Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014609.1 Corchorus olitorius cultivar O-4 contig14642, 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: 49296
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:70 original size:47 final size:47
Alignment explanation
Indices: 1--440 Score: 529
Period size: 47 Copynumber: 9.0 Consensus size: 47
* *
1 TTTAGTTTAATTATCCAGAATTAAACTATTTTCTTCTTCTCTTGCTC
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
* * * * *
48 TTTAGTTTAATTACCCACAATTAAACTCTTTTCATCTTCTTTTACTT
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
* *
95 TTTAGTTTAATTACCCAGAATTAAACTAGCCTCTATGTACTTCTTCTTTTACTC
1 TTTAGTTTAATTACCCAGAATTAAACT---CT-T-T-T-CTTCTTCTCTTGCTC
* * *
149 TTTAGCTTAATTAGCCATAATTAAACTCTTTTCTTCTTCTCTTGCTC
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
* * * *
196 TTCAGTTTAATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTTT
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGC-TC
*
244 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTT
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
* *
291 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTTTTCTCTTGCTT
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
* *
338 TTTAGTTTAGTTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTTAC
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTG--C---T-C
* *
391 TTTTTAGTTTAATTACCCAGAATTGAACTGTTTTCTTCTTCTCTTGCTC
1 --TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
440 T
1 T
441 GGTTTTAATT
Statistics
Matches: 345, Mismatches: 32, Indels: 32
0.84 0.08 0.08
Matches are distributed among these distances:
47 208 0.60
48 44 0.13
49 3 0.01
50 4 0.01
51 3 0.01
52 2 0.01
53 2 0.01
54 37 0.11
55 42 0.12
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.50
Consensus pattern (47 bp):
TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
Found at i:345 original size:142 final size:142
Alignment explanation
Indices: 1--440 Score: 567
Period size: 142 Copynumber: 3.0 Consensus size: 142
* * *
1 TTTAGTTTAATTATCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAC
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAG
* * * *
66 AATTAAACTCTTTTCATCTTCTTTTAC-TTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTA
66 AATTAAACTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTAATTACCCAGAATTAAACT---CT-T-
* *
130 TGTACTTCTTCTTTTACTC
126 T-T-CTTCTTCTCTTGCTC
* * * *
149 TTTAGCTTAATTAGCCATAATTAAACTCTTTTCTTCTTCTCTTGCTCTTCAGTTTAATTACCCAG
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAG
*
214 AATTAAATTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTT
66 AATTAAACTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTT
*
279 CTTCTCTTGCTT
131 CTTCTCTTGCTC
* * *
291 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTTTTCTCTTGCTTTTTAGTTTAGTTACCCAG
1 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAG
* *
356 AATTAAACTGTTTTCTTCTTCTCTTGCTCTTTTACTTTTTAGTTTAATTACCCAGAATTGAACTG
66 AATTAAACTGTTTTCTTCTTCTCTTG--C---T--TTTTTAGTTTAATTACCCAGAATTAAACTC
421 TTTTCTTCTTCTCTTGCTC
124 TTTTCTTCTTCTCTTGCTC
440 T
1 T
441 GGTTTTAATT
Statistics
Matches: 259, Mismatches: 25, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
142 95 0.37
143 1 0.00
144 2 0.01
145 1 0.00
146 2 0.01
147 1 0.00
148 81 0.31
149 76 0.29
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.50
Consensus pattern (142 bp):
TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAG
AATTAAACTGTTTTCTTCTTCTCTTGCTTTTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTT
CTTCTCTTGCTC
Found at i:396 original size:55 final size:55
Alignment explanation
Indices: 335--440 Score: 194
Period size: 55 Copynumber: 1.9 Consensus size: 55
325 TTTTCTCTTG
*
335 CTTTTTAGTTTAGTTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTTA
1 CTTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTTA
*
390 CTTTTTAGTTTAATTACCCAGAATTGAACTGTTTTCTTCTTCTCTTGCTCT
1 CTTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCT
441 GGTTTTAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.18, C:0.21, G:0.09, T:0.52
Consensus pattern (55 bp):
CTTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTTA
Found at i:450 original size:243 final size:243
Alignment explanation
Indices: 1--440 Score: 654
Period size: 243 Copynumber: 1.8 Consensus size: 243
*
1 TTTAGTTTAATTATCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAC
1 TTTAGTTTAATTACCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAC
*
66 AATTAAACTCTTTTCATCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTAT
66 AATTAAACTCTTTTCATCTTCTCTTACTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTAT
* * *
131 GTACTTCTTCTTTTACTCTTTAGCTTAATTAGCCATAATTAAACTCTTTTCTTCTTCTCTTGCTC
131 CTACTTCTTCTTTTACTCTTTAGCTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
196 TTCAGTTTAATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTTT
196 TTCAGTTTAATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTTT
* * *
244 TTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTACCCAG
1 TTTAGTTTAATTACCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAC
* * * * *
309 AATTAAACTCTTTTCTTTTTCTCTTGCTTTTTAGTTTAGTTACCCAGAATTAAACT-GTTTTCTT
66 AATTAAACTCTTTTCATCTTCTCTTACTTTTTAGTTTAATTACCCAGAATTAAACTAG----CCT
* * * *
373 CT-TCT-CTTGC-TCTTTTACTTTTTAGTTTAATTACCCAGAATTGAACTGTTTTCTTCTTCTCT
127 CTATCTACTT-CTTCTTTTACTCTTTAGCTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCT
435 TGCTCT
191 TGCTCT
441 GGTTTTAATT
Statistics
Matches: 175, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
242 1 0.01
243 112 0.64
244 55 0.31
245 3 0.02
246 4 0.02
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.50
Consensus pattern (243 bp):
TTTAGTTTAATTACCCAGAATTAAACTATTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAC
AATTAAACTCTTTTCATCTTCTCTTACTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTAT
CTACTTCTTCTTTTACTCTTTAGCTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTC
TTCAGTTTAATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTTT
Found at i:7548 original size:22 final size:22
Alignment explanation
Indices: 7518--7963 Score: 108
Period size: 22 Copynumber: 20.5 Consensus size: 22
7508 TTAACCTCAT
*
7518 GAAATTTTGATAACCTCCCTAC
1 GAAATTTTGATAACCTCACTAC
* * *
7540 GGAATTTTGAAAACCTCACTAT
1 GAAATTTTGATAACCTCACTAC
* * *
7562 GAAATTTTGATAACTTC-CGAAT
1 GAAATTTTGATAACCTCAC-TAC
** *
7584 GAAATTTTGATAATCAACACTAT
1 GAAATTTTGATAA-CCTCACTAC
* * *
7607 GAGATGTTGATAACCTCTA-TAT
1 GAAATTTTGATAACCTC-ACTAC
* * * ** *
7629 GATATATTGATAACCACGTTAT
1 GAAATTTTGATAACCTCACTAC
* * * *
7651 GAAAATTTAAGAACCTC-C-ATT
1 GAAATTTTGATAACCTCACTA-C
* *
7672 G-AATTGTT-AGTAATCACACT-C
1 GAAATT-TTGA-TAACCTCACTAC
* *
7693 TGAAATTTTGATAA-TTACACTAT
1 -GAAATTTTGATAACCT-CACTAC
* ** *
7716 GAAATTGTGATAACCTTGCTAT
1 GAAATTTTGATAACCTCACTAC
* *
7738 AAAATTTTGATAAACCTC-CTTAT
1 GAAATTTTGAT-AACCTCAC-TAC
* *
7761 AAAATTTTGATAACCTC-CTTAT
1 GAAATTTTGATAACCTCAC-TAC
*
7783 GAAATCTTGAT-A----ACTAC
1 GAAATTTTGATAACCTCACTAC
*
7800 -AAATTTTGATAACCTC-CTTAT
1 GAAATTTTGATAACCTCAC-TAC
* * *
7821 G-ATTTTTGATAACCTCATTAT
1 GAAATTTTGATAACCTCACTAC
* * * *
7842 GAAATTTTGTTAATCTCCCTAA
1 GAAATTTTGATAACCTCACTAC
* * *
7864 GAAATTTTGATCTACAT-ACTAT
1 GAAATTTTGAT-AACCTCACTAC
* *
7886 GAAATTTTGATAACCCTC-TTAT
1 GAAATTTTGATAA-CCTCACTAC
* * *
7908 GAAATTTTGA-AAACTAAACTAT
1 GAAATTTTGATAACCT-CACTAC
* *
7930 GAAATTTTGATAATCTTCA-TAT
1 GAAATTTTGATAA-CCTCACTAC
7952 GAAATTTTGATA
1 GAAATTTTGATA
7964 TACTCCCTGA
Statistics
Matches: 320, Mismatches: 69, Indels: 70
0.70 0.15 0.15
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
18 1 0.00
20 8 0.03
21 33 0.10
22 218 0.68
23 46 0.14
24 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAACCTCACTAC
Found at i:7793 original size:45 final size:43
Alignment explanation
Indices: 7516--8736 Score: 365
Period size: 44 Copynumber: 28.4 Consensus size: 43
7506 TTTTAACCTC
* * *
7516 ATGAAATTTTGATAACCTCCCTACGGAATTTTGAAAACCTCAC-T
1 ATGAAATTTTGATAACCT-CCTATGAAATTTTGATAACCTC-CTT
* * **
7560 ATGAAATTTTGATAACTTCCGAATGAAATTTTGATAATCAACAC-T
1 ATGAAATTTTGATAACCTCC-TATGAAATTTTGATAA-CCTC-CTT
* * * * * * *
7605 ATGAGATGTTGATAACCTCTATATGATATATTGATAACCACGTT
1 ATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCTT
* * * * *
7649 ATGAAAATTTAAGAACCTCC-ATTG-AATTGTT-AGTAATCACAC-T
1 ATGAAATTTTGATAACCTCCTA-TGAAATT-TTGA-TAACCTC-CTT
* * * *
7692 CTGAAATTTTGATAA-TTACACTATGAAATTGTGATAACCTTGC-T
1 ATGAAATTTTGATAACCT-C-CTATGAAATTTTGATAACC-TCCTT
* *
7736 ATAAAATTTTGATAAACCTCCTTATAAAATTTTGATAACCTCCTT
1 ATGAAATTTTGAT-AACCTCC-TATGAAATTTTGATAACCTCCTT
* *
7781 ATGAAATCTTGATAA----CTA-CAAATTTTGATAACCTCCTT
1 ATGAAATTTTGATAACCTCCTATGAAATTTTGATAACCTCCTT
* * * * *
7819 ATG-ATTTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCTT
* * * *
7862 AAGAAATTTTGATCTACATACTATGAAATTTTGATAACC-CTCTT
1 ATGAAATTTTGAT-AACCTCCTATGAAATTTTGATAACCTC-CTT
* * * * *
7906 ATGAAATTTTGA-AAACTAAACTATGAAATTTTGATAATCTTCAT
1 ATGAAATTTTGATAACCT--CCTATGAAATTTTGATAACCTCCTT
* * *
7950 ATGAAATTTTGATATA-CTCC-CTGAAATTTTGATTA-CTCCAT
1 ATGAAATTTTGATA-ACCTCCTATGAAATTTTGATAACCTCCTT
* * * * *
7991 AGTAAAAGTTTAATAACCTTCC--T--AA-TTTGGTAACCATAC-T
1 A-TGAAATTTTGATAACC-TCCTATGAAATTTTGATAACC-TCCTT
* * *
8031 ATGAAATTTTGATAACTTCCCCAT--AA-----AT-ACC-AC-T
1 ATGAAATTTTGATAACCT-CCTATGAAATTTTGATAACCTCCTT
* * * * * *
8065 ATGAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTTT
1 ATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCTT
* * *
8109 ATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACC-CCTCT
1 ATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCT-T
*** * *
8153 ATGAAATTTTGATATTTTCATTATGTAATTTTGATAACCTCGCTT
1 ATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTC-CTT
** *
8198 -TGAAAATTTTGATAACAACACTATGAAATTTTGATAATCTTCC-T
1 ATG-AAATTTTGATAACCTC-CTATGAAATTTTGATAA-CCTCCTT
* * * * *
8242 CT-AAATTTCGATAATTCGATCTCTATAAAATTTCGATAA--TCAC-T
1 ATGAAATTTTGATAA--C-CTC-CTATGAAATTTTGATAACCTC-CTT
* * * * *
8286 CTGAGA-TTTGATAACCTTCTATCAAATTTTGGT-A-CTCCTT
1 ATGAAATTTTGATAACCTCCTATGAAATTTTGATAACCTCCTT
* * *
8326 ATGAAATTAAGACTTTTATAACCTTCATATGAAATTTTGATAACCACAC-T
1 ATGAAA-T-----TTTGATAACC-TCCTATGAAATTTTGATAACCTC-CTT
** * * *
8376 AAAAAATTTTAATAACCACACTATGAAATTTTGATAACCTCCCT
1 ATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACCTCCTT
* * *
8420 ATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACAC-T
1 ATGAAATTTTGA-TAACCTCC-TATGAAATTTTGATAACCTC-CTT
* *
8464 ATGAAATTCTT-ATAACCTCGTTATGACATTTTGATAA--T-C--
1 ATGAAATT-TTGATAACCTC-CTATGAAATTTTGATAACCTCCTT
* * * * * *
8503 -T----CTTTGATAACCTTTCTATAAAATTGTGAAAACCACAC-T
1 ATGAAATTTTGATAACC-TCCTATGAAATTTTGATAACCTC-CTT
* ** * ** * *
8542 ATAAAATTTCAATAACTTTCCTAAAAAAATTTAATAACCTGATCC-T
1 ATGAAATTTTGATAAC-CTCCTATGAAATTTTGATAACC---TCCTT
* * *
8588 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-C
1 ATGAAATTTTGATAACCTC-CTATGAAATTTTGATAACC-TCCTT
* * * * *
8632 ATAAAATTTTGATAACTTCCACATGAAATTTTGGTAACCACAC-T
1 ATGAAATTTTGATAACCTCC-TATGAAATTTTGATAACCTC-CTT
* * *
8676 ATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCAT-CTT
1 ATGAAATTTTGATAACCTCCT-ATGAAATTTTGATAACC-TCCTT
8720 ATGAAATTTTGATAACC
1 ATGAAATTTTGATAACC
8737 ACAAAAAGAC
Statistics
Matches: 872, Mismatches: 201, Indels: 208
0.68 0.16 0.16
Matches are distributed among these distances:
33 3 0.00
34 38 0.04
35 1 0.00
36 5 0.01
37 10 0.01
38 25 0.03
39 24 0.03
40 27 0.03
41 15 0.02
42 38 0.04
43 70 0.08
44 413 0.47
45 117 0.13
46 53 0.06
47 10 0.01
48 13 0.01
49 2 0.00
50 7 0.01
51 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (43 bp):
ATGAAATTTTGATAACCTCCTATGAAATTTTGATAACCTCCTT
Found at i:7828 original size:21 final size:21
Alignment explanation
Indices: 7740--7917 Score: 118
Period size: 22 Copynumber: 8.4 Consensus size: 21
7730 CTTGCTATAA
*
7740 AATTTTGATAAACCTCCTTATAA
1 AATTTTGAT-AACCTCCTTAT-G
7763 AATTTTGATAACCTCCTTATG
1 AATTTTGATAACCTCCTTATG
* *
7784 AAATCTTGATAA-CTAC--A--
1 -AATTTTGATAACCTCCTTATG
7801 AATTTTGATAACCTCCTTATG
1 AATTTTGATAACCTCCTTATG
* *
7822 ATTTTTGATAACCTCATTATG
1 AATTTTGATAACCTCCTTATG
* * * *
7843 AAATTTTGTTAATCTCCCTAAG
1 -AATTTTGATAACCTCCTTATG
* * *
7865 AAATTTTGATCTACATAC-TATG
1 -AATTTTGAT-AACCTCCTTATG
7887 AAATTTTGATAACC-CTCTTATG
1 -AATTTTGATAACCTC-CTTATG
7909 AAATTTTGA
1 -AATTTTGA
7918 AAACTAAACT
Statistics
Matches: 123, Mismatches: 22, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
16 10 0.08
17 3 0.02
19 2 0.02
21 25 0.20
22 71 0.58
23 12 0.10
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (21 bp):
AATTTTGATAACCTCCTTATG
Found at i:7988 original size:19 final size:20
Alignment explanation
Indices: 7951--7988 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7941 AATCTTCATA
7951 TGAAATTTTGATATACTCCC
1 TGAAATTTTGATATACTCCC
7971 TGAAATTTTGAT-TACTCC
1 TGAAATTTTGATATACTCC
7989 ATAGTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (20 bp):
TGAAATTTTGATATACTCCC
Found at i:8091 original size:22 final size:22
Alignment explanation
Indices: 8064--8234 Score: 112
Period size: 22 Copynumber: 7.7 Consensus size: 22
8054 TAAATACCAC
*
8064 TATGAAATTTTGATAATCACATT
1 TATGAAATTTTGATAACCAC-TT
* *
8087 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACTT
* *
8108 TATGAAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCACTT
* * * * *
8130 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCACTT
**** *
8152 TATGAAATTTTGATATTTTCAT
1 TATGAAATTTTGATAACCACTT
* * *
8174 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCAC-TT
* **
8197 T-TGAAAATTTTGATAACAACAC
1 TATG-AAATTTTGATAACCACTT
8219 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
8235 TCTTCCTCTA
Statistics
Matches: 116, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
21 3 0.03
22 95 0.82
23 18 0.16
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACTT
Found at i:8232 original size:67 final size:66
Alignment explanation
Indices: 8063--8233 Score: 173
Period size: 66 Copynumber: 2.6 Consensus size: 66
8053 ATAAATACCA
* * * * *** *
8063 CTATGAAATTTTGATAATC-ACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCT
1 CTATAAAATTTTGATAA-CAACACTATGAAATTTTGATATTTTCATTATGAAATTTTGATAACCT
*
8127 CT
65 CG
* * ** * *
8129 CTATAAAATTTTGTTGACCCCTCTATGAAATTTTGATATTTTCATTATGTAATTTTGATAACCTC
1 CTATAAAATTTTGATAACAACACTATGAAATTTTGATATTTTCATTATGAAATTTTGATAACCTC
8194 G
66 G
*
8195 CTTTGAAAATTTTGATAACAACACTATGAAATTTTGATA
1 CTAT-AAAATTTTGATAACAACACTATGAAATTTTGATA
8234 ATCTTCCTCT
Statistics
Matches: 83, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
65 1 0.01
66 53 0.64
67 29 0.35
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (66 bp):
CTATAAAATTTTGATAACAACACTATGAAATTTTGATATTTTCATTATGAAATTTTGATAACCTC
G
Found at i:8368 original size:22 final size:21
Alignment explanation
Indices: 8351--8500 Score: 106
Period size: 22 Copynumber: 6.9 Consensus size: 21
8341 TTATAACCTT
8351 CATATGAAATTTTGATAACCA
1 CATATGAAATTTTGATAACCA
** *
8372 CACTAAAAAATTTTAATAACCA
1 CA-TATGAAATTTTGATAACCA
*
8394 CACTATGAAATTTTGATAACCTC
1 CA-TATGAAATTTTGATAACC-A
* * *
8417 CCTATGAAATATT-AGTAACCTC
1 CATATGAAATTTTGA-TAACC-A
* *
8439 CTTATGAAATTTTGTTAACCA
1 CATATGAAATTTTGATAACCA
*
8460 CACTATGAAATTCTT-ATAACCT
1 CA-TATGAAATT-TTGATAACCA
* *
8482 CGTTATGACATTTTGATAA
1 C-ATATGAAATTTTGATAA
8501 TCTCTTTGAT
Statistics
Matches: 103, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
21 6 0.06
22 94 0.91
23 3 0.03
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (21 bp):
CATATGAAATTTTGATAACCA
Found at i:8423 original size:66 final size:65
Alignment explanation
Indices: 8339--8500 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 65
8329 AAATTAAGAC
*
8339 TTTTATAACCTTCATATGAAATTTTGATAACCACAC-TAAAAAATTTTAATAACCACACTATGAA
1 TTTTATAACCTCCATATGAAATTTTGATAACCAC-CTTAAAAAATTTTAATAACCACACTATGAA
8403 A
65 A
* * * ** **
8404 TTTTGATAACCTCCCTATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACTATGA
1 TTTT-ATAACCTCCATATGAAATTTTGA-TAACCACCTTAAAAAATTTTAATAACCACACTATGA
8468 AA
64 AA
** *
8470 TTCTTATAACCTCGTTATGACATTTTGATAA
1 TT-TTATAACCTCCATATGAAATTTTGATAA
8501 TCTCTTTGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
65 6 0.08
66 71 0.89
67 3 0.04
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (65 bp):
TTTTATAACCTCCATATGAAATTTTGATAACCACCTTAAAAAATTTTAATAACCACACTATGAAA
Found at i:8613 original size:22 final size:22
Alignment explanation
Indices: 8586--8739 Score: 138
Period size: 22 Copynumber: 7.0 Consensus size: 22
8576 TAACCTGATC
*
8586 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
8608 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* *
8630 CCATAAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
8653 C-ATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
8674 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
8695 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
8718 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
8740 AAAAGACAAG
Statistics
Matches: 107, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.01
21 6 0.06
22 95 0.89
23 4 0.04
24 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:8713 original size:66 final size:66
Alignment explanation
Indices: 8533--8739 Score: 206
Period size: 66 Copynumber: 3.1 Consensus size: 66
8523 AAATTGTGAA
* ** * * *
8533 AACCACACTATAAAATTTCAATAACTTTCCTAAAAAAATT-TAATAACCTGATC-CTATGAAATT
1 AACCACACTATGAAATTTTGATAACCTTCC-CATAAAATTATAATAACC--ATCAC-ATGAAATT
8596 TTGGT
62 TTGGT
* * *
8601 AACCACACTATGAAATTTTGATAACCTTCCCATAAAATTTTGATAA-CTTCCACATGAAATTTTG
1 AACCACACTATGAAATTTTGATAACCTTCCCATAAAATTATAATAACCAT-CACATGAAATTTTG
8665 GT
65 GT
* * **
8667 AACCACACTATGGAATTTTGATAACC-TCCTCATGAAATTATAATAACCATCTTATGAAATTTTG
1 AACCACACTATGAAATTTTGATAACCTTCC-CATAAAATTATAATAACCATCACATGAAATTTTG
*
8731 AT
65 GT
8733 AACCACA
1 AACCACA
8740 AAAAGACAAG
Statistics
Matches: 118, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
65 4 0.03
66 72 0.61
67 11 0.09
68 31 0.26
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (66 bp):
AACCACACTATGAAATTTTGATAACCTTCCCATAAAATTATAATAACCATCACATGAAATTTTGG
T
Found at i:9210 original size:14 final size:13
Alignment explanation
Indices: 9181--9220 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
9171 GTCTAAATTG
9181 AAATTTT-ATAATT
1 AAATTTTAATAA-T
9194 AAATTTTAAATAAT
1 AAATTTT-AATAAT
9208 AAATTTTAATAAT
1 AAATTTTAATAAT
9221 GTCAATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 8 0.32
15 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTTAATAAT
Found at i:9266 original size:165 final size:163
Alignment explanation
Indices: 8956--9281 Score: 449
Period size: 165 Copynumber: 2.0 Consensus size: 163
8946 AATAGTAAAG
*
8956 GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACGTATAATTCGGTCTAAATTGAAATT
1 GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACGTAAAATTCGGTCTAAATTGAAATT
*
9021 TTTAAATAATAGAATTATACTAAATTTTAATAATGGAAATTTAGAAATATAATTGAAAAAAAGGG
66 TTTAAATAATAGAA-TATAATAAATTTTAATAATGGAAATTTAGAAATATAATTG-AAAAAAGGG
9086 TACAATCAGAAACATAAAGTTTCCCATTATTAATA
129 TACAATCAGAAACATAAAGTTTCCCATTATTAATA
* * *
9121 GAAATTTGCATGTTCATCAATGAAAATCAATTTTACAAACTTAAAATTCGGTCTAAATTGAAATT
1 GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACGTAAAATTCGGTCTAAATTGAAATT
* ** ** * * *
9186 TTATAATTAAATTTTAA-ATAATAAATTTTAATAATGTCAATTTAGAAATATATTTG-ATATAGG
66 TT-TAAAT-AA-TAGAATATAATAAATTTTAATAATGGAAATTTAGAAATATAATTGAAAAAAGG
* *
9249 GTACAATCGGAAAACATAAAGTTTTCCATTATT
128 GTACAATCAG-AAACATAAAGTTTCCCATTATT
9282 CATACTTTTA
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
164 14 0.10
165 84 0.59
166 39 0.27
167 2 0.01
168 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (163 bp):
GAAATTTGCATGTTCATCAACGAAAATCAATTTGACAAACGTAAAATTCGGTCTAAATTGAAATT
TTTAAATAATAGAATATAATAAATTTTAATAATGGAAATTTAGAAATATAATTGAAAAAAGGGTA
CAATCAGAAACATAAAGTTTCCCATTATTAATA
Found at i:19365 original size:30 final size:30
Alignment explanation
Indices: 19329--19392 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
19319 GGTCATCATC
19329 CTCCCCCTTATGGCACCCCGCAGCAACCAT
1 CTCCCCCTTATGGCACCCCGCAGCAACCAT
*
19359 CTCCCCCTTATGGCGCCCCGCAGCAACCAT
1 CTCCCCCTTATGGCACCCCGCAGCAACCAT
19389 CTCC
1 CTCC
19393 ATACCATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.17, C:0.52, G:0.14, T:0.17
Consensus pattern (30 bp):
CTCCCCCTTATGGCACCCCGCAGCAACCAT
Found at i:20186 original size:18 final size:18
Alignment explanation
Indices: 20163--20201 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
20153 TATAGTATGC
20163 TAAGAGAAATTATCAAAT
1 TAAGAGAAATTATCAAAT
20181 TAAGAGAAATTATCAAAT
1 TAAGAGAAATTATCAAAT
20199 TAA
1 TAA
20202 ATTACTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (18 bp):
TAAGAGAAATTATCAAAT
Found at i:20273 original size:19 final size:19
Alignment explanation
Indices: 20251--20289 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20241 GACAAGTCAG
20251 ATTTTTTCCTACAATTATT
1 ATTTTTTCCTACAATTATT
20270 ATTTTTTCCTACAATTATT
1 ATTTTTTCCTACAATTATT
20289 A
1 A
20290 AAACCATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTTCCTACAATTATT
Found at i:20435 original size:43 final size:43
Alignment explanation
Indices: 20375--20460 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
20365 GCTAAATTTG
20375 TGCATAAATTTTAGCAATAATTTTGACTTGTCACAATCTTATT
1 TGCATAAATTTTAGCAATAATTTTGACTTGTCACAATCTTATT
* *
20418 TGCATAACTTTTTGCAATAATTTTGACTTGTCACAATCTTATT
1 TGCATAAATTTTAGCAATAATTTTGACTTGTCACAATCTTATT
20461 GGTCGGGACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (43 bp):
TGCATAAATTTTAGCAATAATTTTGACTTGTCACAATCTTATT
Found at i:21952 original size:14 final size:12
Alignment explanation
Indices: 21918--21959 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
21908 TTTATAAAAT
21918 AAATAA-ATAAA
1 AAATAATATAAA
21929 AAATAATATAAA
1 AAATAATATAAA
21941 AAATCAATTATAGAA
1 AAAT-AA-TATA-AA
21956 AAAT
1 AAAT
21960 GTACTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.22
12 9 0.33
13 2 0.07
14 4 0.15
15 6 0.22
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (12 bp):
AAATAATATAAA
Found at i:22135 original size:29 final size:30
Alignment explanation
Indices: 22066--22146 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
22056 GCTCAATTAA
*
22066 GGGCAAAACGTTTCTAGTTCGGCTTAATTTG
1 GGGCAAAACGTTTC-AATTCGGCTTAATTTG
* *
22097 GGGCACAACGTTTCAATTTGG-TCT-ATTTG
1 GGGCAAAACGTTTCAATTCGGCT-TAATTTG
22126 GGGCAAAACGTTTCCAATTCG
1 GGGCAAAACGTTT-CAATTCG
22147 CGTCAATTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.42
30 12 0.28
31 13 0.30
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (30 bp):
GGGCAAAACGTTTCAATTCGGCTTAATTTG
Found at i:22273 original size:16 final size:15
Alignment explanation
Indices: 22252--22283 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
22242 ATATTCGAAA
22252 TAAAATTAATTTTAAT
1 TAAAATTAA-TTTAAT
22268 TAAAATTAATTTAAT
1 TAAAATTAATTTAAT
22283 T
1 T
22284 TTTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAATTAATTTAAT
Found at i:25509 original size:31 final size:31
Alignment explanation
Indices: 25469--25544 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
25459 GCTAAATACC
* *
25469 CAAAA-AATCCCTTGTGTTTTTCTTTTGGGA
1 CAAAATAATCCCTTATATTTTTCTTTTGGGA
* **
25499 CAAAATAATCCCTTATATTTTTTTTTTTTGA
1 CAAAATAATCCCTTATATTTTTCTTTTGGGA
25530 -AAAATTAATCCCTTA
1 CAAAA-TAATCCCTTA
25545 CGTTTCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 9 0.23
31 30 0.77
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (31 bp):
CAAAATAATCCCTTATATTTTTCTTTTGGGA
Found at i:26003 original size:20 final size:20
Alignment explanation
Indices: 25971--26021 Score: 93
Period size: 21 Copynumber: 2.5 Consensus size: 20
25961 ACCTTCGCCG
25971 TTTTAGAATTTTTTTTTTAA
1 TTTTAGAATTTTTTTTTTAA
25991 TTTTCAGAATTTTTTTTTTAA
1 TTTT-AGAATTTTTTTTTTAA
26012 TTTTAGAATT
1 TTTTAGAATT
26022 ATTCTCTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTTAGAATTTTTTTTTTAA
Found at i:26256 original size:27 final size:28
Alignment explanation
Indices: 26195--26256 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
26185 CAGTTTAATG
26195 TTTATAATATATTATATATATAATCAGTT
1 TTTA-AATATATTATATATATAATCAGTT
* *
26224 TATTAAATATATTTTATATATAATTA-TT
1 T-TTAAATATATTATATATATAATCAGTT
26252 TTTAA
1 TTTAA
26257 TTTAGAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.13
28 3 0.10
29 20 0.67
30 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTAAATATATTATATATATAATCAGTT
Found at i:29330 original size:16 final size:16
Alignment explanation
Indices: 29281--29336 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
29271 TTAGACATAT
*
29281 TAAATTAGAATAATAA
1 TAAATTAAAATAATAA
*
29297 TTAAATTTTACAAT--TAA
1 -TAAA--TTAAAATAATAA
29314 TAAATTAAAATAATAA
1 TAAATTAAAATAATAA
29330 TAAATTA
1 TAAATTA
29337 CATAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.18
16 14 0.42
17 7 0.21
19 6 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAATTAAAATAATAA
Found at i:29578 original size:2 final size:2
Alignment explanation
Indices: 29571--29637 Score: 51
Period size: 2 Copynumber: 37.5 Consensus size: 2
29561 TTATAATTAA
* *
29571 AT AT AT AT -T AT AT AT AT A- AA AT A- AT AT -T AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29609 A- AT -T AC AT AT AT A- AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29638 ATTATTAAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
1 8 0.15
2 44 0.85
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:29594 original size:28 final size:28
Alignment explanation
Indices: 29563--29642 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 28
29553 AGTAATATTT
*
29563 ATAATTAAATATATATTATATATATAAA
1 ATAATTAAATATATATTATACATATAAA
* * *
29591 ATAATATTAGATATATATAATTACATATATA
1 AT-A-ATTAAATATATATTA-TACATATAAA
*
29622 ATAATATATATATATAATTAT
1 ATAAT-TAAATATAT-ATTAT
29643 TAAACGGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 2 0.05
29 3 0.07
30 23 0.56
31 13 0.32
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
ATAATTAAATATATATTATACATATAAA
Found at i:29613 original size:14 final size:14
Alignment explanation
Indices: 29596--29641 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
29586 ATAAAATAAT
*
29596 ATTAGATATATATA
1 ATTACATATATATA
29610 ATTACATATATAATA
1 ATTACATATAT-ATA
*
29625 A-TATATATATATA
1 ATTACATATATATA
29638 ATTA
1 ATTA
29642 TTAAACGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.14
14 20 0.71
15 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTACATATATATA
Found at i:43138 original size:24 final size:26
Alignment explanation
Indices: 43087--43138 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
43077 ATTGAGTTCC
43087 CAAATAGGAAAAGATAAGAAGATTTTG
1 CAAATAGGAAAAGAT-AGAAGATTTTG
43114 CAAATAGGAAAAGAT-G-AGATTTTG
1 CAAATAGGAAAAGATAGAAGATTTTG
43138 C
1 C
43139 TTGAGTGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
27 15 0.60
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (26 bp):
CAAATAGGAAAAGATAGAAGATTTTG
Found at i:46451 original size:14 final size:14
Alignment explanation
Indices: 46432--46471 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
46422 GTTGGGTTGG
*
46432 ATTTGGGTTCGGTT
1 ATTTGGGTTAGGTT
46446 ATTTGGGTTAGGTT
1 ATTTGGGTTAGGTT
46460 AGTTTCGGGTTA
1 A-TTT-GGGTTA
46472 AGGAATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.12, C:0.05, G:0.35, T:0.47
Consensus pattern (14 bp):
ATTTGGGTTAGGTT
Found at i:47126 original size:26 final size:27
Alignment explanation
Indices: 47077--47132 Score: 89
Period size: 26 Copynumber: 2.1 Consensus size: 27
47067 TTTTTCTTGA
47077 TTTTACTTTAAAAAAAGCATATAGAAC
1 TTTTACTTTAAAAAAAGCATATAGAAC
47104 TTTTACTTTCAAAAAAAG-A-ATAGAAC
1 TTTTACTTT-AAAAAAAGCATATAGAAC
47130 TTT
1 TTT
47133 GGTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 10 0.36
27 10 0.36
28 8 0.29
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (27 bp):
TTTTACTTTAAAAAAAGCATATAGAAC
Found at i:47148 original size:23 final size:23
Alignment explanation
Indices: 47114--47164 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
47104 TTTTACTTTC
47114 AAAA-AAAGAATAGAACTTTGGT
1 AAAATAAAGAATAGAACTTTGGT
47136 AAAATAAAGAATAGAACTTTGGT
1 AAAATAAAGAATAGAACTTTGGT
47159 AAAATA
1 AAAATA
47165 GTTACTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.24
Consensus pattern (23 bp):
AAAATAAAGAATAGAACTTTGGT
Found at i:48697 original size:73 final size:73
Alignment explanation
Indices: 48579--48727 Score: 237
Period size: 73 Copynumber: 2.0 Consensus size: 73
48569 TTCACATATC
* *
48579 TATCTATACTATATTAAAAAATACGTTCACTTGTAAAACTTTTGAATCACCT-ATTATACCCTTA
1 TATCTATACTATATTAAAAAATACATACACTTGTAAAACTTTTGAATC-CCTCATTATACCCTTA
48643 TTTTTCGAA
65 TTTTTCGAA
* * *
48652 TATCTATACTATATTAAAAAGTACATACTCTTGTAAAACTTTTGAATCGCTCATTATACCCTTAT
1 TATCTATACTATATTAAAAAATACATACACTTGTAAAACTTTTGAATCCCTCATTATACCCTTAT
48717 TTTTCGAA
66 TTTTCGAA
48725 TAT
1 TAT
48728 ATTTCTTAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 2 0.03
73 68 0.97
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (73 bp):
TATCTATACTATATTAAAAAATACATACACTTGTAAAACTTTTGAATCCCTCATTATACCCTTAT
TTTTCGAA
Found at i:48903 original size:129 final size:129
Alignment explanation
Indices: 48753--49143 Score: 685
Period size: 129 Copynumber: 3.0 Consensus size: 129
48743 TTGTTTAAAC
* *
48753 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCTAATATCTTTATAACTA
48818 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAATCTTATATATTAGAATTTTTTAATATAT
66 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAATCTTATATATTAGAATTTTTTAATATAT
48882 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCTAATATCTTTATAACTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCTAATATCTTTATAACTA
48947 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAATCTTATATATTAGAATTTTTTAATATAT
66 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAATCTTATATATTAGAATTTTTTAATATAT
* * *
49011 TTTTATAATTTTACTCAACTAAAAACTTTATTTCTATTTAATAAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCTAATATCTTTATAACTA
* *
49076 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAA-CTTAGATATATTAGAATTTTTAAAATAT
66 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAATCTT--ATATATTAGAATTTTT-TAATAT
49140 AT
128 AT
49142 TT
1 TT
49144 CTTAAATGAC
Statistics
Matches: 252, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
128 3 0.01
129 224 0.89
130 16 0.06
131 9 0.04
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (129 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATTAAATCTAATATCTTTATAACTA
TTTTATTTTTACCATTTTACTATTTTAATTAAAAAATCTTATATATTAGAATTTTTTAATATAT
Done.