Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012820.1 Kokia drynarioides strain JFW-HI SEQ_127833, 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: 23498
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:577 original size:29 final size:29
Alignment explanation
Indices: 545--844 Score: 191
Period size: 29 Copynumber: 10.5 Consensus size: 29
535 AAACTATTCG
* *
545 AAAATTTCATTTTTACCCTCGAACTTCTA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
*
574 AAAATTCCATTTTTAACCTCGAAACTTCCA
1 AAAATTCCATTTTTACCCTCG-AACTTCCA
* *
604 AAACTTCCATTTTTATCCAT-GAACTTCCA
1 AAAATTCCATTTTTA-CCCTCGAACTTCCA
* *
633 TAAATTCCATTTTTACCC-CTAAACTTCCA
1 AAAATTCCATTTTTACCCTC-GAACTTCCA
* * ***
662 AAAAATCCATTTTTAACCC-CAAAACTTTTG
1 AAAATTCCATTTTT-ACCCTC-GAACTTCCA
*
692 AAAATTTCATTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
* *
721 AAAATTCC-GTTTT----T-G-AC-CCCA
1 AAAATTCCATTTTTACCCTCGAACTTCCA
***
742 AAAATTCCATTTTTAACCCAAAAACTTCCA
1 AAAATTCCATTTTT-ACCCTCGAACTTCCA
*
772 AAAATTCCATTTTTGACCC-CAAAAC-TCTC-
1 AAAATTCCATTTTT-ACCCTC-GAACTTC-CA
* * *
801 AAAATTACC-CTTTTACCCCCGAA-TGTCTA
1 AAAATT-CCATTTTTACCCTCGAACT-TCCA
830 AAAATTCCATTTTTA
1 AAAATTCCATTTTTA
845 ACCATGAATT
Statistics
Matches: 213, Mismatches: 35, Indels: 46
0.72 0.12 0.16
Matches are distributed among these distances:
21 11 0.05
22 6 0.03
23 1 0.00
24 1 0.00
28 14 0.07
29 104 0.49
30 74 0.35
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCTCGAACTTCCA
Found at i:629 original size:59 final size:58
Alignment explanation
Indices: 545--785 Score: 200
Period size: 59 Copynumber: 4.2 Consensus size: 58
535 AAACTATTCG
* *
545 AAAATTTCATTTTTACCCTCGAACTTCTAAAAATTCCATTTTTAACCTCGAAACTTCCA
1 AAAATTCCATTTTTACCAT-GAACTTCTAAAAATTCCATTTTTAACCTCGAAACTTCCA
* * * * *
604 AAACTTCCATTTTTATCCATGAACTTCCATAAATTCCATTTTT-ACCCCTAAACTTCCA
1 AAAATTCCATTTTTA-CCATGAACTTCTAAAAATTCCATTTTTAACCTCGAAACTTCCA
* * * * * *
662 AAAAATCCATTTTTAACCCCA-AAACTTTTGAAAATTTCATTTTTACCCTCG-AACTTCCA
1 AAAATTCCATTTTT-A--CCATGAACTTCTAAAAATTCCATTTTTAACCTCGAAACTTCCA
* *
721 AAAATTCCGTTTTTGACC-----C--C-AAAAATTCCATTTTTAACC-CAAAAACTTCCA
1 AAAATTCCATTTTT-ACCATGAACTTCTAAAAATTCCATTTTTAACCTC-GAAACTTCCA
772 AAAATTCCATTTTT
1 AAAATTCCATTTTT
786 GACCCCAAAA
Statistics
Matches: 148, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
49 1 0.01
50 16 0.11
51 21 0.14
53 1 0.01
57 2 0.01
58 25 0.17
59 73 0.49
60 9 0.06
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAATTCCATTTTTACCATGAACTTCTAAAAATTCCATTTTTAACCTCGAAACTTCCA
Found at i:703 original size:88 final size:88
Alignment explanation
Indices: 545--750 Score: 229
Period size: 88 Copynumber: 2.3 Consensus size: 88
535 AAACTATTCG
* * * * * *
545 AAAATTTCATTTTTA-CCCTCGAACTTCTAAAAATTCCATTTTTAACCTCGAAACTTCCAAAACT
1 AAAATTCCATTTTTACCCCT-AAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCCAAAACT
609 TCCATTTTTATCCAT-GAACTTCCA
65 TCCATTTTTA-CCATCGAACTTCCA
* **
633 TAAATTCCATTTTTACCCCTAAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTTTGAAAA-T
1 AAAATTCCATTTTTACCCCTAAACTTCCAAAAAATCCATTTTTAACCCCAAAAC-TTCCAAAACT
* *
697 TTCATTTTTACCCTCGAACTTCCA
65 TCCATTTTTACCATCGAACTTCCA
* * *
721 AAAATTCCGTTTTTGACCCCAAAAATTCCA
1 AAAATTCCATTTTT-ACCCCTAAACTTCCA
751 TTTTTAACCC
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
87 3 0.03
88 73 0.74
89 23 0.23
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (88 bp):
AAAATTCCATTTTTACCCCTAAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCCAAAACTT
CCATTTTTACCATCGAACTTCCA
Found at i:744 original size:21 final size:20
Alignment explanation
Indices: 718--771 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
708 CCTCGAACTT
* *
718 CCAAAAATTCCGTTTTTGACC
1 CCAAAAATTCCATTTTT-AAC
739 CCAAAAATTCCATTTTTAAC
1 CCAAAAATTCCATTTTTAAC
759 CCAAAAACTTCCA
1 CCAAAAA-TTCCA
772 AAAATTCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.30
Consensus pattern (20 bp):
CCAAAAATTCCATTTTTAAC
Found at i:804 original size:30 final size:30
Alignment explanation
Indices: 739--797 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
729 GTTTTTGACC
739 CCAAAAATTCCATTTTTAACCCAAAAACTT
1 CCAAAAATTCCATTTTTAACCCAAAAACTT
* *
769 CCAAAAATTCCATTTTTGACCCCAAAACT
1 CCAAAAATTCCATTTTTAACCCAAAAACT
798 CTCAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.29
Consensus pattern (30 bp):
CCAAAAATTCCATTTTTAACCCAAAAACTT
Found at i:833 original size:109 final size:109
Alignment explanation
Indices: 634--843 Score: 280
Period size: 109 Copynumber: 1.9 Consensus size: 109
624 GAACTTCCAT
** * * *
634 AAATTCCATTTTTACCCCTAAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTTTGAAAATTT
1 AAATTCCATTTTTACCCAAAAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCTCAAAATTA
* * *
699 CATTTTTACCCTCGAACTTCCAAAAATTCCGTTTTTGACCCCAA
66 CACTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAA
* *
743 AAATTCCATTTTTAACCCAAAAACTTCCAAAAATTCCATTTTTGACCCCAAAAC-TCTCAAAATT
1 AAATTCCATTTTT-ACCCAAAAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCTCAAAATT
* *
807 ACCCTTTTACCCCCGAA-TGTCTAAAAATTCCATTTTT
65 ACACTTTTACCCCCGAACT-TCCAAAAATTCCATTTTT
844 AACCATGAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 1 0.01
109 50 0.57
110 36 0.41
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (109 bp):
AAATTCCATTTTTACCCAAAAACTTCCAAAAAATCCATTTTTAACCCCAAAACTTCTCAAAATTA
CACTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAA
Found at i:4991 original size:22 final size:21
Alignment explanation
Indices: 4950--4992 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
4940 CCTAGACAAA
*
4950 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
4971 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
4993 GCAAGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:10421 original size:29 final size:29
Alignment explanation
Indices: 10389--10892 Score: 397
Period size: 29 Copynumber: 17.1 Consensus size: 29
10379 TTTTAAGAGT
*
10389 TTCGAGGTCAAAAATGGAGTTTTTGGACA-
1 TTCGAGGTCAAAAATGGAATTTTTGGA-AG
* * *
10418 TTCG-GGAACAAAAATGGCATTTTTGGAGG
1 TTCGAGG-TCAAAAATGGAATTTTTGGAAG
10447 TTCGAGGGT-AAAAATGGAATTTTTGTGAAAG
1 TTCGA-GGTCAAAAATGGAATTTTTG-G-AAG
*
10478 TTCGAGGGT-AAAAATGGAATTTTTGGGAG
1 TTCGA-GGTCAAAAATGGAATTTTTGGAAG
*
10507 TTTTTG-GGTCAAAAATGGAATTTTTGGAAG
1 --TTCGAGGTCAAAAATGGAATTTTTGGAAG
*
10537 TTCGAGTGT-AAAAATGGAATTTTTGAAAG
1 TTCGAG-GTCAAAAATGGAATTTTTGGAAG
*
10566 TTTCAAGGTCAAAAATGGAATTTTTGGAAG
1 -TTCGAGGTCAAAAATGGAATTTTTGGAAG
*
10596 TT-TAGGAGT-AAAAATGGAATTTTTGGAAG
1 TTCGA-G-GTCAAAAATGGAATTTTTGGAAG
10625 TTTCGAGGTCAAAAAT-GAGATTTTTGGAAG
1 -TTCGAGGTCAAAAATGGA-ATTTTTGGAAG
* * *
10655 TTTGGGGGT-AAAAATGGAATTTTTAGAAG
1 -TTCGAGGTCAAAAATGGAATTTTTGGAAG
* * * *
10684 TTTTGGGGTCAAATATGGGATTTTTGGAAG
1 -TTCGAGGTCAAAAATGGAATTTTTGGAAG
* * *
10714 TTTTGGGGT-AAAAATGGAATTTTTAGAAG
1 -TTCGAGGTCAAAAATGGAATTTTTGGAAG
* * * *
10743 TTTTGAGGTCAAAAATGGGATTTTTAGAAA
1 -TTCGAGGTCAAAAATGGAATTTTTGGAAG
* *
10773 TTCGAGGGT-AAAAATGAAATTTTTAGAAG
1 TTCGA-GGTCAAAAATGGAATTTTTGGAAG
* * * *
10802 TTTTGGGGTTAAAATTTGG-ATTTTTGGAAG
1 -TTCGAGGTCAAAA-ATGGAATTTTTGGAAG
*
10832 TTCGAGGGT-AAAAATGGAATTTTTAGAAG
1 TTCGA-GGTCAAAAATGGAATTTTTGGAAG
* * * *
10861 TTTTGGGGTTAAAAATGGGATTTTTGGAAG
1 -TTCGAGGTCAAAAATGGAATTTTTGGAAG
10891 TT
1 TT
10893 TAGGGGTAAA
Statistics
Matches: 399, Mismatches: 46, Indels: 60
0.79 0.09 0.12
Matches are distributed among these distances:
28 9 0.02
29 189 0.47
30 166 0.42
31 35 0.09
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TTCGAGGTCAAAAATGGAATTTTTGGAAG
Found at i:10550 original size:59 final size:59
Alignment explanation
Indices: 10377--10913 Score: 565
Period size: 59 Copynumber: 9.1 Consensus size: 59
10367 TTAAAAGAGT
* * * * **
10377 AATTTTAAG-AGTTTCGAGGTCAAAAATGGAGTTTTTGGACA-TTCG-GGAACAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGA-AGTTCGAGG-GTAAAAATGG
* * * *
10435 CATTTTT-GGAGGTTCGAGGGT-AAAAATGGAATTTTTGTGAAAGTTCGAGGGTAAAAATGG
1 AATTTTTAGAAGTTTTG-GGGTCAAAAATGGAATTTTTG-G-AAGTTCGAGGGTAAAAATGG
* * * *
10495 AATTTTTGGGAGTTTTTGGGTCAAAAATGGAATTTTTGGAAGTTCGAGTGTAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG
*** *
10554 AATTTTT-GAAAGTTTCAAGGTCAAAAATGGAATTTTTGGAAGTT-TAGGAGTAAAAATGG
1 AATTTTTAG-AAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGG-GTAAAAATGG
* * * * *
10613 AATTTTTGGAAGTTTCGAGGTCAAAAAT-GAGATTTTTGGAAGTTTGGGGGTAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATGGA-ATTTTTGGAAGTTCGAGGGTAAAAATGG
* * *
10672 AATTTTTAGAAGTTTTGGGGTCAAATATGGGATTTTTGGAAGTTTTG-GGGTAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAG-TTCGAGGGTAAAAATGG
* * * * *
10731 AATTTTTAGAAGTTTTGAGGTCAAAAATGGGATTTTTAGAAATTCGAGGGTAAAAATGA
1 AATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG
* *
10790 AATTTTTAGAAGTTTTGGGGTTAAAATTTGG-ATTTTTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTAGAAGTTTTGGGGTCAAAA-ATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG
* * * *
10849 AATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTT-TAGGGGTAAAAACGG
1 AATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGG
10908 AATTTT
1 AATTTT
10914 GGACAATTTA
Statistics
Matches: 419, Mismatches: 41, Indels: 37
0.84 0.08 0.07
Matches are distributed among these distances:
57 1 0.00
58 38 0.09
59 321 0.77
60 35 0.08
61 24 0.06
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (59 bp):
AATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:10923 original size:29 final size:28
Alignment explanation
Indices: 10452--10916 Score: 193
Period size: 30 Copynumber: 15.8 Consensus size: 28
10442 GGAGGTTCGA
* *
10452 GGGTAAAAATGGAATTTTTGTGAAAG-TTCG
1 GGGTAAAAACGGAA-TTTTG-G-AAGTTTAG
* * **
10482 AGGGTAAAAATGGAATTTTTGGGAGTTTTT
1 -GGGTAAAAACGGAA-TTTTGGAAGTTTAG
* *
10512 GGGTCAAAAATGGAATTTTTGGAAG-TTCG
1 GGGT-AAAAACGGAA-TTTTGGAAGTTTAG
* * *
10541 AGTGTAAAAATGGAATTTTTGAAAGTTTCA-
1 -GGGTAAAAACGGAA-TTTTGGAAGTTT-AG
* *
10571 AGGTCAAAAATGGAATTTTTGGAAGTTTAG
1 GGGT-AAAAACGGAA-TTTTGGAAGTTTAG
* * *
10601 GAGTAAAAATGGAATTTTTGGAAGTTTCG
1 GGGTAAAAACGGAA-TTTTGGAAGTTTAG
* * * *
10630 AGGTCAAAAATGAGATTTTTGGAAGTTTGG
1 GGGT-AAAAACG-GAATTTTGGAAGTTTAG
* * *
10660 GGGTAAAAATGGAATTTTTAGAAGTTTTG
1 GGGTAAAAACGGAA-TTTTGGAAGTTTAG
** * *
10689 GGGTCAAATATGGGATTTTTGGAAGTTTTG
1 GGGT-AAA-AACGGAATTTTGGAAGTTTAG
* * *
10719 GGGTAAAAATGGAATTTTTAGAAGTTTTG
1 GGGTAAAAACGGAA-TTTTGGAAGTTTAG
* * * * * *
10748 AGGTCAAAAATGGGATTTTTAGAA-ATTCG
1 GGGT-AAAAA-CGGAATTTTGGAAGTTTAG
* * * *
10777 AGGGTAAAAATGAAATTTTTAGAAGTTTTG
1 -GGGTAAAAACGGAA-TTTTGGAAGTTTAG
** * *
10807 GGGTTAAAATTTGGATTTTTGGAAG-TTCG
1 GGG-TAAAA-ACGGAATTTTGGAAGTTTAG
* * *
10836 AGGGTAAAAATGGAATTTTTAGAAGTTTTG
1 -GGGTAAAAACGGAA-TTTTGGAAGTTTAG
* *
10866 GGGTTAAAAATGGGATTTTTGGAAGTTTAG
1 GGG-TAAAAA-CGGAATTTTGGAAGTTTAG
10896 GGGTAAAAACGGAATTTTGGA
1 GGGTAAAAACGGAATTTTGGA
10917 CAATTTAAGG
Statistics
Matches: 352, Mismatches: 57, Indels: 53
0.76 0.12 0.11
Matches are distributed among these distances:
28 22 0.06
29 142 0.40
30 153 0.43
31 35 0.10
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
GGGTAAAAACGGAATTTTGGAAGTTTAG
Found at i:11974 original size:3 final size:3
Alignment explanation
Indices: 11961--12068 Score: 56
Period size: 3 Copynumber: 34.0 Consensus size: 3
11951 ATTTCCCTTT
* * * * *
11961 TTA TT- TTA TTA TTA ATA TTTA TTA ATG CTA TTTA TTA CTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA -TTA
* * * *
12008 TTA TTA ATA TTA TTA TTA TTTA TTAA ATA GTTA TTA TTG TTA TTAA CTA
1 TTA TTA TTA TTA TTA TTA -TTA TT-A TTA -TTA TTA TTA TTA TT-A TTA
*
12057 TTA TTA CTA TTA
1 TTA TTA TTA TTA
12069 ATGTTACTTA
Statistics
Matches: 78, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
2 2 0.03
3 60 0.77
4 16 0.21
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:12021 original size:19 final size:18
Alignment explanation
Indices: 11961--12068 Score: 87
Period size: 19 Copynumber: 5.7 Consensus size: 18
11951 ATTTCCCTTT
11961 TTATT-TTATTATTAATA
1 TTATTATTATTATTAATA
*
11978 TTTATTAATGCTATTTATTACTA
1 -TTATT-AT--TA-TTATTAATA
12001 TTA-T-TTATTATTAATA
1 TTATTATTATTATTAATA
12017 TTATTATTATTTATTAAATA
1 TTATTATTA-TTATT-AATA
*
12037 GTTATTATTGTTATTAACTA
1 -TTATTATTATTATTAA-TA
*
12057 TTATTACTATTA
1 TTATTATTATTA
12069 ATGTTACTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
16 11 0.15
17 3 0.04
18 8 0.11
19 18 0.24
20 12 0.16
21 9 0.12
22 5 0.07
23 8 0.11
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATTATTATTATTAATA
Found at i:12032 original size:13 final size:13
Alignment explanation
Indices: 11965--12025 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
11955 CCCTTTTTAT
11965 TTTATTATTAATA
1 TTTATTATTAATA
* **
11978 TTTATTAATGCTA
1 TTTATTATTAATA
* *
11991 TTTATTACTATTA
1 TTTATTATTAATA
12004 TTTATTATTAATA
1 TTTATTATTAATA
12017 -TTATTATTA
1 TTTATTATTA
12026 TTTATTAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
12 9 0.22
13 31 0.77
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:12069 original size:16 final size:16
Alignment explanation
Indices: 11992--12070 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
11982 TTAATGCTAT
*
11992 TTATTACTATTATTTA
1 TTATTACTATTAATTA
*
12008 TTATTAATATT-ATTA
1 TTATTACTATTAATTA
* * *
12023 TTATTTATTAAATAGTTA
1 TTA-TTACT-ATTAATTA
** *
12041 TTATTGTTATTAACTA
1 TTATTACTATTAATTA
12057 TTATTACTATTAAT
1 TTATTACTATTAAT
12071 GTTACTTATT
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
15 6 0.12
16 30 0.62
17 6 0.12
18 6 0.12
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATTACTATTAATTA
Found at i:12827 original size:17 final size:17
Alignment explanation
Indices: 12788--12844 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
12778 GTACTTGGAC
*
12788 ATTTAAAATAAATTTTAA
1 ATTTAAAATAAA-CTTAA
*
12806 ATTTAGAATAAACTTAA
1 ATTTAAAATAAACTTAA
* *
12823 TTTTAAAATAAATTTAA
1 ATTTAAAATAAACTTAA
*
12840 GTTTA
1 ATTTA
12845 TTGGGCCCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 22 0.67
18 11 0.33
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
ATTTAAAATAAACTTAA
Found at i:14234 original size:205 final size:205
Alignment explanation
Indices: 13871--14437 Score: 938
Period size: 205 Copynumber: 2.8 Consensus size: 205
13861 GTGATTATCC
* *
13871 ACAAACGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACAACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
*
13936 TGTGAGCAAATCTTCGAAACCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAA
* *
14001 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAAAA
*
14066 GCGAATTGAA
196 GCAAATTGAA
** * *
14076 ACAAATGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACAACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * * * * *
14141 TGTAAGCAAATCTTCGAACCCCAACTTCTTGATGAGACACTGTGAAGCAGGTCAAAACAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAA
*
14206 GGTTAGCTTCCTGATAAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAAAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAAAA
14271 GCAAATTGAA
196 GCAAATTGAA
*
14281 ACAAACAACGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACAACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* *
14346 TGTGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGACATTGAGAAGTAGGTCGAAGCAAT-AAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAA
14410 GGTTAGCTTCCTGATGAGATACTGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAA
14438 AAAGACTAAA
Statistics
Matches: 331, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
204 30 0.09
205 301 0.91
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (205 bp):
ACAAACAACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAAAA
GCAAATTGAA
Found at i:14593 original size:119 final size:119
Alignment explanation
Indices: 14298--14665 Score: 549
Period size: 119 Copynumber: 3.1 Consensus size: 119
14288 ACGCGGTCAT
* *
14298 CTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTTGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* *
14363 ACCCCAGCTTCCTGATGAGACATTGAGAAGTAGGTCGAAGCAAT-AAAGGTTAG
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* * *
14416 CTTCCTGATGAGATACTGAGAAAAAGACTAAATCAAACCCACGCTCGATGTGAGCAAATCATCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* * * * * *
14481 ACCCTAGTTTCCTGATGAGACACTAAGAAGCAGGTTGAAGCGATAAAATGTTAG
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
*
14535 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGTGAGCAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* * * *
14600 ACCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAACGGTTAG
66 ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTAG
*
14655 CTTCCTAATGA
1 CTTCCTGATGA
14666 AATATGGGGA
Statistics
Matches: 220, Mismatches: 28, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
118 97 0.44
119 108 0.49
120 15 0.07
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (119 bp):
CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
ACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
Found at i:15157 original size:6 final size:6
Alignment explanation
Indices: 15119--15210 Score: 73
Period size: 6 Copynumber: 15.8 Consensus size: 6
15109 TATTTTAAGG
* * * * *
15119 TTAAAT TT-ATT TTGAAT ATAAAT TT-ATT TTAAAT TTAAAT TTGAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * *
15165 TAAAAT TAAAAT TT-AAT ATAAAT TTAGAT TTATAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
15211 ACTTATTATA
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
5 12 0.18
6 55 0.82
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:15186 original size:18 final size:18
Alignment explanation
Indices: 15149--15222 Score: 53
Period size: 18 Copynumber: 4.1 Consensus size: 18
15139 AATTTATTTT
*
15149 AAATTTAAATTTGAAT-TA
1 AAATTAAAATTT-AATATA
15167 AAATTAAAATTTAATAT-
1 AAATTAAAATTTAATATA
* * *
15184 AAATTTAGATTTATATTTA
1 AAATTAAAATTTA-ATATA
* * *
15203 AATTTAAAACTTATTATA
1 AAATTAAAATTTAATATA
15221 AA
1 AA
15223 TATTGAAAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
17 14 0.33
18 20 0.47
19 9 0.21
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (18 bp):
AAATTAAAATTTAATATA
Found at i:15223 original size:18 final size:18
Alignment explanation
Indices: 15102--15223 Score: 76
Period size: 17 Copynumber: 6.9 Consensus size: 18
15092 AAACTCATTC
* **
15102 TAAAATTTATTTTAAGGT
1 TAAAATTTATTATAAATT
* * *
15120 T-AAATTTATTTTGAATA
1 TAAAATTTATTATAAATT
*
15137 T-AAATTTATTTTAAATT
1 TAAAATTTATTATAAATT
15154 T-AAATTTGAATTA-AAA-T
1 TAAAATTT--ATTATAAATT
*
15171 TAAAATTTAATATAAATT
1 TAAAATTTATTATAAATT
* *
15189 T-AGATTTATATTTAAATT
1 TAAAATTTAT-TATAAATT
*
15207 TAAAACTTATTATAAAT
1 TAAAATTTATTATAAAT
15224 ATTGAAAGTC
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
16 3 0.04
17 45 0.54
18 26 0.31
19 9 0.11
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (18 bp):
TAAAATTTATTATAAATT
Found at i:15951 original size:7 final size:6
Alignment explanation
Indices: 15938--15990 Score: 52
Period size: 7 Copynumber: 8.2 Consensus size: 6
15928 GATCTTAAGT
* *
15938 ATAATA ATTAATA ATAATTA ATAATTA ATAATA ATTAATA ATATTA TTAATA
1 ATAATA A-TAATA ATAA-TA ATAA-TA ATAATA A-TAATA ATAATA ATAATA
15990 A
1 A
15991 AAAGGAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 15 0.38
7 25 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATAATA
Found at i:15952 original size:3 final size:3
Alignment explanation
Indices: 15938--15990 Score: 52
Period size: 3 Copynumber: 16.3 Consensus size: 3
15928 GATCTTAAGT
* *
15938 ATA ATA ATTA ATA ATA ATTA ATA ATTA ATA ATA ATTA ATA ATA TTA TTA
1 ATA ATA A-TA ATA ATA A-TA ATA A-TA ATA ATA A-TA ATA ATA ATA ATA
15987 ATA A
1 ATA A
15991 AAAGGAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 32 0.73
4 12 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:15953 original size:10 final size:10
Alignment explanation
Indices: 15938--15990 Score: 69
Period size: 10 Copynumber: 5.7 Consensus size: 10
15928 GATCTTAAGT
15938 ATAATAATTA
1 ATAATAATTA
15948 ATAATAA-T-
1 ATAATAATTA
15956 -TAATAATTA
1 ATAATAATTA
15965 ATAATAATTA
1 ATAATAATTA
15975 ATAAT-ATTA
1 ATAATAATTA
*
15984 TTAATAA
1 ATAATAA
15991 AAAGGAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 6 0.16
8 1 0.03
9 9 0.24
10 22 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAATAATTA
Found at i:15961 original size:17 final size:17
Alignment explanation
Indices: 15939--15979 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
15929 ATCTTAAGTA
15939 TAATAATTAATAATAAT
1 TAATAATTAATAATAAT
15956 TAATAATTAATAATAAT
1 TAATAATTAATAATAAT
15973 TAATAAT
1 TAATAAT
15980 ATTATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATTAATAATAAT
Found at i:17200 original size:30 final size:30
Alignment explanation
Indices: 17135--17365 Score: 283
Period size: 30 Copynumber: 7.8 Consensus size: 30
17125 GAAGGTCCCT
*
17135 AAACTGTCAAAAAATTCCATTTTT-ACCCTC-
1 AAACT-TCCAAAAATTCCATTTTTGACCC-CA
* *
17165 GAACTTCAAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
**
17195 AAACTTCCAAAAATTCCATTTTTGACCCTTG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CA
* *
17226 AAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
*
17256 AAACTTCC-AAATTTCCATTTTT-ACCCCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
* *
17284 AAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
*
17314 AAACTTCCAAAATTTCCATTTTTGACCCC-
1 AAACTTCCAAAAATTCCATTTTTGACCCCA
* *
17343 CAACTTCCAAAAATTACATTTTT
1 AAACTTCCAAAAATTCCATTTTT
17366 CCCCCGGATG
Statistics
Matches: 179, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
28 13 0.07
29 65 0.36
30 74 0.41
31 27 0.15
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCA
Found at i:17786 original size:96 final size:96
Alignment explanation
Indices: 17682--17867 Score: 243
Period size: 96 Copynumber: 1.9 Consensus size: 96
17672 AAAACTTTAA
* *
17682 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTTTCGAAA-ATTTGTGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTTCGAAATA-TTGCGCCTTAACTTACTAGGTGCA
** *
17744 ATTTTTCTTCAAATTGAAATAATCGAATACCTGT
63 ACCTTTCTTCAAATCGAAATAATCGAATACCTGT
* *
17778 AATCGAGGCAATGTTTCCTTATCTTCGATTTTGAAATATTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAATATTTCCTTATCTTCGATTTCGAAATATTGCGCCTTAACTTACTAGGTGCAACC
* *
17843 TTTCTTCAAATCGAGATAATTGAAT
66 TTTCTTCAAATCGAAATAATCGAAT
17868 TTCACTTTCC
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
96 69 0.88
97 9 0.12
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTTCGAAATATTGCGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATACCTGT
Found at i:20927 original size:15 final size:15
Alignment explanation
Indices: 20907--20952 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
20897 TTTCGATCTA
*
20907 ATTTAATATATTATT
1 ATTTAAAATATTATT
* *
20922 ATTTAAAATTTTATCG
1 ATTTAAAATATTAT-T
20938 ATTTAAAATATTATT
1 ATTTAAAATATTATT
20953 TATATTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTAAAATATTATT
Done.