Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009873.1 Kokia drynarioides strain JFW-HI SEQ_124608, 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: 91413
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2258 original size:60 final size:59
Alignment explanation
Indices: 2125--2870 Score: 552
Period size: 61 Copynumber: 12.4 Consensus size: 59
2115 GGAAAGTTTA
* ** * *
2125 TGTCGGTCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTATCAGATTAAAAAGGGGTGG
1 TGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCTGA--AAAAA-GGG-GG
* * *
2188 TGTCGGCCA-TGCATGGCAAACACAAAAAAAAATTGAATTTTTTATCTGACGAAAAGGGGG
1 TGTCGGCCATTGCATGGCCAACAC-AAAAAAATTTGAATTTTTTATCTGA-AAAAAGGGGG
* * * * *
2248 TGTCGGCCATGGTATGGCCAACACCAAAAAAATTTCAAATTTTTT-TACTTAAAAAAAGGGG
1 TGTCGGCCATTGCATGGCCAACA-CAAAAAAATTT-GAATTTTTTAT-CTGAAAAAAGGGGG
* ** *
2309 TGTCGGCTATTGCATGGTGAACACAAAAAAATTTTGAAATTTTTATCTGAAAAAA-GGGG
1 TGTCGGCCATTGCATGGCCAACACAAAAAAA-TTTGAATTTTTTATCTGAAAAAAGGGGG
** * *
2368 TGTTAGCCATTGCATGGCCAACACAAAAAAA-TCGAATTTTTTTATCTGCAAAAAGGGGG
1 TGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAA-TTTTTTATCTGAAAAAAGGGGG
* * * **
2427 TGTCGGCCATGGCATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTGCAAAAAGGGTA
1 TGTCGGCCATTGCATGGCCAACACAAAAAAATTTG-AA-TTTTTTATCTGAAAAAAGGGGG
** * * **
2488 TGTAAGCCATTGCATGACCAACACTAAAAAAATTTGAAATTTTTTTAT-TCAAAAAAAGGGAA
1 TGTCGGCCATTGCATGGCCAACAC-AAAAAAATTTG-AA-TTTTTTATCT-GAAAAAAGGGGG
* * ** * *
2550 TGTCGACCATTGCATGGTCAACACCCAAAAATTTGATTTTTTTTAT-TAGATAAATA-GGGG
1 TGTCGGCCATTGCATGGCCAACACAAAAAAATTTGA-ATTTTTTATCT-GA-AAAAAGGGGG
* * *
2610 TGTCGGCCATTGTATGGCCAATACCAAAAAAATTTGAAAATTTTT-T-TGACAAAAAGGGGG
1 TGTCGGCCATTGCATGGCCAACA-CAAAAAAATTTG-AATTTTTTATCTGA-AAAAAGGGGG
** * ** * * *
2670 TGTCATCCATTGCATGGTCAACACCCAAAAATTTGATTTTTTTATCAGATAAATA-GGGG
1 TGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCTGA-AAAAAGGGGG
** * *
2729 TGTCGGCCATTGCATAACCAACACAAAAAAA-TTGAATTTTTTTAAC--AAAAAAGGGGA
1 TGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAA-TTTTTTATCTGAAAAAAGGGGG
* * * * ** * * *
2786 TATCAGCCATTGCATGGTCAATACCCAAAAATTTTATTTTTTTTAT-TAGATTAAAAA-GAGG
1 TGTCGGCCATTGCATGGCCAACACAAAAAAATTTGA-ATTTTTTATCT-GA--AAAAAGGGGG
2847 TGTCGGCCA-TGCAATGGCCAACAC
1 TGTCGGCCATTGC-ATGGCCAACAC
2871 CAAATTTTTT
Statistics
Matches: 542, Mismatches: 111, Indels: 62
0.76 0.16 0.09
Matches are distributed among these distances:
56 4 0.01
57 31 0.06
58 35 0.06
59 114 0.21
60 102 0.19
61 143 0.26
62 85 0.16
63 28 0.05
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (59 bp):
TGTCGGCCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCTGAAAAAAGGGGG
Found at i:2682 original size:302 final size:302
Alignment explanation
Indices: 2125--2772 Score: 705
Period size: 302 Copynumber: 2.1 Consensus size: 302
2115 GGAAAGTTTA
* * * *
2125 TGTCGGTCATTGCATGGCCAACACCCAAAAATTTG-ATTTTTTTATCAGATTAAAAAGGGGTGGT
1 TGTCGGCCATTGCATGGCCAACACCAAAAAATTTGAATTTTTTTATCAGA-CAAAAAGGGGTGAT
** * * ** ** *
2189 GTCGGCCATGCATGGCAAACACAAAAAAAAATTGAATTTTTTATCTGACGAAAAGGGGGTGTCGG
65 GTAAGCCATGCATGACAAACACAAAAAAAAATTGAATTTTTTATCTCAAAAAAAGGGAATGTCGA
* *
2254 CCATGGTATGGCCAACACCAAAAAAATTTCAAATTTTTTTACTTAAAAAAAGGGGTGTCGGCTAT
130 CCATGGCATGGCCAACACCAAAAAAATTTCAAATTTTTTTACTTAAAAAAAGGGGTGTCGGCCAT
** *
2319 TGCATGGTGAACACAAAAAAATTTTGAAATTTTTATCTGAAAAAAGGGGTGTTAGCCATTGCATG
195 TGCATGGCCAACACAAAAAAATTTTGAAATTTTTATCTGAAAAAAGGGGTGTCAGCCATTGCATG
*
2384 GCCAACA-CAAAAAAATCGAATTTTTTTATCTGCA-AAA-AGGGGG
260 GCCAACACCAAAAAAATCG-ATTTTTTTATCAG-ATAAATA-GGGG
* *
2427 TGTCGGCCATGGCATGGCCAACACCAAAAAATTTGAAATTTTTTTATCTG-CAAAAA-GGGT-AT
1 TGTCGGCCATTGCATGGCCAACACCAAAAAATTTG-AATTTTTTTATCAGACAAAAAGGGGTGAT
* * *
2489 GTAAGCCATTGCATGACCAACACTAAAAAAATTTGAAATTTTTTTAT-TCAAAAAAAGGGAATGT
65 GTAAGCCA-TGCATGACAAACACAAAAAAAAATTG-AA-TTTTTTATCTCAAAAAAAGGGAATGT
* * * * * *
2553 CGACCATTGCATGGTCAACACC-CAAAAATTT-GATTTTTTTTA-TTAGATAAATAGGGGTGTCG
127 CGACCATGGCATGGCCAACACCAAAAAAATTTCAAATTTTTTTACTTA-A-AAAAAGGGGTGTCG
* * *
2615 GCCATTGTATGGCCAATACCAAAAAAA-TTTGAAAATTTTT-T-TGACAAAAAGGGGGTGTCATC
190 GCCATTGCATGGCCAACA-CAAAAAAATTTTG-AAATTTTTATCTGA-AAAAA-GGGGTGTCAGC
* * * *
2677 CATTGCATGGTCAACACCCAAAAATTTGATTTTTTTATCAGATAAATAGGGG
251 CATTGCATGGCCAACACCAAAAAAATCGATTTTTTTATCAGATAAATAGGGG
** *
2729 TGTCGGCCATTGCATAACCAACA-CAAAAAAATTGAATTTTTTTA
1 TGTCGGCCATTGCATGGCCAACACCAAAAAATTTGAATTTTTTTA
2773 ACAAAAAAGG
Statistics
Matches: 291, Mismatches: 41, Indels: 30
0.80 0.11 0.08
Matches are distributed among these distances:
299 3 0.01
300 30 0.10
301 81 0.28
302 148 0.51
303 17 0.06
304 12 0.04
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (302 bp):
TGTCGGCCATTGCATGGCCAACACCAAAAAATTTGAATTTTTTTATCAGACAAAAAGGGGTGATG
TAAGCCATGCATGACAAACACAAAAAAAAATTGAATTTTTTATCTCAAAAAAAGGGAATGTCGAC
CATGGCATGGCCAACACCAAAAAAATTTCAAATTTTTTTACTTAAAAAAAGGGGTGTCGGCCATT
GCATGGCCAACACAAAAAAATTTTGAAATTTTTATCTGAAAAAAGGGGTGTCAGCCATTGCATGG
CCAACACCAAAAAAATCGATTTTTTTATCAGATAAATAGGGG
Found at i:2698 original size:120 final size:119
Alignment explanation
Indices: 2125--2874 Score: 588
Period size: 120 Copynumber: 6.2 Consensus size: 119
2115 GGAAAGTTTA
* * * *
2125 TGTCGGTCATTGCATGGCCAACACC-CAAAAATTTG--ATTTTTTTATCAGATTAAAAAGGGGTG
1 TGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTT-T--GA-CAAAAA-GGG-G
* ** * * * *
2187 GTGTCGGCCA-TGCATGG-CAAACACAAAAAAAAATTGAATTTTTTATCT-GACGAAAAGGGGG
60 GTGTCAGCCATTGCATGGTC-AACAC-CCAAAAATTTGATTTTTTTAT-TAGA-TAAAAAGGGG
* * * *
2248 TGTCGGCCATGGTATGGCCAACACCAAAAAAATTT-CAAATTTTTTT-ACTTAAAAAAAGGGGTG
1 TGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTTTGAC---AAAAAGGGGGTG
* * * ** **
2311 TCGGCTATTGCATGGTGAACACAAAAAAATTTTGAAATTTTTATCT-GA-AAAAAGGGG
63 TCAGCCATTGCATGGTCAACACCCAAAAA-TTTGATTTTTTTAT-TAGATAAAAAGGGG
** * **
2368 TGTTAGCCATTGCATGGCCAACA-CAAAAAAA-TCGAATTTTTTTATCTG-CAAAAAGGGGGTGT
1 TGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTT-T-TGACAAAAAGGGGGTGT
* * * * * *
2430 CGGCCATGGCATGGCCAACACCAAAAAATTTGAAATTTTTTTATCT-G-CAAAAAGGGTA
64 CAGCCATTGCATGGTCAACACCCAAAAATTTG--ATTTTTTTAT-TAGATAAAAAGGG-G
** * * * * * **
2488 TGTAAGCCATTGCATGACCAACACTAAAAAAATTTGAAATTTTTTTATTCAAAAAAAGGGAATGT
1 TGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAA-ATTTTT-TTGACAAAAAGGGGGTGT
*
2553 C-GACCATTGCATGGTCAACACCCAAAAATTTGATTTTTTTTATTAGATAAATAGGGG
64 CAG-CCATTGCATGGTCAACACCCAAAAATTTGA-TTTTTTTATTAGATAAAAAGGGG
* *
2610 TGTCGGCCATTGTATGGCCAATACCAAAAAAATTTGAAAATTTTTTTGACAAAAAGGGGGTGTCA
1 TGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTTTGACAAAAAGGGGGTGTCA
* * *
2675 TCCATTGCATGGTCAACACCCAAAAATTTGATTTTTTTATCAGATAAATAGGGG
66 GCCATTGCATGGTCAACACCCAAAAATTTGATTTTTTTATTAGATAAAAAGGGG
** * * *
2729 TGTCGGCCATTGCATAACCAACA-CAAAAAAA-TTG--AATTTTTTTAACAAAAAAGGGGATATC
1 TGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTTTGAC-AAAAAGGGGGTGTC
* * *
2790 AGCCATTGCATGGTCAATACCCAAAAATTTTATTTTTTTTATTAGATTAAAAAGAGG
65 AGCCATTGCATGGTCAACACCCAAAAATTTGA-TTTTTTTATTAGA-TAAAAAGGGG
2847 TGTCGGCCA-TGCAATGGCCAACACCAAA
1 TGTCGGCCATTGC-ATGGCCAACACCAAA
2875 TTTTTTTTTT
Statistics
Matches: 524, Mismatches: 72, Indels: 66
0.79 0.11 0.10
Matches are distributed among these distances:
115 11 0.02
116 41 0.08
117 22 0.04
118 69 0.13
119 78 0.15
120 94 0.18
121 34 0.06
122 79 0.15
123 80 0.15
124 9 0.02
125 7 0.01
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (119 bp):
TGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAAAATTTTTTTGACAAAAAGGGGGTGTCA
GCCATTGCATGGTCAACACCCAAAAATTTGATTTTTTTATTAGATAAAAAGGGG
Found at i:2876 original size:58 final size:59
Alignment explanation
Indices: 2814--2943 Score: 169
Period size: 58 Copynumber: 2.2 Consensus size: 59
2804 CAATACCCAA
* * * *
2814 AAATTTTATTTTTT-TTATTAGATTAAAAAGA-GGTGTCGGCCA-TGCAATGGCCAACACC
1 AAATTTT-TTTTTTCCTATCAGATAAAAAAGAGGGTGTCGGCCATTGC-ATGGCCAACAAC
*
2872 AAATTTTTTTTTTCCTGTCAGATAAAAAAGAGGGTGTCGGCCATTGCATGGCCAACAAC
1 AAATTTTTTTTTTCCTATCAGATAAAAAAGAGGGTGTCGGCCATTGCATGGCCAACAAC
2931 -AATTTTTTTTTTC
1 AAATTTTTTTTTTC
2944 AAATTCTCGT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
57 6 0.09
58 33 0.52
59 22 0.34
60 3 0.05
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (59 bp):
AAATTTTTTTTTTCCTATCAGATAAAAAAGAGGGTGTCGGCCATTGCATGGCCAACAAC
Found at i:2927 original size:59 final size:57
Alignment explanation
Indices: 2833--2943 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 57
2823 TTTTTTTATT
* *
2833 AGATTAAAAAGAGGTGTCGGCCATGCAATGGCCAACACCAAATTTTTTTTTTCCTGTC
1 AGATAAAAAAGAGGTGTCGGCCATGCAATGGCCAACAAC-AATTTTTTTTTTCCTGTC
2891 AGATAAAAAAGAGGGTGTCGGCCATTGC-ATGGCCAACAACAATTTTTTTTTTC
1 AGATAAAAAAGA-GGTGTCGGCCA-TGCAATGGCCAACAACAATTTTTTTTTTC
2944 AAATTCTCGT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
58 24 0.49
59 22 0.45
60 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (57 bp):
AGATAAAAAAGAGGTGTCGGCCATGCAATGGCCAACAACAATTTTTTTTTTCCTGTC
Found at i:3969 original size:27 final size:29
Alignment explanation
Indices: 3906--3965 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 29
3896 AATTCATTTT
3906 CTTTTATTTTGTTTTGTTCTTCAATTAGATCA
1 CTTTT-TTTTGTTTTGTTCTTCAATTA-A-CA
*
3938 CTTTTCTTTTGTTTTGTTCTTTAATTAA
1 CTTTT-TTTTGTTTTGTTCTTCAATTAA
3966 TTTTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.63
Consensus pattern (29 bp):
CTTTTTTTTGTTTTGTTCTTCAATTAACA
Found at i:4068 original size:15 final size:16
Alignment explanation
Indices: 4050--4082 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4040 TATTTCATTG
4050 AAAATAATTTTTA-AA
1 AAAATAATTTTTAGAA
4065 AAAATAATTTTTAGAA
1 AAAATAATTTTTAGAA
4081 AA
1 AA
4083 TAGATTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAATAATTTTTAGAA
Found at i:5017 original size:19 final size:20
Alignment explanation
Indices: 4969--5026 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
4959 TTAACCTTTA
4969 TATT-ACAAA-ATAT-TAAT
1 TATTAACAAATATATATAAT
* *
4986 TATTAATATATATATATAAT
1 TATTAACAAATATATATAAT
*
5006 TA-TAACAAATATTTATAAT
1 TATTAACAAATATATATAAT
5025 TA
1 TA
5027 AAATATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 4 0.12
18 3 0.09
19 20 0.61
20 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAACAAATATATATAAT
Found at i:5404 original size:21 final size:22
Alignment explanation
Indices: 5380--5423 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
5370 ATGTTTAATA
5380 ATATTGAA-ATTATAAT-ATTTT
1 ATATT-AATATTATAATAATTTT
*
5401 ATATTAATATTTTAATAATTTT
1 ATATTAATATTATAATAATTTT
5423 A
1 A
5424 AATATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 12 0.60
22 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATTAATATTATAATAATTTT
Found at i:5547 original size:19 final size:19
Alignment explanation
Indices: 5511--5547 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5501 TTTAAACTTA
*
5511 TAAATTATTTCCCCTTAAT
1 TAAATTATTTCCCATTAAT
*
5530 TAAATTATTTTCCATTAA
1 TAAATTATTTCCCATTAA
5548 ACAAACACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTATTTCCCATTAAT
Found at i:6836 original size:16 final size:17
Alignment explanation
Indices: 6807--6844 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
6797 CAGTTGAAAA
*
6807 TATTTTTTCTCAATGAT
1 TATTTTTTCTCAATGAC
6824 TATTTTTTC-CAATGAC
1 TATTTTTTCTCAATGAC
6840 TATTT
1 TATTT
6845 AATTAACGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (17 bp):
TATTTTTTCTCAATGAC
Found at i:14196 original size:144 final size:145
Alignment explanation
Indices: 13940--14220 Score: 474
Period size: 144 Copynumber: 1.9 Consensus size: 145
13930 GAGTCGTTTT
* *
13940 TTTTGTCAAATCTAAAGATTCCATTTGCCATCCGTGCTTAAGCTCAACATTATTTGCCTCAAAGT
1 TTTTGTCAAAACTAAAGATTCCATTTGCCATCCGTGCTTAAGCTCAACATTATTTGCCTCAAACT
* * *
14005 TGTAGTCACAATCAACTAGAAAATCTTCTTCTATTGTTACCGTAAATTTTTCTAGGACTGATGTG
66 TGTAGTCACAATCAACTAGAAAATCTTCTTCTATTGTCACCGCAAATTCTTCTAGGACTGATGTG
14070 ATGTGCTTCGTTCTA
131 ATGTGCTTCGTTCTA
* *
14085 TTTT-TCAAAACTAAAGATTCCATTTGCCATCTGTGCTTAAGCTCAACATTATTTGCCTCAACCT
1 TTTTGTCAAAACTAAAGATTCCATTTGCCATCCGTGCTTAAGCTCAACATTATTTGCCTCAAACT
* *
14149 TGTAGTCACAATCAACTAGAAAATCTTCTTCTGTTGTCACTGCAAATTCTTCTAGGACTGATGTG
66 TGTAGTCACAATCAACTAGAAAATCTTCTTCTATTGTCACCGCAAATTCTTCTAGGACTGATGTG
14214 ATGTGCT
131 ATGTGCT
14221 CATTAAATTC
Statistics
Matches: 127, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
144 123 0.97
145 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (145 bp):
TTTTGTCAAAACTAAAGATTCCATTTGCCATCCGTGCTTAAGCTCAACATTATTTGCCTCAAACT
TGTAGTCACAATCAACTAGAAAATCTTCTTCTATTGTCACCGCAAATTCTTCTAGGACTGATGTG
ATGTGCTTCGTTCTA
Found at i:18027 original size:38 final size:38
Alignment explanation
Indices: 17970--18046 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
17960 TTATGCAGCG
*
17970 ACAACTCTAGATACCTTCATGCATTGATACTTTTGGAC
1 ACAACTCTAGACACCTTCATGCATTGATACTTTTGGAC
* *
18008 ACAACTCTGGACACTTTCATGCATTGATACTTTTGGAC
1 ACAACTCTAGACACCTTCATGCATTGATACTTTTGGAC
18046 A
1 A
18047 GGTTCTTGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (38 bp):
ACAACTCTAGACACCTTCATGCATTGATACTTTTGGAC
Found at i:35090 original size:16 final size:16
Alignment explanation
Indices: 35069--35099 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35059 ATAATGTGAA
35069 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
35085 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
35100 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:35956 original size:26 final size:26
Alignment explanation
Indices: 35897--35949 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
35887 TTCTAGGCGT
*
35897 AATTTTGGACACGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
*
35923 AATTCTGGACATGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
35949 A
1 A
35950 TTCCTGGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCGAC
Found at i:40798 original size:46 final size:46
Alignment explanation
Indices: 40714--40801 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
40704 ACTATTAATT
* * ** * *
40714 TGTAATATTAGTTATGCACTTGGACGATGTTGTTGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGAAAAATATTGTAGTTATCATGTGG
40760 TGTAATACTAGTTATGCACTTGAAAAATATTGTAGTTATCAT
1 TGTAATACTAGTTATGCACTTGAAAAATATTGTAGTTATCAT
40802 CAATTCGCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (46 bp):
TGTAATACTAGTTATGCACTTGAAAAATATTGTAGTTATCATGTGG
Found at i:44033 original size:26 final size:26
Alignment explanation
Indices: 43972--44022 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
43962 AATTCTGGGC
* *
43972 ACAATTCTAGACACGTTCATGCAGCG
1 ACAATTTTGGACACGTTCATGCAGCG
*
43998 ACAATTTTGGACATGTTCATGCAGC
1 ACAATTTTGGACACGTTCATGCAGC
44023 AATATTCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (26 bp):
ACAATTTTGGACACGTTCATGCAGCG
Found at i:44651 original size:9 final size:9
Alignment explanation
Indices: 44637--44666 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
44627 TGAATTTTAA
*
44637 AATTCGAGT
1 AATTCGAAT
44646 AATTCGAAT
1 AATTCGAAT
44655 AATTCGAAT
1 AATTCGAAT
44664 AAT
1 AAT
44667 AGATTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:44762 original size:19 final size:19
Alignment explanation
Indices: 44734--44794 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
44724 TTTCTTTAAA
* *
44734 AAAATACAAAATAATTTTT
1 AAAATTCAAAATAATTTAT
44753 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
44771 AAAAGTTCAAAA-AA-TTAT
1 AAAA-TTCAAAATAATTTAT
44789 AAAATT
1 AAAATT
44795 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 2 0.05
18 17 0.45
19 19 0.50
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:44773 original size:18 final size:18
Alignment explanation
Indices: 44734--44794 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
44724 TTTCTTTAAA
* *
44734 AAAATACAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
44753 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
*
44771 AAAAGTTCAAAA-AATTAT
1 AAAA-TTCAAAATATTTAT
44789 AAAATT
1 AAAATT
44795 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 2 0.05
18 18 0.47
19 18 0.47
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:44802 original size:29 final size:29
Alignment explanation
Indices: 44760--44840 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
44750 TTTAAAATTC
*
44760 AAAATATTTATAAAAGTTCAAAAAAT-TAT
1 AAAATATTTATAAAAATT-AAAAAATATAT
44789 AAAAT-TTTAATAAAAATTAAAAAATATAT
1 AAAATATTT-ATAAAAATTAAAAAATATAT
* *
44818 ATAAA-AGTTAAAAAAATTAAAAA
1 A-AAATATTTATAAAAATTAAAAA
44841 TTCTCTAGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 10 0.22
29 30 0.67
30 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATATTTATAAAAATTAAAAAATATAT
Found at i:44821 original size:20 final size:20
Alignment explanation
Indices: 44780--44832 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
44770 TAAAAGTTCA
* *
44780 AAAAATTATAAAATTTTAAT
1 AAAAATTAAAAAATTATAAT
44800 AAAAATTAAAAAA-TATATAT
1 AAAAATTAAAAAATTATA-AT
*
44820 AAAAGTTAAAAAA
1 AAAAATTAAAAAA
44833 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATTAAAAAATTATAAT
Found at i:45960 original size:21 final size:21
Alignment explanation
Indices: 45936--46005 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 21
45926 TTAACTTTAC
45936 ATCTCAAAAAATTATAAAAAA
1 ATCTCAAAAAATTATAAAAAA
*
45957 ATCT-AAAGAATATATAAAAAA
1 ATCTCAAAAAAT-TATAAAAAA
* *
45978 AACTTAAAAAA-TATAAAAAA
1 ATCTCAAAAAATTATAAAAAA
45998 A-CTCAAAA
1 ATCTCAAAA
46006 CCCTAAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.14
20 16 0.37
21 16 0.37
22 5 0.12
ACGTcount: A:0.69, C:0.09, G:0.01, T:0.21
Consensus pattern (21 bp):
ATCTCAAAAAATTATAAAAAA
Found at i:45979 original size:22 final size:20
Alignment explanation
Indices: 45941--45998 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
45931 TTTACATCTC
*
45941 AAAAAATTATAAAAAAATC-T
1 AAAAAA-TATAAAAAAAACTT
45961 AAAGAATATATAAAAAAAACTT
1 AAA-AA-ATATAAAAAAAACTT
45983 AAAAAATATAAAAAAA
1 AAAAAATATAAAAAAA
45999 CTCAAAACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 14 0.41
21 15 0.44
22 5 0.15
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAAATATAAAAAAAACTT
Found at i:46045 original size:22 final size:23
Alignment explanation
Indices: 46019--46068 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
46009 TAAAATCCAC
**
46019 AAAACCT-TAACTGTACTTTTAA
1 AAAACCTCTAACCATACTTTTAA
46041 AAAA-CTCTAACCATACTTTTAA
1 AAAACCTCTAACCATACTTTTAA
46063 ACAAAC
1 A-AAAC
46069 AAAACCCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.09
22 18 0.78
23 3 0.13
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAACCTCTAACCATACTTTTAA
Found at i:46074 original size:22 final size:22
Alignment explanation
Indices: 46032--46074 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
46022 ACCTTAACTG
**
46032 TACTTTTAAAAAACTCTAACCA
1 TACTTTTAAAAAACTAAAACCA
46054 TACTTTTAAACAAAC-AAAACC
1 TACTTTTAAA-AAACTAAAACC
46075 CAACACTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (22 bp):
TACTTTTAAAAAACTAAAACCA
Found at i:47005 original size:24 final size:26
Alignment explanation
Indices: 46978--47032 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
46968 AGGTAAAATT
*
46978 ATAATTTAAAAATAAA-TATA-TTTA
1 ATAAATTAAAAATAAATTATATTTTA
**
47002 ATAAATTATTAATAAATTTATATTTTA
1 ATAAATTAAAAATAAA-TTATATTTTA
47029 ATAA
1 ATAA
47033 GCTAACTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 13 0.52
26 4 0.16
27 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAAATTAAAAATAAATTATATTTTA
Found at i:49133 original size:22 final size:22
Alignment explanation
Indices: 49107--49148 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
49097 TTTTGTTGAG
49107 GATAAATATTTTAGATTGATAT
1 GATAAATATTTTAGATTGATAT
*
49129 GATAATTATTTTAGATTGAT
1 GATAAATATTTTAGATTGAT
49149 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
GATAAATATTTTAGATTGATAT
Found at i:54710 original size:14 final size:15
Alignment explanation
Indices: 54693--54721 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54683 TACTTTATTT
54693 TATTTTTAT-CTTTC
1 TATTTTTATGCTTTC
54707 TATTTTTATGCTTTC
1 TATTTTTATGCTTTC
54722 ACACAACTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTTTTATGCTTTC
Found at i:59076 original size:55 final size:55
Alignment explanation
Indices: 58992--59099 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
58982 GAAGCGCTAA
58992 CTTGAATGGATCTAACAACCTCTAAGCTATTCGATTGGATCTCTACTTTGTCAAC
1 CTTGAATGGATCTAACAACCTCTAAGCTATTCGATTGGATCTCTACTTTGTCAAC
59047 CTTGAATGGATCTAACAACCTCTAAGCTATTCGATTGGATCTCTACTTTGTCA
1 CTTGAATGGATCTAACAACCTCTAAGCTATTCGATTGGATCTCTACTTTGTCA
59100 TGGCCTCTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (55 bp):
CTTGAATGGATCTAACAACCTCTAAGCTATTCGATTGGATCTCTACTTTGTCAAC
Found at i:63633 original size:16 final size:16
Alignment explanation
Indices: 63609--63639 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63599 CTTCAAAAAA
63609 CAAAGTAAATATAAAC
1 CAAAGTAAATATAAAC
*
63625 CAAATTAAATATAAA
1 CAAAGTAAATATAAA
63640 AATAATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (16 bp):
CAAAGTAAATATAAAC
Found at i:64141 original size:26 final size:26
Alignment explanation
Indices: 64088--64141 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
64078 AACAAATTAA
* *
64088 AAATACATTAAAAAAGTTATTAATTT
1 AAATACATTAAAAAAGTTATCAACTT
*
64114 AAATAGCATTAAAATAGTTA-CAACTT
1 AAATA-CATTAAAAAAGTTATCAACTT
64140 AA
1 AA
64142 CAAACAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33
Consensus pattern (26 bp):
AAATACATTAAAAAAGTTATCAACTT
Found at i:65314 original size:20 final size:20
Alignment explanation
Indices: 65291--65329 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65281 AATTATGTTT
*
65291 ATTTTTTTTTTTAAATTAAC
1 ATTTATTTTTTTAAATTAAC
*
65311 ATTTATTTTTTTAATTTAA
1 ATTTATTTTTTTAAATTAA
65330 TTTATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTATTTTTTTAAATTAAC
Found at i:65328 original size:25 final size:25
Alignment explanation
Indices: 65288--65349 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
65278 GATAATTATG
*
65288 TTTATTTTTTT-TTTTAAATTAACA
1 TTTATTTTTTTAATTTAAATTAACA
* **
65312 TTTATTTTTTTAATTTAATTTATTA
1 TTTATTTTTTTAATTTAAATTAACA
65337 TTTATTTATTTTA
1 TTTATTT-TTTTA
65350 TTATTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 11 0.34
25 16 0.50
26 5 0.16
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTATTTTTTTAATTTAAATTAACA
Found at i:65349 original size:16 final size:16
Alignment explanation
Indices: 65324--65355 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
65314 TATTTTTTTA
65324 ATTTAATTTATTATTT
1 ATTTAATTTATTATTT
*
65340 ATTTATTTTATTATTT
1 ATTTAATTTATTATTT
65356 TTCACATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTAATTTATTATTT
Found at i:70443 original size:45 final size:45
Alignment explanation
Indices: 70394--70483 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
70384 TTTATTACAA
70394 CTTCGAGGAAATAAGGTTTGGTGTTGTAACTTCAATCTACCCTTT
1 CTTCGAGGAAATAAGGTTTGGTGTTGTAACTTCAATCTACCCTTT
*
70439 CTTCGAGGAAATAAGGTTTGGTGTTGTAACTTTAATCTACCCTTT
1 CTTCGAGGAAATAAGGTTTGGTGTTGTAACTTCAATCTACCCTTT
70484 TGGATTAGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (45 bp):
CTTCGAGGAAATAAGGTTTGGTGTTGTAACTTCAATCTACCCTTT
Found at i:70545 original size:48 final size:42
Alignment explanation
Indices: 70486--70921 Score: 167
Period size: 42 Copynumber: 10.5 Consensus size: 42
70476 TACCCTTTTG
*
70486 GATTAGGGGTAAAACATTGGATGATAGTGACTCCAATCTGCCCCTCTA
1 GATTA-GGGTAAAAGATTGGATG--A-TGACTCCAATCTG-CCCT-TA
* * *
70534 GATTAGCGGTAAGAGATTGGATGATGACTTCAATCTGCCCTTT
1 GATTAG-GGTAAAAGATTGGATGATGACTCCAATCTGCCCTTA
* * *
70577 GGTTAGGGTAAAAGATTGGATG--G-CTTCAATCTGCCC-CA
1 GATTAGGGTAAAAGATTGGATGATGACTCCAATCTGCCCTTA
* * * * * * *
70615 TG-GTCGAGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTTT
1 -GATTAG-GGTAAAAGATTGGATGATGACTCCAATCTGCCCTTA
* * * *
70658 GGTTAGGGTAAAAGAATGGATG--G-CTTCAATCTGCCACAT-
1 GATTAGGGTAAAAGATTGGATGATGACTCCAATCTGCC-CTTA
* * * * * * *
70697 GGTTGGGGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCT-
1 GATTAGGGTAAAAGATTGGATGATGACTCCAATCTGCCCT-TA
* * *
70739 GGTTA-GGTAAAAGATTGGATG--G-CTTCAATCTGCCCCATA
1 GATTAGGGTAAAAGATTGGATGATGACTCCAATCTG-CCCTTA
** * * * * *
70778 G-TCGGGGTAAGAGATTGGATGGTGTCTTCAATCTGGCCTCT-
1 GATTAGGGTAAAAGATTGGATGATGACTCCAATCTGCCCT-TA
* * * *
70819 GGTTAAGGTAAAAGATT--A-GATGGCTTCAATCTGCCC-TA
1 GATTAGGGTAAAAGATTGGATGATGACTCCAATCTGCCCTTA
* * * * * * *
70857 TGGTCAGGGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTA
1 -GATTAGGGTAAAAGATTGGATGATGACTCCAATCTGCCCT-TA
*
70901 G-TGAGGGTAAAAGATTGGATG
1 GATTAGGGTAAAAGATTGGATG
70922 TTCTTCAATC
Statistics
Matches: 313, Mismatches: 47, Indels: 62
0.74 0.11 0.15
Matches are distributed among these distances:
37 1 0.00
38 14 0.04
39 108 0.35
40 5 0.02
41 22 0.07
42 115 0.37
43 9 0.03
44 6 0.02
45 12 0.04
46 1 0.00
47 1 0.00
48 19 0.06
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (42 bp):
GATTAGGGTAAAAGATTGGATGATGACTCCAATCTGCCCTTA
Found at i:70657 original size:81 final size:81
Alignment explanation
Indices: 70541--70941 Score: 590
Period size: 81 Copynumber: 5.0 Consensus size: 81
70531 CTAGATTAGC
* * *
70541 GGTAAGAGATTGGATGATGACTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
70606 TCTGCCCCATGGTCGA
66 TCTGCCCCATGGTCGA
* *
70622 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTTTGGTTAGGGTAAAAGAATGGATGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
* * *
70687 TCTGCCACATGGTTGG
66 TCTGCCCCATGGTCGA
*
70703 GGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTGGTTA-GGTAAAAGATTGGATGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
* *
70767 TCTGCCCCATAGTCGG
66 TCTGCCCCATGGTCGA
* * *
70783 GGTAAGAGATTGGATGGTGTCTTCAATCTGGCCTCTGGTTAAGGTAAAAGATTAGATGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
70848 TCTGCCCTATGGTC-A
66 TCTGCCCCATGGTCGA
* * * *
70863 GGGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTAGTGAGGGTAAAAGATTGGATGTTCTTC
1 -GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATG-GCTTC
*
70928 AATCTGTCCCATGG
64 AATCTGCCCCATGG
70942 GAGATGATGT
Statistics
Matches: 290, Mismatches: 27, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
80 74 0.26
81 200 0.69
82 16 0.06
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (81 bp):
GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
TCTGCCCCATGGTCGA
Found at i:70807 original size:161 final size:162
Alignment explanation
Indices: 70541--70939 Score: 613
Period size: 161 Copynumber: 2.5 Consensus size: 162
70531 CTAGATTAGC
* * * *
70541 GGTAAGAGATTGGATGATGACTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATGGCTTCAA
1 GGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
* * *
70606 TCTGCCCCATGGTCGAGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTTTGGTTAGGGTAAAA
66 TCTGCCCCATAGTCGAGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAAGGTAAAA
* **
70671 GAATGGATGGCTTCAATCTGCCAC-ATGGTTGG
131 GAATAGATGGCTTCAATCTGCC-CTATGGTCAG
70703 GGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTGGTTA-GGTAAAAGATTGGATGGCTTCAA
1 GGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
* *
70767 TCTGCCCCATAGTCGGGGTAAGAGATTGGATGGTGTCTTCAATCTGGCCTCTGGTTAAGGTAAAA
66 TCTGCCCCATAGTCGAGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAAGGTAAAA
*
70832 GATTAGATGGCTTCAATCTGCCCTATGGTCAG
131 GAATAGATGGCTTCAATCTGCCCTATGGTCAG
* * *
70864 GGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTAGTGAGGGTAAAAGATTGGATGTTCTTCA
1 GGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATG-GCTTCA
*
70929 ATCTGTCCCAT
65 ATCTGCCCCAT
70940 GGGAGATGAT
Statistics
Matches: 217, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
160 1 0.00
161 148 0.68
162 53 0.24
163 15 0.07
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (162 bp):
GGTAAGAGATTAGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
TCTGCCCCATAGTCGAGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAAGGTAAAA
GAATAGATGGCTTCAATCTGCCCTATGGTCAG
Found at i:72124 original size:59 final size:60
Alignment explanation
Indices: 72051--72166 Score: 189
Period size: 59 Copynumber: 1.9 Consensus size: 60
72041 GCCCTTCCTT
*
72051 TTTTTTTTGCTAGTTTGAGCAGCCCTTTCAGGTTTTCAACTTAAACTTTTGGATTTTGACC
1 TTTTTTTT-CTAGTTTGAGCAGCCCTTTCAGGTTTTCAACTCAAACTTTTGGATTTTGACC
* *
72112 TTTTTTTT-TAGTTTGAGCCGCCCTTTCAGGTTTTCAACTCAGACTTTTGGATTTT
1 TTTTTTTTCTAGTTTGAGCAGCCCTTTCAGGTTTTCAACTCAAACTTTTGGATTTT
72167 TTAGGCAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 44 0.85
61 8 0.15
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.49
Consensus pattern (60 bp):
TTTTTTTTCTAGTTTGAGCAGCCCTTTCAGGTTTTCAACTCAAACTTTTGGATTTTGACC
Found at i:77214 original size:24 final size:24
Alignment explanation
Indices: 77182--77228 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
77172 ATAACATTAG
77182 CTCTCACGAGCCCAGAATGGTTAC
1 CTCTCACGAGCCCAGAATGGTTAC
*
77206 CTCTTACGAGCCCAGAATGGTTA
1 CTCTCACGAGCCCAGAATGGTTA
77229 ACTAGTTACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (24 bp):
CTCTCACGAGCCCAGAATGGTTAC
Found at i:83549 original size:37 final size:35
Alignment explanation
Indices: 83507--83584 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
83497 CCACAATTGT
*
83507 AAGGACAACATCAGCAACAGTAGCAATTTTCTCAAAA
1 AAGGACAACATC--CAACAGCAGCAATTTTCTCAAAA
* * *
83544 AAGGAC-AGATCCAACAGCAGTAATTTTCTCAACA
1 AAGGACAACATCCAACAGCAGCAATTTTCTCAAAA
83578 AAGGACA
1 AAGGACA
83585 GATCCGATGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 26 0.72
36 4 0.11
37 6 0.17
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (35 bp):
AAGGACAACATCCAACAGCAGCAATTTTCTCAAAA
Found at i:83569 original size:34 final size:34
Alignment explanation
Indices: 83521--83589 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
83511 ACAACATCAG
*
83521 CAACAGTAGCAATTTTCTCAAAAAAGGACAGATC
1 CAACAGCAGCAATTTTCTCAAAAAAGGACAGATC
* *
83555 CAACAGCAGTAATTTTCTCAACAAAGGACAGATC
1 CAACAGCAGCAATTTTCTCAAAAAAGGACAGATC
83589 C
1 C
83590 GATGGCTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.20
Consensus pattern (34 bp):
CAACAGCAGCAATTTTCTCAAAAAAGGACAGATC
Found at i:87874 original size:24 final size:24
Alignment explanation
Indices: 87844--87904 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 24
87834 TCTCATTAAT
87844 ATGATGAGTAAGAAGGGCACTCTA
1 ATGATGAGTAAGAAGGGCACTCTA
*
87868 ATGATGAAGAATAAGAGGGGCACTCTA
1 ATGATG-AG--TAAGAAGGGCACTCTA
87895 ATGATGAGTA
1 ATGATGAGTA
87905 GGGATTGCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.24
25 2 0.06
26 2 0.06
27 21 0.64
ACGTcount: A:0.39, C:0.10, G:0.30, T:0.21
Consensus pattern (24 bp):
ATGATGAGTAAGAAGGGCACTCTA
Found at i:88608 original size:17 final size:18
Alignment explanation
Indices: 88582--88626 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
88572 ATAGTTTGCA
*
88582 TGCATCTTTA-TTGTCAT
1 TGCATTTTTATTTGTCAT
88599 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA-TTTGTCAT
88618 TGCATTTTT
1 TGCATTTTT
88627 TTAATTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.36
19 16 0.64
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (18 bp):
TGCATTTTTATTTGTCAT
Done.