Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023101.1 Corchorus olitorius cultivar O-4 contig23134, 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: 99754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6935 original size:69 final size:69
Alignment explanation
Indices: 6824--6960 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
6814 TTTGCTTGAA
* * * *
6824 GTGCATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATTGTGTTCCTACCATTTTTTC
1 GTGCATTGTCATTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGATCCCACCATTTTTTC
6889 CTTT
66 CTTT
*
6893 GTGCATTGTCATTATATGTAATTTTAGCA-TTGAGATGTAATTAATGGTGATCCCACCTTTTTTT
1 GTGCATTGTCATTATATGTAATTTTAGCATTTG-GATGTAATTAATGGTGATCCCACCATTTTTT
6957 CCTT
65 CCTT
6961 AGTTGTTAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 3 0.05
69 59 0.95
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (69 bp):
GTGCATTGTCATTATATGTAATTTTAGCATTTGGATGTAATTAATGGTGATCCCACCATTTTTTC
CTTT
Found at i:22131 original size:21 final size:21
Alignment explanation
Indices: 22086--22137 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
22076 CCACCTGGGT
* * *
22086 ACCCATATGGTTTCCTTGAGC
1 ACCCATGTGGTTTCCTTAAGA
*
22107 ACCCATGTGGTTTGCTTAAGA
1 ACCCATGTGGTTTCCTTAAGA
*
22128 ACCCAGGTGG
1 ACCCATGTGG
22138 GCAGTCTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (21 bp):
ACCCATGTGGTTTCCTTAAGA
Found at i:23937 original size:22 final size:20
Alignment explanation
Indices: 23908--23957 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
23898 GTAAGTGATG
*
23908 AAGTAGTGAAATTGATGATTA
1 AAGTAGTGAAATTG-TGAATA
*
23929 AAGTGAGTGAATTTGTGAATA
1 AAGT-AGTGAAATTGTGAATA
23950 AAGGTAGT
1 AA-GTAGT
23958 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (20 bp):
AAGTAGTGAAATTGTGAATA
Found at i:26534 original size:21 final size:21
Alignment explanation
Indices: 26501--26549 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
26491 AAGAATTGTA
**
26501 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
26521 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
26542 GCATTCCT
1 GC-TTCCT
26550 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:29372 original size:76 final size:76
Alignment explanation
Indices: 29235--29386 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 76
29225 ACAAGGACCC
* *
29235 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
29300 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
29311 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
29373 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
29387 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.06
76 55 0.85
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:37102 original size:21 final size:21
Alignment explanation
Indices: 37064--37103 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37054 CGACTCGAAG
*
37064 AAAATTCGAGTTCGGCTCGGA
1 AAAATTCGAGTCCGGCTCGGA
37085 AAAATTCGAG-CCGAGCTCG
1 AAAATTCGAGTCCG-GCTCG
37104 AGCTCGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (21 bp):
AAAATTCGAGTCCGGCTCGGA
Found at i:39261 original size:21 final size:21
Alignment explanation
Indices: 39212--39266 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
39202 CGGTGTCTGG
*
39212 GTTATGGTGGTGGGTATCTGA
1 GTTATGGTGGTGGGTATCTAA
39233 GTTATGGTGGTGGTGT-TCTTAA
1 GTTATGGTGGTGG-GTATC-TAA
39255 GTT-TGGTAGGTG
1 GTTATGGT-GGTG
39267 TTCTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.13, C:0.04, G:0.42, T:0.42
Consensus pattern (21 bp):
GTTATGGTGGTGGGTATCTAA
Found at i:53672 original size:2 final size:2
Alignment explanation
Indices: 53660--53700 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
53650 CGTCCCCGAA
53660 AT AT AT A- AT AT AT -T CAT A- 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 AT AT
53700 A
1 A
53701 CATTTTATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 3 0.09
2 31 0.89
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:53877 original size:29 final size:29
Alignment explanation
Indices: 53835--53890 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
53825 CCTTGTACGG
*
53835 TGTTGAAAGCTTGTAATTGTGGTGTTGAT
1 TGTTGAAAACTTGTAATTGTGGTGTTGAT
53864 TGTTGAAAACTTGTAATTGTGGTGTTG
1 TGTTGAAAACTTGTAATTGTGGTGTTG
53891 TAAACTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.04, G:0.30, T:0.45
Consensus pattern (29 bp):
TGTTGAAAACTTGTAATTGTGGTGTTGAT
Found at i:55345 original size:15 final size:15
Alignment explanation
Indices: 55325--55355 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55315 CTTTTATTTG
*
55325 TGTATAAGTAAATTA
1 TGTATAAATAAATTA
55340 TGTATAAATAAATTA
1 TGTATAAATAAATTA
55355 T
1 T
55356 ATATCCTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (15 bp):
TGTATAAATAAATTA
Found at i:56804 original size:11 final size:11
Alignment explanation
Indices: 56788--56812 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56778 ACAGGAAGAT
56788 TAACTATTAAC
1 TAACTATTAAC
56799 TAACTATTAAC
1 TAACTATTAAC
56810 TAA
1 TAA
56813 GGAAAGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (11 bp):
TAACTATTAAC
Found at i:63662 original size:99 final size:97
Alignment explanation
Indices: 63506--63687 Score: 240
Period size: 99 Copynumber: 1.9 Consensus size: 97
63496 ACTCAAATTA
* * *
63506 ATTTTAATTCAAGAATCAAACCTTTAATTTAAAGAGTCTATTTTCAAATCGAAATTAACTCCAAA
1 ATTTTAATTCAAAAATCAAACCTTTAAATTAAAGAGTCTATTTTCAAATCAAAATTAACT-C-AA
63571 AAAAGATTCAAAAATCAATTTAATTTCCAAGTTT
64 AAAAGATTCAAAAATCAATTTAATTTCCAAGTTT
** * * *
63605 ATTTTAATTCAAAAATCAAGTCTTTAAATTAAAG-TTTTAGTTTTCAAATTAAAATTAACTCAAA
1 ATTTTAATTCAAAAATCAAACCTTTAAATTAAAGAGTCTA-TTTTCAAATCAAAATTAACTCAAA
**
63669 AAAGATTCACTAATCAATT
65 AAAGATTCAAAAATCAATT
63688 CCCAAGTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
97 20 0.28
98 4 0.06
99 48 0.67
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (97 bp):
ATTTTAATTCAAAAATCAAACCTTTAAATTAAAGAGTCTATTTTCAAATCAAAATTAACTCAAAA
AAGATTCAAAAATCAATTTAATTTCCAAGTTT
Found at i:63784 original size:40 final size:40
Alignment explanation
Indices: 63653--63787 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 40
63643 AGTTTTCAAA
* * *
63653 TTAAAATTAACTCAAAAAAGATTCACTAATCAATTCCCAAG
1 TTAATATTAATTCAAAAAAGATTCAATAATCAATT-CCAAG
* * * * *
63694 TTAATCTTAATTCAAAAAA-A-TCAA-AGTTTTAATTTTCAAA
1 TTAATATTAATTCAAAAAAGATTCAATA--ATCAA-TTCCAAG
*
63734 TTAAGATTAATT-AAAAAAGATTCAATAATCAATCTCCAAG
1 TTAATATTAATTCAAAAAAGATTCAATAATCAAT-TCCAAG
*
63774 TTAATTTTAATTCA
1 TTAATATTAATTCA
63788 GTATCCAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
38 1 0.01
39 10 0.14
40 35 0.50
41 23 0.33
42 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.35
Consensus pattern (40 bp):
TTAATATTAATTCAAAAAAGATTCAATAATCAATTCCAAG
Found at i:63784 original size:80 final size:80
Alignment explanation
Indices: 63630--63886 Score: 264
Period size: 80 Copynumber: 3.0 Consensus size: 80
63620 TCAAGTCTTT
* * * * *
63630 AAATTAAAGTTTTAGTTTTCAAATTAAAATTAACTCAAAAAAGATTCACTAATCAATTCCCAAGT
1 AAATCAAAGTTTTAATTTTCAAATTAAGATTAACTAAAAAAAGATTCAATAATCAATT-CCAAGT
*
63695 TAATCTTAATTCAAAA
65 TAATTTTAATTCAAAA
*
63711 AAATCAAAGTTTTAATTTTCAAATTAAGATTAA-TTAAAAAAGATTCAATAATCAATCTCCAAGT
1 AAATCAAAGTTTTAATTTTCAAATTAAGATTAACTAAAAAAAGATTCAATAATCAAT-TCCAAGT
63775 TAATTTTAATTCAGTATCCAA
65 TAATTTTAATTCA--A---AA
* *
63796 ACCTTTTAATCAAAGTTTTAATTTTCAAATTAAGCTTAACTAAAAAAAAGGGATTCAATTATCAA
1 A------AATCAAAGTTTTAATTTTCAAATTAAGATTAACT-AAAAAAA--GATTCAATAATCAA
*
63861 TTTTCAAGTTAATTTTAATTCAAAA
57 -TTCCAAGTTAATTTTAATTCAAAA
63886 A
1 A
63887 TCAAAGCTTT
Statistics
Matches: 149, Mismatches: 10, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
80 39 0.26
81 31 0.21
82 1 0.01
85 3 0.02
90 3 0.02
91 31 0.21
92 1 0.01
93 7 0.05
95 32 0.21
96 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.37
Consensus pattern (80 bp):
AAATCAAAGTTTTAATTTTCAAATTAAGATTAACTAAAAAAAGATTCAATAATCAATTCCAAGTT
AATTTTAATTCAAAA
Found at i:63812 original size:91 final size:94
Alignment explanation
Indices: 63712--63923 Score: 270
Period size: 95 Copynumber: 2.3 Consensus size: 94
63702 AATTCAAAAA
*
63712 AATCAAAGTTTTAATTTTCAAATTAAGATTAA-T-TAAAAAA-GATTCAATAATCAATCTCCAAG
1 AATCAAAGTTTTAATTTTCAAATTAAGATTAACTAAAAAAAAGGATTCAATAATCAATCTCCAAG
** *
63774 TTAATTTTAATTC-AGTATCCAAACCTTTT
66 TTAATTTTAATTCAAAAAT-CAAACCTTTC
* * * *
63803 AATCAAAGTTTTAATTTTCAAATTAAGCTTAACTAAAAAAAAGGGATTCAATTATCAATTTTCAA
1 AATCAAAGTTTTAATTTTCAAATTAAGATTAACTAAAAAAAA-GGATTCAATAATCAATCTCCAA
*
63868 GTTAATTTTAATTCAAAAATCAAAGCTTTC
65 GTTAATTTTAATTCAAAAATCAAACCTTTC
** *
63898 AATCAAAGACTCAATTTTCAAATTAA
1 AATCAAAGTTTTAATTTTCAAATTAA
63924 CTTTAACTCA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
91 31 0.30
92 1 0.01
93 6 0.06
95 63 0.61
96 3 0.03
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (94 bp):
AATCAAAGTTTTAATTTTCAAATTAAGATTAACTAAAAAAAAGGATTCAATAATCAATCTCCAAG
TTAATTTTAATTCAAAAATCAAACCTTTC
Found at i:66372 original size:445 final size:446
Alignment explanation
Indices: 65537--66437 Score: 1687
Period size: 445 Copynumber: 2.0 Consensus size: 446
65527 TTTGAGAGCT
*
65537 TAAAGTATGCTTGCAACTACCTTGTTTCTCTGTTGAAATTTGCTTGTTAGCATTGCCTTGATCAA
1 TAAAATATGCTTGCAACTACCTTGTTTCTCTGTTGAAATTTGCTTGTTAGCATTGCCTTGATCAA
*
65602 TTGTTTCAAATTGTCAATTTTATGCCCCTGATTGCATTCTGCTTGTGAGAAGTAGGCTGAAGTAG
66 TTGTATCAAATTGTCAATTTTATGCCCCTGATTGCATTCTGCTTGTGAGAAGTAGGCTGAAGTAG
* *
65667 TTGACCCAAGGATGAAAGCTTTCAAATGCCTCCCAATATTGCTCGTGATCTTGAGCATGTTAATG
131 TTGACCCAAGGATGAAAGCATTCAAATGCCTCCCAATATTGCTAGTGATCTTGAGCATGTTAATG
*
65732 CCATGTTTTTGAGCTTTGCCTTGTGCACTTTTGCAGGTTGTCCAACCATCCATTTCAAAACTGCA
196 CCATGTTTTTGAGCTTTGCCTTGTGCACTTTTGCAGGTTGTCCAACCATCCATTTCAAAACTACA
*
65797 TTAAGCTCATTTAAAGCCATCTCGGTCTTGTGAAATAGAGAAAAGAAGAAGCAAGGTAGGGAAAA
261 TTAAGCTCATTTAAAGCCATCTCGGTCTTGTGAAATAGAGAAAAGAAGAAGCAAGGCAGGGAAAA
*
65862 GTCCCAAAAAATGCAAAAAATTCCAAGATGTAAAAGTAAAATGCTAGCCTATATTTTGTCTTTCT
326 GTCCCAAAAAATGCAAAAAATGCCAAGATGTAAAAGTAAAATGCTAGCCTATATTTTGTCTTTCT
65927 GTAATCGAAAGTGCCAACGTAAATGTAAATGGAAACCTGCCTTTTTGGTATTTTTG
391 GTAATCGAAAGTGCCAACGTAAATGTAAATGGAAACCTGCCTTTTTGGTATTTTTG
* * *
65983 TAAAATATGCTTGCAACTGCCTTGTTTCTCTGTTGGAATTTTCTTGTTAGCATTGCCTTGATCAA
1 TAAAATATGCTTGCAACTACCTTGTTTCTCTGTTGAAATTTGCTTGTTAGCATTGCCTTGATCAA
66048 TTGTATCAAATTGTCAATTTTATGCCCCTGATTGCATTCTGCTTGTGA-AAGTAGGCTGAAGTAG
66 TTGTATCAAATTGTCAATTTTATGCCCCTGATTGCATTCTGCTTGTGAGAAGTAGGCTGAAGTAG
*
66112 TTGACCCAAGGATGAAAGCATTCGAATGCCTCCCAATATTGCTAGTGATCTTGAGCATGTTAATG
131 TTGACCCAAGGATGAAAGCATTCAAATGCCTCCCAATATTGCTAGTGATCTTGAGCATGTTAATG
66177 CCATGTTTTTGAGCTTTGCCTTGTGCACTTTTGCAGGTTGTCCAACCATCCATTTCAAAACTACA
196 CCATGTTTTTGAGCTTTGCCTTGTGCACTTTTGCAGGTTGTCCAACCATCCATTTCAAAACTACA
*
66242 TTGAGCTCATTTAAAGCCATCTCGGTCTTGTGAAATAGAGAAAAGAAGAAGCAAGGCAGGGAAAA
261 TTAAGCTCATTTAAAGCCATCTCGGTCTTGTGAAATAGAGAAAAGAAGAAGCAAGGCAGGGAAAA
66307 GTCCCAAAAAATGCAAAAAATGCCAAGATGTAAAAGTAAAATGCTAGCCTATATTTTGTCTTTCT
326 GTCCCAAAAAATGCAAAAAATGCCAAGATGTAAAAGTAAAATGCTAGCCTATATTTTGTCTTTCT
66372 GTAATCGAAAGTGCCAACGTAAATGTAAATGGAAACCTGCCTTTTTGGTATTTTTG
391 GTAATCGAAAGTGCCAACGTAAATGTAAATGGAAACCTGCCTTTTTGGTATTTTTG
66428 TAAAATATGC
1 TAAAATATGC
66438 AAGCTTAGAA
Statistics
Matches: 443, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
445 335 0.76
446 108 0.24
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (446 bp):
TAAAATATGCTTGCAACTACCTTGTTTCTCTGTTGAAATTTGCTTGTTAGCATTGCCTTGATCAA
TTGTATCAAATTGTCAATTTTATGCCCCTGATTGCATTCTGCTTGTGAGAAGTAGGCTGAAGTAG
TTGACCCAAGGATGAAAGCATTCAAATGCCTCCCAATATTGCTAGTGATCTTGAGCATGTTAATG
CCATGTTTTTGAGCTTTGCCTTGTGCACTTTTGCAGGTTGTCCAACCATCCATTTCAAAACTACA
TTAAGCTCATTTAAAGCCATCTCGGTCTTGTGAAATAGAGAAAAGAAGAAGCAAGGCAGGGAAAA
GTCCCAAAAAATGCAAAAAATGCCAAGATGTAAAAGTAAAATGCTAGCCTATATTTTGTCTTTCT
GTAATCGAAAGTGCCAACGTAAATGTAAATGGAAACCTGCCTTTTTGGTATTTTTG
Found at i:70508 original size:169 final size:167
Alignment explanation
Indices: 70175--70946 Score: 1056
Period size: 169 Copynumber: 4.6 Consensus size: 167
70165 GGATGATTCT
* * * *
70175 GAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTT----A--CAAACTTTGAATAAA
1 GAATTAATACCCGAAGGTTTCTGAATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGA
* * *
70234 GACCTTCAACCAAGGTTCTTAAACTTAAACATGAAATTTCTGATGAAAAACTTGATGAAATGAAA
66 GACCTT-GACCAAGGTT-TTAAACTTAAACATG-AATTT-TGATGAAAAACTTGATAAAATCAAA
* * *
70299 TGGTACCCGGAGGTTTTATCAATTGCCCAGAAGACTTATCA
127 TGATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
*
70340 GAATTAATACCCAAAGGTTTCTGAATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGA
1 GAATTAATACCCGAAGGTTTCTGAATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGA
* *
70405 GACCTTGACCAAGGATTTTAAACTTAAACATGCATCTTTGCTGAAAAACTTGATAAAATCAAATG
66 GACCTTGACCAAGG-TTTTAAACTTAAACATGAAT-TTTGATGAAAAACTTGATAAAATCAAATG
**
70470 ATACCCGGAGGTTTCGTCAATTGCCCGGAGGACTTATCA
129 ATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
* * * *
70509 GAATTAATACCTGGAGGTTTCTGAATTTATGCCTGGAGGTCTTACAAATGCAAACTTTAAATAGA
1 GAATTAATACCCGAAGGTTTCTGAATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGA
**
70574 GACCTTGATTAAGGATTTTAAACTTAAACATGAATGTTTGATGAAAAACTTGATAAAATCAAATG
66 GACCTTGACCAAGG-TTTTAAACTTAAACATGAAT-TTTGATGAAAAACTTGATAAAATCAAATG
*
70639 ATACCCGGAGGTTTTATCAATTGCCCGGAGGACCTATCA
129 ATACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
* *
70678 GAATTAATACCGGAA-GTTTCTGAATTTGTGCCCGGAGGTCTTCCAAATGCAAACTTTAAATAGA
1 GAATTAATACCCGAAGGTTTCTGAATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGA
* * *
70742 GACCTTGAACAAGGTTTTTAAACTTAAACATGAATTTTGATGAAAAACTTGATGAAATGAAATTG
66 GACCTTGACCAAGG-TTTTAAACTTAAACATGAATTTTGATGAAAAACTTGATAAAATCAAA-TG
** * *
70807 -TACCTAAGAGGTTTTACCAATTGCCCGGGGGACTTATCA
129 ATACC-CGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
* * * *
70846 GAATTAATACCCGAAGGTTTCTGAAATCGTGCCCGGAGGTCATACAAATGCAAACTTTGAATAGA
1 GAATTAATACCCGAAGGTTTCTGAATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGA
70911 GACCTTCGACCAAGGTTCTTAAACTTAAACATGAAT
66 GACCTT-GACCAAGGTT-TTAAACTTAAACATGAAT
70947 GTAAACAGGA
Statistics
Matches: 544, Mismatches: 50, Indels: 21
0.88 0.08 0.03
Matches are distributed among these distances:
165 40 0.07
167 29 0.05
168 123 0.23
169 282 0.52
170 49 0.09
171 21 0.04
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (167 bp):
GAATTAATACCCGAAGGTTTCTGAATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGA
GACCTTGACCAAGGTTTTAAACTTAAACATGAATTTTGATGAAAAACTTGATAAAATCAAATGAT
ACCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCA
Found at i:70763 original size:337 final size:340
Alignment explanation
Indices: 70175--70948 Score: 1124
Period size: 337 Copynumber: 2.3 Consensus size: 340
70165 GGATGATTCT
*
70175 GAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTT----A--CAAACTTTGAATAAA
1 GAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTTTGAATAGA
* * *
70234 GACCTTCAACCAAGGTTCTTAAACTTAAACATGAAAT-TTCTGATGAAAAACTTGATGAAATGAA
66 GACCTTCGACCAAGGTTCTTAAACTTAAACATG-AATGTTCTGATGAAAAACTTGATAAAATCAA
* *
70298 ATGGTACCCGGAGGTTTTATCAATTGCCCAGAAGACTTATCAGAATTAATACCCAAAGGTTTCTG
130 ATGATACCCGGAGGTTTTATCAATTGCCCAGAAGACCTATCAGAATTAATACCCAAAGGTTTCTG
*
70363 AATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGAGACCTTGACCAAGGATTTTAAAC
195 AATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGAGACCTTGAACAAGGATTTTAAAC
* * ** **
70428 TTAAACATGCATCTTTGCTGAAAAACTTGATAAAATCAAA-TGATACC-CGGAGGTTTCGTCAAT
260 TTAAACATGAAT-TTTGATGAAAAACTTGATAAAATCAAATTG-TACCTAAGAGGTTTCACCAAT
70491 TGCCCGGAGGACTTATCA
323 TGCCCGGAGGACTTATCA
* * * * *
70509 GAATTAATACCTGGAGGTTTCTGAATTTATGCCTGGAGGTCTTACAAATGCAAACTTTAAATAGA
1 GAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTTTGAATAGA
**
70574 GACCTT-GATTAAGGATT-TTAAACTTAAACATGAATGTT-TGATGAAAAACTTGATAAAATCAA
66 GACCTTCGACCAAGG-TTCTTAAACTTAAACATGAATGTTCTGATGAAAAACTTGATAAAATCAA
* * **
70636 ATGATACCCGGAGGTTTTATCAATTGCCCGGAGGACCTATCAGAATTAATACCGGAA-GTTTCTG
130 ATGATACCCGGAGGTTTTATCAATTGCCCAGAAGACCTATCAGAATTAATACCCAAAGGTTTCTG
* *
70700 AATTTGTGCCCGGAGGTCTTCCAAATGCAAACTTTAAATAGAGACCTTGAACAAGGTTTTTAAAC
195 AATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGAGACCTTGAACAAGGATTTTAAAC
* * *
70765 TTAAACATGAATTTTGATGAAAAACTTGATGAAATGAAATTGTACCTAAGAGGTTTTACCAATTG
260 TTAAACATGAATTTTGATGAAAAACTTGATAAAATCAAATTGTACCTAAGAGGTTTCACCAATTG
*
70830 CCCGGGGGACTTATCA
325 CCCGGAGGACTTATCA
* * *
70846 GAATTAATACCCGAAGGTTTCTGAAATCGTGCCCGGAGGTCATACAAATGCAAACTTTGAATAGA
1 GAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTTTGAATAGA
70911 GACCTTCGACCAAGGTTCTTAAACTTAAACATGAATGT
66 GACCTTCGACCAAGGTTCTTAAACTTAAACATGAATGT
70949 AAACAGGAAA
Statistics
Matches: 388, Mismatches: 40, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
334 39 0.10
336 28 0.07
337 175 0.45
338 103 0.27
339 22 0.06
340 21 0.05
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (340 bp):
GAATTAATACCTGAAGGTTTCTGAAATTGTGCCCGGAGGTCTTACAAATGCAAACTTTGAATAGA
GACCTTCGACCAAGGTTCTTAAACTTAAACATGAATGTTCTGATGAAAAACTTGATAAAATCAAA
TGATACCCGGAGGTTTTATCAATTGCCCAGAAGACCTATCAGAATTAATACCCAAAGGTTTCTGA
ATTTGTGCCCGGAGGTCTTACAAATGCAAACTTTAAATAGAGACCTTGAACAAGGATTTTAAACT
TAAACATGAATTTTGATGAAAAACTTGATAAAATCAAATTGTACCTAAGAGGTTTCACCAATTGC
CCGGAGGACTTATCA
Found at i:73638 original size:15 final size:16
Alignment explanation
Indices: 73614--73653 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
73604 AGAGATTGAA
*
73614 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
73629 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
73645 AGAAAACAA
1 AGAAAACAA
73654 AGAAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:74429 original size:11 final size:11
Alignment explanation
Indices: 74413--74438 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
74403 CCTTTGCCTA
74413 AAAACTAGAAG
1 AAAACTAGAAG
74424 AAAACTAGAAG
1 AAAACTAGAAG
74435 AAAA
1 AAAA
74439 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:75887 original size:2 final size:2
Alignment explanation
Indices: 75875--75915 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
75865 CCTTTCTCAC
*
75875 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75916 ATAGAGGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76171 original size:43 final size:42
Alignment explanation
Indices: 76028--76358 Score: 422
Period size: 43 Copynumber: 7.8 Consensus size: 42
76018 CATAAGGAGA
* *
76028 AATGCCTCTATGTTATATATGTGTTTGAGGACTTTTGTAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAG
*
76071 AGATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAG
*
76114 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
* *
76155 AATTGCCCCTATGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAG
*
76198 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
* *
76239 AATTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGGATATAG
1 AA-TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAG
* * *
76282 -GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAG
1 AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
* *
76323 AGATGCCCCTATGTTATATATGTGTTTGGGGACTTT
1 A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
76359 TTGGTTATTG
Statistics
Matches: 254, Mismatches: 21, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
41 104 0.41
42 16 0.06
43 106 0.42
44 28 0.11
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (42 bp):
AATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAG
Found at i:76180 original size:84 final size:84
Alignment explanation
Indices: 76029--76358 Score: 565
Period size: 84 Copynumber: 3.9 Consensus size: 84
76019 ATAAGGAGAA
* *
76029 ATGCCTCTATGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGATGCCCCTATGTTATATATGT
76094 GTTTGGGGACTTTGATATAG
65 GTTTGGGGACTTTGATATAG
76114 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-ATTGCCCCTATGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA-TGCCCCTATGTTATATATGT
76178 GTTTGGGGACTTTGATATAG
65 GTTTGGGGACTTTGATATAG
*
76198 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-ATTGCCCCTGTGTTATATATGT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA-TGCCCCTATGTTATATATGT
*
76262 GTTTGGGGACTTGGATATAG
65 GTTTGGGGACTTTGATATAG
* *
76282 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAGATGCCCCTATGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTATGTTATATATGTG
76347 TTTGGGGACTTT
66 TTTGGGGACTTT
76359 TTGGTTATTG
Statistics
Matches: 235, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
83 1 0.00
84 203 0.86
85 31 0.13
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTATGTTATATATGTG
TTTGGGGACTTTGATATAG
Found at i:82039 original size:30 final size:31
Alignment explanation
Indices: 81976--82065 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 31
81966 AAAGAAGATA
* *
81976 TTTTTTTTTTCTAAAAACGCAGGAACAAGAAATTT
1 TTTTTTTTTTCAAAAAACGC---AA-AACAAATTT
*
82011 TTTTTTTTTT-AGAAAACGCAAAACAAATTT
1 TTTTTTTTTTCAAAAAACGCAAAACAAATTT
82041 TTTTTTTTTTCAAAAAACGCAAAAC
1 TTTTTTTTTTCAAAAAACGCAAAAC
82066 TAATAAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 18 0.36
31 15 0.30
34 7 0.14
35 10 0.20
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (31 bp):
TTTTTTTTTTCAAAAAACGCAAAACAAATTT
Found at i:82043 original size:31 final size:32
Alignment explanation
Indices: 81967--82074 Score: 105
Period size: 30 Copynumber: 3.2 Consensus size: 32
81957 ACAGAAAATA
* *
81967 AAGAAGATATTTTTTTTTTCTAAAAACGCAGGAAC
1 AAGAA-AT-TTTTTTTTTTTTAAAAACGCA-AAAC
82002 AAGAAATTTTTTTTTTTTTAGAAAACGCAAAAC
1 AAGAAATTTTTTTTTTTTTA-AAAACGCAAAAC
82035 ---AAATTTTTTTTTTTTTCAAAAAACGCAAAAC
1 AAGAAATTTTTTTTTTTTT--AAAAACGCAAAAC
*
82066 TAATAAATT
1 -AAGAAATT
82075 AAAAACGCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
30 16 0.25
31 12 0.19
32 1 0.02
33 15 0.23
34 10 0.16
35 10 0.16
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (32 bp):
AAGAAATTTTTTTTTTTTTAAAAACGCAAAAC
Found at i:82122 original size:26 final size:28
Alignment explanation
Indices: 82075--82129 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
82065 CTAATAAATT
*
82075 AAAAACGCAAGAAAACTTTTTTTTTATG
1 AAAAACGCAAGAAAACCTTTTTTTTATG
82103 AAAAACGC-A-AAAACCTTTTTTTTATG
1 AAAAACGCAAGAAAACCTTTTTTTTATG
82129 A
1 A
82130 CGCAGAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 17 0.65
27 1 0.04
28 8 0.31
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.35
Consensus pattern (28 bp):
AAAAACGCAAGAAAACCTTTTTTTTATG
Found at i:82562 original size:15 final size:16
Alignment explanation
Indices: 82538--82577 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
82528 AGAGATTGAA
*
82538 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
82553 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
82569 AGAAAACAA
1 AGAAAACAA
82578 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:89437 original size:15 final size:15
Alignment explanation
Indices: 89417--89445 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
89407 GCCATAATAT
89417 TAGTTACTAGCTAAG
1 TAGTTACTAGCTAAG
89432 TAGTTACTAGCTAA
1 TAGTTACTAGCTAA
89446 TGAAAATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (15 bp):
TAGTTACTAGCTAAG
Found at i:91310 original size:14 final size:14
Alignment explanation
Indices: 91291--91322 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
91281 GCATATTGTG
91291 AAGTTTGTAAGGGC
1 AAGTTTGTAAGGGC
91305 AAGTTTGTAAGGGC
1 AAGTTTGTAAGGGC
91319 AAGT
1 AAGT
91323 AGAATGGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.34, T:0.28
Consensus pattern (14 bp):
AAGTTTGTAAGGGC
Found at i:95130 original size:6 final size:6
Alignment explanation
Indices: 95119--95147 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
95109 GATATAACTA
95119 ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
95148 CTTACTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
ATCTAT
Found at i:98735 original size:4 final size:4
Alignment explanation
Indices: 98726--98751 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
98716 TAATAATAAT
98726 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
98752 AGAAAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Done.