Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000887.1 Hibiscus syriacus cultivar Beakdansim tig00001732_pilon, 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: 662576
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:4220 original size:13 final size:13
Alignment explanation
Indices: 4202--4241 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
4192 ATATTATGCT
4202 TGAAGAAAAAAAA
1 TGAAGAAAAAAAA
4215 TGAAGAAAAAAAA
1 TGAAGAAAAAAAA
*
4228 AGAAGTAAAAAAAA
1 TGAAG-AAAAAAAA
4242 AGGAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
TGAAGAAAAAAAA
Found at i:4227 original size:15 final size:14
Alignment explanation
Indices: 4203--4271 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 14
4193 TATTATGCTT
*
4203 GAAG-AAAAAAAAT
1 GAAGAAAAAAAAAA
4216 GAAG-AAAAAAAAA
1 GAAGAAAAAAAAAA
4229 GAAGTAAAAAAAAAGGA
1 GAAG-AAAAAAAAA--A
*
4246 AAAGAAAGAAAAAAA
1 GAAGAAA-AAAAAAA
*
4261 AAAGAAAAAAA
1 GAAGAAAAAAA
4272 GAAAAAGGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
13 16 0.33
14 4 0.08
15 16 0.33
16 3 0.06
17 10 0.20
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (14 bp):
GAAGAAAAAAAAAA
Found at i:4237 original size:11 final size:11
Alignment explanation
Indices: 4204--4271 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
4194 ATTATGCTTG
4204 AAGAAAAAAAA
1 AAGAAAAAAAA
4215 TGAAGAAAAAAAAA
1 --AAG-AAAAAAAA
*
4229 GAAGTAAAAAAA
1 -AAGAAAAAAAA
* *
4241 AAG-GAAAAGA
1 AAGAAAAAAAA
4251 AAGAAAAAAAA
1 AAGAAAAAAAA
4262 AAGAAAAAAA
1 AAGAAAAAAA
4272 GAAAAAGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
10 8 0.17
11 18 0.38
12 7 0.15
13 7 0.15
14 8 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:4257 original size:19 final size:19
Alignment explanation
Indices: 4220--4277 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
4210 AAAAATGAAG
*
4220 AAAAA-AAAAGAAGTAAAAA
1 AAAAAGAAAAAAAG-AAAAA
*
4239 AAAAGGAAAAGAAAGAAAAA
1 AAAAAGAAAA-AAAGAAAAA
4259 AAAAAGAAAAAAAGAAAAA
1 AAAAAGAAAAAAAGAAAAA
4278 GGGGGGTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 13 0.38
20 18 0.53
21 3 0.09
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAAAAAGAAAAA
Found at i:4276 original size:14 final size:14
Alignment explanation
Indices: 4208--4278 Score: 65
Period size: 14 Copynumber: 5.0 Consensus size: 14
4198 TGCTTGAAGA
*
4208 AAAAAAATGAAGAA-
1 AAAAAAA-GAAAAAG
*
4222 AAAAAAAGAAGTAA-
1 AAAAAAAGAA-AAAG
*
4236 AAAAAAAGGAAAAG
1 AAAAAAAGAAAAAG
*
4250 AAAGAAAAAAAAAAG
1 AAA-AAAAGAAAAAG
4265 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
4279 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
13 5 0.10
14 31 0.65
15 12 0.25
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:4276 original size:15 final size:15
Alignment explanation
Indices: 4222--4277 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
4212 AAATGAAGAA
**
4222 AAAAAAAGAAGTAA-
1 AAAAAAAGAAAAAAG
*
4236 AAAAAAAG-GAAAAG
1 AAAAAAAGAAAAAAG
4250 AAAGAAAA-AAAAAAG
1 AAA-AAAAGAAAAAAG
4265 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
4278 GGGGGGTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 15 0.44
15 17 0.50
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:5512 original size:82 final size:86
Alignment explanation
Indices: 5412--5591 Score: 269
Period size: 82 Copynumber: 2.1 Consensus size: 86
5402 AATAGAACAA
* *
5412 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGT-TGGA-C-AGA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTATGAACCAAAA
5474 A-CAATCATTGAATTTAGAAG
66 ACCAATCATTGAATTTAGAAG
* *
5494 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGGTTTGGTATGAACCCAAA
1 ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTATGAA-CC-AA
*
5559 AAACCAATCATTGAATTTGGAAG
64 AAACCAATCATTGAATTTAGAAG
5582 ATGAATTTGC
1 ATGAATTTGC
5592 TCATAGTAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
82 52 0.60
83 3 0.03
85 1 0.01
87 3 0.03
88 28 0.32
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (86 bp):
ATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTATGAACCAAAA
ACCAATCATTGAATTTAGAAG
Found at i:6589 original size:113 final size:113
Alignment explanation
Indices: 6383--6938 Score: 949
Period size: 113 Copynumber: 5.0 Consensus size: 113
6373 CAAAGATTCA
* * *
6383 AATCTATCATTTGA-AGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA--TGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
6445 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
6493 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
6558 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
6606 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
6671 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
6719 AATCCATCATTTGAGGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
6784 AGGAAGAAGAAGTTCATAATTAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
6832 AATTCATCAATTGATGGATTATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
6896 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
6939 GCATAATTCT
Statistics
Matches: 429, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
110 13 0.03
111 40 0.09
112 70 0.16
113 306 0.71
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:7276 original size:3 final size:3
Alignment explanation
Indices: 7262--7373 Score: 179
Period size: 3 Copynumber: 37.3 Consensus size: 3
7252 TACCCATATC
* *
7262 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
7310 ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7358 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
7374 AATATATTAA
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:16066 original size:32 final size:32
Alignment explanation
Indices: 16016--16076 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
16006 GCATTGGGTG
* *
16016 CGGGAGCCTCAGTCACCATCGGCAACCCCCGA
1 CGGGAGCCTCAGTAACCATCGACAACCCCCGA
*
16048 CGGGTGCCTCAGTAACCATCGACAACCCC
1 CGGGAGCCTCAGTAACCATCGACAACCCC
16077 AGTCCATTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.43, G:0.23, T:0.11
Consensus pattern (32 bp):
CGGGAGCCTCAGTAACCATCGACAACCCCCGA
Found at i:25379 original size:31 final size:30
Alignment explanation
Indices: 25354--25412 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
25344 TATTAAAATT
*
25354 CCAATTATTTTCAATACTTATTATTAGGAAC
1 CCAATT-TTTTCAATACTTATTATTAGAAAC
*
25385 CCAATTTTTTCAATATTTATTATTAGAA
1 CCAATTTTTTCAATACTTATTATTAGAA
25413 GAATACTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.46
Consensus pattern (30 bp):
CCAATTTTTTCAATACTTATTATTAGAAAC
Found at i:26162 original size:20 final size:20
Alignment explanation
Indices: 26137--26186 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
26127 GGCCATGCAA
26137 TATTGATACTAATTCTA-GGG
1 TATTGATACTAATT-TATGGG
*
26157 TATTGATACTTATTTATGGG
1 TATTGATACTAATTTATGGG
*
26177 TATCGATACT
1 TATTGATACT
26187 GAAAATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (20 bp):
TATTGATACTAATTTATGGG
Found at i:26244 original size:20 final size:20
Alignment explanation
Indices: 26219--26268 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
26209 AAATTAGCAG
26219 GTATCGATACCCTCACCATA
1 GTATCGATACCCTCACCATA
*
26239 GTATCGATAACCTCACCATA
1 GTATCGATACCCTCACCATA
26259 GTATCGATAC
1 GTATCGATAC
26269 TCCCTTAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (20 bp):
GTATCGATACCCTCACCATA
Found at i:27783 original size:31 final size:31
Alignment explanation
Indices: 27748--27833 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
27738 ACTTAATGCG
* *
27748 TTTAGTACCTAAACTATCAGTTTTAGTTCGT
1 TTTAGTACCTAAACTTTCAATTTTAGTTCGT
27779 TTTAGTACCTAAACTTTCAATTTTAGTTCGT
1 TTTAGTACCTAAACTTTCAATTTTAGTTCGT
*
27810 TTTAGTAGCTAAACTTTCAATTTT
1 TTTAGTACCTAAACTTTCAATTTT
27834 TTAAAACTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (31 bp):
TTTAGTACCTAAACTTTCAATTTTAGTTCGT
Found at i:32282 original size:22 final size:23
Alignment explanation
Indices: 32257--32300 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
32247 TGCCAAATTT
*
32257 ATAAAATTATTT-TAAATAGAAA
1 ATAAAATTATTTATAAAAAGAAA
*
32279 ATAAATTTATTTATAAAAAGAA
1 ATAAAATTATTTATAAAAAGAA
32301 CCCAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
ATAAAATTATTTATAAAAAGAAA
Found at i:32581 original size:22 final size:23
Alignment explanation
Indices: 32539--32581 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
32529 AAAAAAATGA
* *
32539 GTTTTTAATTAATAATTTTAATT
1 GTTTTTAAATAATAATATTAATT
32562 GTTTTTAAATAA-AATATTAA
1 GTTTTTAAATAATAATATTAA
32582 AATTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
GTTTTTAAATAATAATATTAATT
Found at i:44887 original size:20 final size:20
Alignment explanation
Indices: 44862--45086 Score: 193
Period size: 20 Copynumber: 11.1 Consensus size: 20
44852 GTTGGAAATT
44862 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
44882 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
* ** **
44902 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGAT-TTTCCATTTC
44923 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
* * ** **
44943 GCGTTGCTATAGTTGAAAATC
1 GCGTTGCGAT-TTTCCATTTC
44964 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
* ** **
44984 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGAT-TTTCCATTTC
*
45005 GCGTTGCGATTTTTCATTTC
1 GCGTTGCGATTTTCCATTTC
* * * *
45025 GCATTGCGATAGTCTACA-AT-
1 GCGTTGCGAT--TTTCCATTTC
45045 GTCGTTGCGATTTTCCATTTC
1 G-CGTTGCGATTTTCCATTTC
45066 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
45086 G
1 G
45087 TATTGCGATA
Statistics
Matches: 157, Mismatches: 40, Indels: 16
0.74 0.19 0.08
Matches are distributed among these distances:
19 4 0.03
20 95 0.61
21 54 0.34
22 4 0.03
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
GCGTTGCGATTTTCCATTTC
Found at i:44925 original size:41 final size:41
Alignment explanation
Indices: 44880--45075 Score: 324
Period size: 41 Copynumber: 4.8 Consensus size: 41
44870 ATTTTCCATT
44880 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
44921 TCGCGTTGCGATTTTCCATTTCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
44962 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* * *
45003 TCGCGTTGCGATTTTTCATTTCGCATTGCGATAGTCT-ACAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAA
45044 T-GTCGTTGCGATTTTCCATTTCGCGTTGCGAT
1 TCG-CGTTGCGATTTTCCATTTCGCGTTGCGAT
45076 TTTCCATTTC
Statistics
Matches: 146, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 1 0.01
41 144 0.99
42 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:44926 original size:21 final size:21
Alignment explanation
Indices: 44900--45014 Score: 117
Period size: 21 Copynumber: 5.6 Consensus size: 21
44890 ATTTTCCATT
44900 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
44921 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
44941 TCGCGTTGCTATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
44962 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
44982 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
45003 TCGCGTTGCGAT
1 TCGCGTTGCGAT
45015 TTTTCATTTC
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 29 0.41
21 41 0.59
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:45099 original size:61 final size:60
Alignment explanation
Indices: 44835--45122 Score: 262
Period size: 61 Copynumber: 4.7 Consensus size: 60
44825 ATTCGAGTTT
44835 CATTTCGCATTGCGATAGTTGGA-AAT-TGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCATTGCGATAGTT--ACAATGT-CGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
* * * * *
44896 CATTTCGCGTTGCGATAGTTGAAAATCG-CGTTGCGATTTTCCATTTCGCGTTGCTATAGTTG
1 CATTTCGCATTGCGATAGTT-ACAAT-GTCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTC
* ** * * * * * ** ** *
44958 AAAATCGCGTTGCGAT--TTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCATTGCGATAGTTACAATGT--CGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
45019 CATTTCGCATTGCGATAGTCTACAATGTCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCATTGCGATAGT-TACAATGTCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
* *
45080 CATTTCGTATTGCGATAGTCTACAATGTCGTTGTGATTTTCCA
1 CATTTCGCATTGCGATAGT-TACAATGTCGTTGCGATTTTCCA
45123 AATTCGTTGC
Statistics
Matches: 182, Mismatches: 34, Indels: 22
0.76 0.14 0.09
Matches are distributed among these distances:
59 2 0.01
60 4 0.02
61 132 0.73
62 38 0.21
63 1 0.01
64 5 0.03
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (60 bp):
CATTTCGCATTGCGATAGTTACAATGTCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
Found at i:45225 original size:6 final size:6
Alignment explanation
Indices: 45214--45264 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
45204 GACACGTATT
45214 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
45262 ACC
1 ACC
45265 CAACCCGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:45764 original size:5 final size:5
Alignment explanation
Indices: 45750--45786 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
45740 CCGCCGCCGC
45750 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
45787 GGTCGTGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:45794 original size:6 final size:6
Alignment explanation
Indices: 45783--45807 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45773 TCGTCTCGTC
45783 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
45808 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:46291 original size:30 final size:28
Alignment explanation
Indices: 46255--46311 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
46245 AAATTATGCA
*
46255 TTTAGTACCTAAACTATCAATCTTGTTTCG
1 TTTAGTACATAAACTATC-AT-TTGTTTCG
*
46285 TTTAGTACATAAACTTTCATTTGTTTC
1 TTTAGTACATAAACTATCATTTGTTTC
46312 AAAACCATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 2 0.08
30 16 0.64
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (28 bp):
TTTAGTACATAAACTATCATTTGTTTCG
Found at i:49777 original size:19 final size:19
Alignment explanation
Indices: 49753--49789 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
49743 CGAGAGTATC
49753 TGAAAGGGGTAAAACAGTT
1 TGAAAGGGGTAAAACAGTT
*
49772 TGAAAGGGGTAAACCAGT
1 TGAAAGGGGTAAAACAGT
49790 ACAGATCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.32, T:0.19
Consensus pattern (19 bp):
TGAAAGGGGTAAAACAGTT
Found at i:50916 original size:58 final size:58
Alignment explanation
Indices: 50825--51104 Score: 404
Period size: 58 Copynumber: 4.9 Consensus size: 58
50815 TCAACTTTTC
* *
50825 CAAAAATAACACACTTACAGAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTA
1 CAAAAATAGCAC-CTAACAGAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTA
* * * * *
50884 CAAAAATAACACCTAGCAAAAATTAATTACCTATTAGGCA-CCTCTT-AAAATATGTA
1 CAAAAATAGCACCTAACAGAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTA
* *
50940 -AAAAATAGCACCTAACATAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTA
1 CAAAAATAGCACCTAACAGAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTA
* *
50997 CAAAAATTGCACCTAACAGAAATTAATTACTTATTAGGCACCCTTTTAAAAATATTTA
1 CAAAAATAGCACCTAACAGAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTA
* * *
51055 CAAAAATAGCACCTAACATAAATTAATCACTTATTAGGCACCCTTTTAAA
1 CAAAAATAGCACCTAACAGAAATTAATTACCTATTAGGCACCCTTTTAAA
51105 TTTTTTTATC
Statistics
Matches: 201, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
55 35 0.17
56 14 0.07
57 14 0.07
58 126 0.63
59 12 0.06
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (58 bp):
CAAAAATAGCACCTAACAGAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTA
Found at i:50976 original size:113 final size:116
Alignment explanation
Indices: 50825--51104 Score: 413
Period size: 113 Copynumber: 2.4 Consensus size: 116
50815 TCAACTTTTC
* * *
50825 CAAAAATAACACACTTACAGAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAA
1 CAAAAATAGCAC-CTAACATAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAA
*
50890 TAACACCTAGCAAAAATTAATTACCTATTAGGCA-CCTCTT-AAAATATGTA
65 TAACACCTAACAAAAATTAATTACCTATTAGGCACCCTCTTAAAAATATGTA
*
50940 -AAAAATAGCACCTAACATAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAAT
1 CAAAAATAGCACCTAACATAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAAT
** * * * *
51004 TGCACCTAACAGAAATTAATTACTTATTAGGCACCCTTTTAAAAATATTTA
66 AACACCTAACAAAAATTAATTACCTATTAGGCACCCTCTTAAAAATATGTA
* *
51055 CAAAAATAGCACCTAACATAAATTAATCACTTATTAGGCACCCTTTTAAA
1 CAAAAATAGCACCTAACATAAATTAATTACCTATTAGGCACCCTTTTAAA
51105 TTTTTTTATC
Statistics
Matches: 149, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
113 78 0.52
114 15 0.10
115 9 0.06
116 47 0.32
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (116 bp):
CAAAAATAGCACCTAACATAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAAT
AACACCTAACAAAAATTAATTACCTATTAGGCACCCTCTTAAAAATATGTA
Found at i:51066 original size:29 final size:29
Alignment explanation
Indices: 50976--51067 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
50966 TACGTATTAG
*
50976 GCACCCTTTTAAAAATATTTACAAAAATT
1 GCACCCTTTTAAAAATATTTACAAAAATA
*** * * ** *
51005 GCA-CCTAACAGAAATTAATTAC-TTATTA
1 GCACCCTTTTA-AAAATATTTACAAAAATA
51033 GGCACCCTTTTAAAAATATTTACAAAAATA
1 -GCACCCTTTTAAAAATATTTACAAAAATA
51063 GCACC
1 GCACC
51068 TAACATAAAT
Statistics
Matches: 42, Mismatches: 17, Indels: 8
0.63 0.25 0.12
Matches are distributed among these distances:
28 6 0.14
29 29 0.69
30 7 0.17
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (29 bp):
GCACCCTTTTAAAAATATTTACAAAAATA
Found at i:51686 original size:20 final size:20
Alignment explanation
Indices: 51661--51698 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51651 ACTTCATTTT
*
51661 TTTTATTCTTAGTGCTATTA
1 TTTTATTCATAGTGCTATTA
*
51681 TTTTATTCATATTGCTAT
1 TTTTATTCATAGTGCTAT
51699 AAGATATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (20 bp):
TTTTATTCATAGTGCTATTA
Found at i:55008 original size:58 final size:58
Alignment explanation
Indices: 54935--55202 Score: 407
Period size: 58 Copynumber: 4.7 Consensus size: 58
54925 CCCTTACAAT
* *
54935 AATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACGTAACAGA
1 AATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACCTAACAGA
* * * *
54993 AATTAATTACGTATTAGGCACCCTCTT-AAAATATGTA-AAAAATAGCACCTCACAGA
1 AATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACCTAACAGA
*
55049 AATTAGTTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACCTAACAGA
1 AATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACCTAACAGA
* *
55107 AATTAATTACTTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACCTAACATA
1 AATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACCTAACAGA
* *
55165 AATTAATCT-CTTATTAGGCACCCTTTTAAAACTATTTA
1 AATTAAT-TACGTATTAGGCACCCTTTTAAAAATATTTA
55203 TCAATAATCT
Statistics
Matches: 192, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
56 41 0.21
57 18 0.09
58 132 0.69
59 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (58 bp):
AATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAACACCTAACAGA
Found at i:55073 original size:114 final size:115
Alignment explanation
Indices: 54914--55202 Score: 413
Period size: 114 Copynumber: 2.5 Consensus size: 115
54904 TCAACTTTTC
*
54914 CAAAAATAGCACCCTTACAATAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAA
1 CAAAAATAGCA-CCTAACAA-AATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAA
*
54979 TAACACGTAACAGAAATTAATTACGTATTAGGCACCCTCTT-AAAATATGTA
64 TAACACCTAACAGAAATTAATTACGTATTAGGCACCCTCTTAAAAATATGTA
* * *
55030 -AAAAATAGCACCTCACAGAAATTAGTTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAAT
1 CAAAAATAGCACCTAACA-AAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAAT
* * *
55094 AACACCTAACAGAAATTAATTACTTATTAGGCACCCTTTTAAAAATATTTA
65 AACACCTAACAGAAATTAATTACGTATTAGGCACCCTCTTAAAAATATGTA
* * *
55145 CAAAAATAACACCTAACATAAATTAATCT-CTTATTAGGCACCCTTTTAAAACTATTTA
1 CAAAAATAGCACCTAACA-AAATTAAT-TACCTATTAGGCACCCTTTTAAAAATATTTA
55203 TCAATAATCT
Statistics
Matches: 156, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
114 86 0.55
115 20 0.13
116 49 0.31
117 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (115 bp):
CAAAAATAGCACCTAACAAAATTAATTACCTATTAGGCACCCTTTTAAAAATATTTACAAAAATA
ACACCTAACAGAAATTAATTACGTATTAGGCACCCTCTTAAAAATATGTA
Found at i:62525 original size:74 final size:74
Alignment explanation
Indices: 62435--62586 Score: 254
Period size: 74 Copynumber: 2.1 Consensus size: 74
62425 TAAAAAAATA
* *
62435 GTTAAAAGCTATTGATCGAGAAATAA-GCA-TTGGTATTCGCAATTAACACCTTGCCGCAGAAGA
1 GTTAAAAGCTAATGATCGAGAAATAACG-AGTTGGTA-TCGCAATTAACACCTTACCGCAGAAGA
62498 ATCACTATGTC
64 ATCACTATGTC
62509 GTTAAAAGCTAATGATCGAGAAATAACGAGTTGGTATCGCAATTAACACCTTACCGCAGAAGAAT
1 GTTAAAAGCTAATGATCGAGAAATAACGAGTTGGTATCGCAATTAACACCTTACCGCAGAAGAAT
62574 CACTATGTC
66 CACTATGTC
62583 GTTA
1 GTTA
62587 TGATATCATT
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
74 67 0.91
75 7 0.09
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (74 bp):
GTTAAAAGCTAATGATCGAGAAATAACGAGTTGGTATCGCAATTAACACCTTACCGCAGAAGAAT
CACTATGTC
Found at i:63423 original size:68 final size:68
Alignment explanation
Indices: 63314--63451 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
63304 CTTGTTGATA
63314 AATATGTCTCTTCATCTTATTACAGTAAAGTGAACCACAAGAAACCTCCCAACTATAACCTTTGT
1 AATATGTCTCTTCATCTTATTACAGTAAAGTGAACCACAAGAAACCTCCCAACTATAACCTTTGT
63379 GTC
66 GTC
63382 AATATGTCTCTTCATCTTATTACAGTAAAGTGAACCACAAGAAACCTCCCAACTATAACCTTTGT
1 AATATGTCTCTTCATCTTATTACAGTAAAGTGAACCACAAGAAACCTCCCAACTATAACCTTTGT
63447 GTC
66 GTC
63450 AA
1 AA
63452 CAAACATAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (68 bp):
AATATGTCTCTTCATCTTATTACAGTAAAGTGAACCACAAGAAACCTCCCAACTATAACCTTTGT
GTC
Found at i:67084 original size:23 final size:22
Alignment explanation
Indices: 67040--67090 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
67030 ATGAGAATGT
*
67040 AATATT-TTTTATTCAACTTAA
1 AATATTATCTTATTCAACTTAA
*
67061 AATATTATCTTATTTAACCTTAA
1 AATATTATCTTATTCAA-CTTAA
*
67084 AAAATTA
1 AATATTA
67091 CTTTATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.24
22 8 0.32
23 11 0.44
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATTATCTTATTCAACTTAA
Found at i:67096 original size:23 final size:21
Alignment explanation
Indices: 67047--67097 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
67037 TGTAATATTT
*
67047 TTTATTCAACTTAAAATATTA
1 TTTATTCAACTTAAAAAATTA
*
67068 TCTTATTTAACCTTAAAAAATTA
1 T-TTATTCAA-CTTAAAAAATTA
67091 CTTTATT
1 -TTTATT
67098 AATAAATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 7 0.28
23 16 0.64
24 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTATTCAACTTAAAAAATTA
Found at i:69568 original size:71 final size:71
Alignment explanation
Indices: 69452--69590 Score: 278
Period size: 71 Copynumber: 2.0 Consensus size: 71
69442 TTATTAGGGG
69452 TTGAATTAGGTTCATACACATGAAAAGCACAATTCAATAGACCATTTTGCTTTCATAACCAAATT
1 TTGAATTAGGTTCATACACATGAAAAGCACAATTCAATAGACCATTTTGCTTTCATAACCAAATT
69517 CATCGT
66 CATCGT
69523 TTGAATTAGGTTCATACACATGAAAAGCACAATTCAATAGACCATTTTGCTTTCATAACCAAATT
1 TTGAATTAGGTTCATACACATGAAAAGCACAATTCAATAGACCATTTTGCTTTCATAACCAAATT
69588 CAT
66 CAT
69591 ACATCGTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (71 bp):
TTGAATTAGGTTCATACACATGAAAAGCACAATTCAATAGACCATTTTGCTTTCATAACCAAATT
CATCGT
Found at i:72641 original size:17 final size:17
Alignment explanation
Indices: 72619--72676 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
72609 CAAGAGCCCT
*
72619 AGGGGTGGCACTTTTTG
1 AGGGGTGACACTTTTTG
72636 AGGGGTGACACTTGTATT-
1 AGGGGTGACACTT-T-TTG
* *
72654 AGGGGTGACACTTGTGG
1 AGGGGTGACACTTTTTG
72671 AGGGGT
1 AGGGGT
72677 TGTTTGGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 18 0.51
18 14 0.40
19 2 0.06
ACGTcount: A:0.17, C:0.10, G:0.43, T:0.29
Consensus pattern (17 bp):
AGGGGTGACACTTTTTG
Found at i:72659 original size:18 final size:17
Alignment explanation
Indices: 72618--72668 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
72608 GCAAGAGCCC
*
72618 TAGGGGTGGCACTT-TT
1 TAGGGGTGACACTTGTT
72634 TGAGGGGTGACACTTGTAT
1 T-AGGGGTGACACTTGT-T
72653 TAGGGGTGACACTTGT
1 TAGGGGTGACACTTGT
72669 GGAGGGGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 12 0.39
18 16 0.52
19 2 0.06
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (17 bp):
TAGGGGTGACACTTGTT
Found at i:76760 original size:23 final size:23
Alignment explanation
Indices: 76734--76778 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
76724 CACCACAGCT
*
76734 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
76757 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
76779 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:77413 original size:19 final size:20
Alignment explanation
Indices: 77376--77413 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
77366 TTTTTATACA
*
77376 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
77396 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
77414 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:77464 original size:21 final size:21
Alignment explanation
Indices: 77440--77482 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
77430 TTCATATTCG
* *
77440 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
77461 TTGAATGTGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
77482 T
1 T
77483 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:83540 original size:23 final size:23
Alignment explanation
Indices: 83514--83558 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
83504 CACCACAGCT
*
83514 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
83537 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
83559 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:84278 original size:21 final size:21
Alignment explanation
Indices: 84254--84296 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
84244 TTCATATTCG
* *
84254 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
84275 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
84296 T
1 T
84297 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:90988 original size:33 final size:31
Alignment explanation
Indices: 90951--91038 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 31
90941 CCCATGTGCA
*
90951 AAGTTGACCACCTACCAAAGATTAATTTCCAAT
1 AAGTTGGCCACCTACCAAAGATT--TTTCCAAT
90984 AAGTTGGCCA-CTAACCAAGATGATTTTTCCAAT
1 AAGTTGGCCACCT-ACCAA-A-GATTTTTCCAAT
*
91017 AAGTTGGCCACCAACCAAAGAT
1 AAGTTGGCCACCTACCAAAGAT
91039 GTCAACTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
31 3 0.06
32 3 0.06
33 37 0.76
34 2 0.04
35 4 0.08
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (31 bp):
AAGTTGGCCACCTACCAAAGATTTTTCCAAT
Found at i:95696 original size:34 final size:35
Alignment explanation
Indices: 95652--95734 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 35
95642 GCAAAATTGG
* * *
95652 CCACCTACCAAAGATGAA-TTTTCCAATAAGTTGA
1 CCACCAACCAAAGATGAATTTTTCCAATAAATTAA
95686 CCACCAACC-AAGAT-AATTTTTCCAATAAATTAA
1 CCACCAACCAAAGATGAATTTTTCCAATAAATTAA
*
95719 CCATCAACCAAAGATG
1 CCACCAACCAAAGATG
95735 TCAACTTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 2 0.05
33 27 0.64
34 13 0.31
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.24
Consensus pattern (35 bp):
CCACCAACCAAAGATGAATTTTTCCAATAAATTAA
Found at i:106084 original size:18 final size:18
Alignment explanation
Indices: 106061--106175 Score: 86
Period size: 22 Copynumber: 5.8 Consensus size: 18
106051 ACTGCATATT
*
106061 TGTCCCGAATGACCATTA
1 TGTCCCGAAGGACCATTA
*
106079 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCA-TTA
* ** *
106098 TTGTTCCGAAAAACCACTA
1 -TGTCCCGAAGGACCATTA
106117 TGTCCCGAAGGACCATTGTATA
1 TGTCCCGAAGGACCA---T-TA
106139 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCA---T-TA
106161 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
106176 CTCCTTAAGA
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
18 26 0.33
19 3 0.04
20 12 0.15
22 38 0.48
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCATTA
Found at i:106107 original size:38 final size:39
Alignment explanation
Indices: 106060--106177 Score: 130
Period size: 38 Copynumber: 2.9 Consensus size: 39
106050 CACTGCATAT
*
106060 TTGTCCCGAATGACCATTATGTCCCGAAGGACCACTG-A
1 TTGTCCCGAAAGACCATTATGTCCCGAAGGACCACTGTA
* * * *
106098 TTGTTCCGAAAAACCACTATGTCCCGAAGGACCATTGTA
1 TTGTCCCGAAAGACCATTATGTCCCGAAGGACCACTGTA
*
106137 TATGTCCCGAAGGACCACTGTATATGTCCCGAAGGACCACT
1 T-TGTCCCGAAAGACCA---T-TATGTCCCGAAGGACCACT
106178 CCTTAAGAAC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
38 32 0.50
39 2 0.03
40 12 0.19
44 18 0.28
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
TTGTCCCGAAAGACCATTATGTCCCGAAGGACCACTGTA
Found at i:106143 original size:22 final size:22
Alignment explanation
Indices: 106077--106177 Score: 124
Period size: 22 Copynumber: 4.9 Consensus size: 22
106067 GAATGACCAT
106077 TATGTCCCGAAGGACCACTG-A
1 TATGTCCCGAAGGACCACTGTA
* **
106098 T-TGTTCCGAAAAACCAC----
1 TATGTCCCGAAGGACCACTGTA
*
106115 TATGTCCCGAAGGACCATTGTA
1 TATGTCCCGAAGGACCACTGTA
106137 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
106159 TATGTCCCGAAGGACCACT
1 TATGTCCCGAAGGACCACT
106178 CCTTAAGAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
17 1 0.01
18 12 0.18
20 13 0.19
21 1 0.01
22 40 0.60
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:106431 original size:24 final size:21
Alignment explanation
Indices: 106375--106432 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
106365 ATATCTTCTC
106375 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
106397 ATTTCAC-TTCATATACACACATGT
1 A--TCACTTTCATATA-A-ACATGT
106421 GATCACTTTCAT
1 -ATCACTTTCAT
106433 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 15 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:111005 original size:25 final size:25
Alignment explanation
Indices: 110955--111005 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
110945 TAAAATTTAT
**
110955 AAAATTTTAAAGAAAATAAACTTAA
1 AAAATTTTAAAGAAAATAAAAATAA
*
110980 AAAATTTTATAGAAAA-AGAAAATAA
1 AAAATTTTAAAGAAAATA-AAAATAA
111005 A
1 A
111006 TTACTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (25 bp):
AAAATTTTAAAGAAAATAAAAATAA
Found at i:113290 original size:10 final size:10
Alignment explanation
Indices: 113270--113323 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
113260 CATTTAAATG
*
113270 ATAAACAAAC
1 ATAAACGAAC
*
113280 ACAAACGAAC
1 ATAAACGAAC
113290 ATAAACGGAAAC
1 ATAAAC-G-AAC
113302 AATAAACGAAC
1 -ATAAACGAAC
113313 ATAAACGAAC
1 ATAAACGAAC
113323 A
1 A
113324 ACATAAACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 24 0.63
11 4 0.11
12 4 0.11
13 6 0.16
ACGTcount: A:0.63, C:0.20, G:0.09, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:113329 original size:23 final size:22
Alignment explanation
Indices: 113276--113331 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
113266 AATGATAAAC
* *
113276 AAACACAAACGAACATAAACGG
1 AAACATAAACGAACATAAACGA
113298 AAACAATAAACGAACATAAACGA
1 AAAC-ATAAACGAACATAAACGA
113321 ACAACATAAAC
1 A-AACATAAAC
113332 ACACAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 4 0.13
23 23 0.77
24 3 0.10
ACGTcount: A:0.62, C:0.21, G:0.09, T:0.07
Consensus pattern (22 bp):
AAACATAAACGAACATAAACGA
Found at i:115290 original size:75 final size:75
Alignment explanation
Indices: 115162--115326 Score: 240
Period size: 75 Copynumber: 2.2 Consensus size: 75
115152 TACCCATGGA
* * *
115162 TCCATTTTGAGAAGCTTGCTGGTCAATTCTATTATCTTCTCGAAGCCAACTGTTGGGAAATGAGA
1 TCCATTTTCAGAAGCCTGCTGGTCAATTCTATTATCATCTCGAAGCCAACTGTTGGGAAATGAGA
*
115227 CACCATTGGG
66 CACCATTGGC
* * * * * *
115237 TCCATTTTCAGAATCCTGCTGGTTAATTCTATTATCATCTTGAAGCCAGCTGTTGGTAAATGATA
1 TCCATTTTCAGAAGCCTGCTGGTCAATTCTATTATCATCTCGAAGCCAACTGTTGGGAAATGAGA
115302 CACCATTGGC
66 CACCATTGGC
115312 TCCATTTTCAGAAGC
1 TCCATTTTCAGAAGC
115327 TTTTGAAGCC
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.34
Consensus pattern (75 bp):
TCCATTTTCAGAAGCCTGCTGGTCAATTCTATTATCATCTCGAAGCCAACTGTTGGGAAATGAGA
CACCATTGGC
Found at i:115358 original size:53 final size:53
Alignment explanation
Indices: 115276--115381 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
115266 TATTATCATC
* * *
115276 TTGAAGCCAGCTGTTGGTAAATGATACACCATTGGCTCCATTTTCAGAAGCTT
1 TTGAAGCCAACTGTTGGGAAATGAAACACCATTGGCTCCATTTTCAGAAGCTT
* *
115329 TTGAAGCCAACTGTTGGGAAATGAAACACCATTGGGTCCATTTTGAGAAGCTT
1 TTGAAGCCAACTGTTGGGAAATGAAACACCATTGGCTCCATTTTCAGAAGCTT
115382 GCCGATCATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (53 bp):
TTGAAGCCAACTGTTGGGAAATGAAACACCATTGGCTCCATTTTCAGAAGCTT
Found at i:115433 original size:128 final size:128
Alignment explanation
Indices: 115203--115455 Score: 323
Period size: 128 Copynumber: 2.0 Consensus size: 128
115193 TTATCTTCTC
* * * *
115203 GAAGCCAACTGTTGGGAAATGAGACACCATTGGGTCCATTTTCAGAATCCTGCTGGTTAATTCTA
1 GAAGCCAACTGTTGGGAAATGAAACACCATTGGGTCCATTTTCAGAAGCCTGCTCGATAATTCTA
* * * * * *
115268 TTATCATCTTGAAGCCAGCTGTTGGTAAATGATACACCATTGGCTCCATTTTCAGAAGCTTTT
66 TGATCACCTTGAAGCCAACTGTTGGGAAATGAGACACCAGTGGCTCCATTTTCAGAAGCTTTT
* * *
115331 GAAGCCAACTGTTGGGAAATGAAACACCATTGGGTCCATTTTGAGAAGCTTGC-CGATCATTGGC
1 GAAGCCAACTGTTGGGAAATGAAACACCATTGGGTCCATTTTCAGAAGCCTGCTCGATAATT--C
* *
115395 -ATGATC-CCGTTGAAGCCAATTGTTGGGAAATGAGACACCAGTGGCTCCATTTTGAGAAGCT
64 TATGATCACC-TTGAAGCCAACTGTTGGGAAATGAGACACCAGTGGCTCCATTTTCAGAAGCT
115456 AGCTGATCAT
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
127 6 0.06
128 100 0.93
129 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (128 bp):
GAAGCCAACTGTTGGGAAATGAAACACCATTGGGTCCATTTTCAGAAGCCTGCTCGATAATTCTA
TGATCACCTTGAAGCCAACTGTTGGGAAATGAGACACCAGTGGCTCCATTTTCAGAAGCTTTT
Found at i:115650 original size:3 final size:3
Alignment explanation
Indices: 115642--115692 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
115632 TGCTAGGGCT
115642 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
115690 TTA
1 TTA
115693 CGTTTGGCCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:127836 original size:24 final size:26
Alignment explanation
Indices: 127794--127841 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
127784 GAACTCAAAA
127794 AAAATTTAGAAGTTCGATTGAAGTCT
1 AAAATTTAGAAGTTCGATTGAAGTCT
*
127820 AAAATTT-G-AGTTTGATTGAAGT
1 AAAATTTAGAAGTTCGATTGAAGT
127842 GAAAAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 1 0.05
26 7 0.33
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (26 bp):
AAAATTTAGAAGTTCGATTGAAGTCT
Found at i:127847 original size:24 final size:26
Alignment explanation
Indices: 127793--127847 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
127783 TGAACTCAAA
127793 AAAAATTTAGAAGTTCGATTGAAGTC
1 AAAAATTTAGAAGTTCGATTGAAGTC
* * *
127819 TAAAATTT-G-AGTTTGATTGAAGTG
1 AAAAATTTAGAAGTTCGATTGAAGTC
127843 AAAAA
1 AAAAA
127848 ATAGTTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 17 0.68
25 1 0.04
26 7 0.28
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.33
Consensus pattern (26 bp):
AAAAATTTAGAAGTTCGATTGAAGTC
Found at i:128217 original size:22 final size:22
Alignment explanation
Indices: 128185--128226 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
128175 TATAAAAAAT
128185 TATTTGTTATTAAATATTTTTGG
1 TATTTGTTATTAAAT-TTTTTGG
*
128208 TATTT-TTATTTAATTTTTT
1 TATTTGTTATTAAATTTTTT
128227 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TATTTGTTATTAAATTTTTTGG
Found at i:128555 original size:20 final size:20
Alignment explanation
Indices: 128508--128749 Score: 294
Period size: 20 Copynumber: 11.8 Consensus size: 20
128498 TGACCAACAA
128508 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
128530 AATCGCAATGCGATT-CATAA
1 AATCGCAACGCGATTCCA-AG
128550 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
*
128572 AATCGCAACGCGATT-CAGAA
1 AATCGCAACGCGATTCCA-AG
128592 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
*
128612 AATCGCGACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
*
128634 AATCGCAACGCGATTCCAAA
1 AATCGCAACGCGATTCCAAG
*
128654 AATCGCAACGCGATT-AAGAG
1 AATCGCAACGCGATTCCA-AG
128674 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
*
128694 AATCGCAACGCGATT-CAGAA
1 AATCGCAACGCGATTCCA-AG
128714 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
*
128734 AATTGCAACGCGATTC
1 AATCGCAACGCGATTC
128750 AGAAAATGAG
Statistics
Matches: 193, Mismatches: 15, Indels: 26
0.82 0.06 0.11
Matches are distributed among these distances:
19 7 0.04
20 132 0.68
21 5 0.03
22 47 0.24
23 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:128607 original size:62 final size:62
Alignment explanation
Indices: 128508--128747 Score: 330
Period size: 62 Copynumber: 3.9 Consensus size: 62
128498 TGACCAACAA
* * *
128508 AATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT-CATAAAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGATCTTCCAAG
*
128572 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCCAAGAATCGCGACGCGATCTTCCAAG
1 AATCGCAACGCGATTCCA-AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCCAAG
*
128634 AATCGCAACGCGATTCCAAAAATCGCAACGCGATT-AAGAGAATCGCAACGCGA--TTCCAAG
1 AATCGCAACGCGATTCCAAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGATCTTCCAAG
*
128694 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCCAAGAATTGCAACGCGAT
1 AATCGCAACGCGATTCCA-AAAATCGCAACGCGATTCCAAGAATCGCAACGCGAT
128748 TCAGAAAATG
Statistics
Matches: 161, Mismatches: 8, Indels: 17
0.87 0.04 0.09
Matches are distributed among these distances:
59 2 0.01
60 53 0.33
61 4 0.02
62 85 0.53
63 4 0.02
64 13 0.08
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.17
Consensus pattern (62 bp):
AATCGCAACGCGATTCCAAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCCAAG
Found at i:128623 original size:40 final size:40
Alignment explanation
Indices: 128506--128756 Score: 360
Period size: 40 Copynumber: 6.1 Consensus size: 40
128496 AATGACCAAC
* *
128506 AAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAG
128548 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAG
*
128590 AAAATCGCAACGCGATTCCAAGAATCGCGACGCGATCTTCCA-
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGA--TT-CAG
* * *
128632 AGAATCGCAACGCGATTCCAAAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
*
128672 AGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
*
128712 AAAATCGCAACGCGATTCCAAGAATTGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
128752 AAAAT
1 AAAAT
128757 GAGTAAATTC
Statistics
Matches: 194, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
39 1 0.01
40 102 0.53
42 89 0.46
43 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
Found at i:128863 original size:6 final size:6
Alignment explanation
Indices: 128852--128900 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
128842 GACACGTATT
128852 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
128898 ACC
1 ACC
128901 CGAGACGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:129548 original size:20 final size:20
Alignment explanation
Indices: 129523--129780 Score: 276
Period size: 20 Copynumber: 12.8 Consensus size: 20
129513 TCATTTTCTG
129523 AATCGCGTTGCGATTCTCTT
1 AATCGCGTTGCGATTCTCTT
* *
129543 AATCGCGTTGCGATTTTCTG
1 AATCGCGTTGCGATTCTCTT
*
129563 AATCGCGTTGCGATTCT-TGG
1 AATCGCGTTGCGATTCTCT-T
129583 AATCGCGTTGCGATTCTCTT
1 AATCGCGTTGCGATTCTCTT
129603 AATCGCGTTGCGATTCTCTT
1 AATCGCGTTGCGATTCTCTT
*
129623 AATCGCGTTGCGATTCTCTG
1 AATCGCGTTGCGATTCTCTT
*
129643 AATCGCGTTGCGATTCT-TGGA
1 AATCGCGTTGCGATTCTCT--T
129664 AGATCGCGTTGCGATTCTCTT
1 A-ATCGCGTTGCGATTCTCTT
* *
129685 AATCGCATTGCGATTCT-TGGA
1 AATCGCGTTGCGATTCTCT--T
*
129706 ATATCGCGTTGCGATTTTCTT
1 A-ATCGCGTTGCGATTCTCTT
* * * *
129727 -TTCAACGTTGCGATTTTCTA
1 AATC-GCGTTGCGATTCTCTT
*
129747 AATCGCGTTGCGATT-T-TG
1 AATCGCGTTGCGATTCTCTT
129765 ATATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
129781 TTGTTGGTCA
Statistics
Matches: 207, Mismatches: 18, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.01
19 20 0.10
20 147 0.71
21 6 0.03
22 30 0.14
23 2 0.01
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTCTT
Found at i:129615 original size:60 final size:59
Alignment explanation
Indices: 129521--129780 Score: 328
Period size: 60 Copynumber: 4.3 Consensus size: 59
129511 ACTCATTTTC
* *
129521 TGAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCT
1 TGAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCT
129580 TGGAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCT
1 T-GAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCT
* *
129640 CTGAATCGCGTTGCGATTCT-TGGAAGATCGCGTTGCGATTCTCTTAATCGCATTGCGATTCT
1 -TGAATCGCGTTGCGATTCTCT--TA-ATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCT
* * * * *
129702 TGGAATATCGCGTTGCGATTTTCTT-TTCAACGTTGCGATTTTCTAAATCGCGTTGCGATT-T
1 T-G-A-ATCGCGTTGCGATTCTCTTAATC-GCGTTGCGATTCTCTTAATCGCGTTGCGATTCT
129763 TGATATCGCGTTGCGATT
1 TGA-ATCGCGTTGCGATT
129781 TTGTTGGTCA
Statistics
Matches: 180, Mismatches: 11, Indels: 20
0.85 0.05 0.09
Matches are distributed among these distances:
59 18 0.10
60 75 0.42
61 7 0.04
62 63 0.35
63 1 0.01
64 15 0.08
65 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (59 bp):
TGAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCTCTTAATCGCGTTGCGATTCT
Found at i:137501 original size:20 final size:20
Alignment explanation
Indices: 137476--137536 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
137466 TTTTGGTGTA
*
137476 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
137496 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
137517 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
137537 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:139205 original size:12 final size:12
Alignment explanation
Indices: 139190--139218 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
139180 AGATGAGCCT
139190 GAGCAGCCCGAG
1 GAGCAGCCCGAG
139202 GAGCAGCCCGAG
1 GAGCAGCCCGAG
139214 GAGCA
1 GAGCA
139219 AGCACAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:142094 original size:24 final size:23
Alignment explanation
Indices: 142067--142154 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 23
142057 TTATGTTATA
*
142067 ATACCTGACCTGGATTCTGATAGG
1 ATACTTGACCTGGATTCTGATA-G
142091 ATACTTGACCTGGATTCTGATCAG
1 ATACTTGACCTGGATTCTGAT-AG
* *
142115 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGAT-AG
142139 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
142155 ATGTTTTGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
24 59 0.98
25 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (23 bp):
ATACTTGACCTGGATTCTGATAG
Found at i:142146 original size:12 final size:13
Alignment explanation
Indices: 142089--142153 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 13
142079 GATTCTGATA
142089 GGATACTTGACCT
1 GGATACTTGACCT
* *
142102 GGATTC-TGATC-
1 GGATACTTGACCT
*
142113 AGATACTTGACCT
1 GGATACTTGACCT
* *
142126 GGAT-TTTGATCT
1 GGATACTTGACCT
142138 -GATACTTGACCT
1 GGATACTTGACCT
142150 GGAT
1 GGAT
142154 TATGTTTTGA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
11 7 0.18
12 20 0.53
13 11 0.29
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (13 bp):
GGATACTTGACCT
Found at i:143205 original size:18 final size:18
Alignment explanation
Indices: 143184--143220 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
143174 TTAGAACTCG
143184 TAAGATCAAAAGAAATGA
1 TAAGATCAAAAGAAATGA
* *
143202 TAAGATCTAAAGAAGTGA
1 TAAGATCAAAAGAAATGA
143220 T
1 T
143221 CAAATGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (18 bp):
TAAGATCAAAAGAAATGA
Found at i:143336 original size:16 final size:15
Alignment explanation
Indices: 143317--143373 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
143307 AATTTATTTA
143317 ATTTTTTAAAAAATCT
1 ATTTTTTAAAAAAT-T
**
143333 ATTTTTGTAACCAATT
1 ATTTTT-TAAAAAATT
*
143349 TTTTTTTAAAATAATT
1 ATTTTTTAAAA-AATT
143365 ATTTTTTAA
1 ATTTTTTAA
143374 TAATATAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 3 0.09
16 24 0.73
17 6 0.18
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTTTTAAAAAATT
Found at i:144737 original size:14 final size:15
Alignment explanation
Indices: 144699--144739 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
144689 GTTTTTTCGG
144699 TTCGGTTCGGGTTTT
1 TTCGGTTCGGGTTTT
144714 TTAACGGTTCGGG-TTT
1 TT--CGGTTCGGGTTTT
144730 TTCGGTTCGG
1 TTCGGTTCGG
144740 TTCGGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 5 0.21
17 9 0.38
ACGTcount: A:0.05, C:0.15, G:0.34, T:0.46
Consensus pattern (15 bp):
TTCGGTTCGGGTTTT
Found at i:144748 original size:17 final size:18
Alignment explanation
Indices: 144692--144750 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
144682 GAAACCGGTT
144692 TTTTCGGTTCGGTTCGGG
1 TTTTCGGTTCGGTTCGGG
144710 TTTT---TTAACGGTTCGGG
1 TTTTCGGTT--CGGTTCGGG
*
144727 TTTTTCGGTTCGGTTCGGT
1 -TTTTCGGTTCGGTTCGGG
144746 TTTTC
1 TTTTC
144751 AATGAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
15 2 0.06
17 9 0.26
18 13 0.38
19 8 0.24
21 2 0.06
ACGTcount: A:0.03, C:0.15, G:0.31, T:0.51
Consensus pattern (18 bp):
TTTTCGGTTCGGTTCGGG
Found at i:147666 original size:5 final size:5
Alignment explanation
Indices: 147656--147695 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
147646 CCACTTCCAC
147656 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTGA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTT
147696 TTTCAATAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:150920 original size:27 final size:27
Alignment explanation
Indices: 150890--150944 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
150880 GTAGCACCAC
150890 AGGATGATAATCACACCAAAATGACTA
1 AGGATGATAATCACACCAAAATGACTA
150917 AGGATGATAATCACACCAAAATGACTA
1 AGGATGATAATCACACCAAAATGACTA
150944 A
1 A
150945 CTTCTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (27 bp):
AGGATGATAATCACACCAAAATGACTA
Found at i:152728 original size:34 final size:34
Alignment explanation
Indices: 152690--152776 Score: 165
Period size: 34 Copynumber: 2.6 Consensus size: 34
152680 AAAGGGGTCG
*
152690 AATGGTTTTCAAAGTTTGGCACCACACTTTGAAA
1 AATGGTTTTCAAAGTTTGGCACCAAACTTTGAAA
152724 AATGGTTTTCAAAGTTTGGCACCAAACTTTGAAA
1 AATGGTTTTCAAAGTTTGGCACCAAACTTTGAAA
152758 AATGGTTTTCAAAGTTTGG
1 AATGGTTTTCAAAGTTTGG
152777 TTAATGTATG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (34 bp):
AATGGTTTTCAAAGTTTGGCACCAAACTTTGAAA
Found at i:158919 original size:23 final size:22
Alignment explanation
Indices: 158878--158920 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
158868 TTTATAATTT
*
158878 TATGAAAATATATTAATTTAAA
1 TATGAAAAGATATTAATTTAAA
*
158900 TATGAATAAGATATTTATTTA
1 TATGAA-AAGATATTAATTTA
158921 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (22 bp):
TATGAAAAGATATTAATTTAAA
Found at i:160546 original size:3 final size:3
Alignment explanation
Indices: 160528--160603 Score: 63
Period size: 3 Copynumber: 26.7 Consensus size: 3
160518 ATGTAATATG
* * * *
160528 TAA TAA TAT TAT TAA TAA TAA -AA -AA T-A TAA TAA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
160573 TAA TAA TAA TAC TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
160604 TTCAAATAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
2 10 0.17
3 48 0.80
4 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:161129 original size:123 final size:118
Alignment explanation
Indices: 160911--161569 Score: 698
Period size: 113 Copynumber: 5.6 Consensus size: 118
160901 AAAAAAATTA
* * *
160911 AACAAGTTCTTCTCATTATGAACATCTTCTT--TTACTTCAGATGGGTTCTTCTCATTATGAACT
1 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTT-CTTCAGATGAGTTCTTCTCATTATGAACT
* ** ** **
160974 TCTCTGGAAAAGTTTATGTTGATCTATCTCCTTCTGTAATACAGTCATGCAAAAGG-TTG
65 TCTCTGGAAAAG-TTATGTTGATCCATCTAATGATG-AAT----TCAAACAAAAGGTTTG
* *
161033 AACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACTT
1 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
* ** * **
161098 CTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTG-TGATAGAGTCATGCAAAAGG-TTG
66 CTCTGGAAAAGTT-ATGTTGATCCA--T-CTAATGATG--A-ATTCAAACAAAAGGTTTG
* *
161156 AACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTT
1 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
*
161221 CTCTGG-AAA---A-GTTGATCCATCGAATGATGAATTCAAACAAAAGGTTTG
66 CTCTGGAAAAGTTATGTTGATCCATCTAATGATGAATTCAAACAAAAGGTTTG
* **
161269 AACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTTTGATGAGTTCTTCTCATTATGAACT
1 AACAAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
161333 TCTCTGG-AAA---A-GTTGATCCATCAAATGATGAATTCAAACAAAAGGTTTG
65 TCTCTGGAAAAGTTATGTTGATCCATCTAATGATGAATTCAAACAAAAGGTTTG
* * *
161382 AATAAATTCTTCTCATTATGAA-TTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AACAAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
161446 TCTCTGG-AAA---A-GTTGATCCATCGAATGATGAATTCAAACAAAAGGTTTG
65 TCTCTGGAAAAGTTATGTTGATCCATCTAATGATGAATTCAAACAAAAGGTTTG
* * *
161495 AACAAATTCTTCTCATTATGAA-TTTATTCTTCATTCTTCATATGAGTTCTTCTCATTATGAACT
1 AACAAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
*
161559 CTTTCTGGAAA
65 -TCTCTGGAAA
161570 TGTTGATCCA
Statistics
Matches: 490, Mismatches: 34, Indels: 33
0.88 0.06 0.06
Matches are distributed among these distances:
112 14 0.03
113 274 0.56
114 9 0.02
115 5 0.01
117 8 0.02
118 1 0.00
122 33 0.07
123 134 0.27
124 2 0.00
125 3 0.01
126 6 0.01
127 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (118 bp):
AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
CTCTGGAAAAGTTATGTTGATCCATCTAATGATGAATTCAAACAAAAGGTTTG
Found at i:161299 original size:113 final size:113
Alignment explanation
Indices: 161146--161594 Score: 731
Period size: 113 Copynumber: 4.0 Consensus size: 113
161136 TAGAGTCATG
** *
161146 CAAAAGG-TTGAACAAGCTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTTTTCT
1 CAAAAGGTTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
161209 CATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
65 CATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
**
161258 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTTTGATGAGTTCTTCTC
1 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
161323 ATTATGAACTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAA
66 ATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
* *
161371 CAAAAGGTTTGAATAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
161436 ATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
66 ATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
* * *
161484 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTATTCTTCATTCTTCATATGAGTTCTTCTC
1 CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
161549 ATTATGAACTCTTTCTGGAAATGTTGATCCATCGAATAATGGATTC
66 ATTATGAACT-TCTCTGGAAAAGTTGATCCATCGAATGATGAATTC
161595 GAATCTTTGC
Statistics
Matches: 314, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
112 10 0.03
113 273 0.87
114 31 0.10
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (113 bp):
CAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAA
Found at i:162772 original size:18 final size:18
Alignment explanation
Indices: 162749--162783 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
162739 TATGTGAAAC
162749 AAATTGAATTTTAAAAAT
1 AAATTGAATTTTAAAAAT
162767 AAATTGAATTTTAAAAA
1 AAATTGAATTTTAAAAA
162784 GATAAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATTGAATTTTAAAAAT
Found at i:163179 original size:19 final size:19
Alignment explanation
Indices: 163136--163193 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 19
163126 CTCCTTTTAT
**
163136 ATTTTTTCTTT-TTTCAAC
1 ATTTTTTCTTTCTTTCTTC
*
163154 TTTTTTTCTTCTTCTTTCTTC
1 ATTTTTTC-T-TTCTTTCTTC
163175 ATTTTTTCTTTCTTTCTTC
1 ATTTTTTCTTTCTTTCTTC
163194 TTCAATCATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 7 0.21
19 11 0.33
20 3 0.09
21 12 0.36
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTCTTTCTTTCTTC
Found at i:163187 original size:22 final size:21
Alignment explanation
Indices: 163155--163197 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
163145 TTTTTCAACT
163155 TTTTTTCTTC-TTCTTTCTTCA
1 TTTTTTCTTCTTTC-TTCTTCA
163176 TTTTTTCTTTCTTTCTTCTTCA
1 TTTTTTC-TTCTTTCTTCTTCA
163198 ATCATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 10 0.50
23 3 0.15
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTTCTTCTTTCTTCTTCA
Found at i:173746 original size:2 final size:2
Alignment explanation
Indices: 173739--173772 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
173729 TAATAAAATA
*
173739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
173773 TATGAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:175951 original size:3 final size:3
Alignment explanation
Indices: 175945--176008 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
175935 TAATATTTAT
*
175945 TAA TAA TAA -AA -AA T-A TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
175990 TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TA
176009 TTCAAATAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 10 0.19
3 42 0.78
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:182632 original size:16 final size:16
Alignment explanation
Indices: 182607--182641 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
182597 GTAAATTATA
*
182607 AAAATATAAATAAGTT
1 AAAATATAAATAAATT
*
182623 AAAATTTAAATAAATT
1 AAAATATAAATAAATT
182639 AAA
1 AAA
182642 CAACACATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATATAAATAAATT
Found at i:183180 original size:21 final size:21
Alignment explanation
Indices: 183097--183192 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
183087 AAAATCGCAA
* *
183097 TGCGATAGTCCGAATTCGCGT
1 TGCGATAGTCCAAATTCGTGT
* *
183118 TGCGATAGTCCAAAATC--AT
1 TGCGATAGTCCAAATTCGTGT
* **
183137 TGCGATA--ACACTGTTCGTCGT
1 TGCGATAGTCCA-AATTCGT-GT
183158 TGCGATAGTCCAAATTCGTGT
1 TGCGATAGTCCAAATTCGTGT
183179 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
183193 ATCATTGCGA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
17 2 0.03
18 2 0.03
19 8 0.14
21 39 0.67
22 5 0.09
23 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCCAAATTCGTGT
Found at i:183192 original size:61 final size:61
Alignment explanation
Indices: 183097--183225 Score: 204
Period size: 61 Copynumber: 2.1 Consensus size: 61
183087 AAAATCGCAA
* * **
183097 TGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCGTCGT
1 TGCGATAGTCCAAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTATTCACCGT
* *
183158 TGCGATAGTCCAAATTCGTGTTGCGATAGTCCAAAATCATTGCGATAGCACTATTCACCGT
1 TGCGATAGTCCAAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTATTCACCGT
183219 TGCGATA
1 TGCGATA
183226 ACACTGTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (61 bp):
TGCGATAGTCCAAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTATTCACCGT
Found at i:183202 original size:19 final size:20
Alignment explanation
Indices: 183157--183205 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
183147 CTGTTCGTCG
* *
183157 TTGCGATAGTCCAAATTCGTG
1 TTGCGATAGTCCAAAATCG-A
183178 TTGCGATAGTCCAAAATC-A
1 TTGCGATAGTCCAAAATCGA
183197 TTGCGATAG
1 TTGCGATAG
183206 CACTATTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
21 17 0.65
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCCAAAATCGA
Found at i:183223 original size:21 final size:21
Alignment explanation
Indices: 183195--183319 Score: 171
Period size: 21 Copynumber: 6.0 Consensus size: 21
183185 AGTCCAAAAT
* *
183195 CATTGCGATAGCACTATTCAC
1 CATTGCGATAACACTGTTCAC
*
183216 CGTTGCGATAACACTGTTCAC
1 CATTGCGATAACACTGTTCAC
* *
183237 CATTGCGATAGCAATGTTCA-
1 CATTGCGATAACACTGTTCAC
183257 CATTGCGATAACACTGTTCAC
1 CATTGCGATAACACTGTTCAC
* *
183278 CGTTGCGATAACGCTGTTCAC
1 CATTGCGATAACACTGTTCAC
*
183299 CATTGCGATAGCACTGTTCAC
1 CATTGCGATAACACTGTTCAC
183320 ATTACGAATT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 18 0.20
21 72 0.80
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (21 bp):
CATTGCGATAACACTGTTCAC
Found at i:183243 original size:61 final size:60
Alignment explanation
Indices: 183117--183309 Score: 194
Period size: 61 Copynumber: 3.1 Consensus size: 60
183107 CGAATTCGCG
** * ** ***
183117 TTGCGATAGTCCAAAATCATTGCGATAACACTGTTCGTCGTTGCGATAGTCCAAATTC-GTG
1 TTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTTGCGATA-ACC-TGTTCACCA
* *
183178 TTGCGATAGTCCAAAATCATTGCGATAGCACTATTCACCGTTGCGATAACACTGTTCACCA
1 TTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTTGCGATAAC-CTGTTCACCA
**
183239 TTGCGATAG--CAATGTTCACATTGCGATAACACTGTTCACCGTTGCGATAACGCTGTTCACCA
1 TTGCGATAGTCCAA-AAT--CATTGCGATAACACTGTTCACCGTTGCGATAAC-CTGTTCACCA
183301 TTGCGATAG
1 TTGCGATAG
183310 CACTGTTCAC
Statistics
Matches: 112, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.03
60 5 0.04
61 54 0.48
62 50 0.45
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (60 bp):
TTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTTGCGATAACCTGTTCACCA
Found at i:183281 original size:62 final size:62
Alignment explanation
Indices: 183195--183322 Score: 220
Period size: 62 Copynumber: 2.1 Consensus size: 62
183185 AGTCCAAAAT
*
183195 CATTGCGATAGCACTATTCACCGTTGCGATAACACTGTTCACCATTGCGATAGCAATGTTCA
1 CATTGCGATAACACTATTCACCGTTGCGATAACACTGTTCACCATTGCGATAGCAATGTTCA
* * *
183257 CATTGCGATAACACTGTTCACCGTTGCGATAACGCTGTTCACCATTGCGATAGCACTGTTCA
1 CATTGCGATAACACTATTCACCGTTGCGATAACACTGTTCACCATTGCGATAGCAATGTTCA
183319 CATT
1 CATT
183323 ACGAATTTGC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.30
Consensus pattern (62 bp):
CATTGCGATAACACTATTCACCGTTGCGATAACACTGTTCACCATTGCGATAGCAATGTTCA
Found at i:183800 original size:16 final size:17
Alignment explanation
Indices: 183771--183822 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
183761 ATCATAAATA
*
183771 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
183788 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
183803 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
183821 AT
1 AT
183823 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:184004 original size:21 final size:21
Alignment explanation
Indices: 183978--184122 Score: 191
Period size: 21 Copynumber: 6.9 Consensus size: 21
183968 AATTCGCAAT
*
183978 GTGAACAGTGTTATCGCAATG
1 GTGAACAGTGTTATCGCAACG
* *
183999 GTGAACAATGTTATCGCAACA
1 GTGAACAGTGTTATCGCAACG
*
184020 GTGAACAGTGTTATCGCAACA
1 GTGAACAGTGTTATCGCAACG
* * *
184041 GTGAACAATGTTATCGTAATG
1 GTGAACAGTGTTATCGCAACG
184062 GTGAACAGTGTTATCGCAACG
1 GTGAACAGTGTTATCGCAACG
**
184083 GTGAACAGTACTATCGCAACG
1 GTGAACAGTGTTATCGCAACG
* *
184104 GTGAACAGTGCTGTCGCAA
1 GTGAACAGTGTTATCGCAA
184123 TGATTCTGGA
Statistics
Matches: 109, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 109 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (21 bp):
GTGAACAGTGTTATCGCAACG
Found at i:184156 original size:21 final size:21
Alignment explanation
Indices: 184125--184294 Score: 120
Period size: 21 Copynumber: 8.1 Consensus size: 21
184115 TGTCGCAATG
* *
184125 ATTCTGGACTATCGCAAAGTGA
1 ATTC-GGACTATCGCAACGCGA
184147 ATTCGGACTATCGCAACGCGA
1 ATTCGGACTATCGCAACGCGA
*
184168 ATTTGGACTATCGCAACGCGA
1 ATTCGGACTATCGCAACGCGA
* *
184189 ATTTGGACTATCGCAACGGTGA
1 ATTCGGACTATCGCAAC-GCGA
* *
184211 A--CAGTG-TTATCGCAACGGTGA
1 ATTC-G-GACTATCGCAAC-GCGA
* * *
184232 A--CAGTATTATCGCAA--TGA
1 ATTC-GGACTATCGCAACGCGA
* *
184250 TTTTGGACTATCGCAACGCGA
1 ATTCGGACTATCGCAACGCGA
*
184271 ATTCGGACTATCGCAACGCAA
1 ATTCGGACTATCGCAACGCGA
184292 ATT
1 ATT
184295 TGGAGTCAGA
Statistics
Matches: 125, Mismatches: 15, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
18 3 0.02
19 10 0.08
21 103 0.82
22 9 0.07
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (21 bp):
ATTCGGACTATCGCAACGCGA
Found at i:184199 original size:103 final size:101
Alignment explanation
Indices: 184092--184298 Score: 272
Period size: 103 Copynumber: 2.0 Consensus size: 101
184082 GGTGAACAGT
* * *
184092 ACTATCGCAACGGTGAACAGTGCTGTCGCAA-TGATTCTGGACTATCGCAAAGTGAATTCGGACT
1 ACTATCGCAACGGTGAACAGTGCTATCGCAAGTGA-ACAGGACTATCGC-AA-TGAATTCGGACT
* *
184156 ATCGCAACGCGAATTTGGACTATCGCAACGCGAATTTGG
63 ATCGCAACGCGAATTCGGACTATCGCAACGCAAATTTGG
* * * * *
184195 ACTATCGCAACGGTGAACAGTGTTATCGCAACGGTGAACAGTATTATCGCAATGATTTTGGACTA
1 ACTATCGCAACGGTGAACAGTGCTATCGCAA--GTGAACAGGACTATCGCAATGAATTCGGACTA
184260 TCGCAACGCGAATTCGGACTATCGCAACGCAAATTTGG
64 TCGCAACGCGAATTCGGACTATCGCAACGCAAATTTGG
184298 A
1 A
184299 GTCAGAATCA
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
103 77 0.85
104 2 0.02
105 9 0.10
106 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (101 bp):
ACTATCGCAACGGTGAACAGTGCTATCGCAAGTGAACAGGACTATCGCAATGAATTCGGACTATC
GCAACGCGAATTCGGACTATCGCAACGCAAATTTGG
Found at i:184201 original size:124 final size:124
Alignment explanation
Indices: 184073--184298 Score: 371
Period size: 124 Copynumber: 1.8 Consensus size: 124
184063 TGAACAGTGT
* *
184073 TATCGCAACGGTGAACAGTACTATCGCAACGGTGAACAGTGCTGTCGCAATGATTCTGGACTATC
1 TATCGCAACGGTGAACAGTACTATCGCAACGGTGAACAGTACTATCGCAATGATTCTGGACTATC
* *
184138 GCAAAGTGAATTCGGACTATCGCAACGCGAATTTGGACTATCGCAACGCGAATTTGGAC
66 GCAAAGCGAATTCGGACTATCGCAACGCAAATTTGGACTATCGCAACGCGAATTTGGAC
** * *
184197 TATCGCAACGGTGAACAGTGTTATCGCAACGGTGAACAGTATTATCGCAATGATTTTGGACTATC
1 TATCGCAACGGTGAACAGTACTATCGCAACGGTGAACAGTACTATCGCAATGATTCTGGACTATC
*
184262 GCAACGCGAATTCGGACTATCGCAACGCAAATTTGGA
66 GCAAAGCGAATTCGGACTATCGCAACGCAAATTTGGA
184299 GTCAGAATCA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 93 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (124 bp):
TATCGCAACGGTGAACAGTACTATCGCAACGGTGAACAGTACTATCGCAATGATTCTGGACTATC
GCAAAGCGAATTCGGACTATCGCAACGCAAATTTGGACTATCGCAACGCGAATTTGGAC
Found at i:184387 original size:19 final size:19
Alignment explanation
Indices: 184363--184399 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
184353 TACGATACTG
*
184363 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
184382 GAGATCGTATTGCGATTT
1 GAGATCGCATTGCGATTT
184400 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:184749 original size:2 final size:2
Alignment explanation
Indices: 184742--184772 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
184732 TATTCAAATA
184742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
184773 ATGAGTATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:184894 original size:2 final size:2
Alignment explanation
Indices: 184887--184976 Score: 166
Period size: 2 Copynumber: 46.0 Consensus size: 2
184877 AAGTAAATTC
184887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184929 AT AT AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
184969 AT AT AT AT
1 AT AT AT AT
184977 GTGAAATTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 84 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:186273 original size:3 final size:3
Alignment explanation
Indices: 186265--186290 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
186255 GGTCATATCA
186265 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
186291 CAAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:191351 original size:17 final size:16
Alignment explanation
Indices: 191322--191361 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
191312 TAATACCATT
*
191322 TTAATGAAAATATTCA
1 TTAATAAAAATATTCA
*
191338 TTAATAAAATATATTTA
1 TTAATAAAA-ATATTCA
191355 TTAATAA
1 TTAATAA
191362 TTTTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TTAATAAAAATATTCA
Found at i:191411 original size:5 final size:5
Alignment explanation
Indices: 191392--191444 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
191382 GTTTTTAATG
*
191392 TTATA TTA-A -TATA TTATA TTATA TTATA TTATA --ATA ATATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
191438 TTATA TT
1 TTATA TT
191445 TTTATTTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
3 5 0.12
4 2 0.05
5 36 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:191418 original size:23 final size:23
Alignment explanation
Indices: 191393--191444 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
191383 TTTTTAATGT
*
191393 TATATTA-ATATATTATATTATAT
1 TATATTATA-ATAATATATTATAT
191416 TATATTATAATAATATATTATAT
1 TATATTATAATAATATATTATAT
191439 TATATT
1 TATATT
191445 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATTATAATAATATATTATAT
Found at i:191432 original size:28 final size:28
Alignment explanation
Indices: 191341--191444 Score: 101
Period size: 28 Copynumber: 3.8 Consensus size: 28
191331 ATATTCATTA
191341 ATAA-AATATATT-TATTA-A-TA-ATT
1 ATAATAATATATTATATTATATTATATT
* * * * *
191364 TTAATAATATAATATATTGTTTTTAATGTT
1 ATAATAATATATTATATT-ATATT-ATATT
*
191394 ATATTAATATATTATATTATATTATATT
1 ATAATAATATATTATATTATATTATATT
191422 ATAATAATATATTATATTATATT
1 ATAATAATATATTATATTATATT
191445 TTTATTTTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
23 3 0.05
24 7 0.11
25 4 0.06
28 27 0.44
29 4 0.06
30 17 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
ATAATAATATATTATATTATATTATATT
Found at i:191527 original size:22 final size:22
Alignment explanation
Indices: 191502--191560 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
191492 ATTAATTTCA
* *
191502 TAAAATAAAATTATTATAAATT
1 TAAAATATAATTATTAAAAATT
*
191524 TAAAATATATTTATTAAAAATT
1 TAAAATATAATTATTAAAAATT
191546 TCAAAAATATAATTA
1 T--AAAATATAATTA
191561 AATATTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 20 0.65
24 11 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATATAATTATTAAAAATT
Found at i:191575 original size:14 final size:14
Alignment explanation
Indices: 191553--191585 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
191543 ATTTCAAAAA
191553 TATAA-TTAAATAT
1 TATAATTTAAATAT
191566 TATAATTTAAATAT
1 TATAATTTAAATAT
*
191580 AATAAT
1 TATAAT
191586 AATAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAATTTAAATAT
Found at i:191612 original size:30 final size:28
Alignment explanation
Indices: 191578--191649 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
191568 TAATTTAAAT
* *
191578 ATAATAATAATAATTTTATTTTAGTAATTA
1 ATAATAATAATAATTTT-TATTA-TAATAA
191608 ATAAT-ATAAT-ATTTTTATTATAATAA
1 ATAATAATAATAATTTTTATTATAATAA
191634 ATAATTAAT-ATAATTT
1 ATAA-TAATAATAATTT
191650 ATAAATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 9 0.24
27 7 0.19
28 11 0.30
29 5 0.14
30 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
ATAATAATAATAATTTTTATTATAATAA
Found at i:191616 original size:26 final size:26
Alignment explanation
Indices: 191579--191644 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
191569 AATTTAAATA
191579 TAATAATAATAAT-TTTATT-TTAGTAAT
1 TAATAAT-ATAATATTT-TTATTA-TAAT
191606 TAATAATATAATATTTTTATTATAAT
1 TAATAATATAATATTTTTATTATAAT
*
191632 AAATAAT-TAATAT
1 TAATAATATAATAT
191645 AATTTATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
25 6 0.17
26 17 0.47
27 13 0.36
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAATAATATAATATTTTTATTATAAT
Found at i:191623 original size:29 final size:29
Alignment explanation
Indices: 191563--191647 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 29
191553 TATAATTAAA
191563 TATTATAATTTAAAT-ATAATAATAATAATTT
1 TATTATAA--TAAATAATAAT-ATAATAATTT
* * * *
191594 TATTTTAGTAATTAATAATATAATATTTT
1 TATTATAATAAATAATAATATAATAATTT
191623 TATTATAATAAATAATTAATATAAT
1 TATTATAATAAATAA-TAATATAAT
191648 TTATAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 25 0.56
30 14 0.31
31 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TATTATAATAAATAATAATATAATAATTT
Found at i:191650 original size:26 final size:26
Alignment explanation
Indices: 191602--191651 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
191592 TTTATTTTAG
* *
191602 TAATTAATAATATAATATTTTTATTA
1 TAATAAATAATATAATATATTTATTA
191628 TAATAAATAAT-TAATATAATTTAT
1 TAATAAATAATATAATAT-ATTTAT
191652 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAATAAATAATATAATATATTTATTA
Found at i:191755 original size:14 final size:14
Alignment explanation
Indices: 191711--191757 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
191701 AAAATTATAG
*
191711 AAATAATATTTTAAT
1 AAATAATA-TTAAAT
*
191726 -AATAATATTGACAT
1 AAATAATATT-AAAT
191740 AAATAATATTAAAT
1 AAATAATATTAAAT
191754 AAAT
1 AAAT
191758 TATTTTACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 2 0.07
14 16 0.59
15 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:201009 original size:21 final size:20
Alignment explanation
Indices: 200980--201023 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
200970 CATATAGGTC
* *
200980 TTGGTAGAGGATTACGAGGAA
1 TTGGAAGAGGATTA-GAAGAA
201001 TTGGAAGAGGATTAGAAGAA
1 TTGGAAGAGGATTAGAAGAA
201021 TTG
1 TTG
201024 TTAACGAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.25
Consensus pattern (20 bp):
TTGGAAGAGGATTAGAAGAA
Found at i:209382 original size:2 final size:2
Alignment explanation
Indices: 209375--209432 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
209365 TAATTTAAAG
209375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
209417 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
209433 TTAAATAACA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209558 original size:107 final size:107
Alignment explanation
Indices: 209442--209635 Score: 298
Period size: 107 Copynumber: 1.8 Consensus size: 107
209432 TTTAAATAAC
* * **
209442 ATATTTATTTATTTAGAAATATAAGAAAAGAGCTTCTAGGTACTTTAAGACAGCTCTTTCTTTTG
1 ATATTTATTTATTTAAAAATATAAGAAAAGAGCTTCTAGGTACTTTAAGACAGCTCTTTCCTTCA
209507 ATATTAAAAAATAAATAAATAAAATTATTTTAATATAGTAAG
66 ATATTAAAAAATAAATAAATAAAATTATTTTAATATAGTAAG
* * * **
209549 ATATTTATTTATTTAAAAATATTAGAAAAGGGCTTCTAGTTGTTTTAAGACAGCTCTTTCCTTCA
1 ATATTTATTTATTTAAAAATATAAGAAAAGAGCTTCTAGGTACTTTAAGACAGCTCTTTCCTTCA
*
209614 ATATTTAAAAATAAATAAATAA
66 ATATTAAAAAATAAATAAATAA
209636 CTAAAACATA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 77 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.40
Consensus pattern (107 bp):
ATATTTATTTATTTAAAAATATAAGAAAAGAGCTTCTAGGTACTTTAAGACAGCTCTTTCCTTCA
ATATTAAAAAATAAATAAATAAAATTATTTTAATATAGTAAG
Found at i:211029 original size:14 final size:15
Alignment explanation
Indices: 211009--211043 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
210999 TTTGTTATTA
211009 GGTTTGGGCCAGTCT
1 GGTTTGGGCCAGTCT
211024 -GTTTGGGCCAGTCT
1 GGTTTGGGCCAGTCT
211038 GGTTTG
1 GGTTTG
211044 TAATCGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.06, C:0.17, G:0.40, T:0.37
Consensus pattern (15 bp):
GGTTTGGGCCAGTCT
Found at i:211144 original size:19 final size:19
Alignment explanation
Indices: 211096--211144 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
211086 ATTAATTATT
* *
211096 TAATAAATATAATAGAATAA
1 TAAT-AATAAAATAAAATAA
*
211116 TAATATTAAAATAAAATAA
1 TAATAATAAAATAAAATAA
*
211135 TACTAATAAA
1 TAATAATAAA
211145 TGAAACAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
TAATAATAAAATAAAATAA
Found at i:211558 original size:113 final size:113
Alignment explanation
Indices: 211380--211797 Score: 538
Period size: 113 Copynumber: 3.7 Consensus size: 113
211370 CTAGCAAAAA
* * *
211380 GTTGAACAAATTCTTCTCATTATAAACTTCTT-TTTCTTCTTCAGATAAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* * * *
211444 ACTTTCTCTGGAAAAGCTAATCCATCGAGTGATGAATTAAAGCGAAAG
66 ACTCTCTCTGGAAATGCTGATCCATCGAATGATGAATTAAAGCGAAAG
* *
211492 GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTTATTATGA
1 GTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
** * * * * ** *
211557 ACTCTAACTGGCACTGCTGATCCACCGATTGATGAATTCGAGCAAAAG
66 ACTCTCTCTGGAAATGCTGATCCATCGAATGATGAATTAAAGCGAAAG
* * *
211605 GTTGAATAAATTCTTCTAATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
* *
211670 ACTCTAC-CTGGCAATGCTGATCCATCGAATGATGAATTTAAGCGAAAAG
66 ACTCT-CTCTGGAAATGCTGATCCATCGAATGATGAATTAAAGCG-AAAG
* * * * *
211719 TTTGAACAAGTTCTTCTAATTATGAACTTATTCTT-TTTCTTCAGATGAGTTCTTCTCATTATGA
1 GTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
211783 ACTCT-TCTGGAAATG
66 ACTCTCTCTGGAAATG
211798 TTTTAAAAAA
Statistics
Matches: 267, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
112 38 0.14
113 194 0.73
114 35 0.13
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
GTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
ACTCTCTCTGGAAATGCTGATCCATCGAATGATGAATTAAAGCGAAAG
Found at i:211695 original size:226 final size:225
Alignment explanation
Indices: 211372--211787 Score: 611
Period size: 226 Copynumber: 1.8 Consensus size: 225
211362 GAAGTAATCT
* *
211372 AGCAAAAAGTTGAACAAATTCTTCTCATTATAAACTTCTTTTTCTTCTTCAGATAAGTTCTTCTC
1 AGCAAAAAGTTGAACAAATTCTTCTAATTATAAACTTCTTTTCCTTCTTCAGATAAGTTCTTCTC
* *
211437 ATTATGAACTTTCTCTGGAAAAGCTAATCCATCGAGTGATGAATTAAAGCG-AAAGGTTGAACAA
66 ATTATGAACTTACTCTGGAAAAGCTAATCCATCGAATGATGAATTAAAGCGAAAAGGTTGAACAA
* * *
211501 ATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTTATTATGAACTCTAACT
131 ATTCTTCTAATTATGAACTTATTCTT-CTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAACT
211566 GGCACTGCTGATCCACCGATTGATGAATTCG
195 GGCACTGCTGATCCACCGATTGATGAATTCG
* * * * *
211597 AGCAAAAGGTTGAATAAATTCTTCTAATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCT
1 AGCAAAAAGTTGAACAAATTCTTCTAATTATAAACTTCTT-TTCCTTCTTCAGATAAGTTCTTCT
* * * * *
211662 CATTATGAACTCTAC-CTGGCAATGCTGATCCATCGAATGATGAATTTAAGCGAAAAGTTTGAAC
65 CATTATGAACT-TACTCTGGAAAAGCTAATCCATCGAATGATGAATTAAAGCGAAAAGGTTGAAC
* * *
211726 AAGTTCTTCTAATTATGAACTTATTCTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCT
129 AAATTCTTCTAATTATGAACTTATTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTCT
211788 TCTGGAAATG
Statistics
Matches: 168, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
225 36 0.21
226 95 0.57
227 37 0.22
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (225 bp):
AGCAAAAAGTTGAACAAATTCTTCTAATTATAAACTTCTTTTCCTTCTTCAGATAAGTTCTTCTC
ATTATGAACTTACTCTGGAAAAGCTAATCCATCGAATGATGAATTAAAGCGAAAAGGTTGAACAA
ATTCTTCTAATTATGAACTTATTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAACTG
GCACTGCTGATCCACCGATTGATGAATTCG
Found at i:211932 original size:76 final size:76
Alignment explanation
Indices: 211815--211987 Score: 274
Period size: 76 Copynumber: 2.3 Consensus size: 76
211805 AAAACATTCC
** * * * * *
211815 GCACTGTAGGGTTTACAGCTGACTCGAAGGTTTTGAAAACATCAAAAAGCTCTCGAAGGCTTTTT
1 GCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
211880 GGAAACATCAT
66 GGAAACATCAT
*
211891 GCACTGTAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
1 GCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
211956 GGAAACATCAT
66 GGAAACATCAT
211967 GCACTGTAGGACTTACAGATG
1 GCACTGTAGGACTTACAGATG
211988 TGGGAAATAG
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 88 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (76 bp):
GCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
GGAAACATCAT
Done.