Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006673.1 Corchorus capsularis cultivar CVL-1 contig06694, 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: 38976
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:965 original size:6 final size:6
Alignment explanation
Indices: 954--980 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
944 ATTAATCTGG
954 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
981 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:12967 original size:26 final size:26
Alignment explanation
Indices: 12931--13013 Score: 87
Period size: 32 Copynumber: 3.0 Consensus size: 26
12921 ACACCGCCCC
12931 TTTACATACTTTGAAAAAGAAATAAG
1 TTTACATACTTTGAAAAAGAAATAAG
*
12957 TTTACATACTTTTGTATTTTACAAA-AATTAAG
1 TTTACATAC-TTTG-A----A-AAAGAAATAAG
12989 TTTACATACTTTGAAAAAGAAATAA
1 TTTACATACTTTGAAAAAGAAATAA
13014 AAACCAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
25 3 0.06
26 15 0.32
27 4 0.09
28 1 0.02
30 1 0.02
31 4 0.09
32 16 0.34
33 3 0.06
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (26 bp):
TTTACATACTTTGAAAAAGAAATAAG
Found at i:14257 original size:14 final size:13
Alignment explanation
Indices: 14235--14266 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
14225 CAGCGGCACC
14235 AAAAAATATACAG
1 AAAAAATATACAG
14248 AAAAATATATACAG
1 AAAAA-ATATACAG
14262 AAAAA
1 AAAAA
14267 GCTAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (13 bp):
AAAAAATATACAG
Found at i:19594 original size:50 final size:50
Alignment explanation
Indices: 19530--19636 Score: 153
Period size: 50 Copynumber: 2.1 Consensus size: 50
19520 AAACAAGAAG
* ** *
19530 TTTTCAAAATAAGATTGTATTCCATTTGTGAGTTGAATATCAAAATTCGA-
1 TTTTCAAAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTC-AC
*
19580 TTTTCATAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCAC
1 TTTTCAAAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCAC
19630 TTTTCAA
1 TTTTCAA
19637 GGGGCATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 1 0.02
50 49 0.98
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (50 bp):
TTTTCAAAATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCAC
Found at i:20305 original size:69 final size:68
Alignment explanation
Indices: 20122--20339 Score: 269
Period size: 69 Copynumber: 3.1 Consensus size: 68
20112 CGAATGCTTC
* * * * *
20122 GACTTTTCCATAAGTCAAACTCGTTTCCATACGAGGTAGCTCAAACTTTGGTTCCACCCAAGCAT
1 GACTTTTCCACAAGCCAAACTCGTTTCCATACGAGGTA-ATCAAGCTTTGGTTCCATCCAAGCA-
*
20187 TCA-A
64 ACATA
* *
20191 GGGCTTTTCGACAAGCCAAACTCGTTTCCATACGAGGTAGATCAAGCTTTGGTTCCATCCAAGCA
1 -GACTTTTCCACAAGCCAAACTCGTTTCCATACGAGGTA-ATCAAGCTTTGGTTCCATCCAAGCA
20256 ACATA
64 ACATA
* *
20261 GCCTTTTCCACAAGCCAAACTCGTTTCCATACGA-GTCAATTCAAGCGTTGGTTCCATCCAAGCA
1 GACTTTTCCACAAGCCAAACTCGTTTCCATACGAGGT-AA-TCAAGCTTTGGTTCCATCCAAGCA
*
20325 ACATG
64 ACATA
20330 GACTTTTCCA
1 GACTTTTCCA
20340 TAACCCAAGT
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
68 3 0.02
69 71 0.54
70 58 0.44
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (68 bp):
GACTTTTCCACAAGCCAAACTCGTTTCCATACGAGGTAATCAAGCTTTGGTTCCATCCAAGCAAC
ATA
Found at i:20538 original size:22 final size:22
Alignment explanation
Indices: 20512--20637 Score: 134
Period size: 22 Copynumber: 5.8 Consensus size: 22
20502 TGACAGTTGG
*
20512 TCAATTTCAATTCTTTAATACT
1 TCAATTTCAATTCTTCAATACT
* *
20534 TCAATTTCAAATCTTCAATCCT
1 TCAATTTCAATTCTTCAATACT
* *
20556 TCAATGTCAATTCTTCAATGCT
1 TCAATTTCAATTCTTCAATACT
20578 TCAATTTCAATTCTTCAAT--T
1 TCAATTTCAATTCTTCAATACT
* **
20598 CCAATTCTTCAATAGTTCAAT--T
1 TCAA-T-TTCAATTCTTCAATACT
20620 TCAATTTCAATTCTTCAA
1 TCAATTTCAATTCTTCAA
20638 ATCAAATCCT
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.17
21 2 0.02
22 72 0.81
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.44
Consensus pattern (22 bp):
TCAATTTCAATTCTTCAATACT
Found at i:20557 original size:8 final size:7
Alignment explanation
Indices: 20512--20944 Score: 95
Period size: 8 Copynumber: 59.7 Consensus size: 7
20502 TGACAGTTGG
20512 TCAAT-T
1 TCAATCT
20518 TCAATTCT
1 TCAA-TCT
*
20526 TTAATACT
1 TCAAT-CT
20534 TCAAT-T
1 TCAATCT
20540 TCAAATCT
1 TC-AATCT
20548 TCAATCCT
1 TCAAT-CT
*
20556 TCAAT-G
1 TCAATCT
20562 TCAATTCT
1 TCAA-TCT
20570 TCAATGCT
1 TCAAT-CT
20578 TCAAT-T
1 TCAATCT
20584 TCAATTCT
1 TCAA-TCT
20592 TCAAT-T
1 TCAATCT
*
20598 CCAATTCT
1 TCAA-TCT
*
20606 TCAATAGT
1 TCAAT-CT
20614 TCAAT-T
1 TCAATCT
20620 TCAAT-T
1 TCAATCT
20626 TCAATTCT
1 TCAA-TCT
20634 TCAAATC-
1 TC-AATCT
*
20641 -AAATCCT
1 TCAAT-CT
*
20648 TCAATGTT
1 TCAAT-CT
20656 TCAAT-T
1 TCAATCT
*
20662 TCAATTTT
1 TCAA-TCT
*
20670 TCAATGTT
1 TCAAT-CT
20678 TCAAT-T
1 TCAATCT
20684 TCAATTCT
1 TCAA-TCT
*
20692 TCAA-AT
1 TCAATCT
20698 TCAATCCT
1 TCAAT-CT
*
20706 CCAATGCT
1 TCAAT-CT
20714 TCAAT-T
1 TCAATCT
20720 TCAAAT-T
1 TC-AATCT
*
20727 CCAAATGC-
1 TC-AAT-CT
20735 -CAATGCT
1 TCAAT-CT
20742 TCAAT-T
1 TCAATCT
**
20748 TCGCTTCT
1 TC-AATCT
20756 TCAATACT
1 TCAAT-CT
*
20764 TCAATAT
1 TCAATCT
* * *
20771 CCATTTT
1 TCAATCT
20778 TCAATTCT
1 TCAA-TCT
20786 TCAAT-T
1 TCAATCT
* *
20792 TCCATTT
1 TCAATCT
20799 CTCAAATCT
1 -TC-AATCT
20808 TCAAT-T
1 TCAATCT
*
20814 TCAATATT
1 TCAAT-CT
20822 TCAATGCT
1 TCAAT-CT
*
20830 TCAGT-T
1 TCAATCT
20836 TCAAT-T
1 TCAATCT
20842 TCAATGCT
1 TCAAT-CT
*
20850 TCAA-GT
1 TCAATCT
20856 TCAATCCT
1 TCAAT-CT
20864 TCAA--T
1 TCAATCT
20869 TCAATGCT
1 TCAAT-CT
*
20877 TCAATTT
1 TCAATCT
**
20884 ATCTTTCT
1 -TCAATCT
20892 TCAATGCT
1 TCAAT-CT
*
20900 TCTATCAT
1 TCAATC-T
*
20908 CCAATGCT
1 TCAAT-CT
20916 TCAATTCT
1 TCAA-TCT
*
20924 TCAATAAT
1 TCAAT-CT
20932 TCAATGCT
1 TCAAT-CT
20940 TCAAT
1 TCAAT
20945 TTACTTCAAA
Statistics
Matches: 323, Mismatches: 50, Indels: 106
0.67 0.10 0.22
Matches are distributed among these distances:
5 8 0.02
6 85 0.26
7 48 0.15
8 175 0.54
9 7 0.02
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (7 bp):
TCAATCT
Found at i:20672 original size:22 final size:21
Alignment explanation
Indices: 20582--20842 Score: 102
Period size: 22 Copynumber: 12.0 Consensus size: 21
20572 AATGCTTCAA
*
20582 TTTCAATTCTTCAATTCCAATT
1 TTTCAATT-TTCAATTTCAATT
* *
20604 CTTCAATAGTTCAATTTCAA--
1 TTTCAAT-TTTCAATTTCAATT
* *
20624 TTTCAATTCTTCAA-ATCAAATC
1 TTTCAATT-TTCAATTTC-AATT
*
20646 CTTCAATGTTTCAATTTCAATT
1 TTTCAAT-TTTCAATTTCAATT
20668 TTTCAATGTTTCAATTTCAATT
1 TTTCAAT-TTTCAATTTCAATT
* * * *
20690 CTTCAA-ATTCAATCCTCCAATG
1 TTTCAATTTTCAAT--TTCAATT
* * *
20712 CTTCAA-TTTCAAATTCCAA-A
1 TTTCAATTTTC-AATTTCAATT
** * **
20732 TGCCAATGCTTCAATTTCGCTT
1 TTTCAAT-TTTCAATTTCAATT
* * * *
20754 CTTCAATACTTCAATATCCATT
1 TTTCAAT-TTTCAATTTCAATT
*
20776 TTTCAATTCTTCAATTTCCATT
1 TTTCAATT-TTCAATTTCAATT
* * *
20798 TCTCAAATCTTCAATTTCAATA
1 TTTC-AATTTTCAATTTCAATT
* *
20820 TTTCAATGCTTCAGTTTCAATT
1 TTTCAAT-TTTCAATTTCAATT
20842 T
1 T
20843 CAATGCTTCA
Statistics
Matches: 182, Mismatches: 41, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
19 2 0.01
20 22 0.12
21 13 0.07
22 136 0.75
23 9 0.05
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTCAATTTTCAATTTCAATT
Found at i:20702 original size:14 final size:14
Alignment explanation
Indices: 20532--20883 Score: 123
Period size: 14 Copynumber: 24.6 Consensus size: 14
20522 TTCTTTAATA
*
20532 CTTCAATTTCAAAT
1 CTTCAATTTCAATT
20546 CTTCAATCCTTCAA-T
1 CTTCAAT--TTCAATT
* *
20561 -GTCAATTCTTCAATG
1 CTTCAA-T-TTCAATT
20576 CTTCAATTTCAATT
1 CTTCAATTTCAATT
*
20590 CTTCAATTCCAATT
1 CTTCAATTTCAATT
20604 CTTCAATAGTTCAA-T
1 CTTCAAT--TTCAATT
20619 -TTCAATTTCAATT
1 CTTCAATTTCAATT
* *
20632 CTTCAA-ATCAAATC
1 CTTCAATTTC-AATT
20646 CTTCAATGTTTCAA-T
1 CTTCAA--TTTCAATT
20661 -TTCAATTTTTCAATGT
1 CTTCAA--TTTCAAT-T
20677 -TTCAATTTCAATT
1 CTTCAATTTCAATT
* *
20690 CTTCAAATTCAATC
1 CTTCAATTTCAATT
*
20704 CTCCAATGCTTCAATTT
1 CTTCAAT--TTCAA-TT
** *
20721 CAAATTCCAAATGCCAATG
1 C---TT-C-AATTTCAATT
**
20740 CTTCAATTTCGCTT
1 CTTCAATTTCAATT
20754 CTTCAATACTTCAATAT
1 CTTCAAT--TTCAAT-T
*
20771 C--CATTTTTCAATT
1 CTTCA-ATTTCAATT
*
20784 CTTCAATTTCCA-T
1 CTTCAATTTCAATT
*
20797 -TTC----TCAAAT
1 CTTCAATTTCAATT
20806 CTTCAATTTCAATAT
1 CTTCAATTTCAAT-T
*
20821 -TTCAATGCTTC-AGT
1 CTTCAAT--TTCAATT
*
20835 -TTCAATTTCAATG
1 CTTCAATTTCAATT
* *
20848 CTTCAAGTTCAATC
1 CTTCAATTTCAATT
*
20862 CTTCAA-TTCAATG
1 CTTCAATTTCAATT
20875 CTTCAATTT
1 CTTCAATTT
20884 ATCTTTCTTC
Statistics
Matches: 258, Mismatches: 38, Indels: 84
0.68 0.10 0.22
Matches are distributed among these distances:
8 3 0.01
9 1 0.00
10 3 0.01
12 11 0.04
13 20 0.08
14 157 0.61
15 11 0.04
16 36 0.14
17 6 0.02
19 2 0.01
20 4 0.02
21 1 0.00
22 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (14 bp):
CTTCAATTTCAATT
Found at i:20745 original size:58 final size:57
Alignment explanation
Indices: 20605--20747 Score: 143
Period size: 58 Copynumber: 2.5 Consensus size: 57
20595 ATTCCAATTC
* * *
20605 TTCAATAGTT-CAAT-TTCAATTTCAATTCTTCAAATCAAATCCTTCAATGTTTCAAT
1 TTCAATA-TTCCAATGTCCAATTTCAATTCTTCAAATCAAATCCTCCAATGCTTCAAT
* * *
20661 TTCAATTTTTCAATGTTTCAATTTCAATTCTTCAAATTC-AATCCTCCAATGCTTCAAT
1 TTCAATATTCCAATG-TCCAATTTCAATTCTTCAAA-TCAAATCCTCCAATGCTTCAAT
20719 TTCAA-ATTCCAAATG-CCAATGCTTCAATT
1 TTCAATATTCC-AATGTCCAAT--TTCAATT
20748 TCGCTTCTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
55 2 0.03
56 14 0.19
57 3 0.04
58 53 0.72
59 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (57 bp):
TTCAATATTCCAATGTCCAATTTCAATTCTTCAAATCAAATCCTCCAATGCTTCAAT
Found at i:20852 original size:28 final size:28
Alignment explanation
Indices: 20532--20944 Score: 137
Period size: 28 Copynumber: 14.2 Consensus size: 28
20522 TTCTTTAATA
20532 CTTCAAT-TTCAAATCTTCAATCCTTCAATG
1 CTTCAATGTTC-AATCTTCAAT--TTCAATG
* *
20562 --TCAATTCTTCAATGCTTCAATTTCAATT
1 CTTCAA-TGTTCAAT-CTTCAATTTCAATG
*
20590 CTTCAAT-TCCAATTCTTCAATAGTTCAAT-
1 CTTCAATGTTCAA-TCTTCAAT--TTCAATG
* *
20619 -TTCAAT-TTCAATTCTTCAA-ATCAAATC
1 CTTCAATGTTCAA-TCTTCAATTTC-AATG
20646 CTTCAATGTTTCAAT-TTCAATTTTTCAATG
1 CTTCAATG-TTCAATCTTCAA--TTTCAATG
* * *
20676 TTTCAAT-TTCAATTCTTCAAATTCAATC
1 CTTCAATGTTCAA-TCTTCAATTTCAATG
* *
20704 CTCCAATGCTTCAAT-TTCAAATTCCAAATG
1 CTTCAATG-TTCAATCTTC-AATTTC-AATG
** *
20734 C--CAATGCTTCAAT-TTCGCTTCTTCAATA
1 CTTCAATG-TTCAATCTTC-AAT-TTCAATG
* * * *
20762 CTTCAATATCCATTTTTCAATTCTTCAAT-
1 CTTCAATGTTCAATCTTCAA-T-TTCAATG
* * *
20791 -TTCCATTTCTCAAATCTTCAATTTCAATA
1 CTTCAATGT-TC-AATCTTCAATTTCAATG
* *
20820 TTTCAATGCTTCAGT-TTCAATTTCAATG
1 CTTCAATG-TTCAATCTTCAATTTCAATG
20848 CTTCAA-GTTCAATCCTTCAA-TTCAATG
1 CTTCAATGTTCAAT-CTTCAATTTCAATG
* ** *
20875 CTTCAATTTATCTTTCTTCAATGCTTCTAT-
1 CTTCAATGT-TCAATCTTCAAT--TTCAATG
*
20905 CATCCAATGCTTCAATTCTTCAATAATTCAATG
1 C-TTCAATG-TTCAA-TCTTCAAT--TTCAATG
20938 CTTCAAT
1 CTTCAAT
20945 TTACTTCAAA
Statistics
Matches: 293, Mismatches: 47, Indels: 84
0.69 0.11 0.20
Matches are distributed among these distances:
25 2 0.01
26 8 0.03
27 14 0.05
28 130 0.44
29 26 0.09
30 78 0.27
31 15 0.05
32 19 0.06
33 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.43
Consensus pattern (28 bp):
CTTCAATGTTCAATCTTCAATTTCAATG
Found at i:21040 original size:8 final size:8
Alignment explanation
Indices: 21027--21097 Score: 64
Period size: 8 Copynumber: 9.6 Consensus size: 8
21017 CAGTTTCAAT
21027 TTCAATTC
1 TTCAATTC
*
21035 TTCAATGC
1 TTCAATTC
21043 TTCAA-T-
1 TTCAATTC
21049 TTCAATTC
1 TTCAATTC
**
21057 TTCAACGC
1 TTCAATTC
21065 TTCAA-T-
1 TTCAATTC
*
21071 TTCAATAC
1 TTCAATTC
21079 TTCAA-T-
1 TTCAATTC
21085 TTCAATTC
1 TTCAATTC
21093 TTCAA
1 TTCAA
21098 ATTCCAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
6 15 0.30
7 2 0.04
8 33 0.66
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.44
Consensus pattern (8 bp):
TTCAATTC
Found at i:21040 original size:14 final size:14
Alignment explanation
Indices: 21021--21305 Score: 97
Period size: 14 Copynumber: 20.1 Consensus size: 14
21011 ATGCCCCAGT
21021 TTCAATTTCAATTC
1 TTCAATTTCAATTC
21035 TTCAATGCTTCAA-T-
1 TTCAAT--TTCAATTC
**
21049 TTCAATTCTTCAACGC
1 TTCAA-T-TTCAATTC
*
21065 TTCAATTTCAATAC
1 TTCAATTTCAATTC
21079 TTCAATTTCAATTC
1 TTCAATTTCAATTC
* *
21093 TTCAAATTCCAAATGC
1 TTC-AATTTC-AATTC
21109 --CAATGCTTCAA-T-
1 TTCAAT--TTCAATTC
21121 TTCAATCCTTCAATGT-
1 TTCAAT--TTCAAT-TC
*
21137 TTCAATTTCAATTT
1 TTCAATTTCAATTC
21151 TTCAATGTTTCAA-T-
1 TTCAA--TTTCAATTC
*
21165 TTCAATATTTCAATGC
1 TTC-A-ATTTCAATTC
* *
21181 TTCAAATCCAATTC
1 TTCAATTTCAATTC
* *
21195 TTCAAATTCCAAAT-
1 TTC-AATTTCAATTC
*
21209 GTCAATGTTTCAA-T-
1 TTCAA--TTTCAATTC
*
21223 TTCAATATGTCAATGC
1 TTCAAT-T-TCAATTC
*
21239 TTCAATTTCGATTC
1 TTCAATTTCAATTC
21253 TTC-----C-ATTGC
1 TTCAATTTCAATT-C
21262 TTCAATTTCAATTC
1 TTCAATTTCAATTC
21276 TTCGAA-TTCAATGT-
1 TTC-AATTTCAAT-TC
21290 TTCAATTTCAATTC
1 TTCAATTTCAATTC
21304 TT
1 TT
21306 TGAAGCCTCT
Statistics
Matches: 212, Mismatches: 21, Indels: 76
0.69 0.07 0.25
Matches are distributed among these distances:
8 3 0.01
9 5 0.02
12 1 0.00
13 10 0.05
14 123 0.58
15 33 0.16
16 37 0.17
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.44
Consensus pattern (14 bp):
TTCAATTTCAATTC
Found at i:21046 original size:22 final size:22
Alignment explanation
Indices: 21021--21199 Score: 175
Period size: 22 Copynumber: 7.9 Consensus size: 22
21011 ATGCCCCAGT
21021 TTCAATTTCAATTCTTCAATGC
1 TTCAATTTCAATTCTTCAATGC
*
21043 TTCAATTTCAATTCTTCAACGC
1 TTCAATTTCAATTCTTCAATGC
*
21065 TTCAATTTCAATACTTCAAT--
1 TTCAATTTCAATTCTTCAATGC
*
21085 TTCAATTCTTCAAATTCCAAATGCCAATGC
1 TTCAA-T-TTC-AATT-C---T-TCAATGC
* *
21115 TTCAATTTCAATCCTTCAATGT
1 TTCAATTTCAATTCTTCAATGC
* *
21137 TTCAATTTCAATTTTTCAATGT
1 TTCAATTTCAATTCTTCAATGC
21159 TTCAATTTCAATAT-TTCAATGC
1 TTCAATTTCAAT-TCTTCAATGC
* *
21181 TTCAAATCCAATTCTTCAA
1 TTCAATTTCAATTCTTCAA
21200 ATTCCAAATG
Statistics
Matches: 132, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.04
21 2 0.02
22 101 0.77
23 5 0.04
24 1 0.01
26 1 0.01
27 4 0.03
28 7 0.05
29 1 0.01
30 5 0.04
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (22 bp):
TTCAATTTCAATTCTTCAATGC
Found at i:21083 original size:58 final size:58
Alignment explanation
Indices: 21021--21247 Score: 212
Period size: 58 Copynumber: 3.9 Consensus size: 58
21011 ATGCCCCAGT
* *
21021 TTCAATTTCAATTCTTCAATGCTTCAATTTCAAT-TCTTCAACGCTTCAATTTCAATAC
1 TTCAATTTCAATTCTTCAATGTTTCAATTTCAATAT-TTCAATGCTTCAATTTCAATAC
* * ** ** **
21079 TTCAATTTCAATTCTTCAA-ATTCCAAATGCCAATGCTTCAAT--TTCAATCCTTCAATGT
1 TTCAATTTCAATTCTTCAATGTTTC-AATTTCAATATTTCAATGCTTCAAT--TTCAATAC
* * * *
21137 TTCAATTTCAATTTTTCAATGTTTCAATTTCAATATTTCAATGCTTCAAATCCAATTC
1 TTCAATTTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAATTTCAATAC
* * * *
21195 TTCAAATTCCAAAT-GTCAATGTTTCAATTTCAATATGTCAATGCTTCAATTTC
1 TTC-AATTTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAATTTC
21248 GATTCTTCCA
Statistics
Matches: 135, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
56 6 0.04
57 2 0.01
58 111 0.82
59 11 0.08
60 5 0.04
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.43
Consensus pattern (58 bp):
TTCAATTTCAATTCTTCAATGTTTCAATTTCAATATTTCAATGCTTCAATTTCAATAC
Found at i:21246 original size:22 final size:20
Alignment explanation
Indices: 21021--21274 Score: 120
Period size: 22 Copynumber: 11.7 Consensus size: 20
21011 ATGCCCCAGT
21021 TTCAATTTCAATTCTTCAATGC
1 TTCAATTTCAA-T-TTCAATGC
*
21043 TTCAATTTCAATTCTTCAACGC
1 TTCAATTTCAA-T-TTCAATGC
21065 TTCAATTTCAATACTTCAAT--
1 TTCAATTTCAAT--TTCAATGC
*
21085 TTCAATTCTTCAAATTCCAAATGC
1 TTCAA-T-TTC-AATTTC-AATGC
*
21109 --CAATGCTTCAATTTCAATCC
1 TTCAAT--TTCAATTTCAATGC
**
21129 TTCAATGTTTCAATTTCAATTT
1 TTCAA--TTTCAATTTCAATGC
**
21151 TTCAATGTTTCAATTTCAATAT
1 TTCAA--TTTCAATTTCAATGC
* * *
21173 TTCAATGCTTCAAATCCAATTC
1 TTCAAT--TTCAATTTCAATGC
* * *
21195 TTCAAATTCCAAATGTCAATGT
1 TTC-AATTTC-AATTTCAATGC
21217 TTCAATTTCAATATGTCAATGC
1 TTCAATTTCAAT-T-TCAATGC
* *
21239 TTCAATTTCGATTCTTCCATTGC
1 TTCAATTTC-AAT-TT-CAATGC
21262 TTCAATTTCAATT
1 TTCAATTTCAATT
21275 CTTCGAATTC
Statistics
Matches: 187, Mismatches: 25, Indels: 41
0.74 0.10 0.16
Matches are distributed among these distances:
20 13 0.07
21 18 0.10
22 132 0.71
23 23 0.12
24 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (20 bp):
TTCAATTTCAATTTCAATGC
Found at i:22132 original size:26 final size:26
Alignment explanation
Indices: 22096--22178 Score: 87
Period size: 32 Copynumber: 3.0 Consensus size: 26
22086 ACACCGCCCC
22096 TTTACATACTTTGAAAAAGAAATAAG
1 TTTACATACTTTGAAAAAGAAATAAG
*
22122 TTTACATACTTTTGTATTTTACAAA-AATTAAG
1 TTTACATAC-TTTG-A----A-AAAGAAATAAG
22154 TTTACATACTTTGAAAAAGAAATAA
1 TTTACATACTTTGAAAAAGAAATAA
22179 AAACCAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
25 3 0.06
26 15 0.32
27 4 0.09
28 1 0.02
30 1 0.02
31 4 0.09
32 16 0.34
33 3 0.06
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (26 bp):
TTTACATACTTTGAAAAAGAAATAAG
Found at i:23395 original size:14 final size:14
Alignment explanation
Indices: 23373--23418 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
23363 CAGCGGCACC
23373 AAAAA-ATATACAG
1 AAAAATATATACAG
23386 AAAAATATATACAG
1 AAAAATATATACAG
23400 AAAAATATATACAG
1 AAAAATATATACAG
23414 AAAAA
1 AAAAA
23419 GCTAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 5 0.16
14 27 0.84
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAATATATACAG
Found at i:23431 original size:28 final size:27
Alignment explanation
Indices: 23373--23432 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
23363 CAGCGGCACC
* *
23373 AAAAAATATACAGAAAAATATATACAG
1 AAAAAATATACAGAAAAAGATATAAAG
*
23400 AAAAATATATACAGAAAAAGCTA-AAAG
1 AAAAA-ATATACAGAAAAAGATATAAAG
23427 AAAAAA
1 AAAAAA
23433 AAGGGAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 13 0.45
28 15 0.52
ACGTcount: A:0.70, C:0.07, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAAATATACAGAAAAAGATATAAAG
Found at i:30874 original size:19 final size:18
Alignment explanation
Indices: 30850--30886 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
30840 TTGAAGATTT
30850 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
30869 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
30887 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:36967 original size:19 final size:18
Alignment explanation
Indices: 36943--36979 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
36933 TTGAAGATTT
36943 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
36962 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
36980 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Done.