Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold563
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: 35135
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:370 original size:20 final size:19
Alignment explanation
Indices: 324--382 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
314 TTGTATCGAT
*
324 ACATTGTATCTATACATGA
1 ACATTGTATCAATACATGA
*
343 TCATTGTATCAATACATGA
1 ACATTGTATCAATACATGA
*
362 ACAATTGTATCGATACATGA
1 AC-ATTGTATCAATACATGA
382 A
1 A
383 ACTGGCAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
ACATTGTATCAATACATGA
Found at i:443 original size:13 final size:13
Alignment explanation
Indices: 425--477 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
415 CGATACATGG
425 TACATTGTATCGA
1 TACATTGTATCGA
438 TACATTGTATCGA
1 TACATTGTATCGA
451 TACA-TG-AT-G-
1 TACATTGTATCGA
460 -A-ATTGTATCGA
1 TACATTGTATCGA
471 TACATTG
1 TACATTG
478 CTTGTAATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:451 original size:33 final size:33
Alignment explanation
Indices: 409--477 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
399 CTACCACTGT
*
409 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
442 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
475 TTG
1 TTG
478 CTTGTAATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:562 original size:72 final size:72
Alignment explanation
Indices: 443--619 Score: 320
Period size: 72 Copynumber: 2.5 Consensus size: 72
433 ATCGATACAT
* *
443 TGTATCGATACATGATGAATTGTATCGATACATTGCTTGTAATGGCTATAAACA-TCTATAATTT
1 TGTATCGATACATTATGAATTGTATCGATACATTGCTTGTAACGGCTATAAACAGT-TATAATTT
507 CAAATCAA
65 CAAATCAA
515 TGTATCGATACATTATGAATTGTATCGATACATTGCTTGTAACGGCTATAAACAGTTATAATTTC
1 TGTATCGATACATTATGAATTGTATCGATACATTGCTTGTAACGGCTATAAACAGTTATAATTTC
580 AAATCAA
66 AAATCAA
587 TGTATCGATACATTATGAATTGTATCGATACAT
1 TGTATCGATACATTATGAATTGTATCGATACAT
620 GGCTATGAGA
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
72 101 0.99
73 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (72 bp):
TGTATCGATACATTATGAATTGTATCGATACATTGCTTGTAACGGCTATAAACAGTTATAATTTC
AAATCAA
Found at i:1486 original size:15 final size:16
Alignment explanation
Indices: 1466--1496 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1456 TTTTTTTATG
1466 AAAATAAAAAA-TTTT
1 AAAATAAAAAAGTTTT
1481 AAAATAAAAAAGTTTT
1 AAAATAAAAAAGTTTT
1497 TTATTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAATAAAAAAGTTTT
Found at i:1575 original size:20 final size:20
Alignment explanation
Indices: 1509--1575 Score: 53
Period size: 22 Copynumber: 3.1 Consensus size: 20
1499 ATTATAATTT
* * *
1509 TTAATAAATAAAAATAATAT
1 TTAATAAATTAAAATATTAA
* *
1529 TTAATTAAGTTTAAAAAATTTACA
1 TTAA-TAA-ATTAAAATA-TTA-A
1553 TTAATAAATTAAAATATTAA
1 TTAATAAATTAAAATATTAA
1573 TTA
1 TTA
1576 TTATGTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
20 8 0.22
21 6 0.17
22 13 0.36
23 5 0.14
24 4 0.11
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
TTAATAAATTAAAATATTAA
Found at i:1650 original size:19 final size:18
Alignment explanation
Indices: 1605--1657 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
1595 AAATTTTAAA
1605 TTTTAAA-ATTTTTTTAT
1 TTTTAAATATTTTTTTAT
* *
1622 TATAATAATATTTTTTTATT
1 TTTTA-AATATTTTTTTA-T
1642 TTTTAAATATATTTTT
1 TTTTAAATAT-TTTTT
1658 GAGAAAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 14 0.50
20 9 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAAATATTTTTTTAT
Found at i:1651 original size:123 final size:123
Alignment explanation
Indices: 1381--1627 Score: 390
Period size: 123 Copynumber: 2.0 Consensus size: 123
1371 TAAGTATTAG
1381 TTTTTAATAAAATTAAAAATAATATTTAATTAAGTTTAAAAAAATTACAGTAACAAATTAAAATA
1 TTTTTAAT-AAA-TAAAAATAATATTTAATTAAGTTTAAAAAAATTACAGTAACAAATTAAAATA
*
1446 TTAATTATTATTTTTTTATGAAAATAAAAAATTTTAAAATAAAAAAGTTTTTTATTATAA
64 TTAATTATTATGTTTTTATGAAAATAAAAAATTTTAAAATAAAAAAGTTTTTTATTATAA
* * *
1506 TTTTTAATAAATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAATAAATTAAAATATT
1 TTTTTAATAAATAAAAATAATATTTAATTAAGTTTAAAAAAATTACAGTAACAAATTAAAATATT
* ** *
1571 AATTATTATGTTTTT-T-AAAATAAAAAATTTTAAATTTTAAAATTTTTTTATTATAA
66 AATTATTATGTTTTTATGAAAATAAAAAATTTTAAAATAAAAAAGTTTTTTATTATAA
1627 T
1 T
1628 AATATTTTTT
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
121 37 0.32
122 1 0.01
123 65 0.57
124 3 0.03
125 8 0.07
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (123 bp):
TTTTTAATAAATAAAAATAATATTTAATTAAGTTTAAAAAAATTACAGTAACAAATTAAAATATT
AATTATTATGTTTTTATGAAAATAAAAAATTTTAAAATAAAAAAGTTTTTTATTATAA
Found at i:1942 original size:20 final size:21
Alignment explanation
Indices: 1918--1988 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 21
1908 ATAAAGATAA
1918 ATTTTTTTAATTCT-TTAA-AT
1 ATTTTTTTAATT-TGTTAATAT
*
1938 -GTTTTTTAATTTGTTAATAT
1 ATTTTTTTAATTTGTTAATAT
*
1958 ATTTTTTTAATTTAATTAAATAT
1 ATTTTTTTAATTT-GTT-AATAT
1981 CATTTTTT
1 -ATTTTTT
1989 ATTTTATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.02
19 14 0.33
20 2 0.05
21 11 0.26
22 2 0.05
23 5 0.12
24 7 0.17
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTTTTTAATTTGTTAATAT
Found at i:1979 original size:23 final size:22
Alignment explanation
Indices: 1939--1998 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
1929 TCTTTAAATG
*
1939 TTTTTTAATTTGTTAATAT-AT
1 TTTTTTAATTTATTAATATCAT
1960 TTTTTTAATTTAATTAAATATCA-
1 TTTTTTAATTT-ATT-AATATCAT
*
1983 TTTTTTATTTTATTAA
1 TTTTTTAATTTATTAA
1999 AAAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 13 0.38
22 5 0.15
23 15 0.44
24 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTTAATTTATTAATATCAT
Found at i:1980 original size:21 final size:20
Alignment explanation
Indices: 1918--1999 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 20
1908 ATAAAGATAA
1918 ATTTTTTTAATTCT-TTAAAT
1 ATTTTTTTAATT-TATTAAAT
* *
1938 -GTTTTTTAATTTGTTAATAT
1 ATTTTTTTAATTTATTAA-AT
1958 ATTTTTTTAATTTAATTAAAT
1 ATTTTTTTAATTT-ATTAAAT
*
1979 ATCATTTTTTATTTTATTAAA
1 AT--TTTTTTAATTTATTAAA
2000 AAATAATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.02
19 14 0.27
20 2 0.04
21 15 0.29
22 10 0.19
23 10 0.19
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTTTTTAATTTATTAAAT
Found at i:2022 original size:32 final size:32
Alignment explanation
Indices: 1984--2046 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1974 TAAATATCAT
*
1984 TTTTTATTTTATTAAAAA-ATAATAATAAATAC
1 TTTTTATTTTA-TAAAAACATAAAAATAAATAC
*
2016 TTTTTATTTTATAAAAACATAAAAATTAATA
1 TTTTTATTTTATAAAAACATAAAAATAAATA
2047 TTTAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (32 bp):
TTTTTATTTTATAAAAACATAAAAATAAATAC
Found at i:2050 original size:29 final size:30
Alignment explanation
Indices: 1985--2054 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
1975 AAATATCATT
*
1985 TTTTATTTTATTAAAAAATAATAATAAATA
1 TTTTATTTTATTAAAAAATAAAAATAAATA
*
2015 CTTTTTATTTTA-TAAAAACATAAAAATTAATA
1 --TTTTATTTTATTAAAAA-ATAAAAATAAATA
*
2047 TTTAATTT
1 TTTTATTT
2055 GTTAATGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.21
31 6 0.18
32 21 0.62
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTTATTTTATTAAAAAATAAAAATAAATA
Found at i:2220 original size:112 final size:107
Alignment explanation
Indices: 1942--2292 Score: 316
Period size: 105 Copynumber: 3.2 Consensus size: 107
1932 TTAAATGTTT
* * * * *
1942 TTTAATTTGTTAATAT-ATTTTTTTAATTTAATTAAATATCATTTTTTATTTTATTAAAA-AATA
1 TTTAATTTATTAATGTAATTTTTTAAAGTTAATTAAATATCA-TTTTTATTTTA-AAAAATAATA
* *
2005 ATAA-----TAA-AT-ACTTTTTATTTTATAAAAACATAAAAATTAATA
64 ATAACTTTTTAATTTAATTTTTTATTTTA-AAAAA-AT---AATTAATA
* *
2047 TTTAATTTGTTAATGTAA-TTTTTAAATTTAATTAAATATCATTTTTATTTATTAAAAAATAATA
1 TTTAATTTATTAATGTAATTTTTTAAAGTTAATTAAATATCATTTTTA-TT-TTAAAAAATAAT-
* *
2111 ATATAAACCCTTTTTAATTTAATTTTTTATTTT-TAACAATAATTAATA
63 A-AT-AA--CTTTTTAATTTAATTTTTTATTTTAAAAAAATAATTAATA
* *
2159 TTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTA-TTTTA--TTAAAAAATAATAA
1 TTTAATTTATTAATGTAA-TTTTTTAAAGTTAATTAAATATCATTTTTATTTTAAAAAATAATAA
*
2221 TAAGTTTTTAATTTAATTTTTTATTTTAAAAAAATAATTAATA
65 TAACTTTTTAATTTAATTTTTTATTTTAAAAAAATAATTAATA
2264 TTTTTAATTTATTAATGTAAATTTTTTAA
1 --TTTAATTTATTAATGT-AATTTTTTAA
2293 TACATTATTA
Statistics
Matches: 209, Mismatches: 15, Indels: 42
0.79 0.06 0.16
Matches are distributed among these distances:
104 29 0.14
105 56 0.27
106 9 0.04
107 26 0.12
108 5 0.02
109 14 0.07
112 24 0.11
113 5 0.02
114 21 0.10
115 2 0.01
116 6 0.03
117 1 0.00
118 11 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (107 bp):
TTTAATTTATTAATGTAATTTTTTAAAGTTAATTAAATATCATTTTTATTTTAAAAAATAATAAT
AACTTTTTAATTTAATTTTTTATTTTAAAAAAATAATTAATA
Found at i:2232 original size:40 final size:39
Alignment explanation
Indices: 2188--2272 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
2178 TTTTTTAAAG
2188 TTAATTAAATATTATTT-TATT-AAAAAATAA-TAATAAGTTT
1 TTAATTAAAT-TT-TTTATATTAAAAAAATAATTAAT-A-TTT
* *
2228 TTAATTTAATTTTTTATTTTAAAAAAATAATTAATATTT
1 TTAATTAAATTTTTTATATTAAAAAAATAATTAATATTT
2267 TTAATT
1 TTAATT
2273 TATTAATGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 3 0.08
39 14 0.35
40 19 0.47
41 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (39 bp):
TTAATTAAATTTTTTATATTAAAAAAATAATTAATATTT
Found at i:2290 original size:109 final size:108
Alignment explanation
Indices: 2039--2292 Score: 304
Period size: 107 Copynumber: 2.3 Consensus size: 108
2029 AAAACATAAA
* * * *
2039 AATTAATATTTAATTTGTTAATGTAA--TTTTTAAATTTAATTAAATATCATTTTTATTTATTAA
1 AATTAATATTTAATTTATTAATATAATTTTTTTAAAGTTAATT-AA-AT-A-TTAT-TTTATTAA
* *
2102 AAAATAATAATATAAACCCTTTTTAATTTAATTTTTTATTTTTAACAAT
61 AAAATAATAATATAAA-CCTTTTTAATTTAATTTTTTATTTTAAAAAAT
2151 AATTAATATTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTATTAAAAAAT
1 AATTAATATTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTATTAAAAAAT
*
2216 AAT-A-AT-AA-GTTTTTAATTTAATTTTTTATTTTAAAAAAAT
66 AATAATATAAACCTTTTTAATTTAATTTTTTATTTT-AAAAAAT
* *
2256 AATTAATATTTTTAATTTATTAATGTAAATTTTTTAA
1 AATTAATA--TTTAATTTATTAATATAATTTTTTTAA
2293 TACATTATTA
Statistics
Matches: 128, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
104 23 0.18
105 13 0.10
106 2 0.02
107 27 0.21
108 1 0.01
109 16 0.12
110 3 0.02
111 1 0.01
112 26 0.20
113 2 0.02
114 14 0.11
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (108 bp):
AATTAATATTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTATTAAAAAAT
AATAATATAAACCTTTTTAATTTAATTTTTTATTTTAAAAAAT
Found at i:5352 original size:18 final size:20
Alignment explanation
Indices: 5326--5364 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
5316 TAAATACATA
*
5326 TTTAGATATA-GAT-AATTT
1 TTTAAATATATGATAAATTT
5344 TTTAAATATATGATAAATTT
1 TTTAAATATATGATAAATTT
5364 T
1 T
5365 AAAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTAAATATATGATAAATTT
Found at i:5912 original size:15 final size:14
Alignment explanation
Indices: 5868--5916 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
5858 TAAACTTATC
5868 AAAAGCAATTCATA
1 AAAAGCAATTCATA
*
5882 AAAA-CAA-TCTAGA
1 AAAAGCAATTC-ATA
5895 AAATAGCAATTCAT-
1 AAA-AGCAATTCATA
5909 AAAAGCAA
1 AAAAGCAA
5917 GGCAACATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
12 2 0.07
13 13 0.45
14 8 0.28
15 4 0.14
16 2 0.07
ACGTcount: A:0.59, C:0.14, G:0.08, T:0.18
Consensus pattern (14 bp):
AAAAGCAATTCATA
Found at i:11051 original size:52 final size:51
Alignment explanation
Indices: 10883--11781 Score: 184
Period size: 52 Copynumber: 17.6 Consensus size: 51
10873 GTATTTACAG
* * * * *
10883 GGCTTGACCTCCTTATAGAA-GTGCCAACTAATGTGGACTTAGATTATAT-A
1 GGCTTGACCTCTTTATA-AAGGTGCCAACTAATATGGATTTGGATTCTATAA
** * * * *
10933 GGCTTGACCT-TCCGATACAA-GAGCTAGCTAATATAGATTTGGATTCTATAA
1 GGCTTGACCTCT-TTATA-AAGGTGCCAACTAATATGGATTTGGATTCTATAA
* * *
10984 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGACTTTGGGTTCTTTAG
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGA-TTTGGATTCTATAA
* * * * * * * * *
11036 GGCTTTACCTTTTTATACAGGTGTCAGCTAATATGGATTTTGACTCTACAG
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGATTTGGATTCTATAA
* ** * ** * * * **
11087 GGCTTGAGCTCCCTATACAA-GTGCTAGTTGATGTGGAGTTAGGGCTCTAT-A
1 GGCTTGACCTCTTTATA-AAGGTGCCAACTAATATGGA-TTTGGATTCTATAA
* * * * * * * * *
11138 GAGCTTGAGCTCTATACACAA-GTGCTAGCTAATGTAGACTTCGACTT-TATAA
1 G-GCTTGACCTCTTTATA-AAGGTGCCAACTAATATGGATTTGGA-TTCTATAA
* * * *
11190 TGCTTGACCTTTTTATACAA-GTGCCAACTAATATGGAGTTTGGGTCCTAT-A
1 GGCTTGACCTCTTTATA-AAGGTGCCAACTAATATGGA-TTTGGATTCTATAA
** * ** * * * *
11241 GTGCTTGACCTCTCCATTCAA-GT-ATAAGCTAGTATGGACTTGGACTCTATAG
1 G-GCTTGACCTCTTTA-TAAAGGTGCCAA-CTAATATGGATTTGGATTCTATAA
* * * * ** * *
11293 GGCTTGACCTCATAATATAGATGCCAGTTAATGTGGATTTTGG-TATCTATTA
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGA-TTTGGAT-TCTATAA
* * * * * * * * * * * *
11345 GGCTTGACATCCTTATATAGGTGCCAGCTAGTGTGAACTTAGTTTCTGTAG
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGATTTGGATTCTATAA
* * * * * * * *
11396 GGACTT--CC-C--TATATAGGTGCCAGCTAGTGTGGACTTGCATTCTCTAG
1 GG-CTTGACCTCTTTATAAAGGTGCCAACTAATATGGATTTGGATTCTATAA
** * * * *
11443 GGCTTGACCTCCCTATATAGGTGCCAGCTAATATGGACTTTGGGTTCTATAG
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGA-TTTGGATTCTATAA
* ** * * * * * * * * *
11495 GGCTTGATCTCCCTATACAGTTTCTAGCTAGTATGGA-TTAGATTTTATGA
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGATTTGGATTCTATAA
* * * * *** * ** * *
11545 GGCTTGTCCTCTCTATACATGTGCCCGTTAATGTAAACTTTGGGTTTTAT-A
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGA-TTTGGATTCTATAA
* ** ** * * * *
11596 GAGCTTAACCTCCCTATGCAGGTGCCAACTAGTGTAGACTTGGATTCTATAA
1 G-GCTTGACCTCTTTATAAAGGTGCCAACTAATATGGATTTGGATTCTATAA
** * * * *
11648 GGCTTGACCTCCCTATACAGGTGCTAGCTAATATGGACATT-GAGTTCTATAA
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGA-TTTGGA-TTCTATAA
* * * * * * *
11700 GGTTTGACCTCCTTATATAGGTGCCAACTACTACGGACTTGGATTTCTATAG
1 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGATTTGGA-TTCTATAA
* * * *
11752 GGCTTGACCTATATATAGAGGTTCCAACTA
1 GGCTTGACCTCTTTATAAAGGTGCCAACTA
11782 GTGTGGATGC
Statistics
Matches: 627, Mismatches: 187, Indels: 68
0.71 0.21 0.08
Matches are distributed among these distances:
46 3 0.00
47 35 0.06
48 2 0.00
49 2 0.00
50 73 0.12
51 200 0.32
52 311 0.50
53 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (51 bp):
GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGATTTGGATTCTATAA
Found at i:11329 original size:206 final size:206
Alignment explanation
Indices: 10878--11329 Score: 461
Period size: 206 Copynumber: 2.2 Consensus size: 206
10868 TTTTGGTATT
* * ** * ** * *
10878 TACAGGGCTTGACCTCCTTATAGAAGTGCCAACTAATGTGGACTTA-GATTATATAG-GCTTGAC
1 TACAGGGCTTGACCTCCATATACAAGTGCCAGTTAATGTGGAGTTAGGGCTCTATAGAGCTTGAG
* * *
10941 CTTCCGAT--ACAAGAGCTAGCTAATATAGATTTGGATTCTATAAGGCTTGACCTCTTTATAAAG
66 C-T-CTATACACAAGAGCTAGCTAATATAGACTTCGATTCTATAAGGCTTGACCTCTTTATAAAG
* * * * ** * * *
11004 GTGCCAACTAATATGGACTTTGGGTTCTTTAGGGCTTTACCTTTTTATACAGGTGTCAGCTAATA
129 GTGCCAACTAATATGGACTTTGGGTCCTATAGGGCTTGACCTCTCCATACAAGTATAAGCTAATA
* *
11069 TGGATTTTGACTC
194 TGGACTTGGACTC
* * * *
11082 TACAGGGCTTGAGCTCCCTATACAAGTGCTAGTTGATGTGGAGTTAGGGCTCTATAGAGCTTGAG
1 TACAGGGCTTGACCTCCATATACAAGTGCCAGTTAATGTGGAGTTAGGGCTCTATAGAGCTTGAG
* * * *
11147 CTCTATACACAAGTGCTAGCTAATGTAGACTTCGACTT-TATAATGCTTGACCTTTTTATACAA-
66 CTCTATACACAAGAGCTAGCTAATATAGACTTCGA-TTCTATAAGGCTTGACCTCTTTATA-AAG
* * * *
11210 GTGCCAACTAATATGGAGTTTGGGTCCTATAGTGCTTGACCTCTCCATTCAAGTATAAGCTAGTA
129 GTGCCAACTAATATGGACTTTGGGTCCTATAGGGCTTGACCTCTCCATACAAGTATAAGCTAATA
11275 TGGACTTGGACTC
194 TGGACTTGGACTC
* *
11288 TATAGGGCTTGACCT-CATAATA-TAGATGCCAGTTAATGTGGA
1 TACAGGGCTTGACCTCCAT-ATACAAG-TGCCAGTTAATGTGGA
11330 TTTTGGTATC
Statistics
Matches: 200, Mismatches: 40, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
204 41 0.20
205 12 0.06
206 143 0.71
207 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (206 bp):
TACAGGGCTTGACCTCCATATACAAGTGCCAGTTAATGTGGAGTTAGGGCTCTATAGAGCTTGAG
CTCTATACACAAGAGCTAGCTAATATAGACTTCGATTCTATAAGGCTTGACCTCTTTATAAAGGT
GCCAACTAATATGGACTTTGGGTCCTATAGGGCTTGACCTCTCCATACAAGTATAAGCTAATATG
GACTTGGACTC
Found at i:11444 original size:47 final size:49
Alignment explanation
Indices: 11349--11482 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 49
11339 CTATTAGGCT
* * * * *
11349 TGACATCCTTATATAGGTGCCAGCTAGTGTGAACTTAGTTTCTGTA-GG
1 TGACCTCCCTATATAGGTGCCAGCTAGTGTGGACTTAGATTCTCTAGGG
*
11397 -GACTTCCCTATATAGGTGCCAGCTAGTGTGGACTT-GCATTCTCTAGGG
1 TGACCTCCCTATATAGGTGCCAGCTAGTGTGGACTTAG-ATTCTCTAGGG
* *
11445 CTTGACCTCCCTATATAGGTGCCAGCTAATATGGACTT
1 --TGACCTCCCTATATAGGTGCCAGCTAGTGTGGACTT
11483 TGGGTTCTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
46 1 0.01
47 38 0.52
48 2 0.03
51 32 0.44
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (49 bp):
TGACCTCCCTATATAGGTGCCAGCTAGTGTGGACTTAGATTCTCTAGGG
Found at i:11726 original size:103 final size:103
Alignment explanation
Indices: 10883--11761 Score: 390
Period size: 103 Copynumber: 8.6 Consensus size: 103
10873 GTATTTACAG
* * * * * * * * *
10883 GGCTTGACCTCCTTATAGAAGTGCCAACTAATGTGGACTTAGATTATAT-AGGCTTGACCTTCCG
1 GGCTTGACCTCCCTATACAGGTGCCAACTAGTATGGACTTGGATTCTATAAGGCTTGACCTCCCT
* * * * *
10947 ATACAAGAGCTAGCTAATATAGA-TTTGGATTCTATAA
66 ATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
** * * * * * * ***
10984 GGCTTGACCTCTTTATAAAGGTGCCAACTAATATGGACTTTGGGTTCTTTAGGGCTTTACCTTTT
1 GGCTTGACCTCCCTATACAGGTGCCAACTAGTATGGAC-TTGGATTCTATAAGGCTTGACCTCCC
* * ** * *
11049 TATACAGGTGTCAGCTAATATGGA-TTTTGACTCTACAG
65 TATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
* * * * * * * ** *
11087 GGCTTGAGCTCCCTATACAAGTG-CTAGTTGATGTGGAGTTAGGGCTCTAT-AGAGCTTGAGCTC
1 GGCTTGACCTCCCTATACAGGTGCCAACTAG-TATGGACTT-GGATTCTATAAG-GCTTGACCTC
** * * * * * * **
11150 TATACACAAGTGCTAGCTAATGTAGACTTCGACTT-TATAA
63 CCTATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
* *** * * * * *
11190 TGCTTGACCTTTTTATACAAGTGCCAACTAATATGGAGTTTGGGTCCTAT-AGTGCTTGACCTCT
1 GGCTTGACCTCCCTATACAGGTGCCAACTAGTATGGA-CTTGGATTCTATAAG-GCTTGACCTC-
* * *** * ** *
11254 CC-ATTCAAGTATAAGCTAGTATGGAC-TTGGACTCTATAG
63 CCTATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
* * * ** * * * * *
11293 GGCTTGACCT-CATAATATAGATGCCAGTTAATGTGGATTTTGG-TATCTATTAGGCTTGACATC
1 GGCTTGACCTCCCT-ATACAGGTGCCAACTAGTATGGA-CTTGGAT-TCTATAAGGCTTGACCTC
* * * * * * * *
11356 CTTATATAGGTGCCAGCTAGTGTGAAC-TTAGTTTCTGT-A
63 CCTATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
* * * * * * *
11395 GG---GACTTCCCTATATAGGTGCCAGCTAGTGTGGACTTGCATTCTCTAGGGCTTGACCTCCCT
1 GGCTTGACCTCCCTATACAGGTGCCAACTAGTATGGACTTGGATTCTATAAGGCTTGACCTCCCT
* *
11457 ATATAGGTGCCAGCTAATATGGACTTTGGGTTCTATAG
66 ATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
* * * * * * * * * *
11495 GGCTTGATCTCCCTATACAGTTTCTAGCTAGTATGGA-TTAGATTTTATGAGGCTTGTCCTCTCT
1 GGCTTGACCTCCCTATACAGGTGCCAACTAGTATGGACTTGGATTCTATAAGGCTTGACCTCCCT
* * * * ** *
11559 ATACATGTGCCCGTTAATGTAAACTTTGGGTTTTAT-A
66 ATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
* * * *
11596 GAGCTTAACCTCCCTATGCAGGTGCCAACTAGTGTAGACTTGGATTCTATAAGGCTTGACCTCCC
1 G-GCTTGACCTCCCTATACAGGTGCCAACTAGTATGGACTTGGATTCTATAAGGCTTGACCTCCC
* * *
11661 TATACAGGTGCTAGCTAATATGGACATTGAGTTCTATAA
65 TATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
* * * * * *
11700 GGTTTGACCTCCTTATATAGGTGCCAACTACTACGGACTTGGATTTCTATAGGGCTTGACCT
1 GGCTTGACCTCCCTATACAGGTGCCAACTAGTATGGACTTGGA-TTCTATAAGGCTTGACCT
11762 ATATATAGAG
Statistics
Matches: 567, Mismatches: 186, Indels: 47
0.71 0.23 0.06
Matches are distributed among these distances:
98 40 0.07
99 33 0.06
100 4 0.01
101 35 0.06
102 95 0.17
103 331 0.58
104 29 0.05
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (103 bp):
GGCTTGACCTCCCTATACAGGTGCCAACTAGTATGGACTTGGATTCTATAAGGCTTGACCTCCCT
ATACAGGTGCCAGCTAATATGGACTTTGGGTTCTATAA
Found at i:12856 original size:16 final size:16
Alignment explanation
Indices: 12823--12869 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
12813 CAATTGTATG
*
12823 TGAGTACGAATGCCCA
1 TGAGTACGAATGCACA
*
12839 TGAGTACGAATGGACA
1 TGAGTACGAATGCACA
* *
12855 TGAATAGGAATGCAC
1 TGAGTACGAATGCAC
12870 GAGCATGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (16 bp):
TGAGTACGAATGCACA
Found at i:14434 original size:22 final size:22
Alignment explanation
Indices: 14392--14434 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
14382 CTTTTCTTGA
*
14392 TTTTGCTTTTATTTTGGTTTTT
1 TTTTGCTTTTATTTTAGTTTTT
*
14414 TTTTGCTTTTCTTTTA-TTTTT
1 TTTTGCTTTTATTTTAGTTTTT
14435 CATTTTGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.05, C:0.07, G:0.09, T:0.79
Consensus pattern (22 bp):
TTTTGCTTTTATTTTAGTTTTT
Found at i:14440 original size:27 final size:28
Alignment explanation
Indices: 14383--14440 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
14373 TTTGTTCCCC
**
14383 TTTTCTTGATTTTGCTTTTATTTTGGTT
1 TTTTCTTGATTTTGCTTTTATTTTGCAT
* * *
14411 TTTTTTTGCTTTT-CTTTTATTTTTCAT
1 TTTTCTTGATTTTGCTTTTATTTTGCAT
14438 TTT
1 TTT
14441 GAGCTTTTGC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.07, C:0.09, G:0.09, T:0.76
Consensus pattern (28 bp):
TTTTCTTGATTTTGCTTTTATTTTGCAT
Found at i:14897 original size:13 final size:13
Alignment explanation
Indices: 14879--14908 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
14869 ATATATTATT
14879 CATTGTATCGATA
1 CATTGTATCGATA
14892 CATTGTATCGATA
1 CATTGTATCGATA
14905 CATT
1 CATT
14909 CTAAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:14923 original size:19 final size:19
Alignment explanation
Indices: 14895--14946 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
14885 ATCGATACAT
14895 TGTATCGATACATTCTAAA
1 TGTATCGATACATTCTAAA
* * *
14914 TGTATGGATACATTTTTCAA
1 TGTATCGATACA-TTCTAAA
14934 TGTATCGATACAT
1 TGTATCGATACAT
14947 CCAGGCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATTCTAAA
Found at i:17384 original size:28 final size:28
Alignment explanation
Indices: 17320--17387 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
17310 AATCGAGGAT
* * * *
17320 ACTCCAACCCTGTTATTTTCGCGGGGAT
1 ACTCCAACCCCGTTATTTTCGAGGGAAA
**
17348 ACTGTAACCCCGTTATTTTCGAGGGAAA
1 ACTCCAACCCCGTTATTTTCGAGGGAAA
17376 ACTCCAACCCCG
1 ACTCCAACCCCG
17388 ATTTTATTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (28 bp):
ACTCCAACCCCGTTATTTTCGAGGGAAA
Found at i:17890 original size:237 final size:237
Alignment explanation
Indices: 17376--17935 Score: 661
Period size: 237 Copynumber: 2.4 Consensus size: 237
17366 TCGAGGGAAA
* * * * * **
17376 ACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCATAATCGAGGATACTCCAATCCTGTT
1 ACTCCAACCCCGATTTTATTTCTAAAAAAACAATTTTTCACAATCGAGGATACTCCAACCCCATT
* * *
17441 ATTTTCGAGGAGATACTCCAACCGCGGTTTTATTTCCAAAACACTAATTTTTCATAATCGGGGAT
66 ATTTTCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGAT
*
17506 ACTCCAACCTCATTATTTCTGAAGGGATACTCCAACCCTGATTTTATTTTCAAAACACCGATTTT
131 ACTCCAACCCCATTATTTCTGAAGGGATACTCCAACCCTGATTTTATTTTCAAAACACCGATTTT
* *
17571 TCACAATCGGGGTTACTCCAACCTCATTATTTCTGAGGGGAT
196 TCACAATCGGGGGTACTCCAACCTCATTATTTCTGAAGGGAT
* * *
17613 ACTCTAACCCCGGTTTTATTTCTAAAAAAACAAATTTTCACAATCG-GGAATACTCCAACCCCAT
1 ACTCCAACCCCGATTTTATTTCTAAAAAAACAATTTTTCACAATCGAGG-ATACTCCAACCCCAT
* * *
17677 TATTTTCGAGTG-GATACTCCAACCCCGATTTTATTTTCAAAACATCT-GTTTTTTACAATCGGG
65 TATTTTCGAG-GAGATACTCCAACCCCGATTTTATTTCCAAAACA-CTAATTTTTCACAATCGGG
* * * *
17740 GATACTCCAACCCCATTATTTTTG-AGAGGATACTCTAACTCC-GATTTTA-TTTCTAAAATACT
128 GATACTCCAACCCCATTATTTCTGAAG-GGATACTCCAAC-CCTGATTTTATTTTC-AAAACACC
17802 GATTTTTCACAATCGGGGGTACTCCAACC-CTATTATTT-TCGAAGGGAT
190 GATTTTTCACAATCGGGGGTACTCCAACCTC-ATTATTTCT-GAAGGGAT
* * * ***** * * *
17850 ACTCCAACCCTGATTTTATTTTTAGAACGTTGATTTTTCACAATCGAGGATACTCCAGCCTCGTT
1 ACTCCAACCCCGATTTTATTTCTAAAAAAACAATTTTTCACAATCGAGGATACTCCAACCCCATT
* *
17915 ATTTTTGA-AAGATACTCCAAC
66 ATTTTCGAGGAGATACTCCAAC
17936 TTTATCTCCA
Statistics
Matches: 274, Mismatches: 39, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
236 21 0.08
237 246 0.90
238 7 0.03
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (237 bp):
ACTCCAACCCCGATTTTATTTCTAAAAAAACAATTTTTCACAATCGAGGATACTCCAACCCCATT
ATTTTCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGGAT
ACTCCAACCCCATTATTTCTGAAGGGATACTCCAACCCTGATTTTATTTTCAAAACACCGATTTT
TCACAATCGGGGGTACTCCAACCTCATTATTTCTGAAGGGAT
Found at i:17917 original size:79 final size:78
Alignment explanation
Indices: 17341--17935 Score: 564
Period size: 79 Copynumber: 7.6 Consensus size: 78
17331 GTTATTTTCG
** * * * *
17341 CGGGGATACTGTAACCCCGTTATTTTCG-AGGGAAAACTCCAACCCCGATTTTATTTCCAAAATA
1 CGGGGATACTCCAACCTCATTATTTTCGAAGGG-ATACTCCAA-CCCGATTTTATTTCCAAAACA
** *
17405 CCAATTTTTCATAAT
64 CTGATTTTTCACAAT
* * *
17420 CGAGGATACTCCAATCCT-GTTATTTTCG-AGGAGATACTCCAACCGCGGTTTTATTTCCAAAAC
1 CGGGGATACTCCAA-CCTCATTATTTTCGAAGG-GATACTCCAACC-CGATTTTATTTCCAAAAC
* *
17483 ACTAATTTTTCATAAT
63 ACTGATTTTTCACAAT
*
17499 CGGGGATACTCCAACCTCATTA-TTTCTGAAGGGATACTCCAACCCTGATTTTATTTTCAAAACA
1 CGGGGATACTCCAACCTCATTATTTTC-GAAGGGATACTCCAACCC-GATTTTATTTCCAAAACA
*
17563 CCGATTTTTCACAAT
64 CTGATTTTTCACAAT
* * * * * *
17578 CGGGGTTACTCCAACCTCATTA-TTTCTGAGGGGATACTCTAACCCCGGTTTTATTTCTAAAAAA
1 CGGGGATACTCCAACCTCATTATTTTC-GAAGGGATACTCCAA-CCCGATTTTATTTC-CAAAAC
* *
17642 AC-AAATTTTCACAAT
63 ACTGATTTTTCACAAT
* * *
17657 CGGGAATACTCCAACCCCATTATTTTCG-AGTGGATACTCCAACCCCGATTTTATTTTCAAAACA
1 CGGGGATACTCCAACCTCATTATTTTCGAAG-GGATACTCCAA-CCCGATTTTATTTCCAAAACA
*
17721 TCTG-TTTTTTACAAT
64 -CTGATTTTTCACAAT
* * * * *
17736 CGGGGATACTCCAACCCCATTATTTTTG-AGAGGATACTCTAACTCCGATTTTATTTCTAAAATA
1 CGGGGATACTCCAACCTCATTATTTTCGAAG-GGATACTCCAAC-CCGATTTTATTTCCAAAACA
17800 CTGATTTTTCACAAT
64 CTGATTTTTCACAAT
* ** * *
17815 CGGGGGTACTCCAACC-CTATTATTTTCGAAGGGATACTCCAACCCTGATTTTATTTTTAGAACG
1 CGGGGATACTCCAACCTC-ATTATTTTCGAAGGGATACTCCAACCC-GATTTTATTTCCAAAACA
*
17879 TTGATTTTTCACAAT
64 CTGATTTTTCACAAT
* * * * *
17894 CGAGGATACTCCAGCCTCGTTATTTTTGAA-AGATACTCCAAC
1 CGGGGATACTCCAACCTCATTATTTTCGAAGGGATACTCCAAC
17936 TTTATCTCCA
Statistics
Matches: 439, Mismatches: 58, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
78 34 0.08
79 383 0.87
80 22 0.05
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (78 bp):
CGGGGATACTCCAACCTCATTATTTTCGAAGGGATACTCCAACCCGATTTTATTTCCAAAACACT
GATTTTTCACAAT
Found at i:17917 original size:158 final size:158
Alignment explanation
Indices: 17341--17936 Score: 654
Period size: 158 Copynumber: 3.8 Consensus size: 158
17331 GTTATTTTCG
** ** * * * *
17341 CGGGGATACTGTAACCCCGTTATTTTCG-AGGGAAAACTCCAACCCCGATTTTATTTCCAAAATA
1 CGGGGATACTCCAACCCTATTATTTTCGAAGGG-ATACTCCAACCCTGATTTTATTTTCAAAACA
*** * * *
17405 CCAATTTTTCATAATCGAGGATACTCCAATCCT-GTTATTTTCGAG-GAGATACTCCAAC-CGCG
65 TTGATTTTTCACAATCGAGGATACTCCAA-CCTCATTATTTTTGAGAG-GATACTCCAACTC-CG
* * *
17467 GTTTTATTTCCAAAACACTAATTTTTCATAAT
127 GTTTTATTTCTAAAAAACTAATTTTTCACAAT
17499 CGGGGATACTCCAA-CCTCATTA-TTTCTGAAGGGATACTCCAACCCTGATTTTATTTTCAAAAC
1 CGGGGATACTCCAACCCT-ATTATTTTC-GAAGGGATACTCCAACCCTGATTTTATTTTCAAAAC
** * * * * * *
17562 ACCGATTTTTCACAATCGGGGTTACTCCAACCTCATTATTTCTGAGGGGATACTCTAACCCCGGT
64 ATTGATTTTTCACAATCGAGGATACTCCAACCTCATTATTTTTGAGAGGATACTCCAACTCCGGT
*
17627 TTTATTTCTAAAAAAAC-AAATTTTCACAAT
129 TTTATTTCT-AAAAAACTAATTTTTCACAAT
* * *
17657 CGGGAATACTCCAACCCCATTATTTTCG-AGTGGATACTCCAACCCCGATTTTATTTTCAAAACA
1 CGGGGATACTCCAACCCTATTATTTTCGAAG-GGATACTCCAACCCTGATTTTATTTTCAAAACA
* * * * *
17721 TCTG-TTTTTTACAATCGGGGATACTCCAACCCCATTATTTTTGAGAGGATACTCTAACTCCGAT
65 T-TGATTTTTCACAATCGAGGATACTCCAACCTCATTATTTTTGAGAGGATACTCCAACTCCGGT
* *
17785 TTTATTTCTAAAATACTGATTTTTCACAAT
129 TTTATTTCTAAAAAACTAATTTTTCACAAT
* * * *
17815 CGGGGGTACTCCAACCCTATTATTTTCGAAGGGATACTCCAACCCTGATTTTATTTTTAGAACGT
1 CGGGGATACTCCAACCCTATTATTTTCGAAGGGATACTCCAACCCTGATTTTATTTTCAAAACAT
* * *
17880 TGATTTTTCACAATCGAGGATACTCCAGCCTCGTTATTTTTGA-AAGATACTCCAACT
66 TGATTTTTCACAATCGAGGATACTCCAACCTCATTATTTTTGAGAGGATACTCCAACT
17937 TTATCTCCAA
Statistics
Matches: 375, Mismatches: 49, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
157 31 0.08
158 323 0.86
159 21 0.06
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (158 bp):
CGGGGATACTCCAACCCTATTATTTTCGAAGGGATACTCCAACCCTGATTTTATTTTCAAAACAT
TGATTTTTCACAATCGAGGATACTCCAACCTCATTATTTTTGAGAGGATACTCCAACTCCGGTTT
TATTTCTAAAAAACTAATTTTTCACAAT
Found at i:24574 original size:20 final size:20
Alignment explanation
Indices: 24549--24642 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
24539 TTTTAACTAG
24549 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
* *
24569 ATGTATCGATACATTGCAGA
1 ATGTATCGATACATTGAATA
* *
24589 ATATATCGATACATT-CATA
1 ATGTATCGATACATTGAATA
* *
24608 CATGTATCGATATATTGAAAA
1 -ATGTATCGATACATTGAATA
*
24629 ATATATCGATACAT
1 ATGTATCGATACAT
24643 CAGGGTAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 3 0.05
20 57 0.92
21 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:24596 original size:40 final size:40
Alignment explanation
Indices: 24552--24642 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
24542 TAACTAGATG
* *
24552 TATCGATACATTGAATA-ATGTATCGATACATTGCAGAATA
1 TATCGATACATT-AATACATGTATCGATACATTGAAAAATA
* *
24592 TATCGATACATTCATACATGTATCGATATATTGAAAAATA
1 TATCGATACATTAATACATGTATCGATACATTGAAAAATA
24632 TATCGATACAT
1 TATCGATACAT
24643 CAGGGTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 3 0.07
40 43 0.93
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (40 bp):
TATCGATACATTAATACATGTATCGATACATTGAAAAATA
Found at i:25353 original size:28 final size:28
Alignment explanation
Indices: 25240--26388 Score: 1201
Period size: 28 Copynumber: 39.9 Consensus size: 28
25230 CGAAAAAAGT
*
25240 TGCCACTGACACGTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTC--GTGGGCTTTG-AAAGAG
** *
25271 TGTTACTGACTTGCGTGGGCTTT-AAAAAGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGA-G
*
25301 TGCCACTGACTTGCGTGGGCTTTGAAAGAA
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGAG
* *
25331 TGCGACTGACTCGTGAGCTTTGAAAG-G
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
*
25358 ATGCCACTGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTCGTGGGCTTTGAAAGAG
* *
25387 TGCCACTGACTCGTGGGCTTTCAAAAAGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
*
25416 TGCCACTAACTCGTGGGCTTTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
* *
25444 TGCCACTGACTTGCGTGGGCTTTAAAAGGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGAG
25474 TGCCACTGACTTGCGTGGGCTTTGAAAG-G
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGAG
*
25503 ATGCCACTGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTCGTGGGCTTTGAAAGAG
25532 TGCCACTGACTCGTGGGCTTTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
*
25560 TGCCACTGACTCGTGGGC-TTGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
*
25587 TGCCACTGACTCGTGGGC-TTGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
* * *
25614 TGCTACTAACTTGTGGGCTTTGAAAGAG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
25642 TGCCACTGACTCGTGGGCTTTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
*
25670 TGCCACTGACTTGCGTGGGCTTTAAAACGAG
1 TGCCACTGAC-T-CGTGGGCTTTGAAA-GAG
* *
25701 TGCCACTGACTTGTGTGGGCTTT-AAAAAGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGA-G
25731 TGCCACTGACTCGTGGGC-TTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
*
25758 TGCCACTGACTCGTGGGC-TTGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
* * *
25785 TGCCACTAACTTGTAGGCTTTGAAAGAG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
25813 TGCCACTGACTCGTGGGCTTTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
*
25841 TGCCACTGACTTGCGTGGGCTTTAAAAGGAG
1 TGCCACTGAC-T-CGTGGGCTTTGAAA-GAG
* *
25872 TGCCACTGACTTGTGTGGGCTTT-AAAAAGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGA-G
25902 TGCCACTGACTCGTGGGC-TTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
* * *
25929 TTCCACTGACTTGTGGGC-TTGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
* *
25956 TGCCACTAACTTGTGGGCTTTGAAAGAG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
25984 TGCCACTGACTCGTGGGCTTTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
*
26012 TGCCACTGACTTGCGTGGGCTTTAAAAGGAG
1 TGCCACTGAC-T-CGTGGGCTTTGAAA-GAG
* *
26043 TGCCACTGACTTGTGTGGGCTTTGAAAGGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGAG
* * *
26073 TGCCACTGACTTGTGGGCTTTAAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGAG
26101 TGCCACTGACTTGCGTGGGCTTTGAAAG-G
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGAG
*
26130 ATGCCACTGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTCGTGGGCTTTGAAAGAG
*
26159 TGCCACTGACTCGTGGGCTTTGAAAAAGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
26188 TGCCACTGACTCGTGGGCTTTGAAA-AGG
1 TGCCACTGACTCGTGGGCTTTGAAAGA-G
* *
26216 TGCCACTGACTTGCGTGGGCTTTAAAAGGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGAG
26246 TGCCACTGACTTGCGTGGGCTTTGAAAG-G
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGAG
* *
26275 ATGCCACGGACTTGTGGGCTTTGAAAGAG
1 -TGCCACTGACTCGTGGGCTTTGAAAGAG
*
26304 TGCCACTGACTTGCGTGGGCTTTAAAAGGAG
1 TGCCACTGAC-T-CGTGGGCTTTGAAA-GAG
* *
26335 TGCCACTGACTTGTGTGGGCTTT-AAAAAGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGA-G
26365 TGCCACTGACTCGTGGGC-TTGAAA
1 TGCCACTGACTCGTGGGCTTTGAAA
26389 AAGGTTTGAG
Statistics
Matches: 987, Mismatches: 78, Indels: 109
0.84 0.07 0.09
Matches are distributed among these distances:
27 144 0.15
28 382 0.39
29 79 0.08
30 260 0.26
31 118 0.12
32 3 0.00
33 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (28 bp):
TGCCACTGACTCGTGGGCTTTGAAAGAG
Found at i:25731 original size:171 final size:172
Alignment explanation
Indices: 25234--26389 Score: 1487
Period size: 171 Copynumber: 6.7 Consensus size: 172
25224 AGGCTTCGAA
* * * ** *
25234 AAAAGTTGCCACTGACACGTGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTT-AAAA
1 AAAAGGTGCCACTGACTC--GTGGGCTTTG-AAAGGGTGCCACTGACTT--GTGGGCTTTGAAAG
* * * *
25298 AGGTGCCACTGACTTGCGTGGGCTTTG-AAAGAATGCGACTGAC-TCGTGAGCTTTGAAAGGA-T
61 A-GTGCCACTGAC-T-CGTGGGCTTTGAAAAG-GTGCCACTGACTTCGTGGGCTTTAAAAGGAGT
* *
25360 GCCACTGAC-T-TGTGGGCTTT-GAAAGAGTGCCACTGACTCGTGGGCTTTCA
122 GCCACTGACTTGTGTGGGCTTTAAAAAG-GTGCCACTGACTCGTGGGCTTT-G
* * * *
25410 AAAAGGTGCCACTAACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGGGT
1 AAAAGGTGCCACTGACTCGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAGAGT
*
25475 GCCACTGACTTGCGTGGGCTTTG-AAAGGATGCCACTGACTT-GTGGGCTTTGAAA-GAGTGCCA
64 GCCACTGAC-T-CGTGGGCTTTGAAAAGG-TGCCACTGACTTCGTGGGCTTTAAAAGGAGTGCCA
* *
25537 CTGAC-T-CGTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGC-TTG
126 CTGACTTGTGTGGGCTTTAAAAAGGTGCCACTGACTCGTGGGCTTTG
* * *
25581 AAAGGGTGCCACTGACTCGTGGGC-TTGAAAGGGTGCTACTAACTTGTGGGCTTTGAAAGAGTGC
1 AAAAGGTGCCACTGACTCGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGC
*
25645 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAACGAGTGCCACTGA
66 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTT-CGTGGGCTTTAAAAGGAGTGCCACTGA
25710 CTTGTGTGGGCTTTAAAAAGGTGCCACTGACTCGTGGGC-TTG
130 CTTGTGTGGGCTTTAAAAAGGTGCCACTGACTCGTGGGCTTTG
* *
25752 AAAAGGTGCCACTGACTCGTGGGC-TTGAAAGGGTGCCACTAACTTGTAGGCTTTGAAAGAGTGC
1 AAAAGGTGCCACTGACTCGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGC
25816 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGA
66 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTT-CGTGGGCTTTAAAAGGAGTGCCACTGA
25881 CTTGTGTGGGCTTTAAAAAGGTGCCACTGACTCGTGGGC-TTG
130 CTTGTGTGGGCTTTAAAAAGGTGCCACTGACTCGTGGGCTTTG
* * *
25923 AAAAGGTTCCACTGACTTGTGGGC-TTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGAGTGC
1 AAAAGGTGCCACTGACTCGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGC
25987 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGA
66 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTT-CGTGGGCTTTAAAAGGAGTGCCACTGA
* * *
26052 CTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-
130 CTTGTGTGGGCTTTAAAAAGGTGCCACTGACTCGTGGGCTTTG
*
26094 AAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAG
1 AAAA-GGTGCCACTGAC-T-CGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAG
26159 TGCCACTGACTCGTGGGCTTTGAAAAAGGTGCCACTGAC-TCGTGGGCTTTGAAAA-G-GTGCCA
63 TGCCACTGACTCGTGGGCTTTG-AAAAGGTGCCACTGACTTCGTGGGCTTT-AAAAGGAGTGCCA
* *
26221 CTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTG
126 CTGACTTGTGTGGGCTTTAAAAAGGTGCCACTGAC-T-CGTGGGCTTTG
* * * *
26270 -AAAGGATGCCACGGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGCGTGGGCTTTAAAAGGA
1 AAAAGG-TGCCACTGACTCGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAA-GA
* * *
26334 GTGCCACTGACTTGTGTGGGCTTTAAAAAGGTGCCACTGAC-TCGTGGGCTTGAAAA
62 GTGCCACTGAC-T-CGTGGGCTTTGAAAAGGTGCCACTGACTTCGTGGGCTTTAAAA
26390 AGGTTTGAGC
Statistics
Matches: 903, Mismatches: 50, Indels: 54
0.90 0.05 0.05
Matches are distributed among these distances:
166 23 0.03
167 6 0.01
168 36 0.04
169 13 0.01
170 19 0.02
171 391 0.43
172 17 0.02
173 180 0.20
174 39 0.04
175 95 0.11
176 48 0.05
177 27 0.03
178 9 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.26
Consensus pattern (172 bp):
AAAAGGTGCCACTGACTCGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGC
CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTCGTGGGCTTTAAAAGGAGTGCCACTGAC
TTGTGTGGGCTTTAAAAAGGTGCCACTGACTCGTGGGCTTTG
Found at i:27617 original size:11 final size:11
Alignment explanation
Indices: 27592--27655 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
27582 GACCCTTCTA
*
27592 TTTTTTTGCTAT
1 TTTTTTTG-TTT
27604 TTTTTTTGTTTT
1 TTTTTTTG-TTT
27616 TTTGTTTTGTTT
1 TTT-TTTTGTTT
*
27628 TTTTATTGTTT
1 TTTTTTTGTTT
* *
27639 TTTTATTATTT
1 TTTTTTTGTTT
27650 TTTTTT
1 TTTTTT
27656 GTGTAAAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
11 22 0.48
12 19 0.41
13 5 0.11
ACGTcount: A:0.06, C:0.02, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:27636 original size:24 final size:23
Alignment explanation
Indices: 27603--27655 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
27593 TTTTTTGCTA
*
27603 TTTTTTTTGTTTTTTTGTT-TTGT
1 TTTTTTTTGTTTTTTTATTATT-T
27626 TTTTTTATTGTTTTTTTATTATTT
1 TTTTTT-TTGTTTTTTTATTATTT
27650 TTTTTT
1 TTTTTT
27656 GTGTAAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 19 0.70
25 2 0.07
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.87
Consensus pattern (23 bp):
TTTTTTTTGTTTTTTTATTATTT
Done.