Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004935.1 Kokia drynarioides strain JFW-HI SEQ_118641, 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: 25037
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1699 original size:91 final size:91
Alignment explanation
Indices: 1564--1737 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 91
1554 TTTAGAGAAG
* * *
1564 TTTGAGGGTTAAAATGTGATTTTGAAAAAGTTTAGGGGTTAAAATATGATTTTGAAAAAGTTTAA
1 TTTGAGGGTCAAAATGTGATTTTGAAAAAGTTTAGGGGTCAAAATATAATTTTGAAAAAGTTT-A
*
1629 GGGGTCAAAATGTAATTTTGGAAATGT
65 GGGGTCAAAATATAATTTTGGAAATGT
* * *
1656 TTTG-GGGTCAAAATGTGATTTTGGAGAAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTAG
1 TTTGAGGGTCAAAATGTGATTTTGAAAAAGTTTAGGGGTCAAAATATAATTTTGAAAAAGTTTAG
1720 GGGTCAAAATATAATTTT
66 GGGTCAAAATATAATTTT
1738 AAAAAAATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
90 19 0.25
91 52 0.69
92 4 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (91 bp):
TTTGAGGGTCAAAATGTGATTTTGAAAAAGTTTAGGGGTCAAAATATAATTTTGAAAAAGTTTAG
GGGTCAAAATATAATTTTGGAAATGT
Found at i:1730 original size:30 final size:30
Alignment explanation
Indices: 1551--1753 Score: 219
Period size: 30 Copynumber: 6.7 Consensus size: 30
1541 ATGAAAATGA
* * * *
1551 AATTTTAGAGAAGTTT-GAGGGTTAAAATGT
1 AATTTTGGAAAAGTTTAG-GGGTCAAAATAT
* * *
1581 GATTTTGAAAAAGTTTAGGGGTTAAAATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATAT
* * *
1611 GATTTTGAAAAAGTTTAAGGGGTCAAAATGT
1 AATTTTGGAAAAGTTT-AGGGGTCAAAATAT
* * *
1642 AATTTTGGAAATGTTTTGGGGTCAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATAT
* *
1672 GATTTTGGAGAAGTTTAGGGGTCAAAATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATAT
1702 AATTTTGGAAAAGTTTAGGGGTCAAAATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATAT
** *
1732 AATTTTAAAAAAATTTAGGGGT
1 AATTTTGGAAAAGTTTAGGGGT
1754 TAAATATGAA
Statistics
Matches: 150, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
30 124 0.83
31 26 0.17
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTAGGGGTCAAAATAT
Found at i:8931 original size:59 final size:60
Alignment explanation
Indices: 8769--9079 Score: 346
Period size: 60 Copynumber: 5.2 Consensus size: 60
8759 TCAAACTTGA
* * * *
8769 AAAATTACATTTTTAA-CCCTAAAC-TTTCCAAAAATCATATTTTAACCCTTATATTTTTCC
1 AAAATTACA-TTTTAACCCCTAAACTTTTCC-AAAATTACATTTTAACCCTTAAACTTTTCC
* * *
8829 AAAATTATATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACTCTTAAATTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
* *
8889 AAAATTACATTTTGA-CCCTAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTT-C
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
* * * * *
8947 AAAATTATATTTTGACCCCAAAACTTTTCTAAAATTACATTTTAACCCCTCAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAA-CCCTTAAACTTTTCC
* * * * * * *
9008 -AAATCATATTTTTACCCCTAAA-TTCTTCCAAAATCACATTTTAACCCTCAAACTTCTCT
1 AAAATTACATTTTAACCCCTAAACTT-TTCCAAAATTACATTTTAACCCTTAAACTTTTCC
*
9067 AAAATTTCATTTT
1 AAAATTACATTTT
9080 CATATCGAGT
Statistics
Matches: 219, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
58 15 0.07
59 87 0.40
60 111 0.51
61 6 0.03
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (60 bp):
AAAATTACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTTCC
Found at i:9071 original size:30 final size:30
Alignment explanation
Indices: 8706--9079 Score: 308
Period size: 30 Copynumber: 12.6 Consensus size: 30
8696 CCCCCGAACC
* *
8706 TTCCAAAGATTACATTTTTGA-CCTCGAAC-T
1 TTCCAAA-ATTACA-TTTTAACCCTCAAACTT
** *
8736 TTCCAAAAACCACATTTTTACCCTCAAAC--
1 TTCC-AAAATTACATTTTAACCCTCAAACTT
**
8765 TTGAAAAATTACATTTTTAACCCT-AAAC-T
1 TTCCAAAATTACA-TTTTAACCCTCAAACTT
* * * * *
8794 TTCCAAAAATCATATTTTAACCCTTATATTT
1 TTCC-AAAATTACATTTTAACCCTCAAACTT
*
8825 TTCCAAAATTATATTTTAACCC-CTAAACTT
1 TTCCAAAATTACATTTTAACCCTC-AAACTT
* * *
8855 TTCCAAAATTACATTTTAACTCTTAAATTT
1 TTCCAAAATTACATTTTAACCCTCAAACTT
*
8885 TTCCAAAATTACATTTTGACCCT-AAACTT
1 TTCCAAAATTACATTTTAACCCTCAAACTT
8914 TTCCAAAATTACATTTTAACCC-CTAAACTT
1 TTCCAAAATTACATTTTAACCCTC-AAACTT
* *
8944 TT-CAAAATTATATTTTGACCC-CAAAACTT
1 TTCCAAAATTACATTTTAACCCTC-AAACTT
*
8973 TTCTAAAATTACATTTTAACCCCTCAAACTT
1 TTCCAAAATTACATTTTAA-CCCTCAAACTT
* * *
9004 TTCC-AAATCATATTTTTACCC-CTAAA-TT
1 TTCCAAAATTACATTTTAACCCTC-AAACTT
*
9032 CTTCCAAAATCACATTTTAACCCTCAAACTT
1 -TTCCAAAATTACATTTTAACCCTCAAACTT
* * *
9063 CTCTAAAATTTCATTTT
1 TTCCAAAATTACATTTT
9080 CATATCGAGT
Statistics
Matches: 282, Mismatches: 43, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
28 14 0.05
29 90 0.32
30 154 0.55
31 23 0.08
32 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
TTCCAAAATTACATTTTAACCCTCAAACTT
Found at i:15292 original size:49 final size:49
Alignment explanation
Indices: 15192--15883 Score: 434
Period size: 49 Copynumber: 14.1 Consensus size: 49
15182 AGGTTTCATA
* * *
15192 ACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGTGAA--TTCAGT
1 ACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTT--GT
* * *
15241 ACCATGAAGATATGGAA-GGAAAGGTTTAAGTCGCAATGGCAAACCTTGT
1 ACCATGAAGATAT-GAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* * * * * *
15290 ACC-TCAGAA-ACATGAAGGGAAATATTTAAGCCGCAACGACGAATCTAGT
1 ACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* * * * * * *
15339 ACCACGAGGACATGGAGGGAATGGTTTAAGTCACAACGGCGAACCTTGT
1 ACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* * * * * *
15388 ACC-T-CAGAATCATGAAGGGAAAGATTTAAGCCGTAATGGCGAATCTAGT
1 ACCATGAAG-AT-ATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* *
15437 ACCACGAAGATATGGAGGGAAAGATTTAAGT-GTTCAACGGCGAACCTTGT
1 ACCATGAAGATATGAAGGGAAAGATTTAAGTCG--CAACGGCGAACCTTGT
* * * * *
15487 ACC-TCAGAA-ACATGAAGGGAAAGATTTAAGTCGCAACGACAAATCTAGT
1 ACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* * * *
15536 ACCACGAAGATATGGAGAGAAAAGGTTTAAGTCGCAACGGCGAACCTTGT
1 ACCATGAAGATATGAAG-GGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* * * * * * *
15586 ACC-TCAGAAG-CATGAATGGAAAGATCTAAGCCGCAATGGCGAATCC-AGC
1 ACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGT
* * *
15635 ACCACGAAGATAAGAAGGGAAA-ATGTTTAAATCGCAACGGCGAACCTTGT
1 ACCATGAAGATATGAAGGGAAAGA--TTTAAGTCGCAACGGCGAACCTTGT
* * * *
15685 ACC-TCAGAAG-CATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCC-GGT
1 ACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGT
* * * * *
15734 ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTAT
1 ACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* * * * *
15783 ACC-TCAGAAG-CATGAAGGGAAAGATTTAAGCCTCAACGGCGAATCTAGT
1 ACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
* * * * * **
15832 ACCACGAAGATTTAAAAGGAAATG-TTTAAGTCGCAATGATGAACCTTGT
1 ACCATGAAGATATGAAGGGAAA-GATTTAAGTCGCAACGGCGAACCTTGT
15881 ACC
1 ACC
15884 TCAGAAACAT
Statistics
Matches: 481, Mismatches: 122, Indels: 80
0.70 0.18 0.12
Matches are distributed among these distances:
47 1 0.00
48 26 0.05
49 323 0.67
50 114 0.24
51 17 0.04
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (49 bp):
ACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGT
Found at i:15515 original size:99 final size:98
Alignment explanation
Indices: 15203--15901 Score: 925
Period size: 98 Copynumber: 7.1 Consensus size: 98
15193 CCACGAAGAT
* * *
15203 ATGAAGGGAAAGATTTAAGCCGCAACGGTGAAT-TCAGTACCATGAAGATATGGAAGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCT-AGTACCACGAAGATATGGAGGGAAAGGTT
* *
15267 TAAGTCGCAATGGCAAACCTTGTACCTCAGAAAC
65 TAAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
* * * * *
15301 ATGAAGGGAAATATTTAAGCCGCAACGACGAATCTAGTACCACGAGGACATGGAGGGAATGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTT
* *
15366 AAGTCACAACGGCGAACCTTGTACCTCAGAATC
66 AAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
* * *
15399 ATGAAGGGAAAGATTTAAGCCGTAATGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGATTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTT
15464 AAGT-GTTCAACGGCGAACCTTGTACCTCAGAAAC
66 AAGTCG--CAACGGCGAACCTTGTACCTCAGAAAC
* * * *
15498 ATGAAGGGAAAGATTTAAGTCGCAACGACAAATCTAGTACCACGAAGATATGGAGAGAAAAGGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAG-GGAAAGGTT
*
15563 TAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
65 TAAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
* * * * * * * *
15597 ATGAATGGAAAGATCTAAGCCGCAATGGCGAATCCAGCACCACGAAGATAAGAAGGGAAAATGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGG-AAAGGTT
* *
15662 TAAATCGCAACGGCGAACCTTGTACCTCAGAAGC
65 TAAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
* **
15696 ATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCGGTACCACGAAGATATGGAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTT
* * *
15761 AAGTCGCAACGGTGAACCTTATACCTCAGAAGC
66 AAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
* * ** * *
15794 ATGAAGGGAAAGATTTAAGCCTCAACGGCGAATCTAGTACCACGAAGATTTAAAAGGAAATGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTT
* **
15859 AAGTCGCAATGATGAACCTTGTACCTCAGAAAC
66 AAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
*
15892 ATAAAGGGAA
1 ATGAAGGGAA
15902 GGTTGAGGCC
Statistics
Matches: 528, Mismatches: 67, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
98 277 0.52
99 238 0.45
100 12 0.02
101 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTT
AAGTCGCAACGGCGAACCTTGTACCTCAGAAAC
Found at i:16868 original size:24 final size:24
Alignment explanation
Indices: 16818--16865 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16808 TCAAATGACC
* *
16818 CAAACACTAAGCCCAATTCTTAAA
1 CAAACACTAAACCCAATTCCTAAA
*
16842 CAAACCCTAAACCCAATTACCTAA
1 CAAACACTAAACCCAATT-CCTAA
16866 CAAGCCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (24 bp):
CAAACACTAAACCCAATTCCTAAA
Found at i:18430 original size:30 final size:29
Alignment explanation
Indices: 18333--18604 Score: 260
Period size: 30 Copynumber: 9.1 Consensus size: 29
18323 CCAAGAAGGA
* * *
18333 CCCCAAACCTTTCAAAATTACATTTTTTA-
1 CCCCAAACTTTTCAAAATCACA-TTTTAAC
* * * *
18362 CACTAAACTTTCTAAAAATCATAATTTT-AC
1 CCCCAAACTTT-TCAAAATCA-CATTTTAAC
** * *
18392 CCTTAAACTTTCTAAAAATAACATTTTAAC
1 CCCCAAACTTT-TCAAAATCACATTTTAAC
*
18422 CCCCAAACTTTTTCAAAATTACATTTTAAC
1 CCCCAAAC-TTTTCAAAATCACATTTTAAC
*
18452 CCCCAAACTTTTCCAAAATTACATTTTAAC
1 CCCCAAACTTTT-CAAAATCACATTTTAAC
* * *
18482 CCATCAAACTTTTCCAAATCATATTTTAAC
1 CC-CCAAACTTTTCAAAATCACATTTTAAC
*
18512 CCCCAAACTTTTCCAAAATTACATTTTAAC
1 CCCCAAACTTTT-CAAAATCACATTTTAAC
*
18542 CCCTCAAACTTTTCCAAAATCATATTTTAAC
1 CCC-CAAACTTTT-CAAAATCACATTTTAAC
*
18573 CCCTAAACTTTTCAAAAATCACATTTTAAC
1 CCCCAAACTTTTC-AAAATCACATTTTAAC
18603 CC
1 CC
18605 TCGAACTTCT
Statistics
Matches: 207, Mismatches: 26, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
29 28 0.14
30 138 0.67
31 41 0.20
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (29 bp):
CCCCAAACTTTTCAAAATCACATTTTAAC
Found at i:18606 original size:60 final size:60
Alignment explanation
Indices: 18333--18621 Score: 320
Period size: 60 Copynumber: 4.8 Consensus size: 60
18323 CCAAGAAGGA
* * * *
18333 CCCCAAACCTTTC-AAAATTACATTTTTTACACT-AAAC-TTTCTAAAAATCATAATTTT-AC
1 CCCCAAACTTTTCAAAAATTACA-TTTTAACCCTCAAACTTTTC-CAAAATCAT-ATTTTAAC
** * * * * *
18392 CCTTAAAC-TTTCTAAAAATAACATTTTAACCCCCAAACTTTTTCAAAATTACATTTTAAC
1 CCCCAAACTTTTC-AAAAATTACATTTTAACCCTCAAACTTTTCCAAAATCATATTTTAAC
*
18452 CCCCAAACTTTTCCAAAATTACATTTTAACCCATCAAACTTTTCC-AAATCATATTTTAAC
1 CCCCAAACTTTTCAAAAATTACATTTTAACCC-TCAAACTTTTCCAAAATCATATTTTAAC
*
18512 CCCCAAACTTTTCCAAAATTACATTTTAACCCCTCAAACTTTTCCAAAATCATATTTTAAC
1 CCCCAAACTTTTCAAAAATTACATTTTAA-CCCTCAAACTTTTCCAAAATCATATTTTAAC
* * * * *
18573 CCCTAAACTTTTCAAAAATCACATTTTAACCCTCGAACTTCTCTAAAAT
1 CCCCAAACTTTTCAAAAATTACATTTTAACCCTCAAACTTTTCCAAAAT
18622 TTCATTTTCA
Statistics
Matches: 197, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
58 4 0.02
59 18 0.09
60 114 0.58
61 61 0.31
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (60 bp):
CCCCAAACTTTTCAAAAATTACATTTTAACCCTCAAACTTTTCCAAAATCATATTTTAAC
Found at i:18628 original size:30 final size:30
Alignment explanation
Indices: 18406--18629 Score: 288
Period size: 30 Copynumber: 7.4 Consensus size: 30
18396 AAACTTTCTA
* *
18406 AAAATAACATTTTAACCCCCAAACTTTTTC
1 AAAATTACATTTTAACCCCCAAACTTTTCC
18436 AAAATTACATTTTAACCCCCAAACTTTTCC
1 AAAATTACATTTTAACCCCCAAACTTTTCC
*
18466 AAAATTACATTTTAACCCATCAAACTTTTCC
1 AAAATTACATTTTAACCC-CCAAACTTTTCC
* *
18497 -AAATCATATTTTAACCCCCAAACTTTTCC
1 AAAATTACATTTTAACCCCCAAACTTTTCC
18526 AAAATTACATTTTAACCCCTCAAACTTTTCC
1 AAAATTACATTTTAACCCC-CAAACTTTTCC
* * * *
18557 AAAATCATATTTTAACCCCTAAACTTTTCA
1 AAAATTACATTTTAACCCCCAAACTTTTCC
* * * * *
18587 AAAATCACATTTTAACCCTCGAACTTCTCT
1 AAAATTACATTTTAACCCCCAAACTTTTCC
*
18617 AAAATTTCATTTT
1 AAAATTACATTTT
18630 CATCCCAAGT
Statistics
Matches: 171, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.06
30 121 0.71
31 39 0.23
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCCAAACTTTTCC
Found at i:20445 original size:15 final size:15
Alignment explanation
Indices: 20415--20444 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
20405 CGTATTTCAA
20415 TGGAAAAGTTAATTT
1 TGGAAAAGTTAATTT
20430 TGGAAAA-TTAATTT
1 TGGAAAAGTTAATTT
20444 T
1 T
20445 TATTTGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (15 bp):
TGGAAAAGTTAATTT
Found at i:21834 original size:29 final size:31
Alignment explanation
Indices: 21751--21837 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 31
21741 ATTAAATCAA
* * * *
21751 AATTAAAGTTTGAAGTATACATTTGAACCAT
1 AATTAAAGTTTCACGTATACAATTGCACCAT
* *
21782 AATTAAAGTTTCACGTGTATAATTGCACCA-
1 AATTAAAGTTTCACGTATACAATTGCACCAT
* *
21812 AATTTAAG-TTCATGTATACAATTGCA
1 AATTAAAGTTTCACGTATACAATTGCA
21838 TATTAAATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
29 15 0.33
30 7 0.15
31 24 0.52
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (31 bp):
AATTAAAGTTTCACGTATACAATTGCACCAT
Found at i:23148 original size:25 final size:24
Alignment explanation
Indices: 23107--23167 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
23097 ACATTTTAAT
*
23107 ATATTATTAAAAAAAATTTATATTA
1 ATATT-TTAAAAAAAATATATATTA
*
23132 ATATTTTAATAATAAATATATATTA
1 ATATTTTAA-AAAAAATATATATTA
*
23157 AAATTTATAAA
1 ATATTT-TAAA
23168 TATTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 4 0.13
25 24 0.77
26 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATTTTAAAAAAAATATATATTA
Found at i:23506 original size:18 final size:18
Alignment explanation
Indices: 23470--23508 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23460 AAATAATTTT
*
23470 AAAAAATACCAAATAAAA
1 AAAAAATACCAAACAAAA
23488 AAAAAAT-CCAAACACAAA
1 AAAAAATACCAAACA-AAA
23506 AAA
1 AAA
23509 TTATCAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.77, C:0.15, G:0.00, T:0.08
Consensus pattern (18 bp):
AAAAAATACCAAACAAAA
Found at i:23843 original size:29 final size:30
Alignment explanation
Indices: 23811--23868 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
23801 AATAGTTTAA
23811 TGTGCAATTATATACATG-AACTTTGATTT
1 TGTGCAATTATATACATGAAACTTTGATTT
* * *
23840 TGTGTAATTGTATACATGAAATTTTGATT
1 TGTGCAATTATATACATGAAACTTTGATT
23869 CGATCACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (30 bp):
TGTGCAATTATATACATGAAACTTTGATTT
Found at i:24064 original size:33 final size:30
Alignment explanation
Indices: 24021--24083 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
24011 AAAATTAAAA
24021 TTTCAAGTATACATT-TGAACCACAATTAAAGTT
1 TTTCAAGTATA-ATTCT--ACCA-AATTAAAGTT
*
24054 TTTCATGTATAATTCTACCAAATTAAAGTT
1 TTTCAAGTATAATTCTACCAAATTAAAGTT
24084 CACGTACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 10 0.36
31 4 0.14
32 3 0.11
33 11 0.39
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (30 bp):
TTTCAAGTATAATTCTACCAAATTAAAGTT
Found at i:24370 original size:23 final size:22
Alignment explanation
Indices: 24334--24382 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
24324 CTAATTTCTG
*
24334 AATTTTTGTAAAATATAAGAATAA
1 AATTTTGGTAAAAT-TAA-AATAA
*
24358 AATTTTGGT-AAATTAAAGTAA
1 AATTTTGGTAAAATTAAAATAA
24379 AATT
1 AATT
24383 AATTTCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 4 0.17
24 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
AATTTTGGTAAAATTAAAATAA
Done.