Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012091.1 Kokia drynarioides strain JFW-HI SEQ_127090, 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: 138870
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:159 original size:27 final size:27
Alignment explanation
Indices: 118--224 Score: 187
Period size: 27 Copynumber: 4.0 Consensus size: 27
108 CAATGTGAGG
118 TTGGTGCCGCCTGTCAGGTAGGCACCT
1 TTGGTGCCGCCTGTCAGGTAGGCACCT
* *
145 CTAGTGCCGCCTGTCAGGTAGGCACCT
1 TTGGTGCCGCCTGTCAGGTAGGCACCT
172 TTGGTGCCGCCTGTCAGGTAGGCACCT
1 TTGGTGCCGCCTGTCAGGTAGGCACCT
*
199 TTGGTGCCGCCTGTCAGATAGGCACC
1 TTGGTGCCGCCTGTCAGGTAGGCACC
225 ACCCCACTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.13, C:0.31, G:0.32, T:0.24
Consensus pattern (27 bp):
TTGGTGCCGCCTGTCAGGTAGGCACCT
Found at i:2468 original size:32 final size:32
Alignment explanation
Indices: 2432--2495 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2422 GACAAATATC
*
2432 TCGATTTGATTTGTTTCTAATCAAATTGATTT
1 TCGATTTGATTTGATTCTAATCAAATTGATTT
*
2464 TCGATTTGATTTGATTCTATTCAAATTGATTT
1 TCGATTTGATTTGATTCTAATCAAATTGATTT
2496 AAAGACTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.53
Consensus pattern (32 bp):
TCGATTTGATTTGATTCTAATCAAATTGATTT
Found at i:2909 original size:46 final size:46
Alignment explanation
Indices: 2856--2967 Score: 109
Period size: 49 Copynumber: 2.3 Consensus size: 46
2846 TCAAATCCTG
* *
2856 TTATTTAAATTGTTTTTAGATCTGATGTTTTA-AAAAATATAAATAT
1 TTATTTAAATT-TTTTTAGATATGATGTTTTACAAAAACATAAATAT
* *
2902 TTATTTAATTTATTTTGTTTAGATATGGTGTTTTACATAAACATAAATAT
1 TTATTTAA---ATTTT-TTTAGATATGATGTTTTACAAAAACATAAATAT
* * *
2952 TTGTTTATATTATTTT
1 TTATTTAAATTTTTTT
2968 GTACAGATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
46 11 0.20
47 4 0.07
48 2 0.04
49 19 0.35
50 18 0.33
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (46 bp):
TTATTTAAATTTTTTTAGATATGATGTTTTACAAAAACATAAATAT
Found at i:2934 original size:49 final size:50
Alignment explanation
Indices: 2870--2969 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
2860 TTAAATTGTT
* *
2870 TTTAGATCTGATGTTTTA-AAAAATATAAATATTTATTTA-ATTTATTTTG
1 TTTAGATATGATGTTTTACAAAAACATAAATATTTATTTATA-TTATTTTG
* * *
2919 TTTAGATATGGTGTTTTACATAAACATAAATATTTGTTTATATTATTTTG
1 TTTAGATATGATGTTTTACAAAAACATAAATATTTATTTATATTATTTTG
2969 T
1 T
2970 ACAGATATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
49 16 0.36
50 27 0.61
51 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (50 bp):
TTTAGATATGATGTTTTACAAAAACATAAATATTTATTTATATTATTTTG
Found at i:2992 original size:50 final size:50
Alignment explanation
Indices: 2894--2992 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
2884 TTTAAAAAAT
** * *
2894 ATAAATATTTATTTAATTTATTTTGTTTAGATATGGTGTTTTACATAAAC
1 ATAAATATTTATTTAATTTATTTTGTACAGATATGGTATTTAACATAAAC
* * *
2944 ATAAATATTTGTTT-ATATTATTTTGTACAGATATTGTATTTAATATAAA
1 ATAAATATTTATTTAAT-TTATTTTGTACAGATATGGTATTTAACATAAA
2993 TTTTTATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.05
50 39 0.95
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (50 bp):
ATAAATATTTATTTAATTTATTTTGTACAGATATGGTATTTAACATAAAC
Found at i:5259 original size:122 final size:121
Alignment explanation
Indices: 5042--5289 Score: 471
Period size: 122 Copynumber: 2.0 Consensus size: 121
5032 GAAAATGGTG
5042 AGATTTGTAAAGGGAGAAAGAGTGAATTCGAGGAGAAGAATTGAACATTGAAGTAAAAGACTGCT
1 AGATTTGTAAAGGGAGAAAGAGTGAATTCGAGGAGAAGAATTGAACATTGAAGTAAAAGACTGCT
*
5107 ACTTTCTACCTTTGGATGGTGCCACCTCACCATATTTGAATTTATTTATTTTTTAAA
66 ACTTTCCACCTTTGGATGGTGCCACCTCACCATATTTGAATTTATTTA-TTTTTAAA
5164 AGATTTGTAAAGGGAGAAAGAGTGAATTCGAGGAGAAGAATTGAACATTGAAGTAAAAGACTGCT
1 AGATTTGTAAAGGGAGAAAGAGTGAATTCGAGGAGAAGAATTGAACATTGAAGTAAAAGACTGCT
5229 ACTTTCCACCTTTGGATGGTGCCACCTCACCATATTTGAATTTATTTATTTTTAAA
66 ACTTTCCACCTTTGGATGGTGCCACCTCACCATATTTGAATTTATTTATTTTTAAA
5285 A-ATTT
1 AGATTT
5290 TTCTGTTTAA
Statistics
Matches: 125, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
120 4 0.03
121 9 0.07
122 112 0.90
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (121 bp):
AGATTTGTAAAGGGAGAAAGAGTGAATTCGAGGAGAAGAATTGAACATTGAAGTAAAAGACTGCT
ACTTTCCACCTTTGGATGGTGCCACCTCACCATATTTGAATTTATTTATTTTTAAA
Found at i:5716 original size:9 final size:9
Alignment explanation
Indices: 5702--5727 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5692 AGGTTCACTT
5702 TTTTTTTTC
1 TTTTTTTTC
5711 TTTTTTTTC
1 TTTTTTTTC
5720 TTTTTTTT
1 TTTTTTTT
5728 AGAGTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:12314 original size:46 final size:46
Alignment explanation
Indices: 12258--12350 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
12248 ATGGTATCAG
12258 AGTTAATTATTTTTTGGGAGTTTGTTTAAAGAATTATGGTGGTTCT
1 AGTTAATTATTTTTTGGGAGTTTGTTTAAAGAATTATGGTGGTTCT
12304 AGTTAATTATTTTTTGGGAGTTTGTTTAAAGAATTATGGTGGTTCT
1 AGTTAATTATTTTTTGGGAGTTTGTTTAAAGAATTATGGTGGTTCT
12350 A
1 A
12351 AAAATAATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.25, C:0.02, G:0.24, T:0.49
Consensus pattern (46 bp):
AGTTAATTATTTTTTGGGAGTTTGTTTAAAGAATTATGGTGGTTCT
Found at i:28258 original size:25 final size:25
Alignment explanation
Indices: 28219--28278 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
28209 TCTCTTTCTC
* *
28219 TTTCTCCTTTCATTTTTAGATTAGGT
1 TTTCT-CTTTCATTTTTAGAGTAGAT
*
28245 TTTCTCTTTTATTTTTAGAGTAGAT
1 TTTCTCTTTCATTTTTAGAGTAGAT
28270 TTTACTCTT
1 TTT-CTCTT
28279 GTAGTTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (25 bp):
TTTCTCTTTCATTTTTAGAGTAGAT
Found at i:28286 original size:26 final size:25
Alignment explanation
Indices: 28232--28286 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
28222 CTCCTTTCAT
* * * *
28232 TTTTAGATTAGGTTTTCTCTTTTAT
1 TTTTAGAGTAGATTTTCTCTTGTAG
28257 TTTTAGAGTAGATTTTACTCTTGTAG
1 TTTTAGAGTAGATTTT-CTCTTGTAG
28283 TTTT
1 TTTT
28287 CTTTTTTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.18, C:0.07, G:0.15, T:0.60
Consensus pattern (25 bp):
TTTTAGAGTAGATTTTCTCTTGTAG
Found at i:30296 original size:44 final size:44
Alignment explanation
Indices: 30246--30340 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
30236 AGTTATCCTT
* *
30246 ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTTATTAATTA
1 ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAACTA
30290 ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAACTA
1 ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAACTA
30334 ATTAACT
1 ATTAACT
30341 AGTCGACCAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (44 bp):
ATTAACTTCAAAATTCGAGTTTTATCGAGTTAGCTAATTAACTA
Found at i:36639 original size:28 final size:27
Alignment explanation
Indices: 36608--36771 Score: 123
Period size: 28 Copynumber: 6.0 Consensus size: 27
36598 CGAGCCCTTG
*
36608 TATACAAACCCCTATAGGCGAACTCCTA
1 TATATAAACCCCTATAGGCGAAC-CCTA
* * * *
36636 TATATGAACCCTTATAAGTGAACCCTA
1 TATATAAACCCCTATAGGCGAACCCTA
* ** *
36663 TATGTAGGCCCTTATAGGC-AAGCCCCTA
1 TATATAAACCCCTATAGGCGAA--CCCTA
* *
36691 TATACAAACCCCTATAGGCAAACTCCTA
1 TATATAAACCCCTATAGGCGAAC-CCTA
* * *
36719 TATATGAACCCCTATAAGTGAACCCTA
1 TATATAAACCCCTATAGGCGAACCCTA
* * * *
36746 TATGTGAGCCCCTATAGACGAACCCT
1 TATATAAACCCCTATAGGCGAACCCT
36772 TGTATGCGAA
Statistics
Matches: 106, Mismatches: 26, Indels: 9
0.75 0.18 0.06
Matches are distributed among these distances:
26 2 0.02
27 43 0.41
28 59 0.56
29 2 0.02
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (27 bp):
TATATAAACCCCTATAGGCGAACCCTA
Found at i:36732 original size:14 final size:14
Alignment explanation
Indices: 36627--36761 Score: 57
Period size: 14 Copynumber: 9.8 Consensus size: 14
36617 CCCTATAGGC
*
36627 GAACTCCTATATAT
1 GAACCCCTATATAT
*
36641 GAACCCTTATA-AGT
1 GAACCCCTATATA-T
*
36655 GAA-CCCTATATGT
1 GAACCCCTATATAT
** *
36668 -AGGCCCT-TATAG
1 GAACCCCTATATAT
*
36680 GCAAGCCCCTATATAC
1 G-AA-CCCCTATATAT
* ***
36696 AAACCCCTATAGGC
1 GAACCCCTATATAT
* *
36710 AAACTCCTATATAT
1 GAACCCCTATATAT
36724 GAACCCCTATA-AGT
1 GAACCCCTATATA-T
*
36738 GAA-CCCTATATGT
1 GAACCCCTATATAT
*
36751 GAGCCCCTATA
1 GAACCCCTATA
36762 GACGAACCCT
Statistics
Matches: 90, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
12 4 0.04
13 23 0.26
14 53 0.59
15 6 0.07
16 4 0.04
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.26
Consensus pattern (14 bp):
GAACCCCTATATAT
Found at i:36746 original size:13 final size:14
Alignment explanation
Indices: 36723--36761 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
36713 CTCCTATATA
36723 TGAACCCCTATAAG
1 TGAACCCCTATAAG
*
36737 TGAA-CCCTATATG
1 TGAACCCCTATAAG
*
36750 TGAGCCCCTATA
1 TGAACCCCTATA
36762 GACGAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (14 bp):
TGAACCCCTATAAG
Found at i:36784 original size:83 final size:82
Alignment explanation
Indices: 36575--36793 Score: 271
Period size: 83 Copynumber: 2.6 Consensus size: 82
36565 CATGTGAACC
* * * * *
36575 CCCTATAGGCGAGCCCCTGTATGCGAGCCCTTGTATACAAACCCCTATAGGCGAACTCCTATATA
1 CCCTATATGTGAGCCCCTATA-GCGAACCCTTGTATACAAACCCCTATAGGCAAACTCCTATATA
*
36640 TGAACCCTTATAAGTGAA
65 TGAACCCCTATAAGTGAA
* * *
36658 CCCTATATGT-AGGCCCTTATAG-GCAAGCCCCTATATACAAACCCCTATAGGCAAACTCCTATA
1 CCCTATATGTGA-GCCCCTATAGCG-AA-CCCTTGTATACAAACCCCTATAGGCAAACTCCTATA
36721 TATGAACCCCTATAAGTGAA
63 TATGAACCCCTATAAGTGAA
* *
36741 CCCTATATGTGAGCCCCTATAGACGAACCCTTGTATGCGAACCCCTTATAGGC
1 CCCTATATGTGAGCCCCTATAG-CGAACCCTTGTATACAAACCCC-TATAGGC
36794 GAGCCCATGT
Statistics
Matches: 115, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
81 1 0.01
82 3 0.03
83 100 0.87
84 10 0.09
85 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (82 bp):
CCCTATATGTGAGCCCCTATAGCGAACCCTTGTATACAAACCCCTATAGGCAAACTCCTATATAT
GAACCCCTATAAGTGAA
Found at i:36804 original size:29 final size:28
Alignment explanation
Indices: 36754--36818 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
36744 TATATGTGAG
* *
36754 CCCCTATAGACGAACCCTTGTATGCGAA
1 CCCCTATAGACGAACCCATGTATGCAAA
* *
36782 CCCCTTATAGGCGAGCCCATGTATGCAAA
1 CCCC-TATAGACGAACCCATGTATGCAAA
36811 CCCTCTAT
1 CCC-CTAT
36819 TTATGTAGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 4 0.13
29 26 0.84
30 1 0.03
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (28 bp):
CCCCTATAGACGAACCCATGTATGCAAA
Found at i:37247 original size:252 final size:251
Alignment explanation
Indices: 36803--37316 Score: 956
Period size: 252 Copynumber: 2.0 Consensus size: 251
36793 CGAGCCCATG
* * * **
36803 TATGCAAACCCTCTATTTATGTAGGGTAAGTTCTGTTATTTTTAAATTGTTGGTTGTATTGTTAT
1 TATGCAAACCCCCCATATATGTAGGGTAAGTGATGTTATTTTTAAATTGTTGGTTGTATTGTTAT
36868 TTTTGTAGCTCTGTTGTTTAGACTAGTGCTAGGAGTATCTTTATTTCTTTTGGTTTGGATATTCT
66 TTTTGTAGCTCTGTTGTTTAGACTAGTGCTAGGAGTATCTTTATTTCTTTTGGTTTGGATATTCT
36933 AATGCCTTAAACTTTGTAAGATTATGACTGAGCAAAAAAAAACATGCGAACCCAAATGCTAAACC
131 AATGCCTTAAACTTTGTAAGATTATGACTGAGCAAAAAAAAACATGCGAACCCAAATGCTAAACC
36998 TTATATGATTTAATGTGCGAGTTTTTAGTATATTTACACGAACTCTAACCGTTTAA
196 TTATATGATTTAATGTGCGAGTTTTTAGTATATTTACACGAACTCTAACCGTTTAA
*
37054 TATGCAAACCCCCCATATATGTAGGGTAAGTGATGTTATTTTTTAAATTGTTGGTTGTATTGTTG
1 TATGCAAACCCCCCATATATGTAGGGTAAGTGATGTTA-TTTTTAAATTGTTGGTTGTATTGTTA
37119 TTTTTGTAGCTCTGTTGTTTAGACTAGTGCTAGGAGTATCTTTATTTCTTTTGGTTTGGATATTC
65 TTTTTGTAGCTCTGTTGTTTAGACTAGTGCTAGGAGTATCTTTATTTCTTTTGGTTTGGATATTC
*
37184 TAATGCCTTAAACTTTGTAAGATTATGACTGAGCAAAAAAAAATATGCGAACCCAAATGCTAAAC
130 TAATGCCTTAAACTTTGTAAGATTATGACTGAGCAAAAAAAAACATGCGAACCCAAATGCTAAAC
37249 CTTATATGATTTAATGTGCGAGTTTTTAGTATATTTACACGAACTCTAACCGTTTAA
195 CTTATATGATTTAATGTGCGAGTTTTTAGTATATTTACACGAACTCTAACCGTTTAA
37306 TATGCAAACCC
1 TATGCAAACCC
37317 TATATGTATA
Statistics
Matches: 255, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
251 33 0.13
252 222 0.87
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (251 bp):
TATGCAAACCCCCCATATATGTAGGGTAAGTGATGTTATTTTTAAATTGTTGGTTGTATTGTTAT
TTTTGTAGCTCTGTTGTTTAGACTAGTGCTAGGAGTATCTTTATTTCTTTTGGTTTGGATATTCT
AATGCCTTAAACTTTGTAAGATTATGACTGAGCAAAAAAAAACATGCGAACCCAAATGCTAAACC
TTATATGATTTAATGTGCGAGTTTTTAGTATATTTACACGAACTCTAACCGTTTAA
Found at i:37501 original size:15 final size:15
Alignment explanation
Indices: 37483--37601 Score: 75
Period size: 15 Copynumber: 8.0 Consensus size: 15
37473 TTATACATGA
*
37483 GAACCCTAGATGTGG
1 GAACCCTAGATGTGC
37498 GAACCCCCTAG--GTGC
1 GAA--CCCTAGATGTGC
* *
37513 GAGCCCTATATGTGC
1 GAACCCTAGATGTGC
*
37528 GAACCCT-GTATGTGT
1 GAACCCTAG-ATGTGC
*
37543 GAACCCTACATGTGC
1 GAACCCTAGATGTGC
* ** *
37558 GAACCTTTTAGGTGC
1 GAACCCTAGATGTGC
* *
37573 AAACCC-ATATGTGC
1 GAACCCTAGATGTGC
*
37587 GAACCCTATATGTGC
1 GAACCCTAGATGTGC
37602 AAGCCCTACT
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
13 5 0.06
14 11 0.14
15 58 0.73
17 6 0.08
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (15 bp):
GAACCCTAGATGTGC
Found at i:37550 original size:30 final size:30
Alignment explanation
Indices: 37483--37609 Score: 114
Period size: 30 Copynumber: 4.3 Consensus size: 30
37473 TTATACATGA
* * **
37483 GAACCCTAGATGTGGGAACCCCCTAGGTGC
1 GAACCCTATATGTGCGAACCCTATAGGTGC
* * * *
37513 GAGCCCTATATGTGCGAACCCTGTATGTGT
1 GAACCCTATATGTGCGAACCCTATAGGTGC
* * *
37543 GAACCCTACATGTGCGAACCTTTTAGGTGC
1 GAACCCTATATGTGCGAACCCTATAGGTGC
* *
37573 AAACCC-ATATGTGCGAACCCTATATGTGC
1 GAACCCTATATGTGCGAACCCTATAGGTGC
37602 -AAGCCCTA
1 GAA-CCCTA
37610 CTTAAGAACC
Statistics
Matches: 77, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
28 2 0.03
29 22 0.29
30 53 0.69
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (30 bp):
GAACCCTATATGTGCGAACCCTATAGGTGC
Found at i:39297 original size:23 final size:25
Alignment explanation
Indices: 39270--39315 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39260 CCAATTAGGG
39270 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
39293 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
39316 GGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:41084 original size:11 final size:11
Alignment explanation
Indices: 41068--41106 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
41058 TGACTTTGCT
41068 ATTCATGCTTG
1 ATTCATGCTTG
* *
41079 ATTCATACTGG
1 ATTCATGCTTG
41090 ATTCATGCTTG
1 ATTCATGCTTG
41101 ATTCAT
1 ATTCAT
41107 AAGAGAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (11 bp):
ATTCATGCTTG
Found at i:43833 original size:19 final size:20
Alignment explanation
Indices: 43790--43830 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
43780 ATTACAAAAT
43790 AATTCAAAATAATATTTAAA
1 AATTCAAAATAATATTTAAA
* *
43810 AATTCAAAATATTTTTTAAA
1 AATTCAAAATAATATTTAAA
43830 A
1 A
43831 TTCTAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTCAAAATAATATTTAAA
Found at i:43859 original size:11 final size:11
Alignment explanation
Indices: 43840--43893 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
43830 ATTCTAATTC
*
43840 TTTATAAAAAT
1 TTTAAAAAAAT
43851 TTTAAAAAAAT
1 TTTAAAAAAAT
43862 TTTAAAAAAAT
1 TTTAAAAAAAT
* *
43873 TCTAAAGAATAT
1 TTTAAA-AAAAT
*
43885 ATTAAAAAA
1 TTTAAAAAA
43894 GATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
11 28 0.78
12 8 0.22
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (11 bp):
TTTAAAAAAAT
Found at i:48738 original size:3 final size:3
Alignment explanation
Indices: 48730--48759 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
48720 ATCTCAATAC
*
48730 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
48760 GTTGTTGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:48764 original size:3 final size:3
Alignment explanation
Indices: 48758--48789 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48748 ATTATTATTA
48758 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
48790 TAAGCCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:66683 original size:25 final size:25
Alignment explanation
Indices: 66655--66707 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
66645 AATTGAAATA
66655 TCCTATTCCTAGTCTATTAGAATTC
1 TCCTATTCCTAGTCTATTAGAATTC
66680 TCCTATTCCTAGTCTATTAGAATTC
1 TCCTATTCCTAGTCTATTAGAATTC
66705 TCC
1 TCC
66708 CTTAACCGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.23, C:0.26, G:0.08, T:0.43
Consensus pattern (25 bp):
TCCTATTCCTAGTCTATTAGAATTC
Found at i:73222 original size:19 final size:19
Alignment explanation
Indices: 73200--73244 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
73190 TTATATTAGG
73200 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
73219 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
73238 ATTTAAT
1 ATTTAAT
73245 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:74078 original size:21 final size:21
Alignment explanation
Indices: 74049--74088 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
74039 ACTTCCCTAT
74049 TTCTATTTCTTTTATTTTTAA
1 TTCTATTTCTTTTATTTTTAA
*
74070 TTCTGTTTCTTTTATTTTT
1 TTCTATTTCTTTTATTTTT
74089 TCCTTAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (21 bp):
TTCTATTTCTTTTATTTTTAA
Found at i:79573 original size:100 final size:100
Alignment explanation
Indices: 79400--79602 Score: 406
Period size: 100 Copynumber: 2.0 Consensus size: 100
79390 ACAAGAACAC
79400 AAGACTAATTGCGATGTTGCAACATGAAGTGTCGATGTCGCAACATAGTAAACAAAGCACTCAAC
1 AAGACTAATTGCGATGTTGCAACATGAAGTGTCGATGTCGCAACATAGTAAACAAAGCACTCAAC
79465 AGGAGCAAACTATCACCAATATTGCAACATAGATA
66 AGGAGCAAACTATCACCAATATTGCAACATAGATA
79500 AAGACTAATTGCGATGTTGCAACATGAAGTGTCGATGTCGCAACATAGTAAACAAAGCACTCAAC
1 AAGACTAATTGCGATGTTGCAACATGAAGTGTCGATGTCGCAACATAGTAAACAAAGCACTCAAC
79565 AGGAGCAAACTATCACCAATATTGCAACATAGATA
66 AGGAGCAAACTATCACCAATATTGCAACATAGATA
79600 AAG
1 AAG
79603 GGTTTGAATG
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (100 bp):
AAGACTAATTGCGATGTTGCAACATGAAGTGTCGATGTCGCAACATAGTAAACAAAGCACTCAAC
AGGAGCAAACTATCACCAATATTGCAACATAGATA
Found at i:83378 original size:18 final size:19
Alignment explanation
Indices: 83355--83409 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
83345 GGAGTCGTGC
*
83355 ACATGGTCATGA-TGATGG
1 ACATGGTCATGAGTCATGG
83373 ACATGGTCAT-AGTCATGG
1 ACATGGTCATGAGTCATGG
*
83391 ACATGGACATG-GTCATGG
1 ACATGGTCATGAGTCATGG
83409 A
1 A
83410 GGTGAGGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 32 0.97
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (19 bp):
ACATGGTCATGAGTCATGG
Found at i:83407 original size:12 final size:12
Alignment explanation
Indices: 83369--83409 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
83359 GGTCATGATG
83369 ATGGACATGGTC
1 ATGGACATGGTC
* * *
83381 ATAGTCATGGAC
1 ATGGACATGGTC
83393 ATGGACATGGTC
1 ATGGACATGGTC
83405 ATGGA
1 ATGGA
83410 GGTGAGGATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (12 bp):
ATGGACATGGTC
Found at i:85001 original size:60 final size:61
Alignment explanation
Indices: 84910--85034 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 61
84900 TTTGTTTTAA
* *
84910 TTAAATTTGATGTTTAATCTCTGGTCATCAATTTTTAGAAAGAGTT-GAATTGATTTTTTT
1 TTAAATTTGATGTTCAATCTCTAGTCATCAATTTTTAGAAAGAGTTCGAATTGATTTTTTT
* *
84970 TTAAATTTGATGTTCAATCTTTAGTCATCAATTTTTAGACAGAGTTCGAATTGATTTTTTT
1 TTAAATTTGATGTTCAATCTCTAGTCATCAATTTTTAGAAAGAGTTCGAATTGATTTTTTT
85031 TTAA
1 TTAA
85035 TTGAAATACT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
60 42 0.70
61 18 0.30
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.50
Consensus pattern (61 bp):
TTAAATTTGATGTTCAATCTCTAGTCATCAATTTTTAGAAAGAGTTCGAATTGATTTTTTT
Found at i:85893 original size:11 final size:13
Alignment explanation
Indices: 85869--85903 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
85859 TTTACTATTT
85869 ATATATTAATAAA
1 ATATATTAATAAA
85882 ATAT-TTAA-AAA
1 ATATATTAATAAA
85893 ATATATTAATA
1 ATATATTAATA
85904 TTTACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.35
12 8 0.40
13 5 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATTAATAAA
Found at i:102799 original size:22 final size:23
Alignment explanation
Indices: 102768--102812 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
102758 TAAAGCAGTC
102768 TTAAAATAT-ATCAAAAT-ATTAT
1 TTAAAATATAAT-AAAATCATTAT
*
102790 TTAAACTATAATAAAATCATTAT
1 TTAAAATATAATAAAATCATTAT
102813 GGATTTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAATATAATAAAATCATTAT
Found at i:102939 original size:21 final size:21
Alignment explanation
Indices: 102915--102955 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
102905 TCTTCCAATC
102915 ATTAATATTTTTAAAAAATAT
1 ATTAATATTTTTAAAAAATAT
*
102936 ATTAATATTTTTTAAAAATA
1 ATTAATATTTTTAAAAAATA
102956 ATGTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAATATTTTTAAAAAATAT
Found at i:105568 original size:3 final size:3
Alignment explanation
Indices: 105560--105603 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
105550 AATAATTCAT
105560 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
105604 ATCAAGGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:119643 original size:9 final size:9
Alignment explanation
Indices: 119625--119677 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
119615 GTCAGCAAAT
119625 AATT-TTAA
1 AATTATTAA
119633 AATTATTAA
1 AATTATTAA
119642 AATTATT--
1 AATTATTAA
119649 --TT-TTAA
1 AATTATTAA
119655 AA-TA-TAA
1 AATTATTAA
119662 AATTATTAA
1 AATTATTAA
119671 AATTATT
1 AATTATT
119678 TTTTTGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.16
8 6 0.16
9 21 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:119649 original size:20 final size:20
Alignment explanation
Indices: 119621--119677 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
119611 TCACGTCAGC
*
119621 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
119641 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
119661 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
119678 TTTTTGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:119672 original size:29 final size:31
Alignment explanation
Indices: 119630--119702 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
119620 CAAATAATTT
119630 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
*
119659 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
119690 TAAAATTATTAAA
1 TAAAATTATTAAA
119703 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 17 0.41
30 10 0.24
31 14 0.34
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAA
Found at i:119709 original size:30 final size:29
Alignment explanation
Indices: 119630--119709 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 29
119620 CAAATAATTT
*
119630 TAAAATTATTAAA-ATTATTTTTTAAAATA
1 TAAAATTATTAAATAAT-TTTTTTAAAATA
* *
119659 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATAATTTTTTTAAAAT-A
119690 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
119710 AATTTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 10 0.23
30 22 0.50
31 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAATAATTTTTTTAAAATA
Found at i:131435 original size:2 final size:2
Alignment explanation
Indices: 131428--131458 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
131418 ATACATAATT
131428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
131459 GCAAAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:132114 original size:21 final size:21
Alignment explanation
Indices: 132067--132116 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
132057 ATTAGTGCAG
* *
132067 ACTTCTACTGATACAAGTGAT
1 ACTTCTACTGAAACAAGTCAT
* *
132088 AGTTCTACTGAAACAAGTCTT
1 ACTTCTACTGAAACAAGTCAT
132109 ACTTCTAC
1 ACTTCTAC
132117 CGATACTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (21 bp):
ACTTCTACTGAAACAAGTCAT
Found at i:132300 original size:21 final size:21
Alignment explanation
Indices: 132276--132315 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
132266 TACCCTGTAC
*
132276 TTCTACCGAAACATGTATGGG
1 TTCTACCGAAACAAGTATGGG
132297 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
132316 CAAAATCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGG
Done.