Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold66
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: 4623749
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 850 characters in sequence are not A, C, G, or T
File 8 of 26
Found at i:1385812 original size:29 final size:29
Alignment explanation
Indices: 1385780--1385843 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1385770 CAATTCTAAT
* *
1385780 AAAATTTTTACACTTCATAAATAAAATTAA
1 AAAATATTTACA-TTCATAAATAAAATAAA
* *
1385810 AAAATATTTATATTCATAAATATAATAAA
1 AAAATATTTACATTCATAAATAAAATAAA
1385839 AAAAT
1 AAAAT
1385844 CAATTAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAATATTTACATTCATAAATAAAATAAA
Found at i:1386484 original size:4 final size:4
Alignment explanation
Indices: 1386475--1386501 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1386465 GAAACCAGTC
1386475 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
1386502 ATATATATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1386906 original size:5 final size:5
Alignment explanation
Indices: 1386892--1387015 Score: 66
Period size: 5 Copynumber: 25.8 Consensus size: 5
1386882 ATATCGTAAT
* ** *
1386892 TTATA GTATA TTATAA TTATA TT-TA AAATG TTATA -TAT- TTATA TTA-A
1 TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * * *
1386939 TTTTA ATAAA TTA-A TAAT- TTATA TTATA -TAAA TTATA ATATA TTTTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1386986 TT-TA TTTATA TTATA TTATA TTATAA TTAT
1 TTATA -TTATA TTATA TTATA TTAT-A TTAT
1387016 TTTTTATCAT
Statistics
Matches: 88, Mismatches: 20, Indels: 21
0.68 0.16 0.16
Matches are distributed among these distances:
4 22 0.25
5 54 0.61
6 12 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:1386937 original size:27 final size:27
Alignment explanation
Indices: 1386892--1386967 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 27
1386882 ATATCGTAAT
*
1386892 TTATAGTATATTATAATTATATTTAA-AATG
1 TTATA-TAT-TTAT-ATTATATTTAATAA-A
1386922 TTATATATTTATATTA-ATTTTAATAAA
1 TTATATATTTATATTATA-TTTAATAAA
1386949 TTA-ATAATTTATATTATAT
1 TTATAT-ATTTATATTATAT
1386968 AAATTATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
26 3 0.07
27 23 0.56
28 7 0.17
29 3 0.07
30 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
TTATATATTTATATTATATTTAATAAA
Found at i:1386978 original size:32 final size:34
Alignment explanation
Indices: 1386925--1387012 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
1386915 TAAAATGTTA
* *
1386925 TATATTTATATTAATTTTAATA-A-ATTAATAATT
1 TATA-TTATATAAATTATAATATATATTAATAATT
* * *
1386958 TATATTATATAAATTATAATATATTTTATTTATT
1 TATATTATATAAATTATAATATATATTAATAATT
*
1386992 TATATTATATTATATTATAAT
1 TATATTATA-TAAATTATAAT
1387013 TATTTTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 15 0.33
33 5 0.11
34 16 0.35
35 10 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATTATATAAATTATAATATATATTAATAATT
Found at i:1387628 original size:18 final size:18
Alignment explanation
Indices: 1387605--1387641 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1387595 TGTAAGCTTT
1387605 ATCCTGACTGAGTCCTGA
1 ATCCTGACTGAGTCCTGA
*
1387623 ATCCTGAGTGAGTCCTGA
1 ATCCTGACTGAGTCCTGA
1387641 A
1 A
1387642 GAAAACGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (18 bp):
ATCCTGACTGAGTCCTGA
Found at i:1388968 original size:19 final size:19
Alignment explanation
Indices: 1388946--1389007 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1388936 ATTATATATA
1388946 AATATATATTTAATATAAT
1 AATATATATTTAATATAAT
* ** *
1388965 AATATTTATTTTTTAAAAT
1 AATATATATTTAATATAAT
* *
1388984 TATATATATTTAATTATCAT
1 AATATATATTTAA-TATAAT
1389004 AATA
1 AATA
1389008 AATAAAATAT
Statistics
Matches: 31, Mismatches: 11, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATATATTTAATATAAT
Found at i:1388971 original size:15 final size:17
Alignment explanation
Indices: 1388941--1388972 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1388931 TGTGTATTAT
1388941 ATATAAATATATATTTA
1 ATATAAATATATATTTA
1388958 ATAT-AATA-ATATTTA
1 ATATAAATATATATTTA
1388973 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAAATATATATTTA
Found at i:1389034 original size:14 final size:12
Alignment explanation
Indices: 1389006--1389051 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1388996 ATTATCATAA
1389006 TAAATAAAATAT
1 TAAATAAAATAT
1389018 TAAATATAAATATT
1 TAAATA-AAATA-T
1389032 TAAA-AAAA-AT
1 TAAATAAAATAT
1389042 TAAATGAAAA
1 TAAAT-AAAA
1389052 CACGAAGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 5 0.17
11 1 0.03
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:1390208 original size:16 final size:16
Alignment explanation
Indices: 1390170--1390200 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1390160 AATTAATTTA
1390170 AAAATA-TATTTTATT
1 AAAATATTATTTTATT
1390185 AAAATATTATTTTATT
1 AAAATATTATTTTATT
1390201 TTAATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAAATATTATTTTATT
Found at i:1390216 original size:16 final size:15
Alignment explanation
Indices: 1390197--1390247 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1390187 AATATTATTT
*
1390197 TATTTTAATATTTATA
1 TATTTTAATAATTA-A
1390213 TATTTT-ATAATTAA
1 TATTTTAATAATTAA
**
1390227 -ATTTTAATAAAAAA
1 TATTTTAATAATTAA
1390241 TATTTTA
1 TATTTTA
1390248 TTATTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 5 0.17
14 7 0.23
15 12 0.40
16 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTTAATAATTAA
Found at i:1390272 original size:17 final size:17
Alignment explanation
Indices: 1390250--1390283 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1390240 ATATTTTATT
1390250 ATTAAA-TAATAATTTAA
1 ATTAAACTAA-AATTTAA
1390267 ATTAAACTAAAATTTAA
1 ATTAAACTAAAATTTAA
1390284 TTCTTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAACTAAAATTTAA
Found at i:1390983 original size:14 final size:14
Alignment explanation
Indices: 1390944--1391002 Score: 68
Period size: 15 Copynumber: 4.2 Consensus size: 14
1390934 TTAACATTAT
1390944 TATT-ATTAAAAAA
1 TATTAATTAAAAAA
*
1390957 TATTGAGTTAAAAAA
1 TATT-AATTAAAAAA
1390972 -ATTAATTAAAAAA
1 TATTAATTAAAAAA
*
1390985 TATATATTTAAAAAA
1 TAT-TAATTAAAAAA
1391000 TAT
1 TAT
1391003 GATAAAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
13 13 0.33
14 5 0.13
15 21 0.54
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
TATTAATTAAAAAA
Found at i:1391117 original size:28 final size:27
Alignment explanation
Indices: 1391070--1391122 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1391060 CTGCAAGAAA
* *
1391070 TTAAAAAATAAATATATAAAGATATCT
1 TTAAAAAATAAAAATATAAAAATATCT
*
1391097 TTAAAATAATAAAAATTTAAAAATAT
1 TTAAAA-AATAAAAATATAAAAATAT
1391123 ATACATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
TTAAAAAATAAAAATATAAAAATATCT
Found at i:1391715 original size:30 final size:30
Alignment explanation
Indices: 1391631--1391714 Score: 134
Period size: 30 Copynumber: 2.8 Consensus size: 30
1391621 TTATATTAAA
* *
1391631 AATTTATTTATATATAAATTAAAAATTATC
1 AATTTATTTAAATATAAATTAAAAATAATC
*
1391661 AATTTATTTAAATATTAATTAAAAATAAT-
1 AATTTATTTAAATATAAATTAAAAATAATC
1391690 AATTTATTTAAATATAAATTAAAAA
1 AATTTATTTAAATATAAATTAAAAA
1391715 ATTAAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 24 0.48
30 26 0.52
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
AATTTATTTAAATATAAATTAAAAATAATC
Found at i:1392188 original size:20 final size:19
Alignment explanation
Indices: 1392132--1392218 Score: 92
Period size: 18 Copynumber: 4.7 Consensus size: 19
1392122 CTATTAAAAT
*
1392132 TATTAAATTAAATTATTT-A
1 TATTAAA-TAAATAATTTAA
1392151 -ATT-AATAAATAATTTAA
1 TATTAAATAAATAATTTAA
1392168 TATTAAATAAATAATTTTAA
1 TATTAAATAAATAA-TTTAA
* * *
1392188 TATTTAATAAAT-GTTAAA
1 TATTAAATAAATAATTTAA
1392206 TATTAAATAAATA
1 TATTAAATAAATA
1392219 TTACTTAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.16
17 3 0.05
18 21 0.36
19 9 0.16
20 16 0.28
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (19 bp):
TATTAAATAAATAATTTAA
Found at i:1392254 original size:15 final size:15
Alignment explanation
Indices: 1392205--1392254 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1392195 TAAATGTTAA
1392205 ATATTAAATAAATATT
1 ATATTAAATAAA-ATT
*
1392221 A-CTT-AATAAAAATTT
1 ATATTAAAT-AAAA-TT
1392236 ATATTAAATAAAATT
1 ATATTAAATAAAATT
1392251 ATAT
1 ATAT
1392255 AATTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 4 0.14
15 14 0.50
16 7 0.25
17 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTAAATAAAATT
Found at i:1392381 original size:18 final size:19
Alignment explanation
Indices: 1392346--1392389 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1392336 ATTTAAACTT
* *
1392346 ATTTTTTATTATTTAATTA
1 ATTTTTTATAATTCAATTA
1392365 ATTTTTT-TAATTCAATTA
1 ATTTTTTATAATTCAATTA
1392383 ATTTTTT
1 ATTTTTT
1392390 CTCCTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTATAATTCAATTA
Found at i:1393306 original size:2 final size:2
Alignment explanation
Indices: 1393299--1393326 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1393289 TATAGCTTTA
1393299 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
1393327 TAAAGTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1394016 original size:19 final size:18
Alignment explanation
Indices: 1393973--1394016 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1393963 TATTACATAT
*
1393973 TAAATAATATTAATTTAA
1 TAAAAAATATTAATTTAA
* *
1393991 TAAAAAATATTTATTTTA
1 TAAAAAATATTAATTTAA
1394009 TAATAAAA
1 TAA-AAAA
1394017 ACTATATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAAATATTAATTTAA
Found at i:1395434 original size:14 final size:14
Alignment explanation
Indices: 1395394--1395435 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1395384 TTAAAATTAT
* *
1395394 ATATATATATTTTA
1 ATATAAATATTTAA
1395408 ATATAAATA-TTAA
1 ATATAAATATTTAA
1395421 ATATAAATATTTAA
1 ATATAAATATTTAA
1395435 A
1 A
1395436 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATAAATATTTAA
Found at i:1395913 original size:15 final size:15
Alignment explanation
Indices: 1395889--1395928 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1395879 TTCTGAATAA
* *
1395889 ATATTATAAATATAT
1 ATATTTTAAATACAT
1395904 ATATTTTAAATACAT
1 ATATTTTAAATACAT
1395919 ATATATTTAA
1 ATAT-TTTAA
1395929 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATTTTAAATACAT
Found at i:1396557 original size:17 final size:17
Alignment explanation
Indices: 1396532--1396578 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1396522 TTAATTTTTG
* *
1396532 TTTAAAAATTAAATTTA
1 TTTATAAATTAAATTAA
1396549 TTTATAAATTAAATTAA
1 TTTATAAATTAAATTAA
* *
1396566 ATTATAATTTAAA
1 TTTATAAATTAAA
1396579 AATTTTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTATAAATTAAATTAA
Found at i:1396565 original size:22 final size:24
Alignment explanation
Indices: 1396537--1396582 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1396527 TTTTGTTTAA
*
1396537 AAATTAAATT-T-ATTTATAAATT
1 AAATTAAATTATAATTTAAAAATT
1396559 AAATTAAATTATAATTTAAAAATT
1 AAATTAAATTATAATTTAAAAATT
1396583 TTAATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTAAATTATAATTTAAAAATT
Found at i:1397425 original size:15 final size:15
Alignment explanation
Indices: 1397405--1397438 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1397395 ATTATTGTTA
*
1397405 AAAAAAATTGAGTTT
1 AAAAAAATTGAGGTT
*
1397420 AAAAAAATTTAGGTT
1 AAAAAAATTGAGGTT
1397435 AAAA
1 AAAA
1397439 TTGTATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (15 bp):
AAAAAAATTGAGGTT
Found at i:1397605 original size:16 final size:15
Alignment explanation
Indices: 1397584--1397628 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1397574 TGAAGATAAT
1397584 AAAATTATTTTATTAA
1 AAAATTATTTT-TTAA
*
1397600 AAAATTAATTTTTAA
1 AAAATTATTTTTTAA
* *
1397615 ATAATAATTTTTTA
1 AAAATTATTTTTTA
1397629 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAAATTATTTTTTAA
Found at i:1397614 original size:15 final size:15
Alignment explanation
Indices: 1397584--1397626 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
1397574 TGAAGATAAT
*
1397584 AAAATTATTTTATTAA
1 AAAATTAATTT-TTAA
1397600 AAAATTAATTTTTAA
1 AAAATTAATTTTTAA
*
1397615 ATAA-TAATTTTT
1 AAAATTAATTTTT
1397627 TATTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.32
15 7 0.28
16 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAAATTAATTTTTAA
Found at i:1398491 original size:64 final size:64
Alignment explanation
Indices: 1398417--1398564 Score: 262
Period size: 64 Copynumber: 2.3 Consensus size: 64
1398407 ATAAATACAA
*
1398417 ATATAAATTTTTTTCTAAATTAAATCACTATAATATATGTTGTGAATTTAGACATGACATGAAT
1 ATATAAATTTTTTTCTAAATTAAATCACTATAATATATGTTGTGAATTTAGACATCACATGAAT
* *
1398481 ATATATATTTTTCTCTAAATTAAATCACTATAATATATGTTGTGAATTTAGACATCACATGAAT
1 ATATAAATTTTTTTCTAAATTAAATCACTATAATATATGTTGTGAATTTAGACATCACATGAAT
1398545 ATATAAATTTTTTT-TAAATT
1 ATATAAATTTTTTTCTAAATT
1398565 CAATACAATG
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 6 0.08
64 73 0.92
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (64 bp):
ATATAAATTTTTTTCTAAATTAAATCACTATAATATATGTTGTGAATTTAGACATCACATGAAT
Found at i:1398538 original size:30 final size:30
Alignment explanation
Indices: 1398440--1398548 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 30
1398430 TCTAAATTAA
1398440 ATCACTATAATATATGTTGTGAATTTAGAC
1 ATCACTATAATATATGTTGTGAATTTAGAC
* * * * *
1398470 ATGACATGAATATATATATTTTTCTCTAAATTA-A-
1 ATCAC-T--ATA-ATATA-TGTTGT-GAATTTAGAC
1398504 ATCACTATAATATATGTTGTGAATTTAGAC
1 ATCACTATAATATATGTTGTGAATTTAGAC
1398534 ATCAC-ATGAATATAT
1 ATCACTAT-AATATAT
1398549 AAATTTTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
28 5 0.08
29 7 0.12
30 21 0.35
31 4 0.07
33 4 0.07
34 9 0.15
35 5 0.08
36 5 0.08
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (30 bp):
ATCACTATAATATATGTTGTGAATTTAGAC
Found at i:1398661 original size:11 final size:11
Alignment explanation
Indices: 1398645--1398672 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1398635 ATTAAAACAT
1398645 AATATAATAAA
1 AATATAATAAA
1398656 AATATAATAAA
1 AATATAATAAA
1398667 AATATA
1 AATATA
1398673 CGAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AATATAATAAA
Found at i:1398832 original size:2 final size:2
Alignment explanation
Indices: 1398825--1398853 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1398815 TGATCTACTC
1398825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1398854 GTTTATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1399266 original size:6 final size:6
Alignment explanation
Indices: 1399248--1399291 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
1399238 GTACTAATTT
*
1399248 ATTTAA ATATAA ATTTAA ATTTTAAA ATTTAA ATTTAAA ATTTA
1 ATTTAA ATTTAA ATTTAA A-TTT-AA ATTTAA ATTT-AA ATTTA
1399292 TTATTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 18 0.55
7 12 0.36
8 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:1399277 original size:14 final size:13
Alignment explanation
Indices: 1399248--1399291 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
1399238 GTACTAATTT
*
1399248 ATTTAAATAT-AA
1 ATTTAAATTTAAA
1399260 ATTTAAATTTTAAA
1 ATTTAAA-TTTAAA
1399274 ATTTAAATTTAAA
1 ATTTAAATTTAAA
1399287 ATTTA
1 ATTTA
1399292 TTATTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 7 0.24
13 13 0.45
14 9 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATTTAAA
Found at i:1399280 original size:20 final size:20
Alignment explanation
Indices: 1399248--1399291 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1399238 GTACTAATTT
1399248 ATTT-AAATATAAATTTAAA
1 ATTTAAAATATAAATTTAAA
* *
1399267 TTTTAAAATTTAAATTTAAA
1 ATTTAAAATATAAATTTAAA
1399287 ATTTA
1 ATTTA
1399292 TTATTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAAATATAAATTTAAA
Found at i:1399291 original size:7 final size:7
Alignment explanation
Indices: 1399258--1399291 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1399248 ATTTAAATAT
1399258 AAATTTA
1 AAATTTA
*
1399265 AATTTTA
1 AAATTTA
1399272 AAATTT-
1 AAATTTA
1399278 AAATTTA
1 AAATTTA
1399285 AAATTTA
1 AAATTTA
1399292 TTATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AAATTTA
Found at i:1399826 original size:27 final size:25
Alignment explanation
Indices: 1399728--1399827 Score: 82
Period size: 23 Copynumber: 4.0 Consensus size: 25
1399718 AATTTATTTA
** *
1399728 ATTAATAAAAAATTAAAAA-ATAAT
1 ATTAATATTAAATTAAAAATTTAAT
* *
1399752 TTTAATATTTAA-TAAAAATTT-AT
1 ATTAATATTAAATTAAAAATTTAAT
1399775 ATTAA-ATTAAATTATATAAATTTTAAT
1 ATTAATATTAAATTA-A-AAA-TTTAAT
1399802 ATTAATATAATAAATTAAAAATTTAA
1 ATTAATAT--TAAATTAAAAATTTAA
1399828 ATCTCGTATA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
22 5 0.08
23 14 0.23
24 10 0.17
25 3 0.05
26 3 0.05
27 12 0.20
28 5 0.08
29 1 0.02
30 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTAATATTAAATTAAAAATTTAAT
Found at i:1399868 original size:15 final size:15
Alignment explanation
Indices: 1399848--1399877 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1399838 TAAATTAAAT
1399848 TTAAAAATATATTTA
1 TTAAAAATATATTTA
*
1399863 TTAAAATTATATTTA
1 TTAAAAATATATTTA
1399878 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAAAATATATTTA
Found at i:1400856 original size:13 final size:14
Alignment explanation
Indices: 1400825--1400866 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1400815 ATTAATTTTA
*
1400825 ATTTTTTTAATAAT
1 ATTTATTTAATAAT
*
1400839 TTTTATTTAAT-AT
1 ATTTATTTAATAAT
*
1400852 ATTTATTTGATAAT
1 ATTTATTTAATAAT
1400866 A
1 A
1400867 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
ATTTATTTAATAAT
Found at i:1401094 original size:25 final size:28
Alignment explanation
Indices: 1401057--1401124 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
1401047 TTATATTTTT
1401057 TATA-TTATAATTATATTTAA-A-A-TAA
1 TATATTTAT-ATTATATTTAATATATTAA
1401082 TATATTTATATTA-ATTTTAATATATTAA
1 TATATTTATATTATA-TTTAATATATTAA
1401110 TA-ATTTATATTATAT
1 TATATTTATATTATAT
1401125 AAATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
24 1 0.03
25 13 0.35
26 5 0.14
27 12 0.32
28 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TATATTTATATTATATTTAATATATTAA
Found at i:1401096 original size:14 final size:14
Alignment explanation
Indices: 1401068--1401132 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
1401058 ATATTATAAT
* *
1401068 TATATTTAAAATAA
1 TATATTTATATTAA
1401082 TATATTTATATTAA
1 TATATTTATATTAA
1401096 T-T-TTAATATATTAA
1 TATATT--TATATTAA
1401110 TA-ATTTATATTATA
1 TATATTTATATTA-A
*
1401124 TAAATTTAT
1 TATATTTAT
1401133 TTTTTATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
12 2 0.05
13 8 0.19
14 25 0.58
15 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATTTATATTAA
Found at i:1401124 original size:20 final size:18
Alignment explanation
Indices: 1401055--1401125 Score: 54
Period size: 20 Copynumber: 3.7 Consensus size: 18
1401045 TATTATATTT
1401055 TTTATATTATA-ATTATA
1 TTTATATTATATATTATA
* *
1401072 TTTAAAATAATATATTTATA
1 TTT-ATATTATATA-TTATA
* *
1401092 TTAATTTTAATATATTAATAA
1 TTTATATT-ATATATT-AT-A
1401113 TTTATATTATATA
1 TTTATATTATATA
1401126 AATTTATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
17 3 0.08
18 6 0.15
19 5 0.12
20 19 0.47
21 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTATATTATATATTATA
Found at i:1407143 original size:19 final size:20
Alignment explanation
Indices: 1407104--1407143 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1407094 GGAAAATGAA
**
1407104 TTTAAATTTAAAATTTTATT
1 TTTAAATTTAAAATTAAATT
1407124 TTTAAATTT-AAATTAAATT
1 TTTAAATTTAAAATTAAATT
1407143 T
1 T
1407144 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAAATTTAAAATTAAATT
Found at i:1407388 original size:168 final size:166
Alignment explanation
Indices: 1407200--1407536 Score: 514
Period size: 170 Copynumber: 2.0 Consensus size: 166
1407190 TGAGCACAAG
*
1407200 AAAATTTAAATTCAAAAATACTAAAACTTAAAAATTTAAAAGT-AAAAAAGTTAAATTCAATTCA
1 AAAATTTAAATTCAAAAATACTAAAACTAAAAAATTTAAAAGTAAAAAAAGTTAAATTCAATTCA
*
1407264 AAATTTTACATAAAATTTAAAAATCACTTGATTAACCCAAATTAAATTAATAAATTTTCAAAAAC
66 AAATTTTACATAAAATTTAAAAATCACTTGATTAACCCAAATTAAATTAATAAAATTTCAAAAAC
1407329 TTCAAAAAAAAAATAAAAAATATAAATCTCAAATTTGAC
131 TTC---AAAAAAATAAAAAATATAAATCTCAAATTTGAC
* * * * *
1407368 AAAATTTAAATTCGAAAATACTGAAACTAAAAAATTTAAAATTAAAAAAAAGTTAAATTTAATTT
1 AAAATTTAAATTCAAAAATACTAAAACTAAAAAATTTAAAAGT-AAAAAAAGTTAAATTCAATTC
* * * * *
1407433 AAAATTTTATATGAATTTTAAAAATTACTTGATTAACCCAAATTTAATTAATAAAATTTCAAAAA
65 AAAATTTTACATAAAATTTAAAAATCACTTGATTAACCCAAATTAAATTAATAAAATTTCAAAAA
*
1407498 CTTCAAAAAAATAAAAAATCTAAATCTCAAATTTGAC
130 CTTCAAAAAAATAAAAAATATAAATCTCAAATTTGAC
1407535 AA
1 AA
1407537 GTGAGGGGTA
Statistics
Matches: 154, Mismatches: 13, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
167 34 0.22
168 39 0.25
170 81 0.53
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (166 bp):
AAAATTTAAATTCAAAAATACTAAAACTAAAAAATTTAAAAGTAAAAAAAGTTAAATTCAATTCA
AAATTTTACATAAAATTTAAAAATCACTTGATTAACCCAAATTAAATTAATAAAATTTCAAAAAC
TTCAAAAAAATAAAAAATATAAATCTCAAATTTGAC
Found at i:1407418 original size:17 final size:17
Alignment explanation
Indices: 1407396--1407429 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1407386 TACTGAAACT
*
1407396 AAAAAATTTAAAATTAA
1 AAAAAAGTTAAAATTAA
*
1407413 AAAAAAGTTAAATTTAA
1 AAAAAAGTTAAAATTAA
1407430 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAAAAGTTAAAATTAA
Found at i:1408484 original size:24 final size:24
Alignment explanation
Indices: 1408456--1408501 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1408446 TTTGGCTCCA
1408456 TTATTATT-ATTAGTATT-TAATTCT
1 TTATT-TTAATTA-TATTCTAATTCT
1408480 TTATTTTAATTATATTCTAATT
1 TTATTTTAATTATATTCTAATT
1408502 GATAAGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (24 bp):
TTATTTTAATTATATTCTAATTCT
Found at i:1409675 original size:13 final size:14
Alignment explanation
Indices: 1409657--1409686 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1409647 TGTGATTTTT
1409657 AAATTA-TTAATTA
1 AAATTATTTAATTA
1409670 AAATTATTTAATTA
1 AAATTATTTAATTA
1409684 AAA
1 AAA
1409687 ATAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTATTTAATTA
Found at i:1410206 original size:16 final size:14
Alignment explanation
Indices: 1410186--1410228 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
1410176 AATATTAAAA
1410186 TTTAAAAATTGAATT
1 TTTAAAAATT-AATT
*
1410201 TATTAAATATTAATT
1 T-TTAAAAATTAATT
1410216 TTT-AAAATTAATT
1 TTTAAAAATTAATT
1410229 ATATGAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 9 0.36
14 2 0.08
15 6 0.24
16 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TTTAAAAATTAATT
Found at i:1410227 original size:13 final size:14
Alignment explanation
Indices: 1410190--1410228 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1410180 TTAAAATTTA
1410190 AAAATTGAATTTATT
1 AAAATT-AATTTATT
1410205 AAATATTAATTT-TT
1 AAA-ATTAATTTATT
1410219 AAAATTAATT
1 AAAATTAATT
1410229 ATATGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 5 0.22
15 8 0.35
16 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
AAAATTAATTTATT
Found at i:1410762 original size:24 final size:26
Alignment explanation
Indices: 1410735--1410798 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
1410725 ACAAATAAAA
*
1410735 TAAT-TAAAAG-AATTATTTTTATAT
1 TAATATAAAAGTAATTAGTTTTATAT
*
1410759 TAATATAAAGGTAATTAG-TTT-TAT
1 TAATATAAAAGTAATTAGTTTTATAT
*
1410783 TAATATAAAAATAATT
1 TAATATAAAAGTAATT
1410799 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 21 0.62
25 8 0.24
26 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
TAATATAAAAGTAATTAGTTTTATAT
Found at i:1412351 original size:27 final size:28
Alignment explanation
Indices: 1412312--1412366 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
1412302 TTGATTATAT
1412312 AAAATTTGAAATTGAATCATATTAAAATC
1 AAAATTT-AAATTGAATCATATTAAAATC
* * *
1412341 AAAATTT-AATTTAATTATTTTAAAAT
1 AAAATTTAAATTGAATCATATTAAAAT
1412367 ATAATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
29 7 0.30
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (28 bp):
AAAATTTAAATTGAATCATATTAAAATC
Found at i:1412530 original size:34 final size:34
Alignment explanation
Indices: 1412487--1412560 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
1412477 AAAATAAAGT
1412487 ACTTATAAGATATATTCATCCTAATTATGCATTG
1 ACTTATAAGATATATTCATCCTAATTATGCATTG
1412521 ACTTATAAGATATATTCATCCTAATTATGCATTG
1 ACTTATAAGATATATTCATCCTAATTATGCATTG
1412555 ACTTAT
1 ACTTAT
1412561 TTATTTATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (34 bp):
ACTTATAAGATATATTCATCCTAATTATGCATTG
Found at i:1413024 original size:26 final size:25
Alignment explanation
Indices: 1412995--1413064 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
1412985 AAATTATCAT
1412995 TTATTTTAATAAAAAATATCAATAAA
1 TTATTTTAAT-AAAAATATCAATAAA
* ** ** *
1413021 TTATTTTTATATCAATATTTATATA
1 TTATTTTAATAAAAATATCAATAAA
1413046 TTATTTTAATTAAAAATAT
1 TTATTTTAA-TAAAAATAT
1413065 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 18 0.53
26 16 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATTTTAATAAAAATATCAATAAA
Found at i:1413067 original size:25 final size:25
Alignment explanation
Indices: 1412987--1413067 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
1412977 TTAAGCTCAA
*
1412987 ATTATCAT-TTATTTTAATAAAAAAT
1 ATTAT-ATATTATTTTAATTAAAAAT
* * * **
1413012 ATCAATAAATTATTTTTA-TATCAAT
1 AT-TATATATTATTTTAATTAAAAAT
1413037 ATTTATATATTATTTTAATTAAAAAT
1 A-TTATATATTATTTTAATTAAAAAT
1413063 ATTAT
1 ATTAT
1413068 TTAAAATTAG
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
25 24 0.59
26 17 0.41
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTATATATTATTTTAATTAAAAAT
Found at i:1413309 original size:2 final size:2
Alignment explanation
Indices: 1413302--1413338 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1413292 TAGATAAGAT
1413302 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 T
1413339 TAAGGAGAGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1415405 original size:24 final size:26
Alignment explanation
Indices: 1415350--1415408 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
1415340 AATTCGTTAA
1415350 ATATTTATATTATTTTTTCGTATCAT
1 ATATTTATATTATTTTTTCGTATCAT
*
1415376 AT-TTTA-ATTATTTTTT-TTAT-ATT
1 ATATTTATATTATTTTTTCGTATCA-T
1415399 ATATTTATAT
1 ATATTTATAT
1415409 CATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.03
23 6 0.21
24 14 0.48
25 6 0.21
26 2 0.07
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (26 bp):
ATATTTATATTATTTTTTCGTATCAT
Found at i:1415576 original size:37 final size:36
Alignment explanation
Indices: 1415501--1415587 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 36
1415491 TATTTTTAAA
* * *
1415501 ATTTTAATTTAATTTTTGAAAACATCATAAAAATAT
1 ATTTTAATCTAATTTTTGAAAACATCAGAAAAACAT
* *
1415537 ATTTTAATCTAATTTTTTAAAACAT-AGCGAAAGACAT
1 ATTTTAATCTAATTTTTGAAAACATCA--GAAAAACAT
*
1415574 ATTCTAATTCTAAT
1 ATTTTAA-TCTAAT
1415588 AAGAGTAGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
35 1 0.02
36 23 0.55
37 12 0.29
38 6 0.14
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.43
Consensus pattern (36 bp):
ATTTTAATCTAATTTTTGAAAACATCAGAAAAACAT
Found at i:1415895 original size:22 final size:21
Alignment explanation
Indices: 1415853--1415942 Score: 70
Period size: 21 Copynumber: 4.4 Consensus size: 21
1415843 TTTAATTTAA
1415853 ATTATTTAA--AAATATTAAAAT
1 ATTATTTAATTAAATA-T-AAAT
1415874 ATTATTTTATATT-AATATAAAT
1 ATTA-TTTA-ATTAAATATAAAT
*
1415896 ATTATTTAATTAAATTTAAAT
1 ATTATTTAATTAAATATAAAT
1415917 ATT-TTT-ATT--A-ATAAAT
1 ATTATTTAATTAAATATAAAT
1415933 AATTATTTAA
1 -ATTATTTAA
1415943 ATTATTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
16 5 0.08
17 4 0.07
18 3 0.05
19 4 0.07
20 6 0.10
21 19 0.32
22 12 0.20
23 2 0.03
24 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATTTAATTAAATATAAAT
Found at i:1415895 original size:41 final size:41
Alignment explanation
Indices: 1415837--1415983 Score: 114
Period size: 41 Copynumber: 3.6 Consensus size: 41
1415827 TTTTTAATAA
*
1415837 ATTTTAT-TTAATTTAAATTATTTAAAAATATTAAAATATT
1 ATTTTATATTAATATAAATTATTTAAAAATATTAAAATATT
1415877 ATTTTATATTAATATAAATATTATTTAATTAAAT-TT--AA-A-T
1 ATTTTATATTAATAT-AA-ATTATTTAA--AAATATTAAAATATT
* * *
1415917 ATTTT-TATTAATAAATAATTATTT-AAATTATTAAAATATA
1 ATTTTATATTAATATA-AATTATTTAAAAATATTAAAATATT
* *
1415957 AATTTATATTGACATA-AAATAATTTAA
1 ATTTTATATT-A-ATATAAATTATTTAA
1415984 TTTTATTAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
35 3 0.03
36 2 0.02
37 1 0.01
38 10 0.12
39 10 0.12
40 17 0.20
41 18 0.21
42 7 0.08
43 12 0.14
44 2 0.02
45 4 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (41 bp):
ATTTTATATTAATATAAATTATTTAAAAATATTAAAATATT
Found at i:1416110 original size:2 final size:2
Alignment explanation
Indices: 1416105--1416139 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1416095 AAAAATCTTT
1416105 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 T
1416140 GCAGTCAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1416506 original size:25 final size:22
Alignment explanation
Indices: 1416478--1416529 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
1416468 GCTAATTTTT
1416478 TAAAATAAAAAATTATTTTATTAAA
1 TAAAAT-AAAAA-TATTTT-TTAAA
* *
1416503 TAAAATATAGATATTTTTTAAA
1 TAAAATAAAAATATTTTTTAAA
1416525 TAAAA
1 TAAAA
1416530 AATTATACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 6 0.24
24 3 0.12
25 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAAATAAAAATATTTTTTAAA
Found at i:1420291 original size:67 final size:67
Alignment explanation
Indices: 1420212--1420343 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
1420202 TCTTAAAGGA
*
1420212 TAGGAAAATGACTAAAAAGTATAAAAATATCCCAAAGGCTCTATTTTGATTAAAAAGTGTTCACA
1 TAGGAAAATGACTAAAAAGTATAAAAATATCCCAAAGGCTCTATTTTGATTAAAAAGTGCTCACA
1420277 AT
66 AT
* * *
1420279 TAGGAAAATGACTAAAAAGTATAAAAATATTCCTAAGGCTCTATTTTGATTAGAAAGTGCTCACA
1 TAGGAAAATGACTAAAAAGTATAAAAATATCCCAAAGGCTCTATTTTGATTAAAAAGTGCTCACA
1420344 CACTGTCTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (67 bp):
TAGGAAAATGACTAAAAAGTATAAAAATATCCCAAAGGCTCTATTTTGATTAAAAAGTGCTCACA
AT
Found at i:1420699 original size:39 final size:39
Alignment explanation
Indices: 1420656--1420730 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
1420646 TAAAAATTTG
1420656 TTTTTGAT-AAACTGGATTCAAT-AGAAGCTAAATGATTCA
1 TTTTTGATGAAA-TGGATTCAATAAG-AGCTAAATGATTCA
*
1420695 TTTTTGATGAAATGTATTCAATAAGAGCTAAATGAT
1 TTTTTGATGAAATGGATTCAATAAGAGCTAAATGAT
1420731 AACCTAGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (39 bp):
TTTTTGATGAAATGGATTCAATAAGAGCTAAATGATTCA
Found at i:1422002 original size:21 final size:21
Alignment explanation
Indices: 1421969--1422019 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1421959 TCAAAATTCT
1421969 TAAACATTAAATAAATATATA
1 TAAACATTAAATAAATATATA
* *
1421990 TAAATATTTAATAAATATATA
1 TAAACATTAAATAAATATATA
* *
1422011 AAAAAATTA
1 TAAACATTA
1422020 TTAATTAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAACATTAAATAAATATATA
Found at i:1429057 original size:3 final size:3
Alignment explanation
Indices: 1429049--1429078 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1429039 GTTATAGGGA
1429049 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1429079 GAGTAACCAA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1430234 original size:20 final size:21
Alignment explanation
Indices: 1430209--1430260 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
1430199 ACATAATTGT
1430209 AATATAATATAAAATA-ATTA
1 AATATAATATAAAATATATTA
1430229 AATAT-ATGAT-AAATATATTA
1 AATATAAT-ATAAAATATATTA
1430249 AAGTA-AATATAA
1 AA-TATAATATAA
1430261 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
AATATAATATAAAATATATTA
Found at i:1430871 original size:17 final size:18
Alignment explanation
Indices: 1430849--1430887 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1430839 TATTAGTTAC
1430849 ATATTT-TAAAATGTTT-T
1 ATATTTATAAAAT-TTTGT
1430866 ATATTTATAAAATTTTGT
1 ATATTTATAAAATTTTGT
1430884 ATAT
1 ATAT
1430888 ATAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
ATATTTATAAAATTTTGT
Found at i:1430881 original size:16 final size:16
Alignment explanation
Indices: 1430849--1430908 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
1430839 TATTAGTTAC
1430849 ATATTT-TAAAATGTTTT
1 ATATTTATAAAA--TTTT
1430866 ATATTTATAAAATTTT
1 ATATTTATAAAATTTT
* * *
1430882 GTATATATAAATAATTT
1 ATATTTATAAA-ATTTT
1430899 ATATTATATA
1 ATATT-TATA
1430909 TTTAATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 13 0.37
17 13 0.37
18 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATTTATAAAATTTT
Found at i:1430906 original size:18 final size:17
Alignment explanation
Indices: 1430863--1430908 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1430853 TTTAAAATGT
*
1430863 TTTATATT-TATAAAAT
1 TTTATATTATATAAAAA
*
1430879 TTTGTA-TATATAAATAA
1 TTTATATTATATAAA-AA
1430896 TTTATATTATATA
1 TTTATATTATATA
1430909 TTTAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 11 0.46
17 6 0.25
18 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTATATTATATAAAAA
Found at i:1430908 original size:22 final size:23
Alignment explanation
Indices: 1430883--1430943 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1430873 TAAAATTTTG
1430883 TATATATAAATAATTTATAT-TA
1 TATATATAAATAATTTATATGTA
* * *
1430905 TATATTTAATTATTTTATATGTA
1 TATATATAAATAATTTATATGTA
1430928 -ATATATTAATATAATT
1 TATATA-TAA-ATAATT
1430944 ATGTTTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 21 0.70
23 5 0.17
24 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TATATATAAATAATTTATATGTA
Found at i:1430940 original size:17 final size:16
Alignment explanation
Indices: 1430898--1430939 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1430888 ATAAATAATT
*
1430898 TATATTATATATTTAA
1 TATATTATATATGTAA
*
1430914 T-TATTTTATATGTAA
1 TATATTATATATGTAA
1430929 TATATTA-ATAT
1 TATATTATATAT
1430940 AATTATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TATATTATATATGTAA
Found at i:1431094 original size:23 final size:23
Alignment explanation
Indices: 1431067--1431110 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1431057 AGCATCTAAA
*
1431067 GCTGTTC-TGCTTGTGCAGCTTTC
1 GCTGTTCTTGC-TGAGCAGCTTTC
1431090 GCTGTTCTTGCTGAGCAGCTT
1 GCTGTTCTTGCTGAGCAGCTT
1431111 CACAGTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.07, C:0.25, G:0.27, T:0.41
Consensus pattern (23 bp):
GCTGTTCTTGCTGAGCAGCTTTC
Found at i:1431213 original size:3 final size:3
Alignment explanation
Indices: 1431198--1431233 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1431188 ACCCACCAAG
*
1431198 CCA CCA TCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1431234 TTCCCACCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.64, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:1431387 original size:48 final size:48
Alignment explanation
Indices: 1431335--1431521 Score: 275
Period size: 48 Copynumber: 3.9 Consensus size: 48
1431325 CCAGTTTATC
* * * *
1431335 CTCCACCCAAGCCCCCTGTTCACCCGCCACCCAAGCCGCCGACGTACG
1 CTCCACCCAAGCCTCCAGTTCACCCACCACCCAAGCCACCGACGTACG
* * *
1431383 CTCCACCTAAGCCTCCAGTTCACCCACCACCCAAGCCGCCAACGTACG
1 CTCCACCCAAGCCTCCAGTTCACCCACCACCCAAGCCACCGACGTACG
*
1431431 CTCCACCCAAGCCTCCAGTTCACCCACCACCCAAGCCACCGACTTACG
1 CTCCACCCAAGCCTCCAGTTCACCCACCACCCAAGCCACCGACGTACG
* * *
1431479 CTCCACCAAAGCCACCAGTTCACCCACCAACCAAGCCACCGAC
1 CTCCACCCAAGCCTCCAGTTCACCCACCACCCAAGCCACCGAC
1431522 ATACTCGCCA
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 127 1.00
ACGTcount: A:0.25, C:0.52, G:0.12, T:0.11
Consensus pattern (48 bp):
CTCCACCCAAGCCTCCAGTTCACCCACCACCCAAGCCACCGACGTACG
Found at i:1431492 original size:24 final size:23
Alignment explanation
Indices: 1431361--1431518 Score: 100
Period size: 24 Copynumber: 6.6 Consensus size: 23
1431351 TGTTCACCCG
* *
1431361 CCACCCAAGCCGCCGACGTACGCT
1 CCACCCAAGCCACC-ACTTACGCT
* * * * *
1431385 CCACCTAAGCCTCCAGTTCACCCA
1 CCACCCAAGCCACCACTT-ACGCT
* *
1431409 CCACCCAAGCCGCCAACGTACGCT
1 CCACCCAAGCCACC-ACTTACGCT
* * * *
1431433 CCACCCAAGCCTCCAGTTCACCCA
1 CCACCCAAGCCACCACTT-ACGCT
1431457 CCACCCAAGCCACCGACTTACGCT
1 CCACCCAAGCCACC-ACTTACGCT
* * * *
1431481 CCACCAAAGCCACCAGTTCACCCA
1 CCACCCAAGCCACCACTT-ACGCT
*
1431505 CCAACCAAGCCACC
1 CCACCCAAGCCACC
1431519 GACATACTCG
Statistics
Matches: 102, Mismatches: 27, Indels: 10
0.73 0.19 0.07
Matches are distributed among these distances:
23 7 0.07
24 90 0.88
25 5 0.05
ACGTcount: A:0.27, C:0.51, G:0.12, T:0.10
Consensus pattern (23 bp):
CCACCCAAGCCACCACTTACGCT
Found at i:1431533 original size:48 final size:48
Alignment explanation
Indices: 1431335--1431551 Score: 265
Period size: 48 Copynumber: 4.5 Consensus size: 48
1431325 CCAGTTTATC
* * * * *
1431335 CTCCACCCAAGCCCCCTGTTCACCCGCCACCCAAGCCGCCGACGTACG
1 CTCCACCAAAGCCACCAGTTCACCCACCACCCAAGCCACCGACGTACG
* * * *
1431383 CTCCACCTAAGCCTCCAGTTCACCCACCACCCAAGCCGCCAACGTACG
1 CTCCACCAAAGCCACCAGTTCACCCACCACCCAAGCCACCGACGTACG
* * *
1431431 CTCCACCCAAGCCTCCAGTTCACCCACCACCCAAGCCACCGACTTACG
1 CTCCACCAAAGCCACCAGTTCACCCACCACCCAAGCCACCGACGTACG
* * *
1431479 CTCCACCAAAGCCACCAGTTCACCCACCAACCAAGCCACCGACATACT
1 CTCCACCAAAGCCACCAGTTCACCCACCACCCAAGCCACCGACGTACG
* *
1431527 CGCCACCTAAA-CCATCAGTTCACCC
1 CTCCACC-AAAGCCACCAGTTCACCC
1431552 TCCAACTAAG
Statistics
Matches: 152, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
48 149 0.98
49 3 0.02
ACGTcount: A:0.26, C:0.51, G:0.12, T:0.12
Consensus pattern (48 bp):
CTCCACCAAAGCCACCAGTTCACCCACCACCCAAGCCACCGACGTACG
Found at i:1436277 original size:20 final size:20
Alignment explanation
Indices: 1436254--1436312 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1436244 TTTTAAATTG
1436254 ATTTATTTGATTTAATTATT
1 ATTTATTTGATTTAATTATT
* ** *
1436274 ATTTATATGATAAAAATATT
1 ATTTATTTGATTTAATTATT
*
1436294 -TTTATTTAAATTTAATTAT
1 ATTTATTT-GATTTAATTAT
1436313 AAAAATAATA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTATTTGATTTAATTATT
Found at i:1436912 original size:6 final size:6
Alignment explanation
Indices: 1436901--1436925 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1436891 ATTTGCAATC
1436901 GGATTA GGATTA GGATTA GGATTA G
1 GGATTA GGATTA GGATTA GGATTA G
1436926 ATAGAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (6 bp):
GGATTA
Found at i:1437140 original size:15 final size:14
Alignment explanation
Indices: 1437121--1437147 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1437111 AATTTAGACT
1437121 TTTTTTTTATTTGA
1 TTTTTTTTATTTGA
1437135 TTTTTTTTATTTG
1 TTTTTTTTATTTG
1437148 GACCTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTTTTATTTGA
Found at i:1438159 original size:11 final size:10
Alignment explanation
Indices: 1438143--1438196 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 10
1438133 TTTTAAAATT
1438143 ATAAATATTAA
1 ATAAATA-TAA
1438154 ATAAATA-AA
1 ATAAATATAA
1438163 ATAAATAT-A
1 ATAAATATAA
1438172 AT-AATAT-A
1 ATAAATATAA
*
1438180 TTAAATATATA
1 ATAAATATA-A
1438191 ATAAAT
1 ATAAAT
1438197 TATTATAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 17 0.46
11 13 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
ATAAATATAA
Found at i:1438217 original size:13 final size:13
Alignment explanation
Indices: 1438201--1438230 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1438191 ATAAATTATT
1438201 ATAACTTAATTTA
1 ATAACTTAATTTA
*
1438214 ATAACTTTATTTA
1 ATAACTTAATTTA
1438227 ATAA
1 ATAA
1438231 ATATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAACTTAATTTA
Found at i:1438746 original size:5 final size:5
Alignment explanation
Indices: 1438736--1438773 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1438726 TTGATTAGTA
1438736 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AAT
1438774 AATTTTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:1439010 original size:2 final size:2
Alignment explanation
Indices: 1439005--1439037 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1438995 ATATATATAT
*
1439005 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1439038 TAAAAGTTAT
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:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1446824 original size:15 final size:15
Alignment explanation
Indices: 1446798--1446835 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1446788 GTTTTAACTT
*
1446798 TTAAAT-AAAATGGA
1 TTAAATAAAAATGAA
1446812 TTAAATAAAAATGAA
1 TTAAATAAAAATGAA
1446827 TTGAAATAA
1 TT-AAATAA
1446836 GCTTGTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 9 0.43
16 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (15 bp):
TTAAATAAAAATGAA
Found at i:1448862 original size:24 final size:25
Alignment explanation
Indices: 1448832--1448882 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
1448822 TTTGGGTGAG
1448832 TTTTAATTTAAA-A-AAATAAAATAT
1 TTTTAATTTAAATATAAATAAAA-AT
1448856 TTTTAATTTAAATATAAATAAAAAT
1 TTTTAATTTAAATATAAATAAAAAT
1448881 TT
1 TT
1448883 GAACTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 12 0.48
25 5 0.20
26 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTTAATTTAAATATAAATAAAAAT
Found at i:1449108 original size:7 final size:7
Alignment explanation
Indices: 1449096--1449120 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1449086 GACCCCCCCA
1449096 ACCACCC
1 ACCACCC
1449103 ACCACCC
1 ACCACCC
1449110 ACCACCC
1 ACCACCC
1449117 ACCA
1 ACCA
1449121 TCCAACCATC
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:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (7 bp):
ACCACCC
Found at i:1449569 original size:15 final size:16
Alignment explanation
Indices: 1449542--1449572 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1449532 ATATTTTATT
1449542 TAAATTAAATTAAATA
1 TAAATTAAATTAAATA
1449558 TAAATT-AATTAAATA
1 TAAATTAAATTAAATA
1449573 ATTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTAAATTAAATA
Found at i:1456755 original size:23 final size:23
Alignment explanation
Indices: 1456728--1456774 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1456718 GATCATATTC
1456728 TTGTATCCATGTCTAAATATATA
1 TTGTATCCATGTCTAAATATATA
*
1456751 TTGTATCCATGTCTGAATATATA
1 TTGTATCCATGTCTAAATATATA
1456774 T
1 T
1456775 CGGGCACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (23 bp):
TTGTATCCATGTCTAAATATATA
Found at i:1460178 original size:18 final size:18
Alignment explanation
Indices: 1460151--1460185 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1460141 GGAAGACTGA
*
1460151 GGAGGAAGAGGCGGAGGC
1 GGAGGAAGAGGCAGAGGC
*
1460169 GGAGGCAGAGGCAGAGG
1 GGAGGAAGAGGCAGAGG
1460186 TGGACGTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.60, T:0.00
Consensus pattern (18 bp):
GGAGGAAGAGGCAGAGGC
Found at i:1460471 original size:13 final size:12
Alignment explanation
Indices: 1460420--1460484 Score: 50
Period size: 11 Copynumber: 5.6 Consensus size: 12
1460410 TGATAATACG
1460420 AATATAATTTATA
1 AATATAATTTA-A
*
1460433 TAAAATAA-TTAA
1 -AATATAATTTAA
*
1460445 AATATAATAT-A
1 AATATAATTTAA
1460456 AATATATATTT-A
1 AATATA-ATTTAA
1460468 AA-ATAA-TTAA
1 AATATAATTTAA
1460478 AATATAA
1 AATATAA
1460485 CATAAATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
9 2 0.05
10 4 0.09
11 20 0.47
12 8 0.19
13 3 0.07
14 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATAATTTAA
Found at i:1460472 original size:24 final size:21
Alignment explanation
Indices: 1460430--1460512 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 21
1460420 AATATAATTT
1460430 ATATAAAATAATTAAAATATA
1 ATATAAAATAATTAAAATATA
*
1460451 ATATAAATATATATTTAAA-ATA
1 ATATAAA-ATA-ATTAAAATATA
*
1460473 AT-TAAAAT-A-TAACATA-A
1 ATATAAAATAATTAAAATATA
1460490 ATGTATAAAATAATTAAAATATA
1 A--TATAAAATAATTAAAATATA
1460513 CTATGAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
17 5 0.10
18 2 0.04
19 1 0.02
20 8 0.16
21 12 0.24
22 14 0.29
23 7 0.14
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (21 bp):
ATATAAAATAATTAAAATATA
Found at i:1460501 original size:29 final size:29
Alignment explanation
Indices: 1460420--1460734 Score: 260
Period size: 29 Copynumber: 10.9 Consensus size: 29
1460410 TGATAATACG
*
1460420 AATATAATTTATATAAAATAATTAAAATAT
1 AATATAA-ATATATAAAATAATTAAAATAT
1460450 AATATAAATATATATTTAAAATAATTAAAATAT
1 AATAT-AA-ATATA--TAAAATAATTAAAATAT
* *
1460483 AACATAAATGTATAAAATAATTAAAATAT
1 AATATAAATATATAAAATAATTAAAATAT
* * *
1460512 ACTATGAATATATAAAGTAATTAAAATAT
1 AATATAAATATATAAAATAATTAAAATAT
* *
1460541 GATATGAATATATAAAATAATTAAAATAT
1 AATATAAATATATAAAATAATTAAAATAT
*
1460570 GATATAAATATATAAAATAATTAAAATAT
1 AATATAAATATATAAAATAATTAAAATAT
** *
1460599 AATATGAATATATATTTTAA-AATT--TATAT
1 AATAT-AA-ATATA-TAAAATAATTAAAATAT
*
1460628 AATATAAAT-TAT-TAATATATTAAAA-AT
1 AATATAAATATATAAAATA-ATTAAAATAT
* ** *
1460655 ATTATAAATATA-AAATATTTTTATACGATTAT
1 AATATAAATATATAAA-ATAATTA-A--AATAT
*
1460687 AATAT-AATA-A-AAAATTA-TAAAA-AT
1 AATATAAATATATAAAATAATTAAAATAT
1460711 AATATAAATATATAAAAT-ATTAAA
1 AATATAAATATATAAAATAATTAAA
1460735 TCTATTTTAT
Statistics
Matches: 239, Mismatches: 25, Indels: 45
0.77 0.08 0.15
Matches are distributed among these distances:
24 10 0.04
25 7 0.03
26 7 0.03
27 22 0.09
28 11 0.05
29 114 0.48
30 11 0.05
31 25 0.10
32 11 0.05
33 21 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
AATATAAATATATAAAATAATTAAAATAT
Found at i:1460558 original size:20 final size:19
Alignment explanation
Indices: 1460429--1460730 Score: 81
Period size: 20 Copynumber: 16.6 Consensus size: 19
1460419 GAATATAATT
1460429 TATATAAAATA-AT-TAAA
1 TATATAAAATATATATAAA
* *
1460446 -ATAT--AATATAAATATA
1 TATATAAAATATATATAAA
*
1460462 TATTTAAAATA-AT-TAAA
1 TATATAAAATATATATAAA
* *
1460479 -ATATAACATAAATGTATAAA
1 TATATAA-A-ATATATATAAA
*
1460499 -ATAATTAAAATATACTATGAA
1 TAT-A-TAAAATATA-TATAAA
*
1460520 TATATAAAGTA-AT-TAAAA
1 TATATAAAATATATAT-AAA
*
1460538 TATGATATGAATATATA-AAA
1 TAT-ATA-AAATATATATAAA
1460558 TA-ATTAAAATATGATATAAA
1 TATA-TAAAATAT-ATATAAA
1460578 TATATAAAATA-AT-TAAA
1 TATATAAAATATATATAAA
* *
1460595 -ATATAATATGA-ATATATA
1 TATATAAAAT-ATATATAAA
* *
1460613 T-TTTAAAAT-T-TATATA
1 TATATAAAATATATATAAA
1460629 -ATAT-AAAT-TAT-T-AA
1 TATATAAAATATATATAAA
1460643 TATATTAAAA-ATATTATAAA
1 TATA-TAAAATATA-TATAAA
* * *
1460663 TATA-AAATATTTTTATACGA
1 TATATAAA-ATATATATA-AA
*
1460683 T-TATAATATA-ATA-AAA
1 TATATAAAATATATATAAA
*
1460699 AATTATAAAA-ATAATATAAA
1 TA-TATAAAATAT-ATATAAA
1460719 TATATAAAATAT
1 TATATAAAATAT
1460731 TAAATCTATT
Statistics
Matches: 208, Mismatches: 32, Indels: 87
0.64 0.10 0.27
Matches are distributed among these distances:
14 5 0.02
15 10 0.05
16 31 0.15
17 22 0.11
18 38 0.18
19 34 0.16
20 52 0.25
21 11 0.05
22 5 0.02
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
TATATAAAATATATATAAA
Found at i:1460632 original size:34 final size:33
Alignment explanation
Indices: 1460576--1460668 Score: 88
Period size: 34 Copynumber: 2.8 Consensus size: 33
1460566 ATATGATATA
1460576 AATATA-T-AAAATAATTA-AAATATAATATGAAT
1 AATATATTAAAAAT-ATTATAAATATAA-ATGAAT
* * *
1460608 -ATATATTTTAAAAT-TTATATAATATAAATTATT
1 AATATA-TTAAAAATATTATA-AATATAAATGAAT
1460641 AATATATTAAAAATATTATAAATATAAA
1 AATATATTAAAAATATTATAAATATAAA
1460669 ATATTTTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
31 5 0.10
32 3 0.06
33 21 0.41
34 22 0.43
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (33 bp):
AATATATTAAAAATATTATAAATATAAATGAAT
Found at i:1460671 original size:16 final size:16
Alignment explanation
Indices: 1460579--1460673 Score: 61
Period size: 16 Copynumber: 5.8 Consensus size: 16
1460569 TGATATAAAT
1460579 ATATAAAATAATTA-AA
1 ATATAAAAT-ATTATAA
* *
1460595 ATATAATATGAATATATA
1 ATATAAAAT-ATTATA-A
* *
1460613 TTTTAAAAT-TTATATA
1 ATATAAAATATTATA-A
* *
1460629 ATATAAATTATTA-AT
1 ATATAAAATATTATAA
1460644 ATATTAAAAATATTATAA
1 ATA-T-AAAATATTATAA
1460662 ATATAAAATATT
1 ATATAAAATATT
1460674 TTTATACGAT
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
15 3 0.05
16 33 0.55
17 13 0.22
18 11 0.18
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
ATATAAAATATTATAA
Found at i:1460714 original size:19 final size:19
Alignment explanation
Indices: 1460690--1460727 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1460680 CGATTATAAT
1460690 ATAATAAAAA-ATTATAAAA
1 ATAATAAAAATA-TATAAAA
*
1460709 ATAATATAAATATATAAAA
1 ATAATAAAAATATATAAAA
1460728 TATTAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATATAAAA
Found at i:1461245 original size:20 final size:20
Alignment explanation
Indices: 1461208--1461244 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1461198 ATACTAAAAC
1461208 TTTTATAAATTATTATATAA
1 TTTTATAAATTATTATATAA
1461228 TTTTA-AAATT-TTATATA
1 TTTTATAAATTATTATATA
1461245 TTATATAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATAAATTATTATATAA
Found at i:1462528 original size:20 final size:20
Alignment explanation
Indices: 1462503--1462542 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1462493 ACTGCCGGCC
1462503 GCCACGCCACCTTTTCTTTG
1 GCCACGCCACCTTTTCTTTG
1462523 GCCACGCCACCTTTTCTTTG
1 GCCACGCCACCTTTTCTTTG
1462543 CTCACTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.40, G:0.15, T:0.35
Consensus pattern (20 bp):
GCCACGCCACCTTTTCTTTG
Found at i:1466121 original size:5 final size:5
Alignment explanation
Indices: 1466111--1466148 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1466101 AAAAATTTGA
1466111 TAAAT TAAAT TAATAT TAAAT TAAAT TAAA- -AAAT TAAA
1 TAAAT TAAAT TAA-AT TAAAT TAAAT TAAAT TAAAT TAAA
1466149 ATAATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
5 22 0.73
6 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
TAAAT
Found at i:1466130 original size:11 final size:10
Alignment explanation
Indices: 1466111--1466148 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
1466101 AAAAATTTGA
1466111 TAAATTAAAT
1 TAAATTAAAT
1466121 TAATATTAAAT
1 TAA-ATTAAAT
1466132 TAAATTAAA-
1 TAAATTAAAT
1466141 -AAATTAAA
1 TAAATTAAA
1466149 ATAATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.30
10 9 0.33
11 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAATTAAAT
Found at i:1466132 original size:16 final size:16
Alignment explanation
Indices: 1466111--1466159 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1466101 AAAAATTTGA
1466111 TAAATTAAATTAATAT
1 TAAATTAAATTAATAT
1466127 TAAATTAAATTAA-A-
1 TAAATTAAATTAATAT
*
1466141 -AAATTAAAATAATAAT
1 TAAATTAAATTAAT-AT
1466157 TAA
1 TAA
1466160 GTTATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.39
15 2 0.07
16 13 0.46
17 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTAAATTAATAT
Found at i:1466248 original size:27 final size:27
Alignment explanation
Indices: 1466204--1466262 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1466194 ACATCATATC
1466204 TATTTTAAAAAACAATATATTAATTA-
1 TATTTTAAAAAACAATATATTAATTAT
* * *
1466230 TATTTTTAAAAATATATATTTTAATTAT
1 TATTTTAAAAAACA-ATATATTAATTAT
1466258 TATTT
1 TATTT
1466263 AATTCTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 12 0.43
27 11 0.39
28 5 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTTTAAAAAACAATATATTAATTAT
Found at i:1467030 original size:26 final size:26
Alignment explanation
Indices: 1466965--1467031 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
1466955 ACTGATATTA
*
1466965 TTATTTAAGTTT-AATTTATATAAAT
1 TTATTTAAATTTAAATTTATATAAAT
* *
1466990 TAAATTTTAAA--TAAATTTATTTAAAT
1 T-TA-TTTAAATTTAAATTTATATAAAT
1467016 TTATTTAAATTTAAAT
1 TTATTTAAATTTAAAT
1467032 AATAATAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
24 6 0.18
25 3 0.09
26 19 0.58
27 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
TTATTTAAATTTAAATTTATATAAAT
Found at i:1467542 original size:19 final size:20
Alignment explanation
Indices: 1467520--1467568 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1467510 TTAATTTCGG
*
1467520 TATTTAAATTAAT-TTAAAT
1 TATTTAAATTAATATTAAAA
1467539 TATTTAAA-TAATATTAAAA
1 TATTTAAATTAATATTAAAA
*
1467558 TATTTATATTA
1 TATTTAAATTA
1467569 TGTTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 20 0.77
20 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTAAATTAATATTAAAA
Found at i:1467545 original size:9 final size:9
Alignment explanation
Indices: 1467520--1467569 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
1467510 TTAATTTCGG
1467520 TATTTAAAT
1 TATTTAAAT
1467529 TAATTTAAAT
1 T-ATTTAAAT
1467539 TATTTAAAT
1 TATTTAAAT
* *
1467548 AATATTAAAA
1 TAT-TTAAAT
*
1467558 TATTTATAT
1 TATTTAAAT
1467567 TAT
1 TAT
1467570 GTTATATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TATTTAAAT
Found at i:1469154 original size:2 final size:2
Alignment explanation
Indices: 1469147--1469186 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1469137 ATTTGCCTAC
* *
1469147 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1469187 CCACGTGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1469453 original size:5 final size:6
Alignment explanation
Indices: 1469437--1469477 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
1469427 TAAATTTTAA
*
1469437 ATTTTT ATTTTT ATTTTT ATTTTT CATATTT ATTATTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT -ATTTTT ATT-TTT ATT
1469478 ATTTTCAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:1469935 original size:28 final size:28
Alignment explanation
Indices: 1469906--1469961 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1469896 TAGTATTAAT
1469906 AAATTAAATAATATTTATTCATTAAAATA
1 AAATTAAAT-ATATTTATTCATTAAAATA
* **
1469935 AAATTATATATATTTATTTTTTAAAAT
1 AAATTAAATATATTTATTCATTAAAAT
1469962 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
AAATTAAATATATTTATTCATTAAAATA
Found at i:1470047 original size:17 final size:19
Alignment explanation
Indices: 1470011--1470061 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1470001 AATATAAATT
*
1470011 TATATAATTATATTTGATA
1 TATATAAATATATTTGATA
1470030 TATATAAAT-TATTT-ATA
1 TATATAAATATATTTGATA
*
1470047 TATTATCAATATATT
1 TA-TATAAATATATT
1470062 AAATAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.18
18 11 0.39
19 12 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TATATAAATATATTTGATA
Found at i:1470144 original size:6 final size:6
Alignment explanation
Indices: 1470133--1470181 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
1470123 AAAAATCAAC
* * * * *
1470133 AAATAT AAATAT AAATAT AAATCT AAACAT ATATAT ATATAT ATATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1470181 A
1 A
1470182 TTCTCTCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (6 bp):
AAATAT
Found at i:1470155 original size:26 final size:27
Alignment explanation
Indices: 1470125--1470179 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1470115 TTAATAAAAA
1470125 AAATC-AACAAATATAAATATAAATAT
1 AAATCAAACAAATATAAATATAAATAT
* * *
1470151 AAATCTAAACATATATATATATATATAT
1 AAATC-AAACAAATATAAATATAAATAT
1470179 A
1 A
1470180 TATTCTCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.21
28 19 0.79
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATCAAACAAATATAAATATAAATAT
Found at i:1470765 original size:18 final size:17
Alignment explanation
Indices: 1470734--1470769 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1470724 ATATATGTAT
1470734 AATCTATAAATAAAAAA
1 AATCTATAAATAAAAAA
*
1470751 AATCATATAATTAAAAAA
1 AATC-TATAAATAAAAAA
1470769 A
1 A
1470770 TAGTTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
AATCTATAAATAAAAAA
Found at i:1471582 original size:12 final size:11
Alignment explanation
Indices: 1471562--1471596 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
1471552 ACTATAACAA
1471562 TTTTTTTAATT
1 TTTTTTTAATT
1471573 TTTATTTTAATT
1 TTT-TTTTAATT
1471585 TTTTTTATAATT
1 TTTTTT-TAATT
1471597 ACTTAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTAATT
Found at i:1472277 original size:18 final size:17
Alignment explanation
Indices: 1472254--1472315 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
1472244 TAAAAAATAA
1472254 TATAAATATATTAAAATT
1 TATAAATATATTAAAA-T
1472272 TATAAATAT-TTAAAA-
1 TATAAATATATTAAAAT
*
1472287 TATAATTATATATAAAAAT
1 TATAA--ATATATTAAAAT
1472306 ATATAAATAT
1 -TATAAATAT
1472316 TATATAAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 5 0.13
17 10 0.26
18 18 0.47
20 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAAATATATTAAAAT
Found at i:1472298 original size:35 final size:35
Alignment explanation
Indices: 1472252--1472327 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
1472242 AATAAAAAAT
* *
1472252 AATATAAATATATTAAAATTTATAAATATT-TA-A
1 AATATAAATATATAAAAATATATAAATATTATATA
1472285 AATATAATTATATATAAAAATATATAAATATTATATA
1 AATATAA--ATATATAAAAATATATAAATATTATATA
1472322 AATATA
1 AATATA
1472328 TAAGTTACCG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 7 0.19
35 21 0.57
36 2 0.05
37 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
AATATAAATATATAAAAATATATAAATATTATATA
Found at i:1472299 original size:10 final size:10
Alignment explanation
Indices: 1472248--1472329 Score: 72
Period size: 10 Copynumber: 8.9 Consensus size: 10
1472238 ATAAAATAAA
1472248 AAATA-ATAT
1 AAATATATAT
1472257 AAATATAT-T
1 AAATATATAT
*
1472266 AAA-ATTTAT
1 AAATATATAT
1472275 AAATAT-T-T
1 AAATATATAT
1472283 -AA-A-ATAT
1 AAATATATAT
*
1472290 AATTATATAT
1 AAATATATAT
*
1472300 AAAAATATAT
1 AAATATATAT
1472310 AAATATTATAT
1 AAATA-TATAT
1472321 AAATATATA
1 AAATATATA
1472330 AGTTACCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
8 5 0.08
9 15 0.25
10 24 0.41
11 10 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATATATAT
Found at i:1472326 original size:27 final size:26
Alignment explanation
Indices: 1472241--1472327 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
1472231 AAACACAATA
1472241 AAATA-AAAAATAATATAAATA-TATT
1 AAATATAAAAAT-ATATAAATATTATT
* * * *
1472266 AAAATTTATAAATATTTAAAATATAATT
1 -AAATATAAAAATATAT-AAATATTATT
*
1472294 ATATATAAAAATATATAAATATTATAT
1 AAATATAAAAATATATAAATATTAT-T
1472321 AAATATA
1 AAATATA
1472328 TAAGTTACCG
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
26 15 0.32
27 29 0.62
28 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATAAAAATATATAAATATTATT
Found at i:1477001 original size:23 final size:22
Alignment explanation
Indices: 1476942--1477002 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 22
1476932 TACTTAATAA
1476942 TTAAAATA-AAATA-GAT-TA-
1 TTAAAATATAAATATGATATAT
*
1476960 -TAAAATATAATTATGATATAT
1 TTAAAATATAAATATGATATAT
*
1476981 TTAAATATATAAATATTATATA
1 TTAAA-ATATAAATATGATATA
1477003 AATATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 3 0.09
20 2 0.06
22 4 0.12
23 14 0.41
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
TTAAAATATAAATATGATATAT
Found at i:1477009 original size:17 final size:16
Alignment explanation
Indices: 1476981--1477028 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
1476971 TATGATATAT
1476981 TTAAATATATAAATATTA
1 TTAAATATA-AAA-ATTA
1476999 TATAAATATAAAAATTA
1 T-TAAATATAAAAATTA
1477016 TTAAATATGAAAA
1 TTAAATAT-AAAA
1477029 CCAATTGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.25
17 9 0.32
18 4 0.14
19 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TTAAATATAAAAATTA
Found at i:1477704 original size:13 final size:13
Alignment explanation
Indices: 1477686--1477714 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1477676 CGGCTGAGTT
1477686 TTTATTTTTTTAA
1 TTTATTTTTTTAA
1477699 TTTATTTTTTTAA
1 TTTATTTTTTTAA
1477712 TTT
1 TTT
1477715 TTTCTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTTTAA
Found at i:1478040 original size:15 final size:16
Alignment explanation
Indices: 1478014--1478044 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1478004 TTTTATCGAT
1478014 TTATATATTTTTTAAA
1 TTATATATTTTTTAAA
1478030 TTATA-ATTTTTTAAA
1 TTATATATTTTTTAAA
1478045 ATATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATATTTTTTAAA
Done.