Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012586.1 Kokia drynarioides strain JFW-HI SEQ_127595, 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: 234085
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:11983 original size:17 final size:17
Alignment explanation
Indices: 11961--11996 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11951 AAATTTTATA
*
11961 TATATTATTTTTTATTT
1 TATATTATTTTTTACTT
*
11978 TATATTGTTTTTTACTT
1 TATATTATTTTTTACTT
11995 TA
1 TA
11997 CTTATTTTAT
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:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (17 bp):
TATATTATTTTTTACTT
Found at i:12715 original size:6 final size:6
Alignment explanation
Indices: 12704--12730 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12694 CAGAATTAAA
12704 TAGCCT TAGCCT TAGCCT TAGCCT TAG
1 TAGCCT TAGCCT TAGCCT TAGCCT TAG
12731 TCTCGATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (6 bp):
TAGCCT
Found at i:14017 original size:20 final size:19
Alignment explanation
Indices: 13981--14018 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13971 TGATAGTTTA
*
13981 ATTTTTTAATTTAATCAAT
1 ATTTTTTAATATAATCAAT
14000 ATTTTTTAATATATATCAA
1 ATTTTTTAATATA-ATCAA
14019 ACAGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTTAATATAATCAAT
Found at i:17570 original size:12 final size:11
Alignment explanation
Indices: 17548--17578 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
17538 TATTCAAAAT
17548 TATTTTTTTCG
1 TATTTTTTTCG
17559 TATTTTTATTCG
1 TATTTTT-TTCG
17571 TATTTTTT
1 TATTTTTT
17579 GGGTGTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.13, C:0.06, G:0.06, T:0.74
Consensus pattern (11 bp):
TATTTTTTTCG
Found at i:25130 original size:22 final size:21
Alignment explanation
Indices: 25105--25153 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
25095 TGTGAAAAAA
*
25105 TTAATTA-GTTTATTTATATATT
1 TTAATTATCTTTATTTAT-TA-T
*
25127 TTAAATATCTTTATTTATTAT
1 TTAATTATCTTTATTTATTAT
25148 TTAATT
1 TTAATT
25154 TATACATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.26
22 8 0.35
23 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (21 bp):
TTAATTATCTTTATTTATTAT
Found at i:33460 original size:6 final size:6
Alignment explanation
Indices: 33449--33478 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
33439 CTAAAACAAC
33449 TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA
1 TCCTAA TCCTAA TCCTAA TCCTAA TCCTAA
33479 CGCCTATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
TCCTAA
Found at i:37867 original size:111 final size:112
Alignment explanation
Indices: 37719--37924 Score: 360
Period size: 111 Copynumber: 1.8 Consensus size: 112
37709 GTGATGGATG
*
37719 GTGGATCGAAGTAGGCCGTTAGTCCTTGTATCTTTACAGAAAATGAAATTTA-ATTTTTATATTT
1 GTGGATCAAAGTAGGCCGTTAGTCCTTGTATCTTTACAGAAAATGAAATTTAGATTTTTATATTT
37783 TAAAAGAAAAATTATTAGGTGAACCTTTTAGAGGTATGGGAATTGTA
66 TAAAAGAAAAATTATTAGGTGAACCTTTTAGAGGTATGGGAATTGTA
* *
37830 GTGGATCAAAGTGGGCCGTTAGTCCTTGTATCTTTACAGAAAATGAAATTTAGTTTTTTATATTT
1 GTGGATCAAAGTAGGCCGTTAGTCCTTGTATCTTTACAGAAAATGAAATTTAGATTTTTATATTT
* *
37895 TAAAAGAAAATTTATTAGGTGAACTTTTTA
66 TAAAAGAAAAATTATTAGGTGAACCTTTTA
37925 CACCGATAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 50 0.56
112 39 0.44
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (112 bp):
GTGGATCAAAGTAGGCCGTTAGTCCTTGTATCTTTACAGAAAATGAAATTTAGATTTTTATATTT
TAAAAGAAAAATTATTAGGTGAACCTTTTAGAGGTATGGGAATTGTA
Found at i:39177 original size:18 final size:17
Alignment explanation
Indices: 39154--39214 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
39144 TTTTAAAATA
39154 ATTTTTATAATTATATAT
1 ATTTTTATAATT-TATAT
*
39172 ATTTTTATAATTTTCTATT
1 ATTTTTATAA-TTTATA-T
* *
39191 ATTTTTTTACATTTTTAT
1 ATTTTTATA-ATTTATAT
39209 ATTTTT
1 ATTTTT
39215 GTATGATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 20 0.54
19 16 0.43
20 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTATAATTTATAT
Found at i:46532 original size:31 final size:29
Alignment explanation
Indices: 46488--46563 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
46478 TTTAGGAGTT
46488 AATTTAAATAAAAATTACTATCAAAATCAA
1 AATTTAAATAAAAATTACTAT-AAAATCAA
*
46518 AATTTAATATAAAAATTACTATAAATTCAA
1 AATTTAA-ATAAAAATTACTATAAAATCAA
* * *
46548 ACTCTAAATAATAATT
1 AATTTAAATAAAAATT
46564 TAAGCTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 8 0.20
30 19 0.46
31 14 0.34
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (29 bp):
AATTTAAATAAAAATTACTATAAAATCAA
Found at i:52177 original size:45 final size:45
Alignment explanation
Indices: 52110--52470 Score: 467
Period size: 45 Copynumber: 8.0 Consensus size: 45
52100 CCAAGTTCTA
* * * *
52110 CGGATCCAAGCTCTAGACCTGCTTCCATCGATCCTAATTATAGAG
1 CGGATCCGAGCTCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
* * * *
52155 CGGATCCAAGCTCCAGATCTGCTTCCATTGATCCCAACTATAGAG
1 CGGATCCGAGCTCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
* *
52200 TGGATCCGAGCTCTAGAGCTGCTCCCATTGATCCCAATTATAGAG
1 CGGATCCGAGCTCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
* * *
52245 TGGATCCGAGCTCTAGAGCTGCTCCCATTGATCCCAATTATAGTG
1 CGGATCCGAGCTCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
* * * *
52290 TGGATCCGAGCTCTAGAGTTGCTTCCATTGATCCTAATTACAGAG
1 CGGATCCGAGCTCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
* *
52335 CGGATCCGAGCGT-TAGAACTGCTTCCATTGAGCCCAATTATAGAG
1 CGGATCCGAGC-TCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
* *
52380 CGGATCCGAGCGCTAGAGCTGCTTCCATTGAGCCCAATTATAGAG
1 CGGATCCGAGCTCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
* *
52425 CGGATCCTG-GCGCTAGAGGTGC-TCCGATTGATCCCAATTATAGAG
1 CGGATCC-GAGCTCTAGAGCTGCTTCC-ATTGATCCCAATTATAGAG
52470 C
1 C
52471 TGCACCAGAG
Statistics
Matches: 285, Mismatches: 27, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
44 3 0.01
45 280 0.98
46 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (45 bp):
CGGATCCGAGCTCTAGAGCTGCTTCCATTGATCCCAATTATAGAG
Found at i:55703 original size:136 final size:136
Alignment explanation
Indices: 55456--55727 Score: 499
Period size: 136 Copynumber: 2.0 Consensus size: 136
55446 CATCTATATT
*
55456 GCATGTTGAAGTTACAACTTTATTCTCATATATGTTCTTTTAAAGTCATTAATCAGATTTTGGCT
1 GCATGTTGAAGTAACAACTTTATTCTCATATATGTTCTTTTAAAGTCATTAATCAGATTTTGGCT
55521 AGTTTACCAGTTTGCTGCAGAAAAATCTGATCACTTCATGTCGATCGTTATTACTGTAACTCTGC
66 AGTTTACCAGTTTGCTGCAGAAAAATCTGATCACTTCATGTCGATCGTTATTACTGTAACTCTGC
55586 ATGAAA
131 ATGAAA
*
55592 GCATGTTGAAGTAACAGCTTTATTCTCATATATGTTCTTTTAAAGTCATTAATCAGATTTTGGCT
1 GCATGTTGAAGTAACAACTTTATTCTCATATATGTTCTTTTAAAGTCATTAATCAGATTTTGGCT
* * *
55657 AGTTTACCAGTTTGCTGCAGAAAAATCTGATCACTTTATGTGGATCGTTATTAGTGTAACTCTGC
66 AGTTTACCAGTTTGCTGCAGAAAAATCTGATCACTTCATGTCGATCGTTATTACTGTAACTCTGC
55722 ATGAAA
131 ATGAAA
55728 AATAGTAGTA
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 131 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (136 bp):
GCATGTTGAAGTAACAACTTTATTCTCATATATGTTCTTTTAAAGTCATTAATCAGATTTTGGCT
AGTTTACCAGTTTGCTGCAGAAAAATCTGATCACTTCATGTCGATCGTTATTACTGTAACTCTGC
ATGAAA
Found at i:62351 original size:14 final size:14
Alignment explanation
Indices: 62332--62360 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62322 TCCCATGATT
62332 TCAATGAAATGTGA
1 TCAATGAAATGTGA
62346 TCAATGAAATGTGA
1 TCAATGAAATGTGA
62360 T
1 T
62361 TGTTGAGAAA
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:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (14 bp):
TCAATGAAATGTGA
Found at i:64940 original size:3 final size:3
Alignment explanation
Indices: 64932--64960 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
64922 CTTAATTGAT
64932 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
64961 TTTAACCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:66535 original size:3 final size:3
Alignment explanation
Indices: 66527--66557 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
66517 TAGATATTAG
66527 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
66558 TGCATAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:67722 original size:2 final size:2
Alignment explanation
Indices: 67715--67739 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67705 AAAATAATAA
67715 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
67740 CAATAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68709 original size:55 final size:55
Alignment explanation
Indices: 68597--68709 Score: 138
Period size: 55 Copynumber: 2.1 Consensus size: 55
68587 TACGAGATTT
* * *
68597 AAAAAAATTTGGTGTTGACCAATGCATGACCGACATCACCTTTTTTGTCAGAGAA
1 AAAAAAAATTGGTGTTGACCAATGCATGACCGACACCACCTTTTTTATCAGAGAA
* ** * *
68652 AAAAAAAATTGGTGTTGA-CTATGCATTGGTCGACACCACCTTTTTTATCTGATAA
1 AAAAAAAATTGGTGTTGACCAATGCA-TGACCGACACCACCTTTTTTATCAGAGAA
68707 AAA
1 AAA
68710 TATTTTTTAG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 6 0.12
55 43 0.88
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (55 bp):
AAAAAAAATTGGTGTTGACCAATGCATGACCGACACCACCTTTTTTATCAGAGAA
Found at i:69435 original size:26 final size:26
Alignment explanation
Indices: 69399--69471 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
69389 CGAAGTACTT
69399 AACAGTAAGCACACAAGTGCTTGGGA
1 AACAGTAAGCACACAAGTGCTTGGGA
69425 AACAGTAAGCACACAAGTGCTTGGGA
1 AACAGTAAGCACACAAGTGCTTGGGA
69451 AACAGTAAGCACACATAGTGC
1 AACAGTAAGCACACA-AGTGC
69472 AATCCAGTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 41 0.89
27 5 0.11
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.15
Consensus pattern (26 bp):
AACAGTAAGCACACAAGTGCTTGGGA
Found at i:69485 original size:23 final size:22
Alignment explanation
Indices: 69453--69531 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
69443 GCTTGGGAAA
*
69453 CAGTAAGCACACATAGTGCAAT
1 CAGTAGGCACACATAGTGCAAT
*
69475 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACATAGTGCAAT
* * *
69498 CAGTAGACGCACATAGCGCAAAT
1 CAGTAGGCACACATAGTGC-AAT
69521 CAGTAGGCACA
1 CAGTAGGCACA
69532 TAAGGTGCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 15 0.32
23 32 0.68
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACATAGTGCAAT
Found at i:74757 original size:23 final size:22
Alignment explanation
Indices: 74729--74850 Score: 129
Period size: 23 Copynumber: 5.4 Consensus size: 22
74719 CTAGCACGCT
* *
74729 TACTGTTTAGCACTGTGTGTACT
1 TACTGTTT-GCACTGTGTGTGCC
74752 TACTGTTTCGCACT-TCGTGTGCC
1 TACTGTTT-GCACTGT-GTGTGCC
* *
74775 TACTGATTTGCACTATGTGCGCC
1 TACTG-TTTGCACTGTGTGTGCC
*
74798 TACTGATTGCACTGTGTGTGCC
1 TACTGTTTGCACTGTGTGTGCC
* *
74820 TACTGGATTGCACTGTGTGTGCT
1 TACT-GTTTGCACTGTGTGTGCC
74843 TACTGTTT
1 TACTGTTT
74851 CCCCAGCATT
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
22 22 0.26
23 60 0.70
24 4 0.05
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (22 bp):
TACTGTTTGCACTGTGTGTGCC
Found at i:75624 original size:59 final size:56
Alignment explanation
Indices: 75527--75908 Score: 245
Period size: 58 Copynumber: 6.5 Consensus size: 56
75517 GAAAAGAGGG
* * * * *
75527 AAAGTTGGTGTCGATCAATGCAGGGCCAATACAAAAAAATTCATTTTTTATCAGATAAA
1 AAAGGTGGTGTCG-CCAA-GCATGGCCAACACAAAAAAAAT-ATTTTTTATCAGATAAA
* * * * * *
75586 AAAGGTGGTGTCAGCCAAACATTGGTCAATACCAAAAAAATA-TTTTTATCTGGTAAAA
1 AAAGGTGGTGTC-GCCAAGCA-TGGCCAACACAAAAAAAATATTTTTTATCAGAT-AAA
* * * * * *
75644 AAATGTTGGTGTCGGCCAATGCATGGCCAACGC---CAAATTTTTTTTTAATTAGAT-AA
1 AAA-GGTGGTGTC-GCCAA-GCATGGCCAACACAAAAAAAATATTTTTT-ATCAGATAAA
* * * *
75700 AAAGGTGGTGTCGACCAAGCAATGGCCAACACAAAAAAATTTGAATATTTTGTCAAATAAA
1 AAAGGTGGTGTCG-CCAAGC-ATGGCCAACACAAAAAAA-AT--ATTTTTTATCAGATAAA
* * *
75761 AAATGTGATGTCGACCAAGCAATGACCAACACAAAAAAAATCATTTTTTATCAGAT-AA
1 AAAGGTGGTGTCG-CCAAGC-ATGGCCAACACAAAAAAAAT-ATTTTTTATCAGATAAA
* ** * *
75819 AAATGTGGTAACAGCCAATGCATGGTCAATACAAAAAAAATATTTTTTATCAGATAAA
1 AAAGGTGGTGTC-GCCAA-GCATGGCCAACACAAAAAAAATATTTTTTATCAGATAAA
* *
75877 AAAAGTGGTGTCGACCAATGCATAGCCAACAC
1 AAAGGTGGTGTCG-CCAA-GCATGGCCAACAC
75909 CAAATATTTT
Statistics
Matches: 254, Mismatches: 49, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
54 3 0.01
55 22 0.09
56 9 0.04
57 30 0.12
58 74 0.29
59 65 0.26
60 8 0.03
61 43 0.17
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (56 bp):
AAAGGTGGTGTCGCCAAGCATGGCCAACACAAAAAAAATATTTTTTATCAGATAAA
Found at i:75951 original size:57 final size:54
Alignment explanation
Indices: 75856--75978 Score: 156
Period size: 57 Copynumber: 2.2 Consensus size: 54
75846 AATACAAAAA
* *
75856 AAATATTTTTTATCAGATAAAAAAAGTGGTGTCGACCAATGCATAGCCAACACC
1 AAATATTTTTTCTCAGATAAAAAAACTGGTGTCGACCAATGCATAGCCAACACC
* * * *
75910 AAATATTTTTTCTCCTGATAAAAGAATACTGGTGTTGACCAATGCATGGCCAACTCC
1 AAATATTTTTTCT-CAGATAAAA-AA-ACTGGTGTCGACCAATGCATAGCCAACACC
*
75967 AAATTTTTTTTC
1 AAATATTTTTTC
75979 AAAATCTCGT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
54 12 0.20
55 8 0.14
56 2 0.03
57 37 0.63
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (54 bp):
AAATATTTTTTCTCAGATAAAAAAACTGGTGTCGACCAATGCATAGCCAACACC
Found at i:77129 original size:10 final size:11
Alignment explanation
Indices: 77112--77137 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
77102 TCAATAACAA
77112 TAAAAAAATAT
1 TAAAAAAATAT
77123 TAAAAAAATAT
1 TAAAAAAATAT
77134 TAAA
1 TAAA
77138 CTATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAAAATAT
Found at i:105789 original size:2 final size:2
Alignment explanation
Indices: 105782--105809 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
105772 CATGGGGGTT
105782 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
105810 AGGGGAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:108445 original size:206 final size:206
Alignment explanation
Indices: 108091--108506 Score: 778
Period size: 206 Copynumber: 2.0 Consensus size: 206
108081 AACGTTATTG
108091 TTTCAAGCTGATGACCCCGACAAGCTTCTGATATTGAGAAATGTAAATTACCTCTGCATTCTCTT
1 TTTCAAGCTGATGACCCCGACAAGCTTCTGATATTGAGAAATGTAAATTACCTCTGCATTCTCTT
108156 TTTGGAAAGTTATCCTCACATTGAGGTTTATTTGGTACTGAATGAGACCACTATTGAAAAGGCTA
66 TTTGGAAAGTTATCCTCACATTGAGGTTTATTTGGTACTGAATGAGACCACTATTGAAAAGGCTA
*
108221 CACCCTTTTTACCTGTGAAAGCTCGGACCTGTTTAGGAATGAAGTTTGGTTCGGCCAGAACCGGA
131 CACCCTTTTTACCTGTGAAAGCTCGGACCTGTTTAGGAATGAAGTTTGGTTCGGCCAGAACCAGA
108286 ATACCGGCCTT
196 ATACCGGCCTT
*
108297 TTTCAAGCTGATGACCCCGACAAGCTTCTGATATTGAGAAATGTAAATTATCTCTGCATTCTCTT
1 TTTCAAGCTGATGACCCCGACAAGCTTCTGATATTGAGAAATGTAAATTACCTCTGCATTCTCTT
108362 TTTGGAAAGTTATCCTCACATTGAGGTTTATTTGGTACTGAATGAGACCACTATTGAAAAGGCTA
66 TTTGGAAAGTTATCCTCACATTGAGGTTTATTTGGTACTGAATGAGACCACTATTGAAAAGGCTA
* * *
108427 CTCCTTTTTTACCTGTGAAAGCTCGGACCTGTTTAGGAATGAAGTTTGGTTCGGCCAGAACCAGC
131 CACCCTTTTTACCTGTGAAAGCTCGGACCTGTTTAGGAATGAAGTTTGGTTCGGCCAGAACCAGA
*
108492 GTACCGGCCTT
196 ATACCGGCCTT
108503 TTTC
1 TTTC
108507 TATTAGATTT
Statistics
Matches: 204, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
206 204 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (206 bp):
TTTCAAGCTGATGACCCCGACAAGCTTCTGATATTGAGAAATGTAAATTACCTCTGCATTCTCTT
TTTGGAAAGTTATCCTCACATTGAGGTTTATTTGGTACTGAATGAGACCACTATTGAAAAGGCTA
CACCCTTTTTACCTGTGAAAGCTCGGACCTGTTTAGGAATGAAGTTTGGTTCGGCCAGAACCAGA
ATACCGGCCTT
Found at i:121700 original size:50 final size:50
Alignment explanation
Indices: 121643--121745 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
121633 AAAAAAAATC
*
121643 ATAAATGATGTGATTGAATAATTCATAAAATAATTTCTCCTAATTATGAG
1 ATAAATGATGTGATTGAATAATTCATAAAATAAATTCTCCTAATTATGAG
*
121693 ATAAATGATGTGATTGAATAATTCATGAAATAAATTCTCCTAATTATGAG
1 ATAAATGATGTGATTGAATAATTCATAAAATAAATTCTCCTAATTATGAG
121743 ATA
1 ATA
121746 TGGTGTAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.37
Consensus pattern (50 bp):
ATAAATGATGTGATTGAATAATTCATAAAATAAATTCTCCTAATTATGAG
Found at i:129937 original size:23 final size:23
Alignment explanation
Indices: 129889--130014 Score: 114
Period size: 23 Copynumber: 5.5 Consensus size: 23
129879 TATACGGAAC
* * *
129889 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
129911 -AACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* * * *
129933 AAACAGAGAGTATACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
129956 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
129979 AATAATAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
130004 AAACAGAGAGC
1 AAACAGAGAGC
130015 GCTAGTGTTC
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
21 11 0.13
22 7 0.08
23 45 0.54
24 2 0.02
25 15 0.18
26 3 0.04
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:129976 original size:46 final size:44
Alignment explanation
Indices: 129889--129980 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 44
129879 TATACGGAAC
*
129889 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGTAACAAAGTACTAACAGAGAGCACACACAGTGCT
129933 AAACAGAGAGTATACAAAGTACTAATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGTA-ACAAAGTACTAA-CAGAGAGCACACACAGTGCT
129979 AA
1 AA
129981 TAATAGAGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 12 0.27
45 11 0.24
46 22 0.49
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (44 bp):
AAACAGAGAGTAACAAAGTACTAACAGAGAGCACACACAGTGCT
Found at i:135345 original size:18 final size:17
Alignment explanation
Indices: 135316--135349 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
135306 CCAACTTCTA
135316 TTAAATTATAATTATTT
1 TTAAATTATAATTATTT
135333 TTAAATGTATAATTATT
1 TTAAAT-TATAATTATT
135350 ACAACTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTAAATTATAATTATTT
Found at i:142715 original size:16 final size:16
Alignment explanation
Indices: 142694--142726 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
142684 TAACTCTTGG
142694 AAACGATCTAAAAACT
1 AAACGATCTAAAAACT
142710 AAACGATCTAAAAACT
1 AAACGATCTAAAAACT
142726 A
1 A
142727 GTGTACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (16 bp):
AAACGATCTAAAAACT
Found at i:146484 original size:5 final size:5
Alignment explanation
Indices: 146474--146502 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
146464 TTATTTTCTC
146474 ACCAA ACCAA ACCAA ACCAA ACCAA ACCA
1 ACCAA ACCAA ACCAA ACCAA ACCAA ACCA
146503 CAATCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCAA
Found at i:175543 original size:16 final size:18
Alignment explanation
Indices: 175512--175544 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
175502 TGAATAATTT
175512 CAGACATTATATAAAAAA
1 CAGACATTATATAAAAAA
175530 CAGACA-TA-ATAAAAA
1 CAGACATTATATAAAAA
175545 TGTATAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (18 bp):
CAGACATTATATAAAAAA
Found at i:192613 original size:38 final size:38
Alignment explanation
Indices: 192562--192652 Score: 139
Period size: 38 Copynumber: 2.4 Consensus size: 38
192552 TTCCCCTTGA
*
192562 GATTTTATTATATTATACAAAGAGTCCCT-TCCATTTAG
1 GATTTTATTATATTATACAAAGAGTCCCTCTCC-TTCAG
* *
192600 GATTTTATTATATTATATAAATAGTCCCTCTCCTTCAG
1 GATTTTATTATATTATACAAAGAGTCCCTCTCCTTCAG
192638 GATTTTATTATATTA
1 GATTTTATTATATTA
192653 AGGAATCAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
38 46 0.94
39 3 0.06
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (38 bp):
GATTTTATTATATTATACAAAGAGTCCCTCTCCTTCAG
Found at i:192986 original size:42 final size:42
Alignment explanation
Indices: 192929--193017 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
192919 GCGACAGCCT
*
192929 TGATGACGATCTACTCCAAGGCAGCGACAGCCATAATGACGA
1 TGATGACGATCTACTCCAAAGCAGCGACAGCCATAATGACGA
* *
192971 TGATGACGATCTACTCCAAAGCAGCGACAGGCATGATGACGA
1 TGATGACGATCTACTCCAAAGCAGCGACAGCCATAATGACGA
*
193013 CGATG
1 TGATG
193018 GTGATGAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.17
Consensus pattern (42 bp):
TGATGACGATCTACTCCAAAGCAGCGACAGCCATAATGACGA
Found at i:194600 original size:6 final size:6
Alignment explanation
Indices: 194589--194630 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
194579 NNNNNNNNNN
194589 CCTGCC CCTGCC CCTGCC CCTGCC CCTGCC CCTGCC CCTGCC
1 CCTGCC CCTGCC CCTGCC CCTGCC CCTGCC CCTGCC CCTGCC
194631 TCCGCTGTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.67, G:0.17, T:0.17
Consensus pattern (6 bp):
CCTGCC
Found at i:195113 original size:2 final size:2
Alignment explanation
Indices: 195106--195134 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
195096 CTTACTAGTC
195106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
195135 TTAGTTCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:196424 original size:223 final size:222
Alignment explanation
Indices: 196187--196616 Score: 586
Period size: 223 Copynumber: 1.9 Consensus size: 222
196177 TGTATAATTG
*
196187 AAAAAAAATTAAAATTGTTAAATAAT-ATCTAAGAAATATAAAACAAAAAATATTTTATCTAATT
1 AAAAAAAATTAAAATTATTAAATAATGA-CTAAGAAATATAAAACAAAAAATATTTTATCTAATT
* *
196251 AAAGTT-AAAAA-GTCCAAATCAAAAAACAATTTTATTTAAATAAAA-TCTAAAGCTAAAAAACA
65 AAAATTAAAAAAGGT-CAAATCAAAAAACAATTTTATTT-AATAAAATTC-AAAACTAAAAAACA
* * *
196313 ATATGAAAATTC-ATACCGAA-TCGAATCAATTTAATACAATTTGGTAATAATCGAA-TTTTTAT
127 ATATGAAAATCCGAT-CCGAACT-GAATCAATTTAATACAATTCGGTAATAA-CCAATTTTTTAT
*
196375 ATTCACTTATTCAGTTTCATTATGAAAACTAAAA
189 ATTCACTGATTCAGTTTCATTATGAAAACTAAAA
*
196409 AAAAAAAAGTTAAAATTATTAAATAATGACTAAGAAATATAAAACAAAGAATATTTTATCTAATT
1 AAAAAAAA-TTAAAATTATTAAATAATGACTAAGAAATATAAAACAAAAAATATTTTATCTAATT
* * * *
196474 AAAATTAAAAAAGGTCAAATCTAAAAATAATTTTATTTAATAAAATTCAAAATTAAAAAATAATA
65 AAAATTAAAAAAGGTCAAATCAAAAAACAATTTTATTTAATAAAATTCAAAACTAAAAAACAATA
** * * *
196539 TGAAAATCCGATTTGAACTGAATCAATTTAGTAGAATTCGGTATTAACCAATTTTTTATATTCAC
130 TGAAAATCCGATCCGAACTGAATCAATTTAATACAATTCGGTAATAACCAATTTTTTATATTCAC
196604 TGATTCAGTTTCA
195 TGATTCAGTTTCA
196617 ATTAAAAAAT
Statistics
Matches: 183, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
222 11 0.06
223 138 0.75
224 32 0.17
225 2 0.01
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (222 bp):
AAAAAAAATTAAAATTATTAAATAATGACTAAGAAATATAAAACAAAAAATATTTTATCTAATTA
AAATTAAAAAAGGTCAAATCAAAAAACAATTTTATTTAATAAAATTCAAAACTAAAAAACAATAT
GAAAATCCGATCCGAACTGAATCAATTTAATACAATTCGGTAATAACCAATTTTTTATATTCACT
GATTCAGTTTCATTATGAAAACTAAAA
Found at i:197269 original size:60 final size:60
Alignment explanation
Indices: 197204--197318 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
197194 ACTCTCTTAA
* * * *
197204 AAATCGATTGTTTATATATTTAAATTGATTGTTATGGTGAAATATTATTTTTTTTCTTTT
1 AAATCGATTATTTATATATTTAAATCGATTATTATGGTGAAATATTATTTCTTTTCTTTT
* * *
197264 AAATCGATTATTTATATATTTAAATCGATTATTATGTTGGAATATTGTTTCTTTT
1 AAATCGATTATTTATATATTTAAATCGATTATTATGGTGAAATATTATTTCTTTT
197319 GAATCGTCTG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (60 bp):
AAATCGATTATTTATATATTTAAATCGATTATTATGGTGAAATATTATTTCTTTTCTTTT
Found at i:208949 original size:4 final size:4
Alignment explanation
Indices: 208940--208969 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
208930 GCTTCTTGCT
208940 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
208970 ATTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:223333 original size:19 final size:20
Alignment explanation
Indices: 223309--223351 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
223299 AAAATATTAC
*
223309 AAAAAA-TATACAGACCTA-A
1 AAAAAACTATA-AAACCTATA
223328 AAAAAACTATAAAACCTATA
1 AAAAAACTATAAAACCTATA
223348 AAAA
1 AAAA
223352 CTTATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAACTATAAAACCTATA
Found at i:228585 original size:18 final size:18
Alignment explanation
Indices: 228547--228581 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
228537 AATGGCTCAT
228547 TTTTTATATTTTGTAAAA
1 TTTTTATATTTTGTAAAA
*
228565 TTTTTAT-TTTTTTAAAA
1 TTTTTATATTTTGTAAAA
228582 ATTTAGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTATATTTTGTAAAA
Found at i:232677 original size:23 final size:23
Alignment explanation
Indices: 232647--232697 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
232637 AGAAGCGTTT
* * *
232647 CACAAGGCAGAGGAAAATCGTGC
1 CACAAGGCACAGGAAAAGCGTAC
232670 CACAAGGCACAGGAAAAGCGTAC
1 CACAAGGCACAGGAAAAGCGTAC
232693 CACAA
1 CACAA
232698 AGACAGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.25, G:0.25, T:0.06
Consensus pattern (23 bp):
CACAAGGCACAGGAAAAGCGTAC
Found at i:234007 original size:16 final size:16
Alignment explanation
Indices: 233986--234023 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
233976 ACCGGATTTG
233986 GAATAGTGATAAAATA
1 GAATAGTGATAAAATA
234002 GAATAGTGATAAAATA
1 GAATAGTGATAAAATA
234018 GAATAG
1 GAATAG
234024 AGAATTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (16 bp):
GAATAGTGATAAAATA
Done.