Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold288
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: 589160
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 14644 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:308531 original size:15 final size:16
Alignment explanation
Indices: 308499--308532 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
308489 TTTCATCGGG
308499 TTTGGGCCATATTTTT
1 TTTGGGCCATATTTTT
308515 TTTGGGCCATATTTTT
1 TTTGGGCCATATTTTT
308531 TT
1 TT
308533 AATGTTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (16 bp):
TTTGGGCCATATTTTT
Found at i:308577 original size:4 final size:4
Alignment explanation
Indices: 308568--308602 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
308558 GGACTGTGTG
308568 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
308603 TTATTGGGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:312673 original size:15 final size:15
Alignment explanation
Indices: 312653--312694 Score: 61
Period size: 13 Copynumber: 2.9 Consensus size: 15
312643 TTATTATATG
312653 TGAAATATTTCAATT
1 TGAAATATTTCAATT
*
312668 TGAAATAATT-AA-T
1 TGAAATATTTCAATT
312681 TGAAATATTTCAAT
1 TGAAATATTTCAAT
312695 CACCACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 10 0.43
14 4 0.17
15 9 0.39
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (15 bp):
TGAAATATTTCAATT
Found at i:313303 original size:5 final size:6
Alignment explanation
Indices: 313263--313315 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
313253 TCAATTACTG
** * *
313263 AAAACA AAAGACA AACCCA AAAATA AAATAAA AAAACA AAAACA AAAACA
1 AAAACA AAA-ACA AAAACA AAAACA AAA-ACA AAAACA AAAACA AAAACA
313313 AAA
1 AAA
313316 TTAAATGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.79, C:0.15, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAACA
Found at i:323508 original size:24 final size:24
Alignment explanation
Indices: 323476--323528 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
323466 TAATAAATAA
*
323476 AAATATATATAATTATTAAATATT
1 AAATATATATAATTAGTAAATATT
* *
323500 AAATATATATAGTTAGTACATATT
1 AAATATATATAATTAGTAAATATT
323524 AAATA
1 AAATA
323529 AAAATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
AAATATATATAATTAGTAAATATT
Found at i:330062 original size:37 final size:37
Alignment explanation
Indices: 329981--330071 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 37
329971 TTAGTGCCGA
* *
329981 GGCGTATTATTAGTTGGATTAGCTCTCATAACCGCTT
1 GGCGTGTTATTGGTTGGATTAGCTCTCATAACCGCTT
* * * ** *
330018 GGAGTGTTATTGGTTGGATTAGCTCTTATGAGTGTTT
1 GGCGTGTTATTGGTTGGATTAGCTCTCATAACCGCTT
330055 GGCGTGTT-TTGGTTGGA
1 GGCGTGTTATTGGTTGGA
330072 CTACTTGTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 9 0.20
37 36 0.80
ACGTcount: A:0.16, C:0.11, G:0.31, T:0.42
Consensus pattern (37 bp):
GGCGTGTTATTGGTTGGATTAGCTCTCATAACCGCTT
Found at i:342875 original size:24 final size:22
Alignment explanation
Indices: 342848--342897 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
342838 CATATATTTG
*
342848 ATTTTGATACTCACTAAATTTTTT
1 ATTTTAATACTCAC--AATTTTTT
**
342872 ATTTTAATGTTCACAATTTTTT
1 ATTTTAATACTCACAATTTTTT
342894 ATTT
1 ATTT
342898 ACCAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
24 11 0.48
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTTAATACTCACAATTTTTT
Found at i:343582 original size:20 final size:21
Alignment explanation
Indices: 343553--343600 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
343543 GTATTCAACC
*
343553 AAAAATTAAAAAGATTGAATT
1 AAAAATTAAAAAAATTGAATT
*
343574 AAAAA-TAAAAAAATTGAA-A
1 AAAAATTAAAAAAATTGAATT
343593 AAAAATTA
1 AAAAATTA
343601 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 14 0.58
21 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (21 bp):
AAAAATTAAAAAAATTGAATT
Found at i:352268 original size:62 final size:62
Alignment explanation
Indices: 352191--352417 Score: 305
Period size: 62 Copynumber: 3.6 Consensus size: 62
352181 CAATGTACCT
352191 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTATAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTATAA
* *
352253 AATTTATAATACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTACAA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTATAA
* * * *
352315 AATTTATATTACAAAGTTTATTACAAGTTTTAATGTTGTAATGT-TGTAATGTTGCA-ATTAATC
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAAT-TT--ATATT-ATA
*
352378 T
62 A
** *
352379 AATTTATGACCATAAAGTTTGTTCCAAGTTTTAATGTTG
1 AATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTG
352418 CAATTAATCT
Statistics
Matches: 146, Mismatches: 14, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
61 5 0.03
62 103 0.71
63 3 0.02
64 9 0.06
65 26 0.18
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTAATTTATATTATAA
Found at i:352320 original size:14 final size:14
Alignment explanation
Indices: 352301--352335 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
352291 TAATGTATTT
352301 AATTTATATTACAA
1 AATTTATATTACAA
352315 AATTTATATTACAA
1 AATTTATATTACAA
*
352329 AGTTTAT
1 AATTTAT
352336 TACAAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (14 bp):
AATTTATATTACAA
Found at i:353559 original size:14 final size:14
Alignment explanation
Indices: 353540--353574 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
353530 CAAATTACAT
353540 GTTAGAATAGTATC
1 GTTAGAATAGTATC
353554 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
353568 ATTAGAA
1 GTTAGAA
353575 AAAAATGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:357962 original size:22 final size:24
Alignment explanation
Indices: 357928--357971 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
357918 AAAAAATAAA
357928 TTATATTATTTTAT-ATTAAATAT
1 TTATATTATTTTATAATTAAATAT
357951 TTATA-TATTTTATAATTAAAT
1 TTATATTATTTTATAATTAAAT
357972 TTAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATATTATTTTATAATTAAATAT
Found at i:359789 original size:28 final size:27
Alignment explanation
Indices: 359752--359824 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 27
359742 ATAAACACCA
359752 AAAAAATATTTTTAAATATAAAAAGAAT
1 AAAAAATATTTTTAAATAT-AAAAGAAT
*
359780 AAAAAATA-TTTTAAA-ATTAAAGAAT
1 AAAAAATATTTTTAAATATAAAAGAAT
*
359805 AAAAAATATTTATTATATAT
1 AAAAAATATTT-TTAAATAT
359825 TCGGGCCGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 15 0.38
26 4 0.10
27 11 0.28
28 10 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AAAAAATATTTTTAAATATAAAAGAAT
Found at i:360126 original size:6 final size:6
Alignment explanation
Indices: 360115--360140 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
360105 AAAAATTAGA
360115 TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TT
360141 TAAGGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:360348 original size:7 final size:7
Alignment explanation
Indices: 360327--360359 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
360317 AAAAATTAGA
360327 TTAGGG-
1 TTAGGGT
360333 TTAGGGT
1 TTAGGGT
*
360340 TTAGAGT
1 TTAGGGT
360347 TTAGGGT
1 TTAGGGT
360354 TTAGGG
1 TTAGGG
360360 AGACATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.18, C:0.00, G:0.42, T:0.39
Consensus pattern (7 bp):
TTAGGGT
Found at i:360775 original size:28 final size:27
Alignment explanation
Indices: 360738--360810 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 27
360728 ATAAACACCA
360738 AAAAAATATTTTTAAATATAAAAAGAAT
1 AAAAAATATTTTTAAATAT-AAAAGAAT
*
360766 AAAAAATA-TTTTAAA-ATTAAAGAAT
1 AAAAAATATTTTTAAATATAAAAGAAT
*
360791 AAAAAATATTTATTATATAT
1 AAAAAATATTT-TTAAATAT
360811 TCATATATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 15 0.38
26 4 0.10
27 11 0.28
28 10 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AAAAAATATTTTTAAATATAAAAGAAT
Found at i:361120 original size:6 final size:6
Alignment explanation
Indices: 361109--361134 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
361099 AAAAATTAGA
361109 TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TT
361135 TAAGGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:361268 original size:994 final size:984
Alignment explanation
Indices: 359379--361351 Score: 3838
Period size: 994 Copynumber: 2.0 Consensus size: 984
359369 CGGAATGGGC
359379 TCATTTTCCCGAAAGCGCATTCACGTCAGCACGATGTCAGGGTACGTGACAGGAAAACGCGTCCC
1 TCATTTTCCCGAAAGCGCATTCACGTCAGCACGATGTCAGGGTACGTGACAGGAAAACGCGTCCC
359444 TGAGGGCGCGCTTTAAGTCCATGAAAGCAAAACGCTCCTTCAAGGACGCGTTTTGCCCGTTTTTG
66 TGAGGGCGCGCTTTAAGTCCATGAAAGCAAAACGCTCCTTCAAGGACGCGTTTTGCCCGTTTTTG
359509 GATTTTAAAGTTTAGGGTTTTAGGATTTAAGATTAAAAATTAAATAAATAAGAGATTAGAATTTA
131 GATTTTAAAGTTTAGGGTTTTAGGATTTAAGATTAAAAATTAAATAAATAAGAGATTAGAATTTA
359574 GGGTAGAGGTGTTCATGGGCCAGGCAATGCTAGGCCCAAAAATTTTTTTGGCCCGCTTCCTAGGC
196 GGGTAGAGGTGTTCATGGGCCAGGCAATGCTAGGCCCAAAAATTTTTTTGGCCCGCTTCCTAGGC
359639 CCGGGGCCGACCCGACCCGAAATATGGGCCTGAAAATTTGTCCAGGCCCGGCGCGAGAAAAAATT
261 CCGGGGCCGACCCGACCCGAAATATGGGCCTGAAAATTTGTCCAGGCCCGGCGCGAGAAAAAATT
359704 TCTAAGCCCGATTCCGGCCCGCCCTGATCCATTATTTAATAAACACCAAAAAAATATTTTTAAAT
326 TCTAAGCCCGATTCCGGCCCGCCCTGATCCATTATTTAATAAACACCAAAAAAATATTTTTAAAT
359769 ATAAAAAGAATAAAAAATATTTTAAAATTAAAGAATAAAAAATATTTATTATATATTCGGGCCGG
391 ATAAAAAGAATAAAAAATATTTTAAAATTAAAGAATAAAAAATATTTATTATATATTCGGGCCGG
359834 ACCGTGCCGGGCTCGAGCCAAAAAAGTGGTGCCCAAGGCCCGACCCGTTTTCTAAACGGGCCTCG
456 ACCGTGCCGGGCTCGAGCCAAAAAAGTGGTGCCCAAGGCCCGACCCGTTTTCTAAACGGGCCTCG
359899 CTTTTTTGCCCAAACCCATATTTTGGGCCTATATTTTTACCCGAACCCTCCCATAATTTTTGCCC
521 CTTTTTTGCCCAAACCCATATTTTGGGCCTATATTTTTACCCGAACCCTCCCATAATTTTTGCCC
359964 GGCCCATGAACACCTCTAGTTTAGGGTTTGTTAATTAAATTATTTATAAATTTTTCATAATTTTG
586 GGCCCATGAACACCTCTAGTTTAGGGTTTGTTAATTAAATTATTTATAAATTTTTCATAATTTTG
360029 TGTATATTATTTTTTAAGAAAAAAGTAATTAAATTAGGGTTTAGGATTACTTGAGTACTTTAATT
651 TGTATATTATTTTTTAAGAAAAAAGTAATTAAATTAGGGTTTAGGATTACTTGAGTACTTTAATT
360094 AAAAAAATTTAAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTAAGGTATTTTTAAGTTA
716 AAAAAAATTTAAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTAAGGTATTTTTAAGTTA
360159 AGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTGTCAATTAAATCATTTATAAATTTTTCA
781 AGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTGTCAATTAAATCATTTATAAATTTTTCA
360224 AAATTGGATTAGTTTTCGTGTTTATTAATTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGT
846 AAATTGGATTAGTTTTCGTGTTTATTAATTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGT
*
360289 TACTTGAGTAATTTAATTAAAAAAATTTAAAAATTAGATTAGGGTTAGGGTTTAGAGTTTAGGGT
911 TACTTGAGTAATTTAATTAAAAAAATTTAAAAATTAGATCAGGGTTAGGG-TTAG-GTTTAGGGT
360354 TTAGGGAGACA
974 TTAGGGAGACA
360365 TCATTTTCCCGAAAGCGCATTCACGTCAGCACGATGTCAGGGTACGTGACAGGAAAACGCGTCCC
1 TCATTTTCCCGAAAGCGCATTCACGTCAGCACGATGTCAGGGTACGTGACAGGAAAACGCGTCCC
360430 TGAGGGCGCGCTTTAAGTCCATGAAAGCAAAACGCTCCTTCAAGGACGCGTTTTGCCCGTTTTTG
66 TGAGGGCGCGCTTTAAGTCCATGAAAGCAAAACGCTCCTTCAAGGACGCGTTTTGCCCGTTTTTG
360495 GATTTTAAAGTTTAGGGTTTTAGGATTTAAGATTAAAAATTAAATAAATAAGAGATTAGAATTTA
131 GATTTTAAAGTTTAGGGTTTTAGGATTTAAGATTAAAAATTAAATAAATAAGAGATTAGAATTTA
360560 GGGTAGAGGTGTTCATGGGCCAGGCAATGCTAGGCCCAAAAATTTTTTTGGCCCGCTTCCTAGGC
196 GGGTAGAGGTGTTCATGGGCCAGGCAATGCTAGGCCCAAAAATTTTTTTGGCCCGCTTCCTAGGC
360625 CCGGGGCCGACCCGACCCGAAATATGGGCCTGAAAATTTGTCCAGGCCCGGCGCGAGAAAAAATT
261 CCGGGGCCGACCCGACCCGAAATATGGGCCTGAAAATTTGTCCAGGCCCGGCGCGAGAAAAAATT
360690 TCTAAGCCCGATTCCGGCCCGCCCTGATCCATTATTTAATAAACACCAAAAAAATATTTTTAAAT
326 TCTAAGCCCGATTCCGGCCCGCCCTGATCCATTATTTAATAAACACCAAAAAAATATTTTTAAAT
360755 ATAAAAAGAATAAAAAATATTTTAAAATTAAAGAATAAAAAATATTTATTATATATTCATATATT
391 ATAAAAAGAATAAAAAATATTTTAAAATTAAAGAAT-AAAAA-A--TA-T-T-TATT-ATATATT
*
360820 CGGGCCGGGCCGTGCCGGGCTCGAGCCAAAAAAGTGGTGCCCAAGGCCCGACCCGTTTTCTAAAC
448 CGGGCCGGACCGTGCCGGGCTCGAGCCAAAAAAGTGGTGCCCAAGGCCCGACCCGTTTTCTAAAC
360885 GGGCCTCGCTTTTTTGCCCAAACCCATATTTTGGGCCTATATTTTTACCCGAACCCTCCCATAAT
513 GGGCCTCGCTTTTTTGCCCAAACCCATATTTTGGGCCTATATTTTTACCCGAACCCTCCCATAAT
360950 TTTTGCCCGGCCCATGAACACCTCTAGTTTAGGGTTTGTTAATTAAATTATTTATAAATTTTTCA
578 TTTTGCCCGGCCCATGAACACCTCTAGTTTAGGGTTTGTTAATTAAATTATTTATAAATTTTTCA
361015 TAATTTTGTGTATATTATTTTTTAAGAAAAAAGTAATTAAATTAGGGTTTAGGATTACTTGAGTA
643 TAATTTTGTGTATATTATTTTTTAAGAAAAAAGTAATTAAATTAGGGTTTAGGATTACTTGAGTA
361080 CTTTAATTAAAAAAATTTAAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTAAGGTATTT
708 CTTTAATTAAAAAAATTTAAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTAAGGTATTT
361145 TTAAGTTAAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTGTCAATTAAATCATTTATAA
773 TTAAGTTAAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTGTCAATTAAATCATTTATAA
361210 ATTTTTCAAAATTGGATTAGTTTTCGTGTTTATTAATTTTTAAGAAAAAATCAATTAAATTAGGG
838 ATTTTTCAAAATTGGATTAGTTTTCGTGTTTATTAATTTTTAAGAAAAAATCAATTAAATTAGGG
361275 TTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTAAAAATTAGATCAGGGTTAGGGTTAGGTT
903 TTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTTAAAAATTAGATCAGGGTTAGGGTTAGGTT
361340 TAGGGTTTAGGG
968 TAGGGTTTAGGG
361352 TGTTTTTAAG
Statistics
Matches: 977, Mismatches: 2, Indels: 10
0.99 0.00 0.01
Matches are distributed among these distances:
986 426 0.44
987 5 0.01
988 1 0.00
990 2 0.00
991 1 0.00
992 16 0.02
993 8 0.01
994 518 0.53
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (984 bp):
TCATTTTCCCGAAAGCGCATTCACGTCAGCACGATGTCAGGGTACGTGACAGGAAAACGCGTCCC
TGAGGGCGCGCTTTAAGTCCATGAAAGCAAAACGCTCCTTCAAGGACGCGTTTTGCCCGTTTTTG
GATTTTAAAGTTTAGGGTTTTAGGATTTAAGATTAAAAATTAAATAAATAAGAGATTAGAATTTA
GGGTAGAGGTGTTCATGGGCCAGGCAATGCTAGGCCCAAAAATTTTTTTGGCCCGCTTCCTAGGC
CCGGGGCCGACCCGACCCGAAATATGGGCCTGAAAATTTGTCCAGGCCCGGCGCGAGAAAAAATT
TCTAAGCCCGATTCCGGCCCGCCCTGATCCATTATTTAATAAACACCAAAAAAATATTTTTAAAT
ATAAAAAGAATAAAAAATATTTTAAAATTAAAGAATAAAAAATATTTATTATATATTCGGGCCGG
ACCGTGCCGGGCTCGAGCCAAAAAAGTGGTGCCCAAGGCCCGACCCGTTTTCTAAACGGGCCTCG
CTTTTTTGCCCAAACCCATATTTTGGGCCTATATTTTTACCCGAACCCTCCCATAATTTTTGCCC
GGCCCATGAACACCTCTAGTTTAGGGTTTGTTAATTAAATTATTTATAAATTTTTCATAATTTTG
TGTATATTATTTTTTAAGAAAAAAGTAATTAAATTAGGGTTTAGGATTACTTGAGTACTTTAATT
AAAAAAATTTAAAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGGTTTAAGGTATTTTTAAGTTA
AGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTGTCAATTAAATCATTTATAAATTTTTCA
AAATTGGATTAGTTTTCGTGTTTATTAATTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGT
TACTTGAGTAATTTAATTAAAAAAATTTAAAAATTAGATCAGGGTTAGGGTTAGGTTTAGGGTTT
AGGGAGACA
Found at i:361566 original size:7 final size:7
Alignment explanation
Indices: 361545--361577 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
361535 AAAAATTAGA
361545 TTAGGG-
1 TTAGGGT
361551 TTAGGGT
1 TTAGGGT
*
361558 TTAGAGT
1 TTAGGGT
361565 TTAGGGT
1 TTAGGGT
361572 TTAGGG
1 TTAGGG
361578 AGACACGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.18, C:0.00, G:0.42, T:0.39
Consensus pattern (7 bp):
TTAGGGT
Found at i:362006 original size:7 final size:7
Alignment explanation
Indices: 361996--362021 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
361986 CATAATACAT
361996 AATACTA
1 AATACTA
362003 AATACTA
1 AATACTA
362010 AATACTA
1 AATACTA
362017 AATAC
1 AATAC
362022 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:362222 original size:20 final size:20
Alignment explanation
Indices: 362184--362222 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
362174 CTATTATTTT
*
362184 TAAAATCTATGTAATAATTG
1 TAAAATCTATATAATAATTG
362204 TAAAATCTAATATAA-AATT
1 TAAAATCT-ATATAATAATT
362223 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAATCTATATAATAATTG
Found at i:369735 original size:95 final size:98
Alignment explanation
Indices: 369607--369923 Score: 315
Period size: 102 Copynumber: 3.1 Consensus size: 98
369597 TTCACTTCTA
* *
369607 CCACCCAAAAATTTTCTGAAGTAACTAATTACCTTATGAAGTATTAACCATCAAAAGGACATAAG
1 CCACCCACAAA-TTTCT-AAGTAACTAAGTACCTTATGAAGTATTAACCATCAAAA-GACATAAG
*
369672 TAAACCAA-ATATATATCTTGATATTAGCAGCCAA-
63 TAAACCAACATATATATCTTGATATGAGCAGCCAAT
369706 CCACCCACAAA-TTC-AAGTAACTAAGTACCTTATGAAGTATTAACCATCAACAAGACATAAGTA
1 CCACCCACAAATTTCTAAGTAACTAAGTACCTTATGAAGTATTAACCATCAA-AAGACATAAGT-
* * *
369769 ACATAACATATACATATATATATTGGTATGAGCAGCCAATT
64 --A-AAC-CA-ACATATATATCTTGATATGAGCAGCCAA-T
** * *
369810 CCACCCACAAATTTTCTTAAGTAACTAAGTACCTTAAAAAGTATTAACCATCAACACG-CAAAAA
1 CCACCCACAAA-TTTC-TAAGTAACTAAGTACCTTATGAAGTATTAACCATCAA-AAGAC-ATAA
* *
369874 GT-AACCAAGTATATATATCTTGATATGAGCAGCAAAT
62 GTAAACCAA-CATATATATCTTGATATGAGCAGCCAAT
* *
369911 -TACCTACAAATTT
1 CCACCCACAAATTT
369924 ATTCAATTCT
Statistics
Matches: 185, Mismatches: 17, Indels: 32
0.79 0.07 0.14
Matches are distributed among these distances:
95 44 0.24
96 2 0.01
97 3 0.02
98 1 0.01
99 16 0.09
100 9 0.05
101 3 0.02
102 47 0.25
103 3 0.02
104 11 0.06
106 3 0.02
107 1 0.01
108 42 0.23
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (98 bp):
CCACCCACAAATTTCTAAGTAACTAAGTACCTTATGAAGTATTAACCATCAAAAGACATAAGTAA
ACCAACATATATATCTTGATATGAGCAGCCAAT
Found at i:369888 original size:108 final size:102
Alignment explanation
Indices: 369680--369878 Score: 265
Period size: 108 Copynumber: 1.9 Consensus size: 102
369670 AGTAAACCAA
* * **
369680 ATATATATCTTGATATTAGCAGCCAACCACCCACAAATTCAAGTAACTAAGTACCTTATGAAGTA
1 ATATATATATTGATATGAGCAGCCAACCACCCACAAATTCAAGTAACTAAGTACCTTAAAAAGTA
*
369745 TTAACCATCAACAAGACATAAGTAACATAACATATAC
66 TTAACCATCAACAAGACAAAAGTAACATAACATATAC
*
369782 ATATATATATTGGTATGAGCAGCCAATTCCACCCACAAATTTTCTTAAGTAACTAAGTACCTTAA
1 ATATATATATTGATATGAGCAGCCAA--CCACCCACAAA--TTC--AAGTAACTAAGTACCTTAA
*
369847 AAAGTATTAACCATCAACACG-CAAAAAGTAAC
60 AAAGTATTAACCATCAACAAGAC-AAAAGTAAC
369879 CAAGTATATA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
102 23 0.28
104 11 0.13
106 3 0.04
107 1 0.01
108 45 0.54
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (102 bp):
ATATATATATTGATATGAGCAGCCAACCACCCACAAATTCAAGTAACTAAGTACCTTAAAAAGTA
TTAACCATCAACAAGACAAAAGTAACATAACATATAC
Found at i:370036 original size:327 final size:323
Alignment explanation
Indices: 369503--370094 Score: 825
Period size: 327 Copynumber: 1.8 Consensus size: 323
369493 GTATTCTCTC
** * * *
369503 AAGTAACTAAGTACCTTATTAAGTATTAACCATCAATAAGACATAAGTAACCAAGTGCATATCTT
1 AAGTAACTAAGTACCTTAAAAAGTATTAACCATCAACAAGACAAAAGTAACCAAGTACATATCTT
** * * * *
369568 GATATGAACAGCCGATTACCCACAAATTATTCACTTCTACCACCCAAAAATTTTCTGAAGTAACT
66 GATATGAACAGCAAATTACCCACAAATTATTCAATTCTACCACCCAAAAAGTCTCTGAAGTAACA
* * * *
369633 AATTACCTTATGAAGTATTAACCATCAAAAGGACATAAGTAAACCAAATATATATCTTGATATTA
131 AAGTACCTTATGAAGTATTAACCATCAAAACGACAAAAGTAAACCAAATATATATCTTGATATGA
*
369698 GCAGCCAACCACCCACAAATT-C-AAGTAACTAAGTACCTT-ATGAAGTATTAACCATCAACAAG
196 GCAGCC-A--A-CCACAAATTCCTAAGCAACTAAGTACCTTAAT-AAGTATTAACCATCAACAAG
369760 ACATAAGTAACATAACATATACATATATATATTGGTATGAGCAGCCAATTCCACCCACAAATTTT
256 ACATAAGTAACATAACATATACATATATATATTGGTATGAGCAGCCAATTCCACCCACAAATTTT
369825 CTT
321 CTT
* *
369828 AAGTAACTAAGTACCTTAAAAAGTATTAACCATCAACACG-CAAAAAGTAACCAAGTATATATAT
1 AAGTAACTAAGTACCTTAAAAAGTATTAACCATCAACAAGAC-AAAAGTAACCAAG--TACATAT
* * * * *
369892 CTTGATATGAGCAGCAAATTACCTACAAATTTATTCAATTCTACCACCTATAAAGTCTCTTAAGT
63 CTTGATATGAACAGCAAATTACCCACAAA-TTATTCAATTCTACCACCCAAAAAGTCTCTGAAGT
* *
369957 AACAAAGTACCTTATTAAGTATTAACCATCAAAACGACAAAAGT-AACCAAGTATATATCTTGAT
127 AACAAAGTACCTTATGAAGTATTAACCATCAAAACGACAAAAGTAAACCAAATATATATCTTGAT
370021 ATGAGCAGCCAACCACAAATTCCCTTAAGCAACTAAGTACCTTAATAAGTATTAACCATCAACAA
192 ATGAGCAGCCAACCACAAATT-CC-TAAGCAACTAAGTACCTTAATAAGTATTAACCATCAACAA
370086 GACATAAGT
255 GACATAAGT
370095 GACAAAGTAC
Statistics
Matches: 233, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
323 9 0.04
324 2 0.01
325 49 0.21
326 1 0.00
327 102 0.44
328 70 0.30
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (323 bp):
AAGTAACTAAGTACCTTAAAAAGTATTAACCATCAACAAGACAAAAGTAACCAAGTACATATCTT
GATATGAACAGCAAATTACCCACAAATTATTCAATTCTACCACCCAAAAAGTCTCTGAAGTAACA
AAGTACCTTATGAAGTATTAACCATCAAAACGACAAAAGTAAACCAAATATATATCTTGATATGA
GCAGCCAACCACAAATTCCTAAGCAACTAAGTACCTTAATAAGTATTAACCATCAACAAGACATA
AGTAACATAACATATACATATATATATTGGTATGAGCAGCCAATTCCACCCACAAATTTTCTT
Found at i:370075 original size:94 final size:94
Alignment explanation
Indices: 369950--370126 Score: 268
Period size: 94 Copynumber: 1.9 Consensus size: 94
369940 TATAAAGTCT
* * *
369950 CTTAAGTAACAAAGTACCTTATTAAGTATTAACCATCAA-AACGACAAAAGTAACCAAGTA-TAT
1 CTTAAGCAACAAAGTACCTTAATAAGTATTAACCATCAACAA-GACAAAAGTAACAAAGTACT-T
370013 ATCTTGATATGAGCAGCCAACCACAAATTCC
64 ATCTTGATATGAGCAGCCAACCACAAATTCC
* * *
370044 CTTAAGCAACTAAGTACCTTAATAAGTATTAACCATCAACAAGACATAAGTGACAAAGTACTTAT
1 CTTAAGCAACAAAGTACCTTAATAAGTATTAACCATCAACAAGACAAAAGTAACAAAGTACTTAT
370109 CTTGATATGAGCAGCCAA
66 CTTGATATGAGCAGCCAA
370127 TTACCCCAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 72 0.96
95 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (94 bp):
CTTAAGCAACAAAGTACCTTAATAAGTATTAACCATCAACAAGACAAAAGTAACAAAGTACTTAT
CTTGATATGAGCAGCCAACCACAAATTCC
Found at i:370222 original size:219 final size:219
Alignment explanation
Indices: 369814--370233 Score: 537
Period size: 219 Copynumber: 1.9 Consensus size: 219
369804 CCAATTCCAC
** * *
369814 CCACAAATTTTCTTAAGTAACTAAGTACCTTAAAAAGTATTAACCATCAACACGCAAAAAGTAAC
1 CCACAAATTCCCTTAAGCAACTAAGTACCTTAAAAAGTATTAACCATCAACAAGCAAAAAGTAAC
* * ** *
369879 CAAGTATATATATCTTGATATGAGCAGCAAATTACCTACAAATTTATTCAATTCTACCACCTATA
66 AAAGTATATATATCTTGATATGAGCAGCAAATTACCAACAAATAGATTCAATTCTACCACCCATA
* *
369944 AAGTCTCTTAAGTAACAAAGTACCTTATTAAGTATTAACCATCAAAACGACAAAAGTAACCAAGT
131 AAATCTCTTAAGTAACAAAGTACCTTATTAAGTATTAACCATCAAAACGAAAAAAGTAACCAAGT
370009 ATATATCTTGATATGAGCAGCCAA
196 ATATATCTTGATATGAGCAGCCAA
* * *
370033 CCACAAATTCCCTTAAGCAACTAAGTACCTTAATAAGTATTAACCATCAACAAG-ACATAAGTGA
1 CCACAAATTCCCTTAAGCAACTAAGTACCTTAAAAAGTATTAACCATCAACAAGCA-AAAAGTAA
* * * *
370097 CAAAGTA-CT-TATCTTGATATGAGCAGCCAATTACCCCAAGAAATAGATTCAATTTTACCACCC
65 CAAAGTATATATATCTTGATATGAGCAGCAAATTA--CCAACAAATAGATTCAATTCTACCACCC
* * * * *
370160 A-AAAATTTCTATCAGTTAACTACGTACCTTCTTAAGTATTAACCATC-AAA-GAAAATAAGTAA
128 ATAAAATCTCT-TAAG-TAACAAAGTACCTTATTAAGTATTAACCATCAAAACGAAAA-AAGTAA
370222 CCAAGTATATAT
190 CCAAGTATATAT
370234 ATATGTATGT
Statistics
Matches: 172, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
217 23 0.13
218 13 0.08
219 108 0.63
220 28 0.16
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (219 bp):
CCACAAATTCCCTTAAGCAACTAAGTACCTTAAAAAGTATTAACCATCAACAAGCAAAAAGTAAC
AAAGTATATATATCTTGATATGAGCAGCAAATTACCAACAAATAGATTCAATTCTACCACCCATA
AAATCTCTTAAGTAACAAAGTACCTTATTAAGTATTAACCATCAAAACGAAAAAAGTAACCAAGT
ATATATCTTGATATGAGCAGCCAA
Found at i:372643 original size:23 final size:23
Alignment explanation
Indices: 372616--372667 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
372606 CAATATTTTG
372616 ATAAATACATGTGTCTATTTATA
1 ATAAATACATGTGTCTATTTATA
** *
372639 ATAAAATTTATGTGTCTATTTGTA
1 AT-AAATACATGTGTCTATTTATA
372663 ATAAA
1 ATAAA
372668 ATTTTTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (23 bp):
ATAAATACATGTGTCTATTTATA
Found at i:372651 original size:24 final size:24
Alignment explanation
Indices: 372624--372671 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
372614 TGATAAATAC
372624 ATGTGTCTATTTATAATAAAATTT
1 ATGTGTCTATTTATAATAAAATTT
*
372648 ATGTGTCTATTTGTAATAAAATTT
1 ATGTGTCTATTTATAATAAAATTT
372672 TTAATCTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATGTGTCTATTTATAATAAAATTT
Found at i:379905 original size:20 final size:20
Alignment explanation
Indices: 379880--379960 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
379870 CAAAAATATT
379880 AAATTA-ATATAAATTCATAA
1 AAATTATATA-AAATTCATAA
*
379900 AAATTATATAAAATTGATAA
1 AAATTATATAAAATTCATAA
* *
379920 AACA-TATCTAAAA-T-ATTTA
1 AA-ATTATATAAAATTCA-TAA
*
379939 AAATTTTATAAAA-TCATAA
1 AAATTATATAAAATTCATAA
379958 AAA
1 AAA
379961 CTCATAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.04
19 18 0.36
20 26 0.52
21 4 0.08
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (20 bp):
AAATTATATAAAATTCATAA
Found at i:379912 original size:10 final size:10
Alignment explanation
Indices: 379875--380038 Score: 57
Period size: 10 Copynumber: 16.8 Consensus size: 10
379865 TCATACAAAA
*
379875 ATATTAAATT
1 ATATAAAATT
379885 A-ATATAAATT
1 ATATA-AAATT
379895 CATA-AAAATT
1 -ATATAAAATT
379905 ATATAAAATT
1 ATATAAAATT
379915 GATA-AAACA-T
1 -ATATAAA-ATT
*
379925 ATCTAAAA-T
1 ATATAAAATT
*
379934 ATTTAAAATT
1 ATATAAAATT
* *
379944 TTATAAAATC
1 ATATAAAATT
*
379954 ATA-AAAACT
1 ATATAAAATT
*
379963 -CATAAAATT
1 ATATAAAATT
379972 -TATTGAAAATT
1 ATA-T-AAAATT
379983 ATA-AGAAATT
1 ATATA-AAATT
*
379993 -TACTAAAAAT
1 ATA-TAAAATT
* *
380003 GT-TAAATTT
1 ATATAAAATT
*
380012 GATATAAACTT
1 -ATATAAAATT
380023 AT-TAAAATT
1 ATATAAAATT
380032 ATA-AAAA
1 ATATAAAA
380039 AATCATAAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 39
0.67 0.10 0.22
Matches are distributed among these distances:
8 1 0.01
9 46 0.39
10 47 0.40
11 20 0.17
12 3 0.03
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (10 bp):
ATATAAAATT
Found at i:380556 original size:9 final size:9
Alignment explanation
Indices: 380534--380646 Score: 79
Period size: 10 Copynumber: 12.0 Consensus size: 9
380524 CCAATTCAAG
*
380534 TTTTTATGAT
1 TTTTTAT-AA
380544 TTTTTATAA
1 TTTTTATAA
380553 TTTTTATAA
1 TTTTTATAA
380562 TTTTATATCAA
1 TTTT-TAT-AA
*
380573 TTTTAAT-A
1 TTTTTATAA
*
380581 TTTTTAATCA
1 TTTTT-ATAA
*
380591 TTTCTA-ATA
1 TTTTTATA-A
*
380600 TTTTTAATGA
1 TTTTT-ATAA
380610 TTTTTATAA
1 TTTTTATAA
*
380619 GTTTTTAAGAA
1 -TTTTT-ATAA
380630 TTTTTAT-A
1 TTTTTATAA
380638 TTTTTATAA
1 TTTTTATAA
380647 AAAATTAAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
8 13 0.16
9 27 0.33
10 34 0.41
11 9 0.11
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:380558 original size:19 final size:18
Alignment explanation
Indices: 380534--380714 Score: 105
Period size: 20 Copynumber: 9.4 Consensus size: 18
380524 CCAATTCAAG
*
380534 TTTTTATGATTTTTTATAA
1 TTTTTAT-ATTTTTAATAA
*
380553 TTTTTATAATTTTATATCAA
1 TTTTTATATTTTTA-AT-AA
* *
380573 TTTTAATATTTTTAATCA
1 TTTTTATATTTTTAATAA
* *
380591 TTTCTAATATTTTTAATGA
1 TTT-TTATATTTTTAATAA
*
380610 TTTTTATAAGTTTTTAAGAA
1 TTTTTAT-A-TTTTTAATAA
*
380630 TTTTTATATTTTTATAAAAA
1 TTTTTATA-TTTT-TAATAA
* ** *
380650 ATTAAATATTTTTATTAA
1 TTTTTATATTTTTAATAA
*
380668 TTTTTAAAGATTTTTAA-AA
1 TTTTT--ATATTTTTAATAA
380687 TTTTTTTATGATCTTTTAAT-A
1 --TTTTTAT-AT-TTTTAATAA
380708 TTTTTAT
1 TTTTTAT
380715 GAGAAATATT
Statistics
Matches: 127, Mismatches: 22, Indels: 26
0.73 0.13 0.15
Matches are distributed among these distances:
18 18 0.14
19 48 0.38
20 49 0.39
21 12 0.09
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTTATATTTTTAATAA
Found at i:380574 original size:11 final size:10
Alignment explanation
Indices: 380542--380645 Score: 53
Period size: 9 Copynumber: 10.8 Consensus size: 10
380532 AGTTTTTATG
*
380542 ATTTTTTATA
1 ATTTTATATA
380552 ATTTT-TATA
1 ATTTTATATA
380561 ATTTTATATCA
1 ATTTTATAT-A
380572 ATTTTA-ATA
1 ATTTTATATA
* *
380581 TTTTTA-ATC
1 ATTTTATATA
380590 ATTTCTA-ATA
1 ATTT-TATATA
* *
380600 TTTTTA-ATG
1 ATTTTATATA
380609 ATTTT-TATA
1 ATTTTATATA
*
380618 AGTTTT-TAAGA
1 A-TTTTAT-ATA
380629 ATTTT-TATA
1 ATTTTATATA
*
380638 TTTTTATA
1 ATTTTATA
380646 AAAAATTAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
9 37 0.49
10 29 0.38
11 10 0.13
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (10 bp):
ATTTTATATA
Found at i:380681 original size:9 final size:9
Alignment explanation
Indices: 380544--380691 Score: 66
Period size: 10 Copynumber: 15.6 Consensus size: 9
380534 TTTTTATGAT
*
380544 TTTTTATAA
1 TTTTTAAAA
*
380553 TTTTTATAA
1 TTTTTAAAA
*
380562 TTTTATATCAA
1 TTTT-TA-AAA
*
380573 -TTTTAATA
1 TTTTTAAAA
*
380581 TTTTTAATCA
1 TTTTTAA-AA
* *
380591 TTTCTAATA
1 TTTTTAAAA
*
380600 TTTTTAATGA
1 TTTTTAA-AA
*
380610 TTTTTATAAG
1 TTTTTA-AAA
380620 TTTTTAAGAA
1 TTTTTAA-AA
*
380630 TTTTT-ATA
1 TTTTTAAAA
380638 TTTTTATAAA
1 TTTTTA-AAA
***
380648 AAATTAAATA
1 TTTTTAAA-A
*
380658 TTTTTATTAA
1 TTTTTA-AAA
380668 TTTTTAAAGA
1 TTTTTAAA-A
380678 TTTTTAAAA
1 TTTTTAAAA
380687 TTTTT
1 TTTTT
380692 TTATGATCTT
Statistics
Matches: 106, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
8 7 0.07
9 39 0.37
10 56 0.53
11 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:380692 original size:21 final size:21
Alignment explanation
Indices: 380668--380712 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
380658 TTTTTATTAA
*
380668 TTTTTAAAGAT-TTTTAAAAT
1 TTTTTTAAGATCTTTTAAAAT
* *
380688 TTTTTTATGATCTTTTAATAT
1 TTTTTTAAGATCTTTTAAAAT
380709 TTTT
1 TTTT
380713 ATGAGAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTTAAGATCTTTTAAAAT
Found at i:383597 original size:23 final size:22
Alignment explanation
Indices: 383562--383610 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
383552 TCAAGCTTGG
383562 TCGACAAAATCAG-ATTTATCATC
1 TCGACAAAATCAGAATTT-TCA-C
* *
383585 TCGACTAACTCAGAATTTTCAC
1 TCGACAAAATCAGAATTTTCAC
383607 TCGA
1 TCGA
383611 TTTGACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (22 bp):
TCGACAAAATCAGAATTTTCAC
Found at i:387929 original size:20 final size:23
Alignment explanation
Indices: 387902--387966 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
387892 CCTGATTAGT
*
387902 ATACGACACAT-AAGTGCTTGA-
1 ATACGACACATAAAGTGCCTGAG
387923 A-ACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
387945 ATACGGCACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
387967 TCGGCAAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.23
21 10 0.26
22 1 0.03
23 19 0.49
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:388583 original size:10 final size:10
Alignment explanation
Indices: 388568--388592 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
388558 ATTAATTTCA
388568 AATTTTCCTC
1 AATTTTCCTC
388578 AATTTTCCTC
1 AATTTTCCTC
388588 AATTT
1 AATTT
388593 AATCGCTAAA
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:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTTTCCTC
Found at i:390329 original size:51 final size:51
Alignment explanation
Indices: 390234--390335 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
390224 ACCTTATGGT
* ** *
390234 TTGTGTTGCAATACTGATGGCAGTCTACTCGTCTTGGGTGTATCTTTAGGG
1 TTGTGTTGCAATACTGATGACAGTCTACTCGTCTTGGGCATATCTTCAGGG
*
390285 TTGTGTTGCGATACTGATGACAGTCTACTCGTCTTGGGCATATCTTCAGGG
1 TTGTGTTGCAATACTGATGACAGTCTACTCGTCTTGGGCATATCTTCAGGG
390336 CTATGTCGCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.37
Consensus pattern (51 bp):
TTGTGTTGCAATACTGATGACAGTCTACTCGTCTTGGGCATATCTTCAGGG
Found at i:390939 original size:54 final size:54
Alignment explanation
Indices: 390861--390966 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
390851 TACTTGAACT
*
390861 TGGGAACTAGATTCATTTTGGTCCCTAAACCTTAAATAAGTTCAAGAACTAAAA
1 TGGGAACTAGATTCATTTTAGTCCCTAAACCTTAAATAAGTTCAAGAACTAAAA
* **
390915 TGGGAACTAGATTCATTTTAGTCCCTAAACCTTGAATAAGTTTGAGAACTAA
1 TGGGAACTAGATTCATTTTAGTCCCTAAACCTTAAATAAGTTCAAGAACTAA
390967 CATGAATCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (54 bp):
TGGGAACTAGATTCATTTTAGTCCCTAAACCTTAAATAAGTTCAAGAACTAAAA
Found at i:391914 original size:22 final size:23
Alignment explanation
Indices: 391860--391933 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 23
391850 CTAATCCTCT
*
391860 CTCAAATTTCCTCTCAATTTCTT
1 CTCAAATTTCCTCTCAATTTCTG
*
391883 CT-AAATTTCCTCTCAATTTGTG
1 CTCAAATTTCCTCTCAATTTCTG
391905 CTCAAA-TTCCT-TCAAAATTTCT-
1 CTCAAATTTCCTCTC--AATTTCTG
391927 CTCAAAT
1 CTCAAAT
391934 CCATATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
21 2 0.05
22 31 0.70
23 11 0.25
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (23 bp):
CTCAAATTTCCTCTCAATTTCTG
Found at i:391933 original size:11 final size:11
Alignment explanation
Indices: 391857--391933 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
391847 AAACTAATCC
391857 TCTCTCAAATT
1 TCTCTCAAATT
391868 TCCTCTC-AATT
1 T-CTCTCAAATT
391879 TCT-TCTAAATT
1 TCTCTC-AAATT
391890 TCCTCTC-AATT
1 T-CTCTCAAATT
*
391901 TGTGCTCAAATT
1 TCT-CTCAAATT
*
391913 CCT-TCAAAATT
1 TCTCTC-AAATT
391924 TCTCTCAAAT
1 TCTCTCAAAT
391934 CCATATTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
9 2 0.04
10 5 0.09
11 30 0.57
12 14 0.26
13 2 0.04
ACGTcount: A:0.26, C:0.27, G:0.03, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:391960 original size:51 final size:51
Alignment explanation
Indices: 391895--391992 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
391885 AAATTTCCTC
391895 TCAATTTGTGCTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGTGCTCAAATTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
* * * *
391946 TCAATTTGCT-CTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTG-TGCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTT
391993 TTAAATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 39 0.95
52 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (51 bp):
TCAATTTGTGCTCAAATTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:392032 original size:10 final size:11
Alignment explanation
Indices: 391989--392015 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
391979 TTAAATCCCT
391989 ATTTTTAAATA
1 ATTTTTAAATA
392000 ATTTTTAAATA
1 ATTTTTAAATA
392011 ATTTT
1 ATTTT
392016 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTTAAATA
Found at i:393610 original size:18 final size:18
Alignment explanation
Indices: 393583--393622 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
393573 CAGGTGCGTT
* *
393583 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
393601 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
393619 TCCT
1 TCCT
393623 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:393904 original size:21 final size:21
Alignment explanation
Indices: 393880--393924 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
393870 GCCCTACTGA
*
393880 AAGAACCAGAATCC-CCGCCAG
1 AAGAACCACAA-CCGCCGCCAG
393901 AAGAACCACAACCGCCGCCAG
1 AAGAACCACAACCGCCGCCAG
393922 AAG
1 AAG
393925 CTGGACAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.40, C:0.38, G:0.20, T:0.02
Consensus pattern (21 bp):
AAGAACCACAACCGCCGCCAG
Found at i:394192 original size:22 final size:22
Alignment explanation
Indices: 394167--394595 Score: 526
Period size: 22 Copynumber: 19.4 Consensus size: 22
394157 TTTAATTGAC
* *
394167 AAACCTTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
394189 AAACCCTAACTCTAACCCTTAAATTAA
1 AAACCCT-A----AACCCTTAACTTAA
*
394216 AAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
394238 AAACCATAATCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
394260 AAACCCTAACCCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
394282 AAACCCT-AACCATTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
394303 AAACCCATAAACCCTTAACCTAA
1 AAACCC-TAAACCCTTAACTTAA
* ** *
394326 AAATCCT-AACTTTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
394347 AAACCCTAAACTCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
394369 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
394391 AAACCCT-AACCTTTTACCTTAA
1 AAACCCTAAACC-CTTAACTTAA
394413 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
394435 AAACTCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
** * *
394457 AAACTGTAACCCCTTAACTAAA
1 AAACCCTAAACCCTTAACTTAA
394479 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
394500 AAATCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
394522 AAACTCTAACCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
394544 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
394565 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
394587 AAACCCTAA
1 AAACCCTAA
394596 CGTGTCAGCA
Statistics
Matches: 350, Mismatches: 45, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
21 74 0.21
22 235 0.67
23 21 0.06
26 1 0.00
27 19 0.05
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:394238 original size:27 final size:27
Alignment explanation
Indices: 394175--394234 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
394165 ACAAACCTTA
** *
394175 AACCCTTAACCTAAAAACCCTAACTCT
1 AACCCTTAAATTAAAAACCCTAACCCT
394202 AACCCTTAAATTAAAAACCCTAAACCCTT
1 AACCCTTAAATTAAAAACCCT-AACCC-T
394231 AACC
1 AACC
394235 TAAAAACCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 19 0.68
28 4 0.14
29 5 0.18
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (27 bp):
AACCCTTAAATTAAAAACCCTAACCCT
Found at i:394271 original size:65 final size:63
Alignment explanation
Indices: 394200--394596 Score: 506
Period size: 65 Copynumber: 6.1 Consensus size: 63
394190 AACCCTAACT
* * *
394200 CTAACCCTTAAATTAAAAACCCTAAACCCTTAACCTAAAAACCATAATCCCTTAACTTAAAAACC
1 CTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACC-TAAACCCTTAACTTAAAAACC
* * * * *
394265 CTAACCCCTTAACCTAAAAACCCTAACCATTAACTTTAAAACCCATAAACCCTTAACCTAAAAAT
1 CTAA-CCCTTAACTTAAAAACCCTAACCCTTAAC-TTAAAAACC-TAAACCCTTAACTTAAAAAC
394330 C
63 C
** * *
394331 CTAACTTTTAACTTTAAAACCCTAAACTCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACC
1 CTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAA-CCTAAACCCTTAACTTAAAAACC
* *
394396 CTAACCTTTTACCTTAAAAACCCTAAACCCTTAACTTAAAAACTCTAAACCCTTAACTTAAAAAC
1 CTAACC-CTTAACTTAAAAACCCT-AACCCTTAACTTAAAAAC-CTAAACCCTTAACTTAAAAAC
*
394461 T
63 C
* * *
394462 GTAACCCCTTAACTAAAAAACCCTAACCCTTAACTTAAAAATCCTAAACCCTTAACTTAAAAACT
1 CTAA-CCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAA-CCTAAACCCTTAACTTAAAAACC
394527 CTAACCCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACC
1 CTAA-CCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAA-CCTAAACCCTTAACTTAAAAACC
394592 CTAAC
1 CTAAC
394597 GTGTCAGCAA
Statistics
Matches: 294, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
64 1 0.00
65 163 0.55
66 128 0.44
67 2 0.01
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (63 bp):
CTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCTAAACCCTTAACTTAAAAACC
Found at i:396410 original size:25 final size:23
Alignment explanation
Indices: 396394--396478 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 23
396384 CTGAATAACA
396394 GGAAGCTCATGCAAGCTAAGTATC
1 GGAAGCTCATGCAAGCTAA-TATC
**
396418 GGAAAGCTCATGTGAGCTAAATATC
1 GG-AAGCTCATGCAAGCT-AATATC
**
396443 GGGAAGCTCATGTGAGCTAAATATC
1 -GGAAGCTCATGCAAGCT-AATATC
396468 GAGAAGCTCAT
1 G-GAAGCTCAT
396479 AAGAGTTGTG
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
24 3 0.05
25 48 0.87
26 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (23 bp):
GGAAGCTCATGCAAGCTAATATC
Found at i:396434 original size:50 final size:50
Alignment explanation
Indices: 396370--396478 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
396360 CTATAAGCGG
* * * *
396370 GAAGCTCCTTTGAGCTGAATAACAGGAAGCTCATGCAAGCTAAGTATCG-
1 GAAGCTCATGTGAGCTAAATAACAGGAAGCTCATGCAAGCTAAATATCGA
* * **
396419 GAAAGCTCATGTGAGCTAAATATCGGGAAGCTCATGTGAGCTAAATATCGA
1 G-AAGCTCATGTGAGCTAAATAACAGGAAGCTCATGCAAGCTAAATATCGA
396470 GAAGCTCAT
1 GAAGCTCAT
396479 AAGAGTTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 48 0.96
51 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (50 bp):
GAAGCTCATGTGAGCTAAATAACAGGAAGCTCATGCAAGCTAAATATCGA
Found at i:398723 original size:25 final size:25
Alignment explanation
Indices: 398671--398723 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
398661 CACTCTCTTT
**
398671 AGCCATAGAATAGGAAGCTCATGTG
1 AGCCATAGAATAGGAAGCTCATCCG
*
398696 AGCCAT-GTAATAGGAAGCTTATCCG
1 AGCCATAG-AATAGGAAGCTCATCCG
398721 AGC
1 AGC
398724 TATAACAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (25 bp):
AGCCATAGAATAGGAAGCTCATCCG
Found at i:399808 original size:19 final size:19
Alignment explanation
Indices: 399786--399823 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
399776 AATATAAAAA
399786 TTACTAAAAACGAGACAAG
1 TTACTAAAAACGAGACAAG
399805 TTACTAAAAACGAGACAAG
1 TTACTAAAAACGAGACAAG
399824 AATTCATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (19 bp):
TTACTAAAAACGAGACAAG
Found at i:402312 original size:23 final size:23
Alignment explanation
Indices: 402284--402411 Score: 148
Period size: 23 Copynumber: 5.5 Consensus size: 23
402274 CAATTTGTCG
* *
402284 TCAATTCATCCTTTACATTGCCG
1 TCAATTCATCCTTTACATTTCCA
* *
402307 TCAATTCATCCTTTACATTACCG
1 TCAATTCATCCTTTACATTTCCA
* *
402330 TCAGTTCCTCCTTTACATTTTCCA
1 TCAATTCATCCTTTACA-TTTCCA
* * *
402354 TTAGTTCCTCCTTTACATTTTCCA
1 TCAATTCATCCTTTACA-TTTCCA
*
402378 TCAATTCATCCTTTACATTTTCA
1 TCAATTCATCCTTTACATTTCCA
402401 TCAATTCATCC
1 TCAATTCATCC
402412 ATTAATAATA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
23 53 0.56
24 41 0.44
ACGTcount: A:0.22, C:0.30, G:0.04, T:0.44
Consensus pattern (23 bp):
TCAATTCATCCTTTACATTTCCA
Found at i:402364 original size:24 final size:24
Alignment explanation
Indices: 402292--402403 Score: 122
Period size: 24 Copynumber: 4.8 Consensus size: 24
402282 CGTCAATTCA
* * * *
402292 TCCTTTACA-TTGCCGTCAATTCA
1 TCCTTTACATTTTCCATCAGTTCC
* *
402315 TCCTTTACA-TTACCGTCAGTTCC
1 TCCTTTACATTTTCCATCAGTTCC
*
402338 TCCTTTACATTTTCCATTAGTTCC
1 TCCTTTACATTTTCCATCAGTTCC
* *
402362 TCCTTTACATTTTCCATCAATTCA
1 TCCTTTACATTTTCCATCAGTTCC
402386 TCCTTTACATTTT-CATCA
1 TCCTTTACATTTTCCATCA
402404 ATTCATCCAT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
23 34 0.43
24 45 0.57
ACGTcount: A:0.21, C:0.30, G:0.04, T:0.45
Consensus pattern (24 bp):
TCCTTTACATTTTCCATCAGTTCC
Found at i:409426 original size:20 final size:20
Alignment explanation
Indices: 409389--409426 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
409379 AAGAAAATAA
*
409389 CGATACCCTAGTGTCAGTAT
1 CGATACCCTAGTGACAGTAT
409409 CGATA-CCTACGTGACAGT
1 CGATACCCTA-GTGACAGT
409427 TTTGGGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
CGATACCCTAGTGACAGTAT
Found at i:415418 original size:16 final size:16
Alignment explanation
Indices: 415397--415448 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
415387 GATTTGCTAT
415397 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
415413 TACACCCCTAATCCAA
1 TACACCTCTAATCCAA
415429 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
415445 TACA
1 TACA
415449 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:418452 original size:28 final size:28
Alignment explanation
Indices: 418386--418450 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
418376 ATTTAATTAT
*
418386 TTTATTTTTTATTTTTAAGTAAATAAGA
1 TTTATTTTTTATTTTGAAGTAAATAAGA
*
418414 TTCATTTTTTATTTTGAA-TCAAATAA-A
1 TTTATTTTTTATTTTGAAGT-AAATAAGA
418441 TTTATTTTTT
1 TTTATTTTTT
418451 TAAAGTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.33
28 22 0.67
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTATTTTTTATTTTGAAGTAAATAAGA
Found at i:419451 original size:28 final size:29
Alignment explanation
Indices: 419420--419476 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
419410 TCTAGTTTCC
419420 TTTG-TTTTTTTCTTTTTAGAATTAATTT
1 TTTGTTTTTTTTCTTTTTAGAATTAATTT
419448 TTTGTTTTTTTTCTTTTTAGAATTAATTT
1 TTTGTTTTTTTTCTTTTTAGAATTAATTT
419477 CCTCAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.72
Consensus pattern (29 bp):
TTTGTTTTTTTTCTTTTTAGAATTAATTT
Found at i:425217 original size:16 final size:16
Alignment explanation
Indices: 425166--425219 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
425156 TTTGGTTCGC
* *
425166 TGTATTGGAATAGAGC
1 TGTAATGGAATAGAGA
* *
425182 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGA
*
425198 TGTAATGGATTAGAGA
1 TGTAATGGAATAGAGA
425214 TGTAAT
1 TGTAAT
425220 AGCAAATCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:425562 original size:14 final size:15
Alignment explanation
Indices: 425523--425564 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
425513 NNNNAACATA
*
425523 ATTATTATTAAATAT
1 ATTATAATTAAATAT
425538 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
425552 A-TATAATTTAATA
1 ATTATAATTAAATA
425565 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:438364 original size:13 final size:13
Alignment explanation
Indices: 438328--438366 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
438318 ATTATTGTTT
438328 TTTATATTCATTTTG
1 TTTATATT-A-TTTG
438343 TTTAT-TTATTTG
1 TTTATATTATTTG
438355 TTTATATTATTT
1 TTTATATTATTT
438367 CTATGTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 7 0.30
14 2 0.09
15 5 0.22
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTATATTATTTG
Found at i:442840 original size:14 final size:15
Alignment explanation
Indices: 442823--442856 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
442813 AAAAAAGATG
442823 GAAAAAATG-AAAAT
1 GAAAAAATGAAAAAT
442837 G-AAAAATGAAAAAT
1 GAAAAAATGAAAAAT
442851 GAAAAA
1 GAAAAA
442857 GGAGAGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.39
14 7 0.39
15 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (15 bp):
GAAAAAATGAAAAAT
Found at i:442842 original size:7 final size:7
Alignment explanation
Indices: 442825--442856 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
442815 AAAAGATGGA
442825 AAAAATG
1 AAAAATG
442832 -AAAATG
1 AAAAATG
442838 AAAAATG
1 AAAAATG
442845 AAAAATG
1 AAAAATG
442852 AAAAA
1 AAAAA
442857 GGAGAGGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:443503 original size:12 final size:12
Alignment explanation
Indices: 443486--443510 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
443476 AAATTGAGAC
443486 TATCCCTTCAGA
1 TATCCCTTCAGA
443498 TATCCCTTCAGA
1 TATCCCTTCAGA
443510 T
1 T
443511 TTTGTTGTCA
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:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TATCCCTTCAGA
Found at i:444260 original size:44 final size:44
Alignment explanation
Indices: 444196--444282 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
444186 CCCTTAGCCT
**
444196 TATCTCCCTGGTCAGTAGTGGAATAAGTT-ACAGATTATGAATCC
1 TATCTCCCTGGTCAACAGTGGAATAAGTTGA-AGATTATGAATCC
* * *
444240 TATCTCCCTGGTTAACAGTGGAATAGGTTGAAGATTGTGAATC
1 TATCTCCCTGGTCAACAGTGGAATAAGTTGAAGATTATGAATC
444283 TTACTTTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
44 36 0.97
45 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (44 bp):
TATCTCCCTGGTCAACAGTGGAATAAGTTGAAGATTATGAATCC
Found at i:444505 original size:169 final size:169
Alignment explanation
Indices: 444301--444938 Score: 943
Period size: 169 Copynumber: 3.8 Consensus size: 169
444291 CTAACGTTAT
* *
444301 AGCGGAGCAGATTAAAGCTAAGGACAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
* * * *
444366 GAAGTAGAGCAGATTAAAGCTGTGGCCAGTGAATCCTATCTCTTTGGCATTATAGTGGAACAAAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
444431 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
* * *
444470 AGCGGAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTAAGAGTTGAAATAGCT
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
* * * * *
444535 GAAGTGAAGCGGATTAAAGCTGTGGGCAGTGAATCTTATCTCTTTGGCATTGTAGTGGAACAGAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
*
444600 TAAAGCTAAAGGTAGCAAATCTTGTTTCCCTAGTGTTGC
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
* * * * *
444639 AGTGGAGCATATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTTGTGTTAAGAGTTGAAATAGCA
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
* * * *
444704 GAAGTGGAACAGATTAAAGCTGTGGGTAGCGAATTCTATCTCTTTGGCATTATAGTGGTACAGAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
*
444769 TAAAGCTAAAGGTAGTGAATCTTGTTTCCCTAGTGTTGC
131 TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
* * * * *
444808 AGCAGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTAGCGTTAAGACTTGGATTAGCT
1 AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
** * * * * *
444873 GAAGTGGAGTGGATTGAAGCTGTGGGTAGCGAATCCTATCTCTTTGGCATTACAGTGAAAAAGAT
66 GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
444938 T
131 T
444939 GAAGTCGCAA
Statistics
Matches: 422, Mismatches: 47, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
169 422 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (169 bp):
AGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTGGTGTTAAGACTTGAAATAGCT
GAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAATCCTATCTCTTTGGCATTATAGTGGAACAGAT
TAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGC
Found at i:444518 original size:51 final size:51
Alignment explanation
Indices: 444372--444519 Score: 125
Period size: 51 Copynumber: 2.9 Consensus size: 51
444362 AGCTGAAGTA
* * * * * * ** * *
444372 GAGCAGATTAAAGCTGTGGCCAGTGAATCCTATCTCTTTGGCATTATAGTG
1 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTACAGCG
* * * * * * * * *
444423 GAACAAATTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTAGTGTTGCAGCG
1 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTACAGCG
444474 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTA
1 GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTA
444520 AGAGTTGAAA
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (51 bp):
GAGCAAATTAAAGCTGAGGGCAGCGAATCTTATCTCCTTGGTGTTACAGCG
Found at i:444672 original size:51 final size:51
Alignment explanation
Indices: 444588--444687 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 51
444578 TTGGCATTGT
* * *
444588 AGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTGTTTCCCTAGTGTTGC
1 AGTGGAACAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTAGTGTTGC
* * * * * *
444639 AGTGGAGCATATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTTGTGTT
1 AGTGGAACAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTAGTGTT
444688 AAGAGTTGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (51 bp):
AGTGGAACAGATTAAAGCTAAAGGCAGCAAATCTTATCTCCCTAGTGTTGC
Found at i:445388 original size:44 final size:43
Alignment explanation
Indices: 445316--445437 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 43
445306 GAAGATGGCG
* * * * * *
445316 AATCTTATCTCCCTAAAGTTGCAATAGAGCAGATTGAAGCCAC
1 AATCTTATCTCCCTGAAGATGCAGTAGAGTAGATTAAAACCAC
*
445359 TAATCTTATCTCCCTGAAG-TGCCAGTAGAGTGGATTAAAACCAC
1 -AATCTTATCTCCCTGAAGATG-CAGTAGAGTAGATTAAAACCAC
**
445403 AGATCTTATCTCTTTGAAGATGCAGTAGAGTAGAT
1 A-ATCTTATCTCCCTGAAGATGCAGTAGAGTAGAT
445438 CACATCGGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
43 3 0.05
44 61 0.92
45 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGATGCAGTAGAGTAGATTAAAACCAC
Found at i:445497 original size:45 final size:44
Alignment explanation
Indices: 445446--445562 Score: 135
Period size: 45 Copynumber: 2.6 Consensus size: 44
445436 ATCACATCGG
* *
445446 GTCTTATCTCCCTGAAGTTCCAGTGGAGCAGACTCAAGAAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAA-CAA
* * * *
445491 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAACAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAACAA
* * * *
445535 ATCCTATCTCCCTAAAGTTGTAGTGGAG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAG
445563 TAGATTAGAA
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 24 0.41
45 35 0.59
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAACAA
Found at i:447678 original size:13 final size:13
Alignment explanation
Indices: 447642--447680 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
447632 ATTATTGTTT
447642 TTTATATTCATTTTG
1 TTTATATT-A-TTTG
447657 TTTAT-TTATTTG
1 TTTATATTATTTG
447669 TTTATATTATTT
1 TTTATATTATTT
447681 CTATGTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 7 0.30
14 2 0.09
15 5 0.22
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTATATTATTTG
Found at i:449321 original size:16 final size:17
Alignment explanation
Indices: 449290--449322 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
449280 TCTAATAAGC
*
449290 ACTTTTGGAGAAAAATT
1 ACTTTTGGAAAAAAATT
449307 ACTTTT-GAAAAAAATT
1 ACTTTTGGAAAAAAATT
449323 TTAAATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (17 bp):
ACTTTTGGAAAAAAATT
Found at i:450269 original size:20 final size:21
Alignment explanation
Indices: 450232--450270 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
450222 AAAACAAAAA
**
450232 AAAAATAAATTTTGAAAGCCG
1 AAAAATAAAACTTGAAAGCCG
450253 AAAAATAAAACTT-AAAGC
1 AAAAATAAAACTTGAAAGC
450271 ATTTGATGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (21 bp):
AAAAATAAAACTTGAAAGCCG
Found at i:455564 original size:17 final size:17
Alignment explanation
Indices: 455542--455584 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
455532 ATTTGTATCG
455542 TCGTGAGCTCTTTAATC
1 TCGTGAGCTCTTTAATC
455559 TCGTGAGCTCTTTAATC
1 TCGTGAGCTCTTTAATC
455576 TCGTGAGCT
1 TCGTGAGCT
455585 AATATACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (17 bp):
TCGTGAGCTCTTTAATC
Found at i:456408 original size:28 final size:28
Alignment explanation
Indices: 456368--456425 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
456358 GCATACTCTG
456368 ATTCATCATTGGGATAAATCAAGATATC
1 ATTCATCATTGGGATAAATCAAGATATC
456396 ATTCATCATTGGGATAAATCAAGATATC
1 ATTCATCATTGGGATAAATCAAGATATC
456424 AT
1 AT
456426 CTATGAACGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (28 bp):
ATTCATCATTGGGATAAATCAAGATATC
Found at i:462287 original size:32 final size:32
Alignment explanation
Indices: 462249--462315 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
462239 ATGATGAGTA
* *
462249 ATATATGGAATTAGTAAATAATTTGAAATGCT
1 ATATATGGAATTAGTAAATAACTGGAAATGCT
462281 ATATATGGAATTAGTAAATAACTGGAAATGCT
1 ATATATGGAATTAGTAAATAACTGGAAATGCT
462313 ATA
1 ATA
462316 GCAAAGGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.34
Consensus pattern (32 bp):
ATATATGGAATTAGTAAATAACTGGAAATGCT
Found at i:466309 original size:26 final size:26
Alignment explanation
Indices: 466258--466336 Score: 104
Period size: 27 Copynumber: 3.0 Consensus size: 26
466248 GCTCGAGGCG
*
466258 ACCGAAATACCGCCATAGGATAAAATA
1 ACCGAAATACC-CCATAGGGTAAAATA
*
466285 ACCGAAATACCCCGTAGGGTAAAATA
1 ACCGAAATACCCCATAGGGTAAAATA
**
466311 ACTAAAATACCCCCATAGGGTAAAAT
1 ACCGAAATA-CCCCATAGGGTAAAAT
466337 GACTGTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 20 0.43
27 26 0.57
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.16
Consensus pattern (26 bp):
ACCGAAATACCCCATAGGGTAAAATA
Found at i:466349 original size:27 final size:27
Alignment explanation
Indices: 466262--466336 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
466252 GAGGCGACCG
* * **
466262 AAATACCGCCATAGGATAAAATAACCG
1 AAATACCCCCATAGGGTAAAATAACTA
*
466289 AAATA-CCCCGTAGGGTAAAATAACTA
1 AAATACCCCCATAGGGTAAAATAACTA
466315 AAATACCCCCATAGGGTAAAAT
1 AAATACCCCCATAGGGTAAAAT
466337 GACTGTTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 21 0.51
27 20 0.49
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATAACTA
Found at i:483475 original size:13 final size:13
Alignment explanation
Indices: 483457--483483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
483447 TTTCCAGAAA
483457 TTATGAATTTATT
1 TTATGAATTTATT
483470 TTATGAATTTATT
1 TTATGAATTTATT
483483 T
1 T
483484 AATGTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:483661 original size:50 final size:50
Alignment explanation
Indices: 483583--483875 Score: 417
Period size: 50 Copynumber: 5.8 Consensus size: 50
483573 ATTTGGGTAA
* * * *
483583 AGAGGTCCCCTGTAAGACTATGTCTGGGACATGGCATTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
483633 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
483683 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
**
483733 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * *
483783 AGAGGTACCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
483833 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
483876 TGTTATTATC
Statistics
Matches: 220, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
50 186 0.85
51 34 0.15
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:490388 original size:13 final size:13
Alignment explanation
Indices: 490370--490395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
490360 TATTAAAATG
490370 AATTAAAAGCCAA
1 AATTAAAAGCCAA
490383 AATTAAAAGCCAA
1 AATTAAAAGCCAA
490396 TTTTTGATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
AATTAAAAGCCAA
Found at i:491212 original size:51 final size:51
Alignment explanation
Indices: 491084--491213 Score: 163
Period size: 50 Copynumber: 2.6 Consensus size: 51
491074 NNNNNNNGGT
* * * ***
491084 CCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACAC
* *
491135 CCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACAC
1 CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACAC
* *
491185 CCCATTTAAGACCATGTTTGGGACATGGC
1 CCCATGTAAGACCATGTCTGGGACATGGC
491214 TTTGGCATGT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
50 42 0.63
51 25 0.37
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.20
Consensus pattern (51 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAACAC
Found at i:496132 original size:105 final size:104
Alignment explanation
Indices: 495950--496302 Score: 447
Period size: 105 Copynumber: 3.4 Consensus size: 104
495940 ACAGATCCTA
* * * * *
495950 ATTTTATAAAGGTTAGCTGATTTAAGATTGCAATCTATTCATCTTTGAGTTAGTTGATTTAATAT
1 ATTTTATAAAGGTTAACTAATTTAAGATTGCAACCTATTCATCTTTGAGTTAGCTGATTTAAAAT
* *
496015 CGCAACTCCTAAATAGCTCAATGACCTATGTTCACAATTG
66 CGCAACTCCTAAATAGCTCGATGACCTAT-TTCACAGTTG
* * * * * *
496055 ATTTTATAAAGGTTAGCTGATTTAAGGTTGCAACCTATTCATTTTTTATTTAGCTGATTTAAAAT
1 ATTTTATAAAGGTTAACTAATTTAAGATTGCAACCTATTCATCTTTGAGTTAGCTGATTTAAAAT
* * * * *
496120 TGTAACTTCTAAATAGCTCGATGACCTACATTCATAGTTG
66 CGCAACTCCTAAATAGCTCGATGACCTA-TTTCACAGTTG
* * *
496160 ATTATATAAAGGTTAACTAATTTAATATTGCAACCTATTCATCTTTGAGTTAGCTGATTTAAGAT
1 ATTTTATAAAGGTTAACTAATTTAAGATTGCAACCTATTCATCTTTGAGTTAGCTGATTTAAAAT
* *
496225 CGCAACTCCTAAACAGCTCGATAACCTACTTTCACAGTTG
66 CGCAACTCCTAAATAGCTCGATGACCTA-TTTCACAGTTG
*
496265 ATTTTAT-AAGTGTTAACTAATTTAAGATCGCAACCTAT
1 ATTTTATAAAG-GTTAACTAATTTAAGATTGCAACCTAT
496303 CTAGCACTAG
Statistics
Matches: 213, Mismatches: 33, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
104 3 0.01
105 210 0.99
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (104 bp):
ATTTTATAAAGGTTAACTAATTTAAGATTGCAACCTATTCATCTTTGAGTTAGCTGATTTAAAAT
CGCAACTCCTAAATAGCTCGATGACCTATTTCACAGTTG
Found at i:505611 original size:18 final size:19
Alignment explanation
Indices: 505569--505611 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
505559 ATTTACCAAC
*
505569 AAAAGTAGAAATAAAATTT
1 AAAAGTAGAAAGAAAATTT
*
505588 AGAAAGT-GAAAGAAATTTT
1 A-AAAGTAGAAAGAAAATTT
505607 AAAAG
1 AAAAG
505612 ATTACCTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 12 0.57
20 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.23
Consensus pattern (19 bp):
AAAAGTAGAAAGAAAATTT
Found at i:506917 original size:31 final size:29
Alignment explanation
Indices: 506851--506915 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
506841 TATCTTATAT
* *
506851 TTTTATAAATTTTAAAAAATTAAATTAAA
1 TTTTATCATTTTTAAAAAATTAAATTAAA
506880 TTTTTATCATTTTTAAAACAATTAAAATATAAA
1 -TTTTATCATTTTTAAAA-AATT-AAAT-TAAA
506913 TTT
1 TTT
506916 ATTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 15 0.50
31 4 0.13
32 7 0.23
33 4 0.13
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTTATCATTTTTAAAAAATTAAATTAAA
Found at i:507060 original size:129 final size:130
Alignment explanation
Indices: 506909--507172 Score: 514
Period size: 129 Copynumber: 2.0 Consensus size: 130
506899 AATTAAAATA
506909 TAAATTTATTTTTATTAATTTAAAATTTTTAAAATTTTAAACCAGGTAAATGAAAATTTTTACAG
1 TAAATTTATTTTTATTAATTTAAAATTTTTAAAATTTTAAACCAGGTAAATGAAAATTTTTACAG
506974 CTGCCGTCTCCTTAGATACCCCCTGCTAAGCGAATCACGTAAATTCTAAAATATAAAGTCCGTTC
66 CTGCCGTCTCCTTAGATACCCCCTGCTAAGCGAATCACGTAAATTCTAAAATATAAAGTCCGTTC
507039 TAAATTTA-TTTTATTAATTTAAAATTTTTAAAATTTTAAACCAGGTAAATGAAAATTTTTACAG
1 TAAATTTATTTTTATTAATTTAAAATTTTTAAAATTTTAAACCAGGTAAATGAAAATTTTTACAG
507103 CTGCCGTCTCCTTAGATACCCCCTGCTAAGCGAATCACGTAAATTCTAAAATATAAAGTCCGTTC
66 CTGCCGTCTCCTTAGATACCCCCTGCTAAGCGAATCACGTAAATTCTAAAATATAAAGTCCGTTC
507168 -AAATT
1 TAAATT
507173 GGATTACCTT
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
128 5 0.04
129 121 0.90
130 8 0.06
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (130 bp):
TAAATTTATTTTTATTAATTTAAAATTTTTAAAATTTTAAACCAGGTAAATGAAAATTTTTACAG
CTGCCGTCTCCTTAGATACCCCCTGCTAAGCGAATCACGTAAATTCTAAAATATAAAGTCCGTTC
Found at i:518901 original size:17 final size:18
Alignment explanation
Indices: 518862--518903 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
518852 TTTAAGAATG
*
518862 TTTTTATCTCAAAAGCGC
1 TTTTTATCTCAAAAGCAC
*
518880 TTTTTATCTCAAAAGTAC
1 TTTTTATCTCAAAAGCAC
518898 TTTTTA
1 TTTTTA
518904 AAAACATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTTTATCTCAAAAGCAC
Found at i:527570 original size:18 final size:18
Alignment explanation
Indices: 527523--527570 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
527513 AGATATATAG
527523 ATATATATAATAAGATAT
1 ATATATATAATAAGATAT
* *
527541 AAATATATAATAAGATGGT
1 ATATATATAATAAGAT-AT
527560 ATATATA-AATA
1 ATATATATAATA
527571 GTTATAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
ATATATATAATAAGATAT
Found at i:528374 original size:15 final size:15
Alignment explanation
Indices: 528351--528380 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
528341 CCCTTTTTTA
*
528351 TATATTATATATATT
1 TATAATATATATATT
528366 TATAATATATATATT
1 TATAATATATATATT
528381 ATTACAAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATAATATATATATT
Found at i:528588 original size:28 final size:28
Alignment explanation
Indices: 528546--528601 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
528536 GAAAGGAAAG
*
528546 AAAGAAAAAACCCCCCTCCTATTACATT
1 AAAGAAAAAAACCCCCTCCTATTACATT
528574 AAAGAAAAAAACCCCCTCCTATTACATT
1 AAAGAAAAAAACCCCCTCCTATTACATT
528602 TGCTTCGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.30, G:0.04, T:0.21
Consensus pattern (28 bp):
AAAGAAAAAAACCCCCTCCTATTACATT
Found at i:529720 original size:100 final size:100
Alignment explanation
Indices: 529614--530457 Score: 1037
Period size: 100 Copynumber: 8.4 Consensus size: 100
529604 ACCGCCAGAG
** * *** * ***
529614 AAGTAAGATTCGTTGTTGTAGCTTCAATCTATTT-AGCCGTAATGTCGGGGAAACAAGATTCGCC
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGTGAGATTCGCC
* * *
529678 GTTGTAGCTTCAATCTGTTCCGTTGCACCGCCTGGA
65 GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGA
* * * * * *
529714 AAGTAAGATTCACCATTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAATGAGATTCGCCG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCG
*
529779 TCGTAGCTTCAATTTGTTCCGCTGCATCGCCTAGG-
66 TCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGA
* * * * ** * * *
529814 AAGTAAGATCCACCGTTGTGGCCTCAATCTTTTAAATTGCAATGTCAGGGAAGCAATATTCACCA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCG
* * * *
529879 TTGTAGCTTCAATCTGTTCCGCTACATTGCCTGGG
66 TCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGA
* * * * *
529914 AAGTAAGATTCGCCATTGTGGCTTTAATCTTTTAAATTGCAATGTAGGGGAAGTGAGATTCACCA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCG
* * * *
529979 TCGTAGCTTCAATTTGTTCTGTTGCATCGCCTGGG
66 TCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGA
* * *
530014 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGTGATTCACCA
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCG
* * *
530079 TCGTAGCTTCAATCTGTTCCGTTGCACCGCCTGGG
66 TCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGA
* *
530114 AAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGGAAGTGAGATTCGCCG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCG
* * * *
530179 TTGTAGCTTCAATCTATTCTGCTGCATCGCCTGGG
66 TCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGA
* * *
530214 AAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTAAATTGTAATGTCGGGGAAGCGAGATTCGCCG
1 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCG
* * *
530279 TTGTAGCTTCAATCTGTTCGGCTGCATCGCTTGGA
66 TCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGA
* * *
530314 AAGGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATTGCAATGTCGGTGAAGTAAGATTCGCC
1 AA-GTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCC
*
530379 GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTAAGA
65 GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-GGA
*
530416 AGGTAAGATTCGCCGTTGTGGTCTT-AATCTTTTAAATTGCAA
1 AAGTAAGATTCGCCGTTGTGG-CTTCAATCTTTTAAATTGCAA
530458 ACTATGGTAT
Statistics
Matches: 654, Mismatches: 84, Indels: 11
0.87 0.11 0.01
Matches are distributed among these distances:
99 5 0.01
100 520 0.80
101 124 0.19
102 5 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (100 bp):
AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCCG
TCGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGA
Found at i:529722 original size:50 final size:50
Alignment explanation
Indices: 529613--530434 Score: 531
Period size: 50 Copynumber: 16.4 Consensus size: 50
529603 CACCGCCAGA
** * * ** * * *
529613 GAAGTAAGATTCGTTGTTGTAGCTTCAATCTATTTAGCCGTAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
** * **
529663 GAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCACCGCCTGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * * * * * *
529713 AAAGTAAGATTCACCATTGTAGCTTCAATCTTTTTAATTGCAATGTCAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * * * * *
529763 GAAATGAGATTCGCCGTCGTAGCTTCAATTTGTTCCGCTGC-ATCGCCTAG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAAT-GCCTGG
* * * * * * * * *
529813 GAAGTAAGATCCACCGTTGTGGCCTCAATCTTTTAAATTGCAATGTCAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * * * * * *
529863 GAAGCAATATTCACCATTGTAGCTTCAATCTGTTCCGCTACATTGCCTGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * * * * ***
529913 GAAGTAAGATTCGCCATTGTGGCTTTAATCTTTTAAATTGCAATGTAGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * * * *
529963 GAAGTGAGATTCACCATCGTAGCTTCAATTTGTTCTGTTGC-ATCGCCTGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAAT-GCCTGG
* * * * * *
530013 GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
** * * * * **
530063 GAAGTGTGATTCACCATCGTAGCTTCAATCTGTTCCGTTGCACCGCCTGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * * * * *
530113 GAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * *
530163 GAAGTGAGATTCGCCGTTGTAGCTTCAATCTATTCTGCTGC-ATCGCCTGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAAT-GCCTGG
* * * * * * * *
530213 GAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTAAATTGTAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
** * * *
530263 GAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCGGCTGC-ATCGCTTGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAAT-GCCTGG
* * * * * * *
530313 AAAGGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAAATTGCAATGTC-GG
1 GAA-GTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
* * * **
530363 TGAAGTAAGATTCGCCGTCGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTAA
1 -GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAAT-GCCTGG
530414 GAAGGTAAGATTCGCCGTTGT
1 GAA-GTAAGATTCGCCGTTGT
530435 GGTCTTAATC
Statistics
Matches: 558, Mismatches: 201, Indels: 25
0.71 0.26 0.03
Matches are distributed among these distances:
49 10 0.02
50 492 0.88
51 54 0.10
52 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (50 bp):
GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCAGTTGCAATGCCTGG
Found at i:536893 original size:18 final size:18
Alignment explanation
Indices: 536846--536893 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
536836 AGATATATAG
536846 ATATATATAATAAGATAT
1 ATATATATAATAAGATAT
* *
536864 AAATATATAATAAGATGGT
1 ATATATATAATAAGAT-AT
536883 ATATATA-AATA
1 ATATATATAATA
536894 GTTATAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
ATATATATAATAAGATAT
Found at i:539105 original size:16 final size:17
Alignment explanation
Indices: 539084--539122 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
539074 AACATATATT
539084 ATTATTTT-AGGCTATC
1 ATTATTTTAAGGCTATC
**
539100 ATTATTTTAAGTTTATC
1 ATTATTTTAAGGCTATC
539117 ATTATT
1 ATTATT
539123 ATTATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (17 bp):
ATTATTTTAAGGCTATC
Found at i:539140 original size:11 final size:11
Alignment explanation
Indices: 539124--539162 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
539114 ATCATTATTA
539124 TTATTTTCAAT
1 TTATTTTCAAT
* *
539135 TTATTTTTTAAA
1 TTA-TTTTCAAT
539147 TTATTTTCAAT
1 TTATTTTCAAT
539158 TTATT
1 TTATT
539163 ATGTGCTATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTTTCAAT
Found at i:548792 original size:29 final size:24
Alignment explanation
Indices: 548721--548771 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
548711 GGGAAAAGCA
548721 TATGAATATTATAAAATAAAAATG
1 TATGAATATTATAAAATAAAAATG
548745 TATGAATATTATAAAATAAAAATG
1 TATGAATATTATAAAATAAAAATG
548769 TAT
1 TAT
548772 ATACGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (24 bp):
TATGAATATTATAAAATAAAAATG
Found at i:548889 original size:22 final size:22
Alignment explanation
Indices: 548863--548907 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
548853 ATAAATGCGC
*
548863 ATATAATATATGC-ATAATAATA
1 ATATAATATA-ACAATAATAATA
548885 ATATAATATAACAATAATAATA
1 ATATAATATAACAATAATAATA
548907 A
1 A
548908 ATGCTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
ATATAATATAACAATAATAATA
Found at i:548919 original size:19 final size:19
Alignment explanation
Indices: 548876--548922 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
548866 TAATATATGC
548876 ATAATAATAATATAATATA
1 ATAATAATAATATAATATA
* *
548895 ACAATAATAATA-AATGCTA
1 ATAATAATAATATAAT-ATA
548914 ATAATAATA
1 ATAATAATA
548923 TAGTAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATAATAATATAATATA
Found at i:549008 original size:15 final size:15
Alignment explanation
Indices: 548983--549019 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
548973 AAATTTTAAA
*
548983 ATCTTAATTAACTTG
1 ATCTAAATTAACTTG
*
548998 ATTTAAATTAACTTG
1 ATCTAAATTAACTTG
549013 ATCTAAA
1 ATCTAAA
549020 ACCAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (15 bp):
ATCTAAATTAACTTG
Found at i:553447 original size:99 final size:100
Alignment explanation
Indices: 553264--553463 Score: 368
Period size: 99 Copynumber: 2.0 Consensus size: 100
553254 TGGAAAAACA
553264 CCAACCTGATGAATTCCATTGAGGTTGAGAAGAAGTGAGCCAAGGCGTAGTAGAATGACCGGAGC
1 CCAACCTGAT-AATTCCATTGAGGTTGAGAAGAAGTGAGCCAAGGCGTAGTAGAATGACCGGAGC
553329 CAACCATGCTGATGTTTGCTTGTGGAG-GAGGCCTGT
65 CAACCATGCTGATGTTTGCTTGTGGAGAG-GGCCTGT
553365 CCAACCTGAT-ATTCCATTGAGGTTGAGAAGAAGTGAGCCAAGGCGTAGTAGAATGACCGGAGCC
1 CCAACCTGATAATTCCATTGAGGTTGAGAAGAAGTGAGCCAAGGCGTAGTAGAATGACCGGAGCC
553429 AACCATGCTGATGTTTGCTTGTGGAGAGGGCCTGT
66 AACCATGCTGATGTTTGCTTGTGGAGAGGGCCTGT
553464 AGTTAGTACT
Statistics
Matches: 98, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
99 87 0.89
100 1 0.01
101 10 0.10
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.23
Consensus pattern (100 bp):
CCAACCTGATAATTCCATTGAGGTTGAGAAGAAGTGAGCCAAGGCGTAGTAGAATGACCGGAGCC
AACCATGCTGATGTTTGCTTGTGGAGAGGGCCTGT
Found at i:560391 original size:79 final size:79
Alignment explanation
Indices: 560260--560424 Score: 296
Period size: 79 Copynumber: 2.1 Consensus size: 79
560250 AGCGGTAAAA
*
560260 GTTAAAAAGTCATGAGCACCGCATTCGAGACATCACGAGTGCGCTCGCGCTCGAGTGGTAAGCTT
1 GTTAAAAAGTCATGAGCACCGCATTCGAGACATCACGAGTGCGCTCGCGCTCGAGTGATAAGCTT
560325 AACGTGCGATACGT
66 AACGTGCGATACGT
560339 GTTAAAAAGTCATGAGCA-CGACATTCGAGACATCACGAGTGCGCTCGCGCTCGAGTGATAAGCT
1 GTTAAAAAGTCATGAGCACCG-CATTCGAGACATCACGAGTGCGCTCGCGCTCGAGTGATAAGCT
560403 TAACGTGCGATACGT
65 TAACGTGCGATACGT
*
560418 GGTAAAA
1 GTTAAAA
560425 TGACCGAATT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
78 2 0.02
79 81 0.98
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (79 bp):
GTTAAAAAGTCATGAGCACCGCATTCGAGACATCACGAGTGCGCTCGCGCTCGAGTGATAAGCTT
AACGTGCGATACGT
Found at i:560544 original size:26 final size:26
Alignment explanation
Indices: 560515--560571 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
560505 ATGACCGTAA
*
560515 TGCCCCTAAAGGGTAAATGACTATTT
1 TGCCCCTAAAGGGTAAATGACTAATT
** * *
560541 TGCCCCTCGAGGTTAAATGATTAATT
1 TGCCCCTAAAGGGTAAATGACTAATT
560567 TGCCC
1 TGCCC
560572 GTGATGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (26 bp):
TGCCCCTAAAGGGTAAATGACTAATT
Found at i:560599 original size:24 final size:24
Alignment explanation
Indices: 560572--560623 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
560562 TAATTTGCCC
560572 GTGATGAAAATGACTGATTTATCT
1 GTGATGAAAATGACTGATTTATCT
** * *
560596 GTGATTTAAATGACTGTTTTGTCT
1 GTGATGAAAATGACTGATTTATCT
560620 GTGA
1 GTGA
560624 ATTGTATGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (24 bp):
GTGATGAAAATGACTGATTTATCT
Found at i:560634 original size:24 final size:24
Alignment explanation
Indices: 560579--560626 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
560569 CCCGTGATGA
*
560579 AAATGACTGATTTATCTGTGATTT
1 AAATGACTGATTTATCTGTGAATT
* *
560603 AAATGACTGTTTTGTCTGTGAATT
1 AAATGACTGATTTATCTGTGAATT
560627 GTATGACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (24 bp):
AAATGACTGATTTATCTGTGAATT
Found at i:560663 original size:16 final size:16
Alignment explanation
Indices: 560644--560674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
560634 TAATTTTGAG
*
560644 CATGACATTCTGCATA
1 CATGACATACTGCATA
560660 CATGACATACTGCAT
1 CATGACATACTGCAT
560675 GGGGTTGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
CATGACATACTGCATA
Found at i:560862 original size:32 final size:32
Alignment explanation
Indices: 560810--560919 Score: 127
Period size: 32 Copynumber: 3.4 Consensus size: 32
560800 GCTGCGATAC
560810 TACTGATGG-TTGTGTACCGATCATATCACTGT
1 TACTGATGGCTT-TGTACCGATCATATCACTGT
*
560842 TACTGATGGCTTTG-ATCCGATCATATTA-TCGT
1 TACTGATGGCTTTGTA-CCGATCATATCACT-GT
* * * *
560874 TACTGATGGCTGTGTGCTGATCATATCACTGC
1 TACTGATGGCTTTGTACCGATCATATCACTGT
560906 TACTGATGGCTTTG
1 TACTGATGGCTTTG
560920 GGCCAATCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
31 2 0.03
32 61 0.92
33 3 0.05
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTACCGATCATATCACTGT
Found at i:560929 original size:64 final size:64
Alignment explanation
Indices: 560810--560932 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 64
560800 GCTGCGATAC
* * * *
560810 TACTGATGGTTGTGTACCGATCATATCACTGTTACTGATGGCTTTGATCCGATCATATTATCGT
1 TACTGATGGCTGTGTACCGATCATATCACTGCTACTGATGGCTTTGAGCCAATCATATTATCGT
* * *
560874 TACTGATGGCTGTGTGCTGATCATATCACTGCTACTGATGGCTTTGGGCCAATCATATT
1 TACTGATGGCTGTGTACCGATCATATCACTGCTACTGATGGCTTTGAGCCAATCATATT
560933 GCTATATTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (64 bp):
TACTGATGGCTGTGTACCGATCATATCACTGCTACTGATGGCTTTGAGCCAATCATATTATCGT
Found at i:560970 original size:22 final size:21
Alignment explanation
Indices: 560939--561004 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
560929 TATTGCTATA
560939 TTTATGGCTTGTAGCCATTCTG
1 TTTATGGCTT-TAGCCATTCTG
* * *
560961 TTTATAGCTTATAGCTATCCTG
1 TTTATGGCTT-TAGCCATTCTG
*
560983 TTTACGGCTCTTAGCCATTCTG
1 TTTATGGCT-TTAGCCATTCTG
561005 ATTACTATCA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTATGGCTTTAGCCATTCTG
Found at i:563983 original size:24 final size:24
Alignment explanation
Indices: 563938--564006 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
563928 CCTCGAGGTT
* **
563938 AAATGATTGATTTGTCCATGATGA
1 AAATGACTGATTTGTCTGTGATGA
**
563962 AAATGACTGATTTGTCTGTGATTT
1 AAATGACTGATTTGTCTGTGATGA
* *
563986 AAATGACTGTTTTTTCTGTGA
1 AAATGACTGATTTGTCTGTGA
564007 ATTGTATGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (24 bp):
AAATGACTGATTTGTCTGTGATGA
Found at i:564015 original size:24 final size:24
Alignment explanation
Indices: 563962--564023 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
563952 TCCATGATGA
* *
563962 AAATGACTGATTTGTCTGTGATTT
1 AAATGACTGATTTTTCTGTGAATT
*
563986 AAATGACTGTTTTTTCTGTGAATT
1 AAATGACTGATTTTTCTGTGAATT
**
564010 GTATGACTGATTTT
1 AAATGACTGATTTT
564024 GAGCATGACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.48
Consensus pattern (24 bp):
AAATGACTGATTTTTCTGTGAATT
Found at i:564046 original size:16 final size:16
Alignment explanation
Indices: 564027--564057 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
564017 TGATTTTGAG
*
564027 CATGACATTCTGCATA
1 CATGACATACTGCATA
564043 CATGACATACTGCAT
1 CATGACATACTGCAT
564058 GGGGTTGGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
CATGACATACTGCATA
Found at i:564202 original size:26 final size:26
Alignment explanation
Indices: 564147--564202 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
564137 TTCTAATTAC
* ** *
564147 TGGCAGATTTGCTGCGATACTGTTGC
1 TGGCAGATTTGCTACGATACTACTGA
*
564173 TGGCAGCTTTGCTACGATACTACTGA
1 TGGCAGATTTGCTACGATACTACTGA
564199 TGGC
1 TGGC
564203 TGTGTACCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (26 bp):
TGGCAGATTTGCTACGATACTACTGA
Found at i:564545 original size:28 final size:28
Alignment explanation
Indices: 564482--564538 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
564472 ACAGTACCGA
* *
564482 TACTGTATTGGGCTAAGGCCTACATTGT
1 TACTGTATTGGGCTAAGGCCCACACTGT
564510 TACTGTATTGGGCTAAGGCCCACACTGT
1 TACTGTATTGGGCTAAGGCCCACACTGT
564538 T
1 T
564539 GTTGTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACACTGT
Found at i:570155 original size:25 final size:25
Alignment explanation
Indices: 570112--570175 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
570102 TCAATATAGT
* *
570112 CTATCTATAATAGTCTCAGTATATA
1 CTATCTATAACAGTCTCAGGATATA
* *
570137 CTATCTATAGCAGTTTCAGGATATA
1 CTATCTATAACAGTCTCAGGATATA
* *
570162 CTATCAATGACAGT
1 CTATCTATAACAGT
570176 TTTAGTTTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (25 bp):
CTATCTATAACAGTCTCAGGATATA
Found at i:571588 original size:109 final size:111
Alignment explanation
Indices: 571404--571623 Score: 408
Period size: 109 Copynumber: 2.0 Consensus size: 111
571394 TCACAGTAGG
571404 GGTGAGCAAAACTCGATTCGACTCGAAAAAATAAAAAAAAAATTAAAATTTTGAGTTAATCGAGA
1 GGTGAGCAAAACTCGATTCGACTCGAAAAAATAAAAAAAAAATTAAAATTTTGAGTTAATCGAGA
571469 GATACGAATCAACTCGAATTTTTTTTTTCAAATTTCGAGTTCGAAT
66 GATACGAATCAACTCGAATTTTTTTTTTCAAATTTCGAGTTCGAAT
571515 GGTGAGC-AAA-TCGATTCGACTCGAAAAAATAAAAAAAAAATTAAAATTTTGAGTTAATCGAGA
1 GGTGAGCAAAACTCGATTCGACTCGAAAAAATAAAAAAAAAATTAAAATTTTGAGTTAATCGAGA
**
571578 GATACGAATCAACTCGAATTTTTTTTTTTTAATTTCGAGTTCGAAT
66 GATACGAATCAACTCGAATTTTTTTTTTCAAATTTCGAGTTCGAAT
571624 CGAGTTGAGT
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
109 97 0.91
110 3 0.03
111 7 0.07
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (111 bp):
GGTGAGCAAAACTCGATTCGACTCGAAAAAATAAAAAAAAAATTAAAATTTTGAGTTAATCGAGA
GATACGAATCAACTCGAATTTTTTTTTTCAAATTTCGAGTTCGAAT
Found at i:573841 original size:49 final size:49
Alignment explanation
Indices: 573769--573868 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
573759 TTGAACAAAT
*
573769 AACACCATAATCACTCTTACCTCGTGATTAATCAAAATCCTGAAACCAA
1 AACACCATAATCAATCTTACCTCGTGATTAATCAAAATCCTGAAACCAA
573818 AACACCATAATCAATCTTACCTCGTGATTAATCAAAATCCTGAAACCAA
1 AACACCATAATCAATCTTACCTCGTGATTAATCAAAATCCTGAAACCAA
573867 AA
1 AA
573869 TACTTACTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (49 bp):
AACACCATAATCAATCTTACCTCGTGATTAATCAAAATCCTGAAACCAA
Found at i:576168 original size:20 final size:20
Alignment explanation
Indices: 576145--576188 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
576135 ATAAAAAGTA
*
576145 TAAAGAATATAGAAAAAA-CT
1 TAAAAAATATA-AAAAAACCT
576165 TAAAAAATATAAAAAAACCT
1 TAAAAAATATAAAAAAACCT
576185 TAAA
1 TAAA
576189 CCTTAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAAAAATATAAAAAAACCT
Found at i:578410 original size:21 final size:21
Alignment explanation
Indices: 578386--578428 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
578376 GAAATGATTT
578386 AAACAAGAAT-TTTGAAATGAC
1 AAACAA-AATATTTGAAATGAC
578407 AAACAAAATAATTTGAAATGAC
1 AAACAAAAT-ATTTGAAATGAC
578429 TTAAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 6 0.30
22 11 0.55
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (21 bp):
AAACAAAATATTTGAAATGAC
Found at i:579419 original size:29 final size:29
Alignment explanation
Indices: 579386--579441 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
579376 AGATACTTCA
* * *
579386 ATTTATTTTTATATTGGATAAATATAATT
1 ATTTATTTATATAATAGATAAATATAATT
*
579415 ATTTATTTATATAATATATAAATATAA
1 ATTTATTTATATAATAGATAAATATAA
579442 AATAATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
ATTTATTTATATAATAGATAAATATAATT
Done.