Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024154.1 Corchorus olitorius cultivar O-4 contig24187, 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: 89918
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:341 original size:151 final size:148
Alignment explanation
Indices: 32--307 Score: 416
Period size: 151 Copynumber: 1.9 Consensus size: 148
22 TAATTATTTG
*
32 ATACATCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTCCATTTTT
1 ATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTCCA-TTTT
* *
97 TGAATTATGAATTAATTAAGTTTTTAATATTTCAATCTAGTCCCTAAAGGACACATGTCACCCTT
65 T--ATTATGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGAACACATGTCACCCTT
* **
162 CAGGACCCGCGTAATTATTTG
128 CAGGACCCGCGTAATTACTAA
183 ATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTCCA-TTTT
1 ATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTCCATTTTT
* * *
247 -TT-T-AATTAATTAAGTTTTAAATGTTTCAATCTAGTCCCTAGAGAATACATGTCACCCTTCA
66 ATTATGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGAACACATGTCACCCTTCA
308 AGGTTTCACT
Statistics
Matches: 119, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
144 53 0.45
145 1 0.01
146 2 0.02
149 4 0.03
151 59 0.50
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (148 bp):
ATACACCGGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAGTTGACACATGTCCATTTTT
ATTATGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGAACACATGTCACCCTTCAG
GACCCGCGTAATTACTAA
Found at i:8854 original size:14 final size:14
Alignment explanation
Indices: 8832--8861 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8822 TATTAGATAC
8832 TTAGATTTATTTTA
1 TTAGATTTATTTTA
*
8846 TTAGGTTTATTTTA
1 TTAGATTTATTTTA
8860 TT
1 TT
8862 TATGTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (14 bp):
TTAGATTTATTTTA
Found at i:11060 original size:1 final size:1
Alignment explanation
Indices: 11009--11046 Score: 67
Period size: 1 Copynumber: 38.0 Consensus size: 1
10999 CAATATTTGG
*
11009 TTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11047 CTCTTTCCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:17091 original size:31 final size:31
Alignment explanation
Indices: 17049--17108 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
17039 GTCATATGTT
17049 ATCAATCGAACATCATGTAAATAAATGGTTA
1 ATCAATCGAACATCATGTAAATAAATGGTTA
*
17080 ATCAATTGAACATCATGTAAATAAATGGT
1 ATCAATCGAACATCATGTAAATAAATGGT
17109 GGTTTATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (31 bp):
ATCAATCGAACATCATGTAAATAAATGGTTA
Found at i:19451 original size:85 final size:85
Alignment explanation
Indices: 19348--19526 Score: 331
Period size: 85 Copynumber: 2.1 Consensus size: 85
19338 CAAATTCAAA
*
19348 CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACCAAACAAATAAAGCCTAACC
1 CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACCAAACAAATAAACCCTAACC
19413 CTAGCAGAGAAATCAAACGT
66 CTAGCAGAGAAATCAAACGT
* *
19433 CAAGAAAGCCTTAAAAACACGCATTTGTTTAATCATTACAAAACCCAAACAAATAAACCCTAACC
1 CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACCAAACAAATAAACCCTAACC
19498 CTAGCAGAGAAATCAAACGT
66 CTAGCAGAGAAATCAAACGT
19518 CAAGAAAGC
1 CAAGAAAGC
19527 TAACCTGATA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.49, C:0.23, G:0.10, T:0.18
Consensus pattern (85 bp):
CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACCAAACAAATAAACCCTAACC
CTAGCAGAGAAATCAAACGT
Found at i:19922 original size:27 final size:27
Alignment explanation
Indices: 19884--19937 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
19874 GCGCTACGCC
*
19884 GCGCAATTAATCTATTAAATTTACTAT
1 GCGCAATTAATCTATTAAACTTACTAT
* *
19911 GCGCAATTAATCTGTTTAACTTACTAT
1 GCGCAATTAATCTATTAAACTTACTAT
19938 CTTAACCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (27 bp):
GCGCAATTAATCTATTAAACTTACTAT
Found at i:21893 original size:2 final size:2
Alignment explanation
Indices: 21886--21910 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21876 ACTTTCAAAA
21886 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21911 AAATTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23308 original size:1 final size:1
Alignment explanation
Indices: 23302--23330 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
23292 TAAGCAATAG
23302 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23331 CTGGACAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23873 original size:29 final size:29
Alignment explanation
Indices: 23828--23883 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
23818 AGACGGTTTG
*
23828 GTGAGAGAAGAAAGAGAAAGAGTGAAAATT
1 GTGAGAGAAGAAAGAGAAAAAG-GAAAATT
23858 GTGA-AGAAGAAAGAGAAAAAGGAAAA
1 GTGAGAGAAGAAAGAGAAAAAGGAAAA
23884 GAAAGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 16 0.64
30 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.32, T:0.09
Consensus pattern (29 bp):
GTGAGAGAAGAAAGAGAAAAAGGAAAATT
Found at i:26617 original size:15 final size:15
Alignment explanation
Indices: 26575--26617 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
26565 AATTTTCTCG
*
26575 GGTCATTCGGGTTCC
1 GGTCATTCGGGTTCA
26590 GGCTCA-TCTGGGTTCA
1 GG-TCATTC-GGGTTCA
26606 GGTCATTCGGGT
1 GGTCATTCGGGT
26618 CTGCTGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.09, C:0.23, G:0.35, T:0.33
Consensus pattern (15 bp):
GGTCATTCGGGTTCA
Found at i:27209 original size:2 final size:2
Alignment explanation
Indices: 27202--27235 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27192 ATTCATAACA
27202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27236 TGAAATCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27926 original size:65 final size:64
Alignment explanation
Indices: 27744--28303 Score: 290
Period size: 66 Copynumber: 8.5 Consensus size: 64
27734 ATGACAAGCT
* * ** * *
27744 TGACCCTTTGACCGAGAGGGCATTTTTGGAAATTGTAAGTAAACTTAAATGC-GTAAATA-AAAA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGGAAA--AAAACTAAACTTAGATGCAG-AAATATAAAA
27807 AAC
62 AAC
* * * *
27810 TGAACCTTTTACTG-AAGGGTCATTTTTGAAAGACAAAGCTAAACTTAGATGCAGAAATATAAAA
1 TGACCCTTTGACCGAAAGGGT-ATTTTGGAAA-A-AAA-CTAAACTTAGATGCAGAAATATAAAA
27874 AAC
62 AAC
* * * **
27877 TGGCCCTTTGACCGAAAGGGTATTTCTAGAAAAAAACTAAACTTAGATGCA-AAA-AGACGAAAC
1 TGACCCTTTGACCGAAAGGGTATTT-TGGAAAAAAACTAAACTTAGATGCAGAAATATAAAAAAC
* * * ** * * **
27940 TGACCTTTTGACCGAAATGGTATTTTAGGAAAACAAAGCCAAAAGTAGATG-TGAAAAATATGAA
1 TGACCCTTTGACCGAAAGGGTATTTT-GGAAAA-AAA-CTAAACTTAGATGCAGAAATATAAAAA
28004 AC
63 AC
* * * * * **
28006 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAAATTGAACTTAGATG-TGAAAAATATGAA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGG-AAA-AAAACTAAACTTAGATGCAGAAATATAAAAA
28070 AC
63 AC
* * * * * *
28072 TGACCCTTTGACTGGAAGGGTATTTTTGGAAAGTAGAA-TAAACTGAAATGCAGAAATGAT--GA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGGAAA--AAAACTAAACTTAGATGCAGAAAT-ATAAAA
28134 AAC
62 AAC
* *
28137 TGACCCTTTCACCGAAAGGGTATTTTTGGAAATCAAAAGTACTAAACTT-GAATGC--AAA-AGA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGG-AA--AAAA--ACTAAACTTAG-ATGCAGAAATATA
*
28198 CAAAAC
59 AAAAAC
* * * * *
28204 CGACCCTTTGACCGAAAGGGTATTTCTGGAAATCAAAATACTAAACTTAAAGGCA-AAAGA-CAA
1 TGACCCTTTGACCGAAAGGGTATTT-TGG-AA--AAAA-ACTAAACTTAGATGCAGAAATATAAA
28267 AAA-
61 AAAC
* * *
28270 TGACCCTTCGACCGAAAGGGTGTTTTTGAAAAAA
1 TGACCCTTTGACCGAAAGGGTATTTTGGAAAAAA
28304 GAAAATACTA
Statistics
Matches: 398, Mismatches: 65, Indels: 66
0.75 0.12 0.12
Matches are distributed among these distances:
62 5 0.01
63 33 0.08
64 8 0.02
65 88 0.22
66 158 0.40
67 81 0.20
68 15 0.04
69 10 0.03
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.24
Consensus pattern (64 bp):
TGACCCTTTGACCGAAAGGGTATTTTGGAAAAAAACTAAACTTAGATGCAGAAATATAAAAAAC
Found at i:28019 original size:66 final size:65
Alignment explanation
Indices: 27719--28228 Score: 315
Period size: 66 Copynumber: 7.7 Consensus size: 65
27709 CTTTTATTCC
* * * * *** *
27719 CTTAAATGTG-AAAATATGACAAGCTTGACCCTTTGACCGAGAGGGCATTTTTGGAAATTGTAAG
1 CTTAGATGTGAAAAATATGA-AA-C-TGACCCTTTGACCGAAAGGGTATTTTAGGAAA-ACAAAC
27783 TAAA
62 TAAA
* * * * * * *
27787 CTTAAATGCGTAAATAA-A-AAAACTGAACCTTTTACTG-AAGGGTCATTTT-TGAAAGACAAAG
1 CTTAGATGTG-AAA-AATATGAAACTGACCCTTTGACCGAAAGGGT-ATTTTAGGAAA-ACAAA-
27848 CTAAA
61 CTAAA
* * ** *
27853 CTTAGATGCAGAAATATAAAAAACTGGCCCTTTGACCGAAAGGGTATTTCTA-GAAAA-AAACTA
1 CTTAGATG-TGAAAAATATGAAACTGACCCTTTGACCGAAAGGGTATTT-TAGGAAAACAAACTA
27916 AA
64 AA
* * * * * *
27918 CTTAGATG-CAAAAAGACGAAACTGACCTTTTGACCGAAATGGTATTTTAGGAAAACAAAGCCAA
1 CTTAGATGTGAAAAATATGAAACTGACCCTTTGACCGAAAGGGTATTTTAGGAAAACAAA-CTAA
27982 A
65 A
** * * * *
27983 AGTAGATGTGAAAAATATGAAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAAATTGA
1 CTTAGATGTGAAAAATATGAAACTGACCCTTTGACCGAAAGGGTATTTTAGGAAAAC-AAACTAA
28048 A
65 A
* * * **
28049 CTTAGATGTGAAAAATATGAAACTGACCCTTTGACTGGAAGGGTATTTTTGGAAAGTAGAA-TAA
1 CTTAGATGTGAAAAATATGAAACTGACCCTTTGACCGAAAGGGTATTTTAGGAAAACA-AACTAA
28113 A
65 A
* * * * * * *
28114 CTGAAATG-CAGAAATGATGAAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATCAAAAGTA
1 CTTAGATGTGAAAAAT-ATGAAACTGACCCTTTGACCGAAAGGGTATTTTAGGAAA--ACAA--A
28178 CTAAA
61 CTAAA
* * * ** *
28183 CTT-GA-ATGCAAAAGACAAAACCGACCCTTTGACCGAAAGGGTATTT
1 CTTAGATGTGAAAAATATGAAACTGACCCTTTGACCGAAAGGGTATTT
28229 CTGGAAATCA
Statistics
Matches: 349, Mismatches: 69, Indels: 49
0.75 0.15 0.10
Matches are distributed among these distances:
62 2 0.01
63 36 0.10
64 8 0.02
65 80 0.23
66 130 0.37
67 54 0.15
68 27 0.08
69 7 0.02
70 3 0.01
71 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (65 bp):
CTTAGATGTGAAAAATATGAAACTGACCCTTTGACCGAAAGGGTATTTTAGGAAAACAAACTAAA
Found at i:28222 original size:67 final size:66
Alignment explanation
Indices: 27873--28378 Score: 397
Period size: 66 Copynumber: 7.7 Consensus size: 66
27863 GAAATATAAA
* * *
27873 AAACTGGCCCTTTGACCGAAAGGGTATTTCT--AGAA-AAAA-ACTAAACTT-AGATGCAAAAAG
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAAACAAAATACTAAACTTGA-ATGC-AAAAG
27933 ACG
64 ACG
* * * ** * * * * * *
27936 AAACTGACCTTTTGACCGAAATGGTATTTTAGGAAAAC-AAAGCCAAAAGTAGATGTGAAAAATA
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAAACAAAATACTAAACTTGA-ATGCAAAAGA
*
28000 TG
65 CG
* * * * *
28002 AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAAACAAAAT--TGAACTTAGATGTGAAAAAT
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAAACAAAATACTAAACTT-GA-ATGCAAAAG
*
28065 ATG
64 ACG
* * ** *
28068 AAACTGACCCTTTGACTGGAAGGGTATTTTTGG-AAAGTAGA-A-TAAAC-TGAAATGCAGAAAT
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAAACAAAATACTAAACTTG-AATGCA-AAA-
*
28129 GATG
63 GACG
* *
28133 AAACTGACCCTTTCACCGAAAGGGTATTTTTGGAAATCAAAAGTACTAAACTTGAATGCAAAAGA
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAAACAAAA-TACTAAACTTGAATGCAAAAGA
*
28198 CA
65 CG
* * * * *
28200 AAACCGACCCTTTGACCGAAAGGGTATTTCTGGAAATCAAAATACTAAACTTAAAGGCAAAAGAC
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAAACAAAATACTAAACTTGAATGCAAAAGAC
*
28265 A
66 G
* * * * * *
28266 AAAATGACCCTTCGACCGAAAGGGTGTTTTTGAAAAAAGAAAATACTAAACTTAAATGCAAAAAG
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTG-GAAAACAAAATACTAAACTTGAATGC-AAAAG
28331 ACG
64 ACG
* * * * *
28334 AAAATAACCCTTCGACCGAAAGGGTATTTCTGGAAAGAGAAAATA
1 AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAA-ACAAAATA
28379 AAACTTTACT
Statistics
Matches: 362, Mismatches: 62, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
63 30 0.08
64 5 0.01
65 51 0.14
66 143 0.40
67 72 0.20
68 48 0.13
69 11 0.03
70 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (66 bp):
AAACTGACCCTTTGACCGAAAGGGTATTTTTGGAAAACAAAATACTAAACTTGAATGCAAAAGAC
G
Found at i:42296 original size:15 final size:15
Alignment explanation
Indices: 42276--42307 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42266 CATTGCTTGA
42276 CATTTCTAGCAAAAG
1 CATTTCTAGCAAAAG
*
42291 CATTTCTAGCTAAAG
1 CATTTCTAGCAAAAG
42306 CA
1 CA
42308 AGGCCAGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (15 bp):
CATTTCTAGCAAAAG
Found at i:43987 original size:27 final size:27
Alignment explanation
Indices: 43953--44012 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
43943 TTAAAAAGCT
*
43953 CACTATAATGCGTGGCAATACAAAACC
1 CACTATAATACGTGGCAATACAAAACC
43980 CACTATAATACGTGGCAATACAAAACC
1 CACTATAATACGTGGCAATACAAAACC
44007 CACTAT
1 CACTAT
44013 GTGACACATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.20
Consensus pattern (27 bp):
CACTATAATACGTGGCAATACAAAACC
Found at i:44107 original size:53 final size:53
Alignment explanation
Indices: 44044--44201 Score: 280
Period size: 53 Copynumber: 3.0 Consensus size: 53
44034 CATGATTAAG
44044 GGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCGAAC
1 GGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCGAAC
* * *
44097 GGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCCTCCCATAGCCCGAAG
1 GGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCGAAC
44150 GGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTTCCCACAGCCCGA
1 GGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCC-TTCCCACAGCCCGA
44202 GAGAGCGAGT
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 87 0.88
54 12 0.12
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (53 bp):
GGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCGAAC
Found at i:45741 original size:25 final size:25
Alignment explanation
Indices: 45713--45819 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
45703 GACAAACAGA
* *
45713 GAAGCCCATTGCCAGGAAGCTCGAT
1 GAAGCTCACTGCCAGGAAGCTCGAT
** * *
45738 GAAGCTCACTGCTGGGATGCTCGTT
1 GAAGCTCACTGCCAGGAAGCTCGAT
*
45763 GAAGCTCGCTGCCAGGAAGCTC-ATT
1 GAAGCTCACTGCCAGGAAGCTCGA-T
* * *
45788 GAAGCTCGCTGCTAGGAAGTTCG-T
1 GAAGCTCACTGCCAGGAAGCTCGAT
45812 CGAAGCTC
1 -GAAGCTC
45820 GCTGTTGGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
24 1 0.02
25 65 0.98
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.21
Consensus pattern (25 bp):
GAAGCTCACTGCCAGGAAGCTCGAT
Found at i:45820 original size:25 final size:25
Alignment explanation
Indices: 45726--45823 Score: 124
Period size: 25 Copynumber: 3.9 Consensus size: 25
45716 GCCCATTGCC
* *
45726 AGGAAGCTCGATGAAGCTCACTGCT
1 AGGAAGCTCGTTGAAGCTCGCTGCT
* * *
45751 GGGATGCTCGTTGAAGCTCGCTGCC
1 AGGAAGCTCGTTGAAGCTCGCTGCT
*
45776 AGGAAGCTCATTGAAGCTCGCTGCT
1 AGGAAGCTCGTTGAAGCTCGCTGCT
* *
45801 AGGAAGTTCGTCGAAGCTCGCTG
1 AGGAAGCTCGTTGAAGCTCGCTG
45824 TTGGAAAGCT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.22
Consensus pattern (25 bp):
AGGAAGCTCGTTGAAGCTCGCTGCT
Found at i:45833 original size:50 final size:50
Alignment explanation
Indices: 45722--45823 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 50
45712 AGAAGCCCAT
* * *
45722 TGCCAGGAAGCTCGATGAAGCTCACTGCTGGGATGCTCGTTGAAGCTCGC
1 TGCCAGGAAGCTCGATGAAGCTCACTGCTAGGAAGCTCGTCGAAGCTCGC
* *
45772 TGCCAGGAAGCTC-ATTGAAGCTCGCTGCTAGGAAGTTCGTCGAAGCTCGC
1 TGCCAGGAAGCTCGA-TGAAGCTCACTGCTAGGAAGCTCGTCGAAGCTCGC
45822 TG
1 TG
45824 TTGGAAAGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.02
50 45 0.98
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (50 bp):
TGCCAGGAAGCTCGATGAAGCTCACTGCTAGGAAGCTCGTCGAAGCTCGC
Found at i:45874 original size:25 final size:25
Alignment explanation
Indices: 45842--45910 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
45832 CTTGCTGCTA
45842 AGAAGCTCGTTGAAGCTCACTACTG
1 AGAAGCTCGTTGAAGCTCACTACTG
* * * *
45867 GGATGCTCGTTAAAGCTCACTGCTG
1 AGAAGCTCGTTGAAGCTCACTACTG
* *
45892 AGAAGCTCGTCGACGCTCA
1 AGAAGCTCGTTGAAGCTCA
45911 TTGTTGGGAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (25 bp):
AGAAGCTCGTTGAAGCTCACTACTG
Found at i:45902 original size:90 final size:90
Alignment explanation
Indices: 45756--45923 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 90
45746 CTGCTGGGAT
* * * * * *
45756 GCTCGTTGAAGCTCGCTGCCAGGAAGCTCATTGAAGCTCGCTGCTAGGAAGTTCGTCGAAGCTCG
1 GCTCGTTGAAGCTCACTACCAGGAAGCTCATTAAAGCTCACTGCTAGGAAGCTCGTCGAAGCTCA
45821 CTGTTGGAAAGCTTGCTGCTAAGAA
66 CTGTTGGAAAGCTTGCTGCTAAGAA
** * * *
45846 GCTCGTTGAAGCTCACTACTGGGATGCTCGTTAAAGCTCACTGCT-GAGAAGCTCGTCGACGCTC
1 GCTCGTTGAAGCTCACTACCAGGAAGCTCATTAAAGCTCACTGCTAG-GAAGCTCGTCGAAGCTC
* *
45910 ATTGTTGGGAAGCT
65 ACTGTTGGAAAGCT
45924 GGCAGAGATA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
89 1 0.02
90 63 0.98
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (90 bp):
GCTCGTTGAAGCTCACTACCAGGAAGCTCATTAAAGCTCACTGCTAGGAAGCTCGTCGAAGCTCA
CTGTTGGAAAGCTTGCTGCTAAGAA
Found at i:51594 original size:29 final size:28
Alignment explanation
Indices: 51558--51634 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 28
51548 ATGTGAACTT
*
51558 AAAAATGACCAAAATGCCCCTGAATGTG
1 AAAAATGACCAAAATGCCCCTGAATATG
* **
51586 CAAAAATGACCATAATGCCATTGAATATG
1 -AAAAATGACCAAAATGCCCCTGAATATG
51615 AAAAATGACCAAAATGCCCC
1 AAAAATGACCAAAATGCCCC
51635 CTGGACGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 17 0.41
29 24 0.59
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.18
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTGAATATG
Found at i:52065 original size:50 final size:49
Alignment explanation
Indices: 52003--52280 Score: 414
Period size: 50 Copynumber: 5.5 Consensus size: 49
51993 CGATCAACTT
* *
52003 CTTTGAATTGTCTTCCAA-TCTAATATCAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTC-AAT-TCAAAAGGACCGTCTTCCGCTTATC
*
52053 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAAT-TCAAAAGGACCGTCTTCCGCTTATC
*
52103 CTTTGAACTGTGTACCAATTCAATTCTATAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATTC---AAAAGGACCGTCTTCCGCTTATC
*
52155 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAAT-TCAAAAGGACCGTCTTCCGCTTATC
52205 CTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATTC---AAAAGGACCGTCTTCCGCTTATC
52257 CTTTGAACTGTCTACCAATTCAAT
1 CTTTGAACTGTCTACCAATTCAAT
52281 CTAAAAAAAG
Statistics
Matches: 211, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
49 2 0.01
50 113 0.54
51 2 0.01
52 93 0.44
53 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (49 bp):
CTTTGAACTGTCTACCAATTCAATTCAAAAGGACCGTCTTCCGCTTATC
Found at i:52162 original size:102 final size:102
Alignment explanation
Indices: 52030--52287 Score: 498
Period size: 102 Copynumber: 2.5 Consensus size: 102
52020 ATCTAATATC
52030 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTC
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTC
*
52095 CGCTTATCCTTTGAACTGTGTACCAATTCAATTCTAT
66 CGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAT
52132 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTC
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTC
52197 CGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAT
66 CGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAT
*
52234 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTAAAAA
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAA
52288 AAGGTAATGC
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 154 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (102 bp):
AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTC
CGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAT
Found at i:52291 original size:52 final size:51
Alignment explanation
Indices: 52030--52288 Score: 468
Period size: 52 Copynumber: 5.1 Consensus size: 51
52020 ATCTAATATC
52030 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT-T
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTAT
*
52080 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTGTACCAATTCAATTCTAT
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TCTAT
52132 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT-T
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTAT
52182 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTAT
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAA-TCTAT
*
52234 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTAA
1 AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTAT
52285 AAAA
1 AAAA
52289 AGGTAATGCA
Statistics
Matches: 202, Mismatches: 3, Indels: 7
0.95 0.01 0.03
Matches are distributed among these distances:
50 92 0.46
51 17 0.08
52 93 0.46
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTAT
Found at i:52375 original size:50 final size:50
Alignment explanation
Indices: 52300--52534 Score: 400
Period size: 50 Copynumber: 4.7 Consensus size: 50
52290 GGTAATGCAC
*
52300 CGTATGGAAACG-GATGTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
1 CGTATGGAAACGAG-TTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
*
52350 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
*
52400 CGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
* *
52450 CGTATGGAAACGAGTTCGGCTTGTGGAAAAGCCTATATTGATAATTGACT
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
*
52500 CATATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
52535 AAGCATTCAG
Statistics
Matches: 177, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
50 176 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (50 bp):
CGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACT
Found at i:52746 original size:78 final size:78
Alignment explanation
Indices: 52617--52824 Score: 337
Period size: 78 Copynumber: 2.7 Consensus size: 78
52607 AATGCCTTTG
* * * *
52617 GAAAATAACTCTGAAT-TCGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAGGGTCCAA
1 GAAAATAACTCTGAATCT-GATGTTATGATTGAAAACTTCTTGATTGATGATGAAAAGGGACCAA
52681 TGTGCGGTCAACTT
65 TGTGCGGTCAACTT
*
52695 GAAAATAACTCTGAGTCTGATGTTATGATTGAAAACTTCTTGATTGATGATGAAAAGGGACCAAT
1 GAAAATAACTCTGAATCTGATGTTATGATTGAAAACTTCTTGATTGATGATGAAAAGGGACCAAT
52760 GTGCGGTCAACTT
66 GTGCGGTCAACTT
*
52773 GAAAAATAACTCTGAATCTGATGTTATGATTGAAAACTTCTTGATTAATGAT
1 G-AAAATAACTCTGAATCTGATGTTATGATTGAAAACTTCTTGATTGATGAT
52825 TTGAATCTTT
Statistics
Matches: 121, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
78 72 0.60
79 49 0.40
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (78 bp):
GAAAATAACTCTGAATCTGATGTTATGATTGAAAACTTCTTGATTGATGATGAAAAGGGACCAAT
GTGCGGTCAACTT
Found at i:53268 original size:50 final size:50
Alignment explanation
Indices: 53214--53363 Score: 210
Period size: 50 Copynumber: 3.0 Consensus size: 50
53204 CTTAAATGCC
* * *
53214 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * *
53264 CTTTGAAAAGCGAATTTTAATCTTTGAACTCTCAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATC-TTGAACTCACAAATGGAAAGCAATCTTA
* * *
53315 TTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTT
53364 GTTATAAAAC
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 44 0.51
51 43 0.49
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:54000 original size:28 final size:27
Alignment explanation
Indices: 53951--54022 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
53941 ATCAATTCTC
** *
53951 TTTTGATTTTGAT-TTTGGTTTTGATTT
1 TTTTGATTTTTTTATTTGATTTTG-TTT
53978 TTTTGATTTTTTTATTTGATTTTGTTT
1 TTTTGATTTTTTTATTTGATTTTGTTT
* *
54005 TTATTTATTTATTTATTT
1 TT-TTGATTTTTTTATTT
54023 TTATTGATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (27 bp):
TTTTGATTTTTTTATTTGATTTTGTTT
Found at i:54030 original size:33 final size:34
Alignment explanation
Indices: 53958--54031 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
53948 CTCTTTTGAT
*
53958 TTTGATTTTGGTTTTGATTTTTTTGATTTTTTTA
1 TTTGATTTTGGTTTTGATTTATTTGATTTTTTTA
*
53992 TTTGATTTT-GTTTTTATTTATTT-ATTTATTTT-
1 TTTGATTTTGGTTTTGATTTATTTGATTT-TTTTA
54024 TATTGATT
1 T-TTGATT
54032 GATTTTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
32 5 0.14
33 22 0.61
34 9 0.25
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (34 bp):
TTTGATTTTGGTTTTGATTTATTTGATTTTTTTA
Found at i:54036 original size:18 final size:18
Alignment explanation
Indices: 54002--54036 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53992 TTTGATTTTG
* *
54002 TTTTTATTTATTTATTTA
1 TTTTTATTGATTGATTTA
54020 TTTTTATTGATTGATTT
1 TTTTTATTGATTGATTT
54037 TTTGAATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTTATTGATTGATTTA
Found at i:63606 original size:29 final size:28
Alignment explanation
Indices: 63570--63646 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 28
63560 ATGTGAACTT
*
63570 AAAAATGACCAAAATGCCCCTGAATGTG
1 AAAAATGACCAAAATGCCCCTGAATATG
* **
63598 CAAAAATGACCATAATGCCATTGAATATG
1 -AAAAATGACCAAAATGCCCCTGAATATG
63627 AAAAATGACCAAAATGCCCC
1 AAAAATGACCAAAATGCCCC
63647 CTGGACGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 17 0.41
29 24 0.59
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.18
Consensus pattern (28 bp):
AAAAATGACCAAAATGCCCCTGAATATG
Found at i:64404 original size:22 final size:22
Alignment explanation
Indices: 64369--64495 Score: 138
Period size: 22 Copynumber: 5.9 Consensus size: 22
64359 TTACTCTAAT
64369 ATTACTCTTT-TTTTACTTCTG
1 ATTACTCTTTCTTTTACTTCTG
64390 ATTACTCTTTCTTTTACTTCTG
1 ATTACTCTTTCTTTTACTTCTG
64412 ATTACTCTTTCTTTTAC-TCAT-
1 ATTACTCTTTCTTTTACTTC-TG
* * *
64433 TTTACTC-TCCTTTTTACTTCTT
1 ATTACTCTTTC-TTTTACTTCTG
* * *
64455 ATTACTCTTCCTTCTACTCCTG
1 ATTACTCTTTCTTTTACTTCTG
64477 ATTACT-TTTCCTTTTACTT
1 ATTACTCTTT-CTTTTACTT
64496 TTTTTAGTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
20 2 0.02
21 27 0.30
22 58 0.64
23 3 0.03
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTACTCTTTCTTTTACTTCTG
Found at i:64419 original size:43 final size:43
Alignment explanation
Indices: 64369--64495 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 43
64359 TTACTCTAAT
64369 ATTACTCTTTTTTTACTTCTGATTACTCTTTCTTTTACTTCTG
1 ATTACTCTTTTTTTACTTCTGATTACTCTTTCTTTTACTTCTG
* * *
64412 ATTACTCTTTCTTTTAC-TCAT-TTTACTC-TCCTTTTTACTTCTT
1 ATTACTCTTT-TTTTACTTC-TGATTACTCTTTC-TTTTACTTCTG
* * *
64455 ATTACTCTTCCTTCTACTCCTGATTACT-TTTCCTTTTACTT
1 ATTACTCTT-TTTTTACTTCTGATTACTCTTT-CTTTTACTT
64496 TTTTTAGTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
42 2 0.03
43 43 0.63
44 22 0.32
45 1 0.01
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.58
Consensus pattern (43 bp):
ATTACTCTTTTTTTACTTCTGATTACTCTTTCTTTTACTTCTG
Found at i:64501 original size:65 final size:64
Alignment explanation
Indices: 64370--64494 Score: 180
Period size: 65 Copynumber: 1.9 Consensus size: 64
64360 TACTCTAATA
* * * *
64370 TTACTCTTTTTTTACTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCTTTTACTCATT
1 TTACTCTCTTTTTACTTCTGATTACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTACTCATT
*
64434 TTACTCTCCTTTTTACTTCTTATTACTCTTCCTTCTACTCCTGATTACT-TTTCCTTTTACT
1 TTACTCT-CTTTTTACTTCTGATTACTCTTCCTTCTACTCCTGATTACTCTTT-CTTTTACT
64495 TTTTTTAGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 10 0.19
65 44 0.81
ACGTcount: A:0.14, C:0.26, G:0.02, T:0.58
Consensus pattern (64 bp):
TTACTCTCTTTTTACTTCTGATTACTCTTCCTTCTACTCCTGATTACTCTTTCTTTTACTCATT
Found at i:64538 original size:58 final size:57
Alignment explanation
Indices: 64474--64609 Score: 202
Period size: 56 Copynumber: 2.4 Consensus size: 57
64464 CCTTCTACTC
* *
64474 CTGATTACTTTTCCTTTTACTTTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTT
1 CTGATTACTTTT-CTTTTACTTTTTTTAGCTTAATTACTCTTAAATTAAACTAATCTT
* *
64532 CTGATTAC-TTTCTTTTACTCTTTTTAGCTTAATTACTCTTAAATTAAGCTAATCTT
1 CTGATTACTTTTCTTTTACTTTTTTTAGCTTAATTACTCTTAAATTAAACTAATCTT
*
64588 CTGATTACTCTTTCTTCTACTT
1 CTGATTACT-TTTCTTTTACTT
64610 CCGATTACTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
56 49 0.70
57 3 0.04
58 18 0.26
ACGTcount: A:0.23, C:0.18, G:0.05, T:0.54
Consensus pattern (57 bp):
CTGATTACTTTTCTTTTACTTTTTTTAGCTTAATTACTCTTAAATTAAACTAATCTT
Found at i:64615 original size:22 final size:22
Alignment explanation
Indices: 64585--64803 Score: 180
Period size: 22 Copynumber: 10.1 Consensus size: 22
64575 TTAAGCTAAT
*
64585 CTTCTGATTACTCTTTCTTCTA
1 CTTCTGATTACTCTTTCTTTTA
* *
64607 CTTCCGATTACTCTGTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
*
64629 CTTCTGATTACTTTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
** **
64651 C-TCTTTTTACTCTCCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* * *
64672 TTTCTGATTACTCTTCCTTTTG
1 CTTCTGATTACTCTTTCTTTTA
*
64694 CTTCCGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
64716 CTTTTGATTACT-TTTTTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* * *
64737 CTCCT-TTTACTC-TCCATTTTA
1 CTTCTGATTACTCTTTC-TTTTA
* * **
64758 CTTCTAATTACTCTTCCTTCAA
1 CTTCTGATTACTCTTTCTTTTA
64780 C-TCTTGATTACT-TTTCCTTTTA
1 CTTC-TGATTACTCTTT-CTTTTA
64802 CT
1 CT
64804 CTTTTTAGTT
Statistics
Matches: 153, Mismatches: 36, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
20 6 0.04
21 39 0.25
22 105 0.69
23 3 0.02
ACGTcount: A:0.14, C:0.26, G:0.04, T:0.57
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTA
Found at i:64869 original size:22 final size:23
Alignment explanation
Indices: 64841--64948 Score: 118
Period size: 22 Copynumber: 4.9 Consensus size: 23
64831 AACTAATCTT
*
64841 CTGATTACTCTTTCTTCTACTTC
1 CTGATTACTCTTTCTTTTACTTC
64864 CT-ATTACTCTTTCTTTTAC-TC
1 CTGATTACTCTTTCTTTTACTTC
* *
64885 TTGATTACTTTTTCTTTTAC-T-
1 CTGATTACTCTTTCTTTTACTTC
** **
64906 CTTTTTACTCTCCCTTTTACTT-
1 CTGATTACTCTTTCTTTTACTTC
64928 CTGATTACTCTTTCTTTTACT
1 CTGATTACTCTTTCTTTTACT
64949 CTTTTTAGCT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
21 17 0.24
22 51 0.73
23 2 0.03
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.58
Consensus pattern (23 bp):
CTGATTACTCTTTCTTTTACTTC
Found at i:64934 original size:145 final size:145
Alignment explanation
Indices: 64694--65093 Score: 531
Period size: 145 Copynumber: 2.8 Consensus size: 145
64684 CTTCCTTTTG
* * ** * * * *
64694 CTTCCGATTACTCTTTCTTTTACTTTTGATTACT-TTTTTTTTACTCCT-TTTAC-TCTCCATTT
1 CTTCTGATTACTCTTTCTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTC-TTT
** * ** *
64756 TACTTCTAATTACTCTTCCTTCAAC-TCTTGATTACTTTTCCTTTTACTCTTTTTAGTTTAATTA
65 TAC-TCTTTTTACTCTCCCTTTTACTTC-TGATTACTTTTCCTTTTACTCTTTTTAGCTTAATTA
*
64820 CTCTTGAATTAAACTAAT
128 CTCTTGAATCAAACTAAT
* *
64838 CTTCTGATTACTCTTTCTTCTACTTCCTATTACTCTTTCTTTTACTCTTGATTACTTTTTCTTTT
1 CTTCTGATTACTCTTTCTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
64903 ACTCTTTTTACTCTCCCTTTTACTTCTGATTACTCTTT-CTTTTACTCTTTTTAGCTTAATTACT
66 ACTCTTTTTACTCTCCCTTTTACTTCTGATTACT-TTTCCTTTTACTCTTTTTAGCTTAATTACT
64967 CTTGAATCAAACTAAT
130 CTTGAATCAAACTAAT
* *
64983 CTTCTGATTAGTCTTTGTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
1 CTTCTGATTACTCTTTCTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
* * *
65048 ACTCTTTTTACTCTCCCTTTTACTTCTGATAACTCTTCCTTCTACT
66 ACTCTTTTTACTCTCCCTTTTACTTCTGATTACTTTTCCTTTTACT
65094 TCCGATTACT
Statistics
Matches: 226, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
144 31 0.14
145 177 0.78
146 15 0.07
147 3 0.01
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.55
Consensus pattern (145 bp):
CTTCTGATTACTCTTTCTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
ACTCTTTTTACTCTCCCTTTTACTTCTGATTACTTTTCCTTTTACTCTTTTTAGCTTAATTACTC
TTGAATCAAACTAAT
Found at i:65028 original size:22 final size:22
Alignment explanation
Indices: 64983--65201 Score: 203
Period size: 22 Copynumber: 10.1 Consensus size: 22
64973 TCAAACTAAT
* * *
64983 CTTCTGATTAGTCTTTGTTCTA
1 CTTCTGATTACTCTTTCTTTTA
*
65005 CTTCCGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
65027 CTCCTGATTACTTTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
** **
65049 C-TCTTTTTACTCTCCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* * *
65070 CTTCTGATAACTCTTCCTTCTA
1 CTTCTGATTACTCTTTCTTTTA
*
65092 CTTCCGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
*
65114 TTTCTGATTACT-TTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
** **
65135 C-TCTTTTTACTCTCCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
65156 CTTCTGATTACTCTTCCTTCTA
1 CTTCTGATTACTCTTTCTTTTA
*
65178 CTGCTGATTACT-TTTCCTTTTA
1 CTTCTGATTACTCTTT-CTTTTA
65200 CT
1 CT
65202 CTTTTTAGCT
Statistics
Matches: 157, Mismatches: 36, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
20 8 0.05
21 34 0.22
22 115 0.73
ACGTcount: A:0.13, C:0.26, G:0.05, T:0.55
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTA
Found at i:65038 original size:398 final size:396
Alignment explanation
Indices: 64529--65259 Score: 1241
Period size: 398 Copynumber: 1.8 Consensus size: 396
64519 TTAAACTAAT
* *
64529 CTTCTGATTACTTTCTTTTACTCTTTTTAGCTTAATTACTCTTAAATTAAGCTAATCTTCTGATT
1 CTTCTGATTACTTTCTTTTACTCTTTTTAGCTTAATTACTCTTAAATCAAACTAATCTTCTGATT
*
64594 ACTCTTTCTTCTACTTCCGATTACTCTGTCTTTTACTTCTGATTACTTTTTCTTTTACTCTTTTT
66 ACTCTTTCTTCTACTTCCGATTACTCTGTCTTTTACTCCTGATTACTTTTTCTTTTACTCTTTTT
* * * *
64659 ACTCTCCCTTTTATTTCTGATTACTCTTCCTTTTGCTTCCGATTACTCTTTCTTTTACTTT-TGA
131 ACTCTCCCTTTTACTTCTGATAACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTA-TTTCTGA
*
64723 TTACTTTTTTTTTACTCCTTTTACTCTCCATTTTACTTCTAATTACTCTTCCTTCAACT-CTTGA
195 TTACTTTTCTTTTACTCCTTTTACTCTCCATTTTACTTCTAATTACTCTTCCTTCAACTGC-TGA
*
64787 TTACTTTTCCTTTTACTCTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCT
259 TTACTTTTCCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCT
64852 TTCTTCTACTTCCTATTACTCTTTCTTTTACTCTTGATTACTTTTTCTTTTACTCTTTTTACTCT
324 TTCTTCTACTTCCTATTACTCTTTCTTTTACTCTTGATTACTTTTTCTTTTACTCTTTTTACTCT
64917 CCCTTTTA
389 CCCTTTTA
*
64925 CTTCTGATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTTGAATCAAACTAATCTTCTGA
1 CTTCTGATTA--CTTTCTTTTACTCTTTTTAGCTTAATTACTCTTAAATCAAACTAATCTTCTGA
* * *
64990 TTAGTCTTTGTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTTACTCTTT
64 TTACTCTTTCTTCTACTTCCGATTACTCTGTCTTTTACTCCTGATTACTTTTTCTTTTACTCTTT
65055 TTACTCTCCCTTTTACTTCTGATAACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTATTTCTG
129 TTACTCTCCCTTTTACTTCTGATAACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTATTTCTG
* * * *
65120 ATTACTTTTCTTTTACTCTTTTTACTCTCCCTTTTACTTCTGATTACTCTTCCTTCTACTGCTGA
194 ATTACTTTTCTTTTACTCCTTTTACTCTCCATTTTACTTCTAATTACTCTTCCTTCAACTGCTGA
*
65185 TTACTTTTCCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTGAACTAATCTTCTGATTACTCT
259 TTACTTTTCCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCT
*
65250 TTCTTTTACT
324 TTCTTCTACT
65260 CTTTTTAGCT
Statistics
Matches: 312, Mismatches: 19, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
396 10 0.03
397 3 0.01
398 298 0.96
399 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.05, T:0.55
Consensus pattern (396 bp):
CTTCTGATTACTTTCTTTTACTCTTTTTAGCTTAATTACTCTTAAATCAAACTAATCTTCTGATT
ACTCTTTCTTCTACTTCCGATTACTCTGTCTTTTACTCCTGATTACTTTTTCTTTTACTCTTTTT
ACTCTCCCTTTTACTTCTGATAACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTATTTCTGAT
TACTTTTCTTTTACTCCTTTTACTCTCCATTTTACTTCTAATTACTCTTCCTTCAACTGCTGATT
ACTTTTCCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTT
CTTCTACTTCCTATTACTCTTTCTTTTACTCTTGATTACTTTTTCTTTTACTCTTTTTACTCTCC
CTTTTA
Found at i:65168 original size:64 final size:63
Alignment explanation
Indices: 65012--65208 Score: 196
Period size: 65 Copynumber: 3.0 Consensus size: 63
65002 CTACTTCCGA
* * * * ** ** **
65012 TTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTTACTCTTTTTACTCTCCCTTTTACTTCTGA
1 TTACTCTTCCTTTTACTTCTGATTACTCTTTCTTTTATTCTGATTACT-TTTCTTTTAC-TCTTT
* * *
65077 TAACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTATTTCTGATTACTTTTCTTTTACTCTTT
1 TTACTCTTCCTTTTACTTCTGATTACTCTTTCTTTTA-TTCTGATTACTTTTCTTTTACTCTTT
* * * *
65141 TTACTCTCCCTTTTACTTCTGATTACTCTTCCTTCTACTGCTGATTACTTTTCCTTTTACTCTTT
1 TTACTCTTCCTTTTACTTCTGATTACTCTTTCTTTTA-TTCTGATTACTTTT-CTTTTACTCTTT
65206 TTA
1 TTA
65209 GCTTAATTAC
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
64 47 0.43
65 54 0.50
66 8 0.07
ACGTcount: A:0.13, C:0.26, G:0.04, T:0.57
Consensus pattern (63 bp):
TTACTCTTCCTTTTACTTCTGATTACTCTTTCTTTTATTCTGATTACTTTTCTTTTACTCTTT
Found at i:65169 original size:86 final size:87
Alignment explanation
Indices: 64983--65202 Score: 345
Period size: 86 Copynumber: 2.5 Consensus size: 87
64973 TCAAACTAAT
* **
64983 CTTCTGATTAGTCTTTGTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
1 CTTCTGATTACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
65048 ACTCTTTTTACTCTCCCTTTTA
66 ACTCTTTTTACTCTCCCTTTTA
* * *
65070 CTTCTGATAACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTATTTCTGATTAC-TTTTCTTTT
1 CTTCTGATTACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
65134 ACTCTTTTTACTCTCCCTTTTA
66 ACTCTTTTTACTCTCCCTTTTA
* *
65156 CTTCTGATTACTCTTCCTTCTACTGCTGATTACT-TTTCCTTTTACTC
1 CTTCTGATTACTCTTCCTTCTACTTCCGATTACTCTTT-CTTTTACTC
65203 TTTTTAGCTT
Statistics
Matches: 121, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
85 3 0.02
86 69 0.57
87 49 0.40
ACGTcount: A:0.13, C:0.27, G:0.05, T:0.55
Consensus pattern (87 bp):
CTTCTGATTACTCTTCCTTCTACTTCCGATTACTCTTTCTTTTACTCCTGATTACTTTTTCTTTT
ACTCTTTTTACTCTCCCTTTTA
Found at i:65247 original size:28 final size:28
Alignment explanation
Indices: 65214--65308 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 28
65204 TTTTAGCTTA
*
65214 ATTACTCTTGAATTGAACTAATCTTCTG
1 ATTACTCTTGAATTAAACTAATCTTCTG
** ** ** * *
65242 ATTACTCTT-TCTTTTACTCTTTTTAGCTTA
1 ATTACTCTTGAATTAAACTAATCTT--C-TG
65272 ATTACTCTTGAATTAAACTAATCTTCTG
1 ATTACTCTTGAATTAAACTAATCTTCTG
65300 ATTACTCTT
1 ATTACTCTT
65309 TCTTTTATTT
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
27 8 0.17
28 19 0.40
29 2 0.04
30 10 0.21
31 8 0.17
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.49
Consensus pattern (28 bp):
ATTACTCTTGAATTAAACTAATCTTCTG
Found at i:65247 original size:58 final size:58
Alignment explanation
Indices: 65181--65546 Score: 410
Period size: 58 Copynumber: 6.3 Consensus size: 58
65171 CCTTCTACTG
*
65181 CTGATTACT-TTTCCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTGAACTAATCTT
1 CTGATTACTCTTT-CTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
65239 CTGATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
1 CTGATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
* ** * * * * * *
65297 CTGATTACTCTTTCTTTTATTTCTGATTACTTTTTCTT--TTGCTCTTTTTAGTTTAATTACTTC
1 CTGATTACTCTTTCTTTTA---CT-CTT--TTTAGCTTAATTACTC--TTGAATTAAACTA-ATC
*
65360 TA
57 TT
*
65362 CTGCTTACTCTTTCTTTTA--CTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
1 CTGATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
* * *
65418 CTGATTACTCTTTCTTTTTA-T-TTTTTAGTTTAATTACTC-TGAATTAAACTTAT-TA
1 CTGATTACTCTTTC-TTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
*
65473 CTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTAC-CTCTGAATTAAACTAATCTT
1 CTGATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCT-TGAATTAAACTAATCTT
65531 CTGATTACTCTTTCTT
1 CTGATTACTCTTTCTT
65547 CTATTCCTGA
Statistics
Matches: 261, Mismatches: 28, Indels: 38
0.80 0.09 0.12
Matches are distributed among these distances:
54 5 0.02
55 17 0.07
56 45 0.17
57 50 0.19
58 89 0.34
59 10 0.04
61 2 0.01
62 7 0.03
64 15 0.06
65 21 0.08
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.54
Consensus pattern (58 bp):
CTGATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
Found at i:65323 original size:22 final size:22
Alignment explanation
Indices: 65295--65336 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
65285 TAAACTAATC
65295 TTCTGATTACTCTTTCTTTTAT
1 TTCTGATTACTCTTTCTTTTAT
*
65317 TTCTGATTACTTTTTCTTTT
1 TTCTGATTACTCTTTCTTTT
65337 GCTCTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.17, G:0.05, T:0.67
Consensus pattern (22 bp):
TTCTGATTACTCTTTCTTTTAT
Found at i:65397 original size:121 final size:123
Alignment explanation
Indices: 65239--65591 Score: 466
Period size: 121 Copynumber: 3.0 Consensus size: 123
65229 AACTAATCTT
65239 CTGATTACTCTTTCTTTTACTCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTA
1 CTGATTACTCTTTCTTTTAC-CTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTA
*
65304 CTCTTTCTTTTATTTCTGATTACTTTTTCTTTTGCTCTTTTTAGTTTAATTACTT-CTA
65 CTCTTTCTTTTATTTCTGATTACTTTTTCTTTTACTCTTTTTAGTTTAATTACTTACTA
*
65362 CTGCTTACTCTTTCTTTTA-CTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTAC
1 CTGATTACTCTTTCTTTTACCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTAC
* ** * * *
65426 TCTTTCTTTTTATTT-T--TTA--GTTT-AATTACTC---TGA-ATTAA--ACTTATTA
66 TCTTTC-TTTTATTTCTGATTACTTTTTCTTTTACTCTTTTTAGTTTAATTACTTACTA
*
65473 CTGATTACTCTTTCTTTTACTCTTTTTAGTTTAATTAC-CTCTGAATTAAACTAATCTTCTGATT
1 CTGATTACTCTTTCTTTTAC-CTTTTTAGCTTAATTACTCT-TGAATTAAACTAATCTTCTGATT
* *
65537 ACTCTTTCTTCTATTCCTGATTACTTTTTCTTTTACTCTTTTTAGTTTAATTACT
64 ACTCTTTCTTTTATTTCTGATTACTTTTTCTTTTACTCTTTTTAGTTTAATTACT
65592 CTGAATTAAA
Statistics
Matches: 196, Mismatches: 17, Indels: 33
0.80 0.07 0.13
Matches are distributed among these distances:
110 4 0.02
111 20 0.10
112 12 0.06
113 50 0.26
115 3 0.02
116 5 0.03
117 6 0.03
118 6 0.03
119 3 0.02
121 54 0.28
122 12 0.06
123 18 0.09
124 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (123 bp):
CTGATTACTCTTTCTTTTACCTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTAC
TCTTTCTTTTATTTCTGATTACTTTTTCTTTTACTCTTTTTAGTTTAATTACTTACTA
Found at i:65453 original size:57 final size:56
Alignment explanation
Indices: 65366--65551 Score: 270
Period size: 56 Copynumber: 3.3 Consensus size: 56
65356 CTTCTACTGC
* *
65366 TTACTCTTTCTTTTACTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGA
1 TTACTCTTTCTTTTATTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGA
* *
65422 TTACTCTTTCTTTTTATTTTTTAGTTTAATTACTC-TGAATTAAACTTAT-TACTGA
1 TTACTCTTTC-TTTTATTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGA
65477 TTACTCTTTCTTTTACTCTTTTTAGTTTAATTAC-CTCTGAATTAAACTAATCTTCTGA
1 TTACTCTTTCTTTTA-T-TTTTTAGTTTAATTACTCT-TGAATTAAACTAATCTTCTGA
*
65535 TTACTCTTTCTTCTATT
1 TTACTCTTTCTTTTATT
65552 CCTGATTACT
Statistics
Matches: 117, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
54 5 0.04
55 17 0.15
56 40 0.34
57 36 0.31
58 19 0.16
ACGTcount: A:0.24, C:0.17, G:0.05, T:0.54
Consensus pattern (56 bp):
TTACTCTTTCTTTTATTTTTTAGTTTAATTACTCTTGAATTAAACTAATCTTCTGA
Found at i:65565 original size:179 final size:178
Alignment explanation
Indices: 65202--65527 Score: 421
Period size: 179 Copynumber: 1.8 Consensus size: 178
65192 TCCTTTTACT
*
65202 CTTTTTAGCTTAATTACTCTTGAATTGAACTAATCTTCTGATTACTCTTTCTTTTACTCTTTTTA
1 CTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTCTTTTACTCTTTTTA
* * *
65267 GCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTCTTTTATTTCTGATTACTTTTT
66 GCTTAATTACTCTTGAATTAAACTAATCTACTGATTACTCTTTCTTTTATCTCTGATTAC-GTTT
** ** ** *** *
65332 CTTTTGCTCTTTTTAGTTTAATTACTTCTACTGCTTACTCTTTCTTTTA
130 AATTACCTCTAATTAAACTAATTACTTCTACTGCTTACTCTTTCTATTA
65381 CTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTCTTTTTA-T-TTTTT
1 CTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTC-TTTTACTCTTTTT
* * **
65444 AGTTTAATTACTC-TGAATTAAACTTAT-TACTGATTACTCTTTCTTTTA-CTCTTTTTA-GTTT
65 AGCTTAATTACTCTTGAATTAAACTAATCTACTGATTACTCTTTCTTTTATCTCTGATTACGTTT
65505 AATTACCTCTGAATTAAACTAAT
130 AATTACCTCT-AATTAAACTAAT
65528 CTTCTGATTA
Statistics
Matches: 128, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
173 9 0.07
174 7 0.05
175 6 0.05
176 20 0.16
177 13 0.10
178 17 0.13
179 51 0.40
180 5 0.04
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (178 bp):
CTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTACTCTTTCTTTTACTCTTTTTA
GCTTAATTACTCTTGAATTAAACTAATCTACTGATTACTCTTTCTTTTATCTCTGATTACGTTTA
ATTACCTCTAATTAAACTAATTACTTCTACTGCTTACTCTTTCTATTA
Found at i:68691 original size:54 final size:54
Alignment explanation
Indices: 68627--68829 Score: 203
Period size: 54 Copynumber: 3.8 Consensus size: 54
68617 AGGACAACCT
* * *
68627 AGCAGTGACTTTCTCCTCAGCAGAATGAGTCTCGCCAGCATCGAGAGGATGTCC
1 AGCAATGACTTGCTCCTCAGCAGAAGGAGTCTCGCCAGCATCGAGAGGATGTCC
* * * * * * * *
68681 AGCAGTGACTTGCTCTTCAGCATG-AGGGGTCTGGCTAGCATCTACAGGATATCC
1 AGCAATGACTTGCTCCTCAGCA-GAAGGAGTCTCGCCAGCATCGAGAGGATGTCC
* * * *
68735 AGCAAAGACTTGTTCCT-AGGCAGAAGGAGTCTCGTCAGCATCGAGAGGATGTCT
1 AGCAATGACTTGCTCCTCA-GCAGAAGGAGTCTCGCCAGCATCGAGAGGATGTCC
* * * *
68789 GGCAATGACTTGCTCCCCAGTAGAAGGATTCTCGCCAGCAT
1 AGCAATGACTTGCTCCTCAGCAGAAGGAGTCTCGCCAGCAT
68830 TAAAGGGAGG
Statistics
Matches: 117, Mismatches: 28, Indels: 8
0.76 0.18 0.05
Matches are distributed among these distances:
53 2 0.02
54 113 0.97
55 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (54 bp):
AGCAATGACTTGCTCCTCAGCAGAAGGAGTCTCGCCAGCATCGAGAGGATGTCC
Found at i:72952 original size:14 final size:14
Alignment explanation
Indices: 72933--72959 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72923 AGAGCTCTCC
72933 AGCAGATCCTCGAT
1 AGCAGATCCTCGAT
72947 AGCAGATCCTCGA
1 AGCAGATCCTCGA
72960 CAAACGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (14 bp):
AGCAGATCCTCGAT
Found at i:72987 original size:28 final size:28
Alignment explanation
Indices: 72947--73100 Score: 204
Period size: 28 Copynumber: 5.5 Consensus size: 28
72937 GATCCTCGAT
*
72947 AGCAGATCCTCGACAAACGAAGCCCTCC
1 AGCAGATCCTCGACAAATGAAGCCCTCC
72975 AGCAGGA-CCTCGACAAATGAAGCCCTCC
1 AGCA-GATCCTCGACAAATGAAGCCCTCC
*
73003 AGCAGATCTTCGACAAATGAAGCCCTCC
1 AGCAGATCCTCGACAAATGAAGCCCTCC
*
73031 AGCAGATCCTCGACAAATGAAGCCCTCT
1 AGCAGATCCTCGACAAATGAAGCCCTCC
* ** *
73059 AGTC-GATTCTCGACAAACAAAGCCCGCC
1 AG-CAGATCCTCGACAAATGAAGCCCTCC
*
73087 AGCAGATTCTCGAC
1 AGCAGATCCTCGAC
73101 GAACAAAGAT
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
27 3 0.03
28 107 0.95
29 3 0.03
ACGTcount: A:0.32, C:0.34, G:0.19, T:0.15
Consensus pattern (28 bp):
AGCAGATCCTCGACAAATGAAGCCCTCC
Found at i:73958 original size:27 final size:27
Alignment explanation
Indices: 73926--74018 Score: 159
Period size: 27 Copynumber: 3.4 Consensus size: 27
73916 GTCAATTTAA
*
73926 AAAGCCCACTATAATGCGTGGCAATAC
1 AAAGCCCACTATAATACGTGGCAATAC
*
73953 AAAGCCCACTATAATACATGGCAATAC
1 AAAGCCCACTATAATACGTGGCAATAC
*
73980 AAAACCCACTATAATACGTGGCAATAC
1 AAAGCCCACTATAATACGTGGCAATAC
74007 AAAGCCCACTAT
1 AAAGCCCACTAT
74019 GTGGCACATG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.18
Consensus pattern (27 bp):
AAAGCCCACTATAATACGTGGCAATAC
Found at i:75073 original size:40 final size:40
Alignment explanation
Indices: 75029--75117 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
75019 ATGACGAGAA
75029 GGGAATAGGAACAACACCTTCCGATGAGGAAGGGCAAAAT
1 GGGAATAGGAACAACACCTTCCGATGAGGAAGGGCAAAAT
* * * *
75069 GGGAATTTA-G-ACAACACCTTCCGGTGGGGAAGGGCGAACT
1 GGGAA--TAGGAACAACACCTTCCGATGAGGAAGGGCAAAAT
75109 GGGAA-AGGA
1 GGGAATAGGA
75118 TAAACTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
40 36 0.88
41 1 0.02
42 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.35, T:0.13
Consensus pattern (40 bp):
GGGAATAGGAACAACACCTTCCGATGAGGAAGGGCAAAAT
Found at i:75262 original size:88 final size:86
Alignment explanation
Indices: 75038--75459 Score: 406
Period size: 88 Copynumber: 4.8 Consensus size: 86
75028 AGGGAATAGG
** *
75038 AACAACACCTTCCGATGAGGAAGGGCAAAATGGGAATTTAGACAACACCTTCCGGTGGGGAAGGG
1 AACAACA-CTTCCGATG-GGAAGGGCAAAACAGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* * * *
75103 CGAACTGGGAAAGGATAAACTTTA
64 CAAACTGGGAAAAG-TAGACTATA
* * * * * * *
75127 AACAACATCTCCCGATGAGGAAGGG-GAAACTGGGAGTTTAACCAACACCATCCGGTGGGTAAGG
1 AACAACA-CTTCCGATG-GGAAGGGCAAAAC-AGGAATTTAAACAACACCTTCCGGTGGGGAAGG
* **
75191 GCAAACTGGGAAAAGTGGGGTATA
63 GCAAACTGGGAAAAGTAGACTATA
*
75215 AACAACACATTCCGATAGGGAAGGGCAAAACAGGAATTTAAACAACACCTTCCGGAGGGGAAGGG
1 AACAACAC-TTCCGAT-GGGAAGGGCAAAACAGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* *
75280 CAAACTGAGAAAAGTGGAC-ATTA
64 CAAACTGGGAAAAGTAGACTA-TA
* **
75303 AACAACACCTTCCGATGGGGAAGGACAAAACAGGAATTTAAACAACACCTTCCGGT-GGGAAGCA
1 AACAACA-CTTCCGAT-GGGAAGGGCAAAACAGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
75367 CAAACTGGGAAAAGTAGACT-TA
64 CAAACTGGGAAAAGTAGACTATA
* * * * * *
75389 GACAACACTGTCCGATGGGGAAGGGC-AAACTAGTAAACTT-AACAACACCTCCCGATGAGGAAG
1 AACAACACT-TCCGAT-GGGAAGGGCAAAAC-AG-GAATTTAAACAACACCTTCCGGTGGGGAAG
75452 GGCAAACT
62 GGCAAACT
75460 TTGGAATATT
Statistics
Matches: 279, Mismatches: 43, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
85 6 0.02
86 39 0.14
87 40 0.14
88 124 0.44
89 70 0.25
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (86 bp):
AACAACACTTCCGATGGGAAGGGCAAAACAGGAATTTAAACAACACCTTCCGGTGGGGAAGGGCA
AACTGGGAAAAGTAGACTATA
Found at i:75268 original size:40 final size:40
Alignment explanation
Indices: 75213--75361 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
75203 AAGTGGGGTA
* *
75213 TAAACAACACATTCCGATAGGGAAGGGCAAAACAGGAATT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAACAGGAATT
*
75253 TAAACAACACCTTCCGGA-GGGGAAGGGC-AAACTGAGAAAAGTGGACAT
1 TAAACAACACCTTCC-GATGGGGAAGGGCAAAAC--AG-GAA-T-----T
*
75301 TAAACAACACCTTCCGATGGGGAAGGACAAAACAGGAATT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAACAGGAATT
*
75341 TAAACAACACCTTCCGGTGGG
1 TAAACAACACCTTCCGATGGG
75362 AAGCACAAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
39 4 0.04
40 44 0.48
41 4 0.04
42 2 0.02
43 1 0.01
45 1 0.01
46 2 0.02
47 4 0.04
48 25 0.27
49 4 0.04
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (40 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAAACAGGAATT
Found at i:75323 original size:48 final size:48
Alignment explanation
Indices: 75252--75419 Score: 148
Period size: 48 Copynumber: 3.7 Consensus size: 48
75242 AAACAGGAAT
75252 TTAAACAACACCTTCCGGA-GGGGAAGGGCAAACTGAGAAAAGTGGACA
1 TTAAACAACACCTTCC-GATGGGGAAGGGCAAACTGAGAAAAGTGGACA
75300 TTAAACAACACCTTCCGATGGGGAA-GG---AC--A-AAACA--GGA-A
1 TTAAACAACACCTTCCGATGGGGAAGGGCAAACTGAGAAA-AGTGGACA
* ** * *
75339 TTTAAACAACACCTTCCGGT-GGGAAGCACAAACTGGGAAAAGTAGAC-
1 -TTAAACAACACCTTCCGATGGGGAAGGGCAAACTGAGAAAAGTGGACA
*
75386 TTAGACAACA-CTGTCCGATGGGGAAGGGCAAACT
1 TTAAACAACACCT-TCCGATGGGGAAGGGCAAACT
75420 AGTAAACTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 31
0.71 0.07 0.23
Matches are distributed among these distances:
39 6 0.06
40 21 0.22
41 3 0.03
42 2 0.02
43 2 0.02
44 2 0.02
45 3 0.03
46 17 0.18
47 18 0.19
48 22 0.23
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (48 bp):
TTAAACAACACCTTCCGATGGGGAAGGGCAAACTGAGAAAAGTGGACA
Found at i:75599 original size:43 final size:43
Alignment explanation
Indices: 75536--75902 Score: 518
Period size: 43 Copynumber: 8.5 Consensus size: 43
75526 AACAAAATAG
* * *
75536 GGACCTTCCAACCAAGAAGGGGCATTTTTGGGAATGAAAAGAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
75579 GAACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACGA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
75622 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* ** * * * *
75665 TGACCTTCCGGCCGGGAAGTGACATTTTTGGAAATGAAAACAG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* * *
75708 GGACCTTCCAATCAGGAAGGGGCATTTTTGTAAAATGAAAACAG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTG-GAAATGAAAACAA
75752 GGACCTTCCAACCAGGAAGGGGCATTTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCA-TTTTTGGAAATGAAAACAA
* ** *
75796 GGACCTTCCGACTGGGAAGGGGCATTTTTTGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
*
75839 GGGCCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
75882 GGACCTTCCGACCGGGAAGGG
1 GGACCTTCCAACCAGGAAGGG
75903 CAGAATGGGA
Statistics
Matches: 285, Mismatches: 37, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
43 212 0.74
44 67 0.24
45 6 0.02
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (43 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
Found at i:81436 original size:35 final size:35
Alignment explanation
Indices: 81386--81463 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
81376 CCGTTGCCAG
* * * *
81386 GAAGCTCGTTGAAGCTCACTGC-TGGGATGCTCGTT
1 GAAGCTCGCTAAAGCTCACTGCAAGGAAT-CTCGTT
**
81421 GAAGCTCGCTAAAGCTTTCTGCAAGGAATCTCGTT
1 GAAGCTCGCTAAAGCTCACTGCAAGGAATCTCGTT
81456 GAAGCTCG
1 GAAGCTCG
81464 ATGCCAGGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (35 bp):
GAAGCTCGCTAAAGCTCACTGCAAGGAATCTCGTT
Found at i:81599 original size:25 final size:25
Alignment explanation
Indices: 81445--81601 Score: 134
Period size: 25 Copynumber: 6.3 Consensus size: 25
81435 CTTTCTGCAA
* * **
81445 GGAATCTCGTTGAAGCTCGATGCCA
1 GGAAGCTCGTTGAAGCTCGCTGCTG
* * * * *
81470 GGAAGTTCATCGAAGCTCGTTGCTA
1 GGAAGCTCGTTGAAGCTCGCTGCTG
* * * * *
81495 GAAAGCTTGCTGAAGCTTGCTGCTA
1 GGAAGCTCGTTGAAGCTCGCTGCTG
* *
81520 AGAAGCTCGTTGAAGCTCACTGCTG
1 GGAAGCTCGTTGAAGCTCGCTGCTG
*
81545 GGATGCTCGTTGAAGCTCGCTGCTG
1 GGAAGCTCGTTGAAGCTCGCTGCTG
* * *
81570 AGAAGCTCGTTGACGCTCGCTGTTG
1 GGAAGCTCGTTGAAGCTCGCTGCTG
81595 GGAAGCT
1 GGAAGCT
81602 GGCAGAGATA
Statistics
Matches: 103, Mismatches: 29, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 103 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (25 bp):
GGAAGCTCGTTGAAGCTCGCTGCTG
Found at i:84728 original size:19 final size:18
Alignment explanation
Indices: 84695--84730 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
84685 TCGAGATAAT
84695 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
84713 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
84731 TAAGTCTTCA
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:86043 original size:2 final size:2
Alignment explanation
Indices: 86038--86071 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
86028 ATAAGTCCAA
*
86038 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86072 GCATGCCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:86926 original size:11 final size:11
Alignment explanation
Indices: 86910--86958 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
86900 AAGTAAGGGA
86910 TTTTTGGTATT
1 TTTTTGGTATT
86921 TTTTTGG-ATTT
1 TTTTTGGTA-TT
**
86932 TTTTTGGTACC
1 TTTTTGGTATT
86943 TTTTTGGTATT
1 TTTTTGGTATT
86954 TTTTT
1 TTTTT
86959 ACTGTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 1 0.03
11 30 0.94
12 1 0.03
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.71
Consensus pattern (11 bp):
TTTTTGGTATT
Found at i:86938 original size:22 final size:23
Alignment explanation
Indices: 86910--86958 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
86900 AAGTAAGGGA
**
86910 TTTTTGGTATTTTTTTGG-ATTT
1 TTTTTGGTACCTTTTTGGTATTT
86932 TTTTTGGTACCTTTTTGGTATTT
1 TTTTTGGTACCTTTTTGGTATTT
86955 TTTT
1 TTTT
86959 ACTGTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.71
Consensus pattern (23 bp):
TTTTTGGTACCTTTTTGGTATTT
Found at i:87261 original size:16 final size:15
Alignment explanation
Indices: 87223--87264 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
87213 ACAGAGGTTG
87223 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
87238 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
87253 ACTAGAAAACAA
1 AC-AGAAAACAA
87265 AACAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.