Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014967.1 Kokia drynarioides strain JFW-HI SEQ_130011, 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: 148366
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 109 characters in sequence are not A, C, G, or T
Found at i:994 original size:37 final size:39
Alignment explanation
Indices: 944--1036 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
934 CGGATAGATT
*
944 CGATGAGGTACTGGGTACCAC-T-TTGCTTCG-ACTAGGC
1 CGATGAGGCACTGGGTACCACTTATTGCTTCGAACTA-GC
* ** *
981 CGATGAGACACTGGGTGTCACTTTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTACCAC-TTATTGCTTCGAACTAGC
1021 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
1037 GCCATTCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 17 0.37
39 1 0.02
40 24 0.52
41 4 0.09
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (39 bp):
CGATGAGGCACTGGGTACCACTTATTGCTTCGAACTAGC
Found at i:8901 original size:202 final size:205
Alignment explanation
Indices: 8396--8948 Score: 548
Period size: 202 Copynumber: 2.7 Consensus size: 205
8386 TACAAAATTA
* * *
8396 AAAACTACTCATAACCCCCTCTCAATCCTTAAATAGGAGGATAATGCGCTTCAATACACTTGAAC
1 AAAACTACTCATAA--CCCTCTCAACCCTTAAATAGGAGGATAATGCGCTTCAGTACACTCGAAC
* * * * * *
8461 TCACGTCCTCCTGTACTGTCAACAATATCGATACCAATCAAGCTAAGATTCAATCGGCAACTTAA
64 CCATGTCCTCCTGTACTGACAACAATATCGATACCAATCGAGCTAAGATTAAATCGACAACTTAA
* ** * * *
8526 AATGTATTATGTATTCTTTTTTTTTTTTTAACATCTCATTATTGGTTATTATCATCTGCTCTTTT
129 AATGTATTATGCATTCTTTTTTTAATATTAACATCTCATTATAGGTTATTATCATCTGCTCTTTG
* *
8591 TTATGCAAAGCCT
194 GTA-GCAAAACCT
* ** * *
8604 AAAACTTCTCATAACTCCTCCTCAACTTTTAAGTAGGAGG---ATGCGCTTCAGCACACTCGAAC
1 AAAACTACTCATAAC-CCT-CTCAACCCTTAAATAGGAGGATAATGCGCTTCAGTACACTCGAAC
* * * *
8666 CAATGTCCTCCTGTACAGGCAACAATATCGATACCAATCGAGCTAAGATTAAATTGACAACTTAA
64 CCATGTCCTCCTGTACTGACAACAATATCGATACCAATCGAGCTAAGATTAAATCGACAACTTAA
*
8731 ACATGTATTATGCA-T-TTTTTTTAATATT-A-ATCTCATTATAGGTTCTTATCATCTGCTC-TT
129 A-ATGTATTATGCATTCTTTTTTTAATATTAACATCTCATTATAGGTTATTATCATCTGCTCTTT
8791 GGTA-CAAAACCT
193 GGTAGCAAAACCT
* * * * * *
8803 AAAACTACTTATAGTCCCTCATCAACCCTTAAATAGGAGGATAATACACTTCAGTGCACTCAAAC
1 AAAACTACTCATA-ACCCTC-TCAACCCTTAAATAGGAGGATAATGCGCTTCAGTACACTCGAAC
** ** * * ** * * * *
8868 CCATGTCCTCCTACACTGACAACGGTGTCGATACTAATCGAATTAAAACTCAATCAACAACTTAA
64 CCATGTCCTCCTGTACTGACAACAATATCGATACCAATCGAGCTAAGATTAAATCGACAACTTAA
*
8933 ATATGAATTATGCATT
129 A-ATGTATTATGCATT
8949 GTTGAAATTA
Statistics
Matches: 281, Mismatches: 55, Indels: 23
0.78 0.15 0.06
Matches are distributed among these distances:
198 1 0.00
199 37 0.13
200 1 0.00
201 4 0.01
202 105 0.37
203 2 0.01
204 10 0.04
205 77 0.27
206 12 0.04
207 3 0.01
208 29 0.10
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (205 bp):
AAAACTACTCATAACCCTCTCAACCCTTAAATAGGAGGATAATGCGCTTCAGTACACTCGAACCC
ATGTCCTCCTGTACTGACAACAATATCGATACCAATCGAGCTAAGATTAAATCGACAACTTAAAA
TGTATTATGCATTCTTTTTTTAATATTAACATCTCATTATAGGTTATTATCATCTGCTCTTTGGT
AGCAAAACCT
Found at i:9256 original size:12 final size:12
Alignment explanation
Indices: 9239--9263 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9229 AATTGTTATA
9239 TGTTTTTTTTTT
1 TGTTTTTTTTTT
9251 TGTTTTTTTTTT
1 TGTTTTTTTTTT
9263 T
1 T
9264 TAATATTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TGTTTTTTTTTT
Found at i:15824 original size:29 final size:30
Alignment explanation
Indices: 15777--15985 Score: 216
Period size: 30 Copynumber: 7.1 Consensus size: 30
15767 CCCTAGATGT
15777 CCCT-AAACTATCCAAAAATTACATTTTTAC
1 CCCTGAAACT-TCCAAAAATTACATTTTTAC
* *
15807 CCCT-AAACTTCCAAAAATTTTCATTTTTAA
1 CCCTGAAACTTCCAAAAA-TTACATTTTTAC
* * *
15837 CCATGGAACTTTCAAAAATTACATTTTTAC
1 CCCTGAAACTTCCAAAAATTACATTTTTAC
*
15867 CCCT-AAACTTCCAAAAATTCCATTTTTAC
1 CCCTGAAACTTCCAAAAATTACATTTTTAC
* *** *
15896 CCCTAAAACTTTTGAAAATTACA-TTTCA-
1 CCCTGAAACTTCCAAAAATTACATTTTTAC
* *
15924 CCCTCAAACTTCCAAAAATTCCATTTTTGA-
1 CCCTGAAACTTCCAAAAATTACATTTTT-AC
15954 CCCTGAAACTTCCAAAAATTACCA-TTTTAC
1 CCCTGAAACTTCCAAAAATTA-CATTTTTAC
15984 CC
1 CC
15986 TCGGATGTCC
Statistics
Matches: 148, Mismatches: 24, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
28 18 0.12
29 42 0.28
30 75 0.51
31 13 0.09
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
CCCTGAAACTTCCAAAAATTACATTTTTAC
Found at i:15963 original size:58 final size:58
Alignment explanation
Indices: 15789--15985 Score: 247
Period size: 58 Copynumber: 3.3 Consensus size: 58
15779 CTAAACTATC
* * *
15789 CAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTTTCATTTTTAACCATGGAACTTT
1 CAAAAATTACATTTTTACCCCTAAACTTCCAAAAA-TTCCATTTTT-ACCCTGAAACTTT
*
15849 CAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCCCTAAAACTTT
1 CAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTA-CCCTGAAACTTT
** * *
15908 TGAAAATTACA-TTTCA-CCCTCAAACTTCCAAAAATTCCATTTTTGACCCTGAAACTTC
1 CAAAAATTACATTTTTACCCCT-AAACTTCCAAAAATTCCATTTTT-ACCCTGAAACTTT
15966 CAAAAATTACCA-TTTTACCC
1 CAAAAATTA-CATTTTTACCC
15986 TCGGATGTCC
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.03
58 45 0.38
59 34 0.28
60 37 0.31
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.35
Consensus pattern (58 bp):
CAAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCCTGAAACTTT
Found at i:27831 original size:34 final size:34
Alignment explanation
Indices: 27784--27851 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
27774 CGCTCCTATC
27784 TTACATTAATCACTTCGAGTCTAGATCATTTTAA
1 TTACATTAATCACTTCGAGTCTAGATCATTTTAA
* *
27818 TTACATTAGTCACTTCGAGTTTAGATCATTTTAA
1 TTACATTAATCACTTCGAGTCTAGATCATTTTAA
27852 GTTTTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (34 bp):
TTACATTAATCACTTCGAGTCTAGATCATTTTAA
Found at i:30264 original size:16 final size:17
Alignment explanation
Indices: 30227--30267 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
30217 TTGATTTAAA
30227 AATTCAAATTTAAAAAT
1 AATTCAAATTTAAAAAT
*
30244 AATTCAAATTT-GAAAT
1 AATTCAAATTTAAAAAT
*
30260 GATTCAAA
1 AATTCAAA
30268 AATAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (17 bp):
AATTCAAATTTAAAAAT
Found at i:43100 original size:17 final size:18
Alignment explanation
Indices: 43063--43111 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
43053 TAAAAATTAA
*
43063 AAATATTTTTTATACTTTTT
1 AAATAATTTTTAT--TTTTT
*
43083 -AATTATTTTTATTTTTT
1 AAATAATTTTTATTTTTT
43100 AAATAATTTTTA
1 AAATAATTTTTA
43112 CAACTCACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 10 0.40
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
AAATAATTTTTATTTTTT
Found at i:46914 original size:26 final size:26
Alignment explanation
Indices: 46884--46936 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
46874 CCTCTCTAAG
*
46884 TATAAATACTTCTCAAAAGTAAAAAT
1 TATAAATACTTCACAAAAGTAAAAAT
46910 TATAAATACTTCACAAAAGTAAAAAT
1 TATAAATACTTCACAAAAGTAAAAAT
46936 T
1 T
46937 TTAAGACTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (26 bp):
TATAAATACTTCACAAAAGTAAAAAT
Found at i:48285 original size:21 final size:21
Alignment explanation
Indices: 48260--48300 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
48250 CCACCACCAG
48260 CCTTTTTCTGCTCCCCTCCAC
1 CCTTTTTCTGCTCCCCTCCAC
48281 CCTTTTTCTGCTCCCCTCCA
1 CCTTTTTCTGCTCCCCTCCA
48301 GCCATATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.51, G:0.05, T:0.39
Consensus pattern (21 bp):
CCTTTTTCTGCTCCCCTCCAC
Found at i:60362 original size:30 final size:29
Alignment explanation
Indices: 60328--60390 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
60318 GTTTGGTGGC
60328 CAAATTTGAATTCTTAGGA-AGTTTAGGAGT
1 CAAATTTGAATTCTTA-GATAGTTT-GGAGT
* *
60358 CAAATTTGAATTTTTAGATAGTTTGGGGT
1 CAAATTTGAATTCTTAGATAGTTTGGAGT
60387 CAAA
1 CAAA
60391 ACATAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (29 bp):
CAAATTTGAATTCTTAGATAGTTTGGAGT
Found at i:62569 original size:41 final size:41
Alignment explanation
Indices: 62525--62780 Score: 223
Period size: 41 Copynumber: 6.5 Consensus size: 41
62515 TGCAAAAGAT
* *
62525 AGAGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTT
1 AGAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC
* * *
62566 AGAGTAATAACGACGCTTAT------G-G--G--A-AGGTC
1 AGAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC
* **
62595 AAAGCAATAGCGGCGCTTATGGACAAGC-CCTGCTAAAACTC
1 AGAGCAATAGCGGCGCTTATGGACAAGCGCC-GCTAAAGGTC
* * *
62636 AGAACAATAGCAGCGCTTATGGGCAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC
* * * *
62677 AGAGCAATAACGGAGCTTATGGGCAAGCGCCACTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC
* * * **
62718 AAAGCAATAGTGGCGCTTATGGAAAATTGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC
*
62759 AGAGCAATAACGGCGCTTATGG
1 AGAGCAATAGCGGCGCTTATGG
62781 GNGTCAAAGC
Statistics
Matches: 168, Mismatches: 33, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
29 20 0.12
30 1 0.01
32 1 0.01
34 1 0.01
35 2 0.01
38 1 0.01
40 1 0.01
41 139 0.83
42 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.18
Consensus pattern (41 bp):
AGAGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAGGTC
Found at i:62653 original size:70 final size:70
Alignment explanation
Indices: 62527--62658 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 70
62517 CAAAAGATAG
* ** * **
62527 AGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTTAGAGTAATAACGACGCTTATGGGAAG
1 AGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAACTCAGAACAATAACGACGCTTATGGGAAG
62592 GTCAA
66 GTCAA
*
62597 AGCAATAGCGGCGCTTATGGACAAGC-CCTGCTAAAACTCAGAACAATAGC-AGCGCTTATGGG
1 AGCAATAGCGGCGCTTATGGACAAGCGCC-GCTAAAACTCAGAACAATAACGA-CGCTTATGGG
62659 CAAGCGCCGC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 3 0.06
70 50 0.94
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (70 bp):
AGCAATAGCGGCGCTTATGGACAAGCGCCGCTAAAACTCAGAACAATAACGACGCTTATGGGAAG
GTCAA
Found at i:62786 original size:27 final size:26
Alignment explanation
Indices: 62755--62807 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
62745 TGCCGCTAAA
*
62755 GGTCAGAGCAATAACGGCGCTTATGG
1 GGTCAAAGCAATAACGGCGCTTATGG
**
62781 GNGTCAAAGCAATAGTGGCGCTTATGG
1 G-GTCAAAGCAATAACGGCGCTTATGG
62808 AAAATTGCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.21
Consensus pattern (26 bp):
GGTCAAAGCAATAACGGCGCTTATGG
Found at i:62824 original size:68 final size:67
Alignment explanation
Indices: 62714--62849 Score: 254
Period size: 68 Copynumber: 2.0 Consensus size: 67
62704 CGCCACTAAA
*
62714 GGTCAAAGCAATAGTGGCGCTTATGGAAAATTGCCGCTAAAGGTCAGAGCAATAACGGCGCTTAT
1 GGTCAAAGCAATAGTGGCGCTTATGGAAAATTGCCGATAAAGGTCAGAGCAATAACGGCGCTTAT
62779 GG
66 GG
62781 GNGTCAAAGCAATAGTGGCGCTTATGGAAAATTGCCGATAAAGGTCAGAGCAATAACGGCGCTTA
1 G-GTCAAAGCAATAGTGGCGCTTATGGAAAATTGCCGATAAAGGTCAGAGCAATAACGGCGCTTA
62846 TGG
65 TGG
62849 G
1 G
62850 AAAGCGCTGC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 1 0.01
68 66 0.99
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (67 bp):
GGTCAAAGCAATAGTGGCGCTTATGGAAAATTGCCGATAAAGGTCAGAGCAATAACGGCGCTTAT
GG
Found at i:62845 original size:41 final size:41
Alignment explanation
Indices: 62783--62986 Score: 239
Period size: 41 Copynumber: 5.0 Consensus size: 41
62773 GCTTATGGGN
* * ** *
62783 GTCAAAGCAATAGTGGCGCTTATGGAAAATTGCCGATAAAG
1 GTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAG
* * *
62824 GTCAGAGCAATAACGGCGCTTATGGGAAAGCGCTGCTAAAG
1 GTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAG
* * * *
62865 GTCATAGCAATAGCGGCGTTTATGGACAAGCACCGCTAAAG
1 GTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAG
**
62906 GTCAGAGCAATAGCAGG-GCTTATGGGCAAGCGCCGCTAAAG
1 GTCAGAGCAATAGC-GGCGCTTATGGAAAAGCGCCGCTAAAG
* *
62947 GTCAGAGCAATAGCGGCGCTTATGGGAAAAACACCGCTAA
1 GTCAGAGCAATAGCGGCGCTTAT-GGAAAAGCGCCGCTAA
62987 TTTATTTAAA
Statistics
Matches: 137, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
40 2 0.01
41 121 0.88
42 14 0.10
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (41 bp):
GTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAG
Found at i:62876 original size:191 final size:192
Alignment explanation
Indices: 62527--62973 Score: 560
Period size: 191 Copynumber: 2.3 Consensus size: 192
62517 CAAAAGATAG
* * * * *
62527 AGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTTAGAGTAATAACGACGCTTATGGGAAG
1 AGCAATAGAGGCGCTTATGGACAAGCGCCGCTAAAGGTCAGAGCAATAACGGCGCTTATGGG-AG
* * *
62592 GTCAAAGCAATAGCGGCGCTTATGGACAAGCCCTGCTAAAACTCAGAACAATAGCAGCGCTTATG
65 GTCAAAGCAATAGCGGCGCTTATGGAAAAGCCCTGATAAAACTCAGAACAATAACAGCGCTTATG
* * *
62657 GGCAAGCGCCGCTAAAGGTCAGAGCAATAACGGAGCTTATGGGCAAGCGCCACTAAAGGTCAA
130 GGAAAGCGCCGCTAAAGGTCAGAGCAATAACGGAGCTTATGGACAAGCACCACTAAAGGTCAA
* * ** *
62720 AGCAATAGTGGCGCTTATGGAAAATTGCCGCTAAAGGTCAGAGCAATAACGGCGCTTATGGG-NG
1 AGCAATAGAGGCGCTTATGGACAAGCGCCGCTAAAGGTCAGAGCAATAACGGCGCTTATGGGAGG
* ** * *
62784 TCAAAGCAATAGTGGCGCTTATGGAAAATTG-CC-GATAAAGGTCAGAGCAATAACGGCGCTTAT
66 TCAAAGCAATAGCGGCGCTTATGGAAAA--GCCCTGATAAAACTCAGAACAATAACAGCGCTTAT
* * * * * * *
62847 GGGAAAGCGCTGCTAAAGGTCATAGCAATAGCGGCGTTTATGGACAAGCACCGCTAAAGGTCAG
129 GGGAAAGCGCCGCTAAAGGTCAGAGCAATAACGGAGCTTATGGACAAGCACCACTAAAGGTCAA
* *
62911 AGCAATAGCAGG-GCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGA
1 AGCAATAG-AGGCGCTTATGGACAAGCGCCGCTAAAGGTCAGAGCAATAACGGCGCTTATGGGA
62974 AAAACACCGC
Statistics
Matches: 217, Mismatches: 33, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
191 158 0.73
192 4 0.02
193 55 0.25
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (192 bp):
AGCAATAGAGGCGCTTATGGACAAGCGCCGCTAAAGGTCAGAGCAATAACGGCGCTTATGGGAGG
TCAAAGCAATAGCGGCGCTTATGGAAAAGCCCTGATAAAACTCAGAACAATAACAGCGCTTATGG
GAAAGCGCCGCTAAAGGTCAGAGCAATAACGGAGCTTATGGACAAGCACCACTAAAGGTCAA
Found at i:62910 original size:82 final size:82
Alignment explanation
Indices: 62783--62986 Score: 266
Period size: 82 Copynumber: 2.5 Consensus size: 82
62773 GCTTATGGGN
* *** *
62783 GTCAAAGCAATAGTGGCGCTTATGGAAAATTGCCGATAAAGGTCAGAGCAATAAC-GGCGCTTAT
1 GTCAAAGCAATAGCGGCGCTTATGGAAAAACACCGCTAAAGGTCAGAGCAATAACAGG-GCTTAT
*
62847 GGGAAAGCGCTGCTAAAG
65 GGGAAAGCGCCGCTAAAG
* * * * *
62865 GTCATAGCAATAGCGGCGTTTATGGACAAGCACCGCTAAAGGTCAGAGCAATAGCAGGGCTTATG
1 GTCAAAGCAATAGCGGCGCTTATGGAAAAACACCGCTAAAGGTCAGAGCAATAACAGGGCTTATG
*
62930 GGCAAGCGCCGCTAAAG
66 GGAAAGCGCCGCTAAAG
*
62947 GTCAGAGCAATAGCGGCGCTTATGGGAAAAACACCGCTAA
1 GTCAAAGCAATAGCGGCGCTTAT-GGAAAAACACCGCTAA
62987 TTTATTTAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
82 89 0.85
83 16 0.15
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (82 bp):
GTCAAAGCAATAGCGGCGCTTATGGAAAAACACCGCTAAAGGTCAGAGCAATAACAGGGCTTATG
GGAAAGCGCCGCTAAAG
Found at i:71408 original size:19 final size:18
Alignment explanation
Indices: 71379--71418 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
71369 AAATAATAGC
71379 ATTTGAAATATTATTTTAGT
1 ATTTGAAATATT-TTTTA-T
71399 ATTT-AAATATTTTTTAT
1 ATTTGAAATATTTTTTAT
71416 ATT
1 ATT
71419 ATCTGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 7 0.35
20 4 0.20
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTGAAATATTTTTTAT
Found at i:77639 original size:14 final size:15
Alignment explanation
Indices: 77610--77642 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
77600 GTTTAGATAC
*
77610 TTTTTAAAATTAATT
1 TTTTTAAAAATAATT
77625 TTTTTAAAAAT-ATT
1 TTTTTAAAAATAATT
77639 TTTT
1 TTTT
77643 ATTTTTCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTAAAAATAATT
Found at i:79828 original size:3 final size:3
Alignment explanation
Indices: 79820--79845 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
79810 CCGTGGCACG
79820 TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TG
79846 GAATCATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:84964 original size:10 final size:10
Alignment explanation
Indices: 84930--84967 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
84920 ATCAACTCAA
84930 TCAGTTAGT-
1 TCAGTTAGTG
84939 TCAGTTAGTG
1 TCAGTTAGTG
* *
84949 TTAGTTAATG
1 TCAGTTAGTG
84959 TCAGTTAGT
1 TCAGTTAGT
84968 CTATTGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.45
Consensus pattern (10 bp):
TCAGTTAGTG
Found at i:91847 original size:19 final size:19
Alignment explanation
Indices: 91823--91865 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
91813 AAACATAAAT
91823 TAAATATAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
91842 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
91861 TAAAT
1 TAAAT
91866 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:93047 original size:20 final size:20
Alignment explanation
Indices: 93024--93064 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
93014 TGATCCTCAC
* *
93024 TAATATTATGTGTACAAAGT
1 TAATATTATATGCACAAAGT
93044 TAATATTATATGCACAAAGT
1 TAATATTATATGCACAAAGT
93064 T
1 T
93065 TGAAGGATAA
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:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (20 bp):
TAATATTATATGCACAAAGT
Found at i:95057 original size:17 final size:17
Alignment explanation
Indices: 95035--95076 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
95025 CTCCTTTGAC
95035 CTTTAACCTTCCATATT
1 CTTTAACCTTCCATATT
*
95052 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
95069 CTTGTAAC
1 CTT-TAAC
95077 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:102219 original size:30 final size:31
Alignment explanation
Indices: 102166--102223 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
102156 ATTTTTATAA
102166 AAATTACAAAAAAACTAAAAAAGTATATATG
1 AAATTACAAAAAAACTAAAAAAGTATATATG
*
102197 AAATTA-AAAAAATC-AAAGAAAGTATAT
1 AAATTACAAAAAAACTAAA-AAAGTATAT
102224 TAAAAAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 3 0.12
30 16 0.64
31 6 0.24
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (31 bp):
AAATTACAAAAAAACTAAAAAAGTATATATG
Found at i:102232 original size:31 final size:30
Alignment explanation
Indices: 102164--102241 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
102154 AAATTTTTAT
*
102164 AAAAATTACAAAAAAACTAAAAAAGTATATA
1 AAAAATTA-AAAAAATCTAAAAAAGTATATA
**
102195 TGAAATTAAAAAAATC-AAAGAAAGTATATTA
1 AAAAATTAAAAAAATCTAAA-AAAGTATA-TA
*
102226 AAAAATTCATAAAAAT
1 AAAAATT-AAAAAAAT
102242 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 3 0.08
30 15 0.39
31 13 0.34
32 7 0.18
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (30 bp):
AAAAATTAAAAAAATCTAAAAAAGTATATA
Found at i:102571 original size:20 final size:20
Alignment explanation
Indices: 102546--102584 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
102536 ATGACAAATT
*
102546 TTCATTGAC-AGATTTAACAA
1 TTCATTAACAAGA-TTAACAA
102566 TTCATTAACAAGATTAACA
1 TTCATTAACAAGATTAACA
102585 CTAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (20 bp):
TTCATTAACAAGATTAACAA
Found at i:105283 original size:6 final size:6
Alignment explanation
Indices: 105274--105358 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
105264 CAAATTTATT
** *
105274 TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATCT TTTCAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-AA TTT-AAA TTTAAA
** *
105323 TTT-GC TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
105359 GATTTAAAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.03
5 9 0.15
6 41 0.67
7 8 0.13
8 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:105324 original size:37 final size:35
Alignment explanation
Indices: 105265--105366 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 35
105255 ACATTGATTC
*
105265 AAATTTATTTTTAAATTTAAATTT-ATCTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTGCT-TTAAATTT
*
105300 AAATTTATCTTTTCAAGTTTAAATTTGCTTTAAATTT
1 AAATTTAT-TTTT-AAATTTAAATTTGCTTTAAATTT
* * *
105337 AAATTTA-ATTAAAATTTAAA-TTGATTTAAA
1 AAATTTATTTTTAAATTTAAATTTGCTTTAAA
105367 ACTTAATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 9 0.16
34 8 0.14
35 10 0.17
36 4 0.07
37 26 0.45
38 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (35 bp):
AAATTTATTTTTAAATTTAAATTTGCTTTAAATTT
Found at i:105367 original size:17 final size:16
Alignment explanation
Indices: 105274--105366 Score: 87
Period size: 17 Copynumber: 5.4 Consensus size: 16
105264 CAAATTTATT
105274 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
105290 TCTTAAATTTAAATTTA
1 T-TTAAATTTAAATTTA
* *
105307 TCTTTTCAAGTTTAAATTTGC
1 ---TTT-AAATTTAAATTT-A
105328 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTT-A
* *
105345 TTAAAATTTAAATTGA
1 TTTAAATTTAAATTTA
105361 TTTAAA
1 TTTAAA
105367 ACTTAATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.11
17 39 0.62
18 3 0.05
19 2 0.03
20 12 0.19
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:107558 original size:6 final size:6
Alignment explanation
Indices: 107549--107633 Score: 61
Period size: 6 Copynumber: 14.3 Consensus size: 6
107539 CAAATTTATT
** *
107549 TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATCT TTTCAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-AA TTT-AAA TTTAAA
** *
107598 TTT-GC TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
107634 GATTTAAAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.03
5 9 0.15
6 41 0.67
7 8 0.13
8 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:107599 original size:37 final size:35
Alignment explanation
Indices: 107540--107641 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 35
107530 ACATTGATTC
*
107540 AAATTTATTTTTAAATTTAAATTT-ATCTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTGCT-TTAAATTT
*
107575 AAATTTATCTTTTCAAGTTTAAATTTGCTTTAAATTT
1 AAATTTAT-TTTT-AAATTTAAATTTGCTTTAAATTT
* * *
107612 AAATTTA-ATTAAAATTTAAA-TTGATTTAAA
1 AAATTTATTTTTAAATTTAAATTTGCTTTAAA
107642 ACTTAATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 9 0.16
34 8 0.14
35 10 0.17
36 4 0.07
37 26 0.45
38 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (35 bp):
AAATTTATTTTTAAATTTAAATTTGCTTTAAATTT
Found at i:107642 original size:17 final size:16
Alignment explanation
Indices: 107549--107641 Score: 87
Period size: 17 Copynumber: 5.4 Consensus size: 16
107539 CAAATTTATT
107549 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
107565 TCTTAAATTTAAATTTA
1 T-TTAAATTTAAATTTA
* *
107582 TCTTTTCAAGTTTAAATTTGC
1 ---TTT-AAATTTAAATTT-A
107603 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTT-A
* *
107620 TTAAAATTTAAATTGA
1 TTTAAATTTAAATTTA
107636 TTTAAA
1 TTTAAA
107642 ACTTAATTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.11
17 39 0.62
18 3 0.05
19 2 0.03
20 12 0.19
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:109521 original size:29 final size:30
Alignment explanation
Indices: 109476--109659 Score: 173
Period size: 29 Copynumber: 6.2 Consensus size: 30
109466 CCGAATATTA
* *
109476 CATTTTTGCCCCCCGAACTTCCAAAAATTC
1 CATTTTTGACCCTCGAACTTCCAAAAATTC
109506 CATTTTTGA-CCTCGAAACTTCC-AAAATTC
1 CATTTTTGACCCTCG-AACTTCCAAAAATTC
* * * *
109535 AATTTTT-ACCCTCGATCTTCTAAAAATTT
1 CATTTTTGACCCTCGAACTTCCAAAAATTC
* ** *
109564 CATTTTCGATCCC-AAAACTTCCAAAAATTA
1 CATTTTTGA-CCCTCGAACTTCCAAAAATTC
* *
109594 CATTTTT-ACCCTCGAACCTCCAAAATTTC
1 CATTTTTGACCCTCGAACTTCCAAAAATTC
*
109623 CATTTTTGACCC-CGAAACTTTCAAAAATTAC
1 CATTTTTGACCCTCG-AACTTCCAAAAATT-C
109654 CATTTT
1 CATTTT
109660 GCCCCCGAGT
Statistics
Matches: 123, Mismatches: 22, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
28 9 0.07
29 55 0.45
30 49 0.40
31 10 0.08
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (30 bp):
CATTTTTGACCCTCGAACTTCCAAAAATTC
Found at i:109627 original size:59 final size:59
Alignment explanation
Indices: 109454--109659 Score: 213
Period size: 59 Copynumber: 3.5 Consensus size: 59
109444 GCCCTAAAGG
* * * * * *
109454 TCCCTAAACTATCCGAATATTACATTTTTGCCCCCCGAACTTCCAAAAATTCCATTTTTGA
1 TCCCGAAACT-TCCAAAAATTACATTTTT-ACCCTCGAACTTCCAAAATTTCCATTTTTGA
* * *
109515 -CCTCGAAACTTCC-AAAATT-CAATTTTTACCCTCGATCTTCTAAAAATTT-CATTTTCGA
1 TCC-CGAAACTTCCAAAAATTAC-ATTTTTACCCTCGAACTTC-CAAAATTTCCATTTTTGA
* *
109573 TCCCAAAACTTCCAAAAATTACATTTTTACCCTCGAACCTCCAAAATTTCCATTTTTGA
1 TCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGA
* *
109632 CCCCGAAACTTTCAAAAATTACCATTTT
1 TCCCGAAACTTCCAAAAATTA-CATTTT
109660 GCCCCCGAGT
Statistics
Matches: 121, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
58 35 0.29
59 68 0.56
60 12 0.10
61 6 0.05
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (59 bp):
TCCCGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAATTTCCATTTTTGA
Found at i:110813 original size:21 final size:21
Alignment explanation
Indices: 110789--110848 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
110779 ATTTCTTCAT
110789 CAATTCATATACATATATATC
1 CAATTCATATACATATATATC
* *
110810 CAATGTCGTATA-ATATA-ATT
1 CAAT-TCATATACATATATATC
110830 CATATTACATAT-CATATAT
1 CA-ATT-CATATACATATAT
110849 CAATAATATC
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 5 0.16
21 20 0.65
22 6 0.19
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (21 bp):
CAATTCATATACATATATATC
Found at i:111732 original size:3 final size:3
Alignment explanation
Indices: 111724--111759 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
111714 CTTTAGTGGA
*
111724 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
111760 CCACCAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:113366 original size:18 final size:18
Alignment explanation
Indices: 113325--113367 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
113315 TTTCAATGTG
113325 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
113343 TCATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
113361 TAATTAA
1 TAATTAA
113368 AAACATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:117084 original size:27 final size:26
Alignment explanation
Indices: 117033--117084 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
117023 TCTAATTTTT
*
117033 TCTATTAATTTTTTTAATTTTTAATTA
1 TCTATTAATTTTTTT-ATTTATAATTA
117060 TCTATTAAATTTGTTTT-TTTATAAT
1 TCTATT-AATTT-TTTTATTTATAAT
117085 AAAATCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 13 0.59
28 5 0.23
29 4 0.18
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (26 bp):
TCTATTAATTTTTTTATTTATAATTA
Found at i:118045 original size:24 final size:24
Alignment explanation
Indices: 118017--118071 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
118007 GACTAATAAG
*
118017 AGTTTGATTCAAACAAATAAACAA
1 AGTTTAATTCAAACAAATAAACAA
* *
118041 AGTTTAATTGAAACAAATAAACAG
1 AGTTTAATTCAAACAAATAAACAA
118065 AGTTTAA
1 AGTTTAA
118072 CTGAAAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (24 bp):
AGTTTAATTCAAACAAATAAACAA
Found at i:118076 original size:24 final size:24
Alignment explanation
Indices: 118027--118077 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
118017 AGTTTGATTC
*
118027 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAACTG
*
118051 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAAAGTTTAACTG
118075 AAA
1 AAA
118078 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAACTG
Found at i:121298 original size:21 final size:20
Alignment explanation
Indices: 121261--121307 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
121251 ATTACATACT
*
121261 TTTTATATTTTTCTTAATAAA
1 TTTTATATTTATCTTAA-AAA
*
121282 TTTTATATTTCAT-TTAACAA
1 TTTTATATTT-ATCTTAAAAA
121302 TTTTAT
1 TTTTAT
121308 CTCAGTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 14 0.61
22 1 0.04
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATATTTATCTTAAAAA
Found at i:122317 original size:31 final size:32
Alignment explanation
Indices: 122277--122338 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
122267 TAACTCAGTG
*
122277 ACTTTAAT-AAAAACTTTCAAATAATTCAATC
1 ACTTAAATAAAAAACTTTCAAATAATTCAATC
* *
122308 ACTTAAATAAAAAATTTTCAGATAATTCAAT
1 ACTTAAATAAAAAACTTTCAAATAATTCAAT
122339 GATAATTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (32 bp):
ACTTAAATAAAAAACTTTCAAATAATTCAATC
Found at i:125923 original size:3 final size:3
Alignment explanation
Indices: 125915--125947 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
125905 CAATGAATTC
125915 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
125948 CACTACAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:126439 original size:24 final size:23
Alignment explanation
Indices: 126412--126458 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
126402 CCCGACCCGA
126412 ATTTATAATAATAATTTTATTTTT
1 ATTTATAATAATAATTTT-TTTTT
* *
126436 ATTTTTAATACTAATTTTTTTTT
1 ATTTATAATAATAATTTTTTTTT
126459 GCTTGTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTATAATAATAATTTTTTTTT
Found at i:127608 original size:59 final size:59
Alignment explanation
Indices: 127545--127685 Score: 237
Period size: 59 Copynumber: 2.4 Consensus size: 59
127535 TACACAATTA
*
127545 CTTTTCTTTTTACTTTTTCTTTAACATTGTCTATGAGGCAAAGCTTGATTGGCACTGAC
1 CTTTTCTTTTTACTTTTTCTTTAACATTGTCTATGAGGCAAAGCTTCATTGGCACTGAC
**
127604 CTTTTCTTTCCACTTTTTCTTTAACATTGTCTATGAGGCAAAGCTTCATTGGCACTGAC
1 CTTTTCTTTTTACTTTTTCTTTAACATTGTCTATGAGGCAAAGCTTCATTGGCACTGAC
127663 CTTTTCTTTTTTCACTTTTTCTT
1 CTTTTC-TTTTT-ACTTTTTCTT
127686 CTAAATATAA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
59 62 0.83
60 3 0.04
61 10 0.13
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.49
Consensus pattern (59 bp):
CTTTTCTTTTTACTTTTTCTTTAACATTGTCTATGAGGCAAAGCTTCATTGGCACTGAC
Found at i:133097 original size:18 final size:17
Alignment explanation
Indices: 133074--133117 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
133064 ATTAAAATAT
*
133074 TTTAAATTTTGAAATCAA
1 TTTAAAATTT-AAATCAA
133092 TTTAAAATTTAAATCATAA
1 TTTAAAATTTAAATC--AA
133111 TTTAAAA
1 TTTAAAA
133118 ATATCCAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 9 0.39
19 9 0.39
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAAATTTAAATCAA
Found at i:136631 original size:20 final size:21
Alignment explanation
Indices: 136606--136645 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
136596 AGGTTTTTAT
*
136606 AAAAAATT-AGAATTTTATGA
1 AAAAAATTAAGAAATTTATGA
136626 AAAAAATTAAGAAATTTATG
1 AAAAAATTAAGAAATTTATG
136646 GTATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAATTAAGAAATTTATGA
Found at i:136675 original size:23 final size:23
Alignment explanation
Indices: 136636--136702 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
136626 AAAAAATTAA
*
136636 GAAA-TTTATGGTATTTTTTTTG
1 GAAATTTTAGGGTATTTTTTTTG
* *
136658 GAAATTTTAGGGTTTTTTTTTTT
1 GAAATTTTAGGGTATTTTTTTTG
* * *
136681 GCATTTTTAGGGAATTTTTTTT
1 GAAATTTTAGGGTATTTTTTTT
136703 ATATTTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.19, C:0.01, G:0.18, T:0.61
Consensus pattern (23 bp):
GAAATTTTAGGGTATTTTTTTTG
Found at i:136708 original size:22 final size:22
Alignment explanation
Indices: 136673--136717 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
136663 TTTAGGGTTT
* *
136673 TTTTTTTTGCATTTTTAGGGAA
1 TTTTTTTTACATTTTTAAGGAA
*
136695 TTTTTTTTATATTTTTAAGGAA
1 TTTTTTTTACATTTTTAAGGAA
136717 T
1 T
136718 ATTAAGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.62
Consensus pattern (22 bp):
TTTTTTTTACATTTTTAAGGAA
Found at i:137006 original size:9 final size:9
Alignment explanation
Indices: 136974--137007 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
136964 TTTAATTATT
*
136974 TTTTTAAAT
1 TTTTTAAAA
*
136983 TTTTTAATA
1 TTTTTAAAA
136992 TTTTTAAAA
1 TTTTTAAAA
137001 TTTTTAA
1 TTTTTAA
137008 GTAAAATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:137139 original size:31 final size:31
Alignment explanation
Indices: 137104--137175 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
137094 ATTACAGGAT
*
137104 TAAAGTATAGGA-ATCAAATTGATAATAAAAA
1 TAAAGTATAGGAGCT-AAATTGATAATAAAAA
* *
137135 TAAAGTACAAGAGCTAAATTGATAATAAAAA
1 TAAAGTATAGGAGCTAAATTGATAATAAAAA
*
137166 AAAAGTATAG
1 TAAAGTATAG
137176 ATACTAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.58, C:0.04, G:0.14, T:0.24
Consensus pattern (31 bp):
TAAAGTATAGGAGCTAAATTGATAATAAAAA
Found at i:137183 original size:31 final size:31
Alignment explanation
Indices: 137119--137187 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
137109 TATAGGAATC
* *
137119 AAATTGATAATAAAAATAAAGTACAAGAGCT
1 AAATTGATAATAAAAAAAAAGTACAAGAACT
*
137150 AAATTGATAATAAAAAAAAAGTA-TAGATACT
1 AAATTGATAATAAAAAAAAAGTACAAGA-ACT
137181 AAATTGA
1 AAATTGA
137188 AAGTTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (31 bp):
AAATTGATAATAAAAAAAAAGTACAAGAACT
Found at i:138040 original size:60 final size:60
Alignment explanation
Indices: 137940--138068 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
137930 AAAAATTCAA
137940 CATAGTTGGGTGACCAAAAAAGACGAAATTGAATAGTTGAGCGACCATTTTATAAC-TTTT
1 CATAGTTGGGTGACCAAAAAAGAC-AAATTGAATAGTTGAGCGACCATTTTATAACTTTTT
* * * * * * *
138000 CATAGTTGGGTGATCAAAAAAGA-AATTTACTAATATTTGAGTGATCATTTTGTAACTTTTT
1 CATAGTTGGGTGACCAAAAAAGACAAATT--GAATAGTTGAGCGACCATTTTATAACTTTTT
*
138061 TATAGTTG
1 CATAGTTG
138069 CGTGTAGAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.07
60 43 0.74
61 11 0.19
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (60 bp):
CATAGTTGGGTGACCAAAAAAGACAAATTGAATAGTTGAGCGACCATTTTATAACTTTTT
Found at i:138822 original size:17 final size:17
Alignment explanation
Indices: 138788--138890 Score: 72
Period size: 17 Copynumber: 6.2 Consensus size: 17
138778 ATGGATGTTC
*
138788 AACCTTTCATC-T-TTT
1 AACCTTCCATCTTCTTT
138803 AACCTTCCATCTTCTTT
1 AACCTTCCATCTTCTTT
138820 AA-CTTCC-T-TTGACCTTT
1 AACCTTCCATCTT---CTTT
*
138837 AACCTTCCATCTTCCTT
1 AACCTTCCATCTTCTTT
* * * **
138854 AATCTCCCTTAATCTTT
1 AACCTTCCATCTTCTTT
*
138871 AACCTTCCATCTTCCTT
1 AACCTTCCATCTTCTTT
138888 AAC
1 AAC
138891 TTTTCATATT
Statistics
Matches: 66, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
14 2 0.03
15 11 0.17
16 6 0.09
17 39 0.59
18 5 0.08
19 1 0.02
20 2 0.03
ACGTcount: A:0.20, C:0.34, G:0.01, T:0.45
Consensus pattern (17 bp):
AACCTTCCATCTTCTTT
Found at i:138838 original size:34 final size:34
Alignment explanation
Indices: 138800--138892 Score: 134
Period size: 34 Copynumber: 2.7 Consensus size: 34
138790 CCTTTCATCT
* * *
138800 TTTAACCTTCCATCTTCTTTAACTTCCTTTGACC
1 TTTAACCTTCCATCTTCCTTAACTTCCCTTAACC
*
138834 TTTAACCTTCCATCTTCCTTAA-TCTCCCTTAATC
1 TTTAACCTTCCATCTTCCTTAACT-TCCCTTAACC
138868 TTTAACCTTCCATCTTCCTTAACTT
1 TTTAACCTTCCATCTTCCTTAACTT
138893 TTCATATTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
33 1 0.02
34 51 0.96
35 1 0.02
ACGTcount: A:0.19, C:0.33, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTAACCTTCCATCTTCCTTAACTTCCCTTAACC
Found at i:146082 original size:18 final size:19
Alignment explanation
Indices: 146054--146089 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
146044 TTTTAAGTTA
146054 CAATGTATAATTATAAATT
1 CAATGTATAATTATAAATT
*
146073 CAAT-TATAATTGTAAAT
1 CAATGTATAATTATAAAT
146090 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (19 bp):
CAATGTATAATTATAAATT
Done.