Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015336.1 Kokia drynarioides strain JFW-HI SEQ_130383, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 257659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 113 characters in sequence are not A, C, G, or T
Found at i:6067 original size:34 final size:34
Alignment explanation
Indices: 6017--6092 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
6007 CGACTGCATC
*
6017 ATGATGCAAAAGGAAACC-AGATATGATATCTACA
1 ATGATGCAAAAGGAAACCGA-ATATGATATCTAAA
* * * *
6051 ATGATGCAATATGAAACCGAATATGATGTTTAAA
1 ATGATGCAAAAGGAAACCGAATATGATATCTAAA
6085 ATGATGCA
1 ATGATGCA
6093 TGAAAATGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (34 bp):
ATGATGCAAAAGGAAACCGAATATGATATCTAAA
Found at i:8284 original size:21 final size:21
Alignment explanation
Indices: 8260--8312 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
8250 AAGTATAATT
8260 TCTACCGATACATGTCATACA
1 TCTACCGATACATGTCATACA
8281 TCTACCGATACATGTCATACA
1 TCTACCGATACATGTCATACA
8302 TCTACCGATAC
1 TCTACCGATAC
8313 TAAAAACTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.28
Consensus pattern (21 bp):
TCTACCGATACATGTCATACA
Found at i:10004 original size:51 final size:51
Alignment explanation
Indices: 9923--10213 Score: 352
Period size: 51 Copynumber: 5.6 Consensus size: 51
9913 GCTATAAACA
*
9923 AAAGAGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCCTTACAGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAGATT
* **
9975 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAGATT
* *
10026 AAAGGTCCGATGACTAAGTGTCATCGTGAGTTAATGAATCCTTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAGATT
* * * * *
10077 AATGGTCCGATGACTACGTATCATCGTGAGTAAATGAATCCATGAC-GAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAG-ATT
* * * * **
10128 AAAGGTCCGATGACTTAGTGTCATCGTGAGTATATGAATTCCTCTACGAAACA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCT-TAC-AGATT
*
10181 AAAGGGTCCGTTGACTATA-TGTCATCGTGAGTA
1 AAA-GGTCCGATGACTA-AGTGTCATCGTGAGTA
10214 TTAAACGAAA
Statistics
Matches: 207, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
50 1 0.00
51 170 0.82
52 6 0.03
53 4 0.02
54 25 0.12
55 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAGATT
Found at i:11362 original size:19 final size:19
Alignment explanation
Indices: 11338--11374 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11328 ATCTCCGTAC
*
11338 AACAAATTTAAATACACAA
1 AACAAATGTAAATACACAA
*
11357 AACAAATGTAAATTCACA
1 AACAAATGTAAATACACA
11375 GGTAATCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (19 bp):
AACAAATGTAAATACACAA
Found at i:11668 original size:52 final size:52
Alignment explanation
Indices: 11605--11823 Score: 237
Period size: 52 Copynumber: 4.2 Consensus size: 52
11595 AATCCACGAG
* * * * *
11605 GGATTCGTATACTCAAGATGACACAGAGTCATCAAACCTCTTAATTCGTAAA
1 GGATTCATATACTCACGATGACACTGAGTCATCAGACCTTTTAATTCGTAAA
* * * *
11657 GGATCCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAA
1 GGATTCATATACTCACGATGACACTGAGTCATCAGACCTTTTAATTCGTAAA
* *
11709 AGATTCATATACTCACGATGTCACTTG-GTCATCAGACCTTTTAATAT-GTAAA
1 GGATTCATATACTCACGATGACAC-TGAGTCATCAGACCTTTTAAT-TCGTAAA
* * * * * *
11761 GGATTCATATACTAATGATTACACTTAGTTATCGGACCTTTTAA-TCTGTAAA
1 GGATTCATATACTCACGATGACACTGAGTCATCAGACCTTTTAATTC-GTAAA
11813 GGATTCATATA
1 GGATTCATATA
11824 GATTAAAAGA
Statistics
Matches: 139, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 136 0.98
53 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (52 bp):
GGATTCATATACTCACGATGACACTGAGTCATCAGACCTTTTAATTCGTAAA
Found at i:11740 original size:104 final size:104
Alignment explanation
Indices: 11558--11823 Score: 302
Period size: 104 Copynumber: 2.6 Consensus size: 104
11548 TCATTTCATT
* * * * * *** * *
11558 CATATACTCACAATGACACATAGCCACCGGACCTTATAATCCACGAGGGATTCGTATACTCAAGA
1 CATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGGATTCATATACTCAAGA
11623 TGACACAGAGTCATCAAACCTCTTAAT-TCGTAAAGGATC
66 TGACACAGAGTCATCAAACCTCTTAATAT-GTAAAGGATC
* *
11662 CATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAAGATTCATATACTCACGA
1 CATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGGATTCATATACTCAAGA
* * * * *
11727 TGTCACTTG-GTCATCAGACCTTTTAATATGTAAAGGATT
66 TGACAC-AGAGTCATCAAACCTCTTAATATGTAAAGGATC
* * * * *
11766 CATATACTAATGATTACACTTAGTTATCGGACCTTTTAATCTGTAAAGGATTCATATA
1 CATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGGATTCATATA
11824 GATTAAAAGA
Statistics
Matches: 137, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
104 135 0.99
105 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (104 bp):
CATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGGATTCATATACTCAAGA
TGACACAGAGTCATCAAACCTCTTAATATGTAAAGGATC
Found at i:11875 original size:70 final size:70
Alignment explanation
Indices: 11757--11893 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
11747 TTTTAATATG
* *
11757 TAAAGGATTCATATACTAATGATTACACTTAGTTATCGGACCTTTTAATCTGTAAAGGATTCATA
1 TAAAAGATTCATATACTAATGATTACACTTAGTTATCGGACCTTTTAATCCGTAAAGGATTCATA
11822 TAGAT
66 TAGAT
*
11827 TAAAAGATTCATATACTCATGATTACACTTAGTTATCGGACCTTTTAATCCGTAAAGGATTCATA
1 TAAAAGATTCATATACTAATGATTACACTTAGTTATCGGACCTTTTAATCCGTAAAGGATTCATA
11892 TA
66 TA
11894 CTCATGATGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (70 bp):
TAAAAGATTCATATACTAATGATTACACTTAGTTATCGGACCTTTTAATCCGTAAAGGATTCATA
TAGAT
Found at i:13213 original size:52 final size:52
Alignment explanation
Indices: 13126--13416 Score: 483
Period size: 52 Copynumber: 5.6 Consensus size: 52
13116 TTCTCATTTA
* * *
13126 ATACTCACGATGACACATAGTCATCGGACCCCATAATCCGAAAAGGATTCGT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
13178 ATACTTACGATGACACATAGTCATCGAACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
13230 ATACTCACGATGACACATAGTCATCGAACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
13282 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
13334 ATAATCACGATGACACATAGTCATCGGGCCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
13386 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
13417 TTTGCATTTA
Statistics
Matches: 225, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 225 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:19264 original size:2 final size:2
Alignment explanation
Indices: 19257--19287 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19247 CTTAAAAGTA
19257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19288 ATAAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21770 original size:4 final size:4
Alignment explanation
Indices: 21761--21815 Score: 73
Period size: 4 Copynumber: 14.8 Consensus size: 4
21751 CACAACAAGA
*
21761 TTTC TTTC TTTC TTTC TTTC -TTC -TTC -TTC -TTC TTTC TTGC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
21805 TTTC TTTC TTT
1 TTTC TTTC TTT
21816 TTTTTTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 12 0.25
4 36 0.75
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:23536 original size:154 final size:154
Alignment explanation
Indices: 23256--23564 Score: 618
Period size: 154 Copynumber: 2.0 Consensus size: 154
23246 ATCAGCAGGT
23256 TGTCGAATATTTACAGATTCAAATATCTCTAAACAAGACGAAACTGATACTTGTGTTAACCTGAG
1 TGTCGAATATTTACAGATTCAAATATCTCTAAACAAGACGAAACTGATACTTGTGTTAACCTGAG
23321 AAACTTATTCAAATGAGTAGTAGTCTACCAAGTTACTGTAAGCAATAATCCAGGCCCCTAAGAAT
66 AAACTTATTCAAATGAGTAGTAGTCTACCAAGTTACTGTAAGCAATAATCCAGGCCCCTAAGAAT
23386 TTCATTCACTTACATCCTCTATGC
131 TTCATTCACTTACATCCTCTATGC
23410 TGTCGAATATTTACAGATTCAAATATCTCTAAACAAGACGAAACTGATACTTGTGTTAACCTGAG
1 TGTCGAATATTTACAGATTCAAATATCTCTAAACAAGACGAAACTGATACTTGTGTTAACCTGAG
23475 AAACTTATTCAAATGAGTAGTAGTCTACCAAGTTACTGTAAGCAATAATCCAGGCCCCTAAGAAT
66 AAACTTATTCAAATGAGTAGTAGTCTACCAAGTTACTGTAAGCAATAATCCAGGCCCCTAAGAAT
23540 TTCATTCACTTACATCCTCTATGC
131 TTCATTCACTTACATCCTCTATGC
23564 T
1 T
23565 CATAACAATA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 155 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (154 bp):
TGTCGAATATTTACAGATTCAAATATCTCTAAACAAGACGAAACTGATACTTGTGTTAACCTGAG
AAACTTATTCAAATGAGTAGTAGTCTACCAAGTTACTGTAAGCAATAATCCAGGCCCCTAAGAAT
TTCATTCACTTACATCCTCTATGC
Found at i:27730 original size:23 final size:23
Alignment explanation
Indices: 27701--27754 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
27691 AAACTTTATG
27701 ATTATATTAAATAAT-TATTAAA
1 ATTATATTAAATAATATATTAAA
*
27723 TATTATATTTAATAATATATTAAA
1 -ATTATATTAAATAATATATTAAA
*
27747 ATAATATT
1 ATTATATT
27755 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 21 0.75
24 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTATATTAAATAATATATTAAA
Found at i:27736 original size:12 final size:12
Alignment explanation
Indices: 27703--27753 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
27693 ACTTTATGAT
27703 TATATTAAATAA
1 TATATTAAATAA
*
27715 T-TATTAAATAT
1 TATATTAAATAA
*
27726 TATATTTAATAA
1 TATATTAAATAA
27738 TATATTAAAATAA
1 TATATT-AAATAA
27751 TAT
1 TAT
27754 TTTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 10 0.30
12 15 0.45
13 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATTAAATAA
Found at i:27811 original size:19 final size:19
Alignment explanation
Indices: 27787--27834 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
27777 TTTATAATAG
*
27787 AAATATTTTAAAACATCAT
1 AAATATTTCAAAACATCAT
*
27806 AAATATCGTTCAAAATATCAT
1 AAATAT--TTCAAAACATCAT
*
27827 TAATATTT
1 AAATATTT
27835 AATGTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.33
21 16 0.67
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (19 bp):
AAATATTTCAAAACATCAT
Found at i:27915 original size:23 final size:22
Alignment explanation
Indices: 27844--27917 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
27834 TAATGTTTCA
* * *
27844 AAATATTTTTTCAAAACCTTAT
1 AAATATTATTTAAAAACTTTAT
*
27866 AAACATTATTTAAAAACTTTAT
1 AAATATTATTTAAAAACTTTAT
*
27888 AAAATATTA-TTAAAACATTTTTAT
1 -AAATATTATTTAAAA-A-CTTTAT
27912 AAATAT
1 AAATAT
27918 GATATTAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 24 0.56
23 14 0.33
24 5 0.12
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATTATTTAAAAACTTTAT
Found at i:35044 original size:28 final size:28
Alignment explanation
Indices: 35013--35089 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
35003 CCCTTTGCAG
* *
35013 CTTCACTGTGATAGTTCGTACCTCAAAA
1 CTTCACTGTGATAGCTCGCACCTCAAAA
* *
35041 CTTCACTGTGATAGCTCGCACCTCACAG
1 CTTCACTGTGATAGCTCGCACCTCAAAA
* * *
35069 CTTCACTATAACAGCTCGCAC
1 CTTCACTGTGATAGCTCGCAC
35090 TTCTTTGTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.27
Consensus pattern (28 bp):
CTTCACTGTGATAGCTCGCACCTCAAAA
Found at i:35210 original size:18 final size:18
Alignment explanation
Indices: 35170--35214 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
35160 GCCCCTTCAC
* *
35170 GTGAGCTTGTCTCTTTAT
1 GTGAGCTCGTCTCTTTAG
35188 GTGAGCTCGTCTCTTT-G
1 GTGAGCTCGTCTCTTTAG
35205 GATGAGCTCG
1 G-TGAGCTCG
35215 CCAAATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.11, C:0.20, G:0.29, T:0.40
Consensus pattern (18 bp):
GTGAGCTCGTCTCTTTAG
Found at i:37486 original size:15 final size:15
Alignment explanation
Indices: 37466--37494 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37456 TTTGAAGCAT
37466 TTTCTAAATCTGAAA
1 TTTCTAAATCTGAAA
37481 TTTCTAAATCTGAA
1 TTTCTAAATCTGAA
37495 TAGTTGTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTCTAAATCTGAAA
Found at i:40747 original size:52 final size:52
Alignment explanation
Indices: 40669--40788 Score: 150
Period size: 52 Copynumber: 2.3 Consensus size: 52
40659 TCTCGATGAT
* * * ** *
40669 TATGTGTCATCATAAGTATATGAATCCTTTACGGATTATGAGGTCTGATAAC
1 TATGTGTCATCGTGAGCATATGAATCCTTTACGGATTAACAGGTCCGATAAC
* *
40721 TATGTGTCATCGTGAGCATATGAATCCTTTATGGATTAACAGGTCCGATGAC
1 TATGTGTCATCGTGAGCATATGAATCCTTTACGGATTAACAGGTCCGATAAC
* *
40773 TATTTATCATCGTGAG
1 TATGTGTCATCGTGAG
40789 TATTAAATGA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (52 bp):
TATGTGTCATCGTGAGCATATGAATCCTTTACGGATTAACAGGTCCGATAAC
Found at i:40833 original size:60 final size:60
Alignment explanation
Indices: 40740--40857 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
40730 TCGTGAGCAT
* * * *
40740 ATGAATCCTTTATGGATTAACAGGTCCGATGACTATTTATCATCGTGAGTATTAAATGAA
1 ATGAATCCATTACGGATTAACAGGTCCGATGACTATGTATCATCGTGAGTATCAAATGAA
* * * *
40800 ATGAATCCCATTACGGATTAA-AGGTCCGGTGACTCTGTGTCATCTTGAGTATCAAATG
1 ATGAAT-CCATTACGGATTAACAGGTCCGATGACTATGTATCATCGTGAGTATCAAATG
40858 CGAATTGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 37 0.76
61 12 0.24
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (60 bp):
ATGAATCCATTACGGATTAACAGGTCCGATGACTATGTATCATCGTGAGTATCAAATGAA
Found at i:41552 original size:21 final size:21
Alignment explanation
Indices: 41526--41582 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
41516 TCGGTAGAAG
*
41526 ACTTGTATCGATAGAACTGTC
1 ACTTGTATCGATAGAACTATC
* *
41547 ACTTGTAT-TAGTAAAACTATC
1 ACTTGTATCGA-TAGAACTATC
*
41568 ACTTGTATCGGTAGA
1 ACTTGTATCGATAGA
41583 GGTATGTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGATAGAACTATC
Found at i:47921 original size:52 final size:52
Alignment explanation
Indices: 47843--47977 Score: 209
Period size: 52 Copynumber: 2.6 Consensus size: 52
47833 AAATGCAAAA
* * *
47843 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAAG
*
47895 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGAATTAAG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAAG
*
47947 AGGT-TCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCT-GATGACTATGTGTCATCGTGAGTAT
47978 TAAATGAAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 1 0.01
52 76 0.99
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAAG
Found at i:49272 original size:24 final size:24
Alignment explanation
Indices: 49245--49400 Score: 123
Period size: 24 Copynumber: 6.2 Consensus size: 24
49235 ATAGTATATT
49245 TACACGTTTACGCTCGTCAGCTTA
1 TACACGTTTACGCTCGTCAGCTTA
* *
49269 TACATATACGTTTACACTCGTCAGCTTG
1 TAC----ACGTTTACGCTCGTCAGCTTA
* * *
49297 CACATGTTTACGCTAGTCAGCTTA
1 TACACGTTTACGCTCGTCAGCTTA
* * *
49321 TACATATGCGTTTACGCTTGCCAGCTTG
1 TAC--A--CGTTTACGCTCGTCAGCTTA
* * * *
49349 CACATGTTTACGCTCGTCTGCTTG
1 TACACGTTTACGCTCGTCAGCTTA
*
49373 CACACGTTTACGCTCGTCAGCTTA
1 TACACGTTTACGCTCGTCAGCTTA
49397 TACA
1 TACA
49401 TATATACATA
Statistics
Matches: 103, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
24 62 0.60
26 2 0.02
28 39 0.38
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (24 bp):
TACACGTTTACGCTCGTCAGCTTA
Found at i:49310 original size:52 final size:52
Alignment explanation
Indices: 49250--49371 Score: 190
Period size: 52 Copynumber: 2.3 Consensus size: 52
49240 ATATTTACAC
*
49250 GTTTACGCTCGTCAGCTTATACATATACGTTTACACTCGTCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTATACATATACGTTTACACTCGCCAGCTTGCACAT
* * * *
49302 GTTTACGCTAGTCAGCTTATACATATGCGTTTACGCTTGCCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTATACATATACGTTTACACTCGCCAGCTTGCACAT
*
49354 GTTTACGCTCGTCTGCTT
1 GTTTACGCTCGTCAGCTT
49372 GCACACGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (52 bp):
GTTTACGCTCGTCAGCTTATACATATACGTTTACACTCGCCAGCTTGCACAT
Found at i:49492 original size:52 final size:52
Alignment explanation
Indices: 49403--49541 Score: 170
Period size: 52 Copynumber: 2.7 Consensus size: 52
49393 CTTATACATA
* * * * *
49403 TATACATATGCGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCGTAAACT
1 TATACATATGCGTTTACTCTCACCAACTTACACACGTTTACGCTCGTAAACT
* * * *
49455 TATACATATGTGTTTACTCTTACCAACTTACAGACGTTTACGCTCGTCAACT
1 TATACATATGCGTTTACTCTCACCAACTTACACACGTTTACGCTCGTAAACT
* * *
49507 TATACATATGCGTTTACTCTCGCCAGCTTGCACAC
1 TATACATATGCGTTTACTCTCACCAACTTACACAC
49542 TCATGCCAAC
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.34
Consensus pattern (52 bp):
TATACATATGCGTTTACTCTCACCAACTTACACACGTTTACGCTCGTAAACT
Found at i:55446 original size:20 final size:20
Alignment explanation
Indices: 55421--55477 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
55411 GCACCAGCAT
*
55421 GCATCGAGCAACATCAGGAA
1 GCATCGAGCAACACCAGGAA
** *
55441 GCATCGAGCAGTACCAGGGA
1 GCATCGAGCAACACCAGGAA
*
55461 GCATCGAGCAATACCAG
1 GCATCGAGCAACACCAG
55478 ACATGGTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.26, G:0.28, T:0.11
Consensus pattern (20 bp):
GCATCGAGCAACACCAGGAA
Found at i:66727 original size:98 final size:98
Alignment explanation
Indices: 66558--66755 Score: 369
Period size: 98 Copynumber: 2.0 Consensus size: 98
66548 AGCTAGTAAC
66558 AGGAACCAGTGGCATACATCAAAAACATTAATCACTAACAATGTTCATCCGTATTAAAGAAAAAG
1 AGGAACCAGTGGCATACATCAAAAACATTAATCACTAACAATGTTCATCCGTATTAAAGAAAAAG
*
66623 AGGTAAGGAACAGGACTACATCTTCCATGCAAA
66 AGGTAAGGAACAGGACTAAATCTTCCATGCAAA
* *
66656 AGGAAGCAGTGTCATACATCAAAAACATTAATCACTAACAATGTTCATCCGTATTAAAGAAAAAG
1 AGGAACCAGTGGCATACATCAAAAACATTAATCACTAACAATGTTCATCCGTATTAAAGAAAAAG
66721 AGGTAAGGAACAGGACTAAATCTTCCATGCAAA
66 AGGTAAGGAACAGGACTAAATCTTCCATGCAAA
66754 AG
1 AG
66756 TTTTTTTACT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (98 bp):
AGGAACCAGTGGCATACATCAAAAACATTAATCACTAACAATGTTCATCCGTATTAAAGAAAAAG
AGGTAAGGAACAGGACTAAATCTTCCATGCAAA
Found at i:78880 original size:14 final size:14
Alignment explanation
Indices: 78861--78888 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
78851 TTTTATTATT
78861 AATAAATTTAATAA
1 AATAAATTTAATAA
78875 AATAAATTTAATAA
1 AATAAATTTAATAA
78889 TATTAACAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAATTTAATAA
Found at i:80014 original size:19 final size:19
Alignment explanation
Indices: 79990--80028 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
79980 CTTCATTTTA
79990 TAAATT-ATAATAATTAAAT
1 TAAATTCAT-ATAATTAAAT
*
80009 TAAATTCATCTAATTAAAT
1 TAAATTCATATAATTAAAT
80028 T
1 T
80029 TAACAATCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATTCATATAATTAAAT
Found at i:88796 original size:21 final size:21
Alignment explanation
Indices: 88772--88825 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
88762 CTTGTGCTAG
88772 TTCTACCGATACAAGT-ATGAT
1 TTCTACCGATACAAGTCATG-T
*
88793 TTCTATCGATACAAGTCATGT
1 TTCTACCGATACAAGTCATGT
**
88814 AACTACCGATAC
1 TTCTACCGATAC
88826 CAAAAACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGT
Found at i:91968 original size:18 final size:18
Alignment explanation
Indices: 91942--91977 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
91932 CAATTTTTTC
91942 CTTTCTTTTTTTTCCCTT
1 CTTTCTTTTTTTTCCCTT
*
91960 CTTTTTTTTTTTTCCCTT
1 CTTTCTTTTTTTTCCCTT
91978 TGAAGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (18 bp):
CTTTCTTTTTTTTCCCTT
Found at i:91969 original size:15 final size:14
Alignment explanation
Indices: 91935--91968 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
91925 TTTATTGCAA
*
91935 TTTTTTCCTTTCTT
1 TTTTTTCCCTTCTT
91949 TTTTTTCCCTTCTT
1 TTTTTTCCCTTCTT
91963 TTTTTT
1 TTTTTT
91969 TTTTCCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCCCTTCTT
Found at i:93088 original size:20 final size:19
Alignment explanation
Indices: 93042--93088 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
93032 ATAAAATAAG
93042 GGAAAAAGAGAAAAGAAAA
1 GGAAAAAGAGAAAAGAAAA
*
93061 GAATAAAAGAGAAGGAA-AAAA
1 GGA-AAAAGAGAA--AAGAAAA
93082 GGAAAAA
1 GGAAAAA
93089 AAAAATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 2 0.09
20 13 0.57
21 6 0.26
22 2 0.09
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (19 bp):
GGAAAAAGAGAAAAGAAAA
Found at i:93546 original size:28 final size:27
Alignment explanation
Indices: 93502--93562 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
93492 ACTCCATACC
93502 ATTTTTTTGAATTTTTTATATTTTT-TA
1 ATTTTTTTGAATTTTTTA-ATTTTTATA
93529 ATTTTTATTGTAA-TTTTTAATTTTTATA
1 ATTTTT-TTG-AATTTTTTAATTTTTATA
*
93557 AATTTT
1 ATTTTT
93563 GAATTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 12 0.40
28 16 0.53
29 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.70
Consensus pattern (27 bp):
ATTTTTTTGAATTTTTTAATTTTTATA
Found at i:93562 original size:17 final size:17
Alignment explanation
Indices: 93505--93573 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 17
93495 CCATACCATT
*
93505 TTTTTGAATTTTT-TATAT
1 TTTTT-AATTTTTATA-AA
*
93523 TTTTTAATTTTTATTGTAA
1 TTTTTAATTTTTA-T-AAA
93542 TTTTTAATTTTTATAAA
1 TTTTTAATTTTTATAAA
*
93559 TTTTGAATTATTTAT
1 TTTTTAATT-TTTAT
93574 TAACATGACA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 17 0.40
18 11 0.26
19 15 0.35
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (17 bp):
TTTTTAATTTTTATAAA
Found at i:96763 original size:2 final size:2
Alignment explanation
Indices: 96756--96808 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
96746 ACTTTTACTC
*
96756 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96798 AT AT AT CAT AT
1 AT AT AT -AT AT
96809 TCTCCTGCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:115262 original size:23 final size:23
Alignment explanation
Indices: 115236--115281 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
115226 TATTTAATAG
115236 AAAA-GGACTTGATCAACGGAAAA
1 AAAATGGAC-TGATCAACGGAAAA
**
115259 AAAATTTACTGATCAACGGAAAA
1 AAAATGGACTGATCAACGGAAAA
115282 TAAGCTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (23 bp):
AAAATGGACTGATCAACGGAAAA
Found at i:115858 original size:7 final size:7
Alignment explanation
Indices: 115848--115873 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
115838 TCTTATATTC
115848 TCAATTT
1 TCAATTT
115855 TCAATTT
1 TCAATTT
115862 TCAATTT
1 TCAATTT
115869 TCAAT
1 TCAAT
115874 CATCAATCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (7 bp):
TCAATTT
Found at i:116984 original size:13 final size:13
Alignment explanation
Indices: 116966--116991 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116956 TTTGATTTAC
116966 AATTTTTTATATT
1 AATTTTTTATATT
116979 AATTTTTTATATT
1 AATTTTTTATATT
116992 TTATATTTAT
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:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTTTATATT
Found at i:118289 original size:6 final size:6
Alignment explanation
Indices: 118264--118302 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
118254 ACAATTCATA
* * *
118264 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
118303 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:120258 original size:27 final size:28
Alignment explanation
Indices: 120217--120283 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
120207 ATTTTAAAAA
*
120217 TATATATTTATATATAAAA-A-TTATTTT
1 TATAT-TTTAAATATAAAATATTTATTTT
120244 TATTATTTTAAATATAAAATATTTATTTT
1 TA-TATTTTAAATATAAAATATTTATTTT
*
120273 TATATTATAAA
1 TATATTTTAAA
120284 AAACAATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 14 0.40
28 12 0.34
29 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATATTTTAAATATAAAATATTTATTTT
Found at i:129089 original size:11 final size:12
Alignment explanation
Indices: 129063--129087 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
129053 ATAGAAAGAA
129063 TTCTTTTTTCTT
1 TTCTTTTTTCTT
129075 TTCTTTTTTCTT
1 TTCTTTTTTCTT
129087 T
1 T
129088 CTGTTAAATG
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:145397 original size:13 final size:12
Alignment explanation
Indices: 145381--145423 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
145371 ACAAAATTCA
145381 AAAAAAAAAAACG
1 AAAAAAAAAAA-G
**
145394 AAAAACGAAAAG
1 AAAAAAAAAAAG
145406 AAAAAAGAAAAAG
1 AAAAAA-AAAAAG
145419 AAAAA
1 AAAAA
145424 TGCCATTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.84, C:0.05, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:158013 original size:20 final size:19
Alignment explanation
Indices: 157974--158013 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
157964 ACTCATTATA
*
157974 ACTTTTATATATATTTTTT
1 ACTTTTATATATAATTTTT
*
157993 ACTTTTATTATCTAATTTTT
1 ACTTTTA-TATATAATTTTT
158013 A
1 A
158014 AGTTCAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
ACTTTTATATATAATTTTT
Found at i:159827 original size:5 final size:5
Alignment explanation
Indices: 159817--159842 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
159807 CATAAAGGCC
159817 AGGTG AGGTG AGGTG AGGTG AGGTG A
1 AGGTG AGGTG AGGTG AGGTG AGGTG A
159843 CAGTCACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.58, T:0.19
Consensus pattern (5 bp):
AGGTG
Found at i:165185 original size:21 final size:21
Alignment explanation
Indices: 165161--165200 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
165151 ATCTTATCTT
**
165161 TATAATATTCAATCTCATTGC
1 TATAATAACCAATCTCATTGC
165182 TATAATAACCAATCTCATT
1 TATAATAACCAATCTCATT
165201 ACTACCGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (21 bp):
TATAATAACCAATCTCATTGC
Found at i:167358 original size:15 final size:15
Alignment explanation
Indices: 167334--167386 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
167324 TATTATTCTC
* *
167334 TTAAACTTAATTTAA
1 TTAAAATTAAATTAA
*
167349 TTAAAATTAAATTAT
1 TTAAAATTAAATTAA
**
167364 TTAAAATTAAACAAA
1 TTAAAATTAAATTAA
167379 TTAAAATT
1 TTAAAATT
167387 TTGAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATTAAATTAA
Found at i:167771 original size:50 final size:50
Alignment explanation
Indices: 167717--167847 Score: 119
Period size: 47 Copynumber: 2.7 Consensus size: 50
167707 GCGGAGCCAA
167717 AAAAAATATTTAATTAATTTAGGTAATTTTATTATTCAATC-ATTCAT-TTT
1 AAAAAATA-TTAATTAATTTAGGTAATTTTATTATTCAATCAATT-ATATTT
* * * ** * *
167767 AAAAAATA-TATTTAGTAT-GAAAATATTA-AATTCAATCAATTATATTT
1 AAAAAATATTAATTAATTTAGGTAATTTTATTATTCAATCAATTATATTT
* *
167814 AATAAATAATAAATTAATTTAGGTAATTTTATTA
1 AAAAAAT-ATTAATTAATTTAGGTAATTTTATTA
167848 AATATGATTG
Statistics
Matches: 59, Mismatches: 16, Indels: 11
0.69 0.19 0.13
Matches are distributed among these distances:
46 10 0.17
47 19 0.32
48 8 0.14
49 6 0.10
50 15 0.25
51 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (50 bp):
AAAAAATATTAATTAATTTAGGTAATTTTATTATTCAATCAATTATATTT
Found at i:170036 original size:52 final size:52
Alignment explanation
Indices: 169923--170166 Score: 217
Period size: 52 Copynumber: 4.7 Consensus size: 52
169913 ATTTCACTTC
* * * * * **
169923 ATTCATATACTCACGATGACACATAGCCACCAGACCTT-ATAATCCA-CGAGAG
1 ATTCATATACTCACGATGACACAGAGTCATCGGA-CTTCTTAATCCATAAAG-G
* * *
169975 ATTCGTATACTCACGATGACACAGAGTCATCGGACTTCTTGATCCGTAAAGG
1 ATTCATATACTCACGATGACACAGAGTCATCGGACTTCTTAATCCATAAAGG
* ** * *
170027 A-TCTATATACTCATGATGACACTTAGTCATCGGACCTT-TAAATCCATAAAGA
1 ATTC-ATATACTCACGATGACACAGAGTCATCGGA-CTTCTTAATCCATAAAGG
* * *
170079 ATTTCATATACTCACGATGACACAGAGTCATCGAACCTCGTAATCCATAAAGG
1 A-TTCATATACTCACGATGACACAGAGTCATCGGACTTCTTAATCCATAAAGG
* * **
170132 ATTCATTTACCCACGATGACACTTAGTCATCGGAC
1 ATTCATATACTCACGATGACACAGAGTCATCGGAC
170167 CCTTTTTCAT
Statistics
Matches: 154, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
51 5 0.03
52 104 0.68
53 43 0.28
54 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACAGAGTCATCGGACTTCTTAATCCATAAAGG
Found at i:177150 original size:316 final size:309
Alignment explanation
Indices: 176581--177182 Score: 823
Period size: 316 Copynumber: 1.9 Consensus size: 309
176571 GCTGATGTAG
* *
176581 CAACTTTCGATATAGATACCATCAGCACTATTTAAAACTCTTAAACATATAGTATCGAAAATTTC
1 CAACTTTCGATATAGATACCATCAACACTAATTAAAACTCTTAAACATATAGTATCGAAAATTTC
* * * *
176646 CGTCAATATGTTTATATTCTTTCAATTTGCATAAGGTACGATTGTAACATACGTTATCAAACATA
66 CGTCAATATATTTATATTCTTTCAATTTGCATAAGGTACAATTGCAACATACATTATCAAACATA
** *
176711 CAGCGTTGCCATTGACGGTTAGAAAATTAGTAAAATTTCAATTATATCCTTAAACATATAGTGAT
131 CAGCGACGCCATTGACGGTTAGAAAATGAGTAAAATTTCAATTATATCCTTAAACATATAGTGAT
* * *
176776 AGTATTAACCGTTGATAAAAAGGTCTTATTGATATTGATATAATAACAATTTTTCTTACACAGGT
196 AGTATTAACCGTTGATAAAAAGGTCTTATTGATATCGATATAATAACAAATGTTCTTACACAGGT
176841 ATAAAATGAAATTCCAATTATATCTACGATTCTTTCAATTTTATATTGA
261 ATAAAATGAAATTCCAATTATATCTACGATTCTTTCAATTTTATATTGA
* * * **
176890 CAACTTTCGATATAGATACCATCAACACTAATTAATATTCTTATACATATAGT-TTTAAAATTTT
1 CAACTTTCGATATAGATACCATCAACACTAATTAAAACTCTTAAACATATAGTATCGAAAA-TTT
176954 CCGTCAATATATTTACACCAATGATTCTTTCAATTTGCATAAGGTACAATTGCAACATACATTAT
65 CCGTCAATATATTT------AT-ATTCTTTCAATTTGCATAAGGTACAATTGCAACATACATTAT
* * * * * *
177019 CAAACATACAGCGACGCCATTGACTGTTGGTAAATGAGTGAATTTTCAATTGTATCCTTAAACAT
123 CAAACATACAGCGACGCCATTGACGGTTAGAAAATGAGTAAAATTTCAATTATATCCTTAAACAT
* * * *
177084 ATAGTGATAGTATTAACCGTTGCTAAAAAGGTTTTATT-A-ATGCGAATATACTGACAAATGTTC
188 ATAGTGATAGTATTAACCGTTGATAAAAAGGTCTTATTGATAT-CG-ATATAATAACAAATGTTC
** *
177147 TTACATGGGTATAAAGTGAAATTCCAATTATATCTA
251 TTACACAGGTATAAAATGAAATTCCAATTATATCTA
177183 TGGACACATC
Statistics
Matches: 253, Mismatches: 30, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
308 5 0.02
309 64 0.25
314 2 0.01
315 4 0.02
316 178 0.70
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (309 bp):
CAACTTTCGATATAGATACCATCAACACTAATTAAAACTCTTAAACATATAGTATCGAAAATTTC
CGTCAATATATTTATATTCTTTCAATTTGCATAAGGTACAATTGCAACATACATTATCAAACATA
CAGCGACGCCATTGACGGTTAGAAAATGAGTAAAATTTCAATTATATCCTTAAACATATAGTGAT
AGTATTAACCGTTGATAAAAAGGTCTTATTGATATCGATATAATAACAAATGTTCTTACACAGGT
ATAAAATGAAATTCCAATTATATCTACGATTCTTTCAATTTTATATTGA
Found at i:179579 original size:8 final size:8
Alignment explanation
Indices: 179568--179608 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
179558 TTATATAAAA
179568 AAATTATT
1 AAATTATT
**
179576 AAA-TAAA
1 AAATTATT
179583 AAATTATT
1 AAATTATT
179591 AAATTATT
1 AAATTATT
179599 AAA-TATT
1 AAATTATT
179606 AAA
1 AAA
179609 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
7 12 0.43
8 16 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATTATT
Found at i:179585 original size:15 final size:15
Alignment explanation
Indices: 179565--179594 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
179555 TAATTATATA
179565 AAAAAATTATTAAAT
1 AAAAAATTATTAAAT
179580 AAAAAATTATTAAAT
1 AAAAAATTATTAAAT
179595 TATTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATTATTAAAT
Found at i:179605 original size:15 final size:16
Alignment explanation
Indices: 179565--179614 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
179555 TAATTATATA
179565 AAAAAATTATTAAA-T
1 AAAAAATTATTAAATT
179580 AAAAAATTATTAAATT
1 AAAAAATTATTAAATT
** *
179596 ATTAAA-TATTAAAAT
1 AAAAAATTATTAAATT
179611 AAAA
1 AAAA
179615 TAAATATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAAATTATTAAATT
Found at i:180887 original size:37 final size:37
Alignment explanation
Indices: 180837--180911 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
180827 CTGGCACAGG
180837 TTGGAGACCACCAGGCATGTGTCCATGATCACTATAA
1 TTGGAGACCACCAGGCATGTGTCCATGATCACTATAA
180874 TTGGAGACCACCAGGCATGTGTCCATGATCACTATAA
1 TTGGAGACCACCAGGCATGTGTCCATGATCACTATAA
180911 T
1 T
180912 CCTTTCGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (37 bp):
TTGGAGACCACCAGGCATGTGTCCATGATCACTATAA
Found at i:190205 original size:29 final size:27
Alignment explanation
Indices: 190143--190211 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 27
190133 AAAAGACCTC
*
190143 AATTTTTTTTTATTTTATCACTAGTAT
1 AATTTTTTTTTATTGTATCACTAGTAT
* * *
190170 ATGTTTTTATTTTATTGTATTACATATTAT
1 A-ATTTTT-TTTTATTGTATCAC-TAGTAT
190200 AATTTTTTTTTA
1 AATTTTTTTTTA
190212 AAAAAGATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 10 0.29
29 17 0.50
30 6 0.18
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (27 bp):
AATTTTTTTTTATTGTATCACTAGTAT
Found at i:193975 original size:17 final size:17
Alignment explanation
Indices: 193941--193975 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
193931 TACTTTTACT
*
193941 AATTTAAAATTTTAAAA
1 AATTTAAAATCTTAAAA
193958 AATTTAAAATGCTTAAAA
1 AATTTAAAAT-CTTAAAA
193976 TGAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAAATCTTAAAA
Found at i:195167 original size:2 final size:2
Alignment explanation
Indices: 195160--195206 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
195150 AATATTCCAA
195160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
195202 AT AT A
1 AT AT A
195207 ACATGTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:196915 original size:22 final size:22
Alignment explanation
Indices: 196887--196935 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
196877 TGATACTTTT
196887 AATTTAATT-TTTT-TTTATTATC
1 AATTTAATTCTTTTCTTT-TTA-C
196909 AATTTAATTCTTTTCTTTTTAC
1 AATTTAATTCTTTTCTTTTTAC
196931 AATTT
1 AATTT
196936 TCTAGTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 15 0.60
23 7 0.28
24 3 0.12
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (22 bp):
AATTTAATTCTTTTCTTTTTAC
Found at i:197406 original size:8 final size:8
Alignment explanation
Indices: 197393--197417 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
197383 ACACCCCACT
197393 GCATAATA
1 GCATAATA
197401 GCATAATA
1 GCATAATA
197409 GCATAATA
1 GCATAATA
197417 G
1 G
197418 GTTATTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (8 bp):
GCATAATA
Found at i:201380 original size:26 final size:26
Alignment explanation
Indices: 201349--201414 Score: 132
Period size: 26 Copynumber: 2.5 Consensus size: 26
201339 CTCGATCCAC
201349 AGCTCGTGTGAGCAGACCCATTTTAT
1 AGCTCGTGTGAGCAGACCCATTTTAT
201375 AGCTCGTGTGAGCAGACCCATTTTAT
1 AGCTCGTGTGAGCAGACCCATTTTAT
201401 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
201415 ATATATGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGACCCATTTTAT
Found at i:207451 original size:16 final size:16
Alignment explanation
Indices: 207415--207452 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
207405 AAATTTTATT
* *
207415 ATTATTTTTAAAAACA
1 ATTATATTTAAAAAAA
207431 A-TATATTTAAAAAAA
1 ATTATATTTAAAAAAA
207446 ATTATAT
1 ATTATAT
207453 AAATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATATTTAAAAAAA
Found at i:212825 original size:20 final size:21
Alignment explanation
Indices: 212802--212841 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
212792 TTTTCAAATG
212802 TATCGATA-ATTTCTTAAAAA
1 TATCGATACATTTCTTAAAAA
* *
212822 TATCGTTACTTTTCTTAAAA
1 TATCGATACATTTCTTAAAA
212842 TCGAGACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (21 bp):
TATCGATACATTTCTTAAAAA
Found at i:212898 original size:32 final size:32
Alignment explanation
Indices: 212862--212932 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
212852 AAGGGCATTC
212862 TATCGATTGGGTATCGATACCATCTCAAATGG
1 TATCGATTGGGTATCGATACCATCTCAAATGG
212894 TATCGATTGGGTATCGATACCATCTCAAATGG
1 TATCGATTGGGTATCGATACCATCTCAAATGG
212926 TATCGAT
1 TATCGAT
212933 AATTTTCATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (32 bp):
TATCGATTGGGTATCGATACCATCTCAAATGG
Found at i:213690 original size:23 final size:23
Alignment explanation
Indices: 213634--213763 Score: 127
Period size: 23 Copynumber: 5.6 Consensus size: 23
213624 TATCGAAGTA
* *
213634 CTAAACAGAGAGCACA-TAAGTG
1 CTAAACAGAGAGCACACAAAGCG
* *
213656 CTAGGCAACAGAGAGCACACACAGTG
1 CTA---AACAGAGAGCACACAAAGCG
*
213682 CTAATCAGAGAGCACACAAAGCG
1 CTAAACAGAGAGCACACAAAGCG
* *
213705 CTAATCAGAGACCACACAAAGCG
1 CTAAACAGAGAGCACACAAAGCG
* * *
213728 CTAAACGGAGAGCAAACAAAGTG
1 CTAAACAGAGAGCACACAAAGCG
*
213751 CTAAACGGAGAGC
1 CTAAACAGAGAGC
213764 GCGCTAGTGT
Statistics
Matches: 93, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
22 3 0.03
23 70 0.75
25 13 0.14
26 7 0.08
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.09
Consensus pattern (23 bp):
CTAAACAGAGAGCACACAAAGCG
Found at i:214638 original size:27 final size:26
Alignment explanation
Indices: 214586--214644 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 26
214576 TTATTCAATC
214586 ACACATTATTATCAACTTATAATTAT
1 ACACATTATTATCAACTTATAATTAT
214612 ACACATTATTATCATACTTATAATTAT
1 ACACATTATTATCA-ACTTATAATTAT
214639 ACACAT
1 ACACAT
214645 CATTTTACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 14 0.44
27 18 0.56
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.41
Consensus pattern (26 bp):
ACACATTATTATCAACTTATAATTAT
Found at i:220442 original size:47 final size:47
Alignment explanation
Indices: 220388--220482 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
220378 TTAATCTTAA
220388 GGGTCGTGTGGTGAGGATGGTTTTGAGTTTTGTACTCGTAACGAATC
1 GGGTCGTGTGGTGAGGATGGTTTTGAGTTTTGTACTCGTAACGAATC
220435 GGGTCGTGTGGTGAGGATGGTTTTGAGTTTTGTACTCGTAACGAATC
1 GGGTCGTGTGGTGAGGATGGTTTTGAGTTTTGTACTCGTAACGAATC
220482 G
1 G
220483 TGAAGCGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.17, C:0.11, G:0.37, T:0.36
Consensus pattern (47 bp):
GGGTCGTGTGGTGAGGATGGTTTTGAGTTTTGTACTCGTAACGAATC
Found at i:220858 original size:13 final size:13
Alignment explanation
Indices: 220840--220864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220830 TTAAATTAAC
220840 ATTATATTTTTAT
1 ATTATATTTTTAT
220853 ATTATATTTTTA
1 ATTATATTTTTA
220865 AATAATAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATATTTTTAT
Found at i:227057 original size:29 final size:29
Alignment explanation
Indices: 227003--227059 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
226993 TGGGGTGGGG
*
227003 ATATTATTTTGATAAATAAATTATTTTTT
1 ATATTATTTTGATAAATAAATCATTTTTT
227032 ATATTATTTT-AGTAAA-AAACTCATTTTT
1 ATATTATTTTGA-TAAATAAA-TCATTTTT
227060 CGTAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
ATATTATTTTGATAAATAAATCATTTTTT
Found at i:227104 original size:12 final size:14
Alignment explanation
Indices: 227087--227118 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
227077 TGTTTTAATA
227087 ATTTTTT-AAA-TT
1 ATTTTTTAAAAGTT
227099 ATTTTTTAAAAGTT
1 ATTTTTTAAAAGTT
227113 ATTTTT
1 ATTTTT
227119 AATAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
ATTTTTTAAAAGTT
Found at i:228221 original size:14 final size:15
Alignment explanation
Indices: 228200--228242 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
228190 TCATTTATTG
228200 TATATTATTTTTAAA
1 TATATTATTTTTAAA
228215 TAT-TTATATTTTAAA
1 TATATTAT-TTTTAAA
*
228230 TTTATTATTTTTA
1 TATATTATTTTTA
228243 CATTCATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTATTTTTAAA
Found at i:229761 original size:11 final size:11
Alignment explanation
Indices: 229745--229852 Score: 67
Period size: 11 Copynumber: 10.4 Consensus size: 11
229735 AATAATCTCT
229745 TTAATATTAAA
1 TTAATATTAAA
229756 TTAATA--AAA
1 TTAATATTAAA
*
229765 -CAATATTAACA
1 TTAATATTAA-A
229776 TTAA-ATTAATA
1 TTAATATTAA-A
229787 TTAATATTAAGA
1 TTAATATTAA-A
*
229799 -TAATCACT---
1 TTAAT-ATTAAA
229807 TTAATATTAAA
1 TTAATATTAAA
229818 TTAATA--AAA
1 TTAATATTAAA
229827 -TAATATTAAA
1 TTAATATTAAA
*
229837 ATAAGTATTAAA
1 TTAA-TATTAAA
229849 TTAA
1 TTAA
229853 ATTTAATATT
Statistics
Matches: 76, Mismatches: 7, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
8 11 0.14
9 10 0.13
10 5 0.07
11 30 0.39
12 20 0.26
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:229786 original size:17 final size:17
Alignment explanation
Indices: 229766--229864 Score: 85
Period size: 17 Copynumber: 5.5 Consensus size: 17
229756 TTAATAAAAC
*
229766 AATATTAACATTAAATT
1 AATATTAATATTAAATT
229783 AATATTAATATTAAGA-T
1 AATATTAATATTAA-ATT
229800 AATCACTTTAATATTAAATT
1 AAT-A--TTAATATTAAATT
* *
229820 AATAAAATAATATTAAAAT
1 AAT--ATTAATATTAAATT
229839 AAGTATTAA-ATTAAATTT
1 AA-TATTAATATTAAA-TT
229857 AATATTAA
1 AATATTAA
229865 ACTATTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
17 29 0.43
18 9 0.13
19 14 0.21
20 15 0.22
21 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATTAATATTAAATT
Found at i:229822 original size:20 final size:20
Alignment explanation
Indices: 229732--229822 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 20
229722 AGAAATTTTC
* *
229732 TAAAATAATCTCTTTAATAT
1 TAAATTAATCACTTTAATAT
* *
229752 TAAATTAATAAAACAATATTAACAT
1 TAAATTAAT----CACT-TTAATAT
229777 TAAATTAAT-A--TTAATAT
1 TAAATTAATCACTTTAATAT
229794 TAAGA-TAATCACTTTAATAT
1 TAA-ATTAATCACTTTAATAT
229814 TAAATTAAT
1 TAAATTAAT
229823 AAAATAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
17 13 0.23
18 2 0.04
19 1 0.02
20 23 0.41
24 2 0.04
25 15 0.27
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.41
Consensus pattern (20 bp):
TAAATTAATCACTTTAATAT
Found at i:229871 original size:37 final size:35
Alignment explanation
Indices: 229745--229882 Score: 127
Period size: 37 Copynumber: 3.8 Consensus size: 35
229735 AATAATCTCT
* *
229745 TTAATATTAAATTAATAAAACAATATTAACATTAAA
1 TTAATATTAAA-TATTAAAATAATATTAACATTAAA
* *
229781 TTAATATT-AATATTAAGATAATCACTTTAATATTAAA
1 TTAATATTAAATATTAAAATAAT-A--TTAACATTAAA
**
229818 TTAATAAAATAATATTAAAATAAGTATTAA-ATTAAA
1 TTAATATTA-AATATTAAAATAA-TATTAACATTAAA
*
229854 TTTAATATTAAACTATTAAAATATTATTA
1 -TTAATATTAAA-TATTAAAATAATATTA
229883 TTTTTGGAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
34 9 0.11
35 3 0.04
36 21 0.25
37 37 0.44
39 13 0.15
40 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (35 bp):
TTAATATTAAATATTAAAATAATATTAACATTAAA
Found at i:238284 original size:13 final size:14
Alignment explanation
Indices: 238254--238286 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
238244 ATAATTAGGA
238254 ATTTGGCTCACAAT
1 ATTTGGCTCACAAT
*
238268 ATTTTGCTCAC-AT
1 ATTTGGCTCACAAT
238281 ATTTGG
1 ATTTGG
238287 GAAGAAGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (14 bp):
ATTTGGCTCACAAT
Found at i:241701 original size:3 final size:3
Alignment explanation
Indices: 241689--241732 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
241679 AATAATGTGG
*
241689 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA GAGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA A
241733 TTGGTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:242821 original size:5 final size:5
Alignment explanation
Indices: 242813--242839 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
242803 ATTTGTGTAA
242813 CCTAC CCTAC CCTAC CCTAC CCTAC CC
1 CCTAC CCTAC CCTAC CCTAC CCTAC CC
242840 AAGCGACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.63, G:0.00, T:0.19
Consensus pattern (5 bp):
CCTAC
Found at i:248353 original size:23 final size:23
Alignment explanation
Indices: 248324--248476 Score: 125
Period size: 23 Copynumber: 6.6 Consensus size: 23
248314 GAACACTAGC
*
248324 GTGCTCTCTGTTTAGCAC-GTCT
1 GTGCTCTCTGTTTAGCACTGTGT
248346 CGTGCTCTCTGTTATTAGCACTGTGT
1 -GTGCTCTCTG-T-TTAGCACTGTGT
* * *
248372 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGTTTAGCACTGTGT
* *
248395 GTACTCTCTATTTAGCACTGTGT
1 GTGCTCTCTGTTTAGCACTGTGT
* *
248418 GTGCTCTCTGTTGCCCAGCACT-TAT
1 GTGCTCTCTGTT---TAGCACTGTGT
* *
248443 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGTTTAGCACTGTGT
*
248464 GTACTCTCTGTTT
1 GTGCTCTCTGTTT
248477 GTTCTGTATA
Statistics
Matches: 105, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.13
22 3 0.03
23 48 0.46
24 2 0.02
25 29 0.28
26 9 0.09
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTGTTTAGCACTGTGT
Found at i:248422 original size:71 final size:69
Alignment explanation
Indices: 248327--248472 Score: 188
Period size: 71 Copynumber: 2.1 Consensus size: 69
248317 CACTAGCGTG
* ** *
248327 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGTT-ATTAGCACTGTGTGTGCTCTCTGATTAGTACT
1 CTCTCTATTTAGCACGTCTCGTGCTCTCTGTTGACCAGCACT-TATGTGCTCTCTG-TTAGTACT
248391 TTGTGTA
64 TTG-GTA
* *
248398 CTCTCTATTTAGCACTGTGT-GTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTT
1 CTCTCTATTTAGCAC-GTCTCGTGCTCTCTGTTGACCAGCACTTATGTGCTCTCTGTTAGTACTT
248462 TGGTA
65 TGGTA
248467 CTCTCT
1 CTCTCT
248473 GTTTGTTCTG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
69 9 0.13
70 11 0.16
71 38 0.57
72 9 0.13
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (69 bp):
CTCTCTATTTAGCACGTCTCGTGCTCTCTGTTGACCAGCACTTATGTGCTCTCTGTTAGTACTTT
GGTA
Found at i:255664 original size:23 final size:23
Alignment explanation
Indices: 255571--255662 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
255561 GCTATCTGTT
255571 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
* * * *
255594 ACTAGCACTTTGTATGCTCTCTA
1 ATTAGCACTGTGTGTGCTCTCTG
* * *
255617 ATTAGTACTTTGTGTACTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
* *
255640 TTTAGCACTGTGTGTGCTTTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
255663 TTGCCCAGAA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (23 bp):
ATTAGCACTGTGTGTGCTCTCTG
Done.