Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014922.1 Kokia drynarioides strain JFW-HI SEQ_129965, 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: 257070
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 291 characters in sequence are not A, C, G, or T
Found at i:108 original size:25 final size:24
Alignment explanation
Indices: 80--155 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
70 AATTTATTTG
80 ATAAAAAATTTTATTATACTTATAA
1 ATAAAAAATTTTATTATA-TTATAA
* * *
105 AT-AAGAATTTTGATTCTATTAAAA
1 ATAAAAAATTTT-ATTATATTATAA
*
129 ATAAATAAA-TTTA-TATATAATAA
1 ATAAA-AAATTTTATTATATTATAA
152 ATAA
1 ATAA
156 TTTCATATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
23 11 0.27
24 16 0.39
25 12 0.29
26 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (24 bp):
ATAAAAAATTTTATTATATTATAA
Found at i:3778 original size:44 final size:44
Alignment explanation
Indices: 3714--3813 Score: 191
Period size: 44 Copynumber: 2.3 Consensus size: 44
3704 TATATATTTC
3714 TTAGACACCTGCCATCCCATTCTTTCATTCCTTGACGAGAACCA
1 TTAGACACCTGCCATCCCATTCTTTCATTCCTTGACGAGAACCA
*
3758 TTAGACACCTGCCATTCCATTCTTTCATTCCTTGACGAGAACCA
1 TTAGACACCTGCCATCCCATTCTTTCATTCCTTGACGAGAACCA
3802 TTAGACACCTGC
1 TTAGACACCTGC
3814 TTCATTGCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.30
Consensus pattern (44 bp):
TTAGACACCTGCCATCCCATTCTTTCATTCCTTGACGAGAACCA
Found at i:5252 original size:21 final size:22
Alignment explanation
Indices: 5219--5259 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5209 AAGTTAATCT
* *
5219 AATCGAGTTATTTGATTTTTCA
1 AATCGAGTAATTTAATTTTTCA
5241 AATC-AGTAATTTAATTTTT
1 AATCGAGTAATTTAATTTTT
5260 TTGTGTTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (22 bp):
AATCGAGTAATTTAATTTTTCA
Found at i:7849 original size:22 final size:24
Alignment explanation
Indices: 7804--7851 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
7794 GAAGTTAGAG
7804 ATTTTTTATAATTAATTTAAAACAT
1 ATTTTTTAT-ATTAATTTAAAACAT
*
7829 ATTTTTTAT-TT-ATTTACAACAT
1 ATTTTTTATATTAATTTAAAACAT
7851 A
1 A
7852 AAAATTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 11 0.50
23 2 0.09
25 9 0.41
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTTTTATATTAATTTAAAACAT
Found at i:8849 original size:4 final size:4
Alignment explanation
Indices: 8840--8909 Score: 54
Period size: 4 Copynumber: 17.5 Consensus size: 4
8830 CAAATAAACG
* * *
8840 AGAA AGAA AGAA ATAA AAAA AGAA AG-A AGAA AGAGA GGAA AGAA AG-A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA-A AGAA AGAA AGAA
* * *
8887 AGAA GGAGA GGAA AGAA AAAA AG
1 AGAA AGA-A AGAA AGAA AGAA AG
8910 GAGAGAAAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
3 6 0.11
4 40 0.75
5 7 0.13
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:8881 original size:20 final size:20
Alignment explanation
Indices: 8858--8904 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
8848 AGAAATAAAA
8858 AAAGAAAGAAGAAAGAGAGG
1 AAAGAAAGAAGAAAGAGAGG
*
8878 AAAGAAAGAAGAAGGAGAGG
1 AAAGAAAGAAGAAAGAGAGG
8898 AAAGAAA
1 AAAGAAA
8905 AAAAGGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAGAAAGAGAGG
Found at i:8915 original size:20 final size:21
Alignment explanation
Indices: 8858--8919 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 21
8848 AGAAATAAAA
8858 AAAGAAAGAAGAA-AGAGAGG
1 AAAGAAAGAAGAAGAGAGAGG
8878 AAAGAAAGAAGAAG-GAGAGG
1 AAAGAAAGAAGAAGAGAGAGG
*
8898 AAAGAAA-AA-AAG-GAGAGA
1 AAAGAAAGAAGAAGAGAGAGG
8916 AAAG
1 AAAG
8920 TAATATGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 12 0.30
19 2 0.05
20 26 0.65
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAGAAGAGAGAGG
Found at i:11995 original size:21 final size:22
Alignment explanation
Indices: 11971--12025 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
11961 TAGGGTATTG
*
11971 AATTTAGGGTTTACT-ATTTAT
1 AATTTAGGGTTTACTGATTTAA
* *
11992 AA-TTAGGGTTTAGTGTTTTAA
1 AATTTAGGGTTTACTGATTTAA
12013 AATTTAGGGTTTA
1 AATTTAGGGTTTA
12026 AGTTTAAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.38
21 8 0.28
22 10 0.34
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (22 bp):
AATTTAGGGTTTACTGATTTAA
Found at i:12030 original size:21 final size:21
Alignment explanation
Indices: 11971--12030 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
11961 TAGGGTATTG
* *
11971 AATTTAGGGTTT-ACTATTTAT
1 AATTTAGGGTTTAAGT-TTTAA
*
11992 AA-TTAGGGTTTAGTGTTTTAA
1 AATTTAGGGTTTA-AGTTTTAA
12013 AATTTAGGGTTTAAGTTT
1 AATTTAGGGTTTAAGTTT
12031 AAGGTTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 9 0.28
21 12 0.38
22 11 0.34
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (21 bp):
AATTTAGGGTTTAAGTTTTAA
Found at i:12364 original size:45 final size:45
Alignment explanation
Indices: 12298--12386 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
12288 GGAGGAGTAG
* * *
12298 AGTATTGCGGTGGCTCATCAAACTGAGCCTGATATCCTTGGCTTC
1 AGTATTACGGTGGCTCATCAAACTCAGCCTAATATCCTTGGCTTC
*
12343 AGTATTACGGTGGCTCGTCAAACTCAGCCTAATATCCTTGGCTT
1 AGTATTACGGTGGCTCATCAAACTCAGCCTAATATCCTTGGCTT
12387 GATGAGCTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.31
Consensus pattern (45 bp):
AGTATTACGGTGGCTCATCAAACTCAGCCTAATATCCTTGGCTTC
Found at i:14304 original size:16 final size:15
Alignment explanation
Indices: 14283--14331 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
14273 TGATGGGGAT
14283 ATTATTTTGGTAATTA
1 ATTATTTT-GTAATTA
14299 ATTATTTT-TATATT-
1 ATTATTTTGTA-ATTA
14313 A-TATTTTGATAATTA
1 ATTATTTTG-TAATTA
14328 ATTA
1 ATTA
14332 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 10 0.36
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
ATTATTTTGTAATTA
Found at i:15323 original size:18 final size:18
Alignment explanation
Indices: 15302--15337 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15292 AATTAAATTT
15302 AAAATTAACCAAACTTAA
1 AAAATTAACCAAACTTAA
* *
15320 AAAATTAATCAAATTTAA
1 AAAATTAACCAAACTTAA
15338 CTTTCTTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTAACCAAACTTAA
Found at i:15495 original size:13 final size:14
Alignment explanation
Indices: 15469--15508 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
15459 CTCATTCTCC
*
15469 TTCTTCCTTCTTTCT
1 TTCTTTCTT-TTTCT
15484 TTCTTT-TTTTTCT
1 TTCTTTCTTTTTCT
15497 TTCTTTCTTTTT
1 TTCTTTCTTTTT
15509 TCCTTCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 11 0.48
14 7 0.30
15 5 0.22
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTCTTTTTCT
Found at i:15496 original size:17 final size:17
Alignment explanation
Indices: 15476--15509 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15466 TCCTTCTTCC
15476 TTCTTTCTTTCTTTTTT
1 TTCTTTCTTTCTTTTTT
15493 TTCTTTCTTTCTTTTTT
1 TTCTTTCTTTCTTTTTT
15510 CCTTCTTCTC
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:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTCTTTCTTTCTTTTTT
Found at i:17113 original size:15 final size:15
Alignment explanation
Indices: 17093--17122 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17083 ATTCCAAATT
17093 AAAAAGAAAAAAGAA
1 AAAAAGAAAAAAGAA
*
17108 AAAAAGAAAGAAGAA
1 AAAAAGAAAAAAGAA
17123 GAAGCAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAGAA
Found at i:18339 original size:21 final size:21
Alignment explanation
Indices: 18315--18354 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18305 AGAAATTGTA
18315 GTGAAGACGAAGATGATGGTG
1 GTGAAGACGAAGATGATGGTG
* * *
18336 GTGATGATGATGATGATGG
1 GTGAAGACGAAGATGATGG
18355 AACACAACTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.42, T:0.25
Consensus pattern (21 bp):
GTGAAGACGAAGATGATGGTG
Found at i:22662 original size:30 final size:30
Alignment explanation
Indices: 22617--22684 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
22607 AATTAATCGG
*
22617 TTAATCGACTGAATTCGGTTAATCACTCAA
1 TTAATCGACTAAATTCGGTTAATCACTCAA
* **
22647 TTAATTGACTAAATTCGGTTAATCACTCGG
1 TTAATCGACTAAATTCGGTTAATCACTCAA
22677 TTAATCGA
1 TTAATCGA
22685 ATTAATTTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (30 bp):
TTAATCGACTAAATTCGGTTAATCACTCAA
Found at i:26641 original size:18 final size:16
Alignment explanation
Indices: 26607--26655 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
26597 TCAATTGTAA
*
26607 TTAATTTAAAAATTTTAA
1 TTAA-TTAAAAA-TTTAT
26625 TTAATT--AAATTTAT
1 TTAATTAAAAATTTAT
26639 TTAATTAAAAATTTAT
1 TTAATTAAAAATTTAT
26655 T
1 T
26656 CTCATCCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 9 0.32
17 2 0.07
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATTAAAAATTTAT
Found at i:30407 original size:205 final size:201
Alignment explanation
Indices: 30030--30434 Score: 571
Period size: 205 Copynumber: 2.0 Consensus size: 201
30020 AATAAGTTTC
* * * * *
30030 TTCTTAGTTCGAGGCTCAGGTGTCAGAGTTGGTTACCATTCTAAAGCATTACTCTTCTATCTGAA
1 TTCTTAGTTCGAGGCTCAGGTGCCAGAGTTAGTTACCATTCCAAAGCATTACACATCTATCTGAA
** *
30095 TGTGACTTTTCATAGCTGCTTGGTTATCAAGAACAAACTCACATGTTATGATTTTTACTTCGATT
66 CATGACTTTTCATAGCTGCTTGGTAATCAAGAACAAACTCACATGTTATGATTTTTACTTCGATT
* *
30160 ATGATATCTTTTCATTGTGGGTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTAAT
131 ATGATATCCTTTCATTGTGAGTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTAAT
30225 TCAAGT
196 TCAAGT
* * *
30231 TTCTTAGTTTGAGG-TCTGGGTGCCAGAGTTAGTTACCATTCCAAAGCTTTACACATCTATCTGA
1 TTCTTAGTTCGAGGCTC-AGGTGCCAGAGTTAGTTACCATTCCAAAGCATTACACATCTATCTGA
* * * * *
30295 ACATTAGTTTTCATTGCTGCTTGGTAATTAAGATGCTCACAAAGTCACATGTTATGA-TTTTACT
65 ACATGACTTTTCATAGCTGCTTGGTAATCAAGA-----ACAAACTCACATGTTATGATTTTTACT
*
30359 TTGATTATGATATCCTTTCATTGTGAGTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATT
125 TCGATTATGATATCCTTTCATTGTGAGTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATT
30424 GTTAATTCAAG
190 GTTAATTCAAG
30435 CTCCCACTTT
Statistics
Matches: 179, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
200 2 0.01
201 79 0.44
205 80 0.45
206 18 0.10
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (201 bp):
TTCTTAGTTCGAGGCTCAGGTGCCAGAGTTAGTTACCATTCCAAAGCATTACACATCTATCTGAA
CATGACTTTTCATAGCTGCTTGGTAATCAAGAACAAACTCACATGTTATGATTTTTACTTCGATT
ATGATATCCTTTCATTGTGAGTGGATTTGTAGTCAGGGTAGTTGGATTTATGAAACATTGTTAAT
TCAAGT
Found at i:36283 original size:52 final size:51
Alignment explanation
Indices: 36188--36380 Score: 160
Period size: 52 Copynumber: 3.7 Consensus size: 51
36178 ATTTCACTTC
* * * *
36188 ATTCATATACTCACGATGACACATAG-CTACCGAATCT-TATAATCCACGAGAG
1 ATTCATATACTCACGATGACACATAGTC-ATCGGACCTCT-TAATCC-CGAAAG
* *
36240 ATTCGTATACTCACGATGACACAAAGTCATCGGACCTCTTAAT-CCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCCG-AAA-G
* * * * * *
36292 ATCCATATACTCAAGATAACACAGAGTCATTGGACCTCGTAAT-CCGTAAAAG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCCG--AAAG
* * *
36344 ATTCATTTACTCACGATGACACTTAGTCATCAGACCT
1 ATTCATATACTCACGATGACACATAGTCATCGGACCT
36381 TTTTTCATTT
Statistics
Matches: 114, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
50 2 0.02
51 3 0.03
52 104 0.91
53 5 0.04
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCCGAAAG
Found at i:37285 original size:20 final size:19
Alignment explanation
Indices: 37237--37285 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
37227 ATTTAGACTT
* *
37237 TCATAATTAGCTTCATTAA
1 TCATATTTAGCTTAATTAA
*
37256 TCACTTTTTAGCTTTAATTAA
1 TCA-TATTTAGC-TTAATTAA
37277 TCATATTTA
1 TCATATTTA
37286 CTTCTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 11 0.46
21 10 0.42
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (19 bp):
TCATATTTAGCTTAATTAA
Found at i:44460 original size:16 final size:16
Alignment explanation
Indices: 44411--44460 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 16
44401 TTATTAAAGT
44411 TTAAAGTTTTATA-TA
1 TTAAAGTTTTATATTA
44426 -TAATA-TTTTATACATTA
1 TTAA-AGTTTTAT--ATTA
44443 TTAAAGTTTTATATTA
1 TTAAAGTTTTATATTA
44459 TT
1 TT
44461 TATAAGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 7 0.24
17 3 0.10
18 9 0.31
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (16 bp):
TTAAAGTTTTATATTA
Found at i:48671 original size:20 final size:23
Alignment explanation
Indices: 48646--48690 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
48636 TTTGACACTA
48646 TTCTTTTA-A-TGCCTTG-TTTT
1 TTCTTTTACAGTGCCTTGATTTT
48666 TTCTTTTACAGTGCCTTGATTTT
1 TTCTTTTACAGTGCCTTGATTTT
48689 TT
1 TT
48691 TTCTGGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 1 0.05
22 7 0.32
23 6 0.27
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.62
Consensus pattern (23 bp):
TTCTTTTACAGTGCCTTGATTTT
Found at i:49473 original size:17 final size:17
Alignment explanation
Indices: 49451--49485 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
49441 TTTTTCTCCC
49451 AAAATATTTG-TAAAAAT
1 AAAATA-TTGATAAAAAT
49468 AAAATATTGATAAAAAT
1 AAAATATTGATAAAAAT
49485 A
1 A
49486 TTTAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAATATTGATAAAAAT
Found at i:49943 original size:15 final size:17
Alignment explanation
Indices: 49923--49955 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
49913 ATTTGTTGGG
49923 TTTTCA-AC-AAATTTT
1 TTTTCACACAAAATTTT
49938 TTTTCACACAAAATTTT
1 TTTTCACACAAAATTTT
49955 T
1 T
49956 CTGCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTCACACAAAATTTT
Found at i:51034 original size:184 final size:181
Alignment explanation
Indices: 50725--51088 Score: 701
Period size: 184 Copynumber: 2.0 Consensus size: 181
50715 AATTTTTCAC
50725 ATAACATACTTATCTTTTTTGATAAGTCTGAAAAGAAGAAATTTCTACCATAATTTATTATTCCT
1 ATAACATACTTATCTTTTTTGATAAGTCTGAAAAGAAGAAATTTCTACCATAATTTATTATTCCT
50790 AAAAATTGTTGAAGTTGTTTTTTATATTCAAATTTTTCAGGAAATTCTTTTATTTTAACTATGAT
66 AAAAATTGTTGAAGTTGTTTTTTATATTCAAATTTTTCAGGAAATTCTTTTATTTTAACTATGAT
50855 GTGATCTTGTAATTGAAGACCATCATTAGATAATTTCTACATTCCTAAAAATTG
131 GTGATCTTGTAATTGAAGACCATCATTAGATAATTT-TA-A-TCCTAAAAATTG
50909 ATAACATACTTATCTTTTTTGATAAGTCTGAAAAGAAGAAATTTCTACCATAATTTATTATTCCT
1 ATAACATACTTATCTTTTTTGATAAGTCTGAAAAGAAGAAATTTCTACCATAATTTATTATTCCT
50974 AAAAATTGTTGAAGTTGTTTTTTATATTCAAATTTTTCAGGAAATTCTTTTATTTTAACTATGAT
66 AAAAATTGTTGAAGTTGTTTTTTATATTCAAATTTTTCAGGAAATTCTTTTATTTTAACTATGAT
51039 GTGATCTTGTAATTGAAGACCATCATTAGATAATTTTAATCCTAAAAATT
131 GTGATCTTGTAATTGAAGACCATCATTAGATAATTTTAATCCTAAAAATT
51089 CTATTTATGT
Statistics
Matches: 180, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
181 11 0.06
182 1 0.01
183 2 0.01
184 166 0.92
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (181 bp):
ATAACATACTTATCTTTTTTGATAAGTCTGAAAAGAAGAAATTTCTACCATAATTTATTATTCCT
AAAAATTGTTGAAGTTGTTTTTTATATTCAAATTTTTCAGGAAATTCTTTTATTTTAACTATGAT
GTGATCTTGTAATTGAAGACCATCATTAGATAATTTTAATCCTAAAAATTG
Found at i:53601 original size:24 final size:24
Alignment explanation
Indices: 53572--53630 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
53562 TTCTGTTACG
53572 ATTCTTTTTCCTAACAAATTTTCTT
1 ATTCTTTTTCCTAA-AAATTTTCTT
** *
53597 -TTCTTTTTATTAAAATTTTTCTT
1 ATTCTTTTTCCTAAAAATTTTCTT
*
53620 ATTCTTATTCC
1 ATTCTTTTTCC
53631 ATGGTTTCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTCTTTTTCCTAAAAATTTTCTT
Found at i:58972 original size:106 final size:107
Alignment explanation
Indices: 58799--59006 Score: 269
Period size: 106 Copynumber: 2.0 Consensus size: 107
58789 AACTCGAGTC
* * * *
58799 CTTCACAACATTGATTGATGTTGTTCAATTTGACTTAACCATGTAAATATAACATGCGGAATGTG
1 CTTCACAACATTGATTGATCTTGTTCAATTCGACTCAACAATGTAAATATAACATGCGGAATGTG
* *
58864 TTAAGATTCAA-TCTGCATTCACGAAAAATACCTAATATTGAA
66 TTAAGATTCAACT-TGCATTCACAAAAAAGACCTAATATTGAA
* * * * *
58906 CTTCATAATATTGATTGATCTTGTTCAA-TCGACTCAATAATGTAAATTTAACACT-TGGAATGT
1 CTTCACAACATTGATTGATCTTGTTCAATTCGACTCAACAATGTAAATATAACA-TGCGGAATGT
*
58969 GTTAAGGTTCAACTTGCATTCACAAAAAAGACCTAATA
65 GTTAAGATTCAACTTGCATTCACAAAAAAGACCTAATA
59007 CTGAGAATAA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
106 60 0.69
107 27 0.31
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (107 bp):
CTTCACAACATTGATTGATCTTGTTCAATTCGACTCAACAATGTAAATATAACATGCGGAATGTG
TTAAGATTCAACTTGCATTCACAAAAAAGACCTAATATTGAA
Found at i:63177 original size:3 final size:3
Alignment explanation
Indices: 63169--63199 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
63159 TTTAACCTTT
63169 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
63200 GTAGATAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:66272 original size:25 final size:23
Alignment explanation
Indices: 66238--66307 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 23
66228 TTTTAAGATC
*
66238 ATATATTATTTTTTATAATTTAAAA
1 ATATAATATTTTTT-TAATTT-AAA
*
66263 ATATCATATTATTTTTAATTTAAA
1 ATATAATATT-TTTTTAATTTAAA
* *
66287 ATTTAATATTTTTTTCATTTA
1 ATATAATATTTTTTTAATTTA
66308 TTAAAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 10 0.26
24 11 0.28
25 14 0.36
26 4 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATAATATTTTTTTAATTTAAA
Found at i:66538 original size:22 final size:23
Alignment explanation
Indices: 66492--66538 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
66482 TTTACATGTT
* *
66492 TAAAATTTTAATTAAAAAATTATA
1 TAAAATTATAATT-AAAAATGATA
66516 TAAAATTATAATT-AAAATGATA
1 TAAAATTATAATTAAAAATGATA
66538 T
1 T
66539 TTTTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAATTATAATTAAAAATGATA
Found at i:73823 original size:21 final size:21
Alignment explanation
Indices: 73798--73854 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
73788 TTTATTTAGC
*
73798 AATTGATTACTTATGTAATAA
1 AATTGATTAATTATGTAATAA
*
73819 GATTGATTAATTATGTAATAA
1 AATTGATTAATTATGTAATAA
*
73840 AATTGATTTATTATG
1 AATTGATTAATTATG
73855 GTAGATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (21 bp):
AATTGATTAATTATGTAATAA
Found at i:74135 original size:16 final size:18
Alignment explanation
Indices: 74096--74137 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
74086 TAAGTTTATA
74096 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
74113 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
74130 A-ATTTATA
1 ATATTTATA
74138 ATATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:74155 original size:16 final size:17
Alignment explanation
Indices: 74130--74171 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
74120 TATATTATGT
*
74130 AATTTATAATATATAAA
1 AATTTATAATAAATAAA
74147 AATTT-TAATAAATAAA
1 AATTTATAATAAATAAA
*
74163 AATATATAA
1 AATTTATAA
74172 ATTTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTATAATAAATAAA
Found at i:74642 original size:12 final size:12
Alignment explanation
Indices: 74603--74645 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
74593 ATTAACTACA
74603 TTTATAATAACT
1 TTTATAATAACT
* *
74615 TTTATTGATAA-A
1 TTTA-TAATAACT
74627 TTTATAATAACT
1 TTTATAATAACT
74639 TTTATAA
1 TTTATAA
74646 AAAATATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.20
12 15 0.60
13 5 0.20
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (12 bp):
TTTATAATAACT
Found at i:74655 original size:24 final size:24
Alignment explanation
Indices: 74602--74656 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
74592 AATTAACTAC
* *
74602 ATTTATAATAACTTTTATTGATAA
1 ATTTATAATAACTTTTATTAAAAA
74626 ATTTATAATAACTTTTA-TAAAAA
1 ATTTATAATAACTTTTATTAAAAA
74649 ATATTATA
1 AT-TTATA
74657 GTTTGCTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTATAATAACTTTTATTAAAAA
Found at i:75574 original size:24 final size:23
Alignment explanation
Indices: 75516--75585 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
75506 TTCGTTAAAC
*
75516 TTAATCGAACATGTTCACGAACA
1 TTAATTGAACATGTTCACGAACA
* * *
75539 TTAAATGAACATGCTCATGAACA
1 TTAATTGAACATGTTCACGAACA
75562 TATAATTGAACATGTTCACGAACA
1 T-TAATTGAACATGTTCACGAACA
75586 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (23 bp):
TTAATTGAACATGTTCACGAACA
Found at i:76629 original size:20 final size:21
Alignment explanation
Indices: 76604--76644 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
76594 AAAAAGCTAC
76604 TGTTGTTTT-CACTGTTTTGG
1 TGTTGTTTTCCACTGTTTTGG
76624 TGTTGTTTTGCCACTGTTTTG
1 TGTTGTTTT-CCACTGTTTTG
76645 CTGGCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.05, C:0.12, G:0.24, T:0.59
Consensus pattern (21 bp):
TGTTGTTTTCCACTGTTTTGG
Found at i:76831 original size:221 final size:221
Alignment explanation
Indices: 76437--76882 Score: 709
Period size: 221 Copynumber: 2.0 Consensus size: 221
76427 AAAAAAAAAG
*
76437 ATTACCAAGAATTAGATTTGATTGGCCTGACCCAAAGAGTCACCTGAAAATAGGAGAGGTTTGGG
1 ATTACCAAGAATTAGACTTGATTGGCCTGACCCAAAGAGTCACCTGAAAATAGGAGAGGTTTGGG
* * *
76502 CAAAGAAACGAGATTCGATTTTTAAACGGGCCGGGCATCGGGTAAATTTTTTTAGCGATTTTTCT
66 CAAAAAAACGAGACTCGATTTTTAAACGGGCCGAGCATCGGGTAAATTTTTTTAGCGATTTTTCT
* *
76567 TGGCCTTGTCTGTCTCAAATTTGCCAAAAAAAGCTACTGTTGTTTTCACTGTTTTGGTGTTGTTT
131 TGGCCTTGCCGGTCTCAAATTTGCCAAAAAAAGCTACTGTTGTTTTCACTGTTTTGGTGTTGTTT
* *
76632 TGCCACTGTTTTGCTGGCATTTCGCT
196 TGCCACTGTTTTACTGACATTTCGCT
* *
76658 ATTACCTAGAATTAGACTTGATTGGCCTGACCCGAAGAGTCACCTGAAAATAGGAG-GGTTTGGG
1 ATTACCAAGAATTAGACTTGATTGGCCTGACCCAAAGAGTCACCTGAAAATAGGAGAGGTTTGGG
* *
76722 CAAAAAAACGAGACTC-ACTTTTTAAACTGGCCGAGCATCGGGTAAGTTTTTTTAGC-AGTTTTT
66 CAAAAAAACGAGACTCGA-TTTTTAAACGGGCCGAGCATCGGGTAAATTTTTTTAGCGA-TTTTT
**
76785 CTTGGCCTTGCCGGTCTTGAATTTGCCAAAAAAAAGCTACTGTTGTTTTCACTGTTTTGGTGTTG
129 CTTGGCCTTGCCGGTCTCAAATTTGCC-AAAAAAAGCTACTGTTGTTTTCACTGTTTTGGTGTTG
*
76850 TTTTGCCACTGTTTTACTGACATTTCGTT
193 TTTTGCCACTGTTTTACTGACATTTCGCT
76879 ATTA
1 ATTA
76883 TATTGTTATT
Statistics
Matches: 207, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
219 2 0.01
220 85 0.41
221 120 0.58
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (221 bp):
ATTACCAAGAATTAGACTTGATTGGCCTGACCCAAAGAGTCACCTGAAAATAGGAGAGGTTTGGG
CAAAAAAACGAGACTCGATTTTTAAACGGGCCGAGCATCGGGTAAATTTTTTTAGCGATTTTTCT
TGGCCTTGCCGGTCTCAAATTTGCCAAAAAAAGCTACTGTTGTTTTCACTGTTTTGGTGTTGTTT
TGCCACTGTTTTACTGACATTTCGCT
Found at i:76850 original size:20 final size:21
Alignment explanation
Indices: 76825--76864 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
76815 AAAAAGCTAC
76825 TGTTGTTTT-CACTGTTTTGG
1 TGTTGTTTTCCACTGTTTTGG
76845 TGTTGTTTTGCCACTGTTTT
1 TGTTGTTTT-CCACTGTTTT
76865 ACTGACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.05, C:0.12, G:0.23, T:0.60
Consensus pattern (21 bp):
TGTTGTTTTCCACTGTTTTGG
Found at i:76900 original size:14 final size:14
Alignment explanation
Indices: 76877--76910 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
76867 TGACATTTCG
*
76877 TTATTATATTGTTA
1 TTATTTTATTGTTA
76891 TTATTTTATTGTTA
1 TTATTTTATTGTTA
76905 TTATTT
1 TTATTT
76911 GGATATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TTATTTTATTGTTA
Found at i:77725 original size:19 final size:19
Alignment explanation
Indices: 77693--77744 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
77683 CATTATTTTT
*
77693 ATTTTCAAAATTTTT-ACTA
1 ATTTTTAAAATTTTTGA-TA
*
77712 ATTTTTAAACTTTTTGATA
1 ATTTTTAAAATTTTTGATA
77731 ATTTTTCAAAATTT
1 ATTTTT-AAAATTT
77745 CATAATGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTAAAATTTTTGATA
Found at i:77922 original size:19 final size:20
Alignment explanation
Indices: 77879--77925 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
77869 AATTTCTATT
*
77879 AATTTTAATAATTTATTCAA
1 AATTTTTATAATTTATTCAA
**
77899 AATTTTTATAATTT-TTTTA
1 AATTTTTATAATTTATTCAA
77918 AATTTTTA
1 AATTTTTA
77926 AATAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTATAATTTATTCAA
Found at i:77922 original size:30 final size:30
Alignment explanation
Indices: 77853--77940 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
77843 AATTTTACTA
* *
77853 TTTTTAATTTTTTCCAAATTTCTATTAATT
1 TTTTTAATTTATTCAAAATTTCTATTAATT
** *
77883 TTAATAATTTATTCAAAATTTTTA-TAATT
1 TTTTTAATTTATTCAAAATTTCTATTAATT
*
77912 TTTTTAAATTT-TTAAATAAGTTTCTATTA
1 TTTTT-AATTTATTCAA-AA-TTTCTATTA
77941 TAAAATAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
29 12 0.27
30 26 0.58
31 5 0.11
32 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTTTAATTTATTCAAAATTTCTATTAATT
Found at i:78150 original size:78 final size:78
Alignment explanation
Indices: 78060--78217 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 78
78050 ATTTATAGAC
*
78060 ATAGAAAGTATAAATGAAATAACTATGATTTTGATGGCTACTAGAATTTAAAGTTTATCCAAACT
1 ATAGAAAGTATAAATGAAATAACTATGATTTTGATGACTACTAGAATTTAAAGTTTATCCAAACT
78125 TATCTTGATATTG
66 TATCTTGATATTG
78138 ATAGAAAGTATAAATGAAATAACTATGATTTTGATGACTACTAGAATTTAAAGTTTATCCAAACT
1 ATAGAAAGTATAAATGAAATAACTATGATTTTGATGACTACTAGAATTTAAAGTTTATCCAAACT
78203 TATCTTGATATTG
66 TATCTTGATATTG
78216 AT
1 AT
78218 GGACATCCAC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (78 bp):
ATAGAAAGTATAAATGAAATAACTATGATTTTGATGACTACTAGAATTTAAAGTTTATCCAAACT
TATCTTGATATTG
Found at i:78500 original size:90 final size:91
Alignment explanation
Indices: 78403--78582 Score: 283
Period size: 90 Copynumber: 2.0 Consensus size: 91
78393 GGGACAAAAC
* *
78403 CTCGGTTAAGGGAAAA-AGAGTACAACTCGTATTTACTCCCCCTCATAAAAA-ATCACATAATAT
1 CTCGGTTAA-GGAAAAGAGAGTACAACGCGTATTTACTCCCCCTCATAAAAACATCACATAATAC
* *
78466 CTCATATTCTATGTATTCAATATTGAT
65 CTCATACTCTACGTATTCAATATTGAT
*
78493 CTCGGTTAAGGAAAAGAGAGTACAACGCGTATTTACTTCCCCTCATAAAAACATCACATAATACC
1 CTCGGTTAAGGAAAAGAGAGTACAACGCGTATTTACTCCCCCTCATAAAAACATCACATAATACC
*
78558 TCATACTCTACGTATTCAATCTTGA
66 TCATACTCTACGTATTCAATATTGA
78583 ATACTAATCT
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 6 0.07
90 42 0.51
91 34 0.41
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (91 bp):
CTCGGTTAAGGAAAAGAGAGTACAACGCGTATTTACTCCCCCTCATAAAAACATCACATAATACC
TCATACTCTACGTATTCAATATTGAT
Found at i:82666 original size:18 final size:18
Alignment explanation
Indices: 82643--82683 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
82633 CATTTTAAAA
82643 AAAAAAAATGGTTTTTTC
1 AAAAAAAATGGTTTTTTC
82661 AAAAAAAATGGTTTTTTC
1 AAAAAAAATGGTTTTTTC
82679 AAAAA
1 AAAAA
82684 TTTAGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (18 bp):
AAAAAAAATGGTTTTTTC
Found at i:84302 original size:95 final size:95
Alignment explanation
Indices: 84193--84381 Score: 342
Period size: 95 Copynumber: 2.0 Consensus size: 95
84183 TTCATGTCTC
*
84193 TATCTACCCATCTTTCTTTTGTATTTTTCCTTCAACTAAGGTTTTTCCTTTTATTTGGTGCTTGG
1 TATCTACCCATCTTTCTTTTGTATTTTTCCTTCAACAAAGGTTTTTCCTTTTATTTGGTGCTTGG
*
84258 AATGTTTATAGAAACTTAGCATTCTTTCTG
66 AATGTTTATAGAAACTTACCATTCTTTCTG
*
84288 TATCTACCCTTCTTTCTTTTGTATTTTTCCTTCAACAAAGGTTTTTCCTTTTATTTGGTGCTTGG
1 TATCTACCCATCTTTCTTTTGTATTTTTCCTTCAACAAAGGTTTTTCCTTTTATTTGGTGCTTGG
*
84353 AATGTTTATAGACACTTACCATTCTTTCT
66 AATGTTTATAGAAACTTACCATTCTTTCT
84382 TTTTGGTTGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.51
Consensus pattern (95 bp):
TATCTACCCATCTTTCTTTTGTATTTTTCCTTCAACAAAGGTTTTTCCTTTTATTTGGTGCTTGG
AATGTTTATAGAAACTTACCATTCTTTCTG
Found at i:91145 original size:17 final size:16
Alignment explanation
Indices: 91108--91150 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
91098 TTTAATTTCT
91108 TAAAATTA-T-AAATA
1 TAAAATTATTAAAATA
91122 TATAAATTATTAAAATAA
1 TA-AAATTATTAAAAT-A
91140 TAAAATTATTA
1 TAAAATTATTA
91151 TTTTACTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 6 0.24
16 1 0.04
17 13 0.52
18 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAATTATTAAAATA
Found at i:92532 original size:26 final size:24
Alignment explanation
Indices: 92503--92550 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
92493 CAAATCTGAT
92503 ATCTATGTTAAATTAATTAGGTTGAC
1 ATCTATGTT-AATTAATT-GGTTGAC
*
92529 ATCTATGTTGATTAATTGGTTG
1 ATCTATGTTAATTAATTGGTTG
92551 TTCTTTTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 7 0.33
26 9 0.43
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (24 bp):
ATCTATGTTAATTAATTGGTTGAC
Found at i:102063 original size:31 final size:30
Alignment explanation
Indices: 102002--102072 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
101992 TATATCATAA
* *
102002 TAGTTATACATATATTAATATTTCTAGTAT
1 TAGTTATATATATAATAATATTTCTAGTAT
*
102032 TAGTTATATATTATAATACTATTT-TATGTAT
1 TAGTTATATA-TATAATAATATTTCTA-GTAT
*
102063 TAGTAATATA
1 TAGTTATATA
102073 CAAATTTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (30 bp):
TAGTTATATATATAATAATATTTCTAGTAT
Found at i:108368 original size:21 final size:20
Alignment explanation
Indices: 108320--108368 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
108310 TAAACGTGAA
* *
108320 ATTTTTTTTTTTTAAATTTG
1 ATTTTTGTTTTTTAAATATG
108340 ATTTTTGTTTTTTAATATAT-
1 ATTTTTGTTTTTTAA-ATATG
108360 ATTTATTGT
1 ATTT-TTGT
108369 ATAGTGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (20 bp):
ATTTTTGTTTTTTAAATATG
Found at i:109000 original size:18 final size:18
Alignment explanation
Indices: 108979--109043 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
108969 ATAAAAAATA
108979 AAAATTTTATAAATTTAT
1 AAAATTTTATAAATTTAT
* *
108997 AAAATTATATAAATATAT
1 AAAATTTTATAAATTTAT
* *
109015 AAAATAATTGATAATATTTTT
1 AAAAT--TTTATAA-ATTTAT
109036 AAAATTTT
1 AAAATTTT
109044 TAATAATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 21 0.57
19 2 0.05
20 5 0.14
21 9 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AAAATTTTATAAATTTAT
Found at i:112151 original size:22 final size:23
Alignment explanation
Indices: 112106--112162 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
112096 ATACAATATC
112106 AAAATAATAACAACAAAATAATA
1 AAAATAATAACAACAAAATAATA
* * *
112129 AAAAT-ATAATAACAGAATGATA
1 AAAATAATAACAACAAAATAATA
112151 ACAAATCAATAA
1 A-AAAT-AATAA
112163 AAAAATAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 15 0.54
23 9 0.32
25 4 0.14
ACGTcount: A:0.68, C:0.09, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAATAATAACAACAAAATAATA
Found at i:124846 original size:23 final size:23
Alignment explanation
Indices: 124816--124860 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
124806 CCTTTTAAAA
124816 TTTAAAAATTCATACAAATTATT
1 TTTAAAAATTCATACAAATTATT
124839 TTTAAAAATTCATACAAATTAT
1 TTTAAAAATTCATACAAATTAT
124861 AAATTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAAAAATTCATACAAATTATT
Found at i:125850 original size:10 final size:9
Alignment explanation
Indices: 125831--125870 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
125821 AATTATAATT
125831 TTTTTATAA
1 TTTTTATAA
125840 TTTTTATTAA
1 TTTTTA-TAA
*
125850 TTTTAATAA
1 TTTTTATAA
*
125859 TTTTTAAAA
1 TTTTTATAA
125868 TTT
1 TTT
125871 ATAAGGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:127074 original size:21 final size:21
Alignment explanation
Indices: 127050--127113 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
127040 AATTTTAAAA
127050 ATTTTAAAAAATATAAAAATT
1 ATTTTAAAAAATATAAAAATT
* *
127071 ATTTTATAAAAT-TAAAAGTT
1 ATTTTAAAAAATATAAAAATT
* *
127091 ATTTTAAAAATTAAAAAAATT
1 ATTTTAAAAAATATAAAAATT
127112 AT
1 AT
127114 AAAAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTTAAAAAATATAAAAATT
Found at i:127092 original size:20 final size:19
Alignment explanation
Indices: 127050--127107 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
127040 AATTTTAAAA
127050 ATTTTAAAAAATATAAAAATT
1 ATTTT-AAAAAT-TAAAAATT
*
127071 ATTTTATAAAATTAAAAGTT
1 ATTTTA-AAAATTAAAAATT
127091 ATTTTAAAAATTAAAAA
1 ATTTTAAAAATTAAAAA
127108 AATTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 14 0.41
21 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTTTAAAAATTAAAAATT
Found at i:136260 original size:27 final size:28
Alignment explanation
Indices: 136207--136262 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
136197 TTTTTATATA
* *
136207 AAATCTATATAAAAAATTTAAACACAAT
1 AAATCTAGATAAAAAATCTAAACACAAT
* *
136235 AAATCTAGA-AAATAATCTAAATACAAT
1 AAATCTAGATAAAAAATCTAAACACAAT
136262 A
1 A
136263 CAATTTGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.27
Consensus pattern (28 bp):
AAATCTAGATAAAAAATCTAAACACAAT
Found at i:140399 original size:23 final size:23
Alignment explanation
Indices: 140373--140425 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
140363 AACGCCTTGC
* *
140373 AAACATCAGCACCTCGCGAGGTG
1 AAACATCAACACCTCGCGAGGCG
* *
140396 AAACATCAACTCCTCGTGAGGCG
1 AAACATCAACACCTCGCGAGGCG
140419 AAACATC
1 AAACATC
140426 CCGCAACCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (23 bp):
AAACATCAACACCTCGCGAGGCG
Found at i:152142 original size:22 final size:18
Alignment explanation
Indices: 152117--152164 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
152107 TTGCAGAAAG
152117 AATTAAATGAAATTTTTTAAA
1 AATTAAAT--AATTTTTT-AA
*
152138 TAATTTAATAATTTTTTAA
1 -AATTAAATAATTTTTTAA
152157 AATTAAAT
1 AATTAAAT
152165 CTTTATAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 2 0.08
20 8 0.33
22 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AATTAAATAATTTTTTAA
Found at i:159509 original size:31 final size:30
Alignment explanation
Indices: 159470--159530 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
159460 AATATTTTTT
159470 ATAATTTTTTAATAATTTT-AATTTTTAAAA
1 ATAATTTTTTAATAATTTTGAA-TTTTAAAA
* *
159500 ATAATTTTTTTTATATTTTTGAATTTTAAAA
1 ATAA-TTTTTTAATAATTTTGAATTTTAAAA
159531 TTTTAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 21 0.78
32 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
ATAATTTTTTAATAATTTTGAATTTTAAAA
Found at i:163107 original size:5 final size:5
Alignment explanation
Indices: 163097--163121 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
163087 TTCAATGGTG
163097 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
163122 ATTCAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:165591 original size:21 final size:22
Alignment explanation
Indices: 165541--165591 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
165531 ATATTGTTTT
165541 TAATTTT-TTTAAATATTTATA
1 TAATTTTATTTAAATATTTATA
** *
165562 TTGTTTTATTTGAATATTTA-A
1 TAATTTTATTTAAATATTTATA
165583 TAATTTTAT
1 TAATTTTAT
165592 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TAATTTTATTTAAATATTTATA
Found at i:173876 original size:8 final size:8
Alignment explanation
Indices: 173865--173896 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
173855 GGATGGGTGG
173865 AAGGATTC
1 AAGGATTC
173873 AAGGATTC
1 AAGGATTC
173881 AAGGATTC
1 AAGGATTC
173889 AATGGATT
1 AA-GGATT
173897 GAAAAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.78
9 5 0.22
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (8 bp):
AAGGATTC
Found at i:192999 original size:19 final size:20
Alignment explanation
Indices: 192961--193003 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
192951 TTATAAAATA
*
192961 TTAAATATTTTTATTTTTAT
1 TTAAATATTTTTATTATTAT
*
192981 TTAAATGTTTTT-TTATTAT
1 TTAAATATTTTTATTATTAT
193000 TTAA
1 TTAA
193004 TTTGAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTAAATATTTTTATTATTAT
Found at i:197776 original size:25 final size:26
Alignment explanation
Indices: 197731--197780 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
197721 GAGACATAGA
* *
197731 CCTATGTTTTCATTTGGTGTTGGATG
1 CCTATGTCTTCATTTGATGTTGGATG
197757 CCTATGTCTT-ATTTGATGTTGGAT
1 CCTATGTCTTCATTTGATGTTGGAT
197781 TTACATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (26 bp):
CCTATGTCTTCATTTGATGTTGGATG
Found at i:206667 original size:15 final size:15
Alignment explanation
Indices: 206647--206685 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
206637 GCACATCAAA
*
206647 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
206662 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
206676 CAAGAATTAA
1 CAAGAATTAA
206686 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:225150 original size:69 final size:69
Alignment explanation
Indices: 225039--225176 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
225029 AGCTGCAATA
225039 AGGGTTTATAAGAAGCGAAAGTGAAGCTACATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAAC
1 AGGGTTTATAAGAAGCGAAAGTGAAGCTACATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAAC
225104 TCAT
66 TCAT
225108 AGGGTTTATAAGAAGCGAAAGTGAAGCTACATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAAC
1 AGGGTTTATAAGAAGCGAAAGTGAAGCTACATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAAC
225173 TCAT
66 TCAT
225177 TGTTTCATTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (69 bp):
AGGGTTTATAAGAAGCGAAAGTGAAGCTACATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAAC
TCAT
Found at i:225178 original size:37 final size:37
Alignment explanation
Indices: 225068--225179 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 37
225058 AGTGAAGCTA
225068 CATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAACT
1 CATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAACT
* ** * * *
225105 CATAGGGT-TTATAAGAAGC----GAAAGTGAAGCTA--
1 CATTGTATGTTA-AA-AAGCTTTAGAATGAGAAGCAACT
225137 CATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAACT
1 CATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAACT
225174 CATTGT
1 CATTGT
225180 TTCATTGTAT
Statistics
Matches: 54, Mismatches: 12, Indels: 18
0.64 0.14 0.21
Matches are distributed among these distances:
31 4 0.07
32 7 0.13
33 3 0.06
34 10 0.19
35 10 0.19
36 3 0.06
37 13 0.24
38 4 0.07
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (37 bp):
CATTGTATGTTAAAAAGCTTTAGAATGAGAAGCAACT
Found at i:237643 original size:44 final size:46
Alignment explanation
Indices: 237590--237691 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 46
237580 TCAACAATAA
* *
237590 TGAGTAAATAATAATATAAAATTTT-ATATAAAAAAATCAAAGG-T
1 TGAGTAAATAATAATATAAAATTTTAAAAGAAAAAAATCAAAGGAT
***
237634 TGAGTAAATAATAATATGTTATTTTAAAAGAAAAAAATCAAAGGAT
1 TGAGTAAATAATAATATAAAATTTTAAAAGAAAAAAATCAAAGGAT
237680 TGAGATAAATAA
1 TGAG-TAAATAA
237692 ACGAGACAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 22 0.44
45 16 0.32
46 5 0.10
47 7 0.14
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (46 bp):
TGAGTAAATAATAATATAAAATTTTAAAAGAAAAAAATCAAAGGAT
Found at i:242348 original size:17 final size:17
Alignment explanation
Indices: 242326--242358 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
242316 CAAAGTTTTG
242326 TTTTAATATTT-TTATAT
1 TTTTAAT-TTTATTATAT
242343 TTTTAATTTTATTATA
1 TTTTAATTTTATTATA
242359 CATGGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTAATTTTATTATAT
Found at i:247724 original size:6 final size:6
Alignment explanation
Indices: 247713--247738 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
247703 GAGAAGCATC
247713 GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GG
247739 TTGCTGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:251868 original size:3 final size:3
Alignment explanation
Indices: 251860--251885 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
251850 GATAGACTTC
251860 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
251886 AACATGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Done.