Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2579
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: 47643
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1642 original size:22 final size:22
Alignment explanation
Indices: 1614--1659 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1604 GTTACACACC
*
1614 AAAAAAAAAAAACAAAA-CAAA
1 AAAAAAAAAAAAAAAAAGCAAA
1635 AAAAAAAAAAAAAAAAAGCAAA
1 AAAAAAAAAAAAAAAAAGCAAA
1657 AAA
1 AAA
1660 TAGAAGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAGCAAA
Found at i:1659 original size:1 final size:1
Alignment explanation
Indices: 1614--1651 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
1604 GTTACACACC
* *
1614 AAAAAAAAAAAACAAAACAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1652 GCAAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1659 original size:18 final size:18
Alignment explanation
Indices: 1613--1651 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1603 CGTTACACAC
1613 CAAAAAAAAAAAACAAAA
1 CAAAAAAAAAAAACAAAA
1631 CAAAAAAAAAAAA-AAAA
1 CAAAAAAAAAAAACAAAA
1648 -AAAA
1 CAAAA
1652 GCAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 13 0.62
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAAAACAAAA
Found at i:2989 original size:57 final size:59
Alignment explanation
Indices: 2893--3105 Score: 247
Period size: 57 Copynumber: 3.6 Consensus size: 59
2883 TTTCCAAGCC
* *
2893 CACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTGAAAAG-CC-
1 CACAAGTCAGTGGCAAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTT-CAAAGCCCA
2951 CACAAGTCAGTGGC-ACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCA
* * * * *
3010 CACAAGTCGGT-GCAACCCATTCCAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTTCAAAG-CC-CACAAGTCAGTGGC-ACTC-TTTCAAAGCCCA
*
3072 CACAAGTCGGTGGCAACCCATTTCAAAGCCCACA
1 CACAAGTCAGTGGCAACCC-TTTCAAAGCCCACA
3106 CAAGTCGGTG
Statistics
Matches: 136, Mismatches: 9, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
57 32 0.24
58 24 0.18
59 20 0.15
60 2 0.01
61 14 0.10
62 29 0.21
63 9 0.07
64 6 0.04
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (59 bp):
CACAAGTCAGTGGCAACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCA
Found at i:3074 original size:32 final size:32
Alignment explanation
Indices: 2893--4101 Score: 1696
Period size: 32 Copynumber: 37.8 Consensus size: 32
2883 TTTCCAAGCC
*
2893 CACAAGTCAGTGGC-ACTCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCAAC-CCATTTCAAAGCCCA
* * *
2924 CA-AA-TCAGTGGC-ACTC-TTTGAAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTT-CAAAGCCCA
*
2951 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2979 CACAAGTCAGTGGC-ACTCC-TTTCAAAGCCCA
1 CACAAGTCGGTGGCAAC-CCATTTCAAAGCCCA
*
3010 CACAAGTCGGT-GCAACCCA-TTCCAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3040 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3072 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3104 CACAAGTCGGTGGCAACCCATTCAGCAAAGTCGGCA
1 CACAAGTCGGTGGCAACCCATT--TCAAAG-C-CCA
* * ** * ** ** **
3140 CCATCAAGCCAAGTCGGTGGCAACCCATTTCAAAGCC-
1 -CA-CAAGTC-GGT--G-GCAACCCATTTCAAAGCCCA
*
3177 CACACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CAC--AAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3211 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3243 CACAAGTCGGTGGCAACCCATTTCAAACCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
3275 CACAAGTCGGTGGCAACCCATTCCAAAACTCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3307 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3339 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3371 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3403 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3435 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3467 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3499 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3531 CACATGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3563 CACAAGTCGGTGGCAACCCATTTCAAACCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3595 CACAAGTCGGTGGCAACCCATTTCAAAACCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3627 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3659 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3691 GACAAGTCGGTGGCAACCCATTTCAAACCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3723 CACAAGTCGGTGGCAACCCATTTCAAAACCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3755 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3787 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3819 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3851 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3883 CACAAGTCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3915 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3947 CACAAGTCGGTGGCAACCCATTTCAAAACCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3979 CACAAGTCAGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
4011 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
4043 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
4075 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
4102 TCACCATATT
Statistics
Matches: 1075, Mismatches: 80, Indels: 45
0.90 0.07 0.04
Matches are distributed among these distances:
27 2 0.00
28 30 0.03
29 38 0.04
30 29 0.03
31 22 0.02
32 906 0.84
33 9 0.01
34 9 0.01
35 2 0.00
36 6 0.01
37 6 0.01
38 6 0.01
39 2 0.00
40 2 0.00
41 1 0.00
42 5 0.00
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:3167 original size:24 final size:23
Alignment explanation
Indices: 3106--3167 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 23
3096 AAAGCCCACA
3106 CAAGTCGGTGGCAACCCATTCAGC
1 CAAGTCGGTGGCAACCCA-TCAGC
*
3130 AAAGTC---GGC-A-CCATCAAGC
1 CAAGTCGGTGGCAACCCATC-AGC
3149 CAAGTCGGTGGCAACCCAT
1 CAAGTCGGTGGCAACCCAT
3168 TTCAAAGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 1 0.03
21 3 0.10
22 3 0.10
23 1 0.03
24 9 0.30
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (23 bp):
CAAGTCGGTGGCAACCCATCAGC
Found at i:4658 original size:20 final size:20
Alignment explanation
Indices: 4630--4704 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
4620 TCATACCCTG
4630 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
4650 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
4670 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
4690 ATGTATCGATACATT
1 ATGTATCGATACATT
4705 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:4697 original size:40 final size:39
Alignment explanation
Indices: 4630--4707 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
4620 TCATACCCTG
* *
4630 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
4670 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
4708 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:9063 original size:47 final size:46
Alignment explanation
Indices: 8959--9079 Score: 124
Period size: 45 Copynumber: 2.7 Consensus size: 46
8949 GCGACAACTG
* * * *
8959 TATTGGCGTTAGGACCTGGTCAAA-TTCTTTTTCCTCATTTGGCTG
1 TATTAGCGTTAGGACCTGGTCAAACTTCTTTTCCCTCATTTGACTA
* * *
9004 TATTAACTTTAGGACCTAGTCAAACTT-TTTTCACCCTCATTTGACTA
1 TATTAGCGTTAGGACCTGGTCAAACTTCTTTT--CCCTCATTTGACTA
*
9051 TTTTAGCGTTAGG-CCTGGTCAAAC-TCTTT
1 TATTAGCGTTAGGACCTGGTCAAACTTCTTT
9080 ATTTCATTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
45 25 0.41
46 15 0.25
47 21 0.34
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (46 bp):
TATTAGCGTTAGGACCTGGTCAAACTTCTTTTCCCTCATTTGACTA
Found at i:9474 original size:36 final size:35
Alignment explanation
Indices: 9411--9478 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
9401 AAGATAGAAA
* **
9411 TCTCCCTATTTTTTCACGGGCTAAGATAGAACTTC
1 TCTCCCTACTTTTTCAAAGGCTAAGATAGAACTTC
*
9446 TCTCCCTACCTTTTTCAAAGGCTGAGATAGAAC
1 TCTCCCTA-CTTTTTCAAAGGCTAAGATAGAAC
9479 CTCTTAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 8 0.29
36 20 0.71
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (35 bp):
TCTCCCTACTTTTTCAAAGGCTAAGATAGAACTTC
Found at i:9963 original size:22 final size:22
Alignment explanation
Indices: 9931--9976 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
9921 TACTATTCAC
9931 ATGTATCGATACATGAACAGTG
1 ATGTATCGATACATGAACAGTG
* *
9953 ATGTATTGATACATGAACATTG
1 ATGTATCGATACATGAACAGTG
9975 AT
1 AT
9977 CAACAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (22 bp):
ATGTATCGATACATGAACAGTG
Found at i:10074 original size:19 final size:20
Alignment explanation
Indices: 10024--10079 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
10014 CTGCTAGTTT
*
10024 TATGTATCAATACAAT-ATA
1 TATGTATCGATACAATGATA
10043 TGATGTAGT-GATACAATGA-A
1 T-ATGTA-TCGATACAATGATA
*
10063 TATGTATCGATATAATG
1 TATGTATCGATACAATG
10080 TATCGATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 14 0.45
21 2 0.06
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (20 bp):
TATGTATCGATACAATGATA
Found at i:10468 original size:47 final size:47
Alignment explanation
Indices: 10391--10497 Score: 144
Period size: 47 Copynumber: 2.3 Consensus size: 47
10381 AAAAGCTTAA
* *
10391 CACCATTGTTTGACTGTACTAACGTTAGGACCTGGTCAAACTCTTT-T
1 CACCATTATTTGACTATACTAACGTTAGGACCTGGTCAAACT-TTTCT
* **
10438 CACTATTATTTGACTATACTGGCGTTAGGACCTGGTCAAACTTTTCT
1 CACCATTATTTGACTATACTAACGTTAGGACCTGGTCAAACTTTTCT
*
10485 CACCATTGTTTGA
1 CACCATTATTTGA
10498 TTGTATTAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 3 0.06
47 49 0.94
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (47 bp):
CACCATTATTTGACTATACTAACGTTAGGACCTGGTCAAACTTTTCT
Found at i:10667 original size:41 final size:42
Alignment explanation
Indices: 10618--10852 Score: 201
Period size: 42 Copynumber: 5.6 Consensus size: 42
10608 CTGTCCGTCT
* * *
10618 GTCGGCTTTGATCTTGGAGACTTCTTTAAC-TTTGTCTGCCC
1 GTCGGCTTTGACCTTGGAGACTTCTTTACCTTTTGTCTGCCA
* * * *
10659 GTCGGCTTTGACCTAGGAGACTTTTTTACCTTTTGTTTACCA
1 GTCGGCTTTGACCTTGGAGACTTCTTTACCTTTTGTCTGCCA
* * * * * *
10701 ATTGGCTTTGACCTTAGAGATTTTTTTACCTTTTGTCTGCCT
1 GTCGGCTTTGACCTTGGAGACTTCTTTACCTTTTGTCTGCCA
* * *
10743 GTTGACTTTGACCTTGGAGACTTCTTTACCTTTAGTCTGCCTA
1 GTCGGCTTTGACCTTGGAGACTTCTTTACCTTTTGTCTGCC-A
* * * *
10786 G-CAGCTTTGA-CTCTAGAGACTT-TTTACCTTTATGT-TGTCT
1 GTCGGCTTTGACCT-TGGAGACTTCTTTACCTTT-TGTCTGCCA
* * *
10826 GTCGGCTTTAACCTTCGAAACTTCTTT
1 GTCGGCTTTGACCTTGGAGACTTCTTT
10853 TTTATCTTTG
Statistics
Matches: 154, Mismatches: 33, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
40 1 0.01
41 54 0.35
42 98 0.64
43 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (42 bp):
GTCGGCTTTGACCTTGGAGACTTCTTTACCTTTTGTCTGCCA
Found at i:10971 original size:42 final size:41
Alignment explanation
Indices: 10912--11048 Score: 170
Period size: 42 Copynumber: 3.3 Consensus size: 41
10902 TTTTCTACCC
10912 GAGACTTCTTTACCTTTAGTCTGCTTATCGGCTTTGACCCTA
1 GAGACTTCTTTACCTTTAGT-TGCTTATCGGCTTTGACCCTA
* *
10954 GAGACTTCTTTACCTTTAGGTTGCTTGTCGGCTTTGACCCTT
1 GAGACTTCTTTACCTTTA-GTTGCTTATCGGCTTTGACCCTA
** * *
10996 GAGACTTCTTTATATTT-TTTGC-TAGTCGGCTTAGACCCTA
1 GAGACTTCTTTACCTTTAGTTGCTTA-TCGGCTTTGACCCTA
*
11036 GAGACTTTTTTAC
1 GAGACTTCTTTAC
11049 ATTTTTCCTG
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.01
40 28 0.34
42 52 0.63
43 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
GAGACTTCTTTACCTTTAGTTGCTTATCGGCTTTGACCCTA
Found at i:11033 original size:40 final size:40
Alignment explanation
Indices: 10912--11660 Score: 168
Period size: 42 Copynumber: 18.3 Consensus size: 40
10902 TTTTCTACCC
* *
10912 GAGACTTCTTTACCTTTAGTCTGCTTA-TCGGCTTTGACCCTA
1 GAGACTTCTTTACATTT--TTTGC-TAGTCGGCTTTGACCCTA
* * * *
10954 GAGACTTCTTTACCTTTAGGTTGCTTGTCGGCTTTGACCCTT
1 GAGACTTCTTTACATTT--TTTGCTAGTCGGCTTTGACCCTA
* *
10996 GAGACTTCTTTATATTTTTTGCTAGTCGGCTTAGACCCTA
1 GAGACTTCTTTACATTTTTTGCTAGTCGGCTTTGACCCTA
* * *** *
11036 GAGACTTTTTTACA-TTTTTCCT-G-C--CCGAGACTTCT-
1 GAGACTTCTTTACATTTTTTGCTAGTCGGCTTTGAC-CCTA
** * * ** * *
11071 -TTAC--CTTT--A-GTCTACCT-GTCGGCTTTGATCTTA
1 GAGACTTCTTTACATTTTTTGCTAGTCGGCTTTGACCCTA
* * * *
11104 GAGATTTCTTTACCTTTAGTTTGCCT-GTCAGCTTTGACCTTA
1 GAGACTTCTTTACATTT--TTTG-CTAGTCGGCTTTGACCCTA
* ** *
11146 GAGACTTCTTTACCTTTAGTTTGCCT-GTCAACTTTGA-CCTGG
1 GAGACTTCTTTACATTT--TTTG-CTAGTCGGCTTTGACCCT-A
* * *
11188 GAGACTTCTTTATC-TTTGTCTGCTCA-TCGACTTTGACCCTG
1 GAGACTTCTTTA-CATTT-TTTGCT-AGTCGGCTTTGACCCTA
* * ** ** * *
11229 GAGACTTCTTTTCCTTTTATTTGCCCGTCAACTTTGAACCTG
1 GAGACTTC-TTTACATTT-TTTGCTAGTCGGCTTTGACCCTA
* * *
11271 GAGACTTCTTTACCTTTTGT-CTACATGTCAGCTTTGACCCTA
1 GAGACTTCTTTACATTTTTTGCT--A-GTCGGCTTTGACCCTA
* * * *
11313 AAGACTTCTTTACCATTTGTCTGCCT-GCCGACTTTGACCCTA
1 GAGACTTCTTTA-CATTT-TTTG-CTAGTCGGCTTTGACCCTA
* * * *
11355 GAAACTTCTTTACCTTTAGTCTGCTTGTCGGCTTTGACCCTA
1 GAGACTTCTTTACATTT--TTTGCTAGTCGGCTTTGACCCTA
* * * * * *
11397 GAAACTTCTTTACCATTAGTCTGCCT-TTCAGCTTTGACCCTG
1 GAGACTTCTTTA-CATT-TTTTG-CTAGTCGGCTTTGACCCTA
* * *
11439 GAGACTTCTTTACCTTTTGTCTGCCTA-TTGGCTTTGACCTTA
1 GAGACTTCTTTACATTTT-T-TG-CTAGTCGGCTTTGACCCTA
* * ** * **
11481 GAGACTTCTTTACCTTTAGTCTGCCGGTTGGCTTTGACCCGG
1 GAGACTTCTTTACATTT--TTTGCTAGTCGGCTTTGACCCTA
* * *
11523 GGGACTTCTTTACCTTTTGTCTGCCTA-TCCGCTTTGACCCTA
1 GAGACTTCTTTACATTTT-T-TG-CTAGTCGGCTTTGACCCTA
* ** *
11565 -AGGACTTCATTACCATTTGTCTACCT-GTCGACTTTGA-CCTAA
1 GA-GACTTCTTTA-CATTT-T-TTGCTAGTCGGCTTTGACCCT-A
* * * * *
11607 AAGATTTCTTTACCTTTTGTTTGCTCGTCGACTTTGA-CCTGA
1 GAGACTTCTTTA-CATTT-TTTGCTAGTCGGCTTTGACCCT-A
*
11649 AAGACTTCTTTA
1 GAGACTTCTTTA
11661 ACTTTTGTAT
Statistics
Matches: 544, Mismatches: 112, Indels: 102
0.72 0.15 0.13
Matches are distributed among these distances:
30 7 0.01
31 1 0.00
32 4 0.01
33 3 0.01
34 3 0.01
35 5 0.01
36 6 0.01
37 1 0.00
38 1 0.00
39 9 0.02
40 37 0.07
41 50 0.09
42 394 0.72
43 16 0.03
44 5 0.01
46 2 0.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (40 bp):
GAGACTTCTTTACATTTTTTGCTAGTCGGCTTTGACCCTA
Found at i:11067 original size:150 final size:151
Alignment explanation
Indices: 10759--11171 Score: 494
Period size: 150 Copynumber: 2.7 Consensus size: 151
10749 TTTGACCTTG
* * * *
10759 GAGACTTCTTTACCTTTAGTCTGCCTAGCAGCTTTGACTCTAGAGACTT-TTTACCTTTATGTTG
1 GAGACTTCTTTACCTTTAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCTTTACCTTTAGGTTG
* * * * * *
10823 -TCTGTCGGCTTTAACCTTCGAAACTTCTTTTTTATCTTTGTTTGCCTATGGGCTTTGACCCTAG
66 CT-TGTCGGCTTTGACCTTAGAGACTTC---TTTATATTTGTTTGCCTATCGGCTTAGACCCTAG
* *
10887 AGACTCCTTTACCTTTTTTCTACCC
127 AGACTCCTTTACATTTTTCCTACCC
*
10912 GAGACTTCTTTACCTTTAGTCTGCTTATCGGCTTTGACCCTAGAGACTTCTTTACCTTTAGGTTG
1 GAGACTTCTTTACCTTTAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCTTTACCTTTAGGTTG
10977 CTTGTCGGCTTTGACCCTT-GAGACTTCTTTATATTT-TTTG-CTAGTCGGCTTAGACCCTAGAG
66 CTTGTCGGCTTTGA-CCTTAGAGACTTCTTTATATTTGTTTGCCTA-TCGGCTTAGACCCTAGAG
** *
11039 ACTTTTTTACATTTTTCCTGCCC
129 ACTCCTTTACATTTTTCCTACCC
* * * * * *
11062 GAGACTTCTTTACCTTTAGTCTACCTGTCGGCTTTGATCTTAGAGATTTCTTTACCTTTAGTTTG
1 GAGACTTCTTTACCTTTAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCTTTACCTTTAGGTTG
* * **
11127 CCTGTCAGCTTTGACCTTAGAGACTTCTTTACCTTTAGTTTGCCT
66 CTTGTCGGCTTTGACCTTAGAGACTTCTTTATATTT-GTTTGCCT
11172 GTCAACTTTG
Statistics
Matches: 226, Mismatches: 26, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
149 7 0.03
150 123 0.54
151 8 0.04
152 4 0.02
153 47 0.21
154 32 0.14
155 5 0.02
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (151 bp):
GAGACTTCTTTACCTTTAGTCTGCCTATCGGCTTTGACCCTAGAGACTTCTTTACCTTTAGGTTG
CTTGTCGGCTTTGACCTTAGAGACTTCTTTATATTTGTTTGCCTATCGGCTTAGACCCTAGAGAC
TCCTTTACATTTTTCCTACCC
Found at i:11131 original size:42 final size:42
Alignment explanation
Indices: 11062--11729 Score: 539
Period size: 42 Copynumber: 15.9 Consensus size: 42
11052 TTTCCTGCCC
* * *
11062 GAGACTTCTTTACCTTTAGTCTACCTGTCGGCTTTGATCTTA
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * *
11104 GAGATTTCTTTACCTTTAGTTTGCCTGTCAGCTTTGACCTTA
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* ** *
11146 GAGACTTCTTTACCTTTAGTTTGCCTGTCAACTTTGA-CCTGG
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCT-A
* * * *
11188 GAGACTTCTTTATCTTT-GTCTG-CTCATCGACTTTGACCCTG
1 GAGACTTCTTTACCTTTAGTCTGCCT-GTCGGCTTTGACCCTA
* * * ** * *
11229 GAGACTTCTTTTCCTTTTA-TTTGCCCGTCAACTTTGAACCTG
1 GAGACTTCTTTACC-TTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * *
11271 GAGACTTCTTTACCTTTTGTCTACATGTCAGCTTTGACCCTA
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * *
11313 AAGACTTCTTTACCATTT-GTCTGCCTGCCGACTTTGACCCTA
1 GAGACTTCTTTACC-TTTAGTCTGCCTGTCGGCTTTGACCCTA
* *
11355 GAAACTTCTTTACCTTTAGTCTGCTTGTCGGCTTTGACCCTA
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * * *
11397 GAAACTTCTTTACCATTAGTCTGCCTTTCAGCTTTGACCCTG
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * *
11439 GAGACTTCTTTACCTTTTGTCTGCCTATTGGCTTTGACCTTA
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * **
11481 GAGACTTCTTTACCTTTAGTCTGCCGGTTGGCTTTGACCCGG
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * *
11523 GGGACTTCTTTACCTTTTGTCTGCCTATCCGCTTTGACCCTA
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * *
11565 -AGGACTTCATTACCATTT-GTCTACCTGTCGACTTTGA-CCTAA
1 GA-GACTTCTTTACC-TTTAGTCTGCCTGTCGGCTTTGACCCT-A
* * * * *
11607 AAGATTTCTTTACCTTTTGTTTG-CTCGTCGACTTTGA-CCTGA
1 GAGACTTCTTTACCTTTAGTCTGCCT-GTCGGCTTTGACCCT-A
* * * * ** * * **
11649 AAGACTTCTTTAACTTTTGTATGCCCATCGACTTTGACTCGG
1 GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
* * * *
11691 GACACTTCGTTACCCTTT-GTCTGCCTGTCAGCTTAGACC
1 GAGACTTCTTTA-CCTTTAGTCTGCCTGTCGGCTTTGACC
11730 TAGGAGATTC
Statistics
Matches: 511, Mismatches: 97, Indels: 36
0.79 0.15 0.06
Matches are distributed among these distances:
40 2 0.00
41 42 0.08
42 453 0.89
43 14 0.03
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (42 bp):
GAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCCTA
Found at i:12234 original size:3 final size:3
Alignment explanation
Indices: 12226--12257 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
12216 TAGGATGGTA
12226 AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12258 TATTATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:16302 original size:43 final size:43
Alignment explanation
Indices: 16244--16353 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 43
16234 GGTAACGAAA
*
16244 TCTCCTAGGTCAAAGCCGATGA-GCAGAAAAAAGATAAAGAAG
1 TCTCCAAGGTCAAAGCCGATGAGGCAGAAAAAAGATAAAGAAG
* * * *
16286 TCTCCCAAGGTCAAAGCCAAT-AGGTAGACAAAGGATAAAGAAG
1 TCT-CCAAGGTCAAAGCCGATGAGGCAGAAAAAAGATAAAGAAG
*
16329 TCTCCGAGGTCAAAGCCGATG-GGCA
1 TCTCCAAGGTCAAAGCCGATGAGGCA
16354 TACAAAGTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
42 22 0.39
43 35 0.61
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (43 bp):
TCTCCAAGGTCAAAGCCGATGAGGCAGAAAAAAGATAAAGAAG
Found at i:16359 original size:42 final size:42
Alignment explanation
Indices: 16219--16846 Score: 245
Period size: 42 Copynumber: 15.0 Consensus size: 42
16209 GGTCTAAGTT
* * *
16219 GATGGGCAGACAAATGG-TAACGAAATCTCCTAGGTCAAAGCC
1 GATGGGCAGACAAA-GGATAAAGAAGTCTCCGAGGTCAAAGCC
* * * *
16261 GATGAGCAGAAAAAAGATAAAGAAGTCTCCCAAGGTCAAAGCC
1 GATGGGCAGACAAAGGATAAAGAAGTCT-CCGAGGTCAAAGCC
* * *
16304 AATAGGTAGACAAAGGATAAAGAAGTCTCCGAGGTCAAAGCC
1 GATGGGCAGACAAAGGATAAAGAAGTCTCCGAGGTCAAAGCC
* * * * *
16346 GATGGGCATACAAAGTATAAACAAATCGCCTG-GGTCAAAGCC
1 GATGGGCAGACAAAGGATAAAGAAGTCTCC-GAGGTCAAAGCC
**** * * * * * ***
16388 GACAAACAGAAAAAGGGTAAAAAAGTTTCTCG-GGTTAAAAAT
1 GATGGGCAGACAAAGGATAAAGAAGTCTC-CGAGGTCAAAGCC
* * *
16430 GACGGGTAAGACAAAGG-TAAAAAAGTCTCCCG-GGTCAAAGCC
1 GATGGG-CAGACAAAGGATAAAGAAGTCT-CCGAGGTCAAAGCC
* *** * * *
16472 AACAAGCAGACAACGG-TAAAGAAGTCTCCCAGGTTAAAGCC
1 GATGGGCAGACAAAGGATAAAGAAGTCTCCGAGGTCAAAGCC
* * * *
16513 -ATGGGTAGACAAAAGG-TCAAA-AAGTCTCCCACGTCAAAGCT
1 GATGGGCAGAC-AAAGGAT-AAAGAAGTCTCCGAGGTCAAAGCC
* * * * * *
16554 GACGGGTAGACAAAAGATAAATAAGTTTCTTG-GGTCAAAGCC
1 GATGGGCAGACAAAGGATAAAGAAGTCTC-CGAGGTCAAAGCC
* * * * * *
16596 GACT-GGCAAAAAAAAGG-TAAAAAAGTCTCCAAGGTCGAAGCT
1 GA-TGGGC-AGACAAAGGATAAAGAAGTCTCCGAGGTCAAAGCC
*** *
16638 GACAAGCAAACAAAGGATAAAGAA-TCTCTCG-GGTCAAAGCC
1 GATGGGCAGACAAAGGATAAAGAAGTCTC-CGAGGTCAAAGCC
* * *
16679 GATGGGTAGACAAAAGG-TAAAGAAGTCT-CTAGGGTCAAAACTC
1 GATGGGCAGAC-AAAGGATAAAGAAGTCTCCGA-GGTCAAAGC-C
* * * * *
16722 -ATAGCCAGACAAAGGATAAAAAAGTCTCTCGA-GTTAAAGTC
1 GATGGGCAGACAAAGGATAAAGAAGTCTC-CGAGGTCAAAGCC
* ** * * * *
16763 AACAGGCATACAAAGGATAAAGAAAT-TACCCGA-GTAAAAACC
1 GATGGGCAGACAAAGGATAAAGAAGTCT--CCGAGGTCAAAGCC
* * * * *
16805 GATAGGTAGACAAAGGGTAAAGAAATCTCTTG-GGTCAAAGCC
1 GATGGGCAGACAAAGGATAAAGAAGTCTC-CGAGGTCAAAGCC
16847 TACAAGCAAA
Statistics
Matches: 434, Mismatches: 119, Indels: 66
0.70 0.19 0.11
Matches are distributed among these distances:
40 9 0.02
41 98 0.23
42 270 0.62
43 55 0.13
44 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (42 bp):
GATGGGCAGACAAAGGATAAAGAAGTCTCCGAGGTCAAAGCC
Found at i:16624 original size:84 final size:83
Alignment explanation
Indices: 16442--16707 Score: 214
Period size: 83 Copynumber: 3.2 Consensus size: 83
16432 CGGGTAAGAC
*** ** * * * * *
16442 AAAGGTAAAAAAGTCTCCCGGGTCAAAGCCAACAAGCAGAC-AACGGTAAAGAAGTCTCCCAGGT
1 AAAGGTAAAAAAGTCTCCAACGTCAAAGCTGACAAGCAAACAAAAGATAAAGAA-TCTCTCGGGT
* * * *
16506 TAAAGCC-ATGGGTAGACA
65 CAAAGCCGATGGGCAAAAA
* * ** * * * * *
16524 AAAGGTCAAAAAGTCTCCCACGTCAAAGCTGACGGGTAGACAAAAGATAAATAAGTTTCTTGGGT
1 AAAGGTAAAAAAGTCTCCAACGTCAAAGCTGACAAGCAAACAAAAGATAAAGAA-TCTCTCGGGT
16589 CAAAGCCGACT-GGCAAAAA
65 CAAAGCCGA-TGGGCAAAAA
* * *
16608 AAAGGTAAAAAAGTCTCCAAGGTCGAAGCTGACAAGCAAACAAAGGATAAAGAATCTCTCGGGTC
1 AAAGGTAAAAAAGTCTCCAACGTCAAAGCTGACAAGCAAACAAAAGATAAAGAATCTCTCGGGTC
* * *
16673 AAAGCCGATGGGTAGACA
66 AAAGCCGATGGGCAAAAA
*
16691 AAAGGTAAAGAAGTCTC
1 AAAGGTAAAAAAGTCTC
16708 TAGGGTCAAA
Statistics
Matches: 145, Mismatches: 35, Indels: 7
0.78 0.19 0.04
Matches are distributed among these distances:
82 34 0.23
83 60 0.41
84 50 0.34
85 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.15
Consensus pattern (83 bp):
AAAGGTAAAAAAGTCTCCAACGTCAAAGCTGACAAGCAAACAAAAGATAAAGAATCTCTCGGGTC
AAAGCCGATGGGCAAAAA
Found at i:16700 original size:208 final size:211
Alignment explanation
Indices: 16251--16749 Score: 480
Period size: 208 Copynumber: 2.4 Consensus size: 211
16241 AAATCTCCTA
* *
16251 GGTCAAAGCCGATGAGCAGAAAAAAGATAAAGAAGTCTCCCAAGGTCAAAGCCAATAGGTAGACA
1 GGTCAAAGCCGATGAGCAGACAAAAGGTAAAGAAGTCTCCCAAGGTCAAAGCCAATAGGTAGACA
* * * *
16316 AAGGATAAAGAAGTCTCCGAGGTCAAAGCCGATGGGCATACAAAGTATAAACAAATCGCCTGGGT
66 AAGGATAAAGAAGTCTCCCACGTCAAAGCCGACGGGCAGACAAAGTATAAACAAATCGCCTGGGT
* * * * * ** *
16381 CAAAGCCGACAAACAGAAAAAGGGTAAAAAAGTTTCTCGGGTTAAAAATGACGGGTAAGACAAAG
131 CAAAGCCGACAAACAAAAAAAAGGTAAAAAAGTCTCTCAGGTCAAAAATGACAAGCAAGACAAAG
16446 GTAAAAAAGTCTCCCG
196 GTAAAAAAGTCTCCCG
* ** * * *
16462 GGTCAAAGCCAACAAGCAGAC-AACGGTAAAGAAGTCTCCC-AGGTTAAAGCC-ATGGGTAGACA
1 GGTCAAAGCCGATGAGCAGACAAAAGGTAAAGAAGTCTCCCAAGGTCAAAGCCAATAGGTAGAC-
* * * * ** *
16524 AAAGG-TCAAA-AAGTCTCCCACGTCAAAGCTGACGGGTAGACAAAAG-ATAAATAAGTTTCTTG
65 AAAGGAT-AAAGAAGTCTCCCACGTCAAAGCCGACGGGCAGAC-AAAGTATAAACAAATCGCCTG
*** * **
16586 GGTCAAAGCCGACTGGCAAAAAAAAGGTAAAAAAGTCTC-CAAGGTCGAAGCTGACAAGCAA-AC
128 GGTCAAAGCCGACAAACAAAAAAAAGGTAAAAAAGTCTCTC-AGGTCAAAAATGACAAGCAAGAC
* *
16649 AAAGGATAAAGAA-TCTCTCG
192 AAAGG-TAAAAAAGTCTCCCG
* * * * * **
16669 GGTCAAAGCCGATGGGTAGACAAAAGGTAAAGAAGTCT-CTAGGGTCAAAACTC-ATAGCCAGAC
1 GGTCAAAGCCGATGAGCAGACAAAAGGTAAAGAAGTCTCCCAAGGTCAAAGC-CAATAGGTAGAC
*
16732 AAAGGATAAAAAAGTCTC
65 AAAGGATAAAGAAGTCTC
16750 TCGAGTTAAA
Statistics
Matches: 230, Mismatches: 48, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
207 31 0.13
208 127 0.55
209 38 0.17
210 17 0.07
211 17 0.07
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (211 bp):
GGTCAAAGCCGATGAGCAGACAAAAGGTAAAGAAGTCTCCCAAGGTCAAAGCCAATAGGTAGACA
AAGGATAAAGAAGTCTCCCACGTCAAAGCCGACGGGCAGACAAAGTATAAACAAATCGCCTGGGT
CAAAGCCGACAAACAAAAAAAAGGTAAAAAAGTCTCTCAGGTCAAAAATGACAAGCAAGACAAAG
GTAAAAAAGTCTCCCG
Found at i:16742 original size:125 final size:126
Alignment explanation
Indices: 16545--16868 Score: 302
Period size: 125 Copynumber: 2.6 Consensus size: 126
16535 AGTCTCCCAC
* * * * * * *
16545 GTCAAAGCTGACGGGTAGACAAAAGATAAATAAGTTTCTTGGGTCAAAGCCGACTGGCAAAAAAA
1 GTCAAAGCCGATGGGTAGACAAAAGGTAAAGAAGTCTCTTGGGTCAAAACCGACTAGCAAAAAAA
* * * *
16610 AGGTAAAAAAGTCTC-CAAGGTCGAAG-CTGACAAGCAAACAAAGGATAAAG-AATCT-CTCGG
66 AGGTAAAAAAGTCTCTCAA-GTCAAAGTC-AACAAGCAAACAAAGGATAAAGAAAT-TACCCGA
* * * *
16670 GTCAAAGCCGATGGGTAGACAAAAGGTAAAGAAGTCTCTAGGGTCAAAACTC-A-TAGCCAGACA
1 GTCAAAGCCGATGGGTAGACAAAAGGTAAAGAAGTCTCTTGGGTCAAAAC-CGACTAGCAAAAAA
* * * *
16733 AAGGATAAAAAAGTCTCTCGAGTTAAAGTCAACAGGCATACAAAGGATAAAGAAATTACCCGA
65 AAGG-TAAAAAAGTCTCTCAAGTCAAAGTCAACAAGCAAACAAAGGATAAAGAAATTACCCGA
* * * * * * * * *
16796 GTAAAAACCGATAGGTAGACAAAGGGTAAAGAAATCTCTTGGGTCAAAGCCTACAAGC-AAACAA
1 GTCAAAGCCGATGGGTAGACAAAAGGTAAAGAAGTCTCTTGGGTCAAAACCGACTAGCAAAAAAA
16860 AGGTAAAAA
66 AGGTAAAAA
16869 TGCCTCTCGG
Statistics
Matches: 163, Mismatches: 28, Indels: 16
0.79 0.14 0.08
Matches are distributed among these distances:
124 10 0.06
125 88 0.54
126 62 0.38
127 3 0.02
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (126 bp):
GTCAAAGCCGATGGGTAGACAAAAGGTAAAGAAGTCTCTTGGGTCAAAACCGACTAGCAAAAAAA
AGGTAAAAAAGTCTCTCAAGTCAAAGTCAACAAGCAAACAAAGGATAAAGAAATTACCCGA
Found at i:16860 original size:126 final size:124
Alignment explanation
Indices: 16647--16877 Score: 288
Period size: 126 Copynumber: 1.8 Consensus size: 124
16637 TGACAAGCAA
* * * * * *
16647 ACAAAGGATAAAGAATCTCTCGGGTCAAAGCCGATGGGTAGACAAAAGGTAAAGAAGTCTCTAGG
1 ACAAAGGATAAAGAATCTCCCGAGTAAAAACCGATAGGTAGACAAAAGGTAAAGAAATCTCTAGG
* *
16712 GTCAAAACTCATAGCCAGACAAAGGATAAAAAAGTCTCTCGAGTTAAAGTCAACAGGCAT
66 GTCAAAACTCATAGCCAAACAAAGG-TAAAAAAGCCTCTCGAGTTAAAGTCAACAGGCAT
* *
16772 ACAAAGGATAAAGAAAT-TACCCGAGTAAAAACCGATAGGTAGACAAAGGGTAAAGAAATCTCTT
1 ACAAAGGATAAAG-AATCT-CCCGAGTAAAAACCGATAGGTAGACAAAAGGTAAAGAAATCTCTA
* *
16836 GGGTCAAAGCCTACA-AG-CAAACAAAGGTAAAAATGCCTCTCG
64 GGGTCAAA-ACT-CATAGCCAAACAAAGGTAAAAAAGCCTCTCG
16878 GGTCAAAGCT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
125 27 0.30
126 57 0.63
127 4 0.04
128 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (124 bp):
ACAAAGGATAAAGAATCTCCCGAGTAAAAACCGATAGGTAGACAAAAGGTAAAGAAATCTCTAGG
GTCAAAACTCATAGCCAAACAAAGGTAAAAAAGCCTCTCGAGTTAAAGTCAACAGGCAT
Found at i:16922 original size:41 final size:41
Alignment explanation
Indices: 16307--16922 Score: 237
Period size: 42 Copynumber: 14.8 Consensus size: 41
16297 CAAAGCCAAT
* * *
16307 AGGTAGACAAAGGATAAAGAAGTCTC-CGAGGTCAAAGCCGAT
1 AGGTAGACAAAGG-TAAAAAAGTCTCTCG-GGTCAAAGCTGAC
* * * * * *
16349 GGGCATACAAA-GTATAAACAAATCGC-CTGGGTCAAAGCCGAC
1 AGGTAGACAAAGGTA-AAA-AAGTCTCTC-GGGTCAAAGCTGAC
*** * * * **
16391 AAACAGAAAAAGGGTAAAAAAGTTTCTCGGGTTAAAAATGAC
1 AGGTAGACAAA-GGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
* * **
16433 GGGTAAGACAAAGGTAAAAAAGTCTCCCGGGTCAAAGCCAAC
1 AGGT-AGACAAAGGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
* * * * * * * * *
16475 AAGCAGACAACGGTAAAGAAGTCTCCCAGGTTAAAGC-CAT
1 AGGTAGACAAAGGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
* * * **
16515 GGGTAGACAAAAGGTCAAAAAGTCTCCCACGTCAAAGCTGAC
1 AGGTAGAC-AAAGGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
* * * * * *
16557 GGGTAGACAAAAGATAAATAAGTTTCTTGGGTCAAAGCCGAC
1 AGGTAGAC-AAAGGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
* * * * * *
16599 TGGCAAAAAAAAGGTAAAAAAGTCTC-CAAGGTCGAAGCTGAC
1 AGG-TAGACAAAGGTAAAAAAGTCTCTC-GGGTCAAAGCTGAC
* * * * * *
16641 AAGCAAACAAAGGATAAAGAA-TCTCTCGGGTCAAAGCCGAT
1 AGGTAGACAAAGG-TAAAAAAGTCTCTCGGGTCAAAGCTGAC
* * * * * *
16682 GGGTAGACAAAAGGTAAAGAAGTCTCTAGGGTCAAAACTCAT
1 AGGTAGAC-AAAGGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
** * * *
16724 AGCCAGACAAAGGATAAAAAAGTCTCTCGAGTTAAAG-TCAAC
1 AGGTAGACAAAGG-TAAAAAAGTCTCTCGGGTCAAAGCT-GAC
* * * * * * * *
16766 AGGCATACAAAGGATAAAGAAA-T-TACCCGAGTAAAAACCGAT
1 AGGTAGACAAAGG-TAAA-AAAGTCT-CTCGGGTCAAAGCTGAC
*
16808 AGGTAGACAAAGGGTAAAGAAA-TCTCTTGGGTCAAAGCCT-AC
1 AGGTAGACAAA-GGTAAA-AAAGTCTCTCGGGTCAAAG-CTGAC
* * * * *
16850 AAGCAAACAAAGGTAAAAATGCCTCTCGGGTCAAAGCTGAC
1 AGGTAGACAAAGGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
* * *
16891 GGGTAAACAAAGGTAAAAAAGTCTCTAGGGTC
1 AGGTAGACAAAGGTAAAAAAGTCTCTCGGGTC
16923 TAAACCGACA
Statistics
Matches: 423, Mismatches: 126, Indels: 51
0.70 0.21 0.09
Matches are distributed among these distances:
40 12 0.03
41 143 0.34
42 245 0.58
43 20 0.05
44 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (41 bp):
AGGTAGACAAAGGTAAAAAAGTCTCTCGGGTCAAAGCTGAC
Found at i:17211 original size:49 final size:47
Alignment explanation
Indices: 17133--17268 Score: 143
Period size: 49 Copynumber: 2.9 Consensus size: 47
17123 TTGTTTATGA
* * *
17133 CTAATGCCAATACAATGAAACGAGAGTGAAAGAGAGAGTTTTACCAAG-C
1 CTAATGCCAATACAATTAAA-TAGAGTGAAA-A-AGAGTTTGACCAAGTC
* *
17182 CTAATGCCAATACAATTAAATATGGGTGAAAAAGAGTTTGACCATGTC
1 CTAATGCCAATACAATTAAATA-GAGTGAAAAAGAGTTTGACCAAGTC
* * *
17230 CTAAAGCCAAAACAGTTAAATA-AG-GAAAAAGAGTTTGAC
1 CTAATGCCAATACAATTAAATAGAGTGAAAAAGAGTTTGAC
17269 TAGGTTTCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
45 15 0.20
46 1 0.01
47 12 0.16
48 22 0.29
49 26 0.34
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (47 bp):
CTAATGCCAATACAATTAAATAGAGTGAAAAAGAGTTTGACCAAGTC
Found at i:17249 original size:48 final size:45
Alignment explanation
Indices: 17157--17268 Score: 118
Period size: 48 Copynumber: 2.4 Consensus size: 45
17147 ATGAAACGAG
* * *
17157 AGTGAAAGAGAGAGTTTTACCAAGCCTAATGCCAATACAATTAAATA
1 AGTGAAA-A-AGAGTTTGACCAAGCCTAAAGCCAAAACAATTAAATA
* * *
17204 TGGGTGAAAAAGAGTTTGACCATGTCCTAAAGCCAAAACAGTTAAATA
1 --AGTGAAAAAGAGTTTGACCAAG-CCTAAAGCCAAAACAATTAAATA
17252 AG-GAAAAAGAGTTTGAC
1 AGTGAAAAAGAGTTTGAC
17269 TAGGTTTCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
45 15 0.27
46 1 0.02
47 12 0.22
48 21 0.38
49 6 0.11
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (45 bp):
AGTGAAAAAGAGTTTGACCAAGCCTAAAGCCAAAACAATTAAATA
Found at i:22830 original size:33 final size:33
Alignment explanation
Indices: 22767--22833 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
22757 AAGTGCACTA
* *
22767 AAGTGCTCATCCATGCGCTCCGAGAATGAAGTG
1 AAGTGCTCATCCATGCGCTACGAAAATGAAGTG
* *
22800 AAGTGCTCATTCATGTGCTAC-AAAAGTGAAGTG
1 AAGTGCTCATCCATGCGCTACGAAAA-TGAAGTG
22833 A
1 A
22834 TCAACTCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (33 bp):
AAGTGCTCATCCATGCGCTACGAAAATGAAGTG
Found at i:30478 original size:20 final size:20
Alignment explanation
Indices: 30453--30506 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
30443 GTTTGAAGCA
*
30453 ATGTATCGATACAGTGT-GCC
1 ATGTATCGATACAATGTAG-C
30473 ATGTATCGATACAATGTAGC
1 ATGTATCGATACAATGTAGC
30493 ATGTATCGATACAA
1 ATGTATCGATACAA
30507 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATGTAGC
Found at i:31514 original size:32 final size:32
Alignment explanation
Indices: 31472--31659 Score: 155
Period size: 33 Copynumber: 5.8 Consensus size: 32
31462 GATGCCATTG
* * *
31472 ACTTGTGTGGGCTTTTGAGAAGGTTGGCACCG
1 ACTTATGTGGGCTTTTGAGAAGGTTGCCACCA
* *
31504 ATTTATGTGGGCTTTAGA-AAGGGTTGCCACCA
1 ACTTATGTGGGCTTTTGAGAA-GGTTGCCACCA
* *
31536 ACTTGTGTGGGC-TTTGAAGAAGGTTGTCACCA
1 ACTTATGTGGGCTTTTG-AGAAGGTTGCCACCA
* * * * * * *
31568 GCTTGTGTTGGCTTTGGAAAAAGGTTTCCATCA
1 ACTTATGTGGGCTTTTG-AGAAGGTTGCCACCA
* * *
31601 ACTTATGTGGGCTTTGGAAAAAGGTTTCCACCA
1 ACTTATGTGGGCTTTTG-AGAAGGTTGCCACCA
*
31634 ACTTATGCGGGCTTTTGAGAAAGGTT
1 ACTTATGTGGGCTTTTGAG-AAGGTT
31660 TCTCCACTAG
Statistics
Matches: 128, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
31 5 0.04
32 56 0.44
33 67 0.52
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.32
Consensus pattern (32 bp):
ACTTATGTGGGCTTTTGAGAAGGTTGCCACCA
Found at i:31548 original size:64 final size:66
Alignment explanation
Indices: 31472--31659 Score: 186
Period size: 64 Copynumber: 2.9 Consensus size: 66
31462 GATGCCATTG
* *
31472 ACTTGTGTGGGCTTTTG-AGAAGGTTGGCACC-GATTTATGTGGGCTTTAG-AAAGGGTTGCCAC
1 ACTTGTGTGGGCTTTTGAAGAAGGTTGGCACCAG-CTTATGTGGGCTTTAGAAAAAGGTTGCCAC
31534 CA
65 CA
* * * * * *
31536 ACTTGTGTGGGC-TTTGAAGAAGGTTGTCACCAGCTTGTGTTGGCTTTGGAAAAAGGTTTCCATC
1 ACTTGTGTGGGCTTTTGAAGAAGGTTGGCACCAGCTTATGTGGGCTTTAGAAAAAGGTTGCCACC
31600 A
66 A
* * * ** * * * *
31601 ACTTATGTGGGCTTTGGAAAAAGGTTTCCACCAACTTATGCGGGCTTTTGAGAAAGGTT
1 ACTTGTGTGGGCTTTTGAAGAAGGTTGGCACCAGCTTATGTGGGCTTTAGAAAAAGGTT
31660 TCTCCACTAG
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
63 4 0.04
64 37 0.37
65 24 0.24
66 36 0.36
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.32
Consensus pattern (66 bp):
ACTTGTGTGGGCTTTTGAAGAAGGTTGGCACCAGCTTATGTGGGCTTTAGAAAAAGGTTGCCACC
A
Found at i:31614 original size:33 final size:33
Alignment explanation
Indices: 31506--31661 Score: 174
Period size: 33 Copynumber: 4.8 Consensus size: 33
31496 TGGCACCGAT
* * *
31506 TTATGTGGGCTTTAG-AAAGGGTTGCCACCAAC
1 TTATGTGGGCTTTGGAAAAAGGTTTCCACCAAC
* * *
31538 TTGTGTGGGCTTT-GAAGAAGGTTGT-CACCAGC
1 TTATGTGGGCTTTGGAAAAAGGTT-TCCACCAAC
* * *
31570 TTGTGTTGGCTTTGGAAAAAGGTTTCCATCAAC
1 TTATGTGGGCTTTGGAAAAAGGTTTCCACCAAC
31603 TTATGTGGGCTTTGGAAAAAGGTTTCCACCAAC
1 TTATGTGGGCTTTGGAAAAAGGTTTCCACCAAC
* * *
31636 TTATGCGGGCTTTTGAGAAAGGTTTC
1 TTATGTGGGCTTTGGAAAAAGGTTTC
31662 TCCACTAGGG
Statistics
Matches: 105, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
31 1 0.01
32 37 0.35
33 67 0.64
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (33 bp):
TTATGTGGGCTTTGGAAAAAGGTTTCCACCAAC
Found at i:37734 original size:59 final size:59
Alignment explanation
Indices: 37642--37760 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
37632 CACTCATTCT
37642 TTTTTATTTTTTTTGAAAAAAGAGCAAATGTCTTAAAAATGGTGGAACAAAATTTGGTG
1 TTTTTATTTTTTTTGAAAAAAGAGCAAATGTCTTAAAAATGGTGGAACAAAATTTGGTG
37701 TTTTTATTTTTTTTGAAAAAAGAGCAAATGTCTTAAAAATGGTGGAACAAAATTTGGTG
1 TTTTTATTTTTTTTGAAAAAAGAGCAAATGTCTTAAAAATGGTGGAACAAAATTTGGTG
37760 T
1 T
37761 CTACACATGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.39
Consensus pattern (59 bp):
TTTTTATTTTTTTTGAAAAAAGAGCAAATGTCTTAAAAATGGTGGAACAAAATTTGGTG
Found at i:39221 original size:31 final size:31
Alignment explanation
Indices: 38880--39224 Score: 233
Period size: 31 Copynumber: 11.0 Consensus size: 31
38870 TCGCTAACTC
* * * *
38880 GTGCAGGCTTAGACTCGGGTGCTGGCAGCTT
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
** *
38911 GTGCCAGCTTTGACTCGGGTGCCGCTAGCTT
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
* ** *
38942 GTGTGGGCTTTGACTCGGGTGTTGCCGGCTT
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
** * * *
38973 GTGCAAGCTTTGACTTGGGTGCCGCTAGCTC
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
* * * * * * *
39004 GTACAGGCTTGGACTCAGGTGCTGTCGACCTGT
1 GTGCGGGCTTTGACTCGGGTGCCG-CCAGCT-T
* ** ** * *
39037 GCGTGCGGGCTTAGACTCAAGTGTTGCCAACTC
1 --GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
* * ** *
39070 GTGTGGGCTTAGACTCGGGTGTTGTCAGCTT
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
**
39101 GTGCGGGCTTTGACTCGGGTG-CGACCTCCTT
1 GTGCGGGCTTTGACTCGGGTGCCG-CCAGCTT
* * * * *
39132 GTGTGGGCTTTGACTTGGCTGTCGCCAACTT
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
* *
39163 GTGTGGGCTTTGACTCGGGTGCCACCAGCTT
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
*
39194 GTGCGGGCTTTGACTCGGGTGCCACCAGCTT
1 GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
39225 ATGCAAGGTT
Statistics
Matches: 246, Mismatches: 62, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
30 1 0.00
31 216 0.88
32 6 0.02
34 4 0.02
35 19 0.08
ACGTcount: A:0.11, C:0.25, G:0.35, T:0.30
Consensus pattern (31 bp):
GTGCGGGCTTTGACTCGGGTGCCGCCAGCTT
Found at i:39245 original size:31 final size:31
Alignment explanation
Indices: 39168--39245 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
39158 AACTTGTGTG
* * * *
39168 GGCTTTGACTCGGGTGCCACCAGCTTGTGCG
1 GGCTTTAACTAGGGTGCCACCAGCTTATGCA
* *
39199 GGCTTTGACTCGGGTGCCACCAGCTTATGCAA
1 GGCTTTAACTAGGGTGCCACCAGCTTATGC-A
39231 GG-TTTAACTAGGGTG
1 GGCTTTAACTAGGGTG
39246 TCCCCAACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 40 0.95
32 2 0.05
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.27
Consensus pattern (31 bp):
GGCTTTAACTAGGGTGCCACCAGCTTATGCA
Found at i:39253 original size:93 final size:93
Alignment explanation
Indices: 39063--39266 Score: 248
Period size: 93 Copynumber: 2.2 Consensus size: 93
39053 TCAAGTGTTG
**** * *
39063 CCAACTCGTGTGGGCTTAGACTCGGGTGTTGTCAGCTTGTGCGGGCTTTGACTCGGGTGCGACCT
1 CCAACTCGTGTGGGCTTAGACTCGGGTGCCACCAGCTTGTGCGGGCTTTGACTCGGGTGCCACCA
* ** * * *
39128 CCTTGTGTGGGCTTTGACTTGGCTGTCG
66 CCTTATGAAGGCTTTAACTAGGCTGTCC
* *
39156 CCAACTTGTGTGGGCTTTGACTCGGGTGCCACCAGCTTGTGCGGGCTTTGACTCGGGTGCCACCA
1 CCAACTCGTGTGGGCTTAGACTCGGGTGCCACCAGCTTGTGCGGGCTTTGACTCGGGTGCCACCA
* *
39221 GCTTATGCAAGG-TTTAACTAGGGTGTCC
66 CCTTATG-AAGGCTTTAACTAGGCTGTCC
39249 CCAACTCGTGTGGGCTTA
1 CCAACTCGTGTGGGCTTA
39267 AAAAGGAGTG
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
93 90 0.98
94 2 0.02
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.30
Consensus pattern (93 bp):
CCAACTCGTGTGGGCTTAGACTCGGGTGCCACCAGCTTGTGCGGGCTTTGACTCGGGTGCCACCA
CCTTATGAAGGCTTTAACTAGGCTGTCC
Found at i:43729 original size:52 final size:52
Alignment explanation
Indices: 43649--43768 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
43639 AAAAGTTACT
* *
43649 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
43701 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
43753 TGCATGTATCGATACA
1 TGCATGTATCGATACA
43769 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:43781 original size:52 final size:52
Alignment explanation
Indices: 43649--43786 Score: 181
Period size: 52 Copynumber: 2.7 Consensus size: 52
43639 AAAAGTTACT
* *
43649 TGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*** *
43701 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*
43753 TGCATGTATCGATACA-AAGATCGGTGTATCGATA
1 TGCATGTATCGATACATAAGAT-AGTGTATCGATA
43787 TAATGTATCG
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
51 4 0.05
52 72 0.95
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:43879 original size:33 final size:33
Alignment explanation
Indices: 43842--43908 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
43832 AGTAGCTTAA
43842 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
43875 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
43908 A
1 A
43909 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:43882 original size:13 final size:13
Alignment explanation
Indices: 43864--43888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43854 CAAAAAAATA
43864 TGTATCGATACAT
1 TGTATCGATACAT
43877 TGTATCGATACA
1 TGTATCGATACA
43889 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:43987 original size:21 final size:21
Alignment explanation
Indices: 43946--43987 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
43936 GTTGGGACCT
*
43946 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
43967 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
43988 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:44170 original size:12 final size:11
Alignment explanation
Indices: 44143--44181 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
44133 TGTCTACACC
*
44143 TTTTTTTCTCTT
1 TTTTTTTGT-TT
44155 TTTTTTTGTTT
1 TTTTTTTGTTT
44166 ATTTTTTTGTTT
1 -TTTTTTTGTTT
44178 TTTT
1 TTTT
44182 AGGCATAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.87
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:45859 original size:19 final size:19
Alignment explanation
Indices: 45814--45869 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
45804 CTGCCAGTTT
*
45814 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
*
45834 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
45853 CATGTATCGATGCAATG
1 CATGTATCGATACAATG
45870 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:45891 original size:20 final size:21
Alignment explanation
Indices: 45866--45918 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
45856 GTATCGATGC
45866 AATGTATCGATACA-AAGCAT
1 AATGTATCGATACATAAGCAT
* * *
45886 AATGTATCAATACATCAGGAT
1 AATGTATCGATACATAAGCAT
45907 -ATGTATCGATAC
1 AATGTATCGATAC
45919 TTTTTAGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
AATGTATCGATACATAAGCAT
Done.