 44
5126590 TTCTTATTCC
* *
5126600 TAATTTAAAACACATTAAATTATAATACAATTTACATGCATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
* * *
5126644 TAATTTAGAGCACATTAAATTACAATACAATATACATACATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
* *
5126688 TATTTTAAAACACATTAAATTATAATACAACATACATACATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
5126732 TAATTTAAAACACATTAAAT
1 TAATTTAAAACACATTAAAT
5126752 GAAACAAATT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 97 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.36
Consensus pattern (44 bp):
TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
Found at i:5126746 original size:22 final size:22
Alignment explanation
Indices: 5126677--5126746 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
5126667 AATACAATAT
*
5126677 ACATACATATTTATTTTAAAAC
1 ACATACATATTTAATTTAAAAC
** * *
5126699 ACATTA-A-ATTATAATACAACAT
1 ACA-TACATATT-TAATTTAAAAC
5126721 ACATACATATTTAATTTAAAAC
1 ACATACATATTTAATTTAAAAC
5126743 ACAT
1 ACAT
5126747 TAAATGAAAC
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
21 5 0.14
22 25 0.71
23 5 0.14
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
ACATACATATTTAATTTAAAAC
Found at i:5127030 original size:6 final size:6
Alignment explanation
Indices: 5127015--5127065 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
5127005 AAGATAATTT
* * * *
5127015 AAAT-G AAATGG AAATGA AAATGA AAATGG AAAT-G AAGTGG AAATAG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
5127061 AAATG
1 AAATG
5127066 AAAAAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
5 8 0.21
6 30 0.79
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:5127034 original size:50 final size:49
Alignment explanation
Indices: 5126784--5127028 Score: 369
Period size: 50 Copynumber: 5.1 Consensus size: 49
5126774 AAATTAATAT
* * *
5126784 GAAAAAAAACGTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGA
1 GAAAAAAAA-TTAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGA
5126834 GAAAAAAAATTAAATTTAAATGGAAAAAAA-ATAATTTAAATGAAATGA
1 GAAAAAAAATTAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGA
*
5126882 G-AAAAAAATTAAATTTAAAAGGAAAAAAAGATAATTTAAATGAAATGA
1 GAAAAAAAATTAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGA
*
5126930 GAAACAAAAATTAAATTTAAATGGAAAGAAAGATAATTTAAATGAAATGA
1 GAAA-AAAAATTAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGA
5126980 G--AAAAAA--AAATTTAAATGGAAAAAAAAGATAATTTAAATGAAATG-
1 GAAAAAAAATTAAATTTAAATGG-AAAAAAAGATAATTTAAATGAAATGA
5127025 GAAA
1 GAAA
5127029 TGAAAATGAA
Statistics
Matches: 182, Mismatches: 7, Indels: 15
0.89 0.03 0.07
Matches are distributed among these distances:
45 13 0.07
46 24 0.13
47 33 0.18
48 39 0.21
49 20 0.11
50 53 0.29
ACGTcount: A:0.63, C:0.01, G:0.13, T:0.22
Consensus pattern (49 bp):
GAAAAAAAATTAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGA
Found at i:5127048 original size:96 final size:95
Alignment explanation
Indices: 5126782--5127028 Score: 376
Period size: 96 Copynumber: 2.6 Consensus size: 95
5126772 AAAAATTAAT
* *
5126782 ATGA-AAAAAAACGTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAAATTA
1 ATGAGAAAAAAA--TAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAATTA
5126846 AATTTAAATGGAAAAAAAATAATTTAAATGAA
64 AATTTAAATGGAAAAAAAATAATTTAAATGAA
*
5126878 ATGAGAAAAAAATTAAATTTAAAAGGAAAAAAAGATAATTTAAATGAAATGAGAAACAAAAATTA
1 ATGAGAAAAAAA-TAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGAGAAA-AAAAATTA
*
5126943 AATTTAAATGGAAAGAAAGATAATTTAAATGAA
64 AATTTAAATGGAAA-AAAAATAATTTAAATGAA
5126976 ATGAG-AAAAAA-AAATTTAAATGGAAAAAAAAGATAATTTAAATGAAATG-GAAA
1 ATGAGAAAAAAATAAATTTAAATGG-AAAAAAAGATAATTTAAATGAAATGAGAAA
5127029 TGAAAATGAA
Statistics
Matches: 141, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
95 15 0.11
96 69 0.49
97 35 0.25
98 22 0.16
ACGTcount: A:0.63, C:0.01, G:0.13, T:0.23
Consensus pattern (95 bp):
ATGAGAAAAAAATAAATTTAAATGGAAAAAAAGATAATTTAAATGAAATGAGAAAAAAAATTAAA
TTTAAATGGAAAAAAAATAATTTAAATGAA
Found at i:5127246 original size:25 final size:25
Alignment explanation
Indices: 5127212--5127277 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
5127202 TGAAATGAGA
5127212 AAAATTTTGAATTTAAATGAAATTT
1 AAAATTTTGAATTTAAATGAAATTT
* ** *
5127237 AAAATTTTGAAATGGAATGATATTT
1 AAAATTTTGAATTTAAATGAAATTT
*
5127262 -AAA-TTTCAATTTAAAT
1 AAAATTTTGAATTTAAAT
5127278 AAGATATGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 9 0.27
24 3 0.09
25 21 0.64
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (25 bp):
AAAATTTTGAATTTAAATGAAATTT
Found at i:5127367 original size:22 final size:20
Alignment explanation
Indices: 5127333--5127391 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
5127323 AATTAATATG
5127333 AAAAAAATATGAAATGAATTGAA
1 AAAAAAAT-TGAAATGAA-T-AA
*
5127356 AAAAAAATTGAATTGAATAA
1 AAAAAAATTGAAATGAATAA
* *
5127376 AGATAAATTGAAATGA
1 AAAAAAATTGAAATGA
5127392 GACTACTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 15 0.47
21 1 0.03
22 8 0.25
23 8 0.25
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.24
Consensus pattern (20 bp):
AAAAAAATTGAAATGAATAA
Done.