Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013101.1 Kokia drynarioides strain JFW-HI SEQ_128119, 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: 321516
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:2565 original size:24 final size:24
Alignment explanation
Indices: 2526--2584 Score: 109
Period size: 24 Copynumber: 2.4 Consensus size: 24
2516 GTTATTTTAA
2526 GAAAAGAAAAATAAATAAATTAAAT
1 GAAAAG-AAAATAAATAAATTAAAT
2551 GAAAAGAAAATAAATAAATTAAAT
1 GAAAAGAAAATAAATAAATTAAAT
2575 GAAAAGAAAA
1 GAAAAGAAAA
2585 ACAGGGATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (24 bp):
GAAAAGAAAATAAATAAATTAAAT
Found at i:2568 original size:19 final size:20
Alignment explanation
Indices: 2538--2579 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2528 AAAGAAAAAT
2538 AAATAAATTAAATGAAAAGA
1 AAATAAATTAAATGAAAAGA
* *
2558 AAATAAA-TAAATTAAATGA
1 AAATAAATTAAATGAAAAGA
2577 AAA
1 AAA
2580 GAAAAACAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (20 bp):
AAATAAATTAAATGAAAAGA
Found at i:3763 original size:5 final size:5
Alignment explanation
Indices: 3746--3775 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3736 CGGTTCTTCC
*
3746 CCCTT CCCAT CCCTT CCCTT CCCTT CCCTT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT
3776 GCATTCAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.60, G:0.00, T:0.37
Consensus pattern (5 bp):
CCCTT
Found at i:16974 original size:411 final size:411
Alignment explanation
Indices: 16207--17036 Score: 1482
Period size: 411 Copynumber: 2.0 Consensus size: 411
16197 TGACTCTAAT
16207 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAATGTTATGATGATTAGAAG
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAATGTTATGATGATTAGAAG
* * * *
16272 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGTTTAACTGATGGAAGGTCTGCCTCA
66 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCATCTCAAGCTTAACTGATGGAAGATCAGCCTCA
16337 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
131 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
* *
16402 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAATGCCCTCCCTAACC
196 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTCCCTAACC
16467 ATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGCCGATTCCATCCAAAAGT
261 ATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGCCGATTCCATCCAAAAGT
*
16532 TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAGTTCATTTCGTTC
326 TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGACTGTTCCAACAGTTCATTTCGTTC
*
16597 TGCCAACCTATAAATCTTGCC
391 TGCCAACCTATAAAACTTGCC
16618 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAA-GATTATGATGATTAGAA
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAATG-TTATGATGATTAGAA
*
16682 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCATCTCAAGCTTAACTGATTGAAGATCAGCCTC
65 GTCATAGTCTCCAATTTTTCAGAAAGTTGATCCATCTCAAGCTTAACTGATGGAAGATCAGCCTC
16747 AAGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAA
130 AAGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAA
*
16812 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTTCCTAAC
195 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTCCCTAAC
* * * **
16877 CATTCAATCTTTTCTTCAGGTTCCATGGGTTGCATTTGTGAGGGCATGTTGATTCCATCCAAAAG
260 CATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGCCGATTCCATCCAAAAG
* * *
16942 TTCCTCCCATTTTTGCACCAAGTGGTTCCTTTCCATTAAGGACTGTTCCAGCATTTCATTTCGTT
325 TTCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGACTGTTCCAACAGTTCATTTCGTT
17007 CTGCCAACCTATAAAACTTGCC
390 CTGCCAACCTATAAAACTTGCC
17029 CTGAAGGT
1 CTGAAGGT
17037 CCTCATATTT
Statistics
Matches: 400, Mismatches: 18, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
410 1 0.00
411 399 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (411 bp):
CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCAAAATGTTATGATGATTAGAAG
TCATAGTCTCCAATTTTTCAGAAAGTTGATCCATCTCAAGCTTAACTGATGGAAGATCAGCCTCA
AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTCCCTAACC
ATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGCCGATTCCATCCAAAAGT
TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGACTGTTCCAACAGTTCATTTCGTTC
TGCCAACCTATAAAACTTGCC
Found at i:22628 original size:6 final size:6
Alignment explanation
Indices: 22617--22648 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
22607 GTTTTTGTCT
22617 GGATTG GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GGATTG GG
22649 TTAGTGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:23180 original size:30 final size:31
Alignment explanation
Indices: 23139--23209 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
23129 GTCACATTTA
* *
23139 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAATAGTCACTAAACTTATCGAAAA-GTG
*
23169 ACAAAATAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAATAGTCACTAAACTTATCGAAAAGTG
23200 AC-AAATAGTC
1 ACAAAATAGTC
23210 CTCTTGTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 25 0.69
31 6 0.17
32 5 0.14
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (31 bp):
ACAAAATAGTCACTAAACTTATCGAAAAGTG
Found at i:24195 original size:30 final size:31
Alignment explanation
Indices: 24127--24198 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
24117 ACAACAAGAG
* *
24127 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACTTTTCGATAACTTGAGT
* *
24158 GATTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCGATAACTTGAGT
24188 GACTGTTTTGT
1 GACTGTTTTGT
24199 TAAATGTGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 17 0.49
31 13 0.37
32 5 0.14
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAACTTGAGT
Found at i:24331 original size:29 final size:30
Alignment explanation
Indices: 24288--24352 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
24278 TGACGGAAAA
* *
24288 GGACTGTTTTATCACA-TTTCAAAGTTGAG
1 GGACTGTTTTATCACATTTTCAAAATCGAG
*
24317 GGACTGTTTTGTCACATTTTCAAAATCGAG
1 GGACTGTTTTATCACATTTTCAAAATCGAG
24347 GGACTG
1 GGACTG
24353 AAATGTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (30 bp):
GGACTGTTTTATCACATTTTCAAAATCGAG
Found at i:27710 original size:118 final size:118
Alignment explanation
Indices: 27517--27752 Score: 463
Period size: 118 Copynumber: 2.0 Consensus size: 118
27507 TGTTAAGGTT
27517 TTTCTCCCAAACGAAAAGATAGTGTAGTTGAAATTGTGCCATGTGCGTTTCATTCTTTATTCCTT
1 TTTCTCCCAAACGAAAAGATAGTGTAGTTGAAATTGTGCCATGTGCGTTTCATTCTTTATTCCTT
27582 AAAATGAAATTAGAAATTGATCAAATTGCTATTTCTTGTTGAATGACAATTGC
66 AAAATGAAATTAGAAATTGATCAAATTGCTATTTCTTGTTGAATGACAATTGC
27635 TTTCTCCCAAACGAAAAGATAGTGTAGTTGAAATTGTGCCATGTGCGTTTCATTCTTTATTCCTT
1 TTTCTCCCAAACGAAAAGATAGTGTAGTTGAAATTGTGCCATGTGCGTTTCATTCTTTATTCCTT
*
27700 AAAATGAAATTAGAAATTGATCAAATTGTTATTTCTTGTTGAATGACAATTGC
66 AAAATGAAATTAGAAATTGATCAAATTGCTATTTCTTGTTGAATGACAATTGC
27753 GCCATTGTGT
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (118 bp):
TTTCTCCCAAACGAAAAGATAGTGTAGTTGAAATTGTGCCATGTGCGTTTCATTCTTTATTCCTT
AAAATGAAATTAGAAATTGATCAAATTGCTATTTCTTGTTGAATGACAATTGC
Found at i:29793 original size:29 final size:30
Alignment explanation
Indices: 29747--29815 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
29737 AAAAATGATG
*
29747 TATAAGAATTGGATC-AAATCAAAATTTAATA
1 TATAA-AATTGCATCAAAATCAAAATTT-ATA
29778 TATAAAATTGCA-CAAAATCAAAATTTATA
1 TATAAAATTGCATCAAAATCAAAATTTATA
29807 TATAAAATT
1 TATAAAATT
29816 ACATATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 13 0.36
30 18 0.50
31 5 0.14
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33
Consensus pattern (30 bp):
TATAAAATTGCATCAAAATCAAAATTTATA
Found at i:30866 original size:28 final size:32
Alignment explanation
Indices: 30807--30866 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 32
30797 TAAGTCATGT
*
30807 AATATTTTTAATTTAAATAAAAATACATAGTTC
1 AATATTTTTAATTT-AATAAAAATACACAGTTC
30840 AATATTTTTAA-TT-A-AAAAATA-ACAGTT
1 AATATTTTTAATTTAATAAAAATACACAGTT
30867 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 5 0.19
29 7 0.27
30 1 0.04
32 2 0.08
33 11 0.42
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
AATATTTTTAATTTAATAAAAATACACAGTTC
Found at i:35694 original size:22 final size:21
Alignment explanation
Indices: 35656--35696 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
35646 AGGGAGGATC
**
35656 AAAGTTAAATTGTAATTTTTA
1 AAAGTTAAATTAAAATTTTTA
35677 AAAGATTAAATTAAAATTTT
1 AAAG-TTAAATTAAAATTTT
35697 ATCATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
AAAGTTAAATTAAAATTTTTA
Found at i:48782 original size:29 final size:27
Alignment explanation
Indices: 48737--48791 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
48727 TAATAAATTA
*
48737 TAAAATAATGAGTAA-TTAAGTTTTTAT
1 TAAAATAATGAGCAATTTAA-TTTTTAT
48764 TAAAATAAATGATGCAATTTAATTTTTA
1 TAAAAT-AATGA-GCAATTTAATTTTTA
48792 AAGTAGTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 5 0.21
29 9 0.38
30 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (27 bp):
TAAAATAATGAGCAATTTAATTTTTAT
Found at i:66006 original size:24 final size:24
Alignment explanation
Indices: 65979--66058 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
65969 CTCTGTCCCC
*
65979 GCCTTTTGCTCTGCTTCTGCT-TCT
1 GCCTTTTGCTCTGCCTCTG-TATCT
* *
66003 GCCTTTGGCTCTGCCTCTGTCTCT
1 GCCTTTTGCTCTGCCTCTGTATCT
*
66027 GTCTTTTGCTCTGCCTCTGTATCT
1 GCCTTTTGCTCTGCCTCTGTATCT
*
66051 GTCTTTTG
1 GCCTTTTG
66059 TTCCACCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 49 0.98
ACGTcount: A:0.01, C:0.31, G:0.19, T:0.49
Consensus pattern (24 bp):
GCCTTTTGCTCTGCCTCTGTATCT
Found at i:66039 original size:48 final size:48
Alignment explanation
Indices: 65967--66080 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 48
65957 AACATTTGCT
* * * * *
65967 ACCTCTGTCCCCGCCTTTTGCTCTGCTTCTGCT-TCTGCCTTTGGCTCT
1 ACCTCTGTCTCTGTCTTTTGCTCTGCCTCTG-TATCTGCCTTTGGCTCC
* * * *
66015 GCCTCTGTCTCTGTCTTTTGCTCTGCCTCTGTATCTGTCTTTTGTTCC
1 ACCTCTGTCTCTGTCTTTTGCTCTGCCTCTGTATCTGCCTTTGGCTCC
66063 ACCTCTGTCTCTGTCTTT
1 ACCTCTGTCTCTGTCTTT
66081 GGCGCTGGCT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.03, C:0.35, G:0.16, T:0.46
Consensus pattern (48 bp):
ACCTCTGTCTCTGTCTTTTGCTCTGCCTCTGTATCTGCCTTTGGCTCC
Found at i:66067 original size:24 final size:24
Alignment explanation
Indices: 66016--66080 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
66006 TTTGGCTCTG
**
66016 CCTCTGTCTCTGTCTTTTGCTCTG
1 CCTCTGTCTCTGTCTTTTGCTCCA
* *
66040 CCTCTGTATCTGTCTTTTGTTCCA
1 CCTCTGTCTCTGTCTTTTGCTCCA
66064 CCTCTGTCTCTGTCTTT
1 CCTCTGTCTCTGTCTTT
66081 GGCGCTGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.03, C:0.32, G:0.14, T:0.51
Consensus pattern (24 bp):
CCTCTGTCTCTGTCTTTTGCTCCA
Found at i:70436 original size:29 final size:31
Alignment explanation
Indices: 70383--70457 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
70373 AAATTTTAAA
* *
70383 TTAATAATGAT-AAAATTATATTTTAACT-T
1 TTAAAAATGATAAAAATTATAATTTAACTAT
*
70412 TTAAAAATGATAAAAATT-TAATTTAATTAT
1 TTAAAAATGATAAAAATTATAATTTAACTAT
*
70442 TTAAAAATCATAAAAA
1 TTAAAAATGATAAAAA
70458 CAATAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (31 bp):
TTAAAAATGATAAAAATTATAATTTAACTAT
Found at i:78697 original size:18 final size:19
Alignment explanation
Indices: 78671--78709 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
78661 ACTATTTTAG
78671 TTTCCCTTTTA-TTTATTT
1 TTTCCCTTTTATTTTATTT
*
78689 TTTCTCTTTTATTTTATTT
1 TTTCCCTTTTATTTTATTT
78708 TT
1 TT
78710 ATACCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCCCTTTTATTTTATTT
Found at i:79112 original size:23 final size:20
Alignment explanation
Indices: 79076--79128 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
79066 CAATTAGTCA
*
79076 TAAATTTT-GAAATAAAAAT
1 TAAATTTTAAAAATAAAAAT
79095 ATAAAATTCTTAAAAATAAAAAT
1 -T-AAATT-TTAAAAATAAAAAT
79118 TAAATTTTAAA
1 TAAATTTTAAA
79129 TTTTAAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 6 0.21
21 10 0.34
22 3 0.10
23 10 0.34
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAATTTTAAAAATAAAAAT
Found at i:84074 original size:17 final size:17
Alignment explanation
Indices: 84052--84087 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
84042 CTGGGATATG
84052 TTGGTTTTTGAACATTA
1 TTGGTTTTTGAACATTA
84069 TTGGTTTTTGAACATTA
1 TTGGTTTTTGAACATTA
84086 TT
1 TT
84088 TTTAAGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (17 bp):
TTGGTTTTTGAACATTA
Found at i:90512 original size:10 final size:10
Alignment explanation
Indices: 90489--90526 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
90479 TTATTAATTT
90489 AAAATTTT-A
1 AAAATTTTAA
90498 AAAATTTTAA
1 AAAATTTTAA
*
90508 AAAATTTAAA
1 AAAATTTTAA
90518 TAAAATTTT
1 -AAAATTTT
90527 TTCATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 10 0.40
11 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:92173 original size:4 final size:4
Alignment explanation
Indices: 92164--92191 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
92154 ACAAAGGGAA
92164 AGGC AGGC AGGC AGGC AGGC AGGC AGGC
1 AGGC AGGC AGGC AGGC AGGC AGGC AGGC
92192 GTATGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.50, T:0.00
Consensus pattern (4 bp):
AGGC
Found at i:114222 original size:30 final size:28
Alignment explanation
Indices: 114188--114247 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
114178 TTTTAATTTG
114188 ATTCAATTAAAATAAATTAT-TAATATAATT
1 ATTCAATTAAAAT--ATTATGTAA-ATAATT
* *
114218 ATTCATTTATAATATTATGTAAATAATT
1 ATTCAATTAAAATATTATGTAAATAATT
114246 AT
1 AT
114248 ATTTATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.48
29 3 0.11
30 11 0.41
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (28 bp):
ATTCAATTAAAATATTATGTAAATAATT
Found at i:132417 original size:56 final size:56
Alignment explanation
Indices: 132324--132436 Score: 181
Period size: 56 Copynumber: 2.0 Consensus size: 56
132314 CTTATAAGCA
* * * *
132324 TGTCAAATGGCACAATGTCGTGAATGACATAGGCCCTTCCATCACCAATCCATGGT
1 TGTCAAATGGCACAATGTCGTAAAGGACACAGACCCTTCCATCACCAATCCATGGT
*
132380 TGTCAAATGGCACAATGTCGTAAAGGACACAGACCCTTCCATCACCGATCCATGGT
1 TGTCAAATGGCACAATGTCGTAAAGGACACAGACCCTTCCATCACCAATCCATGGT
132436 T
1 T
132437 TGGTTAAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (56 bp):
TGTCAAATGGCACAATGTCGTAAAGGACACAGACCCTTCCATCACCAATCCATGGT
Found at i:139396 original size:57 final size:58
Alignment explanation
Indices: 139308--139455 Score: 169
Period size: 58 Copynumber: 2.6 Consensus size: 58
139298 GTTATTAAAC
* * * *
139308 ACTCAAAAAAATATTTTTT-ATTTGTACTTTTTATATGT-TA-ACCATTA-ATTGAAAAAA
1 ACTCAAAAAAATATTTTTTAATTTG-AGTTTTT-T-GGTACAGACCATTAGATGGAAAAAA
* *
139365 ACTCAAAAAAATATTTTTTAATTTGAGTTTTTTGGTACAGATCATTAGGTGGAAAAAA
1 ACTCAAAAAAATATTTTTTAATTTGAGTTTTTTGGTACAGACCATTAGATGGAAAAAA
* *
139423 ACACAACAAAATATTTTTTAATTTGAGTTTTTT
1 ACTCAAAAAAATATTTTTTAATTTGAGTTTTTT
139456 TGATGCCGGC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
55 2 0.03
56 2 0.03
57 31 0.39
58 44 0.56
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (58 bp):
ACTCAAAAAAATATTTTTTAATTTGAGTTTTTTGGTACAGACCATTAGATGGAAAAAA
Found at i:139595 original size:11 final size:11
Alignment explanation
Indices: 139581--139606 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
139571 TTAATTTATT
139581 AATAAAATTAA
1 AATAAAATTAA
139592 AATAAAATTAA
1 AATAAAATTAA
139603 AATA
1 AATA
139607 TCATTTTGTT
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):
AATAAAATTAA
Found at i:145169 original size:18 final size:17
Alignment explanation
Indices: 145148--145191 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
145138 TTATATTCAG
*
145148 TTTTTATTTTCTTTTATA
1 TTTTTATTTTCTTCTA-A
**
145166 TTTTGGTTTTCTTCTAA
1 TTTTTATTTTCTTCTAA
145183 TTTTTATTT
1 TTTTTATTT
145192 GCCTTTGTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTCTTCTAA
Found at i:161846 original size:64 final size:63
Alignment explanation
Indices: 161734--161852 Score: 166
Period size: 64 Copynumber: 1.9 Consensus size: 63
161724 TATTTCAAAT
* ** * *
161734 GATGAAAAGGTTTAATGTTCCAATATTGTTTGGGATGAGTGGAGCTATGTTGCTCATGGGAAA
1 GATGAAAAGGTTTAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGCTGCTCATGGGAAA
* *
161797 GATGAAAAGGTTTAAATTTTTCAATATTGTTGGGGATGAGAAGAACTATGCTGCTC
1 GATGAAAAGGTTT-AATGTTCCAATATTGTTGGGGATGAGAAGAACTATGCTGCTC
161853 TGACTCTTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 13 0.27
64 35 0.73
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (63 bp):
GATGAAAAGGTTTAATGTTCCAATATTGTTGGGGATGAGAAGAACTATGCTGCTCATGGGAAA
Found at i:165831 original size:58 final size:58
Alignment explanation
Indices: 165761--165880 Score: 195
Period size: 58 Copynumber: 2.1 Consensus size: 58
165751 AAAATGAATT
* *
165761 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
1 GTTTAAGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
* * *
165819 GTTTAAGAGTGTTTTTTAAGAATGAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
1 GTTTAAGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
165877 GTTT
1 GTTT
165881 GTTGATGAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (58 bp):
GTTTAAGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGAGTTTA
Found at i:169885 original size:6 final size:6
Alignment explanation
Indices: 169875--169912 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
169865 ATAGATGTCC
* *
169875 ATCAAC ATCAAG ATAAAG ATCAAG ATCAAG ATCAAG AT
1 ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG ATCAAG AT
169913 AATGTTTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.53, C:0.16, G:0.13, T:0.18
Consensus pattern (6 bp):
ATCAAG
Found at i:174145 original size:19 final size:17
Alignment explanation
Indices: 174112--174146 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
174102 TATGCAGCAA
174112 ATTATATTTATTTAATG
1 ATTATATTTATTTAATG
174129 ATTATTATTTAATTTAAT
1 ATTA-TATTT-ATTTAAT
174147 ACTAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTATATTTATTTAATG
Found at i:192715 original size:31 final size:31
Alignment explanation
Indices: 192680--192752 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 31
192670 ATCTAATTTT
* *
192680 TATTTTTTTGTCACAAATAGCACCTAAATTA
1 TATTTTATTATCACAAATAGCACCTAAATTA
* * * * *
192711 TATTTCATTATCCCAAGTGGTACCTAAATTA
1 TATTTTATTATCACAAATAGCACCTAAATTA
*
192742 TATTTTGTTAT
1 TATTTTATTAT
192753 TCAAATTACC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (31 bp):
TATTTTATTATCACAAATAGCACCTAAATTA
Found at i:195248 original size:14 final size:14
Alignment explanation
Indices: 195226--195256 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
195216 ATGAGAAGAC
195226 AATAAAAATTCTTA
1 AATAAAAATTCTTA
*
195240 AATATAAATTCTTA
1 AATAAAAATTCTTA
195254 AAT
1 AAT
195257 GTATGTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAAAAATTCTTA
Found at i:195402 original size:14 final size:14
Alignment explanation
Indices: 195383--195417 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
195373 AAAAAATAAT
*
195383 TCATTTTTCAGAAA
1 TCATTTTTCAAAAA
*
195397 TCATTTTTTAAAAA
1 TCATTTTTCAAAAA
195411 TCATTTT
1 TCATTTT
195418 CAGTGAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.51
Consensus pattern (14 bp):
TCATTTTTCAAAAA
Found at i:199846 original size:22 final size:21
Alignment explanation
Indices: 199817--199857 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
199807 TTTTGACATA
*
199817 TATTTTTTAATATTTATTTTT
1 TATTTTTTAATATATATTTTT
*
199838 TATTATTTTATTATATATTT
1 TATT-TTTTAATATATATTT
199858 ATAGGATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TATTTTTTAATATATATTTTT
Found at i:204633 original size:20 final size:20
Alignment explanation
Indices: 204608--204650 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
204598 CGTCTTCGAG
204608 ACTAAGCAGTGAGGACATGT
1 ACTAAGCAGTGAGGACATGT
204628 ACTAAGCAGTGAGGACATGT
1 ACTAAGCAGTGAGGACATGT
204648 ACT
1 ACT
204651 TCACGGGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (20 bp):
ACTAAGCAGTGAGGACATGT
Found at i:206002 original size:29 final size:30
Alignment explanation
Indices: 205939--206002 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
205929 TAAAATATAT
* *
205939 ATAAATTTTGATTTAATGTGAATTATATAC
1 ATAAATTTTAATTTAATGTGAATTATACAC
**
205969 ATAAATTTTAATTTGGTGT-AATTATACAC
1 ATAAATTTTAATTTAATGTGAATTATACAC
*
205998 GTAAA
1 ATAAA
206003 ACTCTAATTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.44
Consensus pattern (30 bp):
ATAAATTTTAATTTAATGTGAATTATACAC
Found at i:206634 original size:30 final size:30
Alignment explanation
Indices: 206598--206665 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
206588 GATTTTATTT
* *
206598 CAATCACTCAAT-TT-TGAAAAAATGATAAAA
1 CAATCACT-AATGTTAT-AAAAAATAACAAAA
206628 CAATCACTAATGTTATAAAAAATAACAAAA
1 CAATCACTAATGTTATAAAAAATAACAAAA
*
206658 TAATCACT
1 CAATCACT
206666 GATTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 3 0.09
30 29 0.88
31 1 0.03
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (30 bp):
CAATCACTAATGTTATAAAAAATAACAAAA
Found at i:206674 original size:29 final size:30
Alignment explanation
Indices: 206614--206674 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
206604 CTCAATTTTG
* * *
206614 AAAAAATGATAAAACAATCACTAATGTTAT
1 AAAAAATAACAAAACAATCACTAATGTAAT
* *
206644 AAAAAATAACAAAATAATCACTGAT-TAAT
1 AAAAAATAACAAAACAATCACTAATGTAAT
206673 AA
1 AA
206675 TTTTGTTTAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAAAATAACAAAACAATCACTAATGTAAT
Found at i:209895 original size:15 final size:16
Alignment explanation
Indices: 209875--209904 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
209865 AAGTAAAATC
209875 ACAATCAAAA-CAATT
1 ACAATCAAAATCAATT
209890 ACAATCAAAATCAAT
1 ACAATCAAAATCAAT
209905 ACTACTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (16 bp):
ACAATCAAAATCAATT
Found at i:212405 original size:79 final size:79
Alignment explanation
Indices: 212311--212468 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
212301 TATATATATG
*
212311 AATAGTACTGTTGATTAATAATTGAAGAAAAGTTTGCCTGAAAGAATAGAAAGCATATGTATTGC
1 AATAGTACTGTTGATTAATAATTGAAGAAAAGTTTGCCTGAAAAAATAGAAAGCATATGTATTGC
212376 AAATTAATACACTT
66 AAATTAATACACTT
*
212390 AATAGTACTGTTGATTAATAATTGAATAAAAGTTTGCCTGAAAAAATAGAAAGCATATGTATTGC
1 AATAGTACTGTTGATTAATAATTGAAGAAAAGTTTGCCTGAAAAAATAGAAAGCATATGTATTGC
212455 AAATTAATACACTT
66 AAATTAATACACTT
212469 GGGCTTTGGC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (79 bp):
AATAGTACTGTTGATTAATAATTGAAGAAAAGTTTGCCTGAAAAAATAGAAAGCATATGTATTGC
AAATTAATACACTT
Found at i:213825 original size:2 final size:2
Alignment explanation
Indices: 213820--213846 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
213810 CAAAAAAAAA
213820 AT 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 AT A
213847 CAAACCAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:214304 original size:5 final size:5
Alignment explanation
Indices: 214294--214321 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
214284 CTATTCTCAC
214294 CCCTT CCCTT CCCTT CCCTT CCCTT CCC
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCC
214322 CTTTCAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (5 bp):
CCCTT
Found at i:226203 original size:12 final size:12
Alignment explanation
Indices: 226182--226212 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
226172 AATCAACAGT
226182 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
226194 AAAAAGAAAAAG
1 AAAAAAAAAAAG
226206 AAAAAAA
1 AAAAAAA
226213 GGACAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:226785 original size:17 final size:18
Alignment explanation
Indices: 226744--226791 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
226734 CACTTTTTAA
* *
226744 TTATTTTTAATTTCATAAT
1 TTATTTTTAA-TTCAAAAG
226763 TTATTTTTAATT-AAAAG
1 TTATTTTTAATTCAAAAG
*
226780 TTATTTTAAATT
1 TTATTTTTAATT
226792 TTATTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 14 0.54
18 2 0.08
19 10 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTTTTAATTCAAAAG
Found at i:241912 original size:62 final size:62
Alignment explanation
Indices: 241844--241964 Score: 197
Period size: 62 Copynumber: 2.0 Consensus size: 62
241834 TGAATTTGAA
241844 GTGAGGACACAATGAACCCTAATTCTTATTTGCGTTGGTATGGATGAACGGAAAATGCTTAG
1 GTGAGGACACAATGAACCCTAATTCTTATTTGCGTTGGTATGGATGAACGGAAAATGCTTAG
* * * * *
241906 GTGAGGATATAATGAATCCTAATTCTTATTTGCGTTGTTATGGATGAATGGAAAATGCT
1 GTGAGGACACAATGAACCCTAATTCTTATTTGCGTTGGTATGGATGAACGGAAAATGCT
241965 CAAGGATAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (62 bp):
GTGAGGACACAATGAACCCTAATTCTTATTTGCGTTGGTATGGATGAACGGAAAATGCTTAG
Found at i:249254 original size:12 final size:12
Alignment explanation
Indices: 249237--249272 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
249227 AAAGAGGTAG
*
249237 AGAGGAAGAGGA
1 AGAGGACGAGGA
249249 AGAGGACGAGGA
1 AGAGGACGAGGA
*
249261 CGAGGACGAGGA
1 AGAGGACGAGGA
249273 GGGCTCCTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.08, G:0.50, T:0.00
Consensus pattern (12 bp):
AGAGGACGAGGA
Found at i:249265 original size:18 final size:18
Alignment explanation
Indices: 249238--249272 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
249228 AAGAGGTAGA
249238 GAGGAAGAGGAAGAGGAC
1 GAGGAAGAGGAAGAGGAC
* *
249256 GAGGACGAGGACGAGGA
1 GAGGAAGAGGAAGAGGA
249273 GGGCTCCTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.51, T:0.00
Consensus pattern (18 bp):
GAGGAAGAGGAAGAGGAC
Found at i:261361 original size:19 final size:19
Alignment explanation
Indices: 261334--261370 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
261324 AGATATCAAA
*
261334 TTATGTCAAAATTAAAATT
1 TTATGTCAAAAATAAAATT
*
261353 TTATTTCAAAAATAAAAT
1 TTATGTCAAAAATAAAAT
261371 ATAGAGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
TTATGTCAAAAATAAAATT
Found at i:261881 original size:9 final size:9
Alignment explanation
Indices: 261867--261895 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
261857 TACTACTCTA
261867 ATGTAATTT
1 ATGTAATTT
261876 ATGTAATTT
1 ATGTAATTT
261885 ATGTAATTT
1 ATGTAATTT
261894 AT
1 AT
261896 AACACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (9 bp):
ATGTAATTT
Found at i:262497 original size:27 final size:27
Alignment explanation
Indices: 262467--262528 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
262457 ATAAATTTTT
*
262467 TTTTATTTTG-TGATATTCATTTTAGCA
1 TTTTATTTTGATGATATCCATTTTAG-A
262494 TTTT-TGTTTGAATGATATCCATTTTAGA
1 TTTTAT-TTTG-ATGATATCCATTTTAGA
262522 -TTTATTT
1 TTTTATTT
262529 AAGCATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
26 1 0.03
27 13 0.43
28 2 0.07
29 14 0.47
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (27 bp):
TTTTATTTTGATGATATCCATTTTAGA
Found at i:266049 original size:32 final size:33
Alignment explanation
Indices: 266006--266076 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 33
265996 CTAAACTTTT
* *
266006 TTTTTTGTCTAATTTGGTACTTAAACTTGACAC
1 TTTTTTGTCTAATTTGGTACCTAAACTTGAAAC
266039 TTTTTT-TCTAATTTGGTACCTAAACTTGAAAC
1 TTTTTTGTCTAATTTGGTACCTAAACTTGAAAC
266071 TTTTTT
1 TTTTTT
266077 AAGTTGGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.83
33 6 0.17
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (33 bp):
TTTTTTGTCTAATTTGGTACCTAAACTTGAAAC
Found at i:266084 original size:29 final size:31
Alignment explanation
Indices: 266007--266087 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 31
265997 TAAACTTTTT
* * *
266007 TTTTTGTCTAATTTGGTACTTAAACTTGACAC
1 TTTTT-TCTAAGTTGGTACCTAAACTTGAAAC
*
266039 TTTTTTTCTAATTTGGTACCTAAACTTGAAAC
1 -TTTTTTCTAAGTTGGTACCTAAACTTGAAAC
266071 -TTTTT-TAAGTTGGTACC
1 TTTTTTCTAAGTTGGTACC
266088 AAATTAGGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 11 0.24
30 5 0.11
32 24 0.53
33 5 0.11
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (31 bp):
TTTTTTCTAAGTTGGTACCTAAACTTGAAAC
Found at i:266988 original size:18 final size:19
Alignment explanation
Indices: 266951--266988 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
266941 TGTCATTCTT
*
266951 TAATTATAATTTAATGAAA
1 TAATTATAATTAAATGAAA
*
266970 TAATTA-AATTAAATTAAA
1 TAATTATAATTAAATGAAA
266988 T
1 T
266989 TTCAGATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAATTATAATTAAATGAAA
Found at i:267962 original size:17 final size:18
Alignment explanation
Indices: 267940--267981 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
267930 TTTTCAGTTG
267940 TAATTAATTTAAA-TT-TT
1 TAATTAA-TTAAATTTATT
267957 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
267975 TAATTAA
1 TAATTAA
267982 AAAATTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:267977 original size:14 final size:14
Alignment explanation
Indices: 267940--267982 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
267930 TTTTCAGTTG
267940 TAATTAATTTAAATTTT
1 TAATTAA-TTAAA--TT
267957 TAATTAATTAAATT
1 TAATTAATTAAATT
*
267971 TATTTAATTAAA
1 TAATTAATTAAA
267983 AAATTATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATTAATTAAATT
Found at i:267989 original size:16 final size:17
Alignment explanation
Indices: 267940--267990 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
267930 TTTTCAGTTG
*
267940 TAATTAATTTAAATT-TT
1 TAATTAA-TAAAATTATT
*
267957 TAATTAATTAAATTTATT
1 TAATTAA-TAAAATTATT
267975 TAATTAA-AAAATTATT
1 TAATTAATAAAATTATT
267991 CTCATCCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.27
17 13 0.43
18 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTAATAAAATTATT
Found at i:270908 original size:21 final size:21
Alignment explanation
Indices: 270859--270913 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
270849 TAAGATTACA
270859 GGTTATGAGTTTAGGATTCAAG
1 GGTT-TGAGTTTAGGATTCAAG
* * * *
270881 AGCTTGAATTTAGGATTTAAG
1 GGTTTGAGTTTAGGATTCAAG
270902 GGTTTGAGTTTA
1 GGTTTGAGTTTA
270914 CAAGGTATGA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.29, T:0.40
Consensus pattern (21 bp):
GGTTTGAGTTTAGGATTCAAG
Found at i:274740 original size:22 final size:22
Alignment explanation
Indices: 274710--274778 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
274700 ACGCTAGCAC
* *
274710 GCTTACTGTTTAGCAATGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
*
274733 GCTTCTGTTCAGCACTGTGTAT
1 GCTTCTGTTCAGCACTGTGTGT
274755 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
274777 GC
1 GC
274779 CTACTATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 38 0.90
23 4 0.10
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:274818 original size:25 final size:25
Alignment explanation
Indices: 274785--274836 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
274775 GTGCCTACTA
*
274785 TTTCTCCAGCACTTATGTGCTTCTG
1 TTTCCCCAGCACTTATGTGCTTCTG
*
274810 TTTCCCCAGCACTTATGTGCTTTTG
1 TTTCCCCAGCACTTATGTGCTTCTG
274835 TT
1 TT
274837 AAGTACTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.27, G:0.15, T:0.46
Consensus pattern (25 bp):
TTTCCCCAGCACTTATGTGCTTCTG
Found at i:291565 original size:26 final size:28
Alignment explanation
Indices: 291491--291567 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 28
291481 AAATTTTTAT
* *
291491 TATAATAAAAATTTTATTGATTTAATATA
1 TATAA-AAATATTTTATTAATTTAATATA
**
291520 TATAAAAATATAATATTAATTT-ATATA
1 TATAAAAATATTTTATTAATTTAATATA
*
291547 T-TAAAAATATTTTAATAATTT
1 TATAAAAATATTTTATTAATTT
291568 CGTAATTGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 17 0.41
27 6 0.15
28 13 0.32
29 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TATAAAAATATTTTATTAATTTAATATA
Found at i:297632 original size:16 final size:16
Alignment explanation
Indices: 297611--297641 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
297601 GCTTTTGAAA
*
297611 TTCTTTTTTTTCTTTT
1 TTCTTTTTTTACTTTT
297627 TTCTTTTTTTACTTT
1 TTCTTTTTTTACTTT
297642 GGATTATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTCTTTTTTTACTTTT
Found at i:297957 original size:35 final size:37
Alignment explanation
Indices: 297901--297977 Score: 104
Period size: 35 Copynumber: 2.1 Consensus size: 37
297891 TTAGTCATTT
*
297901 TGGGAGATTAAAAAGGGAAATATA-T-TTTTATTAAG
1 TGGGAGATTAAAAAGGAAAATATATTATTTTATTAAG
*
297936 TGGGCGATTAAAAAGGAAAATATACTTTATTTTATTAAG
1 TGGGAGATTAAAAAGGAAAATATA--TTATTTTATTAAG
297975 TGG
1 TGG
297978 ACAATTAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
35 22 0.61
38 1 0.03
39 13 0.36
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (37 bp):
TGGGAGATTAAAAAGGAAAATATATTATTTTATTAAG
Found at i:297985 original size:39 final size:35
Alignment explanation
Indices: 297907--297985 Score: 95
Period size: 39 Copynumber: 2.1 Consensus size: 35
297897 ATTTTGGGAG
* * *
297907 ATTAAAAAGGGAAATATATTTTTATTAAGTGGGCG
1 ATTAAAAAGGAAAATATATTTTTATTAAGTGGACA
297942 ATTAAAAAGGAAAATATACTTTATTTTATTAAGTGGACA
1 ATTAAAAAGGAAAATATA---T-TTTTATTAAGTGGACA
297981 ATTAA
1 ATTAA
297986 GCCTATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 17 0.46
38 1 0.03
39 19 0.51
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.35
Consensus pattern (35 bp):
ATTAAAAAGGAAAATATATTTTTATTAAGTGGACA
Found at i:302634 original size:18 final size:19
Alignment explanation
Indices: 302600--302654 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 19
302590 TTAAAAAATT
302600 ATAATTTTTATATTTTTCT-A
1 ATAA-TTTTATATTTTT-TAA
302620 ATAATTTTA-ATTTTTTAA
1 ATAATTTTATATTTTTTAA
302638 ATAATTTTCATATTTTT
1 ATAATTTT-ATATTTTT
302655 AATTTTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.03
18 15 0.47
19 6 0.19
20 10 0.31
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
ATAATTTTATATTTTTTAA
Found at i:304672 original size:69 final size:67
Alignment explanation
Indices: 304428--304672 Score: 438
Period size: 67 Copynumber: 3.6 Consensus size: 67
304418 AGTGATCTGC
* *
304428 ATGATATTAACTGATGACTATCAATTTGGATTAAGATATATCAAAAACCTCGATCAAGAGATAAA
1 ATGACATTAACTGACGACTATCAATTTGGATTAAGATATATCAAAAACCTCGATCAAGAGATAAA
304493 TA
66 TA
304495 ATGACATTAACTGACGACTATCAATTTGGATTAAGATATATCAAAAACCTCGATCAAGAGATAAA
1 ATGACATTAACTGACGACTATCAATTTGGATTAAGATATATCAAAAACCTCGATCAAGAGATAAA
304560 TA
66 TA
304562 ATGACATTAACTGACGACTATCAATTTGGATTAAGATATATCAAAAACCTCGATCAAGAGATAAA
1 ATGACATTAACTGACGACTATCAATTTGGATTAAGATATATCAAAAACCTCGATCAAGAGATAAA
304627 TTCA
66 -T-A
304631 ATGACATTAACTGACGACTAT-AAGTTTGGATTAAGATATATC
1 ATGACATTAACTGACGACTATCAA-TTTGGATTAAGATATATC
304673 CAATCCATCT
Statistics
Matches: 173, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
67 130 0.75
68 3 0.02
69 40 0.23
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (67 bp):
ATGACATTAACTGACGACTATCAATTTGGATTAAGATATATCAAAAACCTCGATCAAGAGATAAA
TA
Found at i:308823 original size:72 final size:71
Alignment explanation
Indices: 308736--308873 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 71
308726 CCTTGTTATT
*
308736 TATTTTTTAAATTTAACTAGGAAGCAAATGACTTTCTATAGAAAAAATATTATTATGATCATCAT
1 TATTTTTTAAATTTAACTAGGAAGCAAATGACTTTCTATAG-AAAAATATTATTAGGATCATCAT
308801 TTATTAC
65 TTATTAC
* * * * * * * * *
308808 TATTTTTTCACTTTAATTGGGAAGGAAATGACTTTTTATAGGAAAATGTTATTAGGATTATCATT
1 TATTTTTTAAATTTAACTAGGAAGCAAATGACTTTCTATAGAAAAATATTATTAGGATCATCATT
308873 T
66 T
308874 TTTTTTTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
71 21 0.38
72 35 0.62
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (71 bp):
TATTTTTTAAATTTAACTAGGAAGCAAATGACTTTCTATAGAAAAATATTATTAGGATCATCATT
TATTAC
Found at i:311178 original size:52 final size:52
Alignment explanation
Indices: 311095--311210 Score: 146
Period size: 52 Copynumber: 2.2 Consensus size: 52
311085 AATGCTTACG
* *
311095 ACTACCAAAGCTCTATATCATTACAATGAATCAAACA-GACTGTTGTTAATTC
1 ACTACCAAAGCTCTATATCATTACAACGAATCAAACATG-CTGTTATTAATTC
* *
311147 ACTACCAAGGCTCTAT-TACATTACAACGAATCAAACATGCTGTTATTATTTC
1 ACTACCAAAGCTCTATAT-CATTACAACGAATCAAACATGCTGTTATTAATTC
**
311199 ACTGTCAAAGCT
1 ACTACCAAAGCT
311211 TTATGTATGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 1 0.02
52 53 0.96
53 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (52 bp):
ACTACCAAAGCTCTATATCATTACAACGAATCAAACATGCTGTTATTAATTC
Found at i:316115 original size:24 final size:24
Alignment explanation
Indices: 316081--316131 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
316071 AATTTGACTC
* *
316081 AAACAACTAAACAGAGTTTAATTA
1 AAACAAATAAACAGAGTTTAACTA
316105 AAACAAATAAACAGAGTTTAACTA
1 AAACAAATAAACAGAGTTTAACTA
316129 AAA
1 AAA
316132 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTA
Found at i:316903 original size:23 final size:23
Alignment explanation
Indices: 316872--316969 Score: 117
Period size: 23 Copynumber: 4.2 Consensus size: 23
316862 TGTGTTGGGC
*
316872 AACAAAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
316895 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
316918 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
* *
316942 TAATAGAGAGCACGAGACA-TGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
316966 AACA
1 AACA
316970 AAAAGCGCGC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
23 44 0.69
24 2 0.03
25 14 0.22
26 4 0.06
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:320452 original size:24 final size:24
Alignment explanation
Indices: 320425--320499 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
320415 AATTTGACTC
*
320425 AAACAACTAAACAGAATTTAATTG
1 AAACAAATAAACAGAATTTAATTG
320449 AAACAAATAAACAGAATTTAATTG
1 AAACAAATAAACAGAATTTAATTG
* *
320473 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAATTTAATTG
320497 AAA
1 AAA
320500 GATTATTTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAATTG
Done.