Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003338.1 Hibiscus syriacus cultivar Beakdansim tig00007027_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: 74127
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:8579 original size:2 final size:2
Alignment explanation
Indices: 8568--8620 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
8558 ACAAAAATTA
8568 AT AT -T 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
8609 AT AT AT AT AT AT
1 AT AT AT AT AT AT
8621 TGCATCTTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8822 original size:115 final size:119
Alignment explanation
Indices: 8616--8855 Score: 380
Period size: 115 Copynumber: 2.0 Consensus size: 119
8606 TATATATATA
*
8616 TATATTGCATCTTGACATTATAAATGTGAGTCAGAGGTTAAGGGGTAGAGAAAGATAGAAGAAAT
1 TATATTGCATCTTGACATTATAAATGTGAGTCAAAGGTTAAGGGGTAGAGAAAGATAGAAGAAAT
* **
8681 TATTTGATATAAATACATTT-TTAAAAAAA-TAAATTGATTCGATTCAAAGTAT
66 TATTTGATACAAATACATTTAAAAAAAAAAGTAAATTGATTCGATTCAAAGTAT
* * *
8733 TATATTGCATCTTGACATTGTAAATGTGAGTCAAAGG-T-ATGGGTAGATAAAGATAGAAGAAAT
1 TATATTGCATCTTGACATTATAAATGTGAGTCAAAGGTTAAGGGGTAGAGAAAGATAGAAGAAAT
8796 TATTTGATACAAATACATTTAAAAAAAAAAGGTAAATTGATTCGATTCAAAGTAT
66 TATTTGATACAAATACATTTAAAAAAAAAA-GTAAATTGATTCGATTCAAAGTAT
8851 TATAT
1 TATAT
8856 AGTAATATTT
Statistics
Matches: 113, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
115 42 0.37
116 8 0.07
117 35 0.31
118 28 0.25
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.33
Consensus pattern (119 bp):
TATATTGCATCTTGACATTATAAATGTGAGTCAAAGGTTAAGGGGTAGAGAAAGATAGAAGAAAT
TATTTGATACAAATACATTTAAAAAAAAAAGTAAATTGATTCGATTCAAAGTAT
Found at i:13360 original size:24 final size:25
Alignment explanation
Indices: 13324--13373 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
13314 TTTTTTAAAA
*
13324 TAAAAATAATTTAATTTTACAAATAT
1 TAAAAAT-ATTTAATTTTAAAAATAT
13350 TAAAAAT-TTTAATTTTAAAAATAT
1 TAAAAATATTTAATTTTAAAAATAT
13374 AAACAATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.70
26 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAAAATATTTAATTTTAAAAATAT
Found at i:13376 original size:23 final size:23
Alignment explanation
Indices: 13307--13376 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
13297 ATTTTAATAT
* *
13307 AATTTTATTTTTTAAAATA-AAA
1 AATTTTAATTTTAAAAATATAAA
* *
13329 ATAATTTAATTTTACAAATATTAAA
1 A-ATTTTAATTTTAAAAATA-TAAA
13354 AATTTTAATTTTAAAAATATAAA
1 AATTTTAATTTTAAAAATATAAA
13377 CAATGAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 18 0.46
24 16 0.41
25 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTTAATTTTAAAAATATAAA
Found at i:14359 original size:3 final size:3
Alignment explanation
Indices: 14353--14386 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
14343 TAGTCAACTT
14353 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
14387 AATTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21424 original size:45 final size:45
Alignment explanation
Indices: 21358--21447 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
21348 AACTTCTCCC
*
21358 TATTTTATGTAGGTTACGTGAACCACTCCCCAAATATCCTACCAA
1 TATTTTATATAGGTTACGTGAACCACTCCCCAAATATCCTACCAA
* * **
21403 TATTTTATATATGTTATGTGAATTACTCCCCAAATATCCTACCAA
1 TATTTTATATAGGTTACGTGAACCACTCCCCAAATATCCTACCAA
21448 ACCTCATTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (45 bp):
TATTTTATATAGGTTACGTGAACCACTCCCCAAATATCCTACCAA
Found at i:25262 original size:18 final size:18
Alignment explanation
Indices: 25236--25270 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25226 TCGAAATGAC
*
25236 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
25254 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
25271 CCGGATGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:30496 original size:18 final size:18
Alignment explanation
Indices: 30470--30504 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
30460 TCGAAAGGAC
*
30470 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
30488 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
30505 CCGGATGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:40532 original size:2 final size:2
Alignment explanation
Indices: 40525--40554 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40515 TAAATTTTTA
40525 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
40555 GTAGATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42575 original size:23 final size:23
Alignment explanation
Indices: 42549--42593 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42539 CACCACAGCT
*
42549 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
42572 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
42594 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:43337 original size:68 final size:66
Alignment explanation
Indices: 43198--43349 Score: 214
Period size: 67 Copynumber: 2.3 Consensus size: 66
43188 TTTTCCTCAT
* * *
43198 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCAT
1 GGGGGTATCGGTT--CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCAT
43263 TGA
64 TGA
***
43266 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTTGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCATT
43331 GA
65 GA
*
43333 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
43350 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
66 7 0.09
67 57 0.75
68 12 0.16
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCATTG
A
Found at i:43359 original size:21 final size:21
Alignment explanation
Indices: 43329--43371 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
43319 TTCATATTTG
* *
43329 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
43350 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
43371 T
1 T
43372 AACCCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:44589 original size:23 final size:23
Alignment explanation
Indices: 44571--44630 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
44561 CTCGTATAAA
44571 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
44594 TACACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
44617 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
44631 ATATAATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:45383 original size:68 final size:66
Alignment explanation
Indices: 45244--45395 Score: 214
Period size: 67 Copynumber: 2.3 Consensus size: 66
45234 TTTTCCTCAT
* * *
45244 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGT
1 GGGGGTATCGGTT--CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGT
45309 TGA
64 TGA
**
45312 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTTGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
45377 GA
65 GA
* *
45379 AGGGGTATCGATTCCCC
1 GGGGGTATCGGTTCCCC
45396 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
66 7 0.09
67 57 0.75
68 12 0.16
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
A
Found at i:45405 original size:21 final size:21
Alignment explanation
Indices: 45375--45417 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
45365 TTCATATTTG
*
45375 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
45396 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
45417 T
1 T
45418 AACCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:51487 original size:23 final size:23
Alignment explanation
Indices: 51461--51520 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
51451 GCTCGTATAA
51461 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
51484 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
51507 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
51521 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:52271 original size:68 final size:66
Alignment explanation
Indices: 52132--52283 Score: 223
Period size: 67 Copynumber: 2.3 Consensus size: 66
52122 TTTTCCTCAT
* * *
52132 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGT
1 GGGGGTATCGGTT--CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGT
52197 TGA
64 TGA
**
52200 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTTGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
52265 GA
65 GA
*
52267 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
52284 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 7 0.09
67 58 0.75
68 12 0.16
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTG
A
Found at i:52293 original size:21 final size:21
Alignment explanation
Indices: 52263--52305 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52253 TTCATATTTG
* *
52263 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
52284 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
52305 T
1 T
52306 AACCCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:54022 original size:3 final size:3
Alignment explanation
Indices: 54014--54064 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
54004 ATTAATTATT
*
54014 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54060 TAA TA
1 TAA TA
54065 TAAGCAAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 41 0.93
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54661 original size:121 final size:122
Alignment explanation
Indices: 54443--54876 Score: 515
Period size: 121 Copynumber: 3.7 Consensus size: 122
54433 GTTGAACAAG
*
54443 TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTGGAAATGTTGATGCTGATCTAT
1 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TCTTCTGGAAATGTTGATGCTGATCTAT
* *
54508 CTCATTCTGTGATATAATC-ATACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
65 CTCATTCTGTGATAGAATCGAGA-AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* * *
54566 TTCTTCCTCTTCAGATAAGTTTTTCTCATTATGAAC-CTTTTGAAAATGTTGATGCTGATCTATC
1 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGCTGATCTATC
* * * *
54630 TCCTTCTGTGATAGAATCGAGAAAAAGGTTGAATAAATTCTTCTCATTATGAACTTC
66 TCATTCTGTGATAGAATCGAGAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
*
54687 TTCTTCCTTTTCAGATAAGTTCTTCTCATTATGAACT-TTCTGGAAA-----A----G-TCTATC
1 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGCTGATCTATC
** * *
54741 -CATTAAGTGAT-GAATTCGAGCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTC
66 TCATTCTGTGATAGAA-TCGAGAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * * * *
54797 TTC-TCCTTCTTCAGATGAGTTCTTGTCATTATGAACACTTCTGGAAATGTTAATGTTGATATAT
1 TTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGCTGATCTAT
54861 CTTC-TTCTGTGATAGA
65 C-TCATTCTGTGATAGA
54877 GTCATGCAGA
Statistics
Matches: 265, Mismatches: 28, Indels: 36
0.81 0.09 0.11
Matches are distributed among these distances:
109 6 0.02
110 74 0.28
111 15 0.06
112 1 0.00
116 2 0.01
120 1 0.00
121 120 0.45
122 9 0.03
123 37 0.14
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (122 bp):
TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGCTGATCTATC
TCATTCTGTGATAGAATCGAGAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
Found at i:54830 original size:110 final size:111
Alignment explanation
Indices: 54637--54843 Score: 312
Period size: 110 Copynumber: 1.9 Consensus size: 111
54627 ATCTCCTTCT
*
54637 GTGATAGAATCGAGAAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGA
1 GTGATAGAATCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGA
*
54702 TAAGTTCTTCTCATTATGAAC-TTTCTGGAAAAGTCTATCCATTAA
66 TAAGTTCTTCTCATTATGAACACTTCTGGAAAAGTCTATCCATTAA
* * *
54747 GTGAT-GAATTCGAGCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCA
1 GTGATAGAA-TCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT-TTCA
* *
54810 GATGAGTTCTTGTCATTATGAACACTTCTGGAAA
64 GATAAGTTCTTCTCATTATGAACACTTCTGGAAA
54844 TGTTAATGTT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
109 8 0.09
110 70 0.80
111 9 0.10
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (111 bp):
GTGATAGAATCGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGA
TAAGTTCTTCTCATTATGAACACTTCTGGAAAAGTCTATCCATTAA
Found at i:55031 original size:113 final size:113
Alignment explanation
Indices: 54905--55179 Score: 408
Period size: 113 Copynumber: 2.4 Consensus size: 113
54895 CAAACTCTTC
* *
54905 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGTAATGCTGATCCGTCAAATGATGAATT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAATGATGAATT
* * *
54970 CAAACAAAAAGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCT
66 CAAACAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCT
* * *
55018 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAATGATGAATT
** * * *
55083 TGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCT
66 CAAACAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCT
*
55131 TCTTCAGATGAGTTCTTCTCATTATGAACTCTT-TCTGGAAATGTTGATC
1 TCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAATGCTGATC
55180 AATTGTGATG
Statistics
Matches: 146, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
113 144 0.99
114 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAATGATGAATT
CAAACAAAAAGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCT
Found at i:56354 original size:21 final size:21
Alignment explanation
Indices: 56330--56412 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
56320 ATCCATTTAC
*
56330 AAAAGAATAAATTGAATTTCA
1 AAAAAAATAAATTGAATTTCA
*
56351 AAAAAAATAAATTAAATTTCA
1 AAAAAAATAAATTGAATTTCA
*
56372 AAAATAATAAATTGAATTT-A
1 AAAAAAATAAATTGAATTTCA
* *
56392 GAGAAAATAAACTTAGAATTT
1 AAAAAAATAAA-TT-GAATTT
56413 ATTAATAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.17
21 38 0.72
22 6 0.11
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAAATAAATTGAATTTCA
Found at i:56381 original size:42 final size:43
Alignment explanation
Indices: 56330--56412 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
56320 ATCCATTTAC
56330 AAAAGAATAAATTGAATTTCAAAAAAAATAAA-TTA-AATTTCA
1 AAAAGAATAAATTGAATTT-AAAAAAAATAAACTTAGAATTTCA
* * *
56372 AAAATAATAAATTGAATTTAGAGAAAATAAACTTAGAATTT
1 AAAAGAATAAATTGAATTTAAAAAAAATAAACTTAGAATTT
56413 ATTAATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.28
42 21 0.58
43 5 0.14
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (43 bp):
AAAAGAATAAATTGAATTTAAAAAAAATAAACTTAGAATTTCA
Found at i:57632 original size:45 final size:45
Alignment explanation
Indices: 57576--57675 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
57566 AAAATAGTCA
*
57576 ATTGCCACAAGGATGAAACAATGTCCATTCGATGCTTTTGGTGCG
1 ATTGCCCCAAGGATGAAACAATGTCCATTCGATGCTTTTGGTGCG
*
57621 ATTGCCCCAAGGATGAAACAATGTCCATTCGATGCTTTTGGTGTG
1 ATTGCCCCAAGGATGAAACAATGTCCATTCGATGCTTTTGGTGCG
*
57666 ATTTCCCCAA
1 ATTGCCCCAA
57676 TGACGTCTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (45 bp):
ATTGCCCCAAGGATGAAACAATGTCCATTCGATGCTTTTGGTGCG
Found at i:60373 original size:9 final size:9
Alignment explanation
Indices: 60358--60389 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
60348 GAAAAATAAT
60358 GAATGTAAA
1 GAATGTAAA
*
60367 AAATGTAAA
1 GAATGTAAA
60376 GAATGTAAA
1 GAATGTAAA
60385 GAATG
1 GAATG
60390 ATTTCCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
GAATGTAAA
Found at i:64184 original size:15 final size:15
Alignment explanation
Indices: 64166--64197 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
64156 TGCAATGAAT
64166 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
64181 AATGCATGTATGCAA
1 AATGAATGTATGCAA
64196 AA
1 AA
64198 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:67558 original size:28 final size:27
Alignment explanation
Indices: 67507--67560 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
67497 ATATTAATAA
*
67507 AATAATATATATAAATATTATGAAAAT
1 AATAATATATATAAAAATTATGAAAAT
*
67534 AATAAGTATATATAAAAATTTTGAAAA
1 AATAA-TATATATAAAAATTATGAAAA
67561 GAAAGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AATAATATATATAAAAATTATGAAAAT
Found at i:69703 original size:3 final size:3
Alignment explanation
Indices: 69695--69733 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
69685 ATTAATTATT
*
69695 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
69734 TAAGCAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.09
3 29 0.91
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:69729 original size:25 final size:25
Alignment explanation
Indices: 69695--69744 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
69685 ATTAATTATT
69695 TAATAATAATAATATAA-CATAATAA
1 TAATAATAATAATATAAGCA-AATAA
69720 TAATAATAATAATATAAGCAAATAA
1 TAATAATAATAATATAAGCAAATAA
69745 GAGAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (25 bp):
TAATAATAATAATATAAGCAAATAA
Done.