Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010990.1 Kokia drynarioides strain JFW-HI SEQ_125960, 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: 36044
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:182 original size:3 final size:3
Alignment explanation
Indices: 163--216 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
153 AAATAAATAT
* * * *
163 TTA TTA ATA TCA TTA TTA TTA TTA -AA CCTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
208 TTA TTA TTA
1 TTA TTA TTA
217 ATTAATGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:836 original size:17 final size:17
Alignment explanation
Indices: 814--864 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
804 ACATTATTTG
*
814 AATTTAAATTTATAATA
1 AATTTAAATTTAAAATA
831 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
848 AACTTAAATTTTAAAAT
1 AATTTAAA-TTTAAAAT
865 TTGTTAGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 23 0.74
18 8 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:1300 original size:39 final size:39
Alignment explanation
Indices: 1246--1351 Score: 133
Period size: 39 Copynumber: 2.7 Consensus size: 39
1236 GGATAACTAC
* ** * *
1246 GATCTGTCCCAAGCTCCGGGTAGGAGATTGGTTGATGGT
1 GATCTGCCCCAAGCTCCGGGTAAAAGATTGGCTAATGGT
*
1285 GATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTAATGGT
1 GATCTGCCCCAAGCTCCGGGTAAAAGATTGGCTAATGGT
*
1324 GATCTGCCCTAAGCT-CGCGGTAAAAGAT
1 GATCTGCCCCAAGCTCCG-GGTAAAAGAT
1352 CAAAATCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 1 0.02
39 57 0.98
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.25
Consensus pattern (39 bp):
GATCTGCCCCAAGCTCCGGGTAAAAGATTGGCTAATGGT
Found at i:1653 original size:49 final size:49
Alignment explanation
Indices: 1593--2065 Score: 329
Period size: 49 Copynumber: 9.6 Consensus size: 49
1583 AGGTATCGGG
*
1593 TTCGCCATTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGA
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGA
* * * * *
1642 TTCGCCGTTGCGGCTTAAATCTTTCCCTTC--ATGCTTCTGAGGTACAAGG
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCAAAT-CTTC-GTGGTACTAGA
* * * * *
1691 CTCGTCGTTGCGACTTAAACATTTTCCCTTCAAATCTTCATGGTA-TTGTA
1 TTCGCCGTTGCGACTTAAAC-CTTTCCCTTCAAATCTTCGTGGTACTAG-A
* * ** * * *
1741 TTCGCCTTTGC-AGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTACAAGG
1 TTCGCCGTTGCGA-CTTAAACCTTTCCCTTCAAATCTTC-GTGGTACTAGA
* *
1790 TTCGCCGTTGCAACTTAAACCTTTCCCTCCAAATCTTCGTGGTACT-GAA
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAG-A
* * * * * *
1839 TTCGCTGTTGCGGCTTAAATCTTTCCCTTC--ATGGTT-GTGAGGTACAAGG
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCAAAT-CTTCGT--GGTACTAGA
* ** *
1888 TCCGCCGTTGCGACTTAAACCTTTCCC-TCTGTATCTTCGTGGTACTGGA
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTC-AAATCTTCGTGGTACTAGA
* * * *** * * * *
1937 TTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGGCTGT-GAGGAACAAGG
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCT-TCGTGGTACTAGA
* * * * *
1986 TCCGCCGTTGCGACTTAAACCTTTCCCTCCAAATCTTCATGGTATTGGA
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGA
* * *
2035 TTTGCCGTTGCGGCTTAAATCTTTCCCTTCA
1 TTCGCCGTTGCGACTTAAACCTTTCCCTTCA
2066 TGCTTCGAAG
Statistics
Matches: 317, Mismatches: 84, Indels: 46
0.71 0.19 0.10
Matches are distributed among these distances:
47 6 0.02
48 13 0.04
49 250 0.79
50 38 0.12
51 8 0.03
52 2 0.01
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.36
Consensus pattern (49 bp):
TTCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGA
Found at i:1880 original size:98 final size:98
Alignment explanation
Indices: 1591--2067 Score: 652
Period size: 98 Copynumber: 4.9 Consensus size: 98
1581 TAAGGTATCG
* * *
1591 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACT-AGATTCGCCGTTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTGA-ATTCGCTGTTGCGG
*
1655 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
65 CTTAAATCTTTCCCTTCATGGTTCTGAGGTACAA
* * * * * * * *
1689 GGCTCGTCGTTGCGACTTAAACATTTTCCCTTCAAATCTTCATGGTATTGTATTCGCCT-TTGCA
1 GGTTCGCCGTTGCGACTTAAAC-CTTTCCCTCCAAATCTTCGTGGTACTGAATTCG-CTGTTGCG
*
1753 GCTTAAATCTTTCCCTTCATGTTTCTGAGGTACAA
64 GCTTAAATCTTTCCCTTCATGGTTCTGAGGTACAA
*
1788 GGTTCGCCGTTGCAACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTGAATTCGCTGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTGAATTCGCTGTTGCGGC
*
1853 TTAAATCTTTCCCTTCATGGTTGTGAGGTACAA
66 TTAAATCTTTCCCTTCATGGTTCTGAGGTACAA
* *** *
1886 GGTCCGCCGTTGCGACTTAAACCTTTCCCTCTGTATCTTCGTGGTACTGGATTCGCTGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTGAATTCGCTGTTGCGGC
* * *
1951 TTAAATCTTTCCCTTCATGGCTGTGAGGAACAA
66 TTAAATCTTTCCCTTCATGGTTCTGAGGTACAA
* * * * * *
1984 GGTCCGCCGTTGCGACTTAAACCTTTCCCTCCAAATCTTCATGGTATTGGATTTGCCGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTGAATTCGCTGTTGCGGC
2049 TTAAATCTTTCCCTTCATG
66 TTAAATCTTTCCCTTCATG
2068 CTTCGAAGTA
Statistics
Matches: 339, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
97 2 0.01
98 251 0.74
99 85 0.25
100 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (98 bp):
GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTGAATTCGCTGTTGCGGC
TTAAATCTTTCCCTTCATGGTTCTGAGGTACAA
Found at i:3705 original size:15 final size:15
Alignment explanation
Indices: 3685--3715 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3675 GATGTGATGG
3685 AGGTATGTGAATTTT
1 AGGTATGTGAATTTT
3700 AGGTATGTGAATTTT
1 AGGTATGTGAATTTT
3715 A
1 A
3716 TCTCCATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (15 bp):
AGGTATGTGAATTTT
Found at i:13149 original size:12 final size:12
Alignment explanation
Indices: 13132--13156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13122 TTCATGTGAG
13132 TTATACGAAAAA
1 TTATACGAAAAA
13144 TTATACGAAAAA
1 TTATACGAAAAA
13156 T
1 T
13157 CACACCCGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (12 bp):
TTATACGAAAAA
Found at i:13456 original size:59 final size:59
Alignment explanation
Indices: 13377--13659 Score: 299
Period size: 59 Copynumber: 4.8 Consensus size: 59
13367 ATTTGAATAC
** ** * *
13377 AAATGGGAATTTTTGG-AAGTTCGAGGGT-AAAATGGTAATTTTGGGAAAAATCAAGGTCAA
1 AAAT-GGAA-TTTTGGAAAGTTTAAGGGTAAAAAT-GTAATTTTTAGAAAAATTAGGGTCAA
* * * * *
13437 AAATGGAAATTTT-GAAAGTTTGAGTGT--AAATGGTAATTTTCAAAAAAATTAGGGTAAA
1 AAATGG-AATTTTGGAAAGTTTAAGGGTAAAAAT-GTAATTTTTAGAAAAATTAGGGTCAA
* * * * * *
13495 AAATAGAATTTTGGAAAATTTAGGGGTAAAAATGCAATTTTTGGAAAAATTAGGGTTAA
1 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAAAATTAGGGTCAA
* **
13554 AAATGGAATTTTGGAAAATTTAAGGGTAAAAATGTAATTTTTAGAAAGTTTAGGGTCAA
1 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAAAATTAGGGTCAA
13613 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTT-GAAAA
1 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAAA
13660 GTTTGGGGTC
Statistics
Matches: 191, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
57 6 0.03
58 45 0.24
59 130 0.68
60 10 0.05
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (59 bp):
AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAAAATTAGGGTCAA
Found at i:13525 original size:29 final size:29
Alignment explanation
Indices: 13480--13682 Score: 198
Period size: 29 Copynumber: 6.9 Consensus size: 29
13470 TAATTTTCAA
*
13480 AAAAATTA-GGGTAAAAAATAG-AATTTTGG
1 AAAATTTAGGGGT-AAAAAT-GTAATTTTGG
*
13509 AAAATTTAGGGGTAAAAATGCAATTTTTGG
1 AAAATTTAGGGGTAAAAATGTAA-TTTTGG
* * *
13539 AAAAATTAGGGTTAAAAATGGAATTTTGG
1 AAAATTTAGGGGTAAAAATGTAATTTTGG
* *
13568 AAAATTTAAGGGTAAAAATGTAATTTTTAG
1 AAAATTTAGGGGTAAAAATGTAA-TTTTGG
* *
13598 AAAGTTTA-GGGTCAAAAATGGAATTTTGG
1 AAAATTTAGGGGT-AAAAATGTAATTTTGG
* * *
13627 AAAGTTTAAGGGTAAAAATGTAATTTTTG
1 AAAATTTAGGGGTAAAAATGTAATTTTGG
**
13656 AAAAGTTT-GGGGTCGAAATGTAATTTT
1 AAAA-TTTAGGGGTAAAAATGTAATTTT
13683 TGGAGAGTTC
Statistics
Matches: 149, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.01
29 90 0.60
30 58 0.39
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.33
Consensus pattern (29 bp):
AAAATTTAGGGGTAAAAATGTAATTTTGG
Found at i:13661 original size:59 final size:59
Alignment explanation
Indices: 13377--13691 Score: 279
Period size: 59 Copynumber: 5.3 Consensus size: 59
13367 ATTTGAATAC
** * * *
13377 AAATGGGAATTTTTGG-AAGTTCGAGGGT-AAAATGGTAATTTTGGGAAAA-ATCAAGGTCAA
1 AAAT-GGAA-TTTTGGAAAGTTTAAGGGTAAAAAT-GTAATTTT-TGAAAAGATTAGGGTCAA
* * ** * *
13437 AAATGGAAATTTT-GAAAGTTTGAGTGT--AAATGGTAATTTTCAAAAAAATTAGGGTAAA
1 AAATGG-AATTTTGGAAAGTTTAAGGGTAAAAAT-GTAATTTTTGAAAAGATTAGGGTCAA
* * * * *
13495 AAATAGAATTTTGGAAAATTTAGGGGTAAAAATGCAATTTTTGGAAAA-ATTAGGGTTAA
1 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTT-GAAAAGATTAGGGTCAA
* *
13554 AAATGGAATTTTGGAAAATTTAAGGGTAAAAATGTAATTTTT-AGAAAGTTTAGGGTCAA
1 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTGA-AAAGATTAGGGTCAA
* * *
13613 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTTGGGGTC-G
1 AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGATTAGGGTCAA
* *
13671 AAATGTAATTTTTGGAGAGTT
1 AAATGGAA-TTTTGGAAAGTT
13692 CGGGGAACAA
Statistics
Matches: 218, Mismatches: 26, Indels: 23
0.82 0.10 0.09
Matches are distributed among these distances:
57 11 0.05
58 47 0.22
59 145 0.67
60 15 0.07
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (59 bp):
AAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGATTAGGGTCAA
Found at i:14832 original size:3 final size:3
Alignment explanation
Indices: 14813--14868 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
14803 AAATAAATAT
* * * *
14813 TTA TTA ATA TCA TTA TTA TTA TTA -AA CCTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
14859 TTA TTA TTA T
1 TTA TTA TTA T
14869 CAATTAATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 39 0.91
4 3 0.07
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:15590 original size:17 final size:17
Alignment explanation
Indices: 15532--15599 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
15522 ACATTATTTG
*
15532 AATTTAAATTTATAATA
1 AATTTAAATTTAAAATA
**
15549 AATTTAAATTTTCAATA
1 AATTTAAATTTAAAATA
15566 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
**
15583 AACGTAAATTTTAAAAT
1 AATTTAAA-TTTAAAAT
15600 TTGTTGGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:15723 original size:28 final size:28
Alignment explanation
Indices: 15682--15762 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
15672 CTGAACTTTC
*
15682 CCAAAATTACCATTTTGCC-CTCGAGTAT
1 CCAAAATTATCATTTTGCCTC-CGAGTAT
*
15710 CCAAAATTATCATTTTGCCTCCGGGTAT
1 CCAAAATTATCATTTTGCCTCCGAGTAT
* *
15738 CCTAAAA-TCTCATTTTCGACTCCGA
1 CC-AAAATTATCATTTT-GCCTCCGA
15763 TTGTTTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 34 0.76
29 11 0.24
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.33
Consensus pattern (28 bp):
CCAAAATTATCATTTTGCCTCCGAGTAT
Found at i:21401 original size:59 final size:59
Alignment explanation
Indices: 21316--21576 Score: 255
Period size: 59 Copynumber: 4.4 Consensus size: 59
21306 TTGTTCCCCG
* * *
21316 AACTCTCCAAAAATTACA-TTTCGACCCCAAACTTTTCAAAAATTACATTTTTACCCTTA
1 AACTTTCC-AAAATTCCATTTTTGACCCCAAACTTTTCAAAAATTACATTTTTACCCTTA
*
21375 AACTTTCCAAAATTCCATTTTTGACCCTAAAC-TTTCTAAAAATTACATTTTTACCCTTA
1 AACTTTCCAAAATTCCATTTTTGACCCCAAACTTTTC-AAAAATTACATTTTTACCCTTA
* * * * * *
21434 AATTTTCCAAAATTCCATTTTT-AACCCTAATTTTTCCAAAAATTGCATTTTTACCCCTA
1 AACTTTCCAAAATTCCATTTTTGACCCCAAACTTTT-CAAAAATTACATTTTTACCCTTA
* * * * ** ** * *
21493 AATTTTCCAAAATTCTATTTTTTACCCTAATTTTTTTGAAAATTACCA--TTTACACTCA
1 AACTTTCCAAAATTCCATTTTTGACCCCAAACTTTTCAAAAATTA-CATTTTTACCCTTA
21551 AACTTT-CAAAATTTCCATTTTTGACC
1 AACTTTCCAAAA-TTCCATTTTTGACC
21577 TTGATTTTTC
Statistics
Matches: 170, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
57 5 0.03
58 41 0.24
59 112 0.66
60 12 0.07
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (59 bp):
AACTTTCCAAAATTCCATTTTTGACCCCAAACTTTTCAAAAATTACATTTTTACCCTTA
Found at i:21512 original size:29 final size:29
Alignment explanation
Indices: 21325--21527 Score: 198
Period size: 29 Copynumber: 6.9 Consensus size: 29
21315 GAACTCTCCA
** *
21325 AAAATTACATTTCGACCCC-AAACTTTTCA
1 AAAATTACATTTTTACCCCTAAA-TTTTCC
* *
21354 AAAATTACATTTTTACCCTTAAACTTTCC
1 AAAATTACATTTTTACCCCTAAATTTTCC
* * *
21383 AAAATTCCATTTTTGA-CCCTAAACTTTCTA
1 AAAATTACATTTTT-ACCCCTAAATTTTC-C
*
21413 AAAATTACATTTTTACCCTTAAATTTTCC
1 AAAATTACATTTTTACCCCTAAATTTTCC
* * *
21442 AAAATTCCATTTTTAACCCTAATTTTTCC
1 AAAATTACATTTTTACCCCTAAATTTTCC
*
21471 AAAAATTGCATTTTTACCCCTAAATTTTCC
1 -AAAATTACATTTTTACCCCTAAATTTTCC
*
21501 AAAATT-CTATTTTTTA-CCCTAATTTTT
1 AAAATTAC-A-TTTTTACCCCTAAATTTT
21528 TTGAAAATTA
Statistics
Matches: 147, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.01
29 87 0.59
30 59 0.40
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCTAAATTTTCC
Found at i:21868 original size:12 final size:12
Alignment explanation
Indices: 21851--21875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21841 GTCGGGTGTG
21851 ATTTTTCGTATA
1 ATTTTTCGTATA
21863 ATTTTTCGTATA
1 ATTTTTCGTATA
21875 A
1 A
21876 CTCACATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTTTTCGTATA
Found at i:22735 original size:2 final size:2
Alignment explanation
Indices: 22728--22754 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22718 TTATTTTCGT
22728 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 T
22755 TAAACAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28584 original size:96 final size:96
Alignment explanation
Indices: 28417--28591 Score: 239
Period size: 96 Copynumber: 1.8 Consensus size: 96
28407 TTTGACTATC
* * **
28417 TCGATTTGATGAAAGATTGCACCCAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGATACGGAA
1 TCGATTTGAAGAAAAATTGCACCCAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGATAAAGAA
28482 ACATTGCCTCGATTAAGATTATTCGATTATT
66 ACATTGCCTCGATTAAGATTATTCGATTATT
* *
28513 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTT-TGAAACTCGAA-ATAAA-
1 TCGATTTGAAGAAAAATTGCACCCAGTAAGTTAAGGCGCAAATTTTCAG-AA-TCGAAGATAAAG
*
28575 AGAATATTGCCTCGATT
64 A-AACATTGCCTCGATT
28592 TAAAAGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 62 0.90
97 5 0.07
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
TCGATTTGAAGAAAAATTGCACCCAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGATAAAGAA
ACATTGCCTCGATTAAGATTATTCGATTATT
Found at i:28939 original size:59 final size:59
Alignment explanation
Indices: 28830--29050 Score: 188
Period size: 59 Copynumber: 3.8 Consensus size: 59
28820 ACCCGGGGGC
* * * * * * *
28830 AAAATGGTAATTTTTAGAAAGTTT-GGGGTTAAGAATGGAATCTTTAGACATTCGGGAGT
1 AAAATGGTAATTTTT-GGAAGTTTCGGGATCAAAAATGGAATTTTTGGACATTCGGGAGA
* * *
28889 AAAA-GGATAA-TTTT-GAGAGTTTCGAGG-TCGAAAAATGGAGTTTTTGGACATTTGGGGGA
1 AAAATGG-TAATTTTTGGA-AGTTTCG-GGATC-AAAAATGGAATTTTTGGACATTCGGGAGA
* * *
28948 AAAATGGTAATTTTTGGAAGTTTTGGGATCAAAAATGGAATTTTTGGA-AGTTAGGGGGTA
1 AAAATGGTAATTTTTGGAAGTTTCGGGATCAAAAATGGAATTTTTGGACA-TTCGGGAG-A
* *
29008 AAAATGG-AATTTTTGGAAGTTTTGGGGT-AAAAATGGAATTTTT
1 AAAATGGTAATTTTTGGAAGTTTCGGGATCAAAAATGGAATTTTT
29051 AGAAGTTTTG
Statistics
Matches: 138, Mismatches: 13, Indels: 23
0.79 0.07 0.13
Matches are distributed among these distances:
56 1 0.01
57 5 0.04
58 24 0.17
59 84 0.61
60 22 0.16
61 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGTTTCGGGATCAAAAATGGAATTTTTGGACATTCGGGAGA
Found at i:28962 original size:29 final size:28
Alignment explanation
Indices: 28918--29383 Score: 346
Period size: 29 Copynumber: 15.9 Consensus size: 28
28908 TTTCGAGGTC
*
28918 GAAAAATGGAGTTTTTGGACA-TTTGGGG
1 GAAAAATGGAATTTTTGGA-AGTTTGGGG
*
28946 GAAAAATGGTAATTTTTGGAAGTTTTGGGAT
1 GAAAAATGG-AATTTTTGGAAG-TTTGGG-G
* *
28977 CAAAAATGGAATTTTTGGAAGTTAGGGG
1 GAAAAATGGAATTTTTGGAAGTTTGGGG
29005 GTAAAAATGGAATTTTTGGAAGTTTTGGGG
1 G-AAAAATGGAATTTTTGGAAG-TTTGGGG
* *
29035 TAAAAATGGAATTTTTAGAAGTTTTGGGG
1 GAAAAATGGAATTTTTGGAAG-TTTGGGG
* * *
29064 ATTAAAAATGGGATTTTTGGAAGTTCGGGG
1 --GAAAAATGGAATTTTTGGAAGTTTGGGG
* *
29094 GTAAAAAT-GAAATTTTGGAAGTTTTGAGGT
1 G-AAAAATGGAATTTTTGGAAG-TTTG-GGG
* * * *
29124 TAAAAATGGGATTTTTGAAAGTTCAGGGG
1 GAAAAATGGAATTTTTGGAAGTT-TGGGG
* * *
29153 TAAAAATGGAATTTTTTGG-AGTTTCAAGGT
1 GAAAAATGGAA-TTTTTGGAAGTTT--GGGG
* * *
29183 CAAAAATGGGATTTTTGGAAGTTCGGGAG
1 GAAAAATGGAATTTTTGGAAGTTTGGG-G
* *
29212 TAAAAATGAAATTTTTGGAAGTTTTGGGG
1 GAAAAATGGAATTTTTGGAAG-TTTGGGG
* ** *
29241 TTAAAAAT-GAGATTTTTAAAAGTTCGGGG
1 -GAAAAATGGA-ATTTTTGGAAGTTTGGGG
* *
29270 GTAAAATTGAAATTTTTGGAAGTTTTGGGG
1 G-AAAAATGGAATTTTTGGAAG-TTTGGGG
* *
29300 TCAAAAATGGGATTTTTGGAAGTTTGGGG
1 -GAAAAATGGAATTTTTGGAAGTTTGGGG
* *
29329 GTCAAAATGGTATTTTTGGAAGTTTTGGGG
1 G-AAAAATGGAATTTTTGGAAG-TTTGGGG
** *
29359 TCAAAATTGAGATTTTTGGAAGTTT
1 GAAAAATGGA-ATTTTTGGAAGTTT
29384 AGGGACCTTT
Statistics
Matches: 353, Mismatches: 57, Indels: 55
0.76 0.12 0.12
Matches are distributed among these distances:
28 23 0.07
29 176 0.50
30 127 0.36
31 27 0.08
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (28 bp):
GAAAAATGGAATTTTTGGAAGTTTGGGG
Found at i:29383 original size:59 final size:59
Alignment explanation
Indices: 28919--29382 Score: 535
Period size: 59 Copynumber: 7.9 Consensus size: 59
28909 TTCGAGGTCG
* * * ** *
28919 AAAAATGGAGTTTTTGGACA--TTTGGGG-GAAAAATGGTAATTTTTGGAAGTTTTGGGAT
1 AAAAATGGAATTTTTGGA-AGTTTTGGGGTCAAAAATGG-GATTTTTGGAAGTTCGGGGGT
** * **
28977 CAAAAATGGAATTTTTGGAAGTTAGGGGGT-AAAAATGGAATTTTTGGAAGTTTTGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
29036 AAAAATGGAATTTTTAGAAGTTTTGGGGATTAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGG-TCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * *
29096 AAAAAT-GAAATTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGAAAGTTCAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*** *
29154 AAAAATGGAATTTTTTGG-AGTTTCAAGGTCAAAAATGGGATTTTTGGAAGTTCGGGAGT
1 AAAAATGGAA-TTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * **
29213 AAAAATGAAATTTTTGGAAGTTTTGGGGTTAAAAATGAGATTTTTAAAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
29272 AAAATTGAAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * *
29331 CAAAATGGTATTTTTGGAAGTTTTGGGGTCAAAATTGAGATTTTTGGAAGTT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
29383 TAGGGACCTT
Statistics
Matches: 354, Mismatches: 43, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
58 68 0.19
59 235 0.66
60 51 0.14
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:31449 original size:57 final size:56
Alignment explanation
Indices: 31367--31474 Score: 155
Period size: 55 Copynumber: 1.9 Consensus size: 56
31357 TTATTTCAGA
* ** *
31367 AAATTTTTAAATATTTTATATATATCTTTAGAATTTTTTAAATTTTTTTAAAAAATAT
1 AAATTTTTAAATATTTTATAAATATC-TT-GAATTTTAAAAATTATTTTAAAAAATAT
31425 AAATTTTTAAA-ATTTTATAAATATCTTGAATTTTAAAAATTATTTTAAAA
1 AAATTTTTAAATATTTTATAAATATCTTGAATTTTAAAAATTATTTTAAAA
31475 TTTTGAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
55 20 0.43
56 2 0.04
57 13 0.28
58 11 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (56 bp):
AAATTTTTAAATATTTTATAAATATCTTGAATTTTAAAAATTATTTTAAAAAATAT
Found at i:31456 original size:27 final size:27
Alignment explanation
Indices: 31368--31465 Score: 81
Period size: 27 Copynumber: 3.5 Consensus size: 27
31358 TATTTCAGAA
*
31368 AATTTTTAAATATTTTATATATATCTTTAG
1 AATTTTTAAA-ATTTTATAAATATC-TT-G
* * * * *
31398 AATTTTTTAAATTTTTTTAAAAAAT-ATA
1 AA-TTTTTAAAATTTTAT-AAATATCTTG
31426 AATTTTTAAAATTTTATAAATATCTTG
1 AATTTTTAAAATTTTATAAATATCTTG
*
31453 AATTTTAAAAATT
1 AATTTTTAAAATT
31466 ATTTTAAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
26 5 0.09
27 26 0.49
28 2 0.04
29 1 0.02
30 7 0.13
31 12 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
AATTTTTAAAATTTTATAAATATCTTG
Found at i:31497 original size:19 final size:18
Alignment explanation
Indices: 31435--31496 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
31425 AAATTTTTAA
* *
31435 AATTTTATAAATATCTTG
1 AATTTTAAAAATATTTTG
*
31453 AATTTTAAAAATTATTTTAA
1 AATTTTAAAAA-TATTTT-G
*
31473 AATTTTGAAAATATTTTG
1 AATTTTAAAAATATTTTG
31491 AATTTT
1 AATTTT
31497 TTTATAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 16 0.43
19 11 0.30
20 10 0.27
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
AATTTTAAAAATATTTTG
Found at i:32035 original size:23 final size:23
Alignment explanation
Indices: 32001--32059 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
31991 AGTCTCGTTG
*
32001 AAAAATA-ATTAA-AAAAAGTACA
1 AAAAATATTTTAATAAAAA-TACA
* **
32023 AAAAATATTTTAATCACTATACA
1 AAAAATATTTTAATAAAAATACA
32046 AAAAATATTTTAAT
1 AAAAATATTTTAAT
32060 CACTATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 7 0.23
23 22 0.71
24 2 0.06
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAAATATTTTAATAAAAATACA
Found at i:32060 original size:23 final size:23
Alignment explanation
Indices: 32019--32066 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
32009 TTAAAAAAAG
32019 TACAAAAAATATTTTAATCACTA
1 TACAAAAAATATTTTAATCACTA
32042 TACAAAAAATATTTTAATCACTA
1 TACAAAAAATATTTTAATCACTA
32065 TA
1 TA
32067 AAATAAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (23 bp):
TACAAAAAATATTTTAATCACTA
Done.