Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011418.1 Corchorus capsularis cultivar CVL-1 contig11439, 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: 60032
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:5214 original size:39 final size:39
Alignment explanation
Indices: 5160--5293 Score: 214
Period size: 39 Copynumber: 3.4 Consensus size: 39
5150 AAATGATAAT
* * *
5160 GAAGATGAAGAGGAAGATAGTGATAAAGACAACTCAGTG
1 GAAGAAGAAGAGGAAGATAGTGATGAAGACAACTCAATG
*
5199 GAAGATGAAGAGGAAGATAGTGATGAAGACAACTCAATG
1 GAAGAAGAAGAGGAAGATAGTGATGAAGACAACTCAATG
*
5238 GGAGAAGAAGAGGAAGATAGTGATGAAGACAACTCAATG
1 GAAGAAGAAGAGGAAGATAGTGATGAAGACAACTCAATG
*
5277 GGAGAAGAAGAGGAAGA
1 GAAGAAGAAGAGGAAGA
5294 GGAAGATTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.47, C:0.07, G:0.34, T:0.13
Consensus pattern (39 bp):
GAAGAAGAAGAGGAAGATAGTGATGAAGACAACTCAATG
Found at i:5511 original size:23 final size:23
Alignment explanation
Indices: 5467--5512 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5457 CAGTGACACG
* * *
5467 GGATATTCAATGATGAGTAATTA
1 GGATATTCAATAATCAGGAATTA
5490 GGATATTCAATAATCAGGAATTA
1 GGATATTCAATAATCAGGAATTA
5513 AATTTCTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (23 bp):
GGATATTCAATAATCAGGAATTA
Found at i:7903 original size:21 final size:21
Alignment explanation
Indices: 7879--7932 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 21
7869 TGTCATTTGC
7879 TTTCTGTTTCTGATTTCTTTT
1 TTTCTGTTTCTGATTTCTTTT
* *
7900 TTTCTTTTTCT--TTTTTTTT
1 TTTCTGTTTCTGATTTCTTTT
* *
7919 TTTTTGCTTCTGAT
1 TTTCTGTTTCTGAT
7933 GATTGCTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 15 0.58
21 11 0.42
ACGTcount: A:0.04, C:0.13, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTCTGTTTCTGATTTCTTTT
Found at i:7922 original size:14 final size:14
Alignment explanation
Indices: 7892--7921 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
7882 CTGTTTCTGA
7892 TTTCTTTTTTTCTT
1 TTTCTTTTTTTCTT
7906 TTTCTTTTTTT-TT
1 TTTCTTTTTTTCTT
7919 TTT
1 TTT
7922 TTGCTTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:13980 original size:21 final size:21
Alignment explanation
Indices: 13955--13996 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13945 ACACAAAAAG
13955 GCCAAATAAACCCTTGGACTC
1 GCCAAATAAACCCTTGGACTC
*
13976 GCCAAATAAACCGTTGGACTC
1 GCCAAATAAACCCTTGGACTC
13997 TTAAAAGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (21 bp):
GCCAAATAAACCCTTGGACTC
Found at i:17066 original size:334 final size:330
Alignment explanation
Indices: 16473--17323 Score: 1047
Period size: 334 Copynumber: 2.6 Consensus size: 330
16463 GTATACCAAT
* * * * *
16473 CAAATCCTTAAATCCAATATGGCTAAGATTTGATTAGATGAATATAGATATTTTAAGGAGTGTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGGTATTTCAAGGAGTCTTG
* * * **
16538 CCACCAAAAATCATGCAAAACTGAT-CGGGGTCCC-AGAACGCGTTTTTAGCCAAAAAATTG-TG
66 GCGCCAAAAATCATGCAAAACTAATCCGGGGTCCCGA-AACGCGTTTTTAGCCAAAAACGTGATG
* * * * *
16600 ATT-GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCTG-GAATATTTTTCCTCACTTTTT
130 ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAT-TTTTTCCTCAATTCTT
* *
16663 AGCCATAATACTCATAGAATATATATAATTAAACGCCAAAAATATTGGAGGACTCTTCACGCTTT
194 AGCCATAATACTAATAGAATATATATAATTAAACGCCAAAAAGATTGGAGGACTCTTCACGCTTT
* * *
16728 TAATATCGTTTTTAATATTTTTTCTTAATTAATTT-TCAATTAAATCGAAACAAGATTCAGATGC
259 TAATATCGTTTTTAATA-TTTTTCTAAATTAATTTCT-AATTAAATCGAAACAAGATTAAGATGA
16792 TCGTAAAAA
322 TCGTAAAAA
* * *
16801 -AAATCCTTAAATTCAATGTGGTTGAGATTT-ATTTAGATGAATATAGGTATTTCAAGGAGTCTC
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGA-TTAGATGAATATAGGTATTTCAAGGAGTCTT
* * *
16864 GGTGCCAAAAATCATGCAAAACTAATCCCGGGTCCCGAAACACGTTTTTAGCCAAAAACCGTGAT
65 GGCGCCAAAAATCATGCAAAACTAATCCGGGGTCCCGAAACGCGTTTTTAGCCAAAAA-CGTGAT
* * *
16929 GGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAAATGACCCGAAAATTTTTTCCATCAATTCT
129 GATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCC-TCAATTCT
* * * * *
16994 T-GGCATAAATACTAATAATATATATATATAATTTAACGCCAAAAAGATTTGAGGACTTTTCACG
193 TAGCCAT-AATACTAAT-AGA-ATATATATAATTAAACGCCAAAAAGATTGGAGGACTCTTCACG
* * *
17058 CTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAACTCGAAATAAGATTAAGAT
255 CTTTTAATATCGTTTTTAATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTAAGAT
17123 GATCGTAAAAA
320 GATCGTAAAAA
* * * * * * **
17134 CTAATTCTTAAATGCAATGTAGCTGAGATTTGATTAGATAAATAT-GGATATCTCAAATAGTCTT
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGG-TATTTCAAGGAGTCTT
* * * *
17198 GGCGCCAAAAATCATGCAAAACTTATCCGGGGACCCGGAACGCATTTTTAGCCAAAAACGTGATG
65 GGCGCCAAAAATCATGCAAAACTAATCCGGGGTCCCGAAACGCGTTTTTAGCCAAAAACGTGATG
* * * * *
17263 ATTATTACACGATTTCGGTTAAAATTTTGCAAAAATTGACTCGAAAGTTATTTCCTCAATT
130 ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCCTCAATT
17324 TGAAGCCAAA
Statistics
Matches: 446, Mismatches: 62, Indels: 26
0.84 0.12 0.05
Matches are distributed among these distances:
326 1 0.00
327 75 0.17
328 27 0.06
329 3 0.01
330 4 0.01
331 46 0.10
332 24 0.05
333 106 0.24
334 159 0.36
335 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (330 bp):
CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGGTATTTCAAGGAGTCTTG
GCGCCAAAAATCATGCAAAACTAATCCGGGGTCCCGAAACGCGTTTTTAGCCAAAAACGTGATGA
TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAATTTTTTCCTCAATTCTTAG
CCATAATACTAATAGAATATATATAATTAAACGCCAAAAAGATTGGAGGACTCTTCACGCTTTTA
ATATCGTTTTTAATATTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGATCGT
AAAAA
Found at i:19386 original size:331 final size:326
Alignment explanation
Indices: 18666--19802 Score: 1158
Period size: 338 Copynumber: 3.4 Consensus size: 326
18656 CAATGACTGG
* * *
18666 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGCCGCCAAAAATCATT-CAAAATTGAA
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATTGCAAAATTGAG
* * * * *
18730 ATGGGCCACGTAACGCGTTTTTAGCCAAAAATCGTGATGATTATTACACGATTTCGGCTAAAATT
66 CTGGGCCTCGAAACGCGTTTTTAG-CAAAACT-GTGATGGTTATTACACGATTTCGGCTAAAATT
* * *
18795 TTGCAAAAATTGACCCGAAAGA-TATTTCCTCAATTTTTAGCCATAATACTCATAAAAATATATA
129 TTGCAAAAATTGACCCGAAAAATTA-TTCCTCAATTTTT-GGCAAAATACTCATAAAAATATATA
* *
18859 ATTTAATGCTAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTATGA
192 ATTTAATGC-AAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTCTAA
* * * * * *
18924 ATTAATTTCTAATTAAATTGAAACATGATCCAGATCCTCGTAAAAA-AAAGTCTTAAATGCAATG
256 ATTAATTTCTAATTAAATCGAAACAAGAT-TAGATGCTCGTAAAAACAAATTCTTAAATCCAATG
18988 TGGCTAA
320 TGGCTAA
* * *
18995 AATTTTATTAGATGATCATATAGATATTTCAAGGAGTGTCGACGCCAAAAATCA-TGCAAAATTG
1 GATTTGATTAGATGA--ATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATTGCAAAATTG
* ** *
19059 AGCTGGTGCCTCGAAACGCGTTTTTAGCAAAACTGTGATGGTTAGTACACGATTTTTGATAAAAT
64 AGCTGG-GCCTCGAAACGCGTTTTTAGCAAAACTGTGATGGTTATTACACGATTTCGGCTAAAAT
* *
19124 TTTGCAAAAAATAACCCGAAAAATTATTCCTCAATTTTTGGGCAAAATACTCATAAAATATATAT
128 TTTGCAAAAATTGACCCGAAAAATTATTCCTCAATTTTT-GGCAAAATACTCATAAAA-ATATAT
* * * *
19189 AATTTAATGACAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTT
191 AATTTAATG-CAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTCTA
* * *
19254 AATTAATTTCTAATTAAGTCAAAACAAGACTTAGATGCTTC-TAAAAACAAATTTTTAAATCCAA
255 AATTAATTTCTAATTAAATCGAAACAAGA-TTAGATGC-TCGTAAAAACAAATTCTTAAATCCAA
19318 TGTGGCTAA
318 TGTGGCTAA
* * * *
19327 GATTTGATTAGATGAATATATATATCTCAAGGAGTCT-TAGCGCCAAAAATCATTGCAAAAATGA
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGA-CGCCAAAAATCATTGCAAAATTGA
* * * * ** *
19391 GCAGGGGCTCCAGAACGCTTTTTTTTTTTATTAAAAAACAGTGATGGTTATTACACGATTTCGGC
65 GCTGGGCCTCGA-AACGC-----GTTTTTA--GCAAAACTGTGATGGTTATTACACGATTTCGGC
* *
19456 TAAAATTTTGTAAAAATTGA-CCGAAAAGATAATTCCTCAATTTTTGGCTAAAATACTCATAAAA
122 TAAAATTTTGCAAAAATTGACCCGAAAA-ATTATTCCTCAATTTTTGGC-AAAATACTCAT-AAA
* * * * ** * * *
19520 AATATATAACTCAACGCCAAAAAAATTGAAGGGCTTTTGGTG-TTTCTAATATCGTTTCTCCTAA
184 AATATATAATTTAATG-CAAAAAGATTGAAGGGCTTTTGACGCTTT-TAATATCGTTTTTCATAT
* * * *
19584 GTTTTCCAAATTAATTTTTAATTAAATCGAAACAATATTTAGATGCTCGTAAAAACAAATTCTTA
247 TTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGA-TTAGATGCTCGTAAAAACAAATTCTTA
* * *
19649 AATCTAATGTGGGTGA
311 AATCCAATGTGGCTAA
* *
19665 GATTTGATTACATGAATATAGATATTTC----A-TGT--A-GCCAAAAATCA-TGCAAAATTGAG
1 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATTGCAAAATTGAG
* ** * * * * *
19721 CCGGATCGCCAGAACGCGTTTTTAGCCAAAAAGAC-GTGATTTGTTAGTACACAATTTCGGCTAA
66 CTGGGCCTCGA-AACGCGTTTTTAG-C--AAA-ACTGTGA-TGGTTATTACACGATTTCGGCTAA
*
19785 AATTTTGTAAAAATTGAC
125 AATTTTGCAAAAATTGAC
19803 ACTCCTTAAT
Statistics
Matches: 680, Mismatches: 97, Indels: 64
0.81 0.12 0.08
Matches are distributed among these distances:
324 6 0.01
325 7 0.01
326 40 0.06
329 37 0.05
330 123 0.18
331 174 0.26
332 58 0.09
333 2 0.00
334 1 0.00
336 6 0.01
337 15 0.02
338 207 0.30
339 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (326 bp):
GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGACGCCAAAAATCATTGCAAAATTGAG
CTGGGCCTCGAAACGCGTTTTTAGCAAAACTGTGATGGTTATTACACGATTTCGGCTAAAATTTT
GCAAAAATTGACCCGAAAAATTATTCCTCAATTTTTGGCAAAATACTCATAAAAATATATAATTT
AATGCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAA
TTTCTAATTAAATCGAAACAAGATTAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTA
A
Found at i:23238 original size:28 final size:28
Alignment explanation
Indices: 23198--23254 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
23188 TTCTATGATT
*
23198 CACTTGTGAGTCCTCGGCCTAACCCCAC
1 CACTTGTGAGTCCTCGGCCCAACCCCAC
23226 CACTTGTGAGTCCTCGGCCCAACCCCAC
1 CACTTGTGAGTCCTCGGCCCAACCCCAC
23254 C
1 C
23255 GATTCACGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.46, G:0.18, T:0.19
Consensus pattern (28 bp):
CACTTGTGAGTCCTCGGCCCAACCCCAC
Found at i:23544 original size:98 final size:98
Alignment explanation
Indices: 23369--23666 Score: 490
Period size: 98 Copynumber: 3.1 Consensus size: 98
23359 AGCACCAAGG
*
23369 CCCA-CCGAGCAGCTCATATACATAACGGACACCAACTTGAACCCAAAAACCTAAGCTAATGGTT
1 CCCATCCGAGCAGCCCATATACATAACGGACACCAACTTGAACCCAAAAACCTAAGCTAATGGTT
*
23433 TCTTGGATTCTTCATATATATAAGCTACTCTAA
66 TCTTGGATCCTTCATATATATAAGCTACTCTAA
* * *
23466 CTCATCCGAGCAGCCCATATAAATAACGGACACCAACTTGAACCCAAAAACCTAAGTTAATGGTT
1 CCCATCCGAGCAGCCCATATACATAACGGACACCAACTTGAACCCAAAAACCTAAGCTAATGGTT
*
23531 TCTTGGATCCTTCATATATATTAGCTACTCTAA
66 TCTTGGATCCTTCATATATATAAGCTACTCTAA
* * *
23564 CCCATCCAAACAGCCCATATACATAACGGACACCAACTTGAAGCCAAAAACCTAAGCTAATGGTT
1 CCCATCCGAGCAGCCCATATACATAACGGACACCAACTTGAACCCAAAAACCTAAGCTAATGGTT
* *
23629 TCTTGTATCCTTCATATATATAAGCTACTTTAA
66 TCTTGGATCCTTCATATATATAAGCTACTCTAA
23662 CCCAT
1 CCCAT
23667 GTGGGATGTT
Statistics
Matches: 185, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
97 3 0.02
98 182 0.98
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (98 bp):
CCCATCCGAGCAGCCCATATACATAACGGACACCAACTTGAACCCAAAAACCTAAGCTAATGGTT
TCTTGGATCCTTCATATATATAAGCTACTCTAA
Found at i:30692 original size:38 final size:39
Alignment explanation
Indices: 30614--30692 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
30604 TTGAACCTCT
* * *
30614 TAATTATTAAGGAAATAAATTAAATCCAGGTTTACCCCC
1 TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCCC
* *
30653 TAATAATTAAGGTAAGAAATTAAAT-TAGGTTTAACCCC
1 TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCCC
30691 TA
1 TA
30693 GTTATAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
38 13 0.37
39 22 0.63
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (39 bp):
TAATAATTAAGGAAAGAAATTAAATCCAGGTTTAACCCC
Found at i:31341 original size:22 final size:21
Alignment explanation
Indices: 31288--31346 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
31278 TTTTTTATAA
* *
31288 ATATAATTTATATAATACAATT
1 ATAT-ATTTATATATTACAAGT
31310 ATA-ATGTTATATATTACATAGT
1 ATATAT-TTATATATTACA-AGT
31332 ATATATTTATATATT
1 ATATATTTATATATT
31347 TAATATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 11 0.34
22 17 0.53
23 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
ATATATTTATATATTACAAGT
Found at i:35696 original size:16 final size:15
Alignment explanation
Indices: 35665--35695 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35655 TAGGCCTAAT
*
35665 ATTTAAAAATAAAAA
1 ATTTAAAAAAAAAAA
35680 ATTTAAAAAAAAAAA
1 ATTTAAAAAAAAAAA
35695 A
1 A
35696 ACTTTGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATTTAAAAAAAAAAA
Found at i:36174 original size:38 final size:39
Alignment explanation
Indices: 36098--36176 Score: 106
Period size: 38 Copynumber: 2.0 Consensus size: 39
36088 TGAGCCTTTG
* * * *
36098 GGCTCGATTTATATTTTTTTTCAACAGTTGCCCTAGTCAT
1 GGCTCGATTTATA-TTTTGTTCAACAATTACCCAAGTCAT
36138 GGCTCGATTTATA-TTTGTTCAACAATTACCCAAGTCAT
1 GGCTCGATTTATATTTTGTTCAACAATTACCCAAGTCAT
36176 G
1 G
36177 AGGGCAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 22 0.63
40 13 0.37
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (39 bp):
GGCTCGATTTATATTTTGTTCAACAATTACCCAAGTCAT
Found at i:41926 original size:26 final size:25
Alignment explanation
Indices: 41897--41954 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
41887 TTGGCCCATT
41897 ACTTGACTTA-AAAATACAAAATTCCA
1 ACTTGACTTAGAAAATA-AAAA-TCCA
*
41923 ACTTGGGCTTAGAAAATAAAAATCCA
1 ACTT-GACTTAGAAAATAAAAATCCA
*
41949 AATTGA
1 ACTTGA
41955 AGGCCCCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.04
26 11 0.41
27 9 0.33
28 6 0.22
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (25 bp):
ACTTGACTTAGAAAATAAAAATCCA
Found at i:45165 original size:27 final size:27
Alignment explanation
Indices: 45134--45186 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
45124 CCCTCTGTTT
45134 CTTTTTAATTGTCCCCTTCCCTTATTC
1 CTTTTTAATTGTCCCCTTCCCTTATTC
* *
45161 CTTTTTAATTGTCCCTTTCTCTTATT
1 CTTTTTAATTGTCCCCTTCCCTTATT
45187 TTCCAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.11, C:0.28, G:0.04, T:0.57
Consensus pattern (27 bp):
CTTTTTAATTGTCCCCTTCCCTTATTC
Found at i:56383 original size:17 final size:17
Alignment explanation
Indices: 56361--56394 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56351 TTTATCATTC
56361 AATTTTACAATTTTTTT
1 AATTTTACAATTTTTTT
**
56378 AATTTTTTAATTTTTTT
1 AATTTTACAATTTTTTT
56395 TTTGCAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
AATTTTACAATTTTTTT
Found at i:58307 original size:27 final size:27
Alignment explanation
Indices: 58277--58332 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
58267 TTGAAACTCT
58277 TATAAATTGTTTTCAATTGATATAATG
1 TATAAATTGTTTTCAATTGATATAATG
58304 TATAAATTGTTTTCAATTGATATAATG
1 TATAAATTGTTTTCAATTGATATAATG
58331 TA
1 TA
58333 AATTTTCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.48
Consensus pattern (27 bp):
TATAAATTGTTTTCAATTGATATAATG
Found at i:58340 original size:22 final size:24
Alignment explanation
Indices: 58286--58338 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 24
58276 TTATAAATTG
58286 TTTTCAATTGATATAATGTATAAATT
1 TTTTCAATTGATATAATG-ATAAA-T
58312 GTTTTCAATTGATATAATG-TAAAT
1 -TTTTCAATTGATATAATGATAAAT
58336 TTT
1 TTT
58339 CATCTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 3 0.12
24 1 0.04
25 4 0.15
27 18 0.69
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTTCAATTGATATAATGATAAAT
Done.