Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012378.1 Kokia drynarioides strain JFW-HI SEQ_127382, 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: 74879
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 262 characters in sequence are not A, C, G, or T
Found at i:4355 original size:30 final size:30
Alignment explanation
Indices: 4321--4381 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4311 ATTTTTTTTC
*
4321 CGTTTACT-TTTTAAATTTAATTTGTAATTT
1 CGTTT-CTATTTTAAATTTAATTTCTAATTT
* *
4351 CGTTTTTATTTTAAATTTATTTTCTAATTT
1 CGTTTCTATTTTAAATTTAATTTCTAATTT
4381 C
1 C
4382 CTGTATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.62
Consensus pattern (30 bp):
CGTTTCTATTTTAAATTTAATTTCTAATTT
Found at i:5312 original size:62 final size:61
Alignment explanation
Indices: 5240--5421 Score: 184
Period size: 70 Copynumber: 2.8 Consensus size: 61
5230 AGGGGAAGTT
*
5240 GGTGTCGGCCATTACATGGCTAACACCAAAAAAATTTAAAAATTTTTTATCCGAGAAAAGGA
1 GGTGTCGGCCATTGCATGGC-AACACCAAAAAAATTTAAAAATTTTTTATCCGAGAAAAGGA
* **
5302 GGTGTCGGCCATTGCATGACCAACACCAAAAAGATCAAAAATATTTGAAATTTTTTATCCGAGAA
1 GGTGTCGGCCATTGCATG-GCAACACC----A-A--AAAAAT-TTAAAAATTTTTTATCCGAGAA
*
5367 CAGGA
57 AAGGA
* * **
5372 GGTGTCGGCCATTGCATGGGCAACACAAAAAAAATTGAAATTTTTTTTAT
1 GGTGTCGGCCATTGCAT-GGCAACACCAAAAAAATTTAAAAATTTTTTAT
5422 TTGAAATGGC
Statistics
Matches: 98, Mismatches: 12, Indels: 20
0.75 0.09 0.15
Matches are distributed among these distances:
62 33 0.34
63 7 0.07
65 1 0.01
66 2 0.02
67 1 0.01
69 6 0.06
70 47 0.48
71 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (61 bp):
GGTGTCGGCCATTGCATGGCAACACCAAAAAAATTTAAAAATTTTTTATCCGAGAAAAGGA
Found at i:5475 original size:23 final size:24
Alignment explanation
Indices: 5434--5480 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5424 GAAATGGCCA
5434 ACACCCAAAAATACAATTTTTTTG
1 ACACCCAAAAATACAATTTTTTTG
* *
5458 ACACCCAAAAATGCATTTTTTTT
1 ACACCCAAAAATACAATTTTTTT
5481 TCTGAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (24 bp):
ACACCCAAAAATACAATTTTTTTG
Found at i:5823 original size:58 final size:57
Alignment explanation
Indices: 5662--5854 Score: 208
Period size: 60 Copynumber: 3.3 Consensus size: 57
5652 AAAATGCAGT
* * * *
5662 TTTTTTTTTCTGAAAAAGTGGGTGTCGGCCATTGCATGACCAACACAAAAAAAAATTAAA
1 TTTTTTTTTCTCAAAAAG-GGGTGTCGGCCATTGAATGACCAACAC--CAAAAAATGAAA
* * *
5722 TTTTTTTTTCTCAAAAAGGGGTGTCGGCTA-TGCAATGGCCAACACCAAAAAATGCAA
1 TTTTTTTTTCTCAAAAAGGGGTGTCGGCCATTG-AATGACCAACACCAAAAAATGAAA
* * * * *
5779 TTTTTTTTTCTGAAAAAGGGGCTATCGACCATTGTATGATCAACACCAAAAAATTTGAAA
1 TTTTTTTTTCTCAAAAAGGGG-TGTCGGCCATTGAATGACCAACACCAAAAAA--TGAAA
5839 TTTTTTTTTCTCAAAA
1 TTTTTTTTTCTCAAAA
5855 TGGTCGACAC
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
57 29 0.26
58 24 0.21
59 23 0.21
60 36 0.32
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (57 bp):
TTTTTTTTTCTCAAAAAGGGGTGTCGGCCATTGAATGACCAACACCAAAAAATGAAA
Found at i:8568 original size:16 final size:15
Alignment explanation
Indices: 8537--8603 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
8527 TTAAATTTAA
8537 TTTAT-TTTAA-ATTT
1 TTTATATTTAATA-TT
*
8551 TTTATATTATATTATT
1 TTTATATT-TAATATT
*
8567 TTAATATTTAATAATT
1 TTTATATTTAAT-ATT
*
8583 TTATATATTGAA-ATT
1 TT-TATATTTAATATT
8598 TTTATA
1 TTTATA
8604 CAATTATCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.21
15 10 0.23
16 16 0.37
17 8 0.19
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (15 bp):
TTTATATTTAATATT
Found at i:9580 original size:16 final size:17
Alignment explanation
Indices: 9559--9594 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
9549 GTTTCAAATA
9559 TTTAAA-CATTTTCCTT
1 TTTAAATCATTTTCCTT
*
9575 TTTAAATGATTTTCCTT
1 TTTAAATCATTTTCCTT
9592 TTT
1 TTT
9595 TGGTTGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTAAATCATTTTCCTT
Found at i:10173 original size:25 final size:24
Alignment explanation
Indices: 10135--10181 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
10125 TTAAAAAGCG
10135 AAAAAAAAAAAGAAGAAGAAGAGA
1 AAAAAAAAAAAGAAGAAGAAGAGA
10159 AAAAGAAAAAAAGAAGAAGAAGA
1 AAAA-AAAAAAAGAAGAAGAAGA
10182 AAATGGAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAGAAGAAGAAGAGA
Found at i:14503 original size:31 final size:31
Alignment explanation
Indices: 14460--14523 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
14450 TCGTATCTGA
*
14460 CAGTCCCACTCTAGTTTGAGTAGCATAGGTG
1 CAGTCCCACTCTAGTTCGAGTAGCATAGGTG
* *
14491 CAGTCCCCCTCTAGTTCGAGTAGTATAGGTG
1 CAGTCCCACTCTAGTTCGAGTAGCATAGGTG
14522 CA
1 CA
14524 TGTCATTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (31 bp):
CAGTCCCACTCTAGTTCGAGTAGCATAGGTG
Found at i:17699 original size:58 final size:56
Alignment explanation
Indices: 17626--17821 Score: 137
Period size: 58 Copynumber: 3.4 Consensus size: 56
17616 ACTTGGGGGT
* *
17626 AAAATGGTAATTTTTGGAGGTTTTGAGGGTAAAATGCAATTTTTGGAAAGCTC-GGGGTCA
1 AAAATGG-AA-TTTTGGA-G-TTTGAGGGTAAAATACAATTTTTGGAAAGCTCAGGGG-AA
* ** ** *
17686 AAAATGGAATTTTGGAAATTCAAATGTAAAATACAATTTTTGGAAAGTTCAAGGGGAA
1 AAAATGGAATTTTGG-AGTTTGAGGGTAAAATACAATTTTTGGAAAGCTC-AGGGGAA
* * * * * * *
17744 AAAATGTAATTTTGGAAGTTTGGGGGTAAAATAATAATTTTTAGAAAGTTCAGAGG-T
1 AAAATGGAATTTTGG-AGTTTGAGGGTAAAAT-ACAATTTTTGGAAAGCTCAGGGGAA
*
17801 AAAATGTAA-TTTGGAAGTTTG
1 AAAATGGAATTTTGG-AGTTTG
17822 GGGACAAAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
56 12 0.11
57 35 0.31
58 36 0.32
59 23 0.20
60 7 0.06
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (56 bp):
AAAATGGAATTTTGGAGTTTGAGGGTAAAATACAATTTTTGGAAAGCTCAGGGGAA
Found at i:17759 original size:30 final size:29
Alignment explanation
Indices: 17720--17905 Score: 134
Period size: 29 Copynumber: 6.4 Consensus size: 29
17710 TGTAAAATAC
17720 AATTTTTGGAAAGTTCAAGGGGAAAAAATGT
1 AATTTTTGGAAAGTT--AGGGGAAAAAATGT
* ** *
17751 AA-TTTTGG-AAGTTTGGGGGTAAAATAAT
1 AATTTTTGGAAAGTTAGGGGAAAAAAT-GT
* * *
17779 AATTTTTAGAAAGTTCAGAGG-TAAAATGT
1 AATTTTTGGAAAGTT-AGGGGAAAAAATGT
*
17808 AA--TTTGG-AAGTTTGGGGACAAAAATGT
1 AATTTTTGGAAAGTTAGGGGA-AAAAATGT
* *
17835 AATTTTTGGAAAATTTAGGGG-CAAAATGT
1 AATTTTTGG-AAAGTTAGGGGAAAAAATGT
* ** *
17864 AATTTTTGGAAAATTTAGGGGTCAAAATAT
1 AATTTTTGG-AAAGTTAGGGGAAAAAATGT
17894 AATTTTTGGAAA
1 AATTTTTGGAAA
17906 TTTTAGTGGT
Statistics
Matches: 128, Mismatches: 16, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
25 3 0.02
26 5 0.04
27 22 0.17
28 3 0.02
29 49 0.38
30 33 0.26
31 13 0.10
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
AATTTTTGGAAAGTTAGGGGAAAAAATGT
Found at i:17838 original size:56 final size:56
Alignment explanation
Indices: 17720--17905 Score: 180
Period size: 56 Copynumber: 3.2 Consensus size: 56
17710 TGTAAAATAC
**
17720 AATTTTTGGAAAGTTCAAGGGGAAAAAATGTAATTTTGGAAGTTTGGGGGTAAAATAAT
1 AATTTTTGGAAAGTTC-AGGGG-AAAAATGTAA-TTTGGAAGTTTGGGGCAAAAATAAT
* * * *
17779 AATTTTTAGAAAGTTCAGAGGTAAAATGTAATTTGGAAGTTTGGGGACAAAAAT-GT
1 AATTTTTGGAAAGTTCAGGGGAAAAATGTAATTTGGAAGTTTGGGG-CAAAAATAAT
* * * *
17835 AATTTTTGGAAAATTTAGGGGCAAAATGTAATTTTTGGAAAATTTAGGGGTC-AAAAT-AT
1 AATTTTTGGAAAGTTCAGGGGAAAAATGTAA--TTTGG-AAGTTT-GGGG-CAAAAATAAT
17894 AATTTTTGGAAA
1 AATTTTTGGAAA
17906 TTTTAGTGGT
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
56 42 0.39
57 14 0.13
58 9 0.08
59 38 0.35
60 5 0.05
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (56 bp):
AATTTTTGGAAAGTTCAGGGGAAAAATGTAATTTGGAAGTTTGGGGCAAAAATAAT
Found at i:17899 original size:59 final size:56
Alignment explanation
Indices: 17713--17921 Score: 206
Period size: 59 Copynumber: 3.6 Consensus size: 56
17703 ATTCAAATGT
* * *
17713 AAAATACAATTTTTGGAAAGTTCAAGGGGAAAAAATGTAATTTTGGAAGTTTGGGGGT-
1 AAAATATAATTTTTGGAAAGTT-TAGGGG-CAAAATGTAATTTTGGAAGTTT-GGGGTC
* * * * *
17771 AAAATAATAATTTTTAGAAAGTTCAGAGGTAAAATGTAA-TTTGGAAGTTTGGGGAC
1 AAAAT-ATAATTTTTGGAAAGTTTAGGGGCAAAATGTAATTTTGGAAGTTTGGGGTC
* * *
17827 AAAAATGTAATTTTTGGAAAATTTAGGGGCAAAATGTAATTTTTGGAAAATTTAGGGGTC
1 -AAAATATAATTTTTGGAAAGTTTAGGGGCAAAATGTAA-TTTTGG-AAGTTT-GGGGTC
* *
17887 AAAATATAATTTTTGGAAATTTTAGTGGTCAAAAT
1 AAAATATAATTTTTGGAAAGTTTAG-GGGCAAAAT
17922 ATGATTTTTG
Statistics
Matches: 126, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.03
56 38 0.30
57 14 0.11
58 14 0.11
59 43 0.34
60 13 0.10
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (56 bp):
AAAATATAATTTTTGGAAAGTTTAGGGGCAAAATGTAATTTTGGAAGTTTGGGGTC
Found at i:17911 original size:30 final size:30
Alignment explanation
Indices: 17713--17943 Score: 194
Period size: 30 Copynumber: 7.9 Consensus size: 30
17703 ATTCAAATGT
* * **
17713 AAAATACAATTTTTGGAAAGTTCAAGGGGAA
1 AAAATATAATTTTTGGAAAGTT-TAGGGGTC
* *
17744 AAAATGTAA-TTTTGG-AAGTTTGGGGGT-
1 AAAATATAATTTTTGGAAAGTTTAGGGGTC
* * *
17771 AAAATAATAATTTTTAGAAAGTTCAGAGGT-
1 AAAAT-ATAATTTTTGGAAAGTTTAGGGGTC
* *
17801 AAAATGTAA--TTTGG-AAGTTT-GGGGAC
1 AAAATATAATTTTTGGAAAGTTTAGGGGTC
* *
17827 AAAAATGTAATTTTTGGAAAATTTAGGGG-C
1 -AAAATATAATTTTTGGAAAGTTTAGGGGTC
* *
17857 AAAATGTAATTTTTGGAAAATTTAGGGGTC
1 AAAATATAATTTTTGGAAAGTTTAGGGGTC
* *
17887 AAAATATAATTTTTGGAAATTTTAGTGGTC
1 AAAATATAATTTTTGGAAAGTTTAGGGGTC
*
17917 AAAATATGATTTTT-GAAATGTTTAGGG
1 AAAATATAATTTTTGGAAA-GTTTAGGG
17944 ACCTTCTGAG
Statistics
Matches: 167, Mismatches: 22, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
25 3 0.02
26 5 0.03
27 18 0.11
28 7 0.04
29 50 0.30
30 73 0.44
31 11 0.07
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAATATAATTTTTGGAAAGTTTAGGGGTC
Found at i:19090 original size:3 final size:3
Alignment explanation
Indices: 19084--19188 Score: 138
Period size: 3 Copynumber: 34.0 Consensus size: 3
19074 CTTCCTTTTT
* * * * *
19084 TTA TTA TTAA GTA TTA TTA TTA CTG TTA TTA ATA TTTA TTA ATA TTTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA
19132 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19180 TTA TTA TTA
1 TTA TTA TTA
19189 GTAATATTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
3 83 0.93
4 6 0.07
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:20362 original size:209 final size:209
Alignment explanation
Indices: 20013--20897 Score: 1200
Period size: 209 Copynumber: 4.2 Consensus size: 209
20003 TTTGAGTCTA
** * * * * *
20013 GTTTCATTGATTTGGTCAACTTCTTAGTTTCTCATCAGGAAGATGACTGCATCATTTGTTTCAGT
1 GTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT
** * * * * * * **
20078 CTGCTTCTTTGTATTTCACCAGGAAGAC-GAATTTGGTCCACTCCTTAGTATCTCATCATAAAGC
66 CCACTTCTCTGTATCTCATCAGGAAGACAG-ATCTGGTCCACTTCTCAGTATCTCATCAGGAAGC
* * * *
20142 TAACCATTTTATTGCTTCGACCTGTTTCTTAGTATCTCATCAAGAAGTTGGAGTTCGAAGATTTG
130 TAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTG
20207 CTCACTTTGAGCTTG
195 CTCACTTTGAGCTTG
20222 GTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT
1 GTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT
** * * *
20287 CTGCTTCTCTGTATCTCATCAGGAAGAC-GAATTTAGTCCACTTCTCAATATCTCATCAGGAAGC
66 CCACTTCTCTGTATCTCATCAGGAAGACAG-ATCTGGTCCACTTCTCAGTATCTCATCAGGAAGC
* *
20351 TAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTG
130 TAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTG
20416 CTCACTTTGAGCTTG
195 CTCACTTTGAGCTTG
* * * * **
20431 GCTTCATTGATTTGGTCTTCTTCTTAGTACCTCATCAGGAAGATGACCGCATCTCTTGTTTTGAT
1 GTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT
* * *
20496 CCACTTCTCTGTGTCTCATCAAGAAGACAGATCTGGTCTACTTCTCAGTATCTCATCAGGAAGCT
66 CCACTTCTCTGTATCTCATCAGGAAGACAGATCTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
*
20561 AACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGC
131 AACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGC
20626 TCACTTTGAGCTTG
196 TCACTTTGAGCTTG
* * * * * **
20640 GTTTCATTGATTTGGTCTTCTTCTCAATACCTCATCAAGAAGATAACCGCATCTCTTGTTTTGAT
1 GTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT
* *
20705 CCACTTCTCTATGTCTCATCAGGAAGACAGATCTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
66 CCACTTCTCTGTATCTCATCAGGAAGACAGATCTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
* * * *
20770 AACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGGAAACTGGGGTTCGAAGTTTTGC
131 AACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGC
*
20835 TCA-TATTGAGCTTT
196 TCACT-TTGAGCTTG
* * * * * *
20849 GTTTCATTGAGTTGGTATACTTCTCTGCATCTCATCGGGAAGATGACCG
1 GTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCG
20898 ACTCATTATT
Statistics
Matches: 611, Mismatches: 63, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
208 1 0.00
209 609 1.00
210 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
GTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAAT
CCACTTCTCTGTATCTCATCAGGAAGACAGATCTGGTCCACTTCTCAGTATCTCATCAGGAAGCT
AACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGC
TCACTTTGAGCTTG
Found at i:21773 original size:47 final size:47
Alignment explanation
Indices: 21694--21785 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 47
21684 TGGTTTTAAT
* *
21694 ATGCCCTTTGCGGGTTTTCATCTTGACCCTTTTTTTTTAGTATAGAG
1 ATGCCCTTTGCGGGTTTTCATCTTCAACCTTTTTTTTTAGTATAGAG
*
21741 ATGCCCTTTTGCGGGTTTTCATC-TCAATCTTTTTTTTTAGTATAG
1 ATGCCC-TTTGCGGGTTTTCATCTTCAACCTTTTTTTTTAGTATAG
21786 TATTTTTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 25 0.61
48 16 0.39
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.49
Consensus pattern (47 bp):
ATGCCCTTTGCGGGTTTTCATCTTCAACCTTTTTTTTTAGTATAGAG
Found at i:32141 original size:29 final size:29
Alignment explanation
Indices: 32121--32441 Score: 273
Period size: 29 Copynumber: 11.0 Consensus size: 29
32111 TTTTGGATAC
*
32121 TCGAGGGTAAAATGGTAATTTTT-GAAGGT
1 TCGAGGGTAAAAT-GTAATTTTTGGAAAGT
*
32150 TCGGGGGTAAAATGTAATTTTTGGAAAGT
1 TCGAGGGTAAAATGTAATTTTTGGAAAGT
*
32179 TCG-GGGTCAAAAATGGAA-TTTTGGAAA-T
1 TCGAGGGT--AAAATGTAATTTTTGGAAAGT
* * *
32207 TCGGGGGTAAAATATAATTTTTTGAAAGT
1 TCGAGGGTAAAATGTAATTTTTGGAAAGT
*
32236 TCGGGGGGTAGAAATGTAA-TTTTGG-AAGT
1 TC-GAGGGTA-AAATGTAATTTTTGGAAAGT
** *
32265 TCGAGGACAAAAATGTAATTTTTGGAAAAT
1 TCGAGG-GTAAAATGTAATTTTTGGAAAGT
*
32295 TTGAGGGTAAAATGTAATTTTTGGAAAGT
1 TCGAGGGTAAAATGTAATTTTTGGAAAGT
* * *
32324 TTGAGGGAAAAATGTAATTTTTAG-AAGT
1 TCGAGGGTAAAATGTAATTTTTGGAAAGT
*** *
32352 TCGGAGACAAAAATGTAATTTTTAGAAA-T
1 TC-GAGGGTAAAATGTAATTTTTGGAAAGT
* * *
32381 TCAAAGGTAAAAATGTAATTTTTGGAAAAT
1 TCGAGGGT-AAAATGTAATTTTTGGAAAGT
* * *
32411 T-TAGGGGTTAAAATATAATTTTTAGAAAGT
1 TCGA-GGG-TAAAATGTAATTTTTGGAAAGT
32441 T
1 T
32442 TAGGGGTCAT
Statistics
Matches: 243, Mismatches: 32, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
27 7 0.03
28 42 0.17
29 133 0.55
30 53 0.22
31 8 0.03
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
TCGAGGGTAAAATGTAATTTTTGGAAAGT
Found at i:32409 original size:116 final size:117
Alignment explanation
Indices: 32158--32446 Score: 306
Period size: 116 Copynumber: 2.5 Consensus size: 117
32148 GTTCGGGGGT
* * * * * *
32158 AAAATGTAATTTTTGGAAAGTTCG-GGGTCAAAAATGGAA-TTTTGGAAA-TTCGGGGGTAAAAT
1 AAAATGTAATTTTTGGAAAATTTGAGGGT--AAAATGTAATTTTTGGAAAGTTTGAGGGAAAAAT
* * ** * * * *
32220 ATAATTTTTTGAAAGTTCGGGGGGTAGAAATGTAATTTTGGAAGTTCGAGGACA
64 ATAATTTTTAGAAAGTTCGGGAGACAAAAATGTAATTTTAGAAATTCAAGGACA
*
32274 AAAATGTAATTTTTGGAAAATTTGAGGGTAAAATGTAATTTTTGGAAAGTTTGAGGGAAAAATGT
1 AAAATGTAATTTTTGGAAAATTTGAGGGTAAAATGTAATTTTTGGAAAGTTTGAGGGAAAAATAT
*
32339 AATTTTTAG-AAGTTC-GGAGACAAAAATGTAATTTTTAGAAATTCAAAGG-TA
66 AATTTTTAGAAAGTTCGGGAGACAAAAATGTAA-TTTTAGAAATTC-AAGGACA
* *
32390 AAAATGTAATTTTTGGAAAATTT-AGGGGTTAAAATATAATTTTTAGAAAGTTT-AGGG
1 AAAATGTAATTTTTGGAAAATTTGA-GGG-TAAAATGTAATTTTTGGAAAGTTTGAGGG
32447 GTCATAATAT
Statistics
Matches: 148, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
115 21 0.14
116 78 0.53
117 49 0.33
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (117 bp):
AAAATGTAATTTTTGGAAAATTTGAGGGTAAAATGTAATTTTTGGAAAGTTTGAGGGAAAAATAT
AATTTTTAGAAAGTTCGGGAGACAAAAATGTAATTTTAGAAATTCAAGGACA
Found at i:33630 original size:3 final size:3
Alignment explanation
Indices: 33622--33674 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
33612 ACTTCCTTTT
* * * *
33622 TTA TTA TTAA GTA TTA TTA TTA CTG TTA TTA ATA TTA TTTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
33669 TTA TTA
1 TTA TTA
33675 GTAGTAGTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:33653 original size:22 final size:22
Alignment explanation
Indices: 33623--33674 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
33613 CTTCCTTTTT
33623 TATTATTAAGTATTA-TTATTAC
1 TATTATTAA-TATTATTTATTAC
* *
33645 TGTTATTAATATTATTTATTAT
1 TATTATTAATATTATTTATTAC
33667 TATTATTA
1 TATTATTA
33675 GTAGTAGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TATTATTAATATTATTTATTAC
Found at i:33673 original size:13 final size:13
Alignment explanation
Indices: 33622--33673 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
33612 ACTTCCTTTT
**
33622 TTATTATTAAGTA
1 TTATTATTATTTA
33635 TTATTATTACTGTTA
1 TTATTATTA-T-TTA
*
33650 TTAATATTATTTA
1 TTATTATTATTTA
33663 TTATTATTATT
1 TTATTATTATT
33674 AGTAGTAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 22 0.67
14 1 0.03
15 10 0.30
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:34346 original size:12 final size:13
Alignment explanation
Indices: 34329--34357 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
34319 ATTGGGCCCC
34329 AATTTGAG-TTGT
1 AATTTGAGCTTGT
34341 AATTTGAGCTTGT
1 AATTTGAGCTTGT
34354 AATT
1 AATT
34358 GTAATTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (13 bp):
AATTTGAGCTTGT
Found at i:34416 original size:6 final size:6
Alignment explanation
Indices: 34394--34509 Score: 90
Period size: 6 Copynumber: 20.7 Consensus size: 6
34384 GAATATTATT
* *
34394 AATTTA AA--TA AATTTA AACTTA AATTTA AA--TA AATTTA AACTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
** *
34438 AATTTA TAA--TA AATTTA AATTTCA AA--TA AATTTA AACCTA AA-ATA
1 AATTTA -AATTTA AATTTA AATTT-A AATTTA AATTTA AATTTA AATTTA
*
34483 AATTTA AATTTA AA-ATA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
34510 CTATTAAACC
Statistics
Matches: 88, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
4 13 0.15
5 11 0.12
6 59 0.67
7 5 0.06
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:34455 original size:17 final size:17
Alignment explanation
Indices: 34402--34509 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
34392 TTAATTTAAA
*
34402 TAAATTTAAACTTAAATT
1 TAAATTTAAA-ATAAATT
* *
34420 TAAA--TAAATTTAAACT
1 TAAATTTAAA-ATAAATT
*
34436 TAAATTTATAATAAATT
1 TAAATTTAAAATAAATT
*
34453 TAAATTTCAAATAAATT
1 TAAATTTAAAATAAATT
**
34470 TAAACCTAAAATAAATT
1 TAAATTTAAAATAAATT
34487 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
34504 TAAATT
1 TAAATT
34510 CTATTAAACC
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
16 14 0.18
17 55 0.72
18 7 0.09
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:37001 original size:12 final size:14
Alignment explanation
Indices: 36974--37009 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
36964 GTTAAAGATA
36974 TTTATGTATATTTT
1 TTTATGTATATTTT
36988 TTTATG-AT-TTTT
1 TTTATGTATATTTT
37000 TTTAT-TATAT
1 TTTATGTATAT
37010 CATGTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 11 0.55
13 3 0.15
14 6 0.30
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (14 bp):
TTTATGTATATTTT
Found at i:58841 original size:3 final size:3
Alignment explanation
Indices: 58820--58862 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
58810 GTATCTCCAT
*
58820 TTC TTC TTA TTC ATT- TTC TTC TTC TTC -TC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
58863 TTAGTAGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:58852 original size:14 final size:14
Alignment explanation
Indices: 58820--58861 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
58810 GTATCTCCAT
* *
58820 TTCTTCTTATTCATT
1 TTCTTCTTCTTC-TC
58835 TTCTTCTTCTTCTC
1 TTCTTCTTCTTCTC
58849 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
58862 TTTAGTAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCTTCTTCTTCTC
Found at i:65854 original size:17 final size:17
Alignment explanation
Indices: 65832--65864 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65822 TTACAAATAC
65832 AGTCATGCCATAGATAT
1 AGTCATGCCATAGATAT
*
65849 AGTCATGTCATAGATA
1 AGTCATGCCATAGATA
65865 CAGTTAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (17 bp):
AGTCATGCCATAGATAT
Found at i:66084 original size:40 final size:40
Alignment explanation
Indices: 66029--66135 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
66019 ATGACACGTC
* * *
66029 GCAGTGTTTATAGTGTCACTACCAGTTCAGTTGTAATATT
1 GCAGTGTTTACAGTGTCACTACCAGTTCAATTGAAATATT
* *
66069 GCAGTGTTTACAGTGTCACTATC-GATTCAATTGAAATTTT
1 GCAGTGTTTACAGTGTCACTACCAG-TTCAATTGAAATATT
* * * *
66109 GCAGTGTTAACAGCGTCAATGCCAGTT
1 GCAGTGTTTACAGTGTCACTACCAGTT
66136 TAGTAAATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.02
40 53 0.96
41 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (40 bp):
GCAGTGTTTACAGTGTCACTACCAGTTCAATTGAAATATT
Found at i:66728 original size:52 final size:52
Alignment explanation
Indices: 66662--66932 Score: 196
Period size: 55 Copynumber: 5.0 Consensus size: 52
66652 GCCCATGTTC
* * * * *
66662 CCCAGAACAATATACACACACTCTAACACACGCCCATGTGTCAACCCGTGT-
1 CCCAGAACAGTATACACACACCCTAACACACGCCCGTGTGCCAACCTGTGTG
* *
66713 CACCAGAACAGTATACACATACCCTGAA-ACACGTCCGTGTGCCAACCTGTGTG
1 C-CCAGAACAGTATACACACACCCT-AACACACGCCCGTGTGCCAACCTGTGTG
*
66766 CCTCTA-AACAGTATAAACACACACCCTAACACATGCCCGTGTGCCAACCTGTGTG
1 CC-C-AGAACAGTAT--ACACACACCCTAACACACGCCCGTGTGCCAACCTGTGTG
* * *
66821 CCTCTA-AACAGTATGGACACACACCCTGACAC-C-CCCTTGTGTGCCAGCCCGTGTG
1 CC-C-AGAACAGTAT--ACACACACCCTAACACACGCCC--GTGTGCCAACCTGTGTG
* * * * *
66876 CCTTCA-AATAGTATAGACACACACCCTAGACACACTCCCGTGTTCCAGCCCGTGTG
1 CC--CAGAACAGTAT--ACACACACCCTA-ACACACGCCCGTGTGCCAACCTGTGTG
66932 C
1 C
66933 GATCGCAAAG
Statistics
Matches: 186, Mismatches: 20, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
51 1 0.01
52 41 0.22
53 15 0.08
54 3 0.02
55 99 0.53
56 23 0.12
57 1 0.01
58 3 0.02
ACGTcount: A:0.28, C:0.36, G:0.16, T:0.20
Consensus pattern (52 bp):
CCCAGAACAGTATACACACACCCTAACACACGCCCGTGTGCCAACCTGTGTG
Found at i:66792 original size:55 final size:55
Alignment explanation
Indices: 66719--66932 Score: 215
Period size: 55 Copynumber: 3.9 Consensus size: 55
66709 GTGTCACCAG
* *
66719 AACAGTAT--ACACATACCCTGAAACACGTCCGTGTGCCAACCTGTGTGCCTCTA
1 AACAGTATAGACACACACCCTGAAACACGCCCGTGTGCCAACCTGTGTGCCTCTA
* *
66772 AACAGTATAAACACACACCCT-AACACATGCCCGTGTGCCAACCTGTGTGCCTCTA
1 AACAGTATAGACACACACCCTGAA-ACACGCCCGTGTGCCAACCTGTGTGCCTCTA
* * * *
66827 AACAGTATGGACACACACCCTG--ACACCCCCTTGTGTGCCAGCCCGTGTGCCT-TCA
1 AACAGTATAGACACACACCCTGAAACACGCCC--GTGTGCCAACCTGTGTGCCTCT-A
* * * * * *
66882 AATAGTATAGACACACACCCTAGACACACTCCCGTGTTCCAGCCCGTGTGC
1 AACAGTATAGACACACACCCT-GAAACACGCCCGTGTGCCAACCTGTGTGC
66933 GATCGCAAAG
Statistics
Matches: 138, Mismatches: 13, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
53 14 0.10
54 3 0.02
55 96 0.70
56 18 0.13
58 7 0.05
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (55 bp):
AACAGTATAGACACACACCCTGAAACACGCCCGTGTGCCAACCTGTGTGCCTCTA
Found at i:68163 original size:24 final size:24
Alignment explanation
Indices: 68128--68412 Score: 254
Period size: 24 Copynumber: 11.9 Consensus size: 24
68118 TTTATCTGAA
* * *
68128 TAGCTGGCGAGCGTAAATGTACAG
1 TAGCTGACGAGCGTAAACGTACAT
* *
68152 TAGCTGGA-GAGCGTAAACGCATAT
1 TAGCT-GACGAGCGTAAACGTACAT
*
68176 TAGCAT-ACGAGCGTAAACGTACAG
1 TAGC-TGACGAGCGTAAACGTACAT
** * * * *
68200 TAATTGGCGAGCGTAAATGCATAT
1 TAGCTGACGAGCGTAAACGTACAT
* *
68224 TAGCTGACGAGCATAAACGTACAG
1 TAGCTGACGAGCGTAAACGTACAT
* * * *
68248 TAGCTGGCGAGTGTAAACGCATAT
1 TAGCTGACGAGCGTAAACGTACAT
* *
68272 TAGATGACAAGCGTAAACGTACAT
1 TAGCTGACGAGCGTAAACGTACAT
* * *
68296 TAGCTAACGAGCGTAAATGTACAA
1 TAGCTGACGAGCGTAAACGTACAT
* * *
68320 TAGCT-AGCGAGTGTAAACGCATAT
1 TAGCTGA-CGAGCGTAAACGTACAT
*
68344 TAGCTAACGAGCGTAAACGTACAT
1 TAGCTGACGAGCGTAAACGTACAT
68368 TAGCTGACGAGCGTAAACGTACAT
1 TAGCTGACGAGCGTAAACGTACAT
**
68392 TAG-TGGTGAGCGTAAACGTAC
1 TAGCTGACGAGCGTAAACGTAC
68413 TAAACTTGCG
Statistics
Matches: 204, Mismatches: 51, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
23 19 0.09
24 182 0.89
25 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (24 bp):
TAGCTGACGAGCGTAAACGTACAT
Found at i:71359 original size:17 final size:17
Alignment explanation
Indices: 71339--71372 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
71329 TATCAAAAAG
71339 TGATCAAGTCATCCATC
1 TGATCAAGTCATCCATC
71356 TGATCAAGTCATCCATC
1 TGATCAAGTCATCCATC
71373 ACAAAGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
TGATCAAGTCATCCATC
Found at i:72433 original size:17 final size:18
Alignment explanation
Indices: 72408--72451 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
72398 ATGGAATTAG
*
72408 AATTGAATTGA-AAAAAT
1 AATTTAATTGAGAAAAAT
**
72425 AATTTAATTGAGAAATTT
1 AATTTAATTGAGAAAAAT
72443 AATTTAATT
1 AATTTAATT
72452 TAAGTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (18 bp):
AATTTAATTGAGAAAAAT
Done.