Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010505.1 Kokia drynarioides strain JFW-HI SEQ_125416, 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: 109015
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:6188 original size:27 final size:27
Alignment explanation
Indices: 6158--6211 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
6148 TAAAAAAAAG
6158 ATTTTTTGAAAGGTATGTTTATGTTTT
1 ATTTTTTGAAAGGTATGTTTATGTTTT
** *
6185 ATTTTTTGATTGGTATGTTTATTTTTT
1 ATTTTTTGAAAGGTATGTTTATGTTTT
6212 GATTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.65
Consensus pattern (27 bp):
ATTTTTTGAAAGGTATGTTTATGTTTT
Found at i:6207 original size:20 final size:21
Alignment explanation
Indices: 6177--6215 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
6167 AAGGTATGTT
6177 TATGTTTTATTTTTTGATTGG
1 TATGTTTTATTTTTTGATTGG
6198 TATG-TTTATTTTTTGATT
1 TATGTTTTATTTTTTGATT
6216 AATTTTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (21 bp):
TATGTTTTATTTTTTGATTGG
Found at i:6404 original size:24 final size:22
Alignment explanation
Indices: 6352--6405 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
6342 GAAAGATATG
*
6352 TATATTTTTTTTCTTTGTAATT
1 TATATTTTTTTTCTTTATAATT
6374 TACTATTTTTATTTCTAATTATAA-T
1 TA-TATTTTT-TTTCT--TTATAATT
6399 TATATTT
1 TATATTT
6406 GAAAGGTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 2 0.07
23 7 0.26
24 10 0.37
25 3 0.11
26 5 0.19
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (22 bp):
TATATTTTTTTTCTTTATAATT
Found at i:6673 original size:25 final size:26
Alignment explanation
Indices: 6635--6686 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
6625 TTTACAATGT
*
6635 ATTTTTAAATAATAATAATTTTTTTA
1 ATTTTTAAATAATAATAATTTTATTA
*
6661 ATTTTTGAA-AATAATAATTTTATTA
1 ATTTTTAAATAATAATAATTTTATTA
6686 A
1 A
6687 AATATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTTTAAATAATAATAATTTTATTA
Found at i:6694 original size:28 final size:24
Alignment explanation
Indices: 6635--6699 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
6625 TTTACAATGT
*
6635 ATTTTTAAATAATAATAATTTTTTTA
1 ATTTTT-AA-AATAATAATTTTTTAA
6661 ATTTTTGAAAATAATAATTTTATTAAA
1 ATTTTT-AAAATAATAATTTT-TT-AA
6688 ATATTTTAAAAT
1 AT-TTTTAAAAT
6700 GGGTGATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 12 0.35
26 10 0.29
27 8 0.24
28 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTTTAAAATAATAATTTTTTAA
Found at i:8337 original size:45 final size:45
Alignment explanation
Indices: 8273--8364 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
8263 GGGGATCGAG
* *
8273 TATTACGATAGTTCGAGTGCATACAATAAATCTCGACATACCCAA
1 TATTACGACAATTCGAGTGCATACAATAAATCTCGACATACCCAA
*
8318 TATTACGACAATTCGAGTGCATACAATAAATCTTGACATACCCAA
1 TATTACGACAATTCGAGTGCATACAATAAATCTCGACATACCCAA
8363 TA
1 TA
8365 AATTTGGGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (45 bp):
TATTACGACAATTCGAGTGCATACAATAAATCTCGACATACCCAA
Found at i:9144 original size:32 final size:26
Alignment explanation
Indices: 9084--9192 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
9074 AACAAACTCA
* *
9084 GTTTATGCTTGTATTTAATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
9110 GTTTATGTTTGTATTTCATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
9136 GTTTATGTTTGTATTTCATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
* *
9162 GCTTATGTTTGTATTTAATTAATTAT
1 GTTTATGTTTGTATTTCATTAATTAT
9188 GTTTA
1 GTTTA
9193 GGGCTTTGGG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.60
Consensus pattern (26 bp):
GTTTATGTTTGTATTTCATTAATTAT
Found at i:9205 original size:14 final size:14
Alignment explanation
Indices: 9201--9276 Score: 68
Period size: 14 Copynumber: 5.4 Consensus size: 14
9191 TAGGGCTTTG
9201 GGTTTAAGGCTTAA
1 GGTTTAAGGCTTAA
*
9215 GGTTTATGGCTT-A
1 GGTTTAAGGCTTAA
9228 GGATTTAAGG-TTAA
1 GG-TTTAAGGCTTAA
* *
9242 GGCTTT-AGAGTTTAG
1 GG-TTTAAG-GCTTAA
*
9257 GGTTTAAGGCTTAG
1 GGTTTAAGGCTTAA
9271 GGTTTA
1 GGTTTA
9277 GTGTTTATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
13 7 0.13
14 38 0.73
15 7 0.13
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.39
Consensus pattern (14 bp):
GGTTTAAGGCTTAA
Found at i:9219 original size:28 final size:28
Alignment explanation
Indices: 9188--9277 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
9178 AATTAATTAT
9188 GTTTAGGGCTTTGGGTTTAAGGCTTAAG
1 GTTTAGGGCTTTGGGTTTAAGGCTTAAG
* * *
9216 GTTTATGGCTTAGGATTTAAGG-TTAAG
1 GTTTAGGGCTTTGGGTTTAAGGCTTAAG
* *
9243 GCTTTAGAG-TTTAGGGTTTAAGGCTTAGG
1 G-TTTAGGGCTTT-GGGTTTAAGGCTTAAG
9272 GTTTAG
1 GTTTAG
9278 TGTTTATTAC
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
27 8 0.16
28 38 0.75
29 5 0.10
ACGTcount: A:0.21, C:0.06, G:0.33, T:0.40
Consensus pattern (28 bp):
GTTTAGGGCTTTGGGTTTAAGGCTTAAG
Found at i:9277 original size:7 final size:7
Alignment explanation
Indices: 9188--9283 Score: 59
Period size: 7 Copynumber: 13.7 Consensus size: 7
9178 AATTAATTAT
9188 GTTTAGG
1 GTTTAGG
9195 GCTTT-GG
1 G-TTTAGG
*
9202 GTTTAAG
1 GTTTAGG
* *
9209 GCTTAAG
1 GTTTAGG
*
9216 GTTTATG
1 GTTTAGG
*
9223 GCTTAGG
1 GTTTAGG
* *
9230 ATTTAAG
1 GTTTAGG
*
9237 GTTAAGG
1 GTTTAGG
* *
9244 CTTTAGA
1 GTTTAGG
9251 GTTTAGG
1 GTTTAGG
*
9258 GTTTAAG
1 GTTTAGG
*
9265 GCTTAGG
1 GTTTAGG
*
9272 GTTTAGT
1 GTTTAGG
9279 GTTTA
1 GTTTA
9284 TTACTTAATA
Statistics
Matches: 65, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
6 3 0.05
7 59 0.91
8 3 0.05
ACGTcount: A:0.21, C:0.05, G:0.32, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:9277 original size:21 final size:21
Alignment explanation
Indices: 9215--9283 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
9205 TAAGGCTTAA
* * *
9215 GGTTTATGGCTTAGGATTTAA
1 GGTTTAAGGCTTAGGGTTTAG
*
9236 GG-TTAAGGCTTTAGAGTTTAG
1 GGTTTAAGGC-TTAGGGTTTAG
9257 GGTTTAAGGCTTAGGGTTTAG
1 GGTTTAAGGCTTAGGGTTTAG
*
9278 TGTTTA
1 GGTTTA
9284 TTACTTAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.15
21 27 0.68
22 7 0.17
ACGTcount: A:0.22, C:0.04, G:0.32, T:0.42
Consensus pattern (21 bp):
GGTTTAAGGCTTAGGGTTTAG
Found at i:11486 original size:39 final size:39
Alignment explanation
Indices: 11429--11560 Score: 192
Period size: 39 Copynumber: 3.4 Consensus size: 39
11419 ATATTTGGAC
11429 CATCCGGGACCTCGTCATTCAGGCCTTCCTCGTCAATAT
1 CATCCGGGACCTCGTCATTCAGGCCTTCCTCGTCAATAT
* * *
11468 CATCCGGGACCTCATCATTTAGGCCTTCCTTGTCAATAT
1 CATCCGGGACCTCGTCATTCAGGCCTTCCTCGTCAATAT
* * *
11507 CATCCAGGACCTCGTCATTCAGGCTTTCCTCATCAATAT
1 CATCCGGGACCTCGTCATTCAGGCCTTCCTCGTCAATAT
* *
11546 CATCTGAGACCTCGT
1 CATCCGGGACCTCGT
11561 ACACGTCGGG
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.30
Consensus pattern (39 bp):
CATCCGGGACCTCGTCATTCAGGCCTTCCTCGTCAATAT
Found at i:11587 original size:27 final size:27
Alignment explanation
Indices: 11557--11613 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
11547 ATCTGAGACC
*
11557 TCGTACACGTCGGGATCACTATCACTA
1 TCGTACACGTCGAGATCACTATCACTA
*
11584 TCGTCCACGTCGAGATCACTATCACTA
1 TCGTACACGTCGAGATCACTATCACTA
11611 TCG
1 TCG
11614 ACCTCGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.26
Consensus pattern (27 bp):
TCGTACACGTCGAGATCACTATCACTA
Found at i:21652 original size:25 final size:25
Alignment explanation
Indices: 21616--21675 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
21606 ATTAACAAGC
*
21616 CATCATGCAACACCCACATTGGAGT
1 CATCATGTAACACCCACATTGGAGT
*
21641 CATCATGTAACATCCACATTGGAGT
1 CATCATGTAACACCCACATTGGAGT
21666 CATCATGTAA
1 CATCATGTAA
21676 TAGCTCGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (25 bp):
CATCATGTAACACCCACATTGGAGT
Found at i:23512 original size:21 final size:21
Alignment explanation
Indices: 23486--23533 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
23476 GTGTTTAGAA
23486 GTATCGGTAGTTTACATACTT
1 GTATCGGTAGTTTACATACTT
*
23507 GTATCGGTAGTTTGCATACTT
1 GTATCGGTAGTTTACATACTT
23528 GTATCG
1 GTATCG
23534 ATAGAAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (21 bp):
GTATCGGTAGTTTACATACTT
Found at i:23618 original size:21 final size:20
Alignment explanation
Indices: 23577--23645 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
23567 AGAGTTTTTA
23577 GTATCGGTAGAAGTAAG-ACTT
1 GTATCGGTAGAAG--AGTACTT
23598 GTATCGGTAGAAGAGTTACTT
1 GTATCGGTAGAAGAG-TACTT
* * **
23619 GTTTTGGTAGAACTGTCACTT
1 GTATCGGTAGAAGAGT-ACTT
23640 GTATCG
1 GTATCG
23646 ATACAAATCT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 36 0.92
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.35
Consensus pattern (20 bp):
GTATCGGTAGAAGAGTACTT
Found at i:35064 original size:71 final size:72
Alignment explanation
Indices: 34923--35064 Score: 216
Period size: 71 Copynumber: 2.0 Consensus size: 72
34913 AAATAATGAT
* * *
34923 TTCCAAAGGAGCATGAAATTGTAAAACTGTCAGGATCTTTCACGAATGTGGTAGTTTATTTGTCA
1 TTCCAAAGGAGCATGAAATTGTAAAACTGCCAGGATCTTTCACGAAGGTGGCAGTTTATTTGTCA
34988 ATACAAG
66 ATACAAG
* *
34995 TTCCAAAGGAGTATGAAATTGTAAAACTGCCA-GATCTTTCAC-ATAGGTGGCAGTTTTTTTGTC
1 TTCCAAAGGAGCATGAAATTGTAAAACTGCCAGGATCTTTCACGA-AGGTGGCAGTTTATTTGTC
35058 AATACAA
65 AATACAA
35065 CGCTGTGACC
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
70 1 0.02
71 33 0.52
72 30 0.47
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (72 bp):
TTCCAAAGGAGCATGAAATTGTAAAACTGCCAGGATCTTTCACGAAGGTGGCAGTTTATTTGTCA
ATACAAG
Found at i:38194 original size:22 final size:22
Alignment explanation
Indices: 38166--38210 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38156 AAGCCTAAGA
38166 AAAATCAGAATGGAATTAATTT
1 AAAATCAGAATGGAATTAATTT
38188 AAAATCAGAATGGAATTAATTT
1 AAAATCAGAATGGAATTAATTT
38210 A
1 A
38211 TCATGAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (22 bp):
AAAATCAGAATGGAATTAATTT
Found at i:42239 original size:15 final size:17
Alignment explanation
Indices: 42199--42244 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
42189 GTTTTAAATT
*
42199 TTTGTTATTATTATTAG
1 TTTGTTATCATTATTAG
*
42216 TTGGTTATCATT-TTA-
1 TTTGTTATCATTATTAG
42231 TTTGTTATCATTAT
1 TTTGTTATCATTAT
42245 CCTATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 11 0.44
16 4 0.16
17 10 0.40
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTGTTATCATTATTAG
Found at i:49478 original size:29 final size:30
Alignment explanation
Indices: 49423--49486 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
49413 AATAGTTTAT
*
49423 ATTTTTATAATTTTTAAAAAATTAAAT-TAA
1 ATTTTTATAATTTTTAAAAAATCAAATAT-A
* * *
49453 ATTTTTATCA-TTTTGAAAGATCAAATATA
1 ATTTTTATAATTTTTAAAAAATCAAATATA
49482 ATTTT
1 ATTTT
49487 ACTATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAAATCAAATATA
Found at i:53107 original size:9 final size:9
Alignment explanation
Indices: 53060--53120 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
53050 CTTTTAATCG
*
53060 AATTAAATT
1 AATTCAATT
53069 AATT-AATT
1 AATTCAATT
*
53077 AACT-AATT
1 AATTCAATT
53085 AA-TCAAATT
1 AATTC-AATT
53094 AATTCAATT
1 AATTCAATT
* *
53103 CATTCGATT
1 AATTCAATT
53112 AATTCAATT
1 AATTCAATT
53121 TTAATTGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
7 1 0.02
8 13 0.30
9 28 0.64
10 2 0.05
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (9 bp):
AATTCAATT
Found at i:54389 original size:43 final size:42
Alignment explanation
Indices: 54341--54436 Score: 111
Period size: 43 Copynumber: 2.3 Consensus size: 42
54331 CTCAAAAAAG
* * *
54341 GCCGCTATAGAACATGGTCTTTAGCAACGCTTTCCCCACACAC
1 GCCGCTAAAGAACATGGTCTTTAACAACGCTTT-CCCACAAAC
* * ** *
54384 GCCGCTAAAGACCATGTTCTTTAACGGCGGTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAACAACGCTTTCCCACAAAC
54426 GCCGCTAAAGA
1 GCCGCTAAAGA
54437 CCCCGCTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 19 0.42
43 26 0.58
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (42 bp):
GCCGCTAAAGAACATGGTCTTTAACAACGCTTTCCCACAAAC
Found at i:54960 original size:66 final size:66
Alignment explanation
Indices: 54828--54961 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
54818 ATTTTGAAGC
* * * * *
54828 TGTAGTTGCAGTTCGTCATACTTTCTTTGAGACTCTACTTCCCTCGCTGCTGCCTTGCCTTCAAG
1 TGTAGCTGAAGTTCATCATACTTTCGTTGAGACTCTACTTCCCTCGCTGCTGCCTTCCCTTCAAG
54893 T
66 T
* * * * *
54894 TGTAGCTGAAGTTCATCATATTTTCGTTGAGCCTCTGCTTCTCTCGCTGCTGCC-TCCTCTTTAA
1 TGTAGCTGAAGTTCATCATACTTTCGTTGAGACTCTACTTCCCTCGCTGCTGCCTTCC-CTTCAA
54958 GT
65 GT
54960 TG
1 TG
54962 AGCAATTTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 2 0.04
66 55 0.96
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (66 bp):
TGTAGCTGAAGTTCATCATACTTTCGTTGAGACTCTACTTCCCTCGCTGCTGCCTTCCCTTCAAG
T
Found at i:60414 original size:22 final size:22
Alignment explanation
Indices: 60396--60459 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
60386 CGCTCTGATT
60396 AGCACTGTGTGTGCTTCTGTTC
1 AGCACTGTGTGTGCTTCTGTTC
*
60418 AGCATTGTGTGTGCTTCTGTTC
1 AGCACTGTGTGTGCTTCTGTTC
*
60440 AGCACT-TATGTGCTTCTGTT
1 AGCACTGTGTGTGCTTCTGTT
60460 TCCCCAGCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 13 0.33
22 26 0.67
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.44
Consensus pattern (22 bp):
AGCACTGTGTGTGCTTCTGTTC
Found at i:60494 original size:24 final size:25
Alignment explanation
Indices: 60439--60508 Score: 115
Period size: 24 Copynumber: 2.8 Consensus size: 25
60429 TGCTTCTGTT
*
60439 CAGCACTTATGTGCTTCTGTTTCCC
1 CAGCACTTATGCGCTTCTGTTTCCC
60464 CAGCACTTATGCGCTTCTGTTT-CC
1 CAGCACTTATGCGCTTCTGTTTCCC
*
60488 CAGCACTTATGCACTTCTGTT
1 CAGCACTTATGCGCTTCTGTT
60509 AAGTACTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 22 0.51
25 21 0.49
ACGTcount: A:0.14, C:0.31, G:0.16, T:0.39
Consensus pattern (25 bp):
CAGCACTTATGCGCTTCTGTTTCCC
Found at i:62183 original size:22 final size:22
Alignment explanation
Indices: 62157--62240 Score: 141
Period size: 22 Copynumber: 3.8 Consensus size: 22
62147 CTTACTATTC
62157 AGCACTGTGTGTGCTTCTACTA
1 AGCACTGTGTGTGCTTCTACTA
62179 AGCACTGTGTGTGCTTCTACTA
1 AGCACTGTGTGTGCTTCTACTA
*
62201 AGCACTGTGTGTGCTTCTACTC
1 AGCACTGTGTGTGCTTCTACTA
* *
62223 AGCACTCTGTGTGTTTCT
1 AGCACTGTGTGTGCTTCT
62241 GTTTCCCCAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (22 bp):
AGCACTGTGTGTGCTTCTACTA
Found at i:65338 original size:16 final size:16
Alignment explanation
Indices: 65300--65416 Score: 55
Period size: 16 Copynumber: 7.5 Consensus size: 16
65290 TAAATGTTTA
* **
65300 ATTAAATAATTAAAAA
1 ATTAAATAATTGAATT
*
65316 ATGAAATAATTGAATT
1 ATTAAATAATTGAATT
* **
65332 ATTAAATATTTGGTTGT
1 ATTAAATAATTGAAT-T
* *
65349 TTTTAATAATT-AATT
1 ATTAAATAATTGAATT
* *
65364 ATT---TAATTAAATA
1 ATTAAATAATTGAATT
* *
65377 ATGAAATAA-TGAAATA
1 ATTAAATAATTG-AATT
*
65393 ATGAAATAATTGAATT
1 ATTAAATAATTGAATT
65409 ATTAAATA
1 ATTAAATA
65417 TTTGGTTGTT
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
12 5 0.07
13 5 0.07
15 4 0.05
16 50 0.67
17 11 0.15
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (16 bp):
ATTAAATAATTGAATT
Found at i:65378 original size:8 final size:8
Alignment explanation
Indices: 65367--65402 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
65357 ATTAATTATT
*
65367 TAATTAAA
1 TAATGAAA
65375 TAATGAAA
1 TAATGAAA
65383 TAATGAAA
1 TAATGAAA
65391 TAATGAAA
1 TAATGAAA
65399 TAAT
1 TAAT
65403 TGAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (8 bp):
TAATGAAA
Found at i:65378 original size:69 final size:70
Alignment explanation
Indices: 65266--65458 Score: 244
Period size: 77 Copynumber: 2.7 Consensus size: 70
65256 ATTTGAACCG
* * *
65266 AATATTTGGGTTGTTTTTAACAATTAAATGTTTAATTAAATAATTAAAA-AATGAAATAATTGAA
1 AATATTT-GGTTGTTTTTAATAATTAATTATTTAATTAAATAATTAAAATAATGAAATAATTGAA
65330 TTATTA
65 TTATTA
65336 AATATTTGGTTGTTTTTAATAATTAATTATTTAATTAAATAATGAAATAATGAAATAATGAAATA
1 AATATTTGGTTGTTTTTAATAATTAATTATTTAATTAAATAAT----T-A--AAATAATGAAATA
65401 ATTGAATTATTA
59 ATTGAATTATTA
* * * *
65413 AATATTTGGTTGTTTTTAATAAATAATTATATATTTAAATATTTAA
1 AATATTTGGTTGTTTTTAATAATTAATTATTTAATTAAATAATTAA
65459 GTTGTTTTTA
Statistics
Matches: 108, Mismatches: 7, Indels: 16
0.82 0.05 0.12
Matches are distributed among these distances:
69 33 0.31
70 8 0.07
72 1 0.01
73 2 0.02
74 1 0.01
76 3 0.03
77 60 0.56
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.46
Consensus pattern (70 bp):
AATATTTGGTTGTTTTTAATAATTAATTATTTAATTAAATAATTAAAATAATGAAATAATTGAAT
TATTA
Found at i:65398 original size:77 final size:77
Alignment explanation
Indices: 65298--65453 Score: 258
Period size: 77 Copynumber: 2.0 Consensus size: 77
65288 ATTAAATGTT
* * *
65298 TAATTAAATAATTAAAAAATGAAATAATTGAATTATTAAATATTTGGTTGTTTTTAATAATTAAT
1 TAATGAAATAATGAAAAAATGAAATAATTGAATTATTAAATATTTGGTTGTTTTTAATAAATAAT
*
65363 TATTTAATTAAA
66 TATATAATTAAA
*
65375 TAATGAAATAATGAAATAATGAAATAATTGAATTATTAAATATTTGGTTGTTTTTAATAAATAAT
1 TAATGAAATAATGAAAAAATGAAATAATTGAATTATTAAATATTTGGTTGTTTTTAATAAATAAT
*
65440 TATATATTTAAA
66 TATATAATTAAA
65452 TA
1 TA
65454 TTTAAGTTGT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (77 bp):
TAATGAAATAATGAAAAAATGAAATAATTGAATTATTAAATATTTGGTTGTTTTTAATAAATAAT
TATATAATTAAA
Found at i:65486 original size:38 final size:36
Alignment explanation
Indices: 65391--65486 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 36
65381 AATAATGAAA
*
65391 TAATGAAATAATTGAATTA-TTAAATATTTGGTTGTTTT
1 TAAT-AAATAA-T-AATTATTTAAATATTTAGTTGTTTT
*
65429 TAATAAATAATTATATATTTAAATATTTAAGTTGTTTT
1 TAATAAATAATAAT-TATTTAAATATTT-AGTTGTTTT
*
65467 TAATAATTAAATAATTATTT
1 TAATAAAT-AATAATTATTT
65487 TGTAGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
35 2 0.04
36 3 0.06
37 16 0.32
38 24 0.48
39 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (36 bp):
TAATAAATAATAATTATTTAAATATTTAGTTGTTTT
Found at i:69018 original size:2 final size:2
Alignment explanation
Indices: 69011--69041 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
69001 CTTGAATATT
*
69011 AC AC AC AC AC AC CC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
69042 GAGATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:70380 original size:41 final size:41
Alignment explanation
Indices: 70329--70501 Score: 170
Period size: 41 Copynumber: 4.2 Consensus size: 41
70319 TCACTATTGC
* *
70329 TTAACTTTTAGTGGCGTTTTCCCATAAACGCCGCTAATGCT
1 TTAACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAATGCT
** * * * *
70370 TTAACCTTTAGCCACATTTAT-TCATAAATGCCGCTAATGTT
1 TTAACCTTTAGCGGCGTTT-TCCCATAAACGCCGCTAATGCT
* * * *
70411 TTAACCTTTAGCGGTGCTTTCTCATAAACGCGGCTAATGCT
1 TTAACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAATGCT
* * * *
70452 CTGACCTTTAGCGGCGTTTTTCCTATAAACGCCGCTATTGCT
1 TTAACCTTTAGCGGCG-TTTTCCCATAAACGCCGCTAATGCT
70494 TT-ACCTTT
1 TTAACCTTT
70502 TACGACGTTT
Statistics
Matches: 104, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
40 1 0.01
41 81 0.78
42 22 0.21
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (41 bp):
TTAACCTTTAGCGGCGTTTTCCCATAAACGCCGCTAATGCT
Found at i:70500 original size:82 final size:81
Alignment explanation
Indices: 70322--70501 Score: 191
Period size: 82 Copynumber: 2.2 Consensus size: 81
70312 GAAAACGTCA
* * * * *
70322 CTATTGCTTAACTTTTAGTGGCGTTTTCCCATAAACGCCGCTAATGCTTTAACCTTTAGCCACAT
1 CTATTGCTTTACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTAACCTTTAGCCACAT
*
70387 TTATTCATAAATGCCG
66 TTATTCATAAACGCCG
* * * * * * ** *
70403 CTAATGTTTTAACCTTTAGCGGTGCTTTCTCATAAACGCGGCTAATGCTCTGACCTTTAGCGGCG
1 CTATTGCTTT-ACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTAACCTTTAGCCACA
70468 TTT-TTCCTATAAACGCCG
65 TTTATT-C-ATAAACGCCG
70486 CTATTGCTTTACCTTT
1 CTATTGCTTTACCTTT
70502 TACGACGTTT
Statistics
Matches: 79, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
81 9 0.11
82 53 0.67
83 17 0.22
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (81 bp):
CTATTGCTTTACCTTTAGCGGCGCTTTCCCATAAACGCCGCTAATGCTCTAACCTTTAGCCACAT
TTATTCATAAACGCCG
Found at i:82064 original size:7 final size:7
Alignment explanation
Indices: 82052--82077 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
82042 TAACATAATC
82052 ATGGAAA
1 ATGGAAA
82059 ATGGAAA
1 ATGGAAA
82066 ATGGAAA
1 ATGGAAA
82073 ATGGA
1 ATGGA
82078 GAAACACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (7 bp):
ATGGAAA
Found at i:82787 original size:30 final size:32
Alignment explanation
Indices: 82734--82792 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
82724 TTTTAAATTT
**
82734 TTTTAAAAATATTTATATTA-TTTTATTTTCA
1 TTTTAAAAATATTTATACAATTTTTATTTTCA
*
82765 TTTTAATAAT-TTTATACAATTTTTATTT
1 TTTTAAAAATATTTATACAATTTTTATTT
82793 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (32 bp):
TTTTAAAAATATTTATACAATTTTTATTTTCA
Found at i:87606 original size:22 final size:22
Alignment explanation
Indices: 87541--87690 Score: 113
Period size: 22 Copynumber: 6.8 Consensus size: 22
87531 TGTGGTGTAG
* * *
87541 ATCATTAGGCACCATAGTGTAGA
1 ATCAATAGGCACCGTAGTGCA-A
** *
87564 A-CAATAGGCATTGAAGTGCAA
1 ATCAATAGGCACCGTAGTGCAA
* * *
87585 ATTAGTAAGCACCGTAGTGCAA
1 ATCAATAGGCACCGTAGTGCAA
*
87607 ATCAATAGGCACCGTAGTGCAG
1 ATCAATAGGCACCGTAGTGCAA
* * * *
87629 AGCAGTTGGCACCCTAGTGCAA
1 ATCAATAGGCACCGTAGTGCAA
* *
87651 ACCAATAGGCATCGTAGTGCAA
1 ATCAATAGGCACCGTAGTGCAA
* * *
87673 ATTAATAAGCATCGTAGT
1 ATCAATAGGCACCGTAGT
87691 CTAAATAAGT
Statistics
Matches: 97, Mismatches: 29, Indels: 3
0.75 0.22 0.02
Matches are distributed among these distances:
21 2 0.02
22 94 0.97
23 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (22 bp):
ATCAATAGGCACCGTAGTGCAA
Found at i:87626 original size:44 final size:44
Alignment explanation
Indices: 87578--87690 Score: 136
Period size: 44 Copynumber: 2.6 Consensus size: 44
87568 TAGGCATTGA
*
87578 AGTGCAAATTAGTAAGCACCGTAGTGCAAATCAATAGGCACCGT
1 AGTGCAAATTAGTAAGCACCGTAGTGCAAACCAATAGGCACCGT
* ** ** * *
87622 AGTGCAGAGCAGTTGGCACCCTAGTGCAAACCAATAGGCATCGT
1 AGTGCAAATTAGTAAGCACCGTAGTGCAAACCAATAGGCACCGT
* *
87666 AGTGCAAATTAATAAGCATCGTAGT
1 AGTGCAAATTAGTAAGCACCGTAGT
87691 CTAAATAAGT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (44 bp):
AGTGCAAATTAGTAAGCACCGTAGTGCAAACCAATAGGCACCGT
Found at i:87852 original size:17 final size:17
Alignment explanation
Indices: 87830--87862 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
87820 CTATCCCAAG
87830 CCAATTTTATA-AATTCA
1 CCAA-TTTATACAATTCA
87847 CCAATTTATACAATTC
1 CCAATTTATACAATTC
87863 TCAATTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (17 bp):
CCAATTTATACAATTCA
Found at i:91249 original size:16 final size:16
Alignment explanation
Indices: 91228--91258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
91218 TGAGTTGGAT
91228 TTTTTAAATTTTTTTC
1 TTTTTAAATTTTTTTC
*
91244 TTTTTAACTTTTTTT
1 TTTTTAAATTTTTTT
91259 TTTATATTAT
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:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTAAATTTTTTTC
Found at i:91600 original size:12 final size:12
Alignment explanation
Indices: 91558--91602 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
91548 TCTATTACTC
91558 ATTTAATTTTTT
1 ATTTAATTTTTT
* *
91570 ATTTGTATTTTTC
1 ATTT-AATTTTTT
91583 ATTTAATTTTTT
1 ATTTAATTTTTT
*
91595 AGTTAATT
1 ATTTAATT
91603 GCAATCTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (12 bp):
ATTTAATTTTTT
Found at i:93611 original size:17 final size:17
Alignment explanation
Indices: 93589--93622 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
93579 TTACTTCTAG
93589 TATGAATATTGCTAAAA
1 TATGAATATTGCTAAAA
93606 TATGAATATTGCTAAAA
1 TATGAATATTGCTAAAA
93623 GTATTGCGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
TATGAATATTGCTAAAA
Found at i:98773 original size:34 final size:34
Alignment explanation
Indices: 98729--98797 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
98719 ATATGAAAAG
* * *
98729 TTAAGGAAGATGGAAGGTTAAAGGTCAAGGGAGA
1 TTAAGAAAGATGGAAGGTTAAAAGTCAAGAGAGA
98763 TTAAGAAAGATGGAAGGTTAAAAGTCAAGAGAGA
1 TTAAGAAAGATGGAAGGTTAAAAGTCAAGAGAGA
98797 T
1 T
98798 AAAAGGTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.33, T:0.19
Consensus pattern (34 bp):
TTAAGAAAGATGGAAGGTTAAAAGTCAAGAGAGA
Found at i:102744 original size:34 final size:34
Alignment explanation
Indices: 102701--102767 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
102691 AATATAAAAA
*
102701 GTTAAGGAAGATGGAAGGTTAAAGGTCAAGAGAG
1 GTTAAGGAAGATGGAAGGTTAAAAGTCAAGAGAG
102735 GTTAAGGAAGATGGAAGGTTAAAAGTCAAGAGA
1 GTTAAGGAAGATGGAAGGTTAAAAGTCAAGAGA
102768 AATGAAAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.03, G:0.36, T:0.18
Consensus pattern (34 bp):
GTTAAGGAAGATGGAAGGTTAAAAGTCAAGAGAG
Found at i:102753 original size:17 final size:17
Alignment explanation
Indices: 102701--102756 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
102691 AATATAAAAA
102701 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
102718 GTTAAAGGTCAAGA--G-AG
1 GTT-AAGG--AAGATGGAAG
102735 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
102752 GTTAA
1 GTTAA
102757 AAGTCAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 4 0.12
16 5 0.15
17 15 0.45
18 5 0.15
20 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.38, T:0.20
Consensus pattern (17 bp):
GTTAAGGAAGATGGAAG
Found at i:106011 original size:36 final size:36
Alignment explanation
Indices: 105964--106036 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
105954 AAAACGATTT
105964 TCTTCATTATGCCTTTTAGAAAGTCCCACTCCACTC
1 TCTTCATTATGCCTTTTAGAAAGTCCCACTCCACTC
106000 TCTTCATTATGCCTTTTAGAAAGTCCCACTCCACTC
1 TCTTCATTATGCCTTTTAGAAAGTCCCACTCCACTC
106036 T
1 T
106037 ATCTTAAGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (36 bp):
TCTTCATTATGCCTTTTAGAAAGTCCCACTCCACTC
Done.