Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1481
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: 56718
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:67 original size:20 final size:20
Alignment explanation
Indices: 39--113 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
29 TCATACCCTG
39 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
59 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
79 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
99 ATGTATCGATACATT
1 ATGTATCGATACATT
114 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:106 original size:40 final size:39
Alignment explanation
Indices: 39--116 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
29 TCATACCCTG
* *
39 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
79 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
117 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:14152 original size:10 final size:10
Alignment explanation
Indices: 14137--14208 Score: 81
Period size: 10 Copynumber: 6.8 Consensus size: 10
14127 TTACACCCAA
14137 AAAAAAAAAC
1 AAAAAAAAAC
14147 AAAAAAAAACAC
1 -AAAAAAAA-AC
14159 AAAAAAAAAC
1 AAAAAAAAAC
14169 AAAACAAAAAAC
1 -AAA-AAAAAAC
*
14181 AAAAAAAAAG
1 AAAAAAAAAC
* *
14191 AAAAAATAGC
1 AAAAAAAAAC
14201 AAAAAAAA
1 AAAAAAAA
14209 TAGAAGGGTC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
10 22 0.42
11 22 0.42
12 9 0.17
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:14158 original size:26 final size:27
Alignment explanation
Indices: 14135--14208 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
14125 CTTTACACCC
14135 AAAAAAA-AAAACAAAAAAAAACACAA
1 AAAAAAACAAAACAAAAAAAAACACAA
14161 AAAAAAACAAAACAAAAAACAAA-A-AA
1 AAAAAAACAAAACAAAAAA-AAACACAA
*
14187 AAAGAAAA-AATAGCAAAAAAAA
1 AAA-AAAACAA-AACAAAAAAAA
14209 TAGAAGGGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
26 16 0.37
27 24 0.56
28 3 0.07
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.01
Consensus pattern (27 bp):
AAAAAAACAAAACAAAAAAAAACACAA
Found at i:14165 original size:22 final size:21
Alignment explanation
Indices: 14137--14196 Score: 93
Period size: 22 Copynumber: 2.8 Consensus size: 21
14127 TTACACCCAA
14137 AAAAAAAAACAAAAAAAAACAC
1 AAAAAAAAACAAAAAAAAA-AC
14159 AAAAAAAAACAAAACAAAAAAC
1 AAAAAAAAACAAAA-AAAAAAC
*
14181 AAAAAAAAAGAAAAAA
1 AAAAAAAAACAAAAAA
14197 TAGCAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 2 0.06
22 29 0.81
23 5 0.14
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAAAAAC
Found at i:14208 original size:1 final size:1
Alignment explanation
Indices: 14135--14196 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
14125 CTTTACACCC
* * * * * * *
14135 AAAAAAAAAAACAAAAAAAAACACAAAAAAAAACAAAACAAAAAACAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14197 TAGCAAAAAA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:14211 original size:12 final size:11
Alignment explanation
Indices: 14136--14189 Score: 83
Period size: 12 Copynumber: 4.8 Consensus size: 11
14126 TTTACACCCA
14136 AAAAAAAAAAC
1 AAAAAAAAAAC
14147 -AAAAAAAAAC
1 AAAAAAAAAAC
14157 ACAAAAAAAAAC
1 A-AAAAAAAAAC
14169 AAAACAAAAAAC
1 AAAA-AAAAAAC
14181 AAAAAAAAA
1 AAAAAAAAA
14190 GAAAAAATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.25
11 8 0.20
12 22 0.55
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:15982 original size:32 final size:30
Alignment explanation
Indices: 15428--16395 Score: 885
Period size: 32 Copynumber: 32.2 Consensus size: 30
15418 TGTTCATCCC
15428 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
15457 TTTCAAAACCCACA-AA-TCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
* *
15486 TTTCAAAG-CC-CACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* *
15514 TTTCAAAG-CC-CACAAGTCAATGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
15542 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
15571 TTTCAAAGCCCACA-AA-TCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
15600 TTTCAAAG-CC-CACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* *
15628 TTTCAAAG-CC-CACAACTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
15656 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
15685 TTTCAAAG-CC-CACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
*
15713 TTTCAAAG-CC-CACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
* *
15742 TTTCAAAG-CC-CACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* *
15770 TTTCAAAG-CC-CACAAGTCAGTGGTACTCC
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
15799 TTTCAAAG-CC-CACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
15828 TTTCAAAGCCCACA-AA-TCAGTGGCGCTCT
1 TTTCAAAGCCCACACAAGTCAGTGGCAC-CT
*
15857 TTTCAAAG-CC-CACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* *
15885 TTTCAAAG-CC-CACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
* * *
15913 TTTCAGAG-CC-CACAAGTTAGTGGCA-TT
1 TTTCAAAGCCCACACAAGTCAGTGGCACCT
*
15940 CTTTCAAAGCCCACACAAGTCGGTGGCAACCAT
1 -TTTCAAAGCCCACACAAGTCAGTGGC-ACC-T
*
15973 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
*
16005 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* * *
16037 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* * *
16069 TTCCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-AC-CT
* *
16101 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
*
16133 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* *
16165 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* *
16197 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* *
16229 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* * *
16261 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* * *
16293 TTCCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-AC-CT
* *
16325 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
* **
16357 TTTAAAAGCCCATGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCAGTGGC-A-CCT
16389 TTTCAAA
1 TTTCAAA
16396 TCACCATATT
Statistics
Matches: 866, Mismatches: 46, Indels: 51
0.90 0.05 0.05
Matches are distributed among these distances:
27 6 0.01
28 229 0.26
29 198 0.23
30 24 0.03
31 9 0.01
32 395 0.46
33 5 0.01
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (30 bp):
TTTCAAAGCCCACACAAGTCAGTGGCACCT
Found at i:16951 original size:20 final size:20
Alignment explanation
Indices: 16923--16997 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
16913 TCATACCCTG
16923 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
16943 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
16963 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
16983 ATGTATCGATACATT
1 ATGTATCGATACATT
16998 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:16990 original size:40 final size:39
Alignment explanation
Indices: 16923--17000 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
16913 TCATACCCTG
* *
16923 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
16963 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
17001 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:17943 original size:21 final size:21
Alignment explanation
Indices: 17917--17959 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17907 CCATGCATTT
17917 TTTTTTATTATGTTTCATGCA
1 TTTTTTATTATGTTTCATGCA
17938 TTTTTTATTATGTTTCATGCA
1 TTTTTTATTATGTTTCATGCA
17959 T
1 T
17960 ATTTAACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTTTTATTATGTTTCATGCA
Found at i:17970 original size:20 final size:21
Alignment explanation
Indices: 17926--17970 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
17916 TTTTTTTATT
* **
17926 ATGTTTCATGCATTTTTTATT
1 ATGTTTCATGCATTATTTAAC
17947 ATGTTTCATGCA-TATTTAAC
1 ATGTTTCATGCATTATTTAAC
17967 ATGT
1 ATGT
17971 CCAGCATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (21 bp):
ATGTTTCATGCATTATTTAAC
Found at i:23378 original size:146 final size:145
Alignment explanation
Indices: 23089--23386 Score: 515
Period size: 146 Copynumber: 2.0 Consensus size: 145
23079 AAGATTATGG
*
23089 ATTGTTCGTTCCGAAATTACGGTCTTGCAGTTGATAACATAATCGATGCTTGATTTATCGAAGTT
1 ATTGTTCGTTCCGAAATTACGGTCTTGCAGTTGATAACATAATCGATGCTCGATTTATCGAAGTT
23154 AATGTAGAATTCTTGACAGAAAGTCCACGGGAGAAGATCTGTTTTGGGCAAGTCGAGGAAGAGGA
66 AATGTAGAATTCTTGACAGAAAGTCCACGGGAGAAGATCTGTTTTGGGCAAGTCGAGGAAGAGGA
23219 GGAGGTAGCTTTGGA
131 GGAGGTAGCTTTGGA
* *
23234 ATTGTTCGTTCCGAAATTATGGTCTTGCAGTTGATGACATAATCGATGCTCGATTTATCGAAGTT
1 ATTGTTCGTTCCGAAATTACGGTCTTGCAGTTGATAACATAATCGATGCTCGATTTATCGAAGTT
* * * *
23299 AATGTCAGAATTCTTGACAGAAAGTCCATGGGGGAAGATCTGTTTTGGGCAATTCGAGGAAGTGG
66 AATGT-AGAATTCTTGACAGAAAGTCCACGGGAGAAGATCTGTTTTGGGCAAGTCGAGGAAGAGG
23364 AGGAGGTAGCTTTGGA
130 AGGAGGTAGCTTTGGA
*
23380 ATCGTTC
1 ATTGTTC
23387 TGGCATGGAA
Statistics
Matches: 144, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
145 67 0.47
146 77 0.53
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (145 bp):
ATTGTTCGTTCCGAAATTACGGTCTTGCAGTTGATAACATAATCGATGCTCGATTTATCGAAGTT
AATGTAGAATTCTTGACAGAAAGTCCACGGGAGAAGATCTGTTTTGGGCAAGTCGAGGAAGAGGA
GGAGGTAGCTTTGGA
Found at i:24560 original size:7 final size:7
Alignment explanation
Indices: 24548--24581 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
24538 CTATGCCATT
24548 AAATTTA
1 AAATTTA
24555 AAATTTA
1 AAATTTA
*
24562 AATTTTA
1 AAATTTA
*
24569 ATATTTA
1 AAATTTA
24576 AAATTT
1 AAATTT
24582 TTTTCTCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTA
Found at i:25161 original size:15 final size:16
Alignment explanation
Indices: 25143--25176 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
25133 AAAATGCAGG
25143 AAAACAAAA-AAAAAA
1 AAAACAAAATAAAAAA
25158 AAAACAAAATTAAAAAA
1 AAAACAAAA-TAAAAAA
25175 AA
1 AA
25177 GGAATTTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAACAAAATAAAAAA
Found at i:26371 original size:25 final size:25
Alignment explanation
Indices: 26343--26393 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
26333 TTAAGATAAC
26343 CATATGCTGATAGCCTGATATCCGA
1 CATATGCTGATAGCCTGATATCCGA
26368 CATATGCTGATAGCCTGATATCCGA
1 CATATGCTGATAGCCTGATATCCGA
26393 C
1 C
26394 TGCAACATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (25 bp):
CATATGCTGATAGCCTGATATCCGA
Found at i:30346 original size:2 final size:2
Alignment explanation
Indices: 30339--30370 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30329 GTTTAAAGGC
30339 GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30371 TAAGAATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:32818 original size:21 final size:22
Alignment explanation
Indices: 32789--32831 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
32779 AATAAGAATC
*
32789 CTGGGTTTTTTTT-TTCTTTTT
1 CTGGATTTTTTTTATTCTTTTT
*
32810 CTGGATTTTTTTTATTTTTTTT
1 CTGGATTTTTTTTATTCTTTTT
32832 TTCCTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.05, C:0.07, G:0.12, T:0.77
Consensus pattern (22 bp):
CTGGATTTTTTTTATTCTTTTT
Found at i:32842 original size:25 final size:23
Alignment explanation
Indices: 32794--32842 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
32784 GAATCCTGGG
*
32794 TTTTTTTTTTCTTTTTCTGGATT
1 TTTTTTTTTTCTTTTTCTGAATT
*
32817 TTTTTTATTTTTTTTTTCCTGAATT
1 TTTTTT-TTTTCTTTTT-CTGAATT
32842 T
1 T
32843 GGGCGACCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 9 0.41
25 7 0.32
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.78
Consensus pattern (23 bp):
TTTTTTTTTTCTTTTTCTGAATT
Found at i:33206 original size:20 final size:19
Alignment explanation
Indices: 33165--33226 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
33155 AATATTTATT
33165 TAAAATTAAATTTTAAATAA
1 TAAAATT-AATTTTAAATAA
33185 TAAAATTAATTATATAAA-AA
1 TAAAATTAATT-T-TAAATAA
* *
33205 TATAAAATAA-TTTAAATTA
1 TA-AAATTAATTTTAAATAA
33224 TAA
1 TAA
33227 TTTAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 5 0.14
19 8 0.22
20 13 0.36
21 10 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTAATTTTAAATAA
Found at i:33449 original size:30 final size:29
Alignment explanation
Indices: 33413--33469 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
33403 ATATTATTAA
*
33413 TTTTTAATA-AATTAATATTTTTATTTATAT
1 TTTTTAATATAA-TAAT-TTTATATTTATAT
33443 TTTTTAATATAATAATTTTATATTTAT
1 TTTTTAATATAATAATTTTATATTTAT
33470 TAATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTTAATATAATAATTTTATATTTATAT
Found at i:33452 original size:22 final size:21
Alignment explanation
Indices: 33424--33497 Score: 69
Period size: 23 Copynumber: 3.4 Consensus size: 21
33414 TTTTAATAAA
*
33424 TTAATATTTTTATTTATATTTT
1 TTAATA-TATTATTTATATTTT
* *
33446 TTAATATAATAATTTTATATTTA
1 TTAATAT-ATTA-TTTATATTTT
*
33469 TTAATA-AATATTTATATTTT
1 TTAATATATTATTTATATTTT
33489 TTACATATA
1 TTA-ATATA
33498 AAATAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.29
21 6 0.14
22 9 0.21
23 15 0.36
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAATATATTATTTATATTTT
Found at i:33466 original size:23 final size:21
Alignment explanation
Indices: 33434--33498 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 21
33424 TTAATATTTT
33434 TATTTATATTTTTTAATATAA
1 TATTTATATTTTTTAATATAA
*
33455 TAATTTTATATTTATTAATA-AA
1 T-A-TTTATATTTTTTAATATAA
33477 TATTTATATTTTTTACATATAA
1 TATTTATATTTTTTA-ATATAA
33499 AATAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 12 0.32
21 5 0.13
22 6 0.16
23 15 0.39
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTATATTTTTTAATATAA
Found at i:33478 original size:27 final size:27
Alignment explanation
Indices: 33412--33479 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
33402 AATATTATTA
*
33412 ATTT-TTAATAAAT-TAATATTTTTAT
1 ATTTATTAATAAATATAATAATTTTAT
** *
33437 -TTATATTTTTTAATATAATAATTTTAT
1 ATT-TATTAATAAATATAATAATTTTAT
33464 ATTTATTAATAAATAT
1 ATTTATTAATAAATAT
33480 TTATATTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
24 2 0.06
25 1 0.03
26 6 0.19
27 21 0.66
28 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTATTAATAAATATAATAATTTTAT
Found at i:33626 original size:32 final size:32
Alignment explanation
Indices: 33590--33651 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
33580 AATATGATAT
33590 TATATTAATATTATTTTAATTTTTTAAAAATA
1 TATATTAATATTATTTTAATTTTTTAAAAATA
*
33622 TATATTAATGTTATTTTAATTTTTTAAAAA
1 TATATTAATATTATTTTAATTTTTTAAAAA
33652 ATAAATGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
TATATTAATATTATTTTAATTTTTTAAAAATA
Found at i:34960 original size:2 final size:2
Alignment explanation
Indices: 34953--34997 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
34943 AAGGTTATTT
34953 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34995 AG A
1 AG A
34998 AGGGATGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37971 original size:25 final size:25
Alignment explanation
Indices: 37937--37987 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
37927 TCACTTGAAA
37937 GTTATTTTATTCCAATGTTGGTTGT
1 GTTATTTTATTCCAATGTTGGTTGT
37962 GTTATTTTATTCCAATGTTGGTTGT
1 GTTATTTTATTCCAATGTTGGTTGT
37987 G
1 G
37988 AACTCGCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.22, T:0.55
Consensus pattern (25 bp):
GTTATTTTATTCCAATGTTGGTTGT
Found at i:38370 original size:19 final size:19
Alignment explanation
Indices: 38346--38385 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
38336 CAGACATGAG
38346 ATACAAGTATGCGTTTGAT
1 ATACAAGTATGCGTTTGAT
38365 ATACAAGTATGCGTTTGAT
1 ATACAAGTATGCGTTTGAT
38384 AT
1 AT
38386 GAGTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (19 bp):
ATACAAGTATGCGTTTGAT
Found at i:40861 original size:40 final size:40
Alignment explanation
Indices: 40806--40892 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
40796 GAAGTATGCA
*
40806 TTGATCTGTGCTTGTTGATGACTCTTAGTTACTTATGATC
1 TTGATCTGTGCTTGTTGATGACTCTTAGTTAATTATGATC
* *
40846 TTGATCTGTGGTTGTTGATGACTCTTAGTTAATTATGATT
1 TTGATCTGTGCTTGTTGATGACTCTTAGTTAATTATGATC
40886 TTGATCT
1 TTGATCT
40893 TTGGAACAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.49
Consensus pattern (40 bp):
TTGATCTGTGCTTGTTGATGACTCTTAGTTAATTATGATC
Found at i:43629 original size:224 final size:217
Alignment explanation
Indices: 43230--43668 Score: 569
Period size: 224 Copynumber: 2.0 Consensus size: 217
43220 ACTGGAAGTA
* *****
43230 GGTTTTGGAATCTTAATATTATCATACTAGGACCAGGAGAATATTTTACACTTTCTTTTGAGTTT
1 GGTTTTGGAATCTTAATATGATCATACTAGGACCAGGAGAATATTTTACACTTTAAAAAGAGTTT
43295 TCATCATGGCAAAACATTCTACATGTATTTTTTTTTTTGTGTGTGTATTATGCGTACATGCTGGA
66 TCATCATGGCAAAACATTCTACATGTATTTTTTTTTTTGTGTGTGTATTATGCGTACATGCTGGA
43360 AATCCCCTGGGGGAAGCAGATAAATAGATGCTTATATTGGTTTTATTGTAATGTAGCCTAGAGTG
131 AATCCCCTGGGGGAAGCAGATAAATAGATGCTTATATTGGTTTTATTGTAATGTAGCCTAGAGTG
43425 GTACAACTACCTTGGTTTTATT
196 GTACAACTACCTTGGTTTTATT
*
43447 GGTTTTGGAATCTTAATATGATCATAGC-CGGACCAGGAGAATATTTTACAC-TTAAAAAGAGTT
1 GGTTTTGGAATCTTAATATGATCATA-CTAGGACCAGGAGAATATTTTACACTTTAAAAAGAGTT
* ** * *
43510 TTTATTGTGGCAAAACTTTCTAATAGTTCATGTATTTTTTTTTCTTGTTTGGTGTATTTATGCGT
65 TTCATCATGGCAAAACATTC---TA---CATGTATTTTTTTTT-TTGTGT-GTGTA-TTATGCGT
** * * * * * *
43575 ACATTTTGGAAATCCTCT-GGGGAAGCAGGTAAATAGATTCTTTTGTTGGTTTTATTGTTATGTA
121 ACATGCTGGAAATCCCCTGGGGGAAGCAGATAAATAGATGCTTATATTGGTTTTATTGTAATGTA
* *
43639 GCCTAGAGTTGTACAACTACCTTGTTTTTA
186 GCCTAGAGTGGTACAACTACCTTGGTTTTA
43669 GCTTGTGATT
Statistics
Matches: 190, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
216 23 0.12
217 47 0.25
218 1 0.01
219 2 0.01
222 15 0.08
223 5 0.03
224 74 0.39
225 23 0.12
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.42
Consensus pattern (217 bp):
GGTTTTGGAATCTTAATATGATCATACTAGGACCAGGAGAATATTTTACACTTTAAAAAGAGTTT
TCATCATGGCAAAACATTCTACATGTATTTTTTTTTTTGTGTGTGTATTATGCGTACATGCTGGA
AATCCCCTGGGGGAAGCAGATAAATAGATGCTTATATTGGTTTTATTGTAATGTAGCCTAGAGTG
GTACAACTACCTTGGTTTTATT
Found at i:49352 original size:11 final size:10
Alignment explanation
Indices: 49324--49350 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49314 ACTGCTCAGA
49324 TTCCCCCTTC
1 TTCCCCCTTC
49334 TTCCCCCTTC
1 TTCCCCCTTC
49344 TTCCCCC
1 TTCCCCC
49351 CTCCCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (10 bp):
TTCCCCCTTC
Found at i:49767 original size:40 final size:40
Alignment explanation
Indices: 49704--49784 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
49694 CTGTACATAA
* *
49704 TAAAATTTTTTATTTTATATTT-AATTATAAATATTAATTT
1 TAAAATTTTTTATATTATATTTAAATAAT-AATATTAATTT
*
49744 TAAAATTTTTTAATATTAT-TTTAAATAATAATATTGATTT
1 TAAAATTTTTT-ATATTATATTTAAATAATAATATTAATTT
49784 T
1 T
49785 TGAATCAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 25 0.69
41 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (40 bp):
TAAAATTTTTTATATTATATTTAAATAATAATATTAATTT
Found at i:50802 original size:12 final size:13
Alignment explanation
Indices: 50763--50817 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 13
50753 TTTTACTATT
*
50763 TATTATATCATTAAA
1 TATTATAT-ATT-TA
50778 TATTAT-T-TTTA
1 TATTATATATTTA
50789 TATTA-ATATTTA
1 TATTATATATTTA
50801 TATTATATATATTA
1 TATTATATAT-TTA
50815 TAT
1 TAT
50818 AATTAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 7 0.20
12 11 0.31
13 4 0.11
14 7 0.20
15 6 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATATATTTA
Found at i:54302 original size:2 final size:2
Alignment explanation
Indices: 54295--54329 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54285 GACCTGGGAG
54295 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
54330 GGATAACGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.