Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009711.1 Kokia drynarioides strain JFW-HI SEQ_124430, 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: 37051
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3491 original size:36 final size:35
Alignment explanation
Indices: 3445--3513 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 35
3435 CCTAAATTCT
3445 AAGAGATTGCTTACAAGTCAAGTTAAACAAAATCA
1 AAGAGATTGCTTACAAGTCAAGTTAAACAAAATCA
*
3480 AAGAGAATTGCTTGCAAGTCAAGTTAAACAAAAT
1 AAGAG-ATTGCTTACAAGTCAAGTTAAACAAAAT
3514 ATATTATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 5 0.16
36 27 0.84
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (35 bp):
AAGAGATTGCTTACAAGTCAAGTTAAACAAAATCA
Found at i:3565 original size:24 final size:24
Alignment explanation
Indices: 3532--3588 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
3522 TTTCTATAAG
* *
3532 ATTTAGTAGCATAATATATTTAAC
1 ATTTATTAGCATAATAAATTTAAC
*
3556 ATTTATTAGCATAATAAATTTTAC
1 ATTTATTAGCATAATAAATTTAAC
*
3580 ATTAATTAG
1 ATTTATTAG
3589 AATTAGGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (24 bp):
ATTTATTAGCATAATAAATTTAAC
Found at i:6401 original size:2 final size:2
Alignment explanation
Indices: 6394--6422 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6384 GTCAACATGC
6394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6423 ATGATCTCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6804 original size:18 final size:18
Alignment explanation
Indices: 6765--6807 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6755 GAATAGATTT
*
6765 TTAATTAAATAATTTTAT
1 TTAATTAAATAATTTTAA
6783 TTAATTAAA-AATTTTAAA
1 TTAATTAAATAATTTT-AA
6801 TTAATTA
1 TTAATTA
6808 CACATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTAAATAATTTTAA
Found at i:8510 original size:27 final size:27
Alignment explanation
Indices: 8455--8510 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
8445 GACGAATCCT
* *
8455 ATTTTTGTAATCGAATTCAATTTGAAA
1 ATTTTTGTAATCGAATTCAAATTAAAA
8482 ATTTTTCG-AATCGAA-TCAAATTAACAA
1 ATTTTT-GTAATCGAATTCAAATTAA-AA
8509 AT
1 AT
8511 CCTATTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.28
27 17 0.68
28 1 0.04
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (27 bp):
ATTTTTGTAATCGAATTCAAATTAAAA
Found at i:8873 original size:21 final size:19
Alignment explanation
Indices: 8844--8882 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
8834 AAATAACTCG
8844 AATTATTTATTTCAAATTTTC
1 AATTATTTA--TCAAATTTTC
*
8865 AATTTTTTATCAAATTTT
1 AATTATTTATCAAATTTT
8883 TCGAATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTATTTATCAAATTTTC
Found at i:10444 original size:32 final size:32
Alignment explanation
Indices: 10408--10473 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
10398 ACGAGCAGGA
10408 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
1 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
10440 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
1 TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
10472 TT
1 TT
10474 CGTATAAGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (32 bp):
TTTTCCTTAGGACAAGGGCTAATTTGATTTGT
Found at i:13430 original size:33 final size:32
Alignment explanation
Indices: 13385--13484 Score: 100
Period size: 33 Copynumber: 3.1 Consensus size: 32
13375 AATTATAAAT
13385 ATTTAATGATTATATTTAAATATTTAAAATATA
1 ATTTAAT-ATTATATTTAAATATTTAAAATATA
* *
13418 ATTTATATATTATAATTAAA-ATTTATAA-ATA
1 ATTTA-ATATTATATTTAAATATTTAAAATATA
13449 A-TTAATATTAATTATTTAGAAATATTTAAAAT-TA
1 ATTTAATATT-A-TATTT--AAATATTTAAAATATA
13483 AT
1 AT
13485 ATTTCATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
29 5 0.09
30 4 0.07
31 8 0.15
32 7 0.13
33 19 0.35
34 12 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (32 bp):
ATTTAATATTATATTTAAATATTTAAAATATA
Found at i:13471 original size:24 final size:23
Alignment explanation
Indices: 13426--13488 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
13416 TAATTTATAT
* * *
13426 ATTATAATTAAAATTTATAAATA
1 ATTAAAATTAATATTTAGAAATA
*
13449 ATTAATATTAATTATTTAGAAATA
1 ATTAAAATTAA-TATTTAGAAATA
*
13473 TTTAAAATTAATATTT
1 ATTAAAATTAATATTT
13489 CATATATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTAAAATTAATATTTAGAAATA
Found at i:15190 original size:21 final size:19
Alignment explanation
Indices: 15143--15193 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
15133 AGTTTTAGTC
*
15143 ATAACTTTAGAATTTTTTT
1 ATAACTTTATAATTTTTTT
15162 A-AGA-TTTATAATTATTTGTT
1 ATA-ACTTTATAATT-TTT-TT
15182 ATAACTTTATAA
1 ATAACTTTATAA
15194 AATATACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 9 0.35
19 5 0.19
20 4 0.15
21 8 0.31
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (19 bp):
ATAACTTTATAATTTTTTT
Found at i:19389 original size:23 final size:22
Alignment explanation
Indices: 19363--19425 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
19353 TTTTAAATGT
*
19363 ATGTTTATAAACTTTATTAGGGC
1 ATGTTT-TAAACTTTATTAAGGC
* *
19386 ATGTTTTAAGACTTCATTAAGGT
1 ATGTTTTAA-ACTTTATTAAGGC
*
19409 ATGTTTTTTAACTTTAT
1 ATG-TTTTAAACTTTAT
19426 ATTAAGGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 3 0.09
23 25 0.76
24 5 0.15
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (22 bp):
ATGTTTTAAACTTTATTAAGGC
Found at i:26491 original size:15 final size:15
Alignment explanation
Indices: 26435--26491 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
26425 CTTTATACTA
26435 TAAAATATTTATTAT
1 TAAAATATTTATTAT
** *
26450 TATTATATTTATAATT
1 TAAAATATTTATTA-T
26466 GTAATAAATATTTATTAT
1 -T-A-AAATATTTATTAT
26484 TAAAATAT
1 TAAAATAT
26492 ATTGAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 17 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
TAAAATATTTATTAT
Found at i:28021 original size:17 final size:17
Alignment explanation
Indices: 27982--28023 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
27972 TACATGTTTA
*
27982 AATTTTATTTTACTTAT
1 AATTTTAATTTACTTAT
* *
27999 AA-TTTAATTTATTTTT
1 AATTTTAATTTACTTAT
28015 AATTTTAAT
1 AATTTTAAT
28024 ATCATACCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTTAATTTACTTAT
Found at i:29236 original size:29 final size:30
Alignment explanation
Indices: 29181--29251 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
29171 TAATATCTAT
* *
29181 ATTTTTATAATTTTTAAAAAATTAAAT-CA
1 ATTTTTATTATTTTTAAAAAATAAAATACA
* * *
29210 ATTTTTATTATTTTTAGAGAATAAAATATA
1 ATTTTTATTATTTTTAAAAAATAAAATACA
*
29240 ATTTTTTTTATT
1 ATTTTTATTATT
29252 AATTTGAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAAAATAAAATACA
Found at i:30468 original size:27 final size:27
Alignment explanation
Indices: 30430--30482 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
30420 TAATCACCAA
*
30430 AAGTCAGCAAATCG-TGATTCCAATACT
1 AAGTCACCAAAT-GATGATTCCAATACT
30457 AAGTCACCAAATGATGATTCCAATAC
1 AAGTCACCAAATGATGATTCCAATAC
30483 AGGGCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.25
Consensus pattern (27 bp):
AAGTCACCAAATGATGATTCCAATACT
Found at i:36263 original size:29 final size:28
Alignment explanation
Indices: 36163--36262 Score: 80
Period size: 28 Copynumber: 3.5 Consensus size: 28
36153 CCTGGGGGCT
* *
36163 AAATGGTAATTTTGGAC-TCTCGAGGGCA
1 AAATGGTAATTTTAGACATCT-GAGGGTA
* *
36191 AAATGGTAATTTTAGGAAAAT-TTAGGGTTAA
1 AAATGGTAATTTTA-G-ACATCTGAGGG-T-A
*
36222 AAATAGG-ATTTTTAGACATCTGAGGGTA
1 AAAT-GGTAATTTTAGACATCTGAGGGTA
36250 AAATGGTAATTTT
1 AAATGGTAATTTT
36263 TGGAAAATCG
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
27 2 0.04
28 23 0.41
29 9 0.16
30 8 0.14
31 12 0.21
32 2 0.04
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (28 bp):
AAATGGTAATTTTAGACATCTGAGGGTA
Found at i:36275 original size:29 final size:30
Alignment explanation
Indices: 36163--36343 Score: 112
Period size: 29 Copynumber: 6.2 Consensus size: 30
36153 CCTGGGGGCT
*** *
36163 AAATGGTAA-TTTTGGACTCTCGAGGG-CA
1 AAATGGTAATTTTTGGAAAATCGAGGGTAA
* **
36191 AAATGGTAATTTTAGGAAAATTTAGGGTTAA
1 AAATGGTAATTTTTGGAAAATCGAGGG-TAA
* *
36222 AAATAGG--ATTTTTAG-ACATCTGAGGGT-A
1 AAAT-GGTAATTTTTGGAAAATC-GAGGGTAA
*
36250 AAATGGTAATTTTTGGAAAATCGAGGTTAA
1 AAATGGTAATTTTTGGAAAATCGAGGGTAA
* ** *
36280 AAATGG-ATTTTTTGGAAGTTCGGGGGT--
1 AAATGGTAATTTTTGGAAAATCGAGGGTAA
*
36307 AAATGGTAATTTTTGGAAAAAATCG-GGGTCA
1 AAATGGTAATTTTTGG--AAAATCGAGGGTAA
36338 AAATGG
1 AAATGG
36344 AGTTTTTAAG
Statistics
Matches: 116, Mismatches: 23, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
27 8 0.07
28 22 0.19
29 47 0.41
30 26 0.22
31 11 0.09
32 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (30 bp):
AAATGGTAATTTTTGGAAAATCGAGGGTAA
Found at i:36316 original size:57 final size:59
Alignment explanation
Indices: 36184--36326 Score: 170
Period size: 59 Copynumber: 2.5 Consensus size: 59
36174 TTGGACTCTC
* * **
36184 GAGGGCAAAATGGTAATTTTAGGAAAATTTAGGGTTAAAAATAGGATTTTTAGACATCT
1 GAGGGTAAAATGGTAATTTTTGGAAAATCGAGGGTTAAAAATAGGATTTTTAGACATCT
*
36243 GAGGGTAAAATGGTAATTTTTGGAAAATCGA-GGTTAAAAAT-GGATTTTTTGGA-AGT-T
1 GAGGGTAAAATGGTAATTTTTGGAAAATCGAGGGTTAAAAATAGGA-TTTTTAGACA-TCT
*
36300 CGGGGGT-AAATGGTAATTTTTGGAAAA
1 -GAGGGTAAAATGGTAATTTTTGGAAAA
36327 AATCGGGGTC
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
57 25 0.33
58 23 0.31
59 27 0.36
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (59 bp):
GAGGGTAAAATGGTAATTTTTGGAAAATCGAGGGTTAAAAATAGGATTTTTAGACATCT
Found at i:36364 original size:57 final size:56
Alignment explanation
Indices: 36191--36366 Score: 137
Period size: 58 Copynumber: 3.1 Consensus size: 56
36181 CTCGAGGGCA
* ** *
36191 AAATGGTAATTTTAGGAAAATTTAGGGTTAAAAATAGGA-TTTTTAGACA--TCTGAGGGT
1 AAATGGTAATTTTTGGAAAATCGAGGG-TAAAAAT-GGAGTTTTT-GA-AGTTC-AAGGGT
* * **
36249 AAAATGGTAATTTTTGGAAAATCGAGGTTAAAAATGGATTTTTTGGAAGTTCGGGGGT
1 -AAATGGTAATTTTTGGAAAATCGAGGGTAAAAATGGAGTTTTT-GAAGTTCAAGGGT
* *
36307 AAATGGTAATTTTTGGAAAAAATCG-GGGTCAAAATGGAGTTTTT-AAGTTTTAAGGGT
1 AAATGGTAATTTTTGG--AAAATCGAGGGTAAAAATGGAGTTTTTGAAG-TTCAAGGGT
36364 AAA
1 AAA
36367 AATGTAATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
56 3 0.03
57 29 0.29
58 35 0.35
59 32 0.32
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (56 bp):
AAATGGTAATTTTTGGAAAATCGAGGGTAAAAATGGAGTTTTTGAAGTTCAAGGGT
Found at i:36427 original size:59 final size:56
Alignment explanation
Indices: 36332--36653 Score: 186
Period size: 59 Copynumber: 5.5 Consensus size: 56
36322 GAAAAAATCG
* *
36332 GGGTCAAAATGGAGTTTTT-AAGTTTTAAGGGT-AAAAATGTAATTTTCAAGTTTTA
1 GGGTCAAAATGGAATTTTTGAAGTTTT-AGGGTCAAAAATGTAATTTTCAAGTTTAA
* * * *
36387 GGGTCGAAAATGGATTTTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTTGAAGTTTAA
1 GGGTC-AAAATGGA-ATTTTT-GAAGTTTTAGGGTCAAAAATGTAA--TTTTCAAGTTTAA
* * * * **
36448 GGGTAAAAATGTAATTTTTAGAAGTTTTAGGGTCAAAAATTTAATTTTTGGAAGTTCGA
1 GGGTCAAAATGGAATTTTT-GAAGTTTTAGGGTCAAAAATGTAA-TTTT-CAAGTTTAA
* ** * * * **
36507 GGGTAAAAATATAATTTTTGGAAGTTTT-GAGGCCAAAAATGGAATTTTTGAAAGTTCGA
1 GGGTCAAAATGGAATTTTT-GAAGTTTTAG-GGTCAAAAATGTAA-TTTT-CAAGTTTAA
* * * * *
36566 GGGT-ATCAATGTAATTTTTAGAAG-TTCAGGGTCAAAAATATAATTTTGGAAAGTTTAA
1 GGGTCA-AAATGGAATTTTT-GAAGTTTTAGGGTCAAAAATGTAATTTT--CAAGTTTAA
* *
36624 GGGGTAAAAATGTAATTTTTGGATAGTTTT
1 -GGGTCAAAATGGAATTTTT-GA-AGTTTT
36654 GGGACCTCTA
Statistics
Matches: 219, Mismatches: 32, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
55 5 0.02
56 8 0.04
57 9 0.04
58 32 0.15
59 138 0.63
60 10 0.05
61 17 0.08
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (56 bp):
GGGTCAAAATGGAATTTTTGAAGTTTTAGGGTCAAAAATGTAATTTTCAAGTTTAA
Found at i:36443 original size:30 final size:30
Alignment explanation
Indices: 36332--36653 Score: 204
Period size: 29 Copynumber: 11.0 Consensus size: 30
36322 GAAAAAATCG
*
36332 GGGTC-AAAATGG-AGTTTTT-AAGTTTTAA
1 GGGTCAAAAATGGAATTTTTTGAAGTTTT-A
* *
36360 GGGT-AAAAATGTAA--TTTTCAAGTTTTA
1 GGGTCAAAAATGGAATTTTTTGAAGTTTTA
* * *
36387 GGGTCGAAAATGGATTTTTTTGGAAGTTTTG
1 GGGTCAAAAATGGAATTTTTT-GAAGTTTTA
*
36418 GGGTCAAAAATGGAATTTTTTGAAGTTTAA
1 GGGTCAAAAATGGAATTTTTTGAAGTTTTA
* *
36448 GGGT-AAAAATGTAATTTTTAGAAGTTTTA
1 GGGTCAAAAATGGAATTTTTTGAAGTTTTA
** * **
36477 GGGTCAAAAATTTAATTTTTGGAAGTTCGA
1 GGGTCAAAAATGGAATTTTTTGAAGTTTTA
** *
36507 GGGT-AAAAATATAATTTTTGGAAGTTTT-
1 GGGTCAAAAATGGAATTTTTTGAAGTTTTA
* **
36535 GAGGCCAAAAATGGAA-TTTTTGAAAGTTCGA
1 G-GGTCAAAAATGGAATTTTTTG-AAGTTTTA
** * * *
36566 GGGT-ATCAATGTAATTTTTAGAAG-TTCA
1 GGGTCAAAAATGGAATTTTTTGAAGTTTTA
** * *
36594 GGGTCAAAAATATAA-TTTTGGAAAGTTTAA
1 GGGTCAAAAATGGAATTTTTTG-AAGTTTTA
* *
36624 GGGGT-AAAAATGTAATTTTTGGATAGTTTT
1 -GGGTCAAAAATGGAATTTTTTGA-AGTTTT
36654 GGGACCTCTA
Statistics
Matches: 235, Mismatches: 40, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
27 9 0.04
28 36 0.15
29 75 0.32
30 73 0.31
31 42 0.18
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGTCAAAAATGGAATTTTTTGAAGTTTTA
Found at i:36487 original size:118 final size:117
Alignment explanation
Indices: 36351--36654 Score: 330
Period size: 118 Copynumber: 2.6 Consensus size: 117
36341 TGGAGTTTTT
* ** * *
36351 AAGTTTTAAGGGT-AAAAATGTAATTTT-CAAGTTTTAGGGTCGAAAATGGAT-TTTTTTGGAAG
1 AAGTTTT-AGGGTCAAAAATATAATTTTGCAAGTTCGAGGGT-AAAAAT--ATAATTTTTGGAAG
* * *
36413 TTTTGGGGTCAAAAATGGAATTTTTTG-AAGTTTAAGGGTAAAAATGTAATTTTTAG
62 TTTTGAGGCCAAAAATGGAA-TTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTTAG
* *
36469 AAGTTTTAGGGTCAAAAATTTAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTT
1 AAGTTTTAGGGTCAAAAATATAA-TTTTGCAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTT
* **
36534 TGAGGCCAAAAATGGAATTTTTGAAAGTTCGAGGGTATCAATGTAATTTTTAG
65 TGAGGCCAAAAATGGAATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTTAG
* * ** *
36587 AAG-TTCAGGGTCAAAAATATAATTTTGGAAAGTTTAAGGGGTAAAAATGTAATTTTTGGATAGT
1 AAGTTTTAGGGTCAAAAATATAATTTT-GCAAGTTCGA-GGGTAAAAATATAATTTTTGGA-AGT
36651 TTTG
63 TTTG
36655 GGACCTCTAG
Statistics
Matches: 160, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
116 4 0.03
117 37 0.23
118 93 0.58
119 16 0.10
120 10 0.06
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (117 bp):
AAGTTTTAGGGTCAAAAATATAATTTTGCAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTT
GAGGCCAAAAATGGAATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTTAG
Found at i:36515 original size:88 final size:89
Alignment explanation
Indices: 36351--36653 Score: 307
Period size: 88 Copynumber: 3.4 Consensus size: 89
36341 TGGAGTTTTT
* * * *
36351 AAGTTTTAAGGGTAAAAATGTAA-TTTTCAAGTTTTAGGGTCGAAAATGGATTTTTTTGGAAGTT
1 AAGTTTTAAGGGTAAAAATGTAATTTTTGAAGTTTTAGGGTCAAAAATGTA-ATTTTTGGAAG-T
* * *
36415 TTG-GGGTCAAAAATGGAATTTTTTG
64 TCGAGGGTCAAAAATAGAATTTTTGG
*
36440 AAG-TTTAAGGGTAAAAATGTAATTTTTAGAAGTTTTAGGGTCAAAAATTTAATTTTTGGAAGTT
1 AAGTTTTAAGGGTAAAAATGTAATTTTT-GAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTT
*
36504 CGAGGGT-AAAAATATAATTTTTGG
65 CGAGGGTCAAAAATAGAATTTTTGG
* ** * ** ** *
36528 AAGTTTTGAGGCCAAAAATGGAATTTTTGAAAGTTCGAGGGT-ATCAATGTAATTTTTAGAAGTT
1 AAGTTTTAAGGGTAAAAATGTAATTTTTG-AAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTT
*
36592 C-AGGGTCAAAAATATAA-TTTTGG
65 CGAGGGTCAAAAATAGAATTTTTGG
36615 AAAG-TTTAAGGGGTAAAAATGTAATTTTTGGATAGTTTT
1 -AAGTTTTAA-GGGTAAAAATGTAATTTTT-GA-AGTTTT
36654 GGGACCTCTA
Statistics
Matches: 179, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
87 15 0.08
88 89 0.50
89 56 0.31
90 19 0.11
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (89 bp):
AAGTTTTAAGGGTAAAAATGTAATTTTTGAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTC
GAGGGTCAAAAATAGAATTTTTGG
Done.