Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014499.1 Kokia drynarioides strain JFW-HI SEQ_129538, 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: 209467
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:5805 original size:16 final size:16
Alignment explanation
Indices: 5781--5820 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5771 GATATGAACT
*
5781 TTGATTTTGCTGAATTC
1 TTGA-TTTGATGAATTC
*
5798 TTGATTTGATGTATTC
1 TTGATTTGATGAATTC
5814 TTGATTT
1 TTGATTT
5821 CTTTTTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.57
Consensus pattern (16 bp):
TTGATTTGATGAATTC
Found at i:10429 original size:33 final size:33
Alignment explanation
Indices: 10392--10455 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
10382 TTTTAATTCA
10392 AAAATTAAAATTCATCAATTCAAAATTTTATAT
1 AAAATTAAAATTCATCAATTCAAAATTTTATAT
* * *
10425 AAAATTATAATTCATTAATTCAAAGTTTTAT
1 AAAATTAAAATTCATCAATTCAAAATTTTAT
10456 CTCCCCTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (33 bp):
AAAATTAAAATTCATCAATTCAAAATTTTATAT
Found at i:10588 original size:103 final size:103
Alignment explanation
Indices: 10384--10586 Score: 363
Period size: 103 Copynumber: 2.0 Consensus size: 103
10374 ATACTAACTT
* *
10384 TTAATTCAAAAATTAAAATTCATCAATTCAAAATTTTATATAAAATTATAATTCATTAATTCAAA
1 TTAATTCAAAAATTAAAATTCATCAATTCAAAATTTCATATAAAATTATAATTCATTAACTCAAA
10449 GTTTTATCTCCCCTCACTTTAGAGAGAGTTGAGGGGCG
66 GTTTTATCTCCCCTCACTTTAGAGAGAGTTGAGGGGCG
* *
10487 TTAATTTAAAAATTAAAATTCATCAATTTAAAATTTCATATAAAATTATAATTCATTAACTCAAA
1 TTAATTCAAAAATTAAAATTCATCAATTCAAAATTTCATATAAAATTATAATTCATTAACTCAAA
10552 GTTTTATCTCCCCTCACTTTAGAGAGAGTT-AGGGG
66 GTTTTATCTCCCCTCACTTTAGAGAGAGTTGAGGGG
10587 GCACCTCCCG
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 5 0.05
103 91 0.95
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (103 bp):
TTAATTCAAAAATTAAAATTCATCAATTCAAAATTTCATATAAAATTATAATTCATTAACTCAAA
GTTTTATCTCCCCTCACTTTAGAGAGAGTTGAGGGGCG
Found at i:14192 original size:154 final size:154
Alignment explanation
Indices: 13912--14220 Score: 492
Period size: 154 Copynumber: 2.0 Consensus size: 154
13902 AGAATGCTTC
* *
13912 AATTCATATATAACTTCTTTTCCTGATATAGATTTTGTTTTATTTATCTGCATGCTGATAGTTCC
1 AATTCATATACAACTTCTTTTCCTGATATAGATTTTGTTTTATATATCTGCATGCTGATAGTTCC
* * **
13977 CTTTCTTCGTCTGAATATAAGTGTACGGAATTAGTTTTTGCATATGCCAACTTTTTGCAGGTAAG
66 CTTTCTTCATCTGAATATAAGTATACGGAATTAGTTTTTGCATACACCAACTTTTTGCAGGTAAG
*
14042 ATCAAACTAAATAATCTATGGTAG
131 ATCAAACTAAATAATCAATGGTAG
* * *
14066 AATTCATATACATCTTCTTTTTCTGATATAGATTTTGTTTTATATATCTGCATTCTGATAGTTCC
1 AATTCATATACAACTTCTTTTCCTGATATAGATTTTGTTTTATATATCTGCATGCTGATAGTTCC
* * *
14131 CTTTCTTCATTTGAATATAAGTATACGGAATTAGTTTTTGCATACACTAACTTTTTGCAGGTAAT
66 CTTTCTTCATCTGAATATAAGTATACGGAATTAGTTTTTGCATACACCAACTTTTTGCAGGTAAG
*
14196 ATCAAACTAAATCATCAATGGTAG
131 ATCAAACTAAATAATCAATGGTAG
14220 A
1 A
14221 CGCTATTCTC
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
154 141 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (154 bp):
AATTCATATACAACTTCTTTTCCTGATATAGATTTTGTTTTATATATCTGCATGCTGATAGTTCC
CTTTCTTCATCTGAATATAAGTATACGGAATTAGTTTTTGCATACACCAACTTTTTGCAGGTAAG
ATCAAACTAAATAATCAATGGTAG
Found at i:23450 original size:13 final size:13
Alignment explanation
Indices: 23432--23457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23422 TGATATCCTC
23432 TCATTGACATTAT
1 TCATTGACATTAT
23445 TCATTGACATTAT
1 TCATTGACATTAT
23458 ATGATAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TCATTGACATTAT
Found at i:39693 original size:2 final size:2
Alignment explanation
Indices: 39686--39717 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39676 AAATAAGGGT
39686 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39718 ACTCCCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:47404 original size:22 final size:21
Alignment explanation
Indices: 47369--47419 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
47359 GGCATGGAGG
47369 AGGAAAGATGAGAGGCGAGAGA
1 AGGAAA-ATGAGAGGCGAGAGA
* *
47391 AGGAAAATGAAGAGGTGGGAGA
1 AGGAAAATG-AGAGGCGAGAGA
*
47413 AGAAAAA
1 AGGAAAA
47420 AAACAGACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.51, C:0.02, G:0.41, T:0.06
Consensus pattern (21 bp):
AGGAAAATGAGAGGCGAGAGA
Found at i:48710 original size:35 final size:35
Alignment explanation
Indices: 48670--48741 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
48660 ATATATATTG
48670 ACTTAAATTAAATAAATAACTATTGTTCTTTGAAT
1 ACTTAAATTAAATAAATAACTATTGTTCTTTGAAT
*
48705 ACTTAAATTAAATAAATAATTATTGTTCTTTGAAT
1 ACTTAAATTAAATAAATAACTATTGTTCTTTGAAT
48740 AC
1 AC
48742 CCAATGACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (35 bp):
ACTTAAATTAAATAAATAACTATTGTTCTTTGAAT
Found at i:56093 original size:14 final size:14
Alignment explanation
Indices: 56058--56103 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
56048 TTAAAATTAT
*
56058 TAATTA-AATTAAA
1 TAATTATAATTTAA
*
56071 TAAAT-TAATTTAA
1 TAATTATAATTTAA
56084 TAATTATAATTTAA
1 TAATTATAATTTAA
*
56098 TTATTA
1 TAATTA
56104 AGGAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATTATAATTTAA
Found at i:56530 original size:10 final size:10
Alignment explanation
Indices: 56515--56547 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
56505 ATAATTTTTG
56515 AATTTTTAAA
1 AATTTTTAAA
56525 AATTTTTAAA
1 AATTTTTAAA
*
56535 AATTTTAAAA
1 AATTTTTAAA
56545 AAT
1 AAT
56548 AATTAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:56553 original size:20 final size:20
Alignment explanation
Indices: 56515--56554 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
56505 ATAATTTTTG
* **
56515 AATTTTTAAAAATTTTTAAA
1 AATTTTAAAAAATAATTAAA
56535 AATTTTAAAAAATAATTAAA
1 AATTTTAAAAAATAATTAAA
56555 TGTTAATGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTTAAAAAATAATTAAA
Found at i:60107 original size:80 final size:80
Alignment explanation
Indices: 59969--60276 Score: 381
Period size: 80 Copynumber: 3.8 Consensus size: 80
59959 GACAATTATG
* ** **
59969 GCACCCAGTGCTTAGC-GAAATAACTGCGAAA-GTGAGCCCAGCTCTAGTTGGATT-AACCGACA
1 GCACCCAGTGCTTAGCGGATA-AACCAC-AAATGTGAGCCCAGCTCTAG-TCAATTAAACCGACA
*
60031 AATATCCATCAAATCCTA
63 AATATCCATCAAATCTTA
*
60049 GCACCCAGTGCTTAGCGGATAAACCACAAATGTGAGCCTAGCTCTAGTCAATTAAACCGACAAAT
1 GCACCCAGTGCTTAGCGGATAAACCACAAATGTGAGCCCAGCTCTAGTCAATTAAACCGACAAAT
60114 ATCCATCAAATCTTA
66 ATCCATCAAATCTTA
* * **
60129 GCACCCAATGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCGGTTAAACCGACAAAT
1 GCACCCAGTGCTTAGCGGATAAACCACAAATGTGAGCCCAGCTCTAGTCAATTAAACCGACAAAT
*
60194 ATCCGTCAAATCTTA
66 ATCCATCAAATCTTA
* * * * * *
60209 GCACCAAGTGCCTAGCGGATAAA-CAGCAATTGTGAGCCTAGCTCTAGTCAGTTAAACTGACAAC
1 GCACCCAGTGCTTAGCGGATAAACCA-CAAATGTGAGCCCAGCTCTAGTCAATTAAACCGACAA-
60273 ATAT
64 ATAT
60277 ATTCATCAAA
Statistics
Matches: 202, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
79 8 0.04
80 187 0.93
81 7 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (80 bp):
GCACCCAGTGCTTAGCGGATAAACCACAAATGTGAGCCCAGCTCTAGTCAATTAAACCGACAAAT
ATCCATCAAATCTTA
Found at i:60245 original size:160 final size:161
Alignment explanation
Indices: 59969--60276 Score: 446
Period size: 160 Copynumber: 1.9 Consensus size: 161
59959 GACAATTATG
* * *
59969 GCACCCAGTGCTTAGCGAAATAACTGCGAAAGTGAGCCCAGCTCTAGTTGGATTAACCGACAAAT
1 GCACCCAATGCTTAGCGAAATAACCGCGAAAGTGAGCCCAGCTCTAGTCGGATTAACCGACAAAT
* *
60034 ATCCATCAAATCCTAGCACCCAGTGCTTAGCGGATAAACCACAAATGTGAGCCTAGCTCTAGTCA
66 ATCCATCAAATCCTAGCACCAAGTGCCTAGCGGATAAACCACAAATGTGAGCCTAGCTCTAGTCA
60099 ATTAAACCGACAA-ATATCCATCAAATCTTA
131 ATTAAACCGACAACATATCCATCAAATCTTA
*
60129 GCACCCAATGCTTAGCG-GATAAACCGC-AAATGTGAGCCCAGCTCTAGTCGG-TTAAACCGACA
1 GCACCCAATGCTTAGCGAAAT-AACCGCGAAA-GTGAGCCCAGCTCTAGTCGGATT-AACCGACA
* * *
60191 AATATCCGTCAAATCTTAGCACCAAGTGCCTAGCGGATAAA-CAGCAATTGTGAGCCTAGCTCTA
63 AATATCCATCAAATCCTAGCACCAAGTGCCTAGCGGATAAACCA-CAAATGTGAGCCTAGCTCTA
* *
60255 GTCAGTTAAACTGACAACATAT
127 GTCAATTAAACCGACAACATAT
60277 ATTCATCAAA
Statistics
Matches: 132, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
159 9 0.07
160 119 0.90
161 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (161 bp):
GCACCCAATGCTTAGCGAAATAACCGCGAAAGTGAGCCCAGCTCTAGTCGGATTAACCGACAAAT
ATCCATCAAATCCTAGCACCAAGTGCCTAGCGGATAAACCACAAATGTGAGCCTAGCTCTAGTCA
ATTAAACCGACAACATATCCATCAAATCTTA
Found at i:63181 original size:17 final size:17
Alignment explanation
Indices: 63159--63192 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
63149 TAACGCAATC
63159 ATAGTCTTTCAGGAGTT
1 ATAGTCTTTCAGGAGTT
63176 ATAGTCTTTCAGGAGTT
1 ATAGTCTTTCAGGAGTT
63193 CAACCCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (17 bp):
ATAGTCTTTCAGGAGTT
Found at i:64736 original size:19 final size:19
Alignment explanation
Indices: 64701--64740 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
64691 ATATTTTTTT
*
64701 ATAATTTTTAGATTTTCTA
1 ATAATTTTAAGATTTTCTA
64720 ATAATTTTAATGA-TTTCTA
1 ATAATTTTAA-GATTTTCTA
64739 AT
1 AT
64741 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
ATAATTTTAAGATTTTCTA
Found at i:64766 original size:29 final size:29
Alignment explanation
Indices: 64719--64777 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
64709 TAGATTTTCT
64719 AATAATTTTAATGATTTCTAATT-TTTAA
1 AATAATTTTAATGATTTCTAATTCTTTAA
* *
64747 AATAATTTTTATGTTTTTCTAATTCTTTAA
1 AATAATTTTAATG-ATTTCTAATTCTTTAA
64777 A
1 A
64778 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 12 0.44
29 9 0.33
30 6 0.22
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (29 bp):
AATAATTTTAATGATTTCTAATTCTTTAA
Found at i:70960 original size:21 final size:21
Alignment explanation
Indices: 70935--70982 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
70925 TGAGATATAA
*
70935 TTAAAGAAATTTAT-AGTTTTT
1 TTAAAAAAATTTATGA-TTTTT
*
70956 TTAAAAAAAATTTGTGATTTTT
1 TT-AAAAAAATTTATGATTTTT
70978 TTAAA
1 TTAAA
70983 TTTAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.22
22 17 0.74
23 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (21 bp):
TTAAAAAAATTTATGATTTTT
Found at i:70967 original size:22 final size:22
Alignment explanation
Indices: 70941--70982 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
70931 ATAATTAAAG
70941 AAATTTAT-AGTTTTTTTAAAAA
1 AAATTTATGA-TTTTTTTAAAAA
*
70963 AAATTTGTGATTTTTTTAAA
1 AAATTTATGATTTTTTTAAA
70983 TTTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
AAATTTATGATTTTTTTAAAAA
Found at i:75846 original size:29 final size:30
Alignment explanation
Indices: 75791--75901 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
75781 ATCTCAAAAT
* *
75791 TATACAT-AAACTTTGATTTAATGTGCAATTG
1 TATACATGAAACTTTAATTT--GGTGCAATTG
* *
75822 TATACATG-AACTTAAATTTGGTGCAATTA
1 TATACATGAAACTTTAATTTGGTGCAATTG
* * * *
75851 TACACGTGAAACTTTAATTATGGTTCAAATG
1 TATACATGAAACTTTAATT-TGGTGCAATTG
*
75882 TATACTTGAAACTTTAATTT
1 TATACATGAAACTTTAATTT
75902 TGATTTAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
29 14 0.22
30 10 0.15
31 41 0.63
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.41
Consensus pattern (30 bp):
TATACATGAAACTTTAATTTGGTGCAATTG
Found at i:76121 original size:31 final size:29
Alignment explanation
Indices: 76053--76123 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
76043 AAATCAAAAT
*
76053 TTCATGTATAAAATTGCACAAAATCAAAG
1 TTCATGTATAAAATTGCACAAAACCAAAG
* * * *
76082 TTTATGTATACAATTGCCCATTAAACCATAG
1 TTCATGTATAAAATTGCACA--AAACCAAAG
76113 TTCATGTATAA
1 TTCATGTATAA
76124 TTTTGAGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (29 bp):
TTCATGTATAAAATTGCACAAAACCAAAG
Found at i:84222 original size:30 final size:31
Alignment explanation
Indices: 84188--84262 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
84178 ATTACATTTA
*
84188 ACAAAACAATCACTCAA-CTT-T-GAAAATGTG
1 ACAAAACAGTCACT-AATCTTATCGAAAA-GTG
*
84218 ACAAAACAGTCACTAATGTTATCGAAAAGTG
1 ACAAAACAGTCACTAATCTTATCGAAAAGTG
84249 ACAAAACAGTCACT
1 ACAAAACAGTCACT
84263 GATTAATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 2 0.05
30 15 0.38
31 18 0.45
32 5 0.12
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.21
Consensus pattern (31 bp):
ACAAAACAGTCACTAATCTTATCGAAAAGTG
Found at i:93365 original size:52 final size:51
Alignment explanation
Indices: 93284--93575 Score: 381
Period size: 52 Copynumber: 5.6 Consensus size: 51
93274 TTCACATTTA
* * *
93284 ATACTCATGAT-AGCACATTGTCATTGGACCTTATAATTCGAAAAGGATTCAT
1 ATACTCACGATGA-CACATAGTCATCGGACCTTATAA-TCGAAAAGGATTCAT
* **
93336 ATACTTACGATGACACATAGTCATCGGACCTCGTAATCAGTAAAA-GATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATC-G-AAAAGGATTCAT
* *
93388 ATACTCACGATGACACATAGTCATTGGACCTTATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCGA-AAAGGATTCAT
* * *
93440 ATACTCACGATGACACATAGTCATTGGATCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAAT-CGAAAAGGATTCAT
* *
93492 ATACTCACGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAA
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATC-GAAAAGGATTCAT
*
93544 ATACTCACGATGACACATAGTCATCGAACCTT
1 ATACTCACGATGACACATAGTCATCGGACCTT
93576 TTGCATTTAT
Statistics
Matches: 215, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
50 1 0.00
51 6 0.03
52 202 0.94
53 6 0.03
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCGAAAAGGATTCAT
Found at i:93575 original size:156 final size:156
Alignment explanation
Indices: 93284--93575 Score: 451
Period size: 156 Copynumber: 1.9 Consensus size: 156
93274 TTCACATTTA
* * * *
93284 ATACTCATGATAGCACATTGTCATTGGACCTTATAATTCGAAAAGGATTCATATACTTACGATGA
1 ATACTCACGATAGCACATAGTCATTGGACCTTATAATCCGAAAAGGATTCATATACTCACGATGA
* * *
93349 CACATAGTCATCGGACCTCGTAATCAGTAAAAGATTCATATACTCACGATGACACATAGTCATTG
66 CACATAGTCATCGGACCTCATAATCAGTAAAAGATTCAAATACTCACGATGACACATAGTCATCG
*
93414 GACCTTATAATCCATAAAGGATTCAT
131 AACCTTATAATCCATAAAGGATTCAT
* *
93440 ATACTCACGAT-GACACATAGTCATTGGATCTTATAATCCGTAAAGGATTCATATACTCACGATG
1 ATACTCACGATAG-CACATAGTCATTGGACCTTATAATCCGAAAAGGATTCATATACTCACGATG
* * *
93504 ACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAAATACTCACGATGACACATAGTCATC
65 ACACATAGTCATCGGACCTCATAATCAGTAAAAGATTCAAATACTCACGATGACACATAGTCATC
93569 GAACCTT
130 GAACCTT
93576 TTGCATTTAT
Statistics
Matches: 122, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
155 1 0.01
156 121 0.99
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (156 bp):
ATACTCACGATAGCACATAGTCATTGGACCTTATAATCCGAAAAGGATTCATATACTCACGATGA
CACATAGTCATCGGACCTCATAATCAGTAAAAGATTCAAATACTCACGATGACACATAGTCATCG
AACCTTATAATCCATAAAGGATTCAT
Found at i:100302 original size:18 final size:18
Alignment explanation
Indices: 100279--100315 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
100269 ACAATTCATA
100279 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
100297 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
100315 T
1 T
100316 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:104479 original size:20 final size:20
Alignment explanation
Indices: 104456--104496 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
104446 ACTTTCATAA
* *
104456 TTAAGCTTACTTAATCATTT
1 TTAACCTTAATTAATCATTT
*
104476 TTAACCTTAATTATTCATTT
1 TTAACCTTAATTAATCATTT
104496 T
1 T
104497 CTTAACACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAACCTTAATTAATCATTT
Found at i:107050 original size:27 final size:25
Alignment explanation
Indices: 107019--107071 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 25
107009 ATAGTAATCA
107019 TTTGTAATTTAAAAA-AAATCCATTTAT
1 TTTGTAA-TTAAAAATAAAT--ATTTAT
107046 TTTGTAATTAAAAATAAATATTTAT
1 TTTGTAATTAAAAATAAATATTTAT
107071 T
1 T
107072 ATTAACCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.28
26 7 0.28
27 11 0.44
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTGTAATTAAAAATAAATATTTAT
Found at i:107241 original size:33 final size:33
Alignment explanation
Indices: 107199--107265 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
107189 AATTGAACAC
107199 TTGTATAAAAAGATTAAGTATTTATTGCATTTA
1 TTGTATAAAAAGATTAAGTATTTATTGCATTTA
107232 TTGTATAAAAAGATTAAGTATTTATTGCATTTA
1 TTGTATAAAAAGATTAAGTATTTATTGCATTTA
107265 T
1 T
107266 ATACTAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (33 bp):
TTGTATAAAAAGATTAAGTATTTATTGCATTTA
Found at i:108034 original size:23 final size:23
Alignment explanation
Indices: 107992--108035 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
107982 GAGTGATTTG
* **
107992 ATAAAAAAATTAAACTTTAAAAA
1 ATAAAAAAATAAAAAATTAAAAA
108015 ATAAAAAAATAAAAAATTAAA
1 ATAAAAAAATAAAAAATTAAA
108036 TGAAAAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
ATAAAAAAATAAAAAATTAAAAA
Found at i:108036 original size:20 final size:20
Alignment explanation
Indices: 108013--108050 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
108003 AAACTTTAAA
108013 AAATAAAAAAATAAAAAATT
1 AAATAAAAAAATAAAAAATT
* *
108033 AAATGAAAAGATAAAAAA
1 AAATAAAAAAATAAAAAA
108051 GAAAATTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAAAAAAATAAAAAATT
Found at i:108056 original size:20 final size:20
Alignment explanation
Indices: 108012--108056 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
108002 TAAACTTTAA
*
108012 AAAATAAAAAAATAAAAAAT
1 AAAATAAAAAAATAAAAAAG
* * *
108032 TAAATGAAAAGATAAAAAAG
1 AAAATAAAAAAATAAAAAAG
108052 AAAAT
1 AAAAT
108057 TTCATAAAGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (20 bp):
AAAATAAAAAAATAAAAAAG
Found at i:111299 original size:20 final size:20
Alignment explanation
Indices: 111272--111310 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
111262 TTAAAAATAT
111272 TTTAATTAT-TATTTGAAAA
1 TTTAATTATATATTTGAAAA
111291 TTTATATTATAATATTTGAA
1 TTTA-ATTAT-ATATTTGAA
111311 TTAATAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
22 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTAATTATATATTTGAAAA
Found at i:112347 original size:18 final size:18
Alignment explanation
Indices: 112324--112358 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
112314 CAATGAGAAT
*
112324 AAATTTTTAATTAATTAA
1 AAATTTTAAATTAATTAA
112342 AAATTTTAAATTAATTA
1 AAATTTTAAATTAATTA
112359 CAACTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTTTAAATTAATTAA
Found at i:115715 original size:21 final size:20
Alignment explanation
Indices: 115668--115715 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
115658 AAAATAACAA
*
115668 ATTTT-AATAATAAAATAAT
1 ATTTTAAATAATAAAAAAAT
**
115687 ATCATAAATAATTAAAAAAAT
1 ATTTTAAATAA-TAAAAAAAT
115708 ATTTTAAA
1 ATTTTAAA
115716 AAAAACTATC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.14
20 5 0.23
21 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTTAAATAATAAAAAAAT
Found at i:126297 original size:22 final size:21
Alignment explanation
Indices: 126226--126311 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 21
126216 ATTGAGATAA
126226 TAAAAATTATAATATTTTGATTT
1 TAAAAATTATAAT-TTTT-ATTT
* *
126249 TAAATATTATAATTTTCATTTT
1 TAAAAATTATAATTTTTA-TTT
126271 TAAAAATTATAATTTTTATGTT
1 TAAAAATTATAATTTTTAT-TT
* *
126293 AAAAAAATATAATTTTTAT
1 TAAAAATTATAATTTTTAT
126312 CATAATATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
21 2 0.04
22 41 0.75
23 12 0.22
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (21 bp):
TAAAAATTATAATTTTTATTT
Found at i:136200 original size:51 final size:51
Alignment explanation
Indices: 136119--136255 Score: 134
Period size: 53 Copynumber: 2.6 Consensus size: 51
136109 GCTATAAACG
* * * **
136119 AAAGGATCCAATGACTAAGTGTCATTGTGAGTAAAT-AAATCC-ATGATGGATT
1 AAAGG-TCCGATGACT-AGTGTCATCGTGAGTAAATGAAATCCTAT-ACGGAAC
* *
136171 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGGAAC
1 AAAGGTCCGATGACT-AGTGTCATCGTGAGTAAATGAAATCCTATACGGAAC
*
136223 AAGAGGTCCGATGACTATATGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-GTGTCATCGTGAGTA
136256 TTAAATGAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
51 26 0.36
52 17 0.24
53 29 0.40
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAGTGTCATCGTGAGTAAATGAAATCCTATACGGAAC
Found at i:136246 original size:53 final size:57
Alignment explanation
Indices: 136173--136375 Score: 179
Period size: 61 Copynumber: 3.5 Consensus size: 57
136163 GATGGATTAA
*
136173 AGGTCCGATGACTCA-GTGTCATCGTGAGTAT-ATG-A-A-TTCCTATACGGAACAAG
1 AGGTCCGATGACT-ATATGTCATCGTGAGTATAATGAAGAGTTCCTATACGGAACAAG
* *
136226 AGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTTCTTATACGTAACAAG
1 AGGTCCGATGACTATATGTCATCGTGAGTA-T-AATG-AA-GAGTTCCTATACGGAACAAG
* * *
136287 AGGTTCGATGACTATATGTCATCGTGAGTATTAAATAAAATGAGTTCC-A-ATGTGAACAAG
1 AGGTCCGATGACTATATGTCATCGTGAGTA-T-AAT-GAA-GAGTTCCTATACG-GAACAAG
* * *
136347 -GGTCCGATGACTTTGTTTCATCGTGAGTA
1 AGGTCCGATGACTATATGTCATCGTGAGTA
136376 ATAAATACGA
Statistics
Matches: 127, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
52 1 0.01
53 27 0.21
54 1 0.01
56 3 0.02
58 1 0.01
59 27 0.21
60 8 0.06
61 59 0.46
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (57 bp):
AGGTCCGATGACTATATGTCATCGTGAGTATAATGAAGAGTTCCTATACGGAACAAG
Found at i:136308 original size:61 final size:60
Alignment explanation
Indices: 136212--136382 Score: 229
Period size: 61 Copynumber: 2.9 Consensus size: 60
136202 ATATGAATTC
* *
136212 CTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTT
1 CTATACGTAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATAAAATGAGTT
*
136272 CTTATACGTAACAAGAGGTTCGATGACTATATGTCATCGTGAGTATTAAATAAAATGAGTT
1 C-TATACGTAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATAAAATGAGTT
* * * * * *
136333 CCA-ATGTGAACAAG-GGTCCGATGACTTTGTTTCATCGTGAGTAATAAATA
1 CTATACGT-AACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATA
136383 CGAGTGAAAC
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
59 34 0.34
60 8 0.08
61 57 0.58
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (60 bp):
CTATACGTAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATAAAATGAGTT
Found at i:138091 original size:20 final size:20
Alignment explanation
Indices: 138032--138106 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
138022 CTACAGCTTC
*
138032 GTTGTTTCGGTAGAAGC-ATA
1 GTTGTATCGGTAGAAGCGA-A
*
138052 -TTGTATCAGTAGAA-CTGAA
1 GTTGTATCGGTAGAAGC-GAA
138071 GTTGTATCGGTAGAAGCGAA
1 GTTGTATCGGTAGAAGCGAA
* *
138091 GTTCTACCGGTAGAAG
1 GTTGTATCGGTAGAAG
138107 TCCCAAGGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.02
19 13 0.28
20 31 0.67
21 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTGTATCGGTAGAAGCGAA
Found at i:138302 original size:20 final size:20
Alignment explanation
Indices: 138263--138302 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
138253 AGTGTTCAAG
*
138263 GTATCGGTAGAACTGTAGTT
1 GTATCGGTAGAACTGGAGTT
*
138283 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAACTGGAGTT
138303 CTACAGGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.07, G:0.35, T:0.33
Consensus pattern (20 bp):
GTATCGGTAGAACTGGAGTT
Found at i:140305 original size:39 final size:39
Alignment explanation
Indices: 140207--140324 Score: 157
Period size: 39 Copynumber: 3.0 Consensus size: 39
140197 AGAGACTACT
* * *
140207 CTGCAATGATATACTGAATTAGCAGTGACACTGTAAACA
1 CTGCAATGATATACTGAACTGGCAGTTACACTGTAAACA
140246 CTGCAATGATATACTGAACTGGCAGTTACACTGTAAACA
1 CTGCAATGATATACTGAACTGGCAGTTACACTGTAAACA
* * * *
140285 CTGCAATGACATACCGAACTGGC-GTTGAGACTGTGAACA
1 CTGCAATGATATACTGAACTGGCAGTT-ACACTGTAAACA
140324 C
1 C
140325 CGTAATGCTA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
38 3 0.04
39 68 0.96
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (39 bp):
CTGCAATGATATACTGAACTGGCAGTTACACTGTAAACA
Found at i:151171 original size:30 final size:29
Alignment explanation
Indices: 151116--151172 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
151106 TCCTTGGAAT
* *
151116 TATCCATTTTTCATATTGTACCCTATATG
1 TATCCATATTTCATATTATACCCTATATG
151145 TATCACATATTTCATA-TATACTCCTATA
1 TATC-CATATTTCATATTATAC-CCTATA
151173 ATGAATTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.46
Consensus pattern (29 bp):
TATCCATATTTCATATTATACCCTATATG
Found at i:151311 original size:4 final size:4
Alignment explanation
Indices: 151304--151328 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
151294 ACTCACACAA
151304 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
151329 AGAAATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:152504 original size:20 final size:20
Alignment explanation
Indices: 152481--152519 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
152471 TAATTTTATG
*
152481 ACATATATTTTATT-TTTTAA
1 ACATA-ATTATATTATTTTAA
152501 ACATAATTATATTATTTTA
1 ACATAATTATATTATTTTA
152520 CAATCTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
ACATAATTATATTATTTTAA
Found at i:154404 original size:10 final size:10
Alignment explanation
Indices: 154389--154413 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
154379 AAATTGAATA
154389 AATTTTAAAT
1 AATTTTAAAT
154399 AATTTTAAAT
1 AATTTTAAAT
154409 AATTT
1 AATTT
154414 AATTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTTTAAAT
Found at i:154874 original size:14 final size:14
Alignment explanation
Indices: 154855--154885 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
154845 TTAATTTATT
154855 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
154869 TTTAATTAATTAAA
1 TTTAATTAAATAAA
154883 TTT
1 TTT
154886 TCTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:167014 original size:7 final size:7
Alignment explanation
Indices: 167004--167033 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
166994 AAAAATTAAA
167004 AATGTCC
1 AATGTCC
167011 AATGTCC
1 AATGTCC
167018 AATGTCC
1 AATGTCC
167025 AA-GTCC
1 AATGTCC
167031 AAT
1 AAT
167034 TACAACCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (7 bp):
AATGTCC
Found at i:172141 original size:50 final size:50
Alignment explanation
Indices: 172077--172212 Score: 182
Period size: 50 Copynumber: 2.7 Consensus size: 50
172067 GGGGATGTAA
*
172077 AGCCTACGGGTTTGGTACTTGGTGCCCAAGCATGTTTTTGGAGGGATTTT
1 AGCCTACGGGTTTGGTACTTGGTGCCTAAGCATGTTTTTGGAGGGATTTT
* ** ** *
172127 AGGCTACGGGTTTGGTACTTGGTGCCTGGGTGTGCTTTTGGAGGGATTTT
1 AGCCTACGGGTTTGGTACTTGGTGCCTAAGCATGTTTTTGGAGGGATTTT
* * *
172177 AGCCTACGGGCTAGGCACTTGGTGCCTAAGCATGTT
1 AGCCTACGGGTTTGGTACTTGGTGCCTAAGCATGTT
172213 CTTAGTTGGA
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.15, C:0.17, G:0.35, T:0.34
Consensus pattern (50 bp):
AGCCTACGGGTTTGGTACTTGGTGCCTAAGCATGTTTTTGGAGGGATTTT
Found at i:174772 original size:70 final size:70
Alignment explanation
Indices: 174694--174835 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
174684 AAAAGGCAAA
174694 ACATTTTCTAAGGTTAAAAGTCAAAACCATTAATTTAAAAGGTAAAAATACGTCGTTTTGATAAA
1 ACATTTTCTAAGGTTAAAAGTCAAAACCATTAATTTAAAAGGTAAAAATACGTCGTTTTGATAAA
174759 TATTT
66 TATTT
* * *
174764 ACATTTTCTAAGGTTAAAAGTCAAAACCATTAATTTAAAAGGTAAAACTACGTCGTTTTGCTATA
1 ACATTTTCTAAGGTTAAAAGTCAAAACCATTAATTTAAAAGGTAAAAATACGTCGTTTTGATAAA
174829 TATTT
66 TATTT
174834 AC
1 AC
174836 TCATTAAGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (70 bp):
ACATTTTCTAAGGTTAAAAGTCAAAACCATTAATTTAAAAGGTAAAAATACGTCGTTTTGATAAA
TATTT
Found at i:176837 original size:12 final size:12
Alignment explanation
Indices: 176801--176867 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
176791 ATAACATCCA
176801 AACAACAAAAAT
1 AACAACAAAAAT
176813 AACAATC---AA-
1 AACAA-CAAAAAT
176822 AACAACAAAAAT
1 AACAACAAAAAT
* *
176834 AACAGCAAAAAC
1 AACAACAAAAAT
*
176846 AATAACAAAAAT
1 AACAACAAAAAT
*
176858 AACACCAAAA
1 AACAACAAAA
176868 TAGTAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
8 1 0.02
9 5 0.12
10 2 0.05
11 2 0.05
12 32 0.74
13 1 0.02
ACGTcount: A:0.72, C:0.19, G:0.01, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:176844 original size:21 final size:20
Alignment explanation
Indices: 176787--176901 Score: 99
Period size: 21 Copynumber: 5.5 Consensus size: 20
176777 AAAATGCATA
*
176787 AAAAATAACATCCAAACAAC
1 AAAAATAACATCAAAACAAC
176807 AAAAATAACAATCAAAACAAC
1 AAAAATAAC-ATCAAAACAAC
*
176828 AAAAATAACAGCAAAAACAATAAC
1 AAAAATAACATC-AAAAC---AAC
* *
176852 AAAAATAACACCAAAATAGTA-
1 AAAAATAACATCAAAACA--AC
* *
176873 AAAAATAACACCAAAACAGC
1 AAAAATAACATCAAAACAAC
176893 AAAAA-AACA
1 AAAAATAACA
176902 ACACCAAAGC
Statistics
Matches: 81, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.05
20 17 0.21
21 41 0.51
22 1 0.01
23 4 0.05
24 14 0.17
ACGTcount: A:0.70, C:0.19, G:0.03, T:0.09
Consensus pattern (20 bp):
AAAAATAACATCAAAACAAC
Found at i:176904 original size:22 final size:22
Alignment explanation
Indices: 176852--176924 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
176842 AAACAATAAC
* * *
176852 AAAAATAACACCAAAATAG-TA
1 AAAAACAACACCAAAACAGCAA
*
176873 AAAAATAACACCAAAACAGCAA
1 AAAAACAACACCAAAACAGCAA
*
176895 AAAAACAACACCAAAGCAGCAA
1 AAAAACAACACCAAAACAGCAA
176917 CAAAAACA
1 -AAAAACA
176925 TTAAAAAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.39
22 21 0.46
23 7 0.15
ACGTcount: A:0.67, C:0.22, G:0.05, T:0.05
Consensus pattern (22 bp):
AAAAACAACACCAAAACAGCAA
Found at i:176937 original size:23 final size:22
Alignment explanation
Indices: 176885--176939 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
176875 AAATAACACC
**
176885 AAAACAGCAAAAAAACAACACC
1 AAAACAGCAAAAAAACAACAAA
* **
176907 AAAGCAGCAACAAAAACATTAAA
1 AAAACAGCAA-AAAAACAACAAA
176930 AAAACAGCAA
1 AAAACAGCAA
176940 TATAAATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.67, C:0.22, G:0.07, T:0.04
Consensus pattern (22 bp):
AAAACAGCAAAAAAACAACAAA
Found at i:184804 original size:36 final size:35
Alignment explanation
Indices: 184717--184807 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 35
184707 TAATAAATAA
* *
184717 TTTTTAAAATTTTAAATTAATAAAAATAAATTTAC
1 TTTTTAAAATTTAAAAATAATAAAAATAAATTTAC
* ** *
184752 ATTTTAATCTTCTAAAAATAATAAAAATTTAATTT-C
1 TTTTTAAAATT-TAAAAATAATAAAAA-TAAATTTAC
184788 TTTTTAAAATTATAAAAATA
1 TTTTTAAAATT-TAAAAATA
184808 TAAGCCATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
35 8 0.18
36 30 0.68
37 6 0.14
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (35 bp):
TTTTTAAAATTTAAAAATAATAAAAATAAATTTAC
Found at i:193410 original size:97 final size:97
Alignment explanation
Indices: 193235--193428 Score: 223
Period size: 97 Copynumber: 2.0 Consensus size: 97
193225 AACTTTGGAA
** * * * **
193235 AAGGATATTCGATTATCTTGATTTGAATAAAAGTCGCACCTAGTAAGTTAAGGTGCAAAATTTCA
1 AAGGATATTCGATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGCTAAGGCACAAAATTTCA
* *
193300 GAATCAGAGAT-AAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAAG-AACATTGCCTCGATTT
** *
193332 AAGGATATTCGATTA-CACCGATTTGAAGAAAAATCGTGCCTAGTAAGCTAAGGCACAAATTTTC
1 AAGGATATTCGATTATC-CCGATTTGAAGAAAAATCGCACCTAGTAAGCTAAGGCACAAAATTTC
*
193396 AAAACTC-GAAATAAAAGAATATTGCCTCGATTT
65 AAAA-TCAGAAATAAAAGAACATTGCCTCGATTT
193429 TAAAGTTTTC
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
96 1 0.01
97 74 0.91
98 6 0.07
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (97 bp):
AAGGATATTCGATTATCCCGATTTGAAGAAAAATCGCACCTAGTAAGCTAAGGCACAAAATTTCA
AAATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:193813 original size:29 final size:28
Alignment explanation
Indices: 193782--194152 Score: 226
Period size: 29 Copynumber: 12.5 Consensus size: 28
193772 GTTTGGGGCT
193782 AAAATAGTAATTTTTTGAAAAATTAGGGTAA
1 AAAAT-GTAA-TTTTTGAAAAATTAGGGT-A
* * * *
193813 AAAAAGGAA-TTTTGGAAAGTTCAGGGGTA
1 AAAATGTAATTTTTGAAAAATT-A-GGGTA
* * *
193842 AAAATGTATTTTTTTTGTAAAATCAGGGTCA
1 AAAATGTA--ATTTTTGAAAAATTAGGGT-A
* * **
193873 AAAATGGAATTTTGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAAAAATTA-GGGTA
* *
193902 AAAATGTAATTTTGGAAAAA-TCGAGGTAA
1 AAAATGTAATTTTTGAAAAATTAG-GGT-A
* **
193931 AAAATGTAATTTTGGAAAGTTTACGGGTA
1 AAAATGTAATTTTTGAAAAATTA-GGGTA
193960 AAAATGTAATTTTTTGAAAAATTAAGGGTTA
1 AAAATGTAA-TTTTTGAAAAATT-AGGG-TA
* * **
193991 AAAATGGAATTTTGGAAAGTTTAGGGGTAA
1 AAAATGTAATTTTTGAAAAATTA-GGGT-A
194021 AAAATGTAATTTTTTGAAAAATTAGGGTAAA
1 AAAATGTAA-TTTTTGAAAAATTAGGGT--A
* * **
194052 AAAATGGAATTTTGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAAAAATTA-GGGTA
* * *
194081 AAAATGTAATTTTT-AGAAATCGAGGTTA
1 AAAATGTAATTTTTGAAAAAT-TAGGGTA
* * * **
194109 AATATGGAATTTTGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAAAAATTA-GGGTA
194138 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
194153 GATAGTTTAG
Statistics
Matches: 261, Mismatches: 57, Indels: 46
0.72 0.16 0.13
Matches are distributed among these distances:
27 1 0.00
28 33 0.13
29 99 0.38
30 69 0.26
31 50 0.19
32 9 0.03
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAAAATTAGGGTA
Found at i:193864 original size:60 final size:59
Alignment explanation
Indices: 193753--194151 Score: 526
Period size: 60 Copynumber: 6.7 Consensus size: 59
193743 AATCGAGGTC
193753 AAAAATGGAATTTTTGG-AAGTTT-GGGGCT-AAAATAGTAATTTTTTGAAAAATTAGGGTA
1 AAAAATGGAA-TTTTGGAAAGTTTAGGGG-TAAAAAT-GTAATTTTTTGAAAAATTAGGGTA
* * * * * *
193812 AAAAAAGGAATTTTGGAAAGTTCAGGGGTAAAAATGTATTTTTTTTGTAAAATCAGGGTC
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTA-ATTTTTTGAAAAATTAGGGTA
* *
193872 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAA-TTTTGGAAAAA-TCGAGGTA
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAAATTAG-GGTA
* * *
193930 AAAAATGTAATTTTGGAAAGTTTACGGGTAAAAATGTAATTTTTTGAAAAATTAAGGGTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAAATT-AGGGTA
193990 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAAATGTAATTTTTTGAAAAATTAGGGTAA
1 AAAAATGGAATTTTGGAAAGTTTAGGGGT-AAAAATGTAATTTTTTGAAAAATTAGGGT-A
* * *
194051 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAA-TTTTT-AGAAA-TCGAGGTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAAATTAG-GGTA
*
194108 AAATATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT
1 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT
194152 GGATAGTTTA
Statistics
Matches: 302, Mismatches: 26, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
57 41 0.14
58 66 0.22
59 33 0.11
60 108 0.36
61 54 0.18
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAAATTAGGGTA
Found at i:193949 original size:118 final size:117
Alignment explanation
Indices: 193749--194151 Score: 550
Period size: 118 Copynumber: 3.4 Consensus size: 117
193739 GAAGAATCGA
193749 GGTCAAAAATGGAATTTTTGG-AAGTTT-GGGGCT-AAAATAGTAATTTTTTGAAAAATTAGGGT
1 GGTCAAAAATGGAA-TTTTGGAAAGTTTAGGGG-TAAAAAT-GTAATTTTTTGAAAAATTAGGGT
* * *
193811 AAAAAAAGGAATTTTGGAAAGTTCAGGGGTAAAAATGTATTTTTTTTGTAAAATCAG
63 AAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTA-ATTTTTTG-AAAATCAG
* *
193868 GGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAA-TTTTGGAAAAA-TCGAGGTAA
1 GGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAAATTAG-GGTAA
* * *
193931 AAAATGTAATTTTGGAAAGTTTACGGGTAAAAATGTAATTTTTTGAAAAATTAAG
65 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTG-AAAA-TCAG
*
193986 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAAATGTAATTTTTTGAAAAATTAGGGTAA
1 GGTCAAAAATGGAATTTTGGAAAGTTTAGGGGT-AAAAATGTAATTTTTTGAAAAATTAGGGT-A
*
194051 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTAG-AAATC-G
64 AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAATCAG
* *
194103 AGGTTAAATATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT
1 -GGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTT
194152 GGATAGTTTA
Statistics
Matches: 257, Mismatches: 17, Indels: 22
0.87 0.06 0.07
Matches are distributed among these distances:
117 29 0.11
118 122 0.47
119 38 0.15
120 22 0.09
121 46 0.18
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (117 bp):
GGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAAATTAGGGTAAA
AAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTTGAAAATCAG
Found at i:195317 original size:3 final size:3
Alignment explanation
Indices: 195293--195366 Score: 96
Period size: 3 Copynumber: 24.3 Consensus size: 3
195283 TTTTATTAAA
* * *
195293 ATT AAT ATT ATT AATT -TC ATT ATT ATT ATT GTT ATTT ATT ATT ATT
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
195339 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
195367 CTAATGATAC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 55 0.89
4 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:196080 original size:11 final size:11
Alignment explanation
Indices: 196064--196110 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 11
196054 TTTCAAATTT
196064 TAAATTTAAAA
1 TAAATTTAAAA
196075 TAAATTTAAACTTAA
1 TAAATTT-AA---AA
196090 TAAATTTAAAA
1 TAAATTTAAAA
196101 TAAATTTAAA
1 TAAATTTAAA
196111 CTTAATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 19 0.59
12 2 0.06
14 2 0.06
15 9 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:196126 original size:32 final size:31
Alignment explanation
Indices: 196062--196164 Score: 116
Period size: 26 Copynumber: 3.5 Consensus size: 31
196052 TATTTCAAAT
196062 TTTAAATTTAAAATAAATTTAAAC-T--TAA
1 TTTAAATTTAAAATAAATTTAAACTTAATAA
196090 --TAAATTTAAAATAAATTTAAACTTAATATA
1 TTTAAATTTAAAATAAATTTAAACTTAATA-A
*
196120 TTTAAATTTAAAAT-AATTCTAAACTTAA-GA
1 TTTAAATTTAAAATAAATT-TAAACTTAATAA
196150 --TAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
196165 GATTTGGGTT
Statistics
Matches: 66, Mismatches: 1, Indels: 15
0.80 0.01 0.18
Matches are distributed among these distances:
26 22 0.33
27 1 0.02
28 12 0.18
29 4 0.06
30 2 0.03
31 4 0.06
32 21 0.32
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TTTAAATTTAAAATAAATTTAAACTTAATAA
Found at i:196654 original size:49 final size:49
Alignment explanation
Indices: 196601--197103 Score: 325
Period size: 49 Copynumber: 10.3 Consensus size: 49
196591 GTTGCTTAAA
* * *
196601 TTTCCTTTCATGCTTCTGAGGTA-TAGGGTTCGCTATTGCGACTTAATTC
1 TTTCCCTTCATG-TTCTGAGGTACTAGGGTTCGCCATTGCGACTTAAATC
* * * * * * *
196650 TTTCCCTTCGTATTTTCACGGTACT-GGATTCGCCGTTGCGGCTTAAATC
1 TTTCCCTTCATGTTCTGA-GGTACTAGGGTTCGCCATTGCGACTTAAATC
196699 TTTCCCTTCATGTCTCTGAGGTACTA-GGTTCGCCATTGCGACTTAAA-C
1 TTTCCCTTCATGT-TCTGAGGTACTAGGGTTCGCCATTGCGACTTAAATC
* * * * * * *
196747 ATTTCCCTT-GTGTTTTCGTGGTACTA-GATTCGTCGTTGCGGCTTAAATC
1 -TTTCCCTTCATGTTCT-GAGGTACTAGGGTTCGCCATTGCGACTTAAATC
* * *
196796 TTTCCTTTTATGTCTCTGAGGTACTA-GGTTCGCCATTGCGACTTAAACC
1 TTTCCCTTCATGT-TCTGAGGTACTAGGGTTCGCCATTGCGACTTAAATC
* ** * * * * *
196845 TTTTCCTTGGTG-TCTTTATGGTACT-GGATTCGCCGTTACGGCTTAAATC
1 TTTCCCTTCATGTTC-TGA-GGTACTAGGGTTCGCCATTGCGACTTAAATC
*
196894 TTTCCCTTCATGTCTCTGAGGTACTA-GGTTCGTCATTGCGACTTAAATC
1 TTTCCCTTCATGT-TCTGAGGTACTAGGGTTCGCCATTGCGACTTAAATC
* ** * * * ** *
196943 TTTCCATTTGTGTCTTTGTGGTACT-GGATTCGCTGTTGCGGCTTAAATC
1 TTTCCCTTCATGT-TCTGAGGTACTAGGGTTCGCCATTGCGACTTAAATC
* ** * * * * *
196992 TTTCTCTTTGTGCTTTTGAGGTAC-ACGGTTCGCCGTTGTGACTTAAACC
1 TTTCCCTTCATG-TTCTGAGGTACTAGGGTTCGCCATTGCGACTTAAATC
* * * *
197041 TTT-CCTTCCAT-ATCTTCGAGGTACT-GGATTCGCCGTTGCGGCTTAAATC
1 TTTCCCTT-CATGTTC-T-GAGGTACTAGGGTTCGCCATTGCGACTTAAATC
197090 TTTCCCTTCATGTT
1 TTTCCCTTCATGTT
197104 TCATGGTACT
Statistics
Matches: 348, Mismatches: 82, Indels: 47
0.73 0.17 0.10
Matches are distributed among these distances:
47 5 0.01
48 46 0.13
49 281 0.81
50 14 0.04
51 2 0.01
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (49 bp):
TTTCCCTTCATGTTCTGAGGTACTAGGGTTCGCCATTGCGACTTAAATC
Found at i:196740 original size:98 final size:98
Alignment explanation
Indices: 196594--197102 Score: 601
Period size: 98 Copynumber: 5.2 Consensus size: 98
196584 ATCCGCCGTT
* * **
196594 GCTTAAA--TTTCCTTTCATG-CTTCTGAGGTA-TAGGGTTCGCTATTGCGACTTAATTCTTTCC
1 GCTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTA-GGTTCGCCATTGCGACTTAAACCTTTCC
* *
196655 CTTCGTATTTTCACGGTACTGGATTCGCCGTTGCG
64 CTTCGTGTTTTCATGGTACTGGATTCGCCGTTGCG
*
196690 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACATTTCCCT
1 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* * *
196755 T-GTGTTTTCGTGGTACTAGATTCGTCGTTGCG
66 TCGTGTTTTCATGGTACTGGATTCGCCGTTGCG
* * *
196787 GCTTAAATCTTTCCTTTTATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTTCCT
1 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* *
196852 TGGTGTCTTT-ATGGTACTGGATTCGCCGTTACG
66 TCGTGT-TTTCATGGTACTGGATTCGCCGTTGCG
* * *
196885 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGTCATTGCGACTTAAATCTTTCCAT
1 GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT
* * *
196950 TTGTGTCTTT-GTGGTACTGGATTCGCTGTTGCG
66 TCGTGT-TTTCATGGTACTGGATTCGCCGTTGCG
* * * *
196983 GCTTAAATCTTTCTCTT--TGTGCTTTTGAGGTAC-ACGGTTCGCCGTTGTGACTTAAACCTTT-
1 GCTTAAATCTTTCCCTTCATGT-C-TCTGAGGTACTA-GGTTCGCCATTGCGACTTAAACCTTTC
* * *
197044 CCTTCCATATCTTCGA-GGTACTGGATTCGCCGTTGCG
63 CCTT-CGTGTTTTC-ATGGTACTGGATTCGCCGTTGCG
197081 GCTTAAATCTTTCCCTTCATGT
1 GCTTAAATCTTTCCCTTCATGT
197103 TTCATGGTAC
Statistics
Matches: 357, Mismatches: 42, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
96 10 0.03
97 95 0.27
98 243 0.68
99 6 0.02
100 3 0.01
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.40
Consensus pattern (98 bp):
GCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCT
TCGTGTTTTCATGGTACTGGATTCGCCGTTGCG
Found at i:205376 original size:30 final size:31
Alignment explanation
Indices: 205336--205408 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
205326 AAATTAGTTC
*
205336 TTGA-CCCTAAACTTTCTAAAGATTACTA-TT
1 TTGACCCCTAAACTTTCTAAAAATT-CTATTT
205366 TT-ACCCCTAAA-TTTCTAAAAATTCTATTT
1 TTGACCCCTAAACTTTCTAAAAATTCTATTT
205395 TTGACCCC-AAACTT
1 TTGACCCCTAAACTT
205409 CCCGAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
28 3 0.08
29 19 0.50
30 16 0.42
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (31 bp):
TTGACCCCTAAACTTTCTAAAAATTCTATTT
Found at i:205396 original size:29 final size:31
Alignment explanation
Indices: 205336--205426 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 31
205326 AAATTAGTTC
*
205336 TTGA-CCCTAAACTTTCTAAAGATTACTATT
1 TTGACCCCTAAACTTTCTAAAAATTACTATT
205366 TT-ACCCCTAAA-TTTCTAAAAATT-CTATTT
1 TTGACCCCTAAACTTTCTAAAAATTACTA-TT
* ** *
205395 TTGACCCC-AAACTTCCCGAAAATTACCATT
1 TTGACCCCTAAACTTTCTAAAAATTACTATT
205425 TT
1 TT
205427 ACGCTCGAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 3 0.06
29 19 0.37
30 27 0.53
31 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (31 bp):
TTGACCCCTAAACTTTCTAAAAATTACTATT
Found at i:205490 original size:29 final size:29
Alignment explanation
Indices: 205413--205513 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
205403 AAACTTCCCG
* *
205413 AAAATTACCATTTTACGCTCGAACT-TCC
1 AAAATTACCATTTTACCCTCGAAGTATCC
205441 AAAGATT-CCATATTTGA-CCTCGAAGTATCC
1 AAA-ATTACCAT-TTT-ACCCTCGAAGTATCC
* *
205471 AAAATTACCGTTTTACCCTCG-GGTATCC
1 AAAATTACCATTTTACCCTCGAAGTATCC
205499 AAAAATTA-CATTTTA
1 -AAAATTACCATTTTA
205514 TCCCGTCTGC
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
28 20 0.33
29 31 0.51
30 10 0.16
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAAGTATCC
Found at i:207736 original size:19 final size:21
Alignment explanation
Indices: 207698--207738 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
207688 TATTTTTAGC
*
207698 AAAGAGAAGAATTTTTTTTTT
1 AAAGAGAAGAATTATTTTTTT
207719 AAAGAG-AG-ATTATTTTTTT
1 AAAGAGAAGAATTATTTTTTT
207738 A
1 A
207739 CGAGAGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 2 0.11
21 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (21 bp):
AAAGAGAAGAATTATTTTTTT
Found at i:207795 original size:21 final size:21
Alignment explanation
Indices: 207771--207812 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
207761 TAATTTCAAG
207771 TTTAAATT-TGTATTAACTATT
1 TTTAAATTATGT-TTAACTATT
**
207792 TTTATTTTATGTTTAACTATT
1 TTTAAATTATGTTTAACTATT
207813 GTAATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTAAATTATGTTTAACTATT
Done.