Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 209 of 433
Found at i:65587534 original size:20 final size:21
Alignment explanation
Indices: 65587487--65587544 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
65587477 AAAAAGAAAT
* *
65587487 GAGCTGAATCGAGCTGAATTC
1 GAGCTCAAACGAGCTGAATTC
*
65587508 TAGCTCAAACGAGCTGAA-TC
1 GAGCTCAAACGAGCTGAATTC
**
65587528 GAGCTCAAGTGAGCTGA
1 GAGCTCAAACGAGCTGA
65587545 TGGGAGCTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (21 bp):
GAGCTCAAACGAGCTGAATTC
Found at i:65589115 original size:30 final size:30
Alignment explanation
Indices: 65589020--65589116 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
65589010 AGCTCACTCC
* * *
65589020 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
65589050 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
65589080 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
65589110 TAGCTCA
1 TAGCTCA
65589117 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:65593298 original size:13 final size:13
Alignment explanation
Indices: 65593234--65593332 Score: 53
Period size: 13 Copynumber: 7.3 Consensus size: 13
65593224 CAATTGAGAG
65593234 AAAA-AGAAAAGA
1 AAAAGAGAAAAGA
*
65593246 AAAGTGAGAAAA-A
1 AAA-AGAGAAAAGA
* *
65593259 AAAACAAGAATAGCAA
1 AAAA-GAGAAAAG--A
65593275 AAAGAGAGAAAAGA
1 AAA-AGAGAAAAGA
* *
65593289 AAATGAGAAAA-T
1 AAAAGAGAAAAGA
65593301 AAAAGATGAACAAGA
1 AAAAGA-GAA-AAGA
65593316 AAAAGA-AAATAGA
1 AAAAGAGAAA-AGA
65593329 AAAA
1 AAAA
65593333 AAGCTTGATT
Statistics
Matches: 66, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
12 9 0.14
13 28 0.42
14 12 0.18
15 6 0.09
16 10 0.15
17 1 0.02
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (13 bp):
AAAAGAGAAAAGA
Found at i:65593304 original size:27 final size:25
Alignment explanation
Indices: 65593274--65593326 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
65593264 AAGAATAGCA
65593274 AAAAGA-GAGAAAAGAAAATGAGAAAAT
1 AAAAGATGA-AAAAGAAAA--AGAAAAT
*
65593301 AAAAGATGAACAAGAAAAAGAAAAT
1 AAAAGATGAAAAAGAAAAAGAAAAT
65593326 A
1 A
65593327 GAAAAAAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
27 14 0.58
28 2 0.08
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.08
Consensus pattern (25 bp):
AAAAGATGAAAAAGAAAAAGAAAAT
Found at i:65593319 original size:42 final size:43
Alignment explanation
Indices: 65593238--65593321 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
65593228 TGAGAGAAAA
*
65593238 AGAAAAGAAAAGTGAGAAAAAAAAACAAGAATAGCAAAAAGAG
1 AGAAAAGAAAAGTGAGAAAAAAAAACAAGAAAAGCAAAAAGAG
* * *
65593281 AGAAAAGAAAA-TGAGAAAATAAAAGATGAACAAG-AAAAAGA
1 AGAAAAGAAAAGTGAGAAAAAAAAACAAGAA-AAGCAAAAAGA
65593322 AAATAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 23 0.64
43 13 0.36
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.06
Consensus pattern (43 bp):
AGAAAAGAAAAGTGAGAAAAAAAAACAAGAAAAGCAAAAAGAG
Found at i:65595270 original size:17 final size:17
Alignment explanation
Indices: 65595245--65595287 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
65595235 GAGACAGCCA
*
65595245 CCATACATGCACTTAAG
1 CCATTCATGCACTTAAG
* * *
65595262 CCATTCATGCATTTGAT
1 CCATTCATGCACTTAAG
65595279 CCATTCATG
1 CCATTCATG
65595288 GACTAGCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (17 bp):
CCATTCATGCACTTAAG
Found at i:65595718 original size:30 final size:30
Alignment explanation
Indices: 65595684--65595750 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
65595674 TAAACTAAAA
65595684 TGAGCTAAGCTTTAGCTCATGAGCT-AAAG
1 TGAGCTAAGCTTTAGCTCATGAGCTGAAAG
* * *
65595713 TTGAGCTAAGGTTTAGCTCGTGAGTTGAAAG
1 -TGAGCTAAGCTTTAGCTCATGAGCTGAAAG
65595744 TGAGCTA
1 TGAGCTA
65595751 GGAGTGAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTGAAAG
Found at i:65597873 original size:248 final size:248
Alignment explanation
Indices: 65597433--65597929 Score: 825
Period size: 248 Copynumber: 2.0 Consensus size: 248
65597423 AAAAAAGTTC
* * *
65597433 TTGTAACACCCCTTACCAATACCCGAGGCCGGGATAAGGTACGAGGTGTTACTGGACAAACATAC
1 TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGGTGCTACCGGACAAACATAC
*
65597498 AAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACGTTCATTCACTTACA
66 AAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTACA
* * * *
65597563 CATAGTCCCTTATTTGAGTCTATGAAGCCCAAAACATACTTTAGAAAGTGTTCGGGACTAAACCG
131 CATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCAGAACTAAACCG
*
65597628 AGAACTTACAAAAATCTTGGAAATTTCATGCTTTAAGGCTCCACACGCCCGTG
196 AGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
** *
65597681 TTGTAACACCCCTTACCCGTACCCGACGCTGGGATAAGGTACGAGGCT-CTACCGGACAAACATA
1 TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGG-TGCTACCGGACAAACATA
* *
65597745 CAAATATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAGCATTCATTCACTTAC
65 CAAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTAC
* * *
65597810 ACATAGTCCTTTATTTGAGTTTACGGAGCCCAAAACATACTTTAGAAAGGGTTCAGAACTAAACC
130 ACATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCAGAACTAAACC
65597875 GAGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
195 GAGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
65597929 T
1 T
65597930 CCCAAAGTCG
Statistics
Matches: 231, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
248 230 1.00
249 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (248 bp):
TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGGTGCTACCGGACAAACATAC
AAACATTAAACTAAAATACGGGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTACA
CATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCAGAACTAAACCG
AGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
Found at i:65598361 original size:2 final size:2
Alignment explanation
Indices: 65598354--65598383 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
65598344 GAGACTAGTC
65598354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65598384 CATGTCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65599619 original size:63 final size:64
Alignment explanation
Indices: 65599439--65599621 Score: 203
Period size: 63 Copynumber: 2.8 Consensus size: 64
65599429 ATATAGTTCG
* * * *
65599439 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGT
1 GCTCTCTTGT-CTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACA-TATATCCCGT
65599501 A
64 A
* * * *
65599502 GCTCTCTTGTCTACATGGTGTCCTTCACTTGGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCG
65599567 TA
63 TA
* *
65599569 GCTCTC-TGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACAT
65599622 CATAATGTCT
Statistics
Matches: 100, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 46 0.46
66 36 0.36
67 15 0.15
68 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCGTA
Found at i:65600388 original size:30 final size:30
Alignment explanation
Indices: 65600354--65600414 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
65600344 TCCTTAACTC
65600354 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
65600384 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
65600414 A
1 A
65600415 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:65602715 original size:106 final size:106
Alignment explanation
Indices: 65602588--65602807 Score: 440
Period size: 106 Copynumber: 2.1 Consensus size: 106
65602578 CCATGGCGTC
65602588 TTTGCTGAAGAAAAATGATGATATCTCTAGATTTTTCAAATTTGTCTTGTTTTTATATGTTTAAT
1 TTTGCTGAAGAAAAATGATGATATCTCTAGATTTTTCAAATTTGTCTTGTTTTTATATGTTTAAT
65602653 TTGCAAAATTTCCCATTTTGCCCTTGTTTCTCCTTGTCTTT
66 TTGCAAAATTTCCCATTTTGCCCTTGTTTCTCCTTGTCTTT
65602694 TTTGCTGAAGAAAAATGATGATATCTCTAGATTTTTCAAATTTGTCTTGTTTTTATATGTTTAAT
1 TTTGCTGAAGAAAAATGATGATATCTCTAGATTTTTCAAATTTGTCTTGTTTTTATATGTTTAAT
65602759 TTGCAAAATTTCCCATTTTGCCCTTGTTTCTCCTTGTCTTT
66 TTGCAAAATTTCCCATTTTGCCCTTGTTTCTCCTTGTCTTT
65602800 TTTGCTGA
1 TTTGCTGA
65602808 TTTTCTTGTC
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 114 1.00
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (106 bp):
TTTGCTGAAGAAAAATGATGATATCTCTAGATTTTTCAAATTTGTCTTGTTTTTATATGTTTAAT
TTGCAAAATTTCCCATTTTGCCCTTGTTTCTCCTTGTCTTT
Found at i:65603855 original size:2 final size:2
Alignment explanation
Indices: 65603848--65603874 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65603838 GAGACTAGTC
65603848 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
65603875 CATGTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65607108 original size:30 final size:30
Alignment explanation
Indices: 65607074--65607170 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65607064 TAAACTAAAA
65607074 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65607104 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65607134 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65607164 TGAGCTA
1 TGAGCTA
65607171 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65609331 original size:30 final size:29
Alignment explanation
Indices: 65609279--65609363 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
65609269 TTCTTTTGTT
* *
65609279 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCTTC-TCTTTTTCAATC
65609309 TCAAATTTC-TTTTCGTTCTCTTTTTCAATC
1 TC-AATTTCTTTTTC-TTCTCTTTTTCAATC
* *
65609339 TCATTTTCTTTTTCTTTTCTTTTTC
1 TCAATTTCTTTTTCTTCTCTTTTTC
65609364 TTTTCAAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 15 0.31
30 25 0.52
31 8 0.17
ACGTcount: A:0.12, C:0.24, G:0.01, T:0.64
Consensus pattern (29 bp):
TCAATTTCTTTTTCTTCTCTTTTTCAATC
Found at i:65609358 original size:11 final size:11
Alignment explanation
Indices: 65609342--65609368 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
65609332 TTCAATCTCA
65609342 TTTTCTTTTTC
1 TTTTCTTTTTC
65609353 TTTTCTTTTTC
1 TTTTCTTTTTC
65609364 TTTTC
1 TTTTC
65609369 AAAGGCTTTT
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:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:65609393 original size:12 final size:11
Alignment explanation
Indices: 65609363--65609389 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
65609353 TTTTCTTTTT
65609363 CTTTTCAAAGG
1 CTTTTCAAAGG
65609374 CTTTTCAAAGG
1 CTTTTCAAAGG
65609385 CTTTT
1 CTTTT
65609390 TCAAGTTCTC
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:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (11 bp):
CTTTTCAAAGG
Found at i:65609451 original size:5 final size:5
Alignment explanation
Indices: 65609441--65609497 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65609431 CTCTTGCCTC
*
65609441 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
65609488 TCTTT TCTTT
1 TCTTT TCTTT
65609498 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:65609481 original size:15 final size:14
Alignment explanation
Indices: 65609441--65609497 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65609431 CTCTTGCCTC
*
65609441 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
65609456 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
65609471 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
65609488 TCTTTTCTTT
1 TCTTTTCTTT
65609498 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:65609498 original size:21 final size:21
Alignment explanation
Indices: 65609441--65609508 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
65609431 CTCTTGCCTC
* *
65609441 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
65609462 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
65609483 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
65609503 CTCTTT
1 -TCTTT
65609509 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:65612556 original size:30 final size:30
Alignment explanation
Indices: 65612522--65612582 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
65612512 TCCTTAACTC
65612522 AAACTTTAGAAAAATTACAATTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
* * * * *
65612552 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
65612582 A
1 A
65612583 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTGCCCCT
Found at i:65615245 original size:30 final size:31
Alignment explanation
Indices: 65615173--65615260 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 31
65615163 TCAACTCACA
* *
65615173 AGCTAAACCTTAGCTCAACTTCAGCT-TAGG
1 AGCTAAACCTTAGCTCAACTTTAGCTCAAGG
* *
65615203 AGTTTAACCTTAGCTCAACTTTAGCTCAAGG
1 AGCTAAACCTTAGCTCAACTTTAGCTCAAGG
* *
65615234 -GCTAAAGCTTAGCTC-ATTTTAGCTCAA
1 AGCTAAACCTTAGCTCAACTTTAGCTCAA
65615261 ACCCGATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 11 0.22
30 35 0.71
31 3 0.06
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (31 bp):
AGCTAAACCTTAGCTCAACTTTAGCTCAAGG
Found at i:65624341 original size:12 final size:13
Alignment explanation
Indices: 65624324--65624358 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
65624314 CATAAATCAC
65624324 TTTTTTTTTCG-A
1 TTTTTTTTTCGAA
65624336 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
65624349 TTTTTTTTTC
1 TTTTTTTTTC
65624359 AAACTTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:65630788 original size:15 final size:15
Alignment explanation
Indices: 65630768--65630814 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
65630758 AAGATGGGTT
65630768 TTTATGGATATGAAG
1 TTTATGGATATGAAG
* * *
65630783 TTTATGTAGATG-GG
1 TTTATGGATATGAAG
*
65630797 TTTATGGATATAAAG
1 TTTATGGATATGAAG
65630812 TTT
1 TTT
65630815 TTGTAGGTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.45
Consensus pattern (15 bp):
TTTATGGATATGAAG
Found at i:65630806 original size:29 final size:30
Alignment explanation
Indices: 65630759--65630820 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
65630749 AAGGATTCAA
*
65630759 AGATGGGTTTTTATGGATATGAAGTTTATGT
1 AGATGGG-TTTTATGGATATAAAGTTTATGT
*
65630790 AGATGGG-TTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTTATGGATATAAAGTTTATGT
65630819 AG
1 AG
65630821 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 22 0.76
31 7 0.24
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (30 bp):
AGATGGGTTTTATGGATATAAAGTTTATGT
Found at i:65631768 original size:24 final size:24
Alignment explanation
Indices: 65631719--65631769 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
65631709 ATGAATCGGC
* *
65631719 AAAAGCTGAAATGCCAAAATGTCA
1 AAAAGCTGAAATGCCAAAAAGCCA
*
65631743 AAAAGCTTAAATGCCAAAAAGCCA
1 AAAAGCTGAAATGCCAAAAAGCCA
65631767 AAA
1 AAA
65631770 TTTTGGCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.18, G:0.14, T:0.14
Consensus pattern (24 bp):
AAAAGCTGAAATGCCAAAAAGCCA
Found at i:65631770 original size:16 final size:16
Alignment explanation
Indices: 65631731--65631770 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
65631721 AAGCTGAAAT
*
65631731 GCCAAAATGTCAAAAA
1 GCCAAAATGCCAAAAA
**
65631747 GCTTAAATGCCAAAAA
1 GCCAAAATGCCAAAAA
65631763 GCCAAAAT
1 GCCAAAAT
65631771 TTTGGCTTCG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.15
Consensus pattern (16 bp):
GCCAAAATGCCAAAAA
Found at i:65632318 original size:30 final size:30
Alignment explanation
Indices: 65632284--65632384 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
65632274 AGCTCACTCC
*
65632284 TAGCTCATTTTCAACTCACGAGCTAAACCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
** * * * * *
65632314 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
* *
65632344 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ATTTTCAGCTCACGAGCTAAACCT
65632374 TAGCTCATTTT
1 TAGCTCATTTT
65632385 AGTTTAAACT
Statistics
Matches: 53, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
29 4 0.08
30 46 0.87
31 3 0.06
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (30 bp):
TAGCTCATTTTCAGCTCACGAGCTAAACCT
Found at i:65632777 original size:13 final size:13
Alignment explanation
Indices: 65632759--65632783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65632749 TGTATTGATA
65632759 TGTGTTCACACCT
1 TGTGTTCACACCT
65632772 TGTGTTCACACC
1 TGTGTTCACACC
65632784 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:65633891 original size:30 final size:30
Alignment explanation
Indices: 65633796--65633892 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
65633786 AGCTCACTCC
* *
65633796 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* **
65633826 TAGCTCAACTTTAGCAT-AGGAG-TTTAGCCT
1 TAGCTCAACTTTAGC-TCACGAGCTAAAG-CT
*
65633856 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
65633886 TAGCTCA
1 TAGCTCA
65633893 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
29 3 0.06
30 40 0.77
31 9 0.17
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:65635571 original size:10 final size:10
Alignment explanation
Indices: 65635556--65635582 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65635546 TAAGTTGAAG
65635556 TTGAGCTGAT
1 TTGAGCTGAT
65635566 TTGAGCTGAT
1 TTGAGCTGAT
65635576 TTGAGCT
1 TTGAGCT
65635583 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:65635951 original size:17 final size:17
Alignment explanation
Indices: 65635931--65635975 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
65635921 GATGATAGAA
65635931 TGCATGAATGGCTTAAG
1 TGCATGAATGGCTTAAG
65635948 TGCATGAATGGCTTAAG
1 TGCATGAATGGCTTAAG
*
65635965 TGCATGTATGG
1 TGCATGAATGG
65635976 TGGCTATCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (17 bp):
TGCATGAATGGCTTAAG
Found at i:65638128 original size:6 final size:5
Alignment explanation
Indices: 65638104--65638166 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
65638094 AAGAGAAAAC
*
65638104 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
65638152 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
65638167 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:65638134 original size:12 final size:10
Alignment explanation
Indices: 65638104--65638166 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
65638094 AAGAGAAAAC
65638104 AAAGAAAAGA
1 AAAGAAAAGA
65638114 AAAGAAAAAGCA
1 AAAG-AAAAG-A
65638126 AAAGCAAAAGA
1 AAAG-AAAAGA
*
65638137 AGA-AAAAGA
1 AAAGAAAAGA
65638146 AAATGAAATA-A
1 AAA-GAAA-AGA
65638157 AAAGAAAAGA
1 AAAGAAAAGA
65638167 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:65644566 original size:20 final size:23
Alignment explanation
Indices: 65644541--65644591 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 23
65644531 TTTGGCATCT
65644541 ATGTTCACAC-AATA-A-TAAAA
1 ATGTTCACACTAATATATTAAAA
65644561 ATGTTCACACTAATATATTAAAA
1 ATGTTCACACTAATATATTAAAA
65644584 ATGGTTCA
1 AT-GTTCA
65644592 TGAATTCGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.37
21 4 0.15
22 1 0.04
23 7 0.26
24 5 0.19
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (23 bp):
ATGTTCACACTAATATATTAAAA
Found at i:65649624 original size:30 final size:28
Alignment explanation
Indices: 65649553--65649637 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
65649543 TTGAGAGAAA
*
65649553 AAGAAAAGAAAAGTGAGAAAAAGAAAAC
1 AAGAAAAGAAAAGAGAGAAAAAGAAAAC
* *
65649581 AAGAATAGCAAAAGAGAGAGAAAAGAAAAT
1 AAGAAAAG-AAAAGAGAGA-AAAAGAAAAC
* *
65649611 GAGAAAAGAAAA-AGATGAACAAGAAAA
1 AAGAAAAGAAAAGAGA-GAAAAAGAAAA
65649638 AGAAGATAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 18 0.38
29 15 0.31
30 15 0.31
ACGTcount: A:0.69, C:0.04, G:0.22, T:0.05
Consensus pattern (28 bp):
AAGAAAAGAAAAGAGAGAAAAAGAAAAC
Found at i:65649636 original size:15 final size:13
Alignment explanation
Indices: 65649597--65649640 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
65649587 AGCAAAAGAG
65649597 AGAGAAAAGAAAA
1 AGAGAAAAGAAAA
*
65649610 TGAGAAAAGAAAA
1 AGAGAAAAGAAAA
65649623 AGATGAACAAGAAAA
1 AGA-GAA-AAGAAAA
65649638 AGA
1 AGA
65649641 AGATAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 14 0.52
14 3 0.11
15 10 0.37
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (13 bp):
AGAGAAAAGAAAA
Found at i:65650648 original size:21 final size:20
Alignment explanation
Indices: 65650612--65650660 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
65650602 ATCAGCTCAC
*
65650612 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
*
65650632 TTGAGCTCGAATTTAGCTTGT
1 TTGAGCTCG-ATTTAGCTCGT
*
65650653 TTCAGCTC
1 TTGAGCTC
65650661 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:65650902 original size:13 final size:13
Alignment explanation
Indices: 65650884--65650912 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65650874 AATAGTTGTG
65650884 TGTTATTTAATTA
1 TGTTATTTAATTA
65650897 TGTTATTTAATTA
1 TGTTATTTAATTA
65650910 TGT
1 TGT
65650913 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:65653092 original size:18 final size:18
Alignment explanation
Indices: 65653069--65653118 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
65653059 GAAAGAAAAA
*
65653069 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
65653087 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
65653105 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
65653119 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:65653095 original size:24 final size:24
Alignment explanation
Indices: 65653062--65653141 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
65653052 AAGAAATGAA
65653062 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
65653086 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
65653110 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
65653134 AGAAAAAG
1 AGAAAAAG
65653142 CATGTGAACA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:65654797 original size:10 final size:10
Alignment explanation
Indices: 65654784--65654829 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
65654774 AGCTCACTTG
65654784 AGCTCGTTTT
1 AGCTCGTTTT
*
65654794 AGCTCGTTTG
1 AGCTCGTTTT
*
65654804 AGCTCGAATTT
1 AGCTCG-TTTT
*
65654815 AGCTCGTTTC
1 AGCTCGTTTT
65654825 AGCTC
1 AGCTC
65654830 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:65654817 original size:21 final size:20
Alignment explanation
Indices: 65654781--65654829 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
65654771 ATCAGCTCAC
*
65654781 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
65654801 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
65654822 TTCAGCTC
1 TTGAGCTC
65654830 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:65655071 original size:13 final size:13
Alignment explanation
Indices: 65655053--65655081 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65655043 AATAGTTGTG
65655053 TGTTATTTAATTA
1 TGTTATTTAATTA
65655066 TGTTATTTAATTA
1 TGTTATTTAATTA
65655079 TGT
1 TGT
65655082 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:65660119 original size:26 final size:26
Alignment explanation
Indices: 65660090--65660197 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
65660080 TGATACAAAT
65660090 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
65660116 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
65660142 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
65660168 TGATAATGGTTTAGGTAAATGTTCGA
1 TGATAATGGGTTAGGTAAATGTTCCA
65660194 TGAT
1 TGAT
65660198 GGGAATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:65661713 original size:26 final size:26
Alignment explanation
Indices: 65661684--65661736 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
65661674 GTTACAGTTT
*
65661684 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCATAGG-GATAAATTGACCGAAA
* *
65661710 TACCCATAGGGTTAAATTGACCTAAA
1 TACCCATAGGGATAAATTGACCGAAA
65661736 T
1 T
65661737 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCATAGGGATAAATTGACCGAAA
Found at i:65671617 original size:18 final size:19
Alignment explanation
Indices: 65671594--65671632 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
65671584 TTTATCTCAA
*
65671594 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
65671612 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
65671631 TT
1 TT
65671633 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:65671765 original size:5 final size:5
Alignment explanation
Indices: 65671755--65671811 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65671745 CTTTTGCCTC
*
65671755 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
65671802 TCTTT TCTTT
1 TCTTT TCTTT
65671812 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:65671795 original size:15 final size:14
Alignment explanation
Indices: 65671755--65671811 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65671745 CTTTTGCCTC
*
65671755 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
65671770 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
65671785 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
65671802 TCTTTTCTTT
1 TCTTTTCTTT
65671812 GTTTTCTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:65671812 original size:21 final size:21
Alignment explanation
Indices: 65671755--65671816 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
65671745 CTTTTGCCTC
* *
65671755 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
65671776 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
65671797 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
65671817 CTCGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:65674028 original size:29 final size:29
Alignment explanation
Indices: 65673995--65674054 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
65673985 ATAACCAAAC
*
65673995 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
65674024 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
65674053 CT
1 CT
65674055 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:65674047 original size:15 final size:15
Alignment explanation
Indices: 65674001--65674048 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65673991 AAACCTACAA
*
65674001 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
65674016 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
65674030 AAACTTCATATCCAT
1 AAACTTCATATCCAT
65674045 AAAC
1 AAAC
65674049 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:65676813 original size:20 final size:20
Alignment explanation
Indices: 65676790--65676837 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
65676780 AGCTCCGTCT
65676790 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
65676810 AGCTCTTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
65676830 AGCTCAAC
1 AGCTCAAC
65676838 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:65681317 original size:14 final size:14
Alignment explanation
Indices: 65681295--65681342 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
65681285 ACCTAAACCG
* *
65681295 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
65681309 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
65681323 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
65681337 ACCATT
1 ACCATT
65681343 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:65682248 original size:15 final size:14
Alignment explanation
Indices: 65682227--65682268 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
65682217 ACTTTTCCCA
65682227 CTCTTTTTC-TTTT
1 CTCTTTTTCTTTTT
*
65682240 CATTCTTTTTATTTTT
1 C--TCTTTTTCTTTTT
65682256 CTCTTTTTCTTTT
1 CTCTTTTTCTTTT
65682269 GATCTCTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 11 0.46
15 7 0.29
16 5 0.21
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (14 bp):
CTCTTTTTCTTTTT
Found at i:65684552 original size:14 final size:14
Alignment explanation
Indices: 65684533--65684563 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
65684523 CTATTTGAAC
65684533 CTTTCTTAACCTTT
1 CTTTCTTAACCTTT
*
65684547 CTTTCTTAGCCTTT
1 CTTTCTTAACCTTT
65684561 CTT
1 CTT
65684564 CAACTATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.29, G:0.03, T:0.58
Consensus pattern (14 bp):
CTTTCTTAACCTTT
Found at i:65686018 original size:14 final size:14
Alignment explanation
Indices: 65685977--65686020 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
65685967 TATATGTTCT
*
65685977 TTTTTTTATACGAA
1 TTTTTTTATATGAA
*
65685991 TTTTTTTGTATGAA
1 TTTTTTTATATGAA
65686005 TTTTTTTCAT-TGAA
1 TTTTTTT-ATATGAA
65686019 TT
1 TT
65686021 ATAATCTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 25 0.96
15 1 0.04
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64
Consensus pattern (14 bp):
TTTTTTTATATGAA
Found at i:65687118 original size:14 final size:14
Alignment explanation
Indices: 65687099--65687143 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
65687089 AACTCATCTT
*
65687099 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
65687113 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
65687126 AATTTAATTTAATG
1 AGTTTAATTTAATG
65687140 AGTT
1 AGTT
65687144 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:65688134 original size:29 final size:29
Alignment explanation
Indices: 65688101--65688160 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
65688091 ATAACCAAAC
* *
65688101 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
65688130 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
65688159 CT
1 CT
65688161 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:65688153 original size:15 final size:15
Alignment explanation
Indices: 65688107--65688154 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65688097 AAACCTACAA
*
65688107 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
65688122 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
65688136 AAACTTCATATCCAT
1 AAACTTCATATCCAT
65688151 AAAC
1 AAAC
65688155 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:65692553 original size:30 final size:30
Alignment explanation
Indices: 65692519--65692615 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65692509 TAAACTAAAA
65692519 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65692549 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65692579 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65692609 TGAGCTA
1 TGAGCTA
65692616 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65693063 original size:19 final size:19
Alignment explanation
Indices: 65693039--65693078 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
65693029 AGCTCCCATG
65693039 TAGCTCCGCACCAGCTCAT
1 TAGCTCCGCACCAGCTCAT
* *
65693058 TAGCTCGGGACCAGCTCAT
1 TAGCTCCGCACCAGCTCAT
65693077 TA
1 TA
65693079 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (19 bp):
TAGCTCCGCACCAGCTCAT
Found at i:65695925 original size:30 final size:30
Alignment explanation
Indices: 65695840--65695935 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
65695830 TAAACTAAAA
* * *
65695840 TGAGCTAAGCTTTAGCTCGCGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
65695870 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
*
65695900 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-A
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
65695929 TGAGCTA
1 TGAGCTA
65695936 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
29 7 0.14
30 43 0.86
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:65699889 original size:10 final size:10
Alignment explanation
Indices: 65699874--65699900 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65699864 TAAGTTGAAG
65699874 TTGAGCTGAT
1 TTGAGCTGAT
65699884 TTGAGCTGAT
1 TTGAGCTGAT
65699894 TTGAGCT
1 TTGAGCT
65699901 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:65704367 original size:12 final size:12
Alignment explanation
Indices: 65704346--65704400 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
65704336 AAAAAGCCTT
65704346 TGAAAAA-AAAA
1 TGAAAAAGAAAA
*
65704357 -GAAAATGAAAA
1 TGAAAAAGAAAA
* * *
65704368 TGAAAATGAGAT
1 TGAAAAAGAAAA
*
65704380 TGAAAAAGAGAA
1 TGAAAAAGAAAA
65704392 TGAAAAAGA
1 TGAAAAAGA
65704401 GTTTGAGAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
10 5 0.14
11 4 0.11
12 28 0.76
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:65704393 original size:24 final size:24
Alignment explanation
Indices: 65704357--65704420 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
65704347 GAAAAAAAAA
* *
65704357 GAAAATGAAAATGAAAATGAGATT
1 GAAAAAGAAAATGAAAAAGAGATT
* *
65704381 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAATGAAAAAGAGATT
* * *
65704405 GAGAGAGAAAAAGAAA
1 GAAAAAGAAAATGAAA
65704421 TTGAGATAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAAAAGAAAATGAAAAAGAGATT
Found at i:65704401 original size:12 final size:12
Alignment explanation
Indices: 65704366--65704401 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
65704356 AGAAAATGAA
*
65704366 AATGAAAATGAG
1 AATGAAAAAGAG
*
65704378 ATTGAAAAAGAG
1 AATGAAAAAGAG
65704390 AATGAAAAAGAG
1 AATGAAAAAGAG
65704402 TTTGAGAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (12 bp):
AATGAAAAAGAG
Found at i:65709483 original size:10 final size:10
Alignment explanation
Indices: 65709470--65709535 Score: 87
Period size: 10 Copynumber: 6.5 Consensus size: 10
65709460 AGCTCACTTG
65709470 AGCTCGTTTT
1 AGCTCGTTTT
65709480 AGCTCGTTTT
1 AGCTCGTTTT
65709490 AGCTCGTTTT
1 AGCTCGTTTT
* *
65709500 ATCTCGTTTG
1 AGCTCGTTTT
*
65709510 AGCTCGAATTT
1 AGCTCG-TTTT
*
65709521 AGCTCGTTTC
1 AGCTCGTTTT
65709531 AGCTC
1 AGCTC
65709536 ATTCCTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
10 40 0.83
11 8 0.17
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:65712503 original size:30 final size:29
Alignment explanation
Indices: 65712469--65712528 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
65712459 TCCTTAACTC
65712469 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTT-GAAAAATTACAATTTTGCCCCT
* * * *
65712499 AAACTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGAAAAATTACAATTTTGCCCCT
65712528 A
1 A
65712529 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (29 bp):
AAACTTTGAAAAATTACAATTTTGCCCCT
Found at i:65713359 original size:13 final size:13
Alignment explanation
Indices: 65713341--65713366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
65713331 GGCTATTACA
65713341 TATTTAATTATGT
1 TATTTAATTATGT
65713354 TATTTAATTATGT
1 TATTTAATTATGT
65713367 AGGTTAGCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTAATTATGT
Found at i:65719347 original size:10 final size:10
Alignment explanation
Indices: 65719334--65719379 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
65719324 AGCTCACTTG
65719334 AGCTCGTTTT
1 AGCTCGTTTT
*
65719344 AGCTCGTTTG
1 AGCTCGTTTT
*
65719354 AGCTCGAATTT
1 AGCTCG-TTTT
*
65719365 AGCTCGTTTC
1 AGCTCGTTTT
65719375 AGCTC
1 AGCTC
65719380 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:65719367 original size:21 final size:20
Alignment explanation
Indices: 65719331--65719379 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
65719321 ATCAGCTCAC
*
65719331 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
65719351 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
65719372 TTCAGCTC
1 TTGAGCTC
65719380 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:65719622 original size:13 final size:13
Alignment explanation
Indices: 65719604--65719632 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
65719594 AATAGTTGTG
65719604 TGTTATTTAATTA
1 TGTTATTTAATTA
65719617 TGTTATTTAATTA
1 TGTTATTTAATTA
65719630 TGT
1 TGT
65719633 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:65722007 original size:30 final size:30
Alignment explanation
Indices: 65721973--65722069 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65721963 TAAACTAAAA
65721973 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65722003 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65722033 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65722063 TGAGCTA
1 TGAGCTA
65722070 GGAGTGCTCA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65722561 original size:20 final size:20
Alignment explanation
Indices: 65722538--65722585 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
65722528 AGCTCCGTCC
65722538 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
65722558 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
65722578 AGCTCAAC
1 AGCTCAAC
65722586 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:65724533 original size:29 final size:29
Alignment explanation
Indices: 65724500--65724559 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
65724490 AAGGATTCAA
* * *
65724500 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGACATAAAGTTTATGT
*
65724529 AGATGGATTTATGGACATAAAGTTTTTGT
1 AGATGGATTTATGGACATAAAGTTTATGT
65724558 AG
1 AG
65724560 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.40
Consensus pattern (29 bp):
AGATGGATTTATGGACATAAAGTTTATGT
Found at i:65726707 original size:42 final size:42
Alignment explanation
Indices: 65726645--65726741 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
65726635 AGATTATGAG
* * *
65726645 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
65726687 AGAAAATGAGAGAATCTTGAATGAAATCTAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
65726729 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
65726742 AAAGAAAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.57, C:0.05, G:0.23, T:0.15
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:65726768 original size:18 final size:18
Alignment explanation
Indices: 65726745--65726794 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
65726735 GAAAGAAAAA
*
65726745 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
65726763 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
65726781 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
65726795 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:65726771 original size:24 final size:24
Alignment explanation
Indices: 65726738--65726819 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
65726728 AAGAAATGAA
65726738 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
65726762 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
65726786 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
65726810 AGAAAAAGAA
1 AGAAAAAGAA
65726820 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:65726833 original size:48 final size:48
Alignment explanation
Indices: 65726736--65726856 Score: 120
Period size: 48 Copynumber: 2.5 Consensus size: 48
65726726 CAAAGAAATG
* * * **
65726736 AAAGAAAAAGAAAAAGAGATTGAGAGTGAAAAAGAAAATGAGATTGAA
1 AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGAAAGAA
* **
65726784 AAAGAGAATGAAAAAGAGTTTGAGAGAGAAAAAGAATGTGA-ACAAGAA
1 AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGA-AAGAA
* *
65726832 AAA-AGAGTGGAAAAAGAAATTGAGA
1 AAAGAGAAT-GAAAAAGAGATTGAGA
65726857 TAATAGAATC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
47 5 0.08
48 55 0.92
ACGTcount: A:0.60, C:0.01, G:0.26, T:0.12
Consensus pattern (48 bp):
AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGAAAGAA
Found at i:65726848 original size:18 final size:19
Alignment explanation
Indices: 65726812--65726850 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
65726802 TTTGAGAGAG
*
65726812 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
65726831 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
65726849 AA
1 AA
65726851 TTGAGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:65728434 original size:20 final size:20
Alignment explanation
Indices: 65728411--65728458 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65728401 AGCTCCGTCC
*
65728411 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTAAGCTCATTTG
*** *
65728431 AGCTCGTTTAAGCTCGTTTG
1 AGCTCAACTAAGCTCATTTG
65728451 AGCTCAAC
1 AGCTCAAC
65728459 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTAAGCTCATTTG
Found at i:65729800 original size:19 final size:19
Alignment explanation
Indices: 65729776--65729815 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
65729766 AGCTCCCATG
65729776 TAGCTCGGGACCAGCTCAT
1 TAGCTCGGGACCAGCTCAT
65729795 TAGCTCGGGACCAGCTCAT
1 TAGCTCGGGACCAGCTCAT
65729814 TA
1 TA
65729816 TCAGCTCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (19 bp):
TAGCTCGGGACCAGCTCAT
Found at i:65740787 original size:10 final size:10
Alignment explanation
Indices: 65740772--65740798 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65740762 TAAGTTGAAG
65740772 TTGAGCTGAT
1 TTGAGCTGAT
65740782 TTGAGCTGAT
1 TTGAGCTGAT
65740792 TTGAGCT
1 TTGAGCT
65740799 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:65745590 original size:30 final size:30
Alignment explanation
Indices: 65745556--65745637 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
65745546 TAAACTAAAA
65745556 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * * *
65745586 TGAGCTGAGGC-TAAACTCCTAAGCTGAATT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
65745616 TGAGCTAAGGTTTAGCTCGTGA
1 TGAGCTAAGCTTTAGCTCGTGA
65745638 TTTGAAAGTG
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
29 2 0.05
30 32 0.86
31 3 0.08
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65747927 original size:30 final size:30
Alignment explanation
Indices: 65747856--65747938 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
65747846 CTTTTGTTTC
* *
65747856 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
65747887 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
65747916 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
65747939 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:65747938 original size:18 final size:18
Alignment explanation
Indices: 65747889--65747944 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
65747879 CACTCTCAAA
* *
65747889 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
65747906 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
65747924 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
65747943 TT
1 TT
65747945 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:65747945 original size:12 final size:12
Alignment explanation
Indices: 65747914--65747938 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65747904 TTTTTCAATC
65747914 TCATTTTCTTTT
1 TCATTTTCTTTT
65747926 TCATTTTCTTTT
1 TCATTTTCTTTT
65747938 T
1 T
65747939 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:65748017 original size:5 final size:5
Alignment explanation
Indices: 65748007--65748063 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
65747997 CTCTTGCCTC
* * *
65748007 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
65748054 TCTTT TCTTT
1 TCTTT TCTTT
65748064 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 3 0.07
5 30 0.70
6 6 0.14
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:65748039 original size:25 final size:25
Alignment explanation
Indices: 65748011--65748059 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
65748001 TGCCTCTCTT
*
65748011 TTCTTTT-TATTTTGTTTTCTTTTTC
1 TTCTTTTCT-TTTTCTTTTCTTTTTC
65748036 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTTTTTCTTTTCTTTT
65748060 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTTTTTCTTTTCTTTTTC
Found at i:65748064 original size:21 final size:20
Alignment explanation
Indices: 65748020--65748074 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
65748010 TTTCTTTTTA
65748020 TTTTG-TTTTCTTTTTCTTC
1 TTTTGTTTTTCTTTTTCTTC
*
65748039 TTTTGCTTTTTC-TTTTCTTT
1 TTTTG-TTTTTCTTTTTCTTC
65748059 TCTTTGTTTTCTCTTT
1 T-TTTGTTTT-TCTTT
65748075 ACAAGAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 11 0.37
22 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTTCTTTTTCTTC
Found at i:65748952 original size:11 final size:11
Alignment explanation
Indices: 65748936--65748987 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
65748926 ATTAAACACT
*
65748936 TTTTTTTCAGAT
1 TTTTTTTC-GAA
65748948 TTTTTTTCGAA
1 TTTTTTTCGAA
*
65748959 TTTTTTTTGAA
1 TTTTTTTCGAA
65748970 TTTTTTTCGAA
1 TTTTTTTCGAA
65748981 TTTTTTT
1 TTTTTTT
65748988 TTGACTTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
11 29 0.78
12 8 0.22
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:65748952 original size:12 final size:12
Alignment explanation
Indices: 65748935--65748988 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
65748925 CATTAAACAC
65748935 TTTTTTTTC-AGA
1 TTTTTTTTCGA-A
65748947 TTTTTTTTCGAA
1 TTTTTTTTCGAA
65748959 TTTTTTTT-GAA
1 TTTTTTTTCGAA
65748970 -TTTTTTTCGAA
1 TTTTTTTTCGAA
65748981 TTTTTTTT
1 TTTTTTTT
65748989 TGACTTGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.18
11 6 0.15
12 25 0.64
13 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:65749994 original size:30 final size:31
Alignment explanation
Indices: 65749960--65750056 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
65749950 AGCTCACTCC
*
65749960 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
65749990 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
65750020 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
65750050 TAGCTCA
1 TAGCTCA
65750057 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:65753970 original size:30 final size:30
Alignment explanation
Indices: 65753936--65754032 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65753926 TAAACTAAAA
65753936 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
65753966 TGAGCTGAAGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* * *
65753996 TGACCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65754026 TGAGCTA
1 TGAGCTA
65754033 GCAATGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 3 0.06
30 40 0.80
31 7 0.14
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65755718 original size:14 final size:14
Alignment explanation
Indices: 65755679--65755718 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
65755669 TTCATATTCC
65755679 TTCGTTCATACCAT
1 TTCGTTCATACCAT
* *
65755693 TTCATTCCTACCAT
1 TTCGTTCATACCAT
65755707 TTCGTTCATACC
1 TTCGTTCATACC
65755719 CCTCTTTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.05, T:0.42
Consensus pattern (14 bp):
TTCGTTCATACCAT
Found at i:65756204 original size:27 final size:26
Alignment explanation
Indices: 65756159--65756212 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
65756149 TTAATATATG
* *
65756159 TTTAATGTGTCTAGCTTAGGACATAAT
1 TTTAATGTGTCTAACTTAGAACA-AAT
*
65756186 TTTAATGTGTCTAATTTAGAACAAAT
1 TTTAATGTGTCTAACTTAGAACAAAT
65756212 T
1 T
65756213 AATTAGCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (26 bp):
TTTAATGTGTCTAACTTAGAACAAAT
Found at i:65758565 original size:10 final size:10
Alignment explanation
Indices: 65758550--65758586 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
65758540 TACTCCTTCA
65758550 AGCTCAAATC
1 AGCTCAAATC
65758560 AGCTCAAATC
1 AGCTCAAATC
65758570 AGCTCAAATC
1 AGCTCAAATC
65758580 AGCTCAA
1 AGCTCAA
65758587 CTTCAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:65760281 original size:46 final size:46
Alignment explanation
Indices: 65760224--65760330 Score: 178
Period size: 46 Copynumber: 2.3 Consensus size: 46
65760214 ATAGTTAAAT
* *
65760224 TCATTTGATTTGTCTAAATTACTAAAGCAATTTAAGTTGTCTTAGC
1 TCATTTAATTTGTCTAAATTACTAAAGCAATTTAAGTCGTCTTAGC
* *
65760270 TCATTTAATTTGTCCAAATTACTACAGCAATTTAAGTCGTCTTAGC
1 TCATTTAATTTGTCTAAATTACTAAAGCAATTTAAGTCGTCTTAGC
65760316 TCATTTAATTTGTCT
1 TCATTTAATTTGTCT
65760331 TAGTTTGTGC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (46 bp):
TCATTTAATTTGTCTAAATTACTAAAGCAATTTAAGTCGTCTTAGC
Found at i:65761606 original size:24 final size:24
Alignment explanation
Indices: 65761574--65761628 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
65761564 GTTAGGACAT
* *
65761574 ATTAAATTCGTCCACCAGTAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
65761598 ATTAAATTCGTCAACCAGCAGCTC
1 ATTAAATTCGTCAACCAGCAGCTC
65761622 ATTAAAT
1 ATTAAAT
65761629 CTGTCCAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAGCAGCTC
Found at i:65761722 original size:17 final size:18
Alignment explanation
Indices: 65761702--65761736 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
65761692 TGTACACACA
65761702 AATTAATTCA-ACACATT
1 AATTAATTCAGACACATT
*
65761719 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
65761737 TAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:65762002 original size:9 final size:9
Alignment explanation
Indices: 65761988--65762021 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
65761978 AAATTGTTAA
65761988 AACTAATTT
1 AACTAATTT
65761997 AACTAATTT
1 AACTAATTT
65762006 AACTAATTT
1 AACTAATTT
65762015 AACTAAT
1 AACTAAT
65762022 CAGCAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
AACTAATTT
Found at i:65765040 original size:14 final size:14
Alignment explanation
Indices: 65765021--65765069 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
65765011 TTACTAGAAG
65765021 TTTATGTAGATGGA
1 TTTATGTAGATGGA
* * *
65765035 TTTATGGATATGAA
1 TTTATGTAGATGGA
65765049 GTTTATGTAGATGGA
1 -TTTATGTAGATGGA
65765064 TTTATG
1 TTTATG
65765070 GATATAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
TTTATGTAGATGGA
Found at i:65765055 original size:15 final size:15
Alignment explanation
Indices: 65765017--65765081 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 15
65765007 GGGGTTACTA
*
65765017 GAAGTTTATGTAGAT
1 GAAGTTTATGGAGAT
* *
65765032 GGA-TTTATGGATAT
1 GAAGTTTATGGAGAT
*
65765046 GAAGTTTATGTAGAT
1 GAAGTTTATGGAGAT
* *
65765061 GGA-TTTATGGATAT
1 GAAGTTTATGGAGAT
*
65765075 AAAGTTT
1 GAAGTTT
65765082 TTGTAGGTTT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
14 21 0.57
15 16 0.43
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (15 bp):
GAAGTTTATGGAGAT
Found at i:65765059 original size:29 final size:29
Alignment explanation
Indices: 65765017--65765087 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
65765007 GGGGTTACTA
65765017 GAAGTTTATGTAGATGGATTTATGGATAT
1 GAAGTTTATGTAGATGGATTTATGGATAT
65765046 GAAGTTTATGTAGATGGATTTATGGATAT
1 GAAGTTTATGTAGATGGATTTATGGATAT
* *
65765075 AAAGTTTTTGTAG
1 GAAGTTTATGTAG
65765088 GTTTGGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
GAAGTTTATGTAGATGGATTTATGGATAT
Found at i:65780446 original size:20 final size:20
Alignment explanation
Indices: 65780423--65780469 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
65780413 AGCTCCGTCC
65780423 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
*** *
65780443 AGCTTGTTTCAGCTCGTTTG
1 AGCTCAATTCAGCTCATTTG
65780463 AGCTCAA
1 AGCTCAA
65780470 CCAAGATTAC
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:65782082 original size:30 final size:30
Alignment explanation
Indices: 65781987--65782083 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
65781977 AGCTCACTCC
* * *
65781987 TAGCTC-ACTTTCAACTCACAAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
65782017 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
65782047 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
65782077 TAGCTCA
1 TAGCTCA
65782084 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:65784606 original size:21 final size:20
Alignment explanation
Indices: 65784572--65784620 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
65784562 ACATTTTTGT
65784572 AAAGAGAAAACAAAGAAAAG-A
1 AAAGA-AAAACAAA-AAAAGAA
*
65784593 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAA-CAAAAAAAGAA
65784614 AAAGAAA
1 AAAGAAA
65784621 CGAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAAAAACAAAAAAAGAA
Found at i:65784607 original size:6 final size:5
Alignment explanation
Indices: 65784583--65784638 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
65784573 AAGAGAAAAC
* *
65784583 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAAGA AA-AGA
65784629 AAAGA AAAGA
1 AAAGA AAAGA
65784639 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.10
5 28 0.67
6 10 0.24
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:65784715 original size:12 final size:12
Alignment explanation
Indices: 65784707--65784731 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65784697 TTTGAAAAGC
65784707 AAAAAGAAAATG
1 AAAAAGAAAATG
65784719 AAAAAGAAAATG
1 AAAAAGAAAATG
65784731 A
1 A
65784732 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:65784728 original size:18 final size:18
Alignment explanation
Indices: 65784701--65784756 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
65784691 AAAGCCTTTG
65784701 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
65784720 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
65784738 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
65784755 AA
1 AA
65784757 TCTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:65784741 original size:30 final size:31
Alignment explanation
Indices: 65784707--65784788 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
65784697 TTTGAAAAGC
*
65784707 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
65784737 AAAAAGAGAACG-AAAAGAAATCTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
65784767 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
65784789 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.02, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:65786217 original size:30 final size:30
Alignment explanation
Indices: 65786183--65786279 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
65786173 AGCTCACTCC
65786183 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
65786213 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
65786243 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
65786273 TAGCTCA
1 TAGCTCA
65786280 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:65787968 original size:12 final size:11
Alignment explanation
Indices: 65787943--65788009 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 11
65787933 TTATACAAGT
65787943 AAAAAAATTC-
1 AAAAAAATTCA
65787953 AAAAAAATTCGA
1 AAAAAAATTC-A
65787965 AAAAAAATTCGA
1 AAAAAAATTC-A
65787977 AAAAAAATTCAA
1 AAAAAAATTC-A
65787989 AAAAAAAGGTTCA
1 AAAAAAA--TTCA
65788002 AAAAAAAT
1 AAAAAAAT
65788010 GATTTGTGCA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
10 10 0.19
11 1 0.02
12 30 0.58
13 8 0.15
14 3 0.06
ACGTcount: A:0.70, C:0.07, G:0.06, T:0.16
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:65787980 original size:24 final size:23
Alignment explanation
Indices: 65787943--65788009 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 23
65787933 TTATACAAGT
*
65787943 AAAAAAATTC-AAAAAAATTCGA
1 AAAAAAATTCAAAAAAAATTCAA
65787965 AAAAAAATTCGAAAAAAAATTCAA
1 AAAAAAATTC-AAAAAAAATTCAA
65787989 AAAAAAAGGTTCAAAAAAAAT
1 AAAAAAA--TTCAAAAAAAAT
65788010 GATTTGTGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 10 0.25
24 18 0.45
25 9 0.22
26 3 0.08
ACGTcount: A:0.70, C:0.07, G:0.06, T:0.16
Consensus pattern (23 bp):
AAAAAAATTCAAAAAAAATTCAA
Found at i:65788940 original size:9 final size:10
Alignment explanation
Indices: 65788933--65788989 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
65788923 AAGAGAAAAT
65788933 AAAGAAAAGA
1 AAAGAAAAGA
65788943 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
65788955 AAAGAAGA-A
1 AAAGAAAAGA
65788964 AAAGAAAATGA
1 AAAGAAAA-GA
65788975 AATA-AAAAGA
1 AA-AGAAAAGA
65788985 AAAGA
1 AAAGA
65788990 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:65788957 original size:6 final size:5
Alignment explanation
Indices: 65788933--65788989 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65788923 AAGAGAAAAT
*
65788933 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
65788980 AAAGA AAAGA
1 AAAGA AAAGA
65788990 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:65788964 original size:15 final size:14
Alignment explanation
Indices: 65788933--65788989 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65788923 AAGAGAAAAT
65788933 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
65788949 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
65788964 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
65788980 AAAGAAAAGA
1 AAAGAAAAGA
65788990 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:65789066 original size:12 final size:12
Alignment explanation
Indices: 65789058--65789082 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65789048 TTTGAAAAGT
65789058 AAAAAGAAAATG
1 AAAAAGAAAATG
65789070 AAAAAGAAAATG
1 AAAAAGAAAATG
65789082 A
1 A
65789083 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:65789079 original size:18 final size:18
Alignment explanation
Indices: 65789052--65789107 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
65789042 AAAGCCTTTG
65789052 AAAAGTAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
65789071 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
65789089 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
65789106 AA
1 AA
65789108 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Done.