Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1199
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: 59776
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1487 original size:19 final size:19
Alignment explanation
Indices: 1460--1522 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1450 TCACGTGTAC
* *
1460 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1479 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1498 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1517 AGTACC
1 AGTACC
1523 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1873 original size:34 final size:34
Alignment explanation
Indices: 1827--2010 Score: 255
Period size: 34 Copynumber: 5.4 Consensus size: 34
1817 GTAAAAACCA
*
1827 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1861 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1895 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1929 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1963 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1996 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2011 AAACAAAATA
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:8313 original size:20 final size:20
Alignment explanation
Indices: 8274--8313 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
8264 AAGAATTGAA
*
8274 GAGGGATACAAGATAAGGAT
1 GAGGGATACAAGAGAAGGAT
* *
8294 GAGGGATATAAGAGATGGAT
1 GAGGGATACAAGAGAAGGAT
8314 TTGGGAGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.38, T:0.17
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAT
Found at i:8428 original size:25 final size:25
Alignment explanation
Indices: 8366--8435 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
8356 AATAAAAATT
*
8366 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
8390 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
8415 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
8436 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:8481 original size:27 final size:27
Alignment explanation
Indices: 8420--8490 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
8410 AAACAAGCCT
* *
8420 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
8448 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
8475 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
8491 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:8493 original size:24 final size:24
Alignment explanation
Indices: 8368--8493 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
8358 TAAAAATTAG
* *
8368 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
8392 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
8416 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
8445 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
8472 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
8494 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 13 0.15
26 4 0.05
27 20 0.24
28 17 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:13022 original size:25 final size:25
Alignment explanation
Indices: 12960--13029 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
12950 AATAAAAATT
*
12960 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
12984 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
13009 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
13030 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:13075 original size:27 final size:27
Alignment explanation
Indices: 13014--13084 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
13004 AAACAAGCCT
* *
13014 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
13042 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
13069 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
13085 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:13087 original size:24 final size:24
Alignment explanation
Indices: 12962--13087 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
12952 TAAAAATTAG
* *
12962 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
12986 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
13010 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
13039 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
13066 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
13088 GGGTGGCTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.29
25 13 0.15
26 4 0.05
27 20 0.24
28 17 0.20
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:18273 original size:27 final size:26
Alignment explanation
Indices: 18253--18304 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
18243 ATATTATGAT
18253 TATAT-TTAATATATTATATATT-TATA
1 TATATATTAATA-ATT-TATATTATATA
18279 TATATATTAATAATTTATATTATATA
1 TATATATTAATAATTTATATTATATA
18305 AATTTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.25
26 12 0.50
27 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TATATATTAATAATTTATATTATATA
Found at i:18285 original size:19 final size:19
Alignment explanation
Indices: 18261--18383 Score: 72
Period size: 19 Copynumber: 6.9 Consensus size: 19
18251 ATTATATTTA
18261 ATATATTATATATTTATAT
1 ATATATTATATATTTATAT
18280 ATATATTA-ATAATTTATAT
1 ATATATTATAT-ATTTATAT
*
18299 -TATA-TAAAT-TTTA-AT
1 ATATATTATATATTTATAT
* *
18314 ATA-ATTTTTTATTTATA-
1 ATATATTATATATTTATAT
* *
18331 ATATATTTAGATTATTTTTAT
1 ATATA-TTATA-TATTTATAT
18352 ATTATATT-TA-ATTT-T-T
1 A-TATATTATATATTTATAT
*
18368 -TATATTATATTTTTAT
1 ATATATTATATATTTAT
18384 CGCCTAAAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 30
0.68 0.08 0.25
Matches are distributed among these distances:
14 6 0.07
15 5 0.06
16 12 0.15
17 11 0.14
18 14 0.17
19 18 0.22
20 8 0.10
21 3 0.04
22 4 0.05
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
ATATATTATATATTTATAT
Found at i:18301 original size:24 final size:26
Alignment explanation
Indices: 18242--18377 Score: 85
Period size: 24 Copynumber: 5.4 Consensus size: 26
18232 TACGTGTTTG
18242 TATATTATGAT-TATATTTAATATATTA
1 TATATTAT-ATATATA-TTAATATATTA
18269 TATATTTATATATATATTAATA-ATT-
1 TATA-TTATATATATATTAATATATTA
* * *
18294 TATATTATATAAATTTTAATATAATTT
1 TATATTATATATATATTAATAT-ATTA
* *
18321 TTTATT-TATAATATATT--TAGATTA
1 TATATTATAT-ATATATTAATATATTA
* *
18345 T-TTTTATAT-TATATTTAAT-T-TTT
1 TATATTATATATATA-TTAATATATTA
18368 TATATTATAT
1 TATATTATAT
18378 TTTTATCGCC
Statistics
Matches: 87, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
22 4 0.05
23 8 0.09
24 29 0.33
25 7 0.08
26 9 0.10
27 22 0.25
28 8 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
TATATTATATATATATTAATATATTA
Found at i:18337 original size:11 final size:11
Alignment explanation
Indices: 18268--18361 Score: 56
Period size: 11 Copynumber: 8.8 Consensus size: 11
18258 TTAATATATT
18268 ATATATTTATA
1 ATATATTTATA
*
18279 TATATATTAATA
1 -ATATATTTATA
*
18291 ATTTATATTAT-
1 ATATAT-TTATA
*
18302 ATAAATTT-TA
1 ATATATTTATA
18312 ATATAATTT-T-
1 ATAT-ATTTATA
18322 -T-TATTTATA
1 ATATATTTATA
*
18331 ATATATTTAGA
1 ATATATTTATA
* *
18342 TTATTTTTATA
1 ATATATTTATA
*
18353 TTATATTTA
1 ATATATTTA
18362 ATTTTTTATA
Statistics
Matches: 64, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
7 4 0.06
8 2 0.03
9 2 0.03
10 6 0.09
11 37 0.58
12 13 0.20
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (11 bp):
ATATATTTATA
Found at i:18357 original size:22 final size:19
Alignment explanation
Indices: 18273--18379 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 19
18263 ATATTATATA
**
18273 TTTATA-TATATATTAATAA
1 TTTATATTATAT-TTAATTT
*
18292 TTTATATTATA--TAAATT
1 TTTATATTATATTTAATTT
*
18309 TTAATA-TA-ATTT--TTT
1 TTTATATTATATTTAATTT
*
18324 ATTTATAATATATTTAGATTATT
1 -TTTATATTATATTTA-A-T-TT
18347 TTTATATTATATTTAATTT
1 TTTATATTATATTTAATTT
18366 TTTATATTATATTT
1 TTTATATTATATTT
18380 TTATCGCCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
15 3 0.04
16 7 0.10
17 11 0.16
18 4 0.06
19 22 0.31
20 5 0.07
21 1 0.01
22 15 0.21
23 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (19 bp):
TTTATATTATATTTAATTT
Found at i:24988 original size:18 final size:18
Alignment explanation
Indices: 24965--25000 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
24955 TATTTGCATG
24965 GTAAAAACCTTAAGCTTA
1 GTAAAAACCTTAAGCTTA
24983 GTAAAAACCTTAAGCTTA
1 GTAAAAACCTTAAGCTTA
25001 TGTTAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
GTAAAAACCTTAAGCTTA
Found at i:26148 original size:20 final size:20
Alignment explanation
Indices: 26101--26175 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
26091 AAAAAGACAT
*
26101 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
26120 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
26141 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
26161 AATGTATCGATACAT
1 AATGTATCGATACAT
26176 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:26169 original size:40 final size:39
Alignment explanation
Indices: 26098--26175 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
26088 GGTAAAAAGA
* *
26098 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
26137 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
26176 CAGGGTATGA
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:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:26753 original size:32 final size:32
Alignment explanation
Indices: 26704--27337 Score: 1081
Period size: 32 Copynumber: 19.8 Consensus size: 32
26694 AAAATGGTGA
* * **
26704 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
26736 TTTTAAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
26768 TTTGAAATGGGTTGCCGTCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
26800 TTTGAAATGGATTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
26832 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
26864 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
26896 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
26928 TTTGGAATGGGTTTCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
26960 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
26992 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
27024 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
27056 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
27088 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
27120 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
27152 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
27184 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
27216 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
27248 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
27280 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
27312 TTTGAAATGGG-TGCCACGGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
27338 GATTTAAAAG
Statistics
Matches: 578, Mismatches: 24, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
31 13 0.02
32 565 0.98
ACGTcount: A:0.15, C:0.18, G:0.35, T:0.32
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:27354 original size:27 final size:27
Alignment explanation
Indices: 27320--27859 Score: 726
Period size: 27 Copynumber: 19.7 Consensus size: 27
27310 GCTTTGAAAT
27320 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
* * *
27347 GGATGCCACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
*
27374 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
*
27401 GGGTGCCACAGAGTTGTGG-TCTTAAAA
1 GGGTGCCACGGAGTTGTGGAT-TTAAAA
*
27428 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGATTTAAAA
*
27456 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
*
27483 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
* *
27510 GAGTGCCACGGAGTTGTGGACTTAAAGA
1 GGGTGCCACGGAGTTGTGGATTTAAA-A
27538 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-TTTAAAA
* * * *
27566 GAGCGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
*
27593 GGGTGCCACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGA-TTTAAAA
* *
27621 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
27647 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-TTTAAAA
* *
27675 GAGTGCCACGGAGTTGTGGACTTT-GAA
1 GGGTGCCACGGAGTTGTGGA-TTTAAAA
*
27702 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
27729 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-TTTAAAA
*
27757 GAGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-TTTAAAA
*
27785 GAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGATTTAAAA
* * *
27812 GGGTGCCACAGAATTGTGGACTTAAAAA
1 GGGTGCCACGGAGTTGTGGA-TTTAAAA
* *
27840 GGATGCCACAGAGTTGTGGA
1 GGGTGCCACGGAGTTGTGGA
27860 CTTCAAAAAG
Statistics
Matches: 463, Mismatches: 39, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.02
27 278 0.60
28 173 0.37
29 5 0.01
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGATTTAAAA
Found at i:27455 original size:82 final size:81
Alignment explanation
Indices: 27320--27867 Score: 819
Period size: 82 Copynumber: 6.7 Consensus size: 81
27310 GCTTTGAAAT
* * *
27320 GGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
27385 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* *
27401 GGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
27466 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
*
27483 GGGTGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAGAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAA-AGGGTGCCACG
27548 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
* * * * *
27566 GAGCGCTACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTGAAA-GGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
27630 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* **
27647 GGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
27712 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
27729 GGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCAC
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCAC
*
27794 GGAGTTGTGGATTTAAAA
64 GGAGTTGTGGACTTAAAA
* * * *
27812 GGGTGCCACAGAATTGTGGACTTAAAAAGGATGCCACAGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTT-AAAA
27868 AGAAATGCCA
Statistics
Matches: 428, Mismatches: 30, Indels: 16
0.90 0.06 0.03
Matches are distributed among these distances:
81 77 0.18
82 222 0.52
83 125 0.29
84 4 0.01
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:27706 original size:219 final size:218
Alignment explanation
Indices: 27305--27867 Score: 866
Period size: 219 Copynumber: 2.6 Consensus size: 218
27295 CACCGACTTG
* * *
27305 TGTGGGCTTTGAAATGGGTGCCACGGAGTTGTGGA-TTTAAAAGGATGC-CACGAAGTTGTGGAC
1 TGTGGACTTT-AAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GA-GCGCACGGAGTTGTGGAC
*
27368 TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGTCTTAAAAGGGA
63 TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGGA
*
27432 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
127 TGCCACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
27497 TGTGGACTTAAAAGAGTGCCACGGAGT
192 TGTGGACTTAAAAGAGTGCCACGGAGT
27524 TGTGGAC-TTAAAGAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCGCTACGGAGTTGTGGACT
1 TGTGGACTTTAAA-AGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCGC-ACGGAGTTGTGGACT
*
27588 TAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAGGTGCCACAGAGTTGTGGACTTAAAAGGG-TG
64 TAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGATG
**
27652 CCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACGGAGTT
129 CCACGGAGTTGTGGAC-TTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTT
*
27717 GTGGACTTAAAAGGGTGCCACGGAGT
193 GTGGACTTAAAAGAGTGCCACGGAGT
* * *
27743 TGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGATTT
1 TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCG-CACGGAGTTGTGGACTT
* * *
27808 AAAAGGGTGCCACAGAATTGTGGACTTAAAAAGGATGCCACAGAGTTGTGGACTTCAAAA
65 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG-TGCCACAGAGTTGTGGACTT-AAAA
27868 AGAAATGCCA
Statistics
Matches: 318, Mismatches: 16, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
217 5 0.02
218 43 0.14
219 235 0.74
220 31 0.10
221 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.24
Consensus pattern (218 bp):
TGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGCGCACGGAGTTGTGGACTTA
AAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGGATGCC
ACGGAGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTG
GACTTAAAAGAGTGCCACGGAGT
Found at i:35223 original size:18 final size:18
Alignment explanation
Indices: 35200--35235 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35190 TATTTGCATG
35200 GTAAAAACCTTAAGCTTA
1 GTAAAAACCTTAAGCTTA
35218 GTAAAAACCTTAAGCTTA
1 GTAAAAACCTTAAGCTTA
35236 TGTTAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (18 bp):
GTAAAAACCTTAAGCTTA
Found at i:36384 original size:20 final size:20
Alignment explanation
Indices: 36337--36411 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
36327 AAAAAGACAT
*
36337 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
36356 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
36377 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
36397 AATGTATCGATACAT
1 AATGTATCGATACAT
36412 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:36405 original size:40 final size:39
Alignment explanation
Indices: 36334--36411 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
36324 GGTAAAAAGA
* *
36334 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
36373 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
36412 CAGGGTATGA
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:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:38889 original size:12 final size:12
Alignment explanation
Indices: 38872--38922 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
38862 TATAACTTAC
38872 TTATATTATTTT
1 TTATATTATTTT
* *
38884 TTATATAATATT
1 TTATATTATTTT
38896 TTA-ATTATTTT
1 TTATATTATTTT
38907 TTATATTATATTT
1 TTATATTAT-TTT
38920 TTA
1 TTA
38923 AAAGTTTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 9 0.27
12 18 0.55
13 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTATTTT
Found at i:38890 original size:25 final size:23
Alignment explanation
Indices: 38797--38912 Score: 69
Period size: 23 Copynumber: 4.9 Consensus size: 23
38787 TATTTTTATG
* *
38797 TATTATAATTATATTTAATAT-AT
1 TATTAT-ATTATTTTTTATATAAT
* *
38820 TATATTTTTTATTTTTTA-ATATAT
1 TAT-TATATTATTTTTTATATA-AT
* *
38844 TAATAATATTATTCTATTTATA-ACT
1 T-ATTATATTATT-T-TTTATATAAT
38869 TACTTATATTATTTTTTATATAA-
1 TA-TTATATTATTTTTTATATAAT
*
38892 TATTTTAATTATTTTTTATAT
1 TATTAT-ATTATTTTTTATAT
38913 TATATTTTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
22 5 0.07
23 33 0.46
24 14 0.19
25 14 0.19
26 5 0.07
27 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATATTATTTTTTATATAAT
Found at i:38902 original size:23 final size:23
Alignment explanation
Indices: 38876--38920 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
38866 ACTTACTTAT
38876 ATTATTTTTTATATAATATTTTA
1 ATTATTTTTTATATAATATTTTA
*
38899 ATTATTTTTTATATTATATTTT
1 ATTATTTTTTATATAATATTTT
38921 TAAAAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTATTTTTTATATAATATTTTA
Found at i:39938 original size:17 final size:18
Alignment explanation
Indices: 39910--39946 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
39900 AAAAAAAGTG
39910 GAGAAAGCAAAAAGCAAA
1 GAGAAAGCAAAAAGCAAA
39928 GAGAAAG-AAAAAGCAAA
1 GAGAAAGCAAAAAGCAAA
39945 GA
1 GA
39947 AAAATTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (18 bp):
GAGAAAGCAAAAAGCAAA
Found at i:40151 original size:23 final size:22
Alignment explanation
Indices: 40123--40182 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
40113 TGTATTTATG
40123 ATATTTTTTATATGTAA-AATATT
1 ATATTTTTTATAT-TAATAAT-TT
40146 ATATTTTTATATATTAATAATTT
1 ATATTTTT-TATATTAATAATTT
*
40169 ATTTTATTTTATAT
1 ATATT-TTTTATAT
40183 ATATATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATATTTTTTATATTAATAATTT
Found at i:41255 original size:22 final size:24
Alignment explanation
Indices: 41213--41256 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
41203 AAATTATTTT
*
41213 TTAATATTATATTTATGTTATACC
1 TTAATATTATATTTATATTATACC
41237 TTAAT-TTAT-TTTATATTATA
1 TTAATATTATATTTATATTATA
41257 GATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (24 bp):
TTAATATTATATTTATATTATACC
Found at i:41453 original size:18 final size:18
Alignment explanation
Indices: 41430--41466 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41420 TAACAGTCAA
41430 ATTGATGAT-ATGATGATG
1 ATTGATGATGAT-ATGATG
41448 ATTGATGATGATATGATG
1 ATTGATGATGATATGATG
41466 A
1 A
41467 CATCAACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (18 bp):
ATTGATGATGATATGATG
Found at i:42164 original size:2 final size:2
Alignment explanation
Indices: 42157--42187 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
42147 ATTATTATCT
*
42157 TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42188 CATCTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42266 original size:20 final size:20
Alignment explanation
Indices: 42223--42266 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
42213 ATTTCACATA
42223 TAAA-ATAATTATTTTTAAT
1 TAAATATAATTATTTTTAAT
*
42242 CAAATATAATT-TTTTTATAT
1 TAAATATAATTATTTTTA-AT
42262 TAAAT
1 TAAAT
42267 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATATAATTATTTTTAAT
Found at i:42288 original size:22 final size:22
Alignment explanation
Indices: 42263--42304 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
42253 TTTTTATATT
42263 AAATTAAAAA-AATTATTTACCC
1 AAATTAAAAATAATT-TTTACCC
42285 AAATTAAAAATAATTTTTAC
1 AAATTAAAAATAATTTTTAC
42305 TATCAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTAAAAATAATTTTTACCC
Found at i:42722 original size:14 final size:13
Alignment explanation
Indices: 42691--42724 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
42681 TTTTAATTTT
42691 ATTAAATTTTATA
1 ATTAAATTTTATA
42704 A-TAAATATTTATA
1 ATTAAAT-TTTATA
42717 ATTAAATT
1 ATTAAATT
42725 AAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.26
13 9 0.47
14 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAAATTTTATA
Found at i:42740 original size:22 final size:22
Alignment explanation
Indices: 42707--42771 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
42697 TTTTATAATA
*
42707 AATATTTATAATTAAATTAAA-
1 AATATTTTTAATTAAATTAAAT
*
42728 AATTATTTTTAATT-ATTTAAAT
1 AA-TATTTTTAATTAAATTAAAT
* *
42750 AATAATTTAAATTAAATTAAAT
1 AATATTTTTAATTAAATTAAAT
42772 TAATTTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTTTTAATTAAATTAAAT
Found at i:42766 original size:5 final size:5
Alignment explanation
Indices: 42756--42785 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
42746 AAATAATAAT
*
42756 TTAAA TTAAA TTAAA TTAAT TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
42786 AAATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:43687 original size:12 final size:13
Alignment explanation
Indices: 43657--43696 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
43647 AGAGAAAATG
43657 AAAGAAAG-G-AA
1 AAAGAAAGAGAAA
43668 AAAGAAAGA-AAA
1 AAAGAAAGAGAAA
*
43680 AAATAAAGAGAAA
1 AAAGAAAGAGAAA
43693 AAAG
1 AAAG
43697 TGATAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 8 0.33
12 10 0.42
13 6 0.25
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (13 bp):
AAAGAAAGAGAAA
Found at i:43755 original size:16 final size:17
Alignment explanation
Indices: 43729--43771 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
43719 TGTTATTTTT
*
43729 TTAAAAATTTTTAAATA
1 TTAATAATTTTTAAATA
*
43746 TT-ATAATTTTTATATA
1 TTAATAATTTTTAAATA
43762 TTAATAATTT
1 TTAATAATTT
43772 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATAATTTTTAAATA
Found at i:43798 original size:8 final size:8
Alignment explanation
Indices: 43754--43813 Score: 65
Period size: 8 Copynumber: 7.9 Consensus size: 8
43744 TATTATAATT
43754 TTTATATA
1 TTTATATA
*
43762 TTAATA-A
1 TTTATATA
*
43769 TTTATTTTA
1 TTTA-TATA
43778 TTT-TATA
1 TTTATATA
43785 --TATATA
1 TTTATATA
43791 TTTATATA
1 TTTATATA
43799 TTTATATA
1 TTTATATA
43807 TTTATAT
1 TTTATAT
43814 CATGTATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 1 0.02
6 4 0.09
7 7 0.16
8 27 0.63
9 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTATATA
Found at i:44745 original size:10 final size:10
Alignment explanation
Indices: 44713--44745 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
44703 TGATTTGTGT
44713 TTTAATATTA
1 TTTAATATTA
*
44723 TTTTATATT-
1 TTTAATATTA
44732 TTTAATATTA
1 TTTAATATTA
44742 TTTA
1 TTTA
44746 TTTATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATATTA
Found at i:44764 original size:17 final size:18
Alignment explanation
Indices: 44714--44768 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
44704 GATTTGTGTT
44714 TTAATATTATTTTATATTT-
1 TTAATATTA--TTATATTTA
44733 TTAATATTATT-TATTTA
1 TTAATATTATTATATTTA
*
44750 TTGATA-TATTATATTTA
1 TTAATATTATTATATTTA
44767 TT
1 TT
44769 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 9 0.27
17 15 0.45
19 9 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTAATATTATTATATTTA
Found at i:44781 original size:21 final size:22
Alignment explanation
Indices: 44712--44781 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 22
44702 CTGATTTGTG
*
44712 TTTTAA-TATTATTT-TATA-T
1 TTTTAATTATTATTTATTTATT
44731 TTTTAA-TATTATTTATTTA-T
1 TTTTAATTATTATTTATTTATT
**
44751 TGATATATTA-TATTTATTTATT
1 TTTTA-ATTATTATTTATTTATT
44773 TTTTAATTA
1 TTTTAATTA
44782 AATTAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
19 14 0.33
20 7 0.17
21 15 0.36
22 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (22 bp):
TTTTAATTATTATTTATTTATT
Found at i:44797 original size:25 final size:26
Alignment explanation
Indices: 44769--44828 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
44759 TATATTTATT
*
44769 TATTTTTTAAT-TAAATTAA-ATAAAA
1 TATTTTTTAATAT-AATAAACATAAAA
*
44794 TA-TTTCTAATATAATAAACATAAAA
1 TATTTTTTAATATAATAAACATAAAA
*
44819 TATTGTTTAA
1 TATTTTTTAA
44829 AAATATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 12 0.43
25 11 0.39
26 5 0.18
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (26 bp):
TATTTTTTAATATAATAAACATAAAA
Found at i:44841 original size:25 final size:25
Alignment explanation
Indices: 44786--44843 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
44776 TAATTAAATT
44786 AAATAAAATATTTCTAATATAATAA
1 AAATAAAATATTTCTAATATAATAA
* *
44811 ACATAAAATATTGTTTAA-A-AATATA
1 AAATAAAATATT-TCTAATATAATA-A
44836 AAATAAAA
1 AAATAAAA
44844 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 4 0.14
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAAAATATTTCTAATATAATAA
Found at i:45384 original size:109 final size:110
Alignment explanation
Indices: 45170--45411 Score: 269
Period size: 109 Copynumber: 2.2 Consensus size: 110
45160 GAACGCTAAC
*
45170 AATTCATTTTTCGCATAAATTACATAGTATTCGAACACCAAAAGATTGACCCTGAAATAGATCAT
1 AATTCATTTTTCGCATAAATTACATAGTATTCGAACACCAAAAGATTAACCCTGAAATAGATCAT
* * *
45235 TATCTAGAGTCATAAAGTGGAGTACGAGCACCCTTTATATAAAAT
66 TATCTAGAGTCATAAAGTGGAATACAAACACCCTTTATATAAAAT
* ** ** *
45280 AATTCATTTTTCACATAAATTACATAGTATTC-AGGTACCAAGGGATTAACTC-GAAATA-AGTC
1 AATTCATTTTTCGCATAAATTACATAGTATTCGA-ACACCAAAAGATTAACCCTGAAATAGA-TC
* * * **
45342 ATTGTCTAGAGTCATAAAGT-GACATGCAAACACCTTTTATATAGGAT
64 ATTATCTAGAGTCATAAAGTGGA-ATACAAACACCCTTTATATAAAAT
*
45389 AATTCACCTTTT-GCATAAATTAC
1 AATTCA-TTTTTCGCATAAATTAC
45412 TACTCGGACA
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
108 3 0.03
109 61 0.55
110 47 0.42
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (110 bp):
AATTCATTTTTCGCATAAATTACATAGTATTCGAACACCAAAAGATTAACCCTGAAATAGATCAT
TATCTAGAGTCATAAAGTGGAATACAAACACCCTTTATATAAAAT
Found at i:52161 original size:17 final size:18
Alignment explanation
Indices: 52141--52187 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
52131 CTATAAAGCA
52141 AAAAAAGAGTAACAAAGA-
1 AAAAAAGAGTAA-AAAGAG
52159 AAAAAAGA--AAAAAGAG
1 AAAAAAGAGTAAAAAGAG
52175 AAAAGAAGAGTAA
1 AAAA-AAGAGTAA
52188 TAACTTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 5 0.20
16 6 0.24
17 4 0.16
18 8 0.32
19 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAAAAGAGTAAAAAGAG
Found at i:53391 original size:58 final size:58
Alignment explanation
Indices: 53164--53384 Score: 275
Period size: 58 Copynumber: 3.8 Consensus size: 58
53154 GTAAATTAGG
* *
53164 GTCATTTAGGTCATTTTTCATGATCT-AGGGACTTTTATGC-ATTTTATGAATTTTGAT
1 GTCATTTAGGTCATTTTCCATGA-CTAAGGGACTTTGATGCAATTTTATGAATTTTGAT
* * * *
53221 GTCATTTAAGTCATTTTCCATGACAAAGGGACATTGATGCAATTTTATGAATATTGAT
1 GTCATTTAGGTCATTTTCCATGACTAAGGGACTTTGATGCAATTTTATGAATTTTGAT
* * * * * * *
53279 ATCATTTAGGTTATTTTCCATAACTAAGGGATTTTAATGTAATTTTTTGAATTTTGAT
1 GTCATTTAGGTCATTTTCCATGACTAAGGGACTTTGATGCAATTTTATGAATTTTGAT
* * *
53337 GTCATTTAGGTCATTTTCCATGACTTAGAGACTTTGCTGCAATTTTAT
1 GTCATTTAGGTCATTTTCCATGACTAAGGGACTTTGATGCAATTTTAT
53385 ATATTTTAAA
Statistics
Matches: 135, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
56 1 0.01
57 33 0.24
58 101 0.75
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (58 bp):
GTCATTTAGGTCATTTTCCATGACTAAGGGACTTTGATGCAATTTTATGAATTTTGAT
Found at i:53411 original size:116 final size:116
Alignment explanation
Indices: 53204--53415 Score: 275
Period size: 116 Copynumber: 1.8 Consensus size: 116
53194 ACTTTTATGC
*
53204 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCCATGACAAAGGGACATTGATGCAATTTTAT
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCCATGACAAAGAGACATTGATGCAATTTTAT
* * * * *
53269 GAATATTGATATCATTTAGGTTATTTTCCATAACTAAGGGATTTTAATGTA
66 GAATATTAAAATCATTCAAGTCATTTTCCATAACTAAGGGATTTTAATGTA
* * ** * *
53320 ATTTTTTGAATTTTGATGTCATTTAGGTCATTTTCCATGACTTAGAGACTTTGCTGCAATTTTAT
1 ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCCATGACAAAGAGACATTGATGCAATTTTAT
*
53385 -ATATTTTAAAAAT-ATTCAAGTCATTTTCCAT
66 GA-ATATT-AAAATCATTCAAGTCATTTTCCAT
53416 TACTTAAGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
115 1 0.01
116 77 0.95
117 3 0.04
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (116 bp):
ATTTTATGAATTTTGATGTCATTTAAGTCATTTTCCATGACAAAGAGACATTGATGCAATTTTAT
GAATATTAAAATCATTCAAGTCATTTTCCATAACTAAGGGATTTTAATGTA
Found at i:55884 original size:31 final size:31
Alignment explanation
Indices: 55846--55905 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
55836 TAAAAATAAT
*
55846 ATAAATATTAAAATAAATTAT-TTTAATTTTA
1 ATAAATATT-AAATAAAATATATTTAATTTTA
*
55877 ATAAATATTTAATAAAATATATTTAATTT
1 ATAAATATTAAATAAAATATATTTAATTT
55906 AGTAGCATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATAAATATTAAATAAAATATATTTAATTTTA
Found at i:58378 original size:98 final size:99
Alignment explanation
Indices: 58256--58450 Score: 297
Period size: 98 Copynumber: 2.0 Consensus size: 99
58246 CAAGAAATAT
* *
58256 TATTTATTGTTTTAATCATTTTTAATTATC-ATTATTTAAATATTTTTTTAATATAATTTATATA
1 TATTTATTGTTTTAATAATTTTTAATTATCAATTATTTAAA-ATTTTTTGAATATAATTTATATA
*
58320 TAATAGTAATTAAACAAAGATTATG-TTAAATTTAC
65 TAATAGT-ATTAAACAAAGATAATGTTTAAATTTAC
* * *
58355 TATTTGTTG-TTTAATAATTTTTAATTATCAATTATTTAAAATTTTTTGGATGTAATTTATATAT
1 TATTTATTGTTTTAATAATTTTTAATTATCAATTATTTAAAATTTTTTGAATATAATTTATATAT
58419 AATAGTATTAAACAAAGATAATGTTTAAATTT
66 AATAGTATTAAACAAAGATAATGTTTAAATTT
58451 TCGAAGAGTA
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
97 16 0.18
98 54 0.61
99 18 0.20
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (99 bp):
TATTTATTGTTTTAATAATTTTTAATTATCAATTATTTAAAATTTTTTGAATATAATTTATATAT
AATAGTATTAAACAAAGATAATGTTTAAATTTAC
Found at i:59131 original size:24 final size:24
Alignment explanation
Indices: 59104--59182 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
59094 TTATAATCAA
59104 AATTTTTAAAAAAAAAAAATAAAT
1 AATTTTTAAAAAAAAAAAATAAAT
* *
59128 AA--TTCAAAAATAAATAAATAAAAT
1 AATTTTTAAAAA-AAAAAAAT-AAAT
***
59152 AAAAATTAAAAAAAAAACAA-AAAT
1 AATTTTTAAAAAAAAAA-AATAAAT
59176 AATTTTT
1 AATTTTT
59183 TTGAAAATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
22 7 0.17
23 7 0.17
24 16 0.38
25 4 0.10
26 8 0.19
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.27
Consensus pattern (24 bp):
AATTTTTAAAAAAAAAAAATAAAT
Found at i:59136 original size:15 final size:14
Alignment explanation
Indices: 59118--59163 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
59108 TTTAAAAAAA
59118 AAAAATAAATAATT
1 AAAAATAAATAATT
*
59132 CAAAAATAAATAAAT
1 -AAAAATAAATAATT
59147 -AAAATAAA-AATT
1 AAAAATAAATAATT
59159 AAAAA
1 AAAAA
59164 AAAAACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 12 0.43
15 13 0.46
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATAAATAATT
Found at i:59155 original size:19 final size:19
Alignment explanation
Indices: 59110--59177 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
59100 TCAAAATTTT
59110 TAAAA-AAAAA-AAATAAA
1 TAAAATAAAAATAAATAAA
*
59127 T-AATTCAAAAATAAATAAA
1 TAAAAT-AAAAATAAATAAA
59146 TAAAATAAAAATTAAA-AAA
1 TAAAATAAAAA-TAAATAAA
*
59165 -AAAACAAAAATAA
1 TAAAATAAAAATAA
59178 TTTTTTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 14 0.33
19 16 0.37
20 7 0.16
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (19 bp):
TAAAATAAAAATAAATAAA
Found at i:59264 original size:3 final size:3
Alignment explanation
Indices: 59258--59294 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
59248 TCAAAAGCAT
59258 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
59295 ACTTTTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.