Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold333
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: 853475
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:479927 original size:21 final size:18
Alignment explanation
Indices: 479901--479982 Score: 57
Period size: 19 Copynumber: 4.6 Consensus size: 18
479891 AACAATTTGA
479901 ATCGATACAAACTGTAACTGT
1 ATCGATACAAACTGT---TGT
*
479922 ATCGATACATAAGTGTTGT
1 ATCGATACA-AACTGTTGT
479941 ATCGATAC-AA----TGT
1 ATCGATACAAACTGTTGT
* *
479954 ATCGATACATAAGTTTTGT
1 ATCGATACA-AACTGTTGT
479973 ATCGATACAA
1 ATCGATACAA
479983 TGTATCACTA
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
13 11 0.21
15 2 0.04
17 2 0.04
18 1 0.02
19 23 0.43
21 9 0.17
22 5 0.09
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (18 bp):
ATCGATACAAACTGTTGT
Found at i:479943 original size:19 final size:18
Alignment explanation
Indices: 479919--479981 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
479909 AAACTGTAAC
479919 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
479938 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
479951 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
479970 TGTATCGATACA
1 TGTATCGATACA
479982 ATGTATCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:479956 original size:13 final size:13
Alignment explanation
Indices: 479938--479962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
479928 ACATAAGTGT
479938 TGTATCGATACAA
1 TGTATCGATACAA
479951 TGTATCGATACA
1 TGTATCGATACA
479963 TAAGTTTTGT
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:479960 original size:32 final size:32
Alignment explanation
Indices: 479919--479988 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
479909 AAACTGTAAC
479919 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
479951 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
479983 TGTATC
1 TGTATC
479989 ACTACGAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:480036 original size:21 final size:21
Alignment explanation
Indices: 480010--480049 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
480000 ACTGCCAAGA
480010 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
480031 AAATGTATCGATACATTAC
1 AAATGTATCGATACATTAC
480050 ATGCAGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
AAATGTATCGATACATTACTC
Found at i:485505 original size:20 final size:20
Alignment explanation
Indices: 485477--485551 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
485467 TTTTACCTTG
485477 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
485497 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
485517 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
485537 ATGTATCGATACATT
1 ATGTATCGATACATT
485552 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:485544 original size:40 final size:39
Alignment explanation
Indices: 485477--485554 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
485467 TTTTACCTTG
* *
485477 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
485517 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
485555 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:488437 original size:186 final size:185
Alignment explanation
Indices: 488123--488499 Score: 745
Period size: 186 Copynumber: 2.0 Consensus size: 185
488113 TTCTACTAAC
488123 ATTTTTGCTGAATACTATGTGCATTCATGTTTTTTCAAAATTTTGTTACAAAAATCAAAAGGGCA
1 ATTTTTGCTGAATACTATGTGCATTCATGTTTTTTCAAAATTTTGTTACAAAAATCAAAAGGGCA
488188 ATGTTCCGTGTCGGTATCTCTCTAGTGCTTGATACGGAATATCCAGTTTTCAAAATGAAATCCAG
66 ATGTTCCGTGTCGGTATCTCTCTAGTGCTTGATACGGAATATCCAGTTTTCAAAATGAAATCCAG
488253 AGGTCATTTTATGTCTCTATGTTCCCCATCTCTCCGGGGCGCATATGAGATTAAAA
131 AGGTCATTTTATGTCTCTATGTTCCCCATCTCTCCGGGGCGCATATGAGATT-AAA
488309 ATTTTTGCTGAATACTATGTGCATTCATGTTTTTTCAAAATTTTGTTACAAAAATCAAAAGGGCA
1 ATTTTTGCTGAATACTATGTGCATTCATGTTTTTTCAAAATTTTGTTACAAAAATCAAAAGGGCA
488374 ATGTTCCGTGTCGGTATCTCTCTAGTGCTTGATACGGAATATCCAGTTTTCAAAATGAAATCCAG
66 ATGTTCCGTGTCGGTATCTCTCTAGTGCTTGATACGGAATATCCAGTTTTCAAAATGAAATCCAG
488439 AGGTCATTTTATGTCTCTATGTTCCCCATCTCTCCGGGGCGCATATGAGATTAAA
131 AGGTCATTTTATGTCTCTATGTTCCCCATCTCTCCGGGGCGCATATGAGATTAAA
488494 ATTTTT
1 ATTTTT
488500 ATCAAACCTG
Statistics
Matches: 191, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 9 0.05
186 182 0.95
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (185 bp):
ATTTTTGCTGAATACTATGTGCATTCATGTTTTTTCAAAATTTTGTTACAAAAATCAAAAGGGCA
ATGTTCCGTGTCGGTATCTCTCTAGTGCTTGATACGGAATATCCAGTTTTCAAAATGAAATCCAG
AGGTCATTTTATGTCTCTATGTTCCCCATCTCTCCGGGGCGCATATGAGATTAAA
Found at i:499755 original size:20 final size:19
Alignment explanation
Indices: 499729--499789 Score: 81
Period size: 20 Copynumber: 3.3 Consensus size: 19
499719 CTTTACACCC
499729 AAAAAAAAACAAAAAAGAA
1 AAAAAAAAACAAAAAAGAA
*
499748 ACAAAAAAAACAAAACA-AA
1 A-AAAAAAAACAAAAAAGAA
*
499767 AAAACAAAA-AAAAAAGAA
1 AAAAAAAAACAAAAAAGAA
499785 AAAAA
1 AAAAA
499790 TAGCAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 5 0.14
18 13 0.36
19 4 0.11
20 14 0.39
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAGAA
Found at i:499797 original size:11 final size:10
Alignment explanation
Indices: 499729--499804 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
499719 CTTTACACCC
*
499729 AAAAAAAAAC
1 AAAAAAAAAG
*
499739 AAAAAAGAAAC
1 AAAAAA-AAAG
*
499750 AAAAAAAACAA
1 AAAAAAAA-AG
*
499761 AACAAAAAAACA
1 AA-AAAAAAA-G
499773 AAAAAAAAAG
1 AAAAAAAAAG
*
499783 AAAAAAATAG
1 AAAAAAAAAG
* *
499793 CAAAAAATAG
1 AAAAAAAAAG
499803 AA
1 AA
499805 GGGTCTAGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
10 27 0.47
11 21 0.37
12 9 0.16
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:499799 original size:1 final size:1
Alignment explanation
Indices: 499729--499789 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
499719 CTTTACACCC
* * * * * * *
499729 AAAAAAAAACAAAAAAGAAACAAAAAAAACAAAACAAAAAAACAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
499790 TAGCAAAAAA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:501118 original size:28 final size:28
Alignment explanation
Indices: 501017--501921 Score: 1184
Period size: 28 Copynumber: 31.6 Consensus size: 28
501007 GAATGTTCAT
501017 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501045 CTCCTTTCAAAGCCCACAAATCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
501074 CTCTTTTCAAAGCCCACAAGTCAGTGACA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
501103 CCCTTTCAAAGCCCACAAGTCAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501131 CCCTTTCAAAACCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
501159 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501187 CCCTTTCAAAACCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
501215 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
501243 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
501272 CTCTTTTCAAAGCCCACAAATCAGTGACA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
501301 CTCTTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
501330 CCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
501358 CTCCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
** * *
501387 CTTTTTTCAAAGCCCACAAATCAAT-GCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
501415 CTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
501444 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501472 CCCTTTCAGAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501500 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
501528 CCATTGCGAAGCCCACAATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501556 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
501584 CCTTTTTAAAGCCCACACAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* * * *
501614 CTCCTTTTAAAGGTCACGCAAGTCAGTGGTA
1 C-CCTTTCAAA-G-CCCACAAGTCAGTGGCA
* *
501645 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
501673 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
501701 TCCTTTCAAAGCCCACGAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501729 CCCTTTCAAAGCCCACACAAGTCAGTGACA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
*
501759 CTCCTTTTCAAAGCCCACGAGTCAGTGGCA
1 C-CC-TTTCAAAGCCCACAAGTCAGTGGCA
501789 -CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
501816 CTCTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
501844 TCCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* **
501874 CCCTTTTAAAGCCCACGCAAGTCAGTAACA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
501904 CTCTTTTCAAAGCCCACA
1 C-CCTTTCAAAGCCCACA
501922 TGTGTCAGTG
Statistics
Matches: 781, Mismatches: 80, Indels: 31
0.88 0.09 0.03
Matches are distributed among these distances:
27 24 0.03
28 429 0.55
29 192 0.25
30 88 0.11
31 38 0.05
32 10 0.01
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:501624 original size:313 final size:312
Alignment explanation
Indices: 501017--501921 Score: 1309
Period size: 313 Copynumber: 2.9 Consensus size: 312
501007 GAATGTTCAT
*
501017 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
* *
501082 AAAGCCCACAAGTCAGTGACACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAACCCAC
66 AAAGCCCACAAGTCAGTG-CACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
*
501147 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAACCCACAAGTCAGTG
130 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTG
501212 GCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
195 GCA-CCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
501277 TTCAAAGCCCACAAATCAGTGACACTCTTTTTAAA-G-CCCACAAGTCAGTGGCA
258 TTCAAAGCCCACAAATCAGTGACACTCCTTTTAAAGGTCACACAAGTCAGTGGCA
*
501330 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTTTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
* * *
501395 AAAGCCCACAAATCAATGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
66 AAAGCCCACAAGTCAGTGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC
* * *
501460 AAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTG
130 AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTG
* * *
501525 GCACCATTGCGAAGCCCACAATTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTT
195 GCACC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTT
* * * *
501589 TTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGGTCACGCAAGTCAGTGGTA
259 TCAAAGCCCACA-AA-TCAGTGACACTCCTTTTAAAGGTCACACAAGTCAGTGGCA
* * * *
501645 CCTTTTCAAAGCCCACGAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
* * *
501708 AAAGCCCACGAGTTAGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGACACTCCTTTTCAAAGC
66 AAAGCCCACAAGTCAGT-GCACCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CC-TTTCAAAGC
* * *
501773 CCACGAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACGAGTC
126 CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC
* * **
501837 AGTGGCATCCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACGCAAGTCAGTAA
191 AGTGGCA-CCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTCAAAGCCCA--CAAGTCAGTGG
501902 CACTCTTTTCAAAGCCCACA
251 CACTCTTTTCAAAGCCCACA
501922 TGTGTCAGTG
Statistics
Matches: 530, Mismatches: 45, Indels: 26
0.88 0.07 0.04
Matches are distributed among these distances:
311 15 0.03
312 34 0.06
313 252 0.48
314 32 0.06
315 57 0.11
316 63 0.12
317 25 0.05
318 25 0.05
320 12 0.02
321 15 0.03
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (312 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
AAAGCCCACAAGTCAGTGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACA
AGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGG
CACCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
AAAGCCCACAAATCAGTGACACTCCTTTTAAAGGTCACACAAGTCAGTGGCA
Found at i:502559 original size:20 final size:20
Alignment explanation
Indices: 502531--502605 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
502521 TTTTACCTTG
502531 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
502551 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
502571 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
502591 ATGTATCGATACATT
1 ATGTATCGATACATT
502606 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:502598 original size:40 final size:39
Alignment explanation
Indices: 502531--502608 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
502521 TTTTACCTTG
* *
502531 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
502571 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
502609 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:503550 original size:20 final size:20
Alignment explanation
Indices: 503518--503570 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
503508 AGCCTTTGAC
*
503518 CATGCATTTTTTATTATGTTT
1 CATGCA-TTTTTATTATATTT
503539 CATGCATTTTTATTATATTT
1 CATGCATTTTTATTATATTT
503559 CATGCATTTTTA
1 CATGCATTTTTA
503571 ACATGTCCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.23, C:0.11, G:0.08, T:0.58
Consensus pattern (20 bp):
CATGCATTTTTATTATATTT
Found at i:514597 original size:15 final size:15
Alignment explanation
Indices: 514577--514661 Score: 91
Period size: 15 Copynumber: 5.4 Consensus size: 15
514567 CGTCCTCCAG
514577 AAAAAAAAAAAGAAA-
1 AAAAAAAAAAA-AAAC
*
514592 AAAAAAACAACAAAAC
1 AAAAAAA-AAAAAAAC
*
514608 AAAACAAAAAAAAAC
1 AAAAAAAAAAAAAAC
*
514623 AAAAAAAAAACAAAC
1 AAAAAAAAAAAAAAC
514638 AAACAAAAAAACAACAAC
1 AAA-AAAAAAA-AA-AAC
514656 AAAAAA
1 AAAAAA
514662 GGTCCGGATG
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
15 33 0.56
16 16 0.27
17 4 0.07
18 6 0.10
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:514617 original size:34 final size:34
Alignment explanation
Indices: 514579--514661 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
514569 TCCTCCAGAA
*
514579 AAAAAAAAAGAAAAAAAAAAC-AACAAAACAAAAC
1 AAAAAAAAACAAAAAAAAAACAAAC-AAACAAAAC
514613 AAAAAAAAACAAAAAAAAAACAAACAAACAAAA-
1 AAAAAAAAACAAAAAAAAAACAAACAAACAAAAC
* *
514646 AAACAACAACAAAAAA
1 AAAAAAAAACAAAAAA
514662 GGTCCGGATG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 14 0.31
34 28 0.62
35 3 0.07
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (34 bp):
AAAAAAAAACAAAAAAAAAACAAACAAACAAAAC
Found at i:514647 original size:30 final size:30
Alignment explanation
Indices: 514577--514661 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
514567 CGTCCTCCAG
514577 AAAAAAAAAAAGAA-AAAAAAAACAACAAAAC
1 AAAAAAAAAAA-AACAAAAAAAA-AACAAAAC
514608 AAAACAAAAAAAAACAAAAAAAAAAC-AAAC
1 AAAA-AAAAAAAAACAAAAAAAAAACAAAAC
* *
514638 AAACAAAAAAACAACAACAAAAAA
1 AAA-AAAAAAAAAACAAAAAAAAA
514662 GGTCCGGATG
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
30 24 0.49
31 10 0.20
32 15 0.31
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAAACAAAAAAAAAACAAAAC
Found at i:514661 original size:1 final size:1
Alignment explanation
Indices: 514577--514648 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
514567 CGTCCTCCAG
* * * * * * * * *
514577 AAAAAAAAAAAGAAAAAAAAAACAACAAAACAAAACAAAAAAAAACAAAAAAAAAACAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
514642 AAAAAAA
1 AAAAAAA
514649 CAACAACAAA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:516078 original size:30 final size:29
Alignment explanation
Indices: 516042--516207 Score: 185
Period size: 28 Copynumber: 5.7 Consensus size: 29
516032 CATCATTTCC
* *
516042 AAAGCCCACAGGTCAGTGGCACCCTCTTCA
1 AAAGCCCACAAGTCAGTGGCA-ACTCTTCA
* * *
516072 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
516101 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
* * * *
516129 AAAGCCGACAAGTAAGTGGCACCCTTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-AC-TCTTCA
*
516159 AAAGCCCACAAATCAGTGGCAAC-CTTCA
1 AAAGCCCACAAGTCAGTGGCAACTCTTCA
*
516187 AAAGCCCACAAGTCCGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
516208 TCTTTTTCCT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
27 3 0.03
28 41 0.36
29 29 0.25
30 38 0.33
31 3 0.03
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCAACTCTTCA
Found at i:516120 original size:59 final size:57
Alignment explanation
Indices: 516028--516213 Score: 264
Period size: 58 Copynumber: 3.2 Consensus size: 57
516018 TTCGTTGGTT
* * *
516028 GTGGCATCATTTCCAAAGCCCACAGGTCAGTGGCACCCTCTTCAAAAGCCCACAAGTCA
1 GTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCA-AC-CTTCAAAAGCCCACAAGTCA
* *
516087 GTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCGACAAGTAA
1 GTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCA
* * * *
516144 GTGGCACCCTTTTTCAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCCACAAGTCC
1 GTGGCA-TCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCA
516202 GTGGCATCTTTT
1 GTGGCATCTTTT
516214 TCCTTTTAAG
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
57 29 0.25
58 52 0.46
59 33 0.29
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (57 bp):
GTGGCATCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCA
Found at i:516175 original size:87 final size:86
Alignment explanation
Indices: 516042--516207 Score: 226
Period size: 87 Copynumber: 1.9 Consensus size: 86
516032 CATCATTTCC
* * * * * *
516042 AAAGCCCACAGGTCAGTGGCACCCTCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCC
1 AAAGCCCACAAGTAAGTGGCACCCTCTTCAAAAGCCCACAAATCAGTGGCAAC-CTTCAAAAGCC
516107 CACAAGTCAGTGGCAACCTTCA
65 CACAAGTCAGTGGCAACCTTCA
* *
516129 AAAGCCGACAAGTAAGTGGCACCCTTTTTC-AAAGCCCACAAATCAGTGGCAACCTTCAAAAGCC
1 AAAGCCCACAAGTAAGTGGCACCC-TCTTCAAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCC
*
516193 CACAAGTCCGTGGCA
65 CACAAGTCAGTGGCA
516208 TCTTTTTCCT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
86 23 0.33
87 42 0.61
88 4 0.06
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (86 bp):
AAAGCCCACAAGTAAGTGGCACCCTCTTCAAAAGCCCACAAATCAGTGGCAACCTTCAAAAGCCC
ACAAGTCAGTGGCAACCTTCA
Found at i:516253 original size:32 final size:32
Alignment explanation
Indices: 516188--516277 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
516178 CAACCTTCAA
* *
516188 AAGCCCACAAGTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTCCTTTT
*
516221 AAGCCCACAACTCCGTGGCACCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
*
516253 AAGTCCACAACTCCGTGGCACCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
516278 AAGCCCAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 34 0.64
33 19 0.36
ACGTcount: A:0.20, C:0.33, G:0.14, T:0.32
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:516356 original size:35 final size:35
Alignment explanation
Indices: 516316--516427 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
516306 CATATTGGCA
*
516316 CCTTTTCTTTTTTAAGTCCACAACTTCGTGGCACT
1 CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
*
516351 CCTTTTCTTTTTTAAGTCCATAACTCCGTGGCACT
1 CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
* * * *
516386 CTTTTTCTTTTGTAAGCCCACAACTCCGTGGTACT
1 CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
*
516421 CTTTTTC
1 CCTTTTC
516428 CCTTTAAGCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.16, C:0.29, G:0.12, T:0.44
Consensus pattern (35 bp):
CCTTTTCTTTTTTAAGTCCACAACTCCGTGGCACT
Found at i:516441 original size:34 final size:34
Alignment explanation
Indices: 516311--516442 Score: 151
Period size: 35 Copynumber: 3.9 Consensus size: 34
516301 GTCAGCATAT
* *
516311 TGGCAC-C-TTTTCTTTTTTAAGTCCACAACTTCG
1 TGGCACTCTTTTTC-TTTTTAAGCCCACAACTCCG
* * *
516344 TGGCACTCCTTTTCTTTTTTAAGTCCATAACTCCG
1 TGGCACTCTTTTTC-TTTTTAAGCCCACAACTCCG
516379 TGGCACTCTTTTTCTTTTGTAAGCCCACAACTCCG
1 TGGCACTCTTTTTCTTTT-TAAGCCCACAACTCCG
* **
516414 TGGTACTCTTTTTCCCTTTAAGCCCACAA
1 TGGCACTCTTTTTCTTTTTAAGCCCACAA
516443 GTCAGTGACA
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
33 6 0.07
34 16 0.18
35 66 0.75
ACGTcount: A:0.18, C:0.30, G:0.12, T:0.40
Consensus pattern (34 bp):
TGGCACTCTTTTTCTTTTTAAGCCCACAACTCCG
Found at i:516499 original size:28 final size:29
Alignment explanation
Indices: 516433--516502 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
516423 TTTTCCCTTT
*
516433 AAGCCCACAAGTCAGTGACACCCTTTTCAA
1 AAGCCCACAAGTCAGTGACAACC-TTTCAA
*
516463 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGACAACCTTTCAA
*
516491 AAGCACACAAGT
1 AAGCCCACAAGT
516503 TGGTGGTGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 16 0.43
30 21 0.57
ACGTcount: A:0.37, C:0.31, G:0.16, T:0.16
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGACAACCTTTCAA
Found at i:516570 original size:49 final size:49
Alignment explanation
Indices: 516517--516895 Score: 374
Period size: 49 Copynumber: 8.0 Consensus size: 49
516507 GGTGTCTTCT
* *
516517 TTTAAGTCCAATATCGCTGACCTTGAATTAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * *
516566 TTTAAGACCAATCTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
516615 TTTAAGTCCAATATCACTGGTCC-TGAATCAGCATATTAGCACC---ATC
1 TTTAAGTCCAATATCGCTGG-CCTTGAATCAGCATATTGGCACCTTTATC
* ** * *
516661 TCTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGG---C---A--
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * *
516702 --TAAGCCCAATATCACTGGCCTTGAATCAACATATTGGCACC-TTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
516748 TTTAAGACCAATGTCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTTATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TTATC
* * *
516800 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
516849 TTTAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
516896 ACATTCCTAA
Statistics
Matches: 272, Mismatches: 43, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
39 31 0.11
42 1 0.00
43 2 0.01
45 2 0.01
46 32 0.12
48 36 0.13
49 121 0.44
50 3 0.01
52 44 0.16
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
Found at i:516786 original size:87 final size:85
Alignment explanation
Indices: 516617--516788 Score: 238
Period size: 87 Copynumber: 2.0 Consensus size: 85
516607 TCTTCATCTT
* *
516617 TAAGTCCAATATCACTGGTCCTGAATCAGCATATTAGCACCATCTCTAAAACCAATGTCGCTGGC
1 TAAGCCCAATATCACTGGTCCTGAATCAACATATTAGCACCATCTCTAAAACCAATGTCGCTGGC
516682 CTTGAATCAGCACATTGGCA
66 CTTGAATCAGCACATTGGCA
* * * * *
516702 TAAGCCCAATATCACTGG-CCTTGAATCAACATATTGGCACCTTGTCTTTAAGACCAATGTCGTT
1 TAAGCCCAATATCACTGGTCC-TGAATCAACATATTAGCACC--ATCTCTAAAACCAATGTCGCT
*
516766 GGCCTTGAATCAGCATATTGGCA
63 GGCCTTGAATCAGCACATTGGCA
516789 CCTTTGTTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 2 0.03
85 35 0.46
87 39 0.51
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (85 bp):
TAAGCCCAATATCACTGGTCCTGAATCAACATATTAGCACCATCTCTAAAACCAATGTCGCTGGC
CTTGAATCAGCACATTGGCA
Found at i:516912 original size:101 final size:101
Alignment explanation
Indices: 516702--516985 Score: 306
Period size: 101 Copynumber: 2.8 Consensus size: 101
516692 CACATTGGCA
* * * * * *
516702 TAAGCCCAATATCACTGGCCTTGAATCAACATATTGGCACCTT-GTCTTTAAGACCAATGTCGTT
1 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTT
*** *
516766 GGCCTTGAATCAGCATATTGGCACCTTTGTTATCTT
66 GGCCTTGAATCAGCATATTGGCACCTTTAACATCTC
* * *
516802 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATTGTT
1 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTT
*
516867 GGCCTTGAATCAGCATATTGGCATCTTTAACAT-TCC
66 GGCCTTGAATCAGCATATTGGCACCTTTAACATCT-C
* * ** * * * * *
516903 TAAGCCCAATGTCATTAGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAAATCTAATATCGCT
1 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTT
* *
516966 GGCCATGAATCAGCACATTG
66 GGCCTTGAATCAGCATATTG
516986 TCATTCTTCG
Statistics
Matches: 154, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
99 36 0.23
100 39 0.25
101 79 0.51
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (101 bp):
TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGTT
GGCCTTGAATCAGCATATTGGCACCTTTAACATCTC
Found at i:517749 original size:13 final size:13
Alignment explanation
Indices: 517731--517755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
517721 AAACTGTAAC
517731 TGTATCGATACAA
1 TGTATCGATACAA
517744 TGTATCGATACA
1 TGTATCGATACA
517756 TAAGTTTTGT
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:517845 original size:13 final size:13
Alignment explanation
Indices: 517827--517854 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
517817 ATTACTCAAA
517827 TGTATCGATACAT
1 TGTATCGATACAT
517840 TGTATCGATACAT
1 TGTATCGATACAT
517853 TG
1 TG
517855 ACCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:522141 original size:111 final size:112
Alignment explanation
Indices: 522017--522218 Score: 327
Period size: 111 Copynumber: 1.8 Consensus size: 112
522007 TTAAATATTT
* * *
522017 TTTTAATTTGTTAATGTAATTTTTTTAAAATTTAATTAAATATTATTTT-TATTTTATTAAAAAA
1 TTTTAATATGTTAATGTAATTTTTTT-AAACTTAATTAAATATTATTTTCAATTTTATTAAAAAA
*
522081 TAATAATAAAAATAC-TTTTTATTTTTATAAAAACATAATAATTAATA
65 TAATAATAAAAACACTTTTTTATTTTTATAAAAACATAATAATTAATA
522128 TTTTAATATGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTCAATTTTATTAAAAAAT
1 TTTTAATATGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTCAATTTTATTAAAAAAT
* *
522193 AATAATATAAACCCTTTTTTATTTTT
66 AATAATAAAAACACTTTTTTATTTTT
522219 TATTTAAGTT
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
110 21 0.25
111 51 0.61
112 11 0.13
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (112 bp):
TTTTAATATGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTCAATTTTATTAAAAAAT
AATAATAAAAACACTTTTTTATTTTTATAAAAACATAATAATTAATA
Found at i:522369 original size:127 final size:124
Alignment explanation
Indices: 522117--522371 Score: 295
Period size: 127 Copynumber: 2.0 Consensus size: 124
522107 ATAAAAACAT
*
522117 AATAATTAATATTTTAATATGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTTCAATTT
1 AATAATTAATATTTTAATATGTTAATGTAATTTTTTTAAACTTAATTAAATATTA-TTT--ATGT
* * * * *
522182 TATTAAAAAATAATAATATAAACCCTTTTTTATTTTTTATTTAAGTTTTTTTATTTTAAAAA
63 TATTAAAAAATAATAATATAAACACTTTTTTATTATTTATTTAAATTTATTAATTTTAAAAA
*
522244 AATAATTAATATTTTAATTTGTTAATGTAAATTTTTTTAAACTTAATTAAATATTA-TT-TGTTA
1 AATAATTAATATTTTAATATGTTAATGT-AATTTTTTTAAACTTAATTAAATATTATTTATGTTA
* *
522307 TT-AAAAATAATAAT-TAATATATTATTATTTATTAGATTTA-TTAAATTTAATTAATTTATAAA
65 TTAAAAAATAATAATATAA-ACACT-TT-TTTATT--ATTTATTTAAATTT-ATTAATTT-TAAA
522369 AA
123 AA
522371 A
1 A
522372 TTAAACACTT
Statistics
Matches: 111, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
121 3 0.03
122 14 0.13
123 8 0.07
124 6 0.05
125 7 0.06
126 12 0.11
127 34 0.31
128 27 0.24
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (124 bp):
AATAATTAATATTTTAATATGTTAATGTAATTTTTTTAAACTTAATTAAATATTATTTATGTTAT
TAAAAAATAATAATATAAACACTTTTTTATTATTTATTTAAATTTATTAATTTTAAAAA
Found at i:523929 original size:29 final size:29
Alignment explanation
Indices: 523897--523957 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
523887 AACCTACTTA
*
523897 AGCCTTAAAAGT-AAAGAGGTTACTATCTT
1 AGCCTT-AAAGTGAAAGAAGTTACTATCTT
**
523926 AGCCTTAAAGTGTGAGAAGTTACTATCTT
1 AGCCTTAAAGTGAAAGAAGTTACTATCTT
523955 AGC
1 AGC
523958 ATAAGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (29 bp):
AGCCTTAAAGTGAAAGAAGTTACTATCTT
Found at i:525087 original size:14 final size:14
Alignment explanation
Indices: 525068--525098 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
525058 CAGATGGATA
525068 TATCGTATAATTCT
1 TATCGTATAATTCT
525082 TATCGTATAATTCT
1 TATCGTATAATTCT
525096 TAT
1 TAT
525099 ATATATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (14 bp):
TATCGTATAATTCT
Found at i:528446 original size:19 final size:20
Alignment explanation
Indices: 528422--528471 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
528412 TTTGACCAAA
528422 TATCGATACATTCTTC-ATG
1 TATCGATACATTCTTCAATG
528441 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
528461 TATCGATACAT
1 TATCGATACAT
528472 GCAGGCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:529544 original size:20 final size:21
Alignment explanation
Indices: 529519--529571 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
529509 TACAAGCCAA
* *
529519 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
529539 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
529559 TGTATCGATACAA
1 TGTATCGATACAA
529572 GTTTGGCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:529576 original size:19 final size:19
Alignment explanation
Indices: 529519--529577 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
529509 TACAAGCCAA
* *
529519 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
529539 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
529559 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
529578 CTATTGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:532146 original size:13 final size:13
Alignment explanation
Indices: 532128--532166 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
532118 ATAATCCCCC
*
532128 TGTATCGATACAG
1 TGTATCGATACAA
532141 TGTATCGATACAA
1 TGTATCGATACAA
532154 TGTATCGATACAA
1 TGTATCGATACAA
532167 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:538326 original size:13 final size:13
Alignment explanation
Indices: 538308--538333 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
538298 CAATTTTTTG
538308 TGTATCGATACAT
1 TGTATCGATACAT
538321 TGTATCGATACAT
1 TGTATCGATACAT
538334 ACTTTGGTGT
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):
TGTATCGATACAT
Found at i:538330 original size:33 final size:33
Alignment explanation
Indices: 538288--538352 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
538278 TACAAGCCAA
* *
538288 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
538321 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
538353 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:541209 original size:19 final size:18
Alignment explanation
Indices: 541184--541248 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
541174 ATTTCAACAA
541184 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
541202 TGTTGTATTGATAC--AA-
1 T-TTGTATCGATACATAAG
541218 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
541234 TTTTGTATCGATACA
1 -TTTGTATCGATACA
541249 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:541223 original size:32 final size:32
Alignment explanation
Indices: 541186--541256 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
541176 TTCAACAATT
*
541186 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
541218 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
541250 TGTATCG
1 TGTATCG
541257 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:548483 original size:13 final size:13
Alignment explanation
Indices: 548465--548489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
548455 AGTTAAAAAT
548465 TTTAAAATTTAAA
1 TTTAAAATTTAAA
548478 TTTAAAATTTAA
1 TTTAAAATTTAA
548490 TTAATATAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:548489 original size:29 final size:29
Alignment explanation
Indices: 548431--548489 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
548421 GTATATTTTT
*
548431 AAAATTTTAAAAAAAAAATTTATAAGTTA
1 AAAATTTTAAAAAAAAAATTTAAAAGTTA
*** *
548460 AAAATTTTAAAATTTAAATTTAAAATTTA
1 AAAATTTTAAAAAAAAAATTTAAAAGTTA
548489 A
1 A
548490 TTAATATAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (29 bp):
AAAATTTTAAAAAAAAAATTTAAAAGTTA
Found at i:548830 original size:2 final size:2
Alignment explanation
Indices: 548819--548852 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
548809 TTGTCCGAAG
*
548819 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
548853 AGTGGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550070 original size:16 final size:16
Alignment explanation
Indices: 550051--550135 Score: 63
Period size: 16 Copynumber: 5.1 Consensus size: 16
550041 AAGATAATAT
550051 TATATAAATTTATAAA
1 TATATAAATTTATAAA
550067 TATATCAAAATTTATATAA
1 TATAT--AAATTTATA-AA
550086 -A-ATAAA-TTATCAACA
1 TATATAAATTTAT-AA-A
550101 TAT-TAAATTTAGATAAA
1 TATATAAATTT--ATAAA
550118 TATATAATATTTA-AAA
1 TATATAA-ATTTATAAA
550134 TA
1 TA
550136 AGTTTATGTC
Statistics
Matches: 57, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
14 5 0.09
15 5 0.09
16 15 0.26
17 9 0.16
18 15 0.26
19 8 0.14
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (16 bp):
TATATAAATTTATAAA
Found at i:550228 original size:15 final size:17
Alignment explanation
Indices: 550194--550233 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
550184 TTTTCTATTT
550194 TTTCTTCTTTCCTTCATC
1 TTTCTTCTTTCCTT-ATC
550212 TTTCTT-TTTCCTT-TC
1 TTTCTTCTTTCCTTATC
550227 TTTCTTC
1 TTTCTTC
550234 ATAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
17 7 0.33
18 6 0.29
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCTTCTTTCCTTATC
Found at i:550819 original size:18 final size:18
Alignment explanation
Indices: 550796--550830 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
550786 AAGATAATTT
550796 TTAAAACAAA-ATATAAAA
1 TTAAAA-AAATATATAAAA
550814 TTAAAAAAATATATAAA
1 TTAAAAAAATATATAAA
550831 TATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TTAAAAAAATATATAAAA
Found at i:551381 original size:20 final size:20
Alignment explanation
Indices: 551344--551397 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
551334 TTTTACAATT
* *
551344 TGTATCTATACAATAAGTTAA
1 TGTATCGATAC-ATAAGTAAA
*
551365 TGTATGGATACATAAGTAAA
1 TGTATCGATACATAAGTAAA
551385 TGTATCGATACAT
1 TGTATCGATACAT
551398 GCTTGCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAAGTAAA
Found at i:554025 original size:273 final size:273
Alignment explanation
Indices: 553538--554076 Score: 1008
Period size: 273 Copynumber: 2.0 Consensus size: 273
553528 AACCTAATTT
553538 CAAAATTTTATTCCTCCTAGAAAGTAATTTTTTGAGATTTTTAAAGTATTTTTAGATTAACCCTC
1 CAAAATTTTATTCCTCCTAGAAAGTAATTTTTTGAGATTTTTAAAGTATTTTTAGATTAACCCTC
*
553603 ATCGAGTCACCTTTCTAACGATACTTTGTTCACCTTCTAAAACCTTTAAATCAACTTGAAATAAA
66 ATCGAGTCACCTTTCTAACGATACTTTGTTCACCTTCTAAAACCTTCAAATCAACTTGAAATAAA
* *
553668 TTCGAAAAATGAGACAGCGTGATGATGTCCCCTGTTTTTGGTTATGGATCAAAATTTAGTTGTTT
131 TTCAAAAAATGAGACAGCGTGATGATGTCCCCTATTTTTGGTTATGGATCAAAATTTAGTTGTTT
553733 CACCAAGCTTCGTTTCGAGACATTCGATTGTCTCCAAATTATCTCGATCAGCCTCGAAACCCCTT
196 CACCAAGCTTCGTTTCGAGACATTCGATTGTCTCCAAATTATCTCGATCAGCCTCGAAACCCCTT
553798 TTTAGAAAGTGAC
261 TTTAGAAAGTGAC
553811 CAAAATTTTATTCCTCCTAGAAAGTAATTTTTTGAGATTTTTAAAGTATTTTTAGATTAACCCTC
1 CAAAATTTTATTCCTCCTAGAAAGTAATTTTTTGAGATTTTTAAAGTATTTTTAGATTAACCCTC
553876 ATCGAGTCACCTTTCTAACGATACTTTGTTCACCTTCTAAAACCTTCAAATCAACTTGAAATAAA
66 ATCGAGTCACCTTTCTAACGATACTTTGTTCACCTTCTAAAACCTTCAAATCAACTTGAAATAAA
* *
553941 TTCAAAAAATGGGATAGCGTGATGATGTCCCCTATTTTTAGGTTATGG-TCAAAATTTAGTTGTT
131 TTCAAAAAATGAGACAGCGTGATGATGTCCCCTATTTTT-GGTTATGGATCAAAATTTAGTTGTT
*
554005 TCACCGAGCTTCGTTTCGAGACATTCGATTGTCTCCAAATTATCTCGATCAGCCTCGAAACCCCT
195 TCACCAAGCTTCGTTTCGAGACATTCGATTGTCTCCAAATTATCTCGATCAGCCTCGAAACCCCT
554070 TTTTAGA
260 TTTTAGA
554077 CCTTTCTTAG
Statistics
Matches: 259, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
273 251 0.97
274 8 0.03
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (273 bp):
CAAAATTTTATTCCTCCTAGAAAGTAATTTTTTGAGATTTTTAAAGTATTTTTAGATTAACCCTC
ATCGAGTCACCTTTCTAACGATACTTTGTTCACCTTCTAAAACCTTCAAATCAACTTGAAATAAA
TTCAAAAAATGAGACAGCGTGATGATGTCCCCTATTTTTGGTTATGGATCAAAATTTAGTTGTTT
CACCAAGCTTCGTTTCGAGACATTCGATTGTCTCCAAATTATCTCGATCAGCCTCGAAACCCCTT
TTTAGAAAGTGAC
Found at i:554345 original size:26 final size:26
Alignment explanation
Indices: 554282--554348 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
554272 TTCTACAAGA
*
554282 ATACTCCAACCCCATCTTCCAAAGGG
1 ATACTCCAACCTCATCTTCCAAAGGG
*
554308 ATACTCTAACCTCATCTTCCGAAA-GG
1 ATACTCCAACCTCATCTTCC-AAAGGG
554334 ATACTCCAACCTCAT
1 ATACTCCAACCTCAT
554349 TTTTAAACTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 34 0.92
27 3 0.08
ACGTcount: A:0.31, C:0.36, G:0.09, T:0.24
Consensus pattern (26 bp):
ATACTCCAACCTCATCTTCCAAAGGG
Found at i:555434 original size:16 final size:17
Alignment explanation
Indices: 555413--555444 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
555403 ATTGTTACTT
555413 ATAATTT-TTCAATATA
1 ATAATTTATTCAATATA
555429 ATAATTTATTCAATAT
1 ATAATTTATTCAATAT
555445 CGTAAAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAATTTATTCAATATA
Found at i:556305 original size:22 final size:20
Alignment explanation
Indices: 556277--556332 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
556267 AAATTTTTTA
556277 TATTATATATATATATAAAAGG
1 TATTATATATATATAT--AAGG
556299 TA-T-TATATATATATAAGG
1 TATTATATATATATATAAGG
*
556317 TATTATATATAAATAT
1 TATTATATATATATAT
556333 TGATACGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 6 0.19
19 1 0.03
20 21 0.68
21 1 0.03
22 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TATTATATATATATATAAGG
Found at i:556307 original size:20 final size:18
Alignment explanation
Indices: 556284--556327 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
556274 TTATATTATA
*
556284 TATATATATAAAAGGTAT
1 TATATATATATAAGGTAT
556302 TATATATATATAAGGTAT
1 TATATATATATAAGGTAT
556320 TATATATA
1 TATATATA
556328 AATATTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (18 bp):
TATATATATATAAGGTAT
Found at i:558534 original size:13 final size:13
Alignment explanation
Indices: 558512--558564 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 13
558502 TTATAAATAC
558512 AATATAAAAAAATT
1 AATATAAAAAAA-T
558526 AAT-T-AAAAAAT
1 AATATAAAAAAAT
558537 AATAT-AAAAAAT
1 AATATAAAAAAAT
*
558549 AACATAAATAAAAT
1 AATATAAA-AAAAT
558563 AA
1 AA
558565 AAATATATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
11 4 0.11
12 18 0.51
13 3 0.09
14 10 0.29
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (13 bp):
AATATAAAAAAAT
Found at i:558586 original size:29 final size:27
Alignment explanation
Indices: 558554--558611 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
558544 AAAATAACAT
558554 AAATAAAATAAAAA-TATATAAACATATAA
1 AAATAAAA-AAAAATTAT-TAAA-ATATAA
* *
558583 AAATTAAAACAAATTATTAAAATATAA
1 AAATAAAAAAAAATTATTAAAATATAA
558610 AA
1 AA
558612 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 8 0.31
28 8 0.31
29 10 0.38
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (27 bp):
AAATAAAAAAAAATTATTAAAATATAA
Found at i:558632 original size:16 final size:15
Alignment explanation
Indices: 558593--558631 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 15
558583 AAATTAAAAC
558593 AAATTATTAAAATATA
1 AAATT-TTAAAATATA
558609 AAATTTTAAAATAATA
1 AAATTTTAAAAT-ATA
558625 TAAATTT
1 -AAATTT
558632 ATTTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTTAAAATATA
Found at i:558709 original size:9 final size:8
Alignment explanation
Indices: 558691--558728 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
558681 ATTTCTCATA
558691 TTTTCTCT
1 TTTTCTCT
558699 TTTTCTACT
1 TTTTCT-CT
558708 TTTTCT-T
1 TTTTCTCT
558715 TTTTCTCT
1 TTTTCTCT
*
558723 CTTTCT
1 TTTTCT
558729 GTTTCTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 7 0.26
8 12 0.44
9 8 0.30
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTCTCT
Found at i:558727 original size:15 final size:17
Alignment explanation
Indices: 558692--558728 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
558682 TTTCTCATAT
*
558692 TTTCTCTTTTTCTACTT
1 TTTCTCTTTTTCTACTC
558709 TTTCT-TTTTTCT-CTC
1 TTTCTCTTTTTCTACTC
558724 TTTCT
1 TTTCT
558729 GTTTCTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTCTTTTTCTACTC
Found at i:558891 original size:12 final size:12
Alignment explanation
Indices: 558874--558898 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
558864 CAGCCAAGGA
558874 ATAGTACTTGCT
1 ATAGTACTTGCT
558886 ATAGTACTTGCT
1 ATAGTACTTGCT
558898 A
1 A
558899 CACTTACATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
ATAGTACTTGCT
Found at i:558951 original size:22 final size:21
Alignment explanation
Indices: 558923--558968 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
558913 ATTTCTTTTA
558923 ATATAGTTATCTGAACCATAAT
1 ATATAGTTATCTGAACCAT-AT
*
558945 ATATAGTTATCTTAACCATAT
1 ATATAGTTATCTGAACCATAT
558966 ATA
1 ATA
558969 ATGTGAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (21 bp):
ATATAGTTATCTGAACCATAT
Found at i:559140 original size:21 final size:21
Alignment explanation
Indices: 559114--559153 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
559104 TGATACGTAA
559114 TTATTTATTATTT-TATTTTAT
1 TTATTTATT-TTTATATTTTAT
559135 TTATTTATTTTTATATTTT
1 TTATTTATTTTTATATTTT
559154 TATATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTATTTATTTTTATATTTTAT
Found at i:560194 original size:26 final size:26
Alignment explanation
Indices: 560101--560195 Score: 90
Period size: 26 Copynumber: 3.7 Consensus size: 26
560091 ATTTAAATAA
* *
560101 TAATAA-TATAATATTATAATTATTATT
1 TAATAATTATAATAATAT-TTTATTA-T
* *
560128 TACTAATTTTAAT-ATATTTTATTAT
1 TAATAATTATAATAATATTTTATTAT
560153 TAAT-ATTATAATTAATATTTTATTA-
1 TAATAATTATAA-TAATATTTTATTAT
560178 TAATTAATTATAATAATA
1 TAA-TAATTATAATAATA
560196 GCAGTCACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
24 6 0.11
25 8 0.14
26 23 0.40
27 15 0.26
28 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
TAATAATTATAATAATATTTTATTAT
Found at i:560380 original size:2 final size:2
Alignment explanation
Indices: 560373--560413 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
560363 TTCCTCATAG
560373 AT AT AT AT AT 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 AT AT AT AT AT A
560414 AATTACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:564137 original size:68 final size:70
Alignment explanation
Indices: 564043--564173 Score: 194
Period size: 68 Copynumber: 1.9 Consensus size: 70
564033 TCAAATCATA
** *
564043 TTGCAATTTGATTTCAATCTTGCTTGATAAATTT-ACCAAGGTGATTTAAT-TTGATTTCTTGTT
1 TTGCAATTTGAACTCAATCTTGCTTGATAAATTTGACCAAGGTGATTTAATCTTGATGTCTTGTT
564106 TAATG
66 TAATG
* * *
564111 TTGCAATTTGAACTCAATCTTTCTTGATAAATTTGGCCAAGGTGATTTGATCTTGATGTCTTG
1 TTGCAATTTGAACTCAATCTTGCTTGATAAATTTGACCAAGGTGATTTAATCTTGATGTCTTG
564174 CATAAATCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 31 0.56
69 14 0.25
70 10 0.18
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (70 bp):
TTGCAATTTGAACTCAATCTTGCTTGATAAATTTGACCAAGGTGATTTAATCTTGATGTCTTGTT
TAATG
Found at i:567440 original size:23 final size:24
Alignment explanation
Indices: 567400--567449 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
567390 TCGTGCTAAG
567400 GACTATCATTTTAAAACAAAAACAA
1 GACTATCA-TTTAAAACAAAAACAA
567425 GACTATCA-TTAAAACAAAAACAA
1 GACTATCATTTAAAACAAAAACAA
567448 GA
1 GA
567450 ATAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.68
25 8 0.32
ACGTcount: A:0.58, C:0.16, G:0.06, T:0.20
Consensus pattern (24 bp):
GACTATCATTTAAAACAAAAACAA
Found at i:569975 original size:22 final size:21
Alignment explanation
Indices: 569950--569990 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
569940 TCAAATTATA
*
569950 GACTACACTATATAAGATATCC
1 GACTACACT-TAAAAGATATCC
*
569972 GACTATACTTAAAAGATAT
1 GACTACACTTAAAAGATAT
569991 AGTGATGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (21 bp):
GACTACACTTAAAAGATATCC
Found at i:572868 original size:16 final size:16
Alignment explanation
Indices: 572827--572868 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
572817 GAATAGTTTG
*
572827 AATTTAAAATGATTCG
1 AATTTAAAATGATTCA
* *
572843 AACTTGAAATGATTCA
1 AATTTAAAATGATTCA
572859 AATTTAAAAT
1 AATTTAAAAT
572869 ACAATGAACG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (16 bp):
AATTTAAAATGATTCA
Found at i:574421 original size:21 final size:21
Alignment explanation
Indices: 574382--574421 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
574372 AAAAATAAAA
*
574382 ATATTTTATGTTAATATTTTT
1 ATATTTTATATTAATATTTTT
574403 ATATTTTATAATTAA-ATTT
1 ATATTTTAT-ATTAATATTT
574422 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATATTTTATATTAATATTTTT
Found at i:575259 original size:21 final size:20
Alignment explanation
Indices: 575241--575281 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
575231 TAAATTAATT
575241 AAAT-ATAAATTTAATTTAA
1 AAATAATAAATTTAATTTAA
*
575260 AAATAATAATTTATAATTTAA
1 AAATAATAAATT-TAATTTAA
575281 A
1 A
575282 TTGTTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAATAAATTTAATTTAA
Found at i:575351 original size:20 final size:20
Alignment explanation
Indices: 575318--575357 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
575308 AATTTTTTTT
575318 TAAATTTAATTATAAAAATA
1 TAAATTTAATTATAAAAATA
575338 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
575358 ATATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:575377 original size:20 final size:19
Alignment explanation
Indices: 575322--575382 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
575312 TTTTTTTAAA
*
575322 TTTAATTATAAAAATATAAAT
1 TTTAA-TATAAAAATAT-ATT
*
575343 ATTAATATAAAAATAATATT
1 TTTAATATAAAAAT-ATATT
* *
575363 TTTAATATTATAATATATT
1 TTTAATATAAAAATATATT
575382 T
1 T
575383 AAATAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.18
20 22 0.65
21 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATATAAAAATATATT
Found at i:580003 original size:22 final size:23
Alignment explanation
Indices: 579972--580015 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
579962 TTTTTTTAAT
579972 AGAACTGTAATTTTATTTAAAAA
1 AGAACTGTAATTTTATTTAAAAA
*
579995 AGAA-TGTAATTTTTTTTAAAA
1 AGAACTGTAATTTTATTTAAAA
580016 GATAAGGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
AGAACTGTAATTTTATTTAAAAA
Found at i:594720 original size:33 final size:33
Alignment explanation
Indices: 594683--594749 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
594673 TTCAACGATT
594683 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
594716 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
594749 T
1 T
594750 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:594721 original size:13 final size:13
Alignment explanation
Indices: 594703--594727 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
594693 CATAAAATGT
594703 TGTATCGATACAA
1 TGTATCGATACAA
594716 TGTATCGATACA
1 TGTATCGATACA
594728 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:594859 original size:52 final size:50
Alignment explanation
Indices: 594803--594947 Score: 200
Period size: 52 Copynumber: 2.8 Consensus size: 50
594793 GTATCGATAC
*
594803 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
594855 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
594907 TGTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAA
594948 CTTTTCATAT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:601521 original size:88 final size:88
Alignment explanation
Indices: 601248--601527 Score: 233
Period size: 88 Copynumber: 3.2 Consensus size: 88
601238 CCCTTTAAAG
* * * ** * ** *
601248 TAGTAGGGATGGAGTTTCCCTAAGGATAAAATTAAATGAAGGGAATTTAAATTTTTGTTAAA-A-
1 TAGTGGGGATGGAGTTTCCCCAAAGATAAAATTGTACGAAGAAAATTTAAATCTTT-TTAAAGAG
* * *
601311 TGAGGTTAGAGTATCCCATCAGAA
65 CGGGGTTAGAGTATCCCATCGGAA
* * ** * * *
601335 TAGTAGGGATGGAGTTTTCTTAAGGATAAAATTGTTCGAAGAAAATTTAAATCTTTTTGAAGAGC
1 TAGTGGGGATGGAGTTTCCCCAAAGATAAAATTGTACGAAGAAAATTTAAATCTTTTTAAAGAGC
* * ** *
601400 GGGGTTGGAGTGTCCTGTCGGAG
66 GGGGTTAGAGTATCCCATCGGAA
* * * * * *
601423 GAATGAGGATGGAGTTTCCCCAAAGATAAAA-TGTACGAAGGAAAATTTGATTTTTTTTAAAGAG
1 TAGTGGGGATGGAGTTTCCCCAAAGATAAAATTGTACGAA-GAAAATTTAAATCTTTTTAAAGAG
* *
601487 CGGGGTTAGAGTATCCCCTTGGAA
65 CGGGGTTAGAGTATCCCATCGGAA
601511 TAGTGGGGATGGAGTTT
1 TAGTGGGGATGGAGTTT
601528 TTCCAAAATC
Statistics
Matches: 150, Mismatches: 40, Indels: 5
0.77 0.21 0.03
Matches are distributed among these distances:
86 4 0.03
87 55 0.37
88 91 0.61
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.31
Consensus pattern (88 bp):
TAGTGGGGATGGAGTTTCCCCAAAGATAAAATTGTACGAAGAAAATTTAAATCTTTTTAAAGAGC
GGGGTTAGAGTATCCCATCGGAA
Found at i:605263 original size:106 final size:105
Alignment explanation
Indices: 605153--605444 Score: 304
Period size: 106 Copynumber: 2.8 Consensus size: 105
605143 TACATCTTTT
* ** *
605153 TCTTTGAGGACTAAAGT-GGATAGGT-CTCACTAGCTTGTGTGGGCTTTGAGATGGGTAAGTGTT
1 TCTTTGAGGACTAAAGTAGG-TAGGTGC-CACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATC
* * * * *
605216 TTGCTTTTTTAGGGCTAGAGGTAGGTAAGATAAAATG-TCATAC
64 TTGCTCTTTAAAGACTAGAGGTACGTAAGA-AAAA-GATCATAC
** *
605259 TCTTTGAGGA-TTGAGATAGGTAGGTGCCACCAGCTTGTGTGGACTTTGAGATGGGTAAGCATCT
1 TCTTTGAGGACTAAAG-TAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCT
* *
605323 TGCTCTTTAAAGACTAGAGGTACGTAAGAAAAAGCATCCTGC
65 TGCTCTTTAAAGACTAGAGGTACGTAAGAAAAAG-ATCATAC
* * * ** *
605365 TCTTTGAGGACTGAGGTAGGTAGGTGCCACCAACTTGTGTGGGCTTTGAGATGGGTGGGCATCCT
1 TCTTTGAGGACTAAAGTAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCTT
* *
605430 ACTCTTTAAGGACTA
66 GCTCTTTAAAGACTA
605445 AGGAAGATAA
Statistics
Matches: 156, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
104 1 0.01
105 7 0.04
106 143 0.92
107 5 0.03
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.31
Consensus pattern (105 bp):
TCTTTGAGGACTAAAGTAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCTT
GCTCTTTAAAGACTAGAGGTACGTAAGAAAAAGATCATAC
Found at i:605308 original size:279 final size:281
Alignment explanation
Indices: 604784--605412 Score: 915
Period size: 279 Copynumber: 2.2 Consensus size: 281
604774 AGGTAGGTTT
* * * ** *
604784 AAAAAGTATCATGCTCTTTGAGGATTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGTTTTTATG
1 AAAAAGAATCCTGCTCTTTGAGGACTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTGTG
*
604849 TAAGGGTAAAAAAAAAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTCATTAGCTTGTGT
66 TAAGGGT-------AAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGT
* * * *
604914 AGGCTTTGAGATGGGTAAGTGTCTTTCCTTTTGAGGGTTATAGGTAGGTAAGATAAAGTGTCCTA
124 AGGCTTTGAGATGGGTAAGTGTCTTTCCTTTTGAGGGCTAGAGGTAGGTAAGATAAAATGTCATA
*
604979 CTCTTTGAAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGCCTTTGAGATAGGTAAGCATCT
189 CTCTTTGAAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGACTTTGAGATAGGTAAGCATCT
* *
605044 TGCTCTTTGAAGACTAGAGGTAGGTAAG
254 TGCTCTTTAAAGACTAGAGGTACGTAAG
** *
605072 AAAAAGAATTTTGCTCTTTGAGGACTGAGGGTAGGAAAGTGCCACCAACTTGTGTAGGCTTTGTG
1 AAAAAGAATCCTGCTCTTTGAGGACTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTGTG
* *
605137 TAAGGGT-A-CATCTTTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGTGGGCTTT
66 TAAGGGTAAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGTAGGCTTT
* *
605200 GAGATGGGTAAGTGT-TTTGCTTTTTTAGGGCTAGAGGTAGGTAAGATAAAATGTCATACTCTTT
131 GAGATGGGTAAGTGTCTTT-CCTTTTGAGGGCTAGAGGTAGGTAAGATAAAATGTCATACTCTTT
* * *
605264 GAGGATTGAGATAGGTAGGTGCCACCAGCTTGTGTGGACTTTGAGATGGGTAAGCATCTTGCTCT
195 GAAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGACTTTGAGATAGGTAAGCATCTTGCTCT
605329 TTAAAGACTAGAGGTACGTAAG
260 TTAAAGACTAGAGGTACGTAAG
* * *
605351 AAAAAGCATCCTGCTCTTTGAGGACTGA-GGTAGGTAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAAAAGAATCCTGCTCTTTGAGGACTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTG
605413 AGATGGGTGG
Statistics
Matches: 311, Mismatches: 29, Indels: 12
0.88 0.08 0.03
Matches are distributed among these distances:
278 34 0.11
279 212 0.68
280 1 0.00
288 64 0.21
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (281 bp):
AAAAAGAATCCTGCTCTTTGAGGACTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTGTG
TAAGGGTAAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGTAGGCTTT
GAGATGGGTAAGTGTCTTTCCTTTTGAGGGCTAGAGGTAGGTAAGATAAAATGTCATACTCTTTG
AAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGACTTTGAGATAGGTAAGCATCTTGCTCTT
TAAAGACTAGAGGTACGTAAG
Found at i:612743 original size:20 final size:20
Alignment explanation
Indices: 612720--612792 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
612710 TCAATTCAAA
612720 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
612740 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
612761 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
612781 GTATCGATACAT
1 GTATCGATACAT
612793 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:612764 original size:21 final size:21
Alignment explanation
Indices: 612738--612813 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
612728 ACATGTTGCA
612738 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
612759 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
612779 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
612800 ATGTATCGATACAT
1 ATGTATCGATACAT
612814 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:612770 original size:41 final size:41
Alignment explanation
Indices: 612720--612813 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
612710 TCAATTCAAA
*
612720 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
612761 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
612802 GTATCGATACAT
1 GTATCGATACAT
612814 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:612870 original size:13 final size:13
Alignment explanation
Indices: 612852--612877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
612842 TACAGCAAGT
612852 ATGTATCGATACA
1 ATGTATCGATACA
612865 ATGTATCGATACA
1 ATGTATCGATACA
612878 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:617663 original size:3 final size:3
Alignment explanation
Indices: 617655--617742 Score: 113
Period size: 3 Copynumber: 29.3 Consensus size: 3
617645 ATGCAATGTT
* * * *
617655 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TCA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
617703 TCA TCA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
617743 ATAGATGGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:619325 original size:620 final size:601
Alignment explanation
Indices: 618221--619436 Score: 1679
Period size: 620 Copynumber: 2.0 Consensus size: 601
618211 AGTTTAATTG
* * * *
618221 ATTTATCTAAGAGTTAATAATTAATTGAGAAAAATAAAGAACAAGGAATAAAGTAAGAGTATTCT
1 ATTTATCTAAGAGTTAATAATTAATTAAGAAAAATAAAGAAAAAGAAAGAAAGTAAGAGTATTCT
* * * *
618286 TAAATAGAGAATGATAAGACCCATGTATTACACAAGTCGTGTTGATAAAGTCCCATGCTATATGC
66 TAAACAGAGAATGATAAGACCAATGTATTACACAAGTCGTGTTGAGAAAGTCCCATGCTATATAC
618351 TTGTAAAACCTTGAAGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTGAAACAGA
131 TTGTAAAACCTTGAAGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTGAAACAGA
* * *
618416 AAGCATTTGTTATTTCTTTCTTTTGCAGATGATAAATGTATGCATAATAAAATTGAAATAGGAAC
196 AAGCATCTGTTATTTCTTTCTTTTACAGATGATAAATGTATGCATAATAAAATTGAAATAGAAAC
* * *
618481 TTTTTTACCACTGCAATTCACCATGCTTTTTTTTCAATTGCCACAACTTTGCAAAAACTTCCCCT
261 TTTTTTACCACTACAATTCACCATGCTTTTTTTTCAATTGCCACAACTCTGCAAAAACTTCCACT
* ** **
618546 ATAGCAATTTTCAATATTCACAATCGAAAAAAATATAATTTTTTTGCCCCTCTCTCTTTAATTTA
326 ACAGCAATTTTCAATATTCACAATCGAAAAAAATATAATCATTTAACCCCTCTCTCTTTAATTTA
* *
618611 CTTTTCTATTAATTGTTTCTTTGGTTATTTTTTAAATTAATTCTCCTGTTAGGGTCTAATTTTTA
391 CTTTTCTATTAATTGTTTCTTTAGTTATTTTTTAAATTAATTCTCCTGTTAGGGTCCAATTTTTA
* *
618676 TTTTGTAGTTCTGCAAGTTTTTTATTATTTTACATGTA-TTTTTTAATTTTTAACCAAAGATAAA
456 TTTTGTAATTCTGCAAGTTTTTAATTATTTTACATGTATTTTTTTAATTTTTAACCAAAGATAAA
* *
618740 GGTGAGTTAATTATTTAATTAGAATTTTTAGTGATTTATTAAATAATTTTACCTTAGTGATTTAT
521 GGTGAGTTAATTATTTAATTAGAATTTTTAGTGATTTATCAAATAATTTTACCTAAGTGATTTAT
618805 TCAAAAGGCATGATTA
586 TCAAAAGGCATGATTA
* *
618821 ATTTATCT-AGAAGTTAATAATTAATTAAGAAAGAA-CAAGTAAAAAGAAAGAAAGTAAGATTAT
1 ATTTATCTAAG-AGTTAATAATTAATTAAGAAA-AATAAAG-AAAAAGAAAGAAAGTAAGAGTAT
* * * *
618884 TGTTAAACAGGGAATGATAAGACCTAAGTGTTAGTTACACAAGTCGTGTTGAGAAAGTCTCATTC
63 TCTTAAACAGAGAATGATAAGACC-AA-TG-TA-TTACACAAGTCGTGTTGAGAAAGTCCCATGC
*
618949 TATATACTTTTAAAACCTTGAAGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTG
124 TATATACTTGTAAAACCTTGAAGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTG
* * * *
619014 AAATA-AAACGCATCTGTTATTTCTTTCTTTATATAGATGATAAATGTATGCTTAATATAATTGA
189 AAACAGAAA-GCATCTGTTATTTCTTTCTTT-TACAGATGATAAATGTATGCATAATAAAATTGA
*
619078 AATA-AAAGCTTTTTTACTACTACAATTCACCATGCTTGCCTACAACATTTTTTCAATTGCCACA
252 AATAGAAA-CTTTTTTACCACTACAATTCACCATGC-T---T------TTTTTTCAATTGCCACA
* * * *
619142 GAGTCTGTAGAGACTTCTCACTACAGCAATTTTCAATATTCACAATCGAAAAAAAAATATAATCA
306 -ACTCTGCAAAAACTTC-CACTACAGCAATTTTCAATATTCACAATCG--AAAAAAATATAATCA
** * * *
619207 TTTAACCTTTCTCTTTTTAATTTACTTTTTTGTTAATTGTTTCTTTAGTTATTTTTTAAATTAAT
367 TTTAACCCCTCTCTCTTTAATTTACTTTTCTATTAATTGTTTCTTTAGTTATTTTTTAAATTAAT
** * * *
619272 TCTTTTGTTCGGTTCCAATTTTT-TTTTGGTAATTTTGCAAGTTTTTAATTATTTTACATGTATT
432 TCTCCTGTTAGGGTCCAATTTTTATTTT-GTAATTCTGCAAGTTTTTAATTATTTTACATGTATT
*
619336 TTTTTAATTTTTAACCAAAGATACAGGTGAGTTAATTATTTAATTAGAATTTTTAGTGATTTATC
496 TTTTTAATTTTTAACCAAAGATAAAGGTGAGTTAATTATTTAATTAGAATTTTTAGTGATTTATC
* *
619401 AAGTAATTTTACCTAAGTGATTTATTCAAATGGCAT
561 AAATAATTTTACCTAAGTGATTTATTCAAAAGGCAT
619437 TCCCATGTTA
Statistics
Matches: 536, Mismatches: 54, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
599 2 0.00
600 31 0.06
601 42 0.08
602 1 0.00
603 2 0.00
604 5 0.01
605 117 0.22
606 58 0.11
607 1 0.00
610 1 0.00
616 17 0.03
617 11 0.02
618 28 0.05
619 4 0.01
620 119 0.22
621 97 0.18
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (601 bp):
ATTTATCTAAGAGTTAATAATTAATTAAGAAAAATAAAGAAAAAGAAAGAAAGTAAGAGTATTCT
TAAACAGAGAATGATAAGACCAATGTATTACACAAGTCGTGTTGAGAAAGTCCCATGCTATATAC
TTGTAAAACCTTGAAGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTGAAACAGA
AAGCATCTGTTATTTCTTTCTTTTACAGATGATAAATGTATGCATAATAAAATTGAAATAGAAAC
TTTTTTACCACTACAATTCACCATGCTTTTTTTTCAATTGCCACAACTCTGCAAAAACTTCCACT
ACAGCAATTTTCAATATTCACAATCGAAAAAAATATAATCATTTAACCCCTCTCTCTTTAATTTA
CTTTTCTATTAATTGTTTCTTTAGTTATTTTTTAAATTAATTCTCCTGTTAGGGTCCAATTTTTA
TTTTGTAATTCTGCAAGTTTTTAATTATTTTACATGTATTTTTTTAATTTTTAACCAAAGATAAA
GGTGAGTTAATTATTTAATTAGAATTTTTAGTGATTTATCAAATAATTTTACCTAAGTGATTTAT
TCAAAAGGCATGATTA
Found at i:620724 original size:13 final size:13
Alignment explanation
Indices: 620706--620732 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
620696 ACATTATGCT
620706 TTGTATCGATACA
1 TTGTATCGATACA
620719 TTGTATCGATACA
1 TTGTATCGATACA
620732 T
1 T
620733 GAAACTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:620800 original size:13 final size:13
Alignment explanation
Indices: 620782--620806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
620772 ACATGGTAAT
620782 TGTATCGATACAA
1 TGTATCGATACAA
620795 TGTATCGATACA
1 TGTATCGATACA
620807 TGATGAATTG
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:620821 original size:33 final size:32
Alignment explanation
Indices: 620765--620826 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
620755 CCGCTGTTTA
*
620765 TATCGATACATGGTAATTGTATCGATACAATG
1 TATCGATACATGATAATTGTATCGATACAATG
620797 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGAT-AATTGTATCGATACA
620827 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (32 bp):
TATCGATACATGATAATTGTATCGATACAATG
Found at i:628911 original size:22 final size:21
Alignment explanation
Indices: 628881--628936 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
628871 TTATCAAAAT
628881 AAATTTTTATCAAGGGGGAGA
1 AAATTTTTATCAAGGGGGAGA
*
628902 AAATCTTTTATCAAGGGTGAGA
1 AAAT-TTTTATCAAGGGGGAGA
* *
628924 AATTTTTTTTCAA
1 AAATTTTTATCAA
628937 AAGAGAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
AAATTTTTATCAAGGGGGAGA
Found at i:629543 original size:13 final size:13
Alignment explanation
Indices: 629525--629549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
629515 CATTATGCTT
629525 TGTATCGATACAA
1 TGTATCGATACAA
629538 TGTATCGATACA
1 TGTATCGATACA
629550 TGTTCATTGT
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:629549 original size:33 final size:32
Alignment explanation
Indices: 629503--629568 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
629493 TACACACTCA
*
629503 AATGTATCAATACAT-TATGCTTTGTATCGATAC
1 AATGTATCAATACATGT-T-CATTGTATCGATAC
*
629536 AATGTATCGATACATGTTCATTGTATCGATAC
1 AATGTATCAATACATGTTCATTGTATCGATAC
629568 A
1 A
629569 TGGACAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (32 bp):
AATGTATCAATACATGTTCATTGTATCGATAC
Found at i:629580 original size:20 final size:20
Alignment explanation
Indices: 629534--629590 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
629524 TTGTATCGAT
*
629534 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
*
629553 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
629572 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
629591 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 16 0.48
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:629656 original size:13 final size:13
Alignment explanation
Indices: 629635--629664 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
629625 TGATACATGG
*
629635 TACATTGTATCGA
1 TACAATGTATCGA
629648 TACAATGTATCGA
1 TACAATGTATCGA
629661 TACA
1 TACA
629665 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:629657 original size:33 final size:33
Alignment explanation
Indices: 629620--629684 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
629610 TACCACTGTT
* *
629620 TGTATTGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTGTATCGATACAA
629653 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGTATCGATACA
629685 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:632984 original size:20 final size:20
Alignment explanation
Indices: 632959--633097 Score: 119
Period size: 20 Copynumber: 6.8 Consensus size: 20
632949 TTTTCACAAT
632959 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
632979 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
632999 TTGTATCGATACATTG-T-A
1 TTGTATCGATACATTGTTCA
* * *
633017 TCG-ATAC-ATTC-TGGGTTTACCCA
1 TTGTAT-CGATACAT-TG-TT---CA
*
633040 GATGTATCGATACATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
*
633061 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
633081 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
633098 ATCGATACAT
Statistics
Matches: 95, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
16 1 0.01
17 6 0.06
18 4 0.04
19 2 0.02
20 68 0.72
21 3 0.03
23 3 0.03
24 2 0.02
25 5 0.05
26 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:632993 original size:13 final size:13
Alignment explanation
Indices: 632977--633026 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
632967 ATACATTGTT
632977 CATTGTATCGATA
1 CATTGTATCGATA
632990 CATTGT-TC---A
1 CATTGTATCGATA
632999 --TTGTATCGATA
1 CATTGTATCGATA
633010 CATTGTATCGATA
1 CATTGTATCGATA
633023 CATT
1 CATT
633027 CTGGGTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
7 4 0.13
8 2 0.06
9 1 0.03
11 1 0.03
12 2 0.06
13 21 0.68
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:633095 original size:13 final size:13
Alignment explanation
Indices: 633079--633108 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
633069 ATACATTGCT
633079 CATTGTATCGATA
1 CATTGTATCGATA
633092 CATTGTATCGATA
1 CATTGTATCGATA
633105 CATT
1 CATT
633109 ACCCAGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:633121 original size:21 final size:20
Alignment explanation
Indices: 633095--633148 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
633085 ATCGATACAT
*
633095 TGTATCGATACATTACCCAGA
1 TGTATCGATACATTACACA-A
**
633116 TGTATCGATACATTTTACAA
1 TGTATCGATACATTACACAA
633136 TGTATCGATACAT
1 TGTATCGATACAT
633149 ACAGGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTACACAA
Found at i:633140 original size:20 final size:19
Alignment explanation
Indices: 633041--633148 Score: 84
Period size: 20 Copynumber: 5.7 Consensus size: 19
633031 GTTTACCCAG
633041 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTT-CA
* *
633061 TTGTATCGATACATTGCTCA
1 ATGTATCGATACATT-TTCA
*
633081 TTGTATCGATACA---T--
1 ATGTATCGATACATTTTCA
**
633095 -TGTATCGATACATTACCCA
1 ATGTATCGATACATT-TTCA
633114 GATGTATCGATACATTTTACA
1 -ATGTATCGATACATTTT-CA
633135 ATGTATCGATACAT
1 ATGTATCGATACAT
633149 ACAGGCATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 20
0.74 0.05 0.20
Matches are distributed among these distances:
13 12 0.16
16 1 0.01
20 43 0.59
21 17 0.23
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:635607 original size:130 final size:129
Alignment explanation
Indices: 635447--635768 Score: 457
Period size: 130 Copynumber: 2.5 Consensus size: 129
635437 ATTTTTCATC
** * *
635447 TCGGGGATACTCCAACCCCGGTTATATTTCCAAAACATCAATTTTTCATAATCGGGGATACTTTA
1 TCGGGGATACTCCAACTTCGATT-TTTTTCCAAAACATCAATTTTTCATAATCGGGGATACTTTA
*
635512 ATCCCATTATTTCCGAAGAGATACTCCAACCCCGGTTTTATTTCTAAAATACCAAATTTTC-ACA
65 ATCCCATTATTTCCGAAGAGATACTCCAACCCCGGTTTTATTTCTAAAACACC-AATTTTCAACA
635576 A
129 A
*
635577 TCGGGGATACTCCAACTTCGATATTTTTTCCAAAACATCAAATTTTCATAATCGGGGATACTTTA
1 TCGGGGATACTCCAACTTCGAT-TTTTTTCCAAAACATCAATTTTTCATAATCGGGGATACTTTA
* * * *
635642 ATCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCAACAA
65 ATCCCATTATTTCCGAAGAGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCAACAA
* * * * * *
635707 TCGGGGATACTCCAAGTTCGATTTTATTTTCAAAACACCAATCTTCCACAATCGGGGATACT
1 TCGGGGATACTCCAACTTCGATTTT-TTTCCAAAACATCAATTTTTCATAATCGGGGATACT
635769 CCAACTCCGA
Statistics
Matches: 172, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
129 10 0.06
130 161 0.94
131 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (129 bp):
TCGGGGATACTCCAACTTCGATTTTTTTCCAAAACATCAATTTTTCATAATCGGGGATACTTTAA
TCCCATTATTTCCGAAGAGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCAACAA
Found at i:635721 original size:51 final size:50
Alignment explanation
Indices: 635658--635825 Score: 221
Period size: 51 Copynumber: 3.3 Consensus size: 50
635648 TTATTTTCGA
*
635658 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCAACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTC-ACAATC
*** *
635709 GGGGATACTCCAAGTTCGATTTTATTT-TCAAAACACCAATCTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAAT-TTTCACAATC
* * *
635760 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAA-TTTTCACAATC
635811 GGGGATACTCCAACC
1 GGGGATACTCCAACC
635826 TTGTTGTTTC
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.01
51 97 0.95
52 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCACAATC
Found at i:635844 original size:28 final size:28
Alignment explanation
Indices: 635808--635882 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
635798 ATTTTTCACA
* *
635808 ATCGGGGATACTCCAACCTTGTTGTTTC
1 ATCGGGGATACTCCAACCCTGTTATTTC
*
635836 ATCGGGGATACTCCAACCCTGTTATTTT
1 ATCGGGGATACTCCAACCCTGTTATTTC
* * *
635864 TTAGGGGATACTCAAACCC
1 ATCGGGGATACTCCAACCC
635883 CGGCTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCTGTTATTTC
Found at i:635949 original size:51 final size:51
Alignment explanation
Indices: 635871--635969 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
635861 TTTTTAGGGG
* * * * *
635871 ATACTCAAACCCCGGCTTTTTTCCTAAAATATTGATTTCTCACAATCGGGC
1 ATACTCAAACCCAGCCTTATTTCCTAAAACATCGATTTCTCACAATCGGGC
* *
635922 ATACTCCAAACCCAGCCTTATTT-CTAAAGCATCGATTTTTCACAATCG
1 ATACT-CAAACCCAGCCTTATTTCCTAAAACATCGATTTCTCACAATCG
635970 AGGATGCTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 26 0.65
52 14 0.35
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.32
Consensus pattern (51 bp):
ATACTCAAACCCAGCCTTATTTCCTAAAACATCGATTTCTCACAATCGGGC
Found at i:636062 original size:79 final size:79
Alignment explanation
Indices: 635939--636138 Score: 208
Period size: 79 Copynumber: 2.5 Consensus size: 79
635929 AAACCCAGCC
* * * * * * *
635939 TTATTTCTAAAGCATCGATTTTTCACAATC-GAGGATGCTTCAACCCAT-TTATTT-TCGAGGGG
1 TTATTTCCAAAACACCGATTTTCCATAATCAG-GGATACTCCAACCC-TGTTATTTCT-GAGGGG
* * *
636001 ATACTCTAACCTCGATT
63 ATACTCCAACCCCAATT
* * *
636018 TTATTTTCAAAACACTGATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTCTGAGGGGATA
1 TTATTTCCAAAACACCGATTTTCCATAATCAGGGATACTCCAACCCTGTTATTTCTGAGGGGATA
636083 CTCCAACCCCAATT
66 CTCCAACCCCAATT
** *
636097 TTATTTCCCGAACACCGATTTTCCATAATCGGGGATACTCCA
1 TTATTTCCAAAACACCGATTTTCCATAATCAGGGATACTCCA
636139 GCCCCGTTGT
Statistics
Matches: 99, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
78 1 0.01
79 96 0.97
80 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (79 bp):
TTATTTCCAAAACACCGATTTTCCATAATCAGGGATACTCCAACCCTGTTATTTCTGAGGGGATA
CTCCAACCCCAATT
Found at i:652171 original size:1 final size:1
Alignment explanation
Indices: 652167--652246 Score: 61
Period size: 1 Copynumber: 80.0 Consensus size: 1
652157 TCTTTTTTAT
* * * * * * * * *
652167 AAAAACAAAAAAAAATAAAACAAAACAAAAAAACAAAAAAAAAACAAAAAAAAACAAAAGAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
652232 AAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAA
652247 GGAGAGAAAA
Statistics
Matches: 57, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:652186 original size:10 final size:10
Alignment explanation
Indices: 652167--652235 Score: 95
Period size: 10 Copynumber: 7.0 Consensus size: 10
652157 TCTTTTTTAT
652167 AAAAACAAAA
1 AAAAACAAAA
*
652177 AAAAATAAAA
1 AAAAACAAAA
*
652187 CAAAACAAAA
1 AAAAACAAAA
*
652197 AAACA-AAAA
1 AAAAACAAAA
652206 AAAAACAAAA
1 AAAAACAAAA
652216 AAAAACAAAA
1 AAAAACAAAA
*
652226 GAAAACAAAA
1 AAAAACAAAA
652236 CAAAGAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
9 8 0.16
10 43 0.84
ACGTcount: A:0.87, C:0.10, G:0.01, T:0.01
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:652193 original size:20 final size:18
Alignment explanation
Indices: 652167--652246 Score: 97
Period size: 20 Copynumber: 4.1 Consensus size: 18
652157 TCTTTTTTAT
652167 AAAAACAAAAAAAAATAAA
1 AAAAACAAAAAAAAA-AAA
652186 ACAAAACAAAAAAACAAAAA
1 A-AAAACAAAAAAA-AAAAA
652206 AAAAACAAAAAAAAACAAA
1 AAAAACAAAAAAAAA-AAA
652225 AGAAAACAAAACAAAGAAAAA
1 A-AAAACAAAA-AAA-AAAAA
652246 A
1 A
652247 GGAGAGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.04
19 17 0.31
20 25 0.45
21 9 0.16
22 2 0.04
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (18 bp):
AAAAACAAAAAAAAAAAA
Found at i:652217 original size:39 final size:40
Alignment explanation
Indices: 652167--652246 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
652157 TCTTTTTTAT
*
652167 AAAAACAAAAAAAAATAAAACAAAACAAAA-AAACAAAAA
1 AAAAACAAAAAAAAACAAAACAAAACAAAACAAACAAAAA
* *
652206 AAAAACAAAAAAAAACAAAAGAAAACAAAACAAAGAAAAA
1 AAAAACAAAAAAAAACAAAACAAAACAAAACAAACAAAAA
652246 A
1 A
652247 GGAGAGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 28 0.76
40 9 0.24
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (40 bp):
AAAAACAAAAAAAAACAAAACAAAACAAAACAAACAAAAA
Found at i:652245 original size:10 final size:9
Alignment explanation
Indices: 652167--652246 Score: 79
Period size: 10 Copynumber: 8.3 Consensus size: 9
652157 TCTTTTTTAT
652167 AAAAACAAAA
1 AAAAAC-AAA
*
652177 AAAAATAAA
1 AAAAACAAA
652186 ACAAAACAAA
1 A-AAAACAAA
*
652196 AAAACAAAAA
1 AAAA-ACAAA
652206 AAAAACAAAA
1 AAAAAC-AAA
652216 AAAAACAAA
1 AAAAACAAA
652225 AGAAAACAAA
1 A-AAAACAAA
* *
652235 ACAAAGAAA
1 AAAAACAAA
652244 AAA
1 AAA
652247 GGAGAGAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
9 20 0.34
10 39 0.66
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (9 bp):
AAAAACAAA
Found at i:652261 original size:26 final size:25
Alignment explanation
Indices: 652167--652246 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 25
652157 TCTTTTTTAT
652167 AAAAACAAAA-AAAAATAAAACAAAA
1 AAAAACAAAAGAAAAA-AAAACAAAA
*
652192 CAAAAA-AACA-AAAAAAAAACAAAA
1 -AAAAACAAAAGAAAAAAAAACAAAA
*
652216 AAAAACAAAAGAAAACAAAACAAAGA
1 AAAAACAAAAGAAAAAAAAACAAA-A
652242 AAAAA
1 AAAAA
652247 GGAGAGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.10
24 12 0.25
25 20 0.42
26 11 0.23
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.01
Consensus pattern (25 bp):
AAAAACAAAAGAAAAAAAAACAAAA
Found at i:653312 original size:62 final size:62
Alignment explanation
Indices: 653215--653772 Score: 784
Period size: 62 Copynumber: 9.0 Consensus size: 62
653205 TTTCTCTTTT
*
653215 CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
653277 CACTTTTTTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAAGCCCACACGAGTTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGG
* * *
653340 CAC-CTTCTAGTCCTGAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * * * * *
653401 CACTTTTTTAGTCCTCAAGGAGTAGGATGCCTTTTCCTTTCAAAGCCCACATAAGCTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * * *
653463 CAC-CTTC-AGTCCTCAAAGAGTGGGACGTCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* *
653523 CACTTTTCTAGTCCACAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * * *
653585 CACTTTTCTAGCCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * **
653647 AAC-CTTC-AGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * * *
653707 CACTTTTCTAGTCTTCAAAGAGCAGGACACCTTTTCCTTTTAAAAGCCCACACGAGTTGGTGG
1 CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGG
653770 CAC
1 CAC
653773 CTTGAAAGCT
Statistics
Matches: 438, Mismatches: 51, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
60 99 0.23
61 34 0.08
62 259 0.59
63 46 0.11
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (62 bp):
CACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:653546 original size:122 final size:124
Alignment explanation
Indices: 653215--653772 Score: 775
Period size: 122 Copynumber: 4.5 Consensus size: 124
653205 TTTCTCTTTT
* *
653215 CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
653280 TTTTTTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAAGCCCACACGAGTTGGTGG
66 TTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGG
* *
653340 CAC-CTTCTAGTCCTGAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * *
653404 TTTTTTAGTCCTCAAGGAGTAGGATGCCTTTTCCTTTCAAAGCCCACATAAGCTGGTGG
66 TTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
** *
653463 CAC-CTTC-AGTCCTCAAAGAGTGGGACGTCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
1 CACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
653526 TTTTCTAGTCCACAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
66 TTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * * * * *
653585 CACTTTTCTAGCCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGGAAC
1 CACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
* **
653650 -CTTC-AGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
66 TTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * * * *
653707 CACTTTTCTAGTCTTCAAAGAGCAGGACACCTTTTCCTTTTAAAAGCCCACACGAGTTGGTGGCA
1 CACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTCAAAGCCCACACAAGTTGGTGGCA
653772 C
65 C
653773 CTTGAAAGCT
Statistics
Matches: 389, Mismatches: 41, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
122 188 0.48
123 55 0.14
124 143 0.37
125 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (124 bp):
CACTCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCAC
TTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:653565 original size:184 final size:184
Alignment explanation
Indices: 653215--653772 Score: 839
Period size: 184 Copynumber: 3.0 Consensus size: 184
653205 TTTCTCTTTT
* * * *
653215 CACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 CACTTTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGGCAC
* * * * * *
653280 TTTTTTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAAGCCCACACGAGTTGGTGGCAC-C
66 --CTTCAGTCCTCAAAGAGTGGGACGCCTTTTCC-TTTAAAAGCCCACACAAGTTGGTGGCACTT
*
653344 TTCTAGTCCTGAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
128 TTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
653401 CACTTTTTTAGTCCTCAAGGAGTAGGATGCCTTTTCCTTTCAAAGCCCACATAAGCTGGTGGCAC
1 CACTTTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGGCAC
* *
653466 CTTCAGTCCTCAAAGAGTGGGACGTCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
66 CTTCAGTCCTCAAAGAGTGGGACGCCTTTTCCTTTAAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
653531 TAGTCCACAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
131 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* *
653585 CACTTTTCTAGCCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGGAAC
1 CACTTTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGGCAC
* *
653650 CTTCAGTCCTCAAAGAGCGGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
66 CTTCAGTCCTCAAAGAGTGGGACGCCTTTTCCTTTAAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
653715 TAGTCTTCAAAGAGCAGGACACCTTTTCCTTTTAAAAGCCCACACGAGTTGGTGG
131 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGG
653770 CAC
1 CAC
653773 CTTGAAAGCT
Statistics
Matches: 337, Mismatches: 33, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
183 26 0.08
184 230 0.68
185 23 0.07
186 58 0.17
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (184 bp):
CACTTTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGGCAC
CTTCAGTCCTCAAAGAGTGGGACGCCTTTTCCTTTAAAAGCCCACACAAGTTGGTGGCACTTTTC
TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:653573 original size:34 final size:34
Alignment explanation
Indices: 653535--653635 Score: 92
Period size: 34 Copynumber: 3.1 Consensus size: 34
653525 CTTTTCTAGT
653535 CCACAAAGAGTAGGATGCCTTTTCCTTTTAAAGC
1 CCACAAAGAGTAGGATGCCTTTTCCTTTTAAAGC
* *
653569 CCACACA-AGTTGG-TGGCACTTTT-C---T--AGC
1 CCACAAAGAGTAGGAT-GC-CTTTTCCTTTTAAAGC
* *
653597 CCTCAAAGAGTAGGATGCCTTTTCCTTTCAAAGC
1 CCACAAAGAGTAGGATGCCTTTTCCTTTTAAAGC
653631 CCACA
1 CCACA
653636 CAAGCTGGTG
Statistics
Matches: 50, Mismatches: 7, Indels: 20
0.65 0.09 0.26
Matches are distributed among these distances:
28 13 0.26
29 8 0.16
30 2 0.04
32 1 0.02
33 8 0.16
34 18 0.36
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.28
Consensus pattern (34 bp):
CCACAAAGAGTAGGATGCCTTTTCCTTTTAAAGC
Found at i:654578 original size:32 final size:33
Alignment explanation
Indices: 654514--654581 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
654504 CGTTACAAGC
*
654514 CAATGTATCAATACATTTGGTCGTGTATCGATA
1 CAATGTATCAATACATTTGGTCATGTATCGATA
*
654547 CAATGTATCAATAGATCTT-GT-ATGTATCGATA
1 CAATGTATCAATACAT-TTGGTCATGTATCGATA
654579 CAA
1 CAA
654582 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 17 0.53
34 2 0.06
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCAATACATTTGGTCATGTATCGATA
Found at i:657136 original size:13 final size:13
Alignment explanation
Indices: 657118--657155 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
657108 ATAAACCCTT
*
657118 TGTATCGATACAC
1 TGTATCGATACAA
657131 TGTATCGATACAA
1 TGTATCGATACAA
657144 TGTATCGATACA
1 TGTATCGATACA
657156 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:663426 original size:13 final size:13
Alignment explanation
Indices: 663408--663432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
663398 TACAGTGGTC
663408 ATGTATCGATACA
1 ATGTATCGATACA
663421 ATGTATCGATAC
1 ATGTATCGATAC
663433 TATGCATTAT
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):
ATGTATCGATACA
Found at i:664527 original size:20 final size:20
Alignment explanation
Indices: 664442--664536 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
664432 TTTCACAATT
* *
664442 TGTATCTATACATTGTTCAT
1 TGTATCGATACATTGTTCAA
* *
664462 TTTATCGATACATTGTTCAT
1 TGTATCGATACATTGTTCAA
* ***
664482 TGTATTGATACATTACCCAGA
1 TGTATCGATACATTGTTCA-A
664503 TGTATCGATACATT-TTACAA
1 TGTATCGATACATTGTT-CAA
664523 TGTATCGATACATT
1 TGTATCGATACATT
664537 CAGGCATTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTGTTCAA
Done.