Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011696.1 Kokia drynarioides strain JFW-HI SEQ_126690, 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: 540923
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 13 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:235225 original size:19 final size:19
Alignment explanation
Indices: 235187--235225 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
235177 CAGTACAGCA
* *
235187 TATCGCTCTTATGAGTCAG
1 TATCGCTCTTACGAGCCAG
235206 TATCGCTCTTACGAGCCAG
1 TATCGCTCTTACGAGCCAG
235225 T
1 T
235226 TTAGTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (19 bp):
TATCGCTCTTACGAGCCAG
Found at i:237969 original size:20 final size:19
Alignment explanation
Indices: 237936--237973 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
237926 ATAATCTATC
237936 CACTTAAACACTCTTAAAT
1 CACTTAAACACTCTTAAAT
*
237955 CACTCTAAACTCTCTTAAA
1 CACT-TAAACACTCTTAAA
237974 AAAACCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (19 bp):
CACTTAAACACTCTTAAAT
Found at i:243085 original size:152 final size:151
Alignment explanation
Indices: 242639--243119 Score: 549
Period size: 152 Copynumber: 3.1 Consensus size: 151
242629 AAAACCTTCT
** * *
242639 TCTCAAATTTAGTTTTTT-AGAAGCATCAGTACAAAAAAGCGTCCAACTGAAAGC-TTTTTATGT
1 TCTCAAATTTA-TTTTTTCAGAAGCATCAGTACAAAAAA-AATCCAGCTGGAAGCTTTTTTATGT
* * *
242702 ACAATTACTGACTATGGATCCTACTTAGAGGCTTTTTT-AAGAACAAAACAAAATTCATCTCGTC
64 ACTATTACTGACTGTGCATCCTACTTAGA-GCTTTTTTCAA-AACAAAACAAAATTCATCTCGTC
242766 AAAATTATTTTTTCAGAACACATCA
127 AAAATTATTTTTTCAGAACACATCA
* * * ** *
242791 CCTCAAGTTTATTTTTTCAAAAGCATCAAAACAAAAAAAAAACATCCAGCTAGAAGCTTTTTTAT
1 TCTCAAATTTATTTTTTCAGAAGCATCAGTAC---AAAAAAA-ATCCAGCTGGAAGCTTTTTTAT
* * * *
242856 TTACTATTACTGACTGTGCATCCTACTTTATA-CGTTTTTTCAGAACAAAACAAAATTTATCTCG
62 GTACTATTACTGACTGTGCATCCTAC-TTAGAGC-TTTTTTCAAAACAAAACAAAATTCATCTCG
*
242920 TCAAAATTA-TTTTTCAGAACACGTCA
125 TCAAAATTATTTTTTCAGAACACATCA
* * *
242946 TCTCAAATTTCTTTTTTCAGATAGCATCAGTACAAAAAAAATCCAGTTGGAAGCTTTTTTCTGTA
1 TCTCAAATTTATTTTTTCAGA-AGCATCAGTACAAAAAAAATCCAGCTGGAAGCTTTTTTATGTA
* * * * *
243011 GTATTACTGACTGTGCAGCCTACTTAGAGCTTTTTTCAAAACAAAACAAAATCCATTTTGTCAAA
65 CTATTACTGACTGTGCATCCTACTTAGAGCTTTTTTCAAAACAAAACAAAATTCATCTCGTCAAA
*
243076 ATTATTTTTTCAGAACACATTA
130 ATTATTTTTTCAGAACACATCA
** * *
243098 GGTCAAATTAAATTTTTCAGAA
1 TCTCAAATTTATTTTTTCAGAA
243120 CCAATTATTT
Statistics
Matches: 274, Mismatches: 43, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
151 45 0.16
152 94 0.34
153 7 0.03
155 50 0.18
156 73 0.27
157 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (151 bp):
TCTCAAATTTATTTTTTCAGAAGCATCAGTACAAAAAAAATCCAGCTGGAAGCTTTTTTATGTAC
TATTACTGACTGTGCATCCTACTTAGAGCTTTTTTCAAAACAAAACAAAATTCATCTCGTCAAAA
TTATTTTTTCAGAACACATCA
Found at i:249954 original size:29 final size:30
Alignment explanation
Indices: 249922--249985 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
249912 GTGAACTTAT
*
249922 TTGAATTTCTGA-TTT-TTTTCAAGATTAAA
1 TTGAATTT-TGATTTTGTTTTAAAGATTAAA
* *
249951 TTGAGTTTTGATTTTGTTTTAAAGATTAAG
1 TTGAATTTTGATTTTGTTTTAAAGATTAAA
249981 TTGAA
1 TTGAA
249986 AATTTCAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 3 0.10
29 10 0.34
30 16 0.55
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.52
Consensus pattern (30 bp):
TTGAATTTTGATTTTGTTTTAAAGATTAAA
Found at i:254760 original size:21 final size:22
Alignment explanation
Indices: 254730--254771 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
254720 ATTTACATGT
254730 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
254752 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
254772 CTTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:276647 original size:22 final size:22
Alignment explanation
Indices: 276619--276663 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
276609 ATAAGTGTGT
276619 TACCCTCAAAGTATATCCTTCA
1 TACCCTCAAAGTATATCCTTCA
276641 TACCCTCAAAGTATATCCTTCA
1 TACCCTCAAAGTATATCCTTCA
276663 T
1 T
276664 CTCTTTGGGA
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:0.31, C:0.31, G:0.04, T:0.33
Consensus pattern (22 bp):
TACCCTCAAAGTATATCCTTCA
Found at i:278821 original size:23 final size:22
Alignment explanation
Indices: 278795--278838 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
278785 AAAATATTTC
*
278795 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
278818 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
278839 TTATTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:294965 original size:8 final size:8
Alignment explanation
Indices: 294952--294976 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
294942 CAATTAGTAT
294952 GCATTTTG
1 GCATTTTG
294960 GCATTTTG
1 GCATTTTG
294968 GCATTTTG
1 GCATTTTG
294976 G
1 G
294977 AATGGCTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.48
Consensus pattern (8 bp):
GCATTTTG
Found at i:304406 original size:16 final size:17
Alignment explanation
Indices: 304385--304420 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
304375 GTCATCACAT
*
304385 TTTTATT-GTCATTGTA
1 TTTTATTCGTCAATGTA
304401 TTTTATTCGTCAATGTA
1 TTTTATTCGTCAATGTA
304418 TTT
1 TTT
304421 GCATTGTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTTATTCGTCAATGTA
Found at i:306892 original size:17 final size:18
Alignment explanation
Indices: 306870--306907 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
306860 CAACATTTTT
306870 TTTGTTTTC-TCTTCTTC
1 TTTGTTTTCTTCTTCTTC
*
306887 TTTGTTTTCTTTTTCTTC
1 TTTGTTTTCTTCTTCTTC
306905 TTT
1 TTT
306908 TCTATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTGTTTTCTTCTTCTTC
Found at i:306915 original size:21 final size:22
Alignment explanation
Indices: 306869--306915 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
306859 GCAACATTTT
* *
306869 TTTTGTTTTCTCTTCTTCTTTG
1 TTTTCTTTTCTCTTCTTCTTTA
306891 TTTTCTTTT-TCTTCTT-TTCTA
1 TTTTCTTTTCTCTTCTTCTT-TA
306912 TTTT
1 TTTT
306916 TGTACGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 12 0.55
22 8 0.36
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTCTTTTCTCTTCTTCTTTA
Found at i:322726 original size:15 final size:15
Alignment explanation
Indices: 322693--322740 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
322683 TGGCATTTAT
* *
322693 GATGATATCTCTGAT
1 GATGATATCTATGAA
322708 GATGATATCTATGAA
1 GATGATATCTATGAA
*
322723 GATGGGTAT-TATGAA
1 GAT-GATATCTATGAA
322738 GAT
1 GAT
322741 TGGGAGATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 25 0.86
16 4 0.14
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (15 bp):
GATGATATCTATGAA
Found at i:323637 original size:17 final size:16
Alignment explanation
Indices: 323615--323652 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
323605 TCAACGCGAG
323615 GAGAAAAGGAAAATTTT
1 GAGAAAA-GAAAATTTT
*
323632 GAG-AAAGAGAATTTT
1 GAGAAAAGAAAATTTT
323647 GAGAAA
1 GAGAAA
323653 GGGATAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 11 0.58
16 5 0.26
17 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (16 bp):
GAGAAAAGAAAATTTT
Found at i:325962 original size:25 final size:26
Alignment explanation
Indices: 325932--325980 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
325922 AGGACCAAAG
*
325932 AATTAAATTAACCC-AACTATTAAAC
1 AATTAAATAAACCCAAACTATTAAAC
325957 AATTAAATAAACCCAAACTATTAA
1 AATTAAATAAACCCAAACTATTAA
325981 TGAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (26 bp):
AATTAAATAAACCCAAACTATTAAAC
Found at i:327648 original size:15 final size:17
Alignment explanation
Indices: 327613--327649 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
327603 TTTTTAATAG
327613 TTTTAAGACTTTGATTAA
1 TTTTAAGACTTTGA-TAA
327631 TTTTAAGAC-TTG-TAA
1 TTTTAAGACTTTGATAA
327646 TTTT
1 TTTT
327650 GGGGATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (17 bp):
TTTTAAGACTTTGATAA
Found at i:366305 original size:15 final size:16
Alignment explanation
Indices: 366276--366305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
366266 AACAACATGA
366276 TGAAAAGTGAAATAAC
1 TGAAAAGTGAAATAAC
366292 TGAAAAGT-AAATAA
1 TGAAAAGTGAAATAA
366306 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (16 bp):
TGAAAAGTGAAATAAC
Found at i:374092 original size:25 final size:25
Alignment explanation
Indices: 374057--374112 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
374047 AATTAATGCC
* *
374057 AAACTCTACTTCTCGGATCGACGGT
1 AAACTCCACTTCTCGGATCAACGGT
374082 AAACTCCACTTCTCGGATCAACGGT
1 AAACTCCACTTCTCGGATCAACGGT
374107 AAACTC
1 AAACTC
374113 AGTAACTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (25 bp):
AAACTCCACTTCTCGGATCAACGGT
Found at i:376439 original size:45 final size:45
Alignment explanation
Indices: 376346--376432 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
376336 CAGGCTACCA
* *
376346 ATACTTCTATGAACAGTACTACCGAAACTTGTTATATGATTACTG
1 ATACTTCTATGAACAGTACTACCGAAACTTGTTATACGACTACTG
* * ** * *
376391 ATACTTTTATGAATAGTACTATTGATACTTGTTATGCGACTA
1 ATACTTCTATGAACAGTACTACCGAAACTTGTTATACGACTA
376433 TCGATACAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (45 bp):
ATACTTCTATGAACAGTACTACCGAAACTTGTTATACGACTACTG
Found at i:376516 original size:21 final size:21
Alignment explanation
Indices: 376478--376517 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
376468 TACCCTGTAC
*
376478 TTCTACCAATACATGCAAGAG
1 TTCTACCAATACAAGCAAGAG
376499 TTCTACCGAA-ACAAGCAAG
1 TTCTACC-AATACAAGCAAG
376518 TAGAATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (21 bp):
TTCTACCAATACAAGCAAGAG
Found at i:380127 original size:28 final size:27
Alignment explanation
Indices: 380072--380125 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
380062 TTATTATTCA
380072 AATTTTCTTTGAGTTTTTCTTTTCAAG
1 AATTTTCTTTGAGTTTTTCTTTTCAAG
380099 AATTGTTC-TTGAG-TTTTCTTTT-AAG
1 AATT-TTCTTTGAGTTTTTCTTTTCAAG
380124 AA
1 AA
380126 GAGTCTCGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 5 0.19
26 9 0.35
27 9 0.35
28 3 0.12
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (27 bp):
AATTTTCTTTGAGTTTTTCTTTTCAAG
Found at i:392990 original size:30 final size:30
Alignment explanation
Indices: 392921--392990 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
392911 AATAAGTTAA
*
392921 ATTTTT-TATTTATTTTATGTTATAGTATT
1 ATTTTTATATTTATTTTATATTATAGTATT
* * * *
392950 ATTATAATATTTATTTTA-ATTATTGTTGTT
1 ATTTTTATATTTATTTTATATTATAG-TATT
392980 ATTTTTATATT
1 ATTTTTATATT
392991 AATCCTAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (30 bp):
ATTTTTATATTTATTTTATATTATAGTATT
Found at i:395301 original size:37 final size:37
Alignment explanation
Indices: 395259--395330 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
395249 ATATAAAATG
* *
395259 ATAACAATTTGAAATTTTTTTTAAAAAATTAAAAAGT
1 ATAACAATTTGAAATTCTTTTAAAAAAATTAAAAAGT
395296 ATAACAATTTGAAATTCTTTTAAAAAAATTAAAAA
1 ATAACAATTTGAAATTCTTTTAAAAAAATTAAAAA
395331 ATTCTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (37 bp):
ATAACAATTTGAAATTCTTTTAAAAAAATTAAAAAGT
Found at i:395348 original size:37 final size:37
Alignment explanation
Indices: 395259--395348 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 37
395249 ATATAAAATG
* * * *
395259 ATAACAATTTGAAATTTTTTTTAAAAAATTAAAAAGT
1 ATAACAAATTAAAATTCTTTTAAAAAAATTAAAAAGT
* * *
395296 ATAACAATTTGAAATTCTTTTAAAAAAATTAAAAAATT
1 ATAACAAATTAAAATTCTTTTAAAAAAATT-AAAAAGT
*
395334 CTAA-AAATTAAAATT
1 ATAACAAATTAAAATT
395349 AAAACAAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 37 0.80
38 9 0.20
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (37 bp):
ATAACAAATTAAAATTCTTTTAAAAAAATTAAAAAGT
Found at i:397114 original size:21 final size:21
Alignment explanation
Indices: 397090--397134 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
397080 AAAATAGACA
397090 TAATCATGAACATAAAATATT
1 TAATCATGAACATAAAATATT
397111 TAATCATGAACATAAAATATT
1 TAATCATGAACATAAAATATT
397132 TAA
1 TAA
397135 CTTAATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (21 bp):
TAATCATGAACATAAAATATT
Found at i:407865 original size:6 final size:7
Alignment explanation
Indices: 407840--407864 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
407830 ACTAAGTTAG
407840 TTTTTAT
1 TTTTTAT
407847 TTTTTAT
1 TTTTTAT
407854 TTTTTAT
1 TTTTTAT
407861 TTTT
1 TTTT
407865 AGCACTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:408564 original size:23 final size:24
Alignment explanation
Indices: 408516--408576 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
408506 TCAGTCACTT
408516 GAAAAAGGAAAATGAGAAAAAGAAA
1 GAAAAA-GAAAATGAGAAAAAGAAA
408541 GAAAAAGAAAA-GAG-AAAAGAAAA
1 GAAAAAGAAAATGAGAAAAAG-AAA
408564 GAAGAAA-AAAATG
1 GAA-AAAGAAAATG
408577 TTTGCTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
22 5 0.15
23 13 0.39
24 9 0.27
25 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (24 bp):
GAAAAAGAAAATGAGAAAAAGAAA
Found at i:408569 original size:30 final size:29
Alignment explanation
Indices: 408518--408574 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
408508 AGTCACTTGA
408518 AAAAGGAAAATGAGAAAAAGAAAGAAAAAG
1 AAAAGGAAAATGAGAAAAAGAAA-AAAAAG
408548 AAAAGAGAAAA-GA-AAAGAAGAAAAAAA
1 AAAAG-GAAAATGAGAAA-AAGAAAAAAA
408575 TGTTTGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (29 bp):
AAAAGGAAAATGAGAAAAAGAAAAAAAAG
Found at i:409050 original size:211 final size:211
Alignment explanation
Indices: 408682--409107 Score: 789
Period size: 211 Copynumber: 2.0 Consensus size: 211
408672 AATTGTCGGC
*
408682 GCATTATTCTATTATATGAATACAATTTATGTATTAGGATTTTAGGAAATTCAAAGTTACGAGAA
1 GCATTATTCTATTATATGAATACAATTTATGTATTAGGATTTCAGGAAATTCAAAGTTACGAGAA
*
408747 TAATGATTGCGGTGACATGTTTGCTTGTTATTTTGTTAATTTTTGTTTACTTGAGGACAAGTAAA
66 TAATGATTGCGGTGACATGTTTGCTTATTATTTTGTTAATTTTTGTTTACTTGAGGACAAGTAAA
* *
408812 AACTCAAGTTTGGGGGTGTGCTGGTATTACAAATGACATATATTTTCTCCTTAAATTTGGGTATT
131 AACTCAAGTTTAGGGGTGTGATGGTATTACAAATGACATATATTTTCTCCTTAAATTTGGGTATT
408877 AATTGTTTCTTTTGTA
196 AATTGTTTCTTTTGTA
* *
408893 GCATTATTCTATTATATGAATACAATTTGTGTATTAGGATTTCAGGAAATTCAAAGTTGCGAGAA
1 GCATTATTCTATTATATGAATACAATTTATGTATTAGGATTTCAGGAAATTCAAAGTTACGAGAA
*
408958 TAGTGATTGCGGTGACATGTTTGCTTATTATTTTGTTAATTTTTGTTTACTTGAGGACAAGTAAA
66 TAATGATTGCGGTGACATGTTTGCTTATTATTTTGTTAATTTTTGTTTACTTGAGGACAAGTAAA
409023 AACTCAAGTTTAGGGGTGTGATGGTATTACAAATGACATATATTTTCTCCTTAAATTTGGGTATT
131 AACTCAAGTTTAGGGGTGTGATGGTATTACAAATGACATATATTTTCTCCTTAAATTTGGGTATT
409088 AATTGTTTCTTTTGTA
196 AATTGTTTCTTTTGTA
409104 GCAT
1 GCAT
409108 ATTTAGCATG
Statistics
Matches: 208, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
211 208 1.00
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (211 bp):
GCATTATTCTATTATATGAATACAATTTATGTATTAGGATTTCAGGAAATTCAAAGTTACGAGAA
TAATGATTGCGGTGACATGTTTGCTTATTATTTTGTTAATTTTTGTTTACTTGAGGACAAGTAAA
AACTCAAGTTTAGGGGTGTGATGGTATTACAAATGACATATATTTTCTCCTTAAATTTGGGTATT
AATTGTTTCTTTTGTA
Found at i:411859 original size:20 final size:20
Alignment explanation
Indices: 411834--411872 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
411824 CAAGATTGAA
*
411834 GATTGCCTTTTTATTTCTTG
1 GATTGCCTTTTGATTTCTTG
411854 GATTGCCTTTTGATTTCTT
1 GATTGCCTTTTGATTTCTT
411873 TGATATTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.15, G:0.15, T:0.59
Consensus pattern (20 bp):
GATTGCCTTTTGATTTCTTG
Found at i:422568 original size:21 final size:20
Alignment explanation
Indices: 422535--422583 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
422525 TACTTTGTTC
* *
422535 TAAAAAAATAAAAAAATCAA
1 TAAAAAAAAAAAAAAAACAA
*
422555 TAAAAAAGAAAAAAAAAACAT
1 TAAAAAA-AAAAAAAAAACAA
422576 TAAAAAAA
1 TAAAAAAA
422584 CTATGGAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (20 bp):
TAAAAAAAAAAAAAAAACAA
Found at i:426160 original size:46 final size:45
Alignment explanation
Indices: 426091--426206 Score: 144
Period size: 46 Copynumber: 2.6 Consensus size: 45
426081 ATCTTTATCG
***
426091 AAATGATGCC-TAAGTATCTTTCAACTAAGGTCTTAGAACATATTTG
1 AAATGATGCCGT-AGTATCTTTCAACTAAGGTCTTA-AACATATAAA
* *
426137 ATATGATGCCGTAGTATCTTTCAACTATGGTCTTAAACATATAAA
1 AAATGATGCCGTAGTATCTTTCAACTAAGGTCTTAAACATATAAA
* *
426182 AAATGATGTCGTAGTATCTTGCAAC
1 AAATGATGCCGTAGTATCTTTCAAC
426207 CATGATCTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
45 29 0.48
46 31 0.51
47 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (45 bp):
AAATGATGCCGTAGTATCTTTCAACTAAGGTCTTAAACATATAAA
Found at i:426195 original size:45 final size:46
Alignment explanation
Indices: 426091--426215 Score: 146
Period size: 45 Copynumber: 2.7 Consensus size: 46
426081 ATCTTTATCG
* ***
426091 AAATGATGCC-TAAGTATCTTTCAACTAAGGTCTTAGAACATATTTG
1 AAATGATGCCGT-AGTATCTTTCAACTATGGTCTTAGAACATATAAA
*
426137 ATATGATGCCGTAGTATCTTTCAACTATGGTCTTA-AACATATAAA
1 AAATGATGCCGTAGTATCTTTCAACTATGGTCTTAGAACATATAAA
* * * *
426182 AAATGATGTCGTAGTATCTTGCAACCATGATCTT
1 AAATGATGCCGTAGTATCTTTCAACTATGGTCTT
426216 CATTTCAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
45 36 0.53
46 31 0.46
47 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (46 bp):
AAATGATGCCGTAGTATCTTTCAACTATGGTCTTAGAACATATAAA
Found at i:430064 original size:52 final size:53
Alignment explanation
Indices: 430002--430172 Score: 206
Period size: 52 Copynumber: 3.3 Consensus size: 53
429992 TGATGACTGA
*
430002 GTGTCATCATGAGTATATTAATCCTTTACGGATTACAG-GGTCCATTGACTAT
1 GTGTCATCATGAGTATATGAATCCTTTACGGATTACAGAGGTCCATTGACTAT
* * *
430054 GTGTCATCATGAGTATGTGAATCGTTTACGAATTAC-GAGGTCCATTGACTAT
1 GTGTCATCATGAGTATATGAATCCTTTACGGATTACAGAGGTCCATTGACTAT
* * * * * *
430106 TTGTCATCATGAGTATGTGATTCCTTTACGGA--ACAAGAGGTCTAATAACTAT
1 GTGTCATCATGAGTATATGAATCCTTTACGGATTAC-AGAGGTCCATTGACTAT
*
430158 GTGTCATCGTGAGTA
1 GTGTCATCATGAGTA
430173 ATTAATGAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
50 2 0.02
51 1 0.01
52 100 0.97
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (53 bp):
GTGTCATCATGAGTATATGAATCCTTTACGGATTACAGAGGTCCATTGACTAT
Found at i:436971 original size:17 final size:17
Alignment explanation
Indices: 436951--436983 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
436941 TTTAAGGACT
436951 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
436968 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
436984 TAAGTATTTG
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:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:437258 original size:50 final size:50
Alignment explanation
Indices: 437202--437299 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
437192 AGTTAAGTTT
*
437202 GCATCATAAATAATGA-CATGCATTA-AGTAACTTACATGTTAGTTAAATAA
1 GCATCATAAATAAT-ATCATGCATTATA-TAACTCACATGTTAGTTAAATAA
** *
437252 GCATCATAAATCCTATCATGCATTATATAACTCCCATGTTAGTTAAAT
1 GCATCATAAATAATATCATGCATTATATAACTCACATGTTAGTTAAAT
437300 GTATCATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.02
50 40 0.95
51 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (50 bp):
GCATCATAAATAATATCATGCATTATATAACTCACATGTTAGTTAAATAA
Found at i:441597 original size:20 final size:20
Alignment explanation
Indices: 441572--441615 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
441562 ACCATAGAGT
441572 TGAGGCTAATAGCTT-TGAGC
1 TGAGGCTAATAG-TTGTGAGC
441592 TGAGGCTAATAGTTGTGAGC
1 TGAGGCTAATAGTTGTGAGC
441612 TGAG
1 TGAG
441616 ACAGAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.25, C:0.11, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGGCTAATAGTTGTGAGC
Found at i:444537 original size:20 final size:20
Alignment explanation
Indices: 444495--444538 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
444485 TGGCAACGCA
*
444495 TTTTTACATTTACTTTTATC
1 TTTTTACATTTACTTTTAGC
*
444515 TTTTTACTTTTACTTGTT-GC
1 TTTTTACATTTACTT-TTAGC
444535 TTTT
1 TTTT
444539 AAATCTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTACATTTACTTTTAGC
Found at i:446807 original size:18 final size:18
Alignment explanation
Indices: 446781--446834 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
446771 ATGCATAGCA
446781 TTTAGTTGTCATTACATT
1 TTTAGTTGTCATTACATT
* *
446799 TTTAATTGTCATTGCA-T
1 TTTAGTTGTCATTACATT
*
446816 TTTAGTTGTTATTACATT
1 TTTAGTTGTCATTACATT
446834 T
1 T
446835 GCATTATAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTAGTTGTCATTACATT
Found at i:446824 original size:17 final size:17
Alignment explanation
Indices: 446781--446834 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
446771 ATGCATAGCA
446781 TTTAGTTGTCATTACATT
1 TTTAGTTGTCATTACA-T
* *
446799 TTTAATTGTCATTGCAT
1 TTTAGTTGTCATTACAT
*
446816 TTTAGTTGTTATTACAT
1 TTTAGTTGTCATTACAT
446833 TT
1 TT
446835 GCATTATAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.57
Consensus pattern (17 bp):
TTTAGTTGTCATTACAT
Found at i:460639 original size:21 final size:21
Alignment explanation
Indices: 460613--460671 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
460603 TAAGCATAGA
460613 CAGATGCATCCACAACA-AAGC
1 CAGATGCATCCACAACAGAA-C
* *
460634 CAGATGCATCCACACCAGAAT
1 CAGATGCATCCACAACAGAAC
*
460655 CAGATGCAACCACAACA
1 CAGATGCATCCACAACA
460672 CTCTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.42, C:0.34, G:0.14, T:0.10
Consensus pattern (21 bp):
CAGATGCATCCACAACAGAAC
Found at i:469379 original size:5 final size:5
Alignment explanation
Indices: 469359--469398 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
469349 CTTGTTCACC
* *
469359 AAAA- AAAAG AAGAG AAAAG AAAAG AAAAG TAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
469399 GATATATAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:486376 original size:28 final size:27
Alignment explanation
Indices: 486324--486378 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
486314 AAAAATATTG
*
486324 AAAAGATAAAAAAGAAAATAGATGAGT
1 AAAAGATAAAAAAGAAAATACATGAGT
*
486351 AAAA-ATAAAAGAAGAAAAATTCATGAGT
1 AAAAGATAAAA-AAG-AAAATACATGAGT
486379 GAGAAAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 7 0.29
28 11 0.46
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.16
Consensus pattern (27 bp):
AAAAGATAAAAAAGAAAATACATGAGT
Found at i:487007 original size:13 final size:13
Alignment explanation
Indices: 486989--487034 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
486979 TCTTTCTTTG
486989 TTTATTTTATTGC
1 TTTATTTTATTGC
* *
487002 TTTATTTTTTTTC
1 TTTATTTTATTGC
487015 -TTATTTTATTGC
1 TTTATTTTATTGC
*
487027 TTCATTTT
1 TTTATTTT
487035 TGTTTGTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTGC
Found at i:517846 original size:80 final size:80
Alignment explanation
Indices: 517707--517864 Score: 253
Period size: 80 Copynumber: 2.0 Consensus size: 80
517697 TTTTTATGCT
* * * *
517707 TAATTATTTTAAATTCATTAGTATGAGGAGGAATGATCAACTCTTTTATGATTTGTGCATTACTT
1 TAATTATTTTAAATTCATAAGTATGAGGAAGAATGATCAACTCTTTTATAATTTGTGCATTACTC
517772 GGGATGACCAATGAA
66 GGGATGACCAATGAA
* *
517787 TAATTATTTTAAATTCATAAGTATGAGGAAGAATGATCAACTCTTTTGTAATTTTTGCATTACTC
1 TAATTATTTTAAATTCATAAGTATGAGGAAGAATGATCAACTCTTTTATAATTTGTGCATTACTC
*
517852 GGGATGAGCAATG
66 GGGATGACCAATG
517865 TATTAAGTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (80 bp):
TAATTATTTTAAATTCATAAGTATGAGGAAGAATGATCAACTCTTTTATAATTTGTGCATTACTC
GGGATGACCAATGAA
Found at i:521501 original size:109 final size:109
Alignment explanation
Indices: 521311--521515 Score: 279
Period size: 109 Copynumber: 1.9 Consensus size: 109
521301 CAATGCTATT
* * ** * * *
521311 TTATTTTAGGAAATTCAAGAAATTGTGTCCTAATGTGTTGGGTATGGTTTTTCTTTGAACCTAAA
1 TTATTTTAGGAAACTCAAAAAATTGTACCCTAACGTGTTGGGTAAGATTTTTCTTTGAACCTAAA
521376 TAATATAGTATCCTATTTAAAA-CTGATAAATGCTCAATGTTCTG
66 TAATATAGTATCCTATTTAAAATC-GATAAATGCTCAATGTTCTG
**
521420 TTATTTTAGGGGACTCAAAAAATTGTACCCTAACGTGTTGGGTAAGATTTTTCTTTGAACCTAAA
1 TTATTTTAGGAAACTCAAAAAATTGTACCCTAACGTGTTGGGTAAGATTTTTCTTTGAACCTAAA
* *
521485 TAAT-TGGATATTCTATTTAAAATCGATAAAT
66 TAATATAG-TATCCTATTTAAAATCGATAAAT
521516 ATTCTTTGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
108 2 0.02
109 80 0.96
110 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (109 bp):
TTATTTTAGGAAACTCAAAAAATTGTACCCTAACGTGTTGGGTAAGATTTTTCTTTGAACCTAAA
TAATATAGTATCCTATTTAAAATCGATAAATGCTCAATGTTCTG
Found at i:524622 original size:8 final size:7
Alignment explanation
Indices: 524596--524620 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
524586 AGAGAGAGAG
524596 AAAAGAA
1 AAAAGAA
524603 AAAAGAA
1 AAAAGAA
524610 AAAAGAA
1 AAAAGAA
524617 AAAA
1 AAAA
524621 AGGGTGAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:527120 original size:14 final size:14
Alignment explanation
Indices: 527101--527127 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
527091 GAATTTTCAT
527101 CATTTGAAAATTCG
1 CATTTGAAAATTCG
527115 CATTTGAAAATTC
1 CATTTGAAAATTC
527128 TCTGAGACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
CATTTGAAAATTCG
Found at i:528584 original size:17 final size:17
Alignment explanation
Indices: 528559--528603 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
528549 ATAGTATAAC
*
528559 TGTCCCTGCATTTTTAT
1 TGTCACTGCATTTTTAT
528576 TGTCACTGCATTTTTAT
1 TGTCACTGCATTTTTAT
*
528593 TGTCGCTGCAT
1 TGTCACTGCAT
528604 CTACATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.49
Consensus pattern (17 bp):
TGTCACTGCATTTTTAT
Found at i:532438 original size:49 final size:49
Alignment explanation
Indices: 532398--532772 Score: 368
Period size: 49 Copynumber: 7.7 Consensus size: 49
532388 AGATTAAGGA
* * *
532398 AGCAACGGTGAATCTTATACCCTAGAGATATGGAGGGAAAGGTTAAAGCC
1 AGCAACGGTGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAG-C
* *
532448 A-CAACGGTGAACCTTATACCCTAGAGATGTTGA-GGAAACGGTTAAAGC
1 AGCAACGGTGAACCTTATACCCTAGAGATGTGGAGGGAAA-GGTTGAAGC
** * * *
532496 TA-CAATAGTGAACCTTATACCTTAGAGATAT-GATGGGAAAGATTGAAGC
1 -AGCAACGGTGAACCTTATACCCTAGAGATGTGGA-GGGAAAGGTTGAAGC
* * * *
532545 TGCAACGGTGAATCTTACACCCTAGAGATGTGGTGGGAAAGGTTGAAGTC
1 AGCAACGGTGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAG-C
* * *
532595 -GCAATGGCGAACCTTATA-CCTCAGAGATGT-GATGGGAAAGATTGAAGC
1 AGCAACGGTGAACCTTATACCCT-AGAGATGTGGA-GGGAAAGGTTGAAGC
* * * * * *
532643 CGTAACGGTGAATCTTGTACCCTAGAGATATGGAGGGAAAGGTTGTAGC
1 AGCAACGGTGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGC
* ** * *
532692 CGCAACGACGAACCTTATATCCTAGAGATGTGGAGGAAAAGGTTGAAGC
1 AGCAACGGTGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGC
* *
532741 AGCAACGGCGAACCTTATACCTTAGAGATGTG
1 AGCAACGGTGAACCTTATACCCTAGAGATGTG
532773 ATGGGAAGGA
Statistics
Matches: 268, Mismatches: 45, Indels: 25
0.79 0.13 0.07
Matches are distributed among these distances:
48 13 0.05
49 242 0.90
50 13 0.05
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (49 bp):
AGCAACGGTGAACCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGC
Found at i:532654 original size:147 final size:146
Alignment explanation
Indices: 532399--532787 Score: 444
Period size: 147 Copynumber: 2.6 Consensus size: 146
532389 GATTAAGGAA
* * * *
532399 GCAACGGTGAATCTTATACCCTAGAGATATGGAGGGAAAGGTTAAAGCCACAACGGTGAACCTTA
1 GCAACGGTGAATCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAG-CGCAACGGCGAACCTTA
* * * * *
532464 TACC-CTAGAGATGT--TGAGGAAACGGTTAAAGCTACAATAGTGAACCTTATACCTTAGAGATA
65 TACCTC-AGAGATGTGATG-GGAAA-GATTGAAGCCACAACAGTGAACCTTATACCCTAGAGATA
*
532526 T-GATGGGAAAGATTGAAGCT
127 TGGA-GGGAAAGATTGAAGCC
* * *
532546 GCAACGGTGAATCTTACACCCTAGAGATGTGGTGGGAAAGGTTGAAGTCGCAATGGCGAACCTTA
1 GCAACGGTGAATCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAG-CGCAACGGCGAACCTTA
** * * *
532611 TACCTCAGAGATGTGATGGGAAAGATTGAAGCCGTAACGGTGAATCTTGTACCCTAGAGATATGG
65 TACCTCAGAGATGTGATGGGAAAGATTGAAGCCACAACAGTGAACCTTATACCCTAGAGATATGG
* *
532676 AGGGAAAGGTTGTAGCC
130 AGGGAAAGATTGAAGCC
** * * *
532693 GCAACGACGAACCTTATATCCTAGAGATGTGGAGGAAAAGGTTGAAGCAGCAACGGCGAACCTTA
1 GCAACGGTGAATCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGC-GCAACGGCGAACCTTA
* *
532758 TACCTTAGAGATGTGATGGGAAGGATTGAA
65 TACCTCAGAGATGTGATGGGAAAGATTGAA
532788 ACTGTGATAA
Statistics
Matches: 206, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
146 1 0.00
147 195 0.95
148 8 0.04
149 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (146 bp):
GCAACGGTGAATCTTATACCCTAGAGATGTGGAGGGAAAGGTTGAAGCGCAACGGCGAACCTTAT
ACCTCAGAGATGTGATGGGAAAGATTGAAGCCACAACAGTGAACCTTATACCCTAGAGATATGGA
GGGAAAGATTGAAGCC
Found at i:534273 original size:49 final size:48
Alignment explanation
Indices: 534191--534466 Score: 232
Period size: 49 Copynumber: 5.7 Consensus size: 48
534181 AACGATGAAT
** * * *
534191 CTTATACCCTAGAGATGTGGCGAAAAAGGTTGAAGCCGTAATGGCGAAC
1 CTTATACCCTAGAGATGTGAAG-GAAAGATTGAAGCCGTAACGGCGAAC
* *
534240 CTTATACCCTAGAGATGTGATAGGAAAGATTGAAGCCGCAACGACGAAC
1 CTTATACCCTAGAGATGTGA-AGGAAAGATTGAAGCCGTAACGGCGAAC
* * * ** ** *
534289 CTTATACCTTAGAGATGTGATGGGAAAGATAGAAGCCACAACGGTAAAT
1 CTTATACCCTAGAGATGTGA-AGGAAAGATTGAAGCCGTAACGGCGAAC
* * * * * **
534338 CTTGTATCCT--AGATATAAAGGGAAAGGTTGAAGCCGTAACGATGAAC
1 CTTATACCCTAGAGATGTGAA-GGAAAGATTGAAGCCGTAACGGCGAAC
* * * * *
534385 CTTATACTCTAGAGATGTGGAAGGAAAGGTTGAAGTCGTAATGGCGGAC
1 CTTATACCCTAGAGATGT-GAAGGAAAGATTGAAGCCGTAACGGCGAAC
*
534434 CTTATACCCTAAAGATGTGAAGGGAAAGATTGA
1 CTTATACCCTAGAGATGTGAA-GGAAAGATTGA
534467 TGACGTACCG
Statistics
Matches: 180, Mismatches: 41, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
47 33 0.18
48 3 0.02
49 141 0.78
50 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (48 bp):
CTTATACCCTAGAGATGTGAAGGAAAGATTGAAGCCGTAACGGCGAAC
Found at i:538730 original size:17 final size:18
Alignment explanation
Indices: 538693--538732 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
538683 AACAAAAGAG
*
538693 ATGCAGTGACAAAATAAA
1 ATGCAATGACAAAATAAA
*
538711 ATGCAATGACAATA-AAA
1 ATGCAATGACAAAATAAA
538728 ATGCA
1 ATGCA
538733 TGAAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.17
Consensus pattern (18 bp):
ATGCAATGACAAAATAAA
Done.