Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005837.1 Hibiscus syriacus cultivar Beakdansim tig00013681_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: 94097
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1573 original size:9 final size:9
Alignment explanation
Indices: 1559--1584 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1549 TGGAACAAAT
1559 AGACATTGC
1 AGACATTGC
1568 AGACATTGC
1 AGACATTGC
1577 AGACATTG
1 AGACATTG
1585 AACCACCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (9 bp):
AGACATTGC
Found at i:7974 original size:17 final size:18
Alignment explanation
Indices: 7952--7986 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
7942 AATTCCCTCG
*
7952 ACATTTAG-CTCCTTTTT
1 ACATTTAGTCTCATTTTT
7969 ACATTTAGTCTCATTTTT
1 ACATTTAGTCTCATTTTT
7987 TAATTTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (18 bp):
ACATTTAGTCTCATTTTT
Found at i:13917 original size:15 final size:15
Alignment explanation
Indices: 13897--13930 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13887 GAAAATGTGG
* *
13897 AAACCATTTTCAAGA
1 AAACCAATTACAAGA
13912 AAACCAATTACAAGA
1 AAACCAATTACAAGA
13927 AAAC
1 AAAC
13931 AAACAAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.21, G:0.06, T:0.18
Consensus pattern (15 bp):
AAACCAATTACAAGA
Found at i:23461 original size:43 final size:43
Alignment explanation
Indices: 23413--23520 Score: 146
Period size: 43 Copynumber: 2.5 Consensus size: 43
23403 AATGTTGGAC
* * * * *
23413 TTCCAACTTATTTC-TCACACTATGTTGGTGGCTATTACTAGTT
1 TTCCAACTTATTTCTTAAAACTATGTTAG-AGCTATTACTAGCT
23456 TTCCAACTTATTTCTTAAAACTATGTTAGAGCTATTACTAGCT
1 TTCCAACTTATTTCTTAAAACTATGTTAGAGCTATTACTAGCT
*
23499 TTCCAACTTATTTCCTAAAACT
1 TTCCAACTTATTTCTTAAAACT
23521 CTCTCTCTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 47 0.81
44 11 0.19
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (43 bp):
TTCCAACTTATTTCTTAAAACTATGTTAGAGCTATTACTAGCT
Found at i:25617 original size:13 final size:13
Alignment explanation
Indices: 25588--25622 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
25578 ATAACTAATA
*
25588 ATATTAAAT-ATT
1 ATATTAAATAAAT
25600 ATATTAAATAAAT
1 ATATTAAATAAAT
25613 ATATTAAATA
1 ATATTAAATA
25623 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:29332 original size:30 final size:30
Alignment explanation
Indices: 29292--29362 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
29282 TAATTCTAAC
* * *
29292 TAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAATAATTATATAAATAATATATTAA
* *
29322 TAAAAAATAA-TATTTACATAATATATTAA
1 TAAAAAATAATTATATAAATAATATATTAA
29351 TATAAAAATAAT
1 TA-AAAAATAAT
29363 AACTATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAAAAATAATTATATAAATAATATATTAA
Found at i:38464 original size:31 final size:31
Alignment explanation
Indices: 38415--38478 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
38405 CCCTTTTCTT
* * * * *
38415 TTATTTTCCTTAGTCTTTTCTCTAAAATCTC
1 TTATTCTCCATAGCCTTTTCTCCAAAACCTC
38446 TTATTCTCCATAGCCTTTTCTCCAAAACCTC
1 TTATTCTCCATAGCCTTTTCTCCAAAACCTC
38477 TT
1 TT
38479 CTCTTACACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.48
Consensus pattern (31 bp):
TTATTCTCCATAGCCTTTTCTCCAAAACCTC
Found at i:52240 original size:46 final size:46
Alignment explanation
Indices: 52182--52549 Score: 515
Period size: 46 Copynumber: 8.0 Consensus size: 46
52172 TTAATCATTA
* * ** * * * * *
52182 ATTTCAGTTATGGCCTTTTTTCATACCTTAATACATTCTTTCATAC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
* *
52228 ATTTTAGTTATGGCATACTTTCATGCCTTAATGCATTCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
52274 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
52320 ATTTTAGTTATGG-ATTCCTTTCATGCCTTAATGCATCCGTTCATGC
1 ATTTTAGTTATGGCA-TCCTTTCATGCCTTAATGCATCCGTTCATGC
* * *
52366 ATTTTAGTTATGGCATTCTTTCATGCCTTAATACATTCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
* * * *
52412 ATTTTAGTAATGGAATCCTCTCATGCCTTAATGCA-CCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCC-GTTCATGC
* *
52458 ATTTTAGTTATGGAATCCTTTCATACCTTAATGCATCCGTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
*
52504 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
52550 CTTAATGATA
Statistics
Matches: 291, Mismatches: 27, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
45 2 0.01
46 286 0.98
47 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGC
Found at i:52270 original size:20 final size:20
Alignment explanation
Indices: 52247--52411 Score: 69
Period size: 20 Copynumber: 7.3 Consensus size: 20
52237 ATGGCATACT
52247 TTCATGCCTTAATGCATTCG
1 TTCATGCCTTAATGCATTCG
* * *
52267 TTCATGCATTTTAGTTATGGCATCCT
1 TTCATGC--CTTA---AT-GCATTCG
*
52293 TTCATGCCTTAATGCATCCG
1 TTCATGCCTTAATGCATTCG
* * *
52313 TTCATGCATTTTAGTTATGGATTCCT
1 TTCATGC--CTTA---ATGCATT-CG
*
52339 TTCATGCCTTAATGCATCCG
1 TTCATGCCTTAATGCATTCG
* *
52359 TTCATGCATTTTAGTTATGGCATTCT
1 TTCATGC--CTTA---AT-GCATTCG
*
52385 TTCATGCCTTAATACATTCG
1 TTCATGCCTTAATGCATTCG
52405 TTCATGC
1 TTCATGC
52412 ATTTTAGTAA
Statistics
Matches: 108, Mismatches: 19, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
20 40 0.37
21 9 0.08
22 9 0.08
24 9 0.08
25 9 0.08
26 32 0.30
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (20 bp):
TTCATGCCTTAATGCATTCG
Found at i:52500 original size:20 final size:20
Alignment explanation
Indices: 52472--52556 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
52462 TAGTTATGGA
52472 ATCCTTTCATACCTTAATGC
1 ATCCTTTCATACCTTAATGC
* **
52492 ATCCGTTCATGCATTTTAGTTATGGC
1 ATCCTTTCAT--ACCTTA---AT-GC
*
52518 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATACCTTAATGC
* *
52538 ATCCATTCATGCCTTAATG
1 ATCCTTTCATACCTTAATG
52557 ATAACATAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
20 29 0.57
21 2 0.04
22 4 0.08
24 3 0.06
25 2 0.04
26 11 0.22
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (20 bp):
ATCCTTTCATACCTTAATGC
Found at i:55838 original size:20 final size:20
Alignment explanation
Indices: 55813--55883 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 20
55803 ATTGTCTCAT
55813 TTCATTCCTTAATGCATCCG
1 TTCATTCCTTAATGCATCCG
* **
55833 TTCATTCATTTTAGTTATGTCATCTT
1 TTCATTC--CTTA---ATG-CATCCG
55859 TTCATTCCTTAATGCATCCG
1 TTCATTCCTTAATGCATCCG
55879 TTCAT
1 TTCAT
55884 GCATTTTAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 16 0.41
21 3 0.08
22 3 0.08
24 3 0.08
25 3 0.08
26 11 0.28
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (20 bp):
TTCATTCCTTAATGCATCCG
Found at i:55862 original size:46 final size:46
Alignment explanation
Indices: 55812--56194 Score: 550
Period size: 46 Copynumber: 8.3 Consensus size: 46
55802 TATTGTCTCA
* * * *
55812 TTTCATTCCTTAATGCATCCGTTCATTCATTTTAGTTATGTCATCT
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
* * *
55858 TTTCATTCCTTAATGCATCCGTTCATGCATTTTAGTTATGGTATTC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
* *
55904 TTTCATGCCTTAATGTATCCGTTCATGCATTTTAGTTATGGAATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
* * **
55950 TTTGATGCCTTAATGCATCCGTTCATGCATTTTAATTATGAAATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
* * *
55996 TTTTATGTCTTAATGCATTCGTTCATGCATTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
* ** **
56042 TCTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGAAATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
56088 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
* * *
56134 TTTCATGCCTTAATGCATCCATTAATTCATTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
56180 TTTCATGCCTTAATG
1 TTTCATGCCTTAATG
56195 ATAACATAGT
Statistics
Matches: 302, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 302 1.00
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.45
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCC
Found at i:56047 original size:26 final size:26
Alignment explanation
Indices: 56017--56187 Score: 117
Period size: 26 Copynumber: 7.3 Consensus size: 26
56007 AATGCATTCG
56017 TTCATGCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
* * *
56043 CTCATGC--CTTA---AT-GCATCAT
1 TTCATGCATTTTAGTTATGGCATCCT
**
56063 TTCATGCATTTTAGTTATGAAATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
* *
56089 TTCATGC--CTTA---AT-GCATCCG
1 TTCATGCATTTTAGTTATGGCATCCT
56109 TTCATGCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
* *
56135 TTCATGC--CTTA---AT-GCATCCA
1 TTCATGCATTTTAGTTATGGCATCCT
* *
56155 TTAATTCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
56181 TTCATGC
1 TTCATGC
56188 CTTAATGATA
Statistics
Matches: 105, Mismatches: 22, Indels: 36
0.64 0.13 0.22
Matches are distributed among these distances:
20 34 0.32
21 6 0.06
22 9 0.09
24 9 0.09
25 6 0.06
26 41 0.39
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (26 bp):
TTCATGCATTTTAGTTATGGCATCCT
Found at i:56112 original size:20 final size:20
Alignment explanation
Indices: 56036--56153 Score: 74
Period size: 20 Copynumber: 5.3 Consensus size: 20
56026 TTTAGTTATG
*
56036 GCATCCTCTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
56056 GCATCATTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
56081 GAAATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
* *
56102 GCATCCGTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
56127 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
56148 GCATCC
1 GCATCC
56154 ATTAATTCAT
Statistics
Matches: 75, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
20 29 0.39
21 5 0.07
22 6 0.08
24 6 0.08
25 5 0.07
26 24 0.32
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:60157 original size:74 final size:74
Alignment explanation
Indices: 60024--60229 Score: 197
Period size: 74 Copynumber: 2.8 Consensus size: 74
60014 ATGGTGTTAT
* * * *
60024 ATATTTTT-AT-TTT-TTAATGGAAGAAACAATT-TTTATTTTTATTTATAAACTATAATTTACA
1 ATATTTTTAATATTTGTTAAT-GAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTACA
60085 AAAAAATTAC
65 AAAAAATTAC
* ** *
60095 ATATTTTTAATATTTGTTAATTAAAAAATAATTCTTAATTTTTATTTAGGAATTATAGTTTACAA
1 ATATTTTTAATATTTGTTAATGAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTACAA
* *** *
60160 TATTTTTAT
66 AAAAATTAC
* * * * * *
60169 ATATTTTTACTTTTTGTTAGTGAAAAAATCATTCTTAA-ATTTATTTATTAATTATAATTTA
1 ATATTTTTAATATTTGTTAATGAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTA
60230 ATAATTATAT
Statistics
Matches: 109, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
71 8 0.07
72 2 0.02
73 31 0.28
74 68 0.62
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (74 bp):
ATATTTTTAATATTTGTTAATGAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTACAA
AAAAATTAC
Found at i:60435 original size:77 final size:76
Alignment explanation
Indices: 60295--60455 Score: 186
Period size: 76 Copynumber: 2.1 Consensus size: 76
60285 TATATAACTA
*
60295 TTAAATTATAATTAATAAATAGAATAAAAAATTATTTCTTTCATTAAGAAACATTACAAATATAT
1 TTAAATTATAATTAATAAATAAAATAAAAAATTATTTCTTTCATTAAGAAACATTACAAATATAT
60360 AAAAAAATATT
66 AAAAAAATATT
* * * **
60371 TTAAATTATAGTTAATAAATAAAAGTTAAGAATTATTT-TTTCCATT-AGCAAA-ATTTTAAA-A
1 TTAAATTATAATTAATAAATAAAA-TAAAAAATTATTTCTTT-CATTAAG-AAACATTACAAATA
* *
60432 TATATAAAAATGTT
63 TATAAAAAAATATT
*
60446 GTAAATTATA
1 TTAAATTATA
60456 TTCAAATATG
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
75 22 0.30
76 33 0.45
77 18 0.25
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (76 bp):
TTAAATTATAATTAATAAATAAAATAAAAAATTATTTCTTTCATTAAGAAACATTACAAATATAT
AAAAAAATATT
Found at i:62923 original size:95 final size:94
Alignment explanation
Indices: 62757--62930 Score: 224
Period size: 95 Copynumber: 1.8 Consensus size: 94
62747 ACCTAGAATG
* * * *
62757 TAAAAATTGTATCAATATTGAAAGGGAGTATCAGTACCATAGTTTAGTAGTATCGATACTGATAG
1 TAAAAATGGTATCAATATTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAATACTGATAG
*
62822 AAGGGTATCGATACCATGCAACACATAATA
66 -AGGGTACCGATACCATGCAACACATAATA
** * * *
62852 TAAAAATGGTATTTATATTGAAAGGGGGTATCGGTACCATAGTATAGAAGTATCAATACCATGGT
1 TAAAAATGGTATCAATATTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAATA-C-TGAT
62917 AG-GGGTACCGATAC
64 AGAGGGTACCGATAC
62931 TAGTGAGTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
95 61 0.91
96 1 0.01
97 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (94 bp):
TAAAAATGGTATCAATATTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAATACTGATAG
AGGGTACCGATACCATGCAACACATAATA
Found at i:63411 original size:45 final size:45
Alignment explanation
Indices: 63347--63636 Score: 415
Period size: 45 Copynumber: 6.4 Consensus size: 45
63337 AAAATAATAT
* ** *
63347 ATGCATATGGGTGCATTATTGGCATGAAAGGATACCATAACTGAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
* *
63392 ATGCATATTGGTGCATTATTGGCATGAAAGGATGTCATAATT-AGA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGA-A
* *
63437 ATGCATATGGGTGCATTATCGGCATGAAATGATGTCATAACTGAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
* * *
63482 ATGCATATGGGCGCATTAGT-GGCATGAAAAGATGCCATAATTGAA
1 ATGCATATGGGTGCATTA-TCGGCATGAAAGGATGTCATAATTGAA
63527 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
*
63572 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTTATAATTGAAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTG-AA
63618 ATGCATAAT-GGTGCATTAT
1 ATGCAT-ATGGGTGCATTAT
63637 AAGAATGAAT
Statistics
Matches: 223, Mismatches: 16, Indels: 11
0.89 0.06 0.04
Matches are distributed among these distances:
44 2 0.01
45 199 0.89
46 20 0.09
47 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (45 bp):
ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
Found at i:66072 original size:21 final size:22
Alignment explanation
Indices: 66047--66087 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
66037 TTTATAAATA
*
66047 ATTTTCAT-AAATATTATATTT
1 ATTTTCATAAAATATAATATTT
*
66068 ATTTTTATAAAATATAATAT
1 ATTTTCATAAAATATAATAT
66088 AATATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTCATAAAATATAATATTT
Found at i:69035 original size:27 final size:26
Alignment explanation
Indices: 68991--69049 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
68981 ATGAGTCTAT
* *
68991 TAAAAATAATTTTTTAAACTACAAAA
1 TAAAAATAAATTTATAAACTACAAAA
* *
69017 TAAAAATAAAATTTATAAATTTCAAAA
1 TAAAAAT-AAATTTATAAACTACAAAA
69044 -AAAAAT
1 TAAAAAT
69050 GATGGGTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAAAATAAATTTATAAACTACAAAA
Found at i:73521 original size:13 final size:14
Alignment explanation
Indices: 73499--73547 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
73489 TATGTAATGA
73499 AATT-TTTAATAAT
1 AATTATTTAATAAT
*
73512 TA-TATTTAAT-AT
1 AATTATTTAATAAT
73524 AATTATTTAATAACT
1 AATTATTTAATAA-T
*
73539 ATTTATTTA
1 AATTATTTA
73548 TTTCTATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 15 0.52
14 1 0.03
15 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATTTAATAAT
Found at i:73521 original size:25 final size:25
Alignment explanation
Indices: 73485--73536 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
73475 TCATATATTA
73485 AATTTATGTAATGA-AATT-TTTAAT
1 AATTTATGTAAT-ATAATTATTTAAT
*
73509 AATTATATTTAATATAATTATTTAAT
1 AATT-TATGTAATATAATTATTTAAT
73535 AA
1 AA
73537 CTATTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
25 11 0.46
26 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
AATTTATGTAATATAATTATTTAAT
Found at i:73729 original size:2 final size:2
Alignment explanation
Indices: 73722--73753 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
73712 AAACTCTTTA
73722 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
73754 TAATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74806 original size:27 final size:24
Alignment explanation
Indices: 74776--74864 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 24
74766 AAAAACGAAA
74776 AGAAAATAAACAATAAATAAAAAAT
1 AGAAAATAAA-AATAAATAAAAAAT
*
74801 AGAGAAAATAAAAATAAAGT-AAAGAT
1 --AGAAAATAAAAATAAA-TAAAAAAT
74827 A-AAAATAAAAATAAATAAAATAA-
1 AGAAAATAAAAATAAATAAAA-AAT
* *
74850 ATAAAATGAAAATAA
1 AGAAAATAAAAATAA
74865 TAATAATAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
22 1 0.02
23 18 0.33
24 14 0.25
26 11 0.20
27 11 0.20
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (24 bp):
AGAAAATAAAAATAAATAAAAAAT
Found at i:74816 original size:6 final size:6
Alignment explanation
Indices: 74778--74887 Score: 66
Period size: 6 Copynumber: 18.0 Consensus size: 6
74768 AAACGAAAAG
* * *
74778 AAAATA AACAATA AATAA-A AAATAGA GAAAATA AAAAT- AAAGTA AAGATA
1 AAAATA AA-AATA AA-AATA AAA-ATA -AAAATA AAAATA AAAATA AAAATA
* * *
74828 AAAATA AAAATA AATAA-A ATAAAT- AAAATG AAAATA ATAATA ATAATA
1 AAAATA AAAATA AA-AATA A-AAATA AAAATA AAAATA AAAATA AAAATA
* *
74876 ATAATA ATAATA
1 AAAATA AAAATA
74888 TATACACATA
Statistics
Matches: 87, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
5 9 0.10
6 61 0.70
7 14 0.16
8 3 0.03
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:74828 original size:17 final size:15
Alignment explanation
Indices: 74790--74864 Score: 71
Period size: 15 Copynumber: 4.8 Consensus size: 15
74780 AATAAACAAT
*
74790 AAATAAAAAATAGAGA
1 AAAT-AAAAATAAAGA
74806 AAATAAAAATAAAGTA
1 AAATAAAAATAAAG-A
*
74822 AAGATAAAAATAAAAA
1 AA-ATAAAAATAAAGA
*
74838 TAAAT-AAAATAAATA
1 -AAATAAAAATAAAGA
*
74853 AAATGAAAATAA
1 AAATAAAAATAA
74865 TAATAATAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
14 4 0.08
15 25 0.48
16 10 0.19
17 13 0.25
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAATAAAAATAAAGA
Found at i:74835 original size:23 final size:21
Alignment explanation
Indices: 74778--74885 Score: 74
Period size: 23 Copynumber: 4.6 Consensus size: 21
74768 AAACGAAAAG
74778 AAAATAAACAATAAATAAAAAATAGA
1 AAAATAAA-AATAAAT--AAAAT--A
74804 GAAAATAAAAATAAAGTAAAGATA
1 -AAAATAAAAATAAA-TAAA-ATA
74828 AAAATAAAAATAAATAAAATAAA
1 AAAATAAAAATAAATAAAAT--A
*
74851 TAAAATGAAAAT-AATAATAATA
1 -AAAATAAAAATAAATAA-AATA
* *
74873 ATAATAATAATAA
1 AAAATAAAAATAA
74886 TATATACACA
Statistics
Matches: 70, Mismatches: 4, Indels: 19
0.75 0.04 0.20
Matches are distributed among these distances:
21 10 0.14
22 6 0.09
23 20 0.29
24 14 0.20
25 3 0.04
26 8 0.11
27 9 0.13
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAATAAAAATAAATAAAATA
Found at i:74848 original size:9 final size:9
Alignment explanation
Indices: 74806--74903 Score: 56
Period size: 9 Copynumber: 9.8 Consensus size: 9
74796 AAAATAGAGA
74806 AAATAAAAAT
1 AAAT-AAAAT
74816 AAAGTAAAGAT
1 AAA-TAAA-AT
74827 AAAAATAAAAAT
1 --AAAT-AAAAT
74839 AAATAAAAT
1 AAATAAAAT
74848 AAATAAAAT
1 AAATAAAAT
74857 GAAAATAATAAT
1 --AAATAA-AAT
74869 -AATAATAAT
1 AAATAA-AAT
74878 -AATAATAAT
1 AAATAA-AAT
* *
74887 ATATACACAT
1 AAATA-AAAT
74897 AAATAAA
1 AAATAAA
74904 TATTAGAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
9 33 0.45
10 19 0.26
11 10 0.14
12 6 0.08
13 6 0.08
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:74878 original size:15 final size:14
Alignment explanation
Indices: 74828--74887 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 14
74818 AGTAAAGATA
*
74828 AAAATAAAAATAAAT
1 AAAATAATAAT-AAT
74843 AAAATAAATAA-AAT
1 AAAAT-AATAATAAT
74857 GAAAATAATAATAAT
1 -AAAATAATAATAAT
74872 AATAATAATAATAAT
1 AA-AATAATAATAAT
74887 A
1 A
74888 TATACACATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 10 0.25
15 26 0.65
16 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:75141 original size:3 final size:3
Alignment explanation
Indices: 75080--75156 Score: 65
Period size: 3 Copynumber: 26.3 Consensus size: 3
75070 ACAAAGAAGG
*
75080 TAA TAA -AA TAA GAA TAA -AA TAAA TAA -AA TAA -AA -AA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA
* *
75122 AAA GTAA TAA TAT TAA TAA TAA TAA TAA TAA TAA T
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
75157 GGTTATAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
2 10 0.16
3 43 0.70
4 8 0.13
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:77201 original size:43 final size:41
Alignment explanation
Indices: 77104--77225 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 41
77094 TGTAGAGTTA
* * *
77104 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTGG
1 GCACAATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGG
*
77145 GCACAATATCCTCCGTCGTGGAGTTGAAATCGTGGCTTTGTGG
1 GCACAATATCCTCCGTCGTGGAGTTGAAATCGTGG--ATGTGG
* * *
77188 GTATC-ATATCCTCCATCGTGGAGTTAAAATCGTGGATG
1 GCA-CAATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
77226 GCCCCTTCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 34 0.49
43 35 0.50
44 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (41 bp):
GCACAATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGG
Found at i:81565 original size:18 final size:18
Alignment explanation
Indices: 81542--81580 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
81532 ACCCTAAACG
81542 TTTTTCTCTTTTTATTTT
1 TTTTTCTCTTTTTATTTT
81560 TTTTTCTCTTTTTATTTT
1 TTTTTCTCTTTTTATTTT
81578 TTT
1 TTT
81581 GAATTTGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTCTCTTTTTATTTT
Found at i:91880 original size:17 final size:16
Alignment explanation
Indices: 91847--91896 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
91837 TAAACAATAA
*
91847 AAAAATAGAG-AAAAT
1 AAAAATAAAGTAAAAT
91862 AAAAATAAAGTAAAGAT
1 AAAAATAAAGTAAA-AT
*
91879 AAAAATGAA-TAAAAT
1 AAAAATAAAGTAAAAT
91894 AAA
1 AAA
91897 TAAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.45
16 7 0.23
17 10 0.32
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAAATAAAGTAAAAT
Found at i:91881 original size:41 final size:39
Alignment explanation
Indices: 91829--91910 Score: 94
Period size: 41 Copynumber: 2.1 Consensus size: 39
91819 TAAAAAACGA
*
91829 AAAGAAAATAAACAAT-AAAAAAATAGAGAAAATAAAAAT
1 AAAGAAAATAAA-AATGAAAAAAATAAAGAAAATAAAAAT
* * *
91868 AAAGTAAAGATAAAAATGAATAAAATAAATAAAATGAAAAT
1 AAAG-AAA-ATAAAAATGAAAAAAATAAAGAAAATAAAAAT
91909 AA
1 AA
91911 TAATAATAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 4 0.11
40 6 0.17
41 26 0.72
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (39 bp):
AAAGAAAATAAAAATGAAAAAAATAAAGAAAATAAAAAT
Found at i:91901 original size:18 final size:19
Alignment explanation
Indices: 91880--91930 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
91870 AGTAAAGATA
91880 AAAATGAATAA-AATAAAT
1 AAAATGAATAAGAATAAAT
*
91898 AAAATGAA-AATAAT-AAT
1 AAAATGAATAAGAATAAAT
91915 AATAA-GAATAAGAATA
1 AA-AATGAATAAGAATA
91931 TATACACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAATGAATAAGAATAAAT
Found at i:91924 original size:15 final size:14
Alignment explanation
Indices: 91857--91930 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 14
91847 AAAAATAGAG
*
91857 AAAATAAAAATAAAGT
1 AAAATAATAAT-AA-T
*
91873 AAAGATAAAAATGAAT
1 AAA-ATAATAAT-AAT
91889 AAAATAAATAA-AAT
1 AAAAT-AATAATAAT
91903 GAAAATAATAATAAT
1 -AAAATAATAATAAT
*
91918 AAGAATAAGAATA
1 AA-AATAATAATA
91931 TATACACATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
14 10 0.20
15 19 0.38
16 11 0.22
17 10 0.20
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:92139 original size:8 final size:8
Alignment explanation
Indices: 92123--92171 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
92113 AGGTAATAAA
*
92123 ATAAGAAT
1 ATAAAAAT
92131 ATAAAAAT
1 ATAAAAAT
92139 ATAAAAAT
1 ATAAAAAT
92147 ATAAAAA-
1 ATAAAAAT
* *
92154 GTAATAAT
1 ATAAAAAT
92162 ATTAAAAAT
1 A-TAAAAAT
92171 A
1 A
92172 ATAATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
7 5 0.15
8 22 0.65
9 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (8 bp):
ATAAAAAT
Found at i:92162 original size:15 final size:14
Alignment explanation
Indices: 92120--92177 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
92110 ACAAGGTAAT
*
92120 AAAATAAGAATATAA
1 AAAATAATAATAT-A
*
92135 AAATATAAAAATATA
1 AAA-ATAATAATATA
92150 AAAAGTAATAATATTA
1 AAAA-TAATAATA-TA
92166 AAAATAATAATA
1 AAAATAATAATA
92178 ATAACGGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.03
15 22 0.58
16 15 0.39
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAATAATAATATA
Done.