Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013321.1 Corchorus capsularis cultivar CVL-1 contig13342, 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: 8896
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:3256 original size:45 final size:45
Alignment explanation
Indices: 3207--3344 Score: 222
Period size: 45 Copynumber: 3.1 Consensus size: 45
3197 AAAGAAAAAG
*
3207 AAAAAGAGTCATGATTTTCAAAAGGTTTTGATAAAATGGTTTTTC
1 AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTC
* *
3252 AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGATCTTTC
1 AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTC
* * *
3297 AAAAAGAGTCATGGTTTTCAAAGGGTTTTAATAAAATGGTTTTCC
1 AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTC
3342 AAA
1 AAA
3345 GTTGTGTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 85 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (45 bp):
AAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATGGTTTTTC
Found at i:3740 original size:23 final size:24
Alignment explanation
Indices: 3699--3747 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
3689 AAAAGAGACG
3699 AAAAAAGATGAAAATTGAAAGTGA
1 AAAAAAGATGAAAATTGAAAGTGA
3723 AAAAAATGATG-AAA-TGAAAGTGA
1 AAAAAA-GATGAAAATTGAAAGTGA
3746 AA
1 AA
3748 GGAAGGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.46
24 9 0.38
25 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.16
Consensus pattern (24 bp):
AAAAAAGATGAAAATTGAAAGTGA
Found at i:4078 original size:15 final size:16
Alignment explanation
Indices: 4058--4096 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
4048 TTTCAAGTGC
*
4058 CAAAAAAACAA-AAAA
1 CAAAAAAAAAACAAAA
4073 CAAAAAAAAAACAAAA
1 CAAAAAAAAAACAAAA
*
4089 GAAAAAAA
1 CAAAAAAA
4097 GAGGAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAACAAAA
Found at i:4083 original size:11 final size:12
Alignment explanation
Indices: 4062--4095 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
4052 AAGTGCCAAA
4062 AAAACAAAAAAC
1 AAAACAAAAAAC
4074 AAAA-AAAAAAC
1 AAAACAAAAAAC
*
4085 AAAAGAAAAAA
1 AAAACAAAAAA
4096 AGAGGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAAC
Found at i:4491 original size:48 final size:50
Alignment explanation
Indices: 4392--4492 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 50
4382 AAACAAGAAA
* * *
4392 TTTTATAATAAGATTGTATTCCATTTATGAGTCCAAGATCAGAATTCGCT
1 TTTTATAATAAGATTGCATTCCAGTTATGAGTCCAAGATCAAAATTCGCT
* * *
4442 TTTTATAATAATATTGCATTCC-GTT-TGAGTCTAAGATCAAAATTTGCT
1 TTTTATAATAAGATTGCATTCCAGTTATGAGTCCAAGATCAAAATTCGCT
4490 TTT
1 TTT
4493 CAAAGGGCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 23 0.51
49 2 0.04
50 20 0.44
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (50 bp):
TTTTATAATAAGATTGCATTCCAGTTATGAGTCCAAGATCAAAATTCGCT
Found at i:5142 original size:70 final size:69
Alignment explanation
Indices: 4952--5200 Score: 263
Period size: 70 Copynumber: 3.6 Consensus size: 69
4942 GAATTTTGCT
* * * *
4952 TTGGTTCCATCCAAGCA-GCATGGGCTTTTCGACAAGCCAAACTCGTTTCCATACGAGCCAGTTT
1 TTGGTTCCATCCAAGCATTCA-GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTC
*
5016 AAGCC
65 AAGCA
* * * * * *
5021 TCGATTCCATCCGAATCATT--GGGCTTTTCCATAAGTCAAACTCGTTTCCATATGAGTCAGTTC
1 TTGGTTCCATCC-AAGCATTCAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTC
*
5084 GAGCA
65 AAGCA
* *
5089 TTGGTTCCATCCAAGCATTCGAGGGCTTTTCCACAAACCAAACTCGTTACCATACGAGTCAGTTC
1 TTGGTTCCATCCAAGCATTC-AGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTC
5154 AAGCA
65 AAGCA
* * * *
5159 TTAGTTCCATCCAAGTA-ACATGGGGCTTTTCCATAAGCCAAA
1 TTGGTTCCATCCAAGCATTCA--GGGCTTTTCCACAAGCCAAA
5201 TTCAATGAGG
Statistics
Matches: 147, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
67 6 0.04
68 51 0.35
69 11 0.07
70 79 0.54
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (69 bp):
TTGGTTCCATCCAAGCATTCAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCA
AGCA
Found at i:5411 original size:14 final size:13
Alignment explanation
Indices: 5392--5542 Score: 51
Period size: 14 Copynumber: 10.5 Consensus size: 13
5382 ATCTTCAATG
5392 TTTCAATTTCGATA
1 TTTCAATTTC-ATA
5406 TTTCAATGTTTCA-A
1 TTTCAA--TTTCATA
5420 TTTCAATTCTTCA-A
1 TTTCAA-T-TTCATA
* *
5434 ATTCAATCCTTCAATG
1 TTTCAAT--TTC-ATA
5450 TTTCAATTTCGATA
1 TTTCAATTTC-ATA
5464 TTTCAATGTTTCA-A
1 TTTCAA--TTTCATA
5478 TTTCAATTCTTCA-A
1 TTTCAA-T-TTCATA
* *
5492 ATTCAATCCTTCAATG
1 TTTCAAT--TTC-ATA
5508 TTTCAATTTCAATA
1 TTTCAATTTC-ATA
*
5522 TTCCAATGTTTCA-A
1 TTTCAA--TTTCATA
5536 TTTCAAT
1 TTTCAAT
5543 ATTCCAATGC
Statistics
Matches: 110, Mismatches: 13, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
12 1 0.01
13 4 0.04
14 76 0.69
15 5 0.05
16 24 0.22
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (13 bp):
TTTCAATTTCATA
Found at i:5439 original size:58 final size:58
Alignment explanation
Indices: 5384--5765 Score: 307
Period size: 58 Copynumber: 6.6 Consensus size: 58
5374 TTCTTCAAAT
5384 CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAATTTCAATTCTTCAAATTCAATC
1 CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAATTTCAATTCTTCAAATTCAATC
5442 CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAATTTCAATTCTTCAAATTCAATC
1 CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAATTTCAATTCTTCAAATTCAATC
* * *
5500 CTTCAATGTTTCAATTTCAATATTCCAATGTTTCAATTTCAATATTCCAATGCCTCAATTTCAAT
1 CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAATTTC-A-ATT-C--T---TCAAATTCAAT
*
5565 T
58 C
* * * * *
5566 CTTCAA--ATCCAAAATCTTCAATGTTTCAATGCTTCAATTTCAATTCTTCAAATTCAATC
1 CTTCAATGTTTC--AAT-TTCGATATTTCAATGTTTCAATTTCAATTCTTCAAATTCAATC
* * * *
5625 CTTTAATGTTTC-A----G---TTTCATTGTTTCAATTTCAATTCTTCAATTTGAAT-
1 CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAATTTCAATTCTTCAAATTCAATC
* * * * *
5674 -TTCAATGCTTT-AATTTCAAT-TCTTCAA--ATTCAATCCTTCAATGT-TTTAATTTCAATT
1 CTTCAATG-TTTCAATTTCGATAT-TTCAATGTTTCAAT--TTCAAT-TCTTCAAATTCAATC
* *
5731 CTTCAATGCTTCAATTTC-A-ATTTCAATTTTTCAAT
1 CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAAT
5766 GCTTTAAGTT
Statistics
Matches: 266, Mismatches: 27, Indels: 62
0.75 0.08 0.17
Matches are distributed among these distances:
48 6 0.02
49 4 0.02
50 31 0.12
54 6 0.02
55 1 0.00
56 25 0.09
57 5 0.02
58 116 0.44
59 16 0.06
60 3 0.01
61 3 0.01
62 1 0.00
63 1 0.00
64 3 0.01
65 3 0.01
66 20 0.08
67 22 0.08
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (58 bp):
CTTCAATGTTTCAATTTCGATATTTCAATGTTTCAATTTCAATTCTTCAAATTCAATC
Found at i:5504 original size:22 final size:22
Alignment explanation
Indices: 5479--5542 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
5469 ATGTTTCAAT
5479 TTCAAT-TCTTCAAATTCAATCC
1 TTCAATGT-TTCAAATTCAATCC
* *
5501 TTCAATGTTTCAATTTCAAT-A
1 TTCAATGTTTCAAATTCAATCC
*
5522 TTCCAATGTTTCAATTTCAAT
1 TT-CAATGTTTCAAATTCAAT
5543 ATTCCAATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.05
22 35 0.92
23 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.45
Consensus pattern (22 bp):
TTCAATGTTTCAAATTCAATCC
Found at i:5543 original size:22 final size:22
Alignment explanation
Indices: 5503--5564 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
5493 TTCAATCCTT
5503 CAATGTTTCAATTTCAATATTC
1 CAATGTTTCAATTTCAATATTC
5525 CAATGTTTCAATTTCAATATTC
1 CAATGTTTCAATTTCAATATTC
**
5547 CAATGCCTCAATTTCAAT
1 CAATGTTTCAATTTCAAT
5565 TCTTCAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (22 bp):
CAATGTTTCAATTTCAATATTC
Found at i:5571 original size:14 final size:14
Alignment explanation
Indices: 5554--5805 Score: 101
Period size: 14 Copynumber: 17.5 Consensus size: 14
5544 TTCCAATGCC
5554 TCAATTTCAATTCT
1 TCAATTTCAATTCT
* * *
5568 TCAAATCCAAAATCT
1 TCAATTTC-AATTCT
*
5583 TCAATGTTTCAATGCT
1 TCAA--TTTCAATTCT
5599 TCAATTTCAATTCT
1 TCAATTTCAATTCT
* *
5613 TCAAATTCAATCCT
1 TCAATTTCAATTCT
* *
5627 TTAATGTTTC-AGT-T
1 TCAA--TTTCAATTCT
*
5641 TCATTGTTTCAA-T-T
1 TCA--ATTTCAATTCT
5655 TCAATTCTTCAA-T-T
1 TCAA-T-TTCAATTCT
* *
5669 TGAATTTCAATGCT
1 TCAATTTCAATTCT
*
5683 TTAATTTCAATTCT
1 TCAATTTCAATTCT
* *
5697 TCAAATTCAATCCT
1 TCAATTTCAATTCT
*
5711 TCAATGTTTTAA-T-T
1 TCAA--TTTCAATTCT
*
5725 TCAATTCTTCAATGCT
1 TCAA-T-TTCAATTCT
5741 TCAATTTCAA-T-T
1 TCAATTTCAATTCT
*
5753 TCAATTTTTCAATGCT
1 TCAA--TTTCAATTCT
* *
5769 TTAAGTTCAATTCT
1 TCAATTTCAATTCT
*
5783 TCAACTATTCAATGCT
1 TCAA-T-TTCAATTCT
5799 TCAATTT
1 TCAATTT
5806 ATTTCAATGA
Statistics
Matches: 177, Mismatches: 38, Indels: 46
0.68 0.15 0.18
Matches are distributed among these distances:
12 10 0.06
13 3 0.02
14 113 0.64
15 13 0.07
16 36 0.20
17 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (14 bp):
TCAATTTCAATTCT
Found at i:5694 original size:84 final size:84
Alignment explanation
Indices: 5582--5803 Score: 279
Period size: 84 Copynumber: 2.6 Consensus size: 84
5572 ATCCAAAATC
* * *
5582 TTCAATGTTTCAATGCTTCAATTTCAATTCTTCAAATTCAATCCTTTAATGTTTCAGTTTC-ATT
1 TTCAAT-TTTCAATGCTTTAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATT
*
5646 GTTTCAAT-TTCAATTCTTCAAT
65 -CTTCAATCTTCAA-T-TTCAAT
* *
5668 TTGAA-TTTCAATGCTTTAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTTAATTTCAATTC
1 TTCAATTTTCAATGCTTTAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATTC
5732 TTCAATGCTTCAATTTCAAT
66 TTCAAT-CTTCAATTTCAAT
* *
5752 TTCAATTTTTCAATGCTTTAAGTTCAATTCTTCAACTATTCAATGCTTCAAT
1 TTCAA-TTTTCAATGCTTTAATTTCAATTCTTCAA--ATTCAATCCTTCAAT
5804 TTATTTCAAT
Statistics
Matches: 120, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
84 66 0.55
85 4 0.03
86 36 0.30
88 14 0.12
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.48
Consensus pattern (84 bp):
TTCAATTTTCAATGCTTTAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAATTC
TTCAATCTTCAATTTCAAT
Found at i:5713 original size:22 final size:21
Alignment explanation
Indices: 5688--5804 Score: 87
Period size: 22 Copynumber: 5.3 Consensus size: 21
5678 ATGCTTTAAT
*
5688 TTCAATTCTTCAAATTCAATCC
1 TTCAATTCTTCAATTTCAAT-C
*
5710 TTCAATGT-TTTAATTTCAATTC
1 TTCAAT-TCTTCAATTTCAA-TC
*
5732 TTCAATGCTTCAATTTCAAT-
1 TTCAATTCTTCAATTTCAATC
* * *
5752 TTCAATTTTTCAATGCTTTAA-G
1 TTCAATTCTTCAAT--TTCAATC
5774 TTCAATTCTTCAACTATTCAATGC
1 TTCAATTCTTCAA-T-TTCAAT-C
5798 TTCAATT
1 TTCAATT
5805 TATTTCAATG
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
20 12 0.16
21 1 0.01
22 52 0.69
23 3 0.04
24 7 0.09
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (21 bp):
TTCAATTCTTCAATTTCAATC
Found at i:5722 original size:36 final size:34
Alignment explanation
Indices: 5634--5751 Score: 137
Period size: 34 Copynumber: 3.4 Consensus size: 34
5624 CCTTTAATGT
* * * *
5634 TTCAGTTTCATTGTTTCAATTTCAATTCTTCAAT
1 TTCAATTTCAATGTTTTAATTTCAATTCTTCAAA
* *
5668 TTGAATTTCAATGCTTTAATTTCAATTCTTCAAA
1 TTCAATTTCAATGTTTTAATTTCAATTCTTCAAA
*
5702 TTCAATCCTTCAATGTTTTAATTTCAATTCTTCAATGC
1 TTCAAT--TTCAATGTTTTAATTTCAATTCTTCAA--A
5740 TTCAATTTCAAT
1 TTCAATTTCAAT
5752 TTCAATTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
34 33 0.46
36 32 0.45
38 6 0.08
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (34 bp):
TTCAATTTCAATGTTTTAATTTCAATTCTTCAAA
Found at i:5750 original size:50 final size:49
Alignment explanation
Indices: 5366--5805 Score: 178
Period size: 50 Copynumber: 8.7 Consensus size: 49
5356 ACAGTTGGTC
* *
5366 AATTTCAATTCTTCAAATCTTCAATGTTTCAATTTCGATAT-TTCAATGTTTC
1 AATTTCAATTCTTC-AAT-TTCAAT-TTTCAATTTCAAT-TCTTCAATGTTTT
* * *
5418 AATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCGATATTTCAATGTTTC
1 AATTTCAATTCTTCAATTTCAAT-TTTCAA--TTTCAA-TTC-----TTCAATGTTTT
* * * **
5476 AATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAA-T-TTCAATATTCC
1 AATTTCAATTCTTCAATTTCAAT-TTTCAA--TTTCAATTCTTCAATGTTTT
** * **
5526 AATGTTTCAA-T-TTCAATATTCCAATGCCTCAATTTCAATTCTTCAA--ATCC
1 AA--TTTCAATTCTTCAAT-TT-CAAT-TTTCAATTTCAATTCTTCAATGTTTT
* * *
5576 AA----AA-TCTTCAATGTTTCAATGCTTCAATTTCAATTCTTCAA--ATTC
1 AATTTCAATTCTTCAA--TTTCAAT-TTTCAATTTCAATTCTTCAATGTTTT
* * * *
5621 AATCCTTTAATGT-TTCAGTTTCATTGTTTCAATTTCAATTCTTCAA--TTTG
1 AAT--TTCAAT-TCTTCAATTTCAAT-TTTCAATTTCAATTCTTCAATGTTTT
* * * *
5671 AATTTCAATGCTTTAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTT
1 AATTTCAATTCTTCAATTTCAATT-TTCAATTTCAATTCTTCAATGTTTT
* *
5721 AATTTCAATTCTTCAATGCTTCAA-TTTCAATTTCAATTTTTCAATGCTTT
1 AATTTCAATTCTTCAAT--TTCAATTTTCAATTTCAATTCTTCAATGTTTT
* *
5771 AAGTTCAATTCTTCAACTATTCAATGCTTCAATTT
1 AATTTCAATTCTTCAA-T-TTCAAT-TTTCAATTT
5806 ATTTCAATGA
Statistics
Matches: 319, Mismatches: 34, Indels: 70
0.75 0.08 0.17
Matches are distributed among these distances:
44 3 0.01
45 34 0.11
46 2 0.01
47 2 0.01
48 31 0.10
50 128 0.40
51 10 0.03
52 57 0.18
53 2 0.01
56 1 0.00
58 49 0.15
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (49 bp):
AATTTCAATTCTTCAATTTCAATTTTCAATTTCAATTCTTCAATGTTTT
Found at i:5836 original size:58 final size:58
Alignment explanation
Indices: 5774--6085 Score: 394
Period size: 58 Copynumber: 5.4 Consensus size: 58
5764 ATGCTTTAAG
* * *
5774 TTCAATTCTTCAACTATTCAATGCTTCAATTTATTTCAATGATCCAGGGTGGTCTTCC
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTC
* * * *
5832 TTCAATTCTTCAACTATTCAATGCTTCAATTTACTTCAATGATCTAGGGTGGTCCTCC
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTC
* * *
5890 TTCAATTCTTTAATTGTTCATTGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTC
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTC
* * * * * * *
5948 TACAA-T-TTCATTTCTTTAATACTTCCATTTACTTCAATTATCCAGGGTGGTCTTTC
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTC
* ** * * *
6004 TTCAATTCTTCAGTTATTCAATGCTTCCCTTTACTTCAATGATCCATGGCGATCTTTC
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTC
*
6062 TTCGATTCTTCAATTATTCAATGC
1 TTCAATTCTTCAATTATTCAATGC
6086 CTCATTTTGA
Statistics
Matches: 221, Mismatches: 31, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
56 46 0.21
57 2 0.01
58 173 0.78
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (58 bp):
TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTC
Found at i:6037 original size:114 final size:116
Alignment explanation
Indices: 5774--6083 Score: 363
Period size: 114 Copynumber: 2.7 Consensus size: 116
5764 ATGCTTTAAG
* * *
5774 TTCAATTCTTCAACTATTCAATGCTTCAATTTATTTCAATGATCCAGGGTGGTCTTCCTTCAATT
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTCCTACAATT
* *
5839 CTTCAACTATTCAATGCTTCAATTTACTTCAATGATCTAGGGTGGTCCTCC
66 CTTCAACTATTCAATACTTCAATTTACTTCAATGATCCAGGGTGGTCCTCC
* * * *
5890 TTCAATTCTTTAATTGTTCATTGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTTCTACAA-T
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTCCTACAATT
** * * * * * *
5954 -TTCATTTCTTTAATACTTCCATTTACTTCAATTATCCAGGGTGGTCTTTC
66 CTTCAACTATTCAATACTTCAATTTACTTCAATGATCCAGGGTGGTCCTCC
* ** * * * * * *
6004 TTCAATTCTTCAGTTATTCAATGCTTCCCTTTACTTCAATGATCCATGGCGATCTTTCTTCGATT
1 TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTCCTACAATT
*
6069 CTTCAATTATTCAAT
66 CTTCAACTATTCAAT
6084 GCCTCATTTT
Statistics
Matches: 161, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
114 92 0.57
115 2 0.01
116 67 0.42
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (116 bp):
TTCAATTCTTCAATTATTCAATGCTTCAATTTACTTCAATGATCCAGGGTGGTCTTCCTACAATT
CTTCAACTATTCAATACTTCAATTTACTTCAATGATCCAGGGTGGTCCTCC
Found at i:6142 original size:23 final size:22
Alignment explanation
Indices: 6112--6177 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
6102 TGGTGCTTCA
*
6112 ACTTCAATTTCAATTCTTCAAT
1 ACTTCAATTTCAATTCTTCAAC
6134 ACTTTCAATTTCAATTCTTCAAC
1 AC-TTCAATTTCAATTCTTCAAC
* *
6157 GCTTCAATTTCAAGTCTTCAA
1 ACTTCAATTTCAATTCTTCAA
6178 ATTCCAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.50
23 20 0.50
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.42
Consensus pattern (22 bp):
ACTTCAATTTCAATTCTTCAAC
Found at i:6222 original size:16 final size:16
Alignment explanation
Indices: 6201--6235 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6191 ATGCTTCAAT
6201 TTCGATTCTTCAATAC
1 TTCGATTCTTCAATAC
* *
6217 TTCGATTTTTCAATGC
1 TTCGATTCTTCAATAC
6233 TTC
1 TTC
6236 AATTTCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (16 bp):
TTCGATTCTTCAATAC
Found at i:6251 original size:96 final size:97
Alignment explanation
Indices: 6120--6321 Score: 273
Period size: 96 Copynumber: 2.1 Consensus size: 97
6110 CAACTTCAAT
* * * *
6120 TTCAATTCTTCAATACTTTCAATTTCAATTCTTCAACGCTTCAATTTCAAGTCTTCAAATTCCAA
1 TTCAATTTTTCAATACTTTCAATTTCAATTCTTCAAAGCTTCAAATCCAAGTCTTCAAATTCCAA
* * *
6185 ATGTGAATGCTTCAATTTCGATTCTTCAATAC
66 ATGTCAATGCTTCAATTTCAATTCTTAAATAC
* * * *
6217 TTCGATTTTTCAATGC-TTCAATTTCAATAT-TTCAAAGCTTCAAATCCAATTCTTCAAGTTCCA
1 TTCAATTTTTCAATACTTTCAATTTCAAT-TCTTCAAAGCTTCAAATCCAAGTCTTCAAATTCCA
*
6280 AATGTCAATGTTTCAATTTCAATTCTTAAATAC
65 AATGTCAATGCTTCAATTTCAATTCTTAAATAC
6313 TTCAATTTT
1 TTCAATTTT
6322 AATTCGTCCA
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 77 0.85
97 14 0.15
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.43
Consensus pattern (97 bp):
TTCAATTTTTCAATACTTTCAATTTCAATTCTTCAAAGCTTCAAATCCAAGTCTTCAAATTCCAA
ATGTCAATGCTTCAATTTCAATTCTTAAATAC
Found at i:6273 original size:22 final size:22
Alignment explanation
Indices: 6224--6266 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6214 TACTTCGATT
* * *
6224 TTTCAATGCTTCAATTTCAATA
1 TTTCAAAGCTTCAAATCCAATA
6246 TTTCAAAGCTTCAAATCCAAT
1 TTTCAAAGCTTCAAATCCAAT
6267 TCTTCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (22 bp):
TTTCAAAGCTTCAAATCCAATA
Found at i:6339 original size:96 final size:96
Alignment explanation
Indices: 6138--6345 Score: 251
Period size: 96 Copynumber: 2.2 Consensus size: 96
6128 TTCAATACTT
* * * *
6138 TCAATTTCAATTCTTCAACGCTTCAATTTCAAGTCTTCAAATTCCAAATGTGAATGCTTCAATTT
1 TCAATTTCAATTCTTCAAAGCTTCAAATCCAAGTCTTCAAATTCCAAATGTCAATGCTTCAATTT
* * * *
6203 CGATTCTTCAATACTTCGATTTTTCAATGCT
66 CAATTCTTAAATACTTCGAATTTTCAATGCG
* * *
6234 TCAATTTCAATAT-TTCAAAGCTTCAAATCCAATTCTTCAAGTTCCAAATGTCAATGTTTCAATT
1 TCAATTTCAAT-TCTTCAAAGCTTCAAATCCAAGTCTTCAAATTCCAAATGTCAATGCTTCAATT
*
6298 TCAATTCTTAAATACTTC-AATTTT-AATTCG
65 TCAATTCTTAAATACTTCGAATTTTCAATGCG
*
6328 TCCATGCTTCAATTCTTC
1 TCAAT--TTCAATTCTTC
6346 GAATTCAATT
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
94 8 0.08
95 6 0.06
96 80 0.84
97 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.42
Consensus pattern (96 bp):
TCAATTTCAATTCTTCAAAGCTTCAAATCCAAGTCTTCAAATTCCAAATGTCAATGCTTCAATTT
CAATTCTTAAATACTTCGAATTTTCAATGCG
Done.