Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1342
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: 54943
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11172 original size:28 final size:28
Alignment explanation
Indices: 11091--11172 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
11081 TTTTGGAGAT
*
11091 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
11119 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
11147 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
11173 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:11315 original size:51 final size:51
Alignment explanation
Indices: 11155--11325 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
11145 GAAATAACGA
* * *
11155 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
11207 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
11260 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
11311 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
11326 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:11371 original size:27 final size:28
Alignment explanation
Indices: 11308--11383 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
11298 AAAATAAAGT
*
11308 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
11336 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
11363 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
11384 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:13866 original size:13 final size:13
Alignment explanation
Indices: 13848--13873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13838 ACAAAGATCC
13848 ATGTATCGATACA
1 ATGTATCGATACA
13861 ATGTATCGATACA
1 ATGTATCGATACA
13874 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:13869 original size:33 final size:33
Alignment explanation
Indices: 13827--13893 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
13817 AAAATTTCCA
***
13827 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
13860 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
13893 A
1 A
13894 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:13937 original size:19 final size:18
Alignment explanation
Indices: 13913--13980 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
13903 CAGTAGCTAA
13913 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
13932 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
13947 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
13964 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
13981 TCGTTGGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:13953 original size:13 final size:13
Alignment explanation
Indices: 13935--13959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13925 ACAATACTTA
13935 TGTATCGATACAT
1 TGTATCGATACAT
13948 TGTATCGATACA
1 TGTATCGATACA
13960 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13957 original size:32 final size:32
Alignment explanation
Indices: 13916--13978 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
13906 TAGCTAATTA
*
13916 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
13948 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
13979 AATCGTTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:14042 original size:21 final size:22
Alignment explanation
Indices: 14016--14073 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
14006 GTTGGGACCC
*
14016 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGTACAAA
*
14037 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
*
14058 TGTATCGATATATTTG
1 TGTATCGATACATTTG
14074 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:16362 original size:20 final size:20
Alignment explanation
Indices: 16337--16484 Score: 136
Period size: 20 Copynumber: 7.8 Consensus size: 20
16327 TTTTCACAAT
*
16337 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTGTTCA
*
16357 TTGTATCGATACATTGTTTA
1 TTGTATCGATACATTGTTCA
*
16377 TTATATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
16390 TTGTATCGATACATT-TTGCA
1 TTGTATCGATACATTGTT-CA
* *
16410 TTGTATCGATACATGGCTCA
1 TTGTATCGATACATTGTTCA
*
16430 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
16450 TTGTATC-AGTACATT-TTACA
1 TTGTATCGA-TACATTGTT-CA
*
16470 ATGTATCGATACATT
1 TTGTATCGATACATT
16485 CAGGCATTTT
Statistics
Matches: 107, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
13 10 0.09
15 1 0.01
18 1 0.01
19 2 0.02
20 91 0.85
21 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:16397 original size:33 final size:33
Alignment explanation
Indices: 16355--16423 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
16345 ATACATTATT
*
16355 CATTGTATCGATACATTGTT-TATTATATCGATA
1 CATTGTATCGATACATT-TTGCATTATATCGATA
*
16388 CATTGTATCGATACATTTTGCATTGTATCGATA
1 CATTGTATCGATACATTTTGCATTATATCGATA
16421 CAT
1 CAT
16424 GGCTCATTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (33 bp):
CATTGTATCGATACATTTTGCATTATATCGATA
Found at i:16398 original size:13 final size:13
Alignment explanation
Indices: 16380--16404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16370 TTGTTTATTA
16380 TATCGATACATTG
1 TATCGATACATTG
16393 TATCGATACATT
1 TATCGATACATT
16405 TTGCATTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:16417 original size:53 final size:53
Alignment explanation
Indices: 16337--16445 Score: 166
Period size: 53 Copynumber: 2.1 Consensus size: 53
16327 TTTTCACAAT
* * *
16337 TTGTATCGATACATTATTCATTGTATCGATACATTGTTTATTATATCGATACA
1 TTGTATCGATACATTATTCATTGTATCGATACATGGCTCATTATATCGATACA
*
16390 TTGTATCGATACATT-TTGCATTGTATCGATACATGGCTCATTGTATCGATACA
1 TTGTATCGATACATTATT-CATTGTATCGATACATGGCTCATTATATCGATACA
16443 TTG
1 TTG
16446 CTCATTGTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 2 0.04
53 49 0.96
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (53 bp):
TTGTATCGATACATTATTCATTGTATCGATACATGGCTCATTATATCGATACA
Found at i:18977 original size:51 final size:51
Alignment explanation
Indices: 18807--18985 Score: 184
Period size: 51 Copynumber: 3.5 Consensus size: 51
18797 AAATTTCTAG
* * **
18807 ATTTTTCAT-CTCGGGGATACTCCAA-TCCCAGTTCCATTTCGAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACTCCGA-TTTTATTTCGAAAACATCA
* * * *
18857 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATCG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCGAAAACATCA
** * *
18908 ATTTACCGTAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACCA
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTA-TTTCGAAAACATCA
* **
18959 ATTTTTCACAATTAGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
18986 CCCGTTATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 8 0.08
51 90 0.85
52 8 0.08
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCGAAAACATCA
Found at i:19009 original size:28 final size:28
Alignment explanation
Indices: 18973--19044 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
18963 TTCACAATTA
*
18973 GGGATACTCCAACCCCGTTATTTCAT-CG
1 GGGATACTCCAACCCCGTTATTTC-TGAG
*
19001 GGGACACTCCAACCCCGTTATTTCTGAG
1 GGGATACTCCAACCCCGTTATTTCTGAG
19029 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
19045 AGCTTTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCTGAG
Found at i:19185 original size:79 final size:79
Alignment explanation
Indices: 19100--19307 Score: 222
Period size: 79 Copynumber: 2.6 Consensus size: 79
19090 AACCTCGACC
* * *
19100 TTATTTTTAAATTATCAATTTT-TCACAATC-GAGGATACTCCAACCCCGTTATTTTTAAGGGAA
1 TTATTTTCAAAATATCAATTTTCT-ACAATCAG-GGATACTCCAACCCCGTTATTTTCAAGGGAA
*
19163 TACTCCAACCCCGATT
64 TACTCCAACCCCAATT
* * ** * *
19179 TTATTTTCAAAATATCGATTTTCTATAATCAGGGATACTCCAACCTTGTTATTTTCGAGGGGATA
1 TTATTTTCAAAATATCAATTTTCTACAATCAGGGATACTCCAACCCCGTTATTTTCAAGGGAATA
19244 CTCCAACCCCAATT
66 CTCCAACCCCAATT
* * * * * * * *
19258 TTATTTTCAGAACACCAATTTTCCATAGTCGGGGATACTCCAGCCCCGTT
1 TTATTTTCAAAATATCAATTTTCTACAATCAGGGATACTCCAACCCCGTT
19308 GTTATCTCCA
Statistics
Matches: 107, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
79 105 0.98
80 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
TTATTTTCAAAATATCAATTTTCTACAATCAGGGATACTCCAACCCCGTTATTTTCAAGGGAATA
CTCCAACCCCAATT
Found at i:21212 original size:29 final size:29
Alignment explanation
Indices: 21178--21593 Score: 407
Period size: 29 Copynumber: 14.6 Consensus size: 29
21168 TCAATACGAC
*
21178 CCTTTTTAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
21207 CATTTTTAAAGCCCACAAGTCAATGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
*
21236 CCTTTTGAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
21265 CATTTTTAAAGCCCACAAGTTAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
21294 CCTTTCAAAAGCCAACGAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * * *
21323 CC-TTTCAAAGCCCATAAGTTAGTAGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
21351 CCTTTCAAAAGCCCACAAGTTAATGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* *
21380 CCTTTCAAAAGCCCACAAGTTAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
*
21409 CCTTTCAAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * * *
21438 CC-TTTCAAAGCCTATAAGTCAGTGGTA-
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * *
21465 CC-TTTCAAAGCTCACAAGTCAATGGCA-
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * * *
21492 CCTTTCAAAAGCCAACAAGTCAATGG-AA
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* * * * *
21520 CATTTCAAAAGTCAACAAGTCAATGGCA-
1 CCTTTTAAAAGCCCACAAGTCAGTGGCAT
* *
21548 CCTTTTCAAAGCCCACAAGT-AGTGGCAAC
1 CCTTTTAAAAGCCCACAAGTCAGTGGC-AT
*
21577 CCTTTTCAAAGCCCACA
1 CCTTTTAAAAGCCCACA
21594 CAAGTTGGTG
Statistics
Matches: 331, Mismatches: 50, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
27 30 0.09
28 100 0.30
29 201 0.61
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (29 bp):
CCTTTTAAAAGCCCACAAGTCAGTGGCAT
Found at i:21391 original size:115 final size:114
Alignment explanation
Indices: 21185--21593 Score: 486
Period size: 115 Copynumber: 3.6 Consensus size: 114
21175 GACCCTTTTT
* * * * *
21185 AAAGCCCACAAGTCAGTGGCATCATTTTTAAAGCCCACAAGTCAATGGCATCCTTTTGAAAGCCC
1 AAAGCCAACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCC
* * **
21250 ACAAGTCAGTGGCATCATTTTTAAAGCCCACAAGTTAGTGGCATCCTTTCA
64 ACAAGTCAATGGCATCCTTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCA
* * * *
21301 AAAGCCAACGAGTCAGTGGCATCCTTTCAAAGCCCATAAGTTAGTAGCATCCTTTCAAAAGCCCA
1 AAAGCCAACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC-AAAGCCCA
*
21366 CAAGTTAATGGCATCCTTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCA
65 CAAGTCAATGGCATCCTTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCA
* * * * *
21416 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCTATAAGTCAGTGGTA-CCTTTCAAAGCTCAC
1 AAAGCCAACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC
* * * * *
21480 AAGTCAATGGCA-CCTTTCAAAAGCCAACAAGTCAATGG-AACATTTCA
66 AAGTCAATGGCATCCTTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCA
* * *
21527 AAAGTCAACAAGTCAATGGCA-CCTTTTCAAAGCCCACAAGT-AGTGGCAACCCTTTTCAAAGCC
1 AAAGCCAACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGC-ATCC-TTTCAAAGCC
21590 CACA
63 CACA
21594 CAAGTTGGTG
Statistics
Matches: 254, Mismatches: 34, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
110 7 0.03
111 41 0.16
112 25 0.10
113 32 0.13
114 9 0.04
115 119 0.47
116 21 0.08
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.23
Consensus pattern (114 bp):
AAAGCCAACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC
AAGTCAATGGCATCCTTTCAAAAGCCCACAAGTTAGTGGCATCCTTTCA
Found at i:22842 original size:10 final size:10
Alignment explanation
Indices: 22827--22860 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
22817 AGGTTCAACC
22827 AAAAAAGAAA
1 AAAAAAGAAA
22837 AAAAAAGAAA
1 AAAAAAGAAA
*
22847 AAAAGAGAAA
1 AAAAAAGAAA
22857 AAAA
1 AAAA
22861 TAGAGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:23119 original size:3 final size:3
Alignment explanation
Indices: 23111--23157 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
23101 TTACACCACG
23111 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
23158 ATTTCAAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25876 original size:79 final size:79
Alignment explanation
Indices: 25775--26245 Score: 418
Period size: 79 Copynumber: 6.0 Consensus size: 79
25765 CATTGATGTA
* *** * *
25775 TTTATTTCTAAAATATTGATTTTCCACCATCGGGGATACTCCAACCTCGTTAATTCCGAAGGGAT
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCGAAGGGAT
*
25840 ACTCCAACTCTGAT
66 ACTCCAACCCTGAT
* * * ** *
25854 TTTATTTTTAAAACACCAATTTTCCACAATCGGGGATATTCCAACCCCGTTATTTTTGAGGGGAT
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCGAAGGGAT
* **
25919 ACTTCAA---TTTT
66 ACTCCAACCCTGAT
* * * *
25930 TTTATTT-TCAAAACACCAATTTTTCACCATCGGGGATACTCCAGCCTCGTTATTTTC-AAGGAG
1 TTTATTTCT-AAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCGAAGG-G
*
25993 ATACTCTAACCCTGAT
64 ATACTCCAACCCTGAT
* * * * * *
26009 TTTATTTCTAAAACACTAATTTTCTACAATCGAGGATACTCCAACCCCATTATTTCTG--GGAGA
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCGAAGG-G-
** * *
26072 ATTTTTCAACCTTGATT
64 ATACTCCAACCCTGA-T
* * ** * * *
26089 TTTATTTCTAAAACACCGATTTTTCACAATCGAAGATATTCCAACCTTGTTATTTTCGAAGGGAT
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCGAAGGGAT
* *
26154 ACTCCAACCCCAGTT
66 ACTCCAA-CCCTGAT
* ** * *
26169 TTTATTTCTAAAACACTAATTTTTTACAATCGGGGATACTCCAACC-CTGTTATTTCTGAGGGGA
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTC-GTTATTTCCGAAGGGA
26233 TACTCCAACCCTG
65 TACTCCAACCCTG
26246 GTATATTCTA
Statistics
Matches: 310, Mismatches: 69, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
75 4 0.01
76 59 0.19
78 4 0.01
79 120 0.39
80 117 0.38
81 4 0.01
82 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCTCGTTATTTCCGAAGGGAT
ACTCCAACCCTGAT
Found at i:26062 original size:155 final size:157
Alignment explanation
Indices: 25775--26241 Score: 566
Period size: 155 Copynumber: 3.0 Consensus size: 157
25765 CATTGATGTA
* *** * * *
25775 TTTATTTCTAAAATATTGATTTTCCACCATCGGGGATACTCCAACCTCGTTAATTCCGAAGGGAT
1 TTTATTTCTAAAACACCAATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTCGAAGGGAT
* * * * *
25840 ACTCCAACTCTGATTTTATTTTTAAAACACCAATTTTCCACAATCGGGGATATTCCAACCCCGTT
66 ACTCCAACCCTGATTTTATTTCTAAAACACTAATTTTCTACAATCGGGGATACTCCAACCCCGTT
*
25905 ATTTTTGAGGGGATACTTCAA-TT-TT
131 ATTTCTGAGGGGATACTTCAACTTATT
*
25930 TTTATTT-TCAAAACACCAATTTTTCACCATCGGGGATACTCCAGCCTCGTTATTTTC-AAGGAG
1 TTTATTTCT-AAAACACCAATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTCGAAGG-G
* * *
25993 ATACTCTAACCCTGATTTTATTTCTAAAACACTAATTTTCTACAATCGAGGATACTCCAACCCCA
64 ATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTTCTACAATCGGGGATACTCCAACCCCG
* **
26058 TTATTTCTG-GGAGAATTTTTCAACCTTGATT
129 TTATTTCTGAGG-GGATACTTCAA-CTT-ATT
* * ** * *
26089 TTTATTTCTAAAACACCGATTTTTCACAATCGAAGATATTCCAACCTTGTTATTTTCGAAGGGAT
1 TTTATTTCTAAAACACCAATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTCGAAGGGAT
* * * *
26154 ACTCCAACCCCAGTTTTTATTTCTAAAACACTAATTTTTTACAATCGGGGATACTCCAACCCTGT
66 ACTCCAA-CCCTGATTTTATTTCTAAAACACTAATTTTCTACAATCGGGGATACTCCAACCCCGT
*
26219 TATTTCTGAGGGGATACTCCAAC
130 TATTTCTGAGGGGATACTTCAAC
26242 CCTGGTATAT
Statistics
Matches: 263, Mismatches: 38, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
154 7 0.03
155 121 0.46
157 2 0.01
159 60 0.23
160 71 0.27
161 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (157 bp):
TTTATTTCTAAAACACCAATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTCGAAGGGAT
ACTCCAACCCTGATTTTATTTCTAAAACACTAATTTTCTACAATCGGGGATACTCCAACCCCGTT
ATTTCTGAGGGGATACTTCAACTTATT
Found at i:26240 original size:28 final size:29
Alignment explanation
Indices: 26200--26254 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
26190 TTTTACAATC
*
26200 GGGGATACTCCAACCCTGTTAT-TTCTGA
1 GGGGATACTCCAACCCTGGTATATTCTGA
26228 GGGGATACTCCAACCCTGGTATATTCT
1 GGGGATACTCCAACCCTGGTATATTCT
26255 AACTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (29 bp):
GGGGATACTCCAACCCTGGTATATTCTGA
Found at i:26243 original size:80 final size:79
Alignment explanation
Indices: 25775--26245 Score: 411
Period size: 80 Copynumber: 6.0 Consensus size: 79
25765 CATTGATGTA
* *** * * * *
25775 TTTATTTCTAAAATATTGATTTTCCACCATCGGGGATACTCCAA-CCTCGTTAATTCCGAAGGGA
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCCT-GTTATTTCTGAGGGGA
* *
25839 TACTCCAACTCTGAT
65 TACTCCAACCCTGTT
* * * *
25854 TTTATTTTTAAAACACCAATTTTCCACAATCGGGGATATTCCAACCCCGTTATTTTTGAGGGGAT
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGAT
* *
25919 ACTTCAA---TTTT
66 ACTCCAACCCTGTT
* * * * *
25930 TTTATTT-TCAAAACACCAATTTTTCACCATCGGGGATACTCC-AGCCTCGTTATTT-TCAAGGA
1 TTTATTTCT-AAAACACCAATTTTCCACAATCGGGGATACTCCAACCCT-GTTATTTCT-GAGGG
* *
25992 GATACTCTAACCCTGAT
63 GATACTCCAACCCTGTT
* * * ** *
26009 TTTATTTCTAAAACACTAATTTTCTACAATCGAGGATACTCCAACCCCATTATTTCTG-GGAGAA
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGG-GGA
** * *
26073 TTTTTCAACCTTGATT
65 TACTCCAACCCTG-TT
* * ** * * *
26089 TTTATTTCTAAAACACCGATTTTTCACAATCGAAGATATTCCAACCTTGTTATTT-TCGAAGGGA
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCCTGTTATTTCT-GAGGGGA
*
26153 TACTCCAACCCCAGTT
65 TACTCCAA-CCCTGTT
* **
26169 TTTATTTCTAAAACACTAATTTTTTACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGAT
1 TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGAT
26234 ACTCCAACCCTG
66 ACTCCAACCCTG
26246 GTATATTCTA
Statistics
Matches: 308, Mismatches: 68, Indels: 32
0.75 0.17 0.08
Matches are distributed among these distances:
75 5 0.02
76 57 0.19
78 2 0.01
79 113 0.37
80 126 0.41
81 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
TTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCCAACCCTGTTATTTCTGAGGGGAT
ACTCCAACCCTGTT
Found at i:27273 original size:51 final size:51
Alignment explanation
Indices: 27183--27332 Score: 202
Period size: 51 Copynumber: 3.0 Consensus size: 51
27173 TTAAAAATAC
* *
27183 TATTTAAAAATAATAAAAAATT-AAAAATATTTTATATTAAATTTTAAATTAT
1 TATTTAAAAATAAT--AAAATTAAAAAATATTTTATATTAAATCTTGAATTAT
*
27235 TATTTAAAAATAATAAAATTAAAAAATATTTTATATTAAATCTCGAATTAT
1 TATTTAAAAATAATAAAATTAAAAAATATTTTATATTAAATCTTGAATTAT
* *
27286 TAGTTAAAAATTATAAAA-TAAAAAA-A--TTATATTAAATCTTGAATTAT
1 TATTTAAAAATAATAAAATTAAAAAATATTTTATATTAAATCTTGAATTAT
27333 AATAAATAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
47 20 0.22
49 1 0.01
50 13 0.14
51 43 0.47
52 14 0.15
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (51 bp):
TATTTAAAAATAATAAAATTAAAAAATATTTTATATTAAATCTTGAATTAT
Found at i:30840 original size:21 final size:21
Alignment explanation
Indices: 30801--30840 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30791 ATTAAAAAAT
**
30801 TATTTTATAAATATTTTTATA
1 TATTTTATAAATAAATTTATA
*
30822 TATTTTATAACTAAATTTA
1 TATTTTATAAATAAATTTA
30841 AATAAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAAATAAATTTATA
Found at i:32707 original size:20 final size:19
Alignment explanation
Indices: 32682--32730 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
32672 CTCATTTGTG
*
32682 TCGATACATGTCAAAATGTA
1 TCGATACATG-CAAAATATA
* *
32702 TCGATATAATGCACAATATA
1 TCGATA-CATGCAAAATATA
32722 TCGATACAT
1 TCGATACAT
32731 CTAGTTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (19 bp):
TCGATACATGCAAAATATA
Found at i:32771 original size:92 final size:92
Alignment explanation
Indices: 32647--32823 Score: 257
Period size: 92 Copynumber: 1.9 Consensus size: 92
32637 CTGTTGGTAG
* * ** *
32647 TAGTAGCTAAAGAAGTGCTGAAACCCTCATTTGTGTCGATACATGTCAAAATGTATCGATATAAT
1 TAGTAGCTAAAGAAATGCTGAAACCCTCATTTGTATCGATACACATCAAAATGTATCGATACAAT
*
32712 GCACAATATATCGATACATCTAGTTAA
66 ACACAATATATCGATACATCTAGTTAA
* *
32739 TAGTAGCTAAAGAAAT-CTTGAAACCCTTATTTGTATCGATACACATGAAAATGTATCGATACAA
1 TAGTAGCTAAAGAAATGC-TGAAACCCTCATTTGTATCGATACACATCAAAATGTATCGATACAA
*
32803 TACACAATATATTGATACATC
65 TACACAATATATCGATACATC
32824 CCTAAATGTA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
91 1 0.01
92 74 0.99
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (92 bp):
TAGTAGCTAAAGAAATGCTGAAACCCTCATTTGTATCGATACACATCAAAATGTATCGATACAAT
ACACAATATATCGATACATCTAGTTAA
Found at i:39013 original size:20 final size:20
Alignment explanation
Indices: 38988--39025 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38978 TATCACCTCT
38988 CACAAAATTCATCAAATTGC
1 CACAAAATTCATCAAATTGC
*
39008 CACAAATTTCATCAAATT
1 CACAAAATTCATCAAATT
39026 CTTCCTTCCA
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:0.45, C:0.24, G:0.03, T:0.29
Consensus pattern (20 bp):
CACAAAATTCATCAAATTGC
Found at i:44841 original size:51 final size:51
Alignment explanation
Indices: 44778--44892 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
44768 TTGAAGGATG
* ** * *
44778 TATCAATACATTTGGGTCAAAAATCCAAAATGTATCGATAC-ATGGAAAATA
1 TATCGATACATTTGAATCAAAAACCCAAAATGTATCGATACAAT-AAAAATA
* *
44829 TATCGATACATTTGAATTAAAAACCCAAAATGTATCGATACAATAAAAATG
1 TATCGATACATTTGAATCAAAAACCCAAAATGTATCGATACAATAAAAATA
*
44880 TATTGATACATTT
1 TATCGATACATTT
44893 TTTTCAGATT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 53 0.96
52 2 0.04
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.30
Consensus pattern (51 bp):
TATCGATACATTTGAATCAAAAACCCAAAATGTATCGATACAATAAAAATA
Found at i:44954 original size:20 final size:21
Alignment explanation
Indices: 44929--44979 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
44919 CAAGGTAAAA
44929 TATTGATACATTCACTT-ATG
1 TATTGATACATTCACTTGATG
*
44949 TATTGATACATTCACTTGTTG
1 TATTGATACATTCACTTGATG
*
44970 TATCGATACA
1 TATTGATACA
44980 GATTATAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (21 bp):
TATTGATACATTCACTTGATG
Found at i:46053 original size:104 final size:103
Alignment explanation
Indices: 45945--46485 Score: 398
Period size: 104 Copynumber: 5.2 Consensus size: 103
45935 CAATATACTA
* * * * *
45945 ATTCAAGGCCAGTGATATTAGTCTTAAAGATAATAAATGTGCTAATATGCTAATTCAAGGTTAGC
1 ATTCAAGGCCAGCGACATTGGTCTTAAAGATAATAAAAGTGCTAATATGCTAATTCAAGGTTAGT
* * * *
46010 GATATTTAACTTTAAGATGATAAGGGTGCCAACATGTTG
66 GATATTCAACTTAAAGATGACAAGAGTGCCAA-ATGTTG
** * * * * *
46049 ATTCAAACCCAGCGACATCGGACTTAAAGATAATAAAAGGTGCTAATATGCTGATTTAAGGCTAG
1 ATTCAAGGCCAGCGACATTGGTCTTAAAGATAATAAAA-GTGCTAATATGCTAATTCAAGGTTAG
*
46114 TGATA-TCAGACTTAAAGATGACAAGAGTGTC-AATGTACTG
65 TGATATTCA-ACTTAAAGATGACAAGAGTGCCAAATGT--TG
* * * * *
46154 ATTCAAGGTCAACGACATTGGAT-TTAAAGATAATAAAAGTGCCAATATGCTCATTCAAGGTCAG
1 ATTCAAGGCCAGCGACATTGG-TCTTAAAGATAATAAAAGTGCTAATATGCTAATTCAAGGTTAG
** *
46218 TGATATTGGACTTAAATATGACAAGAGTGCC-AATGTGCTG
65 TGATATTCAACTTAAAGATGACAAGAGTGCCAAATGT--TG
* * * * ** * * **
46258 ATTCAAGGCCAGCAACATTTGACTTAAAGATGATAAAAAGTG-TCAATATATTGATTTAAGGCCA
1 ATTCAAGGCCAGCGACATTGGTCTTAAAGATAAT-AAAAGTGCT-AATATGCTAATTCAAGGTTA
* * ** * *
46322 ATGATTTTGGACTTAAAGATGACACGAGTGCCAATGTGTTG
64 GTGATATTCAACTTAAAGATGACAAGAGTGCCAA-ATGTTG
* * * *** * **
46363 -GTCAAGGTCAGGGACATTAAACTTAAAGATAATAAAAAATGCTAATATG-TAGATTCAAGGCCA
1 ATTCAAGGCCAGCGACATTGGTCTTAAAGATAAT-AAAAGTGCTAATATGCTA-ATTCAAGGTTA
* *
46426 GTGATATT-AGACTTAAAAATAACAAGAGTGCC-AATGTACTG
64 GTGATATTCA-ACTTAAAGATGACAAGAGTGCCAAATGT--TG
*
46467 ATTCAAGGCCAGCAACATT
1 ATTCAAGGCCAGCGACATT
46486 AGGCTTAGAA
Statistics
Matches: 348, Mismatches: 72, Indels: 33
0.77 0.16 0.07
Matches are distributed among these distances:
102 3 0.01
103 6 0.02
104 189 0.54
105 146 0.42
106 1 0.00
107 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (103 bp):
ATTCAAGGCCAGCGACATTGGTCTTAAAGATAATAAAAGTGCTAATATGCTAATTCAAGGTTAGT
GATATTCAACTTAAAGATGACAAGAGTGCCAAATGTTG
Found at i:46478 original size:52 final size:52
Alignment explanation
Indices: 45878--46478 Score: 357
Period size: 52 Copynumber: 11.5 Consensus size: 52
45868 GGTTTTGACT
* * * * * **
45878 AGTGTCAATGTGCTGTTTCAAGGCCAATGAAATTTGACTTAAAGATGGTAA-
1 AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
* * * *
45929 ATGTGCCAATATACTAATTCAAGGCCAGTGATATTAGTCTTAAAGATAATAA-
1 A-GTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
* * * ** * * *
45981 ATGTGCTAATATGCTAATTCAAGGTTAGCGATATTTA-ACTTTAAGATGATAAG
1 A-GTGCCAATGTGCTGATTCAAGGCCAGTGATA-TTAGACTTAAAGATAATAAG
* ** * ** * * ** *
46034 GGTGCCAACATGTTGATTCAAACCCAGCGACATCGGACTTAAAGATAATAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
* * * * * * *
46086 AGGTGCTAATATGCTGATTTAAGGCTAGTGATATCAGACTTAAAGATGACAAG
1 A-GTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
* * * ** * * * *
46139 AGTGTCAATGTACTGATTCAAGGTCAACGACATTGGATTTAAAGATAATAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
* * * * * * *
46191 AGTGCCAATATGCTCATTCAAGGTCAGTGATATTGGACTTAAATATGACAAG
1 AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
** * * * *
46243 AGTGCCAATGTGCTGATTCAAGGCCAGCAACATTTGACTTAAAGATGATAAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAAT-AAG
* * ** * * * * * * *
46296 AGTGTCAATATATTGATTTAAGGCCAATGATTTTGGACTTAAAGATGACACG
1 AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
* * * * * * *
46348 AGTGCCAATGTGTTG-GTCAAGGTCAGGGACATTAAACTTAAAGATAATAAAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAAT-AAG
* * * * *
46400 AATGCTAATATG-TAGATTCAAGGCCAGTGATATTAGACTTAAAAATAACAAG
1 AGTGCCAATGTGCT-GATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
*
46452 AGTGCCAATGTACTGATTCAAGGCCAG
1 AGTGCCAATGTGCTGATTCAAGGCCAG
46479 CAACATTAGG
Statistics
Matches: 409, Mismatches: 131, Indels: 19
0.73 0.23 0.03
Matches are distributed among these distances:
51 25 0.06
52 276 0.67
53 108 0.26
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (52 bp):
AGTGCCAATGTGCTGATTCAAGGCCAGTGATATTAGACTTAAAGATAATAAG
Found at i:46485 original size:209 final size:209
Alignment explanation
Indices: 45967--46485 Score: 546
Period size: 209 Copynumber: 2.5 Consensus size: 209
45957 TGATATTAGT
** * * ** * * * * *
45967 CTTAAAGATAATAAATGTGCTAATATGCTAATTCAAGGTTAGCGATATTTA-ACTTTAAGATGAT
1 CTTAAAGATAATAAAAATGCCAATATGCTCATTCAAGGCCAGTGATA-TTAGACTTAAAAATAAC
* ** * ** *
46031 AAGGGTGCCAACATGT--TGATTCAAACCCAGCGACATCGGACTTAAAGATAATAAAAGGTGCTA
65 AAGAGTGCC-A-ATGTACTGATTCAAGGCCAGCAACATTTGACTTAAAGATAATAAAAAGTGCTA
* * * * *
46094 ATATGCTGATTTAAGGCTAGTGATATCAGACTTAAAGATGACAAGAGTGTCAATGTACTGATTCA
128 ATATACTGATTTAAGGCCAATGATATCAGACTTAAAGATGACAAGAGTGCCAATGTACTGAGTCA
**
46159 AGGTCAACGACATTGGA
193 AGGTCAACGACATTAAA
* * * * * *
46176 TTTAAAGATAATAAAAGTGCCAATATGCTCATTCAAGGTCAGTGATATTGGACTTAAATATGACA
1 CTTAAAGATAATAAAAATGCCAATATGCTCATTCAAGGCCAGTGATATTAGACTTAAAAATAACA
* *
46241 AGAGTGCCAATGTGCTGATTCAAGGCCAGCAACATTTGACTTAAAGATGATAAAAAGTG-TCAAT
66 AGAGTGCCAATGTACTGATTCAAGGCCAGCAACATTTGACTTAAAGATAATAAAAAGTGCT-AAT
* * ** * **
46305 ATATTGATTTAAGGCCAATGATTTTGGACTTAAAGATGACACGAGTGCCAATGTGTTG-GTCAAG
130 ATACTGATTTAAGGCCAATGATATCAGACTTAAAGATGACAAGAGTGCCAATGTACTGAGTCAAG
**
46369 GTCAGGGACATTAAA
195 GTCAACGACATTAAA
* *
46384 CTTAAAGATAATAAAAAATGCTAATATG-TAGATTCAAGGCCAGTGATATTAGACTTAAAAATAA
1 CTTAAAGATAAT-AAAAATGCCAATATGCT-CATTCAAGGCCAGTGATATTAGACTTAAAAATAA
46448 CAAGAGTGCCAATGTACTGATTCAAGGCCAGCAACATT
64 CAAGAGTGCCAATGTACTGATTCAAGGCCAGCAACATT
46486 AGGCTTAGAA
Statistics
Matches: 261, Mismatches: 43, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
207 4 0.02
208 32 0.12
209 225 0.86
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (209 bp):
CTTAAAGATAATAAAAATGCCAATATGCTCATTCAAGGCCAGTGATATTAGACTTAAAAATAACA
AGAGTGCCAATGTACTGATTCAAGGCCAGCAACATTTGACTTAAAGATAATAAAAAGTGCTAATA
TACTGATTTAAGGCCAATGATATCAGACTTAAAGATGACAAGAGTGCCAATGTACTGAGTCAAGG
TCAACGACATTAAA
Found at i:46722 original size:33 final size:33
Alignment explanation
Indices: 46501--46780 Score: 216
Period size: 33 Copynumber: 8.7 Consensus size: 33
46491 TAGAAGGAGA
* * *
46501 TGCCACCCACTTATGTGGGCTTTTG--AGAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
**
46532 TGCCACTGACTTGTGTGGGCTTTTG--AAAGGAT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGG-T
* *
46564 TGCCACCAACTTGTGTAGGCTTCTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
* *** * * *
46597 TGTCATTGACTCGTGGGGGC-TTT-AAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
* * * * * * *
46628 TGCCATCGACTTTTGTGAGTTTTTGAAAAATGA
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
* *
46661 TGCTACCAACTTGTGTGGGC-ATTG-AAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
* *
46692 TGCTACTAACTTGTGTGGGCTTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
* * * * *
46725 TGCCACCGACTTGTGTAGGCTTTTTAAAATGGA
1 TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
*
46758 TACCACCAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
46781 AAAAGGGTCA
Statistics
Matches: 194, Mismatches: 48, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
31 70 0.36
32 33 0.17
33 86 0.44
34 5 0.03
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (33 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAAAGGT
Found at i:46728 original size:97 final size:94
Alignment explanation
Indices: 46509--46786 Score: 248
Period size: 97 Copynumber: 2.9 Consensus size: 94
46499 GATGCCACCC
* * * * *
46509 ACTTATGTGGGCTTTTG--AGAGGTTGCCACTGACTTGTGTGGGCTTTTG-AAAGGATTGCCACC
1 ACTTGTGTGGGCTTTTGAAAAAGGTTGCCAC-GACTTGTGTGAGTTTTTGAAAATGA-TGCCACC
* * *
46571 AACTTGTGTAGGCTTCTGAAAAAGGTTGTCATTG
64 AACTTGTGTGGGC-T-TG-AAAAGGTTGTCACTA
* * * * *
46605 ACTCGTGGGGGC-TTT-AAAAGGGTTGCCATCGACTTTTGTGAGTTTTTGAAAAATGATGCTACC
1 ACTTGTGTGGGCTTTTGAAAAAGGTTGCCA-CGACTTGTGTGAGTTTTTG-AAAATGATGCCACC
46668 AACTTGTGTGGGCATTGAAAAGGTTG-CTACTA
64 AACTTGTGTGGGC-TTGAAAAGGTTGTC-ACTA
*
46700 ACTTGTGTGGGCTTTTGAAAAAGGTTGCCACCGACTTGTGT-AGGCTTTTT-AAAATGGATACCA
1 ACTTGTGTGGGCTTTTGAAAAAGGTTGCCA-CGACTTGTGTGA-G-TTTTTGAAAAT-GATGCCA
*
46763 CCAACTTGTGTGGGCTTTAAAAGG
62 CCAACTTGTGTGGGCTTGAAAAGG
46787 GTCATGAAAA
Statistics
Matches: 149, Mismatches: 22, Indels: 22
0.77 0.11 0.11
Matches are distributed among these distances:
94 1 0.01
95 24 0.16
96 52 0.35
97 62 0.42
98 10 0.07
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (94 bp):
ACTTGTGTGGGCTTTTGAAAAAGGTTGCCACGACTTGTGTGAGTTTTTGAAAATGATGCCACCAA
CTTGTGTGGGCTTGAAAAGGTTGTCACTA
Found at i:47714 original size:20 final size:20
Alignment explanation
Indices: 47691--47737 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
47681 CATTTCAAAC
*
47691 ATGTATTTATACATTCACTT
1 ATGTATTAATACATTCACTT
47711 ATGTATTAATACATTCACTT
1 ATGTATTAATACATTCACTT
47731 ATTGTAT
1 A-TGTAT
47738 CGATACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (20 bp):
ATGTATTAATACATTCACTT
Found at i:47743 original size:21 final size:20
Alignment explanation
Indices: 47699--47744 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
47689 ACATGTATTT
*
47699 ATACATTCACTTATGTATTA
1 ATACATTCACTTATGTATCA
*
47719 ATACATTCACTTATTGTATCG
1 ATACATTCACTTA-TGTATCA
47740 ATACA
1 ATACA
47745 AATTGTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (20 bp):
ATACATTCACTTATGTATCA
Found at i:49053 original size:13 final size:13
Alignment explanation
Indices: 49035--49060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49025 TACAGCAAGT
49035 ATGTATCGATACA
1 ATGTATCGATACA
49048 ATGTATCGATACA
1 ATGTATCGATACA
49061 CAAAAAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:50914 original size:27 final size:27
Alignment explanation
Indices: 50855--50967 Score: 115
Period size: 27 Copynumber: 4.1 Consensus size: 27
50845 ACTGAAAGTT
*
50855 TTTTTCAATTAAACTTTGTGCACAT-AAA
1 TTTTT-AATTAAACTTT-TACACATGAAA
*
50883 ATTTTAATTAAA-TTTTCACACATGAAA
1 TTTTTAATTAAACTTTT-ACACATGAAA
* *
50910 TTTTTAATCAAACTTTATACATATG-AA
1 TTTTTAATTAAACTTT-TACACATGAAA
* *
50937 TTTTTAATTAAACTTTTACATATGAAC
1 TTTTTAATTAAACTTTTACACATGAAA
50964 TTTT
1 TTTT
50968 ACATGAAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
25 1 0.01
26 16 0.22
27 42 0.58
28 13 0.18
29 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTTTAATTAAACTTTTACACATGAAA
Found at i:50966 original size:14 final size:14
Alignment explanation
Indices: 50920--50971 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
50910 TTTTTAATCA
50920 AACTTTATACATATG
1 AACTTT-TACATATG
* *
50935 AATTTTTA-AT-TA
1 AACTTTTACATATG
50947 AACTTTTACATATG
1 AACTTTTACATATG
50961 AACTTTTACAT
1 AACTTTTACAT
50972 GAAATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 8 0.26
13 4 0.13
14 14 0.45
15 5 0.16
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (14 bp):
AACTTTTACATATG
Found at i:50980 original size:27 final size:26
Alignment explanation
Indices: 50884--50981 Score: 106
Period size: 27 Copynumber: 3.7 Consensus size: 26
50874 GCACATAAAA
* *
50884 TTTTAATTAAATTTTCACACATGAAAT
1 TTTTAATTAAATTTTTACATATG-AAT
* *
50911 TTTTAATCAAACTTTATACATATGAAT
1 TTTTAATTAAA-TTTTTACATATGAAT
* *
50938 TTTTAATTAAACTTTTACATATGAAC
1 TTTTAATTAAATTTTTACATATGAAT
*
50964 TTTTACATGAAATTTTTA
1 TTTTA-ATTAAATTTTTA
50982 ATCTTTTAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 17 0.29
27 33 0.56
28 9 0.15
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTTAATTAAATTTTTACATATGAAT
Found at i:51477 original size:10 final size:11
Alignment explanation
Indices: 51447--51484 Score: 51
Period size: 10 Copynumber: 3.4 Consensus size: 11
51437 TTTGGAACTT
51447 GAGAAAAAAGAA
1 GAGAAAAAA-AA
51459 GATGAAAAAAAA
1 GA-GAAAAAAAA
51471 -AGAAAAAAAA
1 GAGAAAAAAAA
51481 GAGA
1 GAGA
51485 CGAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 4 0.17
12 4 0.17
13 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (11 bp):
GAGAAAAAAAA
Found at i:52463 original size:17 final size:17
Alignment explanation
Indices: 52441--52473 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52431 CTATTTAGTC
52441 ATGTCAAAATAATCATA
1 ATGTCAAAATAATCATA
52458 ATGTCAAAATAATCAT
1 ATGTCAAAATAATCAT
52474 TCGCTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (17 bp):
ATGTCAAAATAATCATA
Found at i:52610 original size:1 final size:1
Alignment explanation
Indices: 52604--52687 Score: 105
Period size: 1 Copynumber: 84.0 Consensus size: 1
52594 CCATAGTTAC
* * * * **
52604 GGGGGGGGGGGGGGGGGGGGTGGGTGGGCGGGGCGGGGGGGGGGGGGGGTTGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
*
52669 GGGGGGGGCGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGG
52688 CTCCTTACTT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.00, C:0.04, G:0.92, T:0.05
Consensus pattern (1 bp):
G
Found at i:52886 original size:19 final size:18
Alignment explanation
Indices: 52846--52887 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
52836 CCAACAAACA
52846 CAAAACATCAAACACCAAC
1 CAAAACATCAAACACC-AC
52865 CAAAACATACAAAACACC-C
1 CAAAACAT-C-AAACACCAC
52884 CAAA
1 CAAA
52888 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 13 0.62
20 1 0.05
21 7 0.33
ACGTcount: A:0.60, C:0.36, G:0.00, T:0.05
Consensus pattern (18 bp):
CAAAACATCAAACACCAC
Found at i:53036 original size:15 final size:14
Alignment explanation
Indices: 53018--53049 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
53008 CACAAGCCCA
53018 CAACAAACCACCAAC
1 CAACAAACCACC-AC
53033 CAACAAACCACCAC
1 CAACAAACCACCAC
53047 CAA
1 CAA
53050 AATACCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (14 bp):
CAACAAACCACCAC
Found at i:53242 original size:1 final size:1
Alignment explanation
Indices: 53236--53346 Score: 150
Period size: 1 Copynumber: 111.0 Consensus size: 1
53226 AAAACCCACA
* *
53236 CCCCCCCCCACCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* * * * * *
53301 CCACCACCCCCCCACCCCCCCACCCTCCCCCCCCCCCCCACCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
53347 ACACCCCTTA
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.06, C:0.93, G:0.00, T:0.01
Consensus pattern (1 bp):
C
Found at i:53251 original size:8 final size:8
Alignment explanation
Indices: 53238--53409 Score: 138
Period size: 8 Copynumber: 20.9 Consensus size: 8
53228 AACCCACACC
53238 CCCCCCCA
1 CCCCCCCA
*
53246 CCCCCCCCC
1 -CCCCCCCA
53255 CCCCCCCA
1 CCCCCCCA
53263 CCCCCCC-
1 CCCCCCCA
53270 CCCCCCC-
1 CCCCCCCA
53277 CCCCCCC-
1 CCCCCCCA
53284 CCCCCCC-
1 CCCCCCCA
53291 CCCCCCC-
1 CCCCCCCA
53298 CCCCCACCA
1 CCCCC-CCA
53307 CCCCCCCA
1 CCCCCCCA
53315 CCCCCCCA
1 CCCCCCCA
*
53323 CCCTCCCCCC
1 -CC-CCCCCA
53333 CCCCCCCA
1 CCCCCCCA
53341 CCCCCCACA
1 CCCCCC-CA
53350 CCCCTTACCCA
1 CCCC---CCCA
* *
53361 ACCACCCA
1 CCCCCCCA
* ** *
53369 CACTACAA
1 CCCCCCCA
*
53377 CCCACCCA
1 CCCCCCCA
53385 CCCCCCACA
1 CCCCCC-CA
53394 CACCCCCCA
1 C-CCCCCCA
53403 CCCCCCC
1 CCCCCCC
53410 CTCCTTTACC
Statistics
Matches: 137, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
7 33 0.24
8 60 0.44
9 28 0.20
10 10 0.07
11 4 0.03
12 2 0.01
ACGTcount: A:0.14, C:0.84, G:0.00, T:0.02
Consensus pattern (8 bp):
CCCCCCCA
Found at i:53299 original size:44 final size:44
Alignment explanation
Indices: 53234--53353 Score: 181
Period size: 44 Copynumber: 2.8 Consensus size: 44
53224 CTAAAACCCA
* *
53234 CACCCCCCCCCACCCCCCCCCCCCCC-CCACCCCCCCCCCCCCC
1 CACCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCCACCCCCC
*
53277 CCCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCCACCCCCC
1 CACCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCCACCCCCC
* *
53321 CACCCTCCCCCCCCCCCCCACCCCCCA-CACCCC
1 CACCCCCCCCCCCCCCCCCCCCCCCCACCACCCC
53354 TTACCCAACC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
43 30 0.43
44 40 0.57
ACGTcount: A:0.08, C:0.91, G:0.00, T:0.01
Consensus pattern (44 bp):
CACCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCCACCCCCC
Found at i:53369 original size:46 final size:44
Alignment explanation
Indices: 53234--53409 Score: 96
Period size: 47 Copynumber: 3.8 Consensus size: 44
53224 CTAAAACCCA
*
53234 CACCC-CCCCCCACCCCCCC-CCCCCCCCCACCCCCCC--CC-CC
1 CACCCTCCCCCC-CCCCCCCACCCCCCACCACCCCCCCAACCACC
* * * * * * *
53274 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCCACCCCCC
1 CACCCTCCCCCCCCCCCCCACCCCCCACCACCCC---CCCAACCACC
53321 CACCCTCCCCCCCCCCCCCACCCCCCA-CACCCCTTACCCAACCACC
1 CACCCTCCCCCCCCCCCCCACCCCCCACCACCCC---CCCAACCACC
*
53367 CACACTACAACCCACCCACCCCCCACACACCCC-CCACCCCCCC
1 CACCCT-C--CCC-CCC-CCCCCCAC-C-CCCCACCACCCCCCC
53410 CTCCTTTACC
Statistics
Matches: 107, Mismatches: 13, Indels: 22
0.75 0.09 0.15
Matches are distributed among these distances:
40 11 0.10
41 19 0.18
44 3 0.03
46 20 0.19
47 26 0.24
49 3 0.03
50 6 0.06
51 8 0.07
52 1 0.01
53 10 0.09
ACGTcount: A:0.14, C:0.84, G:0.00, T:0.02
Consensus pattern (44 bp):
CACCCTCCCCCCCCCCCCCACCCCCCACCACCCCCCCAACCACC
Found at i:53410 original size:11 final size:11
Alignment explanation
Indices: 53234--53410 Score: 113
Period size: 11 Copynumber: 16.6 Consensus size: 11
53224 CTAAAACCCA
53234 CACCCCCC-CC
1 CACCCCCCACC
53244 CACCCCCC-CC
1 CACCCCCCACC
*
53254 CCCCCCCCACC
1 CACCCCCCACC
53265 C-CCCCCC-CC
1 CACCCCCCACC
*
53274 C-CCCCCCCCC
1 CACCCCCCACC
* *
53284 CCCCCCCCCCC
1 CACCCCCCACC
*
53295 CCCCCCCCA-C
1 CACCCCCCACC
53305 CACCCCCCCACC
1 CA-CCCCCCACC
* *
53317 CCCCCACCCTCC
1 CACCC-CCCACC
*
53329 C-CCCCCCCCC
1 CACCCCCCACC
53339 CACCCCCCA--
1 CACCCCCCACC
**
53348 CACCCCTTACC
1 CACCCCCCACC
*
53359 CAACCACCCACAC
1 C-ACCCCCCAC-C
* **
53372 TACAACCCACC
1 CACCCCCCACC
*
53383 CACCCCCCACA
1 CACCCCCCACC
53394 CACCCCCCACC
1 CACCCCCCACC
53405 C-CCCCC
1 CACCCCC
53411 TCCTTTACCA
Statistics
Matches: 137, Mismatches: 19, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
9 16 0.12
10 39 0.28
11 59 0.43
12 22 0.16
13 1 0.01
ACGTcount: A:0.14, C:0.84, G:0.00, T:0.02
Consensus pattern (11 bp):
CACCCCCCACC
Done.