Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1817
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: 118926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4649 original size:3 final size:3
Alignment explanation
Indices: 4641--4671 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4631 TCTGAGTCAC
*
4641 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
4672 CTTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:6266 original size:13 final size:13
Alignment explanation
Indices: 6248--6277 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6238 TTACAAGATA
6248 TGTATCGATACAG
1 TGTATCGATACAG
*
6261 TGTATCGATACAT
1 TGTATCGATACAG
6274 TGTA
1 TGTA
6278 CCATGTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:6379 original size:75 final size:76
Alignment explanation
Indices: 6280--6429 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 76
6270 ACATTGTACC
6280 ATGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTCATGTATCGATACAATTTGTCCA
1 ATGTATCGATA-AAATAGTGATAGGGTAGCTACTGCCAATTTCATGTATCGATACAATTTGTCCA
*
6345 TGTATTGATATA
65 TGTATCGATATA
6357 ATGTATCGAT-AAATAGTGATAGGGTAGCTACTGCCAATTTCATGTATCGATACAATTTGTCCAT
1 ATGTATCGATAAAATAGTGATAGGGTAGCTACTGCCAATTTCATGTATCGATACAATTTGTCCAT
6421 GTATCGATA
66 GTATCGATA
6430 CATTGAACAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
75 62 0.86
77 10 0.14
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Consensus pattern (76 bp):
ATGTATCGATAAAATAGTGATAGGGTAGCTACTGCCAATTTCATGTATCGATACAATTTGTCCAT
GTATCGATATA
Found at i:6423 original size:21 final size:21
Alignment explanation
Indices: 6397--6452 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
6387 CTGCCAATTT
**
6397 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
6418 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
6437 CATGTATCGATACAAT
1 CATGTATCGATACAAT
6453 GTATCGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:6456 original size:13 final size:13
Alignment explanation
Indices: 6438--6464 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6428 TACATTGAAC
6438 ATGTATCGATACA
1 ATGTATCGATACA
6451 ATGTATCGATACA
1 ATGTATCGATACA
6464 A
1 A
6465 GGTAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9748 original size:18 final size:17
Alignment explanation
Indices: 9717--9750 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9707 ATATCATGGT
*
9717 GAAATTTTTCATTTTTA
1 GAAATTTTTAATTTTTA
9734 GAAATTTTTTAATTTTT
1 GAAA-TTTTTAATTTTT
9751 CTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
GAAATTTTTAATTTTTA
Found at i:10527 original size:16 final size:17
Alignment explanation
Indices: 10495--10528 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10485 TATGTAATTT
10495 AAATCAAATCAAAATAA
1 AAATCAAATCAAAATAA
*
10512 AAATCAAA-CGAAATAA
1 AAATCAAATCAAAATAA
10528 A
1 A
10529 GCAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.71, C:0.12, G:0.03, T:0.15
Consensus pattern (17 bp):
AAATCAAATCAAAATAA
Found at i:12486 original size:18 final size:18
Alignment explanation
Indices: 12463--12499 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12453 ACTTAAAATA
* *
12463 AATAGTCCTTTTTTAATG
1 AATAGTCATTTTGTAATG
12481 AATAGTCATTTTGTAATG
1 AATAGTCATTTTGTAATG
12499 A
1 A
12500 CTATTTAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (18 bp):
AATAGTCATTTTGTAATG
Found at i:13361 original size:18 final size:18
Alignment explanation
Indices: 13338--13373 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13328 TTTTTTTCCC
*
13338 TTTATTTCCATACTTTTA
1 TTTATTTCCATAATTTTA
*
13356 TTTATTTGCATAATTTTA
1 TTTATTTCCATAATTTTA
13374 ACATTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.11, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTATTTCCATAATTTTA
Found at i:17037 original size:32 final size:33
Alignment explanation
Indices: 16998--17081 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 33
16988 ATCTTTCAAC
*
16998 GCTAAGATAGAAACCTCCCTATC-TTTTC-ACG
1 GCTAAGATAGAAACCTCCCTATCTTTTTCAAAG
*
17029 AGCTAAGATAGAACCTTTCTCCCTATCTTTTTCAAAG
1 -GCTAAGATAGAAAC---CTCCCTATCTTTTTCAAAG
17066 GCTAAGATAG-AACCTC
1 GCTAAGATAGAAACCTC
17082 ACAATCACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
32 16 0.36
35 11 0.25
36 15 0.34
37 2 0.05
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (33 bp):
GCTAAGATAGAAACCTCCCTATCTTTTTCAAAG
Found at i:17058 original size:35 final size:36
Alignment explanation
Indices: 17012--17080 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
17002 AGATAGAAAC
*
17012 CTCCCTATC-TTTTC-ACGAGCTAAGATAGAACCTTT
1 CTCCCTATCTTTTTCAAAG-GCTAAGATAGAACCTTT
17047 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCT
17081 CACAATCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
35 9 0.29
36 20 0.65
37 2 0.06
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (36 bp):
CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTTT
Found at i:17571 original size:24 final size:22
Alignment explanation
Indices: 17536--17602 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
17526 CACATGTATC
*
17536 GATACA-AGAACAGTGATGAATA
1 GATACATA-AACAGTGATGAACA
17558 GTGATACATAAACAGTGATGAACA
1 --GATACATAAACAGTGATGAACA
17582 G-TA-ATAAACAGTGATGAACA
1 GATACATAAACAGTGATGAACA
17602 G
1 G
17603 TCATGTATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
20 18 0.44
21 2 0.05
22 1 0.02
24 19 0.46
25 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.19
Consensus pattern (22 bp):
GATACATAAACAGTGATGAACA
Found at i:17581 original size:10 final size:10
Alignment explanation
Indices: 17568--17603 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
17558 GTGATACATA
17568 AACAGTGATG
1 AACAGTGATG
* *
17578 AACAGTAATA
1 AACAGTGATG
17588 AACAGTGATG
1 AACAGTGATG
17598 AACAGT
1 AACAGT
17604 CATGTATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.19
Consensus pattern (10 bp):
AACAGTGATG
Found at i:17590 original size:20 final size:20
Alignment explanation
Indices: 17565--17603 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
17555 ATAGTGATAC
17565 ATAAACAGTGATGAACAGTA
1 ATAAACAGTGATGAACAGTA
17585 ATAAACAGTGATGAACAGT
1 ATAAACAGTGATGAACAGT
17604 CATGTATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.21
Consensus pattern (20 bp):
ATAAACAGTGATGAACAGTA
Found at i:19124 original size:46 final size:46
Alignment explanation
Indices: 19034--19126 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
19024 GGGTGGAAAA
* * * * * **
19034 AGGGTGGAAAAAGTTTAACTAGGTCTTACGCCAATACAGTCAAACG
1 AGGGTGAAAAAAGTTTAACCAGGACTAACGCCAACACAACCAAACG
*
19080 AGGGTGAAAAAAGTTTAACCAGGACTAATGCCAACACAACCAAACG
1 AGGGTGAAAAAAGTTTAACCAGGACTAACGCCAACACAACCAAACG
19126 A
1 A
19127 AGGAAGACAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (46 bp):
AGGGTGAAAAAAGTTTAACCAGGACTAACGCCAACACAACCAAACG
Found at i:19230 original size:91 final size:91
Alignment explanation
Indices: 19087--19253 Score: 210
Period size: 91 Copynumber: 1.8 Consensus size: 91
19077 ACGAGGGTGA
* * * * *
19087 AAAAAGTTTAACCAGGACTAATGCCAACACAACCAAACGAAGGAAGACAGTTTGACGAGGTTCAA
1 AAAAAGTTTAACCAAGACTAACGCCAACACAACCAAACGAAGAAAGACAGTTTGACCAGGTCCAA
*
19152 ATGCCAATACAATTAAAAGAAAGTGG
66 ACGCCAATACAATTAAAAGAAAGTGG
* * * * * *
19178 AAAAAGTTTGACCAAGACTAACGCCAACATAGCCAAATGAA-AATAGATAGTTTGACCAGGTCCT
1 AAAAAGTTTAACCAAGACTAACGCCAACACAACCAAACGAAGAA-AGACAGTTTGACCAGGTCCA
19242 AACGCCAATACA
65 AACGCCAATACA
19254 GTCAAACGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
90 1 0.02
91 62 0.98
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (91 bp):
AAAAAGTTTAACCAAGACTAACGCCAACACAACCAAACGAAGAAAGACAGTTTGACCAGGTCCAA
ACGCCAATACAATTAAAAGAAAGTGG
Found at i:20350 original size:168 final size:169
Alignment explanation
Indices: 20056--20379 Score: 474
Period size: 171 Copynumber: 1.9 Consensus size: 169
20046 AAGGTGATGT
* * *
20056 ATCAATACCATCTAGTGGTTGGATGAAAGGGATATGATTAGGAATGTATGGGCTTTACCCTTTGT
1 ATCAAAACCATCTAGTGGTTGGATGAAAGAGATATGATTAGGAATGTATGGGCTGTACCCTTTGT
* *
20121 GATCATTTGATGCATCAATACCATCTAGCGGCTAAAAGAAAGGGATATGATTGGGAATGAGTGGT
66 GATCA-TTGATGCATCAATACCATCTAGCGGCTAAAAGAAAGGGATATGATTAGAAATGAGTGGT
20186 CGAG-ATATCCTTGGCCCAAGGAAATCCAAGCTTTGTGACGC
130 -GAGAATATCCTT-GCCCAAGGAAATCCAAGCTTTGTGACGC
* * *
20227 ATCAAAACCATCTAGTGGTTGGGTGAAAGAGATATGATTGGGAATGTGTGGGCTGTACCCTTTGT
1 ATCAAAACCATCTAGTGGTTGGATGAAAGAGATATGATTAGGAATGTATGGGCTGTACCCTTTGT
* * * *
20292 GGTCA-T-ATGCATCAATACCATCTAGTGGCTAAAAGAATGGGATATGATTAGAAATGAGTGGTT
66 GATCATTGATGCATCAATACCATCTAGCGGCTAAAAGAAAGGGATATGATTAGAAATGAGTGGTG
* *
20355 AGAATATCCTTGCCCCATGAAATCC
131 AGAATATCCTTGCCCAAGGAAATCC
20380 TTCTTCCAGT
Statistics
Matches: 138, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
167 14 0.10
168 60 0.43
169 1 0.01
171 63 0.46
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (169 bp):
ATCAAAACCATCTAGTGGTTGGATGAAAGAGATATGATTAGGAATGTATGGGCTGTACCCTTTGT
GATCATTGATGCATCAATACCATCTAGCGGCTAAAAGAAAGGGATATGATTAGAAATGAGTGGTG
AGAATATCCTTGCCCAAGGAAATCCAAGCTTTGTGACGC
Found at i:21314 original size:12 final size:11
Alignment explanation
Indices: 21299--21354 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 11
21289 TATTTATTTA
21299 TTTCTTCTTCTT
1 TTTCTTCTT-TT
21311 TTTCTTCTTTT
1 TTTCTTCTTTT
*
21322 TTTGTT-TTTT
1 TTTCTTCTTTT
*
21332 TCTCTT-TTTT
1 TTTCTTCTTTT
*
21342 TTT-TTGTTTT
1 TTTCTTCTTTT
21352 TTT
1 TTT
21355 GATTGCCTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 2 0.05
10 21 0.54
11 7 0.18
12 9 0.23
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.84
Consensus pattern (11 bp):
TTTCTTCTTTT
Found at i:21342 original size:21 final size:21
Alignment explanation
Indices: 21309--21354 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
21299 TTTCTTCTTC
21309 TTTTTC-TTCTTTTTTTGTTT
1 TTTTTCTTTCTTTTTTTGTTT
*
21329 TTTTCTCTTTTTTTTTTTGTTT
1 TTTT-TCTTTCTTTTTTTGTTT
21351 TTTT
1 TTTT
21355 GATTGCCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 2 0.09
22 17 0.74
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (21 bp):
TTTTTCTTTCTTTTTTTGTTT
Found at i:21351 original size:19 final size:19
Alignment explanation
Indices: 21309--21346 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
21299 TTTCTTCTTC
21309 TTTTTCTTCTTTTTTTGTT
1 TTTTTCTTCTTTTTTTGTT
21328 TTTTTC-TCTTTTTTT-TT
1 TTTTTCTTCTTTTTTTGTT
21345 TT
1 TT
21347 GTTTTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 9 0.47
19 6 0.32
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.87
Consensus pattern (19 bp):
TTTTTCTTCTTTTTTTGTT
Found at i:22037 original size:8 final size:8
Alignment explanation
Indices: 22026--22060 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
22016 AATTTTTCAA
22026 TTTTTTCT
1 TTTTTTCT
22034 TTTTTTCTT
1 TTTTTTC-T
22043 TTTTTTCT
1 TTTTTTCT
22051 TTTTTT-T
1 TTTTTTCT
22058 TTT
1 TTT
22061 CAAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 14 0.54
9 8 0.31
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (8 bp):
TTTTTTCT
Found at i:22040 original size:17 final size:17
Alignment explanation
Indices: 22018--22056 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
22008 TGGCACTTAA
22018 TTTTTCAATTTTTTCTT
1 TTTTTCAATTTTTTCTT
**
22035 TTTTTCTTTTTTTTCTT
1 TTTTTCAATTTTTTCTT
22052 TTTTT
1 TTTTT
22057 TTTTCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTCAATTTTTTCTT
Found at i:22058 original size:10 final size:9
Alignment explanation
Indices: 22026--22057 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
22016 AATTTTTCAA
22026 TTTTTTC-T
1 TTTTTTCTT
22034 TTTTTTCTT
1 TTTTTTCTT
22043 TTTTTTCTT
1 TTTTTTCTT
22052 TTTTTT
1 TTTTTT
22058 TTTCAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:27561 original size:52 final size:52
Alignment explanation
Indices: 27483--27631 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 52
27473 CGAAATATGA
*
27483 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
27535 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*** *
27587 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACA
27632 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 88 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:27638 original size:13 final size:13
Alignment explanation
Indices: 27620--27644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27610 CAAAGATTAG
27620 TGTATCGATACAA
1 TGTATCGATACAA
27633 TGTATCGATACA
1 TGTATCGATACA
27645 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:27712 original size:20 final size:20
Alignment explanation
Indices: 27683--27740 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
27673 GCAGTAGCTT
27683 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
27702 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
27722 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
27741 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:32334 original size:11 final size:11
Alignment explanation
Indices: 32320--32347 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
32310 CATTTCTTTT
32320 TTTTTTCTCTC
1 TTTTTTCTCTC
32331 TTTTTTCTCTC
1 TTTTTTCTCTC
32342 TTTTTT
1 TTTTTT
32348 TCTTTCCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTCTCTC
Found at i:32336 original size:13 final size:13
Alignment explanation
Indices: 32314--32348 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
32304 TGCTTTCATT
*
32314 TCTTTTTTTTTTC
1 TCTTTTTTTTCTC
*
32327 TCTCTTTTTTCTC
1 TCTTTTTTTTCTC
32340 TCTTTTTTT
1 TCTTTTTTT
32349 CTTTCCTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTTTTTTCTC
Found at i:32673 original size:5 final size:5
Alignment explanation
Indices: 32663--32691 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
32653 CGAAGAAAAC
32663 AAATA AAATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAAT
32692 TTAAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:32705 original size:20 final size:20
Alignment explanation
Indices: 32663--32713 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
32653 CGAAGAAAAC
*
32663 AAATAAAATAAAATAAAATA
1 AAATAAAATTAAATAAAATA
*
32683 AAATAAAATTTAA-AAAATCA
1 AAATAAAATTAAATAAAAT-A
*
32703 AAAGAAAATTA
1 AAATAAAATTA
32714 GAATCAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAAAATTAAATAAAATA
Found at i:34414 original size:19 final size:19
Alignment explanation
Indices: 34390--34457 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
34380 AATTCAACAA
34390 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
34409 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
34424 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
34441 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
34458 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:34429 original size:13 final size:13
Alignment explanation
Indices: 34411--34435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34401 ACATAAGTTT
34411 TGTATCGATACAA
1 TGTATCGATACAA
34424 TGTATCGATACA
1 TGTATCGATACA
34436 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:34433 original size:32 final size:32
Alignment explanation
Indices: 34392--34454 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
34382 TTCAACAATT
*
34392 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
34424 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
34455 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:37023 original size:28 final size:28
Alignment explanation
Indices: 36990--37061 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
36980 TCATAATCGA
* * *
36990 GGATACTCCAACCTCGTTA-TTTCATTGG
1 GGATACTCCAACCCCGTTACTTCCA-AGG
37018 GGATACTCCAACCCCGTTACTTCCAAGG
1 GGATACTCCAACCCCGTTACTTCCAAGG
37046 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
37062 GCTTTATTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCCAAGG
Found at i:37105 original size:79 final size:78
Alignment explanation
Indices: 37013--37248 Score: 224
Period size: 78 Copynumber: 3.0 Consensus size: 78
37003 TCGTTATTTC
* *
37013 ATTGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCC-GCTTTATTCCCAAAAT
37078 ATTGATTTCTCATA
65 ATTGATTTCTCATA
* * * * * * ** *
37092 ATTGGGGATACTCCAATCCCGTTATTTTCGAGAGGATACTCCAATCTCGATTTATTTTC-TAATC
1 ATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGCTTTATTCCCAAAAT-
* *
37156 ATCGATTTCTCACA
65 ATTGATTTCTCATA
** * * * *
37170 ACCGGGGATACTCCAGCCCCGTTGTTTTCAAGGGAACACTCCAACCCCGCTATTA-TCTCCAAAA
1 ATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGCT-TTATTC-CCAAAA
* *
37234 CATTAAATTTCTCAT
64 TATT-GATTTCTCAT
37249 CGGGAAATAT
Statistics
Matches: 120, Mismatches: 32, Indels: 9
0.75 0.20 0.06
Matches are distributed among these distances:
77 3 0.03
78 60 0.50
79 47 0.39
80 10 0.08
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (78 bp):
ATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGCTTTATTCCCAAAATA
TTGATTTCTCATA
Found at i:38904 original size:27 final size:27
Alignment explanation
Indices: 38837--38908 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
38827 AAGTTAAAAA
38837 AATGGGGTTGGAGTATCCCCTCAGAAG
1 AATGGGGTTGGAGTATCCCCTCAGAAG
** * * * *
38864 AACAGGGTTAGAGTATCTCTTCGGAAG
1 AATGGGGTTGGAGTATCCCCTCAGAAG
*
38891 AATGGGGCTGGAGTATCC
1 AATGGGGTTGGAGTATCC
38909 TGGATAAATA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (27 bp):
AATGGGGTTGGAGTATCCCCTCAGAAG
Found at i:41346 original size:51 final size:53
Alignment explanation
Indices: 41281--41451 Score: 174
Period size: 51 Copynumber: 3.3 Consensus size: 53
41271 TACATTAAAG
* * * * *
41281 AATGTATGGTTACATTTGAGTC-AAAAGCCAGAATGTATAGATATAACG-AAT
1 AATGTATCGATACATTTGAGTCAAAAACCCAGAATGTATAGATACAACGAAAA
* * *
41332 AATGTATCGATACATTTGGGTCAAAAACCCAGAATGTATCGATACAATGAAAA
1 AATGTATCGATACATTTGAGTCAAAAACCCAGAATGTATAGATACAACGAAAA
* * * *
41385 AATGTATCGATACATTTG-GATC--AAACCCAAAATGCATTGATACAA-TAAAA
1 AATGTATCGATACATTTGAG-TCAAAAACCCAGAATGTATAGATACAACGAAAA
*
41435 AATGTATTGATACATTT
1 AATGTATCGATACATTT
41452 TCTTTCCAGA
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
50 20 0.19
51 39 0.38
52 23 0.22
53 22 0.21
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (53 bp):
AATGTATCGATACATTTGAGTCAAAAACCCAGAATGTATAGATACAACGAAAA
Found at i:44352 original size:3 final size:3
Alignment explanation
Indices: 44346--44370 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44336 TAAAAAAACT
44346 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
44371 CTTTTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:45733 original size:20 final size:20
Alignment explanation
Indices: 45710--45766 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
45700 AATCCAACTA
45710 TTTTTCACTATTTTTTCTTAT
1 TTTTTC-CTATTTTTTCTTAT
* *
45731 TTTTTCCTGTTTTTTCTTCCT
1 TTTTTCCTATTTTTTCTT-AT
45752 TTTTTCTCT-TTTTTT
1 TTTTTC-CTATTTTTT
45767 GTTGTTGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.34
21 19 0.59
22 2 0.06
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTCCTATTTTTTCTTAT
Found at i:45765 original size:11 final size:11
Alignment explanation
Indices: 45710--45766 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 11
45700 AATCCAACTA
*
45710 TTTTTCACTAT
1 TTTTTCTCTAT
45721 TTTTTCT-TAT
1 TTTTTCTCTAT
*
45731 TTTTTC-CTGT
1 TTTTTCTCTAT
*
45741 TTTTTCT-TCCT
1 TTTTTCTCT-AT
45752 TTTTTCTCT-T
1 TTTTTCTCTAT
45762 TTTTT
1 TTTTT
45767 GTTGTTGAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 24 0.62
11 14 0.36
12 1 0.03
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTTCTCTAT
Found at i:46458 original size:168 final size:167
Alignment explanation
Indices: 46073--46542 Score: 610
Period size: 168 Copynumber: 2.8 Consensus size: 167
46063 TAATGTATAC
* * *
46073 AAAAAAATTAAAAATTCATG-AAATAAATTGAATTTCTTG-AAACTGATTTAATGA-GATTTAAA
1 AAAAAAATT-AAAACTCATGAAAATAAA-TGAATTT-TTGAAAAATGATTTAAT-ATGAATTAAA
* * * **
46135 TGATGATATTTTATGAATTTTAAAAATTAGAAACCAAG-AAAATGCC-CTCGAAAATATTTATAA
62 TGATGATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAAT-CCTCTCAAAAATATTTATGG
* *
46198 AATAAAAAACTCAATTTTTGGGAAACAGGAAAATTTCAAAGA
126 AATAGAAAACTCAATTTTTGGGAAAAAGGAAAATTTCAAAGA
* * *
46240 AAAAAAATTAAAACTCATGAAAATAAATGAAATTTTCAAAAATGATTTAATATGACTTAAATGAT
1 AAAAAAATTAAAACTCATGAAAATAAATGAATTTTTGAAAAATGATTTAATATGAATTAAATGAT
*
46305 GATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCAAAAATATTTATGGAATAG
66 GATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCTCAAAAATATTTATGGAATAG
**
46370 AAAACTCAATTTTTTGGGAAAAAGGGGAATTTCAAAG-
131 AAAACTCAA-TTTTTGGGAAAAAGGAAAATTTCAAAGA
* * * *
46407 AAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTGAAAAATAATTTAATATGAAATAAATAA
1 AAAAAAATT-AAAACTCATGAAAATAAATGAATTTTTGAAAAATGATTTAATATGAATTAAATGA
* * * * *
46472 TAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCTTCTCAAAAAAATTTACGGAGTA
65 TGATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCTCAAAAATATTTATGGAATA
46537 GAAAAC
130 GAAAAC
46543 CTTGTATTTT
Statistics
Matches: 268, Mismatches: 28, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
165 3 0.01
166 72 0.27
167 56 0.21
168 137 0.51
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (167 bp):
AAAAAAATTAAAACTCATGAAAATAAATGAATTTTTGAAAAATGATTTAATATGAATTAAATGAT
GATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCTCAAAAATATTTATGGAATAG
AAAACTCAATTTTTGGGAAAAAGGAAAATTTCAAAGA
Found at i:46635 original size:156 final size:158
Alignment explanation
Indices: 46093--46699 Score: 487
Period size: 168 Copynumber: 3.7 Consensus size: 158
46083 AAAATTCATG
** * * * *
46093 AAATAAATTGAATTTCTTGAAACTGATTTAATGA-GATTTAAATGATGATATTTTATGAATTTTA
1 AAATAAA-TGAATTT-TCAAAAATGATTTAAT-ATGA-TTAAATAATAATATTTGATGAATTTTA
* * * * *** * * *
46157 AAAATTAGAAACCAAG-AAAATGCC-CTCGAAAATATTTATAAAATAAAAAACTCAATTTTTGGG
62 AAAATTAAAAACCAAGAAAAAT-CCTCCCAAAAAAATTTACGGAGTAGAAAAC-CATTTTTTGGG
* *
46220 AAACAGGAAAATTTCAAAGAAAAAAAATTAAAACTCATGA
125 AAAAAGGGAAATTTCAAAG-AAAAAAATT--AA--CA-GA
* *
46260 AAATAAATGAAATTTTCAAAAATGATTTAATATGACTTAAATGATGATATTTGATGAATTTTAAA
1 AAATAAATG-AATTTTCAAAAATGATTTAATATGA-TTAAATAATAATATTTGATGAATTTTAAA
* * *
46325 AATTAAAAACCAAGAAAAATCCTCCCAAAAATATTTATGGAATAGAAAACTCAATTTTTTGGGAA
64 AATTAAAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGTAGAAAAC-C-ATTTTTTGGGAA
*
46390 AAAGGGGAATTTCAAAGAAAAAAATTCAAAACTCATGA
127 AAAGGGAAATTTCAAAGAAAAAAATT---AA--CA-GA
* * * *
46428 AAATGAATGAATTTTTGAAAAATAATTTAATATGAAATAAATAATAATATTTGATGAATTTTAAA
1 AAATAAATGAA-TTTTCAAAAATGATTTAATATG-ATTAAATAATAATATTTGATGAATTTTAAA
* * *
46493 AATTAAAAACCAAGAAAAATCTTCTCAAAAAAATTTACGGAGTAGAAAACC-TTGTATTTTGGAA
64 AATTAAAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGTAGAAAACCATT-T-TTTGGGAA
* *
46557 ATAGGGAAATTT-TAAGAAAAAAA-T-A-A-A
127 AAAGGGAAATTTCAAAGAAAAAAATTAACAGA
* * * * *
46584 AAATTAATGAATTCTTCAAAATTGATTTAATGGTGATTAAATAATAATATTTAATAAATTTTAAA
1 AAATAAATGAATT-TTCAAAAATGATTTAAT-ATGATTAAATAATAATATTTGATGAATTTTAAA
** ** * *
46649 AATTTTAAACTCTTG-AAAATCCTCCCAAAAAACTTTACGGAGAAGAAAACC
64 AATTAAAAAC-CAAGAAAAATCCTCCCAAAAAAATTTACGGAGTAGAAAACC
46700 CCGTAATTTG
Statistics
Matches: 381, Mismatches: 46, Indels: 37
0.82 0.10 0.08
Matches are distributed among these distances:
155 2 0.01
156 92 0.24
157 4 0.01
158 1 0.00
161 1 0.00
165 4 0.01
166 71 0.19
167 70 0.18
168 135 0.35
169 1 0.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (158 bp):
AAATAAATGAATTTTCAAAAATGATTTAATATGATTAAATAATAATATTTGATGAATTTTAAAAA
TTAAAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGTAGAAAACCATTTTTTGGGAAAAAG
GGAAATTTCAAAGAAAAAAATTAACAGA
Found at i:48206 original size:44 final size:45
Alignment explanation
Indices: 48150--48243 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 45
48140 GTAAACACAG
* *
48150 GATG-AAGAGGTTTACCAAAGACTAAGCCGACAGGTAAACATTAA
1 GATGAAAGAGGTTTACCAAAGACTAAGCCGACAAGTAAACAATAA
* *
48194 GATGAAAG-GGTTTACCAAGGACTAAGCCGACAAGTAAACAATGA
1 GATGAAAGAGGTTTACCAAAGACTAAGCCGACAAGTAAACAATAA
48238 GATGAA
1 GATGAA
48244 GGTTGACTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 42 0.93
45 3 0.07
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (45 bp):
GATGAAAGAGGTTTACCAAAGACTAAGCCGACAAGTAAACAATAA
Found at i:48301 original size:85 final size:85
Alignment explanation
Indices: 48201--48873 Score: 596
Period size: 85 Copynumber: 8.0 Consensus size: 85
48191 TAAGATGAAA
* * * * * * *
48201 GGGTTTACCAAGGACTAAGCCGACAAGTAAACAATGAGATGAAGGTTGACTGAAGACTGAGCTAA
1 GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGAGATAAAGGTTGACTGGAGACTGAGCTGA
*
48266 TAGGTCACCATAGGGGTAAT
66 TAGGTCACCATAGGGGTAAG
* * * *
48286 GGGTTTACC-AGGGACTGAGCCGACAGGTAAATAAT-AGGATAAAGGTTGATTGGAGACTAAGCT
1 GGGTTTACCGA-GGACTGAGCTGACAGGTAAACAATGA-GATAAAGGTTGACTGGAGACTGAGCT
* * *
48349 GACAGGTCCCCATAAGGGTAAG
64 GATAGGTCACCATAGGGGTAAG
* * * * * *
48371 GGGTTTACCAAAGACCGAGCTGATAGGTAAACAATGGGATAAAGGTTGA-TCGGAGACTGAGCTT
1 GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGAGATAAAGGTTGACT-GGAGACTGAGCTG
* *
48435 ATAGGTCAGCATAGGAGTAAAG
65 ATAGGTCACCATAGGGGT-AAG
* * *
48457 GGGTTTACCGAAGACTAAGCTGACAGGTAAACAATGAGATGAAGGTTGAC-GGAAGACTGAGCTG
1 GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGAGATAAAGGTTGACTGG-AGACTGAGCTG
* * *
48521 ACAGGTCACTATAGGGGCAAG
65 ATAGGTCACCATAGGGGTAAG
* * * ** * * *
48542 GGGTTTATCGAAGACTGAGTTGACAGGTAAATGA-GAGGATGAAGGTTGACCGGAGACTGAGTTG
1 GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGA-GATAAAGGTTGACTGGAGACTGAGCTG
* *
48606 ATAGGTCACCATAGAGATAAG
65 ATAGGTCACCATAGGGGTAAG
* * * * *
48627 GGGTTTACCGAGGATTGAGCAGATAGGTAAACAATGGGATGAAGGTTGACT-GAG--T----TGA
1 GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGAGATAAAGGTTGACTGGAGACTGAGCTGA
48685 TAGGTCACCATAGGGGTAAG
66 TAGGTCACCATAGGGGTAAG
* * * * * * * * * *
48705 GGGTTTATCGAGGACCGAGTTGATAGGTAAATAAGGAGATAAAGGTTAACTAGAGACTAAGCTAA
1 GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGAGATAAAGGTTGACTGGAGACTGAGCTGA
* * * *
48770 TTGGTTACCATATGGGTAAT
66 TAGGTCACCATAGGGGTAAG
* * * * * * * *
48790 GGGTTTATCGAGGACTGAGCCGACAGGTAAATAATAAGGTAAAGGTTAACCGGAGACTGAGTTGA
1 GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGAGATAAAGGTTGACTGGAGACTGAGCTGA
* *
48855 CAGGTCACCATAAGGGTAA
66 TAGGTCACCATAGGGGTAA
48874 AGGTGTCTCT
Statistics
Matches: 479, Mismatches: 91, Indels: 36
0.79 0.15 0.06
Matches are distributed among these distances:
78 62 0.13
79 3 0.01
81 1 0.00
82 1 0.00
84 8 0.02
85 331 0.69
86 73 0.15
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (85 bp):
GGGTTTACCGAGGACTGAGCTGACAGGTAAACAATGAGATAAAGGTTGACTGGAGACTGAGCTGA
TAGGTCACCATAGGGGTAAG
Found at i:48656 original size:256 final size:247
Alignment explanation
Indices: 48201--48869 Score: 745
Period size: 256 Copynumber: 2.7 Consensus size: 247
48191 TAAGATGAAA
* *
48201 GGGTTTACC-AAGGACTAAGCCGACAAGTAAACAATGAGATGAAGGTTGACTGAAGACTGAGCTA
1 GGGTTTACCGAA-GACTAAGCTGACAGGTAAACAATGAGATGAAGGTTGAC-GAAGACTGAGCTA
* *
48265 ATAGGTCACCATAGGGGTAATGGGTTTA-CCAGGGACTGAGCCGACAGGTAAATAATAGGATAAA
64 ATAGGTCACCATAGGGGTAATGGGTTTATCGA-GGACTGAGCCGACAGGTAAATAAAAGGATAAA
** * * * * *
48329 GGTTGATTGGAGACTAAGCTGACAGGTCCCCATAAGGGTAAGGGGTTTACCAAAGACCGAGCTGA
128 GGTTGACCGGAGACTGAGTTGACAGGTCACCATAAGGATAAGGGGTTTACCAAAGACCGAGCAGA
*
48394 TAGGTAAACAATGGGATAAAGGTTGATCGGAGACTGAGCTT-ATAGGTCAGCATAGGAGTAAAG
193 TAGGTAAACAATGGGATAAAGG-T--T----GACTGAG-TTGATAGGTCACCATAGGAGT-AAG
*
48457 GGGTTTACCGAAGACTAAGCTGACAGGTAAACAATGAGATGAAGGTTGACGGAAGACTGAGCTGA
1 GGGTTTACCGAAGACTAAGCTGACAGGTAAACAATGAGATGAAGGTTGAC-GAAGACTGAGCTAA
* * * * * ** * * *
48522 CAGGTCACTATAGGGGCAAGGGGTTTATCGAAGACTGAGTTGACAGGTAAATGAGAGGATGAAGG
65 TAGGTCACCATAGGGGTAATGGGTTTATCGAGGACTGAGCCGACAGGTAAATAAAAGGATAAAGG
* * * **
48587 TTGACCGGAGACTGAGTTGATAGGTCACCAT-AGAGATAAGGGGTTTACCGAGGATTGAGCAGAT
130 TTGACCGGAGACTGAGTTGACAGGTCACCATAAG-GATAAGGGGTTTACCAAAGACCGAGCAGAT
* *
48651 AGGTAAACAATGGGATGAAGGTTGACTGAGTTGATAGGTCACCATAGGGGTAAG
194 AGGTAAACAATGGGATAAAGGTTGACTGAGTTGATAGGTCACCATAGGAGTAAG
* * ** * * * * * * * *
48705 GGGTTTATCGAGGACCGAGTTGATAGGTAAATAAGGAGATAAAGGTTAACTAGAGACTAAGCTAA
1 GGGTTTACCGAAGACTAAGCTGACAGGTAAACAATGAGATGAAGGTTGACGA-AGACTGAGCTAA
* * *
48770 TTGGTTACCATATGGGTAATGGGTTTATCGAGGACTGAGCCGACAGGTAAATAATAAGG-TAAAG
65 TAGGTCACCATAGGGGTAATGGGTTTATCGAGGACTGAGCCGACAGGTAAATAA-AAGGATAAAG
*
48834 GTTAACCGGAGACTGAGTTGACAGGTCACCATAAGG
129 GTTGACCGGAGACTGAGTTGACAGGTCACCATAAGG
48870 GTAAAGGTGT
Statistics
Matches: 348, Mismatches: 58, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
247 1 0.00
248 133 0.38
249 28 0.08
253 1 0.00
255 3 0.01
256 178 0.51
257 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (247 bp):
GGGTTTACCGAAGACTAAGCTGACAGGTAAACAATGAGATGAAGGTTGACGAAGACTGAGCTAAT
AGGTCACCATAGGGGTAATGGGTTTATCGAGGACTGAGCCGACAGGTAAATAAAAGGATAAAGGT
TGACCGGAGACTGAGTTGACAGGTCACCATAAGGATAAGGGGTTTACCAAAGACCGAGCAGATAG
GTAAACAATGGGATAAAGGTTGACTGAGTTGATAGGTCACCATAGGAGTAAG
Found at i:48750 original size:78 final size:78
Alignment explanation
Indices: 48596--48751 Score: 215
Period size: 78 Copynumber: 2.0 Consensus size: 78
48586 GTTGACCGGA
**
48596 GACTGAGTTGATAGGTCACCATAGAGATAAGGGGTTTACCGAGGATTGAGCAGATAGGTAAACAA
1 GACTGAGTTGATAGGTCACCATAGAGATAAGGGGTTTACCGAGGACCGAGCAGATAGGTAAACAA
*
48661 TGGGATGAAGGTT
66 TGGGATAAAGGTT
* * * ** *
48674 GACTGAGTTGATAGGTCACCATAGGGGTAAGGGGTTTATCGAGGACCGAGTTGATAGGTAAATAA
1 GACTGAGTTGATAGGTCACCATAGAGATAAGGGGTTTACCGAGGACCGAGCAGATAGGTAAACAA
48739 -GGAGATAAAGGTT
66 TGG-GATAAAGGTT
48752 AACTAGAGAC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 2 0.03
78 66 0.97
ACGTcount: A:0.33, C:0.10, G:0.34, T:0.24
Consensus pattern (78 bp):
GACTGAGTTGATAGGTCACCATAGAGATAAGGGGTTTACCGAGGACCGAGCAGATAGGTAAACAA
TGGGATAAAGGTT
Found at i:48890 original size:85 final size:85
Alignment explanation
Indices: 48674--48903 Score: 255
Period size: 85 Copynumber: 2.7 Consensus size: 85
48664 GATGAAGGTT
* * * *
48674 GACTGAGTTGATAGGTCACCATAGGGGTAAGGGGTTTATCGAGGACCGAGTTGATAGGTAAATAA
1 GACTGAGTTGATAGGTCACCATAAGGGTAAAGGGTTTATCGAGGACTGAGTCGATAGGTAAATAA
* *
48739 GGAGATAAAGGTTAACTAGA
66 GAAGATAAAGGTTAACCAGA
* * * * * * * * *
48759 GACTAAGCTAATTGGTTACCATATGGGTAATGGGTTTATCGAGGACTGAGCCGACAGGTAAATAA
1 GACTGAGTTGATAGGTCACCATAAGGGTAAAGGGTTTATCGAGGACTGAGTCGATAGGTAAATAA
* * *
48824 TAAGGTAAAGGTTAACCGGA
66 GAAGATAAAGGTTAACCAGA
* * *
48844 GACTGAGTTGACAGGTCACCATAAGGGTAAAGGTGTCTCTCG-GGACTGAGTCGATAGGTA
1 GACTGAGTTGATAGGTCACCATAAGGGTAAAGG-GTTTATCGAGGACTGAGTCGATAGGTA
48904 GACAAAGGAT
Statistics
Matches: 116, Mismatches: 28, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
85 110 0.95
86 6 0.05
ACGTcount: A:0.32, C:0.13, G:0.31, T:0.24
Consensus pattern (85 bp):
GACTGAGTTGATAGGTCACCATAAGGGTAAAGGGTTTATCGAGGACTGAGTCGATAGGTAAATAA
GAAGATAAAGGTTAACCAGA
Found at i:48942 original size:41 final size:43
Alignment explanation
Indices: 48872--48957 Score: 113
Period size: 41 Copynumber: 2.0 Consensus size: 43
48862 CCATAAGGGT
* * * * *
48872 AAAGGTGTCTCTCGGGACTGAGTCGATAGGTAGACAAAGGATA
1 AAAGGTGTCTCTCGGGACTAAGCCAATAGGTAAACAAAGAATA
48915 AAAGGTGT-T-TCGGGACTAAGCCAATAGGTAAACAAAGAATA
1 AAAGGTGTCTCTCGGGACTAAGCCAATAGGTAAACAAAGAATA
48956 AA
1 AA
48958 GAAGTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 29 0.76
42 1 0.03
43 8 0.21
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.20
Consensus pattern (43 bp):
AAAGGTGTCTCTCGGGACTAAGCCAATAGGTAAACAAAGAATA
Found at i:49503 original size:58 final size:58
Alignment explanation
Indices: 49413--49533 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 58
49403 CTTGTATCTG
* *
49413 GCACTGTTTATTAAAGAACCAAGTGCTTTTGCCCTTTG-GGCAATTCAGGTTATTTGAT
1 GCACTGTCTATTAAAGAACCAAGTGCTTTTGCCCTTTGAGG-AATTCACGTTATTTGAT
* *
49471 GCACTGTCTATTAAAGAACCAGGTGCTTTTGCCCTTTGAGGAATTCACGTTGTTTGAT
1 GCACTGTCTATTAAAGAACCAAGTGCTTTTGCCCTTTGAGGAATTCACGTTATTTGAT
49529 GCACT
1 GCACT
49534 AATACCATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
58 56 0.97
59 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (58 bp):
GCACTGTCTATTAAAGAACCAAGTGCTTTTGCCCTTTGAGGAATTCACGTTATTTGAT
Found at i:49770 original size:14 final size:14
Alignment explanation
Indices: 49753--49810 Score: 68
Period size: 14 Copynumber: 4.2 Consensus size: 14
49743 CAGTCGGTTT
49753 TTTTATTTATTTTG
1 TTTTATTTATTTTG
49767 TTTTATTTATTTT-
1 TTTTATTTATTTTG
*
49780 TTATTATTTTTTTTG
1 TT-TTATTTATTTTG
49795 -TTT-TTTATTTTTG
1 TTTTATTTA-TTTTG
49808 TTT
1 TTT
49811 ATTCTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 3 0.08
13 9 0.24
14 26 0.68
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (14 bp):
TTTTATTTATTTTG
Found at i:49771 original size:10 final size:9
Alignment explanation
Indices: 49750--49839 Score: 85
Period size: 9 Copynumber: 9.7 Consensus size: 9
49740 TTTCAGTCGG
49750 TTTTTTTAT
1 TTTTTTTAT
* *
49759 TTATTTTGT
1 TTTTTTTAT
*
49768 TTTATTTAT
1 TTTTTTTAT
49777 TTTTTATTA-
1 TTTTT-TTAT
49786 TTTTTTT-T
1 TTTTTTTAT
*
49794 GTTTTTTAT
1 TTTTTTTAT
49803 TTTTGTTTAT
1 TTTT-TTTAT
49813 TCTTTTTTAT
1 T-TTTTTTAT
49823 GGTTTTTTTAT
1 --TTTTTTTAT
49834 TTTTTT
1 TTTTTT
49840 CTTTTTTTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
8 8 0.12
9 32 0.48
10 14 0.21
11 11 0.17
12 1 0.02
ACGTcount: A:0.11, C:0.01, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:49812 original size:40 final size:39
Alignment explanation
Indices: 49750--49845 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 39
49740 TTTCAGTCGG
* *
49750 TTTTTTTATTTA-TTTTGTTTTATTTATTTTTTATTATTT
1 TTTTTTTTTTTATTTTTGTTTTA-TTATTTTTTATGATTT
* *
49789 TTTTTGTTTTTTATTTTTG-TTTATTCTTTTTTATGGTTT
1 TTTTT-TTTTTTATTTTTGTTTTATTATTTTTTATGATTT
*
49828 TTTTATTTTTTTCTTTTT
1 TTTT-TTTTTTTATTTTT
49846 TTATGCATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 33 0.67
40 11 0.22
41 5 0.10
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.82
Consensus pattern (39 bp):
TTTTTTTTTTTATTTTTGTTTTATTATTTTTTATGATTT
Found at i:49812 original size:50 final size:48
Alignment explanation
Indices: 49752--49847 Score: 115
Period size: 50 Copynumber: 2.0 Consensus size: 48
49742 TCAGTCGGTT
* *
49752 TTTTTATTTATT-TTGTTTTAT-TTATTTTTTATTATTTTTTTTGTTTTTTA
1 TTTTTATTTATTCTT-TTTTATGGT-TTTTTTATT-TTTTTCTT-TTTTTTA
*
49802 TTTTTGTTTATTCTTTTTTATGGTTTTTTTATTTTTTTCTTTTTTT
1 TTTTTATTTATTCTTTTTTATGGTTTTTTTATTTTTTTCTTTTTTT
49848 ATGCATAGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 5 0.12
49 7 0.17
50 26 0.63
51 3 0.07
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.82
Consensus pattern (48 bp):
TTTTTATTTATTCTTTTTTATGGTTTTTTTATTTTTTTCTTTTTTTTA
Found at i:49818 original size:13 final size:13
Alignment explanation
Indices: 49750--49819 Score: 56
Period size: 13 Copynumber: 5.3 Consensus size: 13
49740 TTTCAGTCGG
49750 TTTT-TTTATT-T
1 TTTTGTTTATTAT
49761 ATTTTGTTTTATTTAT
1 -TTTTG-TTTA-TTAT
*
49777 TTTT-TATTATTTT
1 TTTTGT-TTATTAT
*
49790 TTTTGTTTTTTAT
1 TTTTGTTTATTAT
*
49803 TTTTGTTTATTCT
1 TTTTGTTTATTAT
49816 TTTT
1 TTTT
49820 TATGGTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
12 4 0.09
13 28 0.60
14 8 0.17
15 6 0.13
16 1 0.02
ACGTcount: A:0.11, C:0.01, G:0.04, T:0.83
Consensus pattern (13 bp):
TTTTGTTTATTAT
Found at i:49819 original size:14 final size:13
Alignment explanation
Indices: 49750--49820 Score: 67
Period size: 14 Copynumber: 5.3 Consensus size: 13
49740 TTTCAGTCGG
*
49750 TTTT-TTTATTTA
1 TTTTGTTTATTTT
49762 TTTTGTTTTATTTAT
1 TTTTG-TTTATTT-T
49777 TTTT-TATTATTTT
1 TTTTGT-TTATTTT
49790 TTTTGTTT-TTTAT
1 TTTTGTTTATTT-T
49803 TTTTGTTTATTCTT
1 TTTTGTTTATT-TT
49817 TTTT
1 TTTT
49821 ATGGTTTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
12 7 0.14
13 17 0.34
14 21 0.42
15 5 0.10
ACGTcount: A:0.11, C:0.01, G:0.04, T:0.83
Consensus pattern (13 bp):
TTTTGTTTATTTT
Found at i:49846 original size:40 final size:39
Alignment explanation
Indices: 49748--49846 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 39
49738 GTTTTCAGTC
* *
49748 GGTTTTTTTATTTATTTTGTTTTATTTATTTTTTATTAT
1 GGTTTTTTTATTTTTTTTTTTTTATTTATTTTTTATTAT
* * *
49787 --TTTTTTT-GTTTTTTATTTTTGTTTATTCTTTT-TTAT
1 GGTTTTTTTATTTTTTTTTTTTTATTTATT-TTTTATTAT
49823 GGTTTTTTTATTTTTTTCTTTTTT
1 GGTTTTTTTATTTTTTT-TTTTTT
49847 TATGCATAGT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
36 19 0.40
37 11 0.23
38 7 0.15
39 6 0.12
40 5 0.10
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (39 bp):
GGTTTTTTTATTTTTTTTTTTTTATTTATTTTTTATTAT
Found at i:49847 original size:10 final size:10
Alignment explanation
Indices: 49751--49839 Score: 90
Period size: 10 Copynumber: 8.7 Consensus size: 10
49741 TTCAGTCGGT
49751 TTTTTTATTTA
1 TTTTTT-TTTA
*
49762 TTTTGTTTTA
1 TTTTTTTTTA
49772 TTTATTTTTTA
1 TTT-TTTTTTA
*
49783 TTATTTTTT-
1 TTTTTTTTTA
*
49792 TTGTTTTTTA
1 TTTTTTTTTA
*
49802 TTTTTGTTTA
1 TTTTTTTTTA
*
49812 TTCTTTTTTA
1 TTTTTTTTTA
*
49822 TGGTTTTTTTA
1 T-TTTTTTTTA
49833 TTTTTTT
1 TTTTTTT
49840 CTTTTTTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
9 8 0.12
10 35 0.55
11 21 0.33
ACGTcount: A:0.11, C:0.01, G:0.06, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:56314 original size:24 final size:21
Alignment explanation
Indices: 56287--56351 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 21
56277 TAGAAAAATC
56287 ACATTTTTACCTAGATGTATCGAT
1 ACATTTTTA-C-A-ATGTATCGAT
56311 ACATTTTT-CAATGTATCGAT
1 ACATTTTTACAATGTATCGAT
*
56331 ACATGTTTA-AATGTATCGAT
1 ACATTTTTACAATGTATCGAT
56351 A
1 A
56352 TATTCTGTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
20 29 0.74
21 1 0.03
22 1 0.03
24 8 0.21
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTTTTACAATGTATCGAT
Found at i:56326 original size:20 final size:20
Alignment explanation
Indices: 56301--56351 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
56291 TTTTACCTAG
* *
56301 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTTTAA
56321 ATGTATCGATACATGTTTAA
1 ATGTATCGATACATGTTTAA
56341 ATGTATCGATA
1 ATGTATCGATA
56352 TATTCTGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTTTAA
Found at i:56406 original size:71 final size:71
Alignment explanation
Indices: 56290--56428 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
56280 AAAAATCACA
* * * * *
56290 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTTTAAATGTATCGATATAT
1 TTTTTACCCAGACGTATCGATACATTTTTCAATGTATCAATACATGTATAAATGTATCGATACAT
56355 TCTGTC
66 TCTGTC
* *
56361 TTTTTACCCAGACGTATCGATGCATTTTTCAATGTATCAATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGACGTATCGATACATTTTTCAATGTATCAATACATGTATAAATGTATCGATACAT
56426 TCT
66 TCT
56429 ATAATGTGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (71 bp):
TTTTTACCCAGACGTATCGATACATTTTTCAATGTATCAATACATGTATAAATGTATCGATACAT
TCTGTC
Found at i:56434 original size:20 final size:21
Alignment explanation
Indices: 56374--56448 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 21
56364 TTACCCAGAC
* * *
56374 GTATCGATGCATT-TTTCAAT
1 GTATCGATACATTCTATGAAT
* *
56394 GTATCAATACA-TGTATGAAT
1 GTATCGATACATTCTATGAAT
56414 GTATCGATACATTCTAT-AAT
1 GTATCGATACATTCTATGAAT
*
56434 GTGTCGATACATTCT
1 GTATCGATACATTCT
56449 GTCTTTTTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.89
21 4 0.09
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
GTATCGATACATTCTATGAAT
Found at i:56486 original size:91 final size:91
Alignment explanation
Indices: 56301--56496 Score: 261
Period size: 91 Copynumber: 2.2 Consensus size: 91
56291 TTTTACCTAG
* * * *
56301 ATGTATCGATACATTTTTCAATGTATCGATACATGTTTAAATGTATCGATATATTCTGTCTTTTT
1 ATGTATCGATACATGTATCAATGTATCGATACATGTCTAAATGTATCGATACATTCTGTCTTTTT
* **
56366 ACCCAGACGTATCGATGCATTTTTCA
66 ACCCAGACGTATCGATACATTAATCA
* * *
56392 ATGTATCAATACATGTATGAATGTATCGATACAT-TCTATAATGTGTCGATACATTCTGTCTTTT
1 ATGTATCGATACATGTATCAATGTATCGATACATGTCTA-AATGTATCGATACATTCTGTCTTTT
*
56456 TACCCAGATGTATCGATACATTGAAT-A
65 TACCCAGACGTATCGATACATT-AATCA
56483 ATGTATCGATACAT
1 ATGTATCGATACAT
56497 CTATTTAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 3 0.03
91 87 0.96
92 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (91 bp):
ATGTATCGATACATGTATCAATGTATCGATACATGTCTAAATGTATCGATACATTCTGTCTTTTT
ACCCAGACGTATCGATACATTAATCA
Found at i:62625 original size:20 final size:19
Alignment explanation
Indices: 62600--62666 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
62590 CTACCACTGT
62600 TTGTATCGATACATGATACA
1 TTGTATCGATACATGATA-A
62620 TTGTATCGATACAT--T-A
1 TTGTATCGATACATGATAA
62636 ---TATCGATACATGATGAA
1 TTGTATCGATACATGAT-AA
62653 TTGTATCGATACAT
1 TTGTATCGATACAT
62667 TGCCTGTAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 25 0.62
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGATAA
Found at i:62632 original size:13 final size:13
Alignment explanation
Indices: 62614--62668 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
62604 ATCGATACAT
62614 GATACATTGTATC
1 GATACATTGTATC
*
62627 GATACATTATATC
1 GATACATTGTATC
62640 GATACA-TG-AT-
1 GATACATTGTATC
62650 G--A-ATTGTATC
1 GATACATTGTATC
62660 GATACATTG
1 GATACATTG
62669 CCTGTAACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
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 2 0.06
13 22 0.65
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:62645 original size:33 final size:33
Alignment explanation
Indices: 62603--62667 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
62593 CCACTGTTTG
62603 TATCGATACATGAT-ACATTGTATCGATACATTA
1 TATCGATACATGATGA-ATTGTATCGATACATTA
62636 TATCGATACATGATGAATTGTATCGATACATT
1 TATCGATACATGATGAATTGTATCGATACATT
62668 GCCTGTAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (33 bp):
TATCGATACATGATGAATTGTATCGATACATTA
Found at i:66590 original size:20 final size:19
Alignment explanation
Indices: 66564--66637 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 19
66554 ATTTGCTTGC
66564 ATGTATCGATACATTGAAT
1 ATGTATCGATACATTGAAT
**
66583 AGTGTATCGATACATCTGGGT
1 A-TGTATCGATACAT-TGAAT
66604 AATGTATCGATACATTGAAT
1 -ATGTATCGATACATTGAAT
66624 CATGTATCGATACA
1 -ATGTATCGATACA
66638 AAACTTATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 29 0.62
21 16 0.34
22 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATTGAAT
Found at i:67834 original size:52 final size:52
Alignment explanation
Indices: 67705--67953 Score: 174
Period size: 49 Copynumber: 4.9 Consensus size: 52
67695 GGGCTTAAAG
** * * *
67705 AATGTCAATGTGCTGATTCACGGCCCGCGACGTTAGACTTGAAGATGAGAAG
1 AATGTCAATGTGCTGATTCACGGCCAACGACATTAGACTTAAAGATGAGAAA
* * * * * * **
67757 AATGCCAATGTGCTAATTTAAGGCCAATGACATTGGGTTTAAAGAT-ACGAAA
1 AATGTCAATGTGCTGATTCACGGCCAACGACATTAGACTTAAAGATGA-GAAA
*
67809 AATGTCAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAAGATGATG---
1 AATGTCAATGTGCTGATTCACGGCCAACGACATTAGACTTAAAGATGA-GAAA
* * * * ** * *
67859 -GTGCCAATGTGCTGATTCAAGGACAGTGACATTGGACTTAAAAAT--G-AA
1 AATGTCAATGTGCTGATTCACGGCCAACGACATTAGACTTAAAGATGAGAAA
* * * *
67907 AGTG-CTAATGTGCCGATTCAAGGCCAGCGACATTAGACTTAAAGATG
1 AATGTC-AATGTGCTGATTCACGGCCAACGACATTAGACTTAAAGATG
67954 CCAATGTGCT
Statistics
Matches: 155, Mismatches: 35, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
46 1 0.01
48 1 0.01
49 76 0.49
51 1 0.01
52 74 0.48
53 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AATGTCAATGTGCTGATTCACGGCCAACGACATTAGACTTAAAGATGAGAAA
Found at i:67890 original size:49 final size:46
Alignment explanation
Indices: 67814--67983 Score: 193
Period size: 49 Copynumber: 3.6 Consensus size: 46
67804 CGAAAAATGT
*
67814 CAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAAGATGATGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAA-ATGA--GTGC
* * *
67863 CAATGTGCTGATTCAAGGACAGTGACATTGGACTTAAAAATGAAAGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTT-AAAATG--AGTGC
* *
67912 TAATGTGCCGATTCAAGGCCAGCGACATTAGACTT-AAA-GA-TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAATGAGTGC
* *
67955 CAATGTGCTGATTCAAGGCTAGTGACATT
1 CAATGTGCTGATTCAAGGCCAGCGACATT
67984 GGGCTTAGAA
Statistics
Matches: 105, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
43 28 0.27
44 1 0.01
46 1 0.01
47 3 0.03
49 68 0.65
50 3 0.03
51 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (46 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAATGAGTGC
Found at i:67940 original size:98 final size:98
Alignment explanation
Indices: 67705--67990 Score: 318
Period size: 104 Copynumber: 2.9 Consensus size: 98
67695 GGGCTTAAAG
* *
67705 AATGTCAATGTGCTGATTCACGGCCCGCGACGTTAGACTTGAAGATGAGAAGAATGCCAATGTGC
1 AATGTCAATGTGCTGATTCACGGCCAGCGACATTAGACTT-AAGATGAG--G--TGCCAATGTGC
* * * *
67770 TAATTTAAGGCCAATGACATTGGGTTTAAAGATACGAAA
61 TGATTCAAGG-CAGTGACATTGGGCTTAAAGATACGAAA
67809 AATGTCAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAAGATGATGGTGCCAATGTGCTGA
1 AATGTCAATGTGCTGATTCACGGCCAGCGACATTAGACTT-AAGATGA-GGTGCCAATGTGCTGA
* *
67874 TTCAAGGACAGTGACATTGGACTTAAA-A-ATG-AA
64 TTCAAGG-CAGTGACATTGGGCTTAAAGATACGAAA
* * *
67907 AGTG-CTAATGTGCCGATTCAAGGCCAGCGACATTAGACTTAA-A-GA--TGCCAATGTGCTGAT
1 AATGTC-AATGTGCTGATTCACGGCCAGCGACATTAGACTTAAGATGAGGTGCCAATGTGCTGAT
67967 TCAAGGCTAGTGACATTGGGCTTA
65 TCAAGGC-AGTGACATTGGGCTTA
67991 GAAGGAAATG
Statistics
Matches: 165, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
91 1 0.01
92 36 0.22
95 2 0.01
96 1 0.01
97 3 0.02
98 37 0.22
99 2 0.01
100 1 0.01
101 35 0.21
103 1 0.01
104 45 0.27
105 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (98 bp):
AATGTCAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAGATGAGGTGCCAATGTGCTGATT
CAAGGCAGTGACATTGGGCTTAAAGATACGAAA
Found at i:67981 original size:92 final size:96
Alignment explanation
Indices: 67711--67990 Score: 266
Period size: 98 Copynumber: 2.9 Consensus size: 96
67701 AAAGAATGTC
* * * * * * *
67711 AATGTGCTGATTCACGGCCCGCGACGTTAGACTTGAAGATGAGAAGAATGCCAATGTGCTAATTT
1 AATGTGCCGATTCAAGGCCAGCGACATTAGACTTAAAGAT--G-AG--TGCCAATGTGCTGATTC
* * ** * *
67776 AAGGCCAATGACATTGGGTTTAAAGATACGAAAAATG-T
61 AAGGACAGTGACATTGGACTTAAA-A-ATG-AAAGTGCT
* *
67814 CAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAAGATGATGGTGCCAATGTGCTGATTCAA
1 -AATGTGCCGATTCAAGGCCAGCGACATTAGACTTAAAGATGA--GTGCCAATGTGCTGATTCAA
67879 GGACAGTGACATTGGACTTAAAAATGAAAGTGCT
63 GGACAGTGACATTGGACTTAAAAATGAAAGTGCT
67913 AATGTGCCGATTCAAGGCCAGCGACATTAGACTT-AA-A-GA-TGCCAATGTGCTGATTCAAGG-
1 AATGTGCCGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGTGCCAATGTGCTGATTCAAGGA
*
67973 CTAGTGACATTGGGCTTA
66 C-AGTGACATTGGACTTA
67991 GAAGGAAATG
Statistics
Matches: 158, Mismatches: 14, Indels: 20
0.82 0.07 0.10
Matches are distributed among these distances:
91 1 0.01
92 36 0.23
95 2 0.01
96 1 0.01
97 2 0.01
98 37 0.23
99 3 0.02
100 1 0.01
101 36 0.23
102 1 0.01
103 1 0.01
104 37 0.23
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (96 bp):
AATGTGCCGATTCAAGGCCAGCGACATTAGACTTAAAGATGAGTGCCAATGTGCTGATTCAAGGA
CAGTGACATTGGACTTAAAAATGAAAGTGCT
Found at i:67992 original size:49 final size:46
Alignment explanation
Indices: 67814--68003 Score: 140
Period size: 49 Copynumber: 4.0 Consensus size: 46
67804 CGAAAAATGT
* * * * **
67814 CAATGTGCTGATTCACGGCCAGCGACATTAGACTTAAAGATGATGGTGC
1 CAATGTGCTGATTCAAGG-CAGTGACATT-GGCTTAGA-ATGAAAGTGC
*
67863 CAATGTGCTGATTCAAGGACAGTGACATTGGACTTAAAAATGAAAGTGC
1 CAATGTGCTGATTCAAGG-CAGTGACATTGG-CTT-AGAATGAAAGTGC
* * * *
67912 TAATGTGCCGATTCAAGGCCAGCGACATTAGACTTA-AA-G--A-TGC
1 CAATGTGCTGATTCAAGG-CAGTGACATT-GGCTTAGAATGAAAGTGC
*
67955 CAATGTGCTGATTCAAGGCTAGTGACATTGGGCTTAGAAGGAAA-TGC
1 CAATGTGCTGATTCAAGGC-AGTGACATT-GGCTTAGAATGAAAGTGC
68002 CA
1 CA
68004 CCAACCTGTG
Statistics
Matches: 117, Mismatches: 16, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
42 1 0.01
43 32 0.27
44 3 0.03
45 1 0.01
46 1 0.01
47 8 0.07
48 2 0.02
49 65 0.56
50 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (46 bp):
CAATGTGCTGATTCAAGGCAGTGACATTGGCTTAGAATGAAAGTGC
Found at i:68046 original size:32 final size:31
Alignment explanation
Indices: 67999--68308 Score: 345
Period size: 32 Copynumber: 9.7 Consensus size: 31
67989 TAGAAGGAAA
*
67999 TGCCACCAACCTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTGAAAGGGT
* *
68031 TGCCATCGACTTGTGTGGGCTTT-AAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAG--GGT
68063 TGCCACCAACTTGTGTGGGCTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGGT
* * *
68094 TGCCACTAACTTGTTTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGGT
* *
68126 TGCCACCAACTTATGTGGGCTTTAGAGAA-AGT
1 TGCCACCAACTTGTGTGGGCTTT-GA-AAGGGT
*
68158 TGCTACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTGAAAGGGT
* ** * *
68190 CGCCACTGACTTGTGTGGGCTTTGGAGGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGGT
* * * *
68221 TGCCACCGACTTATGTGAGCTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTG-AAAGGGT
*
68253 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGC-TTTGAA-AGGGT
68286 TGCCACCAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
68309 AGATAAGGTT
Statistics
Matches: 236, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
30 4 0.02
31 61 0.26
32 131 0.56
33 39 0.17
34 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGGT
Found at i:68146 original size:95 final size:96
Alignment explanation
Indices: 67999--68308 Score: 421
Period size: 95 Copynumber: 3.2 Consensus size: 96
67989 TAGAAGGAAA
* * *
67999 TGCCACCAACCTGTGTGGGCTTTTGAA-AGGGTTGCCATCGACTTGTGTGGGCTTTAAAGAAGGT
1 TGCCACCAACTTGTGTGGGC-TTTGAAGAGGGTTGCCACCGACTTATGTGGGCTTTAAAGAAGGT
68063 TGCCACCAACTTGTGTGGGC-TTTGAAAGGGT
65 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* * * * * *
68094 TGCCACTAACTTGTTTGGGCTTTGAAGAAGGTTGCCACCAACTTATGTGGGCTTTAGAGAAAGTT
1 TGCCACCAACTTGTGTGGGCTTTGAAGAGGGTTGCCACCGACTTATGTGGGCTTTAAAGAAGGTT
*
68159 GCTACCAACTTGTGTGGGCTTTTGAAAGGGT
66 GCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* ** * *
68190 CGCCACTGACTTGTGTGGGCTTTGGAG-GGGTTGCCACCGACTTATGTGAGCTTTGAAA-AAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAGAGGGTTGCCACCGACTTATGTGGGCTTT-AAAGAAGGT
*
68253 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
65 TGCCACCAACTTGTGTGGGCTTTTGAA-AGGGT
68286 TGCCACCAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
68309 AGATAAGGTT
Statistics
Matches: 187, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
94 6 0.03
95 121 0.65
96 60 0.32
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (96 bp):
TGCCACCAACTTGTGTGGGCTTTGAAGAGGGTTGCCACCGACTTATGTGGGCTTTAAAGAAGGTT
GCCACCAACTTGTGTGGGCTTTTGAAAGGGT
Found at i:68225 original size:127 final size:127
Alignment explanation
Indices: 67999--68308 Score: 401
Period size: 127 Copynumber: 2.4 Consensus size: 127
67989 TAGAAGGAAA
* * *
67999 TGCCACCAACCTGTGTGGGCTTTTGA-AAGGGTTGCCATCGACTTGTGTGGGC-TTTAAAGAAGG
1 TGCCACCAACTTGTGTGGGCTTTTGAGAA-GGTTGCCACCAACTTGTGTGGGCTTTTAAAG-AGG
* * * * * *
68062 TTGCCACCAACTTGTGTGGGCTTTGAAAGGGTTGCCACTAACTTGTTTGGGCTTTGAAGAAGGT
64 TCGCCACCAACTTGTGTGGGCTTTGAAAGGGTTGCCACCAACTTATGTGAGCTTTGAAAAAGGT
* * * *
68126 TGCCACCAACTTATGTGGGCTTTAGAGAAAGTTGCTACCAACTTGTGTGGGCTTTTGAAAG-GGT
1 TGCCACCAACTTGTGTGGGCTTTTGAGAAGGTTGCCACCAACTTGTGTGGGCTTTT-AAAGAGGT
** * * *
68190 CGCCACTGACTTGTGTGGGCTTTGGAGGGGTTGCCACCGACTTATGTGAGCTTTGAAAAAGGT
65 CGCCACCAACTTGTGTGGGCTTTGAAAGGGTTGCCACCAACTTATGTGAGCTTTGAAAAAGGT
68253 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTTTG-AGAAGGTTGCCACCAACTTGTGTGGGCTTT
68309 AGATAAGGTT
Statistics
Matches: 157, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
127 120 0.76
128 33 0.21
129 4 0.03
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (127 bp):
TGCCACCAACTTGTGTGGGCTTTTGAGAAGGTTGCCACCAACTTGTGTGGGCTTTTAAAGAGGTC
GCCACCAACTTGTGTGGGCTTTGAAAGGGTTGCCACCAACTTATGTGAGCTTTGAAAAAGGT
Found at i:68535 original size:28 final size:28
Alignment explanation
Indices: 68491--68555 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
68481 TACAGCAAGG
* *
68491 GCCACTG-TTTGTGGACTTCAAAAAGAT
1 GCCACTGACTTGTAGACTTCAAAAAGAT
* ** *
68518 GCCACTGACTTGTAGACTTCGATGAGGT
1 GCCACTGACTTGTAGACTTCAAAAAGAT
68546 GCCACTGACT
1 GCCACTGACT
68556 AGTGGGCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (28 bp):
GCCACTGACTTGTAGACTTCAAAAAGAT
Found at i:69875 original size:1 final size:1
Alignment explanation
Indices: 69869--69929 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
69859 TTCTTCCCCA
* * * * * * * *
69869 TTTTTTTGTTTTTTTGTTTGTTTGTTTGTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
69930 GCAGAGGAAG
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (1 bp):
T
Found at i:69882 original size:8 final size:8
Alignment explanation
Indices: 69869--69929 Score: 79
Period size: 8 Copynumber: 7.5 Consensus size: 8
69859 TTCTTCCCCA
69869 TTTTTTTG
1 TTTTTTTG
69877 TTTTTTTG
1 TTTTTTTG
*
69885 TTTGTTTG
1 TTTTTTTG
*
69893 TTTGTTTGTT
1 TTT-TTT-TG
69903 TTTTTTTG
1 TTTTTTTG
69911 TTTTTTTG
1 TTTTTTTG
69919 TTTTTTT-
1 TTTTTTTG
69926 TTTT
1 TTTT
69930 GCAGAGGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
7 4 0.09
8 34 0.72
9 5 0.11
10 4 0.09
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:69890 original size:4 final size:4
Alignment explanation
Indices: 69873--69921 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
69863 TCCCCATTTT
* *
69873 TTTG TTTT TTTG TTTG TTTG TTTG TTTG TTT- TTT- TTTG TTTT TTTG
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG
69919 TTT
1 TTT
69922 TTTTTTTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 6 0.15
4 34 0.85
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (4 bp):
TTTG
Found at i:69913 original size:26 final size:24
Alignment explanation
Indices: 69877--69929 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 24
69867 CATTTTTTTG
69877 TTTTTTTGTTTGTTTGTTTGTTTGTT
1 TTTTTTTGTTTGTTTGTTT-TTT-TT
*
69903 TTTTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTGTTTGTTTGTTTTTTTT
69927 TTT
1 TTT
69930 GCAGAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 5 0.19
25 3 0.12
26 18 0.69
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (24 bp):
TTTTTTTGTTTGTTTGTTTTTTTT
Found at i:83829 original size:20 final size:20
Alignment explanation
Indices: 83804--83899 Score: 115
Period size: 20 Copynumber: 4.8 Consensus size: 20
83794 AATTTGCCTG
83804 CATGTATCGATACATTGAAT
1 CATGTATCGATACATTGAAT
*
83824 CATGTATCGATACATCT-AGGT
1 CATGTATCGATACAT-TGA-AT
*
83845 AATGTATCGATACATTGAAT
1 CATGTATCGATACATTGAAT
* *
83865 CATGTATCGATACA-AGACT
1 CATGTATCGATACATTGAAT
*
83884 TATGTATCGATACATT
1 CATGTATCGATACATT
83900 CTATCGATAC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.25
20 31 0.48
21 17 0.27
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:85193 original size:21 final size:21
Alignment explanation
Indices: 85167--85208 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
85157 ACTTTGATAT
85167 ATTTTAA-CTTAGAAAACAATC
1 ATTTTAACCTT-GAAAACAATC
85188 ATTTTAAGCCTTGAAAACAAT
1 ATTTTAA-CCTTGAAAACAAT
85209 TACACTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (21 bp):
ATTTTAACCTTGAAAACAATC
Found at i:87070 original size:21 final size:20
Alignment explanation
Indices: 87041--87083 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
87031 GACTAGTGTG
*
87041 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
87062 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
87082 GG
1 GG
87084 TGGTGTTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:87547 original size:13 final size:13
Alignment explanation
Indices: 87525--87563 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
87515 ATAATCCCCC
* *
87525 TGTATTGATACAG
1 TGTATCGATACAA
87538 TGTATCGATACAA
1 TGTATCGATACAA
87551 TGTATCGATACAA
1 TGTATCGATACAA
87564 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:89653 original size:15 final size:15
Alignment explanation
Indices: 89633--89663 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
89623 ATTTCGTTTG
*
89633 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
89648 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
89663 G
1 G
89664 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:93968 original size:20 final size:21
Alignment explanation
Indices: 93943--93982 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
93933 CTTTGATATG
93943 TTTTAA-CTTAAAAACAATCA
1 TTTTAACCTTAAAAACAATCA
*
93963 TTTTAAGCCTTGAAAACAAT
1 TTTTAA-CCTTAAAAACAAT
93983 TTACACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
TTTTAACCTTAAAAACAATCA
Found at i:94376 original size:20 final size:20
Alignment explanation
Indices: 94331--94385 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
94321 CACATAGTAC
94331 TGTATCGATACATTTCAAGCA
1 TGTATCGATACA-TTCAAGCA
* *
94352 GGTATCGATACATTCACA-TA
1 TGTATCGATACATTCA-AGCA
94372 TGTATCGATACATT
1 TGTATCGATACATT
94386 GCCTTATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTCAAGCA
Found at i:96731 original size:33 final size:32
Alignment explanation
Indices: 96667--96731 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
96657 ACAATTGTGT
* *
96667 ATGTATCGATACAATGATCATATATTGATACA
1 ATGTATCGATACAAAGATAATATATTGATACA
* *
96699 ATGTATTGATACAAAGCATAATGTATTGATACA
1 ATGTATCGATACAAAG-ATAATATATTGATACA
96732 TACAAGAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (32 bp):
ATGTATCGATACAAAGATAATATATTGATACA
Found at i:102082 original size:36 final size:37
Alignment explanation
Indices: 102040--102135 Score: 140
Period size: 36 Copynumber: 2.6 Consensus size: 37
102030 CCCACCGATC
102040 ATGCAAGATTAATTTTTAAGTAAATTTCTAG-TGCAT
1 ATGCAAGATTAATTTTTAAGTAAATTTCTAGTTGCAT
* * * *
102076 ATGCAAGATTAATTTTTAAGTGAGTTTTTAGTTTCAT
1 ATGCAAGATTAATTTTTAAGTAAATTTCTAGTTGCAT
*
102113 CTGCAAGATTAATTTTTAAGTAA
1 ATGCAAGATTAATTTTTAAGTAA
102136 TTACTTGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 28 0.53
37 25 0.47
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (37 bp):
ATGCAAGATTAATTTTTAAGTAAATTTCTAGTTGCAT
Found at i:102416 original size:13 final size:14
Alignment explanation
Indices: 102393--102426 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
102383 TTTGATGAAA
102393 AAAATTAAAATTAT
1 AAAATTAAAATTAT
102407 AAAA-TAAAATTAT
1 AAAATTAAAATTAT
*
102420 AATATTA
1 AAAATTA
102427 GATTATGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTAAAATTAT
Found at i:103389 original size:29 final size:30
Alignment explanation
Indices: 103357--103425 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
103347 AATTATTATA
* *
103357 ATTAATTATAAT-AAATATCAATA-ATAAAT
1 ATTAATAATAATAAAATATAAATATA-AAAT
*
103386 ATTAAAAAT-ATAAAATATAAATATAAAAT
1 ATTAATAATAATAAAATATAAATATAAAAT
*
103415 ATTAATCATAA
1 ATTAATAATAA
103426 CATAAATCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.06
29 28 0.88
30 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (30 bp):
ATTAATAATAATAAAATATAAATATAAAAT
Found at i:103396 original size:22 final size:21
Alignment explanation
Indices: 103334--103413 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
103324 ATTACGATTA
*
103334 AAAATAT-AATA-AAAATTATT
1 AAAATATAAATATAAAAATA-T
* *
103354 ATAAT-TAATTATAATAAATAT
1 AAAATATAAATATAA-AAATAT
*
103375 -CAATAATAAATATTAAAAATAT
1 AAAAT-ATAAATA-TAAAAATAT
103397 AAAATATAAATATAAAA
1 AAAATATAAATATAAAA
103414 TATTAATCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 10 0.21
21 8 0.17
22 22 0.47
23 6 0.13
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATATAAATATAAAAATAT
Found at i:104206 original size:2 final size:2
Alignment explanation
Indices: 104199--104237 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
104189 GTAAGCTGTA
104199 AT AT AT AT AT AT AT -T AT AT -T 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
104238 CACGTGTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:104625 original size:27 final size:26
Alignment explanation
Indices: 104551--104625 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
104541 TCTTCCAAAA
* * *
104551 TTTATTATCATATTATTAATTATTTT
1 TTTATTATAATATTATTTATTATTAT
* * *
104577 TTTATGATATATATCATCTATTATTAT
1 TTTATTATA-ATATTATTTATTATTAT
104604 TTTATTCATAATATTATTTATT
1 TTTATT-ATAATATTATTTATT
104626 CATGTAATAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
26 7 0.18
27 28 0.74
28 3 0.08
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (26 bp):
TTTATTATAATATTATTTATTATTAT
Found at i:104711 original size:22 final size:22
Alignment explanation
Indices: 104664--104712 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
104654 ATGAAGTATT
* * *
104664 TACTACTATGTTATTAATCGGT
1 TACTACTATATTATTAATCAGA
104686 TACTACTATATTA-TACATCAGA
1 TACTACTATATTATTA-ATCAGA
104708 TACTA
1 TACTA
104713 TTCTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (22 bp):
TACTACTATATTATTAATCAGA
Found at i:104808 original size:112 final size:112
Alignment explanation
Indices: 104672--104896 Score: 398
Period size: 112 Copynumber: 2.0 Consensus size: 112
104662 TTTACTACTA
104672 TGTTATTAATCGGTTACTACTATATTATACATCAGATACTATTCTTTTATAATTA-TTTTTAAAA
1 TGTTATTAATCGGTTACTACTATATTATACATCAGATACTATTCTTTTATAATTATTTTTTAAAA
104736 ATTATTAAATTTATTAATATATTATCAATTATTTACTAAGTGTCAAAC
66 A-TATTAAATTTATTAATATATTATCAATTATTTACTAAGTGTCAAAC
* * * *
104784 TGTTATTAATCGGTTACTATTATATTATACATCAGATACTATTTTTTTATAATTATTTTTTTATA
1 TGTTATTAATCGGTTACTACTATATTATACATCAGATACTATTCTTTTATAATTATTTTTTAAAA
104849 ATATTAAATTTATTAATATATTATCAATTATTTACTAAGTGTCAAAC
66 ATATTAAATTTATTAATATATTATCAATTATTTACTAAGTGTCAAAC
104896 T
1 T
104897 TTTTGTACTA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
112 100 0.93
113 8 0.07
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.49
Consensus pattern (112 bp):
TGTTATTAATCGGTTACTACTATATTATACATCAGATACTATTCTTTTATAATTATTTTTTAAAA
ATATTAAATTTATTAATATATTATCAATTATTTACTAAGTGTCAAAC
Found at i:104854 original size:16 final size:14
Alignment explanation
Indices: 104823--104850 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
104813 CATCAGATAC
104823 TATTTTTTTATAAT
1 TATTTTTTTATAAT
104837 TATTTTTTTATAAT
1 TATTTTTTTATAAT
104851 ATTAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTTTTATAAT
Found at i:105194 original size:20 final size:21
Alignment explanation
Indices: 105169--105222 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
105159 TTGTAATTAC
*
105169 ATTAAATATCA-ATAATAAAA
1 ATTAAATATCACAAAATAAAA
105189 ATTAAA-ATCACAAAATAAAA
1 ATTAAATATCACAAAATAAAA
105209 ATTATAATATCACA
1 ATTA-AATATCACA
105223 TTACTACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 4 0.13
20 18 0.60
21 2 0.07
22 6 0.20
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTAAATATCACAAAATAAAA
Found at i:105552 original size:25 final size:24
Alignment explanation
Indices: 105524--105586 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
105514 AAATTGATAA
105524 AAATTATTTTATTCAAAATATTTTT
1 AAATTATTTTATTC-AAATATTTTT
*
105549 AAATAAATTTTTATT-AAATATTTTT
1 AAAT-TA-TTTTATTCAAATATTTTT
*
105574 AAATT-TATTATTC
1 AAATTATTTTATTC
105587 TTATTATTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 6 0.19
25 18 0.56
26 1 0.03
27 7 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATTATTTTATTCAAATATTTTT
Found at i:105593 original size:3 final size:3
Alignment explanation
Indices: 105578--105637 Score: 77
Period size: 3 Copynumber: 20.3 Consensus size: 3
105568 ATTTTTAAAT
* * * *
105578 TTA TTA TTC TTA TTA TTG CTA TTA TTA TTA CTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
105625 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
105638 GTGGGCTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:105622 original size:17 final size:17
Alignment explanation
Indices: 105600--105634 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
105590 TTATTGCTAT
105600 TATTATTACTATTATTA
1 TATTATTACTATTATTA
*
105617 TATTATTATTATTATTA
1 TATTATTACTATTATTA
105634 T
1 T
105635 TATGTGGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTATTACTATTATTA
Found at i:110001 original size:3 final size:3
Alignment explanation
Indices: 109993--110040 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
109983 TGGAATAGCA
* *
109993 AAT AAT AAT AAT AAG AAT AAG AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
110041 TAAAAACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:113864 original size:29 final size:29
Alignment explanation
Indices: 113818--113875 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
113808 AAAGATGCTG
113818 GGATAAATTTAATGTTTATGCTTCAAGCA
1 GGATAAATTTAATGTTTATGCTTCAAGCA
* *
113847 GGATAAATTTACTTTTTATGCTTCAAGCA
1 GGATAAATTTAATGTTTATGCTTCAAGCA
113876 TTGAATGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (29 bp):
GGATAAATTTAATGTTTATGCTTCAAGCA
Found at i:116965 original size:16 final size:15
Alignment explanation
Indices: 116932--116983 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
116922 AAAGTTAGGT
116932 AAAAGAAAAAGAAGAAG
1 AAAAGAAAAA-AA-AAG
**
116949 AGGAGAAAAAAGAAAG
1 AAAAGAAAAAA-AAAG
116965 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
116980 AAAA
1 AAAA
116984 AAATATGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 8 0.27
16 13 0.43
17 9 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:116978 original size:19 final size:19
Alignment explanation
Indices: 116932--116986 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
116922 AAAGTTAGGT
*
116932 AAAAGAAAAAG-AAGAAGAG
1 AAAA-AAAAAGAAAGAAAAG
* *
116951 GAGAAAAAAGAAAGAAAAG
1 AAAAAAAAAGAAAGAAAAG
116970 AAAAAAAAAGAAA-AAAA
1 AAAAAAAAAGAAAGAAAA
116987 TATGAAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAGAAAGAAAAG
Found at i:116984 original size:16 final size:16
Alignment explanation
Indices: 116952--116983 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
116942 GAAGAAGAGG
116952 AGAAAAAAGAAAGAAA
1 AGAAAAAAGAAAGAAA
116968 AGAAAAAA-AAAGAAA
1 AGAAAAAAGAAAGAAA
116983 A
1 A
116984 AAATATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAAAAGAAAGAAA
Found at i:116993 original size:11 final size:10
Alignment explanation
Indices: 116954--116986 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
116944 AGAAGAGGAG
116954 AAAAAAG-AA
1 AAAAAAGAAA
*
116963 AGAAAAGAAA
1 AAAAAAGAAA
116973 AAAAAAGAAA
1 AAAAAAGAAA
116983 AAAA
1 AAAA
116987 TATGAAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Done.