Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 5 of 332
Found at i:1399925 original size:16 final size:18
Alignment explanation
Indices: 1399886--1399919 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1399876 TGAGTTTATA
1399886 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
1399903 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
1399920 AATTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:1402248 original size:29 final size:29
Alignment explanation
Indices: 1402216--1402279 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1402206 ATTTAATTTT
*
1402216 AATTAAAGTT-AAATTGAGTTTTTAAAAAA
1 AATTAAAGTTCAAATT-AATTTTTAAAAAA
* * *
1402245 AATTAAATTTCTAATTAATTTTTATAAAA
1 AATTAAAGTTCAAATTAATTTTTAAAAAA
1402274 AATTAA
1 AATTAA
1402280 TTAAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTAAAGTTCAAATTAATTTTTAAAAAA
Found at i:1403520 original size:21 final size:21
Alignment explanation
Indices: 1403494--1403537 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1403484 TCTCGAGGAA
* *
1403494 AATAGAAATCTAGAGGAAAAT
1 AATAGAAAACTAGAGAAAAAT
*
1403515 AATAGAAAACTATAGAAAAAT
1 AATAGAAAACTAGAGAAAAAT
1403536 AA
1 AA
1403538 AAATTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.14, T:0.18
Consensus pattern (21 bp):
AATAGAAAACTAGAGAAAAAT
Found at i:1403546 original size:11 final size:11
Alignment explanation
Indices: 1403532--1403557 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1403522 AACTATAGAA
1403532 AAATAAAAATT
1 AAATAAAAATT
1403543 AAATAAAAATT
1 AAATAAAAATT
1403554 AAAT
1 AAAT
1403558 TTAGATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:1414986 original size:18 final size:17
Alignment explanation
Indices: 1414948--1414980 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1414938 CTAATATTTA
1414948 AAATTAATTACTTTAAAT
1 AAATTAATTA-TTTAAAT
1414966 AAATTAATT-TTTAAA
1 AAATTAATTATTTAAA
1414981 ATTAAACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTAATTATTTAAAT
Found at i:1418867 original size:36 final size:36
Alignment explanation
Indices: 1418820--1418892 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1418810 AGTTTCACAA
1418820 AGATACTCTTAATGATCTTGAAATATTATATCAATG
1 AGATACTCTTAATGATCTTGAAATATTATATCAATG
*
1418856 AGATACTCTTAATGATCTTGAAATATTGTATCAATG
1 AGATACTCTTAATGATCTTGAAATATTATATCAATG
1418892 A
1 A
1418893 CTATGACATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (36 bp):
AGATACTCTTAATGATCTTGAAATATTATATCAATG
Found at i:1424884 original size:7 final size:7
Alignment explanation
Indices: 1424869--1424908 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
1424859 GATTAGACAT
1424869 AGCAAAA
1 AGCAAAA
*
1424876 AGCAGAA
1 AGCAAAA
1424883 AGCAAAA
1 AGCAAAA
1424890 AGCAAAA
1 AGCAAAA
* *
1424897 AGTAGAA
1 AGCAAAA
1424904 AGCAA
1 AGCAA
1424909 GGCCAAACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.65, C:0.12, G:0.20, T:0.03
Consensus pattern (7 bp):
AGCAAAA
Found at i:1424893 original size:21 final size:21
Alignment explanation
Indices: 1424869--1424908 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1424859 GATTAGACAT
1424869 AGCAAAAAGCAGAAAGCAAAA
1 AGCAAAAAGCAGAAAGCAAAA
*
1424890 AGCAAAAAGTAGAAAGCAA
1 AGCAAAAAGCAGAAAGCAA
1424909 GGCCAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.20, T:0.03
Consensus pattern (21 bp):
AGCAAAAAGCAGAAAGCAAAA
Found at i:1426303 original size:4 final size:4
Alignment explanation
Indices: 1426294--1426318 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1426284 TAAGTACTTG
1426294 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
1426319 TTTCTAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:1427446 original size:70 final size:70
Alignment explanation
Indices: 1427314--1427446 Score: 176
Period size: 70 Copynumber: 1.9 Consensus size: 70
1427304 CGAAAACCAG
* * *
1427314 TTGAGGTATTGATCCAGTGAAAGGAAAAAAACCAGGTGACCTGCGAATCGTTATAGACGGGTTGA
1 TTGAGGTATTGATCCAGTGAAAGGAAAAAAACCAGGTGACCCGCGAACCGATATAGACGGGTTGA
1427379 ATCAA
66 ATCAA
* * *** * *
1427384 TTGAGTTATTGATTCAGTGAAAGGAAAAAAATTGGGTGACCCGCGAACCGATATGGATGGGTT
1 TTGAGGTATTGATCCAGTGAAAGGAAAAAAACCAGGTGACCCGCGAACCGATATAGACGGGTT
1427447 AAATTAAGCT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
70 53 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (70 bp):
TTGAGGTATTGATCCAGTGAAAGGAAAAAAACCAGGTGACCCGCGAACCGATATAGACGGGTTGA
ATCAA
Found at i:1427836 original size:20 final size:19
Alignment explanation
Indices: 1427813--1427854 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1427803 AAAACTCTTT
1427813 AAAA-TTTTAAAAATAAAATA
1 AAAAGTTTT-AAAATAAAA-A
1427833 AAAAGTTTTAAAATAAAAA
1 AAAAGTTTTAAAATAAAAA
1427852 AAA
1 AAA
1427855 TCTAAAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAGTTTTAAAATAAAAA
Found at i:1444630 original size:24 final size:26
Alignment explanation
Indices: 1444592--1444644 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
1444582 CATTTTCTTG
* * *
1444592 AGAAAAAACTAAAATTAATTTTAAAA
1 AGAAAAAACTAAAATGAAATTAAAAA
1444618 AGAAAAAA-T-AAATGAAATTAAAAA
1 AGAAAAAACTAAAATGAAATTAAAAA
1444642 AGA
1 AGA
1444645 TAAATTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.62
25 1 0.04
26 8 0.33
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (26 bp):
AGAAAAAACTAAAATGAAATTAAAAA
Found at i:1447600 original size:30 final size:29
Alignment explanation
Indices: 1447564--1447628 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1447554 TAAAAGTTCA
* *
1447564 AAAAAAATTATAAAAACTATTTTAAAAAAT
1 AAAAAAATCATAAAAACTA-TTAAAAAAAT
* *
1447594 AAAAAAATCATTAAAATTATTAAAAAAAT
1 AAAAAAATCATAAAAACTATTAAAAAAAT
*
1447623 ATAAAA
1 AAAAAA
1447629 TATATTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAAAAATCATAAAAACTATTAAAAAAAT
Found at i:1447634 original size:20 final size:21
Alignment explanation
Indices: 1447593--1447634 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1447583 TTTTAAAAAA
1447593 TAAAAAAATCATTAAAATTAT
1 TAAAAAAATCATTAAAATTAT
1447614 TAAAAAAAT-A-TAAAATATAT
1 TAAAAAAATCATTAAAAT-TAT
1447634 T
1 T
1447635 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAAATCATTAAAATTAT
Found at i:1455747 original size:20 final size:20
Alignment explanation
Indices: 1455709--1455747 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1455699 TAAATTTTAC
* * *
1455709 ATTTTAAAAAATAATAATAT
1 ATTTAAAAAAAAAAGAATAT
1455729 ATTTAAAAAAAAAAGAATA
1 ATTTAAAAAAAAAAGAATA
1455748 GATAGTTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
ATTTAAAAAAAAAAGAATAT
Found at i:1458007 original size:29 final size:29
Alignment explanation
Indices: 1457974--1458046 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 29
1457964 AAAATTAAAC
1457974 CATATAAGGAATAGGACCTAAAAGGAAAT
1 CATATAAGGAATAGGACCTAAAAGGAAAT
** * * *
1458003 CATATAAAATAATAGGATCTAAATGTAAAT
1 CATAT-AAGGAATAGGACCTAAAAGGAAAT
* *
1458033 TATACAAGGAATAG
1 CATATAAGGAATAG
1458047 TTTGGCCAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 12 0.35
30 22 0.65
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.23
Consensus pattern (29 bp):
CATATAAGGAATAGGACCTAAAAGGAAAT
Found at i:1460184 original size:51 final size:50
Alignment explanation
Indices: 1460066--1460205 Score: 129
Period size: 51 Copynumber: 2.7 Consensus size: 50
1460056 TATGTAAATG
* * * * * * *
1460066 TTGACAAAATGTGTAAATTTTGTGGGTTAATTTTGTTAAATCAGGATCAAA
1 TTGACAAAATGAGTAAA-TTTGTGAGCTAAATTTATTAAATCAAGATAAAA
** *
1460117 TTGGTAGAAT-ATGTAAATATTGTGAGCTAAATTTATTAAATCAAGATAAAA
1 TTGACAAAATGA-GTAAAT-TTGTGAGCTAAATTTATTAAATCAAGATAAAA
* *
1460168 TTGACAAAATGAGTAAACTTTGAGAACTAAATTTATTA
1 TTGACAAAATGAGTAAA-TTTGTGAGCTAAATTTATTA
1460206 TTATACTAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 1 0.01
51 67 0.96
52 2 0.03
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.36
Consensus pattern (50 bp):
TTGACAAAATGAGTAAATTTGTGAGCTAAATTTATTAAATCAAGATAAAA
Found at i:1462942 original size:13 final size:13
Alignment explanation
Indices: 1462924--1462948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1462914 CATGTTTCTG
1462924 AAGAAAATGTTAC
1 AAGAAAATGTTAC
1462937 AAGAAAATGTTA
1 AAGAAAATGTTA
1462949 AGACAAAACC
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:0.04, G:0.16, T:0.24
Consensus pattern (13 bp):
AAGAAAATGTTAC
Found at i:1467568 original size:42 final size:42
Alignment explanation
Indices: 1467505--1467756 Score: 272
Period size: 42 Copynumber: 5.7 Consensus size: 42
1467495 CTTCGTTTTC
** *
1467505 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* *
1467548 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
* *
1467589 TCGGTGCCATAGCCCAGCTATAGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
* *
1467638 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
*
1467680 TCGGTGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
1467729 TCGATGCCATAGCCCAGCTATGGTCTTA
1 TCGATGCCATAGCCCAGCTATGGTCTTA
1467757 TACAGTAGCA
Statistics
Matches: 177, Mismatches: 17, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
41 2 0.01
42 97 0.55
43 2 0.01
45 4 0.02
46 2 0.01
48 2 0.01
49 68 0.38
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:1467648 original size:49 final size:48
Alignment explanation
Indices: 1467575--1467802 Score: 274
Period size: 49 Copynumber: 4.8 Consensus size: 48
1467565 TATGGTCTTA
* * *
1467575 CACATATTCAGATATCGGTGCCATAGCCCAGCTATAGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGT-AT
1467625 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACAC--AT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAT
* *
1467671 ---AT-TCAGATATCGGTGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGT-AT
* *
1467716 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTATACAGTAG
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACAC-GTAT
* * *
1467765 CATATATCAC--ATCGATGCCATATCCCAGATATGGTCTT
1 CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTT
1467803 GTACGGAAAT
Statistics
Matches: 158, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
42 36 0.23
43 2 0.01
45 2 0.01
46 2 0.01
47 26 0.16
48 2 0.01
49 80 0.51
50 8 0.05
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAT
Found at i:1467772 original size:91 final size:91
Alignment explanation
Indices: 1467540--1467756 Score: 409
Period size: 91 Copynumber: 2.4 Consensus size: 91
1467530 TTACACATCT
1467540 TCACATAAT-GATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATATCGGTGCCATAGCCC
1 TCACAT-ATCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATATCGGTGCCATAGCCC
1467604 AGCTATAGTCTTACACGTAATCACATA
65 AGCTATAGTCTTACACGTAATCACATA
1467631 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATATCGGTGCCATAGCCCA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATATCGGTGCCATAGCCCA
*
1467696 GCTATGGTCTTACACGTAATCACATA
66 GCTATAGTCTTACACGTAATCACATA
1467722 TCACATATCGATGCCATAGCCCAGCTATGGTCTTA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTA
1467757 TACAGTAGCA
Statistics
Matches: 124, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
90 2 0.02
91 122 0.98
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (91 bp):
TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATATCGGTGCCATAGCCCA
GCTATAGTCTTACACGTAATCACATA
Found at i:1467870 original size:31 final size:31
Alignment explanation
Indices: 1467835--1467909 Score: 109
Period size: 31 Copynumber: 2.4 Consensus size: 31
1467825 GTAGCCGAAG
1467835 CTACCACTATTT-ACTGATCAGGTAGCCGGTA
1 CTACCACT-TTTCACTGATCAGGTAGCCGGTA
*
1467866 CTACCACTTTTCACTGATCAGGTAGCC-GAA
1 CTACCACTTTTCACTGATCAGGTAGCCGGTA
1467896 GCTACCACTTTTCA
1 -CTACCACTTTTCA
1467910 TTTGTCATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 5 0.12
31 36 0.88
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (31 bp):
CTACCACTTTTCACTGATCAGGTAGCCGGTA
Found at i:1467990 original size:50 final size:51
Alignment explanation
Indices: 1467887--1468015 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
1467877 CACTGATCAG
* * *
1467887 GTAGCCGAAGCTACCACTTTTCATTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
* *
1467938 GTAGCCAAAGCTATCACTTATCACTT-TCACTTTTTC-TTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
1467988 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
1468016 TTCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 42 0.60
51 28 0.40
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:1470525 original size:23 final size:24
Alignment explanation
Indices: 1470473--1470531 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
1470463 CATGGAATAG
1470473 TATAAGAAATATATACATGAAAACA
1 TATAA-AAATATATACATGAAAACA
* * *
1470498 T-TAAAAATATGTACAT-AATATA
1 TATAAAAATATATACATGAAAACA
*
1470520 TATAAATATATA
1 TATAAAAATATA
1470532 CAATATATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 5 0.18
23 19 0.68
24 3 0.11
25 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (24 bp):
TATAAAAATATATACATGAAAACA
Found at i:1470526 original size:21 final size:21
Alignment explanation
Indices: 1470430--1470540 Score: 57
Period size: 23 Copynumber: 5.0 Consensus size: 21
1470420 TATATTAATA
*
1470430 ATAAATATGTACATAAGATGAT
1 ATAAATATGTACATAATAT-AT
*
1470452 CAT-AATACGTACATGGAATAGTAT
1 -ATAAATATGTACAT--AATA-TAT
* * * *
1470476 AAGAAATATATACATGAAAACATT
1 -ATAAATATGTACAT-AATATA-T
*
1470500 AAAAATATGTACATAATATAT
1 ATAAATATGTACATAATATAT
*
1470521 ATAAATATATAC--AATATAT
1 ATAAATATGTACATAATATAT
1470540 A
1 A
1470541 CCTATATTAG
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
19 8 0.12
21 11 0.16
22 14 0.20
23 15 0.22
24 11 0.16
25 10 0.14
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (21 bp):
ATAAATATGTACATAATATAT
Found at i:1471510 original size:2 final size:2
Alignment explanation
Indices: 1471472--1471498 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1471462 TCAAAAAAAG
1471472 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1471499 AGCCCTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1472509 original size:25 final size:26
Alignment explanation
Indices: 1472481--1472529 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1472471 AGAAAAGTTT
1472481 ATTA-ATTTTATAGTGG-CAAAAATTA
1 ATTACATTTTATAG-GGACAAAAATTA
*
1472506 ATTACCTTTTATAGGGACAAAAAT
1 ATTACATTTTATAGGGACAAAAAT
1472530 CAATAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (26 bp):
ATTACATTTTATAGGGACAAAAATTA
Found at i:1473966 original size:16 final size:16
Alignment explanation
Indices: 1473915--1473970 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
1473905 TGTCAACCTA
1473915 TAAAA-ATTTAATAAAT
1 TAAAATATTT-ATAAAT
* *
1473931 TATAACATTTA-AAAT
1 TAAAATATTTATAAAT
*
1473946 TAAAATATTTATAACT
1 TAAAATATTTATAAAT
1473962 TAAAATATT
1 TAAAATATT
1473971 CAAATTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 13 0.38
16 17 0.50
17 4 0.12
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATTTATAAAT
Found at i:1473975 original size:24 final size:24
Alignment explanation
Indices: 1473930--1473975 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1473920 ATTTAATAAA
*
1473930 TTATAACATTTAAAATTAAAATAT
1 TTATAACATTAAAAATTAAAATAT
*
1473954 TTATAAC-TTAAAATATTCAAAT
1 TTATAACATTAAAA-ATTAAAAT
1473976 TTATCTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (24 bp):
TTATAACATTAAAAATTAAAATAT
Found at i:1476272 original size:20 final size:20
Alignment explanation
Indices: 1476247--1476296 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1476237 TGGCTTAAAA
1476247 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1476267 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1476284 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1476297 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1480910 original size:20 final size:20
Alignment explanation
Indices: 1480885--1480934 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1480875 TGGCTTAAAA
1480885 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1480905 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1480922 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1480935 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1481784 original size:108 final size:108
Alignment explanation
Indices: 1481595--1481803 Score: 307
Period size: 108 Copynumber: 1.9 Consensus size: 108
1481585 CTTTTTTTAC
* ** *
1481595 ATAAAGGCAATGTTCTGTTTTTTGGGATTCGAAAGATAGTGCCCTACTTGCTGGGTTTCGATTTT
1 ATAAAGGCAATATTCACTTTTTTGGGATTCGAAAGATAGTGCCCTACGTGCTGGGTTTCGATTTT
*
1481660 TCTCGTTTGACCCAAATAATCGAATAACCTTTTAAAGTTCTAA
66 TCTCGTTTGACCCAAATAACCGAATAACCTTTTAAAGTTCTAA
*
1481703 ATAAAGGCAATATTCCACTTTTTT-GGATTCGAAAGATTGTGCCCTACGTGCTGGGTTGT-GATT
1 ATAAAGGCAATATT-CACTTTTTTGGGATTCGAAAGATAGTGCCCTACGTGCTGGGTT-TCGATT
*
1481766 TGTT-TCGTTTGACCCAAATAACCGAATAGCCTTTTAAA
64 T-TTCTCGTTTGACCCAAATAACCGAATAACCTTTTAAA
1481804 ATTTCAATGT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
108 81 0.89
109 10 0.11
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (108 bp):
ATAAAGGCAATATTCACTTTTTTGGGATTCGAAAGATAGTGCCCTACGTGCTGGGTTTCGATTTT
TCTCGTTTGACCCAAATAACCGAATAACCTTTTAAAGTTCTAA
Found at i:1483197 original size:29 final size:27
Alignment explanation
Indices: 1483131--1483197 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 27
1483121 TTTTACCTAT
* *
1483131 TTAGTATCTAAACTTTTTGTTATCTAA
1 TTAGTACCTAAACTTTTTGTTAACTAA
* *
1483158 TTGGTAGCTAAA-TTTTTGTTCAGACGTAA
1 TTAGTACCTAAACTTTTTGTT-A-AC-TAA
1483187 TTAGTACCTAA
1 TTAGTACCTAA
1483198 TCTTAAAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 8 0.25
27 11 0.34
28 1 0.03
29 12 0.38
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (27 bp):
TTAGTACCTAAACTTTTTGTTAACTAA
Found at i:1486505 original size:25 final size:25
Alignment explanation
Indices: 1486432--1486493 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
1486422 TTGGTCCTTA
1486432 TTTTTTTCATTTTGAGCAATTTAAT
1 TTTTTTTCATTTTGAGCAATTTAAT
1486457 TTTTTTTCATTTTGAGCAATTTAAT
1 TTTTTTTCATTTTGAGCAATTTAAT
1486482 TTTTTTT-ATTTT
1 TTTTTTTCATTTT
1486494 ATGCTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.14
25 32 0.86
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTTTTTCATTTTGAGCAATTTAAT
Found at i:1487365 original size:31 final size:31
Alignment explanation
Indices: 1487327--1487389 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1487317 AGGTCCTTGT
1487327 ATTATAGGGACTAGATCAAATTAATATTTAC
1 ATTATAGGGACTAGATCAAATTAATATTTAC
1487358 ATTATAGGGACTAGATCAAATTAATATTTAC
1 ATTATAGGGACTAGATCAAATTAATATTTAC
1487389 A
1 A
1487390 GAACCATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
ATTATAGGGACTAGATCAAATTAATATTTAC
Found at i:1489100 original size:31 final size:31
Alignment explanation
Indices: 1489063--1489169 Score: 160
Period size: 31 Copynumber: 3.5 Consensus size: 31
1489053 TTTGAGTGAC
*
1489063 TGATTTGTTACTTTCCAAAAATGTTAGTAAT
1 TGATTTGTTACTTTCCAAAAACGTTAGTAAT
*
1489094 TGATTTGTTACTTTCTAAAAACGTTAGTAAT
1 TGATTTGTTACTTTCCAAAAACGTTAGTAAT
* * * *
1489125 TGATTTGTTACTTTTCATAAACGTTAATAAC
1 TGATTTGTTACTTTCCAAAAACGTTAGTAAT
1489156 TGATTTGTTACTTT
1 TGATTTGTTACTTT
1489170 TGAAAATTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (31 bp):
TGATTTGTTACTTTCCAAAAACGTTAGTAAT
Found at i:1496459 original size:17 final size:17
Alignment explanation
Indices: 1496437--1496469 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1496427 TTATATACTA
1496437 TTGGAGCGAGTAATGGG
1 TTGGAGCGAGTAATGGG
1496454 TTGGAGCGAGTAATGG
1 TTGGAGCGAGTAATGG
1496470 ATAATACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.45, T:0.24
Consensus pattern (17 bp):
TTGGAGCGAGTAATGGG
Found at i:1501718 original size:98 final size:98
Alignment explanation
Indices: 1501547--1501805 Score: 356
Period size: 98 Copynumber: 2.6 Consensus size: 98
1501537 GTACCTCGAC
* * *
1501547 TTTTACAATATCATTGATTAACTCAAATACTTTATTTTGATTAAGACGTTGATGTAACTTTTAAG
1 TTTTATAATATCATTGATTAGCTCAAATACTTTATTTTGATTAAAACGTTGATGTAACTTTTAAG
* * ***
1501612 AATTGTATTTTTGACATAATTTAGTAATTTAAT
66 AATAGTATTTTTGACAAAATTTAGTAACACAAT
*
1501645 TTTTATAATATCATTGATTAGCTCAAATACTTTATTTTGATTAAAACGTTGATGTAACTTTTAAT
1 TTTTATAATATCATTGATTAGCTCAAATACTTTATTTTGATTAAAACGTTGATGTAACTTTTAAG
* * * *
1501710 AGTAGTATTTTTGACAAAATTTGGTACCACGAT
66 AATAGTATTTTTGACAAAATTTAGTAACACAAT
* * ** *
1501743 TTTTATAATATCATTGATTGGCCCAAATACTTTATTTTGATTAAAATATTGATATAACTTTTA
1 TTTTATAATATCATTGATTAGCTCAAATACTTTATTTTGATTAAAACGTTGATGTAACTTTTA
1501806 CGAGTTGTAA
Statistics
Matches: 143, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 143 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (98 bp):
TTTTATAATATCATTGATTAGCTCAAATACTTTATTTTGATTAAAACGTTGATGTAACTTTTAAG
AATAGTATTTTTGACAAAATTTAGTAACACAAT
Found at i:1504684 original size:50 final size:50
Alignment explanation
Indices: 1504560--1504808 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
1504550 GATAATAACA
* * ** * *
1504560 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * *
1504611 TGCCCATGTCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1504661 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
1504711 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
1504766 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
1504809 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1504739 original size:100 final size:104
Alignment explanation
Indices: 1504559--1504808 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
1504549 TGATAATAAC
** *
1504559 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGTCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
1504624 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
1504661 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
1504724 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
1504766 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1504809 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:1504924 original size:13 final size:13
Alignment explanation
Indices: 1504903--1504934 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1504893 GCTTGGATCA
*
1504903 TCATCAAATAAAT
1 TCATAAAATAAAT
1504916 TCATAAAATAAAT
1 TCATAAAATAAAT
1504929 TCATAA
1 TCATAA
1504935 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1505181 original size:30 final size:30
Alignment explanation
Indices: 1505145--1505202 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1505135 CCTCGACTCT
*
1505145 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
1505175 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
1505203 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:1510908 original size:12 final size:12
Alignment explanation
Indices: 1510891--1510922 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1510881 ATCCCGAAAA
1510891 CGACGACGTTTC
1 CGACGACGTTTC
1510903 CGACGACGTTTC
1 CGACGACGTTTC
1510915 CGACGACG
1 CGACGACG
1510923 ACGATGATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.34, G:0.28, T:0.19
Consensus pattern (12 bp):
CGACGACGTTTC
Found at i:1519098 original size:25 final size:24
Alignment explanation
Indices: 1519042--1519103 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1519032 ACCAAACTTA
* * *
1519042 AGTACTAAATTTAGATAAAAATTC
1 AGTACCAAATTGAGACAAAAATTC
1519066 AGTACCAAATTGAGACAAAAATTC
1 AGTACCAAATTGAGACAAAAATTC
* *
1519090 TGGTGCCAAATTGA
1 -AGTACCAAATTGA
1519104 ATACTGAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (24 bp):
AGTACCAAATTGAGACAAAAATTC
Found at i:1529014 original size:25 final size:25
Alignment explanation
Indices: 1528986--1529043 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1528976 AAGCTTTTTC
**
1528986 GAGCCATATAACAG-GAAGCTCATGT
1 GAGCCATATAAC-GTGAAGCTCATAA
*
1529011 GAGCCATGTAACGTGAAGCTCATAA
1 GAGCCATATAACGTGAAGCTCATAA
1529036 GAGCCATA
1 GAGCCATA
1529044 ATCGGAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 1 0.04
25 27 0.96
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGTGAAGCTCATAA
Found at i:1529103 original size:25 final size:24
Alignment explanation
Indices: 1529075--1529139 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 24
1529065 AATATCGGGT
*
1529075 AGCTCCAGAGAGCTATTAATCAGGA
1 AGCTCCAGAGAGCT-TTAATCAGAA
* *
1529100 AGCTCATGAGAGAGCCTTTTATCAGAA
1 AGCTC--CAGAGAG-CTTTAATCAGAA
1529127 AGCTCCAGAGAGC
1 AGCTCCAGAGAGC
1529140 CAATCATCGG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
24 1 0.03
25 11 0.33
27 19 0.58
28 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20
Consensus pattern (24 bp):
AGCTCCAGAGAGCTTTAATCAGAA
Found at i:1529238 original size:25 final size:25
Alignment explanation
Indices: 1529011--1529230 Score: 133
Period size: 25 Copynumber: 8.8 Consensus size: 25
1529001 AAGCTCATGT
* *
1529011 GAGCCATGTAA-CGTGAAGCTCATAA
1 GAGCCAT-TAATCGGGAAGCTCAAAA
* * ***
1529036 GAGCCA-TAATCGGAAAACTCATGC
1 GAGCCATTAATCGGGAAGCTCAAAA
* * * *
1529060 GAGCCAAT-ATCGGGTAGCTCCAGA
1 GAGCCATTAATCGGGAAGCTCAAAA
* * *
1529084 GAGCTATTAATCAGGAAGCTCATGAGA
1 GAGCCATTAATCGGGAAGCTCA--AAA
* * * * * *
1529111 GAGCCTTTTATCAGAAAGCTCCAGA
1 GAGCCATTAATCGGGAAGCTCAAAA
* * * *
1529136 GAGCCAATCATCGGGAAGCTCATAT
1 GAGCCATTAATCGGGAAGCTCAAAA
* * *
1529161 GAGCCA-TAAACGGAAAGCTTAAAA
1 GAGCCATTAATCGGGAAGCTCAAAA
1529185 GAGCCATTAATCGGGAAGCTCAAAA
1 GAGCCATTAATCGGGAAGCTCAAAA
*
1529210 GAGCCATTAATCTGGAAGCTC
1 GAGCCATTAATCGGGAAGCTC
1529231 GTGTGAGCTA
Statistics
Matches: 149, Mismatches: 40, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
23 3 0.02
24 49 0.33
25 77 0.52
27 20 0.13
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCAAAA
Found at i:1535348 original size:15 final size:16
Alignment explanation
Indices: 1535317--1535349 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1535307 TAAGAATTTT
*
1535317 TTTATTTTAATGTAAA
1 TTTATTGTAATGTAAA
1535333 TTTATTGTAA-GTAAA
1 TTTATTGTAATGTAAA
1535348 TT
1 TT
1535350 GTTCTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
TTTATTGTAATGTAAA
Found at i:1544078 original size:23 final size:23
Alignment explanation
Indices: 1544052--1544096 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1544042 CTGGAAGGAT
1544052 TGTTTTTGGTTTATAAGGCTAAG
1 TGTTTTTGGTTTATAAGGCTAAG
1544075 TGTTTTTGGTTTATAAGGCTAA
1 TGTTTTTGGTTTATAAGGCTAA
1544097 TACTTTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.49
Consensus pattern (23 bp):
TGTTTTTGGTTTATAAGGCTAAG
Found at i:1545629 original size:30 final size:30
Alignment explanation
Indices: 1545571--1545630 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1545561 TTCCCGAGCC
*
1545571 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATACAAAAGTT
* *
1545601 TAGGGGCAAAA-TGGTAATTTTACCAAAGTT
1 TAGGGGCAAAAGT-GTAATTATACAAAAGTT
1545631 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAATTATACAAAAGTT
Found at i:1549850 original size:11 final size:11
Alignment explanation
Indices: 1549834--1549858 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1549824 AGTTGAATCT
1549834 AAAAAAAATTA
1 AAAAAAAATTA
1549845 AAAAAAAATTA
1 AAAAAAAATTA
1549856 AAA
1 AAA
1549859 TACTCACTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:1550067 original size:20 final size:21
Alignment explanation
Indices: 1550044--1550090 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1550034 CTTCTCCTTC
*
1550044 TTCTTCTTCT-CTTCTTTCTT
1 TTCTTCTTCTCCCTCTTTCTT
1550064 TTCTTCTTCTCCCTCTTTCTT
1 TTCTTCTTCTCCCTCTTTCTT
1550085 TTCTTC
1 TTCTTC
1550091 ATCCCGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCTTCTTCTCCCTCTTTCTT
Found at i:1550201 original size:27 final size:27
Alignment explanation
Indices: 1550163--1550221 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1550153 GTGCATGAGG
*
1550163 CCAGTGCCGCCTGTGGCAGGCACACCA
1 CCAGTGCCGCCTGTGGAAGGCACACCA
1550190 CCAGTGCCGCCTGTGGAAGGCACACCA
1 CCAGTGCCGCCTGTGGAAGGCACACCA
1550217 CCAGT
1 CCAGT
1550222 TCCAGCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.20, C:0.39, G:0.29, T:0.12
Consensus pattern (27 bp):
CCAGTGCCGCCTGTGGAAGGCACACCA
Found at i:1550253 original size:19 final size:19
Alignment explanation
Indices: 1550224--1550278 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
1550214 CCACCAGTTC
1550224 CAGCTTTTTTTTTTCAGATT
1 CAGC-TTTTTTTTTCAGATT
*
1550244 CAGCTTTTTTTTTCAAATT
1 CAGCTTTTTTTTTCAGATT
*
1550263 CAGCCTTTTTTTTCAG
1 CAGCTTTTTTTTTCAG
1550279 TTTTTTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 28 0.88
20 4 0.12
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.56
Consensus pattern (19 bp):
CAGCTTTTTTTTTCAGATT
Found at i:1558995 original size:14 final size:14
Alignment explanation
Indices: 1558965--1558994 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1558955 TTATTAAGGT
1558965 AATTGTTAAATAAA
1 AATTGTTAAATAAA
1558979 AATTAGTTAAATAAA
1 AATT-GTTAAATAAA
1558994 A
1 A
1558995 TAAAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
AATTGTTAAATAAA
Found at i:1559825 original size:39 final size:40
Alignment explanation
Indices: 1559760--1559894 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
1559750 ATTGATTATT
** *
1559760 TATGGCACTTAGTGTGCGATACGACATAGCTTCGATTATA
1 TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
*
1559800 TATGGCAC-TAGTGTGCGATTTGACATAGCTTCGGCTATA
1 TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
* * * * *
1559839 TATAGCACTTAGTGTGCGATTTGAGATAGTTTCGGCTATG
1 TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
1559879 TATGGCACTTAGTGTG
1 TATGGCACTTAGTGTG
1559895 TGAGATATCG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 34 0.40
40 51 0.60
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (40 bp):
TATGGCACTTAGTGTGCGATTTGACATAGCTTCGACTATA
Found at i:1559936 original size:28 final size:28
Alignment explanation
Indices: 1559878--1559937 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1559868 TTTCGGCTAT
* *
1559878 GTATGGCACTTAGTGTGTGAGATATCGA
1 GTATGGCACTTAGTGTGTGAGACATCAA
*
1559906 GTATGGCACTTAGTGTGCT-AGACATTAA
1 GTATGGCACTTAGTGTG-TGAGACATCAA
1559934 GTAT
1 GTAT
1559938 TCAACGACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
GTATGGCACTTAGTGTGTGAGACATCAA
Found at i:1561906 original size:42 final size:42
Alignment explanation
Indices: 1561859--1562006 Score: 165
Period size: 42 Copynumber: 3.4 Consensus size: 42
1561849 CATAGTTCAA
*
1561859 CTATGGTCTTACACATCTTCACATAAT-GAAGCTATAGCCCAG
1 CTATGGTCTTACACATCTTCACAT-ATCGATGCTATAGCCCAG
* *
1561901 CTATGGTCTTACACATATTCATATATCGATG-TCATAGCCCAG
1 CTATGGTCTTACACATCTTCACATATCGATGCT-ATAGCCCAG
*
1561943 CTATGGTCTTACACGTAATCACATATCACATATCGATGCCATAGCCCAG
1 CTATGGTCTTACAC---AT--C-T-TCACATATCGATGCTATAGCCCAG
1561992 CTATGGTCTTACACA
1 CTATGGTCTTACACA
1562007 AATCATATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 16
0.80 0.05 0.14
Matches are distributed among these distances:
41 3 0.03
42 48 0.53
45 2 0.02
46 1 0.01
48 1 0.01
49 35 0.39
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
CTATGGTCTTACACATCTTCACATATCGATGCTATAGCCCAG
Found at i:1562104 original size:31 final size:31
Alignment explanation
Indices: 1562069--1562186 Score: 166
Period size: 31 Copynumber: 3.8 Consensus size: 31
1562059 CTTGTCACTT
* *
1562069 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1562100 GTAGCCGGTA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
* *
1562131 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
1562162 GTAGCCGAAGTTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
1562187 TGTCATTGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.03
31 74 0.96
32 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:1562230 original size:44 final size:44
Alignment explanation
Indices: 1562162--1562331 Score: 189
Period size: 50 Copynumber: 3.6 Consensus size: 44
1562152 CACTGATCAG
* * *
1562162 GTAGCCGAAGTTACCACTTTTCACTTGTCA-TTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGATCAGATAAGT
1562206 GTAGCCGAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCA----T--TTGATCAGATAAGT
1562256 GTAGCCGAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCA----T--TTGATCAGATAAGT
1562306 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
1562332 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
43 3 0.03
44 23 0.20
50 90 0.78
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (44 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGATCAGATAAGT
Found at i:1562252 original size:50 final size:50
Alignment explanation
Indices: 1562180--1562331 Score: 286
Period size: 50 Copynumber: 3.0 Consensus size: 50
1562170 AGTTACCACT
* *
1562180 TTTCACTTGTCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
1 TTTCACTTTTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
1562230 TTTCACTTTTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
1 TTTCACTTTTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
1562280 TTTCACTTTTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
1 TTTCACTTTTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
1562330 TT
1 TT
1562332 GTTGCCATGG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (50 bp):
TTTCACTTTTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC
Found at i:1564687 original size:39 final size:39
Alignment explanation
Indices: 1564632--1564762 Score: 183
Period size: 39 Copynumber: 3.3 Consensus size: 39
1564622 GTATGAGATT
1564632 GAAAATATATCCGGACATGAAGTCCGCAGGCTATATGCTG
1 GAAAA-ATATCCGGACATGAAGTCCGCAGGCTATATGCTG
*
1564672 GAAAAATATCCGGACATG-AGATCCGCAGGCTATATGCTA
1 GAAAAATATCCGGACATGAAG-TCCGCAGGCTATATGCTG
* * * **
1564711 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTG
1 GAAAAATATCCGGACATGAAGTCCGCAGGCTATATGCTG
1564750 GAAAAATATCCGG
1 GAAAAATATCCGG
1564763 GTTAAAAACC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.02
39 73 0.90
40 6 0.07
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (39 bp):
GAAAAATATCCGGACATGAAGTCCGCAGGCTATATGCTG
Found at i:1564776 original size:78 final size:77
Alignment explanation
Indices: 1564634--1564788 Score: 204
Period size: 78 Copynumber: 2.0 Consensus size: 77
1564624 ATGAGATTGA
* * * *
1564634 AAATATATCCGGACATGAAGTCCGCAGGCTATATGCTGGAAAAATATCCGGACATGAGATCCGCA
1 AAATATATCCGGACATGAAGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAAACCCGCA
1564699 GGCTATATGCTAG
66 GGCT-TATGCTAG
* * * **
1564712 AAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAAACCCGC
1 AAATATATCCGGACATGAAGTCCGCAGGCTACATGCTGGAAAAATATCCGGACAT-AAAACCCGC
1564776 AGGCTTATGCTAG
65 AGGCTTATGCTAG
1564789 TAATGTATTC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 9 0.13
78 58 0.87
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (77 bp):
AAATATATCCGGACATGAAGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAAACCCGCA
GGCTTATGCTAG
Found at i:1581203 original size:39 final size:39
Alignment explanation
Indices: 1581148--1581278 Score: 174
Period size: 39 Copynumber: 3.3 Consensus size: 39
1581138 GTATGAGATT
*
1581148 GAAAATATATCCGGACATGAAGTCCGCAGGCTATATGCTG
1 GAAAA-ATATCCGGACATGAAGTCCGCAGGCTATGTGCTG
* *
1581188 GAAAAATATCCGGACATG-AGATCCGTAGGCTATGTGCTA
1 GAAAAATATCCGGACATGAAG-TCCGCAGGCTATGTGCTG
* * * *
1581227 GAAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTG
1 GAAAAATATCCGGACATGAAGTCCGCAGGCTATGTGCTG
1581266 GAAAAATATCCGG
1 GAAAAATATCCGG
1581279 GTTAAAAACC
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.03
39 71 0.90
40 6 0.08
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (39 bp):
GAAAAATATCCGGACATGAAGTCCGCAGGCTATGTGCTG
Found at i:1581296 original size:78 final size:77
Alignment explanation
Indices: 1581150--1581304 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 77
1581140 ATGAGATTGA
* * * * *
1581150 AAATATATCCGGACATGAAGTCCGCAGGCTATATGCTGGAAAAATATCCGGACATGAGATCCGTA
1 AAATATATCCGGACATGAAGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAAACCCGCA
*
1581215 GGCTATGTGCTAG
66 GGCT-TATGCTAG
* * * **
1581228 AAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAAAATATCCGG-GTTAAAAACCCGC
1 AAATATATCCGGACATGAAGTCCGCAGGCTACATGCTGGAAAAATATCCGGACAT-AAAACCCGC
1581292 AGGCTTATGCTAG
65 AGGCTTATGCTAG
1581305 TAATGTATTC
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
77 8 0.12
78 57 0.88
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (77 bp):
AAATATATCCGGACATGAAGTCCGCAGGCTACATGCTGGAAAAATATCCGGACATAAAACCCGCA
GGCTTATGCTAG
Found at i:1581497 original size:2 final size:2
Alignment explanation
Indices: 1581492--1581535 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1581482 ACGATATATA
1581492 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1581534 TG
1 TG
1581536 AATGAATTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1590203 original size:29 final size:30
Alignment explanation
Indices: 1590166--1590224 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1590156 TTATGTTTAA
*
1590166 TGTGCAATTGTATACAT-AAATTTTGATTT
1 TGTGCAATTGTATACATGAAATCTTGATTT
* *
1590195 TGTGTAATTTTATACATGAAATCTTGATTT
1 TGTGCAATTGTATACATGAAATCTTGATTT
1590225 GATTTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATCTTGATTT
Found at i:1590736 original size:42 final size:42
Alignment explanation
Indices: 1590664--1590745 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 42
1590654 AAATTATTTT
*
1590664 ATATATTTAATGAATTTTTAAATTCGAACAAATTAATATCCCA
1 ATATATTTAATGAA-TTTTAAATTCAAACAAATTAATATCCCA
*
1590707 ATATATTTAATGAGA-TTTAAATTTAAACAAATTAATATC
1 ATATATTTAATGA-ATTTTAAATTCAAACAAATTAATATC
1590746 AATCTAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 22 0.61
43 13 0.36
44 1 0.03
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (42 bp):
ATATATTTAATGAATTTTAAATTCAAACAAATTAATATCCCA
Found at i:1597581 original size:25 final size:23
Alignment explanation
Indices: 1597545--1597591 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1597535 GACGATAGTA
*
1597545 CTATATATACACACATATGGTTT
1 CTATATATACACACAAATGGTTT
1597568 CTATATATACACACAAATGGTTT
1 CTATATATACACACAAATGGTTT
1597591 C
1 C
1597592 CATGAATTAA
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:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (23 bp):
CTATATATACACACAAATGGTTT
Found at i:1601116 original size:2 final size:2
Alignment explanation
Indices: 1601109--1601133 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1601099 AAATGCCCCA
1601109 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1601134 TCCATCACCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1618311 original size:30 final size:30
Alignment explanation
Indices: 1618277--1618338 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1618267 TATTCCTTAA
* *
1618277 GTATTTTACATTACTTAGGTATTTTACTTG
1 GTATTTAACATTACTTAAGTATTTTACTTG
1618307 GTATTTAACATTACTTAAGTATTTTACTTG
1 GTATTTAACATTACTTAAGTATTTTACTTG
1618337 GT
1 GT
1618339 CTCCGGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (30 bp):
GTATTTAACATTACTTAAGTATTTTACTTG
Found at i:1621880 original size:30 final size:29
Alignment explanation
Indices: 1621831--1621892 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
1621821 ACTTAACAAG
1621831 CAAATGCTTCTAAAATAATAACAAAATTAA
1 CAAATGCTTCTAAAATAATAA-AAAATTAA
*
1621861 CAAATGTCTT-TAAAGTAATAAAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAATTAA
1621890 CAA
1 CAA
1621893 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.37
30 16 0.53
31 3 0.10
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.27
Consensus pattern (29 bp):
CAAATGCTTCTAAAATAATAAAAAATTAA
Found at i:1621947 original size:22 final size:22
Alignment explanation
Indices: 1621921--1621969 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1621911 ATATTCAAAC
1621921 AATAACAATAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
* * *
1621943 CATAATAGTAAAATAGTAGCAA
1 AATAACAATAAAATAGTAGCAA
1621965 AATAA
1 AATAA
1621970 GGAGAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.61, C:0.08, G:0.10, T:0.20
Consensus pattern (22 bp):
AATAACAATAAAATAGTAGCAA
Found at i:1621968 original size:11 final size:11
Alignment explanation
Indices: 1621930--1621968 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1621920 CAATAACAAT
1621930 AAAATAGTAGC
1 AAAATAGTAGC
* * *
1621941 AACATAATAGT
1 AAAATAGTAGC
1621952 AAAATAGTAGC
1 AAAATAGTAGC
1621963 AAAATA
1 AAAATA
1621969 AGGAGAAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (11 bp):
AAAATAGTAGC
Found at i:1622400 original size:15 final size:15
Alignment explanation
Indices: 1622359--1622403 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1622349 CATACAAGTG
1622359 CATCTAGGGTTCACA
1 CATCTAGGGTTCACA
* * * *
1622374 CATTTCGAGTTCGCA
1 CATCTAGGGTTCACA
1622389 CATCTAGGGTTCACA
1 CATCTAGGGTTCACA
1622404 TGTATAGAGT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (15 bp):
CATCTAGGGTTCACA
Found at i:1622531 original size:23 final size:23
Alignment explanation
Indices: 1622504--1622560 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
1622494 AAATAACATA
1622504 TAGGGTTCGCATATTAGTGCATG
1 TAGGGTTCGCATATTAGTGCATG
1622527 TAGGGTTCGCATATTAGTGCATG
1 TAGGGTTCGCATATTAGTGCATG
*
1622550 TAGGATTCGCA
1 TAGGGTTCGCA
1622561 AGTTATACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (23 bp):
TAGGGTTCGCATATTAGTGCATG
Found at i:1622539 original size:45 final size:46
Alignment explanation
Indices: 1622431--1622539 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 46
1622421 AATTAGGGTT
* * *
1622431 TGCATATAGAGTTCGCA-AAATAAACAAATAGGGTTTGCATATTCC
1 TGCATGTAGAGTTCGCATAAATAAACAAATAGGGTTCGCATATTAC
* * * *
1622476 TGCAAGTAGAGTTTGCATAAAT-AACATATAGGGTTCGCATATTAG
1 TGCATGTAGAGTTCGCATAAATAAACAAATAGGGTTCGCATATTAC
*
1622521 TGCATGTAGGGTTCGCATA
1 TGCATGTAGAGTTCGCATA
1622540 TTAGTGCATG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 49 0.92
46 4 0.08
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (46 bp):
TGCATGTAGAGTTCGCATAAATAAACAAATAGGGTTCGCATATTAC
Found at i:1622735 original size:29 final size:29
Alignment explanation
Indices: 1622701--1622788 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
1622691 TAGGAGGTCA
*
1622701 CCTATAGGGATTCACATACATGAGGCTCG
1 CCTATAGGGATTCACATACATGGGGCTCG
* * *
1622730 CCTATAGGTG-TTCACATACAGGGGGTTTG
1 CCTATAGG-GATTCACATACATGGGGCTCG
* *
1622759 CCTATAAGGATTCGCATACATGGGGCTCG
1 CCTATAGGGATTCACATACATGGGGCTCG
1622788 C
1 C
1622789 ATACAGGGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
28 1 0.02
29 46 0.96
30 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (29 bp):
CCTATAGGGATTCACATACATGGGGCTCG
Found at i:1625478 original size:3 final size:3
Alignment explanation
Indices: 1625470--1625506 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1625460 CTTATAATGC
1625470 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1625507 GTGGAACACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1626557 original size:29 final size:29
Alignment explanation
Indices: 1626503--1626559 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1626493 ATGGGGCTCG
*
1626503 CCTATAGGTGTTCGCATACAGGGGGTTTT
1 CCTATAGGTGTTCGCATACAGAGGGTTTT
*
1626532 CCTATAAGGT-TTCGCATACATAGGGTTT
1 CCTAT-AGGTGTTCGCATACAGAGGGTTT
1626560 GCATACGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (29 bp):
CCTATAGGTGTTCGCATACAGAGGGTTTT
Found at i:1626582 original size:30 final size:30
Alignment explanation
Indices: 1626542--1626608 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1626532 CCTATAAGGT
* * *
1626542 TTCGCATACATAGGGTTTGCATACGGGGGG
1 TTCGTATACATAAGGTTCGCATACGGGGGG
1626572 TTCGTATACATAAGGTTCGCATACGGGGGG
1 TTCGTATACATAAGGTTCGCATACGGGGGG
1626602 TTCGTAT
1 TTCGTAT
1626609 GTACAGATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (30 bp):
TTCGTATACATAAGGTTCGCATACGGGGGG
Found at i:1628447 original size:11 final size:13
Alignment explanation
Indices: 1628417--1628445 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1628407 TTGTTATTAA
1628417 TTTTTATGAATTT
1 TTTTTATGAATTT
1628430 TTTTTAT-AATTT
1 TTTTTATGAATTT
1628442 TTTT
1 TTTT
1628446 ATTTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTTATGAATTT
Found at i:1629136 original size:7 final size:7
Alignment explanation
Indices: 1629124--1629184 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
1629114 TCCAGATCCA
1629124 TAGGGTT
1 TAGGGTT
1629131 TAGGGTT
1 TAGGGTT
*
1629138 TTGGAGTT
1 TAGG-GTT
*
1629146 TATGGTT
1 TAGGGTT
*
1629153 TAGAGTT
1 TAGGGTT
*
1629160 TTGGGTT
1 TAGGGTT
*
1629167 TAAGGTT
1 TAGGGTT
1629174 TAGGGTT
1 TAGGGTT
1629181 TAGG
1 TAGG
1629185 ATTCAAGACT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 38 0.88
8 5 0.12
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (7 bp):
TAGGGTT
Found at i:1629173 original size:21 final size:22
Alignment explanation
Indices: 1629127--1629181 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
1629117 AGATCCATAG
*
1629127 GGTTTAGGGTTTTGGAGTTTAT
1 GGTTTAGGGTTTTGGAGTTTAA
*
1629149 GGTTTAGAGTTTTGG-GTTTAA
1 GGTTTAGGGTTTTGGAGTTTAA
1629170 GGTTTAGGGTTT
1 GGTTTAGGGTTT
1629182 AGGATTCAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (22 bp):
GGTTTAGGGTTTTGGAGTTTAA
Found at i:1629704 original size:18 final size:19
Alignment explanation
Indices: 1629668--1629704 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1629658 AAAAATAAAA
1629668 TTTATATTTATATTATTTT
1 TTTATATTTATATTATTTT
1629687 TTTA-ATTTAGTATT-TTTT
1 TTTATATTTA-TATTATTTT
1629705 AATTATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTATATTTATATTATTTT
Found at i:1631876 original size:19 final size:19
Alignment explanation
Indices: 1631827--1631878 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1631817 TAGCCCATTG
1631827 TTTT-TAATATTAAACAATA
1 TTTTATAATA-TAAACAATA
*
1631846 TTTTATATTATAAACAATA
1 TTTTATAATATAAACAATA
1631865 TTTGTA-AATATAAA
1 TTT-TATAATATAAA
1631879 GTAAATTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTTATAATATAAACAATA
Found at i:1637004 original size:22 final size:22
Alignment explanation
Indices: 1636974--1637018 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1636964 TATTTTTATA
*
1636974 TTATCAAATTACATTATT-GCCC
1 TTAT-AAAATACATTATTAGCCC
*
1636996 TTATAAAATATATTATTAGCCC
1 TTATAAAATACATTATTAGCCC
1637018 T
1 T
1637019 AAGCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (22 bp):
TTATAAAATACATTATTAGCCC
Found at i:1643998 original size:30 final size:30
Alignment explanation
Indices: 1643962--1644024 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
1643952 AGCTACCACA
*
1643962 AAAGTATTCATTTACTTTGATTGAAGACAT
1 AAAGTATCCATTTACTTTGATTGAAGACAT
1643992 AAAGTATCCATTTACTTTGATTGAAGACAT
1 AAAGTATCCATTTACTTTGATTGAAGACAT
1644022 AAA
1 AAA
1644025 TGATTCAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (30 bp):
AAAGTATCCATTTACTTTGATTGAAGACAT
Found at i:1649645 original size:6 final size:6
Alignment explanation
Indices: 1649634--1649675 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
1649624 ATAAATAATA
1649634 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
1649676 TTGGTATCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:1651525 original size:30 final size:30
Alignment explanation
Indices: 1651489--1651546 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1651479 TTTTTTGTCA
*
1651489 TAAGTGATGCCTAAATTATACTT-TGTTACC
1 TAAGTGATACCTAAATTATA-TTATGTTACC
*
1651519 TAAGTGATACTTAAATTATATTATGTTA
1 TAAGTGATACCTAAATTATATTATGTTA
1651547 TCCAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (30 bp):
TAAGTGATACCTAAATTATATTATGTTACC
Found at i:1652109 original size:26 final size:22
Alignment explanation
Indices: 1652074--1652125 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
1652064 AAATTGAAAA
1652074 TTTTAAATTTAATTATATATATATT
1 TTTTAAATTTAATT-TA-AT-TATT
*
1652099 TTTTATAATTTAGTTTAATTATT
1 TTTTA-AATTTAATTTAATTATT
1652122 TTTT
1 TTTT
1652126 TTTCAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 8 0.32
24 2 0.08
25 7 0.28
26 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTAAATTTAATTTAATTATT
Found at i:1658295 original size:31 final size:31
Alignment explanation
Indices: 1658257--1658321 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1658247 ACTTACTAAT
1658257 GACTAATTTGAATCATTCCCTATAATAAAAG
1 GACTAATTTGAATCATTCCCTATAATAAAAG
1658288 GACTAATTTGAATCATTCCCTATAATAAAAG
1 GACTAATTTGAATCATTCCCTATAATAAAAG
1658319 GAC
1 GAC
1658322 CTGACAGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (31 bp):
GACTAATTTGAATCATTCCCTATAATAAAAG
Found at i:1659880 original size:12 final size:14
Alignment explanation
Indices: 1659863--1659907 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
1659853 AAAATTATTG
1659863 TATATTTA-ATAT-
1 TATATTTATATATA
1659875 TATATTTATATATA
1 TATATTTATATATA
*
1659889 TATATATATATATA
1 TATATTTATATATA
*
1659903 CATAT
1 TATAT
1659908 ATTCTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 8 0.28
13 4 0.14
14 17 0.59
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATTTATATATA
Found at i:1659888 original size:2 final size:2
Alignment explanation
Indices: 1659871--1659909 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1659861 TGTATATTTA
* *
1659871 AT AT -T AT AT TT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1659910 TCTTTTTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1665098 original size:16 final size:17
Alignment explanation
Indices: 1665067--1665099 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1665057 ATCTTTTCTT
*
1665067 AAATATAATAATTAAAA
1 AAATAAAATAATTAAAA
1665084 AAATAAAAT-ATTAAAA
1 AAATAAAATAATTAAAA
1665100 CAATTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAAATAATTAAAA
Found at i:1665574 original size:18 final size:20
Alignment explanation
Indices: 1665550--1665595 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
1665540 AGCTGAACTA
*
1665550 ATTTTATTTATATTTTT-AT
1 ATTTTATTTAGATTTTTAAT
1665569 -TTTTA--TAGATTTTTAAT
1 ATTTTATTTAGATTTTTAAT
1665586 ATTTTATTTA
1 ATTTTATTTA
1665596 ATCGAACCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 10 0.45
20 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTATTTAGATTTTTAAT
Found at i:1666610 original size:6 final size:7
Alignment explanation
Indices: 1666583--1666609 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1666573 CAAAATTTGG
1666583 ATTTTTT
1 ATTTTTT
1666590 ATTTTTT
1 ATTTTTT
1666597 ATTTTTT
1 ATTTTTT
1666604 ATTTTT
1 ATTTTT
1666610 AGAATTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:1676533 original size:11 final size:11
Alignment explanation
Indices: 1676519--1676559 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1676509 TATTTTCTCC
1676519 CTATTTTGCTA
1 CTATTTTGCTA
*
1676530 CTATTTTACTA
1 CTATTTTGCTA
* *
1676541 TTATGTTGCTA
1 CTATTTTGCTA
1676552 CTATTTTG
1 CTATTTTG
1676560 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:1682531 original size:62 final size:60
Alignment explanation
Indices: 1682421--1682587 Score: 160
Period size: 62 Copynumber: 2.8 Consensus size: 60
1682411 CTGCAGTATT
* * * * *
1682421 AGTCACCCAACTGTTAGTAAATTTCTTTTTTGGTTATCTAACTATGAAAAGTTACAAAAA
1 AGTCACTCAACTATTAGTAAATTTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAAA
* * * *
1682481 ATGATCACTCGACTATTAGTGAATTTC-TTTTTGAGTCACCCAACTATGAAAATTTACAAAAT
1 A-G-TCACTCAACTATTAGTAAATTTCTTTTTTG-GTCACCCAACTATGAAAAGTTACAAAAA
** *
1682543 AGTCACTCAACTATTCA--ATTTTATCTTTTTTGGTCACCCGACTAT
1 AGTCACTCAACTATT-AGTAAATT-TCTTTTTTGGTCACCCAACTAT
1682588 CTTAGATTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
59 2 0.02
60 27 0.31
61 15 0.17
62 43 0.49
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (60 bp):
AGTCACTCAACTATTAGTAAATTTCTTTTTTGGTCACCCAACTATGAAAAGTTACAAAAA
Found at i:1700897 original size:31 final size:31
Alignment explanation
Indices: 1700862--1700933 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
1700852 ACTTTTAGTA
* *
1700862 TTTGAACTCGATAATTAAGTTCACTTTGGTC
1 TTTGAACTCGACAATTAAATTCACTTTGGTC
* * *
1700893 TTTGAATTTC-ACAATTAAATTTATTTTGGTC
1 TTTGAA-CTCGACAATTAAATTCACTTTGGTC
*
1700924 ATTGAACTCG
1 TTTGAACTCG
1700934 GATTTAATCT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
30 2 0.06
31 28 0.88
32 2 0.06
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (31 bp):
TTTGAACTCGACAATTAAATTCACTTTGGTC
Found at i:1706893 original size:10 final size:9
Alignment explanation
Indices: 1706868--1706909 Score: 66
Period size: 9 Copynumber: 4.4 Consensus size: 9
1706858 TTATTTTTGA
1706868 AAAATATAT
1 AAAATATAT
1706877 AAAATATAT
1 AAAATATAT
1706886 AAATATATAT
1 AAA-ATATAT
1706896 AAAAATATAT
1 -AAAATATAT
1706906 AAAA
1 AAAA
1706910 ACGTATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 16 0.52
10 12 0.39
11 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAATATAT
Found at i:1706916 original size:12 final size:10
Alignment explanation
Indices: 1706867--1706910 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
1706857 ATTATTTTTG
1706867 AAAAATATAT
1 AAAAATATAT
1706877 -AAAATATAT
1 AAAAATATAT
*
1706886 AAATATATAT
1 AAAAATATAT
1706896 AAAAATATAT
1 AAAAATATAT
1706906 AAAAA
1 AAAAA
1706911 CGTATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 9 0.29
10 22 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:1706916 original size:20 final size:20
Alignment explanation
Indices: 1706867--1706917 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1706857 ATTATTTTTG
1706867 AAAA-ATATATAAAATATATA
1 AAAACATATA-AAAATATATA
* *
1706887 AATATATATAAAAATATATA
1 AAAACATATAAAAATATATA
*
1706907 AAAACGTATAA
1 AAAACATATAA
1706918 TTTTATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAACATATAAAAATATATA
Found at i:1706979 original size:22 final size:22
Alignment explanation
Indices: 1706913--1706995 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 22
1706903 TATAAAAACG
* *
1706913 TATAATTTTATAAAAGTATGTAT
1 TATAAATTTATAAAA-TATATAT
*
1706936 TATAAA---A-AAATTATAATA-
1 TATAAATTTATAAAATAT-ATAT
1706954 TATAAATTTATAAAATATATAT
1 TATAAATTTATAAAATATATAT
*
1706976 TATAAATTTATGAAATATAT
1 TATAAATTTATAAAATATAT
1706996 TATTTTAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
18 9 0.18
19 5 0.10
20 1 0.02
21 4 0.08
22 25 0.51
23 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TATAAATTTATAAAATATATAT
Found at i:1712032 original size:29 final size:29
Alignment explanation
Indices: 1711977--1712035 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1711967 AAATTAAATC
*
1711977 AAATCAAAATGTTATGTATAAAATTACACA
1 AAATCAAAATCTTATG-ATAAAATTACACA
*
1712007 AAATCAAAATTCTTATG-TAACATTACACA
1 AAATCAAAA-TCTTATGATAAAATTACACA
1712036 TTAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 9 0.35
31 6 0.23
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATCAAAATCTTATGATAAAATTACACA
Found at i:1715671 original size:16 final size:14
Alignment explanation
Indices: 1715650--1715683 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
1715640 ATATATTTTT
1715650 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
1715666 TTATAAATTTTATA
1 TTATAAATTTTATA
1715680 TTAT
1 TTAT
1715684 TTTTTACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:1718205 original size:53 final size:53
Alignment explanation
Indices: 1718133--1718241 Score: 175
Period size: 53 Copynumber: 2.1 Consensus size: 53
1718123 TATCACATAA
1718133 TTATACTTCGAACACATATTAAATTACACTTATGATTCTAGACTAATTATCAC
1 TTATACTTCGAACACATATTAAATTACACTTATGATTCTAGACTAATTATCAC
* * *
1718186 TTATACTAT-GAACACATATTAAATTATACTTATTATTCTAGACTAATTGTCAC
1 TTATACT-TCGAACACATATTAAATTACACTTATGATTCTAGACTAATTATCAC
1718239 TTA
1 TTA
1718242 ATTAGTGTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 51 0.98
54 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (53 bp):
TTATACTTCGAACACATATTAAATTACACTTATGATTCTAGACTAATTATCAC
Found at i:1733096 original size:36 final size:36
Alignment explanation
Indices: 1733056--1733130 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1733046 ATTTTAATTT
*
1733056 AATGAATTTAATCACTATTATTTATGTCATAATTAA
1 AATGAATTTAATCACTATTATGTATGTCATAATTAA
1733092 AATGAATTTAATCACTATTATGTATGTCATAATTAA
1 AATGAATTTAATCACTATTATGTATGTCATAATTAA
1733128 AAT
1 AAT
1733131 TTTAAAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (36 bp):
AATGAATTTAATCACTATTATGTATGTCATAATTAA
Found at i:1733381 original size:2 final size:2
Alignment explanation
Indices: 1733374--1733406 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1733364 CTACTAATCC
*
1733374 TA TA TA TA CA 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 T
1733407 GGAATCTAGG
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1735963 original size:39 final size:38
Alignment explanation
Indices: 1735910--1736021 Score: 103
Period size: 39 Copynumber: 3.0 Consensus size: 38
1735900 TTTAATTAAT
* *
1735910 TTTTTAGAATTTAAAATTTTCAAAATATTATAAAAATTA
1 TTTTTAAAAATTAAAATTTT-AAAATATTATAAAAATTA
*
1735949 TTTTTAAAAATTAAAATTATTAAAGA-AGTATAAAAATTA
1 TTTTTAAAAATTAAAATT-TTAAA-ATATTATAAAAATTA
1735988 ----TAAAAATTAAATATTTTTAAAAT-TT-TAAAAATTA
1 TTTTTAAAAATTAAA-A-TTTTAAAATATTATAAAAATTA
1736022 ATTAAATCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
34 9 0.14
35 13 0.20
36 6 0.09
37 2 0.03
39 31 0.48
40 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.43
Consensus pattern (38 bp):
TTTTTAAAAATTAAAATTTTAAAATATTATAAAAATTA
Found at i:1736008 original size:26 final size:26
Alignment explanation
Indices: 1735920--1736022 Score: 76
Period size: 26 Copynumber: 4.2 Consensus size: 26
1735910 TTTTTAGAAT
*
1735920 TTAAA-ATTTTCAAAATATTATAAAAA
1 TTAAATATTTTTAAAA-ATTATAAAAA
*
1735946 -T---TATTTTTAAAAATTA-AAATTA
1 TTAAATATTTTTAAAAATTATAAA-AA
* ** *
1735968 TTAAAGAAGTATAAAAATTATAAAAA
1 TTAAATATTTTTAAAAATTATAAAAA
*
1735994 TTAAATATTTTT-AAAATTTTAAAAA
1 TTAAATATTTTTAAAAATTATAAAAA
1736019 TTAA
1 TTAA
1736023 TTAAATCTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
21 3 0.05
22 5 0.09
23 10 0.17
25 17 0.29
26 20 0.34
27 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (26 bp):
TTAAATATTTTTAAAAATTATAAAAA
Found at i:1745963 original size:25 final size:25
Alignment explanation
Indices: 1745931--1745981 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1745921 AATGTTTGGC
1745931 TTTTATATGACCATTTTGAAATGTT
1 TTTTATATGACCATTTTGAAATGTT
*
1745956 TTTTATATGACTATTTTGAAATGTT
1 TTTTATATGACCATTTTGAAATGTT
1745981 T
1 T
1745982 AACCTCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (25 bp):
TTTTATATGACCATTTTGAAATGTT
Found at i:1746403 original size:3 final size:3
Alignment explanation
Indices: 1746397--1746432 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1746387 AGTTTATATA
*
1746397 GAG GAG GAG GAG GAG GCG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1746433 CTTGATCATG
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:0.31, C:0.03, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:1757059 original size:18 final size:18
Alignment explanation
Indices: 1757024--1757072 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
1757014 TACTATATAT
1757024 AAAATT-TTAATAAA-TAA
1 AAAATTATTAA-AAATTAA
1757041 AAAATTATTAAAAATTAA
1 AAAATTATTAAAAATTAA
1757059 AATAA-TA-TAAAAAT
1 AA-AATTATTAAAAAT
1757073 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 16 0.55
18 11 0.38
19 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTATTAAAAATTAA
Found at i:1758739 original size:11 final size:11
Alignment explanation
Indices: 1758719--1758748 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1758709 GGGCTTTCAA
1758719 TTTTTGTATTAC
1 TTTTT-TATTAC
1758731 TTTTTTATTAC
1 TTTTTTATTAC
1758742 TTTTTTA
1 TTTTTTA
1758749 GAGGGTCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (11 bp):
TTTTTTATTAC
Found at i:1760863 original size:25 final size:25
Alignment explanation
Indices: 1760835--1760882 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1760825 AGAAACTCAT
*
1760835 AAGAGCCAGTTATCAGAAAGCTCTA
1 AAGAGCCAATTATCAGAAAGCTCTA
* *
1760860 AAGAGCCAATTATCGGGAAGCTC
1 AAGAGCCAATTATCAGAAAGCTC
1760883 GCAAGAACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (25 bp):
AAGAGCCAATTATCAGAAAGCTCTA
Found at i:1760888 original size:25 final size:25
Alignment explanation
Indices: 1760835--1760888 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
1760825 AGAAACTCAT
* *
1760835 AAGAGCCAGTTATCAGAAAGCTCTA
1 AAGAGCCAATTATCAGAAAGCTCGA
* * *
1760860 AAGAGCCAATTATCGGGAAGCTCGC
1 AAGAGCCAATTATCAGAAAGCTCGA
1760885 AAGA
1 AAGA
1760889 ACCATATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (25 bp):
AAGAGCCAATTATCAGAAAGCTCGA
Found at i:1762684 original size:50 final size:50
Alignment explanation
Indices: 1762560--1762798 Score: 273
Period size: 50 Copynumber: 4.6 Consensus size: 50
1762550 GATAATAACA
* * ** * *
1762560 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
1762611 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1762661 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
1762711 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
*
1762766 ATGCCAATGCCATGTCCCAGACATGATCTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
1762799 TGAGATCTCT
Statistics
Matches: 161, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.57
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 30 0.19
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1762738 original size:100 final size:105
Alignment explanation
Indices: 1762559--1762805 Score: 344
Period size: 100 Copynumber: 2.4 Consensus size: 105
1762549 TGATAATAAC
**
1762559 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATGGTGCCCATGCCATG
* *
1762624 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
1762661 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGGTGCCCATGCCAT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGAT-GGTGCCCATGCCAT
1762723 GTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 GTCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* * *
1762766 ATGCCAATGCCATGTCCCAGACATGATCTTACATGAGATC
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATC
1762806 TCTTTACCCA
Statistics
Matches: 128, Mismatches: 9, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.39
101 36 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 34 0.27
107 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATGGTGCCCATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:1762924 original size:13 final size:13
Alignment explanation
Indices: 1762903--1762934 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1762893 GCTTGGATCA
*
1762903 TCATCAAATAAAT
1 TCATAAAATAAAT
1762916 TCATAAAATAAAT
1 TCATAAAATAAAT
1762929 TCATAA
1 TCATAA
1762935 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Done.