Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008225.1 Hibiscus syriacus cultivar Beakdansim tig00110858_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: 1890193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:107179 original size:19 final size:18
Alignment explanation
Indices: 107157--107252 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 18
107147 GAAACACAAA
107157 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
107176 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
107192 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
107208 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
107224 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
107241 TGGCATTGCGAT
1 TCGCATTGCGAT
107253 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 3 0.05
18 13 0.21
19 16 0.26
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:107198 original size:14 final size:14
Alignment explanation
Indices: 107179--107236 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
107169 TTTCATTTCG
107179 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
107193 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
107209 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
107225 CGTTGCGATTTT
1 CGTTGCGATTTT
107237 CATTTGGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:107247 original size:33 final size:33
Alignment explanation
Indices: 107162--107252 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
107152 ACAAATCGCA
*
107162 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
107195 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
107227 TTGCGATTTTCATTTGGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
107253 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:107271 original size:20 final size:20
Alignment explanation
Indices: 107246--107291 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
107236 TCATTTGGCA
107246 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
107266 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
107286 TTGCGA
1 TTGCGA
107292 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:107800 original size:18 final size:18
Alignment explanation
Indices: 107774--107818 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
107764 GTCGATCAGA
*
107774 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
107792 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
107810 TGATGGCTC
1 TGATGGCTC
107819 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:109187 original size:20 final size:20
Alignment explanation
Indices: 109139--109197 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
109129 AATAGTTTCT
** *
109139 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
109159 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
109179 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
109198 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:109777 original size:20 final size:20
Alignment explanation
Indices: 109671--109805 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
109661 CGTTTTGAAA
*
109671 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
109692 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
109712 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
109732 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
109753 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
109773 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
109793 ATCGCATTGCGAT
1 ATCGCATTGCGAT
109806 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:109777 original size:61 final size:61
Alignment explanation
Indices: 109671--109808 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
109661 CGTTTTGAAA
* * * *
109671 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
109732 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
109793 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
109809 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:109824 original size:61 final size:61
Alignment explanation
Indices: 109671--109826 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
109661 CGTTTTGAAA
* ** * * * *
109671 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
109732 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
109793 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
109827 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:113499 original size:16 final size:16
Alignment explanation
Indices: 113478--113519 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
113468 GGTGTTATTT
* *
113478 GCAACTTGAGCACGTG
1 GCAACTCGAGCACGTA
113494 GCAACTCGAGCACGTA
1 GCAACTCGAGCACGTA
113510 GCAACTCGAG
1 GCAACTCGAG
113520 GTCCTGCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (16 bp):
GCAACTCGAGCACGTA
Found at i:126400 original size:26 final size:25
Alignment explanation
Indices: 126371--126452 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 25
126361 TTGTTTCATC
*
126371 TATTTGTTTTATTTTATTTATATGTA
1 TATTTCTTTTATTTTATTTATAT-TA
*
126397 TATTTTTTTTATATTTTATTTAT-TTA
1 TA-TTTCTTT-TATTTTATTTATATTA
* * *
126423 TATTACTATTATTTTCTTT-TATTTA
1 TATTTCTTTTATTTTATTTATA-TTA
126448 TATTT
1 TATTT
126453 TATTTCTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 1 0.02
24 9 0.20
25 11 0.24
26 6 0.13
27 7 0.15
28 12 0.26
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (25 bp):
TATTTCTTTTATTTTATTTATATTA
Found at i:126411 original size:11 final size:11
Alignment explanation
Indices: 126377--126472 Score: 71
Period size: 11 Copynumber: 9.1 Consensus size: 11
126367 CATCTATTTG
126377 TTTTATTT-TA
1 TTTTATTTATA
*
126387 TTTATATGTATA
1 TTT-TATTTATA
*
126399 TTTTTTTTATA
1 TTTTATTTATA
126410 TTTTATTTAT-
1 TTTTATTTATA
*
126420 TTATA-TTACTA
1 TTTTATTTA-TA
*
126431 --TTATTT-TC
1 TTTTATTTATA
126439 TTTTATTTATA
1 TTTTATTTATA
*
126450 TTTTATTTCTA
1 TTTTATTTATA
126461 TTCTT-TTTATA
1 TT-TTATTTATA
126472 T
1 T
126473 ACATTAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
8 1 0.01
9 5 0.07
10 16 0.24
11 38 0.57
12 7 0.10
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:126420 original size:20 final size:20
Alignment explanation
Indices: 126397--126472 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
126387 TTTATATGTA
126397 TATTTTTTTTATATTTTATT
1 TATTTTTTTTATATTTTATT
* * *
126417 TATTTATATTACTATTAT-TT
1 TATTTTTTTTA-TATTTTATT
* *
126437 TCTTTTATTTATATTTTATTT
1 TATTTTTTTTATATTTTA-TT
*
126458 CTATTCTTTTTATAT
1 -TATTTTTTTTATAT
126473 ACATTAATAT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 5 0.12
20 18 0.44
21 7 0.17
22 11 0.27
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTTTTTATATTTTATT
Found at i:126424 original size:32 final size:35
Alignment explanation
Indices: 126377--126462 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 35
126367 CATCTATTTG
126377 TTTTATTTTATTTATATGTA-TATT-TTTT-TTATA
1 TTTTATTTTATTTATAT-TACTATTATTTTCTTATA
*
126410 TTTTA-TTTATTTATATTACTATTATTTTCTTTTA
1 TTTTATTTTATTTATATTACTATTATTTTCTTATA
*
126444 TTTATATTTTATTTCTATT
1 TTT-TATTTTATTTATATT
126463 CTTTTTATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
31 2 0.04
32 15 0.33
33 9 0.20
34 7 0.15
35 2 0.04
36 11 0.24
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72
Consensus pattern (35 bp):
TTTTATTTTATTTATATTACTATTATTTTCTTATA
Found at i:126451 original size:6 final size:5
Alignment explanation
Indices: 126377--126462 Score: 59
Period size: 5 Copynumber: 16.4 Consensus size: 5
126367 CATCTATTTG
* *
126377 TTTTA TTTTA TTTATA TGTATA TTTTT TTTATA TTTTA -TTTA -TTTA
1 TTTTA TTTTA TTT-TA T-TTTA TTTTA TTT-TA TTTTA TTTTA TTTTA
* * *
126423 TATTA CTATTA TTTTC TTTTA TTTATA TTTTA TTTCTA TT
1 TTTTA -TTTTA TTTTA TTTTA TTT-TA TTTTA TTT-TA TT
126463 CTTTTTATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
4 8 0.12
5 33 0.50
6 24 0.36
7 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:127005 original size:17 final size:17
Alignment explanation
Indices: 126987--127019 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
126977 TTGCTTTTAT
126987 TTTATTTA-TTATCTTA
1 TTTATTTATTTATCTTA
127003 TTTATTTATTTATCTTA
1 TTTATTTATTTATCTTA
127020 GCTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTATTTATCTTA
Found at i:137487 original size:9 final size:9
Alignment explanation
Indices: 137473--137520 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
137463 CCTAAGTTGA
137473 AAAAAAAAC
1 AAAAAAAAC
137482 AAAAAAAAC
1 AAAAAAAAC
137491 AAAAAAAAC
1 AAAAAAAAC
*
137500 -AAAAACA-
1 AAAAAAAAC
137507 AAAAAAAAC
1 AAAAAAAAC
137516 AAAAA
1 AAAAA
137521 GAGAAAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 12 0.34
9 23 0.66
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:137528 original size:1 final size:1
Alignment explanation
Indices: 137472--137520 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
137462 TCCTAAGTTG
* * * * *
137472 AAAAAAAAACAAAAAAAACAAAAAAAACAAAAACAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
137521 GAGAAAAACG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:137528 original size:16 final size:16
Alignment explanation
Indices: 137472--137520 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
137462 TCCTAAGTTG
*
137472 AAAAAAAAACAAAAAAA
1 AAAAAAAAAC-AAAAAC
137489 ACAAAAAAAACAAAAAC
1 A-AAAAAAAACAAAAAC
137506 AAAAAAAAACAAAAA
1 AAAAAAAAACAAAAA
137521 GAGAAAAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 14 0.47
17 7 0.23
18 9 0.30
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAC
Found at i:137529 original size:24 final size:24
Alignment explanation
Indices: 137472--137520 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
137462 TCCTAAGTTG
137472 AAAA-AAAAACAAAAAAAACAAAA
1 AAAACAAAAACAAAAAAAACAAAA
137495 AAAACAAAAACAAAAAAAAACAAAA
1 AAAACAAAAAC-AAAAAAAACAAAA
137520 A
1 A
137521 GAGAAAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.17
24 6 0.25
25 14 0.58
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAACAAAAACAAAAAAAACAAAA
Found at i:138459 original size:105 final size:105
Alignment explanation
Indices: 138277--138997 Score: 1343
Period size: 105 Copynumber: 6.9 Consensus size: 105
138267 TTATACCCAT
138277 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
138342 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
138382 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
138447 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* *
138487 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
138552 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
138592 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
138657 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
138697 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
138762 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
138802 AACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
138867 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* *
138907 AGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
138972 AAGGGACCGCTGGTTGTCAATAAACA
66 AAGGGACCGCTGGTTGTCAACAAACA
138998 AGTTTGATTT
Statistics
Matches: 601, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 601 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
Found at i:138642 original size:210 final size:210
Alignment explanation
Indices: 138277--139188 Score: 1484
Period size: 210 Copynumber: 4.4 Consensus size: 210
138267 TTATACCCAT
138277 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
138342 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
138407 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
138472 ATTTCTCAGATTCAG
196 ATTTCTCAAATTCAG
* *
138487 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
138552 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
138617 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
138682 ATTGCTCAAATTCAG
196 ATTTCTCAAATTCAG
138697 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
138762 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAACCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
138827 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
138892 ATTTCTCAAATTCGG
196 ATTTCTCAAATTCAG
* *
138907 AGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
138972 AAGGGACCGCTGGTTGTCAATAAACA-AG-T----TT----G---ATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
* *** **
139024 GATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGT---C-AAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
139085 --TTCTCAATTTCAG
196 ATTTCTCAAATTCAG
* *
139098 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
139163 AAGGGACCGCTGGTTGTCAATAAACA
66 AAGGGACCGCTGGTTGTCAACAAACA
139189 ATTTCCCAAT
Statistics
Matches: 672, Mismatches: 30, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
191 98 0.15
193 3 0.00
194 1 0.00
197 71 0.11
204 2 0.00
208 1 0.00
210 496 0.74
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (210 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
ATTTCTCAAATTCAG
Found at i:138853 original size:315 final size:314
Alignment explanation
Indices: 138277--139188 Score: 1491
Period size: 315 Copynumber: 3.0 Consensus size: 314
138267 TTATACCCAT
138277 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
138342 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAA-TTCAGAGCCAATTTCAACTTCACAACGAAG
138407 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
130 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
* * *
138472 ATTTCTCAGATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
195 ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
138537 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
260 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
138592 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
138657 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTGCTC-AATTCAGAGCCAATTTCAACTTCACAACGAAG
138722 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
130 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
138787 ATTTCTCAAATTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
195 ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
138852 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGG
260 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
* *
138907 AGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
138972 AAGGGACCGCTGGTTGTCAATAAACA-AG-T---TT----G---ATTTCAACTTCACAACGAAGG
66 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGG
* *** **
139025 ATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGGGACCGCTGACTGT---C-AAC-
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
* *
139085 -TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGT
196 TTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
* *
139149 TCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACA
261 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
139189 ATTTCCCAAT
Statistics
Matches: 574, Mismatches: 22, Indels: 21
0.93 0.04 0.03
Matches are distributed among these distances:
296 99 0.17
298 3 0.01
299 1 0.00
302 71 0.12
305 1 0.00
309 2 0.00
313 1 0.00
314 1 0.00
315 393 0.68
316 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (314 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTGCTCAATTCAGAGCCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACA
TTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGT
TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
Found at i:139072 original size:92 final size:92
Alignment explanation
Indices: 138915--139216 Score: 374
Period size: 92 Copynumber: 3.2 Consensus size: 92
138905 GGAGCCAATC
* *
138915 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACC
1 TCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
138980 GCTGGTTGTCAATAAACAAGTTT-GATT
66 GCTGGTTGTCAATAAACAA-TTTCGATT
***
139007 TCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAGGGACC
1 TCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
** ***
139072 GCTGACTGTCAACTTCTCAATTTCAGAGCCAATT
66 GCTGGTTGTCAA-TAAACAATTTC---G---ATT
*
139106 TCAACTTCACAACGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACAACGAAGGGAC
1 TCAACTTCACAACGAAGGATATTGGACT-CAAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
139170 CGCTGGTTGTCAATAAACAATTTCCCAATT
65 CGCTGGTTGTCAATAAACAATTT--CGATT
*
139200 TCAGCTTCACAACGAAG
1 TCAACTTCACAACGAAG
139217 TATCTTTGGC
Statistics
Matches: 178, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
92 73 0.41
93 4 0.02
94 19 0.11
96 1 0.01
98 7 0.04
99 70 0.39
100 4 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (92 bp):
TCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
GCTGGTTGTCAATAAACAATTTCGATT
Found at i:139166 original size:191 final size:194
Alignment explanation
Indices: 138805--139216 Score: 616
Period size: 191 Copynumber: 2.1 Consensus size: 194
138795 AATTCAGAAC
* *
138805 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAG
** *
138870 GGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGGAGCCAATCTCAACTTCACAACGAAGGAT
66 GGACCGCTGACTGT--ACAAACA-TTCTCAAATTCAGAGCCAATCTCAACTTCACAACGAAGGAT
* * *
138935 ATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAAG
128 ATTGGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAA-
139000 TTT
192 TTT
* **
139003 -GATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAG
* *
139067 GGACCGCTGACTGT-C-AAC-TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
66 GGACCGCTGACTGTACAAACATTCTCAAATTCAGAGCCAATCTCAACTTCACAACGAAGGATATT
139129 GGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTT
131 GGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
139193 CCCAATTTCAGCTTCACAACGAAG
1 --CAATTTCAACTTCACAACGAAG
139217 TATCTTTGGC
Statistics
Matches: 196, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
190 3 0.02
191 99 0.51
193 22 0.11
194 1 0.01
197 71 0.36
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (194 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACGACGAAG
GGACCGCTGACTGTACAAACATTCTCAAATTCAGAGCCAATCTCAACTTCACAACGAAGGATATT
GGACTCCAAACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTT
Found at i:139182 original size:99 final size:99
Alignment explanation
Indices: 138277--139174 Score: 907
Period size: 105 Copynumber: 8.8 Consensus size: 99
138267 TTATACCCAT
* * *
138277 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
**
138342 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAG
66 AAGGGACCGCTGACTGT---C-AAC--TTCTCAATTTCAG
* * *
138382 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
**
138447 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGA-TTCAG
66 AAGGGACCGCTGACTGT---C-AAC--TTCTCA-ATTTCAG
* * ** *
138487 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
** *
138552 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
66 AAGGGACCGCTGACTGT---C-AAC-TT-CTCAATTTCAG
* * *
138592 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
** *
138657 AAGGGACCGCTGGTTGTCAACAAACATTGCTCAAATTCAG
66 AAGGGACCGCTGACTGT---C-AAC-TT-CTCAATTTCAG
* * *
138697 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
** *
138762 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGACTGT---C-AAC--TTCTCAATTTCAG
* * * *
138802 AACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
** * *
138867 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCGG
66 AAGGGACCGCTGACTGT---C-AAC--TTCTCAATTTCAG
* * * * *
138907 AGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
** ***
138972 AAGGGACCGCTGGTTGTCAA-TAAACAAGTTT---
66 AAGGGACCGCTGACTGTCAACTTCTCAA-TTTCAG
** *
139003 -G---ATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
139064 AAGGGACCGCTGACTGTCAACTTCTCAATTTCAG
66 AAGGGACCGCTGACTGTCAACTTCTCAATTTCAG
*
139098 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACAAC
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT-CAAGACAACACAAGTTCAACTTCACAAC
139162 GAAGGGACCGCTG
65 GAAGGGACCGCTG
139175 GTTGTCAATA
Statistics
Matches: 749, Mismatches: 30, Indels: 34
0.92 0.04 0.04
Matches are distributed among these distances:
92 75 0.10
93 4 0.01
95 1 0.00
96 1 0.00
98 4 0.01
99 66 0.09
100 3 0.00
101 2 0.00
102 1 0.00
104 3 0.00
105 586 0.78
106 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (99 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
AAGGGACCGCTGACTGTCAACTTCTCAATTTCAG
Found at i:139286 original size:20 final size:20
Alignment explanation
Indices: 139261--139302 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
139251 CCAGAACTCT
139261 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
*
139281 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
139301 GA
1 GA
139303 CGAAGGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:140690 original size:5 final size:5
Alignment explanation
Indices: 140680--140761 Score: 51
Period size: 5 Copynumber: 15.4 Consensus size: 5
140670 CATCTATTTG
*
140680 TTTTA TTTTA TTTATA TGTATA TTTT- TTTATA TTTTA -TTTA TTTATA
1 TTTTA TTTTA TTT-TA T-TTTA TTTTA TTT-TA TTTTA TTTTA TTT-TA
* * *
140727 TACTATTA TTTTC TTTTA TTATA TTTTA TTCTA TT
1 T--T-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
140762 CTTTTTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
4 7 0.11
5 35 0.57
6 13 0.21
7 1 0.02
8 4 0.07
9 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (5 bp):
TTTTA
Found at i:140724 original size:15 final size:15
Alignment explanation
Indices: 140680--140771 Score: 64
Period size: 15 Copynumber: 6.1 Consensus size: 15
140670 CATCTATTTG
140680 TTTTATTTTATTTATA
1 TTTTA-TTTATTTATA
* *
140696 TGTATATTTTTTTATA
1 T-TTTATTTATTTATA
140712 TTTTATTTATTTATA
1 TTTTATTTATTTATA
** *
140727 TACTA-TTATTT-TC
1 TTTTATTTATTTATA
140740 TTTTATTATATTT-TA
1 TTTTATT-TATTTATA
* *
140755 TTCTATTCTTTTTATA
1 TTTTATT-TATTTATA
140771 T
1 T
140772 ACATTAATAT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
13 4 0.07
14 7 0.12
15 31 0.53
16 14 0.24
17 3 0.05
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (15 bp):
TTTTATTTATTTATA
Found at i:140728 original size:27 final size:26
Alignment explanation
Indices: 140674--140750 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
140664 TTGTTTCATC
*
140674 TATTTGTTTTATTTTATTTATATGTA
1 TATTTGTTTTATTTTATTTATATATA
* *
140700 TATTTTTTTATATTTTATTTATTTATA
1 TATTTGTTT-TATTTTATTTATATATA
* *
140727 TACTATTATTTTCTTTTA-TTATAT
1 TA-T-TTGTTTTATTTTATTTATAT
140751 TTTATTCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
26 8 0.19
27 22 0.52
28 7 0.17
29 5 0.12
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (26 bp):
TATTTGTTTTATTTTATTTATATATA
Found at i:140752 original size:33 final size:31
Alignment explanation
Indices: 140682--140752 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 31
140672 TCTATTTGTT
*
140682 TTAT-TTTATTTATATGTATATTTTTTTATA
1 TTATATTTATTTATATCTATATTTTTTTATA
*
140712 TTTTATTTATTTATATACTATTATTTTCTTT-TA
1 TTATATTTATTTATAT-CTA-TATTTT-TTTATA
140745 TTATATTT
1 TTATATTT
140753 TATTCTATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 3 0.09
31 11 0.32
32 2 0.06
33 15 0.44
34 3 0.09
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (31 bp):
TTATATTTATTTATATCTATATTTTTTTATA
Found at i:140756 original size:23 final size:23
Alignment explanation
Indices: 140682--140766 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 23
140672 TCTATTTGTT
* *
140682 TTATTTTATTTATATGTATATTTTT
1 TTATTTTCTTT-TAT-TATATTTTA
**
140707 TTATATTT-TATTTATTTATATACTA
1 TTAT-TTTCT-TTTA-TTATATTTTA
140732 TTATTTTCTTTTATTATATTTTA
1 TTATTTTCTTTTATTATATTTTA
* *
140755 TTCTATTCTTTT
1 TTATTTTCTTTT
140767 TATATACATT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 18 0.37
24 7 0.14
25 18 0.37
26 6 0.12
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.71
Consensus pattern (23 bp):
TTATTTTCTTTTATTATATTTTA
Found at i:140839 original size:2 final size:2
Alignment explanation
Indices: 140832--140864 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
140822 TTATTTTAAC
140832 TA TA TA TA 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 TA TA TA TA T
140865 GCTTTTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:141084 original size:19 final size:18
Alignment explanation
Indices: 141042--141085 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
141032 AAACATTTAT
141042 CCTTTTTTAATCTGTATC
1 CCTTTTTTAATCTGTATC
*
141060 CTTTTTTTAAGT-TCGTATC
1 CCTTTTTTAA-TCT-GTATC
141079 CCTTTTT
1 CCTTTTT
141086 CTATTTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.14, C:0.20, G:0.07, T:0.59
Consensus pattern (18 bp):
CCTTTTTTAATCTGTATC
Found at i:141314 original size:17 final size:17
Alignment explanation
Indices: 141296--141328 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
141286 TTGCTTTTAT
141296 TTTATTTA-TTATCTTA
1 TTTATTTATTTATCTTA
141312 TTTATTTATTTATCTTA
1 TTTATTTATTTATCTTA
141329 GCTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTATTTATCTTA
Found at i:149724 original size:18 final size:20
Alignment explanation
Indices: 149688--149728 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
149678 AATGATGAAA
149688 AAATATTTTTTAAACATTTT
1 AAATATTTTTTAAACATTTT
*
149708 AAAT-TTTTTTATA-ATTTT
1 AAATATTTTTTAAACATTTT
149726 AAA
1 AAA
149729 ATAATTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATATTTTTTAAACATTTT
Found at i:156768 original size:3 final size:3
Alignment explanation
Indices: 156760--156789 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
156750 TAATGTCAAA
156760 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
156790 TTCTCAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:157695 original size:39 final size:40
Alignment explanation
Indices: 157610--157722 Score: 108
Period size: 40 Copynumber: 2.8 Consensus size: 40
157600 CTTTTTTATA
**
157610 TTTTT-AATTTTATAAAAAAAATATATATATAAATTTTATG
1 TTTTTAAATTTTA-AAAAAAAATATATATATAAATAATATG
**
157650 AATTTAAATTTTAAAAAAAATATATATATATAAA-AATAT-
1 TTTTTAAATTTTAAAAAAAA-ATATATATATAAATAATATG
* *
157689 TTTTTAACTTGTTAAAAAACAAATGTATA-ATAAA
1 TTTTTAAATT-TTAAAAAA-AAATATATATATAAA
157723 GATAATTTGA
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
39 12 0.20
40 27 0.44
41 22 0.36
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (40 bp):
TTTTTAAATTTTAAAAAAAAATATATATATAAATAATATG
Found at i:159688 original size:2 final size:2
Alignment explanation
Indices: 159681--159726 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
159671 TAAAAGAATA
159681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159722 AT AT A
1 AT AT A
159727 CAATTAGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:161588 original size:20 final size:20
Alignment explanation
Indices: 161563--161607 Score: 83
Period size: 19 Copynumber: 2.3 Consensus size: 20
161553 TTTGTATACT
161563 TCACCCCCTTAAAATTCAAC
1 TCACCCCCTTAAAATTCAAC
161583 TCA-CCCCTTAAAATTCAAC
1 TCACCCCCTTAAAATTCAAC
161602 TCACCC
1 TCACCC
161608 AAATTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.24
Consensus pattern (20 bp):
TCACCCCCTTAAAATTCAAC
Found at i:162947 original size:16 final size:18
Alignment explanation
Indices: 162926--162958 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
162916 TAATTTACCA
162926 TTTTACC-T-AATATGTG
1 TTTTACCATAAATATGTG
162942 TTTTACCATAAATATGT
1 TTTTACCATAAATATGT
162959 CAGGTTCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (18 bp):
TTTTACCATAAATATGTG
Found at i:163244 original size:15 final size:15
Alignment explanation
Indices: 163218--163279 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 15
163208 GGTTAAATTA
163218 AAAAATAAGAAAAAAT
1 AAAAA-AAGAAAAAAT
*
163234 TAAAAAAG-AAAAAT
1 AAAAAAAGAAAAAAT
163248 AAATAAAACGAAATAAAAT
1 AAA-AAAA-G-AA-AAAAT
163267 AAAATAAAGAAAA
1 AAAA-AAAGAAAA
163280 TATTAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
14 8 0.21
15 7 0.18
16 7 0.18
17 2 0.05
18 3 0.08
19 11 0.29
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAAAAAGAAAAAAT
Found at i:164678 original size:18 final size:18
Alignment explanation
Indices: 164655--164722 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
164645 ATATAAGTAT
164655 AATAATAATAAAAATATA
1 AATAATAATAAAAATATA
*
164673 AATAATATTAATATAATATA
1 AATAATAATAA-A-AATATA
* ** *
164693 TATTGTAATGAAAATATA
1 AATAATAATAAAAATATA
164711 TAATATATAATA
1 -AATA-ATAATA
164723 TATAACTATA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 16 0.44
19 4 0.11
20 16 0.44
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AATAATAATAAAAATATA
Found at i:164685 original size:15 final size:15
Alignment explanation
Indices: 164622--164688 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 15
164612 GACCTGAAAA
164622 AAATAA-ATAAATAT
1 AAATAATATAAATAT
164636 AATATATATATATAAGTAT
1 AA-ATA-ATATA-AA-TAT
*
164655 AATAATAATAAAAATAT
1 -A-AATAATATAAATAT
*
164672 AAATAATATTAATAT
1 AAATAATATAAATAT
164687 AA
1 AA
164689 TATATATTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.05
15 17 0.40
16 2 0.05
17 6 0.14
18 4 0.09
19 7 0.16
20 4 0.09
21 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (15 bp):
AAATAATATAAATAT
Found at i:164733 original size:38 final size:37
Alignment explanation
Indices: 164623--164735 Score: 108
Period size: 38 Copynumber: 3.0 Consensus size: 37
164613 ACCTGAAAAA
164623 AATAAATAA-ATATAATATAT-ATATATAAGTATAATAAT
1 AATAAA-AATATATAATATATAATATATAA-TAT-ATAAT
**
164661 AATAAAAATATA-AATAATATTAATATA-ATATATATTGT
1 AATAAAAATATATAAT-ATA-TAATATATA-ATATATAAT
*
164699 AATGAAAATATATAATATATAATATATAACTATATAA
1 AATAAAAATATATAATATATAATATATAA-TATATAA
164736 CTATATAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
37 13 0.21
38 35 0.56
39 8 0.13
40 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (37 bp):
AATAAAAATATATAATATATAATATATAATATATAAT
Found at i:164837 original size:35 final size:35
Alignment explanation
Indices: 164791--164980 Score: 175
Period size: 35 Copynumber: 5.5 Consensus size: 35
164781 TCATATATAT
164791 ATGTTTTCAAAACTATATTATATACGTTTTCAAAA
1 ATGTTTTCAAAACTATATTATATACGTTTTCAAAA
* *
164826 ATGTTTTCAAAACTATATATTATATACATTTGTTTAAAA
1 ATGTTTTCAAAAC--TATATTATATAC-GTT-TTCAAAA
* *
164865 ATGTTTTCTAAAC-----CATAT--GTTTTCAAAA
1 ATGTTTTCAAAACTATATTATATACGTTTTCAAAA
*
164893 ATGTTTTCAAAACCATATATTA-A-ACGTTTTCAAAC
1 ATGTTTTCAAAA-C-TATATTATATACGTTTTCAAAA
* *
164928 ATGTTTTCAAAACCATA-TATTATACATTTTCAAAA
1 ATGTTTTCAAAACTATATTA-TATACGTTTTCAAAA
*
164963 ATATTTTCAAAACTATAT
1 ATGTTTTCAAAACTATAT
164981 ATTATATTTA
Statistics
Matches: 124, Mismatches: 14, Indels: 33
0.73 0.08 0.19
Matches are distributed among these distances:
28 17 0.14
29 3 0.02
32 6 0.05
33 3 0.02
34 3 0.02
35 60 0.48
37 12 0.10
38 2 0.02
39 18 0.15
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.42
Consensus pattern (35 bp):
ATGTTTTCAAAACTATATTATATACGTTTTCAAAA
Found at i:164840 original size:102 final size:102
Alignment explanation
Indices: 164734--164951 Score: 241
Period size: 102 Copynumber: 2.1 Consensus size: 102
164724 ATAACTATAT
* * * *
164734 AACTATATAATATATATATTATGTTTTCAAAAATCG-TTT-TAAA-AAAATCATAT-ATATATGT
1 AACTATATATTATATACATT-TG-TTT-AAAAAT-GTTTTCTAAACAAAATCATATCAAAAATGT
164795 TTTCAAAA-C-TATATTATATACGTTTTCAAAAATGTTTTCAA
62 TTTCAAAACCATATATTA-A-ACGTTTTCAAAAATGTTTTCAA
* * ** *
164836 AACTATATATTATATACATTTGTTTAAAAATGTTTTCTAAACCATATGTTTTCAAAAATGTTTTC
1 AACTATATATTATATACATTTGTTTAAAAATGTTTTCTAAACAAAATCATATCAAAAATGTTTTC
*
164901 AAAACCATATATTAAACGTTTTCAAACATGTTTTCAA
66 AAAACCATATATTAAACGTTTTCAAAAATGTTTTCAA
*
164938 AACCATATATTATA
1 AACTATATATTATA
164952 CATTTTCAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
98 1 0.01
99 9 0.09
100 7 0.07
101 7 0.07
102 66 0.67
103 2 0.02
104 7 0.07
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (102 bp):
AACTATATATTATATACATTTGTTTAAAAATGTTTTCTAAACAAAATCATATCAAAAATGTTTTC
AAAACCATATATTAAACGTTTTCAAAAATGTTTTCAA
Found at i:164898 original size:12 final size:12
Alignment explanation
Indices: 164861--164904 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 12
164851 ACATTTGTTT
164861 AAAAATGTTTTC
1 AAAAATGTTTTC
164873 TAAACCATATGTTTTC
1 -AAA--A-ATGTTTTC
164889 AAAAATGTTTTC
1 AAAAATGTTTTC
164901 AAAA
1 AAAA
164905 CCATATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.43
13 4 0.14
15 4 0.14
16 8 0.29
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (12 bp):
AAAAATGTTTTC
Found at i:164933 original size:12 final size:12
Alignment explanation
Indices: 164881--164938 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
164871 TCTAAACCAT
*
164881 ATGTTTTCAAAA
1 ATGTTTTCAAAC
164893 ATGTTTTCAAAACC
1 ATGTTTTC-AAA-C
* *
164907 ATATATT-AAAC
1 ATGTTTTCAAAC
164918 --GTTTTCAAAC
1 ATGTTTTCAAAC
164928 ATGTTTTCAAA
1 ATGTTTTCAAA
164939 ACCATATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
9 3 0.08
10 4 0.11
11 1 0.03
12 20 0.56
13 3 0.08
14 5 0.14
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAC
Found at i:165611 original size:73 final size:73
Alignment explanation
Indices: 165520--165949 Score: 662
Period size: 73 Copynumber: 5.9 Consensus size: 73
165510 GGCAATCTTC
* *
165520 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTT
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTC
* *
165585 AAAACTTT
66 GAAACTGT
* * *
165593 TGGGCACGATATCATTCGTTGTGAAGTTGAAATCATGGGTGACTCATTCATCGTGAAGTTAAGTC
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTC
* *
165658 CAAAGTGT
66 GAAACTGT
* * * *
165666 TGGGCACGATATCCTTCATTGTGAAGTTGAAATCGTGGATGACTCATTCGTCATGAAGTTAAGTT
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTC
*
165731 GAAACTTT
66 GAAACTGT
*
165739 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCCTTCGTCGTGAAGTTAAGTC
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTC
165804 GAAACTGT
66 GAAACTGT
* * * *
165812 TGGGCATGATATCATTCGTTGTGAAGTTGAAATCATGGGTGACTCCTTCGTCGTGAAGTTAAGTC
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTC
165877 GAAACTGT
66 GAAACTGT
* * *
165885 TGGGCATGATATCCTTCGTTGTGAAGTTAAAATCGTGGGTGACTCATTCGTCGTGAAGTTGAGTC
1 TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTC
165950 TCAATTGAAT
Statistics
Matches: 325, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 325 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (73 bp):
TGGGCACGATATCCTTCGTTGTGAAGTTGAAATCGTGGGTGACTCATTCGTCGTGAAGTTAAGTC
GAAACTGT
Found at i:165764 original size:41 final size:41
Alignment explanation
Indices: 165719--165914 Score: 149
Period size: 41 Copynumber: 5.2 Consensus size: 41
165709 TCATTCGTCA
* *
165719 TGAAGTTAAGTTGAAACTTTTGGGCACGATATCCTTCGTTG
1 TGAAGTTAAGTTGAAACTCTTGGGCATGATATCCTTCGTTG
* * *
165760 T---G--AAGTTGAAA-TCGTGGG--TGA-CTCCTTCGTCG
1 TGAAGTTAAGTTGAAACTCTTGGGCATGATATCCTTCGTTG
* * *
165792 TGAAGTTAAGTCGAAACTGTTGGGCATGATATCATTCGTTG
1 TGAAGTTAAGTTGAAACTCTTGGGCATGATATCCTTCGTTG
* * *
165833 T---G--AAGTTGAAA-TCATGGG--TGA-CTCCTTCGTCG
1 TGAAGTTAAGTTGAAACTCTTGGGCATGATATCCTTCGTTG
* *
165865 TGAAGTTAAGTCGAAACTGTTGGGCATGATATCCTTCGTTG
1 TGAAGTTAAGTTGAAACTCTTGGGCATGATATCCTTCGTTG
165906 TGAAGTTAA
1 TGAAGTTAA
165915 AATCGTGGGT
Statistics
Matches: 115, Mismatches: 22, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
32 19 0.17
33 5 0.04
35 12 0.10
36 17 0.15
37 16 0.14
38 12 0.10
40 6 0.05
41 28 0.24
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (41 bp):
TGAAGTTAAGTTGAAACTCTTGGGCATGATATCCTTCGTTG
Found at i:169750 original size:16 final size:16
Alignment explanation
Indices: 169729--169762 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
169719 TCTCCATATC
*
169729 ATCTGGATGTATTTTG
1 ATCTGGATGTATCTTG
*
169745 ATCTGGTTGTATCTTG
1 ATCTGGATGTATCTTG
169761 AT
1 AT
169763 AATCTGTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.50
Consensus pattern (16 bp):
ATCTGGATGTATCTTG
Found at i:172179 original size:21 final size:21
Alignment explanation
Indices: 172154--172215 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
172144 CCATAAACAG
*
172154 TGCTACAATGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
172175 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
* *
172196 TACTACAGTGCACCGATGCA
1 TGCTACAGTGCATCGATGCA
172216 CTAAAATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:177538 original size:38 final size:40
Alignment explanation
Indices: 177487--177566 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
177477 AGTGAGATGG
*
177487 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
177525 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
177565 TA
1 TA
177567 TATTTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:183227 original size:18 final size:18
Alignment explanation
Indices: 183204--183239 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
183194 TCAACATCAA
*
183204 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
183222 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
183240 GGATTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:183990 original size:37 final size:37
Alignment explanation
Indices: 183941--184028 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 37
183931 ACTAATTTCA
* * *
183941 TCTCTCTGTGAGACAATTTCTT-TTAGAACTAAGTTTTG
1 TCTCTCT-TGAGACAATTT-TTCTTAAAACAAAATTTTG
*
183979 TCTCTCTTGAGACAGTTTTTCTTAAAACAAAATTTTG
1 TCTCTCTTGAGACAATTTTTCTTAAAACAAAATTTTG
*
184016 TCTCCCTTGAGAC
1 TCTCTCTTGAGAC
184029 CGTTTCTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 2 0.05
37 35 0.80
38 7 0.16
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (37 bp):
TCTCTCTTGAGACAATTTTTCTTAAAACAAAATTTTG
Found at i:184044 original size:37 final size:37
Alignment explanation
Indices: 183974--184045 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
183964 TAGAACTAAG
* * *
183974 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* *
184011 TTTTGTCTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
184046 CAGATATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:185097 original size:323 final size:318
Alignment explanation
Indices: 184644--185505 Score: 1169
Period size: 323 Copynumber: 2.7 Consensus size: 318
184634 ATATCACACC
* * * * * *
184644 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTTGTTGTCAACAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAC-ACTGGTTGTCAACAAAACAATTTCC
* * *
184708 TAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATAATGGACTCGAGACAACACAAGTT
65 CAGATT--TT-AGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTT
* * *
184773 CAACTTCACAACGAAGGGACGACTGGTTATCAACAAACCATTACCCAATTTCAGAGCCAATTTCA
127 CAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCATT-CCCAGTTTCAGAGCCAATTTCA
* *
184838 ACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
191 ACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCT
* * * * *
184903 GGTTGTCAATAAACCACTTT-TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATAT
256 GGTTGTCAACAAA-CAATTTCCCA--AT--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
184967 TGG
316 TGG
184970 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACATCTGGTTGTCAACAAAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACA-CTGGTTGTCAACAAAACAATTTCC
* * *
185035 CAG-TTTTAGAGTCAATTTCAACTCCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAA
65 CAGATTTTAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTTCAA
**
185099 CTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTCAGTTTCAGAGCCAATTTCAACT
130 CTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCA-TTCCCAGTTTCAGAGCCAATTTCAACT
185164 TCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGT
194 TCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGT
185229 TGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
259 TGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * **
185289 ACTCAATACGCCACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAAC-AGTCAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAC-ACTGGTTGTCAACAAAACAATTTCC
* * * * *
185353 C-GATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGAACTCGAGACAATACAAGCTCAA
65 CAGATTTTAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTTCAA
* * * * *
185417 CTTCACAGCGAAGGGGCGGCCGGCTGTCAACAAACAATTTCCCAGTTTCAGAGCCAATTTCAACT
130 CTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCA-TTCCCAGTTTCAGAGCCAATTTCAACT
*
185482 TCAC-GACGGAGGATATTGGACTCA
194 TCACAG-CGAAGGATATTGGACTCA
185506 GAACAATACT
Statistics
Matches: 482, Mismatches: 47, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
317 2 0.00
318 141 0.29
319 84 0.17
321 1 0.00
322 5 0.01
323 184 0.38
324 4 0.01
325 1 0.00
326 58 0.12
327 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (318 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACACTGGTTGTCAACAAAACAATTTCCC
AGATTTTAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGTTCAAC
TTCACAACGAAGGGACGGCTGGTTGTCAACAAACCATTCCCAGTTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTG
TCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:185514 original size:106 final size:106
Alignment explanation
Indices: 184644--185505 Score: 1149
Period size: 106 Copynumber: 8.0 Consensus size: 106
184634 ATATCACACC
* * * * * *
184644 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGACTTGTTGTCAACAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
* * * *
184708 TAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATAATGG
65 CAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
184754 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTATCAACAAACCATTACCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
184819 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
184860 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
*
184924 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
**
184970 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACATCTGGTTGTCAACAAAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
* * *
185035 CAGTTTTAGAGTCAATTTCAACTCCACAGCGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
185077 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
185141 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
185183 ACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
185248 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * **
185289 ACTCAATACGCCACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAACAGTCAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
185354 -GATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGA
66 AG-TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
185395 ACTCGAGACAATACAAGCTCAACTTCACAGCGAAGGGGCGGCCGGCTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
*
185460 AGTTTCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
185501 ACTCA
1 ACTCA
185506 GAACAATACT
Statistics
Matches: 672, Mismatches: 67, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
105 6 0.01
106 413 0.61
107 96 0.14
108 2 0.00
109 4 0.01
110 145 0.22
111 6 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:186571 original size:17 final size:18
Alignment explanation
Indices: 186549--186587 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
186539 TATGGATCTT
* *
186549 TTATTCAT-TTATTTTTA
1 TTATTCATGTAATTATTA
186566 TTATTCATGTAATTATTA
1 TTATTCATGTAATTATTA
186584 TTAT
1 TTAT
186588 ACGTATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (18 bp):
TTATTCATGTAATTATTA
Found at i:189991 original size:12 final size:12
Alignment explanation
Indices: 189974--190003 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
189964 AGAGAAGAAG
189974 AAAAAAAGTTTA
1 AAAAAAAGTTTA
189986 AAAAAAAGTTTA
1 AAAAAAAGTTTA
189998 AAAAAA
1 AAAAAA
190004 TAAAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (12 bp):
AAAAAAAGTTTA
Found at i:190063 original size:41 final size:42
Alignment explanation
Indices: 190015--190119 Score: 106
Period size: 44 Copynumber: 2.5 Consensus size: 42
190005 AAAATAAGAC
*
190015 GAAATAAAATAAAGAAAATA-AAGAAAATATT-AAATTTAAAA
1 GAAATAAAA-AAAGAAAAAAGAAGAAAATATTAAAATTTAAAA
* * * *
190056 TAAATAAATAAAAAATAAAAAAGAAGAAAATGTTAAAATTTGAAA
1 GAAAT--A-AAAAAAGAAAAAAGAAGAAAATATTAAAATTTAAAA
*
190101 GAAATAAAAATAGAAAAAA
1 GAAATAAAAAAAGAAAAAA
190120 ACATGTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
41 4 0.08
42 11 0.22
43 10 0.20
44 13 0.25
45 13 0.25
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (42 bp):
GAAATAAAAAAAGAAAAAAGAAGAAAATATTAAAATTTAAAA
Found at i:191394 original size:9 final size:9
Alignment explanation
Indices: 191381--191526 Score: 61
Period size: 9 Copynumber: 17.0 Consensus size: 9
191371 GAAAAAAATA
191381 AATATA-AT
1 AATATATAT
191389 -ATATATAT
1 AATATATAT
191397 AATATATAT
1 AATATATAT
191406 -ATA-AGTAT
1 AATATA-TAT
191414 AATA-ATAAT
1 AATATAT-AT
191423 AATA-ATAAT
1 AATATAT-AT
191432 AATA-ATAAT
1 AATATAT-AT
191441 AATA-ATATT
1 AATATATA-T
191450 AATA-ATAAT
1 AATATAT-AT
191459 AATA-A-AT
1 AATATATAT
*
191466 AATATAAAT
1 AATATATAT
191475 -ATAATATAT
1 AAT-ATATAT
*
191484 AATGTA-AT
1 AATATATAT
* *
191492 GAAAATAAAT
1 -AATATATAT
*
191502 AA-CTATAT
1 AATATATAT
*
191510 AA-CTATAT
1 AATATATAT
191518 AATATATAT
1 AATATATAT
191527 TATGTTTTCA
Statistics
Matches: 117, Mismatches: 7, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
7 12 0.10
8 29 0.25
9 71 0.61
10 5 0.04
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (9 bp):
AATATATAT
Found at i:191407 original size:15 final size:13
Alignment explanation
Indices: 191377--191525 Score: 110
Period size: 12 Copynumber: 11.8 Consensus size: 13
191367 ACATGAAAAA
191377 AATAA-ATATAAT
1 AATAATATATAAT
191389 -AT-ATATATAAT
1 AATAATATATAAT
191400 ATATATATAAGTATAAT
1 A-ATA-AT-A-TATAAT
191417 AATAATA-ATAAT
1 AATAATATATAAT
191429 AATAATA-ATAAT
1 AATAATATATAAT
191441 AATAATAT-TAAT
1 AATAATATATAAT
191453 AATAATA-AT-A-
1 AATAATATATAAT
191463 AATAATATA-AAT
1 AATAATATATAAT
191475 -ATAATATATAAT
1 AATAATATATAAT
*
191487 -GTAATGA-A-AAT
1 AATAAT-ATATAAT
191498 AAATAACTATATAACT
1 -AATAA-TATATAA-T
191514 ATATAATATATA
1 A-ATAATATATA
191526 TTATGTTTTC
Statistics
Matches: 114, Mismatches: 2, Indels: 39
0.74 0.01 0.25
Matches are distributed among these distances:
10 8 0.07
11 23 0.20
12 44 0.39
13 7 0.06
14 3 0.03
15 13 0.11
16 9 0.08
17 7 0.06
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:191421 original size:6 final size:6
Alignment explanation
Indices: 191384--191486 Score: 104
Period size: 6 Copynumber: 16.3 Consensus size: 6
191374 AAAAATAAAT
191384 ATAATA TATATATA ATATATA TATAAGT- ATAATA ATAATA ATAATA ATAATA
1 ATAATA -ATA-ATA ATA-ATA -ATAA-TA ATAATA ATAATA ATAATA ATAATA
*
191436 ATAATA ATAATA TTAATA ATAATA ATAAATA AT-ATA A-ATATA ATATATA
1 ATAATA ATAATA ATAATA ATAATA AT-AATA ATAATA ATA-ATA ATA-ATA
191485 AT
1 AT
191487 GTAATGAAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 16
0.83 0.02 0.15
Matches are distributed among these distances:
5 5 0.06
6 50 0.58
7 24 0.28
8 7 0.08
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (6 bp):
ATAATA
Found at i:191603 original size:64 final size:65
Alignment explanation
Indices: 191519--191673 Score: 162
Period size: 64 Copynumber: 2.4 Consensus size: 65
191509 TAACTATATA
* * *
191519 ATATA-TAT-TATGTTTTCAAAAATCGTTTAAAAAAACCATATATATAT-ATATATGTTTTCAAA
1 ATATATTATATATG-TTTCAAAAATCGTTT-AAAAAACCATACAT-TATCAAAAATGTTTTCAAA
191581 A-C
63 ACC
** *
191583 -TATATTATATATGTTTCAAAAA-CGTTTTCAAAACCATACATTTTCAAAAATGTTTTCAAAACC
1 ATATATTATATATGTTTCAAAAATCGTTTAAAAAACCATACATTATCAAAAATGTTTTCAAAACC
* *
191646 ATATATTATATGTTTTTCAAAAAT-GTTT
1 ATATATTATATATGTTTCAAAAATCGTTT
191674 TCAAAACTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
61 2 0.03
62 25 0.32
63 10 0.13
64 36 0.47
65 4 0.05
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (65 bp):
ATATATTATATATGTTTCAAAAATCGTTTAAAAAACCATACATTATCAAAAATGTTTTCAAAACC
Found at i:191605 original size:23 final size:24
Alignment explanation
Indices: 191559--191603 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
191549 AAAAACCATA
191559 TATATATATATATGTTTTCAAAAC
1 TATATATATATATGTTTTCAAAAC
191583 TATAT-TATATATG-TTTCAAAA
1 TATATATATATATGTTTTCAAAA
191604 ACGTTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (24 bp):
TATATATATATATGTTTTCAAAAC
Found at i:191669 original size:36 final size:36
Alignment explanation
Indices: 191623--191793 Score: 207
Period size: 36 Copynumber: 4.9 Consensus size: 36
191613 AAACCATACA
191623 TTTTCAAAAATGTTTTCAAAACCATATATTATATGT
1 TTTTCAAAAATGTTTTCAAAACCATATATTATATGT
*
191659 TTTTCAAAAATGTTTTCAAAACTATATATTATATACGT
1 TTTTCAAAAATGTTTTCAAAACCATATATTATAT--GT
* *
191697 TTTTTAAAAATGTTTTCAAAACC----A-TACA---
1 TTTTCAAAAATGTTTTCAAAACCATATATTATATGT
* *
191725 TTTTCAAAAATATTTTCAAAACCATATATTATACGT
1 TTTTCAAAAATGTTTTCAAAACCATATATTATATGT
*
191761 TTTT-AAAAATGTTTTCAAAACTATATATTATAT
1 TTTTCAAAAATGTTTTCAAAACCATATATTATAT
191794 CTATACTAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
28 21 0.18
32 1 0.01
33 6 0.05
34 1 0.01
35 26 0.23
36 37 0.32
38 23 0.20
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTCAAAAATGTTTTCAAAACCATATATTATATGT
Found at i:191725 original size:102 final size:99
Alignment explanation
Indices: 191570--191793 Score: 362
Period size: 102 Copynumber: 2.3 Consensus size: 99
191560 ATATATATAT
191570 ATGTTTTCAAAAC--TATATTATATATGTTTCAAAAACGTTTTCAAAACCATACATTTTCAAAAA
1 ATGTTTTCAAAACTATATATTATATATGTTTCAAAAACGTTTTCAAAACCATACATTTTCAAAAA
* *
191633 TGTTTTCAAAACCATATATTATATGTTTTTCAAAA
66 TATTTTCAAAACCATATATTATACGTTTTT-AAAA
* * *
191668 ATGTTTTCAAAACTATATATTATATACGTTTTTTAAAAATGTTTTCAAAACCATACATTTTCAAA
1 ATGTTTTCAAAACTATATATTATATA--TGTTTCAAAAACGTTTTCAAAACCATACATTTTCAAA
191733 AATATTTTCAAAACCATATATTATACGTTTTTAAAA
64 AATATTTTCAAAACCATATATTATACGTTTTTAAAA
191769 ATGTTTTCAAAACTATATATTATAT
1 ATGTTTTCAAAACTATATATTATAT
191794 CTATACTAAA
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
98 13 0.11
100 11 0.09
101 29 0.25
102 64 0.55
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.42
Consensus pattern (99 bp):
ATGTTTTCAAAACTATATATTATATATGTTTCAAAAACGTTTTCAAAACCATACATTTTCAAAAA
TATTTTCAAAACCATATATTATACGTTTTTAAAA
Found at i:191733 original size:28 final size:28
Alignment explanation
Indices: 191697--191750 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
191687 TTATATACGT
* *
191697 TTTTTAAAAATGTTTTCAAAACCATACA
1 TTTTCAAAAATATTTTCAAAACCATACA
191725 TTTTCAAAAATATTTTCAAAACCATA
1 TTTTCAAAAATATTTTCAAAACCATA
191751 TATTATACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (28 bp):
TTTTCAAAAATATTTTCAAAACCATACA
Found at i:191735 original size:66 final size:63
Alignment explanation
Indices: 191659--191781 Score: 201
Period size: 66 Copynumber: 1.9 Consensus size: 63
191649 TATTATATGT
* *
191659 TTTTCAAAAATGTTTTCAAAACTATATATTATATACGTTTTTTAAAAATGTTTTCAAAACCATAC
1 TTTTCAAAAATATTTTCAAAACCATATA-T-TATACG-TTTTTAAAAATGTTTTCAAAACCATAC
191724 A
63 A
191725 TTTTCAAAAATATTTTCAAAACCATATATTATACGTTTTTAAAAATGTTTTCAAAAC
1 TTTTCAAAAATATTTTCAAAACCATATATTATACGTTTTTAAAAATGTTTTCAAAAC
191782 TATATATTAT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 22 0.40
64 6 0.11
65 1 0.02
66 26 0.47
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.42
Consensus pattern (63 bp):
TTTTCAAAAATATTTTCAAAACCATATATTATACGTTTTTAAAAATGTTTTCAAAACCATACA
Found at i:191776 original size:35 final size:35
Alignment explanation
Indices: 191720--191792 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
191710 TTTCAAAACC
191720 ATACATTTTCAAAAATATTTTCAAAACCATATATT
1 ATACATTTTCAAAAATATTTTCAAAACCATATATT
* * * *
191755 ATACGTTTTTAAAAATGTTTTCAAAACTATATATT
1 ATACATTTTCAAAAATATTTTCAAAACCATATATT
191790 ATA
1 ATA
191793 TCTATACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (35 bp):
ATACATTTTCAAAAATATTTTCAAAACCATATATT
Found at i:194794 original size:25 final size:25
Alignment explanation
Indices: 194766--194826 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 25
194756 TTGTAGGAAT
194766 TATAGAGATGATTTGTTACCATTCC
1 TATAGAGATGATTTGTTACCATTCC
*
194791 TATAGAGATATGGTTTGTTACCATTCC
1 TATAGAG--ATGATTTGTTACCATTCC
194818 TATAGAGAT
1 TATAGAGAT
194827 ATGATTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 9 0.27
27 24 0.73
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (25 bp):
TATAGAGATGATTTGTTACCATTCC
Found at i:194812 original size:27 final size:27
Alignment explanation
Indices: 194777--194829 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
194767 ATAGAGATGA
194777 TTTGTTACCATTCCTATAGAGATATGG
1 TTTGTTACCATTCCTATAGAGATATGG
194804 TTTGTTACCATTCCTATAGAGATATG
1 TTTGTTACCATTCCTATAGAGATATG
194830 ATTTTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (27 bp):
TTTGTTACCATTCCTATAGAGATATGG
Found at i:198570 original size:27 final size:27
Alignment explanation
Indices: 198528--198595 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
198518 GTGTAGGAAT
198528 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
198553 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
198580 TATAGAGATATGATTT
1 TATAGAGATATGATTT
198596 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:203649 original size:2 final size:2
Alignment explanation
Indices: 203642--203687 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
203632 TGTTTGTAGT
203642 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
203684 TA TA
1 TA TA
203688 GTGTTAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:205028 original size:12 final size:13
Alignment explanation
Indices: 205011--205043 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
205001 ACCCACTCTA
205011 ATAATAATAATT-
1 ATAATAATAATTC
205023 ATAATAATAATTC
1 ATAATAATAATTC
205036 ATAA-AATA
1 ATAATAATA
205044 TTGTTATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAATAATTC
Found at i:205268 original size:2 final size:2
Alignment explanation
Indices: 205261--205285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
205251 AATAGAATTA
205261 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
205286 AGAACAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:206086 original size:90 final size:90
Alignment explanation
Indices: 205953--206132 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
205943 TAAAAATATT
205953 TATAAGTATTTAGTTAACTTAATTCAGTTATCTAGTTAATTTCATATAAATGTTTAATTTAATAA
1 TATAAGTATTTAGTTAACTTAATTCAGTTATCTAGTTAATTTCATATAAATGTTTAATTTAATAA
206018 TAATTTTATAAATAAATATTAAAAA
66 TAATTTTATAAATAAATATTAAAAA
*
206043 TATAATTATTTAGTTAACTTAATTCAGTTATCTAGTTAATTTCATATAAATGTTTAATTTAATAA
1 TATAAGTATTTAGTTAACTTAATTCAGTTATCTAGTTAATTTCATATAAATGTTTAATTTAATAA
206108 TAATTTTATAAATAAATATTAAAAA
66 TAATTTTATAAATAAATATTAAAAA
206133 GAAAAGTTAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (90 bp):
TATAAGTATTTAGTTAACTTAATTCAGTTATCTAGTTAATTTCATATAAATGTTTAATTTAATAA
TAATTTTATAAATAAATATTAAAAA
Found at i:208140 original size:17 final size:18
Alignment explanation
Indices: 208112--208145 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
208102 AAATTTCTCT
*
208112 AAATATATTATTTTAATA
1 AAATATATTATTCTAATA
208130 AAATATA-TATTCTAAT
1 AAATATATTATTCTAAT
208146 TTTTATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATATTATTCTAATA
Found at i:214808 original size:60 final size:60
Alignment explanation
Indices: 214686--214812 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
214676 TGCATTTTTT
* * * * *
214686 TAAATTAATCCTTAAATTTTTGAATATTCTAACTTCATCCTCAAACTACAATTCTCATTC
1 TAAATTAATCCTTAAACTTTTAAACATTCTAACTTCATCCTCAAACCACAATCCTCATTC
* * **
214746 TAAATTAATCCTTATACTTTTAAACATTCTAATTTCATCC-CTAAACCATTATCCT-ATGTC
1 TAAATTAATCCTTAAACTTTTAAACATTCTAACTTCATCCTC-AAACCACAATCCTCAT-TC
214806 TAAATTA
1 TAAATTA
214813 GCTTTCATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 3 0.05
60 53 0.95
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (60 bp):
TAAATTAATCCTTAAACTTTTAAACATTCTAACTTCATCCTCAAACCACAATCCTCATTC
Found at i:229472 original size:16 final size:17
Alignment explanation
Indices: 229453--229488 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
229443 ATTTTAATAA
229453 AAAATACA-AAAAAATT
1 AAAATACATAAAAAATT
*
229469 AAAATATATAAAAAATT
1 AAAATACATAAAAAATT
229486 AAA
1 AAA
229489 TTTTTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATACATAAAAAATT
Found at i:231751 original size:29 final size:25
Alignment explanation
Indices: 231698--231771 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 25
231688 TTATTTGGGG
*
231698 TTTTATTT-TTATTATTTTATTTTTA
1 TTTTATTTATTATTA-TATATTTTTA
*
231723 CTATTTCTATTATTATTATATATATTTTA
1 -T-TTTAT-TTATTATTATATAT-TTTTA
231752 TTTTATTTATTATTA-ATATT
1 TTTTATTTATTATTATATATT
231772 ATTACAGGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
24 1 0.02
25 4 0.10
26 10 0.24
27 8 0.20
28 7 0.17
29 11 0.27
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTATTTATTATTATATATTTTTA
Found at i:231978 original size:34 final size:35
Alignment explanation
Indices: 231939--232004 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 35
231929 AGAAACCCTA
*
231939 GGGTTATGATACCTAGGG-CACGCACCGCCGCTAG
1 GGGTTATGATACCTAGGGCCACGCAACGCCGCTAG
231973 GGGTTATGATACCTAGGGCCACGCAACGCCGC
1 GGGTTATGATACCTAGGGCCACGCAACGCCGC
232005 CTCTGTGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.21, C:0.30, G:0.32, T:0.17
Consensus pattern (35 bp):
GGGTTATGATACCTAGGGCCACGCAACGCCGCTAG
Found at i:232630 original size:2 final size:2
Alignment explanation
Indices: 232623--232658 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
232613 CTAAATAATA
232623 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
232659 AGGTAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:233154 original size:19 final size:18
Alignment explanation
Indices: 233121--233170 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
233111 ATATGTTTTT
* *
233121 ATTTTATAATTTTTAATC
1 ATTTTTTAATATTTAATC
* *
233139 ATGTTTTTAATATTTATTT
1 AT-TTTTTAATATTTAATC
233158 ATTTTTTAATATT
1 ATTTTTTAATATT
233171 AAGAAAGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTTTAATATTTAATC
Found at i:233165 original size:18 final size:18
Alignment explanation
Indices: 233118--233170 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
233108 TATATATGTT
* *
233118 TTTATTTTATAATTTTTA
1 TTTATTTTTTAATATTTA
* *
233136 ATCATGTTTTTAATATTTA
1 TTTAT-TTTTTAATATTTA
233155 TTTATTTTTTAATATT
1 TTTATTTTTTAATATT
233171 AAGAAAGGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTTTTTAATATTTA
Found at i:235209 original size:41 final size:42
Alignment explanation
Indices: 235151--235235 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 42
235141 TAGCTTTAGA
*
235151 GAAGTTAGGAGGAAAGTTATCCCCTATACGTAAAGTTTTGTT
1 GAAGTTAGGAGGAAAGTTATCCCATATACGTAAAGTTTTGTT
* * * *
235193 GAAG-TAGGATGAAAGTTGTCTCATATATGTAAAGTTTTGTT
1 GAAGTTAGGAGGAAAGTTATCCCATATACGTAAAGTTTTGTT
235234 GA
1 GA
235236 TGCACCGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (42 bp):
GAAGTTAGGAGGAAAGTTATCCCATATACGTAAAGTTTTGTT
Found at i:235411 original size:42 final size:42
Alignment explanation
Indices: 235352--235435 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
235342 ATTCATACGA
*
235352 GAAGTTAGGAGGAAAGTTATCCCCTATACGTAAAGTTTTGTT
1 GAAGTTAGGAGGAAAGTTATCCCATATACGTAAAGTTTTGTT
* * * *
235394 GAAGTTAGGATGAAAGTTGTCTCATATATGTAAAGTTTTGTT
1 GAAGTTAGGAGGAAAGTTATCCCATATACGTAAAGTTTTGTT
235436 TGATGCACCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (42 bp):
GAAGTTAGGAGGAAAGTTATCCCATATACGTAAAGTTTTGTT
Found at i:235519 original size:205 final size:201
Alignment explanation
Indices: 235149--235554 Score: 767
Period size: 205 Copynumber: 2.0 Consensus size: 201
235139 CTTAGCTTTA
235149 GAGAAGTTAGGAGGAAAGTTATCCCCTATACGTAAAGTTTTGTTGAAGTAGGATGAAAGTTGTCT
1 GAGAAGTTAGGAGGAAAGTTATCCCCTATACGTAAAGTTTTGTTGAAGTAGGATGAAAGTTGTCT
235214 CATATATGTAAAGTTTTGTTGATGCACCGAAACTTGTGTGTTGAATGAAATCTTTTAAGACGATC
66 CATATATGTAAAGTTTTGTTGATGCACCGAAACTTGTGTGTTGAATGAAATCTTTTAAGACGATC
235279 ACTCTTGAGTAACAGCTTTTCATACATGCATTTTCATTTCACATCTTTGCATTTTCATTTTGCAT
131 ACTCTTGAGTAACAGCTTTTCATACATGCATTTTCATTTCACATCTTTGCATTTTCATTTTGCAT
235344 TCATAC
196 TCATAC
235350 GAGAAGTTAGGAGGAAAGTTATCCCCTATACGTAAAGTTTTGTTGAAGTTAGGATGAAAGTTGTC
1 GAGAAGTTAGGAGGAAAGTTATCCCCTATACGTAAAGTTTTGTTGAAG-TAGGATGAAAGTTGTC
*
235415 TCATATATGTAAAGTTTTGTTTGATGCACCGAAACTTTTGTGTTGAATGAAATCTGTTTTAAGAC
65 TCATATATGTAAAGTTTTG-TTGATGCACCGAAACTTGTGTGTTGAATGAAATC--TTTTAAGAC
235480 GATCACTCTTGAGTAACAGCTTTTCATACATGCATTTTCATTTCACATCTTTGCATTTTCATTTT
127 GATCACTCTTGAGTAACAGCTTTTCATACATGCATTTTCATTTCACATCTTTGCATTTTCATTTT
235545 GCATTCATAC
192 GCATTCATAC
235555 TTTTATGTTT
Statistics
Matches: 200, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
201 48 0.24
202 35 0.17
203 33 0.17
205 84 0.42
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (201 bp):
GAGAAGTTAGGAGGAAAGTTATCCCCTATACGTAAAGTTTTGTTGAAGTAGGATGAAAGTTGTCT
CATATATGTAAAGTTTTGTTGATGCACCGAAACTTGTGTGTTGAATGAAATCTTTTAAGACGATC
ACTCTTGAGTAACAGCTTTTCATACATGCATTTTCATTTCACATCTTTGCATTTTCATTTTGCAT
TCATAC
Found at i:235551 original size:27 final size:27
Alignment explanation
Indices: 235512--235690 Score: 64
Period size: 26 Copynumber: 6.4 Consensus size: 27
235502 TTCATACATG
235512 CATTTT-CATTTCACATCTTTGCATTTT
1 CATTTTGCA-TTCACATCTTTGCATTTT
* *
235539 CATTTTGCATTCATA-CTTT-TATGTTT
1 CATTTTGCATTCACATCTTTGCAT-TTT
** * * *
235565 GTTTTTGTATTGCACA-ATTTGCATTCAT
1 CATTTTGCATT-CACATCTTTGCATT-TT
* *
235593 -ATTTTTGTATTTCTACATTTTTTTTGCATTTT
1 CA-TTTTGCA-TTC-ACA--TCT-TTGCATTTT
* * *
235625 CATGTTACATTCACATCTTTGCATTTG
1 CATTTTGCATTCACATCTTTGCATTTT
*** *
235652 CA-TTTGCATTTGTATATTTGCATTTT
1 CATTTTGCATTCACATCTTTGCATTTT
235678 GCATATTTGCATT
1 -CAT-TTTGCATT
235691 TTTCGTATAT
Statistics
Matches: 112, Mismatches: 24, Indels: 30
0.67 0.14 0.18
Matches are distributed among these distances:
25 2 0.02
26 32 0.29
27 30 0.27
28 15 0.13
29 13 0.12
30 3 0.03
31 3 0.03
32 6 0.05
33 8 0.07
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (27 bp):
CATTTTGCATTCACATCTTTGCATTTT
Found at i:235692 original size:15 final size:14
Alignment explanation
Indices: 235642--235691 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
235632 CATTCACATC
235642 TTTGCATTTGC--A
1 TTTGCATTTGCATA
*
235654 TTTGCATTTGTATA
1 TTTGCATTTGCATA
235668 TTTGCATTTTGCATA
1 TTTGCA-TTTGCATA
235683 TTTGCATTT
1 TTTGCATTT
235692 TTCGTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 10 0.30
14 10 0.30
15 13 0.39
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.56
Consensus pattern (14 bp):
TTTGCATTTGCATA
Found at i:235702 original size:17 final size:16
Alignment explanation
Indices: 235660--235709 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 16
235650 TGCATTTGCA
235660 TTTGTATATTTGCA-T
1 TTTGTATATTTGCATT
*
235675 TTTGCATATTTGCATT
1 TTTGTATATTTGCATT
*
235691 TTTCGTATATTTACATT
1 TTT-GTATATTTGCATT
235708 TT
1 TT
235710 CATTCTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 13 0.43
16 4 0.13
17 13 0.43
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (16 bp):
TTTGTATATTTGCATT
Found at i:238622 original size:15 final size:15
Alignment explanation
Indices: 238587--238634 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
238577 AAATTCATCT
238587 AAAAA-GAAAAAA-A
1 AAAAATGAAAAAAGA
**
238600 AACGATGAAAAAAGA
1 AAAAATGAAAAAAGA
*
238615 AAAAATGAAAAATGA
1 AAAAATGAAAAAAGA
238630 AAAAA
1 AAAAA
238635 AAGAGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 3 0.11
14 7 0.25
15 18 0.64
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAATGAAAAAAGA
Found at i:238634 original size:17 final size:17
Alignment explanation
Indices: 238614--238648 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
238604 ATGAAAAAAG
*
238614 AAAAAATGA-AAAATGA
1 AAAAAAAGAGAAAATGA
238630 AAAAAAAGAGAAAATGA
1 AAAAAAAGAGAAAATGA
238647 AA
1 AA
238649 GAAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (17 bp):
AAAAAAAGAGAAAATGA
Found at i:238634 original size:24 final size:24
Alignment explanation
Indices: 238607--238659 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
238597 AAAAACGATG
238607 AAAAAAGAAAAAATGAAA-AATGAA
1 AAAAAAGAAAAAATGAAAGAA-GAA
*
238631 AAAAAAGAGAAAATGAAAGAAGAA
1 AAAAAAGAAAAAATGAAAGAAGAA
238655 AAAAA
1 AAAAA
238660 TATTTGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (24 bp):
AAAAAAGAAAAAATGAAAGAAGAA
Found at i:241023 original size:41 final size:40
Alignment explanation
Indices: 240978--241079 Score: 95
Period size: 41 Copynumber: 2.5 Consensus size: 40
240968 TTTCAACGAG
240978 AAATAGAATGTTGGGGCATTTTGAATGC-CTA-ATTCAAACAA
1 AAATAGAATGTTGGGGCATTTTGAATGCTC-ACA-TC-AACAA
* *
241019 AAATA-ATTCATATGGGGCATTTTGAATGCTCACATCAACAA
1 AAATAGAAT-GT-TGGGGCATTTTGAATGCTCACATCAACAA
241060 AAA-AGAAAATGTTGGGGCAT
1 AAATAG--AATGTTGGGGCAT
241080 GCTGAAAGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
40 3 0.06
41 22 0.44
42 21 0.42
43 4 0.08
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (40 bp):
AAATAGAATGTTGGGGCATTTTGAATGCTCACATCAACAA
Found at i:241192 original size:75 final size:75
Alignment explanation
Indices: 241066--241234 Score: 225
Period size: 75 Copynumber: 2.3 Consensus size: 75
241056 ACAAAAAAGA
* * *
241066 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCATAATCAGAAATATTGACGCATTTTGAACGT
1 AAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAATCAGAAATATTGACACATTTTGAACGT
****
241131 TTGTAT-AAGC
66 ACACATCAA-C
* *
241141 AAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAAT-AGGAATGTTGACACATTTTGAACG
1 AAATGTTGGGGCATGTTGAAAGCCCATTTCAATC-AAAATCAGAAATATTGACACATTTTGAACG
241205 TACACATCAAC
65 TACACATCAAC
241216 AAATGTTGGGGCATGTTGA
1 AAATGTTGGGGCATGTTGA
241235 GCGTCCATAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
75 77 0.93
76 6 0.07
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (75 bp):
AAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAATCAGAAATATTGACACATTTTGAACGT
ACACATCAAC
Found at i:242177 original size:54 final size:54
Alignment explanation
Indices: 242085--242192 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
242075 CTGATCAGAA
* * * *
242085 ATCTGTGCATAAGTCACAGGAAATGACGAATATATTGTCAAATGCTTTACGAAC
1 ATCTGGGCAGAAGCCACAAGAAATGACGAATATATTGTCAAATGCTTTACGAAC
* * * **
242139 ATCTGGGCAGAAGCCACAAGAAATGATGAATGTGTTGTCAAATTTTTTACGAAC
1 ATCTGGGCAGAAGCCACAAGAAATGACGAATATATTGTCAAATGCTTTACGAAC
242193 CAGTGATTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAAGAAATGACGAATATATTGTCAAATGCTTTACGAAC
Found at i:242575 original size:20 final size:22
Alignment explanation
Indices: 242550--242604 Score: 87
Period size: 20 Copynumber: 2.6 Consensus size: 22
242540 ACATCTACAT
242550 TCTTCAAAGATGATAG-TT-TC
1 TCTTCAAAGATGATAGATTCTC
242570 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
242592 TTTTCAAAGATGA
1 TCTTCAAAGATGA
242605 AATCTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 16 0.50
21 2 0.06
22 14 0.44
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:243390 original size:36 final size:36
Alignment explanation
Indices: 243349--243464 Score: 124
Period size: 36 Copynumber: 3.2 Consensus size: 36
243339 ATGTATCTTA
243349 CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
1 CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
*** * ** * *
243385 CTTGAGACAATTTTACTCGAAACAACAATTTATCTCA
1 CTTGAGATTGTTTTTCTTAAAACAA-AATTTGTCTCG
* * *
243422 CTTGAGATTGTTTTTCTTAAAATAAGATTCGTCTCG
1 CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
243458 CTTGAGA
1 CTTGAGA
243465 CAGTTTCACT
Statistics
Matches: 60, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
36 33 0.55
37 27 0.45
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (36 bp):
CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
Found at i:243461 original size:73 final size:73
Alignment explanation
Indices: 243342--243488 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 73
243332 AATAGTAATG
* * * *
243342 TATCTTACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAATTTTACTCGAAA
1 TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTAGAAA
*
243407 CAACAATT
66 CAAAAATT
* * *
243415 TATCTCACTTGAGATTGTTTTTCTTAAAATAAGATTCGTCTCGCTTGAGACAGTTTCACTAGAAA
1 TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTAGAAA
243480 CAAAAATT
66 CAAAAATT
243488 T
1 T
243489 CCGTCACTCG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (73 bp):
TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTAGAAA
CAAAAATT
Found at i:243706 original size:20 final size:20
Alignment explanation
Indices: 243644--243707 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
243634 TTCAGAGAAA
243644 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
243664 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
243683 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
243703 GTTCA
1 GTTCA
243708 ACCTTTAGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:243839 original size:129 final size:124
Alignment explanation
Indices: 243510--243955 Score: 567
Period size: 122 Copynumber: 3.6 Consensus size: 124
243500 TGGATCAACA
* * **
243510 TTTCCAAAGGAAGTTCATAATGAGAAGAACCCATCTGAAGA-AGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAGAAGAAGAAGTTCATAATGAGA
* * * * *
243574 AGAACTTGGTCAACCTTTTGTTCGACTCTATCATAGAAGGAGATAGATCATCATACACT
66 AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAAGAGATAGATCAGCATACACT
243633 TTT-CAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAG-GAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAGAAGAAGAAGTTCATAATGAGA
* * *
243696 AGAACTTGTTCAACCTTTAGCTAGAATCTATCACAGAAAGAGATAGATCAGCATACACT
66 AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAAGAGATAGATCAGCATACACT
243755 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAGGAAGAAGAAGTTCATAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG-A-A-G-AGA-GAAGAAGAAGTTCATAA
* *
243820 TGAGAAGAACTTGTTCAACCTTTTGCTCGACGCTATCACAG-AAGAAGATAGATTAGCAT-CA--
61 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAAG-AGATAGATCAGCATACACT
* * *
243881 TTTCCAGAGAGAGTTCATAATAAGAAG-A---ATCTGAAGAGGGAGAAGAA-AA-TCCATAATGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA--GAGAAGAAGAAGTTCATAATGA
*
243940 GAAGAATTTGTTCAAC
64 GAAGAACTTGTTCAAC
243956 ATTGCCTTAA
Statistics
Matches: 291, Mismatches: 21, Indels: 28
0.86 0.06 0.08
Matches are distributed among these distances:
117 24 0.08
118 3 0.01
119 7 0.02
120 3 0.01
121 1 0.00
122 114 0.39
123 36 0.12
124 1 0.00
125 2 0.01
126 26 0.09
127 2 0.01
128 5 0.02
129 67 0.23
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (124 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAAGAGATAGATCAGCATACACT
Found at i:244382 original size:3 final size:3
Alignment explanation
Indices: 244357--244396 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
244347 ATTTTTAATT
*
244357 TTA TTA TT- TTA TTTA TTA CTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
244397 AGGCCTAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:245617 original size:26 final size:26
Alignment explanation
Indices: 245588--245649 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
245578 TTTACTTTCA
*
245588 TTTATTTTTA-ACTATAAGTTTTACTT
1 TTTATTTTTATACTAT-AGTTTTAATT
*
245614 TTTATTTTAATACTATAGTTTTAATT
1 TTTATTTTTATACTATAGTTTTAATT
*
245640 TTTTTTTTTA
1 TTTATTTTTA
245650 GTCACTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTATTTTTATACTATAGTTTTAATT
Found at i:245709 original size:12 final size:12
Alignment explanation
Indices: 245692--245724 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
245682 TTTAAATTTC
245692 AATATGTTTAAT
1 AATATGTTTAAT
245704 AATATGTTTAAT
1 AATATGTTTAAT
*
245716 TATAT-TTTA
1 AATATGTTTA
245725 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (12 bp):
AATATGTTTAAT
Found at i:248190 original size:189 final size:189
Alignment explanation
Indices: 247870--248252 Score: 757
Period size: 189 Copynumber: 2.0 Consensus size: 189
247860 CTTTAAACAT
247870 ATTAAAACAAACATTATCAATAACTATGAAAAGGAATGAGTTAATTATTAAAATTTATTTGATTC
1 ATTAAAACAAACATTATCAATAACTATGAAAAGGAATGAGTTAATTATTAAAATTTATTTGATTC
247935 TTTTTAGCTGTTATTATTTTAATTGTTTTGTGACAATCTTGTATACGATGATATTATACATTAAG
66 TTTTTAGCTGTTATTATTTTAATTGTTTTGTGACAATCTTGTATACGATGATATTATACATTAAG
248000 CTGTCAAATTTTAAAATTAAATAGTATTAAATTTTTTACTGTTTCATTTTTAAAAAAAA
131 CTGTCAAATTTTAAAATTAAATAGTATTAAATTTTTTACTGTTTCATTTTTAAAAAAAA
248059 ATTAAAACAAACATTATCAATAACTATGAAAAGGAATGAGTTAATTATTAAAATTTATTTGATTC
1 ATTAAAACAAACATTATCAATAACTATGAAAAGGAATGAGTTAATTATTAAAATTTATTTGATTC
248124 TTTTTAGCTGTTATTATTTTAATTGTTTTGTGACAATCTTGTATACGATGATATTATACATTAAG
66 TTTTTAGCTGTTATTATTTTAATTGTTTTGTGACAATCTTGTATACGATGATATTATACATTAAG
248189 CTGTCAAATTTTAAAATTAAATAGTATTAAATTTTTTACTGTTTCATTTTTAAAAAAAA
131 CTGTCAAATTTTAAAATTAAATAGTATTAAATTTTTTACTGTTTCATTTTTAAAAAAAA
*
248248 TTTAA
1 ATTAA
248253 CCTCAGAACC
Statistics
Matches: 193, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 193 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (189 bp):
ATTAAAACAAACATTATCAATAACTATGAAAAGGAATGAGTTAATTATTAAAATTTATTTGATTC
TTTTTAGCTGTTATTATTTTAATTGTTTTGTGACAATCTTGTATACGATGATATTATACATTAAG
CTGTCAAATTTTAAAATTAAATAGTATTAAATTTTTTACTGTTTCATTTTTAAAAAAAA
Found at i:255107 original size:40 final size:40
Alignment explanation
Indices: 254999--255116 Score: 192
Period size: 40 Copynumber: 3.0 Consensus size: 40
254989 ACCGTAGTGC
254999 TACACATAAGGTCGTGCCCACCATATACACCGAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCG-AAGTGTAT
255040 TACACATAA-G--GT--CCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
255075 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
255115 TA
1 TA
255117 TAAACCTGCA
Statistics
Matches: 72, Mismatches: 0, Indels: 11
0.87 0.00 0.13
Matches are distributed among these distances:
35 17 0.24
36 16 0.22
38 4 0.06
40 26 0.36
41 9 0.12
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:255494 original size:37 final size:36
Alignment explanation
Indices: 255356--255611 Score: 205
Period size: 37 Copynumber: 6.9 Consensus size: 36
255346 TTTTTTTATT
* *
255356 TATATATTATATAATTTTGAAAACATTTTG-AAA-A
1 TATATAATATATAATTTTAAAAACATTTTGAAAAGA
* * * * *
255390 TATATGATATATAGTTTTTAAAACATTTTAAAAACA
1 TATATAATATATAATTTTAAAAACATTTTGAAAAGA
* * *
255426 TTTATATATTATATAGTTTT-AAAACGTTTTTGAAAAGA
1 --TATATAATATATAATTTTAAAAAC-ATTTTGAAAAGA
* * *
255464 AATATAATATATAATTTTCAAAACATTTTTGAAAATA
1 TATATAATATATAATTTTAAAAACA-TTTTGAAAAGA
* * * * *
255501 TATATATTATATAGTTTTTAAAACGTTTTGAAAATTAA
1 TATATAATATATAATTTTAAAAACATTTTGAAAA--GA
255539 TATATAATATATAATTTTTTGAAAAACATTTTG-AAAGCA
1 TATATAATATATAA--TTTT-AAAAACATTTTGAAAAG-A
* * *
255578 TATATAATATGTATTTTTAAAAACATTTTTAAAA
1 TATATAATATATAATTTTAAAAACATTTTGAAAA
255612 TTATGGTTTT
Statistics
Matches: 179, Mismatches: 29, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
34 25 0.14
35 3 0.02
36 36 0.20
37 47 0.26
38 38 0.21
39 13 0.07
40 7 0.04
41 10 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATAATATATAATTTTAAAAACATTTTGAAAAGA
Found at i:255638 original size:25 final size:27
Alignment explanation
Indices: 255591--255640 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
255581 ATAATATGTA
255591 TTTTTAAAAACATTTTTAAAATTATGG
1 TTTTTAAAAACATTTTTAAAATTATGG
*
255618 TTTTTAAAAA-A-TTTTGAAATTAT
1 TTTTTAAAAACATTTTTAAAATTAT
255641 ATAGTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
27 10 0.45
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (27 bp):
TTTTTAAAAACATTTTTAAAATTATGG
Found at i:255648 original size:26 final size:27
Alignment explanation
Indices: 255591--255654 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
255581 ATAATATGTA
* *
255591 TTTTTAAAAACATTTTTAAAATTATGG
1 TTTTTAAAAACATTTTGAAAATTATAG
*
255618 TTTTTAAAAA-ATTTTGAAATTATATAG
1 TTTTTAAAAACATTTTGAAAAT-TATAG
*
255645 TTTTTTAAAA
1 TTTTTAAAAA
255655 TGTTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (27 bp):
TTTTTAAAAACATTTTGAAAATTATAG
Found at i:255742 original size:3 final size:3
Alignment explanation
Indices: 255730--255789 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
255720 GTTTTTATAT
* *
255730 TTA TTA -TA TTA TTA TTA TTA -TA TTA TTTA TTA TTA TTT TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
255774 CTTA TT- TTA TT- TTA TT
1 -TTA TTA TTA TTA TTA TT
255790 TTTTCCCGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
2 8 0.17
3 34 0.72
4 5 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:255744 original size:11 final size:11
Alignment explanation
Indices: 255730--255766 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
255720 GTTTTTATAT
255730 TTATTATATTA
1 TTATTATATTA
255741 TTATTAT-TATA
1 TTATTATAT-TA
255752 TTATT-TATTA
1 TTATTATATTA
255762 TTATT
1 TTATT
255767 TTTATCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTATATTA
Found at i:255747 original size:14 final size:15
Alignment explanation
Indices: 255730--255765 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
255720 GTTTTTATAT
255730 TTATTATATTA-TTA
1 TTATTATATTATTTA
255744 TTATTATATTATTTA
1 TTATTATATTATTTA
255759 TTATTAT
1 TTATTAT
255766 TTTTATCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTATATTATTTA
Found at i:255762 original size:21 final size:22
Alignment explanation
Indices: 255724--255789 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
255714 TATATAGTTT
*
255724 TTATATTTATTATATTATTATTA
1 TTATACTTATT-TATTATTATTA
*
255747 TTATA-TTATTTATTATTATTT
1 TTATACTTATTTATTATTATTA
255768 TTATCACTTATTTTATT-TTATT
1 TTAT-ACTTA-TTTATTATTATT
255790 TTTTCCCGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
21 14 0.36
22 6 0.15
23 13 0.33
24 6 0.15
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATACTTATTTATTATTATTA
Found at i:255778 original size:23 final size:21
Alignment explanation
Indices: 255711--255792 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 21
255701 TTAAAAATTA
255711 TATTATATAGTTTTTATATTTATT
1 TATTAT-TA-TTTTTATA-TTATT
*
255735 ATATTATTATTATTATATTATT
1 -TATTATTATTTTTATATTATT
255757 TATTATTATTTTTATCACTTATTT
1 TATTATTATTTTTAT-A-TTA-TT
255781 TATT-TTATTTTT
1 TATTATTATTTTT
255793 TCCCGTTTCA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
21 14 0.27
22 6 0.12
23 18 0.35
24 8 0.15
25 6 0.12
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.68
Consensus pattern (21 bp):
TATTATTATTTTTATATTATT
Found at i:257204 original size:21 final size:22
Alignment explanation
Indices: 257178--257230 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
257168 TTTATTTTGA
*
257178 TTATTTTTTTTCTTTTCACTT-
1 TTATTTTTTTTCGTTTCACTTG
* **
257199 TTATTTTATTTCGTTTCTTTTG
1 TTATTTTTTTTCGTTTCACTTG
257221 TTATTTTTTT
1 TTATTTTTTT
257231 ATTATTAGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.77
Consensus pattern (22 bp):
TTATTTTTTTTCGTTTCACTTG
Found at i:257280 original size:17 final size:18
Alignment explanation
Indices: 257258--257305 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
257248 CTAATTTTAT
257258 TTATATTTATTTATC-TA
1 TTATATTTATTTATCTTA
* * *
257275 TTATATTAATTTTTCTTT
1 TTATATTTATTTATCTTA
257293 TTCATATTTATTT
1 TT-ATATTTATTT
257306 TTATTGTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 13 0.52
18 3 0.12
19 9 0.36
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATATTTATTTATCTTA
Found at i:259039 original size:19 final size:19
Alignment explanation
Indices: 259015--259060 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
259005 ATTTAGACAT
259015 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
*
259034 TTTGCATTTTTTTATTTTC
1 TTTGCATTTTGTTATTTTC
*
259053 TTTACATT
1 TTTGCATT
259061 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Done.