Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007932.1 Hibiscus syriacus cultivar Beakdansim tig00110342_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: 1116633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1087723 original size:20 final size:20
Alignment explanation
Indices: 1087698--1087791 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1087688 AATTGGGAAA
*
1087698 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1087718 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1087739 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1087759 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1087779 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1087792 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1088350 original size:19 final size:19
Alignment explanation
Indices: 1088312--1088378 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1088302 TTCGAGAATG
*
1088312 AAAATCGCAACGTGGAAATA
1 AAAATCGCAACG-CGAAATA
**
1088332 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1088351 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1088370 AAAATCGCA
1 AAAATCGCA
1088379 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1088444 original size:33 final size:34
Alignment explanation
Indices: 1088396--1088461 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
1088386 TTTCATTTCG
**
1088396 CGTTGCGATTTTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
1088429 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1088462 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:1088463 original size:20 final size:19
Alignment explanation
Indices: 1088374--1088486 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
1088364 GAAACCAAAA
*
1088374 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1088393 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1088412 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1088426 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1088445 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1088465 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1088485 TC
1 TC
1088487 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 32 0.41
20 31 0.39
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1090637 original size:21 final size:21
Alignment explanation
Indices: 1090613--1090679 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1090603 TCATTCCTCG
1090613 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1090634 AGAGGCCACTATCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1090655 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1090676 AGAG
1 AGAG
1090680 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1090637 original size:42 final size:41
Alignment explanation
Indices: 1090566--1090679 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
1090556 GCCTGCCATC
* * * * * *
1090566 CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-T
1090608 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
1 CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
* * *
1090649 CGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1090680 CCCGATTCAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
41 4 0.07
42 55 0.90
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (41 bp):
CCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCAT
Found at i:1092066 original size:14 final size:14
Alignment explanation
Indices: 1092030--1092066 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1092020 TATTGTTTAA
1092030 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
1092044 GTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
1092058 TTGAATTGT
1 TTGATTTGT
1092067 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1092210 original size:14 final size:14
Alignment explanation
Indices: 1092191--1092247 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1092181 GCGAAATGAA
1092191 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1092205 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1092224 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1092238 AATCGCAACG
1 AATCGCAACG
1092248 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1092218 original size:33 final size:33
Alignment explanation
Indices: 1092173--1092262 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
1092163 AAAAAGTACT
*
1092173 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1092206 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
1092239 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
1092263 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1092232 original size:19 final size:19
Alignment explanation
Indices: 1092173--1092233 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1092163 AAAAAGTACT
*
1092173 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1092192 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1092206 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1092225 ATCGCAACG
1 ATCGCAACG
1092234 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1092280 original size:19 final size:19
Alignment explanation
Indices: 1092258--1092408 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
1092248 CGAAATTAAA
1092258 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1092277 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1092292 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1092310 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
1092324 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1092343 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1092358 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1092376 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1092395 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1092409 AGACATTAAG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 29 0.30
16 6 0.06
17 6 0.06
19 46 0.47
20 10 0.10
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1092304 original size:33 final size:32
Alignment explanation
Indices: 1092262--1092388 Score: 202
Period size: 33 Copynumber: 3.9 Consensus size: 32
1092252 ATTAAATTCG
1092262 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
1092295 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1092328 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1092361 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1092389 AGTAATTTCC
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
31 3 0.03
33 82 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1092338 original size:66 final size:66
Alignment explanation
Indices: 1092255--1092387 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
1092245 ACGCGAAATT
1092255 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1092320 G
66 G
*
1092321 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1092386 G
66 G
1092387 A
1 A
1092388 TAGTAATTTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1094697 original size:12 final size:12
Alignment explanation
Indices: 1094680--1094704 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1094670 TCTTCGGGGA
1094680 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1094692 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1094704 C
1 C
1094705 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1094913 original size:24 final size:24
Alignment explanation
Indices: 1094879--1094932 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1094869 CTGAAACATC
*
1094879 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1094903 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1094927 ATCAAA
1 ATCAAA
1094933 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1095692 original size:20 final size:20
Alignment explanation
Indices: 1095662--1095768 Score: 135
Period size: 20 Copynumber: 5.3 Consensus size: 20
1095652 GATTCTATAT
*
1095662 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1095682 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1095702 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1095722 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1095743 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1095763 TATCGC
1 TATCGC
1095769 ATTACGATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.04
20 57 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1095693 original size:41 final size:40
Alignment explanation
Indices: 1095641--1095777 Score: 139
Period size: 41 Copynumber: 3.4 Consensus size: 40
1095631 GAACTTTGAA
*
1095641 AATCGCATTGCGATTCTATATTATCTCGTTGCGAAAGTCAG
1 AATCGCATTGCGATTCT-TATTATCGCGTTGCGAAAGTCAG
* *** * *
1095682 AATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAG
1 AATCGCATTGCGATTCTTATTATCGCGTTGCGAAAGTCAG
* * * *
1095722 TATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATTCT-TATTATCGCGTTGCGAAAGTCAG
* *
1095763 TATCGCATTACGATT
1 AATCGCATTGCGATT
1095778 TTACCAATTC
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
40 33 0.42
41 46 0.58
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (40 bp):
AATCGCATTGCGATTCTTATTATCGCGTTGCGAAAGTCAG
Found at i:1095789 original size:21 final size:20
Alignment explanation
Indices: 1095765--1095812 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1095755 ATAGTCAGTA
1095765 TCGCATTACGATTTTACCAAT
1 TCGCATTACGA-TTTACCAAT
* * **
1095786 TCGCGTTGCGATTTACTTAT
1 TCGCATTACGATTTACCAAT
1095806 TCGCATT
1 TCGCATT
1095813 GCGAATTGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (20 bp):
TCGCATTACGATTTACCAAT
Found at i:1095790 original size:41 final size:41
Alignment explanation
Indices: 1095702--1095797 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
1095692 CGAAAGTCAG
* * * ** *
1095702 TATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAA
1095743 TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTACCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTT-CCAA
1095785 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1095798 TTACTTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTACGATTTTCCAA
Found at i:1095887 original size:21 final size:21
Alignment explanation
Indices: 1095847--1095887 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1095837 ACTGTAGACC
**
1095847 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1095868 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1095888 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1100426 original size:22 final size:22
Alignment explanation
Indices: 1100355--1100426 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1100345 AACCATCATC
*
1100355 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1100377 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
1100396 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1100418 ATCGCAACG
1 ATCGCAACG
1100427 CGAAATGCAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1100782 original size:30 final size:30
Alignment explanation
Indices: 1100746--1100816 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1100736 TTGGGCCATT
**
1100746 GCTAACGTGCGTTGTGCCCCAAAGAGGTAC
1 GCTAACGTGCACTGTGCCCCAAAGAGGTAC
1100776 GCTAACGTGCACTGTGCCCCAAAGAGGTAC
1 GCTAACGTGCACTGTGCCCCAAAGAGGTAC
1100806 GCTAACGTGCA
1 GCTAACGTGCA
1100817 TCGTTTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (30 bp):
GCTAACGTGCACTGTGCCCCAAAGAGGTAC
Found at i:1107546 original size:46 final size:44
Alignment explanation
Indices: 1107451--1107549 Score: 128
Period size: 47 Copynumber: 2.2 Consensus size: 44
1107441 ATAGCCCCAT
** * *
1107451 TATATATATATATTGAAAACACGTAGTTTTGAAATATATATATA
1 TATATATATATATTGAAAACAAATAATTTTGAAATATATACATA
1107495 TATATATATATATTAGAAAACATAAATAATTTTGAAATATATACATA
1 TATATATATATATT-GAAAAC--AAATAATTTTGAAATATATACATA
1107542 -ATATATAT
1 TATATATAT
1107550 TTTATAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 14 0.29
45 6 0.12
46 8 0.17
47 20 0.42
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (44 bp):
TATATATATATATTGAAAACAAATAATTTTGAAATATATACATA
Found at i:1107563 original size:18 final size:18
Alignment explanation
Indices: 1107542--1107593 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
1107532 TATATACATA
1107542 ATATATATTTTATAAAAT
1 ATATATATTTTATAAAAT
* **
1107560 ATATAGTTTTATTATATTAT
1 ATATA-TATT-TTATAAAAT
*
1107580 ATATATATATTATA
1 ATATATATTTTATA
1107594 TTATAGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 10 0.37
19 5 0.19
20 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATATATTTTATAAAAT
Found at i:1107679 original size:19 final size:19
Alignment explanation
Indices: 1107652--1107700 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1107642 TTTTCATTTC
*
1107652 AGGTTCAAGGTCAAGTTGA
1 AGGTCCAAGGTCAAGTTGA
* *
1107671 AGGTCCAA-GTCCAGTTTA
1 AGGTCCAAGGTCAAGTTGA
*
1107689 TGGTCCAAGGTC
1 AGGTCCAAGGTC
1107701 CAATTCGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (19 bp):
AGGTCCAAGGTCAAGTTGA
Found at i:1107714 original size:23 final size:25
Alignment explanation
Indices: 1107670--1107715 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1107660 GGTCAAGTTG
1107670 AAGGTCCAAGTCCAGTTTATGGTCC
1 AAGGTCCAAGTCCAGTTTATGGTCC
*
1107695 AAGGTCCAA-TTC-GTTTATGGT
1 AAGGTCCAAGTCCAGTTTATGGT
1107716 TCAAAGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 2 0.10
25 9 0.45
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (25 bp):
AAGGTCCAAGTCCAGTTTATGGTCC
Found at i:1111022 original size:12 final size:12
Alignment explanation
Indices: 1111005--1111055 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1110995 CTTCAAGAGG
1111005 TTTTATATTTAA
1 TTTTATATTTAA
1111017 TTTTATA-TTATA
1 TTTTATATTTA-A
*
1111029 TTTGAT-TTTAA
1 TTTTATATTTAA
1111040 TTTTA-ATATTAA
1 TTTTATAT-TTAA
1111052 TTTT
1 TTTT
1111056 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1111110 original size:63 final size:64
Alignment explanation
Indices: 1111017--1111164 Score: 241
Period size: 63 Copynumber: 2.4 Consensus size: 64
1111007 TTATATTTAA
* *
1111017 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATT-ATT
1 TTTTAATATTATATTATAGATATTAATATTAATATTAATTTTTTAAATAAATTAAATATTAATT
1111077 TTTTAATATTATATTATAGATATTAATATTAATATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATATTAATATTAATTTTTTAAATAAATTAAATATTAATT
*
1111141 TTTTAATATTATATTATATATATT
1 TTTTAATATTATATTATAGATATT
1111165 TAATTTTATA
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
60 4 0.05
61 10 0.12
62 1 0.01
63 40 0.49
64 26 0.32
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (64 bp):
TTTTAATATTATATTATAGATATTAATATTAATATTAATTTTTTAAATAAATTAAATATTAATT
Found at i:1111159 original size:24 final size:25
Alignment explanation
Indices: 1111079--1111161 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 25
1111069 ATATTATTTT
* *
1111079 TTAATATT-ATATTATAGATATTAATA
1 TTAATATTAATTTTTTA-ATATT-ATA
*
1111105 TTAATATTAATTTTTTAA-A-TAAA
1 TTAATATTAATTTTTTAATATTATA
1111128 TTAAATATTAATTTTTTAATATTATA
1 TT-AATATTAATTTTTTAATATTATA
1111154 TTATATAT
1 TTA-ATAT
1111162 ATTTAATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
23 4 0.08
24 17 0.35
25 3 0.06
26 18 0.38
27 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TTAATATTAATTTTTTAATATTATA
Found at i:1111165 original size:24 final size:26
Alignment explanation
Indices: 1111096--1111161 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 26
1111086 TATATTATAG
1111096 ATATTAATATTA-ATATTAATTTTTTA
1 ATATT-ATATTATATATTAATTTTTTA
* *
1111122 A-A-TAAATTAAATATTAATTTTTTA
1 ATATTATATTATATATTAATTTTTTA
1111146 ATATTATATTATATAT
1 ATATTATATTATATAT
1111162 ATTTAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 5 0.15
24 16 0.47
25 2 0.06
26 11 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATATTATATTATATATTAATTTTTTA
Found at i:1111166 original size:21 final size:21
Alignment explanation
Indices: 1111078--1111181 Score: 74
Period size: 21 Copynumber: 4.9 Consensus size: 21
1111068 AATATTATTT
*
1111078 TTTAATATTATATTATAGATA
1 TTTAATATTATATTATATATA
*
1111099 -TTAATATTAATATTA-AT-TT
1 TTTAATATT-ATATTATATATA
*
1111118 TTTAAATAAATTAAATATTA-AT-TT
1 TTT-AAT--ATT--ATATTATATATA
1111142 TTTAATATTATATTATATATA
1 TTTAATATTATATTATATATA
* *
1111163 TTTAATTTTATATCATATA
1 TTTAATATTATATTATATA
1111182 AATTATTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
19 7 0.10
20 13 0.19
21 30 0.43
23 6 0.09
24 14 0.20
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTAATATTATATTATATATA
Found at i:1111174 original size:14 final size:15
Alignment explanation
Indices: 1111132--1111198 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 15
1111122 AATAAATTAA
*
1111132 ATATTAATTTTTTA-
1 ATATTAATTTTATAT
*
1111146 ATATT-ATATTATAT
1 ATATTAATTTTATAT
1111160 ATATTTAATTTTATAT
1 ATA-TTAATTTTATAT
* *
1111176 CATATAAATTATTTTAT
1 -ATATTAATT-TTATAT
1111193 ATATTA
1 ATATTA
1111199 TTAAAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.14
14 8 0.19
15 2 0.05
16 18 0.43
17 8 0.19
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTAATTTTATAT
Found at i:1111227 original size:20 final size:19
Alignment explanation
Indices: 1111167--1111228 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1111157 TATATATTTA
*
1111167 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1111186 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1111204 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1111224 ATTTT
1 ATTTT
1111229 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1111726 original size:31 final size:31
Alignment explanation
Indices: 1111688--1111747 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1111678 TAGTTGTATG
* * *
1111688 AATTATTTATATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
1111719 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
1111748 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Done.