Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015042.1 Kokia drynarioides strain JFW-HI SEQ_130086, 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: 366595
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 491 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:301315 original size:24 final size:26
Alignment explanation
Indices: 301267--301319 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
301257 AAAGGCTTAA
*
301267 AACATAGATTTTTTTTTTTGAATATAG
1 AACATAGACTTTTTTTTTT-AATATAG
301294 AACATAG-CTTTTTTTTTT-ATATAG
1 AACATAGACTTTTTTTTTTAATATAG
301318 AA
1 AA
301320 TTGAAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
26 10 0.40
27 7 0.28
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (26 bp):
AACATAGACTTTTTTTTTTAATATAG
Found at i:304783 original size:91 final size:91
Alignment explanation
Indices: 304628--304808 Score: 344
Period size: 91 Copynumber: 2.0 Consensus size: 91
304618 TGGTTTTGCT
304628 AGATTTTAATGTCTCTCATCACCCTACCAAAAGAACCCTTTACAGTATATTTAGCTTTAGAAATG
1 AGATTTTAATGTCTCTCATCACCCTACCAAAAGAACCCTTTACAGTATATTTAGCTTTAGAAATG
304693 AAATTTTAGGGTGGAAATTAAATAGA
66 AAATTTTAGGGTGGAAATTAAATAGA
* *
304719 AGATTTTAATGTCTCTCCTCACCCTACCAAAAGAATCCTTTACAGTATATTTAGCTTTAGAAATG
1 AGATTTTAATGTCTCTCATCACCCTACCAAAAGAACCCTTTACAGTATATTTAGCTTTAGAAATG
304784 AAATTTTAGGGTGGAAATTAAATAG
66 AAATTTTAGGGTGGAAATTAAATAG
304809 CAAAAGCTAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (91 bp):
AGATTTTAATGTCTCTCATCACCCTACCAAAAGAACCCTTTACAGTATATTTAGCTTTAGAAATG
AAATTTTAGGGTGGAAATTAAATAGA
Found at i:311121 original size:21 final size:19
Alignment explanation
Indices: 311075--311113 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
311065 AGGTGTATGC
*
311075 TCGATCTTTACAAGAGAGA
1 TCGATCCTTACAAGAGAGA
311094 TCGATCCTTACAAGAGAGA
1 TCGATCCTTACAAGAGAGA
311113 T
1 T
311114 TTGGATCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (19 bp):
TCGATCCTTACAAGAGAGA
Found at i:311556 original size:44 final size:44
Alignment explanation
Indices: 311507--311610 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
311497 AAAAAAACAT
* * * *
311507 AAAAATAACATCTAAATAACCAAAATAACAATC-AAAACAATAGC
1 AAAAATAACAACAAAACAACAAAAATAACAA-CAAAAACAATAGC
* * *
311551 AAAAATAACAACAAAACAACAAAAATAGCAACAAAAATAATAGG
1 AAAAATAACAACAAAACAACAAAAATAACAACAAAAACAATAGC
**
311595 AAAAATAGTAACAAAA
1 AAAAATAACAACAAAA
311611 ATAAAAGCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.68, C:0.14, G:0.05, T:0.12
Consensus pattern (44 bp):
AAAAATAACAACAAAACAACAAAAATAACAACAAAAACAATAGC
Found at i:311575 original size:20 final size:20
Alignment explanation
Indices: 311507--311586 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
311497 AAAAAAACAT
* * *
311507 AAAAATAACATCTAAATAAC
1 AAAAATAACAACAAAACAAC
*
311527 CAAAATAACAATCAAAACAATAGC
1 AAAAATAACAA-CAAAAC-A-A-C
311551 AAAAATAACAACAAAACAAC
1 AAAAATAACAACAAAACAAC
*
311571 AAAAATAGCAACAAAA
1 AAAAATAACAACAAAA
311587 ATAATAGGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 25 0.50
21 5 0.10
22 2 0.04
23 7 0.14
24 11 0.22
ACGTcount: A:0.69, C:0.17, G:0.03, T:0.11
Consensus pattern (20 bp):
AAAAATAACAACAAAACAAC
Found at i:311664 original size:33 final size:34
Alignment explanation
Indices: 311621--311686 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
311611 ATAAAAGCAT
* **
311621 CAAAATAGT-AAAAAATTGCACAAAAATAGCAAC
1 CAAAACAGTAAAAAAATAACACAAAAATAGCAAC
311654 CAAAACAGTAAAAAAATAACACAAAAATAGCAA
1 CAAAACAGTAAAAAAATAACACAAAAATAGCAA
311687 AAAATACAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 8 0.28
34 21 0.72
ACGTcount: A:0.65, C:0.15, G:0.08, T:0.12
Consensus pattern (34 bp):
CAAAACAGTAAAAAAATAACACAAAAATAGCAAC
Found at i:315884 original size:32 final size:32
Alignment explanation
Indices: 315847--315907 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
315837 AAATATCTCA
*
315847 ATTTGATTTTATTCCAATCAAATTGATTTTCG
1 ATTTGATTTGATTCCAATCAAATTGATTTTCG
* * *
315879 ATTTGATTTGATTCTATTCAAATTTATTT
1 ATTTGATTTGATTCCAATCAAATTGATTT
315908 AAAGACTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (32 bp):
ATTTGATTTGATTCCAATCAAATTGATTTTCG
Found at i:317612 original size:23 final size:23
Alignment explanation
Indices: 317573--317621 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
317563 TAATAGGGAT
317573 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACT-TCAC
*
317596 TTTCAA-TTCCAATTTCACTTCAC
1 TTTCAATTTACAA-TTCACTTCAC
317619 TTT
1 TTT
317622 TACTTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
23 17 0.74
24 1 0.04
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTCAATTTACAATTCACTTCAC
Found at i:337014 original size:18 final size:20
Alignment explanation
Indices: 336993--337029 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
336983 CAACATCATG
336993 TCTA-AAATAAACA-TTTTA
1 TCTACAAATAAACACTTTTA
*
337011 TCTACACATAAACACTTTT
1 TCTACAAATAAACACTTTT
337030 TGACAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 8 0.50
20 4 0.25
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (20 bp):
TCTACAAATAAACACTTTTA
Found at i:337080 original size:12 final size:13
Alignment explanation
Indices: 337050--337082 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
337040 GATTAGTTGA
337050 TTTTCAAAAGTACT
1 TTTTC-AAAGTACT
337064 TTTTCAAAGTA-T
1 TTTTCAAAGTACT
337076 TTTTCAA
1 TTTTCAA
337083 CCTTAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 6 0.32
14 5 0.26
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.48
Consensus pattern (13 bp):
TTTTCAAAGTACT
Found at i:337518 original size:29 final size:29
Alignment explanation
Indices: 337443--337523 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
337433 ATTTAATTAG
*
337443 TTTTTAAATTTTAAAAAATTCAAGAAATAT
1 TTTTTTAATTTTAAAAAATT-AAGAAATAT
* **
337473 GTTTTTAGAAATT-AAAAATTATA-AAATAT
1 TTTTTTA-ATTTTAAAAAATTA-AGAAATAT
337502 TTTTTTAATTTTAAAAAATTAA
1 TTTTTTAATTTTAAAAAATTAA
337524 TTAAATGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
28 4 0.10
29 21 0.51
30 13 0.32
31 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (29 bp):
TTTTTTAATTTTAAAAAATTAAGAAATAT
Found at i:339542 original size:9 final size:9
Alignment explanation
Indices: 339530--339592 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 9
339520 AACTTTTTAA
339530 ATATTTTTT
1 ATATTTTTT
*
339539 ATATTTTAT
1 ATATTTTTT
**
339548 ATAACTTTT
1 ATATTTTTT
339557 ATAGTTTTTT
1 ATA-TTTTTT
339567 -T-TTTTTT
1 ATATTTTTT
*
339574 A-ATTTTTA
1 ATATTTTTT
*
339582 ATATATTTT
1 ATATTTTTT
339591 AT
1 AT
339593 TTAATTTCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
7 6 0.15
8 6 0.15
9 25 0.61
10 4 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (9 bp):
ATATTTTTT
Found at i:339610 original size:21 final size:21
Alignment explanation
Indices: 339566--339610 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
339556 TATAGTTTTT
* * * *
339566 TTTTTTTTAATTTTTAATATA
1 TTTTATTTAATTTCTAACAAA
339587 TTTTATTTAATTTCTAACAAA
1 TTTTATTTAATTTCTAACAAA
339608 TTT
1 TTT
339611 CTATAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATTTAATTTCTAACAAA
Found at i:342309 original size:15 final size:15
Alignment explanation
Indices: 342289--342323 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
342279 ATAAAAATGT
*
342289 AATTTATCTTTTTAA
1 AATTTATATTTTTAA
*
342304 AATTTATATTTTTAT
1 AATTTATATTTTTAA
342319 AATTT
1 AATTT
342324 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTATATTTTTAA
Found at i:342903 original size:24 final size:24
Alignment explanation
Indices: 342876--342931 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
342866 GACTCAAAGG
342876 AATAAACAGAGTTTAATTGAAACA
1 AATAAACAGAGTTTAATTGAAACA
*
342900 AATAAATAGAGTTTAATTGAAACA
1 AATAAACAGAGTTTAATTGAAACA
342924 AATAAACA
1 AATAAACA
342932 ATATTTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.25
Consensus pattern (24 bp):
AATAAACAGAGTTTAATTGAAACA
Found at i:342938 original size:24 final size:24
Alignment explanation
Indices: 342876--342939 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
342866 GACTCAAAGG
*
342876 AATAAACAGAGTTTAATTGAAACA
1 AATAAACAGAATTTAATTGAAACA
* *
342900 AATAAATAGAGTTTAATTGAAACA
1 AATAAACAGAATTTAATTGAAACA
342924 AATAAACA-ATATTTAA
1 AATAAACAGA-ATTTAA
342940 CTAAAAGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (24 bp):
AATAAACAGAATTTAATTGAAACA
Found at i:344902 original size:24 final size:24
Alignment explanation
Indices: 344861--344921 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
344851 AACTAATAAG
* * * * *
344861 AGTTTGACTCAAACAAATAAATAG
1 AGTTTAACTGAAATAAATAAACAA
*
344885 AGTTTAATTGAAATAAATAAACAA
1 AGTTTAACTGAAATAAATAAACAA
344909 AGTTTAACTGAAA
1 AGTTTAACTGAAA
344922 GATTATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (24 bp):
AGTTTAACTGAAATAAATAAACAA
Found at i:346413 original size:23 final size:23
Alignment explanation
Indices: 346383--346428 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
346373 GTAAGCAAAG
346383 AAGAGTTTATGAAATAATAATCC
1 AAGAGTTTATGAAATAATAATCC
346406 AAGAGTTTATGAAATAATAATCC
1 AAGAGTTTATGAAATAATAATCC
346429 CCTAAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (23 bp):
AAGAGTTTATGAAATAATAATCC
Found at i:347663 original size:17 final size:16
Alignment explanation
Indices: 347641--347674 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
347631 AATTGCCACA
*
347641 TATATTTTTTTAATATT
1 TATATTTTATT-ATATT
347658 TATATTTTATTATATT
1 TATATTTTATTATATT
347674 T
1 T
347675 CTATAGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATATTTTATTATATT
Found at i:347909 original size:23 final size:25
Alignment explanation
Indices: 347870--347916 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
347860 ATTTAGATCC
347870 TTAAAATTATTATTTTT-TTATATT
1 TTAAAATTATTATTTTTCTTATATT
347894 TTAAAATT-TTATTTTTCTTATAT
1 TTAAAATTATTATTTTTCTTATAT
347917 ATTCTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
TTAAAATTATTATTTTTCTTATATT
Found at i:347975 original size:19 final size:18
Alignment explanation
Indices: 347953--347988 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
347943 AAAATATAAG
*
347953 TTTTGAAATTTTATAAATA
1 TTTTAAAATTTTA-AAATA
347972 TTTTAAAATTTTAAAAT
1 TTTTAAAATTTTAAAAT
347989 TTAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTAAAATTTTAAAATA
Found at i:347996 original size:14 final size:14
Alignment explanation
Indices: 347977--348006 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
347967 AAATATTTTA
*
347977 AAATTTTAAAATTT
1 AAATTTTAAAAATT
347991 AAATTTTAAAAATT
1 AAATTTTAAAAATT
348005 AA
1 AA
348007 TTTACTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTTAAAAATT
Found at i:353726 original size:60 final size:58
Alignment explanation
Indices: 353659--353816 Score: 148
Period size: 60 Copynumber: 2.7 Consensus size: 58
353649 ATAACATATT
353659 TAAAA-TTTATTAAAAATTAG-AAAAAAA-A-ACTACAAAAATAGTAAAAATTATAGTAAATTG
1 TAAAATTTTA-TAAAAATT-GTAAAAAAATATA-TA-AAAAATAG-AAAAA-TATAGTAAATTG
* *
353719 TAAAATTTTATAAAAATTGTAAAAAAATATATAAAAAATAGAAAAATATAGAAAAAAATTA
1 TAAAATTTTATAAAAATTGTAAAAAAATATATAAAAAATAGAAAAATATAG---TAAATTG
* * *
353780 TAAAATTTTAT-AAAGTCGTAAGAAAAT-TATAAAAAAT
1 TAAAATTTTATAAAAATTGTAAAAAAATATATAAAAAAT
353817 GTAAAGAAAT
Statistics
Matches: 86, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
58 5 0.06
59 16 0.19
60 41 0.48
61 23 0.27
62 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (58 bp):
TAAAATTTTATAAAAATTGTAAAAAAATATATAAAAAATAGAAAAATATAGTAAATTG
Found at i:353749 original size:19 final size:19
Alignment explanation
Indices: 353682--353851 Score: 89
Period size: 20 Copynumber: 8.7 Consensus size: 19
353672 AAATTAGAAA
* * *
353682 AAAAAACTACAAAAATAGT
1 AAAAAATTATAAAAATTGT
*
353701 -AAAAATTATAGTAAATTGT
1 AAAAAATTATA-AAAATTGT
**
353720 AAAATTTTATAAAAATTGT
1 AAAAAATTATAAAAATTGT
*
353739 AAAAAAATATATAAAAAATAG-
1 -AAAAAAT-TAT-AAAAATTGT
* * *
353760 AAAAATATAGAAAAAAATTAT
1 AAAAA-AT-TATAAAAATTGT
** * *
353781 AAAATTTTAT-AAAGTCGT
1 AAAAAATTATAAAAATTGT
*
353799 AAGAAAATTATAAAAAATGT
1 AA-AAAATTATAAAAATTGT
353819 AAAGAAA-TAT-AAAATTCGT
1 AAA-AAATTATAAAAATT-GT
353838 AAAAAATTATAAAA
1 AAAAAATTATAAAA
353852 GTTATAGTAT
Statistics
Matches: 111, Mismatches: 27, Indels: 25
0.68 0.17 0.15
Matches are distributed among these distances:
18 23 0.21
19 32 0.29
20 38 0.34
21 11 0.10
22 7 0.06
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (19 bp):
AAAAAATTATAAAAATTGT
Found at i:354030 original size:21 final size:19
Alignment explanation
Indices: 354005--354069 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
353995 TAAAATGGTC
*
354005 TTTTTGATGCATTTTATAATT
1 TTTTTTATG-ATTTTATAA-T
354026 TTTTTTATGATTTTTATAAAT
1 TTTTTTATGA-TTTTAT-AAT
* *
354047 TTTATAAT-ATTTTATAACT
1 TTTTTTATGATTTTATAA-T
354066 TTTT
1 TTTT
354070 AGCAATTGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.05
19 10 0.27
20 2 0.05
21 21 0.57
22 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTTATGATTTTATAAT
Found at i:354069 original size:29 final size:28
Alignment explanation
Indices: 354028--354088 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
354018 TTATAATTTT
* * *
354028 TTTTATGATTTTTATAAATTTTATAATA
1 TTTTATAATTTTTAGAAATTGTATAATA
* *
354056 TTTTATAACTTTTTAGCAATTGTATAATT
1 TTTTATAA-TTTTTAGAAATTGTATAATA
354085 TTTT
1 TTTT
354089 TTTTCTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTATAATTTTTAGAAATTGTATAATA
Found at i:354150 original size:10 final size:9
Alignment explanation
Indices: 354027--354141 Score: 62
Period size: 9 Copynumber: 12.8 Consensus size: 9
354017 TTTATAATTT
*
354027 TTTTTATGA
1 TTTTTATAA
354036 TTTTTATAA
1 TTTTTATAA
*
354045 ATTTTATAA
1 TTTTTATAA
354054 TATTTTATAA
1 T-TTTTATAA
*
354064 CTTTTTAGCAA
1 -TTTTTA-TAA
*
354075 -TTGTATAA
1 TTTTTATAA
354083 TTTTT-T--
1 TTTTTATAA
354089 TTTTCTA-AA
1 TTTT-TATAA
*
354098 TTTTAAT-A
1 TTTTTATAA
354106 TTTTTATTAAA
1 TTTTTA-T-AA
* * *
354117 ATCTAATAA
1 TTTTTATAA
354126 TTTTTATAA
1 TTTTTATAA
354135 TTTTTAT
1 TTTTTAT
354142 TGATTTTTAC
Statistics
Matches: 79, Mismatches: 15, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 10 0.13
9 43 0.54
10 14 0.18
11 7 0.09
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:362404 original size:5 final size:5
Alignment explanation
Indices: 362394--362418 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
362384 GTTAAAAATA
362394 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
362419 TTAAATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:362843 original size:20 final size:21
Alignment explanation
Indices: 362810--362851 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
362800 TTACCTCAAA
*
362810 CCCCAAATTATTTTACTCCTC
1 CCCCAAAATATTTTACTCCTC
362831 CCCCAAAAT-TTTTACTCCTC
1 CCCCAAAATATTTTACTCCTC
362851 C
1 C
362852 TCACATTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (21 bp):
CCCCAAAATATTTTACTCCTC
Done.