Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010816.1 Kokia drynarioides strain JFW-HI SEQ_125783, 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: 56935
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7052 original size:7 final size:7
Alignment explanation
Indices: 7035--7098 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
7025 AAGTCACCGA
7035 TCAAA-G
1 TCAAAGG
7041 TCAAAGG
1 TCAAAGG
7048 TCAAAGG
1 TCAAAGG
*
7055 TCAATGG
1 TCAAAGG
*
7062 TTAAA-G
1 TCAAAGG
*
7068 TCAACGG
1 TCAAAGG
7075 TCAACA-G
1 TCAA-AGG
7082 TCAAA-G
1 TCAAAGG
*
7088 TCAATGG
1 TCAAAGG
7095 TCAA
1 TCAA
7099 TGGATCGGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
6 15 0.32
7 32 0.68
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (7 bp):
TCAAAGG
Found at i:7058 original size:20 final size:19
Alignment explanation
Indices: 7035--7098 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
7025 AAGTCACCGA
7035 TCAAAGTCAAAGGTCAAAGG
1 TCAAAGTCAAA-GTCAAAGG
* * *
7055 TCAATGGTTAAAGTCAACGG
1 TCAA-AGTCAAAGTCAAAGG
*
7075 TCAACAGTCAAAGTCAATGG
1 TCAA-AGTCAAAGTCAAAGG
7095 TCAA
1 TCAA
7099 TGGATCGGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 31 0.86
21 5 0.14
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (19 bp):
TCAAAGTCAAAGTCAAAGG
Found at i:7067 original size:14 final size:13
Alignment explanation
Indices: 7035--7091 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
7025 AAGTCACCGA
7035 TCAAAGTCAAAGG
1 TCAAAGTCAAAGG
*
7048 TCAAAGGTCAATGG
1 TCAAA-GTCAAAGG
* *
7062 TTAAAGTCAACGG
1 TCAAAGTCAAAGG
7075 TCAACAGTCAAA-G
1 TCAA-AGTCAAAGG
7088 TCAA
1 TCAA
7092 TGGTCAATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 20 0.54
14 17 0.46
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (13 bp):
TCAAAGTCAAAGG
Found at i:7091 original size:40 final size:40
Alignment explanation
Indices: 7020--7101 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
7010 AAAGTTAACG
*
7020 GGTTAAAGTCACCGATCAAAGTCAAAGGTCAAAGGTCAAT
1 GGTTAAAGTCAACGATCAAAGTCAAAGGTCAAAGGTCAAT
* *
7060 GGTTAAAGTCAACGGTCAACAGTCAAA-GTCAATGGTCAAT
1 GGTTAAAGTCAACGATCAA-AGTCAAAGGTCAAAGGTCAAT
7100 GG
1 GG
7102 ATCGGGTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 31 0.82
41 7 0.18
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (40 bp):
GGTTAAAGTCAACGATCAAAGTCAAAGGTCAAAGGTCAAT
Found at i:7511 original size:84 final size:83
Alignment explanation
Indices: 7369--7537 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 83
7359 ATACACGGCG
7369 TCCGACTTTTACACTCACCAATATTCAATTGACGATAGAGCGACGGAGCAGCAAGAGGGACAAAG
1 TCCGACTTTTACACTCACCAATATTCAATTGACGATAGAGCGACGGAGCAGCAAGAGGGACAAAG
*
7434 GTCGAAAGCTTCCCCTTA
66 GCCGAAAGCTTCCCCTTA
7452 TNCCGACTTTTACACTCACCAATATTCAATTGACGATAGAGCGACGGAGCAGCAAGAGGGACAAA
1 T-CCGACTTTTACACTCACCAATATTCAATTGACGATAGAGCGACGGAGCAGCAAGAGGGACAAA
7517 GGCCGAAAGCTTCCCCTTA
65 GGCCGAAAGCTTCCCCTTA
7536 TC
1 TC
7538 GTCACTCATG
Statistics
Matches: 84, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
83 2 0.02
84 82 0.98
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (83 bp):
TCCGACTTTTACACTCACCAATATTCAATTGACGATAGAGCGACGGAGCAGCAAGAGGGACAAAG
GCCGAAAGCTTCCCCTTA
Found at i:9671 original size:38 final size:38
Alignment explanation
Indices: 9624--9706 Score: 116
Period size: 38 Copynumber: 2.2 Consensus size: 38
9614 ATTAACAAAT
* *
9624 AATT-TTAAAATTATTAAAATTAT-TTTTTGAAATATAA
1 AATTATTAAAAATATT-AAATTATATTTTTAAAATATAA
*
9661 AATTATTAAAAATATTATATTATATTTTTAAAATATAA
1 AATTATTAAAAATATTAAATTATATTTTTAAAATATAA
9699 AATTATTA
1 AATTATTA
9707 TATTTTTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
37 10 0.24
38 31 0.76
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
AATTATTAAAAATATTAAATTATATTTTTAAAATATAA
Found at i:10998 original size:14 final size:15
Alignment explanation
Indices: 10974--11002 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10964 AGAAATAAAA
10974 AATAGATTTTAATAT
1 AATAGATTTTAATAT
10989 AATA-ATTTTAATAT
1 AATAGATTTTAATAT
11003 TTTATATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
AATAGATTTTAATAT
Found at i:11324 original size:9 final size:9
Alignment explanation
Indices: 11310--11368 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
11300 TATATTTTGA
11310 TTTAATAAT
1 TTTAATAAT
11319 TTTAATAAT
1 TTTAATAAT
11328 TTT-AT-AT
1 TTTAATAAT
*
11335 TTTAAAAAAT
1 TTT-AATAAT
* *
11345 AATATAATAAA
1 --TTTAATAAT
11356 TTTAATAAT
1 TTTAATAAT
11365 TTTA
1 TTTA
11369 TATTTCAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
7 5 0.13
8 2 0.05
9 24 0.62
10 2 0.05
11 4 0.10
12 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTAATAAT
Found at i:11347 original size:20 final size:21
Alignment explanation
Indices: 11322--11400 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 21
11312 TAATAATTTT
11322 AATAATTTTAT-ATTTTAAAA
1 AATAATTTTATAATTTTAAAA
* * *
11342 AATAATATAATAAATTT----
1 AATAATTTTATAATTTTAAAA
*
11359 AATAATTTTAT-ATTTCAAAAA
1 AATAATTTTATAATTT-TAAAA
11380 AATAATTTTTATAATTTTAAA
1 AATAA-TTTTATAATTTTAAA
11401 TTTATTTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
16 3 0.07
17 9 0.21
20 9 0.21
21 9 0.21
22 9 0.21
23 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAATTTTATAATTTTAAAA
Found at i:11353 original size:37 final size:39
Alignment explanation
Indices: 11312--11399 Score: 126
Period size: 37 Copynumber: 2.3 Consensus size: 39
11302 TATTTTGATT
*
11312 TAATAATTTTAATAATTTTATATTT-TAAAAAATAA-TA
1 TAATAATTTTAATAATTTTATATTTCAAAAAAATAATTA
* *
11349 TAATAAATTTAATAATTTTATATTTCAAAAAAATAATTT
1 TAATAATTTTAATAATTTTATATTTCAAAAAAATAATTA
*
11388 TTATAATTTTAA
1 TAATAATTTTAA
11400 ATTTATTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 24 0.55
38 9 0.20
39 11 0.25
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
TAATAATTTTAATAATTTTATATTTCAAAAAAATAATTA
Found at i:13847 original size:14 final size:14
Alignment explanation
Indices: 13824--13853 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13814 TTGCATTTAA
*
13824 TTTATGTTTATCTT
1 TTTATATTTATCTT
13838 TTTATATTTATCTT
1 TTTATATTTATCTT
13852 TT
1 TT
13854 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:18550 original size:20 final size:18
Alignment explanation
Indices: 18500--18551 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
18490 CTTGTAGATA
18500 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
18517 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
18537 AATATTAAATTAATA
1 AATATTAAATTAATA
18552 AAACACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:20529 original size:18 final size:18
Alignment explanation
Indices: 20495--20527 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20485 TGAGATTAAC
20495 ATATAATCAAACCATATG
1 ATATAATCAAACCATATG
20513 ATAT-ATCAAA-CATAT
1 ATATAATCAAACCATAT
20528 ATCAATCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (18 bp):
ATATAATCAAACCATATG
Found at i:22815 original size:140 final size:139
Alignment explanation
Indices: 22542--22877 Score: 414
Period size: 139 Copynumber: 2.4 Consensus size: 139
22532 ATTTTTTGTG
* * * *
22542 TTTAATTTG-GATTTTAGGGTTGATTTTAGGAAAGTTAATTGTTGATATTTTTAGGTTTGATTTT
1 TTTAATTTGAG-TTTTAGGGTTGATTTTATGAAAGTTAATTGCTAATATTATTAGGTTTGATTTT
* * *
22606 TTCACTATTTTGTTAATAGAATAAATTTAGTGTTAATGTGAATTTGTTTAATTTGTCAGTACAGT
65 TTCACTATTTTATTAATAAAATAAATTTAGTGTTAATGTGAATTTGTTTAATATGTCAGTACAG-
22671 TTGAT-TGTTA
129 TTGATATGTTA
* * * *
22681 TTTAATTTGAGTTTTAGGGTTGGTTTGATAAAAGCTAATTTGCTAATATTATTAGGTTTGAATTT
1 TTTAATTTGAGTTTTAGGGTTGATTTTATGAAAGTTAA-TTGCTAATATTATTAGGTTTG-ATTT
*
22746 TTT-ATTA-TTTATTAATAAAATAAATTTAGTGTTAATTGTGAATTTGTTTAATATGTCAAATGT
64 TTTCACTATTTTATTAATAAAATAAATTTAGTGTTAA-TGTGAATTTGTTTAATATGTC--A-GT
22809 A-A-TTGATAAATGTTA
125 ACAGTTGAT--ATGTTA
* *
22824 TTTAATTGGAGTTTTAGGATTGATTTTATGAAAGTTAATTGCTAATATTATTAG
1 TTTAATTTGAGTTTTAGGGTTGATTTTATGAAAGTTAATTGCTAATATTATTAG
22878 ATAATTATGA
Statistics
Matches: 169, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
139 57 0.34
140 47 0.28
141 7 0.04
142 18 0.11
143 40 0.24
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.50
Consensus pattern (139 bp):
TTTAATTTGAGTTTTAGGGTTGATTTTATGAAAGTTAATTGCTAATATTATTAGGTTTGATTTTT
TCACTATTTTATTAATAAAATAAATTTAGTGTTAATGTGAATTTGTTTAATATGTCAGTACAGTT
GATATGTTA
Found at i:24810 original size:2 final size:2
Alignment explanation
Indices: 24803--24832 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24793 TAGTTGGTTC
24803 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
24833 CAACAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29476 original size:22 final size:22
Alignment explanation
Indices: 29450--29491 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
29440 TTAAAAGAGA
*
29450 CATAATTATTCAAATAATATCT
1 CATAACTATTCAAATAATATCT
*
29472 CATAACTATTCAAGTAATAT
1 CATAACTATTCAAATAATAT
29492 TGATTGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (22 bp):
CATAACTATTCAAATAATATCT
Found at i:39273 original size:9 final size:9
Alignment explanation
Indices: 39259--39294 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
39249 GCTTGCTTGA
39259 GAAATTTTT
1 GAAATTTTT
39268 GAAATTTTT
1 GAAATTTTT
39277 GAGAAATTTTT
1 --GAAATTTTT
39288 GAAATTT
1 GAAATTT
39295 GGGTTATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 16 0.64
11 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (9 bp):
GAAATTTTT
Found at i:39280 original size:20 final size:20
Alignment explanation
Indices: 39255--39294 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39245 ATATGCTTGC
39255 TTGAGAAATTTTTGAAATTT
1 TTGAGAAATTTTTGAAATTT
39275 TTGAGAAATTTTTGAAATTT
1 TTGAGAAATTTTTGAAATTT
39295 GGGTTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (20 bp):
TTGAGAAATTTTTGAAATTT
Found at i:39282 original size:11 final size:11
Alignment explanation
Indices: 39255--39289 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
39245 ATATGCTTGC
39255 TTGAGAAATTT
1 TTGAGAAATTT
39266 TT--GAAATTT
1 TTGAGAAATTT
39275 TTGAGAAATTT
1 TTGAGAAATTT
39286 TTGA
1 TTGA
39290 AATTTGGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (11 bp):
TTGAGAAATTT
Found at i:48060 original size:29 final size:29
Alignment explanation
Indices: 48024--48083 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
48014 AGAAACACAA
*
48024 CCGTGTGAGCCACACGGGCGTGTGCCAGG
1 CCGTGTGAGCCACACAGGCGTGTGCCAGG
*
48053 CCGTGTGAGCCACACAGGTGTGTGCCAGG
1 CCGTGTGAGCCACACAGGCGTGTGCCAGG
48082 CC
1 CC
48084 ATATGGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.32, G:0.38, T:0.15
Consensus pattern (29 bp):
CCGTGTGAGCCACACAGGCGTGTGCCAGG
Found at i:53144 original size:307 final size:308
Alignment explanation
Indices: 52493--53721 Score: 1926
Period size: 308 Copynumber: 4.0 Consensus size: 308
52483 TGCAAGCAAT
* * * *
52493 GATGTGTATTCAAGAATAAGTAACTGGAGTTTGTCCTAGTCCCAAGCAGCTCACTTAACCCACTT
1 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCACCTAACCCACTT
* * * * * * ** * *
52558 GTTAACCTAACTTGTTACCGTATCTCTTGATGTCAGCACACTACAATTTCACTCTCATGCTTAAA
66 GTTAACCTAACCTATCACCGCATCTCTCGATGTCGGTGCACTGCAATTTCACTCTCGTGCTTAAA
* *
52623 GCGATTAGATCTAAGAATAAACAAATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
131 GCGATTAGATCCAAGAATAAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
*
52688 AAGACACTCTCGTATTCGTTTAATATCATCAAAATCCATCATCATTTAAGAAGAATTAAAGAGTA
196 AAGACACTCTCGTATTCATTTAATATCATCAAAATCCATCATCATTTAAGAAGAATTAAAGAGTA
*
52753 CAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTT
261 CAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTC
* *
52801 GATGTGTATTCAAGAATAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCACCTAATCCACTT
1 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCACCTAACCCACTT
* * * *
52866 GTTAACCAAACCTATCACCACATCTCTCGATGTCGGGGCATTGCAATTTCACTCTCGTGCTTAAA
66 GTTAACCTAACCTATCACCGCATCTCTCGATGTCGGTGCACTGCAATTTCACTCTCGTGCTTAAA
*
52931 GCGATTAGATCCAAGAATAAATAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATT-A
131 GCGATTAGATCCAAGAATAAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
* * * *
52995 AAGACACTCTCATATTCATTTAATATCATCAAAGTCTATAATCATTTAAGAAGAATTAAAGAGTA
196 AAGACACTCTCGTATTCATTTAATATCATCAAAATCCATCATCATTTAAGAAGAATTAAAGAGTA
*
53060 CAACGAAGCTTACTATCTCTAGACTACTAGGCTTACTCCCTAATTGTC
261 CAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTC
*
53108 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCGCCTAACCCACTT
1 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCACCTAACCCACTT
* * * *
53173 GTTAACCTAACCTGTCATCGCATCTCTCGATGTCGGTGCACTGTAATTTCACTCTCGTTCTTAAA
66 GTTAACCTAACCTATCACCGCATCTCTCGATGTCGGTGCACTGCAATTTCACTCTCGTGCTTAAA
* * * *
53238 GCGGTTAGATCCATGAATAAACATATAAGCAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
131 GCGATTAGATCCAAGAATAAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
* *
53303 AAGACACTCTCGTATTCATTTAATAT--TCAAAATCCATCATCGTTTAAGAAGAATGAAAGAGTA
196 AAGACACTCTCGTATTCATTTAATATCATCAAAATCCATCATCATTTAAGAAGAATTAAAGAGTA
*
53366 CAACGAAGCTTGCTATCTCTAGACTACTAGGCCTACTCCCTAATTGTC
261 CAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTC
* * * * * * *
53414 GATGTGTATTCAAGAACAAGTAACTAGAATTTGCCCCAATCTCGAGCTGCTCTCACCTAACCTAC
1 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAG--CTCACCTAACCCAC
*
53479 TTGTTAACCTAACCTATCACCGCATCTCTCGATGTCGGTGCACTTCAATTTCACTCTCGTGCTTA
64 TTGTTAACCTAACCTATCACCGCATCTCTCGATGTCGGTGCACTGCAATTTCACTCTCGTGCTTA
* * *
53544 AAGCGGTTAGATCCAAGAATAAACAGATAAGTAGTGTGAAATAAGAGTCAAAATGATTTAACATT
129 AAGCGATTAGATCCAAGAATAAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATT
*
53609 AAAAGACACTCTCGTATTCATTT-ATATCATCAAAATCCATCATCGTTTAAGAAGAATTAAAGAG
194 AAAAGACACTCTCGTATTCATTTAATATCATCAAAATCCATCATCATTTAAGAAGAATTAAAGAG
53673 TACAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGT
259 TACAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGT
53722 TTCTCTTGCT
Statistics
Matches: 845, Mismatches: 71, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
306 121 0.14
307 288 0.34
308 354 0.42
309 82 0.10
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (308 bp):
GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCACCTAACCCACTT
GTTAACCTAACCTATCACCGCATCTCTCGATGTCGGTGCACTGCAATTTCACTCTCGTGCTTAAA
GCGATTAGATCCAAGAATAAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
AAGACACTCTCGTATTCATTTAATATCATCAAAATCCATCATCATTTAAGAAGAATTAAAGAGTA
CAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTC
Found at i:53663 original size:615 final size:614
Alignment explanation
Indices: 52493--53721 Score: 1953
Period size: 615 Copynumber: 2.0 Consensus size: 614
52483 TGCAAGCAAT
* * *
52493 GATGTGTATTCAAGAATAAGTAACTGGAGTTTGTCCTAGTCCCAAGCAGCTCACTTAACCCACTT
1 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCAAGCAGCTCACCTAACCCACTT
* * * *
52558 GTTAACCTAACTTGTTACCGTATCTCTTGATGTCAGCACACTACAATTTCACTCTCATGCTTAAA
66 GTTAACCTAACCTGTCACCGCATCTCTCGATGTCAGCACACTACAATTTCACTCTCATGCTTAAA
* *
52623 GCGATTAGATCTAAGAATAAACAAATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
131 GCGATTAGATCCAAGAATAAACAAATAAGCAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
* *
52688 AAGACACTCTCGTATTCGTTTAATATCATCAAAATCCATCATCATTTAAGAAGAATTAAAGAGTA
196 AAGACACTCTCGTATTCATTTAATAT-ATCAAAATCCATCATCATTTAAGAAGAATGAAAGAGTA
* *
52753 CAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTTGATGTGTATTCAAGAAT
260 CAACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTCGATGTGTATTCAAGAAC
* * * *
52818 AAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCACCTAATCCACTTGTTAACCAAACCTATCA
325 AAGTAACTAGAATTTGCCCCAATCCCGAGCAGCTCACCTAATCCACTTGTTAACCAAACCTATCA
52883 CCACATCTCTCGATGTCGGGGCATTGCAATTTCACTCTCGTGCTTAAAGCGATTAGATCCAAGAA
390 CCACATCTCTCGATGTCGGGGCATTGCAATTTCACTCTCGTGCTTAAAGCGATTAGATCCAAGAA
*
52948 TAAATAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAAAGACACTCTCATATTCA
455 TAAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAAAGACACTCTCATATTCA
* *
53013 TTTAATATCATCAAAGTCTATAATCATTTAAGAAGAATTAAAGAGTACAACGAAGCTTACTATCT
520 TTTAATATCATCAAAATCCATAATCATTTAAGAAGAATTAAAGAGTACAACGAAGCTTACTATCT
*
53078 CTAGACTACTAGGCTTACTCCCTAATTGTC
585 CTAGACTACTAGGCCTACTCCCTAATTGTC
* *
53108 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCGAGCAGCTCGCCTAACCCACTT
1 GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCAAGCAGCTCACCTAACCCACTT
* * ** ** * *
53173 GTTAACCTAACCTGTCATCGCATCTCTCGATGTCGGTGCACTGTAATTTCACTCTCGTTCTTAAA
66 GTTAACCTAACCTGTCACCGCATCTCTCGATGTCAGCACACTACAATTTCACTCTCATGCTTAAA
* * *
53238 GCGGTTAGATCCATGAATAAACATATAAGCAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
131 GCGATTAGATCCAAGAATAAACAAATAAGCAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
*
53303 AAGACACTCTCGTATTCATTTAATAT-TCAAAATCCATCATCGTTTAAGAAGAATGAAAGAGTAC
196 AAGACACTCTCGTATTCATTTAATATATCAAAATCCATCATCATTTAAGAAGAATGAAAGAGTAC
*
53367 AACGAAGCTTGCTATCTCTAGACTACTAGGCCTACTCCCTAATTGTCGATGTGTATTCAAGAACA
261 AACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTCGATGTGTATTCAAGAACA
* * *
53432 AGTAACTAGAATTTGCCCCAATCTCGAGCTGCTCTCACCTAA-CCTACTTGTTAACCTAACCTAT
326 AGTAACTAGAATTTGCCCCAATCCCGAGCAG--CTCACCTAATCC-ACTTGTTAACCAAACCTAT
* * *
53496 CACCGCATCTCTCGATGTCGGTGCACTT-CAATTTCACTCTCGTGCTTAAAGCGGTTAGATCCAA
388 CACCACATCTCTCGATGTCGGGGCA-TTGCAATTTCACTCTCGTGCTTAAAGCGATTAGATCCAA
* * *
53560 GAATAAACAGATAAGTAGTGTGAAATAAGAGTCAAAATGATTTAACATTAAAAGACACTCTCGTA
452 GAATAAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATT-AAAGACACTCTCATA
* *
53625 TTCATTT-ATATCATCAAAATCCATCATCGTTTAAGAAGAATTAAAGAGTACAACGAAGCTTACT
516 TTCATTTAATATCATCAAAATCCATAATCATTTAAGAAGAATTAAAGAGTACAACGAAGCTTACT
53689 ATCTCTAGACTACTAGGCCTACTCCCTAATTGT
581 ATCTCTAGACTACTAGGCCTACTCCCTAATTGT
53722 TTCTCTTGCT
Statistics
Matches: 562, Mismatches: 47, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
613 123 0.22
614 2 0.00
615 414 0.74
616 23 0.04
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (614 bp):
GATGTGTATTCAAGAACAAGTAACTGGAGTTTGTCCCAGTCCCAAGCAGCTCACCTAACCCACTT
GTTAACCTAACCTGTCACCGCATCTCTCGATGTCAGCACACTACAATTTCACTCTCATGCTTAAA
GCGATTAGATCCAAGAATAAACAAATAAGCAGTGTAAAATAAGAATCAAAATGATTTAACATTAA
AAGACACTCTCGTATTCATTTAATATATCAAAATCCATCATCATTTAAGAAGAATGAAAGAGTAC
AACGAAGCTTACTATCTCTAGACTACTAGGCCTACTCCCTAATTGTCGATGTGTATTCAAGAACA
AGTAACTAGAATTTGCCCCAATCCCGAGCAGCTCACCTAATCCACTTGTTAACCAAACCTATCAC
CACATCTCTCGATGTCGGGGCATTGCAATTTCACTCTCGTGCTTAAAGCGATTAGATCCAAGAAT
AAACAGATAAGTAGTGTAAAATAAGAATCAAAATGATTTAACATTAAAGACACTCTCATATTCAT
TTAATATCATCAAAATCCATAATCATTTAAGAAGAATTAAAGAGTACAACGAAGCTTACTATCTC
TAGACTACTAGGCCTACTCCCTAATTGTC
Found at i:54913 original size:12 final size:12
Alignment explanation
Indices: 54896--54928 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
54886 TTAAACATAA
54896 AAAAATAAAATT
1 AAAAATAAAATT
54908 AAAAATAAAA-T
1 AAAAATAAAATT
54919 -AAAATAAAAT
1 AAAAATAAAAT
54929 AAATGTACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATAAAATT
Found at i:54917 original size:5 final size:5
Alignment explanation
Indices: 54897--54931 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
54887 TAAACATAAA
54897 AAAAT AAAATT AAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT AAA
54932 TGTACCTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:54925 original size:22 final size:20
Alignment explanation
Indices: 54885--54928 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
54875 TGACCCCCTT
*
54885 ATTAAACATAAAAAAATAAA
1 ATTAAAAATAAAAAAATAAA
54905 ATTAAAAATAAAATAAAATAAA
1 ATTAAAAAT-AAA-AAAATAAA
54927 AT
1 AT
54929 AAATGTACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
ATTAAAAATAAAAAAATAAA
Done.