Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007884.1 Hibiscus syriacus cultivar Beakdansim tig00110264_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: 2814991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:279595 original size:19 final size:19
Alignment explanation
Indices: 279579--279676 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
279569 AAAAATGACT
279579 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
279598 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
279617 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
279631 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
279650 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
279670 ATCGCAA
1 ATCGCAA
279677 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:279708 original size:53 final size:53
Alignment explanation
Indices: 279579--279695 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
279569 AAAAATGACT
279579 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
279631 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
279684 ATCGCAATGCGA
1 ATCGCAATGCGA
279696 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:279713 original size:19 final size:19
Alignment explanation
Indices: 279685--279906 Score: 241
Period size: 19 Copynumber: 12.7 Consensus size: 19
279675 AACGAGAGAA
*
279685 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
279704 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
279723 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
279739 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
279756 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
279775 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
279791 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
279808 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
279827 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
279843 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
279860 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
279878 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
279894 TCGCATTGCGATT
1 TCGCATTGCGATT
279907 CTCTCGTTGC
Statistics
Matches: 171, Mismatches: 11, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
14 29 0.17
16 22 0.13
17 20 0.12
18 3 0.02
19 86 0.50
20 11 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:279748 original size:52 final size:52
Alignment explanation
Indices: 279691--279878 Score: 358
Period size: 52 Copynumber: 3.6 Consensus size: 52
279681 AGAATCGCAA
279691 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
279743 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
279795 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
279847 TGCGATTTTTATTTCCGCATTGCGATTTTCAT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCAT
279879 GTTGGGATTT
Statistics
Matches: 134, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
52 117 0.87
53 17 0.13
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:279928 original size:33 final size:33
Alignment explanation
Indices: 279709--279920 Score: 225
Period size: 33 Copynumber: 6.2 Consensus size: 33
279699 TCATTTCGCA
279709 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
279742 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
279778 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
279813 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
279846 TTGCGATTTTTATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
279880 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
279913 TTGCGATT
1 TTGCGATT
279921 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 18, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 72 0.49
34 28 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:282237 original size:12 final size:12
Alignment explanation
Indices: 282220--282244 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
282210 TCTTCGGGGA
282220 CTTTTTCTTCTT
1 CTTTTTCTTCTT
282232 CTTTTTCTTCTT
1 CTTTTTCTTCTT
282244 C
1 C
282245 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:282453 original size:24 final size:24
Alignment explanation
Indices: 282419--282465 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
282409 CTGAAACATC
282419 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
282443 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
282466 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:283175 original size:20 final size:20
Alignment explanation
Indices: 283147--283396 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
283137 AAATTTCAGT
* * *
283147 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
283167 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
**
283187 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
283207 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
283227 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
283247 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
283267 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
283287 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
283307 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
283327 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
283347 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
283367 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
283387 GTTGCGATTT
1 GTTGCGATTT
283397 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:283413 original size:21 final size:21
Alignment explanation
Indices: 283383--283465 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
283373 ATTTTCATAT
*
283383 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
283404 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
283425 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
283446 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
283466 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:283456 original size:42 final size:43
Alignment explanation
Indices: 283363--283461 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
283353 ATTTATGTGT
* *
283363 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
283404 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
283446 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
283462 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:284991 original size:83 final size:84
Alignment explanation
Indices: 284883--285081 Score: 260
Period size: 85 Copynumber: 2.4 Consensus size: 84
284873 TATCTTACCG
* * *
284883 TTATTTTTTAATGATAAATAAATAACAAACATTGCAAGAAAAAGA-ATATAATTTAAATTTGTTT
1 TTATTTTTAAATGATAAATGAATAACAAACATAGCAA-AAAAAGATATATAATTTAAATTT-TTT
*
284947 -T-AAAACAATCATTTTATAA
64 ATAAAAACAATCACTTTATAA
* *
284966 TTATTTTTAAATGATAAATGAATAACAAACATAGTAAAAAAATATTATATAATTTAAATTTTTTA
1 TTATTTTTAAATGATAAATGAATAACAAACATAGCAAAAAAAGA-TATATAATTTAAATTTTTTA
* *
285031 TAAAAATAATTACTTTATAA
65 TAAAAACAATCACTTTATAA
* *
285051 TTATTTTTAAATAATAAATGAATAAAAAACA
1 TTATTTTTAAATGATAAATGAATAACAAACA
285082 CCGTAAGAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
82 6 0.06
83 36 0.35
84 16 0.16
85 44 0.43
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (84 bp):
TTATTTTTAAATGATAAATGAATAACAAACATAGCAAAAAAAGATATATAATTTAAATTTTTTAT
AAAAACAATCACTTTATAA
Found at i:295081 original size:13 final size:13
Alignment explanation
Indices: 295053--295086 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
295043 TTTCTTTTAA
295053 TTTATTTTCAATT
1 TTTATTTTCAATT
295066 TTTAGTTTTCAATT
1 TTTA-TTTTCAATT
*
295080 TTCATTT
1 TTTATTT
295087 GTTATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTATTTTCAATT
Found at i:300483 original size:13 final size:13
Alignment explanation
Indices: 300462--300495 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
300452 TATCTTATTT
*
300462 TTATTTTTAGGAA
1 TTATCTTTAGGAA
300475 TTATCTTTAGGAA
1 TTATCTTTAGGAA
300488 TTATCTTT
1 TTATCTTT
300496 TGTTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATCTTTAGGAA
Found at i:306115 original size:20 final size:20
Alignment explanation
Indices: 306087--306126 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
306077 GAGTGTGTGT
*
306087 CTTCTTATGGTTGGCTTGCA
1 CTTCCTATGGTTGGCTTGCA
306107 CTTCCTATGGTTGGCTTGCA
1 CTTCCTATGGTTGGCTTGCA
306127 AAAGTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.25, T:0.42
Consensus pattern (20 bp):
CTTCCTATGGTTGGCTTGCA
Found at i:307013 original size:13 final size:13
Alignment explanation
Indices: 306995--307019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
306985 TGTACCCCGA
306995 CATTTGAAGTGTC
1 CATTTGAAGTGTC
307008 CATTTGAAGTGT
1 CATTTGAAGTGT
307020 TTTCCTTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
CATTTGAAGTGTC
Found at i:307110 original size:15 final size:14
Alignment explanation
Indices: 307092--307131 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
307082 AAAAAATTAA
307092 AAATTAAAATATATT
1 AAATTAAAATA-ATT
*
307107 AAATAAAAATAATT
1 AAATTAAAATAATT
*
307121 AAAATAAAATA
1 AAATTAAAATA
307132 CATAGATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATTAAAATAATT
Found at i:307113 original size:14 final size:16
Alignment explanation
Indices: 307086--307131 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
307076 CATTCAAAAA
307086 AATTAAAAATTAAAATAT
1 AATT-AAAA-TAAAATAT
307104 -ATT-AAATAAAA-AT
1 AATTAAAATAAAATAT
307117 AATTAAAATAAAATA
1 AATTAAAATAAAATA
307132 CATAGATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.08
14 8 0.32
15 11 0.44
16 1 0.04
17 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTAAAATAAAATAT
Found at i:307328 original size:31 final size:31
Alignment explanation
Indices: 307290--307363 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
307280 GTAAATGGTT
307290 CCTAACATTATCGGTCCGT-TCGGTTTAAGTC
1 CCTAACATTATCGGTCCGTCT-GGTTTAAGTC
*
307321 CCTAACATTATCGGTTCGTCTGGTTTAAGTC
1 CCTAACATTATCGGTCCGTCTGGTTTAAGTC
*
307352 CCTAACGTTATC
1 CCTAACATTATC
307364 CATCCATCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (31 bp):
CCTAACATTATCGGTCCGTCTGGTTTAAGTC
Found at i:311391 original size:60 final size:60
Alignment explanation
Indices: 311287--311408 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
311277 GTAAGAAACC
*
311287 CTAAGGTTTTAAGGGTTAGAATTGAGGCCAATATCAATAATAAGATCCTCAGTATCGATA
1 CTAAGGTTTTAAGGGTTAGAATTGAGGCCAATATCAATAATAAGATCCTCAGTATAGATA
* * * * *
311347 CTAAGGTTTTAAGGGTTATAATTGAGGTCAGTATCGATAGTAAGATCCTCAGTATAGATA
1 CTAAGGTTTTAAGGGTTAGAATTGAGGCCAATATCAATAATAAGATCCTCAGTATAGATA
311407 CT
1 CT
311409 CTACCCTCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (60 bp):
CTAAGGTTTTAAGGGTTAGAATTGAGGCCAATATCAATAATAAGATCCTCAGTATAGATA
Found at i:313919 original size:18 final size:18
Alignment explanation
Indices: 313896--313932 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
313886 TGCCATTGTC
*
313896 AGAGCATCATTGTTTGCG
1 AGAGCATCATTGATTGCG
313914 AGAGCATCATTGATTGCG
1 AGAGCATCATTGATTGCG
313932 A
1 A
313933 CTGCAACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (18 bp):
AGAGCATCATTGATTGCG
Found at i:323296 original size:22 final size:22
Alignment explanation
Indices: 323271--323312 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
323261 TAGAAACAAT
323271 AATTAT-TAAATTTATTATGTCA
1 AATTATAT-AATTTATTATGTCA
*
323293 AATTATATTATTTATTATGT
1 AATTATATAATTTATTATGT
323313 ATAAATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTATATAATTTATTATGTCA
Found at i:339262 original size:22 final size:22
Alignment explanation
Indices: 339205--339263 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
339195 ACACGATTCT
*
339205 GACTATCGCATTGCGATTTTCT
1 GACTATCGCATTGCGATTTTCC
* * *
339227 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
339248 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
339264 GTATGACTAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:339364 original size:20 final size:20
Alignment explanation
Indices: 339248--339365 Score: 128
Period size: 20 Copynumber: 5.9 Consensus size: 20
339238 GCGATTTTCC
* * *
339248 GACTATCGCAATGCGAGTAT
1 GACTATCGCAACGCGATTCT
* *
339268 GACTATTGCAACGAGATTCT
1 GACTATCGCAACGCGATTCT
* *
339288 GACTATCGCAACACTATTCT
1 GACTATCGCAACGCGATTCT
*
339308 GACTGTCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
* * *
339328 GACTGTCGCAACACGATGCT
1 GACTATCGCAACGCGATTCT
*
339348 GACTATCGCAATGCGATT
1 GACTATCGCAACGCGATT
339366 TTCAAAGCGT
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 80 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.26
Consensus pattern (20 bp):
GACTATCGCAACGCGATTCT
Found at i:339853 original size:20 final size:20
Alignment explanation
Indices: 339788--339855 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
339778 AGAATCGCAA
* *
339788 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGTGT
** *
339807 TGCGATAGTCATTTTCATGT
1 TGCGATTTTCATTTTCGTGT
339827 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGTGT
339847 TGCGATTTT
1 TGCGATTTT
339856 AAGTTTCAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.17
20 33 0.82
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGTGT
Found at i:339863 original size:40 final size:39
Alignment explanation
Indices: 339788--339863 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 39
339778 AGAATCGCAA
* *
339788 TGCGATTTTAGTTTCGCGTTGCGATAGTCATTTTCATGT
1 TGCGATTTTAGTTTCGCGTTGCGATAGTAAGTTTCATGT
* * **
339827 TGCGATTTTCATTTTCGTGTTGCGATTTTAAGTTTCA
1 TGCGATTTT-AGTTTCGCGTTGCGATAGTAAGTTTCA
339864 GAAACTATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
39 9 0.30
40 21 0.70
ACGTcount: A:0.16, C:0.14, G:0.21, T:0.49
Consensus pattern (39 bp):
TGCGATTTTAGTTTCGCGTTGCGATAGTAAGTTTCATGT
Found at i:343188 original size:20 final size:20
Alignment explanation
Indices: 343163--343367 Score: 123
Period size: 20 Copynumber: 10.8 Consensus size: 20
343153 ACAATTTTCT
*
343163 CGTTGCAATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
* *
343183 CGTTGCGATAAT-AAAATAG
1 CGTTGCGATAATCAAATTCG
*
343202 TCGTTGCGATAGTCAAATTCG
1 -CGTTGCGATAATCAAATTCG
*
343223 CGTTGTGATAGA-CAAATTCG
1 CGTTGCGATA-ATCAAATTCG
*
343243 CGTTGCGAT--T----TTTG
1 CGTTGCGATAATCAAATTCG
* * *
343257 CGTTGCGATAGTTATATTCG
1 CGTTGCGATAATCAAATTCG
* *
343277 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
* *
343297 CATTGCGAT--T----TTTG
1 CGTTGCGATAATCAAATTCG
*
343311 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
* *
343331 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
** *
343351 TATTGCGATATTCAAAT
1 CGTTGCGATAATCAAAT
343368 AAATGTATAA
Statistics
Matches: 142, Mismatches: 27, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
14 22 0.15
16 2 0.01
18 1 0.01
19 5 0.04
20 107 0.75
21 5 0.04
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:343287 original size:54 final size:54
Alignment explanation
Indices: 343203--343359 Score: 224
Period size: 54 Copynumber: 2.9 Consensus size: 54
343193 ATAAAATAGT
* * *
343203 CGTTGCGATAGTCAAATTCGCGTTGTGATAGACAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
* * *
343257 CGTTGCGATAGTTATATTCGTGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
* * * *
343311 AGTTGCGATAATCAAATTCGCGTTACGATAGTCAAATTCGTATTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGAT
343360 ATTCAAATAA
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTTG
Found at i:343590 original size:140 final size:140
Alignment explanation
Indices: 343338--343607 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
343328 TCGCGTTACG
* *
343338 ATAGTCAAATTCGTATTGCGATATTCAAATAAATGTATAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCATTGCGATATTCAAATAAATGTATAATAAGTGATAACAACTGAACAGATCA
343403 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
343468 AATACACATA
131 AATACACATA
* * *
343478 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCATTGCGATATTCAAATAAATGTATAATAAGTGATAACAACTGAACAGATCA
343543 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
343608 TACAACGTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCATTGCGATATTCAAATAAATGTATAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:344314 original size:20 final size:20
Alignment explanation
Indices: 344291--344346 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
344281 ATCGATAATT
*
344291 ATATTCACATTGCGATTTAC
1 ATATTCGCATTGCGATTTAC
*
344311 ATATTCGTATTGCGATTTAC
1 ATATTCGCATTGCGATTTAC
*
344331 ATATTCGCAATGCGAT
1 ATATTCGCATTGCGAT
344347 AGTCGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
ATATTCGCATTGCGATTTAC
Found at i:348476 original size:49 final size:51
Alignment explanation
Indices: 348413--348520 Score: 184
Period size: 51 Copynumber: 2.2 Consensus size: 51
348403 CACGGATCAT
**
348413 GTACCGCGTTATACCTTTACTCCT-A-ATAATTTTATATAGCGCGGGGCAG
1 GTACCGCGACATACCTTTACTCCTGACATAATTTTATATAGCGCGGGGCAG
348462 GTACCGCGACATACCTTTACTCCTGACATAATTTTATATAGCGCGGGGCAG
1 GTACCGCGACATACCTTTACTCCTGACATAATTTTATATAGCGCGGGGCAG
348513 GTACCGCG
1 GTACCGCG
348521 TTTTGTATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
49 22 0.40
50 1 0.02
51 32 0.58
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (51 bp):
GTACCGCGACATACCTTTACTCCTGACATAATTTTATATAGCGCGGGGCAG
Found at i:352657 original size:18 final size:18
Alignment explanation
Indices: 352634--352668 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
352624 GCGATGTCGG
352634 CATCATATATGGCTGCGA
1 CATCATATATGGCTGCGA
352652 CATCATATATGGCTGCG
1 CATCATATATGGCTGCG
352669 GTGGCTGCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (18 bp):
CATCATATATGGCTGCGA
Found at i:354371 original size:110 final size:111
Alignment explanation
Indices: 354177--354397 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 111
354167 ATTACAAAAA
* * * *
354177 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATGAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATGAATAATAATTTAAATTA
* * *
354242 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAACAAAGTGTAGAGATAT
* *
354288 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATGAATAATAATTTAAATTA
354352 AATTAAAACGTTAAAATGTTACCATATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAACAAAGTGTAGAGATAT
354398 ATGATTTCCA
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 68 0.67
111 33 0.33
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATGAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCATATCAACAAAGTGTAGAGATAT
Found at i:354723 original size:50 final size:50
Alignment explanation
Indices: 354669--354787 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 50
354659 AGATATACAG
* **
354669 GTATAGCGCGCTGCAGGGGCCGCACTATA-CCCACGTGGCGCCAGCTCACC
1 GTATAGCGCG-TGCAGGGGCCACACTATACCCCACGTGGCGCCAAATCACC
* * *
354719 GTATAGCGCAGTGCAGGGGGCACGCTATACCCCACGTGGCGCCAAATCATC
1 GTATAGCGC-GTGCAGGGGCCACACTATACCCCACGTGGCGCCAAATCACC
*
354770 TTATAGCGCGGTGCAGGG
1 GTATAGCGC-GTGCAGGG
354788 CGCGCGCTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
50 24 0.41
51 35 0.59
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (50 bp):
GTATAGCGCGTGCAGGGGCCACACTATACCCCACGTGGCGCCAAATCACC
Found at i:355713 original size:29 final size:28
Alignment explanation
Indices: 355659--355739 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
355649 CTTTCTGATA
* *
355659 TGTTATTTATTTT-CAGTTAACTACTAAC
1 TGTTATTT-TTTTGCATTTAACCACTAAC
*
355687 TGTTATTTTTTTGCATATTAACCACTAAT
1 TGTTATTTTTTTGCAT-TTAACCACTAAC
* *
355716 TTTTATTTTATTGCACTTTAACCA
1 TGTTATTTTTTTGCA-TTTAACCA
355740 TTTTTATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.09
28 10 0.22
29 30 0.67
30 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (28 bp):
TGTTATTTTTTTGCATTTAACCACTAAC
Found at i:355883 original size:4 final size:4
Alignment explanation
Indices: 355874--355898 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
355864 ACTCTAACCA
355874 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
355899 GTTTCTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:355957 original size:135 final size:134
Alignment explanation
Indices: 355716--355977 Score: 348
Period size: 135 Copynumber: 1.9 Consensus size: 134
355706 AACCACTAAT
* * *
355716 TTTTATTTTATTGCACTTTAACCATTTTTATTTATTTATTTATTTACTGTTTCTAATATTTGATT
1 TTTTATTTTATTGCACTCTAACCATTTTTATTTATTTATTTATTTACTGTTTCTAATATATGAAT
* * * * *
355781 CGACTTTGTTATGACCAGATCAGGAATATAATCCACATTATTATGGTTTGGACTCTGCTAACTAT
66 CAACCTTGTGATAACCAGATCAGGAATATAATCCACATTATTATGGTTCGGACTCTGCTAACTAT
355846 TGAC
131 TGAC
*
355850 TTTTATTTTATTGCACTCTAACCATTATTTATTTATTTATTTATTTATTGTTTCTAATATATGAA
1 TTTTATTTTATTGCACTCTAACCATT-TTTATTTATTTATTTATTTACTGTTTCTAATATATGAA
* * * * * *
355915 TCAACCTTGTGGTAACTAGATTC-GGGAT-TAGATCTATATTATTATGGTTCGGACTTTGCTAAC
65 TCAACCTTGTGATAACCAGA-TCAGGAATATA-ATCCACATTATTATGGTTCGGACTCTGCTAAC
355978 CTTTAACTTT
Statistics
Matches: 110, Mismatches: 15, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
134 27 0.25
135 81 0.74
136 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.48
Consensus pattern (134 bp):
TTTTATTTTATTGCACTCTAACCATTTTTATTTATTTATTTATTTACTGTTTCTAATATATGAAT
CAACCTTGTGATAACCAGATCAGGAATATAATCCACATTATTATGGTTCGGACTCTGCTAACTAT
TGAC
Found at i:356202 original size:16 final size:16
Alignment explanation
Indices: 356177--356212 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
356167 ATTTCTGTTA
*
356177 TTTAACTTTATGCACT
1 TTTAAATTTATGCACT
*
356193 TTTAAATTTATGCATT
1 TTTAAATTTATGCACT
356209 TTTA
1 TTTA
356213 TTTTCTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:358923 original size:2 final size:2
Alignment explanation
Indices: 358916--358952 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
358906 ACCTTTTATT
358916 TA TA 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 TA TA T
358953 TTATTTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:359018 original size:17 final size:17
Alignment explanation
Indices: 358993--359031 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
358983 GTCTTTGTCC
*
358993 TTTTATTATTATTATAT
1 TTTTTTTATTATTATAT
* *
359010 TTTTTTTATTTTTTTAT
1 TTTTTTTATTATTATAT
359027 TTTTT
1 TTTTT
359032 ATTTTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTATTATTATAT
Found at i:359024 original size:28 final size:29
Alignment explanation
Indices: 358946--359027 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 29
358936 TATATATATA
*
358946 TATATATTTATTTATTATTTTTA--ATTAT
1 TATAT-TTTTTTTATTATTTTTATTATTAT
**
358974 TATATTTTTGTCTT-TGTCCTTTTATTATTAT
1 TATATTTTT-T-TTAT-TATTTTTATTATTAT
359005 TATATTTTTTTTATT-TTTTTATT
1 TATATTTTTTTTATTATTTTTATT
359028 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
27 3 0.07
28 14 0.32
29 11 0.25
30 2 0.05
31 14 0.32
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (29 bp):
TATATTTTTTTTATTATTTTTATTATTAT
Found at i:359325 original size:19 final size:18
Alignment explanation
Indices: 359282--359345 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
359272 CTTGTTTTTA
*
359282 TTTTTATCTTATTCTACTT
1 TTTTTAT-TTATTTTACTT
359301 TGTTTTATTTATTTTACTT
1 T-TTTTATTTATTTTACTT
*
359320 ATTTTT-TTCT-TTTTTCTT
1 -TTTTTATT-TATTTTACTT
359338 TTTTTATT
1 TTTTTATT
359346 GTGCTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.13
18 11 0.28
19 16 0.41
20 7 0.18
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTATTTATTTTACTT
Found at i:359429 original size:21 final size:20
Alignment explanation
Indices: 359381--359433 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 20
359371 TTTTTTTGAG
359381 ATTAGTCTTTTA-TTATTATT
1 ATTAGT-TTTTATTTATTATT
359401 ATTA--TTTTATTTATTATT
1 ATTAGTTTTTATTTATTATT
359419 ATTTAGTTTTTATTT
1 A-TTAGTTTTTATTT
359434 GGGGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 9 0.31
19 3 0.10
20 4 0.14
21 8 0.28
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (20 bp):
ATTAGTTTTTATTTATTATT
Found at i:363093 original size:12 final size:13
Alignment explanation
Indices: 363076--363108 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
363066 AATCTAAAAA
363076 TATATATTTAT-T
1 TATATATTTATAT
363088 TATATATTTATAT
1 TATATATTTATAT
*
363101 TAAATATT
1 TATATATT
363109 AAATTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATATATTTATAT
Found at i:364563 original size:8 final size:8
Alignment explanation
Indices: 364552--364740 Score: 52
Period size: 8 Copynumber: 23.1 Consensus size: 8
364542 AAGAAGAAAA
364552 AAATATAT
1 AAATATAT
*
364560 AAATAAAAT
1 AAAT-ATAT
*
364569 AAATAAAT
1 AAATATAT
*
364577 AAATA-AA
1 AAATATAT
364584 ATAATA-AT
1 A-AATATAT
* *
364592 AAAAAGTAA
1 AAATA-TAT
364601 AAATA-AT
1 AAATATAT
*
364608 ATATATAT
1 AAATATAT
*
364616 ATATATAAT
1 AAATAT-AT
*
364625 AAATAAAT
1 AAATATAT
*
364633 AAA-ATGAA
1 AAATAT-AT
364641 AAATAGTAT
1 AAATA-TAT
364650 ATATATATAT
1 A-A-ATATAT
*
364660 ATATATAT
1 AAATATAT
364668 AAAT-TAAT
1 AAATAT-AT
364676 AAA-ACTGAT
1 AAATA-T-AT
* *
364685 -AATAAAA
1 AAATATAT
364692 AAATA-AT
1 AAATATAT
*
364699 ATATATAT
1 AAATATAT
*
364707 ATATATAT
1 AAATATAT
* *
364715 ATAATCTAA
1 A-AATATAT
* *
364724 AAAAATAA
1 AAATATAT
364732 AAATATAT
1 AAATATAT
364740 A
1 A
364741 CTAAAGTAAA
Statistics
Matches: 136, Mismatches: 27, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
7 18 0.13
8 79 0.58
9 30 0.22
10 6 0.04
11 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (8 bp):
AAATATAT
Found at i:364569 original size:13 final size:13
Alignment explanation
Indices: 364551--364637 Score: 54
Period size: 13 Copynumber: 6.4 Consensus size: 13
364541 AAAGAAGAAA
364551 AAAATATATAAAT
1 AAAATATATAAAT
364564 AAAATAAATAAATAAAT
1 AAAAT--AT--ATAAAT
364581 AAAATA-AT-AAT
1 AAAATATATAAAT
*
364592 AAAA-AGTAAAAAT
1 AAAATA-TATAAAT
*
364605 AATATATATATATAT
1 AA-A-ATATATAAAT
* *
364620 ATAATAAATAAAT
1 AAAATATATAAAT
364633 AAAAT
1 AAAAT
364638 GAAAAATAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
10 1 0.02
11 7 0.12
12 3 0.05
13 22 0.39
14 2 0.04
15 10 0.18
16 1 0.02
17 11 0.19
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (13 bp):
AAAATATATAAAT
Found at i:364572 original size:4 final size:4
Alignment explanation
Indices: 364552--364635 Score: 57
Period size: 4 Copynumber: 20.8 Consensus size: 4
364542 AAGAAGAAAA
* *
364552 AAAT ATAT AAAT AAAAT AAAT AAAT AAAT AAA- ATAAT -AAT AAA- AAGT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
* * * *
364599 AAAA ATAAT ATAT ATAT ATAT ATAAT AAAT AAAT AAA
1 AAAT A-AAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA
364636 ATGAAAAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
3 6 0.09
4 49 0.75
5 10 0.15
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:365937 original size:39 final size:35
Alignment explanation
Indices: 365883--365972 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 35
365873 CGAGGGTTTG
* **
365883 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTC-AAGGGGTTTT-T-T-T
*
365922 GTGTTTCAAGAGAAACAATTTCGAGGGGTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAGGGGTTTTTTT
365957 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
365973 TGTCTCAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 17 0.36
36 1 0.02
37 1 0.02
38 7 0.15
39 21 0.45
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACAATTTCAAGGGGTTTTTTT
Found at i:366050 original size:37 final size:36
Alignment explanation
Indices: 365959--366074 Score: 144
Period size: 36 Copynumber: 3.2 Consensus size: 36
365949 GTTTTTTTGT
* * * *
365959 GTTTCAAGAGAAACTGTCTCAAAAGGGACAAAATTT
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
365995 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTA
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTA
* * *
366032 G-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATTT
1 GTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATTA
366068 GTTTCAA
1 GTTTCAA
366075 GGAAAAGATA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
36 38 0.54
37 32 0.46
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (36 bp):
GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
Found at i:366234 original size:37 final size:37
Alignment explanation
Indices: 366183--366255 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
366173 TCAAGGTTTA
*
366183 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
*
366220 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
366256 AATATCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:366269 original size:102 final size:102
Alignment explanation
Indices: 366158--366395 Score: 368
Period size: 102 Copynumber: 2.3 Consensus size: 102
366148 ATTTTGTGTT
* *
366158 TCAAGGGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGT
* * *
366223 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATA
66 TTCAAAGGAAACTACCCCAAGAGAGACAAAATTAATA
* * *
366260 TCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGT
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGT
* * * *
366325 TTCAAAGGAAACTACCCCAAGCGAGATAAAATTTATT
66 TTCAAAGGAAACTACCCCAAGAGAGACAAAATTAATA
366362 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
366396 GGAGACAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 123 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
TCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGT
TTCAAAGGAAACTACCCCAAGAGAGACAAAATTAATA
Found at i:366422 original size:87 final size:87
Alignment explanation
Indices: 366304--366482 Score: 295
Period size: 87 Copynumber: 2.1 Consensus size: 87
366294 AGAAATTGTC
* *
366304 TCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAAGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
366369 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * * *
366391 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAAGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
*
366456 AATTGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
366478 TCAAG
1 TCAAG
366483 AGAAACTGTC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAAGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:366582 original size:189 final size:189
Alignment explanation
Indices: 366202--366587 Score: 506
Period size: 189 Copynumber: 2.0 Consensus size: 189
366192 AGAAACTATC
*
366202 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATATCAAAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATATCAAAGG
* * * * *
366267 AAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAAG
66 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAATTTAGTTCCAAAA
* * * * * *
366332 GAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTT
131 GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAATATATTCAATATTTATGTT
** * * * *
366391 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATATCAAAGG
* *
366456 AATTGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAATGAAGACAAAATTTAGTTCCAAAA
66 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAATTTAGTTCCAAAA
** * * * *
366521 GAAAATGTCTCAAGGGAGACGAAA-TTAGTTTCAATGAAAATATATTCAAATATTT-TGTT
131 GAAAATACCCCAAGCGAGACAAAATTTA-TTTCAAGGAAAATATATTC-AATATTTATGTT
366580 TCAAGGGA
1 TCAAGGGA
366588 AACTTGGAAA
Statistics
Matches: 169, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
188 3 0.02
189 160 0.95
190 6 0.04
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (189 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATATCAAAGG
AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAATTTAGTTCCAAAA
GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAATATATTCAATATTTATGTT
Found at i:366931 original size:106 final size:106
Alignment explanation
Indices: 366740--367061 Score: 484
Period size: 106 Copynumber: 3.0 Consensus size: 106
366730 GTATTGTTCT
* * * * * ** *
366740 GAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
366805 CCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
366846 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCT-TAGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAATTGTTTGTTGACA
*
366910 ACCAGCCGTCCCTTCGTTGTGAAGTTGAAATTGTGTTGTCTC
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
366952 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
367017 CCAGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
367058 GAGT
1 GAGT
367062 GACACGATAT
Statistics
Matches: 196, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
105 1 0.01
106 194 0.99
107 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:367693 original size:32 final size:32
Alignment explanation
Indices: 367641--367746 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
367631 TGCATCAGGG
* *
367641 TGTTGAATTCTC-AAAGATGCCCCAATATTCGA
1 TGTTGAA-TCTCAAAAAATGCCCCAATATTTGA
*
367673 TGTTGAATCTCAAAAAATGCCCCAATATTTGT
1 TGTTGAATCTCAAAAAATGCCCCAATATTTGA
* * * *
367705 TGTTAAATCTAAAAAAATACCCCAACATTTGA
1 TGTTGAATCTCAAAAAATGCCCCAATATTTGA
*
367737 TGTTTAATCT
1 TGTTGAATCT
367747 TTAAAGATGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 4 0.06
32 60 0.94
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (32 bp):
TGTTGAATCTCAAAAAATGCCCCAATATTTGA
Found at i:368768 original size:69 final size:69
Alignment explanation
Indices: 368685--368822 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
368675 TGTCTCTCTC
* *
368685 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTTAGAAATGATTGTGCTTGATCG-AT
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGAT-GAAT
368749 CTCAT
65 CTCAT
* * *
368754 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATGAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATGAATC
368819 TCAT
66 TCAT
368823 AGTTTGAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 1 0.02
69 62 0.98
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATGAATC
TCAT
Found at i:368947 original size:18 final size:16
Alignment explanation
Indices: 368912--368942 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
368902 TTTTTTCCCT
368912 TTTTATTTTCTCTTTG
1 TTTTATTTTCTCTTTG
368928 TTTTATTTTCTCTTT
1 TTTTATTTTCTCTTT
368943 TTGTTCTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATTTTCTCTTTG
Found at i:372155 original size:25 final size:23
Alignment explanation
Indices: 372099--372214 Score: 78
Period size: 23 Copynumber: 4.9 Consensus size: 23
372089 TAGTAAGTAA
* *
372099 AATAAATATAAAAAATAAAGAAAT
1 AATAAATA-AAAAAAGAAAAAAAT
* *
372123 AA-AGA-AAAAGAAGAAAAAAAT
1 AATAAATAAAAAAAGAAAAAAAT
*
372144 ACATAAATAAAACAAATAAATAAAAT
1 A-ATAAATAAAA-AAAGAAA-AAAAT
372170 AAT-AAT-AAAAAAGTAAAAATAAT
1 AATAAATAAAAAAAG-AAAAA-AAT
* *
372193 ATATATATAAAAAAATAAAAAA
1 A-ATAAATAAAAAAAGAAAAAA
372215 TAGTATATAT
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
21 13 0.18
22 7 0.10
23 14 0.19
24 12 0.17
25 14 0.19
26 12 0.17
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AATAAATAAAAAAAGAAAAAAAT
Found at i:372161 original size:46 final size:46
Alignment explanation
Indices: 372100--372216 Score: 125
Period size: 46 Copynumber: 2.5 Consensus size: 46
372090 AGTAAGTAAA
372100 ATAAATATAAAAAATAAAGAAATAA-AGA-AAAAGAAG-AAAAA-AATAC
1 ATAAATA-AAAAAATAAA-AAATAATA-ATAAAA-AAGTAAAAATAATAC
*
372146 ATAAATAAAACAAATAAATAAAATAATAATAAAAAAGTAAAAATAATAT
1 ATAAATAAAA-AAAT-AA-AAAATAATAATAAAAAAGTAAAAATAATAC
*
372195 ATATATAAAAAAATAAAAAATA
1 ATAAATAAAAAAATAAAAAATA
372217 GTATATATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
45 3 0.05
46 17 0.27
47 14 0.23
48 15 0.24
49 13 0.21
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (46 bp):
ATAAATAAAAAAATAAAAAATAATAATAAAAAAGTAAAAATAATAC
Found at i:372166 original size:17 final size:16
Alignment explanation
Indices: 372098--372216 Score: 79
Period size: 17 Copynumber: 7.6 Consensus size: 16
372088 ATAGTAAGTA
372098 AAATAAATATAAAAAAT
1 AAATAAATA-AAAAAAT
* *
372115 AAAGAAAT-AAAGAA-
1 AAATAAATAAAAAAAT
* *
372129 AAA-GAAGAAAAAAAT
1 AAATAAATAAAAAAAT
*
372144 ACATAAATAAAACAAAT
1 AAATAAATAAAA-AAAT
* *
372161 AAATAAA-ATAATAAT
1 AAATAAATAAAAAAAT
372176 AAA-AAAGTAAAAATAAT
1 AAATAAA-TAAAAA-AAT
* *
372193 ATATATATAAAAAAAT
1 AAATAAATAAAAAAAT
372209 AAA-AAATA
1 AAATAAATA
372217 GTATATATAT
Statistics
Matches: 77, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
13 2 0.03
14 11 0.14
15 17 0.22
16 17 0.22
17 28 0.36
18 2 0.03
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (16 bp):
AAATAAATAAAAAAAT
Found at i:372168 original size:29 final size:28
Alignment explanation
Indices: 372097--372187 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 28
372087 AATAGTAAGT
*
372097 AAAATAAATATAAAAAATAAAGAAATAAAG
1 AAAATAAATA-AAAAAAT-AATAAATAAAG
*
372127 AAAA-AGAAGAAAAAAATACATAAATAAA-
1 AAAATA-AATAAAAAAATA-ATAAATAAAG
*
372155 ACAAATAAATAAAATAATAATAAA-AAAG
1 A-AAATAAATAAAAAAATAATAAATAAAG
372183 TAAAA
1 -AAAA
372188 ATAATATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
27 3 0.06
28 10 0.20
29 30 0.59
30 8 0.16
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.15
Consensus pattern (28 bp):
AAAATAAATAAAAAAATAATAAATAAAG
Found at i:372210 original size:36 final size:36
Alignment explanation
Indices: 372163--372248 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
372153 AAACAAATAA
*
372163 ATAAAATAATAATAAAAAAGTAAAAATA-ATATATAT
1 ATAAAAAAATAA-AAAAAAGTAAAAATATATATATAT
* * *
372199 ATAAAAAAATAAAAAATAGTATATATATATATATAT
1 ATAAAAAAATAAAAAAAAGTAAAAATATATATATAT
**
372235 ATAAATTAATAAAA
1 ATAAAAAAATAAAA
372249 CTGATAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 12 0.28
36 31 0.72
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (36 bp):
ATAAAAAAATAAAAAAAAGTAAAAATATATATATAT
Found at i:372212 original size:8 final size:8
Alignment explanation
Indices: 372096--372214 Score: 59
Period size: 8 Copynumber: 14.9 Consensus size: 8
372086 AAATAGTAAG
372096 TAAAATAAA
1 TAAAA-AAA
372105 TATAAAAAA
1 TA-AAAAAA
*
372114 TAAAGAAA
1 TAAAAAAA
*
372122 T--AAAGA
1 TAAAAAAA
*
372128 -AAAAGAA
1 TAAAAAAA
*
372135 GAAAAAAA
1 TAAAAAAA
* *
372143 TACATAAA
1 TAAAAAAA
372151 TAAAACAAA
1 TAAAA-AAA
372160 TAAATAAAA
1 TAAA-AAAA
*
372169 T--AATAA
1 TAAAAAAA
*
372175 TAAAAAAG
1 TAAAAAAA
372183 TAAAAATAA
1 TAAAAA-AA
* * *
372192 TATATATA
1 TAAAAAAA
372200 TAAAAAAA
1 TAAAAAAA
372208 TAAAAAA
1 TAAAAAA
372215 TAGTATATAT
Statistics
Matches: 80, Mismatches: 21, Indels: 19
0.67 0.17 0.16
Matches are distributed among these distances:
6 7 0.09
7 4 0.05
8 42 0.52
9 23 0.29
10 4 0.05
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:372212 original size:24 final size:24
Alignment explanation
Indices: 372127--372225 Score: 78
Period size: 24 Copynumber: 4.0 Consensus size: 24
372117 AGAAATAAAG
* * * *
372127 AAAAAGAAGAAAAAAATACATAAAT
1 AAAAA-AATAAAATAATATATATAT
*
372152 AAAACAAAT-AAATAAAATA-ATAAT
1 AAAA-AAATAAAATAATATATAT-AT
*
372176 AAAAAAGTAAAAATAATATATATAT
1 AAAAAAAT-AAAATAATATATATAT
372201 AAAAAAATAAAA-AATAGTATATAT
1 AAAAAAATAAAATAATA-TATATAT
372225 A
1 A
372226 TATATATATA
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
23 8 0.13
24 25 0.42
25 24 0.40
26 3 0.05
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAAAAATAAAATAATATATATAT
Found at i:372213 original size:26 final size:25
Alignment explanation
Indices: 372136--372227 Score: 98
Period size: 26 Copynumber: 3.7 Consensus size: 25
372126 GAAAAAGAAG
* *
372136 AAAAAAATACATAAATAAAACAAATA
1 AAAAAAATATATATATAAAA-AAATA
* *
372162 AATAAAATA-ATA-ATAAAAAAGTA
1 AAAAAAATATATATATAAAAAAATA
*
372185 AAAATAATATATATATAAAAAAATA
1 AAAAAAATATATATATAAAAAAATA
*
372210 AAAAATAGTATATATATA
1 AAAAA-AATATATATATA
372228 TATATATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
23 11 0.20
24 9 0.16
25 17 0.30
26 19 0.34
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAAAATATATATATAAAAAAATA
Found at i:372365 original size:11 final size:11
Alignment explanation
Indices: 372349--372375 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
372339 ATATTACATG
372349 AAAAAAAATAA
1 AAAAAAAATAA
372360 AAAAAAAATAA
1 AAAAAAAATAA
372371 AAAAA
1 AAAAA
372376 CAATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:372431 original size:14 final size:15
Alignment explanation
Indices: 372412--372450 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
372402 AAATATGCGT
*
372412 ATAAATAAAATTA-A
1 ATAAATAAAATAATA
372426 ATAAATAAAATAATA
1 ATAAATAAAATAATA
*
372441 ATAATTAAAA
1 ATAAATAAAA
372451 CGTAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:376121 original size:6 final size:6
Alignment explanation
Indices: 376112--376155 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
376102 GCACATATAC
* *
376112 TATCAT TATCAT GATCTT TATCAT TATCAT TATCAT TATCAT TA
1 TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TA
376156 ACTAATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.02, T:0.50
Consensus pattern (6 bp):
TATCAT
Found at i:377733 original size:18 final size:18
Alignment explanation
Indices: 377710--377744 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
377700 CTAGGAGATT
377710 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
377728 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
377745 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:378520 original size:13 final size:14
Alignment explanation
Indices: 378492--378520 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
378482 ATGAAAAGAA
378492 GATATGTGATAAGT
1 GATATGTGATAAGT
378506 GATATGTGA-AAGT
1 GATATGTGATAAGT
378519 GA
1 GA
378521 ATTACAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (14 bp):
GATATGTGATAAGT
Found at i:378799 original size:149 final size:149
Alignment explanation
Indices: 378621--378924 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
378611 GAGTCAAGGG
* *
378621 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGATTCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
378686 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
378751 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
378770 TCTACGCGATTCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGATTCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
378835 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
378900 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
378919 TCTACG
1 TCTACG
378925 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGATTCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:378947 original size:23 final size:23
Alignment explanation
Indices: 378903--378947 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
378893 ATCATTATAT
*
378903 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
378926 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
378948 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:389746 original size:18 final size:18
Alignment explanation
Indices: 389723--389759 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
389713 CGGGTGTAGG
389723 GTGAAAAATACCCGACCC
1 GTGAAAAATACCCGACCC
389741 GTGAAAAATACCCGACCC
1 GTGAAAAATACCCGACCC
389759 G
1 G
389760 ACCTGACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.32, G:0.19, T:0.11
Consensus pattern (18 bp):
GTGAAAAATACCCGACCC
Found at i:390322 original size:17 final size:18
Alignment explanation
Indices: 390296--390342 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
390286 TATGGAATTG
* *
390296 GATTCCAATTCC-TGACA
1 GATTCTAATTCCTTCACA
390313 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTCACA
390331 GATTCTAATTCC
1 GATTCTAATTCC
390343 CTCAGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:395800 original size:27 final size:27
Alignment explanation
Indices: 395745--395802 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
395735 TGAAAAAAAT
*
395745 AAATTTTTAGTTAAACTCAATTTTTTA
1 AAATTTTTAGTTAAACTCAATTTTATA
* *
395772 AAATTTTTCGTTAAATCTTAA-TTTATA
1 AAATTTTTAGTTAAA-CTCAATTTTATA
395799 AAAT
1 AAAT
395803 GAAATTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (27 bp):
AAATTTTTAGTTAAACTCAATTTTATA
Found at i:396192 original size:3 final size:3
Alignment explanation
Indices: 396184--396213 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
396174 TACCAGCTTA
396184 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
396214 ATTCAAGGTC
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:401674 original size:31 final size:31
Alignment explanation
Indices: 401639--401705 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
401629 ACCACCGAGG
*
401639 CACCTAAAATAATAACATTTGTGACGTTAGA
1 CACCTAAAATAATAACATTTGTAACGTTAGA
* * * * *
401670 CACCTAAAGTAGTAACGTTTGTAACTTTAGG
1 CACCTAAAATAATAACATTTGTAACGTTAGA
401701 CACCT
1 CACCT
401706 GGATGAGACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (31 bp):
CACCTAAAATAATAACATTTGTAACGTTAGA
Found at i:404490 original size:22 final size:22
Alignment explanation
Indices: 404437--404496 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
404427 GAACATATTT
* **
404437 TTATGTTTTCATATTTTCATTTA
1 TTATTTTTTCAT-TTTTCATAAA
404460 TT-TTGTTTTCATTTTTCATAAA
1 TTATT-TTTTCATTTTTCATAAA
*
404482 TTATTTTTTAATTTT
1 TTATTTTTTCATTTT
404497 ACAGCCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (22 bp):
TTATTTTTTCATTTTTCATAAA
Found at i:404846 original size:16 final size:18
Alignment explanation
Indices: 404812--404853 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
404802 TATTACAAAA
404812 TATATTTT-TATTATAAT
1 TATATTTTATATTATAAT
404829 TATATTTTATATT-T-AT
1 TATATTTTATATTATAAT
*
404845 TATAGTTTA
1 TATATTTTA
404854 AATTGATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 10 0.43
17 9 0.39
18 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTTATATTATAAT
Found at i:408558 original size:11 final size:11
Alignment explanation
Indices: 408542--408643 Score: 195
Period size: 11 Copynumber: 9.3 Consensus size: 11
408532 TTCAAAGGAT
408542 AATGAAATGGA
1 AATGAAATGGA
408553 AATGAAATGGA
1 AATGAAATGGA
408564 AATGAAATGGA
1 AATGAAATGGA
408575 AATGAAATGGA
1 AATGAAATGGA
408586 AATGAAATGGA
1 AATGAAATGGA
408597 AATGAAATGGA
1 AATGAAATGGA
408608 AATGAAATGGA
1 AATGAAATGGA
*
408619 AATGCAATGGA
1 AATGAAATGGA
408630 AATGAAATGGA
1 AATGAAATGGA
408641 AAT
1 AAT
408644 TGCAAGAAAG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
11 89 1.00
ACGTcount: A:0.54, C:0.01, G:0.26, T:0.19
Consensus pattern (11 bp):
AATGAAATGGA
Found at i:409105 original size:21 final size:21
Alignment explanation
Indices: 409075--409131 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
409065 TCGTTTGCCG
* *
409075 TCACATTATTGATATAGTTGT
1 TCACAGTATTAATATAGTTGT
*
409096 TCACAGTATTAATGTAGTTGT
1 TCACAGTATTAATATAGTTGT
409117 TCAC-GATATTAATAT
1 TCACAG-TATTAATAT
409132 GACAGTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (21 bp):
TCACAGTATTAATATAGTTGT
Found at i:409142 original size:14 final size:14
Alignment explanation
Indices: 409123--409151 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
409113 TTGTTCACGA
409123 TATTAATATGACAG
1 TATTAATATGACAG
409137 TATTAATATGACAG
1 TATTAATATGACAG
409151 T
1 T
409152 CTATAGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
TATTAATATGACAG
Found at i:411776 original size:21 final size:19
Alignment explanation
Indices: 411744--411809 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
411734 TCCAAATTAT
*
411744 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* *
411763 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
411786 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
411805 TCCAA
1 TCCAA
411810 AATCGCAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 13 0.34
21 16 0.42
23 9 0.24
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:412443 original size:6 final size:6
Alignment explanation
Indices: 412432--412458 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
412422 TCTCGTCTCA
412432 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
412459 AATACATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:412580 original size:21 final size:21
Alignment explanation
Indices: 412556--412712 Score: 212
Period size: 21 Copynumber: 7.5 Consensus size: 21
412546 TTTTGGACTA
*
412556 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
412577 TCGCATTGGGATAGT-CAACT
1 TCGCATTGCGATAGTCCAAGT
* *
412597 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
412618 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
412639 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
412660 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
412681 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
412702 TCGCGTTGCGA
1 TCGCATTGCGA
412713 ATCTGGAAAC
Statistics
Matches: 122, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
20 18 0.15
21 103 0.84
22 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:413583 original size:19 final size:19
Alignment explanation
Indices: 413538--413583 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
413528 TTGTTGTTCT
*
413538 TGTGTGTGGGTACTTGCTC
1 TGTGTGTTGGTACTTGCTC
413557 TGTGTGTTGGTACTTGCTC
1 TGTGTGTTGGTACTTGCTC
413576 TGTGTGTT
1 TGTGTGTT
413584 TTATTTTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.04, C:0.13, G:0.35, T:0.48
Consensus pattern (19 bp):
TGTGTGTTGGTACTTGCTC
Found at i:415847 original size:59 final size:59
Alignment explanation
Indices: 415730--415848 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 59
415720 AGATATTTGT
* * * **
415730 TTACACATACATGTGGTATGTGACAGAAGAGAAGGAACATGTGATTATAAGATCAATGA
1 TTACACATACATGTGATATGTGACAGAAAAGAAAGAACATGTGATTATAAGAGAAATGA
* * * *
415789 TTACACGTACATGTGATATGTGACTGAAAAGAAA-AGATATGTGTTTATAAGAGAAATGA
1 TTACACATACATGTGATATGTGACAGAAAAGAAAGA-ACATGTGATTATAAGAGAAATGA
415848 T
1 T
415849 ATGATTAAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 1 0.02
59 49 0.98
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (59 bp):
TTACACATACATGTGATATGTGACAGAAAAGAAAGAACATGTGATTATAAGAGAAATGA
Found at i:416038 original size:62 final size:63
Alignment explanation
Indices: 415940--416096 Score: 208
Period size: 62 Copynumber: 2.5 Consensus size: 63
415930 AGGGTCGAGG
* * * * * *
415940 GTTTACCTATGTTCTTTGGGACATATAGACTATTTACCTATGTTTTTC-AGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGAGGACATATGGACT
*
416002 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGAGGACATATGGACT
* * * *
416065 GATTACCTAGGTTCTTCGGAATATATGGACTG
1 GTTTACCTATGTTCTTCGGGACATATGGACTG
416097 GTCCTTTGGG
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 44 0.53
63 39 0.47
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (63 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGAGGACATATGGACT
Found at i:416096 original size:31 final size:31
Alignment explanation
Indices: 415942--416096 Score: 186
Period size: 31 Copynumber: 5.0 Consensus size: 31
415932 GGTCGAGGGT
* *
415942 TTACCTATGTTCTTTGGGACATATAGACT-A
1 TTACCTATGTTCTTCGGGACATATGGACTGA
* * * * *
415972 TTTACCTATGTTTTTCAGGATATATGGATTGT
1 -TTACCTATGTTCTTCGGGACATATGGACTGA
*
416004 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGA
416035 TTACCTATGTTCTTCGGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGGACATATGGACTGA
* * *
416067 TTACCTAGGTTCTTCGGAATATATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
416097 GTCCTTTGGG
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
31 78 0.73
32 29 0.27
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGA
Found at i:417369 original size:10 final size:11
Alignment explanation
Indices: 417354--417404 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
417344 TTCATTTTTA
417354 ATAATAA-TAT
1 ATAATAATTAT
417364 ATAATAATTTAT
1 ATAATAA-TTAT
* *
417376 ATATTAATGTAC
1 ATAATAAT-TAT
417388 ATAATAA-TAT
1 ATAATAATTAT
417398 ATAATAA
1 ATAATAA
417405 GATAACACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 16 0.47
11 1 0.03
12 17 0.50
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
ATAATAATTAT
Found at i:420498 original size:17 final size:17
Alignment explanation
Indices: 420454--420525 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
420444 ATTCATGCAT
420454 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
420471 GTTAATTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
420489 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
420506 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
420523 CTA
1 CTA
420526 AATCTTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:433114 original size:4 final size:4
Alignment explanation
Indices: 433097--433158 Score: 63
Period size: 4 Copynumber: 15.0 Consensus size: 4
433087 AACAATAATA
* *
433097 AAAT AAAC AAAT AAAT -AAT AAAT GAAAT AAAAT AAAAT AAAT AAAT AGAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT AAAT AAAT AAAT
*
433147 AGAT AAAT AAAT
1 AAAT AAAT AAAT
433159 TAAAAACATT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
3 3 0.06
4 35 0.69
5 13 0.25
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:433131 original size:34 final size:35
Alignment explanation
Indices: 433093--433163 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
433083 AACAAACAAT
433093 AATAAAATAAACAAATAAATA-ATAAATGAAA-TAA
1 AATAAAATAAACAAATAAATAGATAAAT-AAATTAA
* *
433127 AATAAAATAAATAAATAGATAGATAAATAAATTAA
1 AATAAAATAAACAAATAAATAGATAAATAAATTAA
433162 AA
1 AA
433164 ACATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 22 0.67
35 11 0.33
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (35 bp):
AATAAAATAAACAAATAAATAGATAAATAAATTAA
Found at i:433141 original size:30 final size:30
Alignment explanation
Indices: 433093--433163 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
433083 AACAAACAAT
433093 AATAAAAT-AAACAAATAAATA-ATAAATGA
1 AATAAAATAAAACAAATAAATAGATAAAT-A
* *
433122 AATAAAATAAAATAAATAAATAGATAGATA
1 AATAAAATAAAACAAATAAATAGATAAATA
*
433152 AATAAATTAAAA
1 AATAAAATAAAA
433164 ACATTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.22
30 24 0.65
31 5 0.14
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (30 bp):
AATAAAATAAAACAAATAAATAGATAAATA
Found at i:433277 original size:13 final size:13
Alignment explanation
Indices: 433255--433316 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
433245 TATATAATAT
*
433255 ATTTTTAAAACTA
1 ATTTTCAAAACTA
433268 ATTTTCAAAACT-
1 ATTTTCAAAACTA
* *
433280 A-TAT-AATA-TA
1 ATTTTCAAAACTA
*
433290 TATTTTAAAAACTA
1 -ATTTTCAAAACTA
433304 ATTTTCAAAACTA
1 ATTTTCAAAACTA
433317 TATAATATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
9 1 0.03
10 3 0.08
11 3 0.08
12 3 0.08
13 26 0.68
14 2 0.05
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTTCAAAACTA
Found at i:433291 original size:36 final size:36
Alignment explanation
Indices: 433169--433446 Score: 281
Period size: 37 Copynumber: 7.9 Consensus size: 36
433159 TAAAAACATT
* * * * *
433169 TTTTTAAAACTATACAATATATGTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATTTTTAAAACTAA
*
433205 TTTTC-AAACCATAT-ATATAT-TTTTT-AAA--AA
1 TTTTCAAAACTATATAATATATATTTTTAAAACTAA
433235 TTTTCAAAACTATAT-A-ATATATTTTTAAAACTAA
1 TTTTCAAAACTATATAATATATATTTTTAAAACTAA
*
433269 TTTTCAAAACTATATAATATATATTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATTTTTAAAACTAA
**
433305 TTTTCAAAACTATATAATATAT-TTTAAAAAAAACTAA
1 TTTTCAAAACTATATAATATATATTT--TTAAAACTAA
* * **
433342 TTTTCAAAACTATATAATATATGTTTTTCAAAAATGT
1 TTTTCAAAACTATATAATATATATTTTT-AAAACTAA
* *
433379 TTTTTAAAACTATATATATATATATATTTTAAAA-AAA
1 TTTTCAAAACTATATA-ATATATAT-TTTTAAAACTAA
* *
433416 TTTTCAAAACAATAT-ATATATATTTTCAAAA
1 TTTTCAAAACTATATAATATATATTTTTAAAA
433447 ACTATTTATT
Statistics
Matches: 209, Mismatches: 20, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
30 11 0.05
31 14 0.07
32 6 0.03
33 4 0.02
34 30 0.14
35 19 0.09
36 43 0.21
37 64 0.31
38 14 0.07
39 4 0.02
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (36 bp):
TTTTCAAAACTATATAATATATATTTTTAAAACTAA
Found at i:433462 original size:21 final size:22
Alignment explanation
Indices: 433415--433467 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
433405 TTTTAAAAAA
433415 ATTTTCAAAACAATATATATAT
1 ATTTTCAAAACAATATATATAT
* * *
433437 ATTTTCAAAA-ACTATTTATTT
1 ATTTTCAAAACAATATATATAT
433458 ATTTTCAAAA
1 ATTTTCAAAA
433468 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTCAAAACAATATATATAT
Found at i:433473 original size:19 final size:20
Alignment explanation
Indices: 433415--433473 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
433405 TTTTAAAAAA
*
433415 ATTTTCAAAACAATATATATAT
1 ATTTTC-AAA-AATATTTATAT
*
433437 ATTTTCAAAAACTATTTATTT
1 ATTTTCAAAAA-TATTTATAT
433458 ATTTTC-AAAATATTTA
1 ATTTTCAAAAATATTTA
433474 AAAAACCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 6 0.18
20 6 0.18
21 16 0.47
22 6 0.18
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTCAAAAATATTTATAT
Found at i:437566 original size:51 final size:51
Alignment explanation
Indices: 437476--437582 Score: 139
Period size: 51 Copynumber: 2.1 Consensus size: 51
437466 TCTTTGTAGG
* *
437476 AAGGCGCGACCCATGCATCGCACCTTATGTTGATCTGGCG-C-CACGTGGGGT
1 AAGGCGCGACCCATGCACCGCACCTTATGCTGATCTGGCGACACAC-T-GGGT
*
437527 AAGGCGCGACCCATGCACCGCGCCTTATGCTGA-CATGGCGACACACTGGGT
1 AAGGCGCGACCCATGCACCGCACCTTATGCTGATC-TGGCGACACACTGGGT
437578 AAGGC
1 AAGGC
437583 ACGGTGCATG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
50 1 0.02
51 44 0.88
52 2 0.04
53 3 0.06
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.18
Consensus pattern (51 bp):
AAGGCGCGACCCATGCACCGCACCTTATGCTGATCTGGCGACACACTGGGT
Found at i:439283 original size:35 final size:33
Alignment explanation
Indices: 439216--439299 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 33
439206 AGAATAATTT
*
439216 TAAATACAACAAACTTACAATAAGTATTAAATGA
1 TAAATA-AACAAAATTACAATAAGTATTAAATGA
*
439250 TAAATAAA-AAAATTACAATAACTGATATTAAATGG
1 TAAATAAACAAAATTACAATAA--G-TATTAAATGA
439285 T-AATAAACAAAATTA
1 TAAATAAACAAAATTA
439300 ACAAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 12 0.27
33 2 0.05
34 13 0.30
35 17 0.39
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (33 bp):
TAAATAAACAAAATTACAATAAGTATTAAATGA
Found at i:439347 original size:13 final size:13
Alignment explanation
Indices: 439294--439318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
439284 GTAATAAACA
439294 AAATTAACAAAAT
1 AAATTAACAAAAT
439307 AAATTAACAAAA
1 AAATTAACAAAA
439319 AGTCCAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:439382 original size:13 final size:13
Alignment explanation
Indices: 439364--439409 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
439354 AATGATAAAT
439364 AATAAAAAATTAC
1 AATAAAAAATTAC
439377 AATAAAAAACTT-C
1 AATAAAAAA-TTAC
* *
439390 AATAAACAACTA-
1 AATAAAAAATTAC
439402 AATAAAAA
1 AATAAAAA
439410 TATAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 8 0.29
13 18 0.64
14 2 0.07
ACGTcount: A:0.70, C:0.11, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAAAAATTAC
Found at i:440689 original size:20 final size:20
Alignment explanation
Indices: 440639--440692 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
440629 AACAAATCCC
*
440639 TATA-ACACATAT-ACAATA
1 TATACACACATATAAAAATA
*
440657 TATATCATTACATATAAAAATA
1 TATA-CA-CACATATAAAAATA
440679 TATACACACATATA
1 TATACACACATATA
440693 TTCATCACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
20 8 0.28
21 8 0.28
22 9 0.31
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (20 bp):
TATACACACATATAAAAATA
Found at i:441046 original size:23 final size:23
Alignment explanation
Indices: 440981--441049 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
440971 CACCACAGCT
* *
440981 CGTATAAATGCACCGAAGTACCA
1 CGTAAAAATGCACCGAAGTGCCA
* * * *
441004 CGTAGAATTGCACCGTAGTGCCG
1 CGTAAAAATGCACCGAAGTGCCA
441027 CGTAAAAATGCACCGAAGTGCCA
1 CGTAAAAATGCACCGAAGTGCCA
441050 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAAAAATGCACCGAAGTGCCA
Found at i:441446 original size:2 final size:2
Alignment explanation
Indices: 441439--441493 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
441429 TGTCTTATCC
441439 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
441481 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
441494 CACATGTTCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:444944 original size:28 final size:29
Alignment explanation
Indices: 444911--444982 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
444901 CAAAAAAAAT
*
444911 TATTAAATAAAATATTA-AAAAT-TTAAA
1 TATTAAATAAAATATAACAAAATATTAAA
444938 TAATTAAATAAAATACTAACAAAATATTAAA
1 T-ATTAAATAAAATA-TAACAAAATATTAAA
444969 TA-T-AATAAAATATA
1 TATTAAATAAAATATA
444983 TCTTAAAGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 3 0.08
28 22 0.55
29 3 0.08
30 6 0.15
31 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
TATTAAATAAAATATAACAAAATATTAAA
Found at i:444980 original size:17 final size:18
Alignment explanation
Indices: 444948--444981 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
444938 TAATTAAATA
444948 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
444966 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
444982 ATCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:448852 original size:14 final size:14
Alignment explanation
Indices: 448833--448860 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
448823 TGAACCGGTT
448833 TGACCCGACCCGAC
1 TGACCCGACCCGAC
448847 TGACCCGACCCGAC
1 TGACCCGACCCGAC
448861 CATTGACCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:455343 original size:19 final size:19
Alignment explanation
Indices: 455316--455361 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
455306 AAACCGGTTC
*
455316 TGACTGGTATGAACCGATT
1 TGACCGGTATGAACCGATT
*
455335 TGACCGGTATGAACCGGTT
1 TGACCGGTATGAACCGATT
455354 TGACCGGT
1 TGACCGGT
455362 CTGACCCGAC
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:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (19 bp):
TGACCGGTATGAACCGATT
Found at i:458756 original size:16 final size:16
Alignment explanation
Indices: 458735--458769 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
458725 TCGAGAGCAG
458735 TCGATTTTTCAACTTA
1 TCGATTTTTCAACTTA
458751 TCGATTTTTCAACTTA
1 TCGATTTTTCAACTTA
458767 TCG
1 TCG
458770 TACCGAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (16 bp):
TCGATTTTTCAACTTA
Found at i:460526 original size:21 final size:21
Alignment explanation
Indices: 460502--460562 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
460492 TTCAAAGAAA
460502 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
460523 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
460537 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
460558 CATTT
1 CATTT
460563 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:460529 original size:35 final size:35
Alignment explanation
Indices: 460463--460568 Score: 178
Period size: 35 Copynumber: 3.0 Consensus size: 35
460453 AACATCTACC
*
460463 AAAC-TTTACCAAACTTTGAAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCA-TTTTCAAAG
460499 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
460534 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
460569 TTGGTTGTCA
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
35 44 0.65
36 10 0.15
37 14 0.21
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:465113 original size:37 final size:36
Alignment explanation
Indices: 465070--465169 Score: 141
Period size: 35 Copynumber: 2.8 Consensus size: 36
465060 AACAAACATC
* **
465070 TACCAAACTTTGAAAAAACATTTTTCAAAGAAGCATT
1 TACCAAACTTTGAAAAACCA-TTTTCAAAGAAAAATT
465107 TACCAAACTTTG-AAAACCATTTTCAAAGAAAAATT
1 TACCAAACTTTGAAAAACCATTTTCAAAGAAAAATT
*
465142 TATCAAACTTT-AAAAACCATTTTCAAAG
1 TACCAAACTTTGAAAAACCATTTTCAAAG
465170 TTGGTTGCCA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 40 0.69
36 6 0.10
37 12 0.21
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (36 bp):
TACCAAACTTTGAAAAACCATTTTCAAAGAAAAATT
Found at i:465877 original size:14 final size:15
Alignment explanation
Indices: 465858--465890 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
465848 GAAGGGTGAC
*
465858 CAAGGA-AATAAAAA
1 CAAGGACAAAAAAAA
465872 CAAGGACAAAAAAAA
1 CAAGGACAAAAAAAA
465887 CAAG
1 CAAG
465891 TTTCATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.70, C:0.12, G:0.15, T:0.03
Consensus pattern (15 bp):
CAAGGACAAAAAAAA
Found at i:469008 original size:3 final size:3
Alignment explanation
Indices: 469000--469025 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
468990 TGCCCAACAT
469000 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
469026 TCAAACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:469478 original size:20 final size:20
Alignment explanation
Indices: 469455--469493 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
469445 AGTCCTAATT
469455 TAATTAGGAT-AATTAGTTTA
1 TAATTA-GATAAATTAGTTTA
*
469475 TAATTATATAAATTAGTTT
1 TAATTAGATAAATTAGTTT
469494 TGATTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TAATTAGATAAATTAGTTTA
Found at i:472411 original size:35 final size:35
Alignment explanation
Indices: 472358--472452 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
472348 TTATATGTCA
* *
472358 GATTTCAGTTTCTATCAGTTTTAGTTTAGATGACG
1 GATTTCGGTTTCTCTCAGTTTTAGTTTAGATGACG
* *
472393 GGTTTCGGTTTCTCTCAGTTTTAGTTTAGATGTCG
1 GATTTCGGTTTCTCTCAGTTTTAGTTTAGATGACG
*
472428 GATTTTGGTTTCTCTCAGTTTTAGT
1 GATTTCGGTTTCTCTCAGTTTTAGT
472453 CTTTCTTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.49
Consensus pattern (35 bp):
GATTTCGGTTTCTCTCAGTTTTAGTTTAGATGACG
Found at i:477428 original size:20 final size:19
Alignment explanation
Indices: 477403--477456 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
477393 GCGAAATAAA
477403 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
477423 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
477443 AATCGCAACGCGAT
1 AATCGCAACGCGAT
477457 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:477534 original size:20 final size:20
Alignment explanation
Indices: 477506--477558 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
477496 GATTTTCCAT
*
477506 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
*
477526 AATCACAACGCGAACATATA
1 AATCGCAACGCGAACATATA
477546 AATCGCAACGCGA
1 AATCGCAACGCGA
477559 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:477614 original size:20 final size:20
Alignment explanation
Indices: 477567--477775 Score: 177
Period size: 20 Copynumber: 10.3 Consensus size: 20
477557 GATTCTGACT
*
477567 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
477588 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
477608 ATTGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
477629 ATCGCAACACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
477649 ATCACAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
477669 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
477689 ATCGCAACGAGAATACATAA
1 ATCGCAACGCGTATCCGTAA
**
477709 ATCGCAATACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
477729 ATCGTAATGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
477749 ATCGCAATGCGAATCTGTAA
1 ATCGCAACGCGTATCCGTAA
477769 ATCGCAA
1 ATCGCAA
477776 TGAGATTCTG
Statistics
Matches: 149, Mismatches: 36, Indels: 7
0.78 0.19 0.04
Matches are distributed among these distances:
20 117 0.79
21 32 0.21
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:477682 original size:40 final size:40
Alignment explanation
Indices: 477567--477780 Score: 257
Period size: 40 Copynumber: 5.3 Consensus size: 40
477557 GATTCTGACT
* *
477567 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
* * *
477608 ATTGCAACGACAATACGTAAAATCGCAACACGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
* *
477649 ATCACAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* **
477689 ATCGCAACGAGAATACATAAATCGCAATACGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* * * * * *
477729 ATCGTAATGCGAATACGTAAATCGCAATGCGAATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
*
477769 ATCGCAATGAGA
1 ATCGCAACGAGA
477781 TTCTGACTAT
Statistics
Matches: 149, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
40 98 0.66
41 51 0.34
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
Done.