Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002196.1 Hibiscus syriacus cultivar Beakdansim tig00004476_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: 85698
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:948 original size:53 final size:54
Alignment explanation
Indices: 867--969 Score: 199
Period size: 53 Copynumber: 1.9 Consensus size: 54
857 GTTCTGACCT
867 AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCAGGTC
1 AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCAGGTC
921 AATACTTGACTC-AATCAACTTATCATAGACTTCAACTAAATTTAAACCA
1 AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCA
970 AATTTGATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 37 0.76
54 12 0.24
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (54 bp):
AATACTTGACTCGAATCAACTTATCATAGACTTCAACTAAATTTAAACCAGGTC
Found at i:4236 original size:19 final size:19
Alignment explanation
Indices: 4212--4257 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
4202 TTGTAGGGTA
4212 TTGTATCCATGTCACTTTC
1 TTGTATCCATGTCACTTTC
4231 TTGTATCCATGTCACTTTC
1 TTGTATCCATGTCACTTTC
*
4250 TTCTATCC
1 TTGTATCC
4258 TTTAATGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.15, C:0.28, G:0.09, T:0.48
Consensus pattern (19 bp):
TTGTATCCATGTCACTTTC
Found at i:9732 original size:128 final size:128
Alignment explanation
Indices: 9504--10110 Score: 1108
Period size: 128 Copynumber: 4.7 Consensus size: 128
9494 ACTATTTACA
*
9504 TGAAGGCGCGTTCCCGGGGGAGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
9569 TTATGTCACTCATGTCCCTCGGGGATACTATTCATACCAGTACCTATTATTTCTCATGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
9632 TGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
9697 TTATGTCACTCATGTCCATCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
9760 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
9825 TTATGTCACTCATGTCCCTCGGGGACACTATTTATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
9888 TGAAGGCGCGTTCCCGAGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 TGAAGGCGCGTTCCCG-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
9952 ATTATGTCACTCATGTCCCTCAGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
65 ATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
10016 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAAAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
10081 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
10111 GATGGATTGC
Statistics
Matches: 464, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
127 4 0.01
128 456 0.98
129 4 0.01
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:10388 original size:14 final size:14
Alignment explanation
Indices: 10369--10398 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10359 GATAAGTTGA
*
10369 TTTTAATGTATATG
1 TTTTAATATATATG
10383 TTTTAATATATATG
1 TTTTAATATATATG
10397 TT
1 TT
10399 AATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:10546 original size:34 final size:34
Alignment explanation
Indices: 10507--10613 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
10497 TAAGTTGAAA
* *
10507 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
10541 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
10575 TTTTATTTTAAATTTCGAACAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
10609 TTTAA
1 TTTAA
10614 AAACATTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:11182 original size:42 final size:42
Alignment explanation
Indices: 11119--11227 Score: 182
Period size: 42 Copynumber: 2.6 Consensus size: 42
11109 TATGGTATAA
* *
11119 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
11161 AACCCTGCGGGCTCGGAATGTAACCTGGTGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
11203 AACCCGGCGGGCTCGGAATGTAACC
1 AACCCTGCGGGCTCGGAATGTAACC
11228 CTACGGAGAT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:11228 original size:21 final size:21
Alignment explanation
Indices: 11119--11228 Score: 148
Period size: 21 Copynumber: 5.2 Consensus size: 21
11109 TATGGTATAA
* *
11119 AACCCTGCGGGCTAGGCATGT
1 AACCCGGCGGGCTAGGAATGT
*
11140 AACCTGGCGGGCTAGGAATGT
1 AACCCGGCGGGCTAGGAATGT
* *
11161 AACCCTGCGGGCTCGGAATGT
1 AACCCGGCGGGCTAGGAATGT
* *
11182 AACCTGGTGGGCTAGGAATGT
1 AACCCGGCGGGCTAGGAATGT
*
11203 AACCCGGCGGGCTCGGAATGT
1 AACCCGGCGGGCTAGGAATGT
11224 AACCC
1 AACCC
11229 TACGGAGATG
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 76 1.00
ACGTcount: A:0.22, C:0.25, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCGGCGGGCTAGGAATGT
Found at i:11252 original size:63 final size:63
Alignment explanation
Indices: 11127--11257 Score: 169
Period size: 63 Copynumber: 2.1 Consensus size: 63
11117 AAAACCCTGC
* * * *
11127 GGGCTAGGCATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGGAATGTAACCTGGT
1 GGGCTAGGAATGTAACCCGGCGGGCTAGGAATGTAACCCTACGGGATCGGAATGTAACCTGGT
*
11190 GGGCTAGGAATGTAACCCGGCGGGCTCGGAATGTAACCCTACGGAGAT-GGCATATG-AA-CTGG
1 GGGCTAGGAATGTAACCCGGCGGGCTAGGAATGTAACCCTACGG-GATCGG-A-ATGTAACCTGG
11252 T
63 T
11253 GGGCT
1 GGGCT
11258 TGGCATATGA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
63 52 0.87
64 5 0.08
65 3 0.05
ACGTcount: A:0.22, C:0.21, G:0.37, T:0.20
Consensus pattern (63 bp):
GGGCTAGGAATGTAACCCGGCGGGCTAGGAATGTAACCCTACGGGATCGGAATGTAACCTGGT
Found at i:11263 original size:21 final size:21
Alignment explanation
Indices: 11237--11284 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
11227 CCTACGGAGA
*
11237 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
11258 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
11279 GGGCAT
1 TGGCAT
11285 GTACCCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:12842 original size:17 final size:17
Alignment explanation
Indices: 12810--12858 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
12800 ATAAAATATT
* * *
12810 AAAATTAATATAAATTC
1 AAAATAAATTTAAATTA
* *
12827 ATAATAACTTTAAATTA
1 AAAATAAATTTAAATTA
12844 AAAATAAATTTAAAT
1 AAAATAAATTTAAAT
12859 ATTAACATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATAAATTTAAATTA
Found at i:13044 original size:34 final size:33
Alignment explanation
Indices: 13000--13089 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 33
12990 TTAATAATTC
* *
13000 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAA-ATTATATTAA
*
13034 TAAAAAAATAAT-ATT-TATATAATTATATTAA
1 TAAAAAAATAATAATTATATAAAATTATATTAA
* * *
13065 TATAAAATATAATAACTATTTAAAA
1 TA-AAAAAATAATAATTATATAAAA
13090 AAATACTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
31 11 0.24
32 14 0.30
33 5 0.11
34 16 0.35
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAAAAAATAATAATTATATAAAATTATATTAA
Found at i:13045 original size:31 final size:33
Alignment explanation
Indices: 13003--13077 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
12993 ATAATTCTAA
* *
13003 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAATTATATTAAT
* *
13035 A-AAAAAATAA-TATTTATATAATTATATTAAT
1 ATAAAAAATAATTATATAAATAATTATATTAAT
*
13066 ATAAAATATAAT
1 ATAAAAAATAAT
13078 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 19 0.54
32 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAATTATATTAAT
Found at i:15980 original size:19 final size:19
Alignment explanation
Indices: 15956--16005 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
15946 TAAACGTTTT
15956 TATGAATAGTACTATACGG
1 TATGAATAGTACTATACGG
**
15975 TATGAATAGTACTATATTG
1 TATGAATAGTACTATACGG
*
15994 TATGAACAGTAC
1 TATGAATAGTAC
16006 CGTGAACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (19 bp):
TATGAATAGTACTATACGG
Found at i:16035 original size:22 final size:22
Alignment explanation
Indices: 15995--16036 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15985 ACTATATTGT
*
15995 ATGAACAGTACCGTGAACAAAA
1 ATGAACAGTACCATGAACAAAA
* *
16017 ATGAATAGTACCATTAACAA
1 ATGAACAGTACCATGAACAA
16037 TAACTTCAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (22 bp):
ATGAACAGTACCATGAACAAAA
Found at i:17902 original size:15 final size:15
Alignment explanation
Indices: 17882--17919 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
17872 TGGAAAAATT
17882 CTACGTGAAAGTAAA
1 CTACGTGAAAGTAAA
17897 CTACGTGAAAGTAAA
1 CTACGTGAAAGTAAA
*
17912 CTAAGTGA
1 CTACGTGA
17920 CTATGTGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (15 bp):
CTACGTGAAAGTAAA
Found at i:19097 original size:23 final size:24
Alignment explanation
Indices: 19064--19143 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 24
19054 CTCGTATAAT
*
19064 TTTGCACCGAAGTACCGAGTAGAA
1 TTTGCACCGAAGTACCGCGTAGAA
* *
19088 TTTG-TCCGAAGAACCGCGTAGAAA
1 TTTGCACCGAAGTACCGCGTAG-AA
* *
19112 TTTGCACCGATGTGCCGCGTAGAA
1 TTTGCACCGAAGTACCGCGTAGAA
19136 TTT-CACCG
1 TTTGCACCG
19144 TAGTGCCATA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 19 0.40
24 15 0.32
25 13 0.28
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (24 bp):
TTTGCACCGAAGTACCGCGTAGAA
Found at i:19298 original size:23 final size:23
Alignment explanation
Indices: 19268--19330 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
19258 CATATATGTC
19268 CCGAAGGACCACGTAGAATTGTA
1 CCGAAGGACCACGTAGAATTGTA
* *
19291 CCGAAGGATCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAATTGTA
* *
19314 CCGAATGACCGCGTAGA
1 CCGAAGGACCACGTAGA
19331 CCCTCTACTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAATTGTA
Found at i:21467 original size:8 final size:8
Alignment explanation
Indices: 21454--21520 Score: 134
Period size: 8 Copynumber: 8.4 Consensus size: 8
21444 AGTTTACCAA
21454 TATGAATT
1 TATGAATT
21462 TATGAATT
1 TATGAATT
21470 TATGAATT
1 TATGAATT
21478 TATGAATT
1 TATGAATT
21486 TATGAATT
1 TATGAATT
21494 TATGAATT
1 TATGAATT
21502 TATGAATT
1 TATGAATT
21510 TATGAATT
1 TATGAATT
21518 TAT
1 TAT
21521 AGAGATTGGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 59 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (8 bp):
TATGAATT
Found at i:22217 original size:16 final size:16
Alignment explanation
Indices: 22196--22236 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
22186 TAAAATTAAG
22196 TAATTTTTTATAT-AAT
1 TAATTTTTTA-ATGAAT
*
22212 TAATTTTTTAATGATT
1 TAATTTTTTAATGAAT
22228 TAATTTTTT
1 TAATTTTTT
22237 TTACAAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TAATTTTTTAATGAAT
Found at i:22350 original size:2 final size:2
Alignment explanation
Indices: 22343--22392 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
22333 ATCTTCATTA
22343 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
22385 AT AT AT AT
1 AT AT AT AT
22393 TGATGAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22926 original size:31 final size:31
Alignment explanation
Indices: 22890--22948 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
22880 AACTTAAAAG
* *
22890 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
22921 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
22949 CCATATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:22983 original size:14 final size:14
Alignment explanation
Indices: 22964--23016 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
22954 TAACTACAAT
22964 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
22978 AATAAATCAATCCATACA
1 AATAAAT-TAT--TTA-A
22996 AATAAATTATTTAA
1 AATAAATTATTTAA
23010 AATAAAT
1 AATAAAT
23017 CAATCCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 15 0.48
15 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:23000 original size:18 final size:18
Alignment explanation
Indices: 22977--23028 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
22967 AAATTATTTA
22977 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
* *
22995 AAATAAAT-TAT--TTA-
1 AAATAAATCAATCCATAC
23009 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
23027 AA
1 AA
23029 CTACAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
17 4 0.15
18 10 0.38
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATAAATCAATCCATAC
Found at i:23005 original size:32 final size:30
Alignment explanation
Indices: 22964--23300 Score: 176
Period size: 32 Copynumber: 12.1 Consensus size: 30
22954 TAACTACAAT
22964 AATAAATTATTTAAAATAAATCAATCCATAC
1 AATAAA-TATTTAAAATAAATCAATCCATAC
22995 AAATAAATTATTTAAAATAAATCAATCCATAC
1 -AATAAA-TATTTAAAATAAATCAATCCATAC
*
23027 AACTACA-A--T--AATAAATCAATCCAT--
1 AA-TAAATATTTAAAATAAATCAATCCATAC
*
23051 -AT-----TTTAAAATAAATCAATTCATAC
1 AATAAATATTTAAAATAAATCAATCCATAC
* *
23075 TAATAAATTATTTAAAATAAATAAATCAAT-C
1 -AATAAA-TATTTAAAATAAATCAATCCATAC
* **
23106 TATACAA-ATACAATAATAAATCAAT-C---C
1 AATA-AATATTTAA-AATAAATCAATCCATAC
23133 -AT--AT-TTTAAAATAAATCAATCCATAC
1 AATAAATATTTAAAATAAATCAATCCATAC
23159 TAATAAATTATTTAAAATAAATCAAT-C---C
1 -AATAAA-TATTTAAAATAAATCAATCCATAC
23187 -AT--AT-TTTAAAATAAATCAATCCATAC
1 AATAAATATTTAAAATAAATCAATCCATAC
*
23213 TAATAACTTATTTAAAATAAATCAAT-C---C
1 -AATAA-ATATTTAAAATAAATCAATCCATAC
* *
23241 -AT--AT-TTTAAAATAAATTAATACATAC
1 AATAAATATTTAAAATAAATCAATCCATAC
*
23267 TAATAAATTATTTAAAATAAATCAATCTATAC
1 -AATAAA-TATTTAAAATAAATCAATCCATAC
23299 AA
1 AA
23301 CTACAATAAT
Statistics
Matches: 239, Mismatches: 18, Indels: 97
0.68 0.05 0.27
Matches are distributed among these distances:
20 1 0.00
22 57 0.24
23 10 0.04
24 1 0.00
26 26 0.11
27 1 0.00
28 9 0.04
29 4 0.02
30 16 0.07
31 12 0.05
32 102 0.43
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (30 bp):
AATAAATATTTAAAATAAATCAATCCATAC
Found at i:23136 original size:84 final size:84
Alignment explanation
Indices: 22973--23185 Score: 353
Period size: 84 Copynumber: 2.6 Consensus size: 84
22963 TAATAAATTA
* *
22973 TTTAAAATAAATCAATCCATACAAATAAATTATTT---A-AAATAAATCAATCCATACAACTACA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAATCAATCCATACAAATACA
23034 ATAATAAATCAATCCATAT
66 ATAATAAATCAATCCATAT
* *
23053 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATAAATCAATCTATACAAATACA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAATCAATCCATACAAATACA
23118 ATAATAAATCAATCCATAT
66 ATAATAAATCAATCCATAT
*
23137 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAATC
23186 CATATTTTAA
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
80 33 0.27
83 1 0.01
84 89 0.72
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (84 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAATCAATCCATACAAATACA
ATAATAAATCAATCCATAT
Found at i:23166 original size:22 final size:23
Alignment explanation
Indices: 23093--23165 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 23
23083 TATTTAAAAT
* *
23093 AAATAAATCAATCTATACAAATACA
1 AAATAAATCAATCCATACTAAT--A
**
23118 ATAATAAATCAATCCATA-TTTTA
1 A-AATAAATCAATCCATACTAATA
23141 AAATAAATCAATCCATACTAATA
1 AAATAAATCAATCCATACTAATA
23164 AA
1 AA
23166 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
22 16 0.40
23 7 0.17
25 2 0.05
26 15 0.38
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAAATCAATCCATACTAATA
Found at i:23185 original size:54 final size:54
Alignment explanation
Indices: 22973--23620 Score: 355
Period size: 54 Copynumber: 12.0 Consensus size: 54
22963 TAATAAATTA
* *
22973 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * * * * * *
23030 TACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACT-AATAAAT---TA-
1 TTTAA-AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATAT
* * **
23085 TTTAAAATAAATAAATCAAT-CT-ATACAA--ATACAATAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATA-AATTATTTAA-AATAAATCAATCCATAT
23137 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
23191 TTTAAAATAAATCAATCCATACTAATAACTTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * * *
23245 TTTAAAATAAATTAATACATACTAATAAATTATTTAAAATAAATCAATCTATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * * ** * ** * * **
23302 TACAATAATAAATTAATTCATA-TTTTAAAATAAAT-CAATATATACTAATAAAT-T
1 TTTAA-AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT
** * * *
23356 ATTTAAAATAAATCAATCCATA-TTTTAAAATAAATTAATACATACTAATAAAT---TA-
1 -TTTAAAATAAATCAATCCATACTAAT-AAATTATTTAA-A-ATA--AATCAATCCATAT
* * * * * *
23411 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACT-AATAAAT---TA-
1 TTTAAAATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATAT
* * * *
23465 TTTAAAATAAATCAAT--ATA-T-A-CAACTA--CAATAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAA-AATAAATCAATCCATAT
* *
23513 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCGATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
23567 TTTAAAATAAATCAATTCATATTAATAAACTATTTAAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTT-AAAATAAATCAATCCATA
23621 CAACTACAAT
Statistics
Matches: 470, Mismatches: 70, Indels: 104
0.73 0.11 0.16
Matches are distributed among these distances:
42 2 0.00
43 2 0.00
44 7 0.01
45 2 0.00
46 5 0.01
47 4 0.01
48 25 0.05
49 3 0.01
50 3 0.01
51 4 0.01
52 22 0.05
53 8 0.02
54 247 0.53
55 36 0.08
56 7 0.01
57 19 0.04
58 47 0.10
59 6 0.01
60 2 0.00
62 13 0.03
63 6 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:23195 original size:22 final size:22
Alignment explanation
Indices: 23169--23211 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
23159 TAATAAATTA
23169 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
23191 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
23212 CTAATAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:23199 original size:84 final size:83
Alignment explanation
Indices: 22973--23243 Score: 345
Period size: 84 Copynumber: 3.3 Consensus size: 83
22963 TAATAAATTA
* * *
22973 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATA---CAACTACAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTAAAATACAA
23035 TAATAAATCAATCCATAT
66 TAATAAATCAATCCATAT
* * * * *
23053 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATAAATCAATCTATACAAATACA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTA-AAATACA
23118 ATAATAAATCAATCCATAT
65 ATAATAAATCAATCCATAT
23137 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATA-A
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTAAAATACA
** * *
23201 ATCAATCCATACTAATAACTTA-
65 AT-AATAAAT-C-AAT-CCATAT
23223 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
23244 TTTTAAAATA
Statistics
Matches: 166, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
80 48 0.29
83 3 0.02
84 84 0.51
85 4 0.02
86 24 0.14
87 3 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (83 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTAAAATACAA
TAATAAATCAATCCATAT
Found at i:23249 original size:22 final size:22
Alignment explanation
Indices: 23223--23265 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23213 TAATAACTTA
*
23223 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
*
23245 TTTAAAATAAATTAATACATA
1 TTTAAAATAAATCAATACATA
23266 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:23347 original size:134 final size:135
Alignment explanation
Indices: 22973--23696 Score: 663
Period size: 134 Copynumber: 5.4 Consensus size: 135
22963 TAATAAATTA
* * *
22973 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-A
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
* * *
23037 ATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATAAAT
66 ATAAATTAATCCATATTTTAAAATAAATCAATAT-ATACTAATAACTTATTTAAAATAAATCAAT
23101 -CA-AT
130 CCATAT
* * **
23105 CTATACAAATACAAT-AATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATACTAA-TAA
1 -TTTA-AAATA-AATCAATACATACTAATAAATTA-TTTAAAATAAATCAATCCATAC-AACTAA
* **
23165 ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAACTTATTTAAAA
61 A--A--T-AAATAAATTAATCCATATTTTAAAATAAATCAATATATACTAATAACTTATTTAAAA
23230 TAAATCAATCCATAT
121 TAAATCAATCCATAT
* * *
23245 TTTAAAATAAATTAATACATACTAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-A
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
* *
23309 ATAAATTAATTCATATTTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATC
66 ATAAATTAATCCATATTTTAAAATAAATCAATATATACTAATAACTTATTTAAAATAAATCAATC
23374 CATAT
131 CATAT
* ***
23379 TTTAAAATAAATTAATACATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
* * * *
23443 ATCAATTCATACTAATAAATTATTTAAAATAAATCAATATATAC-AACT-AC--A---ATAATAA
66 ATAAATTAAT-C-CAT--A-T-TTTAAAATAAATCAATATATACTAA-TAACTTATTTAAAATAA
*
23501 ATCAATCTATAT
124 ATCAATCCATAT
* * ***
23513 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCGATA-TTTTAAAATAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
** * ** *
23577 ATCAATTCATATTAATAAACTATTTAAAAATAAATCAATCCATAC-AACT-AC--A---ATAATA
66 AT--A---A-ATTAATCCA-TATTTTAAAATAAATCAATATATACTAA-TAACTTATTTAAAATA
*
23635 AATCAATCCATGT
123 AATCAATCCATAT
* *
23648 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAATTCAATC
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATC
23697 TATATTTTAA
Statistics
Matches: 513, Mismatches: 45, Indels: 64
0.82 0.07 0.10
Matches are distributed among these distances:
131 2 0.00
132 29 0.06
133 11 0.02
134 218 0.42
135 93 0.18
136 5 0.01
137 5 0.01
138 76 0.15
139 14 0.03
140 58 0.11
141 2 0.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (135 bp):
TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
ATAAATTAATCCATATTTTAAAATAAATCAATATATACTAATAACTTATTTAAAATAAATCAATC
CATAT
Found at i:23349 original size:188 final size:189
Alignment explanation
Indices: 23036--23853 Score: 1160
Period size: 188 Copynumber: 4.3 Consensus size: 189
23026 CAACTACAAT
*
23036 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTT---A-AAATAAAT
* * *
23101 CAATCTATACAAATACAATAATAAATCAA-TCCATATTTTAAAATAAATCAATCCATACTAATAA
62 CAATCTATACAACTACAATAATAAATCAATTCTATATTTTAAAATAAATCAATCTATACTAATAA
*
23165 ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAACTTATTTAA
127 ATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
23228 AATAAATCAATCCATATTTTAAAATAAATTAATACATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT
* *
23293 CTATACAACTACAATAATAAATTAATTC-ATATTTTAAAATAAATCAATATATACTAATAAATTA
66 CTATACAACTACAATAATAAATCAATTCTATATTTTAAAATAAATCAATCTATACTAATAAATTA
* *
23357 TTTAAAATAAATCAATCCATATTTTAAAATAAATTAATACATACTAATAAATTATTTAA
131 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
23416 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT
*
23481 ATATACAACTACAATAATAAATCAA-TCTATATTTTAAAATAAATCAAT-TCATACTAATAAATT
66 CTATACAACTACAATAATAAATCAATTCTATATTTTAAAATAAATCAATCT-ATACTAATAAATT
* * * *
23544 ATTTAAAATAAATCAATCGATATTTTAAAATAAATCAATTCATATTAATAAACTATTTAAA
130 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT-AA
* * * **
23605 AATAAATCAATCCATA----CAACTACAAT-AATAAAT-C-AATCCATGT-TTTAAAATAAATCA
1 AATAAATCAATCCATATTTTAAAATA-AATCAATACATACTAATAAAT-TATTTAAAATAAATCA
* * * *
23662 ATCCATACTAA-TAAATTATTTAAAATAATTCAA-TCTATATTTTAAAATAAATCAATCGATACT
64 ATCTATAC-AACTACA--A--T--AATAAATCAATTCTATATTTTAAAATAAATCAATCTATACT
23725 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
122 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
23790 TAA
187 TAA
* *
23793 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATCATTTAAAATAAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAAT
23854 TATTTTAAAA
Statistics
Matches: 564, Mismatches: 40, Indels: 42
0.87 0.06 0.07
Matches are distributed among these distances:
183 28 0.05
184 4 0.01
185 10 0.02
186 3 0.01
187 4 0.01
188 315 0.56
189 120 0.21
191 3 0.01
192 59 0.10
193 1 0.00
194 17 0.03
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (189 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT
CTATACAACTACAATAATAAATCAATTCTATATTTTAAAATAAATCAATCTATACTAATAAATTA
TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:23366 original size:32 final size:33
Alignment explanation
Indices: 23325--23486 Score: 107
Period size: 32 Copynumber: 4.7 Consensus size: 33
23315 TAATTCATAT
23325 TTTAAAATAAATCAATATATACT-AATAAATTA
1 TTTAAAATAAATCAATATATACTAAATAAATTA
**
23357 TTTAAAATAAATCAATCCATATTTTAAAATAAATTAA
1 TTTAAAATAAATCAAT--ATATACT-AAATAAATT-A
* * * * * * *
23394 TACATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 T--TTA-AAATAAATCAATATATACTAAATAAAT---TA
23432 TTTTAAAATAAATCAAT-TCATACT-AATAAATTA
1 -TTTAAAATAAATCAATAT-ATACTAAATAAATTA
23465 TTTAAAATAAATCAATATATAC
1 TTTAAAATAAATCAATATATAC
23487 AACTACAATA
Statistics
Matches: 99, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
32 36 0.36
33 3 0.03
34 5 0.05
36 29 0.29
37 12 0.12
38 1 0.01
39 6 0.06
40 7 0.07
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (33 bp):
TTTAAAATAAATCAATATATACTAAATAAATTA
Found at i:23383 original size:22 final size:22
Alignment explanation
Indices: 23357--23399 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
23347 TAATAAATTA
*
23357 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
*
23379 TTTAAAATAAATTAATACATA
1 TTTAAAATAAATCAATACATA
23400 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:23436 original size:22 final size:22
Alignment explanation
Indices: 23411--23453 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
23401 TAATAAATTA
23411 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
23433 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
23454 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:23462 original size:22 final size:22
Alignment explanation
Indices: 23413--23461 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23403 ATAAATTATT
**
23413 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
23435 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
23458 TAAA
1 TAAA
23462 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:23552 original size:32 final size:31
Alignment explanation
Indices: 23513--23621 Score: 101
Period size: 33 Copynumber: 3.7 Consensus size: 31
23503 CAATCTATAT
23513 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAA-TA
*
23545 TTTAAAATAAATC-A---AT-C-GAT--AT-
1 TTTAAAATAAATCAATTCATACTAATAAATA
*
23567 TTTAAAATAAATCAATTCATATTAATAAACTA
1 TTTAAAATAAATCAATTCATACTAATAAA-TA
*
23599 TTTAAAAATAAATCAATCCATAC
1 TTT-AAAATAAATCAATTCATAC
23622 AACTACAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
22 13 0.21
23 2 0.03
24 1 0.02
26 4 0.07
27 1 0.02
28 4 0.07
30 1 0.02
31 2 0.03
32 16 0.26
33 17 0.28
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATTCATACTAATAAATA
Found at i:23677 original size:22 final size:23
Alignment explanation
Indices: 23603--23676 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 23
23593 AAACTATTTA
23603 AAAATAAATCAATCCATAC-AACT
1 AAAATAAATCAATCCATACTAA-T
* **
23626 ACAATAATAAATCAATCCAT-GTTTT
1 --AA-AATAAATCAATCCATACTAAT
23651 AAAATAAATCAATCCATACTAAT
1 AAAATAAATCAATCCATACTAAT
23674 AAA
1 AAA
23677 TTATTTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 15 0.38
23 7 0.17
25 3 0.08
26 15 0.38
ACGTcount: A:0.54, C:0.18, G:0.01, T:0.27
Consensus pattern (23 bp):
AAAATAAATCAATCCATACTAAT
Found at i:23689 original size:32 final size:32
Alignment explanation
Indices: 23648--23853 Score: 175
Period size: 32 Copynumber: 7.4 Consensus size: 32
23638 CAATCCATGT
23648 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
23680 TTTAAAAT-AAT---TCAAT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
23702 TTTAAAATAAATCAATCGATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
23734 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
23756 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
23788 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
23810 TTTAAAATAAATCAATCCATACTAATAAATCA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
23842 TTTAAAATAAAT
1 TTTAAAATAAAT
23854 TATTTTAAAA
Statistics
Matches: 140, Mismatches: 4, Indels: 60
0.69 0.02 0.29
Matches are distributed among these distances:
22 40 0.29
23 8 0.06
24 3 0.02
26 12 0.09
27 4 0.03
28 12 0.09
30 3 0.02
31 6 0.04
32 52 0.37
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:23696 original size:54 final size:54
Alignment explanation
Indices: 23631--23905 Score: 402
Period size: 54 Copynumber: 5.1 Consensus size: 54
23621 CAACTACAAT
*
23631 AATAAATCAATCCATGTTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
23685 AATAATTCAATCTATATTTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
23739 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
23793 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATCATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
23847 AAT--A--AAT---TATTTTAAAATAAATCAATCCATATTTTAAAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA--CT--AATAAATTA-TTTAA
23899 AATAAAT
1 AATAAAT
23906 AACCTTATTA
Statistics
Matches: 203, Mismatches: 10, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
47 24 0.12
49 1 0.00
50 3 0.01
51 8 0.04
52 9 0.04
54 158 0.78
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:23759 original size:108 final size:108
Alignment explanation
Indices: 23308--23905 Score: 560
Period size: 108 Copynumber: 5.6 Consensus size: 108
23298 CAACTACAAT
* * **
23308 AATAAATTAATTCATATTTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
23373 CCATATTTTAAAATAAATTAATACATACTAATAAATTATTTAA
66 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
23416 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
** *** * * *
23481 ATATACAACTACAAT-AATAAATCAAT-CT-AT--A-T-TTTAA
66 CCATA-TTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * *
23518 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCGATATTTTAAAATAAATCAAT
1 AATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATCCATA--CT--AATAAATTATT
* * * * * *
23583 TCATATTAAT-AA-AC-TATTTAAAAATAAATCAATCCATAC-AACTACA--A--T--
52 TAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
* *
23631 AATAAATCAATCCATGTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAATTCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
23696 CTATATTTTAAAATAAATCAATCGATACTAATAAATTATTTAA
66 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
23739 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
23804 CCATATTTTAAAATAAATCAATCCATACTAATAAATCATTTAA
66 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
23847 AAT--A--AAT---TATTTTAAAATAAATCAATCCATATTTTAAAATAAATTATTTTAAAATAAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATA--CT--AATAAATTA-TTTAAAATAAA
23905 T
61 T
23906 AACCTTATTA
Statistics
Matches: 404, Mismatches: 49, Indels: 76
0.76 0.09 0.14
Matches are distributed among these distances:
99 15 0.04
100 2 0.00
101 25 0.06
102 41 0.10
103 26 0.06
104 6 0.01
105 9 0.02
106 17 0.04
107 4 0.01
108 180 0.45
109 6 0.01
110 1 0.00
111 1 0.00
112 25 0.06
113 21 0.05
114 4 0.01
115 4 0.01
116 16 0.04
117 1 0.00
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.36
Consensus pattern (108 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:23760 original size:22 final size:22
Alignment explanation
Indices: 23734--23776 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
23724 TAATAAATTA
23734 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
23756 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
23777 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:23782 original size:18 final size:18
Alignment explanation
Indices: 23761--23841 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
23751 CATATTTTAA
23761 AATAAATCAATCCATACT
1 AATAAATCAATCCATACT
* * *
23779 AATAAAT-TAT--TTA-A
1 AATAAATCAATCCATACT
*
23793 AATAAATCAATCCATATTTT
1 AATAAATCAATCCATA--CT
23813 AAAATAAATCAATCCATACT
1 --AATAAATCAATCCATACT
23833 AATAAATCA
1 AATAAATCA
23842 TTTAAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
14 7 0.15
15 4 0.08
17 4 0.08
18 16 0.33
20 1 0.02
22 16 0.33
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATCAATCCATACT
Found at i:23785 original size:22 final size:22
Alignment explanation
Indices: 23736--23784 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
23726 ATAAATTATT
**
23736 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
23758 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
23781 TAAA
1 TAAA
23785 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:23814 original size:22 final size:22
Alignment explanation
Indices: 23788--23890 Score: 104
Period size: 22 Copynumber: 4.5 Consensus size: 22
23778 TAATAAATTA
23788 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
23810 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** *
23833 AATAAATCATTTAAAATAAAT---TAT
1 TTTAAA--A--T-AAATCAATCCATAT
23857 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
23879 TTTAAAATAAAT
1 TTTAAAATAAAT
23891 TATTTTAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
19 7 0.11
20 1 0.02
22 37 0.56
23 5 0.08
24 5 0.08
25 3 0.05
27 1 0.02
28 7 0.11
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:23862 original size:15 final size:15
Alignment explanation
Indices: 23833--23905 Score: 67
Period size: 15 Copynumber: 4.5 Consensus size: 15
23823 AATCCATACT
*
23833 AATAAATCA-TTTAA
1 AATAAATTATTTTAA
23847 AATAAATTATTTTAA
1 AATAAATTATTTTAA
23862 AATAAATCAATCCATATTTTAA
1 AAT--A--AAT---TATTTTAA
23884 AATAAATTATTTTAA
1 AATAAATTATTTTAA
23899 AATAAAT
1 AATAAAT
23906 AACCTTATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
14 8 0.16
15 23 0.46
17 1 0.02
18 3 0.06
19 3 0.06
20 1 0.02
22 11 0.22
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:26446 original size:23 final size:23
Alignment explanation
Indices: 26391--26448 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
26381 GGCGGGTTAT
*
26391 ATATATTATATTTAATATTTTGAG
1 ATATATTAT-TTTAATATTTTGAA
* *
26415 ATTTTTTATTTT-ATATTGTTGAA
1 ATATATTATTTTAATATT-TTGAA
26438 ATATATTATTT
1 ATATATTATTT
26449 AATTATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 5 0.18
23 16 0.57
24 7 0.25
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
ATATATTATTTTAATATTTTGAA
Found at i:26546 original size:43 final size:42
Alignment explanation
Indices: 26436--26552 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
26426 TATATTGTTG
* *
26436 AAATATATTA-TTTAATTATTAAAA-ATAAAAAATTATTATA
1 AAATATATTATTTTAATTATTAAAATATAATAAATAATTATA
** *
26476 AAATATATTATTTTAACAACTTGAAATATAATAAATAATTAT-
1 AAATATATTATTTTAATTA-TTAAAATATAATAAATAATTATA
26518 AAATATATTATTTTAATTATTTTAAAATATTAATA
1 AAATATATTATTTTAATTA--TTAAAATA-TAATA
26553 TATTTTGATC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
40 10 0.16
41 6 0.10
42 22 0.35
43 20 0.32
44 5 0.08
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (42 bp):
AAATATATTATTTTAATTATTAAAATATAATAAATAATTATA
Found at i:27795 original size:50 final size:51
Alignment explanation
Indices: 27722--27823 Score: 179
Period size: 50 Copynumber: 2.0 Consensus size: 51
27712 AATGTCATTC
*
27722 AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATAT-CAATATTA
1 AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATATGAAATATTA
*
27772 AATAAATTCTATTAACATTATATAAGTTTATATTTAGTATATGAAATATTA
1 AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATATGAAATATTA
27823 A
1 A
27824 TTCTTAACGA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 41 0.84
51 8 0.16
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (51 bp):
AATAAATTCTATTAACATTATATAAGTTTATACTTAGTATATGAAATATTA
Found at i:32033 original size:17 final size:18
Alignment explanation
Indices: 32011--32044 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
32001 TCAGCCGGTC
32011 TGGTTC-GAACGGTTCAG
1 TGGTTCTGAACGGTTCAG
*
32028 TGGTTCTGACCGGTTCA
1 TGGTTCTGAACGGTTCA
32045 CTAATAGCGG
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:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (18 bp):
TGGTTCTGAACGGTTCAG
Found at i:39504 original size:7 final size:7
Alignment explanation
Indices: 39494--39562 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
39484 ATGTTTAATG
*
39494 TTTATGA
1 TTTAGGA
39501 TTTAGGA
1 TTTAGGA
39508 TTTAAGG-
1 TTT-AGGA
*
39515 TTTAGGG
1 TTTAGGA
*
39522 TTTA-TA
1 TTTAGGA
39528 CTTTAGGA
1 -TTTAGGA
*
39536 TTTATGA
1 TTTAGGA
*
39543 TTTAGGT
1 TTTAGGA
*
39550 TTTAGGT
1 TTTAGGA
39557 TTTAGG
1 TTTAGG
39563 GTTCATTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
6 3 0.06
7 44 0.86
8 4 0.08
ACGTcount: A:0.23, C:0.01, G:0.25, T:0.51
Consensus pattern (7 bp):
TTTAGGA
Found at i:39511 original size:14 final size:14
Alignment explanation
Indices: 39494--39553 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
39484 ATGTTTAATG
39494 TTTATGATTTAGGA
1 TTTATGATTTAGGA
* * *
39508 TTTAAGGTTTAGGG
1 TTTATGATTTAGGA
39522 TTTAT-ACTTTAGGA
1 TTTATGA-TTTAGGA
*
39536 TTTATGATTTAGGT
1 TTTATGATTTAGGA
39550 TTTA
1 TTTA
39554 GGTTTTAGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 36 0.97
15 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.22, T:0.52
Consensus pattern (14 bp):
TTTATGATTTAGGA
Found at i:39511 original size:28 final size:28
Alignment explanation
Indices: 39471--39539 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
39461 CACATAATCG
* * *
39471 GATTTAGGGTTTAATGTTTAATGTTTAT
1 GATTTAGGATTTAAGGTTTAAGGTTTAT
*
39499 GATTTAGGATTTAAGGTTTAGGGTTTAT
1 GATTTAGGATTTAAGGTTTAAGGTTTAT
39527 -ACTTTAGGATTTA
1 GA-TTTAGGATTTA
39540 TGATTTAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 1 0.03
28 35 0.97
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.49
Consensus pattern (28 bp):
GATTTAGGATTTAAGGTTTAAGGTTTAT
Found at i:39546 original size:28 final size:28
Alignment explanation
Indices: 39471--39562 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
39461 CACATAATCG
* **
39471 GATTTAGGGTTTAATG-TTTAATGTTTAT
1 GATTTAGGATTTAA-GATTTAGGGTTTAT
*
39499 GATTTAGGATTTAAGGTTTAGGGTTTAT
1 GATTTAGGATTTAAGATTTAGGGTTTAT
* * *
39527 -ACTTTAGGATTTATGATTTAGGTTTTAG
1 GA-TTTAGGATTTAAGATTTAGGGTTTAT
*
39555 GTTTTAGG
1 GATTTAGG
39563 GTTCATTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
27 2 0.04
28 51 0.96
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.50
Consensus pattern (28 bp):
GATTTAGGATTTAAGATTTAGGGTTTAT
Found at i:40113 original size:14 final size:14
Alignment explanation
Indices: 40094--40136 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40084 TTTATAATTA
40094 TTAATAATGTATTT
1 TTAATAATGTATTT
40108 TTAAT-A--TATTT
1 TTAATAATGTATTT
*
40119 TTAATAATGTAATT
1 TTAATAATGTATTT
40133 TTAA
1 TTAA
40137 AAAATCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 10 0.40
12 1 0.04
13 1 0.04
14 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TTAATAATGTATTT
Found at i:44791 original size:59 final size:60
Alignment explanation
Indices: 44722--44897 Score: 293
Period size: 59 Copynumber: 3.0 Consensus size: 60
44712 ATCAAATATC
*
44722 ACTGAACTATACTCAATTGATCGCTTTCATCCTTCAACTTTCAAAAGTTACAATATGG-T
1 ACTGAACTATACTCAATTGATCACTTTCATCCTTCAACTTTCAAAAGTTACAATATGGTT
* *
44781 -CGTGAACTATACTCAATTGATTACTTTCATCCTTCAACTTTCAAAAATTACAATATGGTT
1 AC-TGAACTATACTCAATTGATCACTTTCATCCTTCAACTTTCAAAAGTTACAATATGGTT
*
44841 ACTGAACTATACTCAATTGATCACTTTCATCCTTAAACTTTCAAAAGTTACAATATG
1 ACTGAACTATACTCAATTGATCACTTTCATCCTTCAACTTTCAAAAGTTACAATATG
44898 ATCATTATAA
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
58 1 0.01
59 53 0.49
60 53 0.49
61 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (60 bp):
ACTGAACTATACTCAATTGATCACTTTCATCCTTCAACTTTCAAAAGTTACAATATGGTT
Found at i:47137 original size:21 final size:20
Alignment explanation
Indices: 47085--47138 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
47075 TAATAGAAAG
47085 AAAATAA-ATAAATAAATAA
1 AAAATAATATAAATAAATAA
*
47104 AAACAT-ATAATAAATGAATAA
1 AAA-ATAAT-ATAAATAAATAA
47125 AATAATAATATAAA
1 AA-AATAATATAAA
47139 AATATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.14
20 2 0.07
21 20 0.69
22 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAATAATATAAATAAATAA
Found at i:47259 original size:36 final size:36
Alignment explanation
Indices: 47137--47285 Score: 164
Period size: 37 Copynumber: 4.1 Consensus size: 36
47127 TAATAATATA
* * *
47137 AAAAT-ATTTTAAAAAATTATATAATATACATTTTCCC
1 AAAATAATTTTAAAAAACTATATATTATATATTTT--C
** *
47174 AAAATGTTTTTTAAAAACTATATAATATATATATTTTC
1 AAAATAATTTTAAAAAACTATAT-AT-TATATATTTTC
47212 -AAA-AATGTTTAAAAAACTATATATTATATATTTTC
1 AAAATAAT-TTTAAAAAACTATATATTATATATTTTC
47247 AAAATAATTTTAAAAAACTATATA-T-TATATTTTC
1 AAAATAATTTTAAAAAACTATATATTATATATTTTC
47281 AAAAT
1 AAAAT
47286 GTTTTTTTAA
Statistics
Matches: 98, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
34 14 0.14
35 12 0.12
36 22 0.22
37 25 0.26
38 15 0.15
39 1 0.01
40 9 0.09
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (36 bp):
AAAATAATTTTAAAAAACTATATATTATATATTTTC
Found at i:47269 original size:34 final size:35
Alignment explanation
Indices: 47198--47285 Score: 121
Period size: 34 Copynumber: 2.5 Consensus size: 35
47188 AAACTATATA
47198 ATATATATATTTTC-AAA-AATGTTTAAAAAACTAT
1 ATATATATATTTTCAAAATAATGTTTAAAAAAC-AT
47232 ATATTATATATTTTCAAAATAAT-TTTAAAAAAC-T
1 ATA-TATATATTTTCAAAATAATGTTTAAAAAACAT
47266 ATATATTATATTTTCAAAAT
1 ATATA-TATATTTTCAAAAT
47286 GTTTTTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
33 2 0.04
34 21 0.42
35 11 0.22
36 13 0.26
37 3 0.06
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (35 bp):
ATATATATATTTTCAAAATAATGTTTAAAAAACAT
Found at i:47313 original size:73 final size:76
Alignment explanation
Indices: 47136--47317 Score: 193
Period size: 73 Copynumber: 2.5 Consensus size: 76
47126 ATAATAATAT
* * ** *
47136 AAAAATATTTTAAAAAATTATATAATATACAT-TTTCCCAAAATGTTTTTTAAAAACTATATAAT
1 AAAAATGTTTTAAAAAATTATATAATATATATATTTCCCAAAATAATTTTAAAAAAC-ATATAAT
47200 ATATATATTTTC
65 ATATATATTTTC
* *
47212 AAAAATG-TTTAAAAAACTATAT-AT-TATATATTT-TCAAAATAATTTTAAAAAAC-TAT-ATA
1 AAAAATGTTTTAAAAAATTATATAATATATATATTTCCCAAAATAATTTTAAAAAACATATAATA
47271 T-TATATTTTC
66 TATATATTTTC
* *
47281 -AAAATGTTTTTTTAAAAGTTATATAATATATATATTT
1 AAAAATG--TTTTAAAAAATTATATAATATATATATTT
47318 AAAATGTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
68 6 0.07
69 9 0.10
70 4 0.04
71 15 0.17
72 2 0.02
73 29 0.32
74 5 0.06
75 14 0.16
76 6 0.07
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (76 bp):
AAAAATGTTTTAAAAAATTATATAATATATATATTTCCCAAAATAATTTTAAAAAACATATAATA
TATATATTTTC
Found at i:47322 original size:37 final size:36
Alignment explanation
Indices: 47143--47333 Score: 194
Period size: 36 Copynumber: 5.2 Consensus size: 36
47133 TATAAAAATA
* *
47143 TTTTAAAAAATTATATAATATACATTTTCCCAAAATGT
1 TTTTAAAAAACTATATAATATATATTTT--CAAAATGT
*
47181 TTTTTAAAAACTATATAATATATATATTTTCAAAAATG-
1 TTTTAAAAAACTATAT-A-ATATATATTTTC-AAAATGT
* **
47219 -TTTAAAAAACTATATATTATATATTTTCAAAATAA
1 TTTTAAAAAACTATATAATATATATTTTCAAAATGT
47254 TTTTAAAAAACTATAT-AT-TATATTTTCAAAATGTT
1 TTTTAAAAAACTATATAATATATATTTTCAAAATG-T
* **
47289 TTTTTAAAAGTTATATAATATATATATTT-AAAATGT
1 TTTTAAAAAACTATATAATATATAT-TTTCAAAATGT
*
47325 TTTTCAAAA
1 TTTTAAAAA
47334 GAGAAAATCG
Statistics
Matches: 131, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
34 19 0.15
35 25 0.19
36 27 0.21
37 25 0.19
38 18 0.14
39 7 0.05
40 10 0.08
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTAAAAAACTATATAATATATATTTTCAAAATGT
Found at i:47440 original size:19 final size:20
Alignment explanation
Indices: 47416--47466 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
47406 AATGACCAAT
47416 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
47435 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
47455 AAAATCGCAACG
1 AAAATCGCAACG
47467 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:47460 original size:20 final size:20
Alignment explanation
Indices: 47416--47713 Score: 159
Period size: 20 Copynumber: 14.6 Consensus size: 20
47406 AATGACCAAT
* *
47416 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
47435 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
47455 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
***
47475 AAAATCGCAACG-GACAAAAG
1 AAAATCGCAACGCGA-TTTAG
* * **
47495 AAAATCGCAACACGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
47516 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
47539 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
47559 TCAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
47579 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
47599 AGAGTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
47619 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
* * * *
47642 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
47662 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
47682 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
47702 AAAATCGCAACG
1 AAAATCGCAACG
47714 TTAAAAAGAA
Statistics
Matches: 224, Mismatches: 46, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
19 18 0.08
20 162 0.72
21 15 0.07
22 1 0.00
23 28 0.12
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:47594 original size:40 final size:40
Alignment explanation
Indices: 47520--47711 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
47510 GCTTCCAAGT
***
47520 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTCAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
47563 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
47603 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTT---AGAGAATCGCAATGCGATTGAGAGAA
* * *
47646 TCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
47686 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAGAATCGCAA
47712 CGTTAAAAAG
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
40 78 0.61
42 2 0.02
43 48 0.38
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:47631 original size:83 final size:83
Alignment explanation
Indices: 47520--47703 Score: 287
Period size: 83 Copynumber: 2.2 Consensus size: 83
47510 GCTTCCAAGT
* ** * * *
47520 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTCAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGACAATCGCAATGCGACTGAGAGAATC
*
47585 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAA
* *
47603 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGACAATCGCAATGCGACTGAGAGAATC
47668 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAGAGAA
47686 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
47704 AATCGCAACG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGACAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAA
Found at i:47723 original size:20 final size:20
Alignment explanation
Indices: 47700--47743 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
47690 AACGCGATTT
*
47700 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
47720 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
47740 AGAA
1 AGAA
47744 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:47832 original size:6 final size:6
Alignment explanation
Indices: 47821--47877 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
47811 GACACGTATT
47821 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
47869 ACCACG ACC
1 ACCACG ACC
47878 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:48582 original size:6 final size:6
Alignment explanation
Indices: 48566--48639 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
48556 TCTCGTCTCG
48566 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
48613 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
48640 AATACGTGTC
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:48742 original size:20 final size:20
Alignment explanation
Indices: 48717--48760 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
48707 TTTTTAACTA
*
48717 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
48737 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
48757 TTCT
1 TTCT
48761 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:48770 original size:20 final size:20
Alignment explanation
Indices: 48747--49148 Score: 175
Period size: 20 Copynumber: 19.6 Consensus size: 20
48737 TTCTTTTTAA
48747 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
*
48767 CGTTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
48787 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
48807 CATTGCGATTCTCTTAGTCG
1 CGTTGCGATTTTCTAAATCG
*
48827 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
48850 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
48870 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
48890 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
48910 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
48933 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
48954 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
48972 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
*
48994 TGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
49014 CGTTGCGATTTT-GATATACG
1 CGTTGCGATTTTCTAAAT-CG
* ** *
49034 CGTTGCGATTTATGT-GTTCA
1 CGTTGCGATTT-TCTAAATCG
*
49054 CGTTGCGATTTTC-ATATTCG
1 CGTTGCGATTTTCTA-AATCG
* **
49074 CGTTGCTATTTTGGAAAATCG
1 CGTTGCGATTTT-CTAAATCG
** * * *
49095 CAATGCGAATTTGTACTATCG
1 CGTTGCGATTTTCTA-AATCG
* *
49116 CATTGCGATTTTCAAGAATCG
1 CGTTGCGATTTTCTA-AATCG
49137 CGTTGCGATTTT
1 CGTTGCGATTTT
49149 GGAAACTGAT
Statistics
Matches: 295, Mismatches: 68, Indels: 37
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.01
19 4 0.01
20 197 0.67
21 59 0.20
22 6 0.02
23 27 0.09
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:48791 original size:40 final size:40
Alignment explanation
Indices: 48749--48940 Score: 204
Period size: 40 Copynumber: 4.7 Consensus size: 40
48739 CTTTTTAACG
* *
48749 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTAAATCGCG
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * * *
48789 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTTAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
48829 TTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA-T-T-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * **
48872 TTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
48912 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
48941 ACTTGGAAGC
Statistics
Matches: 123, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
40 71 0.58
41 2 0.02
42 4 0.03
43 46 0.37
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:48855 original size:83 final size:83
Alignment explanation
Indices: 48757--48940 Score: 269
Period size: 83 Copynumber: 2.2 Consensus size: 83
48747 CGTTGCGATT
* * * * * ** *
48757 TTCTAAATCGCGTTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTT
1 TTCTAAATCGCGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
*
48822 AGTCGCATTGCGATTCTC
66 AATCGCATTGCGATTCTC
*
48840 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
1 TTCTAAATCGCGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
*
48905 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTC
48923 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
48941 ACTTGGAAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 90 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
AATCGCATTGCGATTCTC
Found at i:48863 original size:63 final size:62
Alignment explanation
Indices: 48749--48900 Score: 218
Period size: 63 Copynumber: 2.5 Consensus size: 62
48739 CTTTTTAACG
* * * *
48749 TTGCGATTTTCTAAATCGCGTTGCGA-T-TCTCTAAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCTAAATCGCGTTGCGACTCTCTCAATCGCA
* *
48809 TTGCGATTCTCTTAGTCGCATTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTC-TCTAAATCGCGTTGCGACTCTCTCAATCGCA
*
48872 TTGCGATTCTATAAATCGCATTGCGATTC
1 TTGCGATTCTCTAAATCGCATTGCGATTC
48901 AATCAATCGC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
60 22 0.28
61 1 0.01
62 2 0.03
63 55 0.69
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (62 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCTAAATCGCGTTGCGACTCTCTCAATCGCA
Found at i:49337 original size:36 final size:36
Alignment explanation
Indices: 49290--49463 Score: 142
Period size: 36 Copynumber: 4.7 Consensus size: 36
49280 CGATTTTCTC
49290 TTTTCAAAAACTATATAATATATATTTTCAAAATGT
1 TTTTCAAAAACTATATAATATATATTTTCAAAATGT
49326 TTTTCAAAAACTATATATTATATATATATTTCAAAATG-
1 TTTTCAAAAACTATATA--ATATATAT-TTTCAAAATGT
* *
49364 TTTT-AAAAACTATATATTATATTTAAGTTTTCAAAAAATAT
1 TTTTCAAAAACTATATA--ATATAT-A-TTTTC--AAAATGT
* * * *
49405 TTTT-TAAAACCATATATTATATAATTTCCAAAAT-T
1 TTTTCAAAAACTATATAATATAT-ATTTTCAAAATGT
* *
49440 ATTTCAAACTA-TATATAATATATA
1 TTTTCAAA-AACTATATAATATATA
49464 CTTAAAAAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
35 5 0.04
36 34 0.29
37 20 0.17
38 21 0.18
39 17 0.15
40 5 0.04
41 14 0.12
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (36 bp):
TTTTCAAAAACTATATAATATATATTTTCAAAATGT
Found at i:49380 original size:39 final size:38
Alignment explanation
Indices: 49290--49463 Score: 159
Period size: 38 Copynumber: 4.7 Consensus size: 38
49280 CGATTTTCTC
49290 TTTTCAAAAAC--TATATAATATATATTTTCAAAATGT
1 TTTTCAAAAACTATATATAATATATATTTTCAAAATGT
*
49326 TTTTCAAAAACTATATATTATATATATATTTCAAAATG-
1 TTTTCAAAAACTATATATAATATATAT-TTTCAAAATGT
* * *
49364 TTTT-AAAAACTATATATTATATTTAAGTTTTCAAAAAATAT
1 TTTTCAAAAACTATATATAATATAT-A-TTTTC--AAAATGT
* * * *
49405 TTTT-TAAAACCATATATTATATA-ATTTCCAAAAT-T
1 TTTTCAAAAACTATATATAATATATATTTTCAAAATGT
*
49440 ATTTC--AAACTATATATAATATATA
1 TTTTCAAAAACTATATATAATATATA
49464 CTTAAAAAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
34 15 0.13
35 5 0.04
36 16 0.14
37 19 0.16
38 26 0.22
39 12 0.10
40 5 0.04
41 20 0.17
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (38 bp):
TTTTCAAAAACTATATATAATATATATTTTCAAAATGT
Found at i:49742 original size:36 final size:36
Alignment explanation
Indices: 49660--50042 Score: 397
Period size: 36 Copynumber: 10.5 Consensus size: 36
49650 TTCAGCAAAA
* *
49660 ATATTTTCAAAATAATTTTAAAAAACTATAT-AT-T
1 ATATTTTCAAAATATTTTTCAAAAACTATATAATAT
* *
49694 ATATTTTCAAAATATTTTTTAAAAGCTATATAATAT
1 ATATTTTCAAAATATTTTTCAAAAACTATATAATAT
*
49730 ATATATTT-AAAATGTTTTTCAAAAACTATATAATAT
1 ATAT-TTTCAAAATATTTTTCAAAAACTATATAATAT
* *
49766 ATATTTTCAAAATGTTTTTCAAAAACTATATATTAT
1 ATATTTTCAAAATATTTTTCAAAAACTATATAATAT
* *
49802 ATATTTTCAAAATAATTTTAAAAAACTATAT-AT-T
1 ATATTTTCAAAATATTTTTCAAAAACTATATAATAT
* *
49836 ATATTTTCAAAATATTTTTTAAAAGCTATATAATAT
1 ATATTTTCAAAATATTTTTCAAAAACTATATAATAT
*
49872 ATATATTT-AAAATGTTTTTCAAAAACTATATAATAT
1 ATAT-TTTCAAAATATTTTTCAAAAACTATATAATAT
*
49908 ATATTTTCAAAATGTTTTTCAAAAACTATATATATTATAT
1 ATATTTTCAAAATATTTTTCAAAAAC--TATATA--ATAT
*
49948 ATATATTTCAAAAT-GTTTT-AAAAACTATATATTATAT
1 ATAT-TTTCAAAATATTTTTCAAAAACTATATA--ATAT
* * * *
49985 TTAAGTTTTCAAAAAATATTTTT-TAAAACCATATATTAT
1 AT-A-TTTTC--AAAATATTTTTCAAAAACTATATAATAT
*
50024 ATAATTTCCAAAATGATTT
1 AT-ATTTTCAAAAT-ATTT
50043 CAAGCTATAT
Statistics
Matches: 305, Mismatches: 25, Indels: 35
0.84 0.07 0.10
Matches are distributed among these distances:
34 57 0.19
35 11 0.04
36 146 0.48
37 23 0.08
38 15 0.05
39 13 0.04
40 17 0.06
41 23 0.08
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (36 bp):
ATATTTTCAAAATATTTTTCAAAAACTATATAATAT
Found at i:49832 original size:142 final size:145
Alignment explanation
Indices: 49660--49986 Score: 592
Period size: 142 Copynumber: 2.3 Consensus size: 145
49650 TTCAGCAAAA
49660 ATATTTTCAAAATAATTTTAAAAAACTATATATTATATTTTCAAAATATTTTTTAAAAGCTATAT
1 ATATTTTCAAAATAATTTTAAAAAACTATATATTATATTTTCAAAATATTTTTTAAAAGCTATAT
49725 AATATATATATTTAAAATGTTTTTCAAAAACTATATAATATATATTTTCAAAATGTTTTTCAAAA
66 AATATATATATTTAAAATGTTTTTCAAAAACTATATAATATATATTTTCAAAATGTTTTTCAAAA
49790 AC-TATATA-T-TAT
131 ACATATATATTATAT
49802 ATATTTTCAAAATAATTTTAAAAAACTATATATTATATTTTCAAAATATTTTTTAAAAGCTATAT
1 ATATTTTCAAAATAATTTTAAAAAACTATATATTATATTTTCAAAATATTTTTTAAAAGCTATAT
49867 AATATATATATTTAAAATGTTTTTCAAAAACTATATAATATATATTTTCAAAATGTTTTTCAAAA
66 AATATATATATTTAAAATGTTTTTCAAAAACTATATAATATATATTTTCAAAATGTTTTTCAAAA
49932 ACTATATATATTATAT
131 AC-ATATATATTATAT
*
49948 ATATATTTCAAAAT-GTTTT-AAAAACTATATATTATATTT
1 ATAT-TTTCAAAATAATTTTAAAAAACTATATATTATATTT
49987 AAGTTTTCAA
Statistics
Matches: 179, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
142 132 0.74
144 6 0.03
145 21 0.12
146 11 0.06
147 9 0.05
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (145 bp):
ATATTTTCAAAATAATTTTAAAAAACTATATATTATATTTTCAAAATATTTTTTAAAAGCTATAT
AATATATATATTTAAAATGTTTTTCAAAAACTATATAATATATATTTTCAAAATGTTTTTCAAAA
ACATATATATTATAT
Found at i:49848 original size:106 final size:107
Alignment explanation
Indices: 49660--50042 Score: 404
Period size: 106 Copynumber: 3.5 Consensus size: 107
49650 TTCAGCAAAA
* * * * *
49660 ATATTTTCAAAATAATTTTAAAAAACTATATA-T-TATATTTTCAAAATATTTTTTAAAAGCTAT
1 ATATTTTCAAAATATTTTTCAAAAACTATATATTATATATTTTCAAAATAATTTTAAAAAACTAT
49723 ATAATATATATATTT-AAAATGTTTTTCAAAAACTATATAATAT
66 AT-ATATATATATTTCAAAATGTTTTT-AAAAACTATATAATAT
*
49766 ATATTTTCAAAATGTTTTTCAAAAACTATATATTATATATTTTCAAAATAATTTTAAAAAACTAT
1 ATATTTTCAAAATATTTTTCAAAAACTATATATTATATATTTTCAAAATAATTTTAAAAAACTAT
* *
49831 ATAT-TATAT-TTTCAAAATATTTTTTAAAAGCTATATAATAT
66 ATATATATATATTTCAAAAT-GTTTTTAAAAACTATATAATAT
* * **
49872 ATATATTT-AAAATGTTTTTCAAAAACTATATAATATATATTTTCAAAATGTTTTTCAAAAACTA
1 ATAT-TTTCAAAATATTTTTCAAAAACTATATATTATATATTTTCAAAATAATTTT-AAAAA--A
*
49936 TATATATTATATATATATTTCAAAATG-TTTTAAAAACTATATATTATAT
62 -CTATA-TATATATATATTTCAAAATGTTTTTAAAAACTATATA--ATAT
* * * * *
49985 TTAAGTTTTCAAAAAATATTTTT-TAAAACCATATATTATATAATTTCCAAAATGATTT
1 AT-A-TTTTC--AAAATATTTTTCAAAAACTATATATTATAT-ATTTTCAAAATAATTT
50043 CAAGCTATAT
Statistics
Matches: 236, Mismatches: 21, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
105 3 0.01
106 102 0.43
107 16 0.07
108 29 0.12
109 1 0.00
110 4 0.02
111 18 0.08
112 5 0.02
113 14 0.06
114 4 0.02
115 1 0.00
116 15 0.06
117 24 0.10
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (107 bp):
ATATTTTCAAAATATTTTTCAAAAACTATATATTATATATTTTCAAAATAATTTTAAAAAACTAT
ATATATATATATTTCAAAATGTTTTTAAAAACTATATAATAT
Found at i:53136 original size:16 final size:16
Alignment explanation
Indices: 53115--53145 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53105 AAAAACAATT
*
53115 TAAATATTAAATATTA
1 TAAATAGTAAATATTA
53131 TAAATAGTAAATATT
1 TAAATAGTAAATATT
53146 TAATAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATAGTAAATATTA
Found at i:61520 original size:20 final size:20
Alignment explanation
Indices: 61497--61542 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
61487 CCAAAGTATT
61497 GAAACT-TTAATGAAAGTTTC
1 GAAACTCTTAA-GAAAGTTTC
* *
61517 GAAACTCTTGAGATAGTTTC
1 GAAACTCTTAAGAAAGTTTC
61537 GAAACT
1 GAAACT
61543 ATAGGAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (20 bp):
GAAACTCTTAAGAAAGTTTC
Found at i:61734 original size:19 final size:20
Alignment explanation
Indices: 61712--61756 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
61702 TAAAAGACTC
*
61712 ATTTTAAAGATTTGACAA-A
1 ATTTTAAAGATTTGAAAATA
**
61731 ATTTTAGGGATTTGAAAATA
1 ATTTTAAAGATTTGAAAATA
61751 ATTTTA
1 ATTTTA
61757 CGAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.42
Consensus pattern (20 bp):
ATTTTAAAGATTTGAAAATA
Found at i:66727 original size:23 final size:23
Alignment explanation
Indices: 66697--66781 Score: 152
Period size: 23 Copynumber: 3.7 Consensus size: 23
66687 GCACTCCTGC
*
66697 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCGATGCACCTGCCACT
66720 AGTGCATCGATGCACCTGCCACT
1 AGTGCATCGATGCACCTGCCACT
66743 AGTGCATCGATGCACCTGCCACT
1 AGTGCATCGATGCACCTGCCACT
*
66766 AGTTCATCGATGCACC
1 AGTGCATCGATGCACC
66782 ATGCAGTGCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (23 bp):
AGTGCATCGATGCACCTGCCACT
Found at i:66750 original size:46 final size:43
Alignment explanation
Indices: 66676--66800 Score: 153
Period size: 46 Copynumber: 2.8 Consensus size: 43
66666 AGGGTGTCAA
* * *
66676 AGTGTATCCATGCACTCCTGCAGTGCATCCATGCACCTGCCACT
1 AGTGCATCGATGCAC-CATGCAGTGCATCCATGCACCTGCCACT
*
66720 AGTGCATCGATGCACC-TGCCACTAGTGCATCGATGCACCTGCCACT
1 AGTGCATCGATGCACCATG---C-AGTGCATCCATGCACCTGCCACT
*
66766 AGTTCATCGATGCACCATGCAGTGCATCCATGCAC
1 AGTGCATCGATGCACCATGCAGTGCATCCATGCAC
66801 TCCATTTCAA
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
42 2 0.03
43 15 0.21
44 14 0.20
45 1 0.01
46 37 0.52
47 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (43 bp):
AGTGCATCGATGCACCATGCAGTGCATCCATGCACCTGCCACT
Found at i:75040 original size:19 final size:19
Alignment explanation
Indices: 74998--75040 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
74988 TTAACTTTTT
*
74998 CTTTTCTCTTTCTTTATTA
1 CTTTTCTCTTTCTTTATAA
*
75017 TTTTTCTCTTTCATTT-TAA
1 CTTTTCTCTTTC-TTTATAA
75036 CTTTT
1 CTTTT
75041 ACTTTTCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTCTCTTTCTTTATAA
Found at i:78865 original size:17 final size:16
Alignment explanation
Indices: 78834--78867 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
78824 CACGTGAGGA
78834 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
78850 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
78867 T
1 T
78868 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:80319 original size:17 final size:18
Alignment explanation
Indices: 80299--80337 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
80289 TATATTATAA
*
80299 TTATTTTTATAA-AATAT
1 TTATTTTAATAACAATAT
*
80316 TTATTTTAATAACTATAT
1 TTATTTTAATAACAATAT
80334 TTAT
1 TTAT
80338 ATATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTTTAATAACAATAT
Found at i:80327 original size:29 final size:30
Alignment explanation
Indices: 80295--80369 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
80285 AAAATATATT
80295 ATAATTATTTTTATAAAATATT-TATTTTA
1 ATAATTATTTTTATAAAATATTATATTTTA
* * * *
80324 ATAACTATATTTATATATTATTATATTTTA
1 ATAATTATTTTTATAAAATATTATATTTTA
*
80354 ATTATTTATTATTTAT
1 A-TAATTATT-TTTAT
80370 TATATTTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 18 0.50
30 8 0.22
31 5 0.14
32 5 0.14
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (30 bp):
ATAATTATTTTTATAAAATATTATATTTTA
Found at i:80349 original size:10 final size:10
Alignment explanation
Indices: 80334--80407 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 10
80324 ATAACTATAT
80334 TTATATATTA
1 TTATATATTA
*
80344 TTATATTTTAA
1 TTATATATT-A
*
80355 TTATTTATTA
1 TTATATATTA
80365 TT-TAT-TATA
1 TTATATAT-TA
*
80374 TT-TA-ATAA
1 TTATATATTA
80382 TTA-ATATTA
1 TTATATATTA
80391 TTATAT-TTA
1 TTATATATTA
80400 TT-TATATT
1 TTATATATT
80408 CATTTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
8 8 0.16
9 22 0.43
10 13 0.25
11 8 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATATATTA
Found at i:80350 original size:16 final size:16
Alignment explanation
Indices: 80329--80400 Score: 71
Period size: 16 Copynumber: 4.6 Consensus size: 16
80319 TTTTAATAAC
80329 TATATTTATATATTAT
1 TATATTTATATATTAT
80345 TATATTT-TA-ATTATT
1 TATATTTATATATTA-T
80360 TATTATTTATTATATT-T
1 TA-TATTTA-TATATTAT
* *
80377 AATAATTA-ATATTAT
1 TATATTTATATATTAT
80392 TATATTTAT
1 TATATTTAT
80401 TTATATTCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
14 9 0.20
15 12 0.27
16 17 0.38
17 2 0.04
18 2 0.04
19 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATTTATATATTAT
Found at i:80359 original size:25 final size:24
Alignment explanation
Indices: 80330--80398 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 24
80320 TTTAATAACT
80330 ATATTTATATATTATTATATTTTA
1 ATATTTATATATTATTATATTTTA
80354 ATTATTTAT-TATTTATTATA-TTTA
1 A-TATTTATATA-TTATTATATTTTA
*
80378 ATAATTA-ATATTATTATATTT
1 ATATTTATATATTATTATATTT
80399 ATTTATATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 8 0.20
25 15 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTTATATATTATTATATTTTA
Found at i:80876 original size:17 final size:17
Alignment explanation
Indices: 80856--80891 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
80846 CATATAAAAT
80856 ATAAGAAAATATCTAAA
1 ATAAGAAAATATCTAAA
* *
80873 ATAAGAGAATATTTAAA
1 ATAAGAAAATATCTAAA
80890 AT
1 AT
80892 TTTTAGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (17 bp):
ATAAGAAAATATCTAAA
Found at i:84112 original size:2 final size:2
Alignment explanation
Indices: 84105--84133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
84095 TCTTTTAAAC
84105 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 A
84134 CATACCCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84324 original size:12 final size:12
Alignment explanation
Indices: 84299--84368 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
84289 ACGGAGATAT
* *
84299 CAGAAATCAAAA
1 CAGAATTCAGAA
84311 CAGAATTCAGAA
1 CAGAATTCAGAA
*
84323 CA-ACTATCAGAA
1 CAGAAT-TCAGAA
* * *
84335 CAGAATCCATAT
1 CAGAATTCAGAA
* *
84347 TAGAAATCAGAA
1 CAGAATTCAGAA
84359 CAGAATTCAG
1 CAGAATTCAG
84369 GTCATATATC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:84379 original size:24 final size:24
Alignment explanation
Indices: 84298--84405 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
84288 AACGGAGATA
*
84298 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
84321 AACA-ACTATCAGAACAGAATCCATA-
1 -TCAGA-AATCAGAACAGAATTCA-AG
* *
84346 TTAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
84370 TCATATATCATAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
84394 TCAGAAATCAGA
1 TCAGAAATCAGA
84406 TAAAATATTA
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
23 1 0.02
24 59 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:84379 original size:48 final size:48
Alignment explanation
Indices: 84295--84405 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 48
84285 TTAAACGGAG
*
84295 ATATCAGAAATCAAAACAGAATTCAGAACAACTATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACAACTATCAGAACAGAATCC
* ** * *
84343 ATATTAGAAATCAGAACAGAATTCAGGTCATA-TATCATAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACA-ACTATCAGAACAGAATCC
84391 A-AGTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
84406 TAAAATATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACAACTATCAGAACAGAATCC
Found at i:84432 original size:20 final size:21
Alignment explanation
Indices: 84407--84449 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
84397 GAAATCAGAT
84407 AAAATA-TTATATGATTAGGG
1 AAAATATTTATATGATTAGGG
84427 AAAATATTTATATGATTAGGG
1 AAAATATTTATATGATTAGGG
84448 AA
1 AA
84450 CACACCAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.35
Consensus pattern (21 bp):
AAAATATTTATATGATTAGGG
Done.