Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015238.1 Kokia drynarioides strain JFW-HI SEQ_130283, 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: 155225
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 507 characters in sequence are not A, C, G, or T
Found at i:2472 original size:15 final size:16
Alignment explanation
Indices: 2452--2493 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
2442 TCGTTGAATT
2452 TATTTTTATTATA-TA
1 TATTTTTATTATATTA
*
2467 TATTTTTATTTTATTA
1 TATTTTTATTATATTA
2483 TATTTTTATTA
1 TATTTTTATTA
2494 ATTGAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTATTATATTA
Found at i:3323 original size:383 final size:387
Alignment explanation
Indices: 2445--3517 Score: 1552
Period size: 383 Copynumber: 2.8 Consensus size: 387
2435 GAGTTATTCG
* * *
2445 TTGAATTTATTTTTA-T-TATATATAT-TTTTATTTTATTATATTTTTATTAATTGAATCAAAAT
1 TTGAATTCATTTTTATTATATATATATATTTTATTTTATTGTATTTTTATTAATTGAGTCAAAAT
2507 CATTAAATTATCGTACCGAACTCAATCAATAATATTATATTAGGTTAATTTATTGCCTACAATAA
66 CATTAAATTATCGTACCGAACTCAATCAATAATATTATATTAGGTTAATTTATTGCCTACAATAA
2572 TATGAGTGAAACTTTTTATG------ATTATTTATTAAAAAATTATAT-AAAAATAGATAAAGTT
131 TATGAGTGAAACTTTTTATGTAAATAATTATTTATTAAAAAATTATATAAAAAATAGATAAAGTT
* *
2630 TCGGTTGATATTTTGATGTTTTAACTTCAAAGTTTTTAATTTATGAATTTATTTTAAATATAATT
196 TAGGTTGATATTTTGATGTTTTAACTTCAAAGTTTTTAATTTATGAATTTATTTTAAGTATAATT
*
2695 TTATATAATCATAT-ATAATATTTTAAAATTTCAACTAAAATTGATAACGCGTGTGTACACATAT
261 TTATATAATCATATAATAATATTTTAAAATTTCAACTAAAATTGATAA--C-TGCG-ACACA-A-
* *
2759 TTTGCACACACAAATACTCAAATCTGAATCTCTTAAGATGAACAACATTCTCTTTATCACTGAAA
320 -TT---CACACAAATACTCAAATCTGAATATCTTAAGACGAACAACATTCTCTTTATCACTGAAA
* *
2824 TCACTCG
381 CCACTCA
2831 TTGAATTCATTTTTATTATATATATATATATATTTTATTTTATTGTATTTTTATTAATTGAGTCA
1 TTGAATTCA--TTT-TTAT-TATATATATATATTTTATTTTATTGTATTTTTATTAATTGAGTCA
* *
2896 AAATCATTAAATTATCGTACCAAACTCAATCAATAATATTATATTAAGTTAATTTATTGCCTACA
62 AAATCATTAAATTATCGTACCGAACTCAATCAATAATATTATATTAGGTTAATTTATTGCCTACA
* *
2961 ATAATGTGAGTGAAACTTTTTATGTAAATAATTATTTTTTAAAAAATTATATAAAAAATAGATAA
127 ATAATATGAGTGAAACTTTTTATGTAAATAATTATTTATTAAAAAATTATATAAAAAATAGATAA
**
3026 AGTTTAAATTGATATTTTGATGTTTTAACTTCAAAGTTTTTAATTTATGAATTTATTTTAAGTAT
192 AGTTTAGGTTGATATTTTGATGTTTTAACTTCAAAGTTTTTAATTTATGAATTTATTTTAAGTAT
*
3091 AATTTTATATAATAAATATAATAATATTTTAAAATTTCAACTAAAATTGATAA-TGCG-CAC-A-
257 AATTTTATATAAT-CATATAATAATATTTTAAAATTTCAACTAAAATTGATAACTGCGACACAAT
** * * * * * * *
3152 T-ACACAGGTACTCAAATTTGAATATTTTAGGACGAATAACATAT-TTTTTATCACTGAAGCCGC
321 TCACACAAATACTCAAATCTGAATATCTTAAGACGAACAACAT-TCTCTTTATCACTGAAACCAC
3215 TCA
385 TCA
* * *
3218 TT-AGATTCATTTTTATTATATATATATATTTTATTTTATTGTATTATTATTAACTGAGTTAAAA
1 TTGA-ATTCATTTTTATTATATATATATATTTTATTTTATTGTATTTTTATTAATTGAGTCAAAA
* * * *
3282 TCATTAAATTATCTTATCGAATTCAATCAATTATATTATATTAGGTTAATTTATTGCCTACAATA
65 TCATTAAATTATCGTACCGAACTCAATCAATAATATTATATTAGGTTAATTTATTGCCTACAATA
3347 ATATGAGTGAAACTTTTTATGTAAATAATTATTTATTAAAAAATTATATAAAAAATAGATAAAGT
130 ATATGAGTGAAACTTTTTATGTAAATAATTATTTATTAAAAAATTATATAAAAAATAGATAAAGT
*
3412 TTTGGTTGATATTTTGATGTTTTAACTTCAAAGTTTTTAATTTATGAATTTATTTTAAGTATAAT
195 TTAGGTTGATATTTTGATGTTTTAACTTCAAAGTTTTTAATTTATGAATTTATTTTAAGTATAAT
*
3477 TTTATATAATCATATAATAATATTTTAAAATTTCAATTAAA
260 TTTATATAATCATATAATAATATTTTAAAATTTCAACTAAA
3518 TTAATGTTGG
Statistics
Matches: 627, Mismatches: 42, Indels: 40
0.88 0.06 0.06
Matches are distributed among these distances:
382 29 0.05
383 239 0.38
384 4 0.01
385 3 0.00
386 9 0.01
387 57 0.09
388 4 0.01
389 3 0.00
391 2 0.00
392 9 0.01
393 117 0.19
394 1 0.00
396 3 0.00
398 3 0.00
399 21 0.03
400 86 0.14
401 4 0.01
402 33 0.05
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (387 bp):
TTGAATTCATTTTTATTATATATATATATTTTATTTTATTGTATTTTTATTAATTGAGTCAAAAT
CATTAAATTATCGTACCGAACTCAATCAATAATATTATATTAGGTTAATTTATTGCCTACAATAA
TATGAGTGAAACTTTTTATGTAAATAATTATTTATTAAAAAATTATATAAAAAATAGATAAAGTT
TAGGTTGATATTTTGATGTTTTAACTTCAAAGTTTTTAATTTATGAATTTATTTTAAGTATAATT
TTATATAATCATATAATAATATTTTAAAATTTCAACTAAAATTGATAACTGCGACACAATTCACA
CAAATACTCAAATCTGAATATCTTAAGACGAACAACATTCTCTTTATCACTGAAACCACTCA
Found at i:5741 original size:21 final size:21
Alignment explanation
Indices: 5715--5758 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5705 TTTTTTAAAT
5715 TTTAAATTAATAGAAA-AAAAA
1 TTTAAATTAATA-AAAGAAAAA
5736 TTTAAATTAATAAAAGAAAAA
1 TTTAAATTAATAAAAGAAAAA
5757 TT
1 TT
5759 ACATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TTTAAATTAATAAAAGAAAAA
Found at i:13822 original size:72 final size:71
Alignment explanation
Indices: 13732--13916 Score: 298
Period size: 72 Copynumber: 2.6 Consensus size: 71
13722 AAATTCTGTG
*
13732 TCAAAATTTAAAAAATATAGCAATTTATAAATATGTAAATGTTAATAAAATTTTGTGTGAAAATT
1 TCAAAATTTAAAAAATATAGCAATTTATAAATATGTAAATGTTAATAAAATTTTGTGTCAAAATT
13797 TAAATT
66 TAAATT
* * *
13803 TTAAAATTTTAAAAAATATAACAATTTATAAATATGTAAATGTTAATAAGATTTTGTGTCAAAAT
1 TCAAAA-TTTAAAAAATATAGCAATTTATAAATATGTAAATGTTAATAAAATTTTGTGTCAAAAT
13868 TTAAATT
65 TTAAATT
* * *
13875 TCAAAATTTGAAAAATATAGTAATTTACAAATATGTAAATGT
1 TCAAAATTTAAAAAATATAGCAATTTATAAATATGTAAATGT
13917 AGCAAAATAC
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
71 37 0.36
72 67 0.64
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.39
Consensus pattern (71 bp):
TCAAAATTTAAAAAATATAGCAATTTATAAATATGTAAATGTTAATAAAATTTTGTGTCAAAATT
TAAATT
Found at i:21379 original size:39 final size:39
Alignment explanation
Indices: 21336--21415 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
21326 AAGTTCGTTT
21336 ATGTTTTTTTTTTTCCAGTCATTGTATTATAGAAATAGG
1 ATGTTTTTTTTTTTCCAGTCATTGTATTATAGAAATAGG
21375 ATGTTTTTTTTTTTCCAGTCATTGTATTATAGAAATAGG
1 ATGTTTTTTTTTTTCCAGTCATTGTATTATAGAAATAGG
21414 AT
1 AT
21416 TGTTAAATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.51
Consensus pattern (39 bp):
ATGTTTTTTTTTTTCCAGTCATTGTATTATAGAAATAGG
Found at i:25029 original size:22 final size:21
Alignment explanation
Indices: 24981--25038 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
24971 TATCACGTCG
* *
24981 ATAAATATTTTAAAATTTTAAA
1 ATAAATATTTCAAAA-ATTAAA
25003 A-AAATATTTCAAAAATTAAA
1 ATAAATATTTCAAAAATTAAA
25023 TATAAATA-TTCAAAAA
1 -ATAAATATTTCAAAAA
25039 ACAAACATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 21 0.66
22 6 0.19
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
ATAAATATTTCAAAAATTAAA
Found at i:25048 original size:21 final size:22
Alignment explanation
Indices: 25004--25049 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
24994 AATTTTAAAA
** *
25004 AAATATTTCAAAAATTAAATAT
1 AAATATTTCAAAAAACAAACAT
25026 AAATA-TTCAAAAAACAAACAT
1 AAATATTTCAAAAAACAAACAT
25047 AAA
1 AAA
25050 GTACATGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATATTTCAAAAAACAAACAT
Found at i:25527 original size:2 final size:2
Alignment explanation
Indices: 25520--25561 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
25510 AACAATAACC
25520 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25562 GAGTCTTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32295 original size:2 final size:2
Alignment explanation
Indices: 32288--32314 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32278 GCATTGATGT
32288 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
32315 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34345 original size:23 final size:24
Alignment explanation
Indices: 34316--34368 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 24
34306 AATAATGTCA
*
34316 TAATTTTTTTT--AAAAATTGACC
1 TAATTTTTTTTAAAAAAATTAACC
34338 -AATTTTTTTTAAAAAAATTAACC
1 TAATTTTTTTTAAAAAAATTAACC
34361 TAATTTTT
1 TAATTTTT
34369 CAAATAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (24 bp):
TAATTTTTTTTAAAAAAATTAACC
Found at i:45315 original size:2 final size:2
Alignment explanation
Indices: 45308--45336 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45298 CGTTGATAAT
45308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45337 GTATTCCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48166 original size:3 final size:3
Alignment explanation
Indices: 48158--48184 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48148 ACGAGTTGTT
48158 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
48185 AAAATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:49326 original size:6 final size:5
Alignment explanation
Indices: 49277--49325 Score: 71
Period size: 5 Copynumber: 9.2 Consensus size: 5
49267 ATTTTAATTG
49277 AATAA AATAA AATAA AATAA AATAA AATAA ATATAA ATATAA ATATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA A-ATAA A-ATAA A-ATAA
49325 A
1 A
49326 TTTTAGGCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 26 0.60
6 17 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AATAA
Found at i:51916 original size:20 final size:20
Alignment explanation
Indices: 51891--51930 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
51881 AAAAACAATG
51891 ATTATATTAATGTTACTGTT
1 ATTATATTAATGTTACTGTT
51911 ATTATATTAATGTTACTGTT
1 ATTATATTAATGTTACTGTT
51931 CTTTATTGTT
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:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTATATTAATGTTACTGTT
Found at i:62140 original size:19 final size:19
Alignment explanation
Indices: 62089--62156 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
62079 GATATTTTTA
62089 TGTTTATTTTATTGTTTTGG
1 TGTTT-TTTTATTGTTTTGG
62109 T-TACTGATTTTTATTGTTTTGG
1 TGT--T--TTTTTATTGTTTTGG
*
62131 TGTTTTTTTACTGTTTTGG
1 TGTTTTTTTATTGTTTTGG
62150 TGTTTTT
1 TGTTTTT
62157 ACTATTTTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
19 22 0.52
20 1 0.02
21 2 0.05
22 15 0.36
23 2 0.05
ACGTcount: A:0.09, C:0.03, G:0.19, T:0.69
Consensus pattern (19 bp):
TGTTTTTTTATTGTTTTGG
Found at i:62155 original size:17 final size:18
Alignment explanation
Indices: 62116--62167 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
62106 TGGTTACTGA
*
62116 TTTTTATTGTTTTGGTGTT
1 TTTTTACTGTTTTGGTG-T
62135 TTTTTACTGTTTTGGTG-
1 TTTTTACTGTTTTGGTGT
*
62152 TTTTTACTATTTTGGT
1 TTTTTACTGTTTTGGT
62168 TATTGTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 15 0.48
19 16 0.52
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.69
Consensus pattern (18 bp):
TTTTTACTGTTTTGGTGT
Found at i:62182 original size:20 final size:20
Alignment explanation
Indices: 62159--62199 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62149 GTGTTTTTAC
*
62159 TATTTTGGTTATTGTTTTGA
1 TATTTTGGTTACTGTTTTGA
**
62179 TATTTTTTTTACTGTTTTGA
1 TATTTTGGTTACTGTTTTGA
62199 T
1 T
62200 GTTGTTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.68
Consensus pattern (20 bp):
TATTTTGGTTACTGTTTTGA
Found at i:62214 original size:12 final size:12
Alignment explanation
Indices: 62199--62273 Score: 68
Period size: 12 Copynumber: 6.6 Consensus size: 12
62189 ACTGTTTTGA
*
62199 TGTTGTTGTTTT
1 TGTTGTTATTTT
62211 TGTTGTTATTTT
1 TGTTGTTATTTT
62223 TGTTG----TTT
1 TGTTGTTATTTT
* *
62231 TGCTATTATTTT
1 TGTTGTTATTTT
*
62243 TGCTGTTATTTT
1 TGTTGTTATTTT
*
62255 GGTTGTTATTTT
1 TGTTGTTATTTT
*
62267 GGTTGTT
1 TGTTGTT
62274 TAAATGTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
8 6 0.11
12 47 0.89
ACGTcount: A:0.07, C:0.03, G:0.21, T:0.69
Consensus pattern (12 bp):
TGTTGTTATTTT
Found at i:62244 original size:20 final size:20
Alignment explanation
Indices: 62201--62249 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
62191 TGTTTTGATG
* *
62201 TTGTTGTTTTTGTTGTTATTT
1 TTGTTG-TTTTGCTATTATTT
62222 TTGTTGTTTTGCTATTATTT
1 TTGTTGTTTTGCTATTATTT
*
62242 TTGCTGTT
1 TTGTTGTT
62250 ATTTTGGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.06, C:0.04, G:0.18, T:0.71
Consensus pattern (20 bp):
TTGTTGTTTTGCTATTATTT
Found at i:62284 original size:44 final size:44
Alignment explanation
Indices: 62202--62287 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
62192 GTTTTGATGT
* * * ***
62202 TGTTGTTTTTGTTGTTATTTTTGTTGTTTTGCTATTATTTTTGC
1 TGTTATTTTGGTTGTTATTTTGGTTGTTTAAATATTATTTTTGC
*
62246 TGTTATTTTGGTTGTTATTTTGGTTGTTTAAATGTTATTTTT
1 TGTTATTTTGGTTGTTATTTTGGTTGTTTAAATATTATTTTT
62288 ATGCGTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.10, C:0.02, G:0.19, T:0.69
Consensus pattern (44 bp):
TGTTATTTTGGTTGTTATTTTGGTTGTTTAAATATTATTTTTGC
Found at i:63107 original size:10 final size:10
Alignment explanation
Indices: 63088--63120 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
63078 TCAAAATAAG
63088 TTATATTATT
1 TTATATTATT
*
63098 TTATAATATT
1 TTATATTATT
63108 TTA-ATTATT
1 TTATATTATT
63117 TTAT
1 TTAT
63121 TTAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATATTATT
Found at i:63871 original size:30 final size:30
Alignment explanation
Indices: 63837--63901 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
63827 CAACTTAACA
* *
63837 AACAAATGTCTATAAAATAGTAACAAAATT
1 AACAAATGCCTATAAAATAATAACAAAATT
*
63867 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTATAAAATAATAACAAAATT
63897 AACAA
1 AACAA
63902 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTATAAAATAATAACAAAATT
Found at i:69331 original size:2 final size:2
Alignment explanation
Indices: 69324--69348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
69314 GGTAATGTGC
69324 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
69349 CATAAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74972 original size:7 final size:7
Alignment explanation
Indices: 74956--74992 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
74946 TATGGTGTGC
*
74956 TCGCATT
1 TCGCACT
74963 TCGCACT
1 TCGCACT
74970 TCGCACT
1 TCGCACT
74977 TCGCACT
1 TCGCACT
74984 TCGCACT
1 TCGCACT
74991 TC
1 TC
74993 ACAACTGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.41, G:0.14, T:0.32
Consensus pattern (7 bp):
TCGCACT
Found at i:97509 original size:22 final size:24
Alignment explanation
Indices: 97459--97512 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
97449 TTTAAACAAA
97459 ATAAATATTAACAATAATATTTTC
1 ATAAATATTAACAATAATATTTTC
*
97483 TTAAATATTAA-AA-AATCA-TTTC
1 ATAAATATTAACAATAAT-ATTTTC
97505 ATAAATAT
1 ATAAATAT
97513 GCTTTTCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 14 0.52
23 3 0.11
24 10 0.37
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAAATATTAACAATAATATTTTC
Found at i:99187 original size:19 final size:19
Alignment explanation
Indices: 99165--99225 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
99155 ATATATTTTT
99165 CTTCACTATATATTATATG
1 CTTCACTATATATTATATG
** *
99184 CTTCTTTTTATATATT-T-TT
1 CTTC--ACTATATATTATATG
*
99203 CTTCACTACATATTATATG
1 CTTCACTATATATTATATG
99222 CTTC
1 CTTC
99226 TAAGTCTGGC
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
17 7 0.23
18 1 0.03
19 14 0.45
20 1 0.03
21 8 0.26
ACGTcount: A:0.25, C:0.18, G:0.03, T:0.54
Consensus pattern (19 bp):
CTTCACTATATATTATATG
Found at i:99194 original size:38 final size:38
Alignment explanation
Indices: 99150--99226 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
99140 TTAATATTGA
*
99150 TTTTTATATATTTTTCTTCACTATATATTATATGCTTC
1 TTTTTATATATTTTTCTTCACTACATATTATATGCTTC
99188 TTTTTATATATTTTTCTTCACTACATATTATATGCTTC
1 TTTTTATATATTTTTCTTCACTACATATTATATGCTTC
99226 T
1 T
99227 AAGTCTGGCG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.23, C:0.14, G:0.03, T:0.60
Consensus pattern (38 bp):
TTTTTATATATTTTTCTTCACTACATATTATATGCTTC
Found at i:106098 original size:13 final size:13
Alignment explanation
Indices: 106080--106104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106070 GAGGCTCAAA
106080 CTTCGACGCGATG
1 CTTCGACGCGATG
106093 CTTCGACGCGAT
1 CTTCGACGCGAT
106105 AGGAGTCCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (13 bp):
CTTCGACGCGATG
Found at i:116046 original size:18 final size:18
Alignment explanation
Indices: 116023--116065 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
116013 TCTACTGGCC
116023 ATGGAAGAAAATGACATA
1 ATGGAAGAAAATGACATA
116041 ATGGAAGAAAATGACATA
1 ATGGAAGAAAATGACATA
*
116059 GTGGAAG
1 ATGGAAG
116066 CTGAGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.05, G:0.28, T:0.16
Consensus pattern (18 bp):
ATGGAAGAAAATGACATA
Found at i:120294 original size:41 final size:41
Alignment explanation
Indices: 120237--120320 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
120227 CCGGCTAAAA
120237 TAGGATAGGTTTCGCATTGCAGTGCTGAAGCCTCCTTTTCT
1 TAGGATAGGTTTCGCATTGCAGTGCTGAAGCCTCCTTTTCT
*
120278 TAGGATCGGTTTCGCATTGCAGTGCTGAAGCCTCCTTTTCT
1 TAGGATAGGTTTCGCATTGCAGTGCTGAAGCCTCCTTTTCT
120319 TA
1 TA
120321 CTTTTGTTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.37
Consensus pattern (41 bp):
TAGGATAGGTTTCGCATTGCAGTGCTGAAGCCTCCTTTTCT
Found at i:120518 original size:21 final size:21
Alignment explanation
Indices: 120489--120550 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
120479 TTCGTATTTT
120489 AGGTTTTGAATTTTAAGTTT-
1 AGGTTTTGAATTTTAAGTTTG
* * * *
120509 AGATTTTTGAGTTTCAAATTTG
1 AG-GTTTTGAATTTTAAGTTTG
*
120531 AGGTTTTGGATTTTAAGTTT
1 AGGTTTTGAATTTTAAGTTT
120551 CATATTTGAT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.21, T:0.53
Consensus pattern (21 bp):
AGGTTTTGAATTTTAAGTTTG
Found at i:127415 original size:2 final size:2
Alignment explanation
Indices: 127402--127437 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
127392 AGATATACGC
127402 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
127438 AATAGCCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:128248 original size:23 final size:25
Alignment explanation
Indices: 128218--128318 Score: 129
Period size: 27 Copynumber: 4.0 Consensus size: 25
128208 TTAATGTTCA
128218 CGAACATGTT-C-ACGAACATTAAT
1 CGAACATGTTACAACGAACATTAAT
128241 CGAACATGTTCACGAACGAACATTAAT
1 CGAACATGTT-AC-AACGAACATTAAT
128268 CGAACATGTTCACGAACGAACATTAAT
1 CGAACATGTT-AC-AACGAACATTAAT
128295 CGAACATGTT-C-ACGAACATATAAT
1 CGAACATGTTACAACGAACAT-TAAT
128319 TAAACACGTT
Statistics
Matches: 73, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
23 18 0.25
24 4 0.05
25 2 0.03
27 49 0.67
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (25 bp):
CGAACATGTTACAACGAACATTAAT
Found at i:128260 original size:27 final size:27
Alignment explanation
Indices: 128229--128311 Score: 166
Period size: 27 Copynumber: 3.1 Consensus size: 27
128219 GAACATGTTC
128229 ACGAACATTAATCGAACATGTTCACGA
1 ACGAACATTAATCGAACATGTTCACGA
128256 ACGAACATTAATCGAACATGTTCACGA
1 ACGAACATTAATCGAACATGTTCACGA
128283 ACGAACATTAATCGAACATGTTCACGA
1 ACGAACATTAATCGAACATGTTCACGA
128310 AC
1 AC
128312 ATATAATTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (27 bp):
ACGAACATTAATCGAACATGTTCACGA
Found at i:128262 original size:16 final size:16
Alignment explanation
Indices: 128241--128290 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
128231 GAACATTAAT
128241 CGAACATGTTCACGAA
1 CGAACATGTTCACGAA
*
128257 CGAACA--TT-A--AT
1 CGAACATGTTCACGAA
128268 CGAACATGTTCACGAA
1 CGAACATGTTCACGAA
128284 CGAACAT
1 CGAACAT
128291 TAATCGAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
11 7 0.26
13 3 0.11
14 3 0.11
16 14 0.52
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (16 bp):
CGAACATGTTCACGAA
Found at i:129377 original size:21 final size:20
Alignment explanation
Indices: 129345--129383 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
129335 ATCAAAAAAC
*
129345 CTAAAAAAATATTAAAAATT
1 CTAAAAAAATATAAAAAATT
*
129365 CTAAAGAATATATAAAAAA
1 CTAAA-AAAATATAAAAAA
129384 GTTTAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
CTAAAAAAATATAAAAAATT
Found at i:135730 original size:33 final size:31
Alignment explanation
Indices: 135688--135749 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
135678 TTTTTAACTT
135688 TAAATTCAAAATTAATTATTAATATTTTTTAAA
1 TAAATTC-AAATTAATTA-TAATATTTTTTAAA
* *
135721 TAAATTCAAATTTATTATAATTTTTTTTA
1 TAAATTCAAATTAATTATAATATTTTTTA
135750 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 11 0.41
32 9 0.33
33 7 0.26
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (31 bp):
TAAATTCAAATTAATTATAATATTTTTTAAA
Found at i:155175 original size:2 final size:2
Alignment explanation
Indices: 155168--155199 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
155158 CACTACAACC
155168 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
155200 GGTTGTAGTG
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
Done.