Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000384.1 Kokia drynarioides strain JFW-HI SEQ_111185, 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: 92773
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:2174 original size:16 final size:16
Alignment explanation
Indices: 2155--2192 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2145 GATCGAATTT
2155 TAATTTTA-ATTTTTAA
1 TAATTTTATATTTTT-A
2171 TAA-TTTATATTTTTA
1 TAATTTTATATTTTTA
2186 TAATTTT
1 TAATTTT
2193 TAAAAGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATTTTATATTTTTA
Found at i:11252 original size:5 final size:5
Alignment explanation
Indices: 11242--11271 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
11232 TATCAATCAC
11242 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT
1 CCCCT CCCCT CCCCT CCCCT CCCCT CCCCT
11272 GCATGGTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCCT
Found at i:23409 original size:15 final size:14
Alignment explanation
Indices: 23363--23413 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
23353 ACAAGATGAT
23363 AATATAAATAATTAA
1 AATATAAAT-ATTAA
* *
23378 AATGTAACAT-TTTA
1 AATATAA-ATATTAA
23392 AATATAAATGATTAA
1 AATATAAAT-ATTAA
23407 AATATAA
1 AATATAA
23414 CTTAGATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 2 0.07
14 9 0.31
15 16 0.55
16 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (14 bp):
AATATAAATATTAA
Found at i:28063 original size:17 final size:17
Alignment explanation
Indices: 28041--28074 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28031 ACAAAAATTC
*
28041 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
28058 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
28075 TTATTGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:28869 original size:17 final size:17
Alignment explanation
Indices: 28831--28868 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
28821 AATTTAATTC
*
28831 ATTTGATATATTTAAAT
1 ATTTTATATATTTAAAT
28848 ATTTTATATA-TTAAAT
1 ATTTTATATATTTAAAT
28864 ATTTT
1 ATTTT
28869 TTTAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTATATATTTAAAT
Found at i:28881 original size:12 final size:13
Alignment explanation
Indices: 28860--28888 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28850 TTTATATATT
28860 AAATATTTTTTTA
1 AAATATTTTTTTA
28873 AAATA-TTTTTTA
1 AAATATTTTTTTA
28885 AAAT
1 AAAT
28889 GACAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AAATATTTTTTTA
Found at i:30754 original size:6 final size:6
Alignment explanation
Indices: 30743--30781 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
30733 ACTTTCAGCC
* * *
30743 GCCTGA GCCTGA GCTTAA GCTTGA GCCTGA GCCTGA GCC
1 GCCTGA GCCTGA GCCTGA GCCTGA GCCTGA GCCTGA GCC
30782 GTAGCACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.18, C:0.31, G:0.31, T:0.21
Consensus pattern (6 bp):
GCCTGA
Found at i:31382 original size:26 final size:26
Alignment explanation
Indices: 31327--31402 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
31317 GCTAAACCTC
**
31327 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
31353 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
31379 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
31403 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:34216 original size:25 final size:26
Alignment explanation
Indices: 34167--34218 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
34157 AACCTTCTTT
* *
34167 TTCCTTTTCTTCTTCAAAACTTTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
34193 TTCCTTTCCTTCTTCAAAA-ATTTGC
1 TTCCTTTCCTTCTTCAAAACATTTGC
34218 T
1 T
34219 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.17, C:0.27, G:0.04, T:0.52
Consensus pattern (26 bp):
TTCCTTTCCTTCTTCAAAACATTTGC
Found at i:54540 original size:3 final size:3
Alignment explanation
Indices: 54534--54565 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
54524 TTTTTTTTGT
54534 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54566 TTGCAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:57395 original size:6 final size:6
Alignment explanation
Indices: 57384--57410 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
57374 TTAATGGTTC
57384 CTTCTG CTTCTG CTTCTG CTTCTG CTT
1 CTTCTG CTTCTG CTTCTG CTTCTG CTT
57411 ATTAATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
CTTCTG
Found at i:58046 original size:28 final size:26
Alignment explanation
Indices: 58015--58075 Score: 61
Period size: 28 Copynumber: 2.2 Consensus size: 26
58005 AAAATTCGGG
58015 AAAAAAATATAATAT-TAAAAAATATTTT
1 AAAAAAA-A-AATATATAAAAAA-ATTTT
*
58043 AAAATTAAAAAATATATAACAAAATTTT
1 AAAA--AAAAAATATATAAAAAAATTTT
58071 AAAAA
1 AAAAA
58076 TTAGAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
26 1 0.03
28 18 0.62
29 7 0.24
30 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAAAAAAATATATAAAAAAATTTT
Found at i:63137 original size:25 final size:24
Alignment explanation
Indices: 63099--63146 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
63089 GCTTTTGAGG
* * *
63099 ATAAATATATTTATGTAATAAATTT
1 ATAAAAATACTTATATAA-AAATTT
63124 ATAAAAATACTTATATAAAAATT
1 ATAAAAATACTTATATAAAAATT
63147 AAATGTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
ATAAAAATACTTATATAAAAATTT
Found at i:63488 original size:24 final size:25
Alignment explanation
Indices: 63436--63488 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
63426 TTTATTGGTT
* * *
63436 TTTTTCCTCTTATTTTTAGATTAGG
1 TTTTCCCTCTTATTTTTAGAATAGA
*
63461 TTTTCCCT-TTATTTTTAGAATATA
1 TTTTCCCTCTTATTTTTAGAATAGA
63485 TTTT
1 TTTT
63489 ATTTTGTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTTCCCTCTTATTTTTAGAATAGA
Found at i:66983 original size:14 final size:14
Alignment explanation
Indices: 66938--66983 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
66928 AAGTTGTTGC
66938 TTTAATTTCTATA-T
1 TTTAATTT-TATATT
66952 TTTAA-TTTAGTTATT
1 TTTAATTTTA--TATT
66967 TTTAATTTTATATT
1 TTTAATTTTATATT
66981 TTT
1 TTT
66984 TTAAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 14 0.50
15 6 0.21
16 4 0.14
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTAATTTTATATT
Found at i:72331 original size:22 final size:23
Alignment explanation
Indices: 72288--72331 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
72278 GCTATTGTTA
* *
72288 TAAAAAAAATTGGTGTTTATTTT
1 TAAAAAAAATTGGTGCTAATTTT
*
72311 TAAAAAAAGTT-GTGCTAATTT
1 TAAAAAAAATTGGTGCTAATTT
72332 AATTAAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (23 bp):
TAAAAAAAATTGGTGCTAATTTT
Found at i:76708 original size:12 final size:12
Alignment explanation
Indices: 76672--76733 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
76662 AATTTAATAT
*
76672 TATTTTGAGAAG
1 TATTTTGAAAAG
* * *
76684 TGCTTTTAAAAAA
1 T-ATTTTGAAAAG
76697 TATTTTGGAAAAG
1 TATTTT-GAAAAG
*
76710 TTTTTTGAAAAG
1 TATTTTGAAAAG
76722 TACTTTTGAAAA
1 TA-TTTTGAAAA
76734 AATTTGGTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
12 12 0.32
13 26 0.68
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (12 bp):
TATTTTGAAAAG
Found at i:77103 original size:16 final size:18
Alignment explanation
Indices: 77082--77116 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
77072 TTTAGCATTG
77082 GTTTTT-AT-TCAAAAGT
1 GTTTTTCATGTCAAAAGT
77098 GTTTTTCATGTCAAAAGT
1 GTTTTTCATGTCAAAAGT
77116 G
1 G
77117 CTTCTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.46
Consensus pattern (18 bp):
GTTTTTCATGTCAAAAGT
Found at i:77476 original size:40 final size:40
Alignment explanation
Indices: 77432--77517 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
77422 TAATGATATT
77432 AATTTGGTTGAAATATGCTATTCATCTTTGTTTTTATCAA
1 AATTTGGTTGAAATATGCTATTCATCTTTGTTTTTATCAA
77472 AATTTGGTTGAAATATGCTATTCATCTTTGTTTTTATCAA
1 AATTTGGTTGAAATATGCTATTCATCTTTGTTTTTATCAA
*
77512 CATTTG
1 AATTTG
77518 AGTTTTAGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (40 bp):
AATTTGGTTGAAATATGCTATTCATCTTTGTTTTTATCAA
Found at i:80695 original size:2 final size:2
Alignment explanation
Indices: 80688--80719 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
80678 AACAATGTAA
80688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80720 TTCTGGGGAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82491 original size:24 final size:24
Alignment explanation
Indices: 82427--82491 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 24
82417 TTAATATTCA
** *
82427 CGAACATGTTCATTTA-ATTTAAT
1 CGAACATGTTCATAAACATATAAT
* * *
82450 CGAACATTTTCTTGAACATATAAT
1 CGAACATGTTCATAAACATATAAT
*
82474 TGAACATGTTCATAAACA
1 CGAACATGTTCATAAACA
82492 ATGTTAATGA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (24 bp):
CGAACATGTTCATAAACATATAAT
Found at i:90809 original size:60 final size:60
Alignment explanation
Indices: 90623--90828 Score: 204
Period size: 60 Copynumber: 3.4 Consensus size: 60
90613 CGAGAATTTG
* * **
90623 AAAAAATCAAATTTTTTTTGTGTTGATCATGCAATGGCCGACA-TCTCATTTTTTGTCAGAT
1 AAAAAATCAAA-TTTTTTGGTATTGGCCATGCAATGGCCGACACTCTC-TTTTTTGTCAGAT
* * * * * * * * * *
90684 AAAAAA-AATAATTTTTTGGTGTTGGCCATGTAATGACCGACAC-CCCTATTTATCTAATAA
1 AAAAAATCA-AATTTTTTGGTATTGGCCATGCAATGGCCGACACTCTCT-TTTTTGTCAGAT
90744 AAAAAATCAAATTTTTTGGTATTGGCCATGCAATGGCCGACACTCTCTTTTTTGTCAGAT
1 AAAAAATCAAATTTTTTGGTATTGGCCATGCAATGGCCGACACTCTCTTTTTTGTCAGAT
*
90804 AAAAAATTC-AATTTTTTAGTATTGG
1 AAAAAA-TCAAATTTTTTGGTATTGG
90829 TCAAGTATTT
Statistics
Matches: 116, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
59 1 0.01
60 101 0.87
61 14 0.12
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (60 bp):
AAAAAATCAAATTTTTTGGTATTGGCCATGCAATGGCCGACACTCTCTTTTTTGTCAGAT
Found at i:91069 original size:123 final size:122
Alignment explanation
Indices: 90836--91139 Score: 283
Period size: 123 Copynumber: 2.5 Consensus size: 122
90826 TGGTCAAGTA
* * * ** * *
90836 TTTATCTGATAAAAAAAATCAAATTTTTGAGTGTT-AGCCATGCAATTG-GCGACACTTTTTTTT
1 TTTATCAGATAAAAAAAATCAAATTTTTGAGTGTTGA-TCATGCAA-TGACCGACACCCTCTATT
* * * * * *
90899 TTCAAATAACAAAAATTTCAAAATTTTTTTGTGTTGATCATGCAATGGCTGACGC-CTCCTT
64 TGCAGAT-A-AAAAATATCAAAATTTTTTTGTATTGATCATACAATGGCTGACACTC-CCTT
* ** ** *
90960 TTTGT-AGATAAAAAATTTTCAAATTTTTTTTGTGTTGATCATGCAATGGCCGACACCCTCTATT
1 TTTATCAGATAAAAAA-AATCAAA-TTTTTGAGTGTTGATCATGCAATGACCGACACCCTCTATT
* * * *
91024 TGCAGATAAAAAATATCAAATTTTTTTTGTATTGGTCATATAATGGTTGACACTCCCTT
64 TGCAGATAAAAAATATCAAAATTTTTTTGTATTGATCATACAATGGCTGACACTCCCTT
* * *
91083 TTTATCTGATAAAAAAAATCAAATTTTTGAGTGTTGGTCATGTAATGACCGACACCC
1 TTTATCAGATAAAAAAAATCAAATTTTTGAGTGTTGATCATGCAATGACCGACACCC
91140 CCTTTTCTCA
Statistics
Matches: 143, Mismatches: 31, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
122 29 0.20
123 59 0.41
124 22 0.15
125 32 0.22
126 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (122 bp):
TTTATCAGATAAAAAAAATCAAATTTTTGAGTGTTGATCATGCAATGACCGACACCCTCTATTTG
CAGATAAAAAATATCAAAATTTTTTTGTATTGATCATACAATGGCTGACACTCCCTT
Found at i:91094 original size:62 final size:60
Alignment explanation
Indices: 90895--91145 Score: 218
Period size: 62 Copynumber: 4.1 Consensus size: 60
90885 CGACACTTTT
* * * *
90895 TTTTTTCAAATAACAAAAATTTCAAAATTTTTTTGTGTTGATCATGCAATGGCTGACGCCTCC
1 TTTTTTCAGAT-A-AAAAATATCAAATTTTTTTTGTGTTGATCATGCAATGGCTGACACC-CC
* *
90958 TTTTTGT-AGATAAAAAATTTTCAAATTTTTTTTGTGTTGATCATGCAATGGCCGACACCCTC
1 TTTTT-TCAGATAAAAAA-TATCAAATTTTTTTTGTGTTGATCATGCAATGGCTGACACCC-C
* * * * ** *
91020 TATTTGCAGATAAAAAATATCAAATTTTTTTTGTATTGGTCATATAATGGTTGACACTCCC
1 TTTTTTCAGATAAAAAATATCAAATTTTTTTTGTGTTGATCATGCAATGGCTGACAC-CCC
* * ** * * * *
91081 TTTTTATCTGATAAAAAAAATCAAA-TTTTTGAGTGTTGGTCATGTAATGACCGACACCCC
1 TTTTT-TCAGATAAAAAATATCAAATTTTTTTTGTGTTGATCATGCAATGGCTGACACCCC
*
91141 CTTTT
1 TTTTT
91146 CTCATATGGT
Statistics
Matches: 157, Mismatches: 25, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
60 7 0.04
61 69 0.44
62 72 0.46
63 8 0.05
64 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (60 bp):
TTTTTTCAGATAAAAAATATCAAATTTTTTTTGTGTTGATCATGCAATGGCTGACACCCC
Found at i:91143 original size:61 final size:61
Alignment explanation
Indices: 90836--91145 Score: 223
Period size: 61 Copynumber: 5.0 Consensus size: 61
90826 TGGTCAAGTA
* ** * * ***
90836 TTTATCTGATAAAAAAAATCAAATTTTTGAGTGTTAGCCATGCAATTGG-CGACA-CTTTTT
1 TTTATCAGATAAAAAAAATCAAATTTTTTTGTGTTGGTCATGCAA-TGGCCGACACCCCCTT
* * * * * * *
90896 TTTTTCAAATAACAAAAATTTCAAAATTTTTTTGTGTTGATCATGCAATGGCTGACGCCTCCTT
1 TTTATCAGATAA-AAAAA-ATC-AAATTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCCTT
* ** * * *
90960 TTTGT-AGATAAAAAATTTTCAAATTTTTTTTGTGTTGATCATGCAATGGCCGACACCCTCTA
1 TTTATCAGATAAAAAA-AATCAAA-TTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCCTT
* * * ** ** *
91022 TTT-GCAGATAAAAAATATCAAATTTTTTTTGTATTGGTCATATAATGGTTGACACTCCCTT
1 TTTATCAGATAAAAAAAATCAAA-TTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCCTT
* ** * *
91083 TTTATCTGATAAAAAAAATCAAATTTTTGAGTGTTGGTCATGTAATGACCGACACCCCCTT
1 TTTATCAGATAAAAAAAATCAAATTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCCTT
91144 TT
1 TT
91146 CTCATATGGT
Statistics
Matches: 198, Mismatches: 43, Indels: 17
0.77 0.17 0.07
Matches are distributed among these distances:
60 9 0.05
61 79 0.40
62 74 0.37
63 28 0.14
64 8 0.04
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (61 bp):
TTTATCAGATAAAAAAAATCAAATTTTTTTGTGTTGGTCATGCAATGGCCGACACCCCCTT
Found at i:91301 original size:163 final size:163
Alignment explanation
Indices: 91003--91308 Score: 384
Period size: 163 Copynumber: 1.9 Consensus size: 163
90993 GTTGATCATG
* *
91003 CAATGGCCGACACCCTCTATTTGCAGATAAAAAATATCAAATTTTTTTTGTATTGGTCATATAAT
1 CAATGGCCGACACCCTCTATTTGCAGATAAAAAATATCAAAATTTTTTTGTATTGGTCATACAAT
* * * **
91068 GGTTGACACTCCCTTTTTATCTGATAAAAAAAATCAAATTTTTGAGTGTTGGTCATGTAATGACC
66 GGTCGACACTCCCTTTTTATCAGATAAAAAAAATCAAATTTTTGAGTGTTGGCCATACAATGACC
91133 GACACCCCCTTTTCTCATATGGTGTTGGCCATA
131 GACACCCCCTTTTCTCATATGGTGTTGGCCATA
* * * * *
91166 CAATGGCCGACGTCCC-CTTTTTGCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCA
1 CAATGGCCGAC-ACCCTCTATTTGCAGAT-AAAAAATATCAAAATTTTTTTGTATTGGTCATACA
** * **
91230 ATGGTCGACAC-CCCTTTTT-TCAGATAAAAAATTTTAAATTTTTTTGTTGTTGGCCATACAATG
64 ATGGTCGACACTCCCTTTTTATCAGATAAAAAAAATCAAATTTTTGAG-TGTTGGCCATACAATG
** *
91293 GTCGACACCTCCTTTT
128 ACCGACACCCCCTTTT
91309 TTCAGATAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
162 21 0.17
163 56 0.47
164 43 0.36
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (163 bp):
CAATGGCCGACACCCTCTATTTGCAGATAAAAAATATCAAAATTTTTTTGTATTGGTCATACAAT
GGTCGACACTCCCTTTTTATCAGATAAAAAAAATCAAATTTTTGAGTGTTGGCCATACAATGACC
GACACCCCCTTTTCTCATATGGTGTTGGCCATA
Found at i:91383 original size:62 final size:61
Alignment explanation
Indices: 91152--91422 Score: 277
Period size: 62 Copynumber: 4.5 Consensus size: 61
91142 TTTTCTCATA
* * * *
91152 TGGTGTTGGCCATACAATGGCCGACGTCC-CCTTTTTGCAGATAAAAAAATTTCAAAATTTTTT
1 TGGTGTTGGCCATGCAATGGTCGAC-ACCTCCTTTTTTCAGAT-AAAAAATTTC-AAATTTTTT
* *
91215 T-GTGTTGGTCATGCAATGGTCGACACC-CCTTTTTTCAGATAAAAAATTTTAAATTTTTT
1 TGGTGTTGGCCATGCAATGGTCGACACCTCCTTTTTTCAGATAAAAAATTTCAAATTTTTT
* * *
91274 TGTTGTTGGCCATACAATGGTCGACACCTCCTTTTTTCAGATAAAAAAATTTCAATTTTTTT
1 TGGTGTTGGCCATGCAATGGTCGACACCTCCTTTTTTCAGAT-AAAAAATTTCAAATTTTTT
* * ** *
91336 TGGTGTTAGCCATGTC-ATGGTTGACACCTCCTTTTTATTTGGTAAAAAA-TT-AAA-TTTTT
1 TGGTGTTGGCCATG-CAATGGTCGACACCTCCTTTTT-TCAGATAAAAAATTTCAAATTTTTT
* * **
91395 TGGTGTTGGTCATGTAATGACCGACACC
1 TGGTGTTGGCCATGCAATGGTCGACACC
91423 AACTTCCCCT
Statistics
Matches: 177, Mismatches: 25, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
59 36 0.20
60 34 0.19
61 29 0.16
62 73 0.41
63 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (61 bp):
TGGTGTTGGCCATGCAATGGTCGACACCTCCTTTTTTCAGATAAAAAATTTCAAATTTTTT
Found at i:91389 original size:122 final size:120
Alignment explanation
Indices: 91152--91403 Score: 314
Period size: 122 Copynumber: 2.1 Consensus size: 120
91142 TTTTCTCATA
*
91152 TGGTGTTGGCCATACAATGGCCGACGTCCCCTTTTTGCAGATAAAAAAATTTCAAAATTTTTTTG
1 TGGTGTTGGCCATACAATGGCCGACGACCCCTTTTTGCAGATAAAAAAATTTCAAAATTTTTTTG
* *
91217 TGTTGGTCATGCAATGGTCGACACCCCTTTTTTCAGATAAAAAATTTTAAATTTTTT
66 TGTTAGCCATGCAATGGTCGACACCCCTTTTTTCAGATAAAAAA-TTTAAA-TTTTT
* * * *
91274 TGTTGTTGGCCATACAATGGTCGAC-ACCTCCTTTTTTCAGATAAAAAAATTTC-AATTTTTTTT
1 TGGTGTTGGCCATACAATGGCCGACGACC-CCTTTTTGCAGATAAAAAAATTTCAAAATTTTTTT
* ** *
91337 GGTGTTAGCCATGTC-ATGGTTGACACCTCCTTTTTATTTGGTAAAAAA-TTAAATTTTT
65 -GTGTTAGCCATG-CAATGGTCGACACC-CCTTTTT-TCAGATAAAAAATTTAAATTTTT
91395 TGGTGTTGG
1 TGGTGTTGG
91404 TCATGTAATG
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
121 24 0.21
122 72 0.64
123 8 0.07
124 9 0.08
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (120 bp):
TGGTGTTGGCCATACAATGGCCGACGACCCCTTTTTGCAGATAAAAAAATTTCAAAATTTTTTTG
TGTTAGCCATGCAATGGTCGACACCCCTTTTTTCAGATAAAAAATTTAAATTTTT
Found at i:92261 original size:17 final size:17
Alignment explanation
Indices: 92239--92293 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
92229 AAATAATAAC
92239 AATTAGAATATACATGA
1 AATTAGAATATACATGA
92256 AATTAG-A-A-A-ATGA
1 AATTAGAATATACATGA
* *
92269 AATTAAAATATACAGGA
1 AATTAGAATATACATGA
92286 AATTAGAA
1 AATTAGAA
92294 ATTAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 9 0.29
14 2 0.06
15 2 0.06
16 2 0.06
17 16 0.52
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (17 bp):
AATTAGAATATACATGA
Found at i:92273 original size:30 final size:29
Alignment explanation
Indices: 92239--92336 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 29
92229 AAATAATAAC
*
92239 AATTAGAATATACATGAAATTAGAAAATGA
1 AATTAAAATATACATGAAATTAG-AAATGA
* *
92269 AATTAAAATATACAGGAAATTAGAAATTA
1 AATTAAAATATACATGAAATTAGAAATGA
* * * *
92298 AATTTAAAATAAAAATGAAATTACAAATTA
1 AA-TTAAAATATACATGAAATTAGAAATGA
92328 AATTTAAAA
1 AA-TTAAAA
92337 AGTAAACGGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.12
30 53 0.88
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (29 bp):
AATTAAAATATACATGAAATTAGAAATGA
Done.