Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014251.1 Corchorus capsularis cultivar CVL-1 contig14272, 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: 97579
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:146 original size:22 final size:22
Alignment explanation
Indices: 121--162 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
111 GGCTCCCGGA
121 TTGA-CCCCAACCCGGGACCCAG
1 TTGACCCCCAA-CCGGGACCCAG
143 TTGACCCCCAACCGGGACCC
1 TTGACCCCCAACCGGGACCC
163 CGGTTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (22 bp):
TTGACCCCCAACCGGGACCCAG
Found at i:9791 original size:16 final size:15
Alignment explanation
Indices: 9770--9804 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
9760 CGTCTTTCTG
9770 AAAAAATAGAAAAGAAA
1 AAAAAAT-G-AAAGAAA
9787 AAAAAATGAAAGAAA
1 AAAAAATGAAAGAAA
9802 AAA
1 AAA
9805 CGAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 1 0.06
17 7 0.39
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (15 bp):
AAAAAATGAAAGAAA
Found at i:21906 original size:34 final size:33
Alignment explanation
Indices: 21852--21946 Score: 138
Period size: 34 Copynumber: 2.9 Consensus size: 33
21842 CTTTTACAAC
* *
21852 CAATGAAGTT-GCGGGCCTTCATAACGCCGTTA
1 CAATGAAGTTCACGGGCCTTCATCACGCCGTTA
*
21884 CAATGAAGTTACACGGGCCTTCATCACGCCTTTA
1 CAATGAAGTT-CACGGGCCTTCATCACGCCGTTA
*
21918 CAATGAAGTTCATGGGCCTTCATCACGCC
1 CAATGAAGTTCACGGGCCTTCATCACGCC
21947 TACAAGTTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 10 0.18
33 18 0.32
34 29 0.51
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (33 bp):
CAATGAAGTTCACGGGCCTTCATCACGCCGTTA
Found at i:25777 original size:106 final size:104
Alignment explanation
Indices: 25589--25847 Score: 373
Period size: 106 Copynumber: 2.5 Consensus size: 104
25579 AAATTTTAAT
* *
25589 TTTAATTT-TGGCTAAACTTAGTG-AATTAG--TTATATATTATTTCTAAAACCCTATAACAATA
1 TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATA
*
25650 TTATTAATTATGGAATTTACCCTTAAAATAAAAATAAAA
66 TTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAA
* *
25689 TTTAATTTGGGGCTAAACCTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATA
1 TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAAT-
* * *
25754 AATTATTAATTTTGAAATTTACCCTTGAAATAAAAATAAAT
65 -ATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAA
* * *
25795 TTTAATTTGGGACGAAACTTAGTAAAATTAGTTTTATATTTTATTTCTAAAAC
1 TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAAC
25848 TCTGTAATAA
Statistics
Matches: 140, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
100 8 0.06
101 13 0.09
102 6 0.04
104 29 0.21
106 84 0.60
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (104 bp):
TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACAATA
TTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAA
Found at i:25869 original size:106 final size:103
Alignment explanation
Indices: 25567--25871 Score: 332
Period size: 106 Copynumber: 2.9 Consensus size: 103
25557 AATTTTTCTA
* * * * * *
25567 ACCCTTAGAATAAAATTTTAATTTTAATTTTGGCTAAACTTAGTGAATTAG--TTATATATTATT
1 ACCCTTAAAATAAAA-ATAAATTTTAATTTGGGCTAAACTTAGTAAATTAGTTTTATATTTTATT
* * * *
25630 TCTAAAACCCTAT-A-ACAATATTATTAATTATGGAATTT
65 TCTAAAA-CCTATAATAAAAAATTATTAATTTTGAAATTT
* * *
25668 ACCCTTAAAATAAAAATAAAATTTAATTTGGGGCTAAACCTAGTGAAATTAGTTTTGTATTTTAT
1 ACCCTTAAAATAAAAATAAATTTTAATTT-GGGCTAAACTTAGT-AAATTAGTTTTATATTTTAT
* *
25733 TTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
64 TTCTAAAA-CCTATAATAAAAAATTATTAATTTTGAAATTT
* *
25774 ACCCTTGAAATAAAAATAAATTTTAATTTGGGACGAAACTTAGTAAAATTAGTTTTATATTTTAT
1 ACCCTTAAAATAAAAATAAATTTTAATTTGGG-CTAAACTTAGT-AAATTAGTTTTATATTTTAT
*
25839 TTCTAAAACTCTGTAATAAAAAATCT-TTAATTT
64 TTCTAAAAC-CTATAATAAAAAAT-TATTAATTT
25872 CATAATTTGC
Statistics
Matches: 172, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
100 11 0.06
101 26 0.15
102 6 0.03
104 23 0.13
105 5 0.03
106 100 0.58
107 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (103 bp):
ACCCTTAAAATAAAAATAAATTTTAATTTGGGCTAAACTTAGTAAATTAGTTTTATATTTTATTT
CTAAAACCTATAATAAAAAATTATTAATTTTGAAATTT
Found at i:27091 original size:21 final size:21
Alignment explanation
Indices: 27067--27110 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27057 TCCTTGGGGG
*
27067 TTGCTAAAT-ACCGCCCTATTT
1 TTGCT-AATCACCGCCCCATTT
*
27088 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
27109 TT
1 TT
27111 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:27205 original size:33 final size:33
Alignment explanation
Indices: 27158--27349 Score: 219
Period size: 33 Copynumber: 5.9 Consensus size: 33
27148 TTTGCCCTTA
* *
27158 GCCAC-GCGGAGCCTCCCCACTAAGACGGCTCT
1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
* * *
27190 GCCATGGCGGAGCCTCCCCACTAGGGCGGCTCT
1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
* * * *
27223 GCCACGGCCGAGCCTCCCCACTAGGGCGACTCT
1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
* *
27256 GCCACGGTGGAGCCGCCCCACTAGGACGGCCCT
1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
* * *
27289 GCCACGGC-TAGCCGCCCCACTATGACGGCCCT
1 GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
* *
27321 GCCACGGC-TAGCCGCCCCACTAGGGCGGC
1 GCCACGGCGGAGCCGCCCCACTAGGACGGC
27350 AAGGCTTTTT
Statistics
Matches: 142, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
32 53 0.37
33 89 0.63
ACGTcount: A:0.15, C:0.44, G:0.30, T:0.11
Consensus pattern (33 bp):
GCCACGGCGGAGCCGCCCCACTAGGACGGCTCT
Found at i:27457 original size:33 final size:33
Alignment explanation
Indices: 27407--27536 Score: 102
Period size: 33 Copynumber: 3.9 Consensus size: 33
27397 TAGTACCAGT
* * * *
27407 GCCGCCCCAGGGGGGCGGTCTATCCATGGCAGA
1 GCCGCCCCAAGGAGGCGGCCTAGCCATGGCAGA
* * *
27440 GCCGCCCCAAGGAGGCGGCCTGGCCATGGTAGT
1 GCCGCCCCAAGGAGGCGGCCTAGCCATGGCAGA
* * **
27473 GCCGCCCC-AGGAGGGCGGCTTGGCCATGGCTCA
1 GCCGCCCCAAGGA-GGCGGCCTAGCCATGGCAGA
* * *
27506 GTCGCCCC-AGGGGGACGACCTAGCCATGGCA
1 GCCGCCCCAAGGAGG-CGGCCTAGCCATGGCA
27537 AGTCGTCCCC
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
32 6 0.08
33 71 0.92
ACGTcount: A:0.15, C:0.35, G:0.38, T:0.12
Consensus pattern (33 bp):
GCCGCCCCAAGGAGGCGGCCTAGCCATGGCAGA
Found at i:27532 original size:66 final size:66
Alignment explanation
Indices: 27404--27534 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 66
27394 GTTTAGTACC
* * * *
27404 AGTGCCGCCCCAGGGGGGCGGTCTATCCATGGCAGAGCCGCCCCAAGGAGGCGGCCTGGCCATGG
1 AGTGCCGCCCCAGGAGGGCGGTCTATCCATGGCACAGCCGCCCCAAGGAGGCGACCTAGCCATGG
27469 T
66 T
* * *
27470 AGTGCCGCCCCAGGAGGGCGG-CT-TGGCCATGGCTCAGTCGCCCC-AGGGGGACGACCTAGCCA
1 AGTGCCGCCCCAGGAGGGCGGTCTAT--CCATGGCACAGCCGCCCCAAGGAGG-CGACCTAGCCA
27532 TGG
63 TGG
27535 CAAGTCGTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
64 1 0.02
65 7 0.13
66 47 0.85
ACGTcount: A:0.15, C:0.34, G:0.39, T:0.12
Consensus pattern (66 bp):
AGTGCCGCCCCAGGAGGGCGGTCTATCCATGGCACAGCCGCCCCAAGGAGGCGACCTAGCCATGG
T
Found at i:27581 original size:33 final size:31
Alignment explanation
Indices: 27543--27623 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 31
27533 GGCAAGTCGT
27543 CCCCCTGGTGCGGCATTACCAT-GATCAGGCCG
1 CCCCCTGG-GCGGCATTACCATGGATCA-GCCG
** *
27575 CTCCCCTGGGGCGGCCCTACCATGGCTCAGCCG
1 C-CCCCT-GGGCGGCATTACCATGGATCAGCCG
27608 CCCCCTAGGGCGGCAT
1 CCCCCT-GGGCGGCAT
27624 GAGCAATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
32 13 0.32
33 21 0.52
34 6 0.15
ACGTcount: A:0.12, C:0.42, G:0.30, T:0.16
Consensus pattern (31 bp):
CCCCCTGGGCGGCATTACCATGGATCAGCCG
Found at i:30577 original size:50 final size:50
Alignment explanation
Indices: 30502--30602 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
30492 TATGCCCCTA
30502 CAGAAGATAAGATTGATTGTAAGAATTTAAGAGAAATCATTTGTTTTGTG
1 CAGAAGATAAGATTGATTGTAAGAATTTAAGAGAAATCATTTGTTTTGTG
30552 CAGAAGATAAGATTGATTGTAAGAATTTAAGAGAAATCATTTGTTTTGTG
1 CAGAAGATAAGATTGATTGTAAGAATTTAAGAGAAATCATTTGTTTTGTG
30602 C
1 C
30603 CAATAAATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.36
Consensus pattern (50 bp):
CAGAAGATAAGATTGATTGTAAGAATTTAAGAGAAATCATTTGTTTTGTG
Found at i:35119 original size:16 final size:16
Alignment explanation
Indices: 35094--35129 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35084 GCAATCGGAA
35094 AGTGTAGCATATGATG
1 AGTGTAGCATATGATG
* *
35110 AGTGTGGCATGTGATG
1 AGTGTAGCATATGATG
35126 AGTG
1 AGTG
35130 ATGACACCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.06, G:0.39, T:0.31
Consensus pattern (16 bp):
AGTGTAGCATATGATG
Found at i:36931 original size:16 final size:16
Alignment explanation
Indices: 36912--36999 Score: 81
Period size: 16 Copynumber: 5.5 Consensus size: 16
36902 AACCCGTCCG
36912 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATA
36928 ACCCGTA-ACCC-AGATA
1 ACCCG-AGACCCGA-ATA
* *
36944 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATA
* * *
36960 ACCCGAGACCTGTATG
1 ACCCGAGACCCGAATA
* *
36976 ACCCGAAACCCGAAAA
1 ACCCGAGACCCGAATA
36992 ACCCGAGA
1 ACCCGAGA
37000 AATTAACCCG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.03
16 54 0.93
17 2 0.03
ACGTcount: A:0.38, C:0.36, G:0.18, T:0.08
Consensus pattern (16 bp):
ACCCGAGACCCGAATA
Found at i:37009 original size:22 final size:23
Alignment explanation
Indices: 36982--37027 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
36972 TATGACCCGA
36982 AACCCGAAAAACCCGAGAA-ATT
1 AACCCGAAAAACCCGAGAATATT
**
37004 AACCCGAATGACCCGAGAATATT
1 AACCCGAAAAACCCGAGAATATT
37027 A
1 A
37028 TAAACTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (23 bp):
AACCCGAAAAACCCGAGAATATT
Found at i:37582 original size:42 final size:42
Alignment explanation
Indices: 37518--37599 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
37508 TGTTGACACA
*
37518 TACCCCACATGATAATTAATTATGTATTTAATATTCAAAACT
1 TACCCCACATGAAAATTAATTATGTATTTAATATTCAAAACT
*
37560 TACCGCACATGAAAATTAATTATGTATTTAATATTCAAAA
1 TACCCCACATGAAAATTAATTATGTATTTAATATTCAAAA
37600 TTAATATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.37
Consensus pattern (42 bp):
TACCCCACATGAAAATTAATTATGTATTTAATATTCAAAACT
Found at i:37879 original size:48 final size:47
Alignment explanation
Indices: 37811--37927 Score: 130
Period size: 48 Copynumber: 2.5 Consensus size: 47
37801 AACCCGCCCA
* * * *
37811 ACCCGAGACCCG-GTAGACCCGAGATCCGAATGACCCGAA-ACCCGTATG
1 ACCCGAGACCCGAATA-ACCCGAGACCCGAATAACCCGAACA-CAG-ATG
*
37859 ACCCGAGACCCGACTAACCCGAGACCCGAATAACCCGAACACAGATG
1 ACCCGAGACCCGAATAACCCGAGACCCGAATAACCCGAACACAGATG
* *
37906 ACCCGAAACCCGAATGACCCGA
1 ACCCGAGACCCGAATAACCCGA
37928 AAAAACTATT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
47 22 0.37
48 35 0.58
49 3 0.05
ACGTcount: A:0.33, C:0.38, G:0.21, T:0.08
Consensus pattern (47 bp):
ACCCGAGACCCGAATAACCCGAGACCCGAATAACCCGAACACAGATG
Found at i:37923 original size:63 final size:63
Alignment explanation
Indices: 37778--37928 Score: 193
Period size: 63 Copynumber: 2.4 Consensus size: 63
37768 CTGACCCAAT
* * *
37778 TGACCCGAAACACGAATGACCCGAACCCGCCCAACCCGAGACCCGGTAGACCCGAGATCCGAA
1 TGACCCGAAACCCGAATGACCCGAACCCGACCAACCCGAGACCCGATAGACCCGAGATCCGAA
* *
37841 TGACCCGAAACCCGTATGACCCGAGACCCGACTAACCCGAGACCCGAATA-ACCCGA-A-CAC-A
1 TGACCCGAAACCCGAATGACCCGA-ACCCGACCAACCCGAGACCCG-ATAGACCCGAGATC-CGA
37902 GA
63 -A
37904 TGACCCGAAACCCGAATGACCCGAA
1 TGACCCGAAACCCGAATGACCCGAA
37929 AAAACTATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
62 3 0.04
63 48 0.62
64 25 0.32
65 2 0.03
ACGTcount: A:0.34, C:0.38, G:0.21, T:0.07
Consensus pattern (63 bp):
TGACCCGAAACCCGAATGACCCGAACCCGACCAACCCGAGACCCGATAGACCCGAGATCCGAA
Found at i:37928 original size:16 final size:16
Alignment explanation
Indices: 37778--37929 Score: 114
Period size: 16 Copynumber: 9.6 Consensus size: 16
37768 CTGACCCAAT
*
37778 TGACCCGAAACACGAA
1 TGACCCGAAACCCGAA
**
37794 TGACCCG-AACCCGCC
1 TGACCCGAAACCCGAA
** * *
37809 CAACCCGAGACCCG-G
1 TGACCCGAAACCCGAA
* *
37824 TAGACCCGAGATCCGAA
1 T-GACCCGAAACCCGAA
*
37841 TGACCCGAAACCCGTA
1 TGACCCGAAACCCGAA
* *
37857 TGACCCGAGACCCGAC
1 TGACCCGAAACCCGAA
* *
37873 TAACCCGAGACCCGAA
1 TGACCCGAAACCCGAA
* *
37889 TAACCCG-AACAC-AGA
1 TGACCCGAAACCCGA-A
37904 TGACCCGAAACCCGAA
1 TGACCCGAAACCCGAA
37920 TGACCCGAAA
1 TGACCCGAAA
37930 AAACTATTTG
Statistics
Matches: 107, Mismatches: 23, Indels: 12
0.75 0.16 0.08
Matches are distributed among these distances:
14 1 0.01
15 20 0.19
16 84 0.79
17 2 0.02
ACGTcount: A:0.34, C:0.38, G:0.20, T:0.07
Consensus pattern (16 bp):
TGACCCGAAACCCGAA
Found at i:43350 original size:18 final size:18
Alignment explanation
Indices: 43311--43358 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
43301 TAATAATAAA
**
43311 TAAATAATAAATATATTT
1 TAAATAATAAATATATAG
43329 TAAATAATAAATACTA-AG
1 TAAATAATAAATA-TATAG
43347 TAAA-AATAAATA
1 TAAATAATAAATA
43359 AATATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 8 0.30
18 17 0.63
19 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAATAATAAATATATAG
Found at i:43368 original size:42 final size:43
Alignment explanation
Indices: 43289--43374 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 43
43279 TCGTGGATAT
* *
43289 AATAATATATATTAATAATAAATAAATAATAAATATAT-TTTA
1 AATAATAAATACTAATAATAAATAAATAATAAATATATATTTA
*
43331 AATAATAAATACTAAGTAA-AAATAAATAA-ATATTATATATTTA
1 AATAATAAATACTAA-TAATAAATAAATAATA-AATATATATTTA
43374 A
1 A
43375 TTACTAAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
41 1 0.03
42 29 0.76
43 8 0.21
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (43 bp):
AATAATAAATACTAATAATAAATAAATAATAAATATATATTTA
Found at i:43884 original size:12 final size:11
Alignment explanation
Indices: 43867--43892 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43857 TTATTGAACC
43867 AAAAAAAAAAG
1 AAAAAAAAAAG
43878 AAAAAAAAAAG
1 AAAAAAAAAAG
43889 AAAA
1 AAAA
43893 GAGAAACATA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:45338 original size:15 final size:17
Alignment explanation
Indices: 45318--45355 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
45308 CGTTCAAATG
45318 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
45333 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
45350 T-GGGTC
1 TCGGGTC
45356 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:46735 original size:16 final size:16
Alignment explanation
Indices: 46708--46782 Score: 107
Period size: 16 Copynumber: 4.8 Consensus size: 16
46698 GTCAGGTTGA
46708 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTCATT
* *
46724 TTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCATT
*
46740 TCGGGTTCGGGTCGTT
1 TCGGGTTCGGGTCATT
*
46756 T-GGATTCGGGTCATT
1 TCGGGTTCGGGTCATT
46771 TCGGGTTCGGGT
1 TCGGGTTCGGGT
46783 ACCCCAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
15 13 0.26
16 37 0.74
ACGTcount: A:0.05, C:0.15, G:0.40, T:0.40
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:46767 original size:31 final size:32
Alignment explanation
Indices: 46708--46782 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 32
46698 GTCAGGTTGA
* * *
46708 TCGGGTTCGGGTCATTTTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT
46740 TCGGGTTCGGGTC-GTTTGGATTCGGGTCATT
1 TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT
46771 TCGGGTTCGGGT
1 TCGGGTTCGGGT
46783 ACCCCAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 27 0.68
32 13 0.32
ACGTcount: A:0.05, C:0.15, G:0.40, T:0.40
Consensus pattern (32 bp):
TCGGGTTCGGGTCAGTTTGGATTCGGGTCATT
Found at i:47974 original size:21 final size:21
Alignment explanation
Indices: 47909--48016 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
47899 TACCATCTCT
* *
47909 TGGATTTTCAACTCCTTCAGC
1 TGGATTTTCAACTCCATCAAC
** * **
47930 TTCATTATCAA-TACCATCTCC
1 TGGATTTTCAACT-CCATCAAC
*
47951 TGGATTTTCAACTCCTTCAAC
1 TGGATTTTCAACTCCATCAAC
* **
47972 TGGATTTTCAA-TACCAACTCC
1 TGGATTTTCAACT-CCATCAAC
47993 TGGATTTTCAACTCCATCAAC
1 TGGATTTTCAACTCCATCAAC
48014 TGG
1 TGG
48017 CCTCTGAACA
Statistics
Matches: 64, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
20 2 0.03
21 60 0.94
22 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (21 bp):
TGGATTTTCAACTCCATCAAC
Found at i:48016 original size:42 final size:42
Alignment explanation
Indices: 47816--48007 Score: 276
Period size: 42 Copynumber: 4.6 Consensus size: 42
47806 CATGATTAAC
*
47816 ACCATCTCCTGGATTCTCAACTCCTTCAGCTTCATCGTCAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATCGTCAAT
* *
47858 ACCATCTCTTGGATTTTCAACTCCTTCAGCTTCATCGTGAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATCGTCAAT
* **
47900 ACCATCTCTTGGATTTTCAACTCCTTCAGCTTCATTATCAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATCGTCAAT
* ** **
47942 ACCATCTCCTGGATTTTCAACTCCTTCAACTGGATTTTCAAT
1 ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATCGTCAAT
*
47984 ACCAACTCCTGGATTTTCAACTCC
1 ACCATCTCCTGGATTTTCAACTCC
48008 ATCAACTGGC
Statistics
Matches: 138, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 138 1.00
ACGTcount: A:0.23, C:0.31, G:0.09, T:0.36
Consensus pattern (42 bp):
ACCATCTCCTGGATTTTCAACTCCTTCAGCTTCATCGTCAAT
Found at i:49319 original size:19 final size:21
Alignment explanation
Indices: 49297--49337 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
49287 TTTTTTCTGG
49297 ATAAATT-ATTTTATTT-AAA
1 ATAAATTAATTTTATTTCAAA
49316 ATAAATTAATTTTATTTCAAA
1 ATAAATTAATTTTATTTCAAA
49337 A
1 A
49338 ATTAAGTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 9 0.45
21 4 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATTAATTTTATTTCAAA
Found at i:50597 original size:28 final size:29
Alignment explanation
Indices: 50542--50599 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
50532 TCTCGTTTTT
*
50542 AAAAGTTAAGGGGCCAATTTGTCCCCAAA
1 AAAAGTTAAGGGGCCAATTTATCCCCAAA
50571 AAAAGTTAAGGGGCCAATTTAT-CCCAAA
1 AAAAGTTAAGGGGCCAATTTATCCCCAAA
50599 A
1 A
50600 TGGATAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (29 bp):
AAAAGTTAAGGGGCCAATTTATCCCCAAA
Found at i:50833 original size:28 final size:28
Alignment explanation
Indices: 50768--50835 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
50758 ATATAATATA
*
50768 TATTTGATAAAAATCCATATATAAAGTAG
1 TATTTGA-ATAAATCCATATATAAAGTAG
50797 TATTTGAATAAATCCATATATAAAGTAG
1 TATTTGAATAAATCCATATATAAAGTAG
50825 TATTTGAATAA
1 TATTTGAATAA
50836 GAGAGACCTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 31 0.82
29 7 0.18
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (28 bp):
TATTTGAATAAATCCATATATAAAGTAG
Found at i:51016 original size:17 final size:17
Alignment explanation
Indices: 50991--51024 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
50981 AACAAGATTA
50991 AAACAATGTATTAACGC
1 AAACAATGTATTAACGC
*
51008 AAACCATGTATTAACGC
1 AAACAATGTATTAACGC
51025 TAGTCTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.24
Consensus pattern (17 bp):
AAACAATGTATTAACGC
Found at i:51677 original size:78 final size:77
Alignment explanation
Indices: 51534--51685 Score: 241
Period size: 78 Copynumber: 2.0 Consensus size: 77
51524 ATGCTATCTA
* * * *
51534 ATATAAGGCAAAATATTCAATACACTGTCAGTGGAGTTTAGCAGACTACACATGCGGGTCCTGAA
1 ATATAAGGCAAAATATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGGATCCTGAA
51599 GGGTGACATATT
66 GGGTGACATATT
* *
51611 ATATAAAGGCAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGGATCTTGA
1 ATAT-AAGGCAAAATATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGGATCCTGA
51676 AGGGTGACAT
65 AGGGTGACAT
51686 GTGTCCTCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 4 0.06
78 64 0.94
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (77 bp):
ATATAAGGCAAAATATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGGATCCTGAA
GGGTGACATATT
Found at i:53724 original size:66 final size:66
Alignment explanation
Indices: 53618--53749 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 66
53608 CCAGGGAAAA
* *
53618 AGGTCACGGCTTCAGGGGTTGGAGTAAGTCCAAGAACCGATACAAGTCTAGGGACCTAGTGAAGT
1 AGGTCAAGGCTTCAAGGGTTGGAGTAAGTCCAAGAACCGATACAAGTCTAGGGACCTAGTGAAGT
53683 G
66 G
* *
53684 AGGTCAAGGCTTCAAGGGTTGGTGTAAGTCCAAGAACCGATCCAAGTCTAGGGACCTAGTGAAGT
1 AGGTCAAGGCTTCAAGGGTTGGAGTAAGTCCAAGAACCGATACAAGTCTAGGGACCTAGTGAAGT
53749 G
66 G
53750 TTATCACTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.29, C:0.18, G:0.33, T:0.20
Consensus pattern (66 bp):
AGGTCAAGGCTTCAAGGGTTGGAGTAAGTCCAAGAACCGATACAAGTCTAGGGACCTAGTGAAGT
G
Found at i:54200 original size:20 final size:21
Alignment explanation
Indices: 54160--54200 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
54150 TATTTTGATG
54160 ATTTTATTTTTTAAAATAATT
1 ATTTTATTTTTTAAAATAATT
54181 ATTTTATTTTTTAAAA-AATT
1 ATTTTATTTTTTAAAATAATT
54201 TCTTGGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTATTTTTTAAAATAATT
Found at i:54685 original size:17 final size:16
Alignment explanation
Indices: 54644--54697 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
54634 AATTCTTTAC
54644 ATATATATGTAATATA
1 ATATATATGTAATATA
*
54660 ATATAATATTTAATAT-
1 ATAT-ATATGTAATATA
*
54676 ATATATATATAA-ATA
1 ATATATATGTAATATA
*
54691 AAATATA
1 ATATATA
54698 AATAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 2 0.06
15 13 0.39
16 8 0.24
17 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATATATGTAATATA
Found at i:54690 original size:28 final size:29
Alignment explanation
Indices: 54639--54696 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
54629 ACTTAAATTC
* *
54639 TTTACATATATATGTAATATAATATAATA
1 TTTACATATATATATAATATAATAAAATA
54668 TTTA-ATATATATAT-ATATAAATAAAATA
1 TTTACATATATATATAATAT-AATAAAATA
54696 T
1 T
54697 AAATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
28 18 0.69
29 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TTTACATATATATATAATATAATAAAATA
Found at i:58557 original size:25 final size:23
Alignment explanation
Indices: 58519--58565 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
58509 AAATGTCATT
58519 ACTTAAACTACTATAGTTTTATTTA
1 ACTTAAACTACTAT--TTTTATTTA
58544 ACTTAAAACT-CTATTTTTATTT
1 ACTT-AAACTACTATTTTTATTT
58566 TTTTATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (23 bp):
ACTTAAACTACTATTTTTATTTA
Found at i:58843 original size:149 final size:151
Alignment explanation
Indices: 58605--58901 Score: 508
Period size: 149 Copynumber: 2.0 Consensus size: 151
58595 AATTACTTTA
*
58605 TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGAGATATTAAAATTTTTTTAATATGTAGTT
1 TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGAGATATTAAAA-TTTTTTAATATATAGTT
* *
58670 TGATTCTACTAAAAACTCCATTTTCATTTAATTAAATTC-GTATTTTTATAATTATTTTATTTTC
65 TGATTCTACTAAAAACTCCATTTTCAGTTAATTAAATTCAATATTTTTATAATTATTTTATTTTC
58734 ACCATTGTAATTTAAAAGTTTG
130 ACCATTGTAATTTAAAAGTTTG
*
58756 TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAA-TTTTTAATATATAGTTT
1 TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGAGATATTAAAATTTTTTAATATATAGTTT
* *
58820 GATTCTACTAAAAACTCTATTTTCAGTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTA
66 GATTCTACTAAAAACTCCATTTTCAGTTAATTAAATTCAATATTTTTATAATTATTTTATTTTCA
*
58885 CCATTTTAATTTAAAAG
131 CCATTGTAATTTAAAAG
58902 GTTATTGTAA
Statistics
Matches: 138, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 52 0.38
150 40 0.29
151 46 0.33
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.51
Consensus pattern (151 bp):
TTTTTACCATTTTACTATTTTTCATTAAAAACTTGGAGATATTAAAATTTTTTAATATATAGTTT
GATTCTACTAAAAACTCCATTTTCAGTTAATTAAATTCAATATTTTTATAATTATTTTATTTTCA
CCATTGTAATTTAAAAGTTTG
Found at i:77920 original size:13 final size:13
Alignment explanation
Indices: 77902--77938 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
77892 TTAAGTATTG
77902 GGAGGGTCAAATT
1 GGAGGGTCAAATT
*
77915 GGAGGGACAAATT
1 GGAGGGTCAAATT
77928 GGAGGGTCAAA
1 GGAGGGTCAAA
77939 AAGAATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.41, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:79305 original size:2 final size:2
Alignment explanation
Indices: 79298--79324 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
79288 AGCTACACAA
79298 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 A
79325 CTACATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79586 original size:186 final size:186
Alignment explanation
Indices: 79355--79727 Score: 662
Period size: 186 Copynumber: 2.0 Consensus size: 186
79345 AACGTGAAAT
79355 TACTTAACAGTCCTTCCAACTTTTAATCTAGTGAGACCTTATCGCCCCGTTTTAGTAATTTTTTA
1 TACTTAACAGTCCTTCCAACTTTTAATCTAGTGAGACCTTATCGCCCCGTTTTAGTAATTTTTTA
79420 CAAATCATTAATTAACACTTAA-TTAAAAGAGTTATAAAA-CAAAACCATTAACTCCAAATAAAA
66 CAAATCATTAATTAACACTTAATTTAAAA-AGTTATAAAACCAAAA-CATTAACTCCAAATAAAA
* *
79483 ATCAACTCTTCAGATATTCATTGTTGTTATTCCATTTTTTTAAAACCGTTTTAGGTCA
129 ATCAACTCTTCAAATATTCATTGTTGTTATTCCAGTTTTTTAAAACCGTTTTAGGTCA
79541 TACTTAACAGTCCTTCCAACTTTTAATCT-GTTGAGACCTTATCGCCCCGTTTTAGTAATTTTTT
1 TACTTAACAGTCCTTCCAACTTTTAATCTAG-TGAGACCTTATCGCCCCGTTTTAGTAATTTTTT
79605 ACAAATCATTAATTAACACTTAATTTAAAAAGTTATAAAACCAAAACATTAACTCCAAATAAAAA
65 ACAAATCATTAATTAACACTTAATTTAAAAAGTTATAAAACCAAAACATTAACTCCAAATAAAAA
* *
79670 TCAACTCTTCAAATATTCATTGTTGTTATTCCAGTTTTTTAGAACCGTTTTAGTTCA
130 TCAACTCTTCAAATATTCATTGTTGTTATTCCAGTTTTTTAAAACCGTTTTAGGTCA
79727 T
1 T
79728 TGGGAATGAT
Statistics
Matches: 180, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
185 1 0.01
186 168 0.93
187 11 0.06
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (186 bp):
TACTTAACAGTCCTTCCAACTTTTAATCTAGTGAGACCTTATCGCCCCGTTTTAGTAATTTTTTA
CAAATCATTAATTAACACTTAATTTAAAAAGTTATAAAACCAAAACATTAACTCCAAATAAAAAT
CAACTCTTCAAATATTCATTGTTGTTATTCCAGTTTTTTAAAACCGTTTTAGGTCA
Found at i:86987 original size:20 final size:20
Alignment explanation
Indices: 86962--87000 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
86952 TTAACACAAA
86962 ACAAATCTCAGAATAAAACC
1 ACAAATCTCAGAATAAAACC
*
86982 ACAAATCTCAGAATCAAAC
1 ACAAATCTCAGAATAAAAC
87001 AGGAAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.26, G:0.05, T:0.15
Consensus pattern (20 bp):
ACAAATCTCAGAATAAAACC
Found at i:87738 original size:59 final size:59
Alignment explanation
Indices: 87646--87763 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
87636 AAATCCACAC
87646 CTTTTACTGTTTATGTTACTATTCAAAGAACTGTTCATACACTCTCATTTTACTATTCT
1 CTTTTACTGTTTATGTTACTATTCAAAGAACTGTTCATACACTCTCATTTTACTATTCT
* * *
87705 CTTTTACTGTTTATGTTACTGTTCAAAGAACTGTTTATACACTCTCATTTTTCTATTCT
1 CTTTTACTGTTTATGTTACTATTCAAAGAACTGTTCATACACTCTCATTTTACTATTCT
87764 TAGTACTGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (59 bp):
CTTTTACTGTTTATGTTACTATTCAAAGAACTGTTCATACACTCTCATTTTACTATTCT
Found at i:88302 original size:21 final size:21
Alignment explanation
Indices: 88261--88302 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
88251 TTTTTTCCCA
* *
88261 TGCTTTCTTATTCTTTTTCTT
1 TGCTTTCTTATTCTATCTCTT
88282 TGCTTTCTT-TTCTGATCTCTT
1 TGCTTTCTTATTCT-ATCTCTT
88303 CTCCCCCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.05, C:0.21, G:0.07, T:0.67
Consensus pattern (21 bp):
TGCTTTCTTATTCTATCTCTT
Found at i:89959 original size:31 final size:31
Alignment explanation
Indices: 89919--90047 Score: 123
Period size: 31 Copynumber: 4.5 Consensus size: 31
89909 ACGGTGTCCG
*
89919 ACGTGGCACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
89950 ATGTGGCACGCCACATGTACCAAAAAGT---
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
89978 -CGTGTCA---CA--TGTATCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
90003 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
90034 ACGTGGCATGCCAC
1 ACGTGGCACGCCAC
90048 ATGTTTCAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
22 12 0.15
24 2 0.03
26 6 0.08
27 5 0.06
29 2 0.03
31 51 0.65
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.18
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:90058 original size:31 final size:31
Alignment explanation
Indices: 89983--90078 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
89973 AAAGTCGTGT
* * *
89983 CACATGTATCAAAAAGTGACACATGTCACGC
1 CACATGTATCAAAAAGTGACACGTGGCATGC
* *
90014 CACGTGTACCAAAAAGTGACACGTGGCATGC
1 CACATGTATCAAAAAGTGACACGTGGCATGC
* * *
90045 CACATGTTTCAAAATA-TGGCACGTAGCATGC
1 CACATGTATCAAAA-AGTGACACGTGGCATGC
90076 CAC
1 CAC
90079 GTGCACAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 53 0.98
32 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (31 bp):
CACATGTATCAAAAAGTGACACGTGGCATGC
Found at i:92501 original size:27 final size:27
Alignment explanation
Indices: 92450--92501 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
92440 TACTCAACTT
* **
92450 TTCCTACTCCTTTACATTACCAAACGA
1 TTCCTACTCCTTAACAACACCAAACGA
*
92477 TTCCTACTCCTTAACAACACTAAAC
1 TTCCTACTCCTTAACAACACCAAAC
92502 TACACCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31
Consensus pattern (27 bp):
TTCCTACTCCTTAACAACACCAAACGA
Found at i:95160 original size:6 final size:6
Alignment explanation
Indices: 95149--95173 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
95139 GTTCATTAAC
95149 AGACAA AGACAA AGACAA AGACAA A
1 AGACAA AGACAA AGACAA AGACAA A
95174 TGTCAAAAAA
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:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AGACAA
Found at i:96429 original size:15 final size:15
Alignment explanation
Indices: 96411--96443 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
96401 TTTTTAGCTC
96411 TTGCTCTTTTGGCAT
1 TTGCTCTTTTGGCAT
96426 TTGCTCTTTTGGCAT
1 TTGCTCTTTTGGCAT
96441 TTG
1 TTG
96444 GAAATCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.21, T:0.55
Consensus pattern (15 bp):
TTGCTCTTTTGGCAT
Found at i:97106 original size:22 final size:22
Alignment explanation
Indices: 97081--97127 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
97071 ATTTATTCAT
97081 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
97103 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
97125 TAT
1 TAT
97128 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:97123 original size:11 final size:11
Alignment explanation
Indices: 97081--97123 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
97071 ATTTATTCAT
*
97081 TATTAATTAAC
1 TATTAATTAGC
*
97092 TATTAATTAGA
1 TATTAATTAGC
97103 TATTAATTAGC
1 TATTAATTAGC
97114 TATTAATTAG
1 TATTAATTAG
97124 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:97275 original size:2 final size:2
Alignment explanation
Indices: 97262--97296 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
97252 GACAAAAATA
97262 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
97297 CCTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.