Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002030.1 Hibiscus syriacus cultivar Beakdansim tig00004142_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: 78215
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:6152 original size:23 final size:23
Alignment explanation
Indices: 6126--6187 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
6116 GGAACGAATT
6126 TATAAAATTTTAAATGA-AAAAAA
1 TATAAAATTTT-AATGATAAAAAA
* * *
6149 TATAAAACTTTAAGGATATAAAA
1 TATAAAATTTTAATGATAAAAAA
*
6172 TTTAAAATTTTTAATG
1 TATAAAA-TTTTAATG
6188 TTCATCCCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 4 0.13
23 21 0.68
24 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (23 bp):
TATAAAATTTTAATGATAAAAAA
Found at i:6888 original size:32 final size:32
Alignment explanation
Indices: 6831--6920 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
6821 TTAAAAGATA
*
6831 TAAATAATTATTAAA-TTTATCGAATTATTGT
1 TAAATGATTATTAAATTTTATCGAATTATTGT
* *
6862 TAAATGATTTTTAAATTTTATTGAATTATTGT
1 TAAATGATTATTAAATTTTATCGAATTATTGT
* * *
6894 TAAACGATGATAAAATTTTATCGAATT
1 TAAATGATTATTAAATTTTATCGAATT
6921 GTTACAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
31 13 0.26
32 37 0.74
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (32 bp):
TAAATGATTATTAAATTTTATCGAATTATTGT
Found at i:10825 original size:221 final size:221
Alignment explanation
Indices: 10442--10883 Score: 866
Period size: 221 Copynumber: 2.0 Consensus size: 221
10432 CCAAGGAGGC
*
10442 TAAGAAATTCATGAACATTCGGCACCCGAATGTGGTCGGTTTGAGAGGCTACTATTGGGGCCCTA
1 TAAGAAATTCACGAACATTCGGCACCCGAATGTGGTCGGTTTGAGAGGCTACTATTGGGGCCCTA
10507 CTCAACACGAGAAGCTGATTCTTTCAGATTATATCTCACCTGGAAGTCTTGCAAGCTTTCTTTAT
66 CTCAACACGAGAAGCTGATTCTTTCAGATTATATCTCACCTGGAAGTCTTGCAAGCTTTCTTTAT
10572 GGTAAAAACCTGGAGAAATGTTCTTTTTAAGTATCTTTTACACGATATGATATTGGCCAACTTTC
131 GGTAAAAACCTGGAGAAATGTTCTTTTTAAGTATCTTTTACACGATATGATATTGGCCAACTTTC
10637 AGTCTTATTCCTAATCAATCTCATCT
196 AGTCTTATTCCTAATCAATCTCATCT
*
10663 TAAGAAATTTACGAACATTCGGCACCCGAATGTGGTCGGTTTGAGAGGCTACTATTGGGGCCCTA
1 TAAGAAATTCACGAACATTCGGCACCCGAATGTGGTCGGTTTGAGAGGCTACTATTGGGGCCCTA
10728 CTCAACACGAGAAGCTGATTCTTTCAGATTATATCTCACCTGGAAGTCTTGCAAGCTTTCTTTAT
66 CTCAACACGAGAAGCTGATTCTTTCAGATTATATCTCACCTGGAAGTCTTGCAAGCTTTCTTTAT
10793 GGTAAAAACCTGGAGAAATGTTCTTTTTAAGTATCTTTTACACGATATGATATTGGCCAACTTTC
131 GGTAAAAACCTGGAGAAATGTTCTTTTTAAGTATCTTTTACACGATATGATATTGGCCAACTTTC
10858 AGTCTTATTCCTAATCAATCTCATCT
196 AGTCTTATTCCTAATCAATCTCATCT
10884 AAATTTTTCA
Statistics
Matches: 219, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
221 219 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (221 bp):
TAAGAAATTCACGAACATTCGGCACCCGAATGTGGTCGGTTTGAGAGGCTACTATTGGGGCCCTA
CTCAACACGAGAAGCTGATTCTTTCAGATTATATCTCACCTGGAAGTCTTGCAAGCTTTCTTTAT
GGTAAAAACCTGGAGAAATGTTCTTTTTAAGTATCTTTTACACGATATGATATTGGCCAACTTTC
AGTCTTATTCCTAATCAATCTCATCT
Found at i:35613 original size:12 final size:12
Alignment explanation
Indices: 35596--35620 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35586 GGAAAACATT
35596 ACAGATACCAAA
1 ACAGATACCAAA
35608 ACAGATACCAAA
1 ACAGATACCAAA
35620 A
1 A
35621 AGCTACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (12 bp):
ACAGATACCAAA
Found at i:38019 original size:6 final size:6
Alignment explanation
Indices: 38008--38048 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
37998 AGAAGATGGT
*
38008 ACTGGG ACTGGG ACTGGG ACTGGG ACTGGG ACTGGG CCTGG
1 ACTGGG ACTGGG ACTGGG ACTGGG ACTGGG ACTGGG ACTGG
38049 CCAATTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.20, G:0.49, T:0.17
Consensus pattern (6 bp):
ACTGGG
Found at i:51239 original size:21 final size:20
Alignment explanation
Indices: 51213--51254 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
51203 AAAATGATTT
51213 ACTGGAATTTGAATTACTGGA
1 ACTGGAATTTGAATT-CTGGA
51234 ACTGGAATTTGAATTCTGGA
1 ACTGGAATTTGAATTCTGGA
51254 A
1 A
51255 AATTAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (20 bp):
ACTGGAATTTGAATTCTGGA
Found at i:51480 original size:22 final size:22
Alignment explanation
Indices: 51420--51484 Score: 53
Period size: 25 Copynumber: 2.8 Consensus size: 22
51410 ATTACAAATA
51420 TTAAATATATTAAATAATATTATT
1 TTAAA-ATATT-AATAATATTATT
*
51444 TATCATAAA-ACTTAATATTATTATT
1 T-T-A-AAATA-TTAATAATATTATT
51469 TTAAAATATTAA-AATA
1 TTAAAATATTAATAATA
51485 ATTTATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
21 3 0.09
22 7 0.21
23 2 0.06
24 2 0.06
25 14 0.41
26 4 0.12
27 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATATTAATAATATTATT
Found at i:51728 original size:24 final size:24
Alignment explanation
Indices: 51695--51742 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
51685 TTATTAAATA
* *
51695 TAAAAAAAAATTATTATATATTAT
1 TAAAAAAAAAATATAATATATTAT
* *
51719 TAAAATAAAAATATAATATCTTAT
1 TAAAAAAAAAATATAATATATTAT
51743 ATTATTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TAAAAAAAAAATATAATATATTAT
Found at i:51743 original size:29 final size:29
Alignment explanation
Indices: 51676--51754 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
51666 AAATATATAA
51676 TATTAT-TCATTATTAAATATAAAAAAAAAT
1 TATTATAT-ATTATTAAA-ATAAAAAAAAAT
*
51706 TATTATATATTATTAAAATAAAAATATAA-
1 TATTATATATTATTAAAATAAAAA-AAAAT
*
51735 TATCT-TATATTATTATAATA
1 TAT-TATATATTATTAAAATA
51755 TAATTGATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 24 0.55
30 19 0.43
31 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (29 bp):
TATTATATATTATTAAAATAAAAAAAAAT
Found at i:51779 original size:15 final size:16
Alignment explanation
Indices: 51741--51794 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 16
51731 ATAATATCTT
51741 ATATTATTATAATATA
1 ATATTATTATAATATA
*
51757 ATTGATTATT-TTATATA
1 A-T-ATTATTATAATATA
*
51774 ATATTA--AAAATATA
1 ATATTATTATAATATA
51788 ATATTAT
1 ATATTAT
51795 ATTATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 11 0.35
15 4 0.13
16 2 0.06
17 8 0.26
18 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTATTATAATATA
Found at i:51802 original size:34 final size:34
Alignment explanation
Indices: 51761--51826 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
51751 AATATAATTG
* *
51761 ATTATTTTATATAATATTAAA-AATATAATATTAT
1 ATTATTTTAAATAATAATAAATAA-ATAATATTAT
*
51795 ATTATTTTAAATATTAATAAATAAATAATATT
1 ATTATTTTAAATAATAATAAATAAATAATATT
51827 TTGATGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
ATTATTTTAAATAATAATAAATAAATAATATTAT
Found at i:52284 original size:22 final size:21
Alignment explanation
Indices: 52259--52312 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
52249 CCCAGTTTCC
* *
52259 AAATCCGCAACGCGTATTTGGA
1 AAAT-CGCAACACGAATTTGGA
*
52281 AAATCGCAACACGAATTT-GT
1 AAATCGCAACACGAATTTGGA
52301 AAATCGCAACAC
1 AAATCGCAACAC
52313 AGAAGTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.45
21 12 0.41
22 4 0.14
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
AAATCGCAACACGAATTTGGA
Found at i:52337 original size:21 final size:20
Alignment explanation
Indices: 52304--52390 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
52294 AATTTGTAAA
*
52304 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
52324 TCGCAAATACAGAAGTCAAAT
1 TCGC-AACACAAAAGTCAAAT
52345 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
52365 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
52385 TCGCAA
1 TCGCAA
52391 AGCGCGTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 44 0.70
21 19 0.30
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:52349 original size:41 final size:40
Alignment explanation
Indices: 52304--52390 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 40
52294 AATTTGTAAA
* * *
52304 TCGCAACACAGAAGTCAAATTCGCAAATACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGC-AACACAAAAGTCAAAT
52345 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
52385 TCGCAA
1 TCGCAA
52391 AGCGCGTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
40 20 0.47
41 23 0.53
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.16
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:52568 original size:22 final size:22
Alignment explanation
Indices: 52518--52570 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
52508 TCACTCTCTA
*
52518 CGGCGACATCTGTCCCCATCTC
1 CGGCGAAATCTGTCCCCATCTC
**
52540 CAACGAAATCTGTCCCCATCTC
1 CGGCGAAATCTGTCCCCATCTC
52562 CGGCGAAAT
1 CGGCGAAAT
52571 TAGTCTATCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.21
Consensus pattern (22 bp):
CGGCGAAATCTGTCCCCATCTC
Found at i:52960 original size:20 final size:20
Alignment explanation
Indices: 52927--52986 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
52917 CGCAACGCAA
*
52927 TTTTAATTTCGCGTTGCGAT
1 TTTTATTTTCGCGTTGCGAT
*
52947 TTTTATTTTTGCGTTGCGAT
1 TTTTATTTTCGCGTTGCGAT
* *
52967 TTTCATGTTCGCGTTGCGAT
1 TTTTATTTTCGCGTTGCGAT
52987 ATTTGCGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.12, C:0.15, G:0.22, T:0.52
Consensus pattern (20 bp):
TTTTATTTTCGCGTTGCGAT
Found at i:54725 original size:21 final size:21
Alignment explanation
Indices: 54701--54758 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
54691 GAGTTACGTG
54701 ATGAGGTCGGTGCTTTGAGTC
1 ATGAGGTCGGTGCTTTGAGTC
54722 ATGAGGTCGGTGCTTTGAGTC
1 ATGAGGTCGGTGCTTTGAGTC
*
54743 ATGAGGTCGGTACTTT
1 ATGAGGTCGGTGCTTT
54759 ACGTGAAGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.16, C:0.14, G:0.36, T:0.34
Consensus pattern (21 bp):
ATGAGGTCGGTGCTTTGAGTC
Found at i:55225 original size:21 final size:21
Alignment explanation
Indices: 55199--55269 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
55189 CTCCTATTGT
55199 TCAAGAGGCCCCTCTCATC-A
1 TCAAGAGGCCCCTCTCATCGA
* * * *
55219 TCGAAGAAGCCCCTCCCACCGT
1 TC-AAGAGGCCCCTCTCATCGA
* *
55241 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCTCATCGA
55262 TCAAGAGG
1 TCAAGAGG
55270 TCCCGCCCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.24, C:0.37, G:0.21, T:0.18
Consensus pattern (21 bp):
TCAAGAGGCCCCTCTCATCGA
Found at i:55283 original size:42 final size:42
Alignment explanation
Indices: 55197--55289 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
55187 GCCTCCTATT
*
55197 GTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCTCCCACC
1 GTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCACC
* * * * *
55239 GTTCAAGAGGCCCCTGTCATCGTTC-AAGAGGTCCCGCCCGCC
1 GTTCAAGAGGCCCCTCTCATC-ATCGAAGAAGCCCCGCCCACC
55281 GTTCAAGAG
1 GTTCAAGAG
55290 CCTGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.22, C:0.38, G:0.23, T:0.18
Consensus pattern (42 bp):
GTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCACC
Found at i:59250 original size:24 final size:24
Alignment explanation
Indices: 59213--59266 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
59203 CTGAAACATC
*
59213 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
59237 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
59261 ATCAAA
1 ATCAAA
59267 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:59280 original size:24 final size:24
Alignment explanation
Indices: 59229--59280 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
59219 ATCTGAGTAT
* *
59229 TGACCAAGATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
59253 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
59277 TGAC
1 TGAC
59281 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:60256 original size:19 final size:20
Alignment explanation
Indices: 60215--60266 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
60205 ACTAAAACAT
60215 GTTGCGAATTTGAAAATCGA
1 GTTGCGAATTTGAAAATCGA
* *
60235 GTTGAGAATTTGAAATTC-A
1 GTTGCGAATTTGAAAATCGA
60254 GTTGCGAATTTGA
1 GTTGCGAATTTGA
60267 CTTCTGTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGA
Found at i:60279 original size:20 final size:20
Alignment explanation
Indices: 60254--60340 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
60244 TTGAAATTCA
60254 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
60274 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
60294 GTTGCGAATTTGAATTATGT
1 GTTGCGAATTTGACTTCTGT
*
60314 GTTACGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
60334 GTTGCGA
1 GTTGCGA
60341 TTTACAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:60362 original size:40 final size:40
Alignment explanation
Indices: 60274--60365 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
60264 TGACTTCTGT
* * * *
60274 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGAATTATGT
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTTAAATTACGC
*
60314 GTTACGAATTTGACTTCTGTGTTGCG-ATTTACAAATT-CGC
1 GTTGCGAATTTGACTTCTGTGTTGCGAATTT--AAATTACGC
60354 GTTGCGAATTTG
1 GTTGCGAATTTG
60366 GAAACTGAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
39 4 0.09
40 36 0.82
41 4 0.09
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTGTGTTGCGAATTTAAATTACGC
Found at i:64812 original size:37 final size:36
Alignment explanation
Indices: 64753--64872 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
64743 ATCCCATTAT
* *
64753 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
64789 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
*
64825 CA-TTTTCAAAGAAACATTTACCAAAATTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
64860 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
64873 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:64828 original size:21 final size:20
Alignment explanation
Indices: 64804--64864 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
64794 TTCAAAGAAA
64804 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAA-TTTGAAAAC
*
64825 CATTT-TCAAA---G-AAA-
1 CATTTACCAAATTTGAAAAC
64839 CATTTACCAAAATTTGAAAAC
1 CATTTACC-AAATTTGAAAAC
64860 CATTT
1 CATTT
64865 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (20 bp):
CATTTACCAAATTTGAAAAC
Found at i:68182 original size:15 final size:16
Alignment explanation
Indices: 68152--68184 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
68142 AAAATCTTTC
*
68152 TTTCCCGTTTTGGATT
1 TTTCCCGTTCTGGATT
68168 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
68183 TT
1 TT
68185 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.21, G:0.18, T:0.55
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:69504 original size:34 final size:35
Alignment explanation
Indices: 69365--69508 Score: 202
Period size: 35 Copynumber: 4.1 Consensus size: 35
69355 CCATTATCAT
* * * * *
69365 TTTTC-AACAAACATCTATCAAACTTTAAAAAACTA
1 TTTTCAAATAAACATTTACCAAACTTT-GAAAACCA
*
69400 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 -TTTTCAAATAAACATTTACCAAACTTTGAAAACCA
69436 TTTTCAAATAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAATAAACATTTACCAAACTTTGAAAACCA
69471 TTTTCAAATAAACATTTACCAAAC-TTGAAAACCA
1 TTTTCAAATAAACATTTACCAAACTTTGAAAACCA
69505 TTTT
1 TTTT
69509 AATAATTTCA
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
34 14 0.14
35 58 0.57
36 11 0.11
37 18 0.18
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (35 bp):
TTTTCAAATAAACATTTACCAAACTTTGAAAACCA
Found at i:74692 original size:7 final size:6
Alignment explanation
Indices: 74665--74690 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
74655 ATAATTTCAG
74665 AAGAAA AAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AA
74691 AGCTTAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAA
Done.