Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 7 of 210
Found at i:2074449 original size:54 final size:54
Alignment explanation
Indices: 2074374--2074485 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
2074364 TAGACTCAAA
2074374 TAAAGTCGTTTATCAATTTTTCTACTGAAATTTAAACTTGTTCATATTCAAACT
1 TAAAGTCGTTTATCAATTTTTCTACTGAAATTTAAACTTGTTCATATTCAAACT
2074428 TAAAGTCGTTTATCAATTTTTCTACTGAAATTTAAACTTGTTCATATTCAAACT
1 TAAAGTCGTTTATCAATTTTTCTACTGAAATTTAAACTTGTTCATATTCAAACT
2074482 TAAA
1 TAAA
2074486 CTCCTTGGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (54 bp):
TAAAGTCGTTTATCAATTTTTCTACTGAAATTTAAACTTGTTCATATTCAAACT
Found at i:2077248 original size:31 final size:29
Alignment explanation
Indices: 2077197--2077265 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
2077187 GAAAATTCCC
2077197 ATTAAGCCCTCTAAAATTTTAGAAATTTTA
1 ATTAAGCCCTCTAAAATTTTAGAAA-TTTA
* *
2077227 ATTAAGACCCTC-AAATTTTTTATAAATTTA
1 ATTAAG-CCCTCTAAA-ATTTTAGAAATTTA
*
2077257 ATTGAGCCC
1 ATTAAGCCC
2077266 CCATAACTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 18 0.53
31 13 0.38
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (29 bp):
ATTAAGCCCTCTAAAATTTTAGAAATTTA
Found at i:2079328 original size:33 final size:33
Alignment explanation
Indices: 2079281--2079351 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
2079271 TTCAGAGGAC
*
2079281 GCGGGACTAAATTGAAAATATTAAAAAAATTTA
1 GCGGCACTAAATTGAAAATATTAAAAAAATTTA
*
2079314 GCGGCACTAAATTGAAAATATTAAAAAATTTTA
1 GCGGCACTAAATTGAAAATATTAAAAAAATTTA
2079347 G-GGCA
1 GCGGCA
2079352 AATTTTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (33 bp):
GCGGCACTAAATTGAAAATATTAAAAAAATTTA
Found at i:2081992 original size:47 final size:42
Alignment explanation
Indices: 2081896--2081981 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
2081886 GCTTCAATGT
*
2081896 AACTTTCTTAAATTACCTAACTTCCTCTATTATTATGAATAG
1 AACTTTTTTAAATTACCTAACTTCCTCTATTATTATGAATAG
*
2081938 AACTTTTTTAAATTACCTAACTTCCTTTATTATTATGAATAG
1 AACTTTTTTAAATTACCTAACTTCCTCTATTATTATGAATAG
2081980 AA
1 AA
2081982 TTTGGCTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (42 bp):
AACTTTTTTAAATTACCTAACTTCCTCTATTATTATGAATAG
Found at i:2085003 original size:21 final size:22
Alignment explanation
Indices: 2084978--2085033 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
2084968 ATATGTTAGA
*
2084978 AAAAATTAATTTATAAAAATT-
1 AAAAATTAATTTAAAAAAATTC
* *
2084999 AAAAATTGATAGTAAAAAAATTC
1 AAAAATTAAT-TTAAAAAAATTC
2085022 AAAAATATAATT
1 AAAAAT-TAATT
2085034 AGGATCATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 6 0.22
24 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAAATTAATTTAAAAAAATTC
Found at i:2090149 original size:10 final size:11
Alignment explanation
Indices: 2090128--2090152 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2090118 AATTAATGAT
2090128 AATTTCGAAAA
1 AATTTCGAAAA
2090139 AATTTCGAAAA
1 AATTTCGAAAA
2090150 AAT
1 AAT
2090153 AAAAGGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (11 bp):
AATTTCGAAAA
Found at i:2124888 original size:15 final size:15
Alignment explanation
Indices: 2124870--2124898 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2124860 TGAATTTTGA
2124870 TTTGATTATTTTTAT
1 TTTGATTATTTTTAT
2124885 TTTGATTATTTTTA
1 TTTGATTATTTTTA
2124899 AGTAGAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTGATTATTTTTAT
Found at i:2127928 original size:329 final size:330
Alignment explanation
Indices: 2127526--2128185 Score: 1313
Period size: 329 Copynumber: 2.0 Consensus size: 330
2127516 ATAATAGAAA
2127526 TATATTAAAAAAAAGAACGTAATAAAACTATATATTAATTCTATAAGCTAAAATAAAAAAATAAA
1 TATATTAAAAAAAAGAACGTAATAAAACTATATATTAATTCTATAAGCTAAAATAAAAAAATAAA
2127591 GAAATAAATTTAAGAACTCAACAGTTTCACCTCTTTCAAGTAAATCGTACATTAGTATTTATTAT
66 GAAATAAATTTAAGAACTCAACAGTTTCACCTCTTTCAAGTAAATCGTACATTAGTATTTATTAT
2127656 TTAATTTCCACCAAAATAATGAAATGTTAATATTTATCCAAGAAAAAATTAAATGTGAAAATACT
131 TTAATTTCCACCAAAATAATGAAATGTTAATATTTATCCAAGAAAAAATTAAATGTGAAAATACT
2127721 TGGTCGAGTTTGAGTAGGATTTGAAGTTTAAATAATATAAGAAGTTATTTATAATTTAAAAAACT
196 TGGTCGAGTTTGAGTAGGATTTGAAGTTTAAATAATATAAGAAGTTATTTATAATTTAAAAAACT
2127786 TACTTGCTTTCTTCACTTATTACTTTCTTTCTTTTTTTTCACCTGAAACCCTAAATTTTCTCACA
261 TACTTGCTTTCTTCACTTATTACTTTCTTTCTTTTTTTTCACCTGAAACCCTAAATTTTCTCACA
2127851 AAATT
326 AAATT
2127856 TATATT-AAAAAAAGAACGTAATAAAACTATATATTAATTCTATAAGCTAAAATAAAAAAATAAA
1 TATATTAAAAAAAAGAACGTAATAAAACTATATATTAATTCTATAAGCTAAAATAAAAAAATAAA
2127920 GAAATAAATTTAAGAACTCAACAGTTTCACCTCTTTCAAGTAAATCGTACATTAGTATTTATTAT
66 GAAATAAATTTAAGAACTCAACAGTTTCACCTCTTTCAAGTAAATCGTACATTAGTATTTATTAT
2127985 TTAATTTCCACCAAAATAATGAAATGTTAATATTTATCCAAGAAAAAATTAAATGTGAAAATACT
131 TTAATTTCCACCAAAATAATGAAATGTTAATATTTATCCAAGAAAAAATTAAATGTGAAAATACT
2128050 TGGTCGAGTTTGAGTAGGATTTGAAGTTTAAATAATATAAGAAGTTATTTATAATTTAAAAAACT
196 TGGTCGAGTTTGAGTAGGATTTGAAGTTTAAATAATATAAGAAGTTATTTATAATTTAAAAAACT
2128115 TACTTGCTTTCTTCACTTATTACTTTCTTTCTTTTTTTTCACCTGAAACCCTAAATTTTCTCACA
261 TACTTGCTTTCTTCACTTATTACTTTCTTTCTTTTTTTTCACCTGAAACCCTAAATTTTCTCACA
2128180 AAATT
326 AAATT
2128185 T
1 T
2128186 TACCGTCATT
Statistics
Matches: 330, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
329 324 0.98
330 6 0.02
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (330 bp):
TATATTAAAAAAAAGAACGTAATAAAACTATATATTAATTCTATAAGCTAAAATAAAAAAATAAA
GAAATAAATTTAAGAACTCAACAGTTTCACCTCTTTCAAGTAAATCGTACATTAGTATTTATTAT
TTAATTTCCACCAAAATAATGAAATGTTAATATTTATCCAAGAAAAAATTAAATGTGAAAATACT
TGGTCGAGTTTGAGTAGGATTTGAAGTTTAAATAATATAAGAAGTTATTTATAATTTAAAAAACT
TACTTGCTTTCTTCACTTATTACTTTCTTTCTTTTTTTTCACCTGAAACCCTAAATTTTCTCACA
AAATT
Found at i:2132936 original size:2 final size:2
Alignment explanation
Indices: 2132929--2132953 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2132919 TCCAAACATT
2132929 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
2132954 GGTATAAATA
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:2153382 original size:22 final size:22
Alignment explanation
Indices: 2153337--2153382 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2153327 TTTAGCTCCA
* *
2153337 TCTCTGTTTCTTCAAATCTCTG
1 TCTCTGTTTCTTCAAAACTATG
2153359 TCTCTGTTTCTTCAAAACTATG
1 TCTCTGTTTCTTCAAAACTATG
2153381 TC
1 TC
2153383 GATGGTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.26, G:0.09, T:0.48
Consensus pattern (22 bp):
TCTCTGTTTCTTCAAAACTATG
Found at i:2160369 original size:2 final size:2
Alignment explanation
Indices: 2160364--2160406 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
2160354 TATATGCATG
*
2160364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
2160407 AATCAAGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2162643 original size:59 final size:59
Alignment explanation
Indices: 2162511--2162628 Score: 220
Period size: 58 Copynumber: 2.0 Consensus size: 59
2162501 AGTGTTTAAT
2162511 TGATTATTAAATTATTTGTAAAGGACTTTTTTTATATAATAAGCTTAAAGTATTAAATA
1 TGATTATTAAATTATTTGTAAAGGACTTTTTTTATATAATAAGCTTAAAGTATTAAATA
*
2162570 TGATTATTAAATTATTTTTAAAGGAC-TTTTTTATATAATAAGCTTAAAGTATTAAATA
1 TGATTATTAAATTATTTGTAAAGGACTTTTTTTATATAATAAGCTTAAAGTATTAAATA
2162628 T
1 T
2162629 TATATTTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 33 0.57
59 25 0.43
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (59 bp):
TGATTATTAAATTATTTGTAAAGGACTTTTTTTATATAATAAGCTTAAAGTATTAAATA
Found at i:2175478 original size:15 final size:16
Alignment explanation
Indices: 2175458--2175491 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2175448 GACTATTAGT
*
2175458 TTTTTCTATTAA-TCA
1 TTTTTCTAATAATTCA
2175473 TTTTTCTAATAATTCA
1 TTTTTCTAATAATTCA
2175489 TTT
1 TTT
2175492 ATTTGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTCTAATAATTCA
Found at i:2177789 original size:13 final size:13
Alignment explanation
Indices: 2177773--2177806 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2177763 TATATATAAA
2177773 ATATAAAATACAT
1 ATATAAAATACAT
2177786 ATATAAAATACAT
1 ATATAAAATACAT
*
2177799 ATTTAAAA
1 ATATAAAA
2177807 AAGGTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAAATACAT
Found at i:2187123 original size:962 final size:962
Alignment explanation
Indices: 2185259--2187182 Score: 3832
Period size: 962 Copynumber: 2.0 Consensus size: 962
2185249 TTAATATGTA
2185259 CTCAACAACTAAATTTAAAAATTGATTTAAAATATTTTTCGCATCTTTCTTTTTATTCGTTTTTA
1 CTCAACAACTAAATTTAAAAATTGATTTAAAATATTTTTCGCATCTTTCTTTTTATTCGTTTTTA
2185324 AATCGAGTAAAAAGAAAAGGGACAAGCTTTTGCTTACAGAGACAAAAATGATTCCGGGTTATTGT
66 AATCGAGTAAAAAGAAAAGGGACAAGCTTTTGCTTACAGAGACAAAAATGATTCCGGGTTATTGT
2185389 TTACCATCCGCCGACTGCTCACATTAGCATTTGTCGCAAATAAAATATTAATTTATAATTATATT
131 TTACCATCCGCCGACTGCTCACATTAGCATTTGTCGCAAATAAAATATTAATTTATAATTATATT
2185454 TTCAATTATCAATCATCACTTGAATAATATTTTTATTATTTTATTAAACATACATAGCATTATTT
196 TTCAATTATCAATCATCACTTGAATAATATTTTTATTATTTTATTAAACATACATAGCATTATTT
2185519 TCGACAAAAATAAATTAAGATTATTATTACATATATTATGCAAAAATTTCAAAAGAATTTTAGAT
261 TCGACAAAAATAAATTAAGATTATTATTACATATATTATGCAAAAATTTCAAAAGAATTTTAGAT
2185584 TTTTCTAGATACGATTTTTATTTTTTCTAATAGTTTAAAAACTCCTACAATTACTCTTACATTAT
326 TTTTCTAGATACGATTTTTATTTTTTCTAATAGTTTAAAAACTCCTACAATTACTCTTACATTAT
2185649 TCTCAAATTTTTTAAGGATAAATTTTAAAATTATATATGAATTTTTATTTAATTTGTAATTTGAT
391 TCTCAAATTTTTTAAGGATAAATTTTAAAATTATATATGAATTTTTATTTAATTTGTAATTTGAT
2185714 ACATAAAATTTGATTAGTATAATTATATATATTTAAAAAATAAATACATCAAGTTATTTTTATAT
456 ACATAAAATTTGATTAGTATAATTATATATATTTAAAAAATAAATACATCAAGTTATTTTTATAT
2185779 TAGATAAATATAATTATTTGTACACGTAATATATAAACATAAAAAATGATGTTATATTAATAATT
521 TAGATAAATATAATTATTTGTACACGTAATATATAAACATAAAAAATGATGTTATATTAATAATT
2185844 GTGTTAATAATTTTTAAAAATTAGATCAAATTGAAATTTTATTCATAAAATTACATAAAATAAAA
586 GTGTTAATAATTTTTAAAAATTAGATCAAATTGAAATTTTATTCATAAAATTACATAAAATAAAA
2185909 CAGTTTTGATATTTATCTTATTTTTTTAAATAATTATTTGATACATATATCCTTAAATATTTTAA
651 CAGTTTTGATATTTATCTTATTTTTTTAAATAATTATTTGATACATATATCCTTAAATATTTTAA
2185974 CAGGTAAATAAAATAATTAATGTTTAAAATTTAAAAATGATAAATAAAACACATAACCATTTTTA
716 CAGGTAAATAAAATAATTAATGTTTAAAATTTAAAAATGATAAATAAAACACATAACCATTTTTA
2186039 ATTTTCATTTTTAGAATTAATAAATTTTACCTTTAATCTATTAAATAATATGGACAGCGGATATA
781 ATTTTCATTTTTAGAATTAATAAATTTTACCTTTAATCTATTAAATAATATGGACAGCGGATATA
2186104 AAAAAATACCATATATTAAATAATATATTTTTAAAAAATATTTAATGGTAGGGTATACCGAGTAA
846 AAAAAATACCATATATTAAATAATATATTTTTAAAAAATATTTAATGGTAGGGTATACCGAGTAA
2186169 CACCTAACCAAAACTAAGAATCTAACGCTCAAAGCAACATACAGCCACTGAC
911 CACCTAACCAAAACTAAGAATCTAACGCTCAAAGCAACATACAGCCACTGAC
2186221 CTCAACAACTAAATTTAAAAATTGATTTAAAATATTTTTCGCATCTTTCTTTTTATTCGTTTTTA
1 CTCAACAACTAAATTTAAAAATTGATTTAAAATATTTTTCGCATCTTTCTTTTTATTCGTTTTTA
2186286 AATCGAGTAAAAAGAAAAGGGACAAGCTTTTGCTTACAGAGACAAAAATGATTCCGGGTTATTGT
66 AATCGAGTAAAAAGAAAAGGGACAAGCTTTTGCTTACAGAGACAAAAATGATTCCGGGTTATTGT
2186351 TTACCATCCGCCGACTGCTCACATTAGCATTTGTCGCAAATAAAATATTAATTTATAATTATATT
131 TTACCATCCGCCGACTGCTCACATTAGCATTTGTCGCAAATAAAATATTAATTTATAATTATATT
2186416 TTCAATTATCAATCATCACTTGAATAATATTTTTATTATTTTATTAAACATACATAGCATTATTT
196 TTCAATTATCAATCATCACTTGAATAATATTTTTATTATTTTATTAAACATACATAGCATTATTT
2186481 TCGACAAAAATAAATTAAGATTATTATTACATATATTATGCAAAAATTTCAAAAGAATTTTAGAT
261 TCGACAAAAATAAATTAAGATTATTATTACATATATTATGCAAAAATTTCAAAAGAATTTTAGAT
2186546 TTTTCTAGATACGATTTTTATTTTTTCTAATAGTTTAAAAACTCCTACAATTACTCTTACATTAT
326 TTTTCTAGATACGATTTTTATTTTTTCTAATAGTTTAAAAACTCCTACAATTACTCTTACATTAT
2186611 TCTCAAATTTTTTAAGGATAAATTTTAAAATTATATATGAATTTTTATTTAATTTGTAATTTGAT
391 TCTCAAATTTTTTAAGGATAAATTTTAAAATTATATATGAATTTTTATTTAATTTGTAATTTGAT
2186676 ACATAAAATTTGATTAGTATAATTATATATATTTAAAAAATAAATACATCAAGTTATTTTTATAT
456 ACATAAAATTTGATTAGTATAATTATATATATTTAAAAAATAAATACATCAAGTTATTTTTATAT
2186741 TAGATAAATATAATTATTTGTTACACGTAAT-TATAAACATAAAAAATGATGTTATATTAATAAT
521 TAGATAAATATAATTATTTG-TACACGTAATATATAAACATAAAAAATGATGTTATATTAATAAT
2186805 TGTGTTAATAATTTTTAAAAATTAGATCAAATTGAAATTTTATTCATAAAATTACATAAAATAAA
585 TGTGTTAATAATTTTTAAAAATTAGATCAAATTGAAATTTTATTCATAAAATTACATAAAATAAA
2186870 ACAGTTTTGATATTTATCTTATTTTTTTAAATAATTATTTGATACATATATCCTTAAATATTTTA
650 ACAGTTTTGATATTTATCTTATTTTTTTAAATAATTATTTGATACATATATCCTTAAATATTTTA
2186935 ACAGGTAAATAAAATAATTAATGTTTAAAATTTAAAAATGATAAATAAAACACATAACCATTTTT
715 ACAGGTAAATAAAATAATTAATGTTTAAAATTTAAAAATGATAAATAAAACACATAACCATTTTT
2187000 AATTTTCATTTTTAGAATTAATAAATTTTACCTTTAATCTATTAAATAATATGGACAGCGGATAT
780 AATTTTCATTTTTAGAATTAATAAATTTTACCTTTAATCTATTAAATAATATGGACAGCGGATAT
2187065 AAAAAAATACCATATATTAAATAATATATTTTTAAAAAATATTTAATGGTAGGGTATACCGAGTA
845 AAAAAAATACCATATATTAAATAATATATTTTTAAAAAATATTTAATGGTAGGGTATACCGAGTA
2187130 ACACCTAACCAAAACTAAGAATCTAACGCTCAAAGCAACATACAGCCACTGAC
910 ACACCTAACCAAAACTAAGAATCTAACGCTCAAAGCAACATACAGCCACTGAC
2187183 ATATTGTCAA
Statistics
Matches: 961, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
962 951 0.99
963 10 0.01
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (962 bp):
CTCAACAACTAAATTTAAAAATTGATTTAAAATATTTTTCGCATCTTTCTTTTTATTCGTTTTTA
AATCGAGTAAAAAGAAAAGGGACAAGCTTTTGCTTACAGAGACAAAAATGATTCCGGGTTATTGT
TTACCATCCGCCGACTGCTCACATTAGCATTTGTCGCAAATAAAATATTAATTTATAATTATATT
TTCAATTATCAATCATCACTTGAATAATATTTTTATTATTTTATTAAACATACATAGCATTATTT
TCGACAAAAATAAATTAAGATTATTATTACATATATTATGCAAAAATTTCAAAAGAATTTTAGAT
TTTTCTAGATACGATTTTTATTTTTTCTAATAGTTTAAAAACTCCTACAATTACTCTTACATTAT
TCTCAAATTTTTTAAGGATAAATTTTAAAATTATATATGAATTTTTATTTAATTTGTAATTTGAT
ACATAAAATTTGATTAGTATAATTATATATATTTAAAAAATAAATACATCAAGTTATTTTTATAT
TAGATAAATATAATTATTTGTACACGTAATATATAAACATAAAAAATGATGTTATATTAATAATT
GTGTTAATAATTTTTAAAAATTAGATCAAATTGAAATTTTATTCATAAAATTACATAAAATAAAA
CAGTTTTGATATTTATCTTATTTTTTTAAATAATTATTTGATACATATATCCTTAAATATTTTAA
CAGGTAAATAAAATAATTAATGTTTAAAATTTAAAAATGATAAATAAAACACATAACCATTTTTA
ATTTTCATTTTTAGAATTAATAAATTTTACCTTTAATCTATTAAATAATATGGACAGCGGATATA
AAAAAATACCATATATTAAATAATATATTTTTAAAAAATATTTAATGGTAGGGTATACCGAGTAA
CACCTAACCAAAACTAAGAATCTAACGCTCAAAGCAACATACAGCCACTGAC
Found at i:2189003 original size:3 final size:3
Alignment explanation
Indices: 2188995--2189044 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
2188985 AGTATCGTAA
2188995 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2189042 AAT
1 AAT
2189045 GCAAATTAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2190303 original size:46 final size:46
Alignment explanation
Indices: 2190218--2190452 Score: 395
Period size: 45 Copynumber: 5.2 Consensus size: 46
2190208 AATNNNNNNN
*
2190218 TGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
*
2190263 TGATCAGATAAATGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
* * *
2190309 TGATCAGATAAGTGTAGCTAGA-CTACCACTTATCAATTTTTCACT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
2190354 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
*
2190400 TGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCATT
1 TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
2190445 TGATCAGA
1 TGATCAGA
2190453 AGTACTCAAA
Statistics
Matches: 178, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
45 93 0.52
46 85 0.48
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (46 bp):
TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
Found at i:2190373 original size:91 final size:91
Alignment explanation
Indices: 2190218--2190452 Score: 409
Period size: 91 Copynumber: 2.6 Consensus size: 91
2190208 AATNNNNNNN
*
2190218 TGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTA
1 TGATCAGATAAGTGTAGCTAGACTACCACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTA
2190283 AAGCTACCACTTATCACTTTGTCACT
66 AAGCTACCACTTATCACTTTGTCACT
* * *
2190309 TGATCAGATAAGTGTAGCTAGACTACCACTTATCAATTTTTCACTTGATCAGATAAGTGTAGCTA
1 TGATCAGATAAGTGTAGCTAGACTACCACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTA
2190374 AAGCTACCACTTATCACTTTGTCACT
66 AAGCTACCACTTATCACTTTGTCACT
*
2190400 TGATCAGATAAGTGTAGCTA-AGCTACCACTTATCACTTTGTCATTTGATCAGA
1 TGATCAGATAAGTGTAGCTAGA-CTACCACTTATCACTTTGTCACTTGATCAGA
2190453 AGTACTCAAA
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
90 1 0.01
91 135 0.99
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (91 bp):
TGATCAGATAAGTGTAGCTAGACTACCACTTATCACTTTGTCACTTGATCAGATAAATGTAGCTA
AAGCTACCACTTATCACTTTGTCACT
Found at i:2192987 original size:24 final size:24
Alignment explanation
Indices: 2192960--2193007 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2192950 CATAGCTTCA
*
2192960 TACACTAAGAGTTGTAGCCGGTGT
1 TACACTAAGAGTTATAGCCGGTGT
* *
2192984 TACACTAGGAGTTATCGCCGGTGT
1 TACACTAAGAGTTATAGCCGGTGT
2193008 CCACGACGGT
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:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (24 bp):
TACACTAAGAGTTATAGCCGGTGT
Found at i:2195454 original size:24 final size:24
Alignment explanation
Indices: 2195427--2195476 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2195417 TTGAGGCAAG
2195427 GGGGCTCCTTAGGGATACCTTTGA
1 GGGGCTCCTTAGGGATACCTTTGA
2195451 GGGGCTCCTTAGGGATACCTTTGA
1 GGGGCTCCTTAGGGATACCTTTGA
2195475 GG
1 GG
2195477 AGTGTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.36, T:0.28
Consensus pattern (24 bp):
GGGGCTCCTTAGGGATACCTTTGA
Found at i:2209968 original size:5 final size:5
Alignment explanation
Indices: 2209960--2209987 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2209950 ATAAATGAAA
2209960 AATAT AATAT AATAT AATAT AATAT AAT
1 AATAT AATAT AATAT AATAT AATAT AAT
2209988 TTGAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:2212150 original size:30 final size:30
Alignment explanation
Indices: 2212114--2212182 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
2212104 TTAAATTAGT
2212114 AATAATAAAATTGT-ATTTTAACCCTTCAAA
1 AATAATAAAATTGTGA-TTTAACCCTTCAAA
* * *
2212144 AATAATAAAATTTTGATTTAATCCTTTAAA
1 AATAATAAAATTGTGATTTAACCCTTCAAA
*
2212174 AATTATAAA
1 AATAATAAA
2212183 GATAGTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (30 bp):
AATAATAAAATTGTGATTTAACCCTTCAAA
Found at i:2213202 original size:30 final size:31
Alignment explanation
Indices: 2213145--2213221 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
2213135 AACAGTCCAT
* *
2213145 TGACTTAAATAAAAATATTCAATTAGTTTAG
1 TGACTTAAATAAAAACATTCAAATAGTTTAG
2213176 TGACTTAAAT-AAAACATTCAAATAGTTTAG
1 TGACTTAAATAAAAACATTCAAATAGTTTAG
* *
2213206 TCACTTAAATGAAAAC
1 TGACTTAAATAAAAAC
2213222 TTTTGAATAG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 27 0.64
31 15 0.36
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAACATTCAAATAGTTTAG
Found at i:2222828 original size:2 final size:2
Alignment explanation
Indices: 2222823--2222847 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2222813 GTTTTTTTAA
2222823 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 A
2222848 ATTACTGACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2227293 original size:31 final size:29
Alignment explanation
Indices: 2227258--2227327 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
2227248 ATCCTAAAAT
* *
2227258 TATACATGAACTATGGTTTAATGTGTAATTG
1 TATACATGAACTATGATTT--TGTGCAATTG
* * *
2227289 TATACATCAACTTTGATTTTGTGCAATTT
1 TATACATGAACTATGATTTTGTGCAATTG
2227318 TATACATGAA
1 TATACATGAA
2227328 ATTTTGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (29 bp):
TATACATGAACTATGATTTTGTGCAATTG
Found at i:2249650 original size:7 final size:7
Alignment explanation
Indices: 2249631--2249671 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2249621 TCCAGGTCAC
2249631 TTCCTTT
1 TTCCTTT
2249638 TT-CTTT
1 TTCCTTT
2249644 TTCCTTTT
1 TTCC-TTT
*
2249652 TTCGTTT
1 TTCCTTT
2249659 TT-CTTT
1 TTCCTTT
2249665 TTCCTTT
1 TTCCTTT
2249672 CACTTTGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 11 0.38
7 12 0.41
8 6 0.21
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (7 bp):
TTCCTTT
Found at i:2254038 original size:31 final size:30
Alignment explanation
Indices: 2253985--2254056 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
2253975 TTTGATTCAT
* *
2253985 GACTAGAATTTCAAAATTCGAAAAGTAGAAA
1 GACTA-AATTTCAAAATCCGAAAAGTACAAA
* * *
2254016 GACTAAATTTGATAAATCCGAAAGGTACAAG
1 GACTAAATTTCA-AAATCCGAAAAGTACAAA
2254047 GACTTAAATT
1 GAC-TAAATT
2254057 GACCAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 6 0.18
31 22 0.65
32 6 0.18
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (30 bp):
GACTAAATTTCAAAATCCGAAAAGTACAAA
Found at i:2260071 original size:44 final size:44
Alignment explanation
Indices: 2260021--2260171 Score: 175
Period size: 44 Copynumber: 3.4 Consensus size: 44
2260011 ATTATATATG
*
2260021 TTTTGGTGATTTAATTATAAAATAATAATTATTTAATTTCATCT
1 TTTTGGTCATTTAATTATAAAATAATAATTATTTAATTTCATCT
* ** * *
2260065 TTTTGGTCATTTAATTAT--ATTGAATTTTTGGA-TGAATTAT-ATAT
1 TTTTGGTCATTTAATTATAAAAT-AATAATT--ATTTAATT-TCATCT
*
2260109 TTTTGGTGATTTAATTATAAAATAATAATTATTTAATTTCATCT
1 TTTTGGTCATTTAATTATAAAATAATAATTATTTAATTTCATCT
2260153 TTTTGGTCATTTAATTATA
1 TTTTGGTCATTTAATTATA
2260172 TTGAATTTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 7 0.08
44 68 0.79
45 7 0.08
46 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (44 bp):
TTTTGGTCATTTAATTATAAAATAATAATTATTTAATTTCATCT
Found at i:2260124 original size:22 final size:22
Alignment explanation
Indices: 2260010--2260127 Score: 73
Period size: 22 Copynumber: 5.3 Consensus size: 22
2260000 GTAGCCACTA
2260010 AATTATATATGTTTTGGTGATTT
1 AATTATATAT-TTTTGGTGATTT
* * ** ** *
2260033 AATTATAAAATAATAATTATTT
1 AATTATATATTTTTGGTGATTT
* *
2260055 AATT-TCATCTTTTTGGTCATTT
1 AATTAT-ATATTTTTGGTGATTT
*
2260077 AATTATATTGAATTTTT-G-GA-TG
1 AATTATA-T--ATTTTTGGTGATTT
2260099 AATTATATATTTTTGGTGATTT
1 AATTATATATTTTTGGTGATTT
2260121 AATTATA
1 AATTATA
2260128 AAATAATAAT
Statistics
Matches: 68, Mismatches: 19, Indels: 17
0.65 0.18 0.16
Matches are distributed among these distances:
19 6 0.09
20 1 0.01
21 4 0.06
22 40 0.59
23 11 0.16
24 1 0.01
25 5 0.07
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (22 bp):
AATTATATATTTTTGGTGATTT
Found at i:2260138 original size:88 final size:89
Alignment explanation
Indices: 2260010--2260186 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 89
2260000 GTAGCCACTA
2260010 AATTATATATGTTTTGGTGATTTAATTATAAAATAATAATTATTTAATTTCATCTTTTTGGTCAT
1 AATTATATATGTTTTGGTGATTTAATTATAAAATAATAATTATTTAATTTCATCTTTTTGGTCAT
2260075 TTAATTATATTGAATTTTTGGATG
66 TTAATTATATTGAATTTTTGGATG
2260099 AATTATATAT-TTTTGGTGATTTAATTATAAAATAATAATTATTTAATTTCATCTTTTTGGTCAT
1 AATTATATATGTTTTGGTGATTTAATTATAAAATAATAATTATTTAATTTCATCTTTTTGGTCAT
2260163 TTAATTATATTGAATTTTTGGATG
66 TTAATTATATTGAATTTTTGGATG
2260187 TTCCTATTTT
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 78 0.89
89 10 0.11
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (89 bp):
AATTATATATGTTTTGGTGATTTAATTATAAAATAATAATTATTTAATTTCATCTTTTTGGTCAT
TTAATTATATTGAATTTTTGGATG
Found at i:2272090 original size:13 final size:13
Alignment explanation
Indices: 2272074--2272098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2272064 TAAAATTCAA
2272074 TAATCAATTAAAT
1 TAATCAATTAAAT
2272087 TAATCAATTAAA
1 TAATCAATTAAA
2272099 CTGAGGTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATCAATTAAAT
Found at i:2273735 original size:85 final size:86
Alignment explanation
Indices: 2273628--2273799 Score: 337
Period size: 85 Copynumber: 2.0 Consensus size: 86
2273618 AATTTTATAA
2273628 TAAGCTTTAAAAATTAAATTTAAAAATTTTAAAAAAATTGATAATTAAAAATCAAAACGTGATAG
1 TAAGCTTTAAAAATTAAATTTAAAAATTTTAAAAAAATTGATAATTAAAAATCAAAACGTGATAG
2273693 AAAGAAAATAAAATACAATTT
66 AAAGAAAATAAAATACAATTT
2273714 TAAGCTTT-AAAATTAAATTTAAAAATTTTAAAAAAATTGATAATTAAAAATCAAAACGTGATAG
1 TAAGCTTTAAAAATTAAATTTAAAAATTTTAAAAAAATTGATAATTAAAAATCAAAACGTGATAG
2273778 AAAGAAAATAAAATACAATTT
66 AAAGAAAATAAAATACAATTT
2273799 T
1 T
2273800 TACATAATTT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 78 0.91
86 8 0.09
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (86 bp):
TAAGCTTTAAAAATTAAATTTAAAAATTTTAAAAAAATTGATAATTAAAAATCAAAACGTGATAG
AAAGAAAATAAAATACAATTT
Found at i:2282844 original size:58 final size:58
Alignment explanation
Indices: 2282723--2282854 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 58
2282713 TTAGAACAAC
* ** *
2282723 TACCAAGTTCAGGGCCTAACTTAAATAAAAAAAACGTTCAGGCTCCAATATAGAAAAAT
1 TACCAAGTTCAGAGCCTAACTTAAATAAAAAAAAC-TTCAACCTCCAATATAAAAAAAT
* *
2282782 TACCAAGTTCAGAGCTTAACTTAAATAAAAAAAA-TTCAAACCT-TAATATTAAAAAAAT
1 TACCAAGTTCAGAGCCTAACTTAAATAAAAAAAACTTC-AACCTCCAATA-TAAAAAAAT
2282840 TACCAAGTTCA-AGCC
1 TACCAAGTTCAGAGCC
2282855 CCAAATATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
57 10 0.16
58 22 0.34
59 32 0.50
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (58 bp):
TACCAAGTTCAGAGCCTAACTTAAATAAAAAAAACTTCAACCTCCAATATAAAAAAAT
Found at i:2291028 original size:42 final size:43
Alignment explanation
Indices: 2290975--2291060 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
2290965 TTTAAAACAA
*
2290975 AAAAAATTACCTAAAATTACATAGTTTATGAAATT-AAGTTTT
1 AAAAAATTACCTAAAATCACATAGTTTATGAAATTAAAGTTTT
* *
2291017 AAAAAATTACCTAAAATCATATAGTTTGTGAAATTAAAGTTTT
1 AAAAAATTACCTAAAATCACATAGTTTATGAAATTAAAGTTTT
2291060 A
1 A
2291061 GTCTCGTGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 32 0.80
43 8 0.20
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (43 bp):
AAAAAATTACCTAAAATCACATAGTTTATGAAATTAAAGTTTT
Found at i:2292011 original size:24 final size:24
Alignment explanation
Indices: 2291973--2292021 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2291963 TAAAAAAATC
*
2291973 AAAATTACATATCAAATAAATAAA
1 AAAATTAAATATCAAATAAATAAA
*
2291997 AAAATTAAATTTCAAATAAATAAA
1 AAAATTAAATATCAAATAAATAAA
2292021 A
1 A
2292022 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAATTAAATATCAAATAAATAAA
Found at i:2292022 original size:29 final size:30
Alignment explanation
Indices: 2291963--2292020 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2291953 TGTTAGTACC
*
2291963 TAAAAAAATCAAAATTACATATCAAATAAA
1 TAAAAAAATCAAAATTACAAATCAAATAAA
* *
2291993 TAAAAAAAT-TAAATTTCAAAT-AAATAAA
1 TAAAAAAATCAAAATTACAAATCAAATAAA
2292021 ATTTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 9 0.36
30 9 0.36
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (30 bp):
TAAAAAAATCAAAATTACAAATCAAATAAA
Found at i:2292500 original size:22 final size:22
Alignment explanation
Indices: 2292474--2292521 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2292464 CCGTTTGACA
*
2292474 AATATA-AATTTTAAAAATAAAT
1 AATATATAA-TTTAAAAACAAAT
*
2292496 AATATATAATTTAATAACAAAT
1 AATATATAATTTAAAAACAAAT
2292518 AATA
1 AATA
2292522 AATGTTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AATATATAATTTAAAAACAAAT
Found at i:2293175 original size:17 final size:17
Alignment explanation
Indices: 2293149--2293182 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2293139 TACGTTATTA
2293149 TTTAATTTT-AAATTTT
1 TTTAATTTTAAAATTTT
2293165 TTTATATTTTAAAATTTT
1 TTTA-ATTTTAAAATTTT
2293183 AACATTCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTTTAAAATTTT
Found at i:2302230 original size:38 final size:38
Alignment explanation
Indices: 2302188--2302266 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
2302178 TTAATTAAAT
*
2302188 TTTAAATACCTTTGTTTCTATTGTATAAGTAATTTATA
1 TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
2302226 TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
1 TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
2302264 TTT
1 TTT
2302267 GATGTGTGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (38 bp):
TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
Found at i:2303030 original size:18 final size:17
Alignment explanation
Indices: 2302999--2303033 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2302989 TAATCGAACC
*
2302999 AAAAATTTTTATTTTTT
1 AAAAATTTTAATTTTTT
2303016 AAAAATTTTAAATTTTTT
1 AAAAATTTT-AATTTTTT
2303034 TAATTAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAAAATTTTAATTTTTT
Found at i:2303789 original size:12 final size:12
Alignment explanation
Indices: 2303774--2303799 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2303764 AAATTTTCAA
2303774 TAAATATATATT
1 TAAATATATATT
2303786 TAAATATATATT
1 TAAATATATATT
2303798 TA
1 TA
2303800 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2303919 original size:12 final size:12
Alignment explanation
Indices: 2303904--2303929 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2303894 AAATTTTCAA
2303904 TAAATATATATT
1 TAAATATATATT
2303916 TAAATATATATT
1 TAAATATATATT
2303928 TA
1 TA
2303930 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304049 original size:12 final size:12
Alignment explanation
Indices: 2304034--2304059 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2304024 AAATTTTCAA
2304034 TAAATATATATT
1 TAAATATATATT
2304046 TAAATATATATT
1 TAAATATATATT
2304058 TA
1 TA
2304060 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304179 original size:12 final size:12
Alignment explanation
Indices: 2304164--2304189 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2304154 AAATTTTCAA
2304164 TAAATATATATT
1 TAAATATATATT
2304176 TAAATATATATT
1 TAAATATATATT
2304188 TA
1 TA
2304190 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304309 original size:12 final size:12
Alignment explanation
Indices: 2304294--2304319 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2304284 AAATTTTCAA
2304294 TAAATATATATT
1 TAAATATATATT
2304306 TAAATATATATT
1 TAAATATATATT
2304318 TA
1 TA
2304320 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304439 original size:12 final size:12
Alignment explanation
Indices: 2304424--2304449 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2304414 AAATTTTCAA
2304424 TAAATATATATT
1 TAAATATATATT
2304436 TAAATATATATT
1 TAAATATATATT
2304448 TA
1 TA
2304450 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304569 original size:12 final size:12
Alignment explanation
Indices: 2304554--2304579 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2304544 AAATTTTCAA
2304554 TAAATATATATT
1 TAAATATATATT
2304566 TAAATATATATT
1 TAAATATATATT
2304578 TA
1 TA
2304580 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304699 original size:12 final size:12
Alignment explanation
Indices: 2304684--2304709 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2304674 AAATTTTCAA
2304684 TAAATATATATT
1 TAAATATATATT
2304696 TAAATATATATT
1 TAAATATATATT
2304708 TA
1 TA
2304710 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304829 original size:12 final size:12
Alignment explanation
Indices: 2304814--2304839 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2304804 AAATTTTCAA
2304814 TAAATATATATT
1 TAAATATATATT
2304826 TAAATATATATT
1 TAAATATATATT
2304838 TA
1 TA
2304840 TTGAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATATATT
Found at i:2304938 original size:130 final size:130
Alignment explanation
Indices: 2303649--2304899 Score: 2502
Period size: 130 Copynumber: 9.6 Consensus size: 130
2303639 AATGAAAAAA
2303649 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2303714 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2303779 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2303844 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2303909 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2303974 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2304039 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2304104 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2304169 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2304234 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2304299 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2304364 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2304429 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2304494 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2304559 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2304624 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2304689 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2304754 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
66 TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
2304819 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
1 ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
2304884 TAAATTTTAAAATTTA
66 TAAATTTTAAAATTTA
2304900 AAAAATTATT
Statistics
Matches: 1121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 1121 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (130 bp):
ATATATTTAAATATATATTTATTGAAAATTTAAGTAAAAATTAAGTGAAAATTTGATTGAAATGA
TAAATTTTAAAATTTATCATTTCAATCAAATTTTCACTTAATTTTTACTTAAATTTTCAATAAAT
Found at i:2305301 original size:11 final size:11
Alignment explanation
Indices: 2305285--2305406 Score: 75
Period size: 11 Copynumber: 11.6 Consensus size: 11
2305275 TTTAAAATTG
2305285 TAAAATATTTT
1 TAAAATATTTT
2305296 TAAAATACTTTT
1 TAAAATA-TTTT
*
2305308 T--TA-ATTTT
1 TAAAATATTTT
2305316 TAAAATATTTT
1 TAAAATATTTT
2305327 TAAAATACTTTT
1 TAAAATA-TTTT
*
2305339 TTAAAT-TTTT
1 TAAAATATTTT
* *
2305349 T---TTAATTT
1 TAAAATATTTT
2305357 TAAAATATTTT
1 TAAAATATTTT
*
2305368 GAAAATATATTTT
1 -TAAA-ATATTTT
**
2305381 TTTAAT-TTTT
1 TAAAATATTTT
2305391 T-AAA-ATTTT
1 TAAAATATTTT
2305400 TAAAATA
1 TAAAATA
2305407 AATATGGGCC
Statistics
Matches: 85, Mismatches: 12, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
7 1 0.01
8 9 0.11
9 8 0.09
10 15 0.18
11 27 0.32
12 18 0.21
13 7 0.08
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (11 bp):
TAAAATATTTT
Found at i:2305308 original size:31 final size:31
Alignment explanation
Indices: 2305272--2305345 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
2305262 TTTTTTTATT
2305272 TTTTTTAAAATTGTAAAATATTTTTAAAATAC
1 TTTTTT-AAATTGTAAAATATTTTTAAAATAC
* *
2305304 TTTTTTAATTTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATTGTAAAATATTTTTAAAATAC
2305335 TTTTTTAAATT
1 TTTTTTAAATT
2305346 TTTTTTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 33 0.85
32 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTTTTAAATTGTAAAATATTTTTAAAATAC
Found at i:2305314 original size:20 final size:19
Alignment explanation
Indices: 2305291--2305367 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 19
2305281 ATTGTAAAAT
2305291 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATA-TTTTTTA
2305311 ATTTTTAAAATATTTTTAAAATA
1 ATTTTTAAAATATTTTT----TA
* * *
2305334 CTTTTTTAAATTTTTTTTA
1 ATTTTTAAAATATTTTTTA
2305353 A-TTTTAAAATATTTT
1 ATTTTTAAAATATTTT
2305368 GAAAATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
18 12 0.26
19 7 0.15
20 12 0.26
23 16 0.34
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTAAAATATTTTTTA
Found at i:2305357 original size:31 final size:31
Alignment explanation
Indices: 2305291--2305396 Score: 101
Period size: 31 Copynumber: 3.4 Consensus size: 31
2305281 ATTGTAAAAT
***
2305291 ATTTTTAAAATACTTTTTT-AATTTTTAAAA
1 ATTTTTAAAATACTTTTTTAAATTTTTTTTA
2305321 TATTTTTAAAATACTTTTTTAAATTTTTTTTA
1 -ATTTTTAAAATACTTTTTTAAATTTTTTTTA
**
2305353 A-TTTTAAAATA-TTTTGAAAATATATTTTTTTA
1 ATTTTTAAAATACTTTT-TTAA-AT-TTTTTTTA
2305385 ATTTTTTAAAAT
1 A-TTTTTAAAAT
2305397 TTTTAAAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.06
30 12 0.19
31 22 0.34
32 17 0.27
34 9 0.14
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (31 bp):
ATTTTTAAAATACTTTTTTAAATTTTTTTTA
Found at i:2305382 original size:74 final size:73
Alignment explanation
Indices: 2305239--2305406 Score: 223
Period size: 74 Copynumber: 2.3 Consensus size: 73
2305229 NNNNNNNTAA
* * ** *
2305239 TTTTAAAATATTTTTTACATACTTTTTTTTATTTTTTTTAAAATTGTAAAATATTTTTAAAATAC
1 TTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTT-AAATTGTAAAATATTTTAAAAATAC
2305304 TTTTTTAAT
65 TTTTTTAAT
*
2305313 TTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTT-AATTTTAAAATATTTTGAAAATATA
1 TTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTTAAATTGTAAAATATTTT-AAAA-ATA
*
2305377 TTTTTTTAAT
64 CTTTTTTAAT
*
2305387 TTTTTAAA-ATTTTTAAAATA
1 TTTTAAAATATTTTTAAAATA
2305407 AATATGGGCC
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
72 15 0.18
73 15 0.18
74 54 0.64
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (73 bp):
TTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTTAAATTGTAAAATATTTTAAAAATACT
TTTTTAAT
Found at i:2305386 original size:32 final size:31
Alignment explanation
Indices: 2305345--2305406 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 31
2305335 TTTTTTAAAT
2305345 TTTTTTTAA-TTTTAAAATATTTTGAAAATATA
1 TTTTTTTAATTTTTAAAAT-TTTT-AAAATATA
2305377 TTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTTTAA-TTTTTAAAATTTTTAAAATA
2305407 AATATGGGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 15 0.54
33 4 0.14
34 9 0.32
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (31 bp):
TTTTTTTAATTTTTAAAATTTTTAAAATATA
Found at i:2329190 original size:1 final size:1
Alignment explanation
Indices: 2329181--2329212 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
2329171 TAATTTTTTT
*
2329181 GGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2329213 AGAAAGAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:2331175 original size:12 final size:12
Alignment explanation
Indices: 2331160--2331184 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2331150 ATTTATCAAA
2331160 TGGTTTAAATTT
1 TGGTTTAAATTT
2331172 TGGTTTAAATTT
1 TGGTTTAAATTT
2331184 T
1 T
2331185 ACAGAGGGTA
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:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TGGTTTAAATTT
Found at i:2354020 original size:23 final size:24
Alignment explanation
Indices: 2353976--2354020 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2353966 TTTTATTTTT
*
2353976 TAGAAATGTTTATGAAAAAATATC
1 TAGAAATGTTTATCAAAAAATATC
*
2354000 TAGAAAT-TTTATCAAATAATA
1 TAGAAATGTTTATCAAAAAATA
2354021 CCTACAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (24 bp):
TAGAAATGTTTATCAAAAAATATC
Found at i:2354757 original size:3 final size:3
Alignment explanation
Indices: 2354749--2354961 Score: 417
Period size: 3 Copynumber: 71.0 Consensus size: 3
2354739 TATAAATTAC
*
2354749 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2354797 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2354845 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2354893 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2354941 ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
2354962 CATTTTTTAA
Statistics
Matches: 208, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 208 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2360429 original size:19 final size:19
Alignment explanation
Indices: 2360405--2360442 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2360395 GTATTGAATC
2360405 GATCGATTTGAGAATCAAT
1 GATCGATTTGAGAATCAAT
2360424 GATCGATTTGAGAATCAAT
1 GATCGATTTGAGAATCAAT
2360443 ACGGACTGAT
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:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
GATCGATTTGAGAATCAAT
Found at i:2370337 original size:14 final size:15
Alignment explanation
Indices: 2370318--2370362 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
2370308 AATTAATTTA
2370318 TAAAATTCAATTAAT
1 TAAAATTCAATTAAT
* *
2370333 T-AAATTTATTTAAT
1 TAAAATTCAATTAAT
*
2370347 TAAAAATCAATTAAT
1 TAAAATTCAATTAAT
2370362 T
1 T
2370363 TATTTGGCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATTCAATTAAT
Found at i:2377123 original size:17 final size:17
Alignment explanation
Indices: 2377103--2377139 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2377093 TGAACAACTA
*
2377103 ATTTAATAATTAAAGGG
1 ATTTAATAATTAAAGCG
*
2377120 ATTTCATAATTAAAGCG
1 ATTTAATAATTAAAGCG
2377137 ATT
1 ATT
2377140 AACAAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (17 bp):
ATTTAATAATTAAAGCG
Found at i:2379026 original size:50 final size:52
Alignment explanation
Indices: 2378936--2379038 Score: 120
Period size: 50 Copynumber: 2.0 Consensus size: 52
2378926 ATCGCTCAAA
* * * ** *
2378936 TTTTTTTTTTCGTTTTCGTATTGGTGGTGCTGGCTTTTGACATGCCAGAACCC
1 TTTTTTTTTTCATTTTCGTATT-GTGGTGCCGACCATTGACAGGCCAGAACCC
*
2378989 TTTTTTTTTTCATTTTCGTA-T-TGGTGCCGACCATTGACAGGCCAGCACCC
1 TTTTTTTTTTCATTTTCGTATTGTGGTGCCGACCATTGACAGGCCAGAACCC
2379039 AAAATTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 23 0.53
52 1 0.02
53 19 0.44
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (52 bp):
TTTTTTTTTTCATTTTCGTATTGTGGTGCCGACCATTGACAGGCCAGAACCC
Found at i:2379047 original size:53 final size:55
Alignment explanation
Indices: 2378830--2379207 Score: 306
Period size: 53 Copynumber: 7.1 Consensus size: 55
2378820 AAAAAGAAAC
*
2378830 TTTTTTTTCGCTTTT-GTACTGGTGGTGCCGGCCATTAACAGGCCAGCACCCAAAA-
1 TTTTTTTTCG-TTTTCGTACT-GTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* * * * * * * *
2378885 TTTTTTTTCATTTTCGTA--ATGGTGTCGGCCATTGATAGGCCATCGCTCAAATT
1 TTTTTTTTCGTTTTCGTACTGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* * ** * * *
2378938 TTTTTTTTCGTTTTCGTATTGGTGGTGCTGGCTTTTGACATGCCAGAACCC---TT
1 TTTTTTTTCGTTTTCGTACT-GTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* *
2378991 TTTTTTTTCATTTTCGTA-T-TGGTGCCGACCATTGACAGGCCAGCACCCAAAA-
1 TTTTTTTTCGTTTTCGTACTGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* * * *
2379043 TTTTTTAT-GTTTTCGTACTGGCGGTGCCGGCTATTGACAGGCTAGCA-CC-AAA-
1 TTTTTTTTCGTTTTCGTACT-GTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* * * * *
2379095 TTTTTTTTCTTTTTCTTAC--TGGTGCAGGTCATTCACAGGCCAGCACCCAAAAT
1 TTTTTTTTCGTTTTCGTACTGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
* * * *
2379148 TTTTTTTCCGTTTTCGTACTGGTGGTGTCGGTCATTTACAGGCCAGCACCC--AAT
1 TTTTTTTTCGTTTTCGTACT-GTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
2379202 TTTTTT
1 TTTTTT
2379208 GTTATTTATT
Statistics
Matches: 255, Mismatches: 50, Indels: 37
0.75 0.15 0.11
Matches are distributed among these distances:
50 43 0.17
51 10 0.04
52 48 0.19
53 62 0.24
54 35 0.14
55 12 0.05
56 45 0.18
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (55 bp):
TTTTTTTTCGTTTTCGTACTGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAT
Found at i:2379118 original size:104 final size:105
Alignment explanation
Indices: 2378830--2379207 Score: 411
Period size: 106 Copynumber: 3.6 Consensus size: 105
2378820 AAAAAGAAAC
* *
2378830 TTTTTTTTCGCTTTT-GTACTGGTGGTGCCGGCCATTAACAGGCCAGCACCCAAAATTTTTTTTC
1 TTTTTTTTCG-TTTTCGTACTGGTGGTGCCGGCTATTGACAGGCCAGCA-CC-AAATTTTTTTTC
* * * * * *
2378894 ATTTTCGTAATGGTGTCGGCCATTGATAGGCCATCGCTCAAATT
63 ATTTTCGTAATGGTGCCGGCCATTGACAGGCCAGCACCCAAA-A
* * * * * ***
2378938 TTTTTTTTCGTTTTCGTATTGGTGGTGCTGGCTTTTGACATGCCAGAACCCTTTTTTTTTTCATT
1 TTTTTTTTCGTTTTCGTACTGGTGGTGCCGGCTATTGACAGGCCAGCACCAAATTTTTTTTCATT
* *
2379003 TTCGTATTGGTGCCGACCATTGACAGGCCAGCACCCAAAA
66 TTCGTAATGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
* * * *
2379043 TTTTTTAT-GTTTTCGTACTGGCGGTGCCGGCTATTGACAGGCTAGCACCAAATTTTTTTTCTTT
1 TTTTTTTTCGTTTTCGTACTGGTGGTGCCGGCTATTGACAGGCCAGCACCAAATTTTTTTTCATT
* * * * *
2379107 TTCTTACTGGTGCAGGTCATTCACAGGCCAGCACCCAAAA
66 TTCGTAATGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
* * *
2379147 TTTTTTTTCCGTTTTCGTACTGGTGGTGTCGG-TCATTTACAGGCCAGCACCCAATTTTTTT
1 TTTTTTTT-CGTTTTCGTACTGGTGGTGCCGGCT-ATTGACAGGCCAGCACCAAATTTTTTT
2379208 GTTATTTATT
Statistics
Matches: 224, Mismatches: 42, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
104 86 0.38
105 8 0.04
106 88 0.39
107 6 0.03
108 36 0.16
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (105 bp):
TTTTTTTTCGTTTTCGTACTGGTGGTGCCGGCTATTGACAGGCCAGCACCAAATTTTTTTTCATT
TTCGTAATGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
Found at i:2380737 original size:55 final size:53
Alignment explanation
Indices: 2380677--2380825 Score: 129
Period size: 54 Copynumber: 2.7 Consensus size: 53
2380667 GGTGCTAATT
* * * *
2380677 TGTCAATGGCCGACACAAATACGAAAA-TAAAAAAAAAACTTTTTTGGCGCTGGCC
1 TGTCAATGGCCG-CACAAACACAAAAACGAAAAAAAAAA--TTTTGGGCGCTGGCC
* * *
2380732 TGTCAACGGCCTGCACCAACACAAAAACGAAAAAAAAAATTTTGGGTGCTGGCC
1 TGTCAATGGCC-GCACAAACACAAAAACGAAAAAAAAAATTTTGGGCGCTGGCC
* * * *
2380786 TATCAATGGCCGGCACCACCATTATAAAACGAAAAAAAAA
1 TGTCAATGGCC-GCACAAACA-CA-AAAACGAAAAAAAAA
2380826 TGTTAGGTGC
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
54 30 0.38
55 22 0.28
56 26 0.33
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.18
Consensus pattern (53 bp):
TGTCAATGGCCGCACAAACACAAAAACGAAAAAAAAAATTTTGGGCGCTGGCC
Found at i:2380769 original size:56 final size:56
Alignment explanation
Indices: 2380705--2380825 Score: 147
Period size: 54 Copynumber: 2.2 Consensus size: 56
2380695 ATACGAAAAT
* * *
2380705 AAAAAAAAAACTTTTTTGGCGCTGGCCTGTCAACGGCCTGCACCAACA-CA-AAAACG
1 AAAAAAAAAA--TTTTGGGCGCTGGCCTATCAACGGCCGGCACCAACATCATAAAACG
* * * *
2380761 AAAAAAAAAATTTTGGGTGCTGGCCTATCAATGGCCGGCACCACCATTATAAAACG
1 AAAAAAAAAATTTTGGGCGCTGGCCTATCAACGGCCGGCACCAACATCATAAAACG
2380817 AAAAAAAAA
1 AAAAAAAAA
2380826 TGTTAGGTGC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 30 0.54
55 1 0.02
56 25 0.45
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.18
Consensus pattern (56 bp):
AAAAAAAAAATTTTGGGCGCTGGCCTATCAACGGCCGGCACCAACATCATAAAACG
Found at i:2380847 original size:55 final size:57
Alignment explanation
Indices: 2380755--2380871 Score: 148
Period size: 55 Copynumber: 2.1 Consensus size: 57
2380745 CACCAACACA
* * * * *
2380755 AAAACGAAAAAAAAAATTTTGGGTGCTGGCCTATCAATGGCCGGCACCACCATTA-T
1 AAAACGAAAAAAAAAATGTTAGGTGCCGACCTATCAATGGCCGGCACCACCAGTACT
* * *
2380811 AAAACG-AAAAAAAAATGTTAGGTGCCGACTTGTCAATGGTCGGCACCACCAGTACT
1 AAAACGAAAAAAAAAATGTTAGGTGCCGACCTATCAATGGCCGGCACCACCAGTACT
2380867 AAAAC
1 AAAAC
2380872 TAAATTTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 40 0.77
56 12 0.23
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (57 bp):
AAAACGAAAAAAAAAATGTTAGGTGCCGACCTATCAATGGCCGGCACCACCAGTACT
Found at i:2381131 original size:111 final size:113
Alignment explanation
Indices: 2380950--2381381 Score: 361
Period size: 111 Copynumber: 3.8 Consensus size: 113
2380940 CTGGCCTATC
* ** *
2380950 AATGGCCGGCACCACCAGCACAAAAATG--AAAAAAAA--TTGGGTGCTGGTCTGTCAATGGCCA
1 AATGGCCGGCACCACCAGTACAAAAATGAAAAAAAAAATTTTGGGTGCTGACCTGTCAATGGCCG
* * *
2381011 ACACAACCAGTACAAAAAC-AAAAAAAAAATTAGGGTGCAGGCTAGTA
66 ACACCACCAGTACAAAAACGAAAAAAAAAATTTGGGTGCAGGCTAGTT
* * * * *
2381058 AATGGCTGGCAGCACCAGTACGAAAATGAAAAAAAAAA-TTTGGATACTGACCTGTCAATGGCCG
1 AATGGCCGGCACCACCAGTACAAAAATGAAAAAAAAAATTTTGGGTGCTGACCTGTCAATGGCCG
* ** *
2381122 GCACCACCAGTACAAAAAC-AAAAAGAAATTTTTTTTGGGTGCAGGCTTGTT
66 ACACCACCAGTACAAAAACGAAAAA-AAA---AATTTGGGTGCAGGCTAGTT
* ** * *
2381173 AATGGCCGACACCATTAGTACAAAAACGAAAAAAAAATTATTTTTGGGTGCTGGCCTGTCAATGG
1 AATGGCCGGCACCACCAGTACAAAAATGAAAAAAAAA--A-TTTTGGGTGCTGACCTGTCAATGG
* ** * * *
2381238 CCGGCTTCAACA-T--GAAAACGAAAAAAAAAATTTGGGTGCTGGCCTA-TT
63 CCGACACCACCAGTACAAAAACGAAAAAAAAAATTTGGGTGCAGG-CTAGTT
* * *
2381286 AAT-GCCGGCACCACCAGTACGAAAA-CAAAAAATAAAATTTTTTGGGTGCT-AGCCTGTTAATG
1 AATGGCCGGCACCACCAGTACAAAAATGAAAAAA-AAAA--TTTTGGGTGCTGA-CCTGTCAATG
* * *
2381348 GCCGACACCATCAGTACGAAAACTAAAAAAAAAA
62 GCCGACACCACCAGTACAAAAACGAAAAAAAAAA
2381382 GTTTTTTTGG
Statistics
Matches: 259, Mismatches: 46, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
108 24 0.09
110 9 0.03
111 78 0.30
112 25 0.10
113 16 0.06
114 18 0.07
115 45 0.17
116 8 0.03
117 6 0.02
118 1 0.00
119 29 0.11
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (113 bp):
AATGGCCGGCACCACCAGTACAAAAATGAAAAAAAAAATTTTGGGTGCTGACCTGTCAATGGCCG
ACACCACCAGTACAAAAACGAAAAAAAAAATTTGGGTGCAGGCTAGTT
Found at i:2381316 original size:53 final size:55
Alignment explanation
Indices: 2380937--2381918 Score: 539
Period size: 53 Copynumber: 17.7 Consensus size: 55
2380927 GTTTTTTCTT
* * *
2380937 GTGCTGGCCTATCAATGGCCGGCACCACCAGCAC-AAAA-ATGAAAAAAAA-TTGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACA-AAAAAAAAATTTGG
* ** * * *
2380990 GTGCTGGTCTGTCAATGGCCAACACAACCAGTACAAAAACAAAAAAAAAATTAGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAAAAAAAAATTTGG
* * * * *
2381045 GTGCAGG-CTAGTAAATGGCTGGCAGCACCAGTACGAAAATGAAAAAAAAAATTTGG
1 GTGCTGGCCT-GTCAATGGCCGGCACCACCAGTACGAAAA-CAAAAAAAAAATTTGG
* * * * **
2381101 ATACTGACCTGTCAATGGCCGGCACCACCAGTACAAAAACAAAAAGAAATTTTTTTTGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAAAA-AAA---AATTTGG
* * * * ** *
2381160 GTGCAGGCTTGTTAATGGCCGACACCATTAGTACAAAAACGAAAAAAAAATTATTTTTGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAAAAAAAA--A--TTTGG
** *
2381220 GTGCTGGCCTGTCAATGGCCGGCTTCAACA-T--GAAAACGAAAAAAAAAATTTGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAAAAAAAAATTTGG
* *
2381273 GTGCTGGCCTATTAAT-GCCGGCACCACCAGTACGAAAACAAAAAATAAAATTTTTTGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAAAAA-AAAA---TTTGG
* * * * *
2381331 GTGCTAGCCTGTTAATGGCCGACACCATCAGTACGAAAACTAAAAAAAAAAGTTTTTTTG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAAAAAAAAA----TTTGG
* * * *****
2381391 GTGCTTGCCTGTCAATGACCGG---CACCAGTAGGAAAAC--AAATTTTTTTTGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAAAAAAAAATTTGG
* * * * ** *
2381441 GTGCTGGCCTATTAATGGCCGGCATCACCGGTACGAAAATGAAAAAAAAA-TTAG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAAAAAAAAATTTGG
* * * * * ****** *
2381495 GTGCTGGTCTGTTAATGACTGGCACCATCAGTACGAAAACTAAAATTTTTTTTCTTTTTTCG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAAA------AAAAAATTTGG
* **
2381557 GTGCTGGCCTGTCAATGCCCAACACCACCAGTACGAAAAC-AAAAAAAAA-TT-G
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAAAAAAAAATTTGG
* * * * * *
2381609 GTGTTGGCCTGTCAATGG-TGG--GCACTAGTACGAAAACGAAAAAAAAATTTTAG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAAAAAAAAATTTGG
* * * * * *
2381662 GTGCTGACCTATCAATGGTCGG---CACTAGTATGAAAACGAAAAAAAAAAATTGG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAAAAAAAAATTTGG
* * * *
2381715 GTGCTAGCCTGTTAATGGTCGGCACCACCAGTACGAAAACAAAAAAAAAACATTTTTTG
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC-AAAAAAAAA-A--TTTGG
* * * *
2381774 GTGCTGACCTGTCAATGGCCGG---TAGCAGTACAAAAACGAAAAAAAAAAATTT-G
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAC--AAAAAAAAAATTTGG
* * *
2381827 GTGCTGGCCTGTCAATGGCCAGCA-CATCTAGTACGAAAAC-AAAAAAAAA-TTAG
1 GTGCTGGCCTGTCAATGGCCGGCACCA-CCAGTACGAAAACAAAAAAAAAATTTGG
** * ** * *
2381880 GTGCTATCCTATCAATGGTTGGCACCACTAGTACAAAAA
1 GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAA
2381919 TTAAAAATTT
Statistics
Matches: 716, Mismatches: 158, Indels: 110
0.73 0.16 0.11
Matches are distributed among these distances:
49 14 0.02
50 22 0.03
51 8 0.01
52 31 0.04
53 183 0.26
54 65 0.09
55 55 0.08
56 90 0.13
57 41 0.06
58 19 0.03
59 86 0.12
60 66 0.09
62 36 0.05
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (55 bp):
GTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAACAAAAAAAAAATTTGG
Found at i:2381329 original size:171 final size:172
Alignment explanation
Indices: 2381079--2381413 Score: 464
Period size: 171 Copynumber: 2.0 Consensus size: 172
2381069 GCACCAGTAC
* *
2381079 GAAAATGAAAAAAAAAATTTGGATACTGACCTGTCAATGGCCGGCACCACCAGTACAAAAACAAA
1 GAAAACGAAAAAAAAAATTTGGATACTGACCTATCAATGGCCGGCACCACCAGTACAAAAACAAA
** * * *
2381144 AAGAAATTTTTTTTGGGTGC-AGGCTTGTTAATGGCCGACACCATTAGTACAAAAAC-GAAAAAA
66 AAGAAAAATTTTTTGGGTGCTA-GCCTGTTAATGGCCGACACCATCAGTACAAAAACTAAAAAAA
*
2381207 AAA-TTATTTTTGGGTGCTGGCCTGTCAATGGCCGGCTTCAACAT
130 AAAGTT-TTTTT-GGTGCTGGCCTGTCAATGACCGGCTTCAACAT
* * * * *
2381251 GAAAACGAAAAAAAAAATTTGGGTGCTGGCCTATTAAT-GCCGGCACCACCAGTACGAAAACAAA
1 GAAAACGAAAAAAAAAATTTGGATACTGACCTATCAATGGCCGGCACCACCAGTACAAAAACAAA
*
2381315 AA-ATAAAATTTTTTGGGTGCTAGCCTGTTAATGGCCGACACCATCAGTACGAAAACTAAAAAAA
66 AAGA-AAAATTTTTTGGGTGCTAGCCTGTTAATGGCCGACACCATCAGTACAAAAACTAAAAAAA
*
2381379 AAAGTTTTTTTGGTGCTTGCCTGTCAATGACCGGC
130 AAAGTTTTTTTGGTGCTGGCCTGTCAATGACCGGC
2381414 ACCAGTAGGA
Statistics
Matches: 144, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
170 1 0.01
171 94 0.65
172 47 0.33
173 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (172 bp):
GAAAACGAAAAAAAAAATTTGGATACTGACCTATCAATGGCCGGCACCACCAGTACAAAAACAAA
AAGAAAAATTTTTTGGGTGCTAGCCTGTTAATGGCCGACACCATCAGTACAAAAACTAAAAAAAA
AAGTTTTTTTGGTGCTGGCCTGTCAATGACCGGCTTCAACAT
Found at i:2381545 original size:110 final size:108
Alignment explanation
Indices: 2381198--2381547 Score: 295
Period size: 110 Copynumber: 3.2 Consensus size: 108
2381188 TAGTACAAAA
* * * * * *
2381198 ACGAAAA-AAAAATTATTTTTGGGTGCTGGCCTGTCAATGGCCGGCTTCAAC--ATGAAAACGAA
1 ACGAAAACAAAATTTTTTTTTGGGTGCTGGCCTGTTAATGGCCGGCATCAACGTACGAAAATG-A
* *
2381260 AAAAAAAATTTGGGTGCTGGCCTATTAATG-CCGGCACCACCAGT
65 AAAAAAAATTTAGGTGCTGGCCTGTTAATGACCGGCACCA-CAGT
** * * * *
2381304 ACGAAAACAAAAAATAAAATTTTTTGGGTGCTAGCCTGTTAATGGCCGACACCATCAGTACGAAA
1 ACGAAAAC--AAAAT--TTTTTTTTGGGTGCTGGCCTGTTAATGGCCGGCATCAAC-GTACGAAA
* * * *
2381369 ACTAAAAAAAAAAGTTTTTTTGGTGCTTGCCTGTCAATGACCGGCA-C-CAGT
61 A-TGAAAAAAAAA----TTTAGGTGCTGGCCTGTTAATGACCGGCACCACAGT
* * *
2381420 AGGAAAAC-AAA-TTTTTTTTGGGTGCTGGCCTATTAATGGCCGGCATCACCGGTACGAAAATGA
1 ACGAAAACAAAATTTTTTTTTGGGTGCTGGCCTGTTAATGGCCGGCATCAAC-GTACGAAAATGA
* *
2381483 AAAAAAAA-TTAGGTGCTGGTCTGTTAATGACTGGCACCATCAGT
65 AAAAAAAATTTAGGTGCTGGCCTGTTAATGACCGGCACCA-CAGT
2381527 ACGAAAACTAAAATTTTTTTT
1 ACGAAAAC-AAAATTTTTTTT
2381548 CTTTTTTCGG
Statistics
Matches: 191, Mismatches: 33, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
104 23 0.12
105 1 0.01
106 7 0.04
107 11 0.06
109 17 0.09
110 48 0.25
111 30 0.16
113 3 0.02
114 15 0.08
116 11 0.06
118 19 0.10
119 6 0.03
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (108 bp):
ACGAAAACAAAATTTTTTTTTGGGTGCTGGCCTGTTAATGGCCGGCATCAACGTACGAAAATGAA
AAAAAAATTTAGGTGCTGGCCTGTTAATGACCGGCACCACAGT
Found at i:2381813 original size:112 final size:108
Alignment explanation
Indices: 2381597--2381897 Score: 341
Period size: 112 Copynumber: 2.8 Consensus size: 108
2381587 GTACGAAAAC
* * *
2381597 AAAAAAAAATTGGTGTTGGCCTGTCAATGGT-GG-GCACTAGTACGAAAAC-GAAAAAAAAATTT
1 AAAAAAAAATTGGTGCTGGCCTGTCAATGGTCGGCACACTAGTACGAAAACAAAAAAAAAAATTT
* **
2381659 TAGGTGCTGACCTATCAATGGTCGGCACTAGTATGAAAACGAA
66 TAGGTGCTGACCTATCAATGGCCGGCACTAGTACAAAAACGAA
* * *
2381702 AAAAAAAAATTGGGTGCTAGCCTGTTAATGGTCGGCACCACCAGTACGAAAACAAAAAAAAAACA
1 AAAAAAAAATT-GGTGCTGGCCTGTCAATGGTCGGCA-CACTAGTACGAAAACAAAAAAAAAA-A
* * *
2381767 TTTTTTGGTGCTGACCTGTCAATGGCCGGTAGC-AGTACAAAAACGAA
63 -TTTTAGGTGCTGACCTATCAATGGCCGGCA-CTAGTACAAAAACGAA
* *
2381814 AAAAAAAAATTTGGTGCTGGCCTGTCAATGGCCAGCACATCTAGTACGAAAAC--AAAAAAAAA-
1 AAAAAAAAA-TTGGTGCTGGCCTGTCAATGGTCGGCACA-CTAGTACGAAAACAAAAAAAAAAAT
2381876 -TTAGGTGCT-ATCCTATCAATGG
64 TTTAGGTGCTGA-CCTATCAATGG
2381898 TTGGCACCAC
Statistics
Matches: 166, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
105 12 0.07
106 35 0.21
107 2 0.01
109 15 0.09
110 16 0.10
111 3 0.02
112 80 0.48
113 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (108 bp):
AAAAAAAAATTGGTGCTGGCCTGTCAATGGTCGGCACACTAGTACGAAAACAAAAAAAAAAATTT
TAGGTGCTGACCTATCAATGGCCGGCACTAGTACAAAAACGAA
Found at i:2381873 original size:165 final size:156
Alignment explanation
Indices: 2381579--2381918 Score: 362
Period size: 165 Copynumber: 2.1 Consensus size: 156
2381569 CAATGCCCAA
* * ** *
2381579 CACCACCAGTACGAAAACAAAAAAAAATTGGTGTTGGCCTGTCAATGGTGGGCACTAGTACGAAA
1 CACCACCAGTACGAAAACAAAAAAAAATTGGTGCTGACCTGTCAATGGCCGGCACTAGTACAAAA
* * * *
2381644 ACGAAAAAAAAATTTTAGGTGCTGACCTATCAATGGTCGGCACTAGTATGAAAACGAAAAAAAAA
66 ACGAAAAAAAAAATTTAGGTGCTGACCTATCAATGGCCGACACTAGTACGAAAAC--AAAAAAAA
* * *
2381709 AATTGGGTGCTAGCCTGTTAATGGTCGG
129 AATTAGGTGCTAGCCTATCAATGGTCGG
*
2381737 CACCACCAGTACGAAAACAAAAAAAAAACATTTTTTGGTGCTGACCTGTCAATGGCCGGTAGC-A
1 CACCACCAGTACGAAAAC--AAAAAAAA-A----TTGGTGCTGACCTGTCAATGGCCGGCA-CTA
* *
2381801 GTACAAAAACGAAAAAAAAAAATTT-GGTGCTGGCCTGTCAATGGCCAGCACATCTAGTACGAAA
58 GTACAAAAACG-AAAAAAAAAATTTAGGTGCTGACCTATCAATGGCC-G-ACA-CTAGTACGAAA
* *
2381865 AC-AAAAAAAAATTAGGTGCTATCCTATCAATGGTTGG
119 ACAAAAAAAAAATTAGGTGCTAGCCTATCAATGGTCGG
* *
2381902 CACCACTAGTACAAAAA
1 CACCACCAGTACGAAAA
2381919 TTAAAAATTT
Statistics
Matches: 151, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
158 18 0.12
160 8 0.05
161 1 0.01
165 96 0.64
166 14 0.09
167 2 0.01
168 12 0.08
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (156 bp):
CACCACCAGTACGAAAACAAAAAAAAATTGGTGCTGACCTGTCAATGGCCGGCACTAGTACAAAA
ACGAAAAAAAAAATTTAGGTGCTGACCTATCAATGGCCGACACTAGTACGAAAACAAAAAAAAAA
TTAGGTGCTAGCCTATCAATGGTCGG
Found at i:2381990 original size:107 final size:106
Alignment explanation
Indices: 2381879--2382089 Score: 241
Period size: 106 Copynumber: 2.0 Consensus size: 106
2381869 AAAAAAATTA
* * **
2381879 GGTGCT-ATCCTATCAATGGTTGGCACCACTAGTAC-AAAAATTAAA-AA-TTTCTTTTTGGGTG
1 GGTGCTGA-CCTATCAATGGCTGGCACCACCAGTACGAAAAAGAAAAGAATTTTCTTTTT--GT-
* * * *
2381940 CTAGCCTATCAATTGCCGGCATCAGTACGAAAACAAATTTTTTTTG
62 -TAGCCTATCAATGGCCGGCAACAGCACGAAAACAAAATTTTTTTG
* * *
2381986 GGTGCTGACCTATCAATGGCTGGCGCCACCAGTACGAAAACGAAAAGAATTTTCTTTTTGTTGGC
1 GGTGCTGACCTATCAATGGCTGGCACCACCAGTACGAAAAAGAAAAGAATTTTCTTTTTGTTAGC
*
2382051 CTGTCAATGGCCGGCAACAGCACGAAAACAAAATTTTTT
66 CTATCAATGGCCGGCAACAGCACGAAAACAAAATTTTTT
2382090 GTAACAGCCC
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
106 37 0.42
107 30 0.34
108 10 0.11
109 2 0.02
110 9 0.10
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (106 bp):
GGTGCTGACCTATCAATGGCTGGCACCACCAGTACGAAAAAGAAAAGAATTTTCTTTTTGTTAGC
CTATCAATGGCCGGCAACAGCACGAAAACAAAATTTTTTTG
Found at i:2382203 original size:14 final size:15
Alignment explanation
Indices: 2382179--2382207 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2382169 TTTTTCTGTG
2382179 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
2382194 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
2382208 AGTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:2382432 original size:28 final size:28
Alignment explanation
Indices: 2382399--2382455 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
2382389 TATAGTTTTT
2382399 ATAATA-ATTATAAAGGTTATAATAATAA
1 ATAATATATTATAAA-GTTATAATAATAA
*
2382427 ATAATATATTATAAAGTTATTATAATAA
1 ATAATATATTATAAAGTTATAATAATAA
2382455 A
1 A
2382456 AACAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATATATTATAAAGTTATAATAATAA
Found at i:2383402 original size:43 final size:42
Alignment explanation
Indices: 2383341--2383468 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 42
2383331 ATAAGATTCT
* * *
2383341 GATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTCGGCATC
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGT-GACATC
*
2383384 GATATTTGATTACGTGTAAGACC-CTGTCTGGGACAGTGACATC
1 GATATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTGACATC
*
2383427 GATATGTGATTACATGTAAGACCACGTCTGGGACGATGACAT
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACG-TGACAT
2383469 TGTACGAGCT
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.03
43 70 0.93
44 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (42 bp):
GATATGTGATTACGTGTAAGACCACGTCTGGGACGTGACATC
Found at i:2388147 original size:24 final size:24
Alignment explanation
Indices: 2388120--2388193 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
2388110 TGTTACATAT
2388120 ATGCTGTCCAATTTTGATGCTTAA
1 ATGCTGTCCAATTTTGATGCTTAA
* * * *
2388144 ATGCTGCCCAATTTTGTTACAT-A
1 ATGCTGTCCAATTTTGATGCTTAA
*
2388167 ATGCTGTCCAGTTTTGATGCTTAA
1 ATGCTGTCCAATTTTGATGCTTAA
2388191 ATG
1 ATG
2388194 TTGCATATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 18 0.45
24 22 0.55
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (24 bp):
ATGCTGTCCAATTTTGATGCTTAA
Found at i:2388173 original size:47 final size:47
Alignment explanation
Indices: 2388104--2388193 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
2388094 NNNNNNNNGA
2388104 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
2388151 CCAATTTTGTTACATA-ATGCTGTCCAGTTTTGATGCTTAAATG
1 CCAA-TTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATG
2388194 TTGCATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
47 30 0.73
48 11 0.27
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:2388181 original size:23 final size:23
Alignment explanation
Indices: 2388104--2388182 Score: 88
Period size: 24 Copynumber: 3.4 Consensus size: 23
2388094 NNNNNNNNGA
2388104 CCAA-TTTGTTACATATATGCTGT
1 CCAATTTTGTTACATA-ATGCTGT
* * * *
2388127 CCAATTTTGATGCTTAAATGCTGC
1 CCAATTTTGTTACAT-AATGCTGT
2388151 CCAATTTTGTTACATAATGCTGT
1 CCAATTTTGTTACATAATGCTGT
*
2388174 CCAGTTTTG
1 CCAATTTTG
2388183 ATGCTTAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
23 19 0.42
24 25 0.56
25 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (23 bp):
CCAATTTTGTTACATAATGCTGT
Found at i:2388206 original size:35 final size:33
Alignment explanation
Indices: 2388158--2388231 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 33
2388148 TGCCCAATTT
* *
2388158 TGTTACATAATGCTGTCCAGTTTTGATGCTTAAA
1 TGTTGCATAATGCTGTCCAGTTTTGATG-TAAAA
*
2388192 TGTTGCATATATGCTGTCCAGTTTTGGTGTAAAA
1 TGTTGCATA-ATGCTGTCCAGTTTTGATGTAAAA
2388226 TGTTGC
1 TGTTGC
2388232 TCAAACTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 18 0.50
35 18 0.50
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.42
Consensus pattern (33 bp):
TGTTGCATAATGCTGTCCAGTTTTGATGTAAAA
Found at i:2388259 original size:23 final size:23
Alignment explanation
Indices: 2388233--2388282 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2388223 AAATGTTGCT
*
2388233 CAAACTGTTGT-TTATATGCTGCC
1 CAAACTGATGTATT-TATGCTGCC
* *
2388256 CAAATTGATGTATTTATGCTGTC
1 CAAACTGATGTATTTATGCTGCC
2388279 CAAA
1 CAAA
2388283 TTTTGGTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (23 bp):
CAAACTGATGTATTTATGCTGCC
Found at i:2388323 original size:71 final size:68
Alignment explanation
Indices: 2388201--2388331 Score: 158
Period size: 71 Copynumber: 1.9 Consensus size: 68
2388191 ATGTTGCATA
* *
2388201 TATGCTGTCCAGTTTTGGTGTAAAATGTTGCTCAAACTGTTGTTTATATGCTGCCCAAATTGATG
1 TATGCTGTCCAATTTTGGTGTAAAATGTTGCTCAAAC-GTTGTTTAAATGCTGCCCAAATTGATG
2388266 TATT
65 TATT
* *
2388270 TATGCTGTCCAAATTTTGGTGTGAAAATGTTG-TCTAA-GTTGGTATATAAATGCTGTCCAAAT
1 TATGCTGTCC-AATTTTGGTGT-AAAATGTTGCTCAAACGTT-GT-T-TAAATGCTGCCCAAAT
2388332 AGGGTAGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
68 3 0.06
69 12 0.23
70 15 0.28
71 23 0.43
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (68 bp):
TATGCTGTCCAATTTTGGTGTAAAATGTTGCTCAAACGTTGTTTAAATGCTGCCCAAATTGATGT
ATT
Found at i:2389135 original size:55 final size:54
Alignment explanation
Indices: 2389064--2389261 Score: 192
Period size: 55 Copynumber: 3.7 Consensus size: 54
2389054 ATTTTTTTTT
* *
2389064 GGTGTTGGCCTGTCAATGGCCGGCACCACCTGTACGAAAACAAAAAAAAAATTTT
1 GGTGCTGGCCTGTCAATGGCCGGCACCA-CTGTACGAAAACAAAAAAAAAATTTG
* * * ** * *
2389119 GGTGTTGGCCTGTCAATTG-CTGCATTA--GTACGAAAACGAAAAAAAAATTGG
1 GGTGCTGGCCTGTCAATGGCCGGCACCACTGTACGAAAACAAAAAAAAAATTTG
* * * * *
2389170 GGTGCTGGCCTCTTAATGGCTGTCACAACTAGTACGAAAACGAAAAAAAAAA-TTG
1 GGTGCTGGCCTGTCAATGGCCGGCACCACT-GTACGAAAAC-AAAAAAAAAATTTG
*
2389225 GGTGCTGGCCTGTCAATGGCTGGCACCA--GTACGAAAA
1 GGTGCTGGCCTGTCAATGGCCGGCACCACTGTACGAAAA
2389262 TGATTTTTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
51 36 0.31
52 12 0.10
54 5 0.04
55 54 0.47
56 9 0.08
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (54 bp):
GGTGCTGGCCTGTCAATGGCCGGCACCACTGTACGAAAACAAAAAAAAAATTTG
Found at i:2389179 original size:51 final size:50
Alignment explanation
Indices: 2389095--2389261 Score: 190
Period size: 51 Copynumber: 3.2 Consensus size: 50
2389085 GGCACCACCT
* * * * *
2389095 GTACGAAAACAAAAAAAAAATTTTGGTGTTGGCCTGTCAATTGCTGCATTA
1 GTACGAAAACGAAAAAAAAA-TTGGGTGCTGGCCTGTCAATGGCTGCACTA
* *
2389146 GTACGAAAACGAAAAAAAAATTGGGGTGCTGGCCTCTTAATGGCTGTCACAACTA
1 GTACGAAAACGAAAAAAAAATT-GGGTGCTGGCCTGTCAATGGCTG---C-ACTA
*
2389201 GTACGAAAACGAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCTGGCACCA
1 GTACGAAAACG-AAAAAAAAATTGGGTGCTGGCCTGTCAATGGCT-GCACTA
2389253 GTACGAAAA
1 GTACGAAAA
2389262 TGATTTTTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
50 2 0.02
51 37 0.37
52 12 0.12
53 1 0.01
54 1 0.01
55 34 0.34
56 12 0.12
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (50 bp):
GTACGAAAACGAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCTGCACTA
Found at i:2389291 original size:50 final size:50
Alignment explanation
Indices: 2389225--2389492 Score: 230
Period size: 58 Copynumber: 5.0 Consensus size: 50
2389215 AAAAAAATTG
* * *
2389225 GGTGCTGGCCTGTCAATGGCTGGCACCAGTACGAAAATGATTTTTTTTTT
1 GGTGCTGGCCTGTCAATGGCAGGCACCAGTACGAAAAAGAATTTTTTTTT
* * *
2389275 GGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAAAAAGAATTTTTTTTG
1 GGTGCTGGCCTGTCAATGGCAGGCACCAGT------ACG--AAAAAGAATTTTTTTTT
* *
2389333 GGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAACAGAATTTTTTTTTT
1 GGTGCTGGCCTGTCAATGGCAGGCACCAGTACGAAAA-AGAA-TTTTTTTTT
* * * * *
2389385 GATGCTGGCCTATCAATGGCCGGGACCACCAGTACGGAAACGAATTTTTTTTT
1 GGTGCTGGCCTGTCAATGG-CAGG--CACCAGTACGAAAAAGAATTTTTTTTT
* * * *
2389438 GGTGCTGACCTGTCAATGGCCGACACCATCAGTACGAAAACGAAATTTTTTTTT
1 GGTGCTGGCCTGTCAATGGCAGGCA-C--CAGTACGAAAAAG-AATTTTTTTTT
2389492 G
1 G
2389493 TTTTCGTAGT
Statistics
Matches: 178, Mismatches: 23, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
50 34 0.19
51 5 0.03
52 30 0.17
53 38 0.21
54 15 0.08
55 13 0.07
56 3 0.02
58 40 0.22
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (50 bp):
GGTGCTGGCCTGTCAATGGCAGGCACCAGTACGAAAAAGAATTTTTTTTT
Found at i:2389338 original size:58 final size:55
Alignment explanation
Indices: 2388940--2389482 Score: 217
Period size: 53 Copynumber: 10.0 Consensus size: 55
2388930 GGGGTGTTAC
* * *
2388940 ATTTTTTTTGTGGTGCTGGCTTATCAATGGCTGGCACCACCAGTACGAAAACGAAAAGAA
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGG---CACCAGTACGAAAACG-AAAG-A
* * * * *
2389000 AATTTTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCTGTACGAAAAC----TA
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCA---GTACGAAAACGAAAGA
* *
2389054 A-TTTTTTTTTGGTGTTGGCCTGTCAATGGCCGGCACCACCTGTACGAAAAC-AAA-A
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCA---GTACGAAAACGAAAGA
***** * * * * **
2389109 A-AAAAATTTTGGTGTTGGCCTGTCAATTG-CTGCATTAGTACGAAAACGAAA-A
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAGA
**** ** * * * *
2389161 A--AAAATTGGGGTGCTGGCCTCTTAATGGCTGTCACAACTAGTACGAAAACGAAA-A
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCAC--C-AGTACGAAAACGAAAGA
***** * * * *
2389216 A--AAAAATTGGGTGCTGGCCTGTCAATGGCTGGCACCAGTACG--AA--AATG-
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAGA
2389264 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAAAAAGA
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACG----AAAGA
* * ***
2389323 A-TTTTTTTTGGGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAAC---AGA
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAGA
* *
2389374 ATTTTTTTTTTGATGCTGGCCTATCAATGGCCGGGACCACCAGTACGGAAAC----GA
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCC-GG--CACCAGTACGAAAACGAAAGA
* * *
2389428 A-TTTTTTTTTGGTGCTGACCTGTCAATGGCCGACACCATCAGTACGAAAACGAAA
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCA-C--CAGTACGAAAACGAAA
2389483 TTTTTTTTTG
Statistics
Matches: 386, Mismatches: 63, Indels: 71
0.74 0.12 0.14
Matches are distributed among these distances:
48 3 0.01
50 37 0.10
51 36 0.09
52 41 0.11
53 87 0.23
54 10 0.03
55 84 0.22
57 5 0.01
58 45 0.12
59 1 0.00
60 37 0.10
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (55 bp):
ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAGA
Found at i:2389341 original size:108 final size:106
Alignment explanation
Indices: 2388940--2389428 Score: 415
Period size: 108 Copynumber: 4.5 Consensus size: 106
2388930 GGGGTGTTAC
* * * *
2388940 ATTTTTTTTGTGGTGCTGGCTTATCAATGGCTGGCACCACCAGTACGAAAACGAAAAGAAAATTT
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGG---CACCAGTACGAAAACGAAAA-AAAA--A
2389005 TTTTTGGGTGCTGGCCTGTCAATGG-TCGGCACCACCTGTACGAAAACT-A
60 TTTTTGGGTGCTGGCCTGTCAATGGCT-GGCACCA---GTACGAAAACTGA
* * *
2389054 A-TTTTTTTTTGGTGTTGGCCTGTCAATGGCCGGCACCACCTGTACGAAAAC-AAAAAAAAAATT
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCA---GTACGAAAACGAAAAAAAAATTT
* * **
2389117 TT-GGTGTTGGCCTGTCAATTGCT-GCATTAGTACGAAAAC-GAA
63 TTGGGTGCTGGCCTGTCAATGGCTGGCACCAGTACGAAAACTG-A
****** ** * * * * *
2389159 AAAAAAATTGGGGTGCTGGCCTCTTAATGGCTGTCACAACTAGTACGAAAACGAAAAAAAAA--A
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCAC--C-AGTACGAAAACGAAAAAAAAATTT
2389222 TTGGGTGCTGGCCTGTCAATGGCTGGCACCAGTACGAAAA-TG-
63 TTGGGTGCTGGCCTGTCAATGGCTGGCACCAGTACGAAAACTGA
2389264 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAAAAAGAATTTTT
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAAAAA-AA---TT
*** *
2389329 TTTGGGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAACAGA
62 TTTGGGTGCTGGCCTGTCAATGGCTGGCACCAGTACGAAAACTGA
* *
2389374 ATTTTTTTTTTGATGCTGGCCTATCAATGGCCGGGACCACCAGTACGGAAACGAA
1 ATTTTTTTTTTGGTGCTGGCCTATCAATGGCC-GG--CACCAGTACGAAAACGAA
2389429 TTTTTTTTTG
Statistics
Matches: 303, Mismatches: 47, Indels: 51
0.76 0.12 0.13
Matches are distributed among these distances:
102 19 0.06
103 3 0.01
104 10 0.03
105 29 0.10
106 52 0.17
107 27 0.09
108 55 0.18
109 7 0.02
110 36 0.12
111 6 0.02
112 4 0.01
113 54 0.18
114 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (106 bp):
ATTTTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTACGAAAACGAAAAAAAAATTTTTG
GGTGCTGGCCTGTCAATGGCTGGCACCAGTACGAAAACTGA
Found at i:2389436 original size:108 final size:103
Alignment explanation
Indices: 2388990--2389492 Score: 309
Period size: 108 Copynumber: 4.7 Consensus size: 103
2388980 CAGTACGAAA
* * * *
2388990 ACGAAAA-GAAAATTTTTTTTGGGTGCTGGCCTGTCAATGGTCGGCACCACCTGTACGAAAACTA
1 ACGAAAACGAAAATTTTTTTTGGGTGCTGGCCTGTCAAT-G--GGAAGCACCAGTACGAAAACGA
* * *
2389054 A-TTTTTTTTTGGTGTTGGCCTGTCAATGGCCGGCACCACCTGT
63 ATTTTTTTTTTGATGCTGGCCTATCAATGGCCGGCACCA---GT
* **** * * ** **
2389097 ACGAAAACAAAAAAAAAATTTT-GGTGTTGGCCTGTCAAT-TGCTGCATTAGTACGAAAACGAAA
1 ACGAAAAC-GAAAATTTTTTTTGGGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAACG-AA
****** ** * * * * *
2389160 AAAAAATTGGGGTGCTGGCCTCTTAATGGCTGTCACAACTAGT
64 TTTTTTTTTTGATGCTGGCCTATCAATGGCCGGCAC--C-AGT
****** *** *
2389203 ACGAAAACGAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCTGGCACCAGTACGAAAATG-ATT
1 ACGAAAACGAAAATTTTTTTTGGGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAACGAATT
*
2389267 TTTTTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGT
66 TTTTTTTTGATGCTGGCCTATCAATGGCCGGCACCAGT
2389305 ACGAAAACGAAAAAAAGAATTTTTTTTGGGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAA
1 ACGAAAACG-----AA-AATTTTTTTTGGGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAA
2389370 CAGAATTTTTTTTTTGATGCTGGCCTATCAATGGCCGGGACCACCAGT
60 C-GAATTTTTTTTTTGATGCTGGCCTATCAATGGCC-GG--CACCAGT
* * * * *
2389418 ACGGAAACG--AATTTTTTTTTGGTGCTGACCTGTCAATGGCCGACACCATCAGTACGAAAACGA
1 ACGAAAACGAAAATTTTTTTTGGGTGCTGGCCTGTCAATGG--GA-AGCACCAGTACGAAAACGA
*
2389481 AATTTTTTTTTG
63 ATTTTTTTTTTG
2389493 TTTTCGTAGT
Statistics
Matches: 308, Mismatches: 65, Indels: 46
0.74 0.16 0.11
Matches are distributed among these distances:
102 12 0.04
103 1 0.00
104 14 0.05
105 65 0.21
106 49 0.16
107 38 0.12
108 71 0.23
109 10 0.03
110 31 0.10
111 2 0.01
113 15 0.05
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (103 bp):
ACGAAAACGAAAATTTTTTTTGGGTGCTGGCCTGTCAATGGGAAGCACCAGTACGAAAACGAATT
TTTTTTTTGATGCTGGCCTATCAATGGCCGGCACCAGT
Found at i:2389574 original size:54 final size:51
Alignment explanation
Indices: 2389480--2389600 Score: 138
Period size: 54 Copynumber: 2.3 Consensus size: 51
2389470 TACGAAAACG
* * * *
2389480 AAATTTTTTTTTGTTTTCGTAGTAGTGCTGGCCATTGATA-GCCAACACCT
1 AAATTTTTTTTTATTTTCGTAGTAGTGCCGGCCAGTGATAGGCCAACACCC
* *
2389530 AAATTTTTTTTTCATTTTCGTACTGGTGGTGCCGGCCAGTGATAGGCCAGCACCC
1 AAATTTTTTTTT-ATTTTCGTA---GTAGTGCCGGCCAGTGATAGGCCAACACCC
2389585 AAA-TTTTTTTTATTTT
1 AAATTTTTTTTTATTTT
2389601 TTTATTTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
50 12 0.20
51 8 0.13
53 5 0.08
54 24 0.40
55 11 0.18
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (51 bp):
AAATTTTTTTTTATTTTCGTAGTAGTGCCGGCCAGTGATAGGCCAACACCC
Found at i:2391934 original size:77 final size:76
Alignment explanation
Indices: 2391853--2392006 Score: 283
Period size: 76 Copynumber: 2.0 Consensus size: 76
2391843 ATTTTATGAT
2391853 AAAAATTAAATACATGAATATTAT-ATTTTATTTAATAAACGTACATTTATAAATTATCATCTTC
1 AAAAATTAAAT-CATGAATATTATAATTTTATTT-ATAAACGTACATTTATAAATTATCATCTTC
2391917 CCATATATACCAA
64 CCATATATACCAA
2391930 AAAAATTAAATCATGAATATTATAATTTTATTTATAAACGTACATTTATAAATTATCATCTTCCC
1 AAAAATTAAATCATGAATATTATAATTTTATTTATAAACGTACATTTATAAATTATCATCTTCCC
2391995 ATATATACCAA
66 ATATATACCAA
2392006 A
1 A
2392007 TATTATTAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
76 56 0.74
77 20 0.26
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (76 bp):
AAAAATTAAATCATGAATATTATAATTTTATTTATAAACGTACATTTATAAATTATCATCTTCCC
ATATATACCAA
Found at i:2417718 original size:22 final size:21
Alignment explanation
Indices: 2417664--2417719 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2417654 GCCCACCCAT
*
2417664 ATTATTTT-TATTTTTTTAAA
1 ATTATTTTATATTATTTTAAA
* *
2417684 ATTTATATTATATTATTTTAAC
1 A-TTATTTTATATTATTTTAAA
2417706 ATTATTTTAATATT
1 ATTATTTT-ATATT
2417720 TAATTAGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 12 0.41
22 16 0.55
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTTTATATTATTTTAAA
Found at i:2418644 original size:18 final size:18
Alignment explanation
Indices: 2418603--2418637 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2418593 TTTTCTGCAT
*
2418603 CTTTCGCTTTTTTTTTTA
1 CTTTCGCTTTTTCTTTTA
*
2418621 CTTTCGGTTTTTCTTTT
1 CTTTCGCTTTTTCTTTT
2418638 CTGTTCGTTC
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:0.03, C:0.17, G:0.09, T:0.71
Consensus pattern (18 bp):
CTTTCGCTTTTTCTTTTA
Found at i:2421820 original size:35 final size:35
Alignment explanation
Indices: 2421781--2421895 Score: 94
Period size: 35 Copynumber: 3.2 Consensus size: 35
2421771 GATGGAATTA
2421781 TTTAATTTGACTCATTTGATTTATGTCATTAATAT
1 TTTAATTTGACTCATTTGATTTATGTCATTAATAT
* * * ** *
2421816 TTTAATGCTTTTACTTA-TT--TTAAAATCGATGGAAT-T
1 TTTAA---TTTGACTCATTTGATTTATGTC-AT-TAATAT
2421852 ATTTAATTTGACTCATTTGATTTATGTCATTAATAT
1 -TTTAATTTGACTCATTTGATTTATGTCATTAATAT
2421888 TTTAATTT
1 TTTAATTT
2421896 TAATTTAAGA
Statistics
Matches: 58, Mismatches: 12, Indels: 20
0.64 0.13 0.22
Matches are distributed among these distances:
34 7 0.12
35 23 0.40
36 6 0.10
37 15 0.26
38 7 0.12
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.54
Consensus pattern (35 bp):
TTTAATTTGACTCATTTGATTTATGTCATTAATAT
Found at i:2421827 original size:72 final size:72
Alignment explanation
Indices: 2421750--2421893 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
2421740 CAAAACGTTA
*
2421750 GCTTTTACTTATTTTGAAATCGATGGAATTATTTAATTTGACTCATTTGATTTATGTCATTAATA
1 GCTTTTACTTATTTTAAAATCGATGGAATTATTTAATTTGACTCATTTGATTTATGTCATTAATA
2421815 TTTTAAT
66 TTTTAAT
2421822 GCTTTTACTTATTTTAAAATCGATGGAATTATTTAATTTGACTCATTTGATTTATGTCATTAATA
1 GCTTTTACTTATTTTAAAATCGATGGAATTATTTAATTTGACTCATTTGATTTATGTCATTAATA
2421887 TTTTAAT
66 TTTTAAT
2421894 TTTAATTTAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.51
Consensus pattern (72 bp):
GCTTTTACTTATTTTAAAATCGATGGAATTATTTAATTTGACTCATTTGATTTATGTCATTAATA
TTTTAAT
Found at i:2421929 original size:72 final size:72
Alignment explanation
Indices: 2421766--2421915 Score: 183
Period size: 72 Copynumber: 2.1 Consensus size: 72
2421756 ACTTATTTTG
* * **
2421766 AAATCGATGGAATTATTTAATTTGACTCATTTGATTTATGTCATTAATATTTTAATGCTTTTACT
1 AAATCGATGAAAATATTTAATTTGACTCATTTGATTTATGTCATTAATATTTTAATGCTTTTAAG
* **
2421831 TATTTTA
66 AAAGTTA
* * **
2421838 AAATCGATGGAATTATTTAATTTGACTCATTTGATTTATGTCATTAATATTTTAATTTTAATTTA
1 AAATCGATGAAAATATTTAATTTGACTCATTTGATTTATGTCATTAATATTTTAATGCT--TTTA
2421903 AGAAAGTTA
64 AGAAAGTTA
2421912 AAAT
1 AAAT
2421916 GTCGAAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 57 0.83
74 12 0.17
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.49
Consensus pattern (72 bp):
AAATCGATGAAAATATTTAATTTGACTCATTTGATTTATGTCATTAATATTTTAATGCTTTTAAG
AAAGTTA
Found at i:2423099 original size:2 final size:2
Alignment explanation
Indices: 2423092--2423116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2423082 GAAAAATTAA
2423092 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 A
2423117 AATTTTCAGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2424288 original size:4 final size:4
Alignment explanation
Indices: 2424279--2424315 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
2424269 CAGCTCTAAG
*
2424279 GTAT GTAT GTAT GTAT GTAT GTAT GTAT ATAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
2424316 GTCTCATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:2424359 original size:15 final size:15
Alignment explanation
Indices: 2424339--2424375 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2424329 AATGGTAATG
2424339 TTTTTTTCTTGTTTC
1 TTTTTTTCTTGTTTC
* *
2424354 TTTTTTTTTTTTTTC
1 TTTTTTTCTTGTTTC
2424369 TTTTTTT
1 TTTTTTT
2424376 GCAGACTTGA
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:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTTTCTTGTTTC
Found at i:2424858 original size:31 final size:31
Alignment explanation
Indices: 2424807--2424876 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
2424797 AAAACCTTAT
*
2424807 AGTTCAGGCCACAATGTGGGAACAATTGTCA
1 AGTTCAGGCCACAATATGGGAACAATTGTCA
* *
2424838 AGTTTAGGCCCCAATATGGGAACAATTGTCA
1 AGTTCAGGCCACAATATGGGAACAATTGTCA
2424869 AGTTCAGG
1 AGTTCAGG
2424877 GACTAACCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (31 bp):
AGTTCAGGCCACAATATGGGAACAATTGTCA
Found at i:2435308 original size:38 final size:38
Alignment explanation
Indices: 2435266--2435342 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2435256 TTACTTAACA
2435266 ATTTATTTGTGTCGGTAAAATTGAGATTCTAAAATTCC
1 ATTTATTTGTGTCGGTAAAATTGAGATTCTAAAATTCC
2435304 ATTTATTTGTGTCGGTAAAATTGAGATTCTAAAATTCC
1 ATTTATTTGTGTCGGTAAAATTGAGATTCTAAAATTCC
2435342 A
1 A
2435343 ATGCACCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (38 bp):
ATTTATTTGTGTCGGTAAAATTGAGATTCTAAAATTCC
Found at i:2436303 original size:5 final size:5
Alignment explanation
Indices: 2436293--2436317 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2436283 TGATAATCAT
2436293 TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA
2436318 ATGTTGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:2439501 original size:265 final size:256
Alignment explanation
Indices: 2439036--2439529 Score: 744
Period size: 265 Copynumber: 1.9 Consensus size: 256
2439026 AAAGACTCAA
2439036 AATTTTGGGACATCTAGTGCAAATAACCCAGAAAACAAAGCCAAAAAAAGAAAAACAGCTTAACA
1 AATTTTGGGACATCTAGTGCAAATAACCCAGAAAACAAAGCCAAAAAAAGAAAAACAGCTTAACA
* *
2439101 TTCCATTGACTTCAAAATGAACCAAATTCCATTATTGAAACATGAAGAATACAAAGAATATCTCA
66 TTCCATTGACATCAAAATGAACCAAATTCCATTATTGAAACATGAAGAATACAAAGAATACCTCA
*
2439166 AAACAAATCAGCAATGACAGTGTGCTCAAAACAAATGGTCACGAACCATTGGAGAAAGGACTCCA
131 AAACAAATCAGCAATGACAATGTGCTC-AAACAAATGGTCACGAACCATTGGAGAAAGGACTCCA
*
2439231 AAAATTCATTTACATATACAGAAATGGGAAAAGTTTAGGGACCAATCTGAAATTTGGACCAT
195 AAAATTCATTTACATATACAGAAATGAGAAAAGTTTAGGGACCAATCTGAAATTTGGACCAT
* * *
2439293 AATTTTGGGACATCTGGTGCAAATAACCCAGAAAACAAAGCC-AAAAAAGAAAAATAGCTTAGCA
1 AATTTTGGGACATCTAGTGCAAATAACCCAGAAAACAAAGCCAAAAAAAGAAAAACAGCTTAACA
* *
2439357 TTGTGAAACGTTCATTGACATCAAAATGAAGCAAATTCTATTATTGAAACATGAAGAATACAAAG
66 -T-T----C---CATTGACATCAAAATGAACCAAATTCCATTATTGAAACATGAAGAATACAAAG
*
2439422 AATACCTCAAAAC-AATCAGCAAGTGACAATGTGCTC-ATCAAATGGTCACAAAGAA-CATTGGA
122 AATACCTCAAAACAAATCAGCAA-TGACAATGTGCTCAAACAAATGGTCAC---GAACCATTGGA
2439484 GAAAGGACTCCAAAAATTCATTTACATATACAGAAATGAGAAAAGT
183 GAAAGGACTCCAAAAATTCATTTACATATACAGAAATGAGAAAAGT
2439530 ACTTACAAGA
Statistics
Matches: 214, Mismatches: 10, Indels: 18
0.88 0.04 0.07
Matches are distributed among these distances:
256 20 0.09
257 42 0.20
258 1 0.00
262 1 0.00
263 12 0.06
264 9 0.04
265 126 0.59
266 3 0.01
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (256 bp):
AATTTTGGGACATCTAGTGCAAATAACCCAGAAAACAAAGCCAAAAAAAGAAAAACAGCTTAACA
TTCCATTGACATCAAAATGAACCAAATTCCATTATTGAAACATGAAGAATACAAAGAATACCTCA
AAACAAATCAGCAATGACAATGTGCTCAAACAAATGGTCACGAACCATTGGAGAAAGGACTCCAA
AAATTCATTTACATATACAGAAATGAGAAAAGTTTAGGGACCAATCTGAAATTTGGACCAT
Found at i:2441832 original size:125 final size:125
Alignment explanation
Indices: 2441610--2441848 Score: 442
Period size: 125 Copynumber: 1.9 Consensus size: 125
2441600 ACACTTCTTC
2441610 ACAGATGGACTTGGTGACTCAATTGGGTTTAAAATCTGAATAAATAAACACATACAAGTAAGTTG
1 ACAGATGGACTTGGTGACTCAATTGGGTTTAAAATCTGAATAAATAAACACATACAAGTAAGTTG
2441675 AAATGAATCCAGAAATAAAGAGAGTGCAAAGGGGAAGAGAGATAAGAAGCAAAGGGGAAG
66 AAATGAATCCAGAAATAAAGAGAGTGCAAAGGGGAAGAGAGATAAGAAGCAAAGGGGAAG
* *
2441735 ACAGATGGACTTGGTGACTCAATTGGGTTTGAAATCTGAATAAATAAACACATGCAAGTAAGTTG
1 ACAGATGGACTTGGTGACTCAATTGGGTTTAAAATCTGAATAAATAAACACATACAAGTAAGTTG
* *
2441800 AAATGAATCCAGAACTAAAGGGAGTGCAAAGGGGAAGAGAGATAAGAAG
66 AAATGAATCCAGAAATAAAGAGAGTGCAAAGGGGAAGAGAGATAAGAAG
2441849 GAAAAGTGAC
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 110 1.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (125 bp):
ACAGATGGACTTGGTGACTCAATTGGGTTTAAAATCTGAATAAATAAACACATACAAGTAAGTTG
AAATGAATCCAGAAATAAAGAGAGTGCAAAGGGGAAGAGAGATAAGAAGCAAAGGGGAAG
Found at i:2444748 original size:7 final size:7
Alignment explanation
Indices: 2444736--2444760 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2444726 AAAACCAGAA
2444736 AAAATTT
1 AAAATTT
2444743 AAAATTT
1 AAAATTT
2444750 AAAATTT
1 AAAATTT
2444757 AAAA
1 AAAA
2444761 ACTTACTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:2445250 original size:31 final size:31
Alignment explanation
Indices: 2445215--2445273 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2445205 AAATTTGAGC
* *
2445215 CAAACCTTTTAAGA-ATTGGTCATATAAGGAT
1 CAAACATTTTAAGATA-TGCTCATATAAGGAT
*
2445246 CAAACATTTTTAGATATGCTCATATAAG
1 CAAACATTTTAAGATATGCTCATATAAG
2445274 AATTTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (31 bp):
CAAACATTTTAAGATATGCTCATATAAGGAT
Found at i:2445506 original size:25 final size:25
Alignment explanation
Indices: 2445478--2445542 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
2445468 ATTTTAAAAG
2445478 GTTTAGCCTTTATTTAAACACCTTC
1 GTTTAGCCTTTATTTAAACACCTTC
2445503 GTTTAGCCTTTATTTAAACACCTTC
1 GTTTAGCCTTTATTTAAACACCTTC
2445528 GTTTAGCCTTTATTT
1 GTTTAGCCTTTATTT
2445543 GTTTATTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.48
Consensus pattern (25 bp):
GTTTAGCCTTTATTTAAACACCTTC
Found at i:2445921 original size:103 final size:104
Alignment explanation
Indices: 2445720--2445927 Score: 409
Period size: 103 Copynumber: 2.0 Consensus size: 104
2445710 ATCCTTCTAA
2445720 AAATTATGAAAATATAAATTAATATATTATATTTTAATTCAAATATATATTTATATTTATAACAT
1 AAATTATGAAAATATAAATTAATATATTATATTTTAATTCAAATATATATTTATATTTATAACAT
2445785 AATCACAGCTCCCCCCAAACAATATTTAACCTTTCCTTT
66 AATCACAGCTCCCCCCAAACAATATTTAACCTTTCCTTT
2445824 AAATTATG-AAATATAAATTAATATATTATATTTTAATTCAAATATATATTTATATTTATAACAT
1 AAATTATGAAAATATAAATTAATATATTATATTTTAATTCAAATATATATTTATATTTATAACAT
2445888 AATCACAGCTCCCCCCAAACAATATTTAACCTTTCCTTT
66 AATCACAGCTCCCCCCAAACAATATTTAACCTTTCCTTT
2445927 A
1 A
2445928 CATTTATCTA
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 96 0.92
104 8 0.08
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.40
Consensus pattern (104 bp):
AAATTATGAAAATATAAATTAATATATTATATTTTAATTCAAATATATATTTATATTTATAACAT
AATCACAGCTCCCCCCAAACAATATTTAACCTTTCCTTT
Found at i:2452429 original size:50 final size:50
Alignment explanation
Indices: 2452374--2452481 Score: 180
Period size: 50 Copynumber: 2.2 Consensus size: 50
2452364 ATATATAAAC
* *
2452374 ATTGAAAACTAAATTTGTTATTATATCAATCAAAATTATATGCACAATTG
1 ATTGAAAACTAAATTTATTATTATACCAATCAAAATTATATGCACAATTG
*
2452424 ATTGAAAGCTAAATTTATTATTATACCAATCAAAATTATATGCACAATTG
1 ATTGAAAACTAAATTTATTATTATACCAATCAAAATTATATGCACAATTG
*
2452474 ATAGAAAA
1 ATTGAAAA
2452482 TATTAATGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (50 bp):
ATTGAAAACTAAATTTATTATTATACCAATCAAAATTATATGCACAATTG
Found at i:2478205 original size:16 final size:16
Alignment explanation
Indices: 2478170--2478222 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
2478160 ATTGATGTGA
* **
2478170 TTTAATTTTTAATAAA
1 TTTAATTTTTTATATT
2478186 TTTAATTTTTTATATT
1 TTTAATTTTTTATATT
2478202 TTTAGATTTTATATATATT
1 TTTA-ATTTT-T-TATATT
2478221 TT
1 TT
2478223 CTAAAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 17 0.55
17 5 0.16
18 1 0.03
19 8 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTAATTTTTTATATT
Found at i:2478210 original size:17 final size:18
Alignment explanation
Indices: 2478186--2478222 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2478176 TTTTAATAAA
2478186 TTTAATTTT-T-TATATT
1 TTTAATTTTATATATATT
2478202 TTTAGATTTTATATATATT
1 TTTA-ATTTTATATATATT
2478221 TT
1 TT
2478223 CTAAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 5 0.28
18 1 0.06
19 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTAATTTTATATATATT
Found at i:2482067 original size:12 final size:12
Alignment explanation
Indices: 2482050--2482078 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2482040 AATTAAGTTA
2482050 TTATTATTATTG
1 TTATTATTATTG
2482062 TTATTATTATTG
1 TTATTATTATTG
2482074 -TATTA
1 TTATTA
2482079 GTTCATTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:2482357 original size:18 final size:18
Alignment explanation
Indices: 2482336--2482370 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2482326 GTATACCTAC
2482336 TTATATATTTTT-TATACT
1 TTATA-ATTTTTATATACT
2482354 TTATAATTTTTATATAC
1 TTATAATTTTTATATAC
2482371 ATATATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATAATTTTTATATACT
Found at i:2482358 original size:16 final size:17
Alignment explanation
Indices: 2482333--2482367 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2482323 TATGTATACC
*
2482333 TACTTATATATTTTTTA
1 TACTTATATAATTTTTA
2482350 TACTT-TATAATTTTTA
1 TACTTATATAATTTTTA
2482366 TA
1 TA
2482368 TACATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
TACTTATATAATTTTTA
Found at i:2484068 original size:21 final size:21
Alignment explanation
Indices: 2484027--2484068 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
2484017 AATACAAAAT
*
2484027 AAAATTATATTTTAATCTTTCA
1 AAAATTATAATTTAA-CTTTCA
2484049 AAAATTTATAATTTAA-TTTC
1 AAAA-TTATAATTTAACTTTC
2484069 GTCCGCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTATAATTTAACTTTCA
Found at i:2497063 original size:29 final size:29
Alignment explanation
Indices: 2497025--2497080 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
2497015 TTCTTATAAA
*
2497025 TTTAAAATTTAGTCTTTGT-ATTTTTATT
1 TTTAAAATTTAGTCTTTCTAATTTTTATT
2497053 TTTAAGAATTTAGTCTTTCTAATTTTTA
1 TTTAA-AATTTAGTCTTTCTAATTTTTA
2497081 AATGTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 13 0.52
30 7 0.28
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (29 bp):
TTTAAAATTTAGTCTTTCTAATTTTTATT
Found at i:2498963 original size:19 final size:19
Alignment explanation
Indices: 2498939--2498975 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2498929 GAGTAATGTA
2498939 GTTCGAGATTATGTTATTG
1 GTTCGAGATTATGTTATTG
* *
2498958 GTTCGAGTTTTTGTTATT
1 GTTCGAGATTATGTTATT
2498976 CATGCGTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.24, T:0.54
Consensus pattern (19 bp):
GTTCGAGATTATGTTATTG
Found at i:2500673 original size:280 final size:280
Alignment explanation
Indices: 2500172--2500694 Score: 1028
Period size: 280 Copynumber: 1.9 Consensus size: 280
2500162 TTTTACAACT
*
2500172 TATAGGCTTTGGTATCTTGTGTTTTGCATGATCATATTCTTCTGCCTTGTTGCAATTGCATATTC
1 TATAGGCTTTGGTATCTTGTGTTTTGCATGATCATAGTCTTCTGCCTTGTTGCAATTGCATATTC
2500237 ATATTCCTGATTCATACTGAAGTGATCTTTTTTACTGGTGTATGACATTTTTTTGTCTTTCTTTG
66 ATATTCCTGATTCATACTGAAGTGATCTTTTTTACTGGTGTATGACATTTTTTTGTCTTTCTTTG
*
2500302 GACTCTTCATCATTTAAGATATGCTGCACTTTCAAAAGAGACAGAAGAATATACTTCTCATGCGT
131 GACTCTTCACCATTTAAGATATGCTGCACTTTCAAAAGAGACAGAAGAATATACTTCTCATGCGT
2500367 ACTAACAATTTTGCAGAACTTAACTGGAGGTGTCTTGCTGCTTAGAAAATGTCATACATTTTTTT
196 ACTAACAATTTTGCAGAACTTAACTGGAGGTGTCTTGCTGCTTAGAAAATGTCATACATTTTTTT
2500432 ACTGAAGTGATATTTTTGTG
261 ACTGAAGTGATATTTTTGTG
2500452 TATAGGCTTTGGTATCTTGTGTTTTGCATGATCATAGTCTTCTGCCTTGTTGCAATTGCATATTC
1 TATAGGCTTTGGTATCTTGTGTTTTGCATGATCATAGTCTTCTGCCTTGTTGCAATTGCATATTC
2500517 ATATTCCTGATTCATACTGAAGTGATCTTTTTTACTGGTGTATGACATTTTTTTGTCTTTCTTTG
66 ATATTCCTGATTCATACTGAAGTGATCTTTTTTACTGGTGTATGACATTTTTTTGTCTTTCTTTG
2500582 GACTCTTCACCATTTAAGATATGCTGCACTTTCAAAAGAGACAGAAGAATATACTTCTCATGCGT
131 GACTCTTCACCATTTAAGATATGCTGCACTTTCAAAAGAGACAGAAGAATATACTTCTCATGCGT
2500647 ACTAACAATTTTGCAGAACTTAACTGGAGGTGTCTTGCTGCTTAGAAA
196 ACTAACAATTTTGCAGAACTTAACTGGAGGTGTCTTGCTGCTTAGAAA
2500695 CAAGTATTTT
Statistics
Matches: 241, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
280 241 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (280 bp):
TATAGGCTTTGGTATCTTGTGTTTTGCATGATCATAGTCTTCTGCCTTGTTGCAATTGCATATTC
ATATTCCTGATTCATACTGAAGTGATCTTTTTTACTGGTGTATGACATTTTTTTGTCTTTCTTTG
GACTCTTCACCATTTAAGATATGCTGCACTTTCAAAAGAGACAGAAGAATATACTTCTCATGCGT
ACTAACAATTTTGCAGAACTTAACTGGAGGTGTCTTGCTGCTTAGAAAATGTCATACATTTTTTT
ACTGAAGTGATATTTTTGTG
Done.