Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002851.1 Hibiscus syriacus cultivar Beakdansim tig00005866_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: 89199
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1623 original size:236 final size:232
Alignment explanation
Indices: 1171--1608 Score: 528
Period size: 232 Copynumber: 1.9 Consensus size: 232
1161 AATTTATGAT
* * * ** **
1171 AATTTTAAAATCAGTTAAAGCATACTAAATTTTAAATAGATAATCATTTTATTTATTTGGTTTAA
1 AATTTTAAAATCAATCAAAGCATACTAAAGTTTAAATAGATAATCATTTTATTTATCCGGTCCAA
* *
1236 CTTATAGATAGATTTAAATAGAAACATCATCCACTAACTTAATTTTACGAATTTTTTTTTAAAAT
66 CTCATAGATAGATTTAAATAGAAACAACATCCACTAACTTAATTTTACGAATTTTTTTTTAAAAT
*
1301 TGATCAAATCATACCAAATATTGAATAGATAATTACTTTACTACCCGATTCAATTCATAGACAAA
131 TGATCAAATCATACCAAATATTGAATAGATAATTACTTTACTACACGATTCAATTCATAGAC-AA
1366 TCAAATAGACATCATTCATTAAATTAAATTTTACGGTG
195 TCAAATAGACATCATTCATTAAATTAAATTTTACGGTG
* * * * *
1404 AATTTTAAAATTAATCAAATCATACT-AAGTTTAAATAGATGATCGTTTTTTTTATCCGGTCCAA
1 AATTTTAAAATCAATCAAAGCATACTAAAGTTTAAATAGATAATCATTTTATTTATCCGGTCCAA
* * * * *
1468 CTCATGGATAGATTTAAATAGAGACAAC-GCTTATTAACTTAAATTTTACGAGAATTGTTTTTTT
66 CTCATAGATAGATTTAAATAGAAACAACATC-CACTAACTT-AATTTTAC--GAATT-TTTTTTT
* * ** *
1532 AGAATTGATCAAATCATACCAAACT-TTGATTA-ATGGTTACTTTACTTA-ATGATTCAATTCAT
126 AAAATTGATCAAATCATACCAAA-TATTGAATAGATAATTACTTTAC-TACACGATTCAATTCAT
1594 AGAC-ATCTAAATAGA
189 AGACAATC-AAATAGA
1609 AATATCTTTC
Statistics
Matches: 172, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
231 1 0.01
232 61 0.35
233 33 0.19
234 7 0.04
235 32 0.19
236 37 0.22
237 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (232 bp):
AATTTTAAAATCAATCAAAGCATACTAAAGTTTAAATAGATAATCATTTTATTTATCCGGTCCAA
CTCATAGATAGATTTAAATAGAAACAACATCCACTAACTTAATTTTACGAATTTTTTTTTAAAAT
TGATCAAATCATACCAAATATTGAATAGATAATTACTTTACTACACGATTCAATTCATAGACAAT
CAAATAGACATCATTCATTAAATTAAATTTTACGGTG
Found at i:3268 original size:22 final size:23
Alignment explanation
Indices: 3225--3269 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3215 TATACAATGA
*
3225 CAATGACAATAGACCTATTTTTT
1 CAATGACAATAGACCTACTTTTT
* *
3248 CAATGA-AATAGGCTTACTTTTT
1 CAATGACAATAGACCTACTTTTT
3270 AATTATAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (23 bp):
CAATGACAATAGACCTACTTTTT
Found at i:7026 original size:38 final size:38
Alignment explanation
Indices: 6980--7056 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
6970 ACAAAAAAAG
6980 TATGAATCATTGATATTTTGGTTACAAGAGAGTAAGTA
1 TATGAATCATTGATATTTTGGTTACAAGAGAGTAAGTA
*
7018 TATGAATCATTGATATTTTGGTTACAAGTGAGTAAGTA
1 TATGAATCATTGATATTTTGGTTACAAGAGAGTAAGTA
7056 T
1 T
7057 CGAAGAAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (38 bp):
TATGAATCATTGATATTTTGGTTACAAGAGAGTAAGTA
Found at i:16785 original size:29 final size:29
Alignment explanation
Indices: 16743--16804 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
16733 AGATTGCTAG
* * * *
16743 AGAAGTTGTCATGAGTCTCGATCATTTTC
1 AGAAGTCGCCATGAGTCTAGATAATTTTC
16772 AGAAGTCGCCATGAGTCTAGATAATTTTC
1 AGAAGTCGCCATGAGTCTAGATAATTTTC
16801 AGAA
1 AGAA
16805 CTGGTAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (29 bp):
AGAAGTCGCCATGAGTCTAGATAATTTTC
Found at i:18889 original size:18 final size:20
Alignment explanation
Indices: 18863--18912 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
18853 GCCATTTTTG
* *
18863 GTATTGATACTCATGG-A-A
1 GTATCGATACTCAGGGTAGA
*
18881 GTATCGATACTAAGGGTAGA
1 GTATCGATACTCAGGGTAGA
18901 GTATCGATACTC
1 GTATCGATACTC
18913 CCTAATAGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 12 0.46
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (20 bp):
GTATCGATACTCAGGGTAGA
Found at i:28097 original size:14 final size:14
Alignment explanation
Indices: 28078--28128 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
28068 GTCTGAACCA
28078 AGTCAACTCGTATG
1 AGTCAACTCGTATG
*
28092 AGTCAACACAG-ATTG
1 AGTCAACTC-GTA-TG
* *
28107 AGTCAACTCATCTG
1 AGTCAACTCGTATG
28121 AGTCAACT
1 AGTCAACT
28129 TGTTTAAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (14 bp):
AGTCAACTCGTATG
Found at i:30212 original size:20 final size:21
Alignment explanation
Indices: 30166--30229 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 21
30156 TCCTTTCTTG
*
30166 AAAGGGATCGATTCTTTTTCA
1 AAAGGGATCGATTCCTTTTCA
** *
30187 CGAGGGATCGA-TCCTTTTGA
1 AAAGGGATCGATTCCTTTTCA
* * *
30207 AAAGGGGTCAATT-CTTTGCA
1 AAAGGGATCGATTCCTTTTCA
30227 AAA
1 AAA
30230 ACAGAAACTT
Statistics
Matches: 32, Mismatches: 10, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (21 bp):
AAAGGGATCGATTCCTTTTCA
Found at i:32713 original size:16 final size:18
Alignment explanation
Indices: 32682--32720 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
32672 AAAAACAAGC
*
32682 AAATGTAATTTAGATT-A
1 AAATGTAATCTAGATTGA
32699 AAATG-AATCTAGATTGA
1 AAATGTAATCTAGATTGA
32716 AAATG
1 AAATG
32721 GTAAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (18 bp):
AAATGTAATCTAGATTGA
Found at i:34145 original size:17 final size:18
Alignment explanation
Indices: 34113--34146 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34103 ACTGAAATTC
*
34113 AAATTTAATTATAATAAA
1 AAATTAAATTATAATAAA
34131 AAATTAAATTA-AATAA
1 AAATTAAATTATAATAA
34147 TTTCATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTAAATTATAATAAA
Found at i:41633 original size:14 final size:14
Alignment explanation
Indices: 41614--41669 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
41604 CGTTCGTGAA
41614 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
41628 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
41641 --TT-GTTTATGTT
1 CGTTCGATTATGTT
41652 CGTTCGATTATGTT
1 CGTTCGATTATGTT
41666 CGTT
1 CGTT
41670 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:41648 original size:24 final size:24
Alignment explanation
Indices: 41615--41676 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
41605 GTTCGTGAAC
* *
41615 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
41639 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
41663 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
41677 ATTCATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:41686 original size:24 final size:23
Alignment explanation
Indices: 41615--41683 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
41605 GTTCGTGAAC
* *
41615 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
41639 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
41663 GTTCGTTTATGTTCATTCATT
1 GTTCGTTTATGTTCGTTCATT
41684 TATATTTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 3 0.08
24 37 0.93
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:42429 original size:10 final size:10
Alignment explanation
Indices: 42414--42488 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
42404 GGGTCTCCAA
42414 CGTTTATGTT
1 CGTTTATGTT
42424 CGTTTATGTT
1 CGTTTATGTT
42434 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
42445 ATGTTCGTGTT
1 -CGTTTATGTT
42456 CGTTTATGTT
1 CGTTTATGTT
42466 CG----TGTT
1 CGTTTATGTT
42472 CGTTTATGTT
1 CGTTTATGTT
42482 CGTTTAT
1 CGTTTAT
42489 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:42445 original size:16 final size:16
Alignment explanation
Indices: 42420--42484 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
42410 CCAACGTTTA
42420 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
42436 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
42452 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
42468 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
42484 T
1 T
42485 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:42575 original size:16 final size:16
Alignment explanation
Indices: 42554--42586 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42544 AAAAAAATTT
42554 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
42570 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
42586 T
1 T
42587 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:44412 original size:22 final size:23
Alignment explanation
Indices: 44387--44430 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
44377 ACCCAAGATG
*
44387 GTATAGATAC-CCTTATAAAGAA
1 GTATAGATACTCCCTATAAAGAA
* *
44409 GTATTGATGCTCCCTATAAAGA
1 GTATAGATACTCCCTATAAAGA
44431 TATTGATACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (23 bp):
GTATAGATACTCCCTATAAAGAA
Found at i:47396 original size:20 final size:20
Alignment explanation
Indices: 47371--47411 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
47361 CTTATTTTGC
*
47371 ATTTGTTCTATCTCTCAAAT
1 ATTTGTGCTATCTCTCAAAT
*
47391 ATTTGTGCTATGTCTCAAAT
1 ATTTGTGCTATCTCTCAAAT
47411 A
1 A
47412 ATCTCATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (20 bp):
ATTTGTGCTATCTCTCAAAT
Found at i:49381 original size:19 final size:20
Alignment explanation
Indices: 49352--49413 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 20
49342 TATTATAAAA
49352 TTATA-TAATTTTTTATATT
1 TTATATTAATTTTTTATATT
49371 TTA-ATTAATTTTTTA-ATT
1 TTATATTAATTTTTTATATT
* *
49389 ATATATTAACTTGTTTCATATT
1 TTATATTAA-TT-TTTTATATT
49411 TTA
1 TTA
49414 CCTAGTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 6 0.17
19 18 0.51
20 2 0.06
21 4 0.11
22 5 0.14
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (20 bp):
TTATATTAATTTTTTATATT
Found at i:49880 original size:3 final size:3
Alignment explanation
Indices: 49874--49908 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
49864 ATTAAAAAAA
*
49874 AAG AAG AAG AAT AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
49909 TCGTCTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:55885 original size:17 final size:17
Alignment explanation
Indices: 55844--55888 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
55834 CACTACTTGA
55844 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
55861 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
55878 TTAAATATTTA
1 TTAAATATTTA
55889 TTTTTACATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:58447 original size:15 final size:16
Alignment explanation
Indices: 58427--58465 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
58417 GAAAATCAAA
58427 AATAAAGATC-AAGAC
1 AATAAAGATCTAAGAC
*
58442 AATAAAGA-CTAAGAT
1 AATAAAGATCTAAGAC
58457 AATAAAGAT
1 AATAAAGAT
58466 AAATAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.62, C:0.08, G:0.13, T:0.18
Consensus pattern (16 bp):
AATAAAGATCTAAGAC
Found at i:59593 original size:252 final size:245
Alignment explanation
Indices: 59135--59634 Score: 887
Period size: 252 Copynumber: 2.0 Consensus size: 245
59125 TTAAAATATG
59135 TGCATCTTGAGTTCCCGATATCGGACTGATATGATTCAATAACCCTTGGAAATATAACAACCGAT
1 TGCATCTTGAGTTCCCGA-ATCGGACTGATATGATTCAATAACCCTTGGAAATATAACAACCGAT
59200 CTATTCTAGAAGAGTTGTTGACCAAATACACCTGGATCCCATTCAAAGTCCTCACAAGTCTGATG
65 CTATTCTAGAAGAGTTGTTGACCAAATACACCTGGATCCCATTCAAAGTCCTCACAAGTCTGATG
*
59265 CTATTTTGGTCTTCTTTTCCAAGGCTTGGTCGCGTGGATCACTTAGAAGCATCAATCCATCTTCC
130 CTATTTTGGTCTTCTTTTCCAAGGCTTGGTCGCGTGGATCAATTAGAAGCATCAATCCATCTTCC
59330 TATCATGTAAGCCTTTTAGTGCATGTATCATCCTCACTCTCTTCAAAAGGATT
195 TATCATGTAAGCCTTTTAGTGCATGTATCATCCTCACTCTCTTC--AAGGATT
59383 TGCATCTTGAGTTCCCG-ATCGGACTGATATGATTCAATAACCCTTGGAAATATATAGACAACCG
1 TGCATCTTGAGTTCCCGAATCGGACTGATATGATTCAATAACCCTTGG-AA-ATATA-ACAACCG
59447 ATCATATTTCTAGAAGAGTTTGTTGACCAAATA-ACCTGGATCCCATTCAAAAGTCCTCACAAGT
63 ATC-TA-TTCTAGAAGAG-TTGTTGACCAAATACACCTGGATCCCATTC-AAAGTCCTCACAAGT
59511 CTGATGCTATTTTGGTCTTCTTTTCCAAGGCTTGGTCGCGTGGATCAATTAGAAGCATCAATCCA
124 CTGATGCTATTTTGGTCTTCTTTTCCAAGGCTTGGTCGCGTGGATCAATTAGAAGCATCAATCCA
59576 TCTTCCTATCATGTAAGCCTTTTAGTGCATGTATCATCCTCACTCTCTTCAAGGATT
189 TCTTCCTATCATGTAAGCCTTTTAGTGCATGTATCATCCTCACTCTCTTCAAGGATT
59633 TG
1 TG
59635 ACCTCAAATC
Statistics
Matches: 244, Mismatches: 1, Indels: 12
0.95 0.00 0.05
Matches are distributed among these distances:
246 30 0.12
247 2 0.01
248 22 0.09
249 10 0.04
250 11 0.05
251 26 0.11
252 143 0.59
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (245 bp):
TGCATCTTGAGTTCCCGAATCGGACTGATATGATTCAATAACCCTTGGAAATATAACAACCGATC
TATTCTAGAAGAGTTGTTGACCAAATACACCTGGATCCCATTCAAAGTCCTCACAAGTCTGATGC
TATTTTGGTCTTCTTTTCCAAGGCTTGGTCGCGTGGATCAATTAGAAGCATCAATCCATCTTCCT
ATCATGTAAGCCTTTTAGTGCATGTATCATCCTCACTCTCTTCAAGGATT
Found at i:59647 original size:24 final size:25
Alignment explanation
Indices: 59619--59671 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 25
59609 TCATCCTCAC
59619 TCTCTTC-AAGGATTTGACCTCAAA
1 TCTCTTCAAAGGATTTGACCTCAAA
59643 TCTCTTCAAAAGGATTTGACCTCAAA
1 TCTCTTC-AAAGGATTTGACCTCAAA
59669 TCT
1 TCT
59672 GAAACATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 7 0.26
26 20 0.74
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (25 bp):
TCTCTTCAAAGGATTTGACCTCAAA
Found at i:62027 original size:12 final size:11
Alignment explanation
Indices: 62010--62039 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
62000 AATTATTAGA
62010 TTTTTTTTCTCT
1 TTTTTTTTC-CT
62022 TTTTTTTTCCT
1 TTTTTTTTCCT
62033 TTTTTTT
1 TTTTTTT
62040 ATTTTTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTTCCT
Found at i:66636 original size:25 final size:25
Alignment explanation
Indices: 66600--66745 Score: 140
Period size: 25 Copynumber: 5.9 Consensus size: 25
66590 ACAATATTTT
*
66600 ATGAAAGAATTTTGAAAAATTTTTG
1 ATGAAAGAATTTTGAAAAATGTTTG
* * *
66625 ATAAAAGAATTTTGAGAAATATTTG
1 ATGAAAGAATTTTGAAAAATGTTTG
*
66650 ATGAAATAATTTTGAAGAACAT-TTT-
1 ATGAAAGAATTTTGAA-AA-ATGTTTG
* *
66675 ATGAAATAATTTTGAAGAATGTTTG
1 ATGAAAGAATTTTGAAAAATGTTTG
* * *
66700 ATCAAATAATTTTAAAAAAATGTTTG
1 ATGAAAGAATTTT-GAAAAATGTTTG
66726 ATG-AAG--TTTTGAAAAATGTT
1 ATGAAAGAATTTTGAAAAATGTT
66746 GCCCCTTATT
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
22 9 0.09
23 6 0.06
24 4 0.04
25 65 0.63
26 17 0.17
27 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.15, T:0.39
Consensus pattern (25 bp):
ATGAAAGAATTTTGAAAAATGTTTG
Found at i:66648 original size:12 final size:14
Alignment explanation
Indices: 66595--66689 Score: 66
Period size: 13 Copynumber: 7.5 Consensus size: 14
66585 ATTTGACAAT
*
66595 ATTTT-ATGAAAGA
1 ATTTTGATGAAATA
66608 ATTTTGA--AAA-A
1 ATTTTGATGAAATA
* * *
66619 TTTTTGATAAAAGA
1 ATTTTGATGAAATA
66633 ATTTTGA-GAAAT-
1 ATTTTGATGAAATA
66645 A-TTTGATGAAATA
1 ATTTTGATGAAATA
* *
66658 ATTTTGAAG-AA-C
1 ATTTTGATGAAATA
66670 ATTTT-ATGAAATA
1 ATTTTGATGAAATA
66683 ATTTTGA
1 ATTTTGA
66690 AGAATGTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
11 14 0.22
12 16 0.25
13 19 0.30
14 15 0.23
ACGTcount: A:0.44, C:0.01, G:0.14, T:0.41
Consensus pattern (14 bp):
ATTTTGATGAAATA
Found at i:72109 original size:3 final size:3
Alignment explanation
Indices: 72101--72157 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
72091 CTCCTCACTC
* * * * *
72101 TCA TCA TCA TCA TCA CCA TCA CCA CCA CCA CCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
72149 TCA TCA TCA
1 TCA TCA TCA
72158 GGAGTAGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (3 bp):
TCA
Found at i:73250 original size:21 final size:20
Alignment explanation
Indices: 73221--73259 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
73211 GAAATAATTT
73221 TTATTATATACT-AAATAAAA
1 TTATTATATA-TGAAATAAAA
73241 TTATTAATATATGAAATAA
1 TTATT-ATATATGAAATAA
73260 GGATTGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TTATTATATATGAAATAAAA
Found at i:74278 original size:17 final size:17
Alignment explanation
Indices: 74256--74298 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
74246 GTATTTGAAC
74256 GGGTTTGAGCATTAAGA
1 GGGTTTGAGCATTAAGA
* *
74273 GGGTTTGGGCTTTAAGA
1 GGGTTTGAGCATTAAGA
74290 GGGTTTGAG
1 GGGTTTGAG
74299 TAGATTTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.21, C:0.05, G:0.42, T:0.33
Consensus pattern (17 bp):
GGGTTTGAGCATTAAGA
Found at i:77352 original size:20 final size:22
Alignment explanation
Indices: 77299--77354 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
77289 AATTAATTAG
77299 TAATA-AGATTAATAATAATAA
1 TAATATAGATTAATAATAATAA
*
77320 TAATATAGA-TAATAA-AATAC
1 TAATATAGATTAATAATAATAA
77340 TAATATA-ATTAATAA
1 TAATATAGATTAATAA
77355 CATTTTTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 1 0.03
20 17 0.53
21 11 0.34
22 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (22 bp):
TAATATAGATTAATAATAATAA
Found at i:78413 original size:117 final size:107
Alignment explanation
Indices: 78213--78615 Score: 438
Period size: 117 Copynumber: 3.7 Consensus size: 107
78203 AGGTTGAATG
* * *
78213 AGTTCTTCTCATTATGAACTTCTTTTTCCTCGTTA-GATGAGTTCTTCTCATTATGAACTCTTCA
1 AGTTCTTCTCATTATGAA---CTTTCTCCT--TTAGGATGAGTTCTTCTCATTATGAACACTCCA
*
78277 CTGGAAATGTTGATTCACCTCCTTCTGTGATGAAATCGAACAAAGGTTGAACA
61 CTGGAAATGTTGATTCACCTCCTTCTGTGATGAAATTG---AAA-G--GAACA
*
78330 AGTTCTTCTCATTATGAACTTCTTCTTCCTCATT-GGATGAGTTCTTCTCATTATGAACAATCCA
1 AGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACACTCCA
* * * *
78394 CTGAAAATGTTGATCCACCTCTTTCTGTGATGGAACTTGAAAGGAACA
61 CTGGAAATGTTGATTCACCTCCTTCTGTGAT-GAAATTGAAAGGAACA
* **
78442 AGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTAT-AA-ACTCTTCTGGA
1 AGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACACTCCACTGGA
* * * * *
78505 AATATTGGTTCACCTTCTTCTGTGGTGAATTTGAAAGGAACA
66 AATGTTGATTCACCTCCTTCTGTGATGAAATTGAAAGGAACA
* * *
78547 AGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTC-CATTATGAACTCTTCATTGGA
1 AGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACACTCCACTGGA
78611 AATGT
66 AATGT
78616 CGATCCCTCA
Statistics
Matches: 249, Mismatches: 29, Indels: 27
0.82 0.10 0.09
Matches are distributed among these distances:
104 6 0.02
105 59 0.24
106 37 0.15
107 4 0.02
108 19 0.08
109 4 0.02
110 3 0.01
111 1 0.00
112 24 0.10
114 2 0.01
115 4 0.02
116 2 0.01
117 79 0.32
118 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (107 bp):
AGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACACTCCACTGGA
AATGTTGATTCACCTCCTTCTGTGATGAAATTGAAAGGAACA
Found at i:79092 original size:36 final size:36
Alignment explanation
Indices: 79050--79165 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 36
79040 AGTAAAATTG
*
79050 TCTCAAGCAAGACGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGCAAGATGAAGTAGGTTTTAAGAAAAACCA
** * * ** * * **
79086 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
1 TCTCAAGCAAGATGAAGTAGGTTT-TAAGAAAAACCA
*
79123 TCTCAAGCCAGATGAAGTAGGTTTTAAGAAAAACCA
1 TCTCAAGCAAGATGAAGTAGGTTTTAAGAAAAACCA
79159 TCTCAAG
1 TCTCAAG
79166 TGAGATTCAT
Statistics
Matches: 58, Mismatches: 21, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
36 32 0.55
37 26 0.45
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (36 bp):
TCTCAAGCAAGATGAAGTAGGTTTTAAGAAAAACCA
Found at i:79125 original size:73 final size:73
Alignment explanation
Indices: 79013--79259 Score: 314
Period size: 73 Copynumber: 3.4 Consensus size: 73
79003 AGAGAAGCAC
* * *
79013 TCTCAAGTGAGATAAATTTTGTTCCGAAGTAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
79078 AAAAACCA
66 AAAAACCA
* * *
79086 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGCCAGATGAAGTAGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
79151 AAAAACCA
66 AAAAACCA
** * * * ** * *
79159 TCTCAAGTGAGATTCATTTTGTTTCAAGGGAAAGTTGCCTCAAGTGAGACGAACTTGGTTTTAAG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
*
79224 AAAACCCA
66 AAAAACCA
* * *
79232 TCTCAAGGGAGACAAAACTTTGTTTCAA
1 TCTCAAGTGAGA-TAAATTTTGTTTCAA
79260 GAGAAACTGT
Statistics
Matches: 150, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
73 139 0.93
74 11 0.07
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (73 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGCAAGACGAAGTAGGTTTTAAG
AAAAACCA
Found at i:79127 original size:37 final size:37
Alignment explanation
Indices: 79013--79185 Score: 98
Period size: 36 Copynumber: 4.7 Consensus size: 37
79003 AGAGAAGCAC
* * * *
79013 TCTCAAGTGAGATAAATTTTGTTCCGAAGTAAAATTG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGAAAAACTG
** ** * ** * **
79050 TCTCAAGCAAGACGAAGTAGGTTT-TAAGAAAAACCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGAAAAACTG
*
79086 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAACTG
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGAAAAACTG
** * * ** * **
79123 TCTCAAGCCAGATGAAGTAGGTTT-TAAGAAAAACCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGAAAAACTG
**
79159 TCTCAAGTGAGATTCATTTTGTTTCAA
1 TCTCAAGTGAGATAAATTTTGTTTCAA
79186 GGGAAAGTTG
Statistics
Matches: 92, Mismatches: 42, Indels: 4
0.67 0.30 0.03
Matches are distributed among these distances:
36 49 0.53
37 43 0.47
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (37 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAAGAAAAACTG
Found at i:79302 original size:28 final size:29
Alignment explanation
Indices: 79245--79302 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
79235 CAAGGGAGAC
*
79245 AAAACTTTGTTTCAAGAGAAACTGTATCA
1 AAAACTTTGTTTCAAGAGAAACTATATCA
*
79274 AAAAC-TTGTTTCAAGAGAAACTATCTCA
1 AAAACTTTGTTTCAAGAGAAACTATATCA
79302 A
1 A
79303 GGGAGACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (29 bp):
AAAACTTTGTTTCAAGAGAAACTATATCA
Found at i:79320 original size:36 final size:36
Alignment explanation
Indices: 79274--79342 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
79264 AACTGTATCA
79274 AAAACTTGTTTCAAGAGAAACTATCTCAAGGGAGAC
1 AAAACTTGTTTCAAGAGAAACTATCTCAAGGGAGAC
* * *
79310 AAAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
1 AAAACTTGTTTCAAGAGAAACTATCTCAAGGGA
79343 AACTGTCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (36 bp):
AAAACTTGTTTCAAGAGAAACTATCTCAAGGGAGAC
Found at i:79340 original size:15 final size:15
Alignment explanation
Indices: 79320--79354 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
79310 AAAATTTGTT
79320 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
79335 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
79350 TCAAG
1 TCAAG
79355 AGAGATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (15 bp):
TCAAGGGAAACTGTC
Found at i:79352 original size:51 final size:51
Alignment explanation
Indices: 79275--79393 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
79265 ACTGTATCAA
* *
79275 AAACTTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGG
1 AAAC-TGTCTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
* * *
79327 AAACTGTCTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGG
1 AAACTGTCTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
* *
79378 AAACTATCTTAAGAGA
1 AAACTGTCTCAAGAGA
79394 GACAAAACTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 55 0.93
52 4 0.07
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (51 bp):
AAACTGTCTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGG
Found at i:79375 original size:36 final size:36
Alignment explanation
Indices: 79335--79473 Score: 197
Period size: 36 Copynumber: 3.9 Consensus size: 36
79325 GGAAACTGTC
*
79335 TCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTT
1 TCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTT
* * *
79371 TCAAGGGAAACTATCTTAAGAGAGACAAAACTTGTT
1 TCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTT
* * * *
79407 TCGAGGGAAACTGTATCAAGAGAGAAAAAATTTGTT
1 TCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTT
*
79443 TCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TCAAGGGAAACTATCTCAAGAGAGATAAAAT
79474 CTTCTGTTTC
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 88 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (36 bp):
TCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTT
Found at i:79414 original size:72 final size:72
Alignment explanation
Indices: 79338--79472 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
79328 AACTGTCTCA
* * *
79338 AGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTATCTTAAGAGAGACAAAACT
1 AGGGAAACTGTATCAAGAGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
79403 TGTTTCG
66 TGTTTCG
* *
79410 AGGGAAACTGTATCAAGAGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
1 AGGGAAACTGTATCAAGAGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
79473 TCTTCTGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (72 bp):
AGGGAAACTGTATCAAGAGAGAAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
TGTTTCG
Found at i:79509 original size:40 final size:40
Alignment explanation
Indices: 79464--79755 Score: 425
Period size: 40 Copynumber: 7.4 Consensus size: 40
79454 TATCTCAAGC
* * *
79464 GAGATAAAATCTTCTGTTTCAAGAAAAAATAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
79504 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATATTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
79544 GAGATAAAATCTTCTGTTTCAAGGAAAAACAAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAAC-AATCTTGAGT
* * * *
79585 CAGATAAAATCTTTTGTTCCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
79625 GAGATAAAATCTTCTGTTTC------AAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
79659 GAGATAAAATATTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
79699 TAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
79739 GAGATAAAATCTTCTGT
1 GAGATAAAATCTTCTGT
79756 ATTAAATGAG
Statistics
Matches: 224, Mismatches: 21, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
34 32 0.14
40 156 0.70
41 36 0.16
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:84921 original size:6 final size:6
Alignment explanation
Indices: 84900--84940 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
84890 ACAAACGTAA
84900 AAATGC AAAGATGC AAATGC AAATGC AAATGC AAATGC AAA
1 AAATGC -AA-ATGC AAATGC AAATGC AAATGC AAATGC AAA
84941 AGGTATCGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 25 0.76
7 4 0.12
8 4 0.12
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (6 bp):
AAATGC
Found at i:89173 original size:20 final size:20
Alignment explanation
Indices: 89132--89190 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
89122 TAGGCCTAAA
*
89132 AAATATAAT-TAATTAGTAAT
1 AAATATAATATAATTAAT-AT
89152 AAGAT-TAATAATAA-TAATAT
1 AA-ATATAAT-ATAATTAATAT
89172 AAATATAATATAATTAATA
1 AAATATAATATAATTAATA
89191 ACATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
19 6 0.18
20 19 0.58
21 5 0.15
22 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
AAATATAATATAATTAATAT
Done.