Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003965.1 Kokia drynarioides strain JFW-HI SEQ_117058, 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: 98987
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:1500 original size:14 final size:15
Alignment explanation
Indices: 1477--1510 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1467 AACACTTGAT
*
1477 TTTTTTAATACTT-A
1 TTTTTCAATACTTAA
1491 TTTTTCAATACTTAA
1 TTTTTCAATACTTAA
1506 TTTTT
1 TTTTT
1511 AATTTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTCAATACTTAA
Found at i:4621 original size:47 final size:48
Alignment explanation
Indices: 4568--4665 Score: 162
Period size: 47 Copynumber: 2.1 Consensus size: 48
4558 ATTCTTTGAG
* *
4568 GAATTTTAAAGGTAATCGCTTTGGGATGGCTTTGAAGATAGATTTA-A
1 GAATTTTAAAGGTAATCGCTTTAGGATGGCTTCGAAGATAGATTTAGA
*
4615 GAATTTTGAAGGTAATCGCTTTAGGATGGCTTCGAAGATAGATTTAGA
1 GAATTTTAAAGGTAATCGCTTTAGGATGGCTTCGAAGATAGATTTAGA
4663 GAA
1 GAA
4666 GGCTTATGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 43 0.91
48 4 0.09
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.34
Consensus pattern (48 bp):
GAATTTTAAAGGTAATCGCTTTAGGATGGCTTCGAAGATAGATTTAGA
Found at i:10674 original size:21 final size:21
Alignment explanation
Indices: 10650--10700 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
10640 CCAAAATGAA
* *
10650 CCAAACCCATGTGAACTAAGT
1 CCAAACCCATGTGAACCAAGC
* * *
10671 CCAAAACCATTTGAGCCAAGC
1 CCAAACCCATGTGAACCAAGC
10692 CCAAACCCA
1 CCAAACCCA
10701 AACCAAGTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.14
Consensus pattern (21 bp):
CCAAACCCATGTGAACCAAGC
Found at i:10756 original size:7 final size:7
Alignment explanation
Indices: 10744--10785 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
10734 AGCGTGGACC
10744 GACCGTT
1 GACCGTT
10751 GACCGTT
1 GACCGTT
*
10758 GACTGTT
1 GACCGTT
10765 GACCGTT
1 GACCGTT
10772 GACCGTT
1 GACCGTT
10779 GACCGTT
1 GACCGTT
10786 AACTTTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31
Consensus pattern (7 bp):
GACCGTT
Found at i:11855 original size:3 final size:3
Alignment explanation
Indices: 11847--11878 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11837 TTACATCATT
11847 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11879 TTGGTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16250 original size:23 final size:24
Alignment explanation
Indices: 16206--16250 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
16196 AAACATATAC
*
16206 TAAATATATAACACTATTTTAATG
1 TAAATATATAACACTATGTTAATG
16230 TAAATAT-TAACA-TAATGTTAA
1 TAAATATATAACACT-ATGTTAA
16251 AATATTCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 11 0.58
24 7 0.37
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (24 bp):
TAAATATATAACACTATGTTAATG
Found at i:16316 original size:28 final size:27
Alignment explanation
Indices: 16285--16361 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 27
16275 AAGATAACTA
16285 TATAAAA-AATTCAATAAATAAAAAAATG
1 TATAAAATAATT-AA-AAATAAAAAAATG
*
16313 TATAAAATTATTAAAAATAAAAAAATG
1 TATAAAATAATTAAAAATAAAAAAATG
*
16340 TATAAAATTATTAAAAATAAAA
1 TATAAAATAATTAAAAATAAAA
16362 TAATTATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
27 35 0.74
28 9 0.19
29 3 0.06
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (27 bp):
TATAAAATAATTAAAAATAAAAAAATG
Found at i:19141 original size:11 final size:11
Alignment explanation
Indices: 19125--19201 Score: 68
Period size: 11 Copynumber: 6.9 Consensus size: 11
19115 AAAAAATTGA
19125 TATTATTTTAT
1 TATTATTTTAT
19136 TATTATTTT-T
1 TATTATTTTAT
* * *
19146 CACTATTTTTT
1 TATTATTTTAT
*
19157 TATCATTTTACT
1 TATTATTTTA-T
19169 T-TTATTTTAT
1 TATTATTTTAT
*
19179 TGTTAATTTTAT
1 TATT-ATTTTAT
19191 TATTATATTTA
1 TATTAT-TTTA
19202 CATGTATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
10 10 0.19
11 27 0.51
12 16 0.30
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:19210 original size:23 final size:22
Alignment explanation
Indices: 19184--19241 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
19174 TTTATTGTTA
*
19184 ATTTTATTATTATATT-TACAT
1 ATTTTATTATTAAATTGTACAT
*
19205 GTATTTATTTATTAAATTGTACAT
1 AT-TTTA-TTATTAAATTGTACAT
*
19229 ATTTTAGTATTAA
1 ATTTTATTATTAA
19242 GTATAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 13 0.43
24 6 0.20
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (22 bp):
ATTTTATTATTAAATTGTACAT
Found at i:19347 original size:24 final size:25
Alignment explanation
Indices: 19285--19347 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
19275 ATTAAAAAAT
19285 ATTTA-TTTTA-ATATTTTTTAATGA
1 ATTTATTTTTATATATTTTTTAA-GA
* *
19309 ATTTGATGTAT-TATATTTTTTAA-A
1 ATTT-ATTTTTATATATTTTTTAAGA
19333 ATTTATTTTTATATA
1 ATTTATTTTTATATA
19348 AAAAATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
23 4 0.13
24 13 0.42
25 1 0.03
26 13 0.42
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
ATTTATTTTTATATATTTTTTAAGA
Found at i:20501 original size:19 final size:18
Alignment explanation
Indices: 20452--20504 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
20442 ATACAAAATT
*
20452 AAATTATT--TTTTATTT
1 AAATTATTACTTTTATTA
*
20468 AAATTATCACGTTTTCATTA
1 AAATTATTAC-TTTT-ATTA
20488 AAATTATTACTTTTATT
1 AAATTATTACTTTTATT
20505 GTAAACAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.23
18 3 0.10
19 8 0.27
20 12 0.40
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.57
Consensus pattern (18 bp):
AAATTATTACTTTTATTA
Found at i:25872 original size:145 final size:144
Alignment explanation
Indices: 25591--25878 Score: 492
Period size: 145 Copynumber: 2.0 Consensus size: 144
25581 TGTGGGGTAC
*
25591 TTAGCTCAACTCTGTCTCTTTCTCAATGTATCAGCATAGGTATATGAAATTATTGTAGTCTCAGG
1 TTAGCTAAACTCTGTCTCTTTCTCAATGTATCAGCATAGGTATATGAAATTATTGTAGTCTCAGG
* *
25656 CGGTTATTTTTTTATCTTTTATAAATCAAGTGTTCCTTCTTTCATCAAGCATCTGTTTATGAGTA
66 CGGTTATATTTTTATCTATTATAAATCAAGTGTTCCTTCTTTCATCAAGCATCTGTTTATGAGTA
25721 TTCCTCCTTCTGGT
131 TTCCTCCTTCTGGT
25735 TTAGCTAAACTCTGTCTCTTTCTCAATGTATCAGCATAGGTATATGAAATTATTGTAGTCTCTCA
1 TTAGCTAAACTCTGTCTCTTTCTCAATGTATCAGCATAGGTATATGAAATTATTGTAG--TCTCA
25800 GAG-GGTTA-ATTTTTATCTATTATAAATCAAGCT-TTCCTTCTTTCATCAAGCATCTGTTTATG
64 G-GCGGTTATATTTTTATCTATTATAAATCAAG-TGTTCCTTCTTTCATCAAGCATCTGTTTATG
25862 AGTATTCCTCCTTCTGG
127 AGTATTCCTCCTTCTGG
25879 CTGTCTGCTT
Statistics
Matches: 137, Mismatches: 3, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
144 57 0.42
145 67 0.49
146 12 0.09
147 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (144 bp):
TTAGCTAAACTCTGTCTCTTTCTCAATGTATCAGCATAGGTATATGAAATTATTGTAGTCTCAGG
CGGTTATATTTTTATCTATTATAAATCAAGTGTTCCTTCTTTCATCAAGCATCTGTTTATGAGTA
TTCCTCCTTCTGGT
Found at i:48119 original size:2 final size:2
Alignment explanation
Indices: 48112--48146 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
48102 AGTGAAAAGT
*
48112 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
48147 GAAAACCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:48856 original size:22 final size:22
Alignment explanation
Indices: 48830--48884 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
48820 AATTAGGTTA
*
48830 TTTATTATTATGTTGCTATCAT
1 TTTATTATTATATTGCTATCAT
* *
48852 TTTATTATTATATTGTTATTAT
1 TTTATTATTATATTGCTATCAT
48874 TTTATTATTAT
1 TTTATTATTAT
48885 TTTTTGAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTATTATTATATTGCTATCAT
Found at i:48885 original size:11 final size:11
Alignment explanation
Indices: 48830--48936 Score: 63
Period size: 11 Copynumber: 9.4 Consensus size: 11
48820 AATTAGGTTA
48830 TTTATTATTAT
1 TTTATTATTAT
* ** *
48841 GTTGCTATCAT
1 TTTATTATTAT
48852 TTTATTATTAT
1 TTTATTATTAT
* *
48863 ATTGTTATTAT
1 TTTATTATTAT
48874 TTTATTATTAT
1 TTTATTATTAT
*
48885 TTT-TTGAATAT
1 TTTATT-ATTAT
*
48896 TGTATAATTTTTAT
1 T-T-T-ATTATTAT
* *
48910 CTTATTATCAAT
1 TTTATTAT-TAT
*
48922 TTTACTATTAT
1 TTTATTATTAT
48933 TTTA
1 TTTA
48937 GAGGTATTTG
Statistics
Matches: 69, Mismatches: 21, Indels: 12
0.68 0.21 0.12
Matches are distributed among these distances:
10 2 0.03
11 50 0.72
12 10 0.14
13 2 0.03
14 3 0.04
15 2 0.03
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:53062 original size:11 final size:10
Alignment explanation
Indices: 53052--53103 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
53042 TATCTTTTAT
53052 ACTTTAATTA
1 ACTTTAATTA
**
53062 TAAGTTAATTA
1 -ACTTTAATTA
*
53073 ACCTTAATTA
1 ACTTTAATTA
53083 A-TTTAATTAA
1 ACTTTAATT-A
53093 ACTTTAATTA
1 ACTTTAATTA
53103 A
1 A
53104 TTAATCCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 6 0.18
10 13 0.38
11 15 0.44
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (10 bp):
ACTTTAATTA
Found at i:53090 original size:19 final size:20
Alignment explanation
Indices: 53066--53105 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53056 TAATTATAAG
53066 TTAATT-AACCTTAATTAAT
1 TTAATTAAACCTTAATTAAT
*
53085 TTAATTAAACTTTAATTAAT
1 TTAATTAAACCTTAATTAAT
53105 T
1 T
53106 AATCCTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATTAAACCTTAATTAAT
Found at i:57140 original size:41 final size:43
Alignment explanation
Indices: 57094--57179 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
57084 GAACTTTTTC
* *
57094 TTTAAAC-AATCTTATACTC-TACCGAGTCATAAGTCTTCCTT
1 TTTAAACAAATCTCACACTCATACCGAGTCATAAGTCTTCCTT
* * *
57135 TTTAAACATAATCTCACGCTCATTCCGAGTCATGAGTCTTCCTT
1 TTTAAACA-AATCTCACACTCATACCGAGTCATAAGTCTTCCTT
57179 T
1 T
57180 AATCATATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 7 0.19
43 9 0.24
44 21 0.57
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.38
Consensus pattern (43 bp):
TTTAAACAAATCTCACACTCATACCGAGTCATAAGTCTTCCTT
Found at i:57246 original size:40 final size:41
Alignment explanation
Indices: 57125--57262 Score: 165
Period size: 42 Copynumber: 3.3 Consensus size: 41
57115 CCGAGTCATA
* ** *
57125 AGTCTTCCTTTTTAAACATAATCTCACGCTCATTCC-GAGTCATG
1 AGTCTTCC--TTTAATCAT-ATCTCATTCTCA-TCCTGAGACATG
*
57169 AGTCTTCCTTTAATCATATTCTCATTCTCATCTTGAGACATG
1 AGTCTTCCTTTAATCATA-TCTCATTCTCATCCTGAGACATG
57211 AGTCTTCCTTTAATCATA-CTCATTCTCATCCTGAGACATG
1 AGTCTTCCTTTAATCATATCTCATTCTCATCCTGAGACATG
57251 AGTCTT-CTTTAA
1 AGTCTTCCTTTAA
57263 ATATATCCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
39 6 0.07
40 27 0.31
41 3 0.03
42 42 0.49
44 8 0.09
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (41 bp):
AGTCTTCCTTTAATCATATCTCATTCTCATCCTGAGACATG
Found at i:60131 original size:26 final size:27
Alignment explanation
Indices: 60101--60154 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
60091 ATTTTTAAGA
*
60101 AAAG-TAGTATTTTTAAAAAAAAAAAT
1 AAAGTTAGAATTTTTAAAAAAAAAAAT
*
60127 AAAGTTTAGAATTTTTAAAAATAAAAAT
1 AAAG-TTAGAATTTTTAAAAAAAAAAAT
60155 CTGTTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
28 20 0.83
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (27 bp):
AAAGTTAGAATTTTTAAAAAAAAAAAT
Found at i:60336 original size:283 final size:279
Alignment explanation
Indices: 59842--60397 Score: 741
Period size: 283 Copynumber: 2.0 Consensus size: 279
59832 GGTTTTTTTT
*
59842 AAAAAAAAAGTTTAGATTTTTAAAAATAAAAACCTATTTTTTAGTAATTTTAAAGGAAAAGTTTA
1 AAAAAAAAAGTTTAGATTTTTAAAAATAAAAACCTATTTTTTAGTAATTTTAAAGAAAAAGTTTA
* * * * * *
59907 AATTTTTAAACAAAGTTTTTATTTTTTAAATATTTCAAAATAAAGTTTTGCTTTGTAAGAAGAAT
66 AATTTTTAAACAAAGTTTTTATTTTTTAAATATTTCAAAATAAAGCTTTGATTTGAAAAAAAAAA
* *
59972 AGTGATTTAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTTTGTCATGGAAAAAG
131 AGTGATTTAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTCATGGAAAAAG
* * *
60037 TTTATATTTTTAAACAAAGTTTTGATTTTTTAACTATTTCGAAAT-AAAATTTTGATTTTTAAGA
196 TTTAAATTTTTAAACAAAG-TTTGATTTTTTAACCATTTCGAAATAAAAATTTTGATTTTTAAAA
60101 AAAGTAGT-ATTTTTAAAAA
260 AAAGTAGTGATTTTTAAAAA
* * *
60120 AAAAAATAAAGTTTAGAATTTTTAAAAATAAAAATCTGTTTTTTAGTCATTTTAAAGAAAAAAGT
1 AAAAAA-AAAGTTTAG-ATTTTTAAAAATAAAAACCTATTTTTTAGTAATTTTAAAG-AAAAAGT
* * *
60185 TTAAATTTTTTTAAACAAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAGCTTTGATTT-A
63 TTAAA--TTTTTAAACAAAG-TTT--TTATTTTTTAAATATTTCAAAAT-AAAGCTTTGATTTGA
*** *
60249 AAAAAAAAAAGTGATTT-TTTAAAAA-TTTAGATTTTTAAAAATTAAAATATG-TTTTTTAGTCA
122 AAAAAAAAAAGTGATTTAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTCA
*
60311 -GG-AAAAGTTTTAAATTTTTTAAACAAAGTTTGATTTTTTAACCATTTCTAAATAAAAATTTTG
187 TGGAAAAAG-TTTAAA-TTTTTAAACAAAGTTTGATTTTTTAACCATTTCGAAATAAAAATTTTG
60374 ATTTTTAAAAAAAGTAGTGATTTT
250 ATTTTTAAAAAAAGTAGTGATTTT
60398 GTTTAAAAAA
Statistics
Matches: 242, Mismatches: 23, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
278 6 0.02
279 9 0.04
280 37 0.15
281 16 0.07
282 30 0.12
283 62 0.26
284 32 0.13
285 5 0.02
286 34 0.14
287 11 0.05
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (279 bp):
AAAAAAAAAGTTTAGATTTTTAAAAATAAAAACCTATTTTTTAGTAATTTTAAAGAAAAAGTTTA
AATTTTTAAACAAAGTTTTTATTTTTTAAATATTTCAAAATAAAGCTTTGATTTGAAAAAAAAAA
AGTGATTTAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTTAGTCATGGAAAAAG
TTTAAATTTTTAAACAAAGTTTGATTTTTTAACCATTTCGAAATAAAAATTTTGATTTTTAAAAA
AAGTAGTGATTTTTAAAAA
Found at i:60407 original size:134 final size:131
Alignment explanation
Indices: 59838--60397 Score: 511
Period size: 134 Copynumber: 4.0 Consensus size: 131
59828 ATGAGGTTTT
* * *
59838 TTTTAAAAAAAAAGTTTAGATTTTTAAAAATAAAAACCTATTTTTTAGTAATTTTAAAGGAAAAG
1 TTTT-AAAAAAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAG------T-CAGGAAAAG
* * * * * *
59903 TTTAAATTTTTAAACAAAGTTTTTATTTTTTAAATATTTCAAAATAAAGTTTTGCTTTGTAAGAA
58 TTTAAATTTTTAAACAAAGTTTTGATTTTTTAACTATTTCGAAATAAAATTTTGATTTTTAA-AA
*
59968 GAA-TAGTGA
122 AAAGTAGTGA
* * *
59977 TTTAAAAAAAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTTTGTCATGGAAAAAGTTTAT
1 TTTTAAAAAAAAGTTTAGATTTTTAAAAATAAAAATCTG-TTTTTTAGTCA-GG-AAAAGTTTAA
*
60042 ATTTTTAAACAAAGTTTTGATTTTTTAACTATTTCGAAATAAAATTTTGATTTTTAAGAAAAGTA
63 ATTTTTAAACAAAGTTTTGATTTTTTAACTATTTCGAAATAAAATTTTGATTTTTAAAAAAAGTA
60107 GT-A
128 GTGA
60110 TTTTTAAAAAAAAAAATAAAGTTTAGAATTTTTAAAAATAAAAATCTGTTTTTTAGTCATTTTAA
1 -TTTT------AAAAA-AAAGTTTAG-ATTTTTAAAAATAAAAATCTGTTTTTTAGTC-------
* *
60175 AGAAAAAAGTTTAAATTTTTTTAAACAAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAGC
50 AG-GAAAAGTTTAAA--TTTTTAAACAAAGTTTTGA---TTTTTTAACTATTTCGAAATAAAA-T
* **
60240 TTTGA-TTTAAAAAAAAAAAGTGA
108 TTTGATTTTTAAAAAAAGTAGTGA
** * *
60263 TTTT-TTAAAAA-TTTAGATTTTTAAAAATTAAAATATGTTTTTTAGTCAGGAAAAGTTTTAAAT
1 TTTTAAAAAAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTCAGGAAAAG-TTTAAA-
* *
60326 TTTTTAAACAAAG-TTTGATTTTTTAACCATTTCTAAATAAAAATTTTGATTTTTAAAAAAAGTA
64 TTTTTAAACAAAGTTTTGATTTTTTAACTATTTCGAAAT-AAAATTTTGATTTTTAAAAAAAGTA
60390 GTGA
128 GTGA
60394 TTTT
1 TTTT
60398 GTTTAAAAAA
Statistics
Matches: 356, Mismatches: 34, Indels: 70
0.77 0.07 0.15
Matches are distributed among these distances:
130 23 0.06
131 23 0.06
132 1 0.00
133 12 0.03
134 86 0.24
135 8 0.02
138 33 0.09
139 10 0.03
140 5 0.01
141 18 0.05
142 50 0.14
143 5 0.01
144 3 0.01
145 2 0.01
147 11 0.03
148 1 0.00
149 19 0.05
152 40 0.11
153 6 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (131 bp):
TTTTAAAAAAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTCAGGAAAAGTTTAAATT
TTTAAACAAAGTTTTGATTTTTTAACTATTTCGAAATAAAATTTTGATTTTTAAAAAAAGTAGTG
A
Found at i:62987 original size:15 final size:15
Alignment explanation
Indices: 62967--62995 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62957 CTCCACCCTT
62967 CCGCTGCTGCCGCCG
1 CCGCTGCTGCCGCCG
62982 CCGCTGCTGCCGCC
1 CCGCTGCTGCCGCC
62996 TCACTCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.55, G:0.31, T:0.14
Consensus pattern (15 bp):
CCGCTGCTGCCGCCG
Found at i:69139 original size:25 final size:25
Alignment explanation
Indices: 69109--69157 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
69099 TAGACTGCAG
69109 TTTGGCTTGCCATGATTAGATTCAT
1 TTTGGCTTGCCATGATTAGATTCAT
69134 TTTGGCTTGCCATGATTAGATTCA
1 TTTGGCTTGCCATGATTAGATTCA
69158 GTCATTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (25 bp):
TTTGGCTTGCCATGATTAGATTCAT
Found at i:71841 original size:16 final size:15
Alignment explanation
Indices: 71820--71851 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
71810 CTTGATTTTT
71820 AAAAATTAAAATTAAA
1 AAAAATTAAAA-TAAA
71836 AAAAATTAAAATAAA
1 AAAAATTAAAATAAA
71851 A
1 A
71852 GATTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAAATTAAAATAAA
Found at i:76299 original size:23 final size:25
Alignment explanation
Indices: 76273--76318 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
76263 TCAATTAGGG
76273 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
76296 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
76319 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:77405 original size:18 final size:19
Alignment explanation
Indices: 77382--77424 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
77372 TTAGTCATTT
77382 TTTTATTATTT-ATTTTTA
1 TTTTATTATTTCATTTTTA
77400 TTTTATTATTTGCATTTTTA
1 TTTTATTATTT-CATTTTTA
*
77420 ATTTA
1 TTTTA
77425 ATTTTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
20 11 0.50
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTATTATTTCATTTTTA
Found at i:77435 original size:14 final size:14
Alignment explanation
Indices: 77414--77445 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
77404 ATTATTTGCA
77414 TTTT-TAATTTAAT
1 TTTTCTAATTTAAT
77427 TTTTCTAATTTAAT
1 TTTTCTAATTTAAT
77441 TTTTC
1 TTTTC
77446 CCTTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTAATTTAAT
Found at i:80299 original size:12 final size:11
Alignment explanation
Indices: 80275--80322 Score: 62
Period size: 12 Copynumber: 4.2 Consensus size: 11
80265 AATTAGTATA
80275 TTTATTTTCATT
1 TTTATTTT-ATT
80287 TTTAGTTTTA-T
1 TTTA-TTTTATT
80298 TTTATTTTATT
1 TTTATTTTATT
80309 TTTAATTTTATT
1 TTT-ATTTTATT
80321 TT
1 TT
80323 AATTATGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.15
11 9 0.27
12 15 0.45
13 4 0.12
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:80302 original size:5 final size:5
Alignment explanation
Indices: 80275--80323 Score: 53
Period size: 5 Copynumber: 8.8 Consensus size: 5
80265 AATTAGTATA
80275 TTTAT TTTCATT TTTAGT TTTAT TTTAT TTTATT TTTAAT TTTAT TTTA
1 TTTAT TTT-A-T TTTA-T TTTAT TTTAT TTTA-T TTT-AT TTTAT TTTA
80324 ATTATGCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 19 0.49
6 15 0.38
7 5 0.13
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:80316 original size:17 final size:16
Alignment explanation
Indices: 80275--80323 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
80265 AATTAGTATA
80275 TTTATTTTCATTTTTAGT
1 TTTATTTT-A-TTTTAGT
*
80293 TTTATTTTATTTTATT
1 TTTATTTTATTTTAGT
80309 TTTAATTTTATTTTA
1 TTT-ATTTTATTTTA
80324 ATTATGCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 9 0.31
17 12 0.41
18 8 0.28
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTTAGT
Found at i:80322 original size:22 final size:23
Alignment explanation
Indices: 80275--80323 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
80265 AATTAGTATA
*
80275 TTTATTTTCATTTTTAGTTTTAT
1 TTTATTTTCATTTTTAATTTTAT
80298 TTTATTTT-ATTTTTAATTTTAT
1 TTTATTTTCATTTTTAATTTTAT
80320 TTTA
1 TTTA
80324 ATTATGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTATTTTCATTTTTAATTTTAT
Found at i:80323 original size:11 final size:11
Alignment explanation
Indices: 80286--80326 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
80276 TTATTTTCAT
*
80286 TTTTAGTTTTA
1 TTTTAATTTTA
80297 TTTT-ATTTTA
1 TTTTAATTTTA
80307 TTTTTAATTTTA
1 -TTTTAATTTTA
80319 TTTTAATT
1 TTTTAATT
80327 ATGCAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 5 0.19
11 16 0.59
12 6 0.22
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTAATTTTA
Found at i:81273 original size:21 final size:21
Alignment explanation
Indices: 81239--81296 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
81229 ATTGTTTAGA
*
81239 AAAAAAAAAGAAAAAAAAAGGTC
1 AAAAAGAAA-AAAAAAAAA-GTC
* * *
81262 GAAAAGAAAAAAAAAAAATTT
1 AAAAAGAAAAAAAAAAAAGTC
81283 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
81297 GAAGAAGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 14 0.47
22 9 0.30
23 7 0.23
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAGAAAAAAAAAAAAGTC
Found at i:82360 original size:23 final size:25
Alignment explanation
Indices: 82334--82379 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
82324 CCAATTAGGG
82334 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
82357 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
82380 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:87924 original size:61 final size:57
Alignment explanation
Indices: 87829--87981 Score: 220
Period size: 61 Copynumber: 2.6 Consensus size: 57
87819 CATGCAATGA
87829 CCCCTTTTCTC-AAAAAAAATTGCATTTTTGGGTGTTGATCATTGCATGGCCGACAC
1 CCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGATCATTGCATGGCCGACAC
* * *
87885 CCCCTTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGATCATTGCATGGTCGACAC
1 CCCCTTTTCTCGA-AAAAAAATTGC---ATTTTTGGGTGTTGATCATTGCATGGCCGACAC
*
87946 CCCCTTTTCTTGAAAAAAAA-TGCATTTTTGGGTGTT
1 CCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTT
87982 TTCTCGAGAA
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
56 23 0.27
57 1 0.01
58 10 0.12
59 2 0.02
60 7 0.08
61 43 0.50
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (57 bp):
CCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGATCATTGCATGGCCGACAC
Found at i:88055 original size:91 final size:91
Alignment explanation
Indices: 87889--88056 Score: 241
Period size: 91 Copynumber: 1.8 Consensus size: 91
87879 CGACACCCCC
* * *
87889 TTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGATCATTGCATGGTCGACACCCCCTTTT
1 TTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCGCATGGCCGACACCCCCTTTT
*
87954 CTTGAAAAAAAATGCATTTTTGGGTG
66 CTTAAAAAAAAATGCATTTTTGGGTG
* * *
87980 TTTTCTCGAGAAAAAAATTTCAAAATTTTTTTGTGTTGGCCA-CGCAATGGCCGACACCCGCTTT
1 TTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCGC-ATGGCCGACACCCCCTTT
88044 T-TTAAATAAAAAA
65 TCTTAAA-AAAAAA
88057 ATTTCAAATT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
90 6 0.09
91 62 0.91
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (91 bp):
TTTTCTCGAGAAAAAAATTTCAAAATTTTTTGGTGTTGACCATCGCATGGCCGACACCCCCTTTT
CTTAAAAAAAAATGCATTTTTGGGTG
Found at i:88091 original size:61 final size:61
Alignment explanation
Indices: 87990--88105 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 61
87980 TTTTCTCGAG
*
87990 AAAAAAATTTCAAAATTTTTTTGTGTTGGCCACGCAATGGCCGACACCCGCTTTTTTAAAT
1 AAAAAAATTTCAAAATTTTTTTGTGTTGGCCACGCAATGGCCGACACCCCCTTTTTTAAAT
* * *
88051 AAAAAAATTTCAAATTTTTTTTGTGTTGGCCATGCCATGGCCGACACCCCCTTTT
1 AAAAAAATTTCAAAATTTTTTTGTGTTGGCCACGCAATGGCCGACACCCCCTTTT
88106 CTTAGATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (61 bp):
AAAAAAATTTCAAAATTTTTTTGTGTTGGCCACGCAATGGCCGACACCCCCTTTTTTAAAT
Found at i:88355 original size:72 final size:72
Alignment explanation
Indices: 88265--88407 Score: 277
Period size: 72 Copynumber: 2.0 Consensus size: 72
88255 TGGCCATGTA
88265 ATGGCCGACATCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTGATTTTGAAGTTGT
1 ATGGCCGACATCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTGATTTTGAAGTTGT
88330 AAGTAAC
66 AAGTAAC
*
88337 ATGGCCGACATCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTTATTTTGAAGTTGT
1 ATGGCCGACATCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTGATTTTGAAGTTGT
88402 AAGTAA
66 AAGTAA
88408 GAAATATTTC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (72 bp):
ATGGCCGACATCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTGATTTTGAAGTTGT
AAGTAAC
Found at i:89184 original size:17 final size:17
Alignment explanation
Indices: 89164--89220 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
89154 AAAAAAAAAT
89164 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
* **
89181 AATTAGAAGA-A-AAAA
1 AATTAGAATATACAGGA
*
89196 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
*
89213 AAATAGAA
1 AATTAGAA
89221 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 10 0.34
16 2 0.07
17 17 0.59
ACGTcount: A:0.63, C:0.04, G:0.14, T:0.19
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:89194 original size:32 final size:32
Alignment explanation
Indices: 89157--89220 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
89147 AAATTTAAAA
* *
89157 AAAAAATAATTAGAATATACAGGAAATTAGAAG
1 AAAAAA-AATTAAAATATACAGGAAAATAGAAG
89190 AAAAAAAATTAAAATATACAGGAAAATAGAA
1 AAAAAAAATTAAAATATACAGGAAAATAGAA
89221 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.66, C:0.03, G:0.12, T:0.19
Consensus pattern (32 bp):
AAAAAAAATTAAAATATACAGGAAAATAGAAG
Found at i:89234 original size:30 final size:30
Alignment explanation
Indices: 89170--89263 Score: 82
Period size: 30 Copynumber: 3.1 Consensus size: 30
89160 AAATAATTAG
* ** *
89170 AATATACAGGAAATTAGAAGAAAAAAAATTAA
1 AATATACAGGAAAATAG-A-AATTAAATTTAA
89202 AATATACAGGAAAATAGAAATTAAATTTAA
1 AATATACAGGAAAATAGAAATTAAATTTAA
* ** *
89232 AATA-AAAACAAAATTATAAATTAAATTTAA
1 AATATACAGGAAAA-TAGAAATTAAATTTAA
89262 AA
1 AA
89264 AGTAAACAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.11
30 30 0.57
31 1 0.02
32 16 0.30
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.24
Consensus pattern (30 bp):
AATATACAGGAAAATAGAAATTAAATTTAA
Found at i:93833 original size:14 final size:14
Alignment explanation
Indices: 93814--93841 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
93804 TAACTAATTT
93814 AACTTAATTTTTAA
1 AACTTAATTTTTAA
93828 AACTTAATTTTTAA
1 AACTTAATTTTTAA
93842 TTAATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
AACTTAATTTTTAA
Found at i:94651 original size:25 final size:24
Alignment explanation
Indices: 94615--94692 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
94605 TTTGGTGTAG
* *
94615 TTTTTTTGCTATTTTGGTTGTTATT
1 TTTTTTTACTATTTTGG-TGCTATT
94640 TTTTTTTACTATTTTGGTGCTATT
1 TTTTTTTACTATTTTGGTGCTATT
* **
94664 TTTATTGTTA-TTTTTTTTTGCTATT
1 TTT-TT-TTACTATTTTGGTGCTATT
94689 TTTT
1 TTTT
94693 CTATTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 10 0.22
25 33 0.72
26 3 0.07
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.73
Consensus pattern (24 bp):
TTTTTTTACTATTTTGGTGCTATT
Found at i:94654 original size:12 final size:12
Alignment explanation
Indices: 94615--94692 Score: 59
Period size: 12 Copynumber: 6.4 Consensus size: 12
94605 TTTGGTGTAG
94615 TTTTTTTGCTAT
1 TTTTTTTGCTAT
** *
94627 TTTGGTTGTTATT
1 TTTTTTTGCTA-T
*
94640 TTTTTTTACTA-
1 TTTTTTTGCTAT
**
94651 TTTTGGTGCTAT
1 TTTTTTTGCTAT
* *
94663 TTTTATTGTTATT
1 TTTTTTTGCTA-T
94676 TTTTTTTGCTAT
1 TTTTTTTGCTAT
94688 TTTTT
1 TTTTT
94693 CTATTATTTT
Statistics
Matches: 48, Mismatches: 15, Indels: 6
0.70 0.22 0.09
Matches are distributed among these distances:
11 8 0.17
12 22 0.46
13 18 0.38
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTTTTTGCTAT
Found at i:94661 original size:36 final size:36
Alignment explanation
Indices: 94621--94690 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
94611 GTAGTTTTTT
*
94621 TGCTATTTTGGTTGTTATTTTTTTTTACTATTTTGG
1 TGCTATTTTGATTGTTATTTTTTTTTACTATTTTGG
* *
94657 TGCTATTTTTATTGTTATTTTTTTTTGCTATTTT
1 TGCTATTTTGATTGTTATTTTTTTTTACTATTTT
94691 TTCTATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.11, C:0.06, G:0.13, T:0.70
Consensus pattern (36 bp):
TGCTATTTTGATTGTTATTTTTTTTTACTATTTTGG
Found at i:94725 original size:61 final size:60
Alignment explanation
Indices: 94615--94733 Score: 143
Period size: 61 Copynumber: 1.9 Consensus size: 60
94605 TTTGGTGTAG
* * *
94615 TTTTTTTGCTATTTTGGTTGTTATTTTTTTTTACTATTTTGGTGCTATTTTTATTGTTATT
1 TTTTTTTGCTATTTT-GTTGCTATTTTTTTCTACTATTTTGGTGCTATTTTGATTGTTATT
* *
94676 TTTTTTTGCTATTTT-TT-CTATTATTTTTGCTACTGTTTTGGTTGTTATTTTGATTGTT
1 TTTTTTTGCTATTTTGTTGCTATT-TTTTT-CTACTATTTTGG-TGCTATTTTGATTGTT
94734 TGGATGTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 4 0.08
59 7 0.14
60 10 0.20
61 29 0.58
ACGTcount: A:0.11, C:0.06, G:0.13, T:0.70
Consensus pattern (60 bp):
TTTTTTTGCTATTTTGTTGCTATTTTTTTCTACTATTTTGGTGCTATTTTGATTGTTATT
Found at i:94894 original size:17 final size:19
Alignment explanation
Indices: 94874--94908 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
94864 TTTTAATGTA
94874 TTTTTAAT-TTT-TTTTAT
1 TTTTTAATGTTTGTTTTAT
94891 TTTTTAATGTTTGTTTTA
1 TTTTTAATGTTTGTTTTA
94909 AAGTTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTTAATGTTTGTTTTAT
Found at i:95267 original size:10 final size:10
Alignment explanation
Indices: 95252--95287 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
95242 TAACATAATA
95252 ATCTTTTATC
1 ATCTTTTATC
*
95262 ATCTTTT-TT
1 ATCTTTTATC
95271 ATCTTTTATC
1 ATCTTTTATC
95281 ATCTTTT
1 ATCTTTT
95288 TTCTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (10 bp):
ATCTTTTATC
Found at i:95276 original size:19 final size:19
Alignment explanation
Indices: 95252--95289 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
95242 TAACATAATA
95252 ATCTTTTATCATCTTTTTT
1 ATCTTTTATCATCTTTTTT
95271 ATCTTTTATCATCTTTTTT
1 ATCTTTTATCATCTTTTTT
95290 CTTTATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (19 bp):
ATCTTTTATCATCTTTTTT
Done.