Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007268.1 Corchorus capsularis cultivar CVL-1 contig07289, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 77487
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:8923 original size:42 final size:42
Alignment explanation
Indices: 8863--8961 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 42
8853 ATAGCTAAAG
8863 GATCGAATGGCCGGTTGTGACCGGATGGCCCGTGCGATGGCCC
1 GATCG-ATGGCCGGTTGTGACCGGATGGCCCGTGCGATGGCCC
* * *
8906 GATCGATGGCCGGTTGTGGCCGGATGGCTCGTGCGATGTCCC
1 GATCGATGGCCGGTTGTGACCGGATGGCCCGTGCGATGGCCC
*
8948 -ATGCGTTGGCCGGT
1 GAT-CGATGGCCGGT
8962 CATGGCCGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.04
42 44 0.86
43 5 0.10
ACGTcount: A:0.11, C:0.26, G:0.40, T:0.22
Consensus pattern (42 bp):
GATCGATGGCCGGTTGTGACCGGATGGCCCGTGCGATGGCCC
Found at i:10304 original size:36 final size:36
Alignment explanation
Indices: 10257--10435 Score: 259
Period size: 36 Copynumber: 4.9 Consensus size: 36
10247 ATTATTCCCT
* *
10257 TCTTTTATTGACTCCACTTAATTACCCTGAATTAAG
1 TCTTTTATTGACGCTACTTAATTACCCTGAATTAAG
*
10293 TCTTTTATTGACGCTACTTAATTACACTGAATTAAG
1 TCTTTTATTGACGCTACTTAATTACCCTGAATTAAG
* * *
10329 CCTTTTTATTGACACTACTTAATTACCCTCAATTAAG
1 TC-TTTTATTGACGCTACTTAATTACCCTGAATTAAG
* * *
10366 CCCCTTTATTGACGCTGCTTAATTACCCTGAATTAAG
1 -TCTTTTATTGACGCTACTTAATTACCCTGAATTAAG
10403 TCTTTTATTGACGCTACTTAATTACCCTGAATT
1 TCTTTTATTGACGCTACTTAATTACCCTGAATT
10436 TAGTTCCTAA
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
36 64 0.50
37 61 0.48
38 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.41
Consensus pattern (36 bp):
TCTTTTATTGACGCTACTTAATTACCCTGAATTAAG
Found at i:10451 original size:73 final size:71
Alignment explanation
Indices: 10257--10435 Score: 241
Period size: 73 Copynumber: 2.5 Consensus size: 71
10247 ATTATTCCCT
* * *
10257 TCTTTTATTGACTCCACTTAATTACCCTGAATTAAGTCTTTTATTGACGCTACTTAATTACACTG
1 TCTTTTATTGACACTACTTAATTACCCTGAATTAAGTC-CTTATTGACGCTACTTAATTACACTG
10322 AATTAAG
65 AATTAAG
* * * * *
10329 CCTTTTTATTGACACTACTTAATTACCCTCAATTAAGCCCCTTTATTGACGCTGCTTAATTACCC
1 TC-TTTTATTGACACTACTTAATTACCCTGAATTAAG-TCC-TTATTGACGCTACTTAATTACAC
10394 TGAATTAAG
63 TGAATTAAG
*
10403 TCTTTTATTGACGCTACTTAATTACCCTGAATT
1 TCTTTTATTGACACTACTTAATTACCCTGAATT
10436 TAGTTCCTAA
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
72 1 0.01
73 60 0.65
74 32 0.34
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.41
Consensus pattern (71 bp):
TCTTTTATTGACACTACTTAATTACCCTGAATTAAGTCCTTATTGACGCTACTTAATTACACTGA
ATTAAG
Found at i:10523 original size:69 final size:69
Alignment explanation
Indices: 10450--10583 Score: 241
Period size: 69 Copynumber: 1.9 Consensus size: 69
10440 TCCTAACTTG
*
10450 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTC
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGAAATCAAGTC
10515 CTCT
66 CTCT
* *
10519 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGAAATTAAGTC
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGAAATCAAGTC
10584 TGTGCTTTAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (69 bp):
ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGAAATCAAGTC
CTCT
Found at i:10524 original size:32 final size:32
Alignment explanation
Indices: 10450--10583 Score: 115
Period size: 37 Copynumber: 3.9 Consensus size: 32
10440 TCCTAACTTG
* *
10450 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCT
1 ACTTAATTCCCTTCCTTGAAATCAAGT-C----CTCT
*
10487 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCT
1 ACTTAATTCCCTTCCTTGAAATCAAGTCCTCT
* *
10519 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCT
1 ACTTAATTCCCTTCCTTGAAATCAAGT-C----CTCT
* *
10556 ACTTAATTTCCTTCCTTGAAATTAAGTC
1 ACTTAATTCCCTTCCTTGAAATCAAGTC
10584 TGTGCTTTAC
Statistics
Matches: 86, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
32 28 0.33
33 1 0.01
36 2 0.02
37 55 0.64
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (32 bp):
ACTTAATTCCCTTCCTTGAAATCAAGTCCTCT
Found at i:10580 original size:19 final size:19
Alignment explanation
Indices: 10521--10580 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
10511 AGTCCTCTAC
10521 TTAATTTCCTTCCTTGAAA
1 TTAATTTCCTTCCTTGAAA
* * *
10540 TTAA-GTCCTTAACTCT--AC
1 TTAATTTCCTT-CCT-TGAAA
10558 TTAATTTCCTTCCTTGAAA
1 TTAATTTCCTTCCTTGAAA
10577 TTAA
1 TTAA
10581 GTCTGTGCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 1 0.03
18 12 0.40
19 16 0.53
20 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (19 bp):
TTAATTTCCTTCCTTGAAA
Found at i:10850 original size:41 final size:41
Alignment explanation
Indices: 10522--10842 Score: 479
Period size: 41 Copynumber: 7.9 Consensus size: 41
10512 GTCCTCTACT
* * *
10522 TAATTTCCTTCCTTGAAATTAAGTC----CTTAACTCTACT
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
*
10559 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTGCC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
*
10600 TAATTTCCTTCCCTGAAATTAAGTCTGTGCTTTACTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
* * *
10641 TAATTTCTTTCCTTGAAATTAAGTATGTGCTTTACTTCACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
*
10682 TAATTTCCTTCCTTGAAATTAAGTATGTGCTTTACTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
* * * *
10723 TAATTTCTTTCCTTGAAATTAAGTCTGTGTTTTACTTCACT
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
* *
10764 TAATTTCCTTCCTTGAAATTAAGTTTGTGCTTTACTTCACC
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
10805 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTT
1 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTT
10843 GCTTAATTAC
Statistics
Matches: 257, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
37 25 0.10
41 232 0.90
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.47
Consensus pattern (41 bp):
TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACC
Found at i:11006 original size:41 final size:41
Alignment explanation
Indices: 10900--11006 Score: 169
Period size: 41 Copynumber: 2.6 Consensus size: 41
10890 TTAATCGTCT
* *
10900 TGGATTAAAACTTTAACTGTATTTGACTTTCTTAATCACCC
1 TGGATTAAAACTTTAACTATGTTTGACTTTCTTAATCACCC
* *
10941 TGGATTAAAACTTTAACTACGTTTGACTTTCTTAATTACCC
1 TGGATTAAAACTTTAACTATGTTTGACTTTCTTAATCACCC
*
10982 TGGAGTAAAACTTTAACTATGTTTG
1 TGGATTAAAACTTTAACTATGTTTG
11007 TTATCGAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (41 bp):
TGGATTAAAACTTTAACTATGTTTGACTTTCTTAATCACCC
Found at i:11134 original size:71 final size:71
Alignment explanation
Indices: 11017--11179 Score: 227
Period size: 71 Copynumber: 2.2 Consensus size: 71
11007 TTATCGAAAT
* *
11017 TAGGACCTTGACTATACTCCTTTTTTACTCTTAATTACCCCGAATTAAGACTTTACTCTTCTTAA
1 TAGGACCTTGACTGTA--CCTTCTTT--TCTTAATTACCCCGAATTAAGACTTTACTCTTCTTAA
*
11082 CTGCCCAACT
62 CTGCCCAACC
* * * *
11092 TAGGACCTTGATTGTACCTTCTTTTCTTAATTACCCTGAATTAAGACTTTATTCTTCTTAATTGC
1 TAGGACCTTGACTGTACCTTCTTTTCTTAATTACCCCGAATTAAGACTTTACTCTTCTTAACTGC
11157 CCAACC
66 CCAACC
11163 TAGGACCTTGACTGTAC
1 TAGGACCTTGACTGTAC
11180 GTTGCTTAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
71 59 0.74
73 7 0.09
75 14 0.17
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (71 bp):
TAGGACCTTGACTGTACCTTCTTTTCTTAATTACCCCGAATTAAGACTTTACTCTTCTTAACTGC
CCAACC
Found at i:11397 original size:75 final size:71
Alignment explanation
Indices: 11310--11491 Score: 222
Period size: 71 Copynumber: 2.5 Consensus size: 71
11300 TGTTTGTTAT
* * * *
11310 CCAAATTAGGACCTTTACTATACTCCTTTTTTACTCTTAATTACCCCGAATTAAGACTTTATTCT
1 CCAACTTAGGACCTTAACTATACT--TTCTTT--TCTTAAATACCCCGAATTAAGACTTTATTCT
*
11375 TCTTCACTGC
62 TCTTAACTGC
* *
11385 CCAACTTAGGACCTTAACTGTACTTTCTTTTCTTAAATACCCTGAATTAAGACTTTATTCTTCTT
1 CCAACTTAGGACCTTAACTATACTTTCTTTTCTTAAATACCCCGAATTAAGACTTTATTCTTCTT
*
11450 AATTGC
66 AACTGC
* *
11456 CCAACCTAGGACC-TAGACTGTACTTTCTTTTCTTAA
1 CCAACTTAGGACCTTA-ACTATACTTTCTTTTCTTAA
11492 TTCTTTTTGA
Statistics
Matches: 97, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
70 2 0.02
71 69 0.71
73 5 0.05
75 21 0.22
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (71 bp):
CCAACTTAGGACCTTAACTATACTTTCTTTTCTTAAATACCCCGAATTAAGACTTTATTCTTCTT
AACTGC
Found at i:11432 original size:71 final size:71
Alignment explanation
Indices: 11344--11491 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
11334 CCTTTTTTAC
* * *
11344 TCTTAATTACCCCGAATTAAGACTTTATTCTTCTTCACTGCCCAACTTAGGACCTTA-ACTGTAC
1 TCTTAAATACCCCGAATTAAGACTTTATTCTTCTTAACTGCCCAACCTAGGACC-TAGACTGTAC
11408 TTTCTTT
65 TTTCTTT
* *
11415 TCTTAAATACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTAGACTGTACT
1 TCTTAAATACCCCGAATTAAGACTTTATTCTTCTTAACTGCCCAACCTAGGACCTAGACTGTACT
11480 TTCTTT
66 TTCTTT
11486 TCTTAA
1 TCTTAA
11492 TTCTTTTTGA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 2 0.03
71 69 0.97
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.41
Consensus pattern (71 bp):
TCTTAAATACCCCGAATTAAGACTTTATTCTTCTTAACTGCCCAACCTAGGACCTAGACTGTACT
TTCTTT
Found at i:11464 original size:299 final size:299
Alignment explanation
Indices: 10926--11478 Score: 962
Period size: 299 Copynumber: 1.8 Consensus size: 299
10916 CTGTATTTGA
* *
10926 CTTTCTTAATCACCCTGGATTAAAACTTTAACTACGTTTGACTTTCTTAATTACCCTGGAGTAAA
1 CTTTCTTAATCACCCTGGATTAAAACTTTAACTACGTTTGACTTTCTTAATCACCCTAGAGTAAA
*
10991 ACTTTAACTATGTTTGTTATCGAAATTAGGACCTTGACTATACTCCTTTTTTACTCTTAATTACC
66 ACTTTAACTATGTTTGTTATCCAAATTAGGACCTTGACTATACTCCTTTTTTACTCTTAATTACC
* *
11056 CCGAATTAAGACTTTACTCTTCTTAACTGCCCAACTTAGGACCTTGATTGTACCTTCTTTTCTTA
131 CCGAATTAAGACTTTACTCTTCTTAACTGCCCAACTTAGGACCTTAACTGTACCTTCTTTTCTTA
* *
11121 ATTACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTTGACTGTACGTTGCT
196 AATACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTAGACTGTACGTTGCT
11186 TAATTACCATGAATTAAGTTCTTTGAGTGCTATGTTTCC
261 TAATTACCATGAATTAAGTTCTTTGAGTGCTATGTTTCC
** * **
11225 CTTTCTTAATCGTCTTGGATTAAAACTTTAACTGTGTTTGACTTTCTTAATCACCCTAGAGTAAA
1 CTTTCTTAATCACCCTGGATTAAAACTTTAACTACGTTTGACTTTCTTAATCACCCTAGAGTAAA
*
11290 ACTTTAACTATGTTTGTTATCCAAATTAGGACCTTTACTATACTCCTTTTTTACTCTTAATTACC
66 ACTTTAACTATGTTTGTTATCCAAATTAGGACCTTGACTATACTCCTTTTTTACTCTTAATTACC
* * *
11355 CCGAATTAAGACTTTATTCTTCTTCACTGCCCAACTTAGGACCTTAACTGTACTTTCTTTTCTTA
131 CCGAATTAAGACTTTACTCTTCTTAACTGCCCAACTTAGGACCTTAACTGTACCTTCTTTTCTTA
11420 AATACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTAGACTGTAC
196 AATACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTAGACTGTAC
11479 TTTCTTTTCT
Statistics
Matches: 238, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
299 238 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (299 bp):
CTTTCTTAATCACCCTGGATTAAAACTTTAACTACGTTTGACTTTCTTAATCACCCTAGAGTAAA
ACTTTAACTATGTTTGTTATCCAAATTAGGACCTTGACTATACTCCTTTTTTACTCTTAATTACC
CCGAATTAAGACTTTACTCTTCTTAACTGCCCAACTTAGGACCTTAACTGTACCTTCTTTTCTTA
AATACCCTGAATTAAGACTTTATTCTTCTTAATTGCCCAACCTAGGACCTAGACTGTACGTTGCT
TAATTACCATGAATTAAGTTCTTTGAGTGCTATGTTTCC
Found at i:11748 original size:42 final size:43
Alignment explanation
Indices: 11687--11770 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
11677 GGCCATGACC
* *
11687 GGCCAACGCATGGGACATCCGGCCACAACCGGCCA-TCGATCG
1 GGCCAACGCACGGGACATCCGGCCACAACCGACCATTCGATCG
* * *
11729 GGCCATCGCACGGGCCATCCGGCCAGAACCGACCATTCGATC
1 GGCCAACGCACGGGACATCCGGCCACAACCGACCATTCGATC
11771 CTTTAGCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 30 0.83
43 6 0.17
ACGTcount: A:0.23, C:0.39, G:0.27, T:0.11
Consensus pattern (43 bp):
GGCCAACGCACGGGACATCCGGCCACAACCGACCATTCGATCG
Found at i:16345 original size:12 final size:12
Alignment explanation
Indices: 16325--16354 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16315 GAGCGGCCAA
*
16325 CGCATGGGACAT
1 CGCACGGGACAT
16337 CGCACGGGACAT
1 CGCACGGGACAT
16349 CGCACG
1 CGCACG
16355 AGCCATCCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.33, T:0.10
Consensus pattern (12 bp):
CGCACGGGACAT
Found at i:16380 original size:42 final size:42
Alignment explanation
Indices: 16341--16426 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
16331 GGACATCGCA
*
16341 CGGGACATCGCACGAGCCATCCGGCCACAATCGGCCATCGAT
1 CGGGACATCGCACGAGCCATCCGGCCACAACCGGCCATCGAT
* * *
16383 CGGGCCATCGCATGGGCCATCCGGCCACAACCGGCCATTCGAT
1 CGGGACATCGCACGAGCCATCCGGCCACAACCGGCCA-TCGAT
16426 C
1 C
16427 CTTTAGCTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 33 0.85
43 6 0.15
ACGTcount: A:0.21, C:0.40, G:0.27, T:0.13
Consensus pattern (42 bp):
CGGGACATCGCACGAGCCATCCGGCCACAACCGGCCATCGAT
Found at i:22902 original size:13 final size:14
Alignment explanation
Indices: 22878--22907 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22868 CAATTAAAAT
22878 TAAATCTAACTAAG
1 TAAATCTAACTAAG
22892 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
22905 TAA
1 TAA
22908 GCAATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (14 bp):
TAAATCTAACTAAG
Found at i:24216 original size:19 final size:18
Alignment explanation
Indices: 24183--24218 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24173 TTGAAATAAT
24183 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
24201 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
24219 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:27375 original size:18 final size:18
Alignment explanation
Indices: 27352--27493 Score: 131
Period size: 18 Copynumber: 7.9 Consensus size: 18
27342 GCACCAGGCG
* *
27352 CCACACCCAGTGGCCGCA
1 CCACACCAAGTGGTCGCA
27370 CCACACCAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
* * *
27388 CAACCCCAAATGGTCGCA
1 CCACACCAAGTGGTCGCA
* * *
27406 CCACCCCAAATGGCCGCA
1 CCACACCAAGTGGTCGCA
** * *
27424 CCGTATCAAGTGGCCGCA
1 CCACACCAAGTGGTCGCA
** *
27442 CCTTATCAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
*
27460 CCCCACCAAGTGGTCGCA
1 CCACACCAAGTGGTCGCA
*
27478 CCACACCAATTGGTCG
1 CCACACCAAGTGGTCG
27494 TACTTGTTCA
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 105 1.00
ACGTcount: A:0.25, C:0.40, G:0.21, T:0.13
Consensus pattern (18 bp):
CCACACCAAGTGGTCGCA
Found at i:28813 original size:30 final size:30
Alignment explanation
Indices: 28719--28817 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
28709 TAGAGGAAGG
*
28719 TGACGGCACTCTAAATGATGGCACCAAAAT
1 TGACGGCACTCTAGATGATGGCACCAAAAT
** * * * ** **
28749 CCACTGCACCCAAGATGATGGCACCTCAGG
1 TGACGGCACTCTAGATGATGGCACCAAAAT
* *
28779 TGACGGCACTCTAGGTGATGGCACCGAAAT
1 TGACGGCACTCTAGATGATGGCACCAAAAT
28809 TGACGGCAC
1 TGACGGCAC
28818 CAAAGATGAT
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.17
Consensus pattern (30 bp):
TGACGGCACTCTAGATGATGGCACCAAAAT
Found at i:28818 original size:60 final size:60
Alignment explanation
Indices: 28716--28833 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 60
28706 CCATAGAGGA
* * *
28716 AGGTGACGGCACTCTAAATGATGGCACCAAAATCCACTGCACCCAAGATGATGGCACCTC
1 AGGTGACGGCACTCTAAATGATGGCACCAAAATCCACGGCACCAAAGATGATAGCACCTC
** * **
28776 AGGTGACGGCACTCTAGGTGATGGCACCGAAATTGACGGCACCAAAGATGATAGCACC
1 AGGTGACGGCACTCTAAATGATGGCACCAAAATCCACGGCACCAAAGATGATAGCACC
28834 GAAAGTGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.16
Consensus pattern (60 bp):
AGGTGACGGCACTCTAAATGATGGCACCAAAATCCACGGCACCAAAGATGATAGCACCTC
Found at i:35036 original size:21 final size:20
Alignment explanation
Indices: 35011--35050 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35001 TTTAATGGAG
35011 AAAATTCATAAAACTAAAAAC
1 AAAATT-ATAAAACTAAAAAC
* *
35032 AAAATTTTAAAATTAAAAA
1 AAAATTATAAAACTAAAAA
35051 TTGGGTTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAATTATAAAACTAAAAAC
Found at i:40299 original size:13 final size:14
Alignment explanation
Indices: 40275--40304 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
40265 GAATTAAAAT
40275 TAAATCTAACTAAG
1 TAAATCTAACTAAG
40289 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
40302 TAA
1 TAA
40305 GCAATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (14 bp):
TAAATCTAACTAAG
Found at i:53060 original size:18 final size:19
Alignment explanation
Indices: 53027--53063 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
53017 TCCATCGTTG
*
53027 TCTCCATGGTCTCCATGCA
1 TCTCCATGGCCTCCATGCA
53046 TCTCCAT-GCCTCCATGCA
1 TCTCCATGGCCTCCATGCA
53064 GCCCATGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.16, C:0.41, G:0.14, T:0.30
Consensus pattern (19 bp):
TCTCCATGGCCTCCATGCA
Found at i:54031 original size:54 final size:54
Alignment explanation
Indices: 53956--54075 Score: 177
Period size: 54 Copynumber: 2.2 Consensus size: 54
53946 GTCTACTTTG
* **
53956 AAAACTGCTGAAAACTAAGAAAAATGACAGTCTTCGATCAACTTGAGTATACTA
1 AAAACTGCTGAAAACTAAGAAAAATAACAGTCTTCGATCAACTTGAAAATACTA
* * *
54010 AAAACTGTTGAAAACTGAGAAAAATAACCGTCTTCGATCAACTTGAAAATACTA
1 AAAACTGCTGAAAACTAAGAAAAATAACAGTCTTCGATCAACTTGAAAATACTA
*
54064 AAAACTACTGAA
1 AAAACTGCTGAA
54076 CATTTGTGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (54 bp):
AAAACTGCTGAAAACTAAGAAAAATAACAGTCTTCGATCAACTTGAAAATACTA
Found at i:54278 original size:61 final size:61
Alignment explanation
Indices: 54208--54404 Score: 207
Period size: 61 Copynumber: 3.2 Consensus size: 61
54198 AAAATCTTTG
* * *
54208 AGGATCTGTCTTTAGATCCATCTTCGTGAACTGCCTTCACG-TTCACTCTTAAATACCAAAA
1 AGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCA-GATTCACTCTTAAATACCAAAA
* * ** * * * ***
54269 AGGAACTGTCTTCAGACCCATCTTCGTGAACTATCTGAAGATTCATTCCTAAATATCAGTT
1 AGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATACCAAAA
* * ****
54330 AGGAACTGTCTTCAGATCCGTCTTTGTGAACTGTCTTCAGATTCACTCTTAAATACCTTTT
1 AGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATACCAAAA
54391 AGGAACTGTCTTCA
1 AGGAACTGTCTTCA
54405 AAACCCATCT
Statistics
Matches: 111, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
60 1 0.01
61 110 0.99
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (61 bp):
AGGAACTGTCTTCAGATCCATCTTCGTGAACTGTCTTCAGATTCACTCTTAAATACCAAAA
Found at i:54484 original size:58 final size:57
Alignment explanation
Indices: 54098--54660 Score: 410
Period size: 58 Copynumber: 9.5 Consensus size: 57
54088 GTCATGATCC
* * * * * *
54098 GTCTTCAGATTCATTCGTGAGCTGTCTTTAGTCTCAATCTTAAAAGCTTTCAGGAGCT
1 GTCTTCAGATCCATCCGTGAGCTGTCTTCAGCCTCAATCTTAAAATCTTT-AGGAACT
** * *
54156 GTCTTCAGATCCATCTATGAGCTGTCTTCAGCCTCACTCTTTAAAATCTTTGAGGATCT
1 GTCTTCAGATCCATCCGTGAGCTGTCTTCAGCCTCAATC-TTAAAATCTTT-AGGAACT
* * * * * * ***
54215 GTCTTTAGATCCATCTTCGTGAACTGCCTTCA-CGTTCACTCTTAAATACCAAAAAGGAACT
1 GTCTTCAGATCCATC--CGTGAGCTGTCTTCAGC-CTCAATCTTAAA-ATC-TTTAGGAACT
* * * ** ** * * *
54276 GTCTTCAGACCCATCTTCGTGAACTATCTGAAGATTCATTCCTAAATATCAGTTAGGAACT
1 GTCTTCAGATCCATC--CGTGAGCTGTCTTCAGCCTCAATCTTAAA-ATC-TTTAGGAACT
* * * ** * *
54337 GTCTTCAGATCCGTCTTTGTGAACTGTCTTCAGATTCACTCTTAAATACCTTTTAGGAACT
1 GTCTTCAGATCCATC--CGTGAGCTGTCTTCAGCCTCAATCTTAAA-ATC-TTTAGGAACT
* * * * *
54398 GTCTTCAAAACCCATCTGTGAGTTGTCTTCAGCCTCAATCTTAAAATCTTTATGGAATT
1 GTCTTC-AGATCCATCCGTGAGCTGTCTTCAGCCTCAATCTTAAAATCTTTA-GGAACT
* * *
54457 GTCTTCACATCCATCCGTGAGCTGTCTTCAGTCTCTATCTTAAAATCTTTAAGGAACT
1 GTCTTCAGATCCATCCGTGAGCTGTCTTCAGCCTCAATCTTAAAATCTTT-AGGAACT
* * * * * *
54515 ATCTTCAAATCCATCAGTGAGTTATCTTCAGCCTCACTCTTAAAATCTTTCAGGAACT
1 GTCTTCAGATCCATCCGTGAGCTGTCTTCAGCCTCAATCTTAAAATCTTT-AGGAACT
* * * * *
54573 GTCTTCATATCCATCCATGAACTGTCTTCAGACTC-ATACTTAAAATCTTTAAGGAAGT
1 GTCTTCAGATCCATCCGTGAGCTGTCTTCAGCCTCAAT-CTTAAAATCTTT-AGGAACT
*
54631 GTCTTCAGATCCATCTGTGAGCTGTCTTCA
1 GTCTTCAGATCCATCCGTGAGCTGTCTTCA
54661 CACTACTTAA
Statistics
Matches: 408, Mismatches: 86, Indels: 22
0.79 0.17 0.04
Matches are distributed among these distances:
57 1 0.00
58 199 0.49
59 44 0.11
60 30 0.07
61 128 0.31
62 6 0.01
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (57 bp):
GTCTTCAGATCCATCCGTGAGCTGTCTTCAGCCTCAATCTTAAAATCTTTAGGAACT
Found at i:54544 original size:116 final size:115
Alignment explanation
Indices: 54098--54660 Score: 459
Period size: 116 Copynumber: 4.8 Consensus size: 115
54088 GTCATGATCC
* * * * * * * *
54098 GTCTTCAGATTCATTCGTGAGCTGTCTTTAGTCTCAATCTTAAAAGCTTTCAGGAGCTGTCTTCA
1 GTCTTCACATCCATCCGTGAACTGTCTTCAGTCTC-ATCTTAAAATCTTTAAGGAACTGTCTTCA
* * * * * *
54163 GATCCATCTATGAGCTGTCTTCAGCCTCACTCTTTAAAATCTTTGAGGATCT
65 AATCCATCTGTGAGTTGTCTTCAGCCTCAATC-TTAAAATCTTTCAGGAACT
* * * * ***
54215 GTCTTTAGATCCATCTTCGTGAACTGCCTTCACGT-TCACTCTTAAATACCAAAAAGGAACTGTC
1 GTCTTCACATCCATC--CGTGAACTGTCTTCA-GTCTCA-TCTTAAA-ATCTTTAAGGAACTGTC
* * ** * ** ** * * *
54279 TTCAGACCCATCTTCGTGAACTATCTGAAGATTCATTCCTAAATATCAGTT-AGGAACT
61 TTCAAATCCATC-T-GTGAGTTGTCTTCAGCCTCAATCTTAAA-ATC-TTTCAGGAACT
* * * * *
54337 GTCTTCAGATCCGTCTTTGTGAACTGTCTTCAGAT-TCACTCTTAAATACCTTTTAGGAACTGTC
1 GTCTTCACATCCATC--CGTGAACTGTCTTCAG-TCTCA-TCTTAAA-ATCTTTAAGGAACTGTC
* *
54401 TTCAAAACCCATCTGTGAGTTGTCTTCAGCCTCAATCTTAAAATCTTT-ATGGAATT
61 TTC-AAATCCATCTGTGAGTTGTCTTCAGCCTCAATCTTAAAATCTTTCA-GGAACT
* *
54457 GTCTTCACATCCATCCGTGAGCTGTCTTCAGTCTCTATCTTAAAATCTTTAAGGAACTATCTTCA
1 GTCTTCACATCCATCCGTGAACTGTCTTCAGTCTC-ATCTTAAAATCTTTAAGGAACTGTCTTCA
* * *
54522 AATCCATCAGTGAGTTATCTTCAGCCTCACTCTTAAAATCTTTCAGGAACT
65 AATCCATCTGTGAGTTGTCTTCAGCCTCAATCTTAAAATCTTTCAGGAACT
* * * *
54573 GTCTTCATATCCATCCATGAACTGTCTTCAGACTCATACTTAAAATCTTTAAGGAAGTGTCTTCA
1 GTCTTCACATCCATCCGTGAACTGTCTTCAGTCTCAT-CTTAAAATCTTTAAGGAACTGTCTTCA
* *
54638 GATCCATCTGTGAGCTGTCTTCA
65 AATCCATCTGTGAGTTGTCTTCA
54661 CACTACTTAA
Statistics
Matches: 364, Mismatches: 66, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
115 2 0.01
116 120 0.33
117 31 0.09
118 24 0.07
119 25 0.07
120 45 0.12
121 25 0.07
122 82 0.23
123 10 0.03
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (115 bp):
GTCTTCACATCCATCCGTGAACTGTCTTCAGTCTCATCTTAAAATCTTTAAGGAACTGTCTTCAA
ATCCATCTGTGAGTTGTCTTCAGCCTCAATCTTAAAATCTTTCAGGAACT
Found at i:55172 original size:159 final size:161
Alignment explanation
Indices: 54895--55212 Score: 468
Period size: 159 Copynumber: 2.0 Consensus size: 161
54885 TTTTGGATTT
*
54895 AAACGCCGCCATATATGGAAGGAGAAATTATTTTTTTTAGGGAAAAATTCCCTCCCCAATATATA
1 AAACGCAGCCATATATGGAAGGAGAAATTATTTTTTTTAGGGAAAAATTCCCTCCCC-ATATATA
**
54960 ATTATAATAATAATTGTATATTTTCCCTAGAAAATATTGACTATATATAGCAGCGTTTAT-TCGT
65 ATTATAATAATAATAATATATTTTCCCTAGAAAATATTGACTATATATAGCAGCGTTTATGT-GT
55024 GAAACGCCG-CAATTTTGTGGCGTTTAGCACAAA
129 GAAACG-CGACAATTTTGTGGCGTTTAGCACAAA
* * *
55057 AAACGCAGCCATATATGGAGGGAG-AGTT-TTTTTTTTCAGGGAAAAGTTCCCTCCCC-TA-ATA
1 AAACGCAGCCATATATGGAAGGAGAAATTATTTTTTTT-AGGGAAAAATTCCCTCCCCATATATA
* * *
55118 GTTATAATAGTAATAATATATTTTTCCCTAGAAAATATTGATTATATATAGCAGCGTTTATGTGT
65 ATTATAATAATAATAATATA-TTTTCCCTAGAAAATATTGACTATATATAGCAGCGTTTATGTGT
55183 GAAACGCGACAATTTTGTGGCGTTTAGCAC
129 GAAACGCGACAATTTTGTGGCGTTTAGCAC
55213 CAGAAACTCC
Statistics
Matches: 143, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
158 21 0.15
159 70 0.49
160 9 0.06
161 21 0.15
162 22 0.15
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (161 bp):
AAACGCAGCCATATATGGAAGGAGAAATTATTTTTTTTAGGGAAAAATTCCCTCCCCATATATAA
TTATAATAATAATAATATATTTTCCCTAGAAAATATTGACTATATATAGCAGCGTTTATGTGTGA
AACGCGACAATTTTGTGGCGTTTAGCACAAA
Found at i:56985 original size:156 final size:156
Alignment explanation
Indices: 56500--57073 Score: 717
Period size: 156 Copynumber: 3.7 Consensus size: 156
56490 ATGTGGACCA
* * * * * * *
56500 TCTTGGCTAAGTTTCATCCCAAACGGGCTTAAGATGAAAAACTTATGCATGTTTTTTAGTTAAGG
1 TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGG
* * * *
56565 ACAATTTGGGGTGAGAAA-CTAGTTTAGCATGAAGGAGAGCTCGGTGTTACTTAGAATTTTTTCC
66 ACAGTTTGGGGTGAGAAACCTAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCC
*
56629 ATAGTTTTATGGAGATAATCGAAGTC
131 ATAGTTTTATGGAGATAATCTAAGTC
* * *
56655 TCTTGGCCAAA-TTTTATCTCAATCAGACTTAAGATGAAAAACTTATACATGTTTTTCAATTAAG
1 TCTTGG-CAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAG
* * * * *
56719 AACAGTTTGGGGTGAGAAACC-AG-TCACCATTAAGGAAAGCTCGATTTTACTTAGAAATTTTTC
65 GACAGTTTGGGGTGAGAAACCTAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTC
56782 CATAGTTTTATGGAGATAATCTAAGTC
130 CATAGTTTTATGGAGATAATCTAAGTC
* * ** *
56809 TCGTGGCCAAGTTTCATCTCAATTGGACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAAGG
1 TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGG
* * ** * *
56874 ACAGTTTGGGGAGAGAAACCAAGTTCACCACCAAGGAGAGCTCGGTTTTGCTTGGAATTTTTTCC
66 ACAGTTTGGGGTGAGAAACCTAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCC
* * *
56939 ATAGTCTTGTGGGGATAATCTAAGTC
131 ATAGTTTTATGGAGATAATCTAAGTC
* * * * *
56965 CCTTGGCAAAGTTTCATCTCAATTAGACTT-AGAATAAAAAATTTATGCTTGTTTTTCATTTAAG
1 TCTTGGCAAAGTTTCATCTCAATCAGACTTAAG-ATGAAAAACTTATGCATGTTTTTCATTTAAG
* * *
57029 GACAGTTTGGGGTGTGAAGCCTAGTTCACCATGAAGGAGGGCTCG
65 GACAGTTTGGGGTGAGAAACCTAGTTCACCATGAAGGAGAGCTCG
57074 AACTAAGCGA
Statistics
Matches: 359, Mismatches: 54, Indels: 11
0.85 0.13 0.03
Matches are distributed among these distances:
153 3 0.01
154 130 0.36
155 74 0.21
156 152 0.42
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (156 bp):
TCTTGGCAAAGTTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGG
ACAGTTTGGGGTGAGAAACCTAGTTCACCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCC
ATAGTTTTATGGAGATAATCTAAGTC
Found at i:57399 original size:28 final size:28
Alignment explanation
Indices: 57367--57452 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 28
57357 GGAAACATCA
* **
57367 GAAGACTTGCTGTGTGATACATCAAAGG
1 GAAGACTTGCCGCCTGATACATCAAAGG
* * *
57395 GAAGATTTTCCGCCTGATACATCAGAGG
1 GAAGACTTGCCGCCTGATACATCAAAGG
* ** * *
57423 GAAGAATTTTCGCCTGACACATCAGAGG
1 GAAGACTTGCCGCCTGATACATCAAAGG
57451 GA
1 GA
57453 GACGTCATAG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (28 bp):
GAAGACTTGCCGCCTGATACATCAAAGG
Found at i:57719 original size:23 final size:23
Alignment explanation
Indices: 57693--57740 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
57683 CCGTGCAGAA
*
57693 CTCAAGCTCCGTA-CTTATTTTCT
1 CTCAAGCTCCGCACCTT-TTTTCT
*
57716 CTCAGGCTCCGCACCTTTTTTCT
1 CTCAAGCTCCGCACCTTTTTTCT
57739 CT
1 CT
57741 TGTTCATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.12, C:0.35, G:0.10, T:0.42
Consensus pattern (23 bp):
CTCAAGCTCCGCACCTTTTTTCT
Found at i:58760 original size:93 final size:93
Alignment explanation
Indices: 58596--58769 Score: 285
Period size: 93 Copynumber: 1.9 Consensus size: 93
58586 AAAAAGGACA
* *
58596 TGGGGGCCAAGGACTCAGGGGGCAAAACCAACAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTC
1 TGGGGGCCAAGGACTCAGGGGGCAAAACAAAAAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTC
58661 TACAACAAGTCAACAACGAAGAAAGACT
66 TACAACAAGTCAACAACGAAGAAAGACT
* * * *
58689 TGGGGGGCAAGGGCTCGGGGGGCAAAACAAAAAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTT
1 TGGGGGCCAAGGACTCAGGGGGCAAAACAAAAAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTC
*
58754 TGCAACAAGTCAACAA
66 TACAACAAGTCAACAA
58770 TGAGGTGAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.29, T:0.15
Consensus pattern (93 bp):
TGGGGGCCAAGGACTCAGGGGGCAAAACAAAAAACTGCTTGGTGCCCAGCCCGGTGCTCTGCCTC
TACAACAAGTCAACAACGAAGAAAGACT
Found at i:61666 original size:21 final size:21
Alignment explanation
Indices: 61632--61683 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
61622 CAGTAGCTGG
* *
61632 TGGAGTCGACTGCTCGAA-TAA
1 TGGAGTCAAATGCTC-AACTAA
61653 TGGAGTCAAATGCTCAACTTAA
1 TGGAGTCAAATGCTCAAC-TAA
61675 -GGAGTCAAA
1 TGGAGTCAAA
61684 CGACTTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 22 0.81
22 3 0.11
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TGGAGTCAAATGCTCAACTAA
Found at i:63787 original size:155 final size:155
Alignment explanation
Indices: 63538--64110 Score: 654
Period size: 155 Copynumber: 3.7 Consensus size: 155
63528 ATGTGGACCA
* * * * * * *
63538 TCTTGGCTAAGTTTCATCCCAAACGGACTTAAGATGAAAAACTTATGCATGTTTTTTAGTTAAGG
1 TCTTGGCCAAATTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGG
* * *
63603 ACAGTTTGGGGTGAGAAACCAGTTTACCATGATGGAGAGCTCCGTTTTACTTAGAATTTTTTCCA
66 ACAATTTGGGGTGAGAAACCAGTTCACCATGAAGGAGAGCTCCGTTTTACTTAGAATTTTTTCCA
*
63668 TAGTTTTATGGACATAATCTAAGTC
131 TAGTTTTATGGAGATAATCTAAGTC
* * *
63693 TCTTGGCCAAATTTTATCTCAATCAGACTTAAGATGAAAAACTTATACATGTTTTTCAATTAAGG
1 TCTTGGCCAAATTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGG
* * *
63758 ACAATTTGGGGTGAGAAACCAGTTGACCATGAAAGAGAGCTCGGTTTTACTTAGAA-TTTTTCCA
66 ACAATTTGGGGTGAGAAACCAGTTCACCATGAAGGAGAGCTCCGTTTTACTTAGAATTTTTTCCA
*
63822 TCA-TTTTATTGAGATAATCTAAGTC
131 T-AGTTTTATGGAGATAATCTAAGTC
* * *
63847 T-TGTGGCCAAGTTTCATCTCAAT-TGAACTTAAGATGAAAAACTTATGCAAGTTTTTCATTTAA
1 TCT-TGGCCAAATTTCATCTCAATCAG-ACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAA
* * * * * ** * * *
63910 GGACAGTTTAGGGAGAGGAACCATGTTCAACACCAAGGAGAGCTCCATTTTACTTGGAATATTTT
64 GGACAATTTGGGGTGAGAAACCA-GTTCACCATGAAGGAGAGCTCCGTTTTACTTAGAATTTTTT
* *
63975 CCATAGTCTTGTGGAGATAATCTAAGTC
128 CCATAGTTTTATGGAGATAATCTAAGTC
* * * * ***
64003 CCTTGG-GAAAGTTTCATCTCAATCAAACTT-AGAATGAAAAACTTTTTTTTGTTTTTCATTTAA
1 TCTTGGCCAAA-TTTCATCTCAATCAGACTTAAG-ATGAAAAACTTATGCATGTTTTTCATTTAA
* * *
64066 GGACAATTTGGGGTGTGAAGCCTAGTTCACCATGAAGGAGGGCTC
64 GGACAATTTGGGGTGAGAAACC-AGTTCACCATGAAGGAGAGCTC
64111 GAACCAAGCC
Statistics
Matches: 349, Mismatches: 58, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
153 2 0.01
154 101 0.29
155 140 0.40
156 104 0.30
157 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (155 bp):
TCTTGGCCAAATTTCATCTCAATCAGACTTAAGATGAAAAACTTATGCATGTTTTTCATTTAAGG
ACAATTTGGGGTGAGAAACCAGTTCACCATGAAGGAGAGCTCCGTTTTACTTAGAATTTTTTCCA
TAGTTTTATGGAGATAATCTAAGTC
Found at i:64451 original size:28 final size:28
Alignment explanation
Indices: 64420--64489 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
64410 TTGATGTGTG
*
64420 ATACATCAAAGGGAAG-ATTTTCCGCCTC
1 ATACATCAGAGGGAAGAATTTT-CGCCTC
* * *
64448 ATACATTAGTGGGAAGAATTTTCGCCTG
1 ATACATCAGAGGGAAGAATTTTCGCCTC
*
64476 ACACATCAGAGGGA
1 ATACATCAGAGGGA
64490 GACGTCATAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (28 bp):
ATACATCAGAGGGAAGAATTTTCGCCTC
Found at i:65749 original size:21 final size:20
Alignment explanation
Indices: 65710--65763 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
65700 CTTGGTCTTG
* *
65710 AGTCATTTG-TTCTTTAAGT
1 AGTCATTTGACTCCTTAAGT
65729 AAGTCATTTGACTCCTTAAGT
1 -AGTCATTTGACTCCTTAAGT
*
65750 TGATCATTTGACTC
1 AG-TCATTTGACTC
65764 TTTTATTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (20 bp):
AGTCATTTGACTCCTTAAGT
Found at i:67269 original size:88 final size:87
Alignment explanation
Indices: 67106--67274 Score: 216
Period size: 88 Copynumber: 1.9 Consensus size: 87
67096 TTCCTTTTTT
** *
67106 ATATCTTCTAAATCTCCCACAATTTGGCAAGAGTTTAGAAAATATTCTCATTATGATTCAATTCT
1 ATATCTTCTAAATCTCCCACAATTTGGCAAGAGTTTAGAAAATATTCTCATTAAAATTCAATTAT
67171 TATAATTTATTTATTTTCTTAAA
66 TATAATTTA-TTATTTTCTTAAA
* * * **
67194 ATATCTTCTGAATCTCCCACAATTTGGCAAGATTTTTAGAAAATATTCTCTTTACAAATTTTATT
1 ATATCTTCTAAATCTCCCACAATTTGGCAAGA-GTTTAGAAAATATTCTCATTA-AAATTCAATT
*
67259 ATT-TTA-TTATTATTTT
64 ATTATAATTTATTATTTT
67275 ACATGAACTC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
87 7 0.10
88 34 0.49
89 21 0.30
90 8 0.11
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (87 bp):
ATATCTTCTAAATCTCCCACAATTTGGCAAGAGTTTAGAAAATATTCTCATTAAAATTCAATTAT
TATAATTTATTATTTTCTTAAA
Found at i:68324 original size:35 final size:35
Alignment explanation
Indices: 68297--68501 Score: 223
Period size: 35 Copynumber: 5.9 Consensus size: 35
68287 AAATTTCTTG
* *
68297 AAATGAGATCACCTCTAATTGTTGGAAACTACTGA
1 AAATGAGATCAACTCTAATCGTTGGAAACTACTGA
* * *
68332 AAATGTGATCAACTCTGATCGTTGGAAACTACTAA
1 AAATGAGATCAACTCTAATCGTTGGAAACTACTGA
* * *
68367 AAATGCGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGAGATCAACTCTAATCGTTGGAAACTACTGA
* * *
68402 AAATGCGATCAACTTTGATCGTTGGAAACTACTGAA
1 AAATGAGATCAACTCTAATCGTTGGAAACTACTG-A
* * * * * *
68438 AAAT-CGATCACCTATGACCGTTGGAAAATACTGA
1 AAATGAGATCAACTCTAATCGTTGGAAACTACTGA
* *
68472 AAATGCGATCAACTCTGATCGTTGGAAACT
1 AAATGAGATCAACTCTAATCGTTGGAAACT
68502 TCTTGGAATG
Statistics
Matches: 150, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
34 5 0.03
35 140 0.93
36 5 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (35 bp):
AAATGAGATCAACTCTAATCGTTGGAAACTACTGA
Found at i:68391 original size:70 final size:70
Alignment explanation
Indices: 68268--68501 Score: 317
Period size: 70 Copynumber: 3.3 Consensus size: 70
68258 AACTCCTCTA
* * * * ** * * * *
68268 GATCAACTCTGATCATCGGAAATTTCTTGAAATGAGATCACCTCTAATTGTTGGAAACTACTGAA
1 GATCAACTCTGATCGTTGGAAACTACTAAAAATGCGATCACCTCTGATCGTTGGAAAATACTGAA
*
68333 AATGT
66 AATGC
*
68338 GATCAACTCTGATCGTTGGAAACTACTAAAAATGCGATCAACTCTGATCGTTGGAAAATACTGAA
1 GATCAACTCTGATCGTTGGAAACTACTAAAAATGCGATCACCTCTGATCGTTGGAAAATACTGAA
68403 AATGC
66 AATGC
* * *
68408 GATCAACTTTGATCGTTGGAAACTACTGAAAAAT-CGATCACCTATGACCGTTGGAAAATACTGA
1 GATCAACTCTGATCGTTGGAAACTACT-AAAAATGCGATCACCTCTGATCGTTGGAAAATACTGA
68472 AAATGC
65 AAATGC
68478 GATCAACTCTGATCGTTGGAAACT
1 GATCAACTCTGATCGTTGGAAACT
68502 TCTTGGAATG
Statistics
Matches: 146, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
70 140 0.96
71 6 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (70 bp):
GATCAACTCTGATCGTTGGAAACTACTAAAAATGCGATCACCTCTGATCGTTGGAAAATACTGAA
AATGC
Found at i:68460 original size:105 final size:105
Alignment explanation
Indices: 68268--68499 Score: 297
Period size: 105 Copynumber: 2.2 Consensus size: 105
68258 AACTCCTCTA
* * * * * *
68268 GATCAACTCTGATCATCGGAAATTTCTTGAAATGAGATCACCTCTAATTGTTGGAAACTACTGAA
1 GATCAACTCTGATCGTTGGAAAATACTTGAAATGAGATCAACTCTAATCGTTGGAAACTACTGAA
* * * *
68333 AATGTGATCAACTCTGATCGTTGGAAACTACTAAAAATGC
66 AATGCGATCAACTATGACCGTTGGAAAATACTAAAAATGC
* * *
68373 GATCAACTCTGATCGTTGGAAAATAC-TGAAAATGCGATCAACTTTGATCGTTGGAAACTACTGA
1 GATCAACTCTGATCGTTGGAAAATACTTG-AAATGAGATCAACTCTAATCGTTGGAAACTACTG-
* *
68437 AAAAT-CGATCACCTATGACCGTTGGAAAATACTGAAAATGC
64 AAAATGCGATCAACTATGACCGTTGGAAAATACTAAAAATGC
68478 GATCAACTCTGATCGTTGGAAA
1 GATCAACTCTGATCGTTGGAAA
68500 CTTCTTGGAA
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
104 2 0.02
105 103 0.94
106 5 0.05
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (105 bp):
GATCAACTCTGATCGTTGGAAAATACTTGAAATGAGATCAACTCTAATCGTTGGAAACTACTGAA
AATGCGATCAACTATGACCGTTGGAAAATACTAAAAATGC
Found at i:68527 original size:16 final size:16
Alignment explanation
Indices: 68494--68527 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
68484 CTCTGATCGT
*
68494 TGGAAACTTCTTGGAA
1 TGGAAACTTCTTGAAA
*
68510 TGGAAACTTTTTGAAA
1 TGGAAACTTCTTGAAA
68526 TG
1 TG
68528 AGATCAACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (16 bp):
TGGAAACTTCTTGAAA
Found at i:68568 original size:35 final size:35
Alignment explanation
Indices: 68513--68697 Score: 273
Period size: 35 Copynumber: 5.3 Consensus size: 35
68503 CTTGGAATGG
* *
68513 AAACTTTTTGAAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
** *
68548 AAACTTCTTGGAATTTGATCAACTCTGACCTATGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
*
68583 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
* *
68618 AAACTTCTTGGAATTAGATCAACTCTGACCTTTGA
1 AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
*
68653 AAACTTCTT-GATATGAGATCAACTCTGACCTCTGG
1 AAACTTCTTGGA-ATGAGATCAACTCTGACCTCTGA
68688 AAACTTCTTG
1 AAACTTCTTG
68698 AAAGTGAGTG
Statistics
Matches: 133, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
34 2 0.02
35 131 0.98
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (35 bp):
AAACTTCTTGGAATGAGATCAACTCTGACCTCTGA
Found at i:68595 original size:70 final size:70
Alignment explanation
Indices: 68513--68697 Score: 325
Period size: 70 Copynumber: 2.6 Consensus size: 70
68503 CTTGGAATGG
* *
68513 AAACTTTTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATTTGATCAACTCTGACC
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATTAGATCAACTCTGACC
68578 TATGA
66 TATGA
68583 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATTAGATCAACTCTGACC
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATTAGATCAACTCTGACC
*
68648 TTTGA
66 TATGA
* *
68653 AAACTTCTTGATATGAGATCAACTCTGACCTCTGGAAACTTCTTG
1 AAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTG
68698 AAAGTGAGTG
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 110 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (70 bp):
AAACTTCTTGAAATGAGATCAACTCTGACCTCTGAAAACTTCTTGGAATTAGATCAACTCTGACC
TATGA
Found at i:73068 original size:42 final size:42
Alignment explanation
Indices: 73009--73124 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
72999 GACCGGCCAC
** *
73009 CATCGCATGGAGCAACCGGCCATGACCGGCCAACGCATGGAG
1 CATCGCATGGAGCAACCGGCCACAACCAGCCAACGCATGGAG
*
73051 CATCGCATGGGGCAACCGGCCACAACCAGCCAACGCATGG-G
1 CATCGCATGGAGCAACCGGCCACAACCAGCCAACGCATGGAG
* * * *
73092 ACATCGGACGG-GCCATCCGGCCACAACCGGCCA
1 -CATCGCATGGAG-CAACCGGCCACAACCAGCCA
73125 TTCGACCCTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.03
42 62 0.97
ACGTcount: A:0.26, C:0.37, G:0.29, T:0.08
Consensus pattern (42 bp):
CATCGCATGGAGCAACCGGCCACAACCAGCCAACGCATGGAG
Found at i:77487 original size:34 final size:33
Alignment explanation
Indices: 77408--77487 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
77398 TCTTGTTAGA
*
77408 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT
*
77441 TGCAAATAATTCTGTTTTGGTTGATCATAACAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAACAT
77474 TGAAAAATAATTCT
1 TG-AAAATAATTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
33 33 0.77
34 10 0.23
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAACAT
Done.