Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167840.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_111, 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: 81376
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:10383 original size:8 final size:8
Alignment explanation
Indices: 10369--10417 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
10359 CTACACTTGA
10369 AAAAAAATG
1 AAAAAAA-G
*
10378 AAAAAATAA
1 AAAAAA-AG
10387 AAAAAAAG
1 AAAAAAAG
10395 AAAAAAAG
1 AAAAAAAG
*
10403 AAAAAAGG
1 AAAAAAAG
10411 AAAAAAA
1 AAAAAAA
10418 AAAGTGAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 22 0.63
9 12 0.34
10 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:10388 original size:17 final size:16
Alignment explanation
Indices: 10368--10420 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
10358 ACTACACTTG
*
10368 AAAAAAAATGAAAAAA
1 AAAAAAAAAGAAAAAA
10384 TAAAAAAAAAGAAAAAA
1 -AAAAAAAAAGAAAAAA
* *
10401 AGAAAAAAGGAAAAAA
1 AAAAAAAAAGAAAAAA
10417 AAAA
1 AAAA
10421 GTGAATGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 17 0.53
17 15 0.47
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAA
Found at i:11488 original size:42 final size:42
Alignment explanation
Indices: 11442--11900 Score: 310
Period size: 42 Copynumber: 10.8 Consensus size: 42
11432 AGCTATTTAC
*
11442 TTTCCAAAGTCGTCGAGCCTCTGATTAGAGGAGCCATTTATT
1 TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATT
* * * * * *
11484 TTTCCAAAATCGTCGAACCT-TTATTTAGAAGAGCAATTTATT
1 TTTCCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCCATTTATT
** * *
11526 TTT-CAAAGTCGTCAAGCTTCTGATTAAAGGAGCCATTTA-T
1 TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATT
* * * ** * *
11566 TTT-CAAAATTGTTAAGCCTCTGATTAGAAAAGTCACTTATT
1 TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATT
* * *
11607 GTT-CAAAGTTGTTGAGCCCCTGATTAGAGGAG-CATTGT-TT
1 TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATT-TATT
* * * *
11647 ATTTCTTAAAGTTGTTGAGCCTCTGATTAGATGAGCCATTTACT
1 -TTTC-CAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATT
* * * * * *
11691 CTTCAAAAATCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTACT
1 TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGC--CATTTATT
* * *
11735 CTTCAAAAGTCGTTGAGCCTCT-ATTTAGAGGAGCTTTATTTATT
1 TTTCCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGC--CATTTATT
* * * *
11779 TTT-GAAAGTCATCGAGCCTCTGATTAGAGGAG--TTTTATT
1 TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATT
* * * *
11818 CATTTTCAAAGTCATTGAGCCTCTAATTAGAGGAGCATTTATTTATAT
1 --TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGC---CATTTAT-T
* *
11866 TTTTCAAAGTCGTTGAGCCTCTGCTTAGAGGAGCC
1 TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
11901 TTGATCAAAT
Statistics
Matches: 338, Mismatches: 57, Indels: 43
0.77 0.13 0.10
Matches are distributed among these distances:
39 6 0.02
40 36 0.11
41 60 0.18
42 90 0.27
43 54 0.16
44 55 0.16
46 31 0.09
47 5 0.01
48 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (42 bp):
TTTCCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATT
Found at i:11660 original size:43 final size:44
Alignment explanation
Indices: 11611--11899 Score: 247
Period size: 43 Copynumber: 6.7 Consensus size: 44
11601 CTTATTGTTC
* * *
11611 AAAGTTGTTGAGCCCCTGATTAGAGGAGCATTGTTTAT-TTCTT
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCATTATTTATCTTCTT
* * * *
11654 AAAGTTGTTGAGCCTCTGATTAGATGAGC--CATTTACTCTTC-A
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCATTATTTA-TCTTCTT
* * * *
11696 AAAATCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTACTCTTC-A
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCATTATTTA-TCTTCTT
*
11740 AAAGTCGTTGAGCCTCT-ATTTAGAGGAGCTTTATTTAT-TT-TT
1 AAAGTCGTTGAGCCTCTGA-TTAGAGGAGCATTATTTATCTTCTT
* * ** * *
11782 GAAAGTCATCGAGCCTCTGATTAGAGGAGTTTTATTCAT-TT-TC
1 -AAAGTCGTTGAGCCTCTGATTAGAGGAGCATTATTTATCTTCTT
* * * *
11825 AAAGTCATTGAGCCTCTAATTAGAGGAGCATTTATTTATATTTTT
1 AAAGTCGTTGAGCCTCTGATTAGAGGAGCA-TTATTTATCTTCTT
*
11870 CAAAGTCGTTGAGCCTCTGCTTAGAGGAGC
1 -AAAGTCGTTGAGCCTCTGATTAGAGGAGC
11900 CTTGATCAAA
Statistics
Matches: 207, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.02
42 54 0.26
43 73 0.35
44 49 0.24
45 1 0.00
46 26 0.13
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (44 bp):
AAAGTCGTTGAGCCTCTGATTAGAGGAGCATTATTTATCTTCTT
Found at i:11777 original size:129 final size:129
Alignment explanation
Indices: 11608--11899 Score: 308
Period size: 129 Copynumber: 2.2 Consensus size: 129
11598 TCACTTATTG
* * * ** *
11608 TTCAAAGTTGTTGAGCCCCTGATTAGAGGAGCATTGTTTATTTCTT-AAAGTTGTTGAGCCTCTG
1 TTCAAAGTCGTTGAGCCTCT-ATTAGAGGAGCATTATTTATTT-TTGAAAGTCATCGAGCCTCTG
* * **
11672 ATTAGATGAGCCATTTA-C-TCTTCAAAAATCGTTGAGCCTCTGTTTAGAGGAGC-TTTA-TT-T
64 ATTAGAGGAG--ATTTATCATCTTC-AAAATCATTGAGCCTCTAATTAGAGGAGCATTTATTTAT
11732 ACTC
126 ACTC
*
11736 TTCAAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTATTTATTTTTGAAAGTCATCGAGCCTCTG
1 TTC-AAAGTCGTTGAGCCTCTA-TTAGAGGAGCATTATTTATTTTTGAAAGTCATCGAGCCTCTG
* * * *
11801 ATTAGAGGAGTTTTATTCATTTTCAAAGTCATTGAGCCTCTAATTAGAGGAGCATTTATTTATAT
64 ATTAGAGGAGATTTA-TCATCTTCAAAATCATTGAGCCTCTAATTAGAGGAGCATTTATTTATAC
*
11866 TT
128 TC
*
11868 TTCAAAGTCGTTGAGCCTCTGCTTAGAGGAGC
1 TTCAAAGTCGTTGAGCCTCT-ATTAGAGGAGC
11900 CTTGATCAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
127 4 0.03
128 6 0.04
129 84 0.61
130 8 0.06
131 29 0.21
132 6 0.04
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (129 bp):
TTCAAAGTCGTTGAGCCTCTATTAGAGGAGCATTATTTATTTTTGAAAGTCATCGAGCCTCTGAT
TAGAGGAGATTTATCATCTTCAAAATCATTGAGCCTCTAATTAGAGGAGCATTTATTTATACTC
Found at i:11850 original size:85 final size:90
Alignment explanation
Indices: 11705--11899 Score: 265
Period size: 88 Copynumber: 2.2 Consensus size: 90
11695 AAAAATCGTT
* * * *
11705 GAGCCTCTGTTTAGAGGAGCTTTATTTACTCTTCAAAAGTCGTTGAGCCTCTATTTAGAGGAGC-
1 GAGCCTCTGATTAGAGGAGCTTTATTCACTCTTCAAAAGTCATTGAGCCTCTAATTAGAGGAGCA
*
11769 TTTA-TT-TATTTTTGAAAGTCATC
66 TTTATTTATATTTTTCAAAGTCATC
* *
11792 GAGCCTCTGATTAGAGGAGTTTTATTCA-TTTTC-AAAGTCATTGAGCCTCTAATTAGAGGAGCA
1 GAGCCTCTGATTAGAGGAGCTTTATTCACTCTTCAAAAGTCATTGAGCCTCTAATTAGAGGAGCA
* *
11855 TTTATTTATATTTTTCAAAGTCGTT
66 TTTATTTATATTTTTCAAAGTCATC
*
11880 GAGCCTCTGCTTAGAGGAGC
1 GAGCCTCTGATTAGAGGAGC
11900 CTTGATCAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
85 27 0.29
86 8 0.09
87 27 0.29
88 32 0.34
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (90 bp):
GAGCCTCTGATTAGAGGAGCTTTATTCACTCTTCAAAAGTCATTGAGCCTCTAATTAGAGGAGCA
TTTATTTATATTTTTCAAAGTCATC
Found at i:12164 original size:25 final size:26
Alignment explanation
Indices: 12095--12221 Score: 77
Period size: 26 Copynumber: 4.8 Consensus size: 26
12085 CCTTTTTTTC
*
12095 TTATTATT-TATTTTGTATTTTATATT
1 TTATTATTATATTAT-TATTTTATATT
* *
12121 TTATTATTTTATTATTATTTTGTATT
1 TTATTATTATATTATTATTTTATATT
* *
12147 TT-TTATTATATATATATTTCTTTATATC
1 TTATTATTATAT-TAT-TAT-TTTATATT
*
12175 TTATGTATT-TGTTATTTACTATTTAT-TT
1 TTAT-TATTATATTA-TTA-T-TTTATATT
12203 TT-TTATATATATT-TTATTT
1 TTATTAT-TATATTATTATTT
12222 ATCTACTTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
24 2 0.03
25 9 0.11
26 29 0.36
27 9 0.11
28 17 0.21
29 10 0.12
30 4 0.05
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (26 bp):
TTATTATTATATTATTATTTTATATT
Found at i:12164 original size:28 final size:26
Alignment explanation
Indices: 12095--12184 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 26
12085 CCTTTTTTTC
*
12095 TTATTA-TTTATTTTGTATTTTATATT
1 TTATTATTTTATTAT-TATTTTATATT
*
12121 TTATTATTTTATTATTATTTTGTATT
1 TTATTATTTTATTATTATTTTATATT
*
12147 TT-TTATTATATATATATT-TCTTTATATC
1 TTATTATT-T-TAT-TATTAT-TTTATATT
12175 TTATGTATTT
1 TTAT-TATTT
12185 GTTATTTACT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
25 5 0.09
26 19 0.36
27 11 0.21
28 12 0.23
29 2 0.04
30 4 0.08
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (26 bp):
TTATTATTTTATTATTATTTTATATT
Found at i:12218 original size:19 final size:18
Alignment explanation
Indices: 12087--12240 Score: 75
Period size: 19 Copynumber: 8.1 Consensus size: 18
12077 TAGGTCCACC
*
12087 TTTTTTTCTTAT-TATTTA
1 TTTTTTTATTATAT-TTTA
12105 TTTTGTATT-TTATATTTTA
1 TTTT-T-TTATTATATTTTA
* *
12124 TTATTTTATTATTATTTTG
1 TTTTTTTATTA-TATTTTA
*
12143 TATTTTTTATTATATATATA
1 T-TTTTTTATTATAT-TTTA
* *
12163 TTTCTTTA-TATCTTATGTA
1 TTTTTTTATTATATT-T-TA
*
12182 -TTTGTTATT-TACTATTTA
1 TTTTTTTATTATA-T-TTTA
12200 TTTTTTTATATATATTTTA
1 TTTTTTTAT-TATATTTTA
* *
12219 TTTATCTACTTATATATTTA
1 TTTTTTTA-TTATAT-TTTA
12239 TT
1 TT
12241 ATCATTTATC
Statistics
Matches: 105, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.03
18 20 0.19
19 55 0.52
20 25 0.24
21 2 0.02
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTTTATTATATTTTA
Found at i:12221 original size:37 final size:36
Alignment explanation
Indices: 12087--12240 Score: 107
Period size: 37 Copynumber: 4.1 Consensus size: 36
12077 TAGGTCCACC
* *
12087 TTTTTTTCT-TATTATTTATTT-TGTATTTTATATTTTA
1 TTTTTTTATATATT-TTTATTTGT-TATTATATA-TTTA
* * *
12124 TTATTTTATTATTATTTTGTATTTTTTATTATATATATA
1 TTTTTTTA-TA-TATTTT-TATTTGTTATTATATATTTA
* * *
12163 TTTCTTTATATCTTATGTATTTGTTATT-TACTATTTA
1 TTTTTTTATATATT-TTTATTTGTTATTATA-TATTTA
*
12200 TTTTTTTATATATATTTTATTTATCTACTTATATATTTA
1 TTTTTTTATATAT-TTTTATTTGT-TA-TTATATATTTA
12239 TT
1 TT
12241 ATCATTTATC
Statistics
Matches: 92, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
36 2 0.02
37 42 0.46
38 7 0.08
39 21 0.23
40 19 0.21
41 1 0.01
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (36 bp):
TTTTTTTATATATTTTTATTTGTTATTATATATTTA
Found at i:12242 original size:23 final size:23
Alignment explanation
Indices: 12187--12242 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
12177 ATGTATTTGT
* * **
12187 TATTTACTATTTATTTTTTTATA
1 TATTTATTATTTATCTACTTATA
12210 TATATT-TTATTTATCTACTTATA
1 TAT-TTATTATTTATCTACTTATA
12233 TATTTATTAT
1 TATTTATTAT
12243 CATTTATCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTATTATTTATCTACTTATA
Found at i:13257 original size:16 final size:17
Alignment explanation
Indices: 13238--13284 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
13228 AATTGTTTAA
13238 TATTTTTATTTTTA-TT
1 TATTTTTATTTTTATTT
*
13254 TATTTTCATTTTTATTT
1 TATTTTTATTTTTATTT
13271 TATTATTTTATTTT
1 TA-T-TTTTATTTT
13285 CTTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 13 0.50
17 4 0.15
18 1 0.04
19 8 0.31
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TATTTTTATTTTTATTT
Found at i:13446 original size:58 final size:58
Alignment explanation
Indices: 13303--13517 Score: 310
Period size: 58 Copynumber: 3.7 Consensus size: 58
13293 AAAATTCAAA
13303 AAAAAATTATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
1 AAAAAA-TATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTCGAAATT-AAAGTTTTC
* *
13363 AAAAAATATTTTTAGG-GAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAGAGTTTTC
1 AAAAAATATTTTT-GGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
*
13421 AAAAAATATTTTTGGAAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAG-TTTC
1 AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
* * *
13478 AAAAGAATATTTTTAGAGAAACGTTAAAAGTATCAATTTT
1 AAAA-AATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT
13518 TCCTGCACAA
Statistics
Matches: 142, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
57 10 0.07
58 86 0.61
59 39 0.27
60 6 0.04
61 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
Found at i:13474 original size:31 final size:31
Alignment explanation
Indices: 13381--13475 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
13371 TTTTTAGGGA
*
13381 AAAGTTGAAAGTATCAATTTTCCTCAAAATT
1 AAAGTTGAAAGTATCAATTTTCCTCGAAATT
* * ** *
13412 AGAGTTTTCAAAAAAT--ATTTT--TGGAAA--
1 AAAG--TTGAAAGTATCAATTTTCCTCGAAATT
13439 AAAGTTGAAAGTATCAATTTTCCTCGAAATT
1 AAAGTTGAAAGTATCAATTTTCCTCGAAATT
13470 AAAGTT
1 AAAGTT
13476 TCAAAAGAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 16
0.62 0.15 0.22
Matches are distributed among these distances:
25 7 0.16
27 8 0.18
29 9 0.20
31 14 0.31
33 7 0.16
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (31 bp):
AAAGTTGAAAGTATCAATTTTCCTCGAAATT
Found at i:13521 original size:117 final size:118
Alignment explanation
Indices: 13303--13517 Score: 348
Period size: 117 Copynumber: 1.8 Consensus size: 118
13293 AAAATTCAAA
*
13303 AAAAAATTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTCAAAAA
1 AAAAAATTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTCAAAAA
* *
13368 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAGAGTTTTC
66 ATATTTTTAGAGAAAAGTTAAAAGTATCAATTTTCCTCAAAATTAGAGTTTTC
13421 AAAAAA-TATTTTTG-GAAAAAAGTTGAAAGTATCAATTTTCCTCGAAATT-AAAG-TTTCAAAA
1 AAAAAATTATTTTTGAG-AAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTCAAAA
*
13482 GAATATTTTTAGAGAAACGTTAAAAGTATCAATTTT
65 -AATATTTTTAGAGAAAAGTTAAAAGTATCAATTTT
13518 TCCTGCACAA
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
115 8 0.09
116 37 0.41
117 40 0.44
118 6 0.07
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (118 bp):
AAAAAATTATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTCAAAAA
ATATTTTTAGAGAAAAGTTAAAAGTATCAATTTTCCTCAAAATTAGAGTTTTC
Found at i:16157 original size:115 final size:115
Alignment explanation
Indices: 15950--16173 Score: 349
Period size: 115 Copynumber: 1.9 Consensus size: 115
15940 GTTTTCTATA
** **
15950 AAACGTCGCTATATTAACGGTATTTGTATCTGAAAAATACCATTATTTGATTAGCGTTTGTATCT
1 AAACGTCGCTATATTAACGACATTTGTATCTGAAAAATACCATTATTTGAGCAGCGTTTGTATCT
16015 TTGAAATGTCACTAATTTAGTGACATTTTTATCAAAAAAATGCTACTAAT
66 TTGAAATGTCACTAATTTAGTGACATTTTTATCAAAAAAATGCTACTAAT
* * * * * *
16065 AAACGTCGCTATATTAATGACATTTGTATTTGAAAAATATCGTTATTTTAGCAGTGTTTGTATCT
1 AAACGTCGCTATATTAACGACATTTGTATCTGAAAAATACCATTATTTGAGCAGCGTTTGTATCT
*
16130 TTGAAATGTCACTAATTTAGTGGCATTTTTATCAAAAAAATGCT
66 TTGAAATGTCACTAATTTAGTGACATTTTTATCAAAAAAATGCT
16174 GCTGATACGA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 98 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (115 bp):
AAACGTCGCTATATTAACGACATTTGTATCTGAAAAATACCATTATTTGAGCAGCGTTTGTATCT
TTGAAATGTCACTAATTTAGTGACATTTTTATCAAAAAAATGCTACTAAT
Found at i:23656 original size:237 final size:239
Alignment explanation
Indices: 23265--23771 Score: 572
Period size: 238 Copynumber: 2.1 Consensus size: 239
23255 TGAAGTCATT
* * *
23265 TTTTTTGCATTATACTCCTTCAATAATTTGTTTATAGAATTATTAAAGGTGTTTTTTGAGAAAAA
1 TTTTTTGCATTATACGCCTTCAATAATTT-TTCATAGAATTATTAAAGGTATTTTTTGAGAAAAA
** * * * ** * * * *
23330 AAAGCCTTCAATAATTTTCTCTTGAAAACTATTTGTTATTATTAAAGGTGTTTTTTAGTAGAAAA
65 AAAGCCTTCAATAATTACCTATTAAAAACTATTTGTGATTATTAAAGGCATCTTGTAGCAAAAAA
* * * *
23395 CGCCTTCAATATTATATTACTAAAATTTTAAAGGG-TTATTAAAGACACTTATTCGAGAAAGACA
130 CGCCTTAAATATTACATAACTAAAATTTTAAAGGGATTATTAAAGACACTTATTCGAGAAAAACA
* *
23459 CCTTTACTAATTCGTTATAATTTATGAAGGAATTAATTGAAGCCA
195 CCTTTACTAATTCGATATAATTTATGAAAGAATTAATTGAAGCCA
*
23504 TTTTTTGTATTATACGCCTTCAATAATTTTTGCATAG-ATTATTAAAGGTATTTTTTGA-AAAAA
1 TTTTTTGCATTATACGCCTTCAATAATTTTT-CATAGAATTATTAAAGGTATTTTTTGAGAAAAA
* * * *
23567 CACGCCTTCAATAATTACCTATTAAAAATTGTTTAG-GATTATTAAAGGCATCTTGTAGCAAAAA
65 AAAGCCTTCAATAATTACCTATTAAAAACTATTT-GTGATTATTAAAGGCATCTTGTAGCAAAAA
* * * **** ** *
23631 ATGCCTTAAATATTCCATAACTAAAATTTTAAAGGGATTATTGAAGGTGTTTATTTTAGAAAAAT
129 ACGCCTTAAATATTACATAACTAAAATTTTAAAGGGATTATTAAAGACACTTATTCGAGAAAAAC
* * * * * ***
23696 TCCTTTACTAATTTGATCTAATTTTTGAAAGAATTTATTGAAGGTG
194 ACCTTTACTAATTCGATATAATTTATGAAAGAATTAATTGAAGCCA
23742 TTTTTTGCATTATACGCCTTCAATAATTTT
1 TTTTTTGCATTATACGCCTTCAATAATTTT
23772 CTTTCAAAAA
Statistics
Matches: 221, Mismatches: 44, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
237 83 0.38
238 107 0.48
239 31 0.14
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (239 bp):
TTTTTTGCATTATACGCCTTCAATAATTTTTCATAGAATTATTAAAGGTATTTTTTGAGAAAAAA
AAGCCTTCAATAATTACCTATTAAAAACTATTTGTGATTATTAAAGGCATCTTGTAGCAAAAAAC
GCCTTAAATATTACATAACTAAAATTTTAAAGGGATTATTAAAGACACTTATTCGAGAAAAACAC
CTTTACTAATTCGATATAATTTATGAAAGAATTAATTGAAGCCA
Found at i:23843 original size:187 final size:187
Alignment explanation
Indices: 23568--23951 Score: 504
Period size: 187 Copynumber: 2.1 Consensus size: 187
23558 TTGAAAAAAC
* * *
23568 ACGCCTTCAATAATTACCTATTAAAAATTGTTTAGGATTATTAAAGGCATCTTGTAGCAAAAAAT
1 ACGCCTTCAATAATTACCTATTAAAAATTATTTAGGATTATTAAAGGCATCTTCTAGCAAAAAAC
* * * *
23633 GCCTTAAATATTCCATAACTAAAATTTTAAAGGGATTATTGAAGGTGTTTATTTTAGAAAAATTC
66 ACCATAAATATTCCATAACTAAAATTTTAAAGGGATTATTGAAGGTGTTTATTCTAGAAAAATGC
* * *
23698 CTTTACTAATTTGATCTAATTTTTGAAAGAATTTATTGAAGGTGTTTTTTGCATTAT
131 CTTCACTAATTCGATCTAATTTTTGAAAGAATTTAGTGAAGGTGTTTTTTGCATTAT
** * * *
23755 ACGCCTTCAATAATTTTCT-TTCAAAAATTATTT-GAGATTATTAAAGGTATCTTCTAGTAGAAA
1 ACGCCTTCAATAATTACCTATT-AAAAATTATTTAG-GATTATTAAAGGCATCTTCTAGCAAAAA
* * * *
23818 ACACCATCAATATTCCACT-ACTAAAATTTTAAGGGGGTTATTGAAGGTGTTTATTCTATAAAAA
64 ACACCATAAATATTCCA-TAACTAAAATTTTAAAGGGATTATTGAAGGTGTTTATTCTAGAAAAA
* * * *
23882 TGCCTTCACTAATTCGTTTTAGTTTTTGAAAGAATTTGGTGAAGGTGTTTTTTGCATTAT
128 TGCCTTCACTAATTCGATCTAATTTTTGAAAGAATTTAGTGAAGGTGTTTTTTGCATTAT
*
23942 ATGCCTTCAA
1 ACGCCTTCAA
23952 CAACTTTTGT
Statistics
Matches: 170, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
186 3 0.02
187 166 0.98
188 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (187 bp):
ACGCCTTCAATAATTACCTATTAAAAATTATTTAGGATTATTAAAGGCATCTTCTAGCAAAAAAC
ACCATAAATATTCCATAACTAAAATTTTAAAGGGATTATTGAAGGTGTTTATTCTAGAAAAATGC
CTTCACTAATTCGATCTAATTTTTGAAAGAATTTAGTGAAGGTGTTTTTTGCATTAT
Found at i:24111 original size:426 final size:423
Alignment explanation
Indices: 23333--24198 Score: 949
Period size: 426 Copynumber: 2.0 Consensus size: 423
23323 AGAAAAAAAA
* ** * * * *
23333 GCCTTCAATAATTTTCTCTTGAAAACTATTTGTTATTATTAAAGGTGTTTTTTAGTAGAAAACGC
1 GCCTTCAATAATTTTCTCTTAAAAACTATTTGAGATTATTAAAGGTATCTTCTAGTAGAAAACAC
* * * *
23398 CTTCAATATTATATTACTAAAATTTTAAAGGGTTATTAAAGACACTTATTCGAGAAAGACACCTT
66 CATCAATATTACACTACTAAAATTTTAAAGGGTTATTAAAGACACTTATTCGAGAAAAACACCTT
* * * * *
23463 TACTAATTCGTTATAATTTATGAAGGAATTAATTGAAGCCATTTTTTGTATTATACGCCTTCAAT
131 CACTAATTCGTTATAATTTATGAAAGAATTAAGTGAAGCCATTTTTTGCATTATACGCCTTCAAC
* * *
23528 AATTTTTGCATAGATTATTAAAGGTATTTTTTGAAAAAACACGCCTTCAATAATTACCTATTAAA
196 AACTTTTGCACAGATTATTAAAGGTATTTTTTGAAAAAAAACGCCTTCAATAATTA-CTATTAAA
* *
23593 AATTGTTTAGGATTATTAAAGGCATCTTGTAGCAAAAAATGCCTTAAATATTCCATAACTAAAAT
260 AATTATTTAGGATTATTAAAGGCATCTTCTAGCAAAAAATGCCTTAAATATTCCATAACTAAAAT
* * ** ** * * *
23658 TTTAAAGGGATTATTGAAGGTGTTTATTTTAGAAAAATTCCTTTACTAATTTGA-TCTAATTTTT
325 TTTAAAGGGATTATTGAAAGCGTTTATTCCAGAAAAACGCCATCACTAA-TTCATTCTAATTTTT
*
23722 GAA-AGAATTTATTGAAGG-TGTTTTTTGCATTATAC
389 GAAGA-AAATTATTGAAGGAT-TTTTTTGCATTATAC
*
23757 GCCTTCAATAATTTTCT-TTCAAAAATTATTTGAGATTATTAAAGGTATCTTCTAGTAGAAAACA
1 GCCTTCAATAATTTTCTCTT-AAAAACTATTTGAGATTATTAAAGGTATCTTCTAGTAGAAAACA
* * * **** * * **
23821 CCATCAATATTCCACTACTAAAATTTTAAGGGGGTTATTGAAGGTGTTTATTCTATAAAAATGCC
65 CCATCAATATTACACTACTAAAATTTTAA-AGGGTTATTAAAGACACTTATTCGAGAAAAACACC
* * * ** *** *
23886 TTCACTAATTCGTTTTAGTTTTTGAAAGAATTTGGTGAAGGTGTTTTTTGCATTATATGCCTTCA
129 TTCACTAATTCGTTATAATTTATGAAAGAATTAAGTGAAGCCATTTTTTGCATTATACGCCTTCA
* * * *
23951 ACAACTTTTGTACAGAATTATTGAAA-GTATTTTTT-AAAAATAAATGCCTTCAATAATT-TTTT
194 ACAACTTTTGCACAG-ATTATT-AAAGGTATTTTTTGAAAAA-AAACGCCTTCAATAATTACTAT
* * *
24013 TAAAAAAATTATTT-GAGATTATTAAAGGCATCTTCTAGTAAAAAATGCCTTCAATATTTCACT-
256 T--AAAAATTATTTAG-GATTATTAAAGGCATCTTCTAGCAAAAAATGCCTTAAATATTCCA-TA
* * * * *
24076 ATTAAAATTTTAAGGGGGTTGTTGAAAGCGTTTATTCCATAAAAACGCCATCACTAATTCATTCT
317 ACTAAAATTTTAAAGGGATTATTGAAAGCGTTTATTCCAGAAAAACGCCATCACTAATTCATTCT
*
24141 AATTTTTGAAGAAAATTATTGAAGGCATTTTTTTGCATTATAT
382 AATTTTTGAAGAAAATTATTGAAGG-ATTTTTTTGCATTATAC
*
24184 GCCTTTAATAATTTT
1 GCCTTCAATAATTTT
24199 TGTTCATATG
Statistics
Matches: 363, Mismatches: 66, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
423 2 0.01
424 81 0.22
425 96 0.26
426 150 0.41
427 33 0.09
428 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (423 bp):
GCCTTCAATAATTTTCTCTTAAAAACTATTTGAGATTATTAAAGGTATCTTCTAGTAGAAAACAC
CATCAATATTACACTACTAAAATTTTAAAGGGTTATTAAAGACACTTATTCGAGAAAAACACCTT
CACTAATTCGTTATAATTTATGAAAGAATTAAGTGAAGCCATTTTTTGCATTATACGCCTTCAAC
AACTTTTGCACAGATTATTAAAGGTATTTTTTGAAAAAAAACGCCTTCAATAATTACTATTAAAA
ATTATTTAGGATTATTAAAGGCATCTTCTAGCAAAAAATGCCTTAAATATTCCATAACTAAAATT
TTAAAGGGATTATTGAAAGCGTTTATTCCAGAAAAACGCCATCACTAATTCATTCTAATTTTTGA
AGAAAATTATTGAAGGATTTTTTTGCATTATAC
Found at i:24308 original size:241 final size:237
Alignment explanation
Indices: 23755--24309 Score: 695
Period size: 239 Copynumber: 2.3 Consensus size: 237
23745 TTTGCATTAT
* * *
23755 ACGCCTTCAATAATTTTCTTTCAAAAATTATTTGAGATTATTAAAGGTATCTTCTAGTAGAAAA-
1 ACGCCTTCAATAA-TTTCTTTTAAAAATTATTTGAGATTATTAAAGGCATCTTCTAGTAAAAAAT
* * * * * *
23819 CACCATCAATATTCCACTACTAAAATTTTAAGGGGGTTATTGAAGGTGTTTATTCTATAAAAATG
65 GA-CTTCAATATTCCACTACTAAAATTTTAAGGGGGTTATTGAAAGCGTTTATTCCATAAAAACG
* * * * *
23884 CCTTCACTAATTCGTTTTAGTTTTTGAAAGAATTTGGTGAAGGTGTTTTTTGCATTATATGCCTT
129 CCATCACTAATTCATTCTAATTTTTGAAAAAATTT-GTGAAGGTGTTTTTTGCATTATATGCCTT
*
23949 CAACAACTTTTGTACAGAATTATTGAAAGTATTTTTTAAAAATAA
193 CAACAACTTTTGTACAGAATTATTGAAAGTATTTTTAAAAAATAA
*
23994 ATGCCTTCAATAATTT-TTTTAAAAAAATTATTTGAGATTATTAAAGGCATCTTCTAGTAAAAAA
1 ACGCCTTCAATAATTTCTTTT--AAAAATTATTTGAGATTATTAAAGGCATCTTCTAGTAAAAAA
* * * *
24058 TGCCTTCAATATTTCACTATTAAAATTTTAAGGGGGTTGTTGAAAGCGTTTATTCCATAAAAACG
64 TGACTTCAATATTCCACTACTAAAATTTTAAGGGGGTTATTGAAAGCGTTTATTCCATAAAAACG
24123 CCATCACTAATTCATTCTAATTTTTGAAGAAAATTAT-TGAAGGCAT-TTTTTTGCATTATATGC
129 CCATCACTAATTCATTCTAATTTTTGAA-AAAATT-TGTGAAGG--TGTTTTTTGCATTATATGC
* * * * * * *
24186 CTTTAATAATTTTTGTTCATATGTTATTGAAGGTATTTTTAAAAAATAA
190 CTTCAACAACTTTTGTACAGA-ATTATTGAAAGTATTTTTAAAAAATAA
* * * * *
24235 ACGCTTTCAATAATTTCCTTTTAAAAATTGTTTGAGATTATTAAAGGCGTCTTTTAGTATAAAAT
1 ACGCCTTCAATAATTT-CTTTTAAAAATTATTTGAGATTATTAAAGGCATCTTCTAGTAAAAAAT
24300 GACTTCAATA
65 GACTTCAATA
24310 ATTTTAAGGG
Statistics
Matches: 272, Mismatches: 34, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
237 3 0.01
238 3 0.01
239 136 0.50
240 38 0.14
241 88 0.32
243 4 0.01
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (237 bp):
ACGCCTTCAATAATTTCTTTTAAAAATTATTTGAGATTATTAAAGGCATCTTCTAGTAAAAAATG
ACTTCAATATTCCACTACTAAAATTTTAAGGGGGTTATTGAAAGCGTTTATTCCATAAAAACGCC
ATCACTAATTCATTCTAATTTTTGAAAAAATTTGTGAAGGTGTTTTTTGCATTATATGCCTTCAA
CAACTTTTGTACAGAATTATTGAAAGTATTTTTAAAAAATAA
Found at i:25096 original size:28 final size:28
Alignment explanation
Indices: 25038--25100 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
25028 GTGGTTTGTC
* * *
25038 GAATGGTATTGTGTGATATTATTTTGAT
1 GAATGGTATTGTATGATATTAGTATGAT
* *
25066 GAATGGTATTGTATGATATTGGTATGCT
1 GAATGGTATTGTATGATATTAGTATGAT
25094 GAATGGT
1 GAATGGT
25101 TTGCTAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (28 bp):
GAATGGTATTGTATGATATTAGTATGAT
Found at i:25105 original size:12 final size:12
Alignment explanation
Indices: 25085--25124 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
25075 TGTATGATAT
*
25085 TGGTATGCTGAA
1 TGGTTTGCTGAA
*
25097 TGGTTTGCTAAA
1 TGGTTTGCTGAA
25109 TGGTTTGCTGAA
1 TGGTTTGCTGAA
25121 TGGT
1 TGGT
25125 GTTTTTGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (12 bp):
TGGTTTGCTGAA
Found at i:28374 original size:35 final size:36
Alignment explanation
Indices: 28310--28380 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
28300 AAACCAAATG
* * *
28310 TTTTCTGGGCATAAACTTATAATTGACTTCAAATAT
1 TTTTCTGGGCATAAACTTACAACTAACTTCAAATAT
*
28346 TTTTC-GGGCATAAACTTACAACTAACTTCACATAT
1 TTTTCTGGGCATAAACTTACAACTAACTTCAAATAT
28381 ATAATTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 26 0.84
36 5 0.16
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (36 bp):
TTTTCTGGGCATAAACTTACAACTAACTTCAAATAT
Found at i:28707 original size:127 final size:126
Alignment explanation
Indices: 28493--28724 Score: 290
Period size: 127 Copynumber: 1.8 Consensus size: 126
28483 CAAATCCGCT
* * * * *
28493 TTCAATAATCCCACCTAAAAAGTTATTGTGTAGATTATTAAAGGCATTTTGGGCCAAAAATGCCT
1 TTCAATAATCCCACCTAAAAAGTTATTGTGTAGATTATTAAAGGCACTTTCGACCAAAAACGCAT
* * * *
28558 TTAAGAATCTATTCTAACTTTTTTGTATGGATTATTTAAGGCGTTTTTAAAAAAAAAATGCC
66 TCAAGAATCTATTCCAACTTTTTTCTATGGACTA-TTAAGGCGTTTTTAAAAAAAAAATGCC
* *
28620 TTCAATAATCCCACCTAAAAA-TATATTGAT-TGGATTATTGAAGGCACTTTCGACCAAAAACGC
1 TTCAATAATCCCACCTAAAAAGT-TATTG-TGTAGATTATTAAAGGCACTTTCGACCAAAAACGC
* *
28683 ATTCAAGTATCTGTTCCATA-TTTTTTCTATGGACTATTAAGG
64 ATTCAAGAATCTATTCCA-ACTTTTTTCTATGGACTATTAAGG
28725 GCATTTTCCT
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
126 7 0.08
127 80 0.90
128 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (126 bp):
TTCAATAATCCCACCTAAAAAGTTATTGTGTAGATTATTAAAGGCACTTTCGACCAAAAACGCAT
TCAAGAATCTATTCCAACTTTTTTCTATGGACTATTAAGGCGTTTTTAAAAAAAAAATGCC
Found at i:30101 original size:22 final size:22
Alignment explanation
Indices: 30074--30115 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
30064 GTATATTAAT
*
30074 ATTTGTATCTCTAGAATTAAAA
1 ATTTGTATCCCTAGAATTAAAA
30096 ATTTGTATCCCTAGAATTAA
1 ATTTGTATCCCTAGAATTAA
30116 GAATAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
ATTTGTATCCCTAGAATTAAAA
Found at i:34138 original size:22 final size:22
Alignment explanation
Indices: 34113--34155 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
34103 TATATATTTG
*
34113 TATTTGTATCTCTAGAATTAAA
1 TATTTGTATCCCTAGAATTAAA
*
34135 TATTTGTTTCCCTAGAATTAA
1 TATTTGTATCCCTAGAATTAA
34156 GGACAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAA
Found at i:38590 original size:21 final size:20
Alignment explanation
Indices: 38539--38602 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
38529 TAAGTGTATT
38539 TATTTTT-TTAATATAAATTA
1 TATTTTTATTAATATAAA-TA
** *
38559 TAACTTAATTATATATAAATA
1 TATTTTTATTA-ATATAAATA
*
38580 TATTTTTATTAA-ATAAAAA
1 TATTTTTATTAATATAAATA
38599 TATT
1 TATT
38603 AAATAATAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.29
20 5 0.14
21 13 0.37
22 7 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTTTATTAATATAAATA
Found at i:38601 original size:29 final size:30
Alignment explanation
Indices: 38569--38636 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
38559 TAACTTAATT
**
38569 ATATATAAAT-ATATTTTTATTAA-ATAAA
1 ATATATAAATAATAACTTTATTAATATAAA
*
38597 A-ATATTAAATAATAACTTTATTAATATAAT
1 ATATA-TAAATAATAACTTTATTAATATAAA
38627 ATATATAAAT
1 ATATATAAAT
38637 TAGTTAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 3 0.09
28 6 0.18
29 11 0.33
30 10 0.30
31 3 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATATAAATAATAACTTTATTAATATAAA
Found at i:38655 original size:54 final size:50
Alignment explanation
Indices: 38548--38647 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 50
38538 TTATTTTTTT
* **
38548 AATA-TAAATTATAACTTAATTATATATAAATATATTTTTATTAAATAAA
1 AATATTAAATAATAACTTAATTATATATAAATATATAATTATTAAATAAA
*
38597 AATATTAAATAATAACTTTATTA-ATATAATATATATAAATTAGTTAAATAA
1 AATATTAAATAATAACTTAATTATATATAA-ATATAT-AATTA-TTAAATAA
38648 TAAAATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
49 10 0.23
50 22 0.51
51 3 0.07
52 8 0.19
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (50 bp):
AATATTAAATAATAACTTAATTATATATAAATATATAATTATTAAATAAA
Found at i:39556 original size:3 final size:3
Alignment explanation
Indices: 39543--39575 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
39533 ATCTCTACAA
*
39543 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39576 CTATACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40533 original size:18 final size:20
Alignment explanation
Indices: 40489--40554 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 20
40479 TCAAACAAAA
* *
40489 ATTAATTTATATTAAAAGCTT
1 ATTAATATAAATTAAAAG-TT
40510 ATTTATATATAAATTAAAAGTT
1 A-TTA-ATATAAATTAAAAGTT
40532 ATTTAGATATAAATTAAAAGTT
1 A-TTA-ATATAAATTAAAAGTT
40554 A
1 A
40555 AGCACTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.03
22 27 0.68
23 12 0.30
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (20 bp):
ATTAATATAAATTAAAAGTT
Found at i:40536 original size:22 final size:22
Alignment explanation
Indices: 40499--40554 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
40489 ATTAATTTAT
*
40499 ATTAAAAGCTTATTTATATATAA
1 ATTAAAAG-TTATTTAGATATAA
40522 ATTAAAAGTTATTTAGATATAA
1 ATTAAAAGTTATTTAGATATAA
40544 ATTAAAAGTTA
1 ATTAAAAGTTA
40555 AGCACTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (22 bp):
ATTAAAAGTTATTTAGATATAA
Found at i:40564 original size:30 final size:30
Alignment explanation
Indices: 40530--40597 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
40520 AAATTAAAAG
* *
40530 TTATTTAGATATAAATTAAAAGTT-AAGC-AC
1 TTATTTAAATACAAATT-AAAGTTCAA-CAAC
*
40560 TTATTTAAATGCAAATTAAAGTTCAACAAC
1 TTATTTAAATACAAATTAAAGTTCAACAAC
40590 TTATTTAA
1 TTATTTAA
40598 GTATAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.21
30 26 0.79
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (30 bp):
TTATTTAAATACAAATTAAAGTTCAACAAC
Found at i:43179 original size:15 final size:15
Alignment explanation
Indices: 43133--43179 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
43123 GTACCAATGC
43133 AATTTTATTGAATTTT
1 AATTTTATT-AATTTT
*
43149 -ATTATTA-TACTTTT
1 AATT-TTATTAATTTT
43163 AATTTTATTAATTTT
1 AATTTTATTAATTTT
43178 AA
1 AA
43180 ATAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 8 0.31
15 15 0.58
16 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
AATTTTATTAATTTT
Found at i:46682 original size:48 final size:48
Alignment explanation
Indices: 46630--46804 Score: 124
Period size: 47 Copynumber: 3.7 Consensus size: 48
46620 CACCTTAACC
* *
46630 AAAGAGCTTAACTCAATAAATTACCTTCGTAAAAGCCAAGTTTAACAA
1 AAAGAGCTTAACTCAATAAATTACCTTCATAAAAGCCAAGCTTAACAA
* * * * * * * *
46678 AAAGAGTTTATCTTAACAAATTATCTTCATAAAGGCCTAGCTTGACAA
1 AAAGAGCTTAACTCAATAAATTACCTTCATAAAAGCCAAGCTTAACAA
* * * * ** *
46726 AAA-AGCTCAACTCAATAAAGTA-CTATAATAAATGCTTAGCTCAA-AA
1 AAAGAGCTTAACTCAATAAATTACCT-TCATAAAAGCCAAGCTTAACAA
* * *
46772 AAAGAG-TTCATCTCGATAAATTATCTTCATAAA
1 AAAGAGCTT-AACTCAATAAATTACCTTCATAAA
46805 GGGCTTAGCT
Statistics
Matches: 97, Mismatches: 26, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
46 8 0.08
47 46 0.47
48 43 0.44
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (48 bp):
AAAGAGCTTAACTCAATAAATTACCTTCATAAAAGCCAAGCTTAACAA
Found at i:46804 original size:47 final size:47
Alignment explanation
Indices: 46676--46815 Score: 131
Period size: 47 Copynumber: 3.0 Consensus size: 47
46666 CAAGTTTAAC
* * * * * *
46676 AAAAAGAGTTTATCTTAACAAATTATCTTCATAAAGGCCTAGCTTGAC
1 AAAAAGAGTTCATCTCAATAAATTATCTTCATAAAGGCTTAGC-TCAA
* * * * *
46724 AAAAA-AGCTCAACTCAATAAAGTA-CTATAATAAATGCTTAGCTCAA
1 AAAAAGAGTTCATCTCAATAAATTATCT-TCATAAAGGCTTAGCTCAA
*
46770 AAAAAGAGTTCATCTCGATAAATTATCTTCATAAAGGGCTTAGCTC
1 AAAAAGAGTTCATCTCAATAAATTATCTTCATAAA-GGCTTAGCTC
46816 TACTATCTTA
Statistics
Matches: 71, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
46 9 0.13
47 46 0.65
48 16 0.23
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (47 bp):
AAAAAGAGTTCATCTCAATAAATTATCTTCATAAAGGCTTAGCTCAA
Found at i:47536 original size:23 final size:24
Alignment explanation
Indices: 47493--47539 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
47483 TTTTAAAAGA
*
47493 GCTCATCTTTTTAAAATTTTCTTT
1 GCTCATCTTTGTAAAATTTTCTTT
47517 GCTCATCTTTGT-AAATTTTCTTT
1 GCTCATCTTTGTAAAATTTTCTTT
47540 TAATAAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.19, C:0.17, G:0.06, T:0.57
Consensus pattern (24 bp):
GCTCATCTTTGTAAAATTTTCTTT
Found at i:47852 original size:31 final size:31
Alignment explanation
Indices: 47834--47894 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
47824 ATAGATCCAT
*
47834 TTGGCATAAATCCATCTCGATGAAAATCACA
1 TTGGCATAAATCCATCTCGATCAAAATCACA
*
47865 TTGGCATAATTCCATCTCGAT-ATAAATCAC
1 TTGGCATAAATCCATCTCGATCA-AAATCAC
47895 CTCGATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (31 bp):
TTGGCATAAATCCATCTCGATCAAAATCACA
Found at i:58526 original size:18 final size:19
Alignment explanation
Indices: 58483--58526 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
58473 TAGATTTGAA
* *
58483 AAAATATATAAATATTATT
1 AAAATATAAAAATAATATT
58502 AATAATATAAAAATAAT-TT
1 AA-AATATAAAAATAATATT
58521 AAAATA
1 AAAATA
58527 AGTTTTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATAAAAATAATATT
Found at i:61780 original size:20 final size:20
Alignment explanation
Indices: 61755--61792 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
61745 GATTCAATTT
61755 AAAATATTATTTAATTAACA
1 AAAATATTATTTAATTAACA
*
61775 AAAATATTATTTATTTAA
1 AAAATATTATTTAATTAA
61793 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATATTATTTAATTAACA
Found at i:63220 original size:26 final size:27
Alignment explanation
Indices: 63180--63248 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
63170 AATATTTCTT
* *
63180 TAATTTTTTTTTAAATGAT-CATTTAAA
1 TAATTTTTTTATAAATAATAC-TTTAAA
* *
63207 T-ATTTTTATATAAAAAATACTTTAAA
1 TAATTTTTTTATAAATAATACTTTAAA
63233 TAATTTTTTTATAAAT
1 TAATTTTTTTATAAAT
63249 TTATTTAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
TAATTTTTTTATAAATAATACTTTAAA
Found at i:70644 original size:21 final size:21
Alignment explanation
Indices: 70586--70644 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
70576 TGGCAATGTG
*
70586 CTTGAAATGGAAGGAAATGAC
1 CTTGAAATGGAAGGGAATGAC
*
70607 CTTGAAATGGAAAGGAATGAC
1 CTTGAAATGGAAGGGAATGAC
*
70628 CTTGAAATTGAAGGGAA
1 CTTGAAATGGAAGGGAA
70645 CGAGGTTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.29, T:0.20
Consensus pattern (21 bp):
CTTGAAATGGAAGGGAATGAC
Found at i:77923 original size:33 final size:33
Alignment explanation
Indices: 77885--77950 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
77875 ATTTTATCAC
*
77885 TTGTTTAGATGTTTTGCTTATTGGTGGATATTT
1 TTGTTTAGATGTTTTGCTTAGTGGTGGATATTT
77918 TTGTTTAGATGTTTTGCTTAGTGGTGGATATTT
1 TTGTTTAGATGTTTTGCTTAGTGGTGGATATTT
77951 GATTCTACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.03, G:0.26, T:0.56
Consensus pattern (33 bp):
TTGTTTAGATGTTTTGCTTAGTGGTGGATATTT
Done.