Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007825.1 Corchorus capsularis cultivar CVL-1 contig07846, whole genome shotgun sequence
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: 99905
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:886 original size:2 final size:2
Alignment explanation
Indices: 881--935 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
871 GAATGAGATC
* * * *
881 AT AT AT AA AT AT AT AT AT AA AT AT AA AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
923 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
936 GTTTAATAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1938 original size:45 final size:45
Alignment explanation
Indices: 1876--1962 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
1866 TTGAAGACTT
* * * *
1876 CACTATGAAATTTTGATAACTTCCCTATGAAATTTTGATAACTAA
1 CACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACTAA
* *
1921 CACTATGAGATGTTGATAACCTCCATATGATATATTGATAAC
1 CACTATGAAATGTTGATAACCTCCATATGAAATATTGATAAC
1963 CATATTATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (45 bp):
CACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACTAA
Found at i:2181 original size:60 final size:61
Alignment explanation
Indices: 2086--2203 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 61
2076 CCTTCCTATA
*
2086 AAATTTTGATAAACCTCCCTATAGAATTTTTATAACCTCCTTATGAAATCTTGATAATTAC
1 AAATTTTGATAAACCTCCCTATAGAATTTTTATAACCTCATTATGAAATCTTGATAATTAC
* * * *
2147 AAATTTTGAT-AAGCTCCCTAT-GATTTTTTGATAACCTCATTATGAAATTTTGTTAAT
1 AAATTTTGATAAACCTCCCTATAGAATTTTT-ATAACCTCATTATGAAATCTTGATAAT
2204 CTTCCTATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 7 0.14
60 34 0.67
61 10 0.20
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAGAATTTTTATAACCTCATTATGAAATCTTGATAATTAC
Found at i:2324 original size:20 final size:22
Alignment explanation
Indices: 1873--2330 Score: 182
Period size: 22 Copynumber: 20.9 Consensus size: 22
1863 ATTTTGAAGA
1873 CTTCACTATGAAATTTTGATAA-
1 CTTCA-TATGAAATTTTGATAAC
*
1895 CTTCCCTATGAAATTTTGATAA-
1 CTT-CATATGAAATTTTGATAAC
* * *
1917 CTAACACTATGAGATGTTGATAAC
1 CT-TCA-TATGAAATTTTGATAAC
* * *
1941 CTCCATATGATATATTGATAAC
1 CTTCATATGAAATTTTGATAAC
* * *
1963 CAT-ATTATGAAAATTT-AAAAC
1 CTTCA-TATGAAATTTTGATAAC
* *
1984 CTCCATATG-AATTGTT-AGTAAT
1 CTTCATATGAAATT-TTGA-TAAC
* * * *
2006 C-ACACTCTAAAATTTTGATAAT
1 CTTCA-TATGAAATTTTGATAAC
* *
2028 C-ACACTATGAAATTGTGATAACC
1 CTTCA-TATGAAATTTTGATAA-C
**
2051 CCGCTAGCTATGAAATTTTGATAAAC
1 CTTC-A--TATGAAATTTTGAT-AAC
* *
2077 CTTCCTATAAAATTTTGATAAAC
1 CTTCATATGAAATTTTGAT-AAC
* * *
2100 CTCCCTAT-AGAATTTTTATAAC
1 CTTCATATGA-AATTTTGATAAC
* * *
2122 CTCCTTATGAAATCTTGATAA-
1 CTTCATATGAAATTTTGATAAC
* *
2143 --T--TA-CAAATTTTGATAAG
1 CTTCATATGAAATTTTGATAAC
* * **
2160 CTCCCTATGATTTTTTGATAAC
1 CTTCATATGAAATTTTGATAAC
* *
2182 C-TCATTATGAAATTTTGTTAAT
1 CTTCA-TATGAAATTTTGATAAC
* *
2204 CTTCCTATGAAATTTTGATCTAC
1 CTTCATATGAAATTTTGAT-AAC
* *
2227 ATAC-TATGAAATTTTGATAAC
1 CTTCATATGAAATTTTGATAAC
* * * *
2248 CCTCTTATGAAAATTTGA-AAA
1 CTTCATATGAAATTTTGATAAC
**
2269 CTAAACTATGAAATTTTGATAAC
1 CTTCA-TATGAAATTTTGATAAC
*
2292 CTTCATATGAAATTTTGATATC
1 CTTCATATGAAATTTTGATAAC
2314 CTTC-T-TGAAATTTTGAT
1 CTTCATATGAAATTTTGAT
2331 TACTCCATAA
Statistics
Matches: 334, Mismatches: 72, Indels: 62
0.71 0.15 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 15 0.04
21 25 0.07
22 192 0.57
23 66 0.20
24 3 0.01
25 1 0.00
26 17 0.05
27 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
CTTCATATGAAATTTTGATAAC
Found at i:2359 original size:42 final size:42
Alignment explanation
Indices: 2277--2359 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
2267 AACTAAACTA
* * * * *
2277 TGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTTCT
1 TGAAATTTTGATAACCTCCATATAAAAGTTTAATAACCTTCT
*
2319 TGAAATTTTGATTA-CTCCATAATAAAAGTTTAATAACCTTC
1 TGAAATTTTGATAACCTCCAT-ATAAAAGTTTAATAACCTTC
2360 CTAATTTGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.15
42 29 0.85
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (42 bp):
TGAAATTTTGATAACCTCCATATAAAAGTTTAATAACCTTCT
Found at i:2487 original size:22 final size:21
Alignment explanation
Indices: 2438--2579 Score: 99
Period size: 22 Copynumber: 6.6 Consensus size: 21
2428 TCACATTTTG
* *
2438 AAAA-TTTGATAACTCTTTAT
1 AAAATTTTGATAACCCTCTAT
*
2458 GAAATTTTGATAACCCCTCTAT
1 AAAATTTTGATAA-CCCTCTAT
* *
2480 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGAT-AACCCTCTAT
* * *
2502 GAAATTTTGATAACCTTGCTTT
1 AAAATTTTGATAACCCT-CTAT
* * *
2524 GAAATTTTGATAACAACACTAT
1 AAAATTTTGATAAC-CCTCTAT
* * *
2546 AAAATTTTAATAATCTTCCTAT
1 AAAATTTTGATAACCCT-CTAT
2568 -AAATTTTGATAA
1 AAAATTTTGATAA
2580 TCCGATCTCT
Statistics
Matches: 94, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
20 3 0.03
21 23 0.24
22 67 0.71
23 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (21 bp):
AAAATTTTGATAACCCTCTAT
Found at i:2701 original size:22 final size:20
Alignment explanation
Indices: 2672--2832 Score: 79
Period size: 22 Copynumber: 7.4 Consensus size: 20
2662 AAATTGAGAC
*
2672 TTTTATAACCTTCATATGAAA
1 TTTTATAACC-ACATATGAAA
**
2693 TTTTGATAACCACACTAAAAAA
1 TTTT-ATAACCACA-TATGAAA
*
2715 TGTTATTAACCACACTATGAAA
1 TTTTA-TAACCACA-TATGAAA
* **
2737 TTTTGATAACCTCCCCATGAAA
1 TTTT-ATAACC-ACATATGAAA
* *
2759 TATTAGTAACCTACTTATGAAA
1 TTTTA-TAACC-ACATATGAAA
* *
2781 TTTTGTTAACCATACTATGAAA
1 TTTT-ATAACCACA-TATGAAA
* * *
2803 TTCTTATAACCTCGTATGACA
1 TT-TTATAACCACATATGAAA
2824 TTTTGATAA
1 TTTT-ATAA
2833 TCTCTTTGAT
Statistics
Matches: 107, Mismatches: 23, Indels: 20
0.71 0.15 0.13
Matches are distributed among these distances:
20 2 0.02
21 21 0.20
22 80 0.75
23 4 0.04
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTTATAACCACATATGAAA
Found at i:2757 original size:66 final size:65
Alignment explanation
Indices: 2687--2832 Score: 145
Period size: 66 Copynumber: 2.2 Consensus size: 65
2677 TAACCTTCAT
2687 ATGAAATTTTGATAACC-ACACTAAAAAATGTTATTAACCACACTATGAAATT-TTGATAACCTC
1 ATGAAATTTTGATAACCTAC-CTAAAAAATGTTATTAACCACACTATGAAATTCTT-ATAACCT-
2750 CCC
63 CCC
* * ** * * * *
2753 ATGAAATATT-AGTAACCTACTTATGAAATTTTGTTAACCATACTATGAAATTCTTATAACCTCG
1 ATGAAATTTTGA-TAACCTACCTAAAAAATGTTATTAACCACACTATGAAATTCTTATAACCTCC
*
2817 T
65 C
*
2818 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
2833 TCTCTTTGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
65 13 0.20
66 48 0.74
67 4 0.06
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (65 bp):
ATGAAATTTTGATAACCTACCTAAAAAATGTTATTAACCACACTATGAAATTCTTATAACCTCCC
Found at i:2801 original size:44 final size:43
Alignment explanation
Indices: 2674--2832 Score: 144
Period size: 44 Copynumber: 3.7 Consensus size: 43
2664 ATTGAGACTT
* * ** *
2674 TTATAACCTTCATATGAAATTTTGATAACCACACTAAAAAATG
1 TTATAACCTACATATGAAATTTTGATAACCATACTATGAAATA
* *
2717 TTATTAACC-ACACTATGAAATTTTGATAACC-TCCCCATGAAATA
1 TTA-TAACCTACA-TATGAAATTTTGATAACCAT-ACTATGAAATA
* * *
2761 TTAGTAACCTACTTATGAAATTTTGTTAACCATACTATGAAATTC
1 TTA-TAACCTACATATGAAATTTTGATAACCATACTATGAAA-TA
* *
2806 TTATAACCT-CGTATGACATTTTGATAA
1 TTATAACCTACATATGAAATTTTGATAA
2833 TCTCTTTGAT
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
43 20 0.21
44 67 0.71
45 7 0.07
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (43 bp):
TTATAACCTACATATGAAATTTTGATAACCATACTATGAAATA
Found at i:2946 original size:22 final size:21
Alignment explanation
Indices: 2837--3038 Score: 111
Period size: 22 Copynumber: 9.0 Consensus size: 21
2827 TGATAATCTC
*
2837 TTTGATAACCTTTCTAT-AAAT
1 TTTGATAA-CTTACTATGAAAT
**
2858 TTGTGATAATCACACTATGAAAT
1 TT-TGATAA-CTTACTATGAAAT
** * *
2881 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAA-CTTACTATGAAAT
* *
2903 TTTAATAACCTGATCCTATGAAAT
1 TTTGATAA-CT--TACTATGAAAT
* *
2927 TTTGGTAGCTATACTATGAAAT
1 TTTGATAACT-TACTATGAAAT
2949 TTTGATAACCTT-CTCATGAAAT
1 TTTGATAA-CTTACT-ATGAAAT
*
2971 TTTGATAACTTCCATATGAAAT
1 TTTGATAACTTAC-TATGAAAT
* ** *
2993 TTTGGTAACCACACTATGGAAT
1 TTTGATAA-CTTACTATGAAAT
*
3015 TTTGATAAACTTCCTCATGAAAT
1 TTTGAT-AACTTACT-ATGAAAT
3038 T
1 T
3039 ATAATAACCA
Statistics
Matches: 141, Mismatches: 29, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
21 7 0.05
22 97 0.69
23 22 0.16
24 15 0.11
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTGATAACTTACTATGAAAT
Found at i:2989 original size:44 final size:44
Alignment explanation
Indices: 2872--3068 Score: 168
Period size: 44 Copynumber: 4.4 Consensus size: 44
2862 GATAATCACA
** *
2872 CTATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATC-
1 CTATGAAATTTTGATAA-CTTCCTATGAAATTTTAATAACCT--TCT
* * * *
2918 CTATGAAATTTTGGTAGCTATACTATGAAATTTTGATAACCTTCT
1 CTATGAAATTTTGATAACT-TCCTATGAAATTTTAATAACCTTCT
** * *
2963 C-ATGAAATTTTGATAACTTCCATATGAAATTTTGGTAACC-ACA
1 CTATGAAATTTTGATAACTTCC-TATGAAATTTTAATAACCTTCT
* * *
3006 CTATGGAATTTTGATAAACTTCCTCATGAAATTATAATAACCATCT
1 CTATGAAATTTTGAT-AACTTCCT-ATGAAATTTTAATAACCTTCT
*
3052 -TATGAATTTTTGATAAC
1 CTATGAAATTTTGATAAC
3069 CACAAAAAGA
Statistics
Matches: 123, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
43 4 0.03
44 50 0.41
45 36 0.29
46 33 0.27
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
CTATGAAATTTTGATAACTTCCTATGAAATTTTAATAACCTTCT
Found at i:3063 original size:45 final size:44
Alignment explanation
Indices: 2941--3067 Score: 134
Period size: 45 Copynumber: 2.8 Consensus size: 44
2931 GTAGCTATAC
* *
2941 TATGAAATTTTGATAACCTTCTCATGAAATTTTGAT-AACTTCCA
1 TATGAAATTTTGATAACCATCTTATG-AATTTTGATAAACTTCCA
* *
2985 TATGAAATTTTGGTAACCA-CACTATGGAATTTTGATAAACTTCC-
1 TATGAAATTTTGATAACCATC-TTAT-GAATTTTGATAAACTTCCA
* *
3029 TCATGAAATTATAATAACCATCTTATGAATTTTTGATAA
1 T-ATGAAATTTTGATAACCATCTTATGAA-TTTTGATAA
3068 CCACAAAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 32 0.46
45 35 0.51
46 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAACCATCTTATGAATTTTGATAAACTTCCA
Found at i:3067 original size:22 final size:22
Alignment explanation
Indices: 2873--3070 Score: 114
Period size: 22 Copynumber: 8.9 Consensus size: 22
2863 ATAATCACAC
** * *
2873 TATGAAATTTCAATAACCTTCC
1 TATGAAATTTTGATAACCATCT
* * *
2895 TAAGAAATTTTAATAACCTGATCC
1 TATGAAATTTTGATAACC--ATCT
* * *
2919 TATGAAATTTTGGTAGCTATAC-
1 TATGAAATTTTGATAACCAT-CT
*
2941 TATGAAATTTTGATAACCTTCT
1 TATGAAATTTTGATAACCATCT
* * *
2963 CATGAAATTTTGATAA-CTTCCA
1 TATGAAATTTTGATAACCAT-CT
* *
2985 TATGAAATTTTGGTAACCA-CAC
1 TATGAAATTTTGATAACCATC-T
* * *
3007 TATGGAATTTTGATAAACTTCCT
1 TATGAAATTTTGATAACCAT-CT
* * *
3030 CATGAAATTATAATAACCATCT
1 TATGAAATTTTGATAACCATCT
*
3052 TATGAATTTTTGATAACCA
1 TATGAAATTTTGATAACCA
3071 CAAAAAGACA
Statistics
Matches: 134, Mismatches: 33, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
21 5 0.04
22 96 0.72
23 16 0.12
24 17 0.13
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATCT
Found at i:3570 original size:166 final size:165
Alignment explanation
Indices: 3288--3605 Score: 430
Period size: 166 Copynumber: 1.9 Consensus size: 165
3278 AATAGTAAAG
* *
3288 GAAATTTGCTTGTTCATCAACGAAAACCAATTTGACAAACTTATAATTCGGTCTAATTTGAAATT
1 GAAATTTGCATGTTCATCAACGAAAACCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
* * *
3353 TTCAAATAATAAAATTATACTAAATTTTAATTATGGCAATTTATAAATATATTTGAAAAAAATGG
66 TTCAAATAATAAAATTATACTAAATTATAATAATGGCAATTTATAAATATATTTGAAAAAAA-GA
* *
3418 TGCAATCGGATAACATAAAGTTTCCCATTATTCGTA
130 TACAATCGGAAAACATAAAGTTTCCCATTATTCGTA
* * *
3454 GAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTTATAATTCGGTCTAAATTGAAATT
1 GAAATTTGCATGTTCATCAACGAAAACCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
* * *
3519 TT-ATAATTAATTTTTAAA-TA-A-TAAATTATAATAATGTCAATTTA-GAATATATTTGAAAAA
66 TTCA-AA-TAA---TAAAATTATACTAAATTATAATAATGGCAATTTATAAATATATTTGAAAAA
3579 AAGATACAATCGGAAAACATAAAGTTT
126 AAGATACAATCGGAAAACATAAAGTTT
3606 TATATTATTC
Statistics
Matches: 134, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
165 23 0.17
166 81 0.60
167 23 0.17
168 1 0.01
169 2 0.01
170 4 0.03
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (165 bp):
GAAATTTGCATGTTCATCAACGAAAACCAATTTGACAAACTTATAATTCGGTCTAAATTGAAATT
TTCAAATAATAAAATTATACTAAATTATAATAATGGCAATTTATAAATATATTTGAAAAAAAGAT
ACAATCGGAAAACATAAAGTTTCCCATTATTCGTA
Found at i:4481 original size:87 final size:87
Alignment explanation
Indices: 4335--4505 Score: 288
Period size: 87 Copynumber: 2.0 Consensus size: 87
4325 TTGCAAATCA
*
4335 AGAAATTAAGTCTATTGAGAGTTTTCTACTTCATATTAACCAGAACCCACTATGATTATTATTTT
1 AGAAATTAAGTATATTGAGAGTTTTCTACTTCATATTAACCAGAACCCACTATGATTATTATTTT
*
4400 TATATATTTACAAGTTAATCTT
66 CATATATTTACAAGTTAATCTT
* ***
4422 AGAAATTAAGTATATTGAGAGTTTTCTACTTCATATTAACCGGATTTCACTATGATTATTATTTT
1 AGAAATTAAGTATATTGAGAGTTTTCTACTTCATATTAACCAGAACCCACTATGATTATTATTTT
4487 CATATATTTACAAGTTAAT
66 CATATATTTACAAGTTAAT
4506 TTTATTCGAA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (87 bp):
AGAAATTAAGTATATTGAGAGTTTTCTACTTCATATTAACCAGAACCCACTATGATTATTATTTT
CATATATTTACAAGTTAATCTT
Found at i:5921 original size:41 final size:42
Alignment explanation
Indices: 5837--5922 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
5827 TCTAACTTGA
5837 CCCTCCTAATAATTAAGGAAATAAAAATAAATCCAGATTTAG
1 CCCTCCTAATAATTAAGGAAATAAAAATAAATCCAGATTTAG
* * *
5879 CCCTCCTAATAATTAAGGTAA-GAAATTAAATCCA-AGTTTAG
1 CCCTCCTAATAATTAAGGAAATAAAAATAAATCCAGA-TTTAG
5920 CCC
1 CCC
5923 CTAGTTATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 1 0.03
41 19 0.47
42 20 0.50
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (42 bp):
CCCTCCTAATAATTAAGGAAATAAAAATAAATCCAGATTTAG
Found at i:6614 original size:11 final size:11
Alignment explanation
Indices: 6571--6608 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6561 TTCCTATATA
*
6571 AAATAAATTAT
1 AAATTAATTAT
6582 CAAA-TAATTAT
1 -AAATTAATTAT
6593 AAATTAATTAT
1 AAATTAATTAT
6604 AAATT
1 AAATT
6609 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:6857 original size:16 final size:16
Alignment explanation
Indices: 6808--6860 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
6798 TTTCTCATAT
6808 TCTTCATATTTTCTTCG
1 TCTTCATATTTTCTT-G
* *
6825 TCTTCATATTCTATTG
1 TCTTCATATTTTCTTG
6841 TCTCTC-TATTTTCTTG
1 TCT-TCATATTTTCTTG
6857 TCTT
1 TCTT
6861 TTCCATACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 15 0.48
17 15 0.48
ACGTcount: A:0.11, C:0.23, G:0.06, T:0.60
Consensus pattern (16 bp):
TCTTCATATTTTCTTG
Found at i:9140 original size:13 final size:13
Alignment explanation
Indices: 9124--9165 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
9114 CATTAATCAC
9124 TATTATTATATTA
1 TATTATTATATTA
9137 TATTA-TATA-TA
1 TATTATTATATTA
9148 TATTATATATATATA
1 TATTAT-TATAT-TA
9163 TAT
1 TAT
9166 ATGATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.28
12 4 0.16
13 9 0.36
15 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:9147 original size:2 final size:2
Alignment explanation
Indices: 9130--9175 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
9120 TCACTATTAT
9130 TA TA T- TA TA T- TA TA TA TA TA T- TA TA TA TA TA TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
9170 TA TA TA
1 TA TA TA
9176 GTATGATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 3 0.08
2 35 0.88
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9175 original size:13 final size:11
Alignment explanation
Indices: 9127--9174 Score: 71
Period size: 11 Copynumber: 4.3 Consensus size: 11
9117 TAATCACTAT
9127 TATTATAT-TA
1 TATTATATATA
9137 TATTATATATA
1 TATTATATATA
9148 TATTATATATA
1 TATTATATATA
9159 TATATATATGATA
1 TAT-TATAT-ATA
9172 TAT
1 TAT
9175 AGTATGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.23
11 16 0.46
12 5 0.14
13 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TATTATATATA
Found at i:12365 original size:11 final size:12
Alignment explanation
Indices: 12344--12369 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12334 TCCGGATTTC
12344 TTTGTTTTTTTT
1 TTTGTTTTTTTT
12356 TTTGTTTTTTTT
1 TTTGTTTTTTTT
12368 TT
1 TT
12370 CAGTCGTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTGTTTTTTTT
Found at i:18987 original size:33 final size:33
Alignment explanation
Indices: 18945--19011 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
18935 AGATTGATGA
18945 AAAAGTTTGTATTTGACATGTGTAGAAGTGTAT
1 AAAAGTTTGTATTTGACATGTGTAGAAGTGTAT
18978 AAAAGTTTGTATTTGACATGTGTAGAAGTGTAT
1 AAAAGTTTGTATTTGACATGTGTAGAAGTGTAT
19011 A
1 A
19012 TGGTCTACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (33 bp):
AAAAGTTTGTATTTGACATGTGTAGAAGTGTAT
Found at i:23261 original size:44 final size:44
Alignment explanation
Indices: 23192--23279 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
23182 TGTCCTATGA
* * *
23192 TTCTGAGTAAACTAGGGCTCGTTAGAGAGAACCCTACGATCTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
*
23236 TTCTAAGTAAACTTGGGCTCATTAGAGAGAACCCAACGATCTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
23280 AAGAGTTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (44 bp):
TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
Found at i:25528 original size:10 final size:10
Alignment explanation
Indices: 25512--25560 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
25502 TTAGATTTTT
25512 TTAATTATTGA
1 TTAATTATT-A
25523 TT-ATTATTAA
1 TTAATTATT-A
*
25533 TTATTTAATTA
1 TTAATT-ATTA
25544 TTAATTATTA
1 TTAATTATTA
25554 TTAATTA
1 TTAATTA
25561 CATTTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 20 0.61
11 10 0.30
12 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TTAATTATTA
Found at i:25545 original size:25 final size:25
Alignment explanation
Indices: 25511--25560 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
25501 TTTAGATTTT
*
25511 TTTAATTATTGATTATTATTAATTA
1 TTTAATTATTAATTATTATTAATTA
25536 TTTAATTATTAATTATTATTAATTA
1 TTTAATTATTAATTATTATTAATTA
25561 CATTTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTAATTATTAATTATTATTAATTA
Found at i:27443 original size:20 final size:20
Alignment explanation
Indices: 27399--27445 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
27389 GACTAGTTTG
* *
27399 GTTT-ATTATCTTGGTTTTG
1 GTTTGATTATCTTGATTTTA
*
27418 GATTGATTATCTTGATTTTA
1 GTTTGATTATCTTGATTTTA
27438 GTTTGATT
1 GTTTGATT
27446 TATGATCCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.17, C:0.04, G:0.19, T:0.60
Consensus pattern (20 bp):
GTTTGATTATCTTGATTTTA
Found at i:27639 original size:13 final size:12
Alignment explanation
Indices: 27621--27667 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 12
27611 CTATTTTATT
27621 ATTGTTTTATTAA
1 ATTGTTTTA-TAA
27634 ATTGTTTTATAA
1 ATTGTTTTATAA
*
27646 ATGGTTTTAAATAA
1 ATTGTTTT--ATAA
27660 ATTGTTTT
1 ATTGTTTT
27668 GGGTGCATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 10 0.33
13 9 0.30
14 11 0.37
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (12 bp):
ATTGTTTTATAA
Found at i:29271 original size:18 final size:18
Alignment explanation
Indices: 29248--29287 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
29238 GCTCCGACAC
29248 ATCATCAGATCCGACAAA
1 ATCATCAGATCCGACAAA
29266 ATCATCAGATCCGACAAA
1 ATCATCAGATCCGACAAA
29284 ATCA
1 ATCA
29288 GGTTGCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (18 bp):
ATCATCAGATCCGACAAA
Found at i:29288 original size:15 final size:17
Alignment explanation
Indices: 29240--29284 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
29230 CCGGTGATGC
* *
29240 TCCGACACATCATCAGA
1 TCCGACAAAACATCAGA
29257 TCCGACAAAATCATCAGA
1 TCCGACAAAA-CATCAGA
29275 TCCGACAAAA
1 TCCGACAAAA
29285 TCAGGTTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.42, C:0.31, G:0.11, T:0.16
Consensus pattern (17 bp):
TCCGACAAAACATCAGA
Found at i:31356 original size:32 final size:33
Alignment explanation
Indices: 31320--31390 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
31310 GGACGACATG
* *
31320 CCATGGACGTGCCTCCCTGCTAGGACCGCATC-
1 CCATGGACGTGCCGCCCTGATAGGACCGCATCA
* * * *
31352 CCATGGGCTTGCCGCCCTGATAGGGCGGCATCA
1 CCATGGACGTGCCGCCCTGATAGGACCGCATCA
31385 CCATGG
1 CCATGG
31391 CGAGCTGTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 26 0.81
33 6 0.19
ACGTcount: A:0.15, C:0.37, G:0.30, T:0.18
Consensus pattern (33 bp):
CCATGGACGTGCCGCCCTGATAGGACCGCATCA
Found at i:31408 original size:32 final size:32
Alignment explanation
Indices: 31372--31445 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
31362 GCCGCCCTGA
31372 TAGGGCGGCATCACCATGGCGAGCTGTCCTCG
1 TAGGGCGGCATCACCATGGCGAGCTGTCCTCG
31404 TAGGGCGGCATCACCATGGCGAGCTGTCCTCG
1 TAGGGCGGCATCACCATGGCGAGCTGTCCTCG
*
31436 CAGGGCGGCA
1 TAGGGCGGCA
31446 CCGTCATATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.16
Consensus pattern (32 bp):
TAGGGCGGCATCACCATGGCGAGCTGTCCTCG
Found at i:34901 original size:44 final size:45
Alignment explanation
Indices: 34819--34925 Score: 198
Period size: 44 Copynumber: 2.4 Consensus size: 45
34809 AACCATCTTT
*
34819 ATAAGACTATAATCATTCTTTTTTCCTTTTTTTTGTTTTTTAAAA
1 ATAAGACTATAATCATTCTTTTTTCCTTCTTTTTGTTTTTTAAAA
34864 ATAAGACTATAATCATTCTTTTTTCC-TCTTTTTGTTTTTTAAAA
1 ATAAGACTATAATCATTCTTTTTTCCTTCTTTTTGTTTTTTAAAA
34908 ATAAGACTATAATCATTC
1 ATAAGACTATAATCATTC
34926 AATTTTAACA
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
44 35 0.57
45 26 0.43
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (45 bp):
ATAAGACTATAATCATTCTTTTTTCCTTCTTTTTGTTTTTTAAAA
Found at i:35012 original size:103 final size:105
Alignment explanation
Indices: 34905--35117 Score: 385
Period size: 103 Copynumber: 2.0 Consensus size: 105
34895 TTGTTTTTTA
34905 AAAATAAGACTATAATCATTCAATTTTAACATGAAATGTATAATAATGCA-TTTTTTT-AAAAAA
1 AAAATAAGACTATAATCATTCAATTTTAACATGAAATGTATAATAATGCATTTTTTTTAAAAAAA
34968 AATCAATATTGCAGATAAATTTACTTTTAAAACCACAATT
66 AATCAATATTGCAGATAAATTTACTTTTAAAACCACAATT
35008 AAAATAAGACTATAATCATTCAATTTTAACATGAAATGTATAATAATGCATTTTTTTTAAAAAAA
1 AAAATAAGACTATAATCATTCAATTTTAACATGAAATGTATAATAATGCATTTTTTTT---AAAA
35073 AAAAATCAATATTGCAGATAAATTTACTTTTAAAACCACAATT
63 AAAAATCAATATTGCAGATAAATTTACTTTTAAAACCACAATT
35116 AA
1 AA
35118 TTGTGTTCAC
Statistics
Matches: 105, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
103 50 0.48
104 7 0.07
108 48 0.46
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (105 bp):
AAAATAAGACTATAATCATTCAATTTTAACATGAAATGTATAATAATGCATTTTTTTTAAAAAAA
AATCAATATTGCAGATAAATTTACTTTTAAAACCACAATT
Found at i:36805 original size:11 final size:11
Alignment explanation
Indices: 36786--36815 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
36776 GAGGTTAGGG
*
36786 CCTTCTGCGGA
1 CCTTTTGCGGA
36797 CCTTTTGCGGA
1 CCTTTTGCGGA
36808 CCTTTTGC
1 CCTTTTGC
36816 CTCAACTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.33, G:0.23, T:0.37
Consensus pattern (11 bp):
CCTTTTGCGGA
Found at i:42266 original size:53 final size:53
Alignment explanation
Indices: 42196--42333 Score: 181
Period size: 53 Copynumber: 2.6 Consensus size: 53
42186 TAATAGGGTA
* * * *
42196 GAAAGACTTTCCCTAGTTTGGTTGAATTAAAACATGT-GAGAAAGT-AAATGATG
1 GAAACACTTTCCATAGTTTGGTTAAAATAAAACATGTAGA-AAAGTAAAAT-ATG
* *
42249 GAAACACTTTCTATAGTTTCGTTAAAATAAAACATGTAGAAAAGTAAAATATG
1 GAAACACTTTCCATAGTTTGGTTAAAATAAAACATGTAGAAAAGTAAAATATG
*
42302 GAAACACTTTCCACAGTTTGGTTAAAATAAAA
1 GAAACACTTTCCATAGTTTGGTTAAAATAAAA
42334 AAAAAGGTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 68 0.92
54 6 0.08
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (53 bp):
GAAACACTTTCCATAGTTTGGTTAAAATAAAACATGTAGAAAAGTAAAATATG
Found at i:47524 original size:23 final size:24
Alignment explanation
Indices: 47483--47533 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
47473 AACCTAATTG
**
47483 AAATCCCCAATTTTTAAAA-CCCA
1 AAATCCCCAATTTCAAAAAGCCCA
*
47506 AAATCCCCAATTTCAAAAAGCCTA
1 AAATCCCCAATTTCAAAAAGCCCA
47530 AAAT
1 AAAT
47534 ATTAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATCCCCAATTTCAAAAAGCCCA
Found at i:47655 original size:33 final size:35
Alignment explanation
Indices: 47587--47656 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 35
47577 TTGCAAGCAA
* *
47587 AAATCAGAAGAAAATGGAAGCAAACAAAATCAAAG
1 AAATCAGAAGAAAATGAAAGCAAACAAAATAAAAG
* *
47622 AAATCAGAA-AAAAT-AAATCAAAGAAAATAAAAG
1 AAATCAGAAGAAAATGAAAGCAAACAAAATAAAAG
47655 AA
1 AA
47657 CTCATCGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 17 0.55
34 5 0.16
35 9 0.29
ACGTcount: A:0.69, C:0.09, G:0.13, T:0.10
Consensus pattern (35 bp):
AAATCAGAAGAAAATGAAAGCAAACAAAATAAAAG
Found at i:53736 original size:125 final size:125
Alignment explanation
Indices: 53513--54319 Score: 753
Period size: 125 Copynumber: 6.5 Consensus size: 125
53503 ATATATATAT
* * * * * *
53513 TATACTGACGTTTGTAAATGTCGGAACAA-TCTTTTCACATCATTTGATTTCGACGTATTCTGAC
1 TATACCGACGATTATAAATGTCGGAACAAGT-TCTTCACATCATTTGATTTCGACATATTCCGAC
* * * * * * *
53577 ATTTGTAAGCGTTGGTTTTGATATTATATTGTGACAATTATTAAATGTCGCCACAAAATAC
65 ATTTATAAGCGTTGGTATAGATATTATATCGTGACAATTATTAAACGTCGCTATAAAATAC
** * * * * * * **
53638 TATACCGACCCTTTTAATTGTCGGAACAATTTTTTCACATCATTTAATTTTGATGTATTCCGACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
* * * * * *
53703 TTTGTAAGCATTGGTATAGATATTATATCGTGACCATTATTAACCATCGCTACAAAATAC
66 TTTATAAGCGTTGGTATAGATATTATATCGTGACAATTATTAAACGTCGCTATAAAATAC
* ** * * * * *
53763 AATACCGACCCTTGTAAATGTCGGAACAAGTTGTTCACGTCATTTGATTTCGACGTATTCCAACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
*** * * * *
53828 TTTATAATTTTTGGTATAGATATTATATCGTGACAGTTATTAAACGTTGCTATAGAACAC
66 TTTATAAGCGTTGGTATAGATATTATATCGTGACAATTATTAAACGTCGCTATAAAATAC
* * * * * *
53888 TACACCGACAATTACAAATGTCAGAACAAGTTCTTCACATCATTTAATTTTGACATATTCCGACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
* * * * * * *
53953 TCTATAAGCGTTGGTATAAATATTATATTGTGACATTTATTACACGTCACTATAAAA-AA
66 TTTATAAGCGTTGGTATAGATATTATATCGTGACAATTATTAAACGTCGCTATAAAATAC
* * * *
54012 TATACCGACGATTACAATTGTCGGAACAAGTTCTTCACATCATTTCAGTTCGACATATTCCGACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
* * * *
54077 TCTATACA-CGTTGGTATAGATATTATATCATGAC-ATTGATTAAACGTCACTATAAAAAAAC
66 TTTATA-AGCGTTGGTATAGATATTATATCGTGACAATT-ATTAAACGTCGCTAT-AAAATAC
** * * * * *
54138 -ATACCGACGATTATAAATGTCTAAACAAGTTGTACACATTATTTGAGTTCGATATATTCCGACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
* * * * **
54202 TCTT-TAAGCGTTGATATAAATATTATATCGTGATATTTATTAAAAATCGCTATAAAATAC
66 T-TTATAAGCGTTGGTATAGATATTATATCGTGACAATTATTAAACGTCGCTATAAAATAC
* * ** * * * *
54262 TATACCGATGCTTATAAATGTCGGAACACTTTATTCGCATCAATGGATTTCGACATAT
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATAT
54320 GTAAGCATTG
Statistics
Matches: 562, Mismatches: 111, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
123 2 0.00
124 109 0.19
125 446 0.79
126 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (125 bp):
TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
TTTATAAGCGTTGGTATAGATATTATATCGTGACAATTATTAAACGTCGCTATAAAATAC
Found at i:54227 original size:374 final size:375
Alignment explanation
Indices: 53528--54245 Score: 836
Period size: 374 Copynumber: 1.9 Consensus size: 375
53518 TGACGTTTGT
* * * * * * *
53528 AAATGTCGGAACAATCTTTTCACATCATTTGATTTCGACGTATTCTGACATTTGTAAGCGTTGGT
1 AAATGTCAGAACAATCTCTTCACATCATTTAATTTCGACATATTCCGACATCTATAAGCGTTGGT
* ** * * * * **
53593 TTTGATATTATATTGTGACAATTATTAAATGTCGCCACAAAATACTATACCGACCCTTTTAATTG
66 ATAAATATTATATTGTGACAATTATTAAACGTCACCACAAAATAATATACCGACCATTACAATTG
* * * * ** * *
53658 TCGGAACAATTTTTTCACATCATTTAATTTTGATGTATTCCGACATTTGTAAGCATTGGTATAGA
131 TCGGAACAAGTTCTTCACATCATTTAAGTTCGACATATTCCGACATCTATAAGCATTGGTATAGA
* * * * * * * *
53723 TATTATATCGTGACCATTATTAACCATCGCTACAAAATACAATACCGACCCTTGTAAATGTCGGA
196 TATTATATCATGACCATTATTAAACATCACTAAAAAAAACAATACCGACCATTATAAATGTCGAA
* * * * *** * *
53788 ACAAGTTGTTCACGTCATTTGATTTCGACGTATTCCAACATTTATAATTTTTGGTATAGATATTA
261 ACAAGTTGTACACATCATTTGAGTTCGACATATTCCAACATTTATAAGCGTTGATATAAATATTA
53853 TATCGTGACAGTTATTAAACGTTGCTATAGAACACTACACCGACAATTAC
326 TATCGTGACAGTTATTAAACGTTGCTATAGAACACTACACCGACAATTAC
*
53903 AAATGTCAGAACAAGT-TCTTCACATCATTTAATTTTGACATATTCCGACATCTATAAGCGTTGG
1 AAATGTCAGAACAA-TCTCTTCACATCATTTAATTTCGACATATTCCGACATCTATAAGCGTTGG
* * * * *
53967 TATAAATATTATATTGTGACATTTATTACACGTCACTATAAAA-AATATACCGACGATTACAATT
65 TATAAATATTATATTGTGACAATTATTAAACGTCACCACAAAATAATATACCGACCATTACAATT
* *
54031 GTCGGAACAAGTTCTTCACATCATTTCAGTTCGACATATTCCGACATCTATACA-CGTTGGTATA
130 GTCGGAACAAGTTCTTCACATCATTTAAGTTCGACATATTCCGACATCTATA-AGCATTGGTATA
* *
54095 GATATTATATCATGA-CATTGATTAAACGTCACTATAAAAAAAC-ATACCGACGATTATAAATGT
194 GATATTATATCATGACCATT-ATTAAACATCACTA-AAAAAAACAATACCGACCATTATAAATGT
* * * *
54158 CTAAACAAGTTGTACACATTATTTGAGTTCGATATATTCCGACATCTT-TAAGCGTTGATATAAA
257 CGAAACAAGTTGTACACATCATTTGAGTTCGACATATTCCAACAT-TTATAAGCGTTGATATAAA
* *
54222 TATTATATCGTGATATTTATTAAA
321 TATTATATCGTGACAGTTATTAAA
54246 AATCGCTATA
Statistics
Matches: 281, Mismatches: 57, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
373 4 0.01
374 179 0.64
375 97 0.35
376 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (375 bp):
AAATGTCAGAACAATCTCTTCACATCATTTAATTTCGACATATTCCGACATCTATAAGCGTTGGT
ATAAATATTATATTGTGACAATTATTAAACGTCACCACAAAATAATATACCGACCATTACAATTG
TCGGAACAAGTTCTTCACATCATTTAAGTTCGACATATTCCGACATCTATAAGCATTGGTATAGA
TATTATATCATGACCATTATTAAACATCACTAAAAAAAACAATACCGACCATTATAAATGTCGAA
ACAAGTTGTACACATCATTTGAGTTCGACATATTCCAACATTTATAAGCGTTGATATAAATATTA
TATCGTGACAGTTATTAAACGTTGCTATAGAACACTACACCGACAATTAC
Found at i:54503 original size:14 final size:14
Alignment explanation
Indices: 54484--54512 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54474 AATACTAATA
54484 ATTAGAAATTCATT
1 ATTAGAAATTCATT
54498 ATTAGAAATTCATT
1 ATTAGAAATTCATT
54512 A
1 A
54513 CTAATAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATTAGAAATTCATT
Found at i:55852 original size:16 final size:16
Alignment explanation
Indices: 55831--55877 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
55821 CTATCTTTTC
*
55831 TATTTTCTTTTTCTTT
1 TATTTTCTTTTTCCTT
55847 TATTTT-TTTTTCCTT
1 TATTTTCTTTTTCCTT
55862 T-TTTTCCTATTTTCCT
1 TATTTT-CT-TTTTCCT
55878 CTTCTCCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 7 0.26
17 7 0.26
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTCTTTTTCCTT
Found at i:56987 original size:103 final size:102
Alignment explanation
Indices: 56807--57009 Score: 307
Period size: 103 Copynumber: 2.0 Consensus size: 102
56797 TTGGGTTTCA
* * *
56807 ATTTTGAATGTTCTTAGTGTTCTTATGAGCTCATGAGAAAGAGGCGCTTTGCTCTTAATTTGGGA
1 ATTTTGAATGTTCTTAGTGTTCTTATGAGCTCATGAGAAACAGGCGCTTTGATCTTAATTTAGGA
56872 TGAATTTCTGGAAAATTTTGTGTTTTTGGTTGGGTGAG
66 TGAATTTCTGGAAAA-TTTGTGTTTTTGGTTGGGTGAG
* * * * *
56910 ATTTTGAATGTTCTTGGTGTTCTTATGAGTTCATGAGAAACAGGGGTTTTGATCTTATTTTAGGA
1 ATTTTGAATGTTCTTAGTGTTCTTATGAGCTCATGAGAAACAGGCGCTTTGATCTTAATTTAGGA
* *
56975 TGAATTTGTGGAAAATTTGTGTTTTTGTTTGGGTG
66 TGAATTTCTGGAAAATTTGTGTTTTTGGTTGGGTG
57010 TGACTGAGAA
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
102 19 0.21
103 71 0.79
ACGTcount: A:0.21, C:0.07, G:0.27, T:0.45
Consensus pattern (102 bp):
ATTTTGAATGTTCTTAGTGTTCTTATGAGCTCATGAGAAACAGGCGCTTTGATCTTAATTTAGGA
TGAATTTCTGGAAAATTTGTGTTTTTGGTTGGGTGAG
Found at i:57227 original size:30 final size:31
Alignment explanation
Indices: 57165--57236 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
57155 TTGCAATTTC
*
57165 TCCTGAATTGACACAAGCCGATAACGTCGTA
1 TCCTGAATTGACACAAGACGATAACGTCGTA
* *
57196 TCCTGAATTGACACAA-ATGGTAACGGT-GTA
1 TCCTGAATTGACACAAGACGATAAC-GTCGTA
*
57226 TCCTAAATTGA
1 TCCTGAATTGA
57237 ATGTCGCGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
TCCTGAATTGACACAAGACGATAACGTCGTA
Found at i:61630 original size:24 final size:24
Alignment explanation
Indices: 61580--61632 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
61570 CTTTTTTTTC
* **
61580 TCAATAGAATATATTCCTTTCTTT
1 TCAATAGAATATATTCCCTTCAAT
*
61604 TCAATAGAATATATTCCCTTGAAT
1 TCAATAGAATATATTCCCTTCAAT
61628 TCAAT
1 TCAAT
61633 GTCATTGTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (24 bp):
TCAATAGAATATATTCCCTTCAAT
Found at i:61655 original size:3 final size:3
Alignment explanation
Indices: 61647--61675 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
61637 TTGTCTGACA
61647 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
61676 TATATTCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:61709 original size:63 final size:62
Alignment explanation
Indices: 61609--61728 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 62
61599 TCTTTTCAAT
* * *
61609 AGAATATATTCCCTTGAATTCAATGTCATTGTCTGACAAAGAAGAAGAAGAAGAAGAAGAAGA
1 AGAATATATTCCCTTGAATTCAATGTCATTGTATGACAAA-AAAAACAAGAAGAAGAAGAAGA
** *
61672 AGAATATATTCGTTTGAATAT-AATGTCATTGTATGACAAAAAAAACAAGCAGAAGAA
1 AGAATATATTCCCTTGAAT-TCAATGTCATTGTATGACAAAAAAAACAAGAAGAAGAA
61729 TATAATGTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
62 14 0.28
63 35 0.70
64 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.24
Consensus pattern (62 bp):
AGAATATATTCCCTTGAATTCAATGTCATTGTATGACAAAAAAAACAAGAAGAAGAAGAAGA
Found at i:63329 original size:35 final size:35
Alignment explanation
Indices: 63253--63384 Score: 146
Period size: 37 Copynumber: 3.8 Consensus size: 35
63243 GTTATTTAAG
* *
63253 CTACTAGTATTCTCATGTTTA--TG-TTTAGTT-A
1 CTACTAGTATTCTCATGTTTAGTTGTTTTAATTGT
** * *
63284 AAACTAGTATTATCATGTTTAGTTATTTTAATTGT
1 CTACTAGTATTCTCATGTTTAGTTGTTTTAATTGT
63319 CTACTAGTATTTTCTCATGTTTAGTTGTTTTAATTGT
1 CTACTAGTA--TTCTCATGTTTAGTTGTTTTAATTGT
* *
63356 GTACTACTATTCTCATGTTTAGTTGTTTT
1 CTACTAGTATTCTCATGTTTAGTTGTTTT
63385 TATAATTTAT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
31 18 0.22
33 1 0.01
34 6 0.07
35 27 0.33
37 31 0.37
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.54
Consensus pattern (35 bp):
CTACTAGTATTCTCATGTTTAGTTGTTTTAATTGT
Found at i:66135 original size:11 final size:10
Alignment explanation
Indices: 66117--66150 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
66107 AATTGTCTTC
66117 AAATCTTCAA
1 AAATCTTCAA
66127 AATATCTTCAA
1 AA-ATCTTCAA
66138 GAAATCTTCAA
1 -AAATCTTCAA
66149 AA
1 AA
66151 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:66997 original size:18 final size:19
Alignment explanation
Indices: 66945--67002 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
66935 GAGAAAGAAA
*
66945 GGAAGAAAGA-AACAAAGAC
1 GGAAGAAGGAGAA-AAAGAC
* * *
66964 AGAAGAAGAAGGAAAA-AC
1 GGAAGAAGGAGAAAAAGAC
66982 GGAAGAAGGAGAAAAAGAC
1 GGAAGAAGGAGAAAAAGAC
67001 GG
1 GG
67003 TCAATTAACA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 15 0.50
19 14 0.47
20 1 0.03
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (19 bp):
GGAAGAAGGAGAAAAAGAC
Found at i:67231 original size:25 final size:25
Alignment explanation
Indices: 67203--67256 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
67193 GTTTAGGTGA
* *
67203 AGGGGGTCTACCTCAGTATAGGGTC
1 AGGGAGTCTACCTCAGTACAGGGTC
67228 AGGGAGTCTACCTCAGTACAGGGTC
1 AGGGAGTCTACCTCAGTACAGGGTC
67253 AGGG
1 AGGG
67257 TATACAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.20
Consensus pattern (25 bp):
AGGGAGTCTACCTCAGTACAGGGTC
Found at i:68603 original size:2 final size:2
Alignment explanation
Indices: 68596--68627 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
68586 GACCCACTCA
68596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68628 GATCGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71360 original size:323 final size:320
Alignment explanation
Indices: 70727--71369 Score: 1090
Period size: 323 Copynumber: 2.0 Consensus size: 320
70717 TTCTGCAATG
* * *
70727 CGATGACATTTTGATGAAAGAACTGAAGATGAGGTTTTATGGCATCCTGCTGATGCCCAAGCGTG
1 CGATGACATTTTGATGAAAGAACTGAAGATGAGGTTTTACGGCATCCTGCTAATGCCCAAGCATG
* *
70792 GAAAGAATTTGATTCTTTGCATAAGGATTTCACAAAAGATCCTCGTAATGTTTGACTTGGATTAG
66 GAAAGAATTTGATTCTTTGCATAAGGATTTCACAAAAGATCCTCGGAATGTTCGACTTGGATTAG
*
70857 CTAGTGATGGTTTTAATCCTTTTCGAAATATGAACGTTGCGCATAGTACATGGCCTGTGATTCTA
131 CTAGTGATGGATTTAATCCTTTTCGAAATATGAACGTTGCGCATAGTACATGGCCTGTGATTCTA
*
70922 ACTGTGTACAACTTTCCCCCTTGGATGTGCATGAAACAATCTTCTTTTATATTGTCCTTGCTTAT
196 ACTGTGTACAACTTTCCCCCTTGGATGTGCATGAAACAACCTTCTTTTATATTGTCCTTGCTTAT
*
70987 TTCTGGTCCTGAGTCCCCAACAGATAAAATTGATGTATTGTTGCAACCTTTGATCGATGA
261 TTCTGGTCCTAAGTCCCCAACAGATAAAATTGATGTATTGTTGCAACCTTTGATCGATGA
* *
71047 CGATGGCATTTTGATGAAAGAACTGAAGATCATGGGGTTTTACGGCATCCTGCTAATGCCCAAGC
1 CGATGACATTTTGATGAAAGAACTGAAG---ATGAGGTTTTACGGCATCCTGCTAATGCCCAAGC
* * *
71112 ATGGAAAGAGTTTGATTCTTTGCATAAGGATTTCTCAAAAGATTCTCGGAATGTTCGACTTGGAT
63 ATGGAAAGAATTTGATTCTTTGCATAAGGATTTCACAAAAGATCCTCGGAATGTTCGACTTGGAT
*
71177 TAGCTAGTGATGGATTTAATCCTTTTCGAAATATGAACGTTGTGCATAGTACATGGCCTGTGATT
128 TAGCTAGTGATGGATTTAATCCTTTTCGAAATATGAACGTTGCGCATAGTACATGGCCTGTGATT
71242 CTAACTGTGTACAACTTTCCCCCTTGGATGTGCATGAAACAACCTTCTTTTATATTGTCCTTGCT
193 CTAACTGTGTACAACTTTCCCCCTTGGATGTGCATGAAACAACCTTCTTTTATATTGTCCTTGCT
* * *
71307 TATTTCTGGT-CTAAAGTCCCCAAGAGATAAAATTGATGTGTTGTTGTAACCTTTGATCGATGA
258 TATTTCTGGTCCT-AAGTCCCCAACAGATAAAATTGATGTATTGTTGCAACCTTTGATCGATGA
71370 ATTGAAAGAT
Statistics
Matches: 302, Mismatches: 17, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
320 27 0.09
322 2 0.01
323 273 0.90
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (320 bp):
CGATGACATTTTGATGAAAGAACTGAAGATGAGGTTTTACGGCATCCTGCTAATGCCCAAGCATG
GAAAGAATTTGATTCTTTGCATAAGGATTTCACAAAAGATCCTCGGAATGTTCGACTTGGATTAG
CTAGTGATGGATTTAATCCTTTTCGAAATATGAACGTTGCGCATAGTACATGGCCTGTGATTCTA
ACTGTGTACAACTTTCCCCCTTGGATGTGCATGAAACAACCTTCTTTTATATTGTCCTTGCTTAT
TTCTGGTCCTAAGTCCCCAACAGATAAAATTGATGTATTGTTGCAACCTTTGATCGATGA
Found at i:74625 original size:214 final size:213
Alignment explanation
Indices: 73997--74970 Score: 1019
Period size: 214 Copynumber: 4.5 Consensus size: 213
73987 TTGCATTATT
* * * * **
73997 TTAAAACGACGTTT-TATAACAACGTTGTTATAAATGTTGGAAAAGTCTATCTTTAAGCGATGTT
1 TTAAAACGACGTTTCTA-AA-AACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCAACATT
* * * * * * * *
74061 TGTTGATAAATGTCGCATGATTGAACGGCATTTGCGATACACGTCGCTACAAACGTTGCAAAAGC
64 TGTTGATAAATGTCGCATGATTGAACGACATTGGAGA-AAACGTCTCTGCAAACATCGCAAAAGC
* * ** * ** * *
74126 ATAAAGTAA-AGCGATGTTATTAAAAAATGTCACTCAAACTAAAAAAGAGTCGCAAGGT-ATTGT
128 ATAAA-CAAGAGCGACGCAATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGTGA-TGC
* *
74189 GACATTTATTAAAATGTCATATT
191 GACGTTTATTAAAATGTCATATA
* *
74212 TTAAAACGACGTTT-TATAACAACGTTGTTATAAATGTTGGCAAAA-TCTATCTTAAAGCAACAT
1 TTAAAACGACGTTTCTA-AA-AACGTTGCTATAAATGTCGG-AAAAGTCTATCTTAAAGCAACAT
* * * * *
74275 TTGTTGATAAATGTCGCATGATTGAACAACGTTTGAGAAAAACGTCTCTACAAACATCGCAAAAA
63 TTGTTGATAAATGTCGCATGATTGAACGACATTGGAG-AAAACGTCTCTGCAAACATCGCAAAAG
* * ** * ** *
74340 CATAAACTAGAGCGATGTTATTAAAAAACGTCATTTTATTTTAAAAAGTGTCGCAAGGTGATGCG
127 CATAAACAAGAGCGACGCAATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGTGATGCG
74405 ACGTTTATTAAAATGTCATATA
192 ACGTTTATTAAAATGTCATATA
* * * *
74427 TTAAAACGACGTTTCTGAAAAATGTTGCTATAAAAGTCGGAAAATTCTATCTTAAAGCAACGTTT
1 TTAAAACGACGTTTCT-AAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCAACATTT
* * * *
74492 GTTAAAAAATGTCGCATGATTGAATGACATTGGAGAAAACGTCTCTGCAAACATCGCAAAAGTAT
65 GTTGATAAATGTCGCATGATTGAACGACATTGGAGAAAACGTCTCTGCAAACATCGCAAAAGCAT
* * * * *
74557 AAACAAGAGTGACGCAATTAAAAAACGTCAATTAATTTTAAAAAGTGTCGCAATGTGATGCGACG
130 AAACAAGAGCGACGCAATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGTGATGCGACG
74622 TTTATTAAAATGTCATATA
195 TTTATTAAAATGTCATATA
** * * *
74641 TTAAAACGACGTTTCTGAAAAATATTGCTATAAATGTCGGAAAATTCTATCTTAAAGCATCATTC
1 TTAAAACGACGTTTCT-AAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCAACATTT
* * * * *
74706 GTTAAAAAATGTCACATGATTGAACGACATTGGAGAAAACGTCTCTGCAAACATCTCAAAAGTAT
65 GTTGATAAATGTCGCATGATTGAACGACATTGGAGAAAACGTCTCTGCAAACATCGCAAAAGCAT
* * * * * ** * *
74771 AAACAAGAGTGACGCAATTAAAAAACGTCACTCAGTTTTAAAAAAGAGTTGTAAGATTTTGTGAG
130 AAACAAGAGCGACGCAATTAAAAAACGTCACTCAATTTT-AAAAAGAGTCGCAAGGTGATGCGAC
* *
74836 GTTTATTAAAACGTCATTTA
194 GTTTATTAAAATGTCATATA
* * *
74856 TT-AAACAATGTTTCCCT-AAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACATT
1 TTAAAACGACGTTT--CTAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCAACATT
* * * * *
74919 TG-TGATAAATATCGCATAATTGAACGACATTAGACAAAAATGTCTCTGCAAA
64 TGTTGATAAATGTCGCATGATTGAACGACATTGGA-GAAAACGTCTCTGCAAA
74971 TGTCGTAAAA
Statistics
Matches: 662, Mismatches: 86, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
213 26 0.04
214 332 0.50
215 292 0.44
216 11 0.02
217 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (213 bp):
TTAAAACGACGTTTCTAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCAACATTTG
TTGATAAATGTCGCATGATTGAACGACATTGGAGAAAACGTCTCTGCAAACATCGCAAAAGCATA
AACAAGAGCGACGCAATTAAAAAACGTCACTCAATTTTAAAAAGAGTCGCAAGGTGATGCGACGT
TTATTAAAATGTCATATA
Found at i:74842 original size:429 final size:428
Alignment explanation
Indices: 73997--74970 Score: 1052
Period size: 429 Copynumber: 2.3 Consensus size: 428
73987 TTGCATTATT
* * * *
73997 TTAAAACGACGTTT-TATAACAACGTTGTTATAAATGTTGGAAAAGTCTATCTTTAAGCGATGTT
1 TTAAAACGACGTTTCTA-AA-AACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTT
* * * * * * * *
74061 TGTTGATAAATGTCGCATGATTGAACGGCATTTGCGATACACGTCGCTACAAACGTTGCAAAAGC
64 TGTTGATAAATGTCGCATGATTGAACGACATTAGAGA-AAACGTCTCTGCAAACATCGCAAAAGC
* * ** * * *
74126 ATAAAGTAAAGCGATGTTATTAAAAAATGTCACTCAAACTAAAAAAGAGTCGCAAGGTATTGTGA
128 ATAAAGCAAAGCGACGCAATTAAAAAACGTCAATCAAACTAAAAAAGAGTCGCAAGGTATTGCGA
* * * *
74191 CATTTATTAAAATGTCATATTTTAAAACGACGTTTTATAACAACGTTGTTATAAATGTTGGCAAA
193 CATTTATTAAAATGTCATATATTAAAACGACGTTTTATAACAACATTGCTATAAATGTCGGCAAA
* * * * * *
74256 ATCTATCTTAAAGCAACATTTGTTGATAAATGTCGCATGATTGAACAACGTTTGAGAAAAACGTC
258 ATCTATCTTAAAGCAACATTCGTTAAAAAATGTCACATGATTGAACAACATTGGAGAAAAACGTC
* * ** * *
74321 TCTACAAACATCGCAAAAACATAAACTAGAGCGATGTTATTAAAAAACGTCATTTTATTTTAAAA
323 TCTACAAACATCGCAAAAACATAAACAAGAGCGACGCAATTAAAAAACGTCATCTCATTTTAAAA
* * *
74386 AGTGTCGCAAGGTGATGCGACGTTTATTAAAATGTCATATA
388 AGAGTCGCAAGATGATGCGACGTTTATTAAAACGTCATATA
* * * *
74427 TTAAAACGACGTTTCTGAAAAATGTTGCTATAAAAGTCGGAAAATTCTATCTTAAAGCAACGTTT
1 TTAAAACGACGTTTCT-AAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTT
* * * * *
74492 GTTAAAAAATGTCGCATGATTGAATGACATTGGAGAAAACGTCTCTGCAAACATCGCAAAAGTAT
65 GTTGATAAATGTCGCATGATTGAACGACATTAGAGAAAACGTCTCTGCAAACATCGCAAAAGCAT
* * ** * * *
74557 AAA-CAAGAGTGACGCAATTAAAAAACGTCAATTAATTTTAAAAAGTGTCGCAATGTGA-TGCGA
130 AAAGCAA-AGCGACGCAATTAAAAAACGTCAATCAAACTAAAAAAGAGTCGCAAGGT-ATTGCGA
* *
74620 CGTTTATTAAAATGTCATATATTAAAACGACGTTTCTGA-AA-AATATTGCTATAAATGTCGG-A
193 CATTTATTAAAATGTCATATATTAAAACGACGTTT-T-ATAACAACATTGCTATAAATGTCGGCA
* *
74682 AAATTCTATCTTAAAGCATCATTCGTTAAAAAATGTCACATGATTGAACGACATTGGAG-AAAAC
256 AAA-TCTATCTTAAAGCAACATTCGTTAAAAAATGTCACATGATTGAACAACATTGGAGAAAAAC
* * ** *
74746 GTCTCTGCAAACATCTCAAAAGTATAAACAAGAGTGACGCAATTAAAAAACGTCA-CTCAGTTTT
320 GTCTCTACAAACATCGCAAAAACATAAACAAGAGCGACGCAATTAAAAAACGTCATCTCA-TTTT
* * ** * * *
74810 AAAAAAGAGTTGTAAGATTTTGTGAGGTTTATTAAAACGTCATTTA
384 -AAAAAGAGTCGCAAGATGATGCGACGTTTATTAAAACGTCATATA
* * *
74856 TT-AAACAATGTTTCCCT-AAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACATT
1 TTAAAACGACGTTT--CTAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTT
* * * *
74919 TG-TGATAAATATCGCATAATTGAACGACATTAGACAAAAATGTCTCTGCAAA
64 TGTTGATAAATGTCGCATGATTGAACGACATTAGA-GAAAACGTCTCTGCAAA
74971 TGTCGTAAAA
Statistics
Matches: 448, Mismatches: 84, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
427 28 0.06
428 128 0.29
429 200 0.45
430 87 0.19
431 4 0.01
432 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (428 bp):
TTAAAACGACGTTTCTAAAAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCGACGTTTG
TTGATAAATGTCGCATGATTGAACGACATTAGAGAAAACGTCTCTGCAAACATCGCAAAAGCATA
AAGCAAAGCGACGCAATTAAAAAACGTCAATCAAACTAAAAAAGAGTCGCAAGGTATTGCGACAT
TTATTAAAATGTCATATATTAAAACGACGTTTTATAACAACATTGCTATAAATGTCGGCAAAATC
TATCTTAAAGCAACATTCGTTAAAAAATGTCACATGATTGAACAACATTGGAGAAAAACGTCTCT
ACAAACATCGCAAAAACATAAACAAGAGCGACGCAATTAAAAAACGTCATCTCATTTTAAAAAGA
GTCGCAAGATGATGCGACGTTTATTAAAACGTCATATA
Found at i:75962 original size:11 final size:11
Alignment explanation
Indices: 75946--75972 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
75936 TTTATCATTT
75946 TTACTCTTTTC
1 TTACTCTTTTC
75957 TTACTCTTTTC
1 TTACTCTTTTC
75968 TTACT
1 TTACT
75973 TTCTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (11 bp):
TTACTCTTTTC
Found at i:76080 original size:22 final size:21
Alignment explanation
Indices: 76052--76275 Score: 151
Period size: 21 Copynumber: 10.8 Consensus size: 21
76042 ACTGATCACC
76052 TTTTACTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* * *
76074 TTTTACTCTGACTAATTACCA
1 TTTTACTCTTACTGATTACTA
* *
76095 TTTTGCTCATACTGATTACTA
1 TTTTACTCTTACTGATTACTA
76116 TTTTACTCTTACTGATTAC--
1 TTTTACTCTTACTGATTACTA
* *
76135 -----CTTTTACTGATTACTG
1 TTTTACTCTTACTGATTACTA
* *
76151 TCTTACTCTTTACTGATTACCT-
1 TTTTACT-CTTACTGATTA-CTA
* *
76173 TCTTACTTTTTACTGATTACTA
1 TTTTAC-TCTTACTGATTACTA
*
76195 TTTTACTCTTTACTGATTACCA
1 TTTTACTC-TTACTGATTACTA
* * *
76217 TTTTGCCCTCACTGATTA-TCA
1 TTTTACTCTTACTGATTACT-A
* * *
76238 TTTTGCTCTTACTAACTACTA
1 TTTTACTCTTACTGATTACTA
*
76259 TTTTACCTTTTACTGAT
1 TTTTA-CTCTTACTGAT
76276 CATCATTATT
Statistics
Matches: 161, Mismatches: 26, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
14 13 0.08
21 77 0.48
22 68 0.42
23 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:76109 original size:42 final size:41
Alignment explanation
Indices: 76040--76250 Score: 179
Period size: 42 Copynumber: 5.1 Consensus size: 41
76030 ACTCTTTGAA
* *
76040 TTACTGATCACC-TTTTACTCTTTACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTGCTC--TACTGATTACTATTTTACTC
* *
76082 TGACTAATTACCATTTTGCTCATACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTGCTC-TACTGATTACTATTTTACTC
* *
76124 TTACTGATTACC---TT--T-TACTGATTACTGTCTTACTC
1 TTACTGATTACCATTTTGCTCTACTGATTACTATTTTACTC
* *
76159 TTTACTGATTACC-TTCTTACTTTTTACTGATTACTATTTTACTC
1 -TTACTGATTACCATT-TTGC--TCTACTGATTACTATTTTACTC
* *
76203 TTTACTGATTACCATTTTGCCCTCACTGATTA-TCATTTTGCTC
1 -TTACTGATTACCATTTTGCTCT-ACTGATTACT-ATTTTACTC
76246 TTACT
1 TTACT
76251 AACTACTATT
Statistics
Matches: 141, Mismatches: 15, Indels: 26
0.77 0.08 0.14
Matches are distributed among these distances:
35 18 0.13
36 12 0.09
37 1 0.01
39 4 0.03
42 46 0.33
43 24 0.17
44 34 0.24
45 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.07, T:0.49
Consensus pattern (41 bp):
TTACTGATTACCATTTTGCTCTACTGATTACTATTTTACTC
Found at i:76190 original size:44 final size:44
Alignment explanation
Indices: 76131--76215 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
76121 CTCTTACTGA
*
76131 TTACCTTTTACTGATTACTGTCTTACTCTTTACTGATTACCTTC
1 TTACCTTTTACTGATTACTATCTTACTCTTTACTGATTACCTTC
* *
76175 TTACTTTTTACTGATTACTATTTTACTCTTTACTGATTACC
1 TTACCTTTTACTGATTACTATCTTACTCTTTACTGATTACC
76216 ATTTTGCCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (44 bp):
TTACCTTTTACTGATTACTATCTTACTCTTTACTGATTACCTTC
Found at i:76274 original size:43 final size:44
Alignment explanation
Indices: 76131--76282 Score: 127
Period size: 44 Copynumber: 3.5 Consensus size: 44
76121 CTCTTACTGA
* *
76131 TTACCTTTTACTGATTA-C-TGTCTTACTCTTTACTGATTACC-TT
1 TTACCTTTTACTGATTATCAT-T-TTACTCTTTACTAACTACCATT
* * *
76174 CTTACTTTTTACTGATTA-CTATTTTACTCTTTACTGATTACCATT
1 -TTACCTTTTACTGATTATC-ATTTTACTCTTTACTAACTACCATT
* * * * *
76219 TTGCC-CTCACTGATTATCATTTTGCTC-TTACTAACTACTATT
1 TTACCTTTTACTGATTATCATTTTACTCTTTACTAACTACCATT
*
76261 TTACCTTTTACTGATCATCATT
1 TTACCTTTTACTGATTATCATT
76283 ATTATTATTA
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
42 16 0.18
43 30 0.33
44 40 0.44
45 3 0.03
46 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.50
Consensus pattern (44 bp):
TTACCTTTTACTGATTATCATTTTACTCTTTACTAACTACCATT
Found at i:76339 original size:7 final size:7
Alignment explanation
Indices: 76327--76797 Score: 85
Period size: 7 Copynumber: 65.9 Consensus size: 7
76317 ATTTTACTAT
76327 TTTACTC
1 TTTACTC
*
76334 TTTACTG
1 TTTACTC
* *
76341 ATTATCTT
1 TTTA-CTC
*
76349 TTTACTA
1 TTTACTC
* *
76356 ATTACCC
1 TTTACTC
76363 TTTACTC
1 TTTACTC
76370 TTTAC-C
1 TTTACTC
*
76376 ATT-CTTCC
1 TTTAC-T-C
*
76384 TTTACTG
1 TTTACTC
*
76391 ATTACTC
1 TTTACTC
*
76398 TTTACTT
1 TTTACTC
76405 TTTAC-C
1 TTTACTC
*
76411 ATT-CTTC
1 TTTAC-TC
*
76418 TTTTACTG
1 -TTTACTC
*
76426 ATTACTC
1 TTTACTC
*
76433 TTTACTT
1 TTTACTC
76440 TTTA-TC
1 TTTACTC
76446 ATTTTACTC
1 --TTTACTC
76455 TAATTACTC
1 T--TTACTC
* *
76464 CTTACTG
1 TTTACTC
* *
76471 ATTATTC
1 TTTACTC
76478 TTTACTC
1 TTTACTC
76485 TTTAC-C
1 TTTACTC
*
76491 ATTT-TTCC
1 -TTTACT-C
*
76499 TTTACTG
1 TTTACTC
** *
76506 AATACCC
1 TTTACTC
76513 TTTACTC
1 TTTACTC
76520 TTTAC-C
1 TTTACTC
*
76526 ATTT-TTC
1 -TTTACTC
* *
76533 TTTAATA
1 TTTACTC
*
76540 ATTACTC
1 TTTACTC
*
76547 TTTACCC
1 TTTACTC
76554 TTTACTC
1 TTTACTC
*
76561 TTTACTA
1 TTTACTC
*
76568 TTT-TTCC
1 TTTACT-C
*
76575 TTTACTG
1 TTTACTC
*
76582 ATTACTC
1 TTTACTC
*
76589 TTTACTT
1 TTTACTC
76596 TTTAC-C
1 TTTACTC
*
76602 ATTT-GTC
1 -TTTACTC
* *
76609 -TTATTG
1 TTTACTC
* *
76615 ATTAGTC
1 TTTACTC
76622 TTTACTC
1 TTTACTC
76629 TTTACTC
1 TTTACTC
* *
76636 ATTACTAT
1 TTTACT-C
76644 TTTATTCTC
1 TTTA--CTC
* * *
76653 TTGAATT
1 TTTACTC
76660 TAATTAC-C
1 T--TTACTC
76668 ATTTTAC-C
1 --TTTACTC
*
76676 ATTTTTCTC
1 --TTTACTC
*
76685 TTTACTG
1 TTTACTC
*
76692 ATTACTC
1 TTTACTC
76699 TTTACT-
1 TTTACTC
76705 TTTAACTC
1 TTT-ACTC
*
76713 TTTTCTC
1 TTTACTC
*
76720 TTTACTG
1 TTTACTC
*
76727 ATTACTC
1 TTTACTC
*
76734 TATACTC
1 TTTACTC
76741 TTTTAC-C
1 -TTTACTC
*
76748 ATTTTCCTC
1 --TTTACTC
*
76757 TTTACTG
1 TTTACTC
*
76764 ATTACTC
1 TTTACTC
*
76771 TTTACTT
1 TTTACTC
76778 TTTACTC
1 TTTACTC
*
76785 TTTTCTC
1 TTTACTC
76792 TTTACT
1 TTTACT
76798 GATTACTAAT
Statistics
Matches: 321, Mismatches: 103, Indels: 80
0.64 0.20 0.16
Matches are distributed among these distances:
5 4 0.01
6 16 0.05
7 236 0.74
8 45 0.14
9 17 0.05
10 3 0.01
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (7 bp):
TTTACTC
Found at i:76345 original size:52 final size:50
Alignment explanation
Indices: 76289--76400 Score: 136
Period size: 52 Copynumber: 2.2 Consensus size: 50
76279 CATTATTATT
* * * * *
76289 ATTATTTTTTTACTGATTACCTTTTACTATTTTACTATT-TTACTCTTTACTG
1 ATTATCTTTTTACTAATTACCCTTTACT-CTTTACCATTCTT-C-CTTTACTG
76341 ATTATCTTTTTACTAATTACCCTTTACTCTTTACCATTCTTCCTTTACTG
1 ATTATCTTTTTACTAATTACCCTTTACTCTTTACCATTCTTCCTTTACTG
76391 ATTACTCTTT
1 ATTA-TCTTT
76401 ACTTTTTACC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
50 12 0.23
51 14 0.26
52 27 0.51
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.56
Consensus pattern (50 bp):
ATTATCTTTTTACTAATTACCCTTTACTCTTTACCATTCTTCCTTTACTG
Found at i:76395 original size:35 final size:35
Alignment explanation
Indices: 76349--76804 Score: 256
Period size: 35 Copynumber: 12.4 Consensus size: 35
76339 TGATTATCTT
* *
76349 TTTACTAATTACCCTTTACTCTTTACCATTCTTCC
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
* *
76384 TTTACTGATTACTCTTTACTTTTTACCATTCTTCT
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
* *
76419 TTTACTGATTACTCTTTACTTTTTATCATTTTACTCTAATTACTC
1 TTTACTGATTACTCTTTACTCTTTACCA---T--TC---TT-C-C
* * *
76464 CTTACTGATTATTCTTTACTCTTTACCATTTTTCC
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
* * *
76499 TTTACTGAATACCCTTTACTCTTTACCATT-TTTC
1 TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
* * * *
76533 TTTAATAATTACTCTTTACCCTTTACTCTTTACTATTTTTCC
1 TTTACTGATTA--C--T---CTTTACTCTTTACCATTCTTCC
*
76575 TTTACTGATTACTCTTTACTTTTTACCATT-TGT-C
1 TTTACTGATTACTCTTTACTCTTTACCATTCT-TCC
* *
76609 -TTATTGATTAGTCTTTACTCTTTACTCATTACTAT--
1 TTTACTGATTACTCTTTACTCTTTAC-CATT-CT-TCC
* * * *
76644 TTTATTCT-CTTGAATTTAATTAC-CATTTTACCATTTTTCTC
1 TTTA--CTGATT-ACTCT--TTACTC--TTTACCATTCTTC-C
76685 TTTACTGATTACTCTTTACT-TTTAACTC-TT-TTCTC
1 TTTACTGATTACTCTTTACTCTTT-AC-CATTCTTC-C
*
76720 TTTACTGATTACTCTATACTCTTTTACCATT-TTCCTC
1 TTTACTGATTACTCTTTACTC-TTTACCATTCTT-C-C
*
76757 TTTACTGATTACTCTTTACTTTTTACTC-TT-TTCTC
1 TTTACTGATTACTCTTTACTCTTTAC-CATTCTTC-C
76792 TTTACTGATTACT
1 TTTACTGATTACT
76805 AATTTGCAAA
Statistics
Matches: 338, Mismatches: 41, Indels: 84
0.73 0.09 0.18
Matches are distributed among these distances:
33 22 0.07
34 17 0.05
35 145 0.43
36 26 0.08
37 35 0.10
38 7 0.02
39 7 0.02
40 14 0.04
41 25 0.07
42 13 0.04
43 2 0.01
44 1 0.00
45 24 0.07
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTCTTTACCATTCTTCC
Found at i:76573 original size:76 final size:75
Alignment explanation
Indices: 76477--76646 Score: 241
Period size: 76 Copynumber: 2.3 Consensus size: 75
76467 ACTGATTATT
* *
76477 CTTTACTCTTTACCATTTTTCCTTTACTGAATACCCTTTACTCTTTACCATTTTTCTTTAATAAT
1 CTTTACTCTTTACTATTTTTCCTTTACTGAATACCCTTTACTCTTTACCATTTGTC-TTAATAAT
76542 TACTCTTTACC
65 TACTCTTTACC
* * * * *
76553 CTTTACTCTTTACTATTTTTCCTTTACTGATTACTCTTTACTTTTTACCATTTGTCTTATTGATT
1 CTTTACTCTTTACTATTTTTCCTTTACTGAATACCCTTTACTCTTTACCATTTGTCTTAATAATT
* *
76618 AGTCTTTACT
66 ACTCTTTACC
*
76628 CTTTACTCATTACTATTTT
1 CTTTACTCTTTACTATTTT
76647 ATTCTCTTGA
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
75 33 0.39
76 51 0.61
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (75 bp):
CTTTACTCTTTACTATTTTTCCTTTACTGAATACCCTTTACTCTTTACCATTTGTCTTAATAATT
ACTCTTTACC
Found at i:76758 original size:72 final size:72
Alignment explanation
Indices: 76669--76804 Score: 254
Period size: 72 Copynumber: 1.9 Consensus size: 72
76659 TTAATTACCA
*
76669 TTTTACCATTTTTCTCTTTACTGATTACTCTTTACTTTTAACTCTTTTCTCTTTACTGATTACTC
1 TTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTTTAACTCTTTTCTCTTTACTGATTACTC
76734 TATACTC
66 TATACTC
*
76741 TTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTTTTACTCTTTTCTCTTTACTGATTACT
1 TTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTTTAACTCTTTTCTCTTTACTGATTACT
76805 AATTTGCAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.57
Consensus pattern (72 bp):
TTTTACCATTTTCCTCTTTACTGATTACTCTTTACTTTTAACTCTTTTCTCTTTACTGATTACTC
TATACTC
Found at i:77015 original size:40 final size:39
Alignment explanation
Indices: 76970--77476 Score: 173
Period size: 40 Copynumber: 12.8 Consensus size: 39
76960 CCTTTCTTAA
**
76970 TTACTGATTACTAATTTTACTTTCTCTCTTAATTATCAAT
1 TTACTGATTACT-ATTTTACTTTGACTCTTAATTATCAAT
* **
77010 TTACTGA-T-CTATCCCTTTACTCTGACTCTTAATTA-CTGGT
1 TTACTGATTACTAT---TTTACTTTGACTCTTAATTATC-AAT
* * *** * *
77050 CTACTGATTACTACTTTTGCTTCCTCTTTTAATTATGAAT
1 TTACTGATTACTA-TTTTACTTTGACTCTTAATTATCAAT
* ** * *
77090 TTACTGATTAATCCCTTTACCTTGACTCTTAATTA-CTGAT
1 TTACTGATTACT-ATTTTACTTTGACTCTTAATTATC-AAT
* *
77130 TTACTGATCACTA--TTACCTTGACTCTTAATTATCAAT
1 TTACTGATTACTATTTTACTTTGACTCTTAATTATCAAT
**
77167 TTACTGATT-C-ATCTTT--TTT-A--CTTAATTATTGAT
1 TTACTGATTACTAT-TTTACTTTGACTCTTAATTATCAAT
* *
77200 TTACTGAATACTA--TTACCTTGACTCTTAATTATCAAT
1 TTACTGATTACTATTTTACTTTGACTCTTAATTATCAAT
* * * * * * *
77237 TTACTGATTAATCTCTTTTTACTGATTTACTGATTACTGATTACCT
1 TTACTGATT-A-CT-ATTTTACT--TTGACT-CTTAATTATCA-AT
* * * * * * *
77283 TGACTCTTAATTACCAATTTACTGATTAATCTCTT-TTTACTGAA-
1 TTA--C-TGATTACTATTTTACT--TTGA-CTCTTAATTA-TCAAT
77327 TTACTGATTTACTGATTTCTACGTTT-ACTCTTAATTATCAATT
1 TTACTGA-TTACT-ATTT-TAC-TTTGACTCTTAATTATCAA-T
* *
77370 TTACTGA-T-C-ATTATTACTTTGATTCTCAATTATCAATT
1 TTACTGATTACTATT-TTACTTTGACTCTTAATTATCAA-T
* *
77408 TTACTGATTACTA--TTAATTTGACTCTTAATTACTTAAT
1 TTACTGATTACTATTTTACTTTGACTCTTAATTA-TCAAT
* *
77446 TCACTGATTACTA--TTATTTTGACTCTTAATT
1 TTACTGATTACTATTTTACTTTGACTCTTAATT
77477 TATTGGGGTA
Statistics
Matches: 346, Mismatches: 73, Indels: 98
0.67 0.14 0.19
Matches are distributed among these distances:
32 2 0.01
33 19 0.05
34 3 0.01
35 4 0.01
36 3 0.01
37 53 0.15
38 80 0.23
39 9 0.03
40 84 0.24
41 13 0.04
42 16 0.05
43 13 0.04
44 10 0.03
45 10 0.03
46 18 0.05
47 3 0.01
48 2 0.01
49 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (39 bp):
TTACTGATTACTATTTTACTTTGACTCTTAATTATCAAT
Found at i:77104 original size:80 final size:80
Alignment explanation
Indices: 76971--77174 Score: 249
Period size: 80 Copynumber: 2.6 Consensus size: 80
76961 CTTTCTTAAT
*
76971 TACTGATTACTAATTTTACTTTCTCTCTTAATTATCAATTTACTGATCTATCCCTTTA-CTCTGA
1 TACTGATTACTAATTTTACTTCCTCTCTTAATTATCAATTTACTGATCTATCCCTTTACCT-TGA
*
77035 CTCTTAATTACTGGTC
65 CTCTTAATTACTGATC
* * * *
77051 TACTGATTACTACTTTTGCTTCCTCTTTTAATTATGAATTTACTGAT-TAATCCCTTTACCTTGA
1 TACTGATTACTAATTTTACTTCCTCTCTTAATTATCAATTTACTGATCT-ATCCCTTTACCTTGA
*
77115 CTCTTAATTACTGATT
65 CTCTTAATTACTGATC
* **
77131 TACTGATCACT-A--TTACCTT-GACTCTTAATTATCAATTTACTGAT
1 TACTGATTACTAATTTTA-CTTCCTCTCTTAATTATCAATTTACTGAT
77175 TCATCTTTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
77 23 0.21
78 3 0.03
79 1 0.01
80 78 0.73
81 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (80 bp):
TACTGATTACTAATTTTACTTCCTCTCTTAATTATCAATTTACTGATCTATCCCTTTACCTTGAC
TCTTAATTACTGATC
Found at i:77126 original size:32 final size:35
Alignment explanation
Indices: 77090--77161 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 35
77080 AATTATGAAT
*
77090 TTACTGA-TTA-ATCCCT-TTACCTTGACTCTTAA
1 TTACTGATTTACATCACTATTACCTTGACTCTTAA
77122 TTACTGATTTACTGATCACTATTACCTTGACTCTTAA
1 TTACTGATTTAC--ATCACTATTACCTTGACTCTTAA
77159 TTA
1 TTA
77162 TCAATTTACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.21
33 3 0.09
36 5 0.15
37 19 0.56
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (35 bp):
TTACTGATTTACATCACTATTACCTTGACTCTTAA
Found at i:77200 original size:70 final size:70
Alignment explanation
Indices: 77078--77377 Score: 350
Period size: 70 Copynumber: 4.3 Consensus size: 70
77068 GCTTCCTCTT
* *
77078 TTAATTATGAATTTACTGATTAATCCCTTTACCTTGACTCTTAATTACTGATTTACTGATCACTA
1 TTAATTATCAATTTACTGATTAATCTCTTT---TT-A--CTTAATTACTGATTTACTGAT-ACTA
77143 TTACCTTGACTC
59 TTACCTTGACTC
* *
77155 TTAATTATCAATTTACTGATTCATCT-TTTTTACTTAATTATTGATTTACTGAATACTATTACCT
1 TTAATTATCAATTTACTGATTAATCTCTTTTTACTTAATTACTGATTTACTG-ATACTATTACCT
77219 TGACTC
65 TGACTC
* *
77225 TTAATTATCAATTTACTGATTAATCTCTTTTTACTGATTTACTGA-TTACTG-----ATTACCTT
1 TTAATTATCAATTTACTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATACTATTACCTT
77284 GACTC
66 GACTC
* * *
77289 TTAATTACCAATTTACTGATTAATCTCTTTTTACTGAATTACTGATTTACTGAT--T-TCTACGT
1 TTAATTATCAATTTACTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATACTAT-TACCT
*
77351 TTACTC
65 TGACTC
77357 TTAATTATCAATTTTACTGAT
1 TTAATTATCAA-TTTACTGAT
77378 CATTATTACT
Statistics
Matches: 202, Mismatches: 13, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
64 56 0.28
65 6 0.03
67 1 0.00
68 19 0.09
69 9 0.04
70 65 0.32
71 17 0.08
72 1 0.00
73 2 0.01
76 3 0.01
77 23 0.11
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (70 bp):
TTAATTATCAATTTACTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATACTATTACCTT
GACTC
Found at i:77301 original size:64 final size:64
Alignment explanation
Indices: 77196--77377 Score: 267
Period size: 64 Copynumber: 2.8 Consensus size: 64
77186 ACTTAATTAT
*
77196 TGATTTACTGAATACT-ATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTTTAC
1 TGATTTACTGATTACTGATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTTTAC
*
77259 TGATTTACTGATTACTGATTACCTTGACTCTTAATTACCAATTTACTGATTAATCTCTTTTTAC
1 TGATTTACTGATTACTGATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTTTAC
* * *
77323 TGAATTACTGATTTACTGATTTCTACGTTTACTCTTAATTATCAATTTTACTGAT
1 TGATTTACTGA-TTACTGA--T-TACCTTGACTCTTAATTATCAA-TTTACTGAT
77378 CATTATTACT
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
63 15 0.14
64 56 0.52
65 7 0.07
67 1 0.01
68 19 0.18
69 9 0.08
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (64 bp):
TGATTTACTGATTACTGATTACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTTTAC
Found at i:77303 original size:38 final size:36
Alignment explanation
Indices: 77261--77476 Score: 149
Period size: 38 Copynumber: 5.9 Consensus size: 36
77251 CTTTTTACTG
*
77261 ATTTACTGATTACTGATTACCTTGACTCTTAATTACCA
1 ATTTACTGATTA-T-ATTACTTTGACTCTTAATTACCA
* * **
77299 ATTTACTGATTA-ATCT-CTTT--TTACTGAATTACTG
1 ATTTACTGATTATAT-TACTTTGACT-CTTAATTACCA
* *
77333 ATTTACTGATT-T-CTACGTTT-ACTCTTAATTATCA
1 ATTTACTGATTATATTAC-TTTGACTCTTAATTACCA
* * * *
77367 ATTTTACTGATCATTATTACTTTGATTCTCAATTATCA
1 A-TTTACTGATTA-TATTACTTTGACTCTTAATTACCA
* *
77405 ATTTTACTGATTACTATTAATTTGACTCTTAATTACTTA
1 A-TTTACTGATTA-TATTACTTTGACTCTTAATTAC-CA
* *
77444 ATTCACTGATTACTATTATTTTGACTCTTAATT
1 ATTTACTGATTA-TATTACTTTGACTCTTAATT
77477 TATTGGGGTA
Statistics
Matches: 142, Mismatches: 24, Indels: 24
0.75 0.13 0.13
Matches are distributed among these distances:
32 1 0.01
33 2 0.01
34 30 0.21
35 15 0.11
36 1 0.01
37 4 0.03
38 87 0.61
39 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.49
Consensus pattern (36 bp):
ATTTACTGATTATATTACTTTGACTCTTAATTACCA
Found at i:77374 original size:19 final size:19
Alignment explanation
Indices: 77350--77439 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 19
77340 GATTTCTACG
77350 TTTACTCTTAATTATCAAT
1 TTTACTCTTAATTATCAAT
** * * *
77369 TTTACTGATCATTATTACT
1 TTTACTCTTAATTATCAAT
* * *
77388 TTGATTCTCAATTATCAAT
1 TTTACTCTTAATTATCAAT
* * *
77407 TTTACTGATT-ACTATTAAT
1 TTTACT-CTTAATTATCAAT
*
77426 TTGACTCTTAATTA
1 TTTACTCTTAATTA
77440 CTTAATTCAC
Statistics
Matches: 47, Mismatches: 22, Indels: 4
0.64 0.30 0.05
Matches are distributed among these distances:
18 2 0.04
19 44 0.94
20 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTACTCTTAATTATCAAT
Found at i:77439 original size:22 final size:22
Alignment explanation
Indices: 77414--77476 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 22
77404 AATTTTACTG
77414 ATTACTATTAATTTGACTCTTA
1 ATTACTATTAATTTGACTCTTA
* *
77436 ATTAC--TTAA-TT--CAC-TG
1 ATTACTATTAATTTGACTCTTA
*
77452 ATTACTATTATTTTGACTCTTA
1 ATTACTATTAATTTGACTCTTA
77474 ATT
1 ATT
77477 TATTGGGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
16 6 0.20
17 2 0.07
18 3 0.10
19 4 0.13
20 4 0.13
21 2 0.07
22 9 0.30
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (22 bp):
ATTACTATTAATTTGACTCTTA
Found at i:81497 original size:27 final size:27
Alignment explanation
Indices: 81467--81538 Score: 87
Period size: 26 Copynumber: 2.7 Consensus size: 27
81457 TACTACAATT
81467 ACCAAAATGCCCCTGAATGTGC-A-AATG
1 ACCAAAATGCCCCT-AA-GTGCAAGAATG
*
81494 ACCAAAATG-CCCTTAGTGCAAGAATG
1 ACCAAAATGCCCCTAAGTGCAAGAATG
*
81520 ACCAAAATGCCTCTAAGTG
1 ACCAAAATGCCCCTAAGTG
81539 ACCCTAATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 4 0.10
25 2 0.05
26 17 0.44
27 16 0.41
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (27 bp):
ACCAAAATGCCCCTAAGTGCAAGAATG
Found at i:93657 original size:6 final size:6
Alignment explanation
Indices: 93646--93682 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
93636 ATAGTTTTAT
93646 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A
93683 TAATTGAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:94158 original size:74 final size:74
Alignment explanation
Indices: 94080--94236 Score: 244
Period size: 74 Copynumber: 2.1 Consensus size: 74
94070 TAGTCTTTTC
* *
94080 ACACTTTTCAGG-TGACTAAAAAGCCCCTCTATAAGTTTCCCATATTCCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATAAGTTTCCCACATTACTTTTCCTTCTACCCTT
94144 TTTCGTAATT
65 TTTCGTAATT
* * *
94154 ACACTTTTCGGATGACTAAAAAGCCCCTTTATGAGTTTCCCCCATTACTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATAAGTTTCCCACATTACTTTTCCTTCTACCCTTT
94219 TTCGTAATT
66 TTCGTAATT
*
94228 ACACATTTC
1 ACACTTTTC
94237 TCTTCCTTAA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
73 2 0.03
74 74 0.97
ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATAAGTTTCCCACATTACTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:94950 original size:5 final size:5
Alignment explanation
Indices: 94937--94966 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
94927 AATAAAGAGA
*
94937 GAGGT GAGGA GAGGT GAGGT GAGGT GAGGT
1 GAGGT GAGGT GAGGT GAGGT GAGGT GAGGT
94967 TCTATAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.60, T:0.17
Consensus pattern (5 bp):
GAGGT
Found at i:95241 original size:22 final size:23
Alignment explanation
Indices: 95191--95241 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
95181 GTTAGTAAAC
*
95191 AGAAGATTAAAAAAAAAAAGAGAA
1 AGAA-ATTAAAAAAAAAAAGAAAA
* *
95215 GGAAATT-AAAAAAAAAGGAAAA
1 AGAAATTAAAAAAAAAAAGAAAA
95237 AGAAA
1 AGAAA
95242 AAGAATCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 3 0.13
24 3 0.13
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.08
Consensus pattern (23 bp):
AGAAATTAAAAAAAAAAAGAAAA
Done.