Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015260.1 Kokia drynarioides strain JFW-HI SEQ_130305, 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: 591355
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 484 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:347714 original size:7 final size:7
Alignment explanation
Indices: 347702--347757 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
347692 TCGAAAAAAG
347702 TCAACGA
1 TCAACGA
347709 TCAACGA
1 TCAACGA
*
347716 TCAAAG-
1 TCAACGA
*
347722 TCAACGG
1 TCAACGA
*
347729 TCAACGG
1 TCAACGA
*
347736 TTAACGA
1 TCAACGA
*
347743 TCAAAG-
1 TCAACGA
347749 TCAACGA
1 TCAACGA
347756 TC
1 TC
347758 GGTCAACGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 10 0.25
7 30 0.75
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (7 bp):
TCAACGA
Found at i:347741 original size:27 final size:27
Alignment explanation
Indices: 347701--347754 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
347691 TTCGAAAAAA
347701 GTCAACGATCAACGATCAAAGTCAACG
1 GTCAACGATCAACGATCAAAGTCAACG
* *
347728 GTCAACGGTTAACGATCAAAGTCAACG
1 GTCAACGATCAACGATCAAAGTCAACG
347755 ATCGGTCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (27 bp):
GTCAACGATCAACGATCAAAGTCAACG
Found at i:347746 original size:14 final size:13
Alignment explanation
Indices: 347709--347757 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
347699 AAGTCAACGA
347709 TCAACGATCAAAG
1 TCAACGATCAAAG
* *
347722 TCAACGGTCAACGG
1 TCAACGATCAA-AG
*
347736 TTAACGATCAAAG
1 TCAACGATCAAAG
347749 TCAACGATC
1 TCAACGATC
347758 GGTCAACGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (13 bp):
TCAACGATCAAAG
Found at i:354650 original size:25 final size:25
Alignment explanation
Indices: 354622--354678 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
354612 GGTCGGTCAA
354622 TGGTTTGACTTGGTTCAAATGGGTT
1 TGGTTTGACTTGGTTCAAATGGGTT
354647 TGGTTTGACTTGGTTCAAATGGGTT
1 TGGTTTGACTTGGTTCAAATGGGTT
354672 TGGTTTG
1 TGGTTTG
354679 GTTTTTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.14, C:0.07, G:0.33, T:0.46
Consensus pattern (25 bp):
TGGTTTGACTTGGTTCAAATGGGTT
Found at i:368333 original size:3 final size:3
Alignment explanation
Indices: 368325--368349 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
368315 GATATATCTG
368325 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
368350 GTCGAAACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:369129 original size:31 final size:31
Alignment explanation
Indices: 369073--369217 Score: 151
Period size: 30 Copynumber: 4.9 Consensus size: 31
369063 GAGGTCAAAT
* *
369073 TTTG-ATTTTT-GAAAATTTTAGGGGTTAAA
1 TTTGAATTTTTAGAAAAATTTAAGGGTTAAA
* *
369102 TTTTAATTTTTAGAAAAATTTAAGGGTTAGA
1 TTTGAATTTTTAGAAAAATTTAAGGGTTAAA
*
369133 TTTGAATTTTTA-AAAAATTTAAGGGTGAAA
1 TTTGAATTTTTAGAAAAATTTAAGGGTTAAA
* * *
369163 TTTGGATTTTTA-AAAAATTCGAA-GGTCAAA
1 TTTGAATTTTTAGAAAAATT-TAAGGGTTAAA
*
369193 TTTGAATTTTT-G-AAAACTTAAGGGT
1 TTTGAATTTTTAGAAAAATTTAAGGGT
369218 CAAAAAATAA
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
28 2 0.02
29 11 0.11
30 56 0.57
31 29 0.30
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (31 bp):
TTTGAATTTTTAGAAAAATTTAAGGGTTAAA
Found at i:369203 original size:60 final size:59
Alignment explanation
Indices: 369064--369217 Score: 159
Period size: 61 Copynumber: 2.6 Consensus size: 59
369054 CATTAAAATG
* * * * *
369064 AGGTCAAATTTTG-ATTTTTGAAAATTTTAGGGGTTAAATTTTAATTTTTAGAAAAATTTA
1 AGGTCAAA-TTTGAATTTTT-AAAAATTTAAGGGTGAAATTTGAATTTTTAGAAAAATTGA
* * *
369124 AGGGTTAGATTTGAATTTTTAAAAAATTTAAGGGTGAAATTTGGATTTTTA-AAAAATTCGA
1 A-GGTCAAATTTGAATTTTT-AAAAATTTAAGGGTGAAATTTGAATTTTTAGAAAAATT-GA
* *
369185 AGGTCAAATTTGAATTTTTGAAAACTTAAGGGT
1 AGGTCAAATTTGAATTTTTAAAAATTTAAGGGT
369218 CAAAAAATAA
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
59 12 0.15
60 28 0.36
61 38 0.49
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.42
Consensus pattern (59 bp):
AGGTCAAATTTGAATTTTTAAAAATTTAAGGGTGAAATTTGAATTTTTAGAAAAATTGA
Found at i:387403 original size:25 final size:25
Alignment explanation
Indices: 387369--387418 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
387359 CATCCATGTC
*
387369 CGACTGCACTTTGCTCAAGTTTCTT
1 CGACTGCACTCTGCTCAAGTTTCTT
387394 CGACTGCACTCTGCTCAAGTTTCTT
1 CGACTGCACTCTGCTCAAGTTTCTT
387419 TCTTTTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.38
Consensus pattern (25 bp):
CGACTGCACTCTGCTCAAGTTTCTT
Found at i:388482 original size:11 final size:11
Alignment explanation
Indices: 388463--388497 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
388453 AGGTACACAG
*
388463 TTTTATTTTTA
1 TTTTTTTTTTA
388474 TTTTTTTTTTA
1 TTTTTTTTTTA
388485 -TTTTTTTTTA
1 TTTTTTTTTTA
388495 TTT
1 TTT
388498 ATATATAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:388488 original size:10 final size:10
Alignment explanation
Indices: 388463--388497 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
388453 AGGTACACAG
388463 TTTTATTTTTA
1 TTTT-TTTTTA
388474 TTTTTTTTTTA
1 -TTTTTTTTTA
388485 TTTTTTTTTA
1 TTTTTTTTTA
388495 TTT
1 TTT
388498 ATATATAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 6 0.26
12 4 0.17
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:389596 original size:12 final size:13
Alignment explanation
Indices: 389579--389617 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
389569 TTTTATGTTT
389579 AAATATTT-TTTG
1 AAATATTTATTTG
389591 AAATATTATATTT-
1 AAATATT-TATTTG
389604 AAATATTTATTTG
1 AAATATTTATTTG
389617 A
1 A
389618 CTTCAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.50
13 9 0.38
14 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (13 bp):
AAATATTTATTTG
Found at i:390142 original size:17 final size:18
Alignment explanation
Indices: 390119--390217 Score: 125
Period size: 17 Copynumber: 5.7 Consensus size: 18
390109 CCAAACTCAT
390119 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* *
390137 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGA
390154 TTTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
390171 TTTAAATTTAATTTAAG-
1 TTTAAATTTATTTTAAGA
390188 TTTAAATTTATTTTCAA-A
1 TTTAAATTTATTTT-AAGA
*
390206 TTTAAAATTATT
1 TTTAAATTTATT
390218 ATAAATATAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
17 44 0.62
18 27 0.38
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:390158 original size:35 final size:34
Alignment explanation
Indices: 390119--390228 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 34
390109 CCAAACTCAT
**
390119 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAA
*
390154 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
*
390188 TTTAAATTTATTTTCAAATTTAAAATT-ATTATAAA
1 TTTAAATTTATTTT-AAATTTAAATTTAATT-TAAA
*
390223 TATAAA
1 TTTAAA
390229 ATAAATAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 20 0.30
35 46 0.70
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:390162 original size:6 final size:6
Alignment explanation
Indices: 390151--390211 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
390141 ATTTGTTTTA
* *
390151 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
390197 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
390212 ATTATTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 13 0.29
6 28 0.62
7 4 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:390168 original size:11 final size:11
Alignment explanation
Indices: 390154--390209 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
390144 TGTTTTAAAA
390154 TTTAAATTTAT
1 TTTAAATTTAT
*
390165 TTTAAATTTAAA
1 TTTAAATTT-AT
*
390177 TTT-AATTTAAG
1 TTTAAATTT-AT
390188 TTTAAATTTAT
1 TTTAAATTTAT
390199 TTTCAAATTTA
1 TTT-AAATTTA
390210 AAATTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:390186 original size:52 final size:52
Alignment explanation
Indices: 390119--390228 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
390109 CCAAACTCAT
* * * *
390119 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
* *
390171 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
*
390223 TATAAA
1 TTTAAA
390229 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:390333 original size:25 final size:25
Alignment explanation
Indices: 390257--390333 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
390247 CAAAATGTCC
* *
390257 AATTACAA-AGCCCAATTAGGCCTA
1 AATTACAATGGCCCAAATAGGCCTA
* *
390281 AATT-CAAATGACCCAAACTA-ACCTA
1 AATTAC-AATGGCCCAAA-TAGGCCTA
*
390306 AATTACAATGGCCCAAATAGGCCCA
1 AATTACAATGGCCCAAATAGGCCTA
390331 AAT
1 AAT
390334 CGATTAACCC
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
23 1 0.02
24 8 0.20
25 29 0.71
26 3 0.07
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.19
Consensus pattern (25 bp):
AATTACAATGGCCCAAATAGGCCTA
Found at i:391007 original size:9 final size:9
Alignment explanation
Indices: 390990--391036 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
390980 ATAAATGTGT
390990 TATTAATAA
1 TATTAATAA
*
390999 TATTTATAA
1 TATTAATAA
* *
391008 TAATAATAT
1 TATTAATAA
391017 TATTAATGAA
1 TATTAAT-AA
391027 -ATTAATAA
1 TATTAATAA
391035 TA
1 TA
391037 ATAAACAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
8 2 0.07
9 27 0.90
10 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (9 bp):
TATTAATAA
Found at i:391023 original size:15 final size:15
Alignment explanation
Indices: 390972--391023 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
390962 TGTTTGTTAA
390972 TATTAATAATAA-AT
1 TATTAATAATAATAT
* *
390986 GTGTTATTAATAATAT
1 -TATTAATAATAATAT
391002 T-TATAATAATAATAT
1 TAT-TAATAATAATAT
391017 TATTAAT
1 TATTAAT
391024 GAAATTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 27 0.87
16 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (15 bp):
TATTAATAATAATAT
Found at i:391038 original size:27 final size:27
Alignment explanation
Indices: 390969--391101 Score: 85
Period size: 27 Copynumber: 4.7 Consensus size: 27
390959 AAATGTTTGT
* *
390969 TAATATTAATAATAA-ATGTGTTATTAA
1 TAATATTAATAATAATA-ATATTATTAA
*
390996 TAATATTTATAATAATAATATTATTAA
1 TAATATTAATAATAATAATATTATTAA
* *
391023 TGAA-ATTAATAATAATAAACAGTTTTTTTAAA
1 T-AATATTAATAATAAT--A-A-TATTATT-AA
391055 TAATCATTAATAATAATAA-ATGCT-TTAA
1 TAAT-ATTAATAATAATAATAT--TATTAA
* *
391083 TAATAATAATATTAATAAT
1 TAATATTAATAATAATAAT
391102 TAAATAAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 23
0.73 0.08 0.20
Matches are distributed among these distances:
27 46 0.54
28 10 0.12
29 3 0.04
30 3 0.04
31 8 0.09
32 3 0.04
33 12 0.14
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATATTAATAATAATAATATTATTAA
Found at i:401302 original size:205 final size:205
Alignment explanation
Indices: 400853--401561 Score: 1053
Period size: 205 Copynumber: 3.5 Consensus size: 205
400843 AAGCAGGCTC
* * * *
400853 CCTGATGAGATATCGAGAAGCAAGTCGAAGTAATAAAAGGTTAGCTTCCTGATGAGATACTGAGA
1 CCTGATGAGATACCAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGA
* * *
400918 AGTA-GACCAAATCCATTTTCCTGATGAGGTACAGAGAAA-CGGATTGAAACAAACGACGCAGTC
66 AG-AGGACCAAATTCGTTTTCCTGATGAGGTACAGA-AAAGCGGATTGAAACAAACGACGCGGTC
** *
400981 ATCTTCCTAAATGAGATACTGAAAAGAAGACCAAGTCAAACCCACACTCGATGTGAGCAAATCTT
129 ATCTT-CTTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACACTCGATGTGAGCAAATCTT
*
401046 CGAACCCTAACTT
193 CGAACCCTAGCTT
* * *
401059 CCAGATTAGATACCAAGAAGCAGGTCGAAGCAATAAAATGTTAGCTTCCTGATGAGATACTGAGA
1 CCTGATGAGATACCAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGA
401124 AGAGGACCAAATTCGTTTTCCTGATGAGGTACAGAAAAGCGGATTGAAACAAACGACGCGGTCAT
66 AGAGGACCAAATTCGTTTTCCTGATGAGGTACAGAAAAGCGGATTGAAACAAACGACGCGGTCAT
* *
401189 CTTCTTGATGAGATACTGAGAAGAAGACCATGTCAAACCCACACTCGATATGAGCAAATCTTCGA
131 CTTCTTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACACTCGATGTGAGCAAATCTTCGA
401254 ACCCTAGCTT
196 ACCCTAGCTT
* * * * *
401264 TCTGATGAGATACCGAGAAGCAGGTCGAAGCAATAAAATGTTAGCTTCCTGACGAGATATTGAGA
1 CCTGATGAGATACCAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGA
* * * *
401329 AGTGAACCAAATTTGTTTTCCTGATGAGGTACAGAGAAGCGGATTGAAACAAACGACGCGGTCAT
66 AGAGGACCAAATTCGTTTTCCTGATGAGGTACAGAAAAGCGGATTGAAACAAACGACGCGGTCAT
* * * * *
401394 CTTCCTGATGAGATAATAAGAAGAAGACCAAGTCAAACCTACGCTCGATGTGAGCAAATCTTCGA
131 CTTCTTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACACTCGATGTGAGCAAATCTTCGA
*
401459 ACCCCAGCTT
196 ACCCTAGCTT
* * *
401469 CCTGGTGAGACACCAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACGGAGA
1 CCTGATGAGATACCAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGA
* *
401534 AGTGGACCAAATTCGTCTTCCTGATGAG
66 AGAGGACCAAATTCGTTTTCCTGATGAG
401562 ATACTGAGAA
Statistics
Matches: 456, Mismatches: 45, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
205 339 0.74
206 117 0.26
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (205 bp):
CCTGATGAGATACCAAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGA
AGAGGACCAAATTCGTTTTCCTGATGAGGTACAGAAAAGCGGATTGAAACAAACGACGCGGTCAT
CTTCTTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACACTCGATGTGAGCAAATCTTCGA
ACCCTAGCTT
Found at i:404634 original size:20 final size:21
Alignment explanation
Indices: 404609--404651 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
404599 TACTTACTAC
404609 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
404629 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
404650 TA
1 TA
404652 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:405040 original size:4 final size:4
Alignment explanation
Indices: 405033--405074 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
405023 TCCTTCTTCC
* *
405033 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TTTT TTCT T
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT T
405075 CATTTTTCGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:405080 original size:21 final size:21
Alignment explanation
Indices: 405036--405082 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
405026 TTCTTCCTTC
405036 TTTCTTTCTTTCTTTCTCTTT
1 TTTCTTTCTTTCTTTCTCTTT
* *
405057 TTTCTTTCTTTTTTTCTTCATT
1 TTTCTTTCTTTCTTTC-TCTTT
405079 TTTC
1 TTTC
405083 GTTGGTCCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTCTTTCTTTCTCTTT
Found at i:405081 original size:12 final size:12
Alignment explanation
Indices: 405033--405074 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
405023 TCCTTCTTCC
*
405033 TTCTTTCTTTCT
1 TTCTTTCTTTTT
405045 TTCTTTCTCTTTT
1 TTCTTTCT-TTTT
405058 TTCTTTCTTTTT
1 TTCTTTCTTTTT
405070 TTCTT
1 TTCTT
405075 CATTTTTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:414601 original size:19 final size:19
Alignment explanation
Indices: 414552--414603 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
414542 TTCAATATTC
*
414552 AAACTTTAATTCTCCTTTTA
1 AAAC-TTAATTCTCCTTGTA
*
414572 AAAATTCAATT-TACCTTGTA
1 AAACTT-AATTCT-CCTTGTA
414592 AAACTTAATTCT
1 AAACTTAATTCT
414604 TCTTTTACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (19 bp):
AAACTTAATTCTCCTTGTA
Found at i:416332 original size:7 final size:7
Alignment explanation
Indices: 416322--416346 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
416312 CATATTTATA
416322 TTTTAAT
1 TTTTAAT
416329 TTTTAAT
1 TTTTAAT
416336 TTTTAAT
1 TTTTAAT
416343 TTTT
1 TTTT
416347 TTACCTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTAAT
Found at i:416593 original size:20 final size:20
Alignment explanation
Indices: 416552--416602 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
416542 AATAATTTAT
*
416552 AAAT-TATAAAAATATTTGA
1 AAATATATAAAAATATTCGA
416571 AAATATATAAAAAT-TTCGTA
1 AAATATATAAAAATATTCG-A
*
416591 AAA-ATTTAAAAA
1 AAATATATAAAAA
416603 ATTATTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATATATAAAAATATTCGA
Found at i:416745 original size:27 final size:28
Alignment explanation
Indices: 416688--416746 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
416678 AAAAAATAAC
* * **
416688 AATTTAATTCTTTTTGAAAAGTTGATCA
1 AATTTAACTCTTTTTGAAAAATTGAAAA
*
416716 AATTTAACTCTTTTT-AAAAATTTAAAA
1 AATTTAACTCTTTTTGAAAAATTGAAAA
416743 AATT
1 AATT
416747 AAAATTAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (28 bp):
AATTTAACTCTTTTTGAAAAATTGAAAA
Found at i:417837 original size:20 final size:19
Alignment explanation
Indices: 417812--417861 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
417802 TATATTCTTT
*
417812 ATATTTTATAATTTTGTATA
1 ATATTTTATAATTTT-AATA
*
417832 ATATTTGAATAATTTTAATA
1 ATATTT-TATAATTTTAATA
*
417852 AAATTTTATA
1 ATATTTTATA
417862 TATATTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
ATATTTTATAATTTTAATA
Found at i:422134 original size:2 final size:2
Alignment explanation
Indices: 422127--422155 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
422117 TACGGTACCT
422127 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
422156 GTCGTATTTT
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:436759 original size:2 final size:2
Alignment explanation
Indices: 436754--436792 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
436744 AAAAGAGAGA
436754 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
436793 AAATAGCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:443451 original size:46 final size:46
Alignment explanation
Indices: 443390--443481 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
443380 CATGTATAGG
443390 AAACAAGAAAAAATTATATCATATTTCCCATTTAAGCTTCAAATAA
1 AAACAAGAAAAAATTATATCATATTTCCCATTTAAGCTTCAAATAA
* *
443436 AAACAAGAAAGAATTATATCATATTTCCCATTTCAGCTTCAAATAA
1 AAACAAGAAAAAATTATATCATATTTCCCATTTAAGCTTCAAATAA
443482 CAGATGCATC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.30
Consensus pattern (46 bp):
AAACAAGAAAAAATTATATCATATTTCCCATTTAAGCTTCAAATAA
Found at i:445851 original size:29 final size:30
Alignment explanation
Indices: 445797--445865 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
445787 AAATTAAAGG
* * ** *
445797 TAAATTTATCATTATACTTTTTTTTTGT-A
1 TAAATTTACCACTATACTTTAATTTTATAA
445826 TAAATTTACCACTATACTTTAATTTTATAA
1 TAAATTTACCACTATACTTTAATTTTATAA
445856 TAAACTTTAC
1 TAAA-TTTAC
445866 TTTACATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 23 0.70
30 5 0.15
31 5 0.15
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.52
Consensus pattern (30 bp):
TAAATTTACCACTATACTTTAATTTTATAA
Found at i:461794 original size:19 final size:19
Alignment explanation
Indices: 461770--461844 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 19
461760 TAATTTAAAA
*
461770 AATTATTTAAATTTTTTTT
1 AATTATTTAAATTTATTTT
* * *
461789 AATTATTTTAACTTAATTAT
1 AATTA-TTTAAATTTATTTT
* * *
461809 AGTTTTTTAAATTATGTTTT
1 AATTATTTAAATT-TATTTT
461829 AATTATTTAAAATTTA
1 AATTATTT-AAATTTA
461845 ACTATTTTTT
Statistics
Matches: 40, Mismatches: 13, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
19 12 0.30
20 23 0.57
21 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (19 bp):
AATTATTTAAATTTATTTT
Found at i:461821 original size:39 final size:38
Alignment explanation
Indices: 461775--461861 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 38
461765 TAAAAAATTA
* * *
461775 TTTAAATTTTTTTTAATTATTT-TAACTTAATTATAGTTT
1 TTTAAATTTGTTTTAATTATTTAAAACTTAACTAT--TTT
*
461814 TTTAAATTATGTTTTAATTATTTAAAATTTAACTATTTT
1 TTTAAATT-TGTTTTAATTATTTAAAACTTAACTATTTT
461853 TTTAAATTT
1 TTTAAATTT
461862 AGGAAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 1 0.02
39 19 0.45
40 13 0.31
41 9 0.21
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (38 bp):
TTTAAATTTGTTTTAATTATTTAAAACTTAACTATTTT
Found at i:462478 original size:29 final size:29
Alignment explanation
Indices: 462431--462519 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 29
462421 AATTTTTACG
* * *
462431 ATTCATTTTAAGTCGTTTAGGTGAATATT
1 ATTCAATTTAAATCATTTAGGTGAATATT
* ** *
462460 ATTCAATTTAAATTATTTATATAAATATT
1 ATTCAATTTAAATCATTTAGGTGAATATT
* *
462489 -TT--TTTTAAGTCATTTAGGTGAATATT
1 ATTCAATTTAAATCATTTAGGTGAATATT
462515 ATTCA
1 ATTCA
462520 CATAATCCAA
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
26 18 0.41
27 2 0.05
28 2 0.05
29 22 0.50
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.51
Consensus pattern (29 bp):
ATTCAATTTAAATCATTTAGGTGAATATT
Found at i:462512 original size:26 final size:28
Alignment explanation
Indices: 462435--462517 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 28
462425 TTTACGATTC
*
462435 ATTTTAAGTCGTTTAGGTGAATATTATT
1 ATTTTAAGTCATTTAGGTGAATATTATT
* * * ** *
462463 CAATTTAAATTATTTATATAAATATT-TT
1 -ATTTTAAGTCATTTAGGTGAATATTATT
462491 -TTTTAAGTCATTTAGGTGAATATTATT
1 ATTTTAAGTCATTTAGGTGAATATTATT
462518 CACATAATCC
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
26 18 0.45
27 2 0.05
28 2 0.05
29 18 0.45
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (28 bp):
ATTTTAAGTCATTTAGGTGAATATTATT
Found at i:472257 original size:239 final size:239
Alignment explanation
Indices: 471838--472315 Score: 956
Period size: 239 Copynumber: 2.0 Consensus size: 239
471828 ACCTCGTCCA
471838 TACTATGGTAGGAAGGAAAGAAAATGGAGGGAAGAGGAAAAGGTGAGGAAAGAGAAAAAAGAAGA
1 TACTATGGTAGGAAGGAAAGAAAATGGAGGGAAGAGGAAAAGGTGAGGAAAGAGAAAAAAGAAGA
471903 GGAAGGAACGTTATTTTTCCTTCATTGCGTTTGGTAAGAATAATGGAAAATAGAGTATCTTTCAC
66 GGAAGGAACGTTATTTTTCCTTCATTGCGTTTGGTAAGAATAATGGAAAATAGAGTATCTTTCAC
471968 ATTTGGAAGGTTTGAAATTACAAGAGAAGGAAAGGGTCTAAGTCTACTCATTTACTTCCTGTCAC
131 ATTTGGAAGGTTTGAAATTACAAGAGAAGGAAAGGGTCTAAGTCTACTCATTTACTTCCTGTCAC
472033 CTATTTGACTATTTCCTTCCTAATAAAAGGAAACGATGGAAAGG
196 CTATTTGACTATTTCCTTCCTAATAAAAGGAAACGATGGAAAGG
472077 TACTATGGTAGGAAGGAAAGAAAATGGAGGGAAGAGGAAAAGGTGAGGAAAGAGAAAAAAGAAGA
1 TACTATGGTAGGAAGGAAAGAAAATGGAGGGAAGAGGAAAAGGTGAGGAAAGAGAAAAAAGAAGA
472142 GGAAGGAACGTTATTTTTCCTTCATTGCGTTTGGTAAGAATAATGGAAAATAGAGTATCTTTCAC
66 GGAAGGAACGTTATTTTTCCTTCATTGCGTTTGGTAAGAATAATGGAAAATAGAGTATCTTTCAC
472207 ATTTGGAAGGTTTGAAATTACAAGAGAAGGAAAGGGTCTAAGTCTACTCATTTACTTCCTGTCAC
131 ATTTGGAAGGTTTGAAATTACAAGAGAAGGAAAGGGTCTAAGTCTACTCATTTACTTCCTGTCAC
472272 CTATTTGACTATTTCCTTCCTAATAAAAGGAAACGATGGAAAGG
196 CTATTTGACTATTTCCTTCCTAATAAAAGGAAACGATGGAAAGG
472316 AAAGAGTAGC
Statistics
Matches: 239, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 239 1.00
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (239 bp):
TACTATGGTAGGAAGGAAAGAAAATGGAGGGAAGAGGAAAAGGTGAGGAAAGAGAAAAAAGAAGA
GGAAGGAACGTTATTTTTCCTTCATTGCGTTTGGTAAGAATAATGGAAAATAGAGTATCTTTCAC
ATTTGGAAGGTTTGAAATTACAAGAGAAGGAAAGGGTCTAAGTCTACTCATTTACTTCCTGTCAC
CTATTTGACTATTTCCTTCCTAATAAAAGGAAACGATGGAAAGG
Found at i:481200 original size:23 final size:23
Alignment explanation
Indices: 481147--481203 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
481137 TAAAAGTTTT
*
481147 GTTATTTTAATCTTTTCTTCATA
1 GTTATTTTAATCTTTTCTTCAGA
* * *
481170 ATTTTTTTAATCTTTAT-TTTAGA
1 GTTATTTTAATCTTT-TCTTCAGA
481193 GTTATTTTAAT
1 GTTATTTTAAT
481204 TAATATTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (23 bp):
GTTATTTTAATCTTTTCTTCAGA
Found at i:486274 original size:18 final size:19
Alignment explanation
Indices: 486239--486276 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
486229 TTTTACATGC
486239 TTTTAACAAATTAATAATTT
1 TTTTAACAAATT-ATAATTT
*
486259 TTTTATCAAATT-TAATTT
1 TTTTAACAAATTATAATTT
486277 AAATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAACAAATTATAATTT
Found at i:504207 original size:31 final size:31
Alignment explanation
Indices: 504159--504230 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
504149 AAATATTTTT
*
504159 ATAAATTTTAAAATTTATAATTAAATCATCA
1 ATAATTTTTAAAATTTATAATTAAATCATCA
* * **
504190 ATAATTTTTAAATTTTATAATTAATTCATTG
1 ATAATTTTTAAAATTTATAATTAAATCATCA
504221 ATAATTTTTA
1 ATAATTTTTA
504231 TAGTTAAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (31 bp):
ATAATTTTTAAAATTTATAATTAAATCATCA
Found at i:504429 original size:16 final size:16
Alignment explanation
Indices: 504400--504441 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
504390 TTTTCAATTA
*
504400 TTTTTTCTATAAACACT
1 TTTTTTTTATAAACA-T
504417 TTTTTTTTA-AAACAT
1 TTTTTTTTATAAACAT
*
504432 ATTTTTTTAT
1 TTTTTTTTAT
504442 TTTACATCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 5 0.23
17 8 0.36
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTTTTATAAACAT
Found at i:508131 original size:87 final size:87
Alignment explanation
Indices: 507985--508158 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
507975 TGCAACAGTT
507985 TGCTTGTATGAACAACAATGGAGAAGAAAGTGCTACTATGTTCTATGCTACTTACATCAGTTGTC
1 TGCTTGTATGAACAACAATGGAGAAGAAAGTGCTACTATGTTCTATGCTACTTACATCAGTTGTC
508050 TGAATTTCCAAACACTATTTGA
66 TGAATTTCCAAACACTATTTGA
508072 TGCTTGTATGAACAACAATGGAGAAGAAAGTGCTACTATGTTCTATGCTACTTACATCAGTTGTC
1 TGCTTGTATGAACAACAATGGAGAAGAAAGTGCTACTATGTTCTATGCTACTTACATCAGTTGTC
508137 TGAATTTCCAAACACTATTTGA
66 TGAATTTCCAAACACTATTTGA
508159 GGTAACGTAC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (87 bp):
TGCTTGTATGAACAACAATGGAGAAGAAAGTGCTACTATGTTCTATGCTACTTACATCAGTTGTC
TGAATTTCCAAACACTATTTGA
Found at i:512368 original size:15 final size:16
Alignment explanation
Indices: 512342--512371 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
512332 AGACTATATA
512342 AAATATTTAAAAAAAC
1 AAATATTTAAAAAAAC
512358 AAATA-TTAAAAAAA
1 AAATATTTAAAAAAA
512372 GACACATGAC
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:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATATTTAAAAAAAC
Found at i:523300 original size:6 final size:6
Alignment explanation
Indices: 523289--523375 Score: 75
Period size: 6 Copynumber: 13.3 Consensus size: 6
523279 TTCCATCGTC
* * * *
523289 CATCTT CATCTT CAAGCCTC CATCTT CCATCTT CATCTT CATCTT CAAGCCTC
1 CATCTT CATCTT C-A-TCTT CATCTT -CATCTT CATCTT CATCTT C-A-TCTT
523342 CATCTT CCATCTT CCATCTT CATCTT CATCTT CA
1 CATCTT -CATCTT -CATCTT CATCTT CATCTT CA
523376 AGCCTCCATG
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
6 38 0.57
7 23 0.34
8 6 0.09
ACGTcount: A:0.18, C:0.39, G:0.02, T:0.40
Consensus pattern (6 bp):
CATCTT
Found at i:523329 original size:33 final size:33
Alignment explanation
Indices: 523278--523369 Score: 157
Period size: 33 Copynumber: 2.7 Consensus size: 33
523268 TTTTCTCTCA
*
523278 CTTCCATCGTCCATCTTCATCTTCAAGCCTCCAT
1 CTTCCATC-TTCATCTTCATCTTCAAGCCTCCAT
523312 CTTCCATCTTCATCTTCATCTTCAAGCCTCCAT
1 CTTCCATCTTCATCTTCATCTTCAAGCCTCCAT
523345 CTTCCATCTTCCATCTTCATCTTCA
1 CTTCCATCTT-CATCTTCATCTTCA
523370 TCTTCAAGCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
33 34 0.61
34 22 0.39
ACGTcount: A:0.17, C:0.40, G:0.03, T:0.39
Consensus pattern (33 bp):
CTTCCATCTTCATCTTCATCTTCAAGCCTCCAT
Found at i:523354 original size:40 final size:40
Alignment explanation
Indices: 523307--523384 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
523297 TCTTCAAGCC
523307 TCCATCTTCCATCTTCATCTTCATCTTCAAGCCTCCATCT
1 TCCATCTTCCATCTTCATCTTCATCTTCAAGCCTCCATCT
523347 TCCATCTTCCATCTTCATCTTCATCTTCAAGCCTCCAT
1 TCCATCTTCCATCTTCATCTTCATCTTCAAGCCTCCAT
523385 GGTTGGTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.18, C:0.40, G:0.03, T:0.40
Consensus pattern (40 bp):
TCCATCTTCCATCTTCATCTTCATCTTCAAGCCTCCATCT
Found at i:534801 original size:2 final size:2
Alignment explanation
Indices: 534794--534827 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
534784 NNNNNNNNNN
534794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
534828 GTTTGGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:536375 original size:112 final size:112
Alignment explanation
Indices: 536178--536403 Score: 425
Period size: 112 Copynumber: 2.0 Consensus size: 112
536168 ACTCGATTCG
* *
536178 ACTTTATTCGATCGAACGCCGACCCCTACGCACAATTGCTTGCTTCACTATTGCTATCTTGAGAG
1 ACTTTATTCGATCGAACGCCCACCCCTACACACAATTGCTTGCTTCACTATTGCTATCTTGAGAG
*
536243 ATACCTATCAAGTTTGAGATTGAAATACTGAAGGTTAAACAACCTCA
66 ATACCTATCAAGTTTGAGATTGAAATACTAAAGGTTAAACAACCTCA
536290 ACTTTATTCGATCGAACGCCCACCCCTACACACAATTGCTTGCTTCACTATTGCTATCTTGAGAG
1 ACTTTATTCGATCGAACGCCCACCCCTACACACAATTGCTTGCTTCACTATTGCTATCTTGAGAG
536355 ATACCTATCAAGTTTGAGATTGAAATACTAAAGGTTAAACAACCTCA
66 ATACCTATCAAGTTTGAGATTGAAATACTAAAGGTTAAACAACCTCA
536402 AC
1 AC
536404 CAATGGCGTC
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (112 bp):
ACTTTATTCGATCGAACGCCCACCCCTACACACAATTGCTTGCTTCACTATTGCTATCTTGAGAG
ATACCTATCAAGTTTGAGATTGAAATACTAAAGGTTAAACAACCTCA
Found at i:549797 original size:3 final size:3
Alignment explanation
Indices: 549789--549817 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
549779 TCAATTTTTA
549789 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
549818 AAAGTATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:558020 original size:16 final size:16
Alignment explanation
Indices: 557995--558030 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
557985 ACTTATTAGA
*
557995 TTCATTTTTAAGTTGT
1 TTCATCTTTAAGTTGT
*
558011 TTCATCTTTATGTTGT
1 TTCATCTTTAAGTTGT
558027 TTCA
1 TTCA
558031 AGTAGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (16 bp):
TTCATCTTTAAGTTGT
Found at i:559578 original size:22 final size:22
Alignment explanation
Indices: 559553--559600 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
559543 GAAAATTGGC
* *
559553 AAAATATTTGGAAGATCTAATT
1 AAAATATTTGAAAGATCTAATG
* *
559575 AAAATTTTTGAAAGATTTAATG
1 AAAATATTTGAAAGATCTAATG
559597 AAAA
1 AAAA
559601 ATTCCAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.35
Consensus pattern (22 bp):
AAAATATTTGAAAGATCTAATG
Found at i:561895 original size:23 final size:23
Alignment explanation
Indices: 561869--561923 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
561859 AATGATCCTT
561869 TAAAAATTATATTTTTACTATCA
1 TAAAAATTATATTTTTACTATCA
561892 TAAAAATTATATTTTTACTATCA
1 TAAAAATTATATTTTTACTATCA
561915 TAAAAATTA
1 TAAAAATTA
561924 CAATTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAATTATATTTTTACTATCA
Found at i:561930 original size:22 final size:23
Alignment explanation
Indices: 561869--561930 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
561859 AATGATCCTT
* *
561869 TAAAAATTATATTTTTACTATCA
1 TAAAAATTACATATTTACTATCA
* *
561892 TAAAAATTATATTTTTACTATCA
1 TAAAAATTACATATTTACTATCA
561915 TAAAAATTACA-ATTTA
1 TAAAAATTACATATTTA
561931 ATTTCGATCC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 4 0.11
23 33 0.89
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAATTACATATTTACTATCA
Found at i:576660 original size:18 final size:19
Alignment explanation
Indices: 576633--576670 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
576623 TTTTTTATCT
576633 AAAAAATT-A-AATAAAAA
1 AAAAAATTAAGAATAAAAA
576650 AAAAAAGTTAAGAATAAAAA
1 AAAAAA-TTAAGAATAAAAA
576670 A
1 A
576671 CCTGACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 1 0.06
20 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (19 bp):
AAAAAATTAAGAATAAAAA
Found at i:576933 original size:7 final size:7
Alignment explanation
Indices: 576921--576949 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
576911 TTGATTGACC
576921 CAATTCA
1 CAATTCA
576928 CAATTCA
1 CAATTCA
576935 CAATTCA
1 CAATTCA
576942 CAATTCA
1 CAATTCA
576949 C
1 C
576950 GTCTCGCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (7 bp):
CAATTCA
Found at i:577667 original size:4 final size:4
Alignment explanation
Indices: 577660--577688 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
577650 TCTTGTTGTT
577660 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
577689 CTACTTGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:580477 original size:18 final size:18
Alignment explanation
Indices: 580454--580499 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
580444 GTGGTGATTT
*
580454 CGGGTCAGGACCACGTTC
1 CGGGTCAGGACCACGGTC
* *
580472 CGGGTCAAGACCAGGGTC
1 CGGGTCAGGACCACGGTC
*
580490 CGGATCAGGA
1 CGGGTCAGGA
580500 TCGGATTTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.28, G:0.37, T:0.13
Consensus pattern (18 bp):
CGGGTCAGGACCACGGTC
Found at i:585401 original size:33 final size:33
Alignment explanation
Indices: 585373--585453 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
585363 TTTCTTCTTC
*
585373 CTCCTCTTCTTCGTGTTTACTTCCTTCTTCCCG
1 CTCCTCTTCTTCGTGCTTACTTCCTTCTTCCCG
* *
585406 CTCCTCTTCTTCGTGCTTGCTTCCTTCTACCCG
1 CTCCTCTTCTTCGTGCTTACTTCCTTCTTCCCG
* *
585439 TTCCTCCTCTTCGTG
1 CTCCTCTTCTTCGTG
585454 TTTTATTGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.02, C:0.41, G:0.11, T:0.46
Consensus pattern (33 bp):
CTCCTCTTCTTCGTGCTTACTTCCTTCTTCCCG
Done.