Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020790.1 Corchorus olitorius cultivar O-4 contig20823, 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: 165534
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2826 original size:16 final size:16
Alignment explanation
Indices: 2805--2838 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2795 CATGGATACT
2805 TAATTAATATATAATA
1 TAATTAATATATAATA
*
2821 TAATTACTATATAATA
1 TAATTAATATATAATA
2837 TA
1 TA
2839 TCGCACGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTAATATATAATA
Found at i:4598 original size:51 final size:52
Alignment explanation
Indices: 4497--4598 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 52
4487 GTTCTTCATA
* **
4497 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGTTT
1 TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
*
4549 TTCT-CTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TTCTCCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGTT
4599 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 2 0.05
51 37 0.84
52 5 0.11
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (52 bp):
TTCTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGTTT
Found at i:9989 original size:21 final size:22
Alignment explanation
Indices: 9965--10008 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
9955 CAGTTTTCAC
9965 CATAATA-GCATCGTCCTTGCG
1 CATAATACGCATCGTCCTTGCG
9986 CATAATATCGGCATCGTCCTTGC
1 CATAATA-C-GCATCGTCCTTGC
10009 CCAAAACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
24 13 0.65
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (22 bp):
CATAATACGCATCGTCCTTGCG
Found at i:13866 original size:25 final size:26
Alignment explanation
Indices: 13811--13866 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
13801 AAAGATGACA
* * **
13811 TATATATGTGTGCATTTTTTTTTGAGG
1 TATATATGTGTGCATTTCTGTTT-ACC
13838 TATATATGTGTGCATTTCTGTTT-CC
1 TATATATGTGTGCATTTCTGTTTACC
13863 TATA
1 TATA
13867 GCCAATGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 4 0.16
27 21 0.84
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.54
Consensus pattern (26 bp):
TATATATGTGTGCATTTCTGTTTACC
Found at i:17597 original size:15 final size:15
Alignment explanation
Indices: 17579--17613 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
17569 ATATCTAACT
17579 TCATACACACGTTTC
1 TCATACACACGTTTC
17594 TCATACACACGTTTC
1 TCATACACACGTTTC
17609 TCATA
1 TCATA
17614 GATAGATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (15 bp):
TCATACACACGTTTC
Found at i:18882 original size:153 final size:157
Alignment explanation
Indices: 18596--18884 Score: 415
Period size: 153 Copynumber: 1.9 Consensus size: 157
18586 ATGACTAATC
* * *
18596 TCAGGCAACTTACTCATTCCACTTGTCATGGATTTGTCATTGATAGGAGGATTCTGGTATTTGTT
1 TCAGGCAACCTACTCATTCCACCTGTCATGGATTTGTCATTGATAGGA-GATTCTGGTATCTGTT
* *
18661 CCTATGGAAGTTAGTTTGTCTATAGTTGGTGTGAAAGTTATCACCCGTTCGAAGCTCAACCTCCG
65 -CTATGGAAGTTAGTTTGCCTATAGTTGATGTGAAAGTTATCACCCGTTCGAAGCTCAACCTCCG
18726 GAATGCCACTGCCCAGTTGATAATTCCTT
129 GAATGCCACTGCCCAGTTGATAATTCCTT
*
18755 TCAGGCAACCTACTCATTCCACCTGTCATGGATTTTTCATTGAT-GGA-ATTCTGGTATCTG-T-
1 TCAGGCAACCTACTCATTCCACCTGTCATGGATTTGTCATTGATAGGAGATTCTGGTATCTGTTC
* * ** * * *
18816 TATGGAAGTTAGTTTGCCTATGGTTGATGTGAAATTTATCACCTTTTTGAAGCTGAACCTCTGGA
66 TATGGAAGTTAGTTTGCCTATAGTTGATGTGAAAGTTATCACCCGTTCGAAGCTCAACCTCCGGA
18881 ATGC
131 ATGC
18885 GGCTGCTCTC
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
153 60 0.51
155 1 0.01
156 12 0.10
158 3 0.03
159 41 0.35
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (157 bp):
TCAGGCAACCTACTCATTCCACCTGTCATGGATTTGTCATTGATAGGAGATTCTGGTATCTGTTC
TATGGAAGTTAGTTTGCCTATAGTTGATGTGAAAGTTATCACCCGTTCGAAGCTCAACCTCCGGA
ATGCCACTGCCCAGTTGATAATTCCTT
Found at i:34792 original size:1 final size:1
Alignment explanation
Indices: 34786--34838 Score: 106
Period size: 1 Copynumber: 53.0 Consensus size: 1
34776 GTGTTCAAAG
34786 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
34839 CTATATGTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:42460 original size:74 final size:74
Alignment explanation
Indices: 42339--42485 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
42329 GTGTAGTAAC
* *
42339 TATTAGTATCATTCGATAGTTTACAAAAGCCCACCGATAAGTTAATCTACAATAATTTACATTTC
1 TATTAGTATCATTCGATAGTTTACAAAAGCCCACCGACAAGTTAATCTACAATAATTAACATTTC
42404 ACCAAAAGT
66 ACCAAAAGT
* *
42413 TATTAGTATCATTCGATAGTTTACTAAAGCCCATCGACAAGTTAATCTACAATAATTAACATTTC
1 TATTAGTATCATTCGATAGTTTACAAAAGCCCACCGACAAGTTAATCTACAATAATTAACATTTC
42478 ACCAAAAG
66 ACCAAAAG
42486 AAAAGCTTCC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (74 bp):
TATTAGTATCATTCGATAGTTTACAAAAGCCCACCGACAAGTTAATCTACAATAATTAACATTTC
ACCAAAAGT
Found at i:45844 original size:27 final size:27
Alignment explanation
Indices: 45814--45884 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
45804 AAGGGTTTCT
45814 ATCTCTGTTCCTAAAGTAGGGGCTTCC
1 ATCTCTGTTCCTAAAGTAGGGGCTTCC
* * * *
45841 ATCTCTATTCTTGAAGGAGGGGCTTCC
1 ATCTCTGTTCCTAAAGTAGGGGCTTCC
*
45868 GTCTCTGTTCCTAAAGT
1 ATCTCTGTTCCTAAAGT
45885 TCCTAAGGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
ATCTCTGTTCCTAAAGTAGGGGCTTCC
Found at i:46066 original size:18 final size:18
Alignment explanation
Indices: 46043--46081 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
46033 TATACATTCA
46043 AATTTGGACAATATGTGC
1 AATTTGGACAATATGTGC
46061 AATTTGGACAATATGTGC
1 AATTTGGACAATATGTGC
46079 AAT
1 AAT
46082 ATGTAAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (18 bp):
AATTTGGACAATATGTGC
Found at i:46137 original size:57 final size:59
Alignment explanation
Indices: 46075--46187 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
46065 TGGACAATAT
* * *
46075 GTGCAATATGTAAGTACTTG-TCA-TCCTTGTCATCCTTGCTTAAACTTTTAATATGGA
1 GTGCAATATGTAAGTACTTGTTAAGTACTTGTCATCCTTGCTTAAACTTTCAATATGGA
*
46132 GTGCAATATGTAAGTACTTGTTAAGTACTTGTCATCCTTGTTTAAACTTTCAATAT
1 GTGCAATATGTAAGTACTTGTTAAGTACTTGTCATCCTTGCTTAAACTTTCAATAT
46188 ATATGCATTC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 20 0.40
58 2 0.04
59 28 0.56
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (59 bp):
GTGCAATATGTAAGTACTTGTTAAGTACTTGTCATCCTTGCTTAAACTTTCAATATGGA
Found at i:46606 original size:24 final size:25
Alignment explanation
Indices: 46578--46633 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
46568 GTGATTGAAA
*
46578 TTCCAAATTG-GGTAGATTAGCCT-C
1 TTCCAAATCGTGG-AGATTAGCCTCC
*
46602 TTCCAAAACGTGGAGATTAGCCTCC
1 TTCCAAATCGTGGAGATTAGCCTCC
46627 TT-CAAAT
1 TTCCAAAT
46634 GTTGGGATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (25 bp):
TTCCAAATCGTGGAGATTAGCCTCC
Found at i:68307 original size:1 final size:1
Alignment explanation
Indices: 68303--68328 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
68293 AATAAATAAA
68303 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
68329 CTGATTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:70055 original size:33 final size:34
Alignment explanation
Indices: 69991--70058 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
69981 ACAATAGCAA
69991 TGGTTATAATTAGAAAGAAAATTAGGAACATATT
1 TGGTTATAATTAGAAAGAAAATTAGGAACATATT
70025 TGGTTATAATTAGAAAGAAAA-TAGGAACATATT
1 TGGTTATAATTAGAAAGAAAATTAGGAACATATT
70058 T
1 T
70059 AAAAAGCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 13 0.38
34 21 0.62
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (34 bp):
TGGTTATAATTAGAAAGAAAATTAGGAACATATT
Found at i:71657 original size:17 final size:16
Alignment explanation
Indices: 71635--71689 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
71625 CACCCCCCCC
71635 AGATCACTAGTGATCTA
1 AGATCAC-AGTGATCTA
*
71652 AGATCAACAGTGATGTA
1 AGATC-ACAGTGATCTA
* *
71669 AGATCACCGGTGATCAA
1 AGATCA-CAGTGATCTA
71686 AGAT
1 AGAT
71690 TACATGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 29 0.91
18 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (16 bp):
AGATCACAGTGATCTA
Found at i:75986 original size:22 final size:20
Alignment explanation
Indices: 75961--76003 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
75951 ACAAAAGAAA
*
75961 GGGAGTAGAAAATTGAAATATG
1 GGGAG-AGAAAATAG-AATATG
*
75983 GGGAGAGACAATAGAATATG
1 GGGAGAGAAAATAGAATATG
76003 G
1 G
76004 AGAAGGGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.19
Consensus pattern (20 bp):
GGGAGAGAAAATAGAATATG
Found at i:76237 original size:11 final size:11
Alignment explanation
Indices: 76223--76260 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
76213 ATTCATAACA
76223 AATTTATAATT
1 AATTTATAATT
76234 AATTTATAATT
1 AATTTATAATT
76245 -ATTTGATAATT
1 AATTT-ATAATT
*
76256 TATTT
1 AATTT
76261 TATACAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:78584 original size:20 final size:20
Alignment explanation
Indices: 78559--78602 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
78549 ACTCTTCTGG
78559 GAAAATGCTTATTGGTACTA
1 GAAAATGCTTATTGGTACTA
78579 GAAAATGCTTATTGGTACTA
1 GAAAATGCTTATTGGTACTA
78599 GAAA
1 GAAA
78603 CGATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (20 bp):
GAAAATGCTTATTGGTACTA
Found at i:80265 original size:3 final size:3
Alignment explanation
Indices: 80257--80291 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
80247 AGGCTGCTTT
80257 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
80292 TCTTTCTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:82312 original size:56 final size:55
Alignment explanation
Indices: 82252--82372 Score: 129
Period size: 56 Copynumber: 2.2 Consensus size: 55
82242 ATGAATCTAA
82252 TTCATTCATAGAACGAGAATAAAAAAGGTA-T-TAATATATTTGGATGAAATGTTATC
1 TTCATTCATAGAA--A-AATAAAAAAGGTACTATAATATATTTGGATGAAATGTTATC
* ** *** *
82308 TTCATTCGTCTAAAAATGGGAAAGGTACTAGTAATATATTTGGATGAAATGTTTTC
1 TTCATTCATAGAAAAATAAAAAAGGTACTA-TAATATATTTGGATGAAATGTTATC
82364 TTCATTCAT
1 TTCATTCAT
82373 CTAAGAGCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
53 10 0.19
54 2 0.04
56 42 0.78
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (55 bp):
TTCATTCATAGAAAAATAAAAAAGGTACTATAATATATTTGGATGAAATGTTATC
Found at i:85595 original size:6 final size:6
Alignment explanation
Indices: 85584--85615 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
85574 TTAAAGCCGT
85584 AAAAGA AAAAGA AAAAGA AAAAGA AAAA-A AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
85616 GTCAAACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:86396 original size:11 final size:12
Alignment explanation
Indices: 86372--86398 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
86362 AAGTCACATG
86372 TTTTTAAACTTT
1 TTTTTAAACTTT
86384 TTTTTAAACTTT
1 TTTTTAAACTTT
86396 TTT
1 TTT
86399 ATTTAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTAAACTTT
Found at i:90009 original size:28 final size:31
Alignment explanation
Indices: 89947--90012 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 31
89937 AAATTTTACT
89947 AAATTGACAGATTCTATTAAGTAGAGGGACC
1 AAATTGACAGATTCTATTAAGTAGAGGGACC
* *
89978 AAATTGACAG-TT-TTTTAA-TAGGGGGACC
1 AAATTGACAGATTCTATTAAGTAGAGGGACC
90006 AAATTGA
1 AAATTGA
90013 TCCCTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 16 0.48
29 5 0.15
30 2 0.06
31 10 0.30
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (31 bp):
AAATTGACAGATTCTATTAAGTAGAGGGACC
Found at i:90021 original size:29 final size:29
Alignment explanation
Indices: 89963--90036 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
89953 ACAGATTCTA
*
89963 TTAAGTAGAGGGACCAAATTGACAGTTTT
1 TTAAGTAGAGGGACCAAATTGACACTTTT
* *
89992 TTAA-TAGGGGGACCAAATTGATCCCTTTT
1 TTAAGTAGAGGGACCAAATTGA-CACTTTT
*
90021 TGAAAGTAGAGGGACC
1 T-TAAGTAGAGGGACC
90037 TGTACGGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 16 0.43
29 10 0.27
30 2 0.05
31 9 0.24
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (29 bp):
TTAAGTAGAGGGACCAAATTGACACTTTT
Found at i:101788 original size:19 final size:19
Alignment explanation
Indices: 101764--101803 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
101754 TAATAGACCC
101764 TATGATTTAGAACTTATTA
1 TATGATTTAGAACTTATTA
*
101783 TATGATTTAGGACTTATTA
1 TATGATTTAGAACTTATTA
101802 TA
1 TA
101804 GGCATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (19 bp):
TATGATTTAGAACTTATTA
Found at i:127188 original size:29 final size:29
Alignment explanation
Indices: 127156--127213 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
127146 GTTCTTTATC
127156 TTACTGCTTCCTTGTTGCCATTGAAGAAG
1 TTACTGCTTCCTTGTTGCCATTGAAGAAG
127185 TTACTGCTTCCTTGTTGCCATTGAAGAAG
1 TTACTGCTTCCTTGTTGCCATTGAAGAAG
127214 AAGAGTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (29 bp):
TTACTGCTTCCTTGTTGCCATTGAAGAAG
Found at i:129947 original size:60 final size:60
Alignment explanation
Indices: 129879--130036 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 60
129869 ATTAATTGTT
* **
129879 CAAATAAGGGTCTAATGTTTACCAAAATGCTCAAATAAGGGTTCAATATTCTAATTTGGC
1 CAAATAAGGGTCTAATGTTTACAAAAATGCTCAAATAAGGACTCAATATTCTAATTTGGC
* * * * * * *
129939 CAAATAAGGATCTAAAG-TTATCGAAAATGCTCAAATAAGGACTCGATCTTTTAATTTGGT
1 CAAATAAGGGTCTAATGTTTA-CAAAAATGCTCAAATAAGGACTCAATATTCTAATTTGGC
129999 CAAATAAGGGTCTAATGTTATA-AAAAATGCTCAAATAA
1 CAAATAAGGGTCTAATGTT-TACAAAAATGCTCAAATAA
130037 AGGTCTGACG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 3 0.04
60 77 0.93
61 1 0.01
62 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGTCTAATGTTTACAAAAATGCTCAAATAAGGACTCAATATTCTAATTTGGC
Found at i:130036 original size:31 final size:28
Alignment explanation
Indices: 129878--130042 Score: 75
Period size: 31 Copynumber: 5.5 Consensus size: 28
129868 GATTAATTGT
129878 TCAAATAAGGGTCTAATGTTTACCAAAATGC
1 TCAAATAAGGGTCTAATGTTT---AAAATGC
* **
129909 TCAAATAAGGGT-TCAATATTCTAATTTGGC
1 TCAAATAAGGGTCT-AATGTT-TAAAAT-GC
* *
129939 -CAAATAAGGATCTAAAGTTATCGAAAATGC
1 TCAAATAAGGGTCTAATGTT-T--AAAATGC
* * * ** *
129969 TCAAATAA-GGACTCGATCTTTTAATTTGG
1 TCAAATAAGGGTCT-AAT-GTTTAAAATGC
129998 TCAAATAAGGGTCTAATGTTATAAAAAATGC
1 TCAAATAAGGGTCTAATGTT-T--AAAATGC
*
130029 TCAAATAAAGGTCT
1 TCAAATAAGGGTCT
130043 GACGTCAGTT
Statistics
Matches: 97, Mismatches: 24, Indels: 26
0.66 0.16 0.18
Matches are distributed among these distances:
28 2 0.02
29 33 0.34
30 13 0.13
31 46 0.47
32 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (28 bp):
TCAAATAAGGGTCTAATGTTTAAAATGC
Found at i:130123 original size:31 final size:31
Alignment explanation
Indices: 130080--130155 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
130070 TTATCGAGGC
*
130080 TAGACCCTTATTTGAGAATTTTCGATAACGT
1 TAGACCCTTATTTGAGAATTTTCGATAACAT
* *
130111 TAGATCCTTATTTGAGCATTTTCGATAACAT
1 TAGACCCTTATTTGAGAATTTTCGATAACAT
* *
130142 TAGGCCATTATTTG
1 TAGACCCTTATTTG
130156 GCCAAATAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (31 bp):
TAGACCCTTATTTGAGAATTTTCGATAACAT
Found at i:138238 original size:3 final size:3
Alignment explanation
Indices: 138232--138258 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
138222 AAATTAAAAA
138232 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
138259 CTAATCACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:146964 original size:1 final size:1
Alignment explanation
Indices: 146958--146998 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
146948 TTGGGCTATG
146958 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
146999 ATCCTATTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:159435 original size:322 final size:327
Alignment explanation
Indices: 158664--159454 Score: 918
Period size: 333 Copynumber: 2.4 Consensus size: 327
158654 TCTGCTAAAA
* *
158664 TAATATCGTTTTGC-ATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
1 TAATATCGTTTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * *
158728 GTAAAAACAAATCGTTACATCGAATTTCGCTGGGATTTGGTTCGATGAATATAGGTATTTCAAGG
66 GTAAAAACAAATCCTTAAATCCAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGG
* * * * **
158793 AGTCTTTATGCAAAAAATCATGCAAAATTGAGTCAGGACCCCAGAATGTGTTTTTAGCAAAAAAC
131 AGTCTTTATGCAAAAAATCATCCAAAACTGAGCCAGGACCCCAGAACGCATTTTTAGCAAAAAAC
* ** ** * *
158858 CGTGATGGTTAGTATACGGTTTCGGCTAAAATTTTGAAAAAATTGATCCGAAAATTTTTTCCTCA
196 CGTGATGGTTAGTACACAATTTCGGCTAAAATACTG----AACTCA-CCGAAAATTTTTTCCTCA
** * * * * *
158923 ATTATTTTGCGACAATAGTCAGGAAAAATATATAATTCAACAGAAAATAAATTGAAGAGTTTTTC
256 ATTATTCCGCCACAATACTCAGAAAAAATATATAATTCAACACAAAATAAATTGAAGAGCTTTTC
158988 ACGCTTC
321 ACGCTTC
* * *
158995 TAATATCGTTTTTCTATTTTTTTTTGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCT
1 TAATATCGTTTTTCTA-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* * *
159060 CGTAAAAATAAATCCTTAAATCCAATGTAGCTGAGATTTGGTTAGATGAATATAGATATTTCAAG
65 CGTAAAAACAAATCCTTAAATCCAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTCAAG
* * ** * * * *
159125 GAGTCTTTATGCCAAAACTCATCCAAAACTGAGCC-GGGGCACTGAAACGCATTTTTAGCCATAA
130 GAGTCTTTATGCAAAAAATCATCCAAAACTGAGCCAGGACCCCAG-AACGCATTTTTAGCAAAAA
** * * *
159189 ATTGTGATGGTTAGTACATAATTTCGGCTAAAA-ACTG-ACTCA-C-ATAAA-TTTTTGCTGAAT
194 ACCGTGATGGTTAGTACACAATTTCGGCTAAAATACTGAACTCACCGA-AAATTTTTTCCTCAAT
* * * *
159249 T-TTCCGCCACAATACTCATAAAAAATATATAATTCAACACCAAAA-ATATTGACGGGCTTTTCA
258 TATTCCGCCACAATACTCAGAAAAAATATATAATTCAACA-CAAAATAAATTGAAGAGCTTTTCA
*
159312 CTCTTC
322 CGCTTC
* * *
159318 TAATATCGTTTTTCTATTTTTTCTGAATTAATTCCTAATTAAATCAAAAGAAGATTCAGATGCTC
1 TAATATCGTTTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
*
159383 GTAAAAACAAATCCTTATATCCAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTCAA-G
66 GTAAAAACAAATCCTTAAATCCAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGG
159447 AGGTCTTT
131 A-GTCTTT
159455 GCCCCAAAAA
Statistics
Matches: 392, Mismatches: 62, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
321 2 0.01
322 108 0.28
323 67 0.17
324 16 0.04
325 4 0.01
327 3 0.01
331 13 0.03
332 8 0.02
333 171 0.44
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (327 bp):
TAATATCGTTTTTCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
GTAAAAACAAATCCTTAAATCCAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGG
AGTCTTTATGCAAAAAATCATCCAAAACTGAGCCAGGACCCCAGAACGCATTTTTAGCAAAAAAC
CGTGATGGTTAGTACACAATTTCGGCTAAAATACTGAACTCACCGAAAATTTTTTCCTCAATTAT
TCCGCCACAATACTCAGAAAAAATATATAATTCAACACAAAATAAATTGAAGAGCTTTTCACGCT
TC
Found at i:160638 original size:325 final size:325
Alignment explanation
Indices: 159782--160682 Score: 933
Period size: 325 Copynumber: 2.7 Consensus size: 325
159772 AACCCGATTT
* * * *
159782 TTTTTTTCTGAATTTTCTGCTAAAATACTCAGAAAAAATAAATAATTCAACGCCAAAAAAATTTA
1 TTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTCAAC-CCAAAAAAATTGA
* ** **
159847 TGGGCTAGTCACGCTTCTAATA-TCGTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
65 -AGGCTTTTCACGCTTCTAATATTATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * * * * * * *
159911 AACAAGATTCAAATTCTCGTAAAGACAAATCGTTACATCGAATTTGGCTGGGATTT-TTTCGATG
129 AACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATG
* * * * * *
159975 AATATAGGTATTTCAAGGAGTCTTTACGCCAAAAATCATACAAAACTGAGCCGGGATCCCGGAAT
194 AATATAGATATTTCAAGGAGTCTTTATGCCAAAAATAATACAAAACTGAGCCGGGAGCCCGAAAC
** *
160040 GTGTTTTTAGCAAAAAAAACTGTGATGGTTAGTATACGGTTTCGACTAAAATTTTGAAAAAATTG
259 ACGTTTTTAGCAAAAAAAACTGTGATGGTTAG-ATA-----TCGAC-AAAATTTTGAAAAAACTG
* * *
160105 TCCCGAAAT
317 ACCCCAAAA
* * ** * * *
160114 TTTTTTTCCTCAATTATTTTGAGACAATAGTCAGGAAAAATATATAATTCAACCGAAAAAAAATT
1 TTTTTTT-CTGAATT-TTCTGCCACAATACTCAGAAAAAATATATAATTCAACC-CAAAAAAATT
* * * * *
160179 GAAGGGTCTTTCACGCATCTAATATCATTTTTCCATTTTTTTCCGAATTTATTTCAAATTAAATC
63 GAAGGCT-TTTCACGCTTCTAATATTATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATC
* * * * *
160244 GAAACAAGCTATAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGA
127 GAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGA
* * *
160309 TGAATATAGTTATTTCAAGGAGTCTTTATGCCAAAACTAATCCAAAACTGAGCCGGG-GCACCGA
192 TGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATAATACAAAACTGAGCCGGGAGC-CCGA
*** *
160373 AACACGTTTTTAGC-CCGAAAACTGTGATGGTTAG-TA-C-AC-AATTTTTGACTAAAAACTGAC
256 AACACGTTTTTAGCAAAAAAAACTGTGATGGTTAGATATCGACAAAATTTTGA--AAAAACTGAC
160433 CCACAAAA
319 CC-CAAAA
* * *
160441 TTTTTCTCTTGAATTTTCCGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAATATTG
1 TTTTTTTC-TGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTCAAC-CCAAAAAAATTG
* * *
160506 ACGAGCTTTTCACTCTTCTAATATTATTTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATTG
64 AAG-GCTTTTCACGCTTCTAATATTATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCG
* * *
160570 AAAGAAGATTTAGATGCTCGTAAAAACAAATCTTTATATCCAATGTGGCTGAGATTTGATTCGAT
128 AAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGAT
* *
160635 GAATATAGATATTTCAAGGAGT-TTT-TGCCCCAAAAATCATGCAAAACT
193 GAATATAGATATTTCAAGGAGTCTTTATG--CCAAAAATAATACAAAACT
160683 TAGTCCGTTC
Statistics
Matches: 472, Mismatches: 82, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
323 2 0.00
324 11 0.02
325 121 0.26
326 79 0.17
327 18 0.04
332 7 0.01
333 12 0.03
334 53 0.11
335 99 0.21
336 70 0.15
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (325 bp):
TTTTTTTCTGAATTTTCTGCCACAATACTCAGAAAAAATATATAATTCAACCCAAAAAAATTGAA
GGCTTTTCACGCTTCTAATATTATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAA
CAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTCGATGAA
TATAGATATTTCAAGGAGTCTTTATGCCAAAAATAATACAAAACTGAGCCGGGAGCCCGAAACAC
GTTTTTAGCAAAAAAAACTGTGATGGTTAGATATCGACAAAATTTTGAAAAAACTGACCCCAAAA
Found at i:161822 original size:324 final size:321
Alignment explanation
Indices: 160888--161851 Score: 1019
Period size: 332 Copynumber: 3.0 Consensus size: 321
160878 GCTTTTCAGT
* * ** * *
160888 CAAATATCATGCAAAACTGATACGGGGCCCCGAAACGCGTTTTCAGCTCAAAAACCGTGACGGTT
1 CAAAAATCATCCAAAACTGAGCCGGGGCCCCGAAACGCGTTTT-AGCCCAAAAACCGTGATGGTT
* * * * * *
160953 AATACATGATTTCGGCTAAAAACTAATCC-GAAATTTTTCTTTTTCTGAATTTTCAGCTAAAATA
65 AGTACACGATTTCGGCTAAAAACTGA-CCGGAAA--ATT-TTTTCCTGAATTTTCAGCCAAAATA
* *
161017 CTCAG-AAAAA-ATA-AA--CAACGCCAAAAAAATTGACGGGCTTCTCACGCTTCTAATATC-GT
126 CTCAGAAAAAATATATAATTCAAC-CCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCATT
*
161076 TTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
190 TTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTCGTAAAAACA
* * * * * * * * *
161141 AATCGTTACATCGAATTTGGCTGGGATTTGGCTCGATGAATATAGGTATTTCAAGGATTCTTTAT
255 AATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTATTTAT
161206 GC
320 GC
* * * * *
161208 CAAAAATCATGCAAAACTGAGCCGGGACCCCGGAACGTGTTTTTAG-CAAAAAACCGTGATGGTT
1 CAAAAATCATCCAAAACTGAGCCGGGGCCCCGAAACGCG-TTTTAGCCCAAAAACCGTGATGGTT
* * * * * * * **
161272 AGTATACGGTTTCGACTAAAATTTTCAAAAAATTGACTCGG-AAATTTTTTCGTCAGTTATTTTG
65 AGTACACGATTTCGGC--------T--AAAAACTGAC-CGGAAAATTTTTTCCTGAATT-TTCAG
* * * * * *
161336 CGACAATAGTCAGAAAAAATATATAATTCAACCGAAAAAAATTGAAGGGTTTTTCACGCTTCTAA
118 CCAAAATACTCAGAAAAAATATATAATTCAACCCAAAAAAATTGACGGGCTTTTCACGCTTCTAA
* * * * * * *
161401 TATTATTTTCCCATTTTTTTCCAAATTTATTTCAAATTAAATAGAAACAAGATACATATGCTCGT
183 TATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTCGT
* *
161466 AAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
248 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAG
161531 TATTTATGC
313 TATTTATGC
* * * *
161540 CAAAACTCATCCAAAATTGAGCCGGGGCACCGAAACGCGTTTCTAGCCCAAAAACTGTGATGGTT
1 CAAAAATCATCCAAAACTGAGCCGGGGCCCCGAAACGCGTTT-TAGCCCAAAAACCGTGATGGTT
* * * *
161605 AGTACACAATTTCGGCTAAAAACTGACCGGCAAAAATTTTTCCTGAATTTTCCGCCATAATACTC
65 AGTACACGATTTCGGCTAAAAACTGACCGG-AAAATTTTTTCCTGAATTTTCAGCCAAAATACTC
* * *
161670 AGAAAAAATATATAATTCAACACCAAAAATATTGACGAGCTTTTCACTCTTCTAATATCATTTTT
129 AGAAAAAATATATAATTCAAC-CCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCATTTTT
* * * * *
161735 CCATTTTTTTCCGAGTTAATTTCTAGTTAAATCGAAAGAAGATTCATATGCTCTTAAAACCAAAT
193 CCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTCGTAAAAACAAAT
* * *
161800 CCTTATATCTAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTCAAG
258 CCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAG
161852 AGGTCTTTGC
Statistics
Matches: 523, Mismatches: 96, Indels: 46
0.79 0.14 0.07
Matches are distributed among these distances:
319 26 0.05
320 35 0.07
321 4 0.01
322 3 0.01
323 41 0.08
324 150 0.29
325 1 0.00
326 8 0.02
327 16 0.03
328 6 0.01
329 13 0.02
330 3 0.01
331 35 0.07
332 154 0.29
333 28 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (321 bp):
CAAAAATCATCCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTAGCCCAAAAACCGTGATGGTTA
GTACACGATTTCGGCTAAAAACTGACCGGAAAATTTTTTCCTGAATTTTCAGCCAAAATACTCAG
AAAAAATATATAATTCAACCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCA
TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTCGTAAAAACAAATCCT
TAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTATTTATGC
Found at i:163793 original size:646 final size:635
Alignment explanation
Indices: 162111--163727 Score: 2107
Period size: 643 Copynumber: 2.5 Consensus size: 635
162101 AACTGATGCA
* * *
162111 GGGCCCGGAAACGCGTTTTTAGCCCAAAAACCATGACGATTAGTACATGATTTCGGCTAAAAAC-
1 GGGCCCTGAAACGCGTTTTTAGCCCAAAAACCGTGACGGTTAGTACATGATTTCGGCTAAAAACT
* * * *
162175 CATCCGTAATTTTTTTTTTCTGAATTTTCTGCTAAATTACTGAGAAAAAATAAATAATTCAATGC
66 AATCCG-AA--TTTTTTTTCTGAATTTTCTGCTAAA-AACTCAGAAAAAATAAATAATTCAACGC
* *
162240 CAAAAAAATTGACGGGCTTATCACGCTTCTAATACCGTTTTCCATTTTTTTCCGAATTAACTTCT
127 CAAAAAAATTGACGGGCTTATCACGCTTCTAATATCGTTTTCCATTTTTTTCCGAATTAATTTCT
* **
162305 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTACATCGAATTTGTTTGGGAT
192 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTACATCGAATTTGGCTGGGAT
162370 TTGGTTCGATGAATATAGGTATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGG
257 TTGGTTCGATGAATATAGGTATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGG
* ** *
162435 GACCCCGAAACGTGTTTTCAGTAAAAACCGTGATGGTTAGTATACGGTTTCGGCTAAAATTTTG-
322 GA-CCCGAAACGTG-TTTCTGTAAAAA-AATGATGGTTAGTATAC----TCGACTAAAATTTTGA
* *
162499 AAAAATTGACCCGAAAATTTTTTCCTCAATTATTTTGAGACAATAGTAAGGAAAAATATATAATT
380 AAAAATTGACCCGAAAAGTTTTTCCTCAATTATTTTGAGACAATAGTAAGAAAAAATATATAATT
*
162564 CAACCGAAAATAAATTGAAGGGTCTTTCACTCATCTAATATCATTTTTCCATTTTTTTTCCGAAT
445 CAACCGAAAATAAATTGAAGGGTCTTTCACGCATCTAATATCATTTTTCCATTTTTTTTCCGAAT
* * *
162629 TTATTTCAAATTGAATCGAAACAAGCTATAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTG
510 TTATTTCAAATTAAATCGAAACAAGATACAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTG
* *
162694 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTTATGCCAAAACTGAGTCG
575 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAACTAAGTCG
* * * *
162755 GGGCCCTGAAACGCGTTTTCAGCTCAAAAACCGCGACAGTTAGTA-ATGATTTCGGCTAAAAACT
1 GGGCCCTGAAACGCGTTTTTAGCCCAAAAACCGTGACGGTTAGTACATGATTTCGGCTAAAAACT
*
162819 AATCCGATTTTTTTTTTCTGAATTTTCTGCTAAAATACTCAGAAAAAATAAATAATTCAACGCCA
66 AATCCGA-ATTTTTTTTCTGAATTTTCTGCTAAAA-ACTCAGAAAAAATAAATAATTCAACGCCA
* *
162884 AAAAAATTGACGGGCTTCTCACGCTTCTAATATCGTTTTCCATTTTTTTTCTGAATTAATTTCTA
129 AAAAAATTGACGGGCTTATCACGCTTCTAATATCGTTTTCCA-TTTTTTTCCGAATTAATTTCTA
* * *
162949 ATTAAATTGAAACAAGATTCAAATGCTTGTAAAAACAAAT-TGTTACATCGAATTTGGCTGGGAT
193 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCT-TTACATCGAATTTGGCTGGGAT
* *
163013 TTGGTTTGATGAATATAGGTATTTCAAGGAGTGTTTACGCCAAAAATCATGCAAAACTGAGCCGG
257 TTGGTTCGATGAATATAGGTATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGG
* * *
163078 GACCCCGGAACGTGTTTTTAGCAAAAAAAACCGTGATGGTTAGTATACGGTTTCGACTAAAATTT
322 GA-CCCGAAACGTGTTTCT-G-TAAAAAAA---TGATGGTTAGTATAC----TCGACTAAAATTT
* **
163143 TGAAAAAATTGACCCGAAAAGTTTTTCCTCAATTATTTTGCGACAATAGTCTGAAAAAATATATA
377 TGAAAAAATTGACCCGAAAAGTTTTTCCTCAATTATTTTGAGACAATAGTAAGAAAAAATATATA
* * * *
163208 ATTCAACCGGAAAA-ACATTGAAGGGTTTTTCTCGCTTCTAATATCATTTTTCCA-TTTTTTTCC
442 ATTCAACC-GAAAATAAATTGAAGGGTCTTTCACGCATCTAATATCATTTTTCCATTTTTTTTCC
*
163271 GAATTTATTTCAAATTAAATCGAAACAAGATACATATGCTCGTAAAAATAAATCCTTAAATCCAA
506 GAATTTATTTCAAATTAAATCGAAACAAGATACAGATGCTCGTAAAAATAAATCCTTAAATCCAA
163336 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAACCCATCCA
571 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATG-----------CCA
163401 AAACTAAGTCG
625 AAACTAAGTCG
* * *
163412 GGGCACC-GAAACGCGTTTTTAGCCCAAAAACTGTGATGGTTAGTACATAATTTCGGCTAAAAAC
1 GGGC-CCTGAAACGCGTTTTTAGCCCAAAAACCGTGACGGTTAGTACATGATTTCGGCTAAAAAC
* * *** * * *
163476 TGACCCGCAAAACTTTTTCATGAATTTTCCGCTACAAAACTCAGAAAAAATATATAATTCAACAC
65 TAATCCG-AATTTTTTTTC-TGAATTTTCTGCTA-AAAACTCAGAAAAAATAAATAATTCAACGC
** * * * * *
163541 CAAAAATGTTGACGGACTTTTCACTCTTCTATTATCATGTTTTCCATTTATTTCCGAATTAATTT
127 CAAAAAAATTGACGGGCTTATCACGCTTCTAATATC--GTTTTCCATTTTTTTCCGAATTAATTT
* * * * *
163606 CTAATTAAATCGAAAGAAGATTCAGATGCTCGTAAAAACAAATCTTTATATCCAATGTGGCTGAG
190 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTACATCGAATTTGGCTGGG
* * * * *
163671 ATTTGATTCGATGAATATAGATATTTCAA-GAGGTCTTTGCCCCAAAAACCATGCAAA
255 ATTTGGTTCGATGAATATAGGTATTTCAAGGA-GTCTTTACGCCAAAAATCATGCAAA
163728 TCATAGTCGG
Statistics
Matches: 855, Mismatches: 86, Indels: 48
0.86 0.09 0.05
Matches are distributed among these distances:
642 95 0.11
643 173 0.20
644 48 0.06
646 153 0.18
647 100 0.12
648 5 0.01
657 49 0.06
658 30 0.04
659 71 0.08
660 122 0.14
661 9 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (635 bp):
GGGCCCTGAAACGCGTTTTTAGCCCAAAAACCGTGACGGTTAGTACATGATTTCGGCTAAAAACT
AATCCGAATTTTTTTTCTGAATTTTCTGCTAAAAACTCAGAAAAAATAAATAATTCAACGCCAAA
AAAATTGACGGGCTTATCACGCTTCTAATATCGTTTTCCATTTTTTTCCGAATTAATTTCTAATT
AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTACATCGAATTTGGCTGGGATTTGG
TTCGATGAATATAGGTATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGACC
CGAAACGTGTTTCTGTAAAAAAATGATGGTTAGTATACTCGACTAAAATTTTGAAAAAATTGACC
CGAAAAGTTTTTCCTCAATTATTTTGAGACAATAGTAAGAAAAAATATATAATTCAACCGAAAAT
AAATTGAAGGGTCTTTCACGCATCTAATATCATTTTTCCATTTTTTTTCCGAATTTATTTCAAAT
TAAATCGAAACAAGATACAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTG
GTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAACTAAGTCG
Found at i:164856 original size:326 final size:320
Alignment explanation
Indices: 163947--164922 Score: 1018
Period size: 325 Copynumber: 3.0 Consensus size: 320
163937 AAATATCATG
* * * *
163947 CAAAACTGATG-CGGGGCCTCGAAACGCGTTTTCAGCCCAAAAACCGTGACGGTTAGTACATGAT
1 CAAAACTGA-GCCGGGGCC-CGAAACGTGTTTTTAGCCCAAAAACCGTGATGGTTAGTACA-CAT
* * * * * *
164011 TTAGGCTAAAAACT-AACC-CGAATTTTTTTCTTCTGAA-TTTGTACTACAATACTCAGAAAAAA
63 TTCGGCTAAAAACTGACCCACAAATTTTTTTC--CTGAATTTTCTGCCACAATACTCAGAAAAAA
* * * *
164073 TAAATAATTCAACGCCAAAAAAATTGATGGGC-TTCTCACGCTTCTAATATCG-TTTTGCA-TTT
126 TATATAATTCAAC-CCGAAAAAATT-AAGGGCTTTC-CACGCTTCTAATATCGTTTTTCCATTTT
* * *
164135 TTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTACA
188 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* * * * * *
164200 TCGAATTTGGCTGGGATTTGGTTCGATGAATATAGGTATATCAAGGAGTCTTTACGCCAAAAATC
253 TCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAACC
*
164265 ATG
318 ATC
* * * * *
164268 CAAAACTGAGCC--GG---G-AATGTGTTTTTAG-CAAAAAACCGTCATGGTTAGTATACGGTTT
1 CAAAACTGAGCCGGGGCCCGAAACGTGTTTTTAGCCCAAAAACCGTGATGGTTAGTACAC-ATTT
* * * * * * *
164326 CGACTAAAATTTTGAAAAAATTGACCCGA-AAA-GTTTTTCCTCAATTATTTTGCGACAATAGTC
65 CGGC--------T--AAAAACTGACCC-ACAAATTTTTTTCCTGAATT-TTCTGCCACAATACTC
* * * * *
164389 AGAAAAAATATATAATTCAACCGGAAAAAATTGAAGGGTTTTTCTCGCTTCTAATATCATTTTTC
118 AGAAAAAATATATAATTCAACCCGAAAAAATT-AAGGGCTTTCCACGCTTCTAATATCGTTTTTC
* * * * *
164454 CATTTTTTTCCGAATTTATTTCAAATTAAATCGAAACAAGATAT-ATATGCTCGTCAAAATAAAT
182 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT-TCAGATGCTCGTAAAAACAAAT
* *
164518 CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCC
246 CCTTAAATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCC
*
164583 AAAACCCATC
311 AAAAACCATC
*
164593 CAAAACTGAGCCGGGGCACCGAAACGTGTTTTTAGCCCAAAAACTGTGATGGTTAGTACACATTT
1 CAAAACTGAGCCGGGGC-CCGAAACGTGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACA-TT
164658 TCGGCTAAAAACTGACCCACAAATTTTTTTCCTGAATTTTCTGCCACAATACTCAGAAAAAATAT
64 TCGGCTAAAAACTGACCCACAAATTTTTTTCCTGAATTTTCTGCCACAATACTCAGAAAAAATAT
* **
164723 ATAATTCAACACCGAAAATATTAACGGGCTTTCCACTATTCTAATATCGTTTTTTTCCATTTTTT
129 ATAATTCAAC-CCGAAAAAATTAA-GGGCTTTCCACGCTTCTAATATCG--TTTTTCCATTTTTT
* *
164788 TCCGAATTAATTTCTAATTAAATCGAAAGAAGATTCAGATGCTCGTAAAAACAAATCCTTATATC
190 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC
* *
164853 CAATGTCGCTGAGATTTGGTTCGATGAATATAGATATTTCAA-GAGGTCTTTGC-CCTAAAAACC
255 CAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGA-GTCTTTACGCC-AAAAACC
*
164916 ATG
318 ATC
164919 CAAA
1 CAAA
164923 TCATAGTCGG
Statistics
Matches: 535, Mismatches: 81, Indels: 73
0.78 0.12 0.11
Matches are distributed among these distances:
313 25 0.05
314 10 0.02
315 1 0.00
319 2 0.00
320 1 0.00
321 11 0.02
322 5 0.01
323 85 0.16
324 88 0.16
325 136 0.25
326 129 0.24
327 2 0.00
331 1 0.00
332 12 0.02
333 27 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (320 bp):
CAAAACTGAGCCGGGGCCCGAAACGTGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACATTTC
GGCTAAAAACTGACCCACAAATTTTTTTCCTGAATTTTCTGCCACAATACTCAGAAAAAATATAT
AATTCAACCCGAAAAAATTAAGGGCTTTCCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAA
TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
GGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAACCATC
Done.