Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011880.1 Kokia drynarioides strain JFW-HI SEQ_126877, 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: 90107
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 123 characters in sequence are not A, C, G, or T
Found at i:639 original size:106 final size:106
Alignment explanation
Indices: 507--718 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
497 GTATTGCGAC
507 TATCCATCCTTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTCCATTGCCATCT
1 TATCCATCCTTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTCCATTGCCATCT
572 GTTTCGCAATCCATGCTTTTCGATATGAAACTCGATAATGG
66 GTTTCGCAATCCATGCTTTTCGATATGAAACTCGATAATGG
613 TATCCATCCTTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTCCATTGCCATCT
1 TATCCATCCTTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTCCATTGCCATCT
678 GTTTCGCAATCCATGCTTTTCGATATGAAACTCGATAATGG
66 GTTTCGCAATCCATGCTTTTCGATATGAAACTCGATAATGG
719 AATCGTGATT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.33
Consensus pattern (106 bp):
TATCCATCCTTGCAGCTCATTGTATGATGCATCCCAATCACCGAACAATTGTTCCATTGCCATCT
GTTTCGCAATCCATGCTTTTCGATATGAAACTCGATAATGG
Found at i:2196 original size:20 final size:21
Alignment explanation
Indices: 2171--2216 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
2161 AACACATTAC
2171 CTTTCCTCCCCTTCTT-CTTT
1 CTTTCCTCCCCTTCTTCCTTT
2191 CTTTCCTCCCCTTCTTCCTTT
1 CTTTCCTCCCCTTCTTCCTTT
2212 CTTTC
1 CTTTC
2217 TTTCTTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (21 bp):
CTTTCCTCCCCTTCTTCCTTT
Found at i:2225 original size:17 final size:17
Alignment explanation
Indices: 2205--2237 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2195 CCTCCCCTTC
*
2205 TTCCTTTCTTTCTTTCT
1 TTCCTTTATTTCTTTCT
2222 TTCCTTTATTTCTTTC
1 TTCCTTTATTTCTTTC
2238 CTGTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCTTTATTTCTTTCT
Found at i:2499 original size:10 final size:11
Alignment explanation
Indices: 2474--2511 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2464 GTCAGGTATT
2474 TTTTTGTCCTA
1 TTTTTGTCCTA
2485 TTTTTGTCCTA
1 TTTTTGTCCTA
* *
2496 TTTTTCTCATA
1 TTTTTGTCCTA
2507 TTTTT
1 TTTTT
2512 ATGAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (11 bp):
TTTTTGTCCTA
Found at i:3141 original size:18 final size:18
Alignment explanation
Indices: 3111--3155 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
3101 TCTTTCTCAA
*
3111 AAAATATTACAAAAAAT-
1 AAAATATTTCAAAAAATC
3128 AAATATATTTCAAAAAATC
1 AAA-ATATTTCAAAAAATC
3147 AAAATATTT
1 AAAATATTT
3156 ATGAAAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATTTCAAAAAATC
Found at i:3770 original size:16 final size:16
Alignment explanation
Indices: 3749--3781 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3739 ATTTAGATTT
*
3749 TTTAAATTTATAAAAA
1 TTTAAATTAATAAAAA
3765 TTTAAATTAATAAAAA
1 TTTAAATTAATAAAAA
3781 T
1 T
3782 AAAATTGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATTAATAAAAA
Found at i:12878 original size:25 final size:25
Alignment explanation
Indices: 12794--12900 Score: 110
Period size: 26 Copynumber: 4.2 Consensus size: 25
12784 GAGATAAATG
*
12794 AGCAGGCTTCGAGCC-GATGAATATTT
1 AGCAGGCTTCGAGCCAG-TGAAT-GTT
* *
12820 AGCAAGCCTT-GAGCCAGTGAACGTTT
1 AGC-AGGCTTCGAGCCAGTGAATG-TT
*
12846 AGCAGGCTTCGAGCCGGTGAATGTT
1 AGCAGGCTTCGAGCCAGTGAATGTT
*
12871 AGCAGGCTTTGAGCCAGTGAATGTGT
1 AGCAGGCTTCGAGCCAGTGAATGT-T
12897 AGCA
1 AGCA
12901 AGTACTATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
25 29 0.43
26 33 0.49
27 6 0.09
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (25 bp):
AGCAGGCTTCGAGCCAGTGAATGTT
Found at i:12900 original size:51 final size:52
Alignment explanation
Indices: 12794--12900 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 52
12784 GAGATAAATG
* *
12794 AGCAGGCTTCGAGCCGATGAATATTTAGCAAGCCTTGAGCCAGTGAACGTTT
1 AGCAGGCTTCGAGCCGATGAATAGTTAGCAAGCCTTGAGCCAGTGAACGTGT
* * * *
12846 AGCAGGCTTCGAGCCGGTGAAT-GTTAGCAGGCTTTGAGCCAGTGAATGTGT
1 AGCAGGCTTCGAGCCGATGAATAGTTAGCAAGCCTTGAGCCAGTGAACGTGT
12897 AGCA
1 AGCA
12901 AGTACTATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 28 0.57
52 21 0.43
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (52 bp):
AGCAGGCTTCGAGCCGATGAATAGTTAGCAAGCCTTGAGCCAGTGAACGTGT
Found at i:17896 original size:192 final size:193
Alignment explanation
Indices: 17477--17920 Score: 477
Period size: 192 Copynumber: 2.3 Consensus size: 193
17467 GAAATCGACA
* *
17477 CGATGGCTGAGGTACCGCATATGTTGTGAGTCCTCGACAGCTCGTGTGAGCAACATCGTGAGATT
1 CGATGGCTGAGGTACCGCATATGTTGTGAGTCCTCAACAGCTCGTGTGAGCAACATCGTGAGATA
* * *
17542 GAAAATGAGAAAAGAATCCAATAATGGATTACAAGCCCTACGATTGCTAAGATTTATGCATAAGT
66 GAAAATGAGAAAAGAATCCAATAATAGATTACAAGCCCTACGATGGCTAAGATTTATGCATAAAT
* * * * * * *
17607 GCATATTCTCGAAGCTCGTGTGCGCAGCATCATTAGGGAACAGTTATATGCACAGATACTGTAT
131 ACATATTCTCGAAGCTCGTATGAGCAACATCATTAGGGAACAGTTATA-GCAAACAAACTGTAT
* * * *
17671 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCAACAGCTTGTGTAAGCAGCATCGTGAG-TC
1 CGATGGCTGAGGTACCGCATATGTTGTGAGTCCTCAACAGCTCGTGTGAGCAACATCGTGAGAT-
* * * * * * * * *
17735 AGAAAA-GAGATATGAATCCTA-AATAGATTATAGGTCTTACGATGGCTGAGATTTATGCTTAAA
65 AGAAAATGAGAAAAGAATCCAATAATAGATTACAAGCCCTACGATGGCTAAGATTTATGCATAAA
* * *
17798 TACATATTCTCGACAGCTCGTATGAGCAACATCGTTAGGGGATAGTT-TA-CAAACAAACATCGT
130 TACATATTCTCGA-AGCTCGTATGAGCAACATCATTAGGGAACAGTTATAGCAAACAAAC-T-GT
17861 A-
192 AT
* * * * * * *
17862 CTGATGGTTGGGGTATCGCACATGTTATGAGTCCTCAAAAGCTCGTGTGAGCATCATCG
1 C-GATGGCTGAGGTACCGCATATGTTGTGAGTCCTCAACAGCTCGTGTGAGCAACATCG
17921 GGTATTGGTA
Statistics
Matches: 207, Mismatches: 38, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
190 6 0.03
191 2 0.01
192 97 0.47
193 40 0.19
194 62 0.30
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (193 bp):
CGATGGCTGAGGTACCGCATATGTTGTGAGTCCTCAACAGCTCGTGTGAGCAACATCGTGAGATA
GAAAATGAGAAAAGAATCCAATAATAGATTACAAGCCCTACGATGGCTAAGATTTATGCATAAAT
ACATATTCTCGAAGCTCGTATGAGCAACATCATTAGGGAACAGTTATAGCAAACAAACTGTAT
Found at i:21272 original size:23 final size:24
Alignment explanation
Indices: 21219--21273 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
21209 CAAATAAATT
** *
21219 TTTTTTTAAAAAATTATTTTTTTCA
1 TTTTTTT-AAAAATTATTAATTTAA
*
21244 TATTTTT-AAAATTATTAATTTAA
1 TTTTTTTAAAAATTATTAATTTAA
21267 TTTTTTT
1 TTTTTTT
21274 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.76
25 6 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTTTAAAAATTATTAATTTAA
Found at i:24901 original size:33 final size:34
Alignment explanation
Indices: 24825--24901 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 34
24815 CCTATTTACT
* * * *
24825 TAAAATAAATAATTTTAGTCAAAATAAAATTAGA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAGA
24859 -AAAAT-AACAAATTTAATCAAAACAAAATTA-A
1 TAAAATAAACAAATTTAATCAAAACAAAATTAGA
24890 TAAAATAAACAA
1 TAAAATAAACAA
24902 CTTTGACTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 1 0.03
32 26 0.70
33 10 0.27
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (34 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAGA
Found at i:25414 original size:82 final size:82
Alignment explanation
Indices: 25277--25441 Score: 330
Period size: 82 Copynumber: 2.0 Consensus size: 82
25267 AGTTTTGTAG
25277 GGTCTCCTAAGAAGAAAAATTGTTTGAGGAGCTCCACTGGAATTTACCCTAAGAAATACTATTCT
1 GGTCTCCTAAGAAGAAAAATTGTTTGAGGAGCTCCACTGGAATTTACCCTAAGAAATACTATTCT
25342 AAAAGTTGACCAGAAAT
66 AAAAGTTGACCAGAAAT
25359 GGTCTCCTAAGAAGAAAAATTGTTTGAGGAGCTCCACTGGAATTTACCCTAAGAAATACTATTCT
1 GGTCTCCTAAGAAGAAAAATTGTTTGAGGAGCTCCACTGGAATTTACCCTAAGAAATACTATTCT
25424 AAAAGTTGACCAGAAAT
66 AAAAGTTGACCAGAAAT
25441 G
1 G
25442 CCTATACAGA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (82 bp):
GGTCTCCTAAGAAGAAAAATTGTTTGAGGAGCTCCACTGGAATTTACCCTAAGAAATACTATTCT
AAAAGTTGACCAGAAAT
Found at i:37919 original size:10 final size:10
Alignment explanation
Indices: 37904--38009 Score: 55
Period size: 10 Copynumber: 11.2 Consensus size: 10
37894 TTCTTTAGAT
37904 AATTATTAAA
1 AATTATTAAA
37914 AATTA-T-AA
1 AATTATTAAA
**
37922 AATTATGGAA
1 AATTATTAAA
*
37932 AATTATTAAT
1 AATTATTAAA
37942 AATTA-TAAGA
1 AATTATTAA-A
37952 AATTA-TAAA
1 AATTATTAAA
***
37961 AAACCTT-AA
1 AATTATTAAA
**
37970 AATTATTTTA
1 AATTATTAAA
* *
37980 AATAATCAAA
1 AATTATTAAA
*
37990 TA-T-TTAAA
1 AATTATTAAA
37998 AATTATTAAA
1 AATTATTAAA
38008 AA
1 AA
38010 ATATGTTTGG
Statistics
Matches: 69, Mismatches: 20, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
8 12 0.17
9 14 0.20
10 43 0.62
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (10 bp):
AATTATTAAA
Found at i:39016 original size:19 final size:19
Alignment explanation
Indices: 38962--39021 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
38952 TGGTATAATA
* *
38962 TTTATTTTTATATATTATTA
1 TTTATTTTAATATATT-TTT
* *
38982 TTTCTTGTCAACTATATTTTT
1 TTTATT-TTAA-TATATTTTT
39003 TTTATTTTAATATATTTTT
1 TTTATTTTAATATATTTTT
39022 AATTTGTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 9 0.28
20 8 0.25
21 9 0.28
22 6 0.19
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATTTTAATATATTTTT
Found at i:39133 original size:51 final size:51
Alignment explanation
Indices: 39066--39175 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 51
39056 ATATATTTTT
* * * * *
39066 TTAATTTTTTAGAATTAAGATCAAATTGAGATTATTTGTAAATTTTAAAGG
1 TTAAATTTTTAAAATTAAGATCAAATTGAGATAATATGTAAATATTAAAGG
* * * *
39117 TTAAATTTTTAAAATTATGATTAAATTGATATAATATGTAAATATTGAAGG
1 TTAAATTTTTAAAATTAAGATCAAATTGAGATAATATGTAAATATTAAAGG
*
39168 CTAAATTT
1 TTAAATTT
39176 ATTATTATAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.45
Consensus pattern (51 bp):
TTAAATTTTTAAAATTAAGATCAAATTGAGATAATATGTAAATATTAAAGG
Found at i:40722 original size:21 final size:22
Alignment explanation
Indices: 40677--40732 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
40667 TATTTTCGCC
40677 AAAATATATATTATATAAAAGAG
1 AAAATATAT-TTATATAAAAGAG
*
40700 AAAATCTATTTATATAAAA-AG
1 AAAATATATTTATATAAAAGAG
*
40721 AAAATGTATTTA
1 AAAATATATTTA
40733 AAAGTTCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 13 0.42
22 10 0.32
23 8 0.26
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAATATATTTATATAAAAGAG
Found at i:40909 original size:61 final size:60
Alignment explanation
Indices: 40828--40956 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
40818 TTTATATAAA
*
40828 AATAAATTTAATCTTTAATATTTTA-TACTTTCTA-TCAATTTGATTTTAATTTT-AAAATTTT
1 AATAAATTTAATCTTTAATA-TTTACTA-TTT-TAGT-AATTTAATTTTAATTTTAAAAATTTT
40889 AATAAATTTAAT-TTTCAATATTTACCTATTTTAGTAATTTAATTTTAATTTTAAAAATTTT
1 AATAAATTTAATCTTT-AATATTTA-CTATTTTAGTAATTTAATTTTAATTTTAAAAATTTT
40950 AA-AAATT
1 AATAAATT
40957 CAAAAATTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
60 30 0.48
61 30 0.48
62 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (60 bp):
AATAAATTTAATCTTTAATATTTACTATTTTAGTAATTTAATTTTAATTTTAAAAATTTT
Found at i:40929 original size:31 final size:30
Alignment explanation
Indices: 40864--40941 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
40854 ACTTTCTATC
* **
40864 AATTTGATTTTAATTTTA-AAATTTTAATA
1 AATTTAATTTTAATTTTACCTATTTTAATA
*
40893 AATTTAATTTTCAATATTTACCTATTTTAGT-
1 AATTTAATTTT-AAT-TTTACCTATTTTAATA
40924 AATTTAATTTTAATTTTA
1 AATTTAATTTTAATTTTA
40942 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 14 0.33
30 6 0.14
31 15 0.36
32 7 0.17
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (30 bp):
AATTTAATTTTAATTTTACCTATTTTAATA
Found at i:42129 original size:49 final size:48
Alignment explanation
Indices: 42042--42166 Score: 128
Period size: 49 Copynumber: 2.5 Consensus size: 48
42032 AAACTTGAAT
* ** *
42042 CCGTAACCGCATAACCATTGTCAACTGGGCTCCTGAGTTATA-TTCCAAC
1 CCGTGACC-CATAACCACCGTCAACTAGGCTCCTGAGTTATACTT-CAAC
*
42091 CGGTGACCACATAACCACCGTCAACTAGGCT-CTCGAGTTATACTTCAAC
1 CCGTGACC-CATAACCACCGTCAACTAGGCTCCT-GAGTTATACTTCAAC
* *
42140 CCGTGACCCTATAAACACCGTGAACTA
1 CCGTGACCC-ATAACCACCGTCAACTA
42167 AGAGCTTGAG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
48 3 0.05
49 59 0.92
50 2 0.03
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (48 bp):
CCGTGACCCATAACCACCGTCAACTAGGCTCCTGAGTTATACTTCAAC
Found at i:43035 original size:38 final size:38
Alignment explanation
Indices: 42983--43059 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
42973 TTACATCAAA
* * *
42983 TCAAAATTTATGTATCGTTTTGCACGTTGGACCAAAAT
1 TCAAAATTTATGTATCGTATTACACATTGGACCAAAAT
*
43021 TCAAAATTTGTGTATCGTATTACACATTGGACCAAAAT
1 TCAAAATTTATGTATCGTATTACACATTGGACCAAAAT
43059 T
1 T
43060 TGTGTATCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (38 bp):
TCAAAATTTATGTATCGTATTACACATTGGACCAAAAT
Found at i:43060 original size:31 final size:31
Alignment explanation
Indices: 43022--43087 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
43012 GACCAAAATT
43022 CAAAATTTGTGTATCGTATTACACATTGGAC
1 CAAAATTTGTGTATCGTATTACACATTGGAC
* *
43053 CAAAATTTGTGTATCGTATTGCACATTGGAT
1 CAAAATTTGTGTATCGTATTACACATTGGAC
43084 CAAA
1 CAAA
43088 GACTAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (31 bp):
CAAAATTTGTGTATCGTATTACACATTGGAC
Found at i:51093 original size:14 final size:14
Alignment explanation
Indices: 51070--51103 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51060 TGTTATTTCG
*
51070 TTATTATATTGCTA
1 TTATTTTATTGCTA
*
51084 TTATTTTATTGTTA
1 TTATTTTATTGCTA
51098 TTATTT
1 TTATTT
51104 GAATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (14 bp):
TTATTTTATTGCTA
Found at i:59576 original size:39 final size:41
Alignment explanation
Indices: 59517--59593 Score: 97
Period size: 39 Copynumber: 1.9 Consensus size: 41
59507 TTATTTTCAG
59517 TTTTTTCTAAAACTGTTTTTTAAAATTTTAAT-AAAACACAT
1 TTTTTTCTAAAACTGTTTTTT-AAATTTTAATGAAAACACAT
* * *
59558 TTTTTTTTAAAA-TG-TTTTTCAATTTTTATGAAAACA
1 TTTTTTCTAAAACTGTTTTTTAAATTTTAATGAAAACA
59594 AAAATGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 8 0.25
39 11 0.34
40 2 0.06
41 11 0.34
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (41 bp):
TTTTTTCTAAAACTGTTTTTTAAATTTTAATGAAAACACAT
Found at i:70177 original size:72 final size:72
Alignment explanation
Indices: 69938--70193 Score: 287
Period size: 72 Copynumber: 3.6 Consensus size: 72
69928 AAATAGTTAA
* * ** *
69938 TTACACGAGATGGACACACGAGCGTGTACCAGATTGTGTGGACATTCTATGTATGAAATTAGAAA
1 TTACACGGGATGGACACACGGGCGTGTACCAGACCGTGTGGACATTCTATTTATGAAATTAGAAA
70003 CAGTGAG
66 CAGTGAG
* * ** * * *
70010 TTACACGGGCTAGACACATAGGTGTGTACCAAACTGTGTGGACATTCTATTTATGAAATTAGAAA
1 TTACACGGGATGGACACACGGGCGTGTACCAGACCGTGTGGACATTCTATTTATGAAATTAGAAA
70075 CAGTGAG
66 CAGTGAG
** * * * * * *
70082 TTTTACAGGCTGGACACACGGGCGTGTGCTAGACCGTTTGGACATTCTGTTTATGAAATTAGAAA
1 TTACACGGGATGGACACACGGGCGTGTACCAGACCGTGTGGACATTCTATTTATGAAATTAGAAA
*
70147 CAATGAG
66 CAGTGAG
* ** *
70154 TTACACGGGATGGACACATGGGCGTGGGCCAGACCATGTG
1 TTACACGGGATGGACACACGGGCGTGTACCAGACCGTGTG
70194 ACACATACGA
Statistics
Matches: 151, Mismatches: 33, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 151 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (72 bp):
TTACACGGGATGGACACACGGGCGTGTACCAGACCGTGTGGACATTCTATTTATGAAATTAGAAA
CAGTGAG
Found at i:70410 original size:77 final size:78
Alignment explanation
Indices: 70270--70432 Score: 213
Period size: 77 Copynumber: 2.1 Consensus size: 78
70260 CGTCTTTTTG
* * * *
70270 GAAACACTACGATACATTACTGAACTGACAGTGACATTGGAAACACTGCGATACATTACTGAACT
1 GAAACACTACGATACATGACTGAACTGACAGTGACATAGGAAACACTACAATACATTACTGAACT
*
70335 AGCAGTGACGCTA
66 AGCAGTGACACTA
* * *
70348 GAAACACT-TGATACATGACTGAACTGGCAGTGACACTAGG-AACACTACAATACATTATTGAAC
1 GAAACACTACGATACATGACTGAACTGACAGTGACA-TAGGAAACACTACAATACATTACTGAAC
*
70411 TGGCAGTGACACTA
65 TAGCAGTGACACTA
*
70425 TAAACACT
1 GAAACACT
70433 GCAATATTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
77 63 0.85
78 11 0.15
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (78 bp):
GAAACACTACGATACATGACTGAACTGACAGTGACATAGGAAACACTACAATACATTACTGAACT
AGCAGTGACACTA
Found at i:70422 original size:39 final size:39
Alignment explanation
Indices: 70270--70432 Score: 211
Period size: 39 Copynumber: 4.2 Consensus size: 39
70260 CGTCTTTTTG
* * *
70270 GAAACACTACGATACATTACTGAACTGACAGTGACATTG
1 GAAACACTACGATACATTACTGAACTGGCAGTGACACTA
* * *
70309 GAAACACTGCGATACATTACTGAACTAGCAGTGACGCTA
1 GAAACACTACGATACATTACTGAACTGGCAGTGACACTA
* *
70348 GAAACACT-TGATACATGACTGAACTGGCAGTGACACTA
1 GAAACACTACGATACATTACTGAACTGGCAGTGACACTA
* * *
70386 GGAACACTACAATACATTATTGAACTGGCAGTGACACTA
1 GAAACACTACGATACATTACTGAACTGGCAGTGACACTA
*
70425 TAAACACT
1 GAAACACT
70433 GCAATATTAT
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
38 33 0.31
39 73 0.69
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (39 bp):
GAAACACTACGATACATTACTGAACTGGCAGTGACACTA
Found at i:70446 original size:39 final size:39
Alignment explanation
Indices: 70270--70451 Score: 179
Period size: 39 Copynumber: 4.7 Consensus size: 39
70260 CGTCTTTTTG
* * * * *
70270 GAAACACTACGATACATTACTGAACTGACAGTGACATTG
1 GAAACACTACAATACATTATTGAACTGGCAGTGACACTA
* * * * *
70309 GAAACACTGCGATACATTACTGAACTAGCAGTGACGCTA
1 GAAACACTACAATACATTATTGAACTGGCAGTGACACTA
** * *
70348 GAAACACT-TGATACATGACTGAACTGGCAGTGACACTA
1 GAAACACTACAATACATTATTGAACTGGCAGTGACACTA
*
70386 GGAACACTACAATACATTATTGAACTGGCAGTGACACTA
1 GAAACACTACAATACATTATTGAACTGGCAGTGACACTA
* * *
70425 TAAACACTGCAATA-TTATATTGAACTG
1 GAAACACTACAATACAT-TATTGAACTG
70452 ATGGTGTATT
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
38 34 0.28
39 88 0.72
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (39 bp):
GAAACACTACAATACATTATTGAACTGGCAGTGACACTA
Found at i:76140 original size:16 final size:17
Alignment explanation
Indices: 76107--76148 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
76097 ACGAAATTAA
76107 AATTAGATTGAGAAAATT
1 AATTA-ATTGAGAAAATT
*
76125 ATTTAATTGA-AAAATT
1 AATTAATTGAGAAAATT
76141 AATTAATT
1 AATTAATT
76149 TAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
17 5 0.23
18 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (17 bp):
AATTAATTGAGAAAATT
Found at i:80130 original size:29 final size:29
Alignment explanation
Indices: 80097--80179 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 29
80087 CAAGTATTTT
80097 TTAATTCATTTCAAAACAAGTTTTATATA
1 TTAATTCATTTCAAAACAAGTTTTATATA
* *
80126 TTAATGAT-ATTTC----TAAGTATT-T-T-
1 TTAAT--TCATTTCAAAACAAGTTTTATATA
80149 TTAATTCATTTCAAAACAAGTTTTATATA
1 TTAATTCATTTCAAAACAAGTTTTATATA
80178 TT
1 TT
80180 CATGATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 20
0.62 0.06 0.31
Matches are distributed among these distances:
21 1 0.03
22 5 0.12
23 5 0.12
24 1 0.03
25 1 0.03
26 12 0.30
27 1 0.03
28 1 0.03
29 7 0.17
30 5 0.12
31 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (29 bp):
TTAATTCATTTCAAAACAAGTTTTATATA
Found at i:80147 original size:52 final size:51
Alignment explanation
Indices: 80083--80185 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 51
80073 ACTAAACATG
80083 ATTTCAAGTATTTTTTAATTCATTTCAAAACAAGTTTTATATATTAATGAT
1 ATTTCAAGTATTTTTTAATTCATTTCAAAACAAGTTTTATATATTAATGAT
*
80134 ATTTCTAAGTATTTTTTAATTCATTTCAAAACAAGTTTTATATATTCATGAT
1 ATTTC-AAGTATTTTTTAATTCATTTCAAAACAAGTTTTATATATTAATGAT
80186 TATTATGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 5 0.10
52 45 0.90
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (51 bp):
ATTTCAAGTATTTTTTAATTCATTTCAAAACAAGTTTTATATATTAATGAT
Found at i:85634 original size:21 final size:22
Alignment explanation
Indices: 85596--85636 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
85586 TATTATTTAT
* *
85596 TATTTTAAATATTTAATATTAG
1 TATTTTAAATAATAAATATTAG
85618 TATTTT-AATAATAAATATT
1 TATTTTAAATAATAAATATT
85637 TATTACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTTTAAATAATAAATATTAG
Found at i:88265 original size:65 final size:65
Alignment explanation
Indices: 88188--88312 Score: 223
Period size: 65 Copynumber: 1.9 Consensus size: 65
88178 CAATTTATAC
*
88188 TTGTATAGTTGAAAGTATAATGGTTGAAAGTATAAATTGTTTATGTTAAATGGCCATTTAACCAT
1 TTGTATAGTTGAAAGTATAATGGTTGAAAGTATAAATTGTCTATGTTAAATGGCCATTTAACCAT
* *
88253 TTGTATGGTTGAAAGTATAATGGTTGAAAGTATAAATTGTCTATGTTAAATGGTCATTTA
1 TTGTATAGTTGAAAGTATAATGGTTGAAAGTATAAATTGTCTATGTTAAATGGCCATTTA
88313 TTCAACCATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (65 bp):
TTGTATAGTTGAAAGTATAATGGTTGAAAGTATAAATTGTCTATGTTAAATGGCCATTTAACCAT
Found at i:88277 original size:15 final size:15
Alignment explanation
Indices: 88257--88287 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
88247 AACCATTTGT
88257 ATGGTTGAAAGTATA
1 ATGGTTGAAAGTATA
88272 ATGGTTGAAAGTATA
1 ATGGTTGAAAGTATA
88287 A
1 A
88288 ATTGTCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (15 bp):
ATGGTTGAAAGTATA
Done.