Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 11 of 25
Found at i:1629074 original size:11 final size:12
Alignment explanation
Indices: 1629058--1629092 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
1629048 TAAATAAAAA
1629058 ATAAATTTAATT
1 ATAAATTTAATT
1629070 A-AAATTTAATT
1 ATAAATTTAATT
1629081 ATAAATATTAAT
1 ATAAAT-TTAAT
1629093 ATATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
12 5 0.24
13 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAAATTTAATT
Found at i:1629102 original size:15 final size:13
Alignment explanation
Indices: 1629058--1629102 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 13
1629048 TAAATAAAAA
1629058 ATAAAT-TTAATT
1 ATAAATATTAATT
1629070 A-AAAT-TTAATT
1 ATAAATATTAATT
1629081 ATAAATATTAATAT
1 ATAAATATTAAT-T
1629095 ATTAAATA
1 A-TAAATA
1629103 ATTTTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.38
12 5 0.17
13 5 0.17
14 2 0.07
15 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAATATTAATT
Found at i:1629501 original size:21 final size:21
Alignment explanation
Indices: 1629475--1629536 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1629465 AAAAAATTAT
1629475 TTTTATATTAATATTTATATA
1 TTTTATATTAATATTTATATA
*
1629496 TTTTATAATTAA-ATTTAAATA
1 TTTTAT-ATTAATATTTATATA
* *
1629517 ATTTAT-TTAAATATTAATAT
1 TTTTATATT-AATATTTATAT
1629537 TAACTCAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 25 0.74
22 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATATTAATATTTATATA
Found at i:1629539 original size:26 final size:27
Alignment explanation
Indices: 1629417--1629537 Score: 98
Period size: 26 Copynumber: 4.7 Consensus size: 27
1629407 ATTTTGAAAT
*
1629417 TTTATTTAAAT-TTAA-ATTTAATTTAA
1 TTTATTTAAATATTAATATTTAA-ATAA
*
1629443 TTTATTTAAATTATTTATATTTAAA-AA
1 TTTATTTAAA-TATTAATATTTAAATAA
* **
1629470 ATTATTTTTATATTAATATTT--AT-A
1 TTTATTTAAATATTAATATTTAAATAA
* *
1629494 TAT-TTTATA-ATTAA-ATTTAAATAA
1 TTTATTTAAATATTAATATTTAAATAA
1629518 TTTATTTAAATATTAATATT
1 TTTATTTAAATATTAATATT
1629538 AACTCAAAGT
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
21 4 0.05
22 5 0.07
23 7 0.09
24 6 0.08
25 5 0.07
26 25 0.34
27 13 0.18
28 3 0.04
29 6 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTATTTAAATATTAATATTTAAATAA
Found at i:1630455 original size:29 final size:28
Alignment explanation
Indices: 1630393--1630459 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
1630383 GTGATTTGCC
*
1630393 TAATTA-AATTTTCAATTTATATAATTT
1 TAATTATAATTTTCAATTTATATAAATT
*
1630420 TATATTATAATTTT-AATTTTTGAATAAATT
1 TA-ATTATAATTTTCAATTTAT--ATAAATT
1630450 TAATTATAAT
1 TAATTATAAT
1630460 GTAATAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.06
28 10 0.29
29 14 0.41
30 8 0.24
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
TAATTATAATTTTCAATTTATATAAATT
Found at i:1630976 original size:33 final size:30
Alignment explanation
Indices: 1630907--1630977 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
1630897 TCTATTAGGT
* *
1630907 TAAATTTAAATAAATATTTTTAAATTCAAAA
1 TAAATTT-AATAAATATTTTTAAAATAAAAA
*
1630938 -CAATTTAATAAAGTATTATTTATAAATAAAAA
1 TAAATTTAATAAA-TATT-TTTA-AAATAAAAA
1630970 TAAATTTA
1 TAAATTTA
1630978 TTTAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
29 6 0.19
30 9 0.28
31 4 0.12
32 7 0.22
33 6 0.19
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TAAATTTAATAAATATTTTTAAAATAAAAA
Found at i:1631035 original size:18 final size:19
Alignment explanation
Indices: 1630999--1631044 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
1630989 TTATAAAAAC
1630999 TAATATATTAAATAATTTT
1 TAATATATTAAATAATTTT
* *
1631018 TAATAT-TTTAATATTTTT
1 TAATATATTAAATAATTTT
1631036 TAATATATT
1 TAATATATT
1631045 CAACGATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATATATTAAATAATTTT
Found at i:1634118 original size:19 final size:20
Alignment explanation
Indices: 1634081--1634120 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1634071 TAATTTTTTA
1634081 TATATATTTGGATAATTAGAT
1 TATATATTT-GATAATTAGAT
*
1634102 TATATATTT-ATATTTAGAT
1 TATATATTTGATAATTAGAT
1634121 ATGTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (20 bp):
TATATATTTGATAATTAGAT
Found at i:1634886 original size:26 final size:23
Alignment explanation
Indices: 1634841--1634889 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
1634831 TCTCTTTAAT
*
1634841 AAATAAATTTTTTTTAAAAATAA
1 AAATAAATTTTTTTAAAAAATAA
1634864 AAATAATATTATTTTTAATAAAATAA
1 AAATAA-ATT-TTTTTAA-AAAATAA
1634890 TATTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 3 0.14
25 6 0.27
26 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATAAATTTTTTTAAAAAATAA
Found at i:1634891 original size:23 final size:24
Alignment explanation
Indices: 1634841--1634897 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 24
1634831 TCTCTTTAAT
*
1634841 AAATAA-ATTTTTTTTAAAAATAA
1 AAATAATATTATTTTTAAAAATAA
1634864 AAATAATATTATTTTT---AAT-A
1 AAATAATATTATTTTTAAAAATAA
1634884 AAATAATATTATTT
1 AAATAATATTATTT
1634898 AATTTAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 15 0.47
21 3 0.09
23 6 0.19
24 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAATAATATTATTTTTAAAAATAA
Found at i:1636311 original size:12 final size:12
Alignment explanation
Indices: 1636294--1636318 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1636284 GTGTCTTAAC
1636294 TATCCACAGCCA
1 TATCCACAGCCA
1636306 TATCCACAGCCA
1 TATCCACAGCCA
1636318 T
1 T
1636319 CGAATCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.40, G:0.08, T:0.20
Consensus pattern (12 bp):
TATCCACAGCCA
Found at i:1637400 original size:140 final size:140
Alignment explanation
Indices: 1637148--1637427 Score: 524
Period size: 140 Copynumber: 2.0 Consensus size: 140
1637138 ATGAGCTTGT
1637148 CAGAGAAGCTAAGACATCCAATTATTTGAACAGAATATCTAGACTACCGAAAAAGCTGTGCTGGG
1 CAGAGAAGCTAAGACATCCAATTATTTGAACAGAATATCTAGACTACCGAAAAAGCTGTGCTGGG
* * *
1637213 AAATATTCACATCATAGAGAGAGGTTTTCTTGCAAATTCATAGTAATACTCATCTATTCCAGGAA
66 AAATATTCACACCATAGAGAGAGGCTTTCTTGCAAATTCATAGTAATACTCATCTATGCCAGGAA
1637278 AAATAGCAAG
131 AAATAGCAAG
1637288 CAGAGAAGCTAAGACATCCAATTATTTGAACAGAATATCTAGACTACCGAAAAAGCTGTGCTGGG
1 CAGAGAAGCTAAGACATCCAATTATTTGAACAGAATATCTAGACTACCGAAAAAGCTGTGCTGGG
1637353 AAATATTCACACCATAGAGAGAGGCTTTCTTGCAAATTCATAGTAATACTCATCTATGCCAGGAA
66 AAATATTCACACCATAGAGAGAGGCTTTCTTGCAAATTCATAGTAATACTCATCTATGCCAGGAA
*
1637418 ACATAGCAAG
131 AAATAGCAAG
1637428 ATCGAAATTT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (140 bp):
CAGAGAAGCTAAGACATCCAATTATTTGAACAGAATATCTAGACTACCGAAAAAGCTGTGCTGGG
AAATATTCACACCATAGAGAGAGGCTTTCTTGCAAATTCATAGTAATACTCATCTATGCCAGGAA
AAATAGCAAG
Found at i:1638765 original size:24 final size:24
Alignment explanation
Indices: 1638719--1638765 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1638709 AAAACTTTTT
* * * *
1638719 AAAAATCAGGAACAATTAGAAAAA
1 AAAAATAAGGAAAAATAAAAAAAA
1638743 AAAAATAAGGAAAAATAAAAAAA
1 AAAAATAAGGAAAAATAAAAAAA
1638766 TTCTAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (24 bp):
AAAAATAAGGAAAAATAAAAAAAA
Found at i:1638874 original size:15 final size:14
Alignment explanation
Indices: 1638832--1638866 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1638822 TTTTGGTTTA
* *
1638832 AAAGAAAATGTGCT
1 AAAGAAAATGGGTT
1638846 AAAGAAAATGGGTT
1 AAAGAAAATGGGTT
1638860 AAAGAAA
1 AAAGAAA
1638867 CTTGGGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (14 bp):
AAAGAAAATGGGTT
Found at i:1642227 original size:2 final size:2
Alignment explanation
Indices: 1642222--1642253 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1642212 CCAAAAAAGA
1642222 AG AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1642254 TTTTGATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1644439 original size:20 final size:20
Alignment explanation
Indices: 1644409--1644497 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 20
1644399 TATAAATACG
*
1644409 ATATATATTTAAATATATCTT
1 ATATTTATTTAAATATAT-TT
*
1644430 AT-TTTATTTATTACATAAATTTT
1 ATATTTATTTA--A-ATATA-TTT
1644453 ATATTTA-TTAAATATATTT
1 ATATTTATTTAAATATATTT
* *
1644472 ATATTTATAT-AATATTTTT
1 ATATTTATTTAAATATATTT
*
1644491 AAATTTA
1 ATATTTA
1644498 CCAAATTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 24 0.43
20 12 0.21
21 3 0.05
22 1 0.02
23 11 0.20
24 5 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTATTTAAATATATTT
Found at i:1644474 original size:19 final size:19
Alignment explanation
Indices: 1644429--1644497 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1644419 AAATATATCT
*
1644429 TATTT-TATTTATTACATA
1 TATTTATATTTATTAAATA
*
1644447 AATTTTATATTTATTAAATA
1 TA-TTTATATTTATTAAATA
1644467 TATTTATATTTA-TATAATA
1 TATTTATATTTATTA-AATA
* *
1644486 TTTTTAAATTTA
1 TATTTATATTTA
1644498 CCAAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 3 0.07
19 27 0.63
20 13 0.30
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTATATTTATTAAATA
Found at i:1645108 original size:19 final size:19
Alignment explanation
Indices: 1645086--1645134 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1645076 TTTTAGCCAA
1645086 AATTTAATATTAAAAAAAT
1 AATTTAATATTAAAAAAAT
*
1645105 AATTTTAATATTAAAATAAT
1 AA-TTTAATATTAAAAAAAT
* *
1645125 TATTAAATAT
1 AATTTAATAT
1645135 AGTAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTAATATTAAAAAAAT
Found at i:1645410 original size:13 final size:13
Alignment explanation
Indices: 1645377--1645416 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1645367 TTAATTGATC
* *
1645377 TAACTAATCAATC
1 TAACTACTCAATT
1645390 TAACTACTCAATT
1 TAACTACTCAATT
*
1645403 TAATTACTCAATT
1 TAACTACTCAATT
1645416 T
1 T
1645417 GTTTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
TAACTACTCAATT
Found at i:1646084 original size:15 final size:14
Alignment explanation
Indices: 1646062--1646095 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1646052 AATCAATATT
1646062 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
1646076 TAAACAAAATAAAAA
1 TAAA-AAAATAAAAA
1646091 -AAAAA
1 TAAAAA
1646096 GAGTATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 7 0.37
15 10 0.53
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:1646715 original size:14 final size:13
Alignment explanation
Indices: 1646691--1646728 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1646681 TCATAACTTT
*
1646691 TAATATTTAAAAA
1 TAATATATAAAAA
1646704 TATATATATAAAAA
1 TA-ATATATAAAAA
1646718 TAA-ATATAAAA
1 TAATATATAAAA
1646729 TCATTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATATATAAAAA
Found at i:1646751 original size:15 final size:16
Alignment explanation
Indices: 1646731--1646761 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1646721 ATATAAAATC
1646731 ATTTTTTA-CAATTTT
1 ATTTTTTATCAATTTT
1646746 ATTTTTTATCAATTTT
1 ATTTTTTATCAATTTT
1646762 TAACTAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTTATCAATTTT
Found at i:1646870 original size:25 final size:25
Alignment explanation
Indices: 1646823--1646870 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1646813 ATTATACCAA
*
1646823 ATCAAATAAACTTTAAATTTTAAAT
1 ATCAAATAAACTTTAAATGTTAAAT
*
1646848 ATCAAATAAACTTTACATGTTAA
1 ATCAAATAAACTTTAAATGTTAA
1646871 TACATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (25 bp):
ATCAAATAAACTTTAAATGTTAAAT
Found at i:1647821 original size:17 final size:19
Alignment explanation
Indices: 1647787--1647852 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
1647777 ATTAATAATA
1647787 TAAATATAATATAAATTAT
1 TAAATATAATATAAATTAT
1647806 TAAATAT-ATA-AAATTA-
1 TAAATATAATATAAATTAT
* *
1647822 TAAACATAAATATTATATGTAT
1 TAAATAT-AATA-TAAAT-TAT
1647844 TAAATATAA
1 TAAATATAA
1647853 AATTTAGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
16 6 0.16
17 6 0.16
18 6 0.16
19 7 0.18
20 3 0.08
21 4 0.11
22 6 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAATATAATATAAATTAT
Found at i:1647954 original size:18 final size:18
Alignment explanation
Indices: 1647913--1647971 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
1647903 TTAAAAAATA
*
1647913 TATATCAAATTAATAATT
1 TATATAAAATTAATAATT
*
1647931 TTTATAAAATTAA-AATT
1 TATATAAAATTAATAATT
1647948 TAATATAATAATT-AT-ATT
1 T-ATATAA-AATTAATAATT
1647966 TATATA
1 TATATA
1647972 TATATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 10 0.29
18 21 0.60
19 4 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TATATAAAATTAATAATT
Found at i:1648555 original size:32 final size:36
Alignment explanation
Indices: 1648518--1648594 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
1648508 CCTAAATTAT
1648518 TAAAAATTT-A-TTT-TTA-ATATAAAATTTT-AAAA
1 TAAAAATTTAATTTTATTACATA-AAAATTTTAAAAA
1648550 TAAAAATTTAAATTTTATTACATAAAAATTTTAAAAAA
1 TAAAAATTT-AATTTTATTACATAAAAATTTT-AAAAA
1648588 TAAAAAT
1 TAAAAAT
1648595 ACATAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
32 9 0.24
34 1 0.03
35 3 0.08
36 11 0.29
37 3 0.08
38 11 0.29
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (36 bp):
TAAAAATTTAATTTTATTACATAAAAATTTTAAAAA
Found at i:1648564 original size:20 final size:21
Alignment explanation
Indices: 1648539--1648580 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1648529 TTTTAATATA
1648539 AAATTTTA-AAATAAAAATTT
1 AAATTTTATAAATAAAAATTT
*
1648559 AAATTTTATTACATAAAAATTT
1 AAATTTTA-TAAATAAAAATTT
1648581 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTTTATAAATAAAAATTT
Found at i:1649343 original size:11 final size:12
Alignment explanation
Indices: 1649318--1649343 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1649308 TTTATATTTT
1649318 AAAACTTAATAA
1 AAAACTTAATAA
1649330 AAAACTTAATAA
1 AAAACTTAATAA
1649342 AA
1 AA
1649344 GAAATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAACTTAATAA
Found at i:1650843 original size:3 final size:3
Alignment explanation
Indices: 1650829--1650858 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1650819 TTGACTAGTT
*
1650829 TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1650859 CTATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:1652726 original size:2 final size:2
Alignment explanation
Indices: 1652719--1652749 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1652709 ACAAGATACA
1652719 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
1652750 AGTATATTAA
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:1655839 original size:21 final size:22
Alignment explanation
Indices: 1655797--1655836 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1655787 TAATAAGAAA
*
1655797 ATTTTTTTATCAATACTAAATT
1 ATTTTTTAATCAATACTAAATT
1655819 ATTTTTTAAT-AATA-TAAA
1 ATTTTTTAATCAATACTAAA
1655837 ATTTAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTTTAATCAATACTAAATT
Found at i:1655840 original size:18 final size:20
Alignment explanation
Indices: 1655794--1655840 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
1655784 CAATAATAAG
*
1655794 AAAATTTTTTTATCAATACT
1 AAAATTTTTTAATCAATACT
1655814 AAATTATTTTTTAAT-AATA-T
1 AAA--ATTTTTTAATCAATACT
1655834 AAAATTT
1 AAAATTT
1655841 AATATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
20 7 0.29
21 4 0.17
22 9 0.38
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATTTTTTAATCAATACT
Found at i:1655864 original size:27 final size:26
Alignment explanation
Indices: 1655823--1655873 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1655813 TAAATTATTT
*
1655823 TTTAATAATATAAAATTTAATATTAAA
1 TTTAATAATATAAAATATAA-ATTAAA
1655850 TTTAATAAT-TCAAAATATAAATTA
1 TTTAATAATAT-AAAATATAAATTA
1655874 TTTACCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTAATAATATAAAATATAAATTAAA
Found at i:1655865 original size:15 final size:14
Alignment explanation
Indices: 1655823--1655865 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1655813 TAAATTATTT
1655823 TTTAATAATATAAAA
1 TTTAATAAT-TAAAA
1655838 TTTAAT-ATT-AAA
1 TTTAATAATTAAAA
1655850 TTTAATAATTCAAAA
1 TTTAATAATT-AAAA
1655865 T
1 T
1655866 ATAAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 9 0.36
13 4 0.16
14 2 0.08
15 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAATAATTAAAA
Found at i:1656292 original size:21 final size:20
Alignment explanation
Indices: 1656267--1656334 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1656257 CATTATAATT
1656267 ATTAATTTTATTTTAAATTAA
1 ATTAATTTTA-TTTAAATTAA
* * * **
1656288 ATTAAATTAATTAAAAAAAA
1 ATTAATTTTATTTAAATTAA
* *
1656308 ATTATTTTTAATTAAATTAA
1 ATTAATTTTATTTAAATTAA
1656328 ATTAATT
1 ATTAATT
1656335 AAAAGATAAA
Statistics
Matches: 34, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAATTTTATTTAAATTAA
Found at i:1656301 original size:4 final size:5
Alignment explanation
Indices: 1656279--1656337 Score: 50
Period size: 5 Copynumber: 12.0 Consensus size: 5
1656269 TAATTTTATT
** ** *
1656279 TTAAA TTAAA TTAAA TT-AA TTAAAA AAAAA TTATT TTTAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TTAAA
1656329 TT-AA TTAAA
1 TTAAA TTAAA
1656338 AGATAAATAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
4 8 0.20
5 31 0.76
6 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:1659356 original size:51 final size:51
Alignment explanation
Indices: 1659288--1659398 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
1659278 AAATTTGTAA
* * **
1659288 TCTTGACATGATGATTGGATCGAAGTATG-CTAAATTTGATCAGATTTGA-GG
1 TCTTGACATGAAGATTGGATCCAAGTATGTC-AAACCTGATCAGATTT-ACGG
*
1659339 TCTTGACATGAAGATTGGATCCAAGTGTGTCAAACCTGATCAGATTTACGG
1 TCTTGACATGAAGATTGGATCCAAGTATGTCAAACCTGATCAGATTTACGG
1659390 TCTTGACAT
1 TCTTGACAT
1659399 AAAAATTAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
50 1 0.02
51 51 0.96
52 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (51 bp):
TCTTGACATGAAGATTGGATCCAAGTATGTCAAACCTGATCAGATTTACGG
Found at i:1659873 original size:20 final size:20
Alignment explanation
Indices: 1659826--1659873 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1659816 AATTTGTATT
*
1659826 GATACAATAAGTGAATGTATA
1 GATAC-ATAAGTGAATATATA
* *
1659847 GAAACATAAGTGAATATATC
1 GATACATAAGTGAATATATA
1659867 GATACAT
1 GATACAT
1659874 GTCTAAACTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (20 bp):
GATACATAAGTGAATATATA
Found at i:1659993 original size:50 final size:51
Alignment explanation
Indices: 1659930--1660041 Score: 142
Period size: 51 Copynumber: 2.2 Consensus size: 51
1659920 TCTGGAAGGA
* *
1659930 AAATGTA-CAATGCA-T-TTCTATTGTATC-ATACATTTTAGGTTTTTTACCC
1 AAATGTATCAATGCATTATTC-ATTGTATCGATACATTTT-GGGTTTTGACCC
* *
1659979 AAATGTATCGATGCATTATTCATTGTATCGATACATTTTGGGTTTTGACCT
1 AAATGTATCAATGCATTATTCATTGTATCGATACATTTTGGGTTTTGACCC
1660030 AAATGTATCAAT
1 AAATGTATCAAT
1660042 ATAAGCATAC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
49 7 0.13
50 6 0.11
51 29 0.54
52 12 0.22
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (51 bp):
AAATGTATCAATGCATTATTCATTGTATCGATACATTTTGGGTTTTGACCC
Found at i:1662521 original size:79 final size:79
Alignment explanation
Indices: 1662347--1662731 Score: 377
Period size: 79 Copynumber: 4.9 Consensus size: 79
1662337 TAAATTTCTT
* * * * * * *
1662347 CTTCCAAAATTTTGATTTTTCACTATTAGGGATACTCCAATCCCACCATTTTTGA-GGGA-ATTC
1 CTTCCAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCCATCATTTTCGAGGGGATACTC
* **
1662410 -AATCCTGTTTTTA
66 TAACCCCATTTTTA
* * * * *
1662423 CTTTCAAAATATCGATTTTTCATTATCGGGGATACTCCAATCCGATCATTTTCGAGGGGATACTC
1 CTTCCAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCCATCATTTTCGAGGGGATACTC
*
1662488 TAACCCCGTTTTTA
66 TAACCCCATTTTTA
* * * * *
1662502 CTTCCAAAATATCGATTTTTCACCATC-GGGAATAGTCCAACCCCGTCATTTTCGAGAGGATATT
1 CTTCCAAAATATCGATTTTTCACTATCAGGG-ATACTCCAACCCCATCATTTTCGAGGGGATACT
1662566 CTAACCCCATTTTTA
65 CTAACCCCATTTTTA
* * * * *
1662581 TTTCCAAAATATTGATTTTTCACCATCAGGGATACTCTAACCCCATCATTTTCGAGGGGATACAC
1 CTTCCAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCCATCATTTTCGAGGGGATACTC
* *
1662646 CAACCCTATTTTTA
66 TAACCCCATTTTTA
* ** * * * *
1662660 CTTCCCAAATATTAAATTTTTCA-TTTCAGGGATACTCCAACCCCA-CTATCTCCGAGGAGATAC
1 CTTCCAAAATA-TCGATTTTTCACTATCAGGGATACTCCAACCCCATC-ATTTTCGAGGGGATAC
*
1662723 TCCAACCCC
64 TCTAACCCC
1662732 GACTTTCACA
Statistics
Matches: 258, Mismatches: 44, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
76 46 0.18
77 4 0.02
78 7 0.03
79 189 0.73
80 12 0.05
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (79 bp):
CTTCCAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCCATCATTTTCGAGGGGATACTC
TAACCCCATTTTTA
Found at i:1662915 original size:125 final size:124
Alignment explanation
Indices: 1662687--1662978 Score: 368
Period size: 125 Copynumber: 2.3 Consensus size: 124
1662677 TTTTCATTTC
* *
1662687 AGGGATACTCCAACCCCACTATCTCCGAGGAGATACTCCAACCCCGACTTTCACAAAAAATCGAA
1 AGGG-TACTCCAACCCC-CTAT-TCCGAAGAGATACTCCAACCCCGACTTTCACAAAAAATCAAA
* ** *
1662752 TTTCACTATTTTTGAAGTTTCCAAGCTCTTCCAATCAAAGTCTCTTTTAAATATAATCATCG
63 TTTCACTATTTTTGAAGTTTCCAAGCTCTTACAATCAAAGTCTCTTCAAAATATAATCATCA
* * * * * * * *
1662814 GGGGTACTCCAACCCCGTATTCCGAAGAGATACTTCATCTCTGATTTTCACCAAAAATCAAATTT
1 AGGGTACTCCAACCCCCTATTCCGAAGAGATACTCCAACCCCGACTTTCACAAAAAATCAAATTT
* * *
1662879 CTACTCTTTTTGAAGTTTTCAAGCTCTTACAATCAAAGTTTCTTCAAAATATAATCATCA
66 C-ACTATTTTTGAAGTTTCCAAGCTCTTACAATCAAAGTCTCTTCAAAATATAATCATCA
* * *
1662939 AGGGTACTCCAACCCCCTATTCCTAGGAGACACTCCAACC
1 AGGGTACTCCAACCCCCTATTCCGAAGAGATACTCCAACC
1662979 TTGTTTCTTT
Statistics
Matches: 139, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
124 38 0.27
125 86 0.62
126 12 0.09
127 3 0.02
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (124 bp):
AGGGTACTCCAACCCCCTATTCCGAAGAGATACTCCAACCCCGACTTTCACAAAAAATCAAATTT
CACTATTTTTGAAGTTTCCAAGCTCTTACAATCAAAGTCTCTTCAAAATATAATCATCA
Found at i:1670445 original size:25 final size:25
Alignment explanation
Indices: 1670368--1670448 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
1670358 AATTTTAACT
1670368 AAAAATGTATCGATACATCTGGGTA
1 AAAAATGTATCGATACATCTGGGTA
* ** * **
1670393 AGAAAATAGAAT-GTATTGATAT-ATTA
1 A-AAAAT-GTATCG-ATACATCTGGGTA
1670419 AAAAATGTATCGATACATCTGGGTA
1 AAAAATGTATCGATACATCTGGGTA
1670444 AAAAA
1 AAAAA
1670449 CAAAATATAT
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
24 8 0.21
25 14 0.36
26 9 0.23
27 8 0.21
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (25 bp):
AAAAATGTATCGATACATCTGGGTA
Found at i:1674854 original size:18 final size:16
Alignment explanation
Indices: 1674822--1674856 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1674812 AACAAAAATT
1674822 TTAAAAAATTTTAATA
1 TTAAAAAATTTTAATA
1674838 TTAAAGAAATATTTAATA
1 TTAAA-AAAT-TTTAATA
1674856 T
1 T
1674857 ATTAAATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TTAAAAAATTTTAATA
Found at i:1675746 original size:25 final size:25
Alignment explanation
Indices: 1675717--1675791 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
1675707 AATAACTTAA
1675717 ATTTAATACTTATTTTATTGTTTAT
1 ATTTAATACTTATTTTATTGTTTAT
** *
1675742 ATTTAATA---A---TA--ACTTAA
1 ATTTAATACTTATTTTATTGTTTAT
1675759 ATTTAATACTTATTTTATTGTTTAT
1 ATTTAATACTTATTTTATTGTTTAT
1675784 ATTTAATA
1 ATTTAATA
1675792 ATAACTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
17 11 0.31
19 2 0.06
20 1 0.03
22 1 0.03
23 2 0.06
25 19 0.53
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (25 bp):
ATTTAATACTTATTTTATTGTTTAT
Found at i:1675829 original size:42 final size:41
Alignment explanation
Indices: 1675696--1675829 Score: 209
Period size: 42 Copynumber: 3.2 Consensus size: 41
1675686 TTTTACCATA
1675696 TTATATTTAATAATAACTTAAATTTAATACTTATTTTATTGT
1 TTATATTTAATAATAACTTAAATTTAATAC-TATTTTATTGT
1675738 TTATATTTAATAATAACTTAAATTTAATACTTATTTTATTGT
1 TTATATTTAATAATAACTTAAATTTAATAC-TATTTTATTGT
1675780 TTATATTTAATAATAACTTAAATTTAATTA-TATTTGTATT-T
1 TTATATTTAATAATAACTTAAATTTAA-TACTATTT-TATTGT
1675821 TTATTATTT
1 TTA-TATTT
1675830 TTATTTAATA
Statistics
Matches: 89, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
41 9 0.10
42 78 0.88
43 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (41 bp):
TTATATTTAATAATAACTTAAATTTAATACTATTTTATTGT
Found at i:1675846 original size:48 final size:42
Alignment explanation
Indices: 1675696--1675807 Score: 224
Period size: 42 Copynumber: 2.7 Consensus size: 42
1675686 TTTTACCATA
1675696 TTATATTTAATAATAACTTAAATTTAATACTTATTTTATTGT
1 TTATATTTAATAATAACTTAAATTTAATACTTATTTTATTGT
1675738 TTATATTTAATAATAACTTAAATTTAATACTTATTTTATTGT
1 TTATATTTAATAATAACTTAAATTTAATACTTATTTTATTGT
1675780 TTATATTTAATAATAACTTAAATTTAAT
1 TTATATTTAATAATAACTTAAATTTAAT
1675808 TATATTTGTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (42 bp):
TTATATTTAATAATAACTTAAATTTAATACTTATTTTATTGT
Found at i:1675946 original size:18 final size:18
Alignment explanation
Indices: 1675919--1675959 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1675909 TTTAAATTTG
* *
1675919 TTTATTAGGATTTGATTC
1 TTTATCAGGATTTGAATC
1675937 TTTATCAGGATTTGAATC
1 TTTATCAGGATTTGAATC
1675955 TTTAT
1 TTTAT
1675960 TATTAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTATCAGGATTTGAATC
Found at i:1678443 original size:24 final size:24
Alignment explanation
Indices: 1678391--1678443 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1678381 AATATTTTTT
* * * *
1678391 ATTTTTTAAAACAAATAAAGATCA
1 ATTTTTTAAAAAAAAAAAACATAA
*
1678415 TTTTTTTAAAAAAAAAAAACATAA
1 ATTTTTTAAAAAAAAAAAACATAA
1678439 ATTTT
1 ATTTT
1678444 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTTTTTAAAAAAAAAAAACATAA
Found at i:1678989 original size:10 final size:10
Alignment explanation
Indices: 1678976--1679005 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1678966 CCATTTCATA
1678976 TTTTTTCTTT
1 TTTTTTCTTT
1678986 TTTTTTCTTT
1 TTTTTTCTTT
*
1678996 TTCTTTCTTT
1 TTTTTTCTTT
1679006 CTTCTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1678998 original size:16 final size:17
Alignment explanation
Indices: 1678977--1679011 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1678967 CATTTCATAT
*
1678977 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
1678993 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
1679010 TT
1 TT
1679012 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:1680312 original size:32 final size:32
Alignment explanation
Indices: 1680257--1680795 Score: 911
Period size: 32 Copynumber: 16.8 Consensus size: 32
1680247 AAAATGGTGA
* * *
1680257 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1680289 TTTTAAATGGGTTACCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1680321 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
** *
1680353 TTTGAAAAAGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1680385 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1680417 TTT-AGAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
1680449 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1680481 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1680513 TTTGAAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAATGGGTTGCCACCGACTTGTGTGGGC
1680546 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1680578 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1680610 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1680642 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1680674 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1680706 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1680738 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1680770 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
1680796 GATTTAAAAG
Statistics
Matches: 483, Mismatches: 21, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
31 14 0.03
32 436 0.90
33 33 0.07
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:1680813 original size:27 final size:27
Alignment explanation
Indices: 1680778--1681628 Score: 1405
Period size: 27 Copynumber: 31.1 Consensus size: 27
1680768 GCTTTGAAAT
* *
1680778 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
1680805 GGACGCCACGGAGTTGTGGAGTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1680832 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1680859 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1680886 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1680914 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1680942 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1680969 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
1680997 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1681024 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1681051 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1681078 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1681105 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1681132 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1681160 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1681187 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
1681215 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1681242 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1681269 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1681297 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1681324 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1681351 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1681379 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1681406 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
1681434 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1681461 GGGTGCCACGGAATTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1681488 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1681516 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1681543 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1681570 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1681597 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1681625 GGGT
1 GGGT
1681629 CACAGTACTA
Statistics
Matches: 772, Mismatches: 43, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
27 534 0.69
28 238 0.31
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1681212 original size:246 final size:245
Alignment explanation
Indices: 1680778--1681628 Score: 1422
Period size: 246 Copynumber: 3.5 Consensus size: 245
1680768 GCTTTGAAAT
* ** *
1680778 GGGTGCCACAGAGTTGTGGAT-TTAAAAGGACGCCACGGAGTTGTGGAGTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGG-TCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
1680842 GAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TAAAAAGGGTGCCACGGAGTTGTGGA
65 GAGTTGTGGACTAAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGA
*
1680906 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGA
130 CTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-
* *
1680971 GATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
193 GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1681024 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1681089 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TAAAAAGGGTGCCACGGAGTTGTGGAC
66 AGTTGTGGACTAAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGAC
* * *
1681153 TTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGG
131 TTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGG
1681218 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
195 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
1681269 GGGTGCCACGGAGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGTC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
* *
1681334 GAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGA
65 GAGTTGTGGACTAAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGA
* *
1681399 C-TTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
130 CTTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
* *
1681463 GTGCCACGGAATTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTTAAAA
194 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1681516 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* *
1681581 AGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGT
66 AGTTGTGGACTAAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGGT
1681629 CACAGTACTA
Statistics
Matches: 578, Mismatches: 21, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
245 80 0.14
246 422 0.73
247 76 0.13
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.23
Consensus pattern (245 bp):
GGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTAAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGGTGCCACGGAGTTGTGGAC
TTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGT
GCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1681297 original size:219 final size:218
Alignment explanation
Indices: 1680778--1681625 Score: 1500
Period size: 219 Copynumber: 3.9 Consensus size: 218
1680768 GCTTTGAAAT
* * ** *
1680778 GGGTGCCACAGAGTTGTGGATTTAAAAGGACGCCACGGAGTTGTGGAGTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* *
1680843 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-
*
1680908 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
130 TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
1680973 TGCCACGGAGTTATGGACTTAAAA
195 TGCCACGGAGTTATGGACTTAAAA
*
1680997 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1681062 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
1681127 AAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGAT
131 AAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGAT
1681192 GCCACGGAGTTATGGACTTAAAA
196 GCCACGGAGTTATGGACTTAAAA
1681215 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1681280 AGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
66 AGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
*
1681345 TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAGA
130 TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
1681410 TGCCACGGAGTTATGGACTTAAAA
195 TGCCACGGAGTTATGGACTTAAAA
*
1681434 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAATTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
1681499 AGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
66 AGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
* * *
1681564 TTAAAAGGGTGCCACGGAGTTGTGGAC-TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG
130 TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAG
1681626 GGTCACAGTA
Statistics
Matches: 610, Mismatches: 17, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
218 187 0.31
219 423 0.69
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.23
Consensus pattern (218 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
AAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGAT
GCCACGGAGTTATGGACTTAAAA
Found at i:1682663 original size:15 final size:15
Alignment explanation
Indices: 1682645--1682674 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1682635 TTGGTGAAAA
1682645 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
1682660 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
1682675 AGGATTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GGTTTTTTTTTTTTT
Found at i:1689446 original size:10 final size:10
Alignment explanation
Indices: 1689433--1689462 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1689423 CCATTTCATA
1689433 TTTTTTCTTT
1 TTTTTTCTTT
1689443 TTTTTTCTTT
1 TTTTTTCTTT
*
1689453 TTCTTTCTTT
1 TTTTTTCTTT
1689463 CTTCTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1689455 original size:16 final size:17
Alignment explanation
Indices: 1689434--1689468 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1689424 CATTTCATAT
*
1689434 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
1689450 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
1689467 TT
1 TT
1689469 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:1692670 original size:18 final size:18
Alignment explanation
Indices: 1692631--1692670 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1692621 TAAAAAAGAG
* * *
1692631 ATAAAATTAATTTGTTAT
1 ATAAAATGAATTTATTAA
1692649 ATAAAATGAATTTATTAA
1 ATAAAATGAATTTATTAA
1692667 ATAA
1 ATAA
1692671 TTTATTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
ATAAAATGAATTTATTAA
Found at i:1692695 original size:30 final size:30
Alignment explanation
Indices: 1692638--1692695 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1692628 GAGATAAAAT
* * *
1692638 TAATTTGTTATATAAAATGAATTTATTAAA
1 TAATTTATTATAAAAAATGAATATATTAAA
1692668 TAATTTATTATAAAAATATG-ATATATTA
1 TAATTTATTATAAAAA-ATGAATATATTA
1692696 CAAATTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
TAATTTATTATAAAAAATGAATATATTAAA
Found at i:1693916 original size:21 final size:20
Alignment explanation
Indices: 1693872--1693916 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1693862 TATTTTAAAG
*
1693872 ATATTTATATATTAAAATCA
1 ATATTTATATACTAAAATCA
1693892 ATATTTATTAGTACTAAAA-CA
1 ATATTTA-TA-TACTAAAATCA
1693913 ATAT
1 ATAT
1693917 AAAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (20 bp):
ATATTTATATACTAAAATCA
Found at i:1693929 original size:30 final size:30
Alignment explanation
Indices: 1693894--1693954 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
1693884 TAAAATCAAT
1693894 ATTTATTAGTACTAAAA-CAATATAA-AATTA
1 ATTTATTA-TA-TAAAATCAATATAATAATTA
*
1693924 ATTTATTATATAAAATCAATTTAATAATTA
1 ATTTATTATATAAAATCAATATAATAATTA
1693954 A
1 A
1693955 AAGTTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 5 0.18
29 9 0.32
30 14 0.50
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (30 bp):
ATTTATTATATAAAATCAATATAATAATTA
Found at i:1693955 original size:18 final size:18
Alignment explanation
Indices: 1693912--1693956 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1693902 GTACTAAAAC
*
1693912 AATATAAAATTAATTTAT
1 AATATAAAATCAATTTAT
*
1693930 TATATAAAATCAATTTAAT
1 AATATAAAATCAATTT-AT
1693949 AAT-TAAAA
1 AATATAAAA
1693957 GTTTTTTGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAAAATCAATTTAT
Found at i:1694061 original size:3 final size:3
Alignment explanation
Indices: 1694053--1694077 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1694043 GTTTGTGATC
1694053 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1694078 AATTTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1697241 original size:2 final size:2
Alignment explanation
Indices: 1697234--1697258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1697224 ACACCAACAC
1697234 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1697259 GTATTGCTGT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1697750 original size:3 final size:3
Alignment explanation
Indices: 1697729--1697781 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
1697719 ATGGGATTGC
* *
1697729 TGT TGT GGT TGT TGC TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1697777 TGT TG
1 TGT TG
1697782 CTTGGAAGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.02, G:0.36, T:0.62
Consensus pattern (3 bp):
TGT
Found at i:1698058 original size:3 final size:3
Alignment explanation
Indices: 1698050--1698076 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1698040 AACCTTAGCC
1698050 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1698077 CTATACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:1700625 original size:28 final size:28
Alignment explanation
Indices: 1700574--1700631 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1700564 TAATATTTAT
* **
1700574 ATATTTTTATAAATAAATTTTAATAAAA
1 ATATTTCTATAAATAAATAATAATAAAA
* *
1700602 ATATTTCTATAATTAAATAATAATATAA
1 ATATTTCTATAAATAAATAATAATAAAA
1700630 AT
1 AT
1700632 TGAATTGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATTTCTATAAATAAATAATAATAAAA
Found at i:1702543 original size:31 final size:30
Alignment explanation
Indices: 1702477--1702543 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1702467 CAAAGAAACT
* *
1702477 ATTAACTTTTAATTTATATGTAAATAAGTC
1 ATTAATTTTTAATTTATATGTAAATAAGAC
*
1702507 ATTAATTTTTAATTTATATTTAAAATAA-AC
1 ATTAATTTTTAATTTATATGT-AAATAAGAC
1702537 ACTTAAT
1 A-TTAAT
1702544 ATAAATCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (30 bp):
ATTAATTTTTAATTTATATGTAAATAAGAC
Found at i:1702620 original size:29 final size:30
Alignment explanation
Indices: 1702566--1702638 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
1702556 TTTATATTAA
* *
1702566 ATAAAAATTTATTTTAGTACAAATAAAAAG
1 ATAAAAATTTATTTGAATACAAATAAAAAG
* * *
1702596 GTAAAAATTTATTTGAATA-TAATAAAAAT
1 ATAAAAATTTATTTGAATACAAATAAAAAG
1702625 ATAAAAATTTATTT
1 ATAAAAATTTATTT
1702639 ATAAAAAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (30 bp):
ATAAAAATTTATTTGAATACAAATAAAAAG
Found at i:1704018 original size:21 final size:21
Alignment explanation
Indices: 1703959--1704020 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1703949 GCTGTATTGA
**
1703959 TAAAATTAATTATTATAATAG
1 TAAAATTAAGAATTATAATAG
*
1703980 TAAGA-TAAGATATTATAATAG
1 TAAAATTAAGA-ATTATAATAG
1704001 TAAAATTAA-AATTAATAATA
1 TAAAATTAAGAATT-ATAATA
1704021 AAATATGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.18
21 25 0.74
22 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (21 bp):
TAAAATTAAGAATTATAATAG
Found at i:1704175 original size:30 final size:32
Alignment explanation
Indices: 1704117--1704180 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 32
1704107 ATAACTAGTT
*
1704117 ATAAATTATTAAAAATATATTTACATTAAATA
1 ATAAAATATTAAAAATATATTTACATTAAATA
**
1704149 ATAAAATA-TAAAAA-ATATTTGTATTAAATA
1 ATAAAATATTAAAAATATATTTACATTAAATA
1704179 AT
1 AT
1704181 TATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.55
31 6 0.21
32 7 0.24
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (32 bp):
ATAAAATATTAAAAATATATTTACATTAAATA
Found at i:1704208 original size:30 final size:28
Alignment explanation
Indices: 1704120--1704211 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 28
1704110 ACTAGTTATA
*
1704120 AATTATTAAAAATATATTTACATT-AAAT
1 AATTATTAAAAAT-TATTTATATTAAAAT
* * *
1704148 AATAAAATATAAAAAATATTTGTATT-AAAT
1 AAT--TAT-TAAAAATTATTTATATTAAAAT
1704178 AATTATTAAAATATTATTTATATTCAAAAT
1 AATTATTAAAA-ATTATTTATATT-AAAAT
1704208 AATT
1 AATT
1704212 TAATAAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
27 5 0.10
28 15 0.29
30 25 0.49
31 6 0.12
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (28 bp):
AATTATTAAAAATTATTTATATTAAAAT
Found at i:1706368 original size:5 final size:5
Alignment explanation
Indices: 1706358--1706393 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
1706348 ATATTATTTA
1706358 AAAAT AAAAT AAAAT AAAAT AAAAAT AAAACT AAAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA-T AAAA
1706394 AACTTAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1706373 original size:10 final size:10
Alignment explanation
Indices: 1706358--1706393 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
1706348 ATATTATTTA
1706358 AAAATAAAAT
1 AAAATAAAAT
1706368 AAAATAAAAT
1 AAAATAAAAT
1706378 AAAAATAAAACT
1 -AAAATAAAA-T
1706390 AAAA
1 AAAA
1706394 AACTTAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 13 0.54
12 1 0.04
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:1706382 original size:11 final size:11
Alignment explanation
Indices: 1706356--1706394 Score: 62
Period size: 10 Copynumber: 3.5 Consensus size: 11
1706346 ATATATTATT
1706356 TAAAAATAAAA
1 TAAAAATAAAA
1706367 T-AAAATAAAA
1 TAAAAATAAAA
1706377 TAAAAATAAAA
1 TAAAAATAAAA
1706388 CTAAAAA
1 -TAAAAA
1706395 ACTTAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.38
11 10 0.38
12 6 0.23
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:1706912 original size:21 final size:22
Alignment explanation
Indices: 1706888--1706929 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1706878 TTAAAAAAAT
1706888 ATTATAAT-AAATTAAATTTTA
1 ATTATAATAAAATTAAATTTTA
*
1706909 ATTATAATAAAATTAATTTTT
1 ATTATAATAAAATTAAATTTT
1706930 TTAAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTATAATAAAATTAAATTTTA
Found at i:1707387 original size:31 final size:32
Alignment explanation
Indices: 1707352--1707417 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
1707342 GTTATATTAT
* *
1707352 TAAAATATTATATTTTATAAT-TTAATTTAAA
1 TAAAATATTATATTATATAATAATAATTTAAA
* *
1707383 TAAAATTTTTTATTATATAATAATAATTTAAA
1 TAAAATATTATATTATATAATAATAATTTAAA
1707415 TAA
1 TAA
1707418 GATCAGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TAAAATATTATATTATATAATAATAATTTAAA
Found at i:1712976 original size:10 final size:10
Alignment explanation
Indices: 1712946--1712984 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1712936 TTTATTTTAT
*
1712946 TATTTAAAAA
1 TATTTTAAAA
*
1712956 TGATATTAAAA
1 T-ATTTTAAAA
1712967 TATTTTAAAA
1 TATTTTAAAA
1712977 TATTTTAA
1 TATTTTAA
1712985 TATTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:1713601 original size:23 final size:26
Alignment explanation
Indices: 1713524--1713592 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
1713514 TATAATATTA
* * *
1713524 TTATATTAATATAAATATTAAAAAGAG
1 TTATATTATTA-AAATATTAAAAATAT
*
1713551 TAATATTATTAAAATATTAAAAATAT
1 TTATATTATTAAAATATTAAAAATAT
1713577 TTATATTATTAAAATA
1 TTATATTATTAAAATA
1713593 ATAATATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 28 0.76
27 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
TTATATTATTAAAATATTAAAAATAT
Found at i:1714150 original size:25 final size:24
Alignment explanation
Indices: 1714112--1714197 Score: 124
Period size: 25 Copynumber: 3.6 Consensus size: 24
1714102 TATACATGTT
1714112 AACA-CACCTAACATTCTCACCAA
1 AACATCACCTAACATTCTCACCAA
*
1714135 ATACATCACCTAACATTCTCACC-T
1 A-ACATCACCTAACATTCTCACCAA
1714159 AACA-CACCTAACATTCTCACCAA
1 AACATCACCTAACATTCTCACCAA
1714182 ACACATCACCTAACAT
1 A-ACATCACCTAACAT
1714198 ACCTAACATT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
22 17 0.30
23 5 0.09
24 7 0.12
25 27 0.48
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (24 bp):
AACATCACCTAACATTCTCACCAA
Found at i:1714169 original size:22 final size:22
Alignment explanation
Indices: 1714112--1714186 Score: 114
Period size: 22 Copynumber: 3.3 Consensus size: 22
1714102 TATACATGTT
1714112 AACACACCTAACATTCTCACCAA
1 AACACACCTAACATTCTCACC-A
*
1714135 ATACATCACCTAACATTCTCACCT
1 A-ACA-CACCTAACATTCTCACCA
1714159 AACACACCTAACATTCTCACCA
1 AACACACCTAACATTCTCACCA
1714181 AACACA
1 AACACA
1714187 TCACCTAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
22 23 0.48
23 4 0.08
24 4 0.08
25 17 0.35
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (22 bp):
AACACACCTAACATTCTCACCA
Found at i:1714180 original size:47 final size:47
Alignment explanation
Indices: 1714111--1714253 Score: 187
Period size: 56 Copynumber: 2.9 Consensus size: 47
1714101 ATATACATGT
1714111 TAACACACCTAACATTCTCACCAAATACATCACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACATTCTCACC
*
1714158 TAACACACCTAACATTCTCACCAAACACATCACCTAACATACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACC--A-A-AT-A-C-ATC--ACCTAACATTCTCACC
*
1714214 TAACACACCTAACATTCTCACCAAACACATCACCTAACAT
1 TAACACACCTAACATTCTCACCAAATACATCACCTAACAT
1714254 ACCTAACATT
Statistics
Matches: 84, Mismatches: 3, Indels: 18
0.80 0.03 0.17
Matches are distributed among these distances:
47 31 0.37
49 3 0.04
50 2 0.02
51 3 0.04
52 2 0.02
53 2 0.02
54 3 0.04
56 38 0.45
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (47 bp):
TAACACACCTAACATTCTCACCAAATACATCACCTAACATTCTCACC
Found at i:1714195 original size:34 final size:34
Alignment explanation
Indices: 1714153--1714220 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1714143 CCTAACATTC
1714153 TCACCTAACACACCTAACATTCTCACCAAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
* *
1714187 TCACCTAACATACCTAACATTCTCACCTAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
1714221 CCTAACATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.21
Consensus pattern (34 bp):
TCACCTAACACACCTAACATTCTCACCAAACACA
Found at i:1714202 original size:56 final size:56
Alignment explanation
Indices: 1714137--1714269 Score: 257
Period size: 56 Copynumber: 2.4 Consensus size: 56
1714127 CTCACCAAAT
1714137 ACATCACCTAACATTCTCACCTAACACACCTAACATTCTCACCAAACACATCACCTA
1 ACAT-ACCTAACATTCTCACCTAACACACCTAACATTCTCACCAAACACATCACCTA
1714194 ACATACCTAACATTCTCACCTAACACACCTAACATTCTCACCAAACACATCACCTA
1 ACATACCTAACATTCTCACCTAACACACCTAACATTCTCACCAAACACATCACCTA
1714250 ACATACCTAACATTCTCACC
1 ACATACCTAACATTCTCACC
1714270 AAATACATCA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
56 72 0.95
57 4 0.05
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (56 bp):
ACATACCTAACATTCTCACCTAACACACCTAACATTCTCACCAAACACATCACCTA
Found at i:1714203 original size:9 final size:10
Alignment explanation
Indices: 1714137--1714304 Score: 69
Period size: 9 Copynumber: 15.3 Consensus size: 10
1714127 CTCACCAAAT
1714137 ACATCACCTA
1 ACATCACCTA
1714147 ACATTCTCACCTA
1 ACA---TCACCTA
1714160 ACA-CACCTA
1 ACATCACCTA
*
1714169 ACATTCTCACCAAA
1 ACA---TCACC-TA
1714183 CACATCACCTA
1 -ACATCACCTA
1714194 ACAT-ACCTA
1 ACATCACCTA
1714203 ACATTCTCACCTA
1 ACA---TCACCTA
1714216 ACA-CACCTA
1 ACATCACCTA
*
1714225 ACATTCTCACCAAA
1 ACA---TCACC-TA
1714239 CACATCACCTA
1 -ACATCACCTA
1714250 ACAT-ACCTA
1 ACATCACCTA
*
1714259 ACATTCTCACCAAA
1 ACA---TCACC-TA
1714273 TACATCACCTA
1 -ACATCACCTA
1714284 ACA-CACCTA
1 ACATCACCTA
*
1714293 ACA-CACTTA
1 ACATCACCTA
1714302 ACA
1 ACA
1714305 AAGAAATTAA
Statistics
Matches: 126, Mismatches: 7, Indels: 51
0.68 0.04 0.28
Matches are distributed among these distances:
9 51 0.40
10 14 0.11
11 3 0.02
12 17 0.13
13 29 0.23
14 3 0.02
15 9 0.07
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.21
Consensus pattern (10 bp):
ACATCACCTA
Found at i:1714215 original size:22 final size:22
Alignment explanation
Indices: 1714187--1714242 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1714177 ACCAAACACA
*
1714187 TCACCTAACATACCTAACATTC
1 TCACCTAACACACCTAACATTC
1714209 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
*
1714231 TCACCAAACACA
1 TCACCTAACACA
1714243 TCACCTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (22 bp):
TCACCTAACACACCTAACATTC
Found at i:1714247 original size:34 final size:34
Alignment explanation
Indices: 1714209--1714295 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
1714199 CCTAACATTC
1714209 TCACCTAACACACCTAACATTCTCACCAAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
* *
1714243 TCACCTAACATACCTAACATTCTCACCAAATACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
1714277 TCACCTAACACACCTAACA
1 TCACCTAACACACCTAACA
1714296 CACTTAACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (34 bp):
TCACCTAACACACCTAACATTCTCACCAAACACA
Found at i:1716151 original size:13 final size:13
Alignment explanation
Indices: 1716133--1716158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1716123 TACACCAAGT
1716133 ATGTATCGATACA
1 ATGTATCGATACA
1716146 ATGTATCGATACA
1 ATGTATCGATACA
1716159 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1720233 original size:15 final size:15
Alignment explanation
Indices: 1720213--1720243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1720203 TAAAAATGTC
*
1720213 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1720228 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1720243 C
1 C
1720244 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1722318 original size:13 final size:13
Alignment explanation
Indices: 1722300--1722337 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1722290 CATTTTTCTT
1722300 TGTATCGATACAA
1 TGTATCGATACAA
*
1722313 TGTATCGATACAC
1 TGTATCGATACAA
1722326 TGTATCGATACA
1 TGTATCGATACA
1722338 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1722492 original size:20 final size:20
Alignment explanation
Indices: 1722449--1722494 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1722439 AAATCTTTTG
1722449 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1722470 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1722490 CAAAA
1 CAAAA
1722495 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1724924 original size:13 final size:13
Alignment explanation
Indices: 1724906--1724931 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1724896 TACACCAAGT
1724906 ATGTATCGATACA
1 ATGTATCGATACA
1724919 ATGTATCGATACA
1 ATGTATCGATACA
1724932 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1728988 original size:22 final size:22
Alignment explanation
Indices: 1728960--1729015 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1728950 ACCAAATACA
1728960 TCACCTAACACACCTAACATTC
1 TCACCTAACACACCTAACATTC
*
1728982 TCACCTAACACACCTGACATTC
1 TCACCTAACACACCTAACATTC
*
1729004 TCACCAAACACA
1 TCACCTAACACA
1729016 TCACCTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.41, G:0.02, T:0.20
Consensus pattern (22 bp):
TCACCTAACACACCTAACATTC
Found at i:1729017 original size:56 final size:56
Alignment explanation
Indices: 1728931--1729042 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
1728921 ATATACATGT
*
1728931 TAACACACCTAACATTCTCACCAAATACATCACCTAACACACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
* *
1728987 TAACACACCTGACATTCTCACCAAACACATCACCTAACATACCTAACATTCTCACC
1 TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
1729043 AAATACATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.38, C:0.39, G:0.01, T:0.21
Consensus pattern (56 bp):
TAACACACCTAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
Found at i:1729020 original size:34 final size:34
Alignment explanation
Indices: 1728982--1729068 Score: 147
Period size: 34 Copynumber: 2.6 Consensus size: 34
1728972 CCTAACATTC
*
1728982 TCACCTAACACACCTGACATTCTCACCAAACACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
* *
1729016 TCACCTAACATACCTAACATTCTCACCAAATACA
1 TCACCTAACACACCTAACATTCTCACCAAACACA
1729050 TCACCTAACACACCTAACA
1 TCACCTAACACACCTAACA
1729069 CACTTAACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.40, C:0.39, G:0.01, T:0.20
Consensus pattern (34 bp):
TCACCTAACACACCTAACATTCTCACCAAACACA
Found at i:1729032 original size:9 final size:10
Alignment explanation
Indices: 1728957--1729077 Score: 54
Period size: 9 Copynumber: 11.3 Consensus size: 10
1728947 CTCACCAAAT
1728957 ACATCACCTA
1 ACATCACCTA
1728967 ACA-CACCTA
1 ACATCACCTA
1728976 ACATTCTCACCTA
1 ACA---TCACCTA
*
1728989 ACA-CACCTG
1 ACATCACCTA
*
1728998 ACATTCTCACCAAA
1 ACA---TCACC-TA
1729012 CACATCACCTA
1 -ACATCACCTA
1729023 ACAT-ACCTA
1 ACATCACCTA
*
1729032 ACATTCTCACCAAA
1 ACA---TCACC-TA
1729046 TACATCACCTA
1 -ACATCACCTA
1729057 ACA-CACCTA
1 ACATCACCTA
*
1729066 ACA-CACTTA
1 ACATCACCTA
1729075 ACA
1 ACA
1729078 AAGAAATTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 33
0.69 0.05 0.26
Matches are distributed among these distances:
9 42 0.48
10 10 0.11
11 2 0.02
12 11 0.12
13 16 0.18
14 1 0.01
15 6 0.07
ACGTcount: A:0.40, C:0.39, G:0.01, T:0.20
Consensus pattern (10 bp):
ACATCACCTA
Found at i:1729419 original size:26 final size:24
Alignment explanation
Indices: 1729374--1729421 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1729364 TATTTAAAAA
* *
1729374 ATTTTAAAATGAAGTTTTTTTAAT
1 ATTTTAAAATGAAATATTTTTAAT
1729398 ATTTTAACAATGTAAATATTTTTA
1 ATTTTAA-AATG-AAATATTTTTA
1729422 TTAATTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 4 0.20
26 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTTAAAATGAAATATTTTTAAT
Found at i:1731138 original size:13 final size:13
Alignment explanation
Indices: 1731122--1731146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1731112 ATCAATTATA
1731122 ATAAATATTAATT
1 ATAAATATTAATT
1731135 ATAAATATTAAT
1 ATAAATATTAAT
1731147 AATTATAAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAATATTAATT
Found at i:1731149 original size:16 final size:16
Alignment explanation
Indices: 1731083--1731158 Score: 77
Period size: 16 Copynumber: 4.8 Consensus size: 16
1731073 ACATTTATTT
1731083 TAATTATAAAT-ATAA
1 TAATTATAAATAATAA
* *
1731098 TAAATAT-TATAATAA
1 TAATTATAAATAATAA
*
1731113 TCAATTAT-AATAAATAT
1 T-AATTATAAAT-AATAA
*
1731130 TAATTATAAATATTAA
1 TAATTATAAATAATAA
1731146 TAATTATAAATAA
1 TAATTATAAATAA
1731159 AACTCATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
14 2 0.04
15 11 0.22
16 28 0.57
17 8 0.16
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTATAAATAATAA
Found at i:1732065 original size:22 final size:22
Alignment explanation
Indices: 1732013--1732066 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1732003 TAAAATAAAC
*
1732013 AATATAAATAAAAATATAAGTTT
1 AATAT-AATAAAAATATAAGATT
* *
1732036 ACAT-TAATAAAACTTTAAGATT
1 A-ATATAATAAAAATATAAGATT
1732058 AATATAATA
1 AATATAATA
1732067 TGATAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.08
22 20 0.77
23 2 0.08
24 2 0.08
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (22 bp):
AATATAATAAAAATATAAGATT
Found at i:1736693 original size:16 final size:16
Alignment explanation
Indices: 1736669--1736699 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1736659 TTTGGATCAG
*
1736669 TCTCGGGTTCGAGTTC
1 TCTCAGGTTCGAGTTC
1736685 TCTCAGGTTCGAGTT
1 TCTCAGGTTCGAGTT
1736700 TTTTCGAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.23, G:0.29, T:0.39
Consensus pattern (16 bp):
TCTCAGGTTCGAGTTC
Found at i:1736748 original size:16 final size:16
Alignment explanation
Indices: 1736729--1736760 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1736719 TTAAGTTCGG
*
1736729 GCTTTCTCGGGTTTGA
1 GCTTTCTCGAGTTTGA
1736745 GCTTTCTCGAGTTTGA
1 GCTTTCTCGAGTTTGA
1736761 ATTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (16 bp):
GCTTTCTCGAGTTTGA
Found at i:1742045 original size:13 final size:12
Alignment explanation
Indices: 1741997--1742039 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
1741987 ATTTCATTTT
1741997 GAAAAAAAAA-A
1 GAAAAAAAAAGA
* *
1742008 GAACAAAAGA-A
1 GAAAAAAAAAGA
1742019 GAAAAAAAAAGA
1 GAAAAAAAAAGA
1742031 GAAAAAAAA
1 GAAAAAAAA
1742040 GTGAGAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:1742423 original size:2 final size:2
Alignment explanation
Indices: 1742411--1742449 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1742401 TTCAGAGCCA
*
1742411 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1742450 AATGCAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 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):
AT
Found at i:1743597 original size:22 final size:22
Alignment explanation
Indices: 1743572--1743762 Score: 102
Period size: 22 Copynumber: 8.6 Consensus size: 22
1743562 TTATGTATAC
1743572 ATCACAATAATAGAATGTACAT
1 ATCACAATAATAGAATGTACAT
* * *
1743594 ATCATAATAACA-ATATATACAT
1 ATCACAATAATAGA-ATGTACAT
* ** * *
1743616 ATAACTTTCATAGTATGTACAT
1 ATCACAATAATAGAATGTACAT
* **
1743638 ATGATTATAATTA-AATGTACAT
1 ATCACAATAA-TAGAATGTACAT
* * * * *
1743660 ATTATAATAACAGTATATATC-T
1 ATCACAATAATAGAATGTA-CAT
* *
1743682 ATTATAATAATA-AATGTACAT
1 ATCACAATAATAGAATGTACAT
* * *
1743703 ATCACAATAATATAATATATATAT
1 ATCACAATAATA-GA-ATGTACAT
*
1743727 ATCACAATAATAGTATGTACAAT
1 ATCACAATAATAGAATGTAC-AT
1743750 ATCACAATAATAG
1 ATCACAATAATAG
1743763 TCGATTCTTT
Statistics
Matches: 127, Mismatches: 32, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
20 1 0.01
21 17 0.13
22 72 0.57
23 19 0.15
24 18 0.14
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (22 bp):
ATCACAATAATAGAATGTACAT
Found at i:1743753 original size:47 final size:45
Alignment explanation
Indices: 1743644--1743761 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 45
1743634 ACATATGATT
* * * * *
1743644 ATAATTAAATGTACATATTATAATAACAGT-ATATATCTAT-T-ATA
1 ATAA-TAAATGTACATATCACAATAATA-TAATATATATATATCACA
1743688 ATAATAAATGTACATATCACAATAATATAATATATATATATCACA
1 ATAATAAATGTACATATCACAATAATATAATATATATATATCACA
*
1743733 ATAATAGTATGTACAATATCACAATAATA
1 ATAATA-AATGTAC-ATATCACAATAATA
1743762 GTCGATTCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
42 1 0.02
43 29 0.46
44 5 0.08
45 8 0.13
46 6 0.10
47 14 0.22
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (45 bp):
ATAATAAATGTACATATCACAATAATATAATATATATATATCACA
Found at i:1743763 original size:23 final size:22
Alignment explanation
Indices: 1743687--1743761 Score: 89
Period size: 24 Copynumber: 3.3 Consensus size: 22
1743677 TATCTATTAT
*
1743687 AATAATAAATGTAC-ATATCAC
1 AATAATATATGTACAATATCAC
* *
1743708 AATAATATAATATATATATATCAC
1 AATAATAT-ATGTACA-ATATCAC
1743732 AATAATAGTATGTACAATATCAC
1 AATAATA-TATGTACAATATCAC
1743755 AATAATA
1 AATAATA
1743762 GTCGATTCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.16
22 4 0.09
23 14 0.31
24 19 0.42
25 1 0.02
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (22 bp):
AATAATATATGTACAATATCAC
Found at i:1743996 original size:16 final size:16
Alignment explanation
Indices: 1743972--1744005 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1743962 AGTAAAAATA
*
1743972 ATATTTATATATAATT
1 ATATGTATATATAATT
1743988 ATATGTATATATAATT
1 ATATGTATATATAATT
1744004 AT
1 AT
1744006 GTTATATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATATGTATATATAATT
Found at i:1744626 original size:28 final size:28
Alignment explanation
Indices: 1744581--1744639 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1744571 ACATATCATT
* * *
1744581 ATAACAATATATATATA-TATATATCACA
1 ATAACAAAATATACATATTATA-ATAACA
*
1744609 ATAACAAAATGTACATATTATAATAACA
1 ATAACAAAATATACATATTATAATAACA
1744637 ATA
1 ATA
1744640 TATATGACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAACAAAATATACATATTATAATAACA
Found at i:1751498 original size:12 final size:12
Alignment explanation
Indices: 1751481--1751505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1751471 TATATATTAA
1751481 TCATTAAACTTG
1 TCATTAAACTTG
1751493 TCATTAAACTTG
1 TCATTAAACTTG
1751505 T
1 T
1751506 TAGAGAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TCATTAAACTTG
Found at i:1757786 original size:13 final size:12
Alignment explanation
Indices: 1757770--1757803 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1757760 AAAATAAATT
1757770 AAAAAAAAACAAC
1 AAAAAAAAA-AAC
1757783 AAAACAAAAAAAC
1 AAAA-AAAAAAAC
1757796 AAAAAAAA
1 AAAAAAAA
1757804 GAGAGAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1757802 original size:8 final size:8
Alignment explanation
Indices: 1757772--1757802 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1757762 AATAAATTAA
1757772 AAAAAAAC
1 AAAAAAAC
*
1757780 AACAAAAC
1 AAAAAAAC
1757788 AAAAAAAC
1 AAAAAAAC
1757796 AAAAAAA
1 AAAAAAA
1757803 AGAGAGAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1761816 original size:51 final size:51
Alignment explanation
Indices: 1761749--1761864 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
1761739 AAATAACAGG
* * ** *
1761749 GTTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGGAACTAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGA
* * *
1761800 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAAAAATAAAATTGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGA
*
1761851 GTTGGAGTGTCCCC
1 GTTGGAGTATCCCC
1761865 TCGAAAATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAAAAATAAAATCGGA
Found at i:1761864 original size:130 final size:131
Alignment explanation
Indices: 1761717--1761995 Score: 375
Period size: 130 Copynumber: 2.1 Consensus size: 131
1761707 GAAATAAGGC
* *
1761717 CGGGGTTGGAGTATCCCCGT-GAAAATAACAGGGTTGGAGTATCCCCGATTATGAGAAA-TTGGT
1 CGGGGTTGGAGTATCCCCGTCGAAAATAACAGGGTTGGAATATCCCCGATTATGA-AAAGTCGGT
* * * * * *
1761780 GTTTTGGAACTAAAATCGGAGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAAAAATAAA
65 GCTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTATGAAAAATGGGTATTTTAAAAATAAA
1761845 AT
130 AT
* * ** *
1761847 TGGGGTTGGAGTGTCCCC-TCGAAAATAATGGGGTTGGAATATCCCCGATTGTGAAAAGTCGGTG
1 CGGGGTTGGAGTATCCCCGTCGAAAATAACAGGGTTGGAATATCCCCGATTATGAAAAGTCGGTG
* * *
1761911 CTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAA
66 CTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTATGAAAAATGGGTATTTTAAAAATAAAA
1761976 T
131 T
*
1761977 CGGAGTTGGAGTATCCCCG
1 CGGGGTTGGAGTATCCCCG
1761996 ATTAAGAGAA
Statistics
Matches: 127, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
129 4 0.03
130 123 0.97
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (131 bp):
CGGGGTTGGAGTATCCCCGTCGAAAATAACAGGGTTGGAATATCCCCGATTATGAAAAGTCGGTG
CTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTATGAAAAATGGGTATTTTAAAAATAAAA
T
Found at i:1761941 original size:51 final size:51
Alignment explanation
Indices: 1761879--1761999 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
1761869 AAATAATGGG
* *
1761879 GTTGGAATATCCCCGATTGT-GAAAAGTCGGTGCTTTGA-AAATAAAATCGAA
1 GTTGGAGTATCCCCGATTATGGAAAA-TCGGTG-TTTGAGAAATAAAATCGAA
* * *
1761930 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTGAGAAATAAAATCGAA
1761981 GTTGGAGTATCCCCGATTA
1 GTTGGAGTATCCCCGATTA
1762000 AGAGAAATTG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
50 4 0.06
51 54 0.86
52 5 0.08
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTGAGAAATAAAATCGAA
Found at i:1762015 original size:51 final size:51
Alignment explanation
Indices: 1761917--1762043 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 51
1761907 GGTGCTTTGA
* * *
1761917 AAATAAAATCGAAGTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAG
1 AAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGAAAATGGATGTTTTAG
* *
1761968 AAATAAAATCGGAGTTGGAGTATCCCCGATTAA-GAGAAATTGATGTTTTGG
1 AAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGA-AAATGGATGTTTTAG
* *
1762019 AAATGAAACCGG-GATTGGAGTATCC
1 AAATAAAATCGGAG-TTGGAGTATCC
1762044 TCGAGATGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
50 3 0.04
51 64 0.96
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (51 bp):
AAATAAAATCGGAGTTGGAGTATCCCCGATTAAGGAAAATGGATGTTTTAG
Found at i:1764424 original size:20 final size:20
Alignment explanation
Indices: 1764399--1764453 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1764389 AAACTTCCTA
1764399 GATGTATCGATACAAAGATC
1 GATGTATCGATACAAAGATC
1764419 GATGTATCGATACAAAGATC
1 GATGTATCGATACAAAGATC
1764439 GATGTATCGATACAA
1 GATGTATCGATACAA
1764454 TGTATCGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GATGTATCGATACAAAGATC
Found at i:1764458 original size:13 final size:13
Alignment explanation
Indices: 1764440--1764465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1764430 ACAAAGATCG
1764440 ATGTATCGATACA
1 ATGTATCGATACA
1764453 ATGTATCGATACA
1 ATGTATCGATACA
1764466 TTGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1764525 original size:13 final size:13
Alignment explanation
Indices: 1764503--1764560 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1764493 GGTAGTAGCT
*
1764503 TTGTAGCGATACA
1 TTGTATCGATACA
1764516 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
1764532 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1764548 TTGTATCGATACA
1 TTGTATCGATACA
1764561 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1764541 original size:19 final size:19
Alignment explanation
Indices: 1764517--1764602 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
1764507 AGCGATACAT
1764517 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1764536 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1764549 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
1764568 TGTATCGATACATTTACTGTT
1 TGTATCGATACA-AAACT-TA
1764589 TGTATCGATACAAA
1 TGTATCGATACAAA
1764603 TTATTGAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 23 0.43
20 3 0.06
21 13 0.24
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Done.