Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002722.1 Hibiscus syriacus cultivar Beakdansim tig00005615_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: 86367
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:380 original size:16 final size:17
Alignment explanation
Indices: 341--382 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
331 TTGACCGGTC
* *
341 TGACCCAACCCGACCCT
1 TGACCCGACCCGACCCG
358 TGA-CCGACCCGA-CCG
1 TGACCCGACCCGACCCG
373 TGACCCGACC
1 TGACCCGACC
383 AAGTGACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 14 0.64
17 3 0.14
ACGTcount: A:0.21, C:0.50, G:0.19, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCCG
Found at i:435 original size:29 final size:29
Alignment explanation
Indices: 385--487 Score: 131
Period size: 29 Copynumber: 3.6 Consensus size: 29
375 ACCCGACCAA
385 GTGACATTTT-GG-ATTATTTTTTGAAAAAG
1 GTGACATTTTGGGAATTA--TTTTGAAAAAG
* * * *
414 GTAATATTTTAGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAG
443 GTGACATTTTGGGAA-TATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
471 GTGACATTTTGGGAATT
1 GTGACATTTTGGGAATT
488 TGTTTAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
28 27 0.42
29 31 0.48
30 2 0.03
31 4 0.06
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:496 original size:28 final size:28
Alignment explanation
Indices: 385--496 Score: 129
Period size: 28 Copynumber: 3.9 Consensus size: 28
375 ACCCGACCAA
385 GTGACATTTT-GGATTATTTTTTGAAAAAG
1 GTGACATTTTGGGA--ATTTTTTGAAAAAG
* * * *
414 GTAATATTTTAGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATT-TTTTGAAAAAG
*
443 GTGACATTTTGGGAATATTTTGAAAAAG
1 GTGACATTTTGGGAATTTTTTGAAAAAG
471 GTGACATTTTGGGAATTTGTTT-AAAA
1 GTGACATTTTGGGAATTT-TTTGAAAA
497 TAGTGAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
28 34 0.48
29 34 0.48
30 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.42
Consensus pattern (28 bp):
GTGACATTTTGGGAATTTTTTGAAAAAG
Found at i:7959 original size:28 final size:28
Alignment explanation
Indices: 7917--8069 Score: 125
Period size: 28 Copynumber: 5.4 Consensus size: 28
7907 ACCCGACCCA
*
7917 GTGACATTTTGGGAATT-TTTTGAAAAAG
1 GTGACATTTTAGGAATTATTTT-AAAAAG
*
7945 GTGACATTTTAGGAATTATTTTAAAAAT
1 GTGACATTTTAGGAATTATTTTAAAAAG
* *
7973 GTGACATTTTAGGAA-AATTTTAAAAATA
1 GTGACATTTTAGGAATTATTTTAAAAA-G
* * * *
8001 ATGACATTCT-GGTAATTATTTTTAGAACG
1 GTGACATTTTAGG-AATTA-TTTTAAAAAG
*
8030 GTGATATTTT-GGTAATTATTTTTAATAAAG
1 GTGACATTTTAGG-AATTA-TTTTAA-AAAG
*
8060 GTGAAATTTT
1 GTGACATTTT
8070 TGTAATTTTT
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
27 12 0.12
28 46 0.45
29 26 0.25
30 19 0.18
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (28 bp):
GTGACATTTTAGGAATTATTTTAAAAAG
Found at i:8042 original size:29 final size:30
Alignment explanation
Indices: 8010--8076 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
8000 AATGACATTC
* *
8010 TGGTAATTATTTTT-AGAACGGTGATATTT
1 TGGTAATTATTTTTAAGAAAGGTGAAATTT
*
8039 TGGTAATTATTTTTAATAAAGGTGAAATTT
1 TGGTAATTATTTTTAAGAAAGGTGAAATTT
*
8069 TTGTAATT
1 TGGTAATT
8077 TTTGAATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.49
Consensus pattern (30 bp):
TGGTAATTATTTTTAAGAAAGGTGAAATTT
Found at i:10005 original size:22 final size:23
Alignment explanation
Indices: 9937--10014 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 23
9927 TTTTCATCAA
* *
9937 AATATTAATTATTAAAATATTTAA-
1 AATA-TAA-TATTAATATTTTTAAT
* *
9961 AATATATTATTAATATTTATAAT
1 AATATAATATTAATATTTTTAAT
9984 AATATAATATT-ATATTTTTAAT
1 AATATAATATTAATATTTTTAAT
*
10006 ATTATAATA
1 AATATAATA
10015 AAACAATCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 30 0.65
23 12 0.26
24 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATAATATTAATATTTTTAAT
Found at i:10037 original size:31 final size:29
Alignment explanation
Indices: 9963--10038 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 29
9953 ATATTTAAAA
* *
9963 TATATTATTAATATTTATAATAATATAATAT
1 TATATTA-TAATA-TTATAATAAAACAATAT
*
9994 TATATTTTTAATATTATAATAAAACAATCAAT
1 TATA-TTATAATATTATAATAAAACAAT--AT
10026 TATATTATAATAT
1 TATATTATAATAT
10039 AAGATATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 13 0.34
31 17 0.45
32 8 0.21
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
TATATTATAATATTATAATAAAACAATAT
Found at i:10100 original size:28 final size:25
Alignment explanation
Indices: 10050--10127 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 25
10040 AGATATTATA
10050 TTTTTAT-TTTAATAAATATATAATACAT
1 TTTTTATATTTAAT-AATA-ATAAT--AT
10078 TTTTTATATTTAATAATGAATAATAT
1 TTTTTATATTTAATAAT-AATAATAT
* *
10104 TATTTATATATTAATATTAATAAT
1 TTTTTATAT-TTAATAATAATAAT
10128 CTAATAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 16 0.36
27 7 0.16
28 15 0.33
29 7 0.16
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTTTATATTTAATAATAATAATAT
Found at i:10135 original size:17 final size:16
Alignment explanation
Indices: 10087--10138 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
10077 TTTTTTATAT
*
10087 TTAATAATGAATAATA
1 TTAATAATTAATAATA
* * *
10103 TTATTTATATATTAATA
1 TTAATAAT-TAATAATA
10120 TTAATAATCTAATAATA
1 TTAATAAT-TAATAATA
10137 TT
1 TT
10139 TTAATAAAGA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TTAATAATTAATAATA
Found at i:12954 original size:55 final size:55
Alignment explanation
Indices: 12895--13146 Score: 251
Period size: 55 Copynumber: 4.6 Consensus size: 55
12885 TGATAGGTTC
* * * *
12895 GCTCCCTATTCCTTCAGGGAGTACAGAACTTGAACAATATTCAGCAAACGTGTCT
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
* * * *
12950 GCTCCCTATTCGTTCAGGGAGTATA-AGACTCGGATAATCTTCAGCAAACAAGT-TC-
1 GCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAAC--GTGTCT
* * * * * *
13005 GCTCCCTATTCATTCAGGAAGTATAGAACTCGAGCAATCTTCAATAAACATGTCC
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
* * * *
13060 GCACCCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAACAAA-GGGTCT
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
* * * *
13114 TCTCTCTATTCCATCAGAGAGTATAGAACTCGA
1 GCTCCCTATTCCTTCAGGGAGTATAGAACTCGA
13147 TCTTCATAAA
Statistics
Matches: 163, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
53 1 0.01
54 35 0.21
55 122 0.75
56 3 0.02
57 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCT
Found at i:13272 original size:37 final size:37
Alignment explanation
Indices: 13158--13272 Score: 169
Period size: 37 Copynumber: 3.1 Consensus size: 37
13148 CTTCATAAAA
13158 TGAATTTGCTTCACTACTCTTCCGTGAAGGCTTATAGA-
1 TGAA-TTGCTTCACTACTCTTCCGTGAAGGCTTA-AGAT
* *
13196 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTAATAT
1 TGAATTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
* *
13233 TGAATTGCTTGACTACTCTTTCGTGAAGGCTTAAGAT
1 TGAATTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
13270 TGA
1 TGA
13273 CTTGTTTCGA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
36 2 0.03
37 65 0.93
38 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (37 bp):
TGAATTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
Found at i:14472 original size:47 final size:48
Alignment explanation
Indices: 14416--14540 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 48
14406 TTGAACCCCC
*
14416 TTTTATTTTTCTCTATTTTTCATTTTTCATTTTTC-TCTTTATTCT-TT
1 TTTTATTTTTCTCTATTTTTCATTTTTCATTTTTCAT-TTTATTCTCAT
* * *
14463 TTTTATTTTT-TC-ATTTTTTATTTTCACCATTTTTCATTTTTTTCTCAT
1 TTTTATTTTTCTCTATTTTTCATTTT--TCATTTTTCATTTTATTCTCAT
*
14511 TTTTATTTTTTCTTCATTTTTTTCATTTTT
1 TTTTA-TTTTTC-TC-TATTTTTCATTTTT
14541 TTATTTATTC
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
45 11 0.18
46 2 0.03
47 25 0.40
48 7 0.11
49 5 0.08
51 2 0.03
53 10 0.16
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (48 bp):
TTTTATTTTTCTCTATTTTTCATTTTTCATTTTTCATTTTATTCTCAT
Found at i:14480 original size:9 final size:9
Alignment explanation
Indices: 14438--14546 Score: 53
Period size: 8 Copynumber: 13.1 Consensus size: 9
14428 CTATTTTTCA
14438 TTTTTCATT
1 TTTTTCATT
*
14447 TTTCTC--T
1 TTTTTCATT
*
14454 TTATTC-TT
1 TTTTTCATT
14462 TTTTT-A-T
1 TTTTTCATT
14469 TTTTTCA-T
1 TTTTTCATT
14477 TTTTT-ATT
1 TTTTTCATT
***
14485 TTCACCA-T
1 TTTTTCATT
14493 -TTTTCATTT
1 TTTTTCA-TT
14502 TTTTCTCATT
1 TTTT-TCATT
14512 TTTATT--TT
1 TTT-TTCATT
*
14520 TTCTTCATT
1 TTTTTCATT
14529 TTTTTCATT
1 TTTTTCATT
14538 TTTTT-ATT
1 TTTTTCATT
14546 T
1 T
14547 ATTCTTCAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
7 17 0.22
8 24 0.32
9 22 0.29
10 9 0.12
11 4 0.05
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTCATT
Found at i:14519 original size:16 final size:16
Alignment explanation
Indices: 14416--14531 Score: 68
Period size: 16 Copynumber: 7.2 Consensus size: 16
14406 TTGAACCCCC
14416 TTTTA-TTTTTCTCTAT
1 TTTTATTTTTTCTC-AT
14432 TTTTCA--TTTT-TCAT
1 TTTT-ATTTTTTCTCAT
* *
14446 TTTTCTCTTTATTCT-TT
1 TTTTAT-TTT-TTCTCAT
14463 TTTTA-TTTTT-TCAT
1 TTTTATTTTTTCTCAT
* *
14477 TTTT-TATTTTCACCAT
1 TTTTATTTTTTC-TCAT
14493 TTTTCATTTTTTTCTCAT
1 TTTT-A-TTTTTTCTCAT
14511 TTTTATTTTTTCTTCAT
1 TTTTATTTTTTC-TCAT
14528 TTTT
1 TTTT
14532 TTCATTTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
13 1 0.01
14 17 0.22
15 5 0.06
16 24 0.31
17 17 0.22
18 8 0.10
19 6 0.08
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTTCTCAT
Found at i:14527 original size:28 final size:28
Alignment explanation
Indices: 14495--14554 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
14485 TTCACCATTT
*
14495 TTCATTTTTTTC-TCATTTTTATTTTTTC
1 TTCATTTTTTTCAT-ATTTTTATTTATTC
*
14523 TTCATTTTTTTCATTTTTTTATTTATTC
1 TTCATTTTTTTCATATTTTTATTTATTC
14551 TTCA
1 TTCA
14555 AGTGAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (28 bp):
TTCATTTTTTTCATATTTTTATTTATTC
Found at i:14540 original size:7 final size:7
Alignment explanation
Indices: 14430--14503 Score: 58
Period size: 7 Copynumber: 9.9 Consensus size: 7
14420 ATTTTTCTCT
14430 ATTTTTC
1 ATTTTTC
14437 ATTTTTC
1 ATTTTTC
14444 ATTTTTC
1 ATTTTTC
*
14451 TCTTTATTC
1 -ATTT-TTC
* *
14460 TTTTTTT
1 ATTTTTC
14467 ATTTTTTC
1 A-TTTTTC
*
14475 ATTTTTT
1 ATTTTTC
*
14482 ATTTTCACC
1 ATTTT--TC
14491 ATTTTTC
1 ATTTTTC
14498 ATTTTT
1 ATTTTT
14504 TTCTCATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
7 33 0.62
8 12 0.23
9 8 0.15
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTC
Found at i:14541 original size:38 final size:37
Alignment explanation
Indices: 14431--14542 Score: 108
Period size: 34 Copynumber: 3.1 Consensus size: 37
14421 TTTTTCTCTA
* *
14431 TTTTTCATTTTTCATTTTTCTCTTTATTCTTTTT--TTAT
1 TTTTTCATTTTT-ATTTTT-TCTTCATT-TTTTTCATTTT
* **
14469 TTTTTCATTTTT-TATTTTCACCA--TTTTTCATTTT
1 TTTTTCATTTTTATTTTTTCTTCATTTTTTTCATTTT
*
14503 TTTCTCATTTTTATTTTTTCTTCATTTTTTTCATTTT
1 TTTTTCATTTTTATTTTTTCTTCATTTTTTTCATTTT
14540 TTT
1 TTT
14543 ATTTATTCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
32 5 0.08
34 14 0.23
35 11 0.18
36 4 0.07
37 14 0.23
38 12 0.20
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (37 bp):
TTTTTCATTTTTATTTTTTCTTCATTTTTTTCATTTT
Found at i:18964 original size:22 final size:22
Alignment explanation
Indices: 18933--18975 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18923 CGGAATTGCA
*
18933 CCAACCTGATAGAA-CCAAGGCT
1 CCAACATGAT-GAATCCAAGGCT
18955 CCAACATGATGAATCCAAGGC
1 CCAACATGATGAATCCAAGGC
18976 CTTCCCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (22 bp):
CCAACATGATGAATCCAAGGCT
Found at i:27580 original size:14 final size:14
Alignment explanation
Indices: 27561--27594 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
27551 AAATGTAATT
27561 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
27575 CATTTTTCGGAAAA
1 CATTTTACGGAAAA
*
27589 CGTTTT
1 CATTTT
27595 CCAGAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:27628 original size:20 final size:20
Alignment explanation
Indices: 27591--27629 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
27581 TCGGAAAACG
**
27591 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
27611 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
27630 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:27639 original size:15 final size:15
Alignment explanation
Indices: 27603--27669 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
27593 TTCCAGAAAT
**
27603 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
27618 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
27632 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
* *
27647 GTTATTCAAATTTCA
1 GTAATTCAAATTCCA
27662 GTAATTCA
1 GTAATTCA
27670 TTTTCCAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 12 0.29
15 30 0.71
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:27645 original size:29 final size:30
Alignment explanation
Indices: 27603--27676 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
27593 TTCCAGAAAT
27603 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* *
27632 GTAATTCATTTTCCAGTTATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
27662 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
27677 AAACACCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:28589 original size:29 final size:29
Alignment explanation
Indices: 28557--28613 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
28547 TTGGGATGAT
28557 TTCAAATGAGAATGCCTAGACCTATTTAA
1 TTCAAATGAGAATGCCTAGACCTATTTAA
28586 TTCAAATGAGAATGCCTAGACCTATTTA
1 TTCAAATGAGAATGCCTAGACCTATTTA
28614 TAGTGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (29 bp):
TTCAAATGAGAATGCCTAGACCTATTTAA
Found at i:36364 original size:14 final size:14
Alignment explanation
Indices: 36336--36377 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
36326 TGGACAATTA
*
36336 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
36351 TAATAAAAATAAAT
1 AAATAAAAATAAAT
36365 AAATAAAAATAAA
1 AAATAAAAATAAA
36378 CAACAACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:36679 original size:35 final size:36
Alignment explanation
Indices: 36603--36753 Score: 151
Period size: 36 Copynumber: 4.1 Consensus size: 36
36593 TTTTAAAAAT
* **
36603 TATATTTATTTTAAAAATGTTTTTTAAAACCGTATAA
1 TATATTTATTTTAAAAATG-TTTTAAAAACTATATAA
* * *
36640 TATATTT-TCTTAAAAACGTTTTAAAAACTATATAT
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
* *
36675 TATATTTATTTTCAAAGTGTTTTAAAAACTATATAA
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
** * * *
36711 TATATAAATGTTTCAAATATGTTTTCAAAACTATATTA
1 TATATTTAT-TTT-AAAAATGTTTTAAAAACTATATAA
36749 TATAT
1 TATAT
36754 ATATGTATAT
Statistics
Matches: 93, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
35 20 0.22
36 39 0.42
37 10 0.11
38 24 0.26
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
Found at i:36743 original size:38 final size:37
Alignment explanation
Indices: 36544--36759 Score: 148
Period size: 36 Copynumber: 5.9 Consensus size: 37
36534 TAAGTTTTTT
* *
36544 AAAATGATTTCAAAACTATATAATATATATATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATG-TTTC
* *
36582 AAAATGTTTCTTTTTAAAA--AT-T-ATAT-T-TAT-TTTA
1 AAAATG----TTTTAAAAACTATATAATATATATATGTTTC
* ** *
36616 AAAATGTTTTTTAAAACCGTATAATATAT-T-T-TCTTA
1 AAAATG-TTTTAAAAACTATATAATATATATATGT-TTC
* * *
36652 AAAACGTTTTAAAAACTATATATTATATTTAT-TTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* *
36688 AAAGTGTTTTAAAAACTATATAATATATAAATGTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* *
36725 AAATATGTTTTCAAAACTATATTATATATATATGT
1 AAA-ATGTTTTAAAAACTATATAATATATATATGT
36760 ATATATAAAA
Statistics
Matches: 144, Mismatches: 20, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
31 9 0.06
33 1 0.01
34 10 0.07
35 24 0.17
36 43 0.30
37 10 0.07
38 37 0.26
39 1 0.01
40 2 0.01
42 7 0.05
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATAATATATATATGTTTC
Found at i:37830 original size:163 final size:164
Alignment explanation
Indices: 37333--37839 Score: 707
Period size: 163 Copynumber: 3.1 Consensus size: 164
37323 TGACAAATAG
* * * * * *
37333 CCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAAC-TCGG
1 CCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAGG
* * *
37397 GAGTTTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAG
66 G-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAG
37462 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
130 CGTAGTCGAACTCGAAGGTCTTTGG-TGGCAGATAA
* * * ** * **
37498 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCGAAGCTGAGCGTAATCGAACTCGGG
1 CCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAGG
37563 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTA-TGCAAATGATGTGCCTTGGAGCTGAG
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA-TACTGCAAATGATGTGCCTTGGAGCTGAG
* **
37627 CGTAGTCGAACTC-AAGGTCTTTGCTAACAGATAA
130 CGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAA
* * * *
37661 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAGG
*
37726 GGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
* *
37791 GTAGTCGAACTCGAAGGTC-TTGGTGGCAGGTAG
131 GTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAA
*
37824 CCCTTCTGGCCTTGAG
1 CCCTTCTTGCCTTGAG
37840 CTAAGCTGCA
Statistics
Matches: 300, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
162 2 0.01
163 158 0.53
164 16 0.05
165 120 0.40
166 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (164 bp):
CCCTTCTTGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAGG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTGGTGGCAGATAA
Found at i:41217 original size:19 final size:19
Alignment explanation
Indices: 41193--41238 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
41183 AGTTAATGTG
41193 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
41212 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
41231 AATGCAAA
1 AATGCAAA
41239 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:44361 original size:14 final size:14
Alignment explanation
Indices: 44333--44374 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
44323 TGGACAATTA
*
44333 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
44348 TAATAAAAATAAAT
1 AAATAAAAATAAAT
44362 AAATAAAAATAAA
1 AAATAAAAATAAA
44375 CAACAACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:44676 original size:35 final size:36
Alignment explanation
Indices: 44600--44750 Score: 151
Period size: 36 Copynumber: 4.1 Consensus size: 36
44590 TTTTAAAAAT
* **
44600 TATATTTATTTTAAAAATGTTTTTTAAAACCGTATAA
1 TATATTTATTTTAAAAATG-TTTTAAAAACTATATAA
* * *
44637 TATATTT-TCTTAAAAACGTTTTAAAAACTATATAT
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
* *
44672 TATATTTATTTTCAAAGTGTTTTAAAAACTATATAA
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
** * * *
44708 TATATAAATGTTTCAAATATGTTTTCAAAACTATATTA
1 TATATTTAT-TTT-AAAAATGTTTTAAAAACTATATAA
44746 TATAT
1 TATAT
44751 ATATGTATAT
Statistics
Matches: 93, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
35 20 0.22
36 39 0.42
37 10 0.11
38 24 0.26
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
Found at i:44740 original size:38 final size:37
Alignment explanation
Indices: 44541--44756 Score: 148
Period size: 36 Copynumber: 5.9 Consensus size: 37
44531 TAAGTTTTTT
* *
44541 AAAATGATTTCAAAACTATATAATATATATATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATG-TTTC
* *
44579 AAAATGTTTCTTTTTAAAA--AT-T-ATAT-T-TAT-TTTA
1 AAAATG----TTTTAAAAACTATATAATATATATATGTTTC
* ** *
44613 AAAATGTTTTTTAAAACCGTATAATATAT-T-T-TCTTA
1 AAAATG-TTTTAAAAACTATATAATATATATATGT-TTC
* * *
44649 AAAACGTTTTAAAAACTATATATTATATTTAT-TTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* *
44685 AAAGTGTTTTAAAAACTATATAATATATAAATGTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATGTTTC
* *
44722 AAATATGTTTTCAAAACTATATTATATATATATGT
1 AAA-ATGTTTTAAAAACTATATAATATATATATGT
44757 ATATATAAAA
Statistics
Matches: 144, Mismatches: 20, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
31 9 0.06
33 1 0.01
34 10 0.07
35 24 0.17
36 43 0.30
37 10 0.07
38 37 0.26
39 1 0.01
40 2 0.01
42 7 0.05
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATAATATATATATGTTTC
Found at i:46181 original size:20 final size:20
Alignment explanation
Indices: 46158--46206 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
46148 ACAGGAAAAA
*
46158 GAAAATGAAGTAAAAGAAAT
1 GAAAATGAAGGAAAAGAAAT
* *
46178 GAAAATTAAGGAAATGAAAT
1 GAAAATGAAGGAAAAGAAAT
*
46198 GAATATGAA
1 GAAAATGAA
46207 TATGTTGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.18
Consensus pattern (20 bp):
GAAAATGAAGGAAAAGAAAT
Found at i:48198 original size:51 final size:51
Alignment explanation
Indices: 48116--48230 Score: 176
Period size: 51 Copynumber: 2.3 Consensus size: 51
48106 GTAACTACTA
* * * *
48116 AATAAAATAATAATAAACTAAAGATACTATTTTGATTCTATCCTAATTCTT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
* *
48167 AATAAAATAATAATAAACTAAAGGTAATATTTTAACTCTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
48218 AATAAAATAATAA
1 AATAAAATAATAA
48231 ATTTAATCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAGATAATATTTTAACTCTATCCTAATTCCT
Found at i:51690 original size:41 final size:41
Alignment explanation
Indices: 51645--51722 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
51635 ACGTTATAGT
**
51645 CGAAGTTCGTGTTGCGATTCATTCCAAATCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAAATCGTTGCGACAGG
*
51686 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGA
1 CGAAGTTCGCATTGCGATTCATTCCAAATCGTTGCGA
51723 TAGTCCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (41 bp):
CGAAGTTCGCATTGCGATTCATTCCAAATCGTTGCGACAGG
Found at i:51722 original size:20 final size:20
Alignment explanation
Indices: 51655--51723 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
51645 CGAAGTTCGT
*
51655 GTTGCGATTCATTCCAAATC
1 GTTGCGATTCATTCCAATTC
** *
51675 GTTGCGA--CAGGCGAAGTTC
1 GTTGCGATTCATTCCAA-TTC
51694 GCATTGCGATTCATTCCAATTC
1 G--TTGCGATTCATTCCAATTC
51716 GTTGCGAT
1 GTTGCGAT
51724 AGTCCAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
18 5 0.14
19 3 0.08
20 14 0.38
21 6 0.16
22 4 0.11
23 5 0.14
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTGCGATTCATTCCAATTC
Found at i:52518 original size:6 final size:6
Alignment explanation
Indices: 52507--52533 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52497 TCTCGTCCCG
52507 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
52534 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:52667 original size:41 final size:41
Alignment explanation
Indices: 52610--52714 Score: 174
Period size: 41 Copynumber: 2.6 Consensus size: 41
52600 CAATATTTGG
52610 AATGAATCGCAATGCGAACTTCGCCTGTCGCAACAAATTGA
1 AATGAATCGCAATGCGAACTTCGCCTGTCGCAACAAATTGA
* * *
52651 AATGAATCGCAATGCGAACTTCGCCTGTCGCAACGATTTGG
1 AATGAATCGCAATGCGAACTTCGCCTGTCGCAACAAATTGA
*
52692 AATGAATCGCAACGCGAACTTCG
1 AATGAATCGCAATGCGAACTTCG
52715 ACTATCGCGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (41 bp):
AATGAATCGCAATGCGAACTTCGCCTGTCGCAACAAATTGA
Found at i:53557 original size:22 final size:21
Alignment explanation
Indices: 53519--53560 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
53509 TCATTAAAAA
* *
53519 TAAATAAATTTATTATTATTT
1 TAAATAAAATTAATATTATTT
53540 TAAATAATAATTAATATTATT
1 TAAATAA-AATTAATATTATT
53561 ATAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATAAAATTAATATTATTT
Found at i:55773 original size:2 final size:2
Alignment explanation
Indices: 55766--55793 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55756 ATAGAGATGG
55766 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
55794 TCTCTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55962 original size:65 final size:65
Alignment explanation
Indices: 55853--55980 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 65
55843 AGATAATTAA
* * * *
55853 AAATCAGATCTTTCTGTAAGAACAAAGACGAGTCCGAAAGGTTTTGTTTTTAGATTTAAGCTTAC
1 AAATCAGATCTATATGTAAGAACAAAGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTTAC
* *
55918 AAATTAGATCTATATGTAAGAACAAGGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTT
1 AAATCAGATCTATATGTAAGAACAAAGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTT
55981 GAGCTTGCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (65 bp):
AAATCAGATCTATATGTAAGAACAAAGACGAGTCCGAAAGGTTTTCTTTTTAGACTTAAGCTTAC
Found at i:59732 original size:18 final size:18
Alignment explanation
Indices: 59709--59750 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
59699 TATTTCTGAG
59709 GGAATTGGAATCTGTAAA
1 GGAATTGGAATCTGTAAA
*
59727 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTAAA
59745 GGAATT
1 GGAATT
59751 AAAAATCTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTAAA
Found at i:59759 original size:19 final size:18
Alignment explanation
Indices: 59717--59759 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
59707 AGGGAATTGG
**
59717 AATCTGTAAAGGAATTGG
1 AATCTGTAAAGGAATTAA
*
59735 AATCTGTGAAGGAATTAAA
1 AATCTGTAAAGGAATT-AA
59754 AATCTG
1 AATCTG
59760 AATCTGAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (18 bp):
AATCTGTAAAGGAATTAA
Found at i:61931 original size:5 final size:5
Alignment explanation
Indices: 61921--61953 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
61911 TAGTAATGTA
61921 TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
61954 GATCCGACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:66841 original size:32 final size:32
Alignment explanation
Indices: 66777--66841 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
66767 TGAGCACGAT
* ****
66777 ATCCTTCATCGTGAAGTTGAAATCGTGGTCGA
1 ATCCTTCATCGTGAAGTTAAAATCAAACTCGA
*
66809 ATCCTTCATCTTGAAGTTAAAATCAAACTCGA
1 ATCCTTCATCGTGAAGTTAAAATCAAACTCGA
66841 A
1 A
66842 ATCTGAACTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (32 bp):
ATCCTTCATCGTGAAGTTAAAATCAAACTCGA
Found at i:70872 original size:5 final size:5
Alignment explanation
Indices: 70863--71071 Score: 328
Period size: 5 Copynumber: 41.8 Consensus size: 5
70853 ATATAAATAT
* * * * * * * * * *
70863 ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT ATAGT TTAGC
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
70913 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
70963 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
71013 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
71063 ATAGC ATAG
1 ATAGC ATAG
71072 TAGACGGGCT
Statistics
Matches: 201, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 201 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (5 bp):
ATAGC
Found at i:71179 original size:12 final size:11
Alignment explanation
Indices: 71152--71233 Score: 67
Period size: 12 Copynumber: 6.9 Consensus size: 11
71142 AATAAAACAA
*
71152 AAATAAAATAT
1 AAATAATATAT
*
71163 TAATAATTATAT
1 AAATAA-TATAT
71175 AAATAAATATAT
1 AAAT-AATATAT
71187 ATAATATACTATAT
1 A-AATA-A-TATAT
71201 AAAT-ATATAT
1 AAATAATATAT
*
71211 ATACTAATATAT
1 A-AATAATATAT
71223 AATATAATATA
1 AA-ATAATATA
71234 ATATAATACA
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
10 6 0.10
11 9 0.16
12 28 0.48
13 9 0.16
14 6 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATAATATAT
Found at i:71182 original size:22 final size:23
Alignment explanation
Indices: 71152--71241 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 23
71142 AATAAAACAA
71152 AAATAAAATATTA-ATAATTATA-T
1 AAAT-AAATATTATATAA-TATACT
71175 AAATAAATA-TATATAATATACT
1 AAATAAATATTATATAATATACT
* *
71197 ATATAAATATATATATACTAATA-T
1 AAATAAATAT-TATATAAT-ATACT
*
71221 ATAATATAATATAATATAATA
1 A-AATA-AATATTATATAATA
71242 CAGTACAGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
21 6 0.11
22 18 0.33
23 4 0.07
24 10 0.18
25 12 0.22
26 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATAAATATTATATAATATACT
Found at i:71186 original size:2 final size:2
Alignment explanation
Indices: 71170--71238 Score: 58
Period size: 2 Copynumber: 36.0 Consensus size: 2
71160 TATTAATAAT
* * *
71170 TA TA TA AA TA AA TA TA TA TA -A TA TA CTA TA TA AA 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
71212 TA CTA -A TA TA TA -A TA TA -A TA TA -A TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71239 ATACAGTACA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
1 5 0.09
2 45 0.83
3 4 0.07
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:71190 original size:10 final size:11
Alignment explanation
Indices: 71165--71238 Score: 82
Period size: 10 Copynumber: 6.7 Consensus size: 11
71155 TAAAATATTA
*
71165 ATAATTATATAA
1 ATAA-TATATAT
71177 ATAA-ATATAT
1 ATAATATATAT
71187 ATAATATACTAT
1 ATAATATA-TAT
71199 ATAAATATATAT
1 AT-AATATATAT
*
71211 ATACTA-ATAT
1 ATAATATATAT
71221 ATAATATA-AT
1 ATAATATATAT
71231 ATAATATA
1 ATAATATA
71239 ATACAGTACA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
10 28 0.51
11 7 0.13
12 14 0.25
13 6 0.11
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAATATATAT
Found at i:71208 original size:34 final size:34
Alignment explanation
Indices: 71165--71233 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
71155 TAAAATATTA
* *
71165 ATAATTATATAAATAA-ATATATATAATATACTAT
1 ATAAATATATAAATAATA-ATATATAATATAATAT
* *
71199 ATAAATATATATATACTAATATATAATATAATAT
1 ATAAATATATAAATAATAATATATAATATAATAT
71233 A
1 A
71234 ATATAATACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (34 bp):
ATAAATATATAAATAATAATATATAATATAATAT
Found at i:71594 original size:5 final size:5
Alignment explanation
Indices: 71223--71574 Score: 582
Period size: 5 Copynumber: 70.8 Consensus size: 5
71213 ACTAATATAT
* * * * * * * * *
71223 AATAT AATAT AATAT AATAC AGTAC AGTAC AGTAC AGTAC AGTAC AGTAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
* *
71273 AGTAC AATAC AATAC AGTAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
71323 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
71373 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
71423 AATAC AATAC AATAC -A-AC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
71471 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
*
71521 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAT
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC
71571 AATA
1 AATA
71575 TGACAACTAT
Statistics
Matches: 339, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
3 2 0.01
4 2 0.01
5 335 0.99
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.21
Consensus pattern (5 bp):
AATAC
Found at i:76177 original size:24 final size:24
Alignment explanation
Indices: 76133--76178 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
76123 CTTTCAACTT
*
76133 CTTTTTCTTTGTATTTTTTCTTTC
1 CTTTTTCTTTGTATTTCTTCTTTC
76157 CTTTTTCTTTTGT-TTTCTTCTT
1 CTTTTTC-TTTGTATTTCTTCTT
76179 GAGTGCTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.76
Consensus pattern (24 bp):
CTTTTTCTTTGTATTTCTTCTTTC
Found at i:77652 original size:43 final size:42
Alignment explanation
Indices: 77455--77654 Score: 199
Period size: 42 Copynumber: 4.7 Consensus size: 42
77445 GAGTTTGTGA
* * * *
77455 TGAAACATGCCACTATATA-CAT-ACTCAATATCGACGTTTGGG
1 TGAAA-ATGCCACTATATATCATGACT-ATTAGCGGCGTTTGAG
* *
77497 TGAAAATGCCACTAAATACCATGACTATTAGCGGCGTTTGAG
1 TGAAAATGCCACTATATATCATGACTATTAGCGGCGTTTGAG
* * *
77539 TGAAAAATGTCATTATA-ATCATGACTATTAGCGACGTTTGAG
1 TG-AAAATGCCACTATATATCATGACTATTAGCGGCGTTTGAG
* * * *
77581 TGAAAATACTACTATATATCAAGACTATTAGCGGCGTTTGTG
1 TGAAAATGCCACTATATATCATGACTATTAGCGGCGTTTGAG
* * *
77623 TAGGAAACGCCACTATATATCATGGCTATTAG
1 T-GAAAATGCCACTATATATCATGACTATTAG
77655 TGGTGTTTTC
Statistics
Matches: 130, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
41 22 0.17
42 70 0.54
43 38 0.29
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (42 bp):
TGAAAATGCCACTATATATCATGACTATTAGCGGCGTTTGAG
Found at i:79861 original size:20 final size:20
Alignment explanation
Indices: 79832--79869 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
79822 TTTCAAAGTG
79832 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
79852 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
79870 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:85776 original size:24 final size:24
Alignment explanation
Indices: 85744--85823 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 24
85734 ACACTTAACA
85744 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* * *
85768 GTGCATCGATTCAT-CATATGAA-
1 GTGCATCGATGCATCCCTTTGAAT
*
85790 --GCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
85811 GTGCATCGATGCA
1 GTGCATCGATGCA
85824 CAGGGTCGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
20 13 0.30
21 1 0.02
23 16 0.37
24 13 0.30
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Done.