Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013246.1 Kokia drynarioides strain JFW-HI SEQ_128266, 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: 187248
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:2387 original size:22 final size:22
Alignment explanation
Indices: 2359--2403 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2349 GGATAGTAAG
2359 GAACTGGAAGATTCTCAGAATT
1 GAACTGGAAGATTCTCAGAATT
2381 GAACTGGAAGATTCTCAGAATT
1 GAACTGGAAGATTCTCAGAATT
2403 G
1 G
2404 TGATCTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (22 bp):
GAACTGGAAGATTCTCAGAATT
Found at i:4392 original size:28 final size:28
Alignment explanation
Indices: 4361--4444 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
4351 TTTTCATAAA
4361 TATTTTTAAAAATGTCTATTTTTGTAAT
1 TATTTTTAAAAATGTCTATTTTTGTAAT
* **
4389 TATTTTCAAAAATGTCTATTTTCATAAT
1 TATTTTTAAAAATGTCTATTTTTGTAAT
* * * *
4417 TATATCTAAAAA-GCCAATTTTTGTAAT
1 TATTTTTAAAAATGTCTATTTTTGTAAT
4444 T
1 T
4445 TTCCAAAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
27 12 0.26
28 34 0.74
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (28 bp):
TATTTTTAAAAATGTCTATTTTTGTAAT
Found at i:4443 original size:27 final size:28
Alignment explanation
Indices: 4368--4453 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
4358 AAATATTTTT
* * *
4368 AAAAATGTCTATTTTTGTAATTATTTTC
1 AAAAATGCCAATTTTTGTAATTATTCTC
* * **
4396 AAAAATGTCTATTTTCATAATTATATCT-
1 AAAAATGCCAATTTTTGTAATTAT-TCTC
4424 AAAAA-GCCAATTTTTGTAATT-TTC-C
1 AAAAATGCCAATTTTTGTAATTATTCTC
4449 AAAAA
1 AAAAA
4454 CGTAATTAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
25 7 0.14
26 1 0.02
27 12 0.24
28 27 0.55
29 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (28 bp):
AAAAATGCCAATTTTTGTAATTATTCTC
Found at i:4472 original size:28 final size:28
Alignment explanation
Indices: 4435--4504 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
4425 AAAAGCCAAT
* *
4435 TTTTGTAATTTTCCAAAAACGTAATTAG
1 TTTTATAATTTTCCAAAAACATAATTAG
* * *
4463 TTTTATAATTTACCTAAAACATAATTAT
1 TTTTATAATTTTCCAAAAACATAATTAG
4491 TTTTATAATTTTCC
1 TTTTATAATTTTCC
4505 TCAATTGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTTATAATTTTCCAAAAACATAATTAG
Found at i:4515 original size:28 final size:27
Alignment explanation
Indices: 4454--5572 Score: 802
Period size: 28 Copynumber: 39.6 Consensus size: 27
4444 TTTCCAAAAA
* * * *
4454 CGTAATTAGTTTTATAATTTACCTAAAA
1 CGTAATTATTTTTAAAATTTTCCT-AAT
* *
4482 CATAATTATTTTTATAATTTTCCTCAAT
1 CGTAATTATTTTTAAAATTTTCCT-AAT
* * *
4510 TGTAATTATTATAAAAATTTTCCTAAT
1 CGTAATTATTTTTAAAATTTTCCTAAT
*
4537 CCGTAATTATTTTCAAAATTTTCCTAAAT
1 -CGTAATTATTTTTAAAATTTTCCT-AAT
** * *
4566 CGTAATTATTTTCCAATTTTTCTTAAGT
1 CGTAATTATTTTTAAAATTTTCCTAA-T
*
4594 TGTAATTATTTTTAAAATTTTCCTAAT
1 CGTAATTATTTTTAAAATTTTCCTAAT
* *
4621 CCGAAATTATTTTCAAAATTTTCCTCAAT
1 -CGTAATTATTTTTAAAATTTTCCT-AAT
* * **
4650 TGTAATTATTTTCAACAAAATTTTTTTAAGT
1 CGTAATTATTTT---TAAAATTTTCCTAA-T
*
4681 CGTAATTATTTTCAAAA-TTTCCTAAT
1 CGTAATTATTTTTAAAATTTTCCTAAT
*
4707 CCGTAATTA-TTTTAAAATTTTTCTTAAGT
1 -CGTAATTATTTTTAAAA-TTTTCCTAA-T
* *
4736 GGTAATTAATTAATTATTTTTAAAAATTTCCTAAAT
1 CG--------TAATTATTTTTAAAATTTTCCT-AAT
*
4772 CATAATTATTTTTAAAATTTAT-CTAAT
1 CGTAATTATTTTTAAAATTT-TCCTAAT
* *
4799 CCATAATTATTCTTAAAATTTTCCTATAT
1 -CGTAATTATTTTTAAAATTTTCCTA-AT
* *
4828 CATAATT-TTTTCAAAATTTTCCTAAT
1 CGTAATTATTTTTAAAATTTTCCTAAT
* *
4854 CCATAATTATTTTCAAAATTTTCCTAAT
1 -CGTAATTATTTTTAAAATTTTCCTAAT
* * * *
4882 ATGTAATTATTTTTTAAATTTTACAAAT
1 -CGTAATTATTTTTAAAATTTTCCTAAT
* * *
4910 CAATAATTATTTTCAAAATTTTCCTAAGC
1 C-GTAATTATTTTTAAAATTTTCCTAA-T
*
4939 CGTAATTATTTTCAAAATTTTCCTAATT
1 CGTAATTATTTTTAAAATTTTCCTAA-T
* * *
4967 AGTAATTATTTTCAATATTTTCCTAAAT
1 CGTAATTATTTTTAAAATTTTCCT-AAT
* *
4995 CATAATTATTTTCAAAATTTTCCTAAT
1 CGTAATTATTTTTAAAATTTTCCTAAT
* * * *
5022 CCATATTTATTTTGAAATTTTTCCTAAT
1 -CGTAATTATTTTTAAAATTTTCCTAAT
* * *
5050 CCATAATTATTTTCAAAATTTTCCTAGT
1 -CGTAATTATTTTTAAAATTTTCCTAAT
*
5078 CTATAATTATTTTCT-AAATTTTCCTAAAT
1 C-GTAATTATTTT-TAAAATTTTCCT-AAT
*
5107 C-TCAATTATTTTCAAAATTTTCCTAAAT
1 CGT-AATTATTTTTAAAATTTTCCT-AAT
* *
5135 CTTAATTATTTTTAAAATTTTCCTAACC
1 CGTAATTATTTTTAAAATTTTCCTAA-T
*
5163 CGTAATTATTTTTGAAATTTTCCTAAAT
1 CGTAATTATTTTTAAAATTTTCCT-AAT
* *
5191 CATAATTATTTTCAAAATTTTCCTAAT
1 CGTAATTATTTTTAAAATTTTCCTAAT
* **
5218 CCATAATTATTTTCGAAATTTTCCTAAAT
1 -CGTAATTATTTTTAAAATTTTCCT-AAT
* * * *
5247 TGCAATTATATTCAAAA-TTTCCTAAT
1 CGTAATTATTTTTAAAATTTTCCTAAT
* *
5273 CCATAATTATTTTCAAAATTTTCCTAAT
1 -CGTAATTATTTTTAAAATTTTCCTAAT
* * *
5301 TGTAATTATTTCTAAACTTTTCCTAAAT
1 CGTAATTATTTTTAAAATTTTCCT-AAT
*
5329 CTTAATTATTTTTAAAATTTTCCT-AT
1 CGTAATTATTTTTAAAATTTTCCTAAT
* * *
5355 CCAATAATTATTTTCAAAGTTTTCCTAAAT
1 -C-GTAATTATTTTTAAAATTTTCCT-AAT
* * * *
5385 CATAGTAATTTTCAAAATTTTCCTAAAT
1 CGTAATTATTTTTAAAATTTTCCT-AAT
*
5413 CATAATTATTTTTATAATATTCCTTTCCTAAGT
1 CGTAATTATTTTTA-AA-A-T--TTTCCTAA-T
*
5446 CGTAATTATTTTTATAATTTTCCTAAAT
1 CGTAATTATTTTTAAAATTTTCCT-AAT
* * *
5474 TGCAATTATTTTT-AAATTTTCCTATT
1 CGTAATTATTTTTAAAATTTTCCTAAT
*
5500 CCAG-AATTATTTTTATAATTTTCCTAAAT
1 -C-GTAATTATTTTTAAAATTTTCCT-AAT
* *
5529 -GATACTTATTTTTAACATTTTCCTACAT
1 CG-TAATTATTTTTAAAATTTTCCTA-AT
* * *
5557 GGAAACTATTTTTAAA
1 CGTAATTATTTTTAAA
5573 TCGCCTGTTT
Statistics
Matches: 900, Mismatches: 126, Indels: 130
0.78 0.11 0.11
Matches are distributed among these distances:
26 18 0.02
27 115 0.13
28 662 0.74
29 30 0.03
30 6 0.01
31 24 0.03
32 3 0.00
33 20 0.02
36 12 0.01
37 10 0.01
ACGTcount: A:0.35, C:0.13, G:0.03, T:0.49
Consensus pattern (27 bp):
CGTAATTATTTTTAAAATTTTCCTAAT
Found at i:4557 original size:84 final size:83
Alignment explanation
Indices: 4454--5553 Score: 951
Period size: 84 Copynumber: 13.0 Consensus size: 83
4444 TTTCCAAAAA
* * * * **
4454 CGTAATTAGTTTT-ATAATTTACCTAAAACATAATTATTTTTATAATTTTCCTCAATTGTAATTA
1 CGTAATTA-TTTTCAAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCT-AATCATAATTA
* *
4518 TTATAAAAATTTTCCTAATC
64 TTTTCAAAATTTTCCTAATC
* ** * * **
4538 CGTAATTATTTTCAAAATTTTCCTAAATCGTAATTATTTTCCAATTTTTCTTAAGTTGTAATTAT
1 CGTAATTATTTTCAAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCTAA-TCATAATTAT
*
4603 TTTTAAAATTTTCCTAATC
65 TTTCAAAATTTTCCTAATC
* * ** * ** *
4622 CGAAATTATTTTCAAAATTTTCCTCAATTGTAATTATTTTCAACAAAATTTTTTTAAGTCGTAAT
1 CGTAATTATTTTCAAAATTTTCCTAAATCATAATTATTTT---TAAAATTTTCCTAA-TCATAAT
4687 TATTTTCAAAA-TTTCCTAATC
62 TATTTTCAAAATTTTCCTAATC
* * *
4708 CGTAATTATTTT-AAAATTTTTCTTAAGTGGTAATTAATTAATTATTTTTAAAAATTTCCTAAAT
1 CGTAATTATTTTCAAAA-TTTTCCT-A-----AA-TCA-TAATTATTTTTAAAATTTTCCT-AAT
*
4772 CATAATTATTTTTAAAATTTAT-CTAATC
56 CATAATTATTTTCAAAATTT-TCCTAATC
* * *
4800 CATAATTATTCTT-AAAATTTTCCTATATCATAATT-TTTTCAAAATTTTCCTAATCCATAATTA
1 CGTAATTATT-TTCAAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCTAAT-CATAATTA
*
4863 TTTTCAAAATTTTCCTAATA
64 TTTTCAAAATTTTCCTAATC
* ** * * * *
4883 TGTAATTATTTTTTAAATTTTAC-AAATCAATAATTATTTTCAAAATTTTCCTAAGCCGTAATTA
1 CGTAATTATTTTCAAAATTTTCCTAAATC-ATAATTATTTTTAAAATTTTCCTAA-TCATAATTA
*
4947 TTTTCAAAATTTTCCTAATT
64 TTTTCAAAATTTTCCTAATC
* * * *
4967 AGTAATTATTTTCAATATTTTCCTAAATCATAATTATTTTCAAAATTTTCCTAATCCATATTTAT
1 CGTAATTATTTTCAAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCTAAT-CATAATTAT
* *
5032 TTTGAAATTTTTCCTAATC
65 TTTCAAAATTTTCCTAATC
* *
5051 CATAATTATTTTCAAAATTTTCCT-AGTCTATAATTATTTTCT-AAATTTTCCTAAATC-TCAAT
1 CGTAATTATTTTCAAAATTTTCCTAAATC-ATAATTATTTT-TAAAATTTTCCT-AATCAT-AAT
5113 TATTTTCAAAATTTTCCTAAAT-
62 TATTTTCAAAATTTTCCT-AATC
* * ** * *
5135 CTTAATTATTTTTAAAATTTTCCTAACCCGTAATTATTTTTGAAATTTTCCTAAATCATAATTAT
1 CGTAATTATTTTCAAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCT-AATCATAATTAT
5200 TTTCAAAATTTTCCTAATC
65 TTTCAAAATTTTCCTAATC
* * *** * *
5219 CATAATTATTTTCGAAATTTTCCTAAATTGCAATTATATTCAAAA-TTTCCTAATCCATAATTAT
1 CGTAATTATTTTCAAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCTAAT-CATAATTAT
5283 TTTCAAAATTTTCCTAAT-
65 TTTCAAAATTTTCCTAATC
* * *
5301 TGTAATTA-TTTCTAAACTTTTCCTAAATCTTAATTATTTTTAAAATTTTCCT-ATCCAATAATT
1 CGTAATTATTTTC-AAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCTAAT-C-ATAATT
*
5364 ATTTTCAAAGTTTTCCTAAAT-
63 ATTTTCAAAATTTTCCT-AATC
* * * *
5385 CATAGTAATTTTCAAAATTTTCCTAAATCATAATTATTTTTATAATATTCCTTTCCTAAGTCGTA
1 CGTAATTATTTTCAAAATTTTCCTAAATCATAATTATTTTTA-AA-A-T--TTTCCTAA-TCATA
* *
5450 ATTATTTTTATAATTTTCCTAAAT-
60 ATTATTTTCAAAATTTTCCT-AATC
* * * * * * * *
5474 TGCAATTATTTT-TAAATTTTCCT-ATTCCAGAATTATTTTTATAATTTTCCTAAATGATACTTA
1 CGTAATTATTTTCAAAATTTTCCTAAAT-CATAATTATTTTTAAAATTTTCCT-AATCATAATTA
* *
5537 TTTTTAACATTTTCCTA
64 TTTTCAAAATTTTCCTA
5554 CATGGAAACT
Statistics
Matches: 852, Mismatches: 114, Indels: 102
0.80 0.11 0.10
Matches are distributed among these distances:
81 4 0.00
82 49 0.06
83 161 0.19
84 417 0.49
85 27 0.03
86 30 0.04
87 32 0.04
88 23 0.03
89 36 0.04
90 2 0.00
91 26 0.03
92 27 0.03
93 8 0.01
94 10 0.01
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (83 bp):
CGTAATTATTTTCAAAATTTTCCTAAATCATAATTATTTTTAAAATTTTCCTAATCATAATTATT
TTCAAAATTTTCCTAATC
Found at i:4806 original size:64 final size:63
Alignment explanation
Indices: 4683--4807 Score: 148
Period size: 64 Copynumber: 2.0 Consensus size: 63
4673 TTTTAAGTCG
* * * **
4683 TAATTATTTTCAAAATTTCCTAATCCGTAATTATTTTAAAATTTTTCTTAAGTGGTAATTAAT
1 TAATTATTTTAAAAATTTCCTAATCCATAATTATTTTAAAATTTATCTTAAGTCATAATTAAT
4746 TAATTATTTTTAAAAATTTCCTAAAT-CATAATTATTTTTAAAATTTATC-TAA-TCCATAATTA
1 TAATTA-TTTTAAAAATTTCCT-AATCCATAATTA-TTTTAAAATTTATCTTAAGT-CATAATTA
4808 TTCTTAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
63 7 0.13
64 30 0.57
65 16 0.30
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (63 bp):
TAATTATTTTAAAAATTTCCTAATCCATAATTATTTTAAAATTTATCTTAAGTCATAATTAAT
Found at i:5441 original size:33 final size:33
Alignment explanation
Indices: 5403--5469 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
5393 TTTTCAAAAT
5403 TTTCCTAAATCATAATTATTTTTATAATATTCC
1 TTTCCTAAATCATAATTATTTTTATAATATTCC
* * *
5436 TTTCCTAAGTCGTAATTATTTTTATAATTTTCC
1 TTTCCTAAATCATAATTATTTTTATAATATTCC
5469 T
1 T
5470 AAATTGCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.03, T:0.54
Consensus pattern (33 bp):
TTTCCTAAATCATAATTATTTTTATAATATTCC
Found at i:5647 original size:27 final size:27
Alignment explanation
Indices: 5563--5704 Score: 135
Period size: 27 Copynumber: 5.3 Consensus size: 27
5553 ACATGGAAAC
* * *
5563 TATTTTTAAATCGCCTGTTTTCATAAT
1 TATTTTTAAAACACCTATTTTCATAAT
* * * *
5590 TATTTTCGAAAACACCTACTTTCGTATT
1 TATTTT-TAAAACACCTATTTTCATAAT
* * *
5618 TATTTTTATAACACTTATTTCCATAAT
1 TATTTTTAAAACACCTATTTTCATAAT
* *
5645 TA-TTTTAAAAGCACCCATTTTTATAAT
1 TATTTTTAAAA-CACCTATTTTCATAAT
5672 TATTTTTAAAACACCTATTTTCAT-AT
1 TATTTTTAAAACACCTATTTTCATAAT
*
5698 TAATTTT
1 TATTTTT
5705 GCACAGTTAA
Statistics
Matches: 90, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
26 15 0.17
27 47 0.52
28 28 0.31
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (27 bp):
TATTTTTAAAACACCTATTTTCATAAT
Found at i:9793 original size:29 final size:29
Alignment explanation
Indices: 9760--9817 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
9750 TTCTTCAGAG
9760 GTAAACCAATTAGCTGTCTCCGATTTCAT
1 GTAAACCAATTAGCTGTCTCCGATTTCAT
* *
9789 GTAAACCAATTAGCTGTCTCGGGTTTCAT
1 GTAAACCAATTAGCTGTCTCCGATTTCAT
9818 TATTCGGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (29 bp):
GTAAACCAATTAGCTGTCTCCGATTTCAT
Found at i:16172 original size:10 final size:9
Alignment explanation
Indices: 16153--16192 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
16143 GGGGAAAAAA
16153 AAGA-AAAG
1 AAGAGAAAG
16161 AAGAGGAAAG
1 AAGA-GAAAG
16171 AAGAGAAAG
1 AAGAGAAAG
16180 -AGAG-AAG
1 AAGAGAAAG
16187 AAGAGA
1 AAGAGA
16193 TAAAAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
7 3 0.11
8 12 0.43
9 5 0.18
10 8 0.29
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (9 bp):
AAGAGAAAG
Found at i:17389 original size:29 final size:31
Alignment explanation
Indices: 17356--17415 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
17346 GTGTCAATCA
*
17356 ATTTATTATTATAATA-TTAAAA-TTTATTT
1 ATTTATTATTATAAAATTTAAAATTTTATTT
* *
17385 ATTTATTTTTTTAAAATTTAAAATTTTATTT
1 ATTTATTATTATAAAATTTAAAATTTTATTT
17416 TACGTATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 6 0.23
31 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTATTATTATAAAATTTAAAATTTTATTT
Found at i:20429 original size:22 final size:22
Alignment explanation
Indices: 20404--20449 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
20394 TCTCCTACAT
20404 TGGGGCACGTAATAAGAATTGC
1 TGGGGCACGTAATAAGAATTGC
20426 TGGGGCACGTAATAAGAATTGC
1 TGGGGCACGTAATAAGAATTGC
20448 TG
1 TG
20450 ATATTCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (22 bp):
TGGGGCACGTAATAAGAATTGC
Found at i:23511 original size:24 final size:23
Alignment explanation
Indices: 23484--23528 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
23474 CTTGAACTGG
*
23484 ACCATAAGAACAAGAATATGAAAT
1 ACCAAAAGAACAAGAA-ATGAAAT
* *
23508 ACCAAAATAACATGAAATGAA
1 ACCAAAAGAACAAGAAATGAA
23529 CTACAGTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.60, C:0.13, G:0.11, T:0.16
Consensus pattern (23 bp):
ACCAAAAGAACAAGAAATGAAAT
Found at i:28079 original size:98 final size:98
Alignment explanation
Indices: 27910--28113 Score: 401
Period size: 98 Copynumber: 2.1 Consensus size: 98
27900 TTTGAATAAG
27910 TCTGATTTTGTAATACACAAATATACTAGCAGTATATAAAGGTGAAGAGAACATACGGCAAGTTT
1 TCTGATTTTGTAATACACAAATATACTAGCAGTATATAAAGGTGAAGAGAACATACGGCAAGTTT
27975 AAGCTCTATATCACAACGCTGTGAATGCCTCTC
66 AAGCTCTATATCACAACGCTGTGAATGCCTCTC
28008 TCTGATTTTGTAATACACAAATATACTAGCAGTATATAAAGGTGAAGAGAACATACGGCAAGTTT
1 TCTGATTTTGTAATACACAAATATACTAGCAGTATATAAAGGTGAAGAGAACATACGGCAAGTTT
28073 AAGCTCTATATCACAACGCTGTGAATGCCTCTC
66 AAGCTCTATATCACAACGCTGTGAATGCCTCTC
28106 TCTG-TTTT
1 TCTGATTTT
28114 CCTTTTTCAC
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 4 0.04
98 102 0.96
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (98 bp):
TCTGATTTTGTAATACACAAATATACTAGCAGTATATAAAGGTGAAGAGAACATACGGCAAGTTT
AAGCTCTATATCACAACGCTGTGAATGCCTCTC
Found at i:38747 original size:13 final size:14
Alignment explanation
Indices: 38721--38770 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 14
38711 TTTAAAATTA
38721 TTAAAATTAATTTT
1 TTAAAATTAATTTT
38735 TTAAAA-T-ATTTT
1 TTAAAATTAATTTT
* * *
38747 TTAAATATAAAATTA
1 TTAAA-ATTAATTTT
38762 TTAAAATTA
1 TTAAAATTA
38771 TTAATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 10 0.34
13 2 0.07
14 9 0.31
15 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAAATTAATTTT
Found at i:38830 original size:35 final size:35
Alignment explanation
Indices: 38787--38891 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
38777 TTTAATTTCA
38787 TCTTCTTCCCCATTTTTCCATCTAACACCACTTCT
1 TCTTCTTCCCCATTTTTCCATCTAACACCACTTCT
*
38822 TCTTCTTCCCCATTTTTCCATCT-A-A-CACTTCC
1 TCTTCTTCCCCATTTTTCCATCTAACACCACTTCT
38854 TCTTC-TCACCCA-TTTTCTCATCTAACACCACTTCT
1 TCTTCTTC-CCCATTTTTC-CATCTAACACCACTTCT
38889 TCT
1 TCT
38892 CACACAAAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
31 7 0.11
32 20 0.32
33 2 0.03
34 2 0.03
35 32 0.51
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43
Consensus pattern (35 bp):
TCTTCTTCCCCATTTTTCCATCTAACACCACTTCT
Found at i:38894 original size:32 final size:33
Alignment explanation
Indices: 38787--38891 Score: 126
Period size: 32 Copynumber: 3.2 Consensus size: 33
38777 TTTAATTTCA
38787 TCTTCTTC-CCCATTTTTCCATCTAACACCACT
1 TCTTCTTCACCCATTTTTCCATCTAACACCACT
* ** *
38819 TCTTCTTCTTCCCCATTTTTCCATCTAACACTTCC
1 TCTTCTTC--ACCCATTTTTCCATCTAACACCACT
38854 TCTTC-TCACCCA-TTTTCTCATCTAACACCACT
1 TCTTCTTCACCCATTTTTC-CATCTAACACCACT
38886 TCTTCT
1 TCTTCT
38892 CACACAAAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
31 5 0.08
32 28 0.46
34 2 0.03
35 26 0.43
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.43
Consensus pattern (33 bp):
TCTTCTTCACCCATTTTTCCATCTAACACCACT
Found at i:58341 original size:16 final size:17
Alignment explanation
Indices: 58305--58341 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
58295 CTTATAATTA
*
58305 AAATATTATATTTTTAT
1 AAATATAATATTTTTAT
58322 -AATATAAT-TTTTTAT
1 AAATATAATATTTTTAT
58337 AAATA
1 AAATA
58342 GTATCGCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATAATATTTTTAT
Found at i:62884 original size:19 final size:19
Alignment explanation
Indices: 62862--62908 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
62852 AACTACATCC
62862 TTTCGATAAATGTTTATCT
1 TTTCGATAAATGTTTATCT
62881 TTTCGATAAATGTTTATCT
1 TTTCGATAAATGTTTATCT
*
62900 TTTCTATAA
1 TTTCGATAA
62909 TTAAAAGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTCGATAAATGTTTATCT
Found at i:66284 original size:28 final size:28
Alignment explanation
Indices: 66244--66300 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
66234 AGAAAAAGAA
66244 AGAAAGCAATGAATTGCCTGCCTTCACC
1 AGAAAGCAATGAATTGCCTGCCTTCACC
66272 AGAAAGCAATGAATTGCCTGCCTTCACC
1 AGAAAGCAATGAATTGCCTGCCTTCACC
66300 A
1 A
66301 ATCTAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (28 bp):
AGAAAGCAATGAATTGCCTGCCTTCACC
Found at i:66357 original size:3 final size:3
Alignment explanation
Indices: 66336--66373 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
66326 TAAGAAATCT
* *
66336 AGA AGA GGA AGA GGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
66374 TTAGAAATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:69950 original size:52 final size:52
Alignment explanation
Indices: 69871--70108 Score: 300
Period size: 52 Copynumber: 4.6 Consensus size: 52
69861 GTAAATGAAA
* * * *
69871 AGGTCTGATTACTACGTGTCATTGTGAGTATACGAATCATTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATG
* * *
69923 AGGTCCAATGACTTCGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATG
* *
69975 AGGTCCGATGACTACGTGTCCTCGTGAGTATATGAATCATTTATGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATG
* * * * * *
70027 AGGTCCGATGACTACGTGTCATTGTGAGTATGTGATTC-TTTAACGAAGTA-A
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTT-ACGGATTATG
**
70078 AGGTCCGATGACTTTGTGTCATCGTGAGTAT
1 AGGTCCGATGACTACGTGTCATCGTGAGTAT
70109 TTAATATGAA
Statistics
Matches: 162, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
51 31 0.19
52 131 0.81
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCATTTACGGATTATG
Found at i:70814 original size:21 final size:21
Alignment explanation
Indices: 70773--70848 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
70763 GGAGTTTTTA
*
70773 GTATCGGTAGAAGTAAT-ACTT
1 GTATCGGTAGAAG-AGTCACTT
* *
70794 GTTTCGATAGAAGAGTCACTT
1 GTATCGGTAGAAGAGTCACTT
***
70815 GTATCGGTAGACCTGTCACTT
1 GTATCGGTAGAAGAGTCACTT
70836 GTATCGGTAGAAG
1 GTATCGGTAGAAG
70849 TCTGCACTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 2 0.05
21 42 0.95
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGAGTCACTT
Found at i:71810 original size:28 final size:28
Alignment explanation
Indices: 71778--71838 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
71768 CCTCTCGTCT
71778 ACGACTCTTGTCTTTCCTTTCTCTCAGG
1 ACGACTCTTGTCTTTCCTTTCTCTCAGG
71806 ACGACTCTTGTCTTTCCTTTCTCTCAGG
1 ACGACTCTTGTCTTTCCTTTCTCTCAGG
71834 ACGAC
1 ACGAC
71839 ATGATGTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.13, C:0.33, G:0.15, T:0.39
Consensus pattern (28 bp):
ACGACTCTTGTCTTTCCTTTCTCTCAGG
Found at i:75821 original size:29 final size:29
Alignment explanation
Indices: 75779--75843 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
75769 ACACCCACAC
75779 ACACACAATATTTATATCGATGCATACAT
1 ACACACAATATTTATATCGATGCATACAT
75808 ACACACAATATTTATATCGATGCATACAT
1 ACACACAATATTTATATCGATGCATACAT
75837 ACACACA
1 ACACACA
75844 TACATTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (29 bp):
ACACACAATATTTATATCGATGCATACAT
Found at i:76635 original size:20 final size:19
Alignment explanation
Indices: 76612--76660 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
76602 TTTTTAGTAT
76612 ACTTAAAAATTTGAATAAAA
1 ACTTAAAAATTT-AATAAAA
*
76632 ACTTATAAA-TTAATAAAA
1 ACTTAAAAATTTAATAAAA
*
76650 A-TTAAATATTT
1 ACTTAAAAATTT
76661 TATTTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 2 0.08
20 8 0.32
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
ACTTAAAAATTTAATAAAA
Found at i:81749 original size:22 final size:22
Alignment explanation
Indices: 81724--81773 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
81714 AGCGCGCCCT
*
81724 CTGTTTAGCACTGTGTGTGTTA
1 CTGTTTAACACTGTGTGTGTTA
* * *
81746 CTGTTCAACATTGTGTGTGTTT
1 CTGTTTAACACTGTGTGTGTTA
81768 CTGTTT
1 CTGTTT
81774 CCCCAGCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.50
Consensus pattern (22 bp):
CTGTTTAACACTGTGTGTGTTA
Found at i:88436 original size:16 final size:16
Alignment explanation
Indices: 88415--88454 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
88405 CATTTGGTTC
* *
88415 GTTGTATTGGAATAGA
1 GTTGTAATGAAATAGA
*
88431 GTTGTAATGAAATAGG
1 GTTGTAATGAAATAGA
88447 GTTGTAAT
1 GTTGTAAT
88455 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.38
Consensus pattern (16 bp):
GTTGTAATGAAATAGA
Found at i:88639 original size:25 final size:28
Alignment explanation
Indices: 88590--88640 Score: 81
Period size: 25 Copynumber: 1.9 Consensus size: 28
88580 TTTAATAAAA
88590 AAATTTTAAATAGATGATTATTGTTATT
1 AAATTTTAAATAGATGATTATTGTTATT
88618 AAATTTT-AATA-A-GATTATTGTTA
1 AAATTTTAAATAGATGATTATTGTTA
88641 AATATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.48
26 1 0.04
27 4 0.17
28 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (28 bp):
AAATTTTAAATAGATGATTATTGTTATT
Found at i:88682 original size:58 final size:57
Alignment explanation
Indices: 88615--88744 Score: 172
Period size: 58 Copynumber: 2.2 Consensus size: 57
88605 GATTATTGTT
* *
88615 ATTAAATTTTAATA-AGATTATTGTTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTATATTTTAATATA-ATTATTGTTAAATACAATTTAAT-AAAATAATAAATAATTTA
* * *
88673 ATTATATTTTAACATAATTATTTTTAAATACAATTTAATAAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTGTTAAATACAATTTAATAAAATAATAAATAATTTA
*
88730 ATAATATTTTTAATA
1 ATTATA-TTTTAATA
88745 CCCACGTCCA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
57 22 0.35
58 40 0.63
59 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (57 bp):
ATTATATTTTAATATAATTATTGTTAAATACAATTTAATAAAATAATAAATAATTTA
Found at i:90116 original size:13 final size:13
Alignment explanation
Indices: 90079--90118 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 13
90069 AATTTTATTA
90079 AATTGTTTTTATTAT
1 AATT-TTTTT-TTAT
90094 AGATTTTTTTTTAT
1 A-ATTTTTTTTTAT
90108 AATTTTTTTTT
1 AATTTTTTTTT
90119 TTTTAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.42
14 5 0.21
15 6 0.25
16 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (13 bp):
AATTTTTTTTTAT
Found at i:93710 original size:18 final size:17
Alignment explanation
Indices: 93684--93727 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
93674 ATACTACAGG
* *
93684 TAAATTTAAATAAATCAA
1 TAAAATTAAATAAA-AAA
93702 TAAAATTAAATAAAAAA
1 TAAAATTAAATAAAAAA
93719 T-AAATTAAA
1 TAAAATTAAA
93728 CATACCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 13 0.54
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATTAAATAAAAAA
Found at i:94844 original size:20 final size:20
Alignment explanation
Indices: 94807--94847 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
94797 ACTTCTAAAT
**
94807 AAATTATTTTTTAGAAAAAA
1 AAATTATTTTAAAGAAAAAA
*
94827 AAATTATTTTAAATAAAAAA
1 AAATTATTTTAAAGAAAAAA
94847 A
1 A
94848 TTAATCCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATTATTTTAAAGAAAAAA
Found at i:95394 original size:27 final size:27
Alignment explanation
Indices: 95316--95397 Score: 130
Period size: 27 Copynumber: 3.0 Consensus size: 27
95306 TACCTGACAC
* *
95316 CCAATGGAGGAACA-CGAAGTGGCGACA
1 CCAATGGAGGAATATC-AAGTGGCGGCA
95343 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAATATCAAGTGGCGGCA
95370 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAATATCAAGTGGCGGCA
95397 C
1 C
95398 TAAGGGGTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
27 51 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.12
Consensus pattern (27 bp):
CCAATGGAGGAATATCAAGTGGCGGCA
Found at i:107030 original size:45 final size:45
Alignment explanation
Indices: 106980--107167 Score: 252
Period size: 45 Copynumber: 4.2 Consensus size: 45
106970 TGCTGGAGGT
* * *
106980 GCTGGAGGTGCCGGAGGAGGCTGGAAGGGGTTTGGAATAAATGGA
1 GCTGGAGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
* * * *
107025 GCTGGAGGCGCGGGAGGAGGCTGGAAAGGGTTTGGAATAAGTGGA
1 GCTGGAGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
* * *
107070 GCCGGTGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAAGTGGA
1 GCTGGAGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
* *
107115 GCCGGTGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAAGA-GGA
1 GCTGGAGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA-ATGGA
107160 GCTGGAGG
1 GCTGGAGG
107168 AGGCTGAAAG
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
45 130 1.00
ACGTcount: A:0.24, C:0.09, G:0.49, T:0.18
Consensus pattern (45 bp):
GCTGGAGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAAATGGA
Found at i:107030 original size:54 final size:53
Alignment explanation
Indices: 106966--107086 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 53
106956 AGATGAAACC
* *
106966 ATGGTGCTGGAGGTGCTGGAGGTGCCGGAGGAGGCTGGAAGGGGTTTGGAATAA
1 ATGGAGCTGGAGGTGCTGGAGG-GCCGGAGGAGGCTGGAAAGGGTTTGGAATAA
*
107020 ATGGAGCTGGA-G-GC------GCGGGAGGAGGCTGGAAAGGGTTTGGAATAA
1 ATGGAGCTGGAGGTGCTGGAGGGCCGGAGGAGGCTGGAAAGGGTTTGGAATAA
* * *
107065 GTGGAGCCGGTGGTGCTGGAGG
1 ATGGAGCTGGAGGTGCTGGAGG
107087 AGGCTGAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
45 37 0.70
46 1 0.02
47 2 0.04
52 2 0.04
53 1 0.02
54 10 0.19
ACGTcount: A:0.21, C:0.10, G:0.51, T:0.18
Consensus pattern (53 bp):
ATGGAGCTGGAGGTGCTGGAGGGCCGGAGGAGGCTGGAAAGGGTTTGGAATAA
Found at i:107243 original size:36 final size:36
Alignment explanation
Indices: 107119--107236 Score: 182
Period size: 36 Copynumber: 3.3 Consensus size: 36
107109 AGTGGAGCCG
*
107119 GTGGTGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
1 GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
* *
107155 GAGGAGCTGGAGGAGGCTGAAAGGGGTTTGGAATAA
1 GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
* * *
107191 GTGGAGCAGGAGGCGGCTGAAATGGGTTTGGAATAA
1 GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
107227 GTGGAGCTGG
1 GTGGAGCTGG
107237 TGGCGGCAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 74 1.00
ACGTcount: A:0.27, C:0.07, G:0.47, T:0.19
Consensus pattern (36 bp):
GTGGAGCTGGAGGAGGCTGAAAAGGGTTTGGAATAA
Found at i:114615 original size:21 final size:21
Alignment explanation
Indices: 114589--114633 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
114579 AGGTATGTCT
114589 TTACAATTGGGGGTTGTGCAA
1 TTACAATTGGGGGTTGTGCAA
114610 TTACAATTGGGGGTTGTGCAA
1 TTACAATTGGGGGTTGTGCAA
114631 TTA
1 TTA
114634 GTTGGAAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.31, T:0.36
Consensus pattern (21 bp):
TTACAATTGGGGGTTGTGCAA
Found at i:122898 original size:18 final size:19
Alignment explanation
Indices: 122864--122906 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
122854 TTACAAAAAA
*
122864 AAAAATCAAAATCATTTTT
1 AAAAATCAAAATCATTTAT
*
122883 AAAATTCAAAAT-ATTTAT
1 AAAAATCAAAATCATTTAT
122901 AAAAAT
1 AAAAAT
122907 TCCAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATCAAAATCATTTAT
Found at i:122907 original size:19 final size:19
Alignment explanation
Indices: 122863--122913 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
122853 ATTACAAAAA
*
122863 AAAAAATCAAAATCATTTT
1 AAAAATTCAAAATCATTTT
*
122882 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATCATTT-T
122901 AAAAATTCCAAAA
1 AAAAATT-CAAAA
122914 AATATAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATTCAAAATCATTTT
Found at i:123056 original size:2 final size:2
Alignment explanation
Indices: 123049--123093 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
123039 AAGTTTTCAA
123049 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123091 AT A
1 AT A
123094 GTTTCAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:131180 original size:17 final size:18
Alignment explanation
Indices: 131158--131193 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
131148 TTTATCCTCT
*
131158 ATTTTTTAT-TTAAATAA
1 ATTTTTTATGTCAAATAA
131175 ATTTTTTATGTCAAATAA
1 ATTTTTTATGTCAAATAA
131193 A
1 A
131194 ATGTTGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTTTTATGTCAAATAA
Found at i:135046 original size:30 final size:30
Alignment explanation
Indices: 135006--135094 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
134996 TTAATGTCAT
*
135006 ATTTGGTACTTGAATTTGATATTTTTTTTA
1 ATTTGGTACTTGAATTTGATTTTTTTTTTA
* *
135036 ATTTGATACTTAAATTTGATTTTTTTTTTA
1 ATTTGGTACTTGAATTTGATTTTTTTTTTA
*
135066 ATTTGGTACCTGAATTTGATTTTTTTTTT
1 ATTTGGTACTTGAATTTGATTTTTTTTTT
135095 TTTAAATTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.62
Consensus pattern (30 bp):
ATTTGGTACTTGAATTTGATTTTTTTTTTA
Found at i:142053 original size:2 final size:2
Alignment explanation
Indices: 142046--142086 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
142036 CAAGCATACC
*
142046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
142087 TCATTTTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:142834 original size:32 final size:32
Alignment explanation
Indices: 142798--142859 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
142788 ATCTCACATA
*
142798 AAAAAAATAATT-TAAAATTTATAAAAAAATTC
1 AAAAAAA-AATTATAAAAATTATAAAAAAATTC
* *
142830 AAAAATAAATTATAAAAATTATGAAAAAAT
1 AAAAAAAAATTATAAAAATTATAAAAAAAT
142860 ATCATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (32 bp):
AAAAAAAAATTATAAAAATTATAAAAAAATTC
Found at i:142848 original size:33 final size:30
Alignment explanation
Indices: 142800--142868 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 30
142790 CTCACATAAA
142800 AAAAATAATTTAAAATTTATAAAAAAAT-TC
1 AAAAATAATTTAAAA-TTATAAAAAAATATC
*
142830 AAAAATAAATTATAAAAATTATGAAAAAATATC
1 AAAAAT-AATT-T-AAAATTATAAAAAAATATC
*
142863 ATAAAT
1 AAAAAT
142869 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 6 0.18
31 4 0.12
32 12 0.36
33 11 0.33
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (30 bp):
AAAAATAATTTAAAATTATAAAAAAATATC
Found at i:155896 original size:28 final size:28
Alignment explanation
Indices: 155840--155898 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
155830 AGTAAGTCGA
**
155840 GGTTCAAAGATAACAAAAAAGACCGTTT
1 GGTTCAAAGATAACAAAAAAGACAATTT
* *
155868 GGTTCAAAGATAACAAAGAAGATAATTT
1 GGTTCAAAGATAACAAAAAAGACAATTT
155896 GGT
1 GGT
155899 AGAAAGCTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (28 bp):
GGTTCAAAGATAACAAAAAAGACAATTT
Found at i:161738 original size:80 final size:80
Alignment explanation
Indices: 161605--161804 Score: 400
Period size: 80 Copynumber: 2.5 Consensus size: 80
161595 TCCTTAAGAA
161605 GAAAACCAATTCCATTTCTCACTGCACAATATTTAATACAGAATAAAATCCTGTGAGTCCACAGG
1 GAAAACCAATTCCATTTCTCACTGCACAATATTTAATACAGAATAAAATCCTGTGAGTCCACAGG
161670 GGCACTAAAAGAGTT
66 GGCACTAAAAGAGTT
161685 GAAAACCAATTCCATTTCTCACTGCACAATATTTAATACAGAATAAAATCCTGTGAGTCCACAGG
1 GAAAACCAATTCCATTTCTCACTGCACAATATTTAATACAGAATAAAATCCTGTGAGTCCACAGG
161750 GGCACTAAAAGAGTT
66 GGCACTAAAAGAGTT
161765 GAAAACCAATTCCATTTCTCACTGCACAATATTTAATACA
1 GAAAACCAATTCCATTTCTCACTGCACAATATTTAATACA
161805 TAATCTTTTT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 120 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (80 bp):
GAAAACCAATTCCATTTCTCACTGCACAATATTTAATACAGAATAAAATCCTGTGAGTCCACAGG
GGCACTAAAAGAGTT
Found at i:162007 original size:15 final size:15
Alignment explanation
Indices: 161989--162033 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
161979 AAAATTATTT
161989 TTTTTAAATATAAAA
1 TTTTTAAATATAAAA
* **
162004 TTTTTAAA-ATTATT
1 TTTTTAAATATAAAA
162018 TTTTTAAATATAAAA
1 TTTTTAAATATAAAA
162033 T
1 T
162034 CATTAAAATC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTAAATATAAAA
Found at i:162029 original size:29 final size:30
Alignment explanation
Indices: 161969--162042 Score: 123
Period size: 29 Copynumber: 2.5 Consensus size: 30
161959 GCAAATGATT
161969 TAAAATTATTAAAATTATTTTTTTTAAATA
1 TAAAATTATTAAAATTATTTTTTTTAAATA
*
161999 TAAAATTTTTAAAATTA-TTTTTTTAAATA
1 TAAAATTATTAAAATTATTTTTTTTAAATA
*
162028 TAAAATCATTAAAAT
1 TAAAATTATTAAAAT
162043 CATCATCATC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTTTAAATA
Found at i:174782 original size:4 final size:4
Alignment explanation
Indices: 174773--174811 Score: 69
Period size: 4 Copynumber: 9.5 Consensus size: 4
174763 CCAAAACAGG
174773 GGAT GGAT GGAT GGAT GGAT GGAT GGAT GGAT GGGAT GG
1 GGAT GGAT GGAT GGAT GGAT GGAT GGAT GGAT -GGAT GG
174812 GACCCCTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (4 bp):
GGAT
Found at i:184894 original size:25 final size:23
Alignment explanation
Indices: 184866--184924 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
184856 TTTTAAAAAT
184866 ATTTATTTTATTTTATTATTTAATA
1 ATTT-TTTTATTTT-TTATTTAATA
* *
184891 ATTTTATATATTTTTTATTTATTA
1 ATTTT-TTTATTTTTTATTTAATA
*
184915 AATTTTTTAT
1 ATTTTTTTAT
184925 ATAGTCATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 4 0.14
24 14 0.48
25 11 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTTTTATTTTTTATTTAATA
Found at i:184906 original size:27 final size:27
Alignment explanation
Indices: 184876--184927 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
184866 ATTTATTTTA
*
184876 TTTTA-TTATTTAATAATTTTATATATT
1 TTTTATTTATTAAAT-ATTTTATATATT
*
184903 TTTTATTTATTAAATTTTTTATATA
1 TTTTATTTATTAAATATTTTATATA
184928 GTCATCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATTTATTAAATATTTTATATATT
Found at i:184925 original size:25 final size:25
Alignment explanation
Indices: 184866--184926 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
184856 TTTTAAAAAT
184866 ATTTATTT-TATTTTATTATTTAATA
1 ATTT-TTTATATTTTATTATTTAATA
* *
184891 ATTTTATATATTTT-TTATTTATTAA
1 ATTTTTTATATTTTATTATTTAAT-A
184916 ATTTTTTATAT
1 ATTTTTTATAT
184927 AGTCATCTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTTTTTATATTTTATTATTTAATA
Found at i:185297 original size:18 final size:18
Alignment explanation
Indices: 185274--185315 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
185264 CTCTCTAAAA
185274 AAAATT-AAAATAATTTT-T
1 AAAATTCAAAAT--TTTTAT
185292 AAAATTCAAAATTTTTAT
1 AAAATTCAAAATTTTTAT
185310 AAAATT
1 AAAATT
185316 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTCAAAATTTTTAT
Done.