Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012060.1 Corchorus capsularis cultivar CVL-1 contig12081, 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: 67592
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:78 original size:25 final size:27
Alignment explanation
Indices: 40--92 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
30 GCCTCTGAAA
*
40 TATTATATAGGTTGG-GTTTTAATTCTT
1 TATTATATAGGTTGGACTTTT-ATTCTT
67 TATT-TATA-GTTGGACTTTTATTCTT
1 TATTATATAGGTTGGACTTTTATTCTT
92 T
1 T
93 TTAATTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 12 0.50
26 8 0.33
27 4 0.17
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.58
Consensus pattern (27 bp):
TATTATATAGGTTGGACTTTTATTCTT
Found at i:832 original size:23 final size:23
Alignment explanation
Indices: 766--832 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
756 CTATTTAAGC
766 AATTCCAAGAGAAGACTTTTGGA
1 AATTCCAAGAGAAGACTTTTGGA
* * * *
789 AAAT---A-A-AAG-TTTTTAGT
1 AATTCCAAGAGAAGACTTTTGGA
806 AATTCCAAGAGAAGACTTTTGGA
1 AATTCCAAGAGAAGACTTTTGGA
829 AATT
1 AATT
833 AATAAAATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 8 0.27
18 3 0.10
19 1 0.03
20 2 0.07
21 1 0.03
22 3 0.10
23 12 0.40
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (23 bp):
AATTCCAAGAGAAGACTTTTGGA
Found at i:2928 original size:7 final size:7
Alignment explanation
Indices: 2916--2972 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
2906 AGTTTGGGTC
2916 AATTATT
1 AATTATT
2923 AATTATT
1 AATTATT
**
2930 TTTTA-T
1 AATTATT
* *
2936 ATTTTTT
1 AATTATT
2943 AATTATT
1 AATTATT
*
2950 AATCATTT
1 AATTA-TT
2958 AATTATT
1 AATTATT
2965 AATTATT
1 AATTATT
2972 A
1 A
2973 TTAATTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 4 0.10
7 30 0.75
8 6 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (7 bp):
AATTATT
Found at i:10340 original size:15 final size:15
Alignment explanation
Indices: 10322--10353 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10312 TTCTCTTTGG
10322 GTCTTAGTTGTTTAA
1 GTCTTAGTTGTTTAA
10337 GTCTTAGTTGTTTAA
1 GTCTTAGTTGTTTAA
10352 GT
1 GT
10354 TCATTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.22, T:0.53
Consensus pattern (15 bp):
GTCTTAGTTGTTTAA
Found at i:14094 original size:38 final size:39
Alignment explanation
Indices: 14052--14147 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 39
14042 AGTGAAAAGA
* * ** *
14052 AAAAGTAGTAATCAGTCAATTGGTAATTA-AGAGGAAGT
1 AAAAGTAGTAATCAGTAAATTGATAACCACAGAAGAAGT
* *
14090 AAAAGGATTAATCAGTAAATTGATAACCACGAGAAGAAGT
1 AAAAGTAGTAATCAGTAAATTGATAACCAC-AGAAGAAGT
*
14130 AAAAGTAGCAATCAGTAA
1 AAAAGTAGTAATCAGTAA
14148 GTAAGGGTCA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
38 23 0.50
40 23 0.50
ACGTcount: A:0.49, C:0.08, G:0.21, T:0.22
Consensus pattern (39 bp):
AAAAGTAGTAATCAGTAAATTGATAACCACAGAAGAAGT
Found at i:14177 original size:32 final size:32
Alignment explanation
Indices: 14139--14211 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
14129 TAAAAGTAGC
**
14139 AATCAGTAAGTAAGGGTCAAAGTAAAAGG-AT
1 AATCAGTAAGTAAAAGTCAAAGTAAAAGGAAT
* * *
14170 AAGTCAGTAATTAAAAGTCAAGGTAGAAGGAAT
1 AA-TCAGTAAGTAAAAGTCAAAGTAAAAGGAAT
14203 AATCAGTAA
1 AATCAGTAA
14212 ATTGATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 2 0.06
32 29 0.83
33 4 0.11
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (32 bp):
AATCAGTAAGTAAAAGTCAAAGTAAAAGGAAT
Found at i:14357 original size:16 final size:16
Alignment explanation
Indices: 14336--14388 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
14326 ATGGAGTGAA
14336 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
14352 AGTAAAATGGAGTGAA--
1 AGTAAAA-GAAGT-AATC
14368 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
14384 AGTAA
1 AGTAA
14389 GTTGGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 19 0.61
17 4 0.13
18 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.19
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:14363 original size:32 final size:32
Alignment explanation
Indices: 14312--14433 Score: 129
Period size: 32 Copynumber: 3.6 Consensus size: 32
14302 AATAAAAGAG
* *
14312 GAAGTGATCA-TAGAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
14343 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
* *
14375 GAAGTAATCAGTAAGTTGGTAATTAAGAGTAAAAGTAAAA
1 GAAGTAATCAGTAA------AA-T-GGAGTGAAAGTAAAA
14415 GAAGTAATCAGTAAAATGG
1 GAAGTAATCAGTAAAATGG
14434 TAATTAAGAG
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
31 9 0.12
32 35 0.45
33 1 0.01
34 2 0.03
38 2 0.03
39 1 0.01
40 27 0.35
ACGTcount: A:0.50, C:0.03, G:0.25, T:0.21
Consensus pattern (32 bp):
GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
Found at i:14411 original size:40 final size:40
Alignment explanation
Indices: 14361--14469 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
14351 CAGTAAAATG
* **
14361 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
14401 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
*
14441 GAGTAAAAGTAAAAGAAGTAGTCAGTAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAA
14470 TCGGTAAAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (40 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
Found at i:14493 original size:16 final size:17
Alignment explanation
Indices: 14467--14530 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 17
14457 AGTAGTCAGT
*
14467 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
14484 AAAT-GGTAAAAAGTAAA
1 AAATCGGTAAAAAGT-AA
*
14501 GAGTAATCAGTAAAAAGT-A
1 -A--AATCGGTAAAAAGTAA
14520 AAAT-GGTAAAA
1 AAATCGGTAAAA
14531 TGGTAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
15 6 0.15
16 12 0.31
17 6 0.15
18 2 0.05
19 1 0.03
20 3 0.08
21 9 0.23
ACGTcount: A:0.58, C:0.03, G:0.20, T:0.19
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:14494 original size:40 final size:38
Alignment explanation
Indices: 14361--14485 Score: 164
Period size: 40 Copynumber: 3.2 Consensus size: 38
14351 CAGTAAAATG
* *
14361 GAGTGAAAGTAAAAGAAGTAATCAGTAAGTTGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAA-ATGGTAA-TAA
14401 GAGTAAAAGTAAAAGAAGTAATCAGTAAAATGGTAATTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGT-AAATGGTAA-TAA
*
14441 GAGTAAAAGTAAAAGAAGTAGTCAGTAAATCGGT-A-AA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAAAT-GGTAATAA
14478 GAGTAAAA
1 GAGTAAAA
14486 ATGGTAAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
37 10 0.12
39 5 0.06
40 63 0.79
41 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.22
Consensus pattern (38 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAAATGGTAATAA
Found at i:14572 original size:32 final size:33
Alignment explanation
Indices: 14528--14589 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
14518 TAAAATGGTA
14528 AAATGGTAATTAAATTCAAAGAGT-AAAATGAC
1 AAATGGTAATTAAATTCAAAGAGTGAAAATGAC
*
14560 AAATGGTGATTAAATTCAAAGAGTGAAAAT
1 AAATGGTAATTAAATTCAAAGAGTGAAAAT
14590 AGTAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.26
Consensus pattern (33 bp):
AAATGGTAATTAAATTCAAAGAGTGAAAATGAC
Found at i:14597 original size:26 final size:26
Alignment explanation
Indices: 14527--14621 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
14517 GTAAAATGGT
*
14527 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAAGAG-----TG
* *
14558 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATAGTAATTAAATTCAAAGAGTG
14585 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAA-AGAGTG
14611 AAAATAGTAAT
1 AAAATAGTAAT
14622 CAGTAAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 8 0.14
31 1 0.02
32 22 0.37
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAATAGTAATTAAATTCAAAGAGTG
Found at i:14681 original size:27 final size:27
Alignment explanation
Indices: 14611--14702 Score: 121
Period size: 27 Copynumber: 3.4 Consensus size: 27
14601 TCAAGAGAGT
* **
14611 AAAATAGTAATCAGTAAAGAGGAAAAAG
1 AAAAGAGTAATCAGTAAAGA-GAGTAAG
*
14639 TAAAGAGTAATCAGTAAAGAGAGTAAG
1 AAAAGAGTAATCAGTAAAGAGAGTAAG
* *
14666 AAAAGAGTAATTAGTAAAAAGAGTAAG
1 AAAAGAGTAATCAGTAAAGAGAGTAAG
14693 AAAAGAGTAA
1 AAAAGAGTAA
14703 AAATGATAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
27 39 0.68
28 18 0.32
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (27 bp):
AAAAGAGTAATCAGTAAAGAGAGTAAG
Found at i:18851 original size:30 final size:30
Alignment explanation
Indices: 18792--18852 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
18782 ATAAGTTGGT
* * *
18792 TCAAATGCATATTTCATAAATTTAGTGGGG
1 TCAAATACATATTTCACAAATTCAGTGGGG
* *
18822 TCAAATACATATTTCACAACTTCATTGGGG
1 TCAAATACATATTTCACAAATTCAGTGGGG
18852 T
1 T
18853 TAATATAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (30 bp):
TCAAATACATATTTCACAAATTCAGTGGGG
Found at i:22749 original size:6 final size:6
Alignment explanation
Indices: 22738--22763 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22728 TTATAGTATA
22738 AATATT AATATT AATATT AATATT AA
1 AATATT AATATT AATATT AATATT AA
22764 CTAGCCACAG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATATT
Found at i:30504 original size:347 final size:344
Alignment explanation
Indices: 29868--30559 Score: 1066
Period size: 347 Copynumber: 2.0 Consensus size: 344
29858 AACATATATT
*
29868 AAAGTTGAAAATGGAATTACCCTTTTGTCCAGTTATAAGATACACCACATTCACCAAGAACAAAT
1 AAAGTTGAAAATGGAATTACCCTTTTGTCCAGCTATAAGATACACCACATTCACCAAGAACAAAT
* *
29933 TATCAGGGATATTTCGGTACTTTCATGCTCAGTTTCGTTATTATTGTTGATTGTTGAGGGCGTTT
66 TATCAGGGATATTTCGGTACTTTCATGCTCAGTTTCGTTACTATTGTTGATTGTTGAGGGCATTT
* *
29998 TGGAAACTTTAGGATAAAGTTACTATTTGGTTGGTCCCACTCTCAATAAACAAATCATTTTTTGT
131 TGAAAACTTTAGGATAAAGTTACTATTTGGTGGGTCCCACTCTCAATAAACAAATCATTTTTTGT
* * ** * *
30063 TTGATTATTTATCAAATGAATCTCATACTTATATGCTTTATGCTATTTATTCCGTTACAATTATG
196 TGGATTATTTATCAAATGAATCTCATACTTATATGCTTTATGCTATTCAACCCGGTACAATTATC
30128 GGTTGAACGATTGAACGTTTCAGCATTAATTCTTTTATTTTTTGTTATATTTGTCCAATCAAGGT
261 GGTTGAACGATTGAACGTTTCAGCATTAATTCTTTTATTTTTTGTTATATTTGTCCAATCAAGGT
*
30193 GATTCAAGTGTTTATTAAA
326 GATTCAAGTGTCTATTAAA
* *
30212 AAAGTTGAAAATGGAATTACCCTTTTGTCCAGCTATAAGATTCACCACATTCACCTAAGGACAAA
1 AAAGTTGAAAATGGAATTACCCTTTTGTCCAGCTATAAGATACACCACATTCACC-AAGAACAAA
* * * *
30277 TTGTCAGGG-TATTTCGGTATTTTCTTGCTCGGTATTTTCGTTACTATTGTTGATTGTTGAGGGC
65 TTATCAGGGATATTTCGGTACTTTCATGCTC---AGTTTCGTTACTATTGTTGATTGTTGAGGGC
* * * **
30341 ATTTTGAAAACTTTAGGATAATGTTACTATTTGGTGGGTCTCACTCTCAATAAATAAATTGTTTT
127 ATTTTGAAAACTTTAGGATAAAGTTACTATTTGGTGGGTCCCACTCTCAATAAACAAATCATTTT
* *
30406 TTGTTGGATTATTTATCAAATG-TTCCTCATACTTTTATGCTTTATGCTATTCAACCCGGTACAA
192 TTGTTGGATTATTTATCAAATGAAT-CTCATACTTATATGCTTTATGCTATTCAACCCGGTACAA
* *
30470 TTATCGGTTGAACGATTGAACGTTTC-GACATTAATTCTTTTATTTTTTGTTCTATTTGTCCGAT
256 TTATCGGTTGAACGATTGAACGTTTCAG-CATTAATTCTTTTATTTTTTGTTATATTTGTCCAAT
30534 CAAGGTGATTCAAGTGTCTATTAAA
320 CAAGGTGATTCAAGTGTCTATTAAA
30559 A
1 A
30560 GGCAATTTCA
Statistics
Matches: 315, Mismatches: 27, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
344 72 0.23
345 16 0.05
346 2 0.01
347 225 0.71
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (344 bp):
AAAGTTGAAAATGGAATTACCCTTTTGTCCAGCTATAAGATACACCACATTCACCAAGAACAAAT
TATCAGGGATATTTCGGTACTTTCATGCTCAGTTTCGTTACTATTGTTGATTGTTGAGGGCATTT
TGAAAACTTTAGGATAAAGTTACTATTTGGTGGGTCCCACTCTCAATAAACAAATCATTTTTTGT
TGGATTATTTATCAAATGAATCTCATACTTATATGCTTTATGCTATTCAACCCGGTACAATTATC
GGTTGAACGATTGAACGTTTCAGCATTAATTCTTTTATTTTTTGTTATATTTGTCCAATCAAGGT
GATTCAAGTGTCTATTAAA
Found at i:36271 original size:6 final size:6
Alignment explanation
Indices: 36260--36300 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
36250 AGTAACTAAG
* *
36260 AAAATA AAAAT- -AAACA AAAATA AAAATA AAAATG AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA A
36301 CAAAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
4 3 0.10
6 26 0.90
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:36291 original size:28 final size:28
Alignment explanation
Indices: 36260--36325 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
36250 AGTAACTAAG
* *
36260 AAAATAAAAATAA-ACAAAAATAAAAATA
1 AAAATAAAAATAACA-AAAAAGAAAAAGA
*
36288 AAAATGAAAATAACAAAAAAGAAAAAGA
1 AAAATAAAAATAACAAAAAAGAAAAAGA
*
36316 AAAAGAAAAA
1 AAAATAAAAA
36326 GATAAGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (28 bp):
AAAATAAAAATAACAAAAAAGAAAAAGA
Found at i:36297 original size:34 final size:34
Alignment explanation
Indices: 36259--36325 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
36249 AAGTAACTAA
* *
36259 GAAAATAA-AAATAAACAAAAATAAAAATAAAAAT
1 GAAAATAACAAA-AAACAAAAAGAAAAAGAAAAAT
*
36293 GAAAATAACAAAAAAGAAAAAGAAAAAGAAAAA
1 GAAAATAACAAAAAACAAAAAGAAAAAGAAAAA
36326 GATAAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.81, C:0.03, G:0.07, T:0.09
Consensus pattern (34 bp):
GAAAATAACAAAAAACAAAAAGAAAAAGAAAAAT
Found at i:36306 original size:22 final size:22
Alignment explanation
Indices: 36260--36319 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
36250 AGTAACTAAG
36260 AAAATAAAAAT-AAACAAAAATA
1 AAAATAAAAATGAAA-AAAAATA
*
36282 AAAATAAAAATGAAAATAACA-A
1 AAAATAAAAATGAAAA-AAAATA
*
36304 AAAAGAAAAA-GAAAAA
1 AAAATAAAAATGAAAAA
36320 GAAAAAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 5 0.15
22 22 0.65
23 6 0.18
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (22 bp):
AAAATAAAAATGAAAAAAAATA
Found at i:36312 original size:6 final size:6
Alignment explanation
Indices: 36303--36327 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
36293 GAAAATAACA
36303 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
36328 TAAGAAATTC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:40401 original size:72 final size:72
Alignment explanation
Indices: 40314--40452 Score: 197
Period size: 72 Copynumber: 1.9 Consensus size: 72
40304 AAAGACAAGC
** **
40314 CAAGGTGTGAACATTGTCAAAAGGTGGGGCACATGAAAGACCAACGCTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTGTCAAAAGACGGGGCACACAAAAGACCAACGCTATGAGATCATTGGATAT
40379 CCTGCTG
66 CCTGCTG
* * * * *
40386 CAAGGTGTGGACATTGTCAAAAGACGGGGCATACAAAAGATCAATGTTATGAGATCATTGGATAT
1 CAAGGTGTGAACATTGTCAAAAGACGGGGCACACAAAAGACCAACGCTATGAGATCATTGGATAT
40451 CC
66 CC
40453 CGCAGGGTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.23
Consensus pattern (72 bp):
CAAGGTGTGAACATTGTCAAAAGACGGGGCACACAAAAGACCAACGCTATGAGATCATTGGATAT
CCTGCTG
Found at i:43916 original size:6 final size:6
Alignment explanation
Indices: 43905--43938 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
43895 GGTCGAAATT
*
43905 TTTTTA TTTTTA TTTTTA TTTTT- TTTATA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
43939 CGATATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:43922 original size:12 final size:11
Alignment explanation
Indices: 43903--43938 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
43893 CTGGTCGAAA
43903 TTTTTTTATTT
1 TTTTTTTATTT
43914 TTATTTTTATTT
1 TT-TTTTTATTT
*
43926 TTTTTATATTT
1 TTTTTTTATTT
43937 TT
1 TT
43939 CGATATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:50942 original size:32 final size:31
Alignment explanation
Indices: 50903--50962 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
50893 ATGTGGTTGT
*
50903 AAGGGTAAATAAGGTGTTTCATGTAAATTGAC
1 AAGGGTAAATAAGGTGTTCCAT-TAAATTGAC
*
50935 AAGGGTAAATATGGTGTTCCATTAAATT
1 AAGGGTAAATAAGGTGTTCCATTAAATT
50963 TTTTTATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
AAGGGTAAATAAGGTGTTCCATTAAATTGAC
Found at i:63266 original size:30 final size:33
Alignment explanation
Indices: 63230--63295 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
63220 AAGGATCCAT
63230 TGGCCGGTTGT-G-C-GTGGATCCCCCATGCGA
1 TGGCCGGTTGTGGCCGGTGGATCCCCCATGCGA
* *
63260 TGGCCGGTTGTGGCCGGTTGATGCCCCATGCGA
1 TGGCCGGTTGTGGCCGGTGGATCCCCCATGCGA
63293 TGG
1 TGG
63296 TGCATGCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 11 0.35
31 1 0.03
32 1 0.03
33 18 0.58
ACGTcount: A:0.09, C:0.27, G:0.39, T:0.24
Consensus pattern (33 bp):
TGGCCGGTTGTGGCCGGTGGATCCCCCATGCGA
Found at i:64146 original size:20 final size:20
Alignment explanation
Indices: 64121--64161 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
64111 TGAAGATGTC
64121 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
*
64141 TTAAAAATCCACTTAACATA
1 TTAAAAACCCACTTAACATA
64161 T
1 T
64162 CAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (20 bp):
TTAAAAACCCACTTAACATA
Found at i:65418 original size:2 final size:2
Alignment explanation
Indices: 65411--65451 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
65401 ATATGTAGTG
*
65411 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65452 GTCTTATTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:67150 original size:1 final size:1
Alignment explanation
Indices: 67144--67174 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
67134 TGGTATAAGC
67144 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
67175 GGGCAAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.