Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, 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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 55
Found at i:426178 original size:198 final size:198
Alignment explanation
Indices: 425259--427609 Score: 4457
Period size: 199 Copynumber: 11.9 Consensus size: 198
425249 CAATATGGCC
425259 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
*
425324 CCAAAAGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
425389 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
425454 GGAA
195 GGAA
*
425458 AACATGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
425523 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
425588 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
425653 GGAA
195 GGAA
425657 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
425722 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
425787 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
425852 G-A
196 GAA
*
425854 AACATGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
425918 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
425983 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
426048 GAA
196 GAA
426051 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
426116 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
426181 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
426246 GAA
196 GAA
*
426249 AACATGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
426312 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
426376 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
426441 GAA
196 GAA
426444 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
426508 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
426573 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
426638 GAA
196 GAA
*
426641 AACATGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
426706 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
426771 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAA
426836 TGGAA
194 TGGAA
*
426841 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAGAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
426906 CAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
426971 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
427036 GAA
196 GAA
*
427039 AACATGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
427104 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
427169 AATATGTCT-AATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
427232 GAA
196 GAA
427235 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
427300 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGCTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
427365 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
427430 GGAA
195 GGAA
*
427434 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
427499 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
427564 AATATATCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
427610 CTAATTTAAA
Statistics
Matches: 2113, Mismatches: 27, Indels: 24
0.98 0.01 0.01
Matches are distributed among these distances:
195 136 0.06
196 410 0.19
197 321 0.15
198 514 0.24
199 658 0.31
200 74 0.04
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:427787 original size:23 final size:23
Alignment explanation
Indices: 427756--427819 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
427746 ATAGGTAAAC
*
427756 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
427779 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
427802 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
427820 TGGTTATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:427826 original size:23 final size:23
Alignment explanation
Indices: 427756--427828 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
427746 ATAGGTAAAC
* **
427756 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
427779 ATATAATGTAATATGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
427802 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
427825 ATAT
1 ATAT
427829 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:428218 original size:23 final size:23
Alignment explanation
Indices: 428187--428250 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
428177 ATAGGTAAAC
*
428187 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
428210 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
428233 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
428251 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:428257 original size:23 final size:23
Alignment explanation
Indices: 428187--428259 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
428177 ATAGGTAAAC
* **
428187 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
428210 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
428233 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
428256 ATAT
1 ATAT
428260 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:428464 original size:431 final size:431
Alignment explanation
Indices: 427661--428920 Score: 2408
Period size: 431 Copynumber: 2.9 Consensus size: 431
427651 AAATTAATAA
427661 TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
1 TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
*
427726 GTATGTACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
66 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
*
427791 ATGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAA
131 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAA
427856 GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
196 GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
427921 TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTA
261 TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTA
427986 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
326 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
428051 AAATTATTAAATCAATATTGTAGGTGGAAAACACGAAACAC
391 AAATTATTAAATCAATATTGTAGGTGGAAAACACGAAACAC
428092 TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
1 TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
428157 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
66 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
428222 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAA
131 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAA
*
428287 GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTAAGTGAGTTTTAAGA
196 GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
428352 TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTA
261 TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTA
428417 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
326 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
*
428482 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAAACAC
391 AAATTATTAAATCAATATTGTAGGTGGAAAACACGAAACAC
428523 TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
1 TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
428588 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
66 GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
428653 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAA
131 AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAA
428718 GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
196 GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
*
428783 TATTAATTTAGTAATTATAGGCGTATAATGATTTATTTTTTACGTTAC-G-ATATA-TATTATTA
261 TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTA
* *
428845 AATTAAAAATTCTAAATATTA-TTT-TAAAATATCAAAACAATCAAAT--TTTTTTGTGCAAATG
326 AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
428906 AAATTATTAAATCAA
391 AAATTATTAAATCAA
428921 ATAATTCAAA
Statistics
Matches: 821, Mismatches: 8, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
424 30 0.04
426 21 0.03
427 3 0.00
428 28 0.03
429 5 0.01
430 1 0.00
431 733 0.89
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (431 bp):
TGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAAAAA
GTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAAT
AGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAA
GTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGA
TATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTA
AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATG
AAATTATTAAATCAATATTGTAGGTGGAAAACACGAAACAC
Found at i:428649 original size:23 final size:23
Alignment explanation
Indices: 428618--428681 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
428608 ATAGGTAAAC
*
428618 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
428641 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
428664 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
428682 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:428688 original size:23 final size:23
Alignment explanation
Indices: 428618--428690 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
428608 ATAGGTAAAC
* **
428618 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
428641 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
428664 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
428687 ATAT
1 ATAT
428691 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:428986 original size:25 final size:25
Alignment explanation
Indices: 428952--429002 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
428942 ACAACAAATC
*
428952 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
428977 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
429002 A
1 A
429003 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:429272 original size:18 final size:18
Alignment explanation
Indices: 429251--429287 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
429241 GTAATTGGAG
429251 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
429269 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
429287 T
1 T
429288 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:429295 original size:24 final size:24
Alignment explanation
Indices: 429243--429289 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
429233 TTTCATATGT
* *
429243 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
429267 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
429290 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:429589 original size:39 final size:39
Alignment explanation
Indices: 429546--429632 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
429536 TCCGATGCTC
*
429546 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
429585 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
429624 ATCAAAATC
1 ATCAAAATC
429633 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:430067 original size:23 final size:23
Alignment explanation
Indices: 430036--430099 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
430026 ATAGGTAAAC
*
430036 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
430059 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
430082 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
430100 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:430106 original size:23 final size:23
Alignment explanation
Indices: 430036--430108 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
430026 ATAGGTAAAC
* **
430036 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
430059 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
430082 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
430105 ATAT
1 ATAT
430109 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:439791 original size:15 final size:15
Alignment explanation
Indices: 439773--439824 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
439763 TTTCGGAAAA
439773 TGAATTACTGGAATT
1 TGAATTACTGGAATT
439788 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
439803 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
439817 TGAATTAC
1 TGAATTAC
439825 ATTTCTGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.35
15 22 0.65
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:440160 original size:23 final size:23
Alignment explanation
Indices: 440114--440177 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
440104 AGTGTTATAT
* *
440114 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAATATATTAACTAG
* *
440137 TATATTTTAAATATCTTTACTAG
1 TATATTTTAAATATATTAACTAG
440160 TATATGTTTTAAATATAT
1 TATA--TTTTAAATATAT
440178 AAATAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 23 0.68
25 11 0.32
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (23 bp):
TATATTTTAAATATATTAACTAG
Found at i:440220 original size:21 final size:21
Alignment explanation
Indices: 440196--440238 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
440186 AATATTATTC
440196 ATTATTAAATA-TATATAAAAT
1 ATTATTAAATATTAT-TAAAAT
*
440217 ATTATTATATATTATTAAAAT
1 ATTATTAAATATTATTAAAAT
440238 A
1 A
440239 AAAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTATTAAATATTATTAAAAT
Found at i:440223 original size:31 final size:32
Alignment explanation
Indices: 440160--440269 Score: 108
Period size: 31 Copynumber: 3.6 Consensus size: 32
440150 TCTTTACTAG
*
440160 TATATGTT-TTAAATATATAAATAAATAATAT
1 TATATATTATTAAATATATAAATAAATAATAT
* *
440191 TAT-TCATTATTAAATATATATA-AAATATTAT
1 TATAT-ATTATTAAATATATAAATAAATAATAT
*
440222 TATATATTATTAAA-ATA-AAA-ATATAATAT
1 TATATATTATTAAATATATAAATAAATAATAT
440251 CT-TATATTATTATAATATA
1 -TATATATTATTA-AATATA
440270 ATTGATTATA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
29 19 0.28
30 7 0.10
31 28 0.42
32 13 0.19
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TATATATTATTAAATATATAAATAAATAATAT
Found at i:440228 original size:10 final size:10
Alignment explanation
Indices: 440196--440235 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
440186 AATATTATTC
440196 ATTATTAAAT
1 ATTATTAAAT
*
440206 ATATATAAAAT
1 AT-TATTAAAT
*
440217 ATTATTATAT
1 ATTATTAAAT
440227 ATTATTAAA
1 ATTATTAAA
440236 ATAAAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:440248 original size:60 final size:59
Alignment explanation
Indices: 440176--440345 Score: 148
Period size: 52 Copynumber: 3.0 Consensus size: 59
440166 TTTTAAATAT
440176 ATAAATAA-ATAATATTATTCATTATTAAATATATATAAAATATTATTATATATTATTAAA
1 ATAAA-AATATAATATTATT-ATTATTAAATATATATAAAATATTATTATATATTATTAAA
* * * *
440236 ATAAAAATATAATA-TCTTA-TATT-ATTATA-ATATAAT-TGA-T-TATATTATTAAA
1 ATAAAAATATAATATTATTATTATTAAATATATATAAAATATTATTATATATTATTAAA
* *
440288 CTAAAAATATAATATTA-TATTATTATAA-ATATTAATAAATATATT-TTAAATATT-TTAA
1 ATAAAAATATAATATTATTATTATTA-AATATA-T-ATAAA-ATATTATTATATATTATTAA
440346 TAATTAATAT
Statistics
Matches: 88, Mismatches: 10, Indels: 25
0.72 0.08 0.20
Matches are distributed among these distances:
52 27 0.31
53 6 0.07
54 5 0.06
55 7 0.08
56 5 0.06
57 8 0.09
58 3 0.03
59 11 0.12
60 16 0.18
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (59 bp):
ATAAAAATATAATATTATTATTATTAAATATATATAAAATATTATTATATATTATTAAA
Found at i:440265 original size:52 final size:51
Alignment explanation
Indices: 440213--440321 Score: 161
Period size: 52 Copynumber: 2.2 Consensus size: 51
440203 AATATATATA
440213 AAATATTATT-A-TATATTATTAAAATAAAAATATAATATCTTATATTATTAT
1 AAATATTATTGATTATATTATTAAAATAAAAATATAATA--TTATATTATTAT
* *
440264 -AATATAATTGATTATATTATTAAACTAAAAATATAATATTATATTATTAT
1 AAATATTATTGATTATATTATTAAAATAAAAATATAATATTATATTATTAT
440314 AAATATTA
1 AAATATTA
440322 ATAAATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
50 20 0.38
51 7 0.13
52 25 0.48
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (51 bp):
AAATATTATTGATTATATTATTAAAATAAAAATATAATATTATATTATTAT
Found at i:440392 original size:24 final size:22
Alignment explanation
Indices: 440304--440392 Score: 56
Period size: 24 Copynumber: 3.7 Consensus size: 22
440294 ATATAATATT
440304 ATATTATTATAAATATTA-ATAAA
1 ATATT-TTAT-AATATTATATAAA
*
440327 TATATTTTA-AATATTTTAATAATTA
1 -ATATTTTATAATATTAT-ATAA--A
* *
440352 ATATTTGATGAAAATTATATTAAA
1 ATATTTTAT-AATATTATA-TAAA
440376 ATATTTTATTAATATTA
1 ATATTTTA-TAATATTA
440393 AATTCATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
21 6 0.12
23 7 0.14
24 26 0.51
25 3 0.06
26 9 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTTTATAATATTATATAAA
Found at i:441815 original size:21 final size:21
Alignment explanation
Indices: 441786--441826 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
441776 AGAGTTTTTT
441786 AATTACCCACTCATTTCTTCC
1 AATTACCCACTCATTTCTTCC
*
441807 AATTTCCCACTCATTTCTTC
1 AATTACCCACTCATTTCTTC
441827 TTCTTCCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTACCCACTCATTTCTTCC
Found at i:442637 original size:23 final size:23
Alignment explanation
Indices: 442602--442647 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
442592 CGGGTACTCC
* *
442602 TTTTTCTAAAAAAAAGATTTAAT
1 TTTTTCGAAAAAAAAGACTTAAT
* *
442625 TTTTTCGATAAAAGAGACTTAAT
1 TTTTTCGAAAAAAAAGACTTAAT
442648 CCATCTGGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (23 bp):
TTTTTCGAAAAAAAAGACTTAAT
Found at i:443798 original size:16 final size:16
Alignment explanation
Indices: 443770--443809 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
443760 AAATTAGCGA
*
443770 AACCGAAAGTAACCTG
1 AACCGAAAGTAACCCG
* *
443786 AATCGAAATTAACCCG
1 AACCGAAAGTAACCCG
443802 AACCGAAA
1 AACCGAAA
443810 CCAAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.25, G:0.15, T:0.12
Consensus pattern (16 bp):
AACCGAAAGTAACCCG
Found at i:443856 original size:16 final size:16
Alignment explanation
Indices: 443808--443894 Score: 57
Period size: 16 Copynumber: 5.4 Consensus size: 16
443798 CCCGAACCGA
* * *
443808 AACCAAAATTAATCAG
1 AACCGAAATTAACCCG
** *
443824 AACCGAAAGAAAACCG
1 AACCGAAATTAACCCG
*
443840 AACCGAACTTAACCCG
1 AACCGAAATTAACCCG
* * **
443856 ACCCAAAAGCAACCCG
1 AACCGAAATTAACCCG
* *
443872 AACAGAAATTAATCCG
1 AACCGAAATTAACCCG
443888 AACCGAA
1 AACCGAA
443895 TAATAAATTA
Statistics
Matches: 50, Mismatches: 21, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.49, C:0.29, G:0.13, T:0.09
Consensus pattern (16 bp):
AACCGAAATTAACCCG
Found at i:444498 original size:16 final size:16
Alignment explanation
Indices: 444477--444507 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
444467 AACAAATCCA
*
444477 ATATTGACTCGACCCG
1 ATATTGACTCAACCCG
444493 ATATTGACTCAACCC
1 ATATTGACTCAACCC
444508 AAAATCTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (16 bp):
ATATTGACTCAACCCG
Found at i:446530 original size:43 final size:41
Alignment explanation
Indices: 446434--446543 Score: 116
Period size: 43 Copynumber: 2.7 Consensus size: 41
446424 AAACGCCGTA
* *
446434 AAAGGTTAT-ATTTTTAGTGACATTTTTTACAAATGTCGCT
1 AAAGGTTATGATATTTAGTGACATTTTTTACAAACGTCGCT
* * *
446474 AAAAGTAACGATATTTAGT-AGCATTTATTTTACAAACGTCGCT
1 AAAGGTTATGATATTTAGTGA-CA-TT-TTTTACAAACGTCGCT
* *
446517 AAAGGTTATGATATTTAGCGGCATTTT
1 AAAGGTTATGATATTTAGTGACATTTT
446544 CCAAACGCCA
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
40 7 0.13
41 12 0.22
42 4 0.07
43 32 0.58
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (41 bp):
AAAGGTTATGATATTTAGTGACATTTTTTACAAACGTCGCT
Found at i:446638 original size:45 final size:45
Alignment explanation
Indices: 446588--446689 Score: 186
Period size: 45 Copynumber: 2.3 Consensus size: 45
446578 TTTTGTCCCA
446588 AAAACGCCGCTAAATGTTCTGAAATATAGTGGCATTTGTGAATGT
1 AAAACGCCGCTAAATGTTCTGAAATATAGTGGCATTTGTGAATGT
*
446633 AAAACGCCGCTAAATGTTTTGAAATATAGTGGCATTTGTGAATGT
1 AAAACGCCGCTAAATGTTCTGAAATATAGTGGCATTTGTGAATGT
*
446678 AAAACGTCGCTA
1 AAAACGCCGCTA
446690 TTGACTACGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (45 bp):
AAAACGCCGCTAAATGTTCTGAAATATAGTGGCATTTGTGAATGT
Found at i:446918 original size:21 final size:22
Alignment explanation
Indices: 446892--446947 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
446882 ATTATCCAAT
446892 AAACTTGAAAAT-CATAACAAC
1 AAACTTGAAAATCCATAACAAC
*
446913 AAACTTG-AAATCCATAACAAG
1 AAACTTGAAAATCCATAACAAC
446934 AAACTTG-AAATCCA
1 AAACTTGAAAATCCA
446948 CAATAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.20
Consensus pattern (22 bp):
AAACTTGAAAATCCATAACAAC
Found at i:448140 original size:19 final size:19
Alignment explanation
Indices: 448116--448154 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
448106 GCAAGTATGT
448116 TAAATTAAATGTTCTTAAA
1 TAAATTAAATGTTCTTAAA
448135 TAAATTAAATGTTCTTAAA
1 TAAATTAAATGTTCTTAAA
448154 T
1 T
448155 GGGCTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
TAAATTAAATGTTCTTAAA
Found at i:450217 original size:41 final size:41
Alignment explanation
Indices: 450135--450234 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
450125 ACAGTGTTTA
** * *
450135 TATAAAAACACCACTAAAGTACGAGTCTTTACCACCATTTG
1 TATAAAAATGCCACTAAAGTACGAGTCTATAACACCATTTG
* * *
450176 TCTAAAAATGCCACTAAAGTACGAGTCTATAACAGCGTTTG
1 TATAAAAATGCCACTAAAGTACGAGTCTATAACACCATTTG
450217 TATAAAAATGCCACTAAA
1 TATAAAAATGCCACTAAA
450235 ATACATTCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (41 bp):
TATAAAAATGCCACTAAAGTACGAGTCTATAACACCATTTG
Found at i:450417 original size:41 final size:41
Alignment explanation
Indices: 450372--450479 Score: 171
Period size: 41 Copynumber: 2.6 Consensus size: 41
450362 GTACCCTTTT
* *
450372 GTGGCATTTGTTTAAAAATGCCACTAAAGAACGATTCAATG
1 GTGGCGTTTGTTTACAAATGCCACTAAAGAACGATTCAATG
* *
450413 GTGGCGTTTGTTTACAAATACCACTAAAGAACGATTCTATG
1 GTGGCGTTTGTTTACAAATGCCACTAAAGAACGATTCAATG
*
450454 GTGGCGTTTGTTTACAAACGCCACTA
1 GTGGCGTTTGTTTACAAATGCCACTA
450480 CAGTACGAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (41 bp):
GTGGCGTTTGTTTACAAATGCCACTAAAGAACGATTCAATG
Found at i:456477 original size:21 final size:21
Alignment explanation
Indices: 456453--456506 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
456443 TGCGATTTTC
*
456453 CAAATTTACAACACTGAATTT
1 CAAATTCACAACACTGAATTT
*
456474 CAAATTCGCAACACTGAATTT
1 CAAATTCACAACACTGAATTT
*
456495 CAAATTCGCAAC
1 CAAATTCACAAC
456507 GCGAAACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (21 bp):
CAAATTCACAACACTGAATTT
Found at i:457059 original size:19 final size:19
Alignment explanation
Indices: 457037--457084 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
457027 AAATCGCAAC
457037 GCGATTTT-TGTTTCGCGTT
1 GCGATTTTAT-TTTCGCGTT
457056 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-ATTTTCGCGTT
*
457076 GCGAATTTA
1 GCGATTTTA
457085 AGTTTCAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 16 0.62
21 1 0.04
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTTTATTTTCGCGTT
Found at i:457090 original size:20 final size:20
Alignment explanation
Indices: 457046--457090 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
457036 CGCGATTTTT
* *
457046 GTTTCGCGTTGCGATTTTCA
1 GTTTCGCGTTGCGAATTTAA
*
457066 TTTTCGCGTTGCGAATTTAA
1 GTTTCGCGTTGCGAATTTAA
457086 GTTTC
1 GTTTC
457091 AGAAACTACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
GTTTCGCGTTGCGAATTTAA
Found at i:459050 original size:4 final size:4
Alignment explanation
Indices: 459041--459082 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
459031 TTTTTCGGTA
* * *
459041 TTAT TTAT TTAT TTAT TTAT TGAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
459083 TCAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:459301 original size:21 final size:21
Alignment explanation
Indices: 459251--459302 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
459241 TGCCTTCTAT
* * *
459251 CGTTCAAGAGGCCCCTCTCAT
1 CGTTCAAGAGACCCCTCCCAC
*
459272 C-ATCGAAGAGACCCCTCCCAC
1 CGTTC-AAGAGACCCCTCCCAC
459293 CGTTCAAGAG
1 CGTTCAAGAG
459303 GCCCATGTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.25, C:0.38, G:0.19, T:0.17
Consensus pattern (21 bp):
CGTTCAAGAGACCCCTCCCAC
Found at i:460762 original size:64 final size:65
Alignment explanation
Indices: 460649--460822 Score: 244
Period size: 65 Copynumber: 2.6 Consensus size: 65
460639 TGGGTTACAC
460649 TTTTTTGCTTGTTTAATTGCATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATGAGGAAATAA
1 TTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTTGATGAGGAAATAA
460712 GAATTA
60 GAATTA
* *
460718 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTA
* *
460783 TTTTTTTCTTGTTTAATTAATTTGTAAAAGTTGATTTGTT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
460823 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 4, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
64 17 0.17
65 57 0.58
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATTA
Found at i:461263 original size:18 final size:18
Alignment explanation
Indices: 461240--461275 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
461230 AAGCCGGTTG
*
461240 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
461258 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
461276 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:464358 original size:14 final size:15
Alignment explanation
Indices: 464322--464359 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
464312 GAAATCATTG
464322 AAAAATTATATACAA
1 AAAAATTATATACAA
*
464337 ATAAAATTATGTA-AA
1 A-AAAATTATATACAA
464352 AAAAATTA
1 AAAAATTA
464360 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAAATTATATACAA
Found at i:464569 original size:20 final size:19
Alignment explanation
Indices: 464539--464586 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
464529 ATTCGTGTTA
*
464539 CAAATTCGAAAATCTAGTTG
1 CAAATTTGAAAATC-AGTTG
* *
464559 CGAATTTGAAATTCAGTTG
1 CAAATTTGAAAATCAGTTG
464578 CAAATTTGA
1 CAAATTTGA
464587 CTTTTGCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (19 bp):
CAAATTTGAAAATCAGTTG
Found at i:464737 original size:20 final size:19
Alignment explanation
Indices: 464555--464764 Score: 151
Period size: 20 Copynumber: 10.6 Consensus size: 19
464545 CGAAAATCTA
* *
464555 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTG-ACTTCGC
* *
464574 GTTGCAAATTTGACTTTTGC
1 GTTGCGAATTTGAC-TTCGC
*
464594 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
* *
464614 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTT-CGC
464634 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC---TTCGC
464654 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
*
464674 GTTGCGAATTTGACTTCAGT
1 GTTGCGAATTTGACTTC-GC
*
464694 GTTGCGATTTATAGA-TTCGC
1 GTTGCGAATT-T-GACTTCGC
*
464714 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
* *
464734 GTTGCGATTTATAGA-TTCGT
1 GTTGCGAATT-T-GACTTCGC
464754 GTTGCGAATTT
1 GTTGCGAATTT
464765 AGAAAATCGC
Statistics
Matches: 157, Mismatches: 17, Indels: 34
0.75 0.08 0.16
Matches are distributed among these distances:
18 5 0.03
19 27 0.17
20 105 0.67
21 14 0.09
22 6 0.04
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGC
Found at i:464741 original size:40 final size:40
Alignment explanation
Indices: 464670--464764 Score: 172
Period size: 40 Copynumber: 2.4 Consensus size: 40
464660 AATTTGACTA
464670 TCGCGTTGCGAATTTGACTTCAGTGTTGCGATTTATAGAT
1 TCGCGTTGCGAATTTGACTTCAGTGTTGCGATTTATAGAT
*
464710 TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTATAGAT
1 TCGCGTTGCGAATTTGACTTCAGTGTTGCGATTTATAGAT
*
464750 TCGTGTTGCGAATTT
1 TCGCGTTGCGAATTT
464765 AGAAAATCGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTCAGTGTTGCGATTTATAGAT
Found at i:464760 original size:60 final size:60
Alignment explanation
Indices: 464592--464728 Score: 240
Period size: 60 Copynumber: 2.3 Consensus size: 60
464582 TTTGACTTTT
*
464592 GCGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTT-ATGTGTTGCGATTTACAGATTC
1 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCA-GTGTTGCGATTTACAGATTC
*
464652 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCAGTGTTGCGATTTATAGATTC
1 GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCAGTGTTGCGATTTACAGATTC
464712 GCGTTGCGAATTTGACT
1 GCGTTGCGAATTTGACT
464729 TCTGTGTTGC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
60 73 0.99
61 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCAGTGTTGCGATTTACAGATTC
Found at i:464800 original size:20 final size:20
Alignment explanation
Indices: 464634--464801 Score: 91
Period size: 20 Copynumber: 8.3 Consensus size: 20
464624 TGACTTATGT
464634 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
464654 GTTGCGAATTTGAC-TA-TCGC
1 GTTGCG-ATTT-ACAGATTCGC
*
464674 GTTGCGAATTT---GACTTCAGT
1 GTTGCG-ATTTACAGA-TTC-GC
*
464694 GTTGCGATTTATAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
464714 GTTGCGAATTT---GACTTCTGT
1 GTTGCG-ATTTACAGA-TTC-GC
* *
464734 GTTGCGATTTATAGATTCGT
1 GTTGCGATTTACAGATTCGC
* * *
464754 GTTGCGAATTTAGAAAATCGC
1 GTTGCG-ATTTACAGATTCGC
** *
464775 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGC
464795 GTTGCGA
1 GTTGCGA
464802 AATTGGAAAC
Statistics
Matches: 117, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
17 1 0.01
18 2 0.02
19 13 0.11
20 66 0.56
21 29 0.25
22 6 0.05
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:464838 original size:20 final size:19
Alignment explanation
Indices: 464789--464842 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
464779 CGATTTACAT
464789 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
464808 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
464828 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
464843 TTTCTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:465494 original size:29 final size:29
Alignment explanation
Indices: 465429--465536 Score: 76
Period size: 30 Copynumber: 3.6 Consensus size: 29
465419 AAAACATAAG
**
465429 AATAAAAAAAATTATAATAACAATAAATCA
1 AATAAAAAAAAAAAT-ATAACAATAAATCA
* * *
465459 AAGAAAAAAAACAATATATCAATAAAATC-
1 AATAAAAAAAAAAATATAACAAT-AAATCA
* *
465488 AATAAAAATAAAAAATA-AAAAATAAAAATAA
1 AATAAAAA-AAAAAATATAACAAT--AAATCA
465519 AATAAATAAAACAAAATA
1 AATAAA-AAAA-AAAATA
465537 ATAAATAACC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
29 18 0.29
30 29 0.46
31 8 0.13
32 8 0.13
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.19
Consensus pattern (29 bp):
AATAAAAAAAAAAATATAACAATAAATCA
Found at i:465503 original size:7 final size:7
Alignment explanation
Indices: 465491--465520 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
465481 TAAAATCAAT
465491 AAAAATA
1 AAAAATA
465498 AAAAATA
1 AAAAATA
465505 AAAAAT-
1 AAAAATA
465511 AAAAATA
1 AAAAATA
465518 AAA
1 AAA
465521 TAAATAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:465506 original size:13 final size:13
Alignment explanation
Indices: 465488--465544 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
465478 CAATAAAATC
465488 AATAAAAATAAAA
1 AATAAAAATAAAA
465501 AATAAAAA-ATAAA
1 AATAAAAATA-AAA
465514 AAT-AAAATAAATA
1 AATAAAAATAAA-A
*
465527 AA-ACAAAATAATA
1 AATA-AAAATAAAA
465540 AATAA
1 AATAA
465545 CCTAGAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
12 7 0.19
13 22 0.59
14 8 0.22
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.18
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:465529 original size:14 final size:15
Alignment explanation
Indices: 465479--465544 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 15
465469 ACAATATATC
465479 AATAAAATCAATAA-A
1 AATAAAAT-AATAATA
*
465494 AATAAAA-AATAAAA
1 AATAAAATAATAATA
465508 AATAAAAATAA-AATA
1 AAT-AAAATAATAATA
*
465523 AATAAAACAAAATAATA
1 AAT-AAA-ATAATAATA
465540 AATAA
1 AATAA
465545 CCTAGAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 5 0.11
14 4 0.09
15 21 0.48
16 7 0.16
17 7 0.16
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAAAATAATAATA
Found at i:465534 original size:20 final size:20
Alignment explanation
Indices: 465491--465544 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
465481 TAAAATCAAT
*
465491 AAAAATAAAAAATAAAAAAT
1 AAAAATAAAAAATAAAAAAC
*
465511 AAAAATAAAATAA-ATAAAAC
1 AAAAATAAAA-AATAAAAAAC
*
465531 -AAAATAATAAATAA
1 AAAAATAAAAAATAA
465545 CCTAGAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 2 0.07
19 9 0.32
20 15 0.54
21 2 0.07
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAAATAAAAAATAAAAAAC
Found at i:465600 original size:18 final size:15
Alignment explanation
Indices: 465512--465608 Score: 56
Period size: 14 Copynumber: 6.2 Consensus size: 15
465502 ATAAAAAATA
*
465512 AAAATAAAATA-AAT
1 AAAAGAAAATATAAT
*
465526 AAAACAAAATAATAAAT
1 AAAAGAAAAT-AT-AAT
*
465543 AACCTAGAAAA-ATAAT
1 AA--AAGAAAATATAAT
**
465559 ACCAGAAAATATAAT
1 AAAAGAAAATATAAT
465574 AAAAG-AAATATATAT
1 AAAAGAAAATATA-AT
*
465589 AAAGAGTAAAATAAAAT
1 AAA-AG-AAAATATAAT
465606 AAA
1 AAA
465609 GGGACAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
14 22 0.34
15 14 0.22
16 6 0.09
17 12 0.18
18 6 0.09
19 5 0.08
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (15 bp):
AAAAGAAAATATAAT
Found at i:466251 original size:9 final size:9
Alignment explanation
Indices: 466237--466266 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
466227 TAGGGCCTAC
466237 AAAAATAAA
1 AAAAATAAA
466246 AAAAAT-AA
1 AAAAATAAA
466254 AAAAATAAA
1 AAAAATAAA
466263 AAAA
1 AAAA
466267 TATTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:466811 original size:84 final size:83
Alignment explanation
Indices: 466673--467019 Score: 398
Period size: 84 Copynumber: 4.2 Consensus size: 83
466663 GAATGAAATT
* * *
466673 GAACTCGAGGGTCTTTG--G-CAGATAACCCTTTTTGCCTTGAGCTATGCTACAAATGATGGTGC
1 GAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTACAAATGAT-GTGC
* * * *
466735 CTTTGAGTTGAGTGGAGTC
65 CTTGGAGCTGAGCGTAGTC
* * **
466754 GAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCC
1 GAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCC
466819 TTGGAGCTGAGCGTAGTC
66 TTGGAGCTGAGCGTAGTC
* * ** *
466837 GAAATCGAAGGTCTTTTGTTGGA-AAATAACATTTCTTA-CCTTGAGCTATGTTACAAATGATGT
1 GAACTCGAAGGTC-TTTGTT-GACAGATAACCCTTC-TAGCCTTGAGCTATGCTACAAATGATGT
*
466900 GCCTTGGAGCTGAGCGTAATC
63 GCCTTGGAGCTGAGCGTAGTC
** * * ** **
466921 GAACTCGAAGGTCTTCATTGACAGATAACCATTCTAGCCTTGAGTTATGCTGTAAATGATGTGAG
1 GAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCC
466986 TTGGAGCTGAGCGTAGTC
66 TTGGAGCTGAGCGTAGTC
467004 GAACTCGAAGGTCTTT
1 GAACTCGAAGGTCTTT
467020 TGTGTTTCAA
Statistics
Matches: 224, Mismatches: 34, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
81 16 0.07
82 4 0.02
83 99 0.44
84 101 0.45
85 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (83 bp):
GAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTACAAATGATGTGCC
TTGGAGCTGAGCGTAGTC
Found at i:466934 original size:167 final size:168
Alignment explanation
Indices: 466707--467022 Score: 508
Period size: 167 Copynumber: 1.9 Consensus size: 168
466697 ACCCTTTTTG
* * * * **
466707 CCTTGAGCTATGCTACAAATGATGGTGCCTTTGAGTTGAGTGGAGTCGAACTCGAAGGTCTTTGT
1 CCTTGAGCTATGCTACAAATGATGGTGCCTTGGAGCTGAGCGGAATCGAACTCGAAGGTCTTCAT
* *
466772 TGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCTTGGAGCTGAGCGTAGTC
66 TGACAGATAACCATTCTAGCCTTGAGTTATGATGTAAATGATGTGACTTGGAGCTGAGCGTAGTC
466837 GAAATCGAAGGTCTTTTGTTGGAAAATAACATTTCTTA
131 GAAATCGAAGGTCTTTTGTTGGAAAATAACATTTCTTA
* *
466875 CCTTGAGCTATGTTACAAATGAT-GTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTCAT
1 CCTTGAGCTATGCTACAAATGATGGTGCCTTGGAGCTGAGCGGAATCGAACTCGAAGGTCTTCAT
* *
466939 TGACAGATAACCATTCTAGCCTTGAGTTATGCTGTAAATGATGTGAGTTGGAGCTGAGCGTAGTC
66 TGACAGATAACCATTCTAGCCTTGAGTTATGATGTAAATGATGTGACTTGGAGCTGAGCGTAGTC
*
467004 GAACTCGAAGGTCTTTTGT
131 GAAATCGAAGGTCTTTTGT
467023 GTTTCAAGAG
Statistics
Matches: 135, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
167 113 0.84
168 22 0.16
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (168 bp):
CCTTGAGCTATGCTACAAATGATGGTGCCTTGGAGCTGAGCGGAATCGAACTCGAAGGTCTTCAT
TGACAGATAACCATTCTAGCCTTGAGTTATGATGTAAATGATGTGACTTGGAGCTGAGCGTAGTC
GAAATCGAAGGTCTTTTGTTGGAAAATAACATTTCTTA
Found at i:467092 original size:33 final size:33
Alignment explanation
Indices: 467011--467103 Score: 143
Period size: 35 Copynumber: 2.8 Consensus size: 33
467001 GTCGAACTCG
*
467011 AAGGTCTTTTGTGTTTCAAGAGAAACATTTTCA
1 AAGGTTTTTTGTGTTTCAAGAGAAACATTTTCA
467044 AAGGTTTTTTTTGTGTTTCAAGAGAAACGA-TTTCA
1 AAGG--TTTTTTGTGTTTCAAGAGAAAC-ATTTTCA
467079 AAGGTTTTTTGTGTTTCAAGAGAAA
1 AAGGTTTTTTGTGTTTCAAGAGAAA
467104 TTGTCTCCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
33 25 0.45
35 30 0.54
36 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (33 bp):
AAGGTTTTTTGTGTTTCAAGAGAAACATTTTCA
Found at i:467236 original size:36 final size:36
Alignment explanation
Indices: 467161--467394 Score: 232
Period size: 36 Copynumber: 6.6 Consensus size: 36
467151 GGTTGGTGTT
* *
467161 TCAAGAGAGACAAAACTTTTTTTTAAGGGAAACTGTC
1 TCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTC
* *
467198 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTC
* * **
467234 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTC
1 TCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTC
* ** * *
467271 TCAAGGGAGACGGAATTTGTTTCAAGGAAAACATAT-
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-TGTC
* *
467307 TC-A-A-AG----ATTTTGTTTCAAGGGAAACTATC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTC
467336 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTC
*
467372 TCAAGAGAGAAAAAACTTTGTTT
1 TCAAGAGAGACAAAA-TTTGTTT
467395 TGAGTAAATA
Statistics
Matches: 163, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.02
29 19 0.12
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 1 0.01
36 81 0.50
37 53 0.33
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTC
Found at i:467244 original size:73 final size:72
Alignment explanation
Indices: 467161--467300 Score: 199
Period size: 73 Copynumber: 1.9 Consensus size: 72
467151 GGTTGGTGTT
** ** **
467161 TCAAGAGAGACAAAACTTTTTTTTAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAG
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAG-G
467226 AAACTGTC
65 AAACTGTC
**
467234 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAGGA
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGA
467299 AA
66 AA
467301 ACATATTCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 4 0.07
73 55 0.93
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (72 bp):
TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGA
AACTGTC
Found at i:467757 original size:43 final size:43
Alignment explanation
Indices: 467688--467807 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 43
467678 AAGTTGACAC
* *
467688 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTGTG-GCCAT
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGAG-CAT
* * * *
467731 GATATCCTCCGTCGTGGAGTTAAAATCATGGATTTGTGAGTAT
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGAGCAT
* * *
467774 GATATCATCTGTCATGGAGTTGAAATCGTGGATG
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
467808 GCTCTTTCAT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 63 0.98
44 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.33
Consensus pattern (43 bp):
GATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGAGCAT
Found at i:469285 original size:95 final size:95
Alignment explanation
Indices: 469076--469336 Score: 380
Period size: 95 Copynumber: 2.7 Consensus size: 95
469066 GACTAACTGA
* *
469076 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATATCATTGTATAG-AT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTGTAT
*
469140 ATTATAATCACCTTTATCAGGCTAGTTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
469174 ATCCATAAAACTGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* * *
469239 TAATCGCCTTTATCAGGCTAGCTGATTCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
*
469269 ATCCATAAAGCCGGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
469334 ATA
65 ATA
469337 TAATTATAAT
Statistics
Matches: 148, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
94 4 0.03
95 93 0.63
96 6 0.04
97 1 0.01
98 44 0.30
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:471667 original size:30 final size:29
Alignment explanation
Indices: 471629--471686 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
471619 ATGATAATAA
471629 CAATAAATCAA-AGAAAAA-AAACAATAAAT
1 CAATAAATCAATA-AAAAATAAA-AATAAAT
471658 CAATAAAATCAATAAAAAATAAAAATAAA
1 CAAT-AAATCAATAAAAAATAAAAATAAA
471687 AGTAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.16
Consensus pattern (29 bp):
CAATAAATCAATAAAAAATAAAAATAAAT
Found at i:471682 original size:17 final size:18
Alignment explanation
Indices: 471644--471723 Score: 52
Period size: 17 Copynumber: 4.9 Consensus size: 18
471634 AATCAAAGAA
* *
471644 AAAAAACAATAAATCAAT
1 AAAAATCAATAAATAAAT
471662 -AAAATCAATAAA-AAAT
1 AAAAATCAATAAATAAAT
*
471678 AAAAAT-AA-AAGTAAA-
1 AAAAATCAATAAATAAAT
*
471693 AACAA--AATAAATAAA-
1 AAAAATCAATAAATAAAT
471708 ACAAAAT-AATAAATAA
1 A-AAAATCAATAAATAA
471724 CCTAGAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 2 0.04
15 13 0.25
16 11 0.22
17 25 0.49
ACGTcount: A:0.76, C:0.06, G:0.01, T:0.16
Consensus pattern (18 bp):
AAAAATCAATAAATAAAT
Found at i:471720 original size:13 final size:14
Alignment explanation
Indices: 471691--471720 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
471681 AATAAAAGTA
471691 AAAACAAAATAAAT
1 AAAACAAAATAAAT
471705 AAAACAAAAT-AAT
1 AAAACAAAATAAAT
471718 AAA
1 AAA
471721 TAACCTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAACAAAATAAAT
Found at i:471721 original size:21 final size:21
Alignment explanation
Indices: 471630--471723 Score: 54
Period size: 21 Copynumber: 4.4 Consensus size: 21
471620 TGATAATAAC
*
471630 AATAAATCAAAGAAAA--AAAA
1 AATAAAT-AAATAAAAGCAAAA
* *
471650 CAATAAATCAATAAAATCAATAA
1 -AATAAATAAATAAAAGCAA-AA
* *
471673 AA-AATAAAAATAAAAGTAAAA
1 AATAA-ATAAATAAAAGCAAAA
471694 ACA-AAATAAATAAAA-CAAAA
1 A-ATAAATAAATAAAAGCAAAA
471714 TAATAAATAA
1 -AATAAATAA
471724 CCTAGAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
20 11 0.19
21 28 0.48
22 17 0.29
23 2 0.03
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (21 bp):
AATAAATAAATAAAAGCAAAA
Found at i:471753 original size:15 final size:15
Alignment explanation
Indices: 471691--471787 Score: 56
Period size: 16 Copynumber: 6.2 Consensus size: 15
471681 AATAAAAGTA
*
471691 AAAACAAAATA-AAT
1 AAAAGAAAATATAAT
*
471705 AAAACAAAATAATAAAT
1 AAAAGAAAAT-AT-AAT
*
471722 AACCTAGAAAA-ATAAT
1 AA--AAGAAAATATAAT
**
471738 ATCAGAAAATATAAT
1 AAAAGAAAATATAAT
471753 AAAAGAAATATATAA-
1 AAAAGAAA-ATATAAT
*
471768 AAAGAGTAAAATAAAAT
1 AAA-AG-AAAATATAAT
471785 AAA
1 AAA
471788 GGGACAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
14 16 0.24
15 15 0.23
16 17 0.26
17 13 0.20
19 5 0.08
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (15 bp):
AAAAGAAAATATAAT
Found at i:472447 original size:16 final size:17
Alignment explanation
Indices: 472417--472468 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
472407 AGGCCTGCAA
472417 AATAA-AATAATAAAAT
1 AATAATAATAATAAAAT
*
472433 AATAATAATAAAAAATAT
1 AATAATAATAATAAA-AT
472451 ATATAAT-ATAATAAAAT
1 A-ATAATAATAATAAAAT
472468 A
1 A
472469 TTTTTGTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 11 0.35
18 10 0.32
19 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAATAATAATAAAAT
Found at i:472456 original size:19 final size:18
Alignment explanation
Indices: 472417--472469 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
472407 AGGCCTGCAA
*
472417 AATAA-AATAATAAA-AT
1 AATAATAATAAAAAATAT
472433 AATAATAATAAAAAATAT
1 AATAATAATAAAAAATAT
472451 ATATAAT-ATAATAAAATAT
1 A-ATAATAATAA-AAAATAT
472470 TTTTGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 5 0.16
17 8 0.25
18 7 0.22
19 12 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAATAATAAAAAATAT
Found at i:472501 original size:2 final size:2
Alignment explanation
Indices: 472494--472536 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
472484 ATAAAAACGG
472494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
472536 A
1 A
472537 AAAGTCAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:476258 original size:31 final size:31
Alignment explanation
Indices: 476184--476258 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
476174 TTGAAAAAAA
476184 ATAATTGGGTGACTAAAAGAGAACAAAAGTG
1 ATAATTGGGTGACTAAAAGAGAACAAAAGTG
* * * **
476215 ATAGTTGAGTGACTAAAATAGAACTGAAGTG
1 ATAATTGGGTGACTAAAAGAGAACAAAAGTG
*
476246 ATAATAGGGTGAC
1 ATAATTGGGTGAC
476259 CAAATACATA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.23
Consensus pattern (31 bp):
ATAATTGGGTGACTAAAAGAGAACAAAAGTG
Found at i:478645 original size:43 final size:43
Alignment explanation
Indices: 478565--478889 Score: 278
Period size: 43 Copynumber: 7.5 Consensus size: 43
478555 TTTTTGTAGA
* * **
478565 TTCGATTCCATCACAGAAGCAGTTGGATCAGCATCAACATTTTG
1 TTCGATTCCATCACAGAAGGAGTTGAAT-TTCATCAACATTTTG
* * * * **
478609 TTCGATTTCATTATA-AAAGATGTTGAATTTCATCAACATTTCA
1 TTCGATTCCATCACAGAAGGA-GTTGAATTTCATCAACATTTTG
* * * *
478652 CTCGATTCCATCACAGAAGGAGTTGAGTTTTCATCAATATTTCG
1 TTCGATTCCATCACAGAAGGAGTTGA-ATTTCATCAACATTTTG
*
478696 TTCGATTCCATCACTGAAGGAGTTGAATTTCATCAACATTTTG
1 TTCGATTCCATCACAGAAGGAGTTGAATTTCATCAACATTTTG
* * * * *
478739 CTCTATTCCATCACAGAATGAGTTGATTTTCATCAATATTTTG
1 TTCGATTCCATCACAGAAGGAGTTGAATTTCATCAACATTTTG
* * *** *
478782 TTCGATTCCATCATAGAAGGAGTAGAACAACATCAACATTTCG
1 TTCGATTCCATCACAGAAGGAGTTGAATTTCATCAACATTTTG
* * * * * *
478825 ATCAATTCCATCATAGAAAGAGTTGGTCAA--ACATCAACATTTCG
1 TTCGATTCCATCACAGAAGGAGTT-G--AATTTCATCAACATTTTG
*
478869 TCCGATTCCATCACAGAAGGA
1 TTCGATTCCATCACAGAAGGA
478890 ATTGGATCAA
Statistics
Matches: 226, Mismatches: 49, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
43 133 0.59
44 91 0.40
46 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (43 bp):
TTCGATTCCATCACAGAAGGAGTTGAATTTCATCAACATTTTG
Found at i:478721 original size:87 final size:85
Alignment explanation
Indices: 478566--478881 Score: 310
Period size: 87 Copynumber: 3.6 Consensus size: 85
478556 TTTTGTAGAT
* * * * * * * *
478566 TCGATTCCATCACAGAAGCAGTTGGATCAGCATCAACATTTTGTTCGATTTCATTATAAAAGATG
1 TCGATTCCATCACAGAAGGAGTTGG-TTATCATCAACATTTCGTTCGATTCCATCATGAAGGA-G
478631 TTGAATTTCATCAACATTTCAC
64 TTGAATTTCATCAACATTTCAC
* *
478653 TCGATTCCATCACAGAAGGAGTTGAGTTTTCATCAATATTTCGTTCGATTCCATCACTGAAGGAG
1 TCGATTCCATCACAGAAGGAGTTG-GTTATCATCAACATTTCGTTCGATTCCATCA-TGAAGGAG
**
478718 TTGAATTTCATCAACATTTTGC
64 TTGAATTTCATCAACATTTCAC
* * * * * *
478740 TCTATTCCATCACAGAATGAGTTGATTTTCATCAATATTTTGTTCGATTCCATCATAGAAGGAGT
1 TCGATTCCATCACAGAAGGAGTTGGTTATCATCAACATTTCGTTCGATTCCATCAT-GAAGGAGT
* ***
478805 AGAACAACATCAACATTTCGA-
65 TGAATTTCATCAACATTTC-AC
* * * * * *
478826 TCAATTCCATCATAGAAAGAGTTGGTCAAACATCAACATTTCGTCCGATTCCATCA
1 TCGATTCCATCACAGAAGGAGTTGGT-TATCATCAACATTTCGTTCGATTCCATCA
478882 CAGAAGGAAT
Statistics
Matches: 192, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
85 1 0.01
86 73 0.38
87 112 0.58
88 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (85 bp):
TCGATTCCATCACAGAAGGAGTTGGTTATCATCAACATTTCGTTCGATTCCATCATGAAGGAGTT
GAATTTCATCAACATTTCAC
Found at i:478800 original size:130 final size:131
Alignment explanation
Indices: 478565--478804 Score: 304
Period size: 130 Copynumber: 1.8 Consensus size: 131
478555 TTTTTGTAGA
* * * * *
478565 TTCGATTCCATCACAGAAGCAGTTGGATCAGCATCAACATTTTGTTCGATTTCATTATAAAAGAT
1 TTCGATTCCATCACAGAAGCAGTTGAATCAGCATCAACATTTTGCTCGATTCCATCACAAAAGAT
478630 GTTGAATTTCATCAACATTTCACTCGATTCCATCACAGAAGGAGTTGAGTTTTCATCAATATTTC
66 GTTGAATTTCATCAACATTTCACTCGATTCCATCACAGAAGGAGTTGAGTTTTCATCAATATTTC
478695 G
131 G
* * ** * *
478696 TTCGATTCCATCACTGAAGGAGTTGAAT-TTCATCAACATTTTGCTCTATTCCATCACAGAATGA
1 TTCGATTCCATCACAGAAGCAGTTGAATCAGCATCAACATTTTGCTCGATTCCATCACA-AAAGA
* * *** *
478760 -GTTGATTTTCATCAATATTTTGTTCGATTCCATCATAGAAGGAGT
65 TGTTGAATTTCATCAACATTTCACTCGATTCCATCACAGAAGGAGT
478805 AGAACAACAT
Statistics
Matches: 91, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
130 62 0.68
131 29 0.32
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (131 bp):
TTCGATTCCATCACAGAAGCAGTTGAATCAGCATCAACATTTTGCTCGATTCCATCACAAAAGAT
GTTGAATTTCATCAACATTTCACTCGATTCCATCACAGAAGGAGTTGAGTTTTCATCAATATTTC
G
Found at i:478869 original size:173 final size:174
Alignment explanation
Indices: 478569--478889 Score: 391
Period size: 173 Copynumber: 1.9 Consensus size: 174
478559 TGTAGATTCG
* * *
478569 ATTCCATCACAGAAGCAGTTGGATCAGCATCAACATTTTGTTCGATTTCATTATAAAAGATGTTG
1 ATTCCATCACAGAAGCAGTTGGATCAGCATCAACATTTTGTTCGATTCCATCATAAAAGATGTAG
*** * * *** * *
478634 AATTTCATCAACATTTCACTCGATTCCATCACAGAAGGAGTTGAGTTTTCATCAATATTTCGTTC
66 AACAACATCAACATTTCACTCAATTCCATCACAGAAAGAGTTGAGTAAACATCAACATTTCGTCC
*
478699 GATTCCATCACTGAAGGAGTTGAATTTCATCAACATTTTGCTCT
131 GATTCCATCACAGAAGGAGTTGAATTTCATCAACATTTTGCTCT
*** * *
478743 ATTCCATCACAGAATG-AGTT-GATTTTCATCAATATTTTGTTCGATTCCATCATAGAAGGA-GT
1 ATTCCATCACAGAA-GCAGTTGGATCAGCATCAACATTTTGTTCGATTCCATCATA-AAAGATGT
*
478805 AGAACAACATCAACATTTCGA-TCAATTCCATCATAGAAAGAGTTG-GTCAAACATCAACATTTC
64 AGAACAACATCAACATTTC-ACTCAATTCCATCACAGAAAGAGTTGAGT-AAACATCAACATTTC
478868 GTCCGATTCCATCACAGAAGGA
127 GTCCGATTCCATCACAGAAGGA
478890 ATTGGATCAA
Statistics
Matches: 123, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
172 2 0.02
173 97 0.79
174 23 0.19
175 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (174 bp):
ATTCCATCACAGAAGCAGTTGGATCAGCATCAACATTTTGTTCGATTCCATCATAAAAGATGTAG
AACAACATCAACATTTCACTCAATTCCATCACAGAAAGAGTTGAGTAAACATCAACATTTCGTCC
GATTCCATCACAGAAGGAGTTGAATTTCATCAACATTTTGCTCT
Found at i:478908 original size:44 final size:44
Alignment explanation
Indices: 478567--478956 Score: 165
Period size: 44 Copynumber: 8.9 Consensus size: 44
478557 TTTGTAGATT
* * * *
478567 CGATTCCATCACAG-AAGCAGTTGGATCAGCATCAACATTTTGTT
1 CGATTCCATCACAGAAAG-AATTGGATCAACATCAACATTTCGTC
* * * * * ** *
478611 CGATTTCATTATA-AAAGATGTTGAAT-TTCATCAACATTTC-AC
1 CGATTCCATCACAGAAAGA-ATTGGATCAACATCAACATTTCGTC
* * *** * *
478653 TCGATTCCATCACAGAAGGAGTT-GAGTTTTCATCAATATTTCGTT
1 -CGATTCCATCACAGAAAGAATTGGA-TCAACATCAACATTTCGTC
* * * * ** *
478698 CGATTCCATCACTGAAGGAGTTGAAT-TTCATCAACATTTTG-C
1 CGATTCCATCACAGAAAGAATTGGATCAACATCAACATTTCGTC
* * * *** * * *
478740 TCTATTCCATCACAGAATGAGTT-GATTTTCATCAATATTTTGTT
1 -CGATTCCATCACAGAAAGAATTGGATCAACATCAACATTTCGTC
* * * * *
478784 CGATTCCATCATAG-AAGGAGTAGAACAACATCAACATTTCGAT-
1 CGATTCCATCACAGAAAGAATTGGATCAACATCAACATTTCG-TC
* * *
478827 CAATTCCATCATAGAAAGAGTTGG-TCAAACATCAACATTTCGTC
1 CGATTCCATCACAGAAAGAATTGGATC-AACATCAACATTTCGTC
* * * *
478871 CGATTCCATCACAGAAGGAATTGGATCAACTTTAACATTTTG-C
1 CGATTCCATCACAGAAAGAATTGGATCAACATCAACATTTCGTC
* * *
478914 TCGATCCCATCACAAAAAGAATTGGATCAAGCATTAACATTTC
1 -CGATTCCATCACAGAAAGAATTGGATCAA-CATCAACATTTC
478957 ACTCTTTTCC
Statistics
Matches: 269, Mismatches: 58, Indels: 37
0.74 0.16 0.10
Matches are distributed among these distances:
42 6 0.02
43 113 0.42
44 137 0.51
45 13 0.05
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (44 bp):
CGATTCCATCACAGAAAGAATTGGATCAACATCAACATTTCGTC
Found at i:480255 original size:20 final size:20
Alignment explanation
Indices: 480218--480255 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
480208 CTTAAACTTC
*
480218 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
480238 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
480256 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:480422 original size:23 final size:23
Alignment explanation
Indices: 480393--480456 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
480383 CAGCTCGTAT
*
480393 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAG
* *
480416 AATTGCACCGTAA-TGCCGCATAG
1 AAATGCACCG-AAGTGCCACATAG
480439 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
480457 TATAATATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:483453 original size:13 final size:13
Alignment explanation
Indices: 483431--483460 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
483421 ACTAAACACC
483431 TTTC-ACATACCT
1 TTTCAACATACCT
483443 TTTCAACATACCT
1 TTTCAACATACCT
483456 TTTCA
1 TTTCA
483461 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:486295 original size:19 final size:18
Alignment explanation
Indices: 486248--486283 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
486238 TCTTTGCTTT
486248 CTTTGACTTTGCACTTCA
1 CTTTGACTTTGCACTTCA
486266 CTTTGCACTTTGCACTTC
1 CTTTG-ACTTTGCACTTC
486284 TTTTTGTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.14, C:0.31, G:0.11, T:0.44
Consensus pattern (18 bp):
CTTTGACTTTGCACTTCA
Found at i:492077 original size:26 final size:26
Alignment explanation
Indices: 492023--492075 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
492013 AATTATCTCG
*
492023 AATATTTAATTTAAATTAATTAAATA
1 AATATTTAATTTAAATTAAATAAATA
*
492049 AATATTTAA-TTAATTTGAAAT-AATA
1 AATATTTAATTTAAATT-AAATAAATA
492074 AA
1 AA
492076 ATCCCTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
AATATTTAATTTAAATTAAATAAATA
Found at i:492793 original size:23 final size:24
Alignment explanation
Indices: 492752--492797 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
492742 TTTAACTTTT
* *
492752 TTTTATTTTCTTAATTTATTTATC
1 TTTTATCTTCTTAAATTATTTATC
492776 TTTTATCTT-TTAAATTATTTAT
1 TTTTATCTTCTTAAATTATTTAT
492798 TTTAATTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTATCTTCTTAAATTATTTATC
Found at i:498879 original size:21 final size:20
Alignment explanation
Indices: 498853--498893 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
498843 TCAGGGTTTG
*
498853 AGTATCGATACTGGGATGAAT
1 AGTATCAATA-TGGGATGAAT
*
498874 AGTATCAATATTGGATGAAT
1 AGTATCAATATGGGATGAAT
498894 TAGGGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTATCAATATGGGATGAAT
Found at i:499009 original size:20 final size:20
Alignment explanation
Indices: 498984--499038 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
498974 CAAGATGCTG
498984 GTCTCCATACCGAAGGACTA
1 GTCTCCATACCGAAGGACTA
* * *
499004 GTCTCCATACAGAATGACTT
1 GTCTCCATACCGAAGGACTA
* *
499024 TTATCCATACCGAAG
1 GTCTCCATACCGAAG
499039 ATTGAGTATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (20 bp):
GTCTCCATACCGAAGGACTA
Found at i:504080 original size:15 final size:16
Alignment explanation
Indices: 504035--504089 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
504025 TTATAAAAGA
*
504035 AAGAAAATAAAATAAG
1 AAGAATATAAAATAAG
504051 AAGAATATAAGAATAA-
1 AAGAATATAA-AATAAG
504067 AAG-ATATGAAAATAAG
1 AAGAATAT-AAAATAAG
*
504083 AAAAATA
1 AAGAATA
504090 ACTTGTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 9 0.27
16 16 0.48
17 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (16 bp):
AAGAATATAAAATAAG
Found at i:507122 original size:28 final size:28
Alignment explanation
Indices: 507082--507136 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
507072 AAATTAAAAA
507082 TTAAAGATTAAAGTTTTGCTTGGTTGAG
1 TTAAAGATTAAAGTTTTGCTTGGTTGAG
507110 TTAAAGATTAAAGTTTTGCTTGGTTGA
1 TTAAAGATTAAAGTTTTGCTTGGTTGA
507137 AAAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.44
Consensus pattern (28 bp):
TTAAAGATTAAAGTTTTGCTTGGTTGAG
Found at i:507149 original size:28 final size:28
Alignment explanation
Indices: 507090--507153 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
507080 AATTAAAGAT
** * *
507090 TAAAGTTTTGCTTGGTTGAGTTAAAGAT
1 TAAAGTTTTGCTTGGTTGAGAAAAAAAA
507118 TAAAGTTTTGCTTGGTTGA-AAAAATAAA
1 TAAAGTTTTGCTTGGTTGAGAAAAA-AAA
507146 TAAA-TTTT
1 TAAAGTTTT
507154 CATCTTTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (28 bp):
TAAAGTTTTGCTTGGTTGAGAAAAAAAA
Found at i:509104 original size:6 final size:6
Alignment explanation
Indices: 509093--509168 Score: 60
Period size: 6 Copynumber: 13.8 Consensus size: 6
509083 TAAAAGCATT
* *
509093 TTAATA TTAATA TTAATA TGT--T- TTAATA -TAAT- TTTATA CTAATA
1 TTAATA TTAATA TTAATA T-TAATA TTAATA TTAATA TTAATA TTAATA
*
509137 TTAAT- TTAATA TTAA-A ATAAT- TTAATA TTAAT
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAAT
509169 TTATGAATGC
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
3 1 0.02
4 1 0.02
5 22 0.40
6 30 0.55
7 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
TTAATA
Found at i:509118 original size:22 final size:22
Alignment explanation
Indices: 509090--509168 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
509080 AATTAAAAGC
509090 ATTTTAATATTAATATTAATAT
1 ATTTTAATATTAATATTAATAT
* *
509112 GTTTTAATA-TAAT-TTTATACT
1 ATTTTAATATTAATATTAATA-T
* *
509133 AATATTAAT-TTAATATTAAAAT
1 -ATTTTAATATTAATATTAATAT
*
509155 AATTTAATATTAAT
1 ATTTTAATATTAAT
509169 TTATGAATGC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.11
21 11 0.25
22 24 0.55
23 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (22 bp):
ATTTTAATATTAATATTAATAT
Found at i:509135 original size:16 final size:16
Alignment explanation
Indices: 509116--509168 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
509106 TAATATGTTT
*
509116 TAATATAATTTTATAC
1 TAATATAATTTAATAC
*
509132 TAATATTAATTTAATAT
1 TAATA-TAATTTAATAC
* *
509149 TAAAATAATTTAATAT
1 TAATATAATTTAATAC
509165 TAAT
1 TAAT
509169 TTATGAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATAATTTAATAC
Found at i:519908 original size:30 final size:30
Alignment explanation
Indices: 519874--520005 Score: 165
Period size: 30 Copynumber: 4.4 Consensus size: 30
519864 TTACTGTTTA
* * *
519874 AGTCCTTTAAATTTTTATTTTTGTTATTTC
1 AGTCCTTTAAATTTCTATTTTTGCTATTTT
* * *
519904 AGTCCTTTAAATTTTTGTTTTTGTTATTTT
1 AGTCCTTTAAATTTCTATTTTTGCTATTTT
* * * *
519934 AGACCTTTAAATTTCTGTTCTTACTATTTT
1 AGTCCTTTAAATTTCTATTTTTGCTATTTT
519964 AGTCCTTTAAATTTCTATTTTTGCTATTTT
1 AGTCCTTTAAATTTCTATTTTTGCTATTTT
*
519994 GGTCCTTTAAAT
1 AGTCCTTTAAAT
520006 CAAATATGAT
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.59
Consensus pattern (30 bp):
AGTCCTTTAAATTTCTATTTTTGCTATTTT
Found at i:527950 original size:62 final size:62
Alignment explanation
Indices: 527753--527972 Score: 287
Period size: 62 Copynumber: 3.5 Consensus size: 62
527743 CGAGAGGTTC
* * * **
527753 AATATTTTCATCGTCCAGATTCTAAAAGTTAGTTTGGGTTGCCAGGGGTGTTACCGGTGATCTTT
1 AATATCTTCATCGTCCAGATTCTCAAAG--A--TTGGGTTGCCAGCGGTGTTACTAGTGATCTTT
527818 T
62 T
* * * *
527819 AATAACTTCATCGTTCAGATTCTCATAGTTTGGGGGTTGCCAGCGGTGTTACTAGTGATCTTTT
1 AATATCTTCATCGTCCAGATTCTCAAAGATT--GGGTTGCCAGCGGTGTTACTAGTGATCTTTT
* *
527883 AATATCTTCATCGTTCAGATTCTCAAAGATTGGGATGCCAGCGGTGTTACTAGTGATCTTTT
1 AATATCTTCATCGTCCAGATTCTCAAAGATTGGGTTGCCAGCGGTGTTACTAGTGATCTTTT
527945 AATATCTTCATCGTCCAGATTCTCAAAG
1 AATATCTTCATCGTCCAGATTCTCAAAG
527973 TCAAAGCTTG
Statistics
Matches: 138, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
62 59 0.43
64 56 0.41
66 23 0.17
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (62 bp):
AATATCTTCATCGTCCAGATTCTCAAAGATTGGGTTGCCAGCGGTGTTACTAGTGATCTTTT
Found at i:532297 original size:2 final size:2
Alignment explanation
Indices: 532285--532326 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
532275 ATTGTATTTG
532285 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
532326 A
1 A
532327 AATTGGAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:540248 original size:14 final size:15
Alignment explanation
Indices: 540219--540250 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
540209 AAATAATTAA
540219 AATAATATATTTTAT
1 AATAATATATTTTAT
540234 AATAATATA-TTTAT
1 AATAATATATTTTAT
540248 AAT
1 AAT
540251 CACTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:540327 original size:21 final size:20
Alignment explanation
Indices: 540276--540335 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
540266 TTAATTGTTA
*
540276 AAATAATATATTTTTATAAT
1 AAATAATATATTTTAATAAT
* * *
540296 AATTTACTATAATTTAATAATT
1 AA-ATAATATATTTTAATAA-T
540318 AAATAATATATTTTAATA
1 AAATAATATATTTTAATA
540336 GTATAAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATAATATATTTTAATAAT
Found at i:541863 original size:17 final size:16
Alignment explanation
Indices: 541838--541876 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
541828 TTAGATATTA
541838 TTTTAAATAAT-TACAT
1 TTTTAAATAATAT-CAT
541854 TTTTATAATAATATCAT
1 TTTTA-AATAATATCAT
541871 TTTTAA
1 TTTTAA
541877 CTCGTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 14 0.67
18 1 0.05
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAAATAATATCAT
Found at i:543492 original size:33 final size:33
Alignment explanation
Indices: 543455--543621 Score: 201
Period size: 33 Copynumber: 5.1 Consensus size: 33
543445 GAACATATAT
* * *
543455 TAACATGAACTTTCATGGTAAGAAATAATATCA
1 TAACATGAACTTTCATGGCAAGAACTTATATCA
*
543488 TAACATGAACTTTCATGGC-AGTAACTTATATTA
1 TAACATGAACTTTCATGGCAAG-AACTTATATCA
* * * *
543521 CAACAAGCACTTTCATGGCAAGAACTTACATCA
1 TAACATGAACTTTCATGGCAAGAACTTATATCA
* *
543554 TAATATGAACTTTCATGGCAATAACTTATATCA
1 TAACATGAACTTTCATGGCAAGAACTTATATCA
* * *
543587 TAACATGAATTTTCATGACAAGAACTTATCTCA
1 TAACATGAACTTTCATGGCAAGAACTTATATCA
543620 TA
1 TA
543622 TAAATCATAA
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
32 2 0.02
33 108 0.96
34 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (33 bp):
TAACATGAACTTTCATGGCAAGAACTTATATCA
Found at i:544146 original size:51 final size:51
Alignment explanation
Indices: 544060--544224 Score: 215
Period size: 51 Copynumber: 3.2 Consensus size: 51
544050 ATATTATCTT
* * * * ** * *
544060 TTCACAT-GATTTCTTATCTTCGTGTACCAAGTGAGTTGTAGCTATTTATCA
1 TTCACATAG-TTTCTTATCTTGGCGTACTAAATGAGTCATAGCTCTTTCTCA
*
544111 TTCACATAGTTTCTTATCTAGGCGTACTAAATGAGTCATAGCTCTTTCTCA
1 TTCACATAGTTTCTTATCTTGGCGTACTAAATGAGTCATAGCTCTTTCTCA
* *
544162 TTCACATAGTTTCTTATCTTGGCATACTAAATGGGTCATAGCTCTTTCTCA
1 TTCACATAGTTTCTTATCTTGGCGTACTAAATGAGTCATAGCTCTTTCTCA
544213 TTCACATAGTTT
1 TTCACATAGTTT
544225 TCATCATGCT
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 100 0.99
52 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (51 bp):
TTCACATAGTTTCTTATCTTGGCGTACTAAATGAGTCATAGCTCTTTCTCA
Found at i:544321 original size:25 final size:25
Alignment explanation
Indices: 544274--544321 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
544264 GTACGTGTCA
* **
544274 TAACACATATTTACACCCGTGAAAG
1 TAACACATAATTACACCAATGAAAG
544299 TAACACATAATTACACCAATGAA
1 TAACACATAATTACACCAATGAA
544322 CTTTAGCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (25 bp):
TAACACATAATTACACCAATGAAAG
Found at i:547472 original size:102 final size:103
Alignment explanation
Indices: 547306--547493 Score: 261
Period size: 102 Copynumber: 1.8 Consensus size: 103
547296 GTTTCGGATC
* * * * *
547306 TGGCACCAAGATGGATCACTTGTGGTCTTACTCGGCGTACCCTAGTGGTGCACGAGGTGGAGTGA
1 TGGCACCAAGACGGATCACTCGTGCTCTAACTCGGCGTACCCTAGTGGTGCACGAGGTGAAGTGA
* *
547371 TTCGGTGCAATCTG-TCTGACTCTATATGTATGTTATA
66 CTCGGTGCAATATGTTCTGACTCTATATGTATGTTATA
* * * * *
547408 TGGCATCAAGACGGGTCACTCGTGCTCTAACTCGGCTTATCTTAGTGGTGCACGAGGTGAAGTGA
1 TGGCACCAAGACGGATCACTCGTGCTCTAACTCGGCGTACCCTAGTGGTGCACGAGGTGAAGTGA
547473 CTCGGTGCAATATGTTCTGAC
66 CTCGGTGCAATATGTTCTGAC
547494 AGTAAATTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
102 67 0.92
103 6 0.08
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.30
Consensus pattern (103 bp):
TGGCACCAAGACGGATCACTCGTGCTCTAACTCGGCGTACCCTAGTGGTGCACGAGGTGAAGTGA
CTCGGTGCAATATGTTCTGACTCTATATGTATGTTATA
Found at i:547865 original size:5 final size:5
Alignment explanation
Indices: 547855--547879 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
547845 TTTGTTAAAA
547855 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
547880 GGTTGCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:548607 original size:28 final size:28
Alignment explanation
Indices: 548576--548630 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
548566 TATGAGAAGG
548576 ATCTGAATGATACTCACATAGTTCAGAT
1 ATCTGAATGATACTCACATAGTTCAGAT
548604 ATCTGAATGATACTCACATAGTTCAGA
1 ATCTGAATGATACTCACATAGTTCAGA
548631 GACCTGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (28 bp):
ATCTGAATGATACTCACATAGTTCAGAT
Found at i:548637 original size:28 final size:28
Alignment explanation
Indices: 548578--548638 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
548568 TGAGAAGGAT
* *
548578 CTGAATGATACTCACATAGTTCAGATAT
1 CTGAATGATACTCACATAGTTCAGAGAC
548606 CTGAATGATACTCACATAGTTCAGAGAC
1 CTGAATGATACTCACATAGTTCAGAGAC
548634 CTGAA
1 CTGAA
548639 CTAAAATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (28 bp):
CTGAATGATACTCACATAGTTCAGAGAC
Found at i:549366 original size:42 final size:43
Alignment explanation
Indices: 549261--549370 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 43
549251 ACAAAAGATA
**
549261 AAGCTCTATAGC-GTCGTTTTTCTTACAAACATTGCGAAAGGTC
1 AAGCTCTATAGCGGT-GTTTTTCTTACAAACACCGCGAAAGGTC
** **
549304 AAGCTCTATAATGGCCTTTTT-TTACAAACACCGCGAAAGGTC
1 AAGCTCTATAGCGGTGTTTTTCTTACAAACACCGCGAAAGGTC
*
549346 AATCTCTATAGCGGTGTTTTTCTTA
1 AAGCTCTATAGCGGTGTTTTTCTTA
549371 TAAATGCCAC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 35 0.65
43 18 0.33
44 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (43 bp):
AAGCTCTATAGCGGTGTTTTTCTTACAAACACCGCGAAAGGTC
Found at i:552481 original size:22 final size:22
Alignment explanation
Indices: 552453--552497 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
552443 ATTCCCCTAA
552453 AAGAACAAGCAAGGTCCACACC
1 AAGAACAAGCAAGGTCCACACC
552475 AAGAACAAGCAAGGTCCACACC
1 AAGAACAAGCAAGGTCCACACC
552497 A
1 A
552498 TGGAGCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.31, G:0.18, T:0.04
Consensus pattern (22 bp):
AAGAACAAGCAAGGTCCACACC
Found at i:553373 original size:19 final size:20
Alignment explanation
Indices: 553337--553391 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
553327 CATCTTGGTC
553337 AATATAATTTATTAAATATA
1 AATATAATTTATTAAATATA
*
553357 AATATAATTTA-TAAATATT
1 AATATAATTTATTAAATATA
553376 AA-ATAATTTATTAAAT
1 AATATAATTTATTAAAT
553392 CGATATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 8 0.24
19 14 0.42
20 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATAATTTATTAAATATA
Found at i:553400 original size:18 final size:18
Alignment explanation
Indices: 553337--553391 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
553327 CATCTTGGTC
553337 AATATAATTTATTAAATATA
1 AATATAATTTATT-AA-ATA
553357 AATATAATTTA-TAAATA
1 AATATAATTTATTAAATA
553374 TTAA-ATAATTTATTAAAT
1 --AATATAATTTATTAAAT
553392 CGATATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.09
18 10 0.31
19 8 0.25
20 11 0.34
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATAATTTATTAAATA
Found at i:553588 original size:3 final size:3
Alignment explanation
Indices: 553580--553650 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
553570 TTTCATTATG
* *
553580 TTA TTA TTA TTA TTA TTA TTA TTA ATA TATA TTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* *
553626 TTA ATA TACA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
553651 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 53 0.91
4 5 0.09
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:553613 original size:25 final size:25
Alignment explanation
Indices: 553584--553650 Score: 116
Period size: 25 Copynumber: 2.7 Consensus size: 25
553574 ATTATGTTAT
553584 TATTATTATTATTATTATTAATATA
1 TATTATTATTATTATTATTAATATA
*
553609 TATTATTGTTATTATTATTAATATA
1 TATTATTATTATTATTATTAATATA
*
553634 CATTATTATTATTATTA
1 TATTATTATTATTATTA
553651 AATAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (25 bp):
TATTATTATTATTATTATTAATATA
Found at i:553987 original size:17 final size:17
Alignment explanation
Indices: 553962--553996 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
553952 CTCTTGGGAT
553962 CGGTCCGAGCAGAGCAC
1 CGGTCCGAGCAGAGCAC
*
553979 CGGTGCGAGCAGAGCAC
1 CGGTCCGAGCAGAGCAC
553996 C
1 C
553997 TGTGATGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.34, G:0.37, T:0.06
Consensus pattern (17 bp):
CGGTCCGAGCAGAGCAC
Found at i:554974 original size:11 final size:11
Alignment explanation
Indices: 554949--555011 Score: 69
Period size: 11 Copynumber: 5.8 Consensus size: 11
554939 TAATTTGCAA
554949 TATTATTTTAT
1 TATTATTTTAT
554960 TATTACTTTTA-
1 TATTA-TTTTAT
*
554971 TA-T-TTTAAT
1 TATTATTTTAT
*
554980 TATTGCTTTTAT
1 TATT-ATTTTAT
554992 TATTATTTTAT
1 TATTATTTTAT
555003 TATTATTTT
1 TATTATTTT
555012 TATATTAGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 4 0.09
9 2 0.05
10 2 0.05
11 22 0.50
12 14 0.32
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:554983 original size:20 final size:19
Alignment explanation
Indices: 554952--555017 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 19
554942 TTTGCAATAT
554952 TATTTTATTATTACTTTTA
1 TATTTTATTATTACTTTTA
*
554971 TATTTTAATTATTGCTTTTATTA
1 TATTTT-ATTATTAC--TT-TTA
*
554994 TTATTTTATTATTATTTTTA
1 -TATTTTATTATTACTTTTA
555014 TATT
1 TATT
555018 AGTCATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 10 0.26
20 10 0.26
21 2 0.05
22 2 0.05
23 9 0.23
24 6 0.15
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.70
Consensus pattern (19 bp):
TATTTTATTATTACTTTTA
Found at i:555328 original size:157 final size:145
Alignment explanation
Indices: 555052--555457 Score: 411
Period size: 148 Copynumber: 2.7 Consensus size: 145
555042 GTTTAAATAA
* ** * * *
555052 TAATATTTATTTATTTTTAATATCAAAGAAAATGGCAGTCTTAAAGCAACTAGATGTCATATTCT
1 TAATATTTATTTATTTTTAATAT-TAAG-AAATGGTTGTCTTAAAGCACCTAGAAGTCATTTTCT
* * *
555117 GGTATTTTAAATAAATAAATATCTTACTTATAAAAACCAGAAAATAAATATTATTTTATTTAAAT
64 GATATTTCAAATAAATAAATATCTTATTTATAAAAACCAGAAAATAAATATTA---T-TTT-AAT
*
555182 TATTTTCTTAGAAAAATAATCATATTT
124 TA-TTT-TTAGAAAAAT-AT--TATAT
* *
555209 TAATATTTATATATTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCCTTTTCTG
1 TAATATTTATTTATTTTTAATATTAAGAAATG-GTTGTCTTAAAGCACCTAGAAGTCATTTTCTG
* * * ** * *
555274 ATATTCTCAAATAAATAAATATCCTATTTTTATAAATTA-TATATACTAAT-TTATTTTAATTAT
65 ATATT-TCAAATAAATAAATATCTTATTTATAAAAACCAGAAAATA--AATATTATTTTAATTAT
* * *
555337 TTTTATAAAAATGTTGTAT
127 TTTTAGAAAAATATTATAT
*
555356 TAATATTTATTTATTTTTTATTATTAAGAAATGGGTTGTCTTAAAGCACCTAGAAGTCATTTTCT
1 TAATATTTATTTA-TTTTTAATATTAAGAAAT-GGTTGTCTTAAAGCACCTAGAAGTCATTTTCT
*
555421 GATATTTCTAACTAAATAAATATCTTATTTATAAAAA
64 GATATTTC-AAATAAATAAATATCTTATTTATAAAAA
555458 TGAATATATA
Statistics
Matches: 213, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
147 17 0.08
148 77 0.36
149 2 0.01
150 9 0.04
151 3 0.01
152 5 0.02
153 3 0.01
154 1 0.00
155 5 0.02
156 37 0.17
157 51 0.24
158 3 0.01
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (145 bp):
TAATATTTATTTATTTTTAATATTAAGAAATGGTTGTCTTAAAGCACCTAGAAGTCATTTTCTGA
TATTTCAAATAAATAAATATCTTATTTATAAAAACCAGAAAATAAATATTATTTTAATTATTTTT
AGAAAAATATTATAT
Found at i:558088 original size:43 final size:44
Alignment explanation
Indices: 558021--558107 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
558011 TGGCTTTAGA
* *
558021 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAATTATCCCCTATATGTAAAAGTTTTGTT
* *
558064 GAAGTTAGGACTGAAAATTGTCCCCTATATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAATTATCCCCTATATGTAAAAGTTTTGTT
558108 TGATGCATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAATTATCCCCTATATGTAAAAGTTTTGTT
Found at i:558291 original size:20 final size:20
Alignment explanation
Indices: 558268--558334 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
558258 CATATTTACA
558268 TTTACATTTGCATTTGCATT
1 TTTACATTTGCATTTGCATT
** * *
558288 TTTATGTTTGTATTTACATT
1 TTTACATTTGCATTTGCATT
* ** *
558308 TTCATTTTTGCATTTGCATC
1 TTTACATTTGCATTTGCATT
558328 TTTACAT
1 TTTACAT
558335 AATTATATTT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTACATTTGCATTTGCATT
Found at i:564204 original size:70 final size:71
Alignment explanation
Indices: 564019--564210 Score: 226
Period size: 75 Copynumber: 2.7 Consensus size: 71
564009 ATATTAATGA
* *
564019 ATTTTGAACGTTTGTATCAGCAAATATTGGGGCATGCTGAAAGCTCATTTCAATAAGAATCAGGA
1 ATTTTGAACGTTTGTATCAGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATAAGAATCAGGA
*
564084 ATATTGGCGC
66 ATA---G-AC
* * * *
564094 ATTTTGAACGTTTGTATTAGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-TGG
1 ATTTTGAACGTTTGTATCAGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATAAG-AATCAGG
564158 AATA-AC
65 AATAGAC
** * *
564164 ATTTTGAACGTTCATATCAGTAAATGTTGGGGCATGCTGAAGGCCCA
1 ATTTTGAACGTTTGTATCAGCAAATGTTGGGGCATGCTGAAAGCCCA
564211 CATCATTATG
Statistics
Matches: 103, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
70 42 0.41
75 58 0.56
76 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
ATTTTGAACGTTTGTATCAGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATAAGAATCAGGA
ATAGAC
Found at i:565575 original size:22 final size:22
Alignment explanation
Indices: 565550--565604 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
565540 ATCTACATTC
*
565550 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTATT
* *
565572 TTCAAAGATGATATATTTTATT
1 TTCAAAGATGATAGATTCTATT
565594 TTCAAAGATGA
1 TTCAAAGATGA
565605 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTATT
Found at i:566133 original size:45 final size:45
Alignment explanation
Indices: 566069--566440 Score: 663
Period size: 45 Copynumber: 8.2 Consensus size: 45
566059 ATCACACAAA
566069 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
566114 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAATCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
566159 CATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
566204 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
566249 CATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
566295 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
566340 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
566385 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
566430 CATCTGTAAGC
1 CATCTGTAAGC
566441 TCTACAATAC
Statistics
Matches: 312, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 268 0.86
46 44 0.14
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:566372 original size:181 final size:180
Alignment explanation
Indices: 566069--566440 Score: 663
Period size: 181 Copynumber: 2.1 Consensus size: 180
566059 ATCACACAAA
566069 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
*
566134 CAGGATGTTTTCAAAATCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTT
66 CAGGATGTTTTCAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTT
* * *
566199 CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
131 CGGATCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGAGT
*
566249 CATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
* *
566314 GCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCT
65 GCAGGATGTTTTCAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCT
*
566379 TTGGATCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGAGT
130 TCGGATCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGAGT
566430 CATCTGTAAGC
1 CATCTGTAAGC
566441 TCTACAATAC
Statistics
Matches: 183, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
180 31 0.17
181 152 0.83
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (180 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
CAGGATGTTTTCAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTT
CGGATCATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGAGT
Found at i:566635 original size:3 final size:3
Alignment explanation
Indices: 566627--566691 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
566617 TTTCATTCTG
* *
566627 TTA TTA TTA TTA TTA TTA ATA TAAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* *
566673 ATA TACA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA
566692 AATAAAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 48 0.92
4 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:566667 original size:28 final size:28
Alignment explanation
Indices: 566627--566691 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
566617 TTTCATTCTG
566627 TTATTATTATTATTATTAATATAAATTA
1 TTATTATTATTATTATTAATATAAATTA
*
566655 TTATTATTATTATTATTAATATACATTA
1 TTATTATTATTATTATTAATATAAATTA
566683 TTATTATTA
1 TTATTATTA
566692 AATAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TTATTATTATTATTATTAATATAAATTA
Done.