Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014823.1 Kokia drynarioides strain JFW-HI SEQ_129865, 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: 122613
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 201 characters in sequence are not A, C, G, or T
Found at i:1449 original size:347 final size:341
Alignment explanation
Indices: 685--1506 Score: 1090
Period size: 347 Copynumber: 2.4 Consensus size: 341
675 ATATTTTGTT
* * *
685 TCGATTTTAGATAAATTATATTTAAATAATAATTTTTTCAATTTTAATATAATAATATAATTTGA
1 TCGACTTTAGATAAATTATATTTAAATGATAATTTTTTCAATTTTAATATAATAATATAATTTAA
* * * *
750 TTTTCAAGAGTATCCTAAATAAATTTGTTGCCTATTGATATTATTTATTTAGTTATGT-TTTTTT
66 TTTTCAAGTGTATCCTAAATAAGTTTGTTGCCTATTGATATTATTTACTTAGTTATGTCTTTTTA
* * * *
814 TTTAATTAAAAAATTAATTATCTCATGTTTTTATGCAACTAATGACTTCAGATGGAGCTTCTAAG
131 TTAAATTAAAAAATTAATCATCCCATGCTTTTATGCAACTAATGACTTCAGATGGAGCTTC--A-
* * * * *
879 GAATGACTTAGATTCTATGCAAGTGTATGAGATGGCTCCAATGGTAATTTAAAAGCATTGCTATT
193 GAACGAC----ATTCTATGCAAGTCTATGAGATGACTCCAATGGGAATTGAAAAGCATTGCTATT
* *
944 ATTTTCAATGTTTATAGTTGATTAACTATTATTATTAGAATAGTAATTCGATTCAAATTGATTTA
254 ATTTTCAATGTTTATAGTCGATTAACTATTATTATTAGAATAGTAATTCAATTCAAATTGATTTA
*
1009 TCTTGAATTAAATTTTTTTAGGC
319 TCTTGAATTAAATTCTTTTAGGC
* * *
1032 TCGACTTTAGAT-AATTATATTTTAATGAT-ATTTTTTCAATTTTAATAAAATAAAATAATTTAA
1 TCGACTTTAGATAAATTATATTTAAATGATAATTTTTTCAATTTTAATATAATAATATAATTTAA
* *
1095 TTTTCAAGTGTATCCTAAATAAGTTTCTTGTCTATTGATATTATTTACTTAGTTATGTCTTTCTT
66 TTTTCAAGTGTATCCTAAATAAGTTTGTTGCCTATTGATATTATTTACTTAGTTATGTCTTT-TT
*
1160 ATTAAATTAAGAAATTAATCATCCCATGCTTTTATGCAACTAATGACTTCAGGA-GTG-GCTTC-
130 ATTAAATTAAAAAATTAATCATCCCATGCTTTTATGCAACTAATGACTTCA-GATG-GAGCTTCA
* * *
1222 GAACGAC-TTCTGTGCCAACGTCT-T-ATATGACTTCAATGGGAATTGAAAAGGC-TTGCTATTA
193 GAACGACATTCTATG-CAA-GTCTATGAGATGACTCCAATGGGAATTGAAAA-GCATTGCTATTA
1283 TTTTCAATGTTTATAGTCGATTAACTACTACTATTATTATTAGAATAGTAATTCAATTCAAATTG
255 TTTTCAATGTTTATAGTCGA-T---TA--ACTATTATTATTAGAATAGTAATTCAATTCAAATTG
*
1348 ATTTATCTTGAATTACATTCTTTT-GGC
314 ATTTATCTTGAATTAAATTCTTTTAGGC
* *
1375 TCGACTTTAGATAAATTATATTTAAATGATAATCTTTTTTCAATTCTAATATAGTAATATAATTT
1 TCGACTTTAGATAAATTATATTTAAATGATAA--TTTTTTCAATTTTAATATAATAATATAATTT
*
1440 AATTTTCAAGTGTATCCTAAATAAGTTTGTTGCCCATTGATATTATTTACTTAGTTATGTCTTTT
64 AATTTTCAAGTGTATCCTAAATAAGTTTGTTGCCTATTGATATTATTTACTTAGTTATGTCTTTT
1505 TA
129 TA
1507 AAAAAAATAA
Statistics
Matches: 421, Mismatches: 37, Indels: 35
0.85 0.08 0.07
Matches are distributed among these distances:
338 54 0.13
339 7 0.02
340 3 0.01
342 2 0.00
343 21 0.05
344 73 0.17
345 85 0.20
346 21 0.05
347 152 0.36
348 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (341 bp):
TCGACTTTAGATAAATTATATTTAAATGATAATTTTTTCAATTTTAATATAATAATATAATTTAA
TTTTCAAGTGTATCCTAAATAAGTTTGTTGCCTATTGATATTATTTACTTAGTTATGTCTTTTTA
TTAAATTAAAAAATTAATCATCCCATGCTTTTATGCAACTAATGACTTCAGATGGAGCTTCAGAA
CGACATTCTATGCAAGTCTATGAGATGACTCCAATGGGAATTGAAAAGCATTGCTATTATTTTCA
ATGTTTATAGTCGATTAACTATTATTATTAGAATAGTAATTCAATTCAAATTGATTTATCTTGAA
TTAAATTCTTTTAGGC
Found at i:1871 original size:41 final size:41
Alignment explanation
Indices: 1748--2035 Score: 258
Period size: 41 Copynumber: 6.9 Consensus size: 41
1738 GCAGCCATCA
* *
1748 TTCAATCTTTTACCCCTAAGTCAA-AAGGGACAGATTGAAGAT
1 TTCAGTCTTTTACCCTTAA-TCAAGAA-GGACAGATTGAAGAT
* * * *
1790 CATTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGAT
1 --TT-CAGTCTTTTACCCTTAA-TCAAGAAGGACAGATTGAAGAT
* * *
1835 TTTAGTTTTTTACCCTTAATCAAGAAGGACAAATTGAAGAT
1 TTCAGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGAT
* **
1876 TCCAGTCTTTTACCCTTAATCAAGAAGGGTAGATTGAAGAT
1 TTCAGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGAT
* *
1917 TTCAGTCTCTTACCCTTAATCAAGAAGGATAGATTGAAGAT
1 TTCAGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGAT
* * * * * **
1958 TCCAATATTTTACTCC-TAGTCAAGAGGGGTAGATTGAAGAT
1 TTCAGTCTTTTAC-CCTTAATCAAGAAGGACAGATTGAAGAT
* * * *
1999 TCCAATCTTTTACCCCTAGTCAAG-AGGTACAGATTGA
1 TTCAGTCTTTTACCCTTAATCAAGAAGG-ACAGATTGA
2036 CCATTCTAAT
Statistics
Matches: 210, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.02
41 150 0.71
42 15 0.07
43 2 0.01
44 2 0.01
45 36 0.17
46 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (41 bp):
TTCAGTCTTTTACCCTTAATCAAGAAGGACAGATTGAAGAT
Found at i:1915 original size:82 final size:81
Alignment explanation
Indices: 1661--2060 Score: 345
Period size: 82 Copynumber: 4.7 Consensus size: 81
1651 CATCATCCAA
* * * *
1661 TCTTTTACCCTTGAGTCAAGAGGGGCAGATTGTAGCCATCATCCAATCTTTTACCCTTAAATCAA
1 TCTTTTACCCTT-AATCAAGAAGGACAGATTGAAG--AT--TCCAATCTTTTACCC-T-AATCAA
* * * *
1726 GAGAGGTAAATTGCAGCCATCATTCAA
59 GAGGGGTAGATTGAAG--AT--TTCAG
*
1753 TCTTTTACCCCTAAGTCAA-AAGGGACAGATTGAAGATCATTCCAATCTTTTACCCCTAAGTCAA
1 TCTTTTACCCTTAA-TCAAGAA-GGACAGATTGAAG---ATTCCAATCTTTTA-CCCTAA-TCAA
* *
1817 GAGGGGCAGATTGAAGATTTTAG
59 GAGGGGTAGATTGAAGATTTCAG
* * * *
1840 TTTTTTACCCTTAATCAAGAAGGACAAATTGAAGATTCCAGTCTTTTACCCTTAATCAAGAAGGG
1 TCTTTTACCCTTAATCAAGAAGGACAGATTGAAGATTCCAATCTTTTACCC-TAATCAAGAGGGG
1905 TAGATTGAAGATTTCAG
65 TAGATTGAAGATTTCAG
* * * *
1922 TCTCTTACCCTTAATCAAGAAGGATAGATTGAAGATTCCAATATTTTACTCCTAGTCAAGAGGGG
1 TCTTTTACCCTTAATCAAGAAGGACAGATTGAAGATTCCAATCTTTTAC-CCTAATCAAGAGGGG
* *
1987 TAGATTGAAGATTCCAA
65 TAGATTGAAGATTTCAG
* * ** * * *
2004 TCTTTTACCCCTAGTCAAG-AGGTACAGATTGACCATTCTAATCTCTTACCCTGATCA
1 TCTTTTACCCTTAATCAAGAAGG-ACAGATTGAAGATTCCAATCTTTTACCCTAATCA
2061 TGGGGCAGAT
Statistics
Matches: 259, Mismatches: 40, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
81 9 0.03
82 132 0.51
83 18 0.07
86 16 0.06
87 17 0.07
89 2 0.01
90 2 0.01
91 31 0.12
92 29 0.11
93 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (81 bp):
TCTTTTACCCTTAATCAAGAAGGACAGATTGAAGATTCCAATCTTTTACCCTAATCAAGAGGGGT
AGATTGAAGATTTCAG
Found at i:1955 original size:123 final size:127
Alignment explanation
Indices: 1608--2035 Score: 329
Period size: 123 Copynumber: 3.3 Consensus size: 127
1598 TGTCGAAGCC
* * *
1608 ATTCCAATCTTTTACCCCTAAGTAAAG-AGAGACAGATTGAAGCCATCA-TCCAATCTTTTACCC
1 ATTCCAATCTTTTACCCCTAA-TCAAGAAGGGACAGATTGAAG--AT-ATTCCAATCTCTTACCC
* * * * * * *
1671 TTGAGTCAAGAGGGGCAGATTGTAGCCATCATCCAATCTTTTAC-CCTTAAATCAAGAGAGG-TA
62 CTAAGTCAAGAAGGACAGATTGAAG--AT--TCCAATATTTTACTCC-T-AATCAAGA-AGGACA
*
1734 AATTGCAG
120 AATTGAAG
* *
1742 CCATCATTCAATCTTTTACCCCTAAGTCAA-AAGGGACAGATTGAAGATCATTCCAATCTTTTAC
1 --AT--TCCAATCTTTTACCCCTAA-TCAAGAAGGGACAGATTGAAGAT-ATTCCAATCTCTTAC
* * ** * *
1806 CCCTAAGTCAAGAGGGGCAGATTGAAGATTTTAGTTTTTTAC-CCTTAATCAAGAAGGACAAATT
60 CCCTAAGTCAAGAAGGACAGATTGAAGATTCCAATATTTTACTCC-TAATCAAGAAGGACAAATT
1870 GAAG
124 GAAG
* * * * *
1874 ATTCCAGTCTTTTACCCTTAATCAAGAAGGG-TAGATTGAAGAT-TT-CAGTCTCTTACCCTTAA
1 ATTCCAATCTTTTACCCCTAATCAAGAAGGGACAGATTGAAGATATTCCAATCTCTTACCCCTAA
* * * ** *
1936 -TCAAGAAGGATAGATTGAAGATTCCAATATTTTACTCCTAGTCAAGAGGGGTAGATTGAAG
66 GTCAAGAAGGACAGATTGAAGATTCCAATATTTTACTCCTAATCAAGAAGGACAAATTGAAG
* *
1997 ATTCCAATCTTTTACCCCTAGTCAAG-AGGTACAGATTGA
1 ATTCCAATCTTTTACCCCTAATCAAGAAGGGACAGATTGA
2036 CCATTCTAAT
Statistics
Matches: 248, Mismatches: 36, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
122 3 0.01
123 76 0.31
124 16 0.06
125 2 0.01
127 15 0.06
128 21 0.08
130 2 0.01
131 3 0.01
132 16 0.06
133 13 0.05
135 2 0.01
136 6 0.02
137 37 0.15
138 36 0.15
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (127 bp):
ATTCCAATCTTTTACCCCTAATCAAGAAGGGACAGATTGAAGATATTCCAATCTCTTACCCCTAA
GTCAAGAAGGACAGATTGAAGATTCCAATATTTTACTCCTAATCAAGAAGGACAAATTGAAG
Found at i:2227 original size:45 final size:46
Alignment explanation
Indices: 1602--2249 Score: 489
Period size: 46 Copynumber: 14.9 Consensus size: 46
1592 AATTATTGTC
* * *
1602 GAAGCCAT--TCCAATCTTTTACCCCTAAGTAAAGAGAGACAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* *
1646 GAAGCCATCATCCAATCTTTTACCCTTGAGTCAAGAGGGGCAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * * * * *
1692 GTAGCCATCATCCAATCTTTTACCCTTAAATCAAGAGAGGTAAATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * * *
1738 GCAGCCATCATTCAATCTTTTACCCCTAAGTCAAAAGGGACAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
1784 GAAG--ATCATTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
1 GAAGCCATCA-TCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
** * * * * * *
1829 GAAG--AT--TTTAGTTTTTTACCCTTAA-TCAAGAAGGACAAATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * * *
1870 GAAG--AT--TCCAGTCTTTTACCCTTAA-TCAAGAAGGGTAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * * * * **
1911 GAAG--AT--TTCAGTCTCTTACCCTTAA-TCAAGAAGGATAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * *
1952 GAAG--AT--TCCAATATTTTACTCCT-AGTCAAGAGGGGTAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
**
1993 GAAG--AT--TCCAATCTTTTACCCCT-AGTCAAGAGGTACAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * * *
2034 G-A-CCAT--TCTAATCTCTTA-CCCTGA-TC-A-TGGGGCAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * *
2072 GCAA-CTATCATTCAATCTTTTACCCCTAAGTCAAGAGGGGTAGATT
1 G-AAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* *
2118 GTAGCCATCATCCAATCTTTTACCCCTAAGTTAAGAGGGGCAGATT
1 GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* *
2164 GCAA-CCATCATCCAATCTTTTACCCCTAA-TCGAGAGGGGCAGATA
1 G-AAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
* * *
2209 GAAGCCA-CATTTCGATCTTTTACCTCT-AGTCAAGAGGGGCA
1 GAAGCCATCA-TCCAATCTTTTACCCCTAAGTCAAGAGGGGCA
2250 AATCAAACCC
Statistics
Matches: 505, Mismatches: 79, Indels: 39
0.81 0.13 0.06
Matches are distributed among these distances:
38 9 0.02
39 1 0.00
40 12 0.02
41 167 0.33
42 23 0.05
43 5 0.01
44 19 0.04
45 83 0.16
46 185 0.37
47 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (46 bp):
GAAGCCATCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATT
Found at i:4901 original size:7 final size:7
Alignment explanation
Indices: 4889--4929 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
4879 CCCCTCTTTT
4889 TTATTAA
1 TTATTAA
4896 TTATTAA
1 TTATTAA
*
4903 TTAATAA
1 TTATTAA
4910 TTATTAA
1 TTATTAA
4917 -TATT-A
1 TTATTAA
4922 TTATTAA
1 TTATTAA
4929 T
1 T
4930 ATCAAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 8 0.27
7 21 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:4926 original size:12 final size:12
Alignment explanation
Indices: 4895--4931 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4885 TTTTTTATTA
4895 ATTATTAATTAAT
1 ATTATT-ATTAAT
4908 A--ATTATTAAT
1 ATTATTATTAAT
4918 ATTATTATTAAT
1 ATTATTATTAAT
4930 AT
1 AT
4932 CAAAACATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.32
11 3 0.14
12 11 0.50
13 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:5709 original size:17 final size:17
Alignment explanation
Indices: 5669--5780 Score: 129
Period size: 17 Copynumber: 6.5 Consensus size: 17
5659 ATTTATTTTA
5669 AAATTTAAATTTGAAAAT
1 AAATTTAAATTT-AAAAT
* *
5687 -AA-TTAAACTTAAATT
1 AAATTTAAATTTAAAAT
5702 AAATTTAAATTTTAAAAT
1 AAATTTAAA-TTTAAAAT
*
5720 AAATTCAAATTTAAAAT
1 AAATTTAAATTTAAAAT
* *
5737 AAATTTAAATTTTTAAAC
1 AAATTTAAA-TTTAAAAT
*
5755 AAATTTAATTTTAAAAT
1 AAATTTAAATTTAAAAT
5772 AAATTTAAA
1 AAATTTAAA
5781 GGGAGTATGG
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.05
16 9 0.12
17 37 0.47
18 28 0.36
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:5741 original size:35 final size:34
Alignment explanation
Indices: 5669--5780 Score: 145
Period size: 35 Copynumber: 3.3 Consensus size: 34
5659 ATTTATTTTA
* * *
5669 AAATTTAAATTTGAAAAT-AATTAAACTTAAATT
1 AAATTTAAATTTTAAAATAAATTAAATTTAAAAT
5702 AAATTTAAATTTTAAAATAAATTCAAATTTAAAAT
1 AAATTTAAATTTTAAAATAAATT-AAATTTAAAAT
* * *
5737 AAATTTAAATTTTTAAACAAATTTAATTTTAAAAT
1 AAATTTAAATTTTAAAATAAA-TTAAATTTAAAAT
5772 AAATTTAAA
1 AAATTTAAA
5781 GGGAGTATGG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
33 17 0.24
34 4 0.06
35 47 0.67
36 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTTAAAATAAATTAAATTTAAAAT
Found at i:5780 original size:6 final size:6
Alignment explanation
Indices: 5669--5748 Score: 58
Period size: 6 Copynumber: 13.0 Consensus size: 6
5659 ATTTATTTTA
* *
5669 AAATTT AAATTT GAAAATAATT AAACTT AAA-TT AAATTT AAATTTT AAA-AT
1 AAATTT AAATTT --AAAT--TT AAATTT AAATTT AAATTT AAA-TTT AAATTT
* *
5720 AAATTC AAATTT AAA-AT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT
5749 TTAAACAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
5 13 0.22
6 31 0.53
7 6 0.10
8 7 0.12
10 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:10474 original size:30 final size:30
Alignment explanation
Indices: 10440--10516 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
10430 GTTCGAGGTC
***
10440 AAAATGGAATTTTTGAAAATTTTAGGGGTA
1 AAAATGGAATTTTTGAAAAAAATAGGGGTA
* * *
10470 AAAATGTAA-TTTTCAAAAAAATAGGGTTA
1 AAAATGGAATTTTTGAAAAAAATAGGGGTA
*
10499 AAAATGGAATTTTGGAAA
1 AAAATGGAATTTTTGAAA
10517 GTACAAGGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.47, C:0.01, G:0.19, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTTGAAAAAAATAGGGGTA
Found at i:11594 original size:23 final size:25
Alignment explanation
Indices: 11567--11624 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
11557 GTCTCCTTTT
**
11567 TTATTTCATTATT-ACTAATA-TTA
1 TTATTTCATTATTAAAAAATAGTTA
11590 TTA-TT-ATTATTAAAAAATAGTTA
1 TTATTTCATTATTAAAAAATAGTTA
11613 TTATTATCATTA
1 TTATT-TCATTA
11625 ATATTAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
21 6 0.21
22 7 0.25
23 9 0.32
24 1 0.04
25 1 0.04
26 4 0.14
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (25 bp):
TTATTTCATTATTAAAAAATAGTTA
Found at i:11625 original size:23 final size:22
Alignment explanation
Indices: 11583--11625 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
11573 CATTATTACT
*
11583 AATATTATTATTATTATTAAAA
1 AATATTATTATTATCATTAAAA
11605 AATAGTTATTATTATCATTAA
1 AATA-TTATTATTATCATTAA
11626 TATTAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
AATATTATTATTATCATTAAAA
Found at i:11675 original size:31 final size:31
Alignment explanation
Indices: 11610--11677 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
11600 TAAAAAATAG
* * *
11610 TTATTATTATCATTAATATTAATTACGGTTA
1 TTATTATTATCAATAATATTAATTACGCTGA
*
11641 TTATTATTATCAATAATATT-ATTAATGCTGA
1 TTATTATTATCAATAATATTAATT-ACGCTGA
11672 TTATTA
1 TTATTA
11678 AATACGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (31 bp):
TTATTATTATCAATAATATTAATTACGCTGA
Found at i:12383 original size:6 final size:6
Alignment explanation
Indices: 12372--12471 Score: 79
Period size: 6 Copynumber: 17.3 Consensus size: 6
12362 GGTTTCTCTT
* * *
12372 AATTTA AATTTA GAA--TA ATTTTA AATTT- AATAATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AAT-TTA AATTTA AATTTA
* *
12419 AA-TTA AATTTA AATTTA AA-ATA AATTT- AATCTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AAT-TTA AATTTA AATTTA
12464 AATTTA AA
1 AATTTA AA
12472 GAAAAGTGGG
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
4 1 0.01
5 21 0.28
6 46 0.61
7 7 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:12396 original size:17 final size:17
Alignment explanation
Indices: 12372--12471 Score: 139
Period size: 17 Copynumber: 5.8 Consensus size: 17
12362 GGTTTCTCTT
*
12372 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
12389 ATTTTAAATTTAATAATA
1 AATTTAAATTTAA-AATA
* *
12407 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
12424 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
12441 AATTT-AATCTTAAAATA
1 AATTTAAAT-TTAAAATA
12458 AATTTAAATTTAAA
1 AATTTAAATTTAAA
12472 GAAAAGTGGG
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
16 3 0.04
17 52 0.71
18 18 0.25
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:12765 original size:17 final size:17
Alignment explanation
Indices: 12741--12788 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
12731 GACTTCTCTT
* *
12741 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAACA
*
12758 ATTTTAAATTTAAAACA
1 AATTTAAATTTAAAACA
12775 AATTTAAATTTAAA
1 AATTTAAATTTAAA
12789 GAAAAGTGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAAACA
Found at i:15773 original size:13 final size:14
Alignment explanation
Indices: 15755--15823 Score: 50
Period size: 15 Copynumber: 4.8 Consensus size: 14
15745 TAACAAATAC
15755 ATTTTT-TAACAAT
1 ATTTTTCTAACAAT
*
15768 ATTTTTCTATCACAT
1 ATTTTTCTAACA-AT
* *
15783 TTTTTTCTAAAAAT
1 ATTTTTCTAACAAT
* * *
15797 ACTTTTTAATAAAAAC
1 A-TTTTT-CTAACAAT
15813 ATTTTTCTAAC
1 ATTTTTCTAAC
15824 TACAATAGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
13 6 0.14
14 9 0.21
15 21 0.49
16 7 0.16
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTTCTAACAAT
Found at i:16281 original size:9 final size:8
Alignment explanation
Indices: 16268--16297 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16258 CATTTTAATA
16268 ATTTTTTT
1 ATTTTTTT
16276 ATTTTTTT
1 ATTTTTTT
*
16284 ATTTTTTA
1 ATTTTTTT
16292 ATTTTT
1 ATTTTT
16298 AAATTTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
ATTTTTTT
Found at i:18552 original size:20 final size:21
Alignment explanation
Indices: 18499--18615 Score: 82
Period size: 20 Copynumber: 5.7 Consensus size: 21
18489 GACATTAGGA
* *
18499 AAATCTTTAGAAACATTGCTT
1 AAATCTTTAGAAATATTGATT
*
18520 AACT-TTTAGAAATATTG-TT
1 AAATCTTTAGAAATATTGATT
* *
18539 AAATCTTTAGAAATTTTGATA
1 AAATCTTTAGAAATATTGATT
*
18560 AAAGGC-TTAGAAATATTGA-T
1 AAA-TCTTTAGAAATATTGATT
* *
18580 AAA-CACTTAGAAATATTGGTAT
1 AAATC-TTTAGAAATATTGAT-T
* *
18602 AATTATTTAGAAAT
1 AAATCTTTAGAAAT
18616 TTTGGTAAAC
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
18 1 0.01
19 5 0.07
20 39 0.51
21 19 0.25
22 12 0.16
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (21 bp):
AAATCTTTAGAAATATTGATT
Found at i:18590 original size:41 final size:42
Alignment explanation
Indices: 18525--18638 Score: 106
Period size: 41 Copynumber: 2.7 Consensus size: 42
18515 TGCTTAACTT
* * *
18525 TTAGAAATATTGTTAAATC-TTTAGAAATTTTGATA-AAAGGC
1 TTAGAAATATTGATAAA-CACTTAGAAATTTTGATATAAAGAC
* * ** *
18566 TTAGAAATATTGATAAACACTTAGAAATATTGGTATAATTAT
1 TTAGAAATATTGATAAACACTTAGAAATTTTGATATAAAGAC
* * *
18608 TTAGAAATTTTGGTAAACACTTAGATATTTT
1 TTAGAAATATTGATAAACACTTAGAAATTTT
18639 CGTATAACCT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.02
41 29 0.49
42 29 0.49
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.40
Consensus pattern (42 bp):
TTAGAAATATTGATAAACACTTAGAAATTTTGATATAAAGAC
Found at i:18644 original size:42 final size:42
Alignment explanation
Indices: 18566--18645 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
18556 GATAAAAGGC
*
18566 TTAGAAATATTGATAAACACTTAGAAATATTGGTATAATTAT
1 TTAGAAATATTGATAAACACTTAGAAATATTCGTATAATTAT
* * * *
18608 TTAGAAATTTTGGTAAACACTTAGATATTTTCGTATAA
1 TTAGAAATATTGATAAACACTTAGAAATATTCGTATAA
18646 CCTTAAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.40
Consensus pattern (42 bp):
TTAGAAATATTGATAAACACTTAGAAATATTCGTATAATTAT
Found at i:18662 original size:19 final size:21
Alignment explanation
Indices: 18545--18684 Score: 117
Period size: 20 Copynumber: 6.8 Consensus size: 21
18535 TGTTAAATCT
* * **
18545 TTAGAAATTTTGATAAAAGGC
1 TTAGAAATTTTGGTATAACAC
* *
18566 TTAGAAATATTGATA-AACAC
1 TTAGAAATTTTGGTATAACAC
* * *
18586 TTAGAAATATTGGTATAATTAT
1 TTAGAAATTTTGGTATAA-CAC
18608 TTAGAAATTTTGGTA-AACAC
1 TTAGAAATTTTGGTATAACAC
* *
18628 TTAGATATTTTCGTATAAC-C
1 TTAGAAATTTTGGTATAACAC
* *
18648 TTA-AAATTTTGGTATAATTAT
1 TTAGAAATTTTGGTATAA-CAC
18669 TTAGAAATTTTGGTAT
1 TTAGAAATTTTGGTAT
18685 GCCAAAATGT
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
19 12 0.12
20 35 0.36
21 24 0.24
22 27 0.28
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (21 bp):
TTAGAAATTTTGGTATAACAC
Found at i:26224 original size:31 final size:31
Alignment explanation
Indices: 26186--26247 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
26176 TCCCAATTAA
* *
26186 ATACCTAAACTTGGCTTCAAGATGTAATTTG
1 ATACCTAAACTTGGCCTCAAGATGCAATTTG
* *
26217 ATACCTAAATTTGGCCTCAATATGCAATTTG
1 ATACCTAAACTTGGCCTCAAGATGCAATTTG
26248 GTTTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (31 bp):
ATACCTAAACTTGGCCTCAAGATGCAATTTG
Found at i:27014 original size:30 final size:30
Alignment explanation
Indices: 26945--27014 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 30
26935 AGTGACTTAT
*
26945 ATAAAAACTTTTGAATAGTTTAGTGACCAA
1 ATAAAAACTTTTGAATAGTTAAGTGACCAA
*** **
26975 ATTGTAACTTTT-TTTAGTTAAGTGACCAAA
1 ATAAAAACTTTTGAATAGTTAAGTGACC-AA
27005 ATAAAAACTT
1 ATAAAAACTT
27015 ACCCATAGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (30 bp):
ATAAAAACTTTTGAATAGTTAAGTGACCAA
Found at i:28681 original size:19 final size:20
Alignment explanation
Indices: 28641--28683 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28631 TGACTGCATA
*
28641 AAAATAAGAAATTTTGTTAC
1 AAAATAAGAAATTTTGTGAC
28661 AAAATAA-AAATTTCT-TGAC
1 AAAATAAGAAATTT-TGTGAC
28680 AAAA
1 AAAA
28684 AATATGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAATAAGAAATTTTGTGAC
Found at i:28684 original size:20 final size:21
Alignment explanation
Indices: 28640--28684 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
28630 CTGACTGCAT
*
28640 AAAAATAAGAAATTTTGTTAC
1 AAAAATAAGAAATTTTGTGAC
28661 -AAAATAA-AAATTTCT-TGAC
1 AAAAATAAGAAATTT-TGTGAC
28680 AAAAA
1 AAAAA
28685 ATATGTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAATAAGAAATTTTGTGAC
Found at i:38968 original size:28 final size:28
Alignment explanation
Indices: 38895--38970 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
38885 ATATACATAC
* *
38895 TTTTAATTATAAAAATGAAATACACATT
1 TTTTAATTATAAAAATGTAATACACAAT
*
38923 TTTTTATTATAAAAATGTAATACACAAT
1 TTTTAATTATAAAAATGTAATACACAAT
38951 TTTTAATTATAAAAATGTAA
1 TTTTAATTATAAAAATGTAA
38971 CAAATACTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (28 bp):
TTTTAATTATAAAAATGTAATACACAAT
Found at i:38981 original size:28 final size:28
Alignment explanation
Indices: 38887--38984 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
38877 TATTTTTTAT
* *
38887 ATACATAC-TTTTAATTATAAAAATGAA
1 ATACACACTTTTTAATTATAAAAATGTA
* *
38914 ATACACATTTTTTTATTATAAAAATGTA
1 ATACACACTTTTTAATTATAAAAATGTA
*
38942 ATACACAATTTTTAATTATAAAAATGTA
1 ATACACACTTTTTAATTATAAAAATGTA
* * *
38970 ACAAATACTTTTTAA
1 ATACACACTTTTTAA
38985 ACATGATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 6 0.10
28 54 0.90
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (28 bp):
ATACACACTTTTTAATTATAAAAATGTA
Found at i:39696 original size:26 final size:26
Alignment explanation
Indices: 39666--39729 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
39656 CAAAACTCAT
39666 CGTTTCATTTAATGTTTAACACTAAA
1 CGTTTCATTTAATGTTTAACACTAAA
*
39692 CGTTTCATTTAATGTTTGACACTAAA
1 CGTTTCATTTAATGTTTAACACTAAA
*
39718 CGTTTCGTTTAA
1 CGTTTCATTTAA
39730 CTAACAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (26 bp):
CGTTTCATTTAATGTTTAACACTAAA
Found at i:50475 original size:3 final size:3
Alignment explanation
Indices: 50467--50492 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
50457 ATATTAATTG
50467 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
50493 TACATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:58217 original size:16 final size:18
Alignment explanation
Indices: 58191--58223 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
58181 ATTAATTAAC
58191 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
58208 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
58224 CCCAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:63187 original size:27 final size:28
Alignment explanation
Indices: 63135--63187 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
63125 TACTACCGAT
63135 ACTAATAATTTAAGATTAAGATTAATAA
1 ACTAATAATTTAAGATTAAGATTAATAA
*
63163 ACTAATAATTT-ATATTAAGATTAAT
1 ACTAATAATTTAAGATTAAGATTAAT
63188 GTTTTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (28 bp):
ACTAATAATTTAAGATTAAGATTAATAA
Found at i:65291 original size:29 final size:29
Alignment explanation
Indices: 65257--65316 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
65247 AGTCACATGG
*
65257 CATGAAGAACATACCCACATATTTTCTGT
1 CATGAAGAAAATACCCACATATTTTCTGT
* *
65286 CATGAATAAAATACTCACATATTTTCTGT
1 CATGAAGAAAATACCCACATATTTTCTGT
65315 CA
1 CA
65317 CATGGCATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (29 bp):
CATGAAGAAAATACCCACATATTTTCTGT
Found at i:65354 original size:36 final size:36
Alignment explanation
Indices: 65286--65354 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
65276 TATTTTCTGT
* **
65286 CATGAATAAAATACTCACATATTTTCTGTCACATGG
1 CATGAATAAAATACCCACATATTCACTGTCACATGG
* *
65322 CATGAATAACATACCCACATATTCACTTTCACA
1 CATGAATAAAATACCCACATATTCACTGTCACA
65355 ACAGTCATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (36 bp):
CATGAATAAAATACCCACATATTCACTGTCACATGG
Found at i:72396 original size:27 final size:25
Alignment explanation
Indices: 72339--72396 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
72329 CTCAACATAT
* *
72339 ACATCTTTTATCAATTTGACCTTTA
1 ACATTTTTTATCAATTTGACCATTA
**
72364 TTATTTTTTAGTCAAATTTGACCATTA
1 ACATTTTTTA-TC-AATTTGACCATTA
72391 ACATTT
1 ACATTT
72397 CAAAAACAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 7 0.28
26 2 0.08
27 16 0.64
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (25 bp):
ACATTTTTTATCAATTTGACCATTA
Found at i:72561 original size:11 final size:11
Alignment explanation
Indices: 72547--72571 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
72537 AAAAAACTAT
72547 AAAAATTCTAA
1 AAAAATTCTAA
72558 AAAAATTCTAA
1 AAAAATTCTAA
72569 AAA
1 AAA
72572 GTTTATAATT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTCTAA
Found at i:73490 original size:24 final size:24
Alignment explanation
Indices: 73462--73513 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
73452 TTTCTAAAAG
* *
73462 ATTTAGTATTTATTAGTATAATCT
1 ATTTAGCATTTATTAGCATAATCT
*
73486 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATCT
73510 ATTT
1 ATTT
73514 GACCTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATCT
Found at i:77935 original size:18 final size:18
Alignment explanation
Indices: 77913--77998 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 18
77903 AAAATTACAA
*
77913 AAAAATCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTTT
*
77932 AAAATTTTAAAATGATTTTT
1 AAAA-TTCAAAAT-ATTTTT
*
77952 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTT-TT
77971 AAAATTTCAAATATTATATTTT
1 AAAA-TTCAAA-A-TAT-TTTT
77993 AAAATT
1 AAAATT
77999 TTTTAAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
18 4 0.07
19 16 0.29
20 22 0.40
21 3 0.05
22 8 0.15
23 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (18 bp):
AAAATTCAAAATATTTTT
Found at i:77976 original size:19 final size:19
Alignment explanation
Indices: 77912--77996 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 19
77902 AAAAATTACA
*
77912 AAAAAATCAAAATAATTTTT
1 AAAAATTCAAAATAA-TTTT
* * *
77932 AAAATTTTAAAATGATTTT
1 AAAAATTCAAAATAATTTT
*
77951 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
77970 AAAAATTTCAAATATTATATTTT
1 AAAAA-TTCAAA-A-TA-ATTTT
77993 AAAA
1 AAAA
77997 TTTTTTAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 4 0.08
19 19 0.37
20 17 0.33
21 1 0.02
22 1 0.02
23 5 0.10
24 4 0.08
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:79092 original size:16 final size:16
Alignment explanation
Indices: 79061--79102 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
79051 TATAGTTTAA
* *
79061 AATATTTAATTTTCAT
1 AATATATAAATTTCAT
79077 -ATAATATAAATTTCAT
1 AAT-ATATAAATTTCAT
79093 AATATATAAA
1 AATATATAAA
79103 ATGAAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATATAAATTTCAT
Found at i:79109 original size:22 final size:21
Alignment explanation
Indices: 79075--79116 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
79065 TTTAATTTTC
* *
79075 ATATAATATAAATTTCATAAT
1 ATATAAAATAAATATCATAAT
79096 ATATAAAATGAAATATCATAA
1 ATATAAAAT-AAATATCATAA
79117 ATCTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (21 bp):
ATATAAAATAAATATCATAAT
Found at i:79642 original size:27 final size:27
Alignment explanation
Indices: 79612--79666 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
79602 AAAAACTTTA
79612 AAAATTC-TAAAAATT-TCCAAAAAGTTC
1 AAAATTCATAAAAATTAT--AAAAAGTTC
79639 AAAATTCATAAAAATTATAAAAAGTTC
1 AAAATTCATAAAAATTATAAAAAGTTC
79666 A
1 A
79667 TATATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 17 0.65
28 8 0.31
29 1 0.04
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (27 bp):
AAAATTCATAAAAATTATAAAAAGTTC
Found at i:88677 original size:21 final size:20
Alignment explanation
Indices: 88649--88720 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 20
88639 ACTTCATACT
88649 AACTTTTTAAATTTTTTATG
1 AACTTTTTAAATTTTTTATG
*
88669 AACTCTTTTATATTTGTTT-TG
1 AACT-TTTTAAATTT-TTTATG
*
88690 AA-TATTTAAATATTTTTAT-
1 AACTTTTTAAAT-TTTTTATG
*
88709 AA-ATTTTAAATT
1 AACTTTTTAAATT
88721 ATTGGTTGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.02
19 18 0.42
20 8 0.19
21 13 0.30
22 3 0.07
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
AACTTTTTAAATTTTTTATG
Found at i:90584 original size:21 final size:22
Alignment explanation
Indices: 90560--90600 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
90550 AGTTTTTTCA
* *
90560 TATAATATAA-ATTTCATAATT
1 TATAAAATAAGATATCATAATT
90581 TATAAAATAAGATATCATAA
1 TATAAAATAAGATATCATAA
90601 ACTTGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (22 bp):
TATAAAATAAGATATCATAATT
Found at i:91366 original size:20 final size:20
Alignment explanation
Indices: 91337--91385 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
91327 ATCAATTCGA
* *
91337 TTCACATGGGTTGTCATTGT
1 TTCACTTGGGCTGTCATTGT
91357 TTCACTTGGGCTGTCATTGT
1 TTCACTTGGGCTGTCATTGT
91377 TTCAACTTG
1 TTC-ACTTG
91386 TATAGATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTCACTTGGGCTGTCATTGT
Found at i:91955 original size:20 final size:20
Alignment explanation
Indices: 91930--91973 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
91920 ATCAATTCGA
*
91930 TTCACATGGGTTGTCATTGT
1 TTCACATGGGCTGTCATTGT
91950 TTCACATGGGCTGTCATTGT
1 TTCACATGGGCTGTCATTGT
91970 TTCA
1 TTCA
91974 ACTTGTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (20 bp):
TTCACATGGGCTGTCATTGT
Found at i:94512 original size:26 final size:26
Alignment explanation
Indices: 94483--94539 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
94473 ATTCAAAAAC
*
94483 ACATACACAAACAGATACAAATTCTG
1 ACATACACAAACAGATACAAATTCTA
*
94509 ACATACACAAACATATACAAATTCTA
1 ACATACACAAACAGATACAAATTCTA
94535 ACATA
1 ACATA
94540 TTCTCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.53, C:0.23, G:0.04, T:0.21
Consensus pattern (26 bp):
ACATACACAAACAGATACAAATTCTA
Found at i:95167 original size:6 final size:6
Alignment explanation
Indices: 95158--95208 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
95148 TTAATTTGGT
* ** **
95158 TTTAAA TTTAAA ATTATT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
95205 TTTA
1 TTTA
95209 GTTAAATTTG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
5 3 0.09
6 31 0.91
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:95177 original size:17 final size:17
Alignment explanation
Indices: 95157--95241 Score: 82
Period size: 17 Copynumber: 5.0 Consensus size: 17
95147 TTTAATTTGG
95157 TTTTAAATTTAAAATTA
1 TTTTAAATTTAAAATTA
* *
95174 TTTTTAAATTTAAATTTG
1 -TTTTAAATTTAAAATTA
*
95192 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAAATTA
* * *
95209 -GTTAAATTTGAAATGA
1 TTTTAAATTTAAAATTA
* *
95225 TTTTAAACTTAATATTA
1 TTTTAAATTTAAAATTA
95242 AAAACCCAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
16 12 0.22
17 27 0.50
18 15 0.28
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTTAAATTTAAAATTA
Found at i:95180 original size:18 final size:18
Alignment explanation
Indices: 95150--95204 Score: 78
Period size: 17 Copynumber: 3.1 Consensus size: 18
95140 AATTAAGTTT
95150 AATTTGGTTTTAAATTTAA
1 AATTT-GTTTTAAATTTAA
95169 AATTAT-TTTTAAATTT-A
1 AATT-TGTTTTAAATTTAA
95186 AATTTGTTTTAAATTTAA
1 AATTTGTTTTAAATTTAA
95204 A
1 A
95205 TTTAGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 15 0.45
18 12 0.36
19 4 0.12
20 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
AATTTGTTTTAAATTTAA
Found at i:95935 original size:3 final size:3
Alignment explanation
Indices: 95927--95982 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
95917 TAATTTATTA
**
95927 AAT AAT AAT TCT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
95975 AAT AAT AA
1 AAT AAT AA
95983 GAAAGTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:97104 original size:28 final size:28
Alignment explanation
Indices: 97064--97162 Score: 103
Period size: 28 Copynumber: 3.5 Consensus size: 28
97054 GACTTTACTA
* *
97064 AAAATTACATTTTTACCCTAAACTTTCT
1 AAAATTCCATTTTTACCCTAAACTTTCC
* **
97092 GAAATTCCATTTTTTACCCTAATTTTTCC
1 AAAATTCCA-TTTTTACCCTAAACTTTCC
*
97121 AAAATTACCA-TTTTACCCAAGAAC-TTCC
1 AAAATT-CCATTTTTACCCTA-AACTTTCC
97149 AAAATTCCATTTTT
1 AAAATTCCATTTTT
97163 GACTCGATTC
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
27 3 0.05
28 30 0.52
29 22 0.38
30 3 0.05
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.41
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTAAACTTTCC
Found at i:97133 original size:58 final size:58
Alignment explanation
Indices: 97064--97314 Score: 219
Period size: 59 Copynumber: 4.3 Consensus size: 58
97054 GACTTTACTA
* *
97064 AAAATTA-CATTTTTA-CCCTAAACTTTCTGAAATTCCATTTTTTACCCTAATTTTTCC
1 AAAATTACCA-TTTTACCCCTAAACTTTCTAAAATTCCATTTTTGACCCTAATTTTTCC
* * * * * *
97121 AAAATTACCATTTTA-CCCAAGAAC-TTCCAAAATTCCATTTTTGACTC-GATTCTTCAAA
1 AAAATTACCATTTTACCCCTA-AACTTTCTAAAATTCCATTTTTGACCCTAATTTTTC--C
* * * * * *
97179 AAAAATACCATTTTACCCCCAAACTTCCTAAAATTCCATTTTTTACCCCGATTTTTTCC
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTGA-CCCTAATTTTTCC
** * *
97238 AAAATTACCATTTTACCCCTGGA-TGTCTAAAAATTCCATTTTTGA-CCTGAACTTTTCC
1 AAAATTACCATTTTACCCCTAAACTTTCT-AAAATTCCATTTTTGACCCT-AATTTTTCC
*
97296 AAAATTACCATTTTTCCCC
1 AAAATTACCATTTTACCCC
97315 CAGTATCCAA
Statistics
Matches: 155, Mismatches: 29, Indels: 19
0.76 0.14 0.09
Matches are distributed among these distances:
56 6 0.04
57 37 0.24
58 50 0.32
59 55 0.35
60 2 0.01
61 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTGACCCTAATTTTTCC
Found at i:97227 original size:29 final size:27
Alignment explanation
Indices: 97064--97227 Score: 80
Period size: 28 Copynumber: 5.7 Consensus size: 27
97054 GACTTTACTA
* * *
97064 AAAATTACATTTTTACCCTAAACTTTCT
1 AAAATTCCATTTTTACCCCAAAC-TTCC
* * **
97092 GAAATTCCATTTTTTACCCTAATTTTTCC
1 AAAATTCCA-TTTTTACCCCAA-ACTTCC
*
97121 AAAATTACCA-TTTTACCCAAGAACTTCC
1 AAAATT-CCATTTTTACCCCA-AACTTCC
* * ** *
97149 AAAATTCCATTTTTGACTCGATTCTTCAAAA
1 AAAATTCCATTTTT-ACCCCAAACTTC---C
*
97180 AAAATACCA-TTTTACCCCCAAACTTCC
1 AAAATTCCATTTTTA-CCCCAAACTTCC
97207 TAAAATTCCATTTTTTACCCC
1 -AAAATTCCA-TTTTTACCCC
97228 GATTTTTTCC
Statistics
Matches: 102, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
27 3 0.03
28 42 0.41
29 30 0.29
30 19 0.19
31 8 0.08
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAATTCCATTTTTACCCCAAACTTCC
Found at i:97247 original size:59 final size:58
Alignment explanation
Indices: 97064--97316 Score: 232
Period size: 58 Copynumber: 4.4 Consensus size: 58
97054 GACTTTACTA
* * * * *
97064 AAAATTA-CATTTTTA-CCCTAAACTTTCTGAAATTCCATTTTTTACCCTAATTTTTCC
1 AAAATTACCA-TTTTACCCCCAAACTTCCTAAAATTCCATTTTTGACCCGAATTTTTCC
* * * *
97121 AAAATTACCATTTTA-CCCAAGAACTTCC-AAAATTCCATTTTTGACTCG-ATTCTTCAAA
1 AAAATTACCATTTTACCCCCA-AACTTCCTAAAATTCCATTTTTGACCCGAATTTTTC--C
* * *
97179 AAAAATACCATTTTACCCCCAAACTTCCTAAAATTCCATTTTTTACCCCGATTTTTTCC
1 AAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCATTTTTGA-CCCGAATTTTTCC
*** * *
97238 AAAATTACCATTTTACCCCTGGA-TGT-CTAAAAATTCCATTTTTGACCTGAACTTTTCC
1 AAAATTACCATTTTACCCCCAAACT-TCCT-AAAATTCCATTTTTGACCCGAATTTTTCC
*
97296 AAAATTACCATTTTTCCCCCA
1 AAAATTACCATTTTACCCCCA
97317 GTATCCAAAA
Statistics
Matches: 160, Mismatches: 26, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
56 6 0.04
57 32 0.20
58 60 0.38
59 54 0.34
60 3 0.02
61 5 0.03
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCATTTTTGACCCGAATTTTTCC
Found at i:109176 original size:49 final size:49
Alignment explanation
Indices: 109085--109207 Score: 133
Period size: 49 Copynumber: 2.5 Consensus size: 49
109075 GTACCGCAAA
* * * * * * *
109085 ACATGGAGGGAAAGGTTTAAGTTGCAATGGCGAACCTTGTACCTCAGAA-
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCAAACCTAGTACCAC-GAAG
**
109134 TTATGAAGGGAAAGATTTAAGTCGCAACGGCAAATCC-AGTACCACGAAG
1 ACATGAAGGGAAAGATTTAAGTCGCAACGGCAAA-CCTAGTACCACGAAG
109183 ACATGAAGGGAAAGATTTAAGTCGC
1 ACATGAAGGGAAAGATTTAAGTCGC
109208 GTACCACGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
48 3 0.05
49 56 0.92
50 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (49 bp):
ACATGAAGGGAAAGATTTAAGTCGCAACGGCAAACCTAGTACCACGAAG
Found at i:109280 original size:49 final size:49
Alignment explanation
Indices: 109208--109498 Score: 350
Period size: 49 Copynumber: 5.9 Consensus size: 49
109198 TTTAAGTCGC
* **
109208 GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCTT
1 GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
* *
109257 GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGTAACGGCGAATCAA
1 GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
* * *
109306 ATACCACGAAGACATGAAGGGAAAAGATTTAAGCCGTAACGGCGAATCCA
1 GTACCACGAAGACATAAAGGG-AAAGATTTAAGCCGCAACGGCGAATCCA
* * * * * *
109356 GTACCACAAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTT
1 GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-A
* * * *
109405 GTACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCA
1 GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
* * * * *
109454 GTACCGCGAAGACACAAGGGGAAAGGTTTAAGCCGCAATGGCGAA
1 GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAA
109499 CCCTATACCT
Statistics
Matches: 207, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
48 2 0.01
49 159 0.77
50 46 0.22
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (49 bp):
GTACCACGAAGACATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
Found at i:109468 original size:98 final size:98
Alignment explanation
Indices: 109216--109546 Score: 407
Period size: 98 Copynumber: 3.4 Consensus size: 98
109206 GCGTACCACG
* * ** *
109216 AAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCTTGTACCACGAAGACATAAAGGGAAA
1 AAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGGAAA
* * * * * * *
109281 GATTTAAGCCGTAACGGCGAATCAAATACCACG
66 GGTTTAAGCCGCAATGGCGAACCATATACCTCA
* *
109314 AAGACATGAAGGGAAAAGATTTAAGCCGTAACGGCGAATCCAGTACCACAAAGACACAAAGGGAA
1 AAGACATGAAGGG-AAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGGAA
* * *
109379 AGGTTTAAGTCGCAATGGCGAACCTTGTACCTCA
65 AGGTTTAAGCCGCAATGGCGAACCATATACCTCA
* * *
109413 AAGACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCGCGAAGACACAAGGGGAAA
1 AAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGGAAA
*
109478 GGTTTAAGCCGCAATGGCGAACCCTATACCTCA
66 GGTTTAAGCCGCAATGGCGAACCATATACCTCA
* * *
109511 GAAG-CATGAAAGG-AA-ATTTAAGCTGTAACGGCGAAT
1 -AAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAAT
109547 TTAGTACTAG
Statistics
Matches: 202, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
96 18 0.09
97 2 0.01
98 97 0.48
99 85 0.42
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (98 bp):
AAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACAAAGGGAAA
GGTTTAAGCCGCAATGGCGAACCATATACCTCA
Found at i:109523 original size:148 final size:149
Alignment explanation
Indices: 109208--109523 Score: 390
Period size: 148 Copynumber: 2.1 Consensus size: 149
109198 TTTAAGTCGC
* *
109208 GTACCAC-GAAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCTTGTACCACGAAGACAT
1 GTACCACAGAAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCACAAAGACAT
* *
109272 AAAGGGAAAGATTTAAGCCGTAACGGCGAATCAAATACCACGAAGACATGAAGGGAAAAGATTTA
66 AAAGGGAAAGATTTAAGCCGCAACGGCGAATCAAATACCACGAAGACATCAAGGGAAAAGATTTA
* *
109337 AGCCGTAACGGCGAATCCA
131 AGCCGCAACGGCGAACCCA
* * * * * *
109356 GTACCACA-AAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAAAGACAT
1 GTACCACAGAAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCACAAAGACAT
* * * * * * *
109420 GAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCGCGAAGACA-CAAGGGGAAAGGTTTA
66 AAAGGGAAAGATTTAAGCCGCAACGGCGAATCAAATACCACGAAGACATCAAGGGAAAAGATTTA
*
109484 AGCCGCAATGGCGAACCCTA
131 AGCCGCAACGGCGAACCC-A
*
109504 -TACCTCAGAAG-CATGAAAGG
1 GTACCACAGAAGACAT-AAAGG
109524 AAATTTAAGC
Statistics
Matches: 142, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
147 36 0.25
148 106 0.75
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.15
Consensus pattern (149 bp):
GTACCACAGAAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAACCTTGTACCACAAAGACAT
AAAGGGAAAGATTTAAGCCGCAACGGCGAATCAAATACCACGAAGACATCAAGGGAAAAGATTTA
AGCCGCAACGGCGAACCCA
Found at i:109526 original size:49 final size:49
Alignment explanation
Indices: 109209--109546 Score: 282
Period size: 49 Copynumber: 6.9 Consensus size: 49
109199 TTAAGTCGCG
* * *
109209 TACCACGAAGACAT-AAAGGGAAAGATTTAAGCCGCAACGACGAATCTTG
1 TACCACGAAGACATGAAA-GGAAAGATTTAAGCCGCAACGGCGAATCCTA
* **
109258 TACCACGAAGACAT-AAAGGGAAAGATTTAAGCCGTAACGGCGAATCAAA
1 TACCACGAAGACATGAAA-GGAAAGATTTAAGCCGCAACGGCGAATCCTA
* *
109307 TACCACGAAGACATGAAGGGAAAAGATTTAAGCCGTAACGGCGAATCC-A
1 TACCACGAAGACATGAAAGG-AAAGATTTAAGCCGCAACGGCGAATCCTA
* * * * * *
109356 GTACCACAAAGACA-CAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTTG
1 -TACCACGAAGACATGAAA-GGAAAGATTTAAGCCGCAACGGCGAATCC-TA
* * * *
109406 TACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCC-A
1 TACCACGAAGACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCTA
* * * * * *
109454 GTACCGCGAAGACA-CAAGGGGAAAGGTTTAAGCCGCAATGGCGAACCCTA
1 -TACCACGAAGACATGAA-AGGAAAGATTTAAGCCGCAACGGCGAATCCTA
* * *
109504 TACCTCAGAAG-CATGAAAGG-AA-ATTTAAGCTGTAACGGCGAAT
1 TACCAC-GAAGACATGAAAGGAAAGATTTAAGCCGCAACGGCGAAT
109547 TTAGTACTAG
Statistics
Matches: 238, Mismatches: 38, Indels: 28
0.78 0.12 0.09
Matches are distributed among these distances:
47 16 0.07
48 6 0.03
49 163 0.68
50 53 0.22
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (49 bp):
TACCACGAAGACATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCTA
Found at i:110293 original size:3 final size:3
Alignment explanation
Indices: 110285--110333 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
110275 TAATTTATTA
** *
110285 AAT AAT AAT TCT AAT AAT AAT -TT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
110332 AA
1 AA
110334 GAAAGTTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 1 0.03
3 38 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:110311 original size:23 final size:23
Alignment explanation
Indices: 110285--110328 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
110275 TAATTTATTA
**
110285 AATAATAATTCTAATAATAATTT
1 AATAATAATAATAATAATAATTT
110308 AATAATAATAATAATAATAAT
1 AATAATAATAATAATAATAAT
110329 AATAAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAATAATAATAATAATAATTT
Found at i:111401 original size:60 final size:59
Alignment explanation
Indices: 111307--111735 Score: 248
Period size: 59 Copynumber: 7.2 Consensus size: 59
111297 TAGAAATCAT
* * * *
111307 ATTTTGACCCCTAAAATTTTCCAAAATTCCATTTTTGGCCCCGAACTTTCCTAAAAAATA-C
1 ATTTT-ACCCCCAAACTTTT-CAAAATTCCATTTTTGACCCCG-ACTTTCCCAAAAAATATC
* * * * *
111368 ATTTTTACCCTCGAACTTTTCAAAATTCCATTTTTGACCTCGATTTTCCCAAAAATTATC
1 A-TTTTACCCCCAAACTTTTCAAAATTCCATTTTTGACCCCGACTTTCCCAAAAAATATC
* ** * * *
111428 ATTTTACCCCCAAAC-TTCCTAAAATTCCA-TTTTGACCCTTATTCTTCCAAAAAAATTTCC
1 ATTTTACCCCCAAACTTTTC-AAAATTCCATTTTTGACCCCGACT-TTCCCAAAAAATAT-C
* * * * * * *
111488 ATTTTACCTCCAAACTTCT-AAAATTCCATTTTTGACCCCCATTTTTCCAAAAATTACC
1 ATTTTACCCCCAAACTTTTCAAAATTCCATTTTTGACCCCGACTTTCCCAAAAAATATC
*** * * * * *
111546 ATTTTACCCTTGAAC-TTCCAAAATTCTATTTTTGACCTCGA-TTCTTCCAAAAAATTACC
1 ATTTTACCCCCAAACTTTTCAAAATTCCATTTTTGACCCCGACTT-TCCCAAAAAA-TATC
* * * * * * *
111605 ATTTTACCCCCAAAC-TTCCTAAAATTCCATTTTTTACCTCGATTTTTTTCCAAAAATTACC
1 ATTTTACCCCCAAACTTTTC-AAAATTCCATTTTTGACCCCGA--CTTTCCCAAAAAATATC
*** * * * *
111666 ATTTTACCCCTGGA--TGTCTAAAATTTCATTTTTTTACCCCGAACTTTCCC-AAAATTATC
1 ATTTTACCCCCAAACTTTTC-AAAATTCCA-TTTTTGACCCCG-ACTTTCCCAAAAAATATC
*
111725 ATTTTTCCCCC
1 ATTTTACCCCC
111736 GAGTACCTAA
Statistics
Matches: 296, Mismatches: 56, Indels: 34
0.77 0.15 0.09
Matches are distributed among these distances:
57 3 0.01
58 54 0.18
59 100 0.34
60 85 0.29
61 38 0.13
62 14 0.05
63 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.39
Consensus pattern (59 bp):
ATTTTACCCCCAAACTTTTCAAAATTCCATTTTTGACCCCGACTTTCCCAAAAAATATC
Found at i:111408 original size:29 final size:29
Alignment explanation
Indices: 111323--111410 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 29
111313 ACCCCTAAAA
* *
111323 TTTTCCAAAATTCCATTTTTGGCCCCGAAC
1 TTTT-CAAAATTCCATTTTTGACCTCGAAC
* * *
111353 TTTCCTAAAAAATACATTTTT-ACCCTCGAAC
1 TTT--TCAAAATTCCATTTTTGA-CCTCGAAC
111384 TTTTCAAAATTCCATTTTTGACCTCGA
1 TTTTCAAAATTCCATTTTTGACCTCGA
111411 TTTTCCCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
29 19 0.41
30 4 0.09
31 22 0.48
32 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.39
Consensus pattern (29 bp):
TTTTCAAAATTCCATTTTTGACCTCGAAC
Found at i:111420 original size:29 final size:29
Alignment explanation
Indices: 111321--111670 Score: 118
Period size: 29 Copynumber: 11.7 Consensus size: 29
111311 TGACCCCTAA
* *
111321 AATTTTCCAAAATTCCATTTTTGGCCCCG
1 AATTTTCCAAAATTCCATTTTTGACCTCG
* * *
111350 AACTTTCCTAAAAAATACATTTTT-ACCCTCG
1 AATTTTCC--AAAATTCCATTTTTGA-CCTCG
111381 AACTTTT-CAAAATTCCATTTTTGACCTCG
1 AA-TTTTCCAAAATTCCATTTTTGACCTCG
* * *
111410 -ATTTTCCCAAAAATTATCA-TTTT-ACCCCC
1 AATTTT-CC-AAAATT-CCATTTTTGACCTCG
** *
111439 AAACTTCCTAAAATTCCA-TTTTGACC-CT
1 AATTTTCC-AAAATTCCATTTTTGACCTCG
* *
111467 TATTCTTCCAAAAAAATTTCCA-TTTT-ACCTCC
1 AATT-TTCC---AAAA-TTCCATTTTTGACCTCG
** * * *
111499 AAACTTCTAAAATTCCATTTTTGACCCCC
1 AATTTTCCAAAATTCCATTTTTGACCTCG
* *
111528 ATTTTTCCAAAAATTACCA-TTTT-ACCCTTG
1 AATTTTCC-AAAATT-CCATTTTTGA-CCTCG
* *
111558 AA-CTTCCAAAATTCTATTTTTGACCTCG
1 AATTTTCCAAAATTCCATTTTTGACCTCG
* *
111586 -ATTCTTCCAAAAAATTACCA-TTTT-ACCCCC
1 AATT-TTCC--AAAATT-CCATTTTTGACCTCG
** *
111616 AAACTTCCTAAAATTCCATTTTTTACCTCG
1 AATTTTCC-AAAATTCCATTTTTGACCTCG
*
111646 ATTTTTTTCCAAAAATTACCATTTT
1 A--ATTTTCC-AAAATT-CCATTTT
111671 ACCCCTGGAT
Statistics
Matches: 237, Mismatches: 50, Indels: 64
0.68 0.14 0.18
Matches are distributed among these distances:
27 12 0.05
28 34 0.14
29 73 0.31
30 40 0.17
31 45 0.19
32 26 0.11
33 7 0.03
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (29 bp):
AATTTTCCAAAATTCCATTTTTGACCTCG
Found at i:111444 original size:59 final size:58
Alignment explanation
Indices: 111325--111675 Score: 366
Period size: 60 Copynumber: 5.9 Consensus size: 58
111315 CCCTAAAATT
* * * * * * *
111325 TTCCAAAATTCCATTTTTGGCCCCGAACTTTCCTAAAAAATA-CATTTTTACCCTCGAAC
1 TTCCAAAATTCCATTTTTGACCTCG-ATTTTCCCAAAAATTACCA-TTTTACCCCCAAAC
* *
111384 TTTTCAAAATTCCATTTTTGACCTCGATTTTCCCAAAAATTATCATTTTACCCCCAAAC
1 -TTCCAAAATTCCATTTTTGACCTCGATTTTCCCAAAAATTACCATTTTACCCCCAAAC
* * * *
111443 TTCCTAAAATTCCA-TTTTGACC-CTTATTCTTCCAAAAAAATTTCCATTTTACCTCCAAAC
1 TTCC-AAAATTCCATTTTTGACCTC-GATT-TTCC-CAAAAATTACCATTTTACCCCCAAAC
* * * * ***
111503 TTCTAAAATTCCATTTTTGACCCCCATTTTTCCAAAAATTACCATTTTACCCTTGAAC
1 TTCCAAAATTCCATTTTTGACCTCGATTTTCCCAAAAATTACCATTTTACCCCCAAAC
* *
111561 TTCCAAAATTCTATTTTTGACCTCGATTCTTCCAAAAAATTACCATTTTACCCCCAAAC
1 TTCCAAAATTCCATTTTTGACCTCGATT-TTCCCAAAAATTACCATTTTACCCCCAAAC
* *
111620 TTCCTAAAATTCCATTTTTTACCTCGATTTTTTTCCAAAAATTACCATTTTACCCC
1 TTCC-AAAATTCCATTTTTGACCTCGA--TTTTCCCAAAAATTACCATTTTACCCC
111676 TGGATGTCTA
Statistics
Matches: 244, Mismatches: 36, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.00
58 58 0.24
59 79 0.32
60 80 0.33
61 24 0.10
62 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.38
Consensus pattern (58 bp):
TTCCAAAATTCCATTTTTGACCTCGATTTTCCCAAAAATTACCATTTTACCCCCAAAC
Found at i:111524 original size:118 final size:118
Alignment explanation
Indices: 111325--111675 Score: 410
Period size: 118 Copynumber: 3.0 Consensus size: 118
111315 CCCTAAAATT
* * * * *
111325 TTCCAAAATTCCATTTTTGGCCCCGA-ACTTTCCTAAAAAA-TA-CATTTTTACCCTCGAACTT-
1 TTCCAAAATTCCATTTTTGACCTCGATTC-TTCC-AAAAAATTACCA-TTTTACCCCCAAACTTC
* * *
111386 TTCAAAATTCCATTTTTGACCTCGATTTTCCCAAAAATTATCATTTTACCCCCAAAC
63 CT-AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCCCAAAC
* * *
111443 TTCCTAAAATTCCA-TTTTGACC-CTTATTCTTCCAAAAAAATTTCCATTTTACCTCCAAACTT-
1 TTCC-AAAATTCCATTTTTGACCTC-GATTCTTCC-AAAAAATTACCATTTTACCCCCAAACTTC
* * ***
111505 CTAAAATTCCATTTTTGACCCCCATTTTTCCAAAAATTACCATTTTACCCTTGAAC
63 CTAAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCCCAAAC
*
111561 TTCCAAAATTCTATTTTTGACCTCGATTCTTCCAAAAAATTACCATTTTACCCCCAAACTTCCTA
1 TTCCAAAATTCCATTTTTGACCTCGATTCTTCCAAAAAATTACCATTTTACCCCCAAACTTCCTA
*
111626 AAATTCCATTTTTTACCTCGATTTTTTTCCAAAAATTACCATTTTACCCC
66 AAATTCCATTTTTGACCTCGA--TTTTTCCAAAAATTACCATTTTACCCC
111676 TGGATGTCTA
Statistics
Matches: 199, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
117 35 0.18
118 110 0.55
119 26 0.13
120 28 0.14
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.38
Consensus pattern (118 bp):
TTCCAAAATTCCATTTTTGACCTCGATTCTTCCAAAAAATTACCATTTTACCCCCAAACTTCCTA
AAATTCCATTTTTGACCTCGATTTTTCCAAAAATTACCATTTTACCCCCAAAC
Found at i:111699 original size:61 final size:59
Alignment explanation
Indices: 111353--111734 Score: 257
Period size: 59 Copynumber: 6.4 Consensus size: 59
111343 GGCCCCGAAC
* * * *
111353 TTTCCTAAAAAATA-CATTTTTA-CCCTCGAACTTTTCAAAATTCCA-TTTTTGACCTCGATT
1 TTTCC-AAAAATTACCA-TTTTACCCCT-GAACTTCT-AAAATTTCATTTTTTTACCTCGATT
* * ** * * *
111413 TTCCCAAAAATTATCATTTTACCCCCAAACTTCCTAAAATTCCA--TTTTGACC-CTTATT
1 TTTCCAAAAATTACCATTTTACCCCTGAACTT-CTAAAATTTCATTTTTTTACCTC-GATT
* * * * * * *
111471 CTTCCAAAAAAATTTCCATTTTACCTCC-AAACTTCTAAAATTCCA-TTTTTGACCCCCATT
1 TTTCC--AAAAATTACCATTTTACC-CCTGAACTTCTAAAATTTCATTTTTTTACCTCGATT
* * *
111531 TTTCCAAAAATTACCATTTTACCCTTGAACTTCCAAAA-TTC-TATTTTTGACCTCGATT
1 TTTCCAAAAATTACCATTTTACCCCTGAACTTCTAAAATTTCAT-TTTTTTACCTCGATT
* ** *
111589 CTTCCAAAAAATTACCATTTTACCCCCAAACTTCCTAAAATTCCA-TTTTTTACCTCGATTTT
1 TTTCC-AAAAATTACCATTTTACCCCTGAACTT-CTAAAATTTCATTTTTTTACCTCGA--TT
* * **
111651 TTTCCAAAAATTACCATTTTACCCCTGGA-TGTCTAAAATTTCATTTTTTTACCCCGAAC
1 TTTCCAAAAATTACCATTTTACCCCTGAACT-TCTAAAATTTCATTTTTTTACCTCGATT
* * *
111710 TTTCCCAAAATTATCATTTTTCCCC
1 TTTCCAAAAATTACCATTTTACCCC
111735 CGAGTACCTA
Statistics
Matches: 265, Mismatches: 37, Indels: 41
0.77 0.11 0.12
Matches are distributed among these distances:
57 4 0.02
58 58 0.22
59 83 0.31
60 75 0.28
61 39 0.15
62 6 0.02
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (59 bp):
TTTCCAAAAATTACCATTTTACCCCTGAACTTCTAAAATTTCATTTTTTTACCTCGATT
Found at i:114018 original size:9 final size:8
Alignment explanation
Indices: 113996--114119 Score: 59
Period size: 9 Copynumber: 13.8 Consensus size: 8
113986 ATTTTAGGAT
113996 ATTTTTAA
1 ATTTTTAA
*
114004 AATTTTAA
1 ATTTTTAA
114012 CATTTTTAGA
1 -ATTTTTA-A
114022 TATTTTTAGA
1 -ATTTTTA-A
114032 ATTTTTTAA
1 A-TTTTTAA
114041 ATTTTTATA
1 ATTTTTA-A
114050 ATTTTTGTAA
1 A-TTTT-TAA
** *
114060 AAATATAA
1 ATTTTTAA
*
114068 ATTTTGAAA
1 ATTTT-TAA
114077 ATTTTATAA
1 ATTTT-TAA
*
114086 ATATTTTGA
1 AT-TTTTAA
*
114095 ATTTTAAAA
1 ATTTT-TAA
114104 ATTATTTTAA
1 A-T-TTTTAA
114114 ATTTTT
1 ATTTTT
114120 TGTAATTTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
8 25 0.28
9 30 0.34
10 29 0.33
11 5 0.06
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (8 bp):
ATTTTTAA
Found at i:114044 original size:18 final size:17
Alignment explanation
Indices: 113997--114119 Score: 77
Period size: 18 Copynumber: 6.8 Consensus size: 17
113987 TTTTAGGATA
*
113997 TTTTTAAAATTTTAACA-
1 TTTTTAAATTTTTAA-AT
114014 TTTTTAGATATTTTTAGAAT
1 TTTTTA-A-ATTTTTA-AAT
114034 TTTTTAAATTTTTATAAT
1 TTTTTAAATTTTTA-AAT
** *
114052 TTTTGTAAAAATATAAAT
1 TTTT-TAAATTTTTAAAT
**
114070 TTTGAAAATTTTATAAAT
1 TTTTTAAATTTT-TAAAT
* * *
114088 ATTTTGAATTTTAAAAAT
1 TTTTTAAATTTT-TAAAT
114106 TATTTTAAATTTTT
1 T-TTTTAAATTTTT
114120 TGTAATTTTT
Statistics
Matches: 81, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
17 10 0.12
18 39 0.48
19 25 0.31
20 7 0.09
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTTTAAATTTTTAAAT
Found at i:114443 original size:29 final size:27
Alignment explanation
Indices: 114378--114444 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
114368 GCGGTAATTC
114378 TTTTTATTTTAAATATTTTTTTAAGAT
1 TTTTTATTTTAAATATTTTTTTAAGAT
* *
114405 TATTTT-TTTTACATCAATTTTATTTTA-AT
1 T-TTTTATTTTAAAT--ATTTT-TTTAAGAT
114434 TTTTTATTTTA
1 TTTTTATTTTA
114445 TTCATTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
27 8 0.24
28 8 0.24
29 13 0.39
30 4 0.12
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTTTATTTTAAATATTTTTTTAAGAT
Found at i:119451 original size:21 final size:21
Alignment explanation
Indices: 119412--119451 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
119402 TTTTACAAGT
*
119412 AAATAATCAAAAAATTTATCG
1 AAATAATCAAAAAAGTTATCG
* *
119433 AAATAATTAAGAAAGTTAT
1 AAATAATCAAAAAAGTTAT
119452 TTTCCCCAAA
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:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (21 bp):
AAATAATCAAAAAAGTTATCG
Done.