Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015367.1 Kokia drynarioides strain JFW-HI SEQ_130414, 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: 471520
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 729 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:383610 original size:16 final size:15
Alignment explanation
Indices: 383589--383622 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
383579 GTAAGAAAAA
383589 TAATAATTAATATTTT
1 TAATAATTAAT-TTTT
*
383605 TAATAATTTATTTTT
1 TAATAATTAATTTTT
383620 TAA
1 TAA
383623 ACACTATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATAATTAATTTTT
Found at i:399933 original size:6 final size:6
Alignment explanation
Indices: 399922--399949 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
399912 CTTGAGATCG
399922 TTGACC TTGACC TTGACC TTGACC TTGA
1 TTGACC TTGACC TTGACC TTGACC TTGA
399950 GGGATCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.36
Consensus pattern (6 bp):
TTGACC
Found at i:402651 original size:21 final size:21
Alignment explanation
Indices: 402627--402694 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
402617 ATAAAGATTC
402627 TATAAAATAATATTAATGTCA
1 TATAAAATAATATTAATGTCA
*
402648 TATAATTCAA-AATA-AAGAT-TC-
1 TATAA---AATAATATTA-ATGTCA
402669 TATAAAATAATATTAATGTCA
1 TATAAAATAATATTAATGTCA
402690 TATAA
1 TATAA
402695 TTCATGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 2 0.05
19 6 0.16
20 3 0.08
21 15 0.41
22 3 0.08
23 6 0.16
24 2 0.05
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (21 bp):
TATAAAATAATATTAATGTCA
Found at i:402663 original size:42 final size:42
Alignment explanation
Indices: 402608--402698 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
402598 TTGTCCAAAG
402608 ATAA-TCAAAATAAAGATTCTATAAAATAATATTAATGTCAT
1 ATAATTCAAAATAAAGATTCTATAAAATAATATTAATGTCAT
402649 ATAATTCAAAATAAAGATTCTATAAAATAATATTAATGTCAT
1 ATAATTCAAAATAAAGATTCTATAAAATAATATTAATGTCAT
402691 ATAATTCA
1 ATAATTCA
402699 TGTTATAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (42 bp):
ATAATTCAAAATAAAGATTCTATAAAATAATATTAATGTCAT
Found at i:403115 original size:4 final size:4
Alignment explanation
Indices: 403106--403131 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
403096 ATAAAATATC
403106 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
403132 TGATATAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:405008 original size:90 final size:90
Alignment explanation
Indices: 404724--404997 Score: 300
Period size: 90 Copynumber: 3.0 Consensus size: 90
404714 AGGACAAAAG
* *
404724 GAAGGATAAGGAGAAAAAGAAAGAAGAGAAGTCGGATAAAGAGGAT-GATGTAGAAGATGCCAAA
1 GAAGGATAAGAAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGGA-GTAGAAGATGCCAAA
404788 GAGAAGAAGAAGAAGAAGAAGAAAGATAA
65 GAG--G-AGAAGAAGAAGAAGAAAGATAA
* * * * * * * * * ** * * *
404817 TAAGGATAAGGAGATAAAGGAAGACAAGAAGTCTGATACAGAAGACGTCGAAGAA-TTAGCCGAA
1 GAAGGATAAGAAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGGAGTAGAAGAT-GCCAAA
* *
404881 GAAGAGGAGAAGAAGAAGAAAGATAA
65 GAGGAGAAGAAGAAGAAGAAAGATAA
* *
404907 GAAGGATAAGAAGAAAAAGAAAGAAAAGAAGTCGGATAAAGTGGATGGAGTAGAAGATGACAAAG
1 GAAGGATAAGAAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGGAGTAGAAGATGCCAAAG
*
404972 AGGAGAAAAAGAAGAAGAAAGATAA
66 AGGAGAAGAAGAAGAAGAAAGATAA
404997 G
1 G
404998 GAGAAAAAGA
Statistics
Matches: 143, Mismatches: 35, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
90 91 0.64
91 2 0.01
92 1 0.01
93 49 0.34
ACGTcount: A:0.55, C:0.04, G:0.31, T:0.09
Consensus pattern (90 bp):
GAAGGATAAGAAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGGAGTAGAAGATGCCAAAG
AGGAGAAGAAGAAGAAGAAAGATAA
Found at i:408253 original size:2 final size:2
Alignment explanation
Indices: 408248--408277 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
408238 ACACACAAGC
408248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
408278 CCTCTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:411797 original size:33 final size:33
Alignment explanation
Indices: 411755--411821 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
411745 ATCCAATAAA
411755 TGGCTGAAAATCAAGAAAAGATATTTTTCCTCC
1 TGGCTGAAAATCAAGAAAAGATATTTTTCCTCC
*
411788 TGGCTGAAAATCAAGAGAAGATATTTTTCCTCC
1 TGGCTGAAAATCAAGAAAAGATATTTTTCCTCC
411821 T
1 T
411822 TAATCACAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (33 bp):
TGGCTGAAAATCAAGAAAAGATATTTTTCCTCC
Found at i:411918 original size:21 final size:22
Alignment explanation
Indices: 411894--411940 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
411884 ACTTAAAATG
411894 GTCAACAT-CATTGA-TCATCAT
1 GTCAACATCCATTGACT-ATCAT
* *
411915 GTCATCATCCTTTGACTATCAT
1 GTCAACATCCATTGACTATCAT
411937 GTCA
1 GTCA
411941 TCACATGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 14 0.64
23 1 0.05
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (22 bp):
GTCAACATCCATTGACTATCAT
Found at i:412550 original size:20 final size:21
Alignment explanation
Indices: 412520--412559 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
412510 TAATTGTTTT
412520 ATAATTTTTTTTAAAAATATA
1 ATAATTTTTTTTAAAAATATA
*
412541 ATAA-TTTTTTTAAATATAT
1 ATAATTTTTTTTAAAAATAT
412560 TGTGTGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAATTTTTTTTAAAAATATA
Found at i:417662 original size:23 final size:24
Alignment explanation
Indices: 417623--417667 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
417613 TTTTTTATAT
417623 ATAAAATTTTAATAAATTTAAAAA
1 ATAAAATTTTAATAAATTTAAAAA
417647 ATAAAATTATT-A-AAATTTAAA
1 ATAAAATT-TTAATAAATTTAAA
417668 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 9 0.45
25 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAAAATTTTAATAAATTTAAAAA
Found at i:418959 original size:3 final size:3
Alignment explanation
Indices: 418951--418979 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
418941 CTGCCCCTGC
418951 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
418980 ATGAGAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:421379 original size:21 final size:22
Alignment explanation
Indices: 421338--421379 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
421328 ATATATATGA
*
421338 TATACTAGTGGTAGAAATTTTT
1 TATACTAGTGATAGAAATTTTT
*
421360 TATACTAGTGAT-GGAATTTT
1 TATACTAGTGATAGAAATTTT
421380 GTAAGTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (22 bp):
TATACTAGTGATAGAAATTTTT
Found at i:425449 original size:21 final size:22
Alignment explanation
Indices: 425416--425489 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
425406 TTTAATTAAT
* * *
425416 TTTAGGATTTTTTAAATTAGGG
1 TTTAGAATATTTTAAATTAAGG
* * *
425438 TTTTG-GTATTTTAAATAAAGG
1 TTTAGAATATTTTAAATTAAGG
425459 TTTAGAATATTTTAAATTAATGG
1 TTTAGAATATTTTAAATTAA-GG
425482 TTATAGAA
1 TT-TAGAA
425490 AATTGTATGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 16 0.39
22 16 0.39
23 4 0.10
24 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (22 bp):
TTTAGAATATTTTAAATTAAGG
Found at i:425469 original size:22 final size:24
Alignment explanation
Indices: 425444--425489 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
425434 AGGGTTTTGG
425444 TATTTTAAA-TAAAGGTT-TAGAA
1 TATTTTAAATTAAAGGTTATAGAA
*
425466 TATTTTAAATTAATGGTTATAGAA
1 TATTTTAAATTAAAGGTTATAGAA
425490 AATTGTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 7 0.33
24 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (24 bp):
TATTTTAAATTAAAGGTTATAGAA
Found at i:428873 original size:20 final size:20
Alignment explanation
Indices: 428848--428897 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
428838 CTCCAGTGAG
*
428848 ACTTCTACCGGTAGAACTCA
1 ACTTCTACCGGTACAACTCA
* *
428868 ACTTCTACCGTTACAACTCC
1 ACTTCTACCGGTACAACTCA
428888 ACTTCTACCG
1 ACTTCTACCG
428898 ATACCTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.36, G:0.10, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGGTACAACTCA
Found at i:429135 original size:20 final size:19
Alignment explanation
Indices: 429112--429169 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
429102 ACTCTTGTTT
429112 TACCGATACAACTACAGTTC
1 TACCGATACAACTA-AGTTC
* * *
429132 TACCGATATAAGTATGCTTC
1 TACCGATACAACTAAG-TTC
*
429152 TACCGAAACAACTAAGTT
1 TACCGATACAACTAAGTT
429170 GCAGACTACT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (19 bp):
TACCGATACAACTAAGTTC
Found at i:431998 original size:20 final size:20
Alignment explanation
Indices: 431973--432025 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
431963 CTCCAGTGAG
431973 ACTTCTACCGATAGAACTCA
1 ACTTCTACCGATAGAACTCA
* *
431993 ACTTCTACCGATATAACTCC
1 ACTTCTACCGATAGAACTCA
*
432013 ACTTCTATCGATA
1 ACTTCTACCGATA
432026 CCTTGAAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (20 bp):
ACTTCTACCGATAGAACTCA
Found at i:433423 original size:152 final size:149
Alignment explanation
Indices: 433068--433460 Score: 486
Period size: 150 Copynumber: 2.6 Consensus size: 149
433058 TAATTCCTCA
* * * *
433068 AATAGTGGGGGTTGAAGTTTGTAGAGGGAAAATGCTTCAAGTAGGATGCTATGTCAGCAAAAGTA
1 AATAGTGGGGGTTGAAATTTGTAG-GGAAAAATGCTCCAAGTAGGATGCTGTGTCAGCAAAAGTA
* * * * *
433133 TAGTGCCTCTTACTTGGATCATTTTTTAAAAAATTGAAAAAATGGTTCTGAAAAATAACATGGGA
65 AAGTGCATCCTACTTGGAGCATTTTTTAAAAAATTGAAAAAATGGTTCTAAAAAATAACATGGGA
*
433198 TTTCGAGAAATCTGATATCT
130 TTTCGAAAAATCTGATATCT
* ** * * *
433218 AATAATGGAAGTTGAAATTTGTAAGGAAAAAATGCTCCAAGTAGGATGTTGTGTCAGCAGAAGTA
1 AATAGTGGGGGTTGAAATTTGT-AGGGAAAAATGCTCCAAGTAGGATGCTGTGTCAGCAAAAGTA
* * * *
433283 CAGTGCATCCTACTTGGAGC-TTATTTTAAAAAATTTGAGAACATGGTTCTTAAAAAATAACCCT
65 AAGTGCATCCTACTTGGAGCATT-TTTTAAAAAA-TTGAAAAAATGGTTC-TAAAAAATAA-CAT
433347 -GGATTCTCGAAAAATCTGATATCT
126 GGGATT-TCGAAAAATCTGATATCT
* * *
433371 AATAGTGGGGGTTGAAATTTGTTGGGAAAAATGCTCCAAGCAAGATGCTGTGTCAGCAAAAGTAT
1 AATAGTGGGGGTTGAAATTTGTAGGGAAAAATGCTCCAAGTAGGATGCTGTGTCAGCAAAAGTA-
433436 AAG-GCATCCTACTTGGAGCATTTTT
65 AAGTGCATCCTACTTGGAGCATTTTT
433461 CCCTTACAAA
Statistics
Matches: 206, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
149 2 0.01
150 78 0.38
151 15 0.07
152 69 0.33
153 42 0.20
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (149 bp):
AATAGTGGGGGTTGAAATTTGTAGGGAAAAATGCTCCAAGTAGGATGCTGTGTCAGCAAAAGTAA
AGTGCATCCTACTTGGAGCATTTTTTAAAAAATTGAAAAAATGGTTCTAAAAAATAACATGGGAT
TTCGAAAAATCTGATATCT
Found at i:433876 original size:30 final size:31
Alignment explanation
Indices: 433840--433899 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
433830 TCAAAAATGC
*
433840 AAAATTTAGATATATT-GTTTTGAATTTTTT
1 AAAATTTAGATATATTAGTTTTGAAATTTTT
* *
433870 AAAATTTATATATGTTAGTTTTGAAATTTT
1 AAAATTTAGATATATTAGTTTTGAAATTTT
433900 AGAGTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (31 bp):
AAAATTTAGATATATTAGTTTTGAAATTTTT
Found at i:442428 original size:74 final size:72
Alignment explanation
Indices: 442305--442447 Score: 205
Period size: 74 Copynumber: 2.0 Consensus size: 72
442295 TTAGCAAAGA
* *
442305 AAGGACTTGAGGCTTCATCAATAATTTAGATACTAGAAGCTTTACGAGACAAGCTGAGAGACAGT
1 AAGGACCTGAGGCTTCATCAATAATTTAGATACTAAAAGCTTTACGAGACAAGCT-A-AGACAGT
442370 CTTGAACAG
64 CTTGAACAG
* * * * *
442379 AAGGACCTGAGGCTTCGTCGATGATTTAGATACTAAAAGTTTTATGAGACAAGCTAAGACAGTCT
1 AAGGACCTGAGGCTTCATCAATAATTTAGATACTAAAAGCTTTACGAGACAAGCTAAGACAGTCT
442444 TGAA
66 TGAA
442448 GTAGATAGCA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
72 13 0.21
73 1 0.02
74 48 0.77
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (72 bp):
AAGGACCTGAGGCTTCATCAATAATTTAGATACTAAAAGCTTTACGAGACAAGCTAAGACAGTCT
TGAACAG
Found at i:443853 original size:22 final size:23
Alignment explanation
Indices: 443815--443858 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
443805 AAATTCAAAA
443815 TAAATGATAAAAAA-TTTAAATT
1 TAAATGATAAAAAATTTTAAATT
*
443837 TAAAT-ATAAATATATTTTAAAT
1 TAAATGATAAA-AAATTTTAAAT
443859 ATTTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATGATAAAAAATTTTAAATT
Found at i:445672 original size:22 final size:22
Alignment explanation
Indices: 445631--445674 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
445621 ATAATTTACT
*
445631 TAATATAATAATATTTTATAAG
1 TAATATAATAATATTATATAAG
445653 TAATATAATATATATATATATA
1 TAATATAATA-ATAT-TATATA
445675 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TAATATAATAATATTATATAAG
Found at i:448138 original size:3 final size:3
Alignment explanation
Indices: 448130--448154 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
448120 AGTTGAAATT
448130 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
448155 CGACAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:449510 original size:22 final size:23
Alignment explanation
Indices: 449494--449536 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
449484 TAATATATCT
449494 TAAAAA-TAAATTAAATATTCCA
1 TAAAAATTAAATTAAATATTCCA
*
449516 TAAAAATTAAATTAAAGATTC
1 TAAAAATTAAATTAAATATTC
449537 TATCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAATTAAATTAAATATTCCA
Found at i:452971 original size:7 final size:7
Alignment explanation
Indices: 452931--452964 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
452921 ACATTTAACT
452931 AAAAAGAA
1 AAAAAG-A
452939 AAAAAGA
1 AAAAAGA
452946 AAAAAGA
1 AAAAAGA
452953 AAAAAGA
1 AAAAAGA
452960 AAAAA
1 AAAAA
452965 AACAAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:466471 original size:16 final size:17
Alignment explanation
Indices: 466434--466472 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
466424 AATTATAATG
466434 TAATTTTATTATTTTAA
1 TAATTTTATTATTTTAA
*
466451 T-ATTTTA-TATTTTTA
1 TAATTTTATTATTTTAA
466466 TAATTTT
1 TAATTTT
466473 TAAAAGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATTTTATTATTTTAA
Found at i:467116 original size:18 final size:18
Alignment explanation
Indices: 467093--467135 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
467083 GAATAATTTT
467093 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
467111 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
467129 TTAATTA
1 TTAATTA
467136 CAACTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:470355 original size:14 final size:14
Alignment explanation
Indices: 470336--470383 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
470326 AAAAAAAGTT
470336 AACGGTCAACGATC
1 AACGGTCAACGATC
*
470350 AACGGTCAAAG-TC
1 AACGGTCAACGATC
* *
470363 AATGGTCAACAATC
1 AACGGTCAACGATC
470377 AACGGTC
1 AACGGTC
470384 GGTTAACGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (14 bp):
AACGGTCAACGATC
Found at i:470369 original size:27 final size:27
Alignment explanation
Indices: 470330--470383 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
470320 TTTTTGAAAA
* *
470330 AAAGTTAACGGTCAACGATCAACGGTC
1 AAAGTCAACGGTCAACAATCAACGGTC
*
470357 AAAGTCAATGGTCAACAATCAACGGTC
1 AAAGTCAACGGTCAACAATCAACGGTC
470384 GGTTAACGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (27 bp):
AAAGTCAACGGTCAACAATCAACGGTC
Found at i:470447 original size:16 final size:15
Alignment explanation
Indices: 470419--470450 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
470409 AGTCGGTCAA
470419 TGGTTTGACTTGGTT
1 TGGTTTGACTTGGTT
470434 TGGTTTGAACTTGGTT
1 TGGTTTG-ACTTGGTT
470450 T
1 T
470451 AATTGGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.09, C:0.06, G:0.31, T:0.53
Consensus pattern (15 bp):
TGGTTTGACTTGGTT
Found at i:470495 original size:23 final size:23
Alignment explanation
Indices: 470453--470505 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
470443 CTTGGTTTAA
*
470453 TTGGGTTATTGGGTCAAAAGGGT-
1 TTGGGTTATTAGGTCAAAA-GGTC
**
470476 TTGGGTTATTAGGTTTAAAGGTC
1 TTGGGTTATTAGGTCAAAAGGTC
470499 TTGGGTT
1 TTGGGTT
470506 TATAAAGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.19, C:0.04, G:0.36, T:0.42
Consensus pattern (23 bp):
TTGGGTTATTAGGTCAAAAGGTC
Done.