Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009588.1 Kokia drynarioides strain JFW-HI SEQ_124302, 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: 90065
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:5449 original size:26 final size:26
Alignment explanation
Indices: 5409--5502 Score: 116
Period size: 26 Copynumber: 3.6 Consensus size: 26
5399 ATTATAGAGG
* *
5409 TTAGCTCTTATGAGCGTAGATAGAAT
1 TTAGCTCTTACGAGCCTAGATAGAAT
* * * * *
5435 TTAGCTCGTACGAGCCCAAACAGAAA
1 TTAGCTCTTACGAGCCTAGATAGAAT
5461 TTAGCTCTTACGAGCCTAGATAGAAT
1 TTAGCTCTTACGAGCCTAGATAGAAT
*
5487 TTAGCTCATACGAGCC
1 TTAGCTCTTACGAGCC
5503 CAAACAGAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (26 bp):
TTAGCTCTTACGAGCCTAGATAGAAT
Found at i:5487 original size:52 final size:51
Alignment explanation
Indices: 5409--5528 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 51
5399 ATTATAGAGG
* * *
5409 TTAGCTCTTATGAGCGTAGATAGAATTTAGCTCGTACGAGCCCAAACAGAAA
1 TTAGCTCTTACGAGCCTAGATAGAATTTAGCTCATACGAGCCCAAACAG-AA
5461 TTAGCTCTTACGAGCCTAGATAGAATTTAGCTCATACGAGCCCAAACAGAA
1 TTAGCTCTTACGAGCCTAGATAGAATTTAGCTCATACGAGCCCAAACAGAA
* *
5512 TTACACTCTGACGAGCC
1 TTA-GCTCTTACGAGCC
5529 AATTTTCAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 5 0.08
52 57 0.92
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (51 bp):
TTAGCTCTTACGAGCCTAGATAGAATTTAGCTCATACGAGCCCAAACAGAA
Found at i:5511 original size:26 final size:26
Alignment explanation
Indices: 5430--5513 Score: 114
Period size: 26 Copynumber: 3.2 Consensus size: 26
5420 GAGCGTAGAT
*
5430 AGAATTTAGCTCGTACGAGCCCAAAC
1 AGAATTTAGCTCATACGAGCCCAAAC
* * * * *
5456 AGAAATTAGCTCTTACGAGCCTAGAT
1 AGAATTTAGCTCATACGAGCCCAAAC
5482 AGAATTTAGCTCATACGAGCCCAAAC
1 AGAATTTAGCTCATACGAGCCCAAAC
5508 AGAATT
1 AGAATT
5514 ACACTCTGAC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (26 bp):
AGAATTTAGCTCATACGAGCCCAAAC
Found at i:5525 original size:26 final size:24
Alignment explanation
Indices: 5430--5528 Score: 90
Period size: 26 Copynumber: 3.8 Consensus size: 24
5420 GAGCGTAGAT
5430 AGAATTTAGCTCGTACGAGCCCAAAC
1 AGAA-TTAGCTC-TACGAGCCCAAAC
* * *
5456 AGAAATTAGCTCTTACGAGCCTAGAT
1 AG-AATTAGCTC-TACGAGCCCAAAC
5482 AGAATTTAGCTCATACGAGCCCAAAC
1 AGAA-TTAGCTC-TACGAGCCCAAAC
*
5508 AGAATTACACTCTGACGAGCC
1 AGAATTA-GCTCT-ACGAGCC
5529 AATTTTCAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
25 6 0.10
26 52 0.87
27 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
AGAATTAGCTCTACGAGCCCAAAC
Found at i:5646 original size:21 final size:20
Alignment explanation
Indices: 5604--5646 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5594 AACTCAAGAA
*
5604 TATAAACAAGATAAATAATT
1 TATAAACAAAATAAATAATT
* *
5624 TATAAATCAAAATTAATAGTT
1 TATAAA-CAAAATAAATAATT
5645 TA
1 TA
5647 ATTGTACGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
TATAAACAAAATAAATAATT
Found at i:7074 original size:17 final size:17
Alignment explanation
Indices: 7052--7086 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7042 TAAGCACATT
*
7052 AATCAACTAATCTCAAA
1 AATCAACCAATCTCAAA
*
7069 AATCAACCATTCTCAAA
1 AATCAACCAATCTCAAA
7086 A
1 A
7087 TACTTACCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (17 bp):
AATCAACCAATCTCAAA
Found at i:9346 original size:20 final size:20
Alignment explanation
Indices: 9310--9347 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9300 AAATTTCAAT
* *
9310 TATAAAATATTCCTCAATTA
1 TATAAAATACTCATCAATTA
9330 TATAAAATACTCATCAAT
1 TATAAAATACTCATCAAT
9348 AAACTCTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAAAATACTCATCAATTA
Found at i:9600 original size:16 final size:16
Alignment explanation
Indices: 9568--9601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9558 ATTACAAGTT
*
9568 TTCATACATATTAAAA
1 TTCATACATACTAAAA
*
9584 TTCATACATACTCAAA
1 TTCATACATACTAAAA
9600 TT
1 TT
9602 AACGATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (16 bp):
TTCATACATACTAAAA
Found at i:11000 original size:36 final size:36
Alignment explanation
Indices: 10936--11006 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
10926 AATCACTGTC
*
10936 ACATGGCATGAAAGACATACCCACATATTTACTTTT
1 ACATGGCATGAAAGACATACCCACATATTCACTTTT
**
10972 ACATGGCATGAATA-ACATACCCTTATATTCACTTT
1 ACATGGCATGAA-AGACATACCCACATATTCACTTT
11007 CACAATTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (36 bp):
ACATGGCATGAAAGACATACCCACATATTCACTTTT
Found at i:13360 original size:26 final size:27
Alignment explanation
Indices: 13322--13373 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
13312 GTTATTCAAA
*
13322 ATATATTACGGTAGTTCTA-TAAAAAT
1 ATATATTACGGTAGTTATATTAAAAAT
*
13348 ATATATTATGGTAGTTATATTAAAAA
1 ATATATTACGGTAGTTATATTAAAAA
13374 GTATGGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (27 bp):
ATATATTACGGTAGTTATATTAAAAAT
Found at i:14514 original size:79 final size:79
Alignment explanation
Indices: 14379--14535 Score: 260
Period size: 79 Copynumber: 2.0 Consensus size: 79
14369 AATGAGTCAT
* *
14379 TCTCTTCATTAGGATCTAATATAGTTGAAAAGGCATGACATTTCTCCTTAAAGAAGACTTATTGT
1 TCTCTTCATTAGGATCTAATATAGCTGAAAAGACATGACATTTCTCCTTAAAGAAGACTTATTGT
14444 ATCCTTAATGTGTG
66 ATCCTTAATGTGTG
* * * *
14458 TCTCTTCATTAGGATTTGATGTAGCTGAAAAGACATGACATTTCTCCTTAATGAAGACTTATTGT
1 TCTCTTCATTAGGATCTAATATAGCTGAAAAGACATGACATTTCTCCTTAAAGAAGACTTATTGT
14523 ATCCTTAATGTGT
66 ATCCTTAATGTGT
14536 TTATTGGTTG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (79 bp):
TCTCTTCATTAGGATCTAATATAGCTGAAAAGACATGACATTTCTCCTTAAAGAAGACTTATTGT
ATCCTTAATGTGTG
Found at i:19112 original size:16 final size:16
Alignment explanation
Indices: 19091--19121 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19081 TTCAAAACTC
19091 ATAAAAATAATATAAA
1 ATAAAAATAATATAAA
*
19107 ATAAAATTAATATAA
1 ATAAAAATAATATAA
19122 CTTGTCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATAATATAAA
Found at i:29790 original size:27 final size:27
Alignment explanation
Indices: 29752--29805 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29742 TTTAATTCTG
29752 ATTTAATTCTAATTGCACACCATTTTA
1 ATTTAATTCTAATTGCACACCATTTTA
*
29779 ATTTAATTCTAATTTCACACCATTTTA
1 ATTTAATTCTAATTGCACACCATTTTA
29806 GTTCTGATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.46
Consensus pattern (27 bp):
ATTTAATTCTAATTGCACACCATTTTA
Found at i:33871 original size:23 final size:25
Alignment explanation
Indices: 33845--33890 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33835 TCCAATTAAG
33845 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
33868 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
33891 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:35271 original size:90 final size:90
Alignment explanation
Indices: 35118--35302 Score: 370
Period size: 90 Copynumber: 2.1 Consensus size: 90
35108 TGATCGCAAA
35118 AATCGTAAAGAGGTTAGAGATGCTAGGCAAAGTCAGAAAACTTTGGTAGACGATAAAAAAGAAAA
1 AATCGTAAAGAGGTTAGAGATGCTAGGCAAAGTCAGAAAACTTTGGTAGACGATAAAAAAGAAAA
35183 GGATATTACTGTGGAGATAGGTGAC
66 GGATATTACTGTGGAGATAGGTGAC
35208 AATCGTAAAGAGGTTAGAGATGCTAGGCAAAGTCAGAAAACTTTGGTAGACGATAAAAAAGAAAA
1 AATCGTAAAGAGGTTAGAGATGCTAGGCAAAGTCAGAAAACTTTGGTAGACGATAAAAAAGAAAA
35273 GGATATTACTGTGGAGATAGGTGAC
66 GGATATTACTGTGGAGATAGGTGAC
35298 AATCG
1 AATCG
35303 AAATAACCAG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 95 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (90 bp):
AATCGTAAAGAGGTTAGAGATGCTAGGCAAAGTCAGAAAACTTTGGTAGACGATAAAAAAGAAAA
GGATATTACTGTGGAGATAGGTGAC
Found at i:40535 original size:23 final size:22
Alignment explanation
Indices: 40502--40548 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
40492 TATTATTTTT
40502 AAAAAAATGAAAAAAATTCAAA
1 AAAAAAATGAAAAAAATTCAAA
* *
40524 AAAAAAAGTGAAGAAAATTGAAA
1 AAAAAAA-TGAAAAAAATTCAAA
40547 AA
1 AA
40549 TTCAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAAAATGAAAAAAATTCAAA
Found at i:40587 original size:13 final size:12
Alignment explanation
Indices: 40566--40625 Score: 68
Period size: 13 Copynumber: 4.8 Consensus size: 12
40556 AAATTAGTAC
40566 TTTTATTTTCAT
1 TTTTATTTTCAT
40578 TTTGTATTTTC-T
1 TTT-TATTTTCAT
40590 TTTTCATTTTTCAT
1 TTTT-A-TTTTCAT
*
40604 TTTTCATTTTTAT
1 TTTT-ATTTTCAT
40617 TTTTATTTT
1 TTTTATTTT
40626 ATTATGCACT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
11 1 0.02
12 13 0.30
13 22 0.51
14 7 0.16
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTATTTTCAT
Found at i:40599 original size:7 final size:7
Alignment explanation
Indices: 40571--40625 Score: 66
Period size: 7 Copynumber: 8.4 Consensus size: 7
40561 AGTACTTTTA
40571 TTTTCAT
1 TTTTCAT
40578 TTTGT-A-
1 TTT-TCAT
40584 TTTTC-T
1 TTTTCAT
40590 TTTTCAT
1 TTTTCAT
40597 TTTTCAT
1 TTTTCAT
40604 TTTTCAT
1 TTTTCAT
40611 TTTT-AT
1 TTTTCAT
40617 TTTT-AT
1 TTTTCAT
40623 TTT
1 TTT
40626 ATTATGCACT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.02
6 19 0.43
7 23 0.52
8 1 0.02
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (7 bp):
TTTTCAT
Found at i:40644 original size:6 final size:6
Alignment explanation
Indices: 40566--40625 Score: 59
Period size: 6 Copynumber: 9.5 Consensus size: 6
40556 AAATTAGTAC
* *
40566 TTTTAT TTTCAT TTTGTAT TTTCT-T TTTCAT TTTTCAT TTTTCAT TTTTAT
1 TTTTAT TTTTAT TTT-TAT TTT-TAT TTTTAT TTTT-AT TTTT-AT TTTTAT
40617 TTTTAT TTT
1 TTTTAT TTT
40626 ATTATGCACT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
6 27 0.59
7 19 0.41
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:43125 original size:22 final size:25
Alignment explanation
Indices: 43089--43140 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
43079 TTGAATGGAA
43089 TTTGAGAGGACTTTGAAGAC-TGAT
1 TTTGAGAGGACTTTGAAGACTTGAT
*
43113 TTTGA-AGGA-TTTGATGACTTTGAT
1 TTTGAGAGGACTTTGAAGAC-TTGAT
43137 TTTG
1 TTTG
43141 GGTTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 8 0.32
23 4 0.16
24 13 0.52
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (25 bp):
TTTGAGAGGACTTTGAAGACTTGAT
Found at i:43247 original size:63 final size:65
Alignment explanation
Indices: 43158--43293 Score: 204
Period size: 67 Copynumber: 2.1 Consensus size: 65
43148 TATTTTGGTT
*
43158 ATTTATTTATTTATATTCATAAAATAATAAAT-T-AATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAATAATAAATATAAATAATAAAACAAAATAAATATTATTTTAC
* *
43221 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAAGAAAATAAATATTATTTT
1 ATTTATTTATTTATATTCATAAAATAATAAAT--ATAAATAATAAAACAAAATAAATATTATTTT
*
43286 AT
64 AC
43288 ATTTAT
1 ATTTAT
43294 AAAAATAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
63 31 0.48
66 1 0.02
67 33 0.51
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (65 bp):
ATTTATTTATTTATATTCATAAAATAATAAATATAAATAATAAAACAAAATAAATATTATTTTAC
Found at i:43324 original size:67 final size:67
Alignment explanation
Indices: 43179--43333 Score: 163
Period size: 67 Copynumber: 2.3 Consensus size: 67
43169 TATATTCATA
* *** * *
43179 AAATAATAAATTAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCATACA
1 AAATAA-AAA-TAATAATAAAACAAAATAAATATTATTTTACATTTA-TTAAAAATAATAATACA
43244 ATAAT
63 ATAAT
* * *
43249 AAATAAATA-AATAATAAAAGAAAATAAATATTATTTTATATTTA-TAAAAATAATAATA-AATA
1 AAATAAAAATAATAATAAAACAAAATAAATATTATTTTACATTTATTAAAAATAATAATACAAT-
43311 AAT
65 AAT
*
43314 AAATAAAAATAATAAGAAAA
1 AAATAAAAATAATAATAAAA
43334 ATGGAATTGG
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
64 3 0.04
65 20 0.28
66 9 0.12
67 32 0.44
69 2 0.03
70 6 0.08
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (67 bp):
AAATAAAAATAATAATAAAACAAAATAAATATTATTTTACATTTATTAAAAATAATAATACAATA
AT
Found at i:43335 original size:18 final size:18
Alignment explanation
Indices: 43294--43335 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
43284 TTATATTTAT
*
43294 AAAAATAATAATAAATAA
1 AAAAATAAAAATAAATAA
*
43312 ATAAATAAAAAT-AATAA
1 AAAAATAAAAATAAATAA
43329 GAAAAAT
1 -AAAAAT
43336 GGAATTGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAATAAAAATAAATAA
Found at i:43757 original size:11 final size:11
Alignment explanation
Indices: 43741--43770 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
43731 GAGCGAAAAG
43741 AGCGAAAAATA
1 AGCGAAAAATA
43752 AGCGAAAAATA
1 AGCGAAAAATA
43763 AGCGAAAA
1 AGCGAAAA
43771 TCGGACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.10, G:0.20, T:0.07
Consensus pattern (11 bp):
AGCGAAAAATA
Found at i:51962 original size:15 final size:15
Alignment explanation
Indices: 51923--51966 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
51913 ATATTTTACA
*
51923 AAAAATATAAAAATTT
1 AAAAATAT-ATAATTT
51939 -AAAAT-TATAATTT
1 AAAAATATATAATTT
51952 AAAAATATATAATTT
1 AAAAATATATAATTT
51967 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAAATATATAATTT
Found at i:51978 original size:22 final size:23
Alignment explanation
Indices: 51950--52001 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
51940 AAATTATAAT
51950 TTAAAAATATATAATTTTTAAAAA
1 TTAAAAA-ATATAATTTTTAAAAA
51974 -TAAAAAATATAATTTTTAAAAA
1 TTAAAAAATATAATTTTTAAAAA
51996 TTAAAA
1 TTAAAA
52002 CTTATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAAAAATATAATTTTTAAAAA
Found at i:66577 original size:265 final size:259
Alignment explanation
Indices: 66110--66610 Score: 693
Period size: 265 Copynumber: 1.9 Consensus size: 259
66100 CTAAGGTAGC
* *
66110 TGTGTTTCAGTCCCATCTGTTAGGGTTGGATTTTGTATTATCTATTTTCTCTCTGTTGCTTTACT
1 TGTGTTTCAGTCCCATCTGTTAGGGTTGGATTTTGCATTATCTATTTTCTCTCTGTTCCTTTACT
** * * *
66175 TATCATGGATATATGTGATGACCTAAGAACTTTGCAACTTAAAGTCTTTCCTCACTTCTAGTTCT
66 TATCATGGATATATGTGACAACCTAAGAACTTTGCAACTTAAAGACTGTCCTCACTGCTAGTTCT
** * * * *
66240 GTATATGCCCCAAGAATACTTTTATTTTGCCTTGTTTGTAGGGGTCCTAAAATCTAGGCTTCATT
131 CCATATGCCCCAAGAATACCTTTATTTAGCCTTGTTTGGAGAGGTCCTAAAATCTAGGCTTCATT
66305 AATTTCACAAAATCTATATTATTGACATGTTGCTTAAAAATGATCATTGAGGTGGATTTATATT
196 AATTTCACAAAATCTATATTATTGACATGTTGCTTAAAAATGATCATTGAGGTGGATTTATATT
* *
66369 TGTGTTTCAGTGCCATCTGTTAGAGG-TGGATTTTGCGTTATC-AGTTTTCTCTCTGTTCCTTTA
1 TGTGTTTCAGTCCCATCTGTTAG-GGTTGGATTTTGCATTATCTA-TTTTCTCTCTGTTCCTTTA
* * *
66432 -TTATCATGGATTTATGTGACAATCTATGAACTTTGCAATTTGCAACTTAAAGACTGTCCTCACT
64 CTTATCATGGATATATGTGACAACCTAAGAA-----C--TTTGCAACTTAAAGACTGTCCTCACT
* * * *
66496 GCTAGTTCTCCGTATGCCTCAAGAATACCTTTATTTAGCCTTGTTTGGAGAGTTCCTAAAATCTG
122 GCTAGTTCTCCATATGCCCCAAGAATACCTTTATTTAGCCTTGTTTGGAGAGGTCCTAAAATCTA
*
66561 GGCTTCATTAATTTCACAAAATCTATATTATTGACATGTTGCTTGAAAAT
187 GGCTTCATTAATTTCACAAAATCTATATTATTGACATGTTGCTTAAAAAT
66611 AATAATGGAA
Statistics
Matches: 210, Mismatches: 23, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
258 26 0.12
259 54 0.26
260 2 0.01
263 1 0.00
265 127 0.60
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (259 bp):
TGTGTTTCAGTCCCATCTGTTAGGGTTGGATTTTGCATTATCTATTTTCTCTCTGTTCCTTTACT
TATCATGGATATATGTGACAACCTAAGAACTTTGCAACTTAAAGACTGTCCTCACTGCTAGTTCT
CCATATGCCCCAAGAATACCTTTATTTAGCCTTGTTTGGAGAGGTCCTAAAATCTAGGCTTCATT
AATTTCACAAAATCTATATTATTGACATGTTGCTTAAAAATGATCATTGAGGTGGATTTATATT
Found at i:69452 original size:15 final size:15
Alignment explanation
Indices: 69432--69484 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
69422 TTGGAGATAT
*
69432 GAACACTCATGTTGC
1 GAACACTCATATTGC
* * **
69447 GAACACACACAACGC
1 GAACACTCATATTGC
*
69462 GAACACTAATATTGC
1 GAACACTCATATTGC
69477 GAACACTC
1 GAACACTC
69485 GCGTTGCGAG
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (15 bp):
GAACACTCATATTGC
Found at i:77752 original size:20 final size:21
Alignment explanation
Indices: 77710--77762 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 21
77700 AGACAATTTG
77710 TTGAAAATTTATATGGTTTTA
1 TTGAAAATTTATATGGTTTTA
77731 TTGAAGAATTTATAT-G-TTTA
1 TTGAA-AATTTATATGGTTTTA
77751 TTGAATAATTTA
1 TTGAA-AATTTA
77763 CCAAATCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 15 0.50
21 6 0.20
22 9 0.30
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (21 bp):
TTGAAAATTTATATGGTTTTA
Found at i:78467 original size:79 final size:79
Alignment explanation
Indices: 78316--78539 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
78306 ACCGACAGTT
* * * * ** **
78316 TTGACAC-CAAGTGCCTAGCGGATAAACCGCAATTGTGAGCCCAACTCTAGTTGGATT-AACCAA
1 TTGACACTC-AGTGCCTAACGGATAAACCGAAAATGTGAGCCCAGCTCTAGTCAG-TTAAACTGA
**
78379 CAATATCCGTCAAATC
64 CAACGTCCGTCAAATC
* ** * *
78395 TT-AGCAC-CTAGTGCTTAGTGGATAAATCGAAAATGTGAGCCCAGCTCTAGTCATTTAAACTGA
1 TTGA-CACTC-AGTGCCTAACGGATAAACCGAAAATGTGAGCCCAGCTCTAGTCAGTTAAACTGA
78458 CAACGTCCGTCAAATC
64 CAACGTCCGTCAAATC
* * *
78474 TTGACACTCAGTGCCTAACGGATAAACCGCAAATGTGAGCTCAGCTCTAGTTAGTTAAACTGACA
1 TTGACACTCAGTGCCTAACGGATAAACCGAAAATGTGAGCCCAGCTCTAGTCAGTTAAACTGACA
78539 A
66 A
78540 TGTAAATTAT
Statistics
Matches: 119, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
78 3 0.03
79 114 0.96
80 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (79 bp):
TTGACACTCAGTGCCTAACGGATAAACCGAAAATGTGAGCCCAGCTCTAGTCAGTTAAACTGACA
ACGTCCGTCAAATC
Found at i:84395 original size:23 final size:23
Alignment explanation
Indices: 84369--84412 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
84359 TAACAAACAT
*
84369 TCAAATTCATTTAAAACATTCTC
1 TCAAATTCATATAAAACATTCTC
*
84392 TCAAATTCATATAAATCATTC
1 TCAAATTCATATAAAACATTC
84413 AATAAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (23 bp):
TCAAATTCATATAAAACATTCTC
Done.