Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011370.1 Corchorus capsularis cultivar CVL-1 contig11391, 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: 26663
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:138 original size:15 final size:15
Alignment explanation
Indices: 120--150 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
110 TTAGGCTGAG
120 TTTTTTTC-TTTTCT
1 TTTTTTTCTTTTTCT
134 TTTTTTTCTTTTTCT
1 TTTTTTTCTTTTTCT
149 TT
1 TT
151 GAGTTGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTCTTTTTCT
Found at i:851 original size:15 final size:14
Alignment explanation
Indices: 801--854 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
791 ACTCAAAAAC
801 TTTTTTGAAAAC-T
1 TTTTTTGAAAACAT
* *
814 CATTTTTGAAAACCT
1 -TTTTTTGAAAACAT
*
829 TTTCTTGAAAACAAT
1 TTTTTTGAAAAC-AT
844 TTTTTTGAAAA
1 TTTTTTGAAAA
855 GTATCTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (14 bp):
TTTTTTGAAAACAT
Found at i:4045 original size:19 final size:19
Alignment explanation
Indices: 3951--4047 Score: 71
Period size: 19 Copynumber: 5.4 Consensus size: 19
3941 AATTATTTAC
3951 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
* * * *
3970 CTAATT--ACTG-ATTTAC
1 TTAATTACACCGAATTAAG
3986 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
* * * * *
4005 TTGACT--ACTG-ATTTAC
1 TTAATTACACCGAATTAAG
4021 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
4040 TTAATTAC
1 TTAATTAC
4048 CAATTTAATT
Statistics
Matches: 54, Mismatches: 18, Indels: 12
0.64 0.21 0.14
Matches are distributed among these distances:
16 17 0.31
17 6 0.11
18 6 0.11
19 25 0.46
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TTAATTACACCGAATTAAG
Found at i:4054 original size:35 final size:35
Alignment explanation
Indices: 3945--4204 Score: 200
Period size: 35 Copynumber: 7.3 Consensus size: 35
3935 CTATTTAATT
* **
3945 ATTTACTTAATTACACCGAATTAAGCTAATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCA
* * **
3980 ATTTACTTAATTACACCGAATTAAGTTGACTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCA
4015 ATTTACTTAATTACACCGAATTAAGTTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCA
* * * * * *
4050 ATTTAATTGATT-TACC-AGTTTACTTAATTGCACCGA
1 ATTTACTTAATTACACCGAATTAAGTTAATT--ACC-A
* * * *** * * *
4086 ATTAAGTTGATTATCAAATTACTTAATTTAATTATCA
1 ATTTACTTAATTA-C-ACCGAATTAAGTTAATTACCA
* * *
4123 ATTTACTTAATTGCACCGAAATAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCA
* * *
4158 AATTACTTAATAACACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCA
*
4193 AATTACTTAATT
1 ATTTACTTAATT
4205 TAATTGCCAA
Statistics
Matches: 179, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
33 10 0.06
34 3 0.02
35 131 0.73
36 12 0.07
37 10 0.06
38 2 0.01
39 1 0.01
40 10 0.06
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACCA
Found at i:4075 original size:52 final size:54
Alignment explanation
Indices: 4015--4168 Score: 186
Period size: 56 Copynumber: 2.8 Consensus size: 54
4005 TTGACTACTG
* * *
4015 ATTTACTTAATTACACCGAATTAAGTTAATTACCAA-T-TTAATTGATTTACCA
1 ATTTACTTAATTGCACCGAATTAAGTTGATTACCAATTATTAATTGAATTACCA
* * * *
4067 GTTTACTTAATTGCACCGAATTAAGTTGATTATCAAATTACTTAATTTAATTATCA
1 ATTTACTTAATTGCACCGAATTAAGTTGATTA-CCAATTA-TTAATTGAATTACCA
*
4123 ATTTACTTAATTGCACCGAAATAAGTTGATTACCAAATTACTTAAT
1 ATTTACTTAATTGCACCGAATTAAGTTGATTACC-AATTA-TTAAT
4169 AACACCGAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
52 29 0.33
53 3 0.03
54 1 0.01
55 1 0.01
56 53 0.61
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (54 bp):
ATTTACTTAATTGCACCGAATTAAGTTGATTACCAATTATTAATTGAATTACCA
Found at i:4111 original size:21 final size:21
Alignment explanation
Indices: 4087--4132 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
4077 TTGCACCGAA
*
4087 TTAAGTTGATTATCAAATTAC
1 TTAAGTTAATTATCAAATTAC
* *
4108 TTAATTTAATTATCAATTTAC
1 TTAAGTTAATTATCAAATTAC
4129 TTAA
1 TTAA
4133 TTGCACCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (21 bp):
TTAAGTTAATTATCAAATTAC
Found at i:4133 original size:21 final size:21
Alignment explanation
Indices: 4095--4134 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4085 AATTAAGTTG
4095 ATTATCAAATTACTTAATTTA
1 ATTATCAAATTACTTAATTTA
*
4116 ATTATCAATTTACTTAATT
1 ATTATCAAATTACTTAATT
4135 GCACCGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATCAAATTACTTAATTTA
Found at i:4181 original size:91 final size:91
Alignment explanation
Indices: 3947--4340 Score: 469
Period size: 91 Copynumber: 4.4 Consensus size: 91
3937 ATTTAATTAT
* * ** * *
3947 TTACTTAATTACACCGAATTAAGCTAATTACTGATTTACTTAATTACACCGAATTAAGTTGACTA
1 TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGATTA
** * * *
4012 CTGATTTACTTAA-TT-A-CACCGAA
66 CCAAATTACTTAATTTAATTACCAAA
* ** *
4035 TTAAGTTAATT--ACC-AATTTAA-TTGATTTACCAGTTTACTTAATTGCACCGAATTAAGTTGA
1 TT-ACTTAATTACACCGAA-TTAAGTTGA-TTACCAAATTACTTAATTACACCGAATTAAGTTGA
* * *
4096 TTATCAAATTACTTAATTTAATTATCAAT
63 TTACCAAATTACTTAATTTAATTACCAAA
* * *
4125 TTACTTAATTGCACCGAAATAAGTTGATTACCAAATTACTTAATAACACCGAATTAAGTTGATTA
1 TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGATTA
*
4190 CCAAATTACTTAATTTAATTGCCAAA
66 CCAAATTACTTAATTTAATTACCAAA
* *
4216 TTACTTAATTACACCGAATTAAGTTGATTATCAAATTACTTAATTACACCGAATTAAGTCGATTA
1 TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGATTA
*
4281 CCAAATTATTTAATTTAATTACCAAA
66 CCAAATTACTTAATTTAATTACCAAA
* *
4307 TTACTTAATTATACCGAATTAAGTTAATTACCAA
1 TTACTTAATTACACCGAATTAAGTTGATTACCAA
4341 TTTGCTTTTT
Statistics
Matches: 260, Mismatches: 36, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
86 4 0.02
87 49 0.19
88 4 0.02
89 15 0.06
90 5 0.02
91 177 0.68
92 6 0.02
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (91 bp):
TTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTGATTA
CCAAATTACTTAATTTAATTACCAAA
Found at i:4215 original size:56 final size:56
Alignment explanation
Indices: 4155--4260 Score: 194
Period size: 56 Copynumber: 1.9 Consensus size: 56
4145 AAGTTGATTA
4155 CCAAATTACTTAATAACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTG
1 CCAAATTACTTAATAACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTG
* *
4211 CCAAATTACTTAATTACACCGAATTAAGTTGATTATCAAATTACTTAATT
1 CCAAATTACTTAATAACACCGAATTAAGTTGATTACCAAATTACTTAATT
4261 ACACCGAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.37
Consensus pattern (56 bp):
CCAAATTACTTAATAACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATTG
Found at i:4251 original size:35 final size:35
Alignment explanation
Indices: 4211--4295 Score: 143
Period size: 35 Copynumber: 2.4 Consensus size: 35
4201 AATTTAATTG
*
4211 CCAAATTACTTAATTACACCGAATTAAGTTGATTA
1 CCAAATTACTTAATTACACCGAATTAAGTCGATTA
*
4246 TCAAATTACTTAATTACACCGAATTAAGTCGATTA
1 CCAAATTACTTAATTACACCGAATTAAGTCGATTA
*
4281 CCAAATTATTTAATT
1 CCAAATTACTTAATT
4296 TAATTACCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (35 bp):
CCAAATTACTTAATTACACCGAATTAAGTCGATTA
Found at i:4301 original size:21 final size:21
Alignment explanation
Indices: 4277--4316 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4267 AATTAAGTCG
*
4277 ATTACCAAATTATTTAATTTA
1 ATTACCAAATTACTTAATTTA
4298 ATTACCAAATTACTTAATT
1 ATTACCAAATTACTTAATT
4317 ATACCGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:5069 original size:20 final size:20
Alignment explanation
Indices: 5040--5084 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5030 CTAGCCTTCA
* *
5040 TTTTCTTTTTATTTCTTCTC
1 TTTTCGTTTTATTTCTTCCC
5060 TTTTCGTTTTATTTCTTCCC
1 TTTTCGTTTTATTTCTTCCC
5080 TTTTC
1 TTTTC
5085 TTCTTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTCGTTTTATTTCTTCCC
Found at i:5097 original size:20 final size:18
Alignment explanation
Indices: 5040--5093 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
5030 CTAGCCTTCA
*
5040 TTTTCTTTTTATTTCTTCTC
1 TTTTC-TTTT-TTTCTTCCC
5060 TTTTCGTTTTATTTCTTCCC
1 TTTTC-TTTT-TTTCTTCCC
5080 TTTTCTTCTTTTTC
1 TTTTCTT-TTTTTC
5094 CTTCTTCCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTCTTTTTTTCTTCCC
Found at i:7619 original size:59 final size:59
Alignment explanation
Indices: 7547--7666 Score: 179
Period size: 59 Copynumber: 2.0 Consensus size: 59
7537 AAGGACTTAA
* *
7547 GCTCTATGATTAAAATGCAACACTACTAAATTAC-TAGACGAAAAGAAACCATGCAATAT
1 GCTCTATGATTAAAATGCAACACAACTAAATTACTTA-ACAAAAAGAAACCATGCAATAT
* * *
7606 GCTCTATGATTAAAATGCAACACAATTAAATTACTTAATAAAAAGAAATCATGCAATAT
1 GCTCTATGATTAAAATGCAACACAACTAAATTACTTAACAAAAAGAAACCATGCAATAT
7665 GC
1 GC
7667 GAAAATGCTA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 53 0.96
60 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (59 bp):
GCTCTATGATTAAAATGCAACACAACTAAATTACTTAACAAAAAGAAACCATGCAATAT
Found at i:7797 original size:28 final size:28
Alignment explanation
Indices: 7765--7837 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
7755 GTAGATTAAG
*
7765 AATGACCAAAATACCCCCTAAATGCAAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
* **
7793 AATGACCAAAATGCCCCCTAGATGTGAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
7821 AATGACCAAAATGCCCC
1 AATGACCAAAATGCCCC
7838 TGGATGACCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (28 bp):
AATGACCAAAATGCCCCCTAAATGCAAA
Found at i:15480 original size:2 final size:2
Alignment explanation
Indices: 15475--15499 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15465 TGTGTGTGTG
15475 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 T
15500 GTAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15662 original size:5 final size:5
Alignment explanation
Indices: 15654--15703 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
15644 TAAAAAAAAT
*
15654 AATAA AATAA AATAA AATAA TA-AA AATAAA AATAA TAA-AA AAT-A AATAA
1 AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA -AATAA AATAA AATAA
15703 A
1 A
15704 TTACTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 9 0.24
5 22 0.58
6 7 0.18
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:15672 original size:15 final size:14
Alignment explanation
Indices: 15644--15703 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 14
15634 GGTTTTCTTT
15644 TAAAAAAAAT--AA
1 TAAAAAAAATAAAA
15656 TAAAATAAAATAAAA
1 TAAAA-AAAATAAAA
*
15671 TAATAAAAATAAAAA
1 TAAAAAAAAT-AAAA
15686 TAATAAAAAAT-AAA
1 TAA-AAAAAATAAAA
15700 TAAA
1 TAAA
15704 TTACTAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 5 0.12
13 6 0.15
14 11 0.27
15 13 0.32
16 6 0.15
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAAAAAATAAAA
Found at i:15672 original size:18 final size:17
Alignment explanation
Indices: 15644--15699 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
15634 GGTTTTCTTT
15644 TAAAAAAAATAATAAAA
1 TAAAAAAAATAATAAAA
15661 TAAAATAAAATAATAAAAA
1 TAAAA-AAAATAAT-AAAA
*
15680 TAAAAATAATAA-AAAA
1 TAAAAAAAATAATAAAA
15696 TAAA
1 TAAA
15700 TAAATTACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 8 0.22
17 5 0.14
18 14 0.39
19 9 0.25
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAAAAAATAATAAAA
Found at i:15686 original size:33 final size:34
Alignment explanation
Indices: 15648--15713 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
15638 TTCTTTTAAA
*
15648 AAAAATAATAAAATA-AAATAAAATAATAAAAAT
1 AAAAATAATAAAAAATAAATAAAATAATAAAAAT
* *
15681 AAAAATAATAAAAAATAAATAAATTACTAAAAA
1 AAAAATAATAAAAAATAAATAAAATAATAAAAA
15714 CAGACATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (34 bp):
AAAAATAATAAAAAATAAATAAAATAATAAAAAT
Found at i:16771 original size:14 final size:14
Alignment explanation
Indices: 16752--16784 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16742 TATATTAACT
*
16752 TTAGTCCATTTAGC
1 TTAGTCCATTTAGA
16766 TTAGTCCATTTAGA
1 TTAGTCCATTTAGA
16780 TTAGT
1 TTAGT
16785 ATCATAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (14 bp):
TTAGTCCATTTAGA
Found at i:20411 original size:30 final size:31
Alignment explanation
Indices: 20374--20445 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
20364 AGTAAAAAGG
*
20374 GCAATCAGTAATTAAGTTTAATAAGAAA-AA
1 GCAATCAGTAATTAAGTTCAATAAGAAAGAA
* * *
20404 GTAATCAGTGATTAAGTTCAATAAGAAAGAT
1 GCAATCAGTAATTAAGTTCAATAAGAAAGAA
20435 GCAATCAGTAA
1 GCAATCAGTAA
20446 AAGGTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (31 bp):
GCAATCAGTAATTAAGTTCAATAAGAAAGAA
Found at i:20551 original size:15 final size:15
Alignment explanation
Indices: 20498--20556 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
20488 AAAGAGTAAT
*
20498 GGTAATCAGTAAGAA
1 GGTAATCAGTAAAAA
*
20513 -GTAAT-AGTAAACA
1 GGTAATCAGTAAAAA
**
20526 -GTAAAAAAGTAAAAA
1 GGT-AATCAGTAAAAA
20541 GGTAATCAGTAAAAA
1 GGTAATCAGTAAAAA
20556 G
1 G
20557 TAAAAATGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 8 0.23
14 7 0.20
15 18 0.51
16 2 0.06
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.19
Consensus pattern (15 bp):
GGTAATCAGTAAAAA
Found at i:20725 original size:22 final size:22
Alignment explanation
Indices: 20437--20623 Score: 140
Period size: 22 Copynumber: 8.7 Consensus size: 22
20427 AGAAAGATGC
20437 AATCAGTAAA-AGGTAAAATGGT
1 AATCAGTAAAGA-GTAAAATGGT
* *
20459 AATCAGTAAAGAGTAAAGTGAT
1 AATCAGTAAAGAGTAAAATGGT
*
20481 CATCAGTAAAGAGT--AATGGT
1 AATCAGTAAAGAGTAAAATGGT
*
20501 AATCAGT-AAGAAGT--AATAGT
1 AATCAGTAAAG-AGTAAAATGGT
* * *
20521 AAACAGTAAAAAAGTAAAAAGGT
1 AATCAGT-AAAGAGTAAAATGGT
*
20544 AATCAGTAAAAAGTAAAAAT-GT
1 AATCAGTAAAGAGT-AAAATGGT
* *
20566 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAATGGT
* * *
20586 AATTAGTAAAGAGTAAAGTGAT
1 AATCAGTAAAGAGTAAAATGGT
**
20608 AGCCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
20624 TAATCAATAA
Statistics
Matches: 131, Mismatches: 24, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
19 8 0.06
20 31 0.24
21 10 0.08
22 67 0.51
23 15 0.11
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAATGGT
Found at i:20733 original size:22 final size:22
Alignment explanation
Indices: 20666--20897 Score: 81
Period size: 22 Copynumber: 10.5 Consensus size: 22
20656 ATTAAAAAGG
* * *
20666 TAATCAGTAAAAAGTAAAAAGG
1 TAATCAGTAAAGAGTAAAATGA
* * *
20688 T-ATCTG-AAAGGGTAAAATGG
1 TAATCAGTAAAGAGTAAAATGA
* *
20708 TAATTAGTAAAGAGTAAAGTGA
1 TAATCAGTAAAGAGTAAAATGA
*
20730 TAATCAGTAAAGAGT--AATGG
1 TAATCAGTAAAGAGTAAAATGA
*
20750 TAATCAGT-AAGAAGTAATA-G-
1 TAATCAGTAAAG-AGTAAAATGA
* * *
20770 TAAACAGTAAA-AGTAAAAAGGG
1 TAATCAGTAAAGAGT-AAAATGA
*
20792 TAATCGGTAATCA-AGTTCAAAAAGTAATGA
1 TAATCAGTAA--AGAG-T----AA--AATGA
*
20822 TAATCAGT-AAGAGTAAAGT-A
1 TAATCAGTAAAGAGTAAAATGA
* * * **
20842 GTAATTAATAAAAAAGTAAAAAAA
1 -TAATCAGT-AAAGAGTAAAATGA
20866 TAATCAGTAAAGAGTAAAATGA
1 TAATCAGTAAAGAGTAAAATGA
*
20888 TAGTCAGTAA
1 TAATCAGTAA
20898 TTAAATTCAA
Statistics
Matches: 156, Mismatches: 32, Indels: 44
0.67 0.14 0.19
Matches are distributed among these distances:
19 6 0.04
20 37 0.24
21 19 0.12
22 55 0.35
23 16 0.10
24 4 0.03
25 1 0.01
27 2 0.01
28 5 0.03
29 1 0.01
30 10 0.06
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (22 bp):
TAATCAGTAAAGAGTAAAATGA
Found at i:20794 original size:42 final size:42
Alignment explanation
Indices: 20440--20801 Score: 199
Period size: 42 Copynumber: 8.7 Consensus size: 42
20430 AAGATGCAAT
*
20440 CAGTAAA-AGGTAAAATGGTAATCAGTAA-AGAGTAA-AGTGATCAT
1 CAGTAAAGA-GTAAAATGGTAATCAGTAAGA-AGTAATAGT-A--AA
20484 CAGTAAAGAGT--AATGGTAATCAGTAAGAAGTAATAGTAAA
1 CAGTAAAGAGTAAAATGGTAATCAGTAAGAAGTAATAGTAAA
* * * * *
20524 CAGTAAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAATGT-AT
1 CAGT-AAAGAGTAAAATGGTAATCAGTAAGAAGT-AATA-GTAAA
* * * *
20568 CTG-AAAGGGTAAAATGGTAATTAGTAA-AGAGTAA-AGTGATAGC
1 CAGTAAAGAGTAAAATGGTAATCAGTAAGA-AGTAATAGT-A-A-A
*
20611 CAGTAAAGAGT--AA---TAATCAATAAGAAGTAATAGTAAA
1 CAGTAAAGAGTAAAATGGTAATCAGTAAGAAGTAATAGTAAA
* * * * * * *
20648 CTGTAAAAATTAAAAAGGTAATCAGTAAAAAGTAAAAAGGT-AT
1 CAGTAAAGAGTAAAATGGTAATCAGTAAGAAGT-AATA-GTAAA
* * *
20691 CTG-AAAGGGTAAAATGGTAATTAGTAA-AGAGTAA-AGTGATAA
1 CAGTAAAGAGTAAAATGGTAATCAGTAAGA-AGTAATAGT-A-AA
20733 TCAGTAAAGAGT--AATGGTAATCAGTAAGAAGTAATAGTAAA
1 -CAGTAAAGAGTAAAATGGTAATCAGTAAGAAGTAATAGTAAA
* *
20774 CAGTAAA-AGTAAAAAGGGTAATCGGTAA
1 CAGTAAAGAGT-AAAATGGTAATCAGTAA
20802 TCAAGTTCAA
Statistics
Matches: 249, Mismatches: 35, Indels: 70
0.70 0.10 0.20
Matches are distributed among these distances:
37 8 0.03
38 1 0.00
39 23 0.09
40 18 0.07
41 14 0.06
42 116 0.47
43 37 0.15
44 29 0.12
45 3 0.01
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (42 bp):
CAGTAAAGAGTAAAATGGTAATCAGTAAGAAGTAATAGTAAA
Found at i:21013 original size:27 final size:26
Alignment explanation
Indices: 20934--21129 Score: 107
Period size: 27 Copynumber: 7.2 Consensus size: 26
20924 AGTAAAAAAG
* * *
20934 AGTAAGAAATGAGTAAAAAGTGGTGATC
1 AGTAATAAA-GAGTAAAAA-TGGTAATT
* *
20962 AATAAAAAAGAGTAAAAGA-GAGTAATT
1 AGTAATAAAGAGTAAAA-ATG-GTAATT
20989 AGTAATAAAGAGTAAGAAATGGTAATT
1 AGTAATAAAGAGTAA-AAATGGTAATT
*
21016 A--AATGAAAAGAGTAAAAAGTGAT-ATT
1 AGTAAT--AAAGAGTAAAAA-TGGTAATT
* * *
21042 CAGTAA-AAACAGTAAGAAAAGGGGTAATC
1 -AGTAATAAAGAGT-A-AAAA-TGGTAATT
* * *
21071 GGTAAAAAAGAGTAAAATATGGTAATC
1 AGTAATAAAGAGTAAAA-ATGGTAATT
*
21098 AGT-ACAAAGAGTAAAAAATGGTAATT
1 AGTAATAAAGAGT-AAAAATGGTAATT
21124 AGTAAT
1 AGTAAT
21130 CAAAAAATAA
Statistics
Matches: 133, Mismatches: 18, Indels: 35
0.72 0.10 0.19
Matches are distributed among these distances:
25 3 0.02
26 32 0.24
27 64 0.48
28 24 0.18
29 10 0.08
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.21
Consensus pattern (26 bp):
AGTAATAAAGAGTAAAAATGGTAATT
Found at i:23446 original size:20 final size:20
Alignment explanation
Indices: 23421--23459 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
23411 GAGATCTTTC
23421 ATTTCAAACGAATTTTCAGG
1 ATTTCAAACGAATTTTCAGG
23441 ATTTCAAACGAATTTTCAG
1 ATTTCAAACGAATTTTCAG
23460 AACTATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
ATTTCAAACGAATTTTCAGG
Done.