Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_132
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: 182119
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:220 original size:15 final size:14
Alignment explanation
Indices: 197--241 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
187 TTTTGAAATC
197 TCATTTTCATATTTT
1 TCATTTTCAT-TTTT
*
212 TCTTTTTCATTTCTT
1 TCATTTTCATTT-TT
227 TCATTTTCATTTTT
1 TCATTTTCATTTTT
241 T
1 T
242 TTATTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (14 bp):
TCATTTTCATTTTT
Found at i:5688 original size:30 final size:28
Alignment explanation
Indices: 5647--5719 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 28
5637 CTCGCAAGAC
*
5647 TTTCACTTTTTTTTTAACTTGATTTTTT
1 TTTCACTTTTTTTTTAACTCGATTTTTT
**
5675 TTGTCACCTTTTTTTTTTGCTCGATTTTTT
1 TT-TCA-CTTTTTTTTTAACTCGATTTTTT
*
5705 TTTTACTTTTTTTTT
1 TTTCACTTTTTTTTT
5720 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 12 0.31
29 5 0.13
30 22 0.56
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.73
Consensus pattern (28 bp):
TTTCACTTTTTTTTTAACTCGATTTTTT
Found at i:5714 original size:12 final size:12
Alignment explanation
Indices: 5698--5768 Score: 72
Period size: 12 Copynumber: 5.8 Consensus size: 12
5688 TTTTTGCTCG
5698 ATTTTTTTTTTA
1 ATTTTTTTTTTA
* *
5710 CTTTTTTTTTGA
1 ATTTTTTTTTTA
5722 ATTTTTTTTTAATCA
1 ATTTTTTTTT--T-A
*
5737 ATTTTTTTTTCA
1 ATTTTTTTTTTA
*
5749 A-TTTTTTTTTG
1 ATTTTTTTTTTA
5760 ATTTTTTTT
1 ATTTTTTTT
5769 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
11 9 0.19
12 28 0.58
15 11 0.23
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.77
Consensus pattern (12 bp):
ATTTTTTTTTTA
Found at i:5727 original size:39 final size:38
Alignment explanation
Indices: 5684--5768 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 38
5674 TTTGTCACCT
** * * *
5684 TTTTTTTTTGCTCGATTTTTTTTTTACTTTTTTTTTGAA
1 TTTTTTTTTAATCAATTTTTTTTTCAATTTTTTTTTG-A
5723 TTTTTTTTTAATCAATTTTTTTTTCAATTTTTTTTTGA
1 TTTTTTTTTAATCAATTTTTTTTTCAATTTTTTTTTGA
5761 TTTTTTTT
1 TTTTTTTT
5769 GTTACTCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
38 9 0.22
39 32 0.78
ACGTcount: A:0.13, C:0.06, G:0.05, T:0.76
Consensus pattern (38 bp):
TTTTTTTTTAATCAATTTTTTTTTCAATTTTTTTTTGA
Found at i:5729 original size:15 final size:15
Alignment explanation
Indices: 5721--5758 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
5711 TTTTTTTTTG
5721 AATTTTTTTTTAATC
1 AATTTTTTTTTAATC
5736 AA-TTTTTTTT--TC
1 AATTTTTTTTTAATC
5748 AATTTTTTTTT
1 AATTTTTTTTT
5759 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 8 0.36
14 8 0.36
15 2 0.09
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (15 bp):
AATTTTTTTTTAATC
Found at i:8030 original size:30 final size:30
Alignment explanation
Indices: 7996--8092 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
7986 TAAACTAAAA
7996 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
8026 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
8056 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
8085 ATGAGCTA
1 -TGAGCTA
8093 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:10355 original size:6 final size:6
Alignment explanation
Indices: 10339--10388 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
10329 TTTCTTTTTA
*
10339 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
10388 T
1 T
10389 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:10371 original size:37 final size:37
Alignment explanation
Indices: 10328--10398 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
10318 CTTGCCTCTC
10328 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
10365 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
10399 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:10399 original size:16 final size:16
Alignment explanation
Indices: 10324--10384 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
10314 GCCTCTTGCC
*
10324 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
10340 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
10356 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
10372 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
10385 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:11314 original size:26 final size:27
Alignment explanation
Indices: 11274--11334 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
11264 GACTTTTCAC
11274 TTTTTTTTTTCTTTTTTTTTAACTCGA
1 TTTTTTTTTTCTTTTTTTTTAACTCGA
***
11301 TTTTTTTTTT-TTTTTTTTTTTTTCGA
1 TTTTTTTTTTCTTTTTTTTTAACTCGA
11327 TTTTTTTT
1 TTTTTTTT
11335 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.84
Consensus pattern (27 bp):
TTTTTTTTTTCTTTTTTTTTAACTCGA
Found at i:11330 original size:11 final size:12
Alignment explanation
Indices: 11316--11353 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
11306 TTTTTTTTTT
11316 TTTTTTTTCG-A
1 TTTTTTTTCGAA
11327 TTTTTTTT-GAA
1 TTTTTTTTCGAA
11338 TTTTTTTTCTGAA
1 TTTTTTTTC-GAA
11351 TTT
1 TTT
11354 CTTCTCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
13 6 0.25
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:11445 original size:11 final size:11
Alignment explanation
Indices: 11429--11458 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11419 CAACTCAAAA
11429 TTTTTTTT-AT
1 TTTTTTTTGAT
11439 TTTTTTTTGAT
1 TTTTTTTTGAT
11450 TTTTTTTTG
1 TTTTTTTTG
11459 TTACGAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.87
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:13098 original size:30 final size:30
Alignment explanation
Indices: 13064--13160 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
13054 TAAACTAAAA
*
13064 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
13094 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
13124 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
13153 ATGAGCTA
1 -TGAGCTA
13161 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:14067 original size:30 final size:30
Alignment explanation
Indices: 14033--14129 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
14023 TAAACTAAAA
*
14033 TGAGCTAAGTTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
* * * * * * *
14063 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
*
14093 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
14122 ATGAGCTA
1 -TGAGCTA
14130 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
Found at i:14235 original size:969 final size:969
Alignment explanation
Indices: 12358--14296 Score: 3761
Period size: 969 Copynumber: 2.0 Consensus size: 969
12348 AATGGCATGT
*
12358 AAGTTCATAAATGGTAGCATGAACCTAGTAAATTCGTTCTCCCCTTTGTGCATGCACTTAATTCA
1 AAGTTCATAAATGGTAGCATGAACCTAGTAAATTCGTTCTCCCCTTTGTGCATACACTTAATTCA
12423 ATCAATGTGTTGAATTATTGAGTTAATTCCTTCCCTTGGACGTTCTTGAACCCATCCATGCATGT
66 ATCAATGTGTTGAATTATTGAGTTAATTCCTTCCCTTGGACGTTCTTGAACCCATCCATGCATGT
12488 GTAGTAGCCTATAGGTCAATTCAAAGTGTGAACATGCTCAAGGAGCTCTATGGTCAACATAGAAT
131 GTAGTAGCCTATAGGTCAATTCAAAGTGTGAACATGCTCAAGGAGCTCTATGGTCAACATAGAAT
*
12553 TAGTTAGCAGCTACTTCTTGGCCGAATAAGTGCCTTGGAAAGTTAAGAGACAGCCACCATACATG
196 TAGTTAGCAGCTACTTCTTGGCCGAATAAATGCCTTGGAAAGTTAAGAGACAGCCACCATACATG
*
12618 CACTTAAGCCATTCATGCATTCTATCATCCCATGCATTTGATCCATCCATGGACTAGCCTTTAAT
261 CACTTAAGCCATTCATGCATTCTATCAACCCATGCATTTGATCCATCCATGGACTAGCCTTTAAT
12683 GTCCATACATGCATTCGACACATGCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACC
326 GTCCATACATGCATTCGACACATGCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACC
*
12748 AGCATTTAATACTTCTTCATTCATGAGTGTGGAATGCCCAAAAGAGATGTTTCTTCATTCATACA
391 AGCATTTAACACTTCTTCATTCATGAGTGTGGAATGCCCAAAAGAGATGTTTCTTCATTCATACA
*
12813 TTGTACCGTCTAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACT
456 TTGTACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACT
12878 CATAAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCA
521 CATAAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCA
*
12943 ATTTATATAATGACTATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAAT
586 ATTTATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAAT
*
13008 GAATATGTGCAAATTTTATTTAATGTATTAAAGAAAAAACTGAGTTTAAACTAAAATGAGCTAAG
651 GAATATGTGCAAATTTTATTTAATGTATTAAAGAAAAAACCGAGTTTAAACTAAAATGAGCTAAG
*
13073 TTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTA
716 TTTTAGCTCATGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTA
13138 GCTCGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTG
781 GCTCGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTG
*
13203 AATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTTGAAACGAGCTGGGATCAGCTTGCCAA
846 AATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAA
*
13268 CATGTCAATGCTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTATC
911 CATGTCAATACTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTATC
13327 AAGTTCATAAATGGTAGCATGAACCTAGTAAATTCGTTCTCCCCTTTGTGCATACACTTAATTCA
1 AAGTTCATAAATGGTAGCATGAACCTAGTAAATTCGTTCTCCCCTTTGTGCATACACTTAATTCA
13392 ATCAATGTGTTGAATTATTGAGTTAATTCCTTCCCTTGGACGTTCTTGAACCCATCCATGCATGT
66 ATCAATGTGTTGAATTATTGAGTTAATTCCTTCCCTTGGACGTTCTTGAACCCATCCATGCATGT
*
13457 GTAGTAGCCTATAGGTCAATTCAAAGTGTGAACATGTTCAAGGAGCTCTATGGTCAACATAGAAT
131 GTAGTAGCCTATAGGTCAATTCAAAGTGTGAACATGCTCAAGGAGCTCTATGGTCAACATAGAAT
13522 TAGTTAGCAGCTACTTCTTGGCCGAATAAATGCCTTGGAAAGTTAAGAGACAGCCACCATACATG
196 TAGTTAGCAGCTACTTCTTGGCCGAATAAATGCCTTGGAAAGTTAAGAGACAGCCACCATACATG
*
13587 CACTTAAGCCATTCATGCATTCTATCAACCCATGCATTTGATCCATTCATGGACTAGCCTTTAAT
261 CACTTAAGCCATTCATGCATTCTATCAACCCATGCATTTGATCCATCCATGGACTAGCCTTTAAT
*
13652 GTTCATACATGCATTCGACACATGCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACC
326 GTCCATACATGCATTCGACACATGCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACC
13717 AGCATTTAACACTTCTTCATTCATGAGTGTGGAATGCCCAAAAGAGATGTTTCTTCATTCATACA
391 AGCATTTAACACTTCTTCATTCATGAGTGTGGAATGCCCAAAAGAGATGTTTCTTCATTCATACA
13782 TTGTACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACT
456 TTGTACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACT
13847 CATAAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCA
521 CATAAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCA
13912 ATTTATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAAT
586 ATTTATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAAT
13977 GAATATGTGCAAATTTTATTTAATGTATTAAAGAAAAAACCGAGTTTAAACTAAAATGAGCTAAG
651 GAATATGTGCAAATTTTATTTAATGTATTAAAGAAAAAACCGAGTTTAAACTAAAATGAGCTAAG
14042 TTTTAGCTCATGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTA
716 TTTTAGCTCATGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTA
14107 GCTCGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTG
781 GCTCGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTG
14172 AATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAA
846 AATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAA
14237 CATGTCAATACTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTATC
911 CATGTCAATACTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTATC
14296 A
1 A
14297 GCTTAAAGAT
Statistics
Matches: 957, Mismatches: 13, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
969 957 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (969 bp):
AAGTTCATAAATGGTAGCATGAACCTAGTAAATTCGTTCTCCCCTTTGTGCATACACTTAATTCA
ATCAATGTGTTGAATTATTGAGTTAATTCCTTCCCTTGGACGTTCTTGAACCCATCCATGCATGT
GTAGTAGCCTATAGGTCAATTCAAAGTGTGAACATGCTCAAGGAGCTCTATGGTCAACATAGAAT
TAGTTAGCAGCTACTTCTTGGCCGAATAAATGCCTTGGAAAGTTAAGAGACAGCCACCATACATG
CACTTAAGCCATTCATGCATTCTATCAACCCATGCATTTGATCCATCCATGGACTAGCCTTTAAT
GTCCATACATGCATTCGACACATGCATGAATTTGTAGAAACATTGCATCTAGCCGTACATGCACC
AGCATTTAACACTTCTTCATTCATGAGTGTGGAATGCCCAAAAGAGATGTTTCTTCATTCATACA
TTGTACCGTCCAAAGGAATGTACCTACATGAAATAAACAAGTCATTAAGACATCTCATGAACACT
CATAAATTCGGCATGATGTGAACACATTAATGTCATGCATTAATTCGGCTATGTGAACATAATCA
ATTTATATAATGACAATGATATATTAATAACAAATATTAATATAAGACAAGTTTAATGCTTAAAT
GAATATGTGCAAATTTTATTTAATGTATTAAAGAAAAAACCGAGTTTAAACTAAAATGAGCTAAG
TTTTAGCTCATGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTA
GCTCGTGAGCTAAATATGAGCTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATCGAGCTTG
AATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGAGCTGGAAACGAGCTGGGATCAGCTTGCCAA
CATGTCAATACTCGGCTTGACAGACTTGCTCGATGAAGTTCGCGGGGCGTGCTCGTATC
Found at i:15198 original size:14 final size:14
Alignment explanation
Indices: 15176--15215 Score: 57
Period size: 12 Copynumber: 3.0 Consensus size: 14
15166 TAGTAGTTTC
15176 TTCAAAAAAAAATT
1 TTCAAAAAAAAATT
*
15190 TTGAAAAAAAAA--
1 TTCAAAAAAAAATT
15202 TTCAAAAAAAAATT
1 TTCAAAAAAAAATT
15216 GGTTTCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (14 bp):
TTCAAAAAAAAATT
Found at i:15274 original size:14 final size:15
Alignment explanation
Indices: 15252--15291 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
15242 GATATCAAGT
*
15252 TGAAAAAAAAATTTG
1 TGAAAAAAAAATTCG
15267 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
15282 TGAAAAAAAA
1 TGAAAAAAAA
15292 GAAGAAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:20183 original size:13 final size:13
Alignment explanation
Indices: 20165--20197 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
20155 TAGTTTCTTC
20165 AAAAAAAATTTAA
1 AAAAAAAATTTAA
*
20178 AAAAAAAATTTTA
1 AAAAAAAATTTAA
20191 AAAAAAA
1 AAAAAAA
20198 TTGGTTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTTAA
Found at i:20199 original size:12 final size:13
Alignment explanation
Indices: 20165--20197 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
20155 TAGTTTCTTC
20165 AAAAAAAATTTAA
1 AAAAAAAATTTAA
20178 AAAAAAAATTTTAA
1 AAAAAAAA-TTTAA
20192 AAAAAA
1 AAAAAA
20198 TTGGTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTTAA
Found at i:20255 original size:14 final size:15
Alignment explanation
Indices: 20236--20275 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
20226 GATATCAAGT
20236 TGAAAAAAAAA-TCG
1 TGAAAAAAAAATTCG
20250 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
20265 TGAAAAAAAAA
1 TGAAAAAAAAA
20276 AGAAGAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.68, C:0.05, G:0.12, T:0.15
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:25408 original size:22 final size:22
Alignment explanation
Indices: 25378--25421 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25368 TTTGGTATTT
25378 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
25400 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
25422 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:27719 original size:21 final size:21
Alignment explanation
Indices: 27668--27724 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
27658 CTCAATCTCT
*
27668 CTTCTTTC-TTTTCTTTTTCA
1 CTTCTTTCAATTTCTTTTTCA
* *
27688 CTCTCTCTCAATTTCTTTTTCT
1 CT-TCTTTCAATTTCTTTTTCA
* *
27710 GTTCTTTCAAATTCT
1 CTTCTTTCAATTTCT
27725 CCAAAGATGG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.07
21 16 0.55
22 11 0.38
ACGTcount: A:0.11, C:0.26, G:0.02, T:0.61
Consensus pattern (21 bp):
CTTCTTTCAATTTCTTTTTCA
Found at i:28636 original size:45 final size:45
Alignment explanation
Indices: 28572--28803 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
28562 CATGAAATTA
*
28572 AGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
28617 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
28662 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAA-TTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
*
28706 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTA
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
** * * *
28751 AGGAAGCATTTGGTCAACATCATGCATAATTTATGGAACAAATTG
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
28796 AGGAAGCA
1 AGGAAGCA
28804 CCATGGCCGA
Statistics
Matches: 178, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
44 44 0.25
45 134 0.75
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (45 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTG
Found at i:28744 original size:89 final size:89
Alignment explanation
Indices: 28569--28803 Score: 398
Period size: 89 Copynumber: 2.6 Consensus size: 89
28559 CGGCATGAAA
*
28569 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGGAGAATTTGAGGAAGCATTTGACCAA
1 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAA-TTGAGGAAGCATTTGACCAA
28634 CATCATGCATAATTCATGGAAGAAT
65 CATCATGCATAATTCATGGAAGAAT
*
28659 TTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTGAGGAAGCATTTGACCAAC
1 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTGAGGAAGCATTTGACCAAC
28724 ATCATGCATAATTCATGGAAGAAT
66 ATCATGCATAATTCATGGAAGAAT
** * *
28748 TTAAGGAAGCATTTGGTCAACATCATGCATAATTTATGGAACAAATTGAGGAAGCA
1 TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAA-GAATTGAGGAAGCA
28804 CCATGGCCGA
Statistics
Matches: 137, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
89 82 0.60
90 55 0.40
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (89 bp):
TTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTGAGGAAGCATTTGACCAAC
ATCATGCATAATTCATGGAAGAAT
Found at i:33031 original size:22 final size:22
Alignment explanation
Indices: 33001--33042 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
32991 TTTGGTATTT
33001 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
33023 GGGATTTGGTACGAAATGGT
1 GGGAATTGGTACGAAATGGT
33043 TCAAAAAGGT
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:0.31, C:0.05, G:0.38, T:0.26
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39317 original size:28 final size:28
Alignment explanation
Indices: 39268--39323 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
39258 AAATCGTAGC
*
39268 TTCGAAAAAAAAAAGTTAAAAAAAAAGT
1 TTCGAAAAAAAAAAGTCAAAAAAAAAGT
39296 TTCGAAAAAAAAAA-TCCGAAAAAAAAAG
1 TTCGAAAAAAAAAAGT-C-AAAAAAAAAG
39324 AAGGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 14 0.56
29 10 0.40
ACGTcount: A:0.68, C:0.07, G:0.11, T:0.14
Consensus pattern (28 bp):
TTCGAAAAAAAAAAGTCAAAAAAAAAGT
Found at i:39345 original size:14 final size:13
Alignment explanation
Indices: 39328--39354 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39318 AAAAAGAAGG
39328 AAAAAAAAATTGC
1 AAAAAAAAATTGC
39341 AAAAAAAAATTGC
1 AAAAAAAAATTGC
39354 A
1 A
39355 TACGGTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTGC
Found at i:40997 original size:13 final size:13
Alignment explanation
Indices: 40979--41003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40969 TGGTCATCAT
40979 GGTGTGAACACAA
1 GGTGTGAACACAA
40992 GGTGTGAACACA
1 GGTGTGAACACA
41004 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:43244 original size:17 final size:18
Alignment explanation
Indices: 43205--43246 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
43195 AAGAAGAAAA
43205 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
43222 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
43239 TCAAAAGA
1 ACAAAAGA
43247 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:48673 original size:20 final size:20
Alignment explanation
Indices: 48620--48673 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
48610 ATTGAAAGTA
*
48620 AGCTCAGTTGAGCTCAAACG
1 AGCTGAGTTGAGCTCAAACG
**** *
48640 AGCTGAAACAAGCTCAAATG
1 AGCTGAGTTGAGCTCAAACG
48660 AGCTGAGTTGAGCT
1 AGCTGAGTTGAGCT
48674 GGACGGTGCT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
AGCTGAGTTGAGCTCAAACG
Found at i:50356 original size:27 final size:27
Alignment explanation
Indices: 50326--50387 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
50316 CTTTTCAAAC
*
50326 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
50353 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
50380 TCTTTTTC
1 TCTTTTTC
50388 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:50366 original size:13 final size:12
Alignment explanation
Indices: 50350--50469 Score: 63
Period size: 12 Copynumber: 10.0 Consensus size: 12
50340 TTTTTTCGCT
50350 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
50363 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
50377 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
50388 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
50402 -TTTCTTTTTC-
1 TTTTCTTTTTCA
* * *
50412 TTTTGTAATTTCT
1 TTTTCT-TTTTCA
*
50425 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
50437 TTTTCTTTTT-G
1 TTTTCTTTTTCA
50448 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
50458 ATTTCTTTTTCA
1 TTTTCTTTTTCA
50470 ATCTCTTTCT
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 16 0.19
12 30 0.36
13 18 0.22
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:50379 original size:14 final size:14
Alignment explanation
Indices: 50328--50386 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
50318 TTTCAAACTC
*
50328 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
50341 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
50354 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
50369 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
50383 TTTT
1 TTTT
50387 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:50414 original size:18 final size:18
Alignment explanation
Indices: 50393--50451 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
50383 TTTTCTCTCA
50393 CTTTTTTGATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
* *
50411 CTTTTGTAATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
* *
50429 CTTTTTCGTTTTCTTTTT
1 CTTTTTTGATTTCTTTTT
*
50447 GTTTT
1 CTTTT
50452 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (18 bp):
CTTTTTTGATTTCTTTTT
Found at i:50468 original size:6 final size:6
Alignment explanation
Indices: 50348--50455 Score: 60
Period size: 6 Copynumber: 17.7 Consensus size: 6
50338 TCTTTTTTCG
* * * **
50348 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* ** *
50399 -TGATTT CTTTTT CTTTTGT -AATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTT-T CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
50447 -GTTTT CTTT
1 CTTTTT CTTT
50456 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
5 6 0.08
6 54 0.73
7 11 0.15
8 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:51543 original size:21 final size:21
Alignment explanation
Indices: 51519--51577 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
51509 TTGTCACTTC
* *
51519 TTTTTTTTCTTTTTTTTCGAT
1 TTTTTTCTCTTTTTTTTCGAA
*** *
51540 TTTTTTGAATTTTTTTTTGAA
1 TTTTTTCTCTTTTTTTTCGAA
*
51561 TTTCTTCTCTTTTTTTT
1 TTTTTTCTCTTTTTTTT
51578 TAAAATCCAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTTTTCTCTTTTTTTTCGAA
Found at i:51554 original size:12 final size:12
Alignment explanation
Indices: 51539--51563 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51529 TTTTTTTCGA
51539 TTTTTTTGAATT
1 TTTTTTTGAATT
51551 TTTTTTTGAATT
1 TTTTTTTGAATT
51563 T
1 T
51564 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:51658 original size:11 final size:11
Alignment explanation
Indices: 51642--51670 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
51632 CCAACTCAAA
51642 TTTTTTTTGA-
1 TTTTTTTTGAC
51652 TTTTTTTTGAC
1 TTTTTTTTGAC
51663 TTTTTTTT
1 TTTTTTTT
51671 ACATTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:53135 original size:20 final size:20
Alignment explanation
Indices: 53082--53135 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
53072 GCTGAAAGTA
*
53082 AGCTCAGTTGAGCTCAAACG
1 AGCTGAGTTGAGCTCAAACG
**** *
53102 AGCTGAAACAAGCTCAAATG
1 AGCTGAGTTGAGCTCAAACG
53122 AGCTGAGTTGAGCT
1 AGCTGAGTTGAGCT
53136 GGACGGTGCT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
AGCTGAGTTGAGCTCAAACG
Found at i:60230 original size:15 final size:14
Alignment explanation
Indices: 60194--60248 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
60184 TCTATTGATC
60194 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
60208 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
60222 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
60237 GAAAGAAAAGAA
1 GAGA-AAAAGAA
60249 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:66273 original size:13 final size:13
Alignment explanation
Indices: 66257--66294 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
66247 TCTTTTCAAA
66257 AATTTTTTTTTTC
1 AATTTTTTTTTTC
*
66270 AATTTTTTTTTTG
1 AATTTTTTTTTTC
66283 AACTTTTTTTTT
1 AA-TTTTTTTTT
66295 ACGTACCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (13 bp):
AATTTTTTTTTTC
Found at i:66278 original size:16 final size:16
Alignment explanation
Indices: 66237--66281 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
66227 AAACCGTATG
*
66237 CAATTTTTTTTCTTTT
1 CAATTTTTTTTTTTTT
***
66253 CAAAAATTTTTTTTTT
1 CAATTTTTTTTTTTTT
66269 CAATTTTTTTTTT
1 CAATTTTTTTTTT
66282 GAACTTTTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
CAATTTTTTTTTTTTT
Found at i:67001 original size:30 final size:31
Alignment explanation
Indices: 66967--67066 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 31
66957 AGCTCACTCC
66967 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCATACTTTAGCTCACGAGCTAAACCT
* * * * * * *
66997 TAGCTCAAAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTC-ATACTTTAGCTCACGAGCTAAACCT
* *
67029 CAGCTCA-ACTTTAGCTCACGAGCTAAAACT
1 TAGCTCATACTTTAGCTCACGAGCTAAACCT
67059 TAGCTCAT
1 TAGCTCAT
67067 TTTAGTTTAA
Statistics
Matches: 51, Mismatches: 16, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
30 28 0.55
31 3 0.06
32 20 0.39
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCATACTTTAGCTCACGAGCTAAACCT
Found at i:71289 original size:12 final size:12
Alignment explanation
Indices: 71272--71303 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
71262 TAGTTTCTTC
71272 AAAAAAATTCAA
1 AAAAAAATTCAA
71284 AAAAAAATTCAA
1 AAAAAAATTCAA
71296 AAAAAAAT
1 AAAAAAAT
71304 GGTTTCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:71360 original size:15 final size:15
Alignment explanation
Indices: 71340--71396 Score: 96
Period size: 15 Copynumber: 3.7 Consensus size: 15
71330 GATATCAAGT
71340 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
71355 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
71370 TGAAAAAAAAAATTTCG
1 TG-AAAAAAAAA-TTCG
71387 TGAAAAAAAA
1 TGAAAAAAAA
71397 GTAGAAGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 17 0.43
16 17 0.43
17 6 0.15
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.19
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:71364 original size:17 final size:17
Alignment explanation
Indices: 71342--71396 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
71332 TATCAAGTTG
71342 AAAAAAAAATTCGTG--
1 AAAAAAAAATTCGTGAA
71357 AAAAAAAAATTCGTGAA
1 AAAAAAAAATTCGTGAA
*
71374 AAAAAAAATTTCGTGAA
1 AAAAAAAAATTCGTGAA
71391 AAAAAA
1 AAAAAA
71397 GTAGAAGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
15 15 0.41
17 22 0.59
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.18
Consensus pattern (17 bp):
AAAAAAAAATTCGTGAA
Found at i:73286 original size:10 final size:10
Alignment explanation
Indices: 73273--73310 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
73263 TTGTAGCTAA
73273 ATTGAGCTCG
1 ATTGAGCTCG
73283 ATTGAGCT-G
1 ATTGAGCTCG
73292 ACTTGAGCTCG
1 A-TTGAGCTCG
*
73303 AGTGAGCT
1 ATTGAGCT
73311 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:73290 original size:20 final size:20
Alignment explanation
Indices: 73250--73310 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
73240 ACCAATAAAA
73250 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
73270 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
73290 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
73310 T
1 T
73311 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:73311 original size:20 final size:20
Alignment explanation
Indices: 73274--73311 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
73264 TGTAGCTAAA
*
73274 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
73294 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
73312 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:76046 original size:13 final size:13
Alignment explanation
Indices: 76030--76092 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 13
76020 TTTTGCTCGA
*
76030 TTTTTTTTCACTT
1 TTTTTTTTCAATT
*
76043 TTTTTTTTGAATTT
1 TTTTTTTTCAA-TT
76057 TTTTTTTCAATCAATT
1 TTTTTTT---TCAATT
76073 TTTTTTTTCGAATT
1 TTTTTTTTC-AATT
76087 TTTTTT
1 TTTTTT
76093 GATTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
16 9 0.21
17 3 0.07
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:76086 original size:14 final size:14
Alignment explanation
Indices: 76030--76092 Score: 67
Period size: 13 Copynumber: 4.4 Consensus size: 14
76020 TTTTGCTCGA
*
76030 TTTTTTTTC-ACTT
1 TTTTTTTTCGAATT
76043 TTTTTTTT-GAATT
1 TTTTTTTTCGAATT
*
76056 TTTTTTTTCAATCAATT
1 TTTTTTTTC---GAATT
76073 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
76087 TTTTTT
1 TTTTTT
76093 GATTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
13 19 0.45
14 10 0.24
17 13 0.31
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTTTTTCGAATT
Found at i:77503 original size:10 final size:10
Alignment explanation
Indices: 77490--77527 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
77480 TTGTAGCTAA
77490 ATTGAGCTCG
1 ATTGAGCTCG
77500 ATTGAGCT-G
1 ATTGAGCTCG
77509 ACTTGAGCTCG
1 A-TTGAGCTCG
*
77520 AGTGAGCT
1 ATTGAGCT
77528 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:77507 original size:20 final size:20
Alignment explanation
Indices: 77467--77527 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
77457 ACCAATAAAA
77467 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
77487 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
77507 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
77527 T
1 T
77528 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:77528 original size:20 final size:20
Alignment explanation
Indices: 77491--77528 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
77481 TGTAGCTAAA
*
77491 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
77511 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
77529 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:82307 original size:20 final size:20
Alignment explanation
Indices: 82261--82307 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
82251 AGCTTGTTTC
*
82261 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
82281 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
82301 CAGCTCA
1 CAGCTCA
82308 ACCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:83852 original size:10 final size:10
Alignment explanation
Indices: 83837--83877 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
83827 GAAGTGAGCA
83837 AAAAAAAAAG
1 AAAAAAAAAG
83847 AAAAAAAAAG
1 AAAAAAAAAG
83857 TAAAAAAAAA-
1 -AAAAAAAAAG
83867 ACAAAAAAAAG
1 A-AAAAAAAAG
83878 TGAAAAGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.04
10 18 0.64
11 9 0.32
ACGTcount: A:0.88, C:0.02, G:0.07, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:83861 original size:21 final size:21
Alignment explanation
Indices: 83836--83883 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
83826 AGAAGTGAGC
*
83836 AAAAAAAAAAGAAAAAAAAAGT
1 AAAAAAAAAA-CAAAAAAAAGT
83858 AAAAAAAAAACAAAAAAAAGT
1 AAAAAAAAAACAAAAAAAAGT
*
83879 GAAAA
1 AAAAA
83884 GTCTTGTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.85, C:0.02, G:0.08, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAAGT
Found at i:84979 original size:47 final size:46
Alignment explanation
Indices: 84901--85004 Score: 131
Period size: 47 Copynumber: 2.2 Consensus size: 46
84891 GAGTGTCATG
*
84901 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAA-AGAAA-AAATC
* *
84948 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAGAAAAAATC
84995 GAAAAAGAAA
1 GAAAAAGAAA
85005 GAAAAGACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
47 40 0.78
48 8 0.16
49 3 0.06
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (46 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAGAAAAAATC
Found at i:86420 original size:13 final size:13
Alignment explanation
Indices: 86402--86426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
86392 TGGACATCAT
86402 GGTGTGAACACAA
1 GGTGTGAACACAA
86415 GGTGTGAACACA
1 GGTGTGAACACA
86427 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:88655 original size:27 final size:27
Alignment explanation
Indices: 88624--88696 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
88614 TCTTCTTCAA
88624 CATCTTTTTCTTTTTCAATTTT-TTCT
1 CATCTTTTTCTTTTTCAATTTTCTTCT
* *
88650 CAATCTCAATTTCTTTTTCAATTTTCTTTT
1 C-ATCT--TTTTCTTTTTCAATTTTCTTCT
* *
88680 CTTCATTTTCTTTTTCA
1 CATCTTTTTCTTTTTCA
88697 CTCACTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.39
29 18 0.47
30 4 0.11
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (27 bp):
CATCTTTTTCTTTTTCAATTTTCTTCT
Found at i:88660 original size:17 final size:18
Alignment explanation
Indices: 88638--88671 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88628 TTTTTCTTTT
88638 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
88655 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
88672 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:89601 original size:15 final size:15
Alignment explanation
Indices: 89565--89606 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
89555 TTTTTAACTT
*
89565 GATTTTTTTTTGGTC
1 GATTTTTTTTTGCTC
89580 -ACCTTTTTTTTTGCTC
1 GA--TTTTTTTTTGCTC
89596 GATTTTTTTTT
1 GATTTTTTTTT
89607 CACTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 1 0.04
15 9 0.39
16 12 0.52
17 1 0.04
ACGTcount: A:0.07, C:0.12, G:0.12, T:0.69
Consensus pattern (15 bp):
GATTTTTTTTTGCTC
Found at i:89614 original size:13 final size:13
Alignment explanation
Indices: 89598--89637 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
89588 TTTTGCTCGA
*
89598 TTTTTTTTTCACT
1 TTTTTTTTTCAAT
*
89611 TTTTTTTTTGAATT
1 TTTTTTTTTCAA-T
89625 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
89638 CAATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.12, C:0.07, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:90735 original size:13 final size:13
Alignment explanation
Indices: 90717--90741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90707 TGGACATCAT
90717 GGTGTGAACACAA
1 GGTGTGAACACAA
90730 GGTGTGAACACA
1 GGTGTGAACACA
90742 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:94061 original size:17 final size:18
Alignment explanation
Indices: 94039--94072 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
94029 ACAACACTCC
*
94039 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
94056 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
94073 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:94178 original size:15 final size:16
Alignment explanation
Indices: 94153--94190 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
94143 TATCTCACAC
94153 TCATCTTCTTTTTC-TT
1 TCAT-TTCTTTTTCTTT
94169 TCATTTCTTTTTCTTT
1 TCATTTCTTTTTCTTT
94185 TCATTT
1 TCATTT
94191 TCTCGCTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (16 bp):
TCATTTCTTTTTCTTT
Found at i:95118 original size:29 final size:26
Alignment explanation
Indices: 95083--95153 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 26
95073 CTCGCAAGAC
*
95083 TTTTCACTTTTTTTTTAACTTGATTTT
1 TTTTCACTTTTTTTTT-ACTCGATTTT
* *
95110 TTTGGTCACCTTTTTTTTGCTCGATTTT
1 TTT--TCACTTTTTTTTTACTCGATTTT
95138 TTTTCACTTTTTTTTT
1 TTTTCACTTTTTTTTT
95154 TGAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 12 0.32
27 3 0.08
28 11 0.29
29 12 0.32
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (26 bp):
TTTTCACTTTTTTTTTACTCGATTTT
Found at i:95161 original size:12 final size:12
Alignment explanation
Indices: 95146--95203 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
95136 TTTTTTCACT
95146 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
95158 TTTTTTTTCAATCAA
1 TTTTTTTT---TGAA
*
95173 TTTTTTTTCGAA
1 TTTTTTTTTGAA
95185 TTTTTTTTTG-A
1 TTTTTTTTTGAA
95196 TTTTTTTT
1 TTTTTTTT
95204 GTTACTCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.23
12 19 0.49
15 11 0.28
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:98573 original size:20 final size:20
Alignment explanation
Indices: 98527--98573 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
98517 AGCTTGTTTC
*
98527 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
98547 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
98567 CAGCTCA
1 CAGCTCA
98574 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:104023 original size:23 final size:22
Alignment explanation
Indices: 103971--104023 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
103961 TCCACGTCTT
*
103971 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
103993 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
104016 TTTCTTTT
1 TTTCTTTT
104024 TCAATCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:110865 original size:11 final size:11
Alignment explanation
Indices: 110849--110882 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
110839 AGGCATTAAG
110849 ATGTTCACACC
1 ATGTTCACACC
*
110860 ATGTTCA-GCC
1 ATGTTCACACC
110870 ATGTTCACACC
1 ATGTTCACACC
110881 AT
1 AT
110883 TTGGCTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.29
Consensus pattern (11 bp):
ATGTTCACACC
Found at i:116148 original size:20 final size:19
Alignment explanation
Indices: 116125--116182 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
116115 AGCTCAAACG
116125 AGCTAAAGTAAGCTAAATTA
1 AGCTAAAGT-AGCTAAATTA
116145 AGCTCAAACG-AGCTAAATTA
1 AGCT-AAA-GTAGCTAAATTA
* *
116165 AGCTCATGTGAGCTAAAT
1 AGCTAAAGT-AGCTAAAT
116183 CGAGCTGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 26 0.81
21 3 0.09
22 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (19 bp):
AGCTAAAGTAGCTAAATTA
Found at i:116959 original size:30 final size:30
Alignment explanation
Indices: 116903--116959 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
116893 TGGGCTCAAA
* **
116903 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
116933 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
116960 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:120547 original size:17 final size:17
Alignment explanation
Indices: 120488--120547 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
120478 GAGACAGCCA
* * *
120488 CCATACATGCACTTAAG
1 CCATTCATGCATTTAAT
120505 CCATTCATGCATTCT-AT
1 CCATTCATGCATT-TAAT
*
120522 CC-TCCCATGCATTTAAT
1 CCAT-TCATGCATTTAAT
120539 CCATTCATG
1 CCATTCATG
120548 GACTAGCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 30 0.88
18 2 0.06
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.33
Consensus pattern (17 bp):
CCATTCATGCATTTAAT
Found at i:120977 original size:30 final size:30
Alignment explanation
Indices: 120943--121039 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
120933 TAAACTAAAA
*
120943 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
120973 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
121003 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
121032 ATGAGCTA
1 -TGAGCTA
121040 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:131309 original size:21 final size:22
Alignment explanation
Indices: 131285--131329 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
131275 TCATATAATT
131285 ATAACTTAAAAT-AATAACTAA
1 ATAACTTAAAATCAATAACTAA
* *
131306 ATAACTTAATATCACTAACTAA
1 ATAACTTAAAATCAATAACTAA
131328 AT
1 AT
131330 TTGAACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAACTTAAAATCAATAACTAA
Found at i:135665 original size:33 final size:33
Alignment explanation
Indices: 135627--135689 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
135617 GATTACTCAC
135627 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
135660 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
135690 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:135702 original size:13 final size:13
Alignment explanation
Indices: 135686--135741 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
135676 TCAAGCTCTC
135686 TTTCAATTTCTTT
1 TTTCAATTTCTTT
**
135699 TTTCGCTTT-TCTT
1 TTTCAATTTCT-TT
135712 TTTCAATTTTCTTT
1 TTTCAA-TTTCTTT
*
135726 TCTTCATTTTCTTT
1 T-TTCAATTTCTTT
135740 TT
1 TT
135742 CTCTCACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 1 0.03
13 14 0.41
14 14 0.41
15 5 0.15
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTCAATTTCTTT
Found at i:135711 original size:14 final size:13
Alignment explanation
Indices: 135686--135741 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
135676 TCAAGCTCTC
*
135686 TTTCAATTTCTTT
1 TTTCATTTTCTTT
*
135699 TTTCGCTTTTC-TT
1 TTTC-ATTTTCTTT
135712 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
135726 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
135740 TT
1 TT
135742 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 16 0.44
14 17 0.47
15 3 0.08
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:135735 original size:27 final size:26
Alignment explanation
Indices: 135686--135766 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 26
135676 TCAAGCTCTC
*
135686 TTTCAATTTCTTTTTTCGCTTTTCTT
1 TTTCAATTTCTTTTTTCGATTTTCTT
135712 TTTCAATTTTCTTTTCTTC-ATTTTCTT
1 TTTCAA-TTTCTTTT-TTCGATTTTCTT
* *
135739 TTTC--TCTCACTTTTTCGA-TTTCTT
1 TTTCAATTTC-TTTTTTCGATTTTCTT
135763 TTTC
1 TTTC
135767 TTTTGCAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 16 0.33
25 4 0.08
26 6 0.12
27 19 0.40
28 3 0.06
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTCAATTTCTTTTTTCGATTTTCTT
Found at i:135763 original size:12 final size:12
Alignment explanation
Indices: 135748--135809 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
135738 TTTTCTCTCA
*
135748 CTTTTTCGATTT
1 CTTTTTCGTTTT
135760 CTTTTTC-TTTT
1 CTTTTTCGTTTT
** *
135771 GCAATTTCTTTTT
1 -CTTTTTCGTTTT
135784 CTTTTTCGTTTT
1 CTTTTTCGTTTT
135796 CTTTTT-G-TTT
1 CTTTTTCGTTTT
135806 CTTT
1 CTTT
135810 CAATTTCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 7 0.17
11 4 0.10
12 27 0.64
13 4 0.10
ACGTcount: A:0.05, C:0.16, G:0.06, T:0.73
Consensus pattern (12 bp):
CTTTTTCGTTTT
Found at i:135801 original size:18 final size:18
Alignment explanation
Indices: 135705--135822 Score: 85
Period size: 18 Copynumber: 6.3 Consensus size: 18
135695 CTTTTTTCGC
135705 TTTTCTTTTTCAATTTTCTT
1 TTTTCTTTTTC-ATTTTC-T
* *
135725 TTCTTCATTTTCTTTTTCT
1 TT-TTCTTTTTCATTTTCT
* **
135744 CTCACTTTTTCGA-TTTCT
1 TTTTCTTTTTC-ATTTTCT
* *
135762 TTTTCTTTTGCAATTTCT
1 TTTTCTTTTTCATTTTCT
*
135780 TTTTCTTTTTCGTTTTCT
1 TTTTCTTTTTCATTTTCT
* *
135798 TTTTGTTTCTTTCAATTTCT
1 TTTT-CTT-TTTCATTTTCT
135818 TTTTC
1 TTTTC
135823 AATCTCTTTC
Statistics
Matches: 75, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
17 1 0.01
18 42 0.56
19 4 0.05
20 20 0.27
21 8 0.11
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTCTTTTTCATTTTCT
Found at i:135822 original size:6 final size:6
Alignment explanation
Indices: 135705--135801 Score: 68
Period size: 6 Copynumber: 15.7 Consensus size: 6
135695 CTTTTTTCGC
* * * ** *
135705 TTTTCT TTTTCAA TTTTCTT TTCTTCA TTTTCT TTTTCT CTCACT TTTTCG
1 TTTTCT TTTTC-T TTTTC-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * * *
135756 ATTTCT TTTTCT TTTGCA ATTTCT TTTTCT TTTTCG TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
135802 GTTTCTTTCA
Statistics
Matches: 66, Mismatches: 23, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
6 54 0.82
7 9 0.14
8 3 0.05
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
TTTTCT
Found at i:136887 original size:25 final size:25
Alignment explanation
Indices: 136844--136903 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
136834 TTAAACTTGA
**
136844 TTTTTTTTGCTCACCTTTTTTTTTCT
1 TTTTTTTTGCTCA-CTTTTTTTCACT
136870 TTTTTTTTGCTCGA-TTTTTTTCACT
1 TTTTTTTTGCTC-ACTTTTTTTCACT
136895 TTTTTTTTG
1 TTTTTTTTG
136904 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 18 0.58
26 12 0.39
27 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.73
Consensus pattern (25 bp):
TTTTTTTTGCTCACTTTTTTTCACT
Found at i:139177 original size:20 final size:21
Alignment explanation
Indices: 139142--139180 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
139132 CAGCTCGTTG
139142 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
139163 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
139181 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:139587 original size:13 final size:13
Alignment explanation
Indices: 139569--139594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
139559 TGTGTCCTAA
139569 TATGAATTAAATT
1 TATGAATTAAATT
139582 TATGAATTAAATT
1 TATGAATTAAATT
139595 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:140721 original size:9 final size:9
Alignment explanation
Indices: 140707--140740 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
140697 GTAAGTGATT
140707 AAAAAAATA
1 AAAAAAATA
140716 AAAAAAATTGA
1 AAAAAAA-T-A
140727 AAAAAAATA
1 AAAAAAATA
140736 AAAAA
1 AAAAA
140741 GTCAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.57
10 2 0.09
11 8 0.35
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:140747 original size:18 final size:18
Alignment explanation
Indices: 140707--140752 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
140697 GTAAGTGATT
* * *
140707 AAAAAAATAAAAAAAATTG
1 AAAAAAA-ATAAAAAAGTC
140726 AAAAAAAATAAAAAAGTC
1 AAAAAAAATAAAAAAGTC
140744 AAAAAAAAT
1 AAAAAAAAT
140753 TCGTGGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (18 bp):
AAAAAAAATAAAAAAGTC
Found at i:142712 original size:11 final size:10
Alignment explanation
Indices: 142696--142725 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
142686 GTTCGTAACG
142696 AAAAAAAAGTC
1 AAAAAAAA-TC
142707 AAAAAAAATC
1 AAAAAAAATC
142717 AAAAAAAAT
1 AAAAAAAAT
142726 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:142825 original size:11 final size:11
Alignment explanation
Indices: 142809--142844 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
142799 AAAAGAGAAG
142809 AAATTCAAAAA
1 AAATTCAAAAA
142820 AAATTCAAAAA
1 AAATTCAAAAA
*
142831 AAATTGAAAAA
1 AAATTCAAAAA
142842 AAA
1 AAA
142845 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:142900 original size:11 final size:11
Alignment explanation
Indices: 142815--142901 Score: 50
Period size: 11 Copynumber: 7.4 Consensus size: 11
142805 GAAGAAATTC
* *
142815 AAAAAAAATTC
1 AAAAAAAAGTG
*
142826 AAAAAAAATTG
1 AAAAAAAAGTG
**
142837 AAAAAAAAGAA
1 AAAAAAAAGTG
142848 AAAAAAGAAGTG
1 AAAAAA-AAGTG
142860 ACAAAAAAA-TCG
1 A-AAAAAAAGT-G
*
142872 AGTTAAAAAAAGAAG
1 A---AAAAAAAG-TG
142887 AAAAAAAAGTG
1 AAAAAAAAGTG
142898 AAAA
1 AAAA
142902 GTCTTGCGAG
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 30 0.50
12 16 0.27
13 5 0.08
14 7 0.12
15 2 0.03
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (11 bp):
AAAAAAAAGTG
Found at i:143829 original size:15 final size:14
Alignment explanation
Indices: 143806--143853 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
143796 AAATTGAGAG
143806 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
*
143820 TAAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
143835 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
143850 AAGA
1 AAGA
143854 TGAAAATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:143835 original size:21 final size:21
Alignment explanation
Indices: 143802--143853 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
143792 AATGAAATTG
*
143802 AGAGAAGAA-AAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
143822 AGAGAAAAAGAAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
*
143843 AAAGAAAAAGA
1 AGAGAAAAAGA
143854 TGAAAATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
AGAGAAAAAGAAAAAGAAATA
Found at i:147725 original size:6 final size:6
Alignment explanation
Indices: 147700--147798 Score: 83
Period size: 6 Copynumber: 16.0 Consensus size: 6
147690 TAATGAATTC
** *
147700 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
147748 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
147799 TATGAAAATG
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
5 1 0.01
6 59 0.82
7 8 0.11
8 4 0.06
ACGTcount: A:0.74, C:0.01, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:147837 original size:18 final size:18
Alignment explanation
Indices: 147816--147855 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
147806 ATGAGATTTC
147816 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
*
147833 AAAAACAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
147851 AAAAA
1 AAAAA
147856 GAAAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.68, C:0.05, G:0.17, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:147838 original size:17 final size:17
Alignment explanation
Indices: 147816--147865 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
147806 ATGAGATTTC
147816 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
*
147833 AAAAACAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
147851 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
147866 TTGAAAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.17
17 13 0.45
18 11 0.38
ACGTcount: A:0.64, C:0.04, G:0.22, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:147869 original size:18 final size:17
Alignment explanation
Indices: 147823--147897 Score: 54
Period size: 18 Copynumber: 4.5 Consensus size: 17
147813 TTCAAAAACA
*
147823 AAAGAGAG-TGAAAAAC
1 AAAGAGAGTTGAAAAAG
147839 AAA-ATGAGATTGAAAAAG
1 AAAGA-GAG-TTGAAAAAG
147857 AAAGAGAGTTTG-AAAAG
1 AAAGAGAG-TTGAAAAAG
*
147874 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAAAAAG
147890 -AAGAGAGT
1 AAAGAGAGT
147898 GCTCAAACAC
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
15 8 0.17
16 12 0.25
17 11 0.23
18 16 0.33
19 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.28, T:0.12
Consensus pattern (17 bp):
AAAGAGAGTTGAAAAAG
Found at i:149165 original size:20 final size:21
Alignment explanation
Indices: 149130--149168 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
149120 CAGCTCGTTG
149130 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
149151 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
149169 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:149575 original size:13 final size:13
Alignment explanation
Indices: 149557--149582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
149547 TGTGTCCTAA
149557 TATGAATTAAATT
1 TATGAATTAAATT
149570 TATGAATTAAATT
1 TATGAATTAAATT
149583 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:162095 original size:11 final size:11
Alignment explanation
Indices: 162079--162112 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
162069 ATTGGAGTAA
162079 CAAAAAAAAAT
1 CAAAAAAAAAT
*
162090 CAAAAAAAATT
1 CAAAAAAAAAT
162101 CGAAAAAAAAAT
1 C-AAAAAAAAAT
162113 TTGATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (11 bp):
CAAAAAAAAAT
Found at i:162107 original size:13 final size:13
Alignment explanation
Indices: 162080--162167 Score: 60
Period size: 13 Copynumber: 6.7 Consensus size: 13
162070 TTGGAGTAAC
162080 AAAAAAAAA-TC-
1 AAAAAAAAATTCG
162091 -AAAAAAAATTCG
1 AAAAAAAAATTCG
*
162103 AAAAAAAAATTTGATTG
1 AAAAAAAAA--T--TCG
*
162120 AAAAAAAAATTCA
1 AAAAAAAAATTCG
*
162133 AAAAAAAAAGT-G
1 AAAAAAAAATTCG
162145 AAAAAAAAA-TCG
1 AAAAAAAAATTCG
162157 AGCAAAAAAAA
1 A--AAAAAAAA
162168 AAAAAAAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
10 8 0.13
11 3 0.05
12 11 0.18
13 19 0.31
14 8 0.13
15 2 0.03
17 11 0.18
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:162166 original size:25 final size:25
Alignment explanation
Indices: 162091--162154 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
162081 AAAAAAAATC
*
162091 AAAAAAAATTCGAAAAAAAAATTTGATTGA
1 AAAAAAAATTC-AAAAAAAAA----AGTGA
162121 AAAAAAAATTCAAAAAAAAAAGTGA
1 AAAAAAAATTCAAAAAAAAAAGTGA
162146 AAAAAAAAT
1 AAAAAAAAT
162155 CGAGCAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 13 0.39
29 9 0.27
30 11 0.33
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (25 bp):
AAAAAAAATTCAAAAAAAAAAGTGA
Found at i:162202 original size:37 final size:35
Alignment explanation
Indices: 162132--162205 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 35
162122 AAAAAAATTC
*
162132 AAAAAAAAAAGTGAAAAAAAAATCGAGCAAAAAAA
1 AAAAAAAAAAGTGAAAAAAAAATCAAGCAAAAAAA
* **
162167 AAAAAAAAAAGGTGACCAAAAAAATCAAGTTAAAAAA
1 AAAAAAAAAA-GTGA-AAAAAAAATCAAGCAAAAAAA
162204 AA
1 AA
162206 GTGAAAAGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 10 0.30
36 4 0.12
37 19 0.58
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.08
Consensus pattern (35 bp):
AAAAAAAAAAGTGAAAAAAAAATCAAGCAAAAAAA
Found at i:163159 original size:15 final size:16
Alignment explanation
Indices: 163139--163170 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
163129 AGAAAATGAA
163139 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
163154 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
163170 A
1 A
163171 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:163285 original size:17 final size:18
Alignment explanation
Indices: 163253--163286 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
163243 AAAAGAGAGT
*
163253 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
163271 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
163287 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:164142 original size:20 final size:21
Alignment explanation
Indices: 164107--164145 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
164097 CAGCTCGTTG
164107 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
164128 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
164146 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:164553 original size:13 final size:13
Alignment explanation
Indices: 164535--164560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
164525 TGTGTCCTAA
164535 TATGAATTAAATT
1 TATGAATTAAATT
164548 TATGAATTAAATT
1 TATGAATTAAATT
164561 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:165702 original size:12 final size:12
Alignment explanation
Indices: 165687--165716 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
165677 AAAAAATTTT
165687 AAAAAAATAAAA
1 AAAAAAATAAAA
*
165699 AAAAAAGTAAAA
1 AAAAAAATAAAA
165711 AAAAAA
1 AAAAAA
165717 TCGTGGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:166681 original size:6 final size:6
Alignment explanation
Indices: 166656--166754 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
166646 TAATGAATTC
** * * *
166656 GAAAAA GAAAGT GAAGAA GAAAAA GAGAACA -AAAAA GAAAAA GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA GAAAAA GAAAAA
** * * *
166704 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
166755 TATGAAAATG
Statistics
Matches: 68, Mismatches: 20, Indels: 10
0.69 0.20 0.10
Matches are distributed among these distances:
5 3 0.04
6 51 0.75
7 10 0.15
8 4 0.06
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:166737 original size:14 final size:13
Alignment explanation
Indices: 166716--166753 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
166706 AAAAGTGAGA
166716 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
166728 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
166743 GAAAAAGAAAA
1 GAAAAAGAAAA
166754 ATATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:168121 original size:20 final size:21
Alignment explanation
Indices: 168086--168124 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
168076 CAGCTCGTTG
168086 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
168107 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
168125 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:168532 original size:13 final size:13
Alignment explanation
Indices: 168514--168539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168504 TGTGTCCTAA
168514 TATGAATTAAATT
1 TATGAATTAAATT
168527 TATGAATTAAATT
1 TATGAATTAAATT
168540 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:170165 original size:20 final size:20
Alignment explanation
Indices: 170142--170195 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
170132 AGTTTTTTCC
*
170142 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
170162 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
170182 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
170196 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:170177 original size:30 final size:30
Alignment explanation
Indices: 170142--170215 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
170132 AGTTTTTTCC
170142 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
170172 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
170202 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
170216 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:170205 original size:20 final size:20
Alignment explanation
Indices: 170142--170206 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
170132 AGTTTTTTCC
* * * *
170142 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
170162 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
170181 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
170202 AGCTC
1 AGCTC
170207 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:175410 original size:14 final size:14
Alignment explanation
Indices: 175337--175456 Score: 55
Period size: 14 Copynumber: 8.2 Consensus size: 14
175327 CTCGCAAGAC
175337 TTTTCAC-TTTTTT
1 TTTTCACTTTTTTT
*
175350 TTTTAACTTGATTTTT
1 TTTTCACTT--TTTTT
* *
175366 TTGGTCACCTTTTTT
1 TT-TTCACTTTTTTT
* * **
175381 TTTGCTCAATTTTT
1 TTTTCACTTTTTTT
175395 TTTTCAC-TTTTTT
1 TTTTCACTTTTTTT
* * *
175408 TTTTGAATATTTTT
1 TTTTCACTTTTTTT
*
175422 TTTTCAATCAATTTTTT
1 TTTTC-A-C-TTTTTTT
*
175439 TTTTCGAATTTTTTT
1 TTTTC-ACTTTTTTT
175454 TTT
1 TTT
175457 GATTTTTTTT
Statistics
Matches: 77, Mismatches: 22, Indels: 14
0.68 0.19 0.12
Matches are distributed among these distances:
13 16 0.21
14 22 0.29
15 17 0.22
16 7 0.09
17 15 0.19
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (14 bp):
TTTTCACTTTTTTT
Found at i:180009 original size:14 final size:14
Alignment explanation
Indices: 179963--180027 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 14
179953 AAATCGTAGC
*
179963 TTCGAAAAAAAAAA
1 TTCGAAAAAAAAAT
* *
179977 TCCG-AAAAAAAAG
1 TTCGAAAAAAAAAT
*
179990 TT--AAAAAAAAGT
1 TTCGAAAAAAAAAT
180002 TTCGAAAAAAAAAT
1 TTCGAAAAAAAAAT
*
180016 TGC-AAAAAAAAA
1 TTCGAAAAAAAAA
180028 AATTGCATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
12 9 0.22
13 18 0.44
14 14 0.34
ACGTcount: A:0.68, C:0.08, G:0.09, T:0.15
Consensus pattern (14 bp):
TTCGAAAAAAAAAT
Found at i:180022 original size:13 final size:14
Alignment explanation
Indices: 179965--180033 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
179955 ATCGTAGCTT
* *
179965 CGAAAAAAAAAATC
1 CGAAAAAAAAATTG
*
179979 CGAAAAAAAAGTT-
1 CGAAAAAAAAATTG
* *
179992 --AAAAAAAAGTTT
1 CGAAAAAAAAATTG
180004 CGAAAAAAAAATTG
1 CGAAAAAAAAATTG
*
180018 CAAAAAAAAAAATTG
1 C-GAAAAAAAAATTG
180033 C
1 C
180034 ATACGGTCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 11 0.24
14 22 0.48
15 13 0.28
ACGTcount: A:0.67, C:0.09, G:0.10, T:0.14
Consensus pattern (14 bp):
CGAAAAAAAAATTG
Found at i:180028 original size:14 final size:14
Alignment explanation
Indices: 179992--180034 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
179982 AAAAAAAGTT
* * *
179992 AAAAAAAAGTTTCG
1 AAAAAAAAATTGCA
180006 AAAAAAAAATTGCAA
1 AAAAAAAAATTGC-A
180021 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
180035 TACGGTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.16
Consensus pattern (14 bp):
AAAAAAAAATTGCA
Found at i:180028 original size:15 final size:15
Alignment explanation
Indices: 180006--180034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
179996 AAAAGTTTCG
180006 AAAAAAAAATTGCAA
1 AAAAAAAAATTGCAA
180021 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
180035 TACGGTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATTGCAA
Done.