Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011842.1 Kokia drynarioides strain JFW-HI SEQ_126838, 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: 115207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
Found at i:1234 original size:23 final size:23
Alignment explanation
Indices: 1204--1276 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
1194 ACAAAGTACT
*
1204 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
1227 GAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
*
1250 TAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
1273 GAGC
1 GAGC
1277 GCACTAGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.14
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:1379 original size:26 final size:24
Alignment explanation
Indices: 1339--1386 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
1329 TCTACATGGG
1339 CATAATTTCTCATATTCATCATTTCT
1 CATAATTTCTCATA-TCA-CATTTCT
1365 CATAATTTCAT-ATATCACATTT
1 CATAATTTC-TCATATCACATTT
1387 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 12 0.57
27 1 0.05
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (24 bp):
CATAATTTCTCATATCACATTTCT
Found at i:8405 original size:23 final size:23
Alignment explanation
Indices: 8362--8409 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
8352 TTTTTTTTAA
*
8362 TTTTTACATATTTTTCTTTTTTT
1 TTTTTACATATTTTTCATTTTTT
*
8385 TTTTTAC-TTTTTTATCATTTTTT
1 TTTTTACATATTTT-TCATTTTTT
8408 TT
1 TT
8410 CATGGGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTACATATTTTTCATTTTTT
Found at i:12522 original size:31 final size:31
Alignment explanation
Indices: 12477--12545 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
12467 ATTAACAGCC
* *
12477 TAATAACTTGAATAAAAATTTTCAAATAATT
1 TAATAATTTAAATAAAAATTTTCAAATAATT
** *
12508 TAATAATTTAAATAAATTTTTTTAAATAATT
1 TAATAATTTAAATAAAAATTTTCAAATAATT
12539 TAATAAT
1 TAATAAT
12546 GATTTTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (31 bp):
TAATAATTTAAATAAAAATTTTCAAATAATT
Found at i:21797 original size:14 final size:14
Alignment explanation
Indices: 21778--21805 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21768 ACTTTATATA
21778 CAACAAACTAGGGT
1 CAACAAACTAGGGT
21792 CAACAAACTAGGGT
1 CAACAAACTAGGGT
21806 TTATATGTAA
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:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
CAACAAACTAGGGT
Found at i:24744 original size:238 final size:238
Alignment explanation
Indices: 24320--24795 Score: 715
Period size: 238 Copynumber: 2.0 Consensus size: 238
24310 AAAATAATAA
24320 TAATGATAAAAAATCGAATAAGTTGATGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAAATCGAATAAGTTGATGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
* * *
24385 TTAGGCTTTTCTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGGTATTTTACTAGAATT
66 TTAGGCTTTTCTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAAGTATTTTACCAGAATT
* * *
24450 ATTTAAGTATCTTTTAGGGTTCTCGTTAGAAGTAAAAATTTCTAATTTAAGTTTTAAATTAGATA
131 ATTTAAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
* ** *
24515 AGTTTGGTGAACATGTATTAGTTAAGTTACAAATAAATCGGAG
196 AATTCAGTGAACATGTATTAGTCAAGTTACAAATAAATCGGAG
* *
24558 TAATGATAAAAGATTGAATAAGTTG-TAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATT
1 TAATGATAAAAAATCGAATAAGTTGAT-GATGAATTTTAATATTTCTCTTAATTCATTAGTAA--
*
24622 TTTTTAGG-TTTT-TTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAAGTATTTTACCAGA
63 CTTTTAGGCTTTTCTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAAGTATTTTACCAGA
* * * * *
24685 ATTATTTAGGTATCCTTTAGGGTTTTTATTAGGAGTAAAAATCTCTAATTTATGTTTTAAATTAG
128 ATTATTTAAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAG
* * *
24750 ATAAATTCAGTGAACATGTCTTAGTCAAGTTACAAGTAAATTGGAG
193 ATAAATTCAGTGAACATGTATTAGTCAAGTTACAAATAAATCGGAG
24796 GCATTTTTTT
Statistics
Matches: 214, Mismatches: 21, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
237 1 0.00
238 202 0.94
239 4 0.02
240 7 0.03
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (238 bp):
TAATGATAAAAAATCGAATAAGTTGATGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
TTAGGCTTTTCTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAAGTATTTTACCAGAATT
ATTTAAGTATCCTTTAGGGTTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AATTCAGTGAACATGTATTAGTCAAGTTACAAATAAATCGGAG
Found at i:27157 original size:13 final size:13
Alignment explanation
Indices: 27139--27189 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 13
27129 ATGGAAGCTC
27139 TCTCTTCTCTTTT
1 TCTCTTCTCTTTT
27152 TCTCTTCT-TTTCT
1 TCTCTTCTCTTT-T
27165 TCTCTTCTCATCTATT
1 TCTCTTCTC-T-T-TT
27181 TCTCTTCTC
1 TCTCTTCTC
27190 CTCTCCCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 3 0.09
13 17 0.52
15 1 0.03
16 11 0.33
17 1 0.03
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTCTTCTCTTTT
Found at i:28128 original size:19 final size:19
Alignment explanation
Indices: 28104--28145 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
28094 TTGGATGATT
28104 ATTTGATGTAAAATGGTTA
1 ATTTGATGTAAAATGGTTA
28123 ATTTGATGTAAAATGGTTA
1 ATTTGATGTAAAATGGTTA
28142 ATTT
1 ATTT
28146 TATGCTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (19 bp):
ATTTGATGTAAAATGGTTA
Found at i:28714 original size:11 final size:12
Alignment explanation
Indices: 28681--28712 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
28671 TCTTTTTTTA
28681 AAAAAAAAATTG
1 AAAAAAAAATTG
28693 AAAAAAAAATTG
1 AAAAAAAAATTG
28705 AAAGAAAA
1 AAA-AAAA
28713 TTATTACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:28751 original size:6 final size:6
Alignment explanation
Indices: 28727--28782 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
28717 TACAATAAGT
28727 TTTATA TTT-TA -TT-TA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
28772 TTTATA TTTAT
1 TTTATA TTTAT
28783 TTTCATTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 40 0.83
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:28898 original size:22 final size:22
Alignment explanation
Indices: 28857--28898 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28847 TTCCTATCTC
**
28857 TTTATCTTCTTATTCTTTTTTG
1 TTTATCTTCTTATTAGTTTTTG
*
28879 TTTATTTTCTTATTAGTTTT
1 TTTATCTTCTTATTAGTTTT
28899 CTCAGAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTATCTTCTTATTAGTTTTTG
Found at i:34572 original size:21 final size:21
Alignment explanation
Indices: 34530--34586 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
34520 TAACTACTGG
*
34530 ATAAATA-AACAAAT-AA-AA
1 ATAAATATAAAAAATAAACAA
34548 ATAAAATGAT-AAA-ATAAACAA
1 AT-AAAT-ATAAAAAATAAACAA
34569 ATAAATATAAAAAATAAA
1 ATAAATATAAAAAATAAA
34587 AATAATTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
18 2 0.06
19 8 0.26
20 12 0.39
21 9 0.29
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (21 bp):
ATAAATATAAAAAATAAACAA
Found at i:34591 original size:13 final size:14
Alignment explanation
Indices: 34532--34591 Score: 72
Period size: 13 Copynumber: 4.4 Consensus size: 14
34522 ACTACTGGAT
34532 AAATAAACAAATAA
1 AAATAAACAAATAA
*
34546 AAATAAA-ATGAT-A
1 AAATAAACA-AATAA
34559 AAATAAACAAATAA
1 AAATAAACAAATAA
*
34573 ATATAAA-AAATAA
1 AAATAAACAAATAA
34586 AAATAA
1 AAATAA
34592 TTGGGATTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 22 0.56
14 17 0.44
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (14 bp):
AAATAAACAAATAA
Found at i:34591 original size:27 final size:27
Alignment explanation
Indices: 34532--34587 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
34522 ACTACTGGAT
*
34532 AAATAAACAAATAAAAATAAAATGATA
1 AAATAAACAAATAAAAATAAAATAATA
*
34559 AAATAAACAAATAAATATAAAA-AATA
1 AAATAAACAAATAAAAATAAAATAATA
34585 AAA
1 AAA
34588 ATAATTGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18
Consensus pattern (27 bp):
AAATAAACAAATAAAAATAAAATAATA
Found at i:34642 original size:16 final size:16
Alignment explanation
Indices: 34607--34649 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
34597 ATTAGGCATG
*
34607 AAAATAAAT-GACAAA
1 AAAATAAATAAACAAA
*
34622 TAAATAAATAAACAAA
1 AAAATAAATAAACAAA
*
34638 AAAATCAATAAA
1 AAAATAAATAAA
34650 TTAAATGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:34674 original size:25 final size:25
Alignment explanation
Indices: 34634--34681 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
34624 AATAAATAAA
34634 CAAAAAAATCAATAAAT-TAAATGC
1 CAAAAAAATCAATAAATATAAATGC
34658 CAAAATAAA-CAACTAAATATAAAT
1 CAAAA-AAATCAA-TAAATATAAAT
34682 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.21
Consensus pattern (25 bp):
CAAAAAAATCAATAAATATAAATGC
Found at i:35532 original size:28 final size:28
Alignment explanation
Indices: 35501--35554 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
35491 AAGGTGGAAG
*
35501 ATGTGGCCATTTTTGACAATTATGTGAT
1 ATGTGACCATTTTTGACAATTATGTGAT
35529 ATGTGACCATTTTTGACAATTATGTG
1 ATGTGACCATTTTTGACAATTATGTG
35555 GCAATTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (28 bp):
ATGTGACCATTTTTGACAATTATGTGAT
Found at i:44243 original size:29 final size:29
Alignment explanation
Indices: 44201--44259 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
44191 AAAATCAGGT
44201 AAGGATAACAATGGTGCATTAGTCAAACA
1 AAGGATAACAATGGTGCATTAGTCAAACA
*
44230 AAGGATAACGATGGTGCATTAGTCAAACA
1 AAGGATAACAATGGTGCATTAGTCAAACA
44259 A
1 A
44260 TCCTTAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (29 bp):
AAGGATAACAATGGTGCATTAGTCAAACA
Found at i:51292 original size:86 final size:86
Alignment explanation
Indices: 51151--51339 Score: 310
Period size: 86 Copynumber: 2.2 Consensus size: 86
51141 TTTTTATTTG
* *
51151 GGTATCGATATTTT--TCATAAAATATCGATACTAGGGAATTATTATCGATACTACTGGTTTTAC
1 GGTATCGAT-TTTTCATAATAAAATATCGATACTAGGAAATTATTATCGATACTACTGGTTTTAC
*
51214 ATGGAAAACATAATAGAGGTTT
65 ATGGAAAACAGAATAGAGGTTT
51236 GGTATCGATTTTTCATAATAAAATATCGATACTAGGAAATTATTATCGATACTACTGGTTTTACA
1 GGTATCGATTTTTCATAATAAAATATCGATACTAGGAAATTATTATCGATACTACTGGTTTTACA
51301 TGGAAAACAGAATAGAGGTTT
66 TGGAAAACAGAATAGAGGTTT
* *
51322 GGTATCAATTTTCCATAA
1 GGTATCGATTTTTCATAA
51340 GGTATCGATA
Statistics
Matches: 97, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
84 4 0.04
85 9 0.09
86 84 0.87
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (86 bp):
GGTATCGATTTTTCATAATAAAATATCGATACTAGGAAATTATTATCGATACTACTGGTTTTACA
TGGAAAACAGAATAGAGGTTT
Found at i:55547 original size:68 final size:67
Alignment explanation
Indices: 55439--55795 Score: 318
Period size: 68 Copynumber: 5.3 Consensus size: 67
55429 TTCCATAACT
* * * * * * * *
55439 GAGCTATGATTTTACACCTTTTAATCCCATGTTAAATGTCCTAACGGACTCTATTGGTTGTCGTA
1 GAGCTATGGTCTTACACCTTGTAA-CCCATATTTAATGTCCTGACGAACTCTATTGGTTGTCATA
*
55504 GTT
65 GTC
* * *
55507 GAGCTATGGTCTTACACCTTATAAGCCCACATTTAATGTCCTGACGAAATCTATTGGTTGTCATA
1 GAGCTATGGTCTTACACCTTGTAA-CCCATATTTAATGTCCTGACGAACTCTATTGGTTGTCATA
55572 G-C
65 GTC
* * * * * ** *
55574 TAAGATATGGTCTTACACCTTGTAACCTCATGTTTAATGTCTTGGCGGGCTCTATTGGTTGAT-G
1 -GAGCTATGGTCTTACACCTTGTAACC-CATATTTAATGTCCTGACGAACTCTATTGGTTG-TCA
*
55638 TAGCC
63 TAGTC
* * * *
55643 AAGCTATGGTCTTATACATTGTAACCCCATATTTAATGTCCT-AGCAAACTCTATTGGTTGTCAT
1 GAGCTATGGTCTTACACCTTGTAA-CCCATATTTAATGTCCTGA-CGAACTCTATTGGTTGTCAT
55707 AGTC
64 AGTC
* * *
55711 GAGCTATGGTCTTACACATTTTAA-CC----TTAATGT-CTCGACGAACTCTATTGGTTGCCATA
1 GAGCTATGGTCTTACACCTTGTAACCCATATTTAATGTCCT-GACGAACTCTATTGGTTGTCATA
55770 GTC
65 GTC
*
55773 GAGTTATGGTCTTACACCTTGTA
1 GAGCTATGGTCTTACACCTTGTA
55796 CCTCTTTTGA
Statistics
Matches: 238, Mismatches: 42, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
61 2 0.01
62 49 0.21
63 1 0.00
66 2 0.01
67 3 0.01
68 177 0.74
69 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (67 bp):
GAGCTATGGTCTTACACCTTGTAACCCATATTTAATGTCCTGACGAACTCTATTGGTTGTCATAG
TC
Found at i:58135 original size:30 final size:29
Alignment explanation
Indices: 58067--58360 Score: 319
Period size: 30 Copynumber: 10.0 Consensus size: 29
58057 AAAGAATTTG
*
58067 GGGTCAAAATGTAATTTTAGAAAAGTTTA
1 GGGTCAAAATGTGATTTTAGAAAAGTTTA
*
58096 GGGT-AAAATGTGATTTTAAGGAAAGTTTA
1 GGGTCAAAATGTGATTTT-AGAAAAGTTTA
* * *
58125 GGGTTAAAATGTGGTTTTGGGAAAA-TTTA
1 GGGTCAAAATGTGATTTT-AGAAAAGTTTA
* * *
58154 GGGCCAAAATGT-AGTTTCTGGGAAAGTTTA
1 GGGTCAAAATGTGA-TTT-TAGAAAAGTTTA
*
58184 GGGATCAAAATGTGATTTTGGAAAAGTTTAA
1 GGG-TCAAAATGTGATTTTAGAAAAGTTT-A
*
58215 GGGTCAAAATGTGATTTTCGAAAAGTTTA
1 GGGTCAAAATGTGATTTTAGAAAAGTTTA
*
58244 GGGGTCAAAATGTAATTTTAGAAAAGTTTA
1 -GGGTCAAAATGTGATTTTAGAAAAGTTTA
* * *
58274 AGGTC-AAATGTAATTTTAGAAAAATTTA
1 GGGTCAAAATGTGATTTTAGAAAAGTTTA
*
58302 GGGTCAAAATGTGATTTTAAAAAAGTTTA
1 GGGTCAAAATGTGATTTTAGAAAAGTTTA
* *
58331 GGGATC-AAATCGTAATTTTAGAAAATTTTA
1 GGG-TCAAAAT-GTGATTTTAGAAAAGTTTA
58361 AAGGTTAAAA
Statistics
Matches: 229, Mismatches: 24, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
28 38 0.17
29 72 0.31
30 103 0.45
31 15 0.07
32 1 0.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (29 bp):
GGGTCAAAATGTGATTTTAGAAAAGTTTA
Found at i:58375 original size:87 final size:88
Alignment explanation
Indices: 58053--58377 Score: 288
Period size: 87 Copynumber: 3.7 Consensus size: 88
58043 GAAAATGAAG
* * * * * *
58053 TTTTAAAGAA-TTT-GGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGTAAAATGTGATTTTAAG
1 TTTTAAAAAAGTTTAGGGATCAAAATGTAATTTTAGAAAAGTTTAAGGTCAAATATAATTTT-AG
* * * *
58116 GAAAGTTT-AGGGTTAAAATGTGG
65 AAAAATTTAAGGGTCAAAATGTGA
** * * * * * * *
58139 TTTTGGGAAAA-TTTAGGG-CCAAAATGTAGTTTCTGGGAAAGTTTAGGGATCAAAATGTGATTT
1 TTTT-AAAAAAGTTTAGGGATCAAAATGTAATTT-TAGAAAAGTTTAAGG-TC-AAATATAATTT
* *
58202 TGGAAAAGTTTAAGGGTCAAAATGTGA
62 TAGAAAAATTTAAGGGTCAAAATGTGA
** * *
58229 TTTTCGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTAAGGTCAAATGTAATTTTAGA
1 TTTTAAAAAAGTTTAGGGATCAAAATGTAATTTTAGAAAAGTTTAAGGTCAAATATAATTTTAGA
58294 AAAATTT-AGGGTCAAAATGTGA
66 AAAATTTAAGGGTCAAAATGTGA
* *
58316 TTTTAAAAAAGTTTAGGGATC-AAATCGTAATTTTAGAAAATTTTAAAGGTTAAA-ATAATTTT
1 TTTTAAAAAAGTTTAGGGATCAAAAT-GTAATTTTAGAAAAGTTT-AAGGTCAAATATAATTTT
58378 TTGTAAGGTT
Statistics
Matches: 202, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
86 8 0.04
87 75 0.37
88 43 0.21
89 16 0.08
90 48 0.24
91 12 0.06
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.35
Consensus pattern (88 bp):
TTTTAAAAAAGTTTAGGGATCAAAATGTAATTTTAGAAAAGTTTAAGGTCAAATATAATTTTAGA
AAAATTTAAGGGTCAAAATGTGA
Found at i:58651 original size:36 final size:35
Alignment explanation
Indices: 58611--58685 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 35
58601 AACGGTGTCG
*
58611 TTTTGGCACTTTGACCCCTTCCCTTAAACGGCCCCA
1 TTTTGGCACTTTGACCCCTTCCCCTAAAC-GCCCCA
*
58647 TTTTGGCACTTTGACCCCTTCCCCTAAACGCCCCG
1 TTTTGGCACTTTGACCCCTTCCCCTAAACGCCCCA
58682 TTTT
1 TTTT
58686 TCAAACCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 9 0.24
36 28 0.76
ACGTcount: A:0.15, C:0.39, G:0.13, T:0.33
Consensus pattern (35 bp):
TTTTGGCACTTTGACCCCTTCCCCTAAACGCCCCA
Found at i:59963 original size:17 final size:16
Alignment explanation
Indices: 59937--59970 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
59927 ATTTGGACAT
59937 TAAATTAAATTTAAAA
1 TAAATTAAATTTAAAA
59953 TAAATTTAAATTTAAAA
1 TAAA-TTAAATTTAAAA
59970 T
1 T
59971 TCATTCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATTAAATTTAAAA
Found at i:61106 original size:26 final size:25
Alignment explanation
Indices: 61026--61098 Score: 112
Period size: 26 Copynumber: 2.9 Consensus size: 25
61016 TTTCATCCAT
61026 ATTTTACCCTAGTAAAATTTTGACA
1 ATTTTACCCTAGTAAAATTTTGACA
* *
61051 ATTTTACCCTTGATAACATTTTGACA
1 ATTTTACCCTAG-TAAAATTTTGACA
61077 ATTTTACCC-AGTAAAATTTTGA
1 ATTTTACCCTAGTAAAATTTTGA
61099 GAAAATTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 10 0.23
25 12 0.28
26 21 0.49
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTGACA
Found at i:64695 original size:14 final size:13
Alignment explanation
Indices: 64678--64722 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
64668 TTTATTTTTG
*
64678 TTTTAATATTTGAA
1 TTTTTATATTT-AA
64692 TTTTTA-ATTTAA
1 TTTTTATATTTAA
64704 TTTTTATATTTTAA
1 TTTTTATA-TTTAA
64718 TTTTT
1 TTTTT
64723 TTTTATTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 8 0.29
13 5 0.18
14 15 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTTATATTTAA
Found at i:64714 original size:20 final size:20
Alignment explanation
Indices: 64664--64720 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
64654 TACTTTAGCC
**
64664 ATTTTT-TATTTTTGTTTTA
1 ATTTTTATATTTTTAATTTA
*
64683 ATATTTGA-ATTTTTAATTTA
1 AT-TTTTATATTTTTAATTTA
64703 ATTTTTATA-TTTTAATTT
1 ATTTTTATATTTTTAATTT
64721 TTTTTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
ATTTTTATATTTTTAATTTA
Found at i:71054 original size:22 final size:21
Alignment explanation
Indices: 71019--71113 Score: 95
Period size: 22 Copynumber: 4.3 Consensus size: 21
71009 TTACCCTTTC
71019 TTATTTTTATTTTCTTTTATTAT
1 TTATTTTTA-TTT-TTTTATTAT
* *
71042 TTATTTTCATTTCTTTTTTTAT
1 TTATTTTTATTT-TTTTATTAT
71064 TT-TTATTTATTTTTTTATTAT
1 TTATT-TTTATTTTTTTATTAT
*
71085 GTT-GTTTTATTTTATTTATTAT
1 -TTATTTTTATTTT-TTTATTAT
71107 TTATTTT
1 TTATTTT
71114 GTTTTATTAC
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
21 20 0.32
22 34 0.55
23 8 0.13
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (21 bp):
TTATTTTTATTTTTTTATTAT
Found at i:71055 original size:36 final size:33
Alignment explanation
Indices: 71015--71113 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 33
71005 CTTATTACCC
71015 TTTCTTATTTTTATTTTCTTTTATTATTTATTTTCA
1 TTTCTT-TTTTTATTTT-TTTTATTATTTATTTT-A
*
71051 TTTCTTTTTTTA-TTTTTAT-TTATTT-TTTTA
1 TTTCTTTTTTTATTTTTTTTATTATTTATTTTA
* * *
71081 TTATGTTGTTTTATTTTATTTATTATTTATTTT
1 TT-TCTTTTTTTATTTTTTTTATTATTTATTTT
71114 GTTTTATTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
30 3 0.06
31 12 0.22
32 11 0.20
33 9 0.17
34 7 0.13
35 6 0.11
36 6 0.11
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (33 bp):
TTTCTTTTTTTATTTTTTTTATTATTTATTTTA
Found at i:71064 original size:18 final size:18
Alignment explanation
Indices: 71015--71082 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
71005 CTTATTACCC
71015 TTTCTTATTTTTATTTTC-
1 TTTCTT-TTTTTATTTTCA
*
71033 TTT-TATTATTTATTTTCA
1 TTTCT-TTTTTTATTTTCA
*
71051 TTTCTTTTTTTATTTTTA
1 TTTCTTTTTTTATTTTCA
*
71069 TTTATTTTTTTATT
1 TTTCTTTTTTTATT
71083 ATGTTGTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
17 11 0.26
18 31 0.72
19 1 0.02
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTTTATTTTCA
Found at i:71099 original size:26 final size:26
Alignment explanation
Indices: 71064--71121 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
71054 CTTTTTTTAT
*
71064 TTTTA-TTTATTT-TTTTATTATGTTG
1 TTTTATTTTATTTATTAT-TTATGTTG
*
71089 TTTTATTTTATTTATTATTTATTTTG
1 TTTTATTTTATTTATTATTTATGTTG
71115 TTTTATT
1 TTTTATT
71122 ACTGCTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 21 0.72
27 3 0.10
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (26 bp):
TTTTATTTTATTTATTATTTATGTTG
Found at i:81279 original size:29 final size:30
Alignment explanation
Indices: 81214--81270 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
81204 CTAATTGAGT
*
81214 TTTAAAATTTTTAAGTTTCATTTTTTATTG
1 TTTAAAATTTTTAAGTTTCAATTTTTATTG
*
81244 TTTAAAA-TTTTAA-TTTTAATTTTTATT
1 TTTAAAATTTTTAAGTTTCAATTTTTATT
81271 TTAATAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.48
29 6 0.24
30 7 0.28
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (30 bp):
TTTAAAATTTTTAAGTTTCAATTTTTATTG
Found at i:86191 original size:16 final size:16
Alignment explanation
Indices: 86166--86196 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86156 TTGCATACTT
86166 AGGATAATTTGCATTA
1 AGGATAATTTGCATTA
*
86182 AGGATCATTTGCATT
1 AGGATAATTTGCATT
86197 TAGTTTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (16 bp):
AGGATAATTTGCATTA
Found at i:88445 original size:16 final size:16
Alignment explanation
Indices: 88424--88456 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
88414 CGAGTTGCTT
88424 GTAATCCTAAAAATAG
1 GTAATCCTAAAAATAG
88440 GTAATCCTAAAAATAG
1 GTAATCCTAAAAATAG
88456 G
1 G
88457 AGGACATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (16 bp):
GTAATCCTAAAAATAG
Found at i:89179 original size:17 final size:18
Alignment explanation
Indices: 89159--89192 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
89149 AAAATAAGAA
89159 ATAA-AATAAAATTTATC
1 ATAAGAATAAAATTTATC
*
89176 ATAAGATTAAAATTTAT
1 ATAAGAATAAAATTTAT
89193 TAAAATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAAGAATAAAATTTATC
Found at i:90506 original size:13 final size:14
Alignment explanation
Indices: 90480--90511 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
90470 ATTAGCTATA
90480 TTTT-ATTATAAAT
1 TTTTAATTATAAAT
90493 TTTTAATTAT-AAT
1 TTTTAATTATAAAT
90506 TTTTAA
1 TTTTAA
90512 AAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAATTATAAAT
Found at i:93766 original size:86 final size:86
Alignment explanation
Indices: 93621--93796 Score: 352
Period size: 86 Copynumber: 2.0 Consensus size: 86
93611 CAAAATTTGT
93621 GGGAAATAAAATCCTTTTAGTTAGGTATCTAATGCTCTACCGGGAACTTATTCTTATGCATAATG
1 GGGAAATAAAATCCTTTTAGTTAGGTATCTAATGCTCTACCGGGAACTTATTCTTATGCATAATG
93686 CATTGGAAAAGTAAAAGAATA
66 CATTGGAAAAGTAAAAGAATA
93707 GGGAAATAAAATCCTTTTAGTTAGGTATCTAATGCTCTACCGGGAACTTATTCTTATGCATAATG
1 GGGAAATAAAATCCTTTTAGTTAGGTATCTAATGCTCTACCGGGAACTTATTCTTATGCATAATG
93772 CATTGGAAAAGTAAAAGAATA
66 CATTGGAAAAGTAAAAGAATA
93793 GGGA
1 GGGA
93797 TTTAGGTATG
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 90 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (86 bp):
GGGAAATAAAATCCTTTTAGTTAGGTATCTAATGCTCTACCGGGAACTTATTCTTATGCATAATG
CATTGGAAAAGTAAAAGAATA
Found at i:94198 original size:16 final size:17
Alignment explanation
Indices: 94171--94229 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
94161 TTTGAATTTA
*
94171 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
94188 TTAAA-TTATTTAAAAT
1 TTAAATTTATTTTAAAT
*
94204 TTAAATTTATTATAAAT
1 TTAAATTTATTTTAAAT
*
94221 TTAAGTTTA
1 TTAAATTTA
94230 AAATGTCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:94941 original size:14 final size:15
Alignment explanation
Indices: 94924--94961 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
94914 TGAGATTTAT
94924 TATTATTAAAAA-AA
1 TATTATTAAAAATAA
*
94938 TATTATTAAAAATAT
1 TATTATTAAAAATAA
94953 TATTATTAA
1 TATTATTAA
94962 TTAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTATTAAAAATAA
Found at i:94950 original size:12 final size:12
Alignment explanation
Indices: 94933--94957 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94923 TTATTATTAA
94933 AAAAATATTATT
1 AAAAATATTATT
94945 AAAAATATTATT
1 AAAAATATTATT
94957 A
1 A
94958 TTAATTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATATTATT
Found at i:95687 original size:17 final size:17
Alignment explanation
Indices: 95662--95706 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
95652 TATTACCCAA
95662 ATCCGACCCGAAATCTG
1 ATCCGACCCGAAATCTG
*
95679 ATCCAACCCGAAATCTG
1 ATCCGACCCGAAATCTG
95696 ATCCGACCCGA
1 ATCCGACCCGA
95707 CCTAAGATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.38, G:0.16, T:0.16
Consensus pattern (17 bp):
ATCCGACCCGAAATCTG
Found at i:96121 original size:29 final size:28
Alignment explanation
Indices: 96087--96244 Score: 140
Period size: 29 Copynumber: 5.4 Consensus size: 28
96077 GTCCTCGAAC
*
96087 CTTCCAAAAATTACCATCTTACCCTCAAA
1 CTTCCAAAAATTACCATTTTACCC-CAAA
* *
96116 CTTCCAAAAA-TCCCATTTTTGACCCCGAAC
1 CTTCCAAAAATTACCA-TTTT-ACCCC-AAA
* * *
96146 CTTCCAAAAATTACTAATTTACCCCCGAA
1 CTTCCAAAAATTACCATTTTA-CCCCAAA
* *
96175 CTTCCAAAGA-TCCCATTTTGGACCCCAAA
1 CTTCCAAAAATTACCATTTT--ACCCCAAA
*
96204 CCTTCCAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAATTACCATTTTA-CCCCAAA
96234 CTTCCAAAAAT
1 CTTCCAAAAAT
96245 CTCATTTTTG
Statistics
Matches: 103, Mismatches: 16, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
28 10 0.10
29 43 0.42
30 39 0.38
31 11 0.11
ACGTcount: A:0.35, C:0.34, G:0.04, T:0.27
Consensus pattern (28 bp):
CTTCCAAAAATTACCATTTTACCCCAAA
Found at i:96154 original size:59 final size:58
Alignment explanation
Indices: 96082--96257 Score: 262
Period size: 59 Copynumber: 3.0 Consensus size: 58
96072 TCGAGGTCCT
* *
96082 CGAACCTTCCAAAAATTACCATCTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
1 CGAACCTTCCAAAAATTACCAT-TTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
* * *
96141 CGAACCTTCCAAAAATTACTAATTTACCCCCGAACTTCCAAAGATCCCATTTTGGACCC
1 CGAACCTTCCAAAAATTAC-CATTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
* *
96200 CAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACC
1 CGAACCTTCCAAAAATTACCA-TTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC
96258 TCAGACATCT
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
58 1 0.01
59 102 0.97
60 2 0.02
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (58 bp):
CGAACCTTCCAAAAATTACCATTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC
Found at i:96253 original size:29 final size:29
Alignment explanation
Indices: 96105--96253 Score: 112
Period size: 30 Copynumber: 5.1 Consensus size: 29
96095 AATTACCATC
* * *
96105 TTACCCTCAAACTTCCAAAAATCCCATTT
1 TTACCCCCGAACTTCCAAAAATCTCATTT
*
96134 TTGA-CCCCGAACCTTCCAAAAAT-T-ACTAAT
1 TT-ACCCCCGAA-CTTCCAAAAATCTCA-T-TT
* *
96164 TTACCCCCGAACTTCCAAAGATCCCATTT
1 TTACCCCCGAACTTCCAAAAATCTCATTT
* *
96193 TGGA-CCCCAAACCTTCCAAAAAT-TACCA-TT
1 T-TACCCCCGAA-CTTCCAAAAATCT--CATTT
96223 TTACCCCCGAACTTCCAAAAATCTCATTT
1 TTACCCCCGAACTTCCAAAAATCTCATTT
96252 TT
1 TT
96254 GACCTCAGAC
Statistics
Matches: 93, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
28 3 0.03
29 43 0.46
30 44 0.47
31 3 0.03
ACGTcount: A:0.33, C:0.34, G:0.05, T:0.29
Consensus pattern (29 bp):
TTACCCCCGAACTTCCAAAAATCTCATTT
Found at i:103982 original size:33 final size:33
Alignment explanation
Indices: 103944--104011 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
103934 CTTAGAGTCC
103944 TACTTCGAGCAAGATGCGTGTTCGGAAGAGCTT
1 TACTTCGAGCAAGATGCGTGTTCGGAAGAGCTT
103977 TACTTCGAGCAAGATGCGTGTTCGGAAGAGCTT
1 TACTTCGAGCAAGATGCGTGTTCGGAAGAGCTT
104010 TA
1 TA
104012 GGACTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (33 bp):
TACTTCGAGCAAGATGCGTGTTCGGAAGAGCTT
Found at i:108481 original size:77 final size:76
Alignment explanation
Indices: 108353--108508 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 76
108343 TGAGGAACTG
*
108353 TGAAGTGGACCAAATTCGTCTTCGCGATGAGATACAGAGAAGCGGATTGGAACAAACGACGCGGT
1 TGAAGTGGACCAAATCCGTCTTCGCGATGAGATACAGAGAAGCGGATTGGAACAAACGACGCGGT
108418 CATCCTCCTGA
66 CATCCTCCTGA
108429 TNGAAGTGGACCAAATCCGTCTTCGCGATGAGATACAGAGAAGCGGATTGGAACAAACGACGCGG
1 T-GAAGTGGACCAAATCCGTCTTCGCGATGAGATACAGAGAAGCGGATTGGAACAAACGACGCGG
108494 TCATCCTCCTGA
65 TCATCCTCCTGA
108506 TGA
1 TGA
108509 GATACTGAGA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
76 3 0.04
77 75 0.96
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.19
Consensus pattern (76 bp):
TGAAGTGGACCAAATCCGTCTTCGCGATGAGATACAGAGAAGCGGATTGGAACAAACGACGCGGT
CATCCTCCTGA
Found at i:108674 original size:205 final size:205
Alignment explanation
Indices: 108431--109141 Score: 1100
Period size: 205 Copynumber: 3.5 Consensus size: 205
108421 CCTCCTGATN
* * * **
108431 GAAGTGGACCAAATCCGTCTTCGCGATGAGATACAGAGAAGCGGATTGGAACAAACGACGCGGTC
1 GAAGTGGACCAAATTCGTCTTCCCGATGAGAAACAGAGAAGCGGATTAAAACAAACGACGCGGTC
108496 ATCCTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGATGTGAGCAAATCTTC
66 ATCCTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGATGTGAGCAAATCTTC
108561 GAACCGCAGCTTCCTGATGAGATACTGAGAAGCTAGTCGAAGCAATAAAAGGTTAGCTTCCTGAT
131 GAACCGCAGCTTCCTGATGAGATACTGAGAAGCTAGTCGAAGCAATAAAAGGTTAGCTTCCTGAT
108626 GAGAAACTGC
196 GAGAAACTGC
* * *
108636 GAAGTGGACCAAATTCGTCTTCCCGATGAGAAACAGAGAAGCGGATTAGAACAAATGACGCGATC
1 GAAGTGGACCAAATTCGTCTTCCCGATGAGAAACAGAGAAGCGGATTAAAACAAACGACGCGGTC
* * *
108701 ATCCTCCTGATGAGATACTGAGAAGAAAACCAAGTCAAACTCACACTCGATGTGAGCAAATCTTC
66 ATCCTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGATGTGAGCAAATCTTC
* *
108766 GAACCGCANCTTCTTGATGAGATACTGAGAAGCTAGTCGAAGCAATAAAAGGTTAGCTTCCTGAT
131 GAACCGCAGCTTCCTGATGAGATACTGAGAAGCTAGTCGAAGCAATAAAAGGTTAGCTTCCTGAT
108831 GAGAAACTGC
196 GAGAAACTGC
* * * *
108841 GAAGTGGACCAGATTCGTCTTCCTGATGAGATACAAAGAAGCGGATTAAAACAAACGACGCGGTC
1 GAAGTGGACCAAATTCGTCTTCCCGATGAGAAACAGAGAAGCGGATTAAAACAAACGACGCGGTC
*
108906 ATCCTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGATGTGAGAAAATCTTC
66 ATCCTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGATGTGAGCAAATCTTC
* * * *
108971 GAACCGCAGCTTCCTGATGAGATACTGAGAAGATGGTCGAAGCAATAAAAGATTAGCTTCCTAAT
131 GAACCGCAGCTTCCTGATGAGATACTGAGAAGCTAGTCGAAGCAATAAAAGGTTAGCTTCCTGAT
*
109036 GAGAAACTGA
196 GAGAAACTGC
* * * * * * * *
109046 GAAGTAGACCAAATTCGTCTTCTCGATAAGATAA-GGAGAAGCGGAGTGAAACAAACGACACAGT
1 GAAGTGGACCAAATTCGTCTTCCCGATGAGA-AACAGAGAAGCGGATTAAAACAAACGACGCGGT
* * *
109110 CATCCTCTTGATGAGATACTGAGGAGTAGACC
65 CATCCTCCTGATGAGATACTGAGAAGAAGACC
109142 GAATTCGTCT
Statistics
Matches: 461, Mismatches: 44, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
205 460 1.00
206 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (205 bp):
GAAGTGGACCAAATTCGTCTTCCCGATGAGAAACAGAGAAGCGGATTAAAACAAACGACGCGGTC
ATCCTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGATGTGAGCAAATCTTC
GAACCGCAGCTTCCTGATGAGATACTGAGAAGCTAGTCGAAGCAATAAAAGGTTAGCTTCCTGAT
GAGAAACTGC
Found at i:109763 original size:17 final size:17
Alignment explanation
Indices: 109738--109780 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
109728 TTTGAATTTA
**
109738 TTAAGTTTATTTTAAAT
1 TTAAGTTTATAATAAAT
*
109755 TTAAATTTATAATAAAT
1 TTAAGTTTATAATAAAT
109772 TTAAGTTTA
1 TTAAGTTTA
109781 AAATGTCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
TTAAGTTTATAATAAAT
Found at i:110446 original size:14 final size:13
Alignment explanation
Indices: 110429--110462 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
110419 TGAGATTTAT
110429 TATTATTACAAAAA
1 TATTATTA-AAAAA
110443 TATTATT-AAAAA
1 TATTATTAAAAAA
110455 TATTATTA
1 TATTATTA
110463 TTAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.63
14 7 0.37
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTATTAAAAAA
Found at i:111622 original size:29 final size:29
Alignment explanation
Indices: 111577--111672 Score: 108
Period size: 30 Copynumber: 3.3 Consensus size: 29
111567 CCCCGGAGGT
*
111577 CCCCGAA-CTTTCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATCCCATTTTT-A
*
111606 CCCCGAACCTTCCAAAAATTACCA-TTTTA
1 CCCCGAACCTTCCAAAAA-TCCCATTTTTA
111635 CCCCCGAA-CTTCCAAAAATCCCATTTTTTA
1 -CCCCGAACCTTCCAAAAATCCCA-TTTTTA
*
111665 CCTCGAAC
1 CCCCGAAC
111673 ATCTAAAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
28 4 0.07
29 24 0.42
30 25 0.44
31 4 0.07
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.28
Consensus pattern (29 bp):
CCCCGAACCTTCCAAAAATCCCATTTTTA
Found at i:111680 original size:29 final size:29
Alignment explanation
Indices: 111577--111682 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 29
111567 CCCCGGAGGT
* *
111577 CCCCGAACTTTCAAAAATCCCATTTTTGA
1 CCCCGAACTTCCAAAAATCCCATTTTTTA
*
111606 CCCCGAACCTTCCAAAAATTACCA--TTTTA
1 CCCCGAA-CTTCCAAAAA-TCCCATTTTTTA
111635 CCCCCGAACTTCCAAAAATCCCATTTTTTA
1 -CCCCGAACTTCCAAAAATCCCATTTTTTA
* * *
111665 CCTCGAACATCTAAAAAT
1 CCCCGAACTTCCAAAAAT
111683 TACTGCCTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
28 4 0.06
29 36 0.55
30 21 0.32
31 4 0.06
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.28
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATCCCATTTTTTA
Done.