Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013383.1 Corchorus capsularis cultivar CVL-1 contig13404, 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: 67971
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1113 original size:17 final size:17
Alignment explanation
Indices: 1091--1123 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1081 GTAGACTTTC
1091 TTAATTAATTTGTTTGA
1 TTAATTAATTTGTTTGA
*
1108 TTAATTGATTTGTTTG
1 TTAATTAATTTGTTTG
1124 GAGAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (17 bp):
TTAATTAATTTGTTTGA
Found at i:2276 original size:21 final size:21
Alignment explanation
Indices: 2250--2292 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2240 AAAATTTGGA
2250 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
** *
2271 TTGCTATTCACCGTCCCATTT
1 TTGCTAAACACCGCCCCATTT
2292 T
1 T
2293 GACGCTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:2555 original size:33 final size:32
Alignment explanation
Indices: 2510--2573 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
2500 GTGGCGAAGC
2510 CGCCCTCATGGGGCAGCTTCA-CCATGGGCAGGT
1 CGCCCTCATGGGGCAGCTT-AGCCA-GGGCAGGT
*
2543 CGCCC-CACTGGGGCGGCTTAGCCAGGGCAGG
1 CGCCCTCA-TGGGGCAGCTTAGCCAGGGCAGG
2574 CCGTCCCGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.14, C:0.34, G:0.38, T:0.14
Consensus pattern (32 bp):
CGCCCTCATGGGGCAGCTTAGCCAGGGCAGGT
Found at i:2708 original size:33 final size:31
Alignment explanation
Indices: 2658--2775 Score: 100
Period size: 33 Copynumber: 3.6 Consensus size: 31
2648 CCCCACCGGT
2658 GCCGTCCC-CCTGGGGCGGCTGAGCCATGGCCAA
1 GCCG-CCCTCCTGGGGCGGCT-A-CCATGGCCAA
*
2691 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCCTCCTGGGGCGG--CTACCATGGCCAA
2724 GCCG-CCTCCCTGGGGCGGCCCTACCATGG--ATA
1 GCCGCCCT-CCTGGGGCGG--CTACCATGGCCA-A
*
2756 GACCGCCCCCCTGGGGCGGC
1 G-CCGCCCTCCTGGGGCGGC
2776 ACCGATACTA
Statistics
Matches: 74, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
31 2 0.03
32 7 0.09
33 60 0.81
34 3 0.04
35 2 0.03
ACGTcount: A:0.11, C:0.42, G:0.35, T:0.12
Consensus pattern (31 bp):
GCCGCCCTCCTGGGGCGGCTACCATGGCCAA
Found at i:2935 original size:33 final size:33
Alignment explanation
Indices: 2839--2997 Score: 225
Period size: 33 Copynumber: 4.9 Consensus size: 33
2829 AAAAAGCCTT
* * *
2839 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
* * *
2871 GCCGTCCTAGTGGAGCGGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
2903 GCCGTCCTAGTGGGGAGGCTCCGCCGTTGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
2936 GCCGTCCTAGTGGGGAGGCTCCGTCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
2969 GCCGTCCTAGTGGGGAGGCTCCG-CGTGGC
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGC
2998 TAAGGGCAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
32 54 0.46
33 64 0.54
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (33 bp):
GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:2982 original size:66 final size:65
Alignment explanation
Indices: 2839--2997 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 65
2829 AAAAAGCCTT
* * * *
2839 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGAGCCGTCCTAGTGGAGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGTCCTAGTGGAGAGGCTAGCCGTGGCAGA
* * * *
2903 GCCGTCCTAGTGGGGAGGCTCCGCCGTTGCAGAGCCGTCCTAGTGGGGAGGCTCCGTCGTGGCAG
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGTCCTAGTGGAGAGGCT-AGCCGTGGCAG
2968 A
65 A
2969 GCCGTCCTAGTGGGGAGGCTCCG-CGTGGC
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGC
2998 TAAGGGCAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 18 0.21
65 33 0.39
66 33 0.39
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (65 bp):
GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGAGCCGTCCTAGTGGAGAGGCTAGCCGTGGCAGA
Found at i:3793 original size:2 final size:2
Alignment explanation
Indices: 3781--3821 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
3771 TACAGTTTTA
*
3781 AT AT AT TT AT AT AT GAT AT 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
3822 GATTAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7721 original size:17 final size:18
Alignment explanation
Indices: 7696--7731 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
7686 TACTTCATTC
7696 TTCTACTAAT-AGTGACT
1 TTCTACTAATCAGTGACT
*
7713 TTCTGCTAATCAGTGACT
1 TTCTACTAATCAGTGACT
7731 T
1 T
7732 CATTGTGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (18 bp):
TTCTACTAATCAGTGACT
Found at i:16223 original size:31 final size:30
Alignment explanation
Indices: 16185--16289 Score: 108
Period size: 31 Copynumber: 3.5 Consensus size: 30
16175 CATGGCTAAT
*
16185 TGCTCAAATAAGGGCGTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-TCAAAA
**
16216 TGCTCAAATAAGGGCCTAATC-TTTT-AATT
1 TGCTCAAATAAGGGCCTAA-CGTTTTCAAAA
* *
16245 TGGC-CAAATAAGGGCCTAACGTTATCCGAAA
1 T-GCTCAAATAAGGGCCTAACGTT-TTCAAAA
16276 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
16290 TCCGATCTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.02
29 20 0.33
30 6 0.10
31 33 0.54
32 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTTCAAAA
Found at i:16256 original size:60 final size:59
Alignment explanation
Indices: 16189--16352 Score: 206
Period size: 60 Copynumber: 2.7 Consensus size: 59
16179 GCTAATTGCT
* *
16189 CAAATAAGGGCGTAACGTT-TGTCAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
1 CAAATAAGGGC-TAACGTTAT-ACAAAATGCTCAAATAAGGGCCTAATCTTCTAATTTGGC
* * *
16249 CAAATAAGGGCCTAACGTTATCCGAAATGCTCAAATAAGGGTCC-GATCTTCTAATTTGGC
1 CAAATAAGGG-CTAACGTTATACAAAATGCTCAAATAAGGG-CCTAATCTTCTAATTTGGC
* *
16309 CAAATAAGGGTCTAATGTTATAAAAAATGCTCAAATAAGGGCCT
1 CAAATAAGGG-CTAACGTTATACAAAATGCTCAAATAAGGGCCT
16353 GGCGTCAGTT
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
59 2 0.02
60 85 0.93
61 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (59 bp):
CAAATAAGGGCTAACGTTATACAAAATGCTCAAATAAGGGCCTAATCTTCTAATTTGGC
Found at i:27981 original size:15 final size:15
Alignment explanation
Indices: 27961--27992 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27951 CAACGTGATC
27961 ATCATGAACAAAATT
1 ATCATGAACAAAATT
*
27976 ATCATGATCAAAATT
1 ATCATGAACAAAATT
27991 AT
1 AT
27993 AATTTAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (15 bp):
ATCATGAACAAAATT
Found at i:32360 original size:40 final size:40
Alignment explanation
Indices: 32305--32387 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
32295 AAGTCAGAAA
32305 ATACGAAGAAGCAAAAGAGAACATATACAAAAAATGTTGT
1 ATACGAAGAAGCAAAAGAGAACATATACAAAAAATGTTGT
*
32345 ATACGAAGAAGCAAAAGGGAACATATACAAAAAATGTTGT
1 ATACGAAGAAGCAAAAGAGAACATATACAAAAAATGTTGT
32385 ATA
1 ATA
32388 TAAAGAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.54, C:0.10, G:0.18, T:0.18
Consensus pattern (40 bp):
ATACGAAGAAGCAAAAGAGAACATATACAAAAAATGTTGT
Found at i:38161 original size:3 final size:3
Alignment explanation
Indices: 38153--38188 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
38143 ATCCCTAATA
38153 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38189 AAAGAATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:47177 original size:2 final size:2
Alignment explanation
Indices: 47170--47199 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47160 TCTAGGTTAC
47170 AT AT AT AT 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
47200 TAAAGAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47541 original size:17 final size:18
Alignment explanation
Indices: 47516--47551 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
47506 AATAGCAGAA
*
47516 AATTGAAGAG-AAATTAG
1 AATTAAAGAGAAAATTAG
47533 AATTAAAGAGAAAATTAG
1 AATTAAAGAGAAAATTAG
47551 A
1 A
47552 TTAGAGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.22
Consensus pattern (18 bp):
AATTAAAGAGAAAATTAG
Found at i:49578 original size:33 final size:33
Alignment explanation
Indices: 49520--49584 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
49510 ATTATTAACG
*
49520 AGTATTGCTCTACCTCCTTCCAAGAGACTGTCC
1 AGTATTGCTCTACCTACTTCCAAGAGACTGTCC
* * * *
49553 AGTATTGCTCTTCTTACTTCGAAGAGATTGTC
1 AGTATTGCTCTACCTACTTCCAAGAGACTGTC
49585 ACGGGGACGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (33 bp):
AGTATTGCTCTACCTACTTCCAAGAGACTGTCC
Found at i:52717 original size:30 final size:30
Alignment explanation
Indices: 52681--52743 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
52671 TTTCTTAAGA
*
52681 AAAAACTTTCTA-GTCTTAAACTTTCTATAG
1 AAAAACTTTCTACCT-TTAAACTTTCTATAG
*
52711 AAAAACTTTCTACCTTTTAACTTTCTATAG
1 AAAAACTTTCTACCTTTAAACTTTCTATAG
52741 AAA
1 AAA
52744 CTTCCAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAAACTTTCTACCTTTAAACTTTCTATAG
Found at i:56117 original size:2 final size:2
Alignment explanation
Indices: 56110--56136 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56100 CTAGTATAAT
56110 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
56137 TTTGTTATTA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:56197 original size:83 final size:83
Alignment explanation
Indices: 56058--56219 Score: 324
Period size: 83 Copynumber: 2.0 Consensus size: 83
56048 TTATTTTTTT
56058 TTATTATGAATTATTAACACACGTGCGAGGAACGTGCATTAGCTAGTATAATACACACACACACA
1 TTATTATGAATTATTAACACACGTGCGAGGAACGTGCATTAGCTAGTATAATACACACACACACA
56123 CACACACACACACATTTG
66 CACACACACACACATTTG
56141 TTATTATGAATTATTAACACACGTGCGAGGAACGTGCATTAGCTAGTATAATACACACACACACA
1 TTATTATGAATTATTAACACACGTGCGAGGAACGTGCATTAGCTAGTATAATACACACACACACA
56206 CACACACACACACA
66 CACACACACACACA
56220 CATTCCAATC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.23
Consensus pattern (83 bp):
TTATTATGAATTATTAACACACGTGCGAGGAACGTGCATTAGCTAGTATAATACACACACACACA
CACACACACACACATTTG
Found at i:56200 original size:2 final size:2
Alignment explanation
Indices: 56193--56221 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56183 CTAGTATAAT
56193 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
56222 TTCCAATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:58502 original size:42 final size:42
Alignment explanation
Indices: 58443--58530 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
58433 AAGGTAATTA
58443 TTAGATACTTGGCCTAGTTAAAAATAACCAGCTCCTAGTGTG
1 TTAGATACTTGGCCTAGTTAAAAATAACCAGCTCCTAGTGTG
58485 TTAGATACTTGGCCTAGTTAAAAATAACCAGCTCCTAGTGTG
1 TTAGATACTTGGCCTAGTTAAAAATAACCAGCTCCTAGTGTG
58527 TTAG
1 TTAG
58531 CAAAGTATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (42 bp):
TTAGATACTTGGCCTAGTTAAAAATAACCAGCTCCTAGTGTG
Found at i:59071 original size:4 final size:4
Alignment explanation
Indices: 59062--59106 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
59052 CATTAGCTAG
* * * *
59062 TATA TATA TATA TATA TTTA TATA TTTA TTTA TATA TTTA TATA T
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA T
59107 TTATTTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (4 bp):
TATA
Found at i:59083 original size:12 final size:12
Alignment explanation
Indices: 59064--59112 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
59054 TTAGCTAGTA
*
59064 TATATATATATA
1 TATATATATATT
*
59076 TATTTATATATT
1 TATATATATATT
*
59088 TATTTATATATT
1 TATATATATATT
*
59100 TATATATTTATT
1 TATATATATATT
59112 T
1 T
59113 GTTTCTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATATATATT
Found at i:59098 original size:98 final size:99
Alignment explanation
Indices: 58990--59184 Score: 356
Period size: 98 Copynumber: 2.0 Consensus size: 99
58980 TTAATATACG
* *
58990 ATTTATTATATTTATTTATTTATTTGTTTCTATGAATTATTAACACACGTGCGAGGCACGTGCAT
1 ATTTATTATATTTATATATTTATTTGTTTCTATGAATTATTAACACACGCGCGAGGCACGTGCAT
*
59055 TAGCTAGTATATATATATATATATTTATATATTT
66 TAGCTAGTATATATATATATATATATATATATTT
59089 ATTTA-TATATTTATATATTTATTTGTTTCTATGAATTATTAACACACGCGCGAGGCACGTGCAT
1 ATTTATTATATTTATATATTTATTTGTTTCTATGAATTATTAACACACGCGCGAGGCACGTGCAT
59153 TAGCTAGTATATATATATATATATATATATAT
66 TAGCTAGTATATATATATATATATATATATAT
59185 ATATATACAC
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
98 88 0.95
99 5 0.05
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (99 bp):
ATTTATTATATTTATATATTTATTTGTTTCTATGAATTATTAACACACGCGCGAGGCACGTGCAT
TAGCTAGTATATATATATATATATATATATATTT
Found at i:59167 original size:2 final size:2
Alignment explanation
Indices: 59160--59191 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59150 CATTAGCTAG
59160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59192 CACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60665 original size:8 final size:8
Alignment explanation
Indices: 60618--60666 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
60608 ATATATATAC
*
60618 ACACACAC
1 ACACACAT
*
60626 ACACACAC
1 ACACACAT
*
60634 ACATACAT
1 ACACACAT
*
60642 ACATACAT
1 ACACACAT
*
60650 ACATACAT
1 ACACACAT
60658 ACACACAT
1 ACACACAT
60666 A
1 A
60667 AGCATACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.51, C:0.35, G:0.00, T:0.14
Consensus pattern (8 bp):
ACACACAT
Found at i:60665 original size:12 final size:12
Alignment explanation
Indices: 60622--60666 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
60612 ATATACACAC
* *
60622 ACACACACACAC
1 ACACACATACAT
*
60634 ACATACATACAT
1 ACACACATACAT
*
60646 ACATACATACAT
1 ACACACATACAT
60658 ACACACATA
1 ACACACATA
60667 AGCATACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (12 bp):
ACACACATACAT
Found at i:64366 original size:29 final size:29
Alignment explanation
Indices: 64327--64404 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
64317 ACTTGTAGCG
*
64327 TTTGGACATTTTGTCCCCTAAACTTCAAT
1 TTTGGACATTTTGACCCCTAAACTTCAAT
*
64356 TTTGGACATTTT-ACCTCCTAAATTTCAAT
1 TTTGGACATTTTGACC-CCTAAACTTCAAT
* *
64385 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACATTTTGACCCCT
64405 CAACCTAACG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.05
29 27 0.64
30 11 0.26
31 2 0.05
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (29 bp):
TTTGGACATTTTGACCCCTAAACTTCAAT
Done.