Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007346.1 Corchorus capsularis cultivar CVL-1 contig07367, 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: 18992
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3399 original size:2 final size:2
Alignment explanation
Indices: 3392--3427 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3382 AGCAAGTTGG
3392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3428 AGTTAGTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4082 original size:22 final size:22
Alignment explanation
Indices: 4048--4103 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4038 TCTCCATATG
* *
4048 AATTGTTAGTAATCACACTTTAA
1 AATTGTGA-TAATCACACTATAA
* *
4071 AATTTTGATAATCACACTATGA
1 AATTGTGATAATCACACTATAA
4093 AATTGTGATAA
1 AATTGTGATAA
4104 CCTTGTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTGTGATAATCACACTATAA
Found at i:4142 original size:23 final size:23
Alignment explanation
Indices: 4114--4194 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
4104 CCTTGTTATG
4114 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
4137 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
4160 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
4182 AAATCTTGATAAA
1 AAATTTTGATAAA
4195 ATTTTGATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
22 16 0.34
23 31 0.66
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:4190 original size:22 final size:22
Alignment explanation
Indices: 4070--4193 Score: 97
Period size: 22 Copynumber: 5.5 Consensus size: 22
4060 TCACACTTTA
* *
4070 AAATTTTGATAATC-ACACTATG
1 AAATTTTGATAACCTTC-CTATG
* **
4092 AAATTGTGATAACCTTGTTATG
1 AAATTTTGATAACCTTCCTATG
* *
4114 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGAT-AACCTTCCTATG
* * *
4137 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGAT-AACCTTCCTATG
* *
4160 AAATTTTGATAACTTTCTTATG
1 AAATTTTGATAACCTTCCTATG
*
4182 AAATCTTGATAA
1 AAATTTTGATAA
4194 AATTTTGATA
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
22 44 0.54
23 37 0.46
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATG
Found at i:4222 original size:22 final size:22
Alignment explanation
Indices: 4193--4392 Score: 123
Period size: 22 Copynumber: 9.5 Consensus size: 22
4183 AATCTTGATA
*
4193 AAATTTTGATAAGCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** **
4215 ATTTTTTGAT-ACCTCATTATG
1 AAATTTTGATAACCTCCCTATG
* *
4236 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
*
4258 AAATTTTGATAACC-CTCTTATG
1 AAATTTTGATAACCTC-CCTATG
* * **
4280 AAATTTTGAAAATCTAAACTATG
1 AAATTTTGATAACCT-CCCTATG
* * *
4303 AAAATTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATG
* *
4325 AAATTTTGATATCCTCAC--TG
1 AAATTTTGATAACCTCCCTATG
* *
4345 -AATTTCGATATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
* *
4364 -AATTTTGGTATCCTCCC--TG
1 AAATTTTGATAACCTCCCTATG
4383 AAATTTTGAT
1 AAATTTTGAT
4393 TACTCCATTA
Statistics
Matches: 138, Mismatches: 35, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
19 34 0.25
20 10 0.07
21 16 0.12
22 62 0.45
23 16 0.12
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:4294 original size:44 final size:44
Alignment explanation
Indices: 4193--4335 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 44
4183 AATCTTGATA
* **
4193 AAATTTTGATAAGCTCCCTATGATTTTTTGAT-A-CCTCATTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGATAACCCTC-TTATG
*
4236 AAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCTCTTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGATAACCCTCTTATG
* ** * * *
4280 AAATTTTGAAAATCTAAACTATGAAAATTTGATAACCTTCATATG
1 AAATTTTGATAATCT-CCCTATGAAATTTTGATAACCCTCTTATG
4325 AAATTTTGATA
1 AAATTTTGATA
4336 TCCTCACTGA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 28 0.33
44 19 0.22
45 38 0.45
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (44 bp):
AAATTTTGATAATCTCCCTATGAAATTTTGATAACCCTCTTATG
Found at i:4398 original size:19 final size:19
Alignment explanation
Indices: 4326--4392 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
4316 CTTCATATGA
*
4326 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
*
4345 AATTTCGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
4364 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
4383 AAATTTTGAT
1 -AATTTTGAT
4393 TACTCCATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 34 0.81
20 8 0.19
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:4524 original size:22 final size:22
Alignment explanation
Indices: 4499--4745 Score: 152
Period size: 22 Copynumber: 11.3 Consensus size: 22
4489 AATCACATTT
*
4499 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
4521 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
4543 TAAAATTTTGTTGACC-CTTCTA
1 TGAAATTTTGATAACCTCTT-TA
* * * *
4565 TGAATTTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
4587 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
** **
4609 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
4631 TGAAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
4653 T-AAATTTTGATAATCCTATCTTTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
4677 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
4699 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
4719 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
4739 TGAAATT
1 TGAAATT
4746 AAGACTTTTA
Statistics
Matches: 172, Mismatches: 39, Indels: 30
0.71 0.16 0.12
Matches are distributed among these distances:
19 2 0.01
20 17 0.10
21 29 0.17
22 101 0.59
23 4 0.02
24 4 0.02
25 11 0.06
26 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:4594 original size:44 final size:44
Alignment explanation
Indices: 4480--4644 Score: 160
Period size: 44 Copynumber: 3.8 Consensus size: 44
4470 CCACTATTGA
* *
4480 AATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTATG
1 AATTTTTGATAATCACATTATGAAATTTTGATAACCTCTTTATG
* * * * *
4523 AAATTTTGATAA-CATCTTTATAAAATTTTGTTGACC-CTTCTATG
1 AATTTTTGATAATCA-CATTATGAAATTTTGATAACCTCTT-TATG
* *
4567 AATTTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TG
1 AATTTTTGATAATCACATTATGAAATTTTGATAACCTC-TTTATG
* *
4611 AAATTTTGATAA-CAACACTATGAAATTTTGATAA
1 AATTTTTGATAATC-ACATTATGAAATTTTGATAA
4645 TCTTCATATA
Statistics
Matches: 98, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
43 13 0.13
44 80 0.82
45 4 0.04
46 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (44 bp):
AATTTTTGATAATCACATTATGAAATTTTGATAACCTCTTTATG
Found at i:4637 original size:88 final size:87
Alignment explanation
Indices: 4480--4640 Score: 225
Period size: 88 Copynumber: 1.8 Consensus size: 87
4470 CCACTATTGA
* * * **
4480 AATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATCTTTATA
1 AATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACACTATA
4545 AAATTTTGTTGACCCTTCTATG
66 AAATTTTGTTGACCCTTCTATG
* *
4567 AATTTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAACACTA
1 AATTTTTG-TAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACAACACTA
*
4631 TGAAATTTTG
64 TAAAATTTTG
4641 ATAATCTTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
87 8 0.12
88 54 0.84
89 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (87 bp):
AATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACACTATA
AAATTTTGTTGACCCTTCTATG
Found at i:4780 original size:22 final size:22
Alignment explanation
Indices: 4499--4842 Score: 135
Period size: 22 Copynumber: 15.5 Consensus size: 22
4489 AATCACATTT
* *
4499 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
4521 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* * *
4543 TAAAATTTTGTTGACCCTTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* * *
4565 TGAATTTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
4587 TGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
4609 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
4631 TGAAATTTTGATAATCTTCATA
1 TGAAATTTTGATAACCTTCATA
*
4653 T-AAATTTTGATAATCCTATCTTTA
1 TGAAATTTTGATAA-CCT-TC-ATA
*
4677 TGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
4699 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
4719 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
4744 TTAAGACTTTT-ATAACCTTCATA
1 TGAA-A-TTTTGATAACCTTCATA
*
4767 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
4789 TAAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCTTCATA
* * *
4811 TGAAGTATTAATAACCTTC-TAA
1 TGAAATTTTGATAACCTTCAT-A
4833 TGAAATTTTG
1 TGAAATTTTG
4843 TTTACCACAC
Statistics
Matches: 243, Mismatches: 49, Indels: 60
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.00
20 9 0.04
21 37 0.15
22 146 0.60
23 12 0.05
24 6 0.02
25 22 0.09
26 6 0.02
27 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:4989 original size:24 final size:22
Alignment explanation
Indices: 4925--5056 Score: 72
Period size: 22 Copynumber: 5.9 Consensus size: 22
4915 TTGTGATAAT
* *
4925 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
4947 TAACCAACGTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
* **
4969 TAACCCGATCCTATGAAATTTTGG
1 TAA-CC-AACCTATGAAATTTTAA
* **
4993 TAACC-ACTCTATCAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
5015 TAA-CTACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
*
5037 TAACC-ACACTATGGAATTTT
1 TAACCAAC-CTATGAAATTTT
5057 GGTAACCTCC
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.02
22 69 0.76
23 5 0.05
24 15 0.16
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:5009 original size:22 final size:22
Alignment explanation
Indices: 4979--5063 Score: 134
Period size: 22 Copynumber: 3.9 Consensus size: 22
4969 TAACCCGATC
*
4979 CTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGGTAACCACA
* *
5001 CTATCAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
5023 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
5045 CTATGGAATTTTGGTAACC
1 CTATGAAATTTTGGTAACC
5064 TCCCCATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:5072 original size:22 final size:22
Alignment explanation
Indices: 4979--5076 Score: 99
Period size: 22 Copynumber: 4.5 Consensus size: 22
4969 TAACCCGATC
* * *
4979 CTATGAAATTTTGGTAACCACT
1 CTATGGAATTTTGGTAACCTCA
**
5001 CTATCAAATTTTGGTAA-CTACA
1 CTATGGAATTTTGGTAACCT-CA
* *
5023 CTATGAAATTTTGGTAACCACA
1 CTATGGAATTTTGGTAACCTCA
*
5045 CTATGGAATTTTGGTAACCTCC
1 CTATGGAATTTTGGTAACCTCA
*
5067 CCATGGAATT
1 CTATGGAATT
5077 ATAATAACCT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
21 1 0.02
22 63 0.97
23 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (22 bp):
CTATGGAATTTTGGTAACCTCA
Found at i:5252 original size:6 final size:6
Alignment explanation
Indices: 5241--5265 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5231 GTATTGTACA
5241 TGTTAG TGTTAG TGTTAG TGTTAG T
1 TGTTAG TGTTAG TGTTAG TGTTAG T
5266 TTAATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TGTTAG
Found at i:5445 original size:30 final size:31
Alignment explanation
Indices: 5391--5449 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
5381 TGGCAATTTA
5391 GAAATATGTTTTAAAAAAAAGGGTACAATTG
1 GAAATATGTTTTAAAAAAAAGGGTACAATTG
*
5422 GAAATATGTTTT-AAAATAAGGGTACAAT
1 GAAATATGTTTTAAAAAAAAGGGTACAAT
5450 CAGAAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAAAAAGGGTACAATTG
Found at i:5647 original size:22 final size:22
Alignment explanation
Indices: 5622--6182 Score: 192
Period size: 22 Copynumber: 25.7 Consensus size: 22
5612 ATGATCCCAT
5622 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
5644 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * ** **
5666 TATGGAATTTCGAGAATTTTTT
1 TATGAAATTTTGATAACCTTCC
* *
5688 TAT-AAATTTCT-TTAACCTTCT
1 TATGAAATTT-TGATAACCTTCC
* *
5709 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * ** * *
5731 AAAGGAATTTTGACGATC-TCGA
1 TATGAAATTTTGATAACCTTC-C
5753 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
5775 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
5798 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
5819 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
5842 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
5863 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
5886 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
5908 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
5930 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
5953 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * * *
5976 TATAAAATTTTGACAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
5998 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
6015 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* ** *
6036 GATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
6058 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * * *
6080 TTTGAAATTTTAATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
6102 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
6124 TATCAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
6146 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
6168 TATAAAATTTTGATA
1 TATGAAATTTTGATA
6183 TCCTCCCTTA
Statistics
Matches: 391, Mismatches: 118, Indels: 60
0.69 0.21 0.11
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
21 28 0.07
22 281 0.72
23 67 0.17
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:5833 original size:45 final size:45
Alignment explanation
Indices: 5753--5838 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
5743 ACGATCTCGA
* * *
5753 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
* *
5798 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ATGAAATATTGATAACCA
5839 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
Found at i:5960 original size:23 final size:23
Alignment explanation
Indices: 5890--5988 Score: 103
Period size: 23 Copynumber: 4.4 Consensus size: 23
5880 TCACACTCTG
* * * *
5890 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* * *
5912 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTATA
* *
5934 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
5957 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
5980 AAATTTTGA
1 AAATTTTGA
5989 CAACTTTCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
22 27 0.42
23 38 0.58
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:6012 original size:45 final size:45
Alignment explanation
Indices: 5907--6013 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
5897 GATAATCACA
* * *
5907 CTATGAAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATGAAATT-TGATAAACCTCCCTATAAAATTTTGACAAATCTTC
* *
5952 CTATAAAATTTTGATAAACCTCCCTATAAAATTTTGACAACT-TTC
1 CTATGAAA-TTTGATAAACCTCCCTATAAAATTTTGACAAATCTTC
*
5997 TTATGAAATCTTGATAA
1 CTATGAAAT-TTGATAA
6014 CTACAAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.02
45 27 0.52
46 24 0.46
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (45 bp):
CTATGAAATTTGATAAACCTCCCTATAAAATTTTGACAAATCTTC
Found at i:6321 original size:22 final size:22
Alignment explanation
Indices: 6296--6347 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
6286 AATCACATTT
*
6296 TGAAAATTTAATAA-CTTCTTTA
1 TGAAAATTTAATAAGC-ACTTTA
* *
6318 TGAAATTTTGATAAGCACTTTA
1 TGAAAATTTAATAAGCACTTTA
6340 T-AAAATTT
1 TGAAAATTT
6348 TGTTGACCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 6 0.24
22 18 0.72
23 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (22 bp):
TGAAAATTTAATAAGCACTTTA
Found at i:6364 original size:44 final size:45
Alignment explanation
Indices: 6272--6419 Score: 119
Period size: 44 Copynumber: 3.4 Consensus size: 45
6262 GAAATACCAC
* * * * *
6272 TATGAAATTTTTG-TAATCACATTTTGAAAA-TTTAATAACTTC-TT
1 TATGAAA-TTTTGATAAGCACATTAT-AAAATTTTGATAACCTCGCT
* * *
6316 TATGAAATTTTGATAAGCACTTTATAAAATTTTGTTGACC-C-CT
1 TATGAAATTTTGATAAGCACATTATAAAATTTTGATAACCTCGCT
* * **
6359 GTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCT
1 -TATGAAATTTTGATAAGCACATTATAAAATTTTGATAACCTCGCT
6405 T-TGAAATTTTGATAA
1 TATGAAATTTTGATAA
6420 AAACACTATG
Statistics
Matches: 83, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
43 11 0.13
44 68 0.82
45 2 0.02
46 2 0.02
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (45 bp):
TATGAAATTTTGATAAGCACATTATAAAATTTTGATAACCTCGCT
Found at i:6431 original size:22 final size:22
Alignment explanation
Indices: 6360--6432 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
6350 TTGACCCCTG
* * *
6360 TATGAAATTCTGATAATCACAT
1 TATGAAATTTTGATAAACACAC
* * * *
6382 TATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAAACACAC
* *
6404 TTTGAAATTTTGATAAAAACAC
1 TATGAAATTTTGATAAACACAC
6426 TATGAAA
1 TATGAAA
6433 AGTTCATAAT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAAACACAC
Found at i:6645 original size:44 final size:43
Alignment explanation
Indices: 6550--6647 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 43
6540 ATTAAGACTT
* *
6550 TTATAACCTTCATATGAAATTTTGATAACCTCCCCATGAAATA
1 TTATAACCTCCATATGAAATTTTGATAACCTCACCATGAAATA
* * *
6593 TTACTAACCTCC-TAATGAAATTTTGTTAACCAT-ACTATGAAATTC
1 TTA-TAACCTCCAT-ATGAAATTTTGATAACC-TCACCATGAAA-TA
6638 TTATAACCTC
1 TTATAACCTC
6648 GCTATCATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
43 4 0.09
44 37 0.80
45 5 0.11
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (43 bp):
TTATAACCTCCATATGAAATTTTGATAACCTCACCATGAAATA
Found at i:6652 original size:22 final size:21
Alignment explanation
Indices: 6548--6652 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 21
6538 AAATTAAGAC
*
6548 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCCTATGAAA
*
6569 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CCTATGAAA
*
6591 TATT-ACTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCCT-ATGAAA
* *
6613 TTTTGTTAACCATACTATGAAA
1 TTTTGATAACC-TCCTATGAAA
6635 TTCTT-ATAACCTCGCTAT
1 TT-TTGATAACCTC-CTAT
6653 CATTTTGACA
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
21 9 0.13
22 53 0.79
23 5 0.07
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:6809 original size:44 final size:43
Alignment explanation
Indices: 6706--6880 Score: 174
Period size: 44 Copynumber: 4.0 Consensus size: 43
6696 AATTAACCAC
** * *
6706 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGATAACCATA-CTATGAAATTTTGATAA-CT--T
* * *
6752 CCTATGAAATTTTGGTAATCATACTATGAAATTTTGATGACTT
1 CCTATGAAATTTTGATAACCATACTATGAAATTTTGATAACTT
* *
6795 CCATATGAAATTTTGATAACCACACTATGGAATTTTGATAACTT
1 CC-TATGAAATTTTGATAACCATACTATGAAATTTTGATAACTT
* *
6839 CCTCATGAAATTATAATAACCAT-CTTATGAAATTTTGATAAC
1 CCT-ATGAAATTTTGATAACCATAC-TATGAAATTTTGATAAC
6881 CACATAGTGA
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
43 5 0.05
44 70 0.64
45 2 0.02
46 31 0.28
47 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (43 bp):
CCTATGAAATTTTGATAACCATACTATGAAATTTTGATAACTT
Found at i:6881 original size:22 final size:22
Alignment explanation
Indices: 6699--6882 Score: 158
Period size: 22 Copynumber: 8.3 Consensus size: 22
6689 TCATGATAAT
* **
6699 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
6721 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
*
6743 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTGA
* *
6767 TAATCATACTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
* *
6789 TGA-CTTCCATATGAAATTTTGA
1 TAACCATCC-TATGAAATTTTGA
*
6811 TAACCA-CACTATGGAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* * *
6833 TAA-CTTCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTGA
*
6855 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
6877 TAACCA
1 TAACCA
6883 CATAGTGATC
Statistics
Matches: 130, Mismatches: 24, Indels: 16
0.76 0.14 0.09
Matches are distributed among these distances:
21 6 0.05
22 101 0.78
23 6 0.05
24 17 0.13
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:8799 original size:19 final size:20
Alignment explanation
Indices: 8768--8805 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
8758 TATTGACATT
8768 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
8787 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
8806 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:8909 original size:26 final size:24
Alignment explanation
Indices: 8879--8936 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
8869 GTCTAAATTG
* *
8879 AAAATTTTAATTAAGTTTTAAATAAT
1 AAAATTTT-ACTAAATTTT-AATAAT
*
8905 AAAATTATACTAAATTTTAATAAT
1 AAAATTTTACTAAATTTTAATAAT
8929 AGAAATTT
1 A-AAATTT
8937 AGAAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.26
25 13 0.48
26 7 0.26
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
AAAATTTTACTAAATTTTAATAAT
Found at i:10157 original size:228 final size:228
Alignment explanation
Indices: 9754--10210 Score: 770
Period size: 228 Copynumber: 2.0 Consensus size: 228
9744 TTACTAAAAG
* * *
9754 GCCAAATTGAGGATTAATGTGGTGCCACCTTTTGGCTATTTTTGGTCTTTTCTCACTTTTCTGAT
1 GCCAAATTGAGGACTAATGTGGTGCCACCTTATGGCTATTTTTGGTCTTTTCTCACTTTTCGGAT
* * *
9819 GACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTATTCCTTCTACCCTTTTTCGTAATTGCAT
66 GACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTATTCCTTCTACCCTTTTTCGTAATTACAC
*
9884 ATTTCTCTTCCTTAATTGTTTTTAATTAATGTTTAAGACTTTTAATTAATTGCTTCTAAACCCTA
131 ATTTCCCTTCCTTAATTGTTTTTAATTAATGTTTAAGACTTTTAATTAATTGCTTCTAAACCCTA
*
9949 AACCCTTAATTACTTTTAATTAATGTTTCTCTC
196 AACCCTTAATTACTTTTAATTAATATTTCTCTC
*
9982 GCCAAATTGAGGACTAATGTGGTGCTACCTTATGGCTATTTTTGGTCTTTTCTCACTTTTCGGAT
1 GCCAAATTGAGGACTAATGTGGTGCCACCTTATGGCTATTTTTGGTCTTTTCTCACTTTTCGGAT
* * *
10047 GACTTAAAAGCCCCTCTATGAGTTTTCCACATTCCTTTTCCTTCTACCCTTTTTCGTAATTACAC
66 GACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTATTCCTTCTACCCTTTTTCGTAATTACAC
* * **
10112 ATTTCCCTTTCTTAATTTTTTTTAATTAATGTTTAAGGTTTTTAATTAATTGCTTCTAAACCCTA
131 ATTTCCCTTCCTTAATTGTTTTTAATTAATGTTTAAGACTTTTAATTAATTGCTTCTAAACCCTA
10177 AACCCTTAATTACTTTTAATTAATATTTCTCTC
196 AACCCTTAATTACTTTTAATTAATATTTCTCTC
10210 G
1 G
10211 TTGTTTTCTT
Statistics
Matches: 213, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
228 213 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (228 bp):
GCCAAATTGAGGACTAATGTGGTGCCACCTTATGGCTATTTTTGGTCTTTTCTCACTTTTCGGAT
GACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTATTCCTTCTACCCTTTTTCGTAATTACAC
ATTTCCCTTCCTTAATTGTTTTTAATTAATGTTTAAGACTTTTAATTAATTGCTTCTAAACCCTA
AACCCTTAATTACTTTTAATTAATATTTCTCTC
Found at i:11611 original size:37 final size:37
Alignment explanation
Indices: 11523--11618 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
11513 GTCTAAGCCC
* * *
11523 AAATAGAACGTTGGAGACAAAGATAAAAAGCAAAATT
1 AAATAGAACGATGGAAACAAAGACAAAAAGCAAAATT
* * *
11560 AAATACAACAGATGGAAATAAAGACAAAAGGCAAAATT
1 AAATAGAAC-GATGGAAACAAAGACAAAAAGCAAAATT
*
11598 AAATAGGACGATGGAAACAAA
1 AAATAGAACGATGGAAACAAA
11619 AAGGCAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 19 0.39
38 30 0.61
ACGTcount: A:0.58, C:0.09, G:0.19, T:0.14
Consensus pattern (37 bp):
AAATAGAACGATGGAAACAAAGACAAAAAGCAAAATT
Found at i:11990 original size:61 final size:60
Alignment explanation
Indices: 11894--12011 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 60
11884 CTCTTATCCA
* *
11894 TTCAATATATTTGGGATAGTTATATTTAATTTTTTATAGGAGATCCATTCAAAATTTCCG
1 TTCAATATATTTGGGATAGTTATATTGAATTTTTTATAAGAGATCCATTCAAAATTTCCG
*
11954 TTCAATATATTTGGGCATAGTTATATTGAATTTTTTATAAGAGATTCATTCAAAATTT
1 TTCAATATATTTGGG-ATAGTTATATTGAATTTTTTATAAGAGATCCATTCAAAATTT
12012 TGGAAGAGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 15 0.28
61 39 0.72
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (60 bp):
TTCAATATATTTGGGATAGTTATATTGAATTTTTTATAAGAGATCCATTCAAAATTTCCG
Found at i:12035 original size:23 final size:23
Alignment explanation
Indices: 11972--12036 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
11962 ATTTGGGCAT
*
11972 AGTTATATTGAATTTTTTATAAG
1 AGTTATATTGAATTTTTTAGAAG
* * ** *
11995 AGATT-CATTCAAAATTTTGGAAG
1 AG-TTATATTGAATTTTTTAGAAG
12018 AGTTATATTGAATTTTTTA
1 AGTTATATTGAATTTTTTA
12037 TAGGAGATCT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
22 2 0.07
23 25 0.86
24 2 0.07
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (23 bp):
AGTTATATTGAATTTTTTAGAAG
Found at i:12340 original size:18 final size:18
Alignment explanation
Indices: 12319--12357 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12309 CTCTTTTAGA
12319 TTTTTAAATCTTTGTAAT
1 TTTTTAAATCTTTGTAAT
*
12337 TTTTTAGATCTTTGTAAT
1 TTTTTAAATCTTTGTAAT
12355 TTT
1 TTT
12358 AATTTGGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (18 bp):
TTTTTAAATCTTTGTAAT
Found at i:12384 original size:33 final size:33
Alignment explanation
Indices: 12342--12406 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
12332 GTAATTTTTT
**
12342 AGATCTTTGTAATTTTAATTTGGTTCATTATTA
1 AGATCTTTGTAATTTTAATTTGGCACATTATTA
12375 AGATCTTTGTAATTTTAATTTGGCACATTATT
1 AGATCTTTGTAATTTTAATTTGGCACATTATT
12407 TAATTTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (33 bp):
AGATCTTTGTAATTTTAATTTGGCACATTATTA
Found at i:12813 original size:109 final size:109
Alignment explanation
Indices: 12622--12839 Score: 366
Period size: 109 Copynumber: 2.0 Consensus size: 109
12612 TATTTTGGCA
* * *
12622 CCCTAAACATTTAAATTCTATTTTGATGTAGGTGACAGAATATTCAAATCATCATATGCTTCCAT
1 CCCTAAACATTCAAATTCTATTTTGATGTAGGTCACAGAACATTCAAATCATCATATGCTTCCAT
*
12687 CTTGTCCTCTTCCCTTAACCAATCAGACAATATGATTTTGTTAG
66 CTTGTCCTCCTCCCTTAACCAATCAGACAATATGATTTTGTTAG
*
12731 CCCTAAACATTCAAATTCTATTTTGATGTAGGTCACAGAACATTCAAATCATCATATGCTTCCTT
1 CCCTAAACATTCAAATTCTATTTTGATGTAGGTCACAGAACATTCAAATCATCATATGCTTCCAT
*
12796 CTTGTCTTCC-CTCCTTAACCAATCAGACAATATGATTTTGTTAG
66 CTTGTCCTCCTC-CCTTAACCAATCAGACAATATGATTTTGTTAG
12840 ATGACAATGA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.01
109 101 0.99
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (109 bp):
CCCTAAACATTCAAATTCTATTTTGATGTAGGTCACAGAACATTCAAATCATCATATGCTTCCAT
CTTGTCCTCCTCCCTTAACCAATCAGACAATATGATTTTGTTAG
Found at i:13742 original size:13 final size:13
Alignment explanation
Indices: 13724--13750 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13714 GCCAAGGTGC
13724 GGAGGCTAGGGTT
1 GGAGGCTAGGGTT
13737 GGAGGCTAGGGTT
1 GGAGGCTAGGGTT
13750 G
1 G
13751 AAGGGTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.56, T:0.22
Consensus pattern (13 bp):
GGAGGCTAGGGTT
Found at i:15633 original size:20 final size:20
Alignment explanation
Indices: 15610--15648 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15600 TCTCTAATTC
* *
15610 CTCATCCCCTTCTTCTATTT
1 CTCACCCCCTTCTGCTATTT
15630 CTCACCCCCTTCTGCTATT
1 CTCACCCCCTTCTGCTATT
15649 CTATCAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (20 bp):
CTCACCCCCTTCTGCTATTT
Found at i:17718 original size:2 final size:2
Alignment explanation
Indices: 17713--17747 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17703 ATGCCCTAGC
17713 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 T
17748 GTAATGTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17886 original size:20 final size:20
Alignment explanation
Indices: 17863--17901 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17853 TCTCTAATTC
* *
17863 CTCATCCCCTTCTTCTATTT
1 CTCACCCCCTTCTGCTATTT
17883 CTCACCCCCTTCTGCTATT
1 CTCACCCCCTTCTGCTATT
17902 CTATCAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (20 bp):
CTCACCCCCTTCTGCTATTT
Done.