Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011447.1 Kokia drynarioides strain JFW-HI SEQ_126431, 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: 482958
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 26 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:337082 original size:59 final size:60
Alignment explanation
Indices: 336958--337096 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 60
336948 TTGTTTTTTG
* * * * * * *
336958 ACCCTTAAATTTTCCAAAAATTCCAATTTGACCCCTAAACTTTTCTAAAATTCAAATTTG
1 ACCCCTAAATTTTCCAAAAAATCAAATTTAACCCCTAAACTTTCCAAAAATTCAAATTTA
*
337018 A-CCCTAAATTTTCCAAAAAATCAAATTTAACCCTTAAA-TTTCCAAAAATTCAAATTTA
1 ACCCCTAAATTTTCCAAAAAATCAAATTTAACCCCTAAACTTTCCAAAAATTCAAATTTA
*
337076 ACCCCTAAA-TTTCCTAAAAAT
1 ACCCCTAAATTTTCCAAAAAAT
337097 TAACCTCTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 29 0.42
59 39 0.57
60 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (60 bp):
ACCCCTAAATTTTCCAAAAAATCAAATTTAACCCCTAAACTTTCCAAAAATTCAAATTTA
Found at i:337100 original size:23 final size:23
Alignment explanation
Indices: 337073--337122 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
337063 AAATTCAAAT
337073 TTAACCCCTAAA-TTTCCTAAAAA
1 TTAACCCCTAAACTTTCC-AAAAA
* *
337096 TTAACCTCTAAACTTTTCAAAAA
1 TTAACCCCTAAACTTTCCAAAAA
337119 TTAA
1 TTAA
337123 AATTTGACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (23 bp):
TTAACCCCTAAACTTTCCAAAAA
Found at i:346650 original size:30 final size:30
Alignment explanation
Indices: 346601--346718 Score: 159
Period size: 30 Copynumber: 4.0 Consensus size: 30
346591 TAAATTTTTT
* *
346601 ACCCC-AAATTTTTCAAAAATTCCAATTTA
1 ACCCCTAAATTTTCCAAAAATTCAAATTTA
* * *
346630 GCTCCTTAAA-TTTCCAAAAATTTAAATTTA
1 AC-CCCTAAATTTTCCAAAAATTCAAATTTA
346660 ACCCCTAAATTTTCCAAAAATTCAAATTTA
1 ACCCCTAAATTTTCCAAAAATTCAAATTTA
*
346690 ACCCCTAAATTTTCCAAAAATTAAAATTT
1 ACCCCTAAATTTTCCAAAAATTCAAATTT
346719 GGCCCTGTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
29 7 0.09
30 67 0.87
31 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (30 bp):
ACCCCTAAATTTTCCAAAAATTCAAATTTA
Found at i:347341 original size:47 final size:47
Alignment explanation
Indices: 347272--347366 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
347262 TTTGGGCGTG
347272 TAAGAGTGCTAATCCTTCCTTATCCGTAATCGACTCCCGTACTCGTT
1 TAAGAGTGCTAATCCTTCCTTATCCGTAATCGACTCCCGTACTCGTT
347319 TAAGAGTGCTAATCCTTCCTTATCCGTAATCGACTCCCGTACTCGTT
1 TAAGAGTGCTAATCCTTCCTTATCCGTAATCGACTCCCGTACTCGTT
347366 T
1 T
347367 TATGGTTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (47 bp):
TAAGAGTGCTAATCCTTCCTTATCCGTAATCGACTCCCGTACTCGTT
Found at i:350601 original size:158 final size:158
Alignment explanation
Indices: 350304--350626 Score: 457
Period size: 158 Copynumber: 2.0 Consensus size: 158
350294 TGAGATTTAT
* * * *
350304 AGGTTATATGGGTGCTGGTCTTAGATGTCCTACCGATGGCTGAGATCCAACATTTATTACAAATT
1 AGGTTATAGGGGTGCTGATCTTAGATGTCCTACCAATGGCTAAGATCCAACATTTATTACAAATT
* * * * *
350369 CTCCACAACTTGTGTGAGCAACATCGTGTAGCCTAACAACTAGACCCACAACTCGTGTGAGTAGG
66 CTCCACAACTCGTGTGAGCAACATCGTATAGCCCAACAACTAGACCCACAACTCGTGTGAGCAGA
350434 CCCACTTCACAGCTCGTGTGAGCACTAC
131 CCCACTTCACAGCTCGTGTGAGCACTAC
* **
350462 AGGTTATAGGGGTGCTGATCTTAGATGTCCTACCAATGGTTAAGATCCAACATTTATTACGGATT
1 AGGTTATAGGGGTGCTGATCTTAGATGTCCTACCAATGGCTAAGATCCAACATTTATTACAAATT
* ** * * *
350527 CTCCACAGCTCGTGTGAGCAGTATCGTATAGCCCAACATCTCGACCCACAGCTCGTGTGAGCAGA
66 CTCCACAACTCGTGTGAGCAACATCGTATAGCCCAACAACTAGACCCACAACTCGTGTGAGCAGA
* *
350592 CCCATTTCACAGCTCGTGTGAGCATTAC
131 CCCACTTCACAGCTCGTGTGAGCACTAC
*
350620 ATGTTAT
1 AGGTTAT
350627 GGAGATATTA
Statistics
Matches: 144, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 144 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (158 bp):
AGGTTATAGGGGTGCTGATCTTAGATGTCCTACCAATGGCTAAGATCCAACATTTATTACAAATT
CTCCACAACTCGTGTGAGCAACATCGTATAGCCCAACAACTAGACCCACAACTCGTGTGAGCAGA
CCCACTTCACAGCTCGTGTGAGCACTAC
Found at i:355630 original size:3 final size:3
Alignment explanation
Indices: 355624--355653 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
355614 GATGATGATG
355624 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
355654 TGGATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:356747 original size:43 final size:43
Alignment explanation
Indices: 356686--356771 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
356676 AGGTAAGCAT
356686 GATGTGAGACGATGGTGTGGCTTACTAGTATTCTGGCTCAGGC
1 GATGTGAGACGATGGTGTGGCTTACTAGTATTCTGGCTCAGGC
356729 GATGTGAGACGATGGTGTGGCTTACTAGTATTCTGGCTCAGGC
1 GATGTGAGACGATGGTGTGGCTTACTAGTATTCTGGCTCAGGC
356772 AACCAGGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.19, C:0.16, G:0.35, T:0.30
Consensus pattern (43 bp):
GATGTGAGACGATGGTGTGGCTTACTAGTATTCTGGCTCAGGC
Found at i:359088 original size:23 final size:23
Alignment explanation
Indices: 359023--359093 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
359013 GATTATTTAA
*
359023 TTAAAATTTTTATAGT-TTAATAT
1 TTAAAATTATTATA-TATTAATAT
** * *
359046 TTATTACTATCATA-ACTTAATAT
1 TTAAAATTATTATATA-TTAATAT
*
359069 TTAAAATTATTATATATTAAAAT
1 TTAAAATTATTATATATTAATAT
359092 TT
1 TT
359094 TAGGATTGCT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (23 bp):
TTAAAATTATTATATATTAATAT
Found at i:363085 original size:28 final size:28
Alignment explanation
Indices: 363066--363121 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
363056 AATTGAATCC
363066 TAAAAAATTTAAGTAACAAATTAAAAAA
1 TAAAAAATTTAAGTAACAAATTAAAAAA
**
363094 TATTAAATTTAAGTAACAAATTAAAAAA
1 TAAAAAATTTAAGTAACAAATTAAAAAA
363122 ATGTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (28 bp):
TAAAAAATTTAAGTAACAAATTAAAAAA
Found at i:363130 original size:29 final size:29
Alignment explanation
Indices: 363070--363161 Score: 116
Period size: 29 Copynumber: 3.1 Consensus size: 29
363060 GAATCCTAAA
363070 AAATTTAAGTAACAAATT-AAAAAATATT
1 AAATTTAAGTAACAAATTAAAAAAATATT
*
363098 AAATTTAAGTAACAAATTAAAAAAATGTT
1 AAATTTAAGTAACAAATTAAAAAAATATT
* *
363127 AAATTTAAAT-ACTAAATTAAATAAAAACATT
1 AAATTTAAGTAAC-AAATT-AA-AAAAATATT
363158 AAAT
1 AAAT
363162 ATCAAATTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
28 20 0.36
29 23 0.41
30 2 0.04
31 11 0.20
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (29 bp):
AAATTTAAGTAACAAATTAAAAAAATATT
Found at i:363183 original size:15 final size:14
Alignment explanation
Indices: 363159--363196 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
363149 AAAAACATTA
363159 AATATCAAATTACAT
1 AATATCAAATT-CAT
*
363174 AATATTAAATTCAT
1 AATATCAAATTCAT
363188 -ATATCAAAT
1 AATATCAAAT
363197 GTTGTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.38
14 3 0.14
15 10 0.48
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATCAAATTCAT
Found at i:373994 original size:21 final size:21
Alignment explanation
Indices: 373953--373994 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
373943 GGACAATCCC
* *
373953 CATTTTTTATTCTCATTATTA
1 CATTTTTTATTATCATCATTA
373974 CATTTTGTTATTAT-ATCATTA
1 CATTTT-TTATTATCATCATTA
373995 ATTACATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (21 bp):
CATTTTTTATTATCATCATTA
Found at i:374142 original size:18 final size:17
Alignment explanation
Indices: 374102--374143 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
374092 TCCATGCCAA
374102 AATTTATGAAAAAAATT
1 AATTTATGAAAAAAATT
*
374119 ATATTTATTAAAAAAATTT
1 A-ATTTATGAAAAAAA-TT
374138 AATTTA
1 AATTTA
374144 GTTGATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AATTTATGAAAAAAATT
Found at i:374839 original size:27 final size:24
Alignment explanation
Indices: 374805--374868 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 24
374795 TTACATAAAT
374805 AATTGAGAATTTGGTTCTATAAAAAA
1 AATTGAGAATTTGGTTCT-T-AAAAA
374831 AATATGAG-ATATTGGTTCTTAAAAA
1 AAT-TGAGAAT-TTGGTTCTTAAAAA
374856 AATTGAGAATTTG
1 AATTGAGAATTTG
374869 TAAACATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
24 7 0.20
25 10 0.29
26 6 0.17
27 12 0.34
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (24 bp):
AATTGAGAATTTGGTTCTTAAAAA
Found at i:375446 original size:25 final size:26
Alignment explanation
Indices: 375418--375468 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
375408 CTTAAAATTA
* *
375418 GAGTTTGCTTTTAATAGCAC-GTTTT
1 GAGTCTGCTTCTAATAGCACAGTTTT
375443 GAGTCTGCTTCTAATAGCACAGTTTT
1 GAGTCTGCTTCTAATAGCACAGTTTT
375469 TTTGTTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (26 bp):
GAGTCTGCTTCTAATAGCACAGTTTT
Found at i:376113 original size:23 final size:23
Alignment explanation
Indices: 376083--376126 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
376073 CACGATTGGG
376083 GTATGAAAAATTATCGGTATTAT
1 GTATGAAAAATTATCGGTATTAT
* *
376106 GTATGAAACATTGTCGGTATT
1 GTATGAAAAATTATCGGTATT
376127 CTGTTTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (23 bp):
GTATGAAAAATTATCGGTATTAT
Found at i:376858 original size:27 final size:26
Alignment explanation
Indices: 376828--376890 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
376818 TTATCGAGGA
* *
376828 TATTAGTTTATCGATAAATGAATATTT
1 TATTAATTTATAGATAAATGAATA-TT
*
376855 TATTAATTTATAGATAAATTAATATT
1 TATTAATTTATAGATAAATGAATATT
376881 TATTAATTTA
1 TATTAATTTA
376891 GAGAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (26 bp):
TATTAATTTATAGATAAATGAATATT
Found at i:380641 original size:41 final size:41
Alignment explanation
Indices: 380574--380653 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
380564 ATCTTTCAGT
*
380574 TGATAATGGGATAGCTAGACTGCTCATGGGGGATTTTAAGC
1 TGATAATGGGATAGCTAGACTACTCATGGGGGATTTTAAGC
* *
380615 TGATAATGGGATAGCTTGGCTACTCATGGGGGATTTTAA
1 TGATAATGGGATAGCTAGACTACTCATGGGGGATTTTAA
380654 CGAGATTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.31
Consensus pattern (41 bp):
TGATAATGGGATAGCTAGACTACTCATGGGGGATTTTAAGC
Found at i:381699 original size:46 final size:46
Alignment explanation
Indices: 381648--381791 Score: 225
Period size: 46 Copynumber: 3.1 Consensus size: 46
381638 AAGAGTAATG
* * * *
381648 TCAACGCAAGTTGGTTAAAATTGTACAAATCAAAGAATTAAATCTG
1 TCAACGCAATTTGGTTAAAACTGCACAAATCAAAGAATTAAATCTA
* * *
381694 TCAACGCAATTTGGTTAAAACTACACAAATTAAAGAATTAAATCAA
1 TCAACGCAATTTGGTTAAAACTGCACAAATCAAAGAATTAAATCTA
381740 TCAACGCAATTTGGTTAAAACTGCACAAATCAAAGAATTAAATCTA
1 TCAACGCAATTTGGTTAAAACTGCACAAATCAAAGAATTAAATCTA
381786 TCAACG
1 TCAACG
381792 TAAATATAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (46 bp):
TCAACGCAATTTGGTTAAAACTGCACAAATCAAAGAATTAAATCTA
Found at i:384031 original size:17 final size:17
Alignment explanation
Indices: 383998--384033 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
383988 ATGTGAGAAT
*
383998 AATTAAAATGCAGTGAC
1 AATTAAAATGCAATGAC
*
384015 AATTAAAATGTAATGAC
1 AATTAAAATGCAATGAC
384032 AA
1 AA
384034 CTAGAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (17 bp):
AATTAAAATGCAATGAC
Found at i:386308 original size:24 final size:25
Alignment explanation
Indices: 386263--386317 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
386253 TTATTCCTGT
* *
386263 AAAAATTAAAGAAGCAATTTAA-AA
1 AAAAATAAAAGAAGCAAATTAACAA
*
386287 TAAAATAAAAGACA-CAAATTAACAA
1 AAAAATAAAAGA-AGCAAATTAACAA
386312 AAAAAT
1 AAAAAT
386318 TGCAATGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.69, C:0.07, G:0.05, T:0.18
Consensus pattern (25 bp):
AAAAATAAAAGAAGCAAATTAACAA
Found at i:396904 original size:3 final size:3
Alignment explanation
Indices: 396898--396943 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
396888 ATCATATGCA
396898 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
396944 TTTAAAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:406570 original size:28 final size:28
Alignment explanation
Indices: 406539--406596 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
406529 AGTTTTCCAA
* * *
406539 ATAACGAATAATGCGATAGAGATCGCCG
1 ATAACAAATAATACGATAAAGATCGCCG
406567 ATAACAAATAATACGATAAAGATCGCCG
1 ATAACAAATAATACGATAAAGATCGCCG
406595 AT
1 AT
406597 CCCCTCGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (28 bp):
ATAACAAATAATACGATAAAGATCGCCG
Found at i:406859 original size:43 final size:43
Alignment explanation
Indices: 406793--407040 Score: 218
Period size: 43 Copynumber: 5.7 Consensus size: 43
406783 TTCTGAATCA
* * * *
406793 ATCACATACTATCAATATGAGGAAACAATATTCCATTCATTTG
1 ATCACATACTTTCAATATTAGGAAACAATGTTCCATTCATTCG
* * *
406836 ATCACATACTTTTAATATTAGGAAATAGTGTTCCA--CATAATCG
1 ATCACATACTTTCAATATTAGGAAACAATGTTCCATTCAT--TCG
* * * ** *
406879 ATCACATACTTTCAATATTAGGAAATAGTGTTTCACACAATCG
1 ATCACATACTTTCAATATTAGGAAACAATGTTCCATTCATTCG
* *
406922 ATCACATGA-ATTAAATATTAGGAAACAATGTTCCTATT-ATTCG
1 ATCACAT-ACTTTCAATATTAGGAAACAATGTTCC-ATTCATTCG
* * *
406965 ATCACATGCTTTCAATATTAGGAAATAACGTTCC-TCTCATTCG
1 ATCACATACTTTCAATATTAGGAAACAATGTTCCAT-TCATTCG
* * *
407008 GTCACATACTTACAATATTCAGGAAACAGTGTT
1 ATCACATACTTTCAATATT-AGGAAACAATGTT
407041 TCTCTGAATG
Statistics
Matches: 166, Mismatches: 29, Indels: 19
0.78 0.14 0.09
Matches are distributed among these distances:
41 4 0.02
42 1 0.01
43 147 0.89
44 12 0.07
45 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (43 bp):
ATCACATACTTTCAATATTAGGAAACAATGTTCCATTCATTCG
Found at i:406895 original size:86 final size:86
Alignment explanation
Indices: 406788--407040 Score: 253
Period size: 86 Copynumber: 2.9 Consensus size: 86
406778 TCATGTTCTG
* * * * * * *
406788 AATCAATCACATACTATCAATATGAGGAAACAATATTCCATTCATTTGATCACATACTTTTAATA
1 AATCGATCACATACTTTCAATATTAGGAAATAATGTTCCATTCATTCGATCACATACTTTAAATA
*
406853 TTAGGAAATAGTGTTCC-ACAT
66 TTAGGAAACAGTGTTCCTA-AT
* * ** * *
406874 AATCGATCACATACTTTCAATATTAGGAAATAGTGTTTCACACAATCGATCACATGA-ATTAAAT
1 AATCGATCACATACTTTCAATATTAGGAAATAATGTTCCATTCATTCGATCACAT-ACTTTAAAT
* *
406938 ATTAGGAAACAATGTTCCTATT
65 ATTAGGAAACAGTGTTCCTAAT
* * * *
406960 ATTCGATCACATGCTTTCAATATTAGGAAATAACGTTCC-TCTCATTCGGTCACATAC-TTACAA
1 AATCGATCACATACTTTCAATATTAGGAAATAATGTTCCAT-TCATTCGATCACATACTTTA-AA
407023 TATTCAGGAAACAGTGTT
64 TATT-AGGAAACAGTGTT
407041 TCTCTGAATG
Statistics
Matches: 135, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
85 4 0.03
86 117 0.87
87 14 0.10
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.33
Consensus pattern (86 bp):
AATCGATCACATACTTTCAATATTAGGAAATAATGTTCCATTCATTCGATCACATACTTTAAATA
TTAGGAAACAGTGTTCCTAAT
Found at i:407024 original size:129 final size:130
Alignment explanation
Indices: 406806--407042 Score: 327
Period size: 129 Copynumber: 1.8 Consensus size: 130
406796 ACATACTATC
* * **
406806 AATATGAGGAAACAATATTCCATTCATTTGATCACATACTTTTAATATTAGGAAATAGTGTTCCA
1 AATATGAGGAAACAATATTCCATTCATTCGATCACATACTTTCAATATTAGGAAATAACGTTCCA
* *
406871 CATAATCGATCACATACTTTCAATATT-AGGAAATAGTGTTTCACACAATCGATCACATGAATTA
66 CATAATCGATCACATACTTACAATATTCAGGAAACAGTGTTTCACACAATCGATCACATGAATTA
* * *
406935 AATATTAGGAAACAATGTTCCTATT-ATTCGATCACATGCTTTCAATATTAGGAAATAACGTTCC
1 AATATGAGGAAACAATATTCC-ATTCATTCGATCACATACTTTCAATATTAGGAAATAACGTTCC
* * *
406999 TC-TCATTCGGTCACATACTTACAATATTCAGGAAACAGTGTTTC
65 ACAT-AATCGATCACATACTTACAATATTCAGGAAACAGTGTTTC
407043 TCTGAATGTC
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
128 1 0.01
129 75 0.81
130 17 0.18
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (130 bp):
AATATGAGGAAACAATATTCCATTCATTCGATCACATACTTTCAATATTAGGAAATAACGTTCCA
CATAATCGATCACATACTTACAATATTCAGGAAACAGTGTTTCACACAATCGATCACATGAATTA
Found at i:416540 original size:18 final size:18
Alignment explanation
Indices: 416500--416541 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
416490 TTATAGCAAA
416500 CATTTT-TTTCTTCTTTT
1 CATTTTCTTTCTTCTTTT
*
416517 CTTTTTCTTTCTT-TTTCT
1 CATTTTCTTTCTTCTTT-T
416535 CATTTTC
1 CATTTTC
416542 CTTTTTCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (18 bp):
CATTTTCTTTCTTCTTTT
Found at i:421615 original size:20 final size:18
Alignment explanation
Indices: 421582--421619 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
421572 CAATTCAAAT
421582 TTTACTTTTTTTTTTATG
1 TTTACTTTTTTTTTTATG
421600 TTTATCTTTTTATTTTTATG
1 TTTA-CTTTTT-TTTTTATG
421620 CTTTCAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTACTTTTTTTTTTATG
Found at i:426069 original size:16 final size:17
Alignment explanation
Indices: 426036--426069 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
426026 ATGAGTTAGA
*
426036 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
426053 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
426069 A
1 A
426070 GAATTTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:429257 original size:114 final size:114
Alignment explanation
Indices: 429057--429284 Score: 456
Period size: 114 Copynumber: 2.0 Consensus size: 114
429047 CCCGGTAACA
429057 GCGCCAACAACTTGACCGCTCCTGAATGTACTCTAATTCGATGTAAATTTTTGTTTTTGCAAGTA
1 GCGCCAACAACTTGACCGCTCCTGAATGTACTCTAATTCGATGTAAATTTTTGTTTTTGCAAGTA
429122 TACGGTCCAGGTTGTAAATATAGTGTGTTTACAATGGAACACTTATAAG
66 TACGGTCCAGGTTGTAAATATAGTGTGTTTACAATGGAACACTTATAAG
429171 GCGCCAACAACTTGACCGCTCCTGAATGTACTCTAATTCGATGTAAATTTTTGTTTTTGCAAGTA
1 GCGCCAACAACTTGACCGCTCCTGAATGTACTCTAATTCGATGTAAATTTTTGTTTTTGCAAGTA
429236 TACGGTCCAGGTTGTAAATATAGTGTGTTTACAATGGAACACTTATAAG
66 TACGGTCCAGGTTGTAAATATAGTGTGTTTACAATGGAACACTTATAAG
429285 TATTCCAAGG
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (114 bp):
GCGCCAACAACTTGACCGCTCCTGAATGTACTCTAATTCGATGTAAATTTTTGTTTTTGCAAGTA
TACGGTCCAGGTTGTAAATATAGTGTGTTTACAATGGAACACTTATAAG
Found at i:430792 original size:11 final size:11
Alignment explanation
Indices: 430776--430813 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
430766 AAATCTAGCT
430776 AAATATTATGA
1 AAATATTATGA
430787 AAATATT-TCGA
1 AAATATTAT-GA
*
430798 AAATATTACGA
1 AAATATTATGA
430809 AAATA
1 AAATA
430814 CTTGATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.04
11 23 0.96
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (11 bp):
AAATATTATGA
Found at i:430939 original size:43 final size:43
Alignment explanation
Indices: 430892--431122 Score: 263
Period size: 43 Copynumber: 5.3 Consensus size: 43
430882 CATCAATGTG
*
430892 AGGAAACAATGTTCCATTCTTTCGATCACATACTTTCAATATT
1 AGGAAACAATGTTCCATTCATTCGATCACATACTTTCAATATT
* ** * *
430935 AGGAAACATTGTTCCACACAATCGAGCACATACTTTCAATATT
1 AGGAAACAATGTTCCATTCATTCGATCACATACTTTCAATATT
* * *
430978 AGGAAATAGTGTTCCATAT-AATCGATCACATACTTTCAATATT
1 AGGAAACAATGTTCCAT-TCATTCGATCACATACTTTCAATATT
* * *
431021 AGGAAACAATTTTCC-TCTTATTCGATCACATAATTTCAATATT
1 AGGAAACAATGTTCCAT-TCATTCGATCACATACTTTCAATATT
* *
431064 AGGAAACAATGTTCC-TCTCATTCGGTCACATACTTAT-ATTATTT
1 AGGAAACAATGTTCCAT-TCATTCGATCACATACTT-TCAATA-TT
431108 AGGAAACAATGTTCC
1 AGGAAACAATGTTCC
431123 TCCCAATGTC
Statistics
Matches: 162, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
42 2 0.01
43 142 0.88
44 18 0.11
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (43 bp):
AGGAAACAATGTTCCATTCATTCGATCACATACTTTCAATATT
Found at i:436980 original size:24 final size:25
Alignment explanation
Indices: 436948--437012 Score: 96
Period size: 24 Copynumber: 2.6 Consensus size: 25
436938 ACTCTGTCTG
*
436948 GGCTCGTAAGAGCTAACTTTATC-T
1 GGCTCGTAAGAGCTAACCTTATCTT
*
436972 GGCTTGTAAGAGCTAACCTTATCTT
1 GGCTCGTAAGAGCTAACCTTATCTT
*
436997 GGCTCGTATGAGCTAA
1 GGCTCGTAAGAGCTAA
437013 ATTCTAGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 21 0.58
25 15 0.42
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (25 bp):
GGCTCGTAAGAGCTAACCTTATCTT
Found at i:439484 original size:32 final size:32
Alignment explanation
Indices: 439448--439515 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
439438 ATATATATTA
439448 ACTTAAACTAAACTCATTCCCATTACCTAAGC
1 ACTTAAACTAAACTCATTCCCATTACCTAAGC
439480 ACTTAAACTAAACTCATTCCCATTACCTAAGC
1 ACTTAAACTAAACTCATTCCCATTACCTAAGC
439512 ACTT
1 ACTT
439516 CAAAATTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (32 bp):
ACTTAAACTAAACTCATTCCCATTACCTAAGC
Found at i:451858 original size:21 final size:21
Alignment explanation
Indices: 451825--451864 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
451815 TTCCTCCTTC
* *
451825 GCTTGCTCATCTACTTGATTG
1 GCTTCCTCATCTACATGATTG
*
451846 GCTTCCTCTTCTACATGAT
1 GCTTCCTCATCTACATGAT
451865 GTTCACCCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (21 bp):
GCTTCCTCATCTACATGATTG
Found at i:453278 original size:11 final size:12
Alignment explanation
Indices: 453249--453275 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
453239 GAGATGAAGG
453249 TTTTGGAGTGTT
1 TTTTGGAGTGTT
453261 TTTTGGAGTGTT
1 TTTTGGAGTGTT
453273 TTT
1 TTT
453276 GGATGCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (12 bp):
TTTTGGAGTGTT
Found at i:462869 original size:67 final size:67
Alignment explanation
Indices: 462761--462894 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
462751 AATGCTAAAA
* *
462761 ATGTATGATAAAGATGACCAAATGGGAACAACTTAAACAATAAGTAGGGAGAAATCAATGGTTTT
1 ATGTATGATAAAGATAACCAAATGGGAACAACTTAAACAATAAGTAAGGAGAAATCAATGGTTTT
462826 TT
66 TT
*
462828 ATGTATGCTAAAGATAACCAAATGGGAACAACTTAAACAATAAGTAAGGAGAAATCAATGGTTTT
1 ATGTATGATAAAGATAACCAAATGGGAACAACTTAAACAATAAGTAAGGAGAAATCAATGGTTTT
462893 TT
66 TT
462895 CTAGTACTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (67 bp):
ATGTATGATAAAGATAACCAAATGGGAACAACTTAAACAATAAGTAAGGAGAAATCAATGGTTTT
TT
Found at i:470275 original size:20 final size:19
Alignment explanation
Indices: 470252--470297 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
470242 TTTATCCATC
*
470252 TTTATTTTTATTTTAATATT
1 TTTATTTTTAATTTAAT-TT
470272 TTTATTTTTAATTTAATTT
1 TTTATTTTTAATTTAATTT
470291 TTCTATT
1 TT-TATT
470298 ATAATTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTTTAATTTAATTT
Found at i:473039 original size:9 final size:9
Alignment explanation
Indices: 473025--473067 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
473015 TTATTTTTAA
473025 AAAAAATTC
1 AAAAAATTC
*
473034 AAAAAAATTA
1 -AAAAAATTC
473044 AAAAAATTTC
1 AAAAAA-TTC
473054 -AAAAATTC
1 AAAAAATTC
473062 AAAAAA
1 AAAAAA
473068 AATAGTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 3 0.10
9 16 0.55
10 10 0.34
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAAATTC
Found at i:473039 original size:10 final size:10
Alignment explanation
Indices: 473024--473068 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
473014 GTTATTTTTA
473024 AAAAAAATTC
1 AAAAAAATTC
473034 AAAAAAATT-
1 AAAAAAATTC
473043 AAAAAAATTTC
1 AAAAAAA-TTC
473054 --AAAAATTC
1 AAAAAAATTC
473062 AAAAAAA
1 AAAAAAA
473069 ATAGTACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.10
9 12 0.39
10 16 0.52
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:475071 original size:30 final size:30
Alignment explanation
Indices: 475036--475096 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
475026 CAGATTTTAA
* *
475036 GAGCCACACGGGTTGGACACACGGTCATGT
1 GAGCCACACAGGTTGGACACACGGCCATGT
*
475066 GAGCCACACAGGTTGGGCACACGGCCATGT
1 GAGCCACACAGGTTGGACACACGGCCATGT
475096 G
1 G
475097 CCAGACCATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15
Consensus pattern (30 bp):
GAGCCACACAGGTTGGACACACGGCCATGT
Found at i:477640 original size:151 final size:149
Alignment explanation
Indices: 477319--477885 Score: 663
Period size: 154 Copynumber: 3.7 Consensus size: 149
477309 AGAAAGGGGG
* * * * *
477319 AAAGAGAGTTAAATTTTTTTATTGTTTTTAATTTATTTTAAAATTATTTTGTTTTTAATTTAATT
1 AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTG---TT-A-GTAATT
* *
477384 ATTATAAACT-TTAGTTTAGTTTAATGTT-TATAAT-T--TTTTTGTAATAATTTTTTTTTTGTT
61 ATTATAAATTATTTGTTTAGTTTAATGTTGT-TAATGTGATTTTT-T-ATAA--TTTTTTTTGTT
*
477444 TAGTAGAGTAGATTAAAGGGGAAAAAGGTCA
121 TAGTAGAGTAGATTAAA-GAGAAAAA-GTCA
* * *
477475 AAAGAGATGT-ATTTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATATTGTTAGTAATTATTAT
1 AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
* *
477539 AAATTATTTGTTTAGTTTAATGTTGGTTCATGTGATTTTTTATAATTTTTTTTGTTTAGTAAAGT
66 AAATTATTTGTTTAGTTTAATGTT-GTTAATGTGATTTTTTATAATTTTTTTTGTTTAGTAGAGT
477604 AGATTAAAGAGAAGAAAGTCA
130 AGATTAAAGAGAA-AAAGTCA
*
477625 AAAGAGAGGT-AATTTTTTTGTTTTTTTTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTA
1 AAAGAGAGGTAAATTTTTTTG----TTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTA
*
477689 TTATAAATTATTTGTTTAGTTTAATGTTAGTTTATGTGATTTTTTATAATTTTTTTTGTTTAGTA
62 TTATAAATTATTTGTTTAGTTTAATGTT-GTTAATGTGATTTTTTATAATTTTTTTTGTTTAGTA
477754 GAGTAGATTAAA-AGGAAAAAAGAT-A
126 GAGTAGATTAAAGA-G-AAAAAG-TCA
* * *
477779 AAAGAAAGGTAAATTGTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATGATTAT
1 AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
* *
477844 AAATTATTTGTTTCGTTTAAT-TT-TT-ATTTGATTTTTTTATAA
66 AAATTATTTGTTTAGTTTAATGTTGTTAATGTGA-TTTTTTATAA
477886 ATGTAAAATT
Statistics
Matches: 369, Mismatches: 26, Indels: 40
0.85 0.06 0.09
Matches are distributed among these distances:
147 5 0.01
148 12 0.03
150 42 0.11
151 110 0.30
152 5 0.01
153 7 0.02
154 128 0.35
155 52 0.14
156 8 0.02
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (149 bp):
AAAGAGAGGTAAATTTTTTTGTTGTTTTTAATTTAATTTAAAGTTATTTTGTTAGTAATTATTAT
AAATTATTTGTTTAGTTTAATGTTGTTAATGTGATTTTTTATAATTTTTTTTGTTTAGTAGAGTA
GATTAAAGAGAAAAAGTCA
Done.