Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2354
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: 26824
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Found at i:252 original size:20 final size:20
Alignment explanation
Indices: 220--258 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
210 TAAATTTAAA
*
220 TAAAAATATATTTTAATTAT
1 TAAAAATATATTTAAATTAT
240 TAAATAATA-ATTTAAATTA
1 TAAA-AATATATTTAAATTA
259 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAAATATATTTAAATTAT
Found at i:1105 original size:5 final size:5
Alignment explanation
Indices: 1095--1237 Score: 72
Period size: 5 Copynumber: 29.8 Consensus size: 5
1085 ATATTTTTTT
* * * *
1095 TATTA TATTA TAATTA TATTTA AATT- TTTTA T-TTA TA-TA AATT- TAATA
1 TATTA TATTA T-ATTA TA-TTA TATTA TATTA TATTA TATTA TATTA TATTA
* * * * *
1143 TATT- TATAA T-TTA TATTA TA-TA TTTTA AATTA TATTA TTATAA TATAA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA TATTA
* * *
1191 TATTA TATT- TAATTA TTTTA T-TTA TATTA TATTT TTTTA -ATTA TATT
1 TATTA TATTA T-ATTA TATTA TATTA TATTA TATTA TATTA TATTA TATT
1238 TAATATTATC
Statistics
Matches: 104, Mismatches: 20, Indels: 28
0.68 0.13 0.18
Matches are distributed among these distances:
4 28 0.27
5 62 0.60
6 14 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:1145 original size:32 final size:33
Alignment explanation
Indices: 1088--1154 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
1078 ATTGTATATA
*
1088 TTTTTTTTATTATATTATAATTATATTTA-AAT
1 TTTTTTTTATTAAATTATAATTATATTTATAAT
1120 TTTTTATTTATATAAATT-TAA-TATATTTATAAT
1 TTTTT-TTTAT-TAAATTATAATTATATTTATAAT
1153 TT
1 TT
1155 ATATTATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 13 0.42
33 13 0.42
34 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (33 bp):
TTTTTTTTATTAAATTATAATTATATTTATAAT
Found at i:1177 original size:19 final size:19
Alignment explanation
Indices: 1140--1237 Score: 83
Period size: 19 Copynumber: 5.0 Consensus size: 19
1130 TATAAATTTA
*
1140 ATATATTTATAATTTATATT
1 ATATATTT-TAAATTATATT
1160 ATATATTTTAAATTATATT
1 ATATATTTTAAATTATATT
* *
1179 ATTATAATATAATATTATATT
1 A-TATATTTTAA-ATTATATT
*
1200 -TAATTATTTT-ATTTATATT
1 AT-A-TATTTTAAATTATATT
* *
1219 ATATTTTTTTAATTATATT
1 ATATATTTTAAATTATATT
1238 TAATATTATC
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
18 5 0.08
19 28 0.44
20 19 0.30
21 12 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATATTTTAAATTATATT
Found at i:1235 original size:85 final size:83
Alignment explanation
Indices: 1094--1256 Score: 197
Period size: 85 Copynumber: 1.9 Consensus size: 83
1084 TATATTTTTT
* *
1094 TTATTATATTATAATTATATTTAAATTTTTTATTTATATAAATTTAATATATTTATAATTT-ATA
1 TTATTATAATATAATTATATTTAAATTTTTTATTTATATAAATTTAATATAATTAT-ATTTAATA
*
1158 TTATATATTTTAAATTATA
65 TTATATATTATAAATTATA
* * *
1177 TTATTATAATATAATATTATATTT-AATTATTTTATTTATATTATATTT-TTTTAATTATATTTA
1 TTATTATAATAT-A-ATTATATTTAAATT-TTTTATTTATA-TAAATTTAATATAATTATATTTA
*
1240 ATATTATCTATTATAAA
62 ATATTATATATTATAAA
1257 AAAAAATAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
83 11 0.16
84 9 0.13
85 42 0.62
86 6 0.09
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.60
Consensus pattern (83 bp):
TTATTATAATATAATTATATTTAAATTTTTTATTTATATAAATTTAATATAATTATATTTAATAT
TATATATTATAAATTATA
Found at i:1428 original size:14 final size:14
Alignment explanation
Indices: 1409--1446 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1399 AAAATATAGA
*
1409 TAAAAATATTAAATT
1 TAAAAA-ATAAAATT
1424 TAAAAAATAAAATT
1 TAAAAAATAAAATT
1438 TAAAAAATA
1 TAAAAAATA
1447 GGTTCATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAAATAAAATT
Found at i:1887 original size:15 final size:15
Alignment explanation
Indices: 1835--1891 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1825 TAAAAAATTT
* *
1835 ATTAAATTATTTATA
1 ATTAAATTATTAAAA
* *
1850 TTTAAATTTAATAAAATA
1 ATTAAA-TT-ATTAAA-A
1868 ATTAAATTATTAAAA
1 ATTAAATTATTAAAA
1883 ATTAAATTA
1 ATTAAATTA
1892 AAAATATCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 15 0.45
16 7 0.21
17 5 0.15
18 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATTATTAAAA
Found at i:1888 original size:33 final size:33
Alignment explanation
Indices: 1818--1895 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
1808 TATTATAGTG
* * * *
1818 TAAATATTAAAAAATTTATTAAATTATTTATATT
1 TAAAT-TTAAAAAATTAATTAAATTATTAAAAAT
1852 TAAATTTAATAAAA-TAATTAAATTATTAAAAAT
1 TAAATTTAA-AAAATTAATTAAATTATTAAAAAT
1885 TAAA-TTAAAAA
1 TAAATTTAAAAA
1896 TATCTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
31 3 0.08
32 4 0.10
33 23 0.59
34 9 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAATTTAAAAAATTAATTAAATTATTAAAAAT
Found at i:2071 original size:2 final size:2
Alignment explanation
Indices: 2064--2095 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2054 CTATTAGTAG
2064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2096 GAGAAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4396 original size:32 final size:33
Alignment explanation
Indices: 4347--4429 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
4337 AGAGGGGAGG
*
4347 AAAA-AAAAAGAAAAATGAAAAAATGAA-AAAA
1 AAAAGAAAAAGAAAAATGAAAAAAGGAAGAAAA
* *
4378 AAAAGAAAAAGAAGAATGAAGAAAGGAAGGAAAA
1 AAAAGAAAAAGAAAAATGAAAAAAGGAA-GAAAA
*
4412 AAAAGAAAAA-ATAAATGA
1 AAAAGAAAAAGAAAAATGA
4430 GCGGCCTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 4 0.09
32 20 0.45
33 6 0.14
34 14 0.32
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (33 bp):
AAAAGAAAAAGAAAAATGAAAAAAGGAAGAAAA
Found at i:5378 original size:66 final size:66
Alignment explanation
Indices: 5295--5429 Score: 209
Period size: 66 Copynumber: 2.0 Consensus size: 66
5285 CCAAAGAGCA
* *
5295 CTCGTTTGCCTCGAGAAAAGCTAAGATAAAAGAGTTATGATTTTCAAATATGCA-CTATATGGAA
1 CTCGTTTGCCTCAAGAAAAGCTAAGATAAAAGAGTTACGATTTTCAAATATG-AGCTATATGGAA
5359 CC
65 CC
* * *
5361 CTCGTTTGCCTCAAGAAAAGCTAAGATAAAGGAGTTACGATTTTCGAATATGAGTTATATGGAAC
1 CTCGTTTGCCTCAAGAAAAGCTAAGATAAAAGAGTTACGATTTTCAAATATGAGCTATATGGAAC
5426 C
66 C
5427 CTC
1 CTC
5430 AGAACTGGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 1 0.02
66 62 0.98
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (66 bp):
CTCGTTTGCCTCAAGAAAAGCTAAGATAAAAGAGTTACGATTTTCAAATATGAGCTATATGGAAC
C
Found at i:6495 original size:5 final size:5
Alignment explanation
Indices: 6482--6521 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
6472 AGTGTTTTTA
* * *
6482 AAAAA AAAAT AAAAT AAAAT AAAAA AAAAT AAAAA AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
6522 TCCAAATGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:6500 original size:10 final size:10
Alignment explanation
Indices: 6482--6521 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
6472 AGTGTTTTTA
6482 AAAAAAAAAT
1 AAAAAAAAAT
*
6492 AAAATAAAAT
1 AAAAAAAAAT
6502 AAAAAAAAAT
1 AAAAAAAAAT
6512 AAAAAAAAAT
1 AAAAAAAAAT
6522 TCCAAATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:6620 original size:19 final size:19
Alignment explanation
Indices: 6596--6663 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
6586 AATTCAACAA
6596 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
6615 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
6630 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
6647 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
6664 TTGGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:6635 original size:13 final size:13
Alignment explanation
Indices: 6617--6641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6607 ACATAAGTTT
6617 TGTATCGATACAA
1 TGTATCGATACAA
6630 TGTATCGATACA
1 TGTATCGATACA
6642 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6639 original size:32 final size:32
Alignment explanation
Indices: 6598--6660 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
6588 TTCAACAATT
*
6598 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
6630 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
6661 TAATTGGCTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:6721 original size:13 final size:13
Alignment explanation
Indices: 6703--6728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6693 CATTTTTCTG
6703 TGTATCGATACAT
1 TGTATCGATACAT
6716 TGTATCGATACAT
1 TGTATCGATACAT
6729 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:6725 original size:33 final size:33
Alignment explanation
Indices: 6683--6749 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
6673 GCCAAGGAAA
***
6683 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
6716 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
6749 T
1 T
6750 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:9151 original size:51 final size:51
Alignment explanation
Indices: 9090--9263 Score: 204
Period size: 51 Copynumber: 3.4 Consensus size: 51
9080 AATTCTCCAC
* *
9090 AATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTTCAT
1 AATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCAT
* * * * * *
9141 AATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTT
1 AATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTT-TTC-AT
* * * * *
9194 AATCGGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCAC
1 AATCGAGGATACTCCAACTCCGATTTTATTTTC-AAAACACCAATTTTTCAT
9246 AATCGAGGATACTCCAAC
1 AATCGAGGATACTCCAAC
9264 CTCGTTATTT
Statistics
Matches: 101, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 40 0.40
52 18 0.18
53 32 0.32
54 11 0.11
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (51 bp):
AATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCAT
Found at i:9283 original size:28 final size:28
Alignment explanation
Indices: 9247--9328 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
9237 ATTTTTCACA
*
9247 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
9275 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
9303 --CGAGGGAACACTCCAACCTCGCTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
9329 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 40 0.89
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:13172 original size:20 final size:20
Alignment explanation
Indices: 13147--13225 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
13137 GCTGCCAAGG
13147 AAATGTATCGATACATTGCT
1 AAATGTATCGATACATTGCT
*
13167 AAATGTATAGATACA-TGCTT
1 AAATGTATCGATACATTGC-T
*
13187 ACAATTGTATCGATACATTTCT
1 A-AA-TGTATCGATACATTGCT
* * *
13209 CATTATATCGATACATT
1 AAATGTATCGATACATT
13226 CTGGATTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 3 0.06
20 29 0.59
21 3 0.06
22 12 0.24
23 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
AAATGTATCGATACATTGCT
Found at i:14700 original size:21 final size:21
Alignment explanation
Indices: 14675--14717 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14665 AAAATCATTT
14675 TAAAATTCTAAACGATTTTTC
1 TAAAATTCTAAACGATTTTTC
* * *
14696 TAAAATTTTATACTATTTTTC
1 TAAAATTCTAAACGATTTTTC
14717 T
1 T
14718 CGTAAAGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
TAAAATTCTAAACGATTTTTC
Found at i:14891 original size:9 final size:10
Alignment explanation
Indices: 14867--14905 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
14857 CCACTAGAAG
14867 ATTTTTTCAA
1 ATTTTTTCAA
14877 ATTTTTTCAA
1 ATTTTTTCAA
14887 ATTTTTTTCAA
1 A-TTTTTTCAA
14898 TATTTTTT
1 -ATTTTTT
14906 TTTCTAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 11 0.41
11 15 0.56
12 1 0.04
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTTTTTCAA
Found at i:14892 original size:11 final size:11
Alignment explanation
Indices: 14868--14906 Score: 62
Period size: 10 Copynumber: 3.5 Consensus size: 11
14858 CACTAGAAGA
14868 TTTTTTCAAA-
1 TTTTTTCAAAT
14878 TTTTTTCAAAT
1 TTTTTTCAAAT
14889 TTTTTTCAATAT
1 TTTTTTCAA-AT
14901 TTTTTT
1 TTTTTT
14907 TTCTAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.37
11 9 0.33
12 8 0.30
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTCAAAT
Found at i:16744 original size:53 final size:51
Alignment explanation
Indices: 16624--16763 Score: 181
Period size: 53 Copynumber: 2.7 Consensus size: 51
16614 TCTGAAAAGA
* * *
16624 AAATGTATCGATACATTTTTCATTGAATCGATACATTTTGAGTTTTGATCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTGAGTTTTGATCC
* * *
16675 AAATTTATCAATACATTATTCATTGTATCGATACATTCTGAATTTGTTGATCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTG-AGTT-TTGATCC
* * *
16728 AAATGTATCGATACATTCTTCAATGTATTGATACAT
1 AAATGTATCGATACATTATTCATTGTATCGATACAT
16764 GTAAGCTATT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 35 0.46
52 3 0.04
53 38 0.50
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (51 bp):
AAATGTATCGATACATTATTCATTGTATCGATACATTCTGAGTTTTGATCC
Found at i:19098 original size:131 final size:129
Alignment explanation
Indices: 18924--19258 Score: 408
Period size: 131 Copynumber: 2.6 Consensus size: 129
18914 ATATCCGAGG
*
18924 GGATA-TTTCAACCCCGTTTTTATTTTTAAAATATTAAATTTTCATCGCGGGGATACTCCAATCC
1 GGATACTTTCAA-CCCGTTTTTATTTTCAAAATATTAAATTTTCATCGCGGGGATACTCCAATCC
** * * *
18988 TGTTATTTT-TGAGGAGATACTCTAACCCTATTTTTACTTCCAACATATCAATCTTTT-ACTATC
65 TGTTATTTTCAAAGG-GATACTCCAACCCTATTTTTACTTCCAAAATATCAAT-TTTTCACCATC
19051 G-
128 GA
* * * * * *
19052 GTGATACTTTTCAATCCCGTTTTTATTTCCAAAATATTAAAATTTCATTGTGGAGATACTCCAAC
1 G-GATAC-TTTCAA-CCCGTTTTTATTTTCAAAATATTAAATTTTCATCGCGGGGATACTCCAAT
*
19117 CCTGTTATTTTCAAAGGGATACTCCAACCCTATTTTTACTTCCAAAATATCGATTTTTCACCATC
63 CCTGTTATTTTCAAAGGGATACTCCAACCCTATTTTTACTTCCAAAATATCAATTTTTCACCATC
19182 GA
128 GA
* * *
19184 GGATACTCTCTAACCTCATTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAAT
1 GGATACTTTC-AACC-CGTTTTTATTTTCAAAATATTAAA-TTTTCATCGCGGGGATACTCCAAT
*
19249 CCCGTTATTT
63 CCTGTTATTT
19259 AAGAATGGAT
Statistics
Matches: 174, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
128 1 0.01
129 4 0.02
130 9 0.05
131 129 0.74
132 31 0.18
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (129 bp):
GGATACTTTCAACCCGTTTTTATTTTCAAAATATTAAATTTTCATCGCGGGGATACTCCAATCCT
GTTATTTTCAAAGGGATACTCCAACCCTATTTTTACTTCCAAAATATCAATTTTTCACCATCGA
Found at i:19241 original size:53 final size:51
Alignment explanation
Indices: 19132--19247 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 51
19122 TATTTTCAAA
**
19132 GGGATACTCCAACCCTATTTTTACTTCCAAAATATCGATTTTTCACCATCG
1 GGGATACTCCAACCCTATTTTTACTTCCAAAATATAAATTTTTCACCATCG
* * * *
19183 AGGATACTCTCTAA-CCTCATTTTTATTTTCAAAATATTAAATTTTTCATC-TCG
1 GGGATACTC-C-AACCCT-ATTTTTACTTCCAAAATA-TAAATTTTTCACCATCG
19236 GGGATACTCCAA
1 GGGATACTCCAA
19248 TCCCGTTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
51 10 0.19
52 5 0.09
53 29 0.54
54 10 0.19
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (51 bp):
GGGATACTCCAACCCTATTTTTACTTCCAAAATATAAATTTTTCACCATCG
Found at i:19285 original size:79 final size:78
Alignment explanation
Indices: 19191--19833 Score: 507
Period size: 78 Copynumber: 8.2 Consensus size: 78
19181 CGAGGATACT
* *
19191 CTCTAACCTCATTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAATCCCGTTA
1 CTCTAACCCCGTTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAA-CCCGTTA
** *
19256 TTTAAGAATGGATA
65 TTTTCGAAGGGATA
* * * ** *
19270 CTCTAATCTCGTTTTTATTTT-AATAATATTAAATTTTTTATCTTAGGGATATTCCAACCTCGTT
1 CTCTAACCCCGTTTTTATTTTCAA-AATATTAAATTTTTCATCTCGGGGATACTCCAACC-CGTT
*
19334 ATTTTTG-AGGGAATA
64 ATTTTCGAAGGG-ATA
* * * ** * *
19349 CTCTAACCCCGTTTTTATTTCCAAAATATTAAAATTTTCATCTTGAAGATACTCCAACCCCGATG
1 CTCTAACCCCGTTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAA-CCCGTTA
19414 TTTTC-AAGGGAATA
65 TTTTCGAAGGG-ATA
* * * * ** * **
19428 CTCCAACCTCATTTTTATTTTTAAAATATT-AATTTTTCATCTCGAAGATACTCTAACCTTATTA
1 CTCTAACCCCGTTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAACC-CGTTA
*
19492 TTTTCGAGGGGATA
65 TTTTCGAAGGGATA
* * * * * *
19506 TTCCAACCTCGTTTTTATTTTCAAAATATT-AATTTTCCATCTCGGAGATACTCCAACCCCATTA
1 CTCTAACCCCGTTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAA-CCCGTTA
19570 TTTTCG-AGGAGATA
65 TTTTCGAAGG-GATA
* * ** * *
19584 CTCTAACCCC-ATTTTATTTTCAAAATGTTAAATTTTTCATCGAGGGGATACTCTAACTTCGTTA
1 CTCTAACCCCGTTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAAC-CCGTTA
*
19648 TTTTTGAA-GGATA
65 TTTTCGAAGGGATA
* * * * * * * *
19661 CTCCAACCCCGTTTTTA-TCTCTAAAATATTAAGTTTTTTATCGT-AGGGATATTCCACCCCCGC
1 CTCTAACCCCGTTTTTATTTTC-AAAATATTAAATTTTTCATC-TCGGGGATACTCCA-ACCCGT
*
19724 TATTTTCGAGGGGATA
63 TATTTTCGAAGGGATA
* * * * * **
19740 CTCTAACCCCGTCTTTACTTCTAAAAACATTAAATTTCT-ATCTTCGGGGATACTCCAACCCCAC
1 CTCTAACCCCGTTTTTA-TTTTCAAAATATTAAATTTTTCATC-TCGGGGATACTCCAA-CCCGT
* * *
19804 TATCTCCGAGGGGATA
63 TATTTTCGAAGGGATA
*
19820 CTCCAACCCCGTTT
1 CTCTAACCCCGTTT
19834 CTTTTCGAAT
Statistics
Matches: 457, Mismatches: 85, Indels: 43
0.78 0.15 0.07
Matches are distributed among these distances:
77 38 0.08
78 182 0.40
79 177 0.39
80 57 0.12
81 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.39
Consensus pattern (78 bp):
CTCTAACCCCGTTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGGATACTCCAACCCGTTAT
TTTCGAAGGGATA
Found at i:19806 original size:26 final size:27
Alignment explanation
Indices: 19777--19829 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
19767 CATTAAATTT
*
19777 CTATCTTC-GGGGATACTCCAACCCCA
1 CTATCTCCAGGGGATACTCCAACCCCA
19803 CTATCTCCGAGGGGATACTCCAACCCC
1 CTATCTCC-AGGGGATACTCCAACCCC
19830 GTTTCTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
28 17 0.71
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.21
Consensus pattern (27 bp):
CTATCTCCAGGGGATACTCCAACCCCA
Found at i:20882 original size:169 final size:171
Alignment explanation
Indices: 20601--20939 Score: 533
Period size: 169 Copynumber: 2.0 Consensus size: 171
20591 TCATGGTAAC
* * * * *
20601 CATTCGAGACTAATAGGATGAGCAATTCGTCTGATAATCTTTCACCCCCTCCATATTGATCATTA
1 CATTCGAGACTAATAGGATGAGCAAGTCATCTAATAATCTATCACCCCATCCATATTGATCATTA
*
20666 TCATCTTTTATTTTAAGTCAGCGCGCTTTGGCCCTTCAGATCATTCGAAGTACTCAAAGG-TCGG
66 TCATATTTTATTTTAAGTCAGCGCGCTTTGGCCCTTCAGATCATTCGAAGTACTCAAAGGCT-GG
*
20730 GCACGTGTGTCGACAAGTATCATA-CCCCTTCTTTGCTATGGT
130 GCACGTGTGTCGACAAGTATCATATCCCC-TCTTTACTATGGT
* *
20772 CATTCGAGACTAATAGGATGAGCGAGTCATCTAATAATCTATCA-CCCATCCATATT-ATTATTA
1 CATTCGAGACTAATAGGATGAGCAAGTCATCTAATAATCTATCACCCCATCCATATTGATCATTA
*
20835 TCATATTTTATTTTAAGTCAGTGCGCTTTGGCCCTTCAGATCATTCGAAGTACTCAAAGGCTGGG
66 TCATATTTTATTTTAAGTCAGCGCGCTTTGGCCCTTCAGATCATTCGAAGTACTCAAAGGCTGGG
*
20900 CACGTGTGTCGACAAGTATCATATCCGCTCTTTACTATGG
131 CACGTGTGTCGACAAGTATCATATCCCCTCTTTACTATGG
20940 AAAAAAATTA
Statistics
Matches: 155, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
169 101 0.65
170 15 0.10
171 39 0.25
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (171 bp):
CATTCGAGACTAATAGGATGAGCAAGTCATCTAATAATCTATCACCCCATCCATATTGATCATTA
TCATATTTTATTTTAAGTCAGCGCGCTTTGGCCCTTCAGATCATTCGAAGTACTCAAAGGCTGGG
CACGTGTGTCGACAAGTATCATATCCCCTCTTTACTATGGT
Found at i:23934 original size:79 final size:78
Alignment explanation
Indices: 23850--24103 Score: 269
Period size: 79 Copynumber: 3.2 Consensus size: 78
23840 AAAAATTTAA
* * *
23850 TATTTTGGAGATAAAAACGGGGTTGGCGTATCCCCTTCGAAAATAAC-GGGTTAGAGTAT-TCCC
1 TATTTTGGAAATAAAAACGGGGTTAGAGTATCCCC-TC-AAAATAACAGGGTTAGAGTATCT-CC
23913 GATTGTGAAAAATCGG
63 GATTGTGAAAAATCGG
* ** * * * *
23929 TATTTTGAAAATAAAATTGGGGTTAGAGTCTTCCCTCAAAATAACAGGGTTGGAGTATCTTCGAT
1 TATTTTGGAAATAAAAACGGGGTTAGAGTATCCCCTCAAAATAACAGGGTTAGAGTATCTCCGAT
* *
23994 TATGAAAAATTGG
66 TGTGAAAAATCGG
* * ** * * *
24007 TGTTCTGGAAATAAAATTGGAGTTAGAGTATCTCCTCAAAAATAACAAGGTTAGAGTATCTCCGA
1 TATTTTGGAAATAAAAACGGGGTTAGAGTATCCCCTC-AAAATAACAGGGTTAGAGTATCTCCGA
*
24072 TGGTGAAAAATCGG
65 TTGTGAAAAATCGG
*
24086 TATTTTAGAAATAAAAAC
1 TATTTTGGAAATAAAAAC
24104 ATGAATAAAA
Statistics
Matches: 142, Mismatches: 30, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
77 8 0.06
78 58 0.41
79 76 0.54
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (78 bp):
TATTTTGGAAATAAAAACGGGGTTAGAGTATCCCCTCAAAATAACAGGGTTAGAGTATCTCCGAT
TGTGAAAAATCGG
Found at i:24000 original size:78 final size:79
Alignment explanation
Indices: 23889--24101 Score: 265
Period size: 78 Copynumber: 2.7 Consensus size: 79
23879 ATCCCCTTCG
*
23889 AAAATAAC-GGGTTAGAGTAT-TCCCGATTGTGAAAAATCGGTATTTTGAAAATAAAATTGGGGT
1 AAAATAACAGGGTTAGAGTATCT-CCGATTGTGAAAAATCGGTATTTTGAAAATAAAATTGGAGT
*
23952 TAGAGTCT-TCCCTC-
65 TAGAGTATCT-CCTCA
* * * * * * *
23966 AAAATAACAGGGTTGGAGTATCTTCGATTATGAAAAATTGGTGTTCTGGAAATAAAATTGGAGTT
1 AAAATAACAGGGTTAGAGTATCTCCGATTGTGAAAAATCGGTATTTTGAAAATAAAATTGGAGTT
24031 AGAGTATCTCCTCA
66 AGAGTATCTCCTCA
* *
24045 AAAATAACAAGGTTAGAGTATCTCCGATGGTGAAAAATCGGTATTTT-AGAAATAAAA
1 AAAATAACAGGGTTAGAGTATCTCCGATTGTGAAAAATCGGTATTTTGA-AAATAAAA
24102 ACATGAATAA
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
77 8 0.07
78 56 0.50
79 49 0.43
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (79 bp):
AAAATAACAGGGTTAGAGTATCTCCGATTGTGAAAAATCGGTATTTTGAAAATAAAATTGGAGTT
AGAGTATCTCCTCA
Found at i:26520 original size:20 final size:20
Alignment explanation
Indices: 26491--26546 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
26481 GTTAAAACCC
26491 AAAATGTATCGATACAATGA
1 AAAATGTATCGATACAATGA
*
26511 AAAATATATCGATACAATGA
1 AAAATGTATCGATACAATGA
26531 AAAATGTATCGATACA
1 AAAATGTATCGATACA
26547 TCTGGGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (20 bp):
AAAATGTATCGATACAATGA
Found at i:26589 original size:70 final size:71
Alignment explanation
Indices: 26441--26597 Score: 244
Period size: 70 Copynumber: 2.2 Consensus size: 71
26431 AAAAATGCAT
* * *
26441 GAATGTATCGATACATTGAGAAATGTATCGATACATCTGGGTTAAAACCCAAAATGTATCGATAC
1 GAATATATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACCCAAAATGTATCGATAC
26506 AATGAA
66 AATGAA
* * * *
26512 AAATATATCGATACAATGAAAAATGTATCGATACATCTGGG-TAAAACCTAGAATGTATCGATAT
1 GAATATATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACCCAAAATGTATCGATAC
26576 AATGAA
66 AATGAA
26582 GAATATATCGATACAA
1 GAATATATCGATACAA
26598 ATTATTGAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 41 0.53
71 37 0.47
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.27
Consensus pattern (71 bp):
GAATATATCGATACAATGAAAAATGTATCGATACATCTGGGTTAAAACCCAAAATGTATCGATAC
AATGAA
Done.