Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015195.1 Kokia drynarioides strain JFW-HI SEQ_130239, 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: 163993
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 85 characters in sequence are not A, C, G, or T
Found at i:2476 original size:18 final size:17
Alignment explanation
Indices: 2407--2477 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 17
2397 TTTATTGTTT
2407 AAAAAAAAAGAAAAA-A
1 AAAAAAAAAGAAAAAGA
***
2423 AAGTCGAAAAGAAAAATTGA
1 AA-AAAAAAAGAAAAA--GA
2443 GAAAAAAAAAGAAAAAGA
1 -AAAAAAAAAGAAAAAGA
2461 AAAAAAAAAGACAAAAG
1 AAAAAAAAAGA-AAAAG
2478 TGTGTTTGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.05
17 21 0.49
18 7 0.16
20 11 0.26
21 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.04
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAGA
Found at i:3532 original size:25 final size:23
Alignment explanation
Indices: 3491--3536 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
3481 CCAATTAGGG
3491 AATTATTGTTTAGATTTAATTCA
1 AATTATTGTTTAGATTTAATTCA
*
3514 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
3537 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCA
Found at i:4769 original size:6 final size:6
Alignment explanation
Indices: 4751--4782 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4741 AGTTATTTTC
*
4751 TTATTT TTGTTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
4783 TAAGTTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:6523 original size:16 final size:16
Alignment explanation
Indices: 6502--6535 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6492 AATATTTCAC
* *
6502 AATAAATTTTTTTATT
1 AATAAATATTTGTATT
6518 AATAAATATTTGTATT
1 AATAAATATTTGTATT
6534 AA
1 AA
6536 ATATATAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATAAATATTTGTATT
Found at i:18673 original size:16 final size:16
Alignment explanation
Indices: 18652--18682 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18642 TATGGTTTGG
*
18652 GGATACAGAAGGGTGA
1 GGATACAGAAAGGTGA
18668 GGATACAGAAAGGTG
1 GGATACAGAAAGGTG
18683 CAGAAGTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.42, T:0.13
Consensus pattern (16 bp):
GGATACAGAAAGGTGA
Found at i:22264 original size:15 final size:15
Alignment explanation
Indices: 22240--22269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22230 AATGTAATTT
22240 TAAAAATTTTAAAGG
1 TAAAAATTTTAAAGG
*
22255 TAAAATTTTTAAAGG
1 TAAAAATTTTAAAGG
22270 ATAATCATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (15 bp):
TAAAAATTTTAAAGG
Found at i:25548 original size:19 final size:19
Alignment explanation
Indices: 25526--25570 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
25516 TTTAATTAGG
25526 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
25545 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
25564 ATTTAAT
1 ATTTAAT
25571 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:26369 original size:16 final size:17
Alignment explanation
Indices: 26340--26372 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
26330 TGACACTCCT
26340 ATTTTCTATTTCTTTTA
1 ATTTTCTATTTCTTTTA
26357 ATTTTCT-TTTCTTTTA
1 ATTTTCTATTTCTTTTA
26373 TTATTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTCTATTTCTTTTA
Found at i:28967 original size:12 final size:12
Alignment explanation
Indices: 28950--28975 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28940 ACACTGTTTG
28950 ATGATGATTTTA
1 ATGATGATTTTA
28962 ATGATGATTTTA
1 ATGATGATTTTA
28974 AT
1 AT
28976 TCTTATCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
ATGATGATTTTA
Found at i:29181 original size:5 final size:6
Alignment explanation
Indices: 29163--29198 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
29153 GGCAACCCAA
*
29163 TTATTT TTATTT TTATTT TTATTT TTCTATT TTATT
1 TTATTT TTATTT TTATTT TTATTT TTAT-TT TTATT
29199 ATATGTCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:30715 original size:19 final size:19
Alignment explanation
Indices: 30693--30737 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30683 TTTTATTAGG
30693 ATTTAATATTTAAGATGT-T
1 ATTTAATATTTAA-ATGTGT
* *
30712 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATGTGT
30731 ATTTAAT
1 ATTTAAT
30738 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATGTGT
Found at i:31542 original size:22 final size:21
Alignment explanation
Indices: 31498--31552 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
31488 TGCTGTTTAT
31498 TTTTATTTTGACACTTCTATTTTC
1 TTTTATTTT-A-A-TTCTATTTTC
* *
31522 TATTTCTTTTAATTCTGTTTTC
1 T-TTTATTTTAATTCTATTTTC
31544 TTTTATTTT
1 TTTTATTTT
31553 TATTGTTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.26
22 10 0.37
23 1 0.04
24 2 0.07
25 7 0.26
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTATTTTAATTCTATTTTC
Found at i:32145 original size:29 final size:29
Alignment explanation
Indices: 32103--32174 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
32093 TTAATGCATA
*
32103 GATAATCCCTAATAAATTATAGCTAACAC
1 GATAATCCCTAATAAATTATAACTAACAC
* *
32132 GATAATTCCTAATAAATTGTAACTAACAC
1 GATAATCCCTAATAAATTATAACTAACAC
*
32161 GATAGTCCCTAATA
1 GATAATCCCTAATA
32175 TATACAGAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.29
Consensus pattern (29 bp):
GATAATCCCTAATAAATTATAACTAACAC
Found at i:32341 original size:22 final size:20
Alignment explanation
Indices: 32289--32349 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
32279 GATGTTAACC
*
32289 TAAAATTTTAAATTAAAAAA
1 TAAAATATTAAATTAAAAAA
* *
32309 TAAATTAATTAAATTTTAAAAA
1 TAAAAT-ATTAAA-TTAAAAAA
32331 TAAAAATATTAAAATTAAA
1 T-AAAATATT-AAATTAAA
32350 TCGAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 5 0.16
21 5 0.16
22 15 0.47
23 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAATATTAAATTAAAAAA
Found at i:41852 original size:15 final size:16
Alignment explanation
Indices: 41826--41856 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
41816 TATTTTTTCA
41826 TTTTAATATTTAATTT
1 TTTTAATATTTAATTT
41842 TTTTAAT-TTTAATTT
1 TTTTAATATTTAATTT
41857 AGTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATATTTAATTT
Found at i:46074 original size:16 final size:15
Alignment explanation
Indices: 46031--46075 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
46021 GAAAAAATAA
46031 TTAAGTGTTGAATTT
1 TTAAGTGTTGAATTT
* *
46046 TT-ACTGTTAAATTT
1 TTAAGTGTTGAATTT
46060 TATAAGTGTTGAATTT
1 T-TAAGTGTTGAATTT
46076 ATATTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 11 0.46
15 3 0.12
16 10 0.42
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (15 bp):
TTAAGTGTTGAATTT
Found at i:46088 original size:30 final size:30
Alignment explanation
Indices: 46032--46088 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
46022 AAAAAATAAT
* * *
46032 TAAGTGTTGAATTTTTACTGTTAAATTTTA
1 TAAGTGTTGAATTTATACTATAAAATTTTA
*
46062 TAAGTGTTGAATTTATATTATAAAATT
1 TAAGTGTTGAATTTATACTATAAAATT
46089 ATTTGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (30 bp):
TAAGTGTTGAATTTATACTATAAAATTTTA
Found at i:47847 original size:60 final size:59
Alignment explanation
Indices: 47623--48338 Score: 508
Period size: 60 Copynumber: 12.0 Consensus size: 59
47613 AATATTTTGG
* * *
47623 GGTGTTGGCCATGCAATGGTCGACACCCCTTTTTTGTCAGAAAAAAAAAATTTAAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACCCC-CTTTTCTC-G--AAAAAAAATTT-AAATTTTTTT
* **
47687 -GTGTTGGCCAT-CAAATGGTCGACA-CCCCTTTTCTCGTAAAAAAAATTGT--ATTTTTGG
1 GGTGTTGGCCATGC-AATGGCCGACACCCCCTTTTCTCG-AAAAAAAATT-TAAATTTTTTT
*
47744 GTGTGTTGGCCATTGC-ATGGCCGACA-CCCCTTTT-TTGAGAAAAAAATTTCAAATTTTTTT
1 G-GTGTTGGCCA-TGCAATGGCCGACACCCCCTTTTCTCGA-AAAAAAATTT-AAATTTTTTT
* * * * ** *
47804 TGTGTTAGCCATGCAATGGTCGACACCCCCTGTTCTCGAAAAAAAA-TTGCA-TTTTTG
1 GGTGTTGGCCATGCAATGGCCGACACCCCCTTTTCTCGAAAAAAAATTTAAATTTTTTT
* * *
47861 GGTGTTGGCTATTGC-ATGGCCGACACCCCATTTT-TGAGAAAAAAAATTTCAAAATTTTTTT
1 GGTGTTGGCCA-TGCAATGGCCGACACCCCCTTTTCT-CGAAAAAAAATTT--AAATTTTTTT
* * * * * *
47922 -GTGTTGGCCAT-CAAATGGTCGACACTCCTTTTTCTTGGAAAAAAAA-TTATA-TTTTTG
1 GGTGTTGGCCATGC-AATGGCCGACACCCCCTTTTC-TCGAAAAAAAATTTAAATTTTTTT
* * * *
47979 GGTGTTGACCATTGC-ATGGCCGACACCCTCTTTTCTCGAGAAAAAATTTCAAAATTTTTT
1 GGTGTTGGCCA-TGCAATGGCCGACACCCCCTTTTCTCGAAAAAAAATTT-AAATTTTTTT
* * ** *
48039 GGTGTTGGCCAT-CAAATGGCCGACACCCACTTTTCTCGAAAAAAAAATTGTA-TTTTTG
1 GGTGTTGGCCATGC-AATGGCCGACACCCCCTTTTCTCGAAAAAAAATTTAAATTTTTTT
* * * * *
48097 GGTGTTGGCCATGTAATTGCCAACA-CCCCTTGTTATCGGATAAAAAAATTACAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACCCCCTT-TTCTC-GA-AAAAAAATT-TAAATTTTTTT
* * * *
48159 GGTGTTGGCCATGCAATGGCCGACACCCCCCTTTTCTTG--GATAAATTT--TTTTTTTT
1 GGTGTTGGCCATGCAATGGCCGACA-CCCCCTTTTCTCGAAAAAAAATTTAAATTTTTTT
* * * * * *
48215 AGTGTTGGTCATGCAATGGTCGACACACCCTGTTCTCGGATAAAAAAATTGCAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACCCCCTTTTCTC-GA-AAAAAAATT-TAAATTTTTTT
* ** * *
48277 GGTGTTGGTCATGCAATGATCGACACTCCCTTTTCTTGGATAAAAAAATTGTAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACCCCCTTTTC-TCGA-AAAAAAATT-TAAATTTTTTT
48339 TATCGTGCAA
Statistics
Matches: 520, Mismatches: 85, Indels: 96
0.74 0.12 0.14
Matches are distributed among these distances:
55 9 0.02
56 31 0.06
57 65 0.12
58 81 0.16
59 77 0.15
60 106 0.20
61 25 0.05
62 94 0.18
63 26 0.05
64 6 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (59 bp):
GGTGTTGGCCATGCAATGGCCGACACCCCCTTTTCTCGAAAAAAAATTTAAATTTTTTT
Found at i:48166 original size:62 final size:62
Alignment explanation
Indices: 47623--48338 Score: 388
Period size: 62 Copynumber: 12.0 Consensus size: 62
47613 AATATTTTGG
* * * * * **
47623 GGTGTTGGCCATGCAATGGTCGACAC-CCCTTTTTTGTCAGAAAAAAAAAATTTAAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCAACACACCC--TTTTCTC-GGATAAAAAAATTGCAAATTTTTTT
* * * * **
47687 -GTGTTGGCCAT-CAAATGGTCGACAC-CCCTTTTCTCGTA-AAAAAAATTG--TATTTTTGG
1 GGTGTTGGCCATGC-AATGGCCAACACACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* * * *
47744 GTGTGTTGGCCATTGC-ATGGCCGACAC-CCCTTTT-T-TGAGAAAAAAATTTCAAATTTTTTT
1 G-GTGTTGGCCA-TGCAATGGCCAACACACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* * * * * * *
47804 TGTGTTAGCCATGCAATGGTCGACACCCCCTGTTCTC-GA-AAAAAAATTGC--A-TTTTTG
1 GGTGTTGGCCATGCAATGGCCAACACACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* * *
47861 GGTGTTGGCTATTGC-ATGGCCGACAC-CCCATTTT-T-GAGA-AAAAAAATTTCAAAATTTTTT
1 GGTGTTGGCCA-TGCAATGGCCAACACACCC-TTTTCTCG-GATAAAAAAATTGC-AAATTTTTT
47921 T
62 T
* * * * * * *
47922 -GTGTTGGCCAT-CAAATGGTCGACACTCCTTTTTCTTGGA-AAAAAAATT--ATA-TTTTTG
1 GGTGTTGGCCATGC-AATGGCCAACACACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* * * * *
47979 GGTGTTGACCATTGC-ATGGCCGACAC-CCTCTTTTCTC-GA-GAAAAAATTTCAAAATTTTTT
1 GGTGTTGGCCA-TGCAATGGCCAACACACC-CTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* * * *
48039 GGTGTTGGCCAT-CAAATGGCCGACAC-CCACTTTTCTC-GAAAAAAAAATTG--TA-TTTTTG
1 GGTGTTGGCCATGC-AATGGCCAACACACC-CTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* * * *
48097 GGTGTTGGCCATGTAATTGCCAACAC-CCCTTGTTATCGGATAAAAAAATTACAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCAACACACCCTT-TTCTCGGATAAAAAAATTGCAAATTTTTTT
* * * **
48159 GGTGTTGGCCATGCAATGGCCGACACCCCCCTTTTCTTGGAT----AAATT---TTTTTTTTT
1 GGTGTTGGCCATGCAATGGCCAACA-CACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* * * * *
48215 AGTGTTGGTCATGCAATGGTCGACACACCCTGTTCTCGGATAAAAAAATTGCAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCAACACACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
* ** * * * *
48277 GGTGTTGGTCATGCAATGATCGACACTCCCTTTTCTTGGATAAAAAAATTGTAAATTTTTTT
1 GGTGTTGGCCATGCAATGGCCAACACACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
48339 TATCGTGCAA
Statistics
Matches: 529, Mismatches: 73, Indels: 102
0.75 0.10 0.14
Matches are distributed among these distances:
55 13 0.02
56 33 0.06
57 65 0.12
58 79 0.15
59 82 0.16
60 88 0.17
61 38 0.07
62 92 0.17
63 34 0.06
64 5 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (62 bp):
GGTGTTGGCCATGCAATGGCCAACACACCCTTTTCTCGGATAAAAAAATTGCAAATTTTTTT
Found at i:48213 original size:118 final size:114
Alignment explanation
Indices: 47615--48314 Score: 632
Period size: 118 Copynumber: 5.9 Consensus size: 114
47605 TTGAAAAAAA
* * * *
47615 TATTTTGGGGTGTTGGCCA-TGCAATGGTCGACACCCCTTTTTTGTCAGAAAAAAAAAATTTAAA
1 TATTTTTGGGTGTTGGCCATTGC-ATGGCCGACACCCC--TTTT-TC-G-GAAAAAAAATTTCAA
*
47679 ATTTTTTT-GTGTTGGCCATCAAATGGTCGACA-CCCCTTTTCTCGTAAAAAAAATTG
60 ATTTTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTTTTCT--T-GAAAAAATTG
*
47735 TATTTTTGGGTGTGTTGGCCATTGCATGGCCGACACCCCTTTTT-TGAGAAAAAAATTTCAAATT
1 TATTTTT-GG-GTGTTGGCCATTGCATGGCCGACACCCCTTTTTCGGA-AAAAAAATTTCAAATT
* * * *
47799 TTTTTTGTGTTAGCCATGC-AATGGTCGACACCCCCTGTTCTCGAAAAAAAATTG
63 TTTTTGGTGTTGGCCAT-CAAATGGTCGACACCCCCTTTTCTTG--AAAAAATTG
* *
47853 CATTTTTGGGTGTTGGCTATTGCATGGCCGACACCCCATTTTT-GAGAAAAAAAATTTCAAAATT
1 TATTTTTGGGTGTTGGCCATTGCATGGCCGACACCCC-TTTTTCG-GAAAAAAAATTTC-AAATT
* * *
47917 TTTTT-GTGTTGGCCATCAAATGGTCGACACTCCTTTTTCTTGGAAAAAAAATTA
63 TTTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTTTTCTT-G--AAAAAATTG
* * *
47971 TATTTTTGGGTGTTGACCATTGCATGGCCGACACCCTCTTTTCTC-GAGAAAAAATTTCAAAATT
1 TATTTTTGGGTGTTGGCCATTGCATGGCCGACACCC-CTTTT-TCGGAAAAAAAATTTCAAATTT
* * *
48035 TTTTGGTGTTGGCCATCAAATGGCCGACACCCACTTTTCTCGAAAAAAAAATTG
64 TTTTGGTGTTGGCCATCAAATGGTCGACACCCCCTTTTCTTG---AAAAAATTG
* * * *
48089 TATTTTTGGGTGTTGGCCA-TGTAATTGCCAACACCCCTTGTTATCGGATAAAAAAATTACAAAT
1 TATTTTTGGGTGTTGGCCATTG-CATGGCCGACACCCCTT-TT-TCGGA-AAAAAAATTTCAAAT
* * * *
48153 TTTTTTGGTGTTGGCCATGC-AATGGCCGACACCCCCCTTTTCTTGGATAAATTT
62 TTTTTTGGTGTTGGCCAT-CAAATGGTCGACA-CCCCCTTTTCTTGAAAAAATTG
* ** * * * *
48207 TTTTTTTTAGTGTTGGTCA-TGCAATGGTCGACACACCCTGTTCTCGGATAAAAAAATTGCAAAT
1 TATTTTTGGGTGTTGGCCATTGC-ATGGCCGACAC-CCCT-TTTTCGGA-AAAAAAATTTCAAAT
* * *
48271 TTTTTTGGTGTTGGTCATGC-AATGATCGACACTCCCTTTTCTTG
62 TTTTTTGGTGTTGGCCAT-CAAATGGTCGACACCCCCTTTTCTTG
48315 GATAAAAAAA
Statistics
Matches: 496, Mismatches: 56, Indels: 59
0.81 0.09 0.10
Matches are distributed among these distances:
116 29 0.06
117 94 0.19
118 261 0.53
119 20 0.04
120 52 0.10
121 14 0.03
122 23 0.05
123 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (114 bp):
TATTTTTGGGTGTTGGCCATTGCATGGCCGACACCCCTTTTTCGGAAAAAAAATTTCAAATTTTT
TTGGTGTTGGCCATCAAATGGTCGACACCCCCTTTTCTTGAAAAAATTG
Found at i:57537 original size:45 final size:45
Alignment explanation
Indices: 57487--57622 Score: 245
Period size: 45 Copynumber: 3.0 Consensus size: 45
57477 AAAAAGGTTG
*
57487 ATTGCCATTCATTACTTAAAATGTACACAATTTATTTTATTTTAT
1 ATTGCCATTCATTACTTCAAATGTACACAATTTATTTTATTTTAT
*
57532 ATTGCCATTCATTAGTTCAAATGTACACAATTTATTTTATTTTAT
1 ATTGCCATTCATTACTTCAAATGTACACAATTTATTTTATTTTAT
*
57577 ATTTCCATTCATTACTTCAAATGTACACAATTTATTTTATTTTAT
1 ATTGCCATTCATTACTTCAAATGTACACAATTTATTTTATTTTAT
57622 A
1 A
57623 CAACCATTCA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.49
Consensus pattern (45 bp):
ATTGCCATTCATTACTTCAAATGTACACAATTTATTTTATTTTAT
Found at i:62926 original size:28 final size:27
Alignment explanation
Indices: 62880--62939 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
62870 TTTTATATAT
* * *
62880 TTTTTGAAATTTTAGAATTTTTTTAAA
1 TTTTTGAAATTTAAAAATTATTTTAAA
*
62907 TATTTTGAAATTTAAAAATTATTTTGAA
1 T-TTTTGAAATTTAAAAATTATTTTAAA
62935 TTTTT
1 TTTTT
62940 CGAGTATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTTGAAATTTAAAAATTATTTTAAA
Found at i:64736 original size:25 final size:26
Alignment explanation
Indices: 64683--64738 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
64673 GAAAGGGTAC
*** *
64683 ATTTTAAATTTTCAATATTTTTTTTA
1 ATTTTAAATTTTCAATATTAAATTGA
64709 ATTTTAAA-TTTCAATATTAAATTGA
1 ATTTTAAATTTTCAATATTAAATTGA
64734 ATTTT
1 ATTTT
64739 GATTATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTAAATTTTCAATATTAAATTGA
Found at i:67479 original size:43 final size:43
Alignment explanation
Indices: 67412--67551 Score: 190
Period size: 43 Copynumber: 3.3 Consensus size: 43
67402 CACTAAAGAC
* * *
67412 CAAACACCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCCA
1 CAAACGCCGCTGAAGAACATGGTCTTTAGCGGCGCTTTCCCCA
* *
67455 CAAATGCCGCTGAAGAACATGGTCTTTAGCGACGCTTTCCCCA
1 CAAACGCCGCTGAAGAACATGGTCTTTAGCGGCGCTTTCCCCA
* ** *
67498 CAAACGCCACTGAAGAACATGACCTTTAGCGGCGCTTTCTCCA
1 CAAACGCCGCTGAAGAACATGGTCTTTAGCGGCGCTTTCCCCA
*
67541 CAAACGTCGCT
1 CAAACGCCGCT
67552 AAAATTAACA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (43 bp):
CAAACGCCGCTGAAGAACATGGTCTTTAGCGGCGCTTTCCCCA
Found at i:70287 original size:41 final size:41
Alignment explanation
Indices: 70156--70290 Score: 146
Period size: 41 Copynumber: 3.3 Consensus size: 41
70146 AGAAAACGCT
* * * * ***
70156 GCTATTGCT-TAACTTTTAGCAGCGCTTTCCCATAAACACC
1 GCTAATGCTGTAACCTTTAGCGGCACTTTCCCATAAGTGCC
* * * * *
70196 GCTAATTCTATGACCTTTAACGGCACTTTCCCATCAGTGCC
1 GCTAATGCTGTAACCTTTAGCGGCACTTTCCCATAAGTGCC
*
70237 GCTAATGCTGTAACCTTTAGCGGCTCTTTCCCATAAGTGCC
1 GCTAATGCTGTAACCTTTAGCGGCACTTTCCCATAAGTGCC
70278 GCTAATGCTGTAA
1 GCTAATGCTGTAA
70291 AAGCGCCGCT
Statistics
Matches: 77, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 7 0.09
41 70 0.91
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (41 bp):
GCTAATGCTGTAACCTTTAGCGGCACTTTCCCATAAGTGCC
Found at i:74127 original size:17 final size:17
Alignment explanation
Indices: 74097--74130 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
74087 ATTTAAGTCC
**
74097 TTTAAATTTTTAAAAAT
1 TTTAAATTAATAAAAAT
74114 TTTAAATTAATAAAAAT
1 TTTAAATTAATAAAAAT
74131 AAAATTACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAATAAAAAT
Found at i:78182 original size:25 final size:26
Alignment explanation
Indices: 78146--78207 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
78136 ACATATGTTC
* *
78146 TCAAAATTTTA-CTAGGGGAAAATCG
1 TCAAAATTTTACCAAGGGGAAAATCA
* *
78171 TTAAAATTTTACCAAGGGTAAAATCA
1 TCAAAATTTTACCAAGGGGAAAATCA
78197 TCAAAATTTTA
1 TCAAAATTTTA
78208 TTGGGGATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 10 0.32
26 21 0.68
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGGAAAATCA
Found at i:79122 original size:14 final size:13
Alignment explanation
Indices: 79098--79140 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
79088 AGGACTTCTA
79098 TTTTCTATTTTAAT
1 TTTTCT-TTTTAAT
79112 TTTTGCTTTTTAAT
1 TTTT-CTTTTTAAT
*
79126 TTTTCTTATTAAT
1 TTTTCTTTTTAAT
79139 TT
1 TT
79141 ATTTTTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.37
14 15 0.56
15 2 0.07
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTCTTTTTAAT
Found at i:79745 original size:116 final size:116
Alignment explanation
Indices: 79604--79836 Score: 466
Period size: 116 Copynumber: 2.0 Consensus size: 116
79594 TGTAATTTAT
79604 TATATTTTATACACCGAAAAATATATATTTTAAATATATTATTTTTGTTTAATTTACACGGTTCT
1 TATATTTTATACACCGAAAAATATATATTTTAAATATATTATTTTTGTTTAATTTACACGGTTCT
79669 TGGATTATGTTATTACTGTGAAAAATTAGATGAAAATAATAAAGTATGTAA
66 TGGATTATGTTATTACTGTGAAAAATTAGATGAAAATAATAAAGTATGTAA
79720 TATATTTTATACACCGAAAAATATATATTTTAAATATATTATTTTTGTTTAATTTACACGGTTCT
1 TATATTTTATACACCGAAAAATATATATTTTAAATATATTATTTTTGTTTAATTTACACGGTTCT
79785 TGGATTATGTTATTACTGTGAAAAATTAGATGAAAATAATAAAGTATGTAA
66 TGGATTATGTTATTACTGTGAAAAATTAGATGAAAATAATAAAGTATGTAA
79836 T
1 T
79837 GATTTTTGTC
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.43
Consensus pattern (116 bp):
TATATTTTATACACCGAAAAATATATATTTTAAATATATTATTTTTGTTTAATTTACACGGTTCT
TGGATTATGTTATTACTGTGAAAAATTAGATGAAAATAATAAAGTATGTAA
Found at i:80103 original size:37 final size:36
Alignment explanation
Indices: 80062--80136 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
80052 GATATCGTAC
80062 ATATTGCATT-TATTATTAT-TAATTAATTTTAAATCAT
1 ATATTGCATTAT-TTATTATAT-ATTAATTTTAAAT-AT
* *
80099 ATATTTCATTATTTATTATATATTATTTTTAAATAT
1 ATATTGCATTATTTATTATATATTAATTTTAAATAT
80135 AT
1 AT
80137 TTTTATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 4 0.12
37 28 0.82
38 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (36 bp):
ATATTGCATTATTTATTATATATTAATTTTAAATAT
Found at i:80135 original size:34 final size:33
Alignment explanation
Indices: 80072--80162 Score: 87
Period size: 34 Copynumber: 2.6 Consensus size: 33
80062 ATATTGCATT
* *
80072 TATTATTAT-TAATTAATTTTAAATCATATATTTCA
1 TATT-TTATATAATTATTTTTAAAT-ATAT-TTTTA
80107 T-TATTTATTATATATTATTTTTAAATATATTTTTA
1 TAT-TTTA-TATA-ATTATTTTTAAATATATTTTTA
80142 TATTTTATATACATTATTTTT
1 TATTTTATATA-ATTATTTTT
80163 TGACGCATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
34 17 0.35
35 12 0.25
36 7 0.15
37 12 0.25
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (33 bp):
TATTTTATATAATTATTTTTAAATATATTTTTA
Found at i:81580 original size:48 final size:48
Alignment explanation
Indices: 81528--81624 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
81518 ATATTACTAT
81528 AATCAAATATTAAAACAAACATAAATGCACTTAAGAATAAATTCAATA
1 AATCAAATATTAAAACAAACATAAATGCACTTAAGAATAAATTCAATA
81576 AATCAAATATTAAAACAAACATAAATGCACTTAAGAATAAATTCAATA
1 AATCAAATATTAAAACAAACATAAATGCACTTAAGAATAAATTCAATA
81624 A
1 A
81625 TAATTTTATG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (48 bp):
AATCAAATATTAAAACAAACATAAATGCACTTAAGAATAAATTCAATA
Found at i:85260 original size:6 final size:6
Alignment explanation
Indices: 85237--85304 Score: 70
Period size: 6 Copynumber: 11.8 Consensus size: 6
85227 GCTTCATCGT
* * *
85237 CATCAT CATCAT CATCAC CATCA- C--CAC CACCAC CATCAC CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
* *
85282 CATCAC CACCAC CACCAC CATCA
1 CATCAC CATCAC CATCAC CATCA
85305 AAAAGGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 51 0.93
ACGTcount: A:0.34, C:0.51, G:0.00, T:0.15
Consensus pattern (6 bp):
CATCAC
Found at i:85264 original size:9 final size:9
Alignment explanation
Indices: 85246--85304 Score: 64
Period size: 9 Copynumber: 6.6 Consensus size: 9
85236 TCATCATCAT
*
85246 CATCATCAC
1 CATCACCAC
85255 CATCACCAC
1 CATCACCAC
* *
85264 CACCACCAT
1 CATCACCAC
* *
85273 CACCATCAC
1 CATCACCAC
85282 CATCACCAC
1 CATCACCAC
*
85291 CACCACCAC
1 CATCACCAC
85300 CATCA
1 CATCA
85305 AAAAGGTCAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.34, C:0.54, G:0.00, T:0.12
Consensus pattern (9 bp):
CATCACCAC
Found at i:85275 original size:21 final size:21
Alignment explanation
Indices: 85249--85298 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
85239 TCATCATCAT
85249 CATCACCATCACCACCACCAC
1 CATCACCATCACCACCACCAC
*
85270 CATCACCATCACCATCACCAC
1 CATCACCATCACCACCACCAC
*
85291 CACCACCA
1 CATCACCA
85299 CCATCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.56, G:0.00, T:0.10
Consensus pattern (21 bp):
CATCACCATCACCACCACCAC
Found at i:85280 original size:27 final size:27
Alignment explanation
Indices: 85243--85298 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
85233 TCGTCATCAT
*
85243 CATCATCATCACCATCACCACCACCAC
1 CATCACCATCACCATCACCACCACCAC
85270 CATCACCATCACCATCACCACCACCAC
1 CATCACCATCACCATCACCACCACCAC
85297 CA
1 CA
85299 CCATCAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.54, G:0.00, T:0.12
Consensus pattern (27 bp):
CATCACCATCACCATCACCACCACCAC
Found at i:85321 original size:3 final size:3
Alignment explanation
Indices: 85252--85301 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
85242 TCATCATCAT
* * * *
85252 CAC CAT CAC CAC CAC CAC CAT CAC CAT CAC CAT CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
85300 CA
1 CA
85302 TCAAAAAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.58, G:0.00, T:0.08
Consensus pattern (3 bp):
CAC
Found at i:85329 original size:24 final size:24
Alignment explanation
Indices: 85288--85333 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
85278 TCACCATCAC
85288 CACCACCACCACCATCAAAAAGGT
1 CACCACCACCACCATCAAAAAGGT
85312 CACCACCACCACCATCAAAAAG
1 CACCACCACCACCATCAAAAAG
85334 CTNNNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.43, G:0.07, T:0.07
Consensus pattern (24 bp):
CACCACCACCACCATCAAAAAGGT
Found at i:88741 original size:2 final size:2
Alignment explanation
Indices: 88729--88768 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
88719 CAATGTTTTG
*
88729 AT AT GT 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
88769 GTGTGTGTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101355 original size:52 final size:52
Alignment explanation
Indices: 101279--101423 Score: 227
Period size: 52 Copynumber: 2.8 Consensus size: 52
101269 TTGTTTCGTA
* *
101279 AAGGAATTCATATACTCATGATGACACTTAGTCATCGGACCTTATAACCCGTG
1 AAGG-ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAACCCGTG
* * *
101332 AAGGATTCATGTACTCACGATGACACTTAGTTATCAGACCTTATAATCCGTG
1 AAGGATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAACCCGTG
*
101384 AAGGATTCATGTACTCACGATGACACTTAATCATCGGACC
1 AAGGATTCATGTACTCACGATGACACTTAGTCATCGGACC
101424 CTTTTTCATT
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 80 0.95
53 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (52 bp):
AAGGATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAACCCGTG
Found at i:102318 original size:20 final size:21
Alignment explanation
Indices: 102275--102318 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
102265 ACTTTCATCA
* *
102275 TTAAGCTTTAATTAAACATTT
1 TTAACCTTTAATTAAACATAT
*
102296 TTAACCTTT-ATTAAACCTAT
1 TTAACCTTTAATTAAACATAT
102316 TTA
1 TTA
102319 TAATCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAACCTTTAATTAAACATAT
Found at i:103280 original size:18 final size:18
Alignment explanation
Indices: 103257--103292 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
103247 ACTGTGAACT
103257 AATCACAATTCAATTCAA
1 AATCACAATTCAATTCAA
103275 AATCACAATTCAATTCAA
1 AATCACAATTCAATTCAA
103293 CATTTGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (18 bp):
AATCACAATTCAATTCAA
Found at i:106155 original size:17 final size:17
Alignment explanation
Indices: 106133--106167 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
106123 TTTGGCTGGT
106133 AATAAGAGTTTGTACTC
1 AATAAGAGTTTGTACTC
106150 AATAAGAGTTTGTACTC
1 AATAAGAGTTTGTACTC
106167 A
1 A
106168 TTGATAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (17 bp):
AATAAGAGTTTGTACTC
Found at i:113641 original size:6 final size:6
Alignment explanation
Indices: 113630--113656 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
113620 TCGTATTTAA
113630 AATATT AATATT AATATT AATATT AAT
1 AATATT AATATT AATATT AATATT AAT
113657 TTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:116127 original size:4 final size:4
Alignment explanation
Indices: 116118--116169 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
116108 AATAAACGGC
* * *
116118 AAAG AAAG AAAG AAAAG AAAG AAAG AAAG GAAG AAGG AGAGG AAAG AAAG
1 AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG
116168 AA
1 AA
116170 GAAGGAGAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:116142 original size:21 final size:21
Alignment explanation
Indices: 116119--116183 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
116109 ATAAACGGCA
116119 AAGAAAGAAAGAAA-AGAAAGA
1 AAGAAAGAAAGAAAGAG-AAGA
* * *
116140 AAGAAAGGAAGAAGGAGAGGA
1 AAGAAAGAAAGAAAGAGAAGA
* *
116161 AAGAAAG-AAGAAGGAGAGGA
1 AAGAAAGAAAGAAAGAGAAGA
116181 AAG
1 AAG
116184 GTAATGTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 16 0.40
21 22 0.55
22 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAAGAAAGAGAAGA
Found at i:116151 original size:25 final size:25
Alignment explanation
Indices: 116118--116169 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
116108 AATAAACGGC
116118 AAAGAAAGAAAGAAAAGAAAGAAAG
1 AAAGAAAGAAAGAAAAGAAAGAAAG
* * * *
116143 AAAGGAAGAAGGAGAGGAAAGAAAG
1 AAAGAAAGAAAGAAAAGAAAGAAAG
116168 AA
1 AA
116170 GAAGGAGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (25 bp):
AAAGAAAGAAAGAAAAGAAAGAAAG
Found at i:116172 original size:20 final size:20
Alignment explanation
Indices: 116121--116183 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
116111 AAACGGCAAA
*
116121 GAAAGAAAGAA-AA-GA-AA
1 GAAAGAAAGAAGAAGGAGAG
116138 GAAAGAAAGGAAGAAGGAGAG
1 GAAAGAAA-GAAGAAGGAGAG
116159 GAAAGAAAGAAGAAGGAGAG
1 GAAAGAAAGAAGAAGGAGAG
116179 GAAAG
1 GAAAG
116184 GTAATGTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 8 0.20
18 3 0.07
19 2 0.05
20 19 0.46
21 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAAGAAGGAGAG
Found at i:130287 original size:5 final size:5
Alignment explanation
Indices: 130277--130302 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
130267 TTTTATATAT
130277 TCATG TCATG TCATG TCATG TCATG T
1 TCATG TCATG TCATG TCATG TCATG T
130303 GCAGCTTCAG
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:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TCATG
Found at i:132518 original size:21 final size:21
Alignment explanation
Indices: 132492--132532 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
132482 CAATGATAAG
*
132492 ATTATTA-AAGATATTATCAAA
1 ATTATTAGAA-ATATCATCAAA
132513 ATTATTAGAAATATCATCAA
1 ATTATTAGAAATATCATCAA
132533 CATATCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (21 bp):
ATTATTAGAAATATCATCAAA
Found at i:139667 original size:20 final size:20
Alignment explanation
Indices: 139617--139666 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
139607 CAAAAAATAA
*
139617 TTTCTGAAAAATGACTCATT
1 TTTCTGAAAAATGACTCACT
*
139637 TTTTTGAAAAATGACTCACT
1 TTTCTGAAAAATGACTCACT
139657 TTTCT-AAAAA
1 TTTCTGAAAAA
139667 AAGTTATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (20 bp):
TTTCTGAAAAATGACTCACT
Found at i:144244 original size:16 final size:16
Alignment explanation
Indices: 144225--144255 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
144215 TAAATAATTT
*
144225 TAAATTTTTTAAGTTA
1 TAAATATTTTAAGTTA
144241 TAAATATTTTAAGTT
1 TAAATATTTTAAGTT
144256 TTAATTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TAAATATTTTAAGTTA
Found at i:144821 original size:27 final size:25
Alignment explanation
Indices: 144786--144835 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
144776 ATAATATAAT
144786 AATATTTATTAT-ATTAATACTTATCA
1 AATATTTA-TATCATTAATA-TTATCA
144812 AATATATTATATCATTAATATTAT
1 AATAT-TTATATCATTAATATTAT
144836 ATCACATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATTTATATCATTAATATTATCA
Found at i:145497 original size:3 final size:3
Alignment explanation
Indices: 145491--145532 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
145481 ACAACAGAAG
145491 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
145533 GTGAAGAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:146905 original size:14 final size:12
Alignment explanation
Indices: 146872--146903 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
146862 ATCAAGAATA
*
146872 CATATACACACG
1 CATATATACACG
146884 CATATATACACG
1 CATATATACACG
146896 CATATATA
1 CATATATA
146904 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (12 bp):
CATATATACACG
Found at i:150240 original size:23 final size:23
Alignment explanation
Indices: 150212--150255 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
150202 TTCTGCCAAA
*
150212 TTTTATTTATTATTAATATAATT
1 TTTTATTTAATATTAATATAATT
*
150235 TTTTATTTAATATTAGTATAA
1 TTTTATTTAATATTAATATAA
150256 ATACTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTATTTAATATTAATATAATT
Found at i:156710 original size:13 final size:14
Alignment explanation
Indices: 156679--156729 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
156669 AATTAATTAA
* *
156679 TTTAATATTTTAAAA
1 TTTAA-ATTTTATAT
156694 TTTAAATTTT-TAT
1 TTTAAATTTTATAT
*
156707 TTTATATTTTATAT
1 TTTAAATTTTATAT
156721 TTTCAAATT
1 TTT-AAATT
156730 ATCTTTAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 10 0.33
14 11 0.37
15 9 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAAATTTTATAT
Found at i:162785 original size:34 final size:34
Alignment explanation
Indices: 162725--162801 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
162715 CCTAATCAGC
* * *
162725 TTAAATTTATTTTAAAATTAAGTTTATTCTAAAT
1 TTAAATTTATTTGAAAATTAAATTTATTATAAAT
*
162759 TTAAATTT-TGTTGAAATTTAAATTTATTATAAAT
1 TTAAATTTAT-TTGAAAATTAAATTTATTATAAAT
162793 TTAAATTTA
1 TTAAATTTA
162802 AAATTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTATTTGAAAATTAAATTTATTATAAAT
Found at i:162811 original size:17 final size:17
Alignment explanation
Indices: 162725--162801 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
162715 CCTAATCAGC
* *
162725 TTAAATTTATTTTAAAA
1 TTAAATTTATTATAAAT
* *
162742 TTAAGTTTATTCTAAAT
1 TTAAATTTATTATAAAT
162759 TTAAATTT-TGT-TGAAAT
1 TTAAATTTAT-TAT-AAAT
162776 TTAAATTTATTATAAAT
1 TTAAATTTATTATAAAT
162793 TTAAATTTA
1 TTAAATTTA
162802 AAATTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
16 2 0.04
17 48 0.92
18 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTATAAAT
Done.