Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010676.1 Kokia drynarioides strain JFW-HI SEQ_125622, 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: 121402
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:14133 original size:12 final size:12
Alignment explanation
Indices: 14115--14144 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
14105 TACATGCACA
14115 ACAAAGGCAAAG
1 ACAAAGGCAAAG
*
14127 GCAAAGGCAAAG
1 ACAAAGGCAAAG
14139 ACAAAG
1 ACAAAG
14145 AAAAAGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.17, G:0.27, T:0.00
Consensus pattern (12 bp):
ACAAAGGCAAAG
Found at i:16932 original size:8 final size:8
Alignment explanation
Indices: 16919--16958 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
16909 ACAAATATAA
16919 AATATTAT
1 AATATTAT
16927 AATATTAT
1 AATATTAT
16935 -A-A-TA-
1 AATATTAT
16939 AATATTAT
1 AATATTAT
16947 AATATTAT
1 AATATTAT
16955 AATA
1 AATA
16959 AATCTAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 3 0.11
6 2 0.07
7 3 0.11
8 20 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AATATTAT
Found at i:16943 original size:20 final size:20
Alignment explanation
Indices: 16918--16961 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
16908 AACAAATATA
16918 AAATATTATAATATTATAAT
1 AAATATTATAATATTATAAT
16938 AAATATTATAATATTATAAT
1 AAATATTATAATATTATAAT
16958 AAAT
1 AAAT
16962 CTAACTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATTATAATATTATAAT
Found at i:30978 original size:9 final size:9
Alignment explanation
Indices: 30966--31173 Score: 61
Period size: 9 Copynumber: 21.4 Consensus size: 9
30956 TTAAAAAGTC
30966 ATAAAAATT
1 ATAAAAATT
30975 ATAAAAA-T
1 ATAAAAATT
30983 A-AAATAATT
1 ATAAA-AATT
**
30992 AATATTAAAACA
1 -ATA--AAAATT
*
31004 ATAGAAAA-A
1 ATA-AAAATT
31013 ATAAAATATT
1 ATAAAA-ATT
31023 -TAAAAA-T
1 ATAAAAATT
31030 ATATAAAATT
1 ATA-AAAATT
*
31040 GATATAAATTT
1 -ATA-AAAATT
31051 ATAAAAATAT
1 ATAAAAAT-T
31061 ATAATAAATCT
1 ATAA-AAAT-T
*
31072 AT-TAAATT
1 ATAAAAATT
31080 ATAAAAATT
1 ATAAAAATT
*
31089 TTATAAAATT
1 ATA-AAAATT
31099 AATTAAACATATT
1 -A-TAAA-A-ATT
*
31112 -TAAAATTTT
1 ATAAAA-ATT
*
31121 GTAAAAATTT
1 ATAAAAA-TT
*
31131 ATTAAAATTCT
1 A-TAAAAAT-T
* *
31142 ATAAGAATC
1 ATAAAAATT
*
31151 ATAAAAAATC
1 AT-AAAAATT
31161 ATAAAAATT
1 ATAAAAATT
31170 ATAA
1 ATAA
31174 GAAAAAAAAT
Statistics
Matches: 154, Mismatches: 20, Indels: 50
0.69 0.09 0.22
Matches are distributed among these distances:
7 4 0.03
8 13 0.08
9 53 0.34
10 45 0.29
11 29 0.19
12 5 0.03
13 5 0.03
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:31028 original size:10 final size:10
Alignment explanation
Indices: 31015--31226 Score: 57
Period size: 10 Copynumber: 21.1 Consensus size: 10
31005 TAGAAAAAAT
*
31015 AAAATATTTA
1 AAAATATATA
31025 AAAATATAT-
1 AAAATATATA
31034 AAAAT-TGATA
1 AAAATAT-ATA
* *
31044 TAAATTTATA
1 AAAATATATA
31054 AAAATATATA
1 AAAATATATA
*
31064 ATAAATCTAT-
1 A-AAATATATA
*
31074 TAAAT-TATA
1 AAAATATATA
*
31083 AAAATTTTATA
1 AAAA-TATATA
*
31094 AAATTA-ATTA
1 AAAATATA-TA
* *
31104 AACATATTTA
1 AAAATATATA
* * *
31114 AAATTTTGTA
1 AAAATATATA
*
31124 AAAATTTATTA
1 AAAATATA-TA
* *
31135 AAATTCTATA
1 AAAATATATA
*
31145 AGAATCATA-A
1 AAAAT-ATATA
31155 AAAATCATA-A
1 AAAAT-ATATA
* *
31165 AAATTATAAGAA
1 AAAATAT-A-TA
* *
31177 AAAAAATATT
1 AAAATATATA
31187 AAAATCGATATA
1 AAAAT--ATATA
**
31199 AACTTATA-A
1 AAAATATATA
31208 AAAATAT-TA
1 AAAATATATA
31217 AAAA-ATATA
1 AAAATATATA
31226 A
1 A
31227 TAACTCAAAT
Statistics
Matches: 149, Mismatches: 35, Indels: 37
0.67 0.16 0.17
Matches are distributed among these distances:
8 6 0.04
9 31 0.21
10 73 0.49
11 26 0.17
12 13 0.09
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATATATA
Found at i:31055 original size:29 final size:26
Alignment explanation
Indices: 31023--31105 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 26
31013 ATAAAATATT
31023 TAAAAATATATAAAATTGATATAAATTTA
1 TAAAAATATATAAAATT-AT-TAAA-TTA
31052 TAAAAATATATAATAAATCTATTAAATTA
1 TAAAAATATAT-A-AAAT-TATTAAATTA
*
31081 TAAAAATTTTATAAAATTAATTAAA
1 TAAAAA-TATATAAAATT-ATTAAA
31106 CATATTTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
27 1 0.02
28 10 0.21
29 21 0.44
30 9 0.19
31 6 0.12
32 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (26 bp):
TAAAAATATATAAAATTATTAAATTA
Found at i:31508 original size:19 final size:19
Alignment explanation
Indices: 31484--31522 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31474 ATTTAAACCC
31484 ATACCTTTTTAATATTTTT
1 ATACCTTTTTAATATTTTT
31503 ATACCTTTTTAATATTTTT
1 ATACCTTTTTAATATTTTT
31522 A
1 A
31523 CTTTAACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (19 bp):
ATACCTTTTTAATATTTTT
Found at i:36611 original size:41 final size:43
Alignment explanation
Indices: 36523--36607 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
36513 ATGGGTCAAA
* * *
36523 GTGTGTGTATACTGTTCTGGGACACATGGGTTGACACATGGGC
1 GTGTGTCTATACTGTTCTGGGACACATGAGCTGACACATGGGC
*
36566 GTGTGTCTATACTGTTTTGAGGA-ACATGAGCTGACACATGGG
1 GTGTGTCTATACTGTTCTG-GGACACATGAGCTGACACATGGG
36608 TGTGGGTACA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 34 0.92
44 3 0.08
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (43 bp):
GTGTGTCTATACTGTTCTGGGACACATGAGCTGACACATGGGC
Found at i:37092 original size:40 final size:40
Alignment explanation
Indices: 37047--37148 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
37037 TTATTGAGTT
* *
37047 AGCAGTGACACTGTAAACACTGCAATATTATAATTGAACC
1 AGCAGTGACACTGTAAACACTGCAATATTACAACTGAACC
* * * *
37087 GGCAGTGACACTGTAAACACTACAATATTACCACTGAACT
1 AGCAGTGACACTGTAAACACTGCAATATTACAACTGAACC
**
37127 AGTGGTGACACTGTAAACACTG
1 AGCAGTGACACTGTAAACACTG
37149 TAACGTATCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.24
Consensus pattern (40 bp):
AGCAGTGACACTGTAAACACTGCAATATTACAACTGAACC
Found at i:37246 original size:29 final size:30
Alignment explanation
Indices: 37213--37294 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 30
37203 AACGAATAGG
*
37213 GTATCACGTCTGCATCTGTAACTGA-ATTT
1 GTATCACGTCTGCATCTGTAACTGATATAT
* * *
37242 GTATCACGTTTGCGTTTGTAACT-ATATAT
1 GTATCACGTCTGCATCTGTAACTGATATAT
* * *
37271 GTATCATGTCTACATCCGTAACTG
1 GTATCACGTCTGCATCTGTAACTG
37295 TATCTGTGAC
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (30 bp):
GTATCACGTCTGCATCTGTAACTGATATAT
Found at i:37307 original size:29 final size:29
Alignment explanation
Indices: 37275--37338 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
37265 ATATATGTAT
* *
37275 CATGTCTACATCCGTAACTGTATCTGTGA
1 CATGACTACATACGTAACTGTATCTGTGA
** * *
37304 CATGACTGTATATGTAACTGTATCTTTGA
1 CATGACTACATACGTAACTGTATCTGTGA
37333 CATGAC
1 CATGAC
37339 AGTATCTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (29 bp):
CATGACTACATACGTAACTGTATCTGTGA
Found at i:37313 original size:17 final size:17
Alignment explanation
Indices: 37291--37376 Score: 57
Period size: 17 Copynumber: 5.6 Consensus size: 17
37281 TACATCCGTA
37291 ACTGTATCTGTGACATG
1 ACTGTATCTGTGACATG
*
37308 ACTGTATATGT---A--
1 ACTGTATCTGTGACATG
*
37320 ACTGTATCTTTGACATG
1 ACTGTATCTGTGACATG
* *
37337 ACAGTATCTAT-A-AT-
1 ACTGTATCTGTGACATG
*
37351 --TGTATCTGTGGCATG
1 ACTGTATCTGTGACATG
37366 ACTGTATCTGT
1 ACTGTATCTGT
37377 AATCGTATCT
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
12 16 0.31
14 3 0.06
15 3 0.06
16 1 0.02
17 28 0.55
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (17 bp):
ACTGTATCTGTGACATG
Found at i:37343 original size:29 final size:29
Alignment explanation
Indices: 37288--37388 Score: 132
Period size: 29 Copynumber: 3.5 Consensus size: 29
37278 GTCTACATCC
*
37288 GTAACTGTATCTGTGACATGACTGTATAT
1 GTAACTGTATCTGTGACATGACTGTATCT
* *
37317 GTAACTGTATCTTTGACATGACAGTATCT
1 GTAACTGTATCTGTGACATGACTGTATCT
* * *
37346 ATAATTGTATCTGTGGCATGACTGTATCT
1 GTAACTGTATCTGTGACATGACTGTATCT
37375 GTAA-TCGTATCTGT
1 GTAACT-GTATCTGT
37389 ATTATTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 1 0.02
29 61 0.98
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (29 bp):
GTAACTGTATCTGTGACATGACTGTATCT
Found at i:38266 original size:27 final size:27
Alignment explanation
Indices: 38236--38320 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 27
38226 TTAAATCCTT
38236 TTTAATAATTAATGAATTATTTTTAAA
1 TTTAATAATTAATGAATTATTTTTAAA
* * * *
38263 TTTAATTA-TACATGAAATGTTTTAAAA
1 TTTAATAATTA-ATGAATTATTTTTAAA
* *
38290 TTTAAAATATATTAATGAATAATATTTAAA
1 TTT--AATA-ATTAATGAATTATTTTTAAA
38320 T
1 T
38321 AATTTAATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
26 2 0.05
27 23 0.53
29 3 0.07
30 13 0.30
31 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (27 bp):
TTTAATAATTAATGAATTATTTTTAAA
Found at i:40665 original size:22 final size:24
Alignment explanation
Indices: 40629--40672 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
40619 ATGAAATTAA
40629 ATAATTTTTAAATAATT-ATTTTT
1 ATAATTTTTAAATAATTGATTTTT
*
40652 ATAATTTTT-CATAATTGATTT
1 ATAATTTTTAAATAATTGATTT
40673 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
ATAATTTTTAAATAATTGATTTTT
Found at i:41780 original size:19 final size:20
Alignment explanation
Indices: 41743--41780 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
41733 TATATATAAT
**
41743 AATATAAATAATTGGATTTG
1 AATATAAATAATTAAATTTG
41763 AATATAAA-AATTAAATTT
1 AATATAAATAATTAAATTT
41781 CAAATTTGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (20 bp):
AATATAAATAATTAAATTTG
Found at i:48140 original size:31 final size:29
Alignment explanation
Indices: 48065--48142 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
48055 CTTCAAAAAG
* * **
48065 TTAAAATTTTAATTAAGCCCTTAATTGTT
1 TTAAAAATTTAATTAAACCCTTAAAAGTT
*
48094 TTAGAAATCTTAATTAAACCCTTTAAAAGTT
1 TTAAAAAT-TTAATTAAACCC-TTAAAAGTT
48125 TTAAAAATTTCAATTAAA
1 TTAAAAATTT-AATTAAA
48143 TCCTCTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 6 0.15
30 13 0.32
31 21 0.52
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (29 bp):
TTAAAAATTTAATTAAACCCTTAAAAGTT
Found at i:53791 original size:17 final size:17
Alignment explanation
Indices: 53749--53791 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
53739 ACAAAACCTT
53749 GTTTTATA-TTAATTTA
1 GTTTTATATTTAATTTA
*
53765 G-TATATTATTTAATTTA
1 GTTTTA-TATTTAATTTA
53782 GTTTTATATT
1 GTTTTATATT
53792 GTAGCACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 3 0.14
16 3 0.14
17 13 0.59
18 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (17 bp):
GTTTTATATTTAATTTA
Found at i:61827 original size:130 final size:130
Alignment explanation
Indices: 61664--62696 Score: 1221
Period size: 130 Copynumber: 7.7 Consensus size: 130
61654 AAATAAAATT
* *
61664 GATTGCGTTTGCCGGGAGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCAAACCGTTGGA
1 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
* * *
61729 CTACAAAAGCTAGATGTTTAGAAATTTTACAAAAAAGAATATGTTTTTAAGTAATTTATAAAAAG
66 CTACAAACGCTTGATGTTAAGAAATTTTACAAAAAAGAATATGTTTTTAAGTAATTTATAAAAAG
61794 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
1 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
* * *
61859 CTACAAACGCTAGATGTTTAGAAACTTTACAAAAAAGAATATGTTTTTAAGTAATTTATAAAAAG
66 CTACAAACGCTTGATGTTAAGAAATTTTACAAAAAAGAATATGTTTTTAAGTAATTTATAAAAAG
*
61924 TATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
1 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
* * * *
61989 CTACAAACGCCTGATGTAAAGAAATTTTACAAAAAATAATATGTTTTTCAGTAATTTATAAAAAG
66 CTACAAACGCTTGATGTTAAGAAATTTTACAAAAAAGAATATGTTTTTAAGTAATTTATAAAAAG
62054 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
1 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
*
62119 CTACAAACGCTTGATGTTAAGAAATTTTACAAAAAAGAATATGTTTTTCAGTAATTTATAAAAAG
66 CTACAAACGCTTGATGTTAAGAAATTTTACAAAAAAGAATATGTTTTTAAGTAATTTATAAAAAG
*
62184 GATTGCGTTTGCCGGGAGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
1 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
* * * *
62249 CTACAAACGCTTGATGTTCAAGAGTTTAATTTTACAAAATAAAAAGA-ATTTTCAAGTGAATTT-
66 CTACAAACGCTTGATGTT-AAGA----AATTTTACAAAA-AAGAATATGTTTTTAAGT-AATTTA
*
62312 TAAAAAA
124 TAAAAAG
* * *
62319 AATTGCCTGCGTTTACCGGGAGTCGAACCCGGGTCTATTGCCTCTATTGCTTGGAAGGCAATTGT
1 GA-T---TGCGTTTGCCGGGAGTCGAACCC-GG------G--TCTATTGCTTGGAAGGCAATTAT
* *
62384 CCCAACCGTTGGACTACAAACGCTTGATGTTTAGGAGTTTAATTTTACAAAATAA-AA-AGTGTT
53 CCTAACCGTTGGACTACAAACGCTTGATG-TTA--AG--AAATTTTACAAAA-AAGAATA-TGTT
* * *
62447 TTCAAGTGAATTTTAAAAAAATT
111 TTTAAGT-AA-TTTATAAAAA-G
**
62470 GCCTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
1 GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
* *
62535 CTACAAACGCTTGATGTTAAAGAGCTTAATTTTAGAAAATAA-AA-AGTGTTTTCAAGTGAATTT
66 CTACAAACGCTTGATGTT-AAGA----AATTTTACAAAA-AAGAATA-TGTTTTTAAGT-AATTT
62598 -TAAAAA-
123 ATAAAAAG
* * * * *
62604 CATTACCTGCATTTGTCGGGAGTCGAACCTGGGGTC-----C-TGGAAGGCAATTATTCTAACCG
1 GA-T---TGCGTTTGCCGGGAGTCGAACC-CGGGTCTATTGCTTGGAAGGCAATTATCCTAACCG
* * *
62663 TTGAACTACAAACGCTTGATGTTAATAATTTTTA
61 TTGGACTACAAACGCTTGATGTTAAGAAATTTTA
62697 TTTTAAGATA
Statistics
Matches: 812, Mismatches: 51, Indels: 82
0.86 0.05 0.09
Matches are distributed among these distances:
128 6 0.01
130 456 0.56
131 4 0.00
132 3 0.00
133 43 0.05
134 1 0.00
135 26 0.03
136 18 0.02
137 5 0.01
138 103 0.13
139 27 0.03
140 3 0.00
146 3 0.00
147 24 0.03
148 78 0.10
149 5 0.01
150 7 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (130 bp):
GATTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGA
CTACAAACGCTTGATGTTAAGAAATTTTACAAAAAAGAATATGTTTTTAAGTAATTTATAAAAAG
Found at i:62014 original size:260 final size:265
Alignment explanation
Indices: 61484--62685 Score: 1262
Period size: 260 Copynumber: 4.5 Consensus size: 265
61474 TAGGAGTTTT
* * * ** * * *
61484 ATTTTACAAAATAAAATTTGTTTTCAAGTGATTTTTAAAAATTATTTACGTTTGCTGAGAGTCGA
1 ATTTTACAAAATAAAATATGTTTTCAAGTAATTTATAAAAAGGATTTGCGTTTGCCGGGAGTCGA
* ** * * * * * *
61549 ACCTGGGTCTATTG-TGTAAAAGTCAGTTATCTTAACCGTTGGACTACAAATGGTGGATGTTTAG
66 ACCCGGGTCTATTGCT-TGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATGTTTAG
* * * * *
61613 GAGT-TCTATTTA-AAAATAAATGTGTTTTCCTAAGTGATTTTAAATAAAATTGATTGCGTTTGC
130 GA-TAAC--TTTACAAAAAAAATATGTTTT--TAAGTGAATTTAAA-AAAAGTGATTGCGTTTGC
* *
61676 CGGGAGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCAAACCGTTGGACTACAAAAG-CT
189 CGGGAGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCCT
*
61740 AGATGTT-TAGAA
254 -GATGTTAAAGAA
*
61752 ATTTTACAAAA-AAGAATATGTTTTTAAGTAATTTATAAAAAGGA-TTGCGTTTGCCGGGAGTCG
1 ATTTTACAAAATAA-AATATGTTTTCAAGTAATTTATAAAAAGGATTTGCGTTTGCCGGGAGTCG
*
61815 AACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTAGATGTTTA-
65 AACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATGTTTAG
*
61879 GA-AACTTTACAAAAAAGAATATGTTTTTAAGT-AATTTATAAAAAGT-ATTGCGTTTGCCGGGA
130 GATAACTTTACAAAAAA-AATATGTTTTTAAGTGAATTTAAAAAAAGTGATTGCGTTTGCCGGGA
*
61941 GTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCCTGATG-
194 GTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCCTGATGT
62005 TAAAGAA
259 TAAAGAA
62012 ATTTTACAAAA-AATAATATGTTTTTC-AGTAATTTATAAAAAGGA-TTGCGTTTGCCGGGAGTC
1 ATTTTACAAAATAA-AATATG-TTTTCAAGTAATTTATAAAAAGGATTTGCGTTTGCCGGGAGTC
62074 GAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATG-TTA
64 GAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATGTTTA
* * * *
62138 AGA-AATTTTACAAAAAAGAATATGTTTTTCAGT-AATTTATAAAAAG-GATTGCGTTTGCCGGG
129 GGATAACTTTACAAAAAA-AATATGTTTTTAAGTGAATTTAAAAAAAGTGATTGCGTTTGCCGGG
*
62200 AGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATG
193 AGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCCTGATG
*
62265 TTCAAGAGTTTA
258 TT-AA-AG--AA
** *
62277 ATTTTACAAAATAAAA-A-GAATTTTCAAGTGAATTT-TAAAAAAAATTGCCTGCGTTTACCGGG
1 ATTTTACAAAATAAAATATG--TTTTCAAGT-AATTTATAAAAAGGATT---TGCGTTTGCCGGG
* *
62339 AGTCGAACCCGGGTCTATTGCCTCTATTGCTTGGAAGGCAATTGTCCCAACCGTTGGACTACAAA
60 AGTCGAACCC-GG------G--TCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAA
* *
62404 CGCTTGATGTTTAGGAGTTTAATTTTACAAAATAAAA-AGTGTTTTCAAGTGAATTTTAAAAAAA
116 CGCTTGATGTTTAGGA---TAACTTTACAAAA-AAAATA-TGTTTTTAAGTGAA-TTTAAAAAAA
* ** *
62468 TTGCCTGCGTTTGCCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTG
175 GTGATTGCGTTTGCCGGGAGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTG
*
62533 GACTACAAACGCTTGATGTTAAAGAGCTTA
240 GACTACAAACGCCTGATGTTAAAGA----A
* * * *
62563 ATTTTAGAAAATAAAA-AGTGTTTTCAAGTGAATTT-TAAAAA-CATTACCTGCATTTGTCGGGA
1 ATTTTACAAAATAAAATA-TGTTTTCAAGT-AATTTATAAAAAGGATT---TGCGTTTGCCGGGA
* * *
62625 GTCGAACCTGGGGTC-----C-TGGAAGGCAATTATTCTAACCGTTGAACTACAAACGCTTGATG
61 GTCGAACC-CGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATG
62684 TT
125 TT
62686 AATAATTTTT
Statistics
Matches: 823, Mismatches: 62, Indels: 95
0.84 0.06 0.10
Matches are distributed among these distances:
259 4 0.00
260 314 0.38
261 12 0.01
262 8 0.01
263 12 0.01
264 11 0.01
265 34 0.04
266 10 0.01
267 71 0.09
268 36 0.04
269 22 0.03
270 2 0.00
271 41 0.05
272 1 0.00
276 1 0.00
277 2 0.00
278 50 0.06
279 6 0.01
282 1 0.00
283 23 0.03
284 6 0.01
285 37 0.04
286 118 0.14
288 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (265 bp):
ATTTTACAAAATAAAATATGTTTTCAAGTAATTTATAAAAAGGATTTGCGTTTGCCGGGAGTCGA
ACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATGTTTAGG
ATAACTTTACAAAAAAAATATGTTTTTAAGTGAATTTAAAAAAAGTGATTGCGTTTGCCGGGAGT
CGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCCTGATGTTA
AAGAA
Found at i:62710 original size:133 final size:133
Alignment explanation
Indices: 61478--62711 Score: 731
Period size: 130 Copynumber: 9.2 Consensus size: 133
61468 ATTGTTTAGG
* ** * ** * * *
61478 AGTTTTATTTTACA-AAATAAAATTTGTTTTCAAGTG-ATTTT-TAAAAATTATTTACGTTTGCT
1 AGTTTAATTTTA-AGAAATAAAAAGTGTTTTCAAGTGAATTTTAAAAAAATTACCTGCATTTGCC
* * * * * * * * *
61540 GAGAGTCGAACCTGGGTCTATTGTGTAAAAGTCAGTTATCTTAACCGTTGGACTACAAATGGTGG
65 GGGAGTCGAACCCGGGTCTCTTG-G---AAGGCAATTATCCTAACCGTTGGACTACAAACGCTTG
**
61605 ATGTTTAGG
126 ATG-TTAAA
* * *
61614 AGTTCT-A-TTTAA-AAAT-AAATGTGTTTTCCTAAGTG-ATTTTAAATAAAATTGA-TTGCGTT
1 AGTT-TAATTTTAAGAAATAAAAAGTGTTTT-C-AAGTGAATTTTAAA-AAAATT-ACCTGCATT
* * *
61673 TGCCGGGAGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCAAACCGTTGGACTACAAAAG
61 TGCCGGGAGTCGAACCCGGGTC---T-CTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACG
* *
61738 CTAGATGTT--T
122 CTTGATGTTAAA
* * * ** * *
61748 AG--AAATTTTACA-AAA-AAGAATA-TGTTTTTAAGT-AA-TTTATAAAAAGGA-TTGCGTTTG
1 AGTTTAATTTTA-AGAAATAA-AA-AGTGTTTTCAAGTGAATTTTAAAAAAATTACCTGCATTTG
61805 CCGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCT
63 CCGGGAGTCGAACCCGGGTC---T-CTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCT
*
61870 AGATGTTTAGAA
124 TGATG-TTA-AA
* * * * * * * *
61882 ACTTTACA----AA-AAA-GAATA-TGTTTTTAAGT-AA-TTTATAAAAAGTA-TTGCGTTTGCC
1 AGTTTA-ATTTTAAGAAATAAAAAGTGTTTTCAAGTGAATTTTAAAAAAATTACCTGCATTTGCC
*
61937 GGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCCTG
65 GGGAGTCGAACCCGGGTC---T-CTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTG
62002 ATG-T-AA
126 ATGTTAAA
* * * * * ** * *
62008 AG--AAATTTTACAAAAAATAATATGT-TTTTC-AGT-AA-TTTATAAAAAGGA-TTGCGTTTGC
1 AGTTTAATTTT--AAGAAATAAAAAGTGTTTTCAAGTGAATTTTAAAAAAATTACCTGCATTTGC
62066 CGGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTT
64 CGGGAGTCGAACCCGGGTC---T-CTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTT
62131 GATGTT--A
125 GATGTTAAA
* * ** * *
62138 AG--AAATTTTACA-AAA-AAGAATA-TGTTTTTC-AGT-AA-TTTATAAAAAGGA-TTGCGTTT
1 AGTTTAATTTTA-AGAAATAA-AA-AGTG-TTTTCAAGTGAATTTTAAAAAAATTACCTGCATTT
*
62194 GCCGGGAGTCGAACCCGGATCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGC
62 GCCGGGAGTCGAACCCGGGTC---T-CTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGC
*
62259 TTGATGTTCAAG
123 TTGATGTT-AAA
** * * *
62271 AGTTTAATTTTACA-AAATAAAAAGAATTTTCAAGTGAATTTTAAAAAAAATTGCCTGCGTTTAC
1 AGTTTAATTTTA-AGAAATAAAAAGTGTTTTCAAGTGAATTTT-AAAAAAATTACCTGCATTTGC
* *
62335 CGGGAGTCGAACCCGGGTCTATTGCCTCTATTGCTTGGAAGGCAATTGTCCCAACCGTTGGACTA
64 CGGGAGTCGAACCC-GG------G--TC---T-CTTGGAAGGCAATTATCCTAACCGTTGGACTA
**
62400 CAAACGCTTGATGTTTAGG
116 CAAACGCTTGATG-TTAAA
* *
62419 AGTTTAATTTTACA-AAATAAAAAGTGTTTTCAAGTGAATTTTAAAAAAATTGCCTGCGTTTGCC
1 AGTTTAATTTTA-AGAAATAAAAAGTGTTTTCAAGTGAATTTTAAAAAAATTACCTGCATTTGCC
62483 GGGAGTCGAACCCGGGTCTATTGCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTG
65 GGGAGTCGAACCCGGGTC---T-CTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTG
62548 ATGTTAAA
126 ATGTTAAA
* * *
62556 GAGCTTAATTTT-AGAAAATAAAAAGTGTTTTCAAGTGAATTTTAAAAACATTACCTGCATTTGT
1 -AGTTTAATTTTAAG-AAATAAAAAGTGTTTTCAAGTGAATTTTAAAAAAATTACCTGCATTTGC
* * *
62620 CGGGAGTCGAACCTGGGGTC-C-TGGAAGGCAATTATTCTAACCGTTGAACTACAAACGCTTGAT
64 CGGGAGTCGAACC-CGGGTCTCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGAT
62683 GTTAATA
128 GTTAA-A
* * *
62690 ATTTTTATTTTAAGATATAAAA
1 AGTTTAATTTTAAGAAATAAAA
62712 CTGAAAAAGA
Statistics
Matches: 953, Mismatches: 78, Indels: 137
0.82 0.07 0.12
Matches are distributed among these distances:
123 1 0.00
124 1 0.00
126 3 0.00
127 2 0.00
128 7 0.01
129 3 0.00
130 391 0.41
131 13 0.01
132 12 0.01
133 82 0.09
134 24 0.03
135 39 0.04
136 14 0.01
137 71 0.07
138 125 0.13
139 27 0.03
140 5 0.01
141 3 0.00
146 2 0.00
147 34 0.04
148 92 0.10
149 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (133 bp):
AGTTTAATTTTAAGAAATAAAAAGTGTTTTCAAGTGAATTTTAAAAAAATTACCTGCATTTGCCG
GGAGTCGAACCCGGGTCTCTTGGAAGGCAATTATCCTAACCGTTGGACTACAAACGCTTGATGTT
AAA
Found at i:69327 original size:2 final size:2
Alignment explanation
Indices: 69320--69352 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
69310 TACTTTTACC
*
69320 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69353 TAGATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:71043 original size:24 final size:24
Alignment explanation
Indices: 71013--71065 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
71003 TTCTTTAGAG
*
71013 GTTAAAATGTAATTCTATGATTGT
1 GTTAAAATGTAATTCTATGATCGT
71037 GTTAAAATGTAATTCTATGATCGT
1 GTTAAAATGTAATTCTATGATCGT
71061 GTTAA
1 GTTAA
71066 TTTAAAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (24 bp):
GTTAAAATGTAATTCTATGATCGT
Found at i:71145 original size:31 final size:33
Alignment explanation
Indices: 71093--71153 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
71083 GTTTCAAGTC
*
71093 TTTTTATTTTTTGTATATTTAATATTTAATTTT
1 TTTTTATTTTTTGTATATTTAAAATTTAATTTT
71126 TTTTTATTTTATT-T-T-TTTAAAATTTAAT
1 TTTTTATTTT-TTGTATATTTAAAATTTAAT
71154 CTTAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 12 0.46
32 1 0.04
33 11 0.42
34 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (33 bp):
TTTTTATTTTTTGTATATTTAAAATTTAATTTT
Found at i:83906 original size:23 final size:23
Alignment explanation
Indices: 83878--83923 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
83868 AAGTTGATAC
83878 AAAAAATATTTGGACT-CTTAAAA
1 AAAAAAT-TTTGGACTCCTTAAAA
*
83901 AAAAAATTTTGGGCTCCTTAAAA
1 AAAAAATTTTGGACTCCTTAAAA
83924 GTTGTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (23 bp):
AAAAAATTTTGGACTCCTTAAAA
Found at i:86024 original size:17 final size:17
Alignment explanation
Indices: 86002--86035 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
85992 TTGTTTGGTT
*
86002 GTAAATGATTTTCCAAA
1 GTAAATGATTTTACAAA
*
86019 GTAAATTATTTTACAAA
1 GTAAATGATTTTACAAA
86036 CATGGGAAAA
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:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
GTAAATGATTTTACAAA
Found at i:86111 original size:87 final size:87
Alignment explanation
Indices: 86009--86194 Score: 372
Period size: 87 Copynumber: 2.1 Consensus size: 87
85999 GTTGTAAATG
86009 ATTTTCCAAAGTAAATTATTTTACAAACATGGGAAAATGGGAGCGTTTTTTGGGGAAAATGTCTT
1 ATTTTCCAAAGTAAATTATTTTACAAACATGGGAAAATGGGAGCGTTTTTTGGGGAAAATGTCTT
86074 ACGCTTTTTATTTTAGTAAGAT
66 ACGCTTTTTATTTTAGTAAGAT
86096 ATTTTCCAAAGTAAATTATTTTACAAACATGGGAAAATGGGAGCGTTTTTTGGGGAAAATGTCTT
1 ATTTTCCAAAGTAAATTATTTTACAAACATGGGAAAATGGGAGCGTTTTTTGGGGAAAATGTCTT
86161 ACGCTTTTTATTTTAGTAAGAT
66 ACGCTTTTTATTTTAGTAAGAT
86183 ATTTTCCAAAGT
1 ATTTTCCAAAGT
86195 TTTACCTTCT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 99 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (87 bp):
ATTTTCCAAAGTAAATTATTTTACAAACATGGGAAAATGGGAGCGTTTTTTGGGGAAAATGTCTT
ACGCTTTTTATTTTAGTAAGAT
Found at i:86248 original size:6 final size:6
Alignment explanation
Indices: 86239--86306 Score: 100
Period size: 6 Copynumber: 11.3 Consensus size: 6
86229 GGTAAATGCT
* *
86239 TTCTCT TTCTCC TTCTCA TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
* *
86287 TTCTCC TTCCCC TTCCCC TT
1 TTCTCC TTCTCC TTCTCC TT
86307 TCATTGCGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.01, C:0.49, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCTCC
Found at i:86611 original size:6 final size:6
Alignment explanation
Indices: 86602--86705 Score: 136
Period size: 6 Copynumber: 17.3 Consensus size: 6
86592 GGTAAATGCT
* * * * *
86602 TTCTCT TTCTCT TTCTCT TTCTCT TTCTCC TTCTCA TTCTCC TTCTCC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
* *
86650 TTCTCC TTCTCA TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCCCC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
*
86698 TTCCCC TT
1 TTCTCC TT
86706 TCATTGCGTC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 92 1.00
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (6 bp):
TTCTCC
Found at i:88109 original size:96 final size:96
Alignment explanation
Indices: 87927--88119 Score: 232
Period size: 96 Copynumber: 2.0 Consensus size: 96
87917 GAATTTTGGA
* *** **
87927 AAAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGATAAGGTGCAAATTTTC
1 AAAGGATATTAGATTATCTCGATTTGAAGAAAAAATGCACCTAGTAAGATAAGGCACAAATTTTC
87992 AGAATCGATGATAAGAAAATATTGCCTCGATT
66 AGAATCGATGATAAG-AAATATTGCCTCGATT
* *
88024 AAAGG-TATTAGATTATTTCGATTTGAAGAAAAAATGCACCTAGTAAGTTAAGGCACAAAATTTT
1 AAAGGATATTAGATTATCTCGATTTGAAGAAAAAATGCACCTAGTAAGATAAGGCAC-AAATTTT
*
88088 GA-AACTCGAAATGA-AAG-AATATTGCCTCGATT
65 CAGAA-TCG--ATGATAAGAAATATTGCCTCGATT
88120 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
96 60 0.72
97 16 0.19
98 3 0.04
99 4 0.05
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (96 bp):
AAAGGATATTAGATTATCTCGATTTGAAGAAAAAATGCACCTAGTAAGATAAGGCACAAATTTTC
AGAATCGATGATAAGAAATATTGCCTCGATT
Found at i:88503 original size:29 final size:29
Alignment explanation
Indices: 88471--88725 Score: 245
Period size: 29 Copynumber: 8.6 Consensus size: 29
88461 TTGGGACATC
** *
88471 CGAGGTAAAAGGGTAATTTTTGAAAGTTT
1 CGAGGTAAAAATGTAATTTTTGGAAGTTT
*
88500 CGAGGTTAAAAATGAAATTTTTGGAAG-TT
1 CGAGG-TAAAAATGTAATTTTTGGAAGTTT
88529 CGAGGGTAAAAATGTAATTTTTGGAAGTTT
1 CGA-GGTAAAAATGTAATTTTTGGAAGTTT
88559 CGAGGTCAAAAATAG-AATTTTTGGAAG-TT
1 CGAGGT-AAAAAT-GTAATTTTTGGAAGTTT
*
88588 CGGAGGTAAAAATGTAATTTTTGTAAGTTT
1 C-GAGGTAAAAATGTAATTTTTGGAAGTTT
* *
88618 C-AGGGTCAAAAATGGATTTTTTGGAAG-TT
1 CGA-GGT-AAAAATGTAATTTTTGGAAGTTT
* *
88647 CGGGGGTAAAAAATTTAAATTTTTGGAAGTTT
1 C-GAGGT-AAAAATGT-AATTTTTGGAAGTTT
* * *
88679 -TAGGGTTAAAATGGAATTTTTGGAAGTTT
1 CGA-GGTAAAAATGTAATTTTTGGAAGTTT
88708 -GAGGGTAAAAATGTAATT
1 CGA-GGTAAAAATGTAATT
88726 CTTGAATAGT
Statistics
Matches: 189, Mismatches: 22, Indels: 30
0.78 0.09 0.12
Matches are distributed among these distances:
28 2 0.01
29 89 0.47
30 81 0.43
31 15 0.08
32 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
CGAGGTAAAAATGTAATTTTTGGAAGTTT
Found at i:88549 original size:59 final size:60
Alignment explanation
Indices: 88447--88737 Score: 303
Period size: 59 Copynumber: 4.9 Consensus size: 60
88437 AAAATTGGGA
* * * **
88447 TCAAAAACGAAATTTTGGGACA-TCCGA-GGTAAAAGGGTAATTTTTGAAAGTTTCGA-GG
1 TCAAAAATGAAATTTTTGGA-AGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGG
* *
88505 TTAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGA-GG
1 TCAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGG
*
88564 TCAAAAAT-AGAATTTTTGGAAGTTCG-GAGGTAAAAATGTAATTTTTGTAAGTTTC-AGGG
1 TCAAAAATGA-AATTTTTGGAAGTTCGAG-GGTAAAAATGTAATTTTTGAAAGTTTCGAGGG
* * * * * *
88623 TCAAAAATGGATTTTTTGGAAGTTCGGGGGTAAAAAATTTAAATTTTTGGAAGTTT-TAGGG
1 TCAAAAATGAAATTTTTGGAAGTTCGAGGGT-AAAAATGT-AATTTTTGAAAGTTTCGAGGG
* * * *
88684 T-TAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTCTTGAATAGTTT
1 TCAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAA-AGTTT
88738 AGGGACCTTC
Statistics
Matches: 202, Mismatches: 20, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
57 1 0.00
58 32 0.16
59 117 0.58
60 33 0.16
61 19 0.09
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (60 bp):
TCAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGG
Found at i:90398 original size:16 final size:16
Alignment explanation
Indices: 90377--90416 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
90367 AAATCCATTC
90377 AAATTTGAT-CAAATTT
1 AAATTT-ATACAAATTT
90393 AAATTTATAGCAAATTT
1 AAATTTATA-CAAATTT
90410 AAATTTA
1 AAATTTA
90417 AAAAGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 6 0.27
17 14 0.64
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
AAATTTATACAAATTT
Found at i:91125 original size:30 final size:30
Alignment explanation
Indices: 91091--91167 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
91081 CTTGCCTTCT
*
91091 TGTAAATGCAGTTCGTGCAACTGCAATCCG
1 TGTAAATGCAGCTCGTGCAACTGCAATCCG
* * *
91121 TGTAAATGCAACTCGTGCGACTGTAATCCG
1 TGTAAATGCAGCTCGTGCAACTGCAATCCG
*
91151 TGTAAATACAGCTCGTG
1 TGTAAATGCAGCTCGTG
91168 TGATTGTAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (30 bp):
TGTAAATGCAGCTCGTGCAACTGCAATCCG
Found at i:110790 original size:18 final size:19
Alignment explanation
Indices: 110756--110791 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
110746 AAATATTAAA
*
110756 TTAAAATAATATAAATATT
1 TTAAAAAAATATAAATATT
110775 TTAAAAAAAT-TAAATAT
1 TTAAAAAAATATAAATAT
110792 AATATGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAAAAATATAAATATT
Found at i:110810 original size:29 final size:28
Alignment explanation
Indices: 110753--110810 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
110743 ATTAAATATT
* *
110753 AAATTAAAATAATATAAATATTTTAAAA
1 AAATTAAAATAATATAAATAGTCTAAAA
*
110781 AAATTAAATATAATATGAATGAGTCTAAAA
1 AAATTAAA-ATAATATAAAT-AGTCTAAAA
110811 TGAGCTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.32
29 10 0.40
30 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATTAAAATAATATAAATAGTCTAAAA
Found at i:120037 original size:20 final size:18
Alignment explanation
Indices: 119997--120037 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
119987 GGTTCAAAAG
*
119997 TTAGGTTTGGGTTAAGTT
1 TTAGGTTTGGGTTAAGAT
120015 TTAGGTTTAGGGTTTAAGAT
1 TTAGGTTT-GGG-TTAAGAT
120035 TTA
1 TTA
120038 TGATTCAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (18 bp):
TTAGGTTTGGGTTAAGAT
Found at i:120068 original size:40 final size:41
Alignment explanation
Indices: 120019--120112 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
120009 TAAGTTTTAG
* *
120019 GTTTAGGGTTTAAGATTTATGATTC-AGGGTTC-GAGTTTGGA
1 GTTTAGGGTTCAAG-TTTAAGATTCGA-GGTTCGGAGTTTGGA
* *
120060 GTTT-GGGTTCAAGTTTAAGATTCGAGGTTCGGAGTTTAGT
1 GTTTAGGGTTCAAGTTTAAGATTCGAGGTTCGGAGTTTGGA
120100 GTTTAGGGTTCAA
1 GTTTAGGGTTCAA
120113 TATTTTGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 14 0.30
40 20 0.43
41 12 0.26
ACGTcount: A:0.21, C:0.06, G:0.32, T:0.40
Consensus pattern (41 bp):
GTTTAGGGTTCAAGTTTAAGATTCGAGGTTCGGAGTTTGGA
Done.