Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008484.1 Corchorus capsularis cultivar CVL-1 contig08505, 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: 64535
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2095 original size:21 final size:22
Alignment explanation
Indices: 2062--2103 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2052 CTTCACTACT
*
2062 ATATACTAGTATTTGC-ATGATA
1 ATATACTAATA-TTGCAATGATA
2084 ATAT-CTAATATTGCAATGAT
1 ATATACTAATATTGCAATGAT
2104 TATTAAGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (22 bp):
ATATACTAATATTGCAATGATA
Found at i:3971 original size:14 final size:14
Alignment explanation
Indices: 3954--3983 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3944 TAAGATGCTG
3954 TAAATAACTTTCAT
1 TAAATAACTTTCAT
*
3968 TAAATTACTTTCAT
1 TAAATAACTTTCAT
3982 TA
1 TA
3984 TCCTATTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATAACTTTCAT
Found at i:7705 original size:16 final size:16
Alignment explanation
Indices: 7684--7725 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
7674 TGCGTTCGTA
7684 AGAAAGAAAGGAAGGG
1 AGAAAGAAAGGAAGGG
7700 AGAAAGAAAGGAAGGG
1 AGAAAGAAAGGAAGGG
7716 AGAAAGAAAG
1 AGAAAGAAAG
7726 AGACAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAGGAAGGG
Found at i:9683 original size:13 final size:13
Alignment explanation
Indices: 9665--9689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9655 TTTTCATTTC
9665 TCCTATTCCTATT
1 TCCTATTCCTATT
9678 TCCTATTCCTAT
1 TCCTATTCCTAT
9690 AGGATTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (13 bp):
TCCTATTCCTATT
Found at i:10300 original size:5 final size:5
Alignment explanation
Indices: 10284--10324 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
10274 TTATTTAAAC
*
10284 AGCAG AAGCAG AGCAG AGCAG AGCAG ATC-- AGCAG AGCAG AG
1 AGCAG -AGCAG AGCAG AGCAG AGCAG AGCAG AGCAG AGCAG AG
10325 AACAGGGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
3 2 0.06
5 24 0.77
6 5 0.16
ACGTcount: A:0.41, C:0.20, G:0.37, T:0.02
Consensus pattern (5 bp):
AGCAG
Found at i:16035 original size:5 final size:5
Alignment explanation
Indices: 16025--16053 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
16015 TTAACAGTTA
16025 TAAAT TAAAT TAAAT TAAAT TAAAT TAAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAA
16054 CAAATGATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAAAT
Found at i:20842 original size:11 final size:11
Alignment explanation
Indices: 20828--20857 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
20818 TCGAACTCGA
20828 TCTTTTTTTTT
1 TCTTTTTTTTT
20839 TCTTTTTTTTT
1 TCTTTTTTTTT
20850 T-TTTTTTT
1 TCTTTTTTT
20858 ACAATTCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:24984 original size:29 final size:29
Alignment explanation
Indices: 24902--24976 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
24892 TAAAAAATCT
24902 TTCATTGCAAGTTTAATTTTTTGTTGGCC
1 TTCATTGCAAGTTTAATTTTTTGTTGGCC
*
24931 TCCATTGCAAGTTTAATTTTTTGTTGGCC
1 TTCATTGCAAGTTTAATTTTTTGTTGGCC
24960 TTCATTGCAAGTTTAAT
1 TTCATTGCAAGTTTAAT
24977 ACATTGTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (29 bp):
TTCATTGCAAGTTTAATTTTTTGTTGGCC
Found at i:26448 original size:31 final size:31
Alignment explanation
Indices: 26394--26480 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
26384 TTCTGTGCAC
* *
26394 GTGGCATGCCACATG-CCCTTTTTTGAAACAT
1 GTGGCATGCCACGTGTCAC-TTTTTGAAACAT
**
26425 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGAAACAT
* * * *
26456 GTGGCGTGACATGAGTCACTTTTTG
1 GTGGCATGCCACGTGTCACTTTTTG
26481 GTACATATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 45 0.96
32 2 0.04
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGAAACAT
Found at i:26481 original size:31 final size:31
Alignment explanation
Indices: 26421--26486 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
26411 CTTTTTTGAA
* *
26421 ACATGTGGCATGCCACGTGTCACTTTTTGGT
1 ACATGTGGCATGACACGAGTCACTTTTTGGT
* *
26452 ACATGTGGCGTGACATGAGTCACTTTTTGGT
1 ACATGTGGCATGACACGAGTCACTTTTTGGT
26483 ACAT
1 ACAT
26487 ATGTCACAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (31 bp):
ACATGTGGCATGACACGAGTCACTTTTTGGT
Found at i:26828 original size:49 final size:49
Alignment explanation
Indices: 26782--26891 Score: 134
Period size: 49 Copynumber: 2.2 Consensus size: 49
26772 GTCATTAATG
* *
26782 ACATGAATTTGA-AACAATAGGTATTAATTACTTTTTCCTCTTATTAAGA
1 ACATG-ATTTGATAACAATAGGAATTAATTACTTCTTCCTCTTATTAAGA
* * * *
26831 ACTTGATTTGATTACAATTGGAATTAATTACTTCTTCCTCTTATCAAGA
1 ACATGATTTGATAACAATAGGAATTAATTACTTCTTCCTCTTATTAAGA
26880 A-ATTGATTTGAT
1 ACA-TGATTTGAT
26892 TTGAATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 6 0.12
49 46 0.88
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (49 bp):
ACATGATTTGATAACAATAGGAATTAATTACTTCTTCCTCTTATTAAGA
Found at i:26892 original size:49 final size:49
Alignment explanation
Indices: 26795--26892 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
26785 TGAATTTGAA
* * * *
26795 ACAATAGGTATTAATTACTTTTTCCTCTTATTAAGAACTTGATTTGATT
1 ACAATAGGAATTAATTACTTCTTCCTCTTATCAAGAAATTGATTTGATT
*
26844 ACAATTGGAATTAATTACTTCTTCCTCTTATCAAGAAATTGATTTGATT
1 ACAATAGGAATTAATTACTTCTTCCTCTTATCAAGAAATTGATTTGATT
26893 TGAATTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (49 bp):
ACAATAGGAATTAATTACTTCTTCCTCTTATCAAGAAATTGATTTGATT
Found at i:27166 original size:26 final size:26
Alignment explanation
Indices: 27133--27193 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
27123 TAAAAGATTT
27133 TAACAAGTTACCAAGTAAAAGGTTAC
1 TAACAAGTTACCAAGTAAAAGGTTAC
*
27159 TAACAAGTTACCAAGTAAAATGTTAC
1 TAACAAGTTACCAAGTAAAAGGTTAC
27185 TAACAAGTT
1 TAACAAGTT
27194 TAACAAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (26 bp):
TAACAAGTTACCAAGTAAAAGGTTAC
Found at i:29655 original size:15 final size:15
Alignment explanation
Indices: 29635--29664 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29625 TTGATTTTCC
29635 TTCTTTTTCTTTGTT
1 TTCTTTTTCTTTGTT
*
29650 TTCTTTTTGTTTGTT
1 TTCTTTTTCTTTGTT
29665 AAATTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (15 bp):
TTCTTTTTCTTTGTT
Found at i:31543 original size:2 final size:2
Alignment explanation
Indices: 31536--31561 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31526 AGCATTTTGT
31536 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
31562 ATTAGGATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:44368 original size:27 final size:27
Alignment explanation
Indices: 44338--44399 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
44328 CAGCTGGGAG
44338 AGCTGCTGCTGCTGCTGTAACTGTGAA
1 AGCTGCTGCTGCTGCTGTAACTGTGAA
* *
44365 AGCTGCTGCTGCTGCTGTAAGTGTGGA
1 AGCTGCTGCTGCTGCTGTAACTGTGAA
44392 AGCTGCTG
1 AGCTGCTG
44400 TTGTTGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.34, T:0.29
Consensus pattern (27 bp):
AGCTGCTGCTGCTGCTGTAACTGTGAA
Found at i:44396 original size:24 final size:25
Alignment explanation
Indices: 44342--44408 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
44332 TGGGAGAGCT
44342 GCTGCTGCTGCTGTAACTGTGAAAGC
1 GCTGCTGCTGCTGTAACTGTGAAA-C
* *
44368 TGCTGCTGCTGCTGTAAGTGTGGAA-
1 -GCTGCTGCTGCTGTAACTGTGAAAC
* *
44393 GCTGCTGTTGTTGTAA
1 GCTGCTGCTGCTGTAA
44409 TTGTTGCTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 14 0.39
27 22 0.61
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (25 bp):
GCTGCTGCTGCTGTAACTGTGAAAC
Found at i:44479 original size:63 final size:63
Alignment explanation
Indices: 44412--44535 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 63
44402 GTTGTAATTG
* ** ** *
44412 TTGCTGTTGTTGTGGTTGCAGCTGTTGAAGCTGATGCTGTTGCTGCATCTGTGGCAGCTGCGA
1 TTGCTGCTGTTGCAGTTGCAGAAGTTGAAGCTGATGCTGCTGCTGCATCTGTGGCAGCTGCGA
* * * *
44475 TTGCTGCTGTTGCATTTGCGGAAGTTGAGGCTGCTGCTGCTGCTGCATCTGTGGCAGCTGC
1 TTGCTGCTGTTGCAGTTGCAGAAGTTGAAGCTGATGCTGCTGCTGCATCTGTGGCAGCTGC
44536 TGCTGCTGCA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.10, C:0.20, G:0.35, T:0.35
Consensus pattern (63 bp):
TTGCTGCTGTTGCAGTTGCAGAAGTTGAAGCTGATGCTGCTGCTGCATCTGTGGCAGCTGCGA
Found at i:44480 original size:30 final size:29
Alignment explanation
Indices: 44446--44618 Score: 140
Period size: 30 Copynumber: 5.9 Consensus size: 29
44436 TTGAAGCTGA
* * *
44446 TGCTGTTGCTGCATCTGTGGCAGCTGCGAT
1 TGCTGCTGCTGCATCTGTGGAAGCTGCG-C
* * * *
44476 TGCTGCTGTTGCATTTGCGGAAGTTGAGGCTGC
1 TGCTGCTGCTGCATCTGTGGAAGCT---GC-GC
*
44509 TGCTGCTGCTGCATCTGT-G--GC--AGC
1 TGCTGCTGCTGCATCTGTGGAAGCTGCGC
*
44533 TGCTGCTGCTGCATCTGTGAAAGCTGCTGC
1 TGCTGCTGCTGCATCTGTGGAAGCTGC-GC
*
44563 TGCTGCTGTTGCATCTGTGGAAGCTGCGGC
1 TGCTGCTGCTGCATCTGTGGAAGCTGC-GC
* *
44593 TGCTGCTGTTGCATCTGTGGTAGCTG
1 TGCTGCTGCTGCATCTGTGGAAGCTG
44619 TGGTTGCATT
Statistics
Matches: 115, Mismatches: 18, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
24 20 0.17
27 2 0.02
30 74 0.64
32 1 0.01
33 17 0.15
34 1 0.01
ACGTcount: A:0.10, C:0.23, G:0.34, T:0.32
Consensus pattern (29 bp):
TGCTGCTGCTGCATCTGTGGAAGCTGCGC
Found at i:44589 original size:24 final size:24
Alignment explanation
Indices: 44507--44568 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
44497 AGTTGAGGCT
**
44507 GCTGCTGCTGCTGCATCTGTGGCA
1 GCTGCTGCTGCTGCATCTGTGAAA
44531 GCTGCTGCTGCTGCATCTGTGAAA
1 GCTGCTGCTGCTGCATCTGTGAAA
44555 GCTGCTGCTGCTGC
1 GCTGCTGCTGCTGC
44569 TGTTGCATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.10, C:0.29, G:0.32, T:0.29
Consensus pattern (24 bp):
GCTGCTGCTGCTGCATCTGTGAAA
Found at i:44594 original size:24 final size:24
Alignment explanation
Indices: 44507--44598 Score: 94
Period size: 24 Copynumber: 3.6 Consensus size: 24
44497 AGTTGAGGCT
* *
44507 GCTGCTGCTGCTGCATCTGTGGCA
1 GCTGCGGCTGCTGCATCTGTGGAA
* *
44531 GCTGCTGCTGCTGCATCTGTGAAA
1 GCTGCGGCTGCTGCATCTGTGGAA
44555 GCTGCTGCTGCTGCTGTTGCATCTGTGGAA
1 GCTGC-G--GCTGC---TGCATCTGTGGAA
44585 GCTGCGGCTGCTGC
1 GCTGCGGCTGCTGC
44599 TGTTGCATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
24 30 0.52
27 10 0.17
29 1 0.02
30 17 0.29
ACGTcount: A:0.10, C:0.27, G:0.34, T:0.29
Consensus pattern (24 bp):
GCTGCGGCTGCTGCATCTGTGGAA
Found at i:45215 original size:27 final size:27
Alignment explanation
Indices: 45151--45217 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
45141 AAGATTAATA
* ** *
45151 ACATAAGAACTTTGAAAGAATACTGTT
1 ACATAAGAACTTTGAAAGAAGACAATC
*
45178 ATCA-AAAAACTTTGAAAGAAGACAATC
1 A-CATAAGAACTTTGAAAGAAGACAATC
45205 ACATAAGAACTTT
1 ACATAAGAACTTT
45218 TGTATTGCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
26 2 0.06
27 28 0.88
28 2 0.06
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (27 bp):
ACATAAGAACTTTGAAAGAAGACAATC
Found at i:47604 original size:13 final size:13
Alignment explanation
Indices: 47586--47610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47576 TAGTTCCCTG
47586 CTTTTTTTTTTTT
1 CTTTTTTTTTTTT
47599 CTTTTTTTTTTT
1 CTTTTTTTTTTT
47611 GGCTAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:50792 original size:15 final size:15
Alignment explanation
Indices: 50767--50799 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
50757 TCCGGGGGAC
50767 TTTAGTTTTATTTTAT
1 TTTAGTTTTA-TTTAT
50783 TTTA-TTTTATTTAT
1 TTTAGTTTTATTTAT
50797 TTT
1 TTT
50800 CTATTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTAGTTTTATTTAT
Found at i:50797 original size:4 final size:5
Alignment explanation
Indices: 50767--50799 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
50757 TCCGGGGGAC
50767 TTTAGT TTTAT TTTAT TTTAT TTTA- TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
50800 CTATTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:53286 original size:42 final size:43
Alignment explanation
Indices: 53207--53293 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 43
53197 CAGCTGGTAG
*
53207 GCACTCACATTCTCACATCACAGCTTCAATTACATGAATTTTGT
1 GCACTCACATTCTCACAT-ACAGCTTCAATTACATGAATTCTGT
* **
53251 GCACTGACATTCTCACAT-CAGCTTTGATTACATGAATTCTGT
1 GCACTCACATTCTCACATACAGCTTCAATTACATGAATTCTGT
53293 G
1 G
53294 TTTGTAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 22 0.56
44 17 0.44
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (43 bp):
GCACTCACATTCTCACATACAGCTTCAATTACATGAATTCTGT
Found at i:54715 original size:43 final size:42
Alignment explanation
Indices: 54662--54744 Score: 157
Period size: 43 Copynumber: 2.0 Consensus size: 42
54652 TAAATTTATT
54662 TAAATTTATTTATAAAATGGATTCATTAGCCAAATTGTAAAA
1 TAAATTTATTTATAAAATGGATTCATTAGCCAAATTGTAAAA
54704 TAAATTTTATTTATAAAATGGATTCATTAGCCAAATTGTAA
1 TAAA-TTTATTTATAAAATGGATTCATTAGCCAAATTGTAA
54745 GTGACACCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 4 0.10
43 36 0.90
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (42 bp):
TAAATTTATTTATAAAATGGATTCATTAGCCAAATTGTAAAA
Found at i:61341 original size:12 final size:12
Alignment explanation
Indices: 61326--61361 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
61316 TATTTTCTCA
61326 TTTATTTTCATT
1 TTTATTTTCATT
61338 TTTATTTTCATT
1 TTTATTTTCATT
*
61350 TTCATTTTCATT
1 TTTATTTTCATT
61362 GTTGACGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATTTTCATT
Found at i:61344 original size:6 final size:6
Alignment explanation
Indices: 61329--61361 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
61319 TTTCTCATTT
*
61329 ATTTTC ATTTTT ATTTTC ATTTTC ATTTTC ATT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATT
61362 GTTGACGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTC
Found at i:64502 original size:2 final size:2
Alignment explanation
Indices: 64497--64529 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64487 AGAGTTAGTG
64497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64530 GTAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.