Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006024.1 Kokia drynarioides strain JFW-HI SEQ_120469, 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: 99399
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 349 characters in sequence are not A, C, G, or T
Found at i:6883 original size:56 final size:56
Alignment explanation
Indices: 6822--6930 Score: 150
Period size: 56 Copynumber: 1.9 Consensus size: 56
6812 CTTTAGGGGA
* *
6822 CACACGAGCT-GAGCACAC-ATGTGTGTGCCAAACCGTGTGTGTATACTGTTTTGGGT
1 CACACGAGCTAG-GCACACGA-GCGTGTGCCAAACCGTGTGTGCATACTGTTTTGGGT
* *
6878 CACACGGGCTAGGCACACGAGCGTGTGCCAGACCGTGTGTGCATACTGTTTTG
1 CACACGAGCTAGGCACACGAGCGTGTGCCAAACCGTGTGTGCATACTGTTTTG
6931 TGAATTAAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
56 45 0.96
57 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (56 bp):
CACACGAGCTAGGCACACGAGCGTGTGCCAAACCGTGTGTGCATACTGTTTTGGGT
Found at i:7522 original size:20 final size:22
Alignment explanation
Indices: 7497--7553 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
7487 ACATTATATA
*
7497 GTGTGTAGGGATGGAT-A-TTG
1 GTGTGTAGGGATGGATGAGATG
* *
7517 GTGTGTTGGGCTGGATGGAGATG
1 GTGTGTAGGGATGGAT-GAGATG
7540 GTGTGTAGGGATGG
1 GTGTGTAGGGATGG
7554 GATGTGCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 14 0.48
22 1 0.03
23 14 0.48
ACGTcount: A:0.16, C:0.02, G:0.51, T:0.32
Consensus pattern (22 bp):
GTGTGTAGGGATGGATGAGATG
Found at i:7556 original size:24 final size:25
Alignment explanation
Indices: 7504--7557 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
7494 ATAGTGTGTA
* * *
7504 GGGATGGATATTGGTGTGTTGGGCT
1 GGGATGGAGATTGGTGTGTAGGGAT
7529 -GGATGGAGA-TGGTGTGTAGGGAT
1 GGGATGGAGATTGGTGTGTAGGGAT
7552 GGGATG
1 GGGATG
7558 TGCATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.17, C:0.02, G:0.52, T:0.30
Consensus pattern (25 bp):
GGGATGGAGATTGGTGTGTAGGGAT
Found at i:8752 original size:16 final size:17
Alignment explanation
Indices: 8733--8779 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
8723 GTTGAACTAA
8733 TTTTTATAATTT-TCAT
1 TTTTTATAATTTATCAT
* *
8749 TTTTTAT-TTTTATTAT
1 TTTTTATAATTTATCAT
8765 TTTTTAATAATTTAT
1 TTTTT-ATAATTTAT
8780 TTACTTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 15 0.60
17 2 0.08
18 5 0.20
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATAATTTATCAT
Found at i:9091 original size:19 final size:19
Alignment explanation
Indices: 9050--9093 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9040 AAGATTTTTT
* * * *
9050 ATTTTTTTGATAATTTATT
1 ATTTTTTTAAAAATATATA
9069 ATTTTTTTAAAAATATATA
1 ATTTTTTTAAAAATATATA
9088 ATTTTT
1 ATTTTT
9094 AAAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTTAAAAATATATA
Found at i:20239 original size:23 final size:23
Alignment explanation
Indices: 20210--20265 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
20200 GGTTTGTTGG
20210 AATTTATGTGGA-TTAAAAACAT
1 AATTTATGTGGAGTTAAAAACAT
***
20232 AATTTTAT-AAAAGTTAAAAACAT
1 AA-TTTATGTGGAGTTAAAAACAT
20255 AATTTATGTGG
1 AATTTATGTGG
20266 GTTTGTTGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (23 bp):
AATTTATGTGGAGTTAAAAACAT
Found at i:20924 original size:26 final size:26
Alignment explanation
Indices: 20895--21215 Score: 251
Period size: 26 Copynumber: 12.3 Consensus size: 26
20885 CCTAAACAAT
** *
20895 TATATAGCAGGCCTTGAGCCAATGAG
1 TATATAGCAGGCCTTGAGCCGGTGAA
* **
20921 TATATAGCAGGGCTTGAGCTAGTGAA
1 TATATAGCAGGCCTTGAGCCGGTGAA
*
20947 TA-ATTAGCAGGCCTTAAGCCGGTGAA
1 TATA-TAGCAGGCCTTGAGCCGGTGAA
* *
20973 TAAATAGCAGG-CTTCGAGCCGATGAA
1 TATATAGCAGGCCTT-GAGCCGGTGAA
* *
20999 TATATAGCATGCCTTGAGTCGGTGAA
1 TATATAGCAGGCCTTGAGCCGGTGAA
*
21025 TAAATAGCAGG-CTTCGAGCCGGTGAA
1 TATATAGCAGGCCTT-GAGCCGGTGAA
* * *
21051 TATATATCAAGCCTTGAGCCTGTGAA
1 TATATAGCAGGCCTTGAGCCGGTGAA
* * * *
21077 TAAATAGTAAG-CTTCAAGCCGGTGAA
1 TATATAGCAGGCCTT-GAGCCGGTGAA
* * *
21103 TAAATAGCAAG-CTTCAAGCCGGTGAA
1 TATATAGCAGGCCTT-GAGCCGGTGAA
* ** *
21129 TATATAGCAAGCCTTGAATCAGTGAA
1 TATATAGCAGGCCTTGAGCCGGTGAA
*
21155 TA-ATTAGCAGG-CTTCGAGCTGGTGAA
1 TATA-TAGCAGGCCTT-GAGCCGGTGAA
* * * *
21181 TAAATAGCAGGCTTTGAGCCAGTGAT
1 TATATAGCAGGCCTTGAGCCGGTGAA
21207 TATATAGCA
1 TATATAGCA
21216 AGCTTCATGC
Statistics
Matches: 241, Mismatches: 42, Indels: 24
0.79 0.14 0.08
Matches are distributed among these distances:
25 14 0.06
26 214 0.89
27 13 0.05
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (26 bp):
TATATAGCAGGCCTTGAGCCGGTGAA
Found at i:20980 original size:52 final size:52
Alignment explanation
Indices: 20899--21205 Score: 277
Period size: 52 Copynumber: 5.9 Consensus size: 52
20889 AACAATTATA
** * * *
20899 TAGCAGGCCTTGAGCCAATGAGTATATAGCAGGGCTT-GAGCTAGTGAATAAT
1 TAGCAGGCCTTGAGCCGGTGAATAAATAGCA-GGCTTCGAGCCAGTGAATAAT
*
20951 TAGCAGGCCTTAAGCCGGTGAATAAATAGCAGGCTTCGAGCC-GATGAAT-AT
1 TAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCTTCGAGCCAG-TGAATAAT
* * *
21002 ATAGCATGCCTTGAGTCGGTGAATAAATAGCAGGCTTCGAGCCGGTGAAT-AT
1 -TAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCTTCGAGCCAGTGAATAAT
* * * * * * * *
21054 ATATCAAGCCTTGAGCCTGTGAATAAATAGTAAGCTTCAAGCCGGTGAATAAA
1 -TAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCTTCGAGCCAGTGAATAAT
* * * * **
21107 TAGCAAG-CTTCAAGCCGGTGAATATATAGCAAGCCTT-GAATCAGTGAATAAT
1 TAGCAGGCCTT-GAGCCGGTGAATAAATAGC-AGGCTTCGAGCCAGTGAATAAT
* *
21159 TAGCAGG-CTTCGAGCTGGTGAATAAATAGCAGGCTTTGAGCCAGTGA
1 TAGCAGGCCTT-GAGCCGGTGAATAAATAGCAGGCTTCGAGCCAGTGA
21206 TTATATAGCA
Statistics
Matches: 211, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
51 16 0.08
52 189 0.90
53 6 0.03
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (52 bp):
TAGCAGGCCTTGAGCCGGTGAATAAATAGCAGGCTTCGAGCCAGTGAATAAT
Found at i:28418 original size:78 final size:76
Alignment explanation
Indices: 28288--28486 Score: 193
Period size: 78 Copynumber: 2.6 Consensus size: 76
28278 ATCGTAAACA
* * * * * *
28288 AATATATAGCAGGCTTTGAGTCGGTGAATAATTAACAGACTTCGAGCCGGTGAATATATA-ATAG
1 AATATATAGCA-GCCTTGAGCCGATGAATAAATAGCAGGCTTCGAGCCGGTGAATATATACA-AG
28352 ACTTCGAGCCGGTG
64 ACTT-GAGCCGGTG
* *
28366 AATATATAGCAGTCCTTGAGCCGATGAGTAAATAGCAGGCTTCGAGCTGGTGAATATATAGCAAG
1 AATATATAGCAG-CCTTGAGCCGATGAATAAATAGCAGGCTTCGAGCCGGTGAATATATA-CAAG
* *
28431 CCTTGAGCTGGTG
64 ACTTGAGCCGGTG
* * * * * *
28444 AATAAATAGTAGGCTTCGAGCCGATGATTATATAGCAAGCTTC
1 AATATATAGCAGCCTT-GAGCCGATGAATAAATAGCAGGCTTC
28487 TTGCCAATGT
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
77 4 0.04
78 91 0.90
79 5 0.05
80 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (76 bp):
AATATATAGCAGCCTTGAGCCGATGAATAAATAGCAGGCTTCGAGCCGGTGAATATATACAAGAC
TTGAGCCGGTG
Found at i:28478 original size:26 final size:26
Alignment explanation
Indices: 28288--28480 Score: 167
Period size: 26 Copynumber: 7.4 Consensus size: 26
28278 ATCGTAAACA
* * *
28288 AATATATAGCAGGCTTTGAGTCGGTG
1 AATATATAGCAGCCTTCGAGCCGGTG
* *
28314 AATA-ATTAACAGACTTCGAGCCGGTG
1 AATATA-TAGCAGCCTTCGAGCCGGTG
** *
28340 AATATATAATAGACTTCGAGCCGGTG
1 AATATATAGCAGCCTTCGAGCCGGTG
*
28366 AATATATAGCAGTCCTT-GAGCCGATG
1 AATATATAGCAG-CCTTCGAGCCGGTG
* * * *
28392 AGTAAATAGCAGGCTTCGAGCTGGTG
1 AATATATAGCAGCCTTCGAGCCGGTG
*
28418 AATATATAGCAAGCCTT-GAGCTGGTG
1 AATATATAGC-AGCCTTCGAGCCGGTG
* * * *
28444 AATAAATAGTAGGCTTCGAGCCGATG
1 AATATATAGCAGCCTTCGAGCCGGTG
*
28470 ATTATATAGCA
1 AATATATAGCA
28481 AGCTTCTTGC
Statistics
Matches: 136, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
25 9 0.07
26 118 0.87
27 9 0.07
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (26 bp):
AATATATAGCAGCCTTCGAGCCGGTG
Found at i:28481 original size:52 final size:52
Alignment explanation
Indices: 28288--28483 Score: 200
Period size: 52 Copynumber: 3.8 Consensus size: 52
28278 ATCGTAAACA
* * * * * *
28288 AATATATAGCAGGCTTTGAGTCGGTGAATA-ATTAAC-AGACTTCGAGCCGGTG
1 AATAAATAGTAGGCTTCGAGCCGGTGAATATA-TAGCAAGCCTT-GAGCCGGTG
* * * *
28340 AATATATAATAGACTTCGAGCCGGTGAATATATAGC-AGTCCTTGAGCCGATG
1 AATAAATAGTAGGCTTCGAGCCGGTGAATATATAGCAAG-CCTTGAGCCGGTG
* * * *
28392 AGTAAATAGCAGGCTTCGAGCTGGTGAATATATAGCAAGCCTTGAGCTGGTG
1 AATAAATAGTAGGCTTCGAGCCGGTGAATATATAGCAAGCCTTGAGCCGGTG
* *
28444 AATAAATAGTAGGCTTCGAGCCGATGATTATATAGCAAGC
1 AATAAATAGTAGGCTTCGAGCCGGTGAATATATAGCAAGC
28484 TTCTTGCCAA
Statistics
Matches: 120, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
52 114 0.95
53 6 0.05
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (52 bp):
AATAAATAGTAGGCTTCGAGCCGGTGAATATATAGCAAGCCTTGAGCCGGTG
Found at i:29377 original size:25 final size:25
Alignment explanation
Indices: 29338--29389 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
29328 TCAGTCAGAA
*
29338 ATAAAATAATCCTTTTTTATAGTATT
1 ATAAAATAATCC-TTTTTATAGAATT
*
29364 ATAAAA-ATTCCTTTTTATAGAATT
1 ATAAAATAATCCTTTTTATAGAATT
29388 AT
1 AT
29390 TTTTGTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
25 4 0.17
26 6 0.25
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (25 bp):
ATAAAATAATCCTTTTTATAGAATT
Found at i:30170 original size:17 final size:17
Alignment explanation
Indices: 30127--30173 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
30117 CAACATCATC
* *
30127 ATATGAATATATTTAAA
1 ATATGAAAAAATTTAAA
*
30144 A-ATTATAAAAATTTAAA
1 ATATGA-AAAAATTTAAA
30161 ATATGAAAAAATT
1 ATATGAAAAAATT
30174 ATAATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 18 0.75
18 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
ATATGAAAAAATTTAAA
Found at i:43919 original size:3 final size:3
Alignment explanation
Indices: 43911--43938 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43901 TTCCTCTCTG
43911 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
43939 CCTGCCCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:48451 original size:16 final size:16
Alignment explanation
Indices: 48427--48461 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
48417 GTATGGACCT
*
48427 AAATATAAATTGATTC
1 AAATATAAAATGATTC
*
48443 AAATTTAAAATGATTC
1 AAATATAAAATGATTC
48459 AAA
1 AAA
48462 CTCAAAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (16 bp):
AAATATAAAATGATTC
Found at i:51127 original size:35 final size:33
Alignment explanation
Indices: 51081--51149 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 33
51071 AACAAGTGAT
* *
51081 AAAAAATTCAAATTGTTGGATGATCAAAAAAGAAA
1 AAAAAAATCAAATAGTTGGATGAT-AAAAAA-AAA
51116 AAAAAAATCAAATAGTTGGATGATAAAAAAAAA
1 AAAAAAATCAAATAGTTGGATGATAAAAAAAAA
51149 A
1 A
51150 TCAAATAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 4 0.12
34 6 0.19
35 22 0.69
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (33 bp):
AAAAAAATCAAATAGTTGGATGATAAAAAAAAA
Found at i:51151 original size:27 final size:27
Alignment explanation
Indices: 51113--51165 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
51103 ATCAAAAAAG
*
51113 AAAAAAAAAATCAAATAGTTGGATGAT
1 AAAAAAAAAATCAAATAGTTGAATGAT
51140 AAAAAAAAAATCAAATAGTTGAATGA
1 AAAAAAAAAATCAAATAGTTGAATGA
51166 CTATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.21
Consensus pattern (27 bp):
AAAAAAAAAATCAAATAGTTGAATGAT
Found at i:51288 original size:29 final size:29
Alignment explanation
Indices: 51248--51317 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
51238 TTGCCCATTA
*
51248 AAAATTCAATTATTAGACTTATAAAACTC
1 AAAATTTAATTATTAGACTTATAAAACTC
*
51277 AATATTTAATTATTAGACTTATAAAACTC
1 AAAATTTAATTATTAGACTTATAAAACTC
51306 AAAATTTAATTA
1 AAAATTTAATTA
51318 GTTTTAAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39
Consensus pattern (29 bp):
AAAATTTAATTATTAGACTTATAAAACTC
Found at i:53326 original size:55 final size:55
Alignment explanation
Indices: 53172--53347 Score: 214
Period size: 55 Copynumber: 3.2 Consensus size: 55
53162 ATGAATTTTG
* * *
53172 AATCGATTG-TAATGTTGAAATACTGCTTCTTTTGAA-TCGATTGTTTATATATTTA
1 AATCGATTGCT-ATGTTGGAATACTGTTTCTTTTGAATTC-ATTGTTTATATGTTTA
* * * *
53227 AATCGATT-TTATGTTGGAATATTGCCTCTTATTTTGAATCCATTGTTTATATGTTTA
1 AATCGATTGCTATGTTGGAATACTG--T-TTCTTTTGAATTCATTGTTTATATGTTTA
*
53284 AATAGATTGCTATGTTGGAATACTGTTTCTTTTGAATTCATTGTTTATATGTTTA
1 AATCGATTGCTATGTTGGAATACTGTTTCTTTTGAATTCATTGTTTATATGTTTA
53339 AATCGATTG
1 AATCGATTG
53348 TTACGTAGCA
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
54 12 0.12
55 44 0.43
56 1 0.01
57 31 0.30
58 15 0.15
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.49
Consensus pattern (55 bp):
AATCGATTGCTATGTTGGAATACTGTTTCTTTTGAATTCATTGTTTATATGTTTA
Found at i:57581 original size:28 final size:27
Alignment explanation
Indices: 57550--57636 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 27
57540 AAAATTAGAA
*
57550 AAAAATTATAACAATTGTAAAATTTTAT
1 AAAAATTATAA-AATTATAAAATTTTAT
* *
57578 AAAAATCATAAAAAATTATAAAA-TATAT
1 AAAAAT--TATAAAATTATAAAATTTTAT
*
57606 AAAAA-TATAGAAATATAAAAAATTTTAT
1 AAAAATTATA-AAAT-TATAAAATTTTAT
57634 AAA
1 AAA
57637 GCCGTAAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
25 3 0.06
26 4 0.08
27 6 0.12
28 22 0.46
29 9 0.19
30 4 0.08
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAATTATAAAATTATAAAATTTTAT
Found at i:57589 original size:19 final size:18
Alignment explanation
Indices: 57567--57636 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
57557 ATAACAATTG
*
57567 TAAAATTTTATAAAAATCA
1 TAAAAATTTATAAAAAT-A
*
57586 TAAAAAATTATAAAATATA
1 TAAAAATTTATAAAA-ATA
*
57605 TAAAAA--TATAGAAATA
1 TAAAAATTTATAAAAATA
57621 TAAAAAATTTTATAAA
1 T-AAAAA-TTTATAAA
57637 GCCGTAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
16 4 0.10
17 11 0.26
19 20 0.48
20 7 0.17
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
TAAAAATTTATAAAAATA
Found at i:57591 original size:10 final size:9
Alignment explanation
Indices: 57578--57628 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 9
57568 AAAATTTTAT
57578 AAAAATCATA
1 AAAAAT-ATA
57588 AAAAAT-TA
1 AAAAATATA
*
57596 TAAAATATA
1 AAAAATATA
57605 TAAAAATAT-
1 -AAAAATATA
*
57614 AGAAATATA
1 AAAAATATA
57623 AAAAAT
1 AAAAAT
57629 TTTATAAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 14 0.41
9 7 0.21
10 13 0.38
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (9 bp):
AAAAATATA
Found at i:57619 original size:18 final size:16
Alignment explanation
Indices: 57579--57628 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 16
57569 AAATTTTATA
57579 AAAATCATAAAAAATTAT
1 AAAAT-ATAAAAAA-TAT
57597 AAAATATATAAAAATAT
1 AAAATATA-AAAAATAT
57614 AGAAATATAAAAAAT
1 A-AAATATAAAAAAT
57629 TTTATAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAATATAAAAAATAT
Found at i:57985 original size:34 final size:34
Alignment explanation
Indices: 57920--58003 Score: 84
Period size: 34 Copynumber: 2.4 Consensus size: 34
57910 ATTTTACAAG
* *
57920 TTTTTATA-TTTTTACAATATTCATAATATTTTAA
1 TTTTTATATTTTTTAAAATATTAATAATATTTT-A
57954 TTTTTAATATTTTTTAAAAT-TTAATAA-ATTTTA
1 TTTTT-ATATTTTTTAAAATATTAATAATATTTTA
*
57987 TTTATTTTTATTTTTTA
1 -TT-TTTATATTTTTTA
58004 TAACTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
33 1 0.02
34 21 0.49
35 12 0.28
36 9 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (34 bp):
TTTTTATATTTTTTAAAATATTAATAATATTTTA
Found at i:59002 original size:19 final size:20
Alignment explanation
Indices: 58978--59026 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
58968 TTTTTAAATT
58978 TTTTTTATAAAATTTTAT-A
1 TTTTTTATAAAATTTTATAA
* *
58997 TTTTTT-TACGATTTTTATAA
1 TTTTTTATA-AAATTTTATAA
59017 TTTTTTATAA
1 TTTTTTATAA
59027 TTGTTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 7 0.29
21 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTTATAAAATTTTATAA
Found at i:59046 original size:27 final size:28
Alignment explanation
Indices: 59009--59067 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
58999 TTTTTACGAT
59009 TTTTATAA-TTTT-TTATAATTGTTAATAA
1 TTTTATAATTTTTATTA-AATT-TTAATAA
59037 TTTTAT-ATTTTTATTAAATTTTAATAA
1 TTTTATAATTTTTATTAAATTTTAATAA
59064 TTTT
1 TTTT
59068 TTTATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 12 0.41
28 14 0.48
29 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATAATTTTTATTAAATTTTAATAA
Found at i:59066 original size:20 final size:18
Alignment explanation
Indices: 59007--59068 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
58997 TTTTTTTACG
*
59007 ATTTTTATAATTTTTTATA
1 ATTTTTATAA-ATTTTATA
*
59026 ATTGTTA-ATAATTTTAT-
1 ATTTTTATA-AATTTTATA
59043 ATTTTTATTAAATTTTAATA
1 ATTTTTA-TAAATTTT-ATA
59063 ATTTTT
1 ATTTTT
59069 TTATTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
17 6 0.17
18 13 0.37
19 10 0.29
20 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTTATAAATTTTATA
Found at i:59954 original size:19 final size:18
Alignment explanation
Indices: 59926--59961 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
59916 TATATTTTCA
*
59926 ATTTTTATAACTTTTAAT
1 ATTTTTATAAATTTTAAT
59944 ATTTTTAATAAATTTTAA
1 ATTTTT-ATAAATTTTAA
59962 AGGATTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTATAAATTTTAAT
Found at i:60077 original size:20 final size:19
Alignment explanation
Indices: 60052--60114 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
60042 TTATTTTTAA
60052 TAATTTCTAAAATCGTATAC
1 TAATTTCTAAAAT-GTATAC
* * *
60072 TAA-TT-TATAATGTTTAA
1 TAATTTCTAAAATGTATAC
*
60089 TAATTTCTAAAATGGTAAAC
1 TAATTTCTAAAAT-GTATAC
60109 TAATTT
1 TAATTT
60115 ATAATGTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 7 0.21
20 12 0.36
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (19 bp):
TAATTTCTAAAATGTATAC
Found at i:60091 original size:37 final size:37
Alignment explanation
Indices: 60047--60128 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
60037 ATTTTTTATT
*
60047 TTTAATAATTTCTAAAATCGTATACTAATTTATAATG
1 TTTAATAATTTCTAAAATCGTAAACTAATTTATAATG
*
60084 TTTAATAATTTCTAAAATGGTAAACTAATTTATAATG
1 TTTAATAATTTCTAAAATCGTAAACTAATTTATAATG
60121 TTTAATAA
1 TTTAATAA
60129 ATTTTCAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTAATAATTTCTAAAATCGTAAACTAATTTATAATG
Found at i:60131 original size:18 final size:18
Alignment explanation
Indices: 60073--60132 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
60063 ATCGTATACT
60073 AATTTATAATGTTTAATA
1 AATTTATAATGTTTAATA
* * * *
60091 ATTTCTAAAATGGTAAACT-
1 AATT-TATAATGTTTAA-TA
60110 AATTTATAATGTTTAATA
1 AATTTATAATGTTTAATA
60128 AATTT
1 AATTT
60133 TCAACAATAG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 1 0.03
18 17 0.55
19 12 0.39
20 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (18 bp):
AATTTATAATGTTTAATA
Found at i:64668 original size:10 final size:10
Alignment explanation
Indices: 64653--64699 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
64643 TTTGAAAGAG
*
64653 AAAAAACTAA
1 AAAAAAATAA
64663 AAAAAAATAA
1 AAAAAAATAA
64673 AAATAAAA-AA
1 AAA-AAAATAA
64683 TAAAAAAATAGA
1 -AAAAAAATA-A
64695 AAAAA
1 AAAAA
64700 TGTTTATGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 18 0.56
11 13 0.41
12 1 0.03
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.11
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:64680 original size:13 final size:13
Alignment explanation
Indices: 64664--64688 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64654 AAAAACTAAA
64664 AAAAAATAAAAAT
1 AAAAAATAAAAAT
64677 AAAAAATAAAAA
1 AAAAAATAAAAA
64689 AATAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:64700 original size:9 final size:8
Alignment explanation
Indices: 64653--64700 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
64643 TTTGAAAGAG
*
64653 AAAAAACT
1 AAAAAAAT
64661 AAAAAAA-
1 AAAAAAAT
64668 AATAAAAAT
1 AA-AAAAAT
64677 -AAAAAAT
1 AAAAAAAT
64684 AAAAAAAT
1 AAAAAAAT
64692 AGAAAAAAT
1 A-AAAAAAT
64701 GTTTATGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
7 8 0.23
8 20 0.57
9 7 0.20
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:72753 original size:317 final size:318
Alignment explanation
Indices: 72152--72796 Score: 1013
Period size: 317 Copynumber: 2.0 Consensus size: 318
72142 AGAACGTATA
* *
72152 AAGTGTAAGGATAAGTCACTCTAATTAACGTTTGAAAGCTTGAGGTGTTTCCTTGAATTGAATAA
1 AAGTGTGAGGATAAGTCACTCTAATTAACGATTGAAAGCTTGAGGTGTTTCCTTGAATTGAATAA
* * *
72217 AGAAGTGCAAAAGCTCAACCAATCAGAGATGCACTATTTCCAATAAGCAAGTCAACTAGAACTAC
66 AGAAGTGCAAAAGCTCAACAAATCAGAGATGCACTATCTCCAATAAGCAAGCCAACT--AACTAC
* ** * *
72282 AATGTGTGATCCTATCACATTTAAGTATAAGACAACTTATGATTTATTTGAGCCTCTCGTTTATT
129 AATGAGTGATCCTATCACATGCAAGTATAACACAACTTATGATTTATTTGAGCCTCTCATTTATT
* * * *
72347 ATGGAAGAAAGAAAATTAAAAACACATACGAGAACTTAACATCTAAATTCGAAGGAGGTCTATGA
194 ATGAAAGAAAGAAAATCAAAAACACATACGAGAACTTAACATATAAAGTCGAAGGAGGTCTATGA
* * *
72412 TGAGTCATTTGCTTATACCCAACTTGGCGAACTATCTTACACATCGAATATACCTACATT
259 TGAGTCATTTGCTCATACCCAACTTGGCGAACTACCCTACACATCGAATATACCTACATT
* * * * *
72472 GAGTGTGAGGATATGTCACTTTGATTAACGATTGAAAGGTTGAGGTGTTTCCTTGAATTGAATAA
1 AAGTGTGAGGATAAGTCACTCTAATTAACGATTGAAAGCTTGAGGTGTTTCCTTGAATTGAATAA
* *
72537 AGGAGTGCAAAAGCTCAACAAATCAGAGATGCACTATCTCCAATAAGCAAGCCAACT-ACTATAA
66 AGAAGTGCAAAAGCTCAACAAATCAGAGATGCACTATCTCCAATAAGCAAGCCAACTAACTACAA
72601 TGAGTGATCCTATCACATGCAAGTATAACACAACTTATGATTTATTTGAGCCTCTCATTTATTAT
131 TGAGTGATCCTATCACATGCAAGTATAACACAACTTATGATTTATTTGAGCCTCTCATTTATTAT
* * *
72666 GAAAGAAAGAAACTCGAAAACACATATGAGAACTTAACATATAAAGTCGAAGGAGGTCTATGATG
196 GAAAGAAAGAAAATCAAAAACACATACGAGAACTTAACATATAAAGTCGAAGGAGGTCTATGATG
*
72731 AGTCATTTTCTCATACCCAACTTGGCGAACTACCCTACACATCGAATATACCTACATT
261 AGTCATTTGCTCATACCCAACTTGGCGAACTACCCTACACATCGAATATACCTACATT
72789 AAGTGTGA
1 AAGTGTGA
72797 ATCTCTATTG
Statistics
Matches: 296, Mismatches: 29, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
317 185 0.62
320 111 0.38
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (318 bp):
AAGTGTGAGGATAAGTCACTCTAATTAACGATTGAAAGCTTGAGGTGTTTCCTTGAATTGAATAA
AGAAGTGCAAAAGCTCAACAAATCAGAGATGCACTATCTCCAATAAGCAAGCCAACTAACTACAA
TGAGTGATCCTATCACATGCAAGTATAACACAACTTATGATTTATTTGAGCCTCTCATTTATTAT
GAAAGAAAGAAAATCAAAAACACATACGAGAACTTAACATATAAAGTCGAAGGAGGTCTATGATG
AGTCATTTGCTCATACCCAACTTGGCGAACTACCCTACACATCGAATATACCTACATT
Found at i:78026 original size:29 final size:30
Alignment explanation
Indices: 77992--78070 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 30
77982 GGACTCAAAA
* *
77992 AAGTTTATGTACCAACTTA-AAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAGTGTC
78021 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAGGTACCAAATTA-GAAAAAGTGTC
78052 AAGTTTAGGTACCAAATTA
1 AAGTTTAGGTACCAAATTA
78071 TATAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 17 0.37
31 29 0.63
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (30 bp):
AAGTTTAGGTACCAAATTAGAAAAAGTGTC
Found at i:78121 original size:31 final size:30
Alignment explanation
Indices: 77995--78121 Score: 100
Period size: 31 Copynumber: 4.3 Consensus size: 30
77985 CTCAAAAAAG
* * *
77995 TTTATGTACCAACTTAA-AAAAGTGTCAAG
1 TTTAAGTACCAAATTAAGAAAAGTGTCAAA
* * *
78024 TTTAGGTACCAAATTAGGAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAAG-AAAAGTGTCAAA
* * **
78055 TTTAGGTACCAAATTATATAAAA---AAAAA
1 TTTAAGTACCAAATTA-AGAAAAGTGTCAAA
78083 TTTAAGTACCAAATTAAGAAAGAGTGTCAAA
1 TTTAAGTACCAAATTAAGAAA-AGTGTCAAA
*
78114 TTCAAGTA
1 TTTAAGTA
78122 TGAAATTTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
27 4 0.05
28 18 0.23
29 14 0.18
31 42 0.54
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (30 bp):
TTTAAGTACCAAATTAAGAAAAGTGTCAAA
Found at i:78853 original size:22 final size:22
Alignment explanation
Indices: 78825--78869 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
78815 TAAAACTCAA
78825 ATTTATTTTTGCCATTTGCTTT
1 ATTTATTTTTGCCATTTGCTTT
78847 ATTTATTTTTGCCATTTGCTTT
1 ATTTATTTTTGCCATTTGCTTT
78869 A
1 A
78870 AATCTAGGTA
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:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (22 bp):
ATTTATTTTTGCCATTTGCTTT
Found at i:79581 original size:18 final size:18
Alignment explanation
Indices: 79554--79588 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
79544 TTTGTTAGTG
*
79554 TTTAATTTGTTTTAATTT
1 TTTAAATTGTTTTAATTT
79572 TTTAAATTGTTTTAATT
1 TTTAAATTGTTTTAATT
79589 GTGGGTCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTAAATTGTTTTAATTT
Found at i:79627 original size:17 final size:17
Alignment explanation
Indices: 79605--79638 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
79595 CCCAAAATTT
*
79605 TTTTAAATGTTTTTTAA
1 TTTTAAATATTTTTTAA
*
79622 TTTTAATTATTTTTTAA
1 TTTTAAATATTTTTTAA
79639 GTTTGAATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTAAATATTTTTTAA
Found at i:79647 original size:18 final size:18
Alignment explanation
Indices: 79614--79652 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
79604 TTTTTAAATG
*
79614 TTTTTTAATTTTAATT-A
1 TTTTTTAATTTGAATTCA
79631 TTTTTTAAGTTTGAATTCA
1 TTTTTTAA-TTTGAATTCA
79650 TTT
1 TTT
79653 ATTGACGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTTAATTTGAATTCA
Found at i:81816 original size:2 final size:2
Alignment explanation
Indices: 81809--81865 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
81799 CAACCTCATG
*
81809 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
81851 GA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
81866 TGCTTTTGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:83023 original size:18 final size:20
Alignment explanation
Indices: 82984--83020 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
82974 TAAAATTAAG
*
82984 GTAATATAATTCTACAAAAT
1 GTAATATAATTATACAAAAT
83004 GTAATATAA-TATACAAA
1 GTAATATAATTATACAAA
83021 TGTTAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.32
Consensus pattern (20 bp):
GTAATATAATTATACAAAAT
Found at i:85137 original size:16 final size:16
Alignment explanation
Indices: 85099--85130 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
85089 ATATGATTAG
85099 CCTATACACCATTCAC
1 CCTATACACCATTCAC
85115 CCTATACACCATTCAC
1 CCTATACACCATTCAC
85131 GTTATACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.44, G:0.00, T:0.25
Consensus pattern (16 bp):
CCTATACACCATTCAC
Found at i:92513 original size:51 final size:51
Alignment explanation
Indices: 92407--92525 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
92397 ATTATAGCAA
** * *
92407 CATATTCATCAGTAACATTATCCATTCCATCTGATGTTGCAAAATCAACAT
1 CATATTCATCAACAACATTATCCACTCCATCTGATGTTGCAAAATCAACAG
* **
92458 CATATTTATCAACAACATTATCCACTCCATCTGATGTTGCAAAATCAGTAG
1 CATATTCATCAACAACATTATCCACTCCATCTGATGTTGCAAAATCAACAG
*
92509 CATATTCATCAGCAACA
1 CATATTCATCAACAACA
92526 GCTTCACTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.31
Consensus pattern (51 bp):
CATATTCATCAACAACATTATCCACTCCATCTGATGTTGCAAAATCAACAG
Found at i:92626 original size:33 final size:32
Alignment explanation
Indices: 92589--92743 Score: 130
Period size: 33 Copynumber: 4.7 Consensus size: 32
92579 CCTCATAAGC
* * *
92589 TTCTACCCCTCCTACATTACCCTCCCCAACAAT
1 TTCTACCCCTCC-ACATCACCCTCCCCATCAAA
* * * *
92622 TTCTACCCTTTCCAGATCACCTTCACCATCAAA
1 TTCTACCC-CTCCACATCACCCTCCCCATCAAA
* * * *
92655 TTCTACCCTTTCATCATCATCTTCCCCATCAAA
1 TTCTACCCCTCCA-CATCACCCTCCCCATCAAA
* *
92688 TTCTACCCCTCCTACATCACCCTCCCGATCAAC
1 TTCTACCCCTCC-ACATCACCCTCCCCATCAAA
* *
92721 TTCTATCCCTTCATCATCACCCT
1 TTCTACCCCTCCA-CATCACCCT
92744 TCCTACCAGT
Statistics
Matches: 99, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
32 5 0.05
33 90 0.91
34 4 0.04
ACGTcount: A:0.23, C:0.45, G:0.01, T:0.31
Consensus pattern (32 bp):
TTCTACCCCTCCACATCACCCTCCCCATCAAA
Found at i:92681 original size:66 final size:66
Alignment explanation
Indices: 92611--92739 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
92601 TACATTACCC
* * * *
92611 TCCCCAACAATTTCTACCCTTTCC-AGATCACCTTCACC-ATCAAATTCTA-CCCTTTCATCATC
1 TCCCCAACAAATTCTACCC-CTCCTACATCACCCTC-CCGATCAAATTCTATCCC-TTCATCATC
92673 ATCT
63 ATCT
* *
92677 TCCCCATCAAATTCTACCCCTCCTACATCACCCTCCCGATCAACTTCTATCCCTTCATCATCA
1 TCCCCAACAAATTCTACCCCTCCTACATCACCCTCCCGATCAAATTCTATCCCTTCATCATCA
92740 CCCTTCCTAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
65 5 0.09
66 46 0.85
67 3 0.06
ACGTcount: A:0.25, C:0.43, G:0.02, T:0.31
Consensus pattern (66 bp):
TCCCCAACAAATTCTACCCCTCCTACATCACCCTCCCGATCAAATTCTATCCCTTCATCATCATC
T
Found at i:93219 original size:22 final size:23
Alignment explanation
Indices: 93175--93219 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
93165 CACTGTAAGT
*
93175 TACAAAACTCACTAAATTAACAA
1 TACAAAACTCACTAAATCAACAA
*
93198 TACAAAACTCAC-AAATCGACAA
1 TACAAAACTCACTAAATCAACAA
93220 AAAGTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.18
Consensus pattern (23 bp):
TACAAAACTCACTAAATCAACAA
Found at i:93729 original size:33 final size:32
Alignment explanation
Indices: 93621--93725 Score: 140
Period size: 32 Copynumber: 3.3 Consensus size: 32
93611 CATTTTTGAG
**
93621 TTAGGGATTCAACGATTTGGTTTGTAAAAGTT
1 TTAGGGATTCAATAATTTGGTTTGTAAAAGTT
* *
93653 TTAGGGATTTAATAATTTGGGTTGTAAAAGTT
1 TTAGGGATTCAATAATTTGGTTTGTAAAAGTT
* *
93685 TTAGGGATTCAATTATTTGATTTGTTAAAA-TT
1 TTAGGGATTCAATAATTTGGTTTG-TAAAAGTT
93717 TTAGGGATT
1 TTAGGGATT
93726 TCAAGAATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 59 0.92
33 5 0.08
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.45
Consensus pattern (32 bp):
TTAGGGATTCAATAATTTGGTTTGTAAAAGTT
Found at i:93778 original size:17 final size:17
Alignment explanation
Indices: 93752--93795 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
93742 ATGCTAATGA
93752 TTTAGGGATTTTAACAT
1 TTTAGGGATTTTAACAT
* *
93769 TTTGGGGATTTTAATAT
1 TTTAGGGATTTTAACAT
93786 TTTAGGGATT
1 TTTAGGGATT
93796 CAAAGAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.50
Consensus pattern (17 bp):
TTTAGGGATTTTAACAT
Found at i:94508 original size:35 final size:36
Alignment explanation
Indices: 94455--94524 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
94445 GCTCAAACAA
* * *
94455 CAAAAACAACAACCAAAACAGTAG-AAAAATAATAG
1 CAAAAACAAAAACAAAAACAGCAGCAAAAATAATAG
* *
94490 CAAAAACAAAAATAAAAACAGCGGCAAAAATAATA
1 CAAAAACAAAAACAAAAACAGCAGCAAAAATAATA
94525 AAATAACAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.67, C:0.16, G:0.09, T:0.09
Consensus pattern (36 bp):
CAAAAACAAAAACAAAAACAGCAGCAAAAATAATAG
Found at i:98214 original size:23 final size:23
Alignment explanation
Indices: 98184--98741 Score: 830
Period size: 23 Copynumber: 24.3 Consensus size: 23
98174 TATATCTATA
*
98184 CTTAAATATTAATGTAATTTGTG
1 CTTAAATATTAATGTGATTTGTG
98207 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* *
98230 CTTAAGTATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTGTG
* *
98253 CTTAAATATTAATATAATTTGTG
1 CTTAAATATTAATGTGATTTGTG
*
98276 CTCAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
*
98299 CTCAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
*
98322 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
98345 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* * *
98368 CTTAAATATTAATATGATTTATA
1 CTTAAATATTAATGTGATTTGTG
* *
98391 ATTAAATATCAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* *
98414 CTTAAATATTAATGTGATTTATA
1 CTTAAATATTAATGTGATTTGTG
*
98437 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
*
98460 CTCAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
*
98483 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* *
98506 CTCAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTGTG
98529 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
98552 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
*
98575 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* * *
98598 CTCAAATATTAATGTGATATGTT
1 CTTAAATATTAATGTGATTTGTG
*
98621 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* *
98644 CTCAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTGTG
98667 CTTAAATATTAATGTGATTTGTAG
1 CTTAAATATTAATGTGATTTGT-G
* *
98691 -TTAAATATTAATATGATTTATG
1 CTTAAATATTAATGTGATTTGTG
*
98713 ATTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
98736 CTTAAA
1 CTTAAA
98742 GAATTAAGAA
Statistics
Matches: 477, Mismatches: 56, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
22 1 0.00
23 475 1.00
24 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (23 bp):
CTTAAATATTAATGTGATTTGTG
Found at i:98851 original size:36 final size:36
Alignment explanation
Indices: 98811--98924 Score: 158
Period size: 36 Copynumber: 3.2 Consensus size: 36
98801 TGATGACTGT
* * *
98811 TGTGAAAGTGAATATGTGAGTATGTTCTTCATGTCA
1 TGTGACAGAGAATATGTGAGTATGTTCTTCATGCCA
*
98847 TGTGACAGAAAATATGT-AGGTATGTTCTTCATGCCA
1 TGTGACAGAGAATATGTGA-GTATGTTCTTCATGCCA
* *
98883 TGTGACAGAGAATGTGTGGGTATGTTCTTCATGCCA
1 TGTGACAGAGAATATGTGAGTATGTTCTTCATGCCA
98919 TGTGAC
1 TGTGAC
98925 TGATTATATT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 1 0.01
36 68 0.99
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (36 bp):
TGTGACAGAGAATATGTGAGTATGTTCTTCATGCCA
Done.