Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010462.1 Corchorus capsularis cultivar CVL-1 contig10483, 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: 35259
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3570 original size:11 final size:11
Alignment explanation
Indices: 3554--3578 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3544 TAAACTTTTT
3554 TATAATCCAAA
1 TATAATCCAAA
3565 TATAATCCAAA
1 TATAATCCAAA
3576 TAT
1 TAT
3579 GCTAGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (11 bp):
TATAATCCAAA
Found at i:4253 original size:20 final size:20
Alignment explanation
Indices: 4225--4268 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4215 GTTCCGTTGT
*
4225 TTAATATCTAACACAACGAC
1 TTAAAATCTAACACAACGAC
*
4245 TTAAAATCTAACGCAACGAC
1 TTAAAATCTAACACAACGAC
4265 TTAA
1 TTAA
4269 GTATCCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (20 bp):
TTAAAATCTAACACAACGAC
Found at i:4744 original size:202 final size:205
Alignment explanation
Indices: 4398--4797 Score: 662
Period size: 202 Copynumber: 2.0 Consensus size: 205
4388 TTACAACCAC
* * *
4398 TTTAATTGGTTACGGATAACTTTTAAAAACGATTAAATGTCGTTTCCAAAACACTTACATAACGA
1 TTTAATTGGTTACGAATAACTTTTAAAAACGACTAAAAGTCGTTTCCAAAACACTTACATAACGA
*
4463 CCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAAACCCTTACGCAAC
66 CCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAAACCCTTACACAAC
* *
4528 G--A-CGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGTGTAATAATTTT
131 GACATCGTTGTTGTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCGTAATAATTTT
4590 CGCAATCACT
196 CGCAATCACT
*
4600 TTTAATTGGTTACGAATAACTTTTAAAAATGACTAAAAGTCGTTTCCAAAACACTTACATAACGA
1 TTTAATTGGTTACGAATAACTTTTAAAAACGACTAAAAGTCGTTTCCAAAACACTTACATAACGA
*
4665 CCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAAACCCTTACACAAT
66 CCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAAACCCTTACACAAC
**
4730 GACATCGTTTTGGTTGTGGTTGTGAAATCTTTTACGTAGCAGTATTTGATTGGTTGCGTAATAAT
131 GACATCG--TT-GTTGTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCGTAATAAT
4795 TTT
193 TTT
4798 TATATTGATA
Statistics
Matches: 182, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
202 125 0.69
204 1 0.01
205 2 0.01
207 2 0.01
208 52 0.29
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (205 bp):
TTTAATTGGTTACGAATAACTTTTAAAAACGACTAAAAGTCGTTTCCAAAACACTTACATAACGA
CCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGCGAAAACCCTTACACAAC
GACATCGTTGTTGTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCGTAATAATTTT
CGCAATCACT
Found at i:6346 original size:14 final size:14
Alignment explanation
Indices: 6327--6358 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
6317 CCTTGCAAGC
6327 CCCATATATACATG
1 CCCATATATACATG
6341 CCCATATATACATG
1 CCCATATATACATG
6355 CCCA
1 CCCA
6359 AGTAATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.25
Consensus pattern (14 bp):
CCCATATATACATG
Found at i:8414 original size:31 final size:31
Alignment explanation
Indices: 8379--8447 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
8369 AAAAAACTGT
8379 AAAAGTTAAATAAGGATATAATAGGCATTTC
1 AAAAGTTAAATAAGGATATAATAGGCATTTC
*
8410 AAAAGTTAAATAAGGATATAATAGGCGTTTC
1 AAAAGTTAAATAAGGATATAATAGGCATTTC
8441 AAAAGTT
1 AAAAGTT
8448 TCTCAAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (31 bp):
AAAAGTTAAATAAGGATATAATAGGCATTTC
Found at i:8542 original size:15 final size:15
Alignment explanation
Indices: 8503--8554 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
8493 TTGTGATTAT
*
8503 TATATCATTATCATCA
1 TATATAATTATCAT-A
*
8519 TCAT-T-ATTATTATA
1 T-ATATAATTATCATA
8533 TATATAATTATCATA
1 TATATAATTATCATA
8548 TATATAA
1 TATATAA
8555 AATAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 2 0.06
14 3 0.10
15 22 0.71
16 2 0.06
17 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATAATTATCATA
Found at i:8564 original size:21 final size:19
Alignment explanation
Indices: 8536--8604 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 19
8526 TATTATATAT
8536 ATAA-TTATCATATATATAAA
1 ATAATTTAT-ATA-ATATAAA
8556 ATAATTTATATAATATTAAA
1 ATAATTTATATAATA-TAAA
* *
8576 GAAAATTTATTATCAATATATA
1 -ATAATTTA-TAT-AATATAAA
8598 ATAATTT
1 ATAATTT
8605 TAATGCTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.07
20 11 0.27
21 17 0.41
22 6 0.15
23 4 0.10
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (19 bp):
ATAATTTATATAATATAAA
Found at i:8593 original size:23 final size:23
Alignment explanation
Indices: 8539--8598 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
8529 TATATATATA
*
8539 ATTATCATATATATAAAATAATTT
1 ATTATCA-ATATATAAAAAAATTT
8563 A-TAT-AATAT-TAAAGAAAATTT
1 ATTATCAATATATAAA-AAAATTT
8584 ATTATCAATATATAA
1 ATTATCAATATATAA
8599 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.13
21 11 0.35
22 4 0.13
23 8 0.26
24 4 0.13
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTATCAATATATAAAAAAATTT
Found at i:9894 original size:132 final size:132
Alignment explanation
Indices: 9686--10069 Score: 592
Period size: 132 Copynumber: 2.9 Consensus size: 132
9676 ATTTATTGTT
* * *
9686 GCGACTTAATTTGTGGATTCAAAAGTAATTATGTTTTTTTTTGTAGCGACTTTCAAGGTTGCTGT
1 GCGACTTAATTTGTGGCTTCAAAAGTAATTATG---TTTTTTGTAGCGACTTTCAAGGTCGCTGC
*
9751 GAAAATCAATTTGTAAAATATATAAAGCAATGACTAACAATAGTCGTTGCGAAAAGAGTAAGATT
63 GAAAATCAATTTGTAAAATATATAAAGCAACGACTAACAATAGTCGTTGCGAAAAGAGTAAGATT
9816 TCGCA
128 TCGCA
* * * *
9821 GCGACTTAATGTGTGGCTTCAAAAGTACTGATGTTTTTTGTTGCGACTTTCAAGGTCGCTGCGAA
1 GCGACTTAATTTGTGGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAA
* *
9886 AATCAATTTATAAAATATATTAAGCAACGACTAACAATAGTCGTTGCGAAAAGAGTAAGATTTCG
66 AATCAATTTGTAAAATATATAAAGCAACGACTAACAATAGTCGTTGCGAAAAGAGTAAGATTTCG
9951 CA
131 CA
9953 GCGACTTAATTTGTGGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAA
1 GCGACTTAATTTGTGGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAA
* * *
10018 AATCAATTTGTAAAATATATTAAA-CAACTACTAGCAGA-AGTCGTTGTGAAAA
66 AATCAATTTGTAAAATATA-TAAAGCAACGACTAACA-ATAGTCGTTGCGAAAA
10070 TACTATGAAT
Statistics
Matches: 228, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
132 195 0.86
133 4 0.02
135 29 0.13
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (132 bp):
GCGACTTAATTTGTGGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAA
AATCAATTTGTAAAATATATAAAGCAACGACTAACAATAGTCGTTGCGAAAAGAGTAAGATTTCG
CA
Found at i:17232 original size:22 final size:22
Alignment explanation
Indices: 17207--17763 Score: 201
Period size: 22 Copynumber: 25.5 Consensus size: 22
17197 ATGATCCCAT
17207 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * ** *
17229 TATGTAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
17251 TATGGAATGTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
17273 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* * * *
17294 TATAAAATTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
17316 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
*
17338 TATAAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
17360 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
17383 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
17404 ATATGATATATTGATAACC-ACAT
1 -TATGAAATTTTGATAACCTTC-C
* * *
17427 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
17448 ATATG-AATTGTT-AGTAATCACATT-C
1 -TATGAAATT-TTGA-TAA-C-C-TTCC
* *
17473 --TGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
17493 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
17515 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
17538 TAT-AAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
17560 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
17582 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
*
17599 TA-CAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** *
17619 ATATGATTTTTTGATAACC-TCAT
1 -TATGAAATTTTGATAACCTTC-C
* * *
17642 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* ***
17664 TATGAAATTTTGATCTA-CAAAC
1 TATGAAATTTTGAT-AACCTTCC
* *
17686 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
17708 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
17730 AATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
17752 TATGAAATTTTG
1 TATGAAATTTTG
17764 GTATCCTCCC
Statistics
Matches: 389, Mismatches: 108, Indels: 76
0.68 0.19 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 3 0.01
21 28 0.07
22 292 0.75
23 48 0.12
24 3 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:17399 original size:45 final size:44
Alignment explanation
Indices: 17347--17454 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 44
17337 ATATAAAATT
* *
17347 TTGATAACTTCCCA-ATGAAATTTTGATAACCAACACTATGAGATG
1 TTGATAACCT-CCATATGAAATATTGATAACC-ACACTATGAGATG
* * *
17392 TTGATAACCTCCATATGATATATTGATAACCACATTATGAAAAT-
1 TTGATAACCTCCATATGAAATATTGATAACCACACTATG-AGATG
* *
17436 TTAAAAACCTCCATATGAA
1 TTGATAACCTCCATATGAA
17455 TTGTTAGTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
44 26 0.49
45 27 0.51
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (44 bp):
TTGATAACCTCCATATGAAATATTGATAACCACACTATGAGATG
Found at i:17571 original size:45 final size:46
Alignment explanation
Indices: 17475--17597 Score: 139
Period size: 45 Copynumber: 2.8 Consensus size: 46
17465 TCACATTCTG
* * * *
17475 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATTTTGATAAACCTCCCTATA
17519 AAATTTTGATAAATCTTCCTAT-AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
* * *
17564 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAA
17598 CTACAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
44 25 0.37
45 42 0.62
46 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (46 bp):
AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCTCCCTATA
Found at i:18518 original size:22 final size:22
Alignment explanation
Indices: 18493--18739 Score: 159
Period size: 22 Copynumber: 11.3 Consensus size: 22
18483 AATCACATTT
*
18493 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
18515 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
18537 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
*
18559 TGAAATTTTGATAATCC-CATTA
1 TGAAATTTTGATAA-CCTCTTTA
* *
18581 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
18603 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
* *
18625 TGAAAGTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
18647 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
18671 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
18693 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
18713 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
18733 TGAAATT
1 TGAAATT
18740 GAGACTTTTA
Statistics
Matches: 173, Mismatches: 40, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.01
20 16 0.09
21 27 0.16
22 107 0.62
23 4 0.02
24 5 0.03
25 12 0.07
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:18561 original size:44 final size:43
Alignment explanation
Indices: 18468--18617 Score: 124
Period size: 44 Copynumber: 3.4 Consensus size: 43
18458 AGAAATACCA
* * * *
18468 CTATGAAATTTTTG-TAATCACATTTTGAAAA-TTTGATAACCTCT
1 CTATGAAA-TTTTGATAA-CCCATTAT-AAAATTTTGATAACCCCG
* * * * *
18512 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAACC-CATTATAAAATTTTGATAACCCCG
** *
18556 CTATGAAATTTTGATAATCCCATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAA-CCCATTATAAAATTTTGATAACCCCG
*
18600 CTTTGAAATTTTGATAAC
1 CTATGAAATTTTGATAAC
18618 AACACTATGA
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
43 11 0.13
44 73 0.85
45 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCCATTATAAAATTTTGATAACCCCG
Found at i:18990 original size:22 final size:22
Alignment explanation
Indices: 18964--19073 Score: 98
Period size: 22 Copynumber: 5.0 Consensus size: 22
18954 TAACCTGATC
*
18964 CTATGAAATTTTGGTAAGCACA
1 CTATGAAATTTTGGTAACCACA
*
18986 CTATGAAATTTTGGTAACCATA
1 CTATGAAATTTTGGTAACCACA
* * *
19008 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGGTAACCACA
* **
19029 CTTATGAAATTATAATAACCATC-
1 C-TATGAAATTTTGGTAACCA-CA
* *
19052 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGGTAACCACA
19074 TAGAGACAAG
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.03
22 69 0.96
23 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:19035 original size:44 final size:44
Alignment explanation
Indices: 18951--19070 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
18941 TAAGAGATTT
* * * * *
18951 TAATAACCTGATCCTATGAAATTTTGGTAAGCACAC-TATGAAATTT
1 TAATAACC--ATCTTATGAAATTTTGATAACCTC-CTTATGAAATTA
** *
18997 TGGTAACCATAC-TATGGAATTTTGATAACCTCCTTATGAAATTA
1 TAATAACCAT-CTTATGAAATTTTGATAACCTCCTTATGAAATTA
19041 TAATAACCATCTTATGAAATTTTGATAACC
1 TAATAACCATCTTATGAAATTTTGATAACC
19071 ACATAGAGAC
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
43 2 0.03
44 52 0.85
45 1 0.02
46 6 0.10
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (44 bp):
TAATAACCATCTTATGAAATTTTGATAACCTCCTTATGAAATTA
Found at i:19214 original size:6 final size:6
Alignment explanation
Indices: 19203--19228 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19193 AGTATTGTAC
19203 GTGTTA GTGTTA GTGTTA GTGTTA GT
1 GTGTTA GTGTTA GTGTTA GTGTTA GT
19229 TTAATCTTTT
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:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
GTGTTA
Found at i:19479 original size:38 final size:35
Alignment explanation
Indices: 19422--19497 Score: 107
Period size: 38 Copynumber: 2.1 Consensus size: 35
19412 AATTTAAGAC
19422 CAAAGACAAAGCAAAATTAAATACAACGATTGGAAA
1 CAAAGACAAAGCAAAATTAAATACAACG-TTGGAAA
**
19458 CAAAGACAAAAGGCAAAATTAAATAGGACGTTGGAAA
1 CAAAGAC-AAA-GCAAAATTAAATACAACGTTGGAAA
19495 CAA
1 CAA
19498 GAAGGCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 7 0.19
37 13 0.36
38 16 0.44
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (35 bp):
CAAAGACAAAGCAAAATTAAATACAACGTTGGAAA
Found at i:20907 original size:27 final size:27
Alignment explanation
Indices: 20868--20924 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
20858 ATGATACGAT
* ** *
20868 AATACTTAGTAATACGATAGATTCAAA
1 AATACTTAATAATAAAATAGATTAAAA
20895 AATACTTAATAATAAAATAGATTAAAA
1 AATACTTAATAATAAAATAGATTAAAA
20922 AAT
1 AAT
20925 GTCTTCTTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (27 bp):
AATACTTAATAATAAAATAGATTAAAA
Found at i:22543 original size:11 final size:12
Alignment explanation
Indices: 22491--22547 Score: 78
Period size: 12 Copynumber: 4.6 Consensus size: 12
22481 GGGCCGTAGC
22491 TTTTAAATTTCT
1 TTTTAAATTTCT
* *
22503 TTTTAATCTTATGT
1 TTTTAA-ATT-TCT
22517 TTTTAAATTTCT
1 TTTTAAATTTCT
22529 TTTTAAATTTCT
1 TTTTAAATTTCT
22541 TTTTAAA
1 TTTTAAA
22548 AATTTTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 27 0.69
13 4 0.10
14 8 0.21
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (12 bp):
TTTTAAATTTCT
Found at i:23111 original size:17 final size:17
Alignment explanation
Indices: 23089--23121 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23079 CTTTTTTTCT
*
23089 TCGGTTTGGTGGTTTGG
1 TCGGTTTGGCGGTTTGG
23106 TCGGTTTGGCGGTTTG
1 TCGGTTTGGCGGTTTG
23122 AACCGCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.45, T:0.45
Consensus pattern (17 bp):
TCGGTTTGGCGGTTTGG
Found at i:23989 original size:16 final size:16
Alignment explanation
Indices: 23945--24020 Score: 75
Period size: 16 Copynumber: 4.8 Consensus size: 16
23935 TGGGCTTGAG
*
23945 TCGGGTTCGGGTTGGAT
1 TCGGGTTCGGGTT-AAT
* *
23962 TTGGG-TCAGGTTAAT
1 TCGGGTTCGGGTTAAT
23977 TCGGGTTCGGGTTAAT
1 TCGGGTTCGGGTTAAT
* * *
23993 TTGAG-TCAGGTTAAT
1 TCGGGTTCGGGTTAAT
24008 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
24021 CTGCTTGGGT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
15 18 0.39
16 24 0.52
17 4 0.09
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.38
Consensus pattern (16 bp):
TCGGGTTCGGGTTAAT
Found at i:24001 original size:31 final size:32
Alignment explanation
Indices: 23945--24020 Score: 127
Period size: 31 Copynumber: 2.4 Consensus size: 32
23935 TGGGCTTGAG
* *
23945 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGAGTCAGGTTAAT
23977 TCGGGTTCGGGTT-AATTTGAGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGAGTCAGGTTAAT
24008 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
24021 CTGCTTGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.13, C:0.11, G:0.38, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGAGTCAGGTTAAT
Found at i:24006 original size:15 final size:15
Alignment explanation
Indices: 23960--24013 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
23950 TTCGGGTTGG
23960 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
* *
23975 ATTCGGGTTCGGGTTA
1 ATTTGGG-TCAGGTTA
*
23991 ATTTGAGTCAGGTTA
1 ATTTGGGTCAGGTTA
*
24006 ATTCGGGT
1 ATTTGGGT
24014 TCGGGTTCTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.39
Consensus pattern (15 bp):
ATTTGGGTCAGGTTA
Found at i:24189 original size:16 final size:16
Alignment explanation
Indices: 24168--24254 Score: 93
Period size: 16 Copynumber: 5.4 Consensus size: 16
24158 TTTTCATAAA
*
24168 TTTTCGGATTCGGGTT
1 TTTTCGGATTTGGGTT
* *
24184 TTTTCGGATTTGAGCT
1 TTTTCGGATTTGGGTT
*
24200 TTTTCGGGTTTGGGTT
1 TTTTCGGATTTGGGTT
* *
24216 TTTTCGGATTTGAGCT
1 TTTTCGGATTTGGGTT
* **
24232 TTTTCGGGTTCAGGTT
1 TTTTCGGATTTGGGTT
24248 TTTTCGG
1 TTTTCGG
24255 GTTCAAGTTC
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (16 bp):
TTTTCGGATTTGGGTT
Found at i:24215 original size:32 final size:32
Alignment explanation
Indices: 24168--24254 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
24158 TTTTCATAAA
*
24168 TTTTCGGATTCGGGTTTTTTCGGATTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGATTTGAGCT
*
24200 TTTTCGGGTTTGGGTTTTTTCGGATTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGATTTGAGCT
*
24232 TTTTCGGGTTCAGGTTTTTTCGG
1 TTTTCGGGTTCGGGTTTTTTCGG
24255 GTTCAAGTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGATTTGAGCT
Found at i:27580 original size:21 final size:21
Alignment explanation
Indices: 27556--27627 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
27546 TCTCAATTTA
27556 TTGTAATTATGAGTATTATCT
1 TTGTAATTATGAGTATTATCT
* * *
27577 TTGTAATT-TCA-TTTTCAATTT
1 TTGTAATTATGAGTATT--ATCT
27598 ATTGTAATTATGAGTATTATCT
1 -TTGTAATTATGAGTATTATCT
27620 TTGTAATT
1 TTGTAATT
27628 TCATTTTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.08
20 2 0.05
21 19 0.47
22 11 0.28
23 2 0.05
24 3 0.08
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (21 bp):
TTGTAATTATGAGTATTATCT
Found at i:27609 original size:43 final size:43
Alignment explanation
Indices: 27548--27636 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
27538 AGCATTCTTC
27548 TCAATTTATTGTAATTATGAGTATTATCTTTGTAATTTCATTT
1 TCAATTTATTGTAATTATGAGTATTATCTTTGTAATTTCATTT
27591 TCAATTTATTGTAATTATGAGTATTATCTTTGTAATTTCATTT
1 TCAATTTATTGTAATTATGAGTATTATCTTTGTAATTTCATTT
27634 TCA
1 TCA
27637 TAAATGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (43 bp):
TCAATTTATTGTAATTATGAGTATTATCTTTGTAATTTCATTT
Done.