Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 12 of 19
Found at i:1838926 original size:22 final size:23
Alignment explanation
Indices: 1838896--1838939 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1838886 AAATACATTA
1838896 AATA-GTTTTAGTT-AAAAGTTTT
1 AATATGTTTTA-TTGAAAAGTTTT
*
1838918 AATATTTTTTATTGAAAAGTTT
1 AATATGTTTTATTGAAAAGTTT
1838940 CCAAAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (23 bp):
AATATGTTTTATTGAAAAGTTTT
Found at i:1841125 original size:21 final size:20
Alignment explanation
Indices: 1841078--1841128 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
1841068 AGAAAAAAAT
*
1841078 TTTAA-TTTTTAAATTTAAA
1 TTTAATTTTTTAAATTCAAA
1841097 -TTAGATTTATTTAAATTCAAA
1 TTTA-ATTT-TTTAAATTCAAA
1841118 TTTAATTTTTT
1 TTTAATTTTTT
1841129 TTATTTGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 5 0.19
21 15 0.56
22 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTAATTTTTTAAATTCAAA
Found at i:1842012 original size:5 final size:5
Alignment explanation
Indices: 1842002--1842027 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1841992 CTCAGTGGGC
1842002 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
1842028 GCATCATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:1842356 original size:16 final size:17
Alignment explanation
Indices: 1842335--1842367 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1842325 ATAAGATCTA
*
1842335 ATTCAA-AGCTCAACCC
1 ATTCAATAGCTAAACCC
1842351 ATTCAATAGCTAAACCC
1 ATTCAATAGCTAAACCC
1842368 TTTGAAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.21
Consensus pattern (17 bp):
ATTCAATAGCTAAACCC
Found at i:1845023 original size:2 final size:2
Alignment explanation
Indices: 1845016--1845046 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1845006 AATTTAAACT
1845016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1845047 GCTATTGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1848457 original size:12 final size:12
Alignment explanation
Indices: 1848440--1848469 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1848430 ATGTGAGATT
1848440 GCATACATTAAA
1 GCATACATTAAA
1848452 GCATACATTAAA
1 GCATACATTAAA
1848464 GCATAC
1 GCATAC
1848470 TCAATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (12 bp):
GCATACATTAAA
Found at i:1849460 original size:26 final size:26
Alignment explanation
Indices: 1849413--1849463 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1849403 TAATATGTTA
* *
1849413 AAATTCATATAAATATATAAAATATT
1 AAATTCAAATAAATACATAAAATATT
1849439 AAATTCAAATATAATACA-AAAATAT
1 AAATTCAAATA-AATACATAAAATAT
1849464 CATGAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATTCAAATAAATACATAAAATATT
Found at i:1849727 original size:14 final size:15
Alignment explanation
Indices: 1849692--1849728 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1849682 ATTGTTATTT
1849692 AAAT-TTAATTATAA
1 AAATATTAATTATAA
1849706 AAATTATTAA-TATAA
1 AAA-TATTAATTATAA
1849721 AAATATTA
1 AAATATTA
1849729 TTTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.38
15 9 0.43
16 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATTAATTATAA
Found at i:1849784 original size:14 final size:14
Alignment explanation
Indices: 1849765--1849829 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
1849755 TAAAGAAGTG
*
1849765 AATTTTCTGACTAA
1 AATTTTCTGACAAA
***
1849779 AATTTTCTGAGTGA
1 AATTTTCTGACAAA
*
1849793 AATTTT-TGTCAAA
1 AATTTTCTGACAAA
1849806 GAATTATTACTGACAAA
1 -AATT-TT-CTGACAAA
1849823 AATTTTC
1 AATTTTC
1849830 ATCACTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
13 3 0.08
14 23 0.57
15 4 0.10
16 4 0.10
17 6 0.15
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (14 bp):
AATTTTCTGACAAA
Found at i:1851064 original size:17 final size:17
Alignment explanation
Indices: 1851039--1851072 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1851029 AAGTCCAAGG
*
1851039 ATTTTTTTTATAATTTT
1 ATTTATTTTATAATTTT
*
1851056 ATTTATTTTTTAATTTT
1 ATTTATTTTATAATTTT
1851073 TAAAAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTTTATAATTTT
Found at i:1851094 original size:18 final size:19
Alignment explanation
Indices: 1851073--1851109 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1851063 TTTTAATTTT
1851073 TAAAA-AAAT-TATAATACA
1 TAAAACAAATATAT-ATACA
1851091 TAAAACAAATATATATACA
1 TAAAACAAATATATATACA
1851110 CATGTGCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 9 0.53
20 3 0.18
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAACAAATATATATACA
Found at i:1854176 original size:13 final size:13
Alignment explanation
Indices: 1854160--1854186 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1854150 ATCATGTCGT
1854160 ATAAAGAATTATC
1 ATAAAGAATTATC
1854173 ATAAAGAATTATC
1 ATAAAGAATTATC
1854186 A
1 A
1854187 AGTCTATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
ATAAAGAATTATC
Found at i:1858109 original size:21 final size:21
Alignment explanation
Indices: 1858085--1858125 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1858075 ATTATACTCA
1858085 TTGCCT-TATCAAGCTCGCCAT
1 TTGCCTCT-TCAAGCTCGCCAT
1858106 TTGCCTCTTCAAGCTCGCCA
1 TTGCCTCTTCAAGCTCGCCA
1858126 AAGGCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.37, G:0.15, T:0.32
Consensus pattern (21 bp):
TTGCCTCTTCAAGCTCGCCAT
Found at i:1858222 original size:74 final size:74
Alignment explanation
Indices: 1858101--1858251 Score: 302
Period size: 74 Copynumber: 2.0 Consensus size: 74
1858091 TATCAAGCTC
1858101 GCCATTTGCCTCTTCAAGCTCGCCAAAGGCCCTTTCAAGCTCAAACACCTCTCAAGGCAAACAAC
1 GCCATTTGCCTCTTCAAGCTCGCCAAAGGCCCTTTCAAGCTCAAACACCTCTCAAGGCAAACAAC
1858166 TCGCCAAAA
66 TCGCCAAAA
1858175 GCCATTTGCCTCTTCAAGCTCGCCAAAGGCCCTTTCAAGCTCAAACACCTCTCAAGGCAAACAAC
1 GCCATTTGCCTCTTCAAGCTCGCCAAAGGCCCTTTCAAGCTCAAACACCTCTCAAGGCAAACAAC
1858240 TCGCCAAAA
66 TCGCCAAAA
1858249 GCC
1 GCC
1858252 TTTTCCAACC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.30, C:0.37, G:0.14, T:0.19
Consensus pattern (74 bp):
GCCATTTGCCTCTTCAAGCTCGCCAAAGGCCCTTTCAAGCTCAAACACCTCTCAAGGCAAACAAC
TCGCCAAAA
Found at i:1863462 original size:26 final size:27
Alignment explanation
Indices: 1863432--1863483 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1863422 TTTCATAACA
1863432 TTGCATACTTAC-CTTTTAAAAAAAAG
1 TTGCATACTTACTCTTTTAAAAAAAAG
*
1863458 TTGCATACTTACTTTTTTAAAAAAAA
1 TTGCATACTTACTCTTTTAAAAAAAA
1863484 ATATCTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (27 bp):
TTGCATACTTACTCTTTTAAAAAAAAG
Found at i:1864548 original size:317 final size:315
Alignment explanation
Indices: 1863477--1864794 Score: 1096
Period size: 317 Copynumber: 4.2 Consensus size: 315
1863467 TACTTTTTTA
* * ** *
1863477 AAAAAAAATAT-C-TATATATAAATTACTCATTAATAAA-TTTTTAATTGTGATCCTTTATTTAT
1 AAAAAAATTATCCATATATACAAATTACTCATTAATAAATTTTTTAATTGTGATTTTTTATATAT
* *
1863539 GTTGTTTCTCATCCAACCACGTATTTTAATAAATTTTCATTATTTTAAAATTAAAAATTGAATAA
66 GTT-TTT-TCATTCAACCACGTATTTTAATAAATTTT-ATTATTTTAAAATTAAAAATTAAATAA
* * * * * *
1863604 AAATAAATAACAAGTTACCTGATAAATTAAAAAATGTAGAATTATTATTTTACTT-AAATTTACT
128 AAATAAATAA-AAATTACATAATAAATT-AACAATATAGAATTATTATTTTATTTAAAATTTACT
* * *
1863668 CAATAAACAAAACTCTGAGAATT--TAT-TTTTCATCAAA--ATATAAGAATAAATATGTATTTT
191 TAATAAAC-AAACTC-GAGAATTAATATATTTTCATCAAACCATA-AAG-GTAAATATATATTTT
* * **
1863728 TTAAAATTATAAAAAGTAAGTACATTTTCATTAAAATCTCATAATGATTTGCATACTTTATTTTA
252 TT-AAATTATAAAATGTAAGTACATTTTCTTTAAAATCTCATAATGATTTGCATACTTTACCTT-
1863793 T
315 T
** *
1863794 AAAAAAATCTATCCATATATTTAAATTACTTATTAA-AAGATTTTTTAATTGTGATTTTTTATAT
1 AAAAAAAT-TATCCATATATACAAATTACTCATTAATAA-ATTTTTTAATTGTGATTTTTTATAT
* * *
1863858 ATGTTTTTTTATTCAATCACGTATTTTCAT-AA-TTT-TTA--TT----TT-AAAATTAAATAAA
64 ATGTTTTTTCATTCAACCACGTATTTTAATAAATTTTATTATTTTAAAATTAAAAATTAAATAAA
** * * * * *
1863913 AATAAATAAAAAATTATTTGATAATTTAACAATATA-AATTATTAGTCTATTTAAAATTTATTTA
129 AATAAAT-AAAAATTACATAATAAATTAACAATATAGAATTATTATTTTATTTAAAATTTACTTA
* * * * * * * * *
1863977 ATAAATATAACTCAAGAGTTAATCTATTTTTCATC-AATCAT-AAGAATAAGTGTGT-TATTTTT
193 ATAAACA-AACTCGAGAATTAATATA-TTTTCATCAAACCATAAAG-GTAAATATATAT-TTTTT
* * * * * **
1864039 -AATTAT-TAATGGGTATGTGCATTTTGTTTGAAATCTCATAATGATTTGTGTA-TTTAACCTTT
254 AAATTATAAAAT--GTAAGTACATTTTCTTTAAAATCTCATAATGATTTGCATACTTT-ACC-TT
1864101 T
315 T
* * * *** *
1864102 AAAAAAATTTATTCATATATAC-AATTACTTATTAAAAAAAAATTTAATTGTGATTTTTTATTTA
1 AAAAAAA-TTATCCATATATACAAATTACTCATTAATAAATTTTTTAATTGTGATTTTTTATATA
* *
1864166 TGTTTTTTCCATTCAATCACATATTTTAATAAATTTTTATTATTTTAAAATTAAAAATTAAATAA
65 TGTTTTTT-CATTCAACCACGTATTTTAATAAA-TTTTATTATTTTAAAATTAAAAATTAAATAA
* * *
1864231 AAATAAATAATAAATTATATAATAAATTAACAATATATAATTATGATTTTATTTAAAATTTACTT
128 AAATAAATAA-AAATTACATAATAAATTAACAATATAGAATTATTATTTTATTTAAAATTTACTT
** * * * * *
1864296 AATAAACAAACTTCGAGTGTTAATATGTTTTTATCAAACCTTAAAGGTAAACACATATTTTTTAA
192 AATAAACAAAC-TCGAGAATTAATATATTTTCATCAAACCATAAAGGTAAATATATATTTTTTAA
* * * *
1864361 ATTATAAAATGTAAGTATATTTTCTTTAAAA-CTTTATAATTATTTGCTTACTTTA-CTTT
256 ATTATAAAATGTAAGTACATTTTCTTTAAAATC-TCATAATGATTTGCATACTTTACCTTT
* *
1864420 AAAAAAA-TATCCATATATACAAATTACTCACTAATAAATTTTTTTAATTGTGATTTTTTATAAA
1 AAAAAAATTATCCATATATACAAATTACTCATTAATAAA-TTTTTTAATTGTGATTTTTTATATA
* * *
1864484 TGTTTTTTTATTCAACCATGTATTTTAATAAATTCTTATTATTTTAAAATTAAAAATAAAAT-AA
65 TGTTTTTTCATTCAACCACGTATTTTAATAAATT-TTATTATTTTAAAATTAAAAATTAAATAAA
* * ** * * *
1864548 AATAAATAAATAATTACAAAATAAATTAATAAGGGTAGAAATATCATTTTATATAAAATTTACTT
129 AATAAATAAA-AATTACATAATAAATTAACAA-TATAGAATTATTATTTTATTTAAAATTTACTT
* ** *
1864613 AATAAACAAACGTCGAGAATTAAGT-TATTTTCATCAAACCCTAAAATTAAATATATA-TTTTCA
192 AATAAACAAAC-TCGAGAATTAA-TATATTTTCATCAAACCATAAAGGTAAATATATATTTTTTA
* * ** * * * *
1864676 AATTATAAAAGGTCAGTGTA-TTT-TTT--AACCTCATAA-CAGTTTACATAGTTTACCTTT
255 AATTATAAAATGTAAGTACATTTTCTTTAAAATCTCATAATGA-TTTGCATACTTTACCTTT
* * *
1864733 CAAGAAAAACTATCCATATATATACAAATTAGAT-ACTAATAAATTTTTTAAATTGTGATTTT
1 -AA-AAAAATTATCC--ATATATACAAATTA-CTCATTAATAAATTTTTT-AATTGTGATTTT
1864795 GTATTTACAT
Statistics
Matches: 819, Mismatches: 123, Indels: 117
0.77 0.12 0.11
Matches are distributed among these distances:
306 21 0.03
307 78 0.10
308 107 0.13
309 28 0.03
310 8 0.01
311 6 0.01
312 20 0.02
313 7 0.01
314 7 0.01
315 12 0.01
316 70 0.09
317 147 0.18
318 83 0.10
319 77 0.09
320 107 0.13
321 38 0.05
322 3 0.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (315 bp):
AAAAAAATTATCCATATATACAAATTACTCATTAATAAATTTTTTAATTGTGATTTTTTATATAT
GTTTTTTCATTCAACCACGTATTTTAATAAATTTTATTATTTTAAAATTAAAAATTAAATAAAAA
TAAATAAAAATTACATAATAAATTAACAATATAGAATTATTATTTTATTTAAAATTTACTTAATA
AACAAACTCGAGAATTAATATATTTTCATCAAACCATAAAGGTAAATATATATTTTTTAAATTAT
AAAATGTAAGTACATTTTCTTTAAAATCTCATAATGATTTGCATACTTTACCTTT
Found at i:1865439 original size:18 final size:19
Alignment explanation
Indices: 1865412--1865462 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1865402 AGTTATATAT
* *
1865412 TTATAGTTTTTTA-AATAA
1 TTATAATTTTTTAGAAAAA
1865430 TTATAATTTTTTAGAAAAA
1 TTATAATTTTTTAGAAAAA
*
1865449 TCAGTAATTTTTTA
1 TTA-TAATTTTTTA
1865463 CAAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 6 0.21
20 10 0.36
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
TTATAATTTTTTAGAAAAA
Found at i:1866610 original size:72 final size:75
Alignment explanation
Indices: 1866518--1866655 Score: 176
Period size: 72 Copynumber: 1.9 Consensus size: 75
1866508 TTATTAATTA
** * * *
1866518 GATTTATCATATTTTTAAATAAAAAT-TTGAATAATATT-AAATA-TTTGGTTAAAT-AAATTTA
1 GATTTATCATATTTGAAAATAAAAATCTTAAAT-ATATTGAAAAACTTTGGGTAAATGAAATTTA
1866579 TTGAATAATAG
65 TTGAATAATAG
* *
1866590 GATTTATCATATTTGAAAATAAGAATCTTAAATCTATTGAAAAACTTTGGGTAAATGAAATTTAT
1 GATTTATCATATTTGAAAATAAAAATCTTAAATATATTGAAAAACTTTGGGTAAATGAAATTTAT
1866655 T
66 T
1866656 TGATAAGAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
72 27 0.49
73 9 0.16
74 10 0.18
75 9 0.16
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (75 bp):
GATTTATCATATTTGAAAATAAAAATCTTAAATATATTGAAAAACTTTGGGTAAATGAAATTTAT
TGAATAATAG
Found at i:1867359 original size:20 final size:22
Alignment explanation
Indices: 1867334--1867383 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1867324 TTTGATGATA
1867334 TTTATTTT-TAGTTAAT-ATTT
1 TTTATTTTATAGTTAATGATTT
*
1867354 TTTATTTTTATATTTAATGATTT
1 TTTA-TTTTATAGTTAATGATTT
1867377 TTTATTT
1 TTTATTT
1867384 AATATGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 10 0.38
23 8 0.31
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTATTTTATAGTTAATGATTT
Found at i:1867377 original size:22 final size:22
Alignment explanation
Indices: 1867334--1867383 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1867324 TTTGATGATA
1867334 TTTA-TTTTTAGTTAAT-ATTT
1 TTTATTTTTTAGTTAATGATTT
*
1867354 TTTATTTTTATATTTAATGATTT
1 TTTATTTTT-TAGTTAATGATTT
1867377 TTTATTT
1 TTTATTT
1867384 AATATGATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 7 0.27
23 11 0.42
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (22 bp):
TTTATTTTTTAGTTAATGATTT
Found at i:1867380 original size:17 final size:16
Alignment explanation
Indices: 1867358--1867415 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
1867348 ATATTTTTTA
1867358 TTTTTATATTTAATGAT
1 TTTTTAT-TTTAATGAT
*
1867375 TTTTTATTTAATATGA-
1 TTTTTATTTTA-ATGAT
* *
1867391 TATTTATTTTCATGAT
1 TTTTTATTTTAATGAT
1867407 CTTTTTATT
1 -TTTTTATT
1867416 ATTTAATGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 4 0.12
16 11 0.33
17 18 0.55
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (16 bp):
TTTTTATTTTAATGAT
Found at i:1867400 original size:22 final size:21
Alignment explanation
Indices: 1867332--1867400 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 21
1867322 ATTTTGATGA
*
1867332 TATTTATTTTTAGTTAATAT-
1 TATTTATTTTTATTTAATATG
* *
1867352 TTTTTATTTTTATATTTA-ATG
1 TATTTATTTTTAT-TTAATATG
1867373 -A--T-TTTTTATTTAATATG
1 TATTTATTTTTATTTAATATG
1867390 ATATTTATTTT
1 -TATTTATTTT
1867401 CATGATCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
16 3 0.08
17 10 0.28
18 1 0.03
19 1 0.03
20 13 0.36
21 4 0.11
22 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TATTTATTTTTATTTAATATG
Found at i:1868042 original size:20 final size:21
Alignment explanation
Indices: 1868014--1868057 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1868004 TATATCTTAT
*
1868014 ATATAATAAAAATATAAAAAA
1 ATATAATAAAAAGATAAAAAA
* *
1868035 ATAT-ATAAAGAGATAAAATA
1 ATATAATAAAAAGATAAAAAA
1868055 ATA
1 ATA
1868058 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (21 bp):
ATATAATAAAAAGATAAAAAA
Found at i:1868750 original size:22 final size:22
Alignment explanation
Indices: 1868698--1868768 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
1868688 TTGGCCAATC
* *
1868698 AATAAAAAATTATTTAAAT-TT
1 AATAAAAAAATATATAAATATT
*
1868719 AATCATAAAAATATATAAATATT
1 AAT-AAAAAAATATATAAATATT
* * *
1868742 GATAAAAAAATTTATAATATTTT
1 AATAAAAAAATATATAA-ATATT
1868765 AATA
1 AATA
1868769 TATTTTAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 3 0.08
22 25 0.64
23 11 0.28
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
AATAAAAAAATATATAAATATT
Found at i:1870333 original size:26 final size:27
Alignment explanation
Indices: 1870286--1870340 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1870276 TTTTACTAAA
* *
1870286 TTAATTAAATAATTATAGAAATAAAAT
1 TTAATTAAATAAATAAAGAAATAAAAT
* *
1870313 TTAATTAAA-AAATAAATAAATAACAT
1 TTAATTAAATAAATAAAGAAATAAAAT
1870339 TT
1 TT
1870341 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TTAATTAAATAAATAAAGAAATAAAAT
Found at i:1870553 original size:21 final size:21
Alignment explanation
Indices: 1870514--1870553 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1870504 AGTAATATTG
*
1870514 TTAATGCAATGTTTATAAAAA
1 TTAATGCAATATTTATAAAAA
* *
1870535 TTAATGCATTATTTTTAAA
1 TTAATGCAATATTTATAAA
1870554 TTCAATAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
TTAATGCAATATTTATAAAAA
Found at i:1871010 original size:20 final size:20
Alignment explanation
Indices: 1870967--1871010 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1870957 ATTATTTTTA
1870967 ATTTATCATTATAAATATTT
1 ATTTATCATTATAAATATTT
*
1870987 -TTTATTATTAATAAA-ATTT
1 ATTTATCATT-ATAAATATTT
1871006 ATTTA
1 ATTTA
1871011 ATTTATAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTATCATTATAAATATTT
Found at i:1872085 original size:19 final size:19
Alignment explanation
Indices: 1872033--1872085 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1872023 TTTATCAGTA
**
1872033 ATAT-TATTTTTAAATTTG
1 ATATATATTTTTAAAAATG
* * *
1872051 ATATAAAATTTAAAAAATG
1 ATATATATTTTTAAAAATG
1872070 ATATATATTTTTAAAA
1 ATATATATTTTTAAAA
1872086 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
ATATATATTTTTAAAAATG
Found at i:1872893 original size:10 final size:10
Alignment explanation
Indices: 1872872--1872914 Score: 59
Period size: 11 Copynumber: 4.1 Consensus size: 10
1872862 TATTTATAAT
1872872 TTTTAATAATA
1 TTTTAAT-ATA
*
1872883 TTTTAAGATA
1 TTTTAATATA
1872893 TTTTTAATATA
1 -TTTTAATATA
1872904 TTTTAATATA
1 TTTTAATATA
1872914 T
1 T
1872915 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 14 0.48
11 15 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTTAATATA
Found at i:1872897 original size:22 final size:21
Alignment explanation
Indices: 1872870--1872921 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
1872860 TATATTTATA
1872870 ATTTTTAATAATATTTTAAGAT
1 ATTTTTAAT-ATATTTTAAGAT
*
1872892 ATTTTTAATATATTTTAATAT
1 ATTTTTAATATATTTTAAGAT
1872913 ATATTTTAA
1 AT-TTTTAA
1872922 AAATTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTTAATATATTTTAAGAT
Found at i:1875104 original size:2 final size:2
Alignment explanation
Indices: 1875097--1875126 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1875087 CTCACTTCAC
1875097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1875127 ATGTTTAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1876390 original size:2 final size:2
Alignment explanation
Indices: 1876373--1876413 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1876363 TATCTATAAT
*
1876373 TA TA TC TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1876414 AAGCATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1877183 original size:19 final size:18
Alignment explanation
Indices: 1877150--1877190 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1877140 ATATGAATTA
*
1877150 ATTTTATAAAAAATATAT
1 ATTTTATAAAAAATAAAT
*
1877168 ATTTTTTAAAATAATAAAT
1 ATTTTATAAAA-AATAAAT
1877187 ATTT
1 ATTT
1877191 AAATATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTATAAAAAATAAAT
Found at i:1877585 original size:18 final size:18
Alignment explanation
Indices: 1877530--1877588 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1877520 TTATTTATTG
1877530 ATAATAT-TATTTTTAAA
1 ATAATATATATTTTTAAA
* * **
1877547 TTTTATATAATATTTAAAAA
1 -ATAATAT-ATATTTTTAAA
1877567 ATAATATATATTTTTAAA
1 ATAATATATATTTTTAAA
1877585 ATAA
1 ATAA
1877589 ATAAAAATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 18 0.58
19 5 0.16
20 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATATATATTTTTAAA
Found at i:1878432 original size:19 final size:20
Alignment explanation
Indices: 1878398--1878435 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1878388 TTATTTATAT
1878398 ATTTTAAATAAAATTTTAAC
1 ATTTTAAATAAAATTTTAAC
*
1878418 ATTTTTAAT-AAATTTTAA
1 ATTTTAAATAAAATTTTAA
1878436 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAATAAAATTTTAAC
Found at i:1878947 original size:30 final size:32
Alignment explanation
Indices: 1878893--1878956 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1878883 TTTAGATTGA
*
1878893 TTTAATTTATTATTAATAAATAAAA-ATATTT
1 TTTAATATATTATTAATAAATAAAATATATTT
*
1878924 TTTAATATATT-TTAA-ATAATAAAATTTATTT
1 TTTAATATATTATTAATA-AATAAAATATATTT
1878955 TT
1 TT
1878957 AAAATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 11 0.38
31 17 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTTAATATATTATTAATAAATAAAATATATTT
Found at i:1878964 original size:18 final size:18
Alignment explanation
Indices: 1878931--1878968 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1878921 TTTTTTAATA
1878931 TATTTTAAATAATAAAATT
1 TATTTTAAATAAT-AAATT
*
1878950 TATTTTTAA-AATAAATT
1 TATTTTAAATAATAAATT
1878967 TA
1 TA
1878969 ATACAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTAAATAATAAATT
Found at i:1882133 original size:28 final size:29
Alignment explanation
Indices: 1882077--1882134 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1882067 AAAAAATATG
*
1882077 AAAATATTATTTTCGTAATTAAAGTAATA
1 AAAATATTATTTTAGTAATTAAAGTAATA
* *
1882106 AAAATATTATTTTATTAGTTAAA-TAATA
1 AAAATATTATTTTAGTAATTAAAGTAATA
1882134 A
1 A
1882135 TTTTAATCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (29 bp):
AAAATATTATTTTAGTAATTAAAGTAATA
Found at i:1887431 original size:18 final size:19
Alignment explanation
Indices: 1887408--1887445 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1887398 TTAATGTGAT
1887408 TTATTTTT-TAATTATATA
1 TTATTTTTATAATTATATA
*
1887426 TTATTTTTATATTTATATA
1 TTATTTTTATAATTATATA
1887445 T
1 T
1887446 GCTATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTTTATAATTATATA
Found at i:1891231 original size:21 final size:18
Alignment explanation
Indices: 1891187--1891222 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1891177 TAATTACAAA
1891187 ATATATA-TTTTTATAAT
1 ATATATATTTTTTATAAT
1891204 ATATATATTTTTTATAAT
1 ATATATATTTTTTATAAT
1891222 A
1 A
1891223 ATAGTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATATATTTTTTATAAT
Found at i:1891236 original size:21 final size:18
Alignment explanation
Indices: 1891187--1891236 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
1891177 TAATTACAAA
1891187 ATATAT-ATTTTTATAAT
1 ATATATAATTTTTATAAT
*
1891204 ATATATATTTTTTATAAT
1 ATATATAATTTTTATAAT
1891222 AATAGTTATAATTTT
1 -ATA--TATAATTTT
1891237 ATTTTACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 10 0.37
19 3 0.11
21 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
ATATATAATTTTTATAAT
Found at i:1891842 original size:23 final size:23
Alignment explanation
Indices: 1891767--1891851 Score: 68
Period size: 23 Copynumber: 3.6 Consensus size: 23
1891757 ATTTAAATAA
1891767 TATTAAAATATTAAATAATTATTTTA-
1 TATT-AAATATT-AAT-A-TATTTTAT
1891793 TATT-AATATT-ATATATTTTTAT
1 TATTAAATATTAATATA-TTTTAT
* *
1891815 AATTAAATTTTAATATATTTTAT
1 TATTAAATATTAATATATTTTAT
* *
1891838 TATTATATAATAAT
1 TATTAAATATTAAT
1891852 TCATATTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.04
21 6 0.12
22 5 0.10
23 21 0.43
24 11 0.22
26 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAAATATTAATATATTTTAT
Found at i:1892065 original size:21 final size:21
Alignment explanation
Indices: 1892036--1892077 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1892026 AATAAGTTTT
*
1892036 TTATTTAAAT-TTAATTATAAA
1 TTATATAAATATTAA-TATAAA
1892057 TTATATAAATATTAATATAAA
1 TTATATAAATATTAATATAAA
1892078 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATATAAATATTAATATAAA
Found at i:1892253 original size:2 final size:2
Alignment explanation
Indices: 1892241--1892279 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1892231 ATTAAAATGC
*
1892241 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1892280 GTTTAGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1892711 original size:6 final size:7
Alignment explanation
Indices: 1892682--1892723 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1892672 TATTAAATTT
1892682 TATATAAA
1 TATAT-AA
1892690 TATATAA
1 TATATAA
1892697 TATATTAA
1 TATA-TAA
1892705 T-TATAA
1 TATATAA
1892711 T-TATAA
1 TATATAA
1892717 TATATAA
1 TATATAA
1892724 AAATATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 13 0.41
8 9 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TATATAA
Found at i:1892715 original size:15 final size:16
Alignment explanation
Indices: 1892681--1892744 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 16
1892671 ATATTAAATT
1892681 TTATATAAATATATAA
1 TTATATAAATATATAA
*
1892697 -TATATTAAT-TATAA
1 TTATATAAATATATAA
* *
1892711 TTATA-ATATATAAAA
1 TTATATAAATATATAA
* *
1892726 ATATAAAAATATATGAA
1 TTATATAAATATAT-AA
1892743 TT
1 TT
1892745 TTTAAATCTA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
14 7 0.19
15 20 0.56
16 6 0.17
17 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TTATATAAATATATAA
Found at i:1892718 original size:27 final size:27
Alignment explanation
Indices: 1892658--1892723 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
1892648 TCTATATAAC
*
1892658 ATAAAT-TATTAATATATTAAATTTTAT
1 ATAAATATA-TAATATATTAAATTTAAT
1892685 ATAAATATATAATATATT-AATTATAAT
1 ATAAATATATAATATATTAAATT-TAAT
1892712 -TATAATATATAA
1 ATA-AATATATAA
1892724 AAATATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 6 0.17
27 27 0.77
28 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAAATATATAATATATTAAATTTAAT
Found at i:1893890 original size:2 final size:2
Alignment explanation
Indices: 1893885--1893911 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1893875 ATGAGAATTC
1893885 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1893912 AGAAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1894743 original size:3 final size:3
Alignment explanation
Indices: 1894735--1894762 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1894725 GTACATTAAA
1894735 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1894763 TGTTTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1897066 original size:4 final size:4
Alignment explanation
Indices: 1897057--1897081 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1897047 AATGTTAATG
1897057 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
1897082 CTCTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:1898068 original size:2 final size:2
Alignment explanation
Indices: 1898005--1898060 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1897995 TATTTATGAG
*
1898005 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1898047 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1898061 GCATATATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1898509 original size:8 final size:8
Alignment explanation
Indices: 1898492--1898554 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
1898482 TGAACATTTA
1898492 ATAT-AAT
1 ATATAAAT
1898499 ATATAAAT
1 ATATAAAT
*
1898507 ATATATAAA
1 ATATA-AAT
1898516 ATATACAA-
1 ATATA-AAT
*
1898524 ATATTAAT
1 ATATAAAT
*
1898532 ATAAAAAT
1 ATATAAAT
*
1898540 ATATTAAT
1 ATATAAAT
1898548 ATATAAA
1 ATATAAA
1898555 AATAATATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
7 6 0.13
8 30 0.67
9 9 0.20
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATAAAT
Found at i:1902234 original size:54 final size:54
Alignment explanation
Indices: 1902130--1902234 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 54
1902120 ATATTGATAC
* *
1902130 CACTATTTAAAGATGATTACATGAAACAATAAAATTAAGCTTCAAGTTTAATAT
1 CACTATTTAAAGATGATTACATGAAACAATAAAATTAAACTTCAAATTTAATAT
* * * * * *
1902184 CACTATTTAACA-ATGATTGCATGAATCGATTAAATTAAATTTTAAATTTAA
1 CACTATTTAA-AGATGATTACATGAAACAATAAAATTAAACTTCAAATTTAA
1902235 AATATTTATC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (54 bp):
CACTATTTAAAGATGATTACATGAAACAATAAAATTAAACTTCAAATTTAATAT
Found at i:1905587 original size:16 final size:17
Alignment explanation
Indices: 1905563--1905598 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1905553 CAAATTATTT
1905563 ATAATTATTTTTAAAAA
1 ATAATTATTTTTAAAAA
*
1905580 ATAA-TATTTTTTAAAA
1 ATAATTATTTTTAAAAA
1905596 ATA
1 ATA
1905599 TAAGAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATTATTTTTAAAAA
Found at i:1906290 original size:2 final size:2
Alignment explanation
Indices: 1906283--1906315 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1906273 TCTCATAAAG
1906283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1906316 ATTAAAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1907614 original size:27 final size:27
Alignment explanation
Indices: 1907550--1907622 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1907540 AAAAGCCACC
* *
1907550 CTTTATGTTTGTCAACAATGATGGTTA
1 CTTTGTGTTTGTCAAAAATGATGGTTA
*
1907577 CTTTGTATTTGTCAAAAATGATGGTT-
1 CTTTGTGTTTGTCAAAAATGATGGTTA
*
1907603 CTTTTTTGTTTGTCAAAAAT
1 C-TTTGTGTTTGTCAAAAAT
1907623 TATGACTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGATGGTTA
Found at i:1907639 original size:28 final size:27
Alignment explanation
Indices: 1907555--1907639 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
1907545 CCACCCTTTA
* * *
1907555 TGTTTGTCAACAATGATGGTTACTT-TG
1 TGTTTGTCAAAAATGATGCTTA-TTGTT
* * * *
1907582 TATTTGTCAAAAATGATGGTTCTTTTT
1 TGTTTGTCAAAAATGATGCTTATTGTT
*
1907609 TGTTTGTCAAAAATTATGACTTATTGTT
1 TGTTTGTCAAAAATGATG-CTTATTGTT
1907637 TGT
1 TGT
1907640 CAAAATTTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.04
27 36 0.77
28 9 0.19
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATGCTTATTGTT
Found at i:1907754 original size:15 final size:13
Alignment explanation
Indices: 1907707--1907753 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
1907697 GGCTCCTTCC
*
1907707 TCTCTCTTAAGCA
1 TCTCTCTCAAGCA
1907720 TCTCTCTCAAGCA
1 TCTCTCTCAAGCA
*
1907733 TCTCTCTCAAGTA
1 TCTCTCTCAAGCA
*
1907746 TCCCTCTC
1 TCTCTCTC
1907754 TTGTATCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.19, C:0.38, G:0.06, T:0.36
Consensus pattern (13 bp):
TCTCTCTCAAGCA
Found at i:1909452 original size:27 final size:32
Alignment explanation
Indices: 1909400--1909470 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 32
1909390 TAGAAGTATT
1909400 ATTTT-TATATATTATAAACA-TATT-TA-AA
1 ATTTTATATATATTATAAACATTATTATATAA
* *
1909428 ATTTTATATATATTA-ATA-ATTTTTATATAA
1 ATTTTATATATATTATAAACATTATTATATAA
1909458 ATTTTA-ATATATT
1 ATTTTATATATATT
1909471 TATATAGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 1 0.03
28 10 0.27
29 18 0.49
30 8 0.22
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (32 bp):
ATTTTATATATATTATAAACATTATTATATAA
Found at i:1909454 original size:17 final size:17
Alignment explanation
Indices: 1909419--1909456 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1909409 TATTATAAAC
1909419 ATAT-TTAAAATTTTAT
1 ATATATTAAAATTTTAT
1909435 ATATATTAATAATTTT-T
1 ATATATTAA-AATTTTAT
1909452 ATATA
1 ATATA
1909457 AATTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 10 0.50
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATTAAAATTTTAT
Found at i:1909496 original size:46 final size:46
Alignment explanation
Indices: 1909448--1909534 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
1909438 TATTAATAAT
1909448 TTTTATA-TAAATTTTAAT-ATATTTATATAGTTATA-TTATATCATA
1 TTTTATATTAAATTTTAATAAT-TTTATATA-TTATATTTATATCATA
** *
1909493 TTTTATATTATGTTTTAATAATTTTTTATATTATATTTATAT
1 TTTTATATTAAATTTTAATAATTTTATATATTATATTTATAT
1909535 TAAAAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
45 12 0.33
46 22 0.61
47 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (46 bp):
TTTTATATTAAATTTTAATAATTTTATATATTATATTTATATCATA
Found at i:1909500 original size:12 final size:12
Alignment explanation
Indices: 1909448--1909536 Score: 66
Period size: 11 Copynumber: 7.8 Consensus size: 12
1909438 TATTAATAAT
*
1909448 TTTTATA-TAAA
1 TTTTATATTATA
1909459 TTTTA-A-TATA
1 TTTTATATTATA
1909469 TTTATATAGTTATA
1 TTT-TATA-TTATA
*
1909483 --TTATATCATA
1 TTTTATATTATA
*
1909493 TTTTATATTATG
1 TTTTATATTATA
* *
1909505 TTTTA-ATAATT
1 TTTTATATTATA
1909516 TTTTATATTATA
1 TTTTATATTATA
1909528 -TTTATATTA
1 TTTTATATTA
1909537 AAAAATGTCG
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
10 11 0.17
11 29 0.46
12 19 0.30
14 4 0.06
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (12 bp):
TTTTATATTATA
Found at i:1912169 original size:33 final size:34
Alignment explanation
Indices: 1912127--1912190 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
1912117 AACATCACAA
*
1912127 ATATCTAAAAATTTATAT-AATAAAAATTATTGAC
1 ATATCT-AAAATTTATATAAATAAAAAATATTGAC
1912161 ATAT-TAAAATTTATATAAATAAAAAATATT
1 ATATCTAAAATTTATATAAATAAAAAATATT
1912191 TTAAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.39
33 13 0.46
34 4 0.14
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (34 bp):
ATATCTAAAATTTATATAAATAAAAAATATTGAC
Found at i:1914091 original size:16 final size:16
Alignment explanation
Indices: 1914034--1914094 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
1914024 ATTACTTAAG
**
1914034 TTAAATTTAAAGATAT
1 TTAAATTTAATTATAT
*
1914050 TTAAATTTAATTCA-CT
1 TTAAATTTAATT-ATAT
*
1914066 TGATAATTTAATTATAT
1 TTA-AATTTAATTATAT
1914083 TTAAATTTAATT
1 TTAAATTTAATT
1914095 TAATAATAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 23 0.64
17 13 0.36
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
TTAAATTTAATTATAT
Found at i:1914095 original size:21 final size:21
Alignment explanation
Indices: 1914069--1914118 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1914059 ATTCACTTGA
* **
1914069 TAATTTAATTATATTTAAATT
1 TAATTTAATAATAACTAAATT
1914090 TAATTTAATAATAACTAAATT
1 TAATTTAATAATAACTAAATT
*
1914111 AAATTTAA
1 TAATTTAA
1914119 ATTTTTTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATTTAATAATAACTAAATT
Found at i:1914290 original size:9 final size:9
Alignment explanation
Indices: 1914260--1914332 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 9
1914250 TAAGATTTAT
1914260 TAATAAATA
1 TAATAAATA
*
1914269 TAAAAATAATA
1 T-AATA-AATA
1914280 TAATAAATA
1 TAATAAATA
1914289 TAATAAA-A
1 TAATAAATA
* *
1914297 TATTATATA
1 TAATAAATA
*
1914306 T-TTAAATA
1 TAATAAATA
* *
1914314 TGATAAACA
1 TAATAAATA
*
1914323 TAATTAATA
1 TAATAAATA
1914332 T
1 T
1914333 GATATATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
8 13 0.26
9 26 0.52
10 6 0.12
11 5 0.10
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (9 bp):
TAATAAATA
Found at i:1914291 original size:14 final size:14
Alignment explanation
Indices: 1914260--1914298 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1914250 TAAGATTTAT
1914260 TAATAAATATAAAAA
1 TAATAAA-ATAAAAA
* *
1914275 TAATATAATAAATA
1 TAATAAAATAAAAA
1914289 TAATAAAATA
1 TAATAAAATA
1914299 TTATATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAATAAAATAAAAA
Found at i:1914338 original size:33 final size:34
Alignment explanation
Indices: 1914276--1914348 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
1914266 ATATAAAAAT
* *
1914276 AATATAATAAATATAATAAAATATTATATATTTA
1 AATATAATAAACATAATAAAATATGATATATTTA
* *
1914310 AATATGATAAACATAAT-TAATATGATATATTT-
1 AATATAATAAACATAATAAAATATGATATATTTA
1914342 AATATAA
1 AATATAA
1914349 CTATCATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 6 0.18
33 13 0.38
34 15 0.44
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (34 bp):
AATATAATAAACATAATAAAATATGATATATTTA
Found at i:1914418 original size:26 final size:27
Alignment explanation
Indices: 1914369--1914423 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1914359 TTTATTTTAA
* * *
1914369 ATTTTTATTAATAATAATTTATATTAT
1 ATTTTTATTAATAATAAATAATATAAT
*
1914396 ATTTTTATTTAT-ATAAATAATATAAT
1 ATTTTTATTAATAATAAATAATATAAT
1914422 AT
1 AT
1914424 ATATATATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTTATTAATAATAAATAATATAAT
Found at i:1914427 original size:30 final size:27
Alignment explanation
Indices: 1914369--1914429 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
1914359 TTTATTTTAA
*
1914369 ATTTTTATTAATAATAATTTATATTAT
1 ATTTTTATTAATAATAATTAATATTAT
1914396 ATTTTTATTTATATAAATAATATAATATATAT
1 ATTTTTA-TTA-AT-AATAAT-TAATAT-TAT
1914428 AT
1 AT
1914430 ATACGGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 7 0.25
28 3 0.11
29 2 0.07
30 6 0.21
31 5 0.18
32 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTTATTAATAATAATTAATATTAT
Found at i:1914772 original size:18 final size:18
Alignment explanation
Indices: 1914749--1914783 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1914739 GTGAAAATAT
1914749 AATAAA-AATATATATTTA
1 AATAAATAATATA-ATTTA
1914767 AATAAATAATATAATTT
1 AATAAATAATATAATTT
1914784 TTAATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAAATAATATAATTTA
Found at i:1914779 original size:19 final size:20
Alignment explanation
Indices: 1914749--1914794 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1914739 GTGAAAATAT
1914749 AATAAA-AATAT-ATATTTA
1 AATAAATAATATAATATTTA
*
1914767 AATAAATAATATAATTTTTA
1 AATAAATAATATAATATTTA
1914787 ATATAAAT
1 A-ATAAAT
1914795 TTAAAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 5 0.21
20 7 0.29
21 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAAATAATATAATATTTA
Found at i:1914923 original size:2 final size:2
Alignment explanation
Indices: 1914912--1914947 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1914902 TCTCTAATTT
1914912 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1914948 CAAATGGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1924795 original size:2 final size:2
Alignment explanation
Indices: 1924788--1924814 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1924778 ATTCATTGCA
1924788 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1924815 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1924819 original size:2 final size:2
Alignment explanation
Indices: 1924814--1924850 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1924804 TCTCTCTCTC
1924814 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1924851 TAACTTGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1925340 original size:17 final size:17
Alignment explanation
Indices: 1925318--1925355 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1925308 TAAACTGATA
1925318 TTTAAATTATATTTTAT
1 TTTAAATTATATTTTAT
1925335 TTTAAATTATATTTTAT
1 TTTAAATTATATTTTAT
1925352 TTTA
1 TTTA
1925356 TGATTTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAAATTATATTTTAT
Found at i:1926016 original size:35 final size:36
Alignment explanation
Indices: 1925952--1926039 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
1925942 ATTATTCATA
* **
1925952 TTTAAATATATTTTTATTTAATTTTATTAAT-TTTAT
1 TTTAAA-ATATTTTTATGTAATTACATTAATATTTAT
* *
1925988 TTTAAAATATTTTTATGTCATTACATTAATATTTTT
1 TTTAAAATATTTTTATGTAATTACATTAATATTTAT
1926024 TTTAAAAT-TTATTTAT
1 TTTAAAATATT-TTTAT
1926040 TTTTGACGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 22 0.49
36 23 0.51
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (36 bp):
TTTAAAATATTTTTATGTAATTACATTAATATTTAT
Found at i:1928651 original size:19 final size:19
Alignment explanation
Indices: 1928610--1928673 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
1928600 TTTATCTATT
* * * *
1928610 AAAATTAAATATATATGAT
1 AAAATTTAATAAATATTAA
1928629 AAAATTTAATAAATATTAAA
1 AAAATTTAATAAATATT-AA
1928649 AAAATTTAATAAAAATATTAA
1 AAAATTTAAT--AAATATTAA
1928670 AAAA
1 AAAA
1928674 ATAGAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 14 0.37
20 11 0.29
21 6 0.16
22 7 0.18
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTTAATAAATATTAA
Found at i:1928652 original size:20 final size:21
Alignment explanation
Indices: 1928629--1928675 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
1928619 TATATATGAT
1928629 AAAATTTAAT-AAATATTAAA
1 AAAATTTAATAAAATATTAAA
1928649 AAAATTTAATAAAAATATTAAA
1 AAAATTTAAT-AAAATATTAAA
1928671 AAAAT
1 AAAAT
1928676 AGAAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 10 0.40
22 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTTAATAAAATATTAAA
Found at i:1928662 original size:11 final size:10
Alignment explanation
Indices: 1928629--1928675 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
1928619 TATATATGAT
1928629 AAAATTT-AA
1 AAAATTTAAA
*
1928638 TAAATATTAAA
1 AAAAT-TTAAA
1928649 AAAATTTAATA
1 AAAATTTAA-A
1928660 AAAATATTAAA
1 AAAAT-TTAAA
1928671 AAAAT
1 AAAAT
1928676 AGAAAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 4 0.12
10 6 0.19
11 18 0.56
12 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:1928676 original size:11 final size:11
Alignment explanation
Indices: 1928639--1928676 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1928629 AAAATTTAAT
1928639 AAATATTAAAA
1 AAATATTAAAA
1928650 AAAT-TTAATAA
1 AAATATTAA-AA
1928661 AAATATTAAAA
1 AAATATTAAAA
1928672 AAATA
1 AAATA
1928677 GAAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATATTAAAA
Found at i:1928684 original size:22 final size:22
Alignment explanation
Indices: 1928639--1928693 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1928629 AAAATTTAAT
** *
1928639 AAATATTAAAAAAATTTAATAA
1 AAATATTAAAAAAATAGAAAAA
1928661 AAATATTAAAAAAATAGAAAAA
1 AAATATTAAAAAAATAGAAAAA
*
1928683 AAGATAGTAAA
1 AA-ATATTAAA
1928694 TATCCTCAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (22 bp):
AAATATTAAAAAAATAGAAAAA
Found at i:1929920 original size:18 final size:17
Alignment explanation
Indices: 1929894--1930027 Score: 87
Period size: 18 Copynumber: 7.6 Consensus size: 17
1929884 TAAATATGAC
1929894 ATAATTATATAATATAAAT
1 ATAA-TATA-AATATAAAT
* *
1929913 ATGATATAAAAAATAAAT
1 ATAATAT-AAATATAAAT
1929931 ATAATATAAATAGTAAAT
1 ATAATATAAATA-TAAAT
**
1929949 ATTTTATAAACTTATTAAA-
1 ATAATATAAA--TA-TAAAT
*
1929968 ATATATTTAAATATAAA-
1 ATA-ATATAAATATAAAT
* * *
1929985 ATATTTTAAATATAATT
1 ATAATATAAATATAAAT
1930002 ATAATAT-AATA-AAAT
1 ATAATATAAATATAAAT
1930017 ATATATATAAA
1 ATA-ATATAAA
1930028 CTAATAGGTG
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.07
16 19 0.21
17 18 0.20
18 32 0.35
19 6 0.07
20 11 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
ATAATATAAATATAAAT
Found at i:1929947 original size:7 final size:6
Alignment explanation
Indices: 1929894--1930027 Score: 52
Period size: 6 Copynumber: 22.8 Consensus size: 6
1929884 TAAATATGAC
* * *
1929894 ATAATT ATATAAT ATAAAT AT-GAT ATAAAAA ATAAAT AT-AAT ATAAAT
1 ATAAAT ATA-AAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT
** * * *
1929942 AGTAAAT AT-TTT ATAAACTT ATTAAA- ATATAT TTAAAT ATAAA- AT-ATT
1 A-TAAAT ATAAAT ATAAA--T A-TAAAT ATAAAT ATAAAT ATAAAT ATAAAT
* * *
1929990 TTAAAT ATAATT AT-AAT AT-AAT A-AAAT ATATAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
1930028 CTAATAGGTG
Statistics
Matches: 93, Mismatches: 21, Indels: 28
0.65 0.15 0.20
Matches are distributed among these distances:
4 1 0.01
5 30 0.32
6 42 0.45
7 14 0.15
8 2 0.02
9 4 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (6 bp):
ATAAAT
Found at i:1929994 original size:16 final size:17
Alignment explanation
Indices: 1929964--1929999 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1929954 ATAAACTTAT
1929964 TAAAATATATTTAAATA
1 TAAAATATATTTAAATA
1929981 TAAAATAT-TTTAAATA
1 TAAAATATATTTAAATA
1929997 TAA
1 TAA
1930000 TTATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATATATTTAAATA
Found at i:1930017 original size:37 final size:38
Alignment explanation
Indices: 1929927--1930019 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 38
1929917 TATAAAAAAT
*
1929927 AAATATAATATAAATAGT-AAATATTTTATAAACTTATTA
1 AAATATAATA-AAATA-TAAAATATTTTATAAACTAATTA
* *
1929966 AAATATATTTAAATATAAAATATTTTA-AATA-TAATTA
1 AAATATAATAAAATATAAAATATTTTATAA-ACTAATTA
*
1930003 TAATATAATAAAATATA
1 AAATATAATAAAATATA
1930020 TATATAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
37 22 0.48
38 16 0.35
39 8 0.17
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (38 bp):
AAATATAATAAAATATAAAATATTTTATAAACTAATTA
Found at i:1930235 original size:13 final size:12
Alignment explanation
Indices: 1930216--1930278 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
1930206 ATTTTTTTAA
1930216 AAAATTAATTAT
1 AAAATTAATTAT
1930228 ATAAATTAA-TA-
1 A-AAATTAATTAT
* *
1930239 AAAATAAATTTT
1 AAAATTAATTAT
*
1930251 AAAATT-TTTATT
1 AAAATTAATTA-T
*
1930263 AAATTTAATTAT
1 AAAATTAATTAT
1930275 AAAA
1 AAAA
1930279 ATTATAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
10 6 0.16
11 4 0.11
12 18 0.47
13 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAATTAATTAT
Found at i:1930987 original size:10 final size:10
Alignment explanation
Indices: 1930972--1931004 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1930962 AATAAAATTG
1930972 AAATAATCTA
1 AAATAATCTA
*
1930982 AAATAAT-AA
1 AAATAATCTA
1930991 AAATAATCTA
1 AAATAATCTA
1931001 AAAT
1 AAAT
1931005 TTAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATAATCTA
Found at i:1931023 original size:21 final size:20
Alignment explanation
Indices: 1930999--1931049 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
1930989 AAAAATAATC
*
1930999 TAAAATTTAATTTAAATAAAT
1 TAAAATTTAA-TCAAATAAAT
1931020 T-AAATTT-ATCAAATTAAAT
1 TAAAATTTAATCAAA-TAAAT
1931039 TAATAATTTAA
1 TAA-AATTTAA
1931050 CTCGTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.16
19 7 0.28
20 7 0.28
21 6 0.24
22 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAATTTAATCAAATAAAT
Found at i:1931416 original size:22 final size:22
Alignment explanation
Indices: 1931385--1931431 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1931375 TGTTTAAATT
1931385 TTAAAAATTTAATAAATTTAAA
1 TTAAAAATTTAATAAATTTAAA
* * **
1931407 TTAAATATTTATTTTATTTAAA
1 TTAAAAATTTAATAAATTTAAA
1931429 TTA
1 TTA
1931432 TTAAATAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAAAATTTAATAAATTTAAA
Found at i:1933303 original size:16 final size:16
Alignment explanation
Indices: 1933274--1933312 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1933264 TTTATATATT
1933274 ATTT-ATAAAAATAAA
1 ATTTAATAAAAATAAA
*
1933289 ATTTAATAAATATAAA
1 ATTTAATAAAAATAAA
*
1933305 TTTTAATA
1 ATTTAATA
1933313 TTTATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAATAAAAATAAA
Found at i:1933555 original size:3 final size:3
Alignment explanation
Indices: 1933547--1933580 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1933537 TACTGAATGT
*
1933547 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1933581 CATCATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1933585 original size:12 final size:12
Alignment explanation
Indices: 1933549--1933593 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1933539 CTGAATGTTT
*
1933549 ATTATTATTATT
1 ATTATTATTATC
1933561 ATTATTATTATC
1 ATTATTATTATC
*
1933573 ATTATTATCATC
1 ATTATTATTATC
*
1933585 ATAATTATT
1 ATTATTATT
1933594 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:1939216 original size:16 final size:16
Alignment explanation
Indices: 1939195--1939225 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1939185 ATTTGTGTCG
1939195 GATATATTTCGGACAC
1 GATATATTTCGGACAC
1939211 GATATATTTCGGACA
1 GATATATTTCGGACA
1939226 TGAATATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (16 bp):
GATATATTTCGGACAC
Found at i:1941276 original size:13 final size:15
Alignment explanation
Indices: 1941258--1941290 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1941248 TACTGCAAAT
1941258 ATAAATA-TT-AAAA
1 ATAAATATTTAAAAA
1941271 ATAAATATTTAAAAA
1 ATAAATATTTAAAAA
1941286 ATAAA
1 ATAAA
1941291 AAATTCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 2 0.11
15 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAATATTTAAAAA
Found at i:1942476 original size:2 final size:2
Alignment explanation
Indices: 1942469--1942526 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
1942459 GATCAGTTTA
* * * *
1942469 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT CT AT CT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1942511 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1942527 TCATAGAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1942666 original size:2 final size:2
Alignment explanation
Indices: 1942655--1942684 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1942645 CTCACATGTG
1942655 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1942685 CATAATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1945375 original size:32 final size:34
Alignment explanation
Indices: 1945323--1945413 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 34
1945313 TTTATATAAA
* *
1945323 ATAAATAAAAATATAATAATA-ATTTAAAATTTAT
1 ATAAATAAAAATATATTAATATA-TCAAAATTTAT
*
1945357 AT-GATAAAAAT-TATTAATATATCAAAATTTAT
1 ATAAATAAAAATATATTAATATATCAAAATTTAT
1945389 ATAAATATAAAATATATTAAATATA
1 ATAAATA-AAAATATATT-AATATA
1945414 ATTAAATCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 19 0.40
33 12 0.25
34 7 0.15
35 4 0.08
36 6 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (34 bp):
ATAAATAAAAATATATTAATATATCAAAATTTAT
Found at i:1945383 original size:18 final size:16
Alignment explanation
Indices: 1945360--1945414 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
1945350 AATTTATATG
1945360 ATAAAAATTATTAATAT
1 ATAAAAATTATTAA-AT
*
1945377 ATCAAAATTTATATAAAT
1 AT-AAAAATTAT-TAAAT
1945395 AT-AAAATATATTAAAT
1 ATAAAAAT-TATTAAAT
1945411 ATAA
1 ATAA
1945415 TTAAATCGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 11 0.34
17 6 0.19
18 12 0.38
19 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAAATTATTAAAT
Found at i:1945411 original size:16 final size:15
Alignment explanation
Indices: 1945363--1945414 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 15
1945353 TTATATGATA
1945363 AAAATTATTAATATAT
1 AAAATTATTAA-ATAT
1945379 CAAAATTTATATAAATAT
1 -AAAA-TTAT-TAAATAT
1945397 AAAATATATTAAATAT
1 AAAAT-TATTAAATAT
1945413 AA
1 AA
1945415 TTAAATCGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 10 0.31
17 11 0.34
18 8 0.25
19 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATTATTAAATAT
Found at i:1947062 original size:13 final size:13
Alignment explanation
Indices: 1947041--1947072 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1947031 ATTTATTTTT
*
1947041 AATTTTATTACCA
1 AATTATATTACCA
1947054 AATTATATTACCA
1 AATTATATTACCA
1947067 AATTAT
1 AATTAT
1947073 TTATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATATTACCA
Found at i:1947202 original size:13 final size:13
Alignment explanation
Indices: 1947184--1947210 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1947174 ATTAAAAATC
1947184 AATACAAAATTAA
1 AATACAAAATTAA
1947197 AATACAAAATTAA
1 AATACAAAATTAA
1947210 A
1 A
1947211 TTCAATCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (13 bp):
AATACAAAATTAA
Found at i:1954991 original size:10 final size:11
Alignment explanation
Indices: 1954969--1955001 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1954959 TGTTCCTAAG
1954969 GAAAACCTAGAA
1 GAAAA-CTAGAA
1954981 GAAAA-TAGAA
1 GAAAACTAGAA
1954991 GAAAACTAGAA
1 GAAAACTAGAA
1955002 CACCAGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 5 0.25
12 5 0.25
ACGTcount: A:0.64, C:0.09, G:0.18, T:0.09
Consensus pattern (11 bp):
GAAAACTAGAA
Found at i:1955392 original size:24 final size:26
Alignment explanation
Indices: 1955345--1955393 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1955335 TATCTTTAAG
*
1955345 CATTATTTTTATTAAATTTTTTAAAAA
1 CATTATTTTTA-TAAATTTATTAAAAA
1955372 CATTATTTTTA-AAA-TTATTAAA
1 CATTATTTTTATAAATTTATTAAA
1955394 CAGTAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
27 11 0.52
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (26 bp):
CATTATTTTTATAAATTTATTAAAAA
Found at i:1955764 original size:2 final size:2
Alignment explanation
Indices: 1955759--1955803 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
1955749 ATAAAAAAGA
*
1955759 AT AT AT AT -T GT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
1955801 AT A
1 AT A
1955804 AGAACATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1960155 original size:26 final size:26
Alignment explanation
Indices: 1960090--1960156 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
1960080 TTTATATAAA
1960090 TAAATAAAATTTTAATTATTATCAAT
1 TAAATAAAATTTTAATTATTATCAAT
* *
1960116 TAAATATTAA-TTTAATTGTTAT--AT
1 TAAATA-AAATTTTAATTATTATCAAT
1960140 TATTAATAAAATTTTAA
1 TA--AATAAAATTTTAA
1960157 AAATTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 4 0.12
25 2 0.06
26 26 0.76
27 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
TAAATAAAATTTTAATTATTATCAAT
Found at i:1960164 original size:15 final size:15
Alignment explanation
Indices: 1960146--1960184 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1960136 ATATTATTAA
*
1960146 TAAAATTTTAAAAAT
1 TAAAATTTAAAAAAT
1960161 TAAAATTTAAAAAAT
1 TAAAATTTAAAAAAT
1960176 T-AAATTTAA
1 TAAAATTTAA
1960185 TAATTTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATTTAAAAAAT
Found at i:1960171 original size:14 final size:14
Alignment explanation
Indices: 1960146--1960189 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1960136 ATATTATTAA
1960146 TAAAATTTTAAAAAT
1 TAAAA-TTTAAAAAT
1960161 TAAAATTTAAAAAAT
1 TAAAATTT-AAAAAT
*
1960176 T-AAATTTAATAAT
1 TAAAATTTAAAAAT
1960189 T
1 T
1960190 TTATCTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 6 0.22
14 9 0.33
15 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATTTAAAAAT
Found at i:1960336 original size:14 final size:14
Alignment explanation
Indices: 1960317--1960366 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1960307 AATATATGAA
1960317 TATTAAATTATTTT
1 TATTAAATTATTTT
1960331 TATTAAAATTA-TTT
1 TATT-AAATTATTTT
*
1960345 AATTAAATTAATTTAT
1 TATTAAATT-ATTT-T
1960361 TATTAA
1 TATTAA
1960367 TAAGTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.17
14 11 0.37
15 8 0.27
16 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTAAATTATTTT
Found at i:1960577 original size:24 final size:24
Alignment explanation
Indices: 1960550--1960595 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1960540 GTGATTTAAA
1960550 TTATAATATT-TTATTTTATTATAT
1 TTATAATATTGTTA-TTTATTATAT
*
1960574 TTATATTATTGTTATTTATTAT
1 TTATAATATTGTTATTTATTAT
1960596 CGATGTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATAATATTGTTATTTATTATAT
Found at i:1960731 original size:9 final size:9
Alignment explanation
Indices: 1960717--1960774 Score: 62
Period size: 9 Copynumber: 6.1 Consensus size: 9
1960707 GTTTGATAAT
1960717 TTTAATATA
1 TTTAATATA
*
1960726 TTTAATTTA
1 TTTAATATA
*
1960735 TAATAATATA
1 T-TTAATATA
1960745 TTTAATATA
1 TTTAATATA
1960754 TTATAATTATA
1 TT-TAA-TATA
*
1960765 TTTAAAATA
1 TTTAATATA
1960774 T
1 T
1960775 ACTTATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 22 0.54
10 13 0.32
11 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTAATATA
Found at i:1960743 original size:19 final size:19
Alignment explanation
Indices: 1960719--1960775 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1960709 TTGATAATTT
*
1960719 TAATATATTTAATTTATAA
1 TAATATATTTAATATATAA
*
1960738 TAATATATTTAATATATTA
1 TAATATATTTAATATATAA
*
1960757 TAATTATATTTAAAATATA
1 TAA-TATATTTAATATATA
1960776 CTTATTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATATTTAATATATAA
Found at i:1964327 original size:43 final size:43
Alignment explanation
Indices: 1964279--1964367 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 43
1964269 AACCTGAATC
*** * * *
1964279 AACAAAATCTATGTTCAAACTCGACTTAACTGGGATCAAGCTG
1 AACAAAATCTATACCCAAACTCAACTCAACTGAGATCAAGCTG
*
1964322 AACAAAATCTATACCCAAACTCAACTCAACTGAGATCAAGTTG
1 AACAAAATCTATACCCAAACTCAACTCAACTGAGATCAAGCTG
1964365 AAC
1 AAC
1964368 GTACTGCTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.22
Consensus pattern (43 bp):
AACAAAATCTATACCCAAACTCAACTCAACTGAGATCAAGCTG
Found at i:1967209 original size:21 final size:21
Alignment explanation
Indices: 1967163--1967212 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1967153 TAAAATACAT
*
1967163 ATTAATAAAAAATTTTATTAA
1 ATTAATATAAAATTTTATTAA
* *
1967184 ATTAATATAAATTTTTATTAT
1 ATTAATATAAAATTTTATTAA
*
1967205 TTTAATAT
1 ATTAATAT
1967213 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAATATAAAATTTTATTAA
Found at i:1968474 original size:25 final size:26
Alignment explanation
Indices: 1968415--1968474 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
1968405 CATATTTTTT
1968415 TATTAATTATATAAATATAAATAAAA
1 TATTAATTATATAAATATAAATAAAA
*
1968441 TATAAATTAT-TAAATATATAAT-AAA
1 TATTAATTATATAAATATA-AATAAAA
*
1968466 TATTTATTA
1 TATTAATTA
1968475 AATTAATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TATTAATTATATAAATATAAATAAAA
Found at i:1975692 original size:2 final size:2
Alignment explanation
Indices: 1975685--1975715 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1975675 TTATGAGGTA
1975685 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1975716 GGGTGCTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1979725 original size:2 final size:2
Alignment explanation
Indices: 1979718--1979770 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
1979708 CACATTTTGA
1979718 AT AT AT AT -T CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1979760 AT AT AT AT AT A
1 AT AT AT AT AT A
1979771 ACTCTTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 47 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1983321 original size:20 final size:20
Alignment explanation
Indices: 1983296--1983339 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1983286 TAATCAATTC
**
1983296 AAAAATTTATATTATTATTT
1 AAAAATTTATATTACCATTT
1983316 AAAAATTTATATTACCATTT
1 AAAAATTTATATTACCATTT
1983336 AAAA
1 AAAA
1983340 GAACATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATTTATATTACCATTT
Found at i:1986877 original size:15 final size:15
Alignment explanation
Indices: 1986835--1986877 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1986825 TAAAATATTA
* *
1986835 ATTTATATTTATATT
1 ATTTTTATTTAAATT
*
1986850 ATTTTTATATAAATT
1 ATTTTTATTTAAATT
*
1986865 ATTTTTTTTTAAA
1 ATTTTTATTTAAA
1986878 ATTTAATTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTATTTAAATT
Found at i:1987147 original size:13 final size:13
Alignment explanation
Indices: 1987129--1987167 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
1987119 AAATTTAATT
1987129 TAATTAATTTTTA
1 TAATTAATTTTTA
1987142 TAATT-ATTTTTA
1 TAATTAATTTTTA
*
1987154 AAATATAATTTTTA
1 TAAT-TAATTTTTA
1987168 ATATATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATTAATTTTTA
Done.