Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004532.1 Hibiscus syriacus cultivar Beakdansim tig00010009_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: 81271
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2962 original size:21 final size:21
Alignment explanation
Indices: 2936--2975 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2926 AACAAATTGG
2936 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
2957 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
2976 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:3265 original size:20 final size:20
Alignment explanation
Indices: 3240--3288 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
3230 TGCCTGCCAC
3240 TAGTGCATCGATGCACCATG
1 TAGTGCATCGATGCACCATG
3260 TAGTGCATCGATGCACCATG
1 TAGTGCATCGATGCACCATG
3280 TAGTGCATC
1 TAGTGCATC
3289 CATGAACTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (20 bp):
TAGTGCATCGATGCACCATG
Found at i:3419 original size:21 final size:21
Alignment explanation
Indices: 3393--3485 Score: 168
Period size: 21 Copynumber: 4.4 Consensus size: 21
3383 AAAGGGGTAT
*
3393 CGATGCAGCTCGATAGTGCAC
1 CGATGCACCTCGATAGTGCAC
3414 CGATGCACCTCGATAGTGCAC
1 CGATGCACCTCGATAGTGCAC
3435 CGATGCACCTCGATAGTGCAC
1 CGATGCACCTCGATAGTGCAC
*
3456 CGATGCACCTTGATAGTGCAC
1 CGATGCACCTCGATAGTGCAC
3477 CGATGCACC
1 CGATGCACC
3486 ATGTTATGGG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (21 bp):
CGATGCACCTCGATAGTGCAC
Found at i:7547 original size:21 final size:21
Alignment explanation
Indices: 7521--7560 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7511 AACAAATTGG
7521 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
7542 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
7561 CATTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:9240 original size:16 final size:18
Alignment explanation
Indices: 9207--9242 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
9197 TTAAGATTTT
9207 ATATTCGATTTCAAAATA
1 ATATTCGATTTCAAAATA
9225 ATATTCGA-TT-AAAATA
1 ATATTCGATTTCAAAATA
9241 AT
1 AT
9243 CAAATATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (18 bp):
ATATTCGATTTCAAAATA
Found at i:11796 original size:21 final size:21
Alignment explanation
Indices: 11770--11809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11760 AACAAATTGG
11770 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
11791 TAACAATTGTTATCTTTTT
1 TAACAATTGATATCATTTT
11810 CATTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:16318 original size:21 final size:21
Alignment explanation
Indices: 16292--16391 Score: 123
Period size: 21 Copynumber: 4.7 Consensus size: 21
16282 AGGGTGTCAA
16292 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
16313 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
16334 AGTGCATCCATGCACCTTCC-AC
1 AGTGCATCCATGCACC--CCTGC
* * *
16356 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTGC
16377 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
16392 TCCATTTCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
20 14 0.21
21 37 0.54
22 2 0.03
23 15 0.22
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:18896 original size:17 final size:17
Alignment explanation
Indices: 18874--18917 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
18864 GAAAGAGGAG
18874 AGAGAAGAAAAACAAGA
1 AGAGAAGAAAAACAAGA
*
18891 AGAGAAGAAAACCAAGA
1 AGAGAAGAAAAACAAGA
18908 AGAAGAAGAA
1 AG-AGAAGAA
18918 GAAGGAGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (17 bp):
AGAGAAGAAAAACAAGA
Found at i:20593 original size:21 final size:21
Alignment explanation
Indices: 20567--20606 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20557 AACAAATTGG
20567 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
20588 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
20607 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:20886 original size:21 final size:22
Alignment explanation
Indices: 20833--20927 Score: 99
Period size: 21 Copynumber: 4.5 Consensus size: 22
20823 GTCAACGTGT
* *
20833 ATCCATGTACCCCTGC-AGTGC
1 ATCCATGCACCTCTGCTAGTGC
20854 ATCCATGCACCTCTGCT-GTGC
1 ATCCATGCACCTCTGCTAGTGC
**
20875 ATCCATGCACCTGCCACTAGTGC
1 ATCCATGCACCT-CTGCTAGTGC
* *
20898 ATCGATGCA-CTATG-TAGTGC
1 ATCCATGCACCTCTGCTAGTGC
20918 ATCCATGCAC
1 ATCCATGCAC
20928 TCAATTTCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 14 0.23
21 30 0.49
22 5 0.08
23 12 0.20
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (22 bp):
ATCCATGCACCTCTGCTAGTGC
Found at i:21061 original size:21 final size:21
Alignment explanation
Indices: 21035--21085 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
21025 GAAGGGGTAT
21035 CGATGCACCTCGATAGTGCAC
1 CGATGCACCTCGATAGTGCAC
*
21056 CGATGCACCTTGATAGTGCAC
1 CGATGCACCTCGATAGTGCAC
21077 CGATGCACC
1 CGATGCACC
21086 ATGTTATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (21 bp):
CGATGCACCTCGATAGTGCAC
Found at i:24422 original size:59 final size:59
Alignment explanation
Indices: 24359--24821 Score: 412
Period size: 59 Copynumber: 7.8 Consensus size: 59
24349 TTACCAAATG
*
24359 GCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCTATATGGA
1 GCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGA
* *
24418 GCACTATATGTCCTAAAATGATAATGAAATCATACTGAGTGTATGGATTTCCATATGGA
1 GCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGA
* * *
24477 GCACTATATGTGCTAAAATGATAAGGAAATCATACTCAGTGTATGAATTTCCATATGAA
1 GCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGA
* * * *
24536 GCA-T-TGAGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGG-
1 GCACTAT-A-TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGA
* * * * * ***
24595 GCATTATGTGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAAAAA
1 GCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGA
* * * * ** ** *
24654 GCACTA-AGGGTGCTACAAGGATAAGGAAATCATACTAACAGTATGGATTTTTATAT-AA
1 GCACTATA-TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGA
* * * *
24712 GCACT-TCATGTGCTAAAAATGGTAAAGG-GATCATACT-AATGGTATGGATTCTCGA-ATAGG-
1 GCACTAT-ATGTGCT-AAAATGAT-AAGGAAATCATACTGAGT-GTATGGATT-TCCATAT-GGA
* *
24772 GCACT-TCATGTGCTAAAAATGGTAAAGG-AATCATACT-AATGGTATGGATT
1 GCACTAT-ATGTGCT-AAAATGAT-AAGGAAATCATACTGAGT-GTATGGATT
24822 CTCGAATAAG
Statistics
Matches: 340, Mismatches: 49, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.00
58 15 0.04
59 266 0.78
60 57 0.17
61 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (59 bp):
GCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGA
Found at i:24679 original size:177 final size:174
Alignment explanation
Indices: 24366--24926 Score: 473
Period size: 177 Copynumber: 3.2 Consensus size: 174
24356 ATGGCACTAT
* * * *
24366 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTT-CTATATGGAGCACTATATGTC
1 ATGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCAATA-GG-GCATTAT-TGTG
* * * * *** *
24430 CTAAAATGATAATGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTATATGTGCTAAAA
63 CTAAAATGGTAAAGGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTATAGGTGCTAAAA
* * ** *
24495 TGATAAGGAAATCATACTCAGTGTATGAATTTCCATATGAAGCA-TTG
128 GGATAAGGAAATCATACTAACAGTATGAATTTCCATAT-AAGCACTTC
* *
24542 AGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTATGTGTG
1 A-TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCA-ATAGGGCATTAT-TGTG
* *
24607 CTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTA-AGGGTGCTACA
63 CTAAAATGGTAAAGGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTATA-GGTGCTAAA
* **
24671 AGGATAAGGAAATCATACTAACAGTATGGATTTTTATATAAGCACTTC
127 AGGATAAGGAAATCATACTAACAGTATGAATTTCCATATAAGCACTTC
* * *
24719 ATGTGCTAAAAATGGTAAAGG-GATCATACT-AATGGTATGGATTCTCGAATAGGGCACTTCA-T
1 ATGTGCT-AAAATGAT-AAGGAAATCATACTGAAT-GTATGGATT-TCCAATAGGGCA-TT-ATT
* * *
24781 GTGCTAAAAATGGTAAAGGAATCATACT-AATGGTATGGA-TTCTC-GAATAAGGCACT-TCATG
60 GTGCT-AAAATGGTAAAGGAATCATACTGAGT-GTATGGATTTC-CAGAA-AAAGCACTAT-AGG
** * *
24842 TGCTAAAAATGG-TAAAGG-AATCATTACTAATGGTATGGATTCTCGA-ATAAGGCACTTC
120 TGCT-AAAA-GGAT-AAGGAAATCA-TACTAACAGTATGAATT-TCCATATAA-GCACTTC
* * *
24900 GTATGCTAAAATGAGAAGGAAATCATA
1 ATGTGCTAAAATGATAAGGAAATCATA
24927 TTAAGTATAT
Statistics
Matches: 318, Mismatches: 43, Indels: 44
0.79 0.11 0.11
Matches are distributed among these distances:
176 16 0.05
177 180 0.57
178 53 0.17
179 18 0.06
180 37 0.12
181 14 0.04
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (174 bp):
ATGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCAATAGGGCATTATTGTGCTA
AAATGGTAAAGGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACTATAGGTGCTAAAAGGA
TAAGGAAATCATACTAACAGTATGAATTTCCATATAAGCACTTC
Found at i:24731 original size:118 final size:114
Alignment explanation
Indices: 24359--24956 Score: 385
Period size: 118 Copynumber: 5.0 Consensus size: 114
24349 TTACCAAATG
* * * * ***
24359 GCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCTATATGGAGCACTA
1 GCACT-TATGTGCTAAAATGGTAAGGGAATCATACT-AGTGTATGGATTTCCAGAAAAAGCACTA
* * * * *
24424 TATGTCCTAAAATGATAATGAAATCATACTGAGT-GTATGGATTTCCATATGGA
64 -ATGTGCTAAAAGGATAAGGAAATCATACT-AATAGTATGGATTTCCATAT-AA
* * * * ** *
24477 GCACTATATGTGCTAAAATGATAAGGAAATCATACTCAGTGTATGAATTTCCATATGAAGCATTG
1 GCACT-TATGTGCTAAAATGGTAAGGGAATCATACT-AGTGTATGGATTTCCAGAAAAAGCACT-
* * * * *
24542 AGTGTGCTAAAATGATAAGGAAATCATATTGAATA-TATGGATTTCCAGATAGG
63 AATGTGCTAAAAGGATAAGGAAATCATACT-AATAGTATGGATTTCCATATA-A
24595 GCA-TTATGTGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGAAAAAGCACT
1 GCACTTA--TGTGCTAAAATGGTAAGGGAATCATACT-AGTGTATGGATTTCCAGAAAAAGCACT
* * * **
24659 AAGGGTGCTACAAGGATAAGGAAATCATACTAACAGTATGGATTTTTATATAA
63 AA-TGTGCTAAAAGGATAAGGAAATCATACTAATAGTATGGATTTCCATATAA
* **
24712 GCACTTCATGTGCTAAAAATGGTAAAGGG-ATCATACTAATGGTATGGA-TTCTC-GAATAGGGC
1 GCACTT-ATGTGCT-AAAATGGT-AAGGGAATCATACTAGT-GTATGGATTTC-CAGAA-AAAGC
* * *
24774 ACTTCATGTGCTAAAAATGG-TAAAGG-AATCATACTAATGGTATGGATTCTCGA-ATAA
60 AC-TAATGTGCT-AAAA-GGAT-AAGGAAATCATACTAATAGTATGGATT-TCCATATAA
* * *
24831 GGCACTTCATGTGCTAAAAATGGTAAAGGAATCATTACTAATGGTATGGA-TTCTC-GAATAAGG
1 -GCACTT-ATGTGCT-AAAATGGTAAGGGAATCA-TACTAGT-GTATGGATTTC-CAGAA-AAAG
** * * * *
24894 CACTTCGTATGCTAAAATGAGAAGGAAATCATATTAAGTA-TAT-GATATTCCATATATA
59 CAC-TAATGTGCTAAAAGGATAAGGAAATCATACTAA-TAGTATGGAT-TTCCATATA-A
24952 GCACT
1 GCACT
24957 GAGAGTGCTA
Statistics
Matches: 402, Mismatches: 50, Indels: 54
0.79 0.10 0.11
Matches are distributed among these distances:
116 2 0.00
117 22 0.05
118 225 0.56
119 52 0.13
120 61 0.15
121 40 0.10
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (114 bp):
GCACTTATGTGCTAAAATGGTAAGGGAATCATACTAGTGTATGGATTTCCAGAAAAAGCACTAAT
GTGCTAAAAGGATAAGGAAATCATACTAATAGTATGGATTTCCATATAA
Found at i:24912 original size:60 final size:60
Alignment explanation
Indices: 24676--24910 Score: 357
Period size: 60 Copynumber: 3.9 Consensus size: 60
24666 CTACAAGGAT
** **
24676 AAGGAAATCATACTAACAGTATGGATT-TTTATATAA-GCACTTCATGTGCTAAAAATGGTA
1 AAGG-AATCATACTAATGGTATGGATTCTCGA-ATAAGGCACTTCATGTGCTAAAAATGGTA
* *
24736 AAGGGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGGATTCTCGAATAAGGCACTTCATGTGCTAAAAATGGTA
24796 AAGGAATCATACTAATGGTATGGATTCTCGAATAAGGCACTTCATGTGCTAAAAATGGTA
1 AAGGAATCATACTAATGGTATGGATTCTCGAATAAGGCACTTCATGTGCTAAAAATGGTA
* *
24856 AAGGAATCATTACTAATGGTATGGATTCTCGAATAAGGCACTTCGTATGCTAAAA
1 AAGGAATCA-TACTAATGGTATGGATTCTCGAATAAGGCACTTCATGTGCTAAAA
24911 TGAGAAGGAA
Statistics
Matches: 162, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
59 22 0.14
60 97 0.60
61 43 0.27
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (60 bp):
AAGGAATCATACTAATGGTATGGATTCTCGAATAAGGCACTTCATGTGCTAAAAATGGTA
Found at i:24956 original size:120 final size:119
Alignment explanation
Indices: 24676--24956 Score: 326
Period size: 120 Copynumber: 2.3 Consensus size: 119
24666 CTACAAGGAT
* **
24676 AAGGAAATCATACTAACAGTATGGATT-TTTATATA-AGCACTTCATGTGCTAAAAATGGTAAAG
1 AAGG-AATCATACTAA-GGTATGGATTCTCCATATATAGCACTTCATGTGCTAAAAATGGTAAAG
* * *
24739 GGATCATACTAATGGTATGGATTCTCGAATAGGGCACTTCATGTGCTAAAAATGGTA
64 GAATCATACTAATGGTATGGATTCTCGAATAAGGCACTTCATATGCTAAAAATGG-A
*
24796 AAGGAATCATACTAATGGTATGGATTCTCGA-ATA-AGGCACTTCATGTGCTAAAAATGGTAAAG
1 AAGGAATCATACTAA-GGTATGGATTCTCCATATATA-GCACTTCATGTGCTAAAAATGGTAAAG
*
24859 GAATCATTACTAATGGTATGGATTCTCGAATAAGGCACTTCGTATGCT-AAAAT-GA
64 GAATCA-TACTAATGGTATGGATTCTCGAATAAGGCACTTCATATGCTAAAAATGGA
* *
24914 GAAGGAAATCATATTAA-GTATATGATAT-TCCATATATAGCACT
1 -AAGG-AATCATACTAAGGTAT-GGAT-TCTCCATATATAGCACT
24957 GAGAGTGCTA
Statistics
Matches: 141, Mismatches: 11, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
118 5 0.04
119 35 0.25
120 62 0.44
121 39 0.28
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (119 bp):
AAGGAATCATACTAAGGTATGGATTCTCCATATATAGCACTTCATGTGCTAAAAATGGTAAAGGA
ATCATACTAATGGTATGGATTCTCGAATAAGGCACTTCATATGCTAAAAATGGA
Found at i:25126 original size:44 final size:44
Alignment explanation
Indices: 25063--25319 Score: 357
Period size: 44 Copynumber: 6.0 Consensus size: 44
25053 TCAGTAATGC
*
25063 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGATCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
25107 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
25151 AAATTATAGTAAGCATATTGGT---A-AA---TACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
25188 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * *
25232 GAATAATGGTAAGTATATTGGTAAAATAAACTTACGAGCTTAGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * *
25276 GATTTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
25320 TGATTAAATA
Statistics
Matches: 191, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
37 33 0.17
40 3 0.02
41 3 0.02
44 116 0.61
45 36 0.19
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:25189 original size:37 final size:37
Alignment explanation
Indices: 25139--25212 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
25129 AAAATAAGCT
25139 TACGAGCTTATGAAATTATAGTAAGCATATTGGTAAA
1 TACGAGCTTATGAAATTATAGTAAGCATATTGGTAAA
*
25176 TACGAGCTTATGAAATTATAGTAAGTATATTGGTAAA
1 TACGAGCTTATGAAATTATAGTAAGCATATTGGTAAA
25213 ATAAGCTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (37 bp):
TACGAGCTTATGAAATTATAGTAAGCATATTGGTAAA
Found at i:25230 original size:81 final size:83
Alignment explanation
Indices: 25095--25319 Score: 292
Period size: 81 Copynumber: 2.7 Consensus size: 83
25085 AAAATAAGCT
* *
25095 TACGATCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAG
1 TACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATAG
25160 TAAGCATATTGG-TAAA-
66 TAAGCATATTGGATAAAC
* * *
25176 TACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAATAATGG
1 TACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATAG
*
25241 TAAGTATATTGGTAAAATAAAC
66 TAAGCATATTGG----ATAAAC
* * * *
25263 TTACGAGCTTAGGGATTTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 -TACGAGCTTATGAAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
25320 TGATTAAATA
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
81 71 0.57
86 4 0.03
88 14 0.11
89 36 0.29
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.34
Consensus pattern (83 bp):
TACGAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATAG
TAAGCATATTGGATAAAC
Found at i:25309 original size:125 final size:124
Alignment explanation
Indices: 25063--25310 Score: 363
Period size: 125 Copynumber: 2.0 Consensus size: 124
25053 TCAGTAATGC
* * *
25063 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGATCTTATGAAATTATAGTAAGTATATTGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGAAATAATAGTAAGTATATTGG
* *
25128 TAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGCATATTGGTAAATACGAGCTTATG
66 TAAAATAAACTTACGAGCTTAGGAAATTATAGTAAGCATATTGGTAAATAC-AGCTTATG
* *
25188 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTATATTGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGAAATAATAGTAAGTATATTGG
* * * *
25253 TAAAATAAACTTACGAGCTTAGGGATTTAATGGTAAGTATATTGGTAAAATA-AGCTTA
66 TAAAATAAACTTACGAGCTTAGGAAATT-ATAGTAAGCATATTGGT-AAATACAGCTTA
25311 CGAGCTTATT
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
125 90 0.82
126 15 0.14
127 5 0.05
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (124 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGAAATAATAGTAAGTATATTGG
TAAAATAAACTTACGAGCTTAGGAAATTATAGTAAGCATATTGGTAAATACAGCTTATG
Found at i:28320 original size:23 final size:22
Alignment explanation
Indices: 28281--28328 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
28271 TCTCTTAGCA
*
28281 TCATAGTTATATATATTTTATTT
1 TCATAGTTATATATA-TTAATTT
*
28304 TCATAG-TATATTTTATTAATTT
1 TCATAGTTATA-TATATTAATTT
28326 TCA
1 TCA
28329 ATATTATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (22 bp):
TCATAGTTATATATATTAATTT
Found at i:28396 original size:19 final size:18
Alignment explanation
Indices: 28347--28399 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
28337 TTAATATTGA
*
28347 TAATTATATTAATTTATT
1 TAATTATATTATTTTATT
* *
28365 CAGATTAAAATTATTTTATT
1 TA-ATT-ATATTATTTTATT
28385 TAATTGATATTATTT
1 TAATT-ATATTATTT
28400 AAATGATTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TAATTATATTATTTTATT
Found at i:35861 original size:17 final size:16
Alignment explanation
Indices: 35821--35853 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
35811 ACATTTTAAC
35821 TTAAAA-ATAAAATTA
1 TTAAAATATAAAATTA
35836 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
35852 TT
1 TT
35854 TAATATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAATATAAAATTA
Found at i:40198 original size:22 final size:23
Alignment explanation
Indices: 40163--40224 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
40153 AATGTTAGAA
*
40163 AAAAAAAGTGAAAATGAATAAAAT
1 AAAAAAA-TAAAAATGAATAAAAT
*
40187 AAAAAAATAAAAATAAATAAAGA-
1 AAAAAAATAAAAATGAATAAA-AT
40210 AAAAGAAATTAAAAA
1 AAAA-AAA-TAAAAA
40225 AAGAAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 16 0.48
24 11 0.33
25 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (23 bp):
AAAAAAATAAAAATGAATAAAAT
Found at i:40199 original size:14 final size:14
Alignment explanation
Indices: 40182--40251 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
40172 GAAAATGAAT
* *
40182 AAAATAAAAAAATA
1 AAAAGAAAAAAAGA
* *
40196 AAAATAAATAAAGA
1 AAAAGAAAAAAAGA
40210 AAAAGAAATTAAAA-A
1 AAAAGAAA--AAAAGA
40225 AAGAA-AAAGAAAAGA
1 AA-AAGAAA-AAAAGA
40240 AAAAGAAAAAAA
1 AAAAGAAAAAAA
40252 TACATAAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 29 0.63
15 12 0.26
16 5 0.11
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:40201 original size:19 final size:19
Alignment explanation
Indices: 40179--40253 Score: 57
Period size: 20 Copynumber: 3.9 Consensus size: 19
40169 AGTGAAAATG
40179 AATAAAATAAAAAAATAAA
1 AATAAAATAAAAAAATAAA
40198 AAT-AAATAAAGAAAA-AGAA
1 AATAAAATAAA-AAAATA-AA
* * *
40217 ATTAAAAAAAGAAAAAGAAA
1 AATAAAATAA-AAAAATAAA
*
40237 AGA-AAAAGAAAAAAATA
1 A-ATAAAATAAAAAAATA
40254 CATAAGATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 8 0.18
19 17 0.38
20 18 0.40
21 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (19 bp):
AATAAAATAAAAAAATAAA
Found at i:40225 original size:13 final size:14
Alignment explanation
Indices: 40195--40249 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 14
40185 ATAAAAAAAT
*
40195 AAAAATAAATAAAG
1 AAAAAGAAATAAAG
*
40209 AAAAAGAAATTAA-
1 AAAAAGAAATAAAG
40222 AAAAAG-AA-AAAG
1 AAAAAGAAATAAAG
40234 -AAAAG-AA-AAAG
1 AAAAAGAAATAAAG
40245 AAAAA
1 AAAAA
40250 AATACATAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 13 0.36
12 6 0.17
13 6 0.17
14 11 0.31
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (14 bp):
AAAAAGAAATAAAG
Found at i:40237 original size:5 final size:6
Alignment explanation
Indices: 40205--40249 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
40195 AAAAATAAAT
40205 AAAGAA AAAGAA ATTAA-AA AAAGAA AAAG-A AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA A--AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
40250 AATACATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 7 0.20
6 23 0.66
7 3 0.09
8 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:40237 original size:11 final size:11
Alignment explanation
Indices: 40223--40248 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40213 AGAAATTAAA
40223 AAAAGAAAAAG
1 AAAAGAAAAAG
40234 AAAAGAAAAAG
1 AAAAGAAAAAG
40245 AAAA
1 AAAA
40249 AAATACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:40421 original size:3 final size:3
Alignment explanation
Indices: 40399--40457 Score: 50
Period size: 3 Copynumber: 18.7 Consensus size: 3
40389 TTAAGAGAAA
*
40399 AAT ATAT AA- AAT ATAT AAT AAT AAT AAT AAC ATAT ATAT AAT AACT
1 AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT A-AT AAT AA-T
40445 -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
40458 AGAAGGACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
2 3 0.06
3 32 0.67
4 13 0.27
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:40441 original size:14 final size:12
Alignment explanation
Indices: 40419--40454 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
40409 ATATATAATA
40419 ATAATAATAACAT
1 ATAATAATAAC-T
40432 ATATATAATAACT
1 ATA-ATAATAACT
40445 ATAATAATAA
1 ATAATAATAA
40455 TAAAGAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 7 0.32
14 8 0.36
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATAATAACT
Found at i:40457 original size:9 final size:10
Alignment explanation
Indices: 40399--40457 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 10
40389 TTAAGAGAAA
40399 AATATATAA-
1 AATATATAAT
40408 AATATATAAT
1 AATATATAAT
40418 AATA-ATAAT
1 AATATATAAT
*
40427 AACATATATAT
1 AATATATA-AT
40438 AATAACTATAAT
1 AAT-A-TATAAT
40450 AATA-ATAA
1 AATATATAA
40458 AGAAGGACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
9 21 0.49
10 7 0.16
11 5 0.12
12 6 0.14
13 4 0.09
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (10 bp):
AATATATAAT
Found at i:40700 original size:15 final size:15
Alignment explanation
Indices: 40682--40739 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
40672 CAAAGCAAAC
40682 AAAATATAATAATAA
1 AAAATATAATAATAA
*
40697 AAAATAATAA-AGTAA
1 AAAAT-ATAATAATAA
*
40712 AATATATACATAATAA
1 AAAATATA-ATAATAA
40728 ATAAATA-AATAA
1 A-AAATATAATAA
40740 AAGTAAGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 3 0.09
15 18 0.51
16 10 0.29
17 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AAAATATAATAATAA
Found at i:40713 original size:28 final size:28
Alignment explanation
Indices: 40682--40741 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
40672 CAAAGCAAAC
40682 AAAATATAATA-ATAAAAAAT-AATAAAGT
1 AAAATAT-ATACATAAAAAATAAATAAA-T
*
40710 AAAATATATACATAATAAATAAATAAAT
1 AAAATATATACATAAAAAATAAATAAAT
40738 AAAA
1 AAAA
40742 GTAAGAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 20 0.69
29 6 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAATATATACATAAAAAATAAATAAAT
Found at i:40743 original size:34 final size:30
Alignment explanation
Indices: 40685--40745 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 30
40675 AGCAAACAAA
40685 ATATAATAATAAAAAATAATAAAGTAAAAT
1 ATATAATAATAAAAAATAATAAAGTAAAAT
40715 ATATACATAATAAATAAATAAATAAAAGTAA
1 ATATA-ATAATAAA-AAAT-AAT-AAAGTAA
40746 GAAGAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.19
31 8 0.30
32 4 0.15
33 3 0.11
34 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (30 bp):
ATATAATAATAAAAAATAATAAAGTAAAAT
Found at i:43793 original size:84 final size:84
Alignment explanation
Indices: 42665--43785 Score: 1357
Period size: 84 Copynumber: 13.4 Consensus size: 84
42655 AACTCGACAA
* * * * *
42665 TTTTGTTGACAGATAGCCCTTCTTGCCTTGAACTATGATGTAAATTTGATGTGCCTTTGAACTGA
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGA
*
42730 GTGTAATCAAACTCGAAGGTC
64 GTGTAATCGAACTCGAAGGTC
* * *
42751 TTTTGTTAGCAGATATCCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
42816 GTAATCGAACTCGAATGTC
66 GTAATCGAACTCGAAGGTC
* * * * *
42835 TTTTGTTGGCAGATAGCCCTTTTTGCCTTGAGCTATGCTACAAATGATGTGTCTCTGAACTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
** *
42900 ACAATCGAACTTGAAGGTC
66 GTAATCGAACTCGAAGGTC
* *
42919 TTTTGTTGGCAGATAGCTCTTCTTGTCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
42984 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
43003 TTTTGTTGGCATATAGCCCTTCTTGCCTTGAGCTATACTACAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
43068 GTAATCGAACTCGAATGAC
66 GTAATCGAACTCGAAGGTC
* * * * * *
43087 ---T-TTGGCAGATAGCCCTTCTTGCCTTGAGTTATACAGTAAATGATATGTCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
43148 GTAATAGAACTCGAAGATC
66 GTAATCGAACTCGAAGGTC
* * * * *
43167 -TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
43231 GTAATCAAACTCGAAGG--
66 GTAATCGAACTCGAAGGTC
* * * * * *
43248 -TAT-TTGACAGATAACTCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCCGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
43311 GTAATCAAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * *
43330 TTTGGTTGGTAGATAGCCCTTCTTGGCTTGAGCTATGTTGCAAATGAGGTGCTTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
43395 GTAATCGAACTCGAAGGT-
66 GTAATCGAACTCGAAGGTC
* * * * *
43413 TTTTGGTTAGCAGATAACCCTTCTTGCCTTGAGCTATGTTGTAAATGATGTGCCTTTAAGCTGAG
1 TTTT-GTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
*
43478 TGTAATCAAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
** * * * *
43498 TTCGGTTGGTAGATAGTCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
43563 GTAATCAAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * ** * * ** *
43582 -TTTATTGACAGATAACCCTTCAAGCCTTGAGTTATGTTATAAATGATGTGCCTTTGAGCGGAGT
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
43646 GTAATCAAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * * *
43665 TTTGGTTAGCAGATAACCCTTCTTACCTTGA-CTTATACTGCAAATGATGTGCCTTTTAGTTGAG
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGC-TATGCTGCAAATGATGTGCCTTTGAGCTGAG
43729 TGTAATCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* *
43749 TTTTGTTGGCAGATAACCCTTCTCGCCTTGAGCTATG
1 TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATG
43786 ATACAAATAA
Statistics
Matches: 889, Mismatches: 134, Indels: 26
0.85 0.13 0.02
Matches are distributed among these distances:
80 141 0.16
81 3 0.00
82 1 0.00
83 140 0.16
84 564 0.63
85 3 0.00
86 37 0.04
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (84 bp):
TTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:45059 original size:94 final size:94
Alignment explanation
Indices: 44862--45115 Score: 323
Period size: 94 Copynumber: 2.6 Consensus size: 94
44852 GGCTAGCTAG
* * * * *
44862 ATCCATAAAGTCGGGGCGTTTAACCAACTGCTCTAGAGGGTTAGCTCAATATCATTATATAGT-T
1 ATCCATAAAGTCAGGGCGTTTAACCAATTGCTCTAGAGGG-TACCTC-A-A-CCTT-TATTGTAT
*
44926 ATTATAATTACCTTTATCAGGCTAGCTGAATATT
61 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
*
44960 ATCCATAAAGTCAGGGCGTTTAACCAATTGCTCTAGAGGGTACCTCAAGCTTTATTGTATATTAT
1 ATCCATAAAGTCAGGGCGTTTAACCAATTGCTCTAGAGGGTACCTCAACCTTTATTGTATATTAT
*
45025 AATCACCTTTATCAGGCTAGCTGAATCTT
66 AATCACCTTTATCAGGCTAGCTGAATATT
* * * *
45054 ATCCATAAAGCCAGGGTGTTTAACCAATTACTCTAGAGGG-ACAGTTCAACCTTTATTGTATA
1 ATCCATAAAGTCAGGGCGTTTAACCAATTGCTCTAGAGGGTAC--CTCAACCTTTATTGTATA
45116 CATAATATTA
Statistics
Matches: 140, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
93 7 0.05
94 72 0.51
95 17 0.12
96 1 0.01
97 5 0.04
98 38 0.27
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (94 bp):
ATCCATAAAGTCAGGGCGTTTAACCAATTGCTCTAGAGGGTACCTCAACCTTTATTGTATATTAT
AATCACCTTTATCAGGCTAGCTGAATATT
Found at i:50274 original size:11 final size:11
Alignment explanation
Indices: 50244--50285 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
50234 ATTAATGATG
* *
50244 ATAAAATACAT
1 ATAAAATAAAA
50255 ATAATAATAAAA
1 ATAA-AATAAAA
50267 ATAAAATAAAA
1 ATAAAATAAAA
50278 ATAAAATA
1 ATAAAATA
50286 GTATAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:50402 original size:17 final size:17
Alignment explanation
Indices: 50380--50418 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
50370 TATAATACTT
50380 AAATAAAAA-AATTAACC
1 AAATAAAAATAATTAA-C
50397 AAATAAAAATAATTAAC
1 AAATAAAAATAATTAAC
50414 AAATA
1 AAATA
50419 TACATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAAATAATTAAC
Found at i:50490 original size:12 final size:12
Alignment explanation
Indices: 50475--50501 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
50465 ATGTATATAT
50475 ATAAAAATAATA
1 ATAAAAATAATA
50487 ATAAAAATAATA
1 ATAAAAATAATA
50499 ATA
1 ATA
50502 CAAGGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:53697 original size:14 final size:14
Alignment explanation
Indices: 53678--53707 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53668 CCTTTACGAG
53678 TTTTCTCTTTTTTC
1 TTTTCTCTTTTTTC
*
53692 TTTTCTTTTTTTTC
1 TTTTCTCTTTTTTC
53706 TT
1 TT
53708 ATTTGTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTCTTTTTTC
Found at i:53782 original size:11 final size:11
Alignment explanation
Indices: 53768--53807 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
53758 CGTTTTTTCT
53768 TTTTTTTTGTG
1 TTTTTTTTGTG
53779 -TTTTTTTGTG
1 TTTTTTTTGTG
53789 TTTTTTTTGT-
1 TTTTTTTTGTG
53799 TTTGTTTTT
1 TTT-TTTTT
53808 TCATTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTTTTTGTG
Found at i:53784 original size:21 final size:22
Alignment explanation
Indices: 53759--53815 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
53749 TACCCTAAAC
*
53759 GTTTTTTCTTTTTTTTTGTGTT
1 GTTTTTTCATTTTTTTTGTGTT
* *
53781 -TTTTTGT-GTTTTTTTTGTTTT
1 GTTTTT-TCATTTTTTTTGTGTT
53802 GTTTTTTCATTTTT
1 GTTTTTTCATTTTT
53816 CTTCTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (22 bp):
GTTTTTTCATTTTTTTTGTGTT
Found at i:58222 original size:61 final size:61
Alignment explanation
Indices: 58124--58247 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
58114 CCACTTCCTC
* *
58124 ATCTACTTCGATGTATGGGGCCTCCGTGGTCACGCTTGCCACGATATCTTCCTCAGTATTG
1 ATCTACTTCGATGTATGGGGCCTCCGTGATCACGCTTGCCACGATATCTTCCTCAGCATTG
*
58185 ATCTACTTCGATGTATGGGGCCTCCGTGATCATGCTTGCCACGATATCTTCCTCAGCATTG
1 ATCTACTTCGATGTATGGGGCCTCCGTGATCACGCTTGCCACGATATCTTCCTCAGCATTG
58246 AT
1 AT
58248 AATTACTAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (61 bp):
ATCTACTTCGATGTATGGGGCCTCCGTGATCACGCTTGCCACGATATCTTCCTCAGCATTG
Found at i:64195 original size:9 final size:9
Alignment explanation
Indices: 64180--64239 Score: 97
Period size: 9 Copynumber: 6.8 Consensus size: 9
64170 GATTTAGAAG
64180 GGAAAAGGTT
1 GGAAAA-GTT
64190 -GAAAAGTT
1 GGAAAAGTT
64198 GGAAAAGTT
1 GGAAAAGTT
64207 GGAAAAGTT
1 GGAAAAGTT
64216 GGAAAAGTT
1 GGAAAAGTT
64225 GGAAAAGTT
1 GGAAAAGTT
64234 -GAAAAG
1 GGAAAAG
64240 AATGTTAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
8 9 0.18
9 40 0.82
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (9 bp):
GGAAAAGTT
Found at i:64326 original size:24 final size:23
Alignment explanation
Indices: 64285--64336 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
64275 ATTAATGATG
64285 ATAAAATATATATAATAATAAAA
1 ATAAAATATATATAATAATAAAA
*
64308 ATAAAATAGTATA-ATATAATAATA
1 ATAAAATA-TATATA-ATAATAAAA
64332 ATAAA
1 ATAAA
64337 TAAAAACCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
ATAAAATATATATAATAATAAAA
Found at i:65540 original size:9 final size:9
Alignment explanation
Indices: 65518--65648 Score: 51
Period size: 9 Copynumber: 14.9 Consensus size: 9
65508 GGAAAAAAGT
*
65518 GAAAATGAA
1 GAAAATAAA
*
65527 TAAAATAAA
1 GAAAATAAA
65536 GAAAAT--A
1 GAAAATAAA
65543 -AAAATAAA
1 GAAAATAAA
*
65551 TAAAATAAA
1 GAAAATAAA
*
65560 GCAAAAGAAA
1 G-AAAATAAA
* *
65570 -TAGA-AAA
1 GAAAATAAA
65577 GAAAATAAA
1 GAAAATAAA
*
65586 GAAAAGAAAA
1 GAAAA-TAAA
*
65596 GAAAA-AAG
1 GAAAATAAA
65604 GTAAAA-AGAA
1 G-AAAATA-AA
* *
65614 AAAAATACA
1 GAAAATAAA
* * *
65623 TAAGATAAC
1 GAAAATAAA
65632 GAAAATAAA
1 GAAAATAAA
*
65641 GACAATAA
1 GAAAATAA
65649 TGACAATACA
Statistics
Matches: 90, Mismatches: 22, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
6 5 0.06
7 4 0.04
8 8 0.09
9 56 0.62
10 17 0.19
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.11
Consensus pattern (9 bp):
GAAAATAAA
Found at i:65544 original size:14 final size:13
Alignment explanation
Indices: 65525--65602 Score: 61
Period size: 14 Copynumber: 5.7 Consensus size: 13
65515 AGTGAAAATG
65525 AATAAAATAAAGAA
1 AATAAAA-AAAGAA
*
65539 AATAAAAATAAATAA
1 AAT-AAAA-AAAGAA
65554 AATAAAGCAAAAG-A
1 AATAAA--AAAAGAA
*
65568 AAT-AGAAAAGAA
1 AATAAAAAAAGAA
65580 AATAAAGAAAAGAA
1 AATAAA-AAAAGAA
*
65594 AAGAAAAAA
1 AATAAAAAA
65603 GGTAAAAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
11 5 0.09
12 4 0.08
13 5 0.09
14 22 0.42
15 16 0.30
16 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.10, T:0.10
Consensus pattern (13 bp):
AATAAAAAAAGAA
Found at i:65547 original size:24 final size:25
Alignment explanation
Indices: 65519--65595 Score: 79
Period size: 24 Copynumber: 3.1 Consensus size: 25
65509 GAAAAAAGTG
*
65519 AAAATGAATAAAATAAAG-AAAATA
1 AAAATAAATAAAATAAAGCAAAATA
*
65543 AAAATAAATAAAATAAAGCAAAAGA
1 AAAATAAATAAAATAAAGCAAAATA
* *
65568 AATAGA-AAAGAAAATAAAG-AAAAGA
1 AA-A-ATAAATAAAATAAAGCAAAATA
65593 AAA
1 AAA
65596 GAAAAAAGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 18 0.38
25 15 0.32
26 13 0.28
27 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.10, T:0.12
Consensus pattern (25 bp):
AAAATAAATAAAATAAAGCAAAATA
Found at i:65548 original size:15 final size:15
Alignment explanation
Indices: 65528--65559 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
65518 GAAAATGAAT
65528 AAAATAAAGAAAATA
1 AAAATAAAGAAAATA
*
65543 AAAATAAATAAAATA
1 AAAATAAAGAAAATA
65558 AA
1 AA
65560 GCAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (15 bp):
AAAATAAAGAAAATA
Found at i:65568 original size:30 final size:31
Alignment explanation
Indices: 65533--65600 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
65523 TGAATAAAAT
*
65533 AAAGAAAATA-AAAA-TAAATAAA-ATAAAGCA
1 AAAGAAAATAGAAAAGAAAATAAAGA-AAAG-A
65563 AAAG-AAATAGAAAAGAAAATAAAGAAAAGA
1 AAAGAAAATAGAAAAGAAAATAAAGAAAAGA
65593 AAAGAAAA
1 AAAGAAAA
65601 AAGGTAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
29 5 0.15
30 13 0.39
31 14 0.42
32 1 0.03
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (31 bp):
AAAGAAAATAGAAAAGAAAATAAAGAAAAGA
Found at i:65595 original size:19 final size:20
Alignment explanation
Indices: 65563--65600 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
65553 AAATAAAGCA
65563 AAAGAAATAGAAAAGAAAAT
1 AAAGAAATAGAAAAGAAAAT
65583 AAAGAAA-AGAAAAGAAAA
1 AAAGAAATAGAAAAGAAAA
65601 AAGGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAGAAATAGAAAAGAAAAT
Found at i:65598 original size:10 final size:10
Alignment explanation
Indices: 65557--65600 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
65547 TAAATAAAAT
65557 AAAGCAAAAGA
1 AAAG-AAAAGA
65568 AATAGAAAAGA
1 AA-AGAAAAGA
*
65579 AAA-TAAAGA
1 AAAGAAAAGA
65588 AAAGAAAAGA
1 AAAGAAAAGA
65598 AAA
1 AAA
65601 AAGGTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 8 0.28
10 9 0.31
11 10 0.34
12 2 0.07
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:65609 original size:19 final size:20
Alignment explanation
Indices: 65533--65615 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
65523 TGAATAAAAT
*
65533 AAAGAAAATAAA-AATAAATA
1 AAAGAAAATAAAGAA-AAAGA
* *
65553 AAATAAAGCA-AAAGAAATAGA
1 AAAGAAA--ATAAAGAAAAAGA
65574 AAAGAAAATAAAG-AAAAGA
1 AAAGAAAATAAAGAAAAAGA
*
65593 AAAGAAAA-AAGGTAAAAAGA
1 AAAGAAAATAAAG-AAAAAGA
65613 AAA
1 AAA
65616 AAATACATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.06
19 14 0.27
20 19 0.37
21 12 0.24
22 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAGAAAATAAAGAAAAAGA
Found at i:65615 original size:5 final size:5
Alignment explanation
Indices: 65557--65600 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
65547 TAAATAAAAT
*
65557 AAAGCA AAAGA AATAGA AAAGA AAA-T AAAGA AAAGA AAAGA AAA
1 AAAG-A AAAGA AA-AGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
65601 AAGGTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
4 3 0.09
5 22 0.65
6 9 0.26
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:65805 original size:35 final size:33
Alignment explanation
Indices: 65751--65817 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 33
65741 AGGGGAACAA
*
65751 AAAATATATAGAATATATAATAATAATAATAAT
1 AAAATATATAGAATATATAATAAAAATAATAAT
*
65784 AAAATATATATAATAACTATAATAAAAATAATAA
1 AAAATATATAGAAT-A-TATAATAAAAATAATAA
65818 AGAATTACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 13 0.43
34 1 0.03
35 16 0.53
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (33 bp):
AAAATATATAGAATATATAATAAAAATAATAAT
Found at i:65818 original size:9 final size:9
Alignment explanation
Indices: 65769--65840 Score: 56
Period size: 9 Copynumber: 7.2 Consensus size: 9
65759 TAGAATATAT
*
65769 AATAATAAT
1 AATAATAAA
65778 AATAATAAA
1 AATAATAAA
65787 ATATATATAATA
1 A-ATA-ATAA-A
65799 ACTATAATAAA
1 A--ATAATAAA
65810 AATAATAAA
1 AATAATAAA
65819 GAATTACA-AAA
1 -AA-TA-ATAAA
65830 AATAATAAA
1 AATAATAAA
65839 AA
1 AA
65841 AACAAAAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
8 1 0.02
9 24 0.44
10 7 0.13
11 11 0.20
12 7 0.13
13 4 0.07
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:65836 original size:3 final size:3
Alignment explanation
Indices: 65762--65817 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
65752 AAATATATAG
65762 AAT ATAT AAT AAT AAT AAT AAT AA- AAT -AT ATAT AAT AACT -AT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA-T AAT AAT
*
65807 AAA AAT AAT AA
1 AAT AAT AAT AA
65818 AGAATTACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
2 5 0.11
3 33 0.73
4 7 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:65849 original size:20 final size:20
Alignment explanation
Indices: 65807--65849 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
65797 TAACTATAAT
* ** *
65807 AAAAATAATAAAGAATTACA
1 AAAAATAATAAAAAAACAAA
65827 AAAAATAATAAAAAAACAAA
1 AAAAATAATAAAAAAACAAA
65847 AAA
1 AAA
65850 CGTACCCCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (20 bp):
AAAAATAATAAAAAAACAAA
Found at i:66074 original size:43 final size:44
Alignment explanation
Indices: 65991--66086 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
65981 GTAATAAAGT
* *
65991 AAGTAAAGAAAAAAACAATAAAAAATATATACATATAAAAT-ATA
1 AAGTAAA-AAAAAAACAAAAAAAAATATATACATAAAAAATAATA
* *
66035 AGGTAAAAACAAAACAAAACAAACAATA-ATA-ATAAAAAATAATA
1 AAGTAAAAAAAAAACAAAA-AAA-AATATATACATAAAAAATAATA
66079 AAGTAAAA
1 AAGTAAAA
66087 TATATACATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
43 18 0.41
44 22 0.50
45 4 0.09
ACGTcount: A:0.72, C:0.06, G:0.05, T:0.17
Consensus pattern (44 bp):
AAGTAAAAAAAAAACAAAAAAAAATATATACATAAAAAATAATA
Found at i:66212 original size:18 final size:19
Alignment explanation
Indices: 66167--66214 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
66157 AAAATAAAAT
66167 AATGAAAATAATATATATAA
1 AATG-AAATAATATATATAA
*
66187 ATAT-AAATACTA-ATATAA
1 A-ATGAAATAATATATATAA
66205 AATGAAATAA
1 AATGAAATAA
66215 ATAAATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 7 0.29
20 1 0.04
21 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
AATGAAATAATATATATAA
Found at i:66283 original size:9 final size:9
Alignment explanation
Indices: 66273--66334 Score: 63
Period size: 9 Copynumber: 6.4 Consensus size: 9
66263 ATATTTAAAT
66273 AAATAA-AA
1 AAATAATAA
66281 TAAATAATAA
1 -AAATAATAA
66291 AAATAATAA
1 AAATAATAA
66300 AAATAATCATA
1 AAATAAT-A-A
66311 ATAATAATAA
1 A-AATAATAA
*
66321 ACATATATAA
1 AAATA-ATAA
66331 AAAT
1 AAAT
66335 TAAAATATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
9 25 0.54
10 12 0.26
11 3 0.07
12 6 0.13
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
AAATAATAA
Found at i:66298 original size:3 final size:3
Alignment explanation
Indices: 66274--66320 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
66264 TATTTAAATA
* * *
66274 AAT AA- AAT AAAT AAT AAA AAT AAT AAA AAT AAT CAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
66319 AA
1 AA
66321 ACATATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:66298 original size:21 final size:21
Alignment explanation
Indices: 66269--66330 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
66259 TATAATATTT
66269 AAATAAATAAAATAAATAATAA
1 AAAT-AATAAAATAAATAATAA
*
66291 AAATAATAAAA-ATAATCATAA
1 AAATAATAAAATA-AATAATAA
* *
66312 TAATAATAAACATATATAA
1 AAATAATAAA-ATAAATAA
66331 AAATTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.03
21 23 0.70
22 8 0.24
23 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAATAAAATAAATAATAA
Found at i:67538 original size:2 final size:2
Alignment explanation
Indices: 67531--67588 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
67521 TGAAGTGTAA
67531 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
67573 AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT A
67589 CTAACACAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68567 original size:17 final size:16
Alignment explanation
Indices: 68533--68572 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
68523 TCAGACAAGA
* *
68533 AAAAAATGTTATATAT
1 AAAAAATGTTAAAAAT
68549 AAAAAATGTTAAAAAAT
1 AAAAAATGTT-AAAAAT
68566 AAAAAAT
1 AAAAAAT
68573 AAAAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAAATGTTAAAAAT
Found at i:69713 original size:88 final size:88
Alignment explanation
Indices: 69564--69748 Score: 361
Period size: 88 Copynumber: 2.1 Consensus size: 88
69554 AGATGGGTGG
69564 TGAACATGGTTGAGATAATGGTCGGGTAGTGCTGAGATAATGGTGGGTGGTTGGATCTATTTTTT
1 TGAACATGGTTGAGATAATGGTCGGGTAGTGCTGAGATAATGGTGGGTGGTTGGATCTATTTTTT
69629 TGAGTTTCCTAGAATGGTGAGGT
66 TGAGTTTCCTAGAATGGTGAGGT
69652 TGAACATGGTTGAGATAATGGTCGGGTAGTGCTGAGATAATGGTGGGTGGTTGGATCTATTTTTT
1 TGAACATGGTTGAGATAATGGTCGGGTAGTGCTGAGATAATGGTGGGTGGTTGGATCTATTTTTT
69717 TGAGTTTCCTAGAATGGTGAGGT
66 TGAGTTTCCTAGAATGGTGAGGT
*
69740 TAAACATGG
1 TGAACATGG
69749 GGATTGTAAA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 96 1.00
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.36
Consensus pattern (88 bp):
TGAACATGGTTGAGATAATGGTCGGGTAGTGCTGAGATAATGGTGGGTGGTTGGATCTATTTTTT
TGAGTTTCCTAGAATGGTGAGGT
Found at i:69780 original size:88 final size:88
Alignment explanation
Indices: 69596--69774 Score: 218
Period size: 88 Copynumber: 2.0 Consensus size: 88
69586 CGGGTAGTGC
*
69596 TGAGATAATGGTGGGTGGTTGGATCTATTTTTTTGAGTTTCCTAGAATGGTGAGGTTGAACATGG
1 TGAGATAATGGTGGGTGGTTGGATCTATTTTTTTGAGTTTCCTAGAATGGTGAGGTTAAACATGG
* ** *** * **
69661 TTGAGATAATGGTCGGGTAGTGC
66 TTGAGAAAATAATCAAATAATAA
69684 TGAGATAATGGTGGGTGGTTGGATCTATTTTTTTGAGTTTCCTAGAATGGTGAGGTTAAACATGG
1 TGAGATAATGGTGGGTGGTTGGATCTATTTTTTTGAGTTTCCTAGAATGGTGAGGTTAAACAT--
69749 GGATTGTA-AAAATAAT-AAATAATAA
64 GG-TTG-AGAAAATAATCAAATAATAA
69774 T
1 T
69775 AATAATAAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 62 0.81
90 6 0.08
91 8 0.10
92 1 0.01
ACGTcount: A:0.27, C:0.06, G:0.31, T:0.36
Consensus pattern (88 bp):
TGAGATAATGGTGGGTGGTTGGATCTATTTTTTTGAGTTTCCTAGAATGGTGAGGTTAAACATGG
TTGAGAAAATAATCAAATAATAA
Found at i:71077 original size:55 final size:55
Alignment explanation
Indices: 70997--71140 Score: 261
Period size: 55 Copynumber: 2.6 Consensus size: 55
70987 TTGCTGCTTG
* *
70997 TGGGCACGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTGGTTA
1 TGGGTACGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTAAGTTGGTTA
71052 TGGGTACGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTAAGTTGGTTA
1 TGGGTACGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTAAGTTGGTTA
*
71107 TGGGTACGATATCCTTCATTGTGAAGTTGAAATC
1 TGGGTACGATATCCTTCATCGTGAAGTTGAAATC
71141 GTGGATGGTT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 86 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (55 bp):
TGGGTACGATATCCTTCATCGTGAAGTTGAAATCCAATCTTGAGTAAGTTGGTTA
Found at i:71203 original size:121 final size:122
Alignment explanation
Indices: 71059--71627 Score: 629
Period size: 121 Copynumber: 4.7 Consensus size: 122
71049 TTATGGGTAC
* * * * *
71059 GATATCCTTCATCGTGAAGTTGAAATCCAA-TCTTGAGTAAGTTGGTTATGGGTACGATATCCTT
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTGAGTATGTTGCTTGTGGGCACGATATCCTT
* *
71123 CATTGTGAAGTTGAAATCGTGGATGGTTCCTTCATTGTGAAGTTGAGCTTTGAATTA
66 CATTGTGAAGTTGAAATCGTAGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATTA
* *
71180 GATATCCTTCGTCGTGAAGTTGAAATCCAAGGATTGCA-T-TGTTGCTTGTGGGCACGATATCCT
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTG-AGTATGTTGCTTGTGGGCACGATATCCT
* * * ** * *
71243 TAATCGTGAAGTTGAAATCATTTATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATTG
65 TCATTGTGAAGTTGAAATCGTAGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATTA
* * *
71301 GATATCCTTCATCGTGAAGTTGAAATCCAAGGGTT--GTATTGCTACTTGTGGGCACGATATCCT
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTGAGTA-TGTTGCTTGTGGGCACGATATCCT
*
71364 TCATTGTGAAGTTAAAATCGTAGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATTA
65 TCATTGTGAAGTTGAAATCGTAGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATTA
* * * * * * *
71422 GATATCCTTCATCTTGAAGTTGAAATCCAAGGGTTGCA-T-TGCTT-TTTGTGGGAATGATGTTC
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTG-AGTATG-TTGCTTGTGGGCACGATATCC
* * * * **
71484 TTCGTCGTGAAGTTGAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATGG
64 TTCATTGTGAAGTTGAAATCGTAGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATTA
* * * * *
71543 GATATCTTTCGTCGTGAAGTTGAAATCCAA-GCTT-ATGTAAGTTGCATTGTTTCGAGTC-CAAT
1 GATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTGA-GTATGTTGC-TTG--T-G-GGCACGAT
71605 ATCCTTCATTGTGAAGTTGAAAT
60 ATCCTTCATTGTGAAGTTGAAAT
71628 TGACTCTGAA
Statistics
Matches: 375, Mismatches: 55, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
118 1 0.00
119 1 0.00
120 6 0.02
121 333 0.89
122 8 0.02
123 2 0.01
124 1 0.00
125 22 0.06
126 1 0.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (122 bp):
GATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTGAGTATGTTGCTTGTGGGCACGATATCCTT
CATTGTGAAGTTGAAATCGTAGATGGCTCCTTCATTGTGAAGTTGAGCTTTGAATTA
Found at i:71372 original size:242 final size:241
Alignment explanation
Indices: 70868--71573 Score: 785
Period size: 242 Copynumber: 2.9 Consensus size: 241
70858 ATGGATGTTG
* * ** * * * *
70868 CTTGTGGGCACGATATTCTTCGTCATAAAATTGAAATTGTGGATGGCTCCTTCGTTGTGAAGTTG
1 CTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTG
* * * * * * *
70933 AGCTTTTAATTGGATATTCTTCGTTGTGAAGTTGAAATCCAATCTAGATTTGTATTGCTGCTTGT
66 AGCTTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAA---GGA-TTGCATTGTTGCTTGT
*
70998 GGGCACGATATCCTTCGTCGTGAAGTTGAAATCCA-A----T-CTT-G-AGT-AAGTTG-G-TTA
127 GGGCACGATATCCTTCGTCGTGAAGTTGAAAT-CATATGGCTCCTTCGTTGTGAAGTTGAGCTT-
** * * * *
71052 TGGGTACGATATCCTTCATCGTGAAGTTGAAATCCAA-TCTTGAGTAAGTTG
190 TGAATAGGATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTGAGTAAGCTA
* * * *
71103 GTTATGGGTACGATATCCTTCATTGTGAAGTTGAAATCGTGGATGGTTCCTTCATTGTGAAGTTG
1 CTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTG
71168 AGCTTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGTTGCTTGTGGGC
66 AGCTTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGTTGCTTGTGGGC
**
71233 ACGATATCCTTAATCGTGAAGTTGAAATCATTTATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAA
131 ACGATATCCTTCGTCGTGAAGTTGAAATCA--TATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAA
* * *
71298 TTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTT--GTATTGCTA
194 TAGGATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTGAGTA-AGCTA
* *
71345 CTTGTGGGCACGATATCCTTCATTGTGAAGTTAAAATCGTAGATGGCTCCTTCATTGTGAAGTTG
1 CTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTG
* * * *
71410 AGCTTTGAATTAGATATCCTTCATCTTGAAGTTGAAATCCAAGGGTTGCATTGCTT-TTTGTGGG
66 AGCTTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAAGGATTGCATTG-TTGCTTGTGGG
* * * * * *
71474 AATGATGTTCTTCGTCGTGAAGTTGAAATCGTAGATGGCTCATTCGTTGTGAAGTTGAGCTTTGA
130 CACGATATCCTTCGTCGTGAAGTTGAAATC--ATATGGCTCCTTCGTTGTGAAGTTGAGCTTTGA
* * *
71539 ATGGGATATCTTTCGTCGTGAAGTTGAAATCCAAG
193 ATAGGATATCCTTCATCGTGAAGTTGAAATCCAAG
71574 CTTATGTAAG
Statistics
Matches: 401, Mismatches: 52, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
230 2 0.00
231 44 0.11
232 2 0.00
233 1 0.00
235 91 0.23
237 1 0.00
238 3 0.01
239 1 0.00
240 2 0.00
241 9 0.02
242 238 0.59
243 6 0.01
244 1 0.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (241 bp):
CTTGTGGGCACGATATCCTTCATTGTGAAGTTGAAATCGTGGATGGCTCCTTCATTGTGAAGTTG
AGCTTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAAGGATTGCATTGTTGCTTGTGGGC
ACGATATCCTTCGTCGTGAAGTTGAAATCATATGGCTCCTTCGTTGTGAAGTTGAGCTTTGAATA
GGATATCCTTCATCGTGAAGTTGAAATCCAAGGCTTGAGTAAGCTA
Found at i:71672 original size:64 final size:64
Alignment explanation
Indices: 71596--71954 Score: 569
Period size: 64 Copynumber: 5.6 Consensus size: 64
71586 GCATTGTTTC
71596 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
71660 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTATT
1 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*
71724 GAGTCCAATATCCTTCGA-TGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTGTTTGTT
1 GAGTCCAATATCCTTC-ATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * *
71788 GAGTCCAATATCCTTCGA-TGCGAAGTTGAAATTAACTCTGAATGAAACTAGAAAGTCGTTTGTT
1 GAGTCCAATATCCTTC-ATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * *
71852 GAGTCAAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAATGTTGTTTGTT
1 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
71916 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCT
1 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCT
71955 AAAAGCTGCA
Statistics
Matches: 273, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
64 273 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:75051 original size:14 final size:14
Alignment explanation
Indices: 75032--75066 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
75022 ATTTATTTGA
75032 AAATAATCAAAGGT
1 AAATAATCAAAGGT
75046 AAATAATCAAAGGT
1 AAATAATCAAAGGT
75060 AAATAAT
1 AAATAAT
75067 TGGAATCGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (14 bp):
AAATAATCAAAGGT
Found at i:75600 original size:16 final size:17
Alignment explanation
Indices: 75579--75620 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
75569 TCAAAGAAGG
* *
75579 AAAAAATGTT-ATATAT
1 AAAAAATGTTAAAAAAT
75595 AAAAAATGTTAAAAAAT
1 AAAAAATGTTAAAAAAT
75612 AAAAAATGT
1 AAAAAATGT
75621 CAAATGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (17 bp):
AAAAAATGTTAAAAAAT
Found at i:76700 original size:14 final size:17
Alignment explanation
Indices: 76680--76716 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
76670 AACATAGGGC
76680 ATAATAA-AAA-AATAT
1 ATAATAATAAATAATAT
76695 -TAATAATAAATAATAT
1 ATAATAATAAATAATAT
76711 ATAATA
1 ATAATA
76717 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.32
15 3 0.16
16 5 0.26
17 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAATAAATAATAT
Done.