Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013884.1 Corchorus capsularis cultivar CVL-1 contig13905, 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: 42595
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:2598 original size:53 final size:53
Alignment explanation
Indices: 2537--2646 Score: 193
Period size: 53 Copynumber: 2.1 Consensus size: 53
2527 TCAGACTCGA
*
2537 ACCCATGACCACACTTGCAGCAAACCTTACACTCGACTTCCTACCACTAAGCC
1 ACCCATGACCACACTTACAGCAAACCTTACACTCGACTTCCTACCACTAAGCC
* *
2590 ACCCATGACCACACTTACAGCAAACCTTACACTCGACTTCCTGCCACTAAGTC
1 ACCCATGACCACACTTACAGCAAACCTTACACTCGACTTCCTACCACTAAGCC
2643 ACCC
1 ACCC
2647 CCACAGGGGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.30, C:0.42, G:0.09, T:0.19
Consensus pattern (53 bp):
ACCCATGACCACACTTACAGCAAACCTTACACTCGACTTCCTACCACTAAGCC
Found at i:10102 original size:32 final size:32
Alignment explanation
Indices: 10066--10272 Score: 342
Period size: 32 Copynumber: 6.5 Consensus size: 32
10056 CGCGGAGCCT
*
10066 CCCACTAGGACGGCTCTACCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
*
10098 CCCACTAGGACGGCTCTGCCACCGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
* **
10130 CCCACTAGGACGGCTCTGCCACAGCTAGGTGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
*
10162 CCCACTAGGACGGCTCTGCCACGGCTAGGCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
* *
10194 CCTACTAGGACGGCTCTGCCACGGCTAGCCGT
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
10226 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
1 CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
10258 CCCACTAGGACGGCT
1 CCCACTAGGACGGCT
10273 AGGCTTTTTT
Statistics
Matches: 163, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 163 1.00
ACGTcount: A:0.17, C:0.42, G:0.28, T:0.14
Consensus pattern (32 bp):
CCCACTAGGACGGCTCTGCCACGGCTAGCCGC
Found at i:10856 original size:60 final size:60
Alignment explanation
Indices: 10725--10844 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
10715 GATCGATGAC
* *
10725 CCAAACTTCTAGACCTAATTAGATTCAATCTAAGAAATCATGTCTAATTTGAGCATTTCT
1 CCAAACTTTTAGACCTAATTAGATTCAATCTAAGAAATCATGCCTAATTTGAGCATTTCT
*
10785 CCAAACTTTTAGACCTAATTAGATTCAATCTAAGAAATTATGCCTAATTTGAGCATTTCT
1 CCAAACTTTTAGACCTAATTAGATTCAATCTAAGAAATCATGCCTAATTTGAGCATTTCT
10845 TCGTACTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (60 bp):
CCAAACTTTTAGACCTAATTAGATTCAATCTAAGAAATCATGCCTAATTTGAGCATTTCT
Found at i:20847 original size:33 final size:33
Alignment explanation
Indices: 20802--20865 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
20792 CACCGGAAGC
*
20802 ACTGGCCACGGAAGTCTTGGTGGTGGCAGCAGT
1 ACTGGCCACGGAAGTATTGGTGGTGGCAGCAGT
20835 ACTGG-CAGCGGAAGTATTGGTGGTGGCAGCA
1 ACTGGCCA-CGGAAGTATTGGTGGTGGCAGCA
20866 CTGGCGGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.20, C:0.19, G:0.41, T:0.20
Consensus pattern (33 bp):
ACTGGCCACGGAAGTATTGGTGGTGGCAGCAGT
Found at i:20869 original size:30 final size:29
Alignment explanation
Indices: 20799--20884 Score: 95
Period size: 33 Copynumber: 2.9 Consensus size: 29
20789 ATACACCGGA
*
20799 AGCACTGGCCACGGAAGTCTTGGTGGTGGC
1 AGCACTGG-CACGGAAGTATTGGTGGTGGC
20829 AGCAGTACTGGCAGCGGAAGTATTGGTGGTGGC
1 AGC---ACTGGCA-CGGAAGTATTGGTGGTGGC
*
20862 AGCACTGG--CGGAAGCATTGGTGG
1 AGCACTGGCACGGAAGTATTGGTGG
20885 CAGCCCTGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
27 14 0.28
30 8 0.16
32 2 0.04
33 26 0.52
ACGTcount: A:0.20, C:0.19, G:0.42, T:0.20
Consensus pattern (29 bp):
AGCACTGGCACGGAAGTATTGGTGGTGGC
Found at i:23156 original size:59 final size:59
Alignment explanation
Indices: 23064--23181 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
23054 TTATACTTAC
23064 CACATCACATTAGAATTTATGTTACGCACAGACCATTTGGTATTTTACTCATATGAAAA
1 CACATCACATTAGAATTTATGTTACGCACAGACCATTTGGTATTTTACTCATATGAAAA
23123 CACATCACATTAGAATTTATGTTACGCACAGACCATTTGGTATTTTACTCATATGAAAA
1 CACATCACATTAGAATTTATGTTACGCACAGACCATTTGGTATTTTACTCATATGAAAA
23182 TCCTAAAGAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (59 bp):
CACATCACATTAGAATTTATGTTACGCACAGACCATTTGGTATTTTACTCATATGAAAA
Found at i:23990 original size:15 final size:15
Alignment explanation
Indices: 23966--24010 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
23956 TACAAAGCCC
* *
23966 GGCGCCCGACCACCT
1 GGCGCTCGACTACCT
23981 GGCGCTCGACTACCT
1 GGCGCTCGACTACCT
23996 GGCGCTCGACTACCT
1 GGCGCTCGACTACCT
24011 ATGACCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.13, C:0.44, G:0.27, T:0.16
Consensus pattern (15 bp):
GGCGCTCGACTACCT
Found at i:24094 original size:26 final size:26
Alignment explanation
Indices: 24051--24172 Score: 133
Period size: 26 Copynumber: 4.7 Consensus size: 26
24041 GTCAGCTGGC
24051 ACTCCACACGTGACCTCCAACGTACA
1 ACTCCACACGTGACCTCCAACGTACA
*
24077 A-TCCCACACGTGATCTCCGAA-GTACA
1 ACT-CCACACGTGACCTCC-AACGTACA
* *
24103 ACTCCACACGTGACCTCCAACGGATA
1 ACTCCACACGTGACCTCCAACGTACA
* *
24129 CCTTCAACACGTGACCTCCGAA-GTACA
1 AC-TCCACACGTGACCTCC-AACGTACA
*
24156 ACTCTACACGTGACCTC
1 ACTCCACACGTGACCTC
24173 GCGCGTGCGA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.04
26 53 0.66
27 22 0.28
28 2 0.03
ACGTcount: A:0.30, C:0.39, G:0.14, T:0.18
Consensus pattern (26 bp):
ACTCCACACGTGACCTCCAACGTACA
Found at i:24157 original size:53 final size:52
Alignment explanation
Indices: 24051--24172 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 52
24041 GTCAGCTGGC
* *
24051 ACTCCACACGTGACCTCCAACGTACAATCCCACACGTGATCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACGTACAATCCAACACGTGACCTCCGAAGTACA
* *
24103 ACTCCACACGTGACCTCCAACGGATAC-CTTCAACACGTGACCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAAC-G-TACAATCCAACACGTGACCTCCGAAGTACA
*
24156 ACTCTACACGTGACCTC
1 ACTCCACACGTGACCTC
24173 GCGCGTGCGA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
52 21 0.33
53 39 0.62
54 3 0.05
ACGTcount: A:0.30, C:0.39, G:0.14, T:0.18
Consensus pattern (52 bp):
ACTCCACACGTGACCTCCAACGTACAATCCAACACGTGACCTCCGAAGTACA
Found at i:28185 original size:127 final size:128
Alignment explanation
Indices: 27850--28229 Score: 573
Period size: 128 Copynumber: 3.0 Consensus size: 128
27840 TACCTCACGG
* *
27850 ACGCCCCAAAAAGAGGGCTCAACACCAACGGGCGGGGCGATCGACAAGATATGACCCCGACTCAG
1 ACGCCCCAAAAAGAGGGCTCAACGCCAACGGGCGGGGCGATCGACAAGATATGACCCTGACTCAG
27915 CATGGCCCCCAACTTGCAGGCGATGAGTAAAAAACCATCCCTGGACAAGTATGGGAATGAGGA
66 CATGGCCCCCAACTTGCAGGCGATGAGTAAAAAACCATCCCTGGACAAGTATGGGAATGAGGA
* *
27978 ACGCCCCAAAAAGAGGACTCAACGCCAGCGGGCGGGGCGATCGACAAGATATGACCCTGACTCAG
1 ACGCCCCAAAAAGAGGGCTCAACGCCAACGGGCGGGGCGATCGACAAGATATGACCCTGACTCAG
* *
28043 CATGGCCCCCGACTTGCAGGCGATGAGTAAAAAACCATCCCTGGACAAGTATGGGAATGATGA
66 CATGGCCCCCAACTTGCAGGCGATGAGTAAAAAACCATCCCTGGACAAGTATGGGAATGAGGA
* * * * * *
28106 ACGCCCCAAAAA-AGGGTTCAACGCTAACGGGCGGGGCGGTCGATAAGATTTGACCCTGACTTAG
1 ACGCCCCAAAAAGAGGGCTCAACGCCAACGGGCGGGGCGATCGACAAGATATGACCCTGACTCAG
* * * * *
28170 CATGGCCCCCAACTTGCAAGTGGTGAGTAGAAAAAAACCATCCTTGAACAAGTATGGGAA
66 CATGGCCCCCAACTTGCAGGCGATGAGT---AAAAAACCATCCCTGGACAAGTATGGGAA
28230 CAGTGAATGC
Statistics
Matches: 229, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
127 68 0.30
128 134 0.59
130 27 0.12
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.14
Consensus pattern (128 bp):
ACGCCCCAAAAAGAGGGCTCAACGCCAACGGGCGGGGCGATCGACAAGATATGACCCTGACTCAG
CATGGCCCCCAACTTGCAGGCGATGAGTAAAAAACCATCCCTGGACAAGTATGGGAATGAGGA
Found at i:29667 original size:44 final size:44
Alignment explanation
Indices: 29604--29785 Score: 213
Period size: 44 Copynumber: 4.1 Consensus size: 44
29594 GGACCAATAA
* * *
29604 AAGAAAGTAAACAACAGGTCGATCGACCATATCATATTCAAAAC
1 AAGAAAGCAAACAACAGGTCGACCGACCACATCATATTCAAAAC
* * * *
29648 AAGAAAGCAAACAATAGGTCGCCCGACCACATCATATTCGAAGC
1 AAGAAAGCAAACAACAGGTCGACCGACCACATCATATTCAAAAC
* * * *
29692 AAGGAAGTC-AACAACAGGTCGACCGACCATAACATATTCCAAAC
1 AAGAAAG-CAAACAACAGGTCGACCGACCACATCATATTCAAAAC
* * * *
29736 AAGAAAGTAAACAATAGGTCGACCGACTACATCACATTCAAAAC
1 AAGAAAGCAAACAACAGGTCGACCGACCACATCATATTCAAAAC
29780 AAGAAA
1 AAGAAA
29786 ACACCATGTC
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
44 113 0.99
45 1 0.01
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (44 bp):
AAGAAAGCAAACAACAGGTCGACCGACCACATCATATTCAAAAC
Found at i:29719 original size:88 final size:86
Alignment explanation
Indices: 29608--29861 Score: 277
Period size: 88 Copynumber: 3.0 Consensus size: 86
29598 CAATAAAAGA
* * *
29608 AAGTAAACAACAGGTCGATCGACCATATCATATTCAAAACAAGAAAGCAAACAATAGGTCGCCCG
1 AAGT-AACAACAGGTCGACCGACCATAACATATTCAAAACAAGAAAGCAAACAATAGGTCGACCG
* * *
29673 ACCACATCATATTCGAAGCAAGG
65 ACCACATCACATTCAAAACAA-G
* *
29696 AAGTCAACAACAGGTCGACCGACCATAACATATTCCAAACAAGAAAGTAAACAATAGGTCGACCG
1 AAGT-AACAACAGGTCGACCGACCATAACATATTCAAAACAAGAAAGCAAACAATAGGTCGACCG
*
29761 ACTACATCACATTCAAAACAAG
65 ACCACATCACATTCAAAACAAG
* * * * * * *
29783 AA--AACACCATGTCGACCGACCATACCACATTCGAAACAAG--A--AAAGAATTGGTCGACCGA
1 AAGTAACAACAGGTCGACCGACCATAACATATTCAAAACAAGAAAGCAAACAATAGGTCGACCGA
* *
29842 CTACATGACATTCAAAACAA
66 CCACATCACATTCAAAACAA
29862 CATAATACCT
Statistics
Matches: 148, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
80 35 0.24
82 1 0.01
84 33 0.22
87 3 0.02
88 76 0.51
ACGTcount: A:0.44, C:0.25, G:0.15, T:0.15
Consensus pattern (86 bp):
AAGTAACAACAGGTCGACCGACCATAACATATTCAAAACAAGAAAGCAAACAATAGGTCGACCGA
CCACATCACATTCAAAACAAG
Found at i:29788 original size:40 final size:40
Alignment explanation
Indices: 29612--29934 Score: 180
Period size: 40 Copynumber: 7.8 Consensus size: 40
29602 AAAAGAAAGT
* * *
29612 AAACAACAGGTCGATCGACCATATCATATTCAAAACAAGAAA
1 AAACAACAGGTCGACCGACCACATCACATTCAAAACAAG--A
* * * * *
29654 GCAAACAATAGGTCGCCCGACCACATCATATTCGAAGCAAGGA
1 --AAACAACAGGTCGACCGACCACATCACATTCAAAACAA-GA
* * * *
29697 AGTCAACAACAGGTCGACCGACCATAACATATTCCAAACAAGAAA
1 A---AACAACAGGTCGACCGACCACATCACATTCAAAACAAG--A
* *
29742 GTAAACAATAGGTCGACCGACTACATCACATTCAAAACAAGA
1 --AAACAACAGGTCGACCGACCACATCACATTCAAAACAAGA
* * * * *
29784 AAACACCATGTCGACCGACCATACCACATTCGAAACAAGA
1 AAACAACAGGTCGACCGACCACATCACATTCAAAACAAGA
* ** * * *
29824 AAAGAATTGGTCGACCGACTACATGACATTCAAAACAACA
1 AAACAACAGGTCGACCGACCACATCACATTCAAAACAAGA
* * * ** * * *
29864 TAATACCTTGTCGACCGACCATA-CTGCATCCAAAACAAGA
1 AAACAACAGGTCGACCGACCACATC-ACATTCAAAACAAGA
*** * *
29904 AAGGTATAGGTCGGCCGACCACATCACATTC
1 AAACAACAGGTCGACCGACCACATCACATTC
29935 CAAGAGAGAA
Statistics
Matches: 210, Mismatches: 59, Indels: 24
0.72 0.20 0.08
Matches are distributed among these distances:
40 107 0.51
41 2 0.01
42 1 0.00
43 2 0.01
44 95 0.45
45 2 0.01
47 1 0.00
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.16
Consensus pattern (40 bp):
AAACAACAGGTCGACCGACCACATCACATTCAAAACAAGA
Found at i:29853 original size:80 final size:80
Alignment explanation
Indices: 29612--29965 Score: 260
Period size: 80 Copynumber: 4.3 Consensus size: 80
29602 AAAAGAAAGT
* * * * * * * *
29612 AAACAACAGGTCGATCGACCATATCATATTCAAAACAAGAAAGCAAACAATAGGTCGCCCGACCA
1 AAACACCATGTCGACCGACCATACCACATTCAAAACAAG--A--AAAGAATAGGTCGACCGACTA
* * *
29677 CATCATATTCGAAGCAAGGA
62 CATCACATTCAAAACAA-GA
* * * * * *
29697 AGTCAACAACAGGTCGACCGACCATAACATATTCCAAACAAGAAAGTAAACAATAGGTCGACCGA
1 A---AACACCATGTCGACCGACCATACCACATTCAAAACAAG--A--AAAGAATAGGTCGACCGA
29762 CTACATCACATTCAAAACAAGA
59 CTACATCACATTCAAAACAAGA
* * *
29784 AAACACCATGTCGACCGACCATACCACATTCGAAACAAGAAAAGAATTGGTCGACCGACTACATG
1 AAACACCATGTCGACCGACCATACCACATTCAAAACAAGAAAAGAATAGGTCGACCGACTACATC
*
29849 ACATTCAAAACAACA
66 ACATTCAAAACAAGA
* * * ** * * * * *
29864 TAATACCTTGTCGACCGACCATACTGCATCCAAAACAAGAAAGGTATAGGTCGGCCGACCACATC
1 AAACACCATGTCGACCGACCATACCACATTCAAAACAAGAAAAGAATAGGTCGACCGACTACATC
* *
29929 ACATTCCAAGA-GAGAA
66 ACATT-CAAAACAAG-A
* *
29945 AAAGACCAAGTCGACCGACCA
1 AAACACCATGTCGACCGACCA
29966 CAATATATCC
Statistics
Matches: 226, Mismatches: 38, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
80 94 0.42
81 22 0.10
82 1 0.00
84 33 0.15
85 1 0.00
87 3 0.01
88 72 0.32
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.15
Consensus pattern (80 bp):
AAACACCATGTCGACCGACCATACCACATTCAAAACAAGAAAAGAATAGGTCGACCGACTACATC
ACATTCAAAACAAGA
Found at i:31590 original size:43 final size:44
Alignment explanation
Indices: 31366--31582 Score: 375
Period size: 44 Copynumber: 5.0 Consensus size: 44
31356 AAAAAAACCG
*
31366 GTCGATCGACCACATCATATTCAAACCAAGAAGAGAAGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
31410 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
31454 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
31498 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAG-AACTA
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
* * * *
31541 GTCGATCGATCACACCACACTCAAACCAAGAAGATAAG-AACT
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACT
31583 TGGCGATCAA
Statistics
Matches: 168, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
43 43 0.26
44 125 0.74
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (44 bp):
GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTA
Found at i:31611 original size:132 final size:132
Alignment explanation
Indices: 31366--31611 Score: 343
Period size: 132 Copynumber: 1.9 Consensus size: 132
31356 AAAAAAACCG
* * *
31366 GTCGATCGACCACATCATATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACCACATCACATT
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACCACACCACACT
* * * * * * *
31431 CAAACCAAGAAGAGAAGTAACTAGTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAAC
66 CAAACCAAGAAGAGAAGTAACTAGGCGATCAACAAAAACAAATACAAACCAAGAAGAGAAGTAAC
31496 TA
131 TA
*
31498 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAG-AACTAGTCGATCGATCACACCACACT
1 GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACCACACCACACT
* *
31562 CAAACCAAGAAGATAAG-AACTTGGCGATCAACAAAAAACAAAATACAAAC
66 CAAACCAAGAAGAGAAGTAACTAGGCGATCAAC-AAAAAC-AAATACAAAC
31612 TCAAACCAAG
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
130 12 0.12
131 42 0.42
132 45 0.45
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (132 bp):
GTCGATCGACCACATCACATTCAAACCAAGAAGAGAAGTAACTAGTCGATCGACCACACCACACT
CAAACCAAGAAGAGAAGTAACTAGGCGATCAACAAAAACAAATACAAACCAAGAAGAGAAGTAAC
TA
Found at i:31900 original size:37 final size:37
Alignment explanation
Indices: 31770--31987 Score: 339
Period size: 38 Copynumber: 5.8 Consensus size: 37
31760 AAAAAATAGG
*
31770 CGACAAGCTGACAAAATGTGTCGACCGCCATGTCGCT
1 CGACAAGCTGACAAAATGTGTCGACCGCCACGTCGCT
* *
31807 CGACAAAGTTGACAAAATCTGTCGACCGCCACGTCGCT
1 CGAC-AAGCTGACAAAATGTGTCGACCGCCACGTCGCT
*
31845 CGACAAAGCTGACAAAATGTGTCGACCGCCACATCGCT
1 CGAC-AAGCTGACAAAATGTGTCGACCGCCACGTCGCT
*
31883 CGACAAGCTGACAAAATGTGTCGACCGCCACTTCGCT
1 CGACAAGCTGACAAAATGTGTCGACCGCCACGTCGCT
*
31920 CGACAAGGCTGACCAAATGTGTCGACCG-CACGTCGCT
1 CGACAA-GCTGACAAAATGTGTCGACCGCCACGTCGCT
*
31957 CGACAAGCTGAAAAAATGTGTCGACCGCCAC
1 CGACAAGCTGACAAAATGTGTCGACCGCCAC
31988 AGACCACCTC
Statistics
Matches: 167, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
36 19 0.11
37 59 0.35
38 89 0.53
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (37 bp):
CGACAAGCTGACAAAATGTGTCGACCGCCACGTCGCT
Found at i:31911 original size:75 final size:75
Alignment explanation
Indices: 31770--31987 Score: 341
Period size: 75 Copynumber: 2.9 Consensus size: 75
31760 AAAAAATAGG
* * *
31770 CGAC-AAGCTGACAAAATGTGTCGACCGCCATGTCGCTCGACAAAGTTGACAAAATCTGTCGACC
1 CGACAAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGAC-AAGCTGACAAAATGTGTCGACC
31834 GCCACGTCGCT
65 GCCACGTCGCT
*
31845 CGACAAAGCTGACAAAATGTGTCGACCGCCACATCGCTCGACAAGCTGACAAAATGTGTCGACCG
1 CGACAAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAGCTGACAAAATGTGTCGACCG
*
31910 CCACTTCGCT
66 CCACGTCGCT
* * *
31920 CGACAAGGCTGACCAAATGTGTCGACCG-CACGTCGCTCGACAAGCTGAAAAAATGTGTCGACCG
1 CGACAAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAGCTGACAAAATGTGTCGACCG
31984 CCAC
66 CCAC
31988 AGACCACCTC
Statistics
Matches: 133, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
74 38 0.29
75 60 0.45
76 35 0.26
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (75 bp):
CGACAAAGCTGACAAAATGTGTCGACCGCCACGTCGCTCGACAAGCTGACAAAATGTGTCGACCG
CCACGTCGCT
Found at i:32256 original size:61 final size:60
Alignment explanation
Indices: 32175--32291 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 60
32165 ATATGCGGTC
* *
32175 GAGCGCCAAATCCCATATATGGGCTATGGCGCTCGACCAAGAAATCCTCAATATATGGTT
1 GAGCGCCAAACCCCATATATGGGCTATAGCGCTCGACCAAGAAATCCTCAATATATGGTT
* * *
32235 GAGCGCCCAAACCCCATATATGGGCTATAGCGCTCGACCAAGCAATCTTCCATATAT
1 GAGCG-CCAAACCCCATATATGGGCTATAGCGCTCGACCAAGAAATCCTCAATATAT
32292 ATATATGGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 5 0.10
61 46 0.90
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (60 bp):
GAGCGCCAAACCCCATATATGGGCTATAGCGCTCGACCAAGAAATCCTCAATATATGGTT
Found at i:32718 original size:15 final size:15
Alignment explanation
Indices: 32694--32723 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32684 TACAAAGCCC
32694 GGCGCCCGACCACCT
1 GGCGCCCGACCACCT
*
32709 GGCGCTCGACCACCT
1 GGCGCCCGACCACCT
32724 ATGACCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.50, G:0.27, T:0.10
Consensus pattern (15 bp):
GGCGCCCGACCACCT
Found at i:32843 original size:115 final size:115
Alignment explanation
Indices: 32641--32870 Score: 415
Period size: 115 Copynumber: 2.0 Consensus size: 115
32631 ACGGCTGGGG
32641 GGCAATTGTTGAGCATGGCACAATTGCTTGGCGTCCGACTACCTACAAAGCCCGGCGCCCGACCA
1 GGCAATTGTTGAGCATGGCACAATTGCTTGGCGTCCGACTACCTACAAAGCCCGGCGCCCGACCA
*
32706 CCTGGCGCTCGACCACCTATGACCACAAGGAGCCGGACCCTATCGCTAGC
66 CCTGGCGCTCGACCACCTATGACCACAAGGAGCCGGAACCTATCGCTAGC
* * *
32756 GGCAATTGTTGAGTATGGCACAATTGCTTGGCGTCCGACTACCTACAATGTCCGGCGCCCGACCA
1 GGCAATTGTTGAGCATGGCACAATTGCTTGGCGTCCGACTACCTACAAAGCCCGGCGCCCGACCA
*
32821 CCTGGCGTTCGACCACCTATGACCACAAGGAGCCGGAACCTATCGCTAGC
66 CCTGGCGCTCGACCACCTATGACCACAAGGAGCCGGAACCTATCGCTAGC
32871 CAGCTGGCAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.18
Consensus pattern (115 bp):
GGCAATTGTTGAGCATGGCACAATTGCTTGGCGTCCGACTACCTACAAAGCCCGGCGCCCGACCA
CCTGGCGCTCGACCACCTATGACCACAAGGAGCCGGAACCTATCGCTAGC
Found at i:32922 original size:26 final size:26
Alignment explanation
Indices: 32879--33000 Score: 124
Period size: 26 Copynumber: 4.7 Consensus size: 26
32869 GCCAGCTGGC
*
32879 ACTCCACACGTGACCTCCAACGTACG
1 ACTCCACACGTGACCTCCAACGTACA
*
32905 A-TCCCACACGTGATCTCCGAA-GTACA
1 ACT-CCACACGTGACCTCC-AACGTACA
* *
32931 ACTCCACACGTGACCTCCAACGAATA
1 ACTCCACACGTGACCTCCAACGTACA
* *
32957 CCTTCAACACGTGACCTCCGAA-GTACA
1 AC-TCCACACGTGACCTCC-AACGTACA
*
32984 ACTCTACACGTGACCTC
1 ACTCCACACGTGACCTC
33001 GCGCGTGCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
25 3 0.04
26 52 0.66
27 22 0.28
28 2 0.03
ACGTcount: A:0.30, C:0.39, G:0.14, T:0.18
Consensus pattern (26 bp):
ACTCCACACGTGACCTCCAACGTACA
Found at i:32985 original size:53 final size:52
Alignment explanation
Indices: 32879--33000 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 52
32869 GCCAGCTGGC
* *
32879 ACTCCACACGTGACCTCCAACGTACGATCCCACACGTGATCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACGTACGATCCAACACGTGACCTCCGAAGTACA
* *
32931 ACTCCACACGTGACCTCCAACGAATAC-CTTCAACACGTGACCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACG--TACGATCCAACACGTGACCTCCGAAGTACA
*
32984 ACTCTACACGTGACCTC
1 ACTCCACACGTGACCTC
33001 GCGCGTGCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
52 22 0.35
53 38 0.60
54 3 0.05
ACGTcount: A:0.30, C:0.39, G:0.14, T:0.18
Consensus pattern (52 bp):
ACTCCACACGTGACCTCCAACGTACGATCCAACACGTGACCTCCGAAGTACA
Found at i:35246 original size:14 final size:14
Alignment explanation
Indices: 35229--35256 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35219 GCAAGAGCTG
35229 TAAATAAAATCAGT
1 TAAATAAAATCAGT
35243 TAAATAAAATCAGT
1 TAAATAAAATCAGT
35257 ACAGTCGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
TAAATAAAATCAGT
Found at i:37189 original size:10 final size:10
Alignment explanation
Indices: 37166--37215 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
37156 CTTCAGCTTT
37166 TTATA-TAT-
1 TTATATTATA
37174 TTATATTATA
1 TTATATTATA
37184 TTATATTATA
1 TTATATTATA
37194 TTATA-TATA
1 TTATATTATA
37203 -TATATATATA
1 TTATAT-TATA
37213 TTA
1 TTA
37216 GCTCATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 9 0.24
9 7 0.19
10 19 0.51
11 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATTATA
Found at i:37202 original size:2 final size:2
Alignment explanation
Indices: 37167--37213 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
37157 TTCAGCTTTT
*
37167 TA TA TA TT TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37205 TA TA TA TA T
1 TA TA TA TA T
37214 TAGCTCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:37343 original size:2 final size:2
Alignment explanation
Indices: 37336--37373 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37326 TTCGATCGTA
37336 AT AT AT 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 AT AT AT
37374 CAGCATCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40052 original size:78 final size:78
Alignment explanation
Indices: 39901--40056 Score: 215
Period size: 78 Copynumber: 2.0 Consensus size: 78
39891 CAGGAGGCAA
** *
39901 GTCGACAATAGAAAGCCAAGGGTGGAAATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGT
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAACTCATGGTGACCCTATTGAAAAACCTGTAACTGT
*
39966 TTGCAGAAATCCT
66 TCGCAGAAATCCT
* * * *
39979 GTCGACAATAGAAAGCCAGGGGTGGAAATAACTCGTGGTGGCCCTATTGAAACACCTG-AACATG
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAACTCATGGTGACCCTATTGAAAAACCTGTAAC-TG
*
40043 TTCGTAGAAATCCT
65 TTCGCAGAAATCCT
40057 ATCTATGATA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 2 0.03
78 66 0.97
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (78 bp):
GTCGACAATAGAAAGCCAAGGGTGGAAATAACTCATGGTGACCCTATTGAAAAACCTGTAACTGT
TCGCAGAAATCCT
Found at i:41795 original size:11 final size:12
Alignment explanation
Indices: 41767--41797 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
41757 CGATTATTAT
41767 ATAAATGAACAC
1 ATAAATGAACAC
41779 ATAAATGAACA-
1 ATAAATGAACAC
41790 ATAAATGA
1 ATAAATGA
41798 GTCTGTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (12 bp):
ATAAATGAACAC
Done.