Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009506.1 Kokia drynarioides strain JFW-HI SEQ_124217, 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: 72931
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:886 original size:32 final size:32
Alignment explanation
Indices: 850--915 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
840 GCCTTATACG
850 AAACAAATCAAATTAGCCCTTGTCCTAAGGAA
1 AAACAAATCAAATTAGCCCTTGTCCTAAGGAA
882 AAACAAATCAAATTAGCCCTTGTCCTAAGGAA
1 AAACAAATCAAATTAGCCCTTGTCCTAAGGAA
914 AA
1 AA
916 TCCTGCTCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (32 bp):
AAACAAATCAAATTAGCCCTTGTCCTAAGGAA
Found at i:4539 original size:18 final size:18
Alignment explanation
Indices: 4525--4559 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4515 GTAATTAATT
4525 TAAAATT-TTTAATTAAA
1 TAAAATTATTTAATTAAA
4542 TAAAATTATTTAATTAAA
1 TAAAATTATTTAATTAAA
4560 AATCTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTATTTAATTAAA
Found at i:4908 original size:2 final size:2
Alignment explanation
Indices: 4901--4929 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4891 TCGAGATCAT
4901 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 T
4930 GCATGTTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7789 original size:27 final size:24
Alignment explanation
Indices: 7735--7791 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
7725 AAGCCTAATT
* *
7735 CTAATTAATGTAAAATTTATTATG
1 CTAATAAATGTAAAATATATTATG
*
7759 CTAATAAATGTTAAATATATTATG
1 CTAATAAATGTAAAATATATTATG
*
7783 CTACTAAAT
1 CTAATAAAT
7792 CTTATAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:7857 original size:36 final size:35
Alignment explanation
Indices: 7810--7878 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 35
7800 AAGATAATAT
7810 ATTTTGTTTAACTTGACTTGCAAGCAATTCTCTTTG
1 ATTTTGTTTAACTTGACTTGCAAGCAA-TCTCTTTG
*
7846 ATTTTGTTTAACTTGACTTGTAAGCAATCTCTT
1 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTT
7879 AGAATTTAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 6 0.19
36 26 0.81
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTTG
Found at i:11326 original size:24 final size:24
Alignment explanation
Indices: 11299--11346 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11289 TAATAAGTAT
*
11299 GATATAGTTTAGGACTCTAATGTC
1 GATATAGTTTAGGAATCTAATGTC
11323 GATATAGTTTAGGAATCTAATGTC
1 GATATAGTTTAGGAATCTAATGTC
11347 CATTAGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (24 bp):
GATATAGTTTAGGAATCTAATGTC
Found at i:17039 original size:28 final size:31
Alignment explanation
Indices: 16999--17070 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 31
16989 AAAATGATTT
16999 TAAAATTATTAAAATCA-TTTTTT-AAAT-A
1 TAAAATTATTAAAATCATTTTTTTGAAATAA
*
17027 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATCATTTTTTTGAAATAA
17058 TAAAATTATTAAA
1 TAAAATTATTAAA
17071 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 16 0.40
29 6 0.15
30 4 0.10
31 14 0.35
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
TAAAATTATTAAAATCATTTTTTTGAAATAA
Found at i:20188 original size:194 final size:194
Alignment explanation
Indices: 19850--20288 Score: 551
Period size: 194 Copynumber: 2.3 Consensus size: 194
19840 ACGTGATAGC
** * * * *
19850 TGAGGTACTACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCAGGAAATG
1 TGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAACATTGTGAGTCAGGAAAAG
** *
19915 AGAAATGAATCCAAGAATGGATTACAGGCCCTATGATGGCTGGGATTTATGCATAAGTGCATATT
66 AGAAATGAATCCAAGAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAATGCATATT
* * * * * *
19980 CTTGATAGCTCGTGTAAGCAGCATCGTTAGGGAAACAG-TTATATGCACAGATACCGTATCGATT
131 CTCGACAGCTCGTGTAAGAAGCATCGTTAGGG-AACAGATTACA-G-ACAGACACCGTATCGATG
20044 GT
193 GT
* * * * *
20046 TGAGGTACGGGATATGTTGCGAGTCTTTGATAGCTTGTGTGAGCAACATTGTGAGTC-GGAAAAG
1 TGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAACATTGTGAGTCAGGAAAAG
* * * * *
20110 AGATATGAATCCTA-AATGGATTATAGGCCCTACAATGGTTGGGATTTATGCTTAAATGCATATT
66 AGAAATGAATCCAAGAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAATGCATATT
* * *
20174 CTCGACATCTCGTGTGAGAAGCATCGTTAGGGGACAGATTACAGACAGACACCGTATCGATGGT
131 CTCGACAGCTCGTGTAAGAAGCATCGTTAGGGAACAGATTACAGACAGACACCGTATCGATGGT
* * *
20238 TGGGGTACCGCACATGTTGCGAGTCCTCGATAGCTCGTGTGAGCATCATTG
1 TGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAACATTG
20289 AGTACTAGTA
Statistics
Matches: 207, Mismatches: 35, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
192 61 0.29
193 5 0.02
194 75 0.36
195 18 0.09
196 48 0.23
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (194 bp):
TGAGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAACATTGTGAGTCAGGAAAAG
AGAAATGAATCCAAGAATGGATTACAGGCCCTACAATGGCTGGGATTTATGCATAAATGCATATT
CTCGACAGCTCGTGTAAGAAGCATCGTTAGGGAACAGATTACAGACAGACACCGTATCGATGGT
Found at i:22413 original size:20 final size:20
Alignment explanation
Indices: 22363--22415 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
22353 AGAACTCTGG
* *
22363 TATCGATACCACCATAAAAA
1 TATCGATACCTCTATAAAAA
*
22383 TATCGATACCTCTTTAAAAA
1 TATCGATACCTCTATAAAAA
22403 TATCGATACCTCT
1 TATCGATACCTCT
22416 GTCTCAAAAT
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:0.40, C:0.25, G:0.06, T:0.30
Consensus pattern (20 bp):
TATCGATACCTCTATAAAAA
Found at i:23217 original size:23 final size:22
Alignment explanation
Indices: 23189--23378 Score: 190
Period size: 23 Copynumber: 8.4 Consensus size: 22
23179 TGCTAGGAAA
23189 CAGTAAGCACACACAGTGTTAAT
1 CAGTAAGCACACACAGTG-TAAT
* *
23212 CAGTAAGCACACGCAGTGCAAT
1 CAGTAAGCACACACAGTGTAAT
* *
23234 CCAGTAAGCACACACAATGCTGAT
1 -CAGTAAGCACACACAGTG-TAAT
*
23258 CAGTAAGCACACACAGTGCTGAT
1 CAGTAAGCACACACAGTG-TAAT
* *
23281 CAGTAAGCAAACACAGTGCAAT
1 CAGTAAGCACACACAGTGTAAT
*
23303 CCAGTAAGCACACAGC-GCG-AAT
1 -CAGTAAGCACACA-CAGTGTAAT
23325 CAGTAAGCACACACAGTGCTGAA-
1 CAGTAAGCACACACAGTG-T-AAT
23348 CAGTAAGCACACACAGTGCTGAA-
1 CAGTAAGCACACACAGTG-T-AAT
23371 CAGTAAGC
1 CAGTAAGC
23379 GCGCTAATGT
Statistics
Matches: 146, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
20 1 0.01
21 15 0.10
22 8 0.05
23 117 0.80
24 5 0.03
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGTAAT
Found at i:23240 original size:46 final size:46
Alignment explanation
Indices: 23189--23378 Score: 214
Period size: 46 Copynumber: 4.2 Consensus size: 46
23179 TGCTAGGAAA
*
23189 CAGTAAGCACACACAGTGTTAATCAGTAAGCACACGCAGTGC-AAT
1 CAGTAAGCACACACAGTGTTAATCAGTAAGCACACACAGTGCGAAT
* * *
23234 CCAGTAAGCACACACAATGCTGATCAGTAAGCACACACAGTGCTG-AT
1 -CAGTAAGCACACACAGTGTTAATCAGTAAGCACACACAGTGC-GAAT
* * *
23281 CAGTAAGCAAACACAGTG-CAATCCAGTAAG--CACACAGCGCGAAT
1 CAGTAAGCACACACAGTGTTAAT-CAGTAAGCACACACAGTGCGAAT
*
23325 CAGTAAGCACACACAGTGCTGAA-CAGTAAGCACACACAGTGCTGAA-
1 CAGTAAGCACACACAGTG-TTAATCAGTAAGCACACACAGTGC-GAAT
23371 CAGTAAGC
1 CAGTAAGC
23379 GCGCTAATGT
Statistics
Matches: 123, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 35 0.28
45 2 0.02
46 80 0.65
47 5 0.04
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (46 bp):
CAGTAAGCACACACAGTGTTAATCAGTAAGCACACACAGTGCGAAT
Found at i:23283 original size:69 final size:67
Alignment explanation
Indices: 23189--23366 Score: 261
Period size: 69 Copynumber: 2.6 Consensus size: 67
23179 TGCTAGGAAA
* * *
23189 CAGTAAGCACACACAGTGTTAATCAGTAAGCACACGCAGTGCAATCCAGTAAGCACACA-CAATG
1 CAGTAAGCACACACAGTGCTGATCAGTAAGCACACACAGTGCAATCCAGTAAGCACACAGC---G
23253 CTG-AT
63 C-GAAT
*
23258 CAGTAAGCACACACAGTGCTGATCAGTAAGCAAACACAGTGCAATCCAGTAAGCACACAGCGCGA
1 CAGTAAGCACACACAGTGCTGATCAGTAAGCACACACAGTGCAATCCAGTAAGCACACAGCGCGA
23323 AT
66 AT
*
23325 CAGTAAGCACACACAGTGCTGAACAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGCTGATCAGTAAGCACACACAGTGC
23367 TGAACAGTAA
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
66 1 0.01
67 44 0.44
69 55 0.54
70 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (67 bp):
CAGTAAGCACACACAGTGCTGATCAGTAAGCACACACAGTGCAATCCAGTAAGCACACAGCGCGA
AT
Found at i:26552 original size:26 final size:26
Alignment explanation
Indices: 26516--26568 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
26506 AATTCGAGTA
26516 AAATCCTAGTAAACTGATACATGTCC
1 AAATCCTAGTAAACTGATACATGTCC
26542 AAATCCTAGTAAACTGATACATGTCC
1 AAATCCTAGTAAACTGATACATGTCC
26568 A
1 A
26569 TCAGCCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (26 bp):
AAATCCTAGTAAACTGATACATGTCC
Found at i:27744 original size:3 final size:3
Alignment explanation
Indices: 27736--27780 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
27726 TTAAATGAAT
* **
27736 TAA TAA TAA CAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27781 ACCGAAAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:31160 original size:16 final size:16
Alignment explanation
Indices: 31135--31165 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31125 ACATAGAATG
*
31135 AAGAAGTTCAGTGCAA
1 AAGAAATTCAGTGCAA
31151 AAGAAATTCAGTGCA
1 AAGAAATTCAGTGCA
31166 GACCCGATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (16 bp):
AAGAAATTCAGTGCAA
Found at i:31347 original size:18 final size:20
Alignment explanation
Indices: 31310--31347 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
31300 GAAGCAAGAC
*
31310 TTTGAGAAAAGAGCATAGAG
1 TTTGAGAAAAGAGAATAGAG
31330 TTTG-GAAAA-AGAATAGAG
1 TTTGAGAAAAGAGAATAGAG
31348 GCCCTGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.29, T:0.21
Consensus pattern (20 bp):
TTTGAGAAAAGAGAATAGAG
Found at i:40426 original size:171 final size:171
Alignment explanation
Indices: 40141--40464 Score: 452
Period size: 171 Copynumber: 1.9 Consensus size: 171
40131 CAACAAGCTG
* * * * * * *
40141 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAATTTAATGAAATCAGGCTCAAATAGAGCAA
1 GTCATCTTCCTGATAAGATACAGAGAAGAAGACCAAATCAATGAAACCAAGCTCAAATAGAGCAA
* * *
40206 ATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCT
66 ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGATTAGCT
40271 TCCTGATGAGATACCGAGAAGTGAATTGAAACAAGTGATAC
131 TCCTGATGAGATACCGAGAAGTGAATTGAAACAAGTGATAC
* * *
40312 GTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGT-GATCA
1 GTCATCTTCCTGATAAGATACAGAGAAGAAGACCAAATCAATGAAACCAAGCTCAAA-TAGAGCA
* * *
40376 AATTTTCGAACTCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGATTAGC
65 AATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGATTAGC
** * *
40441 TTTTTGATGAGATACTGAGCAGTG
130 TTCCTGATGAGATACCGAGAAGTG
40465 GACCAAATTC
Statistics
Matches: 132, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
171 131 0.99
172 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (171 bp):
GTCATCTTCCTGATAAGATACAGAGAAGAAGACCAAATCAATGAAACCAAGCTCAAATAGAGCAA
ATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGATTAGCT
TCCTGATGAGATACCGAGAAGTGAATTGAAACAAGTGATAC
Found at i:41067 original size:6 final size:6
Alignment explanation
Indices: 41058--41121 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
41048 TTATTTTAGG
* *
41058 TTTAAA TTT--A TTTGAAA TTTAAG TTTAAA TTT--A TTTGAAA TTTAAG
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
41104 TTTAAA TTT--A TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
41122 AATAAGTCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
4 12 0.26
6 26 0.57
7 8 0.17
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:41077 original size:11 final size:10
Alignment explanation
Indices: 41058--41121 Score: 74
Period size: 10 Copynumber: 5.8 Consensus size: 10
41048 TTATTTTAGG
41058 TTTAAATTTA
1 TTTAAATTTA
41068 TTTGAAATTTAA
1 TTT-AAATTT-A
41080 GTTTAAATTTA
1 -TTTAAATTTA
41091 TTTGAAATTTAA
1 TTT-AAATTT-A
41103 GTTTAAATTTA
1 -TTTAAATTTA
41114 TTTAAATT
1 TTTAAATT
41122 AATAAGTCCA
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 14 0.29
11 14 0.29
12 14 0.29
13 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:41078 original size:23 final size:23
Alignment explanation
Indices: 41052--41121 Score: 124
Period size: 23 Copynumber: 3.1 Consensus size: 23
41042 TTAAACTTAT
*
41052 TTTAGGTTTAAATTTATTTGAAA
1 TTTAAGTTTAAATTTATTTGAAA
41075 TTTAAGTTTAAATTTATTTGAAA
1 TTTAAGTTTAAATTTATTTGAAA
41098 TTTAAGTTTAAATTTATTT-AAA
1 TTTAAGTTTAAATTTATTTGAAA
41120 TT
1 TT
41122 AATAAGTCCA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 5 0.11
23 41 0.89
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (23 bp):
TTTAAGTTTAAATTTATTTGAAA
Found at i:43066 original size:29 final size:29
Alignment explanation
Indices: 43021--43197 Score: 203
Period size: 29 Copynumber: 6.0 Consensus size: 29
43011 TATATTTTAA
43021 CCCTCGAACTTCACAAAAATTACATTTTTG
1 CCCTCGAACTTC-CAAAAATTACATTTTTG
*
43051 CCCTCGAACTTACAAAAATTACATTTTTG
1 CCCTCGAACTTCCAAAAATTACATTTTTG
43080 CCCTCGAACTTCCAAAAATTACATTTTTG
1 CCCTCGAACTTCCAAAAATTACATTTTTG
* * * *
43109 ACCC-CGAATTTTCTAAAAGTTACATTTTTT
1 -CCCTCGAA-CTTCCAAAAATTACATTTTTG
* * * * *
43139 ACCTCAAACTTTCCAAAAATCACAATTTTA
1 CCCTCGAAC-TTCCAAAAATTACATTTTTG
* *
43169 CCCCCTAACTTCCAAAAATTACATTTTTG
1 CCCTCGAACTTCCAAAAATTACATTTTTG
43198 AACCCAAAAT
Statistics
Matches: 123, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
29 68 0.55
30 55 0.45
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (29 bp):
CCCTCGAACTTCCAAAAATTACATTTTTG
Found at i:43132 original size:59 final size:58
Alignment explanation
Indices: 43021--43197 Score: 205
Period size: 59 Copynumber: 3.0 Consensus size: 58
43011 TATATTTTAA
43021 CCCTCGAACTTCACAAAAATTACATTTTTG-CCCTCGAACTTACAAAAATTACATTTTTG
1 CCCTCGAACTTC-CAAAAATTACATTTTTGACCC-CGAACTTACAAAAATTACATTTTTG
* * * *
43080 CCCTCGAACTTCCAAAAATTACATTTTTGACCCCGAATTTTCTAAAAGTTACATTTTTT
1 CCCTCGAACTTCCAAAAATTACATTTTTGACCCCGAACTTAC-AAAAATTACATTTTTG
* * * * * *
43139 ACCTCAAACTTTCCAAAAATCACAATTTT-ACCCCCTAACTTCCAAAAATTACATTTTTG
1 CCCTCGAAC-TTCCAAAAATTACATTTTTGA-CCCCGAACTTACAAAAATTACATTTTTG
43198 AACCCAAAAT
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
58 24 0.24
59 51 0.50
60 26 0.26
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (58 bp):
CCCTCGAACTTCCAAAAATTACATTTTTGACCCCGAACTTACAAAAATTACATTTTTG
Found at i:43182 original size:89 final size:88
Alignment explanation
Indices: 43035--43217 Score: 240
Period size: 89 Copynumber: 2.1 Consensus size: 88
43025 CGAACTTCAC
* * * * * *
43035 AAAAATTACATTTTTGCCCTCGAACTTACAAAAATTACATTTTTGCCCTCGAACTTCCAAAAATT
1 AAAAATTACATTTTTGACCTCAAACTTACAAAAATCACAATTTTACCCCCGAACTTCCAAAAATT
* * *
43100 ACATTTTTGACCCCGAATTTTCT
66 ACATTTTTGAACCCAAAATTTCT
* * * *
43123 AAAAGTTACATTTTTTACCTCAAACTTTCCAAAAATCACAATTTTACCCCCTAACTTCCAAAAAT
1 AAAAATTACATTTTTGACCTCAAAC-TTACAAAAATCACAATTTTACCCCCGAACTTCCAAAAAT
43188 TACATTTTTGAACCCAAAATTTCT
65 TACATTTTTGAACCCAAAATTTCT
43212 AAAAAT
1 AAAAAT
43218 CCCATTTAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
88 21 0.26
89 59 0.74
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.35
Consensus pattern (88 bp):
AAAAATTACATTTTTGACCTCAAACTTACAAAAATCACAATTTTACCCCCGAACTTCCAAAAATT
ACATTTTTGAACCCAAAATTTCT
Found at i:43215 original size:29 final size:28
Alignment explanation
Indices: 43034--43217 Score: 116
Period size: 29 Copynumber: 6.2 Consensus size: 28
43024 TCGAACTTCA
** * *
43034 CAAAAATTACATTTTTGCCCTCGAACTTA
1 CAAAAATTACATTTTTAACC-CAAACTTT
** * *
43063 CAAAAATTACATTTTTGCCCTCGAACTTC
1 CAAAAATTACATTTTTAACC-CAAACTTT
* * *
43092 CAAAAATTACATTTTTGACCCCGAATTTT
1 CAAAAATTACATTTTT-AACCCAAACTTT
* *
43121 CTAAAAGTTACATTTTTTACCTCAAACTTT
1 C-AAAAATTACATTTTTAACC-CAAACTTT
* * * * *
43151 CCAAAAATCACAATTTTACCCCCTAACTTC
1 -CAAAAATTACATTTTTA-ACCCAAACTTT
*
43181 CAAAAATTACATTTTTGAACCCAAAATTT
1 CAAAAATTACATTTTT-AACCCAAACTTT
43210 CTAAAAAT
1 C-AAAAAT
43218 CCCATTTAAA
Statistics
Matches: 126, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
29 75 0.60
30 48 0.38
31 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (28 bp):
CAAAAATTACATTTTTAACCCAAACTTT
Found at i:44604 original size:28 final size:28
Alignment explanation
Indices: 44572--44629 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
44562 ATTATAAATT
* * *
44572 AAAT-ATAACATACATACAATAAAATTCA
1 AAATAATAAAATACA-AAAATAAAATGCA
44600 AAATAATAAAATACAAAAATAAAATGCA
1 AAATAATAAAATACAAAAATAAAATGCA
44628 AA
1 AA
44630 GAATCACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (28 bp):
AAATAATAAAATACAAAAATAAAATGCA
Found at i:44620 original size:16 final size:15
Alignment explanation
Indices: 44589--44629 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
44579 ACATACATAC
*
44589 AATAAAATTCAAAAT
1 AATAAAATACAAAAT
44604 AATAAAATAC-AAA-
1 AATAAAATACAAAAT
*
44617 AATAAAATGCAAA
1 AATAAAATACAAA
44630 GAATCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.39
14 5 0.22
15 9 0.39
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (15 bp):
AATAAAATACAAAAT
Found at i:45829 original size:38 final size:38
Alignment explanation
Indices: 45786--45896 Score: 134
Period size: 39 Copynumber: 2.9 Consensus size: 38
45776 ACTAAACTGG
*
45786 CAGTGACACTGTAAACACTACAATACTATACTGACCGA
1 CAGTGACACTGTAAACACTGCAATACTATACTGACCGA
* * **
45824 TAGTGACACTGTAAACACTGCAA-AATAATACTGAATTGA
1 CAGTGACACTGTAAACACTGCAATACT-ATACTG-ACCGA
* *
45863 CAGTGACACTGTAAACACTGTAGTACTATACTGA
1 CAGTGACACTGTAAACACTGCAATACTATACTGA
45897 GTAGGTAGTG
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
37 2 0.03
38 28 0.46
39 29 0.48
40 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (38 bp):
CAGTGACACTGTAAACACTGCAATACTATACTGACCGA
Found at i:45907 original size:39 final size:37
Alignment explanation
Indices: 45787--45920 Score: 124
Period size: 39 Copynumber: 3.5 Consensus size: 37
45777 CTAAACTGGC
* **
45787 AGTGACACTGTAAACACTACAATACTATACTGACCGAT
1 AGTGACACTGTAAACACTGC-ATACTATACTGATAGAT
* * * *
45825 AGTGACACTGTAAACACTGCAAAATAATACTGAATTGAC
1 AGTGACACTGTAAACACTGCATACT-ATACTG-ATAGAT
* *
45864 AGTGACACTGTAAACACTGTAGTACTATACTGAGTAGGT
1 AGTGACACTGTAAACACTGCA-TACTATACTGA-TAGAT
* *
45903 AGTGAAATTGTAAACACT
1 AGTGACACTGTAAACACT
45921 ACCAGACTAG
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 3 0.04
38 26 0.33
39 47 0.60
40 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (37 bp):
AGTGACACTGTAAACACTGCATACTATACTGATAGAT
Found at i:46394 original size:50 final size:50
Alignment explanation
Indices: 46329--46437 Score: 137
Period size: 50 Copynumber: 2.2 Consensus size: 50
46319 TACAAGGGAT
* * ** * *
46329 ATAAGATTTGATGTTGTATCTTTGTTTTGCTCCACTGCAACTTCAGAGCG
1 ATAAGATTCGATGTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAG
* *
46379 ATAAGATTCGCTGTTGTAGCTTCATCTTGCTCTACTGCAACTTCAGAGAG
1 ATAAGATTCGATGTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAG
46429 ATAAAGATT
1 AT-AAGATT
46438 TGCCACTGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
50 44 0.88
51 6 0.12
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (50 bp):
ATAAGATTCGATGTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAG
Found at i:47629 original size:12 final size:12
Alignment explanation
Indices: 47612--47649 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
47602 CCTCTCCTCT
47612 TTTTTTCTTTTC
1 TTTTTTCTTTTC
47624 TTTTTTCTTTT-
1 TTTTTTCTTTTC
**
47635 TTTTCCCTTTTC
1 TTTTTTCTTTTC
47647 TTT
1 TTT
47650 CCTTTTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:47644 original size:11 final size:10
Alignment explanation
Indices: 47606--47657 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
47596 TCCTCTCCTC
47606 TCCTCTTTTTT
1 TCCT-TTTTTT
*
47617 TCTTTTCTTTT
1 TCCTTT-TTTT
*
47628 TTCTTTTTTT
1 TCCTTTTTTT
*
47638 TCCCTTTTCTT
1 T-CCTTTTTTT
47649 TCCTTTTTT
1 TCCTTTTTT
47658 AGGTGAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
10 14 0.42
11 19 0.58
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TCCTTTTTTT
Found at i:51167 original size:21 final size:21
Alignment explanation
Indices: 51143--51198 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
51133 TTAGAGTTTG
51143 TTGTATCGGTAGAAGT-AGTAA
1 TTGTATCGGTAGAAGTCA-TAA
*
51164 TTGTATCGGTAGTAGTCATAA
1 TTGTATCGGTAGAAGTCATAA
*
51185 TTGTATCTGTAGAA
1 TTGTATCGGTAGAA
51199 CCTTCCCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCATAA
Found at i:54918 original size:3 final size:3
Alignment explanation
Indices: 54912--54956 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
54902 GTCAACAAAC
* * *
54912 AAT AAT -AT AAT AAT AAT AAT ATT ATT AAT AAT ATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
54957 GCAAGAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:54942 original size:12 final size:12
Alignment explanation
Indices: 54912--54956 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
54902 GTCAACAAAC
*
54912 AATAAT-ATAAT
1 AATAATAATATT
54923 AATAATAATATT
1 AATAATAATATT
*
54935 ATTAATAATATT
1 AATAATAATATT
54947 AATAATAATA
1 AATAATAATA
54957 GCAAGAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 6 0.20
12 24 0.80
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAATAATATT
Found at i:55260 original size:15 final size:15
Alignment explanation
Indices: 55237--55284 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
55227 CTTAAAGCAG
*
55237 AAATTAAAAAGAATA
1 AAATAAAAAAGAATA
*
55252 AAATAAAAAAGACTA
1 AAATAAAAAAGAATA
*
55267 AATTAAATAAA-AATA
1 AAATAAA-AAAGAATA
55282 AAA
1 AAA
55285 CAACAAGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 24 0.89
16 3 0.11
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (15 bp):
AAATAAAAAAGAATA
Found at i:59830 original size:94 final size:94
Alignment explanation
Indices: 59696--59870 Score: 215
Period size: 94 Copynumber: 1.9 Consensus size: 94
59686 CAATGATCAA
* * * * **
59696 AGTATCGATACCAATTTGAGCTTCGAAGTTTCAAAAAAATTAAGCAGAAATCAAAAGCATTGATA
1 AGTATCAAGACCAATTTGAGCTTCGAAGTTTCAAAAAAATTAAGAAAAAATCAAAAGCATCAATA
*
59761 CTCTTAACAAAGTATCGATATCTTTGCCT
66 CCCTTAACAAAGTATCGATATCTTTGCCT
* * *** * *
59790 AGTATCAAGACCAATTTGAGCTTCGACGTTTTAGGGAAATTGAGAAAAAATCAAAAGTATCAATA
1 AGTATCAAGACCAATTTGAGCTTCGAAGTTTCAAAAAAATTAAGAAAAAATCAAAAGCATCAATA
*
59855 CCCTTAATAAAGTATC
66 CCCTTAACAAAGTATC
59871 AAATATCATA
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
94 66 1.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (94 bp):
AGTATCAAGACCAATTTGAGCTTCGAAGTTTCAAAAAAATTAAGAAAAAATCAAAAGCATCAATA
CCCTTAACAAAGTATCGATATCTTTGCCT
Found at i:69774 original size:36 final size:36
Alignment explanation
Indices: 69723--69816 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
69713 ATGAAAGTGG
* *
69723 ATATGCGGGTATGTTATTCATGCCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGACATGTGACAGTAA
* *
69759 ATATGTTGGTTTGTTATTCATGACATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGACATGTGACAGTAA
69795 ATATGTGGGTATGTTATTCATG
1 ATATGTGGGTATGTTATTCATG
69817 TCGAGTGGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (36 bp):
ATATGTGGGTATGTTATTCATGACATGTGACAGTAA
Found at i:70303 original size:19 final size:20
Alignment explanation
Indices: 70263--70306 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
70253 TTTCTAAGGT
*
70263 ATCGATATTTTTTATTAGAA
1 ATCGATATTTTCTATTAGAA
70283 ATCGATACTTTTCT-TTA-AA
1 ATCGATA-TTTTCTATTAGAA
70302 ATCGA
1 ATCGA
70307 GACCAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 10 0.45
21 5 0.23
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (20 bp):
ATCGATATTTTCTATTAGAA
Found at i:71930 original size:11 final size:10
Alignment explanation
Indices: 71908--71941 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
71898 GTCAAATAGA
71908 TTTT-TTTCT
1 TTTTCTTTCT
71917 TTTTCTTCTCT
1 TTTTCTT-TCT
71928 TTTTCTTTCT
1 TTTTCTTTCT
71938 TTTT
1 TTTT
71942 TGGGTTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.17
10 9 0.39
11 10 0.43
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:71970 original size:3 final size:3
Alignment explanation
Indices: 71962--72009 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
71952 AAGGGCCCAA
* * * * *
71962 ATT ATT ATT ATC ATC ATC ATT ATT CTT ATT ATT CTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72010 TTTAAGGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:72756 original size:148 final size:148
Alignment explanation
Indices: 72432--72931 Score: 589
Period size: 148 Copynumber: 3.4 Consensus size: 148
72422 AAATGTTTTG
* * * *
72432 TTTTTTTAAACAATTTCGAAATAAAAGATTTGATTTTTTTTAAGCAAAATAATGATTTTCTTTAA
1 TTTTTTTTAACTATTTCGAAATAAAAG-TTTGA-TATTTTTAAGTAAAATAATGATTTTCTTTAA
* * * **** ** * *
72497 AAAAGAGAACGTTTATATATATATTTTTTTAAATCTATTTTTTTTAGTTATTTTAAAGAAAAGGT
64 AAAAGAGAAAGTTTATATTTTTAAAAATAAAAATC--TGTTTTTTAGTTATTTTAAAGAAAA-AT
*
72562 TTAAATTTTTAACAAAGTTTTGA
126 TTAAATTTTTAACAAAGTTTTAA
** *
72585 TTTTTCATAACTATTTCGAAATAAAAGTTTGA-ATTTTTAAGTAAAATAGTGATTTTCTTTAAAA
1 TTTTTTTTAACTATTTCGAAATAAAAGTTTGATATTTTTAAGTAAAATAATGATTTTCTTTAAAA
72649 AAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAATTTTAA
66 AAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAA-TTTAA
* *
72714 ATTTTTAATAAAATTTTAA
130 ATTTTTAACAAAGTTTTAA
* * * * *
72733 TTTTTTTTCACTATTTCAAAATAAAAGTTTG-GATTTTTAAGAAAAATAGTGATTTTCTTTAAAA
1 TTTTTTTTAACTATTTCGAAATAAAAGTTTGATATTTTTAAGTAAAATAATGATTTTCTTTAAAA
* * * *
72797 AA-AAAAAGGTTTATATTTTTAAAAATAAAATTTTGTTTTTTAGTTATTTTCAA-AAAAA-TTAA
66 AAGAGAAA-GTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAATTTAA
**
72859 ATTTTTAACAAAGTTTTGTT
130 ATTTTTAACAAAGTTTT-AA
*
72879 TTTTTTTTAACTATTTCGAAATAAAAGTTT-AGATTTTTAAGTAAAATAATGAT
1 TTTTTTTTAACTATTTCGAAATAAAAGTTTGATATTTTTAAGTAAAATAATGAT
Statistics
Matches: 304, Mismatches: 38, Indels: 17
0.85 0.11 0.05
Matches are distributed among these distances:
145 19 0.06
146 48 0.16
147 9 0.03
148 147 0.48
150 53 0.17
152 5 0.02
153 23 0.08
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.47
Consensus pattern (148 bp):
TTTTTTTTAACTATTTCGAAATAAAAGTTTGATATTTTTAAGTAAAATAATGATTTTCTTTAAAA
AAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAATTTAAA
TTTTTAACAAAGTTTTAA
Done.