Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008405.1 Corchorus capsularis cultivar CVL-1 contig08426, 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: 35950
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2736 original size:6 final size:6
Alignment explanation
Indices: 2725--2753 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2715 CTGGTTGCTA
2725 GAAAAT GAAAAT GAAAAT GAAAAT GAAAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAA
2754 CATCCCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (6 bp):
GAAAAT
Found at i:3328 original size:3 final size:3
Alignment explanation
Indices: 3320--3345 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3310 CTGGAATTTT
3320 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3346 TTTGTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12059 original size:23 final size:23
Alignment explanation
Indices: 12028--12073 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
12018 ATAAATAGAT
12028 CATGAAATTAATTTTTAAT-AGACA
1 CATGAAATT-A-TTTTAATCAGACA
12052 CATG-AATTATTTTAATCAGACA
1 CATGAAATTATTTTAATCAGACA
12074 AATGGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 4 0.19
24 4 0.19
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (23 bp):
CATGAAATTATTTTAATCAGACA
Found at i:13104 original size:13 final size:13
Alignment explanation
Indices: 13086--13110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13076 AGAAATTTTC
13086 CTGTCTCAACCTA
1 CTGTCTCAACCTA
13099 CTGTCTCAACCT
1 CTGTCTCAACCT
13111 GTTGTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
CTGTCTCAACCTA
Found at i:14621 original size:22 final size:22
Alignment explanation
Indices: 14587--14697 Score: 150
Period size: 22 Copynumber: 5.0 Consensus size: 22
14577 CGACTATATA
14587 GTGGCCGTGAGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATG
* *
14609 GTGGTCGTTAGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATG
*
14631 GTGGCCGTGAGATTCGACCATG
1 GTGGCCGTGAGATTCGGCCATG
14653 GTGGCCGTGAGATTCGGCCACATG
1 GTGGCCGTGAGATTCGG-C-CATG
* * *
14677 ATGGTCGTGAGATTCGACCAT
1 GTGGCCGTGAGATTCGGCCAT
14698 CCTTCAAAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
22 58 0.74
23 2 0.03
24 18 0.23
ACGTcount: A:0.17, C:0.22, G:0.36, T:0.25
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATG
Found at i:14950 original size:44 final size:43
Alignment explanation
Indices: 14885--14971 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 43
14875 TGGAGAATTC
* *
14885 TAAAAGGCCATGTCAGGTTTTCAATTTGACCAAGGTGGCTGTGA
1 TAAAAAGCCATGTCAGGTTTTCAATTTGACCAAGGCGG-TGTGA
*
14929 TAAAAAGCCATGT-TGGCTTTTCAATTTGACCAAGGCGGTGTGA
1 TAAAAAGCCATGTCAGG-TTTTCAATTTGACCAAGGCGGTGTGA
14972 AGGAAAATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 7 0.18
44 32 0.82
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (43 bp):
TAAAAAGCCATGTCAGGTTTTCAATTTGACCAAGGCGGTGTGA
Found at i:18093 original size:48 final size:47
Alignment explanation
Indices: 18019--18796 Score: 628
Period size: 49 Copynumber: 15.9 Consensus size: 47
18009 AAAGCGAACT
* * * * ** *
18019 TGCCTTTCGTCCGGAAAAGGCATTTTAAGAAAAAGCGAGTAAAACTAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAA-TAA
* * *
18067 TGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAAATTAG
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGT-AAAA-TAA
* ** * ***
18116 TGCCTTCCGTCGGGGAAGGGCACTTTGGGGAAAAGTGGGTAAAAATAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGT-AAAATAA
* * *
18164 -GCGTCTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGTAAAATAA
1 TGC--CTTCCGTCCGGGAAGGGCGTTTTGGGAAAA-AGCAAGTAAAATAA
* * *
18213 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAAAA-CAGGTAAAGATTAG
1 -TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAA-A-TAA
* *
18262 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA-CAGGTAGTAATAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTA-AAATAA
*
18309 GTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAA
1 -TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAA-AT-AA
* * * * *
18359 CGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTT-GGGAAAAAGCAAG-TAAAAT-AA
* * * * *
18409 TGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGCGAAAATAAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAG-TAAAAT-AA
* * * * *
18458 TGACTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAACAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAA
* * * *
18505 GTTG-CTTCCGTCTGGGAAAGGCGCTTTGGGAAATAGCAAGTAAAAATAAA
1 --TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGT-AAAAT-AA
* * * * * *
18555 TGGCTTCCGTCTGGGAAGGGTGTTTTGGGAGATAGCACGTAAAGATGAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAA-AT-AA
** ** *
18604 TGGTTTCCGTCTAGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATAAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAA-AT-AA
* * * * *
18653 TGGCTTCCGTCTGTGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGT-AAAAT-AA
* * * * *
18702 GTGCCTTCCGTACAGGAAGGGTGTTTAGGGAAAAAGCAAATAAAAATTTAA
1 -TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGT-AAAA--TAA
*
18753 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAGGTAAAA
1 TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAA
18797 ACTGAAAATT
Statistics
Matches: 621, Mismatches: 84, Indels: 49
0.82 0.11 0.06
Matches are distributed among these distances:
47 13 0.02
48 156 0.25
49 324 0.52
50 120 0.19
51 7 0.01
52 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (47 bp):
TGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAAGTAAAATAA
Found at i:18407 original size:195 final size:195
Alignment explanation
Indices: 18019--18781 Score: 697
Period size: 195 Copynumber: 3.9 Consensus size: 195
18009 AAAGCGAACT
* * * ** *
18019 TGCCTTTCGTCCGGAAAAGGCATTTTAAGAAA-AAGC-GAGTAAAACT-AATGCCTTCCATCCGG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAA-CAGAGTAAAA-TAAATGCCTTCCGTCCGG
* * * * * *
18081 GAAGGGCGTTTTAGGAAA-AAGCAAGTAAAAATTAGTGCCTTCCGTCGGGGAAGGGCACTTTGGG
64 GAAGGGCGCTTTGGGAAATAA-CAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGC-GTTTTGG
*** * * * * * * * *
18145 GAAA-AGTGGGTAAAAATAAGCGTCTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGTAAA
127 GAAATAGCAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGAAAA
18209 ATAA
192 ATAA
* *
18213 GTGCCTTCCGTCCGGGAAGGGCATTTTGGGAAA-AACAG-GTAAAGATTAGTGCCTTCCGTCCGG
1 -TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGAGTAAA-ATAAATGCCTTCCGTCCGG
* * **
18276 GAAGGGCGTTTTGGGAAA-AACAGGTAGTAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGA
64 GAAGGGCGCTTTGGGAAATAACAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGA
*
18340 AATAGCAAGTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAA
129 AATAGCAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAG-AAAAA
18405 TAAA
193 T-AA
* * ** * * * *
18409 TGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCA-AGCGAAAATAAATGACTTCCGTCTGGG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGAG-TAAAATAAATGCCTTCCGTCCGGG
* * * * *
18473 AAGGGCGCTTTGGGAAATAGCAAGT-AAAACAAGTTG-CTTCCGTCTGGGAAAGGCGCTTTGGGA
65 AAGGGCGCTTTGGGAAATAACAAGTAAAAATAAG-TGCCTTCCGTCCGGGAAGGGCGTTTTGGGA
* * * * *
18536 AATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGTGTTTT-GGGAGATAGCACGTAAAGA
129 AATAGCAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAG-AAAAA
18600 TGAA
193 T-AA
** ** * * * * *
18604 TGGTTTCCGTCTAGGAAGGGCGTTTTGGGAAATAGCA-AGTAAAGATAAATGGCTTCCGTCTGTG
1 TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGAGTAAA-ATAAATGCCTTCCGTCCGGG
* * * * *
18668 AAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAAGTGCCTTCCGTACAGGAAGGGTGTTTAGGGA
65 AAGGGCGCTTTGGGAAATAACAAGTAAAAAT-AAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGA
* * * * *
18733 AAAAGCAAATAAAAATTTAATGCCTTCCGTCCGGGAAGGGCGTTTTGGG
129 AATAGCAAGTAAAAA-TAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGG
18782 AAAAAGCAGG
Statistics
Matches: 477, Mismatches: 74, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
193 9 0.02
194 85 0.18
195 195 0.41
196 114 0.24
197 46 0.10
198 26 0.05
199 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (195 bp):
TGCCTTCCGTCCGGGAAGGGCATTTTGGGAAATAACAGAGTAAAATAAATGCCTTCCGTCCGGGA
AGGGCGCTTTGGGAAATAACAAGTAAAAATAAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA
TAGCAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGAAAAATAA
Found at i:18680 original size:98 final size:99
Alignment explanation
Indices: 18047--18802 Score: 701
Period size: 97 Copynumber: 7.7 Consensus size: 99
18037 GGCATTTTAA
* * * * * * * *
18047 GAAAAAGCGAGTAAAACT-AATGCCTTCCATCCGGGAAGGGCGTTTTAGGAAAAAGCAAGTAAAA
1 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* * * * *
18111 AT-TAGTGCCTTCCGTCGGGGAAGGGCACTTTGGG
66 ATGAAGTGGCTTCCGTCTGGGAAGGGC-GTTTTGG
*** ** * * * * *
18145 GAAA-AGTGGGTAAAAATAAGCGTCTTCCATCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AA
1 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGC-GTTTTGGGAAATAGCAAGTAAA
* * *
18208 AAT-AAGTGCCTTCCGTCCGGGAAGGGCATTTTGG
65 AATGAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGG
* * * * * * * * * **
18242 GAAA-AACAGGTAAAGATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA-AACAGGTAGTA
1 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* *
18305 AT-AAGTGCCTTCCGTCCGGGAAGGGCGTTTTGG
66 ATGAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGG
* * * * *
18338 GAAATAGCAAGTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAA
1 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTT-GGGAAATAGCAAGTAAA
* *
18403 AAT-AAATGGCTTCCGTCTGGGAAGGGCGCTTTGG
65 AATGAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGG
** * *
18437 GAAATAGCAAGCGAAAATAAATGACTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGT-AAA
1 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* * * *
18501 A-CAAGTTGCTTCCGTCTGGGAAAGGCGCTTTGG
66 ATGAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGG
* * * *
18534 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGTGTTTTGGGAGATAGCACGTAAAG
1 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* *
18599 ATGAA-TGGTTTCCGTCTAGGAAGGGCGTTTTGG
66 ATGAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGG
* * *
18632 GAAATAGCAAGTAAAGATAAATGGCTTCCGTCTGTGAAGGGCGCTTTGGGAAATAGCAAGTAAAA
1 GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* * * *
18697 ATGAAGTGCCTTCCGTAC-AGGAAGGGTGTTTAGG
66 ATGAAGTGGCTTCCGT-CTGGGAAGGGCGTTTTGG
* * * * * * *
18731 GAAAAAGCAAATAAAAATTTAATGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGCAGGTAAA
1 GAAATAGCAAGTAAAAA-TAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAA
18796 AACTGAA
65 AA-TGAA
18803 AATTGAAAGA
Statistics
Matches: 553, Mismatches: 92, Indels: 23
0.83 0.14 0.03
Matches are distributed among these distances:
95 5 0.01
96 46 0.08
97 170 0.31
98 157 0.28
99 128 0.23
100 43 0.08
101 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (99 bp):
GAAATAGCAAGTAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
ATGAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGG
Found at i:23094 original size:11 final size:12
Alignment explanation
Indices: 23067--23095 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23057 ATTTTTCATG
23067 TTGCATATAGTT
1 TTGCATATAGTT
23079 TTGCATATAG-T
1 TTGCATATAGTT
23090 TTGCAT
1 TTGCAT
23096 TGTAATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.48
Consensus pattern (12 bp):
TTGCATATAGTT
Found at i:24750 original size:16 final size:17
Alignment explanation
Indices: 24719--24753 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
24709 TTTTTTAAAT
24719 TTTTCAAAAATTTTTGC
1 TTTTCAAAAATTTTTGC
*
24736 TTTTC-AAAGTTTTTGC
1 TTTTCAAAAATTTTTGC
24752 TT
1 TT
24754 CTCTAGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (17 bp):
TTTTCAAAAATTTTTGC
Found at i:25012 original size:18 final size:17
Alignment explanation
Indices: 24971--25013 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
24961 ATTTGTTTGC
*
24971 TTGTCTTTAGTTTTGTT
1 TTGTTTTTAGTTTTGTT
*
24988 TAAGTTTTTAGTTTTTGTT
1 T-TGTTTTTAG-TTTTGTT
25007 TTGTTTT
1 TTGTTTT
25014 CTAGCTTGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 12 0.57
19 8 0.38
ACGTcount: A:0.09, C:0.02, G:0.16, T:0.72
Consensus pattern (17 bp):
TTGTTTTTAGTTTTGTT
Found at i:26887 original size:31 final size:31
Alignment explanation
Indices: 26845--26932 Score: 167
Period size: 31 Copynumber: 2.8 Consensus size: 31
26835 CATGATTACT
26845 CACCAAAAGGTATACCGTAAATACTCCCTACC
1 CACC-AAAGGTATACCGTAAATACTCCCTACC
26877 CACCAAAGGTATACCGTAAATACTCCCTACC
1 CACCAAAGGTATACCGTAAATACTCCCTACC
26908 CACCAAAGGTATACCGTAAATACTC
1 CACCAAAGGTATACCGTAAATACTC
26933 ACCGAGTATT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 52 0.93
32 4 0.07
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.19
Consensus pattern (31 bp):
CACCAAAGGTATACCGTAAATACTCCCTACC
Found at i:27024 original size:45 final size:45
Alignment explanation
Indices: 26956--27041 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
26946 AAGCCAATAG
26956 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA
1 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA
*
27001 GCAGTTACTTCATCAAGAGTGAGGTAACCACCCACGTTCTT
1 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTT
27042 ATTTGAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (45 bp):
GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA
Found at i:29060 original size:36 final size:36
Alignment explanation
Indices: 29004--29129 Score: 162
Period size: 36 Copynumber: 3.5 Consensus size: 36
28994 GGTTGTAATA
* * *
29004 CCGCTGGCCTTGGACGCCCAATACTTGGCTATAACG
1 CCGCTGGCCTTAGTCGCCCAATGCTTGGCTATAACG
* *
29040 CCGCTGGCCTTAGTCACCCAATGCTTGGCTAAAACG
1 CCGCTGGCCTTAGTCGCCCAATGCTTGGCTATAACG
* *
29076 CCACTGGCCTTAGTCGCCCAATGTTTGGCTATAACG
1 CCGCTGGCCTTAGTCGCCCAATGCTTGGCTATAACG
* * *
29112 CCACTGACCTAAGTCGCC
1 CCGCTGGCCTTAGTCGCC
29130 TAATACATAA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 79 1.00
ACGTcount: A:0.21, C:0.34, G:0.22, T:0.23
Consensus pattern (36 bp):
CCGCTGGCCTTAGTCGCCCAATGCTTGGCTATAACG
Found at i:30504 original size:14 final size:13
Alignment explanation
Indices: 30462--30505 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
30452 AATTTAAACT
* *
30462 AAATTCATAAATA
1 AAATTCAAAAAGA
*
30475 AAATTGAAAAAGA
1 AAATTCAAAAAGA
30488 AAATTCAAAAGAGA
1 AAATTCAAAA-AGA
30502 AAAT
1 AAAT
30506 ATAAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 19 0.73
14 7 0.27
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (13 bp):
AAATTCAAAAAGA
Found at i:30719 original size:34 final size:33
Alignment explanation
Indices: 30674--30812 Score: 100
Period size: 34 Copynumber: 3.9 Consensus size: 33
30664 AATCTAATGT
*
30674 TGGGGGAGGCGTTACGCCCCCC-TCCAGTTTTTAA
1 TGGGGG-GGCGTTACGCCCCCCTTCCA-ATTTTAA
30708 TGGGTGGGGCGTACGTACGCCCACCCTTCCAATTTTAA
1 TGGG-GGGGCGT---TACGCCC-CCCTTCCAATTTTAA
* * *
30746 TGGGGTGGCGTTACGCCCCCTATTCCAATTCTAA
1 TGGGGGGGCGTTACGCCCCC-CTTCCAATTTTAA
** * *
30780 TCGGGAAGGTGTTACGCCCTCCTCTTGCAATTT
1 T-GGGGGGGCGTTACGCCC-CC-CTTCCAATTT
30813 AAAACGGGGA
Statistics
Matches: 86, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
33 2 0.02
34 28 0.33
35 16 0.19
36 10 0.12
37 13 0.15
38 13 0.15
39 4 0.05
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (33 bp):
TGGGGGGGCGTTACGCCCCCCTTCCAATTTTAA
Found at i:31923 original size:31 final size:31
Alignment explanation
Indices: 31881--31968 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
31871 CATGATTACT
*
31881 CACCAAAAGGTATACCGTAAATACTCCCTACC
1 CACC-AAAGGTATACCGTAAATACTCCATACC
31913 CACCAAAGGTATACCGTAAATACTCCATACC
1 CACCAAAGGTATACCGTAAATACTCCATACC
*
31944 CACCAAAGGTATACCGTAAACACTC
1 CACCAAAGGTATACCGTAAATACTC
31969 ACCAAGTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
31 50 0.93
32 4 0.07
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (31 bp):
CACCAAAGGTATACCGTAAATACTCCATACC
Found at i:32968 original size:6 final size:6
Alignment explanation
Indices: 32957--32982 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
32947 CTAGCTAGTG
32957 TGTGTT TGTGTT TGTGTT TGTGTT TG
1 TGTGTT TGTGTT TGTGTT TGTGTT TG
32983 CCTGTTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (6 bp):
TGTGTT
Found at i:33446 original size:129 final size:127
Alignment explanation
Indices: 33267--33514 Score: 347
Period size: 129 Copynumber: 1.9 Consensus size: 127
33257 ACCATTGTTC
* * * **
33267 ATAATTTGAACTATAATTTAATTGAAAATTAGATTGATATAAATTAGATTTGATTGTATTTAAAC
1 ATAATTTGAACTATAATTTAACTGAAAATGAGATTAATATAAATTAGATTTGATCATATTTAAAC
* *
33332 TTTGTGGTAGAATTTTAGCCAAAACCACCTAAGAAGTAACAAATGCCTTAACCATTGTACCAAAT
66 TATGTGGTAGAATTTTAGCCAAAACCA--GAA-AAGTAACAAATGCCTTAACCATTGTACCAAAT
33397 ATAA-TTGAACTGATAATTTAACTGAAAATGA-ATTAATATAAATTAGATTTGATCATATTTAAA
1 ATAATTTGAACT-ATAATTTAACTGAAAATGAGATTAATATAAATTAGATTTGATCATATTTAAA
* * * *
33460 CTATGTGGTAGGATTTTATCCAAAACCAGAAAAGTACCAAATGCGTTAACCATTG
65 CTATGTGGTAGAATTTTAGCCAAAACCAGAAAAGTAACAAATGCCTTAACCATTG
33515 CACTAAATTA
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
126 22 0.21
127 2 0.02
129 61 0.58
130 21 0.20
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (127 bp):
ATAATTTGAACTATAATTTAACTGAAAATGAGATTAATATAAATTAGATTTGATCATATTTAAAC
TATGTGGTAGAATTTTAGCCAAAACCAGAAAAGTAACAAATGCCTTAACCATTGTACCAAAT
Found at i:35399 original size:21 final size:22
Alignment explanation
Indices: 35355--35402 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35345 ATAATGTCCA
*
35355 TAGCAAATGTAAATAAAGCGCG
1 TAGCAAATGCAAATAAAGCGCG
*
35377 TAGCAAATGCAAAT-AAGCTCG
1 TAGCAAATGCAAATAAAGCGCG
35398 TAGCA
1 TAGCA
35403 TATAGGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.19
Consensus pattern (22 bp):
TAGCAAATGCAAATAAAGCGCG
Found at i:35850 original size:26 final size:26
Alignment explanation
Indices: 35814--35863 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
35804 TGCCTACAAA
35814 TGCCCAATGCTCCCACACTCATATAC
1 TGCCCAATGCTCCCACACTCATATAC
35840 TGCCCAATGCTCCCACACTCATAT
1 TGCCCAATGCTCCCACACTCATAT
35864 CGATTTGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.42, G:0.08, T:0.24
Consensus pattern (26 bp):
TGCCCAATGCTCCCACACTCATATAC
Done.