Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005493.1 Kokia drynarioides strain JFW-HI SEQ_119555, 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: 9012
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:550 original size:29 final size:30
Alignment explanation
Indices: 505--832 Score: 383
Period size: 30 Copynumber: 11.1 Consensus size: 30
495 CCTTGGAGGT
505 CCCT-AAACTATCCAAAAATTCCATTTTT-A
1 CCCTCAAACT-TCCAAAAATTCCATTTTTGA
*
534 CCCTCAAACTTCTAAAAATTCCATTTTTTGA
1 CCCTCAAACTTCCAAAAATTCCA-TTTTTGA
* * * *
565 CCATAAAACTTCCAAAAAATCCAATTTT-A
1 CCCTCAAACTTCCAAAAATTCCATTTTTGA
594 CCC-CTAAACTTCCAAAAATTCCATTTTTGA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTGA
* *
624 CCCTAAAACTCCCAAAAATTCCATTTTT-A
1 CCCTCAAACTTCCAAAAATTCCATTTTTGA
653 CCCTCAAACTTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTTGA
683 -CCTCGAAACTTCCAAAAATTCCATTTTT-A
1 CCCTC-AAACTTCCAAAAATTCCATTTTTGA
* *
712 CCCCCGAACTTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTTGA
*
742 CCC-CAAAACTTCCAAAAATTCCATTTTTAA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTGA
772 CCC-CAAAACTTCCAAAAATTACCA-TTTT-A
1 CCCTC-AAACTTCCAAAAATT-CCATTTTTGA
* * *
801 CCCCCGAA-TGTCCAAAAACTCCATTTTTGA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTGA
831 CC
1 CC
833 ACAAAACTCT
Statistics
Matches: 263, Mismatches: 20, Indels: 31
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.02
29 114 0.43
30 122 0.46
31 23 0.09
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (30 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTGA
Found at i:804 original size:59 final size:58
Alignment explanation
Indices: 509--837 Score: 412
Period size: 59 Copynumber: 5.5 Consensus size: 58
499 GGAGGTCCCT
* **
509 AAACTATCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATTCCATTTTTTGACCATA
1 AAACT-TCCAAAAATTCCATTTTTACCC-CAAACTTCCAAAAATTCCA-TTTTTGACCCCA
* * *
570 AAACTTCCAAAAAATCCAATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCC-AAACTTCCAAAAATTCCATTTTTGACCCCA
* * *
629 AAACTCCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CAAACTTCCAAAAATTCCATTTTTGACCCCA
*
688 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTA-CCCCAAACTTCCAAAAATTCCATTTTTGACCCCA
*
747 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCA-TTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCC-AAACTTCCAAAAATT-CCATTTTTGACCCCA
* * *
806 GAA-TGTCCAAAAACTCCATTTTTGACCACAAA
1 AAACT-TCCAAAAATTCCATTTTT-ACCCCAAA
838 ACTCTCAAAA
Statistics
Matches: 241, Mismatches: 20, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
58 4 0.02
59 169 0.70
60 60 0.25
61 8 0.03
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAAACTTCCAAAAATTCCATTTTTGACCCCA
Found at i:847 original size:89 final size:88
Alignment explanation
Indices: 509--840 Score: 420
Period size: 89 Copynumber: 3.7 Consensus size: 88
499 GGAGGTCCCT
* * *
509 AAACTATCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATTCCATTTTTTGACCATAAAAC
1 AAACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTTGACCACAAAAC
* * *
574 TTCCAAAAAATCCAATTTTACCCCT
64 TTCCAAAAATTCCATTTTTACCCCA
** * *
599 AAACTTCCAAAAATTCCATTTTTGACCCTAAAACTCCCAAAAATTCCATTTTT-ACC-CTCAAAC
1 AAACTTCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTGACCAC-AAAAC
* *
662 TTCCAAAAATTCCATTTTTGACCTCG
64 TTCCAAAAATTCCATTTTT-ACCCCA
* *
688 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCACAAAACTT
753 CCAAAAATTCCATTTTTAACCCCA
66 CCAAAAATTCCATTTTT-ACCCCA
* *
777 AAACTTCCAAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAACTCCATTTTTGACCACAAAAC
1 AAACTTCCAAAAATT-CCATTTTTACCCCCAAACT-TCCAAAAATTCCATTTTTGACCACAAAAC
840 T
64 T
841 CTCAAAATTA
Statistics
Matches: 216, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
88 50 0.23
89 136 0.63
90 30 0.14
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (88 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCACAAAACTT
CCAAAAATTCCATTTTTACCCCA
Found at i:876 original size:58 final size:59
Alignment explanation
Indices: 515--920 Score: 223
Period size: 59 Copynumber: 6.9 Consensus size: 59
505 CCCTAAACTA
* * * ****
515 TCCAAAAATTCCATTTTTACCCTC-AAACTTCTAAAAATT-CCATTTTTTGACCATAAAACT-
1 TCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATTACCA--TTTT-ACCCCCGAA-TG
* * * * ***
575 TCCAAAAAATCCAATTTT-ACCCCTAAACTTCCAAAAATT-CCATTTTTGACCCTAAAACT-
1 TCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATTACCA-TTTT-ACCCCCGAA-TG
* * * *
634 CCCAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATT-CCATTTTTGA-CCTCGAAACT-
1 TCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATTACCA-TTTT-ACCCCCG-AA-TG
* ** **
693 TCCAAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAATT-CCATTTTTGACCCCAAAACT-
1 TCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATTACCA-TTTT-ACCCCCGAA-TG
*
752 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCCCGAATG
1 TCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATTACCATTTTACCCCCGAATG
* * * **
811 TCCAAAAACTCCATTTTTGACCACAAAAC-TCTC-AAAATTACCCA-TTTACTCTTGAATG
1 TCCAAAAATTCCATTTTTAACCACAAAACTTC-CAAAAATTA-CCATTTTACCCCCGAATG
* * * * ** * *
869 TCTAAAAATTCCGTTTTTAACCTCGAATTTTCCTAAAATTACCATTTCACCC
1 TCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATTACCATTTTACCC
921 TCTATAATCC
Statistics
Matches: 293, Mismatches: 40, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
58 52 0.18
59 177 0.60
60 61 0.21
61 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTAACCACAAAACTTCCAAAAATTACCATTTTACCCCCGAATG
Found at i:2276 original size:58 final size:58
Alignment explanation
Indices: 2205--2589 Score: 317
Period size: 58 Copynumber: 6.6 Consensus size: 58
2195 ATCCGAGGGA
* * * * * * * *
2205 AAAAAGGTAATTTTGGGAAAATTCGGGGTTAAAAACGGAATTTTAGGCA-TTCGGGAGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGG-GT
* ** * *
2263 AAAATGGTAATTTTTGAAAAGAATCG-GGATCAAAAAT-GAATTTTTTTTTAAGTTTGGGAAT
1 AAAATGGTAATTTTTGGAAA-AATCGAGG-TCAAAAATGGAA--TTTTTGGAAGTTCGGG-GT
* * *
2324 AAAATGGTAA-TTTAGGAAGAATCGAGGTCAAAAATGGAATTTTGGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGT
*
2382 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAA-TTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGT
*** * * *
2440 AAAATGGTAATTTTCAAAAAAAATCAAGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAATGGTAATTTT-TGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAG-TTCGGGGT
* *
2500 AAAATGGTAATTTTTGG-AAAA--G-GGT-TAAAATGGAA-TTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGG-AAG-TTCGGGGT
** *
2554 AAAAAT-GTAATTTTTGGAAAGTTTGAGGTCAAAAAT
1 -AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
2590 ATACTTTTGG
Statistics
Matches: 270, Mismatches: 37, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
53 6 0.02
54 32 0.12
55 10 0.04
57 1 0.00
58 79 0.29
59 79 0.29
60 44 0.16
61 19 0.07
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGT
Found at i:2298 original size:59 final size:59
Alignment explanation
Indices: 2235--2521 Score: 282
Period size: 59 Copynumber: 4.8 Consensus size: 59
2225 ATTCGGGGTT
* * * *
2235 AAAAACGGAATTTTAGGCA-TTCGGGAGTAAAATGGTAATTTTTGAAAAGAATC-GGGATC
1 AAAAATGGAATTTTTGGAAGTTCGGG-GTAAAATGGTAATTTTTGAAAAGAATCAAGG-TC
** * * * * *
2294 AAAAAT-GAATTTTTTTTTAAGTTTGGGAATAAAATGGTAA-TTTAG-GAAGAATCGAGGTC
1 AAAAATGGAA--TTTTTGGAAGTTCGGG-GTAAAATGGTAATTTTTGAAAAGAATCAAGGTC
* *
2353 AAAAATGGAATTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAA-AATCAAGGTC
1 AAAAATGGAATTTTTGGAAGTTCG-GGGTAAAATGGTAATTTTTGAAAAGAATCAAGGTC
** * *
2412 AAAAATGGAA-TTTTGGAAGTTCGGGGGTAAAATGGTAATTTTCAAAAAAAATCAAGGTT
1 AAAAATGGAATTTTTGGAAGTTC-GGGGTAAAATGGTAATTTTTGAAAAGAATCAAGGTC
*
2471 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAG
1 AAAAATGGAATTTTTGGAAG-TTCGGGGTAAAATGGTAATTTTT-GAAAAG
2522 GGTTAAAATG
Statistics
Matches: 188, Mismatches: 27, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
58 56 0.30
59 65 0.35
60 44 0.23
61 23 0.12
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.31
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGTAAAATGGTAATTTTTGAAAAGAATCAAGGTC
Found at i:2335 original size:119 final size:117
Alignment explanation
Indices: 2201--2425 Score: 280
Period size: 118 Copynumber: 1.9 Consensus size: 117
2191 AGGTATCCGA
* * * *
2201 GGGAAAAAAGGTAATTTTGGGAA-AATTCGGGGTTAAAAACGGAATTTTAGGCA-TTCG-GGAGT
1 GGGAAAAAAGGTAA-TTTAGGAAGAA-TCGAGGTCAAAAACGGAATTTTAGGAAGTTCGAGG-GT
*
2263 AAAATGGTAATTTTTGAAAAGAATC-GGGATCAAAAAT-GAATTTTTTTTTAAGTTT
63 AAAATGGTAATTTTTGAAAA-AATCAAGG-TCAAAAATGGAATTTTTTTTTAAGTTT
* *
2318 GGGAATAAAATGGTAATTTAGGAAGAATCGAGGTCAAAAATGGAATTTTGGGAAGTTCGAGGGTA
1 GGGAA-AAAA-GGTAATTTAGGAAGAATCGAGGTCAAAAACGGAATTTTAGGAAGTTCGAGGGTA
*
2383 AAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTT
64 AAATGGTAATTTTTGAAAAAATCAAGGTCAAAAATGGAATTTT
2426 GGAAGTTCGG
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
117 5 0.05
118 45 0.48
119 41 0.44
120 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (117 bp):
GGGAAAAAAGGTAATTTAGGAAGAATCGAGGTCAAAAACGGAATTTTAGGAAGTTCGAGGGTAAA
ATGGTAATTTTTGAAAAAATCAAGGTCAAAAATGGAATTTTTTTTTAAGTTT
Found at i:2356 original size:29 final size:28
Alignment explanation
Indices: 2324--2453 Score: 106
Period size: 30 Copynumber: 4.5 Consensus size: 28
2314 GTTTGGGAAT
*
2324 AAAATGGTAATTTAGGAAGAATCGAGGTCA
1 AAAATGGTAATTTTGGAAG-ATCGAGGT-A
*
2354 AAAATGG-AATTTTGGGAAGTTCGAGGGT-
1 AAAATGGTAATTTT-GGAAGATCGA-GGTA
* *
2382 AAAATGGTAATTTTTGGAAAAATCAAGGTCA
1 AAAATGGTAA-TTTTGG-AAGATCGAGGT-A
* *
2413 AAAATGG-AATTTTGGAAGTTCGGGGGT-
1 AAAATGGTAATTTTGGAAGATC-GAGGTA
2440 AAAATGGTAATTTT
1 AAAATGGTAATTTT
2454 CAAAAAAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
27 7 0.09
28 17 0.21
29 25 0.30
30 26 0.32
31 7 0.09
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAGATCGAGGTA
Found at i:2358 original size:30 final size:30
Alignment explanation
Indices: 2324--2490 Score: 107
Period size: 29 Copynumber: 5.6 Consensus size: 30
2314 GTTTGGGAAT
*
2324 AAAATGGTAA-TTTAGGAAGAATCGAGGTCA
1 AAAATGG-AATTTTTGGAAGAATCGAGGTCA
* *
2354 AAAATGGAATTTTGGGAAG-TTCGAGGGT--
1 AAAATGGAATTTTTGGAAGAATCGA-GGTCA
* *
2382 AAAATGGTAATTTTTGGAAAAATCAAGGTCA
1 AAAATGG-AATTTTTGGAAGAATCGAGGTCA
* *
2413 AAAATGGAA-TTTTGGAAG-TTCGGGGGT--
1 AAAATGGAATTTTTGGAAGAATC-GAGGTCA
*** * * *
2440 AAAATGGTAATTTTCAAAAAAAATCAAGGTTA
1 AAAATGG-AATTTT-TGGAAGAATCGAGGTCA
2472 AAAATGGAATTTTTGGAAG
1 AAAATGGAATTTTTGGAAG
2491 TTTAGGGGTA
Statistics
Matches: 103, Mismatches: 21, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
27 7 0.07
28 11 0.11
29 33 0.32
30 30 0.29
31 15 0.15
32 7 0.07
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGAATCGAGGTCA
Found at i:2478 original size:118 final size:116
Alignment explanation
Indices: 2231--2520 Score: 311
Period size: 118 Copynumber: 2.5 Consensus size: 116
2221 GAAAATTCGG
* * * *
2231 GGTTAAAAACGGAATTTTAGGCA-TTCG-GGAGTAAAATGGTAATTTTTGAAAAGAATCGGGATC
1 GGTTAAAAATGGAATTTTAGGAAGTTCGAGG-GTAAAATGGTAATTTTTGGAAA-AATCAGGATC
** * ** * *
2294 AAAAATGAATTTTTTTTTAAGTTTGGGAATAAAATGGTAATTTAGGAAGAATCGA
64 AAAAATGAA--TTTTTGGAAGTTCGGGAATAAAATGGTAATTTAAAAAAAATCAA
* *
2349 GGTCAAAAATGGAATTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCAAGG-TCA
1 GGTTAAAAATGGAATTTTAGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATC-AGGATCA
**
2413 AAAATGGAA-TTTTGGAAGTTCGGGGGTAAAATGGTAATTTTCAAAAAAAATCAA
65 AAAAT-GAATTTTTGGAAGTTCGGGAATAAAATGGTAA-TTT-AAAAAAAATCAA
* *
2467 GGTTAAAAATGGAATTTTTGGAAGTT-TAGGGGTAAAATGGTAATTTTTGGAAAA
1 GGTTAAAAATGGAATTTTAGGAAGTTCGA-GGGTAAAATGGTAATTTTTGGAAAA
2521 GGGTTAAAAT
Statistics
Matches: 147, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
116 23 0.16
117 4 0.03
118 88 0.60
119 30 0.20
120 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.31
Consensus pattern (116 bp):
GGTTAAAAATGGAATTTTAGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCAGGATCAA
AAATGAATTTTTGGAAGTTCGGGAATAAAATGGTAATTTAAAAAAAATCAA
Found at i:2587 original size:29 final size:30
Alignment explanation
Indices: 2472--2669 Score: 159
Period size: 29 Copynumber: 6.9 Consensus size: 30
2462 ATCAAGGTTA
*
2472 AAAATGGAATTTTTGG-AAGTTTAGGGGT-
1 AAAATGTAATTTTTGGAAAGTTTAGGGGTC
*
2500 AAAATGGTAATTTTTGGAAA----A-GGGTT
1 AAAAT-GTAATTTTTGGAAAGTTTAGGGGTC
* *
2526 AAAATGGAA-TTTTGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAAGTTTAGGGGTC
*
2555 AAAATGTAATTTTTGGAAAGTTT-GAGGTC
1 AAAATGTAATTTTTGGAAAGTTTAGGGGTC
* * *
2584 AAAA-ATATACTTTTGGAGAAGTTTA-GGCTC
1 AAAATGTA-ATTTTTGGA-AAGTTTAGGGGTC
*
2614 AAAATATAA-TTTTGGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTTGG-AAAGTTTAGGGGTC
* * **
2644 AAAATATGATTTTTGGGCAGTTTAGG
1 AAAATGTAATTTTTGGAAAGTTTAGG
2670 CTCTCTCCCT
Statistics
Matches: 140, Mismatches: 14, Indels: 30
0.76 0.08 0.16
Matches are distributed among these distances:
24 9 0.06
25 7 0.05
26 6 0.04
28 8 0.06
29 51 0.36
30 50 0.36
31 9 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTAGGGGTC
Found at i:2618 original size:59 final size:60
Alignment explanation
Indices: 2535--2672 Score: 160
Period size: 59 Copynumber: 2.3 Consensus size: 60
2525 TAAAATGGAA
* * *
2535 TTTTGGA-AAGTTTAGGGGTAAAAATGTAATTTTTGG-AAAGTTT-GAGGTCAAAAATAT-AC
1 TTTTGGAGAAGTTTA-GGCTCAAAATATAA-TTTTGGAAAAGTTTAGAGGTC-AAAATATGAC
* *
2594 TTTTGGAGAAGTTTAGGCTCAAAATATAATTTTGGAAAAGTTTAGGGGTCAAAATATGAT
1 TTTTGGAGAAGTTTAGGCTCAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAATATGAC
*
2654 TTTTGG-GCAGTTTAGGCTC
1 TTTTGGAGAAGTTTAGGCTC
2673 TCTCCCTCTC
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
58 6 0.09
59 44 0.64
60 19 0.28
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (60 bp):
TTTTGGAGAAGTTTAGGCTCAAAATATAATTTTGGAAAAGTTTAGAGGTCAAAATATGAC
Found at i:5522 original size:31 final size:30
Alignment explanation
Indices: 5448--5528 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 30
5438 ATCTTAGAAG
* * *
5448 TATACTTGAAATTTTAATTTGGTGTAATTA
1 TATATTTGAAATTTTAATTTAGTGTAAATA
* * *
5478 TACATGTGAAATTTTAATTATAGTTTAAATA
1 TATATTTGAAATTTTAATT-TAGTGTAAATA
5509 TATATTTGAAATTTTAATTT
1 TATATTTGAAATTTTAATTT
5529 TGATTTAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 17 0.40
31 25 0.60
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (30 bp):
TATATTTGAAATTTTAATTTAGTGTAAATA
Found at i:6417 original size:23 final size:24
Alignment explanation
Indices: 6336--6424 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 24
6326 ATTAGAAAAT
*
6336 ATATAATTTTATATATTATGTTAA
1 ATATTATTTTATATATTATGTTAA
* * * * *
6360 ATAATATGTAATTATATAATG-AAA
1 ATATTATTTTA-TATATTATGTTAA
6384 ATATATAATTTTATATATTATGTTAA
1 ATAT-T-ATTTTATATATTATGTTAA
6410 A-ATTATTTTAT-TATT
1 ATATTATTTTATATATT
6425 CAAAAGCATC
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
22 4 0.08
23 7 0.14
24 13 0.26
25 19 0.38
26 7 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
ATATTATTTTATATATTATGTTAA
Found at i:8755 original size:18 final size:18
Alignment explanation
Indices: 8728--8770 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
8718 AGTTTATTTT
8728 ATTT-TTATT-AATTTACA
1 ATTTATTATTAAATTTA-A
8745 ATTTATTATTAAATTTAA
1 ATTTATTATTAAATTTAA
8763 ATTGTATT
1 ATT-TATT
8771 TATATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTATTATTAAATTTAA
Found at i:8871 original size:24 final size:25
Alignment explanation
Indices: 8839--8891 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
8829 TGTGTGCTTA
*
8839 ATATTTTATCAAAATTTA-TAT-AAT
1 ATATCTTAT-AAAATTTATTATAAAT
*
8863 ATATCTTATAAATTTTATTATAAAT
1 ATATCTTATAAAATTTATTATAAAT
8888 ATAT
1 ATAT
8892 AATACACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 11 0.44
25 7 0.28
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATCTTATAAAATTTATTATAAAT
Done.