Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012505.1 Kokia drynarioides strain JFW-HI SEQ_127509, 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: 127659
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 149 characters in sequence are not A, C, G, or T
Found at i:631 original size:59 final size:60
Alignment explanation
Indices: 555--811 Score: 312
Period size: 59 Copynumber: 4.3 Consensus size: 60
545 TACCCTCGAG
**
555 CTTCCAAAAA-TCTCATTTTTACCCTCT-AACTTTCC-AAAATTCCATTTTTAACCTTAAAA
1 CTTCCAAAAATTC-CATTTTTACCCTCTGAAC-TTCCAAAAATTCCATTTTTAACCCCAAAA
* *
614 CTTCCAAAAATTCCATTTTTACCC-CTGAACTTCCCAAAATTCCATTTTTTACCCCAAAA
1 CTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAA
* *
673 CTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCTATTTTTGACCTCCAAAA
1 CTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATTCCATTTTTAACC-CCAAAA
* * * * * *
733 -TTTCAAAAATTCCAATCTTACCCT-TGAGCTTCCAAAAATTTCATTTTTAACCCCGAAA
1 CTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAA
*
791 CTTTCAAAAATTACCATTTTT
1 CTTCCAAAAATT-CCATTTTT
812 TCCTCGGATG
Statistics
Matches: 174, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
58 11 0.06
59 148 0.85
60 15 0.09
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (60 bp):
CTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAA
Found at i:801 original size:30 final size:29
Alignment explanation
Indices: 522--811 Score: 227
Period size: 29 Copynumber: 9.8 Consensus size: 29
512 AGAGGTCCTT
* * *
522 AAACTATCAAAAAATTTCGTTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCC-CG
*
553 -AGCTTCCAAAAA-TCTCATTTTTACCCTC-
1 AAACTTCCAAAAATTC-CATTTTTACCC-CG
* ***
581 TAACTTTCC-AAAATTCCATTTTTAACCTTA
1 AAAC-TTCCAAAAATTCCATTTTT-ACCCCG
611 AAACTTCCAAAAATTCCATTTTTACCCCTG
1 AAACTTCCAAAAATTCCATTTTTACCCC-G
* *
641 -AACTTCCCAAAATTCCATTTTTTACCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCG
670 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
*
700 -AACTTCCAAAAATTCTATTTTTGACCTCC-
1 AAACTTCCAAAAATTCCATTTTT-ACC-CCG
* * * * *
729 AAAATTTCAAAAATTCCAATCTTACCCTTG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
* *
759 -AGCTTCCAAAAATTTCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
788 AAACTTTCAAAAATTACCATTTTT
1 AAACTTCCAAAAATT-CCATTTTT
812 TCCTCGGATG
Statistics
Matches: 208, Mismatches: 32, Indels: 38
0.75 0.12 0.14
Matches are distributed among these distances:
28 2 0.01
29 105 0.50
30 93 0.45
31 8 0.04
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:829 original size:59 final size:57
Alignment explanation
Indices: 531--906 Score: 230
Period size: 59 Copynumber: 6.4 Consensus size: 57
521 TAAACTATCA
* * * *
531 AAAAATTTCGTTTTT-ACCCTCG-AGCTTCCAAAAA-TCTCATTTTTACCCTCTAACTTTCC
1 AAAAATTTCATTTTTAACCC-CGAAACTTTCAAAAATTC-CA-TTTTACCCTCGAA--TTCC
* *** *
590 -AAAATTCCATTTTTAACCTTAAAACTTCCAAAAATTCCATTTTTACCC-CTGAACTTCC
1 AAAAATTTCATTTTTAACCCCGAAACTTTCAAAAATTCCA-TTTTACCCTC-GAA-TTCC
* * * * *
648 CAAAATTCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTTCATTTTTAACCCCGAAACTTTCAAAAATTCCA-TTTTACCCTCGAA-TTCC
* * * * *
707 AAAAA-TTCTATTTTTGACCTCC-AAAATTTCAAAAATTCCAATCTTACCCTTGAGCTTCC
1 AAAAATTTC-ATTTTTAACC-CCGAAACTTTCAAAAATTCC-ATTTTACCCTCGA-ATTCC
** * *
766 AAAAATTTCATTTTTAACCCCGAAACTTTCAAAAATTACCATTTTTTCCTCGGATGTCT
1 AAAAATTTCATTTTTAACCCCGAAACTTTCAAAAATT-CCATTTTACCCTCGAAT-TCC
* * * * * *
825 AAAAATTAT-ATTTTTTACCCCGAAACTCTC-AAAATTACCCTTTTACCCCCAAATGTCT
1 AAAAATT-TCATTTTTAACCCCGAAACTTTCAAAAATT-CCATTTTACCCTCGAAT-TCC
* * *
883 AAAAAGTCCATTTTTAACCTCGAA
1 AAAAATTTCATTTTTAACCCCGAA
907 TGTTCCCAAA
Statistics
Matches: 261, Mismatches: 40, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
58 63 0.24
59 186 0.71
60 12 0.05
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (57 bp):
AAAAATTTCATTTTTAACCCCGAAACTTTCAAAAATTCCATTTTACCCTCGAATTCC
Found at i:857 original size:118 final size:118
Alignment explanation
Indices: 555--858 Score: 307
Period size: 118 Copynumber: 2.6 Consensus size: 118
545 TACCCTCGAG
* ** * *
555 CTTCCAAAAA-TCTCATTTTTACCCTCTAACTTTCC-AAAATTCCATTTTTAACCT-TAAAA-CT
1 CTTCCAAAAATTC-CATTTTTACCCTCGAAC-TTCCAAAAATTATATTTTTGACCTCCAAAATC-
* * * *
616 TCCAAAAATTCCATTTTTACCCCTGAACTTCCCAAAATTCCATTTTTTACCCCAAAA
63 T-CAAAAATTCCAATCTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAA
* *
673 CTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCTATTTTTGACCTCCAAAATTTCA
1 CTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTATATTTTTGACCTCCAAAATCTCA
* * * *
738 AAAATTCCAATCTTACCCTTGAGCTTCCAAAAATTTCATTTTTAACCCCGAAA
66 AAAATTCCAATCTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAA
* * * * * *
791 CTTTCAAAAATTACCATTTTT-TCCTCGGA-TGTCTAAAAATTATATTTTTTACC-CCGAAACTC
1 CTTCCAAAAATT-CCATTTTTACCCTCGAACT-TCCAAAAATTATATTTTTGACCTCC-AAAATC
853 TCAAAA
63 TCAAAA
859 TTACCCTTTT
Statistics
Matches: 158, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
117 7 0.04
118 136 0.86
119 15 0.09
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (118 bp):
CTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTATATTTTTGACCTCCAAAATCTCA
AAAATTCCAATCTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCCAAAA
Found at i:868 original size:29 final size:29
Alignment explanation
Indices: 620--955 Score: 80
Period size: 29 Copynumber: 11.5 Consensus size: 29
610 AAAACTTCCA
*
620 AAAATT-CCATTTTTACCCCTG-AACTTCCC
1 AAAATTACCATTTTTACCCC-GAAAC-TCTC
*
649 AAAATT-CCATTTTTTACCCCAAAACT-TCC
1 AAAATTACCA-TTTTTACCCCGAAACTCT-C
678 AAAAATT-CCATTTTTACCCTCG-AACT-TCC
1 -AAAATTACCATTTTTACCC-CGAAACTCT-C
* * *
707 AAAAATT-CTATTTTTGACCTCC-AAAATTTC
1 -AAAATTACCATTTTT-ACC-CCGAAACTCTC
* * * *
737 AAAAATT-CCAATCTTACCCTTG-AGCT-TCC
1 -AAAATTACCATTTTTACCC-CGAAACTCT-C
* *
766 AAAAATT-TCATTTTTAACCCCGAAACTTTC
1 -AAAATTACCATTTTT-ACCCCGAAACTCTC
* * * ** *
796 AAAAATTACCATTTTTTCCTCGGATGTCTA
1 -AAAATTACCATTTTTACCCCGAAACTCTC
*
826 AAAATTA-TATTTTTTACCCCGAAACTCTC
1 AAAATTACCA-TTTTTACCCCGAAACTCTC
* * * *
855 AAAATTACC-CTTTTACCCCCAAATGTCTA
1 AAAATTACCATTTTTACCCCGAAA-CTCTC
* * ** *
884 AAAAGT-CCATTTTTAACCTCGAATGTTCCC
1 AAAATTACCATTTTT-ACCCCGAA-ACTCTC
* *
914 AAAATTATCA-TTTCACCCCCGAGAA-T-TC
1 AAAATTACCATTTTTA-CCCCGA-AACTCTC
942 AAAATTACCATTTT
1 AAAATTACCATTTT
956 GCCCCCGGTA
Statistics
Matches: 230, Mismatches: 51, Indels: 52
0.69 0.15 0.16
Matches are distributed among these distances:
28 27 0.12
29 104 0.45
30 86 0.37
31 13 0.06
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTTACCCCGAAACTCTC
Found at i:896 original size:58 final size:59
Alignment explanation
Indices: 774--906 Score: 151
Period size: 58 Copynumber: 2.3 Consensus size: 59
764 CCAAAAATTT
* ** * ** *
774 CATTTTTAACCCCGAAACTTTCAAAAATTACCATTTTTTCCTCGGATGTCTAAAAATTA
1 CATTTTTAACCCCGAAACTCTCAAAAATTACCATTTTACCCCCAAATGTCTAAAAAGTA
* * * *
833 TATTTTTTACCCCGAAACTCTC-AAAATTACCCTTTTACCCCCAAATGTCTAAAAAGTC
1 CATTTTTAACCCCGAAACTCTCAAAAATTACCATTTTACCCCCAAATGTCTAAAAAGTA
*
891 CATTTTTAACCTCGAA
1 CATTTTTAACCCCGAA
907 TGTTCCCAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
58 41 0.68
59 19 0.32
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (59 bp):
CATTTTTAACCCCGAAACTCTCAAAAATTACCATTTTACCCCCAAATGTCTAAAAAGTA
Found at i:2679 original size:17 final size:17
Alignment explanation
Indices: 2657--2694 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2647 AGGGTCACTT
2657 GTAGTAATTGCTGAAGA
1 GTAGTAATTGCTGAAGA
2674 GTAGTAATTGCTGAAGA
1 GTAGTAATTGCTGAAGA
2691 -TAGT
1 GTAGT
2695 GCATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (17 bp):
GTAGTAATTGCTGAAGA
Found at i:3844 original size:4 final size:4
Alignment explanation
Indices: 3835--3865 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3825 ATATGAACTA
3835 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
3866 ATGTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:8272 original size:31 final size:32
Alignment explanation
Indices: 8206--8273 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
8196 TTAACAGCCT
* *
8206 AGTGA-TTAAAATGAAAACTTTCGAGTAATTT
1 AGTGACTTAAAATGAAAACTTTCGAATAATTC
* *
8237 AGTGACTT-AAATGAAAACTTTTGAATAGTTC
1 AGTGACTTAAAATGAAAACTTTCGAATAATTC
8268 AGTGAC
1 AGTGAC
8274 CGTTTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.34
Consensus pattern (32 bp):
AGTGACTTAAAATGAAAACTTTCGAATAATTC
Found at i:17579 original size:19 final size:19
Alignment explanation
Indices: 17555--17602 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
17545 CATTAAAATG
17555 GTATTGATACGGGGATAAA
1 GTATTGATACGGGGATAAA
17574 GTATTGATACGGGGATAAA
1 GTATTGATACGGGGATAAA
17593 GTATTGATAC
1 GTATTGATAC
17603 TTGAAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (19 bp):
GTATTGATACGGGGATAAA
Found at i:17612 original size:19 final size:19
Alignment explanation
Indices: 17555--17612 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
17545 CATTAAAATG
* *
17555 GTATTGATACGGGGATAAA
1 GTATTGATACGGGAAAAAA
* *
17574 GTATTGATACGGGGATAAA
1 GTATTGATACGGGAAAAAA
**
17593 GTATTGATACTTGAAAAAA
1 GTATTGATACGGGAAAAAA
17612 G
1 G
17613 GTTCTGATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.28
Consensus pattern (19 bp):
GTATTGATACGGGAAAAAA
Found at i:32226 original size:14 final size:15
Alignment explanation
Indices: 32204--32240 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
32194 TGATTTTAAA
*
32204 AATAATTTTAT-ATT
1 AATATTTTTATAATT
32218 AATATTTTTATAATT
1 AATATTTTTATAATT
32233 AAT-TTTTT
1 AATATTTTT
32241 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATATTTTTATAATT
Found at i:33427 original size:18 final size:17
Alignment explanation
Indices: 33379--33432 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
33369 ATATACTTTT
33379 TTTTTAATTATTTATAA
1 TTTTTAATTATTTATAA
***
33396 TTTTTAAAGCTTTATACA
1 TTTTTAATTATTTATA-A
* *
33414 TTTTTAATTTTTTAGAA
1 TTTTTAATTATTTATAA
33431 TT
1 TT
33433 AAGATAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTTTAATTATTTATAA
Found at i:35288 original size:9 final size:9
Alignment explanation
Indices: 35273--35310 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
35263 TTAATTTTCG
35273 AATTCGAACT
1 AATTCGAA-T
35283 -ATTCGAAT
1 AATTCGAAT
35291 AATTCGAAT
1 AATTCGAAT
*
35300 AAATCGAAT
1 AATTCGAAT
35309 AA
1 AA
35311 AACTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 1 0.04
9 25 0.96
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43862 original size:36 final size:35
Alignment explanation
Indices: 43792--43862 Score: 81
Period size: 36 Copynumber: 2.0 Consensus size: 35
43782 TAGTAACAAA
* *
43792 ATTAATAATAAAATAAATATTATACAATATTAAAAC
1 ATTAACAATAAAATAAATA-TATACAATAATAAAAC
*
43828 ATTAACAATAAAATAACAGTA-ATATAATAATAAAA
1 ATTAACAATAAAATAA-A-TATATACAATAATAAAA
43863 TGATAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 27 0.90
37 1 0.03
38 2 0.07
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (35 bp):
ATTAACAATAAAATAAATATATACAATAATAAAAC
Found at i:48467 original size:21 final size:21
Alignment explanation
Indices: 48425--48487 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
48415 TAATATTATT
* * *
48425 TAAAAAAATTAT-TTTTTTAA
1 TAAAAAAATTATAATTCTAAA
48445 TAAAAAAATTATAATTCTAAA
1 TAAAAAAATTATAATTCTAAA
*
48466 T-AAAAAATTATATATTCGAAA
1 TAAAAAAATTATA-ATTCTAAA
48487 T
1 T
48488 TTGAATTACG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAAAAATTATAATTCTAAA
Found at i:49311 original size:25 final size:24
Alignment explanation
Indices: 49282--49331 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
49272 TTGAGGATAA
* *
49282 TGAAATACAGCTGCCAATTTTAAAT
1 TGAAAAACAGCTGCC-AGTTTAAAT
49307 TGAAAAACAGCTGCCAGTTTAAAT
1 TGAAAAACAGCTGCCAGTTTAAAT
49331 T
1 T
49332 AATTTAACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (24 bp):
TGAAAAACAGCTGCCAGTTTAAAT
Found at i:54682 original size:21 final size:21
Alignment explanation
Indices: 54644--54684 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54634 TAGGAATCGG
**
54644 ATTAAAATAATTTTTTTAATT
1 ATTAAAATAATTCATTTAATT
*
54665 ATTAAATTAATTCATTTAAT
1 ATTAAAATAATTCATTTAAT
54685 AATAGAGGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTAAAATAATTCATTTAATT
Found at i:56613 original size:18 final size:17
Alignment explanation
Indices: 56581--56614 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56571 AAAATGTTTG
*
56581 AAATAATTAATAAAATA
1 AAATAATTAAAAAAATA
56598 AAATAACTTAAAAAAAT
1 AAATAA-TTAAAAAAAT
56615 TAAGAGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATAATTAAAAAAATA
Found at i:62768 original size:73 final size:73
Alignment explanation
Indices: 62681--62826 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
62671 CGAAACGATT
*
62681 CCAAACAAAAACAAACCTGAACTTGAAATGATCTCAATACGAACTCAAAAATGAGACAAACCCCA
1 CCAAACAAAAACAAACCTGAACTTGAAATGACCTCAATACGAACTCAAAAATGAGACAAACCCCA
62746 AAATTAAG
66 AAATTAAG
62754 CCAAACAAAAACAAACCTGAACTTGAAATGACCTCAATACGAACTCAAAAATGAGACAAACCCCA
1 CCAAACAAAAACAAACCTGAACTTGAAATGACCTCAATACGAACTCAAAAATGAGACAAACCCCA
62819 AAATTAAG
66 AAATTAAG
62827 TTACTTGAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.52, C:0.24, G:0.10, T:0.14
Consensus pattern (73 bp):
CCAAACAAAAACAAACCTGAACTTGAAATGACCTCAATACGAACTCAAAAATGAGACAAACCCCA
AAATTAAG
Found at i:64099 original size:19 final size:17
Alignment explanation
Indices: 64067--64110 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
64057 GCTTCCCTAG
* *
64067 TATTTTTATTATTAACCT
1 TATTTTTTTTATTAA-AT
64085 TATTTTTTTTAATTAAAT
1 TATTTTTTTT-ATTAAAT
64103 TATTTTTT
1 TATTTTTT
64111 ATGACAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTTTTATTAAAT
Found at i:72234 original size:41 final size:41
Alignment explanation
Indices: 72174--72261 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
72164 ATTTGATATT
* *
72174 TTTTTACAGTTTTATTTTTGTTTCTAGCATTCACCGTTAAA
1 TTTTTACAGTTTTACTTTTGTTTCTAGCATTCAACGTTAAA
72215 TTTTTACAGTTTTACTTTTGTTTCTAGCATTCAACGTTAAA
1 TTTTTACAGTTTTACTTTTGTTTCTAGCATTCAACGTTAAA
72256 TTTTTA
1 TTTTTA
72262 AAACAACTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (41 bp):
TTTTTACAGTTTTACTTTTGTTTCTAGCATTCAACGTTAAA
Found at i:72329 original size:12 final size:12
Alignment explanation
Indices: 72307--72348 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
72297 TTTTTAGATT
*
72307 TTTATATATTT-
1 TTTATAAATTTA
72318 TTTATCAAATTTAA
1 TTTAT-AAATTT-A
72332 TTTATAAATTTA
1 TTTATAAATTTA
72344 TTTAT
1 TTTAT
72349 TTTAGCTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.19
12 11 0.41
13 6 0.22
14 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATAAATTTA
Found at i:91420 original size:24 final size:24
Alignment explanation
Indices: 91369--91423 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
91359 TCTTTCAGTT
* * *
91369 AAACTCTGTTTAATTGTTTTATTT
1 AAACTCTGTTTAATTGTTTGAGTC
*
91393 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTAATTGTTTGAGTC
91417 AAACTCT
1 AAACTCT
91424 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTGAGTC
Found at i:94110 original size:8 final size:8
Alignment explanation
Indices: 94097--94121 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
94087 ATTTGTGTGT
94097 TCAATTTC
1 TCAATTTC
94105 TCAATTTC
1 TCAATTTC
94113 TCAATTTC
1 TCAATTTC
94121 T
1 T
94122 TCTGCTATTC
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:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:98693 original size:2 final size:2
Alignment explanation
Indices: 98686--98718 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
98676 TTCCTTGCTT
98686 TA TA 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 TA TA T
98719 TAAGACGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:104587 original size:6 final size:6
Alignment explanation
Indices: 104576--104602 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
104566 CATCTTCATA
104576 TCCTCT TCCTCT TCCTCT TCCTCT TCC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCC
104603 ACAATTCCCA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTCT
Found at i:106173 original size:31 final size:31
Alignment explanation
Indices: 106128--106189 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
106118 TCTGCCACTG
*
106128 TACTAAAGTGTTTGAAAATTTTCATTTAAGT
1 TACTAAAGTATTTGAAAATTTTCATTTAAGT
* * *
106159 TACTAAATTATTTGAAAGTTTTTATTTAAGT
1 TACTAAAGTATTTGAAAATTTTCATTTAAGT
106190 CATTGGGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.48
Consensus pattern (31 bp):
TACTAAAGTATTTGAAAATTTTCATTTAAGT
Found at i:106838 original size:20 final size:20
Alignment explanation
Indices: 106801--106867 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 20
106791 ACTTAACAAT
*
106801 TTAAAAAATTATATAAAATC
1 TTAAAAAATTATAAAAAATC
*
106821 TTAAAAACA-TATAAAAAAATTA
1 TTAAAAA-ATTAT-AAAAAA-TC
* *
106843 TTAATAAATTAAAAAAAAATC
1 TTAAAAAATT-ATAAAAAATC
106864 TTAA
1 TTAA
106868 TCCACAACAC
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
20 10 0.27
21 12 0.32
22 14 0.38
23 1 0.03
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAAAAATTATAAAAAATC
Found at i:106839 original size:21 final size:21
Alignment explanation
Indices: 106815--106868 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
106805 AAAATTATAT
106815 AAAATCTTAA-AAACATATAAAA
1 AAAATCTTAATAAA-ATA-AAAA
* * *
106837 AAATTATTAATAAATTAAAAA
1 AAAATCTTAATAAAATAAAAA
106858 AAAATCTTAAT
1 AAAATCTTAAT
106869 CCACAACACG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 13 0.50
22 10 0.38
23 3 0.12
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATCTTAATAAAATAAAAA
Found at i:113942 original size:12 final size:11
Alignment explanation
Indices: 113924--113974 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
113914 ATTGAAATTT
113924 TTATATTAAAA
1 TTATATTAAAA
113935 TGTATATTTAAAA
1 T-TATA-TTAAAA
* *
113948 TTAATATTATAC
1 TT-ATATTAAAA
113960 TTATATT-AAA
1 TTATATTAAAA
113970 TTATA
1 TTATA
113975 AATTAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 6 0.18
11 6 0.18
12 11 0.33
13 10 0.30
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (11 bp):
TTATATTAAAA
Found at i:120020 original size:15 final size:16
Alignment explanation
Indices: 119989--120023 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
119979 GGTTGTCTTG
119989 AGTTCAAGTCAATTTA
1 AGTTCAAGTCAATTTA
*
120005 AGTTCAAG-CGATTTA
1 AGTTCAAGTCAATTTA
120020 AGTT
1 AGTT
120024 TGAGTTGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (16 bp):
AGTTCAAGTCAATTTA
Found at i:127156 original size:18 final size:18
Alignment explanation
Indices: 127133--127169 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
127123 GCATCTAATA
*
127133 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAAATATT
127151 TTGTTCCTTGTAAATATT
1 TTGTTCCTTGTAAATATT
127169 T
1 T
127170 GGCAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (18 bp):
TTGTTCCTTGTAAATATT
Done.