Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2438
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: 77653
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3538 original size:13 final size:14
Alignment explanation
Indices: 3520--3574 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
3510 CTTAATTTTG
3520 AAATAA-ATTATTA
1 AAATAATATTATTA
3533 AAATAATATTATTTTA
1 AAATAATATTA--TTA
* *
3549 AAATTAT-TTATAA
1 AAATAATATTATTA
*
3562 AAATATTATTATT
1 AAATAATATTATT
3575 TTGCTTGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
13 13 0.39
14 8 0.24
15 3 0.09
16 9 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATAATATTATTA
Found at i:3549 original size:16 final size:16
Alignment explanation
Indices: 3500--3552 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3490 GGTAAATTAA
*
3500 TTAAAATAATCTTAATT
1 TTAAAATAATATT-ATT
*
3517 TTGAAATAA-ATTA--
1 TTAAAATAATATTATT
3530 TTAAAATAATATTATT
1 TTAAAATAATATTATT
3546 TTAAAAT
1 TTAAAAT
3553 TATTTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
15 1 0.03
16 9 0.30
17 8 0.27
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TTAAAATAATATTATT
Found at i:3559 original size:29 final size:29
Alignment explanation
Indices: 3492--3576 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
3482 AAACTATAGG
* *
3492 TAAATTAATTAAAATAATCTTAATTTTGAAA
1 TAAATT-ATTAAAATAATATT-ATTTTAAAA
3523 TAAATTATTAAAATAATATTATTTTAAAA
1 TAAATTATTAAAATAATATTATTTTAAAA
* * * *
3552 TTATTTATAAAAATATTATTATTTT
1 TAAATTATTAAAATAATATTATTTT
3577 GCTTGCATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
29 29 0.60
30 13 0.27
31 6 0.12
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TAAATTATTAAAATAATATTATTTTAAAA
Found at i:4079 original size:23 final size:22
Alignment explanation
Indices: 4037--4108 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 22
4027 TATAAATTTT
*
4037 TAATATTTTTAAAATATTAATA
1 TAATAATTTTAAAATATTAATA
*
4059 TAATAATTTTAAATATTTTAATAA
1 TAATAATTTTAAA-ATATTAAT-A
4083 TAACATATATTTTAAAAGTAATTAAT
1 T-A-ATA-ATTTTAAAA-T-ATTAAT
4109 TAACTGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 12 0.30
23 7 0.17
24 2 0.05
25 1 0.03
26 4 0.10
27 9 0.22
28 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (22 bp):
TAATAATTTTAAAATATTAATA
Found at i:4272 original size:29 final size:30
Alignment explanation
Indices: 4240--4307 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
4230 AAAACAGTAA
*
4240 TATTTTAATAAATAATTTTAAAA-TAATAT
1 TATTTTAATAAATAATTTTAAAATTAAAAT
* *
4269 TATTTTAATAATTTATTTTAAAATTAAAAT
1 TATTTTAATAAATAATTTTAAAATTAAAAT
*
4299 TACTTTAAT
1 TATTTTAAT
4308 TAATCTATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTTAATAAATAATTTTAAAATTAAAAT
Found at i:4275 original size:16 final size:16
Alignment explanation
Indices: 4254--4306 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
4244 TTAATAAATA
4254 ATTTTAAAATAATATT
1 ATTTTAAAATAATATT
4270 ATTTT--AATAAT-TT
1 ATTTTAAAATAATATT
*
4283 ATTTTAAAATTAAAATT
1 ATTTTAAAA-TAATATT
*
4300 ACTTTAA
1 ATTTTAA
4307 TTAATCTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 7 0.23
14 6 0.19
15 2 0.06
16 8 0.26
17 8 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAAAATAATATT
Found at i:4278 original size:14 final size:14
Alignment explanation
Indices: 4240--4289 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
4230 AAAACAGTAA
4240 TATTTTAATAA-AT
1 TATTTTAATAATAT
*
4253 AATTTTAAAATAATAT
1 TATTTT--AATAATAT
4269 TATTTTAATAAT-T
1 TATTTTAATAATAT
4282 TATTTTAA
1 TATTTTAA
4290 AATTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 14 0.44
14 6 0.19
15 5 0.16
16 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTTTAATAATAT
Found at i:5153 original size:18 final size:18
Alignment explanation
Indices: 5126--5160 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5116 AATCAAATTT
*
5126 TTAAAGATAAAAATTTAC
1 TTAAAAATAAAAATTTAC
*
5144 TTAAAAATAATAATTTA
1 TTAAAAATAAAAATTTA
5161 ATAATTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
TTAAAAATAAAAATTTAC
Found at i:5321 original size:16 final size:15
Alignment explanation
Indices: 5300--5344 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
5290 TCCACAAAAA
5300 CTCGAATCCGAAAAGG
1 CTCGAATCC-AAAAGG
*
5316 CTCGAATCTAAATAGG
1 CTCGAATCCAAA-AGG
*
5332 CCCGAATCCAAAA
1 CTCGAATCCAAAA
5345 AAGATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (15 bp):
CTCGAATCCAAAAGG
Found at i:5355 original size:16 final size:15
Alignment explanation
Indices: 5336--5379 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
5326 AATAGGCCCG
5336 AATCCAAAAAAGATTA
1 AATCCAAAAAA-ATTA
*
5352 AATCCAAATAAATTTA
1 AATCCAAA-AAAATTA
5368 AATCCGAAAAAA
1 AATCC-AAAAAA
5380 CCCAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.61, C:0.14, G:0.05, T:0.20
Consensus pattern (15 bp):
AATCCAAAAAAATTA
Found at i:7225 original size:17 final size:17
Alignment explanation
Indices: 7203--7259 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
7193 CTACGTCGAG
7203 TTATTTTTAAATTTGAA
1 TTATTTTTAAATTTGAA
*
7220 TTA-TTTTAAGA-TTAAA
1 TTATTTTTAA-ATTTGAA
* *
7236 TTAATTTTAAATTCGAA
1 TTATTTTTAAATTTGAA
*
7253 TAATTTT
1 TTATTTT
7260 GAATTTAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 14 0.44
17 18 0.56
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (17 bp):
TTATTTTTAAATTTGAA
Found at i:7228 original size:16 final size:16
Alignment explanation
Indices: 7207--7265 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
7197 GTCGAGTTAT
7207 TTTTAAATTTGAATTA
1 TTTTAAATTTGAATTA
*
7223 TTTTAAGA-TTAAATTAA
1 TTTTAA-ATTTGAATT-A
* *
7240 TTTTAAATTCGAATAA
1 TTTTAAATTTGAATTA
*
7256 TTTTGAATTT
1 TTTTAAATTT
7266 AGATTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 22 0.65
17 12 0.35
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTAAATTTGAATTA
Found at i:8001 original size:15 final size:15
Alignment explanation
Indices: 7981--8009 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7971 TTTTTTTCTT
7981 TTTTATTAGATTTTG
1 TTTTATTAGATTTTG
7996 TTTTATTAGATTTT
1 TTTTATTAGATTTT
8010 TTTAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTTATTAGATTTTG
Found at i:8879 original size:21 final size:19
Alignment explanation
Indices: 8853--8901 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
8843 AATCTTTATA
8853 TTTTTATTTACAAGATAATAT
1 TTTTTATTTACAAG-TAA-AT
*
8874 TTTTTATTTTCAAGTAAAT
1 TTTTTATTTACAAGTAAAT
*
8893 TTTATATTT
1 TTTTTATTT
8902 TATTTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
20 3 0.12
21 13 0.50
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTTATTTACAAGTAAAT
Found at i:11672 original size:18 final size:17
Alignment explanation
Indices: 11638--11672 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11628 AAGATGTTAT
*
11638 TCAAGAAGTGCTTGATG
1 TCAAGAAGTACTTGATG
11655 TCAAGAAGTACTTTGATG
1 TCAAGAAGTAC-TTGATG
11673 AGGAAGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (17 bp):
TCAAGAAGTACTTGATG
Found at i:16735 original size:3 final size:3
Alignment explanation
Indices: 16725--16762 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
16715 GATGACAACA
16725 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16763 TATTTGCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21498 original size:13 final size:13
Alignment explanation
Indices: 21480--21505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21470 TACAGCAAGT
21480 ATGTATCGATACA
1 ATGTATCGATACA
21493 ATGTATCGATACA
1 ATGTATCGATACA
21506 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:23772 original size:21 final size:21
Alignment explanation
Indices: 23739--23783 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23729 TTGCAAGTTG
*
23739 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
23761 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
23781 AAA
1 AAA
23784 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:25621 original size:16 final size:16
Alignment explanation
Indices: 25585--25621 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
25575 GATAAAAATG
25585 TCCAAAATGAGAAAGC
1 TCCAAAATGAGAAAGC
25601 T-CAAAATGA-AGAAGC
1 TCCAAAATGAGA-AAGC
25616 TCCAAA
1 TCCAAA
25622 CGAAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 13 0.68
16 5 0.26
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (16 bp):
TCCAAAATGAGAAAGC
Found at i:27702 original size:20 final size:20
Alignment explanation
Indices: 27623--27702 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
27613 AATGTCCAAA
*
27623 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
27643 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
27668 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
27688 TTGTATCGATACATT
1 ATGTATCGATACATT
27703 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:27706 original size:13 final size:13
Alignment explanation
Indices: 27688--27713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27678 ACATTTTTCT
27688 TTGTATCGATACA
1 TTGTATCGATACA
27701 TTGTATCGATACA
1 TTGTATCGATACA
27714 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:30273 original size:13 final size:13
Alignment explanation
Indices: 30255--30280 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30245 TACAGCAAGT
30255 ATGTATCGATACA
1 ATGTATCGATACA
30268 ATGTATCGATACA
1 ATGTATCGATACA
30281 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:33331 original size:50 final size:49
Alignment explanation
Indices: 33231--33395 Score: 222
Period size: 50 Copynumber: 3.3 Consensus size: 49
33221 TTTTAACTAG
* * ** *
33231 ATGTATCAATATATTGAAAAAAATATTGATACATTTAGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACA-TTAGGT-AAAAGACAGA
*
33282 ATGTATCGATACATTGAAAAATGTATCGATATATCTAGGTAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACAT-TAGGTAAAAGACAGA
* *
33332 ATGTATCGATACATTAAAAAATGTATCGATACATTTGGATAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATTAGG-TAAAAGACAGA
33382 ATGTATCGATACAT
1 ATGTATCGATACAT
33396 CTGGGAAAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
49 3 0.03
50 68 0.66
51 32 0.31
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (49 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATTAGGTAAAAGACAGA
Found at i:34089 original size:44 final size:44
Alignment explanation
Indices: 34026--34130 Score: 201
Period size: 44 Copynumber: 2.4 Consensus size: 44
34016 GATGTGCTAG
*
34026 TGTGCAGATTTAAGGCTTGGACTTAAAGATAAGAAGGGTGCCAA
1 TGTGCTGATTTAAGGCTTGGACTTAAAGATAAGAAGGGTGCCAA
34070 TGTGCTGATTTAAGGCTTGGACTTAAAGATAAGAAGGGTGCCAA
1 TGTGCTGATTTAAGGCTTGGACTTAAAGATAAGAAGGGTGCCAA
34114 TGTGCTGATTTAAGGCT
1 TGTGCTGATTTAAGGCT
34131 AGTTACAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (44 bp):
TGTGCTGATTTAAGGCTTGGACTTAAAGATAAGAAGGGTGCCAA
Found at i:34160 original size:44 final size:44
Alignment explanation
Indices: 34026--34149 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
34016 GATGTGCTAG
* * *
34026 TGTGCAGATTTAAGGCTTGGACTTAAAGATAAGAAGGGTGCCAA
1 TGTGCTGATTTAAGGCTAGGACTAAAAGATAAGAAGGGTGCCAA
* *
34070 TGTGCTGATTTAAGGCTTGGACTTAAAGATAAGAAGGGTGCCAA
1 TGTGCTGATTTAAGGCTAGGACTAAAAGATAAGAAGGGTGCCAA
* *
34114 TGTGCTGATTTAAGGCTAGTTAC-AAAAGATGAGAAG
1 TGTGCTGATTTAAGGCTAG-GACTAAAAGATAAGAAG
34150 AATGCGAATG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
44 72 0.97
45 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (44 bp):
TGTGCTGATTTAAGGCTAGGACTAAAAGATAAGAAGGGTGCCAA
Found at i:34418 original size:33 final size:31
Alignment explanation
Indices: 34381--34452 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
34371 TGCCATTGAG
*
34381 TTGTGTGGGCCTTTAAAAATAAG-TGCCACCGAC
1 TTGTGTGGG--TTTAAAAA-AAGTTACCACCGAC
* *
34414 TTGTGTGGGTTTGAAAAAGGTTACCACCGAC
1 TTGTGTGGGTTTAAAAAAAGTTACCACCGAC
34445 TTGTGTGG
1 TTGTGTGG
34453 ACTTTGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 2 0.06
31 24 0.69
33 9 0.26
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (31 bp):
TTGTGTGGGTTTAAAAAAAGTTACCACCGAC
Found at i:34444 original size:31 final size:33
Alignment explanation
Indices: 34406--34527 Score: 145
Period size: 31 Copynumber: 3.9 Consensus size: 33
34396 AAAATAAGTG
*
34406 CCACCGACTTGTGTGG-GTTTGAAAA-AGGTTA
1 CCACCGACTTGTGTGGACTTTGAAAAGAGGTTA
34437 CCACCGACTTGTGTGGACTTTGAAAAGAGGTGT-
1 CCACCGACTTGTGTGGACTTTGAAAAGAGGT-TA
*
34470 -CACTGACTTGTG-GG-CTTT-AAAAG-GG-TA
1 CCACCGACTTGTGTGGACTTTGAAAAGAGGTTA
*
34497 TCACCGACTTGTGTGGACTTTGAAAAGAGGT
1 CCACCGACTTGTGTGGACTTTGAAAAGAGGT
34528 GCCATTGACC
Statistics
Matches: 78, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
26 1 0.01
28 13 0.17
29 7 0.09
30 8 0.10
31 23 0.29
32 21 0.27
33 4 0.05
34 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (33 bp):
CCACCGACTTGTGTGGACTTTGAAAAGAGGTTA
Found at i:34502 original size:60 final size:60
Alignment explanation
Indices: 34428--34659 Score: 246
Period size: 60 Copynumber: 4.0 Consensus size: 60
34418 GTGGGTTTGA
* * * *
34428 AAAAGGTTACCACCGACTTGTGTGGACTTTGAAAAGAGGTGTCACTGACTTGTGGGCTTT
1 AAAAGGGTATCACCGACTTGTGTGGACTTTGAAAAGAGGTGCCACTGACTTATGGGCTTT
* *
34488 AAAAGGGTATCACCGACTTGTGTGGACTTTGAAAAGAGGTGCCATTGACCTATGGGCTTT
1 AAAAGGGTATCACCGACTTGTGTGGACTTTGAAAAGAGGTGCCACTGACTTATGGGCTTT
* * *
34548 AAAAGGGTATCACTGACTTGTG-GG-C-TTAAAAAG-GGTGCCACTTACTTATGGGCTTT
1 AAAAGGGTATCACCGACTTGTGTGGACTTTGAAAAGAGGTGCCACTGACTTATGGGCTTT
** ** ** * * *
34604 GGAAGGGTGCCATTGACTTATG-GG-C-TTAAAAAG-GGTGCCACTTACTTATGGGCTTT
1 AAAAGGGTATCACCGACTTGTGTGGACTTTGAAAAGAGGTGCCACTGACTTATGGGCTTT
34660 GGAAGGGTGC
Statistics
Matches: 155, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
56 70 0.45
57 7 0.05
58 1 0.01
59 2 0.01
60 75 0.48
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (60 bp):
AAAAGGGTATCACCGACTTGTGTGGACTTTGAAAAGAGGTGCCACTGACTTATGGGCTTT
Found at i:34589 original size:28 final size:28
Alignment explanation
Indices: 34403--35164 Score: 468
Period size: 28 Copynumber: 26.8 Consensus size: 28
34393 TTAAAAATAA
* *
34403 GTGCCACCGACTTGTGTGGGTTTGAAAAAGG
1 GTGCCACTGACTTGTG-GGCTTT--AAAAGG
* * *
34434 TTACCACCGACTTGTGTGGACTTTGAAAAGAG
1 GTGCCACTGACTTGTG-GG-CTTT-AAAAG-G
*
34466 GTGTCACTGACTTGTGGGCTTTAAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
** *
34494 GTATCACCGACTTGTGTGGACTTTGAAAAGAG
1 GTGCCACTGACTTGTG-GG-CTTT-AAAAG-G
* * *
34526 GTGCCATTGACCTATGGGCTTTAAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
** *
34554 GTATCACTGACTTGTGGGCTTAAAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * **
34582 GTGCCACTTACTTATGGGCTTTGGAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * *
34610 GTGCCATTGACTTATGGGCTTAAAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * **
34638 GTGCCACTTACTTATGGGCTTTGGAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * *
34666 GTGCTACTTG-CTTATGGGCTTTGGAAA-G
1 GTGCCAC-TGACTTGTGGGCTTT-AAAAGG
* * *
34694 GTGCCACCGATTTGTGGGCTTAAAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * * * *
34722 TTGCCACTTG-TTTATGGGCTTTGGAAA-T
1 GTGCCAC-TGACTTGTGGGCTTT-AAAAGG
* *
34750 GTGCCA-TCGACTTGTGGGCTTAAAAAAG
1 GTGCCACT-GACTTGTGGGCTTTAAAAGG
* * * *
34778 GTGCCATTGACTTGTGGACTTTGAATGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * *
34806 ATGCCACTGACCTGTGAGCTTTGAAAA-G
1 GTGCCACTGACTTGTGGGCTTT-AAAAGG
* * *
34834 ATGCCACTGACTTGTGGACTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * *
34862 ATGCCACTGACCTGTGGGCTTT-GAAGAG
1 GTGCCACTGACTTGTGGGCTTTAAAAG-G
* * * *
34890 ATGCTACTCACTTGTGGGGTTTAAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* *
34918 ATGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * * *
34946 ATGCTACTGACCTGTAGGCTTTGAAGAA--
1 GTGCCACTGACTTGTGGGCTTT-AA-AAGG
* * *
34974 ATGCCACTAACTTGTGGGCTTTGAAAAAAG
1 GTGCCACTGACTTGTGGGCTTT--AAAAGG
* * * *
35004 TTGCCACCGACCTGTGGGCTTT-GAAGAG
1 GTGCCACTGACTTGTGGGCTTTAAAAG-G
* * * *
35032 ATGCCACTCAATTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * *
35060 ATGCCATTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* *
35088 ATGCCACTGACCT-TGGGCTTTGAAAA-G
1 GTGCCACTGACTTGTGGGCTTT-AAAAGG
* * *
35115 ATGCCACTGACTTGTAGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTAAAAGG
* * *
35143 ATACCTCTGACTTGTGGGCTTT
1 GTGCCACTGACTTGTGGGCTTT
35165 CAAGAAATGA
Statistics
Matches: 580, Mismatches: 121, Indels: 63
0.76 0.16 0.08
Matches are distributed among these distances:
26 1 0.00
27 40 0.07
28 417 0.72
29 32 0.06
30 32 0.06
31 31 0.05
32 27 0.05
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTAAAAGG
Found at i:34883 original size:56 final size:56
Alignment explanation
Indices: 34404--35164 Score: 545
Period size: 56 Copynumber: 13.4 Consensus size: 56
34394 TAAAAATAAG
* * * * * *
34404 TGCCACCGACTTGTGTGGGTTTGAAAAAGGTTACCACCGACTTGTGTGGACTTTGAAAAGAGG
1 TGCCACTGACTTGTG-GGCTTTG-AAAA-GATGCCACTGACTTGTG-GG-CTTTG-AAAG-GA
* * ** * *
34467 TGTCACTGACTTGTGGGCTTT-AAAAGGGTATCACCGACTTGTGTGGACTTTGAAAAGAGG
1 TGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTG-GG-CTTTG-AAAG-GA
* * * * ** ** *
34527 TGCCATTGACCTATGGGCTTT-AAAAGGGTATCACTGACTTGTGGGCTTAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * * * * ** *
34583 TGCCACTTACTTATGGGCTTTGGAAGGGTGCCATTGACTTATGGGCTTAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * * * *
34639 TGCCACTTACTTATGGGCTTTGGAAGGGTGCTACTTG-CTTATGGGCTTTGGAAAGG-
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCAC-TGACTTGTGGGCTTT-GAAAGGA
* * * * * * *
34695 TGCCACCGATTTGTGGGC-TTAAAAAGGTTGCCACTTG-TTTATGGGCTTTGGAAATG-
1 TGCCACTGACTTGTGGGCTTTGAAAA-GATGCCAC-TGACTTGTGGGCTTT-GAAAGGA
** * * * *
34751 TGCCA-TCGACTTGTGGGCTTAAAAAAGGTGCCATTGACTTGTGGACTTTGAATGGA
1 TGCCACT-GACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
34807 TGCCACTGACCTGTGAGCTTTGAAAAGATGCCACTGACTTGTGGACTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * * *
34863 TGCCACTGACCTGTGGGCTTTGAAGAGATGCTACTCACTTGTGGGGTTTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
34919 TGCCACTGACTTGTGGGCTTTGAAAGGATGCTACTGACCTGTAGGCTTTG-AAGAAA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAG-GA
* * * *
34975 TGCCACTAACTTGTGGGCTTTGAAAAAAGTTGCCACCGACCTGTGGGCTTTG-AAGAGA
1 TGCCACTGACTTGTGGGCTTTG--AAAAGATGCCACTGACTTGTGGGCTTTGAAAG-GA
* * * *
35033 TGCCACTCAATTGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA
* *
35089 TGCCACTGACCT-TGGGCTTTGAAAAGATGCCACTGACTTGTAGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA
* *
35144 TACCTCTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
35165 CAAGAAATGA
Statistics
Matches: 592, Mismatches: 92, Indels: 35
0.82 0.13 0.05
Matches are distributed among these distances:
55 62 0.10
56 361 0.61
57 23 0.04
58 51 0.09
59 2 0.00
60 75 0.13
62 5 0.01
63 13 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (56 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:36411 original size:25 final size:25
Alignment explanation
Indices: 36383--36440 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
36373 TCTAGACCCT
36383 TTTTTTTGTTTATTTGTTTTATT-TA
1 TTTTTTTGTTTATTT-TTTTATTGTA
* * *
36408 TTTTTTTGTTTGTTTTTTTGTTGTT
1 TTTTTTTGTTTATTTTTTTATTGTA
36433 TTTTTTTG
1 TTTTTTTG
36441 GTATGAAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.05, C:0.00, G:0.12, T:0.83
Consensus pattern (25 bp):
TTTTTTTGTTTATTTTTTTATTGTA
Found at i:36423 original size:11 final size:10
Alignment explanation
Indices: 36382--36440 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
36372 GTCTAGACCC
36382 TTTTTTTTG-
1 TTTTTTTTGT
*
36391 -TTTATTTGT
1 TTTTTTTTGT
36400 TTTATTTATT-T
1 TTT-TTT-TTGT
*
36411 TTTTGTTTGT
1 TTTTTTTTGT
36421 TTTTTTGTTGT
1 TTTTTT-TTGT
36432 TTTTTTTTG
1 TTTTTTTTG
36441 GTATGAAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 7 0.17
9 2 0.05
10 13 0.32
11 16 0.40
12 2 0.05
ACGTcount: A:0.05, C:0.00, G:0.12, T:0.83
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:36423 original size:12 final size:12
Alignment explanation
Indices: 36383--36440 Score: 71
Period size: 12 Copynumber: 4.7 Consensus size: 12
36373 TCTAGACCCT
36383 TTTTTTTGTTTA
1 TTTTTTTGTTTA
*
36395 TTTGTTTTATTTA
1 TTT-TTTTGTTTA
*
36408 TTTTTTTGTTTG
1 TTTTTTTGTTTA
*
36420 TTTTTTTGTTGTT
1 TTTTTTTGTT-TA
36433 TTTTTTTG
1 TTTTTTTG
36441 GTATGAAGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
12 20 0.50
13 20 0.50
ACGTcount: A:0.05, C:0.00, G:0.12, T:0.83
Consensus pattern (12 bp):
TTTTTTTGTTTA
Found at i:36429 original size:8 final size:8
Alignment explanation
Indices: 36383--36437 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
36373 TCTAGACCCT
36383 TTTTTTTG
1 TTTTTTTG
*
36391 TTTATTTG
1 TTTTTTTG
*
36399 TTTTATTTA
1 TTTT-TTTG
36408 TTTTTTTG
1 TTTTTTTG
*
36416 TTTGTTT-
1 TTTTTTTG
*
36423 TTTTGTTG
1 TTTTTTTG
36431 TTTTTTT
1 TTTTTTT
36438 TTGGTATGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
7 5 0.14
8 25 0.68
9 7 0.19
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:38239 original size:106 final size:106
Alignment explanation
Indices: 38054--38263 Score: 384
Period size: 106 Copynumber: 2.0 Consensus size: 106
38044 TAACACAAGT
38054 TTCATATTCCGTGATATTATTTATGCAGTCAAAGTTTAACCTTGCTATGAAAGGATAATGACTCC
1 TTCATATTCCGTGATATTATTTATGCAGTCAAAGTTTAACCTTGCTATGAAAGGATAATGACTCC
38119 CATCGAGTGACATCAGTATTAGCCCAATTTCATGACCTATA
66 CATCGAGTGACATCAGTATTAGCCCAATTTCATGACCTATA
* *
38160 TTCATATTCTGTGATATTATTTATGCAGTCAAAGTTTAACCTTGCTGTGAAAGGATAATGACTCC
1 TTCATATTCCGTGATATTATTTATGCAGTCAAAGTTTAACCTTGCTATGAAAGGATAATGACTCC
* *
38225 CATCGGGTGACATCAGTATTGGCCCAATTTCATGACCTA
66 CATCGAGTGACATCAGTATTAGCCCAATTTCATGACCTA
38264 GGGCGTTTGA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 100 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (106 bp):
TTCATATTCCGTGATATTATTTATGCAGTCAAAGTTTAACCTTGCTATGAAAGGATAATGACTCC
CATCGAGTGACATCAGTATTAGCCCAATTTCATGACCTATA
Found at i:42411 original size:13 final size:13
Alignment explanation
Indices: 42393--42417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42383 CAATATTCCT
42393 TGTATCGATACAC
1 TGTATCGATACAC
42406 TGTATCGATACA
1 TGTATCGATACA
42418 TTAGTACTAT
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:44350 original size:15 final size:15
Alignment explanation
Indices: 44332--44362 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
44322 TTTAATTAAG
44332 GGGGAGAAAATTTTT
1 GGGGAGAAAATTTTT
44347 GGGGAGAAAATTTTT
1 GGGGAGAAAATTTTT
44362 G
1 G
44363 AGAATTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (15 bp):
GGGGAGAAAATTTTT
Found at i:44986 original size:20 final size:19
Alignment explanation
Indices: 44940--44996 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
44930 TTGTATCGTT
*
44940 ACATTGTATTGATACATGC
1 ACATTGTATCGATACATGC
* *
44959 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
44978 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
44997 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:45051 original size:20 final size:20
Alignment explanation
Indices: 45026--45124 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 20
45016 TACCATTGTT
45026 TGTATCGATACATGGTAAAA
1 TGTATCGATACATGGTAAAA
45046 TGTATCGATACA---T----
1 TGTATCGATACATGGTAAAA
45059 TGTATCGATACATGGTAAAA
1 TGTATCGATACATGGTAAAA
45079 TGTATCGATACA---T----
1 TGTATCGATACATGGTAAAA
45092 TGTATCGATACATGGTAAAA
1 TGTATCGATACATGGTAAAA
45112 TGTATCGATACAT
1 TGTATCGATACAT
45125 TGTATCGATA
Statistics
Matches: 65, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 24 0.37
16 2 0.03
17 2 0.03
20 37 0.57
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATGGTAAAA
Found at i:45064 original size:13 final size:13
Alignment explanation
Indices: 45046--45159 Score: 84
Period size: 13 Copynumber: 10.2 Consensus size: 13
45036 CATGGTAAAA
45046 TGTATCGATACAT
1 TGTATCGATACAT
45059 TGTATCGATACAT
1 TGTATCGATACAT
*
45072 GGTA---A-A-A-
1 TGTATCGATACAT
45079 TGTATCGATACAT
1 TGTATCGATACAT
45092 TGTATCGATACAT
1 TGTATCGATACAT
*
45105 GGTA---A-A-A-
1 TGTATCGATACAT
45112 TGTATCGATACAT
1 TGTATCGATACAT
45125 TGTATCGATACA-
1 TGTATCGATACAT
45137 TG-AT-GA-A-A-
1 TGTATCGATACAT
45145 TGTATCGATACAT
1 TGTATCGATACAT
45158 TG
1 TG
45160 CTTGTAACGG
Statistics
Matches: 80, Mismatches: 4, Indels: 34
0.68 0.03 0.29
Matches are distributed among these distances:
7 6 0.08
8 5 0.06
9 5 0.06
10 8 0.10
11 5 0.06
12 5 0.06
13 46 0.57
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:45065 original size:33 final size:33
Alignment explanation
Indices: 45025--45159 Score: 252
Period size: 33 Copynumber: 4.1 Consensus size: 33
45015 CTACCATTGT
45025 TTGTATCGATACATGGTAAAATGTATCGATACA
1 TTGTATCGATACATGGTAAAATGTATCGATACA
45058 TTGTATCGATACATGGTAAAATGTATCGATACA
1 TTGTATCGATACATGGTAAAATGTATCGATACA
45091 TTGTATCGATACATGGTAAAATGTATCGATACA
1 TTGTATCGATACATGGTAAAATGTATCGATACA
* *
45124 TTGTATCGATACATGATGAAATGTATCGATACA
1 TTGTATCGATACATGGTAAAATGTATCGATACA
45157 TTG
1 TTG
45160 CTTGTAACGG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 100 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGGTAAAATGTATCGATACA
Found at i:47455 original size:15 final size:15
Alignment explanation
Indices: 47413--47455 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
47403 GGGGTGTATC
47413 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
* * **
47428 GGTAATTAGGTGGTG
1 GATGATTTTGTGGTG
47443 GATGATTTTGTGG
1 GATGATTTTGTGG
47456 CAGATTTGGC
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GATGATTTTGTGGTG
Found at i:55439 original size:20 final size:20
Alignment explanation
Indices: 55414--55451 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55404 ATAAAAAGAC
55414 AGAATGCATCGATACATTGA
1 AGAATGCATCGATACATTGA
*
55434 AGAATGTATCGATACATT
1 AGAATGCATCGATACATT
55452 CGGGTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATACATTGA
Found at i:55483 original size:50 final size:50
Alignment explanation
Indices: 55366--55560 Score: 221
Period size: 50 Copynumber: 3.9 Consensus size: 50
55356 TTTTAACTAG
* * * * *
55366 ATGTATCGATATATTAAAAAATGTATTGATACATTTGGATAAAAAGACAGA
1 ATGTATAGATACATTGAAAAATGTATCGATACATTTGGGT-AAAAGACAGA
* * * *
55417 ATGCATCGATACATTGAAGAATGTATCGATACATTCGGGTAAAAGACAGA
1 ATGTATAGATACATTGAAAAATGTATCGATACATTTGGGTAAAAGACAGA
* * *
55467 ATATATAGATAAATTGAAAAATGTATCGATACGTTTGGGTAAAAGACAGA
1 ATGTATAGATACATTGAAAAATGTATCGATACATTTGGGTAAAAGACAGA
* * * *
55517 ATGTATCA-ATGCATTAAAAAATGTATCGATACATCTAGGTAAAA
1 ATGTAT-AGATACATTGAAAAATGTATCGATACATTTGGGTAAAA
55561 ATGAGACTTT
Statistics
Matches: 122, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
50 88 0.72
51 34 0.28
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (50 bp):
ATGTATAGATACATTGAAAAATGTATCGATACATTTGGGTAAAAGACAGA
Found at i:55558 original size:100 final size:101
Alignment explanation
Indices: 55373--55560 Score: 254
Period size: 100 Copynumber: 1.9 Consensus size: 101
55363 TAGATGTATC
* * * * *
55373 GATATATTAAAAAATGTATTGATACATTTGGATAAAAAGACAGAATGCATCGATACATTGAAGAA
1 GATAAATTAAAAAATGTATCGATACATTTGGATAAAAAGACAGAATGCATCAATACATTAAAAAA
*
55438 TGTATCGATACATTCGGGTAAAAGACAGAATATATA
66 TGTATCGATACATTCAGGTAAAAGACAGAATATATA
* * * * *
55474 GATAAATTGAAAAATGTATCGATACGTTTGGGT-AAAAGACAGAATGTATCAATGCATTAAAAAA
1 GATAAATTAAAAAATGTATCGATACATTTGGATAAAAAGACAGAATGCATCAATACATTAAAAAA
55538 TGTATCGATACA-TCTAGGTAAAA
66 TGTATCGATACATTC-AGGTAAAA
55561 ATGAGACTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
99 2 0.03
100 45 0.60
101 28 0.37
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (101 bp):
GATAAATTAAAAAATGTATCGATACATTTGGATAAAAAGACAGAATGCATCAATACATTAAAAAA
TGTATCGATACATTCAGGTAAAAGACAGAATATATA
Found at i:59034 original size:22 final size:23
Alignment explanation
Indices: 59009--59052 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
58999 TTATGACCTT
*
59009 TTTGAAAATA-TAAAAAGTTTTA
1 TTTGAAAATATTAAAAAATTTTA
* *
59031 TTTGCAAGTATTAAAAAATTTT
1 TTTGAAAATATTAAAAAATTTT
59053 GTTCTAAGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TTTGAAAATATTAAAAAATTTTA
Found at i:62079 original size:28 final size:28
Alignment explanation
Indices: 62045--62126 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
62035 TTTTGGAGAT
*
62045 AATAACGAGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGAGGTTGGAGT-ATCCC-CGATGA
* *
62073 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCCCGATGA
*
62101 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCCCGAT
62127 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 40 0.87
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCCCGATGA
Found at i:62269 original size:51 final size:50
Alignment explanation
Indices: 62109--62279 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 50
62099 GAAATAACGA
* * * *
62109 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATGA-TA-TTTTGAAAATAAAATCGG
** * * * * * *
62161 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGA-AAAATGATATTTTGAAAATAAAATCGG
*
62214 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAT-GATATTTTGAAAATAAAATCGG
62265 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
62280 TCAGAAATAA
Statistics
Matches: 94, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
50 4 0.04
51 35 0.37
52 16 0.17
53 32 0.34
54 3 0.03
55 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATGATATTTTGAAAATAAAATCGG
Found at i:62325 original size:27 final size:28
Alignment explanation
Indices: 62262--62337 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
62252 AAAATAAAGT
*
62262 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
62290 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
62317 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
62338 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:64824 original size:13 final size:13
Alignment explanation
Indices: 64806--64831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64796 ACAAAGATCT
64806 ATGTATCGATACA
1 ATGTATCGATACA
64819 ATGTATCGATACA
1 ATGTATCGATACA
64832 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:64827 original size:33 final size:33
Alignment explanation
Indices: 64785--64851 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
64775 AAAATTTCCA
***
64785 AATGTATCGATACAAAGATCTATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
64818 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
64851 A
1 A
64852 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:64895 original size:19 final size:18
Alignment explanation
Indices: 64871--64938 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
64861 CAGTAGCTAA
64871 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
64890 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
64905 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
64922 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
64939 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:64911 original size:13 final size:13
Alignment explanation
Indices: 64893--64917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64883 ACAATACTTA
64893 TGTATCGATACAT
1 TGTATCGATACAT
64906 TGTATCGATACA
1 TGTATCGATACA
64918 AAACTTATGT
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:64915 original size:32 final size:32
Alignment explanation
Indices: 64874--64936 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
64864 TAGCTAATTA
*
64874 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
64906 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
64937 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:65019 original size:21 final size:21
Alignment explanation
Indices: 64993--65049 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
64983 ACATTTGGGG
64993 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
65014 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
65035 ATGTATCGATACATT
1 ATGTATCGATACATT
65050 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:65059 original size:1 final size:1
Alignment explanation
Indices: 65053--65101 Score: 71
Period size: 1 Copynumber: 49.0 Consensus size: 1
65043 ATACATTTAA
* **
65053 TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTCATTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
65102 CAAACACTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.04, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:65781 original size:55 final size:55
Alignment explanation
Indices: 65697--66428 Score: 990
Period size: 55 Copynumber: 13.3 Consensus size: 55
65687 ATAAATTGTA
* * * * * *
65697 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
65752 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
65807 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
65862 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
65917 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
** *
65972 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
66027 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAAC-T-TGT-GGC-TTGAGGTGAGGGG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGA---AAGGTG
*
66081 T-CTGCTC-TTGAGGACT-AGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
66134 TCCTGCTCTTTGAGGACTGGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
66190 TCCTGCTCTTTGGGGACTGAAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
66246 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
66301 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
66356 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
66411 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
66429 AAAAAGCGGA
Statistics
Matches: 620, Mismatches: 34, Indels: 46
0.89 0.05 0.07
Matches are distributed among these distances:
51 5 0.01
52 24 0.04
53 15 0.02
54 25 0.04
55 432 0.70
56 117 0.19
57 2 0.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:66270 original size:26 final size:26
Alignment explanation
Indices: 66185--66271 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 26
66175 GGGCTTTGAG
66185 AGGTGTCCTGCTCTTTGGGGACTGAAA
1 AGGTGTCCTGCTCTTTGGGGACTG-AA
** * *
66212 AGGTG-CCACCAACTTGTGTGGG-CTTTGAG
1 AGGTGTCCTGC-TCTT-TG-GGGAC--TGAA
66241 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
66267 AGGTG
1 AGGTG
66272 CCACCAACTT
Statistics
Matches: 45, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
26 11 0.24
27 11 0.24
28 6 0.13
29 12 0.27
30 5 0.11
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:67411 original size:1 final size:1
Alignment explanation
Indices: 67393--67471 Score: 122
Period size: 1 Copynumber: 79.0 Consensus size: 1
67383 CTTAAGTAGG
* * * *
67393 TTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
67458 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
67472 GAAGAGAAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.04, G:0.01, T:0.95
Consensus pattern (1 bp):
T
Done.