Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397267.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_204.0, 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: 6982396
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 27749 characters in sequence are not A, C, G, or T
File 10 of 12
Found at i:5845689 original size:125 final size:125
Alignment explanation
Indices: 5845466--5845713 Score: 406
Period size: 125 Copynumber: 2.0 Consensus size: 125
5845456 ACTGACATTA
* * *
5845466 AGATAATTGTTTCAGTGTCTAAGTTGCAAATATGACTTGTATACAGCTAGTATCTTGTATAAGCA
1 AGATAATTGTTTCAGTGTCAAAGTTACAAATATGACTTGTATACAGCTAGTATCTTATATAAGCA
5845531 ATGACCATTTGAGCATTAAAGAACATAGATTTGATTCATTTTATCAAAGTGACTGGACAG
66 ATGACCATTTGAGCATTAAAGAACATAGATTTGATTCATTTTATCAAAGTGACTGGACAG
* ** *
5845591 AGATAATTGTTTCAGTGTCAAAGTTACAAATATGACTTGTTTATGGCTAGTATCTTATATAAGTA
1 AGATAATTGTTTCAGTGTCAAAGTTACAAATATGACTTGTATACAGCTAGTATCTTATATAAGCA
* * *
5845656 ATGACCATTTGAGCATTAAAGAATATAGGTTTGATTCATTTTATCAAAGTGATTGGAC
66 ATGACCATTTGAGCATTAAAGAACATAGATTTGATTCATTTTATCAAAGTGACTGGAC
5845714 GCAACTCTGG
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 113 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (125 bp):
AGATAATTGTTTCAGTGTCAAAGTTACAAATATGACTTGTATACAGCTAGTATCTTATATAAGCA
ATGACCATTTGAGCATTAAAGAACATAGATTTGATTCATTTTATCAAAGTGACTGGACAG
Found at i:5851779 original size:26 final size:26
Alignment explanation
Indices: 5851723--5851800 Score: 88
Period size: 26 Copynumber: 3.1 Consensus size: 26
5851713 TTAAGCGCAT
* **
5851723 ATGTTGAAAAAATATTGTTATATTTC
1 ATGTTGAAAAAATATTGTTACAAATC
* *
5851749 GTGTTGAAAAAATATTGTTACACATC
1 ATGTTGAAAAAATATTGTTACAAATC
*
5851775 ATGTT-AAAAAA-ATTATTACAAATC
1 ATGTTGAAAAAATATTGTTACAAATC
5851799 AT
1 AT
5851801 ATTTAAAGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.29
25 6 0.13
26 26 0.58
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (26 bp):
ATGTTGAAAAAATATTGTTACAAATC
Found at i:5851907 original size:27 final size:27
Alignment explanation
Indices: 5851868--5851929 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
5851858 AAGTTATTTA
*
5851868 AAAAATAATATTGTTACATGTCATGTTC
1 AAAAA-AATATTGTTACATGTCATATTC
* *
5851896 AAAAAAATATTGTTACATGTTATATTG
1 AAAAAAATATTGTTACATGTCATATTC
5851923 AAAAAAA
1 AAAAAAA
5851930 GAGAGTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 26 0.84
28 5 0.16
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (27 bp):
AAAAAAATATTGTTACATGTCATATTC
Found at i:5852178 original size:25 final size:25
Alignment explanation
Indices: 5852137--5852199 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
5852127 GTTAAGCGCA
*
5852137 TGTGTTGAAAAAATATTATTACATAT
1 TGTGTT-AAAAAATATTATTACACAT
* *
5852163 TGTGTTAAAAATTATTGTTACACAT
1 TGTGTTAAAAAATATTATTACACAT
**
5852188 CATGTTAAAAAA
1 TGTGTTAAAAAA
5852200 AAATTGTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 25 0.81
26 6 0.19
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTGTTAAAAAATATTATTACACAT
Found at i:5852215 original size:26 final size:25
Alignment explanation
Indices: 5852139--5852216 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 25
5852129 TAAGCGCATG
* **
5852139 TGTTGAAAAAATATTATTACATATTG
1 TGTT-AAAAAATATTGTTACATATCA
* *
5852165 TGTTAAAAATTATTGTTACACATCA
1 TGTTAAAAAATATTGTTACATATCA
*
5852190 TGTTAAAAAAAAATTGTTACATATCA
1 TGTT-AAAAAATATTGTTACATATCA
5852216 T
1 T
5852217 ATTTAAAGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 20 0.47
26 23 0.53
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (25 bp):
TGTTAAAAAATATTGTTACATATCA
Found at i:5852308 original size:29 final size:28
Alignment explanation
Indices: 5852274--5852342 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
5852264 AAAAAAATAA
5852274 GTTAT-TTAAAAAATAATATTATTACAC
1 GTTATATTAAAAAATAATATTATTACAC
* * *
5852301 GTTATATTCAAAAA-AATATTGTTATAC
1 GTTATATTAAAAAATAATATTATTACAC
5852328 GTTATATTAAAAAAT
1 GTTATATTAAAAAAT
5852343 TTTATATCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 29 0.81
28 7 0.19
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (28 bp):
GTTATATTAAAAAATAATATTATTACAC
Found at i:5852334 original size:414 final size:413
Alignment explanation
Indices: 5851547--5852381 Score: 1152
Period size: 414 Copynumber: 2.0 Consensus size: 413
5851537 TCCTTTCGTA
5851547 TTATTCTTCATTTATTTGGATAAGTAAAAAAAATATAAAAAGAATGATTTTTTTAATCTTCAAAG
1 TTATTCTTCATTTATTTGGATAAGTAAAAAAAATATAAAAAGAATGATTTTTTTAATCTTCAAAG
* * *
5851612 ATAAGATATTTTCAAAATAACTCGTTTTTTTAATTTTAACTGTTTTTAATCAAGAGAAAAAAATT
66 ATAAGATATTTTCAAAATAACTCGATTTTTTAATTTTAACTATTTTTAAGC-A-AGAAAAAAA--
* *
5851677 TTAGACAAAATTATCCTTAATGAAACCTTCTCATATTTAAGCGCATATGTTGAAAAAATATTGTT
127 -TAGACAAAATTATCCTTAATGAAACCTTCTCATAGTTAAGCGCATATGTTGAAAAAATATTATT
*
5851742 ATATTTCGTGTTGAAAAAATATTGTTACACATCATGTTAAAAAAATTATTACAAATCATATTTAA
191 ACATTTCGTGTTGAAAAAATATTGTTACACATCATGTTAAAAAAATTATTACAAATCATATTTAA
* * * *
5851807 AGTTTTTGACTCTAAGAGTTTATGGCGTAATAAAATACAAAGATAAAAATCAAGTTATTTAAAAA
256 AGTGTTTAACTCCAAGAGTTTATGGCGTAATAAAATACAAAGAAAAAAATCAAGTTATTTAAAAA
* * * *
5851872 ATAATATTGTTACATGTCATGTTCAAAAAAATATTGTTACATGTTATATTGAAAAAAAGAGAGTT
321 ATAATATTATTACACGTCATATTCAAAAAAATATTGTTACACGTTATATT----AAAA-A-AGTT
* * *
5851937 TATATCTTAGTTAAATACAAAAATAGAGATCAAG
380 TATATCTTAATTAAATAAAAAAATAGAGACCAAG
*
5851971 TTATTCTTCATTTATTTGGATAAGT-AAAAAAATATAAAAAGAATGATTTTTTTAATCTTCAAAT
1 TTATTCTTCATTTATTTGGATAAGTAAAAAAAATATAAAAAGAATGATTTTTTTAATCTTCAAAG
* * *
5852035 ATAAAGTGTTTTTTTAAAATAACTC-ATTTTTTAATTTTAACTATTTTT-AGC-A-AAAAAAA-A
66 AT-AAG-ATATTTTCAAAATAACTCGATTTTTTAATTTTAACTATTTTTAAGCAAGAAAAAAATA
* * * *
5852095 GATAAAATTGTCCTTAATGAAACCTTCTCGTAGTTAAGCGCATGTGTTGAAAAAATATTATTACA
129 GACAAAATTATCCTTAATGAAACCTTCTCATAGTTAAGCGCATATGTTGAAAAAATATTATTACA
* * *
5852160 TATT-GTGTT-AAAAATTATTGTTACACATCATGTTAAAAAAAAATTGTTACATATCATATTTAA
194 T-TTCGTGTTGAAAAAATATTGTTACACATCATGTT--AAAAAAATTATTACAAATCATATTTAA
*
5852223 AGTGTTTAACTCCAAGAGTTTATGGTC-TAATGAAATACAAA-AAAAAAAT-AAGTTATTTAAAA
256 AGTGTTTAACTCCAAGAGTTTATGG-CGTAATAAAATACAAAGAAAAAAATCAAGTTATTTAAAA
* * *
5852285 AATAATATTATTACACGTTATATTCAAAAAAATATTGTTATACGTTATATTAAAAAATTTTATAT
320 AATAATATTATTACACGTCATATTCAAAAAAATATTGTTACACGTTATATTAAAAAAGTTTATAT
5852350 CTTAATTAAATAAAAAAATAGAGACCAAG
385 CTTAATTAAATAAAAAAATAGAGACCAAG
5852379 TTA
1 TTA
5852382 CACTGTCATA
Statistics
Matches: 373, Mismatches: 32, Indels: 28
0.86 0.07 0.06
Matches are distributed among these distances:
408 37 0.10
409 1 0.00
410 4 0.01
414 82 0.22
415 72 0.19
416 62 0.17
417 1 0.00
419 7 0.02
420 1 0.00
423 42 0.11
424 49 0.13
425 15 0.04
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (413 bp):
TTATTCTTCATTTATTTGGATAAGTAAAAAAAATATAAAAAGAATGATTTTTTTAATCTTCAAAG
ATAAGATATTTTCAAAATAACTCGATTTTTTAATTTTAACTATTTTTAAGCAAGAAAAAAATAGA
CAAAATTATCCTTAATGAAACCTTCTCATAGTTAAGCGCATATGTTGAAAAAATATTATTACATT
TCGTGTTGAAAAAATATTGTTACACATCATGTTAAAAAAATTATTACAAATCATATTTAAAGTGT
TTAACTCCAAGAGTTTATGGCGTAATAAAATACAAAGAAAAAAATCAAGTTATTTAAAAAATAAT
ATTATTACACGTCATATTCAAAAAAATATTGTTACACGTTATATTAAAAAAGTTTATATCTTAAT
TAAATAAAAAAATAGAGACCAAG
Found at i:5861651 original size:16 final size:16
Alignment explanation
Indices: 5861632--5861672 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
5861622 ATTTTATTAT
5861632 TTATTAATTTTAAAAA
1 TTATTAATTTTAAAAA
* *
5861648 TTATTAA-TATATAAA
1 TTATTAATTTTAAAAA
5861663 TTA-TAATTTT
1 TTATTAATTTT
5861673 TCATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTAATTTTAAAAA
Found at i:5873837 original size:28 final size:30
Alignment explanation
Indices: 5873771--5873838 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 30
5873761 AATATTAATC
* *
5873771 ATAAGAATTAATTTAATTTAAAATAAAAAT
1 ATAAAAATTTATTTAATTTAAAATAAAAAT
* *
5873801 ATAAAAATTTATTTAA-TTCAAA-AAATAT
1 ATAAAAATTTATTTAATTTAAAATAAAAAT
5873829 ATAAAAATTT
1 ATAAAAATTT
5873839 TATTAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 15 0.44
29 5 0.15
30 14 0.41
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
ATAAAAATTTATTTAATTTAAAATAAAAAT
Found at i:5890302 original size:22 final size:21
Alignment explanation
Indices: 5890259--5890303 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5890249 ATTTATATTT
5890259 AAATTTAAAAAATAAAACATA
1 AAATTTAAAAAATAAAACATA
* * *
5890280 AAATTGTAAGAAATTAAATATA
1 AAATT-TAAAAAATAAAACATA
5890302 AA
1 AA
5890304 TAATTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (21 bp):
AAATTTAAAAAATAAAACATA
Found at i:5890310 original size:14 final size:14
Alignment explanation
Indices: 5890291--5890317 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5890281 AATTGTAAGA
5890291 AATTAAATATAAAT
1 AATTAAATATAAAT
5890305 AATTAAATATAAA
1 AATTAAATATAAA
5890318 ATATAAGATT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTAAATATAAAT
Found at i:5890521 original size:27 final size:25
Alignment explanation
Indices: 5890473--5890536 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
5890463 GAGTTACTAG
*
5890473 AAAAGAGAAATAAAAATAAAAAGACAA
1 AAAAGAGAAAGAAAAATAAAAA-A-AA
* *
5890500 AAAAGAGAAGAGAAAAA-GAAAAATA
1 AAAAGAGAA-AGAAAAATAAAAAAAA
5890525 AAAAGAGAAAGA
1 AAAAGAGAAAGA
5890537 GGTGTAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 3 0.09
25 10 0.30
26 1 0.03
27 13 0.39
28 6 0.18
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (25 bp):
AAAAGAGAAAGAAAAATAAAAAAAA
Found at i:5891012 original size:24 final size:23
Alignment explanation
Indices: 5890985--5891030 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
5890975 GTATTTTATC
* *
5890985 TTTAACAATATTTAAAGAAGAAAA
1 TTTAAAAAAATTTAAA-AAGAAAA
5891009 TTTAAAAAAATTTAAAAAGAAA
1 TTTAAAAAAATTTAAAAAGAAA
5891031 TGAAAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (23 bp):
TTTAAAAAAATTTAAAAAGAAAA
Found at i:5895437 original size:14 final size:15
Alignment explanation
Indices: 5895401--5895439 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5895391 TAATAGATTT
5895401 ATATTTTAATTGTAA
1 ATATTTTAATTGTAA
5895416 ATATTTTAATT-T-A
1 ATATTTTAATTGTAA
5895429 ATCATTTTAAT
1 AT-ATTTTAAT
5895440 CATATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.13
14 9 0.39
15 11 0.48
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (15 bp):
ATATTTTAATTGTAA
Found at i:5906827 original size:2 final size:2
Alignment explanation
Indices: 5906820--5906847 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5906810 NNNNNNNNNN
5906820 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5906848 TAGCAAAAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5907071 original size:2 final size:2
Alignment explanation
Indices: 5907064--5907122 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
5907054 TGTCTTTCTT
* * *
5907064 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5907106 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
5907123 GAAGACTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5908253 original size:70 final size:71
Alignment explanation
Indices: 5908118--5908253 Score: 184
Period size: 70 Copynumber: 1.9 Consensus size: 71
5908108 TATTTGGCTG
* ** * * * *
5908118 GATAGTTAATGATTTTAGGTTTTACTGTCATTCTGTTGGTCTTAATTTCAAATGCATAATTTTTA
1 GATAGTTAATGATTTTAAGTTCAAATGTCATTCTATTGATATTAATTTCAAATGCATAATTTTTA
5908183 TGTCTC
66 TGTCTC
* *
5908189 GATAGTTAGTGATTTTAAGTTCAAATGTCATTC-ATTGATATTAATTTTAAATGCATAATTTTTA
1 GATAGTTAATGATTTTAAGTTCAAATGTCATTCTATTGATATTAATTTCAAATGCATAATTTTTA
5908253 T
66 T
5908254 AGAACATGAT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
70 28 0.50
71 28 0.50
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.49
Consensus pattern (71 bp):
GATAGTTAATGATTTTAAGTTCAAATGTCATTCTATTGATATTAATTTCAAATGCATAATTTTTA
TGTCTC
Found at i:5908691 original size:49 final size:49
Alignment explanation
Indices: 5908619--5908720 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
5908609 ATAAGAAATT
5908619 TAAACTAATGAGAAATGCATTGCCATATGTACACTTTGTCTAATGCTAA
1 TAAACTAATGAGAAATGCATTGCCATATGTACACTTTGTCTAATGCTAA
5908668 TAAACTAATGAGAAATGCATTGCCATATGTACACTTTGTCTAATGCTAA
1 TAAACTAATGAGAAATGCATTGCCATATGTACACTTTGTCTAATGCTAA
5908717 TAAA
1 TAAA
5908721 TTATACTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (49 bp):
TAAACTAATGAGAAATGCATTGCCATATGTACACTTTGTCTAATGCTAA
Found at i:5908807 original size:2 final size:2
Alignment explanation
Indices: 5908800--5908828 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5908790 AAATAATAAA
5908800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5908829 AAGGAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5911346 original size:2 final size:2
Alignment explanation
Indices: 5911339--5911375 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5911329 TGTACAAGCA
*
5911339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5911376 AACTAATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5919371 original size:83 final size:85
Alignment explanation
Indices: 5919155--5919413 Score: 272
Period size: 83 Copynumber: 3.0 Consensus size: 85
5919145 ATTTTGCATT
** * * * *
5919155 AAGGTGTCACTTTAACTTAAGTAATCAA-GAATAAGAGATTGAAAATTGTGTAAAATAATTTTTT
1 AAGGTGTCACCGTAACTTAGGTAAT-AAGGAATAAGAGAGTGAAAATTGAGTAAAACAA-----T
* * **
5919219 TTAAAAAAGCTCCCTTTATGAAAAAA
60 TAAAAAAACCTCTTTTTATGAAAAAA
* * * * *
5919245 AAGGTGTCACCTTAACTTAGGTAATTAGGAGTAGGAGATTGAAAATTGAGTAAAACAATTAAAAA
1 AAGGTGTCACCGTAACTTAGGTAATAAGGAATAAGAGAGTGAAAATTGAGTAAAACAATTAAAAA
5919310 AACCTC-TTTTATGAAAAAA
66 AACCTCTTTTTATGAAAAAA
* * *
5919329 AA-GTGTCACCGTAGCTTAGGTAATAAGGAATAAGAGAGTGAAAATTGAGTGAAATAATTAAAAA
1 AAGGTGTCACCGTAACTTAGGTAATAAGGAATAAGAGAGTGAAAATTGAGTAAAACAATTAAAAA
*
5919393 AATCTCTTTTTATGAAAAAA
66 AACCTCTTTTTATGAAAAAA
5919413 A
1 A
5919414 CAAATCCAAG
Statistics
Matches: 148, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
83 59 0.40
84 28 0.19
85 11 0.07
89 1 0.01
90 49 0.33
ACGTcount: A:0.46, C:0.08, G:0.17, T:0.29
Consensus pattern (85 bp):
AAGGTGTCACCGTAACTTAGGTAATAAGGAATAAGAGAGTGAAAATTGAGTAAAACAATTAAAAA
AACCTCTTTTTATGAAAAAA
Found at i:5921334 original size:2 final size:2
Alignment explanation
Indices: 5921327--5921351 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5921317 CCAAAGTGTT
5921327 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 T
5921352 GATCTATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5921830 original size:19 final size:20
Alignment explanation
Indices: 5921794--5921832 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5921784 GGATTAGTAA
*
5921794 ATTTAGATTAATTTAAGATT
1 ATTTAAATTAATTTAAGATT
5921814 ATTTAAATTAA-TTAAGATT
1 ATTTAAATTAATTTAAGATT
5921833 GTATGAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
ATTTAAATTAATTTAAGATT
Found at i:5922131 original size:23 final size:24
Alignment explanation
Indices: 5922105--5922155 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
5922095 TAACATCTGT
*
5922105 TAATTACATATAA-TTTAATTATA
1 TAATTAAATATAAGTTTAATTATA
*
5922128 TAATTAAATTTAAGGTTTAATTATA
1 TAATTAAATATAA-GTTTAATTATA
5922153 TAA
1 TAA
5922156 ATTAGTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
25 13 0.54
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
TAATTAAATATAAGTTTAATTATA
Found at i:5923288 original size:25 final size:25
Alignment explanation
Indices: 5923260--5923309 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5923250 CCCTTCTTTC
* * *
5923260 CCAAATCAAATGATCCTTACTAGGG
1 CCAAACCAAATGATCATCACTAGGG
5923285 CCAAACCAAATGATCATCACTAGGG
1 CCAAACCAAATGATCATCACTAGGG
5923310 TGAAGGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (25 bp):
CCAAACCAAATGATCATCACTAGGG
Found at i:5923946 original size:24 final size:25
Alignment explanation
Indices: 5923897--5923948 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
5923887 ACAAAAACAT
*
5923897 AAAAGTGTTGTGAAAATAGAATTTG
1 AAAAGTGTTGTGAAAATAGAACTTG
* *
5923922 AAAAGTGTTTTG-AAATATAACTTG
1 AAAAGTGTTGTGAAAATAGAACTTG
5923946 AAA
1 AAA
5923949 GAACAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.46, C:0.02, G:0.19, T:0.33
Consensus pattern (25 bp):
AAAAGTGTTGTGAAAATAGAACTTG
Found at i:5926342 original size:73 final size:72
Alignment explanation
Indices: 5926218--5926363 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 72
5926208 AATGACAACT
5926218 TAAACATATTTAATTAAGACTGTACTTGTCAATTGGACTTTGAATCTCCTTGAATATGTGTAGGT
1 TAAACATATTTAATTAAGACTGTACTTGTCAATTGGACTTTGAATCTCCTTGAATATGTGTAGGT
*
5926283 GTTCTGG
66 GTACTGG
5926290 TAAACATATTTAATTAAGACTGTACTCTGTCAATTGGACTTTGAATCTCCTTGAATATGTGTAGG
1 TAAACATATTTAATTAAGACTGTACT-TGTCAATTGGACTTTGAATCTCCTTGAATATGTGTAGG
5926355 TGTACTGG
65 TGTACTGG
5926363 T
1 T
5926364 GTGTGCTTGG
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 26 0.36
73 46 0.64
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (72 bp):
TAAACATATTTAATTAAGACTGTACTTGTCAATTGGACTTTGAATCTCCTTGAATATGTGTAGGT
GTACTGG
Found at i:5927104 original size:20 final size:21
Alignment explanation
Indices: 5927069--5927109 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5927059 AATGCTTGAC
5927069 TTTTTTCTTTAGAAAAAAGAA
1 TTTTTTCTTTAGAAAAAAGAA
*
5927090 TTTTTTTTTTA-AAAAAAGAA
1 TTTTTTCTTTAGAAAAAAGAA
5927110 CAGCACTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (21 bp):
TTTTTTCTTTAGAAAAAAGAA
Found at i:5927407 original size:14 final size:15
Alignment explanation
Indices: 5927382--5927413 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5927372 GTTGTTTAAG
5927382 TTATTATTTAAATAT
1 TTATTATTTAAATAT
5927397 TTATT-TTTAAATAT
1 TTATTATTTAAATAT
5927411 TTA
1 TTA
5927414 AGTTGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTTAAATAT
Found at i:5927415 original size:34 final size:35
Alignment explanation
Indices: 5927376--5927449 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
5927366 TGTAATGTTG
5927376 TTTAAGTT-ATTATTT-AAATATTTATTTTTAAATA
1 TTTAAGTTGA-TATTTGAAATATTTATTTTTAAATA
* * *
5927410 TTTAAGTTGATATTTGATATATTTATTTTTTATTA
1 TTTAAGTTGATATTTGAAATATTTATTTTTAAATA
5927445 TTTAA
1 TTTAA
5927450 ATTTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 13 0.37
35 22 0.63
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (35 bp):
TTTAAGTTGATATTTGAAATATTTATTTTTAAATA
Found at i:5930485 original size:21 final size:21
Alignment explanation
Indices: 5930459--5930505 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
5930449 TATAAAAATT
*
5930459 AATAAATAATA-ATCAAATTAA
1 AATAAATAA-ACATAAAATTAA
5930480 AATAAATAAACATAAAATTAA
1 AATAAATAAACATAAAATTAA
5930501 AATAA
1 AATAA
5930506 CTTACTTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AATAAATAAACATAAAATTAA
Found at i:5932667 original size:16 final size:16
Alignment explanation
Indices: 5932642--5932684 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5932632 TGTAATACTT
*
5932642 TTTTTATTATAATTAC
1 TTTTTATTATAATTAA
* *
5932658 TTTTTGTTATGATTAA
1 TTTTTATTATAATTAA
5932674 TTTTTAATTAT
1 TTTTT-ATTAT
5932685 TTGTTGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (16 bp):
TTTTTATTATAATTAA
Found at i:5933503 original size:18 final size:18
Alignment explanation
Indices: 5933476--5933510 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5933466 AGATATTTGG
5933476 ATAACATTAAATAAAAAA
1 ATAACATTAAATAAAAAA
*
5933494 ATAACCTTAAATAAAAA
1 ATAACATTAAATAAAAA
5933511 TGAAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAACATTAAATAAAAAA
Found at i:5939352 original size:2 final size:2
Alignment explanation
Indices: 5939345--5939372 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5939335 NNNNNNNNNN
5939345 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
5939373 TAGAACATTA
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:5942094 original size:2 final size:2
Alignment explanation
Indices: 5942089--5942116 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5942079 TTATATATGC
5942089 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
5942117 CTCGAAATCC
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:5944055 original size:2 final size:2
Alignment explanation
Indices: 5944048--5944103 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
5944038 CCCATTCAAT
*
5944048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5944090 TA TC TA TA TT TA TA
1 TA TA TA TA TA TA TA
5944104 ATCTACAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5955310 original size:29 final size:29
Alignment explanation
Indices: 5955268--5955329 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
5955258 GAAAGGATTG
5955268 TCTAAGATCCAGCAATGACCAATATCACA
1 TCTAAGATCCAGCAATGACCAATATCACA
5955297 TCTAAGATCCAGCAATGACCAATATCACA
1 TCTAAGATCCAGCAATGACCAATATCACA
5955326 TCTA
1 TCTA
5955330 TATTTAGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (29 bp):
TCTAAGATCCAGCAATGACCAATATCACA
Found at i:5956575 original size:15 final size:15
Alignment explanation
Indices: 5956552--5956588 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5956542 TCTTTGTCGC
* *
5956552 CATCCTCACCCTCTT
1 CATCATCACCATCTT
5956567 CATCATCACCATCTT
1 CATCATCACCATCTT
5956582 CATCATC
1 CATCATC
5956589 GCTGTCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.32
Consensus pattern (15 bp):
CATCATCACCATCTT
Found at i:5962463 original size:16 final size:15
Alignment explanation
Indices: 5962442--5962494 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
5962432 AATAAATCAC
5962442 TATAATATAATAAGAT
1 TATAATATAATAA-AT
* *
5962458 TATAATGTAATTATAT
1 TATAATATAA-TAAAT
5962474 TATAAT-TAATAAA-
1 TATAATATAATAAAT
5962487 TATAATAT
1 TATAATAT
5962495 GATTACAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 6 0.19
14 4 0.12
15 3 0.09
16 17 0.53
17 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (15 bp):
TATAATATAATAAAT
Found at i:5962768 original size:27 final size:27
Alignment explanation
Indices: 5962706--5962775 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 27
5962696 TATATTTTTT
*
5962706 TAATAAAATAAAATATATAATATTAAATG
1 TAAT-AAATAAAATATATAAGATTAAA-G
5962735 TAA-AAATAAAATATATAAGATTATAA-
1 TAATAAATAAAATATATAAGATTA-AAG
5962761 TAATAAATGAAAATA
1 TAATAAAT-AAAATA
5962776 AAATCATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 3 0.08
27 23 0.62
28 8 0.22
29 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (27 bp):
TAATAAATAAAATATATAAGATTAAAG
Found at i:5962768 original size:35 final size:34
Alignment explanation
Indices: 5962721--5962786 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
5962711 AAATAAAATA
*
5962721 TATAATATTAAATGTAAAAATAAAAT-ATATAAGAT
1 TATAATAATAAATG--AAAATAAAATCATATAAGAT
5962756 TATAATAATAAATGAAAATAAAATCATATAA
1 TATAATAATAAATGAAAATAAAATCATATAA
5962787 TATATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 10 0.34
34 6 0.21
35 13 0.45
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (34 bp):
TATAATAATAAATGAAAATAAAATCATATAAGAT
Found at i:5962822 original size:14 final size:15
Alignment explanation
Indices: 5962781--5962825 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
5962771 AAATAAAATC
*
5962781 ATATAATATATTAAAA
1 ATATATTATA-TAAAA
5962797 ATATATT-T-TAAAA
1 ATATATTATATAAAA
5962810 A-ATATTATATAAAA
1 ATATATTATATAAAA
5962824 AT
1 AT
5962826 TAATAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
12 5 0.20
13 7 0.28
14 6 0.24
15 1 0.04
16 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATTATATAAAA
Found at i:5962964 original size:12 final size:13
Alignment explanation
Indices: 5962942--5962974 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5962932 ATGTTATTTT
5962942 TTATATATTTTAA
1 TTATATATTTTAA
*
5962955 TTAT-TATTTTAT
1 TTATATATTTTAA
5962967 TTATATAT
1 TTATATAT
5962975 CAAATACTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATATATTTTAA
Found at i:5971874 original size:3 final size:3
Alignment explanation
Indices: 5971866--5971894 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5971856 TCTAATCAAG
5971866 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5971895 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5971899 original size:3 final size:3
Alignment explanation
Indices: 5971893--5971930 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5971883 ATAATAATAA
5971893 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5971931 CAAAGTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5972372 original size:17 final size:17
Alignment explanation
Indices: 5972336--5972373 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5972326 CGCAAAACCC
*
5972336 AAAATAAGATAAAGAGA
1 AAAATAAGATAAAGAAA
5972353 AAAATAAGA-AAACGAAA
1 AAAATAAGATAAA-GAAA
5972370 AAAA
1 AAAA
5972374 AAAATAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAATAAGATAAAGAAA
Found at i:5978151 original size:10 final size:10
Alignment explanation
Indices: 5978132--5978165 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5978122 TACATATATT
5978132 TATATGTATA
1 TATATGTATA
*
5978142 TATGTGTATA
1 TATATGTATA
*
5978152 TATATATATA
1 TATATGTATA
5978162 TATA
1 TATA
5978166 GAGTCACGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
TATATGTATA
Found at i:5981554 original size:22 final size:22
Alignment explanation
Indices: 5981529--5981575 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
5981519 TTCCTCACTT
*
5981529 AATCCATGAACTTCC-ATTACCA
1 AATCCACGAA-TTCCAATTACCA
*
5981551 AATCCACGAATTCCAATTTCCA
1 AATCCACGAATTCCAATTACCA
5981573 AAT
1 AAT
5981576 AATTTCTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (22 bp):
AATCCACGAATTCCAATTACCA
Found at i:5987923 original size:12 final size:12
Alignment explanation
Indices: 5987906--5987952 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
5987896 ATTAACTTTT
5987906 TATATATTTATA
1 TATATATTTATA
5987918 TATATATTAATATA
1 TATATATT--TATA
*
5987932 TATAATATTTTTA
1 TAT-ATATTTATA
5987945 TATATATT
1 TATATATT
5987953 AAGAAGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 13 0.42
13 6 0.19
14 7 0.23
15 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATATATTTATA
Found at i:5988230 original size:22 final size:23
Alignment explanation
Indices: 5988204--5988253 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
5988194 ATATTTTGTA
*
5988204 ATATAAAATAT-TATGAATATA-T
1 ATATAAAAT-TGTATAAATATATT
*
5988226 ATATATAATTGTATAAATATATT
1 ATATAAAATTGTATAAATATATT
5988249 ATATA
1 ATATA
5988254 TACATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATAAAATTGTATAAATATATT
Found at i:5988248 original size:33 final size:31
Alignment explanation
Indices: 5988205--5988272 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
5988195 TATTTTGTAA
*
5988205 TATAAAATATTATGA-ATATATATATATAATT
1 TATAAAATATTAT-ATATACATATATATAATT
*
5988236 GTATAAATATATTATATATACATATATTTAATT
1 -TATAAA-ATATTATATATACATATATATAATT
5988269 TATA
1 TATA
5988273 CTTAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (31 bp):
TATAAAATATTATATATACATATATATAATT
Found at i:5988306 original size:22 final size:22
Alignment explanation
Indices: 5988247--5988309 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
5988237 TATAAATATA
* *
5988247 TTATATATACATA-TATTTAAT
1 TTATACATAAATATTATTTAAT
*
5988268 TTATACTTAAATATTATTATAAT
1 TTATACATAAATATTATT-TAAT
5988291 TTATA-ATAAACT-TTATTTA
1 TTATACATAAA-TATTATTTA
5988310 TATGATCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 12 0.34
22 13 0.37
23 10 0.29
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATACATAAATATTATTTAAT
Found at i:5988334 original size:27 final size:26
Alignment explanation
Indices: 5988294--5988346 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
5988284 TTATAATTTA
*
5988294 TAATAAACTTTATTTATATGATCACATT
1 TAATAAACTGTA-TTA-ATGATCACATT
*
5988322 TAAT-AACTGTATTAATTATCACATT
1 TAATAAACTGTATTAATGATCACATT
5988347 AGATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.43
26 3 0.13
27 6 0.26
28 4 0.17
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (26 bp):
TAATAAACTGTATTAATGATCACATT
Found at i:5988454 original size:28 final size:27
Alignment explanation
Indices: 5988422--5988498 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
5988412 ACATATAAAC
5988422 TATATCTTTAATTTCATATATATATATA
1 TATAT-TTTAATTTCATATATATATATA
** **
5988450 TATATAATAAAGTCATATATTATATATA
1 TATATTTTAATTTCATATA-TATATATA
*
5988478 CATATATTTAATTT-ATATATA
1 TATAT-TTTAATTTCATATATA
5988499 AACATTACTA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
27 12 0.32
28 22 0.58
29 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (27 bp):
TATATTTTAATTTCATATATATATATA
Found at i:5988487 original size:222 final size:220
Alignment explanation
Indices: 5988241--5988879 Score: 865
Period size: 210 Copynumber: 2.9 Consensus size: 220
5988231 TAATTGTATA
* *
5988241 AATATATTATATATACATATATTTAATTTATACTTAAATATTATTATAATTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACTTAAATATTACTATAACTTATAATAAACTTTA
* * * * * *
5988306 TTTATATGATCACATTTAATAACTGTATTAATTATCACATTAGATTTTATAATATATTGTTTATA
66 TTTATATTATTACACTTAATAACTTTATTAGTTATCAC-TTAAATTTTATAATATATTGTTTATA
* *
5988371 ATTAACTATTATTTGTACAAACTTTGATATAAAACATTATAACATATAAACTATATCTTTAATTT
130 ATTAATTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAA-TATATCTTTAATTT
5988436 CATATATATATATATATATAATAAAGT
194 CATATATATATATATATATAATAAAGT
* * * *
5988463 CATATATTATATATACATATATTTAATTTATA-TATAAACATTACTATAACTTATAATAGATTTT
1 AATATATTATATATACATATATTTAATTTATACT-TAAATATTACTATAACTTATAATAAACTTT
*
5988527 ATTTATATTATTACACTTAGTAACTTTATTAGTTATCATCTTAAATTTTATAATATATTGTTTAT
65 ATTTATATTATTACACTTAATAACTTTATTAGTTATCA-CTTAAATTTTATAATATATTGTTTAT
5988592 AATTAATTATTATTTATACAAACTTTGATATAAAACATTAT---A-ATAAATA-AT-TTGT-A-T
129 AATTAATTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAATATATCTT-TAATT
5988649 T-AT-TA-AT-TATATATATAATAAAGT
193 TCATATATATATATATATATAATAAAGT
* * * *
5988673 AATATATTATATATACATATATTTAATTTATACAT-AATCATTACAATAACTAATACTAAACTTT
1 AATATATTATATATACATATATTTAATTTATACTTAAAT-ATTACTATAACTTATAATAAACTTT
* *
5988737 ATTTATATTATTACACTTAATAACTTTATTAGTTATCACTTTAAATTTTATAACATATTATTTAT
65 ATTTATATTATTACACTTAATAACTTTATTAGTTATCAC-TTAAATTTTATAATATATTGTTTAT
* * * ***
5988802 AATTAGTTAGTATTTATACAAACTTTGATATAAAATATTATAACATATAAATTATATCACCAATT
129 AATTAATTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAA-TATATCTTTAATT
5988867 TCATATATATATA
193 TCATATATATATA
5988880 ATTATGAAGG
Statistics
Matches: 366, Mismatches: 32, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
209 3 0.01
210 167 0.46
211 2 0.01
212 2 0.01
213 3 0.01
214 7 0.02
215 5 0.01
216 5 0.01
217 3 0.01
218 7 0.02
219 3 0.01
220 2 0.01
221 3 0.01
222 153 0.42
223 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (220 bp):
AATATATTATATATACATATATTTAATTTATACTTAAATATTACTATAACTTATAATAAACTTTA
TTTATATTATTACACTTAATAACTTTATTAGTTATCACTTAAATTTTATAATATATTGTTTATAA
TTAATTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAATATATCTTTAATTTCA
TATATATATATATATATAATAAAGT
Found at i:5989301 original size:28 final size:30
Alignment explanation
Indices: 5989270--5989343 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 30
5989260 AATTTTTATT
*
5989270 TTAAATTAATTTTTAT-TTTTTATTAT-AA
1 TTAAATAAATTTTTATATTTTTATTATAAA
*
5989298 TT-AATCAAA-TTTTATATTTTTATTTTAAA
1 TTAAAT-AAATTTTTATATTTTTATTATAAA
*
5989327 TAAAATAAATTTTTATA
1 TTAAATAAATTTTTATA
5989344 ATTAACGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 9 0.24
28 13 0.34
29 6 0.16
30 10 0.26
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (30 bp):
TTAAATAAATTTTTATATTTTTATTATAAA
Found at i:5989336 original size:29 final size:27
Alignment explanation
Indices: 5989261--5989339 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 27
5989251 TATTTATAAA
*
5989261 ATTTTTATTTTAAAT--TAATTTTTAT
1 ATTTTTATTTTAAATAATAAATTTTAT
* *
5989286 -TTTTTATTATAATTAATCAAATTTTAT
1 ATTTTTATTTTAAATAAT-AAATTTTAT
5989313 ATTTTTATTTTAAATAAAATAAATTTT
1 ATTTTTATTTTAAAT--AATAAATTTT
5989340 TATAATTAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
24 12 0.28
26 1 0.02
27 8 0.19
28 12 0.28
29 7 0.16
30 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTTTATTTTAAATAATAAATTTTAT
Found at i:5990559 original size:2 final size:2
Alignment explanation
Indices: 5990552--5990588 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5990542 TCCAAAATAC
5990552 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5990589 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5990593 original size:2 final size:2
Alignment explanation
Indices: 5990588--5990624 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5990578 ATATATATAT
5990588 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5990625 AAAGGTCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5991119 original size:106 final size:108
Alignment explanation
Indices: 5990955--5991156 Score: 275
Period size: 106 Copynumber: 1.9 Consensus size: 108
5990945 TTAAAAGGGT
* * * *
5990955 GTTGGGTTGGGTTTCCAGATACTAGGCTCCCTTTGGGCTAAGGTCTTTACGCTTGATGAGTTTGT
1 GTTGGGTTGGGTTTCCAGATACTAGGCTCCCTTTGGGCTAAGGTCATCACGCTCGATGAGCTTGT
5991020 TGAGTTTTCATA-CTTGA-TAGGCTTGCTTTCAAAGGGTGTTGG
66 TGAGTTTTCATAGCTTGATTA-GCTTGCTTTCAAAGGGTGTTGG
* * * * *
5991062 GTTGGG-TGGGTTTGCAGATACTAGGCTGCCTTTGGGTTGAGGTCATCACTCTCGATGAGCTTGT
1 GTTGGGTTGGGTTTCCAGATACTAGGCTCCCTTTGGGCTAAGGTCATCACGCTCGATGAGCTTGT
* *
5991126 TGAGTTTTTATAGTTTGATTAGCTTGCTTTC
66 TGAGTTTTCATAGCTTGATTAGCTTGCTTTC
5991157 GCTTTGTTGG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 60 0.73
107 20 0.24
108 2 0.02
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.40
Consensus pattern (108 bp):
GTTGGGTTGGGTTTCCAGATACTAGGCTCCCTTTGGGCTAAGGTCATCACGCTCGATGAGCTTGT
TGAGTTTTCATAGCTTGATTAGCTTGCTTTCAAAGGGTGTTGG
Found at i:5995279 original size:16 final size:16
Alignment explanation
Indices: 5995258--5995290 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5995248 AAATTTATCT
5995258 GCAAAATGCTTGGCCA
1 GCAAAATGCTTGGCCA
5995274 GCAAAATGCTTGGCCA
1 GCAAAATGCTTGGCCA
5995290 G
1 G
5995291 AATCAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (16 bp):
GCAAAATGCTTGGCCA
Found at i:5998790 original size:5 final size:5
Alignment explanation
Indices: 5998780--5998806 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5998770 TTTATAGGTT
5998780 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
5998807 ACTTTTCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:6000167 original size:19 final size:18
Alignment explanation
Indices: 6000119--6000167 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
6000109 CAAATTGTCA
*
6000119 AAAATAATAATAATATTTT
1 AAAATAATAA-ATTATTTT
6000138 AAAA-AATAAATTATTTT
1 AAAATAATAAATTATTTT
6000155 AAAATATATAAAT
1 AAAATA-ATAAAT
6000168 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 11 0.41
18 6 0.22
19 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATAATAAATTATTTT
Found at i:6020278 original size:12 final size:12
Alignment explanation
Indices: 6020261--6020285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6020251 GATGAAGAAG
6020261 TTATTTATGCTA
1 TTATTTATGCTA
6020273 TTATTTATGCTA
1 TTATTTATGCTA
6020285 T
1 T
6020286 AGAAAAGGAA
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTATTTATGCTA
Found at i:6021027 original size:59 final size:59
Alignment explanation
Indices: 6020961--6021072 Score: 161
Period size: 59 Copynumber: 1.9 Consensus size: 59
6020951 CTAATAAAAA
* * * * * *
6020961 AATTATAAATTCGTCTATTCTTTGAAGTGAATGCAACATTATATAATAATTATTGGCAT
1 AATTATAAATCCATCCATTCCTTGAAGTGAATACAACATCATATAATAATTATTGGCAT
*
6021020 AATTATAAATCCATCCATTCCTTGAAGTGAATACAACATCATTTAATAATTAT
1 AATTATAAATCCATCCATTCCTTGAAGTGAATACAACATCATATAATAATTAT
6021073 GATGGCCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (59 bp):
AATTATAAATCCATCCATTCCTTGAAGTGAATACAACATCATATAATAATTATTGGCAT
Found at i:6021144 original size:26 final size:26
Alignment explanation
Indices: 6021114--6021211 Score: 76
Period size: 26 Copynumber: 3.8 Consensus size: 26
6021104 TTAATTATAC
6021114 TTTTACCACTAGAAGTGGATGGATAA
1 TTTTACCACTAGAAGTGGATGGATAA
** * ** *
6021140 TTTTATTATTAGAA-TCTAAT-AATAA
1 TTTTACCACTAGAAGT-GGATGGATAA
* *
6021165 TTTTACCACTAGAAATGGATAGATAA
1 TTTTACCACTAGAAGTGGATGGATAA
*
6021191 TTTTACCA-TCAAAAGTGGATG
1 TTTTACCACT-AGAAGTGGATG
6021212 AATGCCTTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
25 19 0.36
26 34 0.64
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (26 bp):
TTTTACCACTAGAAGTGGATGGATAA
Found at i:6023802 original size:15 final size:15
Alignment explanation
Indices: 6023782--6023815 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
6023772 ATGCTCAACA
*
6023782 AATATTCAGTCACGT
1 AATATTCAGTCACAT
6023797 AATATTCAGTCACAT
1 AATATTCAGTCACAT
6023812 AATA
1 AATA
6023816 CCAAATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (15 bp):
AATATTCAGTCACAT
Found at i:6024102 original size:18 final size:18
Alignment explanation
Indices: 6024079--6024121 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
6024069 AGAAAGTTAG
* *
6024079 ATGGCAATATAGACCTCA
1 ATGGCAATAGAGACCTAA
* *
6024097 ATGGCATTAGAGAGCTAA
1 ATGGCAATAGAGACCTAA
6024115 ATGGCAA
1 ATGGCAA
6024122 GATATTTACT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (18 bp):
ATGGCAATAGAGACCTAA
Found at i:6027122 original size:17 final size:19
Alignment explanation
Indices: 6027097--6027134 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
6027087 AAATTTTTAT
*
6027097 ATAATAATT-TTTAAA-AA
1 ATAAAAATTATTTAAATAA
6027114 ATAAAAATTATTTAAATAA
1 ATAAAAATTATTTAAATAA
6027133 AT
1 AT
6027135 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAAAATTATTTAAATAA
Found at i:6027160 original size:27 final size:29
Alignment explanation
Indices: 6027123--6027176 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
6027113 AATAAAAATT
6027123 ATTTAAATAAA-TTT-TTATTTTTATTAC
1 ATTTAAATAAATTTTATTATTTTTATTAC
*
6027150 ATTTAATTAAATTTTATTATTTTTATT
1 ATTTAAATAAATTTTATTATTTTTATT
6027177 TTAAGTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
28 3 0.12
29 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTTAAATAAATTTTATTATTTTTATTAC
Found at i:6033856 original size:39 final size:40
Alignment explanation
Indices: 6033803--6033883 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
6033793 TCTTAAATAT
* * *
6033803 ATTTTTAATGTCATATATTTTATTTTTA-TTTTTAATAAA
1 ATTTTTAATATCATATATTTTATTTTAATTTTTTAAAAAA
*
6033842 ATTTTTTATATCATATATTTTATTTTAATTTTTTAAAAAA
1 ATTTTTAATATCATATATTTTATTTTAATTTTTTAAAAAA
6033882 AT
1 AT
6033884 AATATAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 25 0.68
40 12 0.32
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (40 bp):
ATTTTTAATATCATATATTTTATTTTAATTTTTTAAAAAA
Found at i:6038190 original size:51 final size:50
Alignment explanation
Indices: 6038118--6038536 Score: 384
Period size: 51 Copynumber: 8.2 Consensus size: 50
6038108 GGCAGTCTGC
6038118 CTGGC-TCTCTGTCGGGCTGGCTCGCCTAGGGGCTGGTGCTGTGCGCCCTTG
1 CTGGCATC-CTGTCGGGCTGGCTCGCCTAGGGGCT-GTGCTGTGCGCCCTTG
* *
6038169 CTAGCATCCTGTCGGGTTGGCTCGCCTAGGGGCTGGTGCTGTGCGCCCTTG
1 CTGGCATCCTGTCGGGCTGGCTCGCCTAGGGGCT-GTGCTGTGCGCCCTTG
* * * *
6038220 CTAGCACCCTGCCGGGCTGGCTCGCCTAGGGGTTGGTGCTGTGCGCCCTTG
1 CTGGCATCCTGTCGGGCTGGCTCGCCTAGGGGCT-GTGCTGTGCGCCCTTG
* * * * *
6038271 CTAGCACCCTGCCGGGCTGGCTCGCCCAGGGGGCAGTGCTGTGCGCCCTTG
1 CTGGCATCCTGTCGGGCTGGCTCGCCTA-GGGGCTGTGCTGTGCGCCCTTG
* * * * *
6038322 CTGGTA-CCT-TGCAGGGCTAGCTCGCTCAAAGGGCTGTGCTGTGCGCCCCTG
1 CTGGCATCCTGT-C-GGGCTGGCTCGC-CTAGGGGCTGTGCTGTGCGCCCTTG
* * * * *
6038373 CTGGCATCTTGTCGGGCTGGCTCTCCCAGGGGCCTGTGCTATGCGCCCCTG
1 CTGGCATCCTGTCGGGCTGGCTCGCCTAGGGG-CTGTGCTGTGCGCCCTTG
* * * *
6038424 CTGGTA-CCTTGCCAGGCTAGCTCG-CTCAGGGGGCTGTGCTGTGCGTCCCTT-
1 CTGGCATCC-TGTCGGGCTGGCTCGCCT-A-GGGGCTGTGCTGTGCG-CCCTTG
* * * *
6038475 CTGGCATTCTGTCGGGCTAGCTCGCCCAGGGGCCTGTGCTGTGTGACCC-TG
1 CTGGCATCCTGTCGGGCTGGCTCGCCTAGGGG-CTGTGCTGTGCG-CCCTTG
*
6038526 CTGGCACCCTG
1 CTGGCATCCTG
6038537 CACTTGCCTT
Statistics
Matches: 310, Mismatches: 42, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
50 16 0.05
51 272 0.88
52 21 0.07
53 1 0.00
ACGTcount: A:0.07, C:0.33, G:0.36, T:0.25
Consensus pattern (50 bp):
CTGGCATCCTGTCGGGCTGGCTCGCCTAGGGGCTGTGCTGTGCGCCCTTG
Found at i:6038251 original size:102 final size:101
Alignment explanation
Indices: 6038130--6038537 Score: 464
Period size: 102 Copynumber: 4.0 Consensus size: 101
6038120 GGCTCTCTGT
* *
6038130 CGGGCTGGCTCGCCTAGGGGCTGGTGCTGTGCGCCCTTGCTAGCATCCTGTCGGGTTGGCTCGCC
1 CGGGCTAGCTCGCCTAGGGGCT-GTGCTGTGCGCCCTTGCTAGCATCCTGTCGGGCTGGCTCGCC
* *
6038195 TAGGGG-CTGGTGCTGTGCGCCCTTGCTAGCACCCTGC
65 CAGGGGCCT-GTGCTGTGCGCCCTTGCTGGCACCCTGC
* * * *
6038232 CGGGCTGGCTCGCCTAGGGGTTGGTGCTGTGCGCCCTTGCTAGCACCCTGCCGGGCTGGCTCGCC
1 CGGGCTAGCTCGCCTAGGGGCT-GTGCTGTGCGCCCTTGCTAGCATCCTGTCGGGCTGGCTCGCC
* * * *
6038297 CAGGGGGCAGTGCTGTGCGCCCTTGCTGGTACCTTGC
65 CAGGGGCCTGTGCTGTGCGCCCTTGCTGGCACCCTGC
* * * * * * *
6038334 AGGGCTAGCTCGCTCAAAGGGCTGTGCTGTGCGCCCCTGCTGGCATCTTGTCGGGCTGGCTCTCC
1 CGGGCTAGCTCGC-CTAGGGGCTGTGCTGTGCGCCCTTGCTAGCATCCTGTCGGGCTGGCTCGCC
* * * *
6038399 CAGGGGCCTGTGCTATGCGCCCCTGCTGGTACCTTGC
65 CAGGGGCCTGTGCTGTGCGCCCTTGCTGGCACCCTGC
* * * *
6038436 CAGGCTAGCTCG-CTCAGGGGGCTGTGCTGTGCGTCCCTT-CTGGCATTCTGTCGGGCTAGCTCG
1 CGGGCTAGCTCGCCT-A-GGGGCTGTGCTGTGCG-CCCTTGCTAGCATCCTGTCGGGCTGGCTCG
*
6038499 CCCAGGGGCCTGTGCTGTGTGACCC-TGCTGGCACCCTGC
63 CCCAGGGGCCTGTGCTGTGCG-CCCTTGCTGGCACCCTGC
6038538 ACTTGCCTTA
Statistics
Matches: 263, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
100 1 0.00
101 1 0.00
102 247 0.94
103 14 0.05
ACGTcount: A:0.07, C:0.33, G:0.36, T:0.24
Consensus pattern (101 bp):
CGGGCTAGCTCGCCTAGGGGCTGTGCTGTGCGCCCTTGCTAGCATCCTGTCGGGCTGGCTCGCCC
AGGGGCCTGTGCTGTGCGCCCTTGCTGGCACCCTGC
Found at i:6038412 original size:153 final size:152
Alignment explanation
Indices: 6038130--6038537 Score: 432
Period size: 153 Copynumber: 2.7 Consensus size: 152
6038120 GGCTCTCTGT
* * * * *
6038130 CGGGCTGGCTCGCCTA-GGGGCTGGTGCTGTGCGCCCTTGCTAGCATCC-TGTCGGGTTGGCTCG
1 CGGGCTGGCTCGCCCAGGGGGC-AGTGCTGTGCGCCCTTGCTGGCA-CCTTGTCGGGCTAGCTCG
* * * * *
6038193 CCTAGGGGCTGGTGCTGTGCGCCCTTGCTAGCACCCTGCCGGGCTGGCTCGCCTAGGGGTTGGTG
64 CCAAGGGGCT-GTGCTGTGCGCCCCTGCTGGCACCCTGCCGGGCTGGCTCGCCCAGGGGCTGGTG
* *
6038258 CTGTGCGCCCTTGCTAGCACCCTGC
128 CTATGCGCCCCTGCTAGCACCCTGC
*
6038283 CGGGCTGGCTCGCCCAGGGGGCAGTGCTGTGCGCCCTTGCTGGTACCTTG-CAGGGCTAGCTCGC
1 CGGGCTGGCTCGCCCAGGGGGCAGTGCTGTGCGCCCTTGCTGGCACCTTGTC-GGGCTAGCTCGC
* * * * *
6038347 TCAAAGGGCTGTGCTGTGCGCCCCTGCTGGCATCTTGTCGGGCTGGCTCTCCCAGGGGCCT-GTG
65 -CAAGGGGCTGTGCTGTGCGCCCCTGCTGGCACCCTGCCGGGCTGGCTCGCCCAGGGG-CTGGTG
* * *
6038411 CTATGCGCCCCTGCTGGTACCTTGC
128 CTATGCGCCCCTGCTAGCACCCTGC
* * * * *
6038436 CAGGCTAGCTCGCTCAGGGGGCTGTGCTGTGCGTCCCTT-CTGGCA-TTCTGTCGGGCTAGCTCG
1 CGGGCTGGCTCGCCCAGGGGGCAGTGCTGTGCG-CCCTTGCTGGCACCT-TGTCGGGCTAGCTCG
* * *
6038499 CCCAGGGGCCTGTGCTGTGTGACCCTGCTGGCACCCTGC
64 CCAAGGGG-CTGTGCTGTGCGCCCCTGCTGGCACCCTGC
6038538 ACTTGCCTTA
Statistics
Matches: 212, Mismatches: 34, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
152 9 0.04
153 184 0.87
154 19 0.09
ACGTcount: A:0.07, C:0.33, G:0.36, T:0.24
Consensus pattern (152 bp):
CGGGCTGGCTCGCCCAGGGGGCAGTGCTGTGCGCCCTTGCTGGCACCTTGTCGGGCTAGCTCGCC
AAGGGGCTGTGCTGTGCGCCCCTGCTGGCACCCTGCCGGGCTGGCTCGCCCAGGGGCTGGTGCTA
TGCGCCCCTGCTAGCACCCTGC
Found at i:6048686 original size:17 final size:16
Alignment explanation
Indices: 6048658--6048689 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
6048648 CACATAATGA
6048658 TTAAATATATAAATAG
1 TTAAATATATAAATAG
6048674 TTAAATAATATAAATA
1 TTAAAT-ATATAAATA
6048690 AAAAGAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TTAAATATATAAATAG
Found at i:6050005 original size:16 final size:15
Alignment explanation
Indices: 6049952--6049994 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
6049942 AAAACCGAAC
6049952 AATTTTTATTTTTAA
1 AATTTTTATTTTTAA
6049967 AATTTTTATTTTTAA
1 AATTTTTATTTTTAA
6049982 AATTTTTATTTTT
1 AATTTTTATTTTT
6049995 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTTTATTTTTAA
Found at i:6053256 original size:17 final size:17
Alignment explanation
Indices: 6053226--6053259 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6053216 TATTATTTTA
6053226 TTTTAAATTAAATAAAT
1 TTTTAAATTAAATAAAT
6053243 TTTTATAATT-AATAAAT
1 TTTTA-AATTAAATAAAT
6053260 GATAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAAATTAAATAAAT
Found at i:6076351 original size:84 final size:82
Alignment explanation
Indices: 6076211--6076372 Score: 245
Period size: 84 Copynumber: 2.0 Consensus size: 82
6076201 ATATGTAGAC
* * *
6076211 TATTTATGGCATATCCCTTCCGACTGCTAATTTGACAAGGCTAGATATGTCAAGAAATCCTGGCA
1 TATTTATGACATATCCCTTCCGACAGCTAATTCGACAAGGCTAGATATGTCAAGAAATCCTGGCA
6076276 ACCTAGTTGAGCTTCGG
66 ACCTAGTTGAGCTTCGG
* *
6076293 TATTTATGACATAATCCCTTCCGGCAGCTAATTCGGCAAAGGCTAGATATGT-ACAGAAATCCTG
1 TATTTATGACAT-ATCCCTTCCGACAGCTAATTCGAC-AAGGCTAGATATGTCA-AGAAATCCTG
6076357 GCAACCTAGTTGAGCT
63 GCAACCTAGTTGAGCT
6076373 ACAGCATCTG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
82 11 0.15
83 21 0.29
84 40 0.56
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (82 bp):
TATTTATGACATATCCCTTCCGACAGCTAATTCGACAAGGCTAGATATGTCAAGAAATCCTGGCA
ACCTAGTTGAGCTTCGG
Found at i:6084800 original size:20 final size:20
Alignment explanation
Indices: 6084752--6084801 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
6084742 TAAAAATCTG
*
6084752 AAATTATTTTTTAAAAAAAT
1 AAATTAATTTTTAAAAAAAT
* *
6084772 AAATAAATTTTTATAAATAAT
1 AAATTAATTTTTA-AAAAAAT
6084793 -AATTAATTT
1 AAATTAATTT
6084802 AATTAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTAATTTTTAAAAAAAT
Found at i:6087237 original size:15 final size:15
Alignment explanation
Indices: 6087195--6087237 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
6087185 TTATATAATT
*
6087195 TAAATATTAATATTCA
1 TAAA-ATTAGTATTCA
*
6087211 TAAAATTTGTATTCA
1 TAAAATTAGTATTCA
*
6087226 TAAACTTAGTAT
1 TAAAATTAGTAT
6087238 AAAAATGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (15 bp):
TAAAATTAGTATTCA
Found at i:6100030 original size:61 final size:63
Alignment explanation
Indices: 6099946--6100102 Score: 201
Period size: 61 Copynumber: 2.4 Consensus size: 63
6099936 TTAATATATA
6099946 AAATATTAATATTTTATTTATAATTTAAATACTATTATGATTATTTA-TGTTATTTTATTTTT
1 AAATATTAATATTTTATTTATAATTTAAATACTATTATGATTATTTACTGTTATTTTATTTTT
* ** *
6100008 AAATATTAGT-TTTTATTTATAATTTAAATGTTATTATGATTATTTACTTTTATTTTATTTTATT
1 AAATATTAATATTTTATTTATAATTTAAATACTATTATGATTATTTAC-----TGTTATTTTATT
6100072 ATTT
61 -TTT
*
6100076 AAAGATTAATATTTTATTTATAATTTA
1 AAATATTAATATTTTATTTATAATTTA
6100103 GGGTTATTGT
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
61 34 0.42
62 9 0.11
67 11 0.14
68 11 0.14
69 16 0.20
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (63 bp):
AAATATTAATATTTTATTTATAATTTAAATACTATTATGATTATTTACTGTTATTTTATTTTT
Found at i:6100120 original size:68 final size:66
Alignment explanation
Indices: 6099950--6100130 Score: 194
Period size: 68 Copynumber: 2.8 Consensus size: 66
6099940 TATATAAAAT
*** *
6099950 ATTAATATTTTATTTATAATTTAAATACTATTATG---A-TTA-TTTATGTTATTTTATTTTTAA
1 ATTAAT-TTTTATTTATAATTTAAAGGTTATTATGAATATTTATTTTATTTTATTTTATTTTTAA
*
6100010 AT
65 AG
* * *
6100012 ATTAGTTTTTATTTATAATTTAAATGTTATTATGATTATTTACTTTTATTTTATTTTATTATTTA
1 ATTAATTTTTATTTATAATTTAAAGGTTATTATGAATATTTA-TTTTATTTTATTTTATT-TTTA
6100077 AAG
64 AAG
* *
6100080 ATTAATATTTTATTTATAATTT-AGGGTTATTGTGAATATTTATTTTATTTT
1 ATTAAT-TTTTATTTATAATTTAAAGGTTATTATGAATATTTATTTTATTTT
6100131 TAAATATTAA
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
61 26 0.26
62 5 0.05
64 1 0.01
65 3 0.03
67 24 0.24
68 27 0.27
69 15 0.15
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (66 bp):
ATTAATTTTTATTTATAATTTAAAGGTTATTATGAATATTTATTTTATTTTATTTTATTTTTAAA
G
Found at i:6100351 original size:154 final size:154
Alignment explanation
Indices: 6100118--6100550 Score: 712
Period size: 154 Copynumber: 2.8 Consensus size: 154
6100108 ATTGTGAATA
* * * * *
6100118 TTTATTTTATT-TTTAAATATTAA-AAGTTTATAATGTATTTAAAATATTAATAATAGATA-ATT
1 TTTATTTTATTATTTAAATATTAATAA-TTTACAATTTATTTAAAATATTATTGATTGA-ACATT
* * *
6100180 TAAATATCAATACTTTATTTATATTTTAATCTTTAATACTTTAAAATATTCATATTTTATTTATA
64 TTAATATTAATATTTTATTTATATTTTAATCTTTAATACTTTAAAATATTCATATTTTATTTATA
6100245 ATTTAAATGTTATTATGAATATTTCT
129 ATTTAAATGTTATTATGAATATTTCT
6100271 TTTATTTTATTATTTAAATATTAATAATTTACAATTTATTTAAAATATTATTGATTGAACATTTT
1 TTTATTTTATTATTTAAATATTAATAATTTACAATTTATTTAAAATATTATTGATTGAACATTTT
6100336 AATATTAATATTTTATTTATATTTTAATCTTTAATACTTTAAAATATTCATATTTTATTTATAAT
66 AATATTAATATTTTATTTATATTTTAATCTTTAATACTTTAAAATATTCATATTTTATTTATAAT
6100401 TTAAATGTTATTATGAATATTTCT
131 TTAAATGTTATTATGAATATTTCT
6100425 TTTATTTTATTATTTAAATATTAATAATTTACAATTTATTTAAAATATTATTGATTGAACATTTT
1 TTTATTTTATTATTTAAATATTAATAATTTACAATTTATTTAAAATATTATTGATTGAACATTTT
* * *
6100490 AATATTAATATTTTATTTATATTTTAAT-TATTAATATTTTAAAATATTAATATTTCATTTA
66 AATATTAATATTTTATTTATATTTTAATCT-TTAATACTTTAAAATATTCATATTTTATTTA
6100551 CAAATATTAA
Statistics
Matches: 265, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
153 13 0.05
154 250 0.94
155 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (154 bp):
TTTATTTTATTATTTAAATATTAATAATTTACAATTTATTTAAAATATTATTGATTGAACATTTT
AATATTAATATTTTATTTATATTTTAATCTTTAATACTTTAAAATATTCATATTTTATTTATAAT
TTAAATGTTATTATGAATATTTCT
Found at i:6100472 original size:52 final size:51
Alignment explanation
Indices: 6100237--6100473 Score: 132
Period size: 52 Copynumber: 4.6 Consensus size: 51
6100227 ATTCATATTT
* *
6100237 TATTTATAATTTAAATGTTA-TTATGAATATTTCTTTTATTTTATTATTTAAA
1 TATTAATAATTTAAAT-TTATTTA-AAATATTTCTTTTATTTTATTATTTAAA
* * * ** *
6100289 TATTAATAATTTACAATTTATTTAAAATA-TT-ATTGA-TTGAACATTTTAA
1 TATTAATAATTTA-AATTTATTTAAAATATTTCTTTTATTTTATTATTTAAA
* ** * * *** *
6100338 TATTAAT-ATTT-TATTTATATTTTAATCTTTAATACTTTAAAATATTCATATT--T
1 TATTAATAATTTAAATTTAT-TTAAAATATTT-CT--TTTATTTTATT-AT-TTAAA
* *
6100391 TATTTATAATTTAAATGTTA-TTATGAATATTTCTTTTATTTTATTATTTAAA
1 TATTAATAATTTAAAT-TTATTTA-AAATATTTCTTTTATTTTATTATTTAAA
6100443 TATTAATAATTTACAATTTATTTAAAATATT
1 TATTAATAATTTA-AATTTATTTAAAATATT
6100474 ATTGATTGAA
Statistics
Matches: 134, Mismatches: 32, Indels: 38
0.66 0.16 0.19
Matches are distributed among these distances:
46 6 0.04
47 5 0.04
48 6 0.04
49 16 0.12
50 5 0.04
51 4 0.03
52 51 0.38
53 19 0.14
54 9 0.07
55 10 0.07
56 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (51 bp):
TATTAATAATTTAAATTTATTTAAAATATTTCTTTTATTTTATTATTTAAA
Found at i:6100508 original size:42 final size:41
Alignment explanation
Indices: 6100459--6100559 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 41
6100449 TAATTTACAA
6100459 TTTATTTAAAATATTATTGATTGAACATTTT-AATATTAATAT
1 TTTATTTAAAATATTATT-ATT-AACATTTTAAATATTAATAT
* * *
6100501 TTTATTT-ATATTTTAATTATTAATATTTTAAAATATTAATAT
1 TTTATTTAAAATATT-ATTATTAACATTTT-AAATATTAATAT
*
6100543 TTCATTTACAAATATTA
1 TTTATTTA-AAATATTA
6100560 ATATGGGTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
40 7 0.15
41 8 0.17
42 27 0.56
43 1 0.02
44 5 0.10
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (41 bp):
TTTATTTAAAATATTATTATTAACATTTTAAATATTAATAT
Found at i:6100539 original size:16 final size:15
Alignment explanation
Indices: 6100485--6100544 Score: 67
Period size: 16 Copynumber: 4.3 Consensus size: 15
6100475 TTGATTGAAC
6100485 ATTTT-AATATTAAT
1 ATTTTAAATATTAAT
6100499 ATTTT--AT-TT-AT
1 ATTTTAAATATTAAT
*
6100510 ATTTTAATTATTAAT
1 ATTTTAAATATTAAT
6100525 ATTTTAAAATATTAAT
1 ATTTT-AAATATTAAT
6100541 ATTT
1 ATTT
6100545 CATTTACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 7 0.18
12 2 0.05
13 3 0.08
14 7 0.18
15 7 0.18
16 13 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTAAATATTAAT
Found at i:6110302 original size:17 final size:17
Alignment explanation
Indices: 6110280--6110328 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
6110270 TAATATTAGT
6110280 TACTTAAAATTAGATTA
1 TACTTAAAATTAGATTA
**
6110297 TACTTAGGATTAG--T-
1 TACTTAAAATTAGATTA
6110311 TACTTAAAATTAGATTA
1 TACTTAAAATTAGATTA
6110328 T
1 T
6110329 GATTACGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 1 0.04
17 12 0.48
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (17 bp):
TACTTAAAATTAGATTA
Found at i:6110316 original size:14 final size:14
Alignment explanation
Indices: 6110274--6110323 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
6110264 CTATAATAAT
6110274 ATTAGTTACTTAAA
1 ATTAGTTACTTAAA
**
6110288 ATTAGATTATACTTAGG
1 ATTAG--T-TACTTAAA
6110305 ATTAGTTACTTAAA
1 ATTAGTTACTTAAA
6110319 ATTAG
1 ATTAG
6110324 ATTATGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 16 0.55
15 1 0.03
16 1 0.03
17 11 0.38
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (14 bp):
ATTAGTTACTTAAA
Found at i:6110339 original size:31 final size:31
Alignment explanation
Indices: 6110274--6110339 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
6110264 CTATAATAAT
*
6110274 ATTAGTTACTTAAAATTAGATTATACTTAGG
1 ATTAGTTACTTAAAATTAGATTATACTTACG
6110305 ATTAGTTACTTAAAATTAGATTATGA-TTACG
1 ATTAGTTACTTAAAATTAGATTAT-ACTTACG
6110336 ATTA
1 ATTA
6110340 AGCTTATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (31 bp):
ATTAGTTACTTAAAATTAGATTATACTTACG
Found at i:6110351 original size:2 final size:2
Alignment explanation
Indices: 6110344--6110379 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6110334 CGATTAAGCT
6110344 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
6110380 CCTCATTCGC
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:6116911 original size:87 final size:88
Alignment explanation
Indices: 6116749--6116916 Score: 250
Period size: 87 Copynumber: 1.9 Consensus size: 88
6116739 ACCTAACATC
* * * **
6116749 TTCTATCATCCTTGAGAACTCAGAATAAGATTTTTCCTACTGCTAATCCCAGATTACTAATTCTG
1 TTCTATCATCCTTGAGAACTCAGAATAAGAGTTTTCCTACTGCCAATCCAAGATTACTAAGCCTG
6116814 GCACATTAAGCAATGGAAATTGG
66 GCACATTAAGCAATGGAAATTGG
* *
6116837 TTCTATCATCCTTGAGCACTCAGAATAAGACGTTTT-C-ACTGCCAATCCAAGATTTCTAAGCCT
1 TTCTATCATCCTTGAGAACTCAGAATAAGA-GTTTTCCTACTGCCAATCCAAGATTACTAAGCCT
6116900 GGCACATTAAGCAATGG
65 GGCACATTAAGCAATGG
6116917 TACGTTTCAC
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
87 38 0.53
88 30 0.42
89 4 0.06
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (88 bp):
TTCTATCATCCTTGAGAACTCAGAATAAGAGTTTTCCTACTGCCAATCCAAGATTACTAAGCCTG
GCACATTAAGCAATGGAAATTGG
Found at i:6120559 original size:9 final size:9
Alignment explanation
Indices: 6120545--6120569 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6120535 CATATCCTTA
6120545 ACCAAAGGG
1 ACCAAAGGG
6120554 ACCAAAGGG
1 ACCAAAGGG
6120563 ACCAAAG
1 ACCAAAG
6120570 CTACTGAAAA
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:0.48, C:0.24, G:0.28, T:0.00
Consensus pattern (9 bp):
ACCAAAGGG
Found at i:6122952 original size:30 final size:30
Alignment explanation
Indices: 6122918--6122985 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
6122908 TACATTTGAT
6122918 TAAATTCTTATAGTTTT-ATTTTGAATCAAA
1 TAAATTCTTATA-TTTTGATTTTGAATCAAA
* *
6122948 TAAATTTTTATATTTTGATTTTGAGTCAAA
1 TAAATTCTTATATTTTGATTTTGAATCAAA
*
6122978 -AAAGTCTT
1 TAAATTCTT
6122986 TAGGGTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (30 bp):
TAAATTCTTATATTTTGATTTTGAATCAAA
Found at i:6126918 original size:35 final size:35
Alignment explanation
Indices: 6126892--6127067 Score: 194
Period size: 35 Copynumber: 5.0 Consensus size: 35
6126882 CTTAATTGTT
*
6126892 TAATTTAATCAATTAGGCTCAATAACTTAATTAAA
1 TAATTTAATTAATTAGGCTCAATAACTTAATTAAA
*** *
6126927 TAATTTAATTAATTAAATTCAATAATTTAATTAAA
1 TAATTTAATTAATTAGGCTCAATAACTTAATTAAA
* * *
6126962 CAATTTTAATCAATTAGG-TCTAATGACTTAATTAAA
1 TAA-TTTAATTAATTAGGCTC-AATAACTTAATTAAA
*
6126998 TAAATTTAATTAATTAGGC-CAAATGACTTAATTAAA
1 T-AATTTAATTAATTAGGCTC-AATAACTTAATTAAA
* * *
6127034 TAATTTAATTAATTAAGCTTAATAATTTAATTAA
1 TAATTTAATTAATTAGGCTCAATAACTTAATTAA
6127068 TTAGGCATAA
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
35 62 0.53
36 54 0.46
37 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (35 bp):
TAATTTAATTAATTAGGCTCAATAACTTAATTAAA
Found at i:6142515 original size:2 final size:2
Alignment explanation
Indices: 6142508--6142546 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6142498 TCACCCAAGC
6142508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6142547 CACGTAACAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6146089 original size:83 final size:83
Alignment explanation
Indices: 6145989--6146221 Score: 439
Period size: 83 Copynumber: 2.8 Consensus size: 83
6145979 CTAAAAGCAA
*
6145989 ATAAAAGATATGCTTTCACTGATTGGAGACTACAAGTTCAACTTTCATCTAAAAGTAATTGCTCT
1 ATAAAAGATATGCTTTCACTGATTGGAGACTACAAGTTCAACTTTCATCTAAAAGTAATTGCTAT
6146054 ATTGACACTAAAAAGAGC
66 ATTGACACTAAAAAGAGC
*
6146072 ATAAAATATATGCTTTCACTGATTGGAGACTACAAGTTCAACTTTCATCTAAAAGTAATTGCTAT
1 ATAAAAGATATGCTTTCACTGATTGGAGACTACAAGTTCAACTTTCATCTAAAAGTAATTGCTAT
6146137 ATTGACACTAAAAAGAGC
66 ATTGACACTAAAAAGAGC
*
6146155 ATAAAAGATATGCTTTCACTGATTGGAGACTACAAGTTCAACTTTCACCTAAAAGTAATTGCTAT
1 ATAAAAGATATGCTTTCACTGATTGGAGACTACAAGTTCAACTTTCATCTAAAAGTAATTGCTAT
6146220 AT
66 AT
6146222 GAACGCTATA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 146 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (83 bp):
ATAAAAGATATGCTTTCACTGATTGGAGACTACAAGTTCAACTTTCATCTAAAAGTAATTGCTAT
ATTGACACTAAAAAGAGC
Found at i:6159436 original size:17 final size:15
Alignment explanation
Indices: 6159416--6159451 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
6159406 TTTATTTTTT
6159416 TATTTATATTATTTAA
1 TATTTATA-TATTTAA
6159432 CTATTTATATATTTAA
1 -TATTTATATATTTAA
6159448 TATT
1 TATT
6159452 ATGTGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 7 0.37
17 8 0.42
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATATATTTAA
Found at i:6159498 original size:15 final size:14
Alignment explanation
Indices: 6159472--6159521 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
6159462 CTCTGTATCT
*
6159472 TATTTAATCATTTA
1 TATTTTATCATTTA
6159486 TATTTTATACA-TTA
1 TATTTTAT-CATTTA
6159500 TAGTTTTAT-ATTTA
1 TA-TTTTATCATTTA
6159514 GTATTTTA
1 -TATTTTA
6159522 AGCTTAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 1 0.03
14 20 0.65
15 10 0.32
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (14 bp):
TATTTTATCATTTA
Found at i:6172379 original size:33 final size:34
Alignment explanation
Indices: 6172318--6172386 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
6172308 TAAAAAAATT
* *
6172318 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAATATAAAATATAAAAAATTATAATAA
* *
6172352 AAAATAAAA-ATAAAATATATAAGATTATAATAA
1 AAAATAAAATATAAAATATAAAAAATTATAATAA
6172385 AA
1 AA
6172387 TAGTTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 22 0.71
34 9 0.29
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (34 bp):
AAAATAAAATATAAAATATAAAAAATTATAATAA
Found at i:6172590 original size:23 final size:23
Alignment explanation
Indices: 6172542--6172591 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
6172532 CGTTGTAATG
* * *
6172542 TTATTTTTTTTATATTTTAATCA
1 TTATTTTATTTATATCTAAATCA
6172565 TTATTTTATTTATATACTAAAT-A
1 TTATTTTATTTATAT-CTAAATCA
6172588 TTAT
1 TTAT
6172592 AATATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATTTTATTTATATCTAAATCA
Found at i:6184555 original size:3 final size:3
Alignment explanation
Indices: 6184549--6184574 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6184539 AACTAGGAAA
6184549 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
6184575 TTACTGGAAA
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:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6201661 original size:21 final size:21
Alignment explanation
Indices: 6201637--6201676 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6201627 ATCAGGGAGA
* * *
6201637 TACATGCAGGAAATGGAGGTT
1 TACAAGCAGAAAAAGGAGGTT
6201658 TACAAGCAGAAAAAGGAGG
1 TACAAGCAGAAAAAGGAGG
6201677 AAGAAGCTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.33, T:0.15
Consensus pattern (21 bp):
TACAAGCAGAAAAAGGAGGTT
Found at i:6205335 original size:3 final size:3
Alignment explanation
Indices: 6205329--6205372 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
6205319 ATTATTACTA
* * * *
6205329 AAT AAT AAT AAT AAT AAT AAT GAT AAT GAT AAT GAT AAT TAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6205373 CTCTAATTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:6205344 original size:12 final size:12
Alignment explanation
Indices: 6205329--6205372 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
6205319 ATTATTACTA
*
6205329 AATAATAATAAT
1 AATAATAATGAT
6205341 AATAATAATGAT
1 AATAATAATGAT
*
6205353 AATGATAATGAT
1 AATAATAATGAT
*
6205365 AATTATAA
1 AATAATAA
6205373 CTCTAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (12 bp):
AATAATAATGAT
Found at i:6211630 original size:30 final size:30
Alignment explanation
Indices: 6211572--6211630 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
6211562 CAGTTCACCT
* *
6211572 GAAGATAACCATCATCAGACTCCAGCTCCC
1 GAAGAAAACCATCACCAGACTCCAGCTCCC
* * *
6211602 GAAGAAAACCATGACCAGATTCCTGCTCC
1 GAAGAAAACCATCACCAGACTCCAGCTCC
6211631 AGTACCAAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.15, T:0.17
Consensus pattern (30 bp):
GAAGAAAACCATCACCAGACTCCAGCTCCC
Found at i:6211818 original size:12 final size:12
Alignment explanation
Indices: 6211803--6211867 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
6211793 AAATAGTGCT
6211803 AGTGACAGTGGA
1 AGTGACAGTGGA
*
6211815 AGTGATAGT-GA
1 AGTGACAGTGGA
*
6211826 TAGTGACAGTGACAGC
1 -AGTGACAGTG---GA
*
6211842 AGTGATAGTGGA
1 AGTGACAGTGGA
6211854 AGTGACAGTGGA
1 AGTGACAGTGGA
6211866 AG
1 AG
6211868 CCGCAGTAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
11 2 0.05
12 30 0.71
15 9 0.21
16 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.38, T:0.20
Consensus pattern (12 bp):
AGTGACAGTGGA
Found at i:6211847 original size:21 final size:21
Alignment explanation
Indices: 6211821--6211861 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6211811 TGGAAGTGAT
6211821 AGTGATAGT-GACAGTGACAGC
1 AGTGATAGTGGA-AGTGACAGC
6211842 AGTGATAGTGGAAGTGACAG
1 AGTGATAGTGGAAGTGACAG
6211862 TGGAAGCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.34, C:0.10, G:0.37, T:0.20
Consensus pattern (21 bp):
AGTGATAGTGGAAGTGACAGC
Found at i:6211894 original size:30 final size:30
Alignment explanation
Indices: 6211860--6211916 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6211850 TGGAAGTGAC
*
6211860 AGTGGAAGCCGCAGTAGG-AGTAGGAGCAGG
1 AGTGGAAGCC-CAGCAGGAAGTAGGAGCAGG
*
6211890 AGTGGAAGCCCAGCAGGAAGTGGGAGC
1 AGTGGAAGCCCAGCAGGAAGTAGGAGC
6211917 GGTAGTAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.30, C:0.16, G:0.46, T:0.09
Consensus pattern (30 bp):
AGTGGAAGCCCAGCAGGAAGTAGGAGCAGG
Found at i:6212202 original size:30 final size:30
Alignment explanation
Indices: 6212125--6212210 Score: 118
Period size: 30 Copynumber: 2.9 Consensus size: 30
6212115 CAAGATGGTG
* *
6212125 ATGGATCTGATGCAGTTGATATTGAAGGTA
1 ATGGATCTGATGCTGTTGATATTGAGGGTA
*
6212155 ATGGATCTGATGCTGTTGATATTGAGGGTC
1 ATGGATCTGATGCTGTTGATATTGAGGGTA
* * *
6212185 ATGGATCAGATGGTGTTGACATTGAG
1 ATGGATCTGATGCTGTTGATATTGAG
6212211 AAAGACTTGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.26, C:0.08, G:0.33, T:0.34
Consensus pattern (30 bp):
ATGGATCTGATGCTGTTGATATTGAGGGTA
Found at i:6235887 original size:27 final size:27
Alignment explanation
Indices: 6235849--6235903 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6235839 CATCATGATG
6235849 AAGAGGTAGATTAACCACAACAAACTA
1 AAGAGGTAGATTAACCACAACAAACTA
6235876 AAGAGGTAGATTAACCACAACAAACTA
1 AAGAGGTAGATTAACCACAACAAACTA
6235903 A
1 A
6235904 GGAAATCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.15
Consensus pattern (27 bp):
AAGAGGTAGATTAACCACAACAAACTA
Found at i:6246092 original size:18 final size:18
Alignment explanation
Indices: 6246069--6246103 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6246059 TTCACTATCA
*
6246069 TCTATGTAAAGTGGTTAT
1 TCTATGTAAAGTAGTTAT
*
6246087 TCTATGTGAAGTAGTTA
1 TCTATGTAAAGTAGTTA
6246104 ATTTACTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (18 bp):
TCTATGTAAAGTAGTTAT
Found at i:6247706 original size:18 final size:18
Alignment explanation
Indices: 6247683--6247718 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6247673 AAAAACTTAA
6247683 TAATTACAATGTTCAATT
1 TAATTACAATGTTCAATT
6247701 TAATTACAATGTTCAATT
1 TAATTACAATGTTCAATT
6247719 ATGAGGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
TAATTACAATGTTCAATT
Found at i:6267097 original size:26 final size:27
Alignment explanation
Indices: 6267039--6267103 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
6267029 CTCCAACAAT
*
6267039 TTATATCTGTTGACAAAATTCAAAAAA
1 TTATTTCTGTTGACAAAATTCAAAAAA
*
6267066 TATATTTCT-TTGACGAAATTCAAAAAA
1 T-TATTTCTGTTGACAAAATTCAAAAAA
*
6267093 TTATTTTTGTT
1 TTATTTCTGTT
6267104 TGTCTGCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 6 0.18
27 21 0.64
28 6 0.18
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (27 bp):
TTATTTCTGTTGACAAAATTCAAAAAA
Found at i:6273904 original size:28 final size:27
Alignment explanation
Indices: 6273865--6273917 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
6273855 AGATTTCCAT
6273865 ATAAAAATTAATAAT-AATAAGAATAAA
1 ATAAAAATTAATAATAAAT-AGAATAAA
6273892 ATAAAAATATAATAATAAATAGAATA
1 ATAAAAAT-TAATAATAAATAGAATA
6273918 GAAAAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 8 0.33
28 13 0.54
29 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (27 bp):
ATAAAAATTAATAATAAATAGAATAAA
Found at i:6274923 original size:14 final size:14
Alignment explanation
Indices: 6274904--6274930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6274894 TTATTGAGAC
6274904 ATTTATATATATAT
1 ATTTATATATATAT
6274918 ATTTATATATATA
1 ATTTATATATATA
6274931 ATTGAAAAAA
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:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTATATATATAT
Found at i:6279386 original size:9 final size:10
Alignment explanation
Indices: 6279366--6279402 Score: 58
Period size: 11 Copynumber: 3.7 Consensus size: 10
6279356 ATAATGTAAT
6279366 GTCGGTTTCG
1 GTCGGTTTCG
6279376 GTCGG-TTCG
1 GTCGGTTTCG
6279385 GTCGGTTCTCG
1 GTCGGTT-TCG
6279396 GTCGGTT
1 GTCGGTT
6279403 ACAATAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 6 0.24
11 10 0.40
ACGTcount: A:0.00, C:0.22, G:0.41, T:0.38
Consensus pattern (10 bp):
GTCGGTTTCG
Found at i:6279425 original size:26 final size:26
Alignment explanation
Indices: 6279396--6279454 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
6279386 TCGGTTCTCG
6279396 GTCGGTTACAATAACCGACGGTGGCA
1 GTCGGTTACAATAACCGACGGTGGCA
*
6279422 GTCGGTTACAATAACTGACGGTGGCA
1 GTCGGTTACAATAACCGACGGTGGCA
6279448 GTCGGTT
1 GTCGGTT
6279455 GGGCGGTCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (26 bp):
GTCGGTTACAATAACCGACGGTGGCA
Found at i:6279677 original size:66 final size:66
Alignment explanation
Indices: 6279539--6279680 Score: 236
Period size: 68 Copynumber: 2.2 Consensus size: 66
6279529 TGGGGGGGGG
6279539 GGGGGGGGAATCTGGTCGGACTTGCGGGAGGGGAGGGAAGTTTCGTTAGGTTGGCGGACTCGGGT
1 GGGGGGGGAATCTGGTCGGACTTGCGGGAGGGGAGGGAAGTTTCGTTAGGTTGGCGGACTCGGGT
6279604 A
66 A
6279605 GGGGGGGGAATCTGGGTCGGGACTTGCGGGA-GGGAGAGGAAGTTTCGTTAGGTTGGCGGACTC-
1 GGGGGGGGAATCT-GGTC-GGACTTGCGGGAGGGGAG-GGAAGTTTCGTTAGGTTGGCGGACTCG
6279668 GGT-
63 GGTA
6279671 GGGGGGGGAA
1 GGGGGGGGAA
6279681 GTAGTGAGGT
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
66 23 0.32
67 12 0.16
68 38 0.52
ACGTcount: A:0.15, C:0.11, G:0.54, T:0.20
Consensus pattern (66 bp):
GGGGGGGGAATCTGGTCGGACTTGCGGGAGGGGAGGGAAGTTTCGTTAGGTTGGCGGACTCGGGT
A
Found at i:6293981 original size:567 final size:572
Alignment explanation
Indices: 6292947--6294086 Score: 1618
Period size: 567 Copynumber: 2.0 Consensus size: 572
6292937 TAAAAAAAAA
* *
6292947 AACCTGGTCAGCACGTATATTTAGTTAGGTAAAAGGGAGTTAAGAAAAAACCTCAAAGAATTAGA
1 AACCTGGTCAGCACGTATACTTAGTTAGGTAAAAAGGAGTTAAGAAAAAACCTCAAAGAATTAGA
* *
6293012 AAAAAAAAACTTGATTAGCATGTATACTTAGTTAAGAGTTGAGAAAAAGTCTCAATGAGTTAAAA
66 AAAAAAAAACTTGATTAACATGTATACTTAGTTAAGAGTTGAGAAAAAGTCTCAATAAGTTAAAA
*
6293077 AAATTAATAGAGTCATCAACATATTAGGTAGAGTAAAAAAACCAAATTATGGAGTTGAGAAAAAG
131 AAATTAATAGAGT-ATCAACA-ATGAGGTAGAGTAAAAAAACCAAATTATGGAGTTGAGAAAAAG
* * * *
6293142 CTTAAAGGAGTTAGAGAAAAAACTTGATCAGTATATATACTTAATTAGGTAAAAAGAAATTGAAA
194 CTTAAAGGAGTTAGAAAAAAAACTTAATCAGTATATATACTTAATCAAGTAAAAAGAAATTGAAA
* * * *
6293207 AAAAGTCTCAAGGAGTTGGAGAAAAAATCAAAATCTGAAAAAAAAAAATTGGTTAGCATGTATAT
259 AAAAGTCTCAAGGAGTTAGAGAAAAAATAAAAATCTGAAAAAAAAAAACTGGTTAGCATGTATAC
* * * * * *
6293272 TTAGTCAGGAGTTGAGAAAAAGCCTCAACGAGTTAAAAAAATTAATAAGGTCATTAGCGTGGTAA
324 TCAGTCAAGAGTTGAGAAAAAGCCTCAACGAGTTAAAAAAATTAATAAAGTCATTAACATGATAA
* * * *
6293337 ATAAAGTAAAAAAGTCAAATTAGAGAGTTGAGAAAAAGTCTCAAGAAATTAGAGAAAAACTTTAG
389 ATAAAGTAAAAAAGCCAAATTAGAGAGTTGAGAAAAAATCTCAAGAAATTAGAGAAAAACTCTAA
* *
6293402 TCAGCATGTATACTTAGTCATGAGTTGAGAAAAAAAACTTAAAGAGTTAGAAAAAAAACAAAACT
454 TCAGCATGTATACATAGTCAGGAGTTGAG-AAAAAAACTTAAAGAGTTA-AAAAAAAA-AAAA-T
* *
6293467 T-GATCAGTATGTATACTTAGTCAAGTAAAAAAATTAAAATCAAAATACAAAAATTCT
515 TAGATCAGCATGTATACTTAGTCAAGTAAAAAAATTAAAACCAAAATACAAAAATTCT
* * * * *
6293524 AACCTTGTCAGCATGTATACTTAGTTAGGTAAAAAGG-GTTGAGAAAAAGCCTCAAAGAGTTAG-
1 AACCTGGTCAGCACGTATACTTAGTTAGGTAAAAAGGAGTTAAGAAAAAACCTCAAAGAATTAGA
* * *
6293587 AAAAAAAATC-TGATTAACATGTATACTTAGTTAAGAGTTGAGAAAAAGTCTCGATAAGTTAAAG
66 AAAAAAAAACTTGATTAACATGTATACTTAGTTAAGAGTTGAGAAAAAGTCTCAATAAGTTAAAA
* * * *
6293651 AAATTAGTAGAGT-T-ATC-A-GGGGTAGAGTAAAAAAATCAAATTA-GAGAGTTGAGAAAAAGC
131 AAATTAATAGAGTATCAACAATGAGGTAGAGTAAAAAAACCAAATTATG-GAGTTGAGAAAAAGC
* * * * *
6293711 TTAAAGGAGTTAGAAAAAAAATTTAATCAGTATGTATACTTAGTCAAGTAAAAAGAAGTTGAGAA
195 TTAAAGGAGTTAGAAAAAAAACTTAATCAGTATATATACTTAATCAAGTAAAAAGAAATTGAAAA
6293776 AAAGTCTCAAGGAGTTAGAGAAAAAATAAAAATCTG-AAAAAAAAAACTGGTTAGCATGTATACT
260 AAAGTCTCAAGGAGTTAGAGAAAAAATAAAAATCTGAAAAAAAAAAACTGGTTAGCATGTATACT
* * * * *
6293840 CAGTCAAGAGTTGAGAAAAAGTCTCAACGAGTTAGAGAAATTAATAAAGTCATTAATATGATAAG
325 CAGTCAAGAGTTGAGAAAAAGCCTCAACGAGTTAAAAAAATTAATAAAGTCATTAACATGATAAA
* * *
6293905 TAGAGTCAAAAAGCCAAATTAGAGAGTTGAGAAAAAATCTCAAGAAGTTAGAGAAAAAAC-CTAA
390 TAAAGTAAAAAAGCCAAATTAGAGAGTTGAGAAAAAATCTCAAGAAATTAGAG-AAAAACTCTAA
* *
6293969 TCAGCATGTATACATAGTTAGGAGTTGAGAAAAAAACTTAAAGAGTTAAAAAAAAAAAAATTAGG
454 TCAGCATGTATACATAGTCAGGAGTTGAGAAAAAAACTTAAAGAGTTAAAAAAAAAAAAATTAGA
* * *
6294034 TTAGCATGTATACTTAGTCAAGTAAAAAAATTAAAGCCAATATACAAAAATTC
519 TCAGCATGTATACTTAGTCAAGTAAAAAAATTAAAACCAAAATACAAAAATTC
6294087 ACGTAGGCAT
Statistics
Matches: 503, Mismatches: 57, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
563 2 0.00
564 53 0.11
565 8 0.02
566 19 0.04
567 157 0.31
568 133 0.26
569 1 0.00
571 2 0.00
572 1 0.00
574 62 0.12
575 9 0.02
576 23 0.05
577 33 0.07
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (572 bp):
AACCTGGTCAGCACGTATACTTAGTTAGGTAAAAAGGAGTTAAGAAAAAACCTCAAAGAATTAGA
AAAAAAAAACTTGATTAACATGTATACTTAGTTAAGAGTTGAGAAAAAGTCTCAATAAGTTAAAA
AAATTAATAGAGTATCAACAATGAGGTAGAGTAAAAAAACCAAATTATGGAGTTGAGAAAAAGCT
TAAAGGAGTTAGAAAAAAAACTTAATCAGTATATATACTTAATCAAGTAAAAAGAAATTGAAAAA
AAGTCTCAAGGAGTTAGAGAAAAAATAAAAATCTGAAAAAAAAAAACTGGTTAGCATGTATACTC
AGTCAAGAGTTGAGAAAAAGCCTCAACGAGTTAAAAAAATTAATAAAGTCATTAACATGATAAAT
AAAGTAAAAAAGCCAAATTAGAGAGTTGAGAAAAAATCTCAAGAAATTAGAGAAAAACTCTAATC
AGCATGTATACATAGTCAGGAGTTGAGAAAAAAACTTAAAGAGTTAAAAAAAAAAAAATTAGATC
AGCATGTATACTTAGTCAAGTAAAAAAATTAAAACCAAAATACAAAAATTCT
Found at i:6295947 original size:65 final size:66
Alignment explanation
Indices: 6295859--6295991 Score: 162
Period size: 65 Copynumber: 2.0 Consensus size: 66
6295849 TCATGAACAA
* * * *
6295859 ATCAATAACTAAACCCGATGTCAATTTTGAAGATTT-TCAATATTAGATCAAGGGATTCATGGAT
1 ATCAATAACAAAACCCGACGTCAATTTCGAAGATTTCT-AATATTAGATCAAGGGATTCATCGAT
6295923 GG
65 GG
* * * * *
6295925 ATCAAT-ACAAAACCCGACGTCAATTTCGAGGATTTCTAATCTTGGATCTAGGGATTTATCGATG
1 ATCAATAACAAAACCCGACGTCAATTTCGAAGATTTCTAATATTAGATCAAGGGATTCATCGATG
6295989 G
66 G
6295990 AT
1 AT
6295992 TGATAGCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
65 50 0.88
66 7 0.12
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (66 bp):
ATCAATAACAAAACCCGACGTCAATTTCGAAGATTTCTAATATTAGATCAAGGGATTCATCGATG
G
Done.