Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012452.1 Corchorus capsularis cultivar CVL-1 contig12473, 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: 21234
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2735 original size:17 final size:17
Alignment explanation
Indices: 2713--2748 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2703 TATATTTTTG
2713 ATGTTTATAGCTACATC
1 ATGTTTATAGCTACATC
2730 ATGTTTATAGCTACATC
1 ATGTTTATAGCTACATC
2747 AT
1 AT
2749 ATAAATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.42
Consensus pattern (17 bp):
ATGTTTATAGCTACATC
Found at i:2811 original size:36 final size:36
Alignment explanation
Indices: 2767--2841 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
2757 AGGTTCAACA
* * *
2767 ATACATCATGTAGACTTAAATTTAGTGTCATATCAT
1 ATACATCATGTAGACTTAAACTTAGCGTCACATCAT
* *
2803 ATACATCATTTAGACTTAGACTTAGCGTCACATCAT
1 ATACATCATGTAGACTTAAACTTAGCGTCACATCAT
2839 ATA
1 ATA
2842 GACTTAGATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (36 bp):
ATACATCATGTAGACTTAAACTTAGCGTCACATCAT
Found at i:2856 original size:27 final size:27
Alignment explanation
Indices: 2805--2864 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2795 CATATCATAT
* * *
2805 ACATCATTTAGACTTAGACTTAGCGTC
1 ACATCATATAGACTTAGACTCAGCGCC
2832 ACATCATATAGACTTAGA-TCCAGCGCC
1 ACATCATATAGACTTAGACT-CAGCGCC
2859 ACATCA
1 ACATCA
2865 CATGCATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (27 bp):
ACATCATATAGACTTAGACTCAGCGCC
Found at i:2873 original size:36 final size:36
Alignment explanation
Indices: 2832--4289 Score: 1128
Period size: 36 Copynumber: 43.0 Consensus size: 36
2822 ACTTAGCGTC
* *
2832 ACATCATATAGACTTAGATCCAGCGCCACATCACAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
2868 GCATCATATAGATTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* * *
2904 ATATTATATAGACTTA-G---A-----TC--CA-AT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
2928 ACATCATATAGCCTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
2964 ACATCATATAAACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3000 GCATCATATAGACTTAGGTCCAGCG---C--C---T
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
3028 GCATCATATAGATTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3064 ATATCATATAGACTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
3091 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
3127 GCATCATATAGTACTTTGGTCCAGCGCCACATCATAT
1 ACATCATATAG-ACTTAGGTCCAGCGCCACATCATAT
*
3164 ACATCCTATAGACTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
3191 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
3227 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
3263 ACATCATATAGACTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
3290 ACATCATATAGTCTTAGGTCCAACGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* ** * * * ***
3326 ACATCATACAGCGCCACATCATATATACTTAG-GTC-CAGC-GCC
1 ACATCATATA--G--AC-T--TAGGT-C-CAGCGCCACATCATAT
*
3368 ACATCATATAGACTTAGGTCTAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
3404 GCATCATATAGACTTAGGTCCAGCGTCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* **
3440 GCATCATATAGTTTTAGGTCCAGCGCCACATCATATACATCAT
1 ACATCATATAGACTTAGGTCCAGCG-C-CA-C--AT-CAT-AT
3483 ATGCATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 A--CATCATATAGACTTAGGTCCAGCGCCACATCATAT
* ** *
3521 GCATCATATAGTTTTATGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
3557 --A--GT-T---C-TAGGTCCAACGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* **
3584 GCATCATATAGTTTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
3611 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3647 GCATCATATAGACTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* * *
3674 ACATCATATAGTCTTAGGTACAGGGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
**
3710 ACATCATATAGTTTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3737 ACATCATATAGACTTAGGTCCAGCGTCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3773 ACATCATATAGATTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3809 ACATCATATAGACTTAGGTCCAGCGCCACATTATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
**
3845 ACATCATATAGTTTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3872 ACATCATATAGACTTAGGTTCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
3908 GCATCATATAGACTTGGGTCCAGCGCCACATCATATAGACTTAGGT
1 ACATCATATAGACTTAGGTCCAGCGCCACATC------A--TA--T
* * *
3954 CCACATCATATAGACTTATGTCCAGCACTACATCATAT
1 --ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* * *
3992 ACATCATATAGGCTTAGGTCCAGCGTCACATTATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
4028 GCATCATATAGATTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
4064 ACATCATATAGACTTAGGTCCAGCG---C--C----
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
4091 ACATCATATAGTCTTAGGTCCAGCACCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
4127 GCATCATATAGACTTAGGTCCAGCG---C--C--AT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
4156 --ATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
* *
4190 A-GTC-T-TAG---T---TCCAGCGCCATATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
4217 ACATCATATAGACTTAGGTTCAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
4253 ACATCATATAGACTTAGG-CTTAGCGCCACATCATAT
1 ACATCATATAGACTTAGGTC-CAGCGCCACATCATAT
4289 A
1 A
4290 GTCTTAGATC
Statistics
Matches: 1144, Mismatches: 125, Indels: 306
0.73 0.08 0.19
Matches are distributed among these distances:
24 15 0.01
25 3 0.00
27 244 0.21
28 28 0.02
29 4 0.00
30 13 0.01
31 12 0.01
32 12 0.01
33 19 0.02
34 7 0.01
35 11 0.01
36 639 0.56
37 34 0.03
38 8 0.01
39 4 0.00
40 6 0.01
41 3 0.00
42 15 0.01
43 10 0.01
44 6 0.01
45 23 0.02
46 1 0.00
48 27 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (36 bp):
ACATCATATAGACTTAGGTCCAGCGCCACATCATAT
Found at i:2945 original size:60 final size:60
Alignment explanation
Indices: 2869--3248 Score: 210
Period size: 63 Copynumber: 6.0 Consensus size: 60
2859 ACATCACATG
* * * *
2869 CATCATATAGATTTAGGTCCAGCGCCACATCATATATATTATATAGACTTAGATCCAATA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAAACTTAGATCCAATA
* *
2929 CATCATATAGCCTTAGGTCCAGCGCCACATCATATACATCATATAAACTTAGGTCCAGCGCCACA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAAACTTA-G---A---TC-CA
2994 TCATA
58 --ATA
* * * * * ** *
2999 TGCATCATATAGACTTAGGTCCAGCGCCTGCATCATATAGAT-TTAGGTCCAGCGCCACAT-CAT
1 --CATCATATAGACTTAGGTCCAGCGCC-ACATCATATACATCATA--T-AAAC-TTAGATCCA-
3062 ATA
58 ATA
* * * * * ** * *
3065 TATCATATAGACTTAGGTCCAGCGCCACATCATATAGA-CTTAGGTCCAGCGCCACAT-CATATG
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATA--T-AAAC-TTAGATCCA-ATA
* * * * **
3128 CATCATATAGTACTTTGGTCCAGCGCCACATCATATACATCCTATAGACTTAGGTCCAGCGCCA
1 CATCATATAG-ACTTAGGTCCAGCGCCACATCATATACATCATATAAACTTAGATCCA---ATA
* *
3192 CATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTTAGGTCCA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAAACTTAGATCCA
3249 GCGCCACATC
Statistics
Matches: 260, Mismatches: 37, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
60 46 0.18
61 3 0.01
62 3 0.01
63 89 0.34
64 62 0.24
65 3 0.01
66 3 0.01
67 3 0.01
68 2 0.01
70 3 0.01
72 28 0.11
73 11 0.04
74 1 0.00
75 2 0.01
76 1 0.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (60 bp):
CATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAAACTTAGATCCAATA
Found at i:3104 original size:27 final size:27
Alignment explanation
Indices: 3066--3126 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
3056 CATCATATAT
3066 ATCATATAGACTTAGGTCCAGCGCCAC
1 ATCATATAGACTTAGGTCCAGCGCCAC
3093 ATCATATAGACTTAGGTCCAGCGCCAC
1 ATCATATAGACTTAGGTCCAGCGCCAC
3120 ATCATAT
1 ATCATAT
3127 GCATCATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (27 bp):
ATCATATAGACTTAGGTCCAGCGCCAC
Found at i:3228 original size:63 final size:61
Alignment explanation
Indices: 3128--4343 Score: 329
Period size: 63 Copynumber: 19.1 Consensus size: 61
3118 ACATCATATG
*
3128 CATCATATAGTACTTTGGTCCAGCGCCACATCATATACATCCTATAGACTTAGGTCCAGCGCCA
1 CATCATATAG-ACTTAGGTCCAGCGCCACATCATAT-CAT-CTATAGACTTAGGTCCAGCGCCA
3192 CATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACTTAGGTCCAGCGCCACA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATAT-CATC-TATAGACTTAGGTCCAGCG---C-
3257 TCATATA
60 -C----A
* *
3264 CATCATATAGACTTAGGTCCAGCG-C-CA-C--ATCA--TATAGTCTTAGGTCCAACGCCA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATCATCTATAGACTTAGGTCCAGCGCCA
* * *
3318 CATCATATACA-TCA--TACAGCGCCACATC--AT-A--TAT--ACTTAGGTCCAGCGCCA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATCATCTATAGACTTAGGTCCAGCGCCA
*
3369 CATCATATAGACTTAGGTCTAGCGCCACATCATATGCATCATATAGACTTAGGTCCAGCGTCACA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATAT-CATC-TATAGACTTAGGTCCAGCG---C-
3434 TCATA
60 -C--A
**
3439 TGCATCATATAGTTTTAGGTCCAGCGCCACATCATATACATCATATGCATCATATAGACTTAGGT
1 --CATCATATAGACTTAGGTCCAGCG---C--C----ACATCATAT-CATC-TATAGACTTAGGT
3504 CCAGCGCCA
53 CCAGCGCCA
*
3513 CATCATAT-GCATCATATAGTTTTATGTCCAGCGCCACATCATAT-A-GT-T---C-TAGGTCCA
1 CATCATATAG-A-C-T-TAG------GTCCAGCGCCACATCATATCATCTATAGACTTAGGTCCA
*
3570 ACGCCA
56 GCGCCA
* ** ** *
3576 CATCATAT-GCATCATATAGTTTTAG-GTCCAGCGCCACATCA--TATAGACTTAGGTCCAGCGC
1 CATCATATAG-A-C-T-TAGGTCCAGCG-CCA-CATCATATCATCTATAGACTTAGGTCCAGCG-
3637 CACATCATA
59 --C--C--A
* *
3646 TGCATCATATAGACTTAGGTCCAGCGCCACATCATAT-AGTCT-TAGGTAC--AGGGCCA-CATC
1 --CATCATATAGACTTAGGTCCAGCGCCACATCATATCA-TCTATA-G-ACTTAGGTCCAGC-GC
*
3706 ATATA
60 ---CA
** * * * * ***
3711 CATCATATAGTTTTAGGTCCAGCGCCACATCATAT-AGACT-TAG-GTCCAGCGTCACATCATAT
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATCA-TCTATAGACT-TAG-GTC-CAGC-GCC
3773 A
61 A
*
3774 CATCATATAGATTTAGGTCCAGCGCCACATCATATACATCATATAGACTTAGGTCCAGCGCCA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATAT-CATC-TATAGACTTAGGTCCAGCGCCA
* * * ** ** * *
3837 CATTATATACATCATATAGTTTTAG-GTCCAGCGCCACATCA--TATAGACTTAGGTTCAGCGCC
1 CATCATATAGA-C-T-TAGGTCCAGCG-CCA-CATCATATCATCTATAGACTTAGGTCCAGCG--
3899 ACATCATA
59 -C--C--A
* **
3907 TGCATCATATAGACTTGGGTCCAGCG-C-CA-C--ATCA--TATAGACTTAGGTCCA-CATCA
1 --CATCATATAGACTTAGGTCCAGCGCCACATCATATCATCTATAGACTTAGGTCCAGCGCCA
* * * * ** *
3962 TAT-AGACTTATGTC-CA-G--CA-CTACATCAT-ATA-CATCATATAGGCTTAGGTCCAGCGTC
1 CATCATA--TA-GACTTAGGTCCAGCGCCA-CATCATATCATC-TATAGACTTAGGTCCAGCG-C
4019 ACATTATA
60 -C-----A
*
4027 TGCATCATATAGATTTAGGTCCAGCGCCACATCATATACATCATATAGACTTAGGTCCAGCGCCA
1 --CATCATATAGACTTAGGTCCAGCGCCACATCATAT-CATC-TATAGACTTAGGTCCAGCGCCA
* *
4092 CATCATATAGTCTTAGGTCCAGCACCACATCATATGCATCATATAGACTTAGGTCCAGCGCCA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATAT-CATC-TATAGACTTAGGTCCAGCGCCA
* * *
4155 TATCATATAGACTTAGGTCCAGCGCCACATCATAT-AGTCT-TAG--TTCCAGCG-CCATATCAT
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATCA-TCTATAGACTT--AG-GTCC--AGC-G
**
4215 ATA
59 CCA
* *
4218 CATCATATAGACTTAGGTTCAGCGCCACATCATATACATCATATAGACTTAGG-CTTAGCGCCA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATAT-CATC-TATAGACTTAGGTC-CAGCGCCA
* * * *
4281 CATCATATAGTCTTAGATCCAG-TCC-CA-C--ATCA--TATAGTCTTAGGTCCAGCGCCA
1 CATCATATAGACTTAGGTCCAGCGCCACATCATATCATCTATAGACTTAGGTCCAGCGCCA
4335 CATCATATA
1 CATCATATA
4344 CATCATATTG
Statistics
Matches: 889, Mismatches: 112, Indels: 312
0.68 0.09 0.24
Matches are distributed among these distances:
50 1 0.00
51 34 0.04
52 5 0.01
53 13 0.01
54 57 0.06
55 5 0.01
56 3 0.00
57 24 0.03
58 13 0.01
59 2 0.00
60 10 0.01
61 8 0.01
62 10 0.01
63 389 0.44
64 21 0.02
65 18 0.02
66 35 0.04
67 13 0.01
68 16 0.02
69 28 0.03
70 19 0.02
71 7 0.01
72 104 0.12
73 1 0.00
74 2 0.00
75 4 0.00
76 2 0.00
77 1 0.00
78 2 0.00
81 42 0.05
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (61 bp):
CATCATATAGACTTAGGTCCAGCGCCACATCATATCATCTATAGACTTAGGTCCAGCGCCA
Found at i:3345 original size:24 final size:26
Alignment explanation
Indices: 3263--3403 Score: 99
Period size: 27 Copynumber: 5.3 Consensus size: 26
3253 CACATCATAT
* * *
3263 ACATCATATAGACTTAGGTCCAGCGCC
1 ACATCATATACACTCA-GTACAGCGCC
** * * *
3290 ACATCATATAGTCTTAGGTCCAACGCC
1 ACATCATATACACTCA-GTACAGCGCC
3317 ACATCATATACA-TCA-TACAGCGCC
1 ACATCATATACACTCAGTACAGCGCC
* * *
3341 ACATCATATATACTTAGGTCCAGCGCC
1 ACATCATATACACTCA-GTACAGCGCC
* *
3368 ACATCATATAGACTTAGGT-CTAGCGCC
1 ACATCATATACACTCA-GTAC-AGCGCC
3395 ACATCATAT
1 ACATCATAT
3404 GCATCATATA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
24 18 0.18
25 2 0.02
26 3 0.03
27 76 0.77
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (26 bp):
ACATCATATACACTCAGTACAGCGCC
Found at i:3395 original size:78 final size:78
Alignment explanation
Indices: 3263--3411 Score: 253
Period size: 78 Copynumber: 1.9 Consensus size: 78
3253 CACATCATAT
*
3263 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGTCTTAGGTCCAACGCCACATCATATAC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAACGCCACATCATATAC
3328 ATCATACAGCGCC
66 ATCATACAGCGCC
* * * *
3341 ACATCATATATACTTAGGTCCAGCGCCACATCATATAGACTTAGGTCTAGCGCCACATCATATGC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAACGCCACATCATATAC
3406 ATCATA
66 ATCATA
3412 TAGACTTAGG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (78 bp):
ACATCATATAGACTTAGGTCCAGCGCCACATCATATAGACTTAGGTCCAACGCCACATCATATAC
ATCATACAGCGCC
Found at i:3480 original size:45 final size:45
Alignment explanation
Indices: 3431--3529 Score: 171
Period size: 45 Copynumber: 2.2 Consensus size: 45
3421 GTCCAGCGTC
**
3431 ACATCATATGCATCATATAGTTTTAGGTCCAGCGCCACATCATAT
1 ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATAT
3476 ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATAT
1 ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATAT
*
3521 GCATCATAT
1 ACATCATAT
3530 AGTTTTATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (45 bp):
ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATAT
Found at i:3495 original size:81 final size:81
Alignment explanation
Indices: 3395--3557 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
3385 GTCTAGCGCC
*
3395 ACATCATATGCATCATATAGACTTAGGTCCAGCGTCACATCATATGCATCATATAGTTTTAGGTC
1 ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATATGCATCATATAGTTTTAGGTC
3460 CAGCGCCACATCATAT
66 CAGCGCCACATCATAT
*
3476 ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATATGCATCATATAGTTTTATGTC
1 ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATATGCATCATATAGTTTTAGGTC
3541 CAGCGCCACATCATAT
66 CAGCGCCACATCATAT
3557 A
1 A
3558 GTTCTAGGTC
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (81 bp):
ACATCATATGCATCATATAGACTTAGGTCCAGCGCCACATCATATGCATCATATAGTTTTAGGTC
CAGCGCCACATCATAT
Found at i:3959 original size:21 final size:21
Alignment explanation
Indices: 3933--3977 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3923 GGGTCCAGCG
3933 CCACATCATATAGACTTAGGT
1 CCACATCATATAGACTTAGGT
*
3954 CCACATCATATAGACTTATGT
1 CCACATCATATAGACTTAGGT
3975 CCA
1 CCA
3978 GCACTACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (21 bp):
CCACATCATATAGACTTAGGT
Found at i:3997 original size:84 final size:84
Alignment explanation
Indices: 3870--4027 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
3860 AGGTCCAGCG
* * * *
3870 CCACATCATATAGACTTAGGTTCAGCGCCACATCATATGCATCATATAGACTTGGGTCCAGCGCC
1 CCACATCATATAGACTTAGGTCCAGCACCACATCATATACATCATATAGACTTAGGTCCAGCGCC
3935 ACATCATATAGACTTAGGT
66 ACATCATATAGACTTAGGT
* * * *
3954 CCACATCATATAGACTTATGTCCAGCACTACATCATATACATCATATAGGCTTAGGTCCAGCGTC
1 CCACATCATATAGACTTAGGTCCAGCACCACATCATATACATCATATAGACTTAGGTCCAGCGCC
*
4019 ACATTATAT
66 ACATCATAT
4028 GCATCATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 65 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (84 bp):
CCACATCATATAGACTTAGGTCCAGCACCACATCATATACATCATATAGACTTAGGTCCAGCGCC
ACATCATATAGACTTAGGT
Found at i:4182 original size:90 final size:93
Alignment explanation
Indices: 3992--4316 Score: 372
Period size: 99 Copynumber: 3.4 Consensus size: 93
3982 TACATCATAT
* * * * * *
3992 ACATCATATAGGCTTAGGTCCAGCGTCACATTATATGCATCATATAGATTTAGGTCCAGCGCCAC
1 ACATCATATAGTCTTAGATCCAGC-CCACATCATATACATCATATAGACTTAGGTCCAGCG-C-C
4057 ATCATATACATCATATAGACTTAGGTCCAGCGCC
63 A-CA-ATA-ATCATATAGACTTAGGTCCAGCGCC
* *
4091 ACATCATATAGTCTTAGGTCCAGCACCACATCATATGCATCATATAGACTTAGGTCCAGCG-C-C
1 ACATCATATAGTCTTAGATCCAGC-CCACATCATATACATCATATAGACTTAGGTCCAGCGCCAC
4154 -AT-ATCATATAGACTTAGGTCCAGCGCC
65 AATAATCATATAGACTTAGGTCCAGCGCC
* * *
4181 ACATCATATAGTCTTAGTTCCAGCGCCATATCATATACATCATATAGACTTAGGTTCAGCGCCAC
1 ACATCATATAGTCTTAGATCCAGC-CCACATCATATACATCATATAGACTTAGGTCCAGCG-C-C
*
4246 ATCATATACATCATATAGACTTAGG-CTTAGCGCC
63 A-CA-ATA-ATCATATAGACTTAGGTC-CAGCGCC
4280 ACATCATATAGTCTTAGATCCAGTCCCACATCATATA
1 ACATCATATAGTCTTAGATCCAG-CCCACATCATATA
4317 GTCTTAGGTC
Statistics
Matches: 202, Mismatches: 13, Indels: 22
0.85 0.05 0.09
Matches are distributed among these distances:
90 81 0.40
92 2 0.01
93 1 0.00
94 1 0.00
95 1 0.00
96 1 0.00
97 2 0.01
98 1 0.00
99 111 0.55
100 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (93 bp):
ACATCATATAGTCTTAGATCCAGCCCACATCATATACATCATATAGACTTAGGTCCAGCGCCACA
ATAATCATATAGACTTAGGTCCAGCGCC
Found at i:4258 original size:126 final size:126
Alignment explanation
Indices: 4091--4379 Score: 420
Period size: 126 Copynumber: 2.3 Consensus size: 126
4081 GTCCAGCGCC
* *
4091 ACATCATATAGTCTTAGGTCCAGCACCACATCATATGCATCATATAGACTTAGG-TCCAGCGCCA
1 ACATCATATAGACTTAGGTCCAGCACCACATCATATACATCATATAGACTTAGGCT-CAGCGCCA
* * * *
4155 TATCATATAGACTTAGGTCCAG-CGCCACATCATATAGTCTTAGTTCCAGCGCCATATCATAT
65 CATCATATAGACTTAGATCCAGTC-CCACATCATATAGTCTTAGGTCCAGCGCCACATCATAT
* * *
4217 ACATCATATAGACTTAGGTTCAGCGCCACATCATATACATCATATAGACTTAGGCTTAGCGCCAC
1 ACATCATATAGACTTAGGTCCAGCACCACATCATATACATCATATAGACTTAGGCTCAGCGCCAC
*
4282 ATCATATAGTCTTAGATCCAGTCCCACATCATATAGTCTTAGGTCCAGCGCCACATCATAT
66 ATCATATAGACTTAGATCCAGTCCCACATCATATAGTCTTAGGTCCAGCGCCACATCATAT
* * **
4343 ACATCATATTGACATAGACCCAGCACCACATCATATA
1 ACATCATATAGACTTAGGTCCAGCACCACATCATATA
4380 GGTTTATGCA
Statistics
Matches: 145, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
126 143 0.99
127 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (126 bp):
ACATCATATAGACTTAGGTCCAGCACCACATCATATACATCATATAGACTTAGGCTCAGCGCCAC
ATCATATAGACTTAGATCCAGTCCCACATCATATAGTCTTAGGTCCAGCGCCACATCATAT
Found at i:4317 original size:90 final size:90
Alignment explanation
Indices: 4217--4380 Score: 256
Period size: 90 Copynumber: 1.8 Consensus size: 90
4207 CATATCATAT
* * * ** *
4217 ACATCATATAGACTTAGGTTCAGCGCCACATCATATACATCATATAGACTTAGGCTTAGCGCCAC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACATAGACCCAGCACCAC
4282 ATCATATAGTCTTAGATCCAGTCCC
66 ATCATATAGTCTTAGATCCAGTCCC
* *
4307 ACATCATATAGTCTTAGGTCCAGCGCCACATCATATACATCATATTGACATAGACCCAGCACCAC
1 ACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACATAGACCCAGCACCAC
4372 ATCATATAG
66 ATCATATAG
4381 GTTTATGCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 66 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.26
Consensus pattern (90 bp):
ACATCATATAGACTTAGGTCCAGCGCCACATCATATACATCATATAGACATAGACCCAGCACCAC
ATCATATAGTCTTAGATCCAGTCCC
Found at i:4677 original size:37 final size:37
Alignment explanation
Indices: 4636--4707 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
4626 AATAAATGTC
*
4636 GTTTGCTATTGATGTTTGAATGTTGATATATTTGTAT
1 GTTTGCTATTGATGTTTGAATGTTCATATATTTGTAT
4673 GTTTGCTATTGATGTTTGAATGTTCATATATTTGT
1 GTTTGCTATTGATGTTTGAATGTTCATATATTTGT
4708 GTATTTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.54
Consensus pattern (37 bp):
GTTTGCTATTGATGTTTGAATGTTCATATATTTGTAT
Found at i:7027 original size:298 final size:294
Alignment explanation
Indices: 6494--7059 Score: 868
Period size: 298 Copynumber: 1.9 Consensus size: 294
6484 ATTGAATAAT
6494 TATGAAATCGATAATAATTATGTCTGTGAAATCTGCGTTGAGTCAAGGCCCCTAGATAACTCTTT
1 TATGAAATCGATAATAATTATGTCTGTGAAATCTGCGTTGAGTCAAGGCCCCTAGATAACTCTTT
* *
6559 TGGCGTCAAAGGTTGCTCCCACTTTTACTGCATTGATTGCACTGTCAAGTACATCAGATCCAAAC
66 TGGCGTCAAAGGTTGCTCCCACTTTTACTGCATCGATTGCACTGTCAAGTACATCACATCCAAAC
* *
6624 TTGATAAAAACAAAACCCACATCACTTGTCCAGAATCAAACTGTCAAGGGCTTTTGGACCCTGAC
131 TTGATAAAAACAAAACCCACATCACTTGTCCAGAAGCAAACTGTCAAGGGCTTTTGGACCCTCAC
* * *
6689 TTCTGCCGAGAAATCCTCCCAGCAGAATTGTTTGAAAGATGGGGAA-ATGCCCTTTGTGAATCTG
196 TTCTGCCAAGAAATCCTCCCACCAGAATTGTTTAAAAGATGGGGAATA-GCCCTTTGTGAATCTG
6753 CAGTTAATGAAATCGATGATGATTTTTTTGCTACA
260 CAGTTAATGAAATCGATGATGATTTTTTTGCTACA
* * * * * * *
6788 TATGAAATTGATGATGATTATGTGTGTGGAATCTGCGTTGAGTCAAGGCCCCTGGATGACTCTTT
1 TATGAAATCGATAATAATTATGTCTGTGAAATCTGCGTTGAGTCAAGGCCCCTAGATAACTCTTT
*
6853 TGGCGTCAAAGGTTGCTCGCTCCCATTTTTACTGCATCGATTGCACTGTCAAGTACATCACATCC
66 TGGCGTCAAAGG-T--T-GCTCCCACTTTTACTGCATCGATTGCACTGTCAAGTACATCACATCC
* * * *
6918 AAATTTGA-AAATAACGAAACCCGCATCACTTGTCCAGAAGCAAACTGTCAAGGGCTTTTGTACC
127 AAACTTGATAAA-AACAAAACCCACATCACTTGTCCAGAAGCAAACTGTCAAGGGCTTTTGGACC
*
6982 CTCACTTCTGCCAAGAAATCCTCCC-CCAAGAGTTGTTTAAAAGATGGGGAATAGCCCTTTGTGA
191 CTCACTTCTGCCAAGAAATCCTCCCACC-AGAATTGTTTAAAAGATGGGGAATAGCCCTTTGTGA
7046 ATCTGCAGTTAATG
255 ATCTGCAGTTAATG
7060 GGTCTGAGAA
Statistics
Matches: 245, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
294 70 0.29
295 1 0.00
297 5 0.02
298 168 0.69
299 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (294 bp):
TATGAAATCGATAATAATTATGTCTGTGAAATCTGCGTTGAGTCAAGGCCCCTAGATAACTCTTT
TGGCGTCAAAGGTTGCTCCCACTTTTACTGCATCGATTGCACTGTCAAGTACATCACATCCAAAC
TTGATAAAAACAAAACCCACATCACTTGTCCAGAAGCAAACTGTCAAGGGCTTTTGGACCCTCAC
TTCTGCCAAGAAATCCTCCCACCAGAATTGTTTAAAAGATGGGGAATAGCCCTTTGTGAATCTGC
AGTTAATGAAATCGATGATGATTTTTTTGCTACA
Found at i:9913 original size:7 final size:7
Alignment explanation
Indices: 9903--9938 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
9893 CCAAGCCCAA
9903 GCGTAAG
1 GCGTAAG
9910 GCGTAAG
1 GCGTAAG
9917 GCGTAAG
1 GCGTAAG
9924 GCGTAAG
1 GCGTAAG
9931 GCGTAAG
1 GCGTAAG
9938 G
1 G
9939 ACTATGACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.44, T:0.14
Consensus pattern (7 bp):
GCGTAAG
Done.