Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010810.1 Kokia drynarioides strain JFW-HI SEQ_125777, 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: 162367
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:793 original size:424 final size:422
Alignment explanation
Indices: 7--812 Score: 1299
Period size: 424 Copynumber: 1.9 Consensus size: 422
1 CGAATT
*
7 TCTCACAGTTGAAGAAGTCTATACTTCCTTAGCCTCGTATGACAAGATGAAGCATCTTGTGGCTG
1 TCTCACAGATGAAGAAGTCTATACTTCCTTAGCCTCGTATGACAAGATGAAGCATCTTGTGGCTG
* *
72 GATTCAACTCTTAAGGAGAGGGTTTCATTGTTCTTAGGAGATAGAATGAAATATTAGTGATAATC
66 GATTCAACTCTTAAGGAGAGGGTCTCATTGTTCTTAGGAGAAAGAATGAAATATTAGTGATAATC
* * *
137 GTGGGAGGACACAAGGATGAAATCCTTGCAATAAATCTAAGGGTAGATCGAGATCTTCAAACAGA
131 GTAGGAGGACACAAGAATGAAATCCTTGCAATAAATCTAAGGGTAGATCAAGATCTTCAAACAGA
* * *
202 GACAAAACTTGTAATTTCTACAAAAGAAAGGGCACATTAAGTTTGAGTGCTATAAGTTACAGAAC
196 GACAAAACCTGTAATTTCTACAAAAGAAAGGGCACATTAAGTTTCAGTGCTATAAGTTACAAAAC
* * * * * *
267 AAGATCAAAAGGGAGATTGCGAATCAAAAGGGAAAACAAATAGAATAATCCGGTGAAGCTGATGA
261 AAGATCAAAAGGGAGACTGCAAATCAAAAAGGAAAACAAACAAAATAATCCGATGAAGCTGATGA
* *
332 AGTAGAAGACTATAGCAATGGTGAACTCCTGGTTACTTCTATTGACAACTATAAAGTTATTCAAC
326 AGTAGAAGACTATAGCAACGGTGAACTCCTAGTTACTTCTATTGACAACTATAAAGTTATTCAAC
397 CTTTAGAGATACAATTTGTATAGTCATAAATC
391 CTTTAGAGATACAATTTGTATAGTCATAAATC
* * *
429 TCTCACAGATGAAGAAGTCTATACTTCGTTAG-CTACGTATGACAATATGAAGCATCTTGTGGTT
1 TCTCACAGATGAAGAAGTCTATACTTCCTTAGCCT-CGTATGACAAGATGAAGCATCTTGTGGCT
* * * *
493 GGATTCGACTCTTAGGGGGAGGGTCTCATTGTTCTTGGGAGACAAGAATGAAATATTAGTGATAA
65 GGATTCAACTCTTAAGGAGAGGGTCTCATTGTTCTTAGGAGA-AAGAATGAAATATTAGTGATAA
*
558 TCGTAGGAGGACACAAGAATGAAATCCTTGCAATAAATTTAAGGGTAGATCAAGATCTTCAAACA
129 TCGTAGGAGGACACAAGAATGAAATCCTTGCAATAAATCTAAGGGTAGATCAAGATCTTCAAACA
*
623 GAGGCAAAACCTGTAATTTCTACAAAAAGAAAGGGCACATTAAGTTTCAGTGCTATAAGTTACAA
194 GAGACAAAACCTGTAATTTCTAC-AAAAGAAAGGGCACATTAAGTTTCAGTGCTATAAGTTACAA
* * *
688 AATAAGATCAAAAGGGAGACTGCAAATCAAAAAGGAAAACAACCAAAATAATTCGATGAAGCTGA
258 AACAAGATCAAAAGGGAGACTGCAAATCAAAAAGGAAAACAAACAAAATAATCCGATGAAGCTGA
* *
753 TGTAGTAGAAGACTATAGCAACGGTGAACTCCTAGTTACTTCTGTTGACAACTATAAAGT
323 TGAAGTAGAAGACTATAGCAACGGTGAACTCCTAGTTACTTCTATTGACAACTATAAAGT
813 AAGCGAGGAG
Statistics
Matches: 350, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
421 2 0.01
422 94 0.27
423 103 0.29
424 151 0.43
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (422 bp):
TCTCACAGATGAAGAAGTCTATACTTCCTTAGCCTCGTATGACAAGATGAAGCATCTTGTGGCTG
GATTCAACTCTTAAGGAGAGGGTCTCATTGTTCTTAGGAGAAAGAATGAAATATTAGTGATAATC
GTAGGAGGACACAAGAATGAAATCCTTGCAATAAATCTAAGGGTAGATCAAGATCTTCAAACAGA
GACAAAACCTGTAATTTCTACAAAAGAAAGGGCACATTAAGTTTCAGTGCTATAAGTTACAAAAC
AAGATCAAAAGGGAGACTGCAAATCAAAAAGGAAAACAAACAAAATAATCCGATGAAGCTGATGA
AGTAGAAGACTATAGCAACGGTGAACTCCTAGTTACTTCTATTGACAACTATAAAGTTATTCAAC
CTTTAGAGATACAATTTGTATAGTCATAAATC
Found at i:15896 original size:17 final size:18
Alignment explanation
Indices: 15860--15898 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
15850 TTTTATTTAG
*
15860 TTGTCATTGCATTCTCAT
1 TTGTCACTGCATTCTCAT
15878 TTGTCACTGCATT-TCAT
1 TTGTCACTGCATTCTCAT
15895 TTGT
1 TTGT
15899 TAATACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.15, C:0.21, G:0.13, T:0.51
Consensus pattern (18 bp):
TTGTCACTGCATTCTCAT
Found at i:25873 original size:17 final size:18
Alignment explanation
Indices: 25837--25875 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
25827 TTTTATTTAG
*
25837 TTGTCATTGCATTCTCAT
1 TTGTCACTGCATTCTCAT
25855 TTGTCACTGCATT-TCAT
1 TTGTCACTGCATTCTCAT
25872 TTGT
1 TTGT
25876 TAATACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.15, C:0.21, G:0.13, T:0.51
Consensus pattern (18 bp):
TTGTCACTGCATTCTCAT
Found at i:34665 original size:17 final size:17
Alignment explanation
Indices: 34645--34679 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
34635 TCCGTATATT
*
34645 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
34662 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
34679 A
1 A
34680 CGAGTCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:39952 original size:104 final size:104
Alignment explanation
Indices: 39805--40040 Score: 314
Period size: 104 Copynumber: 2.3 Consensus size: 104
39795 GTCCGCAAGA
* *
39805 GATTCGTATACTCACGATGACACAGAGTCAACGGACCTCTTAATCCGTAAAGGATCCATATACTC
1 GATTCATATACTCACGATGACACATAGTCAACGGACCTCTTAATCCGTAAAGGATCCATATACTC
* *
39870 ATGATGACACTTAATCAACGGACCGTTTAATCCGTAAAG
66 ACGATGACACTTAATCAACGAACCGTTTAATCCGTAAAG
* * *
39909 GATTCATATACTCACGATGACACATAGTCATCAGG-CCGT-TTAATCTGTAAAGGATTCATATAC
1 GATTCATATACTCACGATGACACATAGTCAAC-GGACC-TCTTAATCCGTAAAGGATCCATATAC
* * * *
39972 TTACGATGACACTTATTCATCGAACCGTTTAATCTGTAAAG
64 TCACGATGACACTTAATCAACGAACCGTTTAATCCGTAAAG
* * *
40013 GATCCATATACTCATGATGACACTTAGT
1 GATTCATATACTCACGATGACACATAGT
40041 TATCGAACCT
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
104 113 0.97
105 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (104 bp):
GATTCATATACTCACGATGACACATAGTCAACGGACCTCTTAATCCGTAAAGGATCCATATACTC
ACGATGACACTTAATCAACGAACCGTTTAATCCGTAAAG
Found at i:40046 original size:52 final size:52
Alignment explanation
Indices: 39811--40049 Score: 284
Period size: 52 Copynumber: 4.6 Consensus size: 52
39801 AAGAGATTCG
** * *
39811 TATACTCACGATGACACAGAGTCAACGGACC-TCTTAATCCGTAAAGGATCCA
1 TATACTCACGATGACACTTAGTCATCGAACCGT-TTAATCCGTAAAGGATCCA
* * * * *
39863 TATACTCATGATGACACTTAATCAACGGACCGTTTAATCCGTAAAGGATTCA
1 TATACTCACGATGACACTTAGTCATCGAACCGTTTAATCCGTAAAGGATCCA
* * * *
39915 TATACTCACGATGACACATAGTCATC-AGGCCGTTTAATCTGTAAAGGATTCA
1 TATACTCACGATGACACTTAGTCATCGA-ACCGTTTAATCCGTAAAGGATCCA
* * *
39967 TATACTTACGATGACACTTATTCATCGAACCGTTTAATCTGTAAAGGATCCA
1 TATACTCACGATGACACTTAGTCATCGAACCGTTTAATCCGTAAAGGATCCA
* *
40019 TATACTCATGATGACACTTAGTTATCGAACC
1 TATACTCACGATGACACTTAGTCATCGAACC
40050 TCTTCGTTTA
Statistics
Matches: 163, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
52 161 0.99
53 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (52 bp):
TATACTCACGATGACACTTAGTCATCGAACCGTTTAATCCGTAAAGGATCCA
Found at i:47167 original size:52 final size:51
Alignment explanation
Indices: 47110--47359 Score: 278
Period size: 52 Copynumber: 4.8 Consensus size: 51
47100 AATCCACAAG
*
47110 GGATTCGTATACTCACGATGACTTAGAGTCATCGGACCTCTTAATCCGTAAA
1 GGATTCATATACTCACGATGACTTA-AGTCATCGGACCTCTTAATCCGTAAA
*
47162 GGATTCATATACTCACGATGGCACTT-AGTCATCGAACCGT-TTAATCCGTAAA
1 GGATTCATATACTCACGAT-G-ACTTAAGTCATCGGACC-TCTTAATCCGTAAA
* * *
47214 GGATTCATATAGGTC-CGATGACACTT-AGTCATCGGACCGCTTAATCCTTAAA
1 GGATTCATATA-CTCACGATG--ACTTAAGTCATCGGACCTCTTAATCCGTAAA
* * * *
47266 GGATTCGTATAGGTC-CGATGACACTAAGTCATCGGACCGCTTAATCCGTAAA
1 GGATTCATATA-CTCACGATGAC-TTAAGTCATCGGACCTCTTAATCCGTAAA
47318 GGATTCATATACTCACGATGACAGTT-AGTCATCGGACCTCTT
1 GGATTCATATACTCACGATGAC--TTAAGTCATCGGACCTCTT
47360 CGTTTATGGC
Statistics
Matches: 174, Mismatches: 14, Indels: 20
0.84 0.07 0.10
Matches are distributed among these distances:
50 2 0.01
51 4 0.02
52 159 0.91
53 5 0.03
54 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (51 bp):
GGATTCATATACTCACGATGACTTAAGTCATCGGACCTCTTAATCCGTAAA
Found at i:47244 original size:104 final size:104
Alignment explanation
Indices: 47110--47359 Score: 337
Period size: 104 Copynumber: 2.4 Consensus size: 104
47100 AATCCACAAG
*
47110 GGATTCGTATACTCACGATG--ACTTAGAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATA
1 GGATTCATATACTCACGATGACACTT--AGTCATCGGACCTCTTAATCCGTAAAGGATTCATATA
* * *
47173 -CTCACGATGGCACTTAGTCATCGAACCGTTTAATCCGTAAA
64 GCTC-CGATGACACTAAGTCATCGAACCGCTTAATCCGTAAA
* * * *
47214 GGATTCATATAGGTC-CGATGACACTTAGTCATCGGACCGCTTAATCCTTAAAGGATTCGTATAG
1 GGATTCATATA-CTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATAG
* *
47278 GTCCGATGACACTAAGTCATCGGACCGCTTAATCCGTAAA
65 CTCCGATGACACTAAGTCATCGAACCGCTTAATCCGTAAA
*
47318 GGATTCATATACTCACGATGACAGTTAGTCATCGGACCTCTT
1 GGATTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
47360 CGTTTATGGC
Statistics
Matches: 128, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
103 2 0.02
104 118 0.92
105 4 0.03
106 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (104 bp):
GGATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATAGC
TCCGATGACACTAAGTCATCGAACCGCTTAATCCGTAAA
Found at i:53769 original size:21 final size:20
Alignment explanation
Indices: 53745--53783 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
53735 GTTATTTTCG
53745 TTCTTACTCTCACAAGTTTAT
1 TTCTTACTCT-ACAAGTTTAT
* *
53766 TTCTTTCTCTGCAAGTTT
1 TTCTTACTCTACAAGTTT
53784 CTTTTAACCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (20 bp):
TTCTTACTCTACAAGTTTAT
Found at i:55478 original size:20 final size:20
Alignment explanation
Indices: 55446--55490 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
55436 GTAACCCAAT
55446 AAACCCAAAACCTTTAGAACC
1 AAACCCAAAACCTTT-GAACC
*
55467 AAACCC-AAACCTTTGACCC
1 AAACCCAAAACCTTTGAACC
55486 AAACC
1 AAACC
55491 AAGTGGACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.44, C:0.38, G:0.04, T:0.13
Consensus pattern (20 bp):
AAACCCAAAACCTTTGAACC
Found at i:57724 original size:21 final size:21
Alignment explanation
Indices: 57698--57744 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
57688 GGTTGGTTCG
** * *
57698 AAGGACAAGTAGAGGAAGCGC
1 AAGGACAAAAAGAAGAAGCAC
57719 AAGGACAAAAAGAAGAAGCAC
1 AAGGACAAAAAGAAGAAGCAC
57740 AAGGA
1 AAGGA
57745 GGAAAGAGAG
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:0.53, C:0.13, G:0.32, T:0.02
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAGCAC
Found at i:63614 original size:2 final size:2
Alignment explanation
Indices: 63607--63631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63597 TTTTGATTCA
63607 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 A
63632 ATAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63655 original size:24 final size:24
Alignment explanation
Indices: 63615--63698 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
63605 CAATATATAT
*
63615 ATATATATATATATATAATAAATTA
1 ATATA-ATATTTATATAATAAATTA
* * * *
63640 ATATAATATTTTTATATTGAATAA
1 ATATAATATTTATATAATAAATTA
*
63664 ATATAATTATTTATATAATAAAATA
1 ATATAA-TATTTATATAATAAATTA
63689 A-ATAA-ATTTA
1 ATATAATATTTA
63699 AATAGATGTC
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
22 5 0.10
24 24 0.50
25 19 0.40
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
ATATAATATTTATATAATAAATTA
Found at i:69086 original size:26 final size:26
Alignment explanation
Indices: 69057--69126 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
69047 ATACATATTT
*
69057 AATTATTTATATTTAGTCA-TTTACTA
1 AATTATTTATATTTA-TCATTTTAATA
*
69083 AATTATTAATATAATTTATTATTTTAATA
1 AATTATT--TAT-ATTTATCATTTTAATA
69112 AATTATTTGATATTT
1 AATTATTT-ATATTT
69127 CAATTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 7 0.19
29 18 0.49
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (26 bp):
AATTATTTATATTTATCATTTTAATA
Found at i:69170 original size:13 final size:15
Alignment explanation
Indices: 69139--69168 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
69129 ATTTAATTTT
69139 AATAATGAATTTAAA
1 AATAATGAATTTAAA
69154 AATAAT-AATTTAAA
1 AATAATGAATTTAAA
69168 A
1 A
69169 TATTCAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATAATGAATTTAAA
Found at i:69198 original size:15 final size:15
Alignment explanation
Indices: 69180--69236 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
69170 ATTCAATATT
69180 AATATTTTAATAATA
1 AATATTTTAATAATA
*
69195 AATATTTAATATAATTATA
1 AATA-TT--T-TAATAATA
**
69214 AATAAATTAATAATA
1 AATATTTTAATAATA
69229 AATATTTT
1 AATATTTT
69237 GTAGTATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 17 0.53
16 3 0.09
18 1 0.03
19 11 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:75253 original size:21 final size:21
Alignment explanation
Indices: 75235--75275 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
75225 AACTGAATTT
*
75235 AATTTGAAGTTTTTCGAATAC
1 AATTTGAAATTTTTCGAATAC
*
75256 AATTTGAAATTTTTTGAATA
1 AATTTGAAATTTTTCGAATA
75276 GAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (21 bp):
AATTTGAAATTTTTCGAATAC
Found at i:75839 original size:26 final size:26
Alignment explanation
Indices: 75805--75858 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
75795 TTATATCTTG
* *
75805 AATTGTATTTTAGTTTATTTATTAAA
1 AATTATATTTTAATTTATTTATTAAA
*
75831 AATTATATTTTAATTTGTTTATTAAA
1 AATTATATTTTAATTTATTTATTAAA
75857 AA
1 AA
75859 AATAGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (26 bp):
AATTATATTTTAATTTATTTATTAAA
Found at i:76196 original size:22 final size:22
Alignment explanation
Indices: 76171--76214 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
76161 ATATTATTGG
76171 TCAAGAGAAGAATTAGAAGCTA
1 TCAAGAGAAGAATTAGAAGCTA
76193 TCAAGAGAAGAATTAGAAGCTA
1 TCAAGAGAAGAATTAGAAGCTA
76215 CCATATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.23, T:0.18
Consensus pattern (22 bp):
TCAAGAGAAGAATTAGAAGCTA
Found at i:76313 original size:24 final size:23
Alignment explanation
Indices: 76268--76315 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
76258 TAAAATTTTT
76268 AATTTTAATTTAAAAATGTAAAAG
1 AATTTTAATTTAAAAA-GTAAAAG
76292 AATTTTATATTTAGAAAA-TAAAAG
1 AATTTTA-ATTTA-AAAAGTAAAAG
76316 CTTCCAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.59
25 5 0.23
26 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (23 bp):
AATTTTAATTTAAAAAGTAAAAG
Found at i:76327 original size:24 final size:22
Alignment explanation
Indices: 76300--76355 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
76290 AGAATTTTAT
76300 ATTTAGAAAATAAAAGCTTCCAAA
1 ATTTAGAAAA-AAAA-CTTCCAAA
76324 ATTTATG-AAAAAAACTTCCAAA
1 ATTTA-GAAAAAAAACTTCCAAA
* *
76346 AATTATAAAA
1 ATTTAGAAAA
76356 GAACTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 15 0.54
23 4 0.14
24 8 0.29
25 1 0.04
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (22 bp):
ATTTAGAAAAAAAACTTCCAAA
Found at i:76355 original size:21 final size:22
Alignment explanation
Indices: 76311--76361 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
76301 TTTAGAAAAT
* *
76311 AAAAGCTTCCAAAATTTATGAA
1 AAAAACTTCCAAAAATTATGAA
76333 AAAAACTTCCAAAAATTAT-AA
1 AAAAACTTCCAAAAATTATGAA
*
76354 AAGAACTT
1 AAAAACTT
76362 TTTCAAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.55, C:0.14, G:0.06, T:0.25
Consensus pattern (22 bp):
AAAAACTTCCAAAAATTATGAA
Found at i:76541 original size:17 final size:17
Alignment explanation
Indices: 76521--76570 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
76511 AATTTTAGAA
**
76521 TTTTAATTTTAATTTTT
1 TTTTAATTTTAAAATTT
*
76538 TTTTAGTTTTAAAATTT
1 TTTTAATTTTAAAATTT
*
76555 TTATAATTTTAAAATT
1 TTTTAATTTTAAAATT
76571 ATCTGATGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTAATTTTAAAATTT
Found at i:93042 original size:11 final size:11
Alignment explanation
Indices: 93028--93053 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
93018 TCTCCATTTT
93028 TTCTCTTCTTC
1 TTCTCTTCTTC
93039 TTCTCTTCTTC
1 TTCTCTTCTTC
93050 TTCT
1 TTCT
93054 ATTGCATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TTCTCTTCTTC
Found at i:94259 original size:18 final size:19
Alignment explanation
Indices: 94228--94265 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
94218 CATGTTTTGT
94228 ACAAACAAAAG-AAATAAA
1 ACAAACAAAAGAAAATAAA
94246 ACAAA-AAAATGAAAATAAA
1 ACAAACAAAA-GAAAATAAA
94265 A
1 A
94266 ATCAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (19 bp):
ACAAACAAAAGAAAATAAA
Found at i:95818 original size:31 final size:28
Alignment explanation
Indices: 95777--95851 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
95767 AATCTCAAAA
* *
95777 TTATATATAAATTTGATTATAATGAGTAATT
1 TTATACATAAATTTGATT-T--TGAGCAATT
*
95808 TTATACATAAATTTTGATTTTGTGCAATT
1 TTATACATAAA-TTTGATTTTGAGCAATT
95837 TTATACATGAAATTT
1 TTATACAT-AAATTT
95852 TAGTTCGATC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 18 0.46
30 3 0.08
31 11 0.28
32 7 0.18
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.49
Consensus pattern (28 bp):
TTATACATAAATTTGATTTTGAGCAATT
Found at i:95866 original size:30 final size:29
Alignment explanation
Indices: 95804--95866 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
95794 TATAATGAGT
* * *
95804 AATTTTATACATAAATTTTGATTTTGTGC
1 AATTTTATACATAAATTTTGAGTTCGTCC
95833 AATTTTATACATGAAATTTT-AGTTCGATCC
1 AATTTTATACAT-AAATTTTGAGTTCG-TCC
95863 AATT
1 AATT
95867 CTCATAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (29 bp):
AATTTTATACATAAATTTTGAGTTCGTCC
Found at i:97588 original size:19 final size:18
Alignment explanation
Indices: 97553--97592 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
97543 ATTAACCCTA
*
97553 AAAAGAATTAAAGAGATT
1 AAAAGAATTAAAAAGATT
97571 AAAAGAATTGAAAAAGATT
1 AAAAGAATT-AAAAAGATT
97590 AAA
1 AAA
97593 TTTAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (18 bp):
AAAAGAATTAAAAAGATT
Found at i:101168 original size:22 final size:21
Alignment explanation
Indices: 101143--101199 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
101133 TATTTTTTTT
101143 ATATATTATTTAGAACTTTTAA
1 ATATATTATTTAGAA-TTTTAA
* *
101165 ATATA-AATTTTGAATTTTAA
1 ATATATTATTTAGAATTTTAA
*
101185 A-A-ATTATTTTGAATT
1 ATATATTATTTAGAATT
101200 ATTTTGTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 11 0.35
20 7 0.23
21 7 0.23
22 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
ATATATTATTTAGAATTTTAA
Found at i:101195 original size:19 final size:19
Alignment explanation
Indices: 101147--101199 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
101137 TTTTTTATAT
* *
101147 ATTATTTAGAACTTTTAAAT
1 ATTATTTTGAA-TTTTAAAA
*
101167 ATAAATTTTGAATTTTAAAA
1 AT-TATTTTGAATTTTAAAA
101187 ATTATTTTGAATT
1 ATTATTTTGAATT
101200 ATTTTGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 10 0.36
20 11 0.39
21 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (19 bp):
ATTATTTTGAATTTTAAAA
Found at i:127375 original size:17 final size:17
Alignment explanation
Indices: 127353--127387 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
127343 TATCAAAATG
127353 AATGCAGTG-ACAATAAA
1 AATGCAG-GCACAATAAA
127370 AATGCAGGCACAATAAA
1 AATGCAGGCACAATAAA
127387 A
1 A
127388 TACAAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.14
Consensus pattern (17 bp):
AATGCAGGCACAATAAA
Found at i:143128 original size:20 final size:20
Alignment explanation
Indices: 143103--143167 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
143093 TACTCTGAAT
143103 CGCACTACGGTGCCCCTATA
1 CGCACTACGGTGCCCCTATA
* **
143123 CGCACTATGGTGCCTTTATA
1 CGCACTACGGTGCCCCTATA
* * *
143143 TGCACTTCGGTACCCCTATA
1 CGCACTACGGTGCCCCTATA
143163 CGCAC
1 CGCAC
143168 AATGGTGTCC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.26
Consensus pattern (20 bp):
CGCACTACGGTGCCCCTATA
Found at i:143189 original size:40 final size:40
Alignment explanation
Indices: 143104--143191 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
143094 ACTCTGAATC
* * * *
143104 GCACTACGGTGCCCCTATACGCACTATGGTGCCTTTATAT
1 GCACTTCGGTACCCCTATACGCACAATGGTGCCTGTATAT
143144 GCACTTCGGTACCCCTATACGCACAATGGTGTCCCTGTAT-T
1 GCACTTCGGTACCCCTATACGCACAATGGTG--CCTGTATAT
143185 -CACTTCG
1 GCACTTCG
143192 ATGCCCCTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 35 0.83
41 1 0.02
42 6 0.14
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30
Consensus pattern (40 bp):
GCACTTCGGTACCCCTATACGCACAATGGTGCCTGTATAT
Found at i:145269 original size:14 final size:15
Alignment explanation
Indices: 145246--145285 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
145236 TTTCAAAAAA
145246 AAAGTCATTTTCTAG
1 AAAGTCATTTTCTAG
*
145261 AAA-TCATTTT-TTG
1 AAAGTCATTTTCTAG
145274 AAAGTCATTTTC
1 AAAGTCATTTTC
145286 AATAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 5 0.23
14 14 0.64
15 3 0.14
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (15 bp):
AAAGTCATTTTCTAG
Found at i:156300 original size:26 final size:29
Alignment explanation
Indices: 156271--156338 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 29
156261 TTCACCAAAA
156271 AAAATAATCAAAAAAATAATT-TG-AT-T
1 AAAATAATCAAAAAAATAATTATGTATCT
* * * *
156297 AAAATAAACAGATAAATAATTATGTGTCT
1 AAAATAATCAAAAAAATAATTATGTATCT
156326 AAAATAATCAAAA
1 AAAATAATCAAAA
156339 TTATTATGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 18 0.56
27 2 0.06
28 1 0.03
29 11 0.34
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (29 bp):
AAAATAATCAAAAAAATAATTATGTATCT
Found at i:158207 original size:15 final size:15
Alignment explanation
Indices: 158187--158240 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 15
158177 ATATTACAAA
158187 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
158202 ATATTTATAATTATAAT
1 ATATTTATTA-T-TAAT
158219 AAATATTTATTATTAAT
1 --ATATTTATTATTAAT
158236 ATATT
1 ATATT
158241 AATATTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 14 0.42
16 1 0.03
17 8 0.24
18 1 0.03
19 9 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:158246 original size:17 final size:16
Alignment explanation
Indices: 158187--158246 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 16
158177 ATATTACAAA
158187 ATATT-TATTATTAAT
1 ATATTATATTATTAAT
158202 ATATTTATAATTA-TAAT
1 ATA-TTAT-ATTATTAAT
158219 AAATATT-TATTATTAAT
1 --ATATTATATTATTAAT
158236 ATATTAATATT
1 ATATT-ATATT
158247 GAATATTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
15 8 0.22
16 6 0.16
17 14 0.38
18 6 0.16
19 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTATATTATTAAT
Found at i:158326 original size:19 final size:17
Alignment explanation
Indices: 158294--158329 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
158284 ATTATTATTT
158294 ATAAAATTAATATTAAA
1 ATAAAATTAATATTAAA
158311 ATAAAATTGAAATATTAAA
1 ATAAAATT--AATATTAAA
158330 TAATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATAAAATTAATATTAAA
Found at i:158360 original size:22 final size:22
Alignment explanation
Indices: 158320--158375 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
158310 AATAAAATTG
*
158320 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
158340 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
158362 TATTAATAATTTAT
1 AAATAATAAATTAT
158376 TATATGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:158375 original size:16 final size:16
Alignment explanation
Indices: 158354--158386 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
158344 AATAAATTAT
*
158354 ATTTATTATATTAATA
1 ATTTATTATATGAATA
158370 ATTTATTATATGAATA
1 ATTTATTATATGAATA
158386 A
1 A
158387 ATATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
ATTTATTATATGAATA
Found at i:158471 original size:10 final size:9
Alignment explanation
Indices: 158442--158467 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
158432 ATTTTATATT
158442 AATATTTTA
1 AATATTTTA
158451 AATATTTTA
1 AATATTTTA
158460 AATATTTT
1 AATATTTT
158468 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Done.