Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 7 of 14
Found at i:1408584 original size:3 final size:3
Alignment explanation
Indices: 1408578--1408611 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1408568 CTTGATGATG
1408578 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1408612 CAACAACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1409074 original size:3 final size:3
Alignment explanation
Indices: 1409066--1409095 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1409056 AAGATAGAAA
1409066 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1409096 TTGTTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1410584 original size:12 final size:12
Alignment explanation
Indices: 1410549--1410584 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1410539 GATGGTGTCA
*
1410549 ATAATGGTGGTA
1 ATAATGGTGGTG
1410561 ATAATGGTGGTG
1 ATAATGGTGGTG
*
1410573 CTAATGGTGGTG
1 ATAATGGTGGTG
1410585 GTGGTGGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.25, C:0.03, G:0.39, T:0.33
Consensus pattern (12 bp):
ATAATGGTGGTG
Found at i:1412472 original size:2 final size:2
Alignment explanation
Indices: 1412465--1412500 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1412455 AAGATATGCT
1412465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1412501 GAGGGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1414655 original size:2 final size:2
Alignment explanation
Indices: 1414650--1414685 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1414640 TTTAACTCAA
1414650 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
1414686 CCGTAGCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1416064 original size:2 final size:2
Alignment explanation
Indices: 1416057--1416089 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1416047 ACCTGCAGAA
1416057 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 A
1416090 ACCAAAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1416312 original size:31 final size:31
Alignment explanation
Indices: 1416274--1416335 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1416264 AAATTCACCC
1416274 TTTTTATATATGTTGCATGTTCAATTAGAAA
1 TTTTTATATATGTTGCATGTTCAATTAGAAA
1416305 TTTTTATATATGTTGCATGTTCAATTAGAAA
1 TTTTTATATATGTTGCATGTTCAATTAGAAA
1416336 ATGAGTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (31 bp):
TTTTTATATATGTTGCATGTTCAATTAGAAA
Found at i:1418350 original size:12 final size:12
Alignment explanation
Indices: 1418303--1418349 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
1418293 AAATAGACAT
1418303 AATTTTAAATTA
1 AATTTTAAATTA
*
1418315 AATTATAAATTA
1 AATTTTAAATTA
*
1418327 AATTTTAAAATA
1 AATTTTAAATTA
1418339 AATATTTAAAT
1 AAT-TTTAAAT
1418350 ATATAACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AATTTTAAATTA
Found at i:1418749 original size:19 final size:18
Alignment explanation
Indices: 1418704--1418751 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1418694 ATAAAATATA
* *
1418704 AAATAATATATTATAATT
1 AAATAATATGTTAAAATT
*
1418722 ATATAAATATGTTAAAATTT
1 AAAT-AATATGTTAAAA-TT
1418742 AAATAATATG
1 AAATAATATG
1418752 AATAAATATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.12
19 16 0.67
20 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
AAATAATATGTTAAAATT
Found at i:1419226 original size:19 final size:20
Alignment explanation
Indices: 1419189--1419226 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1419179 TATATTAAAA
1419189 TTTAAATAAAATATATAATT
1 TTTAAATAAAATATATAATT
*
1419209 TTTAAATATAAT-TATAAT
1 TTTAAATAAAATATATAAT
1419227 ATAAAATAAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATAAAATATATAATT
Found at i:1419551 original size:17 final size:16
Alignment explanation
Indices: 1419516--1419551 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1419506 TATATTATAA
*
1419516 TTATATTTAAAATATT
1 TTATATTTAAAAAATT
1419532 TTATATTTAAATAAATT
1 TTATATTTAAA-AAATT
1419549 TTA
1 TTA
1419552 ATAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTAAAAAATT
Found at i:1428634 original size:16 final size:16
Alignment explanation
Indices: 1428584--1428662 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 16
1428574 TTTTAATTAA
1428584 TATATTTATATAAATTT
1 TATA-TTATATAAATTT
*
1428601 TA-A-TATATTAAAAATT
1 TATATTATA-T-AAATTT
1428617 TATATTATATAAATTT
1 TATATTATATAAATTT
* *
1428633 TACTATATTTATATATTT
1 TA-TAT-TATATAAATTT
1428651 ATAATATTATAT
1 -T-ATATTATAT
1428663 TTTCTATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.08
15 1 0.02
16 15 0.31
17 7 0.14
18 17 0.35
19 4 0.08
20 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:1428651 original size:33 final size:33
Alignment explanation
Indices: 1428584--1428674 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 33
1428574 TTTTAATTAA
*
1428584 TATATTTATATAAATTTTAATATA-TTAAAAATT
1 TATA-TTATATAAATTTTACTATATTTAAAAATT
* *
1428617 TATATTATATAAATTTTACTATATTTATATATT
1 TATATTATATAAATTTTACTATATTTAAAAATT
* *
1428650 TATAATAT-TATATTTT-CTATTATTT
1 TATATTATATAAATTTTACTA-TATTT
1428675 TTAATTTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.06
32 30 0.59
33 18 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATTATATAAATTTTACTATATTTAAAAATT
Found at i:1429081 original size:16 final size:18
Alignment explanation
Indices: 1429043--1429086 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
1429033 TCAATTTTCT
1429043 ATAATTCTTAATTTTGTATA
1 ATAATT-TT-ATTTTGTATA
1429063 AT-ATTTTATTTTG-ATA
1 ATAATTTTATTTTGTATA
1429079 ATAATTTT
1 ATAATTTT
1429087 GTATTATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 11 0.48
18 2 0.09
19 3 0.13
20 2 0.09
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (18 bp):
ATAATTTTATTTTGTATA
Found at i:1430473 original size:17 final size:18
Alignment explanation
Indices: 1430440--1430480 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1430430 ATAAATAAAG
1430440 TTTAATATTTAATTTATA
1 TTTAATATTTAATTTATA
1430458 TTTAA-ATTT-ATGTTATA
1 TTTAATATTTAAT-TTATA
*
1430475 TATAAT
1 TTTAAT
1430481 GAGAGTGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAATATTTAATTTATA
Found at i:1431000 original size:3 final size:3
Alignment explanation
Indices: 1430992--1431027 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1430982 GAAATTCAAA
1430992 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1431028 AATAATAATA
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1432744 original size:2 final size:2
Alignment explanation
Indices: 1432737--1432767 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1432727 TCATATGTAA
1432737 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1432768 GAAAATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1434039 original size:11 final size:11
Alignment explanation
Indices: 1434023--1434054 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1434013 TATTTTTTTC
*
1434023 TTTTACTTCTT
1 TTTTACTACTT
1434034 TTTTACTACTT
1 TTTTACTACTT
1434045 TTTTACTACT
1 TTTTACTACT
1434055 CCTTTAGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTACTACTT
Found at i:1435972 original size:24 final size:23
Alignment explanation
Indices: 1435945--1436013 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 23
1435935 TTAATATGTA
1435945 TTAAATATTTTATATTAATTATAT
1 TTAAATATTTTATATTAATT-TAT
*
1435969 TTAAATATATTATATTATATTTAT
1 TTAAATATTTTATATTA-ATTTAT
*
1435993 TAAAATATTTTTATACTTAAT
1 TTAAATA-TTTTATA-TTAAT
1436014 AAACATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 25 0.64
25 11 0.28
26 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAAATATTTTATATTAATTTAT
Found at i:1438898 original size:21 final size:21
Alignment explanation
Indices: 1438859--1438898 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1438849 AAATCGATTG
*
1438859 AATTAAAATATAATTAAATAA
1 AATTAAAATATAATAAAATAA
* *
1438880 AATTTAAATATTATAAAAT
1 AATTAAAATATAATAAAAT
1438899 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAAAATATAATAAAATAA
Found at i:1440636 original size:14 final size:14
Alignment explanation
Indices: 1440614--1440654 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1440604 TATGATTGTT
*
1440614 TATAAAATTATATA
1 TATATAATTATATA
1440628 TATATAATTATA-A
1 TATATAATTATATA
*
1440641 T-TATAATTAAATA
1 TATATAATTATATA
1440654 T
1 T
1440655 TTATTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 9 0.38
13 4 0.17
14 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TATATAATTATATA
Found at i:1440932 original size:22 final size:22
Alignment explanation
Indices: 1440907--1440971 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
1440897 AAATTAAATT
1440907 ATAATTAAAATTATTTTATT-TC
1 ATAA-TAAAATTATTTTATTATC
**
1440929 ATAATAATTTTATTTTATTATC
1 ATAATAAAATTATTTTATTATC
*
1440951 ATAA-AATAATTATTTCATTAT
1 ATAATAA-AATTATTTTATTAT
1440972 AATTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATAAAATTATTTTATTATC
Found at i:1441645 original size:21 final size:20
Alignment explanation
Indices: 1441616--1441657 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1441606 AATATTATTT
* *
1441616 TTATTTAAAATTAATTATAAA
1 TTATATAAAAATAATT-TAAA
1441637 TTATATAAAAATAATTTAAA
1 TTATATAAAAATAATTTAAA
1441657 T
1 T
1441658 AGAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATATAAAAATAATTTAAA
Found at i:1441768 original size:22 final size:23
Alignment explanation
Indices: 1441742--1441796 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1441732 AAAATTAAAT
**
1441742 ATTTATTCTAATTT-ATGAATAA
1 ATTTATTCTAATTTAAAAAATAA
*
1441764 ATTTATT-TATTTTAAAAAATAA
1 ATTTATTCTAATTTAAAAAATAA
1441786 ATTT-TTCTAAT
1 ATTTATTCTAAT
1441797 AAAAGAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTATTCTAATTTAAAAAATAA
Found at i:1446858 original size:23 final size:26
Alignment explanation
Indices: 1446812--1446863 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1446802 TTTCATTAAC
* *
1446812 AAAATTATTAATTTCATAACAAAAGT
1 AAAATTAATAATTTCATAACAAAACT
1446838 AAAATTAATAATTT-A-AA-AAAACT
1 AAAATTAATAATTTCATAACAAAACT
1446861 AAA
1 AAA
1446864 TTCTCATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 2 0.08
25 1 0.04
26 13 0.54
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATTAATAATTTCATAACAAAACT
Found at i:1449513 original size:25 final size:22
Alignment explanation
Indices: 1449484--1449530 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
1449474 AAACTTAAGG
1449484 TCAATGTAAAATTCAATTTTTTTTA
1 TCAAT-TAAAA-T-AATTTTTTTTA
*
1449509 TCAATTTAAATAATTTTTTTTA
1 TCAATTAAAATAATTTTTTTTA
1449531 AAAGTGGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 4 0.19
25 5 0.24
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (22 bp):
TCAATTAAAATAATTTTTTTTA
Found at i:1450096 original size:13 final size:13
Alignment explanation
Indices: 1450078--1450102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1450068 TATGAACTCG
1450078 AAAAAGGAAAAAA
1 AAAAAGGAAAAAA
1450091 AAAAAGGAAAAA
1 AAAAAGGAAAAA
1450103 CTCGTGCACA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAA
Found at i:1450199 original size:3 final size:3
Alignment explanation
Indices: 1450191--1450230 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1450181 GTTTATTCAA
1450191 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1450231 CATGAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1450486 original size:2 final size:2
Alignment explanation
Indices: 1450479--1450511 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1450469 ATTTATTATC
1450479 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 A
1450512 AGTTCATGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1455194 original size:24 final size:24
Alignment explanation
Indices: 1455167--1455215 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1455157 ATTAATGATC
1455167 ATCCCAGTGGTAAGAAAAGTTTCA
1 ATCCCAGTGGTAAGAAAAGTTTCA
1455191 ATCCCAGTGGTAAGAAAAGTTTCA
1 ATCCCAGTGGTAAGAAAAGTTTCA
1455215 A
1 A
1455216 GCATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (24 bp):
ATCCCAGTGGTAAGAAAAGTTTCA
Found at i:1455798 original size:23 final size:23
Alignment explanation
Indices: 1455755--1455799 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1455745 TTTATATAAT
*
1455755 TATATTTAAGAAATAATATTTAA
1 TATATTTAAGAAATAAAATTTAA
*
1455778 TATATTTAA-AATTTAAAATTTA
1 TATATTTAAGAA-ATAAAATTTA
1455800 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATTTAAGAAATAAAATTTAA
Found at i:1456850 original size:15 final size:15
Alignment explanation
Indices: 1456830--1456882 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
1456820 ATTCAATAAA
1456830 CATATTTATTAAAAT
1 CATATTTATTAAAAT
* *
1456845 CATATTACTTTTAGAAT
1 CATATT--TATTAAAAT
*
1456862 CACATTTATTAAAAT
1 CATATTTATTAAAAT
1456877 CATATT
1 CATATT
1456883 AGTTTTCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (15 bp):
CATATTTATTAAAAT
Found at i:1457027 original size:38 final size:37
Alignment explanation
Indices: 1456977--1457088 Score: 134
Period size: 38 Copynumber: 3.0 Consensus size: 37
1456967 GGTAGCACGG
*
1456977 GTCGAAACAAAAACTACTATTCTTACTAGTGGTATGA
1 GTCGAAACAAAAACTACTATTCTTACTAGTGGTACGA
* * * * *
1457014 TTCGAAACAAAAAATCACTATTTTTACTGGTGGCACGA
1 GTCGAAACAAAAACT-ACTATTCTTACTAGTGGTACGA
* *
1457052 GTCGAAATAAAAACTATTATTCTTAACTAGTGGTACG
1 GTCGAAACAAAAACTACTATTCTT-ACTAGTGGTACG
1457089 GTTGGAACCG
Statistics
Matches: 60, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
37 20 0.33
38 40 0.67
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (37 bp):
GTCGAAACAAAAACTACTATTCTTACTAGTGGTACGA
Found at i:1457960 original size:15 final size:15
Alignment explanation
Indices: 1457931--1457965 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1457921 AAATAGTACG
1457931 ATTATAAAATAATTT
1 ATTATAAAATAATTT
1457946 ATTA-AAAATATATTT
1 ATTATAAAATA-ATTT
1457961 ATTAT
1 ATTAT
1457966 GTCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATAAAATAATTT
Found at i:1459678 original size:13 final size:13
Alignment explanation
Indices: 1459660--1459695 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1459650 CATATAAATG
1459660 TTATAATAT-GATA
1 TTATAATATAG-TA
1459673 TTATAATATAGTA
1 TTATAATATAGTA
1459686 TTATAATATA
1 TTATAATATA
1459696 AATATTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (13 bp):
TTATAATATAGTA
Found at i:1465636 original size:50 final size:50
Alignment explanation
Indices: 1465582--1465890 Score: 494
Period size: 50 Copynumber: 6.2 Consensus size: 50
1465572 AATTGTTGCC
* * * * *
1465582 ATTGTTGACTATCCTTCACCAACCTTTAACAATAG-AGAGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAG-GAGGTGGCCATA
*
1465632 ATTGTTTACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
* * *
1465682 ATTATTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
*
1465732 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
1465782 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
* *
1465832 ATTGTTGACGATTCTTCACCAACTTTTGACAATGGAGGGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
1465882 ATTGTTGAC
1 ATTGTTGAC
1465891 TCTAAGTATA
Statistics
Matches: 241, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
50 239 0.99
51 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACTTTTGACAATAGAAGGAGGTGGCCATA
Found at i:1472424 original size:21 final size:22
Alignment explanation
Indices: 1472368--1472424 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
1472358 TCAGTTTTGG
1472368 ATTTAA-ATTTATTTTATATTA
1 ATTTAATATTTATTTTATATTA
* *
1472389 A-AT-ATAATTATTTT-TATATA
1 ATTTAATATTTATTTTATAT-TA
1472409 ATTTAATATTTATTTT
1 ATTTAATATTTATTTT
1472425 TAAAAAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 2 0.07
22 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTAATATTTATTTTATATTA
Found at i:1472424 original size:22 final size:23
Alignment explanation
Indices: 1472368--1472426 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
1472358 TCAGTTTTGG
1472368 ATTTAA-ATTTA-TTTTATATTA
1 ATTTAATATTTATTTTTATATTA
* *
1472389 A-AT-ATAATTATTTTTATA-TA
1 ATTTAATATTTATTTTTATATTA
1472409 ATTTAATATTTATTTTTA
1 ATTTAATATTTATTTTTA
1472427 AAAAGTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 1 0.03
20 8 0.27
21 9 0.30
22 12 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTAATATTTATTTTTATATTA
Found at i:1472463 original size:27 final size:29
Alignment explanation
Indices: 1472429--1472496 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
1472419 TATTTTTAAA
1472429 AAGTAAA-TTATTAAATTATTA-ATTTTT
1 AAGTAAATTTATTAAATTATTATATTTTT
*
1472456 AAGTAAATTTTTATTATATTATTATATTTTT
1 AAGTAAA--TTTATTAAATTATTATATTTTT
*
1472487 AA-TATATTTA
1 AAGTAAATTTA
1472497 ATTATTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 7 0.20
28 4 0.11
30 16 0.46
31 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
AAGTAAATTTATTAAATTATTATATTTTT
Found at i:1472502 original size:19 final size:19
Alignment explanation
Indices: 1472462--1472503 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1472452 TTTTAAGTAA
* *
1472462 ATTTTTATTATATTATTAT
1 ATTTTTAATATATTAATAT
1472481 ATTTTTAATATATTTAAT-T
1 ATTTTTAATATA-TTAATAT
1472500 ATTT
1 ATTT
1472504 ATTTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTAATATATTAATAT
Found at i:1472524 original size:20 final size:19
Alignment explanation
Indices: 1472499--1472553 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1472489 TATATTTAAT
*
1472499 TATTTATTTATTAAAATTTA
1 TATTTATATA-TAAAATTTA
1472519 TATTTATATATAAAA-TTA
1 TATTTATATATAAAATTTA
*
1472537 -ATTTGTTATATAAAATT
1 TATTT-ATATATAAAATT
1472554 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 4 0.13
18 12 0.39
19 6 0.19
20 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TATTTATATATAAAATTTA
Found at i:1472567 original size:18 final size:18
Alignment explanation
Indices: 1472528--1472567 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1472518 ATATTTATAT
*
1472528 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
*
1472546 ATAAAATTAATTTTTTAA
1 ATAAAATTAATTTGTTAA
1472564 ATAA
1 ATAA
1472568 TTTATTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:1473258 original size:16 final size:17
Alignment explanation
Indices: 1473227--1473260 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1473217 TATTATGTTA
*
1473227 ACTTTATATTCTATTCT
1 ACTTTATATACTATTCT
1473244 ACTTTAT-TACTATTCT
1 ACTTTATATACTATTCT
1473260 A
1 A
1473261 AGTGTAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
ACTTTATATACTATTCT
Found at i:1473769 original size:16 final size:16
Alignment explanation
Indices: 1473744--1473801 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
1473734 GTTCGAATTC
*
1473744 TCTCGGGTTCAGATTT
1 TCTCGAGTTCAGATTT
* *
1473760 TTTCGAGTTC-GAGCTT
1 TCTCGAGTTCAGA-TTT
* *
1473776 TCTCGAGTTTAGATTA
1 TCTCGAGTTCAGATTT
1473792 TCTCGAGTTC
1 TCTCGAGTTC
1473802 GGACTATTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 2 0.06
16 28 0.88
17 2 0.06
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (16 bp):
TCTCGAGTTCAGATTT
Found at i:1473770 original size:32 final size:32
Alignment explanation
Indices: 1473734--1473802 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
1473724 TCAATCTTGG
* * *
1473734 GTTCGA-ATTCTCTCGGGTTCAGATTTTTTCGA
1 GTTCGAGATT-TCTCGAGTTCAGATTATCTCGA
* *
1473766 GTTCGAGCTTTCTCGAGTTTAGATTATCTCGA
1 GTTCGAGATTTCTCGAGTTCAGATTATCTCGA
1473798 GTTCG
1 GTTCG
1473803 GACTATTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 29 0.94
33 2 0.06
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (32 bp):
GTTCGAGATTTCTCGAGTTCAGATTATCTCGA
Found at i:1474405 original size:41 final size:42
Alignment explanation
Indices: 1474321--1474406 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 42
1474311 TATTATTCAA
** *
1474321 TTATAATATAATTAATAATATTATTATTTGTTATTTATTTAT
1 TTATAATATAATTAATAATATTATTAGATGTTATTTATATAT
1474363 TTATAATAT-ATTAATAATATT-TATAGATGATTATTT-TATAT
1 TTATAATATAATTAATAATATTAT-TAGATG-TTATTTATATAT
1474404 TTA
1 TTA
1474407 AATGCAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
40 1 0.03
41 23 0.59
42 15 0.38
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (42 bp):
TTATAATATAATTAATAATATTATTAGATGTTATTTATATAT
Found at i:1475011 original size:16 final size:15
Alignment explanation
Indices: 1474981--1475049 Score: 67
Period size: 15 Copynumber: 4.8 Consensus size: 15
1474971 TTATGTTATT
1474981 TTTAATT-TTTT-AA
1 TTTAATTATTTTAAA
1474994 TTTAATTTATTTTAAA
1 TTTAA-TTATTTTAAA
1475010 TTTAATT-TTTT--A
1 TTTAATTATTTTAAA
*
1475022 TTTGAGTTATTTTAAA
1 TTT-AATTATTTTAAA
*
1475038 TTTAAATATTTT
1 TTTAATTATTTT
1475050 TTATATTATT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
12 4 0.09
13 8 0.17
14 10 0.22
15 13 0.28
16 11 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTAATTATTTTAAA
Found at i:1475019 original size:28 final size:29
Alignment explanation
Indices: 1474981--1475042 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
1474971 TTATGTTATT
*
1474981 TTTAATTTTTTAATTTAATTTATTTTAAA
1 TTTAATTTTTTAATTTAAGTTATTTTAAA
*
1475010 TTTAATTTTTT-ATTTGAGTTATTTTAAA
1 TTTAATTTTTTAATTTAAGTTATTTTAAA
1475038 TTTAA
1 TTTAA
1475043 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.65
29 11 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (29 bp):
TTTAATTTTTTAATTTAAGTTATTTTAAA
Found at i:1475850 original size:27 final size:29
Alignment explanation
Indices: 1475818--1475874 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 29
1475808 TTAGTATTAT
*
1475818 TATAAAAAATAT-TTTAAAA-AATTAAAA
1 TATAAAAAATATATTTAAAATAATAAAAA
1475845 TATAAAAAATATATTTAAAATAATAAAAA
1 TATAAAAAATATATTTAAAATAATAAAAA
1475874 T
1 T
1475875 TTAAGATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 12 0.44
28 7 0.26
29 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
TATAAAAAATATATTTAAAATAATAAAAA
Found at i:1477781 original size:27 final size:27
Alignment explanation
Indices: 1477751--1477829 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 27
1477741 ATATTTTTTT
1477751 ATAAAATATTATAATTTAAAAATAAAA
1 ATAAAATATTATAATTTAAAAATAAAA
* *
1477778 ATAAATTA-TA-AATATTAAAATTTAAAA
1 ATAAAATATTATAAT-TTAAAA-ATAAAA
*
1477805 TTAATAAATATTAT--TTTAAAAATAA
1 AT-A-AAATATTATAATTTAAAAATAA
1477830 TTATATAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.20
27 16 0.39
28 7 0.17
29 5 0.12
30 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATAAAATATTATAATTTAAAAATAAAA
Found at i:1477793 original size:33 final size:35
Alignment explanation
Indices: 1477749--1477814 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
1477739 TTATATTTTT
*
1477749 TTATAAAATATTATAATTTAAAAATAA-AAATAAA
1 TTATAAAATATTAAAATTTAAAAATAATAAATAAA
*
1477783 TTAT-AAATATTAAAATTTAAAATTAATAAATA
1 TTATAAAATATTAAAATTTAAAAATAATAAATA
1477815 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (35 bp):
TTATAAAATATTAAAATTTAAAAATAATAAATAAA
Found at i:1477813 original size:15 final size:17
Alignment explanation
Indices: 1477749--1477813 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 17
1477739 TTATATTTTT
*
1477749 TTATAAAATATT-ATAAT
1 TTAT-AAATATTAATAAA
* **
1477766 TTAAAAATAAAAATAAA
1 TTATAAATATTAATAAA
1477783 TTATAAATATT-A-AAA
1 TTATAAATATTAATAAA
1477798 TT-TAAA-ATTAATAAA
1 TTATAAATATTAATAAA
1477813 T
1 T
1477814 ATTATTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 3 0.08
14 5 0.13
15 9 0.24
16 6 0.16
17 15 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATAAATATTAATAAA
Found at i:1477869 original size:56 final size:54
Alignment explanation
Indices: 1477748--1477877 Score: 129
Period size: 56 Copynumber: 2.4 Consensus size: 54
1477738 TTTATATTTT
*
1477748 TTTATAAAATATTATAATTTAAAAATAAAAATAAATTATAAATATTAAAATTTAAA
1 TTTATTAAATATTAT--TTTAAAAATAAAAATAAATTATAAATATTAAAATTTAAA
* * * * * *
1477804 ATTAATAAATATTATTTTAAAAATAATTATATAAATTAATTAA-ATTACATTTTAAA
1 TTTATTAAATATTATTTTAAAAATAA--AAATAAATT-ATAAATATTAAAATTTAAA
*
1477860 TTTATTAAAT-TTTTTTTA
1 TTTATTAAATATTATTTTA
1477878 TTTTTTTTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
54 11 0.18
55 7 0.11
56 39 0.64
57 4 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (54 bp):
TTTATTAAATATTATTTTAAAAATAAAAATAAATTATAAATATTAAAATTTAAA
Found at i:1479728 original size:25 final size:26
Alignment explanation
Indices: 1479670--1479725 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
1479660 TCTCGCAAAG
* *
1479670 GTTATGAGTAGTGAAGGACATTCGAA
1 GTTAGGAGTAGTGAAGAACATTCGAA
*
1479696 GTTTTAGGAGTGGTGAAGAACATTCGAA
1 G--TTAGGAGTAGTGAAGAACATTCGAA
1479724 GT
1 GT
1479726 AGGGTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
26 2 0.08
28 23 0.92
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.29
Consensus pattern (26 bp):
GTTAGGAGTAGTGAAGAACATTCGAA
Found at i:1480117 original size:50 final size:50
Alignment explanation
Indices: 1480033--1480267 Score: 353
Period size: 50 Copynumber: 4.7 Consensus size: 50
1480023 GGAAAATACA
** * * *
1480033 TTTGACAATAGAGAGAGGTAACCACAATTATTGACGATTCTTCACTAACC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
*
1480083 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACTAACC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
* *
1480133 TTTGACAATAGAAAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
* * * *
1480183 TTTGACAATAGAGAGAGGTAGCCTTAATTGTTGACGATTATTCACCAACT
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
*
1480233 TTTGACAATAGAGAGATGTGGCCATAATTGTTGAC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
1480268 TCTAAGTATA
Statistics
Matches: 170, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 170 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (50 bp):
TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
Found at i:1484705 original size:50 final size:50
Alignment explanation
Indices: 1484648--1484881 Score: 398
Period size: 50 Copynumber: 4.7 Consensus size: 50
1484638 GGAAAGTACT
***
1484648 TTTGACAATAGAGAGAGGTGGCTGCAATTGTTGACGATTCTTCACCAACC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
1484698 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
*
1484748 TTTGAC-ATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
* *
1484797 TTTGACAATAGAGAGAGATGGCCATAATTGTTGATGATTCTTCACCAACC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
*
1484847 TTTGACAATAGAGAGAGGTGGTCATAATTGTTGAC
1 TTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
1484882 TCTAAGTATA
Statistics
Matches: 173, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
49 48 0.28
50 125 0.72
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (50 bp):
TTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACC
Found at i:1484826 original size:99 final size:100
Alignment explanation
Indices: 1484648--1484881 Score: 407
Period size: 99 Copynumber: 2.4 Consensus size: 100
1484638 GGAAAGTACT
* *
1484648 TTTGACAATAGAGAGAGGTGGCTGCAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAG
1 TTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAG
*
1484713 AGGTGGCCATAATTGTTGACGATTCTTCACCAACC
66 AGATGGCCATAATTGTTGACGATTCTTCACCAACC
1484748 TTTGAC-ATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAG
1 TTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAG
*
1484812 AGATGGCCATAATTGTTGATGATTCTTCACCAACC
66 AGATGGCCATAATTGTTGACGATTCTTCACCAACC
* *
1484847 TTTGACAATAGAGAGAGGTGGTCATAATTGTTGAC
1 TTTGACAATAGAGAGAGGTGGCCGTAATTGTTGAC
1484882 TCTAAGTATA
Statistics
Matches: 127, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
99 95 0.75
100 32 0.25
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (100 bp):
TTTGACAATAGAGAGAGGTGGCCGTAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAG
AGATGGCCATAATTGTTGACGATTCTTCACCAACC
Found at i:1487831 original size:2 final size:2
Alignment explanation
Indices: 1487824--1487854 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1487814 CATAAACATA
1487824 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 A
1487855 CAAACATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1488537 original size:15 final size:16
Alignment explanation
Indices: 1488517--1488546 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1488507 CAACAACAGC
1488517 AACAATAAT-ATTCAT
1 AACAATAATAATTCAT
1488532 AACAATAATAATTCA
1 AACAATAATAATTCA
1488547 ACTGACAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (16 bp):
AACAATAATAATTCAT
Found at i:1489368 original size:14 final size:15
Alignment explanation
Indices: 1489341--1489397 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
1489331 TGATGAAATA
*
1489341 AAAAATAATTATATT
1 AAAAATAATAATATT
1489356 AAAAA-AATAATATT
1 AAAAATAATAATATT
* *
1489370 ATAAATAA-AATA-A
1 AAAAATAATAATATT
1489383 AAAAATATATAATAT
1 AAAAATA-ATAATAT
1489398 GAATGTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 6 0.18
14 17 0.50
15 11 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAATAATAATATT
Found at i:1489379 original size:17 final size:18
Alignment explanation
Indices: 1489336--1489382 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1489326 AAATTTGATG
1489336 AAATAAAA-AATAATTAT
1 AAATAAAATAATAATTAT
*
1489353 ATTAAAAAAATAAT-ATTAT
1 A--AATAAAATAATAATTAT
1489372 AAATAAAATAA
1 AAATAAAATAA
1489383 AAAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 10 0.40
19 12 0.48
20 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATAAAATAATAATTAT
Found at i:1490737 original size:2 final size:2
Alignment explanation
Indices: 1490730--1490766 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1490720 GTATTACAAG
*
1490730 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1490767 TACTCTAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1492045 original size:20 final size:22
Alignment explanation
Indices: 1492020--1492061 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
1492010 GAAAAGTATT
1492020 TTTTTAATTAAA-AT-ATTATA
1 TTTTTAATTAAATATAATTATA
*
1492040 TTTTTATTTAAATATAATTATA
1 TTTTTAATTAAATATAATTATA
1492062 AATTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 2 0.11
22 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTAATTAAATATAATTATA
Found at i:1492072 original size:21 final size:20
Alignment explanation
Indices: 1492043--1492097 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
1492033 TATTATATTT
*
1492043 TTATTTAAATATAATTATAAA
1 TTATATAAATATAATTAT-AA
1492064 TTATATAAATATTAA-TATAA
1 TTATATAAATA-TAATTATAA
1492084 --ATATAAATATAATT
1 TTATATAAATATAATT
1492098 TTTAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 3 0.10
18 10 0.32
20 2 0.06
21 13 0.42
22 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATATAAATATAATTATAA
Found at i:1492075 original size:6 final size:6
Alignment explanation
Indices: 1492048--1492095 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
1492038 TATTTTTATT
* *
1492048 TAAATA TAATTA TAAAT- T--ATA TAAATA TTAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
1492093 TAA
1 TAA
1492096 TTTTTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 1 0.03
6 31 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
TAAATA
Found at i:1492081 original size:12 final size:12
Alignment explanation
Indices: 1492066--1492105 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1492056 ATTATAAATT
1492066 ATATAAATATTA
1 ATATAAATATTA
*
1492078 ATATAAATATAA
1 ATATAAATATTA
* *
1492090 ATATAATTTTTA
1 ATATAAATATTA
1492102 ATAT
1 ATAT
1492106 TTTTTTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATAAATATTA
Found at i:1492203 original size:21 final size:21
Alignment explanation
Indices: 1492179--1492238 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 21
1492169 TTAAGTTTAA
1492179 AATTTAAATTTTTTAAATT-AT
1 AATTT-AATTTTTTAAATTCAT
1492200 AATTTAATTTAATTT-AATTCAT
1 AATTTAATTT--TTTAAATTCAT
1492222 AATATTAA-TTTTTAAAT
1 AAT-TTAATTTTTTAAAT
1492239 AGTTCACGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
20 8 0.24
21 12 0.35
22 10 0.29
23 4 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTAATTTTTTAAATTCAT
Found at i:1492214 original size:10 final size:11
Alignment explanation
Indices: 1492194--1492231 Score: 51
Period size: 10 Copynumber: 3.4 Consensus size: 11
1492184 AAATTTTTTA
1492194 AATTATAATTT
1 AATTATAATTT
1492205 AATT-TAATTT
1 AATTATAATTT
1492215 AATTCATAATATT
1 AATT-ATAAT-TT
1492228 AATT
1 AATT
1492232 TTTAAATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
11 4 0.17
12 4 0.17
13 6 0.25
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTATAATTT
Found at i:1493328 original size:37 final size:36
Alignment explanation
Indices: 1493287--1493384 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 36
1493277 TTATTTTTTA
* *
1493287 TGGATTGGCGCTGCCACCCAAATTCTAATAATCATAG
1 TGGATTGGC-CTGCCACCCAAATACTAACAATCATAG
* * *
1493324 TGGATCGGCACTGCCACCCAAACACTAACACTCATAG
1 TGGATTGGC-CTGCCACCCAAATACTAACAATCATAG
*
1493361 TGGATTGGCCAAGCCACCCAAATA
1 TGGATTGGCC-TGCCACCCAAATA
1493385 TTACTTGTCG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 1 0.02
37 50 0.98
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (36 bp):
TGGATTGGCCTGCCACCCAAATACTAACAATCATAG
Found at i:1498743 original size:42 final size:42
Alignment explanation
Indices: 1498683--1498785 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 42
1498673 AAAAGTTTAT
*
1498683 TTAAAATTTAT-TTATTATTCGA-TTATAATATAATTAATAATA
1 TTAATATTTATATT-TTATT-GATTTATAATATAATTAATAATA
*
1498725 TTAATATTTATATTTTATTTATTTATAATATAATTAATAATA
1 TTAATATTTATATTTTATTGATTTATAATATAATTAATAATA
*
1498767 TT-TTATTTGATTATTTTAT
1 TTAATATTT-A-TATTTTAT
1498786 ATTTAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
41 6 0.11
42 38 0.70
43 10 0.19
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (42 bp):
TTAATATTTATATTTTATTGATTTATAATATAATTAATAATA
Found at i:1499516 original size:31 final size:31
Alignment explanation
Indices: 1499461--1499521 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1499451 AATAGATCTA
* * *
1499461 AGTTATTTTAAATTTAATTTTTTTAGATTTG
1 AGTTATTTTAAATTTAAATATTTTAAATTTG
* *
1499492 AGTTATTTTTAGTTTAAATATTTTAAATTT
1 AGTTATTTTAAATTTAAATATTTTAAATTT
1499522 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (31 bp):
AGTTATTTTAAATTTAAATATTTTAAATTTG
Found at i:1500799 original size:51 final size:51
Alignment explanation
Indices: 1500718--1500816 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
1500708 GAAAAACGTG
* **
1500718 AGAAAAACGTGGCAAAGGAAATTGTAACAAGCAAATTGCCCATTCCAACTC
1 AGAAAAACGTGACAAAGGAAATCATAACAAGCAAATTGCCCATTCCAACTC
* *
1500769 AGAAAAACGTGACAAAGGAAATCATGACAAGCAACTTGCCCATTCCAA
1 AGAAAAACGTGACAAAGGAAATCATAACAAGCAAATTGCCCATTCCAA
1500817 GCAAAGCTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.16
Consensus pattern (51 bp):
AGAAAAACGTGACAAAGGAAATCATAACAAGCAAATTGCCCATTCCAACTC
Found at i:1501361 original size:20 final size:20
Alignment explanation
Indices: 1501336--1501377 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1501326 AGATGGGAGA
*
1501336 AAATATCTATAAATATTTAT
1 AAATATCTACAAATATTTAT
*
1501356 AAATATCTACAGATATTTAT
1 AAATATCTACAAATATTTAT
1501376 AA
1 AA
1501378 CAACAGTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATATCTACAAATATTTAT
Found at i:1504684 original size:25 final size:24
Alignment explanation
Indices: 1504639--1504688 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
1504629 TTACACAACT
1504639 AAATACAATATAAAAATAATAATAA
1 AAATACAATATAAAAATAAT-ATAA
1504664 AAATAC-ATGATATAAAA-AATATAA
1 AAATACAAT-ATA-AAAATAATATAA
1504688 A
1 A
1504689 TACGATTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.30
25 12 0.52
26 4 0.17
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATACAATATAAAAATAATATAA
Found at i:1504798 original size:49 final size:49
Alignment explanation
Indices: 1504673--1504775 Score: 140
Period size: 49 Copynumber: 2.1 Consensus size: 49
1504663 AAAATACATG
* *
1504673 ATATAAAA-AATATAAATA-CGAT-TCGAATATATAGATATATTAAAATTT
1 ATATAAAATAATATAAATATC-ATAT-AAATATATAGATATATCAAAATTT
*
1504721 ATATAAAATAATATAAATATCATATAAATATATAGATATATCAAAGTTT
1 ATATAAAATAATATAAATATCATATAAATATATAGATATATCAAAATTT
1504770 ATATAA
1 ATATAA
1504776 TATGAGTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
48 8 0.16
49 39 0.80
50 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (49 bp):
ATATAAAATAATATAAATATCATATAAATATATAGATATATCAAAATTT
Found at i:1504813 original size:10 final size:10
Alignment explanation
Indices: 1504699--1504754 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
1504689 TACGATTCGA
*
1504699 ATATATAGAT
1 ATATATAAAT
1504709 ATAT-TAAAAT
1 ATATAT-AAAT
*
1504719 TTATATAAA-
1 ATATATAAAT
1504728 ATAATATAAAT
1 AT-ATATAAAT
1504739 ATCATATAAAT
1 AT-ATATAAAT
1504750 ATATA
1 ATATA
1504755 GATATATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 2 0.05
10 23 0.61
11 13 0.34
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
ATATATAAAT
Found at i:1505530 original size:2 final size:2
Alignment explanation
Indices: 1505523--1505563 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1505513 CAGAGCTAGC
1505523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1505564 GTTGTTTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1506437 original size:17 final size:18
Alignment explanation
Indices: 1506404--1506451 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1506394 TTTTAATTAA
1506404 AAAATTTTAAAATATAAAT
1 AAAATTTT-AAATATAAAT
1506423 AAAATTTTAAA-ATAAAT
1 AAAATTTTAAATATAAAT
* *
1506440 ATAAGTTTAAAT
1 AAAATTTTAAAT
1506452 TATATGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 15 0.58
18 3 0.12
19 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATTTTAAATATAAAT
Found at i:1506560 original size:26 final size:24
Alignment explanation
Indices: 1506507--1506562 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
1506497 AAAAACATTT
*
1506507 TTTTAAAAAAAATAACTTTTTTAT
1 TTTTAAAAAAAATAACTTTTTTAA
*
1506531 TTTTAAAAAATTACTAA-TTTTTTAAA
1 TTTTAAAAAA--AATAACTTTTTT-AA
1506557 TTTTAA
1 TTTTAA
1506563 TATATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 10 0.37
25 6 0.22
26 11 0.41
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTAAAAAAAATAACTTTTTTAA
Found at i:1507296 original size:13 final size:13
Alignment explanation
Indices: 1507278--1507302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1507268 AATTTATCTT
1507278 TTTTAAATTCAAA
1 TTTTAAATTCAAA
1507291 TTTTAAATTCAA
1 TTTTAAATTCAA
1507303 TGGTGAAATA
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAATTCAAA
Found at i:1508516 original size:13 final size:13
Alignment explanation
Indices: 1508490--1508528 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1508480 ATTAATTTAA
1508490 TAAAAATTAAATTT
1 TAAAAA-TAAATTT
*
1508504 TAAAAATATATTT
1 TAAAAATAAATTT
*
1508517 AAAAAATAAATT
1 TAAAAATAAATT
1508529 ACAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAATAAATTT
Found at i:1509137 original size:7 final size:7
Alignment explanation
Indices: 1509125--1509149 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1509115 TAAACATTTC
1509125 TATTCTA
1 TATTCTA
1509132 TATTCTA
1 TATTCTA
1509139 TATTCTA
1 TATTCTA
1509146 TATT
1 TATT
1509150 ATGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTCTA
Found at i:1509383 original size:38 final size:39
Alignment explanation
Indices: 1509320--1509402 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 39
1509310 AGACATTTCC
*
1509320 ATTCTA-TAAGTTATACAATGTCCTAATTAAACACTTTT
1 ATTCTATTAAGTTATACAATGACCTAATTAAACACTTTT
*
1509358 ATTCTATTAATTTATACAAT-ACCTAATTAAACACTTTT
1 ATTCTATTAAGTTATACAATGACCTAATTAAACACTTTT
1509396 ATTCTAT
1 ATTCTAT
1509403 ATTGTGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 30 0.71
39 12 0.29
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (39 bp):
ATTCTATTAAGTTATACAATGACCTAATTAAACACTTTT
Found at i:1510451 original size:17 final size:18
Alignment explanation
Indices: 1510431--1510482 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
1510421 AAAATTAAAA
1510431 ATTAATAAAAAATATAT-
1 ATTAATAAAAAATATATG
*
1510448 ATTATTAAAAAA-ATTATG
1 ATTAATAAAAAATA-TATG
*
1510466 ATTAAATAAAAATTATA
1 ATT-AATAAAAAATATA
1510483 AATATTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.04
17 14 0.50
18 3 0.11
19 9 0.32
20 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTAATAAAAAATATATG
Found at i:1510469 original size:18 final size:15
Alignment explanation
Indices: 1510417--1510482 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 15
1510407 AACTTAAAAA
*
1510417 AAAAAAAATTAAAAATT
1 AAAAAAAATT--ATATT
1510434 AATAAAAAATATATATT
1 AA-AAAAAAT-TATATT
1510451 ATTAAAAAAATTATGATT
1 A--AAAAAAATTAT-ATT
1510469 AAATAAAAATTATA
1 AAA-AAAAATTATA
1510483 AATATTAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 3 0.07
17 19 0.45
18 18 0.43
19 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAAAAAATTATATT
Found at i:1511894 original size:86 final size:86
Alignment explanation
Indices: 1511748--1511908 Score: 286
Period size: 86 Copynumber: 1.9 Consensus size: 86
1511738 AAAAAATAGA
* *
1511748 CAAGATCAAGTATTGAAAGCTTCAGTACAGGAGCTTGAAAATCATGTTCTTGATGGTGATAGTTT
1 CAAGATCAAGTATTGAAAGCTTCAGTACAGGAGCTTGAAAATCATGTTCTTGACGGTGATAATTT
*
1511813 TGGGGTCACCCTTACAGTAGT
66 TGGGATCACCCTTACAGTAGT
*
1511834 CAAGATCAAGTATTGAAAGCTTCAGTACAGGAGCTTGAAAATCATGTTCTTGACGTTGATAATTT
1 CAAGATCAAGTATTGAAAGCTTCAGTACAGGAGCTTGAAAATCATGTTCTTGACGGTGATAATTT
1511899 TGGGATCACC
66 TGGGATCACC
1511909 TAGATTTATA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (86 bp):
CAAGATCAAGTATTGAAAGCTTCAGTACAGGAGCTTGAAAATCATGTTCTTGACGGTGATAATTT
TGGGATCACCCTTACAGTAGT
Found at i:1514969 original size:16 final size:15
Alignment explanation
Indices: 1514939--1514993 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
1514929 GAATATTCGT
1514939 TTAAAATTTTTTAAA
1 TTAAAATTTTTTAAA
1514954 TTAAAATTTATTTAAA
1 TTAAAATTT-TTTAAA
** *
1514970 -TACGATTTTATAAA
1 TTAAAATTTTTTAAA
*
1514984 ATAAAATTTT
1 TTAAAATTTT
1514994 ATTTTTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 5 0.15
15 22 0.67
16 6 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
TTAAAATTTTTTAAA
Found at i:1517284 original size:26 final size:27
Alignment explanation
Indices: 1517240--1517313 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 27
1517230 ATATGATGAT
*
1517240 TTATTTATATTAATGTAAATTTAATTA-A
1 TTATTTATATTTAT-TAAATTT-ATTATA
*
1517268 TT-TTATATATTT-TTAAATTTTTTATA
1 TTATT-TATATTTATTAAATTTATTATA
1517294 TTATTTATATTTATTAAATT
1 TTATTTATATTTATTAAATT
1517314 CGACTGTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.08
26 17 0.43
27 12 0.30
28 8 0.20
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (27 bp):
TTATTTATATTTATTAAATTTATTATA
Found at i:1517288 original size:17 final size:18
Alignment explanation
Indices: 1517266--1517305 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1517256 AAATTTAATT
1517266 AATTTTATATATT-TTTA
1 AATTTTATATATTATTTA
*
1517283 AATTTTTTATATTATTTA
1 AATTTTATATATTATTTA
*
1517301 TATTT
1 AATTT
1517306 ATTAAATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTTTATATATTATTTA
Found at i:1518182 original size:2 final size:2
Alignment explanation
Indices: 1518175--1518210 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1518165 TCTATATGTT
1518175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1518211 ATAATTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1519236 original size:2 final size:2
Alignment explanation
Indices: 1519223--1519255 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1519213 ATAAATTCTA
*
1519223 AT AT AA 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 A
1519256 CACACGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1519397 original size:2 final size:2
Alignment explanation
Indices: 1519390--1519423 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1519380 TTGTTATTTG
1519390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1519424 ATACGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1522480 original size:11 final size:11
Alignment explanation
Indices: 1522464--1522529 Score: 63
Period size: 11 Copynumber: 6.5 Consensus size: 11
1522454 AAAATTTATG
1522464 TATTTATATTA
1 TATTTATATTA
1522475 TATTTA-A--A
1 TATTTATATTA
1522483 TATTT-TATTA
1 TATTTATATTA
*
1522493 TATTAATATTA
1 TATTTATATTA
* *
1522504 TATTTAAAATA
1 TATTTATATTA
1522515 T-TTTATATT-
1 TATTTATATTA
1522524 TATTTA
1 TATTTA
1522530 AATTTTAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
8 7 0.16
9 1 0.02
10 16 0.36
11 20 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTATATTA
Found at i:1522501 original size:29 final size:30
Alignment explanation
Indices: 1522464--1522520 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
1522454 AAAATTTATG
*
1522464 TATTTATATTATATTT-AAATATTTTATTA
1 TATTAATATTATATTTAAAATATTTTATTA
1522493 TATTAATATTATATTTAAAATATTTTAT
1 TATTAATATTATATTTAAAATATTTTAT
1522521 ATTTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTAATATTATATTTAAAATATTTTATTA
Found at i:1522515 original size:20 final size:20
Alignment explanation
Indices: 1522495--1522539 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1522485 TTTTATTATA
1522495 TTAATATTATATTTAAAATAT
1 TTAATATT-TATTTAAAATAT
*
1522516 TTTATATTTATTT-AAAT-T
1 TTAATATTTATTTAAAATAT
1522534 TTAATA
1 TTAATA
1522540 CGTTAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 6 0.27
19 4 0.18
20 5 0.23
21 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAATATTTATTTAAAATAT
Found at i:1523074 original size:7 final size:7
Alignment explanation
Indices: 1523064--1523096 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1523054 AAAATAAAAA
1523064 TAATAAT
1 TAATAAT
1523071 TAAT-AT
1 TAATAAT
1523077 TAATAAT
1 TAATAAT
1523084 TAATAAT
1 TAATAAT
1523091 TAATAA
1 TAATAA
1523097 AAAGTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATAAT
Found at i:1523746 original size:24 final size:23
Alignment explanation
Indices: 1523719--1523765 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1523709 CATTTAATCA
*
1523719 ATTTTAATATCAAATATTCAAATT
1 ATTTAAATATCAAA-ATTCAAATT
* *
1523743 ATTTAAATATTAAAATTTAAATT
1 ATTTAAATATCAAAATTCAAATT
1523766 TTATATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAAATATCAAAATTCAAATT
Found at i:1524074 original size:22 final size:22
Alignment explanation
Indices: 1524044--1524089 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1524034 AATAATTTTT
*
1524044 TATTTAAAT-TTAATAATAAAAA
1 TATTAAAATATTAA-AATAAAAA
1524066 TATTAAAATATTAAAATAAAAA
1 TATTAAAATATTAAAATAAAAA
1524088 TA
1 TA
1524090 ACATCATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TATTAAAATATTAAAATAAAAA
Found at i:1524299 original size:16 final size:16
Alignment explanation
Indices: 1524274--1524308 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1524264 AATTAAAATA
* *
1524274 TAAATTTTAAATTTAT
1 TAAATATTAAATTAAT
1524290 TAAATATTAAATTAAT
1 TAAATATTAAATTAAT
1524306 TAA
1 TAA
1524309 TTAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATATTAAATTAAT
Found at i:1530737 original size:29 final size:29
Alignment explanation
Indices: 1530717--1530772 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1530707 TAAGTTATTG
1530717 TATTTTTA-TTATATTTAAATAAATTTTA
1 TATTTTTATTTATATTTAAATAAATTTTA
* *
1530745 TCTTTTTATTTGTATTTAAATAAATTTT
1 TATTTTTATTTATATTTAAATAAATTTT
1530773 TTTTGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
TATTTTTATTTATATTTAAATAAATTTTA
Found at i:1530851 original size:30 final size:30
Alignment explanation
Indices: 1530800--1530893 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
1530790 TTGAATTATA
* * *
1530800 TTAAGGGTTTTTTTAGG-TATAAGTTAAA-G
1 TTAAGAGTTTATTT-GGATATAAATTAAATG
1530829 TTAAAGAGTTTATTTGGATATAAATTAAATG
1 TT-AAGAGTTTATTTGGATATAAATTAAATG
* * *
1530860 TTAAGTGTTTATTT-GAGTGTAAATTAAATA
1 TTAAGAGTTTATTTGGA-TATAAATTAAATG
1530890 TTAA
1 TTAA
1530894 AAATGTATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
29 6 0.11
30 46 0.84
31 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (30 bp):
TTAAGAGTTTATTTGGATATAAATTAAATG
Found at i:1531482 original size:6 final size:6
Alignment explanation
Indices: 1531473--1531498 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1531463 AAAGAAAGAC
1531473 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
1531499 TAAAAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1531598 original size:33 final size:33
Alignment explanation
Indices: 1531542--1531607 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1531532 TCATATTTAA
* *
1531542 AATATTTTATAATTATATTAA-TTTTAATATATT
1 AATAATTTATAATTATATAAATTTTTAA-ATATT
1531575 AATAATTTAT-ATTATATAAAATTTTTAAATATT
1 AATAATTTATAATTATAT-AAATTTTTAAATATT
1531608 TTTTTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 7 0.24
33 16 0.55
34 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
AATAATTTATAATTATATAAATTTTTAAATATT
Found at i:1532909 original size:2 final size:2
Alignment explanation
Indices: 1532902--1532926 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1532892 TTATTCTCAA
1532902 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
1532927 ACAGAAATCC
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:1533596 original size:2 final size:2
Alignment explanation
Indices: 1533584--1533618 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1533574 ATAGAAAGAC
* *
1533584 GA GA GA CA GA GA GA CA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1533619 GGAAAGGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1533597 original size:8 final size:8
Alignment explanation
Indices: 1533580--1533618 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1533570 TTGCATAGAA
1533580 AGAC-GAG
1 AGACAGAG
1533587 AGACAGAG
1 AGACAGAG
1533595 AGACAGAG
1 AGACAGAG
*
1533603 AGAGAGAG
1 AGACAGAG
*
1533611 AGAGAGAG
1 AGACAGAG
1533619 GGAAAGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 4 0.13
8 26 0.87
ACGTcount: A:0.49, C:0.08, G:0.44, T:0.00
Consensus pattern (8 bp):
AGACAGAG
Found at i:1534051 original size:24 final size:24
Alignment explanation
Indices: 1533998--1534051 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1533988 TAAAAATTAT
*
1533998 TAAATTAAATAAATAAATAATTCAA
1 TAAA-TAAATAAATAAATAATTAAA
* * *
1534023 CAAATAAATTAATACATAATTAAA
1 TAAATAAATAAATAAATAATTAAA
1534047 TAAAT
1 TAAAT
1534052 TCAATATCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAATAAATAAATAAATAATTAAA
Found at i:1535540 original size:17 final size:16
Alignment explanation
Indices: 1535494--1535557 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
1535484 CGATTTGGTA
*
1535494 TAATCTAATTTAAATAT
1 TAATTTAATTTAAAT-T
**
1535511 TAA-AAAATTTAAATT
1 TAATTTAATTTAAATT
*
1535526 TAAGTTTATTTTAAAATT
1 TAA-TTTAATTT-AAATT
1535544 TAATTTAATTTAAA
1 TAATTTAATTTAAA
1535558 ATATTTTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
15 4 0.11
16 12 0.32
17 14 0.37
18 8 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTAATTTAAATT
Found at i:1535558 original size:17 final size:18
Alignment explanation
Indices: 1535516--1535559 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1535506 AATATTAAAA
1535516 AATTT-AAATTTAAGTTT
1 AATTTAAAATTTAAGTTT
*
1535533 ATTTTAAAATTTAA-TTT
1 AATTTAAAATTTAAGTTT
1535550 AATTTAAAAT
1 AATTTAAAAT
1535560 ATTTTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTTAAAATTTAAGTTT
Found at i:1535672 original size:13 final size:13
Alignment explanation
Indices: 1535654--1535678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1535644 TAATTTTATT
1535654 ATATATAATTTTC
1 ATATATAATTTTC
1535667 ATATATAATTTT
1 ATATATAATTTT
1535679 TTTAAAAAAA
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATAATTTTC
Found at i:1536287 original size:2 final size:2
Alignment explanation
Indices: 1536280--1536305 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1536270 TAAACATGTT
1536280 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1536306 ATTTTGTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1546340 original size:2 final size:2
Alignment explanation
Indices: 1546335--1546360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1546325 TTTATATTGA
1546335 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
1546361 TCTAACTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1547668 original size:16 final size:16
Alignment explanation
Indices: 1547647--1547702 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
1547637 TCAAATAATG
**
1547647 TTATTTTAAATTTCGA
1 TTATTTTAAATTTAAA
1547663 TTATTTTAAATTTAAA
1 TTATTTTAAATTTAAA
*
1547679 TTATTTTATATTT-AA
1 TTATTTTAAATTTAAA
1547694 TT-TTTTAAA
1 TTATTTTAAA
1547703 AATTTAGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.17
15 4 0.11
16 26 0.72
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
TTATTTTAAATTTAAA
Found at i:1548652 original size:2 final size:2
Alignment explanation
Indices: 1548645--1548669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1548635 ATACAATACC
1548645 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1548670 TGAATTCATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1550288 original size:27 final size:26
Alignment explanation
Indices: 1550230--1550290 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 26
1550220 GTTTTATTTT
* *
1550230 TTAAAATTTTTTTAAATATTTTTAAC
1 TTAAAATTTTTTTAAATATTATCAAC
* *
1550256 TATAAAATTATTTTTAACTATTATCAAG
1 T-TAAAATT-TTTTTAAATATTATCAAC
1550284 TTAAAAT
1 TTAAAAT
1550291 ATAATTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 13 0.45
28 15 0.52
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAAAATTTTTTTAAATATTATCAAC
Found at i:1552308 original size:3 final size:3
Alignment explanation
Indices: 1552302--1552373 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
1552292 ACAACACCAA
1552302 AAT AAT AAT AAT 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 AAT AAT AAT AAT
* * *
1552350 GAT AAT AAT AAT AAA AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
1552374 TCCAATGCTT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1552582 original size:5 final size:5
Alignment explanation
Indices: 1552569--1552602 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1552559 TGATTGGGAA
*
1552569 AAAAG AAAAA AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1552603 AATTTTGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1552998 original size:23 final size:23
Alignment explanation
Indices: 1552953--1553001 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1552943 ATTTTAATTT
*
1552953 AATATAATTTTAATTATCAATAA
1 AATATAATTTTAATGATCAATAA
* **
1552976 AATATAATTTTCATGATTTATAA
1 AATATAATTTTAATGATCAATAA
1552999 AAT
1 AAT
1553002 CGACACGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
AATATAATTTTAATGATCAATAA
Found at i:1553110 original size:2 final size:2
Alignment explanation
Indices: 1553103--1553139 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1553093 AAACAAATGT
* *
1553103 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1553140 CCTAATTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1553322 original size:21 final size:23
Alignment explanation
Indices: 1553280--1553322 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1553270 GTCTAGTTTA
* *
1553280 ATATAAATTTTTAATATTATAAT
1 ATATAAATTTTAAATATAATAAT
1553303 ATATAAA-TTTAAATA-AATAA
1 ATATAAATTTTAAATATAATAA
1553323 AACCATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATAAATTTTAAATATAATAAT
Done.