Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001974.1 Hibiscus syriacus cultivar Beakdansim tig00003997_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: 93026
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:135 original size:63 final size:61
Alignment explanation
Indices: 18--135 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 61
8 GTGTGCAACC
* *
18 CACAAATTTATCATAAATTGATGAACAACATTTAGGCACTAAGTGTGCAACCCACGGAATT
1 CACAAATTCATCATAAATTGATGAACAACATTTAGACACTAAGTGTGCAACCCACGGAATT
* *
79 CACAGAATTCATCATAAGTTGATGAACAACCTTATAGACACTAAGTGTGCAACCCAC
1 CACA-AATTCATCATAAATTGATGAACAACATT-TAGACACTAAGTGTGCAACCCAC
136 ATAATTCATC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
61 4 0.08
62 25 0.49
63 22 0.43
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (61 bp):
CACAAATTCATCATAAATTGATGAACAACATTTAGACACTAAGTGTGCAACCCACGGAATT
Found at i:142 original size:63 final size:61
Alignment explanation
Indices: 18--143 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 61
8 GTGTGCAACC
* * *
18 CACAAATTTATCATAAATTGATGAACAACATTTAGGCACTAAGTGTGCAACCCACGGAATT
1 CACAAATTCATCATAAATTGATGAACAACATTTAGACACTAAGTGTGCAACCCACAGAATT
* * *
79 CACAGAATTCATCATAAGTTGATGAACAACCTTATAGACACTAAGTGTGCAACCCACATAATT
1 CACA-AATTCATCATAAATTGATGAACAACATT-TAGACACTAAGTGTGCAACCCACAGAATT
142 CA
1 CA
144 TCATATGTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 4 0.07
62 25 0.44
63 28 0.49
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (61 bp):
CACAAATTCATCATAAATTGATGAACAACATTTAGACACTAAGTGTGCAACCCACAGAATT
Found at i:290 original size:56 final size:56
Alignment explanation
Indices: 186--293 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 56
176 TATGCGAACC
***
186 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTGTGTGTGCAAAAAAT
1 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTACATGTGCAAAAAAT
*
242 AAGAAATTCATAATAAGTTTATGAATTTCTGTAT-GAGCACTACATGTGCAAA
1 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGA-CACTACATGTGCAAA
294 CTATAGAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
55 2 0.04
56 45 0.96
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (56 bp):
AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTACATGTGCAAAAAAT
Found at i:462 original size:45 final size:44
Alignment explanation
Indices: 375--466 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 44
365 ATAAATTACT
*
375 AAATGCATAACGGTGCATAAAGGCATGAAAGGATGACATAAATG
1 AAATGCATAACGGTGCATAAAGGCATGAAAGAATGACATAAATG
* * *
419 AAATGCATAACGGTGCATTAAAGGCATGAAATAATGCCCTAAATG
1 AAATGCATAACGGTGCA-TAAAGGCATGAAAGAATGACATAAATG
464 AAA
1 AAA
467 ATAATGAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 17 0.40
45 26 0.60
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.20
Consensus pattern (44 bp):
AAATGCATAACGGTGCATAAAGGCATGAAAGAATGACATAAATG
Found at i:3777 original size:41 final size:42
Alignment explanation
Indices: 3719--3835 Score: 191
Period size: 41 Copynumber: 2.8 Consensus size: 42
3709 TATCAATCAA
**
3719 ATTAGGTGAATCATTGGAATTTCCAATATTATTATTAAAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAAAAGT
*
3761 ATTAGG-GAATCATTGGAATTTCCAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAAAAGT
*
3802 ATTAGGTGAATCATTGGAATTTCCAATCGGATTA
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTA
3836 GAAGTTTAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 38 0.54
42 32 0.46
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (42 bp):
ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAAAAGT
Found at i:3992 original size:28 final size:28
Alignment explanation
Indices: 3960--4018 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
3950 ACATATTTAA
*
3960 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
*
3988 AAGTAAACAATAAAACAAATATATTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
4016 AAG
1 AAG
4019 GAAAGATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTAGC
Found at i:4405 original size:28 final size:28
Alignment explanation
Indices: 4373--4427 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
4363 ATACTAAGTT
4373 TGTCGACTAAACATG-AAAGAAATGAGTG
1 TGTCGACTAAACATGCAAA-AAATGAGTG
4401 TGTCGACTAAACATGCAAAAAATGAGT
1 TGTCGACTAAACATGCAAAAAATGAGT
4428 AAGTTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (28 bp):
TGTCGACTAAACATGCAAAAAATGAGTG
Found at i:8935 original size:7 final size:7
Alignment explanation
Indices: 8923--8947 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8913 TATCACTCAT
8923 ACATATC
1 ACATATC
8930 ACATATC
1 ACATATC
8937 ACATATC
1 ACATATC
8944 ACAT
1 ACAT
8948 GTACCATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (7 bp):
ACATATC
Found at i:9134 original size:21 final size:21
Alignment explanation
Indices: 9108--9147 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9098 GCATAGAATT
9108 TGTCCCGAAAGACCACATAGA
1 TGTCCCGAAAGACCACATAGA
*
9129 TGTCCCGAAGGACCACATA
1 TGTCCCGAAAGACCACATA
9148 TAACACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (21 bp):
TGTCCCGAAAGACCACATAGA
Found at i:11839 original size:25 final size:21
Alignment explanation
Indices: 11811--11863 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 21
11801 CACATTCATA
11811 TTCATCTACAGAATAATTCCCTTGC
1 TTCATCTACAG-A-AATT--CTTGC
* *
11836 TTCAACTTCAGAAATTCTTGC
1 TTCATCTACAGAAATTCTTGC
11857 TTCATCT
1 TTCATCT
11864 GTCTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 11 0.44
23 4 0.16
24 1 0.04
25 9 0.36
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (21 bp):
TTCATCTACAGAAATTCTTGC
Found at i:13019 original size:2 final size:2
Alignment explanation
Indices: 13014--13044 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13004 GAACATAAAC
13014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13045 ACTTCAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25705 original size:238 final size:236
Alignment explanation
Indices: 25266--26026 Score: 1010
Period size: 238 Copynumber: 3.2 Consensus size: 236
25256 AACTCATCCG
* * * *
25266 ACAGAGGGGTT-ACCATTTCCTTTGCTCGATTCTCAACACTTCAAATCAGTAACT-CCCCACCAT
1 ACAGAGGGGTTGA-CATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAA-TGCCCCACCAG
* * * ** *
25329 AGGGGTTAACATTTCCTTTGTTTGATTCACAACACTTCGAATTAGCAATACCCCACTAGAGGGGT
64 AGGGGTTAACATTTCCTTTGATCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGT
* * *
25394 TAACATTTCCTTTACTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACAT
129 TAACATTTTCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACAT
*
25459 TTCCTATTGCTCGATTCACAACACTTTGAATCAGCAACGCCCC
194 TTCCTATTGCTCGATTCACAACACTTCGAATCAGCAACGCCCC
*
25502 ATCAGAGGGGTTGACATTTCCTATTGCTCGATTCACAACACTTCGAATCAGCAATGCCTCACCAG
1 A-CAGAGGGGTTGACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAGCAATGCCCCACCAG
* ** *
25567 AGCGGTTAACATTTCGATTGATCGATTCAAAACACTTCGAATCAGCAACGCCCCACCAGAGGGGT
64 AGGGGTTAACATTTCCTTTGATCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGT
* * * ** * *
25632 TAACATTTTCTTTGCTCGATTCACAACACTTCAAATCAGTAGCATCCCACCAGAAGGGTTAAAAT
129 TAACATTTTCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACAT
* *
25697 TTCCTATTGCTCGATTCACAACACTTGGAATCAACAACGCCCC
194 TTCCTATTGCTCGATTCACAACACTTCGAATCAGCAACGCCCC
* * * *
25740 ACCGAAGGGGTTGACATTTCCTATTGCTCGATTCACAATACTTTGAATCAGCAACGCCCCACCAG
1 ACAG-AGGGGTTGACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAGCAATGCCCCACCAG
* *
25805 AGGGGTTAACATGTCCTTTGCTCGATTCACAAC-CTTTCGAATCAGCAACGCCCCACCAGAGGGG
64 AGGGGTTAACATTTCCTTTGATCGATTCACAACAC-TTCGAATCAGCAACGCCCCACCAGAGGGG
* * *
25869 TTAATA-TTTCATTTGCTTGATTCACAACCCTTCGAATCAGCAACGCCCCACCAGAGGGGTTAAC
128 TTAACATTTTC-TTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAAC
* *
25933 ATTTCCT-TTGCTCGATTCACAACACTTCGAATCAGTAAAGCCCC
192 ATTTCCTATTGCTCGATTCACAACACTTCGAATCAGCAACGCCCC
* ** * *
25977 ACCATAGGGGTAAATATTTTCTTTGCTCGATTCACAACACTTCGAATCAG
1 A-CAGAGGGGTTGACATTTCCTTTGCTCGATTCACAACACTTCGAATCAG
26027 TGACATCTCA
Statistics
Matches: 457, Mismatches: 60, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
236 27 0.06
237 73 0.16
238 357 0.78
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (236 bp):
ACAGAGGGGTTGACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAATGCCCCACCAGAG
GGGTTAACATTTCCTTTGATCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTA
ACATTTTCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTTAACATTT
CCTATTGCTCGATTCACAACACTTCGAATCAGCAACGCCCC
Found at i:25850 original size:297 final size:295
Alignment explanation
Indices: 25267--26025 Score: 1042
Period size: 297 Copynumber: 2.6 Consensus size: 295
25257 ACTCATCCGA
* * * * * * *
25267 CAGAGGGGTTACCATTTCCTTTGCTCGATTCTCAACACTTCAAATCAGTAACTCCCCACCATAGG
1 CAGAGGGGTTAACATTT-CATTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGG
* * * * ** * *
25332 GGTTAACATTTCCTTTGTTTGATTCACAACACTTCGAATTAGCAATACCCCACTAGAGGGGTTAA
65 GGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGTAGCA-CCCACCAGAAGGGTTAA
* * * *
25397 CATTTCCTTTACTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATTTC
129 AATTTCCTTTGCTCGATTCACAACACTTCGAATCAACAACGCCCCACCAGAGGGGTTAACATTTC
* * *
25462 CTATTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCATCAGAGGGGTTGACATTTCCTATT
194 CTATTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATGTCCTATT
* *
25527 GCTCGATTCACAACACTTCGAATCAGCAATGCCTCAC
259 GCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * *
25564 CAGAGCGGTTAACATTTCGATTGATCGATTCAAAACACTTCGAATCAGCAACGCCCCACCAGAGG
1 CAGAGGGGTTAACATTTC-ATTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGG
* *
25629 GGTTAACATTTTCTTTGCTCGATTCACAACACTTCAAATCAGTAGCATCCCACCAGAAGGGTTAA
65 GGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGTAGCA-CCCACCAGAAGGGTTAA
* *
25694 AATTTCCTATTGCTCGATTCACAACACTTGGAATCAACAACGCCCCACC-GAAGGGGTTGACATT
129 AATTTCCT-TTGCTCGATTCACAACACTTCGAATCAACAACGCCCCACCAG-AGGGGTTAACATT
*
25758 TCCTATTGCTCGATTCACAATACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATGTCCT-
192 TCCTATTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATGTCCTA
25822 TTGCTCGATTCACAAC-CTTTCGAATCAGCAACGCCCCAC
257 TTGCTCGATTCACAACAC-TTCGAATCAGCAACGCCCCAC
* * *
25861 CAGAGGGGTTAATATTTCATTTGCTTGATTCACAACCCTTCGAATCAGCAACGCCCCACCAGAGG
1 CAGAGGGGTTAACATTTCA-TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGG
* *
25926 GGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGTAAAGC-CCCACCA-TAGGGGTA
65 GGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGT--AGCACCCACCAGAAGGGTTA
*
25989 AATATTTTCTTTGCTCGATTCACAACACTTCGAATCA
128 AA-ATTTCCTTTGCTCGATTCACAACACTTCGAATCA
26026 GTGACATCTC
Statistics
Matches: 410, Mismatches: 44, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
296 37 0.09
297 261 0.64
298 109 0.27
299 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (295 bp):
CAGAGGGGTTAACATTTCATTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGG
GTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGTAGCACCCACCAGAAGGGTTAAAA
TTTCCTTTGCTCGATTCACAACACTTCGAATCAACAACGCCCCACCAGAGGGGTTAACATTTCCT
ATTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCACCAGAGGGGTTAACATGTCCTATTGC
TCGATTCACAACACTTCGAATCAGCAACGCCCCAC
Found at i:26027 original size:59 final size:59
Alignment explanation
Indices: 25267--26026 Score: 1020
Period size: 59 Copynumber: 12.8 Consensus size: 59
25257 ACTCATCCGA
* * * * *
25267 CAGAGGGGTTACCATTTCCTTTGCTCGATTCTCAACACTTCAAATCAGTAACTCCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * * * **
25326 CATAGGGGTTAACATTTCCTTTGTTTGATTCACAACACTTCGAATTAGCAATACCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * *
25385 TAGAGGGGTTAACATTTCCTTTACTCGATTCACAACACTTTGAATCAGCAACGCCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* *
25444 CAGAGGGGTTAACATTTCCTATTGCTCGATTCACAACACTTTGAATCAGCAACGCCCCAT
1 CAGAGGGGTTAACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * *
25504 CAGAGGGGTTGACATTTCCTATTGCTCGATTCACAACACTTCGAATCAGCAATGCCTCAC
1 CAGAGGGGTTAACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* ** * *
25564 CAGAGCGGTTAACATTTCGATTGATCGATTCAAAACACTTCGAATCAGCAACGCCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * * * **
25623 CAGAGGGGTTAACATTTTCTTTGCTCGATTCACAACACTTCAAATCAGTAGCATCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * * *
25682 CAGAAGGGTTAAAATTTCCTATTGCTCGATTCACAACACTTGGAATCAACAACGCCCCAC
1 CAGAGGGGTTAACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * *
25742 C-GAAGGGGTTGACATTTCCTATTGCTCGATTCACAATACTTTGAATCAGCAACGCCCCAC
1 CAG-AGGGGTTAACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
*
25802 CAGAGGGGTTAACATGTCCTTTGCTCGATTCACAAC-CTTTCGAATCAGCAACGCCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACAC-TTCGAATCAGCAACGCCCCAC
* * * *
25861 CAGAGGGGTTAATATTTCATTTGCTTGATTCACAACCCTTCGAATCAGCAACGCCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* *
25920 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGTAAAGCCCCAC
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
* * * *
25979 CATAGGGGTAAATATTTTCTTTGCTCGATTCACAACACTTCGAATCAG
1 CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAG
26027 TGACATCTCA
Statistics
Matches: 615, Mismatches: 80, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
58 1 0.00
59 404 0.66
60 209 0.34
61 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (59 bp):
CAGAGGGGTTAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCAC
Found at i:34408 original size:27 final size:27
Alignment explanation
Indices: 34370--34440 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
34360 AAGTGTCCAA
* *
34370 TCTATGTTTATTTTTTTTAGTTTAGTG
1 TCTAAGTTTATTTTTTATAGTTTAGTG
*
34397 TCTAAGTTTATTTCGTTATAGTTTAGTG
1 TCTAAGTTTATTT-TTTATAGTTTAGTG
*
34425 CCTAACGTTTTATTTT
1 TCTAA-G-TTTATTTT
34441 GTTACTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 12 0.33
28 16 0.44
29 1 0.03
30 7 0.19
ACGTcount: A:0.18, C:0.08, G:0.14, T:0.59
Consensus pattern (27 bp):
TCTAAGTTTATTTTTTATAGTTTAGTG
Found at i:34429 original size:28 final size:30
Alignment explanation
Indices: 34387--34444 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
34377 TTATTTTTTT
*
34387 TAGTTTAGTGTCTAA-G-TTTATTTCGTTA
1 TAGTTTAGTGCCTAACGTTTTATTTCGTTA
*
34415 TAGTTTAGTGCCTAACGTTTTATTTTGTTA
1 TAGTTTAGTGCCTAACGTTTTATTTCGTTA
34445 CTCAAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 14 0.54
29 1 0.04
30 11 0.42
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.53
Consensus pattern (30 bp):
TAGTTTAGTGCCTAACGTTTTATTTCGTTA
Found at i:35579 original size:2 final size:2
Alignment explanation
Indices: 35572--35666 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
35562 AATTATCTTT
35572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35614 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35656 TA TA TA TA TA T
1 TA TA TA TA TA T
35667 TAAGCTAAAG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36554 original size:17 final size:17
Alignment explanation
Indices: 36532--36571 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
36522 TGAATCAAAT
36532 TAATTAAATATTATTTA
1 TAATTAAATATTATTTA
*
36549 TAATTAGATATTATTTA
1 TAATTAAATATTATTTA
36566 -AATTAA
1 TAATTAA
36572 TTGTAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TAATTAAATATTATTTA
Found at i:37202 original size:24 final size:20
Alignment explanation
Indices: 37153--37197 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
37143 TCAATCTCAT
37153 TTTTGAGCTCCAAACCTTCC
1 TTTTGAGCTCCAAACCTTCC
*
37173 TTTTGAGCTCTAAACCTTCC
1 TTTTGAGCTCCAAACCTTCC
37193 TTTTG
1 TTTTG
37198 GTTGAAACGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTTGAGCTCCAAACCTTCC
Found at i:41460 original size:29 final size:29
Alignment explanation
Indices: 41428--41486 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
41418 ATTACCTATA
41428 TAATTATTCAATAAATT-AAAA-TATTTTTT
1 TAATTATT-AA-AAATTAAAAATTATTTTTT
*
41457 TAATTATTAAAATTTAAAAATTATTTTTT
1 TAATTATTAAAAATTAAAAATTATTTTTT
41486 T
1 T
41487 TAAAAATGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 6 0.22
29 17 0.63
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TAATTATTAAAAATTAAAAATTATTTTTT
Found at i:41483 original size:26 final size:29
Alignment explanation
Indices: 41428--41483 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
41418 ATTACCTATA
*
41428 TAATTATTCAATAAATTAAAATATTTTTT
1 TAATTATTCAATAAATTAAAATATTATTT
*
41457 TAATTATT-AA-AATTTAAAA-ATTATTT
1 TAATTATTCAATAAATTAAAATATTATTT
41483 T
1 T
41484 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 8 0.32
28 2 0.08
29 8 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TAATTATTCAATAAATTAAAATATTATTT
Found at i:45630 original size:20 final size:20
Alignment explanation
Indices: 45607--45648 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
45597 TAAAAAATTT
45607 TAAAAAT-AAAAATAATATAA
1 TAAAAATAAAAAATAATA-AA
*
45627 TAAAATTAAAAAATAATAAA
1 TAAAAATAAAAAATAATAAA
45647 TA
1 TA
45649 CCAAGGACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAATAAAAAATAATAAA
Found at i:45645 original size:19 final size:19
Alignment explanation
Indices: 45609--45648 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
45599 AAAAATTTTA
45609 AAAATAAAAATAATATAAT
1 AAAATAAAAATAATATAAT
45628 AAAATTAAAAAATAATA-AAT
1 AAAA-T-AAAAATAATATAAT
45648 A
1 A
45649 CCAAGGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATAAAAATAATATAAT
Found at i:46211 original size:2 final size:2
Alignment explanation
Indices: 46204--46297 Score: 56
Period size: 2 Copynumber: 50.0 Consensus size: 2
46194 AATAATTATT
* *
46204 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
46243 -A TT TA AA TA -A AA AA TA TA TA TT TA TA TA TT TA -A TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46282 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
46298 CCCGGCCCGA
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
1 6 0.09
2 63 0.91
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:46359 original size:12 final size:12
Alignment explanation
Indices: 46295--46359 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
46285 ATATATATAT
*
46295 ATACCCGGCCCG
1 ATACCCGGCCCA
*
46307 ATTCCCGGCCCA
1 ATACCCGGCCCA
**
46319 ATA-CCAACCCA
1 ATACCCGGCCCA
* *
46330 ATATCCGACCCA
1 ATACCCGGCCCA
46342 ATACCCGGCCCA
1 ATACCCGGCCCA
46354 ATACCC
1 ATACCC
46360 ATTTAAATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
11 9 0.20
12 35 0.80
ACGTcount: A:0.28, C:0.48, G:0.12, T:0.12
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:65931 original size:38 final size:38
Alignment explanation
Indices: 65869--65949 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
65859 TAACGAAGTT
* * *
65869 ATAATCCTAGCCCTGGTTTTAAACCCTAAAGATAACTA
1 ATAATCCTAGCCCTAGATTGAAACCCTAAAGATAACTA
* *
65907 ATAATCCTAGTCCTAGATTGAAACCCTAAAGATATCTA
1 ATAATCCTAGCCCTAGATTGAAACCCTAAAGATAACTA
*
65945 GTAAT
1 ATAAT
65950 GTTAGCCGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (38 bp):
ATAATCCTAGCCCTAGATTGAAACCCTAAAGATAACTA
Found at i:66733 original size:17 final size:17
Alignment explanation
Indices: 66711--66751 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
66701 TAATCTTAAT
66711 GAACCCAACTAGAGGAG
1 GAACCCAACTAGAGGAG
*
66728 GAACCCAACTGGAGGAG
1 GAACCCAACTAGAGGAG
66745 GAACCCA
1 GAACCCA
66752 GCAAGAAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.39, C:0.27, G:0.29, T:0.05
Consensus pattern (17 bp):
GAACCCAACTAGAGGAG
Found at i:73037 original size:191 final size:189
Alignment explanation
Indices: 72680--73040 Score: 514
Period size: 187 Copynumber: 1.9 Consensus size: 189
72670 TTCCATCATC
* *
72680 AATGACTGTTCTTCATCTGTTATATATACTGTTGATTAATGGATGCCTCCAGTTTAAGGTGCCAA
1 AATGACTGTTCTTCATCTGTTATATATACTGTTGATTAATGAATGCCTCCAATTTAAGGTGCCAA
* *
72745 ATAATATTGAGGCTGTTTTCAAGTGCCAATTACCATGGATAATTTTTTTAAAAAGTGGTGTTTTA
66 ATAATATTGAGGCTGTTTTCAAGTGCAAATTACCAGGGATAATTTTTTTAAAAAGTGGTGTTTTA
* *
72810 TTCTGCATGCTTGTGTATCGGTTAAGTTGGAATTTTCTCTTGTTTCAAGTGCCAATAAT
131 TTCCGCATGCTTGTGTATCAGTTAAGTTGGAATTTTCTCTTGTTTCAAGTGCCAATAAT
* *
72869 AATGACTGTTCTTCATCTGTTATATA-A-TGTTGATTAATGAATGCCTCCAATTTAAGTTGCCAC
1 AATGACTGTTCTTCATCTGTTATATATACTGTTGATTAATGAATGCCTCCAATTTAAGGTGCCAA
* * * * * *
72932 ATACTATTGAGGTTGTTTTCAAGTGCAAATTTCTAGGGA-GATTTGTTTTAGAAAGTGTGTGGTG
66 ATAATATTGAGGCTGTTTTCAAGTGCAAATTACCAGGGATAATTT-TTTTAAAAAGTG-GT-GT-
72996 TTT-TGATCCGCATGCTTGTGTATCAGTTAAGTTGGAATTTTCTCT
127 TTTAT--TCCGCATGCTTGTGTATCAGTTAAGTTGGAATTTTCTCT
73041 CAGCATGTCT
Statistics
Matches: 152, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
186 4 0.03
187 76 0.50
188 3 0.02
189 29 0.19
190 3 0.02
191 37 0.24
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (189 bp):
AATGACTGTTCTTCATCTGTTATATATACTGTTGATTAATGAATGCCTCCAATTTAAGGTGCCAA
ATAATATTGAGGCTGTTTTCAAGTGCAAATTACCAGGGATAATTTTTTTAAAAAGTGGTGTTTTA
TTCCGCATGCTTGTGTATCAGTTAAGTTGGAATTTTCTCTTGTTTCAAGTGCCAATAAT
Found at i:74805 original size:65 final size:63
Alignment explanation
Indices: 74736--74918 Score: 215
Period size: 65 Copynumber: 2.8 Consensus size: 63
74726 AATTAAATTG
* * *
74736 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACAT-CCATGCACCGATGCACTGAGGATATT-TCAA
* * * ** *
74801 AACATCGAATGCATTTTATGCATCGATGCACCAGCCATGTATCGATGCACTCTGGCTATTTCAA
1 AACATCGAATGCATTTTATGCATCGATGCA-CATCCATGCACCGATGCACTGAGGATATTTCAA
* *
74865 AACATCGAATGTATTTTATGCATCGATGCAC-TCTTAGTGCACCGATGCACTGAG
1 AACATCGAATGCATTTTATGCATCGATGCACATC-CA-TGCACCGATGCACTGAG
74919 AGTCCAACGG
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 45 0.45
65 49 0.49
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTTATGCATCGATGCACATCCATGCACCGATGCACTGAGGATATTTCAA
Found at i:75269 original size:14 final size:14
Alignment explanation
Indices: 75250--75287 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
75240 GTACTCAATT
75250 GTATTCATTTTTGA
1 GTATTCATTTTTGA
75264 GTATTCATTTTTGA
1 GTATTCATTTTTGA
75278 GTATTC-TTTT
1 GTATTCATTTT
75288 CTTTATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.61
Consensus pattern (14 bp):
GTATTCATTTTTGA
Found at i:76089 original size:14 final size:14
Alignment explanation
Indices: 76070--76099 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
76060 TCATTTAAGC
*
76070 CAGTGACATGGGAG
1 CAGTGACATGAGAG
76084 CAGTGACATGAGAG
1 CAGTGACATGAGAG
76098 CA
1 CA
76100 TGGAATGTTG
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:0.33, C:0.17, G:0.37, T:0.13
Consensus pattern (14 bp):
CAGTGACATGAGAG
Found at i:77131 original size:21 final size:20
Alignment explanation
Indices: 77092--77140 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
77082 CTTCGGATTA
* *
77092 TGAAAAATTATTTTTAAAAT
1 TGAAAAATAATTTTCAAAAT
77112 AT-AAAAATAATGTTTCAAAAT
1 -TGAAAAATAAT-TTTCAAAAT
77133 TGAAAAAT
1 TGAAAAAT
77141 GAAAATAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (20 bp):
TGAAAAATAATTTTCAAAAT
Found at i:80975 original size:44 final size:44
Alignment explanation
Indices: 80925--81018 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 44
80915 TTGTGCTTAA
*
80925 TGCATCGATTCA-CTTAACAG-TGCATCGATGCATC-CCTTTGAATG
1 TGCATCGATTCATCTT-ACAGATGCACCGATGCA-CGCC-TTGAATG
* *
80969 TGCATCGATTCATCTTGCTGATGCACCGATGCACGCCTTGAATG
1 TGCATCGATTCATCTTACAGATGCACCGATGCACGCCTTGAATG
81013 TGCATC
1 TGCATC
81019 AATGCACAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 28 0.64
45 16 0.36
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (44 bp):
TGCATCGATTCATCTTACAGATGCACCGATGCACGCCTTGAATG
Found at i:84689 original size:184 final size:184
Alignment explanation
Indices: 84380--84750 Score: 742
Period size: 184 Copynumber: 2.0 Consensus size: 184
84370 ATAATTGTAA
84380 GTTTCCTACACATTCAATGAGAGTGAATTACAGTAAAATTCATGGCTTTTGTCACATATATTTTA
1 GTTTCCTACACATTCAATGAGAGTGAATTACAGTAAAATTCATGGCTTTTGTCACATATATTTTA
84445 GATATTTTCTTTGTTTTTTCTATTGATAATTTTTTTTGCTTCCTAGAATTTTATAAGTTCGTCCC
66 GATATTTTCTTTGTTTTTTCTATTGATAATTTTTTTTGCTTCCTAGAATTTTATAAGTTCGTCCC
84510 TCCCTAAAATGCTTGGACACCATTAATCCACTACCAATTTACGCATGTTGCTAG
131 TCCCTAAAATGCTTGGACACCATTAATCCACTACCAATTTACGCATGTTGCTAG
84564 GTTTCCTACACATTCAATGAGAGTGAATTACAGTAAAATTCATGGCTTTTGTCACATATATTTTA
1 GTTTCCTACACATTCAATGAGAGTGAATTACAGTAAAATTCATGGCTTTTGTCACATATATTTTA
84629 GATATTTTCTTTGTTTTTTCTATTGATAATTTTTTTTGCTTCCTAGAATTTTATAAGTTCGTCCC
66 GATATTTTCTTTGTTTTTTCTATTGATAATTTTTTTTGCTTCCTAGAATTTTATAAGTTCGTCCC
84694 TCCCTAAAATGCTTGGACACCATTAATCCACTACCAATTTACGCATGTTGCTAG
131 TCCCTAAAATGCTTGGACACCATTAATCCACTACCAATTTACGCATGTTGCTAG
84748 GTT
1 GTT
84751 GAGAAGCTTA
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 187 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (184 bp):
GTTTCCTACACATTCAATGAGAGTGAATTACAGTAAAATTCATGGCTTTTGTCACATATATTTTA
GATATTTTCTTTGTTTTTTCTATTGATAATTTTTTTTGCTTCCTAGAATTTTATAAGTTCGTCCC
TCCCTAAAATGCTTGGACACCATTAATCCACTACCAATTTACGCATGTTGCTAG
Found at i:91044 original size:22 final size:21
Alignment explanation
Indices: 91000--91045 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
90990 CATCGATGTG
*
91000 CCACATAATTGTCCCAAATGA
1 CCACATAATTGTCCCAAAGGA
**
91021 CCACATAATTTGTCCTGAAGGA
1 CCACATAA-TTGTCCCAAAGGA
91043 CCA
1 CCA
91046 AATAGAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (21 bp):
CCACATAATTGTCCCAAAGGA
Found at i:91624 original size:21 final size:22
Alignment explanation
Indices: 91583--91624 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
91573 TACTCCCACT
* *
91583 ATAGTATTGATACTTCCCTTCA
1 ATAGTATCGATACTCCCCTTCA
91605 ATAGTATCGATAC-CCCCTTC
1 ATAGTATCGATACTCCCCTTC
91625 GGTACCGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.36
Consensus pattern (22 bp):
ATAGTATCGATACTCCCCTTCA
Done.