Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017144.1 Corchorus olitorius cultivar O-4 contig17177, 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: 28114
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:481 original size:6 final size:6
Alignment explanation
Indices: 464--499 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
454 GTACTTTTAT
464 ATATAG -TATAG ATATAG ATATAG ATATAG ATATAG A
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG A
500 CTGGTAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:1505 original size:13 final size:13
Alignment explanation
Indices: 1487--1512 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1477 GAAGTCTAAC
1487 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1500 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1513 GTACATGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:6394 original size:333 final size:328
Alignment explanation
Indices: 5216--7138 Score: 1600
Period size: 333 Copynumber: 5.8 Consensus size: 328
5206 CCATGATGGT
* * * *
5216 AAAAA-TGAGCCGAAAGATTTTTCCTCAATATTT-GGAAAAAATACTCATAAAATATATATATAA
1 AAAAATTGA-CCGAAAGATTTTT-CTTAATTTTTAGG-CACAATACTCATAAAA-A-ATATATAA
* * * * *
5279 TTCAAC-ACCAAAAAGATT-ATAGGACTTTTCGCGCTTTTAATATCGTTTTTCATATTTTTTTTC
61 TTTAACGA-CAAAAAGATTGA-AGGGCTTTTCACGCTTCTAATATTGTTTTTCATA---TTTTT-
* * **
5342 TGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCAAGTAAAAACAAATCCTTAAATCCA
120 TGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCA
* * * * * *
5407 ATGTGGTTGAGATTTGATTAGGTGAATAAAGATATTTCAAGGAG-CGTCGGCGCCAAAAATCATG
185 ATGTAGATGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC-T-TGCACCAAAAATCATG
** * * * * * *
5471 CAAAA-TAAAGCTGTGGCCCTGGAATGTGTTTTTAGCC-AAAAACC------G-T-G-ACACGAT
248 CAAAACCGACGC-GAGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGATAGTACACGAT
5525 TTCGGCTAAAATTTTGC
312 TTCGGCTAAAATTTTGC
* * * * *
5542 AAATATTGACACGAAAGATGTTTCCTCATTTTTTGGCTA-AGATACTCATAAAAAATATATAATT
1 AAAAATTGAC-CGAAAGATTTTTCTTAATTTTTAGGC-ACA-ATACTCATAAAAAATATATAATT
* * * * * *
5606 TGAC-ATAAAAAAGATTGAAGGGCTTTTAATGCCTCTAATATTGTTTTTCCTATTTTTTCTGAAT
63 TAACGA-CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCATA-TTTTT-TGAAT
* *
5670 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
125 TAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTA
* * *
5735 GTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAAT
190 GATGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT-GCACCAAAAATCATGCAAAAC
* * * * * * *
5800 TGA-GC-AGGGCCTCGGAAA-GCGTTTTTAGTC-GAAAACAGTGATGGCTAGTACATGATTTCGG
254 CGACGCGA-GGCC-CCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGATAGTACACGATTTCGG
5861 CTAAAATTTTGC
317 CTAAAATTTTGC
* * *
5873 AAAAATTGACTCGAAAGATTTTTTTTTCGCAATTTTTAGCCATAATACTCATAAAAAATATATAA
1 AAAAATTGAC-CGAAAGA-TTTTTCTT---AATTTTTAGGCACAATACTCATAAAAAATATATAA
* * * * *
5938 TTCAAC-ACCAAAAAAATTGAA-AGCATTTTTCACGCTTCTAATATCGTTTTTCTTATTTTATTT
61 TTTAACGA-CAAAAAGATTGAAGGGC--TTTTCACGCTTCTAATATTGTTTTTCATA-TTT-TTT
* * * * * * *
6001 CCAAACTAATTTCTGATTAAATCGAAACAAGATTTAAATACTCGTAAAAATAAATCCTTAAATAC
121 --GAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCC
* * *** *
6066 AATGTAGATGAGATTTGGTTAGATGAATATAGATATATTTTAAGGAGTCTTGCTGTAAAAATATA
184 AATGTAGATGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTTGCACCAAAAAT-CA
* *
6131 TGCAAAACCGACGCG-GGCCCCGGAA-GACGTTTTTAGCCAAAAAAAACCGTG-T-GATGGTACA
246 TGCAAAACCGACGCGAGGCCCCGAAACG-CGTTTTTAGCC--AAAAAACCGTGATGGATAGTACA
*
6192 CGATTTCGGCTAAAATTTTTC
308 CGATTTCGGCTAAAATTTTGC
* * * *
6213 AAGAATTGAACCGAAATATTTTTCTTAATTTTTAGGCACAATACTCTTAAAAAATATATAATTCA
1 AAAAATTG-ACCGAAAGATTTTTCTTAATTTTTAGGCACAATACTCATAAAAAATATATAATTTA
* * * *
6278 ACGACAAAAAGATTGAAGGGCTTCTCACGCTTCTGATATTGTTTTTCCTATTTTTTAAAAATTAA
65 ACGACAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCATATTTTTT--GAATTAA
* * * *
6343 TTTCTAAATAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
128 TTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGAT
* * * * * **
6408 AAGATTTGAATAGATGAATATAGATACTTCAATGAGTTTTGCCACCAAAAATCATGCAAAACATA
193 GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG-CACCAAAAATCATGCAAAACCGA
* * *
6473 C-CGAGGCCCCAAAACGCGTTTTTAGCCAAAAAAACGTGAT-G---GTACACGATTTAGGCTAAA
257 CGCGAGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGATAGTACACGATTTCGGCTAAA
*
6533 ATTTTCC
322 ATTTTGC
* * * *
6540 AAAAATTGATCCGAAATATTTTTTTCTCAATTTTTAGCCTCAATACTCATAATATATATCTATAT
1 AAAAATTGA-CCGAAAGA--TTTTTCTTAATTTTTAGGCACAATACTCATAA-A-A-A---ATAT
* * * * * *
6605 ATAATTTAATGTCAAAAAGATTGGAGGACTTTTTACGCTTTTAATATTGTTTTTCATATTTTTTG
57 ATAATTTAACGACAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCATATTTTTTG
* * * * * * *
6670 AATTAATTTATAATTAAA-CTGAAACAAGATTTAGATGTTCGTAAAAATAAATCTTTAAATTCAA
122 AATTAATTTCTAATTAAATC-GAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAA
* * *
6734 TGT-GATTGAGATTTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGCCGCCAAAAATCATGC
186 TGTAGA-TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG-CACCAAAAATCATGC
* * * * *
6798 AAAA-CTAAGCCGAGGCCTCGAAACGCGCTTTTAG-CAAAAAACCGTGATGGTTAGTACACGATT
249 AAAACCGACG-CGAGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGATAGTACACGATT
* *
6861 TCAGCTAAAATTTTGT
313 TCGGCTAAAATTTTGC
* * * * ** *
6877 AAAAAGTGACCCAAAAATTGTTCCTCGATTTTT-GGCTAAAATACTCATAATATATATATATATA
1 AAAAATTGACCGAAAGATT-TTTCTTAATTTTTAGGC-ACAATACTC-----ATA-A-A-A-A-A
* * * * *
6941 TATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
54 TATATAATTTAACGACAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCATATTTT
* * ** *
7006 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAGTACTCGTAAAAACAAATTTTTAAATT
119 T-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATC
* * * * * * *
7071 CAATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGAGTATTGGCGCTAAAAATCAT
183 CAATGTAGATGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT-GCACCAAAAATCAT
7136 GCA
247 GCA
7139 TAGCCAAAAA
Statistics
Matches: 1327, Mismatches: 195, Indels: 136
0.80 0.12 0.08
Matches are distributed among these distances:
322 19 0.01
323 136 0.10
324 3 0.00
325 48 0.04
326 15 0.01
327 68 0.05
328 1 0.00
329 39 0.03
330 6 0.00
331 84 0.06
332 18 0.01
333 210 0.16
334 67 0.05
335 139 0.10
336 58 0.04
337 118 0.09
338 13 0.01
339 111 0.08
340 153 0.12
341 13 0.01
342 8 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (328 bp):
AAAAATTGACCGAAAGATTTTTCTTAATTTTTAGGCACAATACTCATAAAAAATATATAATTTAA
CGACAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATTGTTTTTCATATTTTTTGAATTAATTT
CTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGATGAG
ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGCACCAAAAATCATGCAAAACCGACGCG
AGGCCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTT
TGC
Found at i:8338 original size:343 final size:331
Alignment explanation
Indices: 7589--8420 Score: 955
Period size: 342 Copynumber: 2.5 Consensus size: 331
7579 ATATATATAT
* * * * *
7589 ATATAAAATTCAACGCCAAAAATATTAGAGGACTTTTCACGCTTTTAATATCGTTTT-TCATTTT
1 ATATATAATTCAATGCCAAAAAGATT-GAGGACTTTTCACGCTTCTAATATCGTTTTCTTATTTT
* *
7653 TTGT-T-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATTCTTAA
65 TT-TCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAA
* * * *
7716 ATCCAATGTGGCTGAGATTTGATTAGATAAATATGGATATATCAAAGAGTCTTGGCAGCAAAAAT
129 ATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATCAAAGAGTCTCGGCAGCAAAAAT
* * * *
7781 CATACAAAACTGACCCGGGGCCCCGGAACGCTTTTTTAGCCAAAAACCGTGATGGTTATTACACG
194 CATACAAAACTGACCCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGGTTAATACACG
* *
7846 ATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAAATATTTCCTCAATTTTTGGCTAAAATACT
259 ATTTCGACTAAAATTTTGTAAAAATTGACACGAAAAATATTTCCTCAATTTTTGGCTAAAATACT
7911 CATAAAAA
324 CATAAAAA
* * * * * ** * *
7919 ATATATATTTCAACT-CTAGAAAGATTGAACGACTTTTGACATTTCTATTATCGTTTTTCCTATT
1 ATATATAATTCAA-TGCCAAAAAGATTG-AGGACTTTTCACGCTTCTAATATCG-TTTTCTTATT
* * * * *
7983 TTTTTC-AAATTAATTTCTAATTAAATTGAAACAAAATCCAGATGCTCATTAAAAAAAAATCCTT
63 TTTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTC-GTAAAAACAAATTCTT
* * *
8047 AAATCGAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTC-AAGTAGTCTCGG-AGCTAA
127 AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATCAAAG-AGTCTCGGCAGC-AA
* * ** * *
8110 AAATCATGCAAAATTGAGGCGGGTCCCCGGAATGCGTTTTTAGTCAAAAAAAAAAATCCATGATG
190 AAATCATACAAAACTGACCCGGGGCCCCGGAACGCGTTTTTAG-C-----AAAAAA-CCATGATG
* *
8175 TTTAGTTAATACACGATTT-GACTAAAATTTT-TAAAAAATTGACACGAAAGATTTTTCCTCAAT
248 ----GTTAATACACGATTTCGACTAAAATTTTGT-AAAAATTGACACGAAAAATATTTCCTCAAT
* **
8238 TTTTGGCTAAAATTCTTGT-AAAA
308 TTTTGGCTAAAATACTCATAAAAA
*
8261 ATATATAATTCAATGCCAAAAAGATTGTAGGGCTTTTCACGCTTCTAATATCGTATTTCTTATTT
1 ATATATAATTCAATGCCAAAAAGATTG-AGGACTTTTCACGCTTCTAATATCGT-TTTCTTATTT
*
8326 TTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAA
64 TTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAA
* *
8391 ATCCAATGTTGCTGAAATTTGGTTAGATGA
129 ATCCAATGTGGCTGAGATTTGGTTAGATGA
8421 TGTAAAGTAT
Statistics
Matches: 412, Mismatches: 66, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
329 1 0.00
330 38 0.09
331 5 0.01
332 49 0.12
333 97 0.24
334 1 0.00
339 5 0.01
340 7 0.02
341 2 0.00
342 101 0.25
343 92 0.22
344 14 0.03
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (331 bp):
ATATATAATTCAATGCCAAAAAGATTGAGGACTTTTCACGCTTCTAATATCGTTTTCTTATTTTT
TTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
CCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATATCAAAGAGTCTCGGCAGCAAAAATCA
TACAAAACTGACCCGGGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGGTTAATACACGAT
TTCGACTAAAATTTTGTAAAAATTGACACGAAAAATATTTCCTCAATTTTTGGCTAAAATACTCA
TAAAAA
Found at i:8793 original size:15 final size:16
Alignment explanation
Indices: 8775--8804 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8765 ATAAATAATA
8775 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
8790 ATATTATAATCTAAA
1 ATATTATAATCTAAA
8805 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:8819 original size:13 final size:14
Alignment explanation
Indices: 8801--8830 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8791 TATTATAATC
8801 TAAAAAT-AATTAT
1 TAAAAATAAATTAT
8814 TAAAAATAAATTAT
1 TAAAAATAAATTAT
8828 TAA
1 TAA
8831 TACAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAAATAAATTAT
Found at i:8953 original size:20 final size:20
Alignment explanation
Indices: 8912--8958 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
8902 CATAATTAAT
*
8912 AAAAAAAGTTGAATCATCTA
1 AAAAAAAGTTAAATCATCTA
*
8932 AAAAAAAGTTAAATGA-CTTA
1 AAAAAAAGTTAAATCATC-TA
8952 AAAAAAA
1 AAAAAAA
8959 TACTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.64, C:0.06, G:0.09, T:0.21
Consensus pattern (20 bp):
AAAAAAAGTTAAATCATCTA
Found at i:13691 original size:22 final size:20
Alignment explanation
Indices: 13657--13700 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
13647 AAATATATCT
*
13657 AAAAAATGGGAGAACCAAAAA
1 AAAAAATGAGAGAA-CAAAAA
*
13678 AAAAAATGAAGAGAAGAAAAA
1 AAAAAATG-AGAGAACAAAAA
13699 AA
1 AA
13701 TAGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.73, C:0.05, G:0.18, T:0.05
Consensus pattern (20 bp):
AAAAAATGAGAGAACAAAAA
Found at i:18793 original size:18 final size:18
Alignment explanation
Indices: 18766--18801 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18756 AACTCGCTGC
*
18766 ATGACTGGTTTAGTGGTA
1 ATGACAGGTTTAGTGGTA
18784 ATGACAGGTTTAGTGGTA
1 ATGACAGGTTTAGTGGTA
18802 TCAACCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.33, T:0.36
Consensus pattern (18 bp):
ATGACAGGTTTAGTGGTA
Found at i:20043 original size:20 final size:20
Alignment explanation
Indices: 20015--20057 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
20005 ATTTTGCTTC
*
20015 AGATTTGCTTTGCTTGATGG
1 AGATGTGCTTTGCTTGATGG
20035 AGATGTGCTTTGCTTGATGG
1 AGATGTGCTTTGCTTGATGG
20055 AGA
1 AGA
20058 AGAACTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.40
Consensus pattern (20 bp):
AGATGTGCTTTGCTTGATGG
Found at i:20065 original size:20 final size:20
Alignment explanation
Indices: 20022--20067 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
20012 TTCAGATTTG
* **
20022 CTTTGCTTGATGGAGATGTG
1 CTTTGCTTGATGGAGAAGAA
20042 CTTTGCTTGATGGAGAAGAA
1 CTTTGCTTGATGGAGAAGAA
20062 CTTTGC
1 CTTTGC
20068 ATTGCCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (20 bp):
CTTTGCTTGATGGAGAAGAA
Found at i:20139 original size:41 final size:41
Alignment explanation
Indices: 20086--20171 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
20076 TTGTTGATGG
20086 AGAAAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGAAGA
1 AGAAAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGAAGA
20127 AGAAGAAC-TTGCTTCAGATTTGCTTTGCTTGATGGAGAAGA
1 AGAA-AACTTTGCTTCAGATTTGCTTTGCTTGATGGAGAAGA
20168 AGAA
1 AGAA
20172 TTGCTTGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 41 0.93
42 3 0.07
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (41 bp):
AGAAAACTTTGCTTCAGATTTGCTTTGCTTGATGGAGAAGA
Found at i:20188 original size:18 final size:21
Alignment explanation
Indices: 20151--20192 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20141 CAGATTTGCT
20151 TTGCTTGATGGAGAAGAAGAA
1 TTGCTTGATGGAGAAGAAGAA
20172 TTGCTTGATGGAGAAGAAGAA
1 TTGCTTGATGGAGAAGAAGAA
20193 GAACTTGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.24
Consensus pattern (21 bp):
TTGCTTGATGGAGAAGAAGAA
Found at i:20199 original size:21 final size:21
Alignment explanation
Indices: 20154--20199 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
20144 ATTTGCTTTG
***
20154 CTTGATGGAGAAGAAGAATTG
1 CTTGATGGAGAAGAAGAAGAA
20175 CTTGATGGAGAAGAAGAAGAA
1 CTTGATGGAGAAGAAGAAGAA
20196 CTTG
1 CTTG
20200 CCTTGCCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (21 bp):
CTTGATGGAGAAGAAGAAGAA
Found at i:22287 original size:17 final size:17
Alignment explanation
Indices: 22265--22298 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22255 ATCATCCTCT
22265 CCCTTTTGTCTTGATAG
1 CCCTTTTGTCTTGATAG
22282 CCCTTTTGTCTTGATAG
1 CCCTTTTGTCTTGATAG
22299 AAAGGGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (17 bp):
CCCTTTTGTCTTGATAG
Found at i:22604 original size:47 final size:44
Alignment explanation
Indices: 22533--22756 Score: 241
Period size: 47 Copynumber: 4.8 Consensus size: 44
22523 GGAAATGGTG
**
22533 GGGTTGATTAATTATCGCCCTCTACCTCTGCATCGGTCTCTTGGC
1 GGGTTGATTTTTTATCGCCCTCTACCTCTGCATCGG-CTCTTGGC
* *
22578 GGGATTGATTTTTTTATCGCCCTCTACCTTTGCATCGGCTTCTTGGTG
1 GGG-TTGA-TTTTTTATCGCCCTCTACCTCTGCATCGGC-TCTTGG-C
* * **
22626 GGGTCGATTTTTTATAGCCCTCTACCCTCCACATCGGCTCCTTGGC
1 GGGTTGATTTTTTATCGCCCTCTA-CCTCTGCATCGGCT-CTTGGC
* * * *
22672 GGGGTGATCTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGC
1 GGGTTGATTTTTTATCGCCCTCTACCTCTGCATCGG-CTCTTGGC
22717 GAGGTTGATTTTTTTTATCGCCCTCTACCTCTGCATCGGC
1 G-GGTTGA--TTTTTTATCGCCCTCTACCTCTGCATCGGC
22757 CTTTTATCGC
Statistics
Matches: 148, Mismatches: 21, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
45 19 0.13
46 48 0.32
47 51 0.34
48 30 0.20
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (44 bp):
GGGTTGATTTTTTATCGCCCTCTACCTCTGCATCGGCTCTTGGC
Found at i:22771 original size:29 final size:29
Alignment explanation
Indices: 22729--22790 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
22719 GGTTGATTTT
22729 TTTTATCGCCCTCTACCTCTGCATCGGCC
1 TTTTATCGCCCTCTACCTCTGCATCGGCC
*
22758 TTTTATCGCCCTCTACCTCTGCATCGGCT
1 TTTTATCGCCCTCTACCTCTGCATCGGCC
22787 TTTT
1 TTTT
22791 GGCGGGGCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.10, C:0.37, G:0.13, T:0.40
Consensus pattern (29 bp):
TTTTATCGCCCTCTACCTCTGCATCGGCC
Found at i:22807 original size:77 final size:77
Alignment explanation
Indices: 22680--22833 Score: 254
Period size: 77 Copynumber: 2.0 Consensus size: 77
22670 GCGGGGTGAT
*
22680 CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGTTGATTTTTTTTATCGCCCTCTAC
1 CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGCTGATTTTTTTTATCGCCCTCTAC
22745 CTCTGCATCGGC
66 CTCTGCATCGGC
* * *
22757 CTTTTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTTTTTTATCGCCCTCTAC
1 CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGCTGATTTTTTTTATCGCCCTCTAC
* *
22822 TTCTGGATCGGC
66 CTCTGCATCGGC
22834 TTCTTTGCGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.10, C:0.31, G:0.19, T:0.40
Consensus pattern (77 bp):
CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGCTGATTTTTTTTATCGCCCTCTAC
CTCTGCATCGGC
Found at i:22879 original size:47 final size:46
Alignment explanation
Indices: 22758--22977 Score: 273
Period size: 47 Copynumber: 4.7 Consensus size: 46
22748 TGCATCGGCC
*
22758 TTTTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTT
1 TTTTATCGCCCTCTACCTCTGCATCGGC-TTTTGGCGGGGTTGA-TTT
* * *
22806 TTTTATCGCCCTCTACTTCTGGATCGGCTTCTTTGCGGGGTTGATTT
1 TTTTATCGCCCTCTACCTCTGCATCGGCTT-TTGGCGGGGTTGATTT
** *
22853 TTTTATCGCCCTCTACCTCCACATCGGCTTCTTGGCGGGG-TGA-TC
1 TTTTATCGCCCTCTACCTCTGCATCGGCTT-TTGGCGGGGTTGATTT
*
22898 TTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGGGGTTGATTT
1 TTTTATCGCCCTCTACCTCTGCATCGG-CTTTTGGCGGGGTTGATTT
* * *
22945 TTTTATCCCCCTCTACTTTTGCATCGGCCTTTT
1 TTTTATCGCCCTCTACCTCTGCATCGG-CTTTT
22978 ATCGCCCTCT
Statistics
Matches: 151, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
45 34 0.23
46 9 0.06
47 71 0.47
48 37 0.25
ACGTcount: A:0.10, C:0.29, G:0.20, T:0.41
Consensus pattern (46 bp):
TTTTATCGCCCTCTACCTCTGCATCGGCTTTTGGCGGGGTTGATTT
Found at i:22904 original size:169 final size:168
Alignment explanation
Indices: 22589--22930 Score: 433
Period size: 169 Copynumber: 2.0 Consensus size: 168
22579 GGATTGATTT
* *
22589 TTTTATCGCCCTCTACCTTTGCATCGGCTTCTTGGTGGGGTCGATTTTTTATAGCCCTCTACCCT
1 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTCGATTTTTTATAGCCCTCTACCCT
**
22654 CCACATCGGCTCCTTGGCGGGGTGATCTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGA
66 CCACATCGGCTCCTTGGCGGGGTGATCTTTTATCACCCTCTACCTCCACATCGGCCTTTTGGCGA
* * *
22719 GGTTGATTTTTTTTATCGCCCTCTACCTCTGCATCGGCC
131 GGGTGA-TTCTTTTATCACCCTCTACCTCTGCATCGGCC
* *
22758 TTTTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGG-CTGATTTTTTTTATCGCCCTCTA-
1 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTC-GA--TTTTTTATAGCCCTCTAC
* *** * * * *
22821 CTTCTGGATCGGCTTCTTTGCGGGGTTGATTTTTTTATCGCCCTCTACCTCCACATCGG-CTTCT
63 CCTCCACATCGGCTCCTTGGCGGGG-TGA-TCTTTTATCACCCTCTACCTCCACATCGGCCTT-T
22885 TGGCG-GGGTGA-TCTTTTATCACCCTCTACCTCTGCATCGGCC
125 TGGCGAGGGTGATTCTTTTATCACCCTCTACCTCTGCATCGGCC
22927 TTTT
1 TTTT
22931 GGCGGGGTTG
Statistics
Matches: 150, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
168 1 0.01
169 72 0.48
170 19 0.13
171 27 0.18
172 31 0.21
ACGTcount: A:0.11, C:0.30, G:0.20, T:0.39
Consensus pattern (168 bp):
TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTCGATTTTTTATAGCCCTCTACCCT
CCACATCGGCTCCTTGGCGGGGTGATCTTTTATCACCCTCTACCTCCACATCGGCCTTTTGGCGA
GGGTGATTCTTTTATCACCCTCTACCTCTGCATCGGCC
Found at i:22970 original size:92 final size:94
Alignment explanation
Indices: 22758--22972 Score: 292
Period size: 92 Copynumber: 2.3 Consensus size: 94
22748 TGCATCGGCC
* * * *
22758 TTTTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTTTTTTATCGCCCTCTACT
1 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGCTGA-TTCTTTTATCACCCTCTACC
* *
22823 TCTGGATCGGCTTCTTTGCGGGGTTGATTT
65 TCTGCATCGGCTTCTTGGCGGGGTTGATTT
**
22853 TTTTATCGCCCTCTACCTCCACATCGGCTTCTTGGCGGGG-TGA-TCTTTTATCACCCTCTACCT
1 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGCTGATTCTTTTATCACCCTCTACCT
22916 CTGCATCGGCCTT-TTGGCGGGGTTGATTT
66 CTGCATCGG-CTTCTTGGCGGGGTTGATTT
* * *
22945 TTTTATCCCCCTCTACTTTTGCATCGGC
1 TTTTATCGCCCTCTACCTCTGCATCGGC
22973 CTTTTATCGC
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
92 63 0.59
93 3 0.03
94 3 0.03
95 37 0.35
ACGTcount: A:0.10, C:0.29, G:0.21, T:0.40
Consensus pattern (94 bp):
TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGCTGATTCTTTTATCACCCTCTACCT
CTGCATCGGCTTCTTGGCGGGGTTGATTT
Found at i:22970 original size:216 final size:216
Alignment explanation
Indices: 22544--23100 Score: 881
Period size: 216 Copynumber: 2.6 Consensus size: 216
22534 GGTTGATTAA
* **
22544 TTATCGCCCTCTACCTCTGCATCGG-TCTCTTGGCGGGATTGATTTTTTTATCGCCCTCTACCTT
1 TTATCGCCCTCTACCTCTGCATCGGCT-TTTTGGCGGGGCTGATTTTTTTATCGCCCTCTA-CTT
* * * *
22608 -TGCATCGGCTTCTTGGTGGGGTCGA-TTTTTTATAGCCCTCTACCCTCCACATCGGCTCCTTGG
64 CTGCATCGGCTTCTTGGCGGGGTTGATTTTTTTATCGCCCTCTA-CCTCCACATCGGCTTCTTGG
22671 CGGGGTGATCTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGTTGATTTTTTTTATC
128 CGGGGTGATCTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGTTGATTTTTTTTATC
*
22736 GCCCTCTACCTCTGCATCGGCCTT
193 CCCCTCTACCTCTGCATCGGCCTT
22760 TTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTTTTTTATCGCCCTCTACTTC
1 TTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGA-TTTTTTTATCGCCCTCTACTTC
* *
22825 TGGATCGGCTTCTTTGCGGGGTTGATTTTTTTATCGCCCTCTACCTCCACATCGGCTTCTTGGCG
65 TGCATCGGCTTCTTGGCGGGGTTGATTTTTTTATCGCCCTCTACCTCCACATCGGCTTCTTGGCG
*
22890 GGGTGATCTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGGGGTTGA-TTTTTTTATCCC
130 GGGTGATCTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGTTGATTTTTTTTATCCC
* *
22954 CCTCTACTTTTGCATCGGCCTT
195 CCTCTACCTCTGCATCGGCCTT
*
22976 TTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTTTTTATCGCCCTCTACCTCT
1 TTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTTTTTATCGCCCTCTACTTCT
* ** *
23041 GCATCGGCTTCTTGGCGGGGTTGATTATTTT-TCGCCCTCTACCTCTGCATCGACTTCTTG
66 GCATCGGCTTCTTGGCGGGGTTGATTTTTTTATCGCCCTCTACCTCCACATCGGCTTCTTG
23101 ATGGGTCATG
Statistics
Matches: 317, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
214 26 0.08
215 50 0.16
216 113 0.36
217 112 0.35
218 16 0.05
ACGTcount: A:0.10, C:0.30, G:0.21, T:0.39
Consensus pattern (216 bp):
TTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTTTTTATCGCCCTCTACTTCT
GCATCGGCTTCTTGGCGGGGTTGATTTTTTTATCGCCCTCTACCTCCACATCGGCTTCTTGGCGG
GGTGATCTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGAGGTTGATTTTTTTTATCCCC
CTCTACCTCTGCATCGGCCTT
Found at i:22987 original size:29 final size:29
Alignment explanation
Indices: 22945--23006 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
22935 GGGTTGATTT
* *
22945 TTTTATCCCCCTCTACTTTTGCATCGGCC
1 TTTTATCCCCCTCTACCTCTGCATCGGCC
* *
22974 TTTTATCGCCCTCTACCTCTGCATCGGCT
1 TTTTATCCCCCTCTACCTCTGCATCGGCC
23003 TTTT
1 TTTT
23007 GGCGGGGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.10, C:0.35, G:0.11, T:0.44
Consensus pattern (29 bp):
TTTTATCCCCCTCTACCTCTGCATCGGCC
Found at i:23023 original size:76 final size:76
Alignment explanation
Indices: 22897--23048 Score: 250
Period size: 76 Copynumber: 2.0 Consensus size: 76
22887 GCGGGGTGAT
* *
22897 CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGGGGTTGATTTTTTTATCCCCCTCTACT
1 CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGGGGCTGATTTTTTTATCCCCCTCTACC
*
22962 TTTGCATCGGC
66 TCTGCATCGGC
* * *
22973 CTTTTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTTTTTTATCGCCCTCTACC
1 CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGGGGCTGATTTTTTTATCCCCCTCTACC
23038 TCTGCATCGGC
66 TCTGCATCGGC
23049 TTCTTGGCGG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.10, C:0.32, G:0.18, T:0.39
Consensus pattern (76 bp):
CTTTTATCACCCTCTACCTCTGCATCGGCCTTTTGGCGGGGCTGATTTTTTTATCCCCCTCTACC
TCTGCATCGGC
Found at i:23098 original size:46 final size:47
Alignment explanation
Indices: 22974--23100 Score: 211
Period size: 47 Copynumber: 2.7 Consensus size: 47
22964 TGCATCGGCC
* *
22974 TTTTATCGCCCTCTACCTCTGCATCGGCTTTTTGGCGGGGCTGATTT
1 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGCTGATTA
*
23021 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTA
1 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGCTGATTA
*
23068 TTTT-TCGCCCTCTACCTCTGCATCGACTTCTTG
1 TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTG
23101 ATGGGTCATG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
46 28 0.37
47 48 0.63
ACGTcount: A:0.09, C:0.30, G:0.20, T:0.40
Consensus pattern (47 bp):
TTTTATCGCCCTCTACCTCTGCATCGGCTTCTTGGCGGGGCTGATTA
Found at i:27737 original size:26 final size:25
Alignment explanation
Indices: 27699--27759 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 25
27689 TCCATCAAAT
*
27699 TTCAAACTTTTCAATTCTCTCAACC
1 TTCAAACTTTTCAATTCTCTCAACA
*
27724 TTCAAAACTTTTCAATTCTCTTAACA
1 TTC-AAACTTTTCAATTCTCTCAACA
27750 TTCAAACTTT
1 TTCAAACTTT
27760 CAAAGCTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 10 0.30
26 23 0.70
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (25 bp):
TTCAAACTTTTCAATTCTCTCAACA
Done.