Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004691.1 Hibiscus syriacus cultivar Beakdansim tig00010526_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: 73090
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6243 original size:16 final size:18
Alignment explanation
Indices: 6222--6266 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
6212 AACATTCCCA
6222 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
6238 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
6258 GTAATCTTA
1 GTAATCTTA
6267 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:6260 original size:20 final size:20
Alignment explanation
Indices: 6235--6272 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6225 ATCTTATTCC
6235 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
6255 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
6273 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:12628 original size:62 final size:62
Alignment explanation
Indices: 12555--12682 Score: 166
Period size: 62 Copynumber: 2.1 Consensus size: 62
12545 AATGTTTAGT
* * * * *
12555 TTTTGTTTCATTTTAGTACCTCATTGTTAACAATTTAACATATTCAGTAAGTAAACTATCAA
1 TTTTGTTTCATTTTAGTACCTCAATGTTAAAAACTTAACACATTCAGTAACTAAACTATCAA
* * * * *
12617 TTTTGTTTCATTTTAGTATCTTAATGTTAAAAACTTAACACATTTAGTACCTAAACTTTCAA
1 TTTTGTTTCATTTTAGTACCTCAATGTTAAAAACTTAACACATTCAGTAACTAAACTATCAA
12679 TTTT
1 TTTT
12683 TTTAACTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (62 bp):
TTTTGTTTCATTTTAGTACCTCAATGTTAAAAACTTAACACATTCAGTAACTAAACTATCAA
Found at i:17536 original size:84 final size:84
Alignment explanation
Indices: 17363--17529 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 84
17353 TTTTAACACT
* *
17363 TAAACTTTCAATTTTTTAAAACCAGACCTAACATTTATTTTTTGTTTCATTTTAATACTATCAGT
1 TAAACTTTCAATTTTTTAAAACCAGACCTAACATTTAGTTTTTGTTTCATTTAAATACTATCAGT
17428 TGTGGTCTATTTTAGTACA
66 TGTGGTCTATTTTAGTACA
* * * * * * *
17447 TAAACTTT-TATTTTTTCAAAACCATACCTAACGTTTAGTTTTTGTTTCGTTTAAATATTGTGAG
1 TAAACTTTCAATTTTTT-AAAACCAGACCTAACATTTAGTTTTTGTTTCATTTAAATACTATCAG
* *
17511 TTTTGGTCTGTTTTAGTAC
65 TTGTGGTCTATTTTAGTAC
17530 CAAAACTATC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 7 0.10
84 64 0.90
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (84 bp):
TAAACTTTCAATTTTTTAAAACCAGACCTAACATTTAGTTTTTGTTTCATTTAAATACTATCAGT
TGTGGTCTATTTTAGTACA
Found at i:18204 original size:2 final size:2
Alignment explanation
Indices: 18197--18240 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
18187 ATTTTGATCA
18197 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
18239 AT
1 AT
18241 TGAAGTAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24857 original size:29 final size:29
Alignment explanation
Indices: 24820--24878 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
24810 AAAGGAATTC
24820 CAATATCAAACAGAAGTGACTAGTGGAAT
1 CAATATCAAACAGAAGTGACTAGTGGAAT
24849 CAATATCAAACAGAAGTGACTAGTGGAAT
1 CAATATCAAACAGAAGTGACTAGTGGAAT
24878 C
1 C
24879 TTAAAGAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.20
Consensus pattern (29 bp):
CAATATCAAACAGAAGTGACTAGTGGAAT
Found at i:30933 original size:6 final size:6
Alignment explanation
Indices: 30922--30952 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
30912 ACTTCAGTTC
30922 GGTTTT GGTTTT GGTTTT GGTTTT GGATTTT
1 GGTTTT GGTTTT GGTTTT GGTTTT GG-TTTT
30953 ACCCGAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.03, C:0.00, G:0.32, T:0.65
Consensus pattern (6 bp):
GGTTTT
Found at i:41577 original size:3 final size:3
Alignment explanation
Indices: 41571--41595 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41561 AAAAAAAAAT
41571 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
41596 ATTAACTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41731 original size:16 final size:16
Alignment explanation
Indices: 41712--41744 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41702 AAAACAAAAT
41712 AAACAA-AAGTAATAAA
1 AAACAATAA-TAATAAA
41728 AAACAATAATAATAAA
1 AAACAATAATAATAAA
41744 A
1 A
41745 TAAATTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAACAATAATAATAAA
Found at i:43068 original size:3 final size:3
Alignment explanation
Indices: 43060--43121 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
43050 TTAAATAAGA
* * *
43060 AAT AAT AAT AAT AAAT AA- AAT AAT TAC ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43105 AAAT AAT AAT AAT AAT A
1 -AAT AAT AAT AAT AAT A
43122 TAGTATAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43080 original size:33 final size:33
Alignment explanation
Indices: 43043--43117 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
43033 AACATAAAAC
*
43043 AAAATGATTA-AATAAGAAATAATAATAATAAAT
1 AAAATAATTACAATAA-AAATAATAATAATAAAT
* *
43076 AAAATAATTACACTAATAATAATAATAATAAAT
1 AAAATAATTACAATAAAAATAATAATAATAAAT
43109 AATAATAAT
1 AA-AATAAT
43118 AATATAGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 27 0.73
34 10 0.27
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (33 bp):
AAAATAATTACAATAAAAATAATAATAATAAAT
Found at i:43129 original size:13 final size:12
Alignment explanation
Indices: 43064--43142 Score: 56
Period size: 13 Copynumber: 6.3 Consensus size: 12
43054 ATAAGAAATA
*
43064 ATAATAATAAAT
1 ATAATAATATAT
* *
43076 AAAATAAT-TAC
1 ATAATAATATAT
43087 ACTAATAATA-AT
1 A-TAATAATATAT
43099 AATAATAA-ATAAT
1 -ATAATAATAT-AT
43112 AATAATAATATAGT
1 -ATAATAATATA-T
43126 ATAATATATATAT
1 ATAATA-ATATAT
43139 ATAA
1 ATAA
43143 ATATTTTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
11 3 0.06
12 20 0.37
13 23 0.43
14 8 0.15
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:43129 original size:16 final size:17
Alignment explanation
Indices: 43060--43142 Score: 84
Period size: 16 Copynumber: 4.9 Consensus size: 17
43050 TTAAATAAGA
43060 AATAATAATAATA-AAT
1 AATAATAATAATATAAT
* *
43076 AA-AATAATTACACTAAT
1 AATAATAATAATA-TAAT
43093 AATAATAATAATA-AAT
1 AATAATAATAATATAAT
*
43109 AATAATAATAATATAGT
1 AATAATAATAATATAAT
43126 -ATAATATATATATATAA
1 AATAATA-ATA-ATATAA
43143 ATATTTTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
15 8 0.15
16 24 0.44
17 10 0.18
18 13 0.24
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (17 bp):
AATAATAATAATATAAT
Found at i:43131 original size:19 final size:19
Alignment explanation
Indices: 43060--43121 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
43050 TTAAATAAGA
43060 AATAAT-AATAATAAATAA-
1 AATAATAAATAAT-AATAAT
*
43078 AATAATTACACTAATAATAAT
1 AATAA-TA-AATAATAATAAT
43099 AATAATAAATAATAATAAT
1 AATAATAAATAATAATAAT
43118 AATA
1 AATA
43122 TAGTATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.13
19 16 0.42
20 7 0.18
21 10 0.26
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAATAAATAATAATAAT
Found at i:43266 original size:24 final size:24
Alignment explanation
Indices: 43212--43271 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 24
43202 TATATTAAAA
*
43212 AAATGCTTTAAAAAAAATATATAT
1 AAATGTTTTAAAAAAAATATATAT
* **
43236 ACA--TTTTAAAAACTATATATAT
1 AAATGTTTTAAAAAAAATATATAT
*
43258 AAATGTTTTCAAAA
1 AAATGTTTTAAAAA
43272 TGTTTTCAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 18 0.64
24 10 0.36
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (24 bp):
AAATGTTTTAAAAAAAATATATAT
Found at i:43274 original size:11 final size:11
Alignment explanation
Indices: 43258--43282 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43248 CTATATATAT
43258 AAATGTTTTCA
1 AAATGTTTTCA
43269 AAATGTTTTCA
1 AAATGTTTTCA
43280 AAA
1 AAA
43283 CTATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:43316 original size:38 final size:35
Alignment explanation
Indices: 43239--43328 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 35
43229 TATATATACA
* * *
43239 TTTTAAAAACTATATATATAAATGTTTTCAAAATG
1 TTTTCAAAACTATATATATAAATATTTTCAAAAGG
43274 TTTTCAAAACTATATATCATATAA-ATTTTCAAAAAGG
1 TTTTCAAAACTATATAT-ATA-AATATTTTC-AAAAGG
43311 TTTTTCAAAACTATATAT
1 -TTTTCAAAACTATATAT
43329 TATACGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
35 16 0.33
36 8 0.17
37 7 0.15
38 17 0.35
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (35 bp):
TTTTCAAAACTATATATATAAATATTTTCAAAAGG
Found at i:43344 original size:36 final size:35
Alignment explanation
Indices: 43239--43368 Score: 115
Period size: 36 Copynumber: 3.6 Consensus size: 35
43229 TATATATACA
* * *
43239 TTTTAAAAACTATATATATA-AATGTTTTCAAAATG
1 TTTTCAAAACTATATATATATAA-GTTTTAAAAAGG
*
43274 TTTTCAAAACTATATATCATATAAATTTTCAAAAAGG
1 TTTTCAAAACTATATAT-ATATAAGTTTT-AAAAAGG
* *
43311 TTTTTCAAAACTATATAT-TATACGTTTTAAAAAATGC
1 -TTTTCAAAACTATATATATATAAGTTTT-AAAAA-GG
43348 TTTT-AAATA-TATATATATATA
1 TTTTCAAA-ACTATATATATATA
43369 TATATATATA
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
35 26 0.32
36 29 0.36
37 8 0.10
38 17 0.21
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (35 bp):
TTTTCAAAACTATATATATATAAGTTTTAAAAAGG
Found at i:43359 original size:2 final size:2
Alignment explanation
Indices: 43354--43385 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
43344 ATGCTTTTAA
43354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43386 CATTTCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43381 original size:53 final size:52
Alignment explanation
Indices: 43322--43425 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
43312 TTTTCAAAAC
* *
43322 TATATATTATACGTTTTAAAAAATGCTTTT-AAATA-TATATATATATATATATA
1 TATATATTATAC-ATTTAAAAAATG-TTTTCAAAGACTATATAT-TATATATATA
**
43375 TATATATTATACATTTCCAAAATGTTTTCAAAGACTATATATTATATATAT
1 TATATATTATACATTTAAAAAATGTTTTCAAAGACTATATATTATATATAT
43426 TTTTAAAATG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 22 0.49
53 19 0.42
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (52 bp):
TATATATTATACATTTAAAAAATGTTTTCAAAGACTATATATTATATATATA
Found at i:44385 original size:165 final size:165
Alignment explanation
Indices: 44153--44971 Score: 1417
Period size: 165 Copynumber: 5.0 Consensus size: 165
44143 AACGATATGA
* *
44153 CCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCCTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
* **
44218 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG-GCGACAGATAA
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAG-CAGATAA
44282 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
130 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
* * *
44318 CCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
44383 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
44448 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
131 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
*
44483 CCTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
* *
44548 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCA-CAGATAA
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT-GTTAGCAGATAA
* * * * *
44612 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
130 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
*
44648 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
44713 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
44778 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
131 CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
*
44813 CCTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
**
44878 GCTGCAAATGATGTGCCTTCAAAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAA
66 GCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAA
44943 CCCTTCTTGACTTAAGTTATACTGCAAAT
130 CCCTTCTTGACTTAAGTTATACTGCAAAT
44972 AGTTTGTTAA
Statistics
Matches: 620, Mismatches: 30, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
164 3 0.00
165 541 0.87
166 76 0.12
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
CCTTCTTGACTTAAGTTATACTGCAAATGATGTGC
Found at i:48357 original size:18 final size:19
Alignment explanation
Indices: 48316--48360 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
48306 AGTTAATATG
48316 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
48335 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
48353 AATGCAAA
1 AATGCAAA
48361 ATGTCTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:50063 original size:3 final size:3
Alignment explanation
Indices: 50057--50081 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
50047 AAAAAAAAAT
50057 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
50082 ATTAACTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:50217 original size:16 final size:16
Alignment explanation
Indices: 50198--50230 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50188 AAAACAAAAT
50198 AAACAA-AAGTAATAAA
1 AAACAATAA-TAATAAA
50214 AAACAATAATAATAAA
1 AAACAATAATAATAAA
50230 A
1 A
50231 TAAATTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (16 bp):
AAACAATAATAATAAA
Found at i:50223 original size:13 final size:13
Alignment explanation
Indices: 50179--50230 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
50169 AACAATATTA
50179 AATAAGTAAAAAAC
1 AATAA-TAAAAAAC
50193 AA-AATAAACAAA-
1 AATAATAAA-AAAC
*
50205 AGTAATAAAAAAC
1 AATAATAAAAAAC
50218 AATAATAATAAAA
1 AATAATAA-AAAA
50231 TAAATTTAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 8 0.25
13 18 0.56
14 6 0.19
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (13 bp):
AATAATAAAAAAC
Found at i:51556 original size:3 final size:3
Alignment explanation
Indices: 51548--51614 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
51538 TTAAATAAGA
* * *
51548 AAT AAT AAT AAT AAAT AA- AAT AAT TAC ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
51593 AAAT AAT AAT AAT AAT -AT AAT A
1 -AAT AAT AAT AAT AAT AAT AAT A
51615 GTATAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:51568 original size:33 final size:33
Alignment explanation
Indices: 51531--51605 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
51521 ACATAAAACA
*
51531 AAAATGATTA-AATAAGAAATAATAATAATAAAT
1 AAAATAATTACAATAA-AAATAATAATAATAAAT
* *
51564 AAAATAATTACACTAATAATAATAATAATAAAT
1 AAAATAATTACAATAAAAATAATAATAATAAAT
51597 AATAATAAT
1 AA-AATAAT
51606 AATATAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 27 0.73
34 10 0.27
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (33 bp):
AAAATAATTACAATAAAAATAATAATAATAAAT
Found at i:51614 original size:33 final size:33
Alignment explanation
Indices: 51548--51632 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
51538 TTAAATAAGA
*
51548 AATAATAATAATAAATAAAATAATTACACTAAT
1 AATAATAATAATAAATAAAATAATAACACTAAT
*
51581 AATAATAATAATAAATAATAATAATAATA-TAAT
1 AATAATAATAATAAATAA-AATAATAACACTAAT
51614 AGTATAAT-ATATATAAATA
1 A--ATAATAATA-ATAAATA
51633 TTTTTTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 23 0.50
34 11 0.24
35 12 0.26
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (33 bp):
AATAATAATAATAAATAAAATAATAACACTAAT
Found at i:51620 original size:13 final size:14
Alignment explanation
Indices: 51549--51629 Score: 76
Period size: 13 Copynumber: 5.5 Consensus size: 14
51539 TAAATAAGAA
51549 ATAATAATAATAAAT
1 ATAATAATAAT-AAT
*
51564 AAAATAATTACACTAAT
1 ATAATAA-TA-A-TAAT
51581 AATAATAATAATAA-
1 -ATAATAATAATAAT
51595 ATAATAATAATAAT
1 ATAATAATAATAAT
*
51609 ATAATAGT-ATAAT
1 ATAATAATAATAAT
51622 ATATATAA
1 ATA-ATAA
51630 ATATTTTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
13 21 0.38
14 10 0.18
15 9 0.16
16 3 0.05
17 6 0.11
18 7 0.12
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:51767 original size:11 final size:11
Alignment explanation
Indices: 51751--51775 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
51741 TATAATATAT
51751 AAATGTTTTCA
1 AAATGTTTTCA
51762 AAATGTTTTCA
1 AAATGTTTTCA
51773 AAA
1 AAA
51776 CTATATATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:51789 original size:38 final size:37
Alignment explanation
Indices: 51728--51864 Score: 120
Period size: 38 Copynumber: 3.6 Consensus size: 37
51718 TATATATACA
* *
51728 TTTTTAAAAACTATATAATATATAAATGTTTTC-AAAATG
1 TTTTTCAAAACTATAT-ATATATAAA--TTTTCAAAAAGG
51767 -TTTTCAAAACTATATATCATATAAATTTTCAAAAAAGG
1 TTTTTCAAAACTATATAT-ATATAAATTTTC-AAAAAGG
** * *
51805 TTTTTCAAAACTATATATTATATACGTTTTAAAAAATG
1 TTTTTCAAAACTATATA-TATATAAATTTTCAAAAAGG
*
51843 CTTTT-AAATA-TATATATATATA
1 TTTTTCAAA-ACTATATATATATA
51865 TATATATATA
Statistics
Matches: 85, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
36 11 0.13
37 11 0.13
38 37 0.44
39 25 0.29
40 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTTCAAAACTATATATATATAAATTTTCAAAAAGG
Found at i:51855 original size:2 final size:2
Alignment explanation
Indices: 51850--51885 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
51840 ATGCTTTTAA
51850 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51886 CATTTCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51879 original size:57 final size:56
Alignment explanation
Indices: 51816--51925 Score: 129
Period size: 56 Copynumber: 2.0 Consensus size: 56
51806 TTTTCAAAAC
* *
51816 TATATAT-TA-TATACGTTTTAAAAAATGCTTTT-AAATA-TATATATATATATATATA
1 TATATATATATTATAC-ATTTAAAAAATG-TTTTCAAAGACTATATAT-TATATATATA
**
51871 TATATATATATTATACATTTCCAAAATGTTTTCAAAGACTATATATTATATATAT
1 TATATATATATTATACATTTAAAAAATGTTTTCAAAGACTATATATTATATATAT
51926 TTTTAAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
55 11 0.23
56 24 0.51
57 12 0.26
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (56 bp):
TATATATATATTATACATTTAAAAAATGTTTTCAAAGACTATATATTATATATATA
Found at i:53586 original size:51 final size:51
Alignment explanation
Indices: 53531--53627 Score: 115
Period size: 51 Copynumber: 1.9 Consensus size: 51
53521 TTACTGTTTG
* * * * *
53531 AATTTCATTTAATTA-TATGTTTATATTTTATTTTAATAATTTAAAATTAAT
1 AATTTCACTAAATTATTAT-TTAATAATTTATTTTAATAACTTAAAATTAAT
* *
53582 AATTTTACTAAATTATTATTTAATAATTTATTTTAATTACTTAAAA
1 AATTTCACTAAATTATTATTTAATAATTTATTTTAATAACTTAAAA
53628 ATAAATAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 35 0.92
52 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (51 bp):
AATTTCACTAAATTATTATTTAATAATTTATTTTAATAACTTAAAATTAAT
Found at i:54287 original size:31 final size:31
Alignment explanation
Indices: 54186--54288 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
54176 ATTTGACACG
* * *
54186 AATCAAAAACAATACGAACCGAAAATAACCC
1 AATCCAAAACAATCCGAACCGAAAATAACTC
* * *
54217 AAACTAAAAGCAA-CTCGAACCGAAAATAACCTG
1 AATCCAAAA-CAATC-CGAACCGAAAATAA-CTC
**
54250 AA-CCAAAACAATCCGAACCGAATTTAACTC
1 AATCCAAAACAATCCGAACCGAAAATAACTC
54280 AATCCAAAA
1 AATCCAAAA
54289 TTAATCCGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
30 4 0.07
31 28 0.48
32 23 0.40
33 3 0.05
ACGTcount: A:0.53, C:0.26, G:0.08, T:0.13
Consensus pattern (31 bp):
AATCCAAAACAATCCGAACCGAAAATAACTC
Found at i:58210 original size:44 final size:44
Alignment explanation
Indices: 58161--58246 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
58151 AATATTTTTT
*
58161 ATATTAATATTTTT-AGTATAAAATAATATTTTAAATAACACTTA
1 ATATTAATATTTTTGA-TAAAAAATAATATTTTAAATAACACTTA
58205 ATATTAATATTTTTGATAAAAAATAATATTTTAAATAACACT
1 ATATTAATATTTTTGATAAAAAATAATATTTTAAATAACACT
58247 CTATCTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (44 bp):
ATATTAATATTTTTGATAAAAAATAATATTTTAAATAACACTTA
Found at i:58242 original size:19 final size:19
Alignment explanation
Indices: 58165--58242 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 19
58155 TTTTTTATAT
* * *
58165 TAATATTTTTAGTATAAAA
1 TAATATTTTAAATAAAAAA
58184 TAATATTTTAAATAACACTTAATA
1 TAATATTTTAAATAA-A---AA-A
**
58208 TTAATATTTTTGATAAAAAA
1 -TAATATTTTAAATAAAAAA
58228 TAATATTTTAAATAA
1 TAATATTTTAAATAA
58243 CACTCTATCT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
19 25 0.54
20 2 0.04
21 2 0.04
23 2 0.04
24 2 0.04
25 13 0.28
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
TAATATTTTAAATAAAAAA
Found at i:58468 original size:12 final size:12
Alignment explanation
Indices: 58451--58475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58441 CGTCTCCCTC
58451 GCTTAATGACTA
1 GCTTAATGACTA
58463 GCTTAATGACTA
1 GCTTAATGACTA
58475 G
1 G
58476 TACTAATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GCTTAATGACTA
Found at i:58533 original size:15 final size:16
Alignment explanation
Indices: 58497--58538 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
58487 GGTGTACAAA
58497 TCCGGGTACCCGGATT
1 TCCGGGTACCCGGATT
* *
58513 TTCGGGTATCC-GATT
1 TCCGGGTACCCGGATT
58528 TCCGGGTACCC
1 TCCGGGTACCC
58539 AAAACTTCCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.12, C:0.31, G:0.29, T:0.29
Consensus pattern (16 bp):
TCCGGGTACCCGGATT
Found at i:59004 original size:72 final size:76
Alignment explanation
Indices: 58866--59016 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 76
58856 ACCCGGAAAA
*
58866 ACTAGATTTTGTGACCCAGGCCCGACCCGGAAAATGTTGGGCCGGGTACCCGACCCGGCCGGGTA
1 ACTAGATTTTGTGACCC--GCCCGACCCGGAAAATGTTGGGCCGGGTACCCGACCCGGCAGGGTA
58931 A-TTTTTTTAGAG
64 ATTTTTTTTAGAG
58943 ACTAGATTTTGTGACCC-CCCGACCCGG-AAATGTTGGGCC-GGTACCCGACCCGGCAGGGTAAT
1 ACTAGATTTTGTGACCCGCCCGACCCGGAAAATGTTGGGCCGGGTACCCGACCCGGCAGGGTAAT
59005 TTTTTTTAGAG
66 TTTTTTTAGAG
59016 A
1 A
59017 ATTACCCGAT
Statistics
Matches: 72, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
72 21 0.29
73 24 0.33
74 10 0.14
77 17 0.24
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (76 bp):
ACTAGATTTTGTGACCCGCCCGACCCGGAAAATGTTGGGCCGGGTACCCGACCCGGCAGGGTAAT
TTTTTTTAGAG
Found at i:59696 original size:21 final size:21
Alignment explanation
Indices: 59659--59698 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59649 AATATGTTTA
*
59659 TTTATCTAATTTTAATTTATT
1 TTTATCTAATTTCAATTTATT
59680 TTTATCT-ATTTACAATTTA
1 TTTATCTAATTT-CAATTTA
59699 ATCTACTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATCTAATTTCAATTTATT
Found at i:59829 original size:14 final size:13
Alignment explanation
Indices: 59808--59854 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
59798 AAAGGAAAAG
59808 AAAAATAAAATAA
1 AAAAATAAAATAA
*
59821 AATAAATAAAGTAA
1 AA-AAATAAAATAA
59835 AAAAATAAAAATAA
1 AAAAAT-AAAATAA
59849 CAAAAA
1 -AAAAA
59855 AATGTAGCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.21
14 18 0.62
15 5 0.17
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:59853 original size:17 final size:16
Alignment explanation
Indices: 59778--59857 Score: 54
Period size: 17 Copynumber: 4.8 Consensus size: 16
59768 ATAGAACAAG
* *
59778 ATAAAATAATATAACAA
1 ATAAAAAAAAATAA-AA
* *
59795 ATAAAAGGAAAAGAAAA
1 ATAAAA-AAAAATAAAA
*
59812 ATAAAATAAAATAAATA
1 ATAAAAAAAAATAAA-A
*
59829 A-AGTAAAAAAATAAAA
1 ATA-AAAAAAAATAAAA
59845 ATAACAAAAAAAT
1 ATAA-AAAAAAAT
59858 GTAGCGTAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
16 10 0.20
17 35 0.70
18 5 0.10
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (16 bp):
ATAAAAAAAAATAAAA
Found at i:64350 original size:2 final size:2
Alignment explanation
Indices: 64343--64369 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64333 TGTTGCATTA
64343 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
64370 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64791 original size:15 final size:14
Alignment explanation
Indices: 64773--64807 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
64763 ATATACGTAT
*
64773 TACATGCATACATAA
1 TACATACATACAT-A
64788 TACATACATACATA
1 TACATACATACATA
64802 TACATA
1 TACATA
64808 TATATGTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (14 bp):
TACATACATACATA
Done.