Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009112.1 Corchorus capsularis cultivar CVL-1 contig09133, 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: 22077
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:2766 original size:55 final size:55
Alignment explanation
Indices: 2699--2932 Score: 353
Period size: 55 Copynumber: 4.3 Consensus size: 55
2689 TATTAAGGAG
* * * * *
2699 AAATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTCATAGTAACAGTAATCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
2754 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAACCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
*
2809 AAATCAATAATTAAGT-AAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
2863 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
2918 AAATCGATAACTAAG
1 AAATCAATAATTAAG
2933 AGTTAAAATG
Statistics
Matches: 164, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
54 52 0.32
55 112 0.68
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (55 bp):
AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
Found at i:2799 original size:29 final size:29
Alignment explanation
Indices: 2767--2853 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
2757 TCAATAATTA
2767 AGTAAAAAGAGATTAATCAGAGTCAAAGT
1 AGTAAAAAGAGATTAATCAGAGTCAAAGT
* ** * *
2796 AGTAGTAACCAG-TAAATCA-A-T--AATT
1 AGTA-AAAAGAGATTAATCAGAGTCAAAGT
2821 AAGT-AAAAGAGATTAATCAGAGTCAAAGT
1 -AGTAAAAAGAGATTAATCAGAGTCAAAGT
2850 AGTA
1 AGTA
2854 GTAATCAGTA
Statistics
Matches: 40, Mismatches: 10, Indels: 16
0.61 0.15 0.24
Matches are distributed among these distances:
24 4 0.10
25 9 0.22
26 4 0.10
27 2 0.05
28 4 0.10
29 13 0.32
30 4 0.10
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.23
Consensus pattern (29 bp):
AGTAAAAAGAGATTAATCAGAGTCAAAGT
Found at i:2868 original size:29 final size:29
Alignment explanation
Indices: 2781--2869 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
2771 AAAAGAGATT
*
2781 AATCAGAGTCAAAGTAGTAGTAACCAGTA
1 AATCAGAGTCAAAGTAGTAGTAAACAGTA
* * *
2810 AATCA-A-T--AATTA--AGTAAAAGAGATT
1 AATCAGAGTCAAAGTAGTAGT-AAACAG-TA
*
2835 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTAGTAGTAAACAGTA
2864 AATCAG
1 AATCAG
2870 TAATTAAGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 16
0.65 0.12 0.24
Matches are distributed among these distances:
23 3 0.07
24 4 0.09
25 10 0.23
26 1 0.02
27 2 0.05
28 1 0.02
29 16 0.36
30 4 0.09
31 3 0.07
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (29 bp):
AATCAGAGTCAAAGTAGTAGTAAACAGTA
Found at i:2891 original size:109 final size:110
Alignment explanation
Indices: 2699--2932 Score: 353
Period size: 109 Copynumber: 2.1 Consensus size: 110
2689 TATTAAGGAG
* * *
2699 AAATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTCATAGTAACAGTAATCAGTAAATCAATAA
1 AAATCAATAATTAAGTAAAAAGAGATAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAATAA
*
2764 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAACCAGT
66 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAACCAGT
* ** *
2809 AAATCAATAATTAAGT-AAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGTAAATCAGTAA
1 AAATCAATAATTAAGTAAAAAGAGATAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAATAA
* *
2873 TTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGT
66 TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAACCAGT
* *
2918 AAATCGATAACTAAG
1 AAATCAATAATTAAG
2933 AGTTAAAATG
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
109 97 0.87
110 15 0.13
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (110 bp):
AAATCAATAATTAAGTAAAAAGAGATAAATCAGAGTCAAAGTAACAGTAATCAGTAAATCAATAA
TTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAACCAGT
Found at i:3196 original size:22 final size:21
Alignment explanation
Indices: 3164--3479 Score: 194
Period size: 22 Copynumber: 14.3 Consensus size: 21
3154 ATGGTAAATT
*
3164 AGTAAAGAGTAAAATAGTAATC
1 AGTAAAAAGTAAAA-AGTAATC
*
3186 AGTAAAAAGTAAGAAGGTAATC
1 AGTAAAAAGTAA-AAAGTAATC
* * *
3208 AAT-AAGAGTAAAATAGTAGTC
1 AGTAAAAAGTAAAA-AGTAATC
3229 AGTAAAAAGTAAATAA-TAATC
1 AGTAAAAAGTAAA-AAGTAATC
* *
3250 AGT-AAGAGTAAAAAAGGTAATA
1 AGTAAAAAGT-AAAAA-GTAATC
* * *
3272 AGTAAGAAGTAAAAGGAAATC
1 AGTAAAAAGTAAAAAGTAATC
* *
3293 AGT-AAGAGTAAAAAGGTGATC
1 AGTAAAAAGTAAAAA-GTAATC
* *
3314 AGTAAAGAGTAAAAGGCTAATC
1 AGTAAAAAGTAAAAAG-TAATC
* *
3336 AGCAAGAAGTAAAAAGGTAATC
1 AGTAAAAAGTAAAAA-GTAATC
* *
3358 AGTAAAAAGCAAAAAGGCAATC
1 AGTAAAAAGTAAAAA-GTAATC
3380 AGTAAAAAGTAAAAGAGTAAAATGGTAATC
1 AGTAAAAAGTAAAA-AGT--AA---T---C
**
3410 AGTAAAAAGTAAAAAGGTATC
1 AGTAAAAAGTAAAAAGTAATC
* *
3431 TG-AAAGAGTAAAATAGTAATC
1 AGTAAAAAGTAAAA-AGTAATC
*
3452 AGTACAAAGTAAAATA-TAATC
1 AGTAAAAAGTAAAA-AGTAATC
3473 AGTAAAA
1 AGTAAAA
3480 TAGTGATGCC
Statistics
Matches: 228, Mismatches: 43, Indels: 47
0.72 0.14 0.15
Matches are distributed among these distances:
20 27 0.12
21 58 0.25
22 112 0.49
23 9 0.04
24 3 0.01
27 2 0.01
29 2 0.01
30 15 0.07
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.19
Consensus pattern (21 bp):
AGTAAAAAGTAAAAAGTAATC
Found at i:3216 original size:43 final size:42
Alignment explanation
Indices: 3168--3465 Score: 237
Period size: 43 Copynumber: 6.8 Consensus size: 42
3158 TAAATTAGTA
3168 AAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAAT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-AAGGTAATCAAT
* * *
3211 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAATA-ATAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA-AGGTAATCAAT
* * * * *
3253 AAGAGTAAAAAAGGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGTAAAATA-GTAATCAGTAAAAAGTAAAAGGTAATCAAT
* * **
3296 AAGAGTAAAA-AGGTGATCAGTAAAGAGTAAAAGGCTAATCAGC
1 AAGAGTAAAATA-GTAATCAGTAAAAAGTAAAAGG-TAATCAAT
* *
3339 AAGAAGTAAAA-AGGTAATCAGTAAAAAGCAAAAAGGCAATCAGTAAAAAGT
1 AAG-AGTAAAATA-GTAATCAGTAAAAAG-TAAAAGGTAATC------AA-T
* *
3390 AAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAAAGGT-ATCTGA-
1 --AAGAGTAAAATAGTAATCAGTAAAAAGT-AAAAGGTAATC-AAT
*
3434 AAGAGTAAAATAGTAATCAGTACAAAGTAAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAAA
3466 TATAATCAGT
Statistics
Matches: 210, Mismatches: 28, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
41 4 0.02
42 66 0.31
43 72 0.34
44 26 0.12
45 6 0.03
46 1 0.00
50 1 0.00
51 3 0.01
52 28 0.13
53 3 0.01
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAAAGGTAATCAAT
Found at i:3295 original size:64 final size:64
Alignment explanation
Indices: 3159--3393 Score: 187
Period size: 64 Copynumber: 3.6 Consensus size: 64
3149 GAAAAATGGT
* * * * *
3159 AAATTAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAA-TAAG-AGTAAAAT
1 AAATCAGTAAAAAGT-AAATAATAATCAGTAAAGAGTAAAAAGGTAAT-AAGTAAGAAGTAAAA-
*
3222 AG
63 GG
* *
3224 TAGTCAGTAAAAAGTAAATAATAATCAGT-AAGAGTAAAAAAGGTAATAAGTAAGAAGTAAAAGG
1 AAATCAGTAAAAAGTAAATAATAATCAGTAAAGAGT-AAAAAGGTAATAAGTAAGAAGTAAAAGG
* * * *
3288 AAATCAGT-AAGAGTAAA-AAGGTGATCAGTAAAGAGT-AAAAGGCTAATCAGCAAGAAGTAAAA
1 AAATCAGTAAAAAGTAAATAA--TAATCAGTAAAGAGTAAAAAGG-TAATAAGTAAGAAGT-AAA
3350 AGG
62 AGG
* * * *
3353 TAATCAGTAAAAAGCAAA-AAGGCAATCAGTAAAAAGTAAAA
1 AAATCAGTAAAAAGTAAATAA--TAATCAGTAAAGAGTAAAA
3394 GAGTAAAATG
Statistics
Matches: 140, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
62 2 0.01
63 21 0.15
64 54 0.39
65 37 0.26
66 23 0.16
67 3 0.02
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (64 bp):
AAATCAGTAAAAAGTAAATAATAATCAGTAAAGAGTAAAAAGGTAATAAGTAAGAAGTAAAAGG
Found at i:3400 original size:8 final size:7
Alignment explanation
Indices: 3342--3425 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
3332 AATCAGCAAG
3342 AAGTAAA
1 AAGTAAA
*
3349 AAGGTAAT
1 AA-GTAAA
*
3357 CAGTAAA
1 AAGTAAA
*
3364 AAGCAAA
1 AAGTAAA
* *
3371 AAGGCAAT
1 AA-GTAAA
*
3379 CAGTAAA
1 AAGTAAA
3386 AAGTAAA
1 AAGTAAA
3393 AGAGTAAA
1 A-AGTAAA
* *
3401 ATGGTAAT
1 A-AGTAAA
*
3409 CAGTAAA
1 AAGTAAA
3416 AAGTAAA
1 AAGTAAA
3423 AAG
1 AAG
3426 GTATCTGAAA
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
7 36 0.63
8 21 0.37
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (7 bp):
AAGTAAA
Found at i:3412 original size:30 final size:29
Alignment explanation
Indices: 3358--3425 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 29
3348 AAAGGTAATC
3358 AGTAAAAAGCAAAAAGGCAATCAGTAAAA
1 AGTAAAAAGCAAAAAGGCAATCAGTAAAA
* * *
3387 AGTAAAAGAGTAAAATGGTAATCAGTAAAA
1 AGTAAAA-AGCAAAAAGGCAATCAGTAAAA
3417 AGTAAAAAG
1 AGTAAAAAG
3426 GTATCTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (29 bp):
AGTAAAAAGCAAAAAGGCAATCAGTAAAA
Found at i:7835 original size:18 final size:19
Alignment explanation
Indices: 7784--7835 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
7774 ATAAAAATTA
*
7784 TTTTTGCAAAAGAAAAGAGG
1 TTTTT-CAAAAGAAAAAAGG
**
7804 TTTTTCTCAA-AAAAAAGG
1 TTTTTCAAAAGAAAAAAGG
7822 TTTTT-AAAAGAAAA
1 TTTTTCAAAAGAAAA
7836 TTGTTTTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 16 0.62
19 3 0.12
20 5 0.19
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (19 bp):
TTTTTCAAAAGAAAAAAGG
Found at i:7897 original size:11 final size:11
Alignment explanation
Indices: 7881--7916 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
7871 TGGTGAGGTT
7881 AAGAAAAAAAA
1 AAGAAAAAAAA
*
7892 AAGAAAGAAAA
1 AAGAAAAAAAA
7903 AAGAAAAGAAAA
1 AAGAAAA-AAAA
7915 AA
1 AA
7917 AAATATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:7901 original size:15 final size:16
Alignment explanation
Indices: 7881--7919 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
7871 TGGTGAGGTT
7881 AAGAAAAAA-AAAAGA
1 AAGAAAAAAGAAAAGA
7896 AAGAAAAAAGAAAAGA
1 AAGAAAAAAGAAAAGA
7912 AA-AAAAAA
1 AAGAAAAAA
7920 TATTCAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAAAGA
Found at i:9782 original size:28 final size:29
Alignment explanation
Indices: 9714--9787 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
9704 GGGTCATCCA
9714 GGGGCATTTTGGTCATTTTCACATCTAGG
1 GGGGCATTTTGGTCATTTTCACATCTAGG
** *
9743 GGGGCATTTTGGTCATTTTTGCATTTA-G
1 GGGGCATTTTGGTCATTTTCACATCTAGG
*
9771 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
9788 CTTAATCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 17 0.41
29 24 0.59
ACGTcount: A:0.15, C:0.12, G:0.30, T:0.43
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCACATCTAGG
Found at i:10902 original size:55 final size:55
Alignment explanation
Indices: 10835--11064 Score: 361
Period size: 55 Copynumber: 4.2 Consensus size: 55
10825 TATTAAGGAG
* * * * *
10835 AAATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTCATAGTAACAGTAATCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
10890 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAACCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
*
10945 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
11000 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGT
1 AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
*
11055 AAATCGATAA
1 AAATCAATAA
11065 CGAAGAGTTA
Statistics
Matches: 162, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 162 1.00
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.24
Consensus pattern (55 bp):
AAATCAATAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
Found at i:10935 original size:29 final size:29
Alignment explanation
Indices: 10903--10990 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
10893 TCAATAATTA
10903 AGTAAAAAGAGATTAATCAGAGTCAAAGT
1 AGTAAAAAGAGATTAATCAGAGTCAAAGT
* ** * *
10932 AGTAGTAACCAG-TAAATCA-A-T--AATT
1 AGTA-AAAAGAGATTAATCAGAGTCAAAGT
10957 AAGTAAAAAGAGATTAATCAGAGTCAAAGT
1 -AGTAAAAAGAGATTAATCAGAGTCAAAGT
10987 AGTA
1 AGTA
10991 GTAATCAGTA
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 7 0.17
26 10 0.24
27 2 0.05
28 2 0.05
29 14 0.33
30 7 0.17
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.23
Consensus pattern (29 bp):
AGTAAAAAGAGATTAATCAGAGTCAAAGT
Found at i:10975 original size:26 final size:26
Alignment explanation
Indices: 10891--10976 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
10881 GTAATCAGTA
10891 AATCAATAATTAAGTAAAAAGAGATT
1 AATCAATAATTAAGTAAAAAGAGATT
* * ** *
10917 AATCAGAGTCAAAGT-AGTAGTAACCAG-TA
1 AATCA-A-T--AATTAAGTA-AAAAGAGATT
10946 AATCAATAATTAAGTAAAAAGAGATT
1 AATCAATAATTAAGTAAAAAGAGATT
10972 AATCA
1 AATCA
10977 GAGTCAAAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 7 0.16
26 15 0.35
27 2 0.05
28 2 0.05
29 10 0.23
30 7 0.16
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.24
Consensus pattern (26 bp):
AATCAATAATTAAGTAAAAAGAGATT
Found at i:11004 original size:29 final size:29
Alignment explanation
Indices: 10917--11006 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
10907 AAAAGAGATT
*
10917 AATCAGAGTCAAAGTAGTAGTAACCAGTA
1 AATCAGAGTCAAAGTAGTAGTAAACAGTA
* * * *
10946 AATCA-A-T--AATTAAGTA-AAAAGAGATT
1 AATCAGAGTCAAAGT-AGTAGTAAACAG-TA
*
10972 AATCAGAGTCAAAGTAGTAGTAATCAGTA
1 AATCAGAGTCAAAGTAGTAGTAAACAGTA
11001 AATCAG
1 AATCAG
11007 TAATTAAGTA
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
25 7 0.16
26 10 0.23
27 2 0.05
28 2 0.05
29 16 0.36
30 7 0.16
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (29 bp):
AATCAGAGTCAAAGTAGTAGTAAACAGTA
Found at i:17612 original size:6 final size:6
Alignment explanation
Indices: 17601--17626 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17591 AGTGGTGCCG
17601 TGCCTC TGCCTC TGCCTC TGCCTC TG
1 TGCCTC TGCCTC TGCCTC TGCCTC TG
17627 TCGAACTAAT
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:0.46, G:0.19, T:0.35
Consensus pattern (6 bp):
TGCCTC
Found at i:18548 original size:114 final size:114
Alignment explanation
Indices: 18343--18580 Score: 413
Period size: 114 Copynumber: 2.1 Consensus size: 114
18333 TTAAGGGTAA
* * *
18343 TTGGATTTGAGCTTTAAAGAAACCAAATAGTTGATAAATGTATTGGCAAAGGTTTGCTGTAGTCA
1 TTGGCTTTGAGCTTTAAAGAAACCAAATAGTTGATAAATGTATTGGCAAAGATTTGCTATAGTCA
* *
18408 ACCCAATCCCCTTCTTCACTTCTGAAACTTGCCTCAACTTAAATTCTTG
66 ACCCAATCCCCTTCTTCACTTCTGAAACTTGCATCAACTTAAACTCTTG
*
18457 TTGGCTTTGAGCTTTAAAGAAACCAAATAGTTGATAAATGTATTGGCATAGATTTGCTATAGTCA
1 TTGGCTTTGAGCTTTAAAGAAACCAAATAGTTGATAAATGTATTGGCAAAGATTTGCTATAGTCA
*
18522 ACCCAATCCCCTTCTTCACTTCTGAAACTTGCATTAACTTAAACTCTTG
66 ACCCAATCCCCTTCTTCACTTCTGAAACTTGCATCAACTTAAACTCTTG
18571 TTGGCTTTGA
1 TTGGCTTTGA
18581 AATATAGCTG
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 117 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (114 bp):
TTGGCTTTGAGCTTTAAAGAAACCAAATAGTTGATAAATGTATTGGCAAAGATTTGCTATAGTCA
ACCCAATCCCCTTCTTCACTTCTGAAACTTGCATCAACTTAAACTCTTG
Found at i:21007 original size:12 final size:12
Alignment explanation
Indices: 20990--21014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20980 TTATAAATAT
20990 ATATATCTAACA
1 ATATATCTAACA
21002 ATATATCTAACA
1 ATATATCTAACA
21014 A
1 A
21015 GGAGAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATATCTAACA
Done.