Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 2 of 187
Found at i:502471 original size:14 final size:15
Alignment explanation
Indices: 502452--502489 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
502442 TATTATGTGA
*
502452 TTTATTTTTT-TATT
1 TTTATTTTTTGCATT
502466 TTTATTTTTTGCATT
1 TTTATTTTTTGCATT
502481 TTTAGTTTT
1 TTTA-TTTT
502490 CTTTGTGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 7 0.33
16 4 0.19
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTGCATT
Found at i:505561 original size:458 final size:433
Alignment explanation
Indices: 505036--505851 Score: 1053
Period size: 458 Copynumber: 1.8 Consensus size: 433
505026 ACTTGTAATC
505036 TCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACAC
1 TCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACAC
* * *
505101 AAAAGATATATGTATAGATTCAAACCAATGAATCATATTTCGTTCCTATAAGACTATCCCTATTG
66 AAAAGATATATGTATACATTCAAACCAATGAATCATATTTCATTCCTATAAGACTATCCCTATCG
* *
505166 AATAAGG-TGTCGTATAAGTAACCATTTGCATTTCAATTTCCATTCCTCGTACAGAACCGATCCA
131 AATAAGGAT-TCATATAAGTAACCATTTG------------CATTCCTCATACAGAACCGATCCA
* * *
505230 ATGGCAACCCTCCATTCAAAATACATGAAAATCACTTGTAATCTCATAAACATCACGGAACAACA
183 ATGACAACCCTCCATTCAAAATACAT---AAT--C-----A----AGAAA-ATCAAGGAACAACA
* *
505295 GCAATCCAATTCAGTATGACTAACGATTCGATTATACAAACACAAAAGCTATATGTAGACATTCG
233 GCAATCCAATTCAGTATGACTAACGATTCGATTATACAAACACAAAAGCTATATATAGACATTCA
* * * *
505360 AACCGATGATTTGTA-TTCATTCCTATTAGACTAT-CCCAATCAAATAAGGTTTCCTATAAGTAA
298 AACCGACGAATCGTATTTCATTCCTATTAGACTATGCCCAACCAAATAAGGTTTCCTATAAGTAA
505423 CCATTTGCGTTTAAATATCCATTCCTCATACGGAACTGATCCAATGACAACCCTCCATTCAAAGT
363 CCATTTGCGTTTAAATATCCATTCCTCATACGGAACTGATCCAATGACAACCCTCCATTCAAAGT
505488 ACATAA
428 ACATAA
* * * *
505494 TCATGAAAATCATGGAACAATAGCAATCCAATTCAGTATGATTAACGATTCGATTATATAAACAC
1 TCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACAC
* * * * *
505559 AAAAGCTATATGTATACATTCAAACCGATGAGTCGTATTTCATTCCTATTAGACTATCCCTATCG
66 AAAAGATATATGTATACATTCAAACCAATGAATCATATTTCATTCCTATAAGACTATCCCTATCG
* *
505624 AATAAGGATTCATATAAGTAACCATTTGCGTTCCTCATACCGAACCGATCCAATGACAACCCTCC
131 AATAAGGATTCATATAAGTAACCATTTGCATTCCTCATACAGAACCGATCCAATGACAACCCTCC
* *
505689 ATTCAAAATACATAATCAAGAAAATCAATGAACAATAGCAATCCAATTCAGTATGACTAACGATT
196 ATTCAAAATACATAATCAAGAAAATCAAGGAACAACAGCAATCCAATTCAGTATGACTAACGATT
* * * **
505754 CGATTATATAAACACAAAAGCTATATATATAGATTCAAACCGACGAATCGTATTTTGTTCCTATT
261 CGATTATACAAACACAAAAGCTATATATAGACATTCAAACCGACGAATCGTATTTCATTCCTATT
* *
505819 AGACTATGCCCTACCGAATAAGGTTTCCTATAA
326 AGACTATGCCCAACCAAATAAGGTTTCCTATAA
505852 ACAACCACTC
Statistics
Matches: 321, Mismatches: 34, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
431 83 0.26
432 21 0.07
433 22 0.07
436 1 0.00
441 1 0.00
443 3 0.01
446 46 0.14
458 143 0.45
459 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.29
Consensus pattern (433 bp):
TCATAAAAATCACGAAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACAC
AAAAGATATATGTATACATTCAAACCAATGAATCATATTTCATTCCTATAAGACTATCCCTATCG
AATAAGGATTCATATAAGTAACCATTTGCATTCCTCATACAGAACCGATCCAATGACAACCCTCC
ATTCAAAATACATAATCAAGAAAATCAAGGAACAACAGCAATCCAATTCAGTATGACTAACGATT
CGATTATACAAACACAAAAGCTATATATAGACATTCAAACCGACGAATCGTATTTCATTCCTATT
AGACTATGCCCAACCAAATAAGGTTTCCTATAAGTAACCATTTGCGTTTAAATATCCATTCCTCA
TACGGAACTGATCCAATGACAACCCTCCATTCAAAGTACATAA
Found at i:505807 original size:210 final size:211
Alignment explanation
Indices: 505444--505851 Score: 667
Period size: 210 Copynumber: 1.9 Consensus size: 211
505434 TAAATATCCA
* * * *
505444 TTCCTCATACGGAACTGATCCAATGACAACCCTCCATTCAAAGTACATAATCATGAAAATCATGG
1 TTCCTCATACCGAACCGATCCAATGACAACCCTCCATTCAAAATACATAATCAAGAAAATCATGG
* *
505509 AACAATAGCAATCCAATTCAGTATGATTAACGATTCGATTATATAAACACAAAAGCTATATGTAT
66 AACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACACAAAAGCTATATATAT
* * *
505574 ACATTCAAACCGATGAGTCGTATTTCATTCCTATTAGACTAT-CCCTATCGAATAAGGATTCATA
131 ACATTCAAACCGACGAATCGTATTTCATTCCTATTAGACTATGCCCTACCGAATAAGGATTCATA
505638 TAAGTAACCATTTGCG
196 TAAGTAACCATTTGCG
505654 TTCCTCATACCGAACCGATCCAATGACAACCCTCCATTCAAAATACATAATCAAGAAAATCAAT-
1 TTCCTCATACCGAACCGATCCAATGACAACCCTCCATTCAAAATACATAATCAAGAAAATC-ATG
505718 GAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACACAAAAGCTATATATA
65 GAACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACACAAAAGCTATATATA
* ** * *
505783 TAGATTCAAACCGACGAATCGTATTTTGTTCCTATTAGACTATGCCCTACCGAATAAGGTTTCCT
130 TACATTCAAACCGACGAATCGTATTTCATTCCTATTAGACTATGCCCTACCGAATAAGGATTCAT
505848 ATAA
195 ATAA
505852 ACAACCACTC
Statistics
Matches: 182, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
210 158 0.87
211 24 0.13
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (211 bp):
TTCCTCATACCGAACCGATCCAATGACAACCCTCCATTCAAAATACATAATCAAGAAAATCATGG
AACAATAGCAATCCAATTCAGTATGACTAACGATTCGATTATATAAACACAAAAGCTATATATAT
ACATTCAAACCGACGAATCGTATTTCATTCCTATTAGACTATGCCCTACCGAATAAGGATTCATA
TAAGTAACCATTTGCG
Found at i:506260 original size:185 final size:191
Alignment explanation
Indices: 505936--506348 Score: 633
Period size: 185 Copynumber: 2.2 Consensus size: 191
505926 AATTGTTGAA
* *
505936 AGTAACATTGAAATAAACTAAAACCAGATAACCGAGGACTCCGATTATATAAACTCAAAAGCTAT
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
* *
506001 ATGTATAAATTCAAACGGATGAATCGTATTGAGTTCCTATTAGACTATCCCCTGTCGAATAAGGT
66 ATGTATAAATTCAAACGGATGAATCGCATTCAGTTCCTATTAGACTATCCCCTGTCGAATAAGGT
* **
506066 GT-TAT-A-TAA-G-TTGTGTTCCGATTTTTGCTCCTCGTACCGAACCGATCAGCATTCCT
131 GTCAATAAGTAACGATTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
*
506122 AGTAACATTGAAATAAACTAAAACCAAATAACCAAGGACT-CGATTATATAAACACAAAAGCTAT
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
* *
506186 ATGTATAAATTCAAACTGATGAATCGCATTTCA-TTCCTATTAGACTATCCCCTGTCGAATAATG
66 ATGTATAAATTCAAACGGATGAATCGCA-TTCAGTTCCTATTAGACTATCCCCTGTCGAATAAGG
* *
506250 TGTCATATAAGTAACGATTTGTGTTCCGATTTCCGTTCCTCGTACCGAACCGATCCGCATTCCT
130 TGTCA-ATAAGTAACGA-TTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
*
506314 AGTAAAATTGAAATAAACTAAAACCAGATAACCAA
1 AGTAACATTGAAATAAACTAAAACCAGATAACCAA
506349 ATGACAACCC
Statistics
Matches: 205, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
185 82 0.40
186 41 0.20
187 2 0.01
188 1 0.00
189 3 0.01
190 1 0.00
192 75 0.37
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (191 bp):
AGTAACATTGAAATAAACTAAAACCAGATAACCAAGGACTCCGATTATATAAACACAAAAGCTAT
ATGTATAAATTCAAACGGATGAATCGCATTCAGTTCCTATTAGACTATCCCCTGTCGAATAAGGT
GTCAATAAGTAACGATTGTGTTCCGATTTCCGCTCCTCGTACCGAACCGATCAGCATTCCT
Found at i:508066 original size:10 final size:10
Alignment explanation
Indices: 508051--508075 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
508041 TTTATAACTC
508051 AATTATGAAA
1 AATTATGAAA
508061 AATTATGAAA
1 AATTATGAAA
508071 AATTA
1 AATTA
508076 CAAACGATCA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
AATTATGAAA
Found at i:510661 original size:5 final size:5
Alignment explanation
Indices: 510655--510708 Score: 81
Period size: 5 Copynumber: 10.8 Consensus size: 5
510645 ATATATATAT
* * *
510655 CATAT CATAA CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAT
1 CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC CATAC
510705 CATA
1 CATA
510709 ATCATTGTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (5 bp):
CATAC
Found at i:514379 original size:14 final size:14
Alignment explanation
Indices: 514360--514387 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
514350 TCTAATTAGC
514360 ATTGTTATTTTATT
1 ATTGTTATTTTATT
514374 ATTGTTATTTTATT
1 ATTGTTATTTTATT
514388 GAGCTCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (14 bp):
ATTGTTATTTTATT
Found at i:518940 original size:22 final size:24
Alignment explanation
Indices: 518896--518942 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
518886 TATAATTGTT
*
518896 ATATTTATAATAATAAAACTTTCA
1 ATATATATAATAATAAAACTTTCA
*
518920 ATATATATAA-AATTAAA-TTTCA
1 ATATATATAATAATAAAACTTTCA
518942 A
1 A
518943 GGATTCAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 6 0.29
24 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATATATAATAATAAAACTTTCA
Found at i:520858 original size:51 final size:48
Alignment explanation
Indices: 520758--520872 Score: 194
Period size: 48 Copynumber: 2.4 Consensus size: 48
520748 GCCATCCACC
*
520758 GCAACTCCGCCGCCAACTACCACTCCTGCCACACCACCACCAACCGCA
1 GCAACTCCGCCGCCAACTAACACTCCTGCCACACCACCACCAACCGCA
* *
520806 GCAACTCCGCCGCCAACTAACACTCCTTCTACACCACCACCAACCGCA
1 GCAACTCCGCCGCCAACTAACACTCCTGCCACACCACCACCAACCGCA
*
520854 GCAGCTCCGCCGCCAACTA
1 GCAACTCCGCCGCCAACTA
520873 GTCCTCCCTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.27, C:0.51, G:0.11, T:0.10
Consensus pattern (48 bp):
GCAACTCCGCCGCCAACTAACACTCCTGCCACACCACCACCAACCGCA
Found at i:525134 original size:17 final size:17
Alignment explanation
Indices: 525112--525144 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
525102 TATTAAATTC
525112 TTATTTTTATATAATAG
1 TTATTTTTATATAATAG
*
525129 TTATTTTTATTTAATA
1 TTATTTTTATATAATA
525145 CGTAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTTTTATATAATAG
Found at i:527087 original size:14 final size:14
Alignment explanation
Indices: 527068--527094 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
527058 ATTTATCCCT
527068 AAAATTTATGTATC
1 AAAATTTATGTATC
527082 AAAATTTATGTAT
1 AAAATTTATGTAT
527095 AATTTTAAGG
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:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
AAAATTTATGTATC
Found at i:541267 original size:9 final size:9
Alignment explanation
Indices: 541253--541298 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
541243 TTTGGTTAAA
541253 AATTACCCG
1 AATTACCCG
541262 AATTACCCG
1 AATTACCCG
* *
541271 -ATTAACCA
1 AATTACCCG
*
541279 AATTAACCG
1 AATTACCCG
541288 AATTACCCG
1 AATTACCCG
541297 AA
1 AA
541299 AATTACCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:545148 original size:12 final size:12
Alignment explanation
Indices: 545131--545155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
545121 AAAAACAGAC
545131 TGTTTTGTTTTT
1 TGTTTTGTTTTT
545143 TGTTTTGTTTTT
1 TGTTTTGTTTTT
545155 T
1 T
545156 ATAATTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (12 bp):
TGTTTTGTTTTT
Found at i:545857 original size:199 final size:197
Alignment explanation
Indices: 545475--546031 Score: 665
Period size: 199 Copynumber: 2.8 Consensus size: 197
545465 AACAGGTGCG
* * *
545475 AGAATTTTCTTTCCTACCAAACACGCTCAAACATCCATATTCTTTTTCAGTTTTTCACCACCCCT
1 AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
* * * * * *
545540 AATTCCATTTCTTCCAG-ATTTTTCACTCTGCTAAGCAAACCACTAATCTTGTTTCCGTATTTTT
66 TATT-CA-TTCTT-CTGTTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTTT
* ** *
545604 GCTTTACAATCTATGAACAAGAAAGCTAACGAAGATGACGCTAATCTTTTGTAATGCAGCTAAGT
128 GCTTTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAGT
545669 GAACA
193 GAACA
* *
545674 AGAATTCTT-TTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCTTCTT
1 AGAATT-TTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCT
*
545738 TTATTCATTCTTCTGTTTTTTTTTTCACTCTGCCAAGCAAACCACTAAACTCGTTTTCGTATTTT
65 TTATTCATTCTTCTG---TTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTT
* *
545803 TGCTTTACTATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATC-TTTGTAATGCAGTTAAG
127 TGCTTTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAG
* *
545867 TGAGCC
192 TGAACA
* * * * * * * *
545873 GGAATTTTCTTCCCTACCTAAGACACTCAAACATTAATGTTCTTCTTT-GGTTTTTCACCATCCT
1 AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTT-TTTCAGTTTTTCACCATCCT
* * ** * * *
545937 ATATCCATTTCTTC-CCTTTTTTCTACTCTGCCAAGCTAACCACTAATCTCATTTTCCTAATTTT
65 TTATTCA-TTCTTCTGTTTTTTTC-ACTCTGCCAAGCAAACCACTAATCTCGTTTTCGT-ATTTT
546001 TGCTTTACAATCTATGAACAAGAAAGCTAAT
127 TGCTTTACAATCTATGAACAAGAAAGCTAAT
546032 TATTTCCTTC
Statistics
Matches: 309, Mismatches: 39, Indels: 21
0.84 0.11 0.06
Matches are distributed among these distances:
196 9 0.03
197 35 0.11
198 39 0.13
199 132 0.43
200 94 0.30
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (197 bp):
AGAATTTTCTTTCCTACCAAACACGCTCAAACATTCATATTCTTTTTCAGTTTTTCACCATCCTT
TATTCATTCTTCTGTTTTTTTCACTCTGCCAAGCAAACCACTAATCTCGTTTTCGTATTTTTGCT
TTACAATCTATGAACAAGAAAGCTAATGAAGACAAAGCTAATCTTTTGTAATGCAGCTAAGTGAA
CA
Found at i:560369 original size:3 final size:3
Alignment explanation
Indices: 560361--560394 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
560351 CCATTAACGA
560361 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
560395 ATTGCTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:564946 original size:18 final size:18
Alignment explanation
Indices: 564883--564946 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
564873 CAATAAATAT
*
564883 TTAAATTATATTTTTATAA
1 TTAAATT-TATTTTTAAAA
*
564902 TTTAATTTATTTTTAAAA
1 TTAAATTTATTTTTAAAA
** *
564920 -TATTTTTTATTATTAAAA
1 TTA-AATTTATTTTTAAAA
564938 TTAAATTTA
1 TTAAATTTA
564947 AGTTAAGCCT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.03
18 26 0.74
19 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATTTATTTTTAAAA
Found at i:564947 original size:30 final size:31
Alignment explanation
Indices: 564881--564947 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
564871 ATCAATAAAT
* * * *
564881 ATTTAAATTATATTTTTATAATTTAATTTAT
1 ATTTAAAATATATTTTTATAATTAAAATTAA
* *
564912 TTTTAAAATAT-TTTTTATTATTAAAATTAA
1 ATTTAAAATATATTTTTATAATTAAAATTAA
564942 ATTTAA
1 ATTTAA
564948 GTTAAGCCTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATTTAAAATATATTTTTATAATTAAAATTAA
Found at i:572178 original size:128 final size:128
Alignment explanation
Indices: 572026--572396 Score: 451
Period size: 130 Copynumber: 2.9 Consensus size: 128
572016 AACGAAATCG
* * **
572026 CTTTGCTTTTTTAAAAATTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCTAAACTAAAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCCAAACCGAAA
*
572091 TGTTATCCGCCTAACTTATTGATGTTTGTTTTCACTGTTGTTTATGGTTCAT-TTGATGTGGCT
66 TGTTATCCGCCTAACTTATTGATGTTTGTTTTTACTGTTGTTTATGGTTCATCTT-ATGTGGCT
* ** * *
572154 CTTTGCTTTTTTAAAAACTAGAATACTGTAACCGTAAATTTGTTCAAAATCGATCCAAGCCGAAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCCAAACCGAAA
* *
572219 TGTTATTCGCCTAACTTATTGATGTGTT-TACTTTTACTGTTGTTTATGGTTCATCTTATGTGGT
66 TGTTATCCGCCTAACTTATTGATGT-TTGT--TTTTACTGTTGTTTATGGTTCATCTTATGTGGC
572283 T
128 T
* * * * *
572284 CATTGCTTTTTTAAAAGCTAAAACATTGTAATT-GTAAATTTATTCAAAACCGATCCAAACCGAA
1 CTTTGCTTTTTTAAAAACTAGAATATTGT-ATTCGTAAATTTATTCAAAATCGATCCAAACCGAA
* ** * * *
572348 ATATTATCTACCTAACTTATTGGTGTGTTTGTTTTTACTATTATTTATG
65 ATGTTATCCGCCTAACTTATT-G-ATGTTTGTTTTTACTGTTGTTTATG
572397 CGGTTCTTTG
Statistics
Matches: 206, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
128 81 0.39
129 2 0.01
130 113 0.55
131 6 0.03
132 4 0.02
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (128 bp):
CTTTGCTTTTTTAAAAACTAGAATATTGTATTCGTAAATTTATTCAAAATCGATCCAAACCGAAA
TGTTATCCGCCTAACTTATTGATGTTTGTTTTTACTGTTGTTTATGGTTCATCTTATGTGGCT
Found at i:575074 original size:14 final size:13
Alignment explanation
Indices: 575048--575081 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
575038 TATAAAATTT
575048 TAATAAATAAAAA
1 TAATAAATAAAAA
*
575061 TATTAAATTAAAAA
1 TAATAAA-TAAAAA
575075 TAATAAA
1 TAATAAA
575082 AATATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAATAAATAAAAA
Found at i:579887 original size:16 final size:16
Alignment explanation
Indices: 579866--579914 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
579856 TAATTTGAAG
579866 TGACCAAAACTCAAAA
1 TGACCAAAACTCAAAA
*
579882 TGACCAAAATTCAAAA
1 TGACCAAAACTCAAAA
* * *
579898 TAACCTAAACTCGAAA
1 TGACCAAAACTCAAAA
579914 T
1 T
579915 TAACCCGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.18
Consensus pattern (16 bp):
TGACCAAAACTCAAAA
Found at i:590797 original size:24 final size:24
Alignment explanation
Indices: 590770--590821 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
590760 TTCGTAAGTC
* *
590770 AAATAAATTATACTAATAAATGTT
1 AAATAAATCATACTAATAAATATT
*
590794 AAATATATCATACTAATAAATATT
1 AAATAAATCATACTAATAAATATT
590818 AAAT
1 AAAT
590822 CATCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATAAATCATACTAATAAATATT
Found at i:603082 original size:2 final size:2
Alignment explanation
Indices: 603075--603102 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
603065 TTAAAAAGTC
603075 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
603103 GGTAGTTTTG
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:604234 original size:2 final size:2
Alignment explanation
Indices: 604222--604252 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
604212 TAATATAAAT
*
604222 TA TA GA 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 T
604253 GTTGTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:604642 original size:86 final size:86
Alignment explanation
Indices: 604495--604658 Score: 265
Period size: 86 Copynumber: 1.9 Consensus size: 86
604485 TATATATTAA
* * * *
604495 ATGCACGTTTATTATATTGAATCAGGTTGGGTCTTAATTTGGTTGGTATTGACATAGTTACTAGT
1 ATGCACATTTATTATATTGAATCAGATTGAGTCTTAATTTGGTTGGTATTGACATAGTTACTACT
*
604560 CTAAGTAGACGTGGGTTTGAG
66 CCAAGTAGACGTGGGTTTGAG
**
604581 ATGCACATTTATTATATTGAATCAGATTGAGTCTTAATTTGGTTGGTATTGACATTTTTACTACT
1 ATGCACATTTATTATATTGAATCAGATTGAGTCTTAATTTGGTTGGTATTGACATAGTTACTACT
604646 CCAAGTAGACGTG
66 CCAAGTAGACGTG
604659 AGTTCGAGCG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (86 bp):
ATGCACATTTATTATATTGAATCAGATTGAGTCTTAATTTGGTTGGTATTGACATAGTTACTACT
CCAAGTAGACGTGGGTTTGAG
Found at i:606146 original size:21 final size:20
Alignment explanation
Indices: 606118--606156 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
606108 TTTTGGATTA
606118 AAATATGAAAATGATAATCC
1 AAATATGAAAATGATAATCC
606138 AAATGATGAAAATGATAAT
1 AAAT-ATGAAAATGATAAT
606157 TATTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (20 bp):
AAATATGAAAATGATAATCC
Found at i:608385 original size:14 final size:15
Alignment explanation
Indices: 608361--608389 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
608351 AATAATTGAG
608361 TATTATTATTTATTT
1 TATTATTATTTATTT
608376 TATT-TTATTTATTT
1 TATTATTATTTATTT
608390 ACAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTATTATTTATTT
Found at i:608627 original size:20 final size:19
Alignment explanation
Indices: 608588--608624 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
608578 TCAAAACACT
608588 AGAAAAGTAAATCATTTTC
1 AGAAAAGTAAATCATTTTC
608607 AGAAAAGTAAATCATTTT
1 AGAAAAGTAAATCATTTT
608625 TCATAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (19 bp):
AGAAAAGTAAATCATTTTC
Found at i:611533 original size:61 final size:63
Alignment explanation
Indices: 611440--611562 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 63
611430 CTCTTTTAAA
* *
611440 TTTTTTTCAAAAATCTCATTAATCTCACAAAATTTTTAAAAATTTTAATTAGATCC-CCAAAT
1 TTTTTTTCAAAAATCTCATTAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAAT
** * *
611502 TTTTTTTCAAAAAAT-T-ATTAAACTCGTAAAATTTTTAAAATTTTTATTTAGACCCTCCAAA
1 TTTTTTTC-AAAAATCTCATTAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAA
611563 ACTTAGAGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 33 0.62
62 14 0.26
63 6 0.11
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (63 bp):
TTTTTTTCAAAAATCTCATTAAACTCACAAAATTTTTAAAAATTTTAATTAGACCCTCCAAAT
Found at i:615809 original size:3 final size:3
Alignment explanation
Indices: 615801--615851 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
615791 TTCATGGCCT
*
615801 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ACG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
615849 ATG
1 ATG
615852 TTAGTAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:620166 original size:20 final size:21
Alignment explanation
Indices: 620141--620190 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
620131 AGTCTTTTCC
*
620141 ATAAATATTTCTAAAAAA-AA
1 ATAAATATTTCAAAAAAATAA
620161 ATAAAT-TTTCAAAAAAATAA
1 ATAAATATTTCAAAAAAATAA
*
620181 AAAAATATTT
1 ATAAATATTT
620191 TTCGCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.38
20 13 0.50
21 3 0.12
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAATATTTCAAAAAAATAA
Found at i:620338 original size:25 final size:26
Alignment explanation
Indices: 620300--620373 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
620290 TAGCAAATTT
*
620300 AAAATTAATAAATTATGTTTATTAA-
1 AAAATTATTAAATTATGTTTATTAAG
* * *
620325 AAAGTTATTAAATTGTGTTTTTTAAGG
1 AAAATTATTAAATTATGTTTATTAA-G
620352 AAAATTTTATTAAATTATGTTT
1 AAAA--TTATTAAATTATGTTT
620374 TTGAAATGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 21 0.54
27 3 0.08
29 15 0.38
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (26 bp):
AAAATTATTAAATTATGTTTATTAAG
Found at i:625037 original size:17 final size:19
Alignment explanation
Indices: 625011--625056 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
625001 TATTTATTAT
625011 ATATTATAAAT-A-TAAAA
1 ATATTATAAATAATTAAAA
*
625028 ATATTTTAAATAATTAAAA
1 ATATTATAAATAATTAAAA
*
625047 ATAATATAAA
1 ATATTATAAA
625057 AATGTCAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 1 0.04
19 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATTATAAATAATTAAAA
Found at i:627510 original size:29 final size:31
Alignment explanation
Indices: 627455--627512 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
627445 TATACACATA
*
627455 AATTTTGATTTAATGTGTAATTTTATATATG
1 AATTTTGATTTAATGTGTAATTATATATATG
627486 AATTTTGATTT-A-GTGTAATTATATATA
1 AATTTTGATTTAATGTGTAATTATATATA
627513 CACGTCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 1 0.04
31 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (31 bp):
AATTTTGATTTAATGTGTAATTATATATATG
Found at i:627513 original size:95 final size:95
Alignment explanation
Indices: 627355--627548 Score: 280
Period size: 95 Copynumber: 2.0 Consensus size: 95
627345 TTAAAATTAT
* *
627355 ACATAAAATTTAATTTTATGTGTAATTTGATATATGAATTTTAATTTGGTGTAATTATATATACA
1 ACATAAAATTTAATTTAATGTGTAATTTGATATATGAATTTTAATTTAGTGTAATTATATATACA
* * * *
627420 CGTAAAACTTTTATTGTTGACTAAATATAC
66 CGTAAAACTTTTATCGTGGACCAAATACAC
* * * *
627450 ACATAAATTTTGATTTAATGTGTAATTTTATATATGAATTTTGATTTAGTGTAATTATATATACA
1 ACATAAAATTTAATTTAATGTGTAATTTGATATATGAATTTTAATTTAGTGTAATTATATATACA
* *
627515 CGTCAAATTTTTATCGTGGACCAAATACAC
66 CGTAAAACTTTTATCGTGGACCAAATACAC
627545 ACAT
1 ACAT
627549 TTAAAAAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (95 bp):
ACATAAAATTTAATTTAATGTGTAATTTGATATATGAATTTTAATTTAGTGTAATTATATATACA
CGTAAAACTTTTATCGTGGACCAAATACAC
Found at i:628667 original size:15 final size:16
Alignment explanation
Indices: 628640--628680 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
628630 TTGATTCTGA
628640 TTATAATTA-TTTTAT
1 TTATAATTATTTTTAT
628655 TTAT-ATTATTTTTAT
1 TTATAATTATTTTTAT
628670 TTATAATTATT
1 TTATAATTATT
628681 CAAATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATAATTATTTTTAT
Found at i:631158 original size:14 final size:14
Alignment explanation
Indices: 631139--631168 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
631129 TGTATTGTTC
*
631139 AAAAATATATAAAT
1 AAAAATATAAAAAT
631153 AAAAATATAAAAAT
1 AAAAATATAAAAAT
631167 AA
1 AA
631169 TTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATATAAAAAT
Found at i:642688 original size:133 final size:126
Alignment explanation
Indices: 642367--642679 Score: 374
Period size: 126 Copynumber: 2.4 Consensus size: 126
642357 CAAAAGAAAA
* * * * *
642367 CAATAACAACAATCACAATCATAATAAAGCTAAACATTAACCAATGATTTTAATAATAGTTAAAC
1 CAATAACAACAATCATAATCATAATAAAGTTAAAAATTAACCAATGAATTCAATAATAGTTAAAC
*
642432 TGGGAATTAAACCCTAAACCCTAAAACTAATTAGTAGGCATCAAACAAGAGTAAAATAACG
66 TGAGAATTAAACCCTAAACCCTAAAACTAATTAGTAGGCATCAAACAAGAGTAAAATAACG
* * * * * * ** *
642493 CAATAACAGCAATCATAATAATATTATAGTTAATAATTAACCAGTGAATTGGATAATAGTTAAGC
1 CAATAACAACAATCATAATCATAATAAAGTTAAAAATTAACCAATGAATTCAATAATAGTTAAAC
* * *
642558 TGAGAATTAAACCCTAAACTCTAATACTTAAATTAAGTAGTAGGCGTCAAACAAGAGTAAAAATA
66 TGAGAATTAAACCCTAAACCCTAAAAC-T-AA-T---TAGTAGGCATCAAACAAGAGT-AAAATA
642623 ACG
124 ACG
* * *
642626 CAATAACAACAATCATAATCATAATACAGTTAAAAATTAACCAATTAGTTCAAT
1 CAATAACAACAATCATAATCATAATAAAGTTAAAAATTAACCAATGAATTCAAT
642680 CGAAGTTAAA
Statistics
Matches: 153, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
126 76 0.50
127 1 0.01
128 2 0.01
129 1 0.01
132 20 0.13
133 53 0.35
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (126 bp):
CAATAACAACAATCATAATCATAATAAAGTTAAAAATTAACCAATGAATTCAATAATAGTTAAAC
TGAGAATTAAACCCTAAACCCTAAAACTAATTAGTAGGCATCAAACAAGAGTAAAATAACG
Found at i:644693 original size:24 final size:22
Alignment explanation
Indices: 644652--644703 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
644642 ATAATTATAT
*
644652 AATTAGAAATAATAAAAATTAA
1 AATTAGAAAAAATAAAAATTAA
644674 AATTAGATAAAAATAAAAAATTAA
1 AATTAGA-AAAAAT-AAAAATTAA
*
644698 AGTTAG
1 AATTAG
644704 TAATGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 14 0.54
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (22 bp):
AATTAGAAAAAATAAAAATTAA
Found at i:646492 original size:2 final size:2
Alignment explanation
Indices: 646487--646522 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
646477 TTATTACGTG
646487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
646523 GTTAAAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:647569 original size:3 final size:3
Alignment explanation
Indices: 647561--647594 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
647551 TGTAGATAGA
647561 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
647595 TAGTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:651634 original size:17 final size:16
Alignment explanation
Indices: 651610--651643 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
651600 TTTATAAAAA
*
651610 AATAATTAATATAATT
1 AATAATTAAGATAATT
651626 AATAGATTAAGATAATT
1 AATA-ATTAAGATAATT
651643 A
1 A
651644 TATATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AATAATTAAGATAATT
Found at i:657131 original size:102 final size:101
Alignment explanation
Indices: 656954--657158 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 101
656944 GACTAATTAG
* * *
656954 CTATTTTTTAGTAAAAGGGACAAAATGCAATTTGAGTCTTGTGCAGGAGCCTCTACGGTACTTTT
1 CTATTTTTCAGTAAAAGAGACAAAATGCAATTTGAGTCTTGTGAAGGAGCCTCTACGGTACTTTT
657019 ACCACATATCCTTGTATGTAAAATGTTAATAAGATT
66 ACCACATATCCTTGTATGTAAAATGTTAATAAGATT
*
657055 CTATTTTTCAGTAAAAGAGACAAAATGTAATTTGAGTCTTTGTGAAGGAGCCTCTACGGTACTTT
1 CTATTTTTCAGTAAAAGAGACAAAATGCAATTTGAGTC-TTGTGAAGGAGCCTCTACGGTACTTT
657120 TACCACATATCCTTGTATGTAAAATGTTAATAAGATT
65 TACCACATATCCTTGTATGTAAAATGTTAATAAGATT
657157 CT
1 CT
657159 GTATTTCCTA
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 35 0.35
102 64 0.65
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (101 bp):
CTATTTTTCAGTAAAAGAGACAAAATGCAATTTGAGTCTTGTGAAGGAGCCTCTACGGTACTTTT
ACCACATATCCTTGTATGTAAAATGTTAATAAGATT
Found at i:658093 original size:11 final size:11
Alignment explanation
Indices: 658077--658104 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
658067 GTGATGAAAA
658077 GGGACAATTTT
1 GGGACAATTTT
658088 GGGACAATTTT
1 GGGACAATTTT
658099 GGGACA
1 GGGACA
658105 TGTCTTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.29
Consensus pattern (11 bp):
GGGACAATTTT
Found at i:666712 original size:23 final size:23
Alignment explanation
Indices: 666681--666731 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
666671 ACCTACTTTC
* *
666681 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
666704 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
666727 TTACA
1 TTACA
666732 TAAATTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:667498 original size:26 final size:26
Alignment explanation
Indices: 667454--667504 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
667444 ACGATAGATC
* *
667454 AGAATAAAAATTTAGATATTAAATTA
1 AGAATAAAAATTTAAATATCAAATTA
667480 AGAA-AAAAATTATAAATATCAAATT
1 AGAATAAAAATT-TAAATATCAAATT
667505 GAGAGAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (26 bp):
AGAATAAAAATTTAAATATCAAATTA
Found at i:667899 original size:21 final size:22
Alignment explanation
Indices: 667856--667900 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
667846 AAAATAAGAT
667856 AATACAAAGATTAATACTTACA
1 AATACAAAGATTAATACTTACA
667878 AATACAAA-ATCTAATA-TTACA
1 AATACAAAGAT-TAATACTTACA
667899 AA
1 AA
667901 CAGGGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (22 bp):
AATACAAAGATTAATACTTACA
Found at i:676695 original size:85 final size:84
Alignment explanation
Indices: 676502--676928 Score: 391
Period size: 85 Copynumber: 5.0 Consensus size: 84
676492 GCAAAAATGA
** * *
676502 TATATATACAATTTCCAAAAGAACATTTTAGGTTTCAATAAATC--A-TAT-TCCACTCCTATAC
1 TATATATATGATTTCCAAAAGAACATTTTAGGTTTCAATAAATCGTATTTTGTTC-CTCCTATAC
*
676563 AAACC-GCAGTAGACTATCCCC
65 AAACCAG-AGAAGACTAT-CCC
* *
676584 TATATATA-GAATTTCCAAAAGAACATTTTATGTTTCAATAGATCGTATTTTGTTCCTCCTATAC
1 TATATATATG-ATTTCCAAAAGAACATTTTAGGTTTCAATAAATCGTATTTTGTTCCTCCTATAC
676648 AAACCAGAGAAGACTATCCC
65 AAACCAGAGAAGACTATCCC
* *
676668 TATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTCCTCCTATAC
1 TATATATATGATTTCC-AAAAGAACATTTTAGGTTTCAATAAATCGTATTTTGTTCCTCCTATAC
* *
676733 AAACCGGAGTAGACTATCCC
65 AAACCAGAGAAGACTATCCC
* * * * * * ** *
676753 TATATATGTAATTCCCAAAAGAACAGTTTGGGTTCCAATAAATCGTACTCCT-TTCCTCCTATAT
1 TATATATATGATTTCCAAAAGAACATTTTAGGTTTCAATAAATCGTA-TTTTGTTCCTCCTATAC
* * *
676817 GAACCGGAGAAGACCATCCC
65 AAACCAGAGAAGACTATCCC
* * * * *
676837 TATATATATATGTATATAATTTCAAAAAATAACATTTTAAGTTTCAATAAATCGTATTTCGTTCA
1 --TATATATATG------ATTTC-CAAAAGAACATTTTAGGTTTCAATAAATCGTATTTTGTTCC
* * *
676902 TCCTATACGAACAACAGAAGACTATCC
57 TCCTATACAAACCAGAGAAGACTATCC
676929 TTTTTCGAAT
Statistics
Matches: 282, Mismatches: 44, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
82 40 0.14
84 73 0.26
85 102 0.36
86 11 0.04
92 5 0.02
93 51 0.18
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (84 bp):
TATATATATGATTTCCAAAAGAACATTTTAGGTTTCAATAAATCGTATTTTGTTCCTCCTATACA
AACCAGAGAAGACTATCCC
Found at i:676822 original size:84 final size:84
Alignment explanation
Indices: 676502--676846 Score: 401
Period size: 85 Copynumber: 4.1 Consensus size: 84
676492 GCAAAAATGA
* * *
676502 TATATATACAATTTCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCC---ACTCCTATACA
1 TATATATATAATTCCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCTTTCCTCCTATACA
* *
676564 AACCGCAGTAGACTATCCCC
66 AACCGGAGAAGACTAT-CCC
* * * * * *
676584 TATATATAGAATTTCCAAAAGAACATTTTATGTTTCAATAGATCGTATT-TTGTTCCTCCTATAC
1 TATATATATAATTCCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCT-TTCCTCCTATAC
*
676648 AAACCAGAGAAGACTATCCC
65 AAACCGGAGAAGACTATCCC
* * * *
676668 TATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTCCTCCTATAC
1 TATATATAT-AATTCCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCTTTCCTCCTATAC
*
676733 AAACCGGAGTAGACTATCCC
65 AAACCGGAGAAGACTATCCC
* * * * * * **
676753 TATATATGTAATTCCCAAAAGAACAGTTTGGGTTCCAATAAATCGTACTCCTTTCCTCCTATATG
1 TATATATATAATTCCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCTTTCCTCCTATACA
*
676818 AACCGGAGAAGACCATCCC
66 AACCGGAGAAGACTATCCC
676837 TATATATATA
1 TATATATATA
676847 TGTATATAAT
Statistics
Matches: 222, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
82 45 0.20
84 82 0.37
85 95 0.43
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.32
Consensus pattern (84 bp):
TATATATATAATTCCCAAAAGAACATTTTAGGTTTCAATAAATCATATTCCTTTCCTCCTATACA
AACCGGAGAAGACTATCCC
Found at i:676829 original size:169 final size:171
Alignment explanation
Indices: 676501--676928 Score: 487
Period size: 169 Copynumber: 2.5 Consensus size: 171
676491 CGCAAAAATG
**
676501 ATATATATACAATTTCC-AAAAGAACATTTTAGGTTTCAATAAATCATA-TTC---CACTCCTAT
1 ATATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTC-CTCCTAT
* * * * *
676561 ACAAACCGCAGTAGACTATCCCCTATATATAGAATTTCCAAAAGAACATTTTATGTTTCAATAGA
65 ACAAACCGCAGTAGACTATCCCCTATATATAGAATTCCCAAAAGAACAGTTTAGGTTCCAATAAA
** *
676626 TCGTATTTTGTTCCTCCTATACAAACCAGAGAAGACTATCCC
130 TCGTATCCTGTTCCTCCTATACAAACCAGAGAAGACCATCCC
676668 -TATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTCCTCCTATA
1 ATATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTCCTCCTATA
* *
676732 CAAACCGGAGTAGACTAT-CCCTATATAT-GTAATTCCCAAAAGAACAGTTTGGGTTCCAATAAA
66 CAAACCGCAGTAGACTATCCCCTATATATAG-AATTCCCAAAAGAACAGTTTAGGTTCCAATAAA
** *
676795 TCGTACTCCT-TTCCTCCTATATGAACCGGAGAAGACCATCCC
130 TCGTA-TCCTGTTCCTCCTATACAAACCAGAGAAGACCATCCC
* * * * *
676837 TATATATATATGTATATAATTTCAAAAAATAACATTTTAAGTTTCAATAAATCGTATTTCGTTCA
1 -ATATATATATG------ATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTCC
* ** *
676902 TCCTATACGAACAACAGAAGACTATCC
59 TCCTATACAAACCGCAGTAGACTATCC
676929 TTTTTCGAAT
Statistics
Matches: 220, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
166 14 0.06
167 31 0.14
168 4 0.02
169 70 0.32
170 27 0.12
171 11 0.05
177 62 0.28
178 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (171 bp):
ATATATATATGATTTCCAAAAAGAACATTTTAGGTTTCAATAAATCATATTTCGTTCCTCCTATA
CAAACCGCAGTAGACTATCCCCTATATATAGAATTCCCAAAAGAACAGTTTAGGTTCCAATAAAT
CGTATCCTGTTCCTCCTATACAAACCAGAGAAGACCATCCC
Found at i:678015 original size:15 final size:17
Alignment explanation
Indices: 677995--678027 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
677985 TGGTATTATA
677995 ATAATTT-T-TTATTTG
1 ATAATTTATGTTATTTG
678010 ATAATTTATGTTATTTG
1 ATAATTTATGTTATTTG
678027 A
1 A
678028 ACGATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
ATAATTTATGTTATTTG
Found at i:679319 original size:45 final size:45
Alignment explanation
Indices: 679266--679393 Score: 175
Period size: 45 Copynumber: 2.8 Consensus size: 45
679256 TCATACCGAA
* * * * * *
679266 AACAAGTAAGACCATGGCTGAAAGACGTTATGGCATCCCGATTTT
1 AACAAGTAAAACCATAGCTGAAAGACATTATGGCATCACAATTCT
* *
679311 AACGAGTAAAACCATAGTTGAAAGACATTATGGCATCACAATTCT
1 AACAAGTAAAACCATAGCTGAAAGACATTATGGCATCACAATTCT
*
679356 AACAAGTAAAACCATAGCTGAAAGACATAATGGCATCA
1 AACAAGTAAAACCATAGCTGAAAGACATTATGGCATCA
679394 TGAACCAGAC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (45 bp):
AACAAGTAAAACCATAGCTGAAAGACATTATGGCATCACAATTCT
Found at i:686402 original size:31 final size:31
Alignment explanation
Indices: 686339--686407 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
686329 TGGGTCAAAG
* * *
686339 CTAAAACAGACCAATTCAAAAATTATATGGA
1 CTAAAATAGACCAATTCAAAAATTACAAGGA
*
686370 CTAAAATAGACTAATTCAAATAA-TACAAGGA
1 CTAAAATAGACCAATTCAAA-AATTACAAGGA
*
686401 CTCAAAT
1 CTAAAAT
686408 TAATTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (31 bp):
CTAAAATAGACCAATTCAAAAATTACAAGGA
Found at i:689404 original size:24 final size:24
Alignment explanation
Indices: 689377--689428 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
689367 ATTTTTTTCC
689377 TGAACCAAATGTGGGTTTTACGTT
1 TGAACCAAATGTGGGTTTTACGTT
689401 TGAACCAAATGTGGGTTTTACGTT
1 TGAACCAAATGTGGGTTTTACGTT
689425 TGAA
1 TGAA
689429 AAAAAGTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (24 bp):
TGAACCAAATGTGGGTTTTACGTT
Found at i:693613 original size:2 final size:2
Alignment explanation
Indices: 693606--693639 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
693596 CTTTGATCAT
693606 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
693640 TTGGTATCTT
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:698023 original size:1 final size:1
Alignment explanation
Indices: 697976--698005 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
697966 AGTTAATAGG
697976 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
698006 ATAAGATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:706610 original size:53 final size:53
Alignment explanation
Indices: 706548--706665 Score: 236
Period size: 53 Copynumber: 2.2 Consensus size: 53
706538 TAACTTGATT
706548 AATTTGAATTTAAATCTCATTTAATTATAAAAAATAATAATTTAAATGTGCTC
1 AATTTGAATTTAAATCTCATTTAATTATAAAAAATAATAATTTAAATGTGCTC
706601 AATTTGAATTTAAATCTCATTTAATTATAAAAAATAATAATTTAAATGTGCTC
1 AATTTGAATTTAAATCTCATTTAATTATAAAAAATAATAATTTAAATGTGCTC
706654 AATTTGAATTTA
1 AATTTGAATTTA
706666 GATTAATTTG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (53 bp):
AATTTGAATTTAAATCTCATTTAATTATAAAAAATAATAATTTAAATGTGCTC
Found at i:709039 original size:22 final size:22
Alignment explanation
Indices: 709010--709067 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
709000 CCTCCGAATA
*
709010 TTTAAAAATCTTAATTAAAATT
1 TTTAAAAATTTTAATTAAAATT
* * **
709032 TTTGAAAATTTTTATTAATCTT
1 TTTAAAAATTTTAATTAAAATT
709054 TTTAAAAATTTTAA
1 TTTAAAAATTTTAA
709068 AAGTTTTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTAAAAATTTTAATTAAAATT
Found at i:709654 original size:23 final size:22
Alignment explanation
Indices: 709628--709670 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
709618 GATGTCAAAA
*
709628 TATAATTTTATCATTTATTAATT
1 TATAATTTCATCATTT-TTAATT
709651 TATAATTTCATCATTTTTAA
1 TATAATTTCATCATTTTTAA
709671 GGGACTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (22 bp):
TATAATTTCATCATTTTTAATT
Found at i:714139 original size:29 final size:29
Alignment explanation
Indices: 714105--714160 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
714095 TTTGATTCTT
*
714105 TTTAATTGTACAAGAACTAAATTGATCCA
1 TTTAATTATACAAGAACTAAATTGATCCA
* *
714134 TTTAATTATAGAAGAACTAATTTGATC
1 TTTAATTATACAAGAACTAAATTGATC
714161 AAATCCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
TTTAATTATACAAGAACTAAATTGATCCA
Found at i:716014 original size:11 final size:11
Alignment explanation
Indices: 715994--716071 Score: 85
Period size: 11 Copynumber: 7.4 Consensus size: 11
715984 TTAAAAATTA
715994 AAAAAGTATTTT
1 AAAAA-TATTTT
716006 AAAAATATTTT
1 AAAAATATTTT
*
716017 AAAATTATTTT
1 AAAAATATTTT
*
716028 --AAA-A-TTA
1 AAAAATATTTT
716035 AAAAAT-TTTT
1 AAAAATATTTT
716045 AAAAAGTATTTT
1 AAAAA-TATTTT
716057 AAAAATATTTT
1 AAAAATATTTT
716068 AAAA
1 AAAA
716072 TTAAAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.04
8 1 0.02
9 5 0.09
10 7 0.12
11 27 0.48
12 14 0.25
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:716055 original size:40 final size:39
Alignment explanation
Indices: 715974--716091 Score: 164
Period size: 40 Copynumber: 2.9 Consensus size: 39
715964 ATAAATACCA
715974 AAAATTTATTTTAAAAATTAAAAAAGTATTTTAAAAATATTTT
1 AAAA-TTATTTT-AAAATTAAAAAA-T-TTTTAAAAATATTTT
716017 AAAATTATTTTAAAATTAAAAAATTTTTAAAAAGTATTTT
1 AAAATTATTTTAAAATTAAAAAATTTTTAAAAA-TATTTT
* * *
716057 AAAAATATTTTAAAATTAAAAAAATTTAAAAAATA
1 AAAATTATTTTAAAATTAAAAAATTTTTAAAAATA
716092 AATATATTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
39 11 0.15
40 37 0.52
41 12 0.17
42 7 0.10
43 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (39 bp):
AAAATTATTTTAAAATTAAAAAATTTTTAAAAATATTTT
Found at i:716101 original size:17 final size:17
Alignment explanation
Indices: 716056--716101 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
716046 AAAAGTATTT
* *
716056 TAAAAATATTTTAAAAT
1 TAAAAATATTTAAAAAA
*
716073 TAAAAAAATTTAAAAAA
1 TAAAAATATTTAAAAAA
*
716090 TAAATATATTTA
1 TAAAAATATTTA
716102 TTATATCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAATATTTAAAAAA
Found at i:731748 original size:29 final size:28
Alignment explanation
Indices: 731682--731748 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
731672 TTTTCATAAA
* *
731682 TTTAGAATTTAGTCTCTATAATTTTATT
1 TTTAGAATTTAGTCCCTATAATTTTAAT
*
731710 TTTAAGAATTTAGTCCCTATACTTTTTAGAT
1 TTT-AGAATTTAGTCCCTATA-ATTTTA-AT
731741 TTTA-AATT
1 TTTAGAATT
731749 CAGATTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 3 0.09
29 20 0.61
30 6 0.18
31 4 0.12
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (28 bp):
TTTAGAATTTAGTCCCTATAATTTTAAT
Found at i:751425 original size:29 final size:29
Alignment explanation
Indices: 751380--751435 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
751370 ATATAAGGGC
* *
751380 TAGATCAAATTAGTCCATTTACTATTACA
1 TAGATCAAATTAATCCATGTACTATTACA
*
751409 TAGAT-AAATTAAATCCATGTATTATTA
1 TAGATCAAATT-AATCCATGTACTATTA
751436 AAAAGAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (29 bp):
TAGATCAAATTAATCCATGTACTATTACA
Found at i:754309 original size:28 final size:27
Alignment explanation
Indices: 754269--754321 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
754259 ACTTCCTAAA
754269 TTTAAAATTTAATTTTTATATTTTTAT
1 TTTAAAATTTAATTTTTATATTTTTAT
754296 TTTAAGAATTTAATTTTTATATTTTT
1 TTTAA-AATTTAATTTTTATATTTTT
754322 CAGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTAAAATTTAATTTTTATATTTTTAT
Found at i:756083 original size:2 final size:2
Alignment explanation
Indices: 756076--756123 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
756066 AAAGTTGTGT
756076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
756118 TG TA TA
1 TA TA TA
756124 CACATGTGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:759596 original size:27 final size:26
Alignment explanation
Indices: 759557--759610 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
759547 GGAACAAAAA
*
759557 TTTAACTTAAAGATTTAATTGAAAATT
1 TTTAACTTAAAGA-TGAATTGAAAATT
* * *
759584 TTTAAGTTTAAGATGAATTTAAAATT
1 TTTAACTTAAAGATGAATTGAAAATT
759610 T
1 T
759611 AATCTATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (26 bp):
TTTAACTTAAAGATGAATTGAAAATT
Found at i:769456 original size:16 final size:16
Alignment explanation
Indices: 769437--769531 Score: 59
Period size: 16 Copynumber: 5.9 Consensus size: 16
769427 TTTTAACATC
*
769437 TTTAAGTTATTTTGAG
1 TTTAAGTTATTTTAAG
* *
769453 TTT-AGATTATTTTGAC
1 TTTAAG-TTATTTTAAG
**
769469 TTCGAGATT-TTTTAAG
1 TTTAAG-TTATTTTAAG
* *
769485 TTTGAGTCAATTTTAAG
1 TTTAAGT-TATTTTAAG
* * *
769502 TTAAAATTATTTTAGG
1 TTTAAGTTATTTTAAG
769518 TTTAAGTTATTTTA
1 TTTAAGTTATTTTA
769532 TGTTCGAATC
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
15 3 0.05
16 43 0.69
17 16 0.26
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (16 bp):
TTTAAGTTATTTTAAG
Found at i:771067 original size:27 final size:27
Alignment explanation
Indices: 771037--771101 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
771027 CCTGTCAGGT
*
771037 AGGCGCCAATGAATGTGCCTCATAGAG
1 AGGCGCCAATGAAAGTGCCTCATAGAG
* * * *
771064 AGGCGCCATTAAAAGTGTCTCATAGGG
1 AGGCGCCAATGAAAGTGCCTCATAGAG
771091 AGGCGCCAATG
1 AGGCGCCAATG
771102 CGTAATTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.31, T:0.18
Consensus pattern (27 bp):
AGGCGCCAATGAAAGTGCCTCATAGAG
Found at i:771375 original size:14 final size:13
Alignment explanation
Indices: 771356--771385 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
771346 ATGAAAACTC
771356 TTTTCTTTTCTTTT
1 TTTTCTTTT-TTTT
771370 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
771383 TTT
1 TTT
771386 GTCATTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:776115 original size:23 final size:23
Alignment explanation
Indices: 776085--776139 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
776075 AATTAAAAAG
776085 ATGAAAGCAT-TGTAACTACCATT
1 ATGAAAGCATAT-TAACTACCATT
* *
776108 ATGAAAGCATATTAGCTATCATT
1 ATGAAAGCATATTAACTACCATT
776131 ATGAAAGCA
1 ATGAAAGCA
776140 AAAGATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (23 bp):
ATGAAAGCATATTAACTACCATT
Found at i:776172 original size:23 final size:23
Alignment explanation
Indices: 776144--776195 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
776134 AAAGCAAAAG
776144 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
776167 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
776190 ATGAAA
1 ATGAAA
776196 CCAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:776172 original size:59 final size:59
Alignment explanation
Indices: 776080--776195 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
776070 TTAATAATTA
*
776080 AAAAGATGAAAGCATTGTAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
* * *
776139 AAAAGATGAAAGCATTATAGCTATCATTATGAAAGCATATTAGCTATTATTATGAAA
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAA
776196 CCAAGTTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (59 bp):
AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
Found at i:776278 original size:9 final size:9
Alignment explanation
Indices: 776246--776277 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
776236 ACAAATATTA
776246 AAAATAAAC
1 AAAATAAAC
776255 AAAATAAAC
1 AAAATAAAC
*
776264 AAAATGAAC
1 AAAATAAAC
776273 AAAAT
1 AAAAT
776278 GCACCAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.75, C:0.09, G:0.03, T:0.12
Consensus pattern (9 bp):
AAAATAAAC
Found at i:780668 original size:23 final size:23
Alignment explanation
Indices: 780638--780692 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
780628 AATTAAAAAG
780638 ATGAAAGCAT-TGTAACTACCATT
1 ATGAAAGCATAT-TAACTACCATT
* *
780661 ATGAAAGCATATTAGCTATCATT
1 ATGAAAGCATATTAACTACCATT
780684 ATGAAAGCA
1 ATGAAAGCA
780693 AAAGATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (23 bp):
ATGAAAGCATATTAACTACCATT
Found at i:780725 original size:23 final size:23
Alignment explanation
Indices: 780697--780748 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
780687 AAAGCAAAAG
780697 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
780720 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
780743 ATGAAA
1 ATGAAA
780749 CCAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:780725 original size:59 final size:59
Alignment explanation
Indices: 780633--780748 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
780623 TTAATAATTA
*
780633 AAAAGATGAAAGCATTGTAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
* * *
780692 AAAAGATGAAAGCATTATAGCTATCATTATGAAAGCATATTAGCTATTATTATGAAA
1 AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAA
780749 CCAAGTTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (59 bp):
AAAAGATGAAAGCATTATAACTACCATTATGAAAGCATATTAGCTATCATTATGAAAGC
Found at i:780811 original size:9 final size:9
Alignment explanation
Indices: 780799--780830 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
780789 ACAAATATTA
780799 AAAATAAAC
1 AAAATAAAC
780808 AAAATAAAC
1 AAAATAAAC
780817 AAAATAAAC
1 AAAATAAAC
780826 AAAAT
1 AAAAT
780831 GCACCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAATAAAC
Found at i:793742 original size:21 final size:21
Alignment explanation
Indices: 793726--793769 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
793716 AATTTAATCA
793726 TTATATTTTTATTTTTAAAAT
1 TTATATTTTTATTTTTAAAAT
793747 TTATATTTTTATTTTTAAAAT
1 TTATATTTTTATTTTTAAAAT
793768 TT
1 TT
793770 TTAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATATTTTTATTTTTAAAAT
Found at i:793778 original size:21 final size:21
Alignment explanation
Indices: 793733--793778 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
793723 TCATTATATT
**
793733 TTTATTTTTAAAATTTATATT
1 TTTATTTTTAAAATTTATAAA
*
793754 TTTATTTTTAAAATTTTTAAA
1 TTTATTTTTAAAATTTATAAA
793775 TTTA
1 TTTA
793779 AGTTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTATTTTTAAAATTTATAAA
Found at i:795012 original size:197 final size:195
Alignment explanation
Indices: 794748--795178 Score: 456
Period size: 196 Copynumber: 2.2 Consensus size: 195
794738 CAATTTAATT
* * ** * * * *
794748 TTTAACATTATTTAGTACCTCAA-TTTCTATAATGTCATTGTTACTCTATATACTTCGTTCTGAT
1 TTTAACATAATTTGGTACCTCAACTTT-TATAATGTCATAATCACTCCAAATACTTCCTTCTGAT
** * * * *
794812 TAAAATGTTGGGGTCCACATGTCCATATACAC-GGCCTTTTTACAT-ATTTTTTAAGATAATATA
65 TAAAATGTTGACGTACACATGTCCAAATACACAAG-C-TTTTA-ATGATTTTTTAAGATAACATA
*
794875 ATAATGGTAAAATTTCAATTTAGATCCATAT-ATTATGCTCAAATTTGAAATTTAATCTCAATAC
127 ACAATGGTAAAATTTCAATTTAGATCCATATGATT-TGCTCAAATTTGAAATTTAATCTC-ATAC
794939 TTAAAA
190 TTAAAA
* * *
794945 TTTAACATCATTTGGTACCTCAACTTTTATACTGTCATAATCAGTCCAAATACTTCCTTCTGATT
1 TTTAACATAATTTGGTACCTCAACTTTTATAATGTCATAATCACTCCAAATACTTCCTTCTGATT
* * * * * *
795010 AAAATGTTGACGTATACATGTCCAAATACACAAGCTTTTATTGCTTTTTTCAGATTACATAACAG
66 AAAATGTTGACGTACACATGTCCAAATACACAAGCTTTTAATGATTTTTTAAGATAACATAACAA
* * * * * * * * *
795075 TGGTCAAATTTCAATTTTGGTCCTTATGCTTTGCTTAATTTTGAAATTTAATCTCATACTTTAAT
131 TGGTAAAATTTCAATTTAGATCCATATGATTTGCTCAAATTTGAAATTTAATCTCATACTTAAAA
* *
795140 TTGTGACATAATTTGGTACCTCAACTTTTTTAATGTCAT
1 TT-TAACATAATTTGGTACCTCAACTTTTATAATGTCAT
795179 TAGTTAGTAT
Statistics
Matches: 193, Mismatches: 36, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
195 11 0.06
196 98 0.51
197 80 0.41
198 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (195 bp):
TTTAACATAATTTGGTACCTCAACTTTTATAATGTCATAATCACTCCAAATACTTCCTTCTGATT
AAAATGTTGACGTACACATGTCCAAATACACAAGCTTTTAATGATTTTTTAAGATAACATAACAA
TGGTAAAATTTCAATTTAGATCCATATGATTTGCTCAAATTTGAAATTTAATCTCATACTTAAAA
Found at i:812286 original size:21 final size:21
Alignment explanation
Indices: 812258--812300 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 21
812248 TGCATTTTTT
812258 ATTCGAAAAGTAAA-AA-AAAA
1 ATTCGAAAA-TAAAGAATAAAA
812278 ATTCTGAAAATAAAGAATAAAA
1 ATTC-GAAAATAAAGAATAAAA
812300 A
1 A
812301 CTAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (21 bp):
ATTCGAAAATAAAGAATAAAA
Found at i:815653 original size:23 final size:23
Alignment explanation
Indices: 815627--815675 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
815617 GGTTTTACAC
815627 TTCTTTGAAACCATGGATTTGTT
1 TTCTTTGAAACCATGGATTTGTT
815650 TTCTTTGAAACCATGGATTTGTT
1 TTCTTTGAAACCATGGATTTGTT
815673 TTC
1 TTC
815676 ATTTTAGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.49
Consensus pattern (23 bp):
TTCTTTGAAACCATGGATTTGTT
Found at i:818265 original size:17 final size:17
Alignment explanation
Indices: 818245--818289 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
818235 AAAACGAAAC
*
818245 AAAGAAGGAAAGAAAGA
1 AAAGAAGAAAAGAAAGA
818262 AAAGAAGAAAAGAAAG-
1 AAAGAAGAAAAGAAAGA
*
818278 AAAGGAGAAAAG
1 AAAGAAGAAAAG
818290 TTAGGGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAAGAAAGA
Found at i:818273 original size:25 final size:25
Alignment explanation
Indices: 818224--818289 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
818214 TAAATAGAAA
*
818224 AAGGAGAGAAA-AAAACGAAACAAAG
1 AAGGAAAGAAAGAAAA-GAAACAAAG
818249 AAGGAAAGAAAGAAAAGAAGA-AAAG
1 AAGGAAAGAAAGAAAAGAA-ACAAAG
* *
818274 AAAGAAAG-GAGAAAAG
1 AAGGAAAGAAAGAAAAG
818290 TTAGGGTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.19
25 24 0.67
26 5 0.14
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (25 bp):
AAGGAAAGAAAGAAAAGAAACAAAG
Found at i:819195 original size:37 final size:40
Alignment explanation
Indices: 819104--819228 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 40
819094 GATTTCGACT
*
819104 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAATC
* * *
819145 CGATGAGGCACTGGTTG-CTAA-TT-TACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTC-AATTTATACTTCGGATTAATC
*
819182 CGATGAGACACTGGGTGTCAATTTATTACTTCGAATT-ATC
1 CGATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAATC
*
819222 TGATGAG
1 CGATGAG
819229 GTGATGTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
37 17 0.25
38 15 0.22
39 1 0.01
40 19 0.28
41 17 0.25
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTATACTTCGGATTAATC
Found at i:827391 original size:7 final size:7
Alignment explanation
Indices: 827367--827400 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
827357 GCTTAAAAAA
827367 TAATATT
1 TAATATT
827374 TATATTATT
1 TA-A-TATT
827383 TAATATT
1 TAATATT
827390 TAATATT
1 TAATATT
827397 TAAT
1 TAAT
827401 CTTTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 17 0.68
8 2 0.08
9 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAATATT
Found at i:827398 original size:14 final size:16
Alignment explanation
Indices: 827367--827400 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
827357 GCTTAAAAAA
827367 TAATATTTATATTATT
1 TAATATTTATATTATT
827383 TAATATTTA-A-TATT
1 TAATATTTATATTATT
827397 TAAT
1 TAAT
827401 CTTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 1 0.06
16 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATATTTATATTATT
Found at i:827415 original size:23 final size:23
Alignment explanation
Indices: 827367--827412 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
827357 GCTTAAAAAA
*
827367 TAATATTTATATTATTTAATATT
1 TAATATTTATATTATTTAAAATT
827390 TAATATTTA-ATCT-TTTAAAATT
1 TAATATTTATAT-TATTTAAAATT
827412 T
1 T
827413 TAAATATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATATTTATATTATTTAAAATT
Found at i:835249 original size:9 final size:9
Alignment explanation
Indices: 835221--835262 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
835211 GTTATTTTAA
835221 ATAAAATAT
1 ATAAAATAT
835230 -T-AAAT-T
1 ATAAAATAT
835236 ATAAAATAT
1 ATAAAATAT
*
835245 ATAAAAAAT
1 ATAAAATAT
835254 ATAAAATAT
1 ATAAAATAT
835263 TTAAGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 1 0.04
7 5 0.18
8 5 0.18
9 17 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATAAAATAT
Found at i:847394 original size:16 final size:16
Alignment explanation
Indices: 847365--847410 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
847355 TTAAATTTTT
* *
847365 TAAAAATA-TGAAAAT
1 TAAAAATATTAAAAAA
847380 TAATAAAT-TTAAAAAA
1 TAA-AAATATTAAAAAA
847396 TAAAAATATTAAAAA
1 TAAAAATATTAAAAA
847411 GATATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAAAATATTAAAAAA
Found at i:863287 original size:2 final size:2
Alignment explanation
Indices: 863280--863309 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
863270 CCTTCACTTT
863280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
863310 ACATATCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:864229 original size:23 final size:22
Alignment explanation
Indices: 864187--864229 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
864177 TTTATGATCC
*
864187 AGTCATTTCAAAATTGGGTTCA
1 AGTCATTTCAAAATTAGGTTCA
*
864209 AGTCATTTTCAAATTTAGGTT
1 AGTCA-TTTCAAAATTAGGTT
864230 GAATGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (22 bp):
AGTCATTTCAAAATTAGGTTCA
Found at i:867211 original size:13 final size:14
Alignment explanation
Indices: 867186--867214 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
867176 ATAATCTCAG
867186 CTCAAAAACAAACC
1 CTCAAAAACAAACC
867200 CTCAAAAA-AAACC
1 CTCAAAAACAAACC
867213 CT
1 CT
867215 TTGATCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.34, G:0.00, T:0.10
Consensus pattern (14 bp):
CTCAAAAACAAACC
Found at i:869272 original size:2 final size:2
Alignment explanation
Indices: 869265--869310 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
869255 AGCTCACTTC
869265 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
869308 AT A
1 AT A
869311 ATTAANNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:872401 original size:14 final size:15
Alignment explanation
Indices: 872382--872423 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
872372 AACAATTTCG
872382 ATTTTTATTTTT-AC
1 ATTTTTATTTTTAAC
872396 ATTTTTACTTTTTCAAC
1 ATTTTTA-TTTTT-AAC
872413 ACTTTTTATTT
1 A-TTTTTATTT
872424 CATGATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.29
15 5 0.21
17 6 0.25
18 6 0.25
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTATTTTTAAC
Found at i:879056 original size:20 final size:18
Alignment explanation
Indices: 879031--879077 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 18
879021 TCAAGCTTTT
879031 AAATTAAATCATTTATAATA
1 AAATTAAATCATTT-TAA-A
879051 AAATTAAA--ATTTTAAA
1 AAATTAAATCATTTTAAA
*
879067 AAATCAAATCA
1 AAATTAAATCA
879078 ATTAGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 5 0.21
20 8 0.33
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTAAATCATTTTAAA
Found at i:883206 original size:6 final size:6
Alignment explanation
Indices: 883195--883224 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
883185 TTGTACAATA
883195 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
883225 GCCATGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:883650 original size:51 final size:51
Alignment explanation
Indices: 883502--883939 Score: 180
Period size: 50 Copynumber: 8.9 Consensus size: 51
883492 AGGGTTTGTA
* * * * *
883502 ACTTGTAGCTTCAATCTATTCGACTACAACTTTAGGAAAATAAGACTCGCC
1 ACTTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* * * * *** *
883553 ACAATG-A-CTTCAATCTGTTCCACTGCAATTTCAGGGGTATAGGATTTGCG
1 AC-TTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* * *
883603 ACTTGTAGCTTTAATCTAATCCACTGCAACTTCAGGAAAATAAGA--T---
1 ACTTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* * * * * * **
883649 --TTGTAACTTCAATCTGCTT-CACTACAACTTCAGGGAGATAAGACTCGTT
1 ACTTGTAGCTTCAATCT-ATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* * * * *** *
883698 ACAATG-A-CTTCAATCTGTTCCACTGCAATTTCAGGGGTATAGGATTTGCG
1 AC-TTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* *
883748 ACTTGTAGCTTTAATCTAATCCACTACAACTTCAGGAAAATAAGA--T---
1 ACTTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* * ** * * * * *
883794 --TTGTAACTTCAATTTGCTCCACTACAACTTCAGGGAGATAAGACTCGCC
1 ACTTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* * * ** * *** *
883843 ACAATG-A-CTTCAATCCATTCCATTGTAATTTCAGGGGTATATGATTTGCG
1 AC-TTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
* * * *
883893 ACTTGTAGCTTTAATCTATTCCACTGCAACTTTAGGGAAATAAGATT
1 ACTTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATT
883940 CGCATTTTCA
Statistics
Matches: 278, Mismatches: 84, Indels: 50
0.67 0.20 0.12
Matches are distributed among these distances:
44 70 0.25
45 1 0.00
49 10 0.04
50 99 0.36
51 92 0.33
52 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (51 bp):
ACTTGTAGCTTCAATCTATTCCACTACAACTTCAGGAAAATAAGATTTGCG
Found at i:883677 original size:44 final size:44
Alignment explanation
Indices: 883622--883836 Score: 133
Period size: 44 Copynumber: 4.6 Consensus size: 44
883612 TTTAATCTAA
*
883622 TCCACTGCAACTTCAGGAAAATAAGATTTGTAACTTCAATCTGC
1 TCCACTACAACTTCAGGAAAATAAGATTTGTAACTTCAATCTGC
* * * * * *
883666 TTCACTACAACTTCAGGGAGATAAGACTCGTTACAATGACTTCAATCTGT
1 TCCACTACAACTTCAGGAAAATAAGA-T--TT---GTAACTTCAATCTGC
* * * ** * * * **
883716 TCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAA
1 TCCACTACAACTTCA--GG-A-A--A-ATAAGATTTGTAACTTCAATCTGC
*
883767 TCCACTACAACTTCAGGAAAATAAGATTTGTAACTTCAATTTGC
1 TCCACTACAACTTCAGGAAAATAAGATTTGTAACTTCAATCTGC
* *
883811 TCCACTACAACTTCAGGGAGATAAGA
1 TCCACTACAACTTCAGGAAAATAAGA
883837 CTCGCCACAA
Statistics
Matches: 123, Mismatches: 35, Indels: 26
0.67 0.19 0.14
Matches are distributed among these distances:
44 61 0.50
45 2 0.02
47 3 0.02
48 1 0.01
49 2 0.02
50 24 0.20
51 22 0.18
52 2 0.02
54 3 0.02
57 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (44 bp):
TCCACTACAACTTCAGGAAAATAAGATTTGTAACTTCAATCTGC
Found at i:883767 original size:145 final size:145
Alignment explanation
Indices: 883504--883977 Score: 707
Period size: 145 Copynumber: 3.3 Consensus size: 145
883494 GGTTTGTAAC
* ** * * * *
883504 TTGTAGCTTCAATCTATTCGACTACAACTTTAGGAAAATAAGACTCGCCACAATGACTTCAATCT
1 TTGTAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCCACAATGACTTCAATCT
883569 GTTCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAATCCACTGCAACT
66 GTTCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAATCCACTGCAACT
883634 TCAGGAAAATAAGAT
131 TCAGGAAAATAAGAT
* **
883649 TTGTAACTTCAATCTGCTTCACTACAACTTCAGGGAGATAAGACTCGTTACAATGACTTCAATCT
1 TTGTAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCCACAATGACTTCAATCT
*
883714 GTTCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAATCCACTACAACT
66 GTTCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAATCCACTGCAACT
883779 TCAGGAAAATAAGAT
131 TCAGGAAAATAAGAT
* *
883794 TTGTAACTTCAATTTGCTCCACTACAACTTCAGGGAGATAAGACTCGCCACAATGACTTCAATCC
1 TTGTAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCCACAATGACTTCAATCT
* * * * *
883859 ATTCCATTGTAATTTCAGGGGTATATGATTTGCGACTTGTAGCTTTAATCTATTCCACTGCAACT
66 GTTCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAATCCACTGCAACT
* *
883924 TTAGGGAAATAAGAT
131 TCAGGAAAATAAGAT
* * ** *
883939 TCGCATTTTCAA-CTTGCTCCACTGCAACTTCAGGGAGAT
1 TTGTAACTTCAATC-TGCTCCACTACAACTTCAGGGAGAT
883978 TAGATTTGTA
Statistics
Matches: 298, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
145 298 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (145 bp):
TTGTAACTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCCACAATGACTTCAATCT
GTTCCACTGCAATTTCAGGGGTATAGGATTTGCGACTTGTAGCTTTAATCTAATCCACTGCAACT
TCAGGAAAATAAGAT
Found at i:884001 original size:95 final size:92
Alignment explanation
Indices: 883893--884079 Score: 250
Period size: 95 Copynumber: 2.0 Consensus size: 92
883883 ATGATTTGCG
* * * *
883893 ACTTGTAGCTTTAATCTATTCCACTGCAACTTTAGGGAAATAAGATTCGCATTTTCAA-CTTGCT
1 ACTTGTAGCTTTAATATATTCCACTACAACTTCAGGGAAATAAGATTCGCATATTCAATC-TGCT
*
883957 CCACTGCAACTTCAGGGAGATTAGATTTGTA
65 CCACT---ACTTCAGGGAGATAAGATTTGTA
** * *
883988 ACTTGTATTTTTAATATGTTCCACTATAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTC
1 ACTTGTAGCTTTAATATATTCCACTACAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTC
884053 CACTACTTCAGGGAGATAAGATTTGTA
66 CACTACTTCAGGGAGATAAGATTTGTA
884080 TCTTCAATCT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
92 22 0.27
95 59 0.72
96 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (92 bp):
ACTTGTAGCTTTAATATATTCCACTACAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTC
CACTACTTCAGGGAGATAAGATTTGTA
Found at i:884116 original size:44 final size:44
Alignment explanation
Indices: 884027--884962 Score: 791
Period size: 44 Copynumber: 21.2 Consensus size: 44
884017 CTTCAGGGAA
* * * * *
884027 ATAAGATTCGCATATTCAATCTGCTCCACT---ACTTCAGGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
** * *
884068 ATAAGATTTGTATCTTCAATCTTTTCTACTGTAACTTTAAGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* * * * *
884112 ATAAGATTTATAGCTTTAATCTGCTCTACTGCAACTTCTTA-GAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTT-TAAGGAG
* * * * *
884156 ACAAGATTTGCTATCTTCAATATGCTCTACTGCAACTTCAGGGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* ** * * * *
884201 ATAAGATTTATGGCTTTAATCTGCTCCTCTACAA-TTTCAGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* *
884244 ATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTCAAGGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* ** * * *
884289 ATAATATTTGTGGCTTTAATCTGCTCCACTGTAAC-TTCAGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* * * * * *
884332 ATAAGATTTGCTATTTTCAATTTGCTTCATTACAACTTTAGGGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
** * *
884377 ATAAGATTTGTGGCTTTAATCTGCTCGACTGCAACTTT-AGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* * *
884420 ATAAGATTTGCTATCTTCAATCCGCTCCACTACAACTTTAGGGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
** *
884465 ATAAGATTTGTGGCTTTAATCTGCTCCACTGCAACTTT-AGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* * *
884508 ATAAGATTTGCTATCTTCAATCCGCTCCACTGCAACTTTAGGGGG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
** * * *
884553 ATAAGATTTGTGCCTTTCAATCCGCTCCACTGCAACTTTAGGGGG
1 ATAAGATTTGTATC-TTCAATCTGCTCCACTGCAACTTTAAGGAG
** * * * *
884598 ATAAGATTTGTGCCTTTCAATTTGCTCCACTACAACTTTAGGGGG
1 ATAAGATTTGTATC-TTCAATCTGCTCCACTGCAACTTTAAGGAG
* * ** * * *
884643 ATAATATTTATGGCTTTAATCTGCTCCACTACAACTTCAA-GAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* *
884686 ATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTTAGGGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
884731 ATAAGATTTGTTATCTTCAATCTGCTCCACTGCAAC-TT-AGAGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAG-GAG
** * * * *
884775 ATAAGATTTGTGGCTTTAATATGCTCCTCTGCAAC-TTCAGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* * * * *
884818 ATAAGATTTGCTATCTTTAATCTGCTCTACTGCAGCTTCAGGGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
* * * *
884863 ATAAAATTTGCTATCTTCAATCTACTCTACTGCAAC-TTCAGAGAG
1 ATAAGATTTG-TATCTTCAATCTGCTCCACTGCAACTTTAAG-GAG
** * * * * *
884908 ATAAGATTTGTGGCTTTAATTTGCTCCTCTGCAACTTCAGGGAG
1 ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
*
884952 ATAGGATTTGT
1 ATAAGATTTGT
884963 CATGATAACT
Statistics
Matches: 725, Mismatches: 147, Indels: 43
0.79 0.16 0.05
Matches are distributed among these distances:
41 24 0.03
43 104 0.14
44 330 0.46
45 267 0.37
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (44 bp):
ATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTTAAGGAG
Found at i:884282 original size:88 final size:88
Alignment explanation
Indices: 884044--884961 Score: 1062
Period size: 88 Copynumber: 10.4 Consensus size: 88
884034 TCGCATATTC
** * *
884044 AATCTGCTCCACT---ACTTCAGGGAGATAAGATTTG-TATCTTCAATCTTTTCTACTGTAACTT
1 AATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
* * *
884105 TAAGGAGATAAGATTTATAGCTTT
65 TAGGGAGATAAGATTTGTGGCTTT
* * * *
884129 AATCTGCTCTACTGCAACTTCTTA-GAGACAAGATTTGCTATCTTCAATATGCTCTACTGCAACT
1 AATCTGCTCCACTGCAACTTC--AGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACT
* *
884193 TCAGGGAGATAAGATTTATGGCTTT
64 TTAGGGAGATAAGATTTGTGGCTTT
* * * * *
884218 AATCTGCTCCTCTACAATTTCAGGAGATAAGATTTGCTATCTTTAATCTGCTCCACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
* *
884283 AAGGAGATAATATTTGTGGCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* * * * * *
884306 AATCTGCTCCACTGTAACTTCAGGAGATAAGATTTGCTATTTTCAATTTGCTTCATTACAACTTT
1 AATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
884371 AGGGAGATAAGATTTGTGGCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* * * *
884394 AATCTGCTCGACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCCGCTCCACTACAACTTT
1 AATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
884459 AGGGAGATAAGATTTGTGGCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* *
884482 AATCTGCTCCACTGCAACTTTAGGAGATAAGATTTGCTATCTTCAATCCGCTCCACTGCAACTTT
1 AATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
* *
884547 AGGGGGATAAGATTTGTGCCTTT
66 AGGGAGATAAGATTTGTGGCTTT
* * * ** * *
884570 CAATCCGCTCCACTGCAACTTTAGGGGGATAAGATTTG-TGCCTTTCAATTTGCTCCACTACAAC
1 -AATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTGCTATC-TTCAATCTGCTCCACTGCAAC
* * *
884634 TTTAGGGGGATAATATTTATGGCTTT
63 TTTAGGGAGATAAGATTTGTGGCTTT
* * *
884660 AATCTGCTCCACTACAACTTCAAGAGATAAGATTTGCTATCTTCAATCTACTCCACTGCAACTTT
1 AATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
** *
884725 AGGGAGATAAGATTTGTTATCTTC
66 AGGGAGATAAGATTTG-TGGCTTT
** * * *
884749 AATCTGCTCCACTGCAACTT-AGAGAGATAAGATTTG-TGGCTTTAATATGCTCCTCTGCAACTT
1 AATCTGCTCCACTGCAACTTCAG-GAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
* **
884812 CA-GGAGATAAGATTTGCTATCTTT
65 TAGGGAGATAAGATTTG-TGGCTTT
* * * * *
884836 AATCTGCTCTACTGCAGCTTCAGGGAGATAAAATTTGCTATCTTCAATCTACTCTACTGCAACTT
1 AATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTT
* *
884901 CAGAGAGATAAGATTTGTGGCTTT
65 TAGGGAGATAAGATTTGTGGCTTT
* * *
884925 AATTTGCTCCTCTGCAACTTCAGGGAGATAGGATTTG
1 AATCTGCTCCACTGCAACTTCA-GGAGATAAGATTTG
884962 TCATGATAAC
Statistics
Matches: 715, Mismatches: 101, Indels: 30
0.85 0.12 0.04
Matches are distributed among these distances:
85 12 0.02
87 39 0.05
88 396 0.55
89 200 0.28
90 68 0.10
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (88 bp):
AATCTGCTCCACTGCAACTTCAGGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTT
AGGGAGATAAGATTTGTGGCTTT
Found at i:888103 original size:20 final size:21
Alignment explanation
Indices: 888061--888106 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
888051 TTTTTTTTGC
888061 TTTGGGCTTGTAATAATTTTTAT
1 TTTGGGCTTGTAATAA--TTTAT
*
888084 TTTGGGTTTGTAATAA-TTAT
1 TTTGGGCTTGTAATAATTTAT
888104 TTT
1 TTT
888107 TATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
23 15 0.68
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.59
Consensus pattern (21 bp):
TTTGGGCTTGTAATAATTTAT
Found at i:896997 original size:14 final size:15
Alignment explanation
Indices: 896970--896998 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
896960 TTCTTTCTTT
896970 CCTCTTTATTTTCAA
1 CCTCTTTATTTTCAA
896985 CCTCTTT-TTTTCAA
1 CCTCTTTATTTTCAA
896999 TTATTGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (15 bp):
CCTCTTTATTTTCAA
Found at i:897480 original size:18 final size:18
Alignment explanation
Indices: 897457--897494 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
897447 ACCAAAATTT
897457 TATTTTAAAAATTAAAAA
1 TATTTTAAAAATTAAAAA
*
897475 TATTTTAAAATTTAAAAA
1 TATTTTAAAAATTAAAAA
897493 TA
1 TA
897495 AATATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTTTAAAAATTAAAAA
Found at i:908834 original size:2 final size:2
Alignment explanation
Indices: 908829--908862 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
908819 AAAAAAAAAC
908829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
908863 ATTAAGTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:910028 original size:21 final size:22
Alignment explanation
Indices: 910002--910042 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
909992 AATATTTTTC
910002 AAAAAT-ATTTTTTAAATAAAT
1 AAAAATAATTTTTTAAATAAAT
*
910023 AAAAATAATTTTTTATATAA
1 AAAAATAATTTTTTAAATAA
910043 CATTTCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAATAATTTTTTAAATAAAT
Found at i:911184 original size:24 final size:24
Alignment explanation
Indices: 911152--911200 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
911142 TCTATAACAT
911152 TTATAAATTTAGATTATCATCGTA
1 TTATAAATTTAGATTATCATCGTA
*
911176 TTATAAATTTAGATTATTATCGTA
1 TTATAAATTTAGATTATCATCGTA
911200 T
1 T
911201 GATTTAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (24 bp):
TTATAAATTTAGATTATCATCGTA
Found at i:917122 original size:16 final size:17
Alignment explanation
Indices: 917084--917125 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
917074 AAAAAATACT
917084 CAAAAGTGACTAAATCA
1 CAAAAGTGACTAAATCA
917101 -AGAAAG-GACTAAATCA
1 CA-AAAGTGACTAAATCA
917117 CAAAAGTGA
1 CAAAAGTGA
917126 AAAAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (17 bp):
CAAAAGTGACTAAATCA
Found at i:918918 original size:3 final size:3
Alignment explanation
Indices: 918910--918935 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
918900 TCATATATTT
918910 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
918936 TCCACATCCT
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:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:920668 original size:23 final size:23
Alignment explanation
Indices: 920642--920686 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
920632 TTTCTTACTG
* *
920642 TAGTAATTTTCGGGGTATTACAA
1 TAGTAATTTTCGAGATATTACAA
920665 TAGTAATTTTCGAGATATTACA
1 TAGTAATTTTCGAGATATTACA
920687 TTATGTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (23 bp):
TAGTAATTTTCGAGATATTACAA
Found at i:921362 original size:25 final size:25
Alignment explanation
Indices: 921334--921391 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
921324 AAACCTTAGC
*
921334 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACATTA
921359 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATTA
921384 GTGCTCTC
1 GTGCTCTC
921392 CGTTTAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATTA
Found at i:921432 original size:22 final size:22
Alignment explanation
Indices: 921356--921438 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 22
921346 TATTAGCACG
* *
921356 TTAGTGCTCTCTGATTATTAGCACA
1 TTAGTGCTCTCTG--TA-TAGTACT
* *
921381 TTAGTGCTCTCCGTTTAGCTTA-T
1 TTAGTGCTCTCTGTATAG--TACT
921404 TTA-TGCTCTCTGTATAGTACT
1 TTAGTGCTCTCTGTATAGTACT
921425 TTAGTGCTCTCTGT
1 TTAGTGCTCTCTGT
921439 TTAATAGTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.04
21 4 0.08
22 25 0.52
23 4 0.08
24 1 0.02
25 12 0.25
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (22 bp):
TTAGTGCTCTCTGTATAGTACT
Found at i:922989 original size:3 final size:3
Alignment explanation
Indices: 922981--923006 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
922971 TAAATTTGAG
922981 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
923007 AATTTTAAAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:928203 original size:51 final size:49
Alignment explanation
Indices: 928133--928302 Score: 223
Period size: 51 Copynumber: 3.3 Consensus size: 49
928123 ACGTGACATA
* *
928133 TTGTTAACCTTGCTAGCATGCTGATCTGTCTAATAATTAGTCTTAATTGT
1 TTGTTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAGT-TTAATTGT
* *
928183 TTGTTTAACCTTGTTGGCATGCTGACCTGTGTAATAATTAGTTTTAATTGT
1 TTG-TTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAG-TTTAATTGT
* *
928234 TTGGTTAACCTTACTGGCATGCTGACCTGTCTAAAAATTAGTTTGAATTGT
1 TT-GTTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAGTTT-AATTGT
*
928285 TCAGTTAACCTTGCTGGC
1 T-TGTTAACCTTGCTGGC
928303 GTGCAAATCG
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
50 6 0.06
51 97 0.92
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (49 bp):
TTGTTAACCTTGCTGGCATGCTGACCTGTCTAATAATTAGTTTAATTGT
Found at i:928320 original size:102 final size:103
Alignment explanation
Indices: 928135--928340 Score: 240
Period size: 102 Copynumber: 2.0 Consensus size: 103
928125 GTGACATATT
* * * * *
928135 GTTAACCTTGCTAGCATGCTGATCTGTCTAATAATTAGTCTTAATTGTTTGTTTAACCTTGTTGG
1 GTTAACCTTACTAGCATGCTGACCTGTCTAAAAATTAGTCTTAATTGTTAGTTTAACCTTGCTGG
** * * *
928200 CATGCTGACCTGTGTAATAA-TTAGTTTTAATTGTTTG
66 CATGCAAACCTGTCTAATAACTAAATTTTAATTGTTTG
*
928237 GTTAACCTTACTGGCATGCTGACCTGTCTAAAAATTAGT-TTGAATTGTTCAG-TTAACCTTGCT
1 GTTAACCTTACTAGCATGCTGACCTGTCTAAAAATTAGTCTT-AATTGTT-AGTTTAACCTTGCT
* *
928300 GGCGTGCAAATC-GATCTAATAACTAAATTTTAATTGTTTG
64 GGCATGCAAACCTG-TCTAATAACTAAATTTTAATTGTTTG
928340 G
1 G
928341 CTAGCATGCC
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
101 3 0.03
102 67 0.77
103 17 0.20
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.41
Consensus pattern (103 bp):
GTTAACCTTACTAGCATGCTGACCTGTCTAAAAATTAGTCTTAATTGTTAGTTTAACCTTGCTGG
CATGCAAACCTGTCTAATAACTAAATTTTAATTGTTTG
Found at i:931116 original size:9 final size:9
Alignment explanation
Indices: 931102--931126 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
931092 GAAATAAATA
931102 ATAATAATT
1 ATAATAATT
931111 ATAATAATT
1 ATAATAATT
931120 ATAATAA
1 ATAATAA
931127 ATTTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATAATAATT
Found at i:936336 original size:19 final size:19
Alignment explanation
Indices: 936298--936336 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
936288 TCATACTAGT
*
936298 TGTTAGTTTTGGTATTAAA
1 TGTTAGTTTTGGTATAAAA
936317 TGTTAG-TTTGGATATAAAA
1 TGTTAGTTTTGG-TATAAAA
936336 T
1 T
936337 ATTTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (19 bp):
TGTTAGTTTTGGTATAAAA
Done.