Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 32 of 39
Found at i:6367264 original size:16 final size:19
Alignment explanation
Indices: 6367219--6367257 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6367209 AATGTCGAGT
6367219 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
6367238 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
6367257 T
1 T
6367258 TTTGTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:6367748 original size:197 final size:198
Alignment explanation
Indices: 6367383--6368735 Score: 2461
Period size: 197 Copynumber: 6.9 Consensus size: 198
6367373 CAATATGGCC
* *
6367383 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
6367448 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
6367512 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
6367577 TGGAA
195 TGG-A
6367582 AACAA-GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
6367646 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
* *
6367711 AATATATCTAAATAATGTGTCGACACTAATA-AGTTTGTGTCAATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
6367775 GGA
196 GGA
*
6367778 AACAAGGTGCACCCATAAAGTATCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
6367842 CAAAAGTATAATGTAATATGT-ATTTTTCAATCTAACCGGTACAATTATACCGG-TTT-TGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
6367904 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
6367969 GG-
196 GGA
6367971 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
6368036 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
6368101 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
6368166 GGA
196 GGA
6368169 AACAAGGTGCACCCATAAAGTG-CGATCC--ATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
6368230 CAAAAGTATAATGTAATATGTAATTTTTCAATTTAACCGGTGCAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
6368295 AATATGTCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
6368360 GGA
196 GGA
6368363 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
6368428 CAAACG-AGTAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGA
66 CAAAAGTA-TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
6368492 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
6368556 TGGAA
195 TGG-A
6368561 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
6368624 CAAAAGTATAATGT-ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
6368688 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
6368736 AATTTAAATA
Statistics
Matches: 1120, Mismatches: 18, Indels: 35
0.95 0.02 0.03
Matches are distributed among these distances:
193 70 0.06
194 252 0.22
195 186 0.17
196 104 0.09
197 265 0.24
198 239 0.21
199 4 0.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGA
Found at i:6368674 original size:587 final size:586
Alignment explanation
Indices: 6367383--6368735 Score: 2436
Period size: 587 Copynumber: 2.3 Consensus size: 586
6367373 CAATATGGCC
* *
6367383 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCA-ATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
6367448 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGA
64 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
6367512 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
129 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
6367577 TGGAAAACAAGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
194 TGGAAAACAAGTGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCG
6367642 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
258 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
*
6367707 AGAGAATATATCTAAATAATGTGTCGACACTAATAAGTTTGTGTCAATACTTTTTTCCCAGAATG
323 AGAGAATATATCTAAATAATATGTCGACACTAATAAGTTTGTGTCAATACTTTTTTCCCAGAATG
6367772 AATGGAAACAAGGTGCACCCATAAAGTATCGATCCATATATAAAAGTGTCGATCCCAAAATCATC
388 AATGGAAACAAGGTGCACCCATAAAGTATCGATCCATATATAAAAGTGTCGATCCCAAAATCATC
6367837 GAACCCAAAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAATTATACCGGTTTTGAG
453 GAACCCAAAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAATTATACCGGTTTTGAG
6367902 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
518 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
6367967 ATGG
583 ATGG
6367971 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
6368036 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
6368101 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
6368166 GG-AAACAAGGTGCACCCATAAAGTG-CGATCC-ATATAAAAAGTGTCGATCCC-AAATCATCGA
195 GGAAAACAA-GTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGA
* *
6368227 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATTTAACCGGTGCAATTATACCGGTTTTATGA
259 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
* *
6368292 GAGAATATGTCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATG
324 GAGAATATATCTAAATAATATGTCGACACTAATA-AGTTTGTGTCAATACTTTTTTCCCAGAATG
*
6368357 AATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
388 AATGGAAACAAGGTGCACCCATAAAGTATCGATCCATATAT-AAAAGTGTCGATCCCAAAATCAT
* *
6368422 CGAACCCAAACG-AGTAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTT
452 CGAACCCAAAAGTA-TAATGTAATATGT-ATTTTTCAATCTAACCGGTACAATTATACCGG-TTT
6368486 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAG
514 -TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAG
6368550 AATGAATGG
578 AATGAATGG
6368559 AAAACAAGGTGCACCCATAAAGTGTCGATCC-ATATAAAAAGTGTCGATCCCAAAATCATCGAAC
1 --AACAAGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAAC
6368623 CCAAAAGTATAATGT-ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
64 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
6368687 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
129 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
6368736 AATTTAAATA
Statistics
Matches: 745, Mismatches: 10, Indels: 21
0.96 0.01 0.03
Matches are distributed among these distances:
584 105 0.14
585 90 0.12
586 47 0.06
587 224 0.30
588 197 0.26
589 53 0.07
590 29 0.04
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (586 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
GAAAACAAGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
GAATATATCTAAATAATATGTCGACACTAATAAGTTTGTGTCAATACTTTTTTCCCAGAATGAAT
GGAAACAAGGTGCACCCATAAAGTATCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAA
CCCAAAAGTATAATGTAATATGTATTTTTCAATCTAACCGGTACAATTATACCGGTTTTGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATG
G
Found at i:6370202 original size:3 final size:3
Alignment explanation
Indices: 6370194--6370265 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
6370184 TGAAGCTGAC
* * * * ** * *
6370194 GAT GAT GAT GAT GAC GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
6370242 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
6370266 CCAAACAAGT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:6370262 original size:12 final size:12
Alignment explanation
Indices: 6370179--6370265 Score: 57
Period size: 12 Copynumber: 7.0 Consensus size: 12
6370169 AGCGGTCGCA
* *
6370179 GAAGATGAAGCT
1 GAAGATGATGAT
*
6370191 GACGATGATGAT
1 GAAGATGATGAT
* * *
6370203 GATGACGACGAT
1 GAAGATGATGAT
* **
6370215 GAAGCTGGCGAT
1 GAAGATGATGAT
6370227 GAAGATGATGACGAT
1 GAAGATGAT---GAT
*
6370242 GATGATGATGAT
1 GAAGATGATGAT
6370254 GAAGATGATGAT
1 GAAGATGATGAT
6370266 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
12 46 0.81
15 11 0.19
ACGTcount: A:0.36, C:0.08, G:0.34, T:0.22
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:6371787 original size:162 final size:160
Alignment explanation
Indices: 6371536--6371850 Score: 603
Period size: 162 Copynumber: 2.0 Consensus size: 160
6371526 CGATTGAAAA
*
6371536 ACATCGGAACCCAGATTTAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTT
1 ACATCGGAACCCAGATTTAATGTAATAGATAATTTTGTAATATAACCGGTATAAAAATACCGGTT
6371601 TTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCC
66 TTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCC
6371666 AGATTGGAAGAAAAATGTGTCGACATTTAT
131 AGATTGGAAGAAAAATGTGTCGACATTTAT
6371696 ACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAAATACCGG
1 ACATCGGAACCCAGA-TT-TAATGTAATAGATAATTTTGTAATATAACCGGTATAAAAATACCGG
6371761 TTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGT
64 TTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGT
6371826 CCAGATTGGAAGAAAAATGTGTCGA
129 CCAGATTGGAAGAAAAATGTGTCGA
6371851 TACCATTTAA
Statistics
Matches: 152, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
160 15 0.10
161 2 0.01
162 135 0.89
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (160 bp):
ACATCGGAACCCAGATTTAATGTAATAGATAATTTTGTAATATAACCGGTATAAAAATACCGGTT
TTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATTGTGTCGGTACTTTATGTCC
AGATTGGAAGAAAAATGTGTCGACATTTAT
Found at i:6371970 original size:22 final size:22
Alignment explanation
Indices: 6371934--6371975 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6371924 AACCGGTATA
6371934 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATA-CTTTTTAT
*
6371957 AAAA-GTGTCTATACTTTTT
1 AAAATGTGTCGATACTTTTT
6371976 CACTGTGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (22 bp):
AAAATGTGTCGATACTTTTTAT
Found at i:6375124 original size:20 final size:23
Alignment explanation
Indices: 6375075--6375136 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 23
6375065 ATAGGTAAAC
* *
6375075 ATATGATGTAATAGGTAGTCCTT
1 ATATAATGTAATAGGTAGTCCGT
6375098 ATATAATGTAATAGGTA-T-CGT
1 ATATAATGTAATAGGTAGTCCGT
6375119 -TATAATGTAATAGGTAGT
1 ATATAATGTAATAGGTAGT
6375137 GGTTATTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.44
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTCCGT
Found at i:6375561 original size:22 final size:22
Alignment explanation
Indices: 6375514--6375562 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
6375504 AGGTAGCCCT
* *
6375514 TATATAATGTAATAGGATCGTT
1 TATATAATGTAATAGGATAGTG
6375536 TATATAATGTAATAGG-TAGTGG
1 TATATAATGTAATAGGATAGT-G
6375558 TATAT
1 TATAT
6375563 TGTAAAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (22 bp):
TATATAATGTAATAGGATAGTG
Found at i:6375811 original size:419 final size:424
Alignment explanation
Indices: 6374977--6376242 Score: 2229
Period size: 419 Copynumber: 3.0 Consensus size: 424
6374967 AATTCGCAGT
*
6374977 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAG-ATCGATCATTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
6375041 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGTCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGA-GTAATAGGTAGTCCTTATATAATG
6375106 TAATAGGTATCG--T-TATAATGTAATAGGTAGTGGT-TATTGTAAAGTGTCTATCCTTTTTATA
130 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTATATTGTAAAGTGTCTATCCTTTTTATA
6375167 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
195 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
6375232 GATATTAATTTAGT-ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG-TATATTATTATT
260 GATATTAA-TTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGGATATATTATTATT
*
6375295 AAATT-AAAATTCTAAATAA-ATTTTATAAAATATAAAAAAAATCAAATAATTTTTTGTGCAAAT
323 AAATTAAAAATTCTAAATAATA-TTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAAT
6375358 GAAATTATTAAATC-ATATTGTAGGTGGAAAACATGAA
387 GAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6375395 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
6375460 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGA-TAATAGGTAGCCCTTATATAATGT
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGAGTAATAGGTAGTCCTTATATAATGT
6375524 AATAGG-ATCGTTTATATAATGTAATAGGTAGTGGTATATTGTAAAGTGTCTATCCTTTTTATAA
131 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTATATTGTAAAGTGTCTATCCTTTTTATAA
6375588 AAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT-TCTTTTGAGTGAGTTTTAA
196 AAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
6375652 GATATTAATTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGTATATATTATTATTA
260 GATATTAATTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGG-ATATATTATTATTA
6375717 AATTAAAAATTCTAAATAATATTT-T-AAATATAAAAACAATCAAATAA-TTTTTGTGCAAATGA
324 AATTAAAAATTCTAAATAATATTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGA
6375779 AATTATTAAATCAATATTGTA-GTGGAAAACATGAA
389 AATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6375814 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
6375878 AAAAGTATGGACACTTTCAATATAATAGGTAAAC-TATGATGTAATAGGTAGTCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGA-GTAATAGGTAGTCCTTATATAATG
*
6375942 TAATAGGTATCGTTTATATAATGTAATAGGT-G-GTTATATTGTAAAGTGTCTATCCTTTTTATA
130 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTATATTGTAAAGTGTCTATCCTTTTTATA
6376005 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTTAA
195 AAAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAA
6376069 GATATT-ATTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTAC-GATATATTATTATTAA
260 GATATTAATTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGATATATTATTATTAA
* * *
6376132 ATTAAAAATTCTAAATATTTTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAA
325 ATTAAAAATTCTAAATAATATTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAA
*
6376197 ATTATTAAATTAATATTGTAGGTGGAAAACATGAA
390 ATTATTAAATCAATATTGTAGGTGGAAAACATGAA
6376232 ACACTGTTAAA
1 ACACTGTTAAA
6376243 GTATCGATCC
Statistics
Matches: 819, Mismatches: 9, Indels: 40
0.94 0.01 0.05
Matches are distributed among these distances:
414 36 0.04
415 2 0.00
416 66 0.08
417 123 0.15
418 160 0.20
419 223 0.27
420 141 0.17
421 50 0.06
422 17 0.02
423 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (424 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGAGTAATAGGTAGTCCTTATATAATGT
AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTATATTGTAAAGTGTCTATCCTTTTTATAA
AAGTGTCCATACTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAG
ATATTAATTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGATATATTATTATTAAA
TTAAAAATTCTAAATAATATTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCAAATGAAA
TTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:6375942 original size:23 final size:23
Alignment explanation
Indices: 6375916--6375972 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
6375906 GTAAACTATG
6375916 ATGTAATAGGTAGTC-CTTATATA
1 ATGTAATAGGTA-TCGCTTATATA
*
6375939 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTATCGCTTATATA
6375962 ATGTAATAGGT
1 ATGTAATAGGT
6375973 GGTTATATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 2 0.06
23 30 0.94
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATGTAATAGGTATCGCTTATATA
Found at i:6377602 original size:16 final size:17
Alignment explanation
Indices: 6377581--6377614 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6377571 TTAATAAAGT
6377581 AATATA-AAATTGGCCC
1 AATATACAAATTGGCCC
6377597 AATATACCAAATTGGCCC
1 AATATA-CAAATTGGCCC
6377615 GCTCAAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
AATATACAAATTGGCCC
Found at i:6378899 original size:16 final size:17
Alignment explanation
Indices: 6378868--6378900 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6378858 TATTAATGTA
6378868 TGAATCATTATATTTTT
1 TGAATCATTATATTTTT
*
6378885 TGAAT-ATTTTATTTTT
1 TGAATCATTATATTTTT
6378901 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTATATTTTT
Found at i:6379567 original size:130 final size:130
Alignment explanation
Indices: 6379363--6379610 Score: 426
Period size: 130 Copynumber: 1.9 Consensus size: 130
6379353 AATTTTCTTC
*
6379363 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
6379428 CCAGGTTAAATGATTAATTTTTTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCAGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
6379493 TAATTAGGTGGTGACATGTGTCACCAATGACACTTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
6379558 CCTA-ATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CC-AGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
6379611 TATATAAATA
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
130 110 0.99
131 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCAGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:6380057 original size:35 final size:35
Alignment explanation
Indices: 6380007--6380082 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
6379997 AATTGATTTG
* *
6380007 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
6380042 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
6380077 AATTGA
1 AATTGA
6380083 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:6384280 original size:29 final size:29
Alignment explanation
Indices: 6384189--6384280 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
6384179 ATAGTTGGGT
* * *
6384189 GACCATTTTATAACTTTTAATAGTAAGAG
1 GACCATTTTATAACATTTAATAATCAGAG
****
6384218 GACTCAAAAAAGTAACATCTT-ATAATCA-ATG
1 GAC-CATTTTA-TAACAT-TTAATAATCAGA-G
6384249 GACCATTTTATAACATTTAATAATCAGAG
1 GACCATTTTATAACATTTAATAATCAGAG
6384278 GAC
1 GAC
6384281 TCAATAAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 8 0.17
31 14 0.30
32 2 0.04
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (29 bp):
GACCATTTTATAACATTTAATAATCAGAG
Found at i:6384302 original size:60 final size:60
Alignment explanation
Indices: 6384189--6384305 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
6384179 ATAGTTGGGT
* * * *
6384189 GACCATTTTATAACTTTTAATAGTAAGAGGACTCAAAAAAGTAACATCTTATAATCAATG
1 GACCATTTTATAACATTTAATAATAAGAGGACTCAAAAAAGTAACACCCTATAATCAATG
* *
6384249 GACCATTTTATAACATTTAATAATCAGAGGACTCAATAAAA-TAATACCCTATAATCA
1 GACCATTTTATAACATTTAATAATAAGAGGACTCAA-AAAAGTAACACCCTATAATCA
6384306 GGAGACCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.31
Consensus pattern (60 bp):
GACCATTTTATAACATTTAATAATAAGAGGACTCAAAAAAGTAACACCCTATAATCAATG
Found at i:6384313 original size:60 final size:60
Alignment explanation
Indices: 6384189--6384321 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
6384179 ATAGTTGGGT
* * * * *
6384189 GACCATTTTATAACTTTTAATAGTAAGAGGACTCAAAAAAGTAACATCTTATAATCAATG
1 GACCATTTTATAACATTTAATAATAAGAGGACTCAAAAAAGTAACACCCTATAATCAAGG
* *
6384249 GACCATTTTATAACATTTAATAATCAGAGGACTCAATAAAA-TAATACCCTATAATC-AGG
1 GACCATTTTATAACATTTAATAATAAGAGGACTCAA-AAAAGTAACACCCTATAATCAAGG
6384308 AGACCATTTATATA
1 -GACCATTT-TATA
6384322 TTTTTACCCT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.03
60 53 0.84
61 8 0.13
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (60 bp):
GACCATTTTATAACATTTAATAATAAGAGGACTCAAAAAAGTAACACCCTATAATCAAGG
Found at i:6384597 original size:30 final size:31
Alignment explanation
Indices: 6384557--6384619 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
6384547 GGTTAATATT
* *
6384557 TTTTTTATTTATATCGTAA-TTCATTATCTA
1 TTTTTCATTTAGATCGTAATTTCATTATCTA
* *
6384587 TTTTTCATTTAGATTGTAATTTGATTATCTA
1 TTTTTCATTTAGATCGTAATTTCATTATCTA
6384618 TT
1 TT
6384620 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.60
Consensus pattern (31 bp):
TTTTTCATTTAGATCGTAATTTCATTATCTA
Found at i:6386800 original size:35 final size:35
Alignment explanation
Indices: 6386761--6386828 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
6386751 TTAACAAGTC
* *
6386761 TATTCACCAAGTGACATGACTTATTATTATCATTA
1 TATTCACCAAATGACATAACTTATTATTATCATTA
*
6386796 TATTCACCAAATTACATAACTTATTATTATCAT
1 TATTCACCAAATGACATAACTTATTATTATCAT
6386829 CAATATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (35 bp):
TATTCACCAAATGACATAACTTATTATTATCATTA
Found at i:6387168 original size:36 final size:36
Alignment explanation
Indices: 6387128--6387196 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
6387118 TTAACAAGTC
* *
6387128 TATTCACCAAGTGACATGACTTATTATTATCATTTA
1 TATTCACCAAATGACATAACTTATTATTATCATTTA
*
6387164 TATTCACCAAATTACATAACTTATTATTATCAT
1 TATTCACCAAATGACATAACTTATTATTATCAT
6387197 CAATATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.42
Consensus pattern (36 bp):
TATTCACCAAATGACATAACTTATTATTATCATTTA
Found at i:6387203 original size:36 final size:36
Alignment explanation
Indices: 6387128--6387211 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
6387118 TTAACAAGTC
* * * **
6387128 TATTCACCAAGTGACATGACTTATTATTATCATTTA
1 TATTCACCAAATTACATAACTTATTATTATCATCAA
6387164 TATTCACCAAATTACATAACTTATTATTATCATCAA
1 TATTCACCAAATTACATAACTTATTATTATCATCAA
*
6387200 TATT-ACTAAATT
1 TATTCACCAAATT
6387212 TATCCATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (36 bp):
TATTCACCAAATTACATAACTTATTATTATCATCAA
Found at i:6389022 original size:13 final size:13
Alignment explanation
Indices: 6389004--6389028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6388994 CCCCTCATTC
6389004 CTTCTTTATTCTT
1 CTTCTTTATTCTT
6389017 CTTCTTTATTCT
1 CTTCTTTATTCT
6389029 CCTATTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTCTTTATTCTT
Found at i:6414031 original size:14 final size:14
Alignment explanation
Indices: 6414009--6414039 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6413999 ATGAACTATA
6414009 TTTTCAGAAAACAT
1 TTTTCAGAAAACAT
*
6414023 TTTTTAGAAAACAT
1 TTTTCAGAAAACAT
6414037 TTT
1 TTT
6414040 ACATTGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (14 bp):
TTTTCAGAAAACAT
Found at i:6414719 original size:20 final size:20
Alignment explanation
Indices: 6414696--6414811 Score: 153
Period size: 20 Copynumber: 5.8 Consensus size: 20
6414686 ACCCAGGTTC
* *
6414696 CAAATTCGTAAAGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
6414716 CAAATTCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
6414736 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* *
6414756 CAAATTCGTAACGCAAAAGT
1 CAAATTCGCAACGCGAAAGT
*
6414776 TAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
6414796 TAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
6414812 TACTCCAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 83 0.98
21 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:6414760 original size:60 final size:60
Alignment explanation
Indices: 6414696--6414811 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
6414686 ACCCAGGTTC
*
6414696 CAAATTCGTAAAGCGAAAGTCAAATTCGCAACAC-AGAAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGTAAAGCAAAAGTCAAATTCGCAACACGA-AAGTCAAATTCGCAACGCGAAAGT
* * * *
6414756 CAAATTCGTAACGCAAAAGTTAAATTCGCAACGCGAAAGTTAAATTCGCAACGCGA
1 CAAATTCGTAAAGCAAAAGTCAAATTCGCAACACGAAAGTCAAATTCGCAACGCGA
6414812 TACTCCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 49 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (60 bp):
CAAATTCGTAAAGCAAAAGTCAAATTCGCAACACGAAAGTCAAATTCGCAACGCGAAAGT
Found at i:6414809 original size:40 final size:40
Alignment explanation
Indices: 6414657--6414809 Score: 168
Period size: 40 Copynumber: 3.9 Consensus size: 40
6414647 AAATGACCAA
** * *
6414657 CAAATTCGCAACGCG-ATCTCAAATTCGCAAC-C-CAGGTT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAAAG-T
* * * *
6414695 CCAAATTCGTAAAGCGAAAGTCAAATTCGCAACACAGAAGT
1 -CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAAAGT
*
6414736 CAAATTCGCAACGCGAAAGTCAAATTCGTAACGCAAAAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAAAGT
* *
6414776 TAAATTCGCAACGCGAAAGTTAAATTCGCAACGC
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGC
6414810 GATACTCCAA
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 13 0.13
40 80 0.82
41 2 0.02
42 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCAAAAGT
Found at i:6415246 original size:21 final size:20
Alignment explanation
Indices: 6415220--6415310 Score: 105
Period size: 19 Copynumber: 4.5 Consensus size: 20
6415210 AACAAATGCA
*
6415220 TTGCGATTTTGGACTATCGCG
1 TTGCGAATTT-GACTATCGCG
*
6415241 TTGCGAATTTCGACTTTCGCG
1 TTGCGAATTT-GACTATCGCG
* *
6415262 TTGCGAATTTGAAT-TCTCG
1 TTGCGAATTTGACTATCGCG
*
6415281 TTGCGAATTTGA-GATCGCG
1 TTGCGAATTTGACTATCGCG
6415300 TTGCGAATTTG
1 TTGCGAATTTG
6415311 TTGGTCATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 31 0.50
20 3 0.05
21 28 0.45
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:6416972 original size:8 final size:8
Alignment explanation
Indices: 6416959--6416983 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6416949 TTTAATAAAA
6416959 AAAGGTTC
1 AAAGGTTC
6416967 AAAGGTTC
1 AAAGGTTC
6416975 AAAGGTTC
1 AAAGGTTC
6416983 A
1 A
6416984 CCTTGAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (8 bp):
AAAGGTTC
Found at i:6421496 original size:199 final size:199
Alignment explanation
Indices: 6421156--6421560 Score: 526
Period size: 199 Copynumber: 2.0 Consensus size: 199
6421146 TTATTTGCTT
* * * *
6421156 GCGTAAATAATAAGTATCGATACTTTTATATAGGTATGGAAACTTTTATTTCAGTATGCTTCTCA
1 GCGTAAATAATAAGTATCGATACTTTTATATAGATATAGAAACTTTTATTCCAGTATGATTCTCA
* * * * **
6421221 AACAATTTGTACGCAAAACGTATCGATACACATATATAAAGTATCGATACTTGGAATTTTGAAAC
66 AACAATTTGCACGCAAAACGTATCGATACACACATATAAAATATCGATACTTAGAATTTCAAAAC
** * * * * *
6421286 TTATTACTTTAAAGTAATATGTTAATTAACAATGTAAATGGTAAAAGTCTACC-GATATATTGAT
131 ACATTACTTTAAAATAATAGGTAAATTAACAATGTAAATGGTAAAAGTCTACCAG-TATAATGAA
6421350 AATAG
195 AATAG
* * *
6421355 GCGTAAATACA-ATGTATCGATACTTTTATATAGATATATATACTTTTATTCCAGTATGATTCTC
1 GCGTAAATA-ATAAGTATCGATACTTTTATATAGATATAGAAACTTTTATTCCAGTATGATTCTC
* * *
6421419 AAACAATTTGCATGCAAAATGTATCGATACACACATATAAAATATCGATACTTATAATTTCAAAA
65 AAACAATTTGCACGCAAAACGTATCGATACACACATATAAAATATCGATACTTAGAATTTCAAAA
* * ** *
6421484 CACATTACTTTAAAATAATAGGTAAATTAACATTGTACATGGTAAACTTTTACCAGTATAATGAA
130 CACATTACTTTAAAATAATAGGTAAATTAACAATGTAAATGGTAAAAGTCTACCAGTATAATGAA
6421549 AATAG
195 AATAG
6421554 GCGTAAA
1 GCGTAAA
6421561 ATGTCCAAGT
Statistics
Matches: 176, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
199 174 0.99
200 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (199 bp):
GCGTAAATAATAAGTATCGATACTTTTATATAGATATAGAAACTTTTATTCCAGTATGATTCTCA
AACAATTTGCACGCAAAACGTATCGATACACACATATAAAATATCGATACTTAGAATTTCAAAAC
ACATTACTTTAAAATAATAGGTAAATTAACAATGTAAATGGTAAAAGTCTACCAGTATAATGAAA
ATAG
Found at i:6421723 original size:130 final size:128
Alignment explanation
Indices: 6421452--6421708 Score: 347
Period size: 130 Copynumber: 2.0 Consensus size: 128
6421442 TCGATACACA
* *
6421452 CATATAAAATATCGATACTTATAATTTCAAAACACATTACTTTAAAATAATAGGTAAATTAACAT
1 CATATAAAGTATCGATACTTATAATTTCAAAACACATTACTTTAAAATAATAGGTAAATTAACAA
* * * * * *
6421517 TGTACATGGTAAACTTTTACCAGTATAATGAAAATAGGCGTAAAATGTCCAAGTATCGATACT
66 TGTAAACGATAAACTTTTACCAGTATAATGAAAATAGGCATAAAATGTACAAGTATCAATACT
* * *
6421580 CATATACAAAGTATCGATACTTATAATTTCGAAAC-CTATTACTTTAAAGTAATATGTAAATTAA
1 CATAT--AAAGTATCGATACTTATAATTTCAAAACAC-ATTACTTTAAAATAATAGGTAAATTAA
*
6421644 CAATGTAAACGATAAAAGTTTCTACCAGTATAATGAAAATAGGCAT-AAATGTACAAGTATCAAT
63 CAATGTAAACGAT-AAACTTT-TACCAGTATAATGAAAATAGGCATAAAATGTACAAGTATCAAT
6421708 A
126 A
6421709 TTGTCATATA
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
128 5 0.04
129 1 0.01
130 60 0.54
131 23 0.21
132 23 0.21
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (128 bp):
CATATAAAGTATCGATACTTATAATTTCAAAACACATTACTTTAAAATAATAGGTAAATTAACAA
TGTAAACGATAAACTTTTACCAGTATAATGAAAATAGGCATAAAATGTACAAGTATCAATACT
Found at i:6422719 original size:20 final size:21
Alignment explanation
Indices: 6422695--6422764 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
6422685 ATATATAGAG
6422695 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATGTTTTAA
* * *
6422716 -TAATCATGAATATTTAATTTTAA
1 TTAAT--TAAATATAT-GTTTTAA
*
6422739 TTAATTAAATATA-GATTTAA
1 TTAATTAAATATATGTTTTAA
6422759 TTAATT
1 TTAATT
6422765 TGAAATAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 15 0.39
22 13 0.34
23 6 0.16
24 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (21 bp):
TTAATTAAATATATGTTTTAA
Found at i:6430979 original size:23 final size:23
Alignment explanation
Indices: 6430953--6431005 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
6430943 TTCGGTGAAA
*
6430953 TTCTACGTGGCACTACGGTGCAT
1 TTCTACGCGGCACTACGGTGCAT
**
6430976 TTCTACGCGGCACTTTGGTGCAT
1 TTCTACGCGGCACTACGGTGCAT
*
6430999 TTATACG
1 TTCTACG
6431006 AGCTGTGGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGCACTACGGTGCAT
Found at i:6434947 original size:19 final size:19
Alignment explanation
Indices: 6434923--6434974 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
6434913 ATGTAATTAA
6434923 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
6434942 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
6434961 TGCATCGATGCATA
1 TGCATCGATGCATA
6434975 TGTTAAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:6434988 original size:24 final size:20
Alignment explanation
Indices: 6434961--6435016 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
6434951 GCATAAGGAG
6434961 TGCATCGATGCATATGTTAAGAGA
1 TGCATCGATGCA-ATG-T-AGA-A
* *
6434985 TGCATCGATACACTGTAGAA
1 TGCATCGATGCAATGTAGAA
6435005 TGCATCGATGCA
1 TGCATCGATGCA
6435017 CTTCAAGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 3 0.10
22 1 0.03
23 2 0.07
24 11 0.38
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCAATGTAGAA
Found at i:6436615 original size:23 final size:23
Alignment explanation
Indices: 6436556--6436624 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
6436546 ACATTTTATA
* *
6436556 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
6436579 TGGCA-TTACGGTGCATTTCTACG
1 TGGCACTT-CGGTGCATTTCTACG
* *
6436602 TGGCACTTCAGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
6436625 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.05
23 36 0.90
24 2 0.05
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:6444747 original size:35 final size:34
Alignment explanation
Indices: 6444701--6444813 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
6444691 AAAACCATCC
*
6444701 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
6444736 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
6444771 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
6444806 TCAATTTC
1 TCAATTTC
6444814 TGTCTTTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.90
36 6 0.08
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:6445920 original size:35 final size:34
Alignment explanation
Indices: 6445872--6445983 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
6445862 ATTCCTCCTT
* *
6445872 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
6445907 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
* *
6445942 AAATTGAATTACTTTGGAATTTGGGGTTTACAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
6445977 AAATTGA
1 AAATTGA
6445984 GGAATGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 66 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:6450398 original size:16 final size:16
Alignment explanation
Indices: 6450377--6450408 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6450367 TGCCATAAAA
6450377 AATTGCATGTGCACCG
1 AATTGCATGTGCACCG
6450393 AATTGCATGTGCACCG
1 AATTGCATGTGCACCG
6450409 TTCTTGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (16 bp):
AATTGCATGTGCACCG
Found at i:6461205 original size:231 final size:232
Alignment explanation
Indices: 6460802--6461265 Score: 905
Period size: 232 Copynumber: 2.0 Consensus size: 232
6460792 TATTTTTTTA
6460802 ATTAAAAAATATTAAATTATAAAATTATAAAAAAAATTTGGTTAATTCGAAAATTAACCGAAATT
1 ATTAAAAAATATTAAATTATAAAATTATAAAAAAAATTTGGTTAATTCGAAAATTAACCGAAATT
6460867 TATTCGGTTCGGTTAATACTTCATAAAAAAGTTTGGTTCGGTTAAATAAAAAAAAATTAGTTAAT
66 TATTCGGTTCGGTTAATACTTCATAAAAAAGTTTGGTTCGGTTAAATAAAAAAAAATTAGTTAAT
6460932 TCGGTTAAGGGTATTTCGGTTCGGTTTCGGTTCAGTTTTATCCG-ATGAACACCCCAACTTCAAA
131 TCGGTTAAGGGTATTTCGGTTCGGTTTCGGTTCAGTTTTATCCGAATGAACACCCCAACTTCAAA
6460996 TGATGCGAGTATTTTATTAATCCTCAATGACATATGT
196 TGATGCGAGTATTTTATTAATCCTCAATGACATATGT
6461033 ATTAAAAAATATTAAATTATAAAATTATAAAAAAAATTTGGTTAATTCGAAAATTAACCGAAATT
1 ATTAAAAAATATTAAATTATAAAATTATAAAAAAAATTTGGTTAATTCGAAAATTAACCGAAATT
6461098 TATTCGGTTCGGTTAATACTTTCATAAAAAAGTTTGGTTCGGTTAAATAAAAAAAAATTAGTTAA
66 TATTCGGTTCGGTTAATAC-TTCATAAAAAAGTTTGGTTCGGTTAAATAAAAAAAAATTAGTTAA
6461163 TTCGGTTAAGGGTATTTCGGTTCGG-TTCGGTTCAGTTTTATCCGAATGAACACCCCAACTTCAA
130 TTCGGTTAAGGGTATTTCGGTTCGGTTTCGGTTCAGTTTTATCCGAATGAACACCCCAACTTCAA
6461227 ATGATGCGAGTATTTTATTAATCCTCAATGACATATGT
195 ATGATGCGAGTATTTTATTAATCCTCAATGACATATGT
6461265 A
1 A
6461266 GGCTAGTTTT
Statistics
Matches: 231, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
231 103 0.45
232 128 0.55
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (232 bp):
ATTAAAAAATATTAAATTATAAAATTATAAAAAAAATTTGGTTAATTCGAAAATTAACCGAAATT
TATTCGGTTCGGTTAATACTTCATAAAAAAGTTTGGTTCGGTTAAATAAAAAAAAATTAGTTAAT
TCGGTTAAGGGTATTTCGGTTCGGTTTCGGTTCAGTTTTATCCGAATGAACACCCCAACTTCAAA
TGATGCGAGTATTTTATTAATCCTCAATGACATATGT
Found at i:6467607 original size:25 final size:25
Alignment explanation
Indices: 6467573--6467633 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
6467563 CTATTAATAA
*
6467573 TATATTTTCGCTCCTCC-TAAAATTT
1 TATAATTTCGCTCC-CCTTAAAATTT
*
6467598 TATAATTTCGTTCCCCTTTAAAATTT
1 TATAATTTCGCTCCCC-TTAAAATTT
*
6467624 TATAAATTCG
1 TATAATTTCG
6467634 TCTTCTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.06
25 12 0.39
26 17 0.55
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (25 bp):
TATAATTTCGCTCCCCTTAAAATTT
Found at i:6468953 original size:13 final size:13
Alignment explanation
Indices: 6468930--6468960 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6468920 AGATGTGGTA
6468930 AACAT-TCTTAAT
1 AACATATCTTAAT
6468942 AACATATCTTAAT
1 AACATATCTTAAT
6468955 AACATA
1 AACATA
6468961 CAAATATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
AACATATCTTAAT
Found at i:6472535 original size:21 final size:21
Alignment explanation
Indices: 6472511--6472560 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
6472501 ATTTGTATGC
*
6472511 TATCGAAGTGTGAATTCTGGT
1 TATCGAAGTCTGAATTCTGGT
6472532 TATCGAAGTCTGAATTCTGGT
1 TATCGAAGTCTGAATTCTGGT
*
6472553 TATTGAAG
1 TATCGAAG
6472561 GTAGCATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (21 bp):
TATCGAAGTCTGAATTCTGGT
Found at i:6474497 original size:11 final size:11
Alignment explanation
Indices: 6474481--6474506 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6474471 TGAGAAAAGT
6474481 TTTTTTTTTCA
1 TTTTTTTTTCA
6474492 TTTTTTTTTCA
1 TTTTTTTTTCA
6474503 TTTT
1 TTTT
6474507 AGTGAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:6476267 original size:16 final size:16
Alignment explanation
Indices: 6476246--6476276 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6476236 GGGCTTTACT
6476246 TATATATACATATATC
1 TATATATACATATATC
*
6476262 TATATATACTTATAT
1 TATATATACATATAT
6476277 ATAATAACAT
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:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATACATATATC
Found at i:6476402 original size:2 final size:2
Alignment explanation
Indices: 6476395--6476429 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6476385 ACGTTGGCAT
6476395 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 T
6476430 TTGAAGTGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6476549 original size:3 final size:3
Alignment explanation
Indices: 6476541--6476570 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6476531 TATATATACA
6476541 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6476571 ACATATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6476604 original size:2 final size:2
Alignment explanation
Indices: 6476593--6476646 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
6476583 TTCAACGGTC
* *
6476593 AT AT -T AT AT AT AT AT AT AT AT GT AT GT AT AT GAT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
6476633 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
6476647 TACACGTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 3 0.07
2 39 0.89
3 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6489644 original size:7 final size:7
Alignment explanation
Indices: 6489632--6489665 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
6489622 AATGAATGTA
6489632 AAGAATG
1 AAGAATG
*
6489639 AAGAATA
1 AAGAATG
6489646 AAGAATG
1 AAGAATG
6489653 AAGAATG
1 AAGAATG
6489660 AA-AATG
1 AAGAATG
6489666 TAAATAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (7 bp):
AAGAATG
Found at i:6489649 original size:14 final size:14
Alignment explanation
Indices: 6489630--6489658 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6489620 GAAATGAATG
6489630 TAAAGAATGAAGAA
1 TAAAGAATGAAGAA
6489644 TAAAGAATGAAGAA
1 TAAAGAATGAAGAA
6489658 T
1 T
6489659 GAAAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (14 bp):
TAAAGAATGAAGAA
Found at i:6496269 original size:14 final size:14
Alignment explanation
Indices: 6496250--6496278 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6496240 GCATTTATAA
6496250 AAATAAATAAAAAT
1 AAATAAATAAAAAT
6496264 AAATAAATAAAAAT
1 AAATAAATAAAAAT
6496278 A
1 A
6496279 TGGGGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:6496278 original size:10 final size:10
Alignment explanation
Indices: 6496246--6496270 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6496236 AATTGCATTT
6496246 ATAAAAATAA
1 ATAAAAATAA
6496256 ATAAAAATAA
1 ATAAAAATAA
6496266 ATAAA
1 ATAAA
6496271 TAAAAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:6500879 original size:17 final size:17
Alignment explanation
Indices: 6500857--6500892 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6500847 CGTCAACATT
*
6500857 ACTATTGATTTTTAATG
1 ACTATTAATTTTTAATG
6500874 ACTATTAATTTTTAATG
1 ACTATTAATTTTTAATG
6500891 AC
1 AC
6500893 GGTGTATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (17 bp):
ACTATTAATTTTTAATG
Found at i:6500924 original size:2 final size:2
Alignment explanation
Indices: 6500917--6500955 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
6500907 ACTGTTGACT
6500917 TA TA TA TA TA TA TA TA TA T- 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
6500956 GTGATTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6500940 original size:19 final size:19
Alignment explanation
Indices: 6500916--6500954 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6500906 CACTGTTGAC
6500916 TTATATATATATATATATA
1 TTATATATATATATATATA
6500935 TTATATATATATATATATA
1 TTATATATATATATATATA
6500954 T
1 T
6500955 AGTGATTTTT
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:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATATATATATATATATA
Found at i:6500941 original size:17 final size:17
Alignment explanation
Indices: 6500919--6500952 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6500909 TGTTGACTTA
6500919 TATATATATATATATAT
1 TATATATATATATATAT
6500936 TATATATATATATATAT
1 TATATATATATATATAT
6500953 ATAGTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:6501897 original size:2 final size:2
Alignment explanation
Indices: 6501890--6501968 Score: 130
Period size: 2 Copynumber: 41.5 Consensus size: 2
6501880 ATTGTGAATT
6501890 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
6501931 TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA -A 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
6501969 CTTAGAATTA
Statistics
Matches: 73, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 4 0.05
2 69 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6504594 original size:158 final size:158
Alignment explanation
Indices: 6504306--6504622 Score: 634
Period size: 158 Copynumber: 2.0 Consensus size: 158
6504296 ACAATGACCT
6504306 AAATTATTATTAGACAAAAAAATTTGAGAACACGAGATTATCCATCTTTAATTCGTTCCTTGATT
1 AAATTATTATTAGACAAAAAAATTTGAGAACACGAGATTATCCATCTTTAATTCGTTCCTTGATT
6504371 AAATATTTAATAAATTCTTATATTTTTTAATTTAAATATTTATTTTTACATAAACTAAAATATTA
66 AAATATTTAATAAATTCTTATATTTTTTAATTTAAATATTTATTTTTACATAAACTAAAATATTA
6504436 TTAGATCAAAATTATACCGAATATACAA
131 TTAGATCAAAATTATACCGAATATACAA
6504464 AAATTATTATTAGACAAAAAAATTTGAGAACACGAGATTATCCATCTTTAATTCGTTCCTTGATT
1 AAATTATTATTAGACAAAAAAATTTGAGAACACGAGATTATCCATCTTTAATTCGTTCCTTGATT
6504529 AAATATTTAATAAATTCTTATATTTTTTAATTTAAATATTTATTTTTACATAAACTAAAATATTA
66 AAATATTTAATAAATTCTTATATTTTTTAATTTAAATATTTATTTTTACATAAACTAAAATATTA
6504594 TTAGATCAAAATTATACCGAATATACAA
131 TTAGATCAAAATTATACCGAATATACAA
6504622 A
1 A
6504623 TTTTAACGGC
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (158 bp):
AAATTATTATTAGACAAAAAAATTTGAGAACACGAGATTATCCATCTTTAATTCGTTCCTTGATT
AAATATTTAATAAATTCTTATATTTTTTAATTTAAATATTTATTTTTACATAAACTAAAATATTA
TTAGATCAAAATTATACCGAATATACAA
Found at i:6506884 original size:18 final size:19
Alignment explanation
Indices: 6506849--6506885 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
6506839 CACGGAATGT
6506849 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
6506869 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
6506886 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:6507024 original size:18 final size:18
Alignment explanation
Indices: 6507001--6507048 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
6506991 AAATTGTCCT
*
6507001 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
6507019 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
6507036 TATTTATATATTT
1 TA-TTATATATTT
6507049 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:6512011 original size:130 final size:130
Alignment explanation
Indices: 6511778--6512013 Score: 384
Period size: 130 Copynumber: 1.8 Consensus size: 130
6511768 TTAATTTTAA
* *
6511778 GAAAGAAAACGATAATGTCTAATTATTTCCAATCAATAATAAATGACCTCTCATGCCTTAAAGCA
1 GAAAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCA
*
6511843 GACATTTATTACTTCGATCGAAATGAAGAGATATCACTATTCGTCTTAAAATTCAATATTGATTC
66 GACATTTATTACTCCGATCGAAATGAAGAGATATCACTATTCGTCTTAAAATTCAATATTGATTC
* * * *
6511908 GAAAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAATCA
1 GAAAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCA
*
6511973 -ATCATTTATTACTCCGATCGAAATGAATAGATATCACTATT
66 GA-CATTTATTACTCCGATCGAAATGAAGAGATATCACTATT
6512014 TCCAATATTA
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
129 1 0.01
130 96 0.99
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (130 bp):
GAAAGAAAACGATAATATCTAATTATTTCCAATCAAGAATAAATGACCTCTCATGCCTTAAAGCA
GACATTTATTACTCCGATCGAAATGAAGAGATATCACTATTCGTCTTAAAATTCAATATTGATTC
Found at i:6512514 original size:25 final size:26
Alignment explanation
Indices: 6512471--6512521 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
6512461 TGACTAAAAT
6512471 AAAATAACATAAAAGCAACATGCAAA
1 AAAATAACATAAAAGCAACATGCAAA
*
6512497 AAAATGAA-ATAAAA-CAACATTCAAA
1 AAAAT-AACATAAAAGCAACATGCAAA
6512522 TAGAACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 10 0.43
26 11 0.48
27 2 0.09
ACGTcount: A:0.67, C:0.14, G:0.06, T:0.14
Consensus pattern (26 bp):
AAAATAACATAAAAGCAACATGCAAA
Found at i:6514199 original size:14 final size:15
Alignment explanation
Indices: 6514103--6514205 Score: 109
Period size: 15 Copynumber: 6.5 Consensus size: 15
6514093 TAATAAGGTT
6514103 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
6514118 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
6514133 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
6514148 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
6514167 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
6514185 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
6514199 ATTTATT
1 ATTTATT
6514206 AGTATGGATT
Statistics
Matches: 75, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 12 0.16
15 43 0.57
16 4 0.05
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 4 0.05
22 6 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:6514223 original size:32 final size:32
Alignment explanation
Indices: 6514185--6514282 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 32
6514175 TTTTAAAATA
6514185 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
6514217 ATTTATTTT--A-AA---A-TA-TA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
6514239 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
6514271 ATTTATTTTAAA
1 ATTTATTTTAAA
6514283 ATATGGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 14 0.25
24 3 0.05
25 4 0.07
26 1 0.02
28 1 0.02
29 4 0.07
30 3 0.05
32 26 0.46
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:6514242 original size:69 final size:67
Alignment explanation
Indices: 6514103--6514260 Score: 203
Period size: 69 Copynumber: 2.3 Consensus size: 67
6514093 TAATAAGGTT
*
6514103 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATAGAT
6514168 TG
66 TG
* ** * * * *
6514170 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATA
6514234 GATTG
63 GATTG
6514239 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
6514261 GTATGGATTG
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
66 13 0.16
67 22 0.28
68 13 0.16
69 31 0.39
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATAGAT
TG
Found at i:6514250 original size:54 final size:54
Alignment explanation
Indices: 6514185--6514465 Score: 226
Period size: 54 Copynumber: 5.1 Consensus size: 54
6514175 TTTTAAAATA
6514185 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
*
6514239 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
* * * *
6514293 GTTTA--TT--AT--TGTAGTT-GTATGGATTGCTTTATTTT--AA-ATA-ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATAGATTG
** * * *
6514337 ATTAGTATGGTTTGATTTACTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATT--TAT--TTT-AAATAATTTATTAGTATGGATTGATTTATTTT--A-AA---A-TA-TA--G
6514401 ATTG
51 ATTG
* *
6514405 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
6514459 ATTTATT
1 ATTTATT
6514466 ATTGTAGTTG
Statistics
Matches: 179, Mismatches: 20, Indels: 56
0.70 0.08 0.22
Matches are distributed among these distances:
44 5 0.03
45 2 0.01
46 4 0.02
48 21 0.12
49 2 0.01
50 4 0.02
52 2 0.01
53 1 0.01
54 86 0.48
55 3 0.02
56 1 0.01
57 2 0.01
58 1 0.01
59 1 0.01
61 2 0.01
62 2 0.01
63 7 0.04
64 22 0.12
65 2 0.01
66 3 0.02
68 6 0.03
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
Found at i:6514329 original size:80 final size:80
Alignment explanation
Indices: 6514234--6514505 Score: 420
Period size: 80 Copynumber: 3.3 Consensus size: 80
6514224 TTAAAATATA
*
6514234 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGGTTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
6514299 TATTGTAGTTGTATG
66 TATTGTAGTTGTATG
* * *
6514314 GATTGCTTTATTTTAAATAATTTATTAGTATGGTTTGATTTACTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA-
*
6514379 TTTAAATAATTTA-TTAGTATG
65 -TT--AT--TGTAGTT-GTATG
*
6514400 GATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
6514465 TATTGTAGTTGTATG
66 TATTGTAGTTGTATG
6514480 GATTGATTTATTTTAAATAATTTATT
1 GATTGATTTATTTTAAATAATTTATT
6514506 TTAAATTTCA
Statistics
Matches: 174, Mismatches: 10, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
80 94 0.54
81 2 0.01
82 4 0.02
84 4 0.02
85 2 0.01
86 68 0.39
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (80 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAT
TATTGTAGTTGTATG
Found at i:6514361 original size:32 final size:32
Alignment explanation
Indices: 6514309--6514448 Score: 174
Period size: 32 Copynumber: 4.7 Consensus size: 32
6514299 TATTGTAGTT
*
6514309 GTATGGATTGCTTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
6514341 GTATGGTTTGATTTA-CTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
6514364 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
6514395 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
6514427 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
6514449 ATATGGATTG
Statistics
Matches: 92, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
22 13 0.14
23 3 0.03
25 1 0.01
26 3 0.03
28 3 0.03
29 1 0.01
31 3 0.03
32 65 0.71
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:6514367 original size:22 final size:22
Alignment explanation
Indices: 6514342--6514384 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6514332 AATTTATTAG
*
6514342 TATGGTTTGATTTACTTTAAAA
1 TATGGATTGATTTACTTTAAAA
*
6514364 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTACTTTAAA
6514385 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTACTTTAAAA
Found at i:6514504 original size:14 final size:14
Alignment explanation
Indices: 6514485--6514511 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6514475 GTATGGATTG
6514485 ATTTATTTTAAATA
1 ATTTATTTTAAATA
6514499 ATTTATTTTAAAT
1 ATTTATTTTAAAT
6514512 TTCAGTATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:6514915 original size:3 final size:3
Alignment explanation
Indices: 6514907--6514932 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6514897 TTGAAAACAA
6514907 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6514933 CCCGGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6515225 original size:41 final size:41
Alignment explanation
Indices: 6515180--6515257 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
6515170 ATGAACGCAA
* * *
6515180 CTTGCACG-AAGAACTTATAGATGGCCCGAATGACTTATCAT
1 CTTGCACGAAAG-ACTAACAGATGGCCCGAAGGACTTATCAT
* *
6515221 CTTGCTCGAAAGACTAACAGATGGCCTGAAGGACTTA
1 CTTGCACGAAAGACTAACAGATGGCCCGAAGGACTTA
6515258 CTAATTTTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 28 0.90
42 3 0.10
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (41 bp):
CTTGCACGAAAGACTAACAGATGGCCCGAAGGACTTATCAT
Found at i:6515924 original size:42 final size:41
Alignment explanation
Indices: 6515848--6515957 Score: 139
Period size: 42 Copynumber: 2.7 Consensus size: 41
6515838 TCCCGAAGGT
* *
6515848 CTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * *
6515889 CTTACAGATGACCCGGAGGATTTAGTCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTTA-TCATCATGCTCGAAAGA
* **
6515931 CTTACTGATGGCCCGAAACACTTATCA
1 CTTACAGATGGCCCGAAGGACTTATCA
6515958 ATTTGGGAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 23 0.40
42 34 0.60
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:6516407 original size:40 final size:42
Alignment explanation
Indices: 6516347--6516461 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
6516337 TATGTGTAAA
* *
6516347 CATCTTGCCCG-AAGGTCTTAT-GGTGACCCGAAGGAGTT-AT
1 CATCTTGCTCGAAAGG-CTTATAGATGACCCGAAGGAGTTAAT
* *
6516387 CATCTTGCTCGAAAGGCTTATAGATGACCCGGAGGATTTAAT
1 CATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGAGTTAAT
* * * *
6516429 CATCATCCTTGAAAGGCTTACTA-ATGGCCCGAA
1 CATCTTGCTCGAAAGGCTTA-TAGATGACCCGAA
6516462 AGACTTACCA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
40 15 0.24
41 18 0.29
42 27 0.44
43 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (42 bp):
CATCTTGCTCGAAAGGCTTATAGATGACCCGAAGGAGTTAAT
Found at i:6516487 original size:259 final size:254
Alignment explanation
Indices: 6515781--6516729 Score: 1127
Period size: 259 Copynumber: 3.7 Consensus size: 254
6515771 TTACTAGGTA
* *
6515781 AGAAACTTTGGAAGTCGTTTTCTCATTTTTTTTTTGAAAAACATGTGAAAACATCCTTCCCGAAG
1 AGAAACTTTGGAAATAGTTTTCTCA----TTTTTTGAAAAACATGTGAAAACAT-CTTCCCGAAG
* * * * *
6515846 GTCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGGAGGATT
61 GTCTTACGGATGACCCGAAGGACTTATCACCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATT
* * *
6515911 TAGTCATCATGCTCGAAAGACTTACTGATGGCCCGAAACACTTATCAATTTGGGAAATAGTTTAC
126 TAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACCAATTTGGGAAATAGTTTAC
* *
6515976 TAGGTAAGAAACTTTGGAAACCGTTTTCTTACTTTTCAAAAAAATTT-AATTTTCAAATTTAAAT
191 TAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTC--AAAAATTTCAATTTTCAGATTTAAAT
6516040 G
254 G
* * * *
6516041 AGAAACTTTGGAAA-ACGTTTTCTCATTTTTCGAAAAA-ATGTGAAGATATCATGCCCGAAGGTC
1 AGAAACTTTGGAAATA-GTTTTCTCATTTTTTGAAAAACATGTGAAAACATC-TTCCCGAAGGTC
* * * * * *
6516104 TTACGGATGGCTCGAAGAACTTATCACCTTGCTCGAAAGGCTTATAAATGACCTGAAGAATTTAA
64 TTACGGATGACCCGAAGGACTTATCACCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAA
* * * * *
6516169 TCATCATACTCGAAAGACTTAATGATGGCCCGAATGACTTATCAATTTGGGAAATAGTTTACTAA
129 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACCAATTTGGGAAATAGTTTACTAG
*
6516234 GTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
194 GTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
* *
6516295 AGAAACGTTT-GAAATAGTTTTCTCATTTTTTTTTTTGAAAAATATGTGTAAACATCTTGCCCGA
1 AGAAAC-TTTGGAAATAGTTTTCTCA-----TTTTTTGAAAAACATGTGAAAACATCTT-CCCGA
* * * *
6516359 AGGTCTTATGG-TGACCCGAAGGAGTTATCATCTTGCTCGAAAGGCTTATAGATGACCCGGAGGA
59 AGGTCTTACGGATGACCCGAAGGACTTATCACCTTGCTCGAAAGGCTTATAGATGACCCGAAGGA
* * * * *
6516423 TTTAATCATCATCCTTGAAAGGCTTACTAATGGCCCGAAAGACTTACCAATTTTGGAAATAGTTT
124 TTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACCAATTTGGGAAATAGTTT
* * *
6516488 ACTAGGTAAGAAACTTTGTAAATCGTCTTCTTACTTTTCAAAAATGTCAATTTTCAGTTTAGATT
189 ACTAGGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCAATTTTC-----AGATT
6516553 TAAATG
249 TAAATG
* * **** * *
6516559 AGAAACTTTGGAAATCGTTTTATCATTTAAAAAAAAACATGTGAAAACATCATTCCTGAATGTCT
1 AGAAACTTTGGAAATAGTTTTCTCATTTTTTGAAAAACATGTGAAAACATC-TTCCCGAAGGTCT
* * * *
6516624 TATGGATGGA-CCGAAAGACTTATAACCTTGCTCGAAAGGCTTATAGATGACCCGAAAGATTTAA
65 TACGGAT-GACCCGAAGGACTTATCACCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAA
* * * *
6516688 TCATAATGCTCGAAAGACTTACTGGTTGCCCGAAGGACTTAC
129 TCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTAC
6516730 TAAGTAAGAA
Statistics
Matches: 592, Mismatches: 76, Indels: 42
0.83 0.11 0.06
Matches are distributed among these distances:
253 8 0.01
254 37 0.06
255 172 0.29
256 11 0.02
259 197 0.33
260 132 0.22
261 2 0.00
263 3 0.01
264 30 0.05
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (254 bp):
AGAAACTTTGGAAATAGTTTTCTCATTTTTTGAAAAACATGTGAAAACATCTTCCCGAAGGTCTT
ACGGATGACCCGAAGGACTTATCACCTTGCTCGAAAGGCTTATAGATGACCCGAAGGATTTAATC
ATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTACCAATTTGGGAAATAGTTTACTAGGT
AAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
Found at i:6518318 original size:2 final size:2
Alignment explanation
Indices: 6518311--6518344 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6518301 AAATTTATTG
6518311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6518345 TCTCCTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6518551 original size:3 final size:3
Alignment explanation
Indices: 6518543--6518577 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
6518533 TGTATAGTCT
6518543 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6518578 TTATTAACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6524533 original size:13 final size:13
Alignment explanation
Indices: 6524515--6524540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6524505 TAATATTCTG
6524515 TAAATTTTAGGAT
1 TAAATTTTAGGAT
6524528 TAAATTTTAGGAT
1 TAAATTTTAGGAT
6524541 GAAACACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TAAATTTTAGGAT
Found at i:6525584 original size:90 final size:94
Alignment explanation
Indices: 6525485--6525673 Score: 233
Period size: 90 Copynumber: 2.1 Consensus size: 94
6525475 GACACTCTAC
* * * *
6525485 AAAAAGAATAAGCGCTAAAATGATTATTTAATCAAATGCTAG-GGT-TTTTTACCCTAAAATGAA
1 AAAAAGAATAAGCGATAAAATGATTATTTAACCAAACGCTAGAGATATTTTTACCCTAAAATGAA
*
6525548 ACGTAATGAACTAAAATACT-TCAAAAA-
66 ACGTAATGAACTAAAATACTCTAAAAAAT
* * ** *
6525575 AAAAAGAATAAGGGATAAAATGATTATTTAACCAAACGTTAGAGATATTTTTACTTTAAAGTGAA
1 AAAAAGAATAAGCGATAAAATGATTATTTAACCAAACGCTAGAGATATTTTTACCCTAAAATGAA
* * *
6525640 ATGTTATGAATTAAAATACTCTAAAAAAT
66 ACGTAATGAACTAAAATACTCTAAAAAAT
6525669 AAAAA
1 AAAAA
6525674 AAATGATAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
90 37 0.45
91 2 0.02
92 32 0.39
93 6 0.07
94 5 0.06
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (94 bp):
AAAAAGAATAAGCGATAAAATGATTATTTAACCAAACGCTAGAGATATTTTTACCCTAAAATGAA
ACGTAATGAACTAAAATACTCTAAAAAAT
Found at i:6525960 original size:48 final size:49
Alignment explanation
Indices: 6525889--6525998 Score: 186
Period size: 48 Copynumber: 2.2 Consensus size: 49
6525879 AGGTGCAATG
*
6525889 CATACGGGGCATTAATGAGTAAGGATGCTAGAGACAGAGAC-GGAGGAT
1 CATACAGGGCATTAATGAGTAAGGATGCTAGAGACAGAGACGGGAGGAT
6525937 CATACAGGGCATTAATGAGTAAGGATGCTAGAGACAGAGACGGAGGAGGAT
1 CATACAGGGCATTAATGAGTAAGGATGCTAGAGACAGAGAC-G-GGAGGAT
6525988 CATACAGGGCA
1 CATACAGGGCA
6525999 ATCATCGGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
48 40 0.69
51 18 0.31
ACGTcount: A:0.36, C:0.14, G:0.35, T:0.15
Consensus pattern (49 bp):
CATACAGGGCATTAATGAGTAAGGATGCTAGAGACAGAGACGGGAGGAT
Found at i:6526845 original size:17 final size:17
Alignment explanation
Indices: 6526823--6526859 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6526813 ATGTTATTTG
6526823 TTATTTA-TATTATAATA
1 TTATTTATTATTATAA-A
6526840 TTATTTATTATTATAAA
1 TTATTTATTATTATAAA
6526857 TTA
1 TTA
6526860 AACTTATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTATTATTATAAA
Found at i:6527447 original size:2 final size:2
Alignment explanation
Indices: 6527413--6527439 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6527403 GTTAGGTTTA
6527413 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6527440 GGTATATAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6527869 original size:15 final size:15
Alignment explanation
Indices: 6527849--6527877 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6527839 AATATATATC
6527849 ATAAATTATTAAAAT
1 ATAAATTATTAAAAT
6527864 ATAAATTATTAAAA
1 ATAAATTATTAAAA
6527878 AATTAACGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAATTATTAAAAT
Found at i:6528309 original size:204 final size:204
Alignment explanation
Indices: 6527959--6528365 Score: 814
Period size: 204 Copynumber: 2.0 Consensus size: 204
6527949 CTTAGACGAA
6527959 GTACTCTGAATGGATTAGTCAAGGTTTACAAATTTTGTATCTAAATATAACTAGGAAACATCGTA
1 GTACTCTGAATGGATTAGTCAAGGTTTACAAATTTTGTATCTAAATATAACTAGGAAACATCGTA
6528024 ATTAAGTCGTATCAATACACACAAATTTAATCATATTTCAAACAATTTTTAAGTGCCTCTTTATA
66 ATTAAGTCGTATCAATACACACAAATTTAATCATATTTCAAACAATTTTTAAGTGCCTCTTTATA
6528089 TACTAGCTTATTGTACGATGTGCAAGGTTTACGAATAGTCTTTAGAATTGTTCAAAGTATGATTA
131 TACTAGCTTATTGTACGATGTGCAAGGTTTACGAATAGTCTTTAGAATTGTTCAAAGTATGATTA
6528154 GATGTGGGC
196 GATGTGGGC
6528163 GTACTCTGAATGGATTAGTCAAGGTTTACAAATTTTGTATCTAAATATAACTAGGAAACATCGTA
1 GTACTCTGAATGGATTAGTCAAGGTTTACAAATTTTGTATCTAAATATAACTAGGAAACATCGTA
6528228 ATTAAGTCGTATCAATACACACAAATTTAATCATATTTCAAACAATTTTTAAGTGCCTCTTTATA
66 ATTAAGTCGTATCAATACACACAAATTTAATCATATTTCAAACAATTTTTAAGTGCCTCTTTATA
6528293 TACTAGCTTATTGTACGATGTGCAAGGTTTACGAATAGTCTTTAGAATTGTTCAAAGTATGATTA
131 TACTAGCTTATTGTACGATGTGCAAGGTTTACGAATAGTCTTTAGAATTGTTCAAAGTATGATTA
6528358 GATGTGGG
196 GATGTGGG
6528366 TATTGATACA
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 203 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (204 bp):
GTACTCTGAATGGATTAGTCAAGGTTTACAAATTTTGTATCTAAATATAACTAGGAAACATCGTA
ATTAAGTCGTATCAATACACACAAATTTAATCATATTTCAAACAATTTTTAAGTGCCTCTTTATA
TACTAGCTTATTGTACGATGTGCAAGGTTTACGAATAGTCTTTAGAATTGTTCAAAGTATGATTA
GATGTGGGC
Found at i:6531137 original size:12 final size:12
Alignment explanation
Indices: 6531119--6531172 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
6531109 CAACACCATA
6531119 CTCTTCTTCTTC
1 CTCTTCTTCTTC
* *
6531131 TTCTTCTTCCTC
1 CTCTTCTTCTTC
*
6531143 CTCGTCTTCTTC
1 CTCTTCTTCTTC
6531155 CTCCTCATCTTCTTC
1 CT-CT--TCTTCTTC
6531170 CTC
1 CTC
6531173 GGAGTACATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 21 0.64
13 1 0.03
14 1 0.03
15 10 0.30
ACGTcount: A:0.02, C:0.44, G:0.02, T:0.52
Consensus pattern (12 bp):
CTCTTCTTCTTC
Found at i:6531138 original size:15 final size:15
Alignment explanation
Indices: 6531132--6531172 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
6531122 TTCTTCTTCT
*
6531132 TCTTCTTCCTCCTCG
1 TCTTCTTCCTCCTCA
6531147 TCTTCTTCCTCCTCA
1 TCTTCTTCCTCCTCA
6531162 TCTTCTTCCTC
1 TCTTCTTCCTC
6531173 GGAGTACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.02, C:0.46, G:0.02, T:0.49
Consensus pattern (15 bp):
TCTTCTTCCTCCTCA
Found at i:6531168 original size:18 final size:18
Alignment explanation
Indices: 6531126--6531169 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
6531116 ATACTCTTCT
* *
6531126 TCTTCTTCTTCTTCCTCC
1 TCTTCTTCTTCCTCCTCA
*
6531144 TCGTCTTCTTCCTCCTCA
1 TCTTCTTCTTCCTCCTCA
6531162 TCTTCTTC
1 TCTTCTTC
6531170 CTCGGAGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.02, C:0.43, G:0.02, T:0.52
Consensus pattern (18 bp):
TCTTCTTCTTCCTCCTCA
Found at i:6532095 original size:11 final size:13
Alignment explanation
Indices: 6532064--6532094 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6532054 AGCCACACAC
6532064 TTAT-TATTTAAT
1 TTATATATTTAAT
6532076 TTATATATTTAAT
1 TTATATATTTAAT
6532089 TTATAT
1 TTATAT
6532095 TGTGAACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATATATTTAAT
Found at i:6533527 original size:30 final size:30
Alignment explanation
Indices: 6533493--6533568 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
6533483 GGCTACGCCA
6533493 AATTGGCCCATTAGGGCAATCGGGTAATTT
1 AATTGGCCCATTAGGGCAATCGGGTAATTT
6533523 AATTGGCCCATTAGGGCAATCGGGTAATTT
1 AATTGGCCCATTAGGGCAATCGGGTAATTT
* *
6533553 AATTAGCCTATTAGGG
1 AATTGGCCCATTAGGG
6533569 TATCCAAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (30 bp):
AATTGGCCCATTAGGGCAATCGGGTAATTT
Found at i:6537205 original size:107 final size:106
Alignment explanation
Indices: 6536867--6537246 Score: 478
Period size: 107 Copynumber: 3.6 Consensus size: 106
6536857 AAAATGTATC
* * * * * *
6536867 GGAAGTATTGATACTCACAAGGTAGTATCGACACTACCAACATTGCTCAAATTCCAGAATGTAAA
1 GGAAGTATCGATACTCACAAGGTAGTATCGATACTACTAACATTGCTCAAATTCTAAAATGCAAA
*
6536932 AATGGTACCGATATCCAAAGGGGTATC-ATACCAAAGGTAAT
66 AATGGTA-CGGTATCCAAAGGGGTATCGATACCAAAGGTAAT
** * * * * *
6536973 AAAAGTATCGATACTCACAAGATAGTATCGATACTATTAGCATTGCTCAAATTCTAGAATACAAA
1 GGAAGTATCGATACTCACAAGGTAGTATCGATACTACTAACATTGCTCAAATTCTAAAATGC-AA
* * **
6537038 AAATGGTACTG-ATACATAAAGGAATATCGATACCAAAGGTAAT
65 AAATGGTACGGTAT-C-CAAAGGGGTATCGATACCAAAGGTAAT
* * *
6537081 GGAAGTATCGATTCTCACAAGGTAGTATTGATACTACTAGCATTGCTCAAATTCTAAAATGCAAA
1 GGAAGTATCGATACTCACAAGGTAGTATCGATACTACTAACATTGCTCAAATTCTAAAATGCAAA
* *
6537146 AATGGTATCGGTATCCAAAGGGGTAACGATACCAAAGGTAGT
66 AATGGTA-CGGTATCCAAAGGGGTATCGATACCAAAGGTAAT
6537188 GGAAGTATCGATACTCACAAGGTAGTATCGATACTA-TCAACATTGCTCAAATTCTAAAA
1 GGAAGTATCGATACTCACAAGGTAGTATCGATACTACT-AACATTGCTCAAATTCTAAAA
6537247 GAAATTATTA
Statistics
Matches: 234, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
105 2 0.01
106 54 0.23
107 105 0.45
108 71 0.30
109 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (106 bp):
GGAAGTATCGATACTCACAAGGTAGTATCGATACTACTAACATTGCTCAAATTCTAAAATGCAAA
AATGGTACGGTATCCAAAGGGGTATCGATACCAAAGGTAAT
Found at i:6538625 original size:33 final size:33
Alignment explanation
Indices: 6538578--6538642 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
6538568 CAATTAAATA
* * *
6538578 ATGACAAATTTATTAGAGAATTAAATGGCATTT
1 ATGAAAAATTTATTAGAGAATGAAACGGCATTT
6538611 ATGAAAAATTTATTAGAGAATGAAACGGCATT
1 ATGAAAAATTTATTAGAGAATGAAACGGCATT
6538643 CGGGGAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGAAAAATTTATTAGAGAATGAAACGGCATTT
Found at i:6538952 original size:28 final size:28
Alignment explanation
Indices: 6538920--6538973 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
6538910 TTTAAAATTA
6538920 AAATTAAAACTAATATTTTAATATTTCC
1 AAATTAAAACTAATATTTTAATATTTCC
** *
6538948 AAATTAAATTTAATATTTTCATATTT
1 AAATTAAAACTAATATTTTAATATTT
6538974 ATATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (28 bp):
AAATTAAAACTAATATTTTAATATTTCC
Found at i:6540805 original size:64 final size:64
Alignment explanation
Indices: 6540709--6540891 Score: 264
Period size: 64 Copynumber: 2.9 Consensus size: 64
6540699 GTATTAGTTC
* *
6540709 GGGTGATTACAAGATAATATTTGTTCTA-AATTTTTTTAGTCAATTGACAATGAACGCTAG-TTT
1 GGGTGATTACAAGATAGTATTTGTTC-AGAATTTTCTTAGTCAATTGACAATGAACGCTAGTTTT
* * *
6540772 GAGGTGATAACAATATAGTATTTATTCAGAATTTTCTTAG-CAAATTGACAATGAACGCTAGTTT
1 G-GGTGATTACAAGATAGTATTTGTTCAGAATTTTCTTAGTC-AATTGACAATGAACGCTAGTTT
6540836 T
64 T
*
6540837 GGGTGATTACAAGATAGTATGTGTTCAGAATTTTCTTAGTCAATTGACAATGAAC
1 GGGTGATTACAAGATAGTATTTGTTCAGAATTTTCTTAGTCAATTGACAATGAAC
6540892 TCACACAGAC
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
63 3 0.03
64 98 0.92
65 5 0.05
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (64 bp):
GGGTGATTACAAGATAGTATTTGTTCAGAATTTTCTTAGTCAATTGACAATGAACGCTAGTTTT
Found at i:6548797 original size:2 final size:2
Alignment explanation
Indices: 6548790--6548817 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6548780 TATAAATTTG
6548790 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
6548818 GGGATAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6549374 original size:2 final size:2
Alignment explanation
Indices: 6549367--6549394 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6549357 TTATGTGTCC
6549367 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
6549395 GGTTATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6549441 original size:110 final size:108
Alignment explanation
Indices: 6549273--6549476 Score: 320
Period size: 110 Copynumber: 1.9 Consensus size: 108
6549263 ATCTCAACCC
*
6549273 ATATATATATATATGGTTATACTTTTTCCTTGACCAATGATCTTACATTGCATTATGACATAAAG
1 ATATATATATATATGGTTATACTTTTTCCTTGACCAATGATCTTACATTGAATTATGACATAAAG
** *
6549338 GGTTTATATGGTTATCATTTTATGTGTCCATATATATATATAT
66 GGTTTATACAGTTATCATTGTATGTGTCCATATATATATATAT
* *
6549381 ATATATATATATATGGTTAT-CTTTTTTCTTTTTGACCAATGATCTTCCATTGAATTATGACATA
1 ATATATATATATATGGTTATAC-TTTTTC--CTTGACCAATGATCTTACATTGAATTATGACATA
6549445 AAGGGTTTATACAGTTATCATTGTATGTGTCC
63 AAGGGTTTATACAGTTATCATTGTATGTGTCC
6549477 TCCACCCCCC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 26 0.30
110 60 0.69
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.46
Consensus pattern (108 bp):
ATATATATATATATGGTTATACTTTTTCCTTGACCAATGATCTTACATTGAATTATGACATAAAG
GGTTTATACAGTTATCATTGTATGTGTCCATATATATATATAT
Found at i:6551239 original size:28 final size:28
Alignment explanation
Indices: 6551207--6551265 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
6551197 ACATATTTAA
6551207 AAGT-AATCAATAAAACAAATATAGTAGC
1 AAGTAAAT-AATAAAACAAATATAGTAGC
*
6551235 AAGTAAATAATAAAACAAATATATTAGC
1 AAGTAAATAATAAAACAAATATAGTAGC
6551263 AAG
1 AAG
6551266 GAAGGATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.22
Consensus pattern (28 bp):
AAGTAAATAATAAAACAAATATAGTAGC
Found at i:6557208 original size:30 final size:29
Alignment explanation
Indices: 6557150--6557215 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
6557140 AAATCAATGT
*
6557150 GACCACCGAACTTTCAATTATATCAATCA
1 GACCACCAAACTTTCAATTATATCAATCA
*
6557179 GACCACCAAACTATTTAATTGAT-TCAATCA
1 GACCACCAAACT-TTCAATT-ATATCAATCA
*
6557209 AACCACC
1 GACCACC
6557216 GGCTGTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.34
30 19 0.59
31 2 0.06
ACGTcount: A:0.39, C:0.29, G:0.06, T:0.26
Consensus pattern (29 bp):
GACCACCAAACTTTCAATTATATCAATCA
Found at i:6557810 original size:29 final size:29
Alignment explanation
Indices: 6557768--6557831 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
6557758 ATCGAACCAA
* **
6557768 AATTTATTTGAAAATTATTAACCGAATTG
1 AATTAATTTGAAAATTATTAACCGAACCG
6557797 AATTAATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
6557826 AATTAA
1 AATTAA
6557832 CCGATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:6557939 original size:127 final size:122
Alignment explanation
Indices: 6557773--6558001 Score: 323
Period size: 127 Copynumber: 1.8 Consensus size: 122
6557763 ACCAAAATTT
* * * *
6557773 ATTTGAAAATTATTAACCGAATTGAATTAATTTGAAAATTATTAACCGAACCGAATTAACCGATT
1 ATTTGAAAATTATTAACCGAATCGAACTAATATGAAAATTATTAACCAAACCGAATTAACCGA--
*
6557838 TTTTTTAAAAAATTATTAACTGAATTAATCGAAGCAAAAATTCGATTAAATGGGTTCGGTTA
64 TTTTTT---AAATTATTAACTGAATTAATCGAAACAAAAATTCGATTAAATGGGTTCGGTTA
* * *
6557900 ATTTGAAAATTATTAACTGAATCGAACTAATATGAAAATTATTAATCAAACTGAATTAACCGATT
1 ATTTGAAAATTATTAACCGAATCGAACTAATATGAAAATTATTAACCAAACCGAATTAACCGATT
* *
6557965 TTTTAAATTTTTAATTGAATTAATCGAAACAAAAATT
66 TTTTAAATTATTAACTGAATTAATCGAAACAAAAATT
6558002 AGGTTAATTC
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
122 30 0.33
125 6 0.07
127 56 0.61
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (122 bp):
ATTTGAAAATTATTAACCGAATCGAACTAATATGAAAATTATTAACCAAACCGAATTAACCGATT
TTTTAAATTATTAACTGAATTAATCGAAACAAAAATTCGATTAAATGGGTTCGGTTA
Found at i:6558093 original size:29 final size:29
Alignment explanation
Indices: 6558025--6558094 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
6558015 CGGTTAATCA
* *
6558025 AACCAAAATTTATTTGAAAATTATTAAGCG
1 AACC-AAATTAATTTGAAAATTATTAACCG
**
6558055 AACCGGATTAATTTGAAAATTATTAACCG
1 AACCAAATTAATTTGAAAATTATTAACCG
6558084 AACCAAATTAA
1 AACCAAATTAA
6558095 CCTATTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (29 bp):
AACCAAATTAATTTGAAAATTATTAACCG
Found at i:6558296 original size:17 final size:17
Alignment explanation
Indices: 6558274--6558321 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
6558264 TAATTTAAAT
6558274 AATAATTTGTTTAAACA
1 AATAATTTGTTTAAACA
6558291 AATAATTTGTTTAAACA
1 AATAATTTGTTTAAACA
6558308 AATAATTTGTTTAA
1 AATAATTTGTTTAA
6558322 TTTTTTATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (17 bp):
AATAATTTGTTTAAACA
Found at i:6560555 original size:29 final size:29
Alignment explanation
Indices: 6560533--6560594 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
6560523 TGAACAATTT
6560533 AAAAATTTAGTGATTAAAATGAAAATGAA
1 AAAAATTTAGTGATTAAAATGAAAATGAA
* *
6560562 AAAAATTTAGTGATCAAAATAAAAAAT-AA
1 AAAAATTTAGTGATTAAAAT-GAAAATGAA
6560591 AAAA
1 AAAA
6560595 TTCTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (29 bp):
AAAAATTTAGTGATTAAAATGAAAATGAA
Found at i:6560913 original size:21 final size:20
Alignment explanation
Indices: 6560827--6560984 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
6560817 AAATGACCAA
**
6560827 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
6560846 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
6560866 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
6560886 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
6560907 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
6560928 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
6560948 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
6560969 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
6560985 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:6560975 original size:20 final size:20
Alignment explanation
Indices: 6560951--6561200 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
6560941 CGATTTTCCA
** *
6560951 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
6560971 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
6560991 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
6561011 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
6561031 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
6561051 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
6561071 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
6561091 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
6561111 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
6561131 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
6561151 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
6561171 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
6561191 AAATCACAAC
1 AAATCGCAAC
6561201 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:6561915 original size:24 final size:24
Alignment explanation
Indices: 6561876--6561922 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6561866 AAATTTGGTC
6561876 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
6561900 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
6561923 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:6564493 original size:19 final size:19
Alignment explanation
Indices: 6564453--6564531 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
6564443 GATTCTCTCG
6564453 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
6564473 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6564492 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6564506 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6564525 TTGCGAT
1 TTGCGAT
6564532 AGTCAATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 17 0.33
20 15 0.29
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:6564642 original size:33 final size:33
Alignment explanation
Indices: 6564590--6564738 Score: 133
Period size: 33 Copynumber: 4.3 Consensus size: 33
6564580 CCATTACATT
*
6564590 TCGCAATGCGGAAATGAAAATCGCAACAAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACAAGAAAA
6564624 TCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAA--C--AA-GAAAA
* * * *
6564662 TCGCAACGAGAGAATCG-CAAT-GCGAA-ATGAAAA
1 TCGCAATGCGA-AAT-GAAAATCGC-AACAAGAAAA
* *
6564695 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACAAGAAAA
6564728 TCGCAATGCGA
1 TCGCAATGCGA
6564739 TTTTCATTTC
Statistics
Matches: 93, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
31 1 0.01
32 8 0.09
33 47 0.51
34 10 0.11
35 1 0.01
37 2 0.02
38 15 0.16
39 8 0.09
40 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACAAGAAAA
Found at i:6564646 original size:19 final size:19
Alignment explanation
Indices: 6564590--6564719 Score: 163
Period size: 19 Copynumber: 7.3 Consensus size: 19
6564580 CCATTACATT
6564590 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
6564610 TCGCAA--C--AA-GAGAA
1 TCGCAATGCGAAATGAAAA
6564624 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
6564643 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
6564662 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
6564676 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
6564695 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
6564714 TCGCAA
1 TCGCAA
6564720 CGAGAGAATC
Statistics
Matches: 96, Mismatches: 4, Indels: 21
0.79 0.03 0.17
Matches are distributed among these distances:
14 20 0.21
15 3 0.03
16 3 0.03
17 2 0.02
18 4 0.04
19 58 0.60
20 6 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:6564757 original size:52 final size:52
Alignment explanation
Indices: 6564590--6564738 Score: 280
Period size: 52 Copynumber: 2.8 Consensus size: 52
6564580 CCATTACATT
*
6564590 TCGCAATGCGGAAATGAAAATCGCAACAAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
6564643 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
6564695 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
6564739 TTTTCATTTC
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 86 0.91
53 9 0.09
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:6564771 original size:33 final size:33
Alignment explanation
Indices: 6564734--6565000 Score: 168
Period size: 33 Copynumber: 7.7 Consensus size: 33
6564724 AGAATCGCAA
6564734 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
6564767 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
6564805 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCCACAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCT-CTCGT
** ** **
6564839 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
6564872 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
6564910 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
6564943 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
6564976 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
6565001 AATGTAATGG
Statistics
Matches: 174, Mismatches: 36, Indels: 47
0.68 0.14 0.18
Matches are distributed among these distances:
31 9 0.05
32 10 0.06
33 76 0.44
34 17 0.10
35 9 0.05
36 9 0.05
37 4 0.02
38 16 0.09
39 6 0.03
40 18 0.10
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:6564784 original size:52 final size:52
Alignment explanation
Indices: 6564728--6565000 Score: 456
Period size: 52 Copynumber: 5.2 Consensus size: 52
6564718 AACGAGAGAA
*
6564728 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
6564780 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* ** ** **
6564832 TCCACATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
6564885 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
6564937 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
6564989 TCCGCATTGCGA
1 T-CGCATTGCGA
6565001 AATGTAATGG
Statistics
Matches: 204, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
52 149 0.73
53 55 0.27
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:6564867 original size:105 final size:104
Alignment explanation
Indices: 6564747--6565000 Score: 427
Period size: 105 Copynumber: 2.4 Consensus size: 104
6564737 GATTTTCATT
6564747 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
6564812 CTCTCGTTGCGATTTTCATTTCCACATTGCGAAATGAAAA
66 CTCTCGTTGCGATTTTCATTT-CACATTGCGAAATGAAAA
6564852 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
* ** ** **
6564917 CTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 CTCTCGTTGCGATTTTCATTTCACATTGCGAAATGAAAA
6564956 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGA
6565001 AATGTAATGG
Statistics
Matches: 141, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
104 45 0.32
105 96 0.68
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.43
Consensus pattern (104 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
CTCTCGTTGCGATTTTCATTTCACATTGCGAAATGAAAA
Found at i:6565083 original size:19 final size:19
Alignment explanation
Indices: 6565059--6565156 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
6565049 AAAATTGACT
6565059 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6565078 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
6565092 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6565111 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
6565131 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6565150 ATCGCAA
1 ATCGCAA
6565157 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 36 0.51
20 19 0.27
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6565101 original size:33 final size:33
Alignment explanation
Indices: 6565059--6565175 Score: 171
Period size: 33 Copynumber: 3.4 Consensus size: 33
6565049 AAAATTGACT
6565059 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
6565092 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAGA
6565131 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
6565164 ATCGCAATGCGA
1 ATCGCAATGCGA
6565176 TTTTCATTTC
Statistics
Matches: 76, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
33 41 0.54
34 1 0.01
35 1 0.01
36 2 0.03
37 1 0.01
38 1 0.01
39 29 0.38
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:6565193 original size:19 final size:19
Alignment explanation
Indices: 6565165--6565299 Score: 157
Period size: 19 Copynumber: 7.6 Consensus size: 19
6565155 AACGAGAGAA
*
6565165 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6565184 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
6565198 TCCCA-TGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6565216 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
6565236 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
6565252 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6565269 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6565288 TCGCATTGCGAT
1 TCGCATTGCGAT
6565300 AGTCAATTTT
Statistics
Matches: 99, Mismatches: 5, Indels: 24
0.77 0.04 0.19
Matches are distributed among these distances:
13 5 0.05
14 10 0.10
15 3 0.03
16 7 0.07
17 10 0.10
18 1 0.01
19 49 0.49
20 14 0.14
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:6565228 original size:52 final size:52
Alignment explanation
Indices: 6565165--6565299 Score: 227
Period size: 52 Copynumber: 2.6 Consensus size: 52
6565155 AACGAGAGAA
*
6565165 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTC-CCATGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCCATGCGATTTTCATT
**
6565216 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCCATGCGATTTTCATT
6565269 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
6565300 AGTCAATTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
51 1 0.01
52 63 0.80
53 15 0.19
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCCATGCGATTTTCATT
Found at i:6565422 original size:14 final size:14
Alignment explanation
Indices: 6565403--6565439 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
6565393 CATCAATTAC
6565403 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
6565417 ACAAATCATCTTTT
1 ACAAATCAACTTTT
6565431 ACAAATCAA
1 ACAAATCAA
6565440 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6566863 original size:21 final size:20
Alignment explanation
Indices: 6566833--6566893 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
6566823 GTGAATCGGG
6566833 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGG-C
* * **
6566854 CTCTTCAATGATGACAGTGGC
1 CTCTTGAATGGTGGGAG-GGC
6566875 CTCTTGAATGGTGGGAGGG
1 CTCTTGAATGGTGGGAGGG
6566894 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.26
Consensus pattern (20 bp):
CTCTTGAATGGTGGGAGGGC
Found at i:6567378 original size:20 final size:19
Alignment explanation
Indices: 6567353--6567398 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
6567343 TAGTTTACTT
*
6567353 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAC-CAAAA
*
6567373 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
6567392 TCGCAAC
1 TCGCAAC
6567399 GAAAGAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.46, C:0.30, G:0.13, T:0.11
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Done.