Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015211.1 Kokia drynarioides strain JFW-HI SEQ_130255, 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: 35982
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:7642 original size:141 final size:141
Alignment explanation
Indices: 7387--7645 Score: 299
Period size: 141 Copynumber: 1.8 Consensus size: 141
7377 TTTTTTTTTT
* * ** *
7387 AAAAGCTTGAAATAATATGAAATAAAAAATACAAATGTGCTTAGAAGAGGAATCAAACTTAAGAC
1 AAAAGCTTGAAACAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATCAAACTCAAGAC
* * * * *
7452 TCAATGATAAATCACTATTATTTAAACATCTAATTAGAGAAGTTAATGTGTTATATACAGTAATT
66 TCAATGAAAAATCACTAATATTTAAACATCTAACTAAAGAAGCTAATGTGTTATATACAGTAATT
7517 AAATATAAAAG
131 AAATATAAAAG
* *
7528 AAAAGCTTGAAACAACATGAAATAAAAAATGCAAATGTGAGTAGGAA-AGGAATCTAAC-CAGAG
1 AAAAGCTTGAAACAACATGAAATAAAAAATACAAATGTGAGTA-GAAGAGGAATCAAACTCA-AG
* * * * * * *
7591 ACT-GATGACAAAATCATTAATATTTAACCATTTGACTAAAGGAGCTGATGTGTTA
64 ACTCAATGA-AAAATCACTAATATTTAAACATCTAACTAAAGAAGCTAATGTGTTA
7646 AAAGAGTTAG
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
140 5 0.05
141 88 0.92
142 3 0.03
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (141 bp):
AAAAGCTTGAAACAACATGAAATAAAAAATACAAATGTGAGTAGAAGAGGAATCAAACTCAAGAC
TCAATGAAAAATCACTAATATTTAAACATCTAACTAAAGAAGCTAATGTGTTATATACAGTAATT
AAATATAAAAG
Found at i:9214 original size:2 final size:2
Alignment explanation
Indices: 9207--9247 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9197 ATGAAAGTTC
9207 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
9248 ACCACAGTCA
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:10231 original size:31 final size:31
Alignment explanation
Indices: 10196--10262 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
10186 TAACAACCCT
* *
10196 GTGACTTAAAT-AAAAGTTTTTGAATAGTTCA
1 GTGACTTAAATGAAAA-CTTTCGAATAGTTCA
10227 GTGACTTAAATGAAAACTTTCGAATAGTTCA
1 GTGACTTAAATGAAAACTTTCGAATAGTTCA
*
10258 ATGAC
1 GTGAC
10263 CAACTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (31 bp):
GTGACTTAAATGAAAACTTTCGAATAGTTCA
Found at i:19735 original size:13 final size:14
Alignment explanation
Indices: 19713--19741 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19703 TCAACTTCTG
19713 AAAAGAAAAAAAGA
1 AAAAGAAAAAAAGA
19727 AAAAG-AAAAAAGA
1 AAAAGAAAAAAAGA
19740 AA
1 AA
19742 TAGCAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:24122 original size:21 final size:22
Alignment explanation
Indices: 24075--24116 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
24065 TTTTTAATAT
24075 AATTATTATAAATTACTAAAAA
1 AATTATTATAAATTACTAAAAA
*
24097 AATTA-TATAAATTATTAAAA
1 AATTATTATAAATTACTAAAA
24117 GTATTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTATTATAAATTACTAAAAA
Found at i:24303 original size:19 final size:18
Alignment explanation
Indices: 24279--24317 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
24269 AAATAATTCA
24279 AAAAATAATAGAAAATTAC
1 AAAAAT-ATAGAAAATTAC
*
24298 AAAAATATATAAAATTAC
1 AAAAATATAGAAAATTAC
24316 AA
1 AA
24318 TGAAGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAAATATAGAAAATTAC
Found at i:24605 original size:20 final size:19
Alignment explanation
Indices: 24582--24634 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
24572 TTTGCACTTT
*
24582 TATA-ATTTTTTTAGTTTG
1 TATATATTTTTTTAATTTG
*
24600 TATATATTATTTTGAATTTG
1 TATATATT-TTTTTAATTTG
*
24620 TTTATGATTTTTTTA
1 TATAT-ATTTTTTTA
24635 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 18 0.64
21 3 0.11
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (19 bp):
TATATATTTTTTTAATTTG
Found at i:24634 original size:11 final size:11
Alignment explanation
Indices: 24614--24653 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
24604 TATTATTTTG
*
24614 AATTTGTTTAT
1 AATTTTTTTAT
*
24625 GATTTTTTTAT
1 AATTTTTTTAT
*
24636 AATTTTTTAAT
1 AATTTTTTTAT
24647 AATTTTT
1 AATTTTT
24654 AAAATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (11 bp):
AATTTTTTTAT
Found at i:24661 original size:19 final size:20
Alignment explanation
Indices: 24629--24671 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
24619 GTTTATGATT
*
24629 TTTTTATAATTTTTTAATAA
1 TTTTTATAAATTTTTAATAA
*
24649 TTTTTA-AAATTTTTAATGA
1 TTTTTATAAATTTTTAATAA
24668 TTTT
1 TTTT
24672 AAGTATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATAAATTTTTAATAA
Found at i:24670 original size:10 final size:10
Alignment explanation
Indices: 24628--24671 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
24618 TGTTTATGAT
*
24628 TTTTTTATAA
1 TTTTTAATAA
24638 TTTTTTAATAA
1 -TTTTTAATAA
24649 TTTTTAA-AA
1 TTTTTAATAA
*
24658 TTTTTAATGA
1 TTTTTAATAA
24668 TTTT
1 TTTT
24672 AAGTATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 9 0.30
10 12 0.40
11 9 0.30
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:26860 original size:11 final size:11
Alignment explanation
Indices: 26846--26893 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
26836 CAAAATTGTG
26846 AGAAAACAATA
1 AGAAAACAATA
*
26857 AGAAAATAAT-
1 AGAAAACAATA
26867 AGCAAAACAATA
1 AG-AAAACAATA
* *
26879 AAAAAACAACA
1 AGAAAACAATA
26890 AGAA
1 AGAA
26894 GAAACAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
10 2 0.07
11 27 0.90
12 1 0.03
ACGTcount: A:0.73, C:0.10, G:0.08, T:0.08
Consensus pattern (11 bp):
AGAAAACAATA
Found at i:27709 original size:60 final size:59
Alignment explanation
Indices: 27523--27824 Score: 295
Period size: 59 Copynumber: 5.0 Consensus size: 59
27513 AAAAAAATTA
* * * * *
27523 TGTTGGCCATTGCATGGCAGACACTACCTTTTTAATCTAACAAAAAACCAAATTTCTTTTTTG
1 TGTTGGCCATTGCATGGCCGACACTACCTTTTTTATCTGA-TAAAAATCAAA--T-TTTTTTG
* * * ** *
27586 TGTTGGCCA-TGAATTGGTCGACACCACC-TTTTTATCAAATATAAAAT-TAATTTTTTTGG
1 TGTTGGCCATTGCA-TGGCCGACACTACCTTTTTTATCTGATA-AAAATCAAATTTTTTT-G
* *
27645 TGTTGGTCATTGCATGGCCGACACTACCTTTTTTATTTGATAAAAATCAAAATTTTTTTG
1 TGTTGGCCATTGCATGGCCGACACTACCTTTTTTATCTGATAAAAATC-AAATTTTTTTG
* * *
27705 TGTTGGCCACTGCATGACCGACACTACCTTTTTTATTTGATAAAAATCAAATTTTTTTG
1 TGTTGGCCATTGCATGGCCGACACTACCTTTTTTATCTGATAAAAATCAAATTTTTTTG
* * * * * *
27764 TGTTGGTCATTGCATGGTCGACACCACATATTTTATCTGACAAAAAAATCAAATTTTTTTG
1 TGTTGGCCATTGCATGGCCGACACTACCTTTTTTATCTG--ATAAAAATCAAATTTTTTTG
27825 GTTTTATCTA
Statistics
Matches: 201, Mismatches: 29, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
58 6 0.03
59 69 0.34
60 59 0.29
61 31 0.15
62 16 0.08
63 20 0.10
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (59 bp):
TGTTGGCCATTGCATGGCCGACACTACCTTTTTTATCTGATAAAAATCAAATTTTTTTG
Found at i:27768 original size:119 final size:119
Alignment explanation
Indices: 27523--27824 Score: 324
Period size: 119 Copynumber: 2.5 Consensus size: 119
27513 AAAAAAATTA
* * * * * *
27523 TGTTGGCCATTGCATGGCAGACACTACCTTTTTAATCTAACAAAAAACCAAATTTCTTTTTTGTG
1 TGTTGGTCATTGCATGGCCGACACTACCTTTTTTATCTGA-AAAAAATCAAA-AT-TTTTTTGTG
** *
27588 TTGGCCATGAATTGGTCGACACCACCTTTTTATCAAATATAAAATTAATTTTTTTGG
63 TTGGCCATGAATTGACCGACACCACCTTTTTATCAAATATAAAATAAATTTTTTTGG
* *
27645 TGTTGGTCATTGCATGGCCGACACTACCTTTTTTATTTGATAAAAATCAAAATTTTTTTGTGTTG
1 TGTTGGTCATTGCATGGCCGACACTACCTTTTTTATCTGAAAAAAATCAAAATTTTTTTGTGTTG
* * ***
27710 GCCACTGCA-TGACCGACACTACCTTTTTTATTTGATA-AAAATCAAATTTTTTT-G
66 GCCA-TGAATTGACCGACACCACC-TTTTTATCAAATATAAAAT-AAATTTTTTTGG
* * * *
27764 TGTTGGTCATTGCATGGTCGACACCACATATTTTATCTGACAAAAAAATC-AAATTTTTTTG
1 TGTTGGTCATTGCATGGCCGACACTACCTTTTTTATCTG--AAAAAAATCAAAATTTTTTTG
27825 GTTTTATCTA
Statistics
Matches: 153, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
119 67 0.44
120 34 0.22
121 17 0.11
122 35 0.23
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (119 bp):
TGTTGGTCATTGCATGGCCGACACTACCTTTTTTATCTGAAAAAAATCAAAATTTTTTTGTGTTG
GCCATGAATTGACCGACACCACCTTTTTATCAAATATAAAATAAATTTTTTTGG
Found at i:27854 original size:33 final size:32
Alignment explanation
Indices: 27794--27856 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
27784 ACACCACATA
*
27794 TTTTATCTGACAAAAAAATCAAATTTTTTTGG
1 TTTTATCTAACAAAAAAATCAAATTTTTTTGG
*
27826 TTTTATCTAATAAAAAAATCAAATTTTTTTG
1 TTTTATCTAACAAAAAAATCAAATTTTTTTG
27857 TGTTGGCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (32 bp):
TTTTATCTAACAAAAAAATCAAATTTTTTTGG
Found at i:27892 original size:93 final size:93
Alignment explanation
Indices: 27746--27917 Score: 258
Period size: 93 Copynumber: 1.8 Consensus size: 93
27736 TTTATTTGAT
* *
27746 AAAAATCAAATTTTTTTGTGTTGGTCATTGCATGGTCGACACCACATATTTTATCTGACAAAAAA
1 AAAAATCAAATTTTTTTGTGTTGGCCATTGAATGGTCGACACCACATATTTTATCTGACAAAAAA
*
27811 ATCAAATTTTTTTGGTTTTATCTAATAA
66 ATCAAAATTTTTTGGTTTTATCTAATAA
* *
27839 AAAAATCAAATTTTTTTGTGTTGGCCATTGAATGG-CTGACACCATC-TTTTTTATTTGACAAAA
1 AAAAATCAAATTTTTTTGTGTTGGCCATTGAATGGTC-GACACCA-CATATTTTATCTGACAAAA
*
27902 AATTCAAAATTTTTTG
64 AAATCAAAATTTTTTG
27918 TGTTGGCCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
92 1 0.01
93 69 0.97
94 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (93 bp):
AAAAATCAAATTTTTTTGTGTTGGCCATTGAATGGTCGACACCACATATTTTATCTGACAAAAAA
ATCAAAATTTTTTGGTTTTATCTAATAA
Found at i:27952 original size:60 final size:61
Alignment explanation
Indices: 27826--28343 Score: 503
Period size: 61 Copynumber: 8.6 Consensus size: 61
27816 ATTTTTTTGG
* * * * * *
27826 TTTTATCTAATAAAAAAATCAAATTTTTTTGTGTTGGCCATTG-AATGGCTGACACCATCTT
1 TTTTATCTGAT-AAAAAATCAAAATTTTTTGTGTTGGCCAATGCATTGGCCGACACCACCTT
* * *
27887 TTTTATTTGACAAAAAATTCAAAATTTTTTGTGTTGGCC-TTGCATTGGCCGACACCACC-T
1 TTTTATCTGATAAAAAA-TCAAAATTTTTTGTGTTGGCCAATGCATTGGCCGACACCACCTT
* * * *
27947 TTTTATTTGATAAAAAAATC-AAATTTTTTGGTGTTGGCCATTGCA-TGACCGACATCACCTT
1 TTTTATCTGAT-AAAAAATCAAAATTTTTT-GTGTTGGCCAATGCATTGGCCGACACCACCTT
* ** * *
28008 TTTTATCTGACAAAAAATTCAATTTTTTTTGTGTTAGCC-ATGCATTGGCCGACACTACC-T
1 TTTTATCTGATAAAAAA-TCAAAATTTTTTGTGTTGGCCAATGCATTGGCCGACACCACCTT
* *
28068 TTTTATTTGATAAAGAAAATC-AAATTTTTGGTGTTGGCCAATGC-TTGGCCGACACCACCTT
1 TTTTATCTGAT-AA-AAAATCAAAATTTTTTGTGTTGGCCAATGCATTGGCCGACACCACCTT
* **
28129 TTTTATCTGATAAAAAATC-AAATTTTTTGGTATTGGCC-ATGCATTGGTTGACACCACC-T
1 TTTTATCTGATAAAAAATCAAAATTTTTT-GTGTTGGCCAATGCATTGGCCGACACCACCTT
* * **
28188 TTTTATCTGATAAAAAA-AAATTAATTTTTGGTGTTGGCCAATGC-TTAACCGACACCACCTT
1 TTTTATCTGATAAAAAATCAA--AATTTTTTGTGTTGGCCAATGCATTGGCCGACACCACCTT
* * * * *
28249 TTTTATCTGATAAAAAATCAAATTTTTTTTGTGTTGGCC-ATTCATTGGCCAATACCACCAT
1 TTTTATCTGATAAAAAATCAAA-ATTTTTTGTGTTGGCCAATGCATTGGCCGACACCACCTT
**
28310 TTTTAT-TAGATAAAAAAT-AATTTTTTTTGTGTTG
1 TTTTATCT-GATAAAAAATCAAAATTTTTTGTGTTG
28344 TTCATGCATG
Statistics
Matches: 385, Mismatches: 48, Indels: 50
0.80 0.10 0.10
Matches are distributed among these distances:
59 59 0.15
60 140 0.36
61 173 0.45
62 13 0.03
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (61 bp):
TTTTATCTGATAAAAAATCAAAATTTTTTGTGTTGGCCAATGCATTGGCCGACACCACCTT
Found at i:27962 original size:121 final size:120
Alignment explanation
Indices: 27826--28360 Score: 618
Period size: 121 Copynumber: 4.5 Consensus size: 120
27816 ATTTTTTTGG
* * * * * * *
27826 TTTTATCTAATAAAAAAATCAAATTTTTTTGTGTTGGCCATTGAATGGCTGACACCATCTTTTTT
1 TTTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCCAATGCATGACCGACACCACCTTTTTT
* *
27891 ATTTGACAAAAAATTCAAAATTTTTTGTGTTGGCCTTGCATTGGCCGACACCACCT
66 ATCTGACAAAAAA-TCAAAATTTTTTGTGTTGGCCATGCATTGGCCGACACCACCT
* * *
27947 TTTTATTTGATAAAAAAATCAAATTTTTTGGTGTTGGCCATTGCATGACCGACATCACCTTTTTT
1 TTTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCCAATGCATGACCGACACCACCTTTTTT
** * *
28012 ATCTGACAAAAAATTCAATTTTTTTTGTGTTAGCCATGCATTGGCCGACACTACCT
66 ATCTGACAAAAAA-TCAAAATTTTTTGTGTTGGCCATGCATTGGCCGACACCACCT
* * *
28068 TTTTATTTGATAAAGAAAATCAAA-TTTTTGGTGTTGGCCAATGCTTGGCCGACACCACCTTTTT
1 TTTTATTTGATAAA-AAAATCAAATTTTTTTGTGTTGGCCAATGCATGACCGACACCACCTTTTT
* * **
28132 TATCTGATAAAAAATC-AAATTTTTTGGTATTGGCCATGCATTGGTTGACACCACCT
65 TATCTGACAAAAAATCAAAATTTTTT-GTGTTGGCCATGCATTGGCCGACACCACCT
* * *
28188 TTTTATCTGAT-AAAAAA--AAATTAATTTTTGGTGTTGGCCAATGCTTAACCGACACCACCTTT
1 TTTTATTTGATAAAAAAATCAAATT--TTTTT-GTGTTGGCCAATGCATGACCGACACCACCTTT
* * * * *
28250 TTTATCTGATAAAAAATCAAATTTTTTTTGTGTTGGCCATTCATTGGCCAATACCACCAT
63 TTTATCTGACAAAAAATCAAA-ATTTTTTGTGTTGGCCATGCATTGGCCGACACCACC-T
* * **
28310 TTTTATTAGAT-AAAAAAT-AATTTTTTTTGTGTTGTTC-ATGCATGACCGACA
1 TTTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCCAATGCATGACCGACA
28361 TCAATTTTCC
Statistics
Matches: 360, Mismatches: 44, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
116 3 0.01
117 1 0.00
118 4 0.01
119 25 0.07
120 92 0.26
121 200 0.56
122 31 0.09
123 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (120 bp):
TTTTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGCCAATGCATGACCGACACCACCTTTTTT
ATCTGACAAAAAATCAAAATTTTTTGTGTTGGCCATGCATTGGCCGACACCACCT
Found at i:27978 original size:152 final size:153
Alignment explanation
Indices: 27686--27975 Score: 415
Period size: 152 Copynumber: 1.9 Consensus size: 153
27676 TTTATTTGAT
* * *
27686 AAAAATCAAAATTTTTTTGTGTTGGCCACTGCATGACCGACACTACCTTTTTTATTTGATAAAAA
1 AAAAATCAAAATTTTTTTGTGTTGGCCACTGAATGACCGACACCACCTTTTTTATTTGAAAAAAA
* *
27751 TCAAATTTTTTTGTGTTGGTCATTGCATGGTCGACACCACATATTTTATCTGACAAAAAAATCAA
66 TCAAAATTTTTTGTGTTGGTCATTGCATGGCCGACACCACATATTTTATCTGACAAAAAAATCAA
27816 ATTTTTTTGGTTTTATCTAATAA
131 ATTTTTTTGGTTTTATCTAATAA
* * * *
27839 AAAAATC-AAATTTTTTTGTGTTGGCCATTGAATGGCTGACACCATCTTTTTTATTTGACAAAAA
1 AAAAATCAAAATTTTTTTGTGTTGGCCACTGAATGACCGACACCACCTTTTTTATTTGA-AAAAA
* * * *
27903 ATTCAAAATTTTTTGTGTTGG-CCTTGCATTGGCCGACACCACCT-TTTTATTTGATAAAAAAAT
65 A-TCAAAATTTTTTGTGTTGGTCATTGCA-TGGCCGACACCACATATTTTATCTGACAAAAAAAT
27966 CAAATTTTTT
128 CAAATTTTTT
27976 GGTGTTGGCC
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
152 45 0.37
153 45 0.37
154 31 0.26
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (153 bp):
AAAAATCAAAATTTTTTTGTGTTGGCCACTGAATGACCGACACCACCTTTTTTATTTGAAAAAAA
TCAAAATTTTTTGTGTTGGTCATTGCATGGCCGACACCACATATTTTATCTGACAAAAAAATCAA
ATTTTTTTGGTTTTATCTAATAA
Found at i:31840 original size:11 final size:11
Alignment explanation
Indices: 31814--31851 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31804 GAAGTTGAAA
31814 TTAAAATTATAT
1 TTAAAATTA-AT
31826 TTAAAATTAAT
1 TTAAAATTAAT
*
31837 TTAACATT-AT
1 TTAAAATTAAT
31847 TTAAA
1 TTAAA
31852 TAAAAAGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 6 0.25
11 9 0.38
12 9 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAAAATTAAT
Found at i:31957 original size:46 final size:46
Alignment explanation
Indices: 31906--32162 Score: 154
Period size: 48 Copynumber: 5.5 Consensus size: 46
31896 TTTGACAATA
*
31906 TATTATTTATCAAATTTTAATATTTAAATTTATTTAAGTAAAAAAC
1 TATTATTTATCAAATTTTTATATTTAAATTTATTTAAGTAAAAAAC
* ** * * *
31952 TATTATTATATTATAATTTTTATCAAATAATGTGTTGATTT--G-ATAATA-
1 TATTATT-TATCA-AATTTTTAT-ATTTAA-AT-TT-ATTTAAGTAAAAAAC
* * *
32000 TATTATTTACCAAATTTTTATATTTAAATTTATTTAAATCAAAAAC
1 TATTATTTATCAAATTTTTATATTTAAATTTATTTAAGTAAAAAAC
** * *
32046 TATTATTATATTTC-AATTTTTATCAAATAATATGTTGATTT--G-ACAATAC
1 TATTATT-TA--TCAAATTTTTAT-ATTTAA-AT-TT-ATTTAAGTAAAAAAC
* * *
32095 -ATTATTTGTCAAATTTTAATATTTAAATTTATTTAAATAAAAAAC
1 TATTATTTATCAAATTTTTATATTTAAATTTATTTAAGTAAAAAAC
*
32140 TATTATTATATTACAATTTTTAT
1 TATTATT-TATCA-AATTTTTAT
32163 CAAATAATGT
Statistics
Matches: 154, Mismatches: 33, Indels: 46
0.66 0.14 0.20
Matches are distributed among these distances:
42 8 0.05
43 4 0.03
44 3 0.02
45 18 0.12
46 37 0.24
47 13 0.08
48 38 0.25
49 17 0.11
50 4 0.03
51 4 0.03
52 8 0.05
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (46 bp):
TATTATTTATCAAATTTTTATATTTAAATTTATTTAAGTAAAAAAC
Found at i:31980 original size:94 final size:94
Alignment explanation
Indices: 31835--32365 Score: 721
Period size: 94 Copynumber: 5.8 Consensus size: 94
31825 TTTAAAATTA
* * *
31835 ATTTAACA-TTATTTAAAT-AAAAA-GATTATTATATTTCAATTTATATTAAATAATGTGTTGAT
1 ATTTAA-ATTTATTTAAATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGAT
* *
31897 TTGACAATATATTATTTATCAAATTTTAAT
65 TTGACAATACATTATTTACCAAATTTTAAT
*
31927 ATTTAAATTTATTTAAGTAAAAAACTATTATTATATTAT-AATTTTTATCAAATAATGTGTTGAT
1 ATTTAAATTTATTTAAATAAAAAACTATTATTATATT-TCAATTTTTATCAAATAATGTGTTGAT
* * *
31991 TTGATAATATATTATTTACCAAATTTTTAT
65 TTGACAATACATTATTTACCAAATTTTAAT
* *
32021 ATTTAAATTTATTTAAATCAAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATT
1 ATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATT
**
32086 TGACAATACATTATTTGTCAAATTTTAAT
66 TGACAATACATTATTTACCAAATTTTAAT
* *
32115 ATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTAATT
1 ATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATT
32180 TGACAATACATTATTTACC--A----AAT
66 TGACAATACATTATTTACCAAATTTTAAT
* * *
32203 -TTT-AA--TATTTAAATAAAAAACTATTATTATATTACTATTTTTATCAAATAATATGTTGATT
1 ATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATT
* *
32264 TGATAATACATTATTTACTAAATTTTAAT
66 TGACAATACATTATTTACCAAATTTTAAT
* * * *
32293 ATTTAAATTTAATTAAATCAAAAACTATTATTATATTTCAATCTTTATCAAATAATGTATTGATT
1 ATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATT
*
32358 TGATAATA
66 TGACAATA
32366 TATTTGTCGA
Statistics
Matches: 391, Mismatches: 33, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
84 70 0.18
86 3 0.01
87 3 0.01
88 3 0.01
90 3 0.01
91 4 0.01
92 18 0.05
93 6 0.02
94 280 0.72
95 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (94 bp):
ATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATT
TGACAATACATTATTTACCAAATTTTAAT
Found at i:32195 original size:188 final size:179
Alignment explanation
Indices: 31835--32365 Score: 746
Period size: 178 Copynumber: 2.9 Consensus size: 179
31825 TTTAAAATTA
* * * *
31835 ATTTAACATTATTTAAATAAAAA-GATTATTATATTTCAATTTATATTAAATAATGTGTTGATTT
1 ATTTAA-ATTATTTAAATAAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATTT
* *
31899 GACAATATATTATTTATCAAATTTTAATATTTAAATTTATTTAAGTAAAAAACTATTATTATATT
65 GACAATACATTATTT-TCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATT
* *
31964 ATAATTTTTATCAAATAATGTGTTGATTTGATAATATATTATTTACCAAATTTTTAT
129 ACAATTTTTATCAAATAATGTGTTGATTTGATAATACATTATTTACC-AA-----AT
32021 ATTTAAATTTATTTAAATCAAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATT
1 ATTTAAA-TTATTTAAAT-AAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATT
32086 TGACAATACATTATTTGTCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATAT
64 TGACAATACATTATTT-TCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATAT
* *
32151 TACAATTTTTATCAAATAATGTGTTAATTTGACAATACATTATTTACCAAAT
128 TACAATTTTTATCAAATAATGTGTTGATTTGATAATACATTATTTACCAAAT
* *
32203 -TTT-AA-TATTTAAATAAAAAACTATTATTATATTACTATTTTTATCAAATAATATGTTGATTT
1 ATTTAAATTATTTAAAT-AAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATTT
* * * *
32265 GATAATACATTATTTACTAAATTTTAATATTTAAATTTAATTAAATCAAAAACTATTATTATATT
65 GACAATACATTATTTTC-AAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATT
* * *
32330 TCAATCTTTATCAAATAATGTATTGATTTGATAATA
129 ACAATTTTTATCAAATAATGTGTTGATTTGATAATA
32366 TATTTGTCGA
Statistics
Matches: 318, Mismatches: 23, Indels: 16
0.89 0.06 0.04
Matches are distributed among these distances:
177 1 0.00
178 144 0.45
180 2 0.01
181 3 0.01
182 2 0.01
185 1 0.00
186 16 0.05
187 7 0.02
188 142 0.45
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (179 bp):
ATTTAAATTATTTAAATAAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATTTG
ACAATACATTATTTTCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTAC
AATTTTTATCAAATAATGTGTTGATTTGATAATACATTATTTACCAAAT
Found at i:32234 original size:84 final size:84
Alignment explanation
Indices: 32124--32300 Score: 309
Period size: 84 Copynumber: 2.1 Consensus size: 84
32114 TATTTAAATT
*
32124 TATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTAATTTGACAATAC
1 TATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTGACAATAC
32189 ATTATTTACCAAATTTTAA
66 ATTATTTACCAAATTTTAA
* * *
32208 TATTTAAATAAAAAACTATTATTATATTACTATTTTTATCAAATAATATGTTGATTTGATAATAC
1 TATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTGACAATAC
*
32273 ATTATTTACTAAATTTTAA
66 ATTATTTACCAAATTTTAA
32292 TATTTAAAT
1 TATTTAAAT
32301 TTAATTAAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (84 bp):
TATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATATGTTAATTTGACAATAC
ATTATTTACCAAATTTTAA
Found at i:32358 original size:272 final size:276
Alignment explanation
Indices: 31835--32365 Score: 790
Period size: 272 Copynumber: 1.9 Consensus size: 276
31825 TTTAAAATTA
* * *
31835 ATTTAACATTATTTAAATAAAAAGATTATTATATTTCAATTTATATTAAATAATGTGTTGATTTG
1 ATTTAACATTATTTAAATAAAAAGATTATTATATTACAATTTATATCAAATAATGTGTTAATTTG
* *
31900 ACAATATATTATTTATCAAATTTTAATATTTAAATTTATTTAAGTAAAAAACTATTATTATATTA
66 ACAATACATTATTTACCAAATTTTAATA-TT-AATTTA--TAAGTAAAAAACTATTATTATATTA
* * *
31965 TAATTTTTATCAAATAATGTGTTGATTTGATAATATATTATTTACCAAATTTTTATATTTAAATT
127 TAATTTTTATCAAATAATATGTTGATTTGATAATACATTATTTACCAAATTTTAATATTTAAATT
* * *
32030 TATTTAAATCAAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATTTGACAATAC
192 TAATTAAATCAAAAACTATTATTATATTTCAATCTTTATCAAATAATATATTGATTTGACAATAC
32095 ATTATTTGTCAAATTTTAAT
257 ATTATTTGTCAAATTTTAAT
* *
32115 ATTTAA-ATTTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTAAT
1 ATTTAACA-TTATTTAAAT-AAAAA-GATTATTATATTACAATTTATATCAAATAATGTGTTAAT
32179 TTGACAATACATTATTTACCAAATTTT-A-A-T-ATTTA-AA-TAAAAAACTATTATTATATTAC
63 TTGACAATACATTATTTACCAAATTTTAATATTAATTTATAAGTAAAAAACTATTATTATATTA-
*
32238 T-ATTTTTATCAAATAATATGTTGATTTGATAATACATTATTTACTAAATTTTAATATTTAAATT
127 TAATTTTTATCAAATAATATGTTGATTTGATAATACATTATTTACCAAATTTTAATATTTAAATT
* *
32302 TAATTAAATCAAAAACTATTATTATATTTCAATCTTTATCAAATAATGTATTGATTTGATAATA
192 TAATTAAATCAAAAACTATTATTATATTTCAATCTTTATCAAATAATATATTGATTTGACAATA
32366 TATTTGTCGA
Statistics
Matches: 231, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
272 139 0.60
273 3 0.01
276 5 0.02
278 1 0.00
279 1 0.00
280 17 0.07
281 6 0.03
282 59 0.26
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (276 bp):
ATTTAACATTATTTAAATAAAAAGATTATTATATTACAATTTATATCAAATAATGTGTTAATTTG
ACAATACATTATTTACCAAATTTTAATATTAATTTATAAGTAAAAAACTATTATTATATTATAAT
TTTTATCAAATAATATGTTGATTTGATAATACATTATTTACCAAATTTTAATATTTAAATTTAAT
TAAATCAAAAACTATTATTATATTTCAATCTTTATCAAATAATATATTGATTTGACAATACATTA
TTTGTCAAATTTTAAT
Found at i:33265 original size:28 final size:27
Alignment explanation
Indices: 33234--33293 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
33224 AAAATGAGAC
* *
33234 TTTGGA-TACCCGAGGGTAAAATGGTAAT
1 TTTGGACT-CCCG-GGGCAAAATGATAAT
*
33262 TTTGGACTCTCGGGGCAAAATGATAAT
1 TTTGGACTCCCGGGGCAAAATGATAAT
33289 TTTGG
1 TTTGG
33294 GAAAATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 18 0.64
28 9 0.32
29 1 0.04
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (27 bp):
TTTGGACTCCCGGGGCAAAATGATAAT
Found at i:33534 original size:117 final size:116
Alignment explanation
Indices: 33412--33836 Score: 475
Period size: 117 Copynumber: 3.6 Consensus size: 116
33402 AATGGGGATC
* * * * *
33412 AAAAATAGAGTTTTTGGACGTTCGAGGGTAAAAATGTAATTTTCAAAAGTTTTGAGGTCAAAATG
1 AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAATG
* *
33477 GAATTTTTTAAGGTTT-AGGGGTAAAAATGTAATTTTTGAAAGTTTTGAGGTT
66 GAATTTTTTAA-GTTTGA-GGGTAAAAATATAATTTTTGAAAGTTTCGAGGTT
* * * ** ** * *
33529 TAAAATGGAATTTTTGGAAGTT-TAGGGGT-AAAATGGAATTTTTGGAAGTTTAGAGGTTAAAAA
1 AAAAATAGAATTTTTGGAAGTTCGA-GGGTAAAAATATAATTTTCAGAAGTTTCGAGG-TCAAAA
* *
33592 TGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATATTTTGAAAGTTTCAAGG-T
64 TGGAATTTTT-TAAGTTTGAGGGTAAAAATATAAT-TTTTGAAAGTTTCGAGGTT
* * * *
33646 CAAAAT-GAAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCATAAGTTTCGGGGTTAAAAT
1 AAAAATAG-AATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAAT
* *
33710 GGAATTTTTAGAAGTTCGAGGGTAAAAATATAATTTTT-AGAAGTTTCGAGGTT
65 GGAATTTTT-TAAGTTTGAGGGTAAAAATATAATTTTTGA-AAGTTTCGAGGTT
* *
33763 AAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTCAAAATG
1 AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAATG
* *
33828 AAATATTTT
66 GAATTTTTT
33837 GACAGTTTAA
Statistics
Matches: 260, Mismatches: 37, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
115 1 0.00
116 38 0.15
117 181 0.70
118 40 0.15
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.36
Consensus pattern (116 bp):
AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAATG
GAATTTTTTAAGTTTGAGGGTAAAAATATAATTTTTGAAAGTTTCGAGGTT
Found at i:33837 original size:59 final size:58
Alignment explanation
Indices: 33413--33837 Score: 448
Period size: 58 Copynumber: 7.3 Consensus size: 58
33403 ATGGGGATCA
* * * * * * *
33413 AAAATAGAGTTTTTGGACGTTCGAGGGTAAAAATGTAATTTTCAAAAGTTTTGAGGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
* * * * *
33471 AAAATGGAATTTTT-TAAGGTT-TAGGGGTAAAAATGTAATTTTT-GAAAGTTTTGAGGTTT
1 AAAATGGAATTTTTGGAA-GTTCGA-GGGTAAAAATATAATTTTTAG-AAGTTTCGAGG-TC
* ** * * *
33530 AAAATGGAATTTTTGGAAGTT-TAGGGGT-AAAATGGAATTTTTGGAAGTTTAGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATATAATTTTTAGAAGTTTCGAGG-TC
* *
33588 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATATTTT-GAAAGTTTCAAGGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAAT-TTTTAG-AAGTTTCGAGGTC
* * * * *
33647 AAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCATAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
* *
33705 AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGG-TC
* *
33764 AAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
*
33822 AAAATGAAATATTTTG
1 AAAATGGAAT-TTTTG
33838 ACAGTTTAAG
Statistics
Matches: 317, Mismatches: 37, Indels: 25
0.84 0.10 0.07
Matches are distributed among these distances:
57 2 0.01
58 167 0.53
59 133 0.42
60 15 0.05
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
Found at i:34722 original size:7 final size:7
Alignment explanation
Indices: 34710--34760 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
34700 CTTTTTTTGG
34710 TTATTAA
1 TTATTAA
34717 TTATTAA
1 TTATTAA
34724 TTATT-A
1 TTATTAA
34730 TTATTAA
1 TTATTAA
*
34737 TAATATTTTA
1 T--TA-TTAA
*
34747 TTAATAA
1 TTATTAA
34754 TTATTAA
1 TTATTAA
34761 GGTTATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 6 0.17
7 22 0.61
8 2 0.06
9 2 0.06
10 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATTAA
Found at i:34826 original size:21 final size:19
Alignment explanation
Indices: 34776--34827 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
34766 TTTATTACCG
*
34776 TTATTTATTATTAATATCA
1 TTATTTATTATTAATAACA
*
34795 TTATTAATATTATTAATAAAACC
1 TTATT--TATTATTAAT--AACA
34818 TTATTTATTA
1 TTATTTATTA
34828 CTCATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 5 0.19
21 15 0.56
23 7 0.26
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATTTATTATTAATAACA
Found at i:35537 original size:6 final size:6
Alignment explanation
Indices: 35526--35619 Score: 58
Period size: 6 Copynumber: 16.7 Consensus size: 6
35516 TTTGGACATT
* * * *
35526 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--CA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * *
35572 AA-GTA AATTTA AACTTA AA--TA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
35616 AATT
1 AATT
35620 ATGTTGGGCC
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
4 6 0.09
5 11 0.17
6 46 0.71
7 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:35551 original size:17 final size:16
Alignment explanation
Indices: 35526--35619 Score: 89
Period size: 17 Copynumber: 5.6 Consensus size: 16
35516 TTTGGACATT
*
35526 AATTTAAATTTAAATTT
1 AATTTAAATTTAAA-TA
* * *
35543 AACTCAAATTTATAACA
1 AATTTAAATTTA-AATA
*
35560 AATTTAAATTTTAAGTA
1 AATTTAAA-TTTAAATA
*
35577 AATTTAAACTTAAATA
1 AATTTAAATTTAAATA
*
35593 AATTTAATTTTAAAATA
1 AATTTAAATTT-AAATA
35610 AATTTAAATT
1 AATTTAAATT
35620 ATGTTGGGCC
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
16 15 0.25
17 40 0.66
18 6 0.10
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:35702 original size:46 final size:46
Alignment explanation
Indices: 35652--35798 Score: 129
Period size: 46 Copynumber: 3.2 Consensus size: 46
35642 GCTTCAACAA
*
35652 TATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAAC
1 TATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAAC
* * * * * * ** * *
35698 TATTATTATATTACATTTT-TTA-TCAAATAATGTGTTGATTTGACAATAC
1 TATTATT-TATCAAATTTTAATATTTAAAT--T-TATTTAAAT-AAAAAAC
35747 -ATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAAC
1 TATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAAC
35792 TATTATT
1 TATTATT
35799 ATATTACATT
Statistics
Matches: 72, Mismatches: 21, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
45 10 0.14
46 20 0.28
47 19 0.26
48 13 0.18
49 10 0.14
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (46 bp):
TATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAAC
Found at i:35760 original size:94 final size:94
Alignment explanation
Indices: 35653--35977 Score: 498
Period size: 94 Copynumber: 3.6 Consensus size: 94
35643 CTTCAACAAT
35653 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
35718 TATCAAATAATGTGTTGATTTGACAATAC
66 TATCAAATAATGTGTTGATTTGACAATAC
*
35747 ATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
*
35812 TATCAAATAATGTGTTGATTTGATAATAC
66 TATCAAATAATGTGTTGATTTGACAATAC
* *
35841 ATTATTTACCAAATTTTAATATTT-AA---A--T--A-AAAAAA-TATTATAATATTACAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
* *
35896 TATCATATAA--TG-TG-TTTGACAATAA
66 TATCAAATAATGTGTTGATTTGACAATAC
35921 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATT
35978 TCAAT
Statistics
Matches: 212, Mismatches: 9, Indels: 24
0.87 0.04 0.10
Matches are distributed among these distances:
80 33 0.16
81 4 0.02
82 2 0.01
84 28 0.13
85 6 0.03
86 2 0.01
88 2 0.01
89 6 0.03
90 12 0.06
93 2 0.01
94 115 0.54
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (94 bp):
ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
TATCAAATAATGTGTTGATTTGACAATAC
Found at i:35800 original size:49 final size:48
Alignment explanation
Indices: 35652--35806 Score: 124
Period size: 47 Copynumber: 3.2 Consensus size: 48
35642 GCTTCAACAA
35652 TATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
1 TATTATTTA-CAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
* * * * * * ** *
35701 TATTATATTAC--ATTTT-TTA-TCAAATAATGTGTTGATTTGACAA-TA-
1 TATTAT-TTACAAATTTTAATATTTAAAT-TTAT-TTAAATAAAAAACTAT
*
35746 CATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
1 TATTATTTA-CAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
35795 TATTATATTACA
1 TATTAT-TTACA
35807 TTTTTTATCA
Statistics
Matches: 75, Mismatches: 20, Indels: 22
0.64 0.17 0.19
Matches are distributed among these distances:
44 3 0.04
45 11 0.15
46 6 0.08
47 24 0.32
48 6 0.08
49 19 0.25
50 6 0.08
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (48 bp):
TATTATTTACAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
Done.