Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015284.1 Kokia drynarioides strain JFW-HI SEQ_130329, 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: 395889
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 520 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:319396 original size:27 final size:26
Alignment explanation
Indices: 319345--319427 Score: 69
Period size: 31 Copynumber: 3.0 Consensus size: 26
319335 TGAATCTGAC
* *
319345 TTTTTTTTCTAATTTGATA-TCTAAAA
1 TTTTTTTTTTAATTTGGTACT-TAAAA
*
319371 TTTTTTGTTTTAATTTGGTACTTAAAC
1 TTTTTT-TTTTAATTTGGTACTTAAAA
319398 TTGATACTTTTTTTAAATTTGGTACTTAAA
1 TT--T--TTTTTTT-AATTTGGTACTTAAA
319428 CTTAACACTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 6 0.13
27 17 0.36
28 1 0.02
29 1 0.02
30 4 0.09
31 18 0.38
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (26 bp):
TTTTTTTTTTAATTTGGTACTTAAAA
Found at i:319420 original size:31 final size:31
Alignment explanation
Indices: 319378--319461 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
319368 AAATTTTTTG
* *
319378 TTTTAATTTGGTACTTAAACTTGATACTTT-
1 TTTTAATTTGGTACTTAAACTTAACACTTTA
319408 TTTTAAATTTGGTACTTAAACTTAACACTTTA
1 TTTT-AATTTGGTACTTAAACTTAACACTTTA
*
319440 TTTTAAGTTGGTACTTAAACTT
1 TTTTAATTTGGTACTTAAACTT
319462 TTTGGTGTCC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
30 4 0.08
31 41 0.84
32 4 0.08
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.50
Consensus pattern (31 bp):
TTTTAATTTGGTACTTAAACTTAACACTTTA
Found at i:319516 original size:24 final size:24
Alignment explanation
Indices: 319472--319520 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
319462 TTTGGTGTCC
* *
319472 AATTTGGTACTTGACTCTTTTTCT
1 AATTTGGTACATAACTCTTTTTCT
319496 AATTTGGTACATAA-TCTTTTT-T
1 AATTTGGTACATAACTCTTTTTCT
319518 AAT
1 AAT
319521 ATTAATTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 7 0.30
24 12 0.52
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.53
Consensus pattern (24 bp):
AATTTGGTACATAACTCTTTTTCT
Found at i:324828 original size:13 final size:13
Alignment explanation
Indices: 324810--324851 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
324800 TCGTAAAGTA
324810 TAGGGACTAATAG
1 TAGGGACTAATAG
324823 TAGGGACTAATAG
1 TAGGGACTAATAG
324836 TAGGGACTAATAG
1 TAGGGACTAATAG
324849 TAG
1 TAG
324852 AATTTAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.24
Consensus pattern (13 bp):
TAGGGACTAATAG
Found at i:335876 original size:18 final size:19
Alignment explanation
Indices: 335839--335877 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
335829 AATCTTTAGA
*
335839 TTTTTAAAAAAATTATAAT
1 TTTTTAAAAAAATTAAAAT
*
335858 TTTTTAAAAATA-TAAAAT
1 TTTTTAAAAAAATTAAAAT
335876 TT
1 TT
335878 AAAATTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTAAAAAAATTAAAAT
Found at i:339720 original size:23 final size:24
Alignment explanation
Indices: 339692--339863 Score: 167
Period size: 23 Copynumber: 7.4 Consensus size: 24
339682 TTTAGTTAAC
* *
339692 ATAAACGAACATGTGCG-GAACAT
1 ATAAACGAACATGTTCGCGAACGT
*
339715 ATAAACGAACATGTTCAG-AAACGT
1 ATAAACGAACATGTTC-GCGAACGT
* * *
339739 ATAAATGAACATGTTTGAGAACGT
1 ATAAACGAACATGTTCGCGAACGT
* *
339763 -TAGACGAACATGTTCTCGAACGT
1 ATAAACGAACATGTTCGCGAACGT
* *
339786 -TAAATGAACATGTTCGTGAACGT
1 ATAAACGAACATGTTCGCGAACGT
* **
339809 -TAAACCAACATGTTCGCGAATAT
1 ATAAACGAACATGTTCGCGAACGT
339832 ATAAACGAACATGTTCGCGAAC-T
1 ATAAACGAACATGTTCGCGAACGT
*
339855 CTAAACGAA
1 ATAAACGAA
339864 TCGAGCCTGA
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
23 80 0.65
24 43 0.35
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATAAACGAACATGTTCGCGAACGT
Found at i:339770 original size:47 final size:46
Alignment explanation
Indices: 339693--339863 Score: 150
Period size: 47 Copynumber: 3.7 Consensus size: 46
339683 TTAGTTAACA
* * *
339693 TAAACGAACATGTGCG-GAACATATAAACGAACATGTTC-AGAAACGT
1 TAAATGAACATGTTCGAGAACGT-TAAACGAACATGTTCTAG-AACGT
* * *
339739 ATAAATGAACATGTTTGAGAACGTTAGACGAACATGTTCTCGAACGT
1 -TAAATGAACATGTTCGAGAACGTTAAACGAACATGTTCTAGAACGT
* * ** **
339786 TAAATGAACATGTTCGTGAACGTTAAACCAACATGTTCGCGAATAT
1 TAAATGAACATGTTCGAGAACGTTAAACGAACATGTTCTAGAACGT
* *
339832 ATAAACGAACATGTTCGCGAAC-TCTAAACGAA
1 -TAAATGAACATGTTCGAGAACGT-TAAACGAA
339864 TCGAGCCTGA
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
46 40 0.38
47 58 0.56
48 6 0.06
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (46 bp):
TAAATGAACATGTTCGAGAACGTTAAACGAACATGTTCTAGAACGT
Found at i:343257 original size:16 final size:17
Alignment explanation
Indices: 343225--343257 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
343215 GAATCTTATA
343225 ATTTATTTATGTGTTTT
1 ATTTATTTATGTGTTTT
*
343242 ATTTTTTTAT-TGTTTT
1 ATTTATTTATGTGTTTT
343258 GCGATCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
ATTTATTTATGTGTTTT
Found at i:353482 original size:35 final size:35
Alignment explanation
Indices: 353442--353549 Score: 135
Period size: 35 Copynumber: 3.0 Consensus size: 35
353432 TCCAGTAGAT
*
353442 CTCTTCAAGATTCCCAATAATTTAACTCATCCGAG
1 CTCTTCAAGATTCCCAATAATTTAACTCATACGAG
* *
353477 TTCTTCAAGATTCCCAATAACTTAACTCATACGAG
1 CTCTTCAAGATTCCCAATAATTTAACTCATACGAG
* * * *
353512 CTCTTCTAGACTCCCAGTAATTTTTAACTCTTACGAG
1 CTCTTCAAGATTCCCAATAA--TTTAACTCATACGAG
353549 C
1 C
353550 CCAATCAGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 48 0.77
37 14 0.23
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (35 bp):
CTCTTCAAGATTCCCAATAATTTAACTCATACGAG
Found at i:355038 original size:6 final size:6
Alignment explanation
Indices: 355029--355094 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
355019 CAAATTTATT
** **
355029 TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
355077 TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
355095 GGATTTAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:355070 original size:17 final size:17
Alignment explanation
Indices: 355029--355094 Score: 87
Period size: 17 Copynumber: 3.8 Consensus size: 17
355019 CAAATTTATT
355029 TTTAAATTTAAATTTATC
1 TTTAAATTTAAATTTA-C
*
355047 TTTTAAATTTAAATTTGC
1 -TTTAAATTTAAATTTAC
*
355065 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAC
*
355082 TTAAAATTTAAAT
1 TTTAAATTTAAAT
355095 GGATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 27 0.63
18 1 0.02
19 15 0.35
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:355836 original size:22 final size:22
Alignment explanation
Indices: 355797--355933 Score: 98
Period size: 22 Copynumber: 6.0 Consensus size: 22
355787 TTTTCAATGT
* * * *
355797 ATATTAATTACAACAATAAGTA
1 ATATTAATAATAATAATAAATA
*
355819 ATATTAATAGTAATAATAGTTAATA
1 ATATTAATAATAATAATA---AATA
* *
355844 ATAATAATAACTATTTAATAAATA
1 ATATTAATAA-TA-ATAATAAATA
* *
355868 ATAATAATATTAATAATAAATA
1 ATATTAATAATAATAATAAATA
* *
355890 GTATTAATAAATATTAATAAA-A
1 ATATTAAT-AATAATAATAAATA
*
355912 ATATTAATAATAA-AATGAATA
1 ATATTAATAATAATAATAAATA
355933 A
1 A
355934 AAAAGTGAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
20 5 0.05
21 6 0.07
22 37 0.41
23 12 0.13
24 13 0.14
25 11 0.12
26 2 0.02
27 5 0.05
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATTAATAATAATAATAAATA
Found at i:355843 original size:16 final size:15
Alignment explanation
Indices: 355811--355923 Score: 76
Period size: 16 Copynumber: 7.7 Consensus size: 15
355801 TAATTACAAC
355811 AATAAGTAATATTAAT
1 AATAA-TAATATTAAT
*
355827 AGTAATAATAGTTAAT
1 AATAATAATA-TTAAT
*
355843 AATAATAATA--ACT
1 AATAATAATATTAAT
*
355856 -AT-TTAATA--AAT
1 AATAATAATATTAAT
355867 AATAATAATATTAAT
1 AATAATAATATTAAT
*
355882 AATAAATAGTATTAAT
1 AAT-AATAATATTAAT
* **
355898 AAATATTAATAAAAAT
1 -AATAATAATATTAAT
*
355914 ATTAATAATA
1 AATAATAATA
355924 AAATGAATAA
Statistics
Matches: 77, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
11 7 0.09
12 4 0.05
13 7 0.09
15 19 0.25
16 37 0.48
17 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (15 bp):
AATAATAATATTAAT
Found at i:355845 original size:3 final size:3
Alignment explanation
Indices: 355811--355933 Score: 77
Period size: 3 Copynumber: 38.7 Consensus size: 3
355801 TAATTACAAC
* * * *
355811 AAT AAGT AAT ATT AAT AGT AAT AAT AGTT AAT AAT AAT AAT AACT ATTT
1 AAT AA-T AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA-T A-AT
* * * *
355860 AAT AAAT AAT AAT AAT ATT AAT AAT AAAT AGT ATT AAT AAAT ATT AAT
1 AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT
* *
355908 AAA AAT ATT AAT AAT AA- AAT GAAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AA
355934 AAAAGTGAAA
Statistics
Matches: 92, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
2 2 0.02
3 69 0.75
4 21 0.23
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:355921 original size:12 final size:13
Alignment explanation
Indices: 355866--355925 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
355856 ATTTAATAAA
355866 TAATAAT-AATAT
1 TAATAATAAATAT
*
355878 TAATAATAAATAG
1 TAATAATAAATAT
*
355891 TATTAATAAATAT
1 TAATAATAAATAT
355904 TAATAA-AAATAT
1 TAATAATAAATAT
355916 TAATAATAAA
1 TAATAATAAA
355926 ATGAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
12 19 0.45
13 23 0.55
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAATAATAAATAT
Found at i:356720 original size:32 final size:32
Alignment explanation
Indices: 356658--356721 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
356648 TATTTATGCG
* *
356658 TTTAGTCCTTTCGCATTTTTTTATTGTTTTAA
1 TTTAGTCCTTTCGCATTTTTTAATTATTTTAA
* *
356690 TTTAGTCCTTTTGTA-TTTTTAATTAATTTTAA
1 TTTAGTCCTTTCGCATTTTTTAATT-ATTTTAA
356722 ATTGGCCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.20, C:0.09, G:0.08, T:0.62
Consensus pattern (32 bp):
TTTAGTCCTTTCGCATTTTTTAATTATTTTAA
Found at i:357035 original size:29 final size:29
Alignment explanation
Indices: 356993--357370 Score: 272
Period size: 29 Copynumber: 13.0 Consensus size: 29
356983 GGAGGTCCCT
*
356993 GAACTTCCAAAAATTCTATTTTTTACCCC
1 GAACTTCCAAAAATTCCATTTTTTACCCC
**
357022 GAACTTCCAAAAATTCCATTTTCGACCCC
1 GAACTTCCAAAAATTCCATTTTTTACCCC
*
357051 AAAACTTCCAAAAATTCCA-TTTTTACCCCC
1 -GAACTTCCAAAAATTCCATTTTTTA-CCCC
* **
357081 AAACTTCCAAAAATTCCATTTTCAACCCC
1 GAACTTCCAAAAATTCCATTTTTTACCCC
* *
357110 GAAACTTACAAAAATTACA-TTTTTACCCTC
1 G-AACTTCCAAAAATTCCATTTTTTACCC-C
*
357140 AAACTTCCAAAAATTCCA-TTTTTACCCCC
1 GAACTTCCAAAAATTCCATTTTTTA-CCCC
*
357169 GAACTTCCAAAAATTCCATTTTTGACCCC
1 GAACTTCCAAAAATTCCATTTTTTACCCC
** * *
357198 GAAACTTTTAAAAATT-C-TATTTTACCCTT
1 G-AACTTCCAAAAATTCCATTTTTTACCC-C
* ** **
357227 GAACTTTCAAAAATTCCATTTTCGACCTT
1 GAACTTCCAAAAATTCCATTTTTTACCCC
* * *
357256 GTAACTCCCAAAAATTCTA-TTTTTGCCCTC
1 G-AACTTCCAAAAATTCCATTTTTTACCC-C
* * * ** *
357286 GGA-TGTCCAAAAACTCTATTTTCGACCTC
1 GAACT-TCCAAAAATTCCATTTTTTACCCC
*
357315 GAAAC-TCCAAAAATTTCA--TTTTACCCC
1 G-AACTTCCAAAAATTCCATTTTTTACCCC
* * * *
357342 CAAATGTCTAAAAATTCCATTTTTAACCC
1 GAACT-TCCAAAAATTCCATTTTTTACCC
357371 TATTTTCCCC
Statistics
Matches: 273, Mismatches: 55, Indels: 41
0.74 0.15 0.11
Matches are distributed among these distances:
26 2 0.01
27 6 0.02
28 33 0.12
29 137 0.50
30 95 0.35
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
GAACTTCCAAAAATTCCATTTTTTACCCC
Found at i:357086 original size:59 final size:57
Alignment explanation
Indices: 356994--357248 Score: 296
Period size: 59 Copynumber: 4.4 Consensus size: 57
356984 GAGGTCCCTG
* *
356994 AACTTCCAAAAATTCTATTTTTTA-CCCCGAACTTCCAAAAATTCCATTTTCGACCCCAA
1 AACTTCCAAAAATTCCA-TTTTTACCCCCAAACTTCCAAAAATTCCATTTT--ACCCCAA
*
357053 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTCAACCCCGA
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTT--ACCCCAA
* * * **
357112 AACTTACAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCA-TTTTACCCCAA
* ** * ***
357170 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTTTAAAAATTCTATTTTACCCTTG
1 AACTTCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTACCCCAA
*
357228 AACTTTCAAAAATTCCATTTT
1 AACTTCCAAAAATTCCATTTT
357249 CGACCTTGTA
Statistics
Matches: 174, Mismatches: 19, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
58 60 0.34
59 110 0.63
60 4 0.02
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTACCCCAA
Found at i:357144 original size:88 final size:87
Alignment explanation
Indices: 356994--357370 Score: 342
Period size: 88 Copynumber: 4.3 Consensus size: 87
356984 GAGGTCCCTG
* * * *
356994 AACTTCCAAAAATTCTATTTTTTACCCCG-AACTTCCAAAAATTCCATTTTCGACCC-CAAAACT
1 AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTACAAAAATT-CATTTT-TACCCTC-AAACT
357057 TCCAAAAATTCCATTTTTACCCCCA
63 TCCAAAAATTCCATTTTTACCCCCA
*
357082 AACTTCCAAAAATTCCATTTTCAACCCCGAAACTTACAAAAATTACATTTTTACCCTCAAACTTC
1 AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTACAAAAATT-CATTTTTACCCTCAAACTTC
*
357147 CAAAAATTCCATTTTTACCCCCG
65 CAAAAATTCCATTTTTACCCCCA
* ** ** *
357170 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTTTAAAAATTC-TATTTTACCCTTGAACTTT
1 AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTACAAAAATTCAT-TTTTACCCTCAAACTTC
* ****
357234 CAAAAATTCCATTTTCGACCTTGT
65 CAAAAATTCCATTTT-TACCCCCA
* * * * * * *
357258 AACTCCCAAAAATTCTATTTTT-GCCCTCG-GA-TGTCCAAAAACTCTATTTTCGA-CCTCGAAA
1 AACTTCCAAAAATTCCATTTTTAACCC-CGAAACT-TACAAAAATTC-ATTTT-TACCCTC-AAA
*
357319 C-TCCAAAAATTTCA-TTTTACCCCCA
61 CTTCCAAAAATTCCATTTTTACCCCCA
*
357344 AA-TGTCTAAAAATTCCATTTTTAACCC
1 AACT-TCCAAAAATTCCATTTTTAACCC
357371 TATTTTCCCC
Statistics
Matches: 237, Mismatches: 40, Indels: 25
0.78 0.13 0.08
Matches are distributed among these distances:
85 1 0.00
86 22 0.09
87 48 0.20
88 141 0.59
89 25 0.11
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTAACCCCGAAACTTACAAAAATTCATTTTTACCCTCAAACTTCC
AAAAATTCCATTTTTACCCCCA
Found at i:357520 original size:17 final size:16
Alignment explanation
Indices: 357493--357526 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
357483 TGCACTCGTA
357493 TTTTGCATTTTTGATT
1 TTTTGCATTTTTGATT
*
357509 TTTTGCCATTTTTTATT
1 TTTTG-CATTTTTGATT
357526 T
1 T
357527 ATCTTACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (16 bp):
TTTTGCATTTTTGATT
Found at i:357765 original size:96 final size:96
Alignment explanation
Indices: 357623--357814 Score: 264
Period size: 96 Copynumber: 2.0 Consensus size: 96
357613 AAAACTTTAA
* * **
357623 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTCACTAGGTGCAATT
1 AATCGAGGCAATATTCTCTTATTTCGAGTTTTGAAAATTTGCGCCTTAACTCACTAGGTGCAACC
357688 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTTCTTCAAATCGAAATAATCGAATACCCTT
* *
357719 AATCGAGGCAATGTT-TCCTTATCTTCGA-TTTTG-AAATATTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTCT-CTTAT-TTCGAGTTTTGAAAAT-TTGCGCCTTAACTCACTAGGTGCA
* *
357781 ACCTTTCTTCAAATCGAGATAATCGAATATCCTT
63 ACCTTTCTTCAAATCGAAATAATCGAATACCCTT
357815 TTCACAAAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
95 5 0.06
96 75 0.88
97 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTCTTATTTCGAGTTTTGAAAATTTGCGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATACCCTT
Found at i:358997 original size:23 final size:22
Alignment explanation
Indices: 358971--359022 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
358961 TCTCCTTTAC
358971 TTAGCACATGTAATGCTCTCTGA
1 TTAGCACAT-TAATGCTCTCTGA
**
358994 TTAGCACATTTGTGCTCTCTGA
1 TTAGCACATTAATGCTCTCTGA
359016 TTAGCAC
1 TTAGCAC
359023 CTTGGTGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (22 bp):
TTAGCACATTAATGCTCTCTGA
Found at i:359012 original size:22 final size:22
Alignment explanation
Indices: 358984--359034 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
358974 GCACATGTAA
*
358984 TGCTCTCTGATTAGCACATTTG
1 TGCTCTCTGATTAGCACATTGG
*
359006 TGCTCTCTGATTAGCACCTTGG
1 TGCTCTCTGATTAGCACATTGG
359028 TGCTCTC
1 TGCTCTC
359035 CGTTCATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (22 bp):
TGCTCTCTGATTAGCACATTGG
Found at i:366378 original size:33 final size:34
Alignment explanation
Indices: 366334--366399 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
366324 AATACCATAC
366334 TTTTTGTGAGAATAAAGTAAATTTGTATTTATAA
1 TTTTTGTGAGAATAAAGTAAATTTGTATTTATAA
*
366368 TTTTT-TGAGAATAAGGTAAATTTGTATTTATA
1 TTTTTGTGAGAATAAAGTAAATTTGTATTTATA
366400 CTATCTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (34 bp):
TTTTTGTGAGAATAAAGTAAATTTGTATTTATAA
Found at i:367260 original size:10 final size:10
Alignment explanation
Indices: 367245--367284 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
367235 TTCAACCAGT
367245 ATAATAATAA
1 ATAATAATAA
*
367255 ATAATAATAT
1 ATAATAATAA
*
367265 ATAATAATTA
1 ATAATAATAA
367275 ATATATAATA
1 ATA-ATAATA
367285 TACTACTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATAATAA
Found at i:367276 original size:14 final size:13
Alignment explanation
Indices: 367245--367284 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
367235 TTCAACCAGT
367245 ATAATA-ATAAATA
1 ATAATATAT-AATA
367258 ATAATATATAATA
1 ATAATATATAATA
367271 ATTAATATATAATA
1 A-TAATATATAATA
367285 TACTACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATATAATA
Found at i:367310 original size:16 final size:16
Alignment explanation
Indices: 367261--367311 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
367251 ATAAATAATA
*
367261 ATATATAA-TAATTAAT
1 ATATATAACT-ATTATT
*
367277 ATATAATATACTACTATT
1 ATAT-ATA-ACTATTATT
367295 ATATATAACTATTATT
1 ATATATAACTATTATT
367311 A
1 A
367312 AATTATAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 13 0.45
17 6 0.21
18 9 0.31
19 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATAACTATTATT
Found at i:367454 original size:256 final size:246
Alignment explanation
Indices: 367023--367535 Score: 629
Period size: 256 Copynumber: 2.0 Consensus size: 246
367013 TAACAAACAA
* * * *
367023 TAATATATAATGTCCTACTATTATATATAACTATTATTATATTATAGATTATAATAAAAGATACA
1 TAATATATAATATACTACTATTATATATAACTATTATTAAATTATAGATTATAATAAAAGACACA
* *
367088 GTATTGCAAGATATTATAATGTTTAATCATTGATGCATATATAAACTATTAATATATTATATACT
66 GTATT---AGATATTATAATGTTTAATCATTGATACATATATAAACTATTAATAGATTATATACT
** * * *
367153 ACATGATATGATATAGCATTATATAATATAGTAGGAGGATTAACTTTCAAATATATGAAAAGTAT
128 ACATGATATGATATAGCATTATATAATATAGTAAAAAGATTAACTTTCAAATATAAGAAAAATA-
*
367218 TAGGGCGTAGAACATATTTCAACCAGTATAATAATA-AATAATA-ATATATAATAAT
192 TAGGACGTAGAACATATTTCAACCAGTATAATAA-ACAATAATATAT-TATAATAAT
* * *
367273 TAATATATAATATACTACTATTATATATAACTATTATTAAATTATAGATTATAATAGAATACATA
1 TAATATATAATATACTACTATTATATATAACTATTATTAAATTATAGATTATAATAAAAGACACA
* *
367338 GTATT-GATATTATGATGTTTAATCATTGATATATATATATATATATATAAACTATTAATAGATT
66 GTATTAGATATTATAATGTTTAATCATTG----------ATACATATATAAACTATTAATAGATT
** *
367402 ATATACTATTTGATATGATATAGCATTATATAATATAGTAAAAA-AGTTAACTTTCAAATGTAAG
121 ATATACTACATGATATGATATAGCATTATATAATATAGTAAAAAGA-TTAACTTTCAAATATAAG
* * **
367466 AAAAATATAGGACTTAGAGCATATTTCAATTAGTATAATAAACAATAATATATTATAATAAT
185 AAAAATATAGGACGTAGAACATATTTCAACCAGTATAATAAACAATAATATATTATAATAAT
367528 TAATATAT
1 TAATATAT
367536 TATGTATTAC
Statistics
Matches: 226, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
246 22 0.10
250 63 0.28
254 1 0.00
255 54 0.24
256 86 0.38
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (246 bp):
TAATATATAATATACTACTATTATATATAACTATTATTAAATTATAGATTATAATAAAAGACACA
GTATTAGATATTATAATGTTTAATCATTGATACATATATAAACTATTAATAGATTATATACTACA
TGATATGATATAGCATTATATAATATAGTAAAAAGATTAACTTTCAAATATAAGAAAAATATAGG
ACGTAGAACATATTTCAACCAGTATAATAAACAATAATATATTATAATAAT
Found at i:374775 original size:6 final size:6
Alignment explanation
Indices: 374766--374842 Score: 70
Period size: 6 Copynumber: 13.2 Consensus size: 6
374756 CAAATTTATT
* ** **
374766 TTTAAA TTTAAA TTT-AT TTTAAA TTTATCT TTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA
*
374813 TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
374843 GGATTTAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
5 11 0.20
6 40 0.73
7 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:374787 original size:17 final size:17
Alignment explanation
Indices: 374757--374842 Score: 90
Period size: 17 Copynumber: 5.2 Consensus size: 17
374747 AAATTGATTC
374757 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAATTT
374775 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
374792 --A--TCTTTTAAATTT
1 AAATTTATTTTAAATTT
**
374805 AAATTTGCTTTAAATTT
1 AAATTTATTTTAAATTT
* *
374822 AAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
374839 AAAT
1 AAAT
374843 GGATTTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 38 0.66
18 7 0.12
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:374788 original size:11 final size:12
Alignment explanation
Indices: 374772--374805 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
374762 TATTTTTAAA
374772 TTTAAATTTA-T
1 TTTAAATTTACT
374783 TTTAAATTTATCT
1 TTTAAATTTA-CT
374796 TTTAAATTTA
1 TTTAAATTTA
374806 AATTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAAATTTACT
Found at i:374801 original size:30 final size:28
Alignment explanation
Indices: 374744--374839 Score: 104
Period size: 30 Copynumber: 3.4 Consensus size: 28
374734 TTTTATTGGG
* *
374744 TTTAAATTGATTCAAATTTATTTTTAAA
1 TTTAAATTTATTTAAATTTATTTTTAAA
374772 TTTAAATTTATTTTAAATTTATCTTTTAAA
1 TTTAAATTTA-TTTAAATTTAT-TTTTAAA
* **
374802 TTTAAATTTGCTTTAAATTTAAATTT-AA
1 TTTAAATTT-ATTTAAATTTATTTTTAAA
*
374830 TTAAAATTTA
1 TTTAAATTTA
374840 AATGGATTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
28 19 0.33
29 13 0.22
30 26 0.45
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTAAATTTATTTAAATTTATTTTTAAA
Found at i:374831 original size:11 final size:11
Alignment explanation
Indices: 374770--374840 Score: 54
Period size: 11 Copynumber: 6.2 Consensus size: 11
374760 TTTATTTTTA
374770 AATTTAAATTT
1 AATTTAAATTT
*
374781 ATTTTAAATTT
1 AATTTAAATTT
*
374792 ATCTTTTAAATTT
1 A--ATTTAAATTT
**
374805 AAATTT-GCTTT
1 -AATTTAAATTT
374816 AAATTTAAATTT
1 -AATTTAAATTT
*
374828 AATTAAAATTT
1 AATTTAAATTT
374839 AA
1 AA
374841 ATGGATTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 32 0.65
12 6 0.12
13 10 0.20
14 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:386292 original size:622 final size:612
Alignment explanation
Indices: 385109--386342 Score: 2333
Period size: 622 Copynumber: 2.0 Consensus size: 612
385099 TGCACCCCTT
385109 CCTCCTTTATCACTGAGCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGCTATTTCCCTCTCGA
1 CCTCCTTTATCACTGAGCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGCTATTTCCCTCTCGA
385174 CGATGAAGCTTATCCCCCATCGTCTCACTGGTCGACCTTGACCCTTGTTATTTTGAGGTCATATT
66 CGATGAAGCTTATCCCCCATCGTCTCACTGGTCGACCTTGACCCTTGTTATTTTGAGGTCATATT
385239 TAGTATTCAAAGTTTGCCTCGATTTGGTACCGCTCTCGCGGCCCGCACGGAAATAGTGCTTTACC
131 TAGTATTCAAAGTTTGCCTCGATTTGGTACCGCTCTCGCGGCCCGCACGGAAATAGTGCTTTACC
385304 CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGAAAAACCAGCTAGCTCTGGGTTC
196 CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGAAAAACCAGCTAGCTCTGGGTTC
* * *
385369 GAGTGGTATTTCACCCCTAACCATAACTCATCTGCTGATTCTTCAACATCAGTCGGTTCGGACCT
261 GAGTGGCATTTCACCCCTAACCACAACTCATCCGCTGATTCTTCAACATCAGTCGGTTCGGACCT
385434 CCACTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAGGTTCGGGTCCATGAGT
326 CCACTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAGGTTCGGGTCCATGAGT
385499 AGTGACAATTGCCCTATGTAGACTCGCTTTTGTTACGGCTCTGGTGGGTTCCCTTAACCGAGCCA
391 AGTGACAATTGCCCTATGTAGACTCGCTTTTGTTACGGCTCTGGTGGGTTCCCTTAACCGAGCCA
385564 CTGCCTATGAGTCGTCGGCTCATTCTTCAACAGGCACGCGGTCAGAGTCTTGGGCTCCTCCCACT
456 CTGCCTATGAGTCGTCGGCTCATTCTTCAACAGGCACGCGGTCAGAGTCTTGGGCTCCTCCCACT
385629 GCTTGGGAGCTTACAGTTTCATGTTCTATTTCACTCCCCGACGGGGGTTCTTTTCACCCTTCCCT
521 GCTTGGGAGCTTACAGTTTCATGTTCTATTTCACTCCCCGACGGGGGTTCTTTTCACCCTTCCCT
385694 CACGGTACTACTTCGCTATCGGTCACC
586 CACGGTACTACTTCGCTATCGGTCACC
385721 NNNNNNNNNNCCTCCTTTATCACTGAGCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGCTATT
1 ----------CCTCCTTTATCACTGAGCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGCTATT
385786 TCCCTCTCGACGATGAAGCTTATCCCCCATCGTCTCACTGGTCGACCTTGACCCTTGTTATTTTG
56 TCCCTCTCGACGATGAAGCTTATCCCCCATCGTCTCACTGGTCGACCTTGACCCTTGTTATTTTG
385851 AGGTCATATTTAGTATTCAAAGTTTGCCTCGATTTGGTACCGCTCTCGCGGCCCGCACGGAAATA
121 AGGTCATATTTAGTATTCAAAGTTTGCCTCGATTTGGTACCGCTCTCGCGGCCCGCACGGAAATA
* *
385916 GTGCTTTACCCCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGGAGAACCAGCTAG
186 GTGCTTTACCCCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGAAAAACCAGCTAG
385981 CTCTGGGTTCGAGTGGCATTTCACCCCTAACCACAACTCATCCGCTGATTCTTCAACATCAGTCG
251 CTCTGGGTTCGAGTGGCATTTCACCCCTAACCACAACTCATCCGCTGATTCTTCAACATCAGTCG
386046 GTTCGGACCTCCACTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAGGTTCGG
316 GTTCGGACCTCCACTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAGGTTCGG
386111 GTCCATGAGTAGTGACAATTGCCCTATGTAGACTCGCTTTTGTTACGGCTCTGGTGGGTTCCCTT
381 GTCCATGAGTAGTGACAATTGCCCTATGTAGACTCGCTTTTGTTACGGCTCTGGTGGGTTCCCTT
386176 AACCGAGCCACTGCCTATGAGTCGTCGGCTCATTCTTCAACAGGCACGCGGTCAGAGTCTTGGGC
446 AACCGAGCCACTGCCTATGAGTCGTCGGCTCATTCTTCAACAGGCACGCGGTCAGAGTCTTGGGC
386241 TCCTCCCACTGCTTGGGAGCTTACAGTTTCATGTTCTATTTCACTCCCCGACGGGGGTTCTTTTC
511 TCCTCCCACTGCTTGGGAGCTTACAGTTTCATGTTCTATTTCACTCCCCGACGGGGGTTCTTTTC
386306 ACCCTTCCCTCACGGTACTACTTCGCTATCGGTCACC
576 ACCCTTCCCTCACGGTACTACTTCGCTATCGGTCACC
386343 TAGGAGTATT
Statistics
Matches: 607, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
622 607 1.00
ACGTcount: A:0.18, C:0.30, G:0.22, T:0.30
Consensus pattern (612 bp):
CCTCCTTTATCACTGAGCGGTCATTTAGGGGCCTTAGCTGGTGATCCGGGCTATTTCCCTCTCGA
CGATGAAGCTTATCCCCCATCGTCTCACTGGTCGACCTTGACCCTTGTTATTTTGAGGTCATATT
TAGTATTCAAAGTTTGCCTCGATTTGGTACCGCTCTCGCGGCCCGCACGGAAATAGTGCTTTACC
CCTAGATGTCCAGTCAACTGCTGCGCCTCAACGCATTTCGGGAAAAACCAGCTAGCTCTGGGTTC
GAGTGGCATTTCACCCCTAACCACAACTCATCCGCTGATTCTTCAACATCAGTCGGTTCGGACCT
CCACTTAGTTTCACCCAAGCTTCATCCTGGTCATGGATAGATCACCCAGGTTCGGGTCCATGAGT
AGTGACAATTGCCCTATGTAGACTCGCTTTTGTTACGGCTCTGGTGGGTTCCCTTAACCGAGCCA
CTGCCTATGAGTCGTCGGCTCATTCTTCAACAGGCACGCGGTCAGAGTCTTGGGCTCCTCCCACT
GCTTGGGAGCTTACAGTTTCATGTTCTATTTCACTCCCCGACGGGGGTTCTTTTCACCCTTCCCT
CACGGTACTACTTCGCTATCGGTCACC
Found at i:387627 original size:69 final size:69
Alignment explanation
Indices: 387515--387649 Score: 207
Period size: 69 Copynumber: 2.0 Consensus size: 69
387505 CGGGTGGGTC
* * * *
387515 TTGCAGTCAAGCTCCCTTCTGCCTTTGCACCCGAGGGCCAATCTCCGTCCGGCCTGAGGAAACCT
1 TTGCACTCAAGCTCCCTTCTACCTTTGCACCCGAGAGCCAATCTCCATCCGGCCTGAGGAAACCT
387580 TCCT
66 TCCT
* * *
387584 TTGCACTCAAGCTCCCTTCTACCTTTGCACTCGAGAGCTAATCTCCATCCGGCTTGAGGAAACCT
1 TTGCACTCAAGCTCCCTTCTACCTTTGCACCCGAGAGCCAATCTCCATCCGGCCTGAGGAAACCT
387649 T
66 T
387650 TGCACGCCTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.27
Consensus pattern (69 bp):
TTGCACTCAAGCTCCCTTCTACCTTTGCACCCGAGAGCCAATCTCCATCCGGCCTGAGGAAACCT
TCCT
Done.