Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012234.1 Kokia drynarioides strain JFW-HI SEQ_127235, 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: 113738
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 TGATAACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:940 original size:14 final size:14
Alignment explanation
Indices: 923--955 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
913 AATAAAAGAA
923 AAAATCTAAAATAT
1 AAAATCTAAAATAT
937 AAAATCTAAAATAT
1 AAAATCTAAAATAT
*
951 TAAAT
1 AAAAT
956 ATATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATCTAAAATAT
Found at i:6136 original size:897 final size:892
Alignment explanation
Indices: 4653--7300 Score: 4388
Period size: 897 Copynumber: 3.0 Consensus size: 892
4643 AATTTAGTCC
* *
4653 TTAAACATTAAAATCATAAAAAATCACTTTACAAAATAATCAAATCCAACAACCAAACTTAATAA
1 TTAAACATTAAAATCATTAAAAATCACTTTACAAAATAATCAAATCCAACAACCAAGCTTAATAA
* * * * *
4718 ACTTCAATAATTTTTCAAGAATCAACACATTCATCGATGGAAAGATTTATAAAATTTAACAAATT
66 ACTTCAATAAATTTTCAAGAAACAACACATTCATCAATGGAAAGATTTATAACATTTAACAGATT
* * *
4783 CACAAATTAGTCC-CTGGGTTAGCTAGATTAAGTTAATACGAACTCAAAAATATAAAAATTACTA
131 CACAAATTAGTCCTC-GGGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATAAAAAATACTA
*
4847 AAAACT-GACAAGATTTACATATCAAACCCATGAACTAAAGTTGGCCGAAGCTCCCTCCCATAGG
195 AAAA-TGGGCAAGATTTACATATCAAACCCATGAACTAAAGTTGGCCGAAGCTCCCTCCCAT-GG
*
4911 -GTTCAGGGTTTTTCGGTTCTAAAATAGGTGGAAGAAGATG----------ATTTTTATTATGTT
258 TGTTTAGGGTTTTTCGGTTCTAAAATAGGTGGAAGAAGATGATTTCTTCCAATTTTTATTATGTT
*
4965 TTTATGTTTATAATTGCCCTTTTAACATAATTACATTTTCACGCTTATTTAATTGATTCAATTTC
323 TTTATGTTTATAATTGCCCTTTTAACATAATTACATTTTCACCCTTATTTAATTGATTCAATTTC
* *
5030 AACCAATTTAAAGGCTAAGACCGTGTACTAAACTCCCTAAAGGTATAATTACCCTTTAAGGACCT
388 AACCAATTTAAAGGCTAAGACTGTCTACTAAACTCCCTAAAGGTATAATTACCCTTTAAGGACCT
*
5095 ATCTAGGTCATTCCTTTACAAATTAACATGTTTAATCAATGATTTCTATATTTTACAGCCTTTAC
453 CTCTAGGTCATTCCTTTACAAATTAACATGTTTAATCAATGATTTCTATATTTTACAGCCTTTAC
* *
5160 AATCTAATCCTTTTTACTTTATTAATTATCTATACGATAAAATTTTGTAACCAAATTTTAATACG
518 AATCTAGTCCTTTTTACTTTATTAATTATCTATACGATAAAATTTCGTAACCAAATTTTAATACG
*
5225 ATACTAATAACCTCATAAATATTAAATAAATAATCTTTACGGTTTGACACATCGAAGTTGTGGCC
583 ATACTAATAACCTCATAAATATTAAATAAATAATATTTACGGTTTGACACATCGAAGTTGTGGCC
* *
5290 TC-AAACCCATAATTTCCTATCACACTAAAAATAAATTAACTAGTAAATCCTCATTTTATTAGGA
648 TCGAAA-CCATAATTTCCTATCACACTAAAAATAGACTAACTAGTAAATCCTCATTTTATTAGGA
5354 TTTAATTGCAATTTATAAAAATCTAAAGAGTTTCACATCATTTCTATTTTTGGGCTATTTAAAAG
712 TTTAATTGCAATTTATAAAAATCTAAAGAGTTTCACATCATTTCTATTTTTGGGCTATTTAAAAG
* *
5419 GATCTAATTTCATAATTGGTCTCTCAATTATATTAAATTCCAATTAAAAAAACTTGTTTACAATT
777 GATCTAATTTCATAATTGATCCCTCAATTATATTAAATTCCAATTAAAAAAACTTGTTTACAATT
*
5484 TAGCCTTAAACTAAAAAGGACTAAATGTATAAAAAAAAAAACCTAAACCCGAAACCG
842 TAGCCTTAAACTAAAAAGGACTAAATGAAT-AAAAAAAAAA---AAA-CC-AAACCG
*
5541 TTAAACATTAAAATCATTAAAAATCACTTTACAAAATAATCAAATCCAACAACTAAGCTTAATAA
1 TTAAACATTAAAATCATTAAAAATCACTTTACAAAATAATCAAATCCAACAACCAAGCTTAATAA
* *
5606 ACTTCAATAAATTTTCAAGAAACAACATATTCATCAATGGAAAGATTTATAGCATTTAACAGATT
66 ACTTCAATAAATTTTCAAGAAACAACACATTCATCAATGGAAAGATTTATAACATTTAACAGATT
* *
5671 CACAAATCAGTCCTCGGGTTAACTAGATTAAGCTAATACGAACTCAAAAACATAAAAAATACTAA
131 CACAAATTAGTCCTCGGGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATAAAAAATACTAA
*
5736 AAATGGGCAAGATTTACATATCAAACCCATGAACTAAAGTTGGTCGAAGCTCCCT-CCATGGTGT
196 AAATGGGCAAGATTTACATATCAAACCCATGAACTAAAGTTGGCCGAAGCTCCCTCCCATGGTGT
*
5800 TTAGGGTTTTTCGGTTCTAAAATAGGTTGAAGAAGATGATTTCTTCCAATTTTTATTATGTTTTT
261 TTAGGGTTTTTCGGTTCTAAAATAGGTGGAAGAAGATGATTTCTTCCAATTTTTATTATGTTTTT
* *
5865 ATGTTTAGAATTGCCCTTTTAACATAATTACATTTTCACCCTTATTTAATTGATTCAATTTAAAC
326 ATGTTTATAATTGCCCTTTTAACATAATTACATTTTCACCCTTATTTAATTGATTCAATTTCAAC
*
5930 CAATTTAAAGGCTAAGACTGTCTACTAAACTCCTTAAAGGTATAATTACCCTTTAAGGACCTCTC
391 CAATTTAAAGGCTAAGACTGTCTACTAAACTCCCTAAAGGTATAATTACCCTTTAAGGACCTCTC
*
5995 TAGGTCATTCCTTTACAAATTAACATGTTTAATCAATGATTTCTACATTTTACAGCCTTTACAAT
456 TAGGTCATTCCTTTACAAATTAACATGTTTAATCAATGATTTCTATATTTTACAGCCTTTACAAT
6060 CTAGTCCTTTTTACTTTATTAATTATCTATACGATAAAATTTCGTAACCAAATTTTAATACGATA
521 CTAGTCCTTTTTACTTTATTAATTATCTATACGATAAAATTTCGTAACCAAATTTTAATACGATA
* * * * *
6125 CTAAAAACCTCATAAATATTAAATAAATAATATTTGCGGTTTGACACATTGAAGTTGTGACCCCG
586 CTAATAACCTCATAAATATTAAATAAATAATATTTACGGTTTGACACATCGAAGTTGTGGCCTCG
*
6190 AAACCACT-ATTTCCTATCACATTAAAAATAGACTAACTAGTAAATCCTCATTTTATTAGGATTT
651 AAACCA-TAATTTCCTATCACACTAAAAATAGACTAACTAGTAAATCCTCATTTTATTAGGATTT
6254 AATTGCAATTTATAAAAATCTAAAGAGTTTCACATCATTTCTATTTTTGGGCTATTTAAAAGGAT
715 AATTGCAATTTATAAAAATCTAAAGAGTTTCACATCATTTCTATTTTTGGGCTATTTAAAAGGAT
*
6319 CTAATTTCATAATTGATCCCTCAATTATATTAAATTCCAATTAAAAAAACTTGTTTACAATTTTG
780 CTAATTTCATAATTGATCCCTCAATTATATTAAATTCCAATTAAAAAAACTTGTTTACAATTTAG
*
6384 CCTTAAACTAAAAAGGACTAAATGCAT---AAAAAAAAAACCAAACCG
845 CCTTAAACTAAAAAGGACTAAATGAATAAAAAAAAAAAAACCAAACCG
* * *
6429 TTAAACATTAAAATCATTAAAAATCATTTTGCAAAATAATCAAATCTAACAACCAAGCTTAATAA
1 TTAAACATTAAAATCATTAAAAATCACTTTACAAAATAATCAAATCCAACAACCAAGCTTAATAA
*
6494 ACTTCAATAAATTTTCAAGAAACAAAACATTCATCAATGGAAAGATTTATAACATTTAACAGATT
66 ACTTCAATAAATTTTCAAGAAACAACACATTCATCAATGGAAAGATTTATAACATTTAACAGATT
6559 CACAAATTAGTCCTCGGGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATAAAAAATACTAA
131 CACAAATTAGTCCTCGGGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATAAAAAATACTAA
* * * *
6624 AAAGGGGCAAGATTTACATAACAAACCCATGAACTAAAGTTGGCCAAAGCTCTCTCCCATGGTGT
196 AAATGGGCAAGATTTACATATCAAACCCATGAACTAAAGTTGGCCGAAGCTCCCTCCCATGGTGT
* *
6689 TTAAGGTTTTTCTGTTCTAAAATAGGTGGAAGAAGATGATTTCTTCCAATTTTTATTATGTTTTT
261 TTAGGGTTTTTCGGTTCTAAAATAGGTGGAAGAAGATGATTTCTTCCAATTTTTATTATGTTTTT
6754 ATGTTTATAATTGCCCTTTTTAACATAATTACATTTTCACCC---TTTAATTGATTCAATTTCAA
326 ATGTTTATAATTGCCC-TTTTAACATAATTACATTTTCACCCTTATTTAATTGATTCAATTTCAA
*
6816 CCAATTTAAAGGCTAAGATTGTCTACTAAACTCCCTAAAGGTATAATTACCCTTTAAGGACCTCT
390 CCAATTTAAAGGCTAAGACTGTCTACTAAACTCCCTAAAGGTATAATTACCCTTTAAGGACCTCT
* *
6881 CTAGGTCATTCCTTAACAAATTAATATGTTTAATCAATGATTTCTATATTTTACAGCCTTTACAA
455 CTAGGTCATTCCTTTACAAATTAACATGTTTAATCAATGATTTCTATATTTTACAGCCTTTACAA
* *
6946 TCTAGTCC-TTTTACTTAATTAATTGTCTATACGATAAAATTTCGTAACCAAATTTTAATACGAT
520 TCTAGTCCTTTTTACTTTATTAATTATCTATACGATAAAATTTCGTAACCAAATTTTAATACGAT
* * *
7010 ACTAATAACCTCATAAATATTAAATAAATAATATTTACGATCTGACAGATCGAAGTTGTGGCCTC
585 ACTAATAACCTCATAAATATTAAATAAATAATATTTACGGTTTGACACATCGAAGTTGTGGCCTC
* *
7075 GAAACCACAATTTCCTATCACACTAAAAATAGACTAATTAGTAAATCCTCATTTTATTAGGATTT
650 GAAACCATAATTTCCTATCACACTAAAAATAGACTAACTAGTAAATCCTCATTTTATTAGGATTT
* * *
7140 AATTACAATTTATAAAAATCTAAAGAGTTTCACATCATTTATATTTTTAGGCTATTTAAAAAGGA
715 AATTGCAATTTATAAAAATCTAAAGAGTTTCACATCATTTCTATTTTTGGGCTATTT-AAAAGGA
* *
7205 TTTAATTTCATAATTGATCCCTCAATTATATTAAATTCCAATTAAACAAACTTGTTTACAATTTA
779 TCTAATTTCATAATTGATCCCTCAATTATATTAAATTCCAATTAAAAAAACTTGTTTACAATTTA
* *
7270 GCTTTATACTAAAAAGGACTAAATGAATAAA
844 GCCTTAAACTAAAAAGGACTAAATGAATAAA
7301 TAACTCAAAA
Statistics
Matches: 1650, Mismatches: 88, Indels: 42
0.93 0.05 0.02
Matches are distributed among these distances:
886 228 0.14
887 289 0.18
888 471 0.29
889 89 0.05
890 28 0.02
893 7 0.00
897 534 0.32
898 4 0.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (892 bp):
TTAAACATTAAAATCATTAAAAATCACTTTACAAAATAATCAAATCCAACAACCAAGCTTAATAA
ACTTCAATAAATTTTCAAGAAACAACACATTCATCAATGGAAAGATTTATAACATTTAACAGATT
CACAAATTAGTCCTCGGGTTAGCTAGATTAAGCTAATACGAACTCAAAAACATAAAAAATACTAA
AAATGGGCAAGATTTACATATCAAACCCATGAACTAAAGTTGGCCGAAGCTCCCTCCCATGGTGT
TTAGGGTTTTTCGGTTCTAAAATAGGTGGAAGAAGATGATTTCTTCCAATTTTTATTATGTTTTT
ATGTTTATAATTGCCCTTTTAACATAATTACATTTTCACCCTTATTTAATTGATTCAATTTCAAC
CAATTTAAAGGCTAAGACTGTCTACTAAACTCCCTAAAGGTATAATTACCCTTTAAGGACCTCTC
TAGGTCATTCCTTTACAAATTAACATGTTTAATCAATGATTTCTATATTTTACAGCCTTTACAAT
CTAGTCCTTTTTACTTTATTAATTATCTATACGATAAAATTTCGTAACCAAATTTTAATACGATA
CTAATAACCTCATAAATATTAAATAAATAATATTTACGGTTTGACACATCGAAGTTGTGGCCTCG
AAACCATAATTTCCTATCACACTAAAAATAGACTAACTAGTAAATCCTCATTTTATTAGGATTTA
ATTGCAATTTATAAAAATCTAAAGAGTTTCACATCATTTCTATTTTTGGGCTATTTAAAAGGATC
TAATTTCATAATTGATCCCTCAATTATATTAAATTCCAATTAAAAAAACTTGTTTACAATTTAGC
CTTAAACTAAAAAGGACTAAATGAATAAAAAAAAAAAAACCAAACCG
Found at i:14337 original size:11 final size:11
Alignment explanation
Indices: 14321--14350 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
14311 AAATTGGGAA
14321 TTTGAATTTTT
1 TTTGAATTTTT
14332 TTTGAATTTTT
1 TTTGAATTTTT
*
14343 GTTGAATT
1 TTTGAATT
14351 CTTTATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (11 bp):
TTTGAATTTTT
Found at i:24013 original size:17 final size:17
Alignment explanation
Indices: 23993--24035 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
23983 TCTCCCTTGA
*
23993 TCTTTAACCTTCCATCT
1 TCTTTAACCTTCCATAT
*
24010 TCTTTAACCTTTCATAT
1 TCTTTAACCTTCCATAT
24027 TCTTGTAAC
1 TCTT-TAAC
24036 TATTTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.21, C:0.28, G:0.02, T:0.49
Consensus pattern (17 bp):
TCTTTAACCTTCCATAT
Found at i:27378 original size:30 final size:30
Alignment explanation
Indices: 27325--27564 Score: 274
Period size: 30 Copynumber: 8.1 Consensus size: 30
27315 AAAATGAAGT
* *
27325 TTTTAAG-AA-TTTTGGGGTTAAAATGTGA
1 TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
*
27353 TTTTAAGAAAGTTTAGGGGTCAAAATGTAA
1 TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
* * *
27383 TTTTAAAAAAGTTTAAGGGTTAAAATGTGA
1 TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
* *
27413 TTTTAGGAAAGTTTAGGGGTTAAAATGTGA
1 TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
* * *
27443 TTTT-GGAAAGTTTAAGGGTTACAATGTAA
1 TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
* *
27472 TTTTGAGAAAGTTTAGGAGTTAAAATGTAA
1 TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
* *
27502 TTTT-AGAAAGTTTAGGGGTCAAAATATAA
1 TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
* * *
27531 TTTTGAA-AAAGTTTAAGTGTTAAAATATAA
1 TTTT-AAGAAAGTTTAGGGGTTAAAATGTAA
27561 TTTT
1 TTTT
27565 TAAATAAAAT
Statistics
Matches: 184, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.04
29 54 0.29
30 122 0.66
31 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.22, T:0.38
Consensus pattern (30 bp):
TTTTAAGAAAGTTTAGGGGTTAAAATGTAA
Found at i:27469 original size:89 final size:88
Alignment explanation
Indices: 27338--27564 Score: 294
Period size: 89 Copynumber: 2.5 Consensus size: 88
27328 TAAGAATTTT
* * *
27338 GGGGTTAAAATGTGATTTTAAGAAAGTTTAGGGGTCAAAATGTAATTTTAAAAAAGTTTAAGG-G
1 GGGGTTAAAATGTGATTTT-GGAAAGTTTAAGGGTTAAAATGTAATTTTAAAAAAGTTT-AGGAG
*
27402 TTAAAATGTGATTTTAGGAAAGTTTA
64 TTAAAATGTAATTTTA-GAAAGTTTA
* * *
27428 GGGGTTAAAATGTGATTTTGGAAAGTTTAAGGGTTACAATGTAATTTTGAGAAAGTTTAGGAGTT
1 GGGGTTAAAATGTGATTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTAAAAAAGTTTAGGAGTT
27493 AAAATGTAATTTTAGAAAGTTTA
66 AAAATGTAATTTTAGAAAGTTTA
* * * * * *
27516 GGGGTCAAAATATAATTTTGAAAAAGTTTAAGTGTTAAAATATAATTTT
1 GGGGTTAAAATGTGATTTTG-GAAAGTTTAAGGGTTAAAATGTAATTTT
27565 TAAATAAAAT
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
88 29 0.24
89 73 0.60
90 19 0.16
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (88 bp):
GGGGTTAAAATGTGATTTTGGAAAGTTTAAGGGTTAAAATGTAATTTTAAAAAAGTTTAGGAGTT
AAAATGTAATTTTAGAAAGTTTA
Found at i:27482 original size:59 final size:59
Alignment explanation
Indices: 27339--27564 Score: 283
Period size: 59 Copynumber: 3.8 Consensus size: 59
27329 AAGAATTTTG
* * * *
27339 GGGTTAAAATGTGATTTTAAGAAAGTTTAGGGGTCAAAATGTAATTTTAAAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTT-AGAAAGTTTAA
* * *
27399 GGGTTAAAATGTGATTTT-AGGAAAGTTTAGGGGTTAAAATGTGATTTTGGAAAGTTTAA
1 GGGTTAAAATGTAATTTTGA-GAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGTTTAA
* * *
27458 GGGTTACAATGTAATTTTGAGAAAGTTTAGGAGTTAAAATGTAATTTTAGAAAGTTTAG
1 GGGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGTTTAA
* * * * * *
27517 GGGTCAAAATATAATTTTGAAAAAGTTTAAGTGTTAAAATATAATTTT
1 GGGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTT
27565 TAAATAAAAT
Statistics
Matches: 147, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
59 102 0.69
60 45 0.31
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (59 bp):
GGGTTAAAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGTTTAA
Found at i:29635 original size:15 final size:15
Alignment explanation
Indices: 29615--29671 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
29605 ATTCAATATT
29615 AATATTTTAATAATA
1 AATATTTTAATAATA
*
29630 AATATTTATTAAAATTATA
1 AATA-TT-TT--AATAATA
*
29649 AATATATTAATAATA
1 AATATTTTAATAATA
29664 AATATTTT
1 AATATTTT
29672 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:30632 original size:22 final size:22
Alignment explanation
Indices: 30607--30689 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 22
30597 TGGGCCTTAA
* *
30607 GGTTTAAGATTTTTTAATTTAG
1 GGTTTAAGATATTTTAAATTAG
* * *
30629 GGTTTGAG-TAGTTTAAATAAG
1 GGTTTAAGATATTTTAAATTAG
* * *
30650 AGTTT-TGATTTTTTAAATTAG
1 GGTTTAAGATATTTTAAATTAG
*
30671 GGTTTAGGATATTTTAAAT
1 GGTTTAAGATATTTTAAAT
30690 CAAGGGGTTT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 1 0.02
21 27 0.59
22 18 0.39
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.49
Consensus pattern (22 bp):
GGTTTAAGATATTTTAAATTAG
Found at i:41926 original size:21 final size:19
Alignment explanation
Indices: 41883--41927 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
41873 GTCATTGGTT
*
41883 AAAATCATTTTAATAAATC
1 AAAATCATTTTAAAAAATC
*
41902 AAAATGATTTTAAAACAAGTC
1 AAAATCATTTTAAAA-AA-TC
41923 AAAAT
1 AAAAT
41928 TGCTCCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 2 0.09
21 7 0.32
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAATCATTTTAAAAAATC
Found at i:51065 original size:53 final size:53
Alignment explanation
Indices: 50964--51088 Score: 144
Period size: 53 Copynumber: 2.4 Consensus size: 53
50954 CAAAACAGTG
* * * *
50964 TACACAAACCTTGTCACACGCCCATGTGTCAGCCTATGTATCCTAGAACAACA
1 TACACACACCTTGACACACGCCCATGTGTCAACCCATGTATCCTAGAACAACA
* * * * **
51017 TACACACACCTTGACACTCGTCCATGTTTCAACCCATGTGCTCC-AGAACAGTA
1 TACACACACCTTGACACACGCCCATGTGTCAACCCATGT-ATCCTAGAACAACA
51070 TACACACACCTTGACACAC
1 TACACACACCTTGACACAC
51089 TCATGTGTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 57 0.95
54 3 0.05
ACGTcount: A:0.31, C:0.34, G:0.12, T:0.22
Consensus pattern (53 bp):
TACACACACCTTGACACACGCCCATGTGTCAACCCATGTATCCTAGAACAACA
Found at i:51108 original size:51 final size:51
Alignment explanation
Indices: 50957--51123 Score: 138
Period size: 53 Copynumber: 3.2 Consensus size: 51
50947 TTTGTCTCAA
* * * * *
50957 AACAGTGTACACAAACCTTGTCACACGCCCATGTGTCAGCCTATGT-ATCCTAG
1 AACAGTATACACACACCTTG--ACACACTCATGTGTCAGCCTATGTGCTCC-AG
** * * * *
51010 AACAACATACACACACCTTGACACTCGTCCATGTTTCAACCCATGTGCTCCAG
1 AACAGTATACACACACCTTGACACAC-T-CATGTGTCAGCCTATGTGCTCCAG
* * * *
51063 AACAGTATACACACACCTTGACACACTCATGTGTCAGCTTGTGTGCGCCAA
1 AACAGTATACACACACCTTGACACACTCATGTGTCAGCCTATGTGCTCCAG
*
51114 AATAGTATAC
1 AACAGTATAC
51124 GCAAACCCTG
Statistics
Matches: 90, Mismatches: 21, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
51 31 0.34
52 1 0.01
53 55 0.61
54 3 0.03
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.24
Consensus pattern (51 bp):
AACAGTATACACACACCTTGACACACTCATGTGTCAGCCTATGTGCTCCAG
Found at i:53736 original size:22 final size:25
Alignment explanation
Indices: 53706--53751 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
53696 TTGCAAGGTA
53706 GAAATATT-AA-TTATTATATTTTT
1 GAAATATTAAACTTATTATATTTTT
53729 GAAA-ATTAAACTTATTATATTTT
1 GAAATATTAAACTTATTATATTTT
53752 AATTTCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.14
23 6 0.29
24 12 0.57
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (25 bp):
GAAATATTAAACTTATTATATTTTT
Found at i:54656 original size:19 final size:17
Alignment explanation
Indices: 54628--54681 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
54618 AAATTATTAA
54628 TAAAATTTTATATAAAAT
1 TAAAATTTTAT-TAAAAT
54646 TAAACATTTTATTAAAA-
1 TAAA-ATTTTATTAAAAT
* *
54663 TAATATCTTAATTAAAAT
1 TAAAAT-TTTATTAAAAT
54681 T
1 T
54682 TATTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 12 0.39
18 10 0.32
19 7 0.23
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTTATTAAAAT
Found at i:54661 original size:18 final size:18
Alignment explanation
Indices: 54628--54663 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
54618 AAATTATTAA
54628 TAAAATTTTATATAAAAT
1 TAAAATTTTATATAAAAT
54646 TAAACATTTTAT-TAAAAT
1 TAAA-ATTTTATATAAAAT
54664 AATATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTTATATAAAAT
Found at i:58488 original size:15 final size:15
Alignment explanation
Indices: 58459--58499 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
58449 AATAATATAG
58459 TAATGATAAAAAACAA
1 TAAT-ATAAAAAACAA
*
58475 TAATATAAACAACAA
1 TAATATAAAAAACAA
58490 TAATATAAAA
1 TAATATAAAA
58500 GTAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (15 bp):
TAATATAAAAAACAA
Found at i:58786 original size:10 final size:11
Alignment explanation
Indices: 58767--58808 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
58757 AGCAAAAATT
58767 AATTATTTTTAA
1 AATTA-TTTTAA
58779 AA-TATTTTAA
1 AATTATTTTAA
*
58789 AATTAATTTAA
1 AATTATTTTAA
58800 AATTATTTT
1 AATTATTTT
58809 TTAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 8 0.30
11 17 0.63
12 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:59681 original size:12 final size:13
Alignment explanation
Indices: 59664--59697 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
59654 AAACCCTATT
59664 GAAGGGGAA-GGG
1 GAAGGGGAAGGGG
59676 GAAGGGGAAGGGG
1 GAAGGGGAAGGGG
59689 GAAGGGGAA
1 GAAGGGGAA
59698 AGAGAAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (13 bp):
GAAGGGGAAGGGG
Found at i:59704 original size:12 final size:12
Alignment explanation
Indices: 59664--59715 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
59654 AAACCCTATT
*
59664 GAAGGGGAAGGG
1 GAAGGGGAAGGA
*
59676 GAAGGGGAAGGGG
1 GAAGGGGAA-GGA
*
59689 GAAGGGGAAAGA
1 GAAGGGGAAGGA
* *
59701 GAAGGAGAATGA
1 GAAGGGGAAGGA
59713 GAA
1 GAA
59716 TAAGAGTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 23 0.66
13 12 0.34
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (12 bp):
GAAGGGGAAGGA
Found at i:59704 original size:19 final size:19
Alignment explanation
Indices: 59667--59705 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
59657 CCCTATTGAA
* *
59667 GGGGAAGGGGAAGGGGAAG
1 GGGGAAGGGGAAAGAGAAG
59686 GGGGAAGGGGAAAGAGAAG
1 GGGGAAGGGGAAAGAGAAG
59705 G
1 G
59706 AGAATGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (19 bp):
GGGGAAGGGGAAAGAGAAG
Found at i:59709 original size:6 final size:6
Alignment explanation
Indices: 59664--59697 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
59654 AAACCCTATT
59664 GAAGGG GAAGGG GAAGGG GAAGGGG GAAGGG GAA
1 GAAGGG GAAGGG GAAGGG GAA-GGG GAAGGG GAA
59698 AGAGAAGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:59810 original size:11 final size:11
Alignment explanation
Indices: 59769--59809 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
59759 ATAATTTTAT
*
59769 ATTTAAAAATA
1 ATTTTAAAATA
*
59780 ATTTTAAATTA
1 ATTTTAAAATA
59791 ATTTTAAAAT-
1 ATTTTAAAATA
59801 ATTTTAAAA
1 ATTTTAAAA
59810 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:62733 original size:44 final size:44
Alignment explanation
Indices: 62684--62773 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
62674 TGGTCATGGA
62684 TGATGATTGTTTATGTAGTGGTTATTTTAGGCACTCACTGAGCT
1 TGATGATTGTTTATGTAGTGGTTATTTTAGGCACTCACTGAGCT
*
62728 TGATGATTGTTTATGTAGTGGTTATTTTAGGCACTCATTGAGCT
1 TGATGATTGTTTATGTAGTGGTTATTTTAGGCACTCACTGAGCT
62772 TG
1 TG
62774 TCAAAGCTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.20, C:0.10, G:0.26, T:0.44
Consensus pattern (44 bp):
TGATGATTGTTTATGTAGTGGTTATTTTAGGCACTCACTGAGCT
Found at i:63366 original size:21 final size:19
Alignment explanation
Indices: 63326--63376 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
63316 TTCCAAATAG
63326 TATCGATATCCCTTATAAAA
1 TATCGATA-CCCTTATAAAA
63346 TTATCGATACCCTCT-TCAAAA
1 -TATCGATACCCT-TAT-AAAA
*
63367 TACCGATACC
1 TATCGATACC
63377 TACGTAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (19 bp):
TATCGATACCCTTATAAAA
Found at i:64682 original size:12 final size:12
Alignment explanation
Indices: 64665--64690 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64655 AACGTACTTC
64665 TGATGGTGCTTT
1 TGATGGTGCTTT
64677 TGATGGTGCTTT
1 TGATGGTGCTTT
64689 TG
1 TG
64691 GATGACCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.35, T:0.50
Consensus pattern (12 bp):
TGATGGTGCTTT
Found at i:70820 original size:27 final size:27
Alignment explanation
Indices: 70769--70820 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
70759 CAATAAGATT
*
70769 AAAAGTCATCAAAAATTGATACAAATG
1 AAAAGTCATCAAAAATTAATACAAATG
*
70796 AAAAGTCATGAAATAATTAAT-CAAA
1 AAAAGTCATCAAA-AATTAATACAAA
70821 ATTACACCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (27 bp):
AAAAGTCATCAAAAATTAATACAAATG
Found at i:71590 original size:15 final size:15
Alignment explanation
Indices: 71535--71592 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
71525 TCCATGCTCA
* *
71535 CAACACGAGTGTTCA
1 CAACATGAGTGTTCG
* *
71550 CAACATCAGTGTTTG
1 CAACATGAGTGTTCG
* * *
71565 CAGCTTTAGTGTTCG
1 CAACATGAGTGTTCG
71580 CAACATGAGTGTT
1 CAACATGAGTGTT
71593 GCTCATATCT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (15 bp):
CAACATGAGTGTTCG
Found at i:73385 original size:14 final size:14
Alignment explanation
Indices: 73366--73395 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
73356 CTAGTGTATT
73366 ACTGTTCATTTTTA
1 ACTGTTCATTTTTA
73380 ACTGTTCATTTTTA
1 ACTGTTCATTTTTA
73394 AC
1 AC
73396 ATCATGTTAT
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:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTGTTCATTTTTA
Found at i:81929 original size:21 final size:21
Alignment explanation
Indices: 81904--81970 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
81894 CTACATCTAC
81904 AAATCATCCAGTTCTTACATT
1 AAATCATCCAGTTCTTACATT
81925 AAATCA--CA-TAATCATCTAC---
1 AAATCATCCAGT--TC-T-TACATT
81944 AAATCATCCAGTTCTTACATT
1 AAATCATCCAGTTCTTACATT
81965 AAATCA
1 AAATCA
81971 CATAATTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 20
0.64 0.00 0.36
Matches are distributed among these distances:
18 4 0.11
19 9 0.25
20 4 0.11
21 15 0.42
22 4 0.11
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATCATCCAGTTCTTACATT
Found at i:81952 original size:40 final size:40
Alignment explanation
Indices: 81897--81976 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
81887 TCGTAGTCTA
81897 CATCTACAAATCATCCAGTTCTTACATTAAATCACATAAT
1 CATCTACAAATCATCCAGTTCTTACATTAAATCACATAAT
81937 CATCTACAAATCATCCAGTTCTTACATTAAATCACATAAT
1 CATCTACAAATCATCCAGTTCTTACATTAAATCACATAAT
81977 TGATTCACTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (40 bp):
CATCTACAAATCATCCAGTTCTTACATTAAATCACATAAT
Found at i:87307 original size:3 final size:3
Alignment explanation
Indices: 87299--87364 Score: 59
Period size: 3 Copynumber: 22.7 Consensus size: 3
87289 AATGACCTAC
* *
87299 AAT AAT AAT AAT AA- AAT AAT AAT AACT AA- AAT AAA AAT GA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
*
87342 AA- AAT AAAT AAT AAG AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AA
87365 ATGGTAAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 7 0.14
3 38 0.75
4 6 0.12
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:88121 original size:75 final size:76
Alignment explanation
Indices: 87971--88125 Score: 181
Period size: 75 Copynumber: 2.1 Consensus size: 76
87961 CAAACGCTAA
* *
87971 TGTGTCTAGGCCATGTGCTACTTTTAATTAAAAATAAAAATATCGCCCAGGGGTCACACAGCCTG
1 TGTGTCTAGGCCATGTGCTACTTTGAATTAAAAATAAAAATATCGCCCAGGGGTCACACAGCCTA
*
88036 TCACACGCCCG
66 CCACACGCCCG
* * ** * *
88047 TGTGTCTAGGCCATGTG-T-CATTTCGAATT-GAAATAAAAATATCGGCCATTGGTCACACGGTC
1 TGTGTCTAGGCCATGTGCTAC-TTT-GAATTAAAAATAAAAATATCGCCCAGGGGTCACACAGCC
*
88109 TACCACATGCCCG
64 TACCACACGCCCG
88122 TGTG
1 TGTG
88126 ACCAGGCTGA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
74 1 0.01
75 45 0.67
76 21 0.31
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (76 bp):
TGTGTCTAGGCCATGTGCTACTTTGAATTAAAAATAAAAATATCGCCCAGGGGTCACACAGCCTA
CCACACGCCCG
Found at i:92144 original size:18 final size:17
Alignment explanation
Indices: 92122--92156 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
92112 TTTCTCATCG
*
92122 ATTTTTTGTTTCAACTA
1 ATTTTTTGGTTCAACTA
92139 ATTTTTTGGTTCAACTA
1 ATTTTTTGGTTCAACTA
92156 A
1 A
92157 CACTTTCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (17 bp):
ATTTTTTGGTTCAACTA
Found at i:98580 original size:86 final size:85
Alignment explanation
Indices: 98429--98740 Score: 347
Period size: 86 Copynumber: 3.7 Consensus size: 85
98419 ATATTGACTG
* * * * *
98429 TATGGACCCCTATGATGGCTGGGAT-TGCATATGTTGCAG-TTACCTGACAGCTTGTGTGAGCAG
1 TATGGA-CCCTTTGATGGCTGAGATCTGCATATGTTGCGGATT-CTTGATAGCTTGTGTGAGCAG
98492 CATCGAGAGTAGGTGTTACATT
64 CATCGAGAGTAGGTGTTACATT
* * *
98514 TATGGACCCTTTGATGGTTGAGATCCTGCATATGTTGCGGATTCTTGATAGCTTGTTTGAGTAGC
1 TATGGACCCTTTGATGGCTGAGAT-CTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGC
*
98579 ATCGAGAGTGGGTGTTACATT
65 ATCGAGAGTAGGTGTTACATT
*
98600 TATGGACCCTTCGATGGCTGAGATCTTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGC
1 TATGGACCCTTTGATGGCTGAGATC-TGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGC
*
98665 ATCGTGAGT--G-G-TA-A--
65 ATCGAGAGTAGGTGTTACATT
* ** * *
98679 TATGGACCATATCAATGGCT-ATGATCTTGCATATGTTACGGATTCTTGACAGCTTGTGTGAG
1 TATGGACCCT-TTGATGGCTGA-GATC-TGCATATGTTGCGGATTCTTGATAGCTTGTGTGAG
98741 TAAAATAGTA
Statistics
Matches: 203, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
79 10 0.05
80 46 0.23
81 1 0.00
82 2 0.01
83 1 0.00
84 16 0.08
85 7 0.03
86 118 0.58
87 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (85 bp):
TATGGACCCTTTGATGGCTGAGATCTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGCA
TCGAGAGTAGGTGTTACATT
Found at i:99653 original size:21 final size:21
Alignment explanation
Indices: 99629--99674 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
99619 CACATGGGCT
* *
99629 TGTGTTTGATACACACGATCG
1 TGTGTTTGAGACAAACGATCG
*
99650 TGTGTTTGAGACAAACGGTCG
1 TGTGTTTGAGACAAACGATCG
99671 TGTG
1 TGTG
99675 ACCCCTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
TGTGTTTGAGACAAACGATCG
Found at i:100729 original size:24 final size:24
Alignment explanation
Indices: 100702--100749 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
100692 GCAAATTCTA
*
100702 GGACTGAGGGTGGAGAAGATGTTG
1 GGACTAAGGGTGGAGAAGATGTTG
* *
100726 GGACTAAGGGTGGGGACGATGTTG
1 GGACTAAGGGTGGAGAAGATGTTG
100750 ATAGTAAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.06, G:0.50, T:0.21
Consensus pattern (24 bp):
GGACTAAGGGTGGAGAAGATGTTG
Found at i:102338 original size:11 final size:11
Alignment explanation
Indices: 102322--102387 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
102312 ATCGAGCCCC
102322 TTTTAAATTTA
1 TTTTAAATTTA
102333 TTTT-AA---A
1 TTTTAAATTTA
*
102340 -TTTAGATTTA
1 TTTTAAATTTA
102350 TTTTAAATTTGA
1 TTTTAAATTT-A
* *
102362 ATTTAAATTAA
1 TTTTAAATTTA
*
102373 TCTTAAATTTA
1 TTTTAAATTTA
102384 TTTT
1 TTTT
102388 CAAAATTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
6 3 0.07
7 2 0.05
10 3 0.07
11 24 0.59
12 9 0.22
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:102348 original size:17 final size:17
Alignment explanation
Indices: 102323--102397 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
102313 TCGAGCCCCT
102323 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
102340 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* **
102357 TTTGAATTTAAATT-AA
1 TTTAAATTTATTTTAAA
102373 TCTTAAATTTATTTTCAAA
1 T-TTAAATTTATTTT-AAA
*
102392 ATTAAA
1 TTTAAA
102398 AGTCCAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
16 3 0.07
17 36 0.78
18 5 0.11
19 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:102364 original size:23 final size:23
Alignment explanation
Indices: 102338--102382 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
102328 ATTTATTTTA
* * *
102338 AATTTAGATTTATTTTAAATTTG
1 AATTTAAATTAATCTTAAATTTG
102361 AATTTAAATTAATCTTAAATTT
1 AATTTAAATTAATCTTAAATTT
102383 ATTTTCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
AATTTAAATTAATCTTAAATTTG
Found at i:103253 original size:19 final size:20
Alignment explanation
Indices: 103224--103262 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
103214 AGATAATATT
103224 TATTAAATAATTAATAAAAA
1 TATTAAATAATTAATAAAAA
103244 TATT-AATAATTAATAAAAA
1 TATTAAATAATTAATAAAAA
103263 AAACCGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TATTAAATAATTAATAAAAA
Found at i:104491 original size:58 final size:58
Alignment explanation
Indices: 104392--104549 Score: 203
Period size: 58 Copynumber: 2.7 Consensus size: 58
104382 ATTAACCCCT
* *
104392 AACTTCCAAAAATTCAATTTTCGACCTCAAAACTTCCAAAATTCCATTTT-TAACCCTAA
1 AACTTCCAAAAATTCCATTTT-TACCTCAAAACTTCCAAAATTCCATTTTCT-ACCCTAA
** *
104451 AACTTCCAAAAATTCCATTTTTACCCTC-GTACTTCCAAAATTCCATTTTCTACCCTGA
1 AACTTCCAAAAATTCCATTTTTA-CCTCAAAACTTCCAAAATTCCATTTTCTACCCTAA
* *
104509 AACTTCCAAAAACTCCATTTTTAACCTCAAAACTTCTAAAA
1 AACTTCCAAAAATTCCATTTTT-ACCTCAAAACTTCCAAAA
104550 AAATCAGTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
58 51 0.59
59 35 0.41
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTACCTCAAAACTTCCAAAATTCCATTTTCTACCCTAA
Found at i:104589 original size:29 final size:29
Alignment explanation
Indices: 104392--104620 Score: 207
Period size: 30 Copynumber: 7.7 Consensus size: 29
104382 ATTAACCCCT
* *
104392 AACTTCCAAAAATTCAATTTTCGA-CCTCAA
1 AACTTCCAAAAATTCCATTTT-TACCCT-AA
104422 AACTTCC-AAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTAA
**
104451 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTAA
* *
104480 TACTTCC-AAAATTCCATTTTCTACCCTGA
1 AACTTCCAAAAATTCCATTTT-TACCCTAA
* *
104509 AACTTCCAAAAACTCCATTTTTAACCTCAA
1 AACTTCCAAAAATTCCATTTTTACCCT-AA
* *
104539 AACTTCTAAAAAAAT-CAGTTTTTATCCCT-A
1 AACTTC-CAAAAATTCCA-TTTTTA-CCCTAA
* *
104569 AACCTCCAAAATTTCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTAA
**
104599 AACTTTTAAAAATTACCATTTT
1 AACTTCCAAAAATT-CCATTTT
104621 GCCCCCATAT
Statistics
Matches: 164, Mismatches: 22, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
28 13 0.08
29 64 0.39
30 65 0.40
31 19 0.12
32 3 0.02
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTAA
Done.