Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 25 of 74
Found at i:5835582 original size:5 final size:5
Alignment explanation
Indices: 5835572--5835618 Score: 67
Period size: 5 Copynumber: 9.0 Consensus size: 5
5835562 TAATGGTTGG
*
5835572 TAAAA TAAAA TAAAA TAAAA TAAAA TAAATG TAAAA TAATAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA-A TAAAA TAA-AA TAAAA
5835619 CTAATAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 29 0.76
6 9 0.24
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:5835624 original size:26 final size:25
Alignment explanation
Indices: 5835577--5835627 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
5835567 GTTGGTAAAA
5835577 TAAAATAAAATAAAATAAAATAAATG
1 TAAAATAAAATAAAAT-AAATAAATG
5835603 TAAAATAATAATAAAACT-AATAAAT
1 TAAAATAA-AATAAAA-TAAATAAAT
5835628 AATACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.65
27 7 0.30
28 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (25 bp):
TAAAATAAAATAAAATAAATAAATG
Found at i:5842044 original size:17 final size:17
Alignment explanation
Indices: 5842018--5842062 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
5842008 ATAATTTTTT
5842018 ATTT-AAATTTATCAAA
1 ATTTAAAATTTATCAAA
5842034 ATTTAAAATTTATCAAA
1 ATTTAAAATTTATCAAA
5842051 ATTTAAAATTTA
1 ATTTAAAATTTA
5842063 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAAATTTATCAAA
Found at i:5842497 original size:14 final size:15
Alignment explanation
Indices: 5842473--5842510 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
5842463 TTATACAATT
5842473 TTAATTTATAAT-TAA
1 TTAA-TTATAATATAA
5842488 TTAATTATAATATAA
1 TTAATTATAATATAA
5842503 -TAATTATA
1 TTAATTATA
5842511 TGTGATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTATAATATAA
Found at i:5843508 original size:18 final size:17
Alignment explanation
Indices: 5843487--5843525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5843477 CATGAATTAA
* *
5843487 TTAAATTAAATTTAAAAT
1 TTAAAATAAACTT-AAAT
5843505 TTAAAATAAACTTAAAT
1 TTAAAATAAACTTAAAT
5843522 TTAA
1 TTAA
5843526 TGATGTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAATAAACTTAAAT
Found at i:5851630 original size:2 final size:2
Alignment explanation
Indices: 5851623--5851647 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5851613 GAAATTATCA
5851623 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 T
5851648 TTCTATATCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5851662 original size:2 final size:2
Alignment explanation
Indices: 5851651--5851697 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5851641 TCTCTCTTTC
*
5851651 TA TA TC TA 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 TA TA TA TA
5851693 TA TA T
1 TA TA T
5851698 GCAGGATAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5856469 original size:30 final size:30
Alignment explanation
Indices: 5856433--5856521 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
5856423 GTGGTGCAAG
5856433 GACTTCTATGGGAGTGAAGCCTACGCCAAA
1 GACTTCTATGGGAGTGAAGCCTACGCCAAA
*
5856463 GACTTCTATGGGAGTGAAGCTTACGCCAAA
1 GACTTCTATGGGAGTGAAGCCTACGCCAAA
* * *
5856493 GACTTCTATCGGAGTCAAGCCAACGCCAA
1 GACTTCTATGGGAGTGAAGCCTACGCCAA
5856522 TGACGGAGAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (30 bp):
GACTTCTATGGGAGTGAAGCCTACGCCAAA
Found at i:5857600 original size:14 final size:15
Alignment explanation
Indices: 5857569--5857602 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5857559 TTATTTATAT
5857569 TTTATTTGTTGATTG
1 TTTATTTGTTGATTG
*
5857584 TTTATTTGTT-TTTG
1 TTTATTTGTTGATTG
5857598 TTTAT
1 TTTAT
5857603 CTGATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (15 bp):
TTTATTTGTTGATTG
Found at i:5866661 original size:184 final size:185
Alignment explanation
Indices: 5866345--5866764 Score: 551
Period size: 184 Copynumber: 2.3 Consensus size: 185
5866335 GTTTTCTACT
* * * *
5866345 AAAAATGCCTTCAATAATTTATT-TCAA-TTTCTAAGAGAAAATTATTGAAGGTATTTCTTGAGC
1 AAAAATGCCTTCAATAATTTATTCT-AATTTTTTAA-AG-AATTTATTGAAGGCATTTCTTGAGA
* ** *
5866408 AAAAATGCCTTTAATAATTTTCTTTTAAAAATTGTTTGGAATTATTAAAAACGTCTTTTATAGAA
63 AAAAATGCCTTTAATAATTTCCTTTTAAAAATAATTTGGAATTATTAAAAACGTCTTCTATAGAA
* *
5866473 AATGCCTTTAATATTTCACTACTAAATTTTAAGGGGTTATTGAAGGTGTTTATTCCAA
128 AATGCCTTTAATATTTCACTACTAAATTTTAAGGGGTTATTAAAGGCGTTTATTCCAA
* *
5866531 AAAAATGCCTTTAATAATTCATTCTAATTTTTTAAAGAATTTATT-AAGGCATTTCTTGAGAAAA
1 AAAAATGCCTTCAATAATTTATTCTAATTTTTTAAAGAATTTATTGAAGGCATTTCTTGAGAAAA
** *
5866595 AATGCCTTTAATAATTTCCTTTTAAAAATAATTT-GAGATTATTAAAGGCGTCTTCTATATAAAA
66 AATGCCTTTAATAATTTCCTTTTAAAAATAATTTGGA-ATTATTAAAAACGTCTTCTATAGAAAA
* * **
5866659 TGCCTTTAATATTTTACTACTAAATTTTAAGGGGTTGTTAAAGGCGTTTATTCCTG
130 TGCCTTTAATATTTCACTACTAAATTTTAAGGGGTTATTAAAGGCGTTTATTCCAA
** * * * *
5866715 AAAAACACCTTCACTAATTTGTTCTAATTTTTGAAGGAATTTATTGAAGG
1 AAAAATGCCTTCAATAATTTATTCTAATTTTTTAAAGAATTTATTGAAGG
5866765 TGTTTTATGC
Statistics
Matches: 203, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
183 2 0.01
184 158 0.78
185 11 0.05
186 25 0.12
187 7 0.03
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (185 bp):
AAAAATGCCTTCAATAATTTATTCTAATTTTTTAAAGAATTTATTGAAGGCATTTCTTGAGAAAA
AATGCCTTTAATAATTTCCTTTTAAAAATAATTTGGAATTATTAAAAACGTCTTCTATAGAAAAT
GCCTTTAATATTTCACTACTAAATTTTAAGGGGTTATTAAAGGCGTTTATTCCAA
Found at i:5867127 original size:238 final size:236
Alignment explanation
Indices: 5866571--5867164 Score: 720
Period size: 237 Copynumber: 2.5 Consensus size: 236
5866561 TTTAAAGAAT
** * *
5866571 TTATTAAGGCATTTCTTGAGAAAAAATGCCTTTAATAATTTCCTTTTAAAAATAATTTGAGATTA
1 TTATTAAGGCATTTCTTGAGAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGATTA
* *
5866636 TTAAAGGCGTCTTCTA-T-ATAAAATGCCTTTAATATTTTACTACT-AAATTTTAAGGGGTTGTT
66 TTAAAGGC-TCTTCTAGTGA-AAAATGCCTTCAATATTTCACTACTAAAATTTTAAGGGGTTGTT
* ** ** * * *
5866698 AAAGGCGTTTATTCCTGAAAAACACCTTCACTAATTTGTTCTAATTTTTGAAGGAATTTATTGAA
129 AAAGGCATTTATTCCAAAAAAACACCTTCACTAATTCCTTCTAATATATGAAAGAATTTATTGAA
* * *
5866763 GGTGTTTTATGCATTATATGCCTTCAATAATTTTTATAGATAA
194 GGTATTTTATGCATTAAATGCCTTCAATAATTTTTACAGATAA
* * * *
5866806 TTATTGAAGGCGTTTCATGAGAAAAAACACCTTCAATAATTTTCTTTTAAAAATTATTTGGGATT
1 TTATT-AAGGCATTTCTTGAGAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGATT
* * *
5866871 ATTGAAAGTG-TCTTCTAGTGAAAAATGCCTTCAATATTCCACTAATAAAATTTTAAGATGGTTA
65 ATT-AAAG-GCTCTTCTAGTGAAAAATGCCTTCAATATTTCACTACTAAAATTTTAAG-GGGTT-
* **
5866935 G-TCAAGGCATTTATTCCAAAAAAATGCCTTCACTAATTCCTTC-AA-ATATGAAAGAATTTATT
126 GTTAAAGGCATTTATTCCAAAAAAACACCTTCACTAATTCCTTCTAATATATGAAAGAATTTATT
* * * *
5866997 GAAGGTATTTTTTGTATTAAATGCTTTCAATAATTTTTGCAGATAA
191 GAAGGTATTTTATGCATTAAATGCCTTCAATAATTTTTACAGATAA
*
5867043 TTATTAAAGGCATTTTTTGAGAAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGAT
1 TTATT-AAGGCATTTCTTGAG-AAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGAT
*
5867108 TATTAAAGGCATTTTCTAGTAGAAAACAT--CTTCAATATTTCACTACTAAAATTTTAA
64 TATTAAAGGC-TCTTCTAGT-GAAAA-ATGCCTTCAATATTTCACTACTAAAATTTTAA
5867165 TACGGTTATT
Statistics
Matches: 306, Mismatches: 40, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
235 5 0.02
236 62 0.20
237 100 0.33
238 93 0.30
239 43 0.14
240 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (236 bp):
TTATTAAGGCATTTCTTGAGAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGATTA
TTAAAGGCTCTTCTAGTGAAAAATGCCTTCAATATTTCACTACTAAAATTTTAAGGGGTTGTTAA
AGGCATTTATTCCAAAAAAACACCTTCACTAATTCCTTCTAATATATGAAAGAATTTATTGAAGG
TATTTTATGCATTAAATGCCTTCAATAATTTTTACAGATAA
Found at i:5867204 original size:238 final size:235
Alignment explanation
Indices: 5866571--5867247 Score: 722
Period size: 238 Copynumber: 2.9 Consensus size: 235
5866561 TTTAAAGAAT
** * *
5866571 TTATTAAGGCATTTCTTGAGAAAAAATGCCTTTAATAATTTCCTTTTAAAAATAATTTGAGATTA
1 TTATTAAGGCATTTCTTGAGAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGATTA
* * * ** *
5866636 TTAAAGGCGTCTTCTA-TA-TAAAATGCCTTTAATATTTTACTACT-AAATTTTAAGGGGTTGTT
66 TTAAAGGC-TCTTCTAGTAGAAAAAT--CTTCAATATTTCACTACTAAAATTTTAAACGGTTATT
* * ** * * *
5866698 AAAGGCGTTTATTCCTGAAAAACACCTTCACTAATTTGTTCTAATTTTTGAAGGAATTTATTGAA
128 AAAGGCGTTTATTCCAGAAAAACGCCTTCACTAATTCCTTCTAATATATGAAAGAATTTATTGAA
* * *
5866763 GGTGTTTTATGCATTATATGCCTTCAATAATTTTTATAGATAA
193 GGTATTTTATGCATTAAATGCCTTCAATAATTTTTACAGATAA
* * * *
5866806 TTATTGAAGGCGTTTCATGAGAAAAAACACCTTCAATAATTTTCTTTTAAAAATTATTTGGGATT
1 TTATT-AAGGCATTTCTTGAGAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGATT
* * *
5866871 ATTGAAAGTG-TCTTCTAGT-GAAAAATGCCTTCAATATTCCACTAATAAAATTTTAAGATGGTT
65 ATT-AAAG-GCTCTTCTAGTAGAAAAAT--CTTCAATATTTCACTACTAAAATTTTAA-ACGGTT
* * * * *
5866934 AGTCAAGGCATTTATTCCAAAAAAATGCCTTCACTAATTCCTTC-AA-ATATGAAAGAATTTATT
125 ATTAAAGGCGTTTATTCCAGAAAAACGCCTTCACTAATTCCTTCTAATATATGAAAGAATTTATT
* * * *
5866997 GAAGGTATTTTTTGTATTAAATGCTTTCAATAATTTTTGCAGATAA
190 GAAGGTATTTTATGCATTAAATGCCTTCAATAATTTTTACAGATAA
*
5867043 TTATTAAAGGCATTTTTTGAGAAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGAT
1 TTATT-AAGGCATTTCTTGAG-AAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGAT
*
5867108 TATTAAAGGCATTTTCTAGTAGAAAACATCTTCAATATTTCACTACTAAAATTTTAATACGGTTA
64 TATTAAAGGC-TCTTCTAGTAGAAAA-ATCTTCAATATTTCACTACTAAAATTTTAA-ACGGTTA
* * * * * * * * * *
5867173 TTGAAGGTGTTTATTTCAGGAAAACGCCTTCA-AAATTTCATTCTAGTTTTTAAAAGAATTTATT
126 TTAAAGGCGTTTATTCCAGAAAAACGCCTTCACTAA-TTCCTTCTAATATATGAAAGAATTTATT
*
5867237 GAAGGCATTTT
190 GAAGGTATTTT
5867248 TTTCATTATA
Statistics
Matches: 366, Mismatches: 61, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
235 5 0.01
236 62 0.17
237 102 0.28
238 127 0.35
239 44 0.12
240 26 0.07
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.40
Consensus pattern (235 bp):
TTATTAAGGCATTTCTTGAGAAAAAACACCTTTAATAATTTTCTTTTAAAAATTATTTGAGATTA
TTAAAGGCTCTTCTAGTAGAAAAATCTTCAATATTTCACTACTAAAATTTTAAACGGTTATTAAA
GGCGTTTATTCCAGAAAAACGCCTTCACTAATTCCTTCTAATATATGAAAGAATTTATTGAAGGT
ATTTTATGCATTAAATGCCTTCAATAATTTTTACAGATAA
Found at i:5867287 original size:124 final size:123
Alignment explanation
Indices: 5867133--5867382 Score: 351
Period size: 124 Copynumber: 2.0 Consensus size: 123
5867123 CTAGTAGAAA
* *
5867133 ACATCTTCAATATTTCACTACTAAAATTTTAATACGGTTATTGAAGGTGTTTATTTCAGGAAAA-
1 ACATATTCAATATTTCACTACTAAAATTTTAAGACGGTTATTGAAGGTGTTTA-TTCAGGAAAAT
* * *
5867197 CGCCTTCAAA-ATTTCATTCTAGTTTTTAAAAGAATTTATTGAAGGCATTTTTTTCATTAT
65 CGCC-T-AAACAATTCATTCTAATTTTTAAAAGAATTTATTGAAGGCATTTTTTGCATTAT
* * **
5867257 ACATATTCAATATTTTACTACTAAATTTTTAAGACGGTTATTGAAGGTGTTTATTCTTGAAAATC
1 ACATATTCAATATTTCACTACTAAAATTTTAAGACGGTTATTGAAGGTGTTTATTCAGGAAAATC
* *
5867322 GCCTAAACTAATTCATTCTAATTTTTGAAAGAATTTATTGAAGGCGTTTTTTGCATTAT
66 GCCTAAAC-AATTCATTCTAATTTTTAAAAGAATTTATTGAAGGCATTTTTTGCATTAT
5867381 AC
1 AC
5867383 GCCTTTAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
122 3 0.03
123 9 0.08
124 100 0.89
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (123 bp):
ACATATTCAATATTTCACTACTAAAATTTTAAGACGGTTATTGAAGGTGTTTATTCAGGAAAATC
GCCTAAACAATTCATTCTAATTTTTAAAAGAATTTATTGAAGGCATTTTTTGCATTAT
Found at i:5867690 original size:238 final size:238
Alignment explanation
Indices: 5867278--5868111 Score: 998
Period size: 238 Copynumber: 3.5 Consensus size: 238
5867268 ATTTTACTAC
* * * * * **
5867278 TAAATTTTTAAGACGGTTATTGAAGGTGTTTATTCTTGAAAATCGCCTAAACTAATTCATTCTAA
1 TAAAATTTTAAGACAGTTATTGAAGGCGTTTATTCTAGAAAAACGCCTTCACTAATTCATTCTAA
* * *
5867343 TTTTTGAA-AGAATTTATTGAAGGCGTTTTTTGCATTATACGCCTTTAATAATTTTTGTATAGAA
66 TTTTTGAAGA-AATTTATTAAAGGCGTTTTTTGCATTATACGCCTTCAATAATTTTTGTATAAAA
* * *
5867407 TTATTGAAAGCGTTTTTTTAGAACAAACGCCTTCAATAATTTTCTTTTAAAAATTATTTGGGATT
130 TTATTGAAGGCG-TTTTTTAAAACAAAAGCCTTCAATAATTTTCTTTTAAAAATTATTTGGGATT
* *
5867472 ATTAAAGACATATTCTAGTG-AAAACGCCTTCAATATTCCACTTA
194 ATTAAAGACGTATTCTAGTGAAAAACGCTTTCAATATTCCACTTA
*
5867516 TAAAATTTTAAGACAGTTATTGAAGGCGTTTATTCTAGGAAAACGCCTTCACTAATTCATTCTAA
1 TAAAATTTTAAGACAGTTATTGAAGGCGTTTATTCTAGAAAAACGCCTTCACTAATTCATTCTAA
** * *
5867581 TTTTTGAAGAAATTTATTAAAGGTATTTTTTGCATTATATGCCTTCAATAATTTTTGTACAAAAT
66 TTTTTGAAGAAATTTATTAAAGGCGTTTTTTGCATTATACGCCTTCAATAATTTTTGTATAAAAT
* * * *
5867646 TATTGAAGGCATTTTTTAATAATAAAAGCCTTAAATACTTTTCTTTTAAAAATTATTTGGGATTA
131 TATTGAAGGCGTTTTTTAA-AACAAAAGCCTTCAATAATTTTCTTTTAAAAATTATTTGGGATTA
* * *
5867711 TT-AAGGCGTATTCTAGTGAAAAACGCTTTCAATATTTCACTTC
195 TTAAAGACGTATTCTAGTGAAAAACGCTTTCAATATTCCACTTA
* * ** ** * * *
5867754 TAAAACTTTAATATGGTTATTGAAGGCGTTTATTAAAGAAAAATGCCTTCATTAATTCATTTTAA
1 TAAAATTTTAAGACAGTTATTGAAGGCGTTTATTCTAGAAAAACGCCTTCACTAATTCATTCTAA
* *
5867819 TTTTTGAAGAAATTTATTGAAGGCGTTTTTTGCATTATACGCCTTCAATAATTTGTGTATAAAAT
66 TTTTTGAAGAAATTTATTAAAGGCGTTTTTTGCATTATACGCCTTCAATAATTTTTGTATAAAAT
** * *
5867884 TATTGAAGATGTTTTTTGAAAACAAACA-CCTTCAATAATTTCCTTTTAAAAATTGTTTGGGATT
131 TATTGAAGGCGTTTTTT-AAAACAAA-AGCCTTCAATAATTTTCTTTTAAAAATTATTTGGGATT
* *
5867948 ATTAAA-AGCGTCTTCTAGTGAAAAACACTTTCAATATTCCAC-TA
194 ATTAAAGA-CGTATTCTAGTGAAAAACGCTTTCAATATTCCACTTA
* * * * * ** * *** *
5867992 CTAACATTTTAAGGCAGTTAGTGAAGGCATTT-TTTTCAGAAAAATACTTTCACTAATTTGCTAT
1 -TAAAATTTTAAGACAGTTATTGAAGGCGTTTATTCT-AGAAAAACGCCTTCACTAATTCATTCT
* * * *
5868056 AATTTTTTGAAGGAATTTATTAAAGGCGTTTTCTGCATAATATGCCTTCAATAATT
64 AA-TTTTTGAAGAAATTTATTAAAGGCGTTTTTTGCATTATACGCCTTCAATAATT
5868112 CCTTCCATTC
Statistics
Matches: 508, Mismatches: 78, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
237 21 0.04
238 357 0.70
239 82 0.16
240 48 0.09
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (238 bp):
TAAAATTTTAAGACAGTTATTGAAGGCGTTTATTCTAGAAAAACGCCTTCACTAATTCATTCTAA
TTTTTGAAGAAATTTATTAAAGGCGTTTTTTGCATTATACGCCTTCAATAATTTTTGTATAAAAT
TATTGAAGGCGTTTTTTAAAACAAAAGCCTTCAATAATTTTCTTTTAAAAATTATTTGGGATTAT
TAAAGACGTATTCTAGTGAAAAACGCTTTCAATATTCCACTTA
Found at i:5868751 original size:28 final size:28
Alignment explanation
Indices: 5868720--5868774 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5868710 AATATTGTGG
*
5868720 TTTGCTTAATGATATTGTGTGATATTAT
1 TTTGCTTAATGATATTGTATGATATTAT
*
5868748 TTTGCTTAATGGTATTGTATGATATTA
1 TTTGCTTAATGATATTGTATGATATTA
5868775 ATATGCTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (28 bp):
TTTGCTTAATGATATTGTATGATATTAT
Found at i:5868781 original size:28 final size:28
Alignment explanation
Indices: 5868722--5868790 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
5868712 TATTGTGGTT
* * * *
5868722 TGCTTAATGATATTGTGTGATATTATTT
1 TGCTTAATGGTATTGTATGATATTAATA
5868750 TGCTTAATGGTATTGTATGATATTAATA
1 TGCTTAATGGTATTGTATGATATTAATA
* *
5868778 TGCTGAATCGTAT
1 TGCTTAATGGTAT
5868791 GCTGAATGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.48
Consensus pattern (28 bp):
TGCTTAATGGTATTGTATGATATTAATA
Found at i:5868846 original size:37 final size:37
Alignment explanation
Indices: 5868792--5868882 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 37
5868782 GAATCGTATG
* * *
5868792 CTGAATGCTTTGTTGAATGGTTTGCTAAATAGTGTTT
1 CTGAATGGTTTGTTGAATGATTTGCTAAATAGTATTT
* * * *
5868829 TTGAATGGTTTGCTGAATGATTTGCTTAATGGTATTT
1 CTGAATGGTTTGTTGAATGATTTGCTAAATAGTATTT
*
5868866 CTGAATCGTTTGTTGAA
1 CTGAATGGTTTGTTGAA
5868883 GGTGTTTCTA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (37 bp):
CTGAATGGTTTGTTGAATGATTTGCTAAATAGTATTT
Found at i:5868847 original size:12 final size:12
Alignment explanation
Indices: 5868778--5868882 Score: 77
Period size: 12 Copynumber: 8.6 Consensus size: 12
5868768 GATATTAATA
* *
5868778 TGCTGAATCGTA
1 TGCTGAATGGTT
*
5868790 TGCTGAATGCTT
1 TGCTGAATGGTT
*
5868802 TGTTGAATGGTT
1 TGCTGAATGGTT
*
5868814 TGCTAAATAGTGTT
1 TGCTGAAT-G-GTT
*
5868828 T-TTGAATGGTT
1 TGCTGAATGGTT
*
5868839 TGCTGAATGATT
1 TGCTGAATGGTT
*
5868851 TGCTTAATGGTAT
1 TGCTGAATGGT-T
* *
5868864 TTCTGAATCGTT
1 TGCTGAATGGTT
*
5868876 TGTTGAA
1 TGCTGAA
5868883 GGTGTTTCTA
Statistics
Matches: 71, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
11 4 0.06
12 49 0.69
13 14 0.20
14 4 0.06
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.45
Consensus pattern (12 bp):
TGCTGAATGGTT
Found at i:5872716 original size:2 final size:2
Alignment explanation
Indices: 5872709--5872735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5872699 ATTATCATAT
5872709 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
5872736 ATATATATAT
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:5872740 original size:2 final size:2
Alignment explanation
Indices: 5872735--5872775 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5872725 TCTCTCTCTC
5872735 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
5872776 GCAGGATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5877563 original size:30 final size:30
Alignment explanation
Indices: 5877527--5877594 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
5877517 AACTGTGATG
* * *
5877527 CAAAGACTTCTATGGGAGTGAAGCCTACGC
1 CAAAGACTTCTATCGGAGTCAAGCCAACGC
*
5877557 CAAAGACTTCTATCGGCGTCAAGCCAACGC
1 CAAAGACTTCTATCGGAGTCAAGCCAACGC
*
5877587 CAATGACT
1 CAAAGACT
5877595 GAGACTTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (30 bp):
CAAAGACTTCTATCGGAGTCAAGCCAACGC
Found at i:5883639 original size:13 final size:13
Alignment explanation
Indices: 5883621--5883659 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
5883611 TGATTAAATT
5883621 TAAAAAAATAAAA
1 TAAAAAAATAAAA
5883634 TAAAAAAGATAAAA
1 TAAAAAA-ATAAAA
5883648 -AAATAAAATAAA
1 TAAA-AAAATAAA
5883660 TTTTGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:5887889 original size:13 final size:14
Alignment explanation
Indices: 5887855--5887901 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
5887845 AAAAGGTCTC
5887855 AAAAAGAGAAAGAAA
1 AAAAAGA-AAAGAAA
5887870 AGCAAAATGAAAA-AAA
1 A--AAAA-GAAAAGAAA
5887886 AAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
5887900 AA
1 AA
5887902 TGCCATAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.18
14 9 0.32
15 1 0.04
16 4 0.14
17 7 0.25
18 2 0.07
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAAAGAAAAGAAA
Found at i:5888265 original size:10 final size:10
Alignment explanation
Indices: 5888252--5888322 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
5888242 AATTGATGGG
*
5888252 AAAAGATGAA
1 AAAAAATGAA
5888262 AAAAAATG-A
1 AAAAAATGAA
*
5888271 AAAACA--AA
1 AAAAAATGAA
5888279 AAAAAATGAGA
1 AAAAAATGA-A
**
5888290 AAAATAAACAA
1 AAAA-AATGAA
*
5888301 AAAAAATAAA
1 AAAAAATGAA
5888311 AAAAAAT-AA
1 AAAAAATGAA
5888320 AAA
1 AAA
5888323 TGAGAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
8 6 0.12
9 11 0.22
10 19 0.39
11 10 0.20
12 3 0.06
ACGTcount: A:0.82, C:0.03, G:0.07, T:0.08
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:5888282 original size:19 final size:18
Alignment explanation
Indices: 5888260--5888332 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
5888250 GGAAAAGATG
*
5888260 AAAAAAAATG-AAAAACA
1 AAAAAAAATGAAAAAAAA
5888277 AAAAAAAATGAGAAAAATAA
1 AAAAAAAATGA-AAAAA-AA
5888297 ACAAAAAAA--ATAAAAAAA
1 A-AAAAAAATGA-AAAAAAA
*
5888315 AATAAAAATGAGAAAAAA
1 AAAAAAAATGA-AAAAAA
5888333 GGAAAACTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 16 0.35
18 3 0.07
19 18 0.39
20 2 0.04
21 7 0.15
ACGTcount: A:0.82, C:0.03, G:0.07, T:0.08
Consensus pattern (18 bp):
AAAAAAAATGAAAAAAAA
Found at i:5888315 original size:23 final size:23
Alignment explanation
Indices: 5888272--5888320 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5888262 AAAAAATGAA
* *
5888272 AAACAAAAAAAAATGAGAAAAAT
1 AAACAAAAAAAAATAAAAAAAAT
5888295 AAAC-AAAAAAAATAAAAAAAAAT
1 AAACAAAAAAAAAT-AAAAAAAAT
5888318 AAA
1 AAA
5888321 AATGAGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.84, C:0.04, G:0.04, T:0.08
Consensus pattern (23 bp):
AAACAAAAAAAAATAAAAAAAAT
Found at i:5897546 original size:25 final size:24
Alignment explanation
Indices: 5897530--5897576 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5897520 TTTATTTTTT
*
5897530 TATTTTCCTATTTTTTTTATATAAA
1 TATTTTCC-ATTTTTTTTATTTAAA
*
5897555 TATTTTTCATTTTTTTTATTTA
1 TATTTTCCATTTTTTTTATTTA
5897577 CTTGTGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTTCCATTTTTTTTATTTAAA
Found at i:5897688 original size:22 final size:20
Alignment explanation
Indices: 5897640--5897691 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
5897630 TATTATGACA
*
5897640 TGTATAATTATATTTATTTT
1 TGTATGATTATATTTATTTT
*
5897660 TGCATGATTATAATTTATTATT
1 TGTATGATTAT-ATTTATT-TT
5897682 TGTATGATTA
1 TGTATGATTA
5897692 GTTATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
22 11 0.41
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (20 bp):
TGTATGATTATATTTATTTT
Found at i:5897698 original size:19 final size:19
Alignment explanation
Indices: 5897653--5897733 Score: 83
Period size: 19 Copynumber: 4.2 Consensus size: 19
5897643 ATAATTATAT
5897653 TTATT-TTTGCATGATTATAA
1 TTATTATTTGCATGA-T-TAA
* *
5897673 TTTATTATTTGTATGATTAG
1 -TTATTATTTGCATGATTAA
**
5897693 TTATTATTTGCAACATTAA
1 TTATTATTTGCATGATTAA
*
5897712 TTATTATTTGCATGATTTA
1 TTATTATTTGCATGATTAA
5897731 TTA
1 TTA
5897734 CATGGTATGA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
19 34 0.68
20 2 0.04
21 6 0.12
22 8 0.16
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.56
Consensus pattern (19 bp):
TTATTATTTGCATGATTAA
Found at i:5897767 original size:14 final size:14
Alignment explanation
Indices: 5897748--5897781 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5897738 GTATGATTTT
5897748 ATATTTATT-GCATG
1 ATATTT-TTGGCATG
5897762 ATATTTTTGGCATG
1 ATATTTTTGGCATG
5897776 ATATTT
1 ATATTT
5897782 CTCATTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 17 0.89
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (14 bp):
ATATTTTTGGCATG
Found at i:5899173 original size:29 final size:29
Alignment explanation
Indices: 5899119--5899193 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
5899109 ATGTATCTAC
* * ** *
5899119 TATTTATTCGTGCATATCAAGGTTATCCG
1 TATTTATTCATGTATATCAACATTATCCA
*
5899148 TATTTATTCATGTATATCAACATTATTCA
1 TATTTATTCATGTATATCAACATTATCCA
* *
5899177 TTTTTATTCATATATAT
1 TATTTATTCATGTATAT
5899194 TAGTGTTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.49
Consensus pattern (29 bp):
TATTTATTCATGTATATCAACATTATCCA
Found at i:5911324 original size:16 final size:17
Alignment explanation
Indices: 5911293--5911326 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5911283 AGTACACAAA
*
5911293 TATTTTTTTTCAAATTT
1 TATTATTTTTCAAATTT
5911310 TATTATTTTTC-AATTT
1 TATTATTTTTCAAATTT
5911326 T
1 T
5911327 GAAAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATTTTTCAAATTT
Found at i:5914985 original size:24 final size:24
Alignment explanation
Indices: 5914923--5914986 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
5914913 CGAGAACTCC
* *
5914923 TGGTCCACTGACCAACACAGTTCA
1 TGGTCCACTGACCATCACAGCTCA
* * *
5914947 CGGTCCACTGGCCATCGCAGCTCA
1 TGGTCCACTGACCATCACAGCTCA
5914971 TGGTCCACTGACCATC
1 TGGTCCACTGACCATC
5914987 CCACTTGTGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (24 bp):
TGGTCCACTGACCATCACAGCTCA
Found at i:5919997 original size:2 final size:2
Alignment explanation
Indices: 5919990--5920028 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5919980 ATTCTCATAT
5919990 TC TC TC TC TC TC 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 TC TC TC TC TC TC T
5920029 ATATATATAT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5920033 original size:2 final size:2
Alignment explanation
Indices: 5920028--5920066 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5920018 TCTCTCTCTC
5920028 TA TA TA TA TA 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 TA TA TA TA TA T
5920067 GCAGGATAAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5925673 original size:60 final size:61
Alignment explanation
Indices: 5925540--5925676 Score: 179
Period size: 61 Copynumber: 2.3 Consensus size: 61
5925530 TGGCGTAATA
*
5925540 AAAAACATTTTAAATAATCCTGTTCAATTTTTTTTAGGATTATTTAAAGCAATTTTTGGCT
1 AAAAACATCTTAAATAATCCTGTTCAATTTTTTTTAGGATTATTTAAAGCAATTTTTGGCT
* * ** * * *
5925601 AAAAATACCTTAAATAATTTTGTTCAATTTTTTTTAGGATTATTTAAGGC-GTTTTTAG-T
1 AAAAACATCTTAAATAATCCTGTTCAATTTTTTTTAGGATTATTTAAAGCAATTTTTGGCT
5925660 CAAAAACATCTTAAATA
1 -AAAAACATCTTAAATA
5925677 GTCTATTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 20 0.31
61 44 0.68
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (61 bp):
AAAAACATCTTAAATAATCCTGTTCAATTTTTTTTAGGATTATTTAAAGCAATTTTTGGCT
Found at i:5926260 original size:62 final size:61
Alignment explanation
Indices: 5926092--5926329 Score: 164
Period size: 62 Copynumber: 3.8 Consensus size: 61
5926082 TAATCCCCTT
* * * * ** * *
5926092 TAAACAAAATTAAAGA-TATTTAAGGCATTATTGAT-AAAAACGCCTTAAATAATT-TTTTT
1 TAAA-AAAATTAGAGATTATTTAAAGCATTTTTTATCAAAAATACCTTAAATAATTATCTTG
* * * *
5926151 TAAAAAAAATATTAGAGATTATTTCAGGTAATTTTTTTGTCAAAAATACCTTAAATAA-TATCTT
1 T--AAAAAA-ATTAGAGATTATTTAAAG-CA-TTTTTTATCAAAAATACCTTAAATAATTATCTT
5926215 -
61 G
* * * *
5926215 TTAAAAAATTAAAGAGTATTATTTAAAGCATTTTTTATCAAAAATATCTTAAGTAATTTTCTTG
1 TAAAAAAATT--AGAG-ATTATTTAAAGCATTTTTTATCAAAAATACCTTAAATAATTATCTTG
* * * *
5926279 TAAAAAAATTAGAGATTATTTACAGTA-TTTTTAGACAAAAACACCTTAAAT
1 TAAAAAAATTAGAGATTATTTAAAGCATTTTTTA-TCAAAAATACCTTAAAT
5926330 GATCTTCTCA
Statistics
Matches: 141, Mismatches: 24, Indels: 26
0.74 0.13 0.14
Matches are distributed among these distances:
59 1 0.01
60 9 0.06
61 37 0.26
62 40 0.28
63 11 0.08
64 25 0.18
65 18 0.13
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (61 bp):
TAAAAAAATTAGAGATTATTTAAAGCATTTTTTATCAAAAATACCTTAAATAATTATCTTG
Found at i:5926318 original size:61 final size:60
Alignment explanation
Indices: 5926154--5926329 Score: 178
Period size: 61 Copynumber: 2.9 Consensus size: 60
5926144 TTTTTTTTAA
*
5926154 AAAAAATATTAGAGATTATTT-CAGGTAATTTTTTTGTCAAAAATACCTTAAATAATATCTTT
1 AAAAAA-ATTAGAGATTATTTACA-GT-ATTTTTTAGTCAAAAATACCTTAAATAATATCTTT
* * * * * *
5926216 TAAAAAATTAAAGAGTATTATTTAAAGCATTTTTTA-TCAAAAATATCTTAAGTAATTTTCTTGT
1 AAAAAAATT--AGAG-ATTATTTACAGTATTTTTTAGTCAAAAATACCTTAAATAA-TATCTT-T
* *
5926280 AAAAAAATTAGAGATTATTTACAGTA-TTTTTAGACAAAAACACCTTAAAT
1 AAAAAAATTAGAGATTATTTACAGTATTTTTTAGTCAAAAATACCTTAAAT
5926330 GATCTTCTCA
Statistics
Matches: 93, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
60 6 0.06
61 27 0.29
62 26 0.28
63 16 0.17
64 17 0.18
65 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (60 bp):
AAAAAAATTAGAGATTATTTACAGTATTTTTTAGTCAAAAATACCTTAAATAATATCTTT
Found at i:5929020 original size:7 final size:7
Alignment explanation
Indices: 5928989--5929013 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5928979 ATTATTTAAA
5928989 AAAAAAT
1 AAAAAAT
5928996 AAAAAAT
1 AAAAAAT
5929003 AAAAAAT
1 AAAAAAT
5929010 AAAA
1 AAAA
5929014 TAAAAAAGAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:5929235 original size:59 final size:57
Alignment explanation
Indices: 5929051--5929285 Score: 316
Period size: 58 Copynumber: 4.1 Consensus size: 57
5929041 TTGTGCAGAA
5929051 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAATGTTATTTTTAAAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAT-TTATTTTTAAAG
* *
5929109 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAATTTTATTTTTAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAA-TTTATTTTTAAAG
* ** * *
5929167 AAAATTGATACTTTCAACTTTT-TTCCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCT-CAAAAATCCTTTTTTGAAA-TTT-ATTTTTAAAG
*
5929226 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTG--ATTT-TTATTTAAAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAATTTATT-TTTAAAG
5929281 AAAAT
1 AAAAT
5929286 AGAATAATAA
Statistics
Matches: 156, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
54 2 0.01
55 10 0.06
56 3 0.02
57 2 0.01
58 95 0.61
59 43 0.28
60 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAATTTATTTTTAAAG
Found at i:5929254 original size:117 final size:115
Alignment explanation
Indices: 5929049--5929276 Score: 352
Period size: 116 Copynumber: 2.0 Consensus size: 115
5929039 TCTTGTGCAG
* *
5929049 AAAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTGAAATGTTATTTTTAAAGAAAAT
1 AAAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTGAAATGTTATTTTCAAAGAAAAT
5929114 TGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAATTTTATTTTTAA
66 TGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTG-AATTTTATTTTTAA
* * *
5929165 AAAAAATTGATACTTTCAACTTTT-TTCCAAAAATATTTTTTTGAAACT-TTGATTTTCAAGGAA
1 AAAAAATTGATACTTTCAACTTTTCCT-CAAAAATACTTTTTTGAAA-TGTT-ATTTTCAAAGAA
*
5929228 AATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGATTTTTATTT
63 AATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAATTTTATTT
5929277 AAAGAAAATA
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
115 1 0.01
116 52 0.50
117 50 0.49
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (115 bp):
AAAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTTGAAATGTTATTTTCAAAGAAAAT
TGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAATTTTATTTTTAA
Found at i:5929308 original size:28 final size:26
Alignment explanation
Indices: 5929277--5929363 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 26
5929267 ATTTTTATTT
5929277 AAAGAAAATAGAATAATAAAACAAAATA
1 AAAGAAAATA-AATAATAAAA-AAAATA
*
5929305 AAAGTGAAAATAAATAA-AAAAATAAAGA
1 AAA--GAAAATAAATAATAAAAA-AAATA
*
5929333 AAAGTAAAACAAA-AATAAAAATAAAATA
1 AAAG-AAAATAAATAAT-AAAA-AAAATA
5929361 AAA
1 AAA
5929364 ATAAAAGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
26 3 0.06
27 8 0.16
28 25 0.51
29 6 0.12
30 7 0.14
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (26 bp):
AAAGAAAATAAATAATAAAAAAAATA
Found at i:5929335 original size:11 final size:10
Alignment explanation
Indices: 5929291--5929369 Score: 59
Period size: 11 Copynumber: 7.2 Consensus size: 10
5929281 AAAATAGAAT
*
5929291 AATAAAACAA
1 AATAAAAAAA
*
5929301 AATAAAAGTGAA
1 AATAAAA--AAA
5929313 AATAAATAAAAA
1 AAT-AA-AAAAA
*
5929325 AATAAAGAAA
1 AATAAAAAAA
*
5929335 AGTAAAACAAA
1 AATAAAA-AAA
5929346 AATAAAAATAA
1 AATAAAAA-AA
5929357 AATAAAAATAA
1 AATAAAAA-AA
5929368 AA
1 AA
5929370 GAATATTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
10 17 0.30
11 26 0.46
12 10 0.18
13 2 0.04
14 2 0.04
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:5929347 original size:6 final size:6
Alignment explanation
Indices: 5929299--5929369 Score: 56
Period size: 6 Copynumber: 11.5 Consensus size: 6
5929289 ATAATAAAAC
* * * *
5929299 AAAATA AAAGTG AAAATA AATAA-A AAAATA AAGAAAA GTAAAACA AAAATA
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AA-AATA --AAAATA AAAATA
5929350 AAAAT- AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAA
5929370 GAATATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
5 7 0.13
6 35 0.67
7 5 0.10
8 3 0.06
9 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:5929399 original size:4 final size:4
Alignment explanation
Indices: 5929392--5929423 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
5929382 AACTTAAACT
5929392 AATA AATAA AATA AATA AATA AATA AATA AAT
1 AATA AAT-A AATA AATA AATA AATA AATA AAT
5929424 TCAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:5929412 original size:17 final size:17
Alignment explanation
Indices: 5929312--5929423 Score: 62
Period size: 17 Copynumber: 6.8 Consensus size: 17
5929302 ATAAAAGTGA
*
5929312 AAAT-AAATAAAAAAAT
1 AAATAAAATAAATAAAT
*
5929328 AAAGAAAAGTAAA-ACAA-
1 AAATAAAA-TAAATA-AAT
5929345 AAATAAAAATAAA-ATAA-
1 AAAT-AAAATAAATA-AAT
* *
5929362 AAATAAAA-GAAT-ATT
1 AAATAAAATAAATAAAT
*
5929377 AAATAAACTTAAACT-AAT
1 AAATAAA-ATAAA-TAAAT
5929395 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
5929412 AAAT-AAATAAAT
1 AAATAAAATAAAT
5929424 TCAAAAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.01
15 9 0.12
16 16 0.21
17 31 0.40
18 20 0.26
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:5929423 original size:12 final size:13
Alignment explanation
Indices: 5929312--5929423 Score: 69
Period size: 12 Copynumber: 8.6 Consensus size: 13
5929302 ATAAAAGTGA
5929312 AAATAAATAAAA-
1 AAATAAATAAAAT
*
5929324 AAATAAAGAAAAGT
1 AAATAAATAAAA-T
*
5929338 AAA-ACA-AAAAT
1 AAATAAATAAAAT
5929349 -AA-AAATAAAAT
1 AAATAAATAAAAT
5929360 AAAAATAAA-AGAATATT
1 --AAATAAATA-AA-A-T
*
5929377 AAATAAACTTAAACT
1 AAATAAA--TAAAAT
5929392 -AATAAATAAAAT
1 AAATAAATAAAAT
5929404 AAATAAAT-AAAT
1 AAATAAATAAAAT
5929416 AAATAAAT
1 AAATAAAT
5929424 TCAAAAAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
10 4 0.05
11 6 0.07
12 32 0.40
13 9 0.11
14 12 0.15
15 13 0.16
16 1 0.01
17 3 0.04
18 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:5930325 original size:21 final size:21
Alignment explanation
Indices: 5930301--5930364 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
5930291 AAAAAATAAC
5930301 AGATAATTAAAAATAATAATA
1 AGATAATTAAAAATAATAATA
* * *
5930322 AGATAAATCAAAAAT-ATTACA
1 AGAT-AATTAAAAATAATAATA
*
5930343 AGATAAATAAAAATAATAATA
1 AGATAATTAAAAATAATAATA
5930364 A
1 A
5930365 TAAATAAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 8 0.24
21 17 0.50
22 9 0.26
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (21 bp):
AGATAATTAAAAATAATAATA
Found at i:5930370 original size:4 final size:4
Alignment explanation
Indices: 5930345--5930499 Score: 52
Period size: 4 Copynumber: 37.2 Consensus size: 4
5930335 ATATTACAAG
*
5930345 ATAA ATAA AAATA AT-A AT-A ATAA ATAA ATTATA ATATA AT-A ATAA
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATAA A-TA-A ATA-A ATAA ATAA
* * * * *
5930390 GTAT ATAA CTAG ATAA ATAAA ATACA TATAA ATATTA ACAGA A-AA A-AA
1 ATAA ATAA ATAA ATAA AT-AA ATA-A -ATAA ATA--A ATA-A ATAA ATAA
* * * * * *
5930438 ATAA ATAA ATAA ATAA AGAT ATAC ATAT ATTA ATAC ATAGTA AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA
5930487 ATAA ATAA ATAA A
1 ATAA ATAA ATAA A
5930500 AATACATAAG
Statistics
Matches: 115, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
3 17 0.15
4 70 0.61
5 18 0.16
6 10 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:5930380 original size:14 final size:14
Alignment explanation
Indices: 5930311--5930508 Score: 59
Period size: 14 Copynumber: 13.4 Consensus size: 14
5930301 AGATAATTAA
5930311 AAATAATAATAAGAT
1 AAATAATAATAA-AT
* * *
5930326 AAATCAAAAATATTAC
1 AAAT-AATAATA-AAT
5930342 AAGATAAATAA-AAAT
1 AA-AT-AATAATAAAT
5930357 -AATAATAATAAAT
1 AAATAATAATAAAT
*
5930370 AAATTATAATATAAT
1 AAATAATAATA-AAT
*
5930385 AATAAGTATATAACTAGAT
1 -A-AA-TA-ATAA-TAAAT
5930404 AAATAA-AATACATAT
1 AAATAATAATA-A-AT
* *
5930419 AAATATTAACAGAA-
1 AAATAATAATA-AAT
*
5930433 AAAAAATAAATAAAT
1 AAATAAT-AATAAAT
* *
5930448 AAATAA-AGATATAC
1 AAATAATA-ATAAAT
* * *
5930462 ATATATTAATACAT
1 AAATAATAATAAAT
*
5930476 -AGTAATAATAAAT
1 AAATAATAATAAAT
5930489 AAATAAATAA-AAAT
1 AAAT-AATAATAAAT
*
5930503 ACATAA
1 AAATAA
5930509 GATACAAAGG
Statistics
Matches: 133, Mismatches: 30, Indels: 42
0.65 0.15 0.20
Matches are distributed among these distances:
12 5 0.04
13 20 0.15
14 40 0.30
15 31 0.23
16 17 0.13
17 10 0.08
18 2 0.02
19 6 0.05
20 2 0.02
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:5930406 original size:34 final size:30
Alignment explanation
Indices: 5930345--5930407 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
5930335 ATATTACAAG
5930345 ATAAATAAAAATAATAATAATAAATAAATT
1 ATAAATAAAAATAATAATAATAAATAAATT
* *
5930375 ATAATATAATAATAAGTATATAACTAGATAAAT
1 ATAA-ATAAAAATAA-TA-ATAA-TAAATAAAT
5930408 AAAATACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.15
31 9 0.33
32 2 0.07
33 4 0.15
34 8 0.30
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (30 bp):
ATAAATAAAAATAATAATAATAAATAAATT
Found at i:5930553 original size:17 final size:17
Alignment explanation
Indices: 5930533--5930572 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5930523 AAAAAAAGAT
5930533 ATAAAATAAAAATA-AAA
1 ATAAAAT-AAAATACAAA
*
5930550 ATAATATAAAATACAAA
1 ATAAAATAAAATACAAA
5930567 ATAAAA
1 ATAAAA
5930573 GCCAAATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAATAAAATACAAA
Found at i:5930741 original size:10 final size:10
Alignment explanation
Indices: 5930726--5930761 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
5930716 GACATTTTTA
5930726 TTTTTTGTTT
1 TTTTTTGTTT
5930736 TTTTTTGTTT
1 TTTTTTGTTT
5930746 TTTTTT-TTT
1 TTTTTTGTTT
*
5930755 GTTTTTG
1 TTTTTTG
5930762 ACCAAAGCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:5930746 original size:17 final size:16
Alignment explanation
Indices: 5930720--5930754 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5930710 CAACTCGACA
5930720 TTTTTATTTTTTGTTTT
1 TTTTTATTTTTT-TTTT
*
5930737 TTTTTGTTTTTTTTTT
1 TTTTTATTTTTTTTTT
5930753 TT
1 TT
5930755 GTTTTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (16 bp):
TTTTTATTTTTTTTTT
Found at i:5930749 original size:13 final size:13
Alignment explanation
Indices: 5930720--5930760 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
5930710 CAACTCGACA
*
5930720 TTTTTATTTT-TT
1 TTTTTTTTTTGTT
*
5930732 GTTTTTTTTTGTT
1 TTTTTTTTTTGTT
5930745 TTTTTTTTTTGTT
1 TTTTTTTTTTGTT
5930758 TTT
1 TTT
5930761 GACCAAAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.02, C:0.00, G:0.07, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:5930904 original size:41 final size:41
Alignment explanation
Indices: 5930768--5931070 Score: 322
Period size: 41 Copynumber: 7.1 Consensus size: 41
5930758 TTTGACCAAA
* * * * * *
5930768 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATG
1 GCTCCTCTAAACAGAGGCACCATGACTTTGA-AAA-GTAAATT
* * * ** *
5930811 GCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCATGACTTT-GAAAAGTAAATT
*
5930853 GCTCCTCTAAATAGAGGCACCATGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCATGAC-TTTGAAAAGTAAATT
5930894 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATATAAATT
1 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAG------TAAATT
* *
5930941 GCTCCTCTAAACAGAGGCACCACGAATTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATT
*
5930982 GCTCCTCTAAACAGAGGCACCATGACTTTGAGAAAGTAAATC
1 GCTCCTCTAAACAGAGGCACCATGACTTTGA-AAAGTAAATT
* *
5931024 ACTCCTCTAAACAGAGGCAACA-GAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCATG-ACTTTGAAAAGTAAATT
5931065 GCTCCT
1 GCTCCT
5931071 TGACAATCAT
Statistics
Matches: 229, Mismatches: 20, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
40 4 0.02
41 88 0.38
42 63 0.28
43 33 0.14
44 2 0.01
47 39 0.17
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATT
Found at i:5930911 original size:83 final size:82
Alignment explanation
Indices: 5930768--5931070 Score: 322
Period size: 83 Copynumber: 3.6 Consensus size: 82
5930758 TTTGACCAAA
* * * * * * * *
5930768 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGCTCAA
1 GCTCCTCTAAACAGAGGCACCA-GACTTTGA-AAA-GTAAATTGCTCCTCTAAACAGAGGCACCA
**
5930833 CAACTTTGGAAAAATAAATT
63 TGACTTTGGAAAAATAAATT
*
5930853 GCTCCTCTAAATAGAGGCACCATGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAT
1 GCTCCTCTAAACAGAGGCACCA-GAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAT
*
5930917 GACTTTGAAAAGTAAATATAAATT
64 GACTTTG----G-AAAAATAAATT
*
5930941 GCTCCTCTAAACAGAGGCACCACGAATTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATG
1 GCTCCTCTAAACAGAGGCACCA-GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATG
* *
5931006 ACTTT-GAGAAAGTAAATC
65 ACTTTGGA-AAAATAAATT
* *
5931024 ACTCCTCTAAACAGAGGCAACAGAACTTTGAAAAGTAAATTGCTCCT
1 GCTCCTCTAAACAGAGGCACCAG-ACTTTGAAAAGTAAATTGCTCCT
5931071 TGACAATCAT
Statistics
Matches: 187, Mismatches: 22, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
82 2 0.01
83 80 0.43
84 3 0.02
85 21 0.11
86 4 0.02
87 5 0.03
88 72 0.39
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCAGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATGA
CTTTGGAAAAATAAATT
Found at i:5930962 original size:88 final size:86
Alignment explanation
Indices: 5930768--5931070 Score: 329
Period size: 88 Copynumber: 3.5 Consensus size: 86
5930758 TTTGACCAAA
* * * * * * * *
5930768 GCTCCTCTAAGCAGAGGCTCAACGACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGGCTCAA
1 GCTCCTCTAAACAGAGGCACCA-GACTTTGA-AAA-GTAAATTGCTCCTCTAAACAGAGGCACCA
**
5930833 CAACTTTG-G-AA--AAATAAATT
63 TGACTTTGAGAAAGTAAATAAATT
*
5930853 GCTCCTCTAAATAGAGGCACCATGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAT
1 GCTCCTCTAAACAGAGGCACCA-GAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAT
5930917 GACTTTGA-AAAGTAAATATAAATT
64 GACTTTGAGAAAGT-AA-ATAAATT
*
5930941 GCTCCTCTAAACAGAGGCACCACGAATTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATG
1 GCTCCTCTAAACAGAGGCACCA-GACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATG
*
5931006 ACTTTGAGAAAGTAAAT-CA--
65 ACTTTGAGAAAGTAAATAAATT
*
5931025 -CTCCTCTAAACAGAGGCAACAGAACTTTGAAAAGTAAATTGCTCCT
1 GCTCCTCTAAACAGAGGCACCAG-ACTTTGAAAAGTAAATTGCTCCT
5931071 TGACAATCAT
Statistics
Matches: 190, Mismatches: 18, Indels: 22
0.83 0.08 0.10
Matches are distributed among these distances:
82 1 0.01
83 72 0.38
84 5 0.03
85 21 0.11
86 5 0.03
87 8 0.04
88 73 0.38
89 5 0.03
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (86 bp):
GCTCCTCTAAACAGAGGCACCAGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCATGA
CTTTGAGAAAGTAAATAAATT
Found at i:5931030 original size:130 final size:130
Alignment explanation
Indices: 5930804--5931063 Score: 382
Period size: 130 Copynumber: 2.0 Consensus size: 130
5930794 TTTGAGAAAC
* * *
5930804 ATAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAAATAAATTGCTCCTCTAAATAGAG
1 ATAAATGGCTCCTCTAAACAGAGGCACAACAACTTTGGAAAAATAAATTGCTCCTCTAAACAGAG
* ** *
5930869 GCACCATGACTTTTGAAAGTAAATTGCTCCTCTAAACAGAGGCACCATG-ACTTTGAAAAGTAAA
66 GCACCATGACTTTAGAAAGTAAATCACTCCTCTAAACAGAGGCAACA-GAACTTTGAAAAGTAAA
5930933 T
130 T
* * *
5930934 ATAAATTGCTCCTCTAAACAGAGGCACCACGAA-TTT-GAAAAGTAAATTGCTCCTCTAAACAGA
1 ATAAATGGCTCCTCTAAACAGAGGCACAAC-AACTTTGGAAAAATAAATTGCTCCTCTAAACAGA
5930997 GGCACCATGACTTTGAGAAAGTAAATCACTCCTCTAAACAGAGGCAACAGAACTTTGAAAAGTAA
65 GGCACCATGACTTT-AGAAAGTAAATCACTCCTCTAAACAGAGGCAACAGAACTTTGAAAAGTAA
5931062 AT
129 AT
5931064 TGCTCCTTGA
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
129 40 0.34
130 75 0.64
131 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (130 bp):
ATAAATGGCTCCTCTAAACAGAGGCACAACAACTTTGGAAAAATAAATTGCTCCTCTAAACAGAG
GCACCATGACTTTAGAAAGTAAATCACTCCTCTAAACAGAGGCAACAGAACTTTGAAAAGTAAAT
Found at i:5932737 original size:8 final size:8
Alignment explanation
Indices: 5932726--5932756 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
5932716 GTTTTCTCTT
5932726 TTTTTTCA
1 TTTTTTCA
5932734 TTTTTTCA
1 TTTTTTCA
5932742 TTTTTTCA
1 TTTTTTCA
5932750 TTCTTTT
1 TT-TTTT
5932757 TTTCTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:5932741 original size:27 final size:28
Alignment explanation
Indices: 5932710--5932767 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
5932700 AAAATCACCC
5932710 TTTCAGGTTTTC--TCTTTTTTTTCATTT
1 TTTCAGGTTTTCATTC-TTTTTTTCATTT
** *
5932737 TTTCATTTTTTCATTCTTTTTTTCTTTT
1 TTTCAGGTTTTCATTCTTTTTTTCATTT
5932765 TTT
1 TTT
5932768 TTCTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 10 0.38
28 14 0.54
29 2 0.08
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (28 bp):
TTTCAGGTTTTCATTCTTTTTTTCATTT
Found at i:5932808 original size:32 final size:32
Alignment explanation
Indices: 5932726--5932808 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 32
5932716 GTTTTCTCTT
*
5932726 TTTTTTCATTTTTTCA--TTTTTTCATTC-T-
1 TTTTTTCTTTTTTTCATTTTTTTTCATTCATC
*
5932754 TTTTTTCTTTTTTTTTCTTTTTTTTTCA-TCATC
1 TTTTTTC--TTTTTTTCATTTTTTTTCATTCATC
5932787 TTTTTTCTTTTTTCTCATTTTT
1 TTTTTTCTTTTTT-TCATTTTT
5932809 CATCCATTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
28 7 0.16
30 7 0.16
31 8 0.18
32 16 0.36
33 7 0.16
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.78
Consensus pattern (32 bp):
TTTTTTCTTTTTTTCATTTTTTTTCATTCATC
Found at i:5933144 original size:10 final size:10
Alignment explanation
Indices: 5933129--5933157 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5933119 GTGGCATTTA
5933129 TTTTTTTTTC
1 TTTTTTTTTC
5933139 TTTTTTTTTC
1 TTTTTTTTTC
5933149 TTTTTTTTT
1 TTTTTTTTT
5933158 TATTTTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:5933145 original size:11 final size:11
Alignment explanation
Indices: 5933129--5933164 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
5933119 GTGGCATTTA
5933129 TTTTTTTTTC-
1 TTTTTTTTTCT
5933139 TTTTTTTTTCT
1 TTTTTTTTTCT
*
5933150 TTTTTTTTTAT
1 TTTTTTTTTCT
5933161 TTTT
1 TTTT
5933165 GAGACCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:5933163 original size:10 final size:10
Alignment explanation
Indices: 5933125--5933164 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
5933115 AAGTGTGGCA
5933125 TTTATTTTTT
1 TTTATTTTTT
*
5933135 TTTCTTTTTT
1 TTTATTTTTT
*
5933145 TTTCTTTTTTT
1 TTT-ATTTTTT
5933156 TTTATTTTT
1 TTTATTTTT
5933165 GAGACCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTATTTTTT
Found at i:5935066 original size:12 final size:12
Alignment explanation
Indices: 5935049--5935083 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
5935039 TCCACTTTTA
5935049 CCTTTTCTTTCT
1 CCTTTTCTTTCT
*
5935061 CTTTTTCTTTCT
1 CCTTTTCTTTCT
5935073 CCTTTTCTTTC
1 CCTTTTCTTTC
5935084 AGACCATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
CCTTTTCTTTCT
Found at i:5936168 original size:30 final size:31
Alignment explanation
Indices: 5936107--5936168 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
5936097 GCACATGCTT
*
5936107 ATGAATGACATAATTAACAAAATAAATAAAC
1 ATGAATGACATAATTAACAAAATAAACAAAC
* *
5936138 ATGAATGA-ATAA-TAACACATATATACAAAC
1 ATGAATGACATAATTAACA-AAATAAACAAAC
5936168 A
1 A
5936169 GGTTCAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 14 0.52
31 8 0.30
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (31 bp):
ATGAATGACATAATTAACAAAATAAACAAAC
Found at i:5936927 original size:117 final size:114
Alignment explanation
Indices: 5936714--5937085 Score: 482
Period size: 117 Copynumber: 3.2 Consensus size: 114
5936704 TTGTGCAGAA
* * * *
5936714 AAAATTGATACTTTCAAATTTTTCCTAAAAATATTCTTTT-AAAATTTTAATTTCGAGAAAAATT
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATT-TTTTGAAAATTTTATTTTCAAG-AAAATT
5936778 GATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTTAAGG
64 GATACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTA-TTTTTAAGG
*
5936830 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTGATTTTCAAGAACAATT
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAA-TTTTATTTTCAAGAA-AATT
* *
5936895 GATACTTTCAACTTTTCCTCAAAAACCCTTTTTTG-AAATGTTATTTTTAAAG
64 GATACTTTCAACTTTTCCTCAAAAA-CTTTTTTTGAAAAT-TTATTTTTAAGG
** *
5936947 AAAATTGATACTTTCAAC-TTTTCCTCAAAAACCCTTTTTTG-AAATTTTATTTTTAAAGAAAAT
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAA-TATTTTTTGAAAATTTTA-TTTTCAAGAAAAT
* * * *
5937010 TGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
63 TGATACTTTCAACTTTTCCTCAAAAA-CTTTTTTTGAAAATTT-ATTTTTAAGG
5937064 AAAATTGATACTTTCAACTTTT
1 AAAATTGATACTTTCAACTTTT
5937086 CCTTAAAAAT
Statistics
Matches: 227, Mismatches: 18, Indels: 20
0.86 0.07 0.08
Matches are distributed among these distances:
115 4 0.02
116 86 0.38
117 116 0.51
118 21 0.09
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (114 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAATTTTATTTTCAAGAAAATTGA
TACTTTCAACTTTTCCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGG
Found at i:5936953 original size:175 final size:175
Alignment explanation
Indices: 5936772--5937103 Score: 562
Period size: 175 Copynumber: 1.9 Consensus size: 175
5936762 AATTTCGAGA
* *
5936772 AAAATTGATACTTTCAACTTTTCCTCAAAAA-CTTTTTTTGAAAATTTATTTTTTAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTA-TTTTTAAAGAAAATT
5936836 GATACTTTCAACTTTTTCCCAAAAATA-TTTTTTGAAAACTTTGATTTTCAA-GAACAATTGATA
65 GATACTTTCAACTTTTTCCCAAAAATATTTTTTTG-AAACTTTGATTTTCAAGGAA-AATTGATA
5936899 CTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAATGTTATTTTTAAAG
128 CTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAATGTTATTTTTAAAG
*
5936947 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAATTTTATTTTTAAAGAAAATTG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAAAGAAAATTG
*
5937012 ATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATTGATACTT
66 ATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATTGATACTT
* *
5937077 TCAACTTTTCCTTAAAAATCCTTTTTT
131 TCAACTTTTCCTCAAAAACCCTTTTTT
5937104 TATTTTTATT
Statistics
Matches: 148, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
175 123 0.83
176 25 0.17
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.45
Consensus pattern (175 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAAAGAAAATTG
ATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATTGATACTT
TCAACTTTTCCTCAAAAACCCTTTTTTGAAATGTTATTTTTAAAG
Found at i:5937102 original size:58 final size:56
Alignment explanation
Indices: 5936714--5937102 Score: 399
Period size: 58 Copynumber: 6.7 Consensus size: 56
5936704 TTGTGCAGAA
* ** * * * *
5936714 AAAATTGATACTTTCAAATTTTTCCT-AAAAATATTCTTTTAAAATTTTAATTTCGAGA
1 AAAATTGATACTTTC-AACTTTTCCTCAAAAATCCT-TTTTGAAA-TTTATTTTCAAGG
* *
5936772 AAAATTGATACTTTCAACTTTTCCTCAAAAA-CTTTTTTTGAAAATTTATTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATC-CTTTTTG-AAATTTA-TTTTCAAGG
**
5936830 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGAAAACTTTGATTTTCAA-G
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATCCTTTTTG-AAA-TTT-ATTTTCAAGG
* * *
5936888 AACAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAATGTTATTTTTAAAG
1 AA-AATTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTGAAAT-TTATTTTCAAGG
* * *
5936947 AAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTGAAATTTTATTTTTAAAG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCC-TTTTTGAAA-TTTATTTTCAAGG
* **
5937005 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAT-CCTTTTTGAAA-TTT-ATTTTCAAGG
*
5937064 AAAATTGATACTTTCAACTTTTCCTTAAAAATCCTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTT
5937103 TTATTTTTAT
Statistics
Matches: 291, Mismatches: 24, Indels: 32
0.84 0.07 0.09
Matches are distributed among these distances:
57 17 0.06
58 183 0.63
59 84 0.29
60 7 0.02
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (56 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTGAAATTTATTTTCAAGG
Found at i:5938124 original size:20 final size:20
Alignment explanation
Indices: 5938099--5938155 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
5938089 AAAAAAAAAG
*
5938099 AAAAAAAATCTGATAAACGA
1 AAAAAAAATCAGATAAACGA
5938119 AAAAAAAATCAGATAAACGA
1 AAAAAAAATCAGATAAACGA
*
5938139 AAAAAAATAACAGATAA
1 AAAAAAA-ATCAGATAA
5938156 TTAAAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (20 bp):
AAAAAAAATCAGATAAACGA
Found at i:5938162 original size:21 final size:20
Alignment explanation
Indices: 5938139--5938222 Score: 91
Period size: 21 Copynumber: 4.2 Consensus size: 20
5938129 AGATAAACGA
* *
5938139 AAAAAAATAA-CAGATAATT
1 AAAAAAATAATAAGATAAAT
5938158 AAAAATAATAATAAGATAAAT
1 AAAAA-AATAATAAGATAAAT
* *
5938179 AAAAAATATTACAAGATAAAT
1 AAAAAA-ATAATAAGATAAAT
5938200 AAAAATAATAATAA-ATAAAT
1 AAAAA-AATAATAAGATAAAT
5938220 AAA
1 AAA
5938223 TTATAATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
19 5 0.09
20 15 0.27
21 34 0.62
22 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (20 bp):
AAAAAAATAATAAGATAAAT
Found at i:5938176 original size:42 final size:42
Alignment explanation
Indices: 5938129--5938218 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
5938119 AAAAAAAATC
*
5938129 AGATAAACGAAAAAAAATAAC-AGATAATTAAAAATAATAATA
1 AGATAAA-GAAAAAAAATAACAAGATAAATAAAAATAATAATA
* * *
5938171 AGATAAATAAAAAATATTACAAGATAAATAAAAATAATAATA
1 AGATAAAGAAAAAAAATAACAAGATAAATAAAAATAATAATA
5938213 A-ATAAA
1 AGATAAA
5938219 TAAATTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 15 0.35
42 28 0.65
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (42 bp):
AGATAAAGAAAAAAAATAACAAGATAAATAAAAATAATAATA
Found at i:5938216 original size:4 final size:4
Alignment explanation
Indices: 5938194--5938361 Score: 87
Period size: 4 Copynumber: 41.0 Consensus size: 4
5938184 ATATTACAAG
*
5938194 ATAA ATAA AAATA AT-A ATAA ATAA ATAA ATTATA ATATA AT-A ATAA
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATAA A-TA-A ATA-A ATAA ATAA
* * * * *
5938240 ATAT ATAA CTAG ATAA ATAAA ATACA TATAA AT-A TTAA CAGAA A-AA
1 ATAA ATAA ATAA ATAA AT-AA ATA-A -ATAA ATAA ATAA -ATAA ATAA
* * * * * *
5938286 ATAA ATAA ATAA ATAA AGAT ATAC ATAT ATTA ATAC ATAGTA AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA
*
5938335 ATAA ATAA ATAA AT-A ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
5938362 GATACAAAGG
Statistics
Matches: 126, Mismatches: 23, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
3 17 0.13
4 84 0.67
5 18 0.14
6 7 0.06
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:5938222 original size:8 final size:8
Alignment explanation
Indices: 5938167--5938361 Score: 89
Period size: 8 Copynumber: 23.6 Consensus size: 8
5938157 TAAAAATAAT
5938167 AATAAGATA
1 AATAA-ATA
5938176 AATAAA-A
1 AATAAATA
* *
5938183 AATATTACA
1 AATA-AATA
5938192 AGATAAATA
1 A-ATAAATA
*
5938201 AAAATAAT-
1 AATA-AATA
5938209 AATAAATA
1 AATAAATA
5938217 AATAAATTA
1 AATAAA-TA
5938226 TAATATAAT-
1 -AATA-AATA
5938235 AATAAATA
1 AATAAATA
* *
5938243 TATAACTA
1 AATAAATA
*
5938251 GATAAATAA
1 AATAAAT-A
5938260 AATACATATA
1 AATA-A-ATA
*
5938270 AAT-ATTA
1 AATAAATA
*
5938277 ACAGAAA-A
1 A-ATAAATA
5938285 AATAAATA
1 AATAAATA
5938293 AATAAATA
1 AATAAATA
* *
5938301 AAGATATA
1 AATAAATA
* * *
5938309 CATATATT
1 AATAAATA
*
5938317 AATACATA
1 AATAAATA
5938325 GTAAT-AATA
1 --AATAAATA
5938334 AATAAATA
1 AATAAATA
5938342 AATAAAT-
1 AATAAATA
5938349 AATAAATA
1 AATAAATA
*
5938357 CATAA
1 AATAA
5938362 GATACAAAGG
Statistics
Matches: 143, Mismatches: 24, Indels: 39
0.69 0.12 0.19
Matches are distributed among these distances:
7 28 0.20
8 72 0.50
9 23 0.16
10 16 0.11
11 4 0.03
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.28
Consensus pattern (8 bp):
AATAAATA
Found at i:5938240 original size:42 final size:42
Alignment explanation
Indices: 5938152--5938347 Score: 138
Period size: 42 Copynumber: 4.7 Consensus size: 42
5938142 AAAATAACAG
* * * * *
5938152 ATAATTAAAAATAATAATAAGATAAATAAAAAATATTACAA-G
1 ATAAATAAAAATAATAATAA-ATAAATAAAATATAATATAATA
*
5938194 ATAAATAAAAATAATAATAAATAAATAAATTATAATATAATA
1 ATAAATAAAAATAATAATAAATAAATAAAATATAATATAATA
* * *
5938236 ATAAAT--ATATAACTAGATAAATAAA-ATACATATAA-ATATTA
1 ATAAATAAAAATAA-TA-ATAAATAAATA-AAATATAATATAATA
* * *
5938277 ACAGA-AAAAAT-A-AATAAATAAATAAAGATATACATATATTA
1 ATAAATAAAAATAATAATAAATAAATAAA-ATATA-ATATAATA
* **
5938318 ATACATAGTAATAATAAATAAATAAATAAA
1 ATAAATAAAAATAAT-AATAAATAAATAAA
5938348 TAATAAATAC
Statistics
Matches: 122, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
38 10 0.08
39 7 0.06
40 6 0.05
41 37 0.30
42 47 0.39
43 1 0.01
45 14 0.11
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (42 bp):
ATAAATAAAAATAATAATAAATAAATAAAATATAATATAATA
Found at i:5938259 original size:26 final size:25
Alignment explanation
Indices: 5938194--5938269 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
5938184 ATATTACAAG
* *
5938194 ATAAAT-AAAAATAATAATAAATAA
1 ATAAATGATAAATAATAATAAATAT
*
5938218 ATAAATTATAATATAATAATAAATAT
1 ATAAATGATAA-ATAATAATAAATAT
* *
5938244 ATAACTAGATAAATAA-AATACATAT
1 ATAAAT-GATAAATAATAATAAATAT
5938269 A
1 A
5938270 AATATTAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
24 6 0.14
25 12 0.27
26 22 0.50
27 4 0.09
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (25 bp):
ATAAATGATAAATAATAATAAATAT
Found at i:5938291 original size:29 final size:29
Alignment explanation
Indices: 5938227--5938300 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
5938217 AATAAATTAT
* *
5938227 AATATAAT-AATAAATATATAACTAGATA
1 AATAAAATAAATAAATATATAACTAGAAA
5938255 AATAAAATACATATAAATAT-TAAC-AGAAA
1 AATAAAATA-A-ATAAATATATAACTAGAAA
5938284 AA-ATAAATAAATAAATA
1 AATA-AAATAAATAAATA
5938301 AAGATATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 7 0.17
28 9 0.22
29 11 0.28
30 5 0.12
31 8 0.20
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (29 bp):
AATAAAATAAATAAATATATAACTAGAAA
Found at i:5938405 original size:17 final size:17
Alignment explanation
Indices: 5938385--5938424 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5938375 AAAAAAAGAT
5938385 ATAAAATAAAAATA-AAA
1 ATAAAAT-AAAATACAAA
*
5938402 ATAATATAAAATACAAA
1 ATAAAATAAAATACAAA
5938419 ATAAAA
1 ATAAAA
5938425 GCCAAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAATAAAATACAAA
Found at i:5945244 original size:19 final size:19
Alignment explanation
Indices: 5945205--5945244 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5945195 TGAAAATGCT
* **
5945205 AAAATGTTAATGTTTCTTA
1 AAAATGTTAATGGTTAATA
5945224 AAAATGTTAATGGTTAATA
1 AAAATGTTAATGGTTAATA
5945243 AA
1 AA
5945245 TTTCCTTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (19 bp):
AAAATGTTAATGGTTAATA
Found at i:5946201 original size:16 final size:17
Alignment explanation
Indices: 5946172--5946205 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5946162 AAATGAAAAT
*
5946172 TTTTATTATTATTAGAC
1 TTTTATTATAATTAGAC
5946189 TTTT-TTATAATTAGAC
1 TTTTATTATAATTAGAC
5946205 T
1 T
5946206 AAAAAAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTTATTATAATTAGAC
Found at i:5948349 original size:17 final size:17
Alignment explanation
Indices: 5948304--5948349 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
5948294 GGATTTTAAT
5948304 ATTTTTATATAATAAAA
1 ATTTTTATATAATAAAA
* *
5948321 ATTTATGTATAATAAAA
1 ATTTTTATATAATAAAA
* *
5948338 TTTTTTAAATAA
1 ATTTTTATATAA
5948350 AGGAAAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTTTTATATAATAAAA
Found at i:5950581 original size:11 final size:11
Alignment explanation
Indices: 5950567--5950661 Score: 51
Period size: 11 Copynumber: 8.9 Consensus size: 11
5950557 AATGGATAGT
5950567 TAATAACTTAG
1 TAATAACTTAG
*
5950578 TAATTAA-TTAT
1 TAA-TAACTTAG
*
5950589 TAAAAACTTA-
1 TAATAACTTAG
5950599 -AATGTAA-TTAG
1 TAA--TAACTTAG
5950610 T-ATAACTTAG
1 TAATAACTTAG
* *
5950620 TAGTAA--TAA
1 TAATAACTTAG
5950629 TCAATAACTTAG
1 T-AATAACTTAG
* *
5950641 TAGTAAATTAG
1 TAATAACTTAG
5950652 TAATAACTTA
1 TAATAACTTA
5950662 ACAGTAAATG
Statistics
Matches: 62, Mismatches: 11, Indels: 22
0.65 0.12 0.23
Matches are distributed among these distances:
9 8 0.13
10 14 0.23
11 34 0.55
12 6 0.10
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.38
Consensus pattern (11 bp):
TAATAACTTAG
Found at i:5950640 original size:63 final size:66
Alignment explanation
Indices: 5950568--5950693 Score: 161
Period size: 63 Copynumber: 2.0 Consensus size: 66
5950558 ATGGATAGTT
* * * *
5950568 AATAACTTAGTAATTAATTATTAAAAACTTAA-ATGT-AATTAGT-ATAACTTAGTAG-TAATAA
1 AATAACTTAGTAATAAATTAGTAAAAACTTAACA-GTAAATGAGTAATAACTTAATAGTTAATAA
5950629 TC
65 TC
* *
5950631 AATAACTTAGTAGTAAATTAGTAATAACTTAACAGTAAATGAGTAATAACTTAATAGTTAATA
1 AATAACTTAGTAATAAATTAGTAAAAACTTAACAGTAAATGAGTAATAACTTAATAGTTAATA
5950694 GTTGTTAGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 30 0.57
64 7 0.13
65 11 0.21
66 5 0.09
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (66 bp):
AATAACTTAGTAATAAATTAGTAAAAACTTAACAGTAAATGAGTAATAACTTAATAGTTAATAAT
C
Found at i:5950667 original size:22 final size:22
Alignment explanation
Indices: 5950631--5950684 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
5950621 AGTAATAATC
** *
5950631 AATAACTTAGTAGTAAATTAGT
1 AATAACTTAACAGTAAATGAGT
5950653 AATAACTTAACAGTAAATGAGT
1 AATAACTTAACAGTAAATGAGT
5950675 AATAACTTAA
1 AATAACTTAA
5950685 TAGTTAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (22 bp):
AATAACTTAACAGTAAATGAGT
Found at i:5950864 original size:11 final size:11
Alignment explanation
Indices: 5950859--5950952 Score: 116
Period size: 11 Copynumber: 8.5 Consensus size: 11
5950849 GATAACTTAG
5950859 TAATAATTTAA
1 TAATAATTTAA
5950870 TAATAATTTAA
1 TAATAATTTAA
*
5950881 TAATATTTTAA
1 TAATAATTTAA
*
5950892 TAATATTTTAA
1 TAATAATTTAA
5950903 TAATAATTTAA
1 TAATAATTTAA
*
5950914 TAATAACTTAA
1 TAATAATTTAA
* * *
5950925 TAGTAAATTAG
1 TAATAATTTAA
*
5950936 TGATAATTTAA
1 TAATAATTTAA
5950947 TTAATA
1 -TAATA
5950953 GTAAATTAGT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
11 67 0.94
12 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (11 bp):
TAATAATTTAA
Found at i:5951028 original size:22 final size:21
Alignment explanation
Indices: 5950990--5951106 Score: 74
Period size: 22 Copynumber: 5.4 Consensus size: 21
5950980 TAATTGATAA
*
5950990 TAGTAAATAATAAATAACTTAG
1 TAGTAAATAAT-TATAACTTAG
* *
5951012 TAGTAAATCAATTATAAATTAA
1 TAGTAAAT-AATTATAACTTAG
** *
5951034 TTCTAAATAATTGATAATTTAG
1 TAGTAAATAATT-ATAACTTAG
* * * * *
5951056 TAGTTATTTATTAAAATCTTAA
1 TAGTAAATAATTATAA-CTTAG
*
5951078 AAGTAAATCAA-TATAACTTAG
1 TAGTAAAT-AATTATAACTTAG
5951099 TAGTAAAT
1 TAGTAAAT
5951107 TATCGATAAT
Statistics
Matches: 69, Mismatches: 22, Indels: 9
0.69 0.22 0.09
Matches are distributed among these distances:
21 18 0.26
22 47 0.68
23 4 0.06
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (21 bp):
TAGTAAATAATTATAACTTAG
Found at i:5951270 original size:22 final size:23
Alignment explanation
Indices: 5951245--5951300 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
5951235 TTAAAAATTA
* *
5951245 AATAGTAAATCA-ATGAAAACAT
1 AATAATAAATCATATAAAAACAT
*
5951267 AATAATAAAT-ATATAAAAATAT
1 AATAATAAATCATATAAAAACAT
5951289 AATAATAAATCA
1 AATAATAAATCA
5951301 CTGATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (23 bp):
AATAATAAATCATATAAAAACAT
Found at i:5951324 original size:19 final size:19
Alignment explanation
Indices: 5951302--5951339 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5951292 AATAAATCAC
*
5951302 TGATATTTTAGTAATAAAT
1 TGATAATTTAGTAATAAAT
*
5951321 TGATAATTTAGTACTAAAT
1 TGATAATTTAGTAATAAAT
5951340 CATTAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (19 bp):
TGATAATTTAGTAATAAAT
Found at i:5951409 original size:22 final size:22
Alignment explanation
Indices: 5951291--5951407 Score: 96
Period size: 22 Copynumber: 5.5 Consensus size: 22
5951281 AAAAATATAA
* *
5951291 TAATAAATCACTGATATTTTAG
1 TAATAAATTACTGATAATTTAG
5951313 TAATAAA-T--TGATAATTTAG
1 TAATAAATTACTGATAATTTAG
* * * * * *
5951332 TACTAAATCATTAATAATGTAA
1 TAATAAATTACTGATAATTTAG
* *
5951354 TAGTAAATTACTAATAATTTAG
1 TAATAAATTACTGATAATTTAG
** *
5951376 TTGTAAATTAGTGATAATTTAG
1 TAATAAATTACTGATAATTTAG
5951398 TAATAAATTA
1 TAATAAATTA
5951408 GTTAATCATT
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
19 16 0.21
22 59 0.79
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATAAATTACTGATAATTTAG
Found at i:5951566 original size:22 final size:22
Alignment explanation
Indices: 5951519--5951579 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
5951509 AATAATTGGT
* *
5951519 AAATCATTTATAACTTAATGGA
1 AAATCATTTATAAATTAATGAA
5951541 AAATCATTTATAAATTAAT-AA
1 AAATCATTTATAAATTAATGAA
*
5951562 CAAATCATTCATAAATTA
1 -AAATCATTTATAAATTA
5951580 GCAGTGCATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (22 bp):
AAATCATTTATAAATTAATGAA
Found at i:5952226 original size:58 final size:58
Alignment explanation
Indices: 5952088--5952414 Score: 435
Period size: 58 Copynumber: 5.6 Consensus size: 58
5952078 TCTTGCGTAG
5952088 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTTATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAC-TTTATTTTCAA
* * *
5952147 AGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTCTTAGAAA-TTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTT-TTGGAAACTTTATTTTCAA
5952205 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAACTTT-ATTTTCAA
* * * * *
5952266 GAAAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGGAAACTTTATTTTCAA
** * * * *
5952325 GG-AAATTGATTTTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTATTTTCAA
*
5952382 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA
5952415 AAACTTTTTT
Statistics
Matches: 237, Mismatches: 22, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
56 1 0.00
57 19 0.08
58 100 0.42
59 52 0.22
60 26 0.11
61 38 0.16
63 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTATTTTCAA
Found at i:5952387 original size:177 final size:178
Alignment explanation
Indices: 5952090--5952439 Score: 480
Period size: 177 Copynumber: 2.0 Consensus size: 178
5952080 TTGCGTAGGG
5952090 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTTATTTTCAAAGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTTATTTTCAAAGAAAATT
* *
5952155 GATACTTTCAACTTTTCCCCAAAAATATTTTCTTAGAAATTTATTTTTAAGGAAAATTGATACTT
66 GATACTTTCAACTTTTCCCCAAAAATATTTTCTTAGAAATTTAATTTCAAGGAAAATTGATACTT
* * *
5952220 TCAACTTTTCC-CCAAAAATA-TTTTTTTTGGAAACTTTGATTTTCAAGA
131 TCAACTTTTCCTCAAAAAAAACTTTTTTTT-GAAAATTT-ATTTTCAAGA
* * * *
5952268 AAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTGAAA-TTTTATTTT-TAAGGAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGGAAACTTTTATTTTCAAAGAAAA
** * *
5952330 TTGATTTTTTCAACTTTTCCTCAAAAATATTTT-TT-GAAAACTTTAATTTCGAGGAAAATTGAT
64 TTGATACTTTCAACTTTTCCCCAAAAATATTTTCTTAG-AAA-TTTAATTTCAAGGAAAATTGAT
5952393 ACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTTGAAAATTTATTTT
127 ACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTTGAAAATTTATTTT
5952440 TTTTTAGGAA
Statistics
Matches: 153, Mismatches: 13, Indels: 13
0.85 0.07 0.07
Matches are distributed among these distances:
175 1 0.01
176 5 0.03
177 75 0.49
178 53 0.35
179 18 0.12
180 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.45
Consensus pattern (178 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTTATTTTCAAAGAAAATT
GATACTTTCAACTTTTCCCCAAAAATATTTTCTTAGAAATTTAATTTCAAGGAAAATTGATACTT
TCAACTTTTCCTCAAAAAAAACTTTTTTTTGAAAATTTATTTTCAAGA
Found at i:5952441 original size:119 final size:118
Alignment explanation
Indices: 5952088--5952440 Score: 507
Period size: 119 Copynumber: 3.0 Consensus size: 118
5952078 TCTTGCGTAG
*
5952088 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTTATTTTCAAAGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAC-TTTATTTTCAAGGAAAA
* * * *
5952153 TTGATACTTTCAACTTTTCCCCAAAAATA-TTTTCTTAG-AAATTTATTTTTAA
65 TTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTTGAAAATTTATTTTTAA
*
5952205 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAACTTTGATTTTCAAGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAACTTT-ATTTTCAAGGAA
* *
5952270 AATTGATACTTTCAACTTTTCCTC-AAAAACCTTTTTTTTGAAATTTTATTTTTAA
63 AATTGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTTGAAAATTTATTTTTAA
** * * * *
5952325 GG-AAATTGATTTTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTAATTTCGAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTATTTTCAAGGAAAAT
5952389 TGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTTTTGAAAATTTATTTTT
66 TGATACTTTCAACTTTTCCTC-AAAAAAACTTTTTTTTGAAAATTTATTTTT
5952441 TTTTAGGAAA
Statistics
Matches: 212, Mismatches: 17, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
116 33 0.16
117 49 0.23
118 34 0.16
119 81 0.38
120 15 0.07
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAAAACTTTTTTTTGAAAATTTATTTTTAA
Found at i:5954839 original size:22 final size:23
Alignment explanation
Indices: 5954812--5954862 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
5954802 AGAGGCAACC
5954812 TTTTTT-ATTATTTTCTTG-TTTT
1 TTTTTTAATT-TTTTCTTGCTTTT
*
5954834 TTTTTTAATTTTTTTTTGCTTTT
1 TTTTTTAATTTTTTCTTGCTTTT
5954857 TTTTTT
1 TTTTTT
5954863 TAAATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.08, C:0.04, G:0.04, T:0.84
Consensus pattern (23 bp):
TTTTTTAATTTTTTCTTGCTTTT
Found at i:5954858 original size:25 final size:25
Alignment explanation
Indices: 5954822--5954870 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5954812 TTTTTTATTA
*
5954822 TTTTCTTGTTTTTTTTTTAATTTTT
1 TTTTCTTGTTTTTTTTTAAATTTTT
5954847 TTTTGCTT-TTTTTTTTTAAATTTT
1 TTTT-CTTGTTTTTTTTTAAATTTT
5954871 GATCAAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.82
Consensus pattern (25 bp):
TTTTCTTGTTTTTTTTTAAATTTTT
Found at i:5954969 original size:14 final size:14
Alignment explanation
Indices: 5954952--5954979 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5954942 ACTTTTTTTG
5954952 TTTTTTTTTTTATC
1 TTTTTTTTTTTATC
5954966 TTTTTTTTTTTATC
1 TTTTTTTTTTTATC
5954980 AAAGCTCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTATC
Found at i:5955040 original size:41 final size:41
Alignment explanation
Indices: 5954983--5955442 Score: 625
Period size: 41 Copynumber: 11.1 Consensus size: 41
5954973 TTTTATCAAA
* * * *
5954983 GCTCCTCTAAATAGAGGCTCAACAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
*
5955024 GCTCCTCTAAATAGAGGCACCACGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
* *
5955066 GCTCCTCTAAATAGAGGCACCACGACTTTGGAAA-AATAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTA-AATT
*
5955107 GCTCCTCTAAACAGAGGCACGACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* * * *
5955148 GCTCTTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
5955189 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* * * *
5955230 GCTCCTCTAAGCAGAAGCACCATGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
* * *
5955272 GCTCCTCTAAACAGAGGCATCATGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
*
5955314 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* * * * *
5955355 ACTCCTCTAAATAGAGGCACCACAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
* *
5955396 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
*
5955437 ACTCCT
1 GCTCCT
5955443 TAACAAACAT
Statistics
Matches: 378, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
40 1 0.00
41 258 0.68
42 119 0.31
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
Found at i:5955791 original size:43 final size:42
Alignment explanation
Indices: 5955709--5955814 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 42
5955699 TTCAAGGCTT
* ** *
5955709 TTCAAAGGTTCTCATTTGGCAAACTTGGAATTCATATCCAAAAA
1 TTCAAAGCTTCTCATTT-G-AATTTTGGAATTCACATCCAAAAA
*
5955753 -TCTAAAGCTTTTCATTTGAATTTTGGAGATTCACATCCAAAAA
1 TTC-AAAGCTTCTCATTTGAATTTTGGA-ATTCACATCCAAAAA
5955796 TTCAAAGCTTCTCATTTGA
1 TTCAAAGCTTCTCATTTGA
5955815 GTTCAAAGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 7 0.13
43 32 0.60
44 14 0.26
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (42 bp):
TTCAAAGCTTCTCATTTGAATTTTGGAATTCACATCCAAAAA
Found at i:5957170 original size:19 final size:19
Alignment explanation
Indices: 5957148--5957231 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 19
5957138 AATTTGAATC
* *
5957148 TTTTTTTTCATTTTCTCAT
1 TTTTTTTTCTTTTTTTCAT
*
5957167 TTTTTCTTCTTTTTTTC-T
1 TTTTTTTTCTTTTTTTCAT
5957185 TCTTTTTTTCTTTTTTTTTC-T
1 T-TTTTTTTC--TTTTTTTCAT
5957206 TTTTTTTAT-TTTTTTATCAT
1 TTTTTTT-TCTTTTTT-TCAT
5957226 TTTTTT
1 TTTTTT
5957232 CTCATTTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
18 8 0.15
19 23 0.42
20 13 0.24
21 11 0.20
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTCAT
Found at i:5957171 original size:10 final size:10
Alignment explanation
Indices: 5957158--5957240 Score: 57
Period size: 10 Copynumber: 8.3 Consensus size: 10
5957148 TTTTTTTTCA
5957158 TTTTCTCATT
1 TTTTCTCATT
*
5957168 TTTTCTTCTTT
1 TTTTC-TCATT
5957179 TTTTCTTC-TT
1 TTTTC-TCATT
*
5957189 TTTT-TCTTT
1 TTTTCTCATT
*
5957198 TTTTTTC-TT
1 TTTTCTCATT
*
5957207 TTTT-TTATTT
1 TTTTCTCA-TT
*
5957217 TTTTATCATTT
1 TTTTCTCA-TT
5957228 TTTTCTCATT
1 TTTTCTCATT
5957238 TTT
1 TTT
5957241 CATCCATTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
8 3 0.05
9 12 0.19
10 24 0.38
11 24 0.38
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTCATT
Found at i:5957199 original size:8 final size:8
Alignment explanation
Indices: 5957149--5957233 Score: 54
Period size: 8 Copynumber: 11.1 Consensus size: 8
5957139 ATTTGAATCT
5957149 TTTTTTTC
1 TTTTTTTC
* *
5957157 ATTTTCTC
1 TTTTTTTC
*
5957165 ATTTTTTC
1 TTTTTTTC
*
5957173 -TTCTTT-
1 TTTTTTTC
*
5957179 TTTTCTTC
1 TTTTTTTC
5957187 TTTTTTTC
1 TTTTTTTC
5957195 TTTTTTT-
1 TTTTTTTC
*
5957202 TTCTTTT-
1 TTTTTTTC
*
5957209 TTTTATT-
1 TTTTTTTC
*
5957216 TTTTTATC
1 TTTTTTTC
5957224 ATTTTTTTC
1 -TTTTTTTC
5957233 T
1 T
5957234 CATTTTTCAT
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
7 25 0.42
8 28 0.47
9 7 0.12
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5957236 original size:11 final size:10
Alignment explanation
Indices: 5957158--5957240 Score: 82
Period size: 11 Copynumber: 8.2 Consensus size: 10
5957148 TTTTTTTTCA
*
5957158 TTTTCTCATT
1 TTTTCTCTTT
5957168 TTTTCTTCTTT
1 TTTTC-TCTTT
5957179 TTTTCTTCTTT
1 TTTTC-TCTTT
5957190 TTTTCT-TTT
1 TTTTCTCTTT
5957199 TTTT-TCTTT
1 TTTTCTCTTT
*
5957208 TTTT-TATTT
1 TTTTCTCTTT
*
5957217 TTTTATCATTT
1 TTTTCTC-TTT
5957228 TTTTCTCATTT
1 TTTTCTC-TTT
5957239 TT
1 TT
5957241 CATCCATTGT
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
8 1 0.02
9 22 0.34
10 7 0.11
11 35 0.54
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:5961693 original size:59 final size:58
Alignment explanation
Indices: 5961630--5961838 Score: 300
Period size: 57 Copynumber: 3.6 Consensus size: 58
5961620 TCTTGTGCAG
5961630 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGAAAACTTTTATTTTCAA
1 GGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTG-AAACTTTTATTTTCAA
* *
5961689 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTTTGAAA-TTTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA---TATTTTTTGAAACTTTTATTTTCAA
* *
5961749 GGAAAATTGATACTTTTAACTTTT-CTCAAAAATATTTTTTGGAAAC-TTTAATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAACTTTTATTTTCAA
5961806 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA
5961839 AAACCTTTTT
Statistics
Matches: 136, Mismatches: 7, Indels: 15
0.86 0.04 0.09
Matches are distributed among these distances:
56 7 0.05
57 36 0.26
58 14 0.10
59 34 0.25
60 34 0.25
61 3 0.02
62 8 0.06
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAACTTTTATTTTCAA
Found at i:5961848 original size:117 final size:121
Alignment explanation
Indices: 5961630--5961865 Score: 363
Period size: 118 Copynumber: 2.0 Consensus size: 121
5961620 TCTTGTGCAG
*
5961630 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTTATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTTAATTTCAAGGAAAA
**** *
5961695 TTGATACTTTCAACTTTTCCTC-AAAAACTTTTTTTTTTGAAATTTTAT-TTTTAA
66 TTGATACTTTCAACTTTTCCTCAAAAAAAACCTTTTTTTGAAAATTTATGTTTTAA
* * *
5961749 GGAAAATTGATACTTTTAAC-TTTTCTCAAAAATATTTTTTGGAAAC-TTTAATTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTTAATTTCAAGGAAAA
5961812 TTGATACTTTCAACTTTTCCTCAAAAAAAACCTTTTTTTGAAAATTTATGTTTT
66 TTGATACTTTCAACTTTTCCTCAAAAAAAACCTTTTTTTGAAAATTTATGTTTT
5961866 TTTAGGAAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
117 38 0.36
118 45 0.42
119 23 0.22
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (121 bp):
GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTTAATTTCAAGGAAAA
TTGATACTTTCAACTTTTCCTCAAAAAAAACCTTTTTTTGAAAATTTATGTTTTAA
Found at i:5964357 original size:22 final size:21
Alignment explanation
Indices: 5964332--5964790 Score: 199
Period size: 22 Copynumber: 20.8 Consensus size: 21
5964322 ACAATAAGTA
* *
5964332 ATAACTTAATAGTTAAGAATTG
1 ATAACTTAATAGTAAATAA-TG
5964354 ATAACTTAATAGTAAATAGATG
1 ATAACTTAATAGTAAATA-ATG
*
5964376 ATAATTTAATAGTAAATTAATG
1 ATAACTTAATAGTAAA-TAATG
* *
5964398 ATAACTTAATATTAAATCAATT
1 ATAACTTAATAGTAAAT-AATG
* * *
5964420 TTAATTTAATAGTAATTAATTG
1 ATAACTTAATAGTAAATAA-TG
* * * *
5964442 ATAAATTTAGTAGTAAATCATAA
1 AT-AACTTAATAGTAAATAAT-G
5964465 ATAACTTAATAGTAAATTAATG
1 ATAACTTAATAGTAAA-TAATG
* * * *
5964487 ATAATTTAGTAGTTAATCATTG
1 ATAACTTAATAGTAAAT-AATG
* * *
5964509 AAAATTTAAAAGTAAATCAAT-
1 ATAACTTAATAGTAAAT-AATG
* *
5964530 ATAACTTAATAGTAGTTAATCATCA
1 ATAACTTAATAGTA---AATAAT-G
* *
5964555 ATAATTTAATAGTTAATCAATG
1 ATAACTTAATAGTAAAT-AATG
* * *
5964577 ATAATTTAATAGTAAATCATAA
1 ATAACTTAATAGTAAATAAT-G
5964599 ATAA-TTGAATA-TAAATCAATG
1 ATAACTT-AATAGTAAAT-AATG
* * * *
5964620 ATAACTTGATAATGAATTATAG
1 ATAACTTAATAGTAAATAAT-G
* ** * *
5964642 TTAACTTTGTAATAAATATGTG
1 ATAACTTAATAGTAAATA-ATG
* * ** *
5964664 ATGATTTTGTAGTAAATAATAA
1 ATAACTTAATAGTAAATAAT-G
* *
5964686 AAAAC-TAATTAGTTAATTAATG
1 ATAACTTAA-TAG-TAAATAATG
* *
5964708 ATAACATAATAGTAAATACATA
1 ATAACTTAATAGTAAATA-ATG
* *
5964730 ATAACATAATAGTAAATCATTG
1 ATAACTTAATAGTAAAT-AATG
* *
5964752 ATAATTTAGATA-TAAATTATTG
1 ATAACTTA-ATAGTAAA-TAATG
*
5964774 ATAACTTAATATTAAAT
1 ATAACTTAATAGTAAAT
5964791 TACTAATAAT
Statistics
Matches: 335, Mismatches: 72, Indels: 61
0.72 0.15 0.13
Matches are distributed among these distances:
21 44 0.13
22 234 0.70
23 42 0.13
24 3 0.01
25 12 0.04
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (21 bp):
ATAACTTAATAGTAAATAATG
Found at i:5964571 original size:68 final size:66
Alignment explanation
Indices: 5964378--5964623 Score: 227
Period size: 67 Copynumber: 3.7 Consensus size: 66
5964368 AATAGATGAT
* * ** *
5964378 AATTTAATAGTAAAT--TAATGATAACTTAATATTAAATCAATTTTAATTTAATAG-TAATTAAT
1 AATTTAATAGTAAATCATAA--ATAACTTAATAGTAAATTAATAATAATTTAATAGTTAA-TCAT
5964440 TGATA
63 TGA-A
* * *
5964445 AATTTAGTAGTAAATCATAAATAACTTAATAGTAAATTAATGATAATTTAGTAGTTAATCATTGA
1 AATTTAATAGTAAATCATAAATAACTTAATAGTAAATTAATAATAATTTAATAGTTAATCATTGA
5964510 A
66 A
* * *
5964511 AATTTAAAAGTAAATCA-ATATAACTTAATAGTAGTTAA-TCATCAATAATTTAATAGTTAATCA
1 AATTTAATAGTAAATCATAAATAACTTAATAGTA---AATTAAT-AATAATTTAATAGTTAATCA
* *
5964574 ATGAT
62 TTGAA
* *
5964579 AATTTAATAGTAAATCATAAATAA-TTGAATA-TAAATCAATGATAA
1 AATTTAATAGTAAATCATAAATAACTT-AATAGTAAATTAATAATAA
5964624 CTTGATAATG
Statistics
Matches: 149, Mismatches: 20, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
65 21 0.14
66 18 0.12
67 52 0.35
68 46 0.31
69 12 0.08
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (66 bp):
AATTTAATAGTAAATCATAAATAACTTAATAGTAAATTAATAATAATTTAATAGTTAATCATTGA
A
Found at i:5964579 original size:90 final size:90
Alignment explanation
Indices: 5964376--5964626 Score: 235
Period size: 90 Copynumber: 2.8 Consensus size: 90
5964366 TAAATAGATG
* * * * ** * * *
5964376 ATAATTTAATAGTAAATTAATGATAACTTAATATTAAATCA-ATTTTAATTTAATAGT-AATTAA
1 ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATCATA-AATAATTGAA-AATAAATCAA
*
5964439 TTGATAAATT--TAGTAGTAAATCATAA
64 -TGATAACTTAATAGTAGTAAATCATAA
* * * * *
5964465 ATAACTTAATAGTAAATTAATGATAATTTAGTAGTTAATCATTGAA-AATTTAAAAGTAAATCAA
1 ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATCA-TAAATAATTGAAAA-TAAATCAA
* *
5964529 T-ATAACTTAATAGTAGTTAATCATCA
64 TGATAACTTAATAGTAGTAAATCATAA
* * *
5964555 ATAATTTAATAGTTAATCAATGATAATTTAATAGTAAATCATAAATAATTGAATATAAATCAATG
1 ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATCATAAATAATTGAAAATAAATCAATG
5964620 ATAACTT
66 ATAACTT
5964627 GATAATGAAT
Statistics
Matches: 133, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
88 7 0.05
89 57 0.43
90 69 0.52
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.39
Consensus pattern (90 bp):
ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATCATAAATAATTGAAAATAAATCAATG
ATAACTTAATAGTAGTAAATCATAA
Found at i:5964770 original size:66 final size:65
Alignment explanation
Indices: 5964700--5964835 Score: 157
Period size: 66 Copynumber: 2.1 Consensus size: 65
5964690 CTAATTAGTT
* *
5964700 AATTAATGATAACATAATAGTAAA-TACATAATAACATAATAGTAAATCATTGATAATTTAGATA
1 AATTAATGATAACATAATAGTAAATTAC-TAATAACATAATAGTAAATAAGTGATAATTTAG-TA
*
5964764 TA
64 GA
* * * ** * *
5964766 AATTATTGATAACTTAATATTAAATTACTAATAATTTAGTTGTAAATAAGTGATAATTTAGTAGA
1 AATTAATGATAACATAATAGTAAATTACTAATAACATAATAGTAAATAAGTGATAATTTAGTAGA
5964831 AATTA
1 AATTA
5964836 GTTAATCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 8 0.14
66 48 0.81
67 3 0.05
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (65 bp):
AATTAATGATAACATAATAGTAAATTACTAATAACATAATAGTAAATAAGTGATAATTTAGTAGA
Found at i:5964811 original size:22 final size:22
Alignment explanation
Indices: 5964717--5964835 Score: 64
Period size: 22 Copynumber: 5.5 Consensus size: 22
5964707 GATAACATAA
** *
5964717 TAGTAAA-TACATAATAACATAA
1 TAGTAAATTAC-TAATAATTTAG
* * *
5964739 TAGTAAATCATTGATAATTTAG
1 TAGTAAATTACTAATAATTTAG
* * * *
5964761 ATA-TAAATTATTGATAACTTAA
1 -TAGTAAATTACTAATAATTTAG
*
5964783 TATTAAATTACTAATAATTTAG
1 TAGTAAATTACTAATAATTTAG
* * * *
5964805 TTGTAAATAAGTGATAATTTAG
1 TAGTAAATTACTAATAATTTAG
5964827 TAG-AAATTA
1 TAGTAAATTA
5964836 GTTAATCATT
Statistics
Matches: 74, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
21 7 0.09
22 64 0.86
23 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (22 bp):
TAGTAAATTACTAATAATTTAG
Found at i:5964935 original size:25 final size:24
Alignment explanation
Indices: 5964907--5964989 Score: 64
Period size: 25 Copynumber: 3.4 Consensus size: 24
5964897 TTTATAACAA
5964907 ATCATCAGTAACTTAGTAGTAAATC
1 ATCATCA-TAACTTAGTAGTAAATC
* *
5964932 ATCA--ATAATTTAGTAGT-AATAA
1 ATCATCATAACTTAGTAGTAAAT-C
* *
5964954 ATCAATCATAACTTAATAATAAATC
1 ATC-ATCATAACTTAGTAGTAAATC
*
5964979 ATTCATAATAA
1 A-TCATCATAA
5964990 TTAATGCTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
21 3 0.07
22 14 0.31
23 2 0.04
25 21 0.47
26 5 0.11
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (24 bp):
ATCATCATAACTTAGTAGTAAATC
Found at i:5964973 original size:22 final size:22
Alignment explanation
Indices: 5964875--5964986 Score: 84
Period size: 22 Copynumber: 5.0 Consensus size: 22
5964865 ATCGAAAAAA
* * *
5964875 TTAATAGTAAATCAGTTATAAC
1 TTAATAATAAATCAATCATAAC
* *
5964897 TTTATAACAAATC-ATCAGTAAC
1 TTAATAATAAATCAATCA-TAAC
* * *
5964919 TTAGTAGTAAATC-ATCAATAAT
1 TTAATAATAAATCAATC-ATAAC
5964941 TTAGTAGTAATAAATCAATCATAAC
1 TTA--A-TAATAAATCAATCATAAC
*
5964966 TTAATAATAAATCATTCATAA
1 TTAATAATAAATCAATCATAA
5964987 TAATTAATGC
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.03
22 48 0.69
23 2 0.03
25 15 0.21
26 3 0.04
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (22 bp):
TTAATAATAAATCAATCATAAC
Found at i:5965478 original size:42 final size:42
Alignment explanation
Indices: 5965392--5965499 Score: 128
Period size: 42 Copynumber: 2.5 Consensus size: 42
5965382 ATAAGTTATC
* * * * * *
5965392 AAAAGATTACTAAAATTACATTACGAGATTACTAAAATTTTAT
1 AAAAAATTACTAAAATTATATCACAAG-TTACCAAAATTGTAT
5965435 AAAAAATTA-TCAAAATTATATCACAAGTTACCAAAATTGTAT
1 AAAAAATTACT-AAAATTATATCACAAGTTACCAAAATTGTAT
*
5965477 AAAAAATTACTAAAATTTTATCA
1 AAAAAATTACTAAAATTATATCA
5965500 AAGGTTATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
42 34 0.61
43 22 0.39
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (42 bp):
AAAAAATTACTAAAATTATATCACAAGTTACCAAAATTGTAT
Found at i:5965513 original size:21 final size:21
Alignment explanation
Indices: 5965419--5965497 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
5965409 ACATTACGAG
5965419 ATTACTAAAATTTTATAAAAA
1 ATTACTAAAATTTTATAAAAA
* * *
5965440 ATTA-TCAAAATTATATCACAA
1 ATTACT-AAAATTTTATAAAAA
* * *
5965461 GTTACCAAAATTGTATAAAAA
1 ATTACTAAAATTTTATAAAAA
5965482 ATTACTAAAATTTTAT
1 ATTACTAAAATTTTAT
5965498 CAAAGGTTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.37
Consensus pattern (21 bp):
ATTACTAAAATTTTATAAAAA
Found at i:5965513 original size:42 final size:42
Alignment explanation
Indices: 5965420--5965513 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
5965410 CATTACGAGA
*
5965420 TTACTAAAATTTTATAAAAAATTATCAAAATTATATCACAAG
1 TTACTAAAATTGTATAAAAAATTATCAAAATTATATCACAAG
* *
5965462 TTACCAAAATTGTATAAAAAATTA-CTAAAATTTTATCA-AAGG
1 TTACTAAAATTGTATAAAAAATTATC-AAAATTATATCACAA-G
*
5965504 TTATTAAAAT
1 TTACTAAAAT
5965514 CAAAATTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 3 0.07
42 42 0.93
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (42 bp):
TTACTAAAATTGTATAAAAAATTATCAAAATTATATCACAAG
Found at i:5972934 original size:12 final size:12
Alignment explanation
Indices: 5972919--5972981 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
5972909 TTAAATTATT
5972919 TATTTATTTTTA
1 TATTTATTTTTA
*
5972931 TATTTATTCTTA
1 TATTTATTTTTA
*
5972943 TATTATATATATATA
1 TATT-TAT-T-TTTA
* *
5972958 TATGTAATTTTA
1 TATTTATTTTTA
*
5972970 TATTTATATTTA
1 TATTTATTTTTA
5972982 AAAAATAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
12 27 0.69
13 4 0.10
14 3 0.08
15 5 0.13
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTTATTTTTA
Found at i:5974299 original size:3 final size:3
Alignment explanation
Indices: 5974291--5974326 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5974281 AACTTCTAGC
5974291 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5974327 CTATCTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5974891 original size:2 final size:2
Alignment explanation
Indices: 5974884--5974950 Score: 98
Period size: 2 Copynumber: 32.5 Consensus size: 2
5974874 AGCCTCTTCA
*
5974884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
*
5974927 AT AT AT AT AT AT CAT TT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT A
5974951 AAAGTATAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 55 0.93
3 4 0.07
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5974958 original size:25 final size:24
Alignment explanation
Indices: 5974884--5974951 Score: 104
Period size: 25 Copynumber: 2.9 Consensus size: 24
5974874 AGCCTCTTCA
*
5974884 ATATATAT-ATATATATAT-ATAT
1 ATATATATCATTTATATATAATAT
5974906 ATATATATCATTTATATATATATAT
1 ATATATATCATTTATATATA-ATAT
5974931 ATATATATCATTTATATATAA
1 ATATATATCATTTATATATAA
5974952 AAGTATAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 8 0.19
23 9 0.21
24 1 0.02
25 24 0.57
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATATATCATTTATATATAATAT
Found at i:5975277 original size:151 final size:149
Alignment explanation
Indices: 5974986--5975281 Score: 355
Period size: 151 Copynumber: 2.0 Consensus size: 149
5974976 AATCAAACGA
** * *
5974986 CATAAATACCCTTATAAATTTTAAAAAATAACAAATTTATTTTTAAATTTTTAATATTTTTTATT
1 CATAAATACCCTTATAAATTTTAAAAAATAACAAATTTACGTTTAAATTTCTAACATTTTTTATT
* *
5975051 TATGTATTAATGATTATTTTCCATTAAATATATAGCATTTATTAGTTAATTATTTAAATTAATCC
66 TATGTAATAAAGATTATTTTCCATTAAATATATAGCATTTATTAGTTAATTATTTAAATT-AT-C
**
5975116 AAAAGTATTAAAAATGAATAG
129 AAAACAATTAAAAATGAATAG
* * * *
5975137 CATAAATATCCTTATGAATTTTAAAAAATAACAAATTTACGTTTAAATTTCTAGCGTTTATTTAT
1 CATAAATACCCTTATAAATTTTAAAAAATAACAAATTTACGTTTAAATTTCTAACATTT-TTTAT
* * * *
5975202 TTATTTAATAAAGATTATTTGT-CATTAAATATATATATCTTTTTATTTGTTAATTATTTAAATT
65 TTATGTAATAAAGATTATTT-TCCATT-AA-ATATATAGC-ATTTATTAGTTAATTATTTAAATT
*
5975266 -T-AAATCAATTAAAAAT
126 ATCAAAACAATTAAAAAT
5975282 TTACTAATAT
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
151 63 0.51
152 26 0.21
153 4 0.03
154 8 0.07
155 22 0.18
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (149 bp):
CATAAATACCCTTATAAATTTTAAAAAATAACAAATTTACGTTTAAATTTCTAACATTTTTTATT
TATGTAATAAAGATTATTTTCCATTAAATATATAGCATTTATTAGTTAATTATTTAAATTATCAA
AACAATTAAAAATGAATAG
Done.