Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011717.1 Kokia drynarioides strain JFW-HI SEQ_126711, 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: 4653
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:562 original size:30 final size:29
Alignment explanation
Indices: 500--768 Score: 240
Period size: 29 Copynumber: 9.4 Consensus size: 29
490 AAACTGTCTG
* * *
500 AAAATTCCATTTTTACCGTC-TAACTTCTA
1 AAAATTCCATTTTTACC-CCGAAACTTCCA
*
529 AAAATTTCATTTTTGACCCCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
* *
559 AAAATTTCATTTTTACACTCG-AACTTCCA
1 AAAATTCCATTTTTAC-CCCGAAACTTCCA
*
588 AAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
**
618 AAAATTATATTTTTACCCCCG-AACTTCCA
1 AAAATTCCATTTTTA-CCCCGAAACTTCCA
647 AAAATTCCATTTTTACCCTCG-AACTTCC-
1 AAAATTCCATTTTTACCC-CGAAACTTCCA
* *
675 AAAATTCCCTTTTT-----G--A-TCCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
**
696 AAAATTCCATTTTTACCCTTAAACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTCCA
* *
725 AAAATTCCATTTTTGACCTCGAAACTTTCA
1 AAAATTCCATTTTT-ACCCCGAAACTTCCA
755 AAAATTACCATTTT
1 AAAATT-CCATTTT
769 GCCCGCAAAT
Statistics
Matches: 200, Mismatches: 22, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
20 3 0.01
21 14 0.07
22 1 0.00
28 17 0.09
29 88 0.44
30 70 0.35
31 7 0.04
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCGAAACTTCCA
Found at i:592 original size:59 final size:57
Alignment explanation
Indices: 500--885 Score: 268
Period size: 59 Copynumber: 6.7 Consensus size: 57
490 AAACTGTCTG
* * * *
500 AAAATTCCATTTTTACCGTCTAACTTCTAAAAATTTCATTTTTGACCCCGAAACTTCCA
1 AAAATTTCATTTTTACC-TCGAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTCCA
*
559 AAAATTTCATTTTTACACTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTTCATTTTTAC-CTCGAACTTCCAAAAATTCCATTTTT-ACCCCGAAACTTCCA
*
618 AAAATTAT-ATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCTCG-AACTTCC-
1 AAAATT-TCATTTTTA-CCTCGAACTTCCAAAAATTCCATTTTTACCC-CGAAACTTCCA
** * **
675 AAAA-TTCCCTTTT---T-G-A-TCCCAAAAATTCCATTTTTACCCTTAAACTTCCA
1 AAAATTTCATTTTTACCTCGAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCA
* * *
725 AAAATTCCATTTTTGACCTCGAAACTTTCAAAAATTACCA-TTTT-GCCCGCAAA-TGTCCA
1 AAAATTTCATTTTT-ACCTCG-AACTTCCAAAAATT-CCATTTTTACCCCG-AAACT-TCCA
* * * ** *
784 AAAACTTCATTTTCGACCTCGAAAC-TCTC-AAAATTACC-CTTTTACCCCCGAATGTT-TA
1 AAAATTTCATTTT-TACCTCG-AACTTC-CAAAAATT-CCATTTTTA-CCCCGAAACTTCCA
*
842 AAAATTCCATTTTTAACCTCGAACATTCTC-AAAATTACCATTTT
1 AAAATTTCATTTTT-ACCTCGAAC-TTC-CAAAAATT-CCATTTT
886 GCCCCCGAGA
Statistics
Matches: 265, Mismatches: 33, Indels: 57
0.75 0.09 0.16
Matches are distributed among these distances:
49 29 0.11
50 5 0.02
51 7 0.03
55 2 0.01
56 6 0.02
57 7 0.03
58 47 0.18
59 148 0.56
60 14 0.05
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (57 bp):
AAAATTTCATTTTTACCTCGAACTTCCAAAAATTCCATTTTTACCCCGAAACTTCCA
Found at i:649 original size:88 final size:87
Alignment explanation
Indices: 500--809 Score: 258
Period size: 88 Copynumber: 3.6 Consensus size: 87
490 AAACTGTCTG
* * *
500 AAAATTCCATTTTTACCGTC-TAACTTCTAAAAATTTCATTTTTGACCCCGAAACTTCCAAAAAT
1 AAAATTCCATTTTTACC-CCAAAACTTCCAAAAATTTCATTTTTGACCCCGAAACTTCCAAAAAT
*
564 TTCATTTTTACACTCGAACTTCC
65 TCCATTTTTACACTCGAACTTCC
587 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTAT-ATTTTT-ACCCCCG-AACTTCCAAA
1 -AAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATT-TCATTTTTGA-CCCCGAAACTTCCAAA
*
649 AATTCCATTTTTACCCTCGAACTTCC
62 AATTCCATTTTTACACTCGAACTTCC
* * * * **
675 AAAATTCCCTTTTT-------GA-TCCCAAAAATTCCATTTTT-ACCCTTAAACTTCCAAAAATT
1 AAAATTCCATTTTTACCCCAAAACTTCCAAAAATTTCATTTTTGACCCCGAAACTTCCAAAAATT
*
731 CCATTTTTGAC-CTCGAAACTTTCA
66 CCATTTTT-ACACTCG-AAC-TTCC
* * * *
755 AAAATTACCA-TTTTGCCCGC-AAA-TGTCCAAAAACTTCATTTTCGACCTCGAAACT
1 AAAATT-CCATTTTTACCC-CAAAACT-TCCAAAAATTTCATTTTTGACCCCGAAACT
810 CTCAAAATTA
Statistics
Matches: 182, Mismatches: 21, Indels: 37
0.76 0.09 0.15
Matches are distributed among these distances:
77 3 0.02
78 43 0.24
79 6 0.03
80 13 0.07
81 2 0.01
87 15 0.08
88 64 0.35
89 35 0.19
90 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (87 bp):
AAAATTCCATTTTTACCCCAAAACTTCCAAAAATTTCATTTTTGACCCCGAAACTTCCAAAAATT
CCATTTTTACACTCGAACTTCC
Found at i:721 original size:49 final size:50
Alignment explanation
Indices: 644--740 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 50
634 CCCCGAACTT
* *
644 CCAAAAATTCCATTTTTACCCTCGAACTTCC-AAAATTCCCTTTTTGATC
1 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATC
*
693 CCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGA
1 CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGA
741 CCTCGAAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 29 0.66
50 15 0.34
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (50 bp):
CCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGATC
Found at i:804 original size:137 final size:139
Alignment explanation
Indices: 556--826 Score: 331
Period size: 137 Copynumber: 2.0 Consensus size: 139
546 CCCGAAACTT
* *
556 CCAAAAATTTCATTTTTACACTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAA
1 CCAAAAATTCCATTTTTACACTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAA
* * *
621 ATTATATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCTCG-AACT-TCCAAAATT-CC
66 ATTACATTTTTACCCCCGAAATTCCAAAAATTCCATTTTGACCCTCGAAACTCT-CAAAATTACC
683 CTTTTTGATC
130 CTTTTTGATC
* * * * * *
693 CCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTTCAAAA
1 CCAAAAATTCCATTTTTACACTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAA
* *
758 ATTACCA-TTTTGCCCGC-AAATGTCCAAAAACTT-CATTTTCGA-CCTCGAAACTCTCAAAATT
66 ATTA-CATTTTTACCCCCGAAAT-TCCAAAAA-TTCCATTTT-GACCCTCGAAACTCTCAAAATT
819 ACCCTTTT
127 ACCCTTTT
827 ACCCCCGAAT
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
136 3 0.03
137 88 0.77
138 15 0.13
139 8 0.07
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (139 bp):
CCAAAAATTCCATTTTTACACTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAA
ATTACATTTTTACCCCCGAAATTCCAAAAATTCCATTTTGACCCTCGAAACTCTCAAAATTACCC
TTTTTGATC
Found at i:904 original size:58 final size:56
Alignment explanation
Indices: 725--905 Score: 170
Period size: 59 Copynumber: 3.1 Consensus size: 56
715 TAAACTTCCA
*
725 AAAATTCCATTTTTGACCTCGAAACTT-TCAAAAATTACCATTTTGCCCGC-AAATGTCC
1 AAAATTCCATTTTTGACCTCGAAA-TTCTC-AAAATTACCATTTTGCCCCCGAAA--TCC
* * * * * **
783 AAAAACTT-CATTTTCGACCTCGAAACTCTCAAAATTACCCTTTTACCCCCGAATGTTTA
1 -AAAA-TTCCATTTTTGACCTCGAAATTCTCAAAATTACCATTTTGCCCCCGAA--ATCC
*
842 AAAATTCCATTTTTAACCTCGAACATTCTCAAAATTACCATTTTGCCCCCGAGAATCC
1 AAAATTCCATTTTTGACCTCGAA-ATTCTCAAAATTACCATTTTGCCCCCGA-AATCC
900 AAAATT
1 AAAATT
906 ATCAATTTTC
Statistics
Matches: 98, Mismatches: 16, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
57 2 0.02
58 43 0.44
59 50 0.51
60 3 0.03
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (56 bp):
AAAATTCCATTTTTGACCTCGAAATTCTCAAAATTACCATTTTGCCCCCGAAATCC
Found at i:905 original size:28 final size:30
Alignment explanation
Indices: 871--934 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
861 CGAACATTCT
* *
871 CAAAATTA-CCATTTTGCCCCC-GAGAATC
1 CAAAATTATCAATTTTCCCCCCTGAGAATC
*
899 CAAAATTATCAATTTTCCCCCCTTGAGTATC
1 CAAAATTATCAATTTTCCCCCC-TGAGAATC
930 CAAAA
1 CAAAA
935 AGTCTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
31 11 0.37
ACGTcount: A:0.34, C:0.30, G:0.08, T:0.28
Consensus pattern (30 bp):
CAAAATTATCAATTTTCCCCCCTGAGAATC
Found at i:1402 original size:29 final size:28
Alignment explanation
Indices: 1370--1618 Score: 275
Period size: 30 Copynumber: 8.5 Consensus size: 28
1360 AAACTGTCTG
* * *
1370 AAAATTTCATTTTTACCCTCTAACTTCTA
1 AAAATTCCATTTTTACCC-CAAACTTCCA
*
1399 AAAATTTCATTTTTGACCCCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCC-AAACTTCCA
*
1429 AAAATTTCATTTTTACCCTCAAACTTCCA
1 AAAATTCCATTTTTACCC-CAAACTTCCA
1458 AAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCC-AAACTTCCA
* *
1488 AAAATTCTATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTA-CCCCAAACTTCCA
*
1517 AAAATTCCATTTTTACCCTCGAACTTCC-
1 AAAATTCCATTTTTACCC-CAAACTTCCA
*
1545 AAAATTCCCTTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCC-AAACTTCCA
* *
1575 AAAATTCCATTTTTGACCTCGAAACTTTCA
1 AAAATTCCATTTTT-ACC-CCAAACTTCCA
1605 AAAATTACCATTTT
1 AAAATT-CCATTTT
1619 GCCCCCAGAT
Statistics
Matches: 197, Mismatches: 11, Indels: 22
0.86 0.05 0.10
Matches are distributed among these distances:
28 17 0.09
29 85 0.43
30 87 0.44
31 8 0.04
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCAAACTTCCA
Found at i:1432 original size:30 final size:30
Alignment explanation
Indices: 1370--1659 Score: 282
Period size: 29 Copynumber: 9.9 Consensus size: 30
1360 AAACTGTCTG
* * *
1370 AAAATTTCATTTTT-ACCCTC-TAACTTCTA
1 AAAATTCCATTTTTGACCC-CGAAACTTCCA
*
1399 AAAATTTCATTTTTGACCCCGAAACTTCCA
1 AAAATTCCATTTTTGACCCCGAAACTTCCA
*
1429 AAAATTTCATTTTT-ACCCTC-AAACTTCCA
1 AAAATTCCATTTTTGACCC-CGAAACTTCCA
* *
1458 AAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCCCGAAACTTCCA
*
1488 AAAATTCTATTTTT-ACCCCCG-AACTTCCA
1 AAAATTCCATTTTTGA-CCCCGAAACTTCCA
1517 AAAATTCCATTTTT-ACCCTCG-AACTTCC-
1 AAAATTCCATTTTTGACCC-CGAAACTTCCA
* *
1545 AAAATTCCCTTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTGACCCCGAAACTTCCA
* *
1575 AAAATTCCATTTTTGACCTCGAAACTTTCA
1 AAAATTCCATTTTTGACCCCGAAACTTCCA
* *
1605 AAAATTACCA-TTTTG-CCCCCAGA-TGTCCA
1 AAAATT-CCATTTTTGACCCCGAAACT-TCCA
* *
1634 AAAACTT-CATTTTCGACCTCGAAACT
1 AAAA-TTCCATTTTTGACCCCGAAACT
1660 CTCAAAATTA
Statistics
Matches: 225, Mismatches: 20, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
28 20 0.09
29 101 0.45
30 100 0.44
31 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCCGAAACTTCCA
Found at i:1462 original size:59 final size:59
Alignment explanation
Indices: 1370--1659 Score: 315
Period size: 59 Copynumber: 4.9 Consensus size: 59
1360 AAACTGTCTG
* * * *
1370 AAAATTTCATTTTTACCCTCTAACTTCTAAAAATTTCATTTTTGACCCCGAAACTTCCA
1 AAAATTTCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* * *
1429 AAAATTTCATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTTCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
*
1488 AAAA-TTCTATTTTTACCCCCGAACTTCCAAAAATTCCATTTTT-ACCCTCG-AACTTCC-
1 AAAATTTC-ATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCC-CGAAACTTCCA
* * * * *
1545 AAAATTCCCTTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTTCA
1 AAAATTTCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
* * * * *
1605 AAAATTACCA-TTTTGCCCCCAGA-TGTCCAAAAACTT-CATTTTCGACCTCGAAACT
1 AAAATT-TCATTTTTACCCCCAAACT-TCCAAAAA-TTCCATTTTTGACCCCGAAACT
1660 CTCAAAATTA
Statistics
Matches: 202, Mismatches: 19, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
57 9 0.04
58 46 0.23
59 133 0.66
60 12 0.06
61 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAATTTCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCA
Found at i:1624 original size:117 final size:115
Alignment explanation
Indices: 1391--1743 Score: 341
Period size: 117 Copynumber: 3.0 Consensus size: 115
1381 TTTACCCTCT
* * *
1391 AACTTCTAAAAATTTCATTTTTGACCC-CGAAACTTCCAAAAATTTCATTTTTACCCTCAAACTT
1 AACTTCCAAAAA-TTCATTTTT-ACCCTCGAAACTTCC-AAAATTCCCTTTTTACCC-CAAACTT
* * * * *
1455 CCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATT-CTATTTTTACCCCCG
62 CCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCA-TTTTGCCCCCG
1509 AACTTCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAATTCCCTTTTTGACCCCAAAACTTC
1 AACTTCCAAAAATT-CATTTTTACCCTCGAAACTTCCAAAATTCCCTTTTT-ACCCC-AAACTTC
*
1573 CAAAAATTCCATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTGCCCCC-
63 CAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTGCCCCCG
* *
1625 AGA-TGTCCAAAAACTTCATTTTCGA-CCTCGAAAC-TCTCAAAATTACCC-TTTTACCCCCGAA
1 A-ACT-TCCAAAAA-TTCATTTT-TACCCTCGAAACTTC-CAAAATT-CCCTTTTTA-CCCCAAA
** *
1686 -TGTTTAAAAATTCCATTTTAAACCTCG-AACATTCTC-AAAATTACCATTTTGCCCCCG
59 CT-TCCAAAAATTCCATTTTTAACCTCGAAAC-TT-TCAAAAATTACCATTTTGCCCCCG
1743 A
1 A
1744 GAATCCAAAA
Statistics
Matches: 203, Mismatches: 15, Indels: 34
0.81 0.06 0.13
Matches are distributed among these distances:
116 19 0.09
117 135 0.67
118 46 0.23
119 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (115 bp):
AACTTCCAAAAATTCATTTTTACCCTCGAAACTTCCAAAATTCCCTTTTTACCCCAAACTTCCAA
AAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTGCCCCCG
Found at i:1665 original size:59 final size:58
Alignment explanation
Indices: 1454--1743 Score: 231
Period size: 59 Copynumber: 4.9 Consensus size: 58
1444 CCCTCAAACT
* * * *
1454 TCCAAAAATTCCATTTTTA-ACCCCAAAACT-TCCAAAAATT-CTATTTTTACCCCCGAACT-
1 TCCAAAAATTCCA-TTTTAGACCTCGAAACTCT-C-AAAATTACCA-TTTTGCCCCCGAA-TG
* * * **
1513 TCCAAAAATTCCATTTTTA-CCCTCG-AACT-TCCAAAATTCCCTTTTTGACCCCAAAACT-
1 TCCAAAAATTCCA-TTTTAGACCTCGAAACTCT-CAAAATTACCATTTTG-CCCCCGAA-TG
* *
1571 TCCAAAAATTCCATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTGCCCCC-AGATG
1 TCCAAAAATTCCATTTTAGACCTCGAAACTCTC-AAAATTACCATTTTGCCCCCGA-ATG
* * *
1630 TCCAAAAACTT-CATTTTCGACCTCGAAACTCTCAAAATTACCCTTTTACCCCCGAATG
1 TCCAAAAA-TTCCATTTTAGACCTCGAAACTCTCAAAATTACCATTTTGCCCCCGAATG
** * *
1688 TTTAAAAATTCCATTTTAAACCTCGAACATTCTCAAAATTACCATTTTGCCCCCGA
1 TCCAAAAATTCCATTTTAGACCTCGAA-ACTCTCAAAATTACCATTTTGCCCCCGA
1744 GAATCCAAAA
Statistics
Matches: 195, Mismatches: 24, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
57 16 0.08
58 77 0.39
59 86 0.44
60 16 0.08
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTAGACCTCGAAACTCTCAAAATTACCATTTTGCCCCCGAATG
Found at i:1685 original size:29 final size:28
Alignment explanation
Indices: 1653--1769 Score: 85
Period size: 28 Copynumber: 4.0 Consensus size: 28
1643 TTTTCGACCT
*
1653 CGAAACTCTCAAAATTACCCTTTTACCCC
1 CGAAA-TCTCAAAATTACCATTTTACCCC
* * * * *
1682 CGAATGTTTAAAAATT-CCATTTTAAACCT
1 CGAA-ATCTCAAAATTACCATTTT-ACCCC
*
1711 CGAACATTCTCAAAATTACCATTTTGCCCC
1 CGAA-A-TCTCAAAATTACCATTTTACCCC
* *
1741 CGAGAATC-CAAAATTATCATTTTTCCCC
1 CGA-AATCTCAAAATTACCATTTTACCCC
1769 C
1 C
1770 CTTGAGTATC
Statistics
Matches: 68, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
28 25 0.37
29 21 0.31
30 14 0.21
31 8 0.12
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (28 bp):
CGAAATCTCAAAATTACCATTTTACCCC
Found at i:1762 original size:59 final size:58
Alignment explanation
Indices: 1575--1763 Score: 177
Period size: 59 Copynumber: 3.2 Consensus size: 58
1565 AAAACTTCCA
* ** * *
1575 AAAATTCCATTTTTGACCTCGAAACTTTCAAAAATTACCATTTTGCCCCC-AGATGTCC
1 AAAATTTCATTTTAAACCTCGAAACTCTC-AAAATTACCATTTTGCCCCCGAGATATCC
* ** * * * **
1633 AAAAACTTCATTTTCGACCTCGAAACTCTCAAAATTACCCTTTTACCCCCGA-ATGTTTA
1 -AAAATTTCATTTTAAACCTCGAAACTCTCAAAATTACCATTTTGCCCCCGAGAT-ATCC
* *
1692 AAAATTCCATTTTAAACCTCGAACATTCTCAAAATTACCATTTTGCCCCCGAGA-ATCC
1 AAAATTTCATTTTAAACCTCGAA-ACTCTCAAAATTACCATTTTGCCCCCGAGATATCC
1750 AAAATTATCATTTT
1 AAAATT-TCATTTT
1764 TCCCCCCTTG
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
58 46 0.44
59 58 0.55
60 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (58 bp):
AAAATTTCATTTTAAACCTCGAAACTCTCAAAATTACCATTTTGCCCCCGAGATATCC
Found at i:1784 original size:31 final size:28
Alignment explanation
Indices: 1721--1784 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
1711 CGAACATTCT
*
1721 CAAAATTACCATTTTGCCCCCGAGAATC
1 CAAAATTACCATTTTCCCCCCGAGAATC
* *
1749 CAAAATTATCATTTTTCCCCCCTTGAGTATC
1 CAAAATTACCA-TTTTCCCCCC--GAGAATC
1780 CAAAA
1 CAAAA
1785 AGTCTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 10 0.33
29 9 0.30
31 11 0.37
ACGTcount: A:0.33, C:0.30, G:0.08, T:0.30
Consensus pattern (28 bp):
CAAAATTACCATTTTCCCCCCGAGAATC
Found at i:2691 original size:31 final size:32
Alignment explanation
Indices: 2622--2729 Score: 100
Period size: 31 Copynumber: 3.5 Consensus size: 32
2612 TTAACATTTA
* * * *
2622 CAAAAATGCTCGAATGAA-AGCC-AAATCTTT
1 CAAAAGTGCTCAAATAAAGAGCCAAAATTTTT
2652 C-AAAGTGCTCAAATAAAG-GCCAAAATTTTT
1 CAAAAGTGCTCAAATAAAGAGCCAAAATTTTT
** * * *
2682 TGAGAGTGCTCAAA-CAAGAGCCAAACTTTTT
1 CAAAAGTGCTCAAATAAAGAGCCAAAATTTTT
2713 CAAAAGTGCTCAAATAA
1 CAAAAGTGCTCAAATAA
2730 GGGCTTCTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 16 0.26
30 11 0.18
31 33 0.54
32 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (32 bp):
CAAAAGTGCTCAAATAAAGAGCCAAAATTTTT
Done.