Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012126.1 Corchorus olitorius cultivar O-4 contig12159, 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: 76156
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:15111 original size:38 final size:38
Alignment explanation
Indices: 15068--15150 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
15058 TCAATGCATC
*
15068 ATGATCGGAGTTGATTATCACCTTAGATCCCAGGATGT
1 ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
15106 ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
1 ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
15144 ATGATCG
1 ATGATCG
15151 AAACTTCTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (38 bp):
ATGATCGGAGTAGATTATCACCTTAGATCCCAGGATGT
Found at i:22709 original size:44 final size:44
Alignment explanation
Indices: 22649--22733 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
22639 GGGAATATAT
22649 TATACTTGAACATCATAATCATGGACAGGAAGAATGGTAATTTA
1 TATACTTGAACATCATAATCATGGACAGGAAGAATGGTAATTTA
*
22693 TATACTTGAACATCATAATCATGGACATGAAGAATGGTAAT
1 TATACTTGAACATCATAATCATGGACAGGAAGAATGGTAAT
22734 CAAGAAGGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (44 bp):
TATACTTGAACATCATAATCATGGACAGGAAGAATGGTAATTTA
Found at i:22733 original size:22 final size:22
Alignment explanation
Indices: 22664--22735 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
22654 TTGAACATCA
*
22664 TAATCATGGACAGGAAGAATGG
1 TAATCATGGACATGAAGAATGG
* ** * * **
22686 TAATTTATATACTTGAA-CATCA
1 TAA-TCATGGACATGAAGAATGG
22708 TAATCATGGACATGAAGAATGG
1 TAATCATGGACATGAAGAATGG
22730 TAATCA
1 TAATCA
22736 AGAAGGAAAC
Statistics
Matches: 33, Mismatches: 15, Indels: 4
0.63 0.29 0.08
Matches are distributed among these distances:
21 9 0.27
22 16 0.48
23 8 0.24
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (22 bp):
TAATCATGGACATGAAGAATGG
Found at i:23390 original size:3 final size:3
Alignment explanation
Indices: 23382--23408 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23372 TTGTTACTCG
23382 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
23409 AAGTATGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30209 original size:25 final size:25
Alignment explanation
Indices: 30175--30228 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
30165 ATCACTAAAA
30175 ATTAAGTAAATAAACGAAATGTAAC
1 ATTAAGTAAATAAACGAAATGTAAC
30200 ATTAAGTAAATAAACGAAATGTAAC
1 ATTAAGTAAATAAACGAAATGTAAC
30225 ATTA
1 ATTA
30229 CCTTCTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (25 bp):
ATTAAGTAAATAAACGAAATGTAAC
Found at i:36193 original size:26 final size:25
Alignment explanation
Indices: 36164--36218 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
36154 CAACACAAAA
36164 CAAA-TTTTTTTTTTAAATTAAAAACG
1 CAAACTTTTTTTTTTAAA--AAAAACG
*
36190 CAAAACTTTTTTTTTTCAAAAAAACG
1 C-AAACTTTTTTTTTTAAAAAAAACG
36216 CAA
1 CAA
36219 GACTCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 2 0.08
26 9 0.35
27 3 0.12
28 12 0.46
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.40
Consensus pattern (25 bp):
CAAACTTTTTTTTTTAAAAAAAACG
Found at i:38338 original size:19 final size:18
Alignment explanation
Indices: 38305--38340 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38295 TTGAAATAAT
38305 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
38323 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
38341 TGAGTATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:38733 original size:15 final size:16
Alignment explanation
Indices: 38691--38725 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38681 CGAAATTAAA
* *
38691 ATAAATGTTTTTTATT
1 ATAAAGGTTTTCTATT
38707 ATAAAGGTTTTCTATT
1 ATAAAGGTTTTCTATT
38723 ATA
1 ATA
38726 GAGTTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (16 bp):
ATAAAGGTTTTCTATT
Found at i:50834 original size:16 final size:17
Alignment explanation
Indices: 50805--50838 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
50795 GCAGTAAAAG
50805 TTTCTTTCTTTTTTCTT
1 TTTCTTTCTTTTTTCTT
50822 TTTCTTT-TTTTTTCTT
1 TTTCTTTCTTTTTTCTT
50838 T
1 T
50839 GGGGTGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTCTTTCTTTTTTCTT
Found at i:52614 original size:100 final size:100
Alignment explanation
Indices: 52501--52715 Score: 351
Period size: 100 Copynumber: 2.1 Consensus size: 100
52491 GAGGGCGCAT
*
52501 GCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCC
1 GCCGGTCTTACGGCCCATCATGGGGTCTTACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCC
*
52566 CCAGTG-GGAGAATTATTGCAAAGAATGACGCGTCC
66 ACAGTGCGG-GAATTATTGCAAAGAATGACGCGTCC
*
52601 GCCGGTCTTACGGCCCATCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCC
1 GCCGGTCTTACGGCCCATCATGGGGTCTTACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCC
* * * *
52666 ATAGTGCGGGGATTATTGCAGAGAATGAGGCGTCC
66 ACAGTGCGGGAATTATTGCAAAGAATGACGCGTCC
52701 GCCGGTCTTACGGCC
1 GCCGGTCTTACGGCC
52716 GAGAAAGATG
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 105 0.98
101 2 0.02
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (100 bp):
GCCGGTCTTACGGCCCATCATGGGGTCTTACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCC
ACAGTGCGGGAATTATTGCAAAGAATGACGCGTCC
Found at i:52761 original size:80 final size:80
Alignment explanation
Indices: 52624--52773 Score: 266
Period size: 80 Copynumber: 1.9 Consensus size: 80
52614 CCCATCATGG
*
52624 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCATAGTGCGGGGATTATTGCAGAG
1 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCACAGTGCGGGGATTATTGCAGAG
52689 AATGAGGCGTCCGCC
66 AATGAGGCGTCCGCC
*
52704 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTG-GGGGAATTATTGCAGA
1 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCACAGTGCGGGG-ATTATTGCAGA
52768 GAATGA
65 GAATGA
52774 TGGTGCCTAC
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
79 4 0.06
80 63 0.94
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.20
Consensus pattern (80 bp):
GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCACAGTGCGGGGATTATTGCAGAG
AATGAGGCGTCCGCC
Found at i:52872 original size:51 final size:50
Alignment explanation
Indices: 52716--52872 Score: 140
Period size: 51 Copynumber: 3.1 Consensus size: 50
52706 TCTTACGGCC
52716 GAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCA
1 GAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCA
* * * * ** ** ** * *
52766 GAGAATGATGGTGCCTACCGCTCTTACGGCCCGTCA-T-GGGGTCTTA-CGACC
1 GAGAAAGATGGCG-CT-CGGC-CTGATTGCCCCCCAGTGGGGGAATTATTG-CA
52817 GAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGGAATTATTGCA
1 GAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGT-GGGGGAATTATTGCA
52868 GAGAA
1 GAGAA
52873 TGAGGCGTCC
Statistics
Matches: 75, Mismatches: 24, Indels: 15
0.66 0.21 0.13
Matches are distributed among these distances:
48 9 0.12
49 4 0.05
50 14 0.19
51 34 0.45
52 5 0.07
53 9 0.12
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (50 bp):
GAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCA
Found at i:52899 original size:181 final size:181
Alignment explanation
Indices: 52524--53075 Score: 812
Period size: 181 Copynumber: 3.1 Consensus size: 181
52514 CCCGTCATGG
* * * *
52524 GGTCTTACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCCCCAGTGGGAGAATTATTGCAAAG
1 GGTCTAACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGAG
* * *
52589 AATGACGCGT-CC-GCCGGTCTTACGGCCCATCATGGGGTCTTACGGCCGAGAAAGATGGCGCTC
66 AATGATG-GTGCCTGCCGGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTC
** *
52652 GGCCTGATTGCCCCATAGTGCGGGGATTATTGCAGAGAATGAGGCGTCCGCC
130 GGCCTGATTGCCCCCCAGTGGGGGGATTATTGCAGAGAATGAGGCGTCCGCC
*
52704 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGAG
1 GGTCTAACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGAG
* *
52769 AATGATGGTGCCTACCGCTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
66 AATGATGGTGCCTGCCGGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
52834 GCCTGATTGCCCCCCAGTGGGGGGAATTATTGCAGAGAATGAGGCGTCCGCC
131 GCCTGATTGCCCCCCAGTGGGGGG-ATTATTGCAGAGAATGAGGCGTCCGCC
* * *
52886 GGTC-AACGGCCGAGAAAGATAGCGCTCGGCCTGATTGCCCCCTATTGGGGGAATTATTGCAGCA
1 GGTCTAACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCAG-A
* * *
52950 -AACGATGGTGTCTGCTGGTCTTACGGCCCGTCAT-GGGTCGTTAC-AGCCGAGAAAGATGGCGC
65 GAATGATGGTGCCTGCCGGTCTTACGGCCCGTCATGGGGTC-TTACGA-CCGAGAAAGATGGCGC
*
53012 TCGGCCTGATTG-CCCCCAGTGGGGGGATTATTGCAGAGAATGAGGCATCCGCC
128 TCGGCCTGATTGCCCCCCAGTGGGGGGATTATTGCAGAGAATGAGGCGTCCGCC
* *
53065 TGTCTTACGGC
1 GGTCTAACGGC
53076 TCGTCATGGG
Statistics
Matches: 342, Mismatches: 23, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
179 31 0.09
180 95 0.28
181 184 0.54
182 32 0.09
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (181 bp):
GGTCTAACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGTGGGGGAATTATTGCAGAG
AATGATGGTGCCTGCCGGTCTTACGGCCCGTCATGGGGTCTTACGACCGAGAAAGATGGCGCTCG
GCCTGATTGCCCCCCAGTGGGGGGATTATTGCAGAGAATGAGGCGTCCGCC
Found at i:53114 original size:99 final size:99
Alignment explanation
Indices: 52891--53254 Score: 475
Period size: 99 Copynumber: 3.6 Consensus size: 99
52881 CCGCCGGTCA
* * *
52891 ACGGCCGAGAAAGAT-AGCGCTCGGCCTGATTGCCCCCTATTGGGGGAATTATTGCAGCA-AACG
1 ACGGCCGAGAAAGATGA-CGCTCGGCCTGATTGCCCCC-AGTGGGGGGATTATTGCAG-AGAATG
*
52954 ATGGTGTCTG-CTGGTCTTACGGCCCGTCAT-GGGTCGTT
63 A-GGCGTCTGCCT-GTCTTACGGCCCGTCATGGGGTC-TT
* *
52992 ACAGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCAGTGGGGGGATTATTGCAGAGAATGAGG
1 ACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCCCAGTGGGGGGATTATTGCAGAGAATGAGG
* * *
53057 CATCCGCCTGTCTTACGGCTCGTCATGGGGTCTT
66 CGTCTGCCTGTCTTACGGCCCGTCATGGGGTCTT
* * * *
53091 ACGGCCGACAAAGATGACACTCGGTCTGATTGCCCCCAGTGGGGGGATTATTACAGAGAATGAGG
1 ACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCCCAGTGGGGGGATTATTGCAGAGAATGAGG
*
53156 CGTCTGCCGGTCTTACGGCCCGTCATGGGGTCTT
66 CGTCTGCCTGTCTTACGGCCCGTCATGGGGTCTT
* * *
53190 ACGGCCGAGAAAAGATGGCGCTCAGCCTGGTTGCCCCCCAGTGGGGGGATTATTGCAGAGAATGA
1 ACGGCCGAG-AAAGATGACGCTCGGCCTGATTG-CCCCCAGTGGGGGGATTATTGCAGAGAATGA
53255 TCCAAGGGAA
Statistics
Matches: 231, Mismatches: 26, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
99 121 0.52
100 46 0.20
101 64 0.28
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (99 bp):
ACGGCCGAGAAAGATGACGCTCGGCCTGATTGCCCCCAGTGGGGGGATTATTGCAGAGAATGAGG
CGTCTGCCTGTCTTACGGCCCGTCATGGGGTCTT
Found at i:53234 original size:200 final size:200
Alignment explanation
Indices: 52891--53254 Score: 540
Period size: 200 Copynumber: 1.8 Consensus size: 200
52881 CCGCCGGTCA
* * * *
52891 ACGGCCGAGAAAGATAGCGCTCGGCCTGATTGCCCCCTATTGGGGGAATTATTGCAGCAAACGAT
1 ACGGCCGACAAAGATAGCACTCGGCCTGATTGCCCCCTAGTGGGGGAATTATTACAGCAAACGAT
* * *
52956 GGTGTCTGCTGGTCTTACGGCCCGTCATGGGTCGTTACAGCCGAGAAAGATGGCGCTCGGCCTGA
66 GGCGTCTGCCGGTCTTACGGCCCGTCATGGGTCGTTACAGCCGAGAAAGATGGCGCTCAGCCTGA
53021 TTGCCCCCAGTGGGGGGATTATTGCAGAGAATGAGGCATCCGCCTGTCTTACGGCTCGTCATGGG
131 TTGCCCCCAGTGGGGGGATTATTGCAGAGAATGAGGCATCCGCCTGTCTTACGGCTCGTCATGGG
53086 GTCTT
196 GTCTT
* * *
53091 ACGGCCGACAAAGAT-GACACTCGGTCTGATTGCCCCC-AGTGGGGGGATTATTACAG-AGAATG
1 ACGGCCGACAAAGATAG-CACTCGGCCTGATTGCCCCCTAGTGGGGGAATTATTACAGCA-AACG
*
53153 A-GGCGTCTGCCGGTCTTACGGCCCGTCATGGGGTC-TTACGGCCGAGAAAAGATGGCGCTCAGC
64 ATGGCGTCTGCCGGTCTTACGGCCCGTCAT-GGGTCGTTACAGCCGAG-AAAGATGGCGCTCAGC
*
53216 CTGGTTGCCCCCCAGTGGGGGGATTATTGCAGAGAATGA
127 CTGATTG-CCCCCAGTGGGGGGATTATTGCAGAGAATGA
53255 TCCAAGGGAA
Statistics
Matches: 147, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
198 37 0.25
199 47 0.32
200 63 0.43
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (200 bp):
ACGGCCGACAAAGATAGCACTCGGCCTGATTGCCCCCTAGTGGGGGAATTATTACAGCAAACGAT
GGCGTCTGCCGGTCTTACGGCCCGTCATGGGTCGTTACAGCCGAGAAAGATGGCGCTCAGCCTGA
TTGCCCCCAGTGGGGGGATTATTGCAGAGAATGAGGCATCCGCCTGTCTTACGGCTCGTCATGGG
GTCTT
Found at i:56434 original size:42 final size:43
Alignment explanation
Indices: 56389--56472 Score: 123
Period size: 45 Copynumber: 1.9 Consensus size: 43
56379 CTAAATTTTA
* *
56389 CTCCATCTCTAGGTAATTTATCAAAATAAAGCTAATATTCTACTC
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA--C
*
56434 CTCCATCTCTAGATAATTCATCAAAATAAAGCCAATATT
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
56473 AATTGTTGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (43 bp):
CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTAC
Found at i:61429 original size:69 final size:69
Alignment explanation
Indices: 61320--61457 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
61310 TTTCCTCTTC
61320 TGTGTCTAAGGTGGGTGTGGGTTAGATATATAGGGTGTGCAACTGCAGATATTTTTGCCCGTATC
1 TGTGTCTAAGGTGGGTGTGGGTTAGATATATAGGGTGTGCAACTGCAGATATTTTTGCCCGTATC
61385 TTTG
66 TTTG
61389 TGTGTCTAAGGTGGGTGTGGGTTAGATATATAGGGTGTGCAACTGCAGATATTTTTGCCCGTATC
1 TGTGTCTAAGGTGGGTGTGGGTTAGATATATAGGGTGTGCAACTGCAGATATTTTTGCCCGTATC
61454 TTTG
66 TTTG
61458 CTTCGAAGCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.38
Consensus pattern (69 bp):
TGTGTCTAAGGTGGGTGTGGGTTAGATATATAGGGTGTGCAACTGCAGATATTTTTGCCCGTATC
TTTG
Found at i:69181 original size:30 final size:30
Alignment explanation
Indices: 69145--69684 Score: 605
Period size: 30 Copynumber: 17.8 Consensus size: 30
69135 GAAAGGTAAA
*
69145 ATCATGACAACTTTTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
69175 ATCATGACAACTTCTGGTGTCAATTGAGTAAA
1 ATCATGACAACTTCTGGTGTCAATT--GCAAG
* * * ** * * *
69207 ATTATAACATCTTCAAGTGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATT-GCAA--G
* * * *
69240 ATCATGACAACTTTTGGTGCCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * ***
69272 ATTATGACATCTTCAAATGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
69302 ATCATGACAGCTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
69332 ATCATGACAGCTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * *
69362 ATCATGACAGCTTTTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
69392 ATCATGACAGCTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
69422 ACCATGACAGCTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
** *
69452 GCCATGACGACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
69482 -TCCATGACAACTTCTGGTGTCAATTGCAAG
1 AT-CATGACAACTTCTGGTGTCAATTGCAAG
**
69512 GCCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
**
69542 GCCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
**
69572 GCCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
**
69602 GCCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
69632 ACCATGACAACTTCTGGTGTCATTTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
69662 ACCATGACAACTTCTGGTGTCAA
1 ATCATGACAACTTCTGGTGTCAA
69685 CATATATTAG
Statistics
Matches: 452, Mismatches: 50, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
30 388 0.86
31 3 0.01
32 42 0.09
33 17 0.04
34 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:74171 original size:13 final size:13
Alignment explanation
Indices: 74155--74191 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
74145 AATCTATCTA
74155 TCTATACTATATT
1 TCTATACTATATT
*
74168 TCTATACT-T-TA
1 TCTATACTATATT
74179 TCTATACTATATT
1 TCTATACTATATT
74192 AAAAAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 9 0.45
12 2 0.10
13 9 0.45
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTATACTATATT
Found at i:74184 original size:11 final size:13
Alignment explanation
Indices: 74148--74190 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
74138 AAATATTAAT
*
74148 CTATCTATCTATA
1 CTATATATCTATA
*
74161 CTATATTTCTATA
1 CTATATATCTATA
74174 CT-T-TATCTATA
1 CTATATATCTATA
74185 CTATAT
1 CTATAT
74191 TAAAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
13 14 0.56
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (13 bp):
CTATATATCTATA
Found at i:74424 original size:14 final size:13
Alignment explanation
Indices: 74388--74426 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
74378 TATATATTAG
74388 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
74401 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
74415 AATTTTTTAAAT
1 AATTTTTTAAAT
74427 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Done.