Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold489
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: 192533
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
File 1 of 2
Found at i:626 original size:20 final size:21
Alignment explanation
Indices: 580--632 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
570 GACATGGTCT
*
580 TGTATCGATACATTTCAGACA
1 TGTATCGATACATTTCACACA
* **
601 TATATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACACA
621 TGTATCGATACA
1 TGTATCGATACA
633 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTCACACA
Found at i:1492 original size:15 final size:15
Alignment explanation
Indices: 1466--1512 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
1456 TGCAACTTTT
1466 ATGAATTATAGATAAA
1 ATGAA-TATAGATAAA
1482 ATGAATATAGATAAA
1 ATGAATATAGATAAA
1497 ATGAATATAGATAAA
1 ATGAATATAGATAAA
1512 A
1 A
1513 AAGTATGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 26 0.84
16 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (15 bp):
ATGAATATAGATAAA
Found at i:4167 original size:29 final size:31
Alignment explanation
Indices: 4104--4173 Score: 117
Period size: 29 Copynumber: 2.3 Consensus size: 31
4094 ATTCAATACT
*
4104 TTTAAAAATTATATTTTATTTATTTATAACC
1 TTTAAAAATTATATTTTATTCATTTATAACC
4135 TTTAAAAATTATA-TTTA-TCATTTATAACC
1 TTTAAAAATTATATTTTATTCATTTATAACC
4164 TTTAAAAATT
1 TTTAAAAATT
4174 TTATCATCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 21 0.55
30 4 0.11
31 13 0.34
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTAAAAATTATATTTTATTCATTTATAACC
Found at i:6397 original size:51 final size:52
Alignment explanation
Indices: 6306--6421 Score: 189
Period size: 51 Copynumber: 2.2 Consensus size: 52
6296 TGTCTGCATA
*
6306 TATCGATACATTTGGGTCAAAAACCCAAAATGTATCGATACAATAAAAAATG
1 TATCGATACATTTGGGTCAAAAACCCAAAATGTATCGATACAAGAAAAAATG
* *
6358 TATCGATACATTTGGGTC-AAAACCCAAAATGTATCGATACAAGGAGAAATG
1 TATCGATACATTTGGGTCAAAAACCCAAAATGTATCGATACAAGAAAAAATG
*
6409 TATTGATACATTT
1 TATCGATACATTT
6422 TCTTTTTAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 42 0.70
52 18 0.30
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (52 bp):
TATCGATACATTTGGGTCAAAAACCCAAAATGTATCGATACAAGAAAAAATG
Found at i:6498 original size:20 final size:20
Alignment explanation
Indices: 6475--6516 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6465 CATTTCAGCC
* *
6475 ATGTATTGATACATTCATTT
1 ATGTATCGATACATTCACTT
6495 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
6515 AT
1 AT
6517 TATATGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:7905 original size:40 final size:40
Alignment explanation
Indices: 7861--7938 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
7851 TATATATATA
* * *
7861 TATATAATAAAAATTTATAACAACTAAATTTATCATTATG
1 TATATAATAAAAATTCATAACAACAAAAGTTATCATTATG
* * *
7901 TATATTATAAGAATTCATAATAACAAAAGTTATCATTA
1 TATATAATAAAAATTCATAACAACAAAAGTTATCATTA
7939 AATATAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (40 bp):
TATATAATAAAAATTCATAACAACAAAAGTTATCATTATG
Found at i:8127 original size:11 final size:11
Alignment explanation
Indices: 8111--8135 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8101 AAACTAGTTC
8111 TTATTTTTATT
1 TTATTTTTATT
8122 TTATTTTTATT
1 TTATTTTTATT
8133 TTA
1 TTA
8136 AAAGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:12087 original size:15 final size:16
Alignment explanation
Indices: 12067--12100 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12057 GGATTTATTG
12067 AAAGAAAA-AAAAAGA
1 AAAGAAAAGAAAAAGA
*
12082 AAAGAAAAGAAAAGGA
1 AAAGAAAAGAAAAAGA
12098 AAA
1 AAA
12101 AAGAAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAAGA
Found at i:12099 original size:6 final size:5
Alignment explanation
Indices: 12067--12100 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
12057 GGATTTATTG
*
12067 AAAGA AAAAA AAAGA AAAGA AAAGA AAAGGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAA-GA AAA
12101 AAGAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:13645 original size:29 final size:30
Alignment explanation
Indices: 13577--13657 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
13567 TTTCACCAAT
13577 ACTTTTAAAAATTACATTTTATTTATCTATA
1 ACTTTTAAAAATTACA-TTTATTTATCTATA
*
13608 A-TCTTTAAAAATTATATTTATTGT-T-TATA
1 ACT-TTTAAAAATTACATTTATT-TATCTATA
*
13637 ACTTTTAAAAATTAGATTTAT
1 ACTTTTAAAAATTACATTTAT
13658 CATTCATAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 22 0.49
30 9 0.20
31 14 0.31
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (30 bp):
ACTTTTAAAAATTACATTTATTTATCTATA
Found at i:13666 original size:29 final size:28
Alignment explanation
Indices: 13577--13667 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
13567 TTTCACCAAT
*
13577 ACTTTTAAAAATTACATTTTATTTATCTATA
1 ACTTTTAAAAATTACA-TTTATAT-TC-ATA
* * *
13608 A-TCTTTAAAAATTATATTTATTGTTTATA
1 ACT-TTTAAAAATTACATTTA-TATTCATA
*
13637 ACTTTTAAAAATTAGATTTATCATTCATA
1 ACTTTTAAAAATTACATTTAT-ATTCATA
13666 AC
1 AC
13668 CTGTGAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.02
29 27 0.54
30 7 0.14
31 15 0.30
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (28 bp):
ACTTTTAAAAATTACATTTATATTCATA
Found at i:21295 original size:2 final size:2
Alignment explanation
Indices: 21247--21283 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
21237 ATAAATAAAA
* *
21247 AT AT AT AT GT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21284 CACACATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23370 original size:6 final size:6
Alignment explanation
Indices: 23341--23389 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
23331 AAAATTTTAA
* * * *
23341 ATCATT A-CATC ATCATC ATCATT ATTATT ATCGTT ATCATT ATCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
23388 AT
1 AT
23390 TATTTTGCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (6 bp):
ATCATT
Found at i:28091 original size:52 final size:50
Alignment explanation
Indices: 28034--28134 Score: 112
Period size: 50 Copynumber: 2.0 Consensus size: 50
28024 ATATATCGGT
* * *
28034 ACATTTGGGCCAAAAACCCCGAATATATCGATATAATAAAAAATGTATCGAC
1 ACATTTAGGCC-AAAACCCAGAATATAT-GATACAATAAAAAATGTATCGAC
* * * * *
28086 ACATTTAGGTCAAAACCCATAATGTATGATACAATGAGAAATGTATCGA
1 ACATTTAGGCCAAAACCCAGAATATATGATACAATAAAAAATGTATCGA
28135 TATATTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
50 19 0.46
51 13 0.32
52 9 0.22
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.25
Consensus pattern (50 bp):
ACATTTAGGCCAAAACCCAGAATATATGATACAATAAAAAATGTATCGAC
Found at i:28224 original size:20 final size:21
Alignment explanation
Indices: 28178--28230 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
28168 GACATGGTCT
*
28178 TGTATCGATACATTTCAGACA
1 TGTATCGATACATTTCACACA
* **
28199 TATATCGATACA-TTCACTTA
1 TGTATCGATACATTTCACACA
28219 TGTATCGATACA
1 TGTATCGATACA
28231 AATTGTAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTCACACA
Found at i:29093 original size:17 final size:17
Alignment explanation
Indices: 29067--29118 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
29057 TGCAACTTTT
*
29067 ATGAATTATAGATAAAA
1 ATGAAATATAGATAAAA
29084 ATGAAATATAGATAAAA
1 ATGAAATATAGATAAAA
29101 ATGAAATATAGATAAAA
1 ATGAAATATAGATAAAA
29118 A
1 A
29119 AGTATGAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (17 bp):
ATGAAATATAGATAAAA
Found at i:30452 original size:46 final size:46
Alignment explanation
Indices: 30402--30492 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
30392 CTAAATTAAT
* **
30402 ATCCCAAATTTAAGTAAATTAATTAAATACCTAAATTTTCCTAAGA
1 ATCCCAAATTTAAGTAAATTAATTAAATACCCAAATAATCCTAAGA
* * * *
30448 ATCCCAAATTTCATTGAATTAATTGAATACCCAAATAATCCTAAG
1 ATCCCAAATTTAAGTAAATTAATTAAATACCCAAATAATCCTAAG
30493 GGGAATGCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (46 bp):
ATCCCAAATTTAAGTAAATTAATTAAATACCCAAATAATCCTAAGA
Found at i:30608 original size:27 final size:27
Alignment explanation
Indices: 30577--30649 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
30567 AAAAGCTACC
30577 CTTTGTGTTTGTCAAAAATGATGGTTA
1 CTTTGTGTTTGTCAAAAATGATGGTTA
* * *
30604 CTTTGTATTTGTCAAAAATGGTGGTTC
1 CTTTGTGTTTGTCAAAAATGATGGTTA
*
30631 CTTTTTGTTTGTCAAAAAT
1 CTTTGTGTTTGTCAAAAAT
30650 TATAGCTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.47
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGATGGTTA
Found at i:30667 original size:24 final size:24
Alignment explanation
Indices: 30635--30680 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
30625 TGGTTCCTTT
30635 TTGTTTGTCAAAAATT-ATAGCTTG
1 TTGTTTGTC-AAAATTGATAGCTTG
30659 TTGTTTGTCAAAATTGATAGCT
1 TTGTTTGTCAAAATTGATAGCT
30681 AATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (24 bp):
TTGTTTGTCAAAATTGATAGCTTG
Found at i:33237 original size:21 final size:22
Alignment explanation
Indices: 33208--33253 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
33198 TGTTCAGACA
** *
33208 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
33230 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
33251 AGT
1 AGT
33254 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:35176 original size:27 final size:27
Alignment explanation
Indices: 35138--35208 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
35128 CCACCCTGTG
35138 TTTGTCAAAAATTATGGTTACTTTGTA
1 TTTGTCAAAAATTATGGTTACTTTGTA
* * *
35165 TTTGTCAAAAA-TAGTGGTTCCTTTTTG
1 TTTGTCAAAAATTA-TGGTTACTTTGTA
*
35192 TTTGTTAAAAATTATGG
1 TTTGTCAAAAATTATGG
35209 CTTGTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
27 34 0.89
28 2 0.05
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (27 bp):
TTTGTCAAAAATTATGGTTACTTTGTA
Found at i:37774 original size:2 final size:2
Alignment explanation
Indices: 37767--37793 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37757 TTGTAATCTC
37767 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
37794 TCTTTTTTTG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38348 original size:24 final size:24
Alignment explanation
Indices: 38321--38422 Score: 68
Period size: 28 Copynumber: 4.2 Consensus size: 24
38311 ACATATGTGT
38321 ATATATGTATCCAACCATAAATAA
1 ATATATGTATCCAACCATAAATAA
** * * *
38345 ATATA--TAT-GTA-TATATATAT
1 ATATATGTATCCAACCATAAATAA
* * *
38365 GTATATATATACAACCATAAATAAATA
1 ATATATGTATCCAACCATAAAT--A-A
38392 TATATATGTATCCAACCATAAATAA
1 -ATATATGTATCCAACCATAAATAA
38417 ATATAT
1 ATATAT
38423 ATATATATGT
Statistics
Matches: 56, Mismatches: 14, Indels: 16
0.65 0.16 0.19
Matches are distributed among these distances:
20 10 0.18
21 1 0.02
22 6 0.11
23 1 0.02
24 16 0.29
25 1 0.02
26 2 0.04
28 19 0.34
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATATGTATCCAACCATAAATAA
Found at i:38362 original size:12 final size:12
Alignment explanation
Indices: 38345--38375 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38335 CCATAAATAA
38345 ATATATATGTAT
1 ATATATATGTAT
38357 ATATATATGTAT
1 ATATATATGTAT
38369 ATATATA
1 ATATATA
38376 CAACCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:38385 original size:44 final size:45
Alignment explanation
Indices: 38308--38396 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
38298 TACACACATA
* *
38308 TATACATATGTGTATATATGTATCCAACCATAAATAAATATATATG
1 TATACATATATGTATATA-GTATACAACCATAAATAAATATATATG
*
38354 TATATATATATGTATATA-TATACAACCATAAATAAATATATAT
1 TATACATATATGTATATAGTATACAACCATAAATAAATATATAT
38397 ATGTATCCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 24 0.60
46 16 0.40
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (45 bp):
TATACATATATGTATATAGTATACAACCATAAATAAATATATATG
Found at i:38407 original size:28 final size:28
Alignment explanation
Indices: 38361--38430 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
38351 ATGTATATAT
*
38361 ATATGTATATATATACAACCATAAATAA
1 ATATATATATATATACAACCATAAATAA
* *
38389 ATATATATATGTATCCAACCATAAATAA
1 ATATATATATATATACAACCATAAATAA
38417 ATATATATATATAT
1 ATATATATATATAT
38431 GTATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (28 bp):
ATATATATATATATACAACCATAAATAA
Found at i:39639 original size:28 final size:28
Alignment explanation
Indices: 39581--39641 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
39571 AATGCCACCC
* *
39581 TTTGTATTTATCAAATATGGTGGTTTCT
1 TTTGTATTTATCAAATATGGTGCTATCT
* *
39609 TTTGTATTTGTCAAATGTGGTAGCTAT-T
1 TTTGTATTTATCAAATATGGT-GCTATCT
39637 TTTGT
1 TTTGT
39642 TTGTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (28 bp):
TTTGTATTTATCAAATATGGTGCTATCT
Found at i:39674 original size:24 final size:24
Alignment explanation
Indices: 39638--39683 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
39628 GTAGCTATTT
39638 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
39662 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
39684 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:44215 original size:28 final size:28
Alignment explanation
Indices: 44153--44207 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
44143 CAAATGCCAC
44153 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
44181 CCTTTGTATTTGTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
44208 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.11, G:0.22, T:0.49
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:44248 original size:24 final size:25
Alignment explanation
Indices: 44189--44254 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
44179 TTCCTTTGTA
* *
44189 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG-TATTGTTG
* *
44215 TTTGTAAAAAATGGTGG-CTTGTTG
1 TTTGTCAAAAATGGTGGTATTGTTG
*
44239 TTTGTCAAAATTGGTG
1 TTTGTCAAAAATGGTG
44255 ACTAATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 19 0.56
26 15 0.44
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.47
Consensus pattern (25 bp):
TTTGTCAAAAATGGTGGTATTGTTG
Found at i:45427 original size:6 final size:6
Alignment explanation
Indices: 45408--45456 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
45398 AAAATTTTAA
* * *
45408 ATCATT AT-ATC ATCATC ATCATT ATTATT ATCATT ATCATT ATCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
45455 AT
1 AT
45457 TATTTTACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (6 bp):
ATCATT
Found at i:45442 original size:12 final size:12
Alignment explanation
Indices: 45425--45460 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
45415 TATCATCATC
45425 ATCATTATTATT
1 ATCATTATTATT
*
45437 ATCATTATCATT
1 ATCATTATTATT
45449 ATCATTATTATT
1 ATCATTATTATT
45461 TTACTAATTC
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:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (12 bp):
ATCATTATTATT
Found at i:46240 original size:28 final size:27
Alignment explanation
Indices: 46185--46255 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
46175 GCCACCCATA
46185 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
46212 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
46240 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
46256 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:46357 original size:20 final size:20
Alignment explanation
Indices: 46332--46377 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
46322 AAATAGAGGC
*
46332 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
46352 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
46372 TCCCTC
1 TCCCTC
46378 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:50815 original size:28 final size:27
Alignment explanation
Indices: 50760--50830 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
50750 GCCACCCATA
50760 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
*
50787 TGTTTGTCAAAAATTGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
50815 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
50831 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:50932 original size:20 final size:20
Alignment explanation
Indices: 50907--50952 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
50897 AAATAGAGGC
*
50907 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
* **
50927 TCCCTCATTCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
50947 TCCCTC
1 TCCCTC
50953 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.48, G:0.04, T:0.37
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:52331 original size:27 final size:27
Alignment explanation
Indices: 52296--52350 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
52286 CCGTTACGAT
52296 CACAATATTCCGTTACTCCACTTTTCA
1 CACAATATTCCGTTACTCCACTTTTCA
52323 CACAATATTCCGTTACTCCACTTTTCA
1 CACAATATTCCGTTACTCCACTTTTCA
52350 C
1 C
52351 GACCGCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.35, G:0.04, T:0.36
Consensus pattern (27 bp):
CACAATATTCCGTTACTCCACTTTTCA
Found at i:52521 original size:34 final size:34
Alignment explanation
Indices: 52457--52639 Score: 251
Period size: 34 Copynumber: 5.4 Consensus size: 34
52447 GCGACACAGC
* *
52457 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
52490 TGTTGACTAAATGTGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
52524 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
52558 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
52592 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
52626 TGTTGATTAAATGG
1 TGTTGATTAAATGG
52640 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
33 11 0.08
34 119 0.92
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:53000 original size:19 final size:19
Alignment explanation
Indices: 52944--53006 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
52934 TGGTTGTCGA
**
52944 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
52963 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
52982 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
53001 GTTACT
1 GGTACT
53007 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:57138 original size:34 final size:34
Alignment explanation
Indices: 57072--57256 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
57062 AAGTGGGAGA
* *
57072 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
57105 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
57139 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
57173 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
57207 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
57241 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
57257 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:57603 original size:10 final size:9
Alignment explanation
Indices: 57577--57647 Score: 51
Period size: 8 Copynumber: 8.2 Consensus size: 9
57567 TTCTAAACCC
57577 TATATTATA
1 TATATTATA
57586 T-TATTATA
1 TATATTATA
57594 TATA-TATA
1 TATATTATA
* *
57602 TATATTTTT
1 TATATTATA
* ***
57611 TAAACCCTA
1 TATATTATA
57620 TATA-TAT-
1 TATATTATA
57627 TATATTATA
1 TATATTATA
57636 TATATGTATA
1 TATAT-TATA
57646 TA
1 TA
57648 CACACGTGCG
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
7 4 0.09
8 20 0.43
9 17 0.36
10 6 0.13
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (9 bp):
TATATTATA
Found at i:57646 original size:42 final size:41
Alignment explanation
Indices: 57565--57647 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 41
57555 ATGTCATCGC
57565 TTTTCTAAACCCTATATTATATTATTATATATATATATATA
1 TTTTCTAAACCCTATATTATATTATTATATATATATATATA
* *
57606 TTTTTTAAACCCTATA-TATATTATATTATATATATGTATATA
1 TTTTCTAAACCCTATATTATA-T-TATTATATATATATATATA
57648 CACACGTGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 4 0.11
41 16 0.42
42 18 0.47
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (41 bp):
TTTTCTAAACCCTATATTATATTATTATATATATATATATA
Found at i:57803 original size:2 final size:2
Alignment explanation
Indices: 57796--57821 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57786 TCTTTCAGTA
57796 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
57822 GATGTACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60181 original size:12 final size:12
Alignment explanation
Indices: 60159--60188 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
60149 GCAAAAATAA
60159 ATAAT-TAAAAT
1 ATAATATAAAAT
60170 ATAATATAAAAT
1 ATAATATAAAAT
60182 ATAATAT
1 ATAATAT
60189 TATCAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:60250 original size:31 final size:32
Alignment explanation
Indices: 60193--60252 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
60183 TAATATTATC
* *
60193 AAAAATATATAAATATATTAAAATTTATACAT
1 AAAAATATATAAACATATCAAAATTTATACAT
*
60225 AAAAA-ATATTAACATATCAAAATTTATA
1 AAAAATATATAAACATATCAAAATTTATA
60253 TAAATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAAATATATAAACATATCAAAATTTATACAT
Found at i:60984 original size:3 final size:3
Alignment explanation
Indices: 60958--61006 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
60948 ATTTACTTTC
60958 ATT ATT -TT ATT ATT -TT -TT AGTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
61001 ATT ATT
1 ATT ATT
61007 TACTGAGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 34 0.79
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:63014 original size:4 final size:4
Alignment explanation
Indices: 63007--63031 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
62997 TATATATATA
63007 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
63032 GTGTGTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:63983 original size:81 final size:81
Alignment explanation
Indices: 63809--64010 Score: 228
Period size: 81 Copynumber: 2.5 Consensus size: 81
63799 CAAAGCAAAC
* *
63809 AGCTCCTTCAGCAAATTTTCGGGAAAAA-CGAACTCCACAAGGAATTGATGGGTACAATTCATAC
1 AGCTCCTTCAGCAAATTTTC-AGAAAAAGCGAACTCCACAAGGAATCGATGGGTACAATTCATAC
**
63873 CAAAGTTCGTCTTCGGT
65 CAAAGTTCGTCTTCACT
* * * * * *
63890 AGCTCATCCAGCAAATTTTCTGAAAAAGCGAACTCCACAAGGAATCGGTGGGTGCAATTCATATC
1 AGCTCCTTCAGCAAATTTTCAGAAAAAGCGAACTCCACAAGGAATCGATGGGTACAATTCATACC
**
63955 AAAGTTTTTCTTCCACT
66 AAAGTTCGTCTT-CACT
** * *
63972 -GCTCCTTCAGCAAAAGTTCAGGAAGAGCGAACTCCACAA
1 AGCTCCTTCAGCAAATTTTCAGAAAAAGCGAACTCCACAA
64011 AGTATGGCTG
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
80 6 0.06
81 93 0.92
82 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (81 bp):
AGCTCCTTCAGCAAATTTTCAGAAAAAGCGAACTCCACAAGGAATCGATGGGTACAATTCATACC
AAAGTTCGTCTTCACT
Found at i:65974 original size:2 final size:2
Alignment explanation
Indices: 65969--66012 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
65959 TATATATATA
* **
65969 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TC TG TG CA TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
66011 TG
1 TG
66013 GCTGTTTGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.02, C:0.05, G:0.45, T:0.48
Consensus pattern (2 bp):
TG
Found at i:66208 original size:2 final size:2
Alignment explanation
Indices: 66201--66230 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
66191 TTTAATATGC
66201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66231 GTATTGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67761 original size:2 final size:2
Alignment explanation
Indices: 67754--67784 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
67744 TTTATATTTA
67754 AT AT 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 AT AT A
67785 AACATACGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72550 original size:27 final size:27
Alignment explanation
Indices: 72493--72559 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
72483 CCACCCTTTG
* *
72493 TTTGTCAAAAATGGTGATTATTTTGTG
1 TTTGTCAAAAATGATGATTATTTTGTA
* *
72520 TTTGTCAAAAATGATGGTT-TCTTTTTA
1 TTTGTCAAAAATGATGATTAT-TTTGTA
*
72547 TTTGTAAAAAATG
1 TTTGTCAAAAATG
72560 GTGGCATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.48
Consensus pattern (27 bp):
TTTGTCAAAAATGATGATTATTTTGTA
Found at i:73384 original size:16 final size:16
Alignment explanation
Indices: 73359--73389 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73349 TGATTAAATT
73359 TTTTTCCTTATTTATA
1 TTTTTCCTTATTTATA
*
73375 TTTTTGCTTATTTAT
1 TTTTTCCTTATTTAT
73390 TAATGATTCA
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:0.16, C:0.10, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTCCTTATTTATA
Found at i:74009 original size:13 final size:13
Alignment explanation
Indices: 73991--74015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73981 TCTCACGCCC
73991 TTTTATTTTTTAT
1 TTTTATTTTTTAT
74004 TTTTATTTTTTA
1 TTTTATTTTTTA
74016 AAATTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:76241 original size:20 final size:21
Alignment explanation
Indices: 76210--76255 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 21
76200 TAAAGGTTTA
76210 AATTTTAAAATA-TAAAAA-T
1 AATTTTAAAATATTAAAAAGT
76229 AATTTTAAAAATATTAAAAAGT
1 AATTTT-AAAATATTAAAAAGT
76251 AATTT
1 AATTT
76256 GCTTATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
21 6 0.25
22 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTTAAAATATTAAAAAGT
Found at i:77041 original size:2 final size:2
Alignment explanation
Indices: 77036--77061 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77026 TATATATATA
77036 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
77062 ATTCTGCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:77213 original size:3 final size:3
Alignment explanation
Indices: 77199--77234 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
77189 TTAATATGCT
* *
77199 ATA ATT ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
77235 GCATATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:80937 original size:23 final size:21
Alignment explanation
Indices: 80872--80937 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
80862 TAATATTAAA
* *
80872 AATTAAAATAAAATTAATATTTT
1 AATT-AAATTAAA-TAATAATTT
*
80895 AATTAAATTAAATAAAAATTT
1 AATTAAATTAAATAATAATTT
*
80916 AATTATTATATAAATAATAATT
1 AATTA-AAT-TAAATAATAATT
80938 CAAATTGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 12 0.33
22 9 0.25
23 15 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAAATTAAATAATAATTT
Found at i:90218 original size:90 final size:90
Alignment explanation
Indices: 90065--90241 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 90
90055 GATCATTGGG
* *
90065 ATGTATAACATTAGTTCAGTTGAAACCTCTCATCTAAGATGATTGGGAGTGTACTTCCATTCAGA
1 ATGTATAACATTAGTTCAGTTGAAACCTATCATCTAAGATGATTGGGAGTGCACTTCCATTCAGA
*
90130 TCTATCAATCATGCCATTTGAGGGA
66 TCTATCAATCAAGCCATTTGAGGGA
* *
90155 ATGTATAACATTAGTTCAGTTGGAACCTAT-AGTCTAAGATGATTGCTG-GTGCACTTCCATTCA
1 ATGTATAACATTAGTTCAGTTGAAACCTATCA-TCTAAGATGATTG-GGAGTGCACTTCCATTCA
90218 GATCTATCAATCAAGCCATTTGAG
64 GATCTATCAATCAAGCCATTTGAG
90242 AGTAAAGTAA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
89 1 0.01
90 78 0.98
91 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (90 bp):
ATGTATAACATTAGTTCAGTTGAAACCTATCATCTAAGATGATTGGGAGTGCACTTCCATTCAGA
TCTATCAATCAAGCCATTTGAGGGA
Found at i:91376 original size:2 final size:2
Alignment explanation
Indices: 91369--91398 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
91359 ACAAATCCAT
91369 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91399 AACTACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:96924 original size:117 final size:118
Alignment explanation
Indices: 96755--96984 Score: 340
Period size: 118 Copynumber: 1.9 Consensus size: 118
96745 CTCTCATAAA
* * *
96755 TTTATAATAACTTAAATTTAATTTTAAAAAATAATAATGATCAAATTATAATTAAT-A-TTTTTT
1 TTTATAATAACTCAAATTTAA-TTAAAAAAATAATAATAATCAAATTATAATTAATAATTTTTTT
96818 ATAAAATAAAAAATTTAATGATTAATTATATTTTAATATCATTTTAATCGAATAT
65 ATAAAATAAAAAATTTAATGA-TAATTATATTTTAATATCATTTTAATCGAATAT
*
96873 TTTATAATAACTCAAATTTAA-TAAAAATAATAATAATAATCAAATTGTAATTAATAATTTTTTT
1 TTTATAATAACTCAAATTTAATTAAAAA-AATAATAATAATCAAATTATAATTAATAATTTTTTT
** * *
96937 ATAAAATAAAAGGTTTAATTATAATTGTATTTTAATATCATTTTAATC
65 ATAAAATAAAAAATTTAATGATAATTATATTTTAATATCATTTTAATC
96985 AAATGTTAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
116 5 0.05
117 25 0.25
118 47 0.47
119 24 0.24
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (118 bp):
TTTATAATAACTCAAATTTAATTAAAAAAATAATAATAATCAAATTATAATTAATAATTTTTTTA
TAAAATAAAAAATTTAATGATAATTATATTTTAATATCATTTTAATCGAATAT
Found at i:97025 original size:16 final size:17
Alignment explanation
Indices: 96991--97031 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
96981 AATCAAATGT
96991 TAAAATTTAATATATAA
1 TAAAATTTAATATATAA
97008 TAAAATGTTAA-A-ATAA
1 TAAAAT-TTAATATATAA
97024 T-AAATTTA
1 TAAAATTTA
97032 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 4 0.17
16 5 0.22
17 7 0.30
18 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAAATTTAATATATAA
Found at i:99101 original size:13 final size:13
Alignment explanation
Indices: 99083--99107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
99073 ATTTTGTAAT
99083 TTTTTATTTTTTA
1 TTTTTATTTTTTA
99096 TTTTTATTTTTT
1 TTTTTATTTTTT
99108 TGAAAATCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:100084 original size:14 final size:14
Alignment explanation
Indices: 100067--100114 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
100057 TAATTTCTTC
100067 TATTTAATTTAATT
1 TATTTAATTTAATT
* *
100081 TATTTATTTTATTT
1 TATTTAATTTAATT
* *
100095 TATTTTATTTAGTT
1 TATTTAATTTAATT
100109 TATTTA
1 TATTTA
100115 TTTGTTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (14 bp):
TATTTAATTTAATT
Found at i:100212 original size:19 final size:19
Alignment explanation
Indices: 100185--100224 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
100175 ATTACGTAAG
*
100185 ATTTGAAAAA-AAATATTAA
1 ATTTAAAAAATAAAT-TTAA
100204 ATTTAAAAAATAAATTTAA
1 ATTTAAAAAATAAATTTAA
100223 AT
1 AT
100225 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
ATTTAAAAAATAAATTTAA
Found at i:100219 original size:13 final size:14
Alignment explanation
Indices: 100201--100233 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
100191 AAAAAAATAT
100201 TAAATTTAAA-AAA
1 TAAATTTAAATAAA
100214 TAAATTTAAATAAA
1 TAAATTTAAATAAA
*
100228 AAAATT
1 TAAATT
100234 AGACTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:100229 original size:18 final size:20
Alignment explanation
Indices: 100190--100232 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
100180 GTAAGATTTG
*
100190 AAAAA-AAATATTAAATTTA
1 AAAAATAAATATTAAATTAA
100209 AAAAATAAAT-TTAAA-TAA
1 AAAAATAAATATTAAATTAA
100227 AAAAAT
1 AAAAAT
100233 TAGACTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 10 0.45
20 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATAAATATTAAATTAA
Found at i:100230 original size:19 final size:19
Alignment explanation
Indices: 100190--100231 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
100180 GTAAGATTTG
*
100190 AAAAAAAATATTAAATTTAA
1 AAAAAAAATATTAAA-TAAA
*
100210 AAAATAAAT-TTAAATAAA
1 AAAAAAAATATTAAATAAA
100228 AAAA
1 AAAA
100232 TTAGACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAAAAATATTAAATAAA
Found at i:104058 original size:48 final size:51
Alignment explanation
Indices: 104001--104103 Score: 113
Period size: 52 Copynumber: 2.1 Consensus size: 51
103991 TTGGTAAAAG
*
104001 AGAAAAATGT-CCCG-AAATATGA-AAATTTGCCTGCACGTATCGATACAA
1 AGAAAAATGTACCCGTAAATATGACAAATTTGCCGGCACGTATCGATACAA
* * * * * *
104049 AGAATAATGTATCGGTACATCTGAGCAAATTTGCCGGCATGTATCGATACAA
1 AGAAAAATGTACCCGTAAATATGA-CAAATTTGCCGGCACGTATCGATACAA
104101 AGA
1 AGA
104104 TCATTGTATC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
48 9 0.20
49 2 0.05
50 6 0.14
52 27 0.61
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (51 bp):
AGAAAAATGTACCCGTAAATATGACAAATTTGCCGGCACGTATCGATACAA
Found at i:111210 original size:27 final size:27
Alignment explanation
Indices: 111180--111234 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
111170 AGACAACTGA
111180 AGCCAAGAAAATAAAAGAAAAGTAGAT
1 AGCCAAGAAAATAAAAGAAAAGTAGAT
111207 AGCCAAGAAAATAAAAGAAAAGTAGAT
1 AGCCAAGAAAATAAAAGAAAAGTAGAT
111234 A
1 A
111235 AAAGTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.64, C:0.07, G:0.18, T:0.11
Consensus pattern (27 bp):
AGCCAAGAAAATAAAAGAAAAGTAGAT
Found at i:113808 original size:25 final size:25
Alignment explanation
Indices: 113774--113825 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
113764 TGCAATATAG
*
113774 GAACAGCAAAATATAATTGGATAAT
1 GAACAACAAAATATAATTGGATAAT
113799 GAACAACAAAATATAATTGGATAAT
1 GAACAACAAAATATAATTGGATAAT
113824 GA
1 GA
113826 GAACTAAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (25 bp):
GAACAACAAAATATAATTGGATAAT
Found at i:115534 original size:35 final size:35
Alignment explanation
Indices: 115488--115560 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
115478 CTAAAGTGAT
115488 AAACCAAACTGCCCATAGTTAACCTTCACATTCCA
1 AAACCAAACTGCCCATAGTTAACCTTCACATTCCA
115523 AAACCAAACTGCCCATAGTTAACCTTCACATTCCA
1 AAACCAAACTGCCCATAGTTAACCTTCACATTCCA
115558 AAA
1 AAA
115561 TCCATAGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.22
Consensus pattern (35 bp):
AAACCAAACTGCCCATAGTTAACCTTCACATTCCA
Found at i:117120 original size:28 final size:27
Alignment explanation
Indices: 117089--117153 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
117079 AACAAATTTA
117089 AATATTTTTAATTTTTATATATAATAT
1 AATATTTTTAATTTTTATATATAATAT
* * *
117116 GAATAATTTTAA--TTTATATTTAATGT
1 -AATATTTTTAATTTTTATATATAATAT
117142 AAT-TTTTTAATT
1 AATATTTTTAATT
117154 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 6 0.19
25 3 0.10
26 12 0.39
28 10 0.32
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (27 bp):
AATATTTTTAATTTTTATATATAATAT
Found at i:117674 original size:16 final size:16
Alignment explanation
Indices: 117649--117704 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
117639 GATATCAAGC
*
117649 TAATAATATAGATTTA
1 TAATAATATAAATTTA
*
117665 TAATAGTATAAATTT-
1 TAATAATATAAATTTA
* *
117680 TAA-AATATATATTAA
1 TAATAATATAAATTTA
*
117695 AAATAATATA
1 TAATAATATA
117705 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 8 0.25
15 5 0.16
16 19 0.59
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
TAATAATATAAATTTA
Found at i:118455 original size:18 final size:18
Alignment explanation
Indices: 118415--118469 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
118405 AATTTTACGC
*
118415 ATTAATTATTGAAAAAATAA
1 ATTAATT-TT-AAAAAATTA
*
118435 ATTAATTTTAAGAAATTA
1 ATTAATTTTAAAAAATTA
*
118453 ATTAAATTTAAAAAATT
1 ATTAATTTTAAAAAATT
118470 CATGTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 22 0.71
19 2 0.06
20 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTAATTTTAAAAAATTA
Found at i:118553 original size:22 final size:22
Alignment explanation
Indices: 118501--118568 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
118491 TTATTATTTT
* * *
118501 TTAATCAAA-TAAGAAATAATA
1 TTAATTAAATTAAAAAATTATA
118522 TTTAATTAAATTTAAAAAATTATA
1 -TTAATTAAA-TTAAAAAATTATA
*
118546 TTAA-TAAATTAAAATATTA-A
1 TTAATTAAATTAAAAAATTATA
118566 TTA
1 TTA
118569 TTATATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.10
21 10 0.25
22 12 0.30
23 4 0.10
24 10 0.25
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (22 bp):
TTAATTAAATTAAAAAATTATA
Found at i:118570 original size:23 final size:23
Alignment explanation
Indices: 118514--118576 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
118504 ATCAAATAAG
*
118514 AAATAATATTTAATTAAATTTAAA
1 AAATTATA-TTAATTAAATTTAAA
118538 AAATTATATTAA-TAAA-TTAAA
1 AAATTATATTAATTAAATTTAAA
* *
118559 ATATTA-ATT-ATTATATTT
1 AAATTATATTAATTAAATTT
118577 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 6 0.18
21 12 0.35
22 4 0.12
23 4 0.12
24 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATTATATTAATTAAATTTAAA
Found at i:122868 original size:16 final size:16
Alignment explanation
Indices: 122849--122882 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
122839 TATATTTTGA
122849 AATTGTTATTATAAAT
1 AATTGTTATTATAAAT
* *
122865 AATTTTTATTATTAAT
1 AATTGTTATTATAAAT
122881 AA
1 AA
122883 AATTTATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTGTTATTATAAAT
Found at i:123499 original size:21 final size:21
Alignment explanation
Indices: 123475--123515 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
123465 TCGATTTAGT
123475 TTTAATTTGAGTTTT-ATTAAC
1 TTTAATTT-AGTTTTGATTAAC
123496 TTTAATTTAGTTTTGATTAA
1 TTTAATTTAGTTTTGATTAA
123516 GATAACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (21 bp):
TTTAATTTAGTTTTGATTAAC
Found at i:135781 original size:13 final size:13
Alignment explanation
Indices: 135763--135787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
135753 CATAAAGTGT
135763 TGTATCGATACAA
1 TGTATCGATACAA
135776 TGTATCGATACA
1 TGTATCGATACA
135788 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:135868 original size:13 final size:13
Alignment explanation
Indices: 135850--135874 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
135840 ATCACTTAAA
135850 TGTATCGATACAT
1 TGTATCGATACAT
135863 TGTATCGATACA
1 TGTATCGATACA
135875 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:135939 original size:52 final size:52
Alignment explanation
Indices: 135883--136011 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
135873 CACTGATCTT
* * *
135883 TGTATCGATACATGTAGGCAAATTTGCTCAAATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
* **
135935 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
135987 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
136012 TCATATTCCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:142885 original size:15 final size:15
Alignment explanation
Indices: 142867--142896 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
142857 GTTGCCACTG
*
142867 AACTTGTTCATCCAC
1 AACTCGTTCATCCAC
142882 AACTCGTTCATCCAC
1 AACTCGTTCATCCAC
142897 CTATTTTTTA
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:0.27, C:0.37, G:0.07, T:0.30
Consensus pattern (15 bp):
AACTCGTTCATCCAC
Found at i:143524 original size:14 final size:14
Alignment explanation
Indices: 143507--143658 Score: 65
Period size: 14 Copynumber: 11.1 Consensus size: 14
143497 ATATATAACA
143507 ATAAATTTAATAAT
1 ATAAATTTAATAAT
*
143521 ATAAA-ATAA-AA-
1 ATAAATTTAATAAT
** *
143532 ATAAAAATAGTAAT
1 ATAAATTTAATAAT
*
143546 ATAAAATTAATAAT
1 ATAAATTTAATAAT
* *
143560 A-ATAATATAAAAAT
1 ATA-AATTTAATAAT
143574 ATTAATATTGTAATAAT
1 A-TAA-ATT-TAATAAT
*
143591 ATAAATTAAAT-AT
1 ATAAATTTAATAAT
*
143604 ATAAA--TAAAAATT
1 ATAAATTTAATAA-T
143617 AATAACA-TT-AT-A-
1 -ATAA-ATTTAATAAT
*
143629 ATAAATTTAATAAA
1 ATAAATTTAATAAT
*
143643 ATAAACTTAATAAT
1 ATAAATTTAATAAT
143657 AT
1 AT
143659 TAGTGTCAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
10 1 0.01
11 13 0.12
12 8 0.08
13 15 0.14
14 49 0.46
15 6 0.06
16 7 0.07
17 7 0.07
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (14 bp):
ATAAATTTAATAAT
Found at i:143534 original size:25 final size:25
Alignment explanation
Indices: 143514--143575 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
143504 ACAATAAATT
143514 TAATAATATAAAATAAAAATAAAAA
1 TAATAATATAAAATAAAAATAAAAA
* *
143539 TAGTAATATAAAATTAATAATAATAATA
1 TAATAATATAAAA-TAAAAATAA-AA-A
*
143567 TAAAAATAT
1 TAATAATAT
143576 TAATATTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 12 0.40
26 8 0.27
27 2 0.07
28 8 0.27
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TAATAATATAAAATAAAAATAAAAA
Found at i:143579 original size:20 final size:20
Alignment explanation
Indices: 143514--143580 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
143504 ACAATAAATT
*
143514 TAATAAT-ATAAAATAAAAA
1 TAATAATAATAATATAAAAA
* * *
143533 TAAAAATAGTAATATAAAAT
1 TAATAATAATAATATAAAAA
143553 TAATAATAATAATATAAAAA
1 TAATAATAATAATATAAAAA
*
143573 TATTAATA
1 TAATAATA
143581 TTGTAATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 6 0.15
20 33 0.85
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (20 bp):
TAATAATAATAATATAAAAA
Found at i:144580 original size:3 final size:3
Alignment explanation
Indices: 144537--144568 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
144527 CTTTAATGCT
*
144537 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
144569 GGTTATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:148841 original size:31 final size:31
Alignment explanation
Indices: 148797--148858 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
148787 ATGACCAAAC
* *
148797 TTTTGTTTTTTGATTAAATTTTGACACTCAA
1 TTTTGATTGTTGATTAAATTTTGACACTCAA
** *
148828 TTTTGATTGTTGATTGGATTTTGCCACTCAA
1 TTTTGATTGTTGATTAAATTTTGACACTCAA
148859 CAATGGTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.52
Consensus pattern (31 bp):
TTTTGATTGTTGATTAAATTTTGACACTCAA
Found at i:150157 original size:23 final size:23
Alignment explanation
Indices: 150130--150173 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
150120 AAATTATAAA
*
150130 TATTAAATTTTAATTTTTAAATT
1 TATTAAATATTAATTTTTAAATT
*
150153 TATTAAATATTATTTTTTAAA
1 TATTAAATATTAATTTTTAAA
150174 ATTAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTAAATATTAATTTTTAAATT
Found at i:151351 original size:26 final size:24
Alignment explanation
Indices: 151322--151370 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
151312 CTTAAAAGAT
151322 AATTAAAAATATTTTAAAAATTTTAA
1 AATT-AAAATATTTT-AAAATTTTAA
* *
151348 AATTACAATATTTTTAAATTTTA
1 AATTAAAATATTTTAAAATTTTA
151371 TAATCATTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 9 0.43
26 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTAAAATATTTTAAAATTTTAA
Found at i:151548 original size:16 final size:16
Alignment explanation
Indices: 151527--151559 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
151517 TGATATTAAA
151527 AATTAATAT-TAATTAT
1 AATTAAT-TGTAATTAT
151543 AATTAATTGTAATTAT
1 AATTAATTGTAATTAT
151559 A
1 A
151560 TTGTTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AATTAATTGTAATTAT
Found at i:151914 original size:6 final size:6
Alignment explanation
Indices: 151898--151964 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
151888 TTATTTTGAC
* * * *
151898 AAAGAA GAAGAA AAAGAA AAGAAAA ATAAGAA AAAAAA AGAAAAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AA-AGAA A-AAGAA AAAGAA A-AAGAA AAAGAA
*
151949 AAAGGAA ATAGAA AAA
1 AAA-GAA AAAGAA AAA
151965 AAGATATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 29 0.59
7 19 0.39
8 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:151928 original size:9 final size:9
Alignment explanation
Indices: 151909--151951 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
151899 AAGAAGAAGA
151909 AAAAGAAAAG
1 AAAA-AAAAG
*
151919 AAAAATAAG
1 AAAAAAAAG
151928 AAAAAAAAAG
1 -AAAAAAAAG
151938 AAAAAAAAG
1 AAAAAAAAG
151947 AAAAA
1 AAAAA
151952 GGAAATAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 18 0.60
10 12 0.40
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:151932 original size:10 final size:10
Alignment explanation
Indices: 151905--151966 Score: 65
Period size: 10 Copynumber: 6.0 Consensus size: 10
151895 GACAAAGAAG
151905 AAGAAAAAGAA
1 AAGAAAAA-AA
*
151916 AAG-AAAAAT
1 AAGAAAAAAA
151925 AAGAAAAAAA
1 AAGAAAAAAA
151935 AAG-AAAAAA
1 AAGAAAAAAA
151944 AAGAAAAAGGAA
1 AAGAAAAA--AA
151956 ATAGAAAAAAA
1 A-AGAAAAAAA
151967 GATATAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 13 0.30
10 16 0.36
11 5 0.11
12 3 0.07
13 7 0.16
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:151934 original size:23 final size:23
Alignment explanation
Indices: 151899--151945 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 23
151889 TATTTTGACA
151899 AAGAAGAAGAAAAAGAAAAGAAAAAT
1 AAGAA-AA-AAAAAGAAAA-AAAAAT
151925 AAGAAAAAAAAAGAAAAAAAA
1 AAGAAAAAAAAAGAAAAAAAA
151946 GAAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 2 0.10
26 5 0.24
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAAAAAAAT
Found at i:151936 original size:19 final size:20
Alignment explanation
Indices: 151905--151966 Score: 90
Period size: 19 Copynumber: 3.0 Consensus size: 20
151895 GACAAAGAAG
*
151905 AAGAAAAAGAAAAGAAAAAT
1 AAGAAAAAGAAAAGAAAAAA
151925 AAGAAAAA-AAAAGAAAAAA
1 AAGAAAAAGAAAAGAAAAAA
151944 AAGAAAAAGGAAATAGAAAAAA
1 AAGAAAAA-GAAA-AGAAAAAA
151966 A
1 A
151967 GATATAAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 18 0.47
20 8 0.21
21 3 0.08
22 9 0.24
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
AAGAAAAAGAAAAGAAAAAA
Found at i:151945 original size:33 final size:32
Alignment explanation
Indices: 151902--151966 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
151892 TTTGACAAAG
*
151902 AAGAAGAAAAAG-AAAAGAAAAATAAGAAAAAAA
1 AAGAAAAAAAAGAAAAAG-AAAAT-AGAAAAAAA
*
151935 AAGAAAAAAAAGAAAAAGGAAATAGAAAAAAA
1 AAGAAAAAAAAGAAAAAGAAAATAGAAAAAAA
151967 GATATAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 9 0.31
33 15 0.52
34 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (32 bp):
AAGAAAAAAAAGAAAAAGAAAATAGAAAAAAA
Found at i:153184 original size:6 final size:6
Alignment explanation
Indices: 153175--153216 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
153165 TTATAAAAAT
153175 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
153217 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:153437 original size:15 final size:16
Alignment explanation
Indices: 153402--153432 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
153392 ATGTTATGAG
*
153402 ATCAATTATGAAAAAT
1 ATCAATTAAGAAAAAT
153418 ATCAATTAAGAAAAA
1 ATCAATTAAGAAAAA
153433 CTCAAGATTT
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:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
ATCAATTAAGAAAAAT
Found at i:154533 original size:32 final size:32
Alignment explanation
Indices: 154497--154560 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
154487 AGAAAGAAAG
154497 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
1 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
154529 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
1 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
154561 TTGTTGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (32 bp):
AAAAAAAAGTATTTCACAAATAAAAAATTTGT
Found at i:154558 original size:16 final size:16
Alignment explanation
Indices: 154507--154558 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
154497 AAAAAAAAGT
154507 ATTTCACAAATAAAAA
1 ATTTCACAAATAAAAA
* *
154523 ATTTGTA-AAA-AAAAGT
1 ATTT-CACAAATAAAA-A
154539 ATTTCACAAATAAAAA
1 ATTTCACAAATAAAAA
154555 ATTT
1 ATTT
154559 GTTTGTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.31
Consensus pattern (16 bp):
ATTTCACAAATAAAAA
Found at i:157453 original size:22 final size:21
Alignment explanation
Indices: 157412--157477 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
157402 ATAAATTATT
157412 ATATAAATATGTCAATATATAAA
1 ATATAAATAT-T-AATATATAAA
157435 ATATAAATTATTAATATATTAAA
1 ATATAAA-TATTAATATA-TAAA
* * *
157458 AAATATATATAAATATATAA
1 ATATAAATATTAATATATAA
157478 TATTTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.08
22 15 0.39
23 17 0.45
24 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAAATATTAATATATAAA
Found at i:158368 original size:23 final size:24
Alignment explanation
Indices: 158331--158375 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
158321 GAATATTCTT
*
158331 TATTTTATTTATTTTAAAAATATA
1 TATTTTATATATTTTAAAAATATA
*
158355 TATTTT-TATATTTTATAAATA
1 TATTTTATATATTTTAAAAATA
158376 ATTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTTATATATTTTAAAAATATA
Found at i:160639 original size:31 final size:33
Alignment explanation
Indices: 160601--160675 Score: 100
Period size: 31 Copynumber: 2.3 Consensus size: 33
160591 ATATATATTG
*
160601 TATAGATATAGAGTAAAGATTATAGA-TATA-T
1 TATAGATATAGAGTAAAGATCATAGATTATAGT
* *
160632 TATAGATATATAGTATAGATCATAGATTATAGGT
1 TATAGATATAGAGTAAAGATCATAGATTATA-GT
160666 TATAGATATA
1 TATAGATATA
160676 TAATATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.61
32 4 0.11
34 11 0.29
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.37
Consensus pattern (33 bp):
TATAGATATAGAGTAAAGATCATAGATTATAGT
Found at i:160668 original size:7 final size:7
Alignment explanation
Indices: 160601--160677 Score: 58
Period size: 7 Copynumber: 11.6 Consensus size: 7
160591 ATATATATTG
160601 TATAGA-
1 TATAGAT
*
160607 TATAGAG
1 TATAGAT
*
160614 TAAAGAT
1 TATAGAT
160621 TATAGA-
1 TATAGAT
160627 TAT--AT
1 TATAGAT
160632 TATAGAT
1 TATAGAT
160639 ATATAG--
1 -TATAGAT
160645 TATAGAT
1 TATAGAT
*
160652 CATAGAT
1 TATAGAT
*
160659 TATAGGT
1 TATAGAT
160666 TATAGAT
1 TATAGAT
160673 ATATA
1 -TATA
160678 ATATTTAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
4 1 0.02
5 8 0.14
6 9 0.16
7 29 0.52
8 9 0.16
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (7 bp):
TATAGAT
Found at i:162131 original size:19 final size:19
Alignment explanation
Indices: 162082--162131 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
162072 ATATAAGATA
162082 AAAATAATTTTTTAATATT
1 AAAATAATTTTTTAATATT
** *
162101 TTAAT-ATATTTTAA-ATAT
1 AAAATAATTTTTTAATAT-T
162119 AAAATAATTTTTT
1 AAAATAATTTTTT
162132 CGGATTTTTG
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
17 2 0.09
18 12 0.52
19 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAATAATTTTTTAATATT
Found at i:163820 original size:13 final size:13
Alignment explanation
Indices: 163802--163846 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
163792 TTAACACGTG
163802 ATATAATATAAAA
1 ATATAATATAAAA
163815 ATATAATATAAATA
1 ATATAATATAAA-A
*
163829 A-AT-ATATTAAA
1 ATATAATATAAAA
163840 AT-TAATA
1 ATATAATA
163847 AAACATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 3 0.11
12 9 0.32
13 14 0.50
14 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAATATAAAA
Found at i:163841 original size:25 final size:25
Alignment explanation
Indices: 163807--163856 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
163797 ACGTGATATA
*
163807 ATATAAAAATATAATATAA-ATAAAT
1 ATATAAAAAT-TAATAAAACATAAAT
*
163832 ATATTAAAATTAATAAAACATAAAT
1 ATATAAAAATTAATAAAACATAAAT
163857 GATTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
ATATAAAAATTAATAAAACATAAAT
Found at i:163846 original size:14 final size:15
Alignment explanation
Indices: 163802--163856 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
163792 TTAACACGTG
163802 ATATAATAT-AA-AA
1 ATATAATATAAATAA
163815 ATATAATATAAATAA
1 ATATAATATAAATAA
* *
163830 ATATATTA-AAATTA
1 ATATAATATAAATAA
* *
163844 ATAAAACATAAAT
1 ATATAATATAAAT
163857 GATTAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.26
14 12 0.35
15 13 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATAATATAAATAA
Found at i:163861 original size:24 final size:25
Alignment explanation
Indices: 163812--163862 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
163802 ATATAATATA
* *
163812 AAAATATAATATAAATAAATATATT
1 AAAATATAATAAAAATAAATAGATT
163837 AAAAT-TAATAAAACATAAAT-GATT
1 AAAATATAATAAAA-ATAAATAGATT
163861 AA
1 AA
163863 TTAAGATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATATAATAAAAATAAATAGATT
Found at i:165053 original size:17 final size:19
Alignment explanation
Indices: 164991--165053 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
164981 CATTAGTAAA
164991 ATAAAATAATAATAATTTTT
1 ATAAAAT-ATAATAATTTTT
*
165011 ATAAAATATACATCATTATATT
1 ATAAAATATA-ATAATT-T-TT
165033 ATAAAA-AT-ATAATTTTT
1 ATAAAATATAATAATTTTT
165050 ATAA
1 ATAA
165054 TAAAAGAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 6 0.16
18 1 0.03
19 8 0.21
20 12 0.32
21 3 0.08
22 8 0.21
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAAATATAATAATTTTT
Found at i:166663 original size:17 final size:16
Alignment explanation
Indices: 166637--166678 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
166627 TGAAATCGAT
166637 TAACTCAAACTTCAAAA
1 TAACTCAAACTT-AAAA
*
166654 TAACTTAAACTTAAAA
1 TAACTCAAACTTAAAA
*
166670 TAATTCAAA
1 TAACTCAAA
166679 TCTATATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (16 bp):
TAACTCAAACTTAAAA
Found at i:168687 original size:22 final size:22
Alignment explanation
Indices: 168622--168687 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
168612 CTTGAGTGTC
* * *
168622 AAACTCCATTGGCTTGAATTGTT
1 AAACTCAATTGACTTGAA-TATT
* *
168645 AAACTCAATT-AATTCGTATATT
1 AAACTCAATTGACTT-GAATATT
168667 AAACTCAATTGACTTGAATAT
1 AAACTCAATTGACTTGAATAT
168688 GAATTGATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (22 bp):
AAACTCAATTGACTTGAATATT
Found at i:169684 original size:2 final size:2
Alignment explanation
Indices: 169677--169711 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
169667 AAGAGGCTGT
169677 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
169712 TTGTCTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:170073 original size:19 final size:19
Alignment explanation
Indices: 170039--170078 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
170029 ATATTAATAT
*
170039 TTATAAAAAAATTTAACCA
1 TTATAAAAAAATTTAAACA
170058 TTAT-AAAAAATATTAAACA
1 TTATAAAAAAAT-TTAAACA
170077 TT
1 TT
170079 TGAGATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATAAAAAAATTTAAACA
Found at i:175348 original size:20 final size:20
Alignment explanation
Indices: 175309--175354 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
175299 TTTAATTAAA
*
175309 AAATTTAATTGAAAATTTTT
1 AAATTTAATTGAAAACTTTT
* **
175329 TAATTTAATTGATTACTTTT
1 AAATTTAATTGAAAACTTTT
175349 AAATTT
1 AAATTT
175355 GTTTAGGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
AAATTTAATTGAAAACTTTT
Found at i:177735 original size:29 final size:29
Alignment explanation
Indices: 177703--177846 Score: 108
Period size: 29 Copynumber: 4.8 Consensus size: 29
177693 TTAAATTTTA
**
177703 TTATTTTATTTAAATAATTTTTTATGTTT
1 TTATTTTATTTAAATAATTTTTTAACTTT
* *
177732 TTATTATATTTAAATATTTTTTTAACTTT
1 TTATTTTATTTAAATAATTTTTTAACTTT
* *
177761 TAATTTATACTTAAATAAATTTTTTAATCTTT
1 TTATTT-TATTTAAAT-AATTTTTTAA-CTTT
* * ** * *
177793 TAACTTGTATCAAAATAAGTCTTTTAACGTT
1 TTA-TTTTATTTAAATAA-TTTTTTAACTTT
* *
177824 TAATTTATATTTAAATAAATTTT
1 TTATTT-TATTTAAATAATTTTT
177847 CAAGATAAAT
Statistics
Matches: 90, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
29 29 0.32
30 13 0.14
31 26 0.29
32 20 0.22
33 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TTATTTTATTTAAATAATTTTTTAACTTT
Found at i:177840 original size:31 final size:31
Alignment explanation
Indices: 177691--177846 Score: 140
Period size: 31 Copynumber: 5.1 Consensus size: 31
177681 TAATTAAAAG
*
177691 TTTTAAATTTTATTATTT-TATTTAAAT-AATT
1 TTTTAACTTTTA--ATTTATATTTAAATAAATT
** * *
177722 TTTTATGTTTTTA-TTATATTTAAAT-ATTT
1 TTTTAACTTTTAATTTATATTTAAATAAATT
*
177751 TTTTAACTTTTAATTTATACTTAAATAAATT
1 TTTTAACTTTTAATTTATATTTAAATAAATT
* * ** * *
177782 TTTTAATCTTTTAACTTGTATCAAAATAAGTC
1 TTTTAA-CTTTTAATTTATATTTAAATAAATT
*
177814 TTTTAACGTTTAATTTATATTTAAATAAATT
1 TTTTAACTTTTAATTTATATTTAAATAAATT
177845 TT
1 TT
177847 CAAGATAAAT
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
28 2 0.02
29 23 0.23
30 11 0.11
31 38 0.39
32 24 0.24
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTAACTTTTAATTTATATTTAAATAAATT
Found at i:179501 original size:2 final size:2
Alignment explanation
Indices: 179494--179548 Score: 62
Period size: 2 Copynumber: 29.0 Consensus size: 2
179484 TTTGTTCATA
* *
179494 AT AT AT AT AT AT AT AT -T AT AT CT GT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
179534 AT AT AT GT AT -T AT AT
1 AT AT AT AT AT AT AT AT
179549 CTGCATGCAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:188693 original size:28 final size:29
Alignment explanation
Indices: 188636--188702 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
188626 ACTTATCAGG
*
188636 TTAGTAATTTTCATCATTTGAGGGCTATT
1 TTAGTAATTTTCATCATTTGAGGGCCATT
* *
188665 TTAGTAATTTT-ATTATTTTAGGGCCATT
1 TTAGTAATTTTCATCATTTGAGGGCCATT
* *
188693 TAAGTTATTT
1 TTAGTAATTT
188703 AACAAGGTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.52
Consensus pattern (29 bp):
TTAGTAATTTTCATCATTTGAGGGCCATT
Done.