Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019171.1 Corchorus olitorius cultivar O-4 contig19204, 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: 105369
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--26 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
27 TTCGTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8670 original size:25 final size:25
Alignment explanation
Indices: 8636--8684 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
8626 TTTTAGCTTG
8636 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
8661 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
8685 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:9582 original size:25 final size:25
Alignment explanation
Indices: 9548--9596 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
9538 TGTTAGCTTG
*
9548 TAGAGACCGAGCGAGGGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
9573 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
9597 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:10411 original size:925 final size:905
Alignment explanation
Indices: 8335--10767 Score: 4079
Period size: 925 Copynumber: 2.7 Consensus size: 905
8325 ACACCAAGTA
8335 ATTGTTAGGATTTTGACTCAAATTCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTATTGCTTG
1 ATTGTTAGGATTTTGACTCAAATTCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTATTGCTTG
*
8400 GTGGATAAGAAGACTTGGTGAACAAGAATCCTAGTAGGAAAGGGATTCTTGGAGGCTAAGTTTGT
66 GTGGACAAGAAGACTTGGTGAACAAGAATCCTAGTAGGAAAGGGATTCTTGGAGGCTAAGTTTGT
8465 GCTAGTATAAATAGGGAGTTTCTTTATAGTTTTTTGTATGCTTGGAGAAAAGATGTAGTCTAAGG
131 GCTAGTATAAATAGGGAGTTTCTTTATAGTTTTTTGTATGCTTGGAGAAAAGATGTAGTCTAAGG
*
8530 GCTAGATTTGGGTGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGTGAGTG
196 GTTAGATTTGGGTGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGTGAGTG
*
8595 TCTGTTGTGGTGTTTGGTTTCTTGATGTGATTTTTAGCTTGTAGAGACCGAGCGAGAGTGCTCAA
261 TCTGCTGTGGTGTTT-GTTTCTTGATGTGATTTTTAGCTTGTAGAGACCGAGCGAGAGTGCTCAA
*
8660 ATAGAGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTATGATTGATTGTTATATTGGG
325 ATAGAGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTATGATTGATTGTTAGATTGGG
8725 TTGAGAGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATT
390 TTGAGAGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATT
*
8790 TCTCTTCTCCTCCGTGGACGTAGGCAAGTTCAGTGCCGAACCACGCAAATTCTTTTTTCTTTGTG
455 TCTCTTCTCCTCCGTGGACGTAGGCAAGTTCAGTGCCGAACCACGTAAATTCTTTTTTCTTTGTG
8855 TGGATGATTTATTGTTTTAGTTGCTTCCGCTTGCATTGTTAATTTGATATATTATGGTTTGGGAT
520 TGGATGATTTATTGTTTTAGTTGCTTCCGCTTGCATTGTTAATTTGATATATTATGGTTTGGGAT
**
8920 ATCCGGGTTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCAGTATTCCA
585 ATCCGGGTTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCAGTAGCCCA
8985 AACTTGTGATATGGCTCGTCAGGTTGGTTGTCGTGGAGATTGCCAATTTTCACTGCTTGATGATT
650 AACTTGTGATATGGCTCGTCAGGTTGGTTGTCGTGGAGATTGCCAATTTTCACTGCTTGATGATT
9050 GTTTTGAAGATTGCTCAGATTTGGATGGAAAACAAGATCGGATTCGGAATTAAAGTTGAAGATGA
715 GTTTTGAAGATTGCTCAGATTTGGATGGAAAACAAGATCGGATTCGGAATTAAAGTTGAAGATGA
* * * *
9115 TGTAGTGAAGATGAAGACACACAAAAGAAGATTGCTTAAAGATTGAGAGACTTTCATTGTAGGTG
780 TGCAATGAAGATGAAGACACACAAAAGAAGATTGCTTAAAGATTGAAAGACTTTCATCGTAGGTG
9180 GAGCCAAGCATGTCCTTGAAGATTGAAGATTGAAGATTTGATGGAATTTCAGTCAAGATGGAG
845 GAGCCAAGCATGTCCTTGAAGATT--AGATTGAAGATTTGATGGAATTTCAGTCAAGATGGAG
* * * * *
9243 ATTGTTAGGATTTTGACTCAAATTATATTTCGATTTGGATTTGGATTTTTTAAGCCTATTGCTTG
1 ATTGTTAGGATTTTGACTCAAATTCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTATTGCTTG
* ** *
9308 GTGGACAAAAAGACTTGGTGAACAAGAATCCTAACAGGAAAGGGATTCTTGGAGGCTAAGTTTAT
66 GTGGACAAGAAGACTTGGTGAACAAGAATCCTAGTAGGAAAGGGATTCTTGGAGGCTAAGTTTGT
*
9373 GCTAGTATAAATAGAGAGTTTCTTTATAGTTTTTTGTATGCTTGGAGAAAAGATGTAGTCTAAGG
131 GCTAGTATAAATAGGGAGTTTCTTTATAGTTTTTTGTATGCTTGGAGAAAAGATGTAGTCTAAGG
* * *
9438 GTTAGATTTGGGTGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTTTGTGATTT
196 GTTAGATTTGGGTGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGTGAGTG
* * * *
9503 TTTGCTGTGGTGTTTGCTTTGATAGATGTGATGATTGTTAGCTTGTAGAGACCGAGCGAGGGTGC
261 TCTGCTGTGGTGTTTG-TTT-CTTGATGTGAT--TT-TTAGCTTGTAGAGACCGAGCGAGAGTGC
*
9568 TCAAATAGAGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTAGGATTGATTGTTAGAT
321 TCAAATAGAGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTATGATTGATTGTTAGAT
9633 TGGGTTGAGAGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTG
386 TGGGTTGAGAGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTG
* *
9698 GATTTCTCTTCTCCTCCGTGGATGTAGGCAAGTTCAGTGCCGAACCACGTAAATTCTTTTGTC-T
451 GATTTCTCTTCTCCTCCGTGGACGTAGGCAAGTTCAGTGCCGAACCACGTAAATTCTTTTTTCTT
* * *
9762 TGTGTGGATGA-TTATTATTTTTAGTTGCTTCCGCTTGCA-TGATTAATTTGATAGATTATAGTT
516 TGTGTGGATGATTTATT-GTTTTAGTTGCTTCCGCTTGCATTG-TTAATTTGATATATTATGGTT
*
9825 TGGGATATCCGGGTTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCGGT
579 TGGGATATCCGGGTTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCAGT
* * * *
9890 AGCCCAAACTTGTGATATTGTTCGTCAGATTTGGTTGTCGTGGAGATTGCCAAATTTT-GCTGCT
644 AGCCCAAACTTGTGATATGGCTCGTCAG-GTTGGTTGTCGTGGAGATTGCC-AATTTTCACTGCT
* *
9954 TGATGATTGTTTTTAAGATTGCATGTTGGCTTTTGAAATCAGATTTGGAT-TAAAAGCAAGATCG
707 TGATGATTG-TTTT--GA-AG-A--TT-GC--------TCAGATTTGGATGGAAAA-CAAGATCG
* *
10018 GATTCGGAATTAAAGTTGAAGATGATGCAATGAAGAT-AGAGACACACAAGAGAAGATTGCTTGA
755 GATTCGGAATTAAAGTTGAAGATGATGCAATGAAGATGA-AGACACACAAAAGAAGATTGCTTAA
*
10082 AGATTGAAAGACTTTCATCGTAGGTGGAGCGAAGCATGTCCTTGAAGATT-GATTGAAGATTTGA
819 AGATTGAAAGACTTTCATCGTAGGTGGAGCCAAGCATGTCCTTGAAGATTAGATTGAAGATTTGA
* *
10146 TGGAATTTGAGTCAAGGTGGAG
884 TGGAATTTCAGTCAAGATGGAG
*
10168 ATTGTTAGGATTTTGACTCAAATCCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTATTGCTTG
1 ATTGTTAGGATTTTGACTCAAATTCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTATTGCTTG
10233 GTGGACAAGAAGACTTGGTGAACAAGAATCCTAGTAGGAAAGGGATTCTTGGAGGCTAAGTTTGT
66 GTGGACAAGAAGACTTGGTGAACAAGAATCCTAGTAGGAAAGGGATTCTTGGAGGCTAAGTTTGT
*
10298 GCTAGTATAAATAGGGAGTTTCTCTATAGTTTTTTGTATGCTTGGAGAAAAGATGTAGTCTAAGG
131 GCTAGTATAAATAGGGAGTTTCTTTATAGTTTTTTGTATGCTTGGAGAAAAGATGTAGTCTAAGG
10363 GTTAGATTTGGGTGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGTGAGTG
196 GTTAGATTTGGGTGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGTGAGTG
*
10428 TCTGCTGTGGTGTTTAGTTTCTTGATGTGATTTTTAGCTTGTAGAGACCGAGTGAGAGTGCTCAA
261 TCTGCTGTGGTGTTT-GTTTCTTGATGTGATTTTTAGCTTGTAGAGACCGAGCGAGAGTGCTCAA
10493 ATAGAGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTATGATTGATTGTTAGATTGGG
325 ATAGAGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTATGATTGATTGTTAGATTGGG
*
10558 TTGAGAGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTACTTTTCTATAACTAGTGGATT
390 TTGAGAGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATT
10623 TCTCTTCTCCTCCGTGGACGTAGGCAAGTTCAGTGCCGAACCACGTAAATTCTTTTTTCTTTGTG
455 TCTCTTCTCCTCCGTGGACGTAGGCAAGTTCAGTGCCGAACCACGTAAATTCTTTTTTCTTTGTG
10688 TGGATGATTTATTGTTTTAGTTGCTTCCGCTTGCATTGTTAATTTGATATATTATGGTTTGGGAT
520 TGGATGATTTATTGTTTTAGTTGCTTCCGCTTGCATTGTTAATTTGATATATTATGGTTTGGGAT
*
10753 ATCCAGGTTACAACA
585 ATCCGGGTTACAACA
10768 GTAATTGCAA
Statistics
Matches: 1420, Mismatches: 74, Indels: 48
0.92 0.05 0.03
Matches are distributed among these distances:
907 1 0.00
908 261 0.18
909 9 0.01
910 7 0.00
911 142 0.10
912 250 0.18
913 10 0.01
915 2 0.00
916 1 0.00
917 1 0.00
919 2 0.00
920 2 0.00
921 215 0.15
922 74 0.05
923 7 0.00
924 9 0.01
925 296 0.21
926 1 0.00
927 5 0.00
928 125 0.09
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36
Consensus pattern (905 bp):
ATTGTTAGGATTTTGACTCAAATTCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTATTGCTTG
GTGGACAAGAAGACTTGGTGAACAAGAATCCTAGTAGGAAAGGGATTCTTGGAGGCTAAGTTTGT
GCTAGTATAAATAGGGAGTTTCTTTATAGTTTTTTGTATGCTTGGAGAAAAGATGTAGTCTAAGG
GTTAGATTTGGGTGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGTGAGTG
TCTGCTGTGGTGTTTGTTTCTTGATGTGATTTTTAGCTTGTAGAGACCGAGCGAGAGTGCTCAAA
TAGAGACCGAGCGAGAGTGCTCAAGATTGTTTGGGTTTGGTTTATGATTGATTGTTAGATTGGGT
TGAGAGATTGAGTGAGAGTTATTGATAATTATGTGTTGATGTAATTTTCTATAACTAGTGGATTT
CTCTTCTCCTCCGTGGACGTAGGCAAGTTCAGTGCCGAACCACGTAAATTCTTTTTTCTTTGTGT
GGATGATTTATTGTTTTAGTTGCTTCCGCTTGCATTGTTAATTTGATATATTATGGTTTGGGATA
TCCGGGTTACAACAATTGGTATCAGAGCTCAGGTTGAATGGATTGGAGGTTGCCCAGTAGCCCAA
ACTTGTGATATGGCTCGTCAGGTTGGTTGTCGTGGAGATTGCCAATTTTCACTGCTTGATGATTG
TTTTGAAGATTGCTCAGATTTGGATGGAAAACAAGATCGGATTCGGAATTAAAGTTGAAGATGAT
GCAATGAAGATGAAGACACACAAAAGAAGATTGCTTAAAGATTGAAAGACTTTCATCGTAGGTGG
AGCCAAGCATGTCCTTGAAGATTAGATTGAAGATTTGATGGAATTTCAGTCAAGATGGAG
Found at i:10497 original size:25 final size:25
Alignment explanation
Indices: 10469--10517 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
10459 TTTTAGCTTG
*
10469 TAGAGACCGAGTGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
10494 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
10518 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:13126 original size:40 final size:40
Alignment explanation
Indices: 13071--13151 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
13061 CATTGTTGGG
* *
13071 AATCTCTACAAATGCATTATTGTTGACAAGAAGAATGAGA
1 AATCTCTACAAATGCATAATTGTTGACAAGAAAAATGAGA
*
13111 AATCTCTGCAAATGCATAATTGTTGACAAGAAAAATGAGA
1 AATCTCTACAAATGCATAATTGTTGACAAGAAAAATGAGA
13151 A
1 A
13152 TTATCTGTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (40 bp):
AATCTCTACAAATGCATAATTGTTGACAAGAAAAATGAGA
Found at i:13468 original size:28 final size:27
Alignment explanation
Indices: 13414--13473 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
13404 AAGTATAAAA
* * *
13414 TAAATAATGAGATCATTCAAGCGCAATT
1 TAAATAATAAGATCATTCAAACACAA-T
13442 TAAATAATAAGATCATTCAAACACAAT
1 TAAATAATAAGATCATTCAAACACAAT
13469 TAAAT
1 TAAAT
13474 TAAATATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.28
Consensus pattern (27 bp):
TAAATAATAAGATCATTCAAACACAAT
Found at i:13477 original size:32 final size:31
Alignment explanation
Indices: 13408--13479 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 31
13398 TCTTGAAAGT
* * * *
13408 ATAAAATAAATAATGAGATCATTCAAGCGCA
1 ATAAATTAAATAATAAGATCATTCAAACACA
13439 AT---TTAAATAATAAGATCATTCAAACACA
1 ATAAATTAAATAATAAGATCATTCAAACACA
13467 ATTAAATTAAATA
1 A-TAAATTAAATA
13480 TTACTCCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
28 23 0.70
29 1 0.03
31 2 0.06
32 7 0.21
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (31 bp):
ATAAATTAAATAATAAGATCATTCAAACACA
Found at i:16364 original size:35 final size:35
Alignment explanation
Indices: 16325--16399 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
16315 CAATGTATTC
*
16325 TTCAATTGGTCG-TCTGTCAAGGTAGAATAAATAAA
1 TTCAATTGATCGCT-TGTCAAGGTAGAATAAATAAA
* *
16360 TTCAATTGATCGCTTGTCAATGTAGAATAAATACA
1 TTCAATTGATCGCTTGTCAAGGTAGAATAAATAAA
16395 TTCAA
1 TTCAA
16400 GGAATGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (35 bp):
TTCAATTGATCGCTTGTCAAGGTAGAATAAATAAA
Found at i:16876 original size:21 final size:21
Alignment explanation
Indices: 16852--16891 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16842 GCATATTAAA
* *
16852 TATTTTTTGAAATATAATTTT
1 TATTATTTCAAATATAATTTT
*
16873 TATTATTTCAACTATAATT
1 TATTATTTCAAATATAATT
16892 AGCATATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (21 bp):
TATTATTTCAAATATAATTTT
Found at i:17710 original size:28 final size:28
Alignment explanation
Indices: 17679--17736 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
17669 TAAAATAATT
**
17679 TGTATAGTTAAATGTGATGCTAAATTGC
1 TGTATAGTTAAATCCGATGCTAAATTGC
17707 TGTATAGTTAAATCCGATGCTAAATTGC
1 TGTATAGTTAAATCCGATGCTAAATTGC
17735 TG
1 TG
17737 CTAATTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (28 bp):
TGTATAGTTAAATCCGATGCTAAATTGC
Found at i:17748 original size:36 final size:37
Alignment explanation
Indices: 17707--17778 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
17697 GCTAAATTGC
* *
17707 TGTATAGTTAAATCCGATGCTAAATTGCTGC-TAATT
1 TGTATAGTTAAATACAATGCTAAATTGCTGCATAATT
*
17743 TGTATAGTTAAATACAATGCTAAGTTGCTGCATAAT
1 TGTATAGTTAAATACAATGCTAAATTGCTGCATAAT
17779 GATAAGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (37 bp):
TGTATAGTTAAATACAATGCTAAATTGCTGCATAATT
Found at i:18197 original size:20 final size:20
Alignment explanation
Indices: 18165--18221 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
18155 TACTAAAAGT
*
18165 TTAATAAAGTTATTCAAATA
1 TTAATAAAGTTATTAAAATA
18185 TTAATAACA-TTATTAAAAT-
1 TTAATAA-AGTTATTAAAATA
*
18204 TT-ATCAAGATTATTAAAA
1 TTAATAAAG-TTATTAAAA
18222 ATCTCCAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 1 0.03
18 3 0.09
19 11 0.34
20 16 0.50
21 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (20 bp):
TTAATAAAGTTATTAAAATA
Found at i:19980 original size:11 final size:12
Alignment explanation
Indices: 19964--19996 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
19954 TGCTACAAAC
19964 ACAAAATTACA-
1 ACAAAATTACAG
19975 ACAAAATTA-AG
1 ACAAAATTACAG
19986 ACAAAATTACA
1 ACAAAATTACA
19997 TGTGAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.64, C:0.15, G:0.03, T:0.18
Consensus pattern (12 bp):
ACAAAATTACAG
Found at i:21401 original size:18 final size:20
Alignment explanation
Indices: 21380--21424 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 20
21370 AAAAAAATAA
21380 AAAAAAAAAG-ATTTAAA-G
1 AAAAAAAAAGTATTTAAATG
*
21398 -AAAAAAAAGTTTTTAAATG
1 AAAAAAAAAGTATTTAAATG
21417 AAAAAAAA
1 AAAAAAAA
21425 CGGAAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
19 1 0.04
20 7 0.30
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (20 bp):
AAAAAAAAAGTATTTAAATG
Found at i:24527 original size:14 final size:14
Alignment explanation
Indices: 24502--24542 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
24492 TTTTTAAAAA
*
24502 AAACAAAAACAAAT
1 AAACAAAAACAAAC
24516 AAA-AACAAACAAAC
1 AAACAA-AAACAAAC
24530 AAACAAAAACAAA
1 AAACAAAAACAAA
24543 ACAGAAGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.08
14 20 0.83
15 2 0.08
ACGTcount: A:0.80, C:0.17, G:0.00, T:0.02
Consensus pattern (14 bp):
AAACAAAAACAAAC
Found at i:24529 original size:18 final size:17
Alignment explanation
Indices: 24500--24543 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
24490 GCTTTTTAAA
*
24500 AAAAAC-AAAAACAAAT
1 AAAAACAAAAAACAAAC
24516 AAAAACAAACAAACAAAC
1 AAAAACAAA-AAACAAAC
24534 AAAAACAAAA
1 AAAAACAAAA
24544 CAGAAGTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 6 0.24
17 3 0.12
18 16 0.64
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.02
Consensus pattern (17 bp):
AAAAACAAAAAACAAAC
Found at i:24699 original size:15 final size:15
Alignment explanation
Indices: 24679--24708 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24669 TCAAGATCTT
*
24679 TCCAGAACATTGCAA
1 TCCAGAAAATTGCAA
24694 TCCAGAAAATTGCAA
1 TCCAGAAAATTGCAA
24709 AACAAAAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.20
Consensus pattern (15 bp):
TCCAGAAAATTGCAA
Found at i:25006 original size:11 final size:11
Alignment explanation
Indices: 24990--25016 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
24980 AATTTTGAGA
24990 GAATAGAATTG
1 GAATAGAATTG
25001 GAATAGAATTG
1 GAATAGAATTG
25012 GAATA
1 GAATA
25017 AAGTAAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (11 bp):
GAATAGAATTG
Found at i:25302 original size:25 final size:21
Alignment explanation
Indices: 25254--25337 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 21
25244 TTGGAAATAT
* * *
25254 TTTGTAGAG-ATTCTTTCCAC
1 TTTGCAGAGCATTATTTTCAC
25274 TTTGCAGAGCATTATTTTCAAC
1 TTTGCAGAGCATTATTTTC-AC
**
25296 ATTTTTGCAGAG-ATTCCTTTCAC
1 ---TTTGCAGAGCATTATTTTCAC
25319 TTTGCAGAGCATTATTTTC
1 TTTGCAGAGCATTATTTTC
25338 TTCAATTTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
20 17 0.33
21 14 0.27
22 2 0.04
23 2 0.04
24 7 0.14
25 9 0.18
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (21 bp):
TTTGCAGAGCATTATTTTCAC
Found at i:35220 original size:98 final size:98
Alignment explanation
Indices: 35101--35309 Score: 328
Period size: 98 Copynumber: 2.1 Consensus size: 98
35091 AATTAGCGCT
* * *
35101 TTCCGTCTGGGAAGGGCGTTTTGGGAAATTCTGGTGAAAATTAGTACCTTTCATCCAGAAAGGGC
1 TTCCGTCTGGGAACGGCGTTTTGGGAAATTCTGGTAAAAATTAGCACCTTTCATCCAGAAAGGGC
35166 AGTTTTGGAAATAAACAAGTAAGAATCAACACC
66 AGTTTTGGAAATAAACAAGTAAGAATCAACACC
* * *
35199 TTCCGTGTGGGAACTGCGTTTTGGGAAATTCTGGTAAAAATTAGCATCTTTCATCCAGAAAGGGC
1 TTCCGTCTGGGAACGGCGTTTTGGGAAATTCTGGTAAAAATTAGCACCTTTCATCCAGAAAGGGC
* **
35264 ATTTTTGGAAATAGGCAAGTAAGAATCAACACC
66 AGTTTTGGAAATAAACAAGTAAGAATCAACACC
*
35297 TTCCGTCTCGGAA
1 TTCCGTCTGGGAA
35310 GAGTTTTTGG
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (98 bp):
TTCCGTCTGGGAACGGCGTTTTGGGAAATTCTGGTAAAAATTAGCACCTTTCATCCAGAAAGGGC
AGTTTTGGAAATAAACAAGTAAGAATCAACACC
Found at i:35931 original size:18 final size:18
Alignment explanation
Indices: 35910--35953 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35900 CTAAATTACT
* * *
35910 AAATTAATCTAATTTTGG
1 AAATTAATCCAATCTTAG
*
35928 AAATTAAACCAATCTTAG
1 AAATTAATCCAATCTTAG
35946 AAATTAAT
1 AAATTAAT
35954 TAAAGCTAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (18 bp):
AAATTAATCCAATCTTAG
Found at i:41920 original size:43 final size:41
Alignment explanation
Indices: 41873--42182 Score: 232
Period size: 44 Copynumber: 7.5 Consensus size: 41
41863 AATCTTTAAC
41873 GGGATCTTTCCCCT-AATTAAAAACTTTGAAAAAAAGATTAGAT
1 GGGATCTTT-CCCTAAATTAAAAACTTTGAAAAAAA-ATT-GAT
*
41916 GGGATCTTTCCCTAAATT-AAAACTTCTG--AAAAACTTGAT
1 GGGATCTTTCCCTAAATTAAAAACTT-TGAAAAAAAATTGAT
* * * * *
41955 GGGATCTTTCCTTGAATT-AAAACTTTG---AAGACTGGAT
1 GGGATCTTTCCCTAAATTAAAAACTTTGAAAAAAAATTGAT
*
41992 GGG-TCTTTCCCTAAATTAAAAAACTTT-AAAAAGAAACTGGAT
1 GGGATCTTTCCCTAAATT-AAAAACTTTGAAAAA-AAA-TTGAT
** *
42034 GGGGGCTTTCCCTAAATT-AAAACTTATG--AAAAACTTGAT
1 GGGATCTTTCCCTAAATTAAAAACTT-TGAAAAAAAATTGAT
* * ** *
42073 GGGATCTATCCCTGAATTAAAAAAACTTTGAAAAATACTTTGGT
1 GGGATCTTTCCCTAAATT--AAAAACTTTGAAAAA-AAATTGAT
* ** *
42117 GGGATCTTTCCCTAAATTGAAGTCTTTGAAAAAAATACTTTGGT
1 GGGATCTTTCCCTAAATTAAAAACTTTGAAAAAAA-A--TTGAT
42161 GGGATCTTTCCCTAAATTAAAA
1 GGGATCTTTCCCTAAATTAAAA
42183 CTTCCTTTTG
Statistics
Matches: 218, Mismatches: 28, Indels: 41
0.76 0.10 0.14
Matches are distributed among these distances:
36 12 0.06
37 11 0.05
38 10 0.05
39 44 0.20
40 6 0.03
41 19 0.09
42 39 0.18
43 31 0.14
44 46 0.21
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (41 bp):
GGGATCTTTCCCTAAATTAAAAACTTTGAAAAAAAATTGAT
Found at i:41973 original size:39 final size:38
Alignment explanation
Indices: 41873--42185 Score: 222
Period size: 39 Copynumber: 7.7 Consensus size: 38
41863 AATCTTTAAC
* *
41873 GGGATCTTTCCCCT-AATTAAAAACTTTGAAAAAAAGATTAGAT
1 GGGATCTTT-CCCTAAATT-AAAACTTTG---AAAA-ACTGGAT
*
41916 GGGATCTTTCCCTAAATTAAAACTTCTGAAAAACTTGAT
1 GGGATCTTTCCCTAAATTAAAACTT-TGAAAAACTGGAT
* * *
41955 GGGATCTTTCCTTGAATTAAAACTTTG-AAGACTGGAT
1 GGGATCTTTCCCTAAATTAAAACTTTGAAAAACTGGAT
*
41992 GGG-TCTTTCCCTAAATTAAAAAACTTTAAAAAGAAACTGGAT
1 GGGATCTTTCCCTAAATT--AAAACTTT--GAA-AAACTGGAT
** *
42034 GGGGGCTTTCCCTAAATTAAAACTTATGAAAAACTTGAT
1 GGGATCTTTCCCTAAATTAAAACTT-TGAAAAACTGGAT
* *
42073 GGGATCTATCCCTGAATTAAAAAAACTTTGAAAAATACTTTGG-T
1 GGGATCTTTCCCTAAATT---AAAACTTTG-AAAA-AC--TGGAT
**
42117 GGGATCTTTCCCTAAATTGAAGTCTTTGAAAAAAATACTTTGG-T
1 GGGATCTTTCCCTAAATT-AAAACTTTG---AAAA-AC--TGGAT
42161 GGGATCTTTCCCTAAATTAAAACTT
1 GGGATCTTTCCCTAAATTAAAACTT
42186 CCTTTTGATT
Statistics
Matches: 226, Mismatches: 25, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
36 12 0.05
37 11 0.05
38 10 0.04
39 50 0.22
40 6 0.03
41 10 0.04
42 41 0.18
43 35 0.15
44 49 0.22
45 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (38 bp):
GGGATCTTTCCCTAAATTAAAACTTTGAAAAACTGGAT
Found at i:42023 original size:118 final size:120
Alignment explanation
Indices: 41873--42186 Score: 361
Period size: 118 Copynumber: 2.6 Consensus size: 120
41863 AATCTTTAAC
41873 GGGATCTTTCCCCT-AATTAAAAACTTTGAAAAAAAGATTAGATGGGATCTTTCCCTAAATTAAA
1 GGGATCTTT-CCCTAAATTAAAAACTTTGAAAAAAA-ATTAGATGGGATCTTTCCCTAAATTAAA
* *
41937 ACTTCTGAAAAACTTGATGGGATCTTTCCTTGAATT-AAAACTTTG-AAGAC-TGGAT
64 ACTTCTGAAAAACTTGATGGGATCTATCCCTGAATTAAAAACTTTGAAAGACTTGG-T
* * **
41992 GGG-TCTTTCCCTAAATTAAAAAACTTT-AAAAAGAAACTGGATGGGGGCTTTCCCTAAATTAAA
1 GGGATCTTTCCCTAAATT-AAAAACTTTGAAAAA-AAATTAGATGGGATCTTTCCCTAAATTAAA
* *
42055 ACTTATGAAAAACTTGATGGGATCTATCCCTGAATTAAAAAAACTTTGAAAAATACTTTGGT
64 ACTTCTGAAAAACTTGATGGGATCTATCCCTGAATT--AAAAACTTTG--AAAGAC-TTGGT
* ** * *
42117 GGGATCTTTCCCTAAATTGAAGTCTTTGAAAAAAATACTTTGGTGGGATCTTTCCCTAAATTAAA
1 GGGATCTTTCCCTAAATTAAAAACTTTGAAAAAAA-A-TTAGATGGGATCTTTCCCTAAATTAAA
42182 ACTTC
64 ACTTC
42187 CTTTTGATTT
Statistics
Matches: 163, Mismatches: 17, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
117 4 0.02
118 71 0.44
119 14 0.09
121 9 0.06
124 4 0.02
125 12 0.07
126 23 0.14
127 26 0.16
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (120 bp):
GGGATCTTTCCCTAAATTAAAAACTTTGAAAAAAAATTAGATGGGATCTTTCCCTAAATTAAAAC
TTCTGAAAAACTTGATGGGATCTATCCCTGAATTAAAAACTTTGAAAGACTTGGT
Found at i:42996 original size:2 final size:2
Alignment explanation
Indices: 42989--43022 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
42979 TATGTACATG
42989 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
43023 CTAAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44588 original size:30 final size:30
Alignment explanation
Indices: 44552--44619 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
44542 TTGTTAATGC
* *
44552 TTATGTGGCT-TTCTGATTACCTGTATTTGA
1 TTATGTGGCTCTT-TGATGACATGTATTTGA
*
44582 TTATGTGGCTCTTTGATGACATGTATTTGT
1 TTATGTGGCTCTTTGATGACATGTATTTGA
44612 TTATGTGG
1 TTATGTGG
44620 AGTTATGGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.16, C:0.10, G:0.24, T:0.50
Consensus pattern (30 bp):
TTATGTGGCTCTTTGATGACATGTATTTGA
Found at i:46092 original size:62 final size:62
Alignment explanation
Indices: 46018--46281 Score: 404
Period size: 62 Copynumber: 4.3 Consensus size: 62
46008 CTTTTCATGT
* * * *
46018 ACTGTCTTCAGAACCTATCTTCGTGAACTGTCTTCAGATTCACTCTTAATTACTTTTTAGGA
1 ACTGTCTTCAGAACCCATCTTTGTGAACTGTCTTTAGATTCACTCTTAATTACCTTTTAGGA
46080 ACTGTCTTCAGAACCCATCTTTGTGAACTGTCTTTTAGATTCACTCTTAATTACCTTTTAGGA
1 ACTGTCTTCAGAACCCATCTTTGTGAACTGTC-TTTAGATTCACTCTTAATTACCTTTTAGGA
*
46143 ACTGTCTTCAGAACTCATC-TTGTGAACTGTCTTTAGATTCACTCTTAATTACCTTTTAGGA
1 ACTGTCTTCAGAACCCATCTTTGTGAACTGTCTTTAGATTCACTCTTAATTACCTTTTAGGA
* * * * * *
46204 ACTGTCTTCTGAACCCATCTTTGTGAACTGTCTTTAGATTCACTCTTAAATATCATTCAGGG
1 ACTGTCTTCAGAACCCATCTTTGTGAACTGTCTTTAGATTCACTCTTAATTACCTTTTAGGA
*
46266 ACTGTCTTCGGAACCC
1 ACTGTCTTCAGAACCC
46282 GTCTATGAGC
Statistics
Matches: 187, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
61 47 0.25
62 94 0.50
63 46 0.25
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (62 bp):
ACTGTCTTCAGAACCCATCTTTGTGAACTGTCTTTAGATTCACTCTTAATTACCTTTTAGGA
Found at i:46348 original size:23 final size:23
Alignment explanation
Indices: 46322--46403 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 23
46312 ATTTTAGGAA
46322 CTGTCTTCAGATCCATCTATGAG
1 CTGTCTTCAGATCCATCTATGAG
* * *
46345 CTGTCTTCAGTCTTATCC-TTTAGGAA
1 CTGTCTTCAG----ATCCATCTATGAG
*
46371 CTGTCTTCAGATCCATCTGTGAG
1 CTGTCTTCAGATCCATCTATGAG
46394 CTGTCTTCAG
1 CTGTCTTCAG
46404 CCTTAATCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.09
23 24 0.51
26 15 0.32
27 4 0.09
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (23 bp):
CTGTCTTCAGATCCATCTATGAG
Found at i:46378 original size:49 final size:50
Alignment explanation
Indices: 46314--46525 Score: 203
Period size: 58 Copynumber: 3.9 Consensus size: 50
46304 CTTAAAATAT
*
46314 TTTAGGAACTGTCTTCAGATCCATCTATGAGCTGTCTTCAGTCTT-ATCC
1 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAATCC
*
46363 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCT
1 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAG------TCTT--AATCC
* *
46421 TTTAGGAATTGTCTTCAGATCCATCTGTGAGCTGTGTTCA-TCCTTAATCTTAAAATC
1 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGT-CTTAATC-------C
* *
46478 TTTTAGGAACTGTCTTCAAATCCATCTGTGAGCTGTCTTCAGCCTTAA
1 -TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAA
46526 ATCTTAAAAT
Statistics
Matches: 135, Mismatches: 9, Indels: 29
0.78 0.05 0.17
Matches are distributed among these distances:
49 40 0.30
50 4 0.03
51 1 0.01
52 3 0.02
55 4 0.03
58 83 0.61
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (50 bp):
TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGTCTTAATCC
Found at i:46453 original size:58 final size:58
Alignment explanation
Indices: 46363--46567 Score: 356
Period size: 58 Copynumber: 3.5 Consensus size: 58
46353 AGTCTTATCC
46363 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCT
1 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCT
* * *
46421 TTTAGGAATTGTCTTCAGATCCATCTGTGAGCTGTGTTCATCCTTAATCTTAAAATCT
1 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCT
*
46479 TTTAGGAACTGTCTTCAAATCCATCTGTGAGCTGTCTTCAGCCTTAAATCTTAAAATCT
1 TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTT-AATCTTAAAATCT
*
46538 TTTAGGAACTGTCTTCAGATCCATTTGTGA
1 TTTAGGAACTGTCTTCAGATCCATCTGTGA
46568 TGAATTCTTT
Statistics
Matches: 137, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 96 0.70
59 41 0.30
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (58 bp):
TTTAGGAACTGTCTTCAGATCCATCTGTGAGCTGTCTTCAGCCTTAATCTTAAAATCT
Found at i:47312 original size:3 final size:3
Alignment explanation
Indices: 47304--47340 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
47294 ATATATATAT
47304 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
47341 AAAGATGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:48022 original size:6 final size:6
Alignment explanation
Indices: 48011--48042 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
48001 CGTCGCAATC
48011 TTTGTT TTTGTT TTTGTT TTT-TT TTT-TT TTTG
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTG
48043 CGACCTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTGTT
Found at i:59645 original size:14 final size:14
Alignment explanation
Indices: 59626--59655 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
59616 TTAGAAAGAC
59626 AACTTTTGATCCAG
1 AACTTTTGATCCAG
59640 AACTTTTGATCCAG
1 AACTTTTGATCCAG
59654 AA
1 AA
59656 AGACACTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (14 bp):
AACTTTTGATCCAG
Found at i:60857 original size:21 final size:21
Alignment explanation
Indices: 60833--60873 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60823 ATCTTAAGTT
*
60833 TAGTTTTATTTTA-TTATTTTC
1 TAGTTTGA-TTTAGTTATTTTC
60854 TAGTTTGATTTAGTTATTTT
1 TAGTTTGATTTAGTTATTTT
60874 GAAAAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68
Consensus pattern (21 bp):
TAGTTTGATTTAGTTATTTTC
Found at i:66167 original size:27 final size:27
Alignment explanation
Indices: 66101--66202 Score: 136
Period size: 27 Copynumber: 3.7 Consensus size: 27
66091 AGAATAAACT
* *
66101 AGGGGCATTTTGGTCATTTTTCAATTCT
1 AGGGGCATTTTGGTCATTTTGC-ATTCC
66129 AGGGGCATTTTGGTCATTTGTGCA-TCC
1 AGGGGCATTTTGGTCATTT-TGCATTCC
*
66156 AGGGGCATTTTGGTCA-TTTGCATGTTC
1 AGGGGCATTTTGGTCATTTTGCAT-TCC
66183 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
66203 AAGTTCACAT
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
25 4 0.06
26 2 0.03
27 36 0.54
28 23 0.34
29 2 0.03
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTGCATTCC
Found at i:74395 original size:15 final size:16
Alignment explanation
Indices: 74365--74397 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
74355 AAAAAAAGGG
*
74365 TATAAGAAATAACAAT
1 TATAAGAAAAAACAAT
74381 TATAA-AAAAAACAAT
1 TATAAGAAAAAACAAT
74396 TA
1 TA
74398 AACTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (16 bp):
TATAAGAAAAAACAAT
Found at i:75101 original size:20 final size:19
Alignment explanation
Indices: 75069--75113 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
75059 AGGTGGCTAA
*
75069 AACTAGAAGA-AAAACTAG
1 AACTAGAAGAGAAAAATAG
75087 AACTAGAAGAGAAAAATAG
1 AACTAGAAGAGAAAAATAG
*
75106 ATCTAGAA
1 AACTAGAA
75114 TAGTGATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.60, C:0.09, G:0.18, T:0.13
Consensus pattern (19 bp):
AACTAGAAGAGAAAAATAG
Found at i:78109 original size:152 final size:151
Alignment explanation
Indices: 77814--78116 Score: 471
Period size: 152 Copynumber: 2.0 Consensus size: 151
77804 ATCCTAACTA
* * *
77814 GGCAATGGCCGGTCTTGGCCAGGAAGTGGCGCGGGTTCGCACGGTGCTGGCCTGGCATGGCTCGG
1 GGCAATGGCCGGTCTTGGCCAGGAAGTGGCGCGGGTTCGCACAGTGCTGGCCTAGCATAGCTCGG
* * * *
77879 CTGTGGCAGGCATGAGGCGCAGATGACCAGGCAGCGGGCGGGCAAGCATGCTGGTGCAGCTCGGG
66 CTGTGGCAGGCATGAGGCGCAGATGACAAGGCAACGGCCGGACAAGCATGCTGGTGCAGCTCGGG
77944 CATGGCCAGTCCTGACCGGGC
131 CATGGCCAGTCCTGACCGGGC
* * *
77965 GGCAGTGGCCGGTCTTGGCCAGGCAGTGGCGCGGGTTCGCACAGTGTTGGCCTAGCATAGCTCGG
1 GGCAATGGCCGGTCTTGGCCAGGAAGTGGCGCGGGTTCGCACAGTGCTGGCCTAGCATAGCTCGG
* * *
78030 CTGTGGCAGGGCATGAGGCGCGGATGACAAGGCAATGGCCGGACAAGCATGTTGGTGCAGCTCGG
66 CTGTGGCA-GGCATGAGGCGCAGATGACAAGGCAACGGCCGGACAAGCATGCTGGTGCAGCTCGG
*
78095 GCATGGCCGGTCCTGACCGGGC
130 GCATGGCCAGTCCTGACCGGGC
78117 CTTGTGCAGG
Statistics
Matches: 137, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
151 67 0.49
152 70 0.51
ACGTcount: A:0.15, C:0.26, G:0.42, T:0.16
Consensus pattern (151 bp):
GGCAATGGCCGGTCTTGGCCAGGAAGTGGCGCGGGTTCGCACAGTGCTGGCCTAGCATAGCTCGG
CTGTGGCAGGCATGAGGCGCAGATGACAAGGCAACGGCCGGACAAGCATGCTGGTGCAGCTCGGG
CATGGCCAGTCCTGACCGGGC
Found at i:78410 original size:19 final size:18
Alignment explanation
Indices: 78386--78421 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
78376 TGAAGATTTA
78386 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
78405 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
78422 ATTATTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:83548 original size:33 final size:33
Alignment explanation
Indices: 83503--83583 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
83493 GTGTTTTAGA
* *
83503 TGTTGTTAGTGATGATACTAAACCTAATTTAAG
1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG
** ** *
83536 TGTTGTTTGTGATGACACTAAATTTGTTTTAGG
1 TGTTGTTTGTGATGACACTAAACCTAATTTAAG
83569 TGTTGTTTGTGATGA
1 TGTTGTTTGTGATGA
83584 AACAAATTCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (33 bp):
TGTTGTTTGTGATGACACTAAACCTAATTTAAG
Found at i:83598 original size:33 final size:33
Alignment explanation
Indices: 83530--83598 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
83520 CTAAACCTAA
* *
83530 TTTAAGTGTTGTTTGTGATGACACTAAATTTGT
1 TTTAAGTGTTGTTTGTGATGAAACTAAATTGGT
*
83563 TTTAGGTGTTGTTTGTGATGAAAC-AAATTCGGT
1 TTTAAGTGTTGTTTGTGATGAAACTAAATT-GGT
83596 TTT
1 TTT
83599 GGAAGCTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTAAGTGTTGTTTGTGATGAAACTAAATTGGT
Found at i:85450 original size:21 final size:21
Alignment explanation
Indices: 85424--85662 Score: 329
Period size: 21 Copynumber: 11.4 Consensus size: 21
85414 TGCTAGGAGT
85424 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
85445 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
85466 TCATTGGAGAAGGTTACAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
85487 TCATTGGAGAAGGTCCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
85508 TCATTGGAGAAGGTCCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
85529 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
85550 TCATTGGAGAAGGTCCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
**
85571 TCATTATAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
85592 TCATTGGAGTAGGTCCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* * *
85613 TCTTTGTAGAAGGTTCCAATC
1 TCATTGGAGAAGGTTCCAAGC
*
85634 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
85655 TCATTGGA
1 TCATTGGA
85663 ATTGCCTAAG
Statistics
Matches: 194, Mismatches: 23, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
20 2 0.01
21 192 0.99
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:86620 original size:19 final size:18
Alignment explanation
Indices: 86596--86631 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
86586 TGAAGACTTA
86596 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
86615 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
86632 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:93106 original size:21 final size:21
Alignment explanation
Indices: 93080--93129 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
93070 GGAATGGCGA
**
93080 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
93101 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
93122 TGGCACGG
1 TGGCACGG
93130 TAAATGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:98119 original size:19 final size:18
Alignment explanation
Indices: 98086--98121 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
98076 TTGAAATAAA
98086 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
98104 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
98122 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:101913 original size:21 final size:20
Alignment explanation
Indices: 101883--101927 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
101873 AGTCGTTAAG
101883 AAGGAAGCAAAGTTGTCGACTT
1 AAGGAAGC-AAG-TGTCGACTT
101905 AAGG-AGCAAGTGTCGACTT
1 AAGGAAGCAAGTGTCGACTT
101924 AAGG
1 AAGG
101928 TTGTCGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.57
20 3 0.13
21 3 0.13
22 4 0.17
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (20 bp):
AAGGAAGCAAGTGTCGACTT
Found at i:104018 original size:19 final size:18
Alignment explanation
Indices: 103994--104029 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
103984 TGAAGACTTA
103994 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
104013 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
104030 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Done.