Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015002.1 Kokia drynarioides strain JFW-HI SEQ_130046, 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: 397637
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 163 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:276140 original size:59 final size:58
Alignment explanation
Indices: 275896--276266 Score: 187
Period size: 59 Copynumber: 6.3 Consensus size: 58
275886 CTCAAAACTT
* * * * * *
275896 TCCAAAATTCCA-TTTTTGACCTCAAAACTTTCCAAAATT-CCATTTTTTTA-CCCTAAACTT
1 TCCAAAATTCCATTTTTTTAACTC-GAACTTTCCAAAATTACCA---TTTTACCCCCAGA-TG
* * * * *
275956 TCCAAAATTCCA--TTTTTAACCCCAAAACTTTCCAAAATT-CCATTTTTACCCTCAAATT
1 TCCAAAATTCCATTTTTTTAA-CTC-GAACTTTCCAAAATTACCA-TTTTACCCCCAGATG
* * * * * *
276014 TCCAAAAATTCCA-TTTTTGACCCCAAAACTTTCCAAAATT-CCATTTTTATCCAC-GAACT-
1 TCC-AAAATTCCATTTTTTTAACTC-GAACTTTCCAAAATTACCA-TTTTACCCCCAG-A-TG
* *
276073 TCCAAAAATTCCATTTTTTTAGCTCGAAGCTTTCAAAAATTACCATTTTACCCCCAGATG
1 TCC-AAAATTCCATTTTTTTAACTCGAA-CTTTCCAAAATTACCATTTTACCCCCAGATG
* * * ** * *
276133 TCCAAAATTTCC-TTTTTTGATCCCG-ACTTTTCTCAAAATTACTGTTTT-TCCCCTGAATG
1 TCCAAAA-TTCCATTTTTTTAACTCGAAC-TTTC-CAAAATTACCATTTTACCCCCAG-ATG
* *
276192 TCTAAAATTCCA-TTTTTTAACTCTAAACTTTCCAAAATTACCATTTTACCCCCGAGA-G
1 TCCAAAATTCCATTTTTTTAACTC-GAACTTTCCAAAATTACCATTTTACCCCC-AGATG
276250 TCCAAAATTACCATTTT
1 TCCAAAATT-CCATTTT
276267 GTCCACGGGT
Statistics
Matches: 254, Mismatches: 35, Indels: 44
0.76 0.11 0.13
Matches are distributed among these distances:
57 1 0.00
58 55 0.22
59 114 0.45
60 80 0.31
61 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (58 bp):
TCCAAAATTCCATTTTTTTAACTCGAACTTTCCAAAATTACCATTTTACCCCCAGATG
Found at i:277693 original size:23 final size:22
Alignment explanation
Indices: 277637--277693 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
277627 AAATTAGAAA
*
277637 TTTAGTTTTTATCTTTTTTATT
1 TTTAGATTTTATCTTTTTTATT
* *
277659 TTCAGGAATTTAGTC-TTTTTATTT
1 TTTA-GATTTTA-TCTTTTTTA-TT
277683 TTTAGATTTTA
1 TTTAGATTTTA
277694 AAATTTAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67
Consensus pattern (22 bp):
TTTAGATTTTATCTTTTTTATT
Found at i:277908 original size:29 final size:29
Alignment explanation
Indices: 277857--277935 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
277847 CAATTGAACT
*
277857 TAAATTTTGAAATATAAAAAATA-AAATAAC
1 TAAATTTT-AAAAATAAAAAATACAAA-AAC
*
277887 TAAAATTTTAAAAAT-AAAAATACAGAAAC
1 T-AAATTTTAAAAATAAAAAATACAAAAAC
**
277916 TAAATTTTAAATTTAAAAAA
1 TAAATTTTAAAAATAAAAAA
277936 AAAAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 11 0.26
29 16 0.38
30 8 0.19
31 7 0.17
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (29 bp):
TAAATTTTAAAAATAAAAAATACAAAAAC
Found at i:283750 original size:26 final size:25
Alignment explanation
Indices: 283695--283754 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
283685 TAAGAACATT
* *
283695 AATTAAAATTTAAAATTTATTATTA
1 AATTAAAATTTAAAATTAATAATTA
283720 AATTAAAATTGTAAAATTAAATAATT-
1 AATTAAAATT-TAAAATT-AATAATTA
*
283746 TATTAAAAT
1 AATTAAAAT
283755 AAAAAATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 10 0.33
26 15 0.50
27 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AATTAAAATTTAAAATTAATAATTA
Found at i:283761 original size:33 final size:32
Alignment explanation
Indices: 283698--283765 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
283688 GAACATTAAT
* *
283698 TAAAATTTAAAATTTATTATTAAATTAAAATTG
1 TAAAATTAAAAATTTATTA-TAAATAAAAATTG
283731 TAAAATTAAATAATTTATTA-AAATAAAAAATTG
1 TAAAATTAAA-AATTTATTATAAAT-AAAAATTG
283764 TA
1 TA
283766 TCAATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 4 0.13
33 18 0.58
34 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
TAAAATTAAAAATTTATTATAAATAAAAATTG
Found at i:287255 original size:21 final size:21
Alignment explanation
Indices: 287221--287260 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
287211 ATCCCACTAA
*
287221 TCAGCATTGAGACTGTAAAGC
1 TCAGCATTGAGACTATAAAGC
287242 TCAGCATT-AGGACTATAAA
1 TCAGCATTGA-GACTATAAA
287261 ACATTGCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (21 bp):
TCAGCATTGAGACTATAAAGC
Found at i:289077 original size:96 final size:96
Alignment explanation
Indices: 288903--289084 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
288893 AAGGATATCT
* ** * *
288903 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCGAAGA
1 GATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCGAAGA
*
288968 TAAGGAAACATTGCCTCGATTAAGGGTATTC
66 TAAAGAAACATTGCCTCGATTAAGGGTATTC
* *
288999 GATTATTTCAATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAACCCGAA
1 GATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAA-CCGAA
*
289063 -ATGAAAG-AATATTGCCTCGATT
64 GAT-AAAGAAACATTGCCTCGATT
289085 TTAAAGTATT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 66 0.89
97 7 0.09
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (96 bp):
GATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCGAAGA
TAAAGAAACATTGCCTCGATTAAGGGTATTC
Found at i:289366 original size:28 final size:29
Alignment explanation
Indices: 289308--289370 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
289298 GAATGAGACT
289308 TTTTGGATTCTCGGGGGCAAAAAAGATAA
1 TTTTGGATTCTCGGGGGCAAAAAAGATAA
** *
289337 TTTTGGATTCTCGGGGGTGAAACAG-TAA
1 TTTTGGATTCTCGGGGGCAAAAAAGATAA
289365 TTTTGG
1 TTTTGG
289371 GAAAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.27, C:0.10, G:0.30, T:0.33
Consensus pattern (29 bp):
TTTTGGATTCTCGGGGGCAAAAAAGATAA
Found at i:289416 original size:30 final size:29
Alignment explanation
Indices: 289371--289549 Score: 177
Period size: 29 Copynumber: 6.1 Consensus size: 29
289361 GTAATTTTGG
* * *
289371 GAAAATTTTAGGGTAAAAAATGGGATTTTT
1 GAAAGTTTTGGGGT-AAAAATGGAATTTTT
* *
289401 GGAAGTTTGGGGGTAAAATAT--AATTTTT
1 GAAAGTTTTGGGGTAAAA-ATGGAATTTTT
*
289429 GAAAGTTTTGGGGTTAAAAATGGGATTTTT
1 GAAAGTTTTGGGG-TAAAAATGGAATTTTT
* * *
289459 GGAAGTTTTGGGGTAAAAATAGAATTTTA
1 GAAAGTTTTGGGGTAAAAATGGAATTTTT
*
289488 GAAAGTTTTGAGGTTAAAAATAGG-ATTTTT
1 GAAAGTTTTG-GGGTAAAAAT-GGAATTTTT
*
289518 GAAAG-TTCGGAGGTAAAAATGGAATTTTT
1 GAAAGTTTTGG-GGTAAAAATGGAATTTTT
289547 GAA
1 GAA
289550 CAATTTAGGG
Statistics
Matches: 123, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
28 22 0.18
29 51 0.41
30 49 0.40
31 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (29 bp):
GAAAGTTTTGGGGTAAAAATGGAATTTTT
Found at i:289470 original size:59 final size:58
Alignment explanation
Indices: 289362--289549 Score: 225
Period size: 59 Copynumber: 3.2 Consensus size: 58
289352 GGTGAAACAG
* * * *
289362 TAATTTTGGGAAAATTTTAGGGTAAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATA
1 TAATTTT-TGAAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATA
*
289421 TAATTTTTGAAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGTAAAAATA
1 TAATTTTTGAAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGT-AAAATA
* * * * * * *
289480 GAATTTTAGAAAGTTTTGAGGTTAAAAATAGGATTTTTGAAAGTTCGGAGGTAAAA-A
1 TAATTTTTGAAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATA
289537 TGGAATTTTTGAA
1 T--AATTTTTGAA
289550 CAATTTAGGG
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 1 0.01
58 44 0.40
59 66 0.59
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.37
Consensus pattern (58 bp):
TAATTTTTGAAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATA
Found at i:290693 original size:11 final size:11
Alignment explanation
Indices: 290641--290699 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
290631 TTCGTATTAA
*
290641 ATAATAAATAG
1 ATAATAAATAT
*
290652 ATAATTAATGAT
1 ATAATAAAT-AT
*
290664 CAT-ATTAATAT
1 -ATAATAAATAT
290675 ATAATAAATA-
1 ATAATAAATAT
290685 ATAAGTAAATAT
1 ATAA-TAAATAT
290697 ATA
1 ATA
290700 TTAACATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.15
11 22 0.55
12 10 0.25
13 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (11 bp):
ATAATAAATAT
Found at i:291710 original size:15 final size:15
Alignment explanation
Indices: 291655--291711 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
291645 TTTATACTAC
291655 AAAATATTTATTATT
1 AAAATATTTATTATT
* *
291670 AATATATTTATAATTGT
1 AAAATATTTATTA-T-T
291687 AGTAAATATTTATTATT
1 A--AAATATTTATTATT
291704 AAAATATT
1 AAAATATT
291712 AATATTCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 18 0.53
16 1 0.03
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:291775 original size:13 final size:14
Alignment explanation
Indices: 291739--291776 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
291729 ATAATATATG
291739 AAAAATATTA-TTT
1 AAAAATATTATTTT
291752 AAAAATATTATTTT
1 AAAAATATTATTTT
*
291766 TAAAAT-TTATT
1 AAAAATATTATT
291777 ATCAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAAAATATTATTTT
Found at i:296740 original size:19 final size:19
Alignment explanation
Indices: 296718--296760 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
296708 TATGTATTTT
296718 AAATTTAATAATGTTTT-AA
1 AAATTTAATAAT-TTTTGAA
* *
296737 AAATATGATAATTTTTGAA
1 AAATTTAATAATTTTTGAA
296756 AAATT
1 AAATT
296761 AAAAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (19 bp):
AAATTTAATAATTTTTGAA
Found at i:300405 original size:30 final size:29
Alignment explanation
Indices: 300317--300646 Score: 247
Period size: 30 Copynumber: 11.0 Consensus size: 29
300307 AGAAACAAAC
* *
300317 GGGGTTGAAAATG-AAGTTTTGAAGAATTTTA
1 GGGGTT-AAAATGTAA-TTTTGGA-AAGTTTA
** *
300348 -GGGTTAAAACATATTTTTGGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTA
* *
300377 GGGGTAAAAATGTAATTATGAGAAAGTTTA
1 GGGGTTAAAATGTAATTTTG-GAAAGTTTA
*
300407 GGGGTTAAAATGTGATTTTGGGAAAGTTTA
1 GGGGTTAAAATGTAATTTT-GGAAAGTTTA
* * *
300437 GGGGTCAAAATATGATTTTGGAAAAGTTT-
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTA
* * *
300466 GAGTGTCAAAATGTGATTTTGGAAAAGTTTA
1 G-GGGTTAAAATGTAATTTTGG-AAAGTTTA
*
300497 GTGGTTAAAATGTAATTTTGGAAAAGTTT-
1 GGGGTTAAAATGTAATTTTGG-AAAGTTTA
*
300526 GGGGATTAAAATGTAATTTTGGAAAGTATA
1 GGGG-TTAAAATGTAATTTTGGAAAGTTTA
** * *
300556 GGGGACAAAATGTAGTTTTAGATAAGTTTA
1 GGGGTTAAAATGTAATTTTGGA-AAGTTTA
** *
300586 AAGGTTAAAATGTAATTTT-AAGAAGTTTAA
1 GGGGTTAAAATGTAATTTTGGA-AAGTTT-A
* * * *
300616 AGGGTTAAAATATGATTTTTAGAAAGTTTA
1 GGGGTTAAAATGT-AATTTTGGAAAGTTTA
300646 G
1 G
300647 AGACCTATTG
Statistics
Matches: 245, Mismatches: 40, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
29 48 0.20
30 182 0.74
31 14 0.06
32 1 0.00
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGGTTAAAATGTAATTTTGGAAAGTTTA
Found at i:300456 original size:90 final size:89
Alignment explanation
Indices: 300344--300634 Score: 283
Period size: 90 Copynumber: 3.3 Consensus size: 89
300334 TTTGAAGAAT
*
300344 TTTA-GGGTTAAAACAT-ATTTTTGGAAAAGTTTAGGGGTAAAAATGTAATTATGAGAAAGTTTA
1 TTTAGGGGTTAAAATATGA-TTTTGGAAAAGTTTAGGGGTAAAAATGTAATT-TGAGAAAGTTTA
* *
300407 GGGGTTAAAATGTGATTTTGGGAAAG
64 GAGGTTAAAATGTAATTTTGGGAAAG
* * * *
300433 TTTAGGGGTCAAAATATGATTTTGGAAAAGTTT-GAGTGTCAAAATGTGATTTTG-GAAAAGTTT
1 TTTAGGGGTTAAAATATGATTTTGGAAAAGTTTAG-GGGTAAAAATGT-AATTTGAG-AAAGTTT
* *
300496 AGTGGTTAAAATGTAATTTTGGAAAAG
63 AGAGGTTAAAATGTAATTTTGGGAAAG
* * * * *
300523 TTT-GGGGATTAAAATGTAATTTTGG-AAAGTATAGGGG-ACAAAATGTAGTTTTAGATAAGTTT
1 TTTAGGGG-TTAAAATATGATTTTGGAAAAGTTTAGGGGTA-AAAATGTAATTTGAGA-AAGTTT
* **
300585 AAAGGTTAAAATGTAATTTTAAG-AAG
63 AGAGGTTAAAATGTAATTTTGGGAAAG
*
300611 TTTAAAGGGTTAAAATATGATTTT
1 TTT-AGGGGTTAAAATATGATTTT
300635 TAGAAAGTTT
Statistics
Matches: 166, Mismatches: 24, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
88 11 0.07
89 63 0.38
90 88 0.53
91 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.36
Consensus pattern (89 bp):
TTTAGGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTAAAAATGTAATTTGAGAAAGTTTAGA
GGTTAAAATGTAATTTTGGGAAAG
Found at i:311510 original size:17 final size:17
Alignment explanation
Indices: 311440--311510 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
311430 GGCCCAACAG
**
311440 AATTTAAATTTATTTTA
1 AATTTAAATTTAAATTA
*
311457 AGTTTAAAAATTTAAATT-
1 AATTT--AAATTTAAATTA
* * *
311475 TATTATAAATTTGAGTTA
1 AATT-TAAATTTAAATTA
311493 AATTTAAATTTAAATTA
1 AATTTAAATTTAAATTA
311510 A
1 A
311511 TGTCTAAAAC
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
17 25 0.62
18 5 0.12
19 10 0.25
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:312187 original size:3 final size:3
Alignment explanation
Indices: 312169--312220 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
312159 ACATTGTTTG
* * * * *
312169 TAA TAA GTAT TAA TAA TAA TAA TAA TAA TAT TAT TAA TAA CAT TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
312215 TAA TAA
1 TAA TAA
312221 ACGGTGGTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:313269 original size:29 final size:30
Alignment explanation
Indices: 313228--313515 Score: 197
Period size: 30 Copynumber: 9.7 Consensus size: 30
313218 AGAGGTCCCT
* *
313228 AAACTATCTAAAAATTACATTTTTACCCTC-
1 AAACT-TCCAAAAATTCCATTTTTACCCTCG
*
313258 AAACTTCCAAAAATTTCATTTTTAACCC-CG
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
313288 AAACTTCCAAAAATTCCATTTTCAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCG
*
313318 AAACTTCCAAAATTTCCATTTTTACCC-C-
1 AAACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
313346 TAACCTCCAAAATTTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCG
* *
313376 AAACTTTCAAAAATTACCA-TTTTGCCCTCG
1 AAACTTCCAAAAATT-CCATTTTTACCCTCG
* * *
313406 -AA-TGTCCAAAAAATCTATTTTCGA-CCTCG
1 AAACT-TCCAAAAATTCCATTTT-TACCCTCG
* ** *
313435 AAAC-TCTC-AAAATTACGCTTTTACCCCCG
1 AAACTTC-CAAAAATTCCATTTTTACCCTCG
* *
313464 -AA-TGTCTAAAAATTCCATTTTTAACCTC-
1 AAACT-TCCAAAAATTCCATTTTTACCCTCG
* *
313492 AAATTTTCCCAAAATTACCATTTT
1 AAA-CTTCCAAAAATT-CCATTTT
313516 GCCCCCGGGT
Statistics
Matches: 201, Mismatches: 37, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
28 30 0.15
29 73 0.36
30 87 0.43
31 11 0.05
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:313330 original size:59 final size:58
Alignment explanation
Indices: 313237--313491 Score: 227
Period size: 58 Copynumber: 4.4 Consensus size: 58
313227 TAAACTATCT
* *
313237 AAAAATTACATTTTTACCCTC-AAACTTCCAAAAATTTCATTTTTAACCCCGAAACT-TCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC-AAAATTTCATTTTT-ACCCCG-AACTGTCC
* * *
313296 AAAAATTCCATTTTCAACCTCGAAACTTCCAAAATTTCCATTTTTACCCCTAAC-CTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCCAAAATTT-CATTTTTACCCCGAACTGTCC
* * * *
313354 AAAATTTCCATTTTTAACCTCGAAACTTTCAAAAATTACCA-TTTTGCCCTCGAA-TGTCC
1 AAAAATTCCATTTTTAACCTCGAAAC-TTCCAAAATT-TCATTTTTACCC-CGAACTGTCC
* * ** * ** *
313413 AAAAAATCTATTTTCGACCTCGAAAC-TCTCAAAATTACGCTTTTACCCCCGAA-TGTCT
1 AAAAATTCCATTTTTAACCTCGAAACTTC-CAAAATTTCATTTTTA-CCCCGAACTGTCC
313471 AAAAATTCCATTTTTAACCTC
1 AAAAATTCCATTTTTAACCTC
313492 AAATTTTCCC
Statistics
Matches: 161, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
57 3 0.02
58 72 0.45
59 71 0.44
60 15 0.09
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAAATTCCATTTTTAACCTCGAAACTTCCAAAATTTCATTTTTACCCCGAACTGTCC
Found at i:313373 original size:58 final size:60
Alignment explanation
Indices: 313237--313515 Score: 213
Period size: 59 Copynumber: 4.7 Consensus size: 60
313227 TAAACTATCT
* * *
313237 AAAAATTACATTTTTACCCTC-AAACTTCCAAAAATTT-CATTTTTAACCCCGAAACTTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCC-AAAATTTCCATTTTTAACCCCGAAACCTCC
* *
313296 AAAAATTCCATTTTCAACCTCGAAACTTCCAAAATTTCCATTTTT-ACCCC-TAACCTCC
1 AAAAATTCCATTTTTAACCTCGAAACTTCCAAAATTTCCATTTTTAACCCCGAAACCTCC
* * * * **
313354 AAAATTTCCATTTTTAACCTCGAAACTTTCAAAAATTACCA-TTTT-GCCCTCG-AATGTCC
1 AAAAATTCCATTTTTAACCTCGAAAC-TTCCAAAATTTCCATTTTTAACCC-CGAAACCTCC
* * ** * * ** *
313413 AAAAAATCTATTTTCGACCTCGAAAC-TCTCAAAATTACGC--TTTTACCCCCG-AATGTCT
1 AAAAATTCCATTTTTAACCTCGAAACTTC-CAAAATTTC-CATTTTTAACCCCGAAACCTCC
* *
313471 AAAAATTCCATTTTTAACCTC-AAATTTTCCCAAAATTACCATTTT
1 AAAAATTCCATTTTTAACCTCGAAA-CTT-CCAAAATTTCCATTTT
313516 GCCCCCGGGT
Statistics
Matches: 182, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
57 5 0.03
58 75 0.41
59 83 0.46
60 19 0.10
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (60 bp):
AAAAATTCCATTTTTAACCTCGAAACTTCCAAAATTTCCATTTTTAACCCCGAAACCTCC
Found at i:313405 original size:88 final size:88
Alignment explanation
Indices: 313245--313407 Score: 233
Period size: 88 Copynumber: 1.8 Consensus size: 88
313235 CTAAAAATTA
*
313245 CATTTTTACCCTCAAACTTCCAAAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTT
1 CATTTTTACCCTCAAACCTCCAAAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTT
313310 CAACCTCGAAACTTCCAAAATTTC
66 C-ACCTCGAAACTTCCAAAATTTC
* * *
313334 CATTTTTACCC-CTAACCTCC-AAAATTTCCATTTTTAACCTCGAAACTTTCAAAAATTACCATT
1 CATTTTTACCCTCAAACCTCCAAAAATTT-CATTTTTAACCCCGAAACTTCCAAAAATT-CCATT
313397 TTGC-CCTCGAA
64 TT-CACCTCGAA
313408 TGTCCAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
87 7 0.10
88 41 0.61
89 18 0.27
90 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (88 bp):
CATTTTTACCCTCAAACCTCCAAAAATTTCATTTTTAACCCCGAAACTTCCAAAAATTCCATTTT
CACCTCGAAACTTCCAAAATTTC
Found at i:313433 original size:117 final size:117
Alignment explanation
Indices: 313237--313519 Score: 303
Period size: 117 Copynumber: 2.4 Consensus size: 117
313227 TAAACTATCT
* * * *
313237 AAAAATTACATTTTTACCCTCAAAC-TTCCAAAAATT-TCATTTTTAACCC-CGAAACT-TCCAA
1 AAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTACCA-TTTT-GCCCTCG-AA-TGTCCAA
* * *
313298 AAATTCCATTTTCAACCTCGAAACT-TCCAAAATTTC-CATTTTTA-CCCCTAACCTCC
62 AAAATCCATTTTCAACCTCGAAACTCT-CAAAATTACGC--TTTTACCCCCGAACCTCC
*
313354 AAAATTTCCATTTTTAACCTCGAAACTTT-CAAAAATTACCATTTTGCCCTCGAATGTCCAAAAA
1 AAAAATTCCATTTTTAACCTC-AAACTTTCCAAAAATTACCATTTTGCCCTCGAATGTCCAAAAA
* * ** *
313418 ATCTATTTTCGACCTCGAAACTCTCAAAATTACGCTTTTACCCCCGAATGTCT
65 ATCCATTTTCAACCTCGAAACTCTCAAAATTACGCTTTTACCCCCGAACCTCC
* *
313471 AAAAATTCCATTTTTAACCTCAAATTTTCCCAAAATTACCATTTTGCCC
1 AAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTGCCC
313520 CCGGGTATCC
Statistics
Matches: 141, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
116 12 0.09
117 105 0.74
118 20 0.14
119 4 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (117 bp):
AAAAATTCCATTTTTAACCTCAAACTTTCCAAAAATTACCATTTTGCCCTCGAATGTCCAAAAAA
TCCATTTTCAACCTCGAAACTCTCAAAATTACGCTTTTACCCCCGAACCTCC
Found at i:313534 original size:59 final size:58
Alignment explanation
Indices: 313293--313522 Score: 232
Period size: 58 Copynumber: 3.9 Consensus size: 58
313283 CCCCGAAACT
* * ** * **
313293 TCCAAAAATTCCATTTTCAACCTCGAAACTTCCAAAATTTCCATTTTTACCCCTAACC
1 TCCAAAAATTCCATTTTCAACCTCGAAATTTCCAAAATTACCATTTTGCCCCCGAATG
* * * *
313351 TCCAAAATTTCCATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTGCCCTCGAATG
1 TCCAAAAATTCCATTTTCAACCTCGAAA-TTTCCAAAATTACCATTTTGCCCCCGAATG
* * * * *
313410 TCCAAAAAATCTATTTTCGACCTCGAAA-CTCTCAAAATTACGC-TTTTACCCCCGAATG
1 TCCAAAAATTCCATTTTCAACCTCGAAATTTC-CAAAATTAC-CATTTTGCCCCCGAATG
* *
313468 TCTAAAAATTCCATTTTTAACCTC-AAATTTTCCCAAAATTACCATTTTGCCCCCG
1 TCCAAAAATTCCATTTTCAACCTCGAAA-TTT-CCAAAATTACCATTTTGCCCCCG
313523 GGTATCCAAA
Statistics
Matches: 138, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
57 5 0.04
58 67 0.49
59 65 0.47
60 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTCAACCTCGAAATTTCCAAAATTACCATTTTGCCCCCGAATG
Found at i:325800 original size:205 final size:206
Alignment explanation
Indices: 325028--325898 Score: 1214
Period size: 206 Copynumber: 4.2 Consensus size: 206
325018 CACAAACAGC
* * * * * * * * * *
325028 GATGCGGTTATCTTCCTAATGAGATACTGAGAAGTAGACCAAATAAATGAAACGAGGCTCAAAGC
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT-CA--AACCCACGCTCGATGA
* * * *
325093 GAGCGAATCTTCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAATGG
63 GAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGG
*
325158 TTAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATGAG-AA-AGAGAAGC
128 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAAACAGAGAAGC
**
325221 GGATTGAAACAAGT
193 GGATCAAAACAAGT
* *
325235 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAGATCAAACCCACGCTTGATGAGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGAGAG
*
325300 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTTA
* * * * *
325365 GCTTCCTGATAAGATACTGAAAAGTGGAACAAATTCGTCTTCTTGATGAGAAACATAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAAACAGAGAAGCGGA
325430 TCAAAACAAGT
196 TCAAAACAAGT
* * *
325441 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAACTCACGCTCTATGAGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGAGAG
* *
325506 CAAATCTTCGAACACCAGTTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTTA
* *
325571 GCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGAAACAGAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAAACAGAGAAGCGGA
** *
325636 TTGAAACAAGC
196 TCAAAACAAGT
325647 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA-CAAATCAAACCCACGCTCGATGAGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGAGAG
* * ** **
325711 CAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTTGAAGCAATAAAGCGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTTA
* * * *
325776 GCTTCCTGATGAGATACAGAGAAGTGAACCAAA-TCTGTCTTCCCGAT-A-AAACATAGAGAAGT
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTC-GTCTTCCTGATGAGAAAC--AGAGAAGC
325838 GGATCAAAACAAGT
193 GGATCAAAACAAGT
* * *
325852 GATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
325899 TAAAACCAGA
Statistics
Matches: 595, Mismatches: 63, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
203 4 0.01
204 120 0.20
205 176 0.30
206 255 0.43
207 40 0.07
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (206 bp):
GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGAGAG
CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTTA
GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAAACAGAGAAGCGGA
TCAAAACAAGT
Found at i:325859 original size:411 final size:412
Alignment explanation
Indices: 325028--325893 Score: 1305
Period size: 411 Copynumber: 2.1 Consensus size: 412
325018 CACAAACAGC
* * * * *
325028 GATGCGGTTATCTTCCTAATGAGATACTGAGAAGTAGACCAAATAAATGAAACGAGGCTCAAAGC
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATAAA-GAAACGACGCTCAAAGA
* * * *
325093 GAGCGAATCTTCGAACTCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAATAAAATGG
65 GAGCAAATCTTCGAACACCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGG
325158 TTAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATGAGAAAGAGAAGCGG
130 TTAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATGAGAAAGAGAAGCGG
* *
325223 ATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAGATCAAACCCAC
195 ATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCAC
*
325288 GCTTGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCA
260 GCTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCA
* * **
325353 ATAAAATGGTTAGCTTCCTGATAAGATACTGAAAAGTGGAACAAATTCGTCTTCTTGATGAGAAA
325 ATAAAACGGTTAGCTTCCTGATAAGATACAGAAAAGTGGAACAAATTCGTCTTCCCGATGAGAAA
325418 CATAGAAGCGGATCAAAACAAGT
390 CATAGAAGCGGATCAAAACAAGT
* * ** * *
325441 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGATCAAATCAA-ACTC-ACGCTCTATGAG
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATAAAGAAACGACGCTCAAAGAG
*
325504 AGCAAATCTTCGAACACCAGTTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGT
66 AGCAAATCTTCGAACACCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGT
* * *
325569 TAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGAAACAGAGAAGCG
131 TAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATGAG-AA-AGAGAAGCG
325634 GATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGA-CAAATCAAACCCA
194 GATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA
* **
325698 CGCTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGAGAAGCAGGTTGAAGC
259 CGCTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGC
* * *
325763 AATAAAGCGGTTAGCTTCCTGATGAGATACAGAGAAGT-GAACCAAA-TCTGTCTTCCCGAT-A-
324 AATAAAACGGTTAGCTTCCTGATAAGATACAGAAAAGTGGAA-CAAATTC-GTCTTCCCGATGAG
*
325824 AAACATAGAGAAGTGGATCAAAACAAGT
387 AAACAT--AGAAGCGGATCAAAACAAGT
* *
325852 GATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGGCCAA
1 GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
325894 GTCAATAAAA
Statistics
Matches: 411, Mismatches: 36, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
409 6 0.01
410 123 0.30
411 181 0.44
412 59 0.14
413 42 0.10
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (412 bp):
GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATAAAGAAACGACGCTCAAAGAG
AGCAAATCTTCGAACACCAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGT
TAGCTTCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATGAGAAAGAGAAGCGGA
TTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
CTCGATGAGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAA
TAAAACGGTTAGCTTCCTGATAAGATACAGAAAAGTGGAACAAATTCGTCTTCCCGATGAGAAAC
ATAGAAGCGGATCAAAACAAGT
Found at i:326231 original size:6 final size:6
Alignment explanation
Indices: 326220--326314 Score: 60
Period size: 6 Copynumber: 16.7 Consensus size: 6
326210 GGCCCAACAG
* * *
326220 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGA-TTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA A-ATTTA AATTTA
* * * *
326265 ACTTAA AATTTA AATTT- -ATTATA AATTT- GAGTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA
326311 AATT
1 AATT
326315 AATGTCCAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 18
0.67 0.14 0.18
Matches are distributed among these distances:
4 3 0.05
5 16 0.24
6 44 0.67
7 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:326245 original size:17 final size:17
Alignment explanation
Indices: 326223--326289 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
326213 CCAACAGAAT
326223 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
326240 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAAA
*
326257 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
*
326273 TTTAAATTTATTATAAA
1 -TTAAATTTATTTTAAA
326290 TTTGAGTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
16 5 0.12
17 34 0.79
18 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:326290 original size:17 final size:17
Alignment explanation
Indices: 326220--326314 Score: 88
Period size: 17 Copynumber: 5.6 Consensus size: 17
326210 GGCCCAACAG
*
326220 AATTTAAATTTATTTTA
1 AATTTAAATTTATTATA
* *
326237 AAATTAAATTTATTTTA
1 AATTTAAATTTATTATA
326254 AGA-TTAAATTTACTTA-A
1 A-ATTTAAATTTA-TTATA
326271 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
* * *
326288 AATTTGAGTTAAATT-TA
1 AATTTAAATT-TATTATA
326305 AATTTAAATT
1 AATTTAAATT
326315 AATGTCCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.06
17 56 0.85
18 6 0.09
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:327011 original size:9 final size:9
Alignment explanation
Indices: 326971--327033 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
326961 ATATTGTTTG
326971 TAATAAGTAT
1 TAATAA-TAT
*
326981 TAATAATAA
1 TAATAATAT
** *
326990 TAATTGTTT
1 TAATAATAT
*
326999 TAATAATAA
1 TAATAATAT
327008 TAATAATAT
1 TAATAATAT
*
327017 TAATAACAT
1 TAATAATAT
327026 TAATAATA
1 TAATAATA
327034 AACGGTGGTA
Statistics
Matches: 41, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
9 35 0.85
10 6 0.15
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (9 bp):
TAATAATAT
Found at i:327019 original size:18 final size:18
Alignment explanation
Indices: 326971--327033 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
326961 ATATTGTTTG
326971 TAATAAGTATTAATAATAA
1 TAATAA-TATTAATAATAA
** *
326990 TAATTGTTTTAATAATAA
1 TAATAATATTAATAATAA
* *
327008 TAATAATATTAATAACAT
1 TAATAATATTAATAATAA
327026 TAATAATA
1 TAATAATA
327034 AACGGTGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 32 0.89
19 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATAATATTAATAATAA
Found at i:328303 original size:29 final size:29
Alignment explanation
Indices: 328270--328375 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 29
328260 AAACTATCTG
328270 AAAATTCCATTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTGACCCCAAAACTTCCA
*
328299 AAAATTCCATTTTTGACCCCAAAACTTTCA
1 AAAATTCCA-TTTTGACCCCAAAACTTCCA
* *
328329 AAAATTACCCTTTT-ACCCCCAAA-TGTCCA
1 AAAATT-CCATTTTGACCCCAAAACT-TCCA
*
328358 AAAACTCCATTTTCGACC
1 AAAATTCCATTTT-GACC
328376 TCGAAACTCT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
28 7 0.11
29 25 0.38
30 32 0.48
31 2 0.03
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAATTCCATTTTGACCCCAAAACTTCCA
Found at i:328358 original size:59 final size:58
Alignment explanation
Indices: 328270--328465 Score: 180
Period size: 59 Copynumber: 3.3 Consensus size: 58
328260 AAACTATCTG
* *
328270 AAAATT-CCATTTTGACCCCAAAACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTTC
1 AAAATTACCATTTT-ACCCCCAAA-TGTCCAAAAATTCCATTTTTGACCCCAAAACTCTC
* * * * *
328328 AAAAATTACCCTTTTACCCCCAAATGTCCAAAAACTCCATTTTCGACCTCGAAACTCTC
1 -AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAAACTCTC
* * * * * * *** *
328387 GAAATTACCTTTTTACCCCCGAATGTCTAAAAATTCCAATTTTAACCCCGAATTTTCCC
1 AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCC-AAAACTCTC
*
328446 AAAATTACCATTTTGCCCCC
1 AAAATTACCATTTTACCCCC
328466 TGAGAATACA
Statistics
Matches: 110, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
58 41 0.37
59 63 0.57
60 6 0.05
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTGACCCCAAAACTCTC
Found at i:329786 original size:20 final size:20
Alignment explanation
Indices: 329758--329795 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
329748 ATATAGTGAT
* *
329758 TAAATTAATTTATTTAATAA
1 TAAAATAATTAATTTAATAA
329778 TAAAATAATTAATTTAAT
1 TAAAATAATTAATTTAAT
329796 TTAGTTTTTA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATAATTAATTTAATAA
Found at i:342368 original size:16 final size:16
Alignment explanation
Indices: 342333--342370 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
342323 TATATATACA
342333 AATTTAATAAAAAAGT
1 AATTTAATAAAAAAGT
* *
342349 -ATTTAATTAAAAATT
1 AATTTAATAAAAAAGT
342364 AATTTAA
1 AATTTAA
342371 GTATATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AATTTAATAAAAAAGT
Found at i:356040 original size:9 final size:9
Alignment explanation
Indices: 355989--356039 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
355979 TGTGGTATTA
*
355989 GTGGGACTT
1 GTGGGACCT
*
355998 GTGGGACTT
1 GTGGGACCT
356007 GTGGGACCT
1 GTGGGACCT
*
356016 GTGGGACCA
1 GTGGGACCT
*
356025 GTGGGATCT
1 GTGGGACCT
356034 GTGGGA
1 GTGGGA
356040 TTTCTGGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.14, C:0.14, G:0.47, T:0.25
Consensus pattern (9 bp):
GTGGGACCT
Found at i:357337 original size:21 final size:22
Alignment explanation
Indices: 357305--357376 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
357295 CTTTAATTTT
* *
357305 AGTTTAAAGCATATTGGGTTCA
1 AGTTTAAAGCATATTAGGTTCG
357327 AGTTT-AAGCATATTAGGTTCG
1 AGTTTAAAGCATATTAGGTTCG
* *
357348 AGTTTAAAGCGTATTAAGTTCG
1 AGTTTAAAGCATATTAGGTTCG
357370 AGTTTAA
1 AGTTTAA
357377 GGCCTAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.42
22 26 0.58
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (22 bp):
AGTTTAAAGCATATTAGGTTCG
Found at i:357969 original size:11 final size:11
Alignment explanation
Indices: 357953--357977 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
357943 GTTTTAATTA
357953 TTTTCTTTTTT
1 TTTTCTTTTTT
357964 TTTTCTTTTTT
1 TTTTCTTTTTT
357975 TTT
1 TTT
357978 CTAAATCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:360517 original size:19 final size:19
Alignment explanation
Indices: 360488--360529 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
360478 TCAACAAAAT
*
360488 AAAATATTTTAAAATATTTA
1 AAAATATTTTAAAA-AATTA
360508 AAAATA-TTTAAAAAATTA
1 AAAATATTTTAAAAAATTA
360526 AAAA
1 AAAA
360530 ACTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATTTTAAAAAATTA
Found at i:360521 original size:10 final size:10
Alignment explanation
Indices: 360488--360529 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
360478 TCAACAAAAT
*
360488 AAAATATTTT
1 AAAATATTTA
360498 AAAATATTTA
1 AAAATATTTA
360508 AAAATATTTA
1 AAAATATTTA
360518 AAAA-A-TTA
1 AAAATATTTA
360526 AAAA
1 AAAA
360530 ACTTTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 23 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATTTA
Found at i:360530 original size:19 final size:20
Alignment explanation
Indices: 360488--360530 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
360478 TCAACAAAAT
* *
360488 AAAATATTTTAAAATATTTA
1 AAAATATTTTAAAAAATTAA
360508 AAAATA-TTTAAAAAATTAA
1 AAAATATTTTAAAAAATTAA
360527 AAAA
1 AAAA
360531 CTTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATATTTTAAAAAATTAA
Found at i:360536 original size:10 final size:9
Alignment explanation
Indices: 360495--360537 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
360485 AATAAAATAT
*
360495 TTTAAAATA
1 TTTAAAAAA
360504 TTTAAAAATA
1 TTTAAAAA-A
360514 TTTAAAAAA
1 TTTAAAAAA
360523 -TTAAAAAA
1 TTTAAAAAA
360531 CTTTAAA
1 -TTTAAA
360538 TTTAACTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.27
9 8 0.27
10 14 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:392075 original size:2 final size:2
Alignment explanation
Indices: 392068--392094 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
392058 AGAAAGAATG
392068 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
392095 TTTTGTTTCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:394064 original size:16 final size:17
Alignment explanation
Indices: 394039--394072 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
394029 GTTTTTTTAA
394039 TAAATGTTATA-TATTT
1 TAAATGTTATATTATTT
*
394055 TAAATTTTATATTATTT
1 TAAATGTTATATTATTT
394072 T
1 T
394073 TAACTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TAAATGTTATATTATTT
Found at i:394856 original size:30 final size:30
Alignment explanation
Indices: 394816--394873 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
394806 ATTTGAATTT
*
394816 TGAAATATAAAAAG-TAAATGAACTAAATTAC
1 TGAAATATAAAAGGAT-AATG-ACTAAATTAC
394847 TGAAA-ATAAAAGGATAATGACTAAATT
1 TGAAATATAAAAGGATAATGACTAAATT
394874 TCAAACTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 8 0.32
30 11 0.44
31 6 0.24
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (30 bp):
TGAAATATAAAAGGATAATGACTAAATTAC
Done.