Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012750.1 Corchorus olitorius cultivar O-4 contig12783, 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: 35945
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:2477 original size:18 final size:18
Alignment explanation
Indices: 2439--2491 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
2429 CTTCAACATT
**
2439 ACCTTCAACTTGACCAAC
1 ACCTTCAACTTGACCTTC
*
2457 ACCTTCAGCTTGACCTTC
1 ACCTTCAACTTGACCTTC
* * *
2475 ACCATCACCTTAACCTT
1 ACCTTCAACTTGACCTT
2492 GACCAGGACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.40, G:0.06, T:0.28
Consensus pattern (18 bp):
ACCTTCAACTTGACCTTC
Found at i:2483 original size:24 final size:24
Alignment explanation
Indices: 2451--2526 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
2441 CTTCAACTTG
* *
2451 ACCAACACCTTCAGCTTGACCTTC
1 ACCATCACCTTCACCTTGACCTTC
* ***
2475 ACCATCACCTTAACCTTGACCAGG
1 ACCATCACCTTCACCTTGACCTTC
* *
2499 ACCATCACCTTCACCTTCATCTTC
1 ACCATCACCTTCACCTTGACCTTC
2523 ACCA
1 ACCA
2527 GGACCATCAT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.26, C:0.42, G:0.07, T:0.25
Consensus pattern (24 bp):
ACCATCACCTTCACCTTGACCTTC
Found at i:2507 original size:30 final size:30
Alignment explanation
Indices: 2468--2535 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
2458 CCTTCAGCTT
* *
2468 GACCTTCACCATCACCTTAACCTTGACCAG
1 GACCATCACCATCACCTTAACCTTCACCAG
* * *
2498 GACCATCACCTTCACCTTCATCTTCACCAG
1 GACCATCACCATCACCTTAACCTTCACCAG
2528 GACCATCA
1 GACCATCA
2536 TCACCACCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.41, G:0.09, T:0.24
Consensus pattern (30 bp):
GACCATCACCATCACCTTAACCTTCACCAG
Found at i:4683 original size:11 final size:11
Alignment explanation
Indices: 4667--4692 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4657 CTAGCCCTAA
4667 AAAACTAGAAG
1 AAAACTAGAAG
4678 AAAACTAGAAG
1 AAAACTAGAAG
4689 AAAA
1 AAAA
4693 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:15073 original size:9 final size:9
Alignment explanation
Indices: 15059--15084 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
15049 TTGATATAAT
15059 TCTTCAAAG
1 TCTTCAAAG
15068 TCTTCAAAG
1 TCTTCAAAG
15077 TCTTCAAA
1 TCTTCAAA
15085 TTATCTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (9 bp):
TCTTCAAAG
Found at i:17511 original size:39 final size:40
Alignment explanation
Indices: 17440--17693 Score: 244
Period size: 39 Copynumber: 6.6 Consensus size: 40
17430 AGAAGTATCA
* * *
17440 TTTAAGTAAAACCTGCTTAGGTCCT-TGTTTAGAATTCCCG
1 TTTAAGTCAAACCTGCTTAGGT-CTATGCTTAGAATTCTCG
* * *
17480 TTTAAGT-GAACCTACTTAGGTCTATGCTTAGAGTT-TCG
1 TTTAAGTCAAACCTGCTTAGGTCTATGCTTAGAATTCTCG
*
17518 TTTAA-TCAAACCTGCTTAGGTCCT-TGTTTAGAATTCTCG
1 TTTAAGTCAAACCTGCTTAGGT-CTATGCTTAGAATTCTCG
* * * *
17557 TTTAAGT-GAACCTGCTTAGATCTATGCTTAGAGTT-TTG
1 TTTAAGTCAAACCTGCTTAGGTCTATGCTTAGAATTCTCG
* *
17595 TTTAA-TCAAACCTGCTTAGGTCCT-TGTTTAGAATTCCCG
1 TTTAAGTCAAACCTGCTTAGGT-CTATGCTTAGAATTCTCG
* * *
17634 TTTAAGT-GAACCTGCTTAGGTCTATGCTTAGAGTT-TCT
1 TTTAAGTCAAACCTGCTTAGGTCTATGCTTAGAATTCTCG
*
17672 TTTAA-TCAAACCTGCTCAGGTC
1 TTTAAGTCAAACCTGCTTAGGTC
17694 CATCTTTAAA
Statistics
Matches: 175, Mismatches: 27, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
37 3 0.02
38 81 0.46
39 82 0.47
40 9 0.05
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (40 bp):
TTTAAGTCAAACCTGCTTAGGTCTATGCTTAGAATTCTCG
Found at i:17511 original size:101 final size:101
Alignment explanation
Indices: 17336--17518 Score: 260
Period size: 101 Copynumber: 1.8 Consensus size: 101
17326 GTTCAGAATT
* ** * * *
17336 TCATTTAAGAAAACCTGCTTAGGGCCTTCATTTAGAGTTTTCATTTGAGTAAACCTATTTAGGTT
1 TCATTTAAGAAAACCTGCTTAGGGCCTTCATTTAGAATTCCCATTTAAGTAAACCTACTTAGGTC
17401 TATGCTTAGAGTTTCGTAGAACCTGCTTTAGAAGTA
66 TATGCTTAGAGTTTCGTAGAACCTGCTTTAGAAGTA
* * * *
17437 TCATTTAAGTAAAACCTGCTTAGGTCCTT-GTTTAGAATTCCCGTTTAAGTGAACCTACTTAGGT
1 TCATTTAAG-AAAACCTGCTTAGGGCCTTCATTTAGAATTCCCATTTAAGTAAACCTACTTAGGT
17501 CTATGCTTAGAGTTTCGT
65 CTATGCTTAGAGTTTCGT
17519 TTAATCAAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 53 0.75
102 18 0.25
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (101 bp):
TCATTTAAGAAAACCTGCTTAGGGCCTTCATTTAGAATTCCCATTTAAGTAAACCTACTTAGGTC
TATGCTTAGAGTTTCGTAGAACCTGCTTTAGAAGTA
Found at i:17531 original size:77 final size:77
Alignment explanation
Indices: 17448--17694 Score: 440
Period size: 77 Copynumber: 3.2 Consensus size: 77
17438 CATTTAAGTA
*
17448 AAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTGAACCTACTTAGGTCTATGCTTAGAG
1 AAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTGAACCTGCTTAGGTCTATGCTTAGAG
17513 TTTCGTTTAATC
66 TTTCGTTTAATC
* *
17525 AAACCTGCTTAGGTCCTTGTTTAGAATTCTCGTTTAAGTGAACCTGCTTAGATCTATGCTTAGAG
1 AAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTGAACCTGCTTAGGTCTATGCTTAGAG
*
17590 TTTTGTTTAATC
66 TTTCGTTTAATC
17602 AAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTGAACCTGCTTAGGTCTATGCTTAGAG
1 AAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTGAACCTGCTTAGGTCTATGCTTAGAG
*
17667 TTTCTTTTAATC
66 TTTCGTTTAATC
*
17679 AAACCTGCTCAGGTCC
1 AAACCTGCTTAGGTCC
17695 ATCTTTAAAA
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 161 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (77 bp):
AAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTGAACCTGCTTAGGTCTATGCTTAGAG
TTTCGTTTAATC
Found at i:19739 original size:18 final size:20
Alignment explanation
Indices: 19704--19741 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
19694 CACCACTACC
*
19704 AAGCACAAACAAAGAAAGGA
1 AAGCACAAACAAAAAAAGGA
19724 AAGCA-AAA-AAAAAAAGGA
1 AAGCACAAACAAAAAAAGGA
19742 GCTAAACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.71, C:0.11, G:0.18, T:0.00
Consensus pattern (20 bp):
AAGCACAAACAAAAAAAGGA
Found at i:21500 original size:19 final size:18
Alignment explanation
Indices: 21467--21502 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21457 TTGAAATTAT
21467 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
21485 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
21503 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:24461 original size:22 final size:23
Alignment explanation
Indices: 24412--24461 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
24402 ATGGTCGATG
* *
24412 GTTTTGCTTCCTTAAATCGACTA
1 GTTTTGCCTCCTTAAATCGACAA
*
24435 GTTTTGCCTCCTT-AGTCGACAA
1 GTTTTGCCTCCTTAAATCGACAA
*
24457 TTTTT
1 GTTTT
24462 CTTCCACTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.46
Consensus pattern (23 bp):
GTTTTGCCTCCTTAAATCGACAA
Found at i:24492 original size:21 final size:21
Alignment explanation
Indices: 24466--24507 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24456 ATTTTTCTTC
*
24466 CACTTGTCGACTTACTTGCTT
1 CACTTGTCAACTTACTTGCTT
*
24487 CACTTGTCAACTTATTTGCTT
1 CACTTGTCAACTTACTTGCTT
24508 AAGTCGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.12, T:0.45
Consensus pattern (21 bp):
CACTTGTCAACTTACTTGCTT
Found at i:27128 original size:22 final size:23
Alignment explanation
Indices: 27089--27131 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
27079 AATCCTAATC
27089 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
27112 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
27132 ACTCCTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:27550 original size:22 final size:22
Alignment explanation
Indices: 27515--28071 Score: 220
Period size: 22 Copynumber: 25.4 Consensus size: 22
27505 TAATTACACT
* *
27515 AATTTTTATGACCTCCTTATGA
1 AATTTTGATAACCTCCTTATGA
* *
27537 AATTTTGATAACCTTCGTATGA
1 AATTTTGATAACCTCCTTATGA
* * *
27559 AATTTTGATAACGATAC-TATGG
1 AATTTTGATAAC-CTCCTTATGA
* * * ** ** *
27581 AGTTTCGAGAATTTATTTATTA
1 AATTTTGATAACCTCCTTATGA
* * *
27603 ACTTTT-TTAACCTTCTTATGA
1 AATTTTGATAACCTCCTTATGA
* * * *
27624 AATTTTGTTAACCTCCCTAAGG
1 AATTTTGATAACCTCCTTATGA
*
27646 AATTTTGA-AGACTTCAC-TATGA
1 AATTTTGATA-ACCTC-CTTATGA
* **
27668 AATTTTGATAACTTCCCAATGA
1 AATTTTGATAACCTCCTTATGA
*
27690 AATTTTGATAACCAGCAC-TATGA
1 AATTTTGATAACC-TC-CTTATGA
* * * *
27713 GATGTTAATAACCTCCATATGA
1 AATTTTGATAACCTCCTTATGA
* * * *
27735 TATATTGATAACCACGTTATGA
1 AATTTTGATAACCTCCTTATGA
* * * *
27757 AAATTTAAAAACCTCCATATG-
1 AATTTTGATAACCTCCTTATGA
27778 AATTGTTAGTAATAACACT-C---TGA
1 AATT-TT-G--ATAAC-CTCCTTATGA
* *
27801 AATTTTGATAATCACAC-TATGA
1 AATTTTGATAACCTC-CTTATGA
* * * *
27823 AATTGTAATAATCTCGTTATGA
1 AATTTTGATAACCTCCTTATGA
* *
27845 AATATTGATAAACCTTCCTATAAATAA
1 AATTTTGAT-AACC-TCCT-T--ATGA
* *
27872 AATTTTGATAAACCTCCCTATAA
1 AATTTTGAT-AACCTCCTTATGA
27895 AATTTTGATAACCTCCTTATGA
1 AATTTTGATAACCTCCTTATGA
* *
27917 AATCTTGATAA----C-TA-AA
1 AATTTTGATAACCTCCTTATGA
* *
27933 AATTTTGATAATCTCCATATGA
1 AATTTTGATAACCTCCTTATGA
** *
27955 TTTTTTGATAACCTCATTATGA
1 AATTTTGATAACCTCCTTATGA
27977 AATTTTGATAACC-CTCTTATGA
1 AATTTTGATAACCTC-CTTATGA
* * **
27999 AATCTTGAAAACCAAAC-TATGA
1 AATTTTGATAACC-TCCTTATGA
* *
28021 AATTTTGATAACCTTCATATGA
1 AATTTTGATAACCTCCTTATGA
* *
28043 AATTTTGATATCCTCC--CTGA
1 AATTTTGATAACCTCCTTATGA
28063 AATTTTGAT
1 AATTTTGAT
28072 TACTCGATAA
Statistics
Matches: 403, Mismatches: 96, Indels: 74
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 2 0.00
19 4 0.01
20 14 0.03
21 26 0.06
22 272 0.67
23 40 0.10
24 4 0.01
25 7 0.02
26 5 0.01
27 16 0.04
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCCTTATGA
Found at i:27724 original size:45 final size:45
Alignment explanation
Indices: 27660--27779 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 45
27650 TTGAAGACTT
* * * *
27660 CACTATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAG
1 CACTATGAAATGTTAATAACCT-CCATATGAAATATTGATAACCAG
* *
27705 CACTATGAGATGTTAATAACCTCCATATGATATATTGATAACCA-
1 CACTATGAAATGTTAATAACCTCCATATGAAATATTGATAACCAG
** *
27749 CGTTATGAAAAT-TTAAAAACCTCCATATGAA
1 CACTATG-AAATGTTAATAACCTCCATATGAA
27780 TTGTTAGTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
44 25 0.40
45 37 0.60
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (45 bp):
CACTATGAAATGTTAATAACCTCCATATGAAATATTGATAACCAG
Found at i:27874 original size:27 final size:27
Alignment explanation
Indices: 27844--27895 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
27834 TCTCGTTATG
*
27844 AAATATTGATAAACCTTCCTATAAATA
1 AAATATTGATAAACCTCCCTATAAATA
*
27871 AAATTTTGATAAACCTCCCTATAAA
1 AAATATTGATAAACCTCCCTATAAA
27896 ATTTTGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (27 bp):
AAATATTGATAAACCTCCCTATAAATA
Found at i:27964 original size:60 final size:61
Alignment explanation
Indices: 27870--27988 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 61
27860 TCCTATAAAT
* *
27870 AAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAACTA
1 AAAATTTTGATAAACCTCCATATAAAATTTTGATAACCTCATTATGAAATCTTGATAACTA
* * ** *
27931 AAAATTTTGAT-AATCTCCATATGATTTTTTGATAACCTCATTATGAAATTTTGATAAC
1 AAAATTTTGATAAACCTCCATATAAAATTTTGATAACCTCATTATGAAATCTTGATAAC
27989 CCTCTTATGA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 40 0.78
61 11 0.22
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (61 bp):
AAAATTTTGATAAACCTCCATATAAAATTTTGATAACCTCATTATGAAATCTTGATAACTA
Found at i:27998 original size:44 final size:44
Alignment explanation
Indices: 27619--28572 Score: 206
Period size: 44 Copynumber: 22.0 Consensus size: 44
27609 TTAACCTTCT
* * * * *
27619 TATGAAATTTTGTTAA-CCTCCCTAAGGAATTTTGA-AGACTTCAC
1 TATGAAATTTTGATAACCCT-CATATGAAATTTTGATA-ACCTCAC
*
27663 TATGAAATTTTGATAACTTCC-CA-ATGAAATTTTGATAACCAGCAC
1 TATGAAATTTTGATAAC--CCTCATATGAAATTTTGATAACC-TCAC
* * * * * * **
27708 TATGAGATGTTAATAA-CCTCCATATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCCT-CATATGAAATTTTGATAACCTCAC
* * * ***
27752 TATGAAAATTT-AAAAACCTCCATATG-AATTGTT-AGTAATAACAC
1 TATGAAATTTTGATAACCCT-CATATGAAATT-TTGA-TAACCTCAC
* * * * * * **
27796 TCTGAAATTTTGATAA-TCACACTATGAAATTGTAATAATCTCGT
1 TATGAAATTTTGATAACCCTCA-TATGAAATTTTGATAACCTCAC
* * * *
27840 TATGAAATATTGATAAACCTTCCTATAAATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCCT-C-AT--ATGAAATTTTGAT-AACCTCAC
* * *
27890 TATAAAATTTTGATAA-CCTCCTTATGAAATCTTGATAA-CT-A-
1 TATGAAATTTTGATAACCCT-CATATGAAATTTTGATAACCTCAC
* ** *
27931 -A--AAATTTTGATAA-TCTCCATATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCCT-CATATGAAATTTTGATAACCTCAC
* * * **
27972 TATGAAATTTTGATAACCCTCTTATGAAATCTTGAAAACCAAAC
1 TATGAAATTTTGATAACCCTCATATGAAATTTTGATAACCTCAC
* *
28016 TATGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCCTCATATGAAATTTTGATAACCTCAC
* * * * *
28059 -CTGAAATTTTGATTA--CTCGATAATAAAAGTTTAATAACCTTC-C
1 TATGAAATTTTGATAACCCTC-AT-ATGAAATTTTGATAACC-TCAC
* * *
28102 --T--AA-TTTGCTAACCAT-ACTATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCCTCA-TATGAAATTTTGATAACCTCAC
* * * * * *
28141 CA-G-AA-----AT-A-CCAC-TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCCTCATATGAAATTTTGATAACCTCAC
* * * * *
28175 TTTGAAAATTTGATAA-CCTCTATATTAAATTGTGATAACCTCTC
1 TATGAAATTTTGATAACCCTC-ATATGAAATTTTGATAACCTCAC
* * *
28219 TAT-AGAATTTTGTTGACCCCTC-TATGAAATTTTGAT-A-CTAACAT
1 TATGA-AATTTTGAT-AACCCTCATATGAAATTTTGATAACCT--CAC
* * * ***
28263 TAT-ATAATTTTGATAA-TCTCGCTTTGAAATTTTGATAATAGCAC
1 TATGA-AATTTTGATAACCCTC-ATATGAAATTTTGATAACCTCAC
* * * * *
28307 TATGAAATTTTGTTAATCTTCCTAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAACCCTCATATGAAATTTTGATAA-CC--TCAC
* * *
28353 TATGAAATTTTGATAATCACTC-TATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAA-CCCTCATATGAAATTTTGATAACCTCAC
* *
28395 TATCAAATTTCGAT-ACTCCTCATGAAATTGAGACA-TTT-ATAACCTTCA-
1 TATGAAATTTTGATAAC-CCTCAT---A-TGA-A-ATTTTGATAACC-TCAC
* * * * *
28443 TATGAAATTTT-ATTAA-TCACACTA-AAAACTTTGGATAACCACAC
1 TATGAAATTTTGA-TAACCCTCA-TATGAAA-TTTTGATAACCTCAC
* * ** *
28487 TATGAAATTTTGATAATCTTCCCATGAAATTTTGATAACTTC-C
1 TATGAAATTTTGATAACCCTCATATGAAATTTTGATAACCTCAC
* ** *
28530 ATATGAAATTTTGGTAA-CGACACTATGGAATTTTGATAACCTC
1 -TATGAAATTTTGATAACCCTCA-TATGAAATTTTGATAACCTC
28573 GTCATGAAAT
Statistics
Matches: 661, Mismatches: 161, Indels: 176
0.66 0.16 0.18
Matches are distributed among these distances:
34 17 0.03
35 2 0.00
36 3 0.00
37 1 0.00
38 31 0.05
39 24 0.04
40 8 0.01
41 12 0.02
42 55 0.08
43 38 0.06
44 295 0.45
45 70 0.11
46 35 0.05
47 19 0.03
48 21 0.03
49 13 0.02
50 17 0.03
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACCCTCATATGAAATTTTGATAACCTCAC
Found at i:28378 original size:68 final size:63
Alignment explanation
Indices: 28263--28409 Score: 154
Period size: 68 Copynumber: 2.2 Consensus size: 63
28253 ATACTAACAT
* *
28263 TATATAATTTTGATAATCTCGCTTTGAAATTTTGATAATAGCACTATGAAATTTTGTTAATCTTC
1 TATA-AATTTTGATAATCTCGCTTTGAAATTTTGATAATAGCACTATGAAA-TTTGATAACCTT-
28328 C
63 C
* *
28329 TATAAATTTTGATAATC-CGATCTCTATGAAATTTTGATAATCA-CTCTATGAGATTTGATAACC
1 TATAAATTTTGATAATCTCG--CT-T-TGAAATTTTGATAAT-AGCACTATGAAATTTGATAACC
28392 TTC
61 TTC
*
28395 TATCAAATTTCGATA
1 TAT-AAATTTTGATA
28410 CTCCTCATGA
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
64 2 0.03
65 13 0.19
66 10 0.14
67 21 0.30
68 23 0.33
69 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (63 bp):
TATAAATTTTGATAATCTCGCTTTGAAATTTTGATAATAGCACTATGAAATTTGATAACCTTC
Found at i:28583 original size:22 final size:20
Alignment explanation
Indices: 27871--28615 Score: 138
Period size: 22 Copynumber: 34.7 Consensus size: 20
27861 CCTATAAATA
*
27871 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCT--CTATG
27894 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCT-C-TATG
* *
27916 AAATCTTGATAA---CTA-A
1 AAATTTTGATAACCTCTATG
*
27932 AAATTTTGATAATCTCCATATG
1 AAATTTTGATAACCT-C-TATG
**
27954 ATTTTTTGATAACCTCATTATG
1 AAATTTTGATAACCTC--TATG
27976 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAA-CCTC-TATG
* * *
27998 AAATCTTGAAAACCAAACTATG
1 AAATTTTGATAACC--TCTATG
28020 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACC-TC-TATG
* **
28042 AAATTTTGATATCCTCCCTG
1 AAATTTTGATAACCTCTATG
* *
28062 AAATTTTGATTA-CTCGATAATA
1 AAATTTTGATAACCTC--T-ATG
* * *
28084 AAAGTTTAATAACCT-TCCT-
1 AAATTTTGATAACCTCT-ATG
*
28103 -AA-TTTGCTAACCATACTATG
1 AAATTTTGATAACC-T-CTATG
*
28123 AAATTTTGATAACCTCCCCA-G
1 AAATTTTGATAACCT--CTATG
*
28144 -AA-----AT-ACCACTATG
1 AAATTTTGATAACCTCTATG
* *
28157 AAATTTTGGTAATCACAT-TTTG
1 AAATTTTGATAA-C-C-TCTATG
* *
28179 AAAATTTGATAACCTCTATATT
1 AAATTTTGATAACCTC--TATG
*
28201 AAATTGTGATAACCTCTCTAT-
1 AAATTTTGATAA-C-CTCTATG
* *
28222 AGAATTTTGTTGACCCCTCTATG
1 A-AATTTTGAT-A-ACCTCTATG
*
28245 AAATTTTGATACTAACAT-TAT-
1 AAATTTTG--A-TAACCTCTATG
* *
28266 ATAATTTTGATAATCTCGCTTTG
1 A-AATTTTGATAA-C-CTCTATG
* *
28289 AAATTTTGATAATAGCACTATG
1 AAATTTTGAT-A-ACCTCTATG
* *
28311 AAATTTTGTTAATCTTCCTAT-
1 AAATTTTGATAA-CCT-CTATG
28332 AAATTTTGATAATCCGATCTCTATG
1 AAATTTTGATAA--C---CTCTATG
28357 AAATTTTGATAATCACTCTATG
1 AAATTTTGATAA-C-CTCTATG
* *
28379 AGA-TTTGATAACCTTCTATC
1 AAATTTTGATAACC-TCTATG
* *
28399 AAATTTCGATACTCCTC-ATG
1 AAATTTTGATA-ACCTCTATG
*
28419 AAATTGAGACATTTATAACCTTCATATG
1 AAATT------TTGATAACC-TC-TATG
* *
28447 AAATTTT-ATTAATCACACTA-A
1 AAATTTTGA-TAA-C-CTCTATG
* *
28468 AAACTTTGGATAACCACACTATG
1 AAA-TTTTGATAA-C-CTCTATG
* *
28491 AAATTTTGATAATCTTCCCATG
1 AAATTTTGATAA-CCT-CTATG
*
28513 AAATTTTGATAACTTCCATATG
1 AAATTTTGATAACCT-C-TATG
* *
28535 AAATTTTGGTAACGACACTATG
1 AAATTTTGATAAC--CTCTATG
*
28557 GAATTTTGATAACCTCGTCATG
1 AAATTTTGATAACCTC-T-ATG
* * *
28579 AAATTATAATAAACATCTTTATG
1 AAATTTTGAT-AAC--CTCTATG
*
28602 AAATCTTGATAACC
1 AAATTTTGATAACC
28616 ACAGAGACAA
Statistics
Matches: 533, Mismatches: 102, Indels: 177
0.66 0.13 0.22
Matches are distributed among these distances:
12 2 0.00
13 1 0.00
14 5 0.01
15 2 0.00
16 11 0.02
17 10 0.02
18 4 0.01
19 10 0.02
20 41 0.08
21 56 0.11
22 302 0.57
23 45 0.08
24 12 0.02
25 18 0.03
26 6 0.01
28 8 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
AAATTTTGATAACCTCTATG
Found at i:28818 original size:20 final size:20
Alignment explanation
Indices: 28780--28818 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28770 TATCAACATT
28780 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
28800 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
28819 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:29105 original size:13 final size:13
Alignment explanation
Indices: 29069--29106 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
29059 TCTAAATTGA
29069 AATTTT-ATAATT
1 AATTTTAATAATT
29081 AATTTTTAAATAATT
1 AA-TTTT-AATAATT
29096 AATTTTAATAA
1 AATTTTAATAA
29107 CATCAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 4 0.17
15 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTTAATAATT
Found at i:29558 original size:27 final size:27
Alignment explanation
Indices: 29526--29579 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
29516 TACACTAAGG
*
29526 GCATATTCAGGGGCATTTTAGTCATTT
1 GCATATCCAGGGGCATTTTAGTCATTT
*
29553 GCATATCCAGGGGCATTTTGGTCATTT
1 GCATATCCAGGGGCATTTTAGTCATTT
29580 CAAGTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (27 bp):
GCATATCCAGGGGCATTTTAGTCATTT
Found at i:32516 original size:19 final size:18
Alignment explanation
Indices: 32463--32517 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
32453 GGGTATCTTC
32463 TATGATTTGGGCTTTTAT
1 TATGATTTGGGCTTTTAT
* *
32481 TCT-ATTTTGGGC-ATTAT
1 TATGA-TTTGGGCTTTTAT
32498 TGATGATTTGGGCTTTTAT
1 T-ATGATTTGGGCTTTTAT
32517 T
1 T
32518 TATGCATTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 6 0.21
ACGTcount: A:0.16, C:0.07, G:0.22, T:0.55
Consensus pattern (18 bp):
TATGATTTGGGCTTTTAT
Done.