Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002267.1 Kokia drynarioides strain JFW-HI SEQ_114289, 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: 32858
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:826 original size:21 final size:21
Alignment explanation
Indices: 800--845 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
790 AAGAAAAAAG
*
800 AAAGAATTTATATA-TATTTTT
1 AAAGAACTTATATACT-TTTTT
821 AAAGAACTTATATACTTTTTT
1 AAAGAACTTATATACTTTTTT
842 AAAG
1 AAAG
846 TTTTTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (21 bp):
AAAGAACTTATATACTTTTTT
Found at i:2943 original size:52 final size:51
Alignment explanation
Indices: 2866--3052 Score: 252
Period size: 52 Copynumber: 3.6 Consensus size: 51
2856 AATAAAAAAG
* *
2866 GTCCGATGAC--TGTGTCATTGTGAGTATATGAATCCTTTACAGATCATGA
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGA
*
2915 GATCCGATGACTATGTGTCATCGTGAGTACATGAATCCTTTACGGATCATGA
1 G-TCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGA
* * * *
2967 CGTCCGATGATTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATGA
1 -GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGA
* *
3019 GGTTCGATGACTATGTGTCCTCGTGAGTATATGA
1 -GTCCGATGACTATGTGTCATCGTGAGTATATGA
3053 TTCCCAATAT
Statistics
Matches: 121, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
49 1 0.01
50 9 0.07
52 110 0.91
53 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (51 bp):
GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATCATGA
Found at i:3081 original size:52 final size:52
Alignment explanation
Indices: 2863--3101 Score: 216
Period size: 52 Copynumber: 4.6 Consensus size: 52
2853 GTAAATAAAA
* ** ** *
2863 AAGGTCCGATGAC--TGTGTCATTGTGAGTATATGAATCCTTTACAGATCAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCAATATGGATTAT
* * * ** * *
2913 GAGATCCGATGACTATGTGTCATCGTGAGTACATGAATCCTTTACGGATCAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCAATATGGATTAT
* * * * **
2965 GACGTCCGATGATTATGTGTCATCGTGAATATATGAATCCTTTATGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCAATATGGATTAT
* * * *
3017 GAGGTTCGATGACTATGTGTCCTCGTGAGTATATGATTCCCAATATGGATTA-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CCAATATGGATTAT
*
3069 AAGGTCCAATGACTCA-GTGTCATCGTGAGTATA
1 AAGGTCCGATGACT-ATGTGTCATCGTGAGTATA
3102 AAAGAAATAA
Statistics
Matches: 161, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 11 0.07
52 138 0.86
53 12 0.07
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCAATATGGATTAT
Found at i:3089 original size:104 final size:102
Alignment explanation
Indices: 2862--3101 Score: 275
Period size: 104 Copynumber: 2.3 Consensus size: 102
2852 CGTAAATAAA
*
2862 AAAGGTCCGATGACT-GTGTCATTGTGAGTATATGAATCCTTTACAGATCATGAGATCCGATGAC
1 AAAGGTCCGATGACTAGTGTCATCGTGAGTATATGAATCCTTTACAGATCATGAGATCCGATGAC
**
2926 TATGTGTCATCGTGAGTACATGAATCCTTTACGGATC
66 TATGTGTCATCGTGAGTACATGAATCCAATACGGATC
* * * * ** * * *
2963 ATGACGTCCGATGATTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATGAGGTTCGATG
1 A-AAGGTCCGATGACTA-GTGTCATCGTGAGTATATGAATCCTTTACAGATCATGAGATCCGATG
* * * * *
3028 ACTATGTGTCCTCGTGAGTATATGATTCCCAATATGGATT
64 ACTATGTGTCATCGTGAGTACATGAAT-CCAATACGGATC
*
3068 AAAGGTCCAATGACTCAGTGTCATCGTGAGTATA
1 AAAGGTCCGATGACT-AGTGTCATCGTGAGTATA
3102 AAAGAAATAA
Statistics
Matches: 112, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
101 1 0.01
102 11 0.10
104 90 0.80
105 10 0.09
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (102 bp):
AAAGGTCCGATGACTAGTGTCATCGTGAGTATATGAATCCTTTACAGATCATGAGATCCGATGAC
TATGTGTCATCGTGAGTACATGAATCCAATACGGATC
Found at i:3250 original size:43 final size:43
Alignment explanation
Indices: 3201--3287 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
3191 TTTAACTTTA
3201 TGAACTTACTAAGCTTTGAAGTGCTTACTTGTGGAAACTATTG
1 TGAACTTACTAAGCTTTGAAGTGCTTACTTGTGGAAACTATTG
3244 TGAACTTACTAAGCTTTGAAGTGCTTACTTGTGGAAACTATTG
1 TGAACTTACTAAGCTTTGAAGTGCTTACTTGTGGAAACTATTG
3287 T
1 T
3288 TGTTTTGTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (43 bp):
TGAACTTACTAAGCTTTGAAGTGCTTACTTGTGGAAACTATTG
Found at i:7095 original size:87 final size:86
Alignment explanation
Indices: 6974--7175 Score: 230
Period size: 87 Copynumber: 2.3 Consensus size: 86
6964 GATGCCTGGG
** * * * * *
6974 GGTAAAATGGTAATTTTTATAGGTTCGGGGGTAAAACGGTAATTTTTGGACACTT-AGGGGT-GA
1 GGTAAAATGGTAATTTTTGGAAGTTCGGAGGTAAAAC-ATAATTTTTGGAAACTTCA-GGGTCAA
*
7037 AAATGTAATTTTTGG-ACATTCAAC
64 AAATGTAATTTTGGGAAC-TT-AAC
* *
7061 GGTAAAATGGTAATTTTTGGATGTTCGGAGGTAAAACATAATTTTTGGAAAGTTCAGGGTCAAAA
1 GGTAAAATGGTAATTTTTGGAAGTTCGGAGGTAAAACATAATTTTTGGAAACTTCAGGGTCAAAA
*
7126 ATGTAATTTTGGGAAGCTTAAG
66 ATGTAATTTTGGGAA-CTTAAC
*
7148 GGTAAAATAGTAATTTTTGGAAGTTCGG
1 GGTAAAATGGTAATTTTTGGAAGTTCGG
7176 GGGGCAAAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
86 18 0.18
87 77 0.78
88 3 0.03
89 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (86 bp):
GGTAAAATGGTAATTTTTGGAAGTTCGGAGGTAAAACATAATTTTTGGAAACTTCAGGGTCAAAA
ATGTAATTTTGGGAACTTAAC
Found at i:7135 original size:30 final size:28
Alignment explanation
Indices: 7002--7349 Score: 215
Period size: 29 Copynumber: 11.9 Consensus size: 28
6992 ATAGGTTCGG
* * *
7002 GGGTAAAACGGTAATTTTTGGACACTT-A
1 GGGTAAAA-TGTAATTTTTGGAAAGTTCA
*
7030 GGGGTGAAAATGTAATTTTTGGACA-TTCAA
1 -GGGT-AAAATGTAATTTTTGGAAAGTTC-A
* * *
7060 CGGTAAAATGGTAATTTTTGG-ATGTTCG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTCA
**
7088 GAGGTAAAACATAATTTTTGGAAAGTTCA
1 G-GGTAAAATGTAATTTTTGGAAAGTTCA
* *
7117 GGGTCAAAAATGTAA-TTTTGGGAAGCTTAA
1 GGGT--AAAATGTAATTTTTGGAAAG-TTCA
*
7147 GGGTAAAATAGTAATTTTTGG-AAGTTCGGG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTC--A
* * * *
7177 GGGCAAAAATGTGATTTTTGGAAGGTTCGG
1 GGG-TAAAATGTAATTTTTGGAAAGTTC-A
7207 GGGTAAAATGGTAA-TTTTGG-AAGTTCA
1 GGGTAAAAT-GTAATTTTTGGAAAGTTCA
* **
7234 GGGTCAAAATTTAATTTTTTAAAAGTTCGA
1 GGGT-AAAATGTAATTTTTGGAAAGTTC-A
* * *
7264 GGTTAAAATGTAATTTTTGAGAAATTTAA
1 GGGTAAAATGTAATTTTTG-GAAAGTTCA
* * * *
7293 GGGTTAAAATTTATTTTTTAGAAAGTTTAA
1 GGG-TAAAATGTAATTTTTGGAAAG-TTCA
*
7323 GGGTTAAAATATAATTTTTGGAAAGTT
1 GGG-TAAAATGTAATTTTTGGAAAGTT
7350 TAAGGGTCAA
Statistics
Matches: 255, Mismatches: 40, Indels: 48
0.74 0.12 0.14
Matches are distributed among these distances:
27 7 0.03
28 41 0.16
29 103 0.40
30 94 0.37
31 10 0.04
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGGAAAGTTCA
Found at i:7166 original size:59 final size:59
Alignment explanation
Indices: 7031--7361 Score: 222
Period size: 59 Copynumber: 5.6 Consensus size: 59
7021 GGACACTTAG
* * * * *
7031 GGGTGAAAAT-GTAATTTTTGGACA-TTCAACGGT--AAAATGGTAATTTTTGGATGTTC-G
1 GGGT-AAAATAGTAATTTTTGGAAAGTTC-AGGGTCAAAAAT-GTAATTTTTGAAAGTTCAA
* * *
7088 GAGGTAAAACA-TAATTTTTGGAAAGTTCAGGGTCAAAAATGTAATTTTGGGAAGCTT-AA
1 G-GGTAAAATAGTAATTTTTGGAAAGTTCAGGGTCAAAAATGTAATTTTTGAAAG-TTCAA
* * * * **
7147 GGGTAAAATAGTAATTTTTGG-AAGTTCGGGGGGCAAAAATGTGATTTTTGGAAGGTTCGG
1 GGGTAAAATAGTAATTTTTGGAAAGTTC-AGGGTCAAAAATGTAATTTTT-GAAAGTTCAA
* * * *
7207 GGGTAAAATGGTAA-TTTTGG-AAGTTCAGGGTC-AAAATTTAATTTTTTAAAAGTTCGA
1 GGGTAAAATAGTAATTTTTGGAAAGTTCAGGGTCAAAAATGTAA-TTTTTGAAAGTTCAA
* * * * * * *
7264 GGTTAAAAT-GTAATTTTTGAGAAATTTAAGGGT-TAAAATTTATTTTTTAGAAAGTTTAA
1 GGGTAAAATAGTAATTTTTG-GAAAGTTCAGGGTCAAAAATGTAATTTTT-GAAAGTTCAA
*
7323 GGGTTAAAATA-TAATTTTTGGAAAGTTTAAGGGTCAAAA
1 GGG-TAAAATAGTAATTTTTGGAAAG-TTCAGGGTCAAAA
7362 CGTGATTTAT
Statistics
Matches: 220, Mismatches: 33, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
56 4 0.02
57 48 0.22
58 47 0.21
59 79 0.36
60 39 0.18
61 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (59 bp):
GGGTAAAATAGTAATTTTTGGAAAGTTCAGGGTCAAAAATGTAATTTTTGAAAGTTCAA
Found at i:7237 original size:87 final size:83
Alignment explanation
Indices: 6973--7252 Score: 224
Period size: 87 Copynumber: 3.2 Consensus size: 83
6963 GGATGCCTGG
** * * * * * * * *
6973 GGGTAAAATGGTAATTTTTATAGGTTCGGGGGTAAAACGGTAATTTTTGGACACTTAGGGGTGAA
1 GGGTAAAAT-GTAATTTTTGGAAGTTCGGAGGCAAAAC-ATAATTTTTGGAAAGTTCGGGGTAAA
7038 AATGTAATTTTTGGACA-TTCAA
64 AATGTAA-TTTTGGA-AGTTC-A
* * * *
7060 CGGTAAAATGGTAATTTTTGGATGTTCGGAGGTAAAACATAATTTTTGGAAAGTTCAGGGTCAAA
1 GGGTAAAAT-GTAATTTTTGGAAGTTCGGAGGCAAAACATAATTTTTGGAAAGTTCGGGGT-AAA
*
7125 AATGTAATTTTGGGAAGCTTAA
64 AATGTAATTTT-GGAAG-TTCA
* * *
7147 GGGTAAAATAGTAATTTTTGGAAGTTCGGGGGGCAAAA-ATGTGATTTTTGGAAGGTTCGGGGGT
1 GGGTAAAAT-GTAATTTTTGGAAGTTC-GGAGGCAAAACA--TAATTTTTGGAAAGTTC-GGGGT
7211 -AAAATGGTAATTTTGGAAGTTCA
61 AAAAAT-GTAATTTTGGAAGTTCA
*
7234 GGGTCAAAATTTAATTTTT
1 GGGT-AAAATGTAATTTTT
7253 TAAAAGTTCG
Statistics
Matches: 161, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
86 23 0.14
87 86 0.53
88 25 0.16
89 23 0.14
90 4 0.02
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (83 bp):
GGGTAAAATGTAATTTTTGGAAGTTCGGAGGCAAAACATAATTTTTGGAAAGTTCGGGGTAAAAA
TGTAATTTTGGAAGTTCA
Found at i:7350 original size:30 final size:30
Alignment explanation
Indices: 7012--7361 Score: 183
Period size: 30 Copynumber: 12.0 Consensus size: 30
7002 GGGTAAAACG
* * * *
7012 GTAATTTTTGGACA-CTTAGGGGTGAAAAT
1 GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
* * *
7041 GTAATTTTTGGACA-TTCAACGG-TAAAAT
1 GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
* * * *
7069 GGTAATTTTTGG-ATG-TT-CGGAGGTAAAAC
1 -GTAATTTTTGGAAAGTTTAAGG-GTTAAAAT
* * *
7098 ATAATTTTTGGAAAG-TTCAGGGTCAAAAAT
1 GTAATTTTTGGAAAGTTTAAGGGT-TAAAAT
* *
7128 GTAA-TTTTGGGAAGCTTAAGGG-TAAAAT
1 GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
*** **
7156 AGTAATTTTTGG-AAGTTCGGGGGGCAAAAAT
1 -GTAATTTTTGGAAAGTT-TAAGGGTTAAAAT
* * ** *
7187 GTGATTTTTGG-AAGGTTCGGGGGTAAAAT
1 GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
* *
7216 GGTAA-TTTTGG-AAG-TTCAGGGTCAAAAT
1 -GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
* ** **
7244 TTAATTTTTTAAAAGTTCGA-GGTTAAAAT
1 GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
7273 GTAATTTTTGAGAAA-TTTAAGGGTTAAAAT
1 GTAATTTTTG-GAAAGTTTAAGGGTTAAAAT
* * *
7303 TTATTTTTTAGAAAGTTTAAGGGTTAAAAT
1 GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
* *
7333 ATAATTTTTGGAAAGTTTAAGGGTCAAAA
1 GTAATTTTTGGAAAGTTTAAGGGTTAAAA
7362 CGTGATTTAT
Statistics
Matches: 248, Mismatches: 54, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
27 4 0.02
28 37 0.15
29 100 0.40
30 102 0.41
31 5 0.02
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
GTAATTTTTGGAAAGTTTAAGGGTTAAAAT
Found at i:9018 original size:17 final size:17
Alignment explanation
Indices: 8996--9047 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
8986 GATTAAATTT
8996 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
**
9013 TAAATTTAAACGCAAAA
1 TAAATTTAAATTCAAAA
* *
9030 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
9047 T
1 T
9048 TTAAAATTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:10366 original size:209 final size:208
Alignment explanation
Indices: 9581--10450 Score: 1095
Period size: 208 Copynumber: 4.2 Consensus size: 208
9571 TTAATCGCAT
* * * * *
9581 TTGATTTGGTCTACTCCTCTA-TATCTTATCAGGAAGATGACCGCATCA-T-TTTTAATTCGCTT
1 TTGATTTGGTCTACTTCTC-AGTATCTCATCAGGAAGATGACCGTATCATTGTTTTAATCCACTT
* * * *** **
9643 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAAGAAGACGACCAT
65 CTCTGTATCTCATCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGGTAACCGC
* * * * **
9708 TTTATTGCTTCGACCTACTTCTCAGTACCTCATCAAGAAGCTAGGGTTCGAAGTTTCGCTCATAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCGCAT
**
9773 TGAGCTTTATTTCA
195 TGAGCTTGGTTTCA
* * *
9787 TTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCT-TCATTGTTTTGATCCACCT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCG-TATCATTGTTTTAATCCACTT
* * * * *
9851 CTCTGTGTC-CTATCAGGAAGACGGATCTGGTTCACTTCTCTGTACCTCATCAGGAACGTAACCG
65 CTCTGTATCTC-ATCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGGTAACCG
* * * * *
9915 CTTTATTGCTTCGACCTTCGTCTCAGTATCTCATCACGAAGTTGAGGTTCGAAGTTTCGCTCGCA
129 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCGCA
*
9980 TTGAGCTTGGTTTTA
194 TTGAGCTTGGTTTCA
* * * * * *
9995 TTGATTTGGTCTACTTCTCAATATCTCATCAGGAAGATGACTGTCTCGTTGTTTTGATCCACTTA
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGTATCATTGTTTTAATCCACTTC
* * * * *
10060 TTTGTGTCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCT
66 TCTGTATCTCATCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCT
* * * *
10125 TTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGTTTCACTTGCATT
131 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCGCATT
10190 GAGCTTGGTTTCA
196 GAGCTTGGTTTCA
* * *
10203 TTTATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGTATCACTTGTTTCAATCCGCTT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGTATCA-TTGTTTTAATCCACTT
* * *
10268 CTTTGTATCTCATCAGGAAGACGAATTTAGTCCACTTCTCTGTATCTCATCAGGAAGGTAACCGC
65 CTCTGTATCTCATCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGGTAACCGC
*
10333 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCGCTT
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCGCAT
*
10398 TGAGCTTTGTTTCA
195 TGAGCTTGGTTTCA
* * * * *
10412 TTGAGTTGGTATACTTCTCTGTATCACATCATGAA-ATGA
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA
10451 TGTAGTTTGA
Statistics
Matches: 576, Mismatches: 80, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
205 1 0.00
206 41 0.07
207 3 0.01
208 357 0.62
209 174 0.30
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (208 bp):
TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGTATCATTGTTTTAATCCACTTC
TCTGTATCTCATCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCT
TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCGCATT
GAGCTTGGTTTCA
Found at i:10787 original size:50 final size:50
Alignment explanation
Indices: 10719--11372 Score: 361
Period size: 50 Copynumber: 13.1 Consensus size: 50
10709 TTGTCTTCAT
* * * * * *
10719 GGTATCGGATTCGCCGTTACGACCTTAATCTTTTCCATCGCATCTTCTTA
1 GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTTA
* * * *
10769 GGTACCGGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCACTTCTTTTTA
1 GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTTA
* * * * *
10819 GGTACCGGGTTCGCCGTTGCGGA-CTCAACCTTTCCCTTTATATCTTTTTAA
1 GGTACCGGGTTCGCCGTTAC-GACCTCAACCTTTCCCATCACATCTTCTT-A
** * * * * * *
10870 GGTATTGGATTTGCTGTTGCGACCTTAATCC--TCCC-TTATCATC-TCTTCA
1 GGTACCGGGTTCGCCGTTACGACCTCAA-CCTTTCCCATCA-CATCTTCTT-A
* * * ** *
10919 TGGTACTGGATTCGTCGTTGTGACCTCAATCC-TTCCCATCGCATCTT-TCTA
1 -GGTACCGGGTTCGCCGTTACGACCTCAA-CCTTTCCCATCACATCTTCT-TA
* * * * * * *
10970 GGTAACGGGTTCGCCATTGC-AGCCCCAACCTTTCCCTTTACATCTTTTTAA
1 GGTACCGGGTTCGCCGTTACGA-CCTCAACCTTTCCCATCACATCTTCTT-A
* * * * * * ** *
11021 GGTATCGGATTCACCGTTGCGGCCTCAATCC--TCCCCTGTCATCGTT-TCA
1 GGTACCGGGTTCGCCGTTACGACCTCAA-CCTTTCCCATCACATC-TTCTTA
* *
11070 TGGTACTGGGTTCGCCATT--GTAGCCTCAACCTTTCCCATCACATCTTCTTA
1 -GGTACCGGGTTCGCCGTTACG-A-CCTCAACCTTTCCCATCACATCTTCTTA
* * * * *
11121 GGTACTGGGTTCGCCGTTGCGACCTCAACCTTTCCCTTTACATCTTATTA
1 GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTTA
* ** ** * * * *
11171 GGTACCCGGTTCGCCGTTGTGGTCTTAACCTTTCCCTTTACATCTTCAT-
1 GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTTA
* * ** * *
11220 GGTAGCGGGTTCACCGTTGTGGCCTCAACCTTTCCCATCACATCTTTTTA
1 GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTTA
* *
11270 GGTACCGGGTTTGCCGTTGC-AGCCTCAACCTTTCCCATCACATCTTCTTA
1 GGTACCGGGTTCGCCGTTACGA-CCTCAACCTTTCCCATCACATCTTCTTA
** * ** *
11320 GGTATTGGGTTCGTCGTTGTGGCCTCAACCTTTCCCATCA-ATCTT-TTAA
1 GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTT-A
11369 GGTA
1 GGTA
11373 TTGGATTTGC
Statistics
Matches: 480, Mismatches: 95, Indels: 59
0.76 0.15 0.09
Matches are distributed among these distances:
48 3 0.01
49 63 0.13
50 338 0.70
51 68 0.14
52 8 0.02
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (50 bp):
GGTACCGGGTTCGCCGTTACGACCTCAACCTTTCCCATCACATCTTCTTA
Found at i:10924 original size:151 final size:150
Alignment explanation
Indices: 10719--11344 Score: 628
Period size: 151 Copynumber: 4.2 Consensus size: 150
10709 TTGTCTTCAT
* * *
10719 GGTATCGGATTCGCCGTTACGACCTTAAT-CT---TTTCCATCGCATCTTCTTAGGTACCGGGTT
1 GGTATCGGATTCGCCGTTGCGGCCTTAATCCTCCCTTT-CAT--CATCTTCAT-GGTACCGGGTT
** * * *
10780 CGCCGTTACGGCCTCAACCTTTCCCTTCACTTCTTTTTAGGTACCGGGTTCGCCGTTGCGGACTC
62 CGCCGTTGTGGCCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCAGACTC
*
10845 AACCTTTCCCTTTATATCTTTTTAA
127 AACCTTTCCCTTTACATCTTTTT-A
* * * * * * *
10870 GGTATTGGATTTGCTGTTGCGACCTTAATCCTCCCTTATCATC-TCTTCATGGTACTGGATTCGT
1 GGTATCGGATTCGCCGTTGCGGCCTTAATCCTCCCTT-TCATCATCTTCATGGTACCGGGTTCGC
* * * * * * *
10934 CGTTGTGACCTCAATCC-TTCCCATCGCATCTTTCTAGGTAACGGGTTCGCCATTGCAGCCCCAA
65 CGTTGTGGCCTCAA-CCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCAGACTCAA
10998 CCTTTCCCTTTACATCTTTTTAA
129 CCTTTCCCTTTACATCTTTTT-A
* * * * *
11021 GGTATCGGATTCACCGTTGCGGCCTCAATCCTCCCCTGTCATCGT-TTCATGGTACTGGGTTCGC
1 GGTATCGGATTCGCCGTTGCGGCCTTAATCCT-CCCTTTCATCATCTTCATGGTACCGGGTTCGC
* * * *
11085 CATTGTAGCCTCAACCTTTCCCATCACATCTTCTTAGGTACTGGGTTCGCCGTTGC-GACCTCAA
65 CGTTGTGGCCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCAGA-CTCAA
*
11149 CCTTTCCCTTTACATCTTATTA
129 CCTTTCCCTTTACATCTTTTTA
* * * *
11171 GGTACCCGG-TTCGCCGTTGTGGTCTTAA-CCTTTCCCTTT-A-CATCTTCATGGTAGCGGGTTC
1 GGTA-TCGGATTCGCCGTTGCGGCCTTAATCC--TCCCTTTCATCATCTTCATGGTACCGGGTTC
* * *
11232 ACCGTTGTGGCCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTTGCCGTTGCAGCCTCA
63 GCCGTTGTGGCCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCAGACTCA
* * *
11297 ACCTTTCCCATCACATCTTCTTA
128 ACCTTTCCCTTTACATCTTTTTA
* * * *
11320 GGTATTGGGTTCGTCGTTGTGGCCT
1 GGTATCGGATTCGCCGTTGCGGCCT
11345 CAACCTTTCC
Statistics
Matches: 394, Mismatches: 65, Indels: 34
0.80 0.13 0.07
Matches are distributed among these distances:
148 4 0.01
149 112 0.28
150 29 0.07
151 227 0.58
152 15 0.04
153 1 0.00
155 5 0.01
156 1 0.00
ACGTcount: A:0.15, C:0.30, G:0.19, T:0.36
Consensus pattern (150 bp):
GGTATCGGATTCGCCGTTGCGGCCTTAATCCTCCCTTTCATCATCTTCATGGTACCGGGTTCGCC
GTTGTGGCCTCAACCTTTCCCATCACATCTTTTTAGGTACCGGGTTCGCCGTTGCAGACTCAACC
TTTCCCTTTACATCTTTTTA
Found at i:12450 original size:30 final size:30
Alignment explanation
Indices: 12414--12475 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
12404 GCAGGTCTTT
12414 TCCGTCCATTTCGACCAGAATCAAAACTTC
1 TCCGTCCATTTCGACCAGAATCAAAACTTC
12444 TCCGTCCATTTCGACCAGAATCAAAACTTC
1 TCCGTCCATTTCGACCAGAATCAAAACTTC
12474 TC
1 TC
12476 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (30 bp):
TCCGTCCATTTCGACCAGAATCAAAACTTC
Found at i:15655 original size:6 final size:6
Alignment explanation
Indices: 15635--15712 Score: 65
Period size: 6 Copynumber: 13.5 Consensus size: 6
15625 TATTAAACAA
** * **
15635 AAATTT AAAAAT AAATTT AAACTT AAA-TT AAATTT AAATTT AAA-AC
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
15681 AAATTT AAATTT -AATCTT AAA-AT AAATTT AAA
1 AAATTT AAATTT AAAT-TT AAATTT AAATTT AAA
15713 AAAGTGGGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 15 0.27
6 39 0.70
7 2 0.04
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
AAATTT
Found at i:15668 original size:17 final size:17
Alignment explanation
Indices: 15635--15694 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
15625 TATTAAACAA
15635 AAATTTAAAAATAAATTT
1 AAATTT-AAAATAAATTT
* *
15653 AAACTTAAATTAAATTT
1 AAATTTAAAATAAATTT
*
15670 AAATTTAAAACAAATTT
1 AAATTTAAAATAAATTT
15687 AAATTTAA
1 AAATTTAA
15695 TCTTAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 32 0.86
18 5 0.14
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAAATAAATTT
Found at i:15672 original size:23 final size:23
Alignment explanation
Indices: 15635--15712 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
15625 TATTAAACAA
**
15635 AAATTTAAAAATAAATTT-AAAC
1 AAATTTAAATTTAAATTTAAAAC
15657 TTAAA-TTAAATTTAAATTTAAAAC
1 --AAATTTAAATTTAAATTTAAAAC
*
15681 AAATTTAAATTT-AATCTTAAAAT
1 AAATTTAAATTTAAAT-TTAAAAC
15704 AAATTTAAA
1 AAATTTAAA
15713 AAAGTGGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 6 0.12
23 35 0.73
24 7 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTAAATTTAAATTTAAAAC
Found at i:16478 original size:209 final size:209
Alignment explanation
Indices: 16094--17637 Score: 1544
Period size: 209 Copynumber: 7.5 Consensus size: 209
16084 TTTTACTAGA
* * ** * * * * * **
16094 AAGACGAATTTGGCTCACTTCTCTGCGTCTCGTCAGGAAGATGATCATTTTATTGCTTTAACCTG
1 AAGACGAATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACCTG
* * * ** * * *
16159 CTTCTCCGTATCTCATC-GAGAATCTGAGGTTTAAAG-TTTCGCTCGCATCGAGCTTTGGTTTCG
66 CTTCTCAGTATCTCATCAG-GAAGCTGGGGTTCGAAGATTT-GCTCACTTCGAGC-CTGGTTTCG
* * * *
16222 TTGATTTGGTCTATTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATTCATTT
128 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
* * *
16287 CTTTGTGTCTCATTAGG
193 CTCTGTGTCTCATCAAG
* **** * * *
16304 AAGACGAATTTAACCCACTTCACTATATCTCATCAAGAAGGTAACCATTTTATTGCTTCAACCTG
1 AAGACGAATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACCTG
* * *
16369 CTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTTACTTTGAGCCTGGTTTCGTTG
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTCGAGCCTGGTTTCGTTG
* * *
16434 ATTTGGTCTACTTCTTAGTATCTCATCAGAAAGATGATCGCATCATTTGTTTTGATCCACTTCTC
131 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCTC
16499 TGTGTCTCATC-AG
196 TGTGTCTCATCAAG
* * *
16512 AAAGA-TAGATTTGGTTCACTTCTCTGTATCTCATC----AGG-------TTTATTGCTTCAACC
1 -AAGACGA-ATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACC
* * * * * ** *
16565 TGCTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGATTTGCTCATTTTGAGCCTTATTTCAT
64 TGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTCGAGCCTGGTTTCGT
* * * * *
16630 TGATTTGGTCTACTTCTTAGTACCTCATCAGAAAGATGATTGTATCA-TTGGTTTTGA-CTCACT
129 TGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTT-GTTTTGATC-CACT
*
16693 TCTCTGTGTCTCATCAGG
192 TCTCTGTGTCTCATCAAG
*
16711 AAGACGAATCTAGTTCACTTCTCTGTATCTCAT-AAGGAAGGTAACCATTTTATTGCTTCGACCT
1 AAGACGAATCTGGTTCACTTCTCTGTATCTCATCAA-GAAGGTAACCATTTTATTGCTTCGACCT
* * * * * *
16775 GGTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGCATCAAGCTTTGGTTTCGT
65 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTCGAGC-CTGGTTTCGT
* * * * *
16840 TGATTAGGTCTACTTCTCAGTATCTCAGCAGGAAGATGATTGCTTCACTTATTTTGATCCACTTC
129 TGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTC
*
16905 TCTGTGTCTCATCAGG
194 TCTGTGTCTCATCAAG
* * * *
16921 ACGA-TAGACCTGGTTCACTTCTC--TATATC-TC----A-G----CATTTTATTGCTTCGA-CT
1 AAGACGA-ATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACCT
* * ** *
16972 AGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACTTGGAGCCTTATTTCAT
65 -GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTCGAGCCTGGTTTCGT
*
17037 TGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGTATCA-TTGGTTTTGATCCACTT
129 TGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTT-GTTTTGATCCACTT
*
17101 CTCTATGTCTCATCAAG
193 CTCTGTGTCTCATCAAG
* * * *
17118 AAGATGGATCGGGTTCACTTCTCTGTATCTTAT-AAGGAAGGTAACCATTTTATTGCTTCGACCT
1 AAGACGAATCTGGTTCACTTCTCTGTATCTCATCAA-GAAGGTAACCATTTTATTGCTTCGACCT
* * ** * * *
17182 GCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTCGCTTGCATCGAGCTTTGGTTTCAT
65 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTCGAGC-CTGGTTTCGT
* * * *
17247 TTATTTGGTTTACTGCTCAGTATCTCAAT-AGGAAGATGACCGCATCACTTGTTTTGATCCACTT
129 TGATTTGGTCTACTTCTCAGTATCTC-ATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
*
17311 CTTTGTGTCTCATCAAG
193 CTCTGTGTCTCATCAAG
* * * *** *
17328 AAGAC-AGATTTGGTTCACTTCTCTGTATATCATCAGGAAGGTAACTGCTTTATTGCTTCGACCA
1 AAGACGA-ATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACCT
* * * * *
17392 GCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAATATTTGCTCACTTGGAGTCTTGTTTCGTT
65 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTCGAGCCTGGTTTCGTT
* * * * *
17457 GATTTGGTCTACTTCTCAATATCTCATTAGGAAGATGACCACATCACTTGTTTTAATCCACTTCT
130 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCT
* *
17522 CTGTGTTTTATCAAG
195 CTGTGTCTCATCAAG
* ***
17537 AAGAC-AGATCTGATTCACTTCTCTGTATCTCATC-AGAAAGGTAACTGCTTTATTGCTTCGACC
1 AAGACGA-ATCTGGTTCACTTCTCTGTATCTCATCAAG-AAGGTAACCATTTTATTGCTTCGACC
* * * *
17600 TGCTTCTTAATATCTCATTAGGAAGCTGGGTTTCGAAG
64 TGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAG
17638 TTTCACTCAC
Statistics
Matches: 1116, Mismatches: 169, Indels: 99
0.81 0.12 0.07
Matches are distributed among these distances:
196 2 0.00
197 98 0.09
198 232 0.21
199 6 0.01
200 1 0.00
202 4 0.00
203 1 0.00
204 1 0.00
205 4 0.00
207 1 0.00
208 10 0.01
209 392 0.35
210 352 0.32
211 12 0.01
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (209 bp):
AAGACGAATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACCTG
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTCGAGCCTGGTTTCGTTG
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCTC
TGTGTCTCATCAAG
Found at i:16963 original size:407 final size:408
Alignment explanation
Indices: 16141--17637 Score: 1774
Period size: 407 Copynumber: 3.6 Consensus size: 408
16131 AAGATGATCA
* * * ** *
16141 TTTTATTGCTTTAACCTGCTTCTCCGTATCTCATCGAGAA-TCTGAGGTTTAAAG-TTTCGCTCG
1 TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGT-TGAGGTTCGAAGATTT-GCTCA
* * * * * *
16204 CATCGAGCTTTGGTTTCGTTGATTTGGTCTATTTCTCAGTATCTCATCAGGAAGATGACCGCATC
64 CTTGGAGCCTT-ATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATC
* * * * * * *** * *
16269 ACTTGTTTTGATTCATTTCTTTGTGTCTCATTAGGAAGACGAATTTAACCCACTTCACTATATCT
128 ACTTGTTTTGATCCACTTCTCTGTGTCTCATCAAGAAGACGAATCTAGTTCACTTCTCTGTATCT
* *
16334 CATCAA-GAAGGTAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGG
193 CAT-AAGGAAGGTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGG
* * * * * * *
16398 TTCGAAGATTTGCTTACTTTGAGC-CTGGTTTCGTTGATTTGGTCTACTTCTTAGTATCTCATCA
257 TTCGAAGATTCGCTTGCATCGAGCTTTGGTTTCGTTGATTTGGTCTACTTCTCAGTATCTCAACA
* * *
16462 GAAAGATGATCGCATCATTTGTTTTGATCCACTTCTCTGTGTCTCATCAGAAAGATAGATTTGGT
322 GGAAGATGATCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGATAGATTTGGT
* * *
16527 TCACTTCTCTGTATCTCATCAG
387 TCACTTCTCTATATCTCAGCAC
* *
16549 GTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGATTTGCTCATT
1 TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGATTTGCTCACT
* * * * ** *
16614 TTGAGCCTTATTTCATTGATTTGGTCTACTTCTTAGTACCTCATCAGAAAGATGATTGTATCA-T
66 TGGAGCCTTATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
*
16678 TGGTTTTGA-CTCACTTCTCTGTGTCTCATCAGGAAGACGAATCTAGTTCACTTCTCTGTATCTC
131 T-GTTTTGATC-CACTTCTCTGTGTCTCATCAAGAAGACGAATCTAGTTCACTTCTCTGTATCTC
*
16742 ATAAGGAAGGTAACCATTTTATTGCTTCGACCTGGTTCTCAGTATCTCATCAGGAAGCTGGGGTT
194 ATAAGGAAGGTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTT
* * * *
16807 CGAAGATTCGCTCGCATCAAGCTTTGGTTTCGTTGATTAGGTCTACTTCTCAGTATCTCAGCAGG
259 CGAAGATTCGCTTGCATCGAGCTTTGGTTTCGTTGATTTGGTCTACTTCTCAGTATCTCAACAGG
* * * * **
16872 AAGATGATTGCTTCACTTATTTTGATCCACTTCTCTGTGTCTCATCAGGACGATAGACCTGGTTC
324 AAGATGATCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGATAGATTTGGTTC
16937 ACTTCTCTATATCTCAGCA-
389 ACTTCTCTATATCTCAGCAC
* * *
16956 TTTTATTGCTTCGA-CTAGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCAC
1 TTTTATTGCTTCAACCT-GCTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGATTTGCTCAC
* *
17020 TTGGAGCCTTATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGTATCA-
65 TTGGAGCCTTATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCAC
* * * ** *
17084 TTGGTTTTGATCCACTTCTCTATGTCTCATCAAGAAGATGGATCGGGTTCACTTCTCTGTATCTT
130 TT-GTTTTGATCCACTTCTCTGTGTCTCATCAAGAAGACGAATCTAGTTCACTTCTCTGTATCTC
*
17149 ATAAGGAAGGTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTT
194 ATAAGGAAGGTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTT
* * * * *
17214 CGAAGATTCGCTTGCATCGAGCTTTGGTTTCATTTATTTGGTTTACTGCTCAGTATCTCAATAGG
259 CGAAGATTCGCTTGCATCGAGCTTTGGTTTCGTTGATTTGGTCTACTTCTCAGTATCTCAACAGG
* * * *
17279 AAGATGACCGCATCACTTGTTTTGATCCACTTCTTTGTGTCTCATCAAGAAGACAGATTTGGTTC
324 AAGATGATCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGATAGATTTGGTTC
*
17344 ACTTCTCTGTATATCATCAGGAAGGTAAC
389 ACTTCTC--TATATC-TC----A-G-CAC
* * * * * * *
17373 TGCTTTATTGCTTCGACCAGCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAATATTTGCTCA
1 T--TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGATTTGCTCA
* * * * * *
17438 CTTGGAGTCTTGTTTCGTTGATTTGGTCTACTTCTCAATATCTCATTAGGAAGATGACCACATCA
64 CTTGGAGCCTTATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCA
* * *
17503 CTTGTTTTAATCCACTTCTCTGTGTTTTATCAAGAAGAC-AGATCT-GATTCACTTCTCTGTATC
129 CTTGTTTTGATCCACTTCTCTGTGTCTCATCAAGAAGACGA-ATCTAG-TTCACTTCTCTGTATC
* * *** * * * *
17566 TCATCAGAAAGGTAACTGCTTTATTGCTTCGACCTGCTTCTTAATATCTCATTAGGAAGCTGGGT
192 TCATAAGGAAGGTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGG
17631 TTCGAAG
257 TTCGAAG
17638 TTTCACTCAC
Statistics
Matches: 942, Mismatches: 123, Indels: 37
0.85 0.11 0.03
Matches are distributed among these distances:
406 6 0.01
407 523 0.56
408 169 0.18
409 10 0.01
410 2 0.00
414 1 0.00
415 1 0.00
416 1 0.00
417 1 0.00
418 1 0.00
419 224 0.24
420 3 0.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (408 bp):
TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGATTTGCTCACT
TGGAGCCTTATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACT
TGTTTTGATCCACTTCTCTGTGTCTCATCAAGAAGACGAATCTAGTTCACTTCTCTGTATCTCAT
AAGGAAGGTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCG
AAGATTCGCTTGCATCGAGCTTTGGTTTCGTTGATTTGGTCTACTTCTCAGTATCTCAACAGGAA
GATGATCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGATAGATTTGGTTCAC
TTCTCTATATCTCAGCAC
Found at i:17285 original size:617 final size:604
Alignment explanation
Indices: 16094--17568 Score: 1653
Period size: 617 Copynumber: 2.4 Consensus size: 604
16084 TTTTACTAGA
* ** * * * * **
16094 AAGACGAATTTGGCTCACTTCTCTGCGTCTCGTCAGGAAGATGATCATTTTATTGCTTTAACCTG
1 AAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCATTTTATTGCTTCGACCTG
* * * ** *
16159 CTTCTCCGTATCTCATC-GAGAATCTGAGGTTTAAAGTTTCGCTCGCATCGAGCTTTGGTTTCGT
66 CTTCTCAGTATCTCATCAG-GAAGCTGGGGTTCGAAGATTCGCTCGCATCGAGCTTTGGTTTCGT
* * *
16223 TGATTTGGTCTATTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATTCATTTC
130 TGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTC
* * * * ** *
16288 TTTGTGTCTCATTAGGAAGACGAATTTA-ACC-CACTTCACTATATCTCATCAAGAAGGTAACCA
195 TCTGTGTCTCATCA-G--GACG-A--TAGACCTGA-TTCAC--T-TCTC-T--A-TATCTCACCA
* *
16351 TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTTACT
246 TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACT
* * * *
16416 TTGAGCCTGGTTTCGTTGATTTGGTCTACTTCTTAGTATCTCATCAGAAAGATGATCGCATCATT
311 TGGAGCCTGATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGAAAGATGATCGCATCATT
* * **
16481 TGTTTTGATCCACTTCTCTGTGTCTCATCAGAAAGATAGATTTGGTTCACTTCTCTGTATCTCAT
376 GGTTTTGATCCACTTCTCTATGTCTCATCAGAAAGATAGATCGGGTTCACTTCTCTGTATCTCAT
* * *
16546 CAGGTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTTGAGGTTCGAAGATTTGCTC
441 AAGGTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTAGAGGTTCGAAGATTCGCTC
* * * ** *
16611 ATTTTGAGCCTTATTTCATTGATTTGGTCTACTTCTTAGTACCTCATCAGAAAGATGATTGTATC
506 A-TTCGAGCCTTATTTCATTGATTTGGTCTACTGCTCAGTACCTCATCAGAAAGATGACCGCATC
*
16676 A-TTGGTTTTGA-CTCACTTCTCTGTGTCTCATCAGG
570 ACTT-GTTTTGATC-CACTTCTCTGTGTCTCATCAAG
* * *
16711 AAGACGAATCTAGTTCACTTCTCTGTATCTCATAAGGAAGGTAACCATTTTATTGCTTCGACCTG
1 AAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCATTTTATTGCTTCGACCTG
* *
16776 GTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGCATCAAGCTTTGGTTTCGTT
66 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGCATCGAGCTTTGGTTTCGTT
* * ** * *
16841 GATTAGGTCTACTTCTCAGTATCTCAGCAGGAAGATGATTGCTTCACTTATTTTGATCCACTTCT
131 GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCT
* * *
16906 CTGTGTCTCATCAGGACGATAGACCTGGTTCACTTCTCTATATCTCAGCATTTTATTGCTTCGA-
196 CTGTGTCTCATCAGGACGATAGACCTGATTCACTTCTCTATATCTCACCATTTTATTGCTTCAAC
* *
16970 CTAGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACTTGGAGCCTTATTTC
261 CT-GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTGGAGCCTGATTTC
* *
17035 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGTATCATTGGTTTTGATCCACT
325 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGAAAGATGATCGCATCATTGGTTTTGATCCACT
* *
17100 TCTCTATGTCTCATCA-AGAAGATGGATCGGGTTCACTTCTCTGTATCTTATAAGGAAGGTAACC
390 TCTCTATGTCTCATCAGA-AAGATAGATCGGGTTCACTTCTCTGTATCTCAT----AAGG-----
* *
17164 ATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAG-GGTTCGAAGATTCGCTTG
445 --TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAG-TAGAGGTTCGAAGATTCGC-T-
* * * * * *
17228 CA-TCGAGCTTTGGTTTCATTTATTTGGTTTACTGCTCAGTATCTCAAT-AGGAAGATGACCGCA
505 CATTCGAGCCTT-ATTTCATTGATTTGGTCTACTGCTCAGTACCTC-ATCAGAAAGATGACCGCA
*
17291 TCACTTGTTTTGATCCACTTCTTTGTGTCTCATCAAG
568 TCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAAG
* *** *
17328 AAGAC-AGATTTGGTTCACTTCTCTGTATATCATCAGGAAGGTAACTGCTTTATTGCTTCGACCA
1 AAGACGA-ATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCATTTTATTGCTTCGACCT
* * * * * *
17392 GCTTCTTAGTATCTCATCAGGAAGCTGGGGTTCGAATATTTGCTCACTTGGAG-TCTT-GTTTCG
65 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGCATCGAGCT-TTGGTTTCG
* * * *
17455 TTGATTTGGTCTACTTCTCAATATCTCATTAGGAAGATGACCACATCACTTGTTTTAATCCACTT
129 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTT
* * * * * * *
17520 CTCTGTGTTTTATCAAGAAGACAGATCTGATTCACTTCTCTGTATCTCA
194 CTCTGTGTCTCATCAGGACGATAGACCTGATTCACTTCTCTATATCTCA
17569 TCAGAAAGGT
Statistics
Matches: 725, Mismatches: 108, Indels: 51
0.82 0.12 0.06
Matches are distributed among these distances:
604 3 0.00
605 178 0.25
606 1 0.00
608 1 0.00
609 7 0.01
610 1 0.00
611 2 0.00
612 8 0.01
613 1 0.00
614 4 0.01
616 164 0.23
617 347 0.48
618 8 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (604 bp):
AAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCATTTTATTGCTTCGACCTG
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGCATCGAGCTTTGGTTTCGTT
GATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCT
CTGTGTCTCATCAGGACGATAGACCTGATTCACTTCTCTATATCTCACCATTTTATTGCTTCAAC
CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTGGAGCCTGATTTCA
TTGATTTGGTCTACTTCTCAGTATCTCATCAGAAAGATGATCGCATCATTGGTTTTGATCCACTT
CTCTATGTCTCATCAGAAAGATAGATCGGGTTCACTTCTCTGTATCTCATAAGGTTTATTGCTTC
AACCTGCTTCTCAGTATCTCATCAAGAAGTAGAGGTTCGAAGATTCGCTCATTCGAGCCTTATTT
CATTGATTTGGTCTACTGCTCAGTACCTCATCAGAAAGATGACCGCATCACTTGTTTTGATCCAC
TTCTCTGTGTCTCATCAAG
Found at i:28548 original size:35 final size:32
Alignment explanation
Indices: 28508--28589 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 32
28498 ATAAATGGAC
28508 AACTAATA-ATGAAGATAAATAACGCAAAACAAAGA
1 AACTAATAGAT-AA-ATAAAT-ACGCAAAACAAA-A
*
28543 AACTAAATAGATAAATAAATACGCAAAATAAAA
1 AACT-AATAGATAAATAAATACGCAAAACAAAA
28576 AA-TAATAGTATAAA
1 AACTAATAG-ATAAA
28590 ATACGAAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
31 5 0.12
32 6 0.14
33 3 0.07
34 11 0.26
35 10 0.23
36 6 0.14
37 2 0.05
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (32 bp):
AACTAATAGATAAATAAATACGCAAAACAAAA
Found at i:28583 original size:31 final size:36
Alignment explanation
Indices: 28522--28589 Score: 92
Period size: 34 Copynumber: 2.0 Consensus size: 36
28512 AATAATGAAG
28522 ATAAATAACGCAAAACAAAGAAACTAAATAG-ATAA
1 ATAAATAACGCAAAACAAAGAAACTAAATAGTATAA
*
28557 ATAAAT-ACGCAAAATAAA-AAA-T-AATAGTATAA
1 ATAAATAACGCAAAACAAAGAAACTAAATAGTATAA
28589 A
1 A
28590 ATACGAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 5 0.16
32 6 0.19
33 3 0.10
34 11 0.35
35 6 0.19
ACGTcount: A:0.66, C:0.09, G:0.07, T:0.18
Consensus pattern (36 bp):
ATAAATAACGCAAAACAAAGAAACTAAATAGTATAA
Found at i:28697 original size:28 final size:28
Alignment explanation
Indices: 28658--28787 Score: 97
Period size: 29 Copynumber: 4.5 Consensus size: 28
28648 AACAGAGTCA
* *
28658 AAAAT-GTAATTTTTAGATGCCAAGGGT
1 AAAATGGTAATTTTTAGAAGCCGAGGGT
* * **
28685 AAAATGGTAATTTTTGGAAGTTCGAGGAC
1 AAAATGGTAATTTTTAGAAG-CCGAGGGT
*
28714 AAAATGGTAATTTTAAGACA-CTCGAGGGT
1 AAAATGGTAATTTTTAGA-AGC-CGAGGGT
*
28743 GAAAATGGTAATTTTT-GACA-CTTCGAGGTT
1 -AAAATGGTAATTTTTAGA-AGC--CGAGGGT
28773 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
28788 GAACACTTAC
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.06
28 12 0.14
29 45 0.54
30 22 0.26
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (28 bp):
AAAATGGTAATTTTTAGAAGCCGAGGGT
Found at i:28718 original size:29 final size:29
Alignment explanation
Indices: 28685--28989 Score: 123
Period size: 29 Copynumber: 10.5 Consensus size: 29
28675 TGCCAAGGGT
28685 AAAATGGTAATTTTTGGAAGTTCGAGGAC
1 AAAATGGTAATTTTTGGAAGTTCGAGGAC
** * **
28714 AAAATGGTAATTTTAAGACA-CTCGAGGGTG
1 AAAATGGTAATTTTTGGA-AGTTCGA-GGAC
* **
28744 AAAATGGTAATTTTT-GACACTTCGAGGTT
1 AAAATGGTAATTTTTGGA-AGTTCGAGGAC
* * *
28773 AAAATGGTAATTTTTGAACACTTACTG-GTA-
1 AAAATGGTAATTTTTGGA-AGTT-C-GAGGAC
* * **
28803 AAAAT-GCAATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGAC
* *
28831 AAAATGGTAATTTTTTGAAAGCTCGA-G--
1 AAAATGGTAA-TTTTTGGAAGTTCGAGGAC
* *** * *
28858 AAAATGATAATTTTCAAAAAATTCGAGGTC
1 AAAATGGTAATTTT-TGGAAGTTCGAGGAC
* **
28888 AAAAATGAT-ATTTTTGGAAGTTCGAGGGT
1 -AAAATGGTAATTTTTGGAAGTTCGAGGAC
** *
28917 AAAATGGTAATTTTTAAAAGTTCGAGGGTAA
1 AAAATGGTAATTTTTGGAAGTTCGA-GG-AC
* *
28948 AAAAT-GT-ATTTTTGGAAAGTT-TAGGGGC
1 AAAATGGTAATTTTTGG-AAGTTCGA-GGAC
28976 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
28990 TTGAAATCTA
Statistics
Matches: 214, Mismatches: 42, Indels: 40
0.72 0.14 0.14
Matches are distributed among these distances:
26 5 0.02
27 17 0.08
28 23 0.11
29 95 0.44
30 58 0.27
31 15 0.07
32 1 0.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGAGGAC
Found at i:28756 original size:59 final size:57
Alignment explanation
Indices: 28680--28844 Score: 174
Period size: 59 Copynumber: 2.8 Consensus size: 57
28670 TTAGATGCCA
*
28680 AGGGTAAAATGGTAATTTTTGGAAGTTCGAGGACAAAATGGTAATTTTA-AGACACTCG
1 AGGGTAAAATGGTAATTTTTGGAAGTTCGAGGATAAAATGGTAATTTTAGA-ACACT-G
* * * *
28738 AGGGTGAAAATGGTAATTTTT-GACACTTCGAGGTTAAAATGGTAATTTTTGAACACTT
1 AGGGT-AAAATGGTAATTTTTGGA-AGTTCGAGGATAAAATGGTAATTTTAGAACACTG
* * * *
28796 ACTGGTAAAAAT-GCAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTT
1 A-GGGT-AAAATGGTAATTTTTGGAAGTTCGAGGATAAAATGGTAATTTT
28845 TTGAAAGCTC
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
58 38 0.42
59 52 0.57
60 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (57 bp):
AGGGTAAAATGGTAATTTTTGGAAGTTCGAGGATAAAATGGTAATTTTAGAACACTG
Found at i:28807 original size:30 final size:29
Alignment explanation
Indices: 28685--28845 Score: 129
Period size: 29 Copynumber: 5.5 Consensus size: 29
28675 TGCCAAGGGT
*
28685 AAAATGGTAATTTTTGGA-AGTTCGAGG-A
1 AAAATGGTAATTTTT-GACACTTCGAGGTA
* *
28713 CAAAATGGTAATTTTAAGACAC-TCGAGGGTG
1 -AAAATGGTAATTTT-TGACACTTCGA-GGTA
*
28744 AAAATGGTAATTTTTGACACTTCGAGGTT
1 AAAATGGTAATTTTTGACACTTCGAGGTA
*
28773 AAAATGGTAATTTTTGAACACTTAC-TGGTA
1 AAAATGGTAATTTTTG-ACACTT-CGAGGTA
* * *
28803 AAAAT-GCAATTTTTGGA-AGTTTGAGGGT-
1 AAAATGGTAATTTTT-GACACTTCGA-GGTA
28831 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
28846 TGAAAGCTCG
Statistics
Matches: 109, Mismatches: 12, Indels: 22
0.76 0.08 0.15
Matches are distributed among these distances:
28 8 0.07
29 64 0.59
30 36 0.33
31 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGACACTTCGAGGTA
Found at i:28893 original size:58 final size:59
Alignment explanation
Indices: 28831--28966 Score: 138
Period size: 59 Copynumber: 2.3 Consensus size: 59
28821 GTTTGAGGGT
*
28831 AAAATGGTAATTTTTTGAAAGCTCGA-G-AAAATGATAATTTTCAAAAAATTCGA-GGTCA
1 AAAATGGT-ATTTTTTGAAAGCTCGAGGTAAAATGATAATTTT-AAAAAATTCGAGGGTAA
* * * * * *
28889 AAAATGATA-TTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTAAAAGTTCGAGGGTAA
1 AAAATGGTATTTTTTGAAAGCTCGA-GGTAAAATGATAATTTTAAAAAATTCGAGGGTAA
*
28948 AAAAT-GTATTTTTGGAAAG
1 AAAATGGTATTTTTTGAAAG
28967 TTTAGGGGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
56 13 0.21
57 1 0.02
58 19 0.30
59 30 0.48
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (59 bp):
AAAATGGTATTTTTTGAAAGCTCGAGGTAAAATGATAATTTTAAAAAATTCGAGGGTAA
Found at i:28968 original size:59 final size:58
Alignment explanation
Indices: 28858--28989 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 58
28848 AAAGCTCGAG
* * * *
28858 AAAATGATAATTTTCAAAAAATTCGAGGTCAAAAATGATATTTTTGGAAGTTCGA-GGGT
1 AAAATGGTAATTTT-TAAAAATTCGAGGTAAAAAATGATATTTTTGGAAGTT-GAGGGGC
* *
28917 AAAATGGTAATTTTTAAAAGTTCGAGGGTAAAAAATG-TATTTTTGGAAAGTTTAGGGGC
1 AAAATGGTAATTTTTAAAAATTCGA-GGTAAAAAATGATATTTTTGG-AAGTTGAGGGGC
28976 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
28990 TTGAAATCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 28 0.44
59 36 0.56
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTAAAAATTCGAGGTAAAAAATGATATTTTTGGAAGTTGAGGGGC
Found at i:28979 original size:28 final size:30
Alignment explanation
Indices: 28947--29060 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 30
28937 TTCGAGGGTA
28947 AAAAATGT-ATTTTTGGAAAGTTTAGGGGC
1 AAAAATGTAATTTTTGGAAAGTTTAGGGGC
* *
28976 -AAAATGTAATTTTTTTGAAA-TCTAGGGGC
1 AAAAATGTAA-TTTTTGGAAAGTTTAGGGGC
*
29005 AAAAATGTAATTTTTGTG-AAG--TATGGGC
1 AAAAATGTAATTTTTG-GAAAGTTTAGGGGC
29033 AAAAATGTAA-TTTTGGAAAGTTTAGGGG
1 AAAAATGTAATTTTTGGAAAGTTTAGGGG
29061 GTTAAAATAT
Statistics
Matches: 72, Mismatches: 5, Indels: 16
0.77 0.05 0.17
Matches are distributed among these distances:
26 1 0.01
27 8 0.11
28 23 0.32
29 21 0.29
30 19 0.26
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAAATGTAATTTTTGGAAAGTTTAGGGGC
Found at i:28990 original size:30 final size:29
Alignment explanation
Indices: 28948--29138 Score: 126
Period size: 30 Copynumber: 6.5 Consensus size: 29
28938 TCGAGGGTAA
28948 AAAATGT-ATTTTTGGAAAGTTTAGGGGC
1 AAAATGTAATTTTTGGAAAGTTTAGGGGC
* *
28976 AAAATGTAATTTTTTTGAAA-TCTAGGGGC
1 AAAATGTAA-TTTTTGGAAAGTTTAGGGGC
*
29005 AAAAATGTAATTTTTGTG-AAG--TATGGGC
1 -AAAATGTAATTTTTG-GAAAGTTTAGGGGC
*
29033 AAAAATGTAA-TTTTGGAAAGTTTAGGGGGTT
1 -AAAATGTAATTTTTGGAAAGTTTA-GGGG-C
* * ** * *
29064 AAAATATATTTTTTTTAAAAATTTGAGGGTC
1 AAAATGTA-ATTTTTGGAAAGTTT-AGGGGC
* *
29095 AAAATATAATTTTT-GAGAAGTTTGAGGGTC
1 AAAATGTAATTTTTGGA-AAGTTT-AGGGGC
*
29125 AAAATATAATTTTT
1 AAAATGTAATTTTT
29139 TTTAGAGTTT
Statistics
Matches: 133, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
26 1 0.01
27 8 0.06
28 23 0.17
29 19 0.14
30 60 0.45
31 8 0.06
32 13 0.10
33 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTTAGGGGC
Found at i:29148 original size:31 final size:31
Alignment explanation
Indices: 29059--29149 Score: 107
Period size: 30 Copynumber: 3.0 Consensus size: 31
29049 AAAGTTTAGG
* * *
29059 GGGTTAAAATAT-ATTTTTTTTAAAAATTTGA
1 GGGTCAAAATATAATTTTTTTT-AGAGTTTGA
*
29090 GGGTCAAAATATAA--TTTTTGAGAAGTTTGA
1 GGGTCAAAATATAATTTTTTTTAG-AGTTTGA
29120 GGGTCAAAATATAATTTTTTTTAGAGTTTG
1 GGGTCAAAATATAATTTTTTTTAGAGTTTG
29150 GGGACCTTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 25 0.49
31 17 0.33
32 8 0.16
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (31 bp):
GGGTCAAAATATAATTTTTTTTAGAGTTTGA
Found at i:30306 original size:15 final size:15
Alignment explanation
Indices: 30286--30315 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30276 TCTTCTTTTT
30286 TTGTTATTAGTATTA
1 TTGTTATTAGTATTA
*
30301 TTGTTATTATTATTA
1 TTGTTATTAGTATTA
30316 ATATTAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (15 bp):
TTGTTATTAGTATTA
Found at i:31038 original size:17 final size:17
Alignment explanation
Indices: 31015--31107 Score: 116
Period size: 17 Copynumber: 5.4 Consensus size: 17
31005 TACTTTATTT
*
31015 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
*
31032 TTTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
* * *
31050 GTTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
31067 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
31084 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
31101 ATTTAAA
1 ATTTAAA
31108 AAAGTGAGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
16 3 0.05
17 46 0.71
18 16 0.25
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:31042 original size:6 final size:6
Alignment explanation
Indices: 31015--31107 Score: 63
Period size: 6 Copynumber: 16.2 Consensus size: 6
31005 TACTTTATTT
* ** * *
31015 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA AAATAA GTTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
31062 A-TTAA ATTTAA ATTTAA A-ATAA ATTT-A ATCTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
31107 A
1 A
31108 AAAGTGAGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
4 1 0.02
5 18 0.27
6 43 0.65
7 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:31108 original size:11 final size:12
Alignment explanation
Indices: 31035--31089 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 12
31025 AGAATAATTT
*
31035 TAAATTTAAAAA
1 TAAATTTAAACA
* *
31047 TAAGTTTAAACT
1 TAAATTTAAACA
**
31059 TAAA-TTAAATT
1 TAAATTTAAACA
31070 TAAATTTAAA-A
1 TAAATTTAAACA
31081 TAAATTTAA
1 TAAATTTAA
31090 TCTTAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
11 19 0.53
12 17 0.47
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (12 bp):
TAAATTTAAACA
Found at i:32410 original size:93 final size:92
Alignment explanation
Indices: 32288--32473 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 92
32278 TCTTATCAAT
* *
32288 ATGAATGAAATGATTTCTTATTAATTACTAACATATTTACATGAACTTTATTATATATTCATCGA
1 ATGAATGAAATGATTTCTTATTAACTACTAACATATTTACATGAACTTGATTATATATTCATCGA
*
32353 ACTTGAATTTATATTCTTGTATAAGAA
66 ACTTGAATTTATATTATTGTATAAGAA
* * *
32380 ATGAATGAAATGATATTCTTATTAACTACTATCATATTTACATGAACTTGATTATATATTCCTTG
1 ATGAATGAAATGAT-TTCTTATTAACTACTAACATATTTACATGAACTTGATTATATATTCATCG
* *
32445 AACTTGAATTTGTATTATTGTATATGAA
65 AACTTGAATTTATATTATTGTATAAGAA
32473 A
1 A
32474 CCCATGAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 14 0.16
93 71 0.84
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (92 bp):
ATGAATGAAATGATTTCTTATTAACTACTAACATATTTACATGAACTTGATTATATATTCATCGA
ACTTGAATTTATATTATTGTATAAGAA
Done.