Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006175.1 Kokia drynarioides strain JFW-HI SEQ_120740, 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: 102808
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1419 original size:15 final size:15
Alignment explanation
Indices: 1401--1453 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
1391 TAGCTTATTT
1401 TTATTTATT-AAATTA
1 TTATTT-TTAAAATTA
*
1416 TTATTTTTTAATTAATTT
1 TTA-TTTTTAA--AATTA
1434 TTATTTTTAAAATTA
1 TTATTTTTAAAATTA
1449 TTATT
1 TTATT
1454 ATTGTTCACC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 14 0.44
16 4 0.12
17 7 0.22
18 7 0.22
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTTTAAAATTA
Found at i:1425 original size:18 final size:18
Alignment explanation
Indices: 1395--1453 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
1385 TCATTCTAGC
1395 TTATT-TTTATTTATTAAA
1 TTATTATTT-TTTATTAAA
1413 TTATTATTTTTTAATT-AA
1 TTATTATTTTTT-ATTAAA
*
1431 TTTTTA-TTTTTA--AAA
1 TTATTATTTTTTATTAAA
1446 TTATTATT
1 TTATTATT
1454 ATTGTTCACC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 7 0.20
16 2 0.06
17 5 0.14
18 15 0.43
19 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTATTTTTTATTAAA
Found at i:1455 original size:18 final size:18
Alignment explanation
Indices: 1411--1456 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1401 TTATTTATTA
*
1411 AATTATTATTTTTTAATT
1 AATTATTATTTTTAAATT
*
1429 AATTTTTATTTTTAAAATT
1 AATTATTATTTTT-AAATT
1448 -ATTATTATT
1 AATTATTATT
1457 GTTCACCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AATTATTATTTTTAAATT
Found at i:3218 original size:122 final size:119
Alignment explanation
Indices: 3085--3460 Score: 533
Period size: 132 Copynumber: 3.0 Consensus size: 119
3075 TTGAACATTA
*
3085 AATAAAATTATTTCTTTCTTTATTTTTTTCATATCAGATATTTTAACTTTTAACTTTAAATAAAT
1 AATAAAATTATTTCTTTCTTTATTTTTTTCATATCATATATTTTAACTTTTAACTTTAAATAAAT
*
3150 ATTTATTTTTTTATTTCTTTTTTTCATATCATATATTTTAAATTTAAATATTTATAT
66 ATTT-TTTTTTTA-TT-TTTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
3207 AATAAAATTATTTCTTTCTTTATTTTTTTTCCATATCATATATTTTAACTTTTTAACTTTTTAAC
1 AATAAAATTATTTCTTTCTTTA-TTTTTTT-CATATCATATATTTTAAC-TTTTAAC--TTT-A-
3272 TTTAAGTAAATATTTTCTTTTTTATTTATTTTTTCATATCATATATTTTAACTTTAAATATTTAT
59 ---AA-TAAATATTTT-TTTTTTATTT-TTTTTTCATATCATATATTTTAACTTTAAATATTTAT
3337 AT
118 AT
* *
3339 AATAAAATTATTTCTTTCTTTATTTTTTCCATATCATATATTTTAACTGTTTAATTTTAAATAAA
1 AATAAAATTATTTCTTTCTTTATTTTTTTCATATCATATATTTTAACT-TTTAACTTTAAATAAA
3404 TATTTCTTTTTTTA---TTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
65 TATTT-TTTTTTTATTTTTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
3457 AATA
1 AATA
3461 TACTTCAACT
Statistics
Matches: 235, Mismatches: 4, Indels: 34
0.86 0.01 0.12
Matches are distributed among these distances:
118 43 0.18
122 38 0.16
123 10 0.04
124 17 0.07
125 7 0.03
127 4 0.02
128 4 0.02
129 1 0.00
130 23 0.10
131 7 0.03
132 65 0.28
133 16 0.07
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (119 bp):
AATAAAATTATTTCTTTCTTTATTTTTTTCATATCATATATTTTAACTTTTAACTTTAAATAAAT
ATTTTTTTTTTATTTTTTTTTCATATCATATATTTTAACTTTAAATATTTATAT
Found at i:3262 original size:8 final size:8
Alignment explanation
Indices: 3249--3274 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3239 ATATCATATA
3249 TTTTAACT
1 TTTTAACT
3257 TTTTAACT
1 TTTTAACT
3265 TTTTAACT
1 TTTTAACT
3273 TT
1 TT
3275 AAGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTAACT
Found at i:3478 original size:56 final size:57
Alignment explanation
Indices: 3298--3480 Score: 192
Period size: 56 Copynumber: 3.1 Consensus size: 57
3288 CTTTTTTATT
*
3298 TATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATAAAATT-ATTTCTTTC
1 TATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATATAATTCA--TC-TTC
* * * * * *
3357 TTTATTTTTTCCATATCATATATTTTAACTGTTTAAT-TTTAAATAA-ATATTTCTTTTTT
1 --TATTTTTT-CATATCATATATTTTAACT-TTAAATATTTATATAATATAATTCATCTTC
* *
3416 TATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATATACTTCAACTTC
1 TATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATATAATTCATCTTC
*
3473 TTTTTTTT
1 TATTTTTT
3481 TAGATGATAA
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
55 5 0.05
56 27 0.26
57 23 0.23
59 2 0.02
60 1 0.01
61 12 0.12
62 27 0.26
63 5 0.05
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (57 bp):
TATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATATAATTCATCTTC
Found at i:3478 original size:62 final size:59
Alignment explanation
Indices: 3296--3478 Score: 230
Period size: 62 Copynumber: 3.1 Consensus size: 59
3286 TTCTTTTTTA
* *
3296 TTTATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATAAAATTATTTCTTT
1 TTTATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAAT-ATATTACTTCTTT
* * *
3356 CTTTATTTTTTCCATATCATATATTTTAACTGTTTAAT-TTTAAATAA-ATATTTC-T-TTT
1 -TTTATTTTTT-CATATCATATATTTTAACT-TTAAATATTTATATAATATATTACTTCTTT
3414 TTTATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATATACTTCAACTTCTTT
1 TTTATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATATA-TT--ACTTCTTT
3476 TTT
1 TTT
3479 TTTAGATGAT
Statistics
Matches: 105, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
55 5 0.05
56 27 0.26
57 13 0.12
58 5 0.05
59 1 0.01
60 5 0.05
61 11 0.10
62 33 0.31
63 5 0.05
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (59 bp):
TTTATTTTTTCATATCATATATTTTAACTTTAAATATTTATATAATATATTACTTCTTT
Found at i:6224 original size:17 final size:15
Alignment explanation
Indices: 6194--6245 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
6184 TAACTTATTT
6194 TTATTTATT-AAATTA
1 TTATTT-TTAAAATTA
*
6209 TTATTTTTAATTAATTT
1 TTATTTTTAA--AATTA
6226 TTATTTTTAAAATTA
1 TTATTTTTAAAATTA
6241 TTATT
1 TTATT
6246 ATTGTTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 2 0.06
15 16 0.50
17 14 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTTTTAAAATTA
Found at i:14787 original size:43 final size:41
Alignment explanation
Indices: 14717--14931 Score: 225
Period size: 41 Copynumber: 5.1 Consensus size: 41
14707 ATGGAGAAAG
* * ** *
14717 AGTGGCAATTTATTTGC-AATATGTTGTGCATCCGCAGTCG
1 AGTGGCAGTTTATTTGCAAATATGTTGTGCATCCACAACCC
*
14757 AGTGGCAGTTTTTATTTGCAAATATGTTGTGCATCCATAACCC
1 AGTGGCAG--TTTATTTGCAAATATGTTGTGCATCCACAACCC
* *
14800 AGTGACAGTTTTTATTTGCATTAAATATTTTGTGCATCCACAACCC
1 AGTGGCAG--TTTATTTGC---AAATATGTTGTGCATCCACAACCC
* * * * *
14846 AGTGGAAGTTTATCTGCAAATACGTTGTGCATCCACAATCG
1 AGTGGCAGTTTATTTGCAAATATGTTGTGCATCCACAACCC
* *
14887 AGTGGTAGTTTATCTGCAAATATGTTGTGCATCCACAACCC
1 AGTGGCAGTTTATTTGCAAATATGTTGTGCATCCACAACCC
14928 AGTG
1 AGTG
14932 ATAGTTTTTA
Statistics
Matches: 149, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
40 7 0.05
41 61 0.41
42 9 0.06
43 36 0.24
44 8 0.05
46 28 0.19
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (41 bp):
AGTGGCAGTTTATTTGCAAATATGTTGTGCATCCACAACCC
Found at i:14880 original size:87 final size:82
Alignment explanation
Indices: 14725--14931 Score: 209
Period size: 87 Copynumber: 2.5 Consensus size: 82
14715 AGAGTGGCAA
* * ** * * * *
14725 TTTATTTGC-AATATGTTGTGCATCCGCAGTCGAGTGGCAGTTTTTATTTGCAAATATGTTGTGC
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGAAG--TTTATCTGCAAATACGTTGTGC
*
14789 ATCCATAACCCAGTGACAG
64 ATCCACAACCCAGTGACAG
* *
14808 TTTTTATTTGCATTAAATATTTTGTGCATCCACAACCCAGTGGAAGTTTATCTGCAAATACGTTG
1 --TTTATCTGC---AAATATGTTGTGCATCCACAACCCAGTGGAAGTTTATCTGCAAATACGTTG
* * **
14873 TGCATCCACAATCGAGTGGTAG
61 TGCATCCACAACCCAGTGACAG
14895 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTG
1 TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTG
14932 ATAGTTTTTA
Statistics
Matches: 103, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
82 27 0.26
85 17 0.17
87 34 0.33
89 25 0.24
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (82 bp):
TTTATCTGCAAATATGTTGTGCATCCACAACCCAGTGGAAGTTTATCTGCAAATACGTTGTGCAT
CCACAACCCAGTGACAG
Found at i:14969 original size:128 final size:126
Alignment explanation
Indices: 14717--14971 Score: 291
Period size: 128 Copynumber: 2.0 Consensus size: 126
14707 ATGGAGAAAG
* * * * *
14717 AGTGGCAATTTATTTGCAATATGTTGTGCATCCGCAGTCGAGTGGCAGTTTTTATTTGCAAATAT
1 AGTGGCAATTTATCTGCAATACGTTGTGCATCCACAATCGAGTGGCAG-TTTTATCTGCAAATAT
* ** * * *
14782 GTTGTGCATCCATAACCCAGTGACAGTTTTTATTTGCATTAAATATTTTGTGCATCCACAACCC
65 GTTGTGCATCCACAACCCAGTGACAGTTTTTACCTG-A-TAAATATGTGGTGAATCCACAACCC
*
14846 AGTGG-AAGTTTATCTGCAAATACGTTGTGCATCCACAATCGAGTGGTAG-TTTATCTGCAAATA
1 AGTGGCAA-TTTATCTGC-AATACGTTGTGCATCCACAATCGAGTGGCAGTTTTATCTGCAAATA
* *
14909 TGTTGTGCATCCACAACCCAGTGATAGTTTTTACCTG-TAAATCAATGGTGGTTAATCCACAAC
64 TGTTGTGCATCCACAACCCAGTGACAGTTTTTACCTGATAAAT--AT-GTGGTGAATCCACAAC
14972 TCGATGTATA
Statistics
Matches: 107, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
125 5 0.05
127 2 0.02
128 60 0.56
129 13 0.12
130 27 0.25
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (126 bp):
AGTGGCAATTTATCTGCAATACGTTGTGCATCCACAATCGAGTGGCAGTTTTATCTGCAAATATG
TTGTGCATCCACAACCCAGTGACAGTTTTTACCTGATAAATATGTGGTGAATCCACAACCC
Found at i:15973 original size:10 final size:10
Alignment explanation
Indices: 15946--15993 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
15936 CCCTCCTACT
*
15946 ATATTATATG
1 ATATAATATG
15956 ATAT-ATATG
1 ATATAATATG
*
15965 ATATAATATA
1 ATATAATATG
* *
15975 ATATTATATC
1 ATATAATATG
15985 ATATAATAT
1 ATATAATAT
15994 ATTTATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 9 0.27
10 24 0.73
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (10 bp):
ATATAATATG
Found at i:16011 original size:11 final size:11
Alignment explanation
Indices: 15958--16011 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
15948 ATTATATGAT
15958 ATATATGATATA
1 ATATAT-ATATA
15970 ATATA-ATAT-
1 ATATATATATA
15979 -TATATCATATA
1 ATATAT-ATATA
*
15990 ATATATTTATA
1 ATATATATATA
*
16001 ATTTATATATA
1 ATATATATATA
16012 TGCATTGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
8 4 0.11
10 8 0.23
11 13 0.37
12 10 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
ATATATATATA
Found at i:26148 original size:3 final size:3
Alignment explanation
Indices: 26140--26170 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
26130 GTCATCACCC
*
26140 TCA TCA TCA TCA TCA TCA TCA TCG TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
26171 TTCCTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:29374 original size:24 final size:24
Alignment explanation
Indices: 29346--29408 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29336 AGAAATAATC
* *
29346 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
*
29370 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
29394 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
29409 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:30180 original size:22 final size:22
Alignment explanation
Indices: 30152--30194 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
30142 TTGATTACTT
30152 TTTTAAATTTTATGTTGATGTC
1 TTTTAAATTTTATGTTGATGTC
30174 TTTTAAATTTTATGTTGATGT
1 TTTTAAATTTTATGTTGATGT
30195 TAAAGTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.60
Consensus pattern (22 bp):
TTTTAAATTTTATGTTGATGTC
Found at i:30310 original size:21 final size:21
Alignment explanation
Indices: 30247--30317 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
30237 GAATAATAGT
*
30247 TTTTTAAAGGGATTAAACATAA
1 TTTTT-AAGTGATTAAACATAA
* * * **
30269 TGTATTAATTTATTATTCATAA
1 T-TTTTAAGTGATTAAACATAA
*
30291 TTTTTAAGTGATTAAACATAT
1 TTTTTAAGTGATTAAACATAA
30312 TTTTTA
1 TTTTTA
30318 TCATTTTGAG
Statistics
Matches: 36, Mismatches: 12, Indels: 3
0.71 0.24 0.06
Matches are distributed among these distances:
21 20 0.56
22 13 0.36
23 3 0.08
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (21 bp):
TTTTTAAGTGATTAAACATAA
Found at i:43725 original size:29 final size:29
Alignment explanation
Indices: 43662--43764 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 29
43652 TAGAAATAAT
*
43662 ACAGACACAATTACAGATATC-GTCATGTC
1 ACAGATACAATTACAGATA-CAGTCATGTC
*
43691 ACAGATACAATTACAAATACAGTCATGTC
1 ACAGATACAATTACAGATACAGTCATGTC
* * * *
43720 ACAGATACAGTTATAGATGCAGACATGAT-
1 ACAGATACAATTACAGATACAGTCATG-TC
*
43749 ACAGATACAGTTACAG
1 ACAGATACAATTACAG
43765 TTACGGATGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.02
29 62 0.97
30 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (29 bp):
ACAGATACAATTACAGATACAGTCATGTC
Found at i:43729 original size:17 final size:17
Alignment explanation
Indices: 43674--43730 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
43664 AGACACAATT
43674 ACAGATATC-GTCATGTC
1 ACAGATA-CAGTCATGTC
43691 ACAGATACA---AT-T-
1 ACAGATACAGTCATGTC
*
43703 ACAAATACAGTCATGTC
1 ACAGATACAGTCATGTC
43720 ACAGATACAGT
1 ACAGATACAGT
43731 TATAGATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
12 8 0.25
13 1 0.03
14 2 0.06
15 2 0.06
16 2 0.06
17 17 0.53
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (17 bp):
ACAGATACAGTCATGTC
Found at i:43774 original size:35 final size:35
Alignment explanation
Indices: 43720--43798 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 35
43710 CAGTCATGTC
* *
43720 ACAGATACAGTTATAGATGCAGACATGATACAGAT
1 ACAGTTACAGTTACAGATGCAGACATGATACAGAT
* *
43755 ACAGTTACAGTTACGGATGCAGATATGATACAGAT
1 ACAGTTACAGTTACAGATGCAGACATGATACAGAT
**
43790 GTAGTTACA
1 ACAGTTACA
43799 AATGCAGACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (35 bp):
ACAGTTACAGTTACAGATGCAGACATGATACAGAT
Found at i:43784 original size:29 final size:29
Alignment explanation
Indices: 43691--43814 Score: 106
Period size: 29 Copynumber: 4.1 Consensus size: 29
43681 TCGTCATGTC
* * *
43691 ACAGATACAATTACAAATACAGTCATG-T
1 ACAGATACAGTTACAAATGCAGACATGAT
* *
43719 CACAGATACAGTTATAGATGCAGACATGAT
1 -ACAGATACAGTTACAAATGCAGACATGAT
*
43749 ACAGATACAGTTACAGTTACGGATGCAGATATGAT
1 ACAGATACAGTTACA---A---ATGCAGACATGAT
**
43784 ACAGATGTAGTTACAAATGCAGACATGAT
1 ACAGATACAGTTACAAATGCAGACATGAT
43813 AC
1 AC
43815 CCTCATCCGT
Statistics
Matches: 77, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
29 50 0.65
30 1 0.01
32 1 0.01
35 25 0.32
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (29 bp):
ACAGATACAGTTACAAATGCAGACATGAT
Found at i:44399 original size:41 final size:40
Alignment explanation
Indices: 44354--44443 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
44344 TTATTACAGA
**
44354 CCATGTGTCTTAAAACAATATACACACACCCTGACACACAC
1 CCATGTGTCCCAAAACAATATA-ACACACCCTGACACACAC
* * * *
44395 CCATGTGCCCCAAAACAGTATAACATACCCTGACACACGC
1 CCATGTGTCCCAAAACAATATAACACACCCTGACACACAC
*
44435 CCATATGTC
1 CCATGTGTC
44444 AGCCCGTGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 23 0.56
41 18 0.44
ACGTcount: A:0.36, C:0.36, G:0.10, T:0.19
Consensus pattern (40 bp):
CCATGTGTCCCAAAACAATATAACACACCCTGACACACAC
Found at i:44759 original size:20 final size:20
Alignment explanation
Indices: 44723--44772 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
44713 ATTAGCATGA
44723 TTTATATTAAGTGTAAATAG-G
1 TTTA-ATTAAGTGTAAA-AGCG
44744 TTTAATTAAGAT-TAAAAGCG
1 TTTAATTAAG-TGTAAAAGCG
*
44764 ATTAATTAA
1 TTTAATTAA
44773 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (20 bp):
TTTAATTAAGTGTAAAAGCG
Found at i:45946 original size:35 final size:36
Alignment explanation
Indices: 45853--45955 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 36
45843 TAGTAACAGG
*
45853 CATGACCTTTAGGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
*
45889 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
*
45925 CATGACC-TTGGGTCAATAGGGAATAAAATGA
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGA
45956 TTAAAGATCA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 22 0.35
36 41 0.65
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
Found at i:46683 original size:21 final size:21
Alignment explanation
Indices: 46638--46695 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
46628 TAGAAGTAAG
* **
46638 ACTTGTTTCGGTAGAACAGTT
1 ACTTGTATCGGTAGAACAGCC
*
46659 ACTTGTATCGGTAGAACTGCC
1 ACTTGTATCGGTAGAACAGCC
*
46680 ACTTGTATCGATAGAA
1 ACTTGTATCGGTAGAA
46696 GTCTGCATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGCC
Found at i:56946 original size:35 final size:36
Alignment explanation
Indices: 56850--56948 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 36
56840 GGTAATAGGC
* * *
56850 ATGACCTTTGGATCAACAGGGAGTAAAATGAGCATC
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAACATA
* * *
56886 ATGATCTTTGGGTTAACAGGAAGTAAAATGAACATA
1 ATGACCTTTGGGTCAACAGGGAGTAAAATGAACATA
*
56922 ATGA-CTTTGGGTCAATAGGGAGTAAAA
1 ATGACCTTTGGGTCAACAGGGAGTAAAA
56949 CGATTAACGA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 20 0.37
36 34 0.63
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.25
Consensus pattern (36 bp):
ATGACCTTTGGGTCAACAGGGAGTAAAATGAACATA
Found at i:64564 original size:18 final size:19
Alignment explanation
Indices: 64538--64575 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
64528 GATTACCAGA
64538 AGAAGAAAAAGAA-AAGAG
1 AGAAGAAAAAGAAGAAGAG
*
64556 AGAATAAAAAGAAGAAGAG
1 AGAAGAAAAAGAAGAAGAG
64575 A
1 A
64576 ATGACGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (19 bp):
AGAAGAAAAAGAAGAAGAG
Found at i:65043 original size:19 final size:19
Alignment explanation
Indices: 65019--65065 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
65009 ATAGTTTTCA
*
65019 TGCATTTTTATTTTGTCAT
1 TGCATTTTTATTTCGTCAT
65038 TGCATTTTTATTTCGTCAT
1 TGCATTTTTATTTCGTCAT
65057 TGCATTTTT
1 TGCATTTTT
65066 GTTAAGTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.13, G:0.11, T:0.62
Consensus pattern (19 bp):
TGCATTTTTATTTCGTCAT
Found at i:65092 original size:11 final size:11
Alignment explanation
Indices: 65076--65105 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
65066 GTTAAGTTAG
65076 TTACATTTTCA
1 TTACATTTTCA
65087 TTACATTTTCA
1 TTACATTTTCA
*
65098 TTATATTT
1 TTACATTT
65106 GTATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (11 bp):
TTACATTTTCA
Found at i:65676 original size:15 final size:15
Alignment explanation
Indices: 65657--65686 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
65647 GAAAAATGAT
65657 AAAAAGGAAGAAAAAG
1 AAAAA-GAAGAAAAAG
65673 AAAAAGAAGAAAAA
1 AAAAAGAAGAAAAA
65687 AATTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAAG
Found at i:81765 original size:11 final size:11
Alignment explanation
Indices: 81749--81778 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
81739 GAACCTTGAG
81749 AAAAAATAAAT
1 AAAAAATAAAT
81760 AAAAAATAAAT
1 AAAAAATAAAT
*
81771 AAATAATA
1 AAAAAATA
81779 GAAGATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:82576 original size:14 final size:14
Alignment explanation
Indices: 82559--82588 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
82549 TTTAAACTCT
*
82559 AAAAGATAAATCTA
1 AAAAGATAAATATA
82573 AAAAGATAAATATA
1 AAAAGATAAATATA
82587 AA
1 AA
82589 TTAAATATAA
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:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:82630 original size:13 final size:13
Alignment explanation
Indices: 82604--82639 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
82594 TATAAACAAT
82604 ATCCT-AATAATA
1 ATCCTAAATAATA
*
82616 ATCCTAAATATTA
1 ATCCTAAATAATA
82629 ATCCTAAATAA
1 ATCCTAAATAA
82640 AAATAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (13 bp):
ATCCTAAATAATA
Found at i:85115 original size:21 final size:21
Alignment explanation
Indices: 85065--85139 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
85055 CAATGTATTT
* *
85065 TTCTACTGATACAAGTGAT-AG
1 TTCTACCGATACAAGTG-TCAC
* *
85086 TCCTGCCGATACAAGTGTCAC
1 TTCTACCGATACAAGTGTCAC
*
85107 TTCTACCGAAACAA--GTCATGC
1 TTCTACCGATACAAGTGTCA--C
85128 TTCTACCGATAC
1 TTCTACCGATAC
85140 TAAAAATTCC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.09
20 1 0.02
21 38 0.88
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTGTCAC
Found at i:86983 original size:21 final size:22
Alignment explanation
Indices: 86953--86994 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
86943 ATTTAGGCTT
86953 TCTTAATTAG-CTTAACTAATC
1 TCTTAATTAGCCTTAACTAATC
* *
86974 TCTTACTTAGCCTTAATTAAT
1 TCTTAATTAGCCTTAACTAAT
86995 ATTTCTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (22 bp):
TCTTAATTAGCCTTAACTAATC
Found at i:98520 original size:24 final size:24
Alignment explanation
Indices: 98464--98512 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
98454 CACATTCATG
98464 CACAACTAAGTTAAAATAAACTAA
1 CACAACTAAGTTAAAATAAACTAA
98488 CACAACTAAGTTAAAATAAACTAA
1 CACAACTAAGTTAAAATAAACTAA
98512 C
1 C
98513 TTACCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.18, G:0.04, T:0.20
Consensus pattern (24 bp):
CACAACTAAGTTAAAATAAACTAA
Done.