Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011749.1 Corchorus capsularis cultivar CVL-1 contig11770, 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: 122768
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2900 original size:15 final size:15
Alignment explanation
Indices: 2876--2907 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2866 CAAACTAACT
*
2876 TTAAGTGTGGAATTG
1 TTAAGGGTGGAATTG
2891 TTAAGGGTGGAATTG
1 TTAAGGGTGGAATTG
2906 TT
1 TT
2908 TTAAGCATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTAAGGGTGGAATTG
Found at i:5357 original size:6 final size:6
Alignment explanation
Indices: 5346--5372 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5336 CCTGCTCTCT
5346 TTTTTC TTTTTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT
5373 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:12948 original size:29 final size:29
Alignment explanation
Indices: 12903--12978 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
12893 TTAGGCTAAA
* *
12903 GGGGCAAAATGTCCCAAAATTGAAGTTTAG
1 GGGGCAAAATGT-CCAAAATTAAAGTTCAG
*
12933 GGGGTAAAATGTCCAAAATTAAAGTTCAG
1 GGGGCAAAATGTCCAAAATTAAAGTTCAG
*
12962 GGTGCAAAATGTCCAAA
1 GGGGCAAAATGTCCAAA
12979 CGCTACAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 30 0.73
30 11 0.27
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.22
Consensus pattern (29 bp):
GGGGCAAAATGTCCAAAATTAAAGTTCAG
Found at i:13002 original size:31 final size:28
Alignment explanation
Indices: 12902--13002 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 28
12892 GTTAGGCTAA
* * * *
12902 AGGGGCAAAATGTCCCAAAATTGAAGTTT
1 AGGGGGAAAATGT-CCAAAACTAAAGTTC
*
12931 AGGGGGTAAAATGTCCAAAATTAAAGTTC
1 AGGGGG-AAAATGTCCAAAACTAAAGTTC
* *
12960 AGGGTGCAAAATGTCCAAACGCTACAAGTTC
1 AGGG-GGAAAATGTCCAAA-ACTA-AAGTTC
12991 AAGGGGGAAAAT
1 -AGGGGGAAAAT
13003 TGTAGTTTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 34 0.57
30 10 0.17
31 12 0.20
32 4 0.07
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (28 bp):
AGGGGGAAAATGTCCAAAACTAAAGTTC
Found at i:13334 original size:31 final size:31
Alignment explanation
Indices: 13288--13385 Score: 151
Period size: 31 Copynumber: 3.2 Consensus size: 31
13278 GTGTCCGACG
* * *
13288 TGGCACGCCACGTGTACCAAAAAGTGACATA
1 TGGCACGTCATGTGTACCAAAAAGTGACACA
13319 TGGCACGTCATGTGTACCAAAAAGTGACACA
1 TGGCACGTCATGTGTACCAAAAAGTGACACA
* *
13350 TGTCACGTCATGTGTACCAAAAAGTGACACG
1 TGGCACGTCATGTGTACCAAAAAGTGACACA
13381 TGGCA
1 TGGCA
13386 TGCCACATGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (31 bp):
TGGCACGTCATGTGTACCAAAAAGTGACACA
Found at i:15827 original size:22 final size:21
Alignment explanation
Indices: 15758--15827 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
15748 ATTTGAATAG
*
15758 TTTTCAAGTTAAGAATATTTT
1 TTTTCACGTTAAGAATATTTT
* *
15779 TTATTCACATTAAG-ATTTTTT
1 TT-TTCACGTTAAGAATATTTT
*
15800 TCTTTCACGTAAAGAAATATTTT
1 T-TTTCACGTTAAG-AATATTTT
15823 TTTTC
1 TTTTC
15828 TCAAAAGGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
21 18 0.46
22 14 0.36
23 7 0.18
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTCACGTTAAGAATATTTT
Found at i:35798 original size:22 final size:22
Alignment explanation
Indices: 35770--35836 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
35760 TGGATAAGTG
35770 TTTTAAATGGTTGTTATCAAAA
1 TTTTAAATGGTTGTTATCAAAA
35792 TTTTAAAT-GTTGGTT-TACAAAA
1 TTTTAAATGGTT-GTTAT-CAAAA
* * * *
35814 TTTCAAAAGGTAGTTAGCAAAA
1 TTTTAAATGGTTGTTATCAAAA
35836 T
1 T
35837 CTCATTGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 4 0.11
22 31 0.84
23 2 0.05
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
TTTTAAATGGTTGTTATCAAAA
Found at i:43630 original size:16 final size:16
Alignment explanation
Indices: 43611--43644 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43601 CTTTGTTTGC
*
43611 TTTCTTGGGTTCTTCT
1 TTTCTTGAGTTCTTCT
*
43627 TTTCTTGAGTTTTTCT
1 TTTCTTGAGTTCTTCT
43643 TT
1 TT
43645 AAAGCCCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.15, T:0.68
Consensus pattern (16 bp):
TTTCTTGAGTTCTTCT
Found at i:51841 original size:6 final size:6
Alignment explanation
Indices: 51825--51863 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
51815 ATGGACCTTG
**
51825 TAAAAT T-AAAT TAAAAT TTTAAT TAAAAT TAAAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAA
51864 CATTTCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAAAT
Found at i:51850 original size:12 final size:12
Alignment explanation
Indices: 51825--51868 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
51815 ATGGACCTTG
51825 TAAAA-TTAAAT
1 TAAAATTTAAAT
*
51836 TAAAATTTTAAT
1 TAAAATTTAAAT
*
51848 TAAAATTAAAAT
1 TAAAATTTAAAT
51860 TAAACATTT
1 TAAA-ATTT
51869 CATTGTTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 5 0.19
12 19 0.70
13 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATTTAAAT
Found at i:55967 original size:445 final size:446
Alignment explanation
Indices: 55431--56323 Score: 1654
Period size: 446 Copynumber: 2.0 Consensus size: 446
55421 ACATTGAACT
55431 ATCAGATAGAAAATGTCAATCATAATTACTTTTTAAATTAAAAATGGTAAAAATAAAAAAAACTT
1 ATCAGATAGAAAATGTCAATCATAATTACTTTTTAAATTAAAAATGGTAAAAATAAAAAAAACTT
*
55496 ATATAAAATATTGAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTCG
66 ATATAAAATATTGAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
55561 AAAAATTTTAATATATCCAAA-TTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAAT
131 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAAT
55625 TAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTATATCC-AA
196 TAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAA
* *
55689 TTTTTTGTGTAGAGATAAAGTAATTATAAAGATATTAGATTTTATTTAATTGAATAAAAATAGAG
261 TTTTTT-TGTAAAAATAAAGTAATTATAAAGATATTAGATTTTATTTAATTGAATAAAAATAGAG
*
55754 TTTCTAGTAGAATAAAATTATAATAGTTAAGTAAGGGCATTTAAGACAATATATTTGAAAAATAA
325 TTTCTAGTAGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATATATTTGAAAAATAA
55819 GGGTACAATAGGCAATTCAAAAGTTTCTCAAAACTCGTACTTTTATATATAGTATAG
390 GGGTACAATAGGCAATTCAAAAGTTTCTCAAAACTCGTACTTTTATATATAGTATAG
55876 ATCAGATAGAAAATGTCAATCATAATTACATTTTTTAAAATT-AAAATGGTAAAAA-ATAAAAAA
1 ATCAGATAGAAAATGTCAATCATAATTAC--TTTTT-AAATTAAAAATGGTAAAAATA-AAAAAA
55939 A-TTATATAAAATATTG-AATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATA
62 ACTTATATAAAATATTGAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATA
56002 TTAGAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATT
127 TTAGAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATT
56067 TAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTATATC
192 TAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTATATC
56132 CAAATTTTTTTGTAAAAATAAAGTAATTATAAAGATATTAGATTTTATTTAATTGAATAAAAATA
257 CAAATTTTTTTGTAAAAATAAAGTAATTATAAAGATATTAGATTTTATTTAATTGAATAAAAATA
56197 GAGTTTCTAGTAGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATATATTTGAAAAA
322 GAGTTTCTAGTAGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATATATTTGAAAAA
*
56262 TAAGGGTACAATAGGCAATTCAAGAGTTTCTCAAAACTCGTACTTTTATATATAGTATAG
387 TAAGGGTACAATAGGCAATTCAAAAGTTTCTCAAAACTCGTACTTTTATATATAGTATAG
56322 AT
1 AT
56324 GTGCTACCTT
Statistics
Matches: 437, Mismatches: 5, Indels: 11
0.96 0.01 0.02
Matches are distributed among these distances:
445 100 0.23
446 299 0.68
447 33 0.08
448 5 0.01
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (446 bp):
ATCAGATAGAAAATGTCAATCATAATTACTTTTTAAATTAAAAATGGTAAAAATAAAAAAAACTT
ATATAAAATATTGAAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAAT
TAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAA
TTTTTTTGTAAAAATAAAGTAATTATAAAGATATTAGATTTTATTTAATTGAATAAAAATAGAGT
TTCTAGTAGAATAAAACTATAATAGTTAAGTAAGGGCATTTAAGACAATATATTTGAAAAATAAG
GGTACAATAGGCAATTCAAAAGTTTCTCAAAACTCGTACTTTTATATATAGTATAG
Found at i:56147 original size:109 final size:109
Alignment explanation
Indices: 55511--56216 Score: 517
Period size: 109 Copynumber: 6.4 Consensus size: 109
55501 AAATATTGAA
*
55511 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTCGAAAAATTTTAATATA
1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAATTTTAATATA
55576 TCCAAA-TTTTTGGTAAAAATAAAGTAATTATAAAGATATTAG-
66 TCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGT
*
55618 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTAT
1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG-AAAAATTTTAATAT
* *
55683 ATCC-AATTTTTTGTGTAGAGATAAAGTAATTATAAAGATATTAGATTTT
65 ATCCAAATTTTTTG-GTAAAAATAAAGTAATTATAAAGATATTAG----T
* * * * **
55732 ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAATTATAATAGTTAAGTAAGGGCA-TTT
1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGT-ATA-TT-AG-AA--AAATTTT
* * * * ** * **
55796 -A-AGA--C-AATATATTT-G-AAAAATAAGGGTACAATAGGCAA-TTCAAAAGT
60 AATATATCCAAAT-TTTTTGGTAAAAATAA-AGTA-ATTA-TAAAGAT-ATTAGT
** ** * * * * * *
55843 -TTCTCAAAACTCGTACTTTTATATATAG--TATAGATCAG-ATAGAAAATGTCA-ATCATAATT
1 ATT-T---AA-T--TAAATGAAAATAGAGTTTTTAG-T-AGAATA-AAATTGT-ATATTAGAA--
* *** ** * *
55903 ACATTTT--T-TA---AAATTAAAATGGTAAAAAATAAAAAAATTATATAAAATATT-GA
53 AAATTTTAATATATCCAAATT-TTTTGGT-AAAAATAAAGTAATTATA-AAGATATTAGT
55956 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAATTTTAATATA
1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAATTTTAATATA
56021 TCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAG-
66 TCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGT
*
56064 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAAATTTTAGTAT
1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG-AAAAATTTTAATAT
*
56129 ATCCAAATTTTTTTGTAAAAATAAAGTAATTATAAAGATATTAGATTTT
65 ATCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAG----T
* * *
56178 ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAA
56217 CTATAATAGT
Statistics
Matches: 470, Mismatches: 74, Indels: 103
0.73 0.11 0.16
Matches are distributed among these distances:
105 6 0.01
106 1 0.00
107 74 0.16
108 86 0.18
109 106 0.23
110 8 0.02
111 7 0.01
112 7 0.01
113 16 0.03
114 98 0.21
115 20 0.04
116 17 0.04
117 20 0.04
118 3 0.01
119 1 0.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (109 bp):
ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGAAAAATTTTAATATA
TCCAAATTTTTTGGTAAAAATAAAGTAATTATAAAGATATTAGT
Found at i:66299 original size:62 final size:63
Alignment explanation
Indices: 66220--66340 Score: 217
Period size: 62 Copynumber: 1.9 Consensus size: 63
66210 TCTAAATGAG
*
66220 AAATCAACTTCAAAGTAATAAACTATCATAAATAAACCATTTACCTACTAAATACACAACGAA
1 AAATCAACTTCAAAGTAAGAAACTATCATAAATAAACCATTTACCTACTAAATACACAACGAA
*
66283 AAATCAAC-TCAAAGTAAGAAACTATCATAAATAAACCATTTACTTACTAAATACACAA
1 AAATCAACTTCAAAGTAAGAAACTATCATAAATAAACCATTTACCTACTAAATACACAA
66341 ATAAACAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 48 0.86
63 8 0.14
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.24
Consensus pattern (63 bp):
AAATCAACTTCAAAGTAAGAAACTATCATAAATAAACCATTTACCTACTAAATACACAACGAA
Found at i:75706 original size:6 final size:6
Alignment explanation
Indices: 75695--75740 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
75685 AATAATTACT
* * * *
75695 CTATTA CTATTA CTATTA CTATTA TTATTA TTATTA TTACTA CTAT
1 CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTATTA CTAT
75741 ATAACTTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (6 bp):
CTATTA
Found at i:77623 original size:21 final size:21
Alignment explanation
Indices: 77598--77654 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
77588 GCAACAGCGC
* *
77598 CATGGGTAATATTAGCGCAGA
1 CATGGGTAATATGAGCACAGA
*
77619 CATGGGTAATATGAGCACAGC
1 CATGGGTAATATGAGCACAGA
*
77640 CATGGATAATATGAG
1 CATGGGTAATATGAG
77655 ATTAGACCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (21 bp):
CATGGGTAATATGAGCACAGA
Found at i:77883 original size:78 final size:79
Alignment explanation
Indices: 77699--77895 Score: 288
Period size: 78 Copynumber: 2.5 Consensus size: 79
77689 TTACCGAGTG
* * * *
77699 CAGATCGAATTTCCGAGTTGGCCGAGGATGTTATGAACAATATTAGATTAGACCCTGTTGTTGAT
1 CAGATCGAATTTCCGAGTTGGCCGAGGATGTTATGAATAATATGAGACTAGACCC--TTGTTGAC
77764 GCTTCACAGAGTGCAA
64 GCTTCACAGAGTGCAA
* * *
77780 CATATCGAATTTCGGAGTTGGCCGAGGATGTTATGAATAATATGGGACTAGACCC-TGTTGACGC
1 CAGATCGAATTTCCGAGTTGGCCGAGGATGTTATGAATAATATGAGACTAGACCCTTGTTGACGC
*
77844 TTCACCGAGTGCAA
66 TTCACAGAGTGCAA
*
77858 CAGATCGAATTTCCGAGTTGCCCGAGGATGTTATGAAT
1 CAGATCGAATTTCCGAGTTGGCCGAGGATGTTATGAAT
77896 CGTATCCTCT
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
78 56 0.53
81 49 0.47
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (79 bp):
CAGATCGAATTTCCGAGTTGGCCGAGGATGTTATGAATAATATGAGACTAGACCCTTGTTGACGC
TTCACAGAGTGCAA
Found at i:83473 original size:25 final size:25
Alignment explanation
Indices: 83439--83488 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
83429 ACTACTAAAC
83439 CCCCACTATGAATAATGGAATATTG
1 CCCCACTATGAATAATGGAATATTG
83464 CCCCACTATGAATAATGGAATATTG
1 CCCCACTATGAATAATGGAATATTG
83489 GTAGTACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (25 bp):
CCCCACTATGAATAATGGAATATTG
Found at i:84807 original size:1 final size:1
Alignment explanation
Indices: 84801--84830 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
84791 AGTTTTCAGG
84801 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
84831 AACTCTCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:100431 original size:21 final size:21
Alignment explanation
Indices: 100405--100447 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
100395 CCCTCATTAA
100405 CGGACCATCAGTCACAAAACC
1 CGGACCATCAGTCACAAAACC
100426 CGGACCATCAGTCACAAAACC
1 CGGACCATCAGTCACAAAACC
100447 C
1 C
100448 TATGTGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.40, G:0.14, T:0.09
Consensus pattern (21 bp):
CGGACCATCAGTCACAAAACC
Found at i:100542 original size:31 final size:29
Alignment explanation
Indices: 100499--100573 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 29
100489 CTTAATACAC
*
100499 TTTTGCCCCTTAAACTTGTACGGTTTGGACG
1 TTTTGCCCCTTAAACTT-TA-AGTTTGGACG
* *
100530 TTTTGCCTCTTAAACTTTAATTTTGGACG
1 TTTTGCCCCTTAAACTTTAAGTTTGGACG
*
100559 TTTTGTCCC-TAAACT
1 TTTTGCCCCTTAAACT
100574 CTTAGTGCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.15
29 15 0.38
30 2 0.05
31 16 0.41
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTTGCCCCTTAAACTTTAAGTTTGGACG
Found at i:102812 original size:78 final size:78
Alignment explanation
Indices: 102683--102845 Score: 263
Period size: 78 Copynumber: 2.1 Consensus size: 78
102673 AGAGGATACG
* * *
102683 ATTCATAACATCCTCGGGCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCATTAGCAGGGT
1 ATTCATAACATCCTCGGCCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCATCAGCAGAGT
102748 CTAATCTCATATT
66 CTAATCTCATATT
* *
102761 ATTCATAACATCCTCGGCCAACTTGGAAATTCGATCTGTTGCACTTGGTGAAGCATCAGCAGAGT
1 ATTCATAACATCCTCGGCCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCATCAGCAGAGT
*
102826 TTAATCTCATATT
66 CTAATCTCATATT
*
102839 ATCCATA
1 ATTCATA
102846 GTTGTGCTCA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (78 bp):
ATTCATAACATCCTCGGCCAACTCGGAAATTCGATCTGTTGCACTCGGTGAAGCATCAGCAGAGT
CTAATCTCATATT
Found at i:103240 original size:16 final size:16
Alignment explanation
Indices: 103219--103252 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
103209 AATCCTTACA
*
103219 AACAATGGGTTGGATC
1 AACAATGAGTTGGATC
103235 AACAATGAGTTGGATC
1 AACAATGAGTTGGATC
103251 AA
1 AA
103253 GTGGTAAATG
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:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (16 bp):
AACAATGAGTTGGATC
Found at i:112642 original size:30 final size:32
Alignment explanation
Indices: 112598--112663 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
112588 TTTAAATCGT
* * *
112598 GACAATTTGTCTCCTGAA-TTTCTAAATTCAA
1 GACAATTAGTCTCCTAAATTTTCCAAATTCAA
*
112629 GACAATTAG-CTCCTAAATTTTCCAAGTTCAA
1 GACAATTAGTCTCCTAAATTTTCCAAATTCAA
112660 GACA
1 GACA
112664 TTTTATTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (32 bp):
GACAATTAGTCTCCTAAATTTTCCAAATTCAA
Found at i:119590 original size:200 final size:198
Alignment explanation
Indices: 119012--120514 Score: 1698
Period size: 200 Copynumber: 7.5 Consensus size: 198
119002 TCAAATCACT
* * * *
119012 TTATATAATTTTTCTTATAGGAGTATTATACAATACACTTTTTCAGTGTAAATTTTGCACTCCCT
1 TTATATAATTTTTCTTATAGGATTATTATACAATACAC--TGTCAGTGTAAATTTTGGACTCCAT
* * *
119077 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAAAACAT
64 AAGCGGGTTAAGAAGTTGACACATACCTCATTT-ATAATTAATTAAATATTTAATATTAATACAT
* * * * * *
119142 ATTCCTTAAGGGGACACATGTCAACCCTTAAACTCTCCACGTGCAGTCCGCTAAATTCGACTGAC
128 ATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGAC
*
119207 AGTGTA
193 GGTGTA
* * * * *
119213 -TAGTATAATTTTTCTTATAAGATCATTATACAATCCACTGTGAGTGTAAATTTTGGAATCCATA
1 TTA-TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATA
* *
119277 AACGGGTTAAGAAGTTGACATATACCTCATTTCATAATTAATTAAATATTTAATTTAATATTAAT
65 AGCGGGTTAAGAAGTTGACACATACCTCATTT-ATAATTAATT-AA-A--T-ATTTAATATTAAT
* * * * *
119342 ACACATTCCCTAAGGGGACACATGTCAACCCTTCAACCCCGTACGTGCAGTCTGCTAAAATCCAC
124 ACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAC
*
119407 TGGCGGTGTA
189 TGACGGTGTA
* * * * *
119417 TTATATAATTTTTCTTATA-GAGTTATCATACAACACGCTGTCAGTGTAAATTTTTAGACTCTAT
1 TTATATAATTTTTCTTATAGGA-TTATTATACAATACACTGTCAGTGTAAA-TTTTGGACTCCAT
* * * * *
119481 AAGAGGGTTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATATATAATATTAGTACAT
64 AAGCGGGTTAAGAAGTTGACACATACCTCATTT-ATAATTAATTAAATATTTAATATTAATACAT
* * *
119546 ATTCCCTAAGGAGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAATTAC
128 ATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGAC
119611 GGTGTA
193 GGTGTA
* * * * *
119617 -TAGTATAATTTTTCTTATAGGATTATTATACAATAAACTATCACTGTAAATTTTGGAATCCAAA
1 TTA-TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATA
* *
119681 AGCGGGTTAAGAAATTGACACATACCTTATTTCATAATT-A--AAATATTTAATATTAATACATA
65 AGCGGGTTAAGAAGTTGACACATACCTCATTT-ATAATTAATTAAATATTTAATATTAATACATA
* *
119743 TTCCTTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTCCAGCACGTGCAGTCTACTAAACT
129 TTCCCTAAGGGGACACATGTCAACCCTTAAA---C-C-C-T---GCACGTGCAGTCTGCTAAACT
** * *
119808 TGACTGGCGTTGTA
185 CCACTGACGGTGTA
* * * * *
119822 TTGTACAATTTTTCTTATAGGATTATTATACAATACACAT-TAAATGTAAATTTTGGACTCAATA
1 TTATATAATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTGGACTCCATA
* * * * * * *
119886 AGCGGGTTAAGAAGTTGAAATATGCCTTATTTTATAATTAATCAAACAATTTAATATTAATACCT
65 AGCGGGTTAAGAAGTTGACACATACCTCA-TTTATAATTAATTAAA-TATTTAATATTAATACAT
* * * *
119951 ATTCCCAAAGGGGACACATGTCAACCTTTAAACCCTGCACGCGCAGTCTGCTAAACTCCATTGAC
128 ATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGAC
120016 GGTGTA
193 GGTGTA
* * * * * *
120022 CTGTATAATTGTTCTTATAGGATTATTATACAATAAATTGTCAATGTAAAATTTTGGACTCCATA
1 TTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGT-AAATTTTGGACTCCATA
* * *
120087 AGCGGGTTAAGAAGTTGACGCATACCCCCACTTTATAATTAAATAAATATTTAATATTAATACAT
65 AGCGGGTTAAGAAGTTGACACATA-CCTCA-TTTATAATTAATTAAATATTTAATATTAATACAT
* * * *
120152 ATTCCCTAAGAGGACACATGTCTACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCTACTTAC
128 ATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGAC
120217 GGTGTA
193 GGTGTA
* * * *
120223 -TAGTATAATATTTCTTATAGGATTATTTTACAATAAACTGTCAGTGTAAATTTTGAACTCCATA
1 TTA-TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATA
*
120287 AGCGGGTTAAGAAGTTGATACATTACC-CATTTCATAATT-A--AAATATTTAATATTAATACAT
65 AGCGGGTTAAGAAGTTGACACA-TACCTCATTT-ATAATTAATTAAATATTTAATATTAATACAT
* * * *
120348 ATTCCTTAAAGGGACACATGTCAACCTTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTTAC
128 ATTCCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGAC
*
120413 GGTATA
193 GGTGTA
* * * * * * * *
120419 TAATATAATTTTTCTTATAGGATTATTATACAATAAATTGTCCGTATAAGTTTTGAATTCCATAA
1 TTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAA
* * *
120484 GCGGATTAAGAAGTTGACACACATCTCATTT
66 GCGGGTTAAGAAGTTGACACATACCTCATTT
120515 CACAAAAATA
Statistics
Matches: 1112, Mismatches: 155, Indels: 75
0.83 0.12 0.06
Matches are distributed among these distances:
195 2 0.00
196 213 0.19
197 1 0.00
198 5 0.00
199 116 0.10
200 226 0.20
201 192 0.17
202 18 0.02
203 5 0.00
204 116 0.10
205 163 0.15
206 7 0.01
208 3 0.00
209 45 0.04
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (198 bp):
TTATATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAA
GCGGGTTAAGAAGTTGACACATACCTCATTTATAATTAATTAAATATTTAATATTAATACATATT
CCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTGACGGT
GTA
Found at i:119895 original size:404 final size:396
Alignment explanation
Indices: 119015--120516 Score: 1760
Period size: 404 Copynumber: 3.7 Consensus size: 396
119005 AATCACTTTA
* * * *
119015 TATAATTTTTCTTATAGGAGTATTATACAATACACTTTTTCAGTGTAAATTTTGCACTCCCTAAG
1 TATAATTTTTCTTATAGGATTATTATACAATACAC--TGTCAGTGTAAATTTTGGACTCCATAAG
* *
119080 CGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAAAACATATT
64 CGGGTTAAGAAGTTGACACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATT
* * * * * * * * *
119145 CCTTAAGGGGACACATGTCAACCCTTAAACTCTCCACGTGCAGTCCGCTAAATTCGACTGACAGT
129 CCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAATTACGGT
* * ** * *
119210 GTATAGTATAATTTTTCTTATAAGATCATTATACAATCCACTGTGAGTGTAAATTTTGGAATCCA
194 GTATAGTATAATTTTTCTTATAGGATTATTATACAATAAACTGTCACTGTAAATTTTGGAATCCA
*
119275 TAAA-CGGGTTAAGAAGTTGACATATACCTCATTTCATAATTAATTAAATATTTAATTTAATATT
259 -AAAGCGGGTTAAGAAGTTGACACATACCTCATTTC---A-TAATTAAA-A--T-ATTTAATATT
* * *
119339 AATACACATTCCCTAAGGGGACACATGTCAACCCTTCAACCCCGT--ACGTGCAGTCTGCTAAAA
315 AATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGTGCACGTGCAGTCTGCTAAAC
* *
119402 TCCACTGGCGGTGTATTA
380 T-TACTGGCGGTGTATTG
* * * * *
119420 TATAATTTTTCTTATA-GAGTTATCATACAACACGCTGTCAGTGTAAATTTTTAGACTCTATAAG
1 TATAATTTTTCTTATAGGA-TTATTATACAATACACTGTCAGTGTAAA-TTTTGGACTCCATAAG
* * * *
119484 AGGGTTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATATATAATATTAGTACATATT
64 CGGGTTAAGAAGTTGACACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATT
*
119549 CCCTAAGGAGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAATTACGGT
129 CCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAATTACGGT
*
119614 GTATAGTATAATTTTTCTTATAGGATTATTATACAATAAACTATCACTGTAAATTTTGGAATCCA
194 GTATAGTATAATTTTTCTTATAGGATTATTATACAATAAACTGTCACTGTAAATTTTGGAATCCA
* *
119679 AAAGCGGGTTAAGAAATTGACACATACCTTATTTCATAATTAAAATATTTAATATTAATACATAT
259 AAAGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAAAATATTTAATATTAATACATAT
* *
119744 TCCTTAAGGGGACACATGTCAACCCTTAAACCCCGCACGTCCAGCACGTGCAGTCTACTAAACTT
324 TCCCTAAGGGGACACATGTCAACCCTTAAA--CC-C-CGT---GCACGTGCAGTCTGCTAAACTT
*
119809 GACTGGCGTTGTATTG
382 -ACTGGCGGTGTATTG
* * * *
119825 TACAATTTTTCTTATAGGATTATTATACAATACACAT-TAAATGTAAATTTTGGACTCAATAAGC
1 TATAATTTTTCTTATAGGATTATTATACAATACAC-TGTCAGTGTAAATTTTGGACTCCATAAGC
* * * * * * * * *
119889 GGGTTAAGAAGTTGAAATATGCCTTATTTTATAATTAATCAAACAATTTAATATTAATACCTATT
65 GGGTTAAGAAGTTGACACATACCTCATTTCATAATCAATTAAA-TATTTAATATTAATACATATT
* * *
119954 CCCAAAGGGGACACATGTCAACCTTTAAACCCTGCACGCGCAGTCTGCTAAACTCC-ATTGACGG
129 CCCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAATT-ACGG
* * * *
120018 TGTACT-GTATAATTGTTCTTATAGGATTATTATACAATAAATTGTCAATGTAAAATTTTGGACT
193 TGTA-TAGTATAATTTTTCTTATAGGATTATTATACAATAAACTGTCACTGT-AAATTTTGGAAT
* * *
120082 CCATAAGCGGGTTAAGAAGTTGACGCATACCCCCACTTT-ATAATTAAATAAATATTTAATATTA
256 CCAAAAGCGGGTTAAGAAGTTGACACATA-CCTCA-TTTCATAATT--A-AAATATTTAATATTA
* *
120146 ATACATATTCCCTAAGAGGACACATGTCTACCCTTAAA-CCC-TGCACGTGCAGTCTGCTAAACT
316 ATACATATTCCCTAAGGGGACACATGTCAACCCTTAAACCCCGTGCACGTGCAGTCTGCTAAACT
** *
120209 CTACTTACGGTGTATAG
381 -TACTGGCGGTGTATTG
* * * *
120226 TATAATATTTCTTATAGGATTATTTTACAATAAACTGTCAGTGTAAATTTTGAACTCCATAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCG
* *
120291 GGTTAAGAAGTTGATACATTACC-CATTTCATAAT---TAAAATATTTAATATTAATACATATTC
66 GGTTAAGAAGTTGACACA-TACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTC
* * * * *
120352 CTTAAAGGGACACATGTCAACCTTTAAACCCTGCACGTGCAGTCTGCTAAACTCCACTTACGGTA
130 CCTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAATTACGGTG
* *
120417 TATAATATAATTTTTCTTATAGGATTATTATACAATAAATTGTC-C-GTATAAGTTTT-GAATTC
195 TATAGTATAATTTTTCTTATAGGATTATTATACAATAAACTGTCACTGTA-AA-TTTTGGAA-TC
* * * *
120479 CATAAGCGGATTAAGAAGTTGACACACATCTCATTTCA
257 CAAAAGCGGGTTAAGAAGTTGACACATACCTCATTTCA
120517 CAAAAATAAT
Statistics
Matches: 947, Mismatches: 117, Indels: 76
0.83 0.10 0.07
Matches are distributed among these distances:
394 4 0.00
395 10 0.01
396 78 0.08
397 117 0.12
398 8 0.01
399 2 0.00
400 12 0.01
401 112 0.12
402 4 0.00
403 14 0.01
404 267 0.28
405 213 0.22
406 42 0.04
407 10 0.01
408 3 0.00
409 1 0.00
410 50 0.05
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (396 bp):
TATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCG
GGTTAAGAAGTTGACACATACCTCATTTCATAATCAATTAAATATTTAATATTAATACATATTCC
CTAAGGGGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAACTCCAATTACGGTGT
ATAGTATAATTTTTCTTATAGGATTATTATACAATAAACTGTCACTGTAAATTTTGGAATCCAAA
AGCGGGTTAAGAAGTTGACACATACCTCATTTCATAATTAAAATATTTAATATTAATACATATTC
CCTAAGGGGACACATGTCAACCCTTAAACCCCGTGCACGTGCAGTCTGCTAAACTTACTGGCGGT
GTATTG
Found at i:120243 original size:606 final size:603
Alignment explanation
Indices: 119015--120389 Score: 1801
Period size: 606 Copynumber: 2.3 Consensus size: 603
119005 AATCACTTTA
* * * * * *
119015 TATAATTTTTCTTATAGGAGTATTATACAATACACTTTTTCAGTGTAAATTTTGCACTCCCTAAG
1 TATAATTTTTCTTATAGGATTATTATACAATAAAC--TATCAGTGTAAATTTTGGAATCCATAAG
* *
119080 CGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATTAAAACATATT
64 CGGGTTAAGAAGTTGACACATA-CCCATTTCATAAT---TAAAATATTTAATATTAATACATATT
* *
119145 CCTTAAGGGGACACATGTCAACCCTTAAA----CTC-TCCACGTGCAGTCCGCTAAATTCGACTG
125 CCTTAAGGGGACACATGTCAACCCTTAAACCCGCACGTCCACGTGCAGTCCACTAAATTCGACTG
* * * *
119205 ACAGTGTATAGTATAATTTTTCTTATAAGATCATTATACAATCCACTGTGAGTGTAAATTTTGGA
190 ACAGTGTATAGTACAATTTTTCTTATAAGATCATTATACAATACACTGTAAATGTAAATTTTGGA
* * *
119270 ATCCATAAACGGGTTAAGAAGTTGACATATACCTCATTTCATAATTAATTAAATATTTAATTTAA
255 ATCAATAAACGGGTTAAGAAGTTGAAATATACCTCATTTCATAATTAATTAAATA-TCAATTTAA
* * * *
119335 TATTAATACACATTCCCTAAGGGGACACATGTCAACCCTTCAACCCCGTACGTGCAGTCTGCTAA
319 TATTAATACACATTCCCAAAGGGGACACATGTCAACCCTTAAACCCCGCACGCGCAGTCTGCTAA
* * * ** *
119400 AATCCACTGGCGGTGTATTATATAATTTTTCTTATAGAGTTATCATACAACACGCTGTCAGTGTA
384 AATCCACTGACGGTGTACTATATAATTGTTCTTATAGAGTTATCATACAACAAACTGTCAATGTA
* * * * *
119465 AATTTTTAGACTCTATAAGAGGGTTAAGAAGTTGACACATACCTCATTTCATCATCAATTAAATA
449 AAATTTTAGACTCCATAAGAGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAAATAAATA
*
119530 TATAATATTAGTACATATTCCCTAAGGAGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCT
514 TATAATATTAATACATATTCCCTAAGGAGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCT
119595 GCTAAACTCCAATTACGGTGTATAG
579 GCTAAACTCCAATTACGGTGTATAG
* *
119620 TATAATTTTTCTTATAGGATTATTATACAATAAACTATCACTGTAAATTTTGGAATCCAAAAGCG
1 TATAATTTTTCTTATAGGATTATTATACAATAAACTATCAGTGTAAATTTTGGAATCCATAAGCG
* *
119685 GGTTAAGAAATTGACACATACCTTATTTCATAATTAAAATATTTAATATTAATACATATTCCTTA
66 GGTTAAGAAGTTGACACATACC-CATTTCATAATTAAAATATTTAATATTAATACATATTCCTTA
*
119750 AGGGGACACATGTCAACCCTTAAACCCCGCACGTCCAGCACGTGCAGTCTACTAAACTT-GACTG
130 AGGGGACACATGTCAACCCTTAAA-CCCGCACGT-C--CACGTGCAGTCCACTAAA-TTCGACTG
* * * *
119814 GC-GTTGTATTGTACAATTTTTCTTATAGGATTATTATACAATACACAT-TAAATGTAAATTTTG
190 ACAG-TGTATAGTACAATTTTTCTTATAAGATCATTATACAATACAC-TGTAAATGTAAATTTTG
* * * * * *
119877 GACTCAATAAGCGGGTTAAGAAGTTGAAATATGCCTTATTTTATAATTAA-TCAA-A-CAATTTA
253 GAATCAATAAACGGGTTAAGAAGTTGAAATATACCTCATTTCATAATTAATTAAATATCAATTTA
* *
119939 ATATTAATAC-CTATTCCCAAAGGGGACACATGTCAACCTTTAAACCCTGCACGCGCAGTCTGCT
318 ATATTAATACAC-ATTCCCAAAGGGGACACATGTCAACCCTTAAACCCCGCACGCGCAGTCTGCT
* * * * * *
120003 AAACTCCATTGACGGTGTACTGTATAATTGTTCTTATAG-GATTATTATACAATAAATTGTCAAT
382 AAAATCCACTGACGGTGTACTATATAATTGTTCTTATAGAG-TTATCATACAACAAACTGTCAAT
* * * *
120067 GTAAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACGCATACCCCCACTTT-ATAATTAAAT
446 GTAAAATTTTAGACTCCATAAGAGGGTTAAGAAGTTGACACATA-CCCCA-TTTCATAATCAAAT
* *
120131 AAATATTTAATATTAATACATATTCCCTAA-GAGGACACATGTCTACCCTTAAACCCTGCACGTG
509 AAATATATAATATTAATACATATTCCCTAAGGA-GACACATGTCAACCCTTAAACCCTGCACGTG
* *
120195 CAGTCTGCTAAACTCTACTTACGGTGTATAG
573 CAGTCTGCTAAACTCCAATTACGGTGTATAG
* * *
120226 TATAATATTTCTTATAGGATTATTTTACAATAAACTGTCAGTGTAAATTTT-GAACTCCATAAGC
1 TATAATTTTTCTTATAGGATTATTATACAATAAACTATCAGTGTAAATTTTGGAA-TCCATAAGC
*
120290 GGGTTAAGAAGTTGATACATTACCCATTTCATAATTAAAATATTTAATATTAATACATATTCCTT
65 GGGTTAAGAAGTTGACACA-TACCCATTTCATAATTAAAATATTTAATATTAATACATATTCCTT
* *
120355 AAAGGGACACATGTCAACCTTTAAACCCTGCACGT
129 AAGGGGACACATGTCAACCCTTAAACCC-GCACGT
120390 GCAGTCTGCT
Statistics
Matches: 675, Mismatches: 74, Indels: 41
0.85 0.09 0.05
Matches are distributed among these distances:
600 53 0.08
602 2 0.00
603 53 0.08
604 2 0.00
605 194 0.29
606 240 0.36
607 9 0.01
608 4 0.01
609 115 0.17
610 3 0.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (603 bp):
TATAATTTTTCTTATAGGATTATTATACAATAAACTATCAGTGTAAATTTTGGAATCCATAAGCG
GGTTAAGAAGTTGACACATACCCATTTCATAATTAAAATATTTAATATTAATACATATTCCTTAA
GGGGACACATGTCAACCCTTAAACCCGCACGTCCACGTGCAGTCCACTAAATTCGACTGACAGTG
TATAGTACAATTTTTCTTATAAGATCATTATACAATACACTGTAAATGTAAATTTTGGAATCAAT
AAACGGGTTAAGAAGTTGAAATATACCTCATTTCATAATTAATTAAATATCAATTTAATATTAAT
ACACATTCCCAAAGGGGACACATGTCAACCCTTAAACCCCGCACGCGCAGTCTGCTAAAATCCAC
TGACGGTGTACTATATAATTGTTCTTATAGAGTTATCATACAACAAACTGTCAATGTAAAATTTT
AGACTCCATAAGAGGGTTAAGAAGTTGACACATACCCCATTTCATAATCAAATAAATATATAATA
TTAATACATATTCCCTAAGGAGACACATGTCAACCCTTAAACCCTGCACGTGCAGTCTGCTAAAC
TCCAATTACGGTGTATAG
Found at i:122278 original size:16 final size:16
Alignment explanation
Indices: 122257--122287 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
122247 TTGAAAAATA
122257 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
122273 TTACTAAATTTTTAT
1 TTACTAAATATTTAT
122288 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTACTAAATATTTATT
Done.