Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010126.1 Corchorus capsularis cultivar CVL-1 contig10147, 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: 70248
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5199 original size:136 final size:136
Alignment explanation
Indices: 5031--5304 Score: 512
Period size: 136 Copynumber: 2.0 Consensus size: 136
5021 TCCCCAGAAG
5031 TAGCATTGGCATTAGCACAAATGAAAGATGAAAGTCCTCCTCAAAAAATTGGTGCTAAAGCAGCA
1 TAGCATTGGCATTAGCACAAATGAAAGATGAAAGTCCTCCTCAAAAAATTGGTGCTAAAGCAGCA
5096 AAGATTTCAAAAAATAGAGAGATTGTTTTACACAAACCAAAGTCTCTCACAAATATTTCAAAACA
66 AAGATTTCAAAAAATAGAGAGATTGTTTTACACAAACCAAAGTCTCTCACAAATATTTCAAAACA
5161 ACTATC
131 ACTATC
* * * *
5167 TAGCATTGGCATTAGCATAAATGAAAGATGAAAGTTCTCTTCAAAAAATTGGTGCTGAAGCAGCA
1 TAGCATTGGCATTAGCACAAATGAAAGATGAAAGTCCTCCTCAAAAAATTGGTGCTAAAGCAGCA
5232 AAGATTTCAAAAAATAGAGAGATTGTTTTACACAAACCAAAGTCTCTCACAAATATTTCAAAACA
66 AAGATTTCAAAAAATAGAGAGATTGTTTTACACAAACCAAAGTCTCTCACAAATATTTCAAAACA
5297 ACTATC
131 ACTATC
5303 TA
1 TA
5305 TTCAAGAGAT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 134 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (136 bp):
TAGCATTGGCATTAGCACAAATGAAAGATGAAAGTCCTCCTCAAAAAATTGGTGCTAAAGCAGCA
AAGATTTCAAAAAATAGAGAGATTGTTTTACACAAACCAAAGTCTCTCACAAATATTTCAAAACA
ACTATC
Found at i:6440 original size:20 final size:20
Alignment explanation
Indices: 6415--6454 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6405 CCAAGAAAAT
6415 CTCTGCAAAGTTCAATAATG
1 CTCTGCAAAGTTCAATAATG
6435 CTCTGCAAAGTTCAATAATG
1 CTCTGCAAAGTTCAATAATG
6455 GAAGACAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
CTCTGCAAAGTTCAATAATG
Found at i:6961 original size:10 final size:10
Alignment explanation
Indices: 6946--6972 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6936 ATCTTTTAGG
6946 AGAAAAGGTT
1 AGAAAAGGTT
6956 AGAAAAGGTT
1 AGAAAAGGTT
6966 AGAAAAG
1 AGAAAAG
6973 TTATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (10 bp):
AGAAAAGGTT
Found at i:6981 original size:2 final size:2
Alignment explanation
Indices: 6974--7012 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
6964 TTAGAAAAGT
* *
6974 TA TA TA TA TA TA TA TA TA TA TA TA TC TG TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
7013 AAAGTATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:8050 original size:20 final size:20
Alignment explanation
Indices: 8013--8051 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8003 TACTATTATT
8013 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
8033 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
8052 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:8290 original size:22 final size:22
Alignment explanation
Indices: 8263--8385 Score: 104
Period size: 22 Copynumber: 5.5 Consensus size: 22
8253 ATTCCATGAG
8263 GAGGTTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGT
* *
8285 GTGGTTACCAAAATTTCATACGAT
1 GAGGTTATCAAAATTTCATA-G-T
* * *
8309 CAGGTTATTAAAATTTCTTAG-
1 GAGGTTATCAAAATTTCATAGT
*
8330 GAAAGTTATCAAAATTTCATAGT
1 G-AGGTTATCAAAATTTCATAGT
* * * * *
8353 GTGATTATCACAATTTTATAGA
1 GAGGTTATCAAAATTTCATAGT
*
8375 AAGGTTATCAA
1 GAGGTTATCAA
8386 GAGATTATCA
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
22 57 0.75
23 3 0.04
24 16 0.21
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGT
Found at i:8444 original size:22 final size:22
Alignment explanation
Indices: 8390--8720 Score: 133
Period size: 22 Copynumber: 14.9 Consensus size: 22
8380 TATCAAGAGA
* * * *
8390 TTATCAATATGTCATAGCGAGC
1 TTATCAAAATTTCATAGTGAGG
*
8412 TTAT-AAGAATTTCATAGTGCGG
1 TTATCAA-AATTTCATAGTGAGG
*
8434 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * * *
8456 TTA-CTAATATTTCATGGGGAGA
1 TTATC-AAAATTTCATAGTGAGG
* * *
8478 TTATTAAAATTTCATAGTGTGT
1 TTATCAAAATTTCATAGTGAGG
** *
8500 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
8522 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
8544 TTATATAAGTCTCAATTTCATA-AGAAG
1 TTAT-CAA-----AATTTCATAGTGAGG
* * *
8571 -TACCAAAATTTGATAGTAAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
8592 TTATC--AATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
*
8612 TTATCAAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
8636 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
* **
8658 TTATAAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
8680 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
8702 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
8721 GTATTTTTGT
Statistics
Matches: 230, Mismatches: 56, Indels: 46
0.69 0.17 0.14
Matches are distributed among these distances:
20 22 0.10
21 19 0.08
22 147 0.64
23 8 0.03
24 6 0.03
25 14 0.06
26 2 0.01
27 2 0.01
28 10 0.04
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:8659 original size:21 final size:24
Alignment explanation
Indices: 8610--8673 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
8600 CTCATAGAGT
*
8610 GATTATCAAAATTTCATAGAGATCG
1 GATTATCAAAATTTCATAGAGA-CA
8635 GATTATCAAAATTT-ATAG-GA-A
1 GATTATCAAAATTTCATAGAGACA
*
8656 GATTATAAAAATTTCATA
1 GATTATCAAAATTTCATA
8674 AAGAGGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 13 0.36
22 3 0.08
23 2 0.06
24 4 0.11
25 14 0.39
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (24 bp):
GATTATCAAAATTTCATAGAGACA
Found at i:8963 original size:21 final size:20
Alignment explanation
Indices: 8938--9039 Score: 59
Period size: 21 Copynumber: 5.0 Consensus size: 20
8928 TAACAAAATT
*
8938 TCATAATGAGGTTATCGAAAA
1 TCATAAGGAGGTTATC-AAAA
*
8959 TCATAGGGAGGTTATCAAAA
1 TCATAAGGAGGTTATCAAAA
* * *
8979 T--T-TGTA-GTTATCAAGATT
1 TCATAAGGAGGTTATCAA-A-A
*
8997 TCATAAGGAGTTTATCAAAA
1 TCATAAGGAGGTTATCAAAA
* *
9017 TTTATAGGGAGGTTTATCAAAA
1 -TCATAAGGAGG-TTATCAAAA
9039 T
1 T
9040 TTTATAGGAA
Statistics
Matches: 61, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
16 8 0.13
17 3 0.05
18 2 0.03
20 6 0.10
21 26 0.43
22 16 0.26
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (20 bp):
TCATAAGGAGGTTATCAAAA
Found at i:9043 original size:23 final size:23
Alignment explanation
Indices: 8986--9061 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
8976 AAATTTGTAG
* * *
8986 TTATCAAGATTTCATAAGGA-GT
1 TTATCAAAATTTTATAGGGAGGT
9008 TTATCAAAA-TTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
9030 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
9053 TTATCAAAA
1 TTATCAAAA
9062 AAAATTCATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
21 8 0.17
22 19 0.40
23 21 0.44
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:9094 original size:22 final size:22
Alignment explanation
Indices: 8799--9113 Score: 157
Period size: 22 Copynumber: 14.5 Consensus size: 22
8789 TTATGGAGTA
* *
8799 ATCAAAATTTCA-GGGAGG-AT
1 ATCAAAATTTCATAGGAGGTTT
* *
8819 ATCAAAATTGCATATGAAGG-TT
1 ATCAAAATTTCATA-GGAGGTTT
*
8841 ATCAAAATTTCATAGTTTA-GTTT
1 ATCAAAATTTCATAG--GAGGTTT
* *
8864 -TCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAGGAGGTTT
* * **
8885 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAGGAGGTTT
* *
8907 ATCAAAATTTCATTGG-GAGATT
1 ATCAAAATTTCATAGGAG-GTTT
* *
8929 AACAAAATTTCATAATGAGG-TT
1 ATCAAAATTTCAT-AGGAGGTTT
8951 ATCGAAAA--TCATAGGGAGG-TT
1 ATC-AAAATTTCATA-GGAGGTTT
*
8972 ATCAAAA-TT--T-GTA-G-TT
1 ATCAAAATTTCATAGGAGGTTT
*
8988 ATCAAGATTTCATAAGGA-GTTT
1 ATCAAAATTTCAT-AGGAGGTTT
9010 ATCAAAATTT-ATAGGGAGGTTT
1 ATCAAAATTTCATA-GGAGGTTT
*
9032 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGG-AGGTTT
*
9055 ATCAAAAAAAATTCATAGCGA-GTTT
1 ATC---AAAATTTCATAG-GAGGTTT
* * *
9080 ATCACAATTTCATA-GTGTTATT
1 ATCAAAATTTCATAGGAGGT-TT
9102 ATCAAAATTTCA
1 ATCAAAATTTCA
9114 GAGTGTAATC
Statistics
Matches: 229, Mismatches: 37, Indels: 56
0.71 0.11 0.17
Matches are distributed among these distances:
16 9 0.04
17 4 0.02
19 2 0.01
20 19 0.08
21 27 0.12
22 127 0.55
23 21 0.09
24 1 0.00
25 7 0.03
26 11 0.05
27 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAGGTTT
Found at i:9225 original size:23 final size:23
Alignment explanation
Indices: 8985--9292 Score: 103
Period size: 22 Copynumber: 13.7 Consensus size: 23
8975 AAAATTTGTA
* *
8985 GTTATCAAGATTTCATA-AGGAG
1 GTTATCAAAATTTCATAGTGGAG
*
9007 TTTATCAAAATTT-ATAG-GGAG
1 GTTATCAAAATTTCATAGTGGAG
* *
9028 GTTTATCAAAATTTTATAG-GAAG
1 G-TTATCAAAATTTCATAGTGGAG
* *
9051 GTTTATCAAAAAAAATTCATAG-CGAG
1 G-TTATC---AAAATTTCATAGTGGAG
* * *
9077 TTTATCACAATTTCATAGTGTTA-
1 GTTATCAAAATTTCATAGTG-GAG
* *
9100 -TTATCAAAATTTCAGAGTGTA-
1 GTTATCAAAATTTCATAGTGGAG
* *
9121 ATCA-CTAACAATTT-ATA-TGGAG
1 GTTATC-AA-AATTTCATAGTGGAG
** * ** *
9143 GTT-TTTAGATGTTCATA-ACGTG
1 GTTATCAAAAT-TTCATAGTGGAG
* *
9165 GTTATCAATATATCATA-TGGAG
1 GTTATCAAAATTTCATAGTGGAG
* * **
9187 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAGTGGAG
* *
9210 GTTATCAAAATTTCATTG-GGAA
1 GTTATCAAAATTTCATAGTGGAG
*
9232 GTTATCAAAATTTCATAGT-AAG
1 GTTATCAAAATTTCATAGTGGAG
* * *
9254 GTCT-TCAAAATTCCTTA-AGGAG
1 GT-TATCAAAATTTCATAGTGGAG
*
9276 GTTAACAAAATTTCATA
1 GTTATCAAAATTTCATA
9293 AAAAGCTTTA
Statistics
Matches: 212, Mismatches: 53, Indels: 42
0.69 0.17 0.14
Matches are distributed among these distances:
20 2 0.01
21 17 0.08
22 133 0.63
23 42 0.20
24 1 0.00
25 5 0.02
26 12 0.06
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (23 bp):
GTTATCAAAATTTCATAGTGGAG
Found at i:9236 original size:45 final size:45
Alignment explanation
Indices: 9163--9250 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
9153 GTTCATAACG
* * *
9163 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
9208 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGT
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGT
9251 AAGGTCTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:10459 original size:29 final size:31
Alignment explanation
Indices: 10409--10477 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
10399 AACTATTGCG
* *
10409 TCAAGACGTTTTGTGTCATGAAGTT-CAAA-
1 TCAAGACATTTTGTGTCATGAACTTCCAAAT
*
10438 TCAAGACATTTTGCT-TCCTGAACTTCCAAAT
1 TCAAGACATTTTG-TGTCATGAACTTCCAAAT
*
10469 TCAAAACAT
1 TCAAGACAT
10478 CTTGGAAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 20 0.61
30 5 0.15
31 8 0.24
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (31 bp):
TCAAGACATTTTGTGTCATGAACTTCCAAAT
Found at i:11667 original size:126 final size:126
Alignment explanation
Indices: 11442--11692 Score: 493
Period size: 126 Copynumber: 2.0 Consensus size: 126
11432 CTTGATCTTG
*
11442 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATGAAGATCGAGAGAAATTTATTTGCTTCAAG
1 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATGAAGATCGAGAGAAATTTACTTGCTTCAAG
11507 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTTC
66 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTTC
11568 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATGAAGATCGAGAGAAATTTACTTGCTTCAAG
1 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATGAAGATCGAGAGAAATTTACTTGCTTCAAG
11633 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTT
66 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTT
11693 GGTGAAGATC
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 124 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (126 bp):
AATAAACAAGAATAATCTTCTCTAAATGTGTTGATGAAGATCGAGAGAAATTTACTTGCTTCAAG
GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTTC
Found at i:11949 original size:126 final size:126
Alignment explanation
Indices: 11795--12045 Score: 475
Period size: 126 Copynumber: 2.0 Consensus size: 126
11785 CTTGATCTTG
*
11795 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATGAAGATCGAGAGAAATTTATTTGCTTCAAG
1 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATAAAGATCGAGAGAAATTTATTTGCTTCAAG
*
11860 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAAGAGAATTAATCTTCTCCGAATTTGTTC
66 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTTC
*
11921 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATAAAGATCGAGAGAATTTTATTTGCTTCAAG
1 AATAAACAAGAATAATCTTCTCTAAATGTGTTGATAAAGATCGAGAGAAATTTATTTGCTTCAAG
11986 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTT
66 GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTT
12046 GGTGAAGATC
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (126 bp):
AATAAACAAGAATAATCTTCTCTAAATGTGTTGATAAAGATCGAGAGAAATTTATTTGCTTCAAG
GGTCTTCGATTTGGTAGACTTGATCTTGAACAAACAGAATTAATCTTCTCCGAATTTGTTC
Found at i:12050 original size:353 final size:353
Alignment explanation
Indices: 11404--12107 Score: 1372
Period size: 353 Copynumber: 2.0 Consensus size: 353
11394 ATCTTCTTCA
11404 ATGAATTTGATTCAAGGGTCTTGATAGACTTGATCTTGAATAAACAAGAATAATCTTCTCTAAAT
1 ATGAATTTGATTCAAGGGTCTTGATAGACTTGATCTTGAATAAACAAGAATAATCTTCTCTAAAT
11469 GTGTTGATGAAGATCGAGAGAAATTTATTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTT
66 GTGTTGATGAAGATCGAGAGAAATTTATTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTT
11534 GAACAAACAGAATTAATCTTCTCCGAATTTGTTCAATAAACAAGAATAATCTTCTCTAAATGTGT
131 GAACAAACAGAATTAATCTTCTCCGAATTTGTTCAATAAACAAGAATAATCTTCTCTAAATGTGT
*
11599 TGATGAAGATCGAGAGAAATTTACTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTTGAAC
196 TGATAAAGATCGAGAGAAATTTACTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTTGAAC
11664 AAACAGAATTAATCTTCTCCGAATTTGTTGGTGAAGATCAAAACAATGATTTCTTGAATTTTGGT
261 AAACAGAATTAATCTTCTCCGAATTTGTTGGTGAAGATCAAAACAATGATTTCTTGAATTTTGGT
11729 GAAGATCAAACCAAGAAATATCTGAAGT
326 GAAGATCAAACCAAGAAATATCTGAAGT
11757 ATGAATTTGATTCAAGGGTCTTGATAGACTTGATCTTGAATAAACAAGAATAATCTTCTCTAAAT
1 ATGAATTTGATTCAAGGGTCTTGATAGACTTGATCTTGAATAAACAAGAATAATCTTCTCTAAAT
11822 GTGTTGATGAAGATCGAGAGAAATTTATTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTT
66 GTGTTGATGAAGATCGAGAGAAATTTATTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTT
*
11887 GAACAAAGAGAATTAATCTTCTCCGAATTTGTTCAATAAACAAGAATAATCTTCTCTAAATGTGT
131 GAACAAACAGAATTAATCTTCTCCGAATTTGTTCAATAAACAAGAATAATCTTCTCTAAATGTGT
* *
11952 TGATAAAGATCGAGAGAATTTTATTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTTGAAC
196 TGATAAAGATCGAGAGAAATTTACTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTTGAAC
12017 AAACAGAATTAATCTTCTCCGAATTTGTTGGTGAAGATCAAAACAATGATTTCTTGAATTTTGGT
261 AAACAGAATTAATCTTCTCCGAATTTGTTGGTGAAGATCAAAACAATGATTTCTTGAATTTTGGT
12082 GAAGATCAAACCAAGAAATATCTGAA
326 GAAGATCAAACCAAGAAATATCTGAA
12108 ATACTTCAGA
Statistics
Matches: 347, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
353 347 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (353 bp):
ATGAATTTGATTCAAGGGTCTTGATAGACTTGATCTTGAATAAACAAGAATAATCTTCTCTAAAT
GTGTTGATGAAGATCGAGAGAAATTTATTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTT
GAACAAACAGAATTAATCTTCTCCGAATTTGTTCAATAAACAAGAATAATCTTCTCTAAATGTGT
TGATAAAGATCGAGAGAAATTTACTTGCTTCAAGGGTCTTCGATTTGGTAGACTTGATCTTGAAC
AAACAGAATTAATCTTCTCCGAATTTGTTGGTGAAGATCAAAACAATGATTTCTTGAATTTTGGT
GAAGATCAAACCAAGAAATATCTGAAGT
Found at i:13341 original size:3 final size:3
Alignment explanation
Indices: 13333--13371 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
13323 CCCTTCCCCA
* * *
13333 ACC ACC ACC ACC ACC ACT ACC ACC ACT ACC ACC TCC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
13372 TCCTCCCCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.62, G:0.00, T:0.08
Consensus pattern (3 bp):
ACC
Found at i:24105 original size:21 final size:21
Alignment explanation
Indices: 24062--24105 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
24052 ATAATGGGGG
* * *
24062 TTGCTAAATACCGTCCTAGTT
1 TTGCTAAATACCGCCCCACTT
24083 TTGCTAAATACCGCCCCACTT
1 TTGCTAAATACCGCCCCACTT
24104 TT
1 TT
24106 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCACTT
Found at i:24124 original size:15 final size:16
Alignment explanation
Indices: 24103--24147 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
24093 CCGCCCCACT
*
24103 TTTTACACTTTTGCCC
1 TTTTACACTTTTACCC
24119 -TTTACA-TTTTACCC
1 TTTTACACTTTTACCC
24133 TTTTTACACTTTTAC
1 -TTTTACACTTTTAC
24148 ACTGAGCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 6 0.24
17 6 0.24
ACGTcount: A:0.18, C:0.27, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTTACACTTTTACCC
Found at i:24193 original size:33 final size:33
Alignment explanation
Indices: 24151--24229 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
24141 CTTTTACACT
*
24151 GAGCCTCCCCACTA-GGACGGCTCAGCCACGACG
1 GAGCCTCCCCACTAGGGA-GGCTCAACCACGACG
*
24184 GAGCCTCCCCACTAGGGAGGCTCAACCACGGCG
1 GAGCCTCCCCACTAGGGAGGCTCAACCACGACG
24217 GAGCCTCCCCACT
1 GAGCCTCCCCACT
24230 GGGGCGGCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 40 0.93
34 3 0.07
ACGTcount: A:0.20, C:0.43, G:0.27, T:0.10
Consensus pattern (33 bp):
GAGCCTCCCCACTAGGGAGGCTCAACCACGACG
Found at i:25742 original size:30 final size:29
Alignment explanation
Indices: 25687--25743 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
25677 TTTTACTCAT
25687 TGAACTTCAATTTTGGACATTTTGCCCCA
1 TGAACTTCAATTTTGGACATTTTGCCCCA
*
25716 TGAACTTCAATTTTGGGACGTTTTGCCC
1 TGAACTTCAATTTT-GGACATTTTGCCC
25744 TCTCAGACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (29 bp):
TGAACTTCAATTTTGGACATTTTGCCCCA
Found at i:27029 original size:42 final size:43
Alignment explanation
Indices: 26982--27062 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
26972 TGTTTGGTTA
* *
26982 ATCGTGTGTCGTGTCGA-AATCGTGTC-GGACACGATTAAGATT
1 ATCGTGTGTCGGGTC-ATAATCGTGTCACGACACGATTAAGATT
*
27024 ATCGTGTTTCGGGTCATAATCGTGTCACGACACGATTAA
1 ATCGTGTGTCGGGTCATAATCGTGTCACGACACGATTAA
27063 CACGTTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 1 0.03
42 22 0.65
43 11 0.32
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
ATCGTGTGTCGGGTCATAATCGTGTCACGACACGATTAAGATT
Found at i:27077 original size:20 final size:21
Alignment explanation
Indices: 27052--27092 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
27042 ATCGTGTCAC
27052 GACACGATTAACAC-GTTTAA
1 GACACGATTAACACGGTTTAA
*
27072 GACACGATTGACACGGTTTAA
1 GACACGATTAACACGGTTTAA
27093 TTACCGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GACACGATTAACACGGTTTAA
Found at i:27146 original size:2 final size:2
Alignment explanation
Indices: 27139--27163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27129 TTAGACACGT
27139 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
27164 TTATTTATTT
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:29995 original size:22 final size:23
Alignment explanation
Indices: 29970--30194 Score: 235
Period size: 23 Copynumber: 10.0 Consensus size: 23
29960 TGTTTTTTTT
29970 TGTTGAAAATGTTGCTGTTTTG-
1 TGTTGAAAATGTTGCTGTTTTGA
* *
29992 TGTTGAAAATTTTGTTGTTTTG-
1 TGTTGAAAATGTTGCTGTTTTGA
30014 TGTT-AATAATGTTGCTGTTTTG-
1 TGTTGAA-AATGTTGCTGTTTTGA
* * *
30036 TGTTGAAAATGCTACTGTTTTGC
1 TGTTGAAAATGTTGCTGTTTTGA
* * *
30059 TGTTGAAAATGCTGCTGGTTTGC
1 TGTTGAAAATGTTGCTGTTTTGA
* * *
30082 TGTTGAAATTGCTGCTGTTTTGC
1 TGTTGAAAATGTTGCTGTTTTGA
* *
30105 TGTTCAAAATGTTGTTGTTTTGA
1 TGTTGAAAATGTTGCTGTTTTGA
* *
30128 TGTTCAAAATGTTTCTGTTTTGA
1 TGTTGAAAATGTTGCTGTTTTGA
***
30151 TGTT-CTCATGTTGCTGTTTTGA
1 TGTTGAAAATGTTGCTGTTTTGA
*
30173 TGTTCAAAATGTTGCTGTTTTG
1 TGTTGAAAATGTTGCTGTTTTG
30195 CTTATTTGTA
Statistics
Matches: 175, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
21 2 0.01
22 72 0.41
23 101 0.58
ACGTcount: A:0.18, C:0.08, G:0.24, T:0.50
Consensus pattern (23 bp):
TGTTGAAAATGTTGCTGTTTTGA
Found at i:35074 original size:1 final size:1
Alignment explanation
Indices: 35068--35092 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35058 GTCAACTTTT
35068 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
35093 GCTTTGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:35593 original size:20 final size:20
Alignment explanation
Indices: 35555--35593 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35545 AGTTTCTAAG
**
35555 AGAAGAAAGAGGTGAGAAGT
1 AGAAGAAAGAGAAGAGAAGT
*
35575 AGAAGAAAGAGAAGGGAAG
1 AGAAGAAAGAGAAGAGAAG
35594 CAGAGGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (20 bp):
AGAAGAAAGAGAAGAGAAGT
Found at i:38535 original size:137 final size:137
Alignment explanation
Indices: 38289--38564 Score: 552
Period size: 137 Copynumber: 2.0 Consensus size: 137
38279 AAGGCATAAC
38289 CAGGAACTCGTAGTGGCCGTCGAAAGTGTGAAAAGCTGTTTTTCCAATGTCCGTTTCAGCCATCC
1 CAGGAACTCGTAGTGGCCGTCGAAAGTGTGAAAAGCTGTTTTTCCAATGTCCGTTTCAGCCATCC
38354 TAATTTGGTGGTAACCAGCCCTCAAATCAATTTTCGAAAATACCGAAGCTCCATGAAGCTCATCT
66 TAATTTGGTGGTAACCAGCCCTCAAATCAATTTTCGAAAATACCGAAGCTCCATGAAGCTCATCT
38419 ATCAACT
131 ATCAACT
38426 CAGGAACTCGTAGTGGCCGTCGAAAGTGTGAAAAGCTGTTTTTCCAATGTCCGTTTCAGCCATCC
1 CAGGAACTCGTAGTGGCCGTCGAAAGTGTGAAAAGCTGTTTTTCCAATGTCCGTTTCAGCCATCC
38491 TAATTTGGTGGTAACCAGCCCTCAAATCAATTTTCGAAAATACCGAAGCTCCATGAAGCTCATCT
66 TAATTTGGTGGTAACCAGCCCTCAAATCAATTTTCGAAAATACCGAAGCTCCATGAAGCTCATCT
38556 ATCAACT
131 ATCAACT
38563 CA
1 CA
38565 TCCACGGTGG
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 139 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (137 bp):
CAGGAACTCGTAGTGGCCGTCGAAAGTGTGAAAAGCTGTTTTTCCAATGTCCGTTTCAGCCATCC
TAATTTGGTGGTAACCAGCCCTCAAATCAATTTTCGAAAATACCGAAGCTCCATGAAGCTCATCT
ATCAACT
Found at i:40693 original size:20 final size:20
Alignment explanation
Indices: 40655--40693 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40645 AGTTTCTAAG
**
40655 AGAAGAAAGAGGTGAGAAGT
1 AGAAGAAAGAGAAGAGAAGT
*
40675 AGAAGAAAGAGAAGGGAAG
1 AGAAGAAAGAGAAGAGAAG
40694 CAGAGGAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (20 bp):
AGAAGAAAGAGAAGAGAAGT
Found at i:57303 original size:5 final size:5
Alignment explanation
Indices: 57293--57317 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
57283 TAACAATGCT
57293 CAATC CAATC CAATC CAATC CAATC
1 CAATC CAATC CAATC CAATC CAATC
57318 AGTATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CAATC
Found at i:57899 original size:6 final size:6
Alignment explanation
Indices: 57888--57918 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
57878 TACTATTCCC
57888 CAGAGG CAGAGG CAGAGG CAGAGG CAGAGG C
1 CAGAGG CAGAGG CAGAGG CAGAGG CAGAGG C
57919 GATCAAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.48, T:0.00
Consensus pattern (6 bp):
CAGAGG
Found at i:62128 original size:104 final size:105
Alignment explanation
Indices: 61995--62198 Score: 383
Period size: 104 Copynumber: 2.0 Consensus size: 105
61985 TGTCCTATTC
*
61995 TGCTCTGGTACTGTTGCATTTGATGCCATGCCACTCATAGCAAGATGAGTTTGTTATATC-TAAA
1 TGCTCTGGTACTGTTGCATCTGATGCCATGCCACTCATAGCAAGATGAGTTTGTTATATCTTAAA
*
62059 TGTTTTTGGATCTTAAATAGTTTGATTTGGCCCGATAGTT
66 TGTTTTTGGATCTTAAATAATTTGATTTGGCCCGATAGTT
62099 TGCTCTGGTACTGTTGCATCTGATGCCATGCCACTCATAGCAAGATGAGTTTGTTATATCTTAAA
1 TGCTCTGGTACTGTTGCATCTGATGCCATGCCACTCATAGCAAGATGAGTTTGTTATATCTTAAA
62164 TGTTTTTGGATCTTAAATAATTTGATTTGGCCCGA
66 TGTTTTTGGATCTTAAATAATTTGATTTGGCCCGA
62199 CACCTGACAA
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 59 0.61
105 38 0.39
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (105 bp):
TGCTCTGGTACTGTTGCATCTGATGCCATGCCACTCATAGCAAGATGAGTTTGTTATATCTTAAA
TGTTTTTGGATCTTAAATAATTTGATTTGGCCCGATAGTT
Found at i:64379 original size:1 final size:1
Alignment explanation
Indices: 64373--64399 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
64363 CCATGTCTAC
64373 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
64400 AAAAACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.