Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013669.1 Kokia drynarioides strain JFW-HI SEQ_128697, 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: 79635
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:3870 original size:33 final size:34
Alignment explanation
Indices: 3807--3873 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
3797 AGACTCTACA
* *
3807 CATTCATACTCCTTTTTATTATCAATATTAACAT
1 CATTCATACTCCTTTTTATTAACAACATTAACAT
* *
3841 CATTCA-AGTCCTTTTTATTAACAGCATTAACAT
1 CATTCATACTCCTTTTTATTAACAACATTAACAT
3874 TATTAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 23 0.79
34 6 0.21
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (34 bp):
CATTCATACTCCTTTTTATTAACAACATTAACAT
Found at i:7057 original size:18 final size:18
Alignment explanation
Indices: 7030--7085 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
7020 ACTTAATAAG
7030 TTTT-TATATTTTTGAAT
1 TTTTATATATTTTTGAAT
*
7047 TTTTATATATTTTAG-AT
1 TTTTATATATTTTTGAAT
*
7064 ATTATATATATTTTTGAAT
1 -TTTTATATATTTTTGAAT
7083 TTT
1 TTT
7086 GAGTAGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 6 0.19
18 24 0.75
19 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTATATATTTTTGAAT
Found at i:13940 original size:216 final size:216
Alignment explanation
Indices: 13596--14025 Score: 752
Period size: 216 Copynumber: 2.0 Consensus size: 216
13586 CCTCCACTTG
* *
13596 TCAATCCCTCATAGAGTGATTAATTTCTCATGGTTTTTATAAATGATATAAAATCGATGTATGAG
1 TCAATCCCTCATAGAGGGATTAATTTCTCATGGTTTTTATAAATGATATAAAATCGATGTATGAC
* *
13661 GTAAACATAAAGAGCAAAACGAAAATATAAGATTCAGGAAAAAAGCTTGATTTGTATTAAGAATT
66 GTAAACATAAAGAGCAAAACGAAAATATAAGATTCAGGAAAAAAGCCTGATTTGTATTAAGAATC
* * *
13726 GAAATGAATCCACAACGTTTGATCGTATTCACAAATTGGATCTCCTGAAATAAAGAAAGACAAAA
131 GAAATGAATCCACAACGTCTGATCATATTCACAAATTGGATCTCCCGAAATAAAGAAAGACAAAA
13791 CAAAAATAAACTAAAACCTTT
196 CAAAAATAAACTAAAACCTTT
* *
13812 TCAATTCCTCATAGTGGGATTAATTTCTCATGGTTTTTATAAATGATATAAAATCGATGTATGAC
1 TCAATCCCTCATAGAGGGATTAATTTCTCATGGTTTTTATAAATGATATAAAATCGATGTATGAC
* *
13877 GTAAACATAAAGAGCAAATCGAAAATATAAGATTTAGGAAAAAAGCCTGATTTGTATTAAGAATC
66 GTAAACATAAAGAGCAAAACGAAAATATAAGATTCAGGAAAAAAGCCTGATTTGTATTAAGAATC
*
13942 GAAATGAATCCACAACGTCTGATCATATTCATAAATTGGATCTCCCGAAATAAAGAAAGACAAAA
131 GAAATGAATCCACAACGTCTGATCATATTCACAAATTGGATCTCCCGAAATAAAGAAAGACAAAA
14007 CAAAAATAAACTAAAACCT
196 CAAAAATAAACTAAAACCT
14026 AAGAAAAAGA
Statistics
Matches: 202, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
216 202 1.00
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.28
Consensus pattern (216 bp):
TCAATCCCTCATAGAGGGATTAATTTCTCATGGTTTTTATAAATGATATAAAATCGATGTATGAC
GTAAACATAAAGAGCAAAACGAAAATATAAGATTCAGGAAAAAAGCCTGATTTGTATTAAGAATC
GAAATGAATCCACAACGTCTGATCATATTCACAAATTGGATCTCCCGAAATAAAGAAAGACAAAA
CAAAAATAAACTAAAACCTTT
Found at i:14168 original size:81 final size:81
Alignment explanation
Indices: 14033--14194 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
14023 CCTAAGAAAA
14033 AGAGAAAAACCTAAACTAAACTAAAGAGAGAAAATTTAAGCTAATGGAATGGTGTGTAAAACAAG
1 AGAGAAAAACCTAAACTAAACTAAAGAGAGAAAATTTAAGCTAATGGAATGGTGTGTAAAACAAG
14098 TGCCAAAGGAGCCTAT
66 TGCCAAAGGAGCCTAT
14114 AGAGAAAAACCTAAACTAAACTAAAGAGAGAAAATTTAAGCTAATGGAATGGTGTGTAAAACAAG
1 AGAGAAAAACCTAAACTAAACTAAAGAGAGAAAATTTAAGCTAATGGAATGGTGTGTAAAACAAG
14179 TGCCAAAGGAGCCTAT
66 TGCCAAAGGAGCCTAT
14195 TTATAGATTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (81 bp):
AGAGAAAAACCTAAACTAAACTAAAGAGAGAAAATTTAAGCTAATGGAATGGTGTGTAAAACAAG
TGCCAAAGGAGCCTAT
Found at i:16183 original size:30 final size:30
Alignment explanation
Indices: 16147--16435 Score: 160
Period size: 30 Copynumber: 9.6 Consensus size: 30
16137 TAAAAGTGAT
*
16147 GCCTTTGTGACTGTTCTCTGATATGTGAAA
1 GCCTTTGTGACTGTTCTTTGATATGTGAAA
* * * *
16177 GTCTTTGTGACTATTTTTTGATATGTAAAA
1 GCCTTTGTGACTGTTCTTTGATATGTGAAA
*
16207 GCCTTTGTTG-CTGTTTTTTGATATGTGAAA
1 GCCTTTG-TGACTGTTCTTTGATATGTGAAA
* *
16237 GCCTTTGT-AGCTGTTCTATGATATGTGGAA
1 GCCTTTGTGA-CTGTTCTTTGATATGTGAAA
** * *
16267 GCCTTTGTGGTTGTTCCTTATAACATGTG--A
1 GCCTTTGTGACTGTT-CTT-TGATATGTGAAA
**** * ** *
16297 GCCCCAATGGC-GAAACTTGTTATATGTGAAA
1 GCCTTTGTGACTG-TTCTT-TGATATGTGAAA
* * *
16328 GCCTTTGTGGCTGTTCTCTGATATGTGGAA
1 GCCTTTGTGACTGTTCTTTGATATGTGAAA
* *
16358 GCCTTTGTGACTGTTCCTTATTACATGTG--A
1 GCCTTTGTGACTGTT-CTT-TGATATGTGAAA
* * * ** * *
16388 GCCTTAGTGGCAGAACTTGTTATATGTGGAA
1 GCCTTTGTGACTGTTCTT-TGATATGTGAAA
16419 GCCTTTGTGACTGTTCT
1 GCCTTTGTGACTGTTCT
16436 CTGCTTTATA
Statistics
Matches: 194, Mismatches: 51, Indels: 27
0.71 0.19 0.10
Matches are distributed among these distances:
29 23 0.12
30 127 0.65
31 29 0.15
32 15 0.08
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (30 bp):
GCCTTTGTGACTGTTCTTTGATATGTGAAA
Found at i:16341 original size:91 final size:91
Alignment explanation
Indices: 16227--16435 Score: 312
Period size: 91 Copynumber: 2.3 Consensus size: 91
16217 CTGTTTTTTG
* **
16227 ATATGTGAAAGCCTTTGTAGCTGTTCTATGATATGTGGAAGCCTTTGTGGTTGTTCCTTATAACA
1 ATATGTGAAAGCCTTTGTGGCTGTTCTATGATATGTGGAAGCCTTTGTGACTGTTCCTTATAACA
16292 TGTGAGCCCCAATGGC-GAAACTTGTT
66 TGTGAGCCCCAATGGCAG-AACTTGTT
* *
16318 ATATGTGAAAGCCTTTGTGGCTGTTCTCTGATATGTGGAAGCCTTTGTGACTGTTCCTTATTACA
1 ATATGTGAAAGCCTTTGTGGCTGTTCTATGATATGTGGAAGCCTTTGTGACTGTTCCTTATAACA
** *
16383 TGTGAGCCTTAGTGGCAGAACTTGTT
66 TGTGAGCCCCAATGGCAGAACTTGTT
* *
16409 ATATGTGGAAGCCTTTGTGACTGTTCT
1 ATATGTGAAAGCCTTTGTGGCTGTTCT
16436 CTGCTTTATA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 106 0.99
92 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (91 bp):
ATATGTGAAAGCCTTTGTGGCTGTTCTATGATATGTGGAAGCCTTTGTGACTGTTCCTTATAACA
TGTGAGCCCCAATGGCAGAACTTGTT
Found at i:16576 original size:30 final size:30
Alignment explanation
Indices: 16540--16615 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
16530 ATCTAGGTGC
* *
16540 CTTTGTGGCTATCTAATGATGTCTGGATTA
1 CTTTGTGGCTATCTAATGATATCTGGATGA
* * *
16570 CTTTGTGACTATCTAATGATATGTGGATGC
1 CTTTGTGGCTATCTAATGATATCTGGATGA
*
16600 CTCTGTGGCTATCTAA
1 CTTTGTGGCTATCTAA
16616 GTTAAGTGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (30 bp):
CTTTGTGGCTATCTAATGATATCTGGATGA
Found at i:21613 original size:16 final size:17
Alignment explanation
Indices: 21577--21615 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21567 TACCAAAAAG
21577 AATGCAGTGACAATAAA
1 AATGCAGTGACAATAAA
21594 AATGCAG-GCACAAT-AA
1 AATGCAGTG-ACAATAAA
21610 AATGCA
1 AATGCA
21616 AGAATGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (17 bp):
AATGCAGTGACAATAAA
Found at i:32390 original size:23 final size:23
Alignment explanation
Indices: 32360--32405 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
32350 AATGTGCTCC
32360 TACAGTAGCAATATCATGAAAAA
1 TACAGTAGCAATATCATGAAAAA
32383 TACAGTAGCAATATCATGAAAAA
1 TACAGTAGCAATATCATGAAAAA
32406 AAAATTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (23 bp):
TACAGTAGCAATATCATGAAAAA
Found at i:40700 original size:31 final size:31
Alignment explanation
Indices: 40663--40755 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
40653 GGTTTTCTTG
40663 GTAAGGTTTTTAATAAGGCAATATATTATGC
1 GTAAGGTTTTTAATAAGGCAATATATTATGC
40694 GTAAGGTTTTTAATAAGGCAATATATTATGC
1 GTAAGGTTTTTAATAAGGCAATATATTATGC
*
40725 GTAAGGTTTTTAATAAGGCAACATATTATGC
1 GTAAGGTTTTTAATAAGGCAATATATTATGC
40756 TTATTATAGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (31 bp):
GTAAGGTTTTTAATAAGGCAATATATTATGC
Found at i:42420 original size:24 final size:24
Alignment explanation
Indices: 42368--42420 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
42358 TTTTTAAATG
* *
42368 ATTAAATTAAAATTTTATCATTTTT
1 ATTAAATTAAAATGTAAT-ATTTTT
42393 -TTAAATTAAAATGTAAT-TTTATT
1 ATTAAATTAAAATGTAATATTT-TT
42416 ATTAA
1 ATTAA
42421 TAATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 2 0.08
24 19 0.79
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTAAATTAAAATGTAATATTTTT
Found at i:44361 original size:26 final size:28
Alignment explanation
Indices: 44314--44384 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
44304 ATTTTTTTAA
* * *
44314 AATATTTATTTTATTTTATTTTA-ATATTT
1 AATATTT-TTATATATT-TTTTATATATTG
*
44343 AATATTTTTATATATTTTTTATTTATTG
1 AATATTTTTATATATTTTTTATATATTG
*
44371 AATTTTTTTATATA
1 AATATTTTTATATA
44385 ATCATCTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.14
28 24 0.67
29 7 0.19
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (28 bp):
AATATTTTTATATATTTTTTATATATTG
Found at i:44365 original size:17 final size:16
Alignment explanation
Indices: 44327--44381 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
44317 ATTTATTTTA
44327 TTTTA-TTTTAATATT
1 TTTTATTTTTAATATT
**
44342 TAATATTTTTATATATT
1 TTTTATTTTTA-ATATT
44359 TTTTATTTATTGAAT-TT
1 TTTTATTT-TT-AATATT
44376 TTTTAT
1 TTTTAT
44382 ATAATCATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.09
16 5 0.16
17 19 0.59
18 4 0.12
19 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTATTTTTAATATT
Found at i:45519 original size:26 final size:25
Alignment explanation
Indices: 45490--45539 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
45480 AATCTACTAA
*
45490 CTTTTAAGAAGTTTAAAATTTTTTAC
1 CTTTTAAG-AGTTCAAAATTTTTTAC
* *
45516 CTTTTGAGGGTTCAAAATTTTTTA
1 CTTTTAAGAGTTCAAAATTTTTTA
45540 TCAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (25 bp):
CTTTTAAGAGTTCAAAATTTTTTAC
Found at i:45588 original size:28 final size:28
Alignment explanation
Indices: 45530--45588 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
45520 TGAGGGTTCA
* ** *
45530 AAATTTTTTATCAATTTTTAAAGGTTTT
1 AAATTTTTTATCAACTTTTAAAAATTAT
* *
45558 AAATTTTTTTTCGACTTTTAAAAATTAT
1 AAATTTTTTATCAACTTTTAAAAATTAT
45586 AAA
1 AAA
45589 ACTCTATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (28 bp):
AAATTTTTTATCAACTTTTAAAAATTAT
Found at i:48152 original size:31 final size:30
Alignment explanation
Indices: 48119--48301 Score: 102
Period size: 31 Copynumber: 6.2 Consensus size: 30
48109 GATTAAGTAT
*
48119 CAAATTAGAATAAAATGTCAAGTTTAAATAT
1 CAAATTAGAATAAAATGTCAA-TTTAAATAC
* * *
48150 CAAATTGGACCTCAAAA----AATTTAAGTAC
1 CAAATTAGA-AT-AAAATGTCAATTTAAATAC
* * *
48178 CAAATTAAAAAAAAATGTTAAATTTAAATAC
1 CAAATTAGAATAAAATG-TCAATTTAAATAC
* *
48209 CAAATTAAGAAAAAAATATCAACTTTAAATAC
1 CAAATT-AGAATAAAATGTCAA-TTTAAATAC
* *
48241 TAAATTA-AATAAAA---AAATTTAAATAC
1 CAAATTAGAATAAAATGTCAATTTAAATAC
*
48267 TAAATTA-AA-AAAA--TCAAATTTAAATAC
1 CAAATTAGAATAAAATGTC-AATTTAAATAC
48294 CAATATTA
1 CAA-ATTA
48302 TATTAAACCT
Statistics
Matches: 123, Mismatches: 17, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
25 4 0.03
26 22 0.18
27 15 0.12
28 18 0.15
29 2 0.02
30 6 0.05
31 28 0.23
32 24 0.20
33 4 0.03
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.29
Consensus pattern (30 bp):
CAAATTAGAATAAAATGTCAATTTAAATAC
Found at i:48236 original size:32 final size:31
Alignment explanation
Indices: 48166--48301 Score: 128
Period size: 32 Copynumber: 4.6 Consensus size: 31
48156 GGACCTCAAA
* * *
48166 AAATTTAAGTACCAAATTAAAAAAAAATGTT
1 AAATTTAAATACCAAATTAAAAAAAAATATC
48197 AAATTTAAATACCAAATTAAGAAAAAAATATC
1 AAATTTAAATACCAAATTAA-AAAAAAATATC
* * *
48229 AACTTTAAATACTAAATT--AAATAAA-A--
1 AAATTTAAATACCAAATTAAAAAAAAATATC
*
48255 AAATTTAAATACTAAATT---AAAAAA-ATC
1 AAATTTAAATACCAAATTAAAAAAAAATATC
48282 AAATTTAAATACCAATATTA
1 AAATTTAAATACCAA-ATTA
48302 TATTAAACCT
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
25 6 0.07
26 17 0.19
27 14 0.15
28 4 0.04
29 6 0.07
31 19 0.21
32 25 0.27
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (31 bp):
AAATTTAAATACCAAATTAAAAAAAAATATC
Found at i:48250 original size:12 final size:12
Alignment explanation
Indices: 48233--48275 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
48223 AATATCAACT
48233 TTAAATACTAAA
1 TTAAATACTAAA
**
48245 TTAAATAAAAAAA
1 TTAAAT-ACTAAA
48258 TTTAAATACTAAA
1 -TTAAATACTAAA
48271 TTAAA
1 TTAAA
48276 AAAATCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 11 0.44
13 8 0.32
14 6 0.24
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (12 bp):
TTAAATACTAAA
Found at i:48285 original size:21 final size:21
Alignment explanation
Indices: 48246--48285 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48236 AATACTAAAT
*
48246 TAAATAAAAAAATTTAAATAC
1 TAAATAAAAAAATTCAAATAC
48267 TAAATTAAAAAAA-TCAAAT
1 TAAA-TAAAAAAATTCAAAT
48286 TTAAATACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAATAAAAAAATTCAAATAC
Found at i:48293 original size:27 final size:27
Alignment explanation
Indices: 48219--48293 Score: 109
Period size: 26 Copynumber: 2.8 Consensus size: 27
48209 CAAATTAAGA
*
48219 AAAAAATATCAACTTTAAATACTAAATT
1 AAAAAA-ATCAAATTTAAATACTAAATT
48247 AAATAAAA--AAATTTAAATACTAAATT
1 AAA-AAAATCAAATTTAAATACTAAATT
48273 AAAAAAATCAAATTTAAATAC
1 AAAAAAATCAAATTTAAATAC
48294 CAATATTATA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 4 0.09
26 20 0.47
27 12 0.28
28 4 0.09
29 3 0.07
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAAAAATCAAATTTAAATACTAAATT
Found at i:53772 original size:195 final size:191
Alignment explanation
Indices: 53451--53826 Score: 457
Period size: 195 Copynumber: 1.9 Consensus size: 191
53441 GATGCTTGTT
* *
53451 TGTGCTATAAACTGTTCCCTAATGATGCTACTCACACGAGCTGTCGAGAGTATCCATAAAGCATA
1 TGTGCTATAAACTGTTCCCTAATGATGCTACTCACACGAGCTATCGAGAATATCCATAAAGCATA
*
53516 GTCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGATTCATGATACT
66 GTCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGACTCATGATACT
* *
53581 GCTCACATGAGCTGTCAAGGACTCACAACATAGGTGGTACCTCAGCCATCGATACGATATC
131 GCTCACATGAGCTGTCAAGGACTCACAACATAGGCGGTACCTCAACCATCGATACGATATC
* * * * * *
53642 TGTGCCTAT-AACTGTTCCCTAATGATGCTGCTTACACGAGCTATTGAGAATATGCACTTATGCA
1 TGTG-CTATAAACTGTTCCCTAATGATGCTACTCACACGAGCTATCGAGAATATCCA-TAAAGCA
* * * * * * * * *
53706 TAGATCTCAGCCATTGTAGGGCTTGTAATCCATTCTTGGATTCTTTTCTCATTTCTTGACTCATG
64 TAG-TCCCAGCCATCGTAGGGCCTATAATCCATT-TAGGATCCATATCTC-TTTCTCGACTCATG
* ** ** * *
53771 ATGCTGCTTGCATGAGCTGTTGAGGACTCGCAACATATGCGGTACCTCAACCATCG
126 ATACTGCTCACATGAGCTGTCAAGGACTCACAACATAGGCGGTACCTCAACCATCG
53827 CTTCGGTTTC
Statistics
Matches: 153, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
191 45 0.29
192 12 0.08
193 26 0.17
194 11 0.07
195 59 0.39
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (191 bp):
TGTGCTATAAACTGTTCCCTAATGATGCTACTCACACGAGCTATCGAGAATATCCATAAAGCATA
GTCCCAGCCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGACTCATGATACT
GCTCACATGAGCTGTCAAGGACTCACAACATAGGCGGTACCTCAACCATCGATACGATATC
Found at i:57951 original size:54 final size:54
Alignment explanation
Indices: 57849--58078 Score: 313
Period size: 54 Copynumber: 4.3 Consensus size: 54
57839 TCGTAAATGC
* * *
57849 TAAAAGGTCTGATGACTTTGTGTAATCGTGAGTTATATG-AATCCTATTACGGAT
1 TAAAA-GTCCGATGACTCTGTGTCATCGTGAGTTATATGAAATCCTATTACGGAT
*
57903 TAAAAGTCCGATGACTCTGTGTCATCGTGAGTTATATGAAATCCTATTATGGAT
1 TAAAAGTCCGATGACTCTGTGTCATCGTGAGTTATATGAAATCCTATTACGGAT
* * *
57957 TAAAGGTCCGATGACTCTGTGTCATCGGGATTTATATGAAATCCTATTACGGAT
1 TAAAAGTCCGATGACTCTGTGTCATCGTGAGTTATATGAAATCCTATTACGGAT
* * * *
58011 T-AAAGATCCGATGACTTTGTGTCATCGTGAGTCATAT-TAATCCTATTATGGAT
1 TAAAAG-TCCGATGACTCTGTGTCATCGTGAGTTATATGAAATCCTATTACGGAT
*
58064 TAAAGGTCCGATGAC
1 TAAAAGTCCGATGAC
58079 AGAGCTCCTA
Statistics
Matches: 157, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
53 57 0.36
54 100 0.64
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (54 bp):
TAAAAGTCCGATGACTCTGTGTCATCGTGAGTTATATGAAATCCTATTACGGAT
Found at i:58062 original size:107 final size:107
Alignment explanation
Indices: 57851--58078 Score: 352
Period size: 107 Copynumber: 2.1 Consensus size: 107
57841 GTAAATGCTA
* * *
57851 AAAGGTCTGATGACTTTGTGTAATCGTGAGTTATATGAATCCTATTACGGATTAAAAGTCCGATG
1 AAAGGTCCGATGACTCTGTGTAATCGGGAGTTATATGAATCCTATTACGGATTAAAAGTCCGATG
*
57916 ACTCTGTGTCATCGTGAGTTATATGAAATCCTATTATGGATT
66 ACTCTGTGTCATCGTGAGTCATATGAAATCCTATTATGGATT
* *
57958 AAAGGTCCGATGACTCTGTGTCATCGGGATTTATATGAAATCCTATTACGGATT-AAAGATCCGA
1 AAAGGTCCGATGACTCTGTGTAATCGGGAGTTATATG-AATCCTATTACGGATTAAAAG-TCCGA
* *
58022 TGACTTTGTGTCATCGTGAGTCATAT-TAATCCTATTATGGATT
64 TGACTCTGTGTCATCGTGAGTCATATGAAATCCTATTATGGATT
58065 AAAGGTCCGATGAC
1 AAAGGTCCGATGAC
58079 AGAGCTCCTA
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
107 66 0.59
108 45 0.41
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (107 bp):
AAAGGTCCGATGACTCTGTGTAATCGGGAGTTATATGAATCCTATTACGGATTAAAAGTCCGATG
ACTCTGTGTCATCGTGAGTCATATGAAATCCTATTATGGATT
Found at i:58740 original size:21 final size:23
Alignment explanation
Indices: 58698--58753 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
58688 TACTAACAAA
*
58698 AGTATCGGTAGTTCTGTTAATAGT
1 AGTATCGGTAGTTCTG-TAATACT
58722 AGTATCGGTAGTT-TG-AATACT
1 AGTATCGGTAGTTCTGTAATACT
*
58743 TGTATCGGTAG
1 AGTATCGGTAG
58754 AAGTTGCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 15 0.50
23 2 0.07
24 13 0.43
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (23 bp):
AGTATCGGTAGTTCTGTAATACT
Found at i:62935 original size:54 final size:54
Alignment explanation
Indices: 62824--63149 Score: 399
Period size: 54 Copynumber: 6.1 Consensus size: 54
62814 AAATGCAAAT
* * * * * *
62824 AGGTCCGATGACTCTATGTCATCGTGTGTTACATG-AATCCTATTACGGATTAA
1 AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACAGATTAA
*
62877 AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTATAGATTAA
1 AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACAGATTAA
* * *
62931 AGGTCCGATGACTTTGTGTCATCATGAGTTATATGAAATCCTATTA-GGATTAA
1 AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACAGATTAA
* ** * * * *
62984 AAGTCTGATGACTCAGTGTCATCGTGAATTATATGAAATCCTATTACAGGTTAA
1 AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACAGATTAA
* * *
63038 AGGTCCAATGACTCTATGTCATCATGAGTTATATGAAATCCTATTGCAAATTAA
1 AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACAGATTAA
* * * * *
63092 AGGTTCAATGACTTTGTGTCAT-TTGAGTAATATG-AATCCTATTACGGATTAA
1 AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACAGATTAA
63144 AGGTCC
1 AGGTCC
63150 GATAACGGAG
Statistics
Matches: 234, Mismatches: 37, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
52 20 0.09
53 86 0.37
54 128 0.55
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (54 bp):
AGGTCCAATGACTCTGTGTCATCATGAGTTATATGAAATCCTATTACAGATTAA
Found at i:63016 original size:107 final size:108
Alignment explanation
Indices: 62824--63152 Score: 405
Period size: 107 Copynumber: 3.1 Consensus size: 108
62814 AAATGCAAAT
* * * *
62824 AGGTCCGATGACTCTATGTCATCGTGTGTTACATG-AATCCTATTACGGATTAAAGGTCCAATGA
1 AGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTACGGATTAAAAGTCCAATGA
* * *
62888 CTCTGTGTCATCATGAGTTATATGAAATCCTATTATAGATTAA
66 CTCAGTGTCATCATGAATTATATGAAATCCTATTACAGATTAA
* * **
62931 AGGTCCGATGACTTTGTGTCATCATGAGTTATATGAAATCCTATTA-GGATTAAAAGTCTGATGA
1 AGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTACGGATTAAAAGTCCAATGA
* *
62995 CTCAGTGTCATCGTGAATTATATGAAATCCTATTACAGGTTAA
66 CTCAGTGTCATCATGAATTATATGAAATCCTATTACAGATTAA
* * ** * *
63038 AGGTCCAATGACTCTATGTCATCATGAGTTATATGAAATCCTATTGCAAATTAAAGGTTCAATGA
1 AGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTACGGATTAAAAGTCCAATGA
** * * * *
63103 CTTTGTGTCAT-TTGAGTAATATG-AATCCTATTACGGATTAA
66 CTCAGTGTCATCATGAATTATATGAAATCCTATTACAGATTAA
63144 AGGTCCGAT
1 AGGTCCGAT
63153 AACGGAGCTC
Statistics
Matches: 189, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
106 24 0.13
107 134 0.71
108 31 0.16
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (108 bp):
AGGTCCGATGACTCTATGTCATCATGAGTTATATGAAATCCTATTACGGATTAAAAGTCCAATGA
CTCAGTGTCATCATGAATTATATGAAATCCTATTACAGATTAA
Found at i:63094 original size:161 final size:159
Alignment explanation
Indices: 62830--63144 Score: 465
Period size: 161 Copynumber: 2.0 Consensus size: 159
62820 AAATAGGTCC
** *
62830 GATGACTCTATGTCATCGTGTGTTACATGAATCCTATTACGGATTAAAGGTCCAATGACTCTGTG
1 GATGACTCTATGTCATCGTGAATTACATGAATCCTATTACGGATTAAAGGTCCAATGACTCTATG
* * *
62895 TCATCATGAGTTATATGAAATCCTATTATAGATTAAAGGTCCGATGACTTTGTGTCATCATGAGT
66 TCATCATGAGTTATATGAAATCCTATTACAAATTAAAGGTCCAATGACTTTGTGTCAT-ATGAGT
*
62960 TATATGAAATCCTATTA-GGATTAAAAGTCT
130 AATATG-AATCCTATTACGGATTAAAAGTCT
*
62990 GATGACTC-AGTGTCATCGTGAATTATATGAAATCCTATTACAGG-TTAAAGGTCCAATGACTCT
1 GATGACTCTA-TGTCATCGTGAATTACATG-AATCCTATTAC-GGATTAAAGGTCCAATGACTCT
* * *
63053 ATGTCATCATGAGTTATATGAAATCCTATTGCAAATTAAAGGTTCAATGACTTTGTGTCATTTGA
63 ATGTCATCATGAGTTATATGAAATCCTATTACAAATTAAAGGTCCAATGACTTTGTGTCATATGA
63118 GTAATATGAATCCTATTACGGATTAAA
128 GTAATATGAATCCTATTACGGATTAAA
63145 GGTCCGATAA
Statistics
Matches: 140, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
159 11 0.08
160 42 0.30
161 85 0.61
162 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (159 bp):
GATGACTCTATGTCATCGTGAATTACATGAATCCTATTACGGATTAAAGGTCCAATGACTCTATG
TCATCATGAGTTATATGAAATCCTATTACAAATTAAAGGTCCAATGACTTTGTGTCATATGAGTA
ATATGAATCCTATTACGGATTAAAAGTCT
Found at i:64016 original size:14 final size:14
Alignment explanation
Indices: 63997--64025 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
63987 TACTTATCTA
63997 ATAAGTATCGGTAG
1 ATAAGTATCGGTAG
64011 ATAAGTATCGGTAG
1 ATAAGTATCGGTAG
64025 A
1 A
64026 AGTCTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (14 bp):
ATAAGTATCGGTAG
Found at i:64975 original size:21 final size:21
Alignment explanation
Indices: 64949--64988 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
64939 AACACTTAGT
64949 GGTGTTCGACATTGTCATGTC
1 GGTGTTCGACATTGTCATGTC
64970 GGTGTTCGACATTGTCATG
1 GGTGTTCGACATTGTCATG
64989 CCCCAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.38
Consensus pattern (21 bp):
GGTGTTCGACATTGTCATGTC
Found at i:68086 original size:43 final size:43
Alignment explanation
Indices: 68038--68171 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 43
68028 AAACACATAA
68038 TCACATATAAGGCAACAAACATGAATCATAATACACATCAATT
1 TCACATATAAGGCAACAAACATGAATCATAATACACATCAATT
* * ** ***
68081 TCACATAACTTTAGG-ATC--ACATTTATCATCAAT--GTTTCTAA--
1 TCACAT-A--TAAGGCAACAAACATGAATCAT-AATACACATC-AATT
*
68122 TCACATATAAGGCAACAAACATGAATCATCATACACATCAATT
1 TCACATATAAGGCAACAAACATGAATCATAATACACATCAATT
68165 TCACATA
1 TCACATA
68172 ACTTTAGGAT
Statistics
Matches: 64, Mismatches: 15, Indels: 24
0.62 0.15 0.23
Matches are distributed among these distances:
38 4 0.06
39 2 0.03
40 3 0.05
41 17 0.27
42 4 0.06
43 24 0.38
44 4 0.06
45 2 0.03
46 4 0.06
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (43 bp):
TCACATATAAGGCAACAAACATGAATCATAATACACATCAATT
Found at i:68176 original size:84 final size:84
Alignment explanation
Indices: 68035--68200 Score: 314
Period size: 84 Copynumber: 2.0 Consensus size: 84
68025 AATAAACACA
68035 TAATCACATATAAGGCAACAAACATGAATCATAATACACATCAATTTCACATAACTTTAGGATCA
1 TAATCACATATAAGGCAACAAACATGAATCATAATACACATCAATTTCACATAACTTTAGGATCA
*
68100 CATTTATCATCAATGTTTC
66 CATATATCATCAATGTTTC
*
68119 TAATCACATATAAGGCAACAAACATGAATCATCATACACATCAATTTCACATAACTTTAGGATCA
1 TAATCACATATAAGGCAACAAACATGAATCATAATACACATCAATTTCACATAACTTTAGGATCA
68184 CATATATCATCAATGTT
66 CATATATCATCAATGTT
68201 GCTATGCATG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (84 bp):
TAATCACATATAAGGCAACAAACATGAATCATAATACACATCAATTTCACATAACTTTAGGATCA
CATATATCATCAATGTTTC
Found at i:68430 original size:48 final size:48
Alignment explanation
Indices: 68355--68447 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
68345 ACATAAACAC
* * * *
68355 ATAATCACTTTGTAGATAAATTGCCACATAATTGCCAAAAATGACCCT
1 ATAATCACTTTGCACATAAACTACCACATAATTGCCAAAAATGACCCT
*
68403 ATAATCACTTTGCACATAAGCTACCACATAATTGCCAAAAATGAC
1 ATAATCACTTTGCACATAAACTACCACATAATTGCCAAAAATGAC
68448 TACTTATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.27
Consensus pattern (48 bp):
ATAATCACTTTGCACATAAACTACCACATAATTGCCAAAAATGACCCT
Found at i:70769 original size:19 final size:19
Alignment explanation
Indices: 70745--70782 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
70735 GTGGGATCGT
70745 TATCTAATAGACTTACATC
1 TATCTAATAGACTTACATC
* *
70764 TATCTATTATACTTACATC
1 TATCTAATAGACTTACATC
70783 GATAGTGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (19 bp):
TATCTAATAGACTTACATC
Found at i:74226 original size:19 final size:18
Alignment explanation
Indices: 74202--74253 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
74192 GAATATTTGT
74202 TATTTTTTTATTTTTCTC
1 TATTTTTTTATTTTTCTC
*
74220 GTA--TTTTTCTTTTTCTC
1 -TATTTTTTTATTTTTCTC
74237 TACTTTTTTTCATTTTT
1 TA-TTTTTTT-ATTTTT
74254 TTTGTGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
19 7 0.26
20 5 0.19
ACGTcount: A:0.10, C:0.13, G:0.02, T:0.75
Consensus pattern (18 bp):
TATTTTTTTATTTTTCTC
Found at i:77066 original size:15 final size:15
Alignment explanation
Indices: 77046--77076 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
77036 ACAAAACGCA
*
77046 AACACTGATGTTGCG
1 AACACTCATGTTGCG
77061 AACACTCATGTTGCG
1 AACACTCATGTTGCG
77076 A
1 A
77077 GCATCGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (15 bp):
AACACTCATGTTGCG
Found at i:79339 original size:26 final size:26
Alignment explanation
Indices: 79303--79353 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
79293 CCCAAAATAC
*
79303 ATAGTTTATAAAAAGTCAGATTCGAG
1 ATAGTCTATAAAAAGTCAGATTCGAG
79329 ATAGTCTATAAAAAGTCAGATTCGA
1 ATAGTCTATAAAAAGTCAGATTCGA
79354 AATATCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (26 bp):
ATAGTCTATAAAAAGTCAGATTCGAG
Done.