Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012101.1 Corchorus olitorius cultivar O-4 contig12134, 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: 63517
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:8899 original size:5 final size:6
Alignment explanation
Indices: 8884--8908 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8874 TTATGAATTA
8884 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
8909 ATTAGACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:23197 original size:13 final size:12
Alignment explanation
Indices: 23174--23220 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
23164 AAGTTTATTG
23174 ATAATATATAAT
1 ATAATATATAAT
23186 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
23199 ATAACAT-TATT
1 ATAATATATAAT
23210 ATCAATATATA
1 AT-AATATATA
23221 TAAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:23800 original size:2 final size:2
Alignment explanation
Indices: 23795--23823 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
23785 TTATATAAGT
23795 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23824 GTAGTTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23802 original size:11 final size:9
Alignment explanation
Indices: 23772--23800 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
23762 TCTTTTGCTT
23772 TAAGTTATA
1 TAAGTTATA
23781 TAAGTTATA
1 TAAGTTATA
23790 TAAGTTATA
1 TAAGTTATA
23799 TA
1 TA
23801 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (9 bp):
TAAGTTATA
Found at i:23815 original size:9 final size:9
Alignment explanation
Indices: 23776--23820 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
23766 TTGCTTTAAG
23776 TTATATA-A
1 TTATATATA
23784 GTTATATA-A
1 -TTATATATA
23793 GTTATATATA
1 -TTATATATA
23803 -TATATATA
1 TTATATATA
23811 TTATATATA
1 TTATATATA
23820 T
1 T
23821 ATAGTAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.24
9 25 0.74
10 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (9 bp):
TTATATATA
Found at i:23863 original size:24 final size:24
Alignment explanation
Indices: 23836--23882 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
23826 AGTTTAACAT
*
23836 TTTTTATATTGATTATTGAATCAC
1 TTTTTATATTGATTAATGAATCAC
23860 TTTTTATATTGATTAATGAATCA
1 TTTTTATATTGATTAATGAATCA
23883 TTTAATTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTTTATATTGATTAATGAATCAC
Found at i:24058 original size:17 final size:17
Alignment explanation
Indices: 24026--24066 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
24016 TATTTTGGGT
*
24026 TCGGGATCGGGCTCGGTC
1 TCGGG-TCGGGCTCGGGC
*
24044 TCGGGTCGGGTTCGGGC
1 TCGGGTCGGGCTCGGGC
24061 TCGGGT
1 TCGGGT
24067 TGCCTCGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.02, C:0.24, G:0.49, T:0.24
Consensus pattern (17 bp):
TCGGGTCGGGCTCGGGC
Found at i:24065 original size:12 final size:12
Alignment explanation
Indices: 24026--24087 Score: 60
Period size: 12 Copynumber: 5.4 Consensus size: 12
24016 TATTTTGGGT
*
24026 TCGGGATCGGGC
1 TCGGGTTCGGGC
24038 TC-GGTCTCGGG-
1 TCGGGT-TCGGGC
24049 TCGGGTTCGGGC
1 TCGGGTTCGGGC
*
24061 TCGGGTT--GCC
1 TCGGGTTCGGGC
*
24071 TCGGGTTCGGGT
1 TCGGGTTCGGGC
24083 TCGGG
1 TCGGG
24088 ACATTGACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 9 0.22
11 9 0.22
12 23 0.56
ACGTcount: A:0.02, C:0.24, G:0.48, T:0.26
Consensus pattern (12 bp):
TCGGGTTCGGGC
Found at i:24080 original size:6 final size:6
Alignment explanation
Indices: 24022--24087 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
24012 AAATTATTTT
* * *
24022 GGGTTC GGGATC GGGCTC -GGTCTC GGG-TC GGGTTC GGGCTC GGGTT-
1 GGGTTC GGGTTC GGGTTC GGGT-TC GGGTTC GGGTTC GGGTTC GGGTTC
**
24068 -GCCTC GGGTTC GGGTTC GGG
1 GGGTTC GGGTTC GGGTTC GGG
24088 ACATTGACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
4 2 0.04
5 7 0.15
6 35 0.76
7 2 0.04
ACGTcount: A:0.02, C:0.23, G:0.50, T:0.26
Consensus pattern (6 bp):
GGGTTC
Found at i:27211 original size:31 final size:31
Alignment explanation
Indices: 27169--27227 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
27159 TTAGACGAAA
* * *
27169 TAAAAGGTTTGGTACTAAGTTGGGATTTTCT
1 TAAAAGATTTGGTACTAAATTGAGATTTTCT
27200 TAAAAGATTTGGTACTAAATTGAGATTT
1 TAAAAGATTTGGTACTAAATTGAGATTT
27228 CAGCCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (31 bp):
TAAAAGATTTGGTACTAAATTGAGATTTTCT
Found at i:29878 original size:13 final size:12
Alignment explanation
Indices: 29860--29897 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
29850 AACCACTGGG
29860 TTTTTATTTTTT
1 TTTTTATTTTTT
29872 ATTTTTATTTTTT
1 -TTTTTATTTTTT
*
29885 TTATTATTTTTT
1 TTTTTATTTTTT
29897 T
1 T
29898 AAAGTATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTATTTTTT
Found at i:39795 original size:19 final size:19
Alignment explanation
Indices: 39773--39831 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
39763 CTGCACCTAA
39773 CACACACATATGAATATT-
1 CACACACATATGAATATTC
* *
39791 -TCACACATATGGATATTC
1 CACACACATATGAATATTC
* * *
39809 CACACACACATAAATATCC
1 CACACACATATGAATATTC
39828 CACA
1 CACA
39832 AATAAAATAC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 15 0.47
19 17 0.53
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (19 bp):
CACACACATATGAATATTC
Found at i:39812 original size:15 final size:17
Alignment explanation
Indices: 39775--39814 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
39765 GCACCTAACA
39775 CACACATATGAATATTT
1 CACACATATGAATATTT
* *
39792 CACACATATGGATATTC
1 CACACATATGAATATTT
39809 CACACA
1 CACACA
39815 CACATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (17 bp):
CACACATATGAATATTT
Found at i:44266 original size:21 final size:21
Alignment explanation
Indices: 44242--44284 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
44232 CGCGGTCTGG
44242 GCGGTAGCTCGTCACCCCAAA
1 GCGGTAGCTCGTCACCCCAAA
44263 GCGGTAGCTCGTCACCCCAAA
1 GCGGTAGCTCGTCACCCCAAA
44284 G
1 G
44285 GTGCCAACCA
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:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (21 bp):
GCGGTAGCTCGTCACCCCAAA
Found at i:46744 original size:22 final size:20
Alignment explanation
Indices: 46704--46744 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
46694 CGTCGGGTTC
46704 AGAAAAAAAAAGAAATATAT
1 AGAAAAAAAAAGAAATATAT
*
46724 AGAAAAATATAAATAAATATA
1 AGAAAAA-A-AAAGAAATATA
46745 GGGGAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AGAAAAAAAAAGAAATATAT
Found at i:49404 original size:199 final size:198
Alignment explanation
Indices: 49086--49691 Score: 628
Period size: 199 Copynumber: 3.1 Consensus size: 198
49076 CGAGAGGGCA
* *
49086 TTTTTGGAAATTGTAAGTAAACTCAAATGCGAAAATGGAGAAACTGAACCTTTCACCGAAGGGGC
1 TTTTTGAAAATTGTAAGTAAACTCAAATGCGAAAATGAAGAAACTGAACCTTTCACCGAAGGGGC
* * * ** *
49151 ATTTTTGGAAGACAAGGCTAAACTTAGATGCAAAAATATAAAAAGCTGGCCCTTTGA-CAAAAGG
66 A-TTTTGGAAAACAAAGCTAAACTTAGATGCAGAAATATAAAAAAATGGCCCTTTGACCGAAAGG
* *
49215 GTATTTTGGAAAAAGAAAATACTAGACTTAAATGCAAAAAGATGAAAATGACCCTTCGATCGAAA
130 GTATTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGA-CGAAA
49280 GGGTG
194 GGGTG
49285 TTTTT-AAATATTGTAAGTAAACTCAAATGCGAAAATGAAGAAACTGAACCTTTCACCGAAGGGG
1 TTTTTGAAA-ATTGTAAGTAAACTCAAATGCGAAAATGAAGAAACTGAACCTTTCACCGAAGGGG
*
49349 CATTTCTGGAATACAAAGCTAAACTTAGATGCAGAAATATAAAAAAATGGCCCTTTGACCGAAAG
65 CATTT-TGGAAAACAAAGCTAAACTTAGATGCAGAAATATAAAAAAATGGCCCTTTGACCGAAAG
* * *
49414 GGTATTTCTGG--AAATAAAA-ACTAAACTTAGA--CAAAAAGACGAAACTGACCCATT-GACTG
129 GGTATTT-TGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCC-TTCGAC-G
*
49473 AAAGGGTAT
191 AAAGGGT-G
*** ** * * * * * *
49482 TTTTTGGAAAA-CAAAACCAAAC-CTAGATGTGAAAAAT-ATGAAACTGACCCTTTGACCGAAAG
1 TTTTT-GAAAATTGTAAGTAAACTC-AAATGCG-AAAATGAAGAAACTGAACCTTTCACCGAAGG
** * * * * * ** * * *
49544 GATACTTTGGGAAAAGAAAACT-AACTTAGATAC-GAAAAAGT-TGAAATTGACCCTTCGACCGA
63 GGCA-TTTTGGAAAACAAAGCTAAACTTAGATGCAGAAATA-TAAAAAAATGGCCCTTTGACCGA
49606 AAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGAC
126 AAGGGTA-TTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGA-
49671 CGAAAGGGTG
189 CGAAAGGGTG
49681 TTTTTGGAAAA
1 TTTTT-GAAAA
49692 AGAAAATACT
Statistics
Matches: 344, Mismatches: 42, Indels: 42
0.80 0.10 0.10
Matches are distributed among these distances:
195 32 0.09
196 43 0.12
197 58 0.17
198 35 0.10
199 131 0.38
200 41 0.12
201 4 0.01
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (198 bp):
TTTTTGAAAATTGTAAGTAAACTCAAATGCGAAAATGAAGAAACTGAACCTTTCACCGAAGGGGC
ATTTTGGAAAACAAAGCTAAACTTAGATGCAGAAATATAAAAAAATGGCCCTTTGACCGAAAGGG
TATTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGACGAAAGG
GTG
Found at i:49421 original size:67 final size:65
Alignment explanation
Indices: 49064--49752 Score: 224
Period size: 66 Copynumber: 10.4 Consensus size: 65
49054 ATGACAAGCT
* * *** * * * *
49064 TGACCCTTTGACCGAGAGGGCATTTTTGGAAATTGTAAG-TAAACTCAAATGC-GAAAATGGAGA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGG-AATACAAAGCTAAACTTAGATGCAGAAAAT-AAAA
*
49127 AAC
63 AAA
* * * * * *
49130 TGAACCTTTCACCGAAGGGGCATTTTTGGAAGACAAGGCTAAACTTAGATGCA-AAAATATAAAA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGGAATACAAAGCTAAACTTAGATGCAGAAAATA-AAAA
*
49194 AGC
64 A-A
* * * * * * * * **
49197 TGGCCCTTTGA-CAAAAGGGTATTTTGGAAAAAGAAAATACTAGACTTAAATGCA-AAAAGATGA
1 TGACCCTTTGACCGAAAGGGTATTTTGG-AATA-CAAA-GCTAAACTTAGATGCAGAAAATAAAA
49260 AAA
63 AAA
* * * ** ** * * *
49263 TGACCCTTCGATCGAAAGGGTGTTTTTAAATATTGTAAG-TAAACTCAAATGC-GAAAATGAAGA
1 TGACCCTTTGACCGAAAGGGTATTTTGGAATA--CAAAGCTAAACTTAGATGCAGAAAAT-AAAA
*
49326 AAC
63 AAA
* * * *
49329 TGAACCTTTCACCGAAGGGGCATTTCTGGAATACAAAGCTAAACTTAGATGCAGAAATATAAAAA
1 TGACCCTTTGACCGAAAGGGTATTT-TGGAATACAAAGCTAAACTTAGATGCAGAAA-ATAAAAA
49394 AA
64 AA
* * * **
49396 TGGCCCTTTGACCGAAAGGGTATTTCTGGAAATA-AAAACTAAACTTAGA--CA-AAAAGACGAA
1 TGACCCTTTGACCGAAAGGGTATTT-TGG-AATACAAAGCTAAACTTAGATGCAGAAAATAAAAA
*
49457 AC
64 AA
* * * * * * * **
49459 TGACCCATTGACTGAAAGGGTATTTTTTGGAAAACAAAACCAAACCTAGATG-TGAAAAATATGA
1 TGACCCTTTGACCGAAAGGGTA--TTTTGGAATACAAAGCTAAACTTAGATGCAG-AAAATAAAA
*
49523 AAC
63 AAA
* * * * * * **
49526 TGACCCTTTGACCGAAAGGATACTTTGGGAAAAGAAAACT-AACTTAGATAC-GAAAA-AGTTGA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGGAATACAAAGCTAAACTTAGATGCAGAAAATA--AAA
*
49588 AAT
63 AAA
* * * * * * **
49591 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCA-AAAAGACG
1 TGACCCTTTGACCGAAAGGGTA-TTTTGG-AATA-CAAA-GCTAAACTTAGATGCAGAAAATAAA
49655 AAAA
62 AAAA
* * * * * * * **
49659 TGACCCTTCGACCGAAAGGGTGTTTTTGGAAAAAGAAAATACTAAACTTAAATGCA-AAAAGACG
1 TGACCCTTTGACCGAAAGGGT-ATTTTGG-AATA-CAAA-GCTAAACTTAGATGCAGAAAATAAA
*
49723 AGAA
62 AAAA
49727 TGACCCTTTGACCGAAAGGGTATTTT
1 TGACCCTTTGACCGAAAGGGTATTTT
49753 TGAAAAAAGA
Statistics
Matches: 488, Mismatches: 102, Indels: 65
0.75 0.16 0.10
Matches are distributed among these distances:
63 28 0.06
64 23 0.05
65 72 0.15
66 119 0.24
67 116 0.24
68 116 0.24
69 13 0.03
70 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (65 bp):
TGACCCTTTGACCGAAAGGGTATTTTGGAATACAAAGCTAAACTTAGATGCAGAAAATAAAAAAA
Found at i:49595 original size:65 final size:65
Alignment explanation
Indices: 49064--49802 Score: 415
Period size: 68 Copynumber: 11.1 Consensus size: 65
49054 ATGACAAGCT
* * * * * * * * *
49064 TGACCCTTTGACCGAGAGGGCATTTTTGGAAATTG-TAAGTAAACTCAAATGCGAAAATGGA-GA
1 TGACCCTTTGACCGAAAGGGTATTTTGGGAAA-AGAAAACTAAACTTAGATGC-AAAA-AGACGA
49127 AAC
63 AAC
* * * * * * * ** * **
49130 TGAACCTTTCACCGAAGGGGCATTTTTGGAAGACAAGGCTAAACTTAGATGCAAAAATATAAAAA
1 TGACCCTTTGACCGAAAGGGTATTTTGGGAAAAGAAAACTAAACTTAGATGCAAAAAGA-CGAAA
49195 GC
65 -C
* * * * * *
49197 TGGCCCTTTGA-CAAAAGGGTATTTTGGAAAAAGAAAATACTAGACTTAAATGCAAAAAGATGAA
1 TGACCCTTTGACCGAAAGGGTATTTTGGGAAAAG-AAA-ACTAAACTTAGATGCAAAAAGACGAA
*
49261 AA
64 AC
* * * * * * * * * *
49263 TGACCCTTCGATCGAAAGGGTGTTTT--TAAATATTG-TAAGTAAACTCAAATGCGAAAATGAAG
1 TGACCCTTTGACCGAAAGGGTATTTTGGGAAA-A--GAAAACTAAACTTAGATGC-AAAAAGACG
49325 AAAC
62 AAAC
* * * * * * * * **
49329 TGAACCTTTCACCGAAGGGGCATTTCT-GGAATACAAAGCTAAACTTAGATGCAGAAATATAAAA
1 TGACCCTTTGACCGAAAGGGTATTT-TGGGAAAAGAAAACTAAACTTAGATGCA-AAA-AGACGA
*
49393 AAA
63 AAC
*
49396 TGGCCCTTTGACCGAAAGGGTATTTCT-GGAAATA-AAAACTAAACTTAGA--CAAAAAGACGAA
1 TGACCCTTTGACCGAAAGGGTATTT-TGGGAAA-AGAAAACTAAACTTAGATGCAAAAAGACGAA
49457 AC
64 AC
* * * * * * * * *
49459 TGACCCATTGACTGAAAGGGTATTTTTTGGAAAACAAAACCAAACCTAGATGTGAAAAATATGAA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGGGAAAAGAAAACTAAACTTAGATG-CAAAAAGACGAA
49524 AC
64 AC
* * * **
49526 TGACCCTTTGACCGAAAGGATACTTTGGGAAAAGAAAACT-AACTTAGATACGAAAAAGTTGAAA
1 TGACCCTTTGACCGAAAGGGTATTTTGGGAAAAGAAAACTAAACTTAGATGC-AAAAAGACGAAA
*
49590 T
65 C
* * *
49591 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGGGAAAAG-AAA-ACTAAACTTAGATGCAAAAAGACGA
*
49656 AAA
63 AAC
* * * *
49659 TGACCCTTCGACCGAAAGGGTGTTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGA
1 TGACCCTTTGACCGAAAGGGT-ATTTTGGGAAAAG-AAA-ACTAAACTTAGATGCAAAAAGACGA
49724 GAA-
63 -AAC
** * * *
49727 TGACCCTTTGACCGAAAGGGTATTTTTGAAAAAAGAAAATACTAAACCTAAATGCAAAAAAACGA
1 TGACCCTTTGACCGAAAGGGTA-TTTTGGGAAAAG-AAA-ACTAAACTTAGATGCAAAAAGACGA
*
49792 AAA
63 AAC
49795 TGACCCTT
1 TGACCCTT
49803 CGACAGGGTA
Statistics
Matches: 529, Mismatches: 112, Indels: 62
0.75 0.16 0.09
Matches are distributed among these distances:
63 26 0.05
64 25 0.05
65 60 0.11
66 134 0.25
67 108 0.20
68 165 0.31
69 11 0.02
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (65 bp):
TGACCCTTTGACCGAAAGGGTATTTTGGGAAAAGAAAACTAAACTTAGATGCAAAAAGACGAAAC
Found at i:49663 original size:68 final size:67
Alignment explanation
Indices: 49210--49828 Score: 486
Period size: 68 Copynumber: 9.4 Consensus size: 67
49200 CCCTTTGACA
* *
49210 AAAGGGTA-TTTTGGAAAAAGAAAATACTAGACTTAAATGCAAAAAGATGAAAATGACCCTTCGA
1 AAAGGGTATTTTTGGAAAAAGAAAA-ACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGA
*
49274 TCG
65 CCG
* * **** * * * * * *
49277 AAAGGGTGTTTTT--AAATATTGTAAGTAAACTCAAATGCGAAAATGAAGAAACTGAACCTTTC-
1 AAAGGGTATTTTTGGAAAAAGAAAAACTAAACTTAAATGC-AAAAAGACGAAAATG-ACCCTTCG
49339 ACCG
64 ACCG
* * * * * * * * ** * *
49343 AAGGGGCATTTCTGG-AATA-CAAAGCTAAACTTAGATGCAGAAATATAAAAAAATGGCCCTTTG
1 AAAGGGTATTTTTGGAAAAAGAAAAACTAAACTTAAATGCA-AAA-AGACGAAAATGACCCTTCG
49406 ACCG
64 ACCG
* * * *
49410 AAAGGGTATTTCTGG--AAATAAAAACTAAACTTAGA--CAAAAAGACGAAACTGACCCATT-GA
1 AAAGGGTATTTTTGGAAAAAGAAAAACTAAACTTAAATGCAAAAAGACGAAAATGACCC-TTCGA
*
49470 CTG
65 CCG
* * * * * * * * *
49473 AAAGGGTATTTTTTGG-AAAA-CAAAACCAAACCTAGATGTGAAAAATATGAAACTGACCCTTTG
1 AAAGGGTA-TTTTTGGAAAAAGAAAAACTAAACTTAAATG-CAAAAAGACGAAAATGACCCTTCG
49536 ACCG
64 ACCG
* * * * * ** *
49540 AAAGGATA-CTTTGGGAAAAG-AAAACT-AACTTAGATACGAAAAAGTTGAAATTGACCCTTCGA
1 AAAGGGTATTTTTGGAAAAAGAAAAACTAAACTTAAATGC-AAAAAGACGAAAATGACCCTTCGA
49602 CCG
65 CCG
49605 AAAGGGTATTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGA
1 AAAGGGTATTTTTGGAAAAAGAAAA-ACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGA
49670 CCG
65 CCG
* * *
49673 AAAGGGTGTTTTTGGAAAAAGAAAATACTAAACTTAAATGCAAAAAGACGAGAATGACCCTTTGA
1 AAAGGGTATTTTTGGAAAAAGAAAA-ACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGA
49738 CCG
65 CCG
* * *
49741 AAAGGGTATTTTTGAAAAAAGAAAATACTAAACCTAAATGCAAAAAAACGAAAATGACCCTTCGA
1 AAAGGGTATTTTTGGAAAAAGAAAA-ACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGA
49806 -C-
65 CCG
*
49807 --AGGGTATTTTTGGAATAAGAAA
1 AAAGGGTATTTTTGGAAAAAGAAA
49829 GGAACCGATG
Statistics
Matches: 449, Mismatches: 80, Indels: 49
0.78 0.14 0.08
Matches are distributed among these distances:
63 22 0.05
64 44 0.10
65 61 0.14
66 71 0.16
67 87 0.19
68 155 0.35
69 9 0.02
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (67 bp):
AAAGGGTATTTTTGGAAAAAGAAAAACTAAACTTAAATGCAAAAAGACGAAAATGACCCTTCGAC
CG
Found at i:52940 original size:11 final size:11
Alignment explanation
Indices: 52926--52955 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
52916 TGAAGATTTA
52926 TTGAAGATAAT
1 TTGAAGATAAT
52937 TTGAAGATAAT
1 TTGAAGATAAT
52948 TTGAAGAT
1 TTGAAGAT
52956 TTGAAGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (11 bp):
TTGAAGATAAT
Found at i:53582 original size:19 final size:18
Alignment explanation
Indices: 53558--53600 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
53548 ACAATCACAA
*
53558 TTCTAGATCTATTTTTCTC
1 TTCTAGATCTAGTTTT-TC
* *
53577 TTCTAGTTTTAGTTTTTC
1 TTCTAGATCTAGTTTTTC
53595 TTCTAG
1 TTCTAG
53601 TTTTTAGGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (18 bp):
TTCTAGATCTAGTTTTTC
Found at i:57063 original size:69 final size:69
Alignment explanation
Indices: 56986--57202 Score: 389
Period size: 69 Copynumber: 3.1 Consensus size: 69
56976 GTCCGGTGTT
* * * *
56986 GCTTGGATGGAACCAAGGCTTAAATTGTCTCGTATGGAAACGAGCTTGGCTTTTGGAAAAGCCTA
1 GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
57051 TGTG
66 TGTG
*
57055 GCTTGGATGGAACCGAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
57120 TGTG
66 TGTG
57124 GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
1 GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
57189 TGTG
66 TGTG
57193 GCTTGGATGG
1 GCTTGGATGG
57203 TGTAGACACC
Statistics
Matches: 142, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 142 1.00
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (69 bp):
GCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
TGTG
Found at i:58888 original size:17 final size:18
Alignment explanation
Indices: 58861--58900 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
58851 AACACCGCAG
*
58861 GATCAAGAGTCAACAAAA
1 GATCAAAAGTCAACAAAA
*
58879 -ATCAAAAGTCAGCAAAA
1 GATCAAAAGTCAACAAAA
58896 GATCA
1 GATCA
58901 TCACCATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.55, C:0.17, G:0.15, T:0.12
Consensus pattern (18 bp):
GATCAAAAGTCAACAAAA
Found at i:60388 original size:24 final size:24
Alignment explanation
Indices: 60361--60406 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
60351 TTTACTATTT
* *
60361 GATGCAATTTGGTCCCCGATTTAG
1 GATGAAATTTGATCCCCGATTTAG
*
60385 GATGAAATTTGATCCTCGATTT
1 GATGAAATTTGATCCCCGATTT
60407 TAGAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (24 bp):
GATGAAATTTGATCCCCGATTTAG
Found at i:62221 original size:88 final size:87
Alignment explanation
Indices: 62114--62331 Score: 368
Period size: 87 Copynumber: 2.5 Consensus size: 87
62104 ATACCTTTGG
* *
62114 AAAATAACTCTGAA-TCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGACCAAT
1 AAAATAACTCT-AAGTCTGATGTTGTGA-TTAAAACTTCTTGATTGATGATGAAAGAGGACCAAT
62178 TTGCGGTCAACTTTGATAACTTGA
64 TTGCGGTCAACTTTGATAACTTGA
* *
62202 AAAATAACTCTTAGTCTGATGTTGTGATTAAAACTTCTTGATTAATGATGAAAGAGGACCAATTT
1 AAAATAACTCTAAGTCTGATGTTGTGATTAAAACTTCTTGATTGATGATGAAAGAGGACCAATTT
62267 GCGGTCAACTTTGATAACTTGA
66 GCGGTCAACTTTGATAACTTGA
62289 AAAATAACTCTAAGT-TGATGTTGTGATTAAAACTTCTTGATTG
1 AAAATAACTCTAAGTCTGATGTTGTGATTAAAACTTCTTGATTG
62332 TTGCTTTGAA
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
86 27 0.22
87 73 0.59
88 23 0.19
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (87 bp):
AAAATAACTCTAAGTCTGATGTTGTGATTAAAACTTCTTGATTGATGATGAAAGAGGACCAATTT
GCGGTCAACTTTGATAACTTGA
Found at i:63073 original size:50 final size:50
Alignment explanation
Indices: 63019--63114 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
63009 TAAAATGCCC
* *
63019 TTTGAAAAGCAAATTTTGATCTTGGACTCCCAAATGGAATGCAATCTCAT
1 TTTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTCAT
*
63069 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATC
1 TTTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAAAGCAATC
63115 CTATTATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (50 bp):
TTTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTCAT
Done.