Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold436
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: 700632
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:146398 original size:43 final size:43
Alignment explanation
Indices: 146289--146426 Score: 195
Period size: 43 Copynumber: 3.1 Consensus size: 43
146279 GCACCTTCAT
*
146289 CTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CAC
146337 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
146380 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
146423 CTTT
1 CTTT
146427 TCCATCTTTA
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
43 47 0.55
48 39 0.45
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:146516 original size:56 final size:52
Alignment explanation
Indices: 146380--146518 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 52
146370 ACATTGGCAC
* *
146380 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCCAT
* * *
146432 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACA-CC-TTTTC--CAT
* * * *
146488 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
146519 ACATATTGGC
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
52 37 0.51
53 2 0.03
54 5 0.07
56 28 0.39
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATCGACACCTTTTCCAT
Found at i:147371 original size:33 final size:33
Alignment explanation
Indices: 147334--147400 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
147324 TTCAACGATT
147334 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
147367 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
147400 T
1 T
147401 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:147372 original size:13 final size:13
Alignment explanation
Indices: 147354--147378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
147344 CATAAAATGT
147354 TGTATCGATACAA
1 TGTATCGATACAA
147367 TGTATCGATACA
1 TGTATCGATACA
147379 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:147459 original size:13 final size:13
Alignment explanation
Indices: 147441--147465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
147431 ATTACTCAAA
147441 TGTATCGATACAT
1 TGTATCGATACAT
147454 TGTATCGATACA
1 TGTATCGATACA
147466 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:156321 original size:28 final size:28
Alignment explanation
Indices: 156240--156321 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
156230 TTTTGGAGAT
*
156240 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
156268 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
156296 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
156322 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:156464 original size:51 final size:51
Alignment explanation
Indices: 156304--156474 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
156294 GAAATAACGA
* * * *
156304 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGA
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
156356 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
156409 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
156460 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
156475 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 39 0.41
52 16 0.17
53 31 0.32
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:156520 original size:27 final size:28
Alignment explanation
Indices: 156457--156532 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
156447 AAAATAAAGT
*
156457 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
156485 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
156512 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
156533 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:159572 original size:55 final size:54
Alignment explanation
Indices: 159468--160440 Score: 1328
Period size: 55 Copynumber: 17.6 Consensus size: 54
159458 AAGAGGAAAA
* * * * * * *
159468 TAAAGTGTATCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTT
1 TAAAG-GTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
159523 TGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
159578 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* ** *
159633 TGAAA-ATAAAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTT
1 T-AAAGGT-----G--TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
**
159694 TAAAAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
159749 TGAAAGGTGTCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
159804 TGAGAGGTGTCCTGCTCTTTGAGGACT-AGAAGGCGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTT
159859 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
* * *
159915 TGAGAGGTGTCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
159970 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
*
160025 TGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
160080 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
*
160135 TGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
*
160190 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
160245 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
160300 TAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
* *
160355 TAAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTATGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
160410 TAAGAGGTGTCCTGCTCTTTGAGGACTGAAA
1 TAA-AGGTGTCCTGCTCTTTGAGGACTGAAA
160441 AGCGGAAGGA
Statistics
Matches: 841, Mismatches: 49, Indels: 57
0.89 0.05 0.06
Matches are distributed among these distances:
54 24 0.03
55 695 0.83
56 72 0.09
57 3 0.00
59 1 0.00
61 45 0.05
62 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (54 bp):
TAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:159611 original size:26 final size:26
Alignment explanation
Indices: 159523--159612 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
159513 GTGTGGGCTT
* *
159523 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
159549 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
159576 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
159604 TGAAAGGTG
1 TGAAAGGTG
159613 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:160166 original size:27 final size:27
Alignment explanation
Indices: 160026--160166 Score: 65
Period size: 28 Copynumber: 5.1 Consensus size: 27
160016 GGTGGGCTTT
*
160026 GAAAGGTGTCCTGCTCTTTGGGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
** * * * *
160052 GAAAGGTG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
160080 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
160108 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
160136 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
160163 GAAA
1 GAAA
160167 ATGCCACCAA
Statistics
Matches: 78, Mismatches: 27, Indels: 19
0.63 0.22 0.15
Matches are distributed among these distances:
25 6 0.08
26 16 0.21
27 17 0.22
28 20 0.26
29 13 0.17
30 6 0.08
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:160223 original size:26 final size:26
Alignment explanation
Indices: 160194--160334 Score: 92
Period size: 26 Copynumber: 5.2 Consensus size: 26
160184 GGGCTTTAAG
160194 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
160220 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
160248 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
160275 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
160303 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
160330 AGGTG
1 AGGTG
160335 CCACCAACTT
Statistics
Matches: 85, Mismatches: 16, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
25 6 0.07
26 21 0.25
27 18 0.21
28 18 0.21
29 16 0.19
30 6 0.07
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:161432 original size:25 final size:23
Alignment explanation
Indices: 161404--161478 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
161394 TAAGTAGGTT
*
161404 TTTTTCTTTTCTCTCTTTTTCTTTG
1 TTTTT-TTTTCTCT-TTTTTTTTTG
* *
161429 TTTTGTTTTTTTGTTTTTTTTTTTG
1 TTTT-TTTTTCT-CTTTTTTTTTTG
161454 TTTTTTTTTTGCTCTTTTTTTTTTG
1 -TTTTTTTTT-CTCTTTTTTTTTTG
161479 AAGAGAAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 34 0.83
26 7 0.17
ACGTcount: A:0.00, C:0.09, G:0.08, T:0.83
Consensus pattern (23 bp):
TTTTTTTTTCTCTTTTTTTTTTG
Found at i:161451 original size:12 final size:12
Alignment explanation
Indices: 161419--161478 Score: 77
Period size: 11 Copynumber: 4.8 Consensus size: 12
161409 CTTTTCTCTC
*
161419 TTTTTCTTTGTT
1 TTTTTTTTTGTT
161431 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
161444 TTTTTTTTTG-T
1 TTTTTTTTTGTT
161455 TTTTTTTTTGCTCT
1 TTTTTTTTTG-T-T
161469 TTTTTTTTTG
1 TTTTTTTTTG
161479 AAGAGAAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
11 11 0.26
12 10 0.23
13 11 0.26
14 11 0.26
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:163168 original size:62 final size:63
Alignment explanation
Indices: 163068--163225 Score: 205
Period size: 63 Copynumber: 2.5 Consensus size: 63
163058 TCTACAAGTA
* * *
163068 GCATTTTGT-CTCAAAGTCCACGACTTAGTGGCATC-TTT-TTCTTCAAAGCCCACGAATCAGTG
1 GCATTTTGTCCT-AAAGTCCACGACTCAGTGGCACCTTTTCTTC-TCAAAGCCCACGAATCAATG
* * *
163130 GCATTTTGTCCTAAAGTCCACGACTCCGTGGCACCTTTTCTTCTCAAAGCCCGCGACTCAATG
1 GCATTTTGTCCTAAAGTCCACGACTCAGTGGCACCTTTTCTTCTCAAAGCCCACGAATCAATG
* *
163193 GCATTTTGTCCTAAAGTCCACAATTCAGTGGCA
1 GCATTTTGTCCTAAAGTCCACGACTCAGTGGCA
163226 TCTCCTTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
62 29 0.35
63 52 0.62
64 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.30
Consensus pattern (63 bp):
GCATTTTGTCCTAAAGTCCACGACTCAGTGGCACCTTTTCTTCTCAAAGCCCACGAATCAATG
Found at i:163240 original size:31 final size:30
Alignment explanation
Indices: 163204--163348 Score: 91
Period size: 31 Copynumber: 4.8 Consensus size: 30
163194 CATTTTGTCC
163204 TAAAGTCCACAATTCAGTGGCATCTCCTTCT
1 TAAAGTCCACAATTCAGTGGCATC-CCTTCT
* * *
163235 TAAAGTTCACGACTT-AGTGGCAACCTCTTCT
1 TAAAGTCCAC-AATTCAGTGGCATCC-CTTCT
* * ** * * **
163266 CAAAGCCCATGACTCAATGGCAT-TTTGTCCT
1 TAAAGTCCACAATTCAGTGGCATCCCT-T-CT
*
163297 AAAAGTCCACAATTCAGTGGCATCCCTT-T
1 TAAAGTCCACAATTCAGTGGCATCCCTTCT
* *
163326 T-AAGTCCACGACTCAGTGGCATC
1 TAAAGTCCACAATTCAGTGGCATC
163349 AAAGTCCACA
Statistics
Matches: 83, Mismatches: 25, Indels: 15
0.67 0.20 0.12
Matches are distributed among these distances:
28 20 0.24
29 2 0.02
30 3 0.04
31 54 0.65
32 4 0.05
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (30 bp):
TAAAGTCCACAATTCAGTGGCATCCCTTCT
Found at i:163280 original size:92 final size:90
Alignment explanation
Indices: 163143--163346 Score: 295
Period size: 92 Copynumber: 2.2 Consensus size: 90
163133 TTTTGTCCTA
* *
163143 AAGTCCACGACTCCGTGGC-ACCTTTTCTTCTCAAAGCCCGCGACTCAATGGCATTTTGTCCT-A
1 AAGTCCACGACTCAGTGGCAACC---TCTTCTCAAAGCCCACGACTCAATGGCATTTTGTCCTAA
163206 AAGTCCACAATTCAGTGGCATCTCCTTCTT
63 AAGTCCACAATTCAGTGGCATC-CCTT-TT
* * *
163236 AAAGTTCACGACTTAGTGGCAACCTCTTCTCAAAGCCCATGACTCAATGGCATTTTGTCCTAAAA
1 -AAGTCCACGACTCAGTGGCAACCTCTTCTCAAAGCCCACGACTCAATGGCATTTTGTCCTAAAA
163301 GTCCACAATTCAGTGGCATCCCTTTT
65 GTCCACAATTCAGTGGCATCCCTTTT
163327 AAGTCCACGACTCAGTGGCA
1 AAGTCCACGACTCAGTGGCA
163347 TCAAAGTCCA
Statistics
Matches: 101, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
90 18 0.18
91 2 0.02
92 39 0.39
93 23 0.23
94 16 0.16
95 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (90 bp):
AAGTCCACGACTCAGTGGCAACCTCTTCTCAAAGCCCACGACTCAATGGCATTTTGTCCTAAAAG
TCCACAATTCAGTGGCATCCCTTTT
Found at i:163444 original size:36 final size:35
Alignment explanation
Indices: 163373--163624 Score: 215
Period size: 27 Copynumber: 7.7 Consensus size: 35
163363 TGTGGCACCA
*
163373 TTTTAAGCCCACAACTCCGTGGTA-TCTTTTTCCT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
*
163407 TTTTAAAGCCCACAACTACGTGGCACTCTTTTTCCT
1 TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCT
163443 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC-
1 TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCT
* *
163478 TTCTAAGTCCACAACTCCGTGGCA--C-----CC-
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
*
163505 GTTTAAGCCCACAACTCCGTGGCA--C-----CC-
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
* *
163532 TTTTAAGTCCACGACTCCGTGGCAAC-CTTTTTTCC-
1 TTTTAAGCCCACAACTCCGTGGC-ACTC-TTTTTCCT
* *
163567 TTTAAAGCCCACAACTACGTGGCACTC-TTTTCC-
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
* *
163600 TTTTAAGTCCACGACTCCGTGGCAC
1 TTTTAAGCCCACAACTCCGTGGCAC
163625 CTTCTTCTAA
Statistics
Matches: 188, Mismatches: 19, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
27 46 0.24
28 1 0.01
29 1 0.01
32 1 0.01
33 27 0.14
34 25 0.13
35 43 0.23
36 44 0.23
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.32
Consensus pattern (35 bp):
TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
Found at i:163661 original size:33 final size:33
Alignment explanation
Indices: 163618--163729 Score: 174
Period size: 33 Copynumber: 3.4 Consensus size: 33
163608 CCACGACTCC
163618 GTGGC-ACCTTCTTCTAAAGCCCACACAAGTCG
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
*
163650 GTGGCAACCTTCTTCCAAAGCCCACACAAGTCG
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
*
163683 GTGGCAACC-ACTCTCTAAAGCCCACACAAGTCG
1 GTGGCAACCTTCT-TCTAAAGCCCACACAAGTCG
163716 GTGGCAACCCTTCT
1 GTGGCAA-CCTTCT
163730 AAGTCCAATG
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
32 7 0.10
33 61 0.85
34 2 0.03
35 2 0.03
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.20
Consensus pattern (33 bp):
GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
Found at i:163843 original size:49 final size:47
Alignment explanation
Indices: 163729--164048 Score: 368
Period size: 49 Copynumber: 6.8 Consensus size: 47
163719 GCAACCCTTC
* *
163729 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC----CAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTATCTT
* *
163772 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--TTATCTT
* *
163821 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTT-ATCTT
* *
163870 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CTTATCTT
*
163918 TAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATTGGCAC----CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTATCTT
* * *
163961 TAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--TT--ATCTT
* *
164013 TAAGTTCAATGTAGCTGGCCTTGAATCAACACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
164049 ACATCCTTTT
Statistics
Matches: 238, Mismatches: 22, Indels: 25
0.84 0.08 0.09
Matches are distributed among these distances:
43 75 0.32
44 1 0.00
47 1 0.00
48 44 0.18
49 82 0.34
50 1 0.00
52 34 0.14
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (47 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACTTATCTT
Found at i:164036 original size:52 final size:55
Alignment explanation
Indices: 163958--164476 Score: 254
Period size: 52 Copynumber: 9.6 Consensus size: 55
163948 ACATTGGCAC
* * * *
163958 CTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
* *
164010 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
* * * * *
164065 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATT-G-A-C---ATC-C-TTT-T--TC-TC
164130 AT
54 AT
* * * * *
164132 CTTTAAGTCCAATATTGTTGGCCTTGAACCAGCACATTGGCA-CC----T-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
* * * *
164181 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA--C-----CTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
* * * *
164229 CTTTAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATTGGCA----------C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
* * * * *
164272 CTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTAC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
* * * *
164324 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
* * * * *
164379 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATT-G-A-C---ATC-C-TTT-T--TC-TC
164444 AT
54 AT
*
164446 CTTTAAGTCCAATATTGCTGGCCTTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
164477 GCATATTGGC
Statistics
Matches: 377, Mismatches: 50, Indels: 65
0.77 0.10 0.13
Matches are distributed among these distances:
43 38 0.10
45 1 0.00
48 45 0.12
49 42 0.11
50 1 0.00
51 1 0.00
52 72 0.19
53 4 0.01
54 9 0.02
55 66 0.18
56 2 0.01
57 2 0.01
58 2 0.01
59 1 0.00
60 1 0.00
61 7 0.02
62 2 0.01
63 6 0.02
64 3 0.01
66 5 0.01
67 67 0.18
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
Found at i:164180 original size:49 final size:49
Alignment explanation
Indices: 164126--164358 Score: 300
Period size: 49 Copynumber: 4.8 Consensus size: 49
164116 CTTTTCTCAT
* * * *
164126 CTTCATCTTTAAGTCCAATATTGTTGGCCTTGAACCAGCACATTGGCAC
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
164175 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
164224 C-TCACCTTTAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
164271 ---C--CTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
*
164315 CTTTACCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
1 C-TT--CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCAC
164359 GTTGACATCC
Statistics
Matches: 161, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
43 38 0.24
45 1 0.01
48 44 0.27
49 46 0.29
50 1 0.01
52 31 0.19
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:164290 original size:43 final size:43
Alignment explanation
Indices: 164181--164319 Score: 197
Period size: 43 Copynumber: 3.1 Consensus size: 43
164171 GCACCTTCAT
164181 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
164229 CTTTAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * *
164272 CTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
164315 CTTTA
1 CTTTA
164320 CCATCTTTAA
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
43 47 0.55
48 39 0.45
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:164312 original size:91 final size:93
Alignment explanation
Indices: 164181--164358 Score: 270
Period size: 91 Copynumber: 1.9 Consensus size: 93
164171 GCACCTTCAT
* * *
164181 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-T-CACCTTTAAGTCCAGTGT
1 CTTTAACTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTACACCTTTAAGTCCAATGT
164244 AGCTGGCCTTGAATCAGCACATTGGCAC
66 AGCTGGCCTTGAATCAGCACATTGGCAC
* * *
164272 CTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTTCAAT
1 CTTTAACTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TTA-CACCTTTAAGTCCAAT
164337 GTAGCTGGCCTTGAATCAGCAC
64 GTAGCTGGCCTTGAATCAGCAC
164359 GTTGACATCC
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
91 41 0.53
93 1 0.01
95 35 0.45
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (93 bp):
CTTTAACTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTACACCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:164385 original size:314 final size:314
Alignment explanation
Indices: 163816--164493 Score: 1223
Period size: 314 Copynumber: 2.2 Consensus size: 314
163806 TGGCACTTTT
* * *
163816 ATCTTTAAGACCAATGTAGCTGGCCTTG-ACTCAGCACATTGGCACCTTCATCTTTAAGTCCAAT
1 ATCTTTAAGTCCAATATTGCTGGCCTTGAAC-CAGCACATTGGCACCTTCATCTTTAAGTCCAAT
163880 GTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAGTGTAGCTGGCCTTGAATC
65 GTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAGTGTAGCTGGCCTTGAATC
* * *
163945 AGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTTCCAT
130 AGCACATTGGCACCTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCAT
164010 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCATCTTTAAGCCC
195 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCATCTTTAAGCCC
* *
164075 AATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
260 AATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
*
164130 ATCTTTAAGTCCAATATTGTTGGCCTTGAACCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
1 ATCTTTAAGTCCAATATTGCTGGCCTTGAACCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
164195 TAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAGTGTAGCTGGCCTTGAATCA
66 TAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAGTGTAGCTGGCCTTGAATCA
164260 GCACATTGGCACCTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATC
131 GCACATTGGCACCTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATC
* *
164325 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCA
196 TTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCATCTTTAAGCCCA
164390 ATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
261 ATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
* *
164444 ATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCA
1 ATCTTTAAGTCCAATATTGCTGGCCTTGAACCAGCACATTGGCACCTTCA
164494 GCATCTCTAA
Statistics
Matches: 349, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
314 347 0.99
315 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (314 bp):
ATCTTTAAGTCCAATATTGCTGGCCTTGAACCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAGTGTAGCTGGCCTTGAATCA
GCACATTGGCACCTTTAACTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATC
TTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCATCTTTAAGCCCA
ATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATC
Found at i:165321 original size:13 final size:13
Alignment explanation
Indices: 165303--165327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
165293 CATAAAGTGT
165303 TGTATCGATACAA
1 TGTATCGATACAA
165316 TGTATCGATACA
1 TGTATCGATACA
165328 TTTTTTTTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:165409 original size:13 final size:13
Alignment explanation
Indices: 165391--165418 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
165381 ATTACTCAAA
165391 TGTATCGATACAT
1 TGTATCGATACAT
165404 TGTATCGATACAT
1 TGTATCGATACAT
165417 TG
1 TG
165419 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:165468 original size:52 final size:52
Alignment explanation
Indices: 165424--165543 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
165414 CATTGATCTT
165424 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
* *
165476 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
165528 TGTATCGATACATGCA
1 TGTATCGATACATGCA
165544 AGCAACTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:169216 original size:22 final size:20
Alignment explanation
Indices: 169191--169239 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
169181 TAATGTGCAA
*
169191 ATATTAGTAATATTTAAAATAT
1 ATATTAGAAATA-TTAAAAT-T
*
169213 ATATTTAGAAATATTAAAGTT
1 ATA-TTAGAAATATTAAAATT
169234 ATATTA
1 ATATTA
169240 AAAAAAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 4 0.17
22 9 0.38
23 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (20 bp):
ATATTAGAAATATTAAAATT
Found at i:171086 original size:21 final size:21
Alignment explanation
Indices: 171061--171104 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
171051 AAAATAAGTG
171061 TATTAATATTATT-TAATTTAA
1 TATTAATATTATTATAA-TTAA
*
171082 TATTAATTTTATTATAATTAA
1 TATTAATATTATTATAATTAA
171103 TA
1 TA
171105 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATATTATTATAATTAA
Found at i:179320 original size:11 final size:11
Alignment explanation
Indices: 179304--179370 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
179294 AAATAATTTA
179304 TATATTTATAT
1 TATATTTATAT
179315 TATA-TT-TA-
1 TATATTTATAT
179323 TATATTT-TAT
1 TATATTTATAT
179333 TATA-TTATAAT
1 TATATTTAT-AT
* *
179344 TATATTTAAAA
1 TATATTTATAT
179355 TAT-TTTATATT
1 TATATTTATA-T
179366 TATAT
1 TATAT
179371 AAATTTTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 4 0.09
9 8 0.18
10 12 0.27
11 17 0.38
12 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:179462 original size:19 final size:19
Alignment explanation
Indices: 179434--179475 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
179424 TATTTTATTT
*
179434 TATTCGTGTCATATTTATA
1 TATTCATGTCATATTTATA
*
179453 TATTCATGTCGTATTTATA
1 TATTCATGTCATATTTATA
179472 TATT
1 TATT
179476 TTATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (19 bp):
TATTCATGTCATATTTATA
Found at i:179567 original size:27 final size:27
Alignment explanation
Indices: 179480--179571 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 27
179470 TATATTTTAT
* *
179480 TATATTATA-ATAATATTTAAAATAT-TT
1 TATATTATATA-AAT-TTTAATATATATA
179507 TATATTTATATAAATTTTAATAATTTAATAATA
1 TATA-TTATATAAATTTTAAT-A--T-AT-ATA
179540 TATATTATATAAATTTTAATATATATA
1 TATATTATATAAATTTTAATATATATA
179567 TATAT
1 TATAT
179572 ATTGTTGTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
27 17 0.31
28 11 0.20
29 2 0.04
30 1 0.02
31 3 0.05
32 16 0.29
33 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TATATTATATAAATTTTAATATATATA
Found at i:179574 original size:147 final size:147
Alignment explanation
Indices: 179299--179567 Score: 439
Period size: 147 Copynumber: 1.8 Consensus size: 147
179289 ATAATAAATA
* * *
179299 ATTTATATATTTATATTATATTTATATATTTTATTATATTATAATTATATTTAAAATATTTTATA
1 ATTTATATATTCATATCATATTTATATATTTTATTATATTATAATAATATTTAAAATATTTTATA
* * *
179364 TTTATATAAATTTTGATAAGTTAATAATTTATATTATATAGATTTTAAAAAATATATTCATATTT
66 TTTATATAAATTTTAATAAGTTAATAATATATATTATATAAATTTTAAAAAATATATTCATATTT
179429 TATTTTATTCGTGTCAT
131 TATTTTATTCGTGTCAT
* *
179446 ATTTATATATTCATGTCGTATTTATATATTTTATTATATTATAATAATATTTAAAATATTTTATA
1 ATTTATATATTCATATCATATTTATATATTTTATTATATTATAATAATATTTAAAATATTTTATA
* * *
179511 TTTATATAAATTTTAATAATTTAATAATATATATTATATAAATTTTAATATATATAT
66 TTTATATAAATTTTAATAAGTTAATAATATATATTATATAAATTTTAAAAAATATAT
179568 ATATATTGTT
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
147 111 1.00
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (147 bp):
ATTTATATATTCATATCATATTTATATATTTTATTATATTATAATAATATTTAAAATATTTTATA
TTTATATAAATTTTAATAAGTTAATAATATATATTATATAAATTTTAAAAAATATATTCATATTT
TATTTTATTCGTGTCAT
Found at i:179698 original size:21 final size:21
Alignment explanation
Indices: 179672--179730 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
179662 AAAGATATAT
179672 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAA-GAATGCATTGG
**
179693 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCATTGG
*
179714 TTGGATGAAAAAATGCA
1 TTGGATGAAAGAATGCA
179731 ACTTTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGGATGAAAGAATGCATTGG
Found at i:179736 original size:21 final size:21
Alignment explanation
Indices: 179693--179736 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
179683 GATGCATTGG
* **
179693 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATGCAACTT
179714 TTGGATGAAAAAATGCAACTT
1 TTGGATGAAAAAATGCAACTT
179735 TT
1 TT
179737 AATAACCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:182569 original size:28 final size:29
Alignment explanation
Indices: 182509--182590 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 29
182499 TTTTGGAGAT
*
182509 AATAATGGGGTTGAAGTATCCCC--TCGA
1 AATAATGGGGTTGGAGTATCCCCGATCGA
*
182536 AGATAACGGGGTTGGAGTATCCCCGAT-GA
1 A-ATAATGGGGTTGGAGTATCCCCGATCGA
* *
182565 AATAATGAGGTTGGAGTATCCTCGAT
1 AATAATGGGGTTGGAGTATCCCCGAT
182591 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.02
28 42 0.89
29 3 0.06
30 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (29 bp):
AATAATGGGGTTGGAGTATCCCCGATCGA
Found at i:182723 original size:51 final size:51
Alignment explanation
Indices: 182573--182791 Score: 251
Period size: 51 Copynumber: 4.3 Consensus size: 51
182563 GAAATAATGA
* ** *
182573 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCTCGATTATGAAAAATTAATG-TTTTAGAAATAAAACCGG
* * * * ** *
182625 AGTTGGAGTATCCTAGATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGG
1 GGTTGGAGTATCCTCGATT-ATGAAAAATTAATGTTTTAGAAATAAAACCGG
*
182677 GGTTGGAGTATCCTCGATTGTGAAAAATTAATGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCTCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGG
* * * * *
182728 GGTTGGAGTAT-CTCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCT-CGATTATGAAAAATTAATGTTTTAGAAATAAAACCGG
182779 GGTTGGAGTATCC
1 GGTTGGAGTATCC
182792 CTTCGAAAAT
Statistics
Matches: 143, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.01
51 79 0.55
52 51 0.36
53 11 0.08
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCTCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGG
Found at i:182860 original size:79 final size:79
Alignment explanation
Indices: 182725--182903 Score: 297
Period size: 79 Copynumber: 2.3 Consensus size: 79
182715 GAAATAAAAC
* * *
182725 CGGGGTTGGAGTATCTCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCAGGGGTTGGAGTAT
*
182790 CCCTTCGAAAATAA
66 CCCCTCGAAAATAA
*
182804 TGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTA-AGAATAAAGCAGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGA-AATAAAGCAGGGGTTGGAGTA
182868 TCCCCTCGAAAATAA
65 TCCCCTCGAAAATAA
182883 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
182904 AATTAACGGG
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 1 0.01
79 92 0.99
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGCAGGGGTTGGAGTAT
CCCCTCGAAAATAA
Found at i:182890 original size:28 final size:28
Alignment explanation
Indices: 182856--182925 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 28
182846 GAATAAAGCA
182856 GGGGTTGGAGTATCCCCTCGA-AAATAAC
1 GGGGTTGGAGTATCCCC-CGATAAATAAC
*
182884 GGGGTTGGAGTAT-CCCCGATAATTAAC
1 GGGGTTGGAGTATCCCCCGATAAATAAC
182911 GGGGTTGGAGTATCC
1 GGGGTTGGAGTATCC
182926 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 3 0.08
27 22 0.56
28 14 0.36
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCCGATAAATAAC
Found at i:182975 original size:53 final size:52
Alignment explanation
Indices: 182914--183046 Score: 153
Period size: 51 Copynumber: 2.6 Consensus size: 52
182904 AATTAACGGG
* ** *
182914 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATT-GTGCGTTTTGAAAATAAAATCGGA
*
182967 GTTGGAGTATCCCCGATTAT-AGAAAATT-TGCGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGTGCGTTTTGAAAATAAAATCGGA
* * * *
183018 GTGGGAATATCCCCGATTGCGAAGAATTG
1 GTTGGAGTATCCCCGATTGTGAAAAATTG
183047 AGAAACTCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
51 41 0.61
52 2 0.03
53 24 0.36
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGTGCGTTTTGAAAATAAAATCGGA
Found at i:185407 original size:21 final size:21
Alignment explanation
Indices: 185381--185433 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
185371 GTAAACTTCC
185381 TAGATGTATCGACACAAAGAA
1 TAGATGTATCGACACAAAGAA
* *
185402 TAGATGTATCGATACACAGAA
1 TAGATGTATCGACACAAAGAA
*
185423 -AAATGTATCGA
1 TAGATGTATCGA
185434 TATAATGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (21 bp):
TAGATGTATCGACACAAAGAA
Found at i:185430 original size:20 final size:20
Alignment explanation
Indices: 185384--185470 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
185374 AACTTCCTAG
* * *
185384 ATGTATCGACACAAAGAATAG
1 ATGTATCGATACACAGAA-AA
185405 ATGTATCGATACACAGAAAA
1 ATGTATCGATACACAGAAAA
*
185425 ATGTATCGAT-------ATA
1 ATGTATCGATACACAGAAAA
185438 ATGTATCGATACACAGAAAA
1 ATGTATCGATACACAGAAAA
185458 ATGTATCGATACA
1 ATGTATCGATACA
185471 TTTCCTTGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 12 0.22
20 26 0.48
21 16 0.30
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (20 bp):
ATGTATCGATACACAGAAAA
Found at i:185442 original size:13 final size:13
Alignment explanation
Indices: 185424--185448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185414 TACACAGAAA
185424 AATGTATCGATAT
1 AATGTATCGATAT
185437 AATGTATCGATA
1 AATGTATCGATA
185449 CACAGAAAAA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:185447 original size:33 final size:33
Alignment explanation
Indices: 185405--185468 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
185395 CAAAGAATAG
185405 ATGTATCGATACACAGAAAAATGTATCGATATA
1 ATGTATCGATACACAGAAAAATGTATCGATATA
185438 ATGTATCGATACACAGAAAAATGTATCGATA
1 ATGTATCGATACACAGAAAAATGTATCGATA
185469 CATTTCCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACACAGAAAAATGTATCGATATA
Found at i:185526 original size:19 final size:20
Alignment explanation
Indices: 185502--185555 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
185492 AGCGATACCT
*
185502 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGAA
**
185521 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACTGAA
185542 TGTATCGATACAAA
1 TGTATCGATACAAA
185556 TTATTGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAAAACTGAA
Found at i:185617 original size:21 final size:22
Alignment explanation
Indices: 185591--185648 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
185581 GTTGGGACCT
* *
185591 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGCACAAA
*
185612 TGTATCGATACA-TTCCACAAA
1 TGTATCGATACATTTGCACAAA
185633 TGTATCGATACATTTG
1 TGTATCGATACATTTG
185649 GATAAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
TGTATCGATACATTTGCACAAA
Found at i:186448 original size:55 final size:55
Alignment explanation
Indices: 186353--186975 Score: 695
Period size: 55 Copynumber: 10.9 Consensus size: 55
186343 ATAAAGTGAA
* * * *
186353 TCCTGCTCTTTGAGGACTAAAAAGTGCCACTAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
186408 TCCTACTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
186463 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
186518 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
186573 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
186628 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* *
186689 TCCTGCTCTTTGAGGGCTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
186744 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
* *
186805 TCCTGCTATTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
** *
186864 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* *
186925 TCCTGCTCTTTGAGGACTG-AAGGTACCACCAACTTGTGTGGGCTTTAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
186976 AAAAAAGCAT
Statistics
Matches: 497, Mismatches: 40, Indels: 58
0.84 0.07 0.10
Matches are distributed among these distances:
54 12 0.02
55 261 0.53
56 26 0.05
59 34 0.07
60 76 0.15
61 87 0.18
62 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:187993 original size:14 final size:13
Alignment explanation
Indices: 187974--188028 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 13
187964 AAGCAGATTC
*
187974 TTCTTTTTTCTTTT
1 TTCTTTTTT-TTTG
187988 TTCTTTTTTTTTG
1 TTCTTTTTTTTTG
188001 TTCATTTTTTTGTTG
1 TTC-TTTTTTT-TTG
*
188016 TTTTTTTTTTTTG
1 TTCTTTTTTTTTG
188029 CTTTAGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 9 0.24
14 23 0.62
15 5 0.14
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (13 bp):
TTCTTTTTTTTTG
Found at i:187999 original size:12 final size:12
Alignment explanation
Indices: 187978--188026 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
187968 AGATTCTTCT
187978 TTTTTCTTTTTTC
1 TTTTT-TTTTTTC
187991 TTTTTTTTTGTTC
1 TTTTTTTTT-TTC
* * *
188004 ATTTTTTTGTTG
1 TTTTTTTTTTTC
188016 TTTTTTTTTTT
1 TTTTTTTTTTT
188027 TGCTTTAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 15 0.50
13 15 0.50
ACGTcount: A:0.02, C:0.06, G:0.06, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:188028 original size:16 final size:18
Alignment explanation
Indices: 188005--188043 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
187995 TTTTTGTTCA
188005 TTTTTTTG-TT-GTTTTT
1 TTTTTTTGCTTAGTTTTT
188021 TTTTTTTGCTTTAGTTTTT
1 TTTTTTTGC-TTAGTTTTT
188040 TTTT
1 TTTT
188044 AATAGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.85
Consensus pattern (18 bp):
TTTTTTTGCTTAGTTTTT
Found at i:188038 original size:29 final size:29
Alignment explanation
Indices: 187977--188040 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
187967 CAGATTCTTC
* *
187977 TTTTTTCTTTTTTCTTTTTTTTTGTTCAT
1 TTTTTTCTTGTTTCTTTTTTTTTGTTCAG
* *
188006 TTTTTTGTTGTTT-TTTTTTTTTGCTTTAG
1 TTTTTTCTTGTTTCTTTTTTTTTG-TTCAG
188035 TTTTTT
1 TTTTTT
188041 TTTAATAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.03, C:0.06, G:0.08, T:0.83
Consensus pattern (29 bp):
TTTTTTCTTGTTTCTTTTTTTTTGTTCAG
Found at i:200491 original size:28 final size:28
Alignment explanation
Indices: 200431--200515 Score: 111
Period size: 28 Copynumber: 3.0 Consensus size: 28
200421 TTTTGGAGAT
200431 AATAACGAGGTTGGAGTATCGCCTCGA--A
1 AATAACGAGGTTGGAGTAT--CCTCGATGA
* *
200459 GATAACGGGGTTGGAGTATCCTCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
*
200487 AATAATGAGGTTGGAGTATCCTCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
200515 A
1 A
200516 GAAAAATTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 6 0.12
28 44 0.88
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:200645 original size:51 final size:51
Alignment explanation
Indices: 200495--200714 Score: 253
Period size: 51 Copynumber: 4.3 Consensus size: 51
200485 GAAATAATGA
* * * ** *
200495 GGTTGGAGTATCCTCGATGAAGAAAAATTGGTGTTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTAATG-TTTTAGAAATAAAACCGG
* * ** *
200547 AGTTGGAGTATCTCCGATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-AAGGAAAATTAATGTTTTAGAAATAAAACCGG
*
200599 GGTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTAATGTTTTAGAAATAAAACCGG
* * * * *
200650 GGTTGGAGTATCCCCGATT-ATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTAAGGA-AAATTAATGTTTTAGAAATAAAACCGG
200701 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
200715 TTCGGAAATA
Statistics
Matches: 147, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
50 2 0.01
51 84 0.57
52 48 0.33
53 13 0.09
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTAAGGAAAATTAATGTTTTAGAAATAAAACCGG
Found at i:200741 original size:79 final size:79
Alignment explanation
Indices: 200647--200825 Score: 281
Period size: 79 Copynumber: 2.3 Consensus size: 79
200637 GAAATAAAAC
* *
200647 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTT-GGAAATAAAGCCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAG-AATAAAGCAGGGGTTGGAGTA
*
200711 -TCCCTTCGGAAATAA
65 TTCCC-TCAGAAATAA
*
200726 CGGGGTTGGAGTATCCCCGATTATGAGAAATCCATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
200791 TCCCTCAGAAATAA
66 TCCCTCAGAAATAA
*
200805 TGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
200826 GATTAACGGG
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
79 88 0.95
80 5 0.05
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
TCCCTCAGAAATAA
Found at i:200916 original size:53 final size:51
Alignment explanation
Indices: 200836--200957 Score: 147
Period size: 51 Copynumber: 2.4 Consensus size: 51
200826 GATTAACGGG
* * * * *
200836 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGCG--TTTTGAAAATAAAATCAGA
200889 GTTGGAGTATCCCCGATTAT-AGAAAATTAGCGTTTTGAAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGCGTTTTGAAAATAAAATCAGA
* *
200940 GTGGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
200958 GCGAAGAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
51 33 0.54
52 1 0.02
53 27 0.44
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGCGTTTTGAAAATAAAATCAGA
Found at i:203343 original size:13 final size:13
Alignment explanation
Indices: 203325--203350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
203315 CAAAGAATAG
203325 ATGTATCGATACA
1 ATGTATCGATACA
203338 ATGTATCGATACA
1 ATGTATCGATACA
203351 CAGGAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:203426 original size:19 final size:20
Alignment explanation
Indices: 203402--203455 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
203392 AGCGATACCT
*
203402 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGAA
**
203421 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACTGAA
203442 TGTATCGATACAAA
1 TGTATCGATACAAA
203456 TTATTGGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAAAACTGAA
Found at i:203519 original size:21 final size:22
Alignment explanation
Indices: 203493--203548 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
203483 TGGGACCTTA
* *
203493 TATCGATACATTTGTA-GAATG
1 TATCGATACATTTGCACAAATG
*
203514 TATCGATACA-TTCCACAAATG
1 TATCGATACATTTGCACAAATG
203535 TATCGATACATTTG
1 TATCGATACATTTG
203549 GATAAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCGATACATTTGCACAAATG
Found at i:204338 original size:55 final size:55
Alignment explanation
Indices: 204254--204903 Score: 688
Period size: 55 Copynumber: 11.3 Consensus size: 55
204244 ATAAAGTGCA
* * *
204254 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
204309 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
204364 TCTTACTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
204419 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAGCTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
204474 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
204529 TCCTGCTCTTTGGGGACTGAAAGGTGCAACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* *
204590 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
204645 TCCTGCTATTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
204706 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* *
204765 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * * *
204826 TCTTGCTCTTTAAGGACTG-AAGGTACCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G--AAAGGCG
204886 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
204904 AAAAAGCGGA
Statistics
Matches: 517, Mismatches: 40, Indels: 71
0.82 0.06 0.11
Matches are distributed among these distances:
54 12 0.02
55 258 0.50
56 26 0.05
59 34 0.07
60 93 0.18
61 87 0.17
62 1 0.00
64 1 0.00
65 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:206160 original size:31 final size:30
Alignment explanation
Indices: 206099--206159 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 30
206089 TCAATGGTAC
206099 TAAAATATAATAATAAATTTTTATACAAAAT
1 TAAAATATAATAATAAATTTTTATA-AAAAT
206130 TAAAATATAATAATAAATTTAATTATAAAA
1 TAAAATATAATAATAAATTT--TTATAAAA
206160 TCTTAATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 20 0.71
32 3 0.11
33 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TAAAATATAATAATAAATTTTTATAAAAAT
Found at i:207139 original size:20 final size:20
Alignment explanation
Indices: 207114--207289 Score: 138
Period size: 20 Copynumber: 8.8 Consensus size: 20
207104 TTTTCACAAT
207114 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
207134 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
207154 TTGTATCGATACATTCTGGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
*
207182 GATGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
*
207203 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
*
207223 TTGTATC---A-A---TACA
1 TTGTATCGATACATTGTTCA
*
207236 TTGTATC-ATACATTGCTCA
1 TTGTATCGATACATTGTTCA
207255 TTGTATCGATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
207275 ATGTATCGATACATT
1 TTGTATCGATACATT
207290 CAGGCATTTT
Statistics
Matches: 128, Mismatches: 10, Indels: 36
0.74 0.06 0.21
Matches are distributed among these distances:
13 9 0.07
15 1 0.01
16 2 0.02
17 1 0.01
19 10 0.08
20 79 0.62
21 4 0.03
22 1 0.01
23 2 0.02
24 1 0.01
25 2 0.02
27 1 0.01
28 3 0.02
29 12 0.09
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:207248 original size:12 final size:13
Alignment explanation
Indices: 207221--207250 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
207211 ATACATTGCT
207221 CATTGTATCAATA
1 CATTGTATCAATA
207234 CATTGTATC-ATA
1 CATTGTATCAATA
207246 CATTG
1 CATTG
207251 CTCATTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:207251 original size:32 final size:33
Alignment explanation
Indices: 207201--207269 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
207191 ATACATTTTG
207201 CATTGTATCGATACATTGCTCATTGTATCAATA
1 CATTGTATCGATACATTGCTCATTGTATCAATA
*
207234 CATTGTATC-ATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCAATA
207266 CATT
1 CATT
207270 TTACAATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCAATA
Found at i:207280 original size:52 final size:53
Alignment explanation
Indices: 207184--207289 Score: 137
Period size: 52 Copynumber: 2.0 Consensus size: 53
207174 TTTACCCAGA
* *
207184 TGTATCGATACATTTTGCATTGTATCGATACATTGCTCATTGTATCAATACAT
1 TGTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCAATACAT
* *
207237 TGTATC-ATACATTGCT-CATTGTATCGATACATT-TTACAATGTATCGATACAT
1 TGTATCGATACATT-CTGCATTGTATCGATACATTGCT-CAATGTATCAATACAT
207289 T
1 T
207290 CAGGCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
51 1 0.02
52 39 0.83
53 7 0.15
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (53 bp):
TGTATCGATACATTCTGCATTGTATCGATACATTGCTCAATGTATCAATACAT
Found at i:209646 original size:51 final size:51
Alignment explanation
Indices: 209584--209752 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 51
209574 ATTTTTCATC
* * * *
209584 TCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTCATTTCCAAAACACCAATTTTCCATAA
* * * *
209635 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAATACCCATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACCAATTTTCCATAA
** * * * *
209686 TCGGGGATACTCCAACTCCGATTTTGTTTTCAAAACACTGACTTTT-CACAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACAC-CAATTTTCCATAA
*
209737 TCTGGGATACTCCAAC
1 TCGGGGATACTCCAAC
209753 CTCGCTATTT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
51 94 0.95
52 5 0.05
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACCAATTTTCCATAA
Found at i:216166 original size:61 final size:61
Alignment explanation
Indices: 216054--216552 Score: 569
Period size: 61 Copynumber: 8.3 Consensus size: 61
216044 TAGCTCTTCC
* * *
216054 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACGCC-TTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
* * *
216116 AGTTCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
* * * *
216177 AGTCCTCAAAGAGCAGGATGCCTTTCTTCTTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTT
1 AGTCCTCAAAGAGCAGGACGCC-TT-TTCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
* * *
216239 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACCCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
* *
216300 AGTCCTTAAAGAGCAGGACGCC---T-C-TT-AAAGCCCACACAAGTTGGTGGCA-CTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
* * **
216354 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 -AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC-CCTCT
* **
216417 AGTCCTCAAAGAGCAGGATGCC---T--TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC-CCTCT
* * * * ** *
216473 AGTCCTCAAAGAGTAGGACG-CTTTTCCTTTTCAAAGCCTATACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
216534 AGTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
216553 ACACTTTATT
Statistics
Matches: 392, Mismatches: 26, Indels: 39
0.86 0.06 0.09
Matches are distributed among these distances:
54 3 0.01
55 44 0.11
56 50 0.13
57 4 0.01
58 3 0.01
59 2 0.01
60 31 0.08
61 134 0.34
62 89 0.23
63 32 0.08
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT
Found at i:216275 original size:123 final size:118
Alignment explanation
Indices: 216054--216552 Score: 607
Period size: 123 Copynumber: 4.2 Consensus size: 118
216044 TAGCTCTTCC
* * *
216054 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTCCAGT
1 AGTCCTCAAAGAGCAGGACGCC----TCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGT
* * * *
216119 TCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTCC
61 CCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCT
*
216177 AGTCCTCAAAGAGCAGGATGCCTTTCTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAG
1 AGTCCTCAAAGAGCAGGACG-C---C-TC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAG
* *
216241 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGCACCCTTT
60 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCT
*
216300 AGTCCTTAAAGAGCAGGACGCCTC--TTAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTC
* **
216362 AAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
65 AAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CCTCT
* *
216417 AGTCCTCAAAGAGCAGGATG-C-CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTC
1 AGTCCTCAAAGAGCAGGACGCCTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTC
* * * * ** *
216480 AAAGAGTAGGACG-CTTTTCCTTTTCAAAGCCTATACGAGTTGGTGGCACTTTTT
65 AAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCCTCT
216534 AGTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
216553 ACACTTTATT
Statistics
Matches: 336, Mismatches: 27, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
114 3 0.01
115 27 0.08
116 55 0.16
117 77 0.23
118 42 0.12
119 5 0.01
122 1 0.00
123 92 0.27
124 29 0.09
125 4 0.01
127 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (118 bp):
AGTCCTCAAAGAGCAGGACGCCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCA
AAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCCTCT
Found at i:216414 original size:28 final size:28
Alignment explanation
Indices: 216382--216470 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
216372 ACGCCTTCTC
216382 CTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTTAAAGCCCACACAAGTTGGTGGCA
** * * * **
216410 CTTTTCTAGTCCTCAAAGAGCAGGAT-GC-
1 CTTTTAAAGCCCACACA-AGTTGG-TGGCA
216438 CTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTTAAAGCCCACACAAGTTGGTGGCA
216466 CTTTT
1 CTTTT
216471 CTAGTCCTCA
Statistics
Matches: 43, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
26 1 0.02
27 6 0.14
28 29 0.67
29 6 0.14
30 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (28 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:216501 original size:117 final size:117
Alignment explanation
Indices: 216207--216552 Score: 538
Period size: 117 Copynumber: 3.0 Consensus size: 117
216197 CCTTTCTTCT
*
216207 TTTTAAAGCCCACACAAGTTGGTGGCAC-CTT-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
** *
216270 TAAAGCCCATACAAGTTGGTGGCACCCTTTAGTCCTTAAAGAGCAGGACGCC
66 TAAAGCCCATACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCC
* * *
216322 TCTTAAAGCCCACACAAGTTGGTGGCACTTCTC-AGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* *
216386 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCC
66 TAAAGCCCATACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGACGCC
*
216439 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACG-CTTTTCCTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* *
216503 TCAAAGCCTATACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGAC
66 T-AAAGCCCATACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGAC
216553 ACACTTTATT
Statistics
Matches: 209, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
115 27 0.13
116 57 0.27
117 81 0.39
118 44 0.21
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (117 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
TAAAGCCCATACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCC
Found at i:216613 original size:42 final size:45
Alignment explanation
Indices: 216534--216640 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 45
216524 GGCACTTTTT
* **
216534 AGTCCTCAAAGAGCAGGACACACTTTATTTTCCTC-TTTC-CTT-
1 AGTCCTCAAAGAGCAGGACACACTTCATTCCCCTCTTTTCTCTTC
*
216576 TGTCCTCAAAGAGCAGGACACACTTCA-TCCCCTTCTTTTCTCTTCC
1 AGTCCTCAAAGAGCAGGACACACTTCATTCCCC-TCTTTTCTCTT-C
216622 AGTCCTCAAAGAGCAGGAC
1 AGTCCTCAAAGAGCAGGAC
216641 GCCTTTCCTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 3 0.05
42 27 0.49
43 4 0.07
44 3 0.05
46 18 0.33
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (45 bp):
AGTCCTCAAAGAGCAGGACACACTTCATTCCCCTCTTTTCTCTTC
Found at i:216730 original size:42 final size:42
Alignment explanation
Indices: 216678--216850 Score: 183
Period size: 42 Copynumber: 4.1 Consensus size: 42
216668 TTGGTGGCAT
* * *
216678 TTTTTTCCTCAAAGAGGAGGACACACTTTATTTTCCTCTTTC
1 TTTTGTCCTCAAAGAGCAAGACACACTTTATTTTCCTCTTTC
* * *
216720 TTTTGTCCTCAAAGAGTAAGACACACTTCATTCCCTT-CTTTTCTC
1 TTTTGTCCTCAAAGAGCAAGACACACTTTATT---TTCCTCTT-TC
* *
216765 TTTTGTCCTCAAAGAGCATGACGCACTTTATTTTCCTCTTTC
1 TTTTGTCCTCAAAGAGCAAGACACACTTTATTTTCCTCTTTC
* *
216807 TTTTGTCCTCAAAGAGCATGACGCA-TTTCATTTTCCT-TTT-
1 TTTTGTCCTCAAAGAGCAAGACACACTTT-ATTTTCCTCTTTC
216847 TTTT
1 TTTT
216851 CCTTTATCCT
Statistics
Matches: 115, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
40 4 0.03
41 6 0.05
42 65 0.57
43 4 0.03
44 4 0.03
45 32 0.28
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.44
Consensus pattern (42 bp):
TTTTGTCCTCAAAGAGCAAGACACACTTTATTTTCCTCTTTC
Found at i:216743 original size:147 final size:148
Alignment explanation
Indices: 216473--216793 Score: 493
Period size: 147 Copynumber: 2.2 Consensus size: 148
216463 GCACTTTTCT
* * * *
216473 AGTCCTCAAAGAGTAGGACGCTTTTCCTTTTCAAAGCCTATACGAGTTGGTGGCACTTTTTAGTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
*
216538 CTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAGGACACACTTCA
66 CTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAAGACACACTTCA
216603 TCCCCTTCTTTTCTCTTCC
131 TCCCCTTCTTTTCTCTT-C
*
216622 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCA-TTTTT-TTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
* * *
216685 CTCAAAGAGGAGGACACACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGTAAGACACACTTCA
66 CTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAAGACACACTTCA
* *
216750 TTCCCTTCTTTTCTCTTT
131 TCCCCTTCTTTTCTCTTC
* *
216768 TGTCCTCAAAGAGCATGACGCACTTT
1 AGTCCTCAAAGAGCAGGACGC-CTTT
216794 ATTTTCCTCT
Statistics
Matches: 158, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
146 19 0.12
147 83 0.53
148 5 0.03
149 51 0.32
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (148 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTC
CTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCCTTTGTCCTCAAAGAGCAAGACACACTTCA
TCCCCTTCTTTTCTCTTC
Found at i:216837 original size:87 final size:87
Alignment explanation
Indices: 216678--216873 Score: 252
Period size: 87 Copynumber: 2.3 Consensus size: 87
216668 TTGGTGGCAT
* * *
216678 TTTTTTCCTCAAAGAGGAGGACACACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGTAAGACA
1 TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAAGACA
216743 CACTTCATTCCCTTCTTTTCTC
66 CACTTCATTCCCTTCTTTTCTC
* * * *
216765 TTTTGTCCTCAAAGAGCATGACGCACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCATGACG
1 TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAAGACA
* * *
216830 CATTTCATTTTCCTT-TTTTTTC
66 CACTTCA-TTCCCTTCTTTTCTC
* *
216852 CTTTATCCTCGAAA-AGCAGGAC
1 TTTTGTCCTC-AAAGAGCAGGAC
216874 GTACTCTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
87 85 0.90
88 9 0.10
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (87 bp):
TTTTGTCCTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCTTTTGTCCTCAAAGAGCAAGACA
CACTTCATTCCCTTCTTTTCTC
Found at i:216967 original size:41 final size:40
Alignment explanation
Indices: 216877--216976 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 40
216867 GCAGGACGTA
* * *
216877 CTCTTTTTCGCTTTGTCCTCAAGAAGCAGGACACTTTCCTT
1 CTCTTTTTC-CTTTGTCCTCAAGAAGCAAGACAATTTCATT
* * *
216918 TTCTTTTTTCCTTTGTCCTCAAGGAGCAAGATATATTTCATT
1 CTC-TTTTTCCTTTGTCCTCAAGAAGCAAGACA-ATTTCATT
216960 CTCTTTTT-CTTTGTCCT
1 CTCTTTTTCCTTTGTCCT
216977 TAAAAAGTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
40 9 0.18
41 27 0.54
42 14 0.28
ACGTcount: A:0.16, C:0.25, G:0.12, T:0.47
Consensus pattern (40 bp):
CTCTTTTTCCTTTGTCCTCAAGAAGCAAGACAATTTCATT
Found at i:217611 original size:13 final size:13
Alignment explanation
Indices: 217595--217624 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
217585 ATACATTGTT
217595 CATTGTATCGATA
1 CATTGTATCGATA
217608 CATTGTATCGATA
1 CATTGTATCGATA
217621 CATT
1 CATT
217625 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:217669 original size:20 final size:20
Alignment explanation
Indices: 217644--217694 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
217634 CCTAGATGTT
*
217644 TCGATACATT-TTGCATTATA
1 TCGATACATTGCT-CATTATA
*
217664 TCGATACATTGCTCATTGTA
1 TCGATACATTGCTCATTATA
217684 TCGATACATTG
1 TCGATACATTG
217695 TATCGATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (20 bp):
TCGATACATTGCTCATTATA
Found at i:217704 original size:33 final size:33
Alignment explanation
Indices: 217657--217726 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
217647 ATACATTTTG
*
217657 CATTATATCGATACATTGCTCATTGTATCGATA
1 CATTATATCGATACATTGATCATTGTATCGATA
*
217690 CATTGTATCGATACATTGATCATTGTATCGATA
1 CATTATATCGATACATTGATCATTGTATCGATA
217723 CATT
1 CATT
217727 TTACAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (33 bp):
CATTATATCGATACATTGATCATTGTATCGATA
Found at i:217713 original size:20 final size:20
Alignment explanation
Indices: 217687--217746 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
217677 CATTGTATCG
217687 ATACATTGTATCGATACATT
1 ATACATTGTATCGATACATT
217707 GAT-CATTGTATCGATACATT
1 -ATACATTGTATCGATACATT
* *
217727 TTACAATGTATCGATACATT
1 ATACATTGTATCGATACATT
217747 CAGGCATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.03
20 33 0.92
21 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATACATTGTATCGATACATT
Found at i:217719 original size:53 final size:53
Alignment explanation
Indices: 217644--217746 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
217634 CCTAGATGTT
* *
217644 TCGATACATTTTGCATTATATCGATACATTGCT-CATTGTATCGATACATTGTA
1 TCGATACATTATGCATTATATCGATACATT-CTACAATGTATCGATACATTGTA
* *
217697 TCGATACATTGAT-CATTGTATCGATACATTTTACAATGTATCGATACATT
1 TCGATACATT-ATGCATTATATCGATACATTCTACAATGTATCGATACATT
217747 CAGGCATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 1 0.02
53 42 0.95
54 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (53 bp):
TCGATACATTATGCATTATATCGATACATTCTACAATGTATCGATACATTGTA
Found at i:217726 original size:13 final size:13
Alignment explanation
Indices: 217677--217707 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
217667 ATACATTGCT
217677 CATTGTATCGATA
1 CATTGTATCGATA
217690 CATTGTATCGATA
1 CATTGTATCGATA
217703 CATTG
1 CATTG
217708 ATCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:220131 original size:51 final size:51
Alignment explanation
Indices: 220092--220212 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
220082 CAATATTTCT
*
220092 TAATCGAGGATACTCCAACTCCGATTTTATTTCTGAAACACCCATTTTCCA
1 TAATCGAGGATACTCCAACTCCGATTTTATTTCTGAAACACCAATTTTCCA
* * *
220143 TAATCGGGGATACTCCAACTCCGATTTTATTT-TCAAAACACTAACTTTT-CA
1 TAATCGAGGATACTCCAACTCCGATTTTATTTCT-GAAACACCAA-TTTTCCA
* *
220194 CAATCGGGGATACTCCAAC
1 TAATCGAGGATACTCCAAC
220213 CTCGTTATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
50 1 0.02
51 58 0.92
52 4 0.06
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (51 bp):
TAATCGAGGATACTCCAACTCCGATTTTATTTCTGAAACACCAATTTTCCA
Found at i:220239 original size:79 final size:78
Alignment explanation
Indices: 220148--220555 Score: 502
Period size: 79 Copynumber: 5.2 Consensus size: 78
220138 TTCCATAATC
*
220148 GGGGATACTCCAACTCCGATTTTATTT-TCAAAACA-CTAACTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACATC-AA-TTTTCACAATCGGGGATACTCCA
*
220211 ACCTCGTTATTTTCGA
63 ACCCCGTTATTTTCGA
* * * *
220227 GGGGACACTCCAACCCCTG-TTTCATTTCTAAAACATCAATTTT-TC-GTCGGGGATACTCCAAC
1 GGGGATACTCCAACCCC-GATTTTATTTCTAAAACATCAATTTTCACAATCGGGGATACTCCAAC
*
220289 CCCATTATTTTCGA
65 CCCGTTATTTTCGA
* * * * *
220303 GGGGGATACCCCAACCCCGACTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
1 -GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTT-TCACAATCGGGGATACTCCAA
* *
220368 CCCCGTTATTTCCAA
64 CCCCGTTATTTTCGA
* * * * *
220383 GGGGATACTCCAACCCTGGTTTCATTTCTAAAACATCAATTTTTCATAGTCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAA-TTTTCACAATCGGGGATACTCCAAC
*
220448 CTCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * *
220462 GGGGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATC-AATTTTCACAATCGGGGATACTCCAAC
220527 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
220541 GGGGATACTCCAACC
1 GGGGATACTCCAACC
220556 TCGTTATTAT
Statistics
Matches: 279, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
76 29 0.10
77 35 0.13
78 5 0.02
79 176 0.63
80 34 0.12
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:221315 original size:21 final size:21
Alignment explanation
Indices: 221291--221332 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
221281 CGAGTTTTAT
221291 GACTTGAAACATAGGTTTCAA
1 GACTTGAAACATAGGTTTCAA
221312 GACTTGAAACATAGGTTTCAA
1 GACTTGAAACATAGGTTTCAA
221333 TAGGCATCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (21 bp):
GACTTGAAACATAGGTTTCAA
Found at i:222218 original size:16 final size:16
Alignment explanation
Indices: 222197--222228 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
222187 ATGCATGGAA
222197 CATGCAGCACGTGAAG
1 CATGCAGCACGTGAAG
*
222213 CATGCAGCATGTGAAG
1 CATGCAGCACGTGAAG
222229 TGCTGAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (16 bp):
CATGCAGCACGTGAAG
Found at i:222612 original size:26 final size:28
Alignment explanation
Indices: 222556--222614 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
222546 CAGCTTCCAA
*
222556 CAGCATCCACTCCAGCAAGCAGCAGCTTC
1 CAGCATCCACTCCAACAAGCAGCA-CTTC
*
222585 CAGCGTCCACTCCAACAAGCAG-A-TTC
1 CAGCATCCACTCCAACAAGCAGCACTTC
222611 CAGC
1 CAGC
222615 CCACGAGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.25
28 1 0.04
29 20 0.71
ACGTcount: A:0.29, C:0.41, G:0.17, T:0.14
Consensus pattern (28 bp):
CAGCATCCACTCCAACAAGCAGCACTTC
Found at i:222768 original size:74 final size:73
Alignment explanation
Indices: 222628--222840 Score: 259
Period size: 74 Copynumber: 2.9 Consensus size: 73
222618 CGAGCTCTAG
* * * *
222628 CAGCGGCAACATCCACTCCAGCAAGCAGC--TTCCAACCCACGAACATCGACAGCAGCTCCAGTA
1 CAGCGACAACATCCACTCCAGCAAGCAGCAGTTCCAGCCCACGAACACCGACAGCAGCTCCAGCA
*
222691 GCTTCCAG
66 GCTTCCAA
* * * *
222699 TAGCGACAACATCCACTCCAGCAAGCAGCAGTTTCCAGCCCAGGAACACCGGCAGCAGCTCTAGC
1 CAGCGACAACATCCACTCCAGCAAGCAGCAG-TTCCAGCCCACGAACACCGACAGCAGCTCCAGC
222764 AGCTTCCAA
65 AGCTTCCAA
* * * * **
222773 CAGCGACAGCATCCACTCCAGCAAGCAGCAGCTTCTAGCCCACGAACAACGATAATAGCTCCAGC
1 CAGCGACAACATCCACTCCAGCAAGCAGCAG-TTCCAGCCCACGAACACCGACAGCAGCTCCAGC
222838 AGC
65 AGC
222841 GACAGTATCC
Statistics
Matches: 119, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
71 27 0.23
74 92 0.77
ACGTcount: A:0.31, C:0.38, G:0.19, T:0.13
Consensus pattern (73 bp):
CAGCGACAACATCCACTCCAGCAAGCAGCAGTTCCAGCCCACGAACACCGACAGCAGCTCCAGCA
GCTTCCAA
Found at i:227331 original size:184 final size:184
Alignment explanation
Indices: 227022--227375 Score: 690
Period size: 184 Copynumber: 1.9 Consensus size: 184
227012 AACCGAAGAG
227022 ATACGTGAGCTCAAGGAATAATTAAAAGCATGGAAGGCCAAAACTTTGAAAGCAGAGACTAAATT
1 ATACGTGAGCTCAAGGAATAATTAAAAGCATGGAAGGCCAAAACTTTGAAAGCAGAGACTAAATT
227087 AGCCATGTATAAGGGTGAAAGGAGCGAGCACGTGAACACACGGATTCAGTTGAGAAGAGTTGAGC
66 AGCCATGTATAAGGGTGAAAGGAGCGAGCACGTGAACACACGGATTCAGTTGAGAAGAGTTGAGC
227152 AAAGGAATCAACAACTTCGAGTTGCATTGGAAAGAGAGCATGGAAGGCCAAGGA
131 AAAGGAATCAACAACTTCGAGTTGCATTGGAAAGAGAGCATGGAAGGCCAAGGA
*
227206 ATACGTGAGTTCAAGGAATAATTAAAAGCATGGAAGGCCAAAACTTTGAAAGCAGAGACTAAATT
1 ATACGTGAGCTCAAGGAATAATTAAAAGCATGGAAGGCCAAAACTTTGAAAGCAGAGACTAAATT
*
227271 AGCCATGTATAAGGGTGAAAGGAGCGAGCACGTGAACACATGGATTCAGTTGAGAAGAGTTGAGC
66 AGCCATGTATAAGGGTGAAAGGAGCGAGCACGTGAACACACGGATTCAGTTGAGAAGAGTTGAGC
227336 AAAGGAATCAACAACTTCGAGTTGCATTGGAAAGAGAGCA
131 AAAGGAATCAACAACTTCGAGTTGCATTGGAAAGAGAGCA
227376 ACACTGGGTG
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 168 1.00
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (184 bp):
ATACGTGAGCTCAAGGAATAATTAAAAGCATGGAAGGCCAAAACTTTGAAAGCAGAGACTAAATT
AGCCATGTATAAGGGTGAAAGGAGCGAGCACGTGAACACACGGATTCAGTTGAGAAGAGTTGAGC
AAAGGAATCAACAACTTCGAGTTGCATTGGAAAGAGAGCATGGAAGGCCAAGGA
Found at i:234220 original size:9 final size:9
Alignment explanation
Indices: 234206--234231 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
234196 ATATGGTTGA
234206 AAATGCCAC
1 AAATGCCAC
234215 AAATGCCAC
1 AAATGCCAC
234224 AAATGCCA
1 AAATGCCA
234232 AATCTATGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.31, G:0.12, T:0.12
Consensus pattern (9 bp):
AAATGCCAC
Found at i:235980 original size:21 final size:22
Alignment explanation
Indices: 235947--235996 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
235937 CAGGTGGAGT
*
235947 AAATCAAGCCATAAAAATGAA-C
1 AAATCAAGACATAAAAA-GAATC
*
235969 AAAT-AAGACATAGAAAGAATC
1 AAATCAAGACATAAAAAGAATC
235990 AAATCAA
1 AAATCAA
235997 ATCATGAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 6 0.25
ACGTcount: A:0.62, C:0.14, G:0.10, T:0.14
Consensus pattern (22 bp):
AAATCAAGACATAAAAAGAATC
Found at i:236902 original size:296 final size:293
Alignment explanation
Indices: 236283--237086 Score: 837
Period size: 296 Copynumber: 2.7 Consensus size: 293
236273 CCCCATCTAC
* * * * * * * *
236283 AGTCTACCTGCCGACTTTGACCTTGGAGACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCC
1 AGTCTACCTGTCGGCTTTAACCCTAGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCTTTGACCC
* *
236348 TGGAGATTGCCTCATCTAAAGTCTGCCTATCGACTTTGACCCTGGAGACTAACCCATATAAAGTC
66 TGGAGACTGCCTCATCTAAAGTCTGCCTATCGACTTTGACCCTGGAGAC-AACTCATATAAAGTC
* * * * * * *
236413 TGCCTGTCGGCTTTGACCCTAGAGAC-TACCCAT-CTAAAGTCTACCTATCGACTTTGACCCTGG
130 TGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCTTAA-TCTGCCTATCGGCTTTGA-CCTGG
** * * * * *
236476 AGACTGCCTCGCTTAAAGTTTGCCCGTCGGCTTTGTCCTTGGAGACTTTCTTATCCCTAAGTCTA
193 AGACTGCCTCATTTAAAGTTTGCCCGTCAGCTTTGTCCCTAGAGACTTTCCTATCCCCAAGTCTA
** * **
236541 CCTGTCGGCTTTGACCCTGGAGACTACCTCATCCAA
258 CCTGTCAACTTTAACCCTAAAGACTACCTCATCCAA
* * * *
236577 AGTCTACCTGTTGGCTTTGACCTTAGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCTTTGACCT
1 AGTCTACCTGTCGGCTTTAACCCTAGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCTTTGACCC
* * * * * * *
236642 TTGAGACTGCTTCATCTAAAGTCTACCTATC-AGCTTTAACCCTAGAGACCACTTCATCTAAAGT
66 TGGAGACTGCCTCATCTAAAGTCTGCCTATCGA-CTTTGACCCTGGAGACAAC-TCATATAAAGT
* *
236706 CTGCTTGTCAGG-TTTAACCTTGGAGACTTTCCTATCCTTCAATCTGCCTATCGGCTTTGACCTT
129 CTGCCTGTC-GGCTTTGACCTTGGAGACTTTCCTATCCTT-AATCTGCCTATCGGCTTTGACC-T
* *
236770 GGAGACTGTCTCATTTAAAGTTTGCCTGTCAGCTTTGTCCCTAGAGACTTTCCTATCCCCAAGTC
191 GGAGACTGCCTCATTTAAAGTTTGCCCGTCAGCTTTGTCCCTAGAGACTTTCCTATCCCCAAGTC
* *** * *
236835 TGCCTGTCAACTTTAACCCTAAAGACTTTTTTA-CCTTA
256 TACCTGTCAACTTTAACCCTAAAGACTACCTCATCC-AA
* * * * *
236873 AGTCTGCTTGTCGGCTTTAACCCTAGAGACTTTTCTAT-CTTCAGTCTACCTGTCGACTTTGACC
1 AGTCTACCTGTCGGCTTTAACCCTAGAGACTTTCCT-TCCTTCAGTCTGCCTGTCGGCTTTGACC
* * * * * ** *
236937 CTGGAGACTGCCTCATTTAAAGTATGTCTGTCGACTTTGATCCTGGAGACTGCCTCATTTAAAGT
65 CTGGAGACTGCCTCATCTAAAGTCTGCCTATCGACTTTGACCCTGGAGAC-AACTCATATAAAGT
* * *
237002 CTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTATCCCTTAGTCTGCCTGTCGGCTTTGAGCCTG
129 CTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTAT-CCTTAATCTGCCTATCGGCTTTGA-CCTG
* *
237067 GAGACTACCTCATTTTAAGT
192 GAGACTGCCTCATTTAAAGT
237087 CTGCTTGTTG
Statistics
Matches: 420, Mismatches: 76, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
293 3 0.01
294 127 0.30
295 13 0.03
296 266 0.63
297 11 0.03
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (293 bp):
AGTCTACCTGTCGGCTTTAACCCTAGAGACTTTCCTTCCTTCAGTCTGCCTGTCGGCTTTGACCC
TGGAGACTGCCTCATCTAAAGTCTGCCTATCGACTTTGACCCTGGAGACAACTCATATAAAGTCT
GCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCTTAATCTGCCTATCGGCTTTGACCTGGAGA
CTGCCTCATTTAAAGTTTGCCCGTCAGCTTTGTCCCTAGAGACTTTCCTATCCCCAAGTCTACCT
GTCAACTTTAACCCTAAAGACTACCTCATCCAA
Found at i:237087 original size:211 final size:209
Alignment explanation
Indices: 236276--237094 Score: 564
Period size: 211 Copynumber: 3.9 Consensus size: 209
236266 AAGGCTGCCC
* * * * * * * * *
236276 CATCTACAGTCTACCTG-CCGACTTTGACCTTGGAGACTTTCCTACCCTAAGTCTGCCTGTCGGC
1 CATCTAAAGTCTACCTGTCAG-CTTTAACCCTGGAGACTTGCCTATCTTAAATATGCCTGTCGGC
* * * * * * ** *
236340 TTTGACCCTGGAGATTGCCTCATCTAAAGTCTGCCTATCGACTTTGACCCTGGAGACTAACCCAT
65 TTTGA-CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCCTAT
* * * * * * *
236405 --ATAAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTAC-CCATCTAAAGTCTACCTATC-GACT
129 CCCT-TAGTCTGCCTGTCGGCTTTGA-CCTAGAGACTACTTCATCTTAAGTCTGCTTGTCAG-CT
* * ** *
236466 TTGACCCTGGAGACTGCCT
191 TTAACCCTAGAGACCACTT
* * * * * ** * * * * * * *
236485 C-GCTTAAAGTTTGCCCGTCGGCTTTGTCCTTGGAGACTTTCTTATCCCTAAGTCTACCTGTCGG
1 CATC-TAAAGTCTACCTGTCAGCTTTAACCCTGGAGACTTGCCTAT-CTTAAATATGCCTGTCGG
* ** * *
236549 CTTTGACCCTGGAGACTACCTCATCCAAAGTCTACCTGTTGGCTTTGACCTTAGAGACTTTCCT-
64 CTTTGA-CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCCTA
* * * * * *
236613 T-CCTTCAGTCTGCCTGTCGGCTTTGACCTTTGAGACTGCTTCATCTAAAGTCTACCTATCAGCT
128 TCCCTT-AGTCTGCCTGTCGGCTTTGACC-TAGAGACTACTTCATCTTAAGTCTGCTTGTCAGCT
236677 TTAACCCTAGAGACCACTT
191 TTAACCCTAGAGACCACTT
* * * * * * * *
236696 CATCTAAAGTCTGCTTGTCAGGTTTAACCTTGGAGACTTTCCTATCCTTCAATCTGCCTATCGGC
1 CATCTAAAGTCTACCTGTCAGCTTTAACCCTGGAGACTTGCCTAT-CTTAAATATGCCTGTCGGC
* * * * *
236761 TTTGACCTTGGAGACTGTCTCATTTAAAGTTTGCCTGTCAGCTTTGTCCCTAGAGACTTTCCTAT
65 TTTGACC-TGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCCTAT
** ** * * ** * * *
236826 CCCCAAGTCTGCCTGTCAACTTTAACCCTAAAGACTTTTTTACCTTAAGTCTGCTTGTCGGCTTT
129 CCCTTAGTCTGCCTGTCGGCTTTGA-CCTAGAGACTACTTCATCTTAAGTCTGCTTGTCAGCTTT
**
236891 AACCCTAGAGA-CTTTT
193 AACCCTAGAGACCACTT
** * *
236907 CTATCTTCAGTCTACCTGTC-GACTTTGACCCTGGAGAC-TGCCTCAT-TTAAAGTATGTCTGTC
1 C-ATCTAAAGTCTACCTGTCAG-CTTTAACCCTGGAGACTTGCCT-ATCTTAAA-TATGCCTGTC
* * *
236969 GACTTTGATCCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTC
62 GGCTTTGA-CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCC
* * *
237034 TATCCCTTAGTCTGCCTGTCGGCTTTGAGCCTGGAGACTACCTCATTTTAAGTCTGCTTGT
126 TATCCCTTAGTCTGCCTGTCGGCTTTGA-CCTAGAGACTACTTCATCTTAAGTCTGCTTGT
237095 TGTCTTTGAC
Statistics
Matches: 484, Mismatches: 108, Indels: 34
0.77 0.17 0.05
Matches are distributed among these distances:
208 1 0.00
209 34 0.07
210 106 0.22
211 251 0.52
212 88 0.18
213 4 0.01
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34
Consensus pattern (209 bp):
CATCTAAAGTCTACCTGTCAGCTTTAACCCTGGAGACTTGCCTATCTTAAATATGCCTGTCGGCT
TTGACCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTTTCCTATCC
CTTAGTCTGCCTGTCGGCTTTGACCTAGAGACTACTTCATCTTAAGTCTGCTTGTCAGCTTTAAC
CCTAGAGACCACTT
Found at i:237102 original size:42 final size:42
Alignment explanation
Indices: 236241--237108 Score: 467
Period size: 42 Copynumber: 20.6 Consensus size: 42
236231 GTTTGCCCTC
* * * * * *
236241 AGTCTGCCTGTCTGCTTTGACCAC-GAAGGCTGCCCCATCTAC
1 AGTCTGCCTGTCGGCTTTGACC-CTGGAGACTGCCTCATTTAA
* * * * * **
236283 AGTCTACCTGCCGACTTTGACCTTGGAGACTTTCCT-ACCCT-A
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TGCCTCA-TTTAA
* *
236325 AGTCTGCCTGTCGGCTTTGACCCTGGAGATTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * *
236367 AGTCTGCCTATCGACTTTGACCCTGGAGACTAACC-CATATAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-GCCTCATTTAA
* * *
236409 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTACC-CATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * **
236450 AGTCTACCTATCGACTTTGACCCTGGAGACTGCCTCGCTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * * ** * *
236492 AGTTTGCCCGTCGGCTTTGTCCTTGGAGACTTTCTTATCCCT-A
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCAT--TTAA
* * **
236535 AGTCTACCTGTCGGCTTTGACCCTGGAGACTACCTCATCCAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * * * * *
236577 AGTCTACCTGTTGGCTTTGACCTTAGAGACTTTCCTTC-CTT-C
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TGCC-TCATTTAA
* * * *
236619 AGTCTGCCTGTCGGCTTTGACCTTTGAGACTGCTTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * * * ** * *
236661 AGTCTACCTATCAGCTTTAACCCTAGAGACCACTTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * * *
236703 AGTCTGCTTGTCAGG-TTTAACCTTGGAGACTTTCCT-ATCCTTCA
1 AGTCTGCCTGTC-GGCTTTGACCCTGGAGAC-TGCCTCAT--TTAA
* * *
236747 A-TCTGCCTATCGGCTTTGACCTTGGAGACTGTCTCATTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * * * ***
236788 AGTTTGCCTGTCAGCTTTGTCCCTAGAGACTTTCCT-ATCCCCA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TGCCTCAT-TTAA
** * ** *** * *
236831 AGTCTGCCTGTCAACTTTAACCCTAAAGACTTTTTTACCTT-A
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCA-TTTAA
* * * ** *
236873 AGTCTGCTTGTCGGCTTTAACCCTAGAGACT-TTTCTATCTT-C
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTC-AT-TTAA
* *
236915 AGTCTACCTGTCGACTTTGACCCTGGAGACTGCCTCATTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * * *
236957 AGTATGTCTGTCGACTTTGATCCTGGAGACTGCCTCATTTAA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* **
236999 AGTCTGCCTGTCGGCTTTGACCTTGGAGACT-TTTCTATCCCTT--
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTC-AT---TTAA
* * *
237042 AGTCTGCCTGTCGGCTTTGAGCCTGGAGACTACCTCATTTTA
1 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
* * *
237084 AGTCTGCTTGTTGTCTTTGACCCTG
1 AGTCTGCCTGTCGGCTTTGACCCTG
237109 CAAACTTTCC
Statistics
Matches: 637, Mismatches: 153, Indels: 72
0.74 0.18 0.08
Matches are distributed among these distances:
40 4 0.01
41 59 0.09
42 433 0.68
43 131 0.21
44 8 0.01
45 2 0.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.34
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTTAA
Found at i:237116 original size:85 final size:84
Alignment explanation
Indices: 236964--237130 Score: 217
Period size: 85 Copynumber: 2.0 Consensus size: 84
236954 TAAAGTATGT
* * * * *
236964 CTGTCGACTTTGATCCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
1 CTGTCGACTTTGAGCCTGGAGACTACCTCATTTAAAGTCTGCCTGTCGGCTTTGACCCTGCAAAC
* *
237029 TTTTCTATCCCTTAGTCTGC
66 TTTCCTA-CCCTCAGTCTGC
* * * * *
237049 CTGTCGGCTTTGAGCCTGGAGACTACCTCATTTTAAGTCTGCTTGTTGTCTTTGACCCTGCAAAC
1 CTGTCGACTTTGAGCCTGGAGACTACCTCATTTAAAGTCTGCCTGTCGGCTTTGACCCTGCAAAC
237114 TTTCCTACCCTCAGTCT
66 TTTCCTACCCTCAGTCT
237131 ACCATCGGTT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
84 9 0.13
85 61 0.87
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.37
Consensus pattern (84 bp):
CTGTCGACTTTGAGCCTGGAGACTACCTCATTTAAAGTCTGCCTGTCGGCTTTGACCCTGCAAAC
TTTCCTACCCTCAGTCTGC
Found at i:237683 original size:8 final size:8
Alignment explanation
Indices: 237672--237716 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
237662 ATCAAAAATT
237672 AAAAATAA
1 AAAAATAA
237680 AAAAAT-A
1 AAAAATAA
237687 AAAAATAA
1 AAAAATAA
*
237695 TAAAAATCA
1 -AAAAATAA
*
237704 AATAATAA
1 AAAAATAA
237712 AAAAA
1 AAAAA
237717 ATCATGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 7 0.23
8 17 0.55
9 7 0.23
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:237710 original size:17 final size:15
Alignment explanation
Indices: 237665--237716 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
237655 AGTAGAAATC
*
237665 AAAAATTAAAAATAA
1 AAAAATCAAAAATAA
*
237680 AAAAATAAAAAATAA
1 AAAAATCAAAAATAA
237695 TAAAAATCAAATAATAA
1 -AAAAATCAAA-AATAA
237712 AAAAA
1 AAAAA
237717 ATCATGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 14 0.42
16 14 0.42
17 5 0.15
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATCAAAAATAA
Found at i:237717 original size:17 final size:16
Alignment explanation
Indices: 237665--237720 Score: 69
Period size: 17 Copynumber: 3.5 Consensus size: 16
237655 AGTAGAAATC
*
237665 AAAAATTAAAAAT-AA
1 AAAAATCAAAAATAAA
* *
237680 AAAAATAAAAAATAAT
1 AAAAATCAAAAATAAA
237696 AAAAATCAAATAATAAA
1 AAAAATCAAA-AATAAA
237713 AAAAATCA
1 AAAAATCA
237721 TGAAATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 12 0.34
16 10 0.29
17 13 0.37
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAATCAAAAATAAA
Found at i:237941 original size:16 final size:16
Alignment explanation
Indices: 237920--237951 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
237910 ACACATGGAA
237920 CATGCAGCACGTGAAG
1 CATGCAGCACGTGAAG
237936 CATGCAGCACGTGAAG
1 CATGCAGCACGTGAAG
237952 TGCTGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.31, T:0.12
Consensus pattern (16 bp):
CATGCAGCACGTGAAG
Found at i:239198 original size:19 final size:19
Alignment explanation
Indices: 239155--239227 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
239145 CTCACCCAGA
*
239155 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
239175 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
239194 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
*
239214 TATATCGATACATG
1 TGTATCGATACATG
239228 AAATTGGTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:247396 original size:22 final size:22
Alignment explanation
Indices: 247371--247425 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
247361 AGATTTGACA
*
247371 AAGGGGGAGAAATGCCTTGATT
1 AAGGGGGAGAAATGCCTTAATT
* *
247393 AAGGGGGAGAAATTCTTTAATT
1 AAGGGGGAGAAATGCCTTAATT
247415 AAGGGGGAGAA
1 AAGGGGGAGAA
247426 GAATGAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.22
Consensus pattern (22 bp):
AAGGGGGAGAAATGCCTTAATT
Found at i:247988 original size:13 final size:13
Alignment explanation
Indices: 247970--247996 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
247960 ACATTATGCT
247970 TTGTATCGATACA
1 TTGTATCGATACA
247983 TTGTATCGATACA
1 TTGTATCGATACA
247996 T
1 T
247997 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:247993 original size:33 final size:32
Alignment explanation
Indices: 247951--248014 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
247941 CTCACCCAGA
*
247951 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
247984 TGTATCGATACATGTTCATTGTATCGATACA
1 TGTATCGATACATGTTCATTGTATCGATACA
248015 AGGACAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:248026 original size:20 final size:19
Alignment explanation
Indices: 247980--248036 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
247970 TTGTATCGAT
* *
247980 ACATTGTATCGATACATGT
1 ACATTGTATCGATACAAGG
*
247999 TCATTGTATCGATACAAGG
1 ACATTGTATCGATACAAGG
248018 ACAATTGTATCGATACAAG
1 AC-ATTGTATCGATACAAG
248037 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACAAGG
Found at i:248103 original size:20 final size:20
Alignment explanation
Indices: 248066--248103 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
248056 TACCACTGTT
*
248066 TGTATCGATATATGGTATAA
1 TGTATCGATACATGGTATAA
*
248086 TGTATCGATACATTGTAT
1 TGTATCGATACATGGTAT
248104 CGATAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATGGTATAA
Found at i:248107 original size:33 final size:33
Alignment explanation
Indices: 248065--248133 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
248055 CTACCACTGT
*
248065 TTGTATCGATATATGGTAT-AA-TGTATCGATACA
1 TTGTATCGATAAAT-G-ATGAATTGTATCGATACA
248098 TTGTATCGATAAATGATGAATTGTATCGATACA
1 TTGTATCGATAAATGATGAATTGTATCGATACA
248131 TTG
1 TTG
248134 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 2 0.06
32 3 0.09
33 28 0.85
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (33 bp):
TTGTATCGATAAATGATGAATTGTATCGATACA
Found at i:262222 original size:55 final size:55
Alignment explanation
Indices: 262109--262339 Score: 302
Period size: 55 Copynumber: 4.2 Consensus size: 55
262099 TTTCTTTTCA
* * *
262109 AAGTCCACAACTCCATGGCATCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTA
1 AAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT
*
262163 AAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACCACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT
* * * * *
262218 AAGTCCACAACTTCGTTGCATCCTTTTAAAGTCCACAACTCTGTGGCATCCTTTT
1 AAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT
* * ** *
262273 AAAGTCCACAACTCCATGGCACCCTTTTAAAGCCCACAAGTTAGTGGCATCATTTT
1 -AAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT
*
262329 AAAGCCCACAA
1 -AAGTCCACAA
262340 GTCAGTGGCA
Statistics
Matches: 155, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 26 0.17
55 73 0.47
56 56 0.36
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.27
Consensus pattern (55 bp):
AAGTCCACAACTCCATGGCACCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT
Found at i:262349 original size:56 final size:56
Alignment explanation
Indices: 262090--263026 Score: 553
Period size: 56 Copynumber: 16.0 Consensus size: 56
262080 AGTCCACGAT
* * * * * *
262090 TCAGTGGCATTTCTTTTCAAAGTCCACAACTCCA-TGGCATCCTTTT-AAGTCCACAAC
1 TCAGTGGCA--TCATTTCAAAGCCCACAAGT-CAGTGGCACCCTTTTAAAGCCCACAAG
* * * * * * * *
262147 TCCGTGGCACCCTTT-AAAGTCCACAACTCCA-TGGCACCCTTTTAAAGTCCACCAC
1 TCAGTGGCATCATTTCAAAGCCCACAAGT-CAGTGGCACCCTTTTAAAGCCCACAAG
* * * * * * * * *
262202 TCCGTGGCATCCTTT-TAAGTCCACAACTTC-GTTGCATCCTTTTAAAGTCCACAAC
1 TCAGTGGCATCATTTCAAAGCCCACAA-GTCAGTGGCACCCTTTTAAAGCCCACAAG
* * * * *
262257 TCTGTGGCATCCTTTTAAAGTCCACAACTCCA-TGGCACCCTTTTAAAGCCCACAAG
1 TCAGTGGCATCATTTCAAAGCCCACAAGT-CAGTGGCACCCTTTTAAAGCCCACAAG
* * ** * *
262313 TTAGTGGCATCATTTTAAAGCCCACAAGTCAGTGGCATTCTTTCAAAGACCACAAG
1 TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAG
* * *** * * *
262369 TCAGTAGCATCATTTCAAAGCCCATAAGTCAGTGGCATTATTTCAAAGCTTACATAAG
1 TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGC--CCACAAG
* * * ** *
262427 TCGGTGGCAACTTATTTGAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCGTACAAG
1 TCAGTGGC-A-TCATTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTTAAAGCCC--ACAAG
* * **
262491 AT-GGTGGCAACTCATTTGAAAGCCCACACAAGTTGGTGGCAACCCATTTTAAAGCTCACACAAG
1 -TCAGTGGC-A-TCATTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTTAAAGC-C-CACAAG
** * * * *
262555 TTGGTGGGTAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACAAG
1 TCAGT-GG-CA-TCATTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-TTTTAAAGCCCACAAG
* *
262618 TCAGTGGCATCATTTCAAAGCCCACACAAGTC-GATGGCAACTCATTTGAAAGCCCACACAAG
1 TCAGTGGCATCATTTCAAAG-CC-CACAAGTCAG-TGGC-AC-CCTTTTAAAG-CC-CACAAG
** * * *
262680 TTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCTATTTCAAAGCCCACAAG
1 TCAGTGGC-A-TCATTTCAAAG-CC-CACAAGTCAGTGGCACCCT-TTT-AAAGCCCACAAG
* * *
262742 TCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAG
* * *
262798 TCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAG
* * * *
262854 TCAGT-GCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCATAAG
1 TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACAAG
* * * *
262910 TTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAG
1 TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACAAG
* * * * * * *
262967 TAAATGGTAACTCTTTTCAAAGCCCACACGAATCGGTGGCAACTCTTTTCAAAGCCCACA
1 TCAGTGG-CA-TCATTTCAAAGCCCACA--AGTCAGTGGC-ACCCTTTT-AAAGCCCACA
263027 CAAGTTAGTG
Statistics
Matches: 753, Mismatches: 88, Indels: 73
0.82 0.10 0.08
Matches are distributed among these distances:
54 27 0.04
55 111 0.15
56 207 0.27
57 65 0.09
58 29 0.04
59 19 0.03
60 54 0.07
61 15 0.02
62 59 0.08
63 17 0.02
64 102 0.14
65 47 0.06
66 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (56 bp):
TCAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCACAAG
Found at i:262368 original size:28 final size:28
Alignment explanation
Indices: 262090--263050 Score: 382
Period size: 28 Copynumber: 32.7 Consensus size: 28
262080 AGTCCACGAT
* *
262090 TCAGTGGCATTTCTTTTCAAAGTCCACAAC
1 TCAGTGGCA-TTCTTTT-AAAGCCCACAAG
* * *
262120 TCCA-TGGCATCCTTTT-AAGTCCACAAC
1 T-CAGTGGCATTCTTTTAAAGCCCACAAG
* * * * *
262147 TCCGTGGCA-CCCTTTAAAGTCCACAAC
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
** * * *
262174 TCCA-TGGCACCCTTTTAAAGTCCACCAC
1 T-CAGTGGCATTCTTTTAAAGCCCACAAG
* * * *
262202 TCCGTGGCATCCTTTT-AAGTCCACAACT
1 TCAGTGGCATTCTTTTAAAGCCCACAA-G
* * * *
262230 TC-GTTGCATCCTTTTAAAGTCCACAAC
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
* * * *
262257 TCTGTGGCATCCTTTTAAAGTCCACAAC
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
**
262285 TCCA-TGGCACCCTTTTAAAGCCCACAAG
1 T-CAGTGGCATTCTTTTAAAGCCCACAAG
*
262313 TTAGTGGCA-TCATTTTAAAGCCCACAAG
1 TCAGTGGCATTC-TTTTAAAGCCCACAAG
* *
262341 TCAGTGGCATTCTTTCAAAGACCACAAG
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
* * *
262369 TCAGTAGCA-TCATTTCAAAGCCCATAAG
1 TCAGTGGCATTC-TTTTAAAGCCCACAAG
* * * *
262397 TCAGTGGCATTATTTCAAAGCTTACATAAG
1 TCAGTGGCATTCTTTTAAAGC--CCACAAG
* * *
262427 TCGGTGGCAACTTATTTGAAAGCCCACACAAG
1 TCAGTGGC-A-TTCTTTTAAAG-CC-CACAAG
** ** *
262459 TTGGTGGCAACCCATTTCAAAGCCCGTACAAG
1 TCAGTGGC-ATTC-TTTTAAAGCCC--ACAAG
* * *
262491 AT-GGTGGCAACTCATTTGAAAGCCCACACAAG
1 -TCAGTGGC-ATTC-TTTTAAAG-CC-CACAAG
** **
262523 TTGGTGGCAACCCATTTTAAAGCTCACACAAG
1 TCAGTGGC-ATTC-TTTTAAAGC-C-CACAAG
** * ** *
262555 TTGGTGGGTAACCCATTTCAAAGCCCACACAAG
1 TCAGT-GG-CATTC-TTTTAAAG-CC-CACAAG
* ** *
262588 TCGGTGGCAACCCATTTCAAAGCCCACAAG
1 TCAGTGGC-ATTC-TTTTAAAGCCCACAAG
*
262618 TCAGTGGCA-TCATTTCAAAGCCCACACAAG
1 TCAGTGGCATTC-TTTTAAAG-CC-CACAAG
* *
262648 TC-GATGGCAACTCATTTGAAAGCCCACACAAG
1 TCAG-TGGC-ATTC-TTTTAAAG-CC-CACAAG
** ** *
262680 TTGGTGGCAACCCATTTCAAAGCCCACACAAG
1 TCAGTGGC-ATTC-TTTTAAAG-CC-CACAAG
* **
262712 TTAGTGGCAACCTATTTCAAAGCCCACAAG
1 TCAGTGGCATTCT-TTT-AAAGCCCACAAG
* *
262742 TCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
* *
262770 TCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
* *
262798 TCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
* *
262826 TCAGTGGCATCCTTTCAAAGCCCACAAG
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
** *
262854 TCAGT-GCACCCTTTCAAAGCCCACAAG
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
* *
262881 TCAGTGGCACTCTTTTCAAAGCCCATAAG
1 TCAGTGGCATTCTTTT-AAAGCCCACAAG
* ** *
262910 TTAGTGGCACCCTTTCAAAGCCCACAAG
1 TCAGTGGCATTCTTTTAAAGCCCACAAG
*
262938 TCAGTGGCACTCTTTTCAAAGCCCACAAG
1 TCAGTGGCATTCTTTT-AAAGCCCACAAG
* * * * *
262967 TAAATGGTAACTCTTTTCAAAGCCCACACGAA
1 TCAGTGG-CATTCTTTT-AAAGCCCACA--AG
* *
262999 TCGGTGGCAACTCTTTTCAAAGCCCACACAAG
1 TCAGTGGC-ATTCTTTT-AAAG-CC-CACAAG
* *
263031 TTAGTGGCACTTTTTTTAAA
1 TCAGTGGCA-TTCTTTTAAA
263051 AAAAATTCGA
Statistics
Matches: 799, Mismatches: 81, Indels: 101
0.81 0.08 0.10
Matches are distributed among these distances:
26 6 0.01
27 88 0.11
28 313 0.39
29 57 0.07
30 82 0.10
31 21 0.03
32 193 0.24
33 33 0.04
34 6 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
TCAGTGGCATTCTTTTAAAGCCCACAAG
Found at i:262449 original size:32 final size:32
Alignment explanation
Indices: 262322--263031 Score: 498
Period size: 32 Copynumber: 23.7 Consensus size: 32
262312 GTTAGTGGCA
* * *
262322 TCATTTTAAAG-CC-CACAAGTCAGTGGC-AT
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
262351 TC-TTTCAAAG-AC-CACAAGTCAGTAGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262378 TCATTTCAAAG-CC-CATAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* ** *
262406 TTATTTCAAAGCTTACATAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * *
262438 TTATTTGAAAGCCCACACAAGTTGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* **
262470 CCATTTCAAAGCCCGTACAAGAT-GGTGGCAAC
1 TCATTTCAAAGCCCACACAAG-TCGGTGGCAAC
* *
262502 TCATTTGAAAGCCCACACAAGTTGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * * * *
262534 CCATTTTAAAGCTCACACAAGTTGGTGGGTAAC
1 TCATTTCAAAGCCCACACAAGTCGGT-GGCAAC
*
262567 CCATTTCAAAGCCCACACAAGTCGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262599 CCATTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
262627 TCATTTCAAAGCCCACACAAGTCGATGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262659 TCATTTGAAAGCCCACACAAGTTGGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* **
262691 CCATTTCAAAGCCCACACAAGTTAGTGGCAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
262723 -CTATTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TC-ATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262751 TCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262779 TCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262807 TCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262835 TCCTTTCAAAG-CC-CACAAGTCAGT-GC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262863 -CCTTTCAAAG-CC-CACAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* * **
262891 TCTTTTCAAAG-CC-CATAAGTTAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *
262920 -CCTTTCAAAG-CC-CACAAGTCAGTGGC-AC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
* *** *
262948 TCTTTTCAAAG-CC-CACAAGTAAATGGTAAC
1 TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
*
262978 TCTTTTCAAAGCCCACACGAA-TCGGTGGCAAC
1 TCATTTCAAAGCCCACAC-AAGTCGGTGGCAAC
*
263010 TCTTTTCAAAGCCCACACAAGT
1 TCATTTCAAAGCCCACACAAGT
263032 TAGTGGCACT
Statistics
Matches: 600, Mismatches: 58, Indels: 43
0.86 0.08 0.06
Matches are distributed among these distances:
27 28 0.05
28 198 0.33
29 54 0.09
30 64 0.11
31 12 0.02
32 213 0.35
33 31 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (32 bp):
TCATTTCAAAGCCCACACAAGTCGGTGGCAAC
Found at i:262648 original size:189 final size:180
Alignment explanation
Indices: 262353--263039 Score: 639
Period size: 189 Copynumber: 3.8 Consensus size: 180
262343 AGTGGCATTC
* * * * * * ***
262353 TTTCAAAGACCACAAGTCAGTAGCATCATTTCAAAGCCCATAAGTCAGTGGCATTATTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGAACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* * * * * * *
262418 TTACATAAGTCGGTGGCAACTTATTTGAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCC
66 --CCACAAGTCAGTGGC-A-TCATTTCAAAGCCCACACAAGTCGATGGCAACCCATTTCAAAGCC
** * * *
262483 CGTACAAGATGGTGGCAACTCATTTGAAAGCCCACACAAGTTGGTGGCAACCCA
127 CACACAAGATGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCA
* ** *
262537 TTTTAAAGCTCACACAAGTTGGTGGGTAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGC-C-CACAAGTCAGT-GG-AACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
* *
262602 TTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCGATGGCAACTCATTTGA
57 TTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCGATGGCAACCCATTTCA
* *
262667 AAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCTA
122 AAGCCCACACAAGATGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCA
* * *
262726 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGAACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* *
262791 CCACAAGTCAGTGGCATCCTTTCAAAG-CC-CACAAGTC-AGTGGC-ATCC-TTTCAAAG-CC-C
66 CCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCGA-TGGCAACCCATTTCAAAGCCCAC
* * * *
262849 ACAAG-TCAGT-GC-ACCC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCT
130 ACAAGAT-GGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCA
* * * *
262894 TTTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGAACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAG
* * * * * * *
262959 CCCACAAGTAAATGGTAACTCTTTTCAAAGCCCACACGAA-TCGGTGGCAACTCTTTTCAAAGCC
65 CCCACAAGTCAGTGG-CA-TCATTTCAAAGCCCACAC-AAGTCGATGGCAACCCATTTCAAAGCC
* *
263023 CACACAAGTTAGTGGCA
127 CACACAAGATGGTGGCA
263040 CTTTTTTTAA
Statistics
Matches: 421, Mismatches: 57, Indels: 55
0.79 0.11 0.10
Matches are distributed among these distances:
168 52 0.12
169 35 0.08
170 3 0.01
171 18 0.04
172 6 0.01
173 12 0.03
174 12 0.03
175 10 0.02
176 9 0.02
177 12 0.03
178 15 0.04
179 2 0.00
180 35 0.08
181 3 0.01
182 13 0.03
183 2 0.00
184 15 0.04
185 4 0.01
186 11 0.03
187 10 0.02
188 3 0.01
189 102 0.24
190 3 0.01
191 24 0.06
192 1 0.00
193 9 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (180 bp):
TTTCAAAGCCCACAAGTCAGTGGAACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
CCACAAGTCAGTGGCATCATTTCAAAGCCCACACAAGTCGATGGCAACCCATTTCAAAGCCCACA
CAAGATGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCCA
Found at i:263038 original size:32 final size:29
Alignment explanation
Indices: 262240--263046 Score: 546
Period size: 28 Copynumber: 27.2 Consensus size: 29
262230 TCGTTGCATC
* * *
262240 CTTTT-AAAGTCCACAACTCTGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
262267 CCTTTT-AAAGTCCACAACTCCA-TGGCACC
1 -CTTTTCAAAGCCCACAAGT-CAGTGGCACT
*
262296 CTTTT-AAAGCCCACAAGTTAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
262323 CATTTT-AAAGCCCACAAGTCAGTGGCATT
1 C-TTTTCAAAGCCCACAAGTCAGTGGCACT
* *
262352 C-TTTCAAAGACCACAAGTCAGTAGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
262379 CATTTCAAAGCCCATAAGTCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
262407 -TATTTCAAAGCTTACATAAGTCGGTGGCAACT
1 CT-TTTCAAAGC--CCACAAGTCAGTGGC-ACT
* ** *
262439 -TATTTGAAAGCCCACACAAGTTGGTGGCAACC
1 CT-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT
* *
262471 CATTTCAAAGCCCGTACAAGAT-GGTGGCAACT
1 CTTTTCAAAGCCC--ACAAG-TCAGTGGC-ACT
* * ** *
262503 CATTTGAAAGCCCACACAAGTTGGTGGCAACC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
** * *
262535 CATTTT-AAAGCTCACACAAGTTGGTGGGTAACC
1 C-TTTTCAAAGC-C-CACAAGTCAGT-GG-CACT
* * *
262568 CATTTCAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
*
262600 CATTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
262628 CATTTCAAAGCCCACACAAGTC-GATGGCAACT
1 CTTTTCAAAG-CC-CACAAGTCAG-TGGC-ACT
* * ** *
262660 CATTTGAAAGCCCACACAAGTTGGTGGCAACC
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
* *
262692 CATTTCAAAGCCCACACAAGTTAGTGGCAAC-
1 CTTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
262723 CTATTTCAAAGCCCACAAGTCAGTGGCA-T
1 CT-TTTCAAAGCCCACAAGTCAGTGGCACT
*
262752 CCTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
262780 CCTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
262808 CCTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
262836 CCTTTCAAAGCCCACAAGTCAGT-GCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
262863 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
262892 CTTTTCAAAGCCCATAAGTTAGTGGCAC-
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
*
262920 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
262949 CTTTTCAAAGCCCACAAGTAAATGGTAACT
1 CTTTTCAAAGCCCACAAGTCAGTGG-CACT
* *
262979 CTTTTCAAAGCCCACACGAATCGGTGGCAACT
1 CTTTTCAAAGCCCACA--AGTCAGTGGC-ACT
*
263011 CTTTTCAAAGCCCACACAAGTTAGTGGCACT
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCACT
*
263042 TTTTT
1 CTTTT
263047 TAAAAAAAAT
Statistics
Matches: 674, Mismatches: 59, Indels: 89
0.82 0.07 0.11
Matches are distributed among these distances:
27 33 0.05
28 263 0.39
29 56 0.08
30 71 0.11
31 18 0.03
32 195 0.29
33 32 0.05
34 6 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (29 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:267719 original size:30 final size:30
Alignment explanation
Indices: 267685--267741 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
267675 TTAAGAAAAT
* *
267685 ATGGATTCC-TAAGGGAGCAAAAGTTATAAA
1 ATGGA-TCCATAAAGGAACAAAAGTTATAAA
267715 ATGGATCCATAAAGGAACAAAAGTTAT
1 ATGGATCCATAAAGGAACAAAAGTTAT
267742 GAACACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.23
Consensus pattern (30 bp):
ATGGATCCATAAAGGAACAAAAGTTATAAA
Found at i:271463 original size:31 final size:31
Alignment explanation
Indices: 271426--271492 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
271416 GTTTTCAATC
271426 TCAAATTT-CATCAATTCCTTTTCAAATTTCA
1 TCAAATTTACATC-ATTCCTTTTCAAATTTCA
* **
271457 TCAAATTTACATCATTTCTTTTCATTTTTCA
1 TCAAATTTACATCATTCCTTTTCAAATTTCA
271488 TCAAA
1 TCAAA
271493 ACTTCATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (31 bp):
TCAAATTTACATCATTCCTTTTCAAATTTCA
Found at i:279367 original size:13 final size:13
Alignment explanation
Indices: 279349--279408 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
279339 ACATTATGCT
279349 TTGTATCGATACA
1 TTGTATCGATACA
279362 TTGTATCGATACA
1 TTGTATCGATACA
*
279375 -TG-AAC-A-AC-
1 TTGTATCGATACA
279383 -TGTATCGATACA
1 TTGTATCGATACA
279395 TTGTATCGATACA
1 TTGTATCGATACA
279408 T
1 T
279409 GAACAACTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 2 0.05
9 4 0.10
10 2 0.05
11 4 0.10
12 2 0.05
13 26 0.65
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:279374 original size:33 final size:33
Alignment explanation
Indices: 279350--279425 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
279340 CATTATGCTT
279350 TGTATCGATACATTGTATCGATACATGAACAAC
1 TGTATCGATACATTGTATCGATACATGAACAAC
279383 TGTATCGATACATTGTATCGATACATGAACAAC
1 TGTATCGATACATTGTATCGATACATGAACAAC
279416 TGTATCGATA
1 TGTATCGATA
279426 TATGAAACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATTGTATCGATACATGAACAAC
Found at i:279388 original size:20 final size:20
Alignment explanation
Indices: 279363--279431 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
279353 ATCGATACAT
279363 TGTATCGATACATGAACAAC
1 TGTATCGATACATGAACAAC
279383 TGTATCGATACAT-------
1 TGTATCGATACATGAACAAC
279396 TGTATCGATACATGAACAAC
1 TGTATCGATACATGAACAAC
*
279416 TGTATCGATATATGAA
1 TGTATCGATACATGAA
279432 ACTGGCAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
13 13 0.32
20 28 0.68
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAACAAC
Found at i:279495 original size:13 final size:13
Alignment explanation
Indices: 279477--279501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
279467 TACATAGTAC
279477 ATTGTATCGATAT
1 ATTGTATCGATAT
279490 ATTGTATCGATA
1 ATTGTATCGATA
279502 CATGATGAAT
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:279514 original size:33 final size:33
Alignment explanation
Indices: 279458--279526 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
279448 CTACCACTAT
* *
279458 TTGTATCGATACATAGTACATTGTATCGATATA
1 TTGTATCGATACATAGTACATTGTATCAATACA
279491 TTGTATCGATACAT-GATGA-ATTGTATCAATACA
1 TTGTATCGATACATAG-T-ACATTGTATCAATACA
279524 TTG
1 TTG
279527 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 1 0.03
33 30 0.94
34 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATAGTACATTGTATCAATACA
Found at i:284965 original size:20 final size:20
Alignment explanation
Indices: 284940--284977 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
284930 AAAATTTTCC
284940 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
284960 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
284978 TGGAAAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:285028 original size:13 final size:13
Alignment explanation
Indices: 285010--285062 Score: 97
Period size: 13 Copynumber: 4.1 Consensus size: 13
285000 ACAACATTCC
*
285010 TTGTATGGATACA
1 TTGTATCGATACA
285023 TTGTATCGATACA
1 TTGTATCGATACA
285036 TTGTATCGATACA
1 TTGTATCGATACA
285049 TTGTATCGATACA
1 TTGTATCGATACA
285062 T
1 T
285063 GGGTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Done.