Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014551.1 Kokia drynarioides strain JFW-HI SEQ_129590, whole genome shotgun sequence
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: 184219
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Warning! 112 characters in sequence are not A, C, G, or T
Found at i:1383 original size:30 final size:28
Alignment explanation
Indices: 1347--1416 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
1337 ATTAATAAAC
* * *
1347 ATAAAATTATATTTTAATTCTTTTAAAATT
1 ATAAAATTATAATTTAA-TC-TTCAAAAAT
*
1377 ATAAAATTTTAATTTAATCTTCAAAAAT
1 ATAAAATTATAATTTAATCTTCAAAAAT
*
1405 ATAAAAATATAA
1 ATAAAATTATAA
1417 ACTAATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 17 0.50
29 2 0.06
30 15 0.44
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
ATAAAATTATAATTTAATCTTCAAAAAT
Found at i:2008 original size:114 final size:114
Alignment explanation
Indices: 1808--2041 Score: 380
Period size: 114 Copynumber: 2.1 Consensus size: 114
1798 AGAGTGTAAG
* * *
1808 TGTCCTTCCTGCGAACACTCAATATCATATGAACTCGATACGCGAACCATGTAGAATCCGATCCG
1 TGTCCTTCCTGCGAACACTCAATATCATACGAACTCGATACACGAACCATGTAGAATCCGACCCG
** * *
1873 AATCCATTCGAATTGTGAATCAATACTATTAAGTATCATAACAAAATTT
66 AATCCATTAAAATTGTGAATCAATACTAATAAGTATCATAACAAAATAT
* *
1922 TGTCCTTCCTGTGAACACTCAATATCATACGAACTCGATACACGAACCATGTAGAATCTGACCCG
1 TGTCCTTCCTGCGAACACTCAATATCATACGAACTCGATACACGAACCATGTAGAATCCGACCCG
1987 AATCCATTAAAATTGTGAATCAATACTAATAAGTATCATAACAAAATAT
66 AATCCATTAAAATTGTGAATCAATACTAATAAGTATCATAACAAAATAT
2036 T-TCCTT
1 TGTCCTT
2042 TTTTCAAAAA
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
113 5 0.05
114 106 0.95
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (114 bp):
TGTCCTTCCTGCGAACACTCAATATCATACGAACTCGATACACGAACCATGTAGAATCCGACCCG
AATCCATTAAAATTGTGAATCAATACTAATAAGTATCATAACAAAATAT
Found at i:3435 original size:15 final size:17
Alignment explanation
Indices: 3405--3443 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
3395 TAGTAAAAAT
3405 ATAATTTCACCATCTTA
1 ATAATTTCACCATCTTA
*
3422 ATAATTT-A-CATCTTT
1 ATAATTTCACCATCTTA
3437 ATAATTT
1 ATAATTT
3444 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 1 0.05
17 7 0.33
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTTCACCATCTTA
Found at i:7539 original size:16 final size:16
Alignment explanation
Indices: 7518--7548 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
7508 TCAAAGAGTT
7518 AAAAAAGTATAAACAG
1 AAAAAAGTATAAACAG
7534 AAAAAAGTATAAACA
1 AAAAAAGTATAAACA
7549 AATACTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAAAGTATAAACAG
Found at i:9742 original size:22 final size:22
Alignment explanation
Indices: 9714--9830 Score: 83
Period size: 22 Copynumber: 5.3 Consensus size: 22
9704 GGGTAGGATA
9714 TGATATGTTATAAGATATGCTC
1 TGATATGTTATAAGATATGCTC
** * * *
9736 TGATATGAAATCTA-ATATGATA
1 TGATATGTTAT-AAGATATGCTC
*
9758 TGTTATGTTATAAGATATGCTC
1 TGATATGTTATAAGATATGCTC
* ** * * *
9780 CGATATGAAATATGATATGATA
1 TGATATGTTATAAGATATGCTC
* *
9802 TGCTATGTTATAAGACATGCTC
1 TGATATGTTATAAGATATGCTC
*
9824 CGATATG
1 TGATATG
9831 AAATATGATA
Statistics
Matches: 65, Mismatches: 28, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
21 1 0.02
22 63 0.97
23 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGATATGTTATAAGATATGCTC
Found at i:9837 original size:44 final size:44
Alignment explanation
Indices: 9710--9840 Score: 208
Period size: 44 Copynumber: 3.0 Consensus size: 44
9700 ATGGGGGTAG
* * *
9710 GATATGATATGTTATAAGATATGCTCTGATATGAAATCTAATAT
1 GATATGATATGTTATAAGATATGCTCCGATATGAAATATGATAT
*
9754 GATATGTTATGTTATAAGATATGCTCCGATATGAAATATGATAT
1 GATATGATATGTTATAAGATATGCTCCGATATGAAATATGATAT
* *
9798 GATATGCTATGTTATAAGACATGCTCCGATATGAAATATGATA
1 GATATGATATGTTATAAGATATGCTCCGATATGAAATATGATA
9841 CATTCTGACA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (44 bp):
GATATGATATGTTATAAGATATGCTCCGATATGAAATATGATAT
Found at i:17013 original size:44 final size:44
Alignment explanation
Indices: 16958--17130 Score: 229
Period size: 44 Copynumber: 3.9 Consensus size: 44
16948 GAGGGGAGGA
* * * *
16958 TATGTTATGTTATAAGATATGCTCCAATATGAAATCTGACATGA
1 TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATATGC
* * * *
17002 TAAGATATGTTATAAGATATGCTTCGATATGATATTTGATATGC
1 TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATATGC
*
17046 TATGATATGTTATAAGATATGCTCCGATATGAAATCTAATATGC
1 TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATATGC
* ** *
17090 TATGATATGTTATAAGATATGCACTTATATGAAATATGATA
1 TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATA
17131 CATTTTGGCA
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 111 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (44 bp):
TATGATATGTTATAAGATATGCTCCGATATGAAATCTGATATGC
Found at i:17016 original size:12 final size:12
Alignment explanation
Indices: 17001--17068 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 12
16991 ATCTGACATG
*
17001 ATAAGATATGTT
1 ATAAGATATGCT
17013 ATAAGATATGCT
1 ATAAGATATGCT
* *
17025 -T-CGATATGAT
1 ATAAGATATGCT
**
17035 ATTTGATATGCT
1 ATAAGATATGCT
*
17047 AT--GATATGTT
1 ATAAGATATGCT
17057 ATAAGATATGCT
1 ATAAGATATGCT
17069 CCGATATGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
10 16 0.36
11 2 0.04
12 27 0.60
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (12 bp):
ATAAGATATGCT
Found at i:17030 original size:22 final size:22
Alignment explanation
Indices: 17005--17111 Score: 110
Period size: 22 Copynumber: 4.9 Consensus size: 22
16995 GACATGATAA
17005 GATATGTTATAAGATATGCT-T
1 GATATGTTATAAGATATGCTAT
* **
17026 CGATATGATATTTGATATGCTAT
1 -GATATGTTATAAGATATGCTAT
**
17049 GATATGTTATAAGATATGCTCC
1 GATATGTTATAAGATATGCTAT
** *
17071 GATATGAAATCTA-ATATGCTAT
1 GATATGTTAT-AAGATATGCTAT
17093 GATATGTTATAAGATATGC
1 GATATGTTATAAGATATGC
17112 ACTTATATGA
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 63 0.95
23 2 0.03
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
GATATGTTATAAGATATGCTAT
Found at i:20660 original size:21 final size:20
Alignment explanation
Indices: 20604--20653 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
20594 ATTATTATGA
*
20604 GTTATATTAAG-TATAAATAGG
1 GTTA-ATTAAGAT-TAAAAAGG
*
20625 TTTAATTAAGATTAAAAAGG
1 GTTAATTAAGATTAAAAAGG
20645 GTTAATTAA
1 GTTAATTAA
20654 AGCTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (20 bp):
GTTAATTAAGATTAAAAAGG
Found at i:22553 original size:21 final size:21
Alignment explanation
Indices: 22500--22546 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
22490 TTAATATCGA
* * *
22500 TAGAAGCATGACTTGTTTCAG
1 TAGAAGCTTCACTTGTATCAG
*
22521 TAGAAGCTTCACTTGTATCGG
1 TAGAAGCTTCACTTGTATCAG
22542 TAGAA
1 TAGAA
22547 CTGTCACAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (21 bp):
TAGAAGCTTCACTTGTATCAG
Found at i:27901 original size:21 final size:20
Alignment explanation
Indices: 27845--27894 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
27835 ATTAGCATGA
*
27845 GTTATATTAAG-TATAAATAGG
1 GTTA-ATTAAGAT-TAAAAAGG
*
27866 TTTAATTAAGATTAAAAAGG
1 GTTAATTAAGATTAAAAAGG
27886 GTTAATTAA
1 GTTAATTAA
27895 AGCTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (20 bp):
GTTAATTAAGATTAAAAAGG
Found at i:28424 original size:62 final size:62
Alignment explanation
Indices: 28327--28452 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
28317 TTGTTGGGAA
**
28327 TTGTTTAAGAATAAAGAATGTTCTATTATGGAGTATTTAAAAAGAAAAGGGTATTTTGCATG
1 TTGTTTAAGAATAAAGAATGTTCTATTATAAAGTATTTAAAAAGAAAAGGGTATTTTGCATG
*
28389 TTGTTTAAGAATAAAGAATGTTCTATTATAAAGTATTTAAAAAGAAAAGGGTATTTTTCATG
1 TTGTTTAAGAATAAAGAATGTTCTATTATAAAGTATTTAAAAAGAAAAGGGTATTTTGCATG
28451 TT
1 TT
28453 TTGTATTGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (62 bp):
TTGTTTAAGAATAAAGAATGTTCTATTATAAAGTATTTAAAAAGAAAAGGGTATTTTGCATG
Found at i:29777 original size:21 final size:20
Alignment explanation
Indices: 29715--29777 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
29705 TTGGAGTTTT
* *
29715 TTGTATCGATAGAAGTATGAC
1 TTGTATCGATAGAACT-TCAC
* * *
29736 TTGTTTCGGTAAAAGCTTCAC
1 TTGTATCGATAGAA-CTTCAC
29757 TTGTATCGATAGAACTGTCAC
1 TTGTATCGATAGAACT-TCAC
29778 AGATATCGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGTATCGATAGAACTTCAC
Found at i:33482 original size:21 final size:22
Alignment explanation
Indices: 33458--33511 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
33448 ATGACATGTT
**
33458 TCGGTAGAAGTCAT-ACTTGTA
1 TCGGTAGAAGTCATCACAAGTA
* *
33479 TCGGTAG-TGTTATCACAAGTA
1 TCGGTAGAAGTCATCACAAGTA
33500 TCGGTAGAAGTC
1 TCGGTAGAAGTC
33512 TGCACTGTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (22 bp):
TCGGTAGAAGTCATCACAAGTA
Found at i:38222 original size:21 final size:21
Alignment explanation
Indices: 38174--38225 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
38164 AGAGTTTTTA
*
38174 GTATCGGTAAAAGCATGACAT
1 GTATCGGTAGAAGCATGACAT
* *
38195 GTTTCGGTAGAAGTCAT-ACTT
1 GTATCGGTAGAAG-CATGACAT
38216 GTATCGGTAG
1 GTATCGGTAG
38226 TGTTATCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACAT
Found at i:46562 original size:18 final size:18
Alignment explanation
Indices: 46539--46584 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
46529 CAACAGTAAG
46539 CTGAAGAAGAAGAAGATC
1 CTGAAGAAGAAGAAGATC
*
46557 CTGAAGAAGAAGAGGATC
1 CTGAAGAAGAAGAAGATC
*
46575 CTGAGGAAGA
1 CTGAAGAAGA
46585 TCCTATGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.33, T:0.11
Consensus pattern (18 bp):
CTGAAGAAGAAGAAGATC
Found at i:52746 original size:26 final size:26
Alignment explanation
Indices: 52687--52739 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
52677 TTCTGGGCGT
52687 AATTCTGGACACGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
* *
52713 AATTCTGGACATGTTCATGTAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
52739 A
1 A
52740 TTCCTGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCGAC
Found at i:52774 original size:37 final size:37
Alignment explanation
Indices: 52733--52809 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
52723 ATGTTCATGT
* **
52733 AGCGACATTCCTGGGTGCAATTGAAGAATACTTATGC
1 AGCGACAGTCCTGAATGCAATTGAAGAATACTTATGC
* * *
52770 AGCGATAGTCCTGAATGCAATTGAATAATATTTATGC
1 AGCGACAGTCCTGAATGCAATTGAAGAATACTTATGC
52807 AGC
1 AGC
52810 AATAGTCTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (37 bp):
AGCGACAGTCCTGAATGCAATTGAAGAATACTTATGC
Found at i:52870 original size:37 final size:37
Alignment explanation
Indices: 52817--52924 Score: 144
Period size: 37 Copynumber: 2.9 Consensus size: 37
52807 AGCAATAGTC
* * ** *
52817 TTGGGTGCATTTTGGAAATATTCATGCGGCGACAGTT
1 TTGGGTGCAATTTGGAAGTGCTCATGCGGCGACAATT
* *
52854 TTGGGTGCAATCTGGAAGTGCTCATGCGACGACAATT
1 TTGGGTGCAATTTGGAAGTGCTCATGCGGCGACAATT
*
52891 TTGGGTGCAATTTAGAAGTGCTCATGCGGCGACA
1 TTGGGTGCAATTTGGAAGTGCTCATGCGGCGACA
52925 TTAGTAGTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (37 bp):
TTGGGTGCAATTTGGAAGTGCTCATGCGGCGACAATT
Found at i:55055 original size:12 final size:12
Alignment explanation
Indices: 55014--55058 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
55004 TATCTCAAAT
*
55014 TCTCAAA-TCAC
1 TCTCAAATTCTC
55025 TCTCAAATTC-C
1 TCTCAAATTCTC
55036 TCTCAAATTCTC
1 TCTCAAATTCTC
*
55048 TCTTAAATTCT
1 TCTCAAATTCT
55059 ATTTATATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 18 0.58
12 13 0.42
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (12 bp):
TCTCAAATTCTC
Found at i:55055 original size:23 final size:22
Alignment explanation
Indices: 55014--55057 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
55004 TATCTCAAAT
55014 TCTCAAATCACTCTCAAATTCC
1 TCTCAAATCACTCTCAAATTCC
* *
55036 TCTCAAATTCTCTCTTAAATTC
1 TCTCAAA-TCACTCTCAAATTC
55058 TATTTATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
TCTCAAATCACTCTCAAATTCC
Found at i:55252 original size:19 final size:19
Alignment explanation
Indices: 55218--55278 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
55208 TTTCAATAAA
*
55218 TTTCATTTTTTTTATTTTAT
1 TTTCA-TTTTTATATTTTAT
*
55238 TTTCATTTTTATATTTTAA
1 TTTCATTTTTATATTTTAT
* *
55257 CTTAATATTTTATATTTT-T
1 TTTCAT-TTTTATATTTTAT
55276 TTT
1 TTT
55279 ACGTAAATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCATTTTTATATTTTAT
Found at i:64302 original size:11 final size:12
Alignment explanation
Indices: 64274--64306 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
64264 CAATTTGTAC
64274 ATTGTTTTAAGA
1 ATTGTTTTAAGA
*
64286 ATTGTTTTAA-T
1 ATTGTTTTAAGA
64297 ATTGTTTTAA
1 ATTGTTTTAA
64307 ATTTATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (12 bp):
ATTGTTTTAAGA
Found at i:67511 original size:78 final size:78
Alignment explanation
Indices: 67377--67521 Score: 272
Period size: 78 Copynumber: 1.9 Consensus size: 78
67367 TTCAATCAAC
*
67377 TTTGGAAAATTTTCGTCACACCCTAAACTTTGGAAAAATTAAAGTAAGGTCTCAAATATTTGTAA
1 TTTGGAAAATTTTCGTCACACCCTAAACTTTGGAAAAATTAAAGTAAGGTCCCAAATATTTGTAA
67442 ATATTTGTAAATT
66 ATATTTGTAAATT
*
67455 TTTGGAAAATTTTCGTCACACCCTAAACTTTGGAAAAATTAAAGTAATGTCCCAAATATTTGTAA
1 TTTGGAAAATTTTCGTCACACCCTAAACTTTGGAAAAATTAAAGTAAGGTCCCAAATATTTGTAA
67520 AT
66 AT
67522 TTTAGAAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (78 bp):
TTTGGAAAATTTTCGTCACACCCTAAACTTTGGAAAAATTAAAGTAAGGTCCCAAATATTTGTAA
ATATTTGTAAATT
Found at i:68648 original size:69 final size:69
Alignment explanation
Indices: 68557--68758 Score: 273
Period size: 69 Copynumber: 2.9 Consensus size: 69
68547 GTAAATGATA
*
68557 CCATGATTATTGATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTT
1 CCATGATTATCGATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTT
68622 ATGC
66 ATGC
* * * * *
68626 CCATGATTATCAATGGAATATGATTGCTTAGGAATGATTA-TTTAATCCATCATTGATTATGTTT
1 CCATGATTATCGATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTT
68690 ATGC
66 ATGC
* * * * *
68694 TCATGA-TAACTGATCGAATATGATTACTTAAAGAATGATTATTTTAATCCGTGAATGATTATGT
1 CCATGATTATC-GATAGAATATGATTGCTT-AGGAATGATTATTTTAATCCGTGAATGATTATGT
68758 T
64 T
68759 CATACTAAAT
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
67 3 0.03
68 45 0.39
69 47 0.41
70 20 0.17
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (69 bp):
CCATGATTATCGATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTT
ATGC
Found at i:68713 original size:68 final size:68
Alignment explanation
Indices: 68557--68758 Score: 271
Period size: 68 Copynumber: 2.9 Consensus size: 68
68547 GTAAATGATA
68557 CCATGATTATTGATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTT
1 CCATGATTA-TGATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTT
68622 ATGC
65 ATGC
* * * * *
68626 CCATGATTATCAATGGAATATGATTGCTTAGGAATGATTA-TTTAATCCATCATTGATTATGTTT
1 CCATGATTAT-GATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTT
68690 ATGC
65 ATGC
* * * * *
68694 TCATGATAACTGATCGAATATGATTACTTAAAGAATGATTATTTTAATCCGTGAATGATTATGTT
1 CCATGATTA-TGATAGAATATGATTGCTT-AGGAATGATTATTTTAATCCGTGAATGATTATGTT
68759 CATACTAAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
68 48 0.42
69 47 0.41
70 20 0.17
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (68 bp):
CCATGATTATGATAGAATATGATTGCTTAGGAATGATTATTTTAATCCGTGAATGATTATGTTTA
TGC
Found at i:69142 original size:110 final size:109
Alignment explanation
Indices: 68949--69269 Score: 331
Period size: 110 Copynumber: 2.9 Consensus size: 109
68939 GACCACTGTG
* * ** * * * *
68949 TATTCACAAATTAACAGATTCCAACTACGACTATATGTACAAATCATTCACGATTTCC-TCTAAT
1 TATTCACAGATTAGCAGATTCCAACTACGACTATATGTACGGAGCATCCATGATTTCCTTCGAA-
* *
69013 GTCTTTTTTTTGCGAGGGATTGTGAATCCTCAACCATTCCGCTATA
65 G-CTTTTATTTGCGAGGGATTGTGAATCCTCAACCATTCCACTATA
* * *
69059 TATTCACAGATTAGCAGGTTCCAAGTGCGACTATATGTACGGAGCATCCATGATTTCCTTCGATA
1 TATTCACAGATTAGCAGATTCCAACTACGACTATATGTACGGAGCATCCATGATTTCCTTCGA-A
* * *
69124 GCTTTTATTTGCGAGGGATTGT-AGATCCTCAAACATTCCACTGTG
65 GCTTTTATTTGCGAGGGATTGTGA-ATCCTCAACCATTCCACTATA
* * * * ** * *
69169 TATTAACAGATTAGCATATTCAAACTACAAAAATATGTACGGAGCATCCATGATTTTCTTTGACA
1 TATTCACAGATTAGCAGATTCCAACTACGACTATATGTACGGAGCATCCATGATTTCCTTCGA-A
* * * *
69234 ACTTTTATCTGCGAGGGGTTGTGGATCCTCAACCAT
65 GCTTTTATTTGCGAGGGATTGTGAATCCTCAACCAT
69270 CCGGCAGCTT
Statistics
Matches: 174, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
109 1 0.01
110 168 0.97
111 4 0.02
112 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (109 bp):
TATTCACAGATTAGCAGATTCCAACTACGACTATATGTACGGAGCATCCATGATTTCCTTCGAAG
CTTTTATTTGCGAGGGATTGTGAATCCTCAACCATTCCACTATA
Found at i:76937 original size:19 final size:19
Alignment explanation
Indices: 76913--76950 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
76903 AATTTAAAAC
76913 AAAAGGATTGCAAAAGCAT
1 AAAAGGATTGCAAAAGCAT
* *
76932 AAAAGGGTTGCAGAAGCAT
1 AAAAGGATTGCAAAAGCAT
76951 CAAATACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.16
Consensus pattern (19 bp):
AAAAGGATTGCAAAAGCAT
Found at i:82800 original size:29 final size:29
Alignment explanation
Indices: 82766--82825 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
82756 TATTATAATA
82766 AAATTTAAAATAATTTT-AATTTTAAAAAT
1 AAATTTAAAA-AATTTTAAATTTTAAAAAT
*
82795 AAATTTAAAAAATTTTAAATTTTATAAAT
1 AAATTTAAAAAATTTTAAATTTTAAAAAT
82824 AA
1 AA
82826 TATATATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATTTAAAAAATTTTAAATTTTAAAAAT
Found at i:83188 original size:31 final size:31
Alignment explanation
Indices: 83152--83255 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 31
83142 TTTTTGATCC
83152 AATTTGGTACCTGAACTTGACATTTTTTCCT
1 AATTTGGTACCTGAACTTGACATTTTTTCCT
* * *
83183 AATTTGGTACCT-AAATT---TTTTTTTGACCC
1 AATTTGGTACCTGAACTTGACATTTTTT--CCT
*
83212 AATTTGGTAGCTGAACTTGACATTTTTTTCCT
1 AATTTGGTACCTGAACTTGACA-TTTTTTCCT
*
83244 AATTTGGCACCT
1 AATTTGGTACCT
83256 AAGCTTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
27 6 0.11
29 13 0.23
30 8 0.14
31 12 0.21
32 12 0.21
34 6 0.11
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.45
Consensus pattern (31 bp):
AATTTGGTACCTGAACTTGACATTTTTTCCT
Found at i:83219 original size:60 final size:61
Alignment explanation
Indices: 83117--83286 Score: 227
Period size: 60 Copynumber: 2.8 Consensus size: 61
83107 AATTTGGTAC
* * * *
83117 TTTTCTTAATTTGATACTTAAA-CTTTTTTTGATCCAATTTGGTACCTGAACTTGACA-TT
1 TTTTCCTAATTTGGTACCTAAATTTTTTTTTGATCCAATTTGGTACCTGAACTTGACATTT
* *
83176 TTTTCCTAATTTGGTACCTAAATTTTTTTTTGACCCAATTTGGTAGCTGAACTTGACATTT
1 TTTTCCTAATTTGGTACCTAAATTTTTTTTTGATCCAATTTGGTACCTGAACTTGACATTT
* * *
83237 TTTTCCTAATTTGGCACCTAAGCTTTTTTTTTAGATTCAATTTGGTACCT
1 TTTTCCTAATTTGGTACCTAA-ATTTTTTTTT-GATCCAATTTGGTACCT
83287 AAATGCATTA
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 19 0.20
60 32 0.33
61 22 0.23
62 9 0.09
63 14 0.15
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.49
Consensus pattern (61 bp):
TTTTCCTAATTTGGTACCTAAATTTTTTTTTGATCCAATTTGGTACCTGAACTTGACATTT
Found at i:83558 original size:31 final size:31
Alignment explanation
Indices: 83517--83575 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
83507 CAACTTTAAA
83517 AAAAAGTGTCAAGGTTAGA-TACCAAATTAGG
1 AAAAAGTGTCAA-GTTAGAGTACCAAATTAGG
* *
83548 AAAACGTGTCAAGTTTGAGTACCAAATT
1 AAAAAGTGTCAAGTTAGAGTACCAAATT
83576 GAACTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTAGAGTACCAAATTAGG
Found at i:86579 original size:22 final size:22
Alignment explanation
Indices: 86554--86614 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
86544 AGTGCACTTA
*
86554 CTGTTTAGTACTGTGTGTGCTT
1 CTGTTTAGCACTGTGTGTGCTT
* *
86576 CTGTTCAGCATTGTGTGTGCTT
1 CTGTTTAGCACTGTGTGTGCTT
86598 CTGTTTAGCACTGTGTG
1 CTGTTTAGCACTGTGTG
86615 CCTACTGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.10, C:0.16, G:0.28, T:0.46
Consensus pattern (22 bp):
CTGTTTAGCACTGTGTGTGCTT
Found at i:86634 original size:25 final size:24
Alignment explanation
Indices: 86604--86673 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
86594 GCTTCTGTTT
*
86604 AGCACTGTGTGCCTACTGTTTCCCC
1 AGCACTATGTG-CTACTGTTTCCCC
*
86629 AGCACTTATGTGCTTCTGTTTCCCC
1 AGCAC-TATGTGCTACTGTTTCCCC
* *
86654 AGCACTTATGCGCTTCTGTT
1 AGCAC-TATGTGCTACTGTT
86674 AAGTACTTCG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 36 0.88
26 5 0.12
ACGTcount: A:0.13, C:0.31, G:0.19, T:0.37
Consensus pattern (24 bp):
AGCACTATGTGCTACTGTTTCCCC
Found at i:90220 original size:24 final size:22
Alignment explanation
Indices: 90201--90241 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
90191 TAAATATATT
90201 TGTTTATTTTTATGAT-AATAG
1 TGTTTATTTTTATGATAAATAG
90222 TGTTTATTTTTATGATAAAT
1 TGTTTATTTTTATGATAAAT
90242 GTCAAATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (22 bp):
TGTTTATTTTTATGATAAATAG
Found at i:92369 original size:16 final size:16
Alignment explanation
Indices: 92338--92372 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
92328 TATTTTTTAA
*
92338 TTTAAAAATAATTTTG
1 TTTAAAAATAACTTTG
*
92354 TTTAAAAATACCTTTG
1 TTTAAAAATAACTTTG
92370 TTT
1 TTT
92373 GTCAGATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (16 bp):
TTTAAAAATAACTTTG
Found at i:97464 original size:20 final size:20
Alignment explanation
Indices: 97427--97465 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
97417 ATGCAAAGAA
97427 GAGAATGAAAAAGAAAAAAG
1 GAGAATGAAAAAGAAAAAAG
* *
97447 GAGAA-GAAATAGAGAAAAG
1 GAGAATGAAAAAGAAAAAAG
97466 AAAGCGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (20 bp):
GAGAATGAAAAAGAAAAAAG
Found at i:98317 original size:20 final size:20
Alignment explanation
Indices: 98287--98343 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
98277 AAATATAAAT
98287 TTTTGAA-TTTTTATAACTA
1 TTTTGAATTTTTTATAACTA
* *
98306 TTTTGAATTTTTTTTAAATTA
1 TTTTGAATTTTTTAT-AACTA
*
98327 TTTTAAATTATTTTATA
1 TTTTGAATT-TTTTATA
98344 TTTTTTATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 7 0.23
20 6 0.19
21 13 0.42
22 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTTTTATAACTA
Found at i:98330 original size:10 final size:10
Alignment explanation
Indices: 98317--98350 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
98307 TTTGAATTTT
98317 TTTTAAATTA
1 TTTTAAATTA
98327 TTTTAAATTA
1 TTTTAAATTA
*
98337 TTTTATATT-
1 TTTTAAATTA
98346 TTTTA
1 TTTTA
98351 TTGAGAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTAAATTA
Found at i:98545 original size:13 final size:13
Alignment explanation
Indices: 98527--98560 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
98517 TGTAATATAT
*
98527 ATATATATAAATC
1 ATATATAAAAATC
98540 ATATATAAAAATC
1 ATATATAAAAATC
*
98553 ATAAATAA
1 ATATATAA
98561 TATATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATATAAAAATC
Found at i:111582 original size:22 final size:22
Alignment explanation
Indices: 111536--111607 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 22
111526 AATGTATAGA
* * *
111536 ATTTTATATTAAATCAGTATAAT
1 ATTTTATATTAAA-AAATATTAT
111559 ATTTTAT-TTAAAAAATATGTAT
1 ATTTTATATTAAAAAATAT-TAT
*
111581 ATTTAATATTAAAAAATATT-T
1 ATTTTATATTAAAAAATATTAT
111602 ATTTTA
1 ATTTTA
111608 AATACGTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
21 10 0.24
22 14 0.33
23 18 0.43
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (22 bp):
ATTTTATATTAAAAAATATTAT
Found at i:115926 original size:63 final size:63
Alignment explanation
Indices: 115827--115947 Score: 242
Period size: 63 Copynumber: 1.9 Consensus size: 63
115817 CAGTAACGTA
115827 AATCGTGTCTCTCCGAAGAACCCATATGCCTTCAATAAAGCCGCAAGCCTCCACCCTAACCTG
1 AATCGTGTCTCTCCGAAGAACCCATATGCCTTCAATAAAGCCGCAAGCCTCCACCCTAACCTG
115890 AATCGTGTCTCTCCGAAGAACCCATATGCCTTCAATAAAGCCGCAAGCCTCCACCCTA
1 AATCGTGTCTCTCCGAAGAACCCATATGCCTTCAATAAAGCCGCAAGCCTCCACCCTA
115948 TGAGAGTTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (63 bp):
AATCGTGTCTCTCCGAAGAACCCATATGCCTTCAATAAAGCCGCAAGCCTCCACCCTAACCTG
Found at i:125896 original size:39 final size:39
Alignment explanation
Indices: 125853--125934 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
125843 ATCTATTTCG
125853 TTTTATTAATTTAAAATAATGAA-CTTTTATTTTGGGTTT
1 TTTTATTAATTTAAAATAATGAATCTTTTA-TTTGGGTTT
125892 TTTTATTAATTTAAAATAATGAATTTCTTTTATTTGGGTTT
1 TTTTATTAATTTAAAATAATGAA--TCTTTTATTTGGGTTT
125933 TT
1 TT
125935 AGAACTCTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
39 23 0.57
41 11 0.28
42 6 0.15
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (39 bp):
TTTTATTAATTTAAAATAATGAATCTTTTATTTGGGTTT
Found at i:127026 original size:92 final size:94
Alignment explanation
Indices: 126856--127075 Score: 345
Period size: 92 Copynumber: 2.4 Consensus size: 94
126846 AATTAAAATA
* * *
126856 TCAACATTTGGTCTAAACAATTTATCAATACATAGTTACCCCTCAGTAATTATGGTATTCTTCCC
1 TCAACATTTGGTCTCAACAATTTATCAATACATAGTCACCCCTCAGTAATTACGGTATTCTTCCC
126921 TCAAATCTTAGAATATAAACCATAATTGC
66 TCAAATCTTAGAATATAAACCATAATTGC
* *
126950 TCAACATTTGGTCTCAACAATTTATCAATACAT-G-CACTCCTCAGTAATTACGGTATTCTTCCT
1 TCAACATTTGGTCTCAACAATTTATCAATACATAGTCACCCCTCAGTAATTACGGTATTCTTCCC
*
127013 TCAACTCTTAGAATATAAACCATAATTGC
66 TCAAATCTTAGAATATAAACCATAATTGC
* * *
127042 TCAACATTTGGTTTCAACAAGTAATCAATACATA
1 TCAACATTTGGTCTCAACAATTTATCAATACATA
127076 TTTACTTCGG
Statistics
Matches: 116, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
92 83 0.72
93 1 0.01
94 32 0.28
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (94 bp):
TCAACATTTGGTCTCAACAATTTATCAATACATAGTCACCCCTCAGTAATTACGGTATTCTTCCC
TCAAATCTTAGAATATAAACCATAATTGC
Found at i:128322 original size:23 final size:23
Alignment explanation
Indices: 128296--128340 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
128286 CACATTAATC
* *
128296 ACATTATCATTTGAGCATAAATT
1 ACATTAACATTTAAGCATAAATT
*
128319 ACATTAACTTTTAAGCATAAAT
1 ACATTAACATTTAAGCATAAAT
128341 CACCTATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (23 bp):
ACATTAACATTTAAGCATAAATT
Found at i:131814 original size:21 final size:21
Alignment explanation
Indices: 131785--131824 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
131775 CCTTACTGCA
* * *
131785 ATAGTGGAAGCAGGTGAAGTG
1 ATAGAGGAAGAAGGCGAAGTG
131806 ATAGAGGAAGAAGGCGAAG
1 ATAGAGGAAGAAGGCGAAG
131825 GGATTACCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.42, T:0.12
Consensus pattern (21 bp):
ATAGAGGAAGAAGGCGAAGTG
Found at i:135736 original size:20 final size:20
Alignment explanation
Indices: 135711--135771 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
135701 GCATTGACCG
135711 AATGCTAAATGGTTGTTCCA
1 AATGCTAAATGGTTGTTCCA
135731 AATGCTAAATGGTTGTTCCA
1 AATGCTAAATGGTTGTTCCA
*
135751 AATGCTAAATGATTGTTCCA
1 AATGCTAAATGGTTGTTCCA
135771 A
1 A
135772 GGATAAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (20 bp):
AATGCTAAATGGTTGTTCCA
Found at i:136498 original size:25 final size:25
Alignment explanation
Indices: 136452--136499 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
136442 TGAAGTTTGT
* * *
136452 TGGTTTGCTTGATGATTGTTTGTTC
1 TGGTTTGCTTGATAACTATTTGTTC
*
136477 TGGTTTGCTTTATAACTATTTGT
1 TGGTTTGCTTGATAACTATTTGT
136500 GTTCAAATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.12, C:0.08, G:0.23, T:0.56
Consensus pattern (25 bp):
TGGTTTGCTTGATAACTATTTGTTC
Found at i:140490 original size:25 final size:25
Alignment explanation
Indices: 140443--140494 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
140433 ATGAAGTTTG
* *
140443 TTGGTTTGCTTTATGATTGTTTGTT
1 TTGGTTTGCTATATGATTATTTGTT
140468 TTGGTTTGCTATATG-TCTATTTGTT
1 TTGGTTTGCTATATGAT-TATTTGTT
140493 TT
1 TT
140495 CAAATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.10, C:0.06, G:0.21, T:0.63
Consensus pattern (25 bp):
TTGGTTTGCTATATGATTATTTGTT
Found at i:141718 original size:25 final size:25
Alignment explanation
Indices: 141690--141759 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
141680 AGTTTTTTTG
*
141690 TTTGCTTTATGACTGTTTGTGCTGA
1 TTTGCTTTATGACTATTTGTGCTGA
141715 TTTGCTTTATGACTATTTGTGCTGA
1 TTTGCTTTATGACTATTTGTGCTGA
141740 TTTGCTTTATGACTATTTGT
1 TTTGCTTTATGACTATTTGT
141760 TTTCAAATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.54
Consensus pattern (25 bp):
TTTGCTTTATGACTATTTGTGCTGA
Found at i:143829 original size:19 final size:18
Alignment explanation
Indices: 143807--143877 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
143797 TAAAAATGAA
143807 AAAAATACAAAAAATTATT
1 AAAAATA-AAAAAATTATT
* *
143826 AAAATGTAGAAAAATTA-T
1 AAAA-ATAAAAAAATTATT
* *
143844 AAAATTACAATAAA-TATAT
1 AAAAATA-AAAAAATTAT-T
143863 AAAAATAAAAAAATT
1 AAAAATAAAAAAATT
143878 TCTATTTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 4 0.10
18 14 0.35
19 20 0.50
20 2 0.05
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAATAAAAAAATTATT
Found at i:144110 original size:18 final size:19
Alignment explanation
Indices: 144087--144129 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
144077 TAAAATATTA
144087 AAATTTATAAT-ATTTTTT
1 AAATTTATAATAATTTTTT
* *
144105 AAATTTTTAGTAATTTTTT
1 AAATTTATAATAATTTTTT
144124 AAATTT
1 AAATTT
144130 TGTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AAATTTATAATAATTTTTT
Found at i:144151 original size:14 final size:15
Alignment explanation
Indices: 144099--144161 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
144089 ATTTATAATA
144099 TTTTTTAAATTTTTAGT
1 TTTTTTAAA-TTTT-GT
144116 AATTTTTTAAATTTTGT
1 --TTTTTTAAATTTTGT
*
144133 TTTTTT-AATTTTTT
1 TTTTTTAAATTTTGT
144147 ATTTTCTTAAATTTT
1 -TTTT-TTAAATTTT
144162 TTGTAATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 7 0.17
15 10 0.25
16 2 0.05
17 8 0.20
18 4 0.10
19 9 0.22
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTTTAAATTTTGT
Found at i:144200 original size:19 final size:19
Alignment explanation
Indices: 144157--144210 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
144147 ATTTTCTTAA
144157 ATTTTTTGTAATTTTTAATT
1 ATTTTTTGTAATTTTT-ATT
*
144177 A-TTTTTGTACTTTTT-TGT
1 ATTTTTTGTAATTTTTAT-T
*
144195 ATTTTTT-TCATTTTTA
1 ATTTTTTGTAATTTTTA
144211 AAGATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 1 0.04
18 8 0.29
19 18 0.64
20 1 0.04
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTTTTGTAATTTTTATT
Found at i:144552 original size:24 final size:23
Alignment explanation
Indices: 144520--144569 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
144510 AATATTAATA
*
144520 TTTAAAATTTCATTAAAAATAT-TT
1 TTTAAAATTT-A-AAAAAATATATT
*
144544 TTTATAATTTAAAAAAATATATT
1 TTTAAAATTTAAAAAAATATATT
144567 TTT
1 TTT
144570 GAATGAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 6 0.26
24 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAAATTTAAAAAAATATATT
Found at i:145211 original size:54 final size:54
Alignment explanation
Indices: 145129--145237 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
145119 AATTTTTATT
*
145129 TCTATCCTCGTCCCACCACTCACGTAGGTCCTTAAATCCATCAAATCCCAACTG
1 TCTATCCTCGTCCCACCACTCACATAGGTCCTTAAATCCATCAAATCCCAACTG
145183 TCTATCCTCGTCCCACCACTCACATAGGTCCTTAAATCCATCAAATCCCAACTG
1 TCTATCCTCGTCCCACCACTCACATAGGTCCTTAAATCCATCAAATCCCAACTG
145237 T
1 T
145238 ATCCGTCTCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.27, C:0.39, G:0.08, T:0.27
Consensus pattern (54 bp):
TCTATCCTCGTCCCACCACTCACATAGGTCCTTAAATCCATCAAATCCCAACTG
Found at i:146842 original size:32 final size:29
Alignment explanation
Indices: 146805--146874 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 29
146795 ATGTCACATT
* *
146805 TGGTACTTATACTTTCATAAAATGTCTCAATG
1 TGGTACTTATAATTT--GAAAATGTC-CAATG
*
146837 TGGTACATATAATTTGAAAATGTCCAATG
1 TGGTACTTATAATTTGAAAATGTCCAATG
*
146866 TGATACTTA
1 TGGTACTTA
146875 AACTATCCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 12 0.36
30 8 0.24
32 13 0.39
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (29 bp):
TGGTACTTATAATTTGAAAATGTCCAATG
Found at i:147073 original size:93 final size:91
Alignment explanation
Indices: 146814--147080 Score: 272
Period size: 93 Copynumber: 2.9 Consensus size: 91
146804 TTGGTACTTA
* * * *
146814 TACTTTCATAAAATGTCTCAATGTGGTACATATAATTTG-AAAATGTCCAATGTGATACTTAAAC
1 TACTTTCATAAAATATC-CAA-AT-GTACATATACTTTGAAAAATATCCAATGTGATACTTAAAC
* * * *
146878 TATCCATATGTATTTTTATTATGGTACTTG
63 TATCAATATGT-GTTTTATTATAGTACATG
* *** * * *
146908 CACTTTCATAAAATATCC-AATG-GGGTAT-CTTTTAAAAATATCCAATGTAATACTTGAACTAT
1 TACTTTCATAAAATATCCAAATGTACATATACTTTGAAAAATATCCAATGTGATACTTAAACTAT
146970 CAATATGTGTTTTATTATAGTACATG
66 CAATATGTGTTTTATTATAGTACATG
* * * * *
146996 TACTTTCATAAAATATCCAACATGATACCTATACTTTGAAAAAAATCCAATGTGGTACCTAAAGT
1 TACTTTCATAAAATATCCAA-ATG-TACATATACTTTGAAAAATATCCAATGTGATACTTAAACT
147061 ATCAATATGTGTTTTATTAT
64 ATCAATATGTGTTTTATTAT
147081 GGTGTTTGAC
Statistics
Matches: 141, Mismatches: 26, Indels: 13
0.78 0.14 0.07
Matches are distributed among these distances:
88 35 0.25
89 36 0.26
90 4 0.03
91 1 0.01
92 4 0.03
93 46 0.33
94 15 0.11
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (91 bp):
TACTTTCATAAAATATCCAAATGTACATATACTTTGAAAAATATCCAATGTGATACTTAAACTAT
CAATATGTGTTTTATTATAGTACATG
Found at i:147867 original size:19 final size:19
Alignment explanation
Indices: 147843--147879 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
147833 AAATAAAGAG
147843 ATTAAAAAAAACTAGAAAA
1 ATTAAAAAAAACTAGAAAA
*
147862 ATTAAAAAAAATTAGAAA
1 ATTAAAAAAAACTAGAAA
147880 TACAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (19 bp):
ATTAAAAAAAACTAGAAAA
Found at i:148342 original size:12 final size:12
Alignment explanation
Indices: 148327--148365 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
148317 GAAAAAAACT
148327 AAAATATAAAAG
1 AAAATATAAAAG
*
148339 AAAATA-ATAAG
1 AAAATATAAAAG
148350 AAAATATAAAAG
1 AAAATATAAAAG
148362 AAAA
1 AAAA
148366 GTTAGTTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAATATAAAAG
Found at i:148544 original size:29 final size:29
Alignment explanation
Indices: 148507--148575 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
148497 TTTCTGGAAA
148507 TTAA-GAATTTAATATATGTATTTGTATT
1 TTAAGGAATTTAATATATGTATTTGTATT
* * *
148535 TTAAGGAATTTAGTCTTTGTATTTGTATT
1 TTAAGGAATTTAATATATGTATTTGTATT
* *
148564 TTTAGGAGTTTA
1 TTAAGGAATTTA
148576 GTGTCTTTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (29 bp):
TTAAGGAATTTAATATATGTATTTGTATT
Found at i:148793 original size:30 final size:30
Alignment explanation
Indices: 148754--148840 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 30
148744 ATTAATGATT
148754 AGATATAAATTTTAAAATTCGAAAAGTAAAG
1 AGAT-TAAATTTTAAAATTCGAAAAGTAAAG
* ** *
148785 AGATTAAATTTCTAAAAATATAAAA-TATAG
1 AGATTAAATTT-TAAAATTCGAAAAGTAAAG
*
148815 TGATTAAA-TTTAAAATTTTCGAAAAG
1 AGATTAAATTTTAAAA--TTCGAAAAG
148841 CACATATTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
28 5 0.11
29 2 0.05
30 23 0.52
31 14 0.32
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.33
Consensus pattern (30 bp):
AGATTAAATTTTAAAATTCGAAAAGTAAAG
Found at i:149375 original size:53 final size:53
Alignment explanation
Indices: 149312--149413 Score: 186
Period size: 53 Copynumber: 1.9 Consensus size: 53
149302 TTCATCAGCG
* *
149312 TTCTCTACTTCAATGGAGTTTCTAAGAGCAATAAATTCATATTCGATTTAACT
1 TTCTCTACTTCAATGGAGTTCCCAAGAGCAATAAATTCATATTCGATTTAACT
149365 TTCTCTACTTCAATGGAGTTCCCAAGAGCAATAAATTCATATTCGATTT
1 TTCTCTACTTCAATGGAGTTCCCAAGAGCAATAAATTCATATTCGATTT
149414 CATTAGCAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (53 bp):
TTCTCTACTTCAATGGAGTTCCCAAGAGCAATAAATTCATATTCGATTTAACT
Found at i:149445 original size:16 final size:16
Alignment explanation
Indices: 149421--149454 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
149411 TTTCATTAGC
* *
149421 AGGATAAATCTTCTTT
1 AGGACAAATCTTCATT
149437 AGGACAAATCTTCATT
1 AGGACAAATCTTCATT
149453 AG
1 AG
149455 CAATCGGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (16 bp):
AGGACAAATCTTCATT
Found at i:154810 original size:2 final size:2
Alignment explanation
Indices: 154803--154831 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
154793 AAATTACATA
154803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
154832 ACATAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:154842 original size:10 final size:12
Alignment explanation
Indices: 154797--154841 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
154787 TGTTCTAAAT
154797 TACATA-ATATA
1 TACATATATATA
*
154808 TATATATATATA
1 TACATATATATA
*
154820 TATATATATATA
1 TACATATATATA
154832 -ACATA-ATATA
1 TACATATATATA
154842 AAGTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 5 0.16
11 9 0.29
12 17 0.55
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (12 bp):
TACATATATATA
Found at i:165117 original size:17 final size:17
Alignment explanation
Indices: 165095--165138 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
165085 TTGCATGCAT
*
165095 ATTTTTTTTGTCATTGC
1 ATTTTTTTTGTCACTGC
* *
165112 ATTTTTATTGTCCCTGC
1 ATTTTTTTTGTCACTGC
*
165129 ATTTTATTTG
1 ATTTTTTTTG
165139 GTTTAATAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (17 bp):
ATTTTTTTTGTCACTGC
Found at i:168472 original size:2 final size:2
Alignment explanation
Indices: 168465--168492 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
168455 TTCTATCCTT
168465 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
168493 TGTTAATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:170897 original size:34 final size:34
Alignment explanation
Indices: 170857--170944 Score: 131
Period size: 34 Copynumber: 2.6 Consensus size: 34
170847 GTACACGATT
*
170857 AACCATCCAACACACTAGATGCTCGTATAAGCCA
1 AACCATCCAACACACCAGATGCTCGTATAAGCCA
* * *
170891 ATCCATCCAACACACCAGATGCTTGTATGAGCCA
1 AACCATCCAACACACCAGATGCTCGTATAAGCCA
*
170925 AACCATCTAACACACCAGAT
1 AACCATCCAACACACCAGAT
170945 AACATTGTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.38, C:0.33, G:0.11, T:0.18
Consensus pattern (34 bp):
AACCATCCAACACACCAGATGCTCGTATAAGCCA
Found at i:176782 original size:20 final size:19
Alignment explanation
Indices: 176754--176826 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
176744 AATAAAAAAG
*
176754 ATAAGAAATATCAAATTTTA
1 ATAAAAAATAT-AAATTTTA
*
176774 ATAAAAAATGTAAATTTTA
1 ATAAAAAATATAAATTTTA
* * * *
176793 TTAAAAACTAGAAATTTTTT
1 ATAAAAAATATAAA-TTTTA
*
176813 ATAAAAAATGTAAA
1 ATAAAAAATATAAA
176827 AAATTATAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 18 0.44
20 23 0.56
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (19 bp):
ATAAAAAATATAAATTTTA
Found at i:176790 original size:19 final size:19
Alignment explanation
Indices: 176766--176859 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 19
176756 AAGAAATATC
176766 AAATTTTAATAAAAAATGT-
1 AAATTTT-ATAAAAAATGTA
*
176785 AAATTTTATTAAAAACTAG-A
1 AAATTTTA-TAAAAAAT-GTA
*
176805 AATTTTTTATAAAAAATGTA
1 AA-ATTTTATAAAAAATGTA
**
176825 AAAAATTATAAAAAATTGTA
1 AAATTTTATAAAAAA-TGTA
176845 AAATTTTATAAAAAA
1 AAATTTTATAAAAAA
176860 ATTATAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
19 25 0.41
20 30 0.49
21 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (19 bp):
AAATTTTATAAAAAATGTA
Found at i:176836 original size:10 final size:10
Alignment explanation
Indices: 176811--176868 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
176801 TAGAAATTTT
176811 TTATAAAAAA
1 TTATAAAAAA
*
176821 -TGTAAAAAA
1 TTATAAAAAA
176830 TTATAAAAAA
1 TTATAAAAAA
* **
176840 TTGTAAAATT
1 TTATAAAAAA
176850 TTATAAAAAAA
1 TTAT-AAAAAA
176861 TTATAAAA
1 TTATAAAA
176869 TGCATCAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 8 0.21
10 22 0.58
11 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:176852 original size:39 final size:38
Alignment explanation
Indices: 176766--176859 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
176756 AAGAAATATC
** *
176766 AAATTTTAATAAAAAATGTAAATTTTATTAAAAACTAGA
1 AAATTTT-ATAAAAAATGTAAAAATTATTAAAAAATAGA
* *
176805 AATTTTTTATAAAAAATGTAAAAAATTA-TAAAAAATTGTA
1 AA-ATTTTATAAAAAATGT-AAAAATTATTAAAAAATAG-A
176845 AAATTTTATAAAAAA
1 AAATTTTATAAAAAA
176860 ATTATAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
39 33 0.72
40 13 0.28
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (38 bp):
AAATTTTATAAAAAATGTAAAAATTATTAAAAAATAGA
Found at i:178299 original size:19 final size:19
Alignment explanation
Indices: 178252--178300 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
178242 CTATAAATTT
178252 TTTTATAAAAATTGTAAAA
1 TTTTATAAAAATTGTAAAA
**
178271 -AATATAAAAAATTGTAAAA
1 TTTTAT-AAAAATTGTAAAA
178290 TTTTATAAAAA
1 TTTTATAAAAA
178301 AAATTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 18 0.75
20 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (19 bp):
TTTTATAAAAATTGTAAAA
Found at i:178640 original size:8 final size:9
Alignment explanation
Indices: 178624--178650 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
178614 ATAAAATTTA
178624 ATAATTTTT
1 ATAATTTTT
178633 ATAATTTTT
1 ATAATTTTT
178642 ATAATTTTT
1 ATAATTTTT
178651 TATTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATAATTTTT
Found at i:178651 original size:10 final size:10
Alignment explanation
Indices: 178565--178653 Score: 56
Period size: 10 Copynumber: 8.6 Consensus size: 10
178555 CTTTATAAAA
*
178565 TTTTATATTT
1 TTTTATAATT
*
178575 TTTTCTAATT
1 TTTTATAATT
*
178585 TTTAATAAAAATAT
1 TTT--T-ATAAT-T
*
178599 TTTTATAGTT
1 TTTTATAATT
**
178609 TTTTAATAAAA
1 TTTT-ATAATT
*
178620 TTTAATAA-T
1 TTTTATAATT
178629 TTTTATAA-T
1 TTTTATAATT
178638 TTTTATAATT
1 TTTTATAATT
178648 TTTTAT
1 TTTTAT
178654 TTTTTGTCAC
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
9 16 0.26
10 27 0.44
11 9 0.15
12 2 0.03
13 3 0.05
14 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:180596 original size:8 final size:8
Alignment explanation
Indices: 180568--180640 Score: 51
Period size: 8 Copynumber: 8.5 Consensus size: 8
180558 ACATGTGGCA
180568 AAAAACTAT
1 AAAAA-TAT
180577 ATAAAA-AT
1 A-AAAATAT
180585 AAAAATAT
1 AAAAATAT
180593 AAAAATAT
1 AAAAATAT
**
180601 CAAATTTTAAT
1 -AAA-AAT-AT
180612 AAAAATAT
1 AAAAATAT
180620 AAAAATTATT
1 AAAAA-TA-T
180630 AAAAAT-T
1 AAAAATAT
180637 AAAA
1 AAAA
180641 TTTTTGTATA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
7 9 0.17
8 20 0.38
9 8 0.15
10 14 0.26
11 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAATAT
Found at i:180667 original size:40 final size:39
Alignment explanation
Indices: 180605--180703 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 39
180595 AAATATCAAA
* *
180605 TTTTAATAAAAATAT-AAAAATTATTAAAA-ATT-AAAATT
1 TTTT-ATAAAAATATAAAAAATTATAAAAAGATTGAAAA-C
180643 TTTGTATAAAAATCATAAAAAATTATAAAAAGATTGAAAAC
1 TTT-TATAAAAAT-ATAAAAAATTATAAAAAGATTGAAAAC
180684 TTTTATAAAAATTATAAAAA
1 TTTTATAAAAA-TATAAAAA
180704 GCATCAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
38 11 0.21
39 3 0.06
40 28 0.53
41 7 0.13
42 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (39 bp):
TTTTATAAAAATATAAAAAATTATAAAAAGATTGAAAAC
Found at i:181258 original size:93 final size:88
Alignment explanation
Indices: 181073--181281 Score: 224
Period size: 93 Copynumber: 2.3 Consensus size: 88
181063 TAAGAGTGAC
* ** *
181073 TCAAGTACTCAATTGAGTGCAAAAAAATTAAAGGGCTTAATTGCTTTTTTTGAATATTTTTTAGG
1 TCAAGTAC-CAATTGAGTGCAAAAAAATTAAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGG
* * * *
181138 GCCTTTTTGATGCATTTTGAAAGT
65 GACTTTTTAATGCATTTTCAAAAT
*
181162 TCAAGTATCCAATTGAGTGCAAAAAAGATGT-AGGGGCTTAATTGCTTTTTTTTTTGAAAAAGTT
1 TCAAGTA-CCAATTGAGTGCAAAAAA-AT-TAAAGGGCTTAATTGC---TTTTTTTGAAAAAGTT
181226 TGAGGGACTTTTTAATGCA-TTTCAATAAT
60 TGAGGGACTTTTTAATGCATTTTCAA-AAT
* *
181255 TCAAATACCTAATTGAATGCAAAAAAA
1 TCAAGTACC-AATTGAGTGCAAAAAAA
181282 AAAAGAAAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
89 24 0.24
90 16 0.16
91 1 0.01
92 8 0.08
93 52 0.51
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (88 bp):
TCAAGTACCAATTGAGTGCAAAAAAATTAAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG
ACTTTTTAATGCATTTTCAAAAT
Found at i:181412 original size:8 final size:7
Alignment explanation
Indices: 181386--181410 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
181376 AGGATTTCCA
181386 TTTTGTT
1 TTTTGTT
181393 TTTTGTT
1 TTTTGTT
181400 TTTTGTT
1 TTTTGTT
181407 TTTT
1 TTTT
181411 TGGATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:182619 original size:90 final size:87
Alignment explanation
Indices: 182465--182720 Score: 252
Period size: 90 Copynumber: 2.9 Consensus size: 87
182455 CTTCAAGCTT
* * * * * * *
182465 GTTTAAAAAAAAATAATTATGCTTCTCTT-TATTTTTGTACTCAATTGAGTACTTGAAGTGTCAA
1 GTTTAAAAAAAAACAATTAAGC--CCCTTATTTTTTTGCACTCAATTGGGTACTTGAACTGTCAA
182529 AATGCATCAAAAAGACCCGCAAAC
64 AATGCATCAAAAAGACCCGCAAAC
* * * *
182553 -TTTAAAAAAAAAAACAATTAAG-CCCTTGCCCTTTTTTTGCACTCAATTGGGTGCTTTAACTTT
1 GTTT--AAAAAAAAACAATTAAGCCCCTT---ATTTTTTTGCACTCAATTGGGTACTTGAACTGT
* *
182616 CAAAATGCATAAAAAAAACCCGCAAAC
61 CAAAATGCATCAAAAAGACCCGCAAAC
* * * * *
182643 GTTTTAAAAAGAGCAATTAAGCCCCTTATTTTTTT-CACTGAATTGGGTAATTGAACTGTC-AAA
1 GTTTAAAAAAAAACAATTAAGCCCCTTATTTTTTTGCACTCAATTGGGTACTTGAACTGTCAAAA
182706 TGCATCAAAAAGACC
66 TGCATCAAAAAGACC
182721 TTTCGACTAT
Statistics
Matches: 137, Mismatches: 23, Indels: 19
0.77 0.13 0.11
Matches are distributed among these distances:
85 16 0.12
86 24 0.18
87 10 0.07
89 29 0.21
90 55 0.40
91 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (87 bp):
GTTTAAAAAAAAACAATTAAGCCCCTTATTTTTTTGCACTCAATTGGGTACTTGAACTGTCAAAA
TGCATCAAAAAGACCCGCAAAC
Found at i:182931 original size:9 final size:9
Alignment explanation
Indices: 182894--182950 Score: 51
Period size: 10 Copynumber: 5.9 Consensus size: 9
182884 AGAATTTTTT
182894 TTATAAAAA
1 TTATAAAAA
*
182903 TCATTAAAAA
1 TTA-TAAAAA
182913 TATATAAAAAA
1 T-TAT-AAAAA
* *
182924 TTGTAAAATT
1 TTATAAAA-A
182934 TTATAAAAA
1 TTATAAAAA
182943 TTATAAAA
1 TTATAAAA
182951 TGCATTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 14 0.37
10 17 0.45
11 7 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:182931 original size:19 final size:19
Alignment explanation
Indices: 182895--182951 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
182885 GAATTTTTTT
* *
182895 TATAAAAATCATTAAAAATA
1 TATAAAAATTA-TAAAATTA
* *
182915 TATAAAAAATTGTAAAATTT
1 TAT-AAAAATTATAAAATTA
182935 TATAAAAATTATAAAAT
1 TATAAAAATTATAAAAT
182952 GCATTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 13 0.42
20 12 0.39
21 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TATAAAAATTATAAAATTA
Found at i:183494 original size:90 final size:89
Alignment explanation
Indices: 183335--183508 Score: 246
Period size: 90 Copynumber: 1.9 Consensus size: 89
183325 TTAAATACCC
**
183335 AATTGAGTGCAAAAAAATTAGGGGTTTAATTGCTATTTTTTGAAAAAAGTTTGAGGGCCTTTTTG
1 AATTGAGTGCAAAAAAATTAGGGCCTTAATTGCTATTTTTTGAAAAAAGTTT-AGGGCCTTTTTG
183400 ATGCATTTTGAAAGTTCAAGTATCA
65 ATGCATTTTGAAAGTTCAAGTATCA
*
183425 AATTGAGTGCAAAAAAGATGTAGGGCCTTAATTGCT-TTTTTT-AAAAAAGTTT-GTGCACTTTT
1 AATTGAGTGCAAAAAA-AT-TAGGGCCTTAATTGCTATTTTTTGAAAAAAGTTTAGGGC-CTTTT
*
183487 TGAATGCATTTTGATAGTTCAA
63 TG-ATGCATTTTGAAAGTTCAA
183509 ATACCTAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
88 3 0.04
89 7 0.09
90 44 0.58
91 8 0.11
92 14 0.18
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (89 bp):
AATTGAGTGCAAAAAAATTAGGGCCTTAATTGCTATTTTTTGAAAAAAGTTTAGGGCCTTTTTGA
TGCATTTTGAAAGTTCAAGTATCA
Found at i:183529 original size:90 final size:91
Alignment explanation
Indices: 183344--183530 Score: 213
Period size: 90 Copynumber: 2.1 Consensus size: 91
183334 CAATTGAGTG
**
183344 CAAAAAA-AT-TAGGGGTTTAATTGCTATTTTTTGAAAAAAGTTTGAGGGCCTTTTTGATGCATT
1 CAAAAAAGATGTAGGGCCTTAATTGCTATTTTTTGAAAAAAGTTT-AGGGCCTTTTTGATGCATT
* * * * *
183407 TTGAAAGTTCAAGTATCAAATTGAGTG
65 TTGAAAGTTCAAATACCAAATTAAATA
*
183434 CAAAAAAGATGTAGGGCCTTAATTGCT-TTTTTT-AAAAAAGTTT-GTGCACTTTTTGAATGCAT
1 CAAAAAAGATGTAGGGCCTTAATTGCTATTTTTTGAAAAAAGTTTAGGGC-CTTTTTG-ATGCAT
* *
183496 TTTGATAGTTCAAATACCTAATTAAATA
64 TTTGAAAGTTCAAATACCAAATTAAATA
*
183524 TAAAAAA
1 CAAAAAA
183531 AACAGGGATT
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
88 3 0.04
89 7 0.09
90 50 0.61
91 8 0.10
92 14 0.17
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (91 bp):
CAAAAAAGATGTAGGGCCTTAATTGCTATTTTTTGAAAAAAGTTTAGGGCCTTTTTGATGCATTT
TGAAAGTTCAAATACCAAATTAAATA
Done.