Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001581.1 Hibiscus syriacus cultivar Beakdansim tig00003147_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: 220942
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:172 original size:2 final size:2
Alignment explanation
Indices: 167--208 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
157 ATAATGCCTC
167 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
209 TAATTGGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8354 original size:18 final size:18
Alignment explanation
Indices: 8331--8366 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8321 TCAAATGCAA
*
8331 AGAGTTATATTTAAAGAG
1 AGAGTTACATTTAAAGAG
*
8349 AGAGTTGCATTTAAAGAG
1 AGAGTTACATTTAAAGAG
8367 GCATACCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (18 bp):
AGAGTTACATTTAAAGAG
Found at i:8566 original size:36 final size:36
Alignment explanation
Indices: 8519--8852 Score: 189
Period size: 37 Copynumber: 9.0 Consensus size: 36
8509 TGGGGCAAGT
8519 CAATCTTAAGCCTTCACTAGAGAGTAGTGAAGCAAA
1 CAATCTTAAGCCTTCACTAGAGAGTAGTGAAGCAAA
* *
8555 CAATCTGAAGCCTTCACTGGAGAGTAGTGAAGCAAA
1 CAATCTTAAGCCTTCACTAGAGAGTAGTGAAGCAAA
** *
8591 CCGTCTTAAGCCTTCAC-CGAAGAGTAGTGAAGCAAA
1 CAATCTTAAGCCTTCACTAG-AGAGTAGTGAAGCAAA
* ** * *** **
8627 TCCATCAGCAAGCCTTCCGAGCATA-ATGATTAAGT-CCTCATGG
1 -CAATC-TTAAGCCTT-C-A-C-TAGA-GAGT-AGTGAAGCA-AA
* * * * *
8670 CAATCTTAAGCCTCCACCAGA-AGGAGTGAATCAATTT
1 CAATCTTAAGCCTTCACTAGAGAGTAGTGAAGCAA--A
* *
8707 C-ATCTTAAGCCTTCACCT-GAGAATAGTGAAGTAAA
1 CAATCTTAAGCCTTCA-CTAGAGAGTAGTGAAGCAAA
* * *
8742 TCCATCTTAAGCCTTCACCT-GAGAATAATGAAGCAAA
1 -CAATCTTAAGCCTTCA-CTAGAGAGTAGTGAAGCAAA
* * *
8779 TCCATCTTAAGCCTTCACCT-GAGAATAGTGAAACAAA
1 -CAATCTTAAGCCTTCA-CTAGAGAGTAGTGAAGCAAA
* *
8816 TCAATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAA
1 -CAATCTTAAGCCTTCACTAGAGAGTAGTGAAGCAAA
8853 TTCATCTATA
Statistics
Matches: 235, Mismatches: 43, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
35 4 0.02
36 85 0.36
37 113 0.48
38 9 0.04
39 2 0.01
40 2 0.01
41 8 0.03
42 9 0.04
43 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (36 bp):
CAATCTTAAGCCTTCACTAGAGAGTAGTGAAGCAAA
Found at i:8748 original size:37 final size:37
Alignment explanation
Indices: 8672--8868 Score: 236
Period size: 37 Copynumber: 5.3 Consensus size: 37
8662 CCTCATGGCA
* * * * *
8672 ATCTTAAGCCTCCACC--AGAAGGAGTGAATCAATTTC
1 ATCTTAAGCCTTCACCTGAGAA-TAGTGAAGCAAATCC
*
8708 ATCTTAAGCCTTCACCTGAGAATAGTGAAGTAAATCC
1 ATCTTAAGCCTTCACCTGAGAATAGTGAAGCAAATCC
*
8745 ATCTTAAGCCTTCACCTGAGAATAATGAAGCAAATCC
1 ATCTTAAGCCTTCACCTGAGAATAGTGAAGCAAATCC
* *
8782 ATCTTAAGCCTTCACCTGAGAATAGTGAAACAAATCA
1 ATCTTAAGCCTTCACCTGAGAATAGTGAAGCAAATCC
** * *
8819 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATTC
1 ATCTTAAGCCTTCACCTGAGAATAGTGAAGCAAATCC
*
8856 ATCTATAACCCTT
1 ATCT-TAAGCCTT
8869 TAGAGCAAGA
Statistics
Matches: 140, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
36 15 0.11
37 114 0.81
38 11 0.08
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCTGAGAATAGTGAAGCAAATCC
Found at i:9090 original size:42 final size:41
Alignment explanation
Indices: 9013--9114 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
9003 TTCACAATTT
* * * * *
9013 ATAAGTCCTTCGGGCCAT-TAATAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCT-GTAAGCCTTTAGAGCAAGATG
* *
9054 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATG
9096 ATAAATCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
9115 CATAAGACCT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
41 17 0.34
42 32 0.64
43 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCTGTAAGCCTTTAGAGCAAGATG
Found at i:9282 original size:42 final size:41
Alignment explanation
Indices: 9221--9352 Score: 147
Period size: 42 Copynumber: 3.2 Consensus size: 41
9211 AATTTATAAG
* *
9221 TCCTTCGGACTATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG-TTAAA
* * * * * * *
9263 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTAAA
*
9304 TCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG-TTAAA
*
9346 TTCTTCG
1 TCCTTCG
9353 AGTAATTTGT
Statistics
Matches: 70, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
41 33 0.47
42 37 0.53
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTAAA
Found at i:9291 original size:203 final size:203
Alignment explanation
Indices: 8942--9317 Score: 671
Period size: 203 Copynumber: 1.9 Consensus size: 203
8932 AATTTGAAAG
* *
8942 TGAAAAAATGATGTCTTAAGAAGTTGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCA
1 TGAAAAAATGATGTCTTAAGAAGATGAAATTTTTGAAAACTAAGAATGAGATTTTCAAAATTTCA
* *
9007 CAATTTATAAGTCCTTCGGGCCATTAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
66 CAATTTATAAGTCCTTCGGACCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
9072 TCTGTAAGCCTTTAGAGCAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGTAGGATG
131 TCTGTAAGCCTTTAGAGCAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGTAGGATG
9137 TTTTCAAA
196 TTTTCAAA
*
9145 TGAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGAGATTTTCAAAATTTCA
1 TGAAAAAATGATGTCTTAAGAAGATGAAATTTTTGAAAACTAAGAATGAGATTTTCAAAATTTCA
* *
9210 CAATTTATAAGTCCTTCGGACTATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
66 CAATTTATAAGTCCTTCGGACCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
* *
9275 TCTGTAAGCCTTTAGAGCAAGATGATAAGTCTTTCGGGCCATC
131 TCTGTAAGCCTTTAGAGCAAGATGATAAATCCTTCGGGCCATC
9318 AGTAAGTCTT
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
203 164 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (203 bp):
TGAAAAAATGATGTCTTAAGAAGATGAAATTTTTGAAAACTAAGAATGAGATTTTCAAAATTTCA
CAATTTATAAGTCCTTCGGACCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCA
TCTGTAAGCCTTTAGAGCAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGTAGGATG
TTTTCAAA
Found at i:9323 original size:41 final size:41
Alignment explanation
Indices: 9216--9341 Score: 153
Period size: 41 Copynumber: 3.0 Consensus size: 41
9206 TTCACAATTT
* *
9216 ATAAGTCCTTCGGACTATCAGTAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
* * * * * * *
9257 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
*
9299 ATAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
9340 AT
1 AT
9342 TAAATTCTTC
Statistics
Matches: 67, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
41 35 0.52
42 32 0.48
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (41 bp):
ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
Found at i:9364 original size:83 final size:83
Alignment explanation
Indices: 9216--9369 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 83
9206 TTCACAATTT
* * * *
9216 ATAAGTCCTTCGGACTATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATCTGTA
9281 AGCCTTTAGAGCAAGATG
66 AGCCTTTAGAGCAAGATG
* * * *
9299 ATAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATTCTTCGAGTAATTTGTA
1 ATAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATCTGTA
9364 AGCCTT
66 AGCCTT
9370 CACCAAAGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 63 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (83 bp):
ATAAGTCCTTCGGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATCTGTA
AGCCTTTAGAGCAAGATG
Found at i:9505 original size:56 final size:54
Alignment explanation
Indices: 9399--9629 Score: 209
Period size: 56 Copynumber: 4.2 Consensus size: 54
9389 AGAATCACAC
* * *
9399 CAGAAGATTGTTCGAGTTC-ATACCCCTT-AAAGAAAGAGGGAGTGAACCCATTTT
1 CAGAAGATT-TTCGAGTTCTATACTCCTTGAAAG-AATAGGGAGCGAACCCATTTT
* *
9453 CAGAAGATTATTCTAGTTCTGTACTCCTTGAAAAGAATAGGGAGCGAACCCATTTT
1 CAGAAGATT-TTCGAGTTCTATACTCCTTG-AAAGAATAGGGAGCGAACCCATTTT
* * * * *
9509 GAGAAGATTTCTCGAGTTATATACT-CTCTGAAAGAATAGGGAGC-ATACACGTTTG
1 CAGAAGATTT-TCGAGTTCTATACTCCT-TGAAAGAATAGGGAGCGA-ACCCATTTT
* * * * * *
9564 CTGAAGATTGTTCGAGTTCTATACTCCCTGAAAGTAATAAGGAGCAAACTCGTTTT
1 CAGAAGATT-TTCGAGTTCTATACTCCTTGAAAG-AATAGGGAGCGAACCCATTTT
9620 CAGAAGATTT
1 CAGAAGATTT
9630 CTTGTACTCT
Statistics
Matches: 146, Mismatches: 21, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
54 18 0.12
55 57 0.39
56 66 0.45
57 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (54 bp):
CAGAAGATTTTCGAGTTCTATACTCCTTGAAAGAATAGGGAGCGAACCCATTTT
Found at i:9570 original size:55 final size:56
Alignment explanation
Indices: 9506--9631 Score: 159
Period size: 55 Copynumber: 2.3 Consensus size: 56
9496 GCGAACCCAT
* * *
9506 TTTG-AGAAGATTTCTCGAGTTATATACTCTCTGAAAG-AATAGGGAGCATACACG
1 TTTGCAGAAGATTTCTCGAGTTATATACTCCCTGAAAGTAATAAGGAGCAAACACG
* * *
9560 TTTGCTGAAGATTGT-TCGAGTTCTATACTCCCTGAAAGTAATAAGGAGCAAACTCG
1 TTTGCAGAAGATT-TCTCGAGTTATATACTCCCTGAAAGTAATAAGGAGCAAACACG
*
9616 TTTTCAGAAGATTTCT
1 TTTGCAGAAGATTTCT
9632 TGTACTCTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.07
55 29 0.48
56 27 0.45
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (56 bp):
TTTGCAGAAGATTTCTCGAGTTATATACTCCCTGAAAGTAATAAGGAGCAAACACG
Found at i:9979 original size:3 final size:3
Alignment explanation
Indices: 9973--10032 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
9963 TATAATAATA
* * *
9973 ATT ATT ATT A-T ATT ATT A-T ATT ATT ATT AAT AAT ATT AAT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
10020 ATGT TTT ATT ATT
1 AT-T ATT ATT ATT
10033 TTGCAGACCA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.09
3 38 0.81
4 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:9988 original size:8 final size:8
Alignment explanation
Indices: 9975--9999 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9965 TAATAATAAT
9975 TATTATTA
1 TATTATTA
9983 TATTATTA
1 TATTATTA
9991 TATTATTA
1 TATTATTA
9999 T
1 T
10000 TAATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTATTA
Found at i:14036 original size:6 final size:6
Alignment explanation
Indices: 14027--14051 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14017 GGGATGATAA
14027 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
14052 AAACCCATTT
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:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:14151 original size:12 final size:13
Alignment explanation
Indices: 14115--14158 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
14105 GCCCCGATTA
14115 CCCGATTACCCGC
1 CCCGATTACCCGC
14128 CCCGATTACCCGC
1 CCCGATTACCCGC
*
14141 CCCGA-TACCCGA
1 CCCGATTACCCGC
14153 CCCGAT
1 CCCGAT
14159 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:14239 original size:30 final size:31
Alignment explanation
Indices: 14188--14256 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
14178 TTATATATAT
14188 ATATAATATTAATAAATTTAATTTAAATAAAA
1 ATAT-ATATTAATAAATTTAATTTAAATAAAA
* * *
14220 ATATATATT-ATATATTTAATTTAAATATAT
1 ATATATATTAATAAATTTAATTTAAATAAAA
14250 ATATATA
1 ATATATA
14257 CCCGACCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 25 0.74
31 5 0.15
32 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
ATATATATTAATAAATTTAATTTAAATAAAA
Found at i:14291 original size:12 final size:12
Alignment explanation
Indices: 14254--14308 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
14244 ATATATATAT
*
14254 ATACCCGACCCG
1 ATACCCGACCCA
* * *
14266 ATTCTCGGCCCA
1 ATACCCGACCCA
14278 ATACCCGACCCA
1 ATACCCGACCCA
14290 ATACCCGACCCA
1 ATACCCGACCCA
14302 ATACCCG
1 ATACCCG
14309 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.27, C:0.47, G:0.13, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:14913 original size:25 final size:22
Alignment explanation
Indices: 14881--14947 Score: 53
Period size: 25 Copynumber: 2.8 Consensus size: 22
14871 CCGTTTATCG
*
14881 TTAAAAATTAATTTTATAATAATT
1 TTAAAAA-TAACTTT-TAATAATT
*
14905 TTAAGAAATAACTTTTAATATTTTT
1 TTAA-AAATAACTTTTAATA--ATT
*
14930 TTCAAAATATACTTTTAA
1 TTAAAAATA-ACTTTTAA
14948 AAAAATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 5 0.14
24 15 0.42
25 16 0.44
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (22 bp):
TTAAAAATAACTTTTAATAATT
Found at i:15922 original size:242 final size:243
Alignment explanation
Indices: 15541--16017 Score: 539
Period size: 242 Copynumber: 2.0 Consensus size: 243
15531 AACTCTTCTA
** ** * * *
15541 ACTTACTTGATGATGTGGTCTTTAAACTTATCCTATTAAAATATCAACCACTCCTAATATTTGTT
1 ACTTACTTGATGACATACTCTTTAAACTTATCATATTAAAATATCAACCACTCCTAATACTTATT
* * * ** * ** * *
15606 TAAATAATCACTTTGTCACATCCAAATAATAGTTCAGTCGATTTCTGAGTCTTCGGACGCACCCC
66 TAAATAATCACTTTGTCACATACAAATAAGAGTCCAAACGACTTAAGAGTCTTCGAACACACCCC
* * *
15671 TTCACCAATAAATGC-CTTTTGTCATTATTTATCAACTCAAAA-CATCAAATAAGATAATTTGAC
131 TTAACCAATAAATGCTCTTTTGTCATTATTCATCAACTCAAAATCAT-AAATAAGATAATTTGAA
* *
15734 AAATTCAATTATCCCATCATCCGGGACGGAGGCACTAAGTCCCTAACTC
195 AAATTCAATCATCCCATCATCAGGGACGGAGGCACTAAGTCCCTAACTC
* * **
15783 ACTTACTTGATGACATACTCTTTAAATTTATTATATTAAAATATCAATTACTCCTAATACTTATT
1 ACTTACTTGATGACATACTCTTTAAACTTATCATATTAAAATATCAACCACTCCTAATACTTATT
* * * *
15848 TAAATAATCACTTTGTCATATACAACTCACGA-TCCAAACGACCTTAAGAGTCTTCGAACATACC
66 TAAATAATCACTTTGTCACATACAAAT-AAGAGTCCAAACGA-CTTAAGAGTCTTCGAACACACC
* * * * *
15912 CC-TAACCAATAAATGCATTTTTTTTTCATTATTCATCAGCTCAAAATCGTAGATAAGATAATTT
129 CCTTAACCAATAAATGC--TCTTTTGTCATTATTCATCAACTCAAAATCATAAATAAGATAATTT
* * *
15976 GAAAAATTCAATCATCTCATCGTCAGGGACGGATGCACTAAG
192 GAAAAATTCAATCATCCCATCATCAGGGACGGAGGCACTAAG
16018 CATTTTAAGG
Statistics
Matches: 191, Mismatches: 38, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
242 97 0.51
243 20 0.10
245 72 0.38
246 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.34
Consensus pattern (243 bp):
ACTTACTTGATGACATACTCTTTAAACTTATCATATTAAAATATCAACCACTCCTAATACTTATT
TAAATAATCACTTTGTCACATACAAATAAGAGTCCAAACGACTTAAGAGTCTTCGAACACACCCC
TTAACCAATAAATGCTCTTTTGTCATTATTCATCAACTCAAAATCATAAATAAGATAATTTGAAA
AATTCAATCATCCCATCATCAGGGACGGAGGCACTAAGTCCCTAACTC
Found at i:18960 original size:60 final size:60
Alignment explanation
Indices: 18804--18962 Score: 178
Period size: 60 Copynumber: 2.6 Consensus size: 60
18794 ATAGTTTGAA
* * **
18804 ATGAAATTAGAATGTTCAAAAATTTTGGAGACTAATTTAGAATGAAGGTCATAGTTTGGGG
1 ATGAAATTAAAATGTTTAAAAATTTAAG-GACTAATTTAGAATGAAGGTCATAGTTTGGGG
* * ** * *
18865 ATGAAATTGAAATGTTTAAAAGTTCGAGAATTAATTTAGAATGATA-GTCATAGTTTAGGGG
1 ATGAAATTAAAATGTTTAAAAATTTAAGGACTAATTTAGAATGA-AGGTCATAGTTT-GGGG
*
18926 -TGAAATTAAAATATTTAAAAATTTAAGGACTAATTTA
1 ATGAAATTAAAATGTTTAAAAATTTAAGGACTAATTTA
18963 AAATAAAAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
60 54 0.68
61 26 0.32
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.35
Consensus pattern (60 bp):
ATGAAATTAAAATGTTTAAAAATTTAAGGACTAATTTAGAATGAAGGTCATAGTTTGGGG
Found at i:25753 original size:60 final size:61
Alignment explanation
Indices: 25687--25864 Score: 197
Period size: 60 Copynumber: 3.0 Consensus size: 61
25677 ATGAATGTAT
** *
25687 GGATGAAATTGA-AATATTAAAAAGTTTGGGGACTAATTTAGAAA-G-GAGTCCATAGTTTAG
1 GGATGAAATTGATAATATTAAAAAGTTTAAGGACTAATTTA-AAATGAGAGT-CATAGTTTAA
* *
25747 GGATGAAATT-ATAATTTTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTAA
1 GGATGAAATTGATAATATTAAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTAA
** * * *
25807 GGATGAAATTGGAT--TATTCGAAAGTTTAAAGACCAATTTAAAATGAGAGTTATAGTTT
1 GGATGAAATT-GATAATATTAAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTT
25865 GGAGACATAT
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
59 4 0.04
60 93 0.90
61 4 0.04
62 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (61 bp):
GGATGAAATTGATAATATTAAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTAA
Found at i:28489 original size:22 final size:20
Alignment explanation
Indices: 28459--28500 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
28449 TTGTGATGTA
28459 TAAAATATTTTTATATAATATT
1 TAAAATA-TTTTATA-AATATT
*
28481 TAAATTATTTTATAAATATT
1 TAAAATATTTTATAAATATT
28501 CTAATTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAAATATTTTATAAATATT
Found at i:36572 original size:40 final size:38
Alignment explanation
Indices: 36514--36625 Score: 145
Period size: 40 Copynumber: 2.9 Consensus size: 38
36504 TCTTTAAAAC
*
36514 ACTATCCAATCAAGACTAGATTGAGACAGCGGAAGGGA
1 ACTATCCAATCAGGACTAGATTGAGACAGCGGAAGGGA
* *
36552 ACTCAATCCAATCAGGACTAGATTAAGACAGCGGAA-GGT
1 ACT--ATCCAATCAGGACTAGATTGAGACAGCGGAAGGGA
* * *
36591 ACTATCCAATCAGTACTAAATTGAGACAGAGGAAG
1 ACTATCCAATCAGGACTAGATTGAGACAGCGGAAG
36626 AAGATTCAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
37 27 0.42
38 3 0.05
39 5 0.08
40 29 0.45
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (38 bp):
ACTATCCAATCAGGACTAGATTGAGACAGCGGAAGGGA
Found at i:37413 original size:16 final size:17
Alignment explanation
Indices: 37374--37414 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
37364 TTTTTTATTT
37374 GAGTTTAAAATTAATTG
1 GAGTTTAAAATTAATTG
*
37391 GATTTTAAATATTAA-TG
1 GAGTTTAAA-ATTAATTG
37408 G-GTTTAA
1 GAGTTTAA
37415 GGTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (17 bp):
GAGTTTAAAATTAATTG
Found at i:37511 original size:23 final size:24
Alignment explanation
Indices: 37470--37516 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
37460 TGGCATAAAT
37470 ATAAATGAACGAACATAAACGAAC
1 ATAAATGAACGAACATAAACGAAC
37494 ATAAAT-AAC-AAGCATAAACGAAC
1 ATAAATGAACGAA-CATAAACGAAC
37517 GAATTATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.09
23 14 0.64
24 6 0.27
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (24 bp):
ATAAATGAACGAACATAAACGAAC
Found at i:39513 original size:2 final size:2
Alignment explanation
Indices: 39506--39536 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39496 TTAGATTACT
39506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39537 TAATTTCAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40002 original size:3 final size:3
Alignment explanation
Indices: 39994--40023 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
39984 TATATATTTA
*
39994 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40024 TATTCATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:42852 original size:16 final size:16
Alignment explanation
Indices: 42819--42859 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
42809 CGTTCATTTA
42819 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
42833 ATAAATGAACACGTAC
1 ATAAATGAACACGAAC
*
42849 ATAAACGAACA
1 ATAAATGAACA
42860 ATTTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 15 0.65
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.15
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:42949 original size:16 final size:16
Alignment explanation
Indices: 42920--42986 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
42910 CGTATATTTA
42920 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
42934 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
42950 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
*
42966 ATAAATGAATACGAAC
1 ATAAATGAACACGAAC
42982 ATAAA
1 ATAAA
42987 CGAATATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 40 0.83
ACGTcount: A:0.60, C:0.16, G:0.10, T:0.13
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:42964 original size:32 final size:32
Alignment explanation
Indices: 42928--42990 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
42918 TAATAAATAA
42928 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAATGAACACGAACATAAACGAAC
*
42960 ACGAACATAAATGAATACGAACATAAACGAA
1 ACGAACATAAATGAACACGAACATAAACGAA
42991 TATAAACGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.57, C:0.19, G:0.13, T:0.11
Consensus pattern (32 bp):
ACGAACATAAATGAACACGAACATAAACGAAC
Found at i:44089 original size:10 final size:10
Alignment explanation
Indices: 44074--44107 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
44064 ATAAATGAAT
*
44074 GAACATAAAC
1 GAACATAACC
44084 GAACATAACC
1 GAACATAACC
44094 GAACATAACC
1 GAACATAACC
44104 GAAC
1 GAAC
44108 GTTCACGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.53, C:0.26, G:0.12, T:0.09
Consensus pattern (10 bp):
GAACATAACC
Found at i:44893 original size:18 final size:18
Alignment explanation
Indices: 44866--44903 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
44856 AAAACTAATA
* *
44866 AAAAATAATAATAAAATG
1 AAAAAGAATAAAAAAATG
44884 AAAAAGAATAAAAAAATG
1 AAAAAGAATAAAAAAATG
44902 AA
1 AA
44904 TATGCTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (18 bp):
AAAAAGAATAAAAAAATG
Found at i:45031 original size:30 final size:27
Alignment explanation
Indices: 44945--45035 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 27
44935 AAAACAAATC
* *
44945 AAAATAAAATAAT-AAATTAAAA-ATA
1 AAAATAAAATAGTAAAAATAAAATATA
* *
44970 AGAATAAAAGA-T-AAAATAAAATATA
1 AAAATAAAATAGTAAAAATAAAATATA
*
44995 ATAATAATAATAGTAAAAAGTAAAGATATA
1 AAAATAA-AATAGTAAAAA-TAAA-ATATA
45025 AAAATAAAATA
1 AAAATAAAATA
45036 AAAGAGAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
24 9 0.17
25 18 0.33
26 3 0.06
27 1 0.02
28 4 0.07
29 8 0.15
30 11 0.20
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (27 bp):
AAAATAAAATAGTAAAAATAAAATATA
Found at i:45046 original size:48 final size:45
Alignment explanation
Indices: 44952--45046 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 45
44942 ATCAAAATAA
* * *
44952 AATAATAAATTAAAAATAAGAATAAAAGATAAAATAAAATATAAT
1 AATAATAAAGTAAAAATAAGAATAAAAGATAAAATAAAAGAGAAT
44997 AATAATAATAGTAAAAAGTAAAGATATAAAA-ATAAAATAAAAGAGAAT
1 AATAATAA-AGTAAAAA-T-AAGA-ATAAAAGATAAAATAAAAGAGAAT
45045 AA
1 AA
45047 AAAAACAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
45 8 0.19
46 7 0.16
47 1 0.02
48 21 0.49
49 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (45 bp):
AATAATAAAGTAAAAATAAGAATAAAAGATAAAATAAAAGAGAAT
Found at i:45139 original size:3 final size:3
Alignment explanation
Indices: 45125--45156 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
45115 TGAAATACAA
*
45125 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
45157 AAGGTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45222 original size:16 final size:15
Alignment explanation
Indices: 45201--45235 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
45191 ATTAAAAAGG
45201 AAAATAAATAATAAGA
1 AAAATAAATAATAA-A
45217 AAAATAAATAATAAA
1 AAAATAAATAATAAA
45232 AAAA
1 AAAA
45236 GGAATAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAATAAATAATAAA
Found at i:47111 original size:84 final size:84
Alignment explanation
Indices: 46967--47148 Score: 265
Period size: 84 Copynumber: 2.2 Consensus size: 84
46957 ATTTGCCTTT
* * * *
46967 GAAGGTCTTTGGTTTGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATAATGTGCCTTAGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATAATATGCCTTAGA
47032 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * * * * *
47051 TAAGGTATTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGA
1 GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATAATATGCCTTAGA
47116 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
47135 GAAGGTCTTTTGTT
1 GAAGGTCTTTTGTT
47149 TCAAGAGAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (84 bp):
GAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATAATATGCCTTAGA
GCTGAGCGTAGTCGAACTC
Found at i:47224 original size:33 final size:33
Alignment explanation
Indices: 47145--47279 Score: 207
Period size: 33 Copynumber: 4.0 Consensus size: 33
47135 GAAGGTCTTT
*
47145 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTG
1 TGTTTCAAGAGAAACAATTTCAAAGG-TTTTT-TG
* *
47180 TATGTTTCAAGAGAAACAATCTCAAAGGCTTTTTG
1 --TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
47215 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
47248 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTT
47280 TTCAAGAGAA
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
33 63 0.68
35 2 0.02
36 4 0.04
37 24 0.26
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:47383 original size:66 final size:66
Alignment explanation
Indices: 47248--47373 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
47238 AGGTTTTTTG
* * * * * *
47248 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTCAAGAGAAATTGCGTCCAGGGAGGCAAAATT
1 TGTTTCAAGAGAAACAATTTCAAAGGTTGTGTTTAAAGAGAAACTGCGTCAAGGGAGACAAAATT
47313 T
66 T
47314 TGTTTCAAGAGAAAC-ATATTCAAAGGTTGGTGTTTAAAGAGAAACTGTC-TCAAGGGAGAC
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTT-GTGTTTAAAGAGAAACTG-CGTCAAGGGAGAC
47374 GGAATTTGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
65 2 0.04
66 25 0.49
67 23 0.45
68 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (66 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTGTGTTTAAAGAGAAACTGCGTCAAGGGAGACAAAATT
T
Found at i:47599 original size:36 final size:36
Alignment explanation
Indices: 47542--47720 Score: 115
Period size: 36 Copynumber: 5.1 Consensus size: 36
47532 TAAAAGTTTA
* * * *
47542 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
47578 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
** * * * * *
47614 CATTTCAGGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATT
* * * *
47642 ATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
* *
47679 TGTTTCAAGGGAAACTATCACAAGAGAGATAAAATCT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT-T
47716 TGTTT
1 TGTTT
47721 ATAAAAGACA
Statistics
Matches: 106, Mismatches: 25, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
28 2 0.02
29 14 0.13
30 2 0.02
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.02
36 75 0.71
37 8 0.08
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:47665 original size:101 final size:102
Alignment explanation
Indices: 47521--47713 Score: 325
Period size: 101 Copynumber: 1.9 Consensus size: 102
47511 TTGTTTCAAT
* *
47521 GGAAACTGTTTTAAAAGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAA
1 GGAAACTGTTTTAAAAGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
*
47586 GGGAAACTATCTCAAGAGAGACAAAATTCATTTCAGG
66 GGGAAACTATCACAAGAGAGACAAAATTCATTTCAGG
* *
47623 GGAAA-TGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
1 GGAAACTGTTTTAAAAGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
*
47687 GGGAAACTATCACAAGAGAGATAAAAT
66 GGGAAACTATCACAAGAGAGACAAAAT
47714 CTTGTTTATA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 80 0.94
102 5 0.06
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (102 bp):
GGAAACTGTTTTAAAAGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
GGGAAACTATCACAAGAGAGACAAAATTCATTTCAGG
Found at i:47805 original size:72 final size:72
Alignment explanation
Indices: 47723--47878 Score: 222
Period size: 72 Copynumber: 2.2 Consensus size: 72
47713 TCTTGTTTAT
* * *
47723 AAAAGACAATCTTGAGGGAAATAAATTTTCTTTCGAGTAAAACAGTATCAAGTGAGACAAAGTCT
1 AAAA-ACAATCTTGAGGGAAATAAATCTTCTTTCGAGTAAAACAGTATCAAGCGAGACAAAGTAT
47788 GTTTTAAG
65 GTTTTAAG
* * * *
47796 AAAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGTAAAACAGTCTTAAGCGAGACAAGGTATG
1 AAAAACAATCTTGAGGGAAATAAATCTTCTTTCGAGTAAAACAGTATCAAGCGAGACAAAGTATG
47861 TTTTAAG
66 TTTTAAG
**
47868 AATGACAATCT
1 AAAAACAATCT
47879 CAAGTGAGAT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 70 0.95
73 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (72 bp):
AAAAACAATCTTGAGGGAAATAAATCTTCTTTCGAGTAAAACAGTATCAAGCGAGACAAAGTATG
TTTTAAG
Found at i:47837 original size:36 final size:36
Alignment explanation
Indices: 47728--47843 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
47718 TTTATAAAAG
* *
47728 ACAATCTTGAGGGAAATAAATTTTCTTTCGAGTAAA
1 ACAATCTTGAGTGAAATAAATCTTCTTTCGAGTAAA
* * ** * * * *
47764 ACAGTATCAAGTGAGACAAAGTCTGT-TTT-AAGAAAA
1 ACAATCTTGAGTGAAATAAA-TCT-TCTTTCGAGTAAA
47800 ACAATCTTGAGTGAAATAAATCTTCTTTCGAGTAAA
1 ACAATCTTGAGTGAAATAAATCTTCTTTCGAGTAAA
*
47836 ACAGTCTT
1 ACAATCTT
47844 AAGCGAGACA
Statistics
Matches: 57, Mismatches: 19, Indels: 8
0.68 0.23 0.10
Matches are distributed among these distances:
34 1 0.02
35 6 0.11
36 44 0.77
37 5 0.09
38 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (36 bp):
ACAATCTTGAGTGAAATAAATCTTCTTTCGAGTAAA
Found at i:52805 original size:43 final size:42
Alignment explanation
Indices: 52730--53062 Score: 235
Period size: 43 Copynumber: 7.8 Consensus size: 42
52720 AACAAAAAAT
* *
52730 GCCGCAATAGGTCAATATCTATTA-C-GACGTTTTTTGAACAAAC
1 GCCGCAAAAGGTC-ATATCTA-TAGCAG-CGTTTTTGGAACAAAC
* *
52773 GCCGCAAAAGGTCGATATCTATAGCAGTGTTTTTGGAATAAAC
1 GCCGCAAAAGGTC-ATATCTATAGCAGCGTTTTTGGAACAAAC
* * * * * * *
52816 GCCGCAAAAAGTTATGATATATAGCGGCGTTTATAGAAAAAAC
1 GCCGCAAAAGGTCAT-ATCTATAGCAGCGTTTTTGGAACAAAC
* * * *
52859 ACTGCAAAAGGTCAGACCTATAGCAGCGTTTTTGGACACAAAC
1 GCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGA-ACAAAC
* * * *
52902 GCCGCAAAAGGTCAGACCTATAAC-GACGTTTTTGAACACAAAC
1 GCCGCAAAAGGTCATATCTATAGCAG-CGTTTTTGGA-ACAAAC
* * * * * * *
52945 GCCGCAAAAGAG-AAGACCTATA-CTGGCATTTTTAGAAGAAAC
1 GCCGCAAAAG-GTCATATCTATAGC-AGCGTTTTTGGAACAAAC
* * *
52987 GCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAAC
1 GCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGA-ACAAAC
* * * *
53030 GCCGCAAAAAGTCAGACCTATAGCGGCGTTTTT
1 GCCGCAAAAGGTCATATCTATAGCAGCGTTTTT
53063 TTTGATACAA
Statistics
Matches: 241, Mismatches: 38, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.00
42 56 0.23
43 181 0.75
44 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
GCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGAACAAAC
Found at i:52891 original size:128 final size:128
Alignment explanation
Indices: 52757--53062 Score: 361
Period size: 128 Copynumber: 2.4 Consensus size: 128
52747 TCTATTACGA
* * * * * * *
52757 CGTTTTTTGA-ACAAACGCCGCAAAAGGTCGATATCTATAGC-AGTGTTTTTGGA-ATAAACGCC
1 CGTTTTTGGACACAAACGCCGCAAAAGGTC-AGACCTATAACGA-CGTTTTTGAACACAAACGCC
* * * *
52819 GCAAAA-AGTTATGATATATAGC-GGCGTTTATAGAAAAAACACTGCAAAAGGTCAGACCTATAG
64 GCAAAAGAG--AAGACATATA-CTGGCATTTATAGAAAAAACACCGCAAAAGGTCAGACCTATAG
52882 CAG
126 CAG
52885 CGTTTTTGGACACAAACGCCGCAAAAGGTCAGACCTATAACGACGTTTTTGAACACAAACGCCGC
1 CGTTTTTGGACACAAACGCCGCAAAAGGTCAGACCTATAACGACGTTTTTGAACACAAACGCCGC
* * * * *
52950 AAAAGAGAAGACCTATACTGGCATTTTTAGAAGAAACGCCGCAAAAGGTCAGACCTATAGCGG
66 AAAAGAGAAGACATATACTGGCATTTATAGAAAAAACACCGCAAAAGGTCAGACCTATAGCAG
* * *
53013 CGTTTTTGGACACAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTT
1 CGTTTTTGGACACAAACGCCGCAAAAGGTCAGACCTATAACGACGTTTTT
53063 TTTGATACAA
Statistics
Matches: 154, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
127 1 0.01
128 117 0.76
129 34 0.22
130 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (128 bp):
CGTTTTTGGACACAAACGCCGCAAAAGGTCAGACCTATAACGACGTTTTTGAACACAAACGCCGC
AAAAGAGAAGACATATACTGGCATTTATAGAAAAAACACCGCAAAAGGTCAGACCTATAGCAG
Found at i:52932 original size:85 final size:84
Alignment explanation
Indices: 52730--53062 Score: 294
Period size: 86 Copynumber: 3.9 Consensus size: 84
52720 AACAAAAAAT
* * * * * * *
52730 GCCGCAATAGGTCAATATCTATTACGACGTTTTTTGAACAAACGCCGCAAAAGGTCGATATCTAT
1 GCCGCAAAAGGTC-AGACCTATAACGACGTTTTTTGAAAAAACGCCGCAAAAGGTC-AGACCTAT
* *
52795 AGCAGTGTTTTTGGAATAAAC
64 AGCAGCGTTTTTGGAACAAAC
* * ** * * * * * *
52816 GCCGCAAAAAGTTATGATATATAGCGGCGTTTATAGAAAAAACACTGCAAAAGGTCAGACCTATA
1 GCCGCAAAAGGTCA-GACCTATAACGACGTTTTTTGAAAAAACGCCGCAAAAGGTCAGACCTATA
52881 GCAGCGTTTTTGGACACAAAC
65 GCAGCGTTTTTGGA-ACAAAC
*
52902 GCCGCAAAAGGTCAGACCTATAACGACG-TTTTTGAACACAAACGCCGCAAAAGAG-AAGACCTA
1 GCCGCAAAAGGTCAGACCTATAACGACGTTTTTTGAA-A-AAACGCCGCAAAAG-GTCAGACCTA
* * * *
52965 TA-CTGGCATTTTTAGAAGAAAC
63 TAGC-AGCGTTTTTGGAACAAAC
* * * * *
52987 GCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAAAGTCAGACCTATA
1 GCCGCAAAAGGTCAGACCTATAACGACGTTTTTTGA-AAAAACGCCGCAAAAGGTCAGACCTATA
*
53052 GCGGCGTTTTT
65 GCAGCGTTTTT
53063 TTTGATACAA
Statistics
Matches: 198, Mismatches: 39, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
84 7 0.04
85 94 0.47
86 95 0.48
87 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (84 bp):
GCCGCAAAAGGTCAGACCTATAACGACGTTTTTTGAAAAAACGCCGCAAAAGGTCAGACCTATAG
CAGCGTTTTTGGAACAAAC
Found at i:56964 original size:41 final size:41
Alignment explanation
Indices: 56917--57301 Score: 346
Period size: 41 Copynumber: 9.4 Consensus size: 41
56907 TTGTAAACAC
* * * *
56917 AAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
56958 AAACGCCACTAAAGTATGAGTCTTTAGTGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * *
56999 AAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
57040 AAATGCCACTAAATTATGAGTCT-TTGCGGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-A
* * * *
57081 CAAACGCCACTATAGTAC-ATGTGTATAACGACGTTTGTATAA
1 -AAACGCCACTAAAGTACGA-GTCTATAGCGGCGTTTGTATAA
* * *
57123 AAACGCCACTAAAGTACAATTATATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
57164 AAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
57205 AAATGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT--AA
* * * * *
57247 AAACGCCACTATAG-ATGAATCTATTGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
**
57287 AAACGCTGCTAAAGT
1 AAACGCCACTAAAGT
57302 TACCATTTGT
Statistics
Matches: 281, Mismatches: 54, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
40 28 0.10
41 208 0.74
42 33 0.12
43 12 0.04
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:57099 original size:165 final size:166
Alignment explanation
Indices: 56898--57260 Score: 518
Period size: 165 Copynumber: 2.2 Consensus size: 166
56888 ATTTGTAAAC
* * *
56898 TTGCGGTGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCGTTTGAATAAAAACG
1 TTGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACG
** * * * *
56963 CCACTAAAGTATGAGTCTTTAGTGACGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCG
66 CCACTAAAGTACAAGTATATAGCGACGTTTGTATAAAAATGCCAATAAAGTACGAGTCTTTAGCG
* *
57028 GCGTTTGTATAAAAATGCCACTAAATTA-TGAGTC-T
131 GCGTTTGTATAAAAATGCCACTAAAGTACT-ACTCTT
* *
57063 TTGCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGACGTTTGTATAAAAACG
1 TTGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACG
* * * *
57128 CCACTAAAGTACAATTATATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCG
66 CCACTAAAGTACAAGTATATAGCGACGTTTGTATAAAAATGCCAATAAAGTACGAGTCTTTAGCG
57193 GCGTTTGTATAAAAATGCCACTAAAGTACTACTCTT
131 GCGTTTGTATAAAAATGCCACTAAAGTACTACTCTT
*
57229 TTGCGGCGTTTGTTGAA-A-AAACGCCACTATAG
1 TTGCGGCGTTTG-TAAACACAAACGCCACTATAG
57261 ATGAATCTAT
Statistics
Matches: 177, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
165 159 0.90
166 15 0.08
167 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (166 bp):
TTGCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACG
CCACTAAAGTACAAGTATATAGCGACGTTTGTATAAAAATGCCAATAAAGTACGAGTCTTTAGCG
GCGTTTGTATAAAAATGCCACTAAAGTACTACTCTT
Found at i:57249 original size:124 final size:122
Alignment explanation
Indices: 56941--57257 Score: 372
Period size: 124 Copynumber: 2.6 Consensus size: 122
56931 TACAAGTGTA
* * * *
56941 TAGCGGCGTTTGAATAAAAACGCCACTAAAGTA-TGAGTCTTTAGTGACGTTTGTATAAAAATGT
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACT-A-TCTTTAGCGACGTTTGTATAAAAACGC
* * * * *
57005 CAATAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAATTATGAGTCTT
64 CACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTT
* * * *
57064 T-GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATAACGACGTTTGTATAAAAAC
1 TAGCGGCGTTTGTATA-A-AAACGCCACTAAAGTACTATCT-T-TAGCGACGTTTGTATAAAAAC
*
57127 GCCACTAAAGTACAATTATATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTT
62 GCCACTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTT
* * *
57188 TAGCGGCGTTTGTATAAAAATGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACG
1 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTA-TCTTTAGCGACGTTTGTAT--AAAAACG
57252 CCACTA
63 CCACTA
57258 TAGATGAATC
Statistics
Matches: 163, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
122 15 0.09
123 29 0.18
124 104 0.64
125 15 0.09
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (122 bp):
TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTATCTTTAGCGACGTTTGTATAAAAACGCCA
CTAAAGTACAAGTATATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTT
Found at i:58159 original size:17 final size:18
Alignment explanation
Indices: 58133--58168 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
58123 AAGTAAAGCA
58133 AAAATAAAAAAAAT-AAT
1 AAAATAAAAAAAATGAAT
*
58150 AAAATGAAAAAAATGAAT
1 AAAATAAAAAAAATGAAT
58168 A
1 A
58169 TGCTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAATAAAAAAAATGAAT
Found at i:58240 original size:12 final size:12
Alignment explanation
Indices: 58208--58303 Score: 56
Period size: 12 Copynumber: 7.9 Consensus size: 12
58198 AAAACAAATC
*
58208 AAAATAAAATAAT
1 AAAATAAAA-GAT
*
58221 AAATTAAAA-AT
1 AAAATAAAAGAT
58232 AAGAATAAAAGAT
1 AA-AATAAAAGAT
*
58245 AAAATAAAATAT
1 AAAATAAAAGAT
*
58257 AATAATAATA-AT
1 AA-AATAAAAGAT
**
58269 AGCA-AAAAG-T
1 AAAATAAAAGAT
*
58279 AAAGATAGAAAAAT
1 AAA-ATA-AAAGAT
58293 AAAATAAAAGA
1 AAAATAAAAGA
58304 GAATAAAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
10 5 0.08
11 6 0.09
12 25 0.39
13 24 0.38
14 4 0.06
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (12 bp):
AAAATAAAAGAT
Found at i:58358 original size:2 final size:2
Alignment explanation
Indices: 58351--58375 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58341 AATAAAAATG
58351 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
58376 AAATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58412 original size:11 final size:11
Alignment explanation
Indices: 58398--58429 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
58388 TTGAAATATA
58398 AAAATAATAGT
1 AAAATAATAGT
58409 AAAATAATAGT
1 AAAATAATAGT
58420 AATAATAATA
1 AA-AATAATA
58430 AGAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:58417 original size:3 final size:3
Alignment explanation
Indices: 58395--58445 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
58385 AAATTGAAAT
* * * *
58395 ATA AAA ATA ATA GTA A-A ATA ATA GTA ATA ATA ATA AGA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
58440 ATA ATA
1 ATA ATA
58446 TAAAAGGTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:58509 original size:19 final size:19
Alignment explanation
Indices: 58485--58536 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
58475 AACAAAACAT
58485 TAAAAAGGAAAATAAATAA
1 TAAAAAGGAAAATAAATAA
**
58504 TAAAAATAATAAAT-AATAA
1 TAAAAAGGA-AAATAAATAA
58523 -AAAAAGGAATAATA
1 TAAAAAGGAA-AATA
58537 GCAAGGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 1 0.04
18 9 0.35
19 12 0.46
20 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
TAAAAAGGAAAATAAATAA
Found at i:58516 original size:16 final size:16
Alignment explanation
Indices: 58495--58525 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58485 TAAAAAGGAA
58495 AATAAATAATAAAAAT
1 AATAAATAATAAAAAT
58511 AATAAATAATAAAAA
1 AATAAATAATAAAAA
58526 AAGGAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATAAATAATAAAAAT
Found at i:60315 original size:4 final size:4
Alignment explanation
Indices: 60308--60341 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
60298 TTTTTTTTAT
*
60308 ATAA ATAA ATAA ATAA GTAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
60342 TTGGAGTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:63058 original size:23 final size:21
Alignment explanation
Indices: 63007--63070 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
62997 TATTCATTTT
*
63007 TCATTTTTTTCTTCTTTTTTC
1 TCATTTTTTTCTTCTTTGTTC
*
63028 TTACTTTTTTT-TTACATTTGTTC
1 TCA-TTTTTTTCTT-C-TTTGTTC
*
63051 TCATTTTTCT-TTCTTT-TTC
1 TCATTTTTTTCTTCTTTGTTC
63070 T
1 T
63071 TTTTTATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 4 0.11
20 3 0.08
21 5 0.14
22 16 0.44
23 8 0.22
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (21 bp):
TCATTTTTTTCTTCTTTGTTC
Found at i:65287 original size:22 final size:22
Alignment explanation
Indices: 65255--65297 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
65245 CAAACCATTC
*
65255 AGGGGGGAATCGGTACCCTCTT
1 AGGGGGAAATCGGTACCCTCTT
*
65277 AGGGGGAAATCGGTTCCCTCT
1 AGGGGGAAATCGGTACCCTCT
65298 GAGCAATCTA
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:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (22 bp):
AGGGGGAAATCGGTACCCTCTT
Found at i:67902 original size:23 final size:23
Alignment explanation
Indices: 67843--67902 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
67833 ACCCTCAGGT
*
67843 GGTATCGATTCCCCTTCAAAGGG
1 GGTATCGATTCCCTTTCAAAGGG
* * *
67866 GGAATCGGTTCCCTTTCAAGGGG
1 GGTATCGATTCCCTTTCAAAGGG
67889 GGTATCGATTCCCT
1 GGTATCGATTCCCT
67903 ATGCACCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
GGTATCGATTCCCTTTCAAAGGG
Found at i:71136 original size:19 final size:20
Alignment explanation
Indices: 71112--71152 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
71102 TGAAAATGTT
*
71112 ATGCATTAAAACTAA-AAAA
1 ATGCATAAAAACTAAGAAAA
*
71131 ATGCATAAAAATTAAGAAAA
1 ATGCATAAAAACTAAGAAAA
71151 AT
1 AT
71153 TTAAGGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (20 bp):
ATGCATAAAAACTAAGAAAA
Found at i:80700 original size:17 final size:18
Alignment explanation
Indices: 80680--80722 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
80670 TCCCCCCAAA
*
80680 ATCTTTCTTTT-ATTTTT
1 ATCTTTCTTTTCACTTTT
80697 ATC-TTCTTTTCACTTTT
1 ATCTTTCTTTTCACTTTT
80714 A-CTTTCTTT
1 ATCTTTCTTT
80723 CATCTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (18 bp):
ATCTTTCTTTTCACTTTT
Found at i:88323 original size:39 final size:39
Alignment explanation
Indices: 88280--88355 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
88270 AGCACAACAC
**
88280 AACTTTTTGATCGA-ATAATACCTTGCCTCACAATCAGTG
1 AACTTTTTG-TCGAGATAATAAATTGCCTCACAATCAGTG
* *
88319 AACTTTTTGTTGAGATAGTAAATTGCCTCACAATCAG
1 AACTTTTTGTCGAGATAATAAATTGCCTCACAATCAG
88356 GAAATACCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (39 bp):
AACTTTTTGTCGAGATAATAAATTGCCTCACAATCAGTG
Found at i:89696 original size:6 final size:6
Alignment explanation
Indices: 89685--90553 Score: 1359
Period size: 6 Copynumber: 143.8 Consensus size: 6
89675 GAACAAGAGG
* * *
89685 ATACAT ATACAT ATACAT ATACAT ATGCAT ATATGCAT ATGCAT ATGCAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATA--CAT ATACAT ATACAT
* * * * *
89735 ATTCAT ATGCAT ATACAT ATACAT ATGCAT ATGCAT ATACAT ATGCAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
89783 ATATAT ATACAT ATACAT ATGCAT ATACAT ATACAT ATGCAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
89831 ATACAT ATACAT ATAC-- ATACAT ATACATAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATAC--AT ATACAT ATACAT ATACAT
89879 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
89927 ATACAT ATACAT ATGCATAT ATACAT ATACAT ATAC-- ATACAT ATACAT
1 ATACAT ATACAT AT--ACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* *
89975 ATACAT ATACAT ATACAT ATGCAT ATACAT ATACAT ATGCAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
90023 ATACAT ATGCAT ATACAT ATGCAT ATACAT ATGCAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
90071 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
90119 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
90167 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
90215 ATACAT ATACAT ATACATAT ATACAT ATACAT ATACAT ATACATAT ATACAT
1 ATACAT ATACAT ATAC--AT ATACAT ATACAT ATACAT ATAC--AT ATACAT
90267 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
90315 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
90363 ATACAT ATACAT ATACAT ATACAT ATACAT ATACGT ATACGT ATACGT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* *
90411 ATACAT ATACAT ATACAT ATACGT ATACAT ATACAT ATACGT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
90459 ATACGT ATACAT ATACAT ATACAT ATACGT ATACAT ATACAT ATACGT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * * *
90507 ATACAT ATACAT ATACGT ATACGT ATACGT ATACAT ATACAC ATACA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACA
90554 CATATAAGAG
Statistics
Matches: 806, Mismatches: 43, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
4 8 0.01
6 770 0.96
8 28 0.03
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:95445 original size:36 final size:36
Alignment explanation
Indices: 95405--95541 Score: 238
Period size: 36 Copynumber: 3.8 Consensus size: 36
95395 GGTGCTGAAT
* *
95405 ATTGATACATGAATGTAGCAAAGCTGATATGATAAC
1 ATTGATACACGAATGTATCAAAGCTGATATGATAAC
95441 ATTGATACACGAATGTATCAAAGCTGATATGATAAC
1 ATTGATACACGAATGTATCAAAGCTGATATGATAAC
95477 ATTGATACACGAATGTATCAAAGCTGATATGATAAC
1 ATTGATACACGAATGTATCAAAGCTGATATGATAAC
**
95513 ATTGATACACGAATACATCAAAGCTGATA
1 ATTGATACACGAATGTATCAAAGCTGATA
95542 ATGGATAAAT
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (36 bp):
ATTGATACACGAATGTATCAAAGCTGATATGATAAC
Found at i:99952 original size:26 final size:25
Alignment explanation
Indices: 99911--99980 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 25
99901 AAAACCACCC
99911 CTTTATTTTTCTCTCTCTCACTATTTC-T
1 CTTTATTTTTC-CTCT-TCA-T-TTTCAT
99939 CTTT-TTTTTCCTCTTCATTTTCAT
1 CTTTATTTTTCCTCTTCATTTTCAT
99963 CTTTATATTTTCCTCTTC
1 CTTTAT-TTTTCCTCTTC
99981 CCCTAAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.10
24 6 0.15
25 4 0.10
26 15 0.38
27 6 0.15
28 4 0.10
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (25 bp):
CTTTATTTTTCCTCTTCATTTTCAT
Found at i:108029 original size:22 final size:22
Alignment explanation
Indices: 108003--108059 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
107993 ATAATCAATT
*
108003 ATAACAAATTTATTTAGTCACA
1 ATAACAAATTTATTTAGTCAAA
* * *
108025 ATAACATATTAAATTTTGTCAAA
1 ATAACAAATT-TATTTAGTCAAA
108048 ATAA-AAATTTAT
1 ATAACAAATTTAT
108060 GTTAAATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.07
22 13 0.46
23 13 0.46
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAACAAATTTATTTAGTCAAA
Found at i:108218 original size:201 final size:198
Alignment explanation
Indices: 107796--108623 Score: 986
Period size: 196 Copynumber: 4.2 Consensus size: 198
107786 TCCTCAAAAC
* * * * * * *
107796 AACAAATTATGA-TAATTTATTTAGACAAAATAACAAATTAAATTTAGTTAAAATAAAAAAATTA
1 AACAAATTATAACAAATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAAT-AAAAAGTTA
* * * * ** * *
107860 TGTCAAATTTATTT-AGTCAAAATATTTCCTCAAAATAAAAAATTATAAAAAATTTAAATAGTTA
65 TGTCAAATTTATTTCA-TCAAAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTTAATCA
* * * * *
107924 TAATAACAAATTATTAATAAATATTAATTTCTCAATATAAAAAGTTATGACAAATAATATTTTTT
129 AAATAACAATTTA-TAACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTT
107989 CACAAT
193 CACAAT
* *
107995 AATC-AATTATAACAAATTTATTTAGTCACAATAACATATTAAATTTTGTCAAAATAAAAATTTA
1 AA-CAAATTATAACAAATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAAGTTA
* * *
108059 TGTTAAATTTATTTCATCAAAATATTTTCTCAAAA-AATAATAACTTTTGACAAATTTATTTAGT
65 TGTCAAATTTATTTCATCAAAATATTTTCTCAAAATAA-AA-AA-TTGTGACAAATTTATTTAAT
* *
108123 CATAATAACAATTTATAACAAATATTAATTCCTCAATATAAACAAATTATGACAAATAATATTCT
127 CAAAATAACAATTTATAACAAATATTAATTTCTCAATATAAA-AAATTATGACAAATAATATTCT
108188 TTCACAAT
191 TTCACAAT
* * * * * * *
108196 AACAAAATGTAAGAAGTTTATTTAATTACAATAACATAGTAAATTTAGTCAAAATAAAAAGTTAT
1 AACAAATTATAACAAATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAAGTTAT
* ** *
108261 GTTAAATTTATTTTGTCACAAA-ATTTTGTCAAAATAAAAAATTGTGACAAATTTATTTAATCAA
66 GTCAAATTTATTTCATCA-AAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTTAATCAA
* * * *
108325 AATAATAATTTATAACAAATATTAATTTCTCAGTATAAAAAATTGTGACAAGTAATATTCTTTCA
130 AATAACAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCA
108390 CAAT
195 CAAT
** * ** * *
108394 AACAAATTATAA-AAAAATATTTAGTCATAATAACACGTTAAATTTAGTC-TAAGAAAAAGTTAT
1 AACAAATTATAACAAATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAAGTTAT
* ** *
108457 GTCGAATTTATTTCATCCCAATATTTTGTCAAAATAAAAAATTGTGACAAATTTATTTAATCAAA
66 GTCAAATTTATTTCATCAAAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTTAATCAAA
* * * *
108522 ATAACAATTTATAACAAATATTAACTTCTCATTATAAAAAATTGTGAAAAATAATATTCTTTCAC
131 ATAACAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCAC
108587 AAT
196 AAT
* * *
108590 AACAATTTGTAACAAAATTATTTAGTCACAATAA
1 AACAAATTATAACAAATTTATTTAGTCACAATAA
108624 AAAGTTATAA
Statistics
Matches: 548, Mismatches: 69, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
195 2 0.00
196 141 0.26
197 47 0.09
198 40 0.07
199 106 0.19
200 68 0.12
201 139 0.25
202 5 0.01
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (198 bp):
AACAAATTATAACAAATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAAGTTAT
GTCAAATTTATTTCATCAAAATATTTTCTCAAAATAAAAAATTGTGACAAATTTATTTAATCAAA
ATAACAATTTATAACAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCAC
AAT
Found at i:108329 original size:32 final size:33
Alignment explanation
Indices: 108289--108375 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 33
108279 CAAAATTTTG
108289 TCAAAATAAAAAATTGTGACAAAT-TT-ATTTAA
1 TCAAAATAAAAAATTGTGACAAATATTAATTT-A
* * * * *
108321 TCAAAATAATAATTTATAACAAATATTAATTTC
1 TCAAAATAAAAAATTGTGACAAATATTAATTTA
**
108354 TCAGTATAAAAAATTGTGACAA
1 TCAAAATAAAAAATTGTGACAA
108376 GTAATATTCT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
32 20 0.48
33 18 0.43
34 4 0.10
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (33 bp):
TCAAAATAAAAAATTGTGACAAATATTAATTTA
Found at i:108644 original size:30 final size:32
Alignment explanation
Indices: 108583--108659 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
108573 TAATATTCTT
* * *
108583 TCACAATAACAATTTGTAACAAAATTATTTAG
1 TCACAATAAAAAGTTATAACAAAATTATTTAG
108615 TCACAATAAAAAGTTATAA-AAAA-TATTTAG
1 TCACAATAAAAAGTTATAACAAAATTATTTAG
* *
108645 TGACAAAATAAAAGT
1 TCACAATA-AAAAGT
108660 AGTGAGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 13 0.33
31 10 0.26
32 16 0.41
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (32 bp):
TCACAATAAAAAGTTATAACAAAATTATTTAG
Found at i:110875 original size:206 final size:206
Alignment explanation
Indices: 110615--111090 Score: 738
Period size: 206 Copynumber: 2.3 Consensus size: 206
110605 TGATCGTAGA
* * **
110615 TAAGACTCTACTTCTAGATTACTCATCGGATCAGTGGATCGTCATTTAAGTCTCGAATGTTGCAT
1 TAAGATTCTACTGCTAGATTACTCATCAAATCAGTGGATCGTCATTTAAGTCTCGAATGTTGCAT
110680 GATCTTCGAGCTCACTGCTTCATCTCAGATCTTTGTATTTGGATCTGATGCCCCTCAAAGCTCTA
66 GATCTTCGAGCTCACTGCTTCATCTCAGATCTTTGTATTTGGATCTGATGCCCCTCAAAGCTCTA
* *
110745 TAAACTAACTCCGTTAATGCCTCAGCGGTGATGAAGCCATTGCGTTGCTCATTGATGACTAGCGA
131 TAAACTAACTACATTAATGCCTCAGCGGTGATGAAGCCATTGCGTTGCTCATTGATGACTAGCGA
110810 TTG-CATGATTG
196 -TGACATGATTG
* * *
110821 TAAGATTCTACTGCTAGATTACTCCTCAAATTAGTGGATCGTCATTTAAGTCTCGAATATTGCAT
1 TAAGATTCTACTGCTAGATTACTCATCAAATCAGTGGATCGTCATTTAAGTCTCGAATGTTGCAT
* * * * *
110886 GATCTTCGAGCTCACTGCTTCATTTCGGATCTTTTTATTTGGATCTGATGCCCCTCAATGCTCTG
66 GATCTTCGAGCTCACTGCTTCATCTCAGATCTTTGTATTTGGATCTGATGCCCCTCAAAGCTCTA
* * *
110951 TAAACTAACTACATTAATGCCTCAGTGGTGCTGAAGCCATTGCGTTGCTCCTTGATGACTAGCGA
131 TAAACTAACTACATTAATGCCTCAGCGGTGATGAAGCCATTGCGTTGCTCATTGATGACTAGCGA
111016 TGACATGATTG
196 TGACATGATTG
* * * * *
111027 TAAGATTCTACTGCTAGATTACTCTTCAAATCAATGGATCATCATTTCAGTCTTGAATGTTGCA
1 TAAGATTCTACTGCTAGATTACTCATCAAATCAGTGGATCGTCATTTAAGTCTCGAATGTTGCA
111091 CTACTTTCTA
Statistics
Matches: 245, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
205 2 0.01
206 243 0.99
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (206 bp):
TAAGATTCTACTGCTAGATTACTCATCAAATCAGTGGATCGTCATTTAAGTCTCGAATGTTGCAT
GATCTTCGAGCTCACTGCTTCATCTCAGATCTTTGTATTTGGATCTGATGCCCCTCAAAGCTCTA
TAAACTAACTACATTAATGCCTCAGCGGTGATGAAGCCATTGCGTTGCTCATTGATGACTAGCGA
TGACATGATTG
Found at i:111338 original size:30 final size:32
Alignment explanation
Indices: 111280--111339 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
111270 TGACCAAATG
*
111280 ACACAAACAAAAGAGAAGAAATAAGTTAGTGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
*
111312 ACACAAATAAAAGA-AA-AAACAAGTTAGT
1 ACACAAACAAAAGAGAAGAAACAAGTTAGT
111340 ACAAACATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 11 0.42
31 2 0.08
32 13 0.50
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAACAAGTTAGTGT
Found at i:115054 original size:12 final size:12
Alignment explanation
Indices: 115037--115146 Score: 57
Period size: 12 Copynumber: 9.2 Consensus size: 12
115027 TGAATGTTTT
115037 ATTTGATTTCTG
1 ATTTGATTTCTG
*
115049 ATTTGAATTCTG
1 ATTTGATTTCTG
*
115061 -TTCTGATTTTTG
1 ATT-TGATTTCTG
* * *
115073 ATCTGAATTATG
1 ATTTGATTTCTG
*
115085 TTTTGATTTCTG
1 ATTTGATTTCTG
*
115097 ATCTGGA-TTCTG
1 AT-TTGATTTCTG
* *
115109 -TTCTGATATATG
1 ATT-TGATTTCTG
*
115121 ATCTGAATTT-TG
1 ATTTG-ATTTCTG
*
115133 TTTTGATTTCTG
1 ATTTGATTTCTG
115145 AT
1 AT
115147 ATCTTCGTTT
Statistics
Matches: 70, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
10 1 0.01
11 9 0.13
12 52 0.74
13 8 0.11
ACGTcount: A:0.19, C:0.09, G:0.17, T:0.55
Consensus pattern (12 bp):
ATTTGATTTCTG
Found at i:115068 original size:24 final size:24
Alignment explanation
Indices: 115040--115146 Score: 133
Period size: 24 Copynumber: 4.5 Consensus size: 24
115030 ATGTTTTATT
*
115040 TGATTTCTGATTTGAATTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTC
* * *
115064 TGATTTTTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTCTGTTC
*
115088 TGATTTCTGATCTGGATTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTC
* * * *
115112 TGATATATGATCTGAATTTTGTTT
1 TGATTTCTGATCTGAATTCTGTTC
115136 TGATTTCTGAT
1 TGATTTCTGAT
115147 ATCTTCGTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.19, C:0.09, G:0.18, T:0.54
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTC
Found at i:115092 original size:48 final size:48
Alignment explanation
Indices: 115038--115146 Score: 173
Period size: 48 Copynumber: 2.3 Consensus size: 48
115028 GAATGTTTTA
* * *
115038 TTTGATTTCTGATTTGAATTCTGTTCTGATTTTTGATCTGAATTATGT
1 TTTGATTTCTGATCTGAATTCTGTTCTGATATATGATCTGAATTATGT
* *
115086 TTTGATTTCTGATCTGGATTCTGTTCTGATATATGATCTGAATTTTGT
1 TTTGATTTCTGATCTGAATTCTGTTCTGATATATGATCTGAATTATGT
115134 TTTGATTTCTGAT
1 TTTGATTTCTGAT
115147 ATCTTCGTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.18, C:0.09, G:0.17, T:0.55
Consensus pattern (48 bp):
TTTGATTTCTGATCTGAATTCTGTTCTGATATATGATCTGAATTATGT
Found at i:116474 original size:16 final size:15
Alignment explanation
Indices: 116439--116479 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
116429 GTGTCTTTTA
116439 AAAAACAATTTTAAG
1 AAAAACAATTTTAAG
*
116454 AAAAACATTTTTAAG
1 AAAAACAATTTTAAG
116469 ACAAAACAATT
1 A-AAAACAATT
116480 GGTATGTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (15 bp):
AAAAACAATTTTAAG
Found at i:117243 original size:30 final size:30
Alignment explanation
Indices: 117209--117485 Score: 181
Period size: 30 Copynumber: 9.2 Consensus size: 30
117199 ACTTAGTGAT
117209 TTAAAGGACCAAAATAGCAAAAACAAG-AAC
1 TTAAAGGACCAAAATAGCAAAAA-AAGAAAC
* * *
117239 TTAAAGGACTC--ATTAGAAAAAAATAGAAAT
1 TTAAAGGAC-CAAAATAGCAAAAAA-AGAAAC
* *
117269 TTAAATGACCAAAATAGTAAAAAAATAGAAA-
1 TTAAAGGACCAAAATAG-CAAAAAA-AGAAAC
* * * * *
117300 TTTAAGGACTAAAATAACAAAAATAGAAAA
1 TTAAAGGACCAAAATAGCAAAAAAAGAAAC
* * * * * *
117330 TTATATGACTAAAATAACAAAATAA-AAAT
1 TTAAAGGACCAAAATAGCAAAAAAAGAAAC
* * * *
117359 TTATAGGACTAAAATAGTAAAAATAGAAAC
1 TTAAAGGACCAAAATAGCAAAAAAAGAAAC
* * *
117389 TTACAGGGCTAAAATAGCAAAAATAA-AAAC
1 TTAAAGGACCAAAATAGCAAAAA-AAGAAAC
* * *
117419 TTAAAGG-CCTAAAATAGCTAAAACAGAAAG
1 TTAAAGGACC-AAAATAGCAAAAAAAGAAAC
* * *
117449 TTTAAGGACCAAAATAGCTAAAATAGAAAC
1 TTAAAGGACCAAAATAGCAAAAAAAGAAAC
117479 TTAAAGG
1 TTAAAGG
117486 GTAAACAATA
Statistics
Matches: 199, Mismatches: 36, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.01
29 42 0.21
30 122 0.61
31 21 0.11
32 13 0.07
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (30 bp):
TTAAAGGACCAAAATAGCAAAAAAAGAAAC
Found at i:117375 original size:90 final size:91
Alignment explanation
Indices: 117213--117471 Score: 242
Period size: 90 Copynumber: 2.8 Consensus size: 91
117203 AGTGATTTAA
* * * * * * ** * *
117213 AGGACCAAAATAGCAAAAACAAGAACTTAAAGGACT-CATTAGAAAAAAATAGAAATTTAAATGA
1 AGGACTAAAATAACAAAAATAAAAACTTAAAGGACTAAAATA-ACTAAAATAAAAATTT-AAGGA
*
117277 CCAAAATAGTAAAAAAATAGAAATTTA-
64 CCAAAATAGTAAAAAAATAGAAACTTAC
* *
117304 AGGACTAAAATAACAAAAATAGAAAA-TTATATGACTAAAATAAC-AAAATAAAAATTTATAGGA
1 AGGACTAAAATAACAAAAATA-AAAACTTAAAGGACTAAAATAACTAAAATAAAAATTTA-AGGA
*
117367 CTAAAATAGT--AAAAATAGAAACTTAC
64 CCAAAATAGTAAAAAAATAGAAACTTAC
* * * * * *
117393 AGGGCTAAAATAGCAAAAATAAAAACTTAAAGGCCTAAAATAGCTAAAACAGAAAGTTTAAGGAC
1 AGGACTAAAATAACAAAAATAAAAACTTAAAGGACTAAAATAACTAAAATA-AAAATTTAAGGAC
117458 CAAAATAGCTAAAA
65 CAAAATAG-TAAAA
117472 TAGAAACTTA
Statistics
Matches: 136, Mismatches: 22, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
88 18 0.13
89 34 0.25
90 41 0.30
91 35 0.26
92 6 0.04
93 2 0.01
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.19
Consensus pattern (91 bp):
AGGACTAAAATAACAAAAATAAAAACTTAAAGGACTAAAATAACTAAAATAAAAATTTAAGGACC
AAAATAGTAAAAAAATAGAAACTTAC
Found at i:117386 original size:59 final size:58
Alignment explanation
Indices: 117257--117441 Score: 181
Period size: 59 Copynumber: 3.1 Consensus size: 58
117247 CTCATTAGAA
* * * * **
117257 AAAAATAGAAATTTAAATGACCAAAATAGTAAAAAAATAGAAATTTAAGGACTAAAATAAC
1 AAAAATAGAAAATTAAATGA-CTAAA-A-TAACAAAATAAAAATTTAAGGACTAAAATAGT
*
117318 AAAAATAGAAAATTATATGACTAAAATAACAAAATAAAAATTTATAGGACTAAAATAGT
1 AAAAATAGAAAATTAAATGACTAAAATAACAAAATAAAAATTTA-AGGACTAAAATAGT
* * * * * * *
117377 AAAAATAGAAACTTACAGGGCTAAAATAGCAAAAATAAAAACTTAAAGGCCTAAAATAGCT
1 AAAAATAGAAAATTAAATGACTAAAATAAC-AAAATAAAAA-TTTAAGGACTAAAATAG-T
117438 AAAA
1 AAAA
117442 CAGAAAGTTT
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
58 16 0.15
59 38 0.36
60 26 0.25
61 26 0.25
ACGTcount: A:0.61, C:0.08, G:0.10, T:0.21
Consensus pattern (58 bp):
AAAAATAGAAAATTAAATGACTAAAATAACAAAATAAAAATTTAAGGACTAAAATAGT
Found at i:117447 original size:60 final size:59
Alignment explanation
Indices: 117212--117485 Score: 205
Period size: 60 Copynumber: 4.6 Consensus size: 59
117202 TAGTGATTTA
* * * * * ** *
117212 AAGGACCAAAATAGCAAAAACAAGAACTTAAAGGACT-CATTAGAAAAAAATAGAAATTT
1 AAGGACTAAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAG-CTAAAATAGAAAATT
* * * * * * *
117271 AAATGACCAAAATAGTAAAAA-AATAGAAATTTAAGGACTAAAATAACAAAAATAGAAAATT
1 -AAGGACTAAAATAGCAAAAATAA-A-AACTTAAAGGACTAAAATAGCTAAAATAGAAAATT
* * * * *
117332 ATATGACTAAAATAAC-AAAATAAAAATTTATAGGACTAAAATAG-TAAAAATAGAAACTT
1 A-AGGACTAAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAGCT-AAAATAGAAAATT
* * * *
117391 ACAGGGCTAAAATAGCAAAAATAAAAACTTAAAGGCCTAAAATAGCTAAAACAGAAAGTTT
1 A-AGGACTAAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAGCTAAAATAGAAA-ATT
* * *
117452 AAGGACCAAAATAGCTAAAATAGAAACTTAAAGG
1 AAGGACTAAAATAGCAAAAATAAAAACTTAAAGG
117486 GTAAACAATA
Statistics
Matches: 173, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
59 42 0.24
60 87 0.50
61 41 0.24
62 3 0.02
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.19
Consensus pattern (59 bp):
AAGGACTAAAATAGCAAAAATAAAAACTTAAAGGACTAAAATAGCTAAAATAGAAAATT
Found at i:118922 original size:3 final size:3
Alignment explanation
Indices: 118914--118980 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
118904 TGTAAACATA
118914 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
118962 -AT AAT AAT AAT ACT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
118981 AATTAATATT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:119714 original size:27 final size:27
Alignment explanation
Indices: 119676--119731 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
119666 ATGAAGATCT
*
119676 TGATGCTGTGGACTTTCAAGTTCAAAG
1 TGATGCTATGGACTTTCAAGTTCAAAG
*
119703 TGATGCTATGGAGTTTCAAGTTCAAAG
1 TGATGCTATGGACTTTCAAGTTCAAAG
119730 TG
1 TG
119732 GTGATGGCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (27 bp):
TGATGCTATGGACTTTCAAGTTCAAAG
Found at i:120866 original size:2 final size:2
Alignment explanation
Indices: 120859--120891 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
120849 CTTAGATTAC
120859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
120892 TAATTTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:126400 original size:24 final size:24
Alignment explanation
Indices: 126351--126402 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
126341 TTAACAATAG
* * *
126351 AAAATTAGAATATGTCCATTAGGA
1 AAAATTAGAATATATCCATAAAGA
126375 AAAATTAGAATATATACCA-AAAGA
1 AAAATTAGAATATAT-CCATAAAGA
126399 AAAA
1 AAAA
126403 CATATCATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (24 bp):
AAAATTAGAATATATCCATAAAGA
Found at i:128143 original size:4 final size:4
Alignment explanation
Indices: 128134--128163 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
128124 TGTTTTTTAT
*
128134 ATAA ATAA ATAA GTAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT
128164 TTGGAATCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:150285 original size:12 final size:12
Alignment explanation
Indices: 150268--150293 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
150258 TTATGAGCCA
150268 CATTTTATTACT
1 CATTTTATTACT
150280 CATTTTATTACT
1 CATTTTATTACT
150292 CA
1 CA
150294 CTATCACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (12 bp):
CATTTTATTACT
Found at i:157416 original size:20 final size:21
Alignment explanation
Indices: 157379--157417 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
157369 CTCTGATCTC
*
157379 TTTTTTCTTCCTATTTTTTTA
1 TTTTTTCTTCCTAATTTTTTA
*
157400 TTTTTT-TTTCTAATTTTT
1 TTTTTTCTTCCTAATTTTT
157418 CAATTCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTCCTAATTTTTTA
Found at i:159449 original size:131 final size:130
Alignment explanation
Indices: 159303--159561 Score: 353
Period size: 131 Copynumber: 2.0 Consensus size: 130
159293 TGGATTTTAA
* *
159303 GAGAGAAAATGATAATATCTAATTATTTCCAATCT-AGAATAAATGACCTCTCATGCCTTAAACC
1 GAGAGAAAACGATAATATCTAATCATTTCCAAT-TGAGAATAAATGACCTCTCATGCCTTAAACC
* * *
159367 AATCATTTATTACTCCAATCAAAATGAAGAGATA-TCACTATCTT-GTCTTAAAATTCAATATTG
65 AATCATTTATTACTCCAACCAAAATGAAAAGATAGT-ACTAT-TTCGTCCTAAAA-TCAATATTG
159430 ATTC
127 ATTC
* * *
159434 GAGAGAAAACGATAATATCTAATCATTTCTAATTGAGAATAAATGACCTCTTATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATCATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAACCA
* * * *
159499 CTCATTTATTGCTCCAACCGAAATGAAAAGATAGTACTATTTCGTCCTAAAATCATTATTGAT
66 ATCATTTATTACTCCAACCAAAATGAAAAGATAGTACTATTTCGTCCTAAAATCAATATTGAT
159562 AAAAGTGTTA
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
130 13 0.12
131 99 0.88
132 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATCATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAACCA
ATCATTTATTACTCCAACCAAAATGAAAAGATAGTACTATTTCGTCCTAAAATCAATATTGATTC
Found at i:160064 original size:60 final size:61
Alignment explanation
Indices: 159997--160133 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 61
159987 AAAACTAATT
*
159997 AGTGACTAAAATGAAACAATATAAAAGCAACATG-CAAAAATTAAAATAAAA-AAA-TAG-AAA
1 AGTGACTAAAATGAAACAA-AT-AAAGCAACATGTCAAAAATTAAAACAAAATAAAGT-GCAAA
* * * *
160057 TAG-GACTAAAATATAAACCAATAAATCATCATGTCAAAAATTAAAACAAAATAAAGTGCAAA
1 -AGTGACTAAAAT-GAAACAAATAAAGCAACATGTCAAAAATTAAAACAAAATAAAGTGCAAA
160119 AGTGACTAAAATGAA
1 AGTGACTAAAATGAA
160134 CATTTTTAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
59 9 0.14
60 27 0.42
61 15 0.23
62 13 0.20
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (61 bp):
AGTGACTAAAATGAAACAAATAAAGCAACATGTCAAAAATTAAAACAAAATAAAGTGCAAA
Found at i:161845 original size:44 final size:44
Alignment explanation
Indices: 161796--161880 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
161786 CTCGGGCCCA
*
161796 AGTTTTGGGTTTGTAACTGGGTATTATGTTATTAGTTGTACCCG
1 AGTTTTGGGTTTGTAACTGGGTATTAGGTTATTAGTTGTACCCG
* * * *
161840 AGTTTTGGGTTTGTAATTGGTTATTGGGTTATTGGTTGTAC
1 AGTTTTGGGTTTGTAACTGGGTATTAGGTTATTAGTTGTAC
161881 TTGGGCCCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.16, C:0.06, G:0.29, T:0.48
Consensus pattern (44 bp):
AGTTTTGGGTTTGTAACTGGGTATTAGGTTATTAGTTGTACCCG
Found at i:162417 original size:133 final size:133
Alignment explanation
Indices: 162204--162538 Score: 472
Period size: 133 Copynumber: 2.5 Consensus size: 133
162194 TGCTCCGCTG
* * * * ** *
162204 CTTCTTCAGGGTATATCAGATCTTGAAGTGTTGATTCATTCCACTGTTCTTCAAGGAAAATTGAA
1 CTTCTTCAGGGAAAATCAGATATGGAAACGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAA
* * * * *
162269 TCGAGATAGACTTGTTCCACTGCTACTTAGGGAAGATCAAATCTGGAAAGAGGGGATTTGTTCTG
66 TCGAGACAGAATTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGGATTTGTTCTA
* *
162334 TTG
131 CTA
* * *
162337 TTTCTTCAGGGAAAATCAGATATGGAGACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAA
1 CTTCTTCAGGGAAAATCAGATATGGAAACGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAA
*
162402 TCGATACAGAATTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGGATTTGTTCTA
66 TCGAGACAGAATTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGGATTTGTTCTA
162467 CTA
131 CTA
* * * *
162470 CTTCTTTAGGGAAAATCATATTTGGAAACTTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAA
1 CTTCTTCAGGGAAAATCAGATATGGAAACGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAA
162535 TCGA
66 TCGA
162539 ATTTGATTGC
Statistics
Matches: 177, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
133 177 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (133 bp):
CTTCTTCAGGGAAAATCAGATATGGAAACGTTGATTCATTCCACTGTTCTTCAAGGAAGATTGAA
TCGAGACAGAATTGTTCCACTGCTACTCAGGGAAGATCAAATATGGAAAGAGGGGATTTGTTCTA
CTA
Found at i:162951 original size:42 final size:41
Alignment explanation
Indices: 162874--162960 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
162864 ACCCGAAGCT
* *
162874 CTTATAGATGGCCCAAAGAACTTATCATCTCGCTCGAAAGG
1 CTTATAGATGACCCAAAGAACTTATCATCTCGCTCGAAAGA
* * *
162915 CTTATAGATGACCCGAAGGATTTAATCATCAT-GCTCGAAAGA
1 CTTATAGATGACCCAAAGAACTT-ATCATC-TCGCTCGAAAGA
162957 CTTA
1 CTTA
162961 CTGATAACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 19 0.49
42 19 0.49
43 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (41 bp):
CTTATAGATGACCCAAAGAACTTATCATCTCGCTCGAAAGA
Found at i:163430 original size:241 final size:238
Alignment explanation
Indices: 162998--163739 Score: 860
Period size: 241 Copynumber: 3.1 Consensus size: 238
162988 TGGAAATAGT
* * * * *** *
162998 TTACTAGGTAAGAAACTTTGGAGATTGTTTTTTTACTTTTCAAAA-ATTTCAATTTTCATAAAAT
1 TTACTAAGTAAGAAACTTTTGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAAAAAAT
* * * * *
163062 ATTTAAATGAGAAACTTTGGAAATCGTTCTCATTTTTCGAAAAACATGTGAAAACATCATGCCCA
66 GTTTAAATGAGAAACTTTGGAATTCTTTCTCATTTTTTG-AAAACATGTGAAAACATCATGCCCG
* * * * **
163127 AAGGTGTTATGGATTGCCCGAAGGACTTATCATCTTGGTTGAAAGACTTACGGATGACCCGAAGG
130 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACGGATGACCCGAAGG
163192 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGAC
195 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGAC
* *
163236 TTACTAAGTAAGAAAGTTTTGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAGAAAAT
1 TTACTAAGTAAGAAACTTTTGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAAAAAAT
* * * * *
163301 GTTTAAATGAGAAACTTTGGAATTTGCTTTCTCATTTTTTGAGAAACATATGAAGACATCCTACT
66 GTTTAAATGAGAAACTTTGGAA-TT-CTTTCTCATTTTTTGA-AAACATGTGAAAACATCATGCC
* * * * * *
163366 CGAAGGCCTTATAGATGGCTCGGAGGATTTATCATCTTGCTCAAAATACTTACGGATTACCCGAA
128 CGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACGGATGACCCGAA
* * *
163431 GGATTTAAGCATCATGCTCGAAAGACATACTAATGGCC-CAGAGGAC
193 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGA-AGGAC
** * * *
163477 TTACTAAGTAAGAAACTTTTGAAATCATTTTCTTACTTTTCAAAAGAAACAAATTATCAAAAAAG
1 TTACTAAGTAAGAAACTTTTGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAAAAAAT
*
163542 GTTTAAATGAGAAACTTTGGAAATTACTTTCTAATTATTTTTTTTTGAAAATCATGTGAAAACAT
66 GTTTAAATGAGAAACTTTGG-AATT-CTTTC---TCA---TTTTTTGAAAA-CATGTGAAAACAT
* * * * * *
163607 GATGCCCGAATGTCTTATTGATGGCCCGAAAGACTTATCATATTGCTCAAAAGACTTACTGATGA
122 CATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACGGATGA
* * **
163672 CCTGAATGATTTAAGTGTCATGCTCGAAAGACTTACTGATGG-CTCGAAGGAC
187 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCT-GAAGGAC
*
163724 TTACTAAGTGAGAAAC
1 TTACTAAGTAAGAAAC
163740 CCGTGAAGAT
Statistics
Matches: 421, Mismatches: 68, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
238 40 0.10
239 36 0.09
240 3 0.01
241 208 0.49
242 2 0.00
244 2 0.00
246 4 0.01
247 125 0.30
248 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (238 bp):
TTACTAAGTAAGAAACTTTTGAAATTGTTTTCTTACTTTTCAAAAGAAACCAATTTTCAAAAAAT
GTTTAAATGAGAAACTTTGGAATTCTTTCTCATTTTTTGAAAACATGTGAAAACATCATGCCCGA
AGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTACGGATGACCCGAAGGA
TTTAAGCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGAC
Found at i:163643 original size:20 final size:19
Alignment explanation
Indices: 163606--163644 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
163596 TGTGAAAACA
* *
163606 TGATGCCCGAATGTCTTAT
1 TGATGCCCGAAAGACTTAT
163625 TGATGGCCCGAAAGACTTAT
1 TGAT-GCCCGAAAGACTTAT
163645 CATATTGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (19 bp):
TGATGCCCGAAAGACTTAT
Found at i:165436 original size:44 final size:44
Alignment explanation
Indices: 165357--165467 Score: 150
Period size: 44 Copynumber: 2.5 Consensus size: 44
165347 GTATTCCTGG
* * * *
165357 ATGATATGGGCCTTTAAAAGTGCCATACCATTTATCATTTCTGA
1 ATGATATGGGCCTTAAAAAATGCCATAACACTTATCATTTCTGA
* * * *
165401 ATGATATGGGCCTTCAAAAATGTCTTAACACTTATCATTTCTGG
1 ATGATATGGGCCTTAAAAAATGCCATAACACTTATCATTTCTGA
165445 ATGATATGGGCCTTAAAAAATGC
1 ATGATATGGGCCTTAAAAAATGC
165468 GCCAACATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (44 bp):
ATGATATGGGCCTTAAAAAATGCCATAACACTTATCATTTCTGA
Found at i:167420 original size:12 final size:12
Alignment explanation
Indices: 167398--167436 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
167388 AAATTAATAC
*
167398 AATGAAAATGCA
1 AATGTAAATGCA
*
167410 AATGTAGATGCAA
1 AATGTAAATGC-A
167423 AATGTAAATGCA
1 AATGTAAATGCA
167435 AA
1 AA
167437 AGGTGTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.21
Consensus pattern (12 bp):
AATGTAAATGCA
Found at i:167427 original size:13 final size:13
Alignment explanation
Indices: 167398--167437 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
167388 AAATTAATAC
*
167398 AATGAAAATGC-A
1 AATGTAAATGCAA
*
167410 AATGTAGATGCAA
1 AATGTAAATGCAA
167423 AATGTAAATGCAA
1 AATGTAAATGCAA
167436 AA
1 AA
167438 GGTGTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (13 bp):
AATGTAAATGCAA
Found at i:169651 original size:131 final size:130
Alignment explanation
Indices: 169417--169675 Score: 364
Period size: 131 Copynumber: 2.0 Consensus size: 130
169407 GGATTTTAAG
* * *
169417 AGAGAAAACGATAATATCTAATTATTTCCAATGGAGAATAAATGATCTTTCATGCCTTAAAGCAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATGGAGAATAAATGACCTTTCATACCTTAAAACAA
* *
169482 TAATTTATTACTCCAATCGAAATGAAGAGATATCACTATCTT-GTCT-TAAAATTCAATATTGAT
66 TAATTTATTACTCCAACCGAAATGAAAAGATATCACTAT-TTCGT-TGTAAAA-TCAATATTGAT
169545 TCA
128 TCA
*
169548 AGAGAAAACGATAATATCTAATTATTTCCAATTGAGAATAAATGACCTCTT-ATACCTTAAAACA
1 AGAGAAAACGATAATATCTAATTATTTCCAATGGAGAATAAATGACCT-TTCATACCTTAAAACA
* * *
169612 ATCATTTATTGA-TCCAACCGAAATGAAAAGATATTACTATTTCGTTGTAAAATCAGTATTGATT
65 ATAATTTATT-ACTCCAACCGAAATGAAAAGATATCACTATTTCGTTGTAAAATCAATATTGATT
169676 TGAGTGTTAC
Statistics
Matches: 115, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
130 14 0.12
131 98 0.85
132 3 0.03
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (130 bp):
AGAGAAAACGATAATATCTAATTATTTCCAATGGAGAATAAATGACCTTTCATACCTTAAAACAA
TAATTTATTACTCCAACCGAAATGAAAAGATATCACTATTTCGTTGTAAAATCAATATTGATTCA
Found at i:170048 original size:42 final size:42
Alignment explanation
Indices: 169989--170072 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
169979 TATACGTTAA
169989 GACAGTCACTTTACGACAATCTTAAAATGAACGAATATTACC
1 GACAGTCACTTTACGACAATCTTAAAATGAACGAATATTACC
170031 GACAGTCACTTTACGACAATCTTAAAATGAACGAATATTACC
1 GACAGTCACTTTACGACAATCTTAAAATGAACGAATATTACC
170073 CTTAGACAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (42 bp):
GACAGTCACTTTACGACAATCTTAAAATGAACGAATATTACC
Found at i:176127 original size:75 final size:75
Alignment explanation
Indices: 175991--176132 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 75
175981 GAATCTAGCT
* * *
175991 TTGCCAGATTTTGAATTGGCTTTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGA
1 TTGCAAGAGTTTGAATTGGCTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGA
176056 TAATATTGCA
66 TAATATTGCA
* * *
176066 TTGCAAGAGTTTGAATTGGCTCTGAAGCAGTCAAAGAATCCAGTTCCAACTCAATATTCTACTGA
1 TTGCAAGAGTTTGAATTGGCTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGA
176131 TA
66 TA
176133 TCATTAATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (75 bp):
TTGCAAGAGTTTGAATTGGCTCTGAAGCAGTCAAAGAATCCAGTACCAACTCAAGACTCTACTGA
TAATATTGCA
Found at i:178914 original size:19 final size:19
Alignment explanation
Indices: 178882--178919 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
178872 ACCCTATCCG
178882 AAATAATATATTTATTCAA
1 AAATAATATATTTATTCAA
* *
178901 AAATATTATTTTTATTCAA
1 AAATAATATATTTATTCAA
178920 TAAAACTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATAATATATTTATTCAA
Found at i:179947 original size:13 final size:14
Alignment explanation
Indices: 179929--179959 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
179919 ATTGTGATTT
179929 ATATCCG-ATCTAA
1 ATATCCGAATCTAA
179942 ATATCCGAATCTAA
1 ATATCCGAATCTAA
179956 ATAT
1 ATAT
179960 AAAACTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (14 bp):
ATATCCGAATCTAA
Found at i:183117 original size:29 final size:28
Alignment explanation
Indices: 183083--183164 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 28
183073 AATGCTTAAC
183083 AAGTAAATGCATAAATTAAAATAACATA
1 AAGTAAATGCATAAATTAAAATAACATA
*
183111 AATGTAAAGGCA-AAATTATAAATAACATA
1 AA-GTAAATGCATAAATTA-AAATAACATA
* **
183140 AAATAAATTAATTAAATTAAAATAA
1 AAGTAAATGCA-TAAATTAAAATAA
183165 AAAATAGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 13 0.29
29 26 0.58
30 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (28 bp):
AAGTAAATGCATAAATTAAAATAACATA
Found at i:183274 original size:4 final size:4
Alignment explanation
Indices: 183265--183294 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
183255 TTCGAACAAA
183265 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
183295 CAAGTTGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:184436 original size:27 final size:27
Alignment explanation
Indices: 184401--184454 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
184391 ATGGCTTGGG
* *
184401 GCTGTTGTAGTGCAGAGATTTGGTGCA
1 GCTGCTGTAGAGCAGAGATTTGGTGCA
*
184428 GCTGCTGTAGAGCTGAGATTTGGTGCA
1 GCTGCTGTAGAGCAGAGATTTGGTGCA
184455 TATATTAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.37, T:0.31
Consensus pattern (27 bp):
GCTGCTGTAGAGCAGAGATTTGGTGCA
Found at i:185793 original size:118 final size:118
Alignment explanation
Indices: 185560--185844 Score: 329
Period size: 118 Copynumber: 2.4 Consensus size: 118
185550 ATCTTCTTAT
* * * *
185560 GTGATGGAATCGAGCTAATGTTGAACGATTTCTTCTCATTATGAACTTCTTCTCCCTCAACGGAT
1 GTGATGGAATCGAGCCAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCAACGGAT
* * * * * *
185625 GAGTTCTTCTCATTACGAACCTTTCCATTGGAAATATTGATCAACTTCCTTCT
66 GAGTTCTTCTCATTACGAACCCTTCCATTCGAAATATTAAACAACATCCTTCC
* * * **
185678 GTGATGTAATTGAGCC-AAGATTGAACAAGTTCTTCTCATTCTGAACTTCTTCTCCCTCATTGGA
1 GTGATGGAATCGAGCCAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCAACGGA
* * * **
185742 TGAGTTCTTCTCATTACGAGCCCTTCTATTCGAAATGTTAAACCGCATCCTTCC
65 TGAGTTCTTCTCATTACGAACCCTTCCATTCGAAATATTAAACAACATCCTTCC
** * *
185796 GTGATGGAATCGAGTGAAATGTTGAACAAGTTCTTCTTATTAGGAACTT
1 GTGATGGAATCGAGCCAAA-GTTGAACAAGTTCTTCTCATTATGAACTT
185845 TTTCATTGGA
Statistics
Matches: 137, Mismatches: 27, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
117 2 0.01
118 107 0.78
119 27 0.20
120 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (118 bp):
GTGATGGAATCGAGCCAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCAACGGAT
GAGTTCTTCTCATTACGAACCCTTCCATTCGAAATATTAAACAACATCCTTCC
Found at i:186708 original size:64 final size:63
Alignment explanation
Indices: 186618--186754 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
186608 TTCAATGTGA
* * *
186618 ATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG-AGAGC
1 ATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGGTAGAGC
* * * * * *
186681 ATCGATGCATCCCTTTAAA-ATGAAAACATCAAAGGTAATTTGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCA-CCCTTTAAAGAAG-AAACATCAAAGGCAATTAGTGCATCGATGCATAGGTAGAGC
186745 ATCGATGCAC
1 ATCGATGCAC
186755 ATGTTAAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
63 14 0.23
64 48 0.77
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (63 bp):
ATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCATAGGTAGAGC
Found at i:186769 original size:24 final size:20
Alignment explanation
Indices: 186742--186799 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
186732 GCATGGGTAG
186742 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
186766 TGCATCAATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
186786 TACATCGATGCACT
1 TGCATCGATGCACT
186800 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:187595 original size:18 final size:18
Alignment explanation
Indices: 187572--187751 Score: 226
Period size: 18 Copynumber: 10.0 Consensus size: 18
187562 AAGGGTCTAT
187572 GTGGTCCTTCGGGACAAA
1 GTGGTCCTTCGGGACAAA
*
187590 GTGGTCCTTAGGGA-AATA
1 GTGGTCCTTCGGGACAA-A
*
187608 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACAAA
*
187626 GTGGTTCTTCGGGACATAA
1 GTGGTCCTTCGGGACA-AA
187645 -TGGTCCTTCGGGACATAA
1 GTGGTCCTTCGGGACA-AA
187663 -TGGTCCTTCGGGACATAA
1 GTGGTCCTTCGGGACA-AA
187681 -TGGTCCTTCGGGACATAA
1 GTGGTCCTTCGGGACA-AA
*
187699 -TGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACAAA
*
187716 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACAAA
*
187734 GTGGTCCTACGGGACAAA
1 GTGGTCCTTCGGGACAAA
187752 TTCTACGTGC
Statistics
Matches: 148, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
17 3 0.02
18 143 0.97
19 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACAAA
Found at i:187667 original size:54 final size:54
Alignment explanation
Indices: 187572--187749 Score: 268
Period size: 54 Copynumber: 3.3 Consensus size: 54
187562 AAGGGTCTAT
* * *
187572 GTGGTCCTTCGGGACA-AAGTGGTCCTTAGGGAAATAGTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATAA-TGGTCCTTCGGGACATAGTGGTCCTTCGGGACATA
* *
187626 GTGGTTCTTCGGGACATAATGGTCCTTCGGGACATAATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATAATGGTCCTTCGGGACATAGTGGTCCTTCGGGACATA
* *
187680 ATGGTCCTTCGGGACATAATGGTCCTTCGGGACACAGTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATAATGGTCCTTCGGGACATAGTGGTCCTTCGGGACATA
*
187734 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
187750 AATTCTACGT
Statistics
Matches: 112, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
54 110 0.98
55 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (54 bp):
GTGGTCCTTCGGGACATAATGGTCCTTCGGGACATAGTGGTCCTTCGGGACATA
Found at i:189360 original size:38 final size:37
Alignment explanation
Indices: 189277--189367 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 37
189267 TTCTAAGGAG
* *
189277 ATAATCCTAAGAATAACTCAAACGACATTCTAGATAA
1 ATAATCCTAAGAATGACTCAAACGACATTCTAGAAAA
* *
189314 ACAGTCCTAAGAATGACTCAAACGA-ATTTTCTAGAAAA
1 ATAATCCTAAGAATGACTCAAACGACA--TTCTAGAAAA
189352 ATAATCCTAAGAATGA
1 ATAATCCTAAGAATGA
189368 TAAAATAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.02
37 22 0.48
38 23 0.50
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (37 bp):
ATAATCCTAAGAATGACTCAAACGACATTCTAGAAAA
Found at i:190338 original size:56 final size:54
Alignment explanation
Indices: 190269--190380 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 54
190259 CAGTTATCAG
190269 CAAGAAACACCTAAAAATCAGGCTTAGCTCCTTTAAAAAAAATCATTTGAAAACAT
1 CAAGAAACACCTAAAAATCAGGCTTAGCTCCTTT--AAAAAATCATTTGAAAACAT
* * * * * *
190325 CAAGAAACCCCTAAAAATCATGTTTAGCTTCTTTTAAAATTCATTTGAAAACAT
1 CAAGAAACACCTAAAAATCAGGCTTAGCTCCTTTAAAAAATCATTTGAAAACAT
190379 CA
1 CA
190381 TATTGTTTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 20 0.40
56 30 0.60
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.28
Consensus pattern (54 bp):
CAAGAAACACCTAAAAATCAGGCTTAGCTCCTTTAAAAAATCATTTGAAAACAT
Found at i:198136 original size:18 final size:19
Alignment explanation
Indices: 198109--198146 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
198099 ATAATTTTTA
198109 TTTTACTATTA-TTTTAAT
1 TTTTACTATTATTTTTAAT
*
198127 TTTTATTATTATTTTTAAT
1 TTTTACTATTATTTTTAAT
198146 T
1 T
198147 AATTAGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTACTATTATTTTTAAT
Found at i:198148 original size:23 final size:23
Alignment explanation
Indices: 198100--198167 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 23
198090 TGAACATAAA
* * *
198100 TAATTTTTATTTTACTATTATTT
1 TAATTTTTATTTTATTTTTATAT
198123 TAATTTTTATTATTATTTTTA-AT
1 TAATTTTTATT-TTATTTTTATAT
198146 TAATTAGGTTTATTTTATTTTT
1 TAATT---TTTATTTTATTTTT
198168 GCAAGGATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 17 0.45
24 7 0.18
25 8 0.21
26 6 0.16
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (23 bp):
TAATTTTTATTTTATTTTTATAT
Found at i:204593 original size:19 final size:18
Alignment explanation
Indices: 204561--204624 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 18
204551 CGTCTTGAAG
*
204561 TTTTTTTTCTTTTTTCTT
1 TTTTTTTTATTTTTTCTT
204579 TTTTTTTTATGTTTTTCTT
1 TTTTTTTTAT-TTTTTCTT
* *
204598 CTTTTTGTTATATCTTCTCTT
1 -TTTTT-TT-TATTTTTTCTT
204619 TTTTTT
1 TTTTTT
204625 CTCTGTGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 9 0.23
19 9 0.23
20 10 0.26
21 8 0.21
22 3 0.08
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTTTTTATTTTTTCTT
Found at i:206924 original size:28 final size:26
Alignment explanation
Indices: 206868--206929 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
206858 AAAATATAGA
* *
206868 ACTAAAATTAAAACATTAAGTAAAGG
1 ACTAAAATGAAAACATTAAGTAAAAG
206894 ACTAAAATGAAAGACATCATAA-TAAAAG
1 ACTAAAATGAAA-ACAT--TAAGTAAAAG
*
206922 ACTTAAAT
1 ACTAAAAT
206930 TAAGAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 11 0.37
27 4 0.13
28 12 0.40
29 3 0.10
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (26 bp):
ACTAAAATGAAAACATTAAGTAAAAG
Found at i:207016 original size:29 final size:28
Alignment explanation
Indices: 206984--207051 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
206974 TGTAAATGCT
206984 GAAAAGTAAATGCATAAATTA-AAATAACA
1 GAAAA-TAAATGCA-AAATTATAAATAACA
* * *
207013 GAAATTTAAAGGCAAAATTATAAATAACG
1 GAAA-ATAAATGCAAAATTATAAATAACA
207042 GAAAATAAAT
1 GAAAATAAAT
207052 TAATCGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (28 bp):
GAAAATAAATGCAAAATTATAAATAACA
Found at i:208816 original size:60 final size:60
Alignment explanation
Indices: 208739--208870 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
208729 GCATCACACA
* * * * *
208739 TCCCTAAACTATGACTCTC-TTTTTATATTAGTTCT-TAAACTTTTGAACATTCCAATTTCA-
1 TCCC-AAACTATAACTCTCATTCTGA-ATTA-TTCTCTAAACTTTTGAAAATTCCAAGTTCAT
208799 TCCTCAAACTATAACTCTCATTCTGAATTATTCTCTAAACTTTTGAAAATTCCAAGTTCAT
1 TCC-CAAACTATAACTCTCATTCTGAATTATTCTCTAAACTTTTGAAAATTCCAAGTTCAT
208860 TCCCAAACTAT
1 TCCCAAACTAT
208871 GATCCCCATT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
59 4 0.06
60 51 0.81
61 8 0.13
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (60 bp):
TCCCAAACTATAACTCTCATTCTGAATTATTCTCTAAACTTTTGAAAATTCCAAGTTCAT
Found at i:208897 original size:60 final size:60
Alignment explanation
Indices: 208765--208906 Score: 139
Period size: 60 Copynumber: 2.4 Consensus size: 60
208755 CTCTTTTTAT
* * * * *
208765 ATTAGTTCTTAAACTTTTGAACATTCCAATTTCATCCTCAAACTATAACTCTCATTCTGA
1 ATTAGTCCCTAAACTTTTGAAAATTCCAAGTTCATCCTCAAACTATAACTCCCATTCTGA
* * *
208825 ATTATTCTCTAAACTTTTGAAAATTCCAAGTTCATTCC-CAAACTATGA-TCCCCATTCT-A
1 ATTAGTCCCTAAACTTTTGAAAATTCCAAGTTCA-TCCTCAAACTATAACT-CCCATTCTGA
* *
208884 TATTGGTCCCTAAACCTTT-AAAA
1 -ATTAGTCCCTAAACTTTTGAAAA
208907 GATACAATAA
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
59 6 0.09
60 58 0.87
61 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (60 bp):
ATTAGTCCCTAAACTTTTGAAAATTCCAAGTTCATCCTCAAACTATAACTCCCATTCTGA
Found at i:210186 original size:26 final size:26
Alignment explanation
Indices: 210140--210189 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
210130 TTTGAAACAA
*
210140 TTATAATATATTAATATATATAAACT
1 TTATAATATAATAATATATATAAACT
210166 TTATAATAATAAT-ATATATATAAA
1 TTATAAT-ATAATAATATATATAAA
210190 TTATATAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TTATAATATAATAATATATATAAACT
Done.