Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009128.1 Corchorus capsularis cultivar CVL-1 contig09149, 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: 52451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5499 original size:19 final size:20
Alignment explanation
Indices: 5456--5500 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
5446 GCACGCACAT
*
5456 ATGTACCAAAAAGTCATGCCAC
1 ATGTACCAAAAAG--ATGACAC
5478 ATGTACCAAAAAG-TGACAC
1 ATGTACCAAAAAGATGACAC
5497 ATGT
1 ATGT
5501 CACGCCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
22 13 0.59
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (20 bp):
ATGTACCAAAAAGATGACAC
Found at i:5505 original size:54 final size:52
Alignment explanation
Indices: 5419--5522 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 52
5409 GACGTGGCAC
* *
5419 GCCACGTGTACCAAAAAGTGACATGTAGCACGCACATATGTACCAAAAAGTCAT
1 GCCACATGTACCAAAAAGTGACATGTA-CACGC-CACATGTACCAAAAAGTCAT
*
5473 GCCACATGTACCAAAAAGTGACACATGT-CACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTG--ACATGTACACGCCACATGTACCAAAAAGT
5523 GACACATGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
53 15 0.33
54 24 0.53
56 6 0.13
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (52 bp):
GCCACATGTACCAAAAAGTGACATGTACACGCCACATGTACCAAAAAGTCAT
Found at i:5514 original size:31 final size:31
Alignment explanation
Indices: 5468--5570 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
5458 GTACCAAAAA
5468 GTCATGCCACATGTACCAAAAAGTGACACAT
1 GTCATGCCACATGTACCAAAAAGTGACACAT
* *
5499 GTCACGCCACGTGTACCAAAAAGTGACACAT
1 GTCATGCCACATGTACCAAAAAGTGACACAT
* ** * * *
5530 GGCATGCCACATGTTTCAAAAAATGGCACGT
1 GTCATGCCACATGTACCAAAAAGTGACACAT
*
5561 GGCATGCCAC
1 GTCATGCCAC
5571 GTGCACAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.18
Consensus pattern (31 bp):
GTCATGCCACATGTACCAAAAAGTGACACAT
Found at i:6371 original size:2 final size:2
Alignment explanation
Indices: 6366--6411 Score: 56
Period size: 2 Copynumber: 22.0 Consensus size: 2
6356 CAAAAAAACC
* *
6366 TA TA TA CTA CA TA TA TA CTT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
6410 TA
1 TA
6412 CTCTCTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 35 0.92
3 3 0.08
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8432 original size:23 final size:23
Alignment explanation
Indices: 8402--8445 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
8392 ATTCGTCCGA
8402 TTAAGGTAA-TTCATGTGTCTATT
1 TTAAGGTAATTTCATG-GTCTATT
8425 TTAAGGTAATTTCATGGTCTA
1 TTAAGGTAATTTCATGGTCTA
8446 CAACTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (23 bp):
TTAAGGTAATTTCATGGTCTATT
Found at i:10241 original size:156 final size:155
Alignment explanation
Indices: 9873--10233 Score: 392
Period size: 156 Copynumber: 2.3 Consensus size: 155
9863 CAGATTTCGT
* * * * * * *
9873 ATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAGTTTGAGGTGTCAAACCAACTTCTCTATGC
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCTAGTTCACCATGC
* * * * *
9938 TAGAGAGTTTGGTTTTACTTAGAATTTTTTCCATAGCTTAATGGGGATAATCTAAGTCTACTGGT
66 AAGAGAGCTCGATTTTACTTAGAATTTTTTCCATAGCTTAATGGAGATAATCTAAGTCTACT-GT
* *
10003 GGAAAATCAGCTTCGTTGGACTTAGA
130 GGAAAATCAGCTTCATTAGACTTAGA
* **** * *
10029 GTGAAAAACTTATGCTAGTTTTTCATTTAAGGACA-ACCCAGGGAGAGAAACCTAGTTCACCAT-
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGA-GGTGTGAAACCTAGTTCACCATG
* * *
10092 CAAGGGGAGCTCGATTTTACTTAGAATTTTTTCCATAG-TCTCATGGAGATAATCTAAGTC-CCT
65 CAA-GAGAGCTCGATTTTACTTAGAATTTTTTCCATAGCT-TAATGGAGATAATCTAAGTCTACT
10155 -TGGAAAAGTTTCAGC-TCATTCAGACTTAGA
128 GTGGAAAA---TCAGCTTCATT-AGACTTAGA
10185 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAA
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAA
10234 GTCTAGTTTG
Statistics
Matches: 166, Mismatches: 31, Indels: 16
0.78 0.15 0.08
Matches are distributed among these distances:
153 7 0.04
155 10 0.06
156 148 0.89
157 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (155 bp):
ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCTAGTTCACCATGC
AAGAGAGCTCGATTTTACTTAGAATTTTTTCCATAGCTTAATGGAGATAATCTAAGTCTACTGTG
GAAAATCAGCTTCATTAGACTTAGA
Found at i:13484 original size:13 final size:14
Alignment explanation
Indices: 13460--13498 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
13450 ATTAAAAAAA
13460 TACTACTAATATAG
1 TACTACTAATATAG
13474 TACTA-TAATATAG
1 TACTACTAATATAG
13487 TACTACT-ATATA
1 TACTACTAATATA
13499 TGTTTCTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (14 bp):
TACTACTAATATAG
Found at i:14591 original size:31 final size:31
Alignment explanation
Indices: 14518--14595 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
14508 TTTGTAAAAC
14518 TTTTGAAACGCCTATTGTACCCTTATTTAAT
1 TTTTGAAACGCCTATTGTACCCTTATTTAAT
**
14549 TTTTGTTACGCCTATTGTACCCTTATTTAAT
1 TTTTGAAACGCCTATTGTACCCTTATTTAAT
*
14580 TTTTAAAACGCCTATT
1 TTTTGAAACGCCTATT
14596 ATATCCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.09, T:0.47
Consensus pattern (31 bp):
TTTTGAAACGCCTATTGTACCCTTATTTAAT
Found at i:17588 original size:22 final size:24
Alignment explanation
Indices: 17560--17607 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
17550 CAATCTAATC
*
17560 TCATAGAG-TC-ATTATCAGAATT
1 TCATAGAGATCGATTATCAAAATT
17582 TCATAGAGATCGGATTATCAAAATT
1 TCATAGAGATC-GATTATCAAAATT
17607 T
1 T
17608 ACAGGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
25 12 0.55
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (24 bp):
TCATAGAGATCGATTATCAAAATT
Found at i:17932 original size:2 final size:2
Alignment explanation
Indices: 17916--17957 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
17906 AAAATTGATA
17916 AT AT AT CAT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17958 TTGCAAAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21387 original size:15 final size:14
Alignment explanation
Indices: 21356--21397 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
21346 ATATTATTAG
21356 TTTTTTTTTTTTT-
1 TTTTTTTTTTTTTC
21369 TTTTTTTTTTTTTC
1 TTTTTTTTTTTTTC
**
21383 ATTTTCATTTTTTTC
1 -TTTTTTTTTTTTTC
21398 CCAACTAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.52
15 12 0.48
ACGTcount: A:0.05, C:0.07, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTTC
Found at i:21396 original size:1 final size:1
Alignment explanation
Indices: 21356--21381 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
21346 ATATTATTAG
21356 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
21382 CATTTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24211 original size:543 final size:543
Alignment explanation
Indices: 23184--24268 Score: 1945
Period size: 543 Copynumber: 2.0 Consensus size: 543
23174 ATTTTGTTTT
* *
23184 GGCCCACAATAACTATTTTATGCATATTCCAATCAATTGGGGCCAAACGAATATCTTATAAAGGT
1 GGCCCACAATAACTATTTTATGCATATTCCAATCAATTGAGGCCAAACGAATACCTTATAAAGGT
*
23249 AATATATATCCACATGCGGTAATTATGATTCATATATAATTAAATGATTTGGTATATTTTACACC
66 AATATATATCCACATGCGGTAATTATGATTCATATATAATTAAATGATTTGGTATATTTAACACC
* * *
23314 AAAAAACTGATTGGTATATCATCTTAACTATGATGTTTGTAAGGTAAGTGATAGTTGTTCAATAA
131 AAAAAACTAATTGGTATATCATCTTAACTATGAGGTTTCTAAGGTAAGTGATAGTTGTTCAATAA
* *
23379 GGGAGTCCAAAATCAGCTGCATTAAATATTTGTTCAATAATTAGATAGCTACTTAAGTTGGTACC
196 GGGAGTCCAAAATCAACTGCATTAAATATCTGTTCAATAATTAGATAGCTACTTAAGTTGGTACC
* *
23444 AAGTGATATTAAAGGTTCTACCTGTCACAAATGGTGAAATGTGGGTATTTGACCACCGTAAGAAA
261 AAGTGATATTAAAGGTCCTACCTGTCACAAATGGTGAAAGGTGGGTATTTGACCACCGTAAGAAA
*
23509 AGTCAAATAAGAAAAACGAAGACACCATTCGAGCCTCCCTAATAGAAAGAGAAGAGAAATTGCTT
326 AGTCAAATAAGAAAAACGAAGACACCATTCGAGCCTCCCTAATAGAAAGAGAAAAGAAATTGCTT
23574 GCGCGCTTCGTCAAGTGAGAGAGAGGATCACATATCTCATGGTTGATTCCAGAACATGCTAGATT
391 GCGCGCTTCGTCAAGTGAGAGAGAGGATCACATATCTCATGGTTGATTCCAGAACATGCTAGATT
23639 TCTAACTTTGTAGGAGTCTAAGCAAACTTTCGAAATGTTTATTTTATGGGTAATTGAAGGAGGCT
456 TCTAACTTTGTAGGAGTCTAAGCAAACTTTCGAAATGTTTATTTTATGGGTAATTGAAGGAGGCT
*
23704 TTTCTCAAGAAAATAATGACAGG
521 TTCCTCAAGAAAATAATGACAGG
23727 GGCCCACAATAACTATTTTATGCATATTCCAATCAATTGAGGCCAAACGAATACCTTATAAAGGT
1 GGCCCACAATAACTATTTTATGCATATTCCAATCAATTGAGGCCAAACGAATACCTTATAAAGGT
* **
23792 AATATATATCCACATGCGGTAATTATGATTCATATATAATTGAATTTTTTGGTATATTTAACACC
66 AATATATATCCACATGCGGTAATTATGATTCATATATAATTAAATGATTTGGTATATTTAACACC
* * *
23857 AAAAAACTAATTGGTATATTATCTTAACTGTGAGGTTTCTAAGGTAAGTGATATTTGTTCAATAA
131 AAAAAACTAATTGGTATATCATCTTAACTATGAGGTTTCTAAGGTAAGTGATAGTTGTTCAATAA
23922 GGGAGTCCAAAATCAACTGCATTAAATATCTGTTCAATAATTAGATAGCTACTTAAGTTGGTACC
196 GGGAGTCCAAAATCAACTGCATTAAATATCTGTTCAATAATTAGATAGCTACTTAAGTTGGTACC
*
23987 AAGTGATATTAAAGGTCCTACCTGTCACAAATGGTGAAAGGTGGGTATTTGACCACTGTAAGAAA
261 AAGTGATATTAAAGGTCCTACCTGTCACAAATGGTGAAAGGTGGGTATTTGACCACCGTAAGAAA
**
24052 AGTCAAATAAGAAAATTGAAGACACCATTCGAGCCTCCCTAATAGAAAGAGAAAAGAAATTGCTT
326 AGTCAAATAAGAAAAACGAAGACACCATTCGAGCCTCCCTAATAGAAAGAGAAAAGAAATTGCTT
24117 GCGCGCTTCGTCAAGTGAGAGAGAGGATCACATATCTCATGGTTGATTCCAGAACATGCTAGATT
391 GCGCGCTTCGTCAAGTGAGAGAGAGGATCACATATCTCATGGTTGATTCCAGAACATGCTAGATT
* * * *
24182 TCTAACTTTGTAGGAGTCTGAGCAAACTTTTGAAGTGTTTATTTTATGGGTGATTGAAGGAGGCT
456 TCTAACTTTGTAGGAGTCTAAGCAAACTTTCGAAATGTTTATTTTATGGGTAATTGAAGGAGGCT
24247 TTCCTCAAGAAAATAATGACAG
521 TTCCTCAAGAAAATAATGACAG
24269 AATTCTCTGT
Statistics
Matches: 517, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
543 517 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (543 bp):
GGCCCACAATAACTATTTTATGCATATTCCAATCAATTGAGGCCAAACGAATACCTTATAAAGGT
AATATATATCCACATGCGGTAATTATGATTCATATATAATTAAATGATTTGGTATATTTAACACC
AAAAAACTAATTGGTATATCATCTTAACTATGAGGTTTCTAAGGTAAGTGATAGTTGTTCAATAA
GGGAGTCCAAAATCAACTGCATTAAATATCTGTTCAATAATTAGATAGCTACTTAAGTTGGTACC
AAGTGATATTAAAGGTCCTACCTGTCACAAATGGTGAAAGGTGGGTATTTGACCACCGTAAGAAA
AGTCAAATAAGAAAAACGAAGACACCATTCGAGCCTCCCTAATAGAAAGAGAAAAGAAATTGCTT
GCGCGCTTCGTCAAGTGAGAGAGAGGATCACATATCTCATGGTTGATTCCAGAACATGCTAGATT
TCTAACTTTGTAGGAGTCTAAGCAAACTTTCGAAATGTTTATTTTATGGGTAATTGAAGGAGGCT
TTCCTCAAGAAAATAATGACAGG
Found at i:26951 original size:74 final size:73
Alignment explanation
Indices: 26799--26958 Score: 196
Period size: 73 Copynumber: 2.2 Consensus size: 73
26789 TACAAGAAAG
* * ** * * *
26799 AATTTATTCCAAGAATGAAATTCGGTCAAATTTATTCAAGAATTCATTTTCAACCCAATTAAATT
1 AATTTATACCAAGAATGAAATTCGGCCAAATTTATTCAAGAATTCAAATTCAACCAAATAAAAAT
26864 CTTGCCCA
66 CTTGCCCA
** *
26872 AATTTATACCAAGAATTTAATTCGGCCAAATTTATTACAAGAATTCAAATTC-ACTAAATAAAAA
1 AATTTATACCAAGAATGAAATTCGGCCAAATTTATT-CAAGAATTCAAATTCAACCAAAT-AAAA
26936 ATCTTGCCCA
64 ATCTTGCCCA
*
26946 AATTTATGCCAAG
1 AATTTATACCAAG
26959 TTCAGAAAAG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
73 37 0.50
74 37 0.50
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (73 bp):
AATTTATACCAAGAATGAAATTCGGCCAAATTTATTCAAGAATTCAAATTCAACCAAATAAAAAT
CTTGCCCA
Found at i:27101 original size:12 final size:12
Alignment explanation
Indices: 27063--27104 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
27053 GAAAAAAGGA
*
27063 AAAAATGGGAAG
1 AAAAATGGCAAG
*
27075 AAAAA-GGTAAG
1 AAAAATGGCAAG
*
27086 AAAAATGGCAAC
1 AAAAATGGCAAG
27098 AAAAATG
1 AAAAATG
27105 CTTTGAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.62, C:0.05, G:0.24, T:0.10
Consensus pattern (12 bp):
AAAAATGGCAAG
Found at i:30426 original size:11 final size:11
Alignment explanation
Indices: 30410--30441 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
30400 GAAGTTCGTG
30410 TTTGAAGATTA
1 TTTGAAGATTA
*
30421 TTTGAAGATAA
1 TTTGAAGATTA
30432 TTTGAAGATT
1 TTTGAAGATT
30442 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:30444 original size:19 final size:18
Alignment explanation
Indices: 30420--30457 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
30410 TTTGAAGATT
*
30420 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
30439 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
30457 A
1 A
30458 ATTAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:31773 original size:6 final size:6
Alignment explanation
Indices: 31762--31792 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
31752 ATAATTGCTA
31762 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
31793 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:33219 original size:15 final size:15
Alignment explanation
Indices: 33191--33246 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
33181 TTGCCAAGCA
*
33191 AGAAGTTGAGCCACC
1 AGAAGATGAGCCACC
*
33206 AGAAGATGAACCACC
1 AGAAGATGAGCCACC
33221 AGAAGATGAGCCACC
1 AGAAGATGAGCCACC
33236 AGAAGATGAGC
1 AGAAGATGAGC
33247 AACTTGGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (15 bp):
AGAAGATGAGCCACC
Found at i:36135 original size:11 final size:11
Alignment explanation
Indices: 36119--36158 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
36109 TAAGTTCGTG
36119 TTTGAAGATTA
1 TTTGAAGATTA
*
36130 TTTGAAGATAA
1 TTTGAAGATTA
*
36141 TTTGAAGACTA
1 TTTGAAGATTA
36152 -TTGAAGA
1 TTTGAAGA
36159 ATTAATTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 7 0.27
11 19 0.73
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.38
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:42617 original size:31 final size:32
Alignment explanation
Indices: 42579--42655 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
42569 CGCTGACGTA
42579 GCAATGCCACGTCATT-GTTTGGTCCGACATG
1 GCAATGCCACGTCATTAGTTTGGTCCGACATG
*
42610 GCAATGCCACGTCATTAGTTTGGTCCGACGTG
1 GCAATGCCACGTCATTAGTTTGGTCCGACATG
*
42642 GCAATGCCATGTCA
1 GCAATGCCACGTCA
42656 ACATGTGCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 16 0.37
32 27 0.63
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (32 bp):
GCAATGCCACGTCATTAGTTTGGTCCGACATG
Found at i:42752 original size:29 final size:30
Alignment explanation
Indices: 42677--42754 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
42667 ATCGTTTGAG
** *
42677 AGGGGGCAAAACGTAAAAAATTGACAATTC
1 AGGGGGCAAAACGTCCAAAATTGACAATTA
* * *
42707 AGGAGGCAAAATGTCCAAAATTGA-AGTTA
1 AGGGGGCAAAACGTCCAAAATTGACAATTA
*
42736 AGGGGGCAAAACATCCAAA
1 AGGGGGCAAAACGTCCAAA
42755 TGCTACAAGT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.15
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCAAAATTGACAATTA
Found at i:42877 original size:11 final size:11
Alignment explanation
Indices: 42857--42888 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
42847 AAAATCGTAG
*
42857 CGCCTCCTCCT
1 CGCCTTCTCCT
42868 CGCCTTCTCCT
1 CGCCTTCTCCT
42879 CGCCTTCTCC
1 CGCCTTCTCC
42889 CCTTTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.59, G:0.09, T:0.31
Consensus pattern (11 bp):
CGCCTTCTCCT
Found at i:46386 original size:86 final size:85
Alignment explanation
Indices: 46283--46594 Score: 353
Period size: 86 Copynumber: 3.7 Consensus size: 85
46273 TTAACAAAAT
* *
46283 TAATAATAAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGCTTTAGGAGATATTTTAAGAAAA
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAA
46348 CAAATAAATTAAAAATAGAA
66 CAAATAAATTAAAAATAGAA
*
46368 TTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGG--G----A-GATAT-TTTTAAGAAA
1 -TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAA
*
46425 TA-AAAT-AA-TAACAAA-ATAA
65 -ACAAATAAATTAA-AAATAGAA
*
46444 TAATAAAGTTGGGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAG-
1 TAAT-AA--TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
*
46508 AAACAAATAAATAATAAAAATTGAA
63 AAACAAATAAAT--TAAAAATAGAA
* * * *
46533 TAGTAATGAGAATATTTCTTTAAATCTTGCCAGATTGTGGGAGATTTAGGAGATATATTTAA
1 TAATAATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATAT-TTTAA
46595 TAATGATAAT
Statistics
Matches: 193, Mismatches: 12, Indels: 40
0.79 0.05 0.16
Matches are distributed among these distances:
75 4 0.02
76 8 0.04
77 5 0.03
78 46 0.24
79 5 0.03
80 2 0.01
84 3 0.02
85 10 0.05
86 57 0.30
87 35 0.18
88 10 0.05
89 8 0.04
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (85 bp):
TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAAA
CAAATAAATTAAAAATAGAA
Found at i:46431 original size:78 final size:76
Alignment explanation
Indices: 46330--46577 Score: 234
Period size: 78 Copynumber: 3.1 Consensus size: 76
46320 GGAAGCTTTA
46330 GGAGATA-TTTTAAGAAAACAAATAAATTAAAAATAGAATTAATAATGAGAATATTTTCTAAATC
1 GGAGATATTTTTAAGAAAA-AAATAAATTAAAAATAGAA-TAATAATGAGAATATTTTCTAAATC
46394 TTGCCAAATTGTG
64 TTGCCAAATTGTG
* *
46407 GGAGATATTTTTAAGAAATAAAAT-AA-TAACAAA-ATAATAATAAAGTTGGGAATATTTTCTAA
1 GGAGATATTTTTAAGAAA-AAAATAAATTAA-AAATAGAATAAT-AA--TGAGAATATTTTCTAA
46469 ATCTTGCCAAATTGTG
61 ATCTTGCCAAATTGTG
* * * *
46485 GAAGATTTAGGAGATATTTTAAGAAACAAATAAATAATAAAAATTGAATAGTAATGAGAATATTT
1 G--G----A-GATAT-TTTTAAGAAAAAAATAAAT--TAAAAATAGAATAATAATGAGAATATTT
* *
46550 CTTTAAATCTTGCCAGATTGTG
56 -TCTAAATCTTGCCAAATTGTG
46572 GGAGAT
1 GGAGAT
46578 TTAGGAGATA
Statistics
Matches: 140, Mismatches: 11, Indels: 37
0.74 0.06 0.20
Matches are distributed among these distances:
75 4 0.03
76 8 0.06
77 12 0.09
78 46 0.33
79 1 0.01
80 3 0.02
81 1 0.01
84 1 0.01
85 9 0.06
86 22 0.16
87 20 0.14
88 5 0.04
89 8 0.06
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (76 bp):
GGAGATATTTTTAAGAAAAAAATAAATTAAAAATAGAATAATAATGAGAATATTTTCTAAATCTT
GCCAAATTGTG
Found at i:46520 original size:89 final size:89
Alignment explanation
Indices: 46422--46594 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 89
46412 TATTTTTAAG
*
46422 AAATAAAATAATAACAAAAT-AATAATAAAGTTGGGAATATTT-TCTAAATCTTGCCAAATTGTG
1 AAATAAAATAATAA-AAAATGAATAAT-AA--TGAGAATATTTCTCTAAATCTTGCCAAATTGTG
46485 GAAGATTTAGGAGATAT-TTTAAGAAAC
62 GAAGATTTAGGAGATATATTTAAGAAAC
* * * * *
46512 AAAT-AAATAATAAAAATTGAATAGTAATGAGAATATTTCTTTAAATCTTGCCAGATTGTGGGAG
1 AAATAAAATAATAAAAAATGAATAATAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGAAG
46576 ATTTAGGAGATATATTTAA
66 ATTTAGGAGATATATTTAA
46595 TAATGATAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
86 10 0.14
87 35 0.47
88 11 0.15
89 14 0.19
90 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.33
Consensus pattern (89 bp):
AAATAAAATAATAAAAAATGAATAATAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGAAG
ATTTAGGAGATATATTTAAGAAAC
Done.