Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013790.1 Corchorus capsularis cultivar CVL-1 contig13811, 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: 40798
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:3418 original size:26 final size:27
Alignment explanation
Indices: 3369--3420 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3359 TAGATTTAGA
*
3369 TTTAGATTTAATTTGCTTTGCTTTATT
1 TTTAGATTTAATTTGCTTTCCTTTATT
3396 TTTAG-TTTAATATTG-TTTCCTTTAT
1 TTTAGATTTAAT-TTGCTTTCCTTTAT
3421 AATTGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.63
Consensus pattern (27 bp):
TTTAGATTTAATTTGCTTTCCTTTATT
Found at i:4373 original size:10 final size:10
Alignment explanation
Indices: 4358--4403 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
4348 TGGCTTATTG
4358 TCTTCAATGC
1 TCTTCAATGC
*
4368 TCTTCAATTGA
1 TCTTCAA-TGC
*
4379 TCTTCAATGG
1 TCTTCAATGC
4389 TCTTCAA-GC
1 TCTTCAATGC
4398 -CTTCAA
1 TCTTCAA
4404 GATGATGTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 6 0.19
9 1 0.03
10 16 0.50
11 9 0.28
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (10 bp):
TCTTCAATGC
Found at i:4382 original size:21 final size:20
Alignment explanation
Indices: 4354--4395 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
4344 TCCTTGGCTT
4354 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCTCTTCA
*
4374 ATTGATCTTCAATGGTCTTCA
1 ATTG-TCTTCAATGCTCTTCA
4395 A
1 A
4396 GCCTTCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (20 bp):
ATTGTCTTCAATGCTCTTCA
Found at i:6196 original size:22 final size:22
Alignment explanation
Indices: 6154--6197 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6144 TATTCATATG
*
6154 AAATTATGATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
6176 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
6198 TTTTATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:6237 original size:22 final size:22
Alignment explanation
Indices: 6212--7408 Score: 247
Period size: 22 Copynumber: 54.5 Consensus size: 22
6202 ATGATCCCAT
6212 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
6234 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
6256 TATGGAATTTCGATAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** * *
6278 TAT-AAATTTTTTTAACATTCT
1 TATGAAATTTTGATAACCTTCC
* *
6299 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
6321 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
* *
6343 TATGAAAATTTGATAA-TTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
6365 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
6388 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** * * *
6409 ATATGGTATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
6432 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
6453 ATATG-AATTGTT-AGTAATCATAC
1 -TATGAAATT-TTGA-TAACCTTCC
* * * *
6476 TCTGAAATTTTAATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
6498 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
6520 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
6543 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
6566 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
6588 TATGAAATCTTGA-AA----AC
1 TATGAAATTTTGATAACCTTCC
*
6605 TA-CAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** **
6625 -ATGATTTTTTGATAACCTTAT
1 TATGAAATTTTGATAACCTTCC
* * *
6646 TATGAAATTTTGTTAATCTGCC
1 TATGAAATTTTGATAACCTTCC
* * *
6668 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
6690 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
6712 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
6734 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
*
6755 -ATGAAATTTTGATTA--TTCC
1 TATGAAATTTTGATAACCTTCC
* * **
6774 ATAATAAAAGTTTTTGA-AAACTAAAC
1 -T-ATGAAA--TTTTGATAACCT-TCC
*
6800 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
*
6821 -ATGAAATTTTGATTA--TTCC
1 TATGAAATTTTGATAACCTTCC
* * *
6840 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
6864 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
6881 TATGAAATTTTTG-TAATCACATT--
1 TATGAAA-TTTTGATAA-C-C-TTCC
* *
6904 T-TGAAAATTTGATAACC-TCTT
1 TATGAAATTTTGATAACCTTC-C
*
6925 TATGAAATTTTCATAATCTCTT--
1 TATGAAATTTTGATAA-C-CTTCC
* * *
6947 TATAAAATTTTG-TCGACC-CCTC
1 TATGAAATTTTGAT-AACCTTC-C
* *
6969 TATGAAATTCTGATAATCACAT--
1 TATGAAATTTTGATAA-C-CTTCC
* *
6991 TATGTAATTTTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
* ** *
7013 TTTGAAATTTTGATAACAATAC
1 TATGAAATTTTGATAACCTTCC
* *
7035 TATGAAATTTTGATAATCAGAAATACCAC
1 TATGAAATTTTGATAA-C----CT-TC-C
*
7064 TATGAAATTTTTATAATCACTT--
1 TATGAAATTTTGATAA-C-CTTCC
* * * *
7086 TTTCAAAATTTGATAACC-TCTT
1 TATGAAATTTTGATAACCTTC-C
* * *
7108 TATGAAATTTTGTTGACC-CCTC
1 TATGAAATTTTGATAACCTTC-C
* *
7130 TATGAAATTCTGATAATCACAT--
1 TATGAAATTTTGATAA-C-CTTCC
* *
7152 TATGTAATTTTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
* *
7174 TTTGAAATTTTGATAA--TAACAC
1 TATGAAATTTTGATAACCT-TC-C
*
7196 TATGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCTTCC
*
7218 TAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAA-CC-TTC-C
** *
7242 TATGAAATTTCAATAACC-ACTC
1 TATGAAATTTTGATAACCTTC-C
*
7264 TATGAGA-TTTGATAACCTT-C
1 TATGAAATTTTGATAACCTTCC
* * * *
7284 TATCAAATTTTGGTACTCCTT-G
1 TATGAAATTTTGATA-ACCTTCC
* *
7306 TGAATTGAGACTTTT-ATAACCTTCA
1 T--A-TGA-AATTTTGATAACCTTCC
*
7331 TATGAAATTTTGATAACC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
7353 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
7375 GATGAAATATT-AGTAACC-TCC
1 TATGAAATTTTGA-TAACCTTCC
7396 TAATGAAATTTTG
1 T-ATGAAATTTTG
7409 TTAGCCACAC
Statistics
Matches: 848, Mismatches: 214, Indels: 225
0.66 0.17 0.17
Matches are distributed among these distances:
16 8 0.01
17 14 0.02
18 3 0.00
19 11 0.01
20 51 0.06
21 79 0.09
22 517 0.61
23 86 0.10
24 33 0.04
25 19 0.02
26 8 0.01
27 1 0.00
29 18 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:6550 original size:23 final size:23
Alignment explanation
Indices: 6497--6581 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
6487 AATAATCACA
* * *
6497 CTATGAAATTGTGAT-AACCTCG
1 CTATAAAATTTTGATAAACCTCC
* * *
6519 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAACCTCC
6542 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
6565 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
6582 CTTTCTTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 14 0.25
23 41 0.75
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:6760 original size:20 final size:20
Alignment explanation
Indices: 6735--6833 Score: 67
Period size: 20 Copynumber: 4.7 Consensus size: 20
6725 AAACTAAACT
6735 ATGAAATTTTGATATCCTCC
1 ATGAAATTTTGATATCCTCC
*
6755 ATGAAATTTTGATTATTCCAT-A
1 ATGAAATTTTGA-TA-TCC-TCC
* ** *
6777 ATAAAAGTTTTTGA-AAACTAAACT
1 ATGAAA--TTTTGATATCCT---CC
6801 ATGAAATTTTGATATCCTCC
1 ATGAAATTTTGATATCCTCC
6821 ATGAAATTTTGAT
1 ATGAAATTTTGAT
6834 TATTCCATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
20 27 0.45
21 3 0.05
22 15 0.25
23 4 0.07
24 11 0.18
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (20 bp):
ATGAAATTTTGATATCCTCC
Found at i:7423 original size:22 final size:22
Alignment explanation
Indices: 7061--7676 Score: 138
Period size: 22 Copynumber: 28.1 Consensus size: 22
7051 TCAGAAATAC
* *
7061 CACTATGAAATTTTTATAATCA
1 CACTATGAAATTTTGATAACCA
** * * * *
7083 CTTTTTCAAAATTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** * * *
7105 CTTTATGAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAACCA
* * *
7127 CTCTATGAAATTCTGATAATCA
1 CACTATGAAATTTTGATAACCA
* * *
7149 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
** * **
7171 CGTTTTGAAATTTTGATAATAA
1 CACTATGAAATTTTGATAACCA
**
7193 CACTATGAAATTTTGATAATCTT
1 CACTATGAAATTTTGATAA-CCA
7216 C-CTAT-AAATTTTGATAATCCGA
1 CACTATGAAATTTTGATAA-CC-A
* **
7238 TCTCTATGAAATTTCAATAACCA
1 -CACTATGAAATTTTGATAACCA
* *
7261 CTCTATGAGA-TTTGATAACC-
1 CACTATGAAATTTTGATAACCA
** * *
7281 TTCTATCAAATTTTGGT-ACTC-
1 CACTATGAAATTTTGATAAC-CA
** * *
7302 CTTGTGAATTGAGACTTTT-ATAACCTT
1 C-ACT--A-TGA-AATTTTGATAACC-A
7329 CA-TATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
* *
7350 CACTATAAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * * *
7372 CCCGATGAAATATT-AGTAACCT
1 CACTATGAAATTTTGA-TAACCA
* *
7394 C-CTAATGAAATTTTGTTAGCCA
1 CACT-ATGAAATTTTGATAACCA
*
7416 CACTATGAAATTCTT-ATAACCT
1 CACTATGAAATT-TTGATAACCA
* * * * *
7438 CGCTGTGACATTTCGATAA--T
1 CACTATGAAATTTTGATAACCA
* *
7458 CTCTTTGATAACCTTTCT-ATAA--A
1 CACTATGA-AA--TTT-TGATAACCA
* * *
7481 -ATTGTGATAA---T--CAACCA
1 CACTATGA-AATTTTGATAACCA
* **
7498 CCCTATGAAATTTCAATAACCA
1 CACTATGAAATTTTGATAACCA
* *
7520 -ACCTAAGAAATTTTAATAACCTA
1 CA-CTATGAAATTTTGATAACC-A
*
7543 -ATCCTATATGAAATTTTGGTAACCA
1 CA--C--TATGAAATTTTGATAACCA
**
7568 CACTATGAAATTTTGATAACTTT
1 CACTATGAAATTTTGATAAC-CA
*
7591 CA-TATGAAATTTTGGTAACCA
1 CACTATGAAATTTTGATAACCA
*
7612 CACTATGGAATTTTGATAA-C-
1 CACTATGAAATTTTGATAACCA
* * *
7632 CTC-ATGAAATTATAATAACCA
1 CACTATGAAATTTTGATAACCA
*
7653 TC-TTATGAAATTTTGATAACCA
1 -CACTATGAAATTTTGATAACCA
7675 CA
1 CA
7677 TAGAGACAAG
Statistics
Matches: 436, Mismatches: 110, Indels: 96
0.68 0.17 0.15
Matches are distributed among these distances:
15 2 0.00
16 1 0.00
17 3 0.01
18 4 0.01
19 12 0.03
20 19 0.04
21 43 0.10
22 283 0.65
23 19 0.04
24 10 0.02
25 16 0.04
26 23 0.05
27 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:7610 original size:44 final size:43
Alignment explanation
Indices: 7548--7678 Score: 160
Period size: 44 Copynumber: 3.1 Consensus size: 43
7538 ACCTAATCCT
*
7548 ATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTTTC
1 ATATGAAATTTTGGTAACCACACTATGAAATTTTGATAAC-CTC
*
7592 ATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTC
1 ATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC
* ** * *
7635 --ATGAAATTATAATAACCATC-TTATGAAATTTTGATAACCAC
1 ATATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACCTC
7676 ATA
1 ATA
7679 GAGACAAGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
41 33 0.43
42 1 0.01
43 3 0.04
44 39 0.51
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.36
Consensus pattern (43 bp):
ATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTC
Found at i:7651 original size:41 final size:42
Alignment explanation
Indices: 7562--7673 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 42
7552 GAAATTTTGG
* * **
7562 TAACCACACTATGAAATTTTGATAACTTTCATATGAAATTTTGG
1 TAACCACACTATGAAATTTTGATAAC-CTCA-ATGAAATTATAA
*
7606 TAACCACACTATGGAATTTTGATAACCTC-ATGAAATTATAA
1 TAACCACACTATGAAATTTTGATAACCTCAATGAAATTATAA
*
7647 TAACCATC-TTATGAAATTTTGATAACC
1 TAACCA-CACTATGAAATTTTGATAACC
7674 ACATAGAGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
41 32 0.53
42 1 0.02
43 2 0.03
44 25 0.42
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (42 bp):
TAACCACACTATGAAATTTTGATAACCTCAATGAAATTATAA
Found at i:9782 original size:3 final size:3
Alignment explanation
Indices: 9774--9798 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9764 CCATTTCCCC
9774 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
9799 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12170 original size:11 final size:11
Alignment explanation
Indices: 12154--12178 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12144 TGTGAATACC
12154 CAAGGTTTCCT
1 CAAGGTTTCCT
12165 CAAGGTTTCCT
1 CAAGGTTTCCT
12176 CAA
1 CAA
12179 TGCTGATGCT
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:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (11 bp):
CAAGGTTTCCT
Found at i:19706 original size:4 final size:4
Alignment explanation
Indices: 19697--19722 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19687 GAGAAGAGAA
19697 GAGG GAGG GAGG GAGG GAGG GAGG GA
1 GAGG GAGG GAGG GAGG GAGG GAGG GA
19723 TAGGGCGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:19832 original size:7 final size:7
Alignment explanation
Indices: 19799--19824 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19789 CGTGTTCCTC
19799 TTTTTCT
1 TTTTTCT
19806 TTTTTCT
1 TTTTTCT
19813 TTTTTCT
1 TTTTTCT
19820 TTTTT
1 TTTTT
19825 TTTGTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:24844 original size:58 final size:56
Alignment explanation
Indices: 24746--25225 Score: 291
Period size: 67 Copynumber: 7.9 Consensus size: 56
24736 CACTTTTGAG
* * *
24746 TACGATTTAAGGATCGTTTTAATTTTGATAAAACGATCTCGAAGGAGACGTTCGTCTTT
1 TACGATTCAAGGATCG-TTCAATTTTGATAAAACGGTCTCGAAGGAGACGTTCG--TTT
*
24805 TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAGGGAGACGTTCGTTT
1 TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAAGGAGACGTTCGTTT
*
24861 TACGATTCAAGGATCGTTCAATTTTGATAAAATGGTCTC----GA-A-------TT
1 TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAAGGAGACGTTCGTTT
* * *
24905 TACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTGAAG
1 TACGATTCAAGGATCG-TTCAATTTTGATAAAACGGTCTCGAAGGAGACGTTCG------T----
24970 TT
55 TT
* *
24972 TACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTCAAG
1 TACGATTCAAGGATCGTTCAA-TTTTGATAAAACGGTCTCGAAGGAGACGTTCG------T----
25037 TT
55 TT
* *
25039 TACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAAC
1 TACGATTCAAGGATCGTTCAA-TTTTGATAAAACGGTCTCGAAGGAGACGTTCG-------T---
25104 TT
55 TT
* *
25106 TACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTAAA
1 TACGATTCAAGGATCGTTCAA-TTTTGATAAAACGGTCTCGAAGGAGACGTTCG-------T---
25171 TT
55 TT
* * *
25173 TACGATTCAAGGATCGTTCAATTCTCGGTAAAACGGTCTCGAGGGAGACGTTC
1 TACGATTCAAGGATCGTTCAATT-TTGATAAAACGGTCTCGAAGGAGACGTTC
25226 ATCTTACTTA
Statistics
Matches: 377, Mismatches: 18, Indels: 44
0.86 0.04 0.10
Matches are distributed among these distances:
44 18 0.05
45 20 0.05
49 2 0.01
50 1 0.00
51 1 0.00
52 2 0.01
56 41 0.11
58 34 0.09
59 15 0.04
66 6 0.02
67 235 0.62
68 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (56 bp):
TACGATTCAAGGATCGTTCAATTTTGATAAAACGGTCTCGAAGGAGACGTTCGTTT
Found at i:24909 original size:44 final size:45
Alignment explanation
Indices: 24859--24946 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
24849 AGACGTTCGT
*
24859 TTTACGATTCAAGGATCG-TTCAATTTTGATAAAATGGTCTCGAA
1 TTTACGATTCAAGGATCGTTTCAATTTTGATAAAACGGTCTCGAA
* *
24903 TTTACGATTCAAGGATCGTTTTAATTTTGGTAAAACGGTCTCGA
1 TTTACGATTCAAGGATCGTTTCAATTTTGATAAAACGGTCTCGA
24947 GGGAGACGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (45 bp):
TTTACGATTCAAGGATCGTTTCAATTTTGATAAAACGGTCTCGAA
Found at i:24984 original size:67 final size:67
Alignment explanation
Indices: 24903--25265 Score: 638
Period size: 67 Copynumber: 5.4 Consensus size: 67
24893 TGGTCTCGAA
* *
24903 TTTACGATTCAAGGATCGTTTTAA-TTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTG
1 TTTACGATTCAAGGATCG-TTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTT
24967 AAG
65 AAG
*
24970 TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTCA
1 TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
25035 AG
66 AG
25037 TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
1 TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
*
25102 AC
66 AG
25104 TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
1 TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
*
25169 AA
66 AG
* * *
25171 TTTACGATTCAAGGATCGTTCAATTCTCGGTAAAACGGTCTCGAGGGAGACGTTCATCTTACTTA
1 TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
25236 AG
66 AG
25238 TTTACGATTCAAGGATCGTTCAATTTTT
1 TTTACGATTCAAGGATCGTTCAATTTTT
25266 CGTCTTACTT
Statistics
Matches: 284, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
66 4 0.01
67 280 0.99
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (67 bp):
TTTACGATTCAAGGATCGTTCAATTTTTGGTAAAACGGTCTCGAGGGAGACGTTCGTCTTACTTA
AG
Found at i:25284 original size:41 final size:41
Alignment explanation
Indices: 25227--25312 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
25217 GAGACGTTCA
25227 TCTTACTTAAGTTTACGATTCAAGGATCGTTCAATTTTTCG
1 TCTTACTTAAGTTTACGATTCAAGGATCGTTCAATTTTTCG
* *
25268 TCTTACTTAAGTTTACGATTCAAGGGTCGTTCAATTTTTGG
1 TCTTACTTAAGTTTACGATTCAAGGATCGTTCAATTTTTCG
25309 TCTT
1 TCTT
25313 CAAGGGGACG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (41 bp):
TCTTACTTAAGTTTACGATTCAAGGATCGTTCAATTTTTCG
Found at i:32732 original size:2 final size:2
Alignment explanation
Indices: 32725--32763 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
32715 GTCCTATTAC
32725 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32764 TGTTGAAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33160 original size:60 final size:58
Alignment explanation
Indices: 33012--33170 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 58
33002 GCTAATTACT
*
33012 CAAATAAGGGCCTAACGTTTTATCAAAATGCTCAAATAAGGACTCGATCTTTTAATTTGGC
1 CAAATAA-GGCCTAACG--TTATCAAAATGCTCAAATAAGGACTCGATATTTTAATTTGGC
* * * * *
33073 CAAATAATGGCCTAGCATTTGTCAAAATGCTCAAATAAGG-GTCTGGTATTTTAATTTGGC
1 CAAATAA-GGCCTAAC-GTTATCAAAATGCTCAAATAAGGACTC-GATATTTTAATTTGGC
*
33133 CAAATAAGGATCTAACGTTATCGAAAATGCTCAAATAA
1 CAAATAAGG-CCTAACGTTATC-AAAATGCTCAAATAA
33171 AGGCCTAACG
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
59 8 0.10
60 61 0.73
61 14 0.17
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.30
Consensus pattern (58 bp):
CAAATAAGGCCTAACGTTATCAAAATGCTCAAATAAGGACTCGATATTTTAATTTGGC
Found at i:33253 original size:31 final size:28
Alignment explanation
Indices: 33217--33382 Score: 86
Period size: 31 Copynumber: 5.5 Consensus size: 28
33207 TCAATACCAA
33217 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTT--A-AACGTTAG
** *
33248 GCCCTTATTTG-GCCAAATTAAAAGATT-G
1 GCCCTTATTTGAG-CATTTTAAACG-TTAG
* *
33276 GACCCCTATTTGAGCATTTTCAATAACGTTCG
1 G-CCCTTATTTGAGCATTTT--A-AACGTTAG
* ** *
33308 GTCCTTATTTG-GCCAAATTAAAAGATTAG
1 GCCCTTATTTGAG-CATTTTAAACG-TTAG
* *
33337 ACCCTTATTTGAACATTTTAGCAAACGTTAG
1 GCCCTTATTTGAGCATTTT---AAACGTTAG
33368 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
33383 ATTAGCCTAA
Statistics
Matches: 100, Mismatches: 21, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
28 8 0.08
29 33 0.33
30 3 0.03
31 47 0.47
32 9 0.09
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (28 bp):
GCCCTTATTTGAGCATTTTAAACGTTAG
Found at i:33294 original size:60 final size:60
Alignment explanation
Indices: 33222--33378 Score: 235
Period size: 60 Copynumber: 2.6 Consensus size: 60
33212 ACCAAGCCCT
*
33222 TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTGGACCCC
1 TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTAGACCCC
* * * *
33282 TATTTGAGCATTTTCAATAACGTTCGGTCCTTATTTGGCCAAATTAAAAGATTAGACCCT
1 TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTAGACCCC
* *
33342 TATTTGAACATTTTAGCA-AACGTTAGGCCCTTATTTG
1 TATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
33379 AGCAATTAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 85 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (60 bp):
TATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTAGACCCC
Found at i:33344 original size:29 final size:29
Alignment explanation
Indices: 33244--33347 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 29
33234 TTCGATAACG
*
33244 TTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TTAGACCCTTATTTGGCCAAATTAAAAGA
* * **
33273 TTGGACCCCTATTTGAG-CATTTTCAATAACG-
1 TTAGACCCTTATTTG-GCCAAATT-AA-AA-GA
* **
33304 TTCGGTCCTTATTTGGCCAAATTAAAAGA
1 TTAGACCCTTATTTGGCCAAATTAAAAGA
33333 TTAGACCCTTATTTG
1 TTAGACCCTTATTTG
33348 AACATTTTAG
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 1 0.02
29 30 0.55
30 6 0.11
31 17 0.31
32 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (29 bp):
TTAGACCCTTATTTGGCCAAATTAAAAGA
Found at i:35354 original size:2 final size:2
Alignment explanation
Indices: 35349--35376 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35339 TATATATATA
35349 TG 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 TG
35377 CTATGTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:37853 original size:33 final size:33
Alignment explanation
Indices: 37816--37892 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
37806 TCATGCCGCT
* *
37816 CTCTTGGGGCGGCCTTAGCCATGGGATG-CTGCC
1 CTCTTAGGGCGGCCTGAGCCATGGGATGTC-GCC
37849 CTCTTAGGGCGGCCTGAGCCATGGGATGTCGCC
1 CTCTTAGGGCGGCCTGAGCCATGGGATGTCGCC
*
37882 CTCCTAGGGCG
1 CTCTTAGGGCG
37893 ACATATACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 39 0.98
34 1 0.03
ACGTcount: A:0.10, C:0.31, G:0.36, T:0.22
Consensus pattern (33 bp):
CTCTTAGGGCGGCCTGAGCCATGGGATGTCGCC
Found at i:38053 original size:31 final size:33
Alignment explanation
Indices: 37996--38056 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
37986 TAATTTTTAT
**
37996 ATTTGTTTAATTATTAATTATTATTAATTAAAA
1 ATTTGTTTAATTATTAATTAAGATTAATTAAAA
38029 ATTTGTTTAA-T-TTAATTAAGATTAATTA
1 ATTTGTTTAATTATTAATTAAGATTAATTA
38057 TTGTTAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 15 0.58
32 1 0.04
33 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (33 bp):
ATTTGTTTAATTATTAATTAAGATTAATTAAAA
Found at i:38917 original size:9 final size:9
Alignment explanation
Indices: 38901--38953 Score: 70
Period size: 9 Copynumber: 5.9 Consensus size: 9
38891 TTACAAATAC
38901 AAATGTTAT
1 AAATGTTAT
*
38910 ACATGTTAT
1 AAATGTTAT
*
38919 AAATGTTCT
1 AAATGTTAT
*
38928 AAATGTTAA
1 AAATGTTAT
*
38937 AAATGTTAA
1 AAATGTTAT
38946 AAATGTTA
1 AAATGTTA
38954 ACAGTAATAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (9 bp):
AAATGTTAT
Found at i:40684 original size:13 final size:14
Alignment explanation
Indices: 40649--40678 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40639 AATTAATAAG
40649 TAAATTAATTTAAC
1 TAAATTAATTTAAC
40663 TAAATTAATTT-AC
1 TAAATTAATTTAAC
40676 TAA
1 TAA
40679 TCTAATACTC
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATTAATTTAAC
Done.