Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2551
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: 79150
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:192 original size:15 final size:16
Alignment explanation
Indices: 172--232 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 16
162 GTGAATTATA
172 TTTGAA-TTAAATTTT
1 TTTGAATTTAAATTTT
187 TTTGAATTTAAATTTGATT
1 TTTGAATTTAAA-TT--TT
* *
206 TTTTATATTTAAAATTT
1 TTTGA-ATTTAAATTTT
223 TTT-AATTTAA
1 TTTGAATTTAA
233 GTCGAGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 12 0.31
16 6 0.15
17 7 0.18
19 7 0.18
20 7 0.18
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTGAATTTAAATTTT
Found at i:542 original size:2 final size:2
Alignment explanation
Indices: 535--565 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
525 CAGAGACATG
535 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 G
566 TACCTTCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:766 original size:2 final size:2
Alignment explanation
Indices: 761--798 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
751 TCTCTCTCTC
* *
761 TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
799 GGCAGTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1383 original size:2 final size:2
Alignment explanation
Indices: 1376--1405 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1366 CCTGACATCC
1376 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1406 CACTTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1558 original size:16 final size:16
Alignment explanation
Indices: 1542--1597 Score: 94
Period size: 16 Copynumber: 3.4 Consensus size: 16
1532 AATTAAAAAA
1542 TTAATAATAATTTAAAT
1 TTAA-AATAATTTAAAT
1559 TTAAAATAATTTAAAT
1 TTAAAATAATTTAAAT
*
1575 TTAAAAAAATTTAAAT
1 TTAAAATAATTTAAAT
1591 TTAAAAT
1 TTAAAAT
1598 GATCATATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
16 33 0.89
17 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAATAATTTAAAT
Found at i:9217 original size:19 final size:20
Alignment explanation
Indices: 9186--9223 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
9176 ATATAAATTA
9186 TTAACATATTAAT-TTTTAT
1 TTAACATATTAATATTTTAT
9205 TTAA-ATATATAATATTTTA
1 TTAACATAT-TAATATTTTA
9224 AATATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAACATATTAATATTTTAT
Found at i:9232 original size:33 final size:36
Alignment explanation
Indices: 9167--9232 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
9157 ATATATAAAA
*
9167 ATTTATATAATATAAATTATTAACATATTAATTTTT
1 ATTTAAATAATATAAATTATTAACATATTAATTTTT
9203 ATTTAAAT-ATATAATATT-TTAA-ATA-TAATT
1 ATTTAAATAATATAA-ATTATTAACATATTAATT
9233 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 5 0.18
34 3 0.11
35 10 0.36
36 10 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (36 bp):
ATTTAAATAATATAAATTATTAACATATTAATTTTT
Found at i:11247 original size:21 final size:22
Alignment explanation
Indices: 11199--11253 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
11189 TATTCAAATC
** *
11199 TTAATTTTTAATTAGTTTTTAT
1 TTAATTTTTAATTAAATTTAAT
*
11221 TCAATTTTT-ATTAAATTTAAT
1 TTAATTTTTAATTAAATTTAAT
11242 TTAA-TTTTAATT
1 TTAATTTTTAATT
11254 TAGATAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.15
21 15 0.56
22 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTAATTTTTAATTAAATTTAAT
Found at i:11663 original size:31 final size:30
Alignment explanation
Indices: 11597--11664 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
11587 TAATCTAACC
*
11597 TATTTTAAAATTATATAATATATATTAATTT
1 TATTTTAAAATTATATAATATATATT-ATTA
11628 TATTTTAAAATTATATAATATATTACTT-TTA
1 TATTTTAAAATTATATAATATA-TA-TTATTA
11659 TATTTT
1 TATTTT
11665 TATATATTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 30 0.88
32 2 0.06
33 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
TATTTTAAAATTATATAATATATATTATTA
Found at i:11667 original size:26 final size:26
Alignment explanation
Indices: 11638--11691 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
11628 TATTTTAAAA
* *
11638 TTATATAATATATTACTTTTATATTT
1 TTATATAATAGATCACTTTTATATTT
* *
11664 TTATATATTAGATCATTTTTATATTT
1 TTATATAATAGATCACTTTTATATTT
11690 TT
1 TT
11692 TAAATAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTATATAATAGATCACTTTTATATTT
Found at i:11989 original size:10 final size:10
Alignment explanation
Indices: 11966--12019 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
11956 CGGTCAAATC
11966 TTAATTTTTAA
1 TTAATTTTT-A
*
11977 TTAGTTTTTA
1 TTAATTTTTA
11987 TTAATTTTTA
1 TTAATTTTTA
*
11997 TTGAA-TTTAA
1 TT-AATTTTTA
12007 TTTAATTTTTA
1 -TTAATTTTTA
12018 TT
1 TT
12020 TGAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
10 20 0.56
11 16 0.44
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (10 bp):
TTAATTTTTA
Found at i:12020 original size:11 final size:11
Alignment explanation
Indices: 11966--12020 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
11956 CGGTCAAATC
*
11966 TTAATTTTTAA
1 TTAATTTTTAT
*
11977 TTAGTTTTTA-
1 TTAATTTTTAT
11987 TTAATTTTTAT
1 TTAATTTTTAT
* *
11998 TGAA-TTTAAT
1 TTAATTTTTAT
12008 TTAATTTTTAT
1 TTAATTTTTAT
12019 TT
1 TT
12021 GAAAAATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 17 0.47
11 19 0.53
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (11 bp):
TTAATTTTTAT
Found at i:12033 original size:22 final size:20
Alignment explanation
Indices: 11986--12033 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
11976 ATTAGTTTTT
**
11986 ATTAATTTTTATTGAATTTA
1 ATTAATTTTTATTGAAAATA
12006 ATTTAATTTTTATTTGAAAAATA
1 A-TTAATTTTTA-TTG-AAAATA
12029 ATTAA
1 ATTAA
12034 GTATATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 10 0.43
22 7 0.30
23 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
ATTAATTTTTATTGAAAATA
Found at i:12393 original size:26 final size:26
Alignment explanation
Indices: 12364--12439 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 26
12354 AATCTAATTC
*
12364 ATTTTATAATTATATAATA-TATATTA
1 ATTTTATAATTATATAATATTA-AATA
*
12390 ATTTTATAATTTTAT-ATATTAAATA
1 ATTTTATAATTATATAATATTAAATA
12415 ATTTTTATAAATATATATAATATTA
1 A-TTTTAT-AAT-TATATAATATTA
12440 TAGTATAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 7 0.17
26 22 0.52
27 3 0.07
28 4 0.10
29 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTTATAATTATATAATATTAAATA
Found at i:13550 original size:2 final size:2
Alignment explanation
Indices: 13531--13568 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
13521 ATTATAGTAA
* *
13531 AT AT AT AA AT AT AA 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 AT AT AT
13569 TTGAGGGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:15247 original size:2 final size:2
Alignment explanation
Indices: 15240--15270 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15230 AACTCTTCAT
15240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15271 TAAATGATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15851 original size:34 final size:34
Alignment explanation
Indices: 15805--15989 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
15795 GTAAAAACCA
*
15805 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
15839 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
15873 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
15907 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
15941 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
15974 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
15990 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:20082 original size:19 final size:19
Alignment explanation
Indices: 20055--20117 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
20045 TCACGTGTAC
* *
20055 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
20074 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
20093 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
20112 AGTACC
1 AGTACC
20118 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:20468 original size:34 final size:34
Alignment explanation
Indices: 20422--20604 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
20412 GTAAAAACCA
*
20422 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
20456 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
20490 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
20524 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
20558 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
20591 CCATTTAATCAACA
1 CCATTTAATCAACA
20605 TTATCCAACT
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.12
34 113 0.85
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:20869 original size:2 final size:2
Alignment explanation
Indices: 20862--20886 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20852 ATTGGGTGAA
20862 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20887 GGTGGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21039 original size:18 final size:17
Alignment explanation
Indices: 20997--21039 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
20987 GATATAGGTA
20997 TTTTTA-TTATATTAAT
1 TTTTTATTTATATTAAT
* *
21013 ATTTAATTTATAATTAAT
1 TTTTTATTTAT-ATTAAT
21031 TTTTTATTT
1 TTTTTATTT
21040 TGTATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTATTTATATTAAT
Found at i:25206 original size:21 final size:21
Alignment explanation
Indices: 25158--25206 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25148 TTGAGGACGA
*
25158 TTAATAATTATCTTTAAAAGAT
1 TTAA-AATCATCTTTAAAAGAT
** *
25180 AAAAAATCATCTTTAAAAGTT
1 TTAAAATCATCTTTAAAAGAT
25201 TTAAAA
1 TTAAAA
25207 GATGAAATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (21 bp):
TTAAAATCATCTTTAAAAGAT
Found at i:25723 original size:17 final size:18
Alignment explanation
Indices: 25701--25734 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
25691 GAGCTTTGAT
25701 AAGTTTATA-TTAATAAA
1 AAGTTTATATTTAATAAA
25718 AAGTTTATATTTAATAA
1 AAGTTTATATTTAATAA
25735 TATATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AAGTTTATATTTAATAAA
Found at i:28701 original size:16 final size:16
Alignment explanation
Indices: 28680--28713 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28670 TTTATTTATG
28680 ATATTAGTACATATTA
1 ATATTAGTACATATTA
28696 ATATTAGTACATATTA
1 ATATTAGTACATATTA
28712 AT
1 AT
28714 CTACGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
ATATTAGTACATATTA
Found at i:29165 original size:2 final size:2
Alignment explanation
Indices: 29158--29198 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
29148 TTTAAAACCG
29158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29199 ATGAACTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36792 original size:22 final size:22
Alignment explanation
Indices: 36764--36808 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
36754 TTACAAGAAT
36764 GTCAGATAAGGCAAATCCAAAA
1 GTCAGATAAGGCAAATCCAAAA
36786 GTCAGATAAGGCAAATCCAAAA
1 GTCAGATAAGGCAAATCCAAAA
36808 G
1 G
36809 CTCCTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (22 bp):
GTCAGATAAGGCAAATCCAAAA
Found at i:37939 original size:51 final size:51
Alignment explanation
Indices: 37875--37984 Score: 118
Period size: 51 Copynumber: 2.1 Consensus size: 51
37865 TGATTAATAT
* *
37875 TTTAATAATTTAATTGTAAAAT-TTAATAATATAATTATAATATATAAAAAAAA
1 TTTAATAATTTAATT-TAAAATCTTAATAATATAA--ATAAAAAATAAAAAAAA
* * *
37928 TTTAA-AA-TTAATTTGATATCTTAATTATATAAATAAAAAATAAAAAAAA
1 TTTAATAATTTAATTTAAAATCTTAATAATATAAATAAAAAATAAAAAAAA
37977 TATTAATA
1 T-TTAATA
37985 TTTTTAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
49 16 0.33
50 8 0.16
51 18 0.37
52 2 0.04
53 5 0.10
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (51 bp):
TTTAATAATTTAATTTAAAATCTTAATAATATAAATAAAAAATAAAAAAAA
Found at i:40500 original size:18 final size:18
Alignment explanation
Indices: 40466--40511 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40456 AAATATAACA
* *
40466 TTATATTTTACTGAATAAT
1 TTATATATTATTGAAT-AT
40485 TT-TATATTATTGAATAT
1 TTATATATTATTGAATAT
40502 TTATATATTA
1 TTATATATTA
40512 AGAAGCACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TTATATATTATTGAATAT
Found at i:41032 original size:15 final size:15
Alignment explanation
Indices: 41012--41041 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41002 ACCAAAAATG
41012 TTGTTATTAAATATA
1 TTGTTATTAAATATA
41027 TTGTTATTAAATATA
1 TTGTTATTAAATATA
41042 ACAAAAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TTGTTATTAAATATA
Found at i:45234 original size:2 final size:2
Alignment explanation
Indices: 45227--45252 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45217 TTGGATCCTT
45227 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
45253 AGGTGACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47916 original size:36 final size:36
Alignment explanation
Indices: 47876--47948 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
47866 CATTAATATT
* *
47876 TAATTTATTTTACTTATAATATTAATGATTAAATCA
1 TAATTTATGTTACATATAATATTAATGATTAAATCA
47912 TAATTTATGTTACATATAATATTAATGATTAAATCA
1 TAATTTATGTTACATATAATATTAATGATTAAATCA
47948 T
1 T
47949 GTTTAATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (36 bp):
TAATTTATGTTACATATAATATTAATGATTAAATCA
Found at i:48519 original size:2 final size:2
Alignment explanation
Indices: 48514--48539 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48504 ATTCTTTGAG
48514 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
48540 GAAAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48842 original size:22 final size:22
Alignment explanation
Indices: 48816--48857 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
48806 CTAATTAAAA
*
48816 GTTTA-ATGTTTATTTAATTTTG
1 GTTTAGAT-TTTATTGAATTTTG
48838 GTTTAGATTTTATTGAATTT
1 GTTTAGATTTTATTGAATTT
48858 AATTCGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (22 bp):
GTTTAGATTTTATTGAATTTTG
Found at i:49401 original size:2 final size:2
Alignment explanation
Indices: 49345--49383 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
49335 TTTTTAACTT
49345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49384 GAAACCACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50269 original size:45 final size:45
Alignment explanation
Indices: 50127--51852 Score: 2406
Period size: 45 Copynumber: 38.2 Consensus size: 45
50117 CTTAGTCAAC
* * *
50127 TAAAAAAGAACCCAAAAAAAACTCATTTTGTAAGTTTTGGT--ATA
1 TAAAAAA-AACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*** ** * *
50171 TAAAAAATATTTCAAGAAAATTTTTTTTTGTAAGTCTTGATCAATA
1 TAAAAAA-AACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* * ** *
50217 TAAAAAAAAACTCAAGAAAAACTTTTTTTGTAAGTCTTATTTAATA
1 T-AAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* *
50263 TAAAAAAAACTCAAGAAAAACTCTTTTTGTAAGTCTTGATCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
50308 T-AAAAAAACCCAAGAAAAACTCATTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
50352 TAAAAAAAACCTAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
50397 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* * *
50442 TAAAAAAAAACCAAGAAAAACTTTTTTTGTAAGTCTTCGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
**
50487 TAAAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTCTTCAATA
1 T--AAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
50534 T-AAAAAAA-CCAAGAAAAACTCTTTTTGTAAGTCTTCGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* * *
50577 TAAAAAAAATCCAAGAAAAACTCTTTTTATAAGTCTTCGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
50622 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* *
50667 TAAAAAAAACCCAAGAAAAACTCATTTTGTAAGTCTTGGTTAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
50712 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
50757 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
50802 TAAAAAAAACCCAAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCC-AAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
50848 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
50893 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* * *
50938 TAAAAAAAAACCAAGAAAAACTCTTTTTGTAAGTCTTCGTTAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* * ** *
50983 TAAAAAAAA-TCAAGAAAAACTCTTTTTGTAAGTTTTCATTAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
51027 T-AAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGATCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
51071 TAAAAAAAA-CCAAGAAAAACTCTTTTTGTAAGTCTTGATCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
51115 T-AAAAAAACCCAAGAAAAACTCATTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
**
51159 TAAAAAAAACTTAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
51204 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
** *
51249 TAAAAAAAAATCAAGAAAAACTCTTTTTGTAAGTCTTCGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
51294 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
51339 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
51384 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGATCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
51429 T-AAAAAAA-CTAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
51472 T-AAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGATCAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
*
51516 TAAAAAAAAAATCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
1 T--AAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* *
51563 TAAAAAAAACCCAAGAAAAACTTTTTTTTGTAAGTCTTCGTCAATA
1 TAAAAAAAACCCAAGAAAAAC-TCTTTTTGTAAGTCTTGGTCAATA
* *
51609 T-AAAAAAACCTAAAAAAAACTCTTTTTGTAAGTATTTTTGTAAGTCTTGGTCAATA
1 TAAAAAAAACCCAAGAAAAACTC------------TTTTTGTAAGTCTTGGTCAATA
* * * * *
51665 TAAAAAAAAACCTAAAAAAAAAT-TTTTTGTAAGTTTTGATCAATA
1 TA-AAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
** ** * *
51710 T-AAAAAAACTTAA-AAAATTTTTTTTTTGTAAGTCTTGGACAATA
1 TAAAAAAAACCCAAGAAAA-ACTCTTTTTGTAAGTCTTGGTCAATA
* * * * ** *
51754 T-AAAAAAATCCAAAAAAAACTCTTTTTATAAATCTTAATTAATA
1 TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
* * * * * * *
51798 TAAAAAAAACTCAAAAAAAAAATTTTTTTGTATGTTTTGATCAATA
1 TAAAAAAAAC-CCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
51844 TAAAAAAAA
1 TAAAAAAAA
51853 TTAAAAAAAA
Statistics
Matches: 1534, Mismatches: 111, Indels: 72
0.89 0.06 0.04
Matches are distributed among these distances:
42 4 0.00
43 102 0.07
44 309 0.20
45 849 0.55
46 139 0.09
47 90 0.06
56 22 0.01
58 19 0.01
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (45 bp):
TAAAAAAAACCCAAGAAAAACTCTTTTTGTAAGTCTTGGTCAATA
Found at i:51649 original size:56 final size:56
Alignment explanation
Indices: 51587--51698 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
51577 GAAAAACTTT
*
51587 TTTTTGTAAGTCTTCGTCAATAT-AAAAAAACCTAAAAAAAACTCTTTTTGTAAGTA
1 TTTTTGTAAGTCTTCGTCAATATAAAAAAAACCTAAAAAAAAAT-TTTTTGTAAGTA
*
51643 TTTTTGTAAGTCTTGGTCAATATAAAAAAAAACCTAAAAAAAAATTTTTTGTAAGT
1 TTTTTGTAAGTCTTCGTCAATAT-AAAAAAAACCTAAAAAAAAATTTTTTGTAAGT
51699 TTTGATCAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
56 22 0.42
57 11 0.21
58 19 0.37
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (56 bp):
TTTTTGTAAGTCTTCGTCAATATAAAAAAAACCTAAAAAAAAATTTTTTGTAAGTA
Found at i:51742 original size:101 final size:102
Alignment explanation
Indices: 51541--51726 Score: 288
Period size: 101 Copynumber: 1.8 Consensus size: 102
51531 AGAAAAACTC
**
51541 TTTTTGTAAGTCTTGGTCAATATAAAAAAAACCCAAGAAAAACTTTTTTTTGTAAGTCTTCGTCA
1 TTTTTGTAAGTCTTGGTCAATATAAAAAAAACCCAAGAAAAACAATTTTTTGTAAGTCTTCGTCA
51606 ATATAAAAAAACCTAAAAAAAACTCTTTTTGTAAGTA
66 ATATAAAAAAACCTAAAAAAAACTCTTTTTGTAAGTA
* *
51643 TTTTTGTAAGTCTTGGTCAATATAAAAAAAAACCTAA-AAAAA-AATTTTTTGTAAGT-TTTGAT
1 TTTTTGTAAGTCTTGGTCAATAT-AAAAAAAACCCAAGAAAAACAATTTTTTGTAAGTCTTCG-T
*
51705 CAATATAAAAAAACTTAAAAAA
64 CAATATAAAAAAACCTAAAAAA
51727 TTTTTTTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
100 3 0.04
101 34 0.44
102 28 0.36
103 12 0.16
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (102 bp):
TTTTTGTAAGTCTTGGTCAATATAAAAAAAACCCAAGAAAAACAATTTTTTGTAAGTCTTCGTCA
ATATAAAAAAACCTAAAAAAAACTCTTTTTGTAAGTA
Found at i:51859 original size:45 final size:44
Alignment explanation
Indices: 51643--51862 Score: 203
Period size: 44 Copynumber: 4.9 Consensus size: 44
51633 TTTGTAAGTA
* * *
51643 TTTTTGTAAGTCTTGGTCAATATAAAAAAAAACCTAAAAAAAAA-T
1 TTTTTGTAAGTTTTGATCAATAT-AAAAAAAA-TTAAAAAAAAATT
* ***
51688 TTTTTGTAAGTTTTGATCAATATAAAAAAACTTAAAAAATTTTT
1 TTTTTGTAAGTTTTGATCAATATAAAAAAAATTAAAAAAAAATT
* * * *
51732 TTTTTGTAAGTCTTGGA-CAATAT-AAAAAAATCCAAAAAAAACTC
1 TTTTTGTAAGT-TTTGATCAATATAAAAAAAAT-TAAAAAAAAATT
* * * * * *
51776 TTTTTATAAATCTTAATTAATATAAAAAAAACTCAAAAAAAAAATT
1 TTTTTGTAAGTTTTGATCAATATAAAAAAAA-T-TAAAAAAAAATT
*
51822 TTTTTGTATGTTTTGATCAATATAAAAAAAATTAAAAAAAA
1 TTTTTGTAAGTTTTGATCAATATAAAAAAAATTAAAAAAAA
51863 CTCTTGTTAT
Statistics
Matches: 139, Mismatches: 30, Indels: 13
0.76 0.16 0.07
Matches are distributed among these distances:
43 16 0.12
44 54 0.39
45 33 0.24
46 36 0.26
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.36
Consensus pattern (44 bp):
TTTTTGTAAGTTTTGATCAATATAAAAAAAATTAAAAAAAAATT
Found at i:52979 original size:24 final size:23
Alignment explanation
Indices: 52930--52972 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
52920 TTAAATTGTA
*
52930 TTTAAATAATTCATATAATTATT
1 TTTAAATAATTAATATAATTATT
52953 TTTAAA-AATTAATAT-ATTAT
1 TTTAAATAATTAATATAATTAT
52973 ATGTTTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAAATAATTAATATAATTATT
Found at i:53350 original size:22 final size:22
Alignment explanation
Indices: 53322--53391 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
53312 TTTTTTTTAA
53322 TAATAATACGTATTAATATTTT
1 TAATAATACGTATTAATATTTT
* * * *
53344 TAGTAATAAACAT-TTGATTTTTT
1 TAATAAT--ACGTATTAATATTTT
53367 AATAATAATACGTATTAATATTTT
1 --TAATAATACGTATTAATATTTT
53391 T
1 T
53392 TTTAATAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
22 7 0.20
23 11 0.31
24 11 0.31
25 6 0.17
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (22 bp):
TAATAATACGTATTAATATTTT
Found at i:53350 original size:28 final size:28
Alignment explanation
Indices: 53310--53410 Score: 114
Period size: 28 Copynumber: 3.9 Consensus size: 28
53300 CTAAACCTAT
53310 TATTTTTTTTAATAATAATACGTATTAA
1 TATTTTTTTTAATAATAATACGTATTAA
*
53338 TA---TTTTTAGTAATAA-AC--ATT--
1 TATTTTTTTTAATAATAATACGTATTAA
53358 TGA--TTTTTTAATAATAATACGTATTAA
1 T-ATTTTTTTTAATAATAATACGTATTAA
53385 TATTTTTTTTAATAATAATACGTATT
1 TATTTTTTTTAATAATAATACGTATT
53411 TATAGTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 15 0.24
23 2 0.03
24 2 0.03
25 15 0.24
26 1 0.02
27 1 0.02
28 24 0.39
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (28 bp):
TATTTTTTTTAATAATAATACGTATTAA
Found at i:53420 original size:47 final size:47
Alignment explanation
Indices: 53314--53421 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 47
53304 ACCTATTATT
* **
53314 TTTTTTAATAATAATACGTATTAATATTTTTAGTAATAAACATTTGA
1 TTTTATAATAATAATACGTATTAATATTTTTAGTAATAAACATACGA
* **
53361 TTTTTTAATAATAATACGTATTAATATTTTTTTTAATAATA-ATACG-
1 TTTTATAATAATAATACGTATTAATATTTTTAGTAATAA-ACATACGA
*
53407 TATTTATAGTAATAA
1 T-TTTATAATAATAA
53422 ACATTTGATT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.96
48 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTTATAATAATAATACGTATTAATATTTTTAGTAATAAACATACGA
Found at i:53491 original size:13 final size:11
Alignment explanation
Indices: 53463--53501 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
53453 CAGTTTTAGA
53463 TTTATTAATAT
1 TTTATTAATAT
53474 TTTATTAATAT
1 TTTATTAATAT
53485 TTT-TTATATAT
1 TTTATTA-ATAT
53496 ATTTAT
1 -TTTAT
53502 AATTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 18 0.72
12 3 0.12
13 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:53728 original size:16 final size:15
Alignment explanation
Indices: 53719--53787 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
53709 AAAATGTAAT
53719 TATAAAAAAATAAAA
1 TATAAAAAAATAAAA
*
53734 TATAAAAAATTAAAA
1 TATAAAAAAATAAAA
*
53749 TTGATTTAAAAAATAAAA
1 -T-A-TAAAAAAATAAAA
* *
53767 TAAATAAAAAATTAAA
1 TATA-AAAAAATAAAA
53783 T-TAAA
1 TATAAA
53788 TCAACTAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
14 2 0.05
15 15 0.35
16 13 0.30
17 2 0.05
18 11 0.26
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (15 bp):
TATAAAAAAATAAAA
Found at i:69547 original size:80 final size:81
Alignment explanation
Indices: 69401--69563 Score: 256
Period size: 80 Copynumber: 2.0 Consensus size: 81
69391 TATAGACCCC
* * *
69401 TTAAGACACTCAAGTATAAATAGACAGGATAGTCATTCACAAACTATTCTACTTCTATTTCCCTA
1 TTAAGACACTCAAGTATAAAAAGACAGGAAAGTCATTCACAAACTATTCTACTTCTACTTCCCTA
**
69466 CTTTGCCATTCTATAT
66 CTTTAACATTCTATAT
* *
69482 TTAA-ACACTCAAGTATAAAAAGATAGGAAAGTCATTCACAAACTATTCTACTTCTACTTCTCTA
1 TTAAGACACTCAAGTATAAAAAGACAGGAAAGTCATTCACAAACTATTCTACTTCTACTTCCCTA
69546 CTTTAACATTCTATAT
66 CTTTAACATTCTATAT
69562 TT
1 TT
69564 GCTCTAAAGC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
80 71 0.95
81 4 0.05
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (81 bp):
TTAAGACACTCAAGTATAAAAAGACAGGAAAGTCATTCACAAACTATTCTACTTCTACTTCCCTA
CTTTAACATTCTATAT
Found at i:72685 original size:18 final size:17
Alignment explanation
Indices: 72643--72691 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
72633 GATATAGGTA
72643 TTTTTA-TTATATTAAT
1 TTTTTATTTATATTAAT
* *
72659 ATTTAATTTATAATTAAT
1 TTTTTATTTAT-ATTAAT
72677 TTTTTATTTTATATT
1 TTTTTA-TTTATATT
72692 TTTTGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 13 0.50
19 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTATTTATATTAAT
Found at i:74605 original size:21 final size:21
Alignment explanation
Indices: 74579--74618 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
74569 AAAGATATCT
*
74579 TTGAATGAAATGATGTATTGG
1 TTGAATGAAATAATGTATTGG
74600 TTGAATGAAATAATGTATT
1 TTGAATGAAATAATGTATT
74619 TTTTAGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.40
Consensus pattern (21 bp):
TTGAATGAAATAATGTATTGG
Found at i:74642 original size:20 final size:21
Alignment explanation
Indices: 74604--74643 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
74594 TATTGGTTGA
**
74604 ATGAAATAATGTATTTTTTAG
1 ATGAAATAATGTAACTTTTAG
74625 ATGAAA-AATGTAACTTTTA
1 ATGAAATAATGTAACTTTTA
74644 ATAATCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGAAATAATGTAACTTTTAG
Found at i:77993 original size:21 final size:21
Alignment explanation
Indices: 77968--78022 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
77958 GTATCTTTGA
*
77968 ATGAAATGATGCATTGGTTGG
1 ATGAAATAATGCATTGGTTGG
**
77989 ATGAAATAATGCATTTTTTGG
1 ATGAAATAATGCATTGGTTGG
*
78010 ATGAAAAAATGCA
1 ATGAAATAATGCA
78023 ACTTCTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (21 bp):
ATGAAATAATGCATTGGTTGG
Done.