Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2429
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: 89756
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Found at i:345 original size:37 final size:37
Alignment explanation
Indices: 301--390 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
291 ATTTTTTCAA
* ** *
301 TGGCACAGTTCGAAACAAAAATTACTATTCTTACTGG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
* *
338 TGGCACAGGTCGGAACAAAAAGCACTATTTTTACTAG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
375 TGGCACAGGTCGAAAC
1 TGGCACAGGTCGAAAC
391 CAGTTTTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (37 bp):
TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
Found at i:359 original size:74 final size:74
Alignment explanation
Indices: 233--390 Score: 169
Period size: 74 Copynumber: 2.1 Consensus size: 74
223 TTTGTAGCAT
* * *
233 AGGTTGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGCTATTATTTTTT
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGC-ACTATTTTTA
298 C-AATGGCAC
65 CTAATGGCAC
* * * * * **
307 AGTTCGAAACAAAAATTACTATTCTTA-CTGGTGGCACAGG-TCGGAACAAAAAGCACTATTTTT
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCAC-GGTTCAAAAC-AAAAGCACTATTTTT
*
370 ACTAGTGGCAC
64 ACTAATGGCAC
381 AGGTCGAAAC
1 AGGTCGAAAC
391 CAGTTTTTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
73 22 0.32
74 47 0.68
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (74 bp):
AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGCACTATTTTTAC
TAATGGCAC
Found at i:543 original size:15 final size:16
Alignment explanation
Indices: 523--552 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
513 ACAAAAGCAA
523 AAATCACA-TATTTAT
1 AAATCACATTATTTAT
538 AAATCACATTATTTA
1 AAATCACATTATTTA
553 CAAAGCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATCACATTATTTAT
Found at i:3970 original size:13 final size:13
Alignment explanation
Indices: 3952--4008 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
3942 CATAAAGTGT
3952 TGTATCGATACAA
1 TGTATCGATACAA
3965 TGTATCGATACATAA
1 TGTATCGATAC--AA
3980 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
3997 TGTATCGATACA
1 TGTATCGATACA
4009 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3987 original size:32 final size:32
Alignment explanation
Indices: 3932--4029 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
3922 TTCAACGATT
3932 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
3965 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
3997 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
4029 T
1 T
4030 TTAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3989 original size:19 final size:18
Alignment explanation
Indices: 3930--4027 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
3920 ATTTCAACGA
3930 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
3949 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
3965 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3981 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
3997 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
4013 TTTTGTATCGATACA
1 -TTTGTATCGATACA
4028 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:8313 original size:19 final size:18
Alignment explanation
Indices: 8271--8314 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
8261 ATGACGTGTT
*
8271 TGATGACGTTGCTAATGT
1 TGATGACGTTGCTAATGA
* *
8289 TGATGACGTTGTTTATTGA
1 TGATGACGTTG-CTAATGA
8308 TGATGAC
1 TGATGAC
8315 ATGGCATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (18 bp):
TGATGACGTTGCTAATGA
Found at i:9568 original size:2 final size:2
Alignment explanation
Indices: 9561--9592 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9551 TTAGCTATGC
9561 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
9593 TGGTATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9622 original size:22 final size:23
Alignment explanation
Indices: 9597--9641 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
9587 ATATATTGGT
9597 ATAAAAAAATCAT-AATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
9619 ATAAAAAAATCATAAATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
9642 TTTAAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAAAATCATAAATTTAAAA
Found at i:10078 original size:2 final size:2
Alignment explanation
Indices: 10071--10097 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10061 TATGAAATGG
10071 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 A
10098 AAAGACTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11921 original size:4 final size:4
Alignment explanation
Indices: 11912--11963 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
11902 GTTTGGTGAA
* *
11912 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -GAG AAA- AAA- AAGG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
11957 AAAG AAA
1 AAAG AAA
11964 AAAATTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 7 0.17
4 35 0.83
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:12379 original size:4 final size:4
Alignment explanation
Indices: 12364--12424 Score: 83
Period size: 4 Copynumber: 15.8 Consensus size: 4
12354 TCAAGAGGGA
*
12364 AAAG AGAG AAAG AAAG AAAG AAAG AGAA- AAA- AAAG AAA- AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
12410 AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAA
12425 AGGAGAATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 8 0.15
4 42 0.81
5 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:12431 original size:12 final size:12
Alignment explanation
Indices: 12362--12431 Score: 60
Period size: 12 Copynumber: 5.9 Consensus size: 12
12352 GTTCAAGAGG
12362 GAAAAGAGAGAAA
1 GAAAAGA-AGAAA
12375 G-AAAGAAAGAAA
1 GAAAAG-AAGAAA
12387 GAGAAA-AA-AAA
1 GA-AAAGAAGAAA
12398 GAAAA-AAGAAA
1 GAAAAGAAGAAA
12409 G-AAAGAAAGAAA
1 GAAAAG-AAGAAA
*
12421 GAAAAGGAGAA
1 GAAAAGAAGAA
12432 TAAATTTACG
Statistics
Matches: 49, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
10 8 0.16
11 9 0.18
12 23 0.47
13 6 0.12
14 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAAAGAAGAAA
Found at i:12762 original size:14 final size:14
Alignment explanation
Indices: 12743--12772 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12733 TTGCGTATTA
*
12743 ATTTATATATATAT
1 ATTTATACATATAT
12757 ATTTATACATATAT
1 ATTTATACATATAT
12771 AT
1 AT
12773 ATAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATACATATAT
Found at i:12785 original size:20 final size:20
Alignment explanation
Indices: 12746--12787 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12736 CGTATTAATT
*
12746 TATATATATATATTTATACA
1 TATATATATATATTAATACA
12766 TATATATATA-ATTAATTACA
1 TATATATATATATTAA-TACA
12786 TA
1 TA
12788 AAGAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATATATATATTAATACA
Found at i:13997 original size:15 final size:16
Alignment explanation
Indices: 13977--14006 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13967 TTTTTAAATA
13977 AATTTTA-TTAATTAT
1 AATTTTATTTAATTAT
13992 AATTTTATTTAATTA
1 AATTTTATTTAATTA
14007 AAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTTAATTAT
Found at i:14320 original size:18 final size:20
Alignment explanation
Indices: 14280--14319 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
14270 AAATTGTATT
14280 TAAAATATTATATATTTATA
1 TAAAATATTATATATTTATA
14300 TAAAAT-TTGATATATTTATA
1 TAAAATATT-ATATATTTATA
14320 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TAAAATATTATATATTTATA
Found at i:14406 original size:21 final size:23
Alignment explanation
Indices: 14353--14417 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
14343 CGTTTCTGTA
14353 TTTATGTTATA-TTCATATTATT
1 TTTATGTTATATTTCATATTATT
* *
14375 TTTCATATTATATTTTA-ATT-TT
1 TTT-ATGTTATATTTCATATTATT
*
14397 TTTATGTTATA-TTCATTTTAT
1 TTTATGTTATATTTCATATTAT
14418 ATAATCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 3 0.09
21 9 0.26
22 9 0.26
23 10 0.29
24 3 0.09
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (23 bp):
TTTATGTTATATTTCATATTATT
Found at i:14736 original size:15 final size:15
Alignment explanation
Indices: 14716--14760 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
14706 GAAGCTCTTA
14716 TTTATTTATATTATT
1 TTTATTTATATTATT
*
14731 TTTA-TTACTCTTATT
1 TTTATTTA-TATTATT
14746 TTTATTT-TATT-TT
1 TTTATTTATATTATT
14759 TT
1 TT
14761 AAATTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 4 0.15
14 6 0.23
15 14 0.54
16 2 0.08
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTATATTATT
Found at i:14905 original size:3 final size:3
Alignment explanation
Indices: 14897--14932 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
14887 AAATGTATTA
14897 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14933 TCAAAAGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16638 original size:33 final size:30
Alignment explanation
Indices: 16587--16678 Score: 80
Period size: 32 Copynumber: 3.0 Consensus size: 30
16577 TATGGTATCA
* *
16587 ATATAATTATATTTTAAAAATTTATATAATAT
1 ATATAATTATATATT-AAAATTAATATAA-AT
*
16619 ATATTATTAATATATTAAAATTAATATAAAT
1 ATATAATT-ATATATTAAAATTAATATAAAT
* * *
16650 ATA-AAATATA-ATTATAATATAATAAAAAT
1 ATATAATTATATATTAAAAT-TAATATAAAT
16679 TTTATGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.14
29 12 0.24
30 2 0.04
31 5 0.10
32 19 0.37
33 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATAATTATATATTAAAATTAATATAAAT
Found at i:16651 original size:18 final size:20
Alignment explanation
Indices: 16609--16676 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
16599 TTTAAAAATT
*
16609 TATATAATATAT-ATTATTAA
1 TATATAAAATATAATTA-TAA
16629 TATATTAAAAT-TAA-TATAA
1 TATA-TAAAATATAATTATAA
16648 -ATATAAAATATAATTATAA
1 TATATAAAATATAATTATAA
16667 TATAATAAAA
1 TAT-ATAAAA
16677 ATTTTATGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 8 0.20
20 9 0.22
21 12 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAAAATATAATTATAA
Found at i:19206 original size:70 final size:70
Alignment explanation
Indices: 19093--19234 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
19083 ACAAATTGGT
*
19093 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATGG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
19158 GAGTC
66 GAGTC
19163 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
19228 GAGTC
66 GAGTC
19233 AC
1 AC
19235 TTTTAGAATC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (70 bp):
ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAGCATACTATAG
GAGTC
Found at i:22455 original size:37 final size:37
Alignment explanation
Indices: 22411--22500 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
22401 ATTTTTTTAA
* ** *
22411 TGGCACAGTTCGAAACAAAAATTACTATTCTTACTGG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
* *
22448 TGGCACAGGTCGGAACAAAAAGCACTATTTTTACTAG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
22485 TGGCACAGGTCGAAAC
1 TGGCACAGGTCGAAAC
22501 CAGTTTTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (37 bp):
TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
Found at i:22469 original size:74 final size:74
Alignment explanation
Indices: 22343--22500 Score: 169
Period size: 74 Copynumber: 2.1 Consensus size: 74
22333 TTTGTAGCAT
* *
22343 AGGTTGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGCTATTATTTTT-
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGC-ACTATTTTTA
*
22407 TTAATGGCAC
65 CTAATGGCAC
* * * * * **
22417 AGTTCGAAACAAAAATTACTATTCTTA-CTGGTGGCACAGG-TCGGAACAAAAAGCACTATTTTT
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCAC-GGTTCAAAAC-AAAAGCACTATTTTT
*
22480 ACTAGTGGCAC
64 ACTAATGGCAC
22491 AGGTCGAAAC
1 AGGTCGAAAC
22501 CAGTTTTTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
73 21 0.30
74 48 0.70
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (74 bp):
AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGCACTATTTTTAC
TAATGGCAC
Found at i:22654 original size:16 final size:16
Alignment explanation
Indices: 22633--22667 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22623 ACAAAAGCAA
22633 AAATCACA-TATTTTAC
1 AAATCACATTA-TTTAC
22649 AAATCACATTATTTAC
1 AAATCACATTATTTAC
22665 AAA
1 AAA
22668 GCAATTGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATCACATTATTTAC
Found at i:26094 original size:32 final size:32
Alignment explanation
Indices: 26039--26132 Score: 170
Period size: 32 Copynumber: 2.9 Consensus size: 32
26029 TTCAACGATT
26039 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
26072 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
26104 TGTATCGATACATAAGTTTTGTATCGATA
1 TGTATCGATACATAAGTGTTGTATCGATA
26133 TAATTTAAGC
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 47 0.78
33 13 0.22
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:26096 original size:19 final size:18
Alignment explanation
Indices: 26037--26132 Score: 86
Period size: 13 Copynumber: 5.7 Consensus size: 18
26027 ATTTCAACGA
26037 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
26056 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
26072 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
26088 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
26104 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
26120 TTTTGTATCGATA
1 -TTTGTATCGATA
26133 TAATTTAAGC
Statistics
Matches: 64, Mismatches: 0, Indels: 26
0.71 0.00 0.29
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 22 0.34
20 12 0.19
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:30426 original size:19 final size:18
Alignment explanation
Indices: 30384--30427 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30374 ATGACGTGTT
*
30384 TGATGACGTTGCTAATGT
1 TGATGACGTTGCTAATGA
* *
30402 TGATGACGTTGTTTATTGA
1 TGATGACGTTG-CTAATGA
30421 TGATGAC
1 TGATGAC
30428 ATGGCATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (18 bp):
TGATGACGTTGCTAATGA
Found at i:30872 original size:24 final size:24
Alignment explanation
Indices: 30845--30898 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
30835 AAAGAATTCT
* *
30845 TAATAAGAATCTCTAATATTATGC
1 TAATAAGAATCACTAATATGATGC
*
30869 TAATTAGAATCACTAATATGATGC
1 TAATAAGAATCACTAATATGATGC
*
30893 TGATAA
1 TAATAA
30899 AGTCAACTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (24 bp):
TAATAAGAATCACTAATATGATGC
Found at i:30960 original size:22 final size:22
Alignment explanation
Indices: 30930--30973 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30920 ACAATCCAAT
*
30930 GCAAGATATGCAAGATATTCTA
1 GCAACATATGCAAGATATTCTA
30952 GCAACATATGCAAGATATTCTA
1 GCAACATATGCAAGATATTCTA
30974 ACAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (22 bp):
GCAACATATGCAAGATATTCTA
Found at i:31113 original size:14 final size:14
Alignment explanation
Indices: 31085--31133 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
31075 AATTTATTGA
31085 AAAAATATTAAATTT
1 AAAAATA-TAAATTT
*
31100 AAAAATATATATTT
1 AAAAATATAAATTT
*
31114 AAAAA-ATAAATTA
1 AAAAATATAAATTT
31127 AAAAATA
1 AAAAATA
31134 AAGTATGAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 11 0.37
14 12 0.40
15 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATATAAATTT
Found at i:31130 original size:13 final size:12
Alignment explanation
Indices: 31093--31135 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
31083 GAAAAAATAT
31093 TAAATTTAAAAATA
1 TAAA-TTAAAAA-A
*
31107 TATATTTAAAAAA
1 TA-AATTAAAAAA
31120 TAAATTAAAAAA
1 TAAATTAAAAAA
31132 TAAA
1 TAAA
31136 GTATGAGCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 13 0.50
13 3 0.12
14 9 0.35
15 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATTAAAAAA
Found at i:31482 original size:30 final size:28
Alignment explanation
Indices: 31447--31539 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 28
31437 AAGTCAAAGG
31447 ATTTATTTATAAGTATATTAAAAATTAAA
1 ATTTATTTA-AAGTATATTAAAAATTAAA
* *
31476 ATTT-TATTCAAGTATAAATTAAAAATTATA
1 ATTTAT-TTAAAGTAT--ATTAAAAATTAAA
*
31506 ATTTATTTAAA-TATAATAAAAATATAAAA
1 ATTTATTTAAAGTATATTAAAAAT-T-AAA
31535 ATTTA
1 ATTTA
31540 AGTAATATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
27 8 0.15
28 8 0.15
29 16 0.30
30 20 0.38
31 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTTATTTAAAGTATATTAAAAATTAAA
Found at i:31537 original size:29 final size:28
Alignment explanation
Indices: 31447--31553 Score: 92
Period size: 29 Copynumber: 3.7 Consensus size: 28
31437 AAGTCAAAGG
*
31447 ATTTATTTATAAGTATATTAAAAATTAAAA
1 ATTTATTTA-AA-TATAATAAAAATTAAAA
* * * *
31477 TTTTATTCAAGTATAAATTAAAAATT-ATA
1 ATTTATTTAAATAT-AA-TAAAAATTAAAA
31506 ATTTATTTAAATATAATAAAAATATAAAA
1 ATTTATTTAAATATAATAAAAAT-TAAAA
**
31535 ATTTAAGT-AATATAATAAA
1 ATTTATTTAAATATAATAAA
31554 TTTAACTTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
27 7 0.11
28 17 0.27
29 23 0.37
30 15 0.24
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
ATTTATTTAAATATAATAAAAATTAAAA
Found at i:33968 original size:20 final size:20
Alignment explanation
Indices: 33945--34029 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
33935 AAGTACCCAG
33945 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
33965 ATGTATCGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
33995 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
34016 ATGTATCGATACAT
1 ATGTATCGATACAT
34030 CTAGTTAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
20 27 0.50
21 2 0.04
24 5 0.09
27 5 0.09
30 2 0.04
31 13 0.24
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:34475 original size:13 final size:14
Alignment explanation
Indices: 34453--34481 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34443 ATATCTTAGC
34453 AAAACATCAACACA
1 AAAACATCAACACA
34467 AAAAC-TCAACACA
1 AAAACATCAACACA
34480 AA
1 AA
34482 TCTATTCCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACATCAACACA
Found at i:38116 original size:16 final size:16
Alignment explanation
Indices: 38095--38125 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38085 AATCAAAAAA
38095 ATTAATTTAGATTTGG
1 ATTAATTTAGATTTGG
*
38111 ATTAATTTAGCTTTG
1 ATTAATTTAGATTTG
38126 ACATTATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (16 bp):
ATTAATTTAGATTTGG
Found at i:38935 original size:21 final size:20
Alignment explanation
Indices: 38903--38943 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
38893 TTATCACTTA
*
38903 AAAAATTAATAAAAAATAAT
1 AAAAATAAATAAAAAATAAT
*
38923 AAAAATAACATAAAAACTAAT
1 AAAAATAA-ATAAAAAATAAT
38944 TTTATGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAATAAATAAAAAATAAT
Found at i:39562 original size:5 final size:5
Alignment explanation
Indices: 39552--39577 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39542 ATGGATGCAT
39552 GCGAG GCGAG GCGAG GCGAG GCGAG G
1 GCGAG GCGAG GCGAG GCGAG GCGAG G
39578 GGCTAGTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.62, T:0.00
Consensus pattern (5 bp):
GCGAG
Found at i:42743 original size:2 final size:2
Alignment explanation
Indices: 42736--42791 Score: 55
Period size: 2 Copynumber: 29.0 Consensus size: 2
42726 AATTTAAACC
* * *
42736 AT AT AT AT AT AT A- AT AT TT AT AT -T TT GT AT -T AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
42776 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
42792 TGCACAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 3 0.07
2 41 0.89
3 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
AT
Found at i:44741 original size:64 final size:65
Alignment explanation
Indices: 44611--44743 Score: 171
Period size: 64 Copynumber: 2.1 Consensus size: 65
44601 TCGTGTTTTA
* * * * * *
44611 TTTAAATTTGAATGTTTGATTATAAGGGATTTTTATTGAATTAAAATTTAAAATAATTTTAAATT
1 TTTAAATTTGAATCTCTGATTAAAAAGGATTTTTATTGAATCAAAATTTAAAATAATATTAAATT
* *
44676 TTTAAATTTGAATACTCTG-TTAAAAAGGATTTTT-TTGGATCAAAATTTAAAATTATATTAAAT
1 TTTAAATTTGAAT-CTCTGATTAAAAAGGATTTTTATTGAATCAAAATTTAAAATAATATTAAAT
44739 T
65 T
44740 TTTA
1 TTTA
44744 TGAATATAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
64 30 0.51
65 26 0.44
66 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (65 bp):
TTTAAATTTGAATCTCTGATTAAAAAGGATTTTTATTGAATCAAAATTTAAAATAATATTAAATT
Found at i:46267 original size:2 final size:2
Alignment explanation
Indices: 46260--46299 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
46250 TTAGCTATGC
46260 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
46300 TGGTATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46329 original size:22 final size:23
Alignment explanation
Indices: 46304--46348 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
46294 ATATATTGGT
46304 ATAAAAAAATCAT-AATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
46326 ATAAAAAAATCATAAATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
46349 TTTAAAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAAAATCATAAATTTAAAA
Found at i:46787 original size:2 final size:2
Alignment explanation
Indices: 46780--46816 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46770 TATGAAATGG
46780 AT AT AT AT 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 AT AT AT AT A
46817 AAAGACTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48098 original size:13 final size:13
Alignment explanation
Indices: 48080--48104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48070 AAGATAAATT
48080 AAAATATAATACG
1 AAAATATAATACG
48093 AAAATATAATAC
1 AAAATATAATAC
48105 AACATAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAATATAATACG
Found at i:48286 original size:21 final size:20
Alignment explanation
Indices: 48257--48301 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
48247 ATTATATATG
*
48257 AATATATTATAATACATATAA
1 AATAAATTATAATACATA-AA
*
48278 AATAAATTATTAATATATAAA
1 AATAAATTA-TAATACATAAA
48299 AAT
1 AAT
48302 TAATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTATAATACATAAA
Found at i:48615 original size:4 final size:4
Alignment explanation
Indices: 48606--48640 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
48596 GTTTGGTGAA
48606 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
48641 AAAATTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:48700 original size:10 final size:10
Alignment explanation
Indices: 48685--48746 Score: 69
Period size: 10 Copynumber: 6.5 Consensus size: 10
48675 TTTAAAATAT
48685 TATATTTTTA
1 TATATTTTTA
48695 TATATTTTT-
1 TATATTTTTA
* *
48704 TATATATTAA
1 TATATTTTTA
48714 TA-ATTTATT-
1 TATATTT-TTA
48723 T-TATTTTTA
1 TATATTTTTA
48732 TATATTTTTA
1 TATATTTTTA
48742 TATAT
1 TATAT
48747 ACGTGTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 2 0.05
9 16 0.37
10 25 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATTTTTA
Found at i:48960 original size:4 final size:4
Alignment explanation
Indices: 48951--48977 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
48941 TAATTTTTTA
48951 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
48978 ACATACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:49071 original size:4 final size:4
Alignment explanation
Indices: 49056--49109 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
49046 TCAAGAGGGA
* *
49056 AAAG AGAG AAAG AAAG AAAG AAAG AGAA- AAAA AAAG AAA- AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
49103 AAAG AAA
1 AAAG AAA
49110 AAGAGAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
3 5 0.11
4 37 0.84
5 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:49737 original size:23 final size:22
Alignment explanation
Indices: 49706--49755 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
49696 GTCATATTCA
*
49706 TTTTTTTATATTATATTTTAAT
1 TTTTTTTATATCATATTTTAAT
* *
49728 TATTTTTTATGTCATATTTTTAT
1 T-TTTTTTATATCATATTTTAAT
49751 TTTTT
1 TTTTT
49756 GTACATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTTATATCATATTTTAAT
Found at i:50685 original size:15 final size:16
Alignment explanation
Indices: 50665--50694 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50655 TTTTTAAATA
50665 AATTTTA-TTAATTAT
1 AATTTTATTTAATTAT
50680 AATTTTATTTAATTA
1 AATTTTATTTAATTA
50695 AAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTTAATTAT
Found at i:50991 original size:20 final size:20
Alignment explanation
Indices: 50970--51007 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50960 ATTATATTTA
50970 AAATATT-ATATATTTATAT
1 AAATATTGATATATTTATAT
*
50989 AAATTTTGATATATTTATA
1 AAATATTGATATATTTATA
51008 ATTTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATATTGATATATTTATAT
Found at i:51138 original size:15 final size:14
Alignment explanation
Indices: 51114--51144 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
51104 ATATAATCAT
51114 ATTGTATTATTCTA
1 ATTGTATTATTCTA
51128 ATTGATATTATTCTA
1 ATTG-TATTATTCTA
51143 AT
1 AT
51145 AACTCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (14 bp):
ATTGTATTATTCTA
Found at i:51425 original size:15 final size:15
Alignment explanation
Indices: 51405--51449 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
51395 GAAGCTCTTA
51405 TTTATTTATATTATT
1 TTTATTTATATTATT
*
51420 TTTA-TTACTCTTATT
1 TTTATTTA-TATTATT
51435 TTTATTT-TATT-TT
1 TTTATTTATATTATT
51448 TT
1 TT
51450 AAATTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 4 0.15
14 6 0.23
15 14 0.54
16 2 0.08
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTATATTATT
Found at i:52779 original size:20 final size:20
Alignment explanation
Indices: 52751--52788 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52741 TTTATATTAT
52751 ATATAATAATTTAAAAATATA
1 ATATAATAA-TTAAAAATATA
52772 ATAT-ATAATTAAAAATA
1 ATATAATAATTAAAAATA
52789 AAAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATAATAATTAAAAATATA
Found at i:52908 original size:15 final size:16
Alignment explanation
Indices: 52876--52928 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
52866 ATCAACTTTC
*
52876 AAAATTAAATAATTTA
1 AAAATTAAATAATATA
*
52892 AAAATTGAAT-ATAT-
1 AAAATTAAATAATATA
52906 AAAATTAAATTAAT-T-
1 AAAATTAAA-TAATATA
52921 AAAATTAA
1 AAAATTAA
52929 TCGATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.25
15 13 0.41
16 11 0.34
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAATTAAATAATATA
Found at i:53134 original size:33 final size:30
Alignment explanation
Indices: 53083--53174 Score: 80
Period size: 32 Copynumber: 3.0 Consensus size: 30
53073 TATGGTATCA
* *
53083 ATATAATTATATTTTAAAAATTTATATAATAT
1 ATATAATTATATATT-AAAATTAATATAA-AT
*
53115 ATATTATTAATATATTAAAATTAATATAAAT
1 ATATAATT-ATATATTAAAATTAATATAAAT
* * *
53146 ATA-AAATATA-ATTATAATATAATAAAAAT
1 ATATAATTATATATTAAAAT-TAATATAAAT
53175 TTTATGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.14
29 12 0.24
30 2 0.04
31 5 0.10
32 19 0.37
33 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATAATTATATATTAAAATTAATATAAAT
Found at i:53147 original size:18 final size:20
Alignment explanation
Indices: 53105--53172 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
53095 TTTAAAAATT
*
53105 TATATAATATAT-ATTATTAA
1 TATATAAAATATAATTA-TAA
53125 TATATTAAAAT-TAA-TATAA
1 TATA-TAAAATATAATTATAA
53144 -ATATAAAATATAATTATAA
1 TATATAAAATATAATTATAA
53163 TATAATAAAA
1 TAT-ATAAAA
53173 ATTTTATGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 6 0.15
18 6 0.15
19 8 0.20
20 9 0.22
21 12 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAAAATATAATTATAA
Found at i:53527 original size:21 final size:21
Alignment explanation
Indices: 53503--53544 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53493 GATTTATGAT
53503 AAAATATTTAAA-AAGTAATTA
1 AAAATA-TTAAATAAGTAATTA
*
53524 AAAATATTAAATAATTAATTA
1 AAAATATTAAATAAGTAATTA
53545 TACTTGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATATTAAATAAGTAATTA
Found at i:55659 original size:70 final size:70
Alignment explanation
Indices: 55546--55687 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
55536 ACAAATTGGT
*
55546 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATGG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATAG
55611 GAGTC
66 GAGTC
* *
55616 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGTTGAAATGAACTAAGTAGCATACTATAG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATAG
55681 GAGTC
66 GAGTC
55686 AC
1 AC
55688 TTTTAGAATC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (70 bp):
ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATAG
GAGTC
Found at i:58907 original size:37 final size:37
Alignment explanation
Indices: 58863--58952 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
58853 ATTTTTTCAA
* ** *
58863 TGGCACAGTTCGAAACAAAAATTACTATTCTTACTGG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
* *
58900 TGGCACAGGTCGGAACAAAAAGCACTATTTTTACTAG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
58937 TGGCACAGGTCGAAAC
1 TGGCACAGGTCGAAAC
58953 CAGTTTTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (37 bp):
TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
Found at i:58921 original size:74 final size:74
Alignment explanation
Indices: 58795--58952 Score: 169
Period size: 74 Copynumber: 2.1 Consensus size: 74
58785 TTTGTAGCAT
* * *
58795 AGGTTGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGCTATTATTTTTT
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGC-ACTATTTTTA
58860 C-AATGGCAC
65 CTAATGGCAC
* * * * * **
58869 AGTTCGAAACAAAAATTACTATTCTTA-CTGGTGGCACAGG-TCGGAACAAAAAGCACTATTTTT
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCAC-GGTTCAAAAC-AAAAGCACTATTTTT
*
58932 ACTAGTGGCAC
64 ACTAATGGCAC
58943 AGGTCGAAAC
1 AGGTCGAAAC
58953 CAGTTTTTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
73 22 0.32
74 47 0.68
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (74 bp):
AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGCACTATTTTTAC
TAATGGCAC
Found at i:62525 original size:13 final size:13
Alignment explanation
Indices: 62507--62563 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
62497 CATAAAGTGT
62507 TGTATCGATACAA
1 TGTATCGATACAA
62520 TGTATCGATACATAA
1 TGTATCGATAC--AA
62535 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
62552 TGTATCGATACA
1 TGTATCGATACA
62564 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:62542 original size:32 final size:32
Alignment explanation
Indices: 62487--62584 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
62477 TTCAACGATT
62487 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
62520 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
62552 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
62584 T
1 T
62585 TTAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:62544 original size:19 final size:18
Alignment explanation
Indices: 62485--62582 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
62475 ATTTCAACGA
62485 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
62504 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
62520 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
62536 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
62552 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
62568 TTTTGTATCGATACA
1 -TTTGTATCGATACA
62583 ATTTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:66866 original size:19 final size:18
Alignment explanation
Indices: 66824--66867 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
66814 ATGACGTGTT
*
66824 TGATGACGTTGCTAATGT
1 TGATGACGTTGCTAATGA
* *
66842 TGATGACGTTGTTTATTGA
1 TGATGACGTTG-CTAATGA
66861 TGATGAC
1 TGATGAC
66868 ATGGCATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (18 bp):
TGATGACGTTGCTAATGA
Found at i:68121 original size:2 final size:2
Alignment explanation
Indices: 68114--68147 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
68104 TTAGCTATGC
68114 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
68148 TGGTATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68177 original size:22 final size:23
Alignment explanation
Indices: 68152--68196 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
68142 ATATATTGGT
68152 ATAAAAAAATCAT-AATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
68174 ATAAAAAAATCATAAATTTAAAA
1 ATAAAAAAATCATAAATTTAAAA
68197 TTTAAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAAAATCATAAATTTAAAA
Found at i:68633 original size:2 final size:2
Alignment explanation
Indices: 68626--68650 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68616 TATGAAATGG
68626 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 A
68651 AAAGACTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69289 original size:2 final size:2
Alignment explanation
Indices: 69282--69313 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
69272 TTGTATGATC
69282 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
69314 TGTACAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70481 original size:4 final size:4
Alignment explanation
Indices: 70472--70523 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
70462 GTTTGGTGAA
* *
70472 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -GAG AAA- AAA- AAGG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
70517 AAAG AAA
1 AAAG AAA
70524 AAAATTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 7 0.17
4 35 0.83
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:70938 original size:4 final size:4
Alignment explanation
Indices: 70923--70982 Score: 74
Period size: 4 Copynumber: 15.8 Consensus size: 4
70913 TCAAGAGGGA
*
70923 AAAG AGAG AAAG AAAG AAAG AAAG AGAA- AAA- AAAG -AA- AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
70968 AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAA
70983 AGGAGAATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
3 9 0.18
4 39 0.78
5 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:70959 original size:15 final size:14
Alignment explanation
Indices: 70933--70976 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
70923 AAAGAGAGAA
*
70933 AGAAAGAAAGAAAG
1 AGAAAAAAAGAAAG
*
70947 AGAAAAAAAAGAAAA
1 AG-AAAAAAAGAAAG
*
70962 AGAAAGAAAGAAAG
1 AGAAAAAAAGAAAG
70976 A
1 A
70977 AAGAAAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAAAG
Found at i:71320 original size:14 final size:14
Alignment explanation
Indices: 71301--71330 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
71291 TTGCGTATTA
*
71301 ATTTATATATATAT
1 ATTTATACATATAT
71315 ATTTATACATATAT
1 ATTTATACATATAT
71329 AT
1 AT
71331 ATAATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTATACATATAT
Found at i:71343 original size:20 final size:20
Alignment explanation
Indices: 71304--71345 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
71294 CGTATTAATT
*
71304 TATATATATATATTTATACA
1 TATATATATATATTAATACA
71324 TATATATATA-ATTAATTACA
1 TATATATATATATTAA-TACA
71344 TA
1 TA
71346 AAGAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATATATATATTAATACA
Found at i:71608 original size:23 final size:22
Alignment explanation
Indices: 71577--71626 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
71567 GTCATATTCA
*
71577 TTTTTTTATATTATATTTTAAT
1 TTTTTTTATATCATATTTTAAT
* *
71599 TATTTTTTATGTCATATTTTTAT
1 T-TTTTTTATATCATATTTTAAT
71622 TTTTT
1 TTTTT
71627 GTACATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTTTTATATCATATTTTAAT
Found at i:72557 original size:15 final size:16
Alignment explanation
Indices: 72537--72566 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
72527 TTTTTAAATA
72537 AATTTTA-TTAATTAT
1 AATTTTATTTAATTAT
72552 AATTTTATTTAATTA
1 AATTTTATTTAATTA
72567 AAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTTAATTAT
Found at i:72880 original size:18 final size:20
Alignment explanation
Indices: 72840--72879 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
72830 AAATTGTATT
72840 TAAAATATTATATATTTATA
1 TAAAATATTATATATTTATA
72860 TAAAAT-TTGATATATTTATA
1 TAAAATATT-ATATATTTATA
72880 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TAAAATATTATATATTTATA
Found at i:72966 original size:21 final size:23
Alignment explanation
Indices: 72913--72977 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
72903 CGTTTCTGTA
72913 TTTATGTTATA-TTCATATTATT
1 TTTATGTTATATTTCATATTATT
* *
72935 TTTCATATTATATTTTA-ATT-TT
1 TTT-ATGTTATATTTCATATTATT
*
72957 TTTATGTTATA-TTCATTTTAT
1 TTTATGTTATATTTCATATTAT
72978 ATAATCATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 3 0.09
21 9 0.26
22 9 0.26
23 10 0.29
24 3 0.09
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (23 bp):
TTTATGTTATATTTCATATTATT
Found at i:73297 original size:15 final size:15
Alignment explanation
Indices: 73277--73315 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
73267 GAAGCTCTTA
73277 TTTATTTATATTATT
1 TTTATTTATATTATT
*
73292 TTTA-TTACTCTTATT
1 TTTATTTA-TATTATT
73307 TTTATTTAT
1 TTTATTTAT
73316 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 15 0.71
16 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTATATTATT
Found at i:73465 original size:3 final size:3
Alignment explanation
Indices: 73457--73492 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
73447 AAATGTATTA
73457 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
73493 TCAAAAGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:74970 original size:15 final size:16
Alignment explanation
Indices: 74938--74990 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
74928 ATCAACTTTC
*
74938 AAAATTAAATAATTTA
1 AAAATTAAATAATATA
*
74954 AAAATTGAAT-ATAT-
1 AAAATTAAATAATATA
74968 AAAATTAAATTAAT-T-
1 AAAATTAAA-TAATATA
74983 AAAATTAA
1 AAAATTAA
74991 TCGATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 8 0.25
15 13 0.41
16 11 0.34
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAATTAAATAATATA
Found at i:75124 original size:5 final size:5
Alignment explanation
Indices: 75087--75230 Score: 56
Period size: 5 Copynumber: 29.2 Consensus size: 5
75077 TGATAACATG
* *
75087 ATAAT AT-AT ATACAT -TACAT A-AAT ATAAT -TAAT ATAAT ATTAT GAAAAT
1 ATAAT ATAAT ATA-AT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
** * * * *
75136 ATGGT ATCAAT ATAATT ATATT TTAA- A-AAT -TTAT ATAAT AT-AT ATTAT
1 ATAAT AT-AAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
75184 -TAAT ATATT AAAAT -TAAT ATAAT ATAAAAT ATAATT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT--AAT ATAA-T ATAAT ATAAT
75230 A
1 A
75231 AAAATTATAT
Statistics
Matches: 103, Mismatches: 19, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
3 2 0.02
4 23 0.22
5 56 0.54
6 17 0.17
7 5 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:75210 original size:37 final size:37
Alignment explanation
Indices: 75168--75254 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 37
75158 TTAAAAATTT
*
75168 ATATAATATATATTATTAATAT-ATTAAAATTA-ATATA
1 ATATAA-ATATATTA-TAATATAATAAAAATTATATATA
*
75205 ATATAAAATATAATTATAATATAATAAAAATTATATGTA
1 ATAT-AAATAT-ATTATAATATAATAAAAATTATATATA
75244 ATATAAATATA
1 ATATAAATATA
75255 CGAAGTAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
37 15 0.34
38 21 0.48
39 8 0.18
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (37 bp):
ATATAAATATATTATAATATAATAAAAATTATATATA
Found at i:75224 original size:18 final size:16
Alignment explanation
Indices: 75161--75228 Score: 68
Period size: 18 Copynumber: 4.1 Consensus size: 16
75151 TTATATTTTA
*
75161 AAAATTTATATAATAT
1 AAAATTAATATAATAT
*
75177 ATATTATTAATAT-AT-T
1 A-A-AATTAATATAATAT
75193 AAAATTAATATAATAT
1 AAAATTAATATAATAT
75209 AAAATATAATTATAATAT
1 AAAAT-TAA-TATAATAT
75227 AA
1 AA
75229 TAAAAATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 8 0.19
15 3 0.07
16 9 0.21
17 6 0.14
18 17 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTAATATAATAT
Found at i:77760 original size:70 final size:70
Alignment explanation
Indices: 77647--77788 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
77637 ACAAATTGGT
*
77647 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATGG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATAG
77712 GAGTC
66 GAGTC
* *
77717 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGTTGAAATGAACTAAGTAGCATACTATAG
1 ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATAG
77782 GAGTC
66 GAGTC
77787 AC
1 AC
77789 CTTTAGAATC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (70 bp):
ACAGGTTGCCACAAATGATGTCAGAGCAATGCACTAGCTGAAATGAACTAAGTAACATACTATAG
GAGTC
Found at i:81000 original size:37 final size:37
Alignment explanation
Indices: 80959--81048 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
80949 TTTTTTTCAA
* ** *
80959 TGGCACAGTTCGAAACAAAAATTACTATTCTTACTGG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
* *
80996 TGGCACGGGTCGAAACAAAAAGCACTATTTTTACTAG
1 TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
81033 TGGCACAGGTCGAAAC
1 TGGCACAGGTCGAAAC
81049 CAGTTTTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (37 bp):
TGGCACAGGTCGAAACAAAAAGCACTATTCTTACTAG
Found at i:81037 original size:74 final size:75
Alignment explanation
Indices: 80890--81048 Score: 180
Period size: 74 Copynumber: 2.1 Consensus size: 75
80880 CTTGTAGCAT
* * * *
80890 AGGTTGAAACAAAAATCACTATTCTAATCCGATGGCACGGTTCAAAACAAAAGCTATTATTTTTT
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGGTCAAAACAAAAGCTACTATTTTTC
80955 TCAATGGCAC
66 TCAATGGCAC
* * * * * *
80965 AGTTCGAAACAAAAATTACTATTCTTA-CTGGTGGCACGGGTCGAAACAAAAAGC-ACTATTTTT
1 AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGGTCAAAAC-AAAAGCTACTATTTTT
*
81028 ACT-AGTGGCAC
65 -CTCAATGGCAC
81039 AGGTCGAAAC
1 AGGTCGAAAC
81049 CAGTTTTTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
74 40 0.57
75 30 0.43
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (75 bp):
AGGTCGAAACAAAAATCACTATTCTAATCCGATGGCACGGGTCAAAACAAAAGCTACTATTTTTC
TCAATGGCAC
Found at i:81202 original size:16 final size:16
Alignment explanation
Indices: 81181--81215 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
81171 ACAAAAGCAA
81181 AAATCACA-TATTTCAC
1 AAATCACATTATTT-AC
81197 AAATCACATTATTTAC
1 AAATCACATTATTTAC
81213 AAA
1 AAA
81216 GCAATTGCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATCACATTATTTAC
Found at i:84625 original size:13 final size:13
Alignment explanation
Indices: 84607--84631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84597 CATAAAGTGT
84607 TGTATCGATACAA
1 TGTATCGATACAA
84620 TGTATCGATACA
1 TGTATCGATACA
84632 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:84647 original size:32 final size:33
Alignment explanation
Indices: 84587--84652 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
84577 TTCAACGATT
84587 TGTATCAATACATAAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTGTATCGATACAA
* *
84620 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTGTATCGATACAA
84652 T
1 T
84653 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (33 bp):
TGTATCAATACATAAAGTGTTGTATCGATACAA
Found at i:84717 original size:20 final size:21
Alignment explanation
Indices: 84672--84724 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
84662 TGCCAAAAAA
* *
84672 TGTATCGATACATTACTCAAT
1 TGTATCGATACACTAATCAAT
*
84693 TGTATCGATACACTAATC-TT
1 TGTATCGATACACTAATCAAT
84713 TGTATCGATACA
1 TGTATCGATACA
84725 TGTAGGCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (21 bp):
TGTATCGATACACTAATCAAT
Found at i:88915 original size:19 final size:18
Alignment explanation
Indices: 88873--88916 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
88863 ATGACGTGTT
*
88873 TGATGACGTTGCTAATGT
1 TGATGACGTTGCTAATGA
* *
88891 TGATGACGTTGTTTATTGA
1 TGATGACGTTG-CTAATGA
88910 TGATGAC
1 TGATGAC
88917 ATGGCATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (18 bp):
TGATGACGTTGCTAATGA
Found at i:89361 original size:23 final size:24
Alignment explanation
Indices: 89330--89382 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
89320 AAAGAATCCT
* *
89330 TAATAAGAATC-TTAATATTATGC
1 TAATAAGAATCACTAATATGATGC
*
89353 TAATTAGAATCACTAATATGATGC
1 TAATAAGAATCACTAATATGATGC
*
89377 TGATAA
1 TAATAA
89383 AGTCAACTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (24 bp):
TAATAAGAATCACTAATATGATGC
Found at i:89588 original size:13 final size:13
Alignment explanation
Indices: 89572--89617 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
89562 ATTTATTGAA
89572 AAAAATTAAATTT
1 AAAAATTAAATTT
*
89585 AAAAATATATATTT
1 AAAAAT-TAAATTT
* *
89599 AAAAAATAAATTA
1 AAAAATTAAATTT
89612 AAAAAT
1 AAAAAT
89618 AAAGTATGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATTAAATTT
Found at i:89614 original size:12 final size:12
Alignment explanation
Indices: 89571--89620 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 12
89561 AATTTATTGA
89571 AAAAAATTAAATTT
1 AAAAAA-TAAA-TT
*
89585 AAAAATATATATTT
1 AAAAA-ATA-AATT
89599 AAAAAATAAATT
1 AAAAAATAAATT
89611 AAAAAATAAA
1 AAAAAATAAA
89621 GTATGAGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 13 0.41
13 3 0.09
14 14 0.44
15 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAAATAAATT
Done.