Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012342.1 Kokia drynarioides strain JFW-HI SEQ_127344, 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: 96128
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Warning! 254 characters in sequence are not A, C, G, or T
Found at i:1664 original size:25 final size:27
Alignment explanation
Indices: 1631--1680 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1621 ACAAAATTTA
1631 AACACTGAATT-TT-TTGTTTTTAATT
1 AACACTGAATTGTTATTGTTTTTAATT
* *
1656 AACATTGAATTGTTATTTTTTTTAA
1 AACACTGAATTGTTATTGTTTTTAA
1681 ATATACTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 2 0.10
27 9 0.43
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (27 bp):
AACACTGAATTGTTATTGTTTTTAATT
Found at i:3384 original size:30 final size:30
Alignment explanation
Indices: 3350--3406 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3340 AAAATATTCA
3350 TATTTATGTTCATATT-TCTTTATTTAAAAT
1 TATTTATGTTCATATTCT-TTTATTTAAAAT
* *
3380 TATTTTTGTTTATATTCTTTTATTTAA
1 TATTTATGTTCATATTCTTTTATTTAA
3407 TATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (30 bp):
TATTTATGTTCATATTCTTTTATTTAAAAT
Found at i:6611 original size:2 final size:2
Alignment explanation
Indices: 6604--6648 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
6594 TTTGCTTTTC
*
6604 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6646 CT C
1 CT C
6649 ACAAAAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:8595 original size:123 final size:123
Alignment explanation
Indices: 8376--8615 Score: 462
Period size: 123 Copynumber: 2.0 Consensus size: 123
8366 TTGCTGAAAT
8376 CAAGATAGTTGCACACCTTGCTCTCTGATTACGGTCAGTAAACATCTTTTATCATAATTGCCTTG
1 CAAGATAGTTGCACACCTTGCTCTCTGATTACGGTCAGTAAACATCTTTTATCATAATTGCCTTG
*
8441 ATCCGTTGTGTTTTATCCTAATTCACATCCAGGGCCATTGATGGACCTATATTTTGAG
66 ATCCGTTGTGTTATATCCTAATTCACATCCAGGGCCATTGATGGACCTATATTTTGAG
8499 CAAGATAGTTGCACACCTTGCTCTCTGATTACGGTCAGTAAACATCTTTTATCATAATTGCCTTG
1 CAAGATAGTTGCACACCTTGCTCTCTGATTACGGTCAGTAAACATCTTTTATCATAATTGCCTTG
*
8564 ATCCGTTGTGTTATATTCTAATTCACATCCAGGGCCATTGATGGACCTATAT
66 ATCCGTTGTGTTATATCCTAATTCACATCCAGGGCCATTGATGGACCTATAT
8616 CGGTGCTCTG
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 115 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (123 bp):
CAAGATAGTTGCACACCTTGCTCTCTGATTACGGTCAGTAAACATCTTTTATCATAATTGCCTTG
ATCCGTTGTGTTATATCCTAATTCACATCCAGGGCCATTGATGGACCTATATTTTGAG
Found at i:8962 original size:16 final size:16
Alignment explanation
Indices: 8941--8972 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8931 AACTTTTTGG
8941 ACCACTATCTCAATGT
1 ACCACTATCTCAATGT
*
8957 ACCACTATCTCCATGT
1 ACCACTATCTCAATGT
8973 TAGCTGGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.31
Consensus pattern (16 bp):
ACCACTATCTCAATGT
Found at i:17060 original size:9 final size:10
Alignment explanation
Indices: 17034--17059 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
17024 TTTGTATTTT
17034 TAAAAAATTC
1 TAAAAAATTC
17044 TAAAAAATTC
1 TAAAAAATTC
17054 TAAAAA
1 TAAAAA
17060 TATATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAAAAATTC
Found at i:18213 original size:30 final size:29
Alignment explanation
Indices: 18173--18230 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
18163 TTCGTAAACA
18173 TTAAACAAACGAACATAAACACAAAATATT
1 TTAAACAAACGAACATAAACA-AAAATATT
* *
18203 TTAAATAAACGAACATGAACAAAAATAT
1 TTAAACAAACGAACATAAACAAAAATAT
18231 GAAATTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.60, C:0.14, G:0.05, T:0.21
Consensus pattern (29 bp):
TTAAACAAACGAACATAAACAAAAATATT
Found at i:19526 original size:23 final size:23
Alignment explanation
Indices: 19499--19552 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
19489 TAATTCAAAT
*
19499 TTCGAGTTAA-TCAAATTAAGTTA
1 TTCGAGTTAACTCAAA-TAAGTAA
19522 TTCGAGTTAACTCAAATAAGTAA
1 TTCGAGTTAACTCAAATAAGTAA
19545 TTCGAGTT
1 TTCGAGTT
19553 TTATGTTCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 24 0.83
24 5 0.17
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (23 bp):
TTCGAGTTAACTCAAATAAGTAA
Found at i:19690 original size:20 final size:20
Alignment explanation
Indices: 19665--19713 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
19655 TCTCTCTCAA
*
19665 CAAAATTTACAAAAAAATTT
1 CAAAATTTACAAAAAAATTC
* *
19685 CAAAATATT-TATAAAAATTC
1 CAAAAT-TTACAAAAAAATTC
19705 CAAAATTTA
1 CAAAATTTA
19714 TATCTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAAATTTACAAAAAAATTC
Found at i:22663 original size:9 final size:9
Alignment explanation
Indices: 22646--22676 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22636 TTGCCTCTAT
*
22646 GCAGCAGCA
1 GCAGGAGCA
22655 GCAGGAGCA
1 GCAGGAGCA
22664 GCAGGAGCA
1 GCAGGAGCA
22673 GCAG
1 GCAG
22677 CAAGTATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.26, G:0.42, T:0.00
Consensus pattern (9 bp):
GCAGGAGCA
Found at i:22907 original size:102 final size:102
Alignment explanation
Indices: 22731--22937 Score: 360
Period size: 102 Copynumber: 2.0 Consensus size: 102
22721 CATTCTCCTG
* *
22731 AACAACAATTCACGAACTGTGCTTCCAAATAGCATGAGGACCCTAGGAGGCAATCTTTTAGCAGG
1 AACAACAATTCACAAACTGTGCTTCCAAATAGCATGAGGACCCGAGGAGGCAATCTTTTAGCAGG
** *
22796 TCCGAATATGGTCGACAATGGTGCGGGGATGAATAAT
66 TCAAAATATGGTCGACAATGGTGCAGGGATGAATAAT
22833 AACAACAATTCACAAACTGTGCTTCCAAATAGCATGAGGACCCGAGGAGGCAATCTTTTAGCAGG
1 AACAACAATTCACAAACTGTGCTTCCAAATAGCATGAGGACCCGAGGAGGCAATCTTTTAGCAGG
*
22898 TCAAAATATGGTTGACAATGGTGCAGGGATGAATAAT
66 TCAAAATATGGTCGACAATGGTGCAGGGATGAATAAT
22935 AAC
1 AAC
22938 TCAACATATC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (102 bp):
AACAACAATTCACAAACTGTGCTTCCAAATAGCATGAGGACCCGAGGAGGCAATCTTTTAGCAGG
TCAAAATATGGTCGACAATGGTGCAGGGATGAATAAT
Found at i:23944 original size:226 final size:228
Alignment explanation
Indices: 23458--24001 Score: 874
Period size: 226 Copynumber: 2.4 Consensus size: 228
23448 TGATCATTTG
*
23458 AATATAGGAAGATATTTTGGTATTATTTTTTGTTTCTTTATATTGAGATCCAAAATGCTAA-TTA
1 AATATAGGAAGAGATTTTGGTATTATTTTTTGTTTCTTTATATTGAGATCCAAAATGC-AAGTTA
*
23522 TAATTGC-T-TGTGC--GCATGAAATCAAAATTTTTTTTTATATCATTTGAATATAAATTTATAA
65 TAATTGCTTGTGTGCAGGAATGAAATCAAAA-TTTTTTTTATATCATTTGAATATAAATTTAT--
23583 AATTTTATTACATAGTAAAAATATAAATTTATTATTTTAATAATTTATTTCTTTATAATTTTAAT
127 -ATTTTATTACATAGTAAAAATATAAATTTATTATTTTAATAATTTATTTCTTTATAATTTTAAT
23648 TTTTTATTAAGCTCCAAAATGCTAATTTTAAACTTGAA
191 TTTTTATTAAGCTCCAAAATGCTAATTTTAAACTTGAA
23686 AATATAGGAAGAGATTTTGGTATTATTTTTTTGTTTCTTTATATTGAGATCCAAAATGCAAGTTA
1 AATATAGGAAGAGATTTTGGTATTA-TTTTTTGTTTCTTTATATTGAGATCCAAAATGCAAGTTA
23751 TAATTGCTTGTGTGCAGGAATGAAATCAGAAA-TTTTTTTATATCATTTGAATAT-AATTT-T-T
65 TAATTGCTTGTGTGCAGGAATGAAATCA-AAATTTTTTTTATATCATTTGAATATAAATTTATAT
23812 TTT-TTACATAGTAAAAATATAAATTTATTATTTTAATAATTTATTTCTTTATAATTTTAATTTT
129 TTTATTACATAGTAAAAATATAAATTTATTATTTTAATAATTTATTTCTTTATAATTTTAA-TTT
* *
23876 TTTATTAAGCTCCAAAATGCTAGTTTTAAATTTGAA
193 TTTATTAAGCTCCAAAATGCTAATTTTAAACTTGAA
* *
23912 AATATAGGAAGAGATTTTGGTATTTATTTTTTGTTTCTTTATATTGAGATCTAAAATGCTAGTTA
1 AATATAGGAAGAGATTTTGGTA-TTATTTTTTGTTTCTTTATATTGAGATCCAAAATGCAAGTTA
*
23977 TAATTGCTTGTGTGCAGGGATGAAA
65 TAATTGCTTGTGTGCAGGAATGAAA
24002 CTAGTGTTTT
Statistics
Matches: 300, Mismatches: 7, Indels: 20
0.92 0.02 0.06
Matches are distributed among these distances:
225 57 0.19
226 124 0.41
227 3 0.01
228 26 0.09
229 43 0.14
230 2 0.01
231 10 0.03
232 22 0.07
233 10 0.03
234 3 0.01
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (228 bp):
AATATAGGAAGAGATTTTGGTATTATTTTTTGTTTCTTTATATTGAGATCCAAAATGCAAGTTAT
AATTGCTTGTGTGCAGGAATGAAATCAAAATTTTTTTTATATCATTTGAATATAAATTTATATTT
TATTACATAGTAAAAATATAAATTTATTATTTTAATAATTTATTTCTTTATAATTTTAATTTTTT
ATTAAGCTCCAAAATGCTAATTTTAAACTTGAA
Found at i:24874 original size:17 final size:18
Alignment explanation
Indices: 24848--24889 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
24838 TTTGGAGTTT
24848 ATAA-TATAAAGA-AGTAA
1 ATAATTATAAAGATA-TAA
24865 A-AATTATAAAGATATAA
1 ATAATTATAAAGATATAA
24882 ATAATTAT
1 ATAATTAT
24890 TAAAATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (18 bp):
ATAATTATAAAGATATAA
Found at i:29551 original size:12 final size:12
Alignment explanation
Indices: 29523--29569 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
29513 TTCACAAACA
29523 AGCTCGTTTATTG
1 AGCTCGTTTA-TG
*
29536 -GCTCATTTATG
1 AGCTCGTTTATG
29547 AGCTCGTTTATCG
1 AGCTCGTTTAT-G
29560 A-CTCGTTTAT
1 AGCTCGTTTAT
29570 TTATTAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 2 0.07
12 26 0.87
13 2 0.07
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (12 bp):
AGCTCGTTTATG
Found at i:29568 original size:24 final size:24
Alignment explanation
Indices: 29523--29569 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29513 TTCACAAACA
* *
29523 AGCTCGTTTATTGGCTCATTTATG
1 AGCTCGTTTATCGACTCATTTATG
*
29547 AGCTCGTTTATCGACTCGTTTAT
1 AGCTCGTTTATCGACTCATTTAT
29570 TTATTAATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (24 bp):
AGCTCGTTTATCGACTCATTTATG
Found at i:34404 original size:88 final size:88
Alignment explanation
Indices: 34255--34432 Score: 329
Period size: 88 Copynumber: 2.0 Consensus size: 88
34245 CACTATAATA
*
34255 TCTAATCTTATCATCACCGTTGTTTTTATATTAACTATAAGTAAACACACCGTTCATCCAAACTA
1 TCTAATCTTATCATCACCGTTGTTTTTACATTAACTATAAGTAAACACACCGTTCATCCAAACTA
*
34320 AATTTTAGCATCACTAGTCTTTT
66 AATCTTAGCATCACTAGTCTTTT
*
34343 TCTAATCTTATCATCGCCGTTGTTTTTACATTAACTATAAGTAAACACACCGTTCATCCAAACTA
1 TCTAATCTTATCATCACCGTTGTTTTTACATTAACTATAAGTAAACACACCGTTCATCCAAACTA
34408 AATCTTAGCATCACTAGTCTTTT
66 AATCTTAGCATCACTAGTCTTTT
34431 TC
1 TC
34433 AAACTAATGT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (88 bp):
TCTAATCTTATCATCACCGTTGTTTTTACATTAACTATAAGTAAACACACCGTTCATCCAAACTA
AATCTTAGCATCACTAGTCTTTT
Found at i:37344 original size:2 final size:2
Alignment explanation
Indices: 37337--37365 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
37327 GCTTATGATA
37337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37366 CTACTCCCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38092 original size:22 final size:21
Alignment explanation
Indices: 38066--38120 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
38056 TACTTTTTTA
*
38066 AAAAATTTAAATTAAAAAGTT
1 AAAAATTTAAATTAAAAAATT
**
38087 ATAAAATTTATTTTAAAAAATT
1 A-AAAATTTAAATTAAAAAATT
38109 AAAAATATTAAA
1 AAAAAT-TTAAA
38121 ATCATTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAAATTTAAATTAAAAAATT
Found at i:43954 original size:31 final size:30
Alignment explanation
Indices: 43911--43972 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
43901 AGACCTCAAA
*
43911 AAGTTTAAGTACCAACTTACA-AAAAGAGTGT
1 AAGTTTAAGTACCAAATTA-AGAAAA-AGTGT
*
43942 AAGTTTAGGTACCAAATTAAGAAAAAGTGT
1 AAGTTTAAGTACCAAATTAAGAAAAAGTGT
43972 A
1 A
43973 GGTACCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.26
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAAGAAAAAGTGT
Found at i:43969 original size:24 final size:24
Alignment explanation
Indices: 43942--43991 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
43932 AAAAGAGTGT
* *
43942 AAGTTTAGGTACCAAATTAAGAAA
1 AAGTGTAGGTACCAAATTAAAAAA
43966 AAGTGTAGGTACCAAATTAAAAAA
1 AAGTGTAGGTACCAAATTAAAAAA
43990 AA
1 AA
43992 TGTCAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (24 bp):
AAGTGTAGGTACCAAATTAAAAAA
Found at i:49219 original size:72 final size:73
Alignment explanation
Indices: 49101--49277 Score: 234
Period size: 72 Copynumber: 2.5 Consensus size: 73
49091 TTCAAAGATC
* * * *
49101 TCGTCTCCATATTTTCGTTTATCACTACATG-TTCAAGAATTTTCTTCTCATTCAAAGGCTTTTT
1 TCGTCTCCGTATTTTCGTTTATCACCACCTGCTTCAAGAATTGTCTTCTCATTCAAAGGCTTTTT
49165 GATTATCA
66 GATTATCA
* *
49173 TCGTCTCCGTATTTTCGTGTATCACCACCTGCTT-GAGAATTGTCTTCTCATTCAAAGGCTTTTT
1 TCGTCTCCGTATTTTCGTTTATCACCACCTGCTTCAAGAATTGTCTTCTCATTCAAAGGCTTTTT
* *
49237 GATTCTGA
66 GATTATCA
* *
49245 TCGTCTCGGTATTTTCATTTAT-AGCCACCTGCT
1 TCGTCTCCGTATTTTCGTTTATCA-CCACCTGCT
49278 CGAGTGACGG
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
71 1 0.01
72 89 0.97
73 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.44
Consensus pattern (73 bp):
TCGTCTCCGTATTTTCGTTTATCACCACCTGCTTCAAGAATTGTCTTCTCATTCAAAGGCTTTTT
GATTATCA
Found at i:53253 original size:18 final size:19
Alignment explanation
Indices: 53225--53264 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
53215 ATTACAAAAT
*
53225 AAATTCAAAATAATTTTTA
1 AAATTCAAAATAATTTATA
*
53244 AAATTC-AAATTATTTATA
1 AAATTCAAAATAATTTATA
53262 AAA
1 AAA
53265 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTCAAAATAATTTATA
Found at i:53265 original size:19 final size:19
Alignment explanation
Indices: 53225--53267 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
53215 ATTACAAAAT
*
53225 AAATTCAAAATAATTTTTA
1 AAATTCAAAATAATTTTAA
*
53244 AAATTC-AAATTATTTATAA
1 AAATTCAAAATAATTT-TAA
53263 AAATT
1 AAATT
53268 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTCAAAATAATTTTAA
Found at i:55298 original size:25 final size:26
Alignment explanation
Indices: 55239--55299 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
55229 TTAAAAAAAT
*
55239 ATTTATTT-TATTTTAATATTTAATA
1 ATTTTTTTATATTTTAATATTTAATA
* * *
55264 A-TTTTATATATTTTTA-ATTTATTA
1 ATTTTTTTATATTTTAATATTTAATA
55288 ATTTTTTTATAT
1 ATTTTTTTATAT
55300 AATCATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
ATTTTTTTATATTTTAATATTTAATA
Found at i:56011 original size:2 final size:2
Alignment explanation
Indices: 55971--55996 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55961 ATGATCAAAC
55971 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
55997 CCCACTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56780 original size:19 final size:19
Alignment explanation
Indices: 56739--56780 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
56729 TTTTTTTCTT
* *
56739 TTTTATTGTTTTGCTGCTT
1 TTTTATTGTTTTGCTACTA
56758 TTTTATTGTTTT-CTCACTA
1 TTTTATTGTTTTGCT-ACTA
56777 TTTT
1 TTTT
56781 GTTATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.10, C:0.12, G:0.10, T:0.69
Consensus pattern (19 bp):
TTTTATTGTTTTGCTACTA
Found at i:58416 original size:15 final size:16
Alignment explanation
Indices: 58396--58429 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
58386 ATGTAAAAGA
*
58396 ATTAAAAAT-TATTTT
1 ATTAAAAATATATATT
58411 ATTAAAAATATATATT
1 ATTAAAAATATATATT
58427 ATT
1 ATT
58430 GTAATAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAAAAATATATATT
Found at i:74367 original size:6 final size:6
Alignment explanation
Indices: 74356--74382 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
74346 TCTTCTTGGT
74356 ATGCAC ATGCAC ATGCAC ATGCAC ATG
1 ATGCAC ATGCAC ATGCAC ATGCAC ATG
74383 ATGTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (6 bp):
ATGCAC
Found at i:75440 original size:18 final size:18
Alignment explanation
Indices: 75417--75455 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
75407 AGCTTTACTT
*
75417 TATTTTTT-TTAAAAATA
1 TATTTTTTATAAAAAATA
*
75434 TATTTTTTATAAAAAATT
1 TATTTTTTATAAAAAATA
75452 TATT
1 TATT
75456 AATTAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTTTATAAAAAATA
Found at i:77168 original size:18 final size:18
Alignment explanation
Indices: 77132--77169 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
77122 TAGATTTTTG
*
77132 TTTGTTTTAGTTTTTAAA
1 TTTGTTTTAGTTTTCAAA
77150 TTTGTTTTA-TTTGTCAAA
1 TTTGTTTTAGTTT-TCAAA
77168 TT
1 TT
77170 AATTAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.21, C:0.03, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTGTTTTAGTTTTCAAA
Found at i:79041 original size:21 final size:21
Alignment explanation
Indices: 79017--79076 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
79007 TATTTTTTGC
*
79017 TGTTTCGATGTTGTGTTTTAT
1 TGTTTCGATGTTATGTTTTAT
* * *
79038 TGTTTTGGTGTTATTTTTTAT
1 TGTTTCGATGTTATGTTTTAT
* *
79059 TGTTTTGAT-TGATGTTTT
1 TGTTTCGATGTTATGTTTT
79077 TGCTATTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.10, C:0.02, G:0.22, T:0.67
Consensus pattern (21 bp):
TGTTTCGATGTTATGTTTTAT
Found at i:79153 original size:20 final size:22
Alignment explanation
Indices: 79116--79166 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
79106 TGTTTTGCTG
*
79116 TTATTTTTTGCTGCTTTGGTTC
1 TTATTTTTTGCTGCTTTGGATC
* *
79138 TTATTTTTT-TTG-TTTGGATG
1 TTATTTTTTGCTGCTTTGGATC
79158 TTATTTTTT
1 TTATTTTTT
79167 ATGCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.58
21 2 0.08
22 9 0.35
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.71
Consensus pattern (22 bp):
TTATTTTTTGCTGCTTTGGATC
Found at i:89286 original size:17 final size:19
Alignment explanation
Indices: 89259--89294 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
89249 AACGAAAATG
89259 GGAAGAAAG-AAAAGGGGA
1 GGAAGAAAGAAAAAGGGGA
89277 GGAA-AAAGAAAAAGGGGA
1 GGAAGAAAGAAAAAGGGGA
89295 AACTAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (19 bp):
GGAAGAAAGAAAAAGGGGA
Done.