Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 32
Found at i:4118365 original size:44 final size:43
Alignment explanation
Indices: 4118311--4118405 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 43
4118301 TGCACTGAGT
* *
4118311 ACCATATAAATGTCCCGAAAGACCACGTAGAAATGTCCCC-AAGG
1 ACCACATAAATGTCCCCAAAGACCAC--AGAAATGTCCCCGAAGG
* *
4118355 ACCACATAAATGTCCCCAAGGACCACATAAATGTCCCCGAAGG
1 ACCACATAAATGTCCCCAAAGACCACAGAAATGTCCCCGAAGG
4118398 ACCACATA
1 ACCACATA
4118406 GAATTGTCTC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 11 0.24
43 12 0.26
44 23 0.50
ACGTcount: A:0.39, C:0.31, G:0.16, T:0.15
Consensus pattern (43 bp):
ACCACATAAATGTCCCCAAAGACCACAGAAATGTCCCCGAAGG
Found at i:4118401 original size:66 final size:65
Alignment explanation
Indices: 4118311--4118470 Score: 185
Period size: 66 Copynumber: 2.4 Consensus size: 65
4118301 TGCACTGAGT
* * * *
4118311 ACCATATAAATGTCCCGAAAGACCACGTAGAAATGTCCCCAAGGACCACATAAATGTCCCCAAGG
1 ACCAAATAAATGTCCCGAAGGACCACATAGAAATGTCCCCAAGGACCACATAAATGTCCCAAAGG
* * * * * * *
4118376 ACCACATAAATGTCCCCGAAGGACCACATAGAATTGTCTCTAAGGACCACATATATGTTCCAAAT
1 ACCAAATAAATGT-CCCGAAGGACCACATAGAAATGTCCCCAAGGACCACATAAATGTCCCAAAG
4118441 G
65 G
* * *
4118442 ACCAAATATATGTCCCAAAGGACCGCATA
1 ACCAAATAAATGTCCCGAAGGACCACATA
4118471 TATGTTCCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 26 0.32
66 54 0.68
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.19
Consensus pattern (65 bp):
ACCAAATAAATGTCCCGAAGGACCACATAGAAATGTCCCCAAGGACCACATAAATGTCCCAAAGG
Found at i:4118507 original size:21 final size:21
Alignment explanation
Indices: 4118311--4118499 Score: 164
Period size: 21 Copynumber: 8.8 Consensus size: 21
4118301 TGCACTGAGT
*
4118311 ACCATATAAATGTCCCGAAA-G
1 ACCACATAAATGTCCC-AAAGG
* *
4118332 ACCACGTAGAAATGTCCCCAAGG
1 ACCAC--ATAAATGTCCCAAAGG
*
4118355 ACCACATAAATGTCCCCAAGG
1 ACCACATAAATGTCCCAAAGG
*
4118376 ACCACATAAATGTCCCCGAAGG
1 ACCACATAAATGT-CCCAAAGG
* *
4118398 ACCACATAGAATTGTCTCTAAGG
1 ACCACATA-AA-TGTCCCAAAGG
* * *
4118421 ACCACATATATGTTCCAAATG
1 ACCACATAAATGTCCCAAAGG
* *
4118442 ACCAAATATATGTCCCAAAGG
1 ACCACATAAATGTCCCAAAGG
* * *
4118463 ACCGCATATATGTTCCAAAGG
1 ACCACATAAATGTCCCAAAGG
* *
4118484 ACCATATATATGTCCC
1 ACCACATAAATGTCCC
4118500 GAATGACCGC
Statistics
Matches: 141, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
21 88 0.62
22 18 0.13
23 32 0.23
24 3 0.02
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (21 bp):
ACCACATAAATGTCCCAAAGG
Found at i:4119226 original size:23 final size:23
Alignment explanation
Indices: 4119196--4119251 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
4119186 ACAAGTACAA
*
4119196 TACCGATACCTCTATGGTTATAG
1 TACCGATACCTCTATGCTTATAG
4119219 TACCGATACCTCTATGCTTATAG
1 TACCGATACCTCTATGCTTATAG
4119242 TACCGATACC
1 TACCGATACC
4119252 ATCATACGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (23 bp):
TACCGATACCTCTATGCTTATAG
Found at i:4121773 original size:13 final size:14
Alignment explanation
Indices: 4121746--4121774 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4121736 CTATCAATAT
4121746 TCTTATAATTTATA
1 TCTTATAATTTATA
4121760 TCTTATAA-TTATA
1 TCTTATAATTTATA
4121773 TC
1 TC
4121775 CTATTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTATAATTTATA
Found at i:4122134 original size:23 final size:23
Alignment explanation
Indices: 4122108--4122170 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
4122098 CGTATAAATA
*
4122108 CACCGAAGTGCCATATAGAATTG
1 CACCGAAGTGCCATATAGAACTG
***
4122131 CACCGAAGTGCCGCGTAGAACTG
1 CACCGAAGTGCCATATAGAACTG
**
4122154 GTCCGAAGTGCCATATA
1 CACCGAAGTGCCATATA
4122171 AAATGTCCCT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CACCGAAGTGCCATATAGAACTG
Found at i:4127265 original size:23 final size:23
Alignment explanation
Indices: 4127245--4127299 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
4127235 TAAATGCATT
*
4127245 GAAGTGTCACGTAGAATTGCACC
1 GAAGTGCCACGTAGAATTGCACC
*
4127268 GAAGTGCCGCGTAGAATTGCACC
1 GAAGTGCCACGTAGAATTGCACC
4127291 GAAGTGCCA
1 GAAGTGCCA
4127300 TATAAAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (23 bp):
GAAGTGCCACGTAGAATTGCACC
Found at i:4136089 original size:22 final size:22
Alignment explanation
Indices: 4136040--4136089 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4136030 AGGTTTTAAG
* * * *
4136040 GTTTAAAGGTTATGTAGTTATG
1 GTTTAGAGGATATGTAGTAATA
4136062 GTTTAGAGGATATGTAGTAATA
1 GTTTAGAGGATATGTAGTAATA
4136084 GTTTAG
1 GTTTAG
4136090 GGTTTAGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (22 bp):
GTTTAGAGGATATGTAGTAATA
Found at i:4139842 original size:41 final size:41
Alignment explanation
Indices: 4139777--4139874 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 41
4139767 CAGCTAATAT
*
4139777 ATTCATTCTTGAATGCCCGACTTTGGTTGATTTAATATCTTC
1 ATTC-TTCTTGAATGGCCGACTTTGGTTGATTTAATATCTTC
* *
4139819 ATTCTTCTTGAATGGCTGGCTTTGGTTGATTTAATATCTTC
1 ATTCTTCTTGAATGGCCGACTTTGGTTGATTTAATATCTTC
4139860 ATTCTTCTTGAATGG
1 ATTCTTCTTGAATGG
4139875 TAACTGTATG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 49 0.92
42 4 0.08
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.47
Consensus pattern (41 bp):
ATTCTTCTTGAATGGCCGACTTTGGTTGATTTAATATCTTC
Found at i:4143548 original size:14 final size:14
Alignment explanation
Indices: 4143526--4143565 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4143516 CATTATCTTG
*
4143526 TTCGTTTATATTCG
1 TTCGTTTATATTCA
4143540 TGT-GTTTATATTCA
1 T-TCGTTTATATTCA
4143554 TTCGTTTATATT
1 TTCGTTTATATT
4143566 TAGTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60
Consensus pattern (14 bp):
TTCGTTTATATTCA
Found at i:4148266 original size:20 final size:20
Alignment explanation
Indices: 4148250--4148288 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4148240 TAATTTTAGT
*
4148250 TTTATGATATTTTTTTTATC
1 TTTATGATATATTTTTTATC
*
4148270 TTTATTATATATTTTTTAT
1 TTTATGATATATTTTTTAT
4148289 GTCATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTATGATATATTTTTTATC
Found at i:4151317 original size:30 final size:30
Alignment explanation
Indices: 4151281--4151382 Score: 168
Period size: 30 Copynumber: 3.4 Consensus size: 30
4151271 TGTTTGGTCG
*
4151281 AATGAAGGTCGCCGGGTGGTCTGGGAGACC
1 AATGAAGGTCGCCGGGTGGTCTGGGCGACC
*
4151311 AATGAAGGTCGTCGGGTGGTCTGGGCGACC
1 AATGAAGGTCGCCGGGTGGTCTGGGCGACC
*
4151341 AATGAAGGTCGCCGGGTGATCTGGGCGACC
1 AATGAAGGTCGCCGGGTGGTCTGGGCGACC
*
4151371 AATGAATGTCGC
1 AATGAAGGTCGC
4151383 GTGATCCATG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.19
Consensus pattern (30 bp):
AATGAAGGTCGCCGGGTGGTCTGGGCGACC
Found at i:4151589 original size:50 final size:50
Alignment explanation
Indices: 4151526--4151627 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
4151516 TTTATCCTAT
4151526 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
4151576 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
4151626 TT
1 TT
4151628 CAATAAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:4152653 original size:3 final size:3
Alignment explanation
Indices: 4152641--4152673 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4152631 TAATGCAACG
*
4152641 CTT C-T CTT CTT CTT CTT CTT CTT CTT CAT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
4152674 AGCAAGGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:4157552 original size:30 final size:30
Alignment explanation
Indices: 4157469--4157587 Score: 98
Period size: 31 Copynumber: 3.9 Consensus size: 30
4157459 TAACCTAAGG
4157469 GAACATCTTAGGGCCTG-AGAGCCTACCCAA
1 GAACATCTTAGGGCC-GCAGAGCCTACCCAA
* * ** * *
4157499 GATAGAT-TTCGGGGCCGTGGGGCCTACCTAA
1 GA-ACATCTT-AGGGCCGCAGAGCCTACCCAA
* *
4157530 GAACATCTTAGGGCCGCAGGGCCTACCCGA
1 GAACATCTTAGGGCCGCAGAGCCTACCCAA
* *
4157560 GAATGATCTCAGGGCCGCAGAGCCTACC
1 GAA-CATCTTAGGGCCGCAGAGCCTACC
4157588 TAAGTGTCAC
Statistics
Matches: 70, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
30 27 0.39
31 43 0.61
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.17
Consensus pattern (30 bp):
GAACATCTTAGGGCCGCAGAGCCTACCCAA
Found at i:4157575 original size:61 final size:61
Alignment explanation
Indices: 4157469--4157591 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 61
4157459 TAACCTAAGG
* * ** *
4157469 GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAA
1 GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAA
* *
4157530 GAACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAA
1 GAACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAA
4157591 G
1 G
4157592 TGTCACATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 2 0.04
61 51 0.96
ACGTcount: A:0.25, C:0.28, G:0.29, T:0.17
Consensus pattern (61 bp):
GAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAA
Found at i:4159125 original size:18 final size:18
Alignment explanation
Indices: 4159102--4159136 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4159092 TTCCATCCGG
*
4159102 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
4159120 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4159137 GTCATTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:4163231 original size:32 final size:31
Alignment explanation
Indices: 4163195--4163270 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
4163185 CGGGGCCGTG
*
4163195 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
4163227 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
4163258 GAGCCTACCTAAG
1 GGGCCTACCTAAG
4163271 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:4163254 original size:63 final size:63
Alignment explanation
Indices: 4163148--4163270 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
4163138 ACCTAAGGGA
* * ** *
4163148 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
4163211 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
4163271 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:4164803 original size:18 final size:18
Alignment explanation
Indices: 4164780--4164814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4164770 TTCCATCCGG
*
4164780 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
4164798 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4164815 GTCATTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:4169671 original size:184 final size:184
Alignment explanation
Indices: 4169451--4169815 Score: 730
Period size: 184 Copynumber: 2.0 Consensus size: 184
4169441 ATTGCGAAAT
4169451 ATATACTATTGACCTCCTAATCAGTGAATATTGACTTACATTTAAAATCGGTCGCAATCAATCAA
1 ATATACTATTGACCTCCTAATCAGTGAATATTGACTTACATTTAAAATCGGTCGCAATCAATCAA
4169516 TTGATTAAAGACCTACTTACACTAGGTGGGTTAATTAAAGGCTTCTCCTAACTTAAAGTGTCAAA
66 TTGATTAAAGACCTACTTACACTAGGTGGGTTAATTAAAGGCTTCTCCTAACTTAAAGTGTCAAA
4169581 TTATGAAGTTTAAAGAACCTAGAAGACTAAACCTGAAAAATGGAGTCTCTAGAA
131 TTATGAAGTTTAAAGAACCTAGAAGACTAAACCTGAAAAATGGAGTCTCTAGAA
4169635 ATATACTATTGACCTCCTAATCAGTGAATATTGACTTACATTTAAAATCGGTCGCAATCAATCAA
1 ATATACTATTGACCTCCTAATCAGTGAATATTGACTTACATTTAAAATCGGTCGCAATCAATCAA
4169700 TTGATTAAAGACCTACTTACACTAGGTGGGTTAATTAAAGGCTTCTCCTAACTTAAAGTGTCAAA
66 TTGATTAAAGACCTACTTACACTAGGTGGGTTAATTAAAGGCTTCTCCTAACTTAAAGTGTCAAA
4169765 TTATGAAGTTTAAAGAACCTAGAAGACTAAACCTGAAAAATGGAGTCTCTA
131 TTATGAAGTTTAAAGAACCTAGAAGACTAAACCTGAAAAATGGAGTCTCTA
4169816 ATATTAATCC
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 181 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (184 bp):
ATATACTATTGACCTCCTAATCAGTGAATATTGACTTACATTTAAAATCGGTCGCAATCAATCAA
TTGATTAAAGACCTACTTACACTAGGTGGGTTAATTAAAGGCTTCTCCTAACTTAAAGTGTCAAA
TTATGAAGTTTAAAGAACCTAGAAGACTAAACCTGAAAAATGGAGTCTCTAGAA
Found at i:4170657 original size:20 final size:22
Alignment explanation
Indices: 4170627--4170668 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4170617 AAGTTGATAT
4170627 AGTGAATTTTC-GGGCATGAAC
1 AGTGAATTTTCTGGGCATGAAC
*
4170648 AGTG-ATTTTCTGGGCTTGAAC
1 AGTGAATTTTCTGGGCATGAAC
4170669 GAAAATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (22 bp):
AGTGAATTTTCTGGGCATGAAC
Found at i:4171220 original size:22 final size:23
Alignment explanation
Indices: 4171195--4171248 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
4171185 TGATATGCCA
*
4171195 TATATGAAAA-TAAAATATGAAT
1 TATATGAAAAGGAAAATATGAAT
** *
4171217 TATA-GAAAAGGATTATATGAGT
1 TATATGAAAAGGAAAATATGAAT
4171239 TATATGAAAA
1 TATATGAAAA
4171249 AGATGATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 16 0.62
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (23 bp):
TATATGAAAAGGAAAATATGAAT
Found at i:4171300 original size:21 final size:21
Alignment explanation
Indices: 4171262--4171302 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4171252 TGATTCAAAG
*
4171262 CATATGTGAAGTATATATGAA
1 CATATGTGAAGTAGATATGAA
4171283 CATATGTGAA-TAAGATATGA
1 CATATGTGAAGT-AGATATGA
4171303 TATACATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (21 bp):
CATATGTGAAGTAGATATGAA
Found at i:4171579 original size:21 final size:21
Alignment explanation
Indices: 4171555--4171600 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4171545 ATAGGTCATT
*
4171555 GGGACAATATAGTGGTCCTTC
1 GGGACAATACAGTGGTCCTTC
*
4171576 GGGATAATACAGTGGTCCTTC
1 GGGACAATACAGTGGTCCTTC
4171597 GGGA
1 GGGA
4171601 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGACAATACAGTGGTCCTTC
Found at i:4172364 original size:22 final size:21
Alignment explanation
Indices: 4172322--4172365 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4172312 TACGGAAGTA
*
4172322 CTGTAGCAGGGTATCGATTCC
1 CTGTAGCAGGGAATCGATTCC
*
4172343 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCA-GGGAATCGATTCC
4172365 C
1 C
4172366 CTTTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
CTGTAGCAGGGAATCGATTCC
Found at i:4173726 original size:28 final size:28
Alignment explanation
Indices: 4173686--4173769 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
4173676 CATGAGTCAG
*
4173686 ATAATTTATTTCATGATTCTCTAGTTGC
1 ATAATTTCTTTCATGATTCTCTAGTTGC
*
4173714 ATAATTTCTTTCATGGTTCTCTAGTTGC
1 ATAATTTCTTTCATGATTCTCTAGTTGC
4173742 ATAATTTCTTTCATGATTCTCTAGTTGC
1 ATAATTTCTTTCATGATTCTCTAGTTGC
4173770 TTTGAAGTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (28 bp):
ATAATTTCTTTCATGATTCTCTAGTTGC
Found at i:4177067 original size:19 final size:19
Alignment explanation
Indices: 4177043--4177112 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
4177033 AGAATGTCCA
4177043 GGGGGTA-CAGATTCCCCTG
1 GGGGGTATC-GATTCCCCTG
4177062 GGGGGTATCGATTCCCC--
1 GGGGGTATCGATTCCCCTG
* *
4177079 --GGGAATAGATTCCCCTG
1 GGGGGTATCGATTCCCCTG
4177096 GGGGGTATCGATTCCCC
1 GGGGGTATCGATTCCCC
4177113 CTAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 13 0.31
19 28 0.67
20 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.34, T:0.23
Consensus pattern (19 bp):
GGGGGTATCGATTCCCCTG
Found at i:4178105 original size:31 final size:31
Alignment explanation
Indices: 4178067--4178408 Score: 569
Period size: 31 Copynumber: 11.0 Consensus size: 31
4178057 AGGGTCGAGG
4178067 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4178098 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4178129 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4178160 TTTTACCTATGTTCTTCGGGGCATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4178191 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
4178222 GTTTACCTATGTTCTTCAGGATATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4178253 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4178284 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4178315 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4178346 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
** * *
4178377 AATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
4178408 G
1 G
4178409 GTCCTTTGGG
Statistics
Matches: 293, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 292 1.00
32 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4181446 original size:19 final size:19
Alignment explanation
Indices: 4181422--4181490 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
4181412 GAATGTCCAA
4181422 GGGGTACAGATTCCCCTGG
1 GGGGTACAGATTCCCCTGG
**
4181441 GGGGTATTGATTCCCC---
1 GGGGTACAGATTCCCCTGG
*
4181457 -GGGAACAGATTCCCCTGG
1 GGGGTACAGATTCCCCTGG
4181475 GGGGTATC-GATTCCCC
1 GGGGTA-CAGATTCCCC
4181491 CTAAATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
15 12 0.31
19 26 0.67
20 1 0.03
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (19 bp):
GGGGTACAGATTCCCCTGG
Found at i:4182515 original size:61 final size:62
Alignment explanation
Indices: 4182445--4182586 Score: 250
Period size: 61 Copynumber: 2.3 Consensus size: 62
4182435 AGGGTCGAGG
4182445 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
*
4182506 GTTTACCTATGTTCTTCGGGACATATGGATTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
* *
4182568 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
4182587 AATTTATGGA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
61 47 0.61
62 30 0.39
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4182599 original size:31 final size:31
Alignment explanation
Indices: 4182445--4182586 Score: 250
Period size: 31 Copynumber: 4.6 Consensus size: 31
4182435 AGGGTCGAGG
4182445 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4182476 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
4182506 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
4182537 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
4182568 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
4182587 AATTTATGGA
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
30 30 0.28
31 76 0.72
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:4183374 original size:40 final size:39
Alignment explanation
Indices: 4183275--4183400 Score: 189
Period size: 39 Copynumber: 3.2 Consensus size: 39
4183265 TATGCATCGT
* * *
4183275 AGTGCTTACACATAATGTTGTGCCCACCATATTCACCGA
1 AGTGCTTACACATAAGGTTGTGCCCACCATATGCACTGA
*
4183314 AGTGCTTACACATAAGGTTGTGCCCACCATATGAACTGA
1 AGTGCTTACACATAAGGTTGTGCCCACCATATGCACTGA
* *
4183353 AGTGCATTACACATAAGGTTGTGCCCATCATACGCACTGA
1 AGTGC-TTACACATAAGGTTGTGCCCACCATATGCACTGA
4183393 AGTGCTTA
1 AGTGCTTA
4183401 AACGATATGC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 43 0.54
40 36 0.46
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (39 bp):
AGTGCTTACACATAAGGTTGTGCCCACCATATGCACTGA
Found at i:4188813 original size:17 final size:17
Alignment explanation
Indices: 4188793--4188843 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
4188783 GGAAGTCAAC
4188793 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
4188810 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4188827 GGT---CGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4188841 GGT
1 GGT
4188844 TGGTCGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
14 13 0.41
17 19 0.59
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:4188837 original size:14 final size:14
Alignment explanation
Indices: 4188799--4188853 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 14
4188789 CAACGGTCAA
4188799 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
*
4188813 CAACAGTCGGGTCGGGT
1 ---CGGTCGGGTCGGGT
4188830 CGGTCGGGTCGGGT
1 CGGTCGGGTCGGGT
*
4188844 TGGTCGGGTC
1 CGGTCGGGTC
4188854 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 22 0.63
17 13 0.37
ACGTcount: A:0.05, C:0.22, G:0.51, T:0.22
Consensus pattern (14 bp):
CGGTCGGGTCGGGT
Found at i:4188880 original size:10 final size:9
Alignment explanation
Indices: 4188850--4188889 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
4188840 GGGTTGGTCG
*
4188850 GGTCAGACC
1 GGTCAGAAC
4188859 GGTCAGAAC
1 GGTCAGAAC
*
4188868 GGTTCAGACC
1 GG-TCAGAAC
4188878 GGTCAGAAC
1 GGTCAGAAC
4188887 GGT
1 GGT
4188890 TCGAACCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (9 bp):
GGTCAGAAC
Found at i:4188897 original size:19 final size:19
Alignment explanation
Indices: 4188852--4188891 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
4188842 GTTGGTCGGG
4188852 TCAGACCGGTCAGAACGGT
1 TCAGACCGGTCAGAACGGT
4188871 TCAGACCGGTCAGAACGGT
1 TCAGACCGGTCAGAACGGT
4188890 TC
1 TC
4188892 GAACCGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAGAACGGT
Found at i:4197113 original size:6 final size:6
Alignment explanation
Indices: 4197099--4197133 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4197089 TATAAAAGAA
* *
4197099 AATAAC AATAGC AATAAC AATAAC AATAAA AATAA
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAA
4197134 ATATAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.11, G:0.03, T:0.17
Consensus pattern (6 bp):
AATAAC
Found at i:4197139 original size:18 final size:17
Alignment explanation
Indices: 4197087--4197139 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
4197077 AAAGGTAAAT
*
4197087 AATATAAAAGAAAATAAC
1 AATA-AAAATAAAATAAC
**
4197105 AATAGCAATAACAATAAC
1 AATAAAAATAA-AATAAC
4197123 AATAAAAATAAATATAA
1 AATAAAAATAAA-ATAA
4197140 AATGTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.70, C:0.08, G:0.04, T:0.19
Consensus pattern (17 bp):
AATAAAAATAAAATAAC
Found at i:4197817 original size:28 final size:27
Alignment explanation
Indices: 4197769--4197821 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
4197759 TTTTAGTGTG
*
4197769 TAAATGTCTTACTTAAAATATATTTTT
1 TAAATATCTTACTTAAAATATATTTTT
*
4197796 TAAATATCTTAACTTCAAATATATTT
1 TAAATATCTT-ACTTAAAATATATTT
4197822 AAATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
TAAATATCTTACTTAAAATATATTTTT
Found at i:4197859 original size:31 final size:32
Alignment explanation
Indices: 4197824--4197891 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
4197814 ATATATTTAA
*
4197824 ATATTTTATTCTTATATTTAA-TTTA-AAATAT
1 ATATTTTATTATTATATTTAACTTTATAAA-AT
*
4197855 ATATTTTATTATTATCTTTAACTTTATAAAAT
1 ATATTTTATTATTATATTTAACTTTATAAAAT
4197887 ATATT
1 ATATT
4197892 AAAATATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 19 0.58
32 11 0.33
33 3 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (32 bp):
ATATTTTATTATTATATTTAACTTTATAAAAT
Found at i:4198086 original size:15 final size:16
Alignment explanation
Indices: 4198058--4198106 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
4198048 TTAATGGAAT
4198058 AGTTAAATATATTTTA
1 AGTTAAATATATTTTA
4198074 AGTTAAA-ATATTTT-
1 AGTTAAATATATTTTA
*
4198088 A-TAAAATATATTTTTA
1 AGTTAAATATA-TTTTA
4198104 AGT
1 AGT
4198107 GATGATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 11 0.39
16 8 0.29
17 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (16 bp):
AGTTAAATATATTTTA
Found at i:4198121 original size:29 final size:28
Alignment explanation
Indices: 4198062--4198194 Score: 106
Period size: 30 Copynumber: 4.5 Consensus size: 28
4198052 TGGAATAGTT
***
4198062 AAATATA-TTTTAAGTTAAAATATTTTATA
1 AAATATATTTTTAAG-TAAAATA-AAAATA
** *
4198091 AAATATATTTTTAAGTGATGATAAAACTA
1 AAATATATTTTTAAGT-AAAATAAAAATA
*
4198120 AAATATAAATTTTTACACTAAAATAAAAATA
1 AAATAT--ATTTTTA-AGTAAAATAAAAATA
*
4198151 AAATATATTTATTAAGTTAAAACAAAAATA
1 AAATATATTT-TTAAG-TAAAATAAAAATA
*
4198181 AAAGATATTTTTAA
1 AAATATATTTTTAA
4198195 AATTTAAGAT
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
29 25 0.30
30 35 0.42
31 22 0.26
32 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (28 bp):
AAATATATTTTTAAGTAAAATAAAAATA
Found at i:4198783 original size:2 final size:2
Alignment explanation
Indices: 4198770--4198801 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4198760 TATTTTAAAA
4198770 AT AT AT -T A- 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
4198802 TAAAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4198809 original size:10 final size:12
Alignment explanation
Indices: 4198770--4198815 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
4198760 TATTTTAAAA
4198770 ATATATTAATAT
1 ATATATTAATAT
4198782 ATATATATATATAT
1 ATATAT-TA-ATAT
*
4198796 ATATATTAAAAT
1 ATATATTAATAT
*
4198808 ATTTATTA
1 ATATATTA
4198816 TTTTCATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 16 0.53
13 4 0.13
14 10 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATTAATAT
Found at i:4198824 original size:21 final size:21
Alignment explanation
Indices: 4198800--4198848 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4198790 ATATATATAT
** *
4198800 ATTAAAATATTTATTATTTTC
1 ATTAAAATATCCATTACTTTC
4198821 ATTAAAATATCCATTACTTTC
1 ATTAAAATATCCATTACTTTC
*
4198842 ATAAAAA
1 ATTAAAA
4198849 ATAATTCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAAAATATCCATTACTTTC
Found at i:4199433 original size:43 final size:42
Alignment explanation
Indices: 4199368--4199892 Score: 204
Period size: 43 Copynumber: 11.9 Consensus size: 42
4199358 AATCCTAAAA
* * *
4199368 AATCTCATTTTTTTACATTTATAATTAATGACCCTAATTTTTTA
1 AATCTCA-CTTTTTACCTTTATAATTAA-GACCCTAATTTTTTC
* * * *
4199412 AATCTCATTTTTTACCTTTATAATTGAG-CTTCTAATTCTTTTT
1 AATCTCACTTTTTACCTTTATAATTAAGAC-CCTAATT-TTTTC
* * * * *
4199455 AATCTCGCTTTCTATCTTTATAAGTGAGACCCTAATTTTTTC
1 AATCTCACTTTTTACCTTTATAATTAAGACCCTAATTTTTTC
* * **
4199497 -ATCTCACTTTTTAACTTTATAATTAAGGCCCCTAAAATTTTC
1 AATCTCACTTTTTACCTTTATAATTAA-GACCCTAATTTTTTC
* *
4199539 AATC-CTACATTTTTA-CTTATATAATTTAGGCCTCTAATTTTTTC
1 AATCTC-AC-TTTTTACCTT-TATAATTAAGACC-CTAATTTTTTC
* * * *
4199583 AATCTCACATTTTATCTTTAAAATTGAAGCCCCTAATTTTTTTC
1 AATCTCACTTTTTACCTTTATAATT-AAGACCCTAA-TTTTTTC
* ** * * *
4199627 AATCT-ATTTTTTTAAATTTTTAATTTTTAA-ATCCTTTTAATAGCTTTTAATT
1 AATCTCA-CTTTTTACCTTTATAA---TTAAGA-CC--CTAAT---TTTT--TC
* * * * * * * *
4199679 ATTTTTAATATCGCTTTCTATCTTTATAAGTGAGCCCCTAATTTTTTC
1 A-ATCT--CA-C-TTTT-TACCTTTATAATTAAGACCCTAATTTTTTC
* * *
4199727 -ATCTCACTTTTTAACTTTATAATTAAGGCCCCTAAATTTTTC
1 AATCTCACTTTTTACCTTTATAATTAA-GACCCTAATTTTTTC
* * * * *
4199769 AATCTCACATTTTATCTTTAAAATCGAAGCCCCTAATTTTTT-
1 AATCTCACTTTTTACCTTTATAAT-TAAGACCCTAATTTTTTC
* * ** * *
4199811 TATCTCACTTATTATATTTATAATTTAAGTCCCTAATTTTTTA
1 AATCTCACTTTTTACCTTTATAA-TTAAGACCCTAATTTTTTC
* * *
4199854 AATCAT-ACTTTTTACTTTTCTAATTTAAGTCCCTAATTT
1 AATC-TCACTTTTTACCTTTATAA-TTAAGACCCTAATTT
4199893 AATCATTTTT
Statistics
Matches: 370, Mismatches: 73, Indels: 77
0.71 0.14 0.15
Matches are distributed among these distances:
41 34 0.09
42 74 0.20
43 145 0.39
44 70 0.19
45 1 0.00
46 6 0.02
47 3 0.01
48 4 0.01
50 8 0.02
52 2 0.01
53 6 0.02
55 4 0.01
56 2 0.01
57 3 0.01
58 8 0.02
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.50
Consensus pattern (42 bp):
AATCTCACTTTTTACCTTTATAATTAAGACCCTAATTTTTTC
Found at i:4199562 original size:128 final size:129
Alignment explanation
Indices: 4199369--4199624 Score: 299
Period size: 128 Copynumber: 2.0 Consensus size: 129
4199359 ATCCTAAAAA
* * * **
4199369 ATCTCATTTTTTTACATTTATAATTAATGACCCTAATTTTTTAAATCTCATTTTTTACCTTTATA
1 ATCTCACTTTTTAACATTTATAATTAAGGACCCTAAAATTTTAAATCTCATTTTTTACCTTTATA
* * * *
4199434 ATTGA-GCTTCTAATTCTTTTTAATCTCGC-TTTCTATCTTTATAAGTG-AGACCCTAATTTTTT
66 ATTGAGGCCTCTAATT-TTTTCAATCTCACATTT-TATCTTTAAAAGTGAAGACCCTAATTTTTT
4199496 C
129 C
* *
4199497 ATCTCACTTTTTAAC-TTTATAATTAAGGCCCCTAAAATTTTCAATCCTACA-TTTTTA-CTTAT
1 ATCTCACTTTTTAACATTTATAATTAAGGACCCTAAAATTTTAAAT-CT-CATTTTTTACCTT-T
* * *
4199559 ATAATTTAGGCCTCTAATTTTTTCAATCTCACATTTTATCTTTAAAATTGAAGCCCCTAATTTTT
63 ATAATTGAGGCCTCTAATTTTTTCAATCTCACATTTTATCTTTAAAAGTGAAGACCCTAATTTTT
4199624 T
128 T
4199625 TCAATCTATT
Statistics
Matches: 108, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
127 28 0.26
128 52 0.48
129 28 0.26
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (129 bp):
ATCTCACTTTTTAACATTTATAATTAAGGACCCTAAAATTTTAAATCTCATTTTTTACCTTTATA
ATTGAGGCCTCTAATTTTTTCAATCTCACATTTTATCTTTAAAAGTGAAGACCCTAATTTTTTC
Found at i:4199640 original size:44 final size:42
Alignment explanation
Indices: 4199368--4199631 Score: 207
Period size: 43 Copynumber: 6.1 Consensus size: 42
4199358 AATCCTAAAA
* * *
4199368 AATCTCATTTTTTTACATTTATAATT-AATGACCCTAATTTTTTA
1 AATCTCA-CTTTTTAC-TTTATAATTGAA-GCCCCTAATTTTTTC
* ** *
4199412 AATCTCATTTTTTACCTTTATAATTG-AGCTTCTAATTCTTTTT
1 AATCTCACTTTTTA-CTTTATAATTGAAGCCCCTAATT-TTTTC
* * * *
4199455 AATCTCGCTTTCTATCTTTATAAGTG-AGACCCTAATTTTTTC
1 AATCTCACTTTTTA-CTTTATAATTGAAGCCCCTAATTTTTTC
**
4199497 -ATCTCACTTTTTAACTTTATAATT-AAGGCCCCTAAAATTTTC
1 AATCTCACTTTTT-ACTTTATAATTGAA-GCCCCTAATTTTTTC
* * *
4199539 AATC-CTACATTTTTACTTATATAATTTAGGCCTCTAATTTTTTC
1 AATCTC-AC-TTTTTACTT-TATAATTGAAGCCCCTAATTTTTTC
* *
4199583 AATCTCACATTTTATCTTTAAAATTGAAGCCCCTAATTTTTTTC
1 AATCTCACTTTTTA-CTTTATAATTGAAGCCCCTAA-TTTTTTC
4199627 AATCT
1 AATCT
4199632 ATTTTTTTAA
Statistics
Matches: 178, Mismatches: 28, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
41 20 0.11
42 25 0.14
43 78 0.44
44 53 0.30
45 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (42 bp):
AATCTCACTTTTTACTTTATAATTGAAGCCCCTAATTTTTTC
Found at i:4199746 original size:230 final size:228
Alignment explanation
Indices: 4199438--4199852 Score: 629
Period size: 230 Copynumber: 1.8 Consensus size: 228
4199428 TTTATAATTG
* *
4199438 AGCTTCTAATTCTTTTTAATCTCGCTTTCTATCTTTATAAGTGAGACCCTAATTTTTTCATCTCA
1 AGCTTCTAATTATTTTTAATATCGCTTTCTATCTTTATAAGTGAGACCCTAATTTTTTCATCTCA
* **
4199503 CTTTTTAACTTTATAATTAAGGCCCCTAAAATTTTCAATC-CTACATTTT-TACTTATATAATTT
66 CTTTTTAACTTTATAATTAAGGCCCCTAAAATTTTCAATCTC-ACATTTTAT-CTT-TAAAATCG
* * *
4199566 AGGCCTCTAATTTTTTCAATCTCACATT-TTATCTTTAAAATTGAAGCCCCTAATTTTTTTCAAT
128 AAGCCCCTAATTTTTT-AATCTCAC-TTATTATATTTAAAATTGAAGCCCCTAATTTTTTTCAAT
4199630 CTATTTTTTTAAATTTTTAATTTTTAAATCCTTTTAAT
191 CTATTTTTTTAAATTTTTAATTTTTAAATCCTTTTAAT
* *
4199668 AGCTTTTAATTATTTTTAATATCGCTTTCTATCTTTATAAGTGAGCCCCTAATTTTTTCATCTCA
1 AGCTTCTAATTATTTTTAATATCGCTTTCTATCTTTATAAGTGAGACCCTAATTTTTTCATCTCA
*
4199733 CTTTTTAACTTTATAATTAAGGCCCCTAAATTTTTCAATCTCACATTTTATCTTTAAAATCGAAG
66 CTTTTTAACTTTATAATTAAGGCCCCTAAAATTTTCAATCTCACATTTTATCTTTAAAATCGAAG
* * * *
4199798 CCCCTAATTTTTTTATCTCACTTATTATATTTATAATTTAAGTCCCTAATTTTTT
131 CCCCTAATTTTTTAATCTCACTTATTATATTTAAAATTGAAGCCCCTAATTTTTT
4199853 AAATCATACT
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
227 2 0.01
228 34 0.20
229 19 0.11
230 110 0.66
231 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (228 bp):
AGCTTCTAATTATTTTTAATATCGCTTTCTATCTTTATAAGTGAGACCCTAATTTTTTCATCTCA
CTTTTTAACTTTATAATTAAGGCCCCTAAAATTTTCAATCTCACATTTTATCTTTAAAATCGAAG
CCCCTAATTTTTTAATCTCACTTATTATATTTAAAATTGAAGCCCCTAATTTTTTTCAATCTATT
TTTTTAAATTTTTAATTTTTAAATCCTTTTAAT
Found at i:4199867 original size:85 final size:84
Alignment explanation
Indices: 4199711--4199871 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 84
4199701 TTTATAAGTG
* *
4199711 AGCCCCTAATTTTTTCATCTCACTTTTTAACTTTATAATTAAGGCCCCTAAATTTTTCAATCTCA
1 AGCCCCTAATTTTTTCATCTCACTTATTAACTTTATAATTAAGGCCCCTAAATTTTTAAATCTCA
4199776 CATTTTATCTTTAAAATCGA
66 CATTTTA-CTTTAAAATCGA
* * *
4199796 AGCCCCTAATTTTTTTATCTCACTTATTATA-TTTATAATTTAA-GTCCCTAATTTTTTAAATCA
1 AGCCCCTAATTTTTTCATCTCACTTATTA-ACTTTATAA-TTAAGGCCCCTAAATTTTTAAATC-
*
4199859 T-ACTTTTTACTTT
63 TCACATTTTACTTT
4199872 TCTAATTTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
84 4 0.06
85 57 0.85
86 6 0.09
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.48
Consensus pattern (84 bp):
AGCCCCTAATTTTTTCATCTCACTTATTAACTTTATAATTAAGGCCCCTAAATTTTTAAATCTCA
CATTTTACTTTAAAATCGA
Found at i:4204905 original size:90 final size:91
Alignment explanation
Indices: 4204752--4204930 Score: 335
Period size: 90 Copynumber: 2.0 Consensus size: 91
4204742 CCATGCTTGC
4204752 TTAACCGTACTATCTTTATTCCCACCTCTAAGGATACAACTGAAAGTCACTTTCCAATCTTTTGC
1 TTAACCGTACTATCTTTATTCCCACCTCTAAGGATACAACTGAAAGTCACTTTCCAATCTTTTGC
4204817 TAAGA-CTTAT-TATAGTGTTGTAGGG
66 TAAGACCTTATCTAT-GTGTTGTAGGG
4204842 TTAACCGTACTATCTTTATTCCCACCTCTAAGGATACAACTGAAAGTCACTTTCCAATCTTTTGC
1 TTAACCGTACTATCTTTATTCCCACCTCTAAGGATACAACTGAAAGTCACTTTCCAATCTTTTGC
4204907 TAAGACCTTATCTATGTGTTGTAG
66 TAAGACCTTATCTATGTGTTGTAG
4204931 TAGGGTTAAG
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
90 70 0.80
91 14 0.16
92 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (91 bp):
TTAACCGTACTATCTTTATTCCCACCTCTAAGGATACAACTGAAAGTCACTTTCCAATCTTTTGC
TAAGACCTTATCTATGTGTTGTAGGG
Found at i:4207535 original size:28 final size:30
Alignment explanation
Indices: 4207472--4207545 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
4207462 GTCATACTTT
4207472 TAATAAATTATATATTTTTAAATGAAAATGAA
1 TAATAAA--ATATATTTTTAAATGAAAATGAA
* *
4207504 -AATAAAATAT-TTTTTAAAT-TAAATTAA
1 TAATAAAATATATTTTTAAATGAAAATGAA
4207531 TAATAAAATATATTT
1 TAATAAAATATATTT
4207546 AATAAGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 6 0.16
28 19 0.50
29 7 0.18
31 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TAATAAAATATATTTTTAAATGAAAATGAA
Found at i:4210157 original size:43 final size:43
Alignment explanation
Indices: 4210091--4210205 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
4210081 AGTTTTGATG
* * * * *
4210091 TTTAGCGACATTTTTAGCGAAAACGCCGCAATATGTGTTGTGA
1 TTTAGCGACGTTTTTAGCTAAAACGCCGCAATAGGCGTTGAGA
4210134 TTTAGCGACGTTTTTAGCTAAAACGCCGCAATAGGCGTTGAGA
1 TTTAGCGACGTTTTTAGCTAAAACGCCGCAATAGGCGTTGAGA
* * *
4210177 TTTAACGGCGTTTTTA-ATATAAACGCCGC
1 TTTAGCGACGTTTTTAGCTA-AAACGCCGC
4210206 TAAAAATTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 2 0.03
43 61 0.97
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
TTTAGCGACGTTTTTAGCTAAAACGCCGCAATAGGCGTTGAGA
Found at i:4224914 original size:21 final size:21
Alignment explanation
Indices: 4224888--4224927 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4224878 CAGAACCCCA
*
4224888 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
4224909 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
4224928 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:4228787 original size:22 final size:21
Alignment explanation
Indices: 4228745--4228784 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4228735 GAGTTTGTTT
*
4228745 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4228766 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4228785 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4233028 original size:20 final size:20
Alignment explanation
Indices: 4232995--4233032 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4232985 TTTGGTTCAC
* *
4232995 GGAATGTAATATTACTAGTG
1 GGAATATAAGATTACTAGTG
4233015 GGAATATAAGATTACTAG
1 GGAATATAAGATTACTAG
4233033 AGAATATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (20 bp):
GGAATATAAGATTACTAGTG
Found at i:4241538 original size:3 final size:3
Alignment explanation
Indices: 4241530--4241622 Score: 62
Period size: 3 Copynumber: 31.0 Consensus size: 3
4241520 CTGTAATATG
* * * *
4241530 TAA TAA TAA TATT TAT TAA TAA -AA AAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
4241575 TTA TAA TAT TTA TAA CAA TTA TAA TAA TTA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4241623 AACAGGCAAA
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
2 2 0.03
3 63 0.94
4 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4241981 original size:23 final size:22
Alignment explanation
Indices: 4241945--4241990 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
4241935 GTTGAACAAG
4241945 TTCTTCTCATTATGAACTTCTTC
1 TTCTTCTCATTATG-ACTTCTTC
*
4241968 TTCTTCTTCA-TATGAGTTCTTC
1 TTCTTC-TCATTATGACTTCTTC
4241990 T
1 T
4241991 CATTATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 10 0.48
24 3 0.14
ACGTcount: A:0.15, C:0.24, G:0.07, T:0.54
Consensus pattern (22 bp):
TTCTTCTCATTATGACTTCTTC
Found at i:4242096 original size:122 final size:120
Alignment explanation
Indices: 4241849--4242096 Score: 313
Period size: 122 Copynumber: 2.0 Consensus size: 120
4241839 TCTGCTCCTT
4241849 CTTCTTCAGATGAGTTCTTCTCATTACAAACACTTCTGAAAATGTTGATGCTAATCTATCTCCTT
1 CTTCTTCAGATGAGTTCTTCTCATTACAAACACTTCTGAAAATGTTGATGCTAATCTATCTCCTT
* * *
4241914 CTGTGATAGATCATACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT
66 CTGTGATAGATCATACAAAAGGTTGAACAAGCTCTTCTCATGATGAAC-TCTTCTC
* ** ** * *
4241970 CTTCTTCATATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-GTTGATGTTGATCTATCTCC
1 CTTCTTCAGATGAGTTCTTCTCATTACAAACACT-TCT-GAAAATGTTGATGCTAATCTATCTCC
* *
4242034 TTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCGATGCT-AA-TCTATCTC
64 TTCTGTGATAGA-TCATACAAAAGGTTGAACAAGCTCTTCTC-ATGATGAACTCT-TCTC
4242092 CTTCT
1 CTTCT
4242097 GTGATAGATC
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
121 32 0.29
122 41 0.37
123 34 0.31
124 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (120 bp):
CTTCTTCAGATGAGTTCTTCTCATTACAAACACTTCTGAAAATGTTGATGCTAATCTATCTCCTT
CTGTGATAGATCATACAAAAGGTTGAACAAGCTCTTCTCATGATGAACTCTTCTC
Found at i:4242100 original size:181 final size:181
Alignment explanation
Indices: 4241895--4242256 Score: 706
Period size: 181 Copynumber: 2.0 Consensus size: 181
4241885 TGAAAATGTT
4241895 GATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAGTTCTTCTCATTATGA
1 GATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAGTTCTTCTCATTATGA
*
4241960 ACTTCTTCTTCTTCTTCATATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGA
66 ACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGA
4242025 TCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTC
131 TCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTC
4242076 GATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAGTTCTTCTCATTATGA
1 GATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAGTTCTTCTCATTATGA
4242141 ACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGA
66 ACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGA
*
4242206 TCTATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTC
131 TCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTC
4242257 ATTATGAACT
Statistics
Matches: 179, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 179 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (181 bp):
GATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAGTTCTTCTCATTATGA
ACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGA
TCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTC
Found at i:4242319 original size:124 final size:124
Alignment explanation
Indices: 4242083--4242571 Score: 831
Period size: 124 Copynumber: 4.0 Consensus size: 124
4242073 CTCGATGCTA
* * *
4242083 ATCTATCTCCTTCTGTGATAGA-TCATACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
*
4242147 TCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
66 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGTTG
4242205 ATCTATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* *
4242270 TCTTCCTTCTTCAGATGAGTTCTTTTTATTATGAACTTTTTCTGGAAAAGTTGATGTTG
66 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGTTG
* *
4242329 ATCTATCTCCTTCTGTGATAGATTTATGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
*
4242394 TCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTTTCTGGAAAAGTTGATGTTG
66 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGTTG
* *
4242453 ATCTATCTCATTCTGTGATATAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
1 ATCTATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
* * *
4242518 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCTTCCGGAAATGTTGAT
66 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGAT
4242572 CCATAGAATG
Statistics
Matches: 348, Mismatches: 17, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
122 22 0.06
123 58 0.17
124 268 0.77
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (124 bp):
ATCTATCTCCTTCTGTGATAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGTTGATGTTG
Found at i:4243769 original size:18 final size:18
Alignment explanation
Indices: 4243746--4243780 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4243736 TATATGAAAC
4243746 AAATTGAATTTCAAAAAT
1 AAATTGAATTTCAAAAAT
4243764 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
4243781 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:4244175 original size:15 final size:14
Alignment explanation
Indices: 4244143--4244189 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
4244133 CTTTCACTCA
*
4244143 TTTTT-TTCATTTT
1 TTTTTCTTCATTAT
*
4244156 ATTTTTCTTTTATTAT
1 -TTTTTC-TTCATTAT
4244172 TTTTTCTTCATTAT
1 TTTTTCTTCATTAT
4244186 TTTT
1 TTTT
4244190 CATTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 16 0.57
15 6 0.21
16 6 0.21
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTTCATTAT
Found at i:4244191 original size:10 final size:10
Alignment explanation
Indices: 4244140--4244219 Score: 62
Period size: 11 Copynumber: 8.1 Consensus size: 10
4244130 TCTCTTTCAC
4244140 TCATT-TTTT
1 TCATTATTTT
4244149 TCATTTTATTTT
1 TCA--TTATTTT
*
4244161 TC-TT-TTAT
1 TCATTATTTT
*
4244169 T-ATTTTTTCT
1 TCATTATTT-T
4244179 TCATTATTTT
1 TCATTATTTT
4244189 TCATTATTTTT
1 TCATTA-TTTT
*
4244200 TCCTT-TTTT
1 TCATTATTTT
4244209 TCATTATTTT
1 TCATTATTTT
4244219 T
1 T
4244220 TTCTTCAAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
8 6 0.11
9 15 0.26
10 14 0.25
11 16 0.28
12 6 0.11
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (10 bp):
TCATTATTTT
Found at i:4244199 original size:24 final size:23
Alignment explanation
Indices: 4244163--4244226 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
4244153 TTTATTTTTC
4244163 TTTT-ATTATTTTTTCTTCATTAT
1 TTTTCATTATTTTTTCTTCATT-T
4244186 TTTTCATTATTTTTTC--C-TTT
1 TTTTCATTATTTTTTCTTCATTT
4244206 TTTTCATTATTTTTTTCTTCA
1 TTTTCATTA-TTTTTTCTTCA
4244227 AGCATAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 5 0.14
24 11 0.31
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTCATTATTTTTTCTTCATTT
Found at i:4254954 original size:28 final size:26
Alignment explanation
Indices: 4254899--4254956 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
4254889 AAACATTAAT
*
4254899 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
4254925 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
4254953 AAAA
1 AAAA
4254957 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:4255797 original size:18 final size:18
Alignment explanation
Indices: 4255771--4255827 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
4255761 AATATATTGC
4255771 AAATAAACATATAAAATT
1 AAATAAACATATAAAATT
*
4255789 AAATCAACA-ACTAAAA-T
1 AAATAAACATA-TAAAATT
*
4255806 AAATGAA-AT-TAAAATT
1 AAATAAACATATAAAATT
*
4255822 ATATAA
1 AAATAA
4255828 TAAAACTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.16
16 6 0.19
17 8 0.25
18 13 0.41
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAACATATAAAATT
Found at i:4257173 original size:3 final size:3
Alignment explanation
Indices: 4257155--4257222 Score: 66
Period size: 3 Copynumber: 23.0 Consensus size: 3
4257145 TATTATTTAT
* * * * *
4257155 TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA TTA TAA TAA TTA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4257202 TTA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
4257223 AACTGGCAAA
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4260643 original size:17 final size:17
Alignment explanation
Indices: 4260621--4260663 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
4260611 ACCCTCGTAT
4260621 GATTCATAAGTTGTTAA
1 GATTCATAAGTTGTTAA
4260638 GATTCATAAGTTGTTAA
1 GATTCATAAGTTGTTAA
4260655 GATTCATAA
1 GATTCATAA
4260664 ATCTCTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (17 bp):
GATTCATAAGTTGTTAA
Found at i:4262021 original size:16 final size:16
Alignment explanation
Indices: 4261970--4262041 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 16
4261960 TTATAAGGTA
*
4261970 TATTTTATTATATTTAA
1 TATTTTATTAT-TTTAT
* *
4261987 TATTTTGTTAGTATT-T
1 TATTTTATTA-TTTTAT
*
4262003 TATTTTATTATTGTAT
1 TATTTTATTATTTTAT
* *
4262019 TATTTAAATATTTTAT
1 TATTTTATTATTTTAT
4262035 T-TTTTAT
1 TATTTTAT
4262042 AGTTATAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
15 6 0.14
16 24 0.57
17 11 0.26
18 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
TATTTTATTATTTTAT
Found at i:4262138 original size:21 final size:21
Alignment explanation
Indices: 4262114--4262157 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4262104 AATTGTTGTA
* *
4262114 TTATTTAATTTTTTTATTATT
1 TTATTTAAATATTTTATTATT
*
4262135 TTATTTAAATATTTTATTTTT
1 TTATTTAAATATTTTATTATT
4262156 TT
1 TT
4262158 GCAGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTAAATATTTTATTATT
Found at i:4262139 original size:117 final size:119
Alignment explanation
Indices: 4261977--4262190 Score: 308
Period size: 117 Copynumber: 1.8 Consensus size: 119
4261967 GTATATTTTA
* * *
4261977 TTATATTTAATATTTTGTTAGTATTTTATTTTATTATTGTATTATTTAAATATTTTATTTTTTAT
1 TTATATTTAATATGTTGTTAGTATTTAATTTTATTATTATATTATTTAAATATTTTATTTTTT-T
*
4262042 -AGTTATAAAATGAAAAGCGGTTTGCTTCGTTATATTTAATATTTTGTTAATATT
65 CAGTTATAAAATGAAAAGCGGTCTGCTTCGTTATATTTAATATTTTGTTAATATT
* * *
4262096 TTATATTTAAT-TGTTG-TATTATTTAATTTTTTTATTATTTTATTTAAATATTTTATTTTTTTG
1 TTATATTTAATATGTTGTTAGTATTTAATTTTATTATTATATTATTTAAATATTTTATTTTTTT-
* *
4262159 CAGTTATAAAATGGAAAGTGGTCTGCTTCGTT
65 CAGTTATAAAATGAAAAGCGGTCTGCTTCGTT
4262191 TGGATGAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
116 1 0.01
117 40 0.48
118 32 0.38
119 11 0.13
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (119 bp):
TTATATTTAATATGTTGTTAGTATTTAATTTTATTATTATATTATTTAAATATTTTATTTTTTTC
AGTTATAAAATGAAAAGCGGTCTGCTTCGTTATATTTAATATTTTGTTAATATT
Found at i:4262140 original size:16 final size:16
Alignment explanation
Indices: 4262094--4262140 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
4262084 TTTGTTAATA
*
4262094 TTTTA-TATTTAATTG
1 TTTTATTATTTAATTT
*
4262109 TTGTATTATTTAATTT
1 TTTTATTATTTAATTT
*
4262125 TTTTATTATTTTATTT
1 TTTTATTATTTAATTT
4262141 AAATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (16 bp):
TTTTATTATTTAATTT
Found at i:4263195 original size:5 final size:6
Alignment explanation
Indices: 4263177--4263202 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4263167 TAATAAGAAC
4263177 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
4263203 GTCAATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:4263382 original size:14 final size:14
Alignment explanation
Indices: 4263363--4263389 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4263353 AGATATATAA
4263363 AAATAAAATAAAAT
1 AAATAAAATAAAAT
4263377 AAATAAAATAAAA
1 AAATAAAATAAAA
4263390 AAGTTAGTGG
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):
AAATAAAATAAAAT
Found at i:4263409 original size:125 final size:125
Alignment explanation
Indices: 4263267--4263504 Score: 379
Period size: 125 Copynumber: 1.9 Consensus size: 125
4263257 AAAGTTAGTG
*
4263267 GTTAGTGGTCAGTAGAGTCCGGACCATAATAATGTAGATCTTACCTC-GGATCGGGTCACCACAA
1 GTTAGTGGTCAGTAGAGTCCGAACCATAATAATGTAGATCTTACC-CAGGATCGGGTCACCACAA
* *
4263331 GGTCGAATTGAATAACGCAAACAGATATATAAAAATAAAATAAAATAAATAAAATAAAAAA
65 GGTCGAATCGAATAACGCAAACAAATATATAAAAATAAAATAAAATAAATAAAATAAAAAA
* * * *
4263392 GTTAGTGGTTAGTAGAGTTCGAACCATAATAATGTGGATCTTACCCAGGATCGTGTCACCACAAG
1 GTTAGTGGTCAGTAGAGTCCGAACCATAATAATGTAGATCTTACCCAGGATCGGGTCACCACAAG
* *
4263457 GTCGAATCGAATAACGTAAACAAATATATAAAAATAAACTAAAATAAA
66 GTCGAATCGAATAACGCAAACAAATATATAAAAATAAAATAAAATAAA
4263505 AAAGTTAGTG
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
124 1 0.01
125 102 0.99
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (125 bp):
GTTAGTGGTCAGTAGAGTCCGAACCATAATAATGTAGATCTTACCCAGGATCGGGTCACCACAAG
GTCGAATCGAATAACGCAAACAAATATATAAAAATAAAATAAAATAAATAAAATAAAAAA
Found at i:4273706 original size:2 final size:2
Alignment explanation
Indices: 4273701--4273725 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4273691 ATATATATAT
4273701 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
4273726 ATCGTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4274752 original size:43 final size:44
Alignment explanation
Indices: 4274701--4274852 Score: 118
Period size: 44 Copynumber: 3.5 Consensus size: 44
4274691 TGAAGCTTTG
4274701 AAGTTTTTTCAATCTCAATTTCTACATTCATAATTGAGGTCTCT
1 AAGTTTTTTCAATCTCAATTTCTACATTCATAATTGAGGTCTCT
*** * *
4274745 -AGTTTTTT--ATCCTTGTTTTTTTA-ACTTTATAATTGAGGTCAT-T
1 AAGTTTTTTCAAT-C-TCAATTTCTACA-TTCATAATTGAGGTC-TCT
* * * * *
4274788 AAGTTTTTTTAATCTCACTTTCTAACTTTC-TAATTGAGGGCCCT
1 AAGTTTTTTCAATCTCAATTTCT-ACATTCATAATTGAGGTCTCT
*
4274832 AAGTTTTTTCGATCTCAATTT
1 AAGTTTTTTCAATCTCAATTT
4274853 ATAATTGAGA
Statistics
Matches: 82, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 29 0.35
44 43 0.52
45 4 0.05
46 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.50
Consensus pattern (44 bp):
AAGTTTTTTCAATCTCAATTTCTACATTCATAATTGAGGTCTCT
Found at i:4274779 original size:87 final size:88
Alignment explanation
Indices: 4274676--4274840 Score: 219
Period size: 87 Copynumber: 1.9 Consensus size: 88
4274666 GTAATATCAC
* *
4274676 TTTTAATTTTATAATTGAAG-CTTTGAAGTTTTTTCAATCTCAATTTCT-ACATTCATAATTGAG
1 TTTTAACTTTATAATTGAAGTCATT-AAGTTTTTTCAATCTCAATTTCTAACATTC-TAATTGAG
* *
4274739 GTCTCT-AGTTTTTTATCCTTGTTT
64 GGCCCTAAGTTTTTTATCCTTGTTT
* * * *
4274763 TTTTAACTTTATAATTGAGGTCATTAAGTTTTTTTAATCTCACTTTCTAACTTTCTAATTGAGGG
1 TTTTAACTTTATAATTGAAGTCATTAAGTTTTTTCAATCTCAATTTCTAACATTCTAATTGAGGG
4274828 CCCTAAGTTTTTT
66 CCCTAAGTTTTTT
4274841 CGATCTCAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
87 51 0.76
88 16 0.24
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (88 bp):
TTTTAACTTTATAATTGAAGTCATTAAGTTTTTTCAATCTCAATTTCTAACATTCTAATTGAGGG
CCCTAAGTTTTTTATCCTTGTTT
Found at i:4274814 original size:44 final size:42
Alignment explanation
Indices: 4274549--4274824 Score: 158
Period size: 43 Copynumber: 6.4 Consensus size: 42
4274539 AAATATTATT
* *
4274549 TTTTACCTTTATAATTGATA-TCTTAA-TATTATTTAATCTCAC
1 TTTTAACTTTATAATTGA-AGTCTTAAGT-TTTTTTAATCTCAC
* * * *
4274591 ATTTTATCTTTATAATTGAAGTCTTTATTTTTTTTCAAT-TCATT
1 -TTTTAACTTTATAATTGAAGTCTTAAGTTTTTTT-AATCTCA-C
* * * *
4274635 TTTTACCTTTATAATTGAAGTTTCTAA--TTTTGTAATATCAC
1 TTTTAACTTTATAATTGAAGTCT-TAAGTTTTTTTAATCTCAC
* * *
4274676 TTTTAATTTTATAATTGAAG-CTTTGAAGTTTTTTCAATCTCAA
1 TTTTAACTTTATAATTGAAGTC-TT-AAGTTTTTTTAATCTCAC
* * ***
4274719 TTTCT-ACATTCATAATTGAGGTCTCT-AG-TTTTTT-ATCCTTGTTT
1 TTT-TAAC-TTTATAATTGAAGTCT-TAAGTTTTTTTAAT-C-T-CAC
*
4274763 TTTTAACTTTATAATTGAGGTCATTAAGTTTTTTTAATCTCAC
1 TTTTAACTTTATAATTGAAGTC-TTAAGTTTTTTTAATCTCAC
*
4274806 TTTCTAACTTTCTAATTGA
1 TTT-TAACTTTATAATTGA
4274825 GGGCCCTAAG
Statistics
Matches: 182, Mismatches: 28, Indels: 45
0.71 0.11 0.18
Matches are distributed among these distances:
40 1 0.01
41 26 0.14
42 15 0.08
43 87 0.48
44 42 0.23
45 9 0.05
46 2 0.01
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (42 bp):
TTTTAACTTTATAATTGAAGTCTTAAGTTTTTTTAATCTCAC
Found at i:4274868 original size:36 final size:35
Alignment explanation
Indices: 4274818--4274887 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
4274808 TCTAACTTTC
* *
4274818 TAATTGAGGGCCCTAAGTTTTTTCGATCTCAATTTA
1 TAATTGAGAGCCCT-AGTTTTTTCAATCTCAATTTA
* *
4274854 TAATTGAGATCCCTATTTTTTTCAATCTCAATTT
1 TAATTGAGAGCCCTAGTTTTTTCAATCTCAATTT
4274888 CCACCTTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 18 0.60
36 12 0.40
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (35 bp):
TAATTGAGAGCCCTAGTTTTTTCAATCTCAATTTA
Found at i:4278400 original size:2 final size:2
Alignment explanation
Indices: 4278393--4278475 Score: 124
Period size: 2 Copynumber: 44.5 Consensus size: 2
4278383 GTTAAGTGAT
4278393 TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4278432 TA TA TA TA TA TA -A TA TA TA T- TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4278471 TA TA T
1 TA TA T
4278476 GAGATTATTA
Statistics
Matches: 75, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
1 6 0.08
2 69 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4278441 original size:35 final size:35
Alignment explanation
Indices: 4278393--4278475 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 35
4278383 GTTAAGTGAT
4278393 TATAT-ATATATATATATATAAT-TATA-TATATA
1 TATATAATATATATATATATAATATATATTATATA
4278425 TATAT--TATATATATATATAATATATATTATATA
1 TATATAATATATATATATATAATATATATTATATA
4278458 TATATAATATATATATAT
1 TATATAATATATATATAT
4278476 GAGATTATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
31 16 0.34
32 9 0.19
33 11 0.23
35 11 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TATATAATATATATATATATAATATATATTATATA
Found at i:4285526 original size:2 final size:2
Alignment explanation
Indices: 4285519--4285580 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
4285509 GCTGCTATTG
4285519 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
4285561 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
4285581 TAATATTTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4289189 original size:54 final size:54
Alignment explanation
Indices: 4289107--4289286 Score: 306
Period size: 54 Copynumber: 3.3 Consensus size: 54
4289097 GTAAGTTTAC
* * *
4289107 GCAGTTTGGTTCATTAACATCTAGATCATAGGTTATTTTGTAGCAATATGATCA
1 GCAGTTTGGTTCATTAACATCTAGATCATAGGTTATTTTGTATCAATGTGATGA
* *
4289161 GCAGTTTGGTTCATTAACATCGAGATCATAAGTTATTTTGTATCAATGTGATGA
1 GCAGTTTGGTTCATTAACATCTAGATCATAGGTTATTTTGTATCAATGTGATGA
*
4289215 GCAGTTTGGTTGATTAACATCTAGATCATAGGTTATTTTGTATCAATGTGATGA
1 GCAGTTTGGTTCATTAACATCTAGATCATAGGTTATTTTGTATCAATGTGATGA
4289269 GCAGTTTGGTTCATTAAC
1 GCAGTTTGGTTCATTAAC
4289287 CTTGTGGGGA
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 117 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (54 bp):
GCAGTTTGGTTCATTAACATCTAGATCATAGGTTATTTTGTATCAATGTGATGA
Found at i:4289991 original size:6 final size:6
Alignment explanation
Indices: 4289980--4290005 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4289970 CATCACCAAC
4289980 GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GG
4290006 CTTGTATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:4290387 original size:25 final size:25
Alignment explanation
Indices: 4290328--4290388 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
4290318 TATGATTTTA
* *
4290328 ATTT-TTTTAATTTAGTATTTATTT
1 ATTTATTTTAAATTAGTATTTAATT
* *
4290352 ATTTGTATTAAATTAGTATTTAAATT
1 ATTTATTTTAAATTAGTATTT-AATT
4290378 -TTTATTTTAAA
1 ATTTATTTTAAA
4290389 AAAAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 4 0.13
25 23 0.77
26 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
ATTTATTTTAAATTAGTATTTAATT
Found at i:4294530 original size:103 final size:103
Alignment explanation
Indices: 4294341--4294541 Score: 244
Period size: 103 Copynumber: 2.0 Consensus size: 103
4294331 AGAACATATT
* * * * *
4294341 AGCACATACAATGCTATTATATCATAATCATAATATGGACACAAAGTGCAATCACATCTGAAATA
1 AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCTGAAATA
* * ** *
4294406 TACTAGTATACTTACTTGTAACACCACAATATAACATA
66 TACCAATATACCCACTGGTAACACCACAATATAACATA
* *
4294444 AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTTCAATCATATC-GAAAAT
1 AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCTG-AAAT
* *
4294508 ATACCAATGTACCCA-TCGGTAACACCACAGTATA
65 ATACCAATATACCCACT-GGTAACACCACAATATA
4294542 TCAATCATTC
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
102 2 0.02
103 80 0.98
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.25
Consensus pattern (103 bp):
AGCACACACAATGCTATCACATCAGAATCATAATATGCACACAAAGTGCAATCACATCTGAAATA
TACCAATATACCCACTGGTAACACCACAATATAACATA
Found at i:4297132 original size:21 final size:21
Alignment explanation
Indices: 4297106--4297146 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
4297096 ATACTTCTAC
4297106 ATTTAATAAACTTGAAATCAT
1 ATTTAATAAACTTGAAATCAT
4297127 ATTTAATAAACTTGAAATCA
1 ATTTAATAAACTTGAAATCA
4297147 AGTCCCTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.37
Consensus pattern (21 bp):
ATTTAATAAACTTGAAATCAT
Found at i:4298306 original size:30 final size:30
Alignment explanation
Indices: 4298270--4298351 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
4298260 TAAAATATAT
**
4298270 AACTTTTCAAAA-TTATATTTTTGGTCCCTA
1 AACTTTTCAAAACTTATATTTTT-ACCCCTA
* *
4298300 AACTTTTACAAAATTTATAATTTTACCCCTA
1 AACTTTT-CAAAACTTATATTTTTACCCCTA
*
4298331 AAC-TTTCAAAACTTACATTTT
1 AACTTTTCAAAACTTATATTTT
4298352 AGTCACTAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 12 0.27
30 10 0.23
31 13 0.30
32 9 0.20
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.44
Consensus pattern (30 bp):
AACTTTTCAAAACTTATATTTTTACCCCTA
Found at i:4301747 original size:20 final size:20
Alignment explanation
Indices: 4301719--4301769 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
4301709 TACCAGTTTG
*
4301719 GAGCCGTTGGAGATTGATTA
1 GAGCTGTTGGAGATTGATTA
4301739 GAGCTGTTGGAGATTGATTA
1 GAGCTGTTGGAGATTGATTA
4301759 GAGCTGTTGGA
1 GAGCTGTTGGA
4301770 ATCTTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.08, G:0.37, T:0.31
Consensus pattern (20 bp):
GAGCTGTTGGAGATTGATTA
Found at i:4302118 original size:14 final size:14
Alignment explanation
Indices: 4302099--4302134 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4302089 CACTTTAAAG
4302099 TTGTTTATGACAAA
1 TTGTTTATGACAAA
4302113 TTGTTTATGACAAA
1 TTGTTTATGACAAA
*
4302127 TTTTTTAT
1 TTGTTTAT
4302135 AAAAGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (14 bp):
TTGTTTATGACAAA
Found at i:4313520 original size:28 final size:29
Alignment explanation
Indices: 4313486--4313542 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
4313476 ATCACAAGAT
*
4313486 AAATAAATAAAAATGAAG-AAAATGTTAA
1 AAATAAAAAAAAATGAAGAAAAATGTTAA
*
4313514 AAATAAAAAAAAATTAAGAAAAATGTTAA
1 AAATAAAAAAAAATGAAGAAAAATGTTAA
4313543 TTTCTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (29 bp):
AAATAAAAAAAAATGAAGAAAAATGTTAA
Found at i:4313599 original size:3 final size:3
Alignment explanation
Indices: 4313591--4313629 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4313581 AAAAATAGAA
4313591 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4313630 TTTTTATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4315697 original size:84 final size:84
Alignment explanation
Indices: 4315273--4316149 Score: 1042
Period size: 84 Copynumber: 10.5 Consensus size: 84
4315263 ATGTGTCGTC
* * * * * * *
4315273 GAGCTGAATGGAATCGAACTCGTCA-GT-TTTTGCTGACAGATAACCCTTCTTACCTCGAGCTAT
1 GAGCTGAGTGTAATCGAACTCG-AAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTAT
* **
4315336 GCTGTAAATTTGATACGCCTTT
65 GCTGCAAA--TGATGTGCCTTT
* * * * * * *
4315358 GAGCTAAATGTAATCGAACTCGAAGGTC-TTTGATGACAGATAACCCTTCTCGCCTTGAGTTATA
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
4315422 CTGCAAATGATGTGCCTTT
66 CTGCAAATGATGTGCCTTT
* * * *
4315441 GAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGTAGATAAACCTTCTTGCCTTAAGCTATT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
4315502 CTGCAAATGATGTGCCTTT
66 CTGCAAATGATGTGCCTTT
* * * *
4315521 GAGCTGAGTGTAATCGAACTCGAAGGT-TTCATTGTTGACAGATAGCCCTTCTCGCCTTGAGTTA
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTT--TTGTTGGCAGATAACCCTTCTTGCCTTGAGCTA
4315585 TGCTGCAAATGATGTGCCTTT
64 TGCTGCAAATGATGTGCCTTT
* * * *
4315606 TAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
* *
4315671 TTGCAAATGAAGTGCCTTT
66 CTGCAAATGATGTGCCTTT
* * * * *
4315690 GAACTGAGTGTAATCGAACTCAAAGGTC---T-TTGGCAAATATCCCTTCTTACCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
*
4315751 CTGCAAATGATGTGTCTTT
66 CTGCAAATGATGTGCCTTT
* * * *
4315770 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATAGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
*
4315835 CTGTAAATGATGTGCCTTT
66 CTGCAAATGATGTGCCTTT
* * * *
4315854 GAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCTTTCTTGCCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
* * *
4315919 ATGCAAATCATGTGTCTTT
66 CTGCAAATGATGTGCCTTT
* * *
4315938 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
*
4316002 CTGTAAATGATGTGCCTTT
66 CTGCAAATGATGTGCCTTT
* * * * *
4316021 GAGATGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGAAGAAAACACTTCTTGCCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
* *
4316086 CTACAAATGATGTGCCTCT
66 CTGCAAATGATGTGCCTTT
* * * *
4316105 AAGCTGAGTGTAATCGAACTCAAAGGTCTTTTATTGACAGATAAC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAAC
4316150 TCATTCGTCG
Statistics
Matches: 681, Mismatches: 97, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
80 141 0.21
81 2 0.00
83 110 0.16
84 300 0.44
85 126 0.19
86 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (84 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATG
CTGCAAATGATGTGCCTTT
Found at i:4315777 original size:164 final size:166
Alignment explanation
Indices: 4315273--4316136 Score: 1005
Period size: 167 Copynumber: 5.2 Consensus size: 166
4315263 ATGTGTCGTC
* * * * * * *
4315273 GAGCTGAATGGAATCGAACTCGTCA-GT-TTTTGCTGACAGATAACCCTTCTTA-CCTCGAGCTA
1 GAGCTGAGTGTAATCGAACTCG-AAGGTCTTTTGTTGGCAAATAACCCTTC-TAGCCTTGAGCTA
* ** * *
4315335 TGCTGTAAATTTGATACGCCTTTGAGCTAAATGTAATCGAACTCGAAGGTC-TTTGATGACAGAT
64 TGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TG-CAGAT
* * *
4315399 AACCCTTCTCGCCTTGAGTTATACTGCAAATGATGTGCCTTT
125 AACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTT
* * * * * *
4315441 GAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGTAGATAAACCTTCTTGCCTTAAGCTATT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTATG
*
4315502 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-TTCATTGTTGACAGATAG
66 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT--TTG-TG-CAGATAA
* *
4315566 CCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTT
127 CCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTT
* * *
4315606 TAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTATG
* * * * * *
4315671 TTGCAAATGAAGTGCCTTTGAACTGAGTGTAATCGAACTCAAAGGTC-TTTG-GCAAATATCCCT
66 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTGCAGATAACCCT
* *
4315734 TCTTACCTTGAGCTATGCTGCAAATGATGTGTCTTT
131 TCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTT
* *
4315770 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATAGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTATG
* * *
4315835 CTGTAAATGATGTGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCC
66 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TG-CAGATAACC
* * * *
4315900 TTTCTTGCCTTGAGCTATGATGCAAATCATGTGTCTTT
129 CTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTT
* * *
4315938 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTATG
* * * * * *
4316002 CTGTAAATGATGTGCCTTTGAGATGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGAAGAAAACA
66 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-T-GCAGATAACC
* *
4316067 CTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTCT
129 CTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTT
* *
4316105 AAGCTGAGTGTAATCGAACTCAAAGGTCTTTT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTT
4316137 ATTGACAGAT
Statistics
Matches: 607, Mismatches: 72, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
163 36 0.06
164 143 0.24
165 110 0.18
166 1 0.00
167 152 0.25
168 96 0.16
169 69 0.11
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (166 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTAGCCTTGAGCTATG
CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTGCAGATAACCCT
TCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTT
Found at i:4315947 original size:248 final size:247
Alignment explanation
Indices: 4315273--4316149 Score: 1084
Period size: 248 Copynumber: 3.5 Consensus size: 247
4315263 ATGTGTCGTC
* * * * * *
4315273 GAGCTGAATGGAATCGAACTCGTCA-GTTTTTGCTGACAGATAACCCTTCTTA-CCTCGAGCTAT
1 GAGCTGAGTGTAATCGAACTCG-AAGGTTTTTGTTGACAAATAACCCTTC-TAGCCTTGAGCTAT
* ** * * *
4315336 GCTGTAAATTTGATACGCCTTTGAGCTAAATGTAATCGAACTCGAAGGTC-TTTGATGACAGATA
64 GCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATA
*
4315400 ACCCTTCTCGCCTTGAGTTAT-ACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
127 ACCCTTCTCGCCTTGAGCTATGA-TGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
* * * * *
4315464 AGGTCTTTGGTAGATAAACCTTCTTGCCTTAAGCTATTCTGCAAATGATGTGCCTTT
191 AGGTCTTTGGCAGATAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCCTTT
* * * *
4315521 GAGCTGAGTGTAATCGAACTCGAAGGTTTCATTGTTGACAGATAGCCCTTCTCGCCTTGAGTTAT
1 GAGCTGAGTGTAATCGAACTCGAAGGTTT--TTGTTGACAAATAACCCTTCTAGCCTTGAGCTAT
* * * *
4315586 GCTGCAAATGATGTGCCTTTTAGCTGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGCAAATAAC
64 GCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAAC
* * * *
4315651 CCTTCTCGCCTTGAGCTATGTTGCAAATGAAGTGCCTTTGAACTGAGTGTAATCGAACTCAAAGG
129 CCTTCTCGCCTTGAGCTATGATGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * *
4315716 TCTTTGGCAAATATCCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGTCTTT
194 TCTTTGGCAGATAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCCTTT
* * *
4315770 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATAGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGT-TTTTGTTGACAAATAACCCTTCTAGCCTTGAGCTATG
* * *
4315835 CTGTAAATGATGTGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCC
65 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACC
* * * *
4315900 TTTCTTGCCTTGAGCTATGATGCAAATCATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
130 CTTCTCGCCTTGAGCTATGATGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
* *
4315965 CTTTGTTGACAGATAACCCTTC-TAGCCTTGAGTTATGCTGTAAATGATGTGCCTTT
195 CTTTG--G-CAGATAACCCTTCTTA-CCTTGAGCTATGCTGCAAATGATGTGCCTTT
* * * *
4316021 GAGATGAGTGTAATCGAACTTGAAGGTCTTTTGTTGGA-AGAA-AACACTTCTTGCCTTGAGCTA
1 GAGCTGAGTGTAATCGAACTCGAAGGT-TTTTGTT-GACA-AATAACCCTTCTAGCCTTGAGCTA
* * * * *
4316084 TGCTACAAATGATGTGCCTCTAAGCTGAGTGTAATCGAACTCAAAGGTCTTTTATTGACAGATAA
63 TGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAA
4316149 C
128 C
4316150 TCATTCGTCG
Statistics
Matches: 545, Mismatches: 71, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
247 1 0.00
248 208 0.38
249 146 0.27
250 39 0.07
251 148 0.27
252 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (247 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTTTTTGTTGACAAATAACCCTTCTAGCCTTGAGCTATGC
TGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCC
TTCTCGCCTTGAGCTATGATGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
TTTGGCAGATAACCCTTCTTACCTTGAGCTATGCTGCAAATGATGTGCCTTT
Found at i:4317058 original size:32 final size:32
Alignment explanation
Indices: 4317017--4317136 Score: 179
Period size: 32 Copynumber: 3.8 Consensus size: 32
4317007 TCCGCATCAG
* * *
4317017 GATGTTGAATCCCCAAAGATGCCCTAA-TATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACT-TTT
4317049 GATGTTGAATCTCCAAAGATGCCCCAACTTTT
1 GATGTTGAATCTCCAAAGATGCCCCAACTTTT
4317081 GATGTTGAATCTCCAAAGATGCCCCAACTTTT
1 GATGTTGAATCTCCAAAGATGCCCCAACTTTT
**
4317113 GATGTTGAATCTTTAAAGATGCCC
1 GATGTTGAATCTCCAAAGATGCCC
4317137 TCTATTGCTT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
32 81 0.99
33 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACTTTT
Found at i:4320820 original size:29 final size:29
Alignment explanation
Indices: 4320787--4320852 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
4320777 CTTAAACTTA
4320787 TAATTTCGCTCAAAAAGACAACTAGAAAT
1 TAATTTCGCTCAAAAAGACAACTAGAAAT
4320816 TAATTTCGCTCAAAAAGACAACTAGAAAT
1 TAATTTCGCTCAAAAAGACAACTAGAAAT
4320845 TAATTTCG
1 TAATTTCG
4320853 GCCTAACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (29 bp):
TAATTTCGCTCAAAAAGACAACTAGAAAT
Found at i:4321339 original size:20 final size:20
Alignment explanation
Indices: 4321302--4321339 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4321292 AAAATCAAAC
*
4321302 AAAATATTAGATGGTAAAAT
1 AAAATATTAGATGCTAAAAT
4321322 AAAATATT-GAATGCTAAA
1 AAAATATTAG-ATGCTAAA
4321340 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATATTAGATGCTAAAAT
Found at i:4321479 original size:27 final size:26
Alignment explanation
Indices: 4321417--4321470 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
4321407 ATCACAAGAT
4321417 AAATAAATAAAAATGAAGAAAATGTTAA
1 AAATAAA-AAAAAT-AAGAAAATGTTAA
4321445 AAATAAAAAAAATAAGAAAATGTTAA
1 AAATAAAAAAAATAAGAAAATGTTAA
4321471 TTTCTAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 13 0.50
27 6 0.23
28 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (26 bp):
AAATAAAAAAAATAAGAAAATGTTAA
Found at i:4325642 original size:135 final size:136
Alignment explanation
Indices: 4325475--4325738 Score: 424
Period size: 136 Copynumber: 1.9 Consensus size: 136
4325465 GTAACAATGC
* * *
4325475 TTGGAGGTATTTCTGGTTCTACTCTCTTCTGTTATATTGTATCACCCTTC-CTTTTTGATAGAAT
1 TTGGAGGTATTTCTGATTCTACTATCTTCTGTTATATTGTATCACCCTTCTCTTTTTGATAGAAA
*
4325539 CGGGAAGTCAAGGTACATGGGATGAAGGGTTCGTCTGCATAGCTTGTTCAGGGTAGTGAGTGTTA
66 CGGGAAGCCAAGGTACATGGGATGAAGGGTTCGTCTGCATAGCTTGTTCAGGGTAGTGAGTGTTA
4325604 ACATAT
131 ACATAT
* *
4325610 TTGGAGGTATTTCTAGATT-TACTATCTTCTGTTATATTGTATCACCCTTCTTTTTTTTATAGAA
1 TTGGAGGTATTTCT-GATTCTACTATCTTCTGTTATATTGTATCACCCTTCTCTTTTTGATAGAA
* * *
4325674 ACTGGAAGCCAAGGTACGTGGGATGAAGGGTTCGTCTGTATAGCTTGTTCAGGGTAGTGAGTGTT
65 ACGGGAAGCCAAGGTACATGGGATGAAGGGTTCGTCTGCATAGCTTGTTCAGGGTAGTGAGTGTT
4325739 GTTGAAAGTC
Statistics
Matches: 118, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
135 44 0.37
136 74 0.63
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (136 bp):
TTGGAGGTATTTCTGATTCTACTATCTTCTGTTATATTGTATCACCCTTCTCTTTTTGATAGAAA
CGGGAAGCCAAGGTACATGGGATGAAGGGTTCGTCTGCATAGCTTGTTCAGGGTAGTGAGTGTTA
ACATAT
Found at i:4326227 original size:135 final size:135
Alignment explanation
Indices: 4325979--4326238 Score: 346
Period size: 135 Copynumber: 1.9 Consensus size: 135
4325969 ACTTTCAACA
*
4325979 AGTGTTAACTTATTTGGAGGTATTTCTGGATTTACTATCTTTTGTTATATTGCATCACCCTTGTT
1 AGTGTTAACATATTTGGAGGTATTTCTGGATTTACTATCTTTTGTTATATTGCATCACCCTTGTT
* * * ** * * *
4326044 TTTTGATATAAACTTGAAGTCGAGGTATGTGGGATGAATAGTTTGTCTGTATAACTTGTTTAAGG
66 TTTTGATAGAAACTTGAAGTCAAGGTACGTGAAATAAAGAGTTCGTCTGTATAACTTGTTTAAGG
4326109 TAGCT
131 TAGCT
* *
4326114 AGTGTTAACATATTTGGAGGTATTTTTGGATTTACTAT-TTTCTGTTATATTGTATCACCCTT-T
1 AGTGTTAACATATTTGGAGGTATTTCTGGATTTACTATCTTT-TGTTATATTGCATCACCCTTGT
* * *
4326177 CTTTTTGGTAGAAA-TTGGAAGTCAAGGTACGTGAAATAAAGGGTTCGTCTGTATAGCTTGTT
65 -TTTTTGATAGAAACTT-GAAGTCAAGGTACGTGAAATAAAGAGTTCGTCTGTATAACTTGTT
4326239 CAGAGCAGTG
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
134 6 0.06
135 102 0.94
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (135 bp):
AGTGTTAACATATTTGGAGGTATTTCTGGATTTACTATCTTTTGTTATATTGCATCACCCTTGTT
TTTTGATAGAAACTTGAAGTCAAGGTACGTGAAATAAAGAGTTCGTCTGTATAACTTGTTTAAGG
TAGCT
Found at i:4329344 original size:13 final size:13
Alignment explanation
Indices: 4329326--4329377 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
4329316 GTCATGAATC
4329326 TATGACGCGCATT
1 TATGACGCGCATT
* *
4329339 TATGACACGTATT
1 TATGACGCGCATT
*
4329352 TATGACGCACATT
1 TATGACGCGCATT
*
4329365 TATGACGCTCATT
1 TATGACGCGCATT
4329378 GCACGCCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:4329473 original size:85 final size:85
Alignment explanation
Indices: 4329384--4329571 Score: 256
Period size: 85 Copynumber: 2.2 Consensus size: 85
4329374 CATTGCACGC
* *
4329384 CATTGAAGCCACCGTCATAAAT-TAAG-ATGACACACATTTGTGTGTCATAAATTTATGACATGC
1 CATTGAAGCCACCGTCATAAATCT--GCATGACACACAATTGTGTGTCATAAATTTATGACACGC
*
4329447 ATGTATGCCTTACATTGAGCGT
64 ATGTATGACTTACATTGAGCGT
* * *
4329469 CATTGAAGCCCCCGTCATAAATCTGCTTGACTCACAATTGTGTGTCATAAATTTATGACACGCAT
1 CATTGAAGCCACCGTCATAAATCTGCATGACACACAATTGTGTGTCATAAATTTATGACACGCAT
* *
4329534 GTATGACTTACATTGCGTGT
66 GTATGACTTACATTGAGCGT
4329554 CATTGAAG-CACACGTCAT
1 CATTGAAGCCAC-CGTCAT
4329572 TAAAAAAATT
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
84 3 0.03
85 87 0.96
86 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (85 bp):
CATTGAAGCCACCGTCATAAATCTGCATGACACACAATTGTGTGTCATAAATTTATGACACGCAT
GTATGACTTACATTGAGCGT
Found at i:4329623 original size:2 final size:2
Alignment explanation
Indices: 4329616--4329682 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
4329606 TTTCGTAAAT
4329616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4329658 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4329683 TGTAGATTGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4334695 original size:30 final size:30
Alignment explanation
Indices: 4334661--4334737 Score: 154
Period size: 30 Copynumber: 2.6 Consensus size: 30
4334651 GGGCTACTCG
4334661 ATGAAACTTGTAAATATTTTTTTTTGATAA
1 ATGAAACTTGTAAATATTTTTTTTTGATAA
4334691 ATGAAACTTGTAAATATTTTTTTTTGATAA
1 ATGAAACTTGTAAATATTTTTTTTTGATAA
4334721 ATGAAACTTGTAAATAT
1 ATGAAACTTGTAAATAT
4334738 ATAACACAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (30 bp):
ATGAAACTTGTAAATATTTTTTTTTGATAA
Found at i:4337985 original size:22 final size:20
Alignment explanation
Indices: 4337952--4337991 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
4337942 GATTTCTATG
4337952 TTTTTTTTTGTTTTTTCTTA
1 TTTTTTTTTGTTTTTTCTTA
4337972 TTTTATTTCTTGTTTTTTCT
1 TTTT-TTT-TTGTTTTTTCT
4337992 AAAGTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTGTTTTTTCTTA
Found at i:4337990 original size:10 final size:10
Alignment explanation
Indices: 4337944--4337991 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
4337934 TATAGCTCGA
4337944 TTTCTATGTTT
1 TTTCT-TGTTT
*
4337955 TTTTTTGTTT
1 TTTCTTGTTT
*
4337965 TTTCTTATTTT
1 TTTCTT-GTTT
4337976 ATTTCTTGTTT
1 -TTTCTTGTTT
4337987 TTTCT
1 TTTCT
4337992 AAAGTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 15 0.48
11 10 0.32
12 6 0.19
ACGTcount: A:0.06, C:0.08, G:0.06, T:0.79
Consensus pattern (10 bp):
TTTCTTGTTT
Found at i:4338382 original size:12 final size:11
Alignment explanation
Indices: 4338359--4338397 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4338349 TTTGCTTTAG
*
4338359 AAAAAGTAAGA
1 AAAAAATAAGA
4338370 AATAAAATAAGA
1 AA-AAAATAAGA
*
4338382 AAAAAACAAGA
1 AAAAAATAAGA
4338393 AAAAA
1 AAAAA
4338398 CATAGAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.08
Consensus pattern (11 bp):
AAAAAATAAGA
Found at i:4342903 original size:16 final size:16
Alignment explanation
Indices: 4342874--4342913 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
4342864 TATATAATAT
*
4342874 ATAAT-TTTTGAAATC
1 ATAATATTTTAAAATC
*
4342889 ATAATATTTTAAAATT
1 ATAATATTTTAAAATC
4342905 ATAATATTT
1 ATAATATTT
4342914 AGTTTTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
ATAATATTTTAAAATC
Found at i:4344423 original size:18 final size:18
Alignment explanation
Indices: 4344400--4344436 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4344390 ATATAACACA
4344400 TATGTCCCG-ATGGACCAC
1 TATGTCCCGAAT-GACCAC
4344418 TATGTCCCGAATGACCAC
1 TATGTCCCGAATGACCAC
4344436 T
1 T
4344437 CCTTAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (18 bp):
TATGTCCCGAATGACCAC
Found at i:4349762 original size:18 final size:18
Alignment explanation
Indices: 4349739--4349775 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4349729 ATATAACACA
* *
4349739 TATGTCTCGAATGACCAC
1 TATGTCCCGAAGGACCAC
4349757 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
4349775 T
1 T
4349776 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:4353567 original size:18 final size:18
Alignment explanation
Indices: 4353544--4353580 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4353534 ATTAAAAACC
4353544 ATTACATTTATTTAAGTA
1 ATTACATTTATTTAAGTA
4353562 ATTACATTTATTTAAGTA
1 ATTACATTTATTTAAGTA
4353580 A
1 A
4353581 AAGGGATCAA
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:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTACATTTATTTAAGTA
Found at i:4360583 original size:21 final size:22
Alignment explanation
Indices: 4360559--4360657 Score: 76
Period size: 24 Copynumber: 4.4 Consensus size: 22
4360549 CACCGAAGTG
4360559 CCACATA-TTTGTCCCAAAAGA
1 CCACATAGTTTGTCCCAAAAGA
* *
4360580 CCACATAGGTTTTGTCCCGAATGA
1 CCACATA-G-TTTGTCCCAAAAGA
* **
4360604 CCACATAGTTT-TATCCTGAAGAA
1 CCACATAGTTTGT-CCCAAAAG-A
* *
4360627 CCACATAGGTTTGTCCCGAATGA
1 CCACATA-GTTTGTCCCAAAAGA
4360650 CCACATAG
1 CCACATAG
4360658 AACCCTCGAC
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
21 8 0.13
22 8 0.13
23 17 0.28
24 27 0.44
25 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (22 bp):
CCACATAGTTTGTCCCAAAAGA
Found at i:4360629 original size:23 final size:23
Alignment explanation
Indices: 4360551--4360657 Score: 114
Period size: 23 Copynumber: 4.7 Consensus size: 23
4360541 ATAATTTGCA
4360551 CCGAAGTG-CCACATA--TTTGTC
1 CCGAA-TGACCACATAGTTTTGTC
* *
4360572 CCAAAAGACCACATAGGTTTTGTC
1 CCGAATGACCACATA-GTTTTGTC
*
4360596 CCGAATGACCACATAGTTTTATC
1 CCGAATGACCACATAGTTTTGTC
* *
4360619 CTGAA-GAACCACATAGGTTTGTC
1 CCGAATG-ACCACATAGTTTTGTC
4360642 CCGAATGACCACATAG
1 CCGAATGACCACATAG
4360658 AACCCTCGAC
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
20 1 0.01
21 11 0.15
22 1 0.01
23 38 0.54
24 20 0.28
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (23 bp):
CCGAATGACCACATAGTTTTGTC
Found at i:4367454 original size:21 final size:21
Alignment explanation
Indices: 4367437--4367519 Score: 78
Period size: 24 Copynumber: 3.7 Consensus size: 21
4367427 ATAATTTGCA
4367437 CCGAAGTG-CCACATATTTGTC
1 CCGAAG-GACCACATATTTGTC
4367458 CCGAAGGACCACATAGGTTTTGTC
1 CCGAAGGACCACATA---TTTGTC
*
4367482 CCAAAGGACCACATAGTCTTGTC
1 CCGAAGGACCACATA-T-TTGTC
* *
4367505 CCAAATGACCACATA
1 CCGAAGGACCACATA
4367520 GAACCCTCGA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.02
21 13 0.24
22 1 0.02
23 19 0.35
24 20 0.37
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (21 bp):
CCGAAGGACCACATATTTGTC
Found at i:4367488 original size:24 final size:24
Alignment explanation
Indices: 4367452--4367520 Score: 104
Period size: 23 Copynumber: 2.9 Consensus size: 24
4367442 GTGCCACATA
*
4367452 TTTGTCCCGAAGGACCACATAGGT
1 TTTGTCCCAAAGGACCACATAGGT
4367476 TTTGTCCCAAAGGACCACATA-GT
1 TTTGTCCCAAAGGACCACATAGGT
* *
4367499 CTTGTCCCAAATGACCACATAG
1 TTTGTCCCAAAGGACCACATAG
4367521 AACCCTCGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (24 bp):
TTTGTCCCAAAGGACCACATAGGT
Found at i:4374838 original size:26 final size:24
Alignment explanation
Indices: 4374776--4374838 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
4374766 CATTTTCATC
4374776 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
4374800 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
4374823 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
4374839 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Done.