Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 13 of 26
Found at i:2193330 original size:23 final size:22
Alignment explanation
Indices: 2193304--2193346 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2193294 TACTCAAATT
2193304 ATATCATAAAAGTTATCAAAAAA
1 ATAT-ATAAAAGTTATCAAAAAA
*
2193327 ATATATTAAAGTTATCAAAA
1 ATATATAAAAGTTATCAAAA
2193347 TATTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (22 bp):
ATATATAAAAGTTATCAAAAAA
Found at i:2193348 original size:19 final size:19
Alignment explanation
Indices: 2193324--2193373 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
2193314 AGTTATCAAA
*
2193324 AAAATATATTAAAGTTATC
1 AAAATATATTAAAGTTAGC
2193343 AAAATATTATTTAAAGTTAGC
1 AAAATA-TA-TTAAAGTTAGC
2193364 AAAAT-TATTA
1 AAAATATATTA
2193374 TAAATGATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 8 0.29
20 2 0.07
21 15 0.54
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (19 bp):
AAAATATATTAAAGTTAGC
Found at i:2193356 original size:21 final size:22
Alignment explanation
Indices: 2193312--2193375 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
2193302 TTATATCATA
* *
2193312 AAAGTTATCAAAAAAATATATT
1 AAAGTTATCAAAATATTATATT
2193334 AAAGTTATCAAAATATTAT-TT
1 AAAGTTATCAAAATATTATATT
*
2193355 AAAGTTAGCAAAATTATTATA
1 AAAGTTATCAAAA-TATTATA
2193376 AATGATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (22 bp):
AAAGTTATCAAAATATTATATT
Found at i:2193388 original size:21 final size:21
Alignment explanation
Indices: 2193364--2193404 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2193354 TAAAGTTAGC
2193364 AAAA-TTATTATAAATGATATT
1 AAAAGTTATTA-AAATGATATT
*
2193385 AAAAGTTATTAAAATTATAT
1 AAAAGTTATTAAAATGATAT
2193405 GTGAGCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
AAAAGTTATTAAAATGATATT
Found at i:2198777 original size:13 final size:13
Alignment explanation
Indices: 2198747--2198795 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
2198737 AAAATATATT
*
2198747 AATTTAAAA-TAA
1 AATTAAAAATTAA
*
2198759 ATTTAAAAATTAA
1 AATTAAAAATTAA
*
2198772 AATTAAAAATAAA
1 AATTAAAAATTAA
*
2198785 AAATAAAAATT
1 AATTAAAAATT
2198796 TATTTTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 7 0.23
13 23 0.77
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTAAAAATTAA
Found at i:2198903 original size:14 final size:14
Alignment explanation
Indices: 2198880--2198931 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
2198870 AGTTTAAGAA
* *
2198880 TAAATTAAAACTTT
1 TAAAATAAAAATTT
2198894 TAAAA-AAAAA-TT
1 TAAAATAAAAATTT
2198906 TAAAATACAAAATTT
1 TAAAATA-AAAATTT
*
2198921 AAAAATAAAAA
1 TAAAATAAAAA
2198932 CCTAAGTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 7 0.22
13 5 0.16
14 12 0.38
15 8 0.25
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAATAAAAATTT
Found at i:2199564 original size:16 final size:17
Alignment explanation
Indices: 2199532--2199575 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2199522 TGTTAAATTT
2199532 TTAAAAA-TTTA-TTAA
1 TTAAAAATTTTATTTAA
*
2199547 TT-ATAATTTTATTTAA
1 TTAAAAATTTTATTTAA
2199563 TTAAAAATTTTAT
1 TTAAAAATTTTAT
2199576 AAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 3 0.12
15 6 0.25
16 6 0.25
17 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAAATTTTATTTAA
Found at i:2199980 original size:20 final size:20
Alignment explanation
Indices: 2199955--2199992 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2199945 ACATATCATT
*
2199955 TTTTTTCTTTCTTTCTTTTC
1 TTTTTTCTTTCTTCCTTTTC
*
2199975 TTTTTTTTTTCTTCCTTT
1 TTTTTTCTTTCTTCCTTT
2199993 GTCTCTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTCTTCCTTTTC
Found at i:2199984 original size:24 final size:27
Alignment explanation
Indices: 2199953--2200010 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
2199943 AAACATATCA
*
2199953 TTTTTTTTCTTTC-TT-TCT-TTTCTT
1 TTTTTTTTCTTCCTTTGTCTCTTTCTT
2199977 TTTTTTTTCTTCCTTTGTCTCTTTCTT
1 TTTTTTTTCTTCCTTTGTCTCTTTCTT
2200004 TTTTTTT
1 TTTTTTT
2200011 CAGCAAACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 12 0.40
25 2 0.07
26 3 0.10
27 13 0.43
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTTTTTTCTTCCTTTGTCTCTTTCTT
Found at i:2201133 original size:14 final size:14
Alignment explanation
Indices: 2201100--2201138 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
2201090 ATAAATTAAA
*
2201100 AAAAATTTAAAAAT
1 AAAAACTTAAAAAT
2201114 ACAAAACTTAAAAAT
1 A-AAAACTTAAAAAT
2201129 AAAAACTTAA
1 AAAAACTTAA
2201139 GTGATTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAACTTAAAAAT
Found at i:2201368 original size:19 final size:18
Alignment explanation
Indices: 2201331--2201379 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
2201321 AAAATATAAC
2201331 ATAAAAATGATATGCACAT
1 ATAAAAAT-ATATGCACAT
* *
2201350 AATATAAATATATGTACAT
1 -ATAAAAATATATGCACAT
2201369 ATAAAAATATA
1 ATAAAAATATA
2201380 CATAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.38
19 9 0.35
20 7 0.27
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAAAATATATGCACAT
Found at i:2201498 original size:16 final size:17
Alignment explanation
Indices: 2201472--2201521 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
2201462 TATAAAATTT
2201472 TTTCTCTTTTTTCTTT-C
1 TTTCTCTTTTTT-TTTCC
2201489 TTTC-CTTTTTTTTTCC
1 TTTCTCTTTTTTTTTCC
2201505 TTTCTTTCTTTTTTTTT
1 TTTC--TCTTTTTTTTT
2201522 TTTACCTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
17 4 0.14
19 10 0.34
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTCTTTTTTTTTCC
Found at i:2201508 original size:24 final size:22
Alignment explanation
Indices: 2201481--2201524 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
2201471 TTTTCTCTTT
2201481 TTTCTTTCTTTCCTTTTTTTTTCC
1 TTTCTTTCTTT--TTTTTTTTTCC
2201505 TTTCTTTCTTTTTTTTTTTT
1 TTTCTTTCTTTTTTTTTTTT
2201525 ACCTACTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTCTTTCTTTTTTTTTTTTCC
Found at i:2201522 original size:20 final size:19
Alignment explanation
Indices: 2201478--2201521 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
2201468 ATTTTTTCTC
2201478 TTTTTTCTTTCTTTCCTTT
1 TTTTTTCTTTCTTTCCTTT
2201497 TTTTTTCCTTTCTTT-CTTT
1 TTTTTT-CTTTCTTTCCTTT
2201516 TTTTTT
1 TTTTTT
2201522 TTTACCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTCTTTCTTTCCTTT
Found at i:2210147 original size:2 final size:2
Alignment explanation
Indices: 2210140--2210191 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2210130 ATATTTGTGA
2210140 AT AT AT AT AT AT 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
2210182 AT AT AT AT AT
1 AT AT AT AT AT
2210192 GAAATAAGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2211437 original size:28 final size:26
Alignment explanation
Indices: 2211387--2211491 Score: 83
Period size: 25 Copynumber: 4.0 Consensus size: 26
2211377 ATGCTTTGAT
* *
2211387 AAATTATATAATTACACAAATATTAAAAA
1 AAATTATATAAATATA-AAATATT--AAA
2211416 AAATTAATATAAA-ATAAAATA-TAAA
1 AAATT-ATATAAATATAAAATATTAAA
**
2211441 AAATTATATAAATATAATAATATT-TT
1 AAATTATATAAATATAA-AATATTAAA
*
2211467 AAATT-TATACAATATAAATTATTAA
1 AAATTATATA-AATATAAAATATTAA
2211492 TATATTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
24 7 0.11
25 21 0.33
26 16 0.25
27 2 0.03
28 5 0.08
29 7 0.11
30 6 0.09
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATTATATAAATATAAAATATTAAA
Found at i:2211463 original size:14 final size:13
Alignment explanation
Indices: 2211420--2211463 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
2211410 TAAAAAAAAT
2211420 TAATATAAAATAA
1 TAATATAAAATAA
2211433 -AATATAAAA-AA
1 TAATATAAAATAA
*
2211444 TTATATAAATATAA
1 TAATATAAA-ATAA
2211458 TAATAT
1 TAATAT
2211464 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.08
12 16 0.62
13 1 0.04
14 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATATAAAATAA
Found at i:2211504 original size:33 final size:32
Alignment explanation
Indices: 2211446--2211507 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
2211436 ATAAAAAATT
**
2211446 ATATAAATATAATAATATTTTAAATTTATACA
1 ATATAAATATAATAATATTAAAAATTTATACA
2211478 ATATAAATTATTAAT-ATATTAAAAATTTAT
1 ATATAAA-TA-TAATAATATTAAAAATTTAT
2211508 TAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 7 0.27
33 15 0.58
34 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (32 bp):
ATATAAATATAATAATATTAAAAATTTATACA
Found at i:2212101 original size:42 final size:43
Alignment explanation
Indices: 2212042--2212126 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
2212032 TTAACATGTT
*
2212042 AAAAAAATTATATACATTTAA-TATAT-TATTTTTATTAAATTCA
1 AAAAAAATTATAAACA-TTAATTATATAT-TTTTTATTAAATTCA
*
2212085 AAAAAAATTA-AAACATTAATTATATATTTTTTATTATATTCA
1 AAAAAAATTATAAACATTAATTATATATTTTTTATTAAATTCA
2212127 TATTATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
41 4 0.11
42 23 0.61
43 11 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (43 bp):
AAAAAAATTATAAACATTAATTATATATTTTTTATTAAATTCA
Found at i:2214530 original size:21 final size:21
Alignment explanation
Indices: 2214506--2214545 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2214496 ACAAAAAAAT
2214506 ATTAA-TATAAATAAAATATAA
1 ATTAAGTATAAA-AAAATATAA
*
2214527 ATTAAGTTTAAAAAAATAT
1 ATTAAGTATAAAAAAATAT
2214546 TATAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATTAAGTATAAAAAAATATAA
Found at i:2214808 original size:2 final size:2
Alignment explanation
Indices: 2214793--2214840 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
2214783 GACCAACTTG
* * * *
2214793 AT AT AT AA AA AT AT AT AA AT CAT AT TT 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
2214836 AT AT A
1 AT AT A
2214841 ATTTAATAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2214938 original size:19 final size:20
Alignment explanation
Indices: 2214910--2214952 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2214900 AAAAAAATTA
*
2214910 AAATATATAAATATA-ATAT
1 AAATAGATAAATATATATAT
2214929 AAATAGATAAATATATATAT
1 AAATAGATAAATATATATAT
2214949 AAAT
1 AAAT
2214953 TTATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATAGATAAATATATATAT
Found at i:2214985 original size:32 final size:35
Alignment explanation
Indices: 2214920--2214993 Score: 109
Period size: 32 Copynumber: 2.2 Consensus size: 35
2214910 AAATATATAA
2214920 ATATAATATAAATAGATAAATATATATATAAATTT
1 ATATAATATAAATAGATAAATATATATATAAATTT
* *
2214955 ATATAATATAAA-ATATTAATATAT-TA-AAATTT
1 ATATAATATAAATAGATAAATATATATATAAATTT
2214987 ATATAAT
1 ATATAAT
2214994 TATATAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 13 0.35
33 2 0.05
34 10 0.27
35 12 0.32
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (35 bp):
ATATAATATAAATAGATAAATATATATATAAATTT
Found at i:2214997 original size:40 final size:42
Alignment explanation
Indices: 2214913--2215001 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
2214903 AAAATTAAAA
*
2214913 TATATAA-ATATAATATAAATAGATAAATATATATATAAATT
1 TATATAATATAAAATATAAATAGATAAATATATATATAAATT
* * *
2214954 TATATAATATAAAATATTAATATATTAAA-ATTTATAT-AA-T
1 TATATAATATAAAATATAAATAGA-TAAATATATATATAAATT
2214994 TATATAAT
1 TATATAAT
2215002 TTTTTAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 9 0.21
41 9 0.21
42 20 0.48
43 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (42 bp):
TATATAATATAAAATATAAATAGATAAATATATATATAAATT
Found at i:2217473 original size:18 final size:17
Alignment explanation
Indices: 2217450--2217483 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2217440 AAAATATAAT
*
2217450 TAATATGATATAAAAATA
1 TAATATAATA-AAAAATA
2217468 TAATATAATAAAAAAT
1 TAATATAATAAAAAAT
2217484 TATTTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
TAATATAATAAAAAATA
Found at i:2217513 original size:14 final size:14
Alignment explanation
Indices: 2217442--2217522 Score: 64
Period size: 14 Copynumber: 6.1 Consensus size: 14
2217432 TATGGATAAA
2217442 AATATAATTAATAT
1 AATATAATTAATAT
* *
2217456 GATATAA-AAATAT
1 AATATAATTAATAT
2217469 AATATAA-TAA-A-
1 AATATAATTAATAT
* * *
2217480 AA-ATTATTTATTT
1 AATATAATTAATAT
2217493 AAATATAATTAATAT
1 -AATATAATTAATAT
*
2217508 AATATATTTAATAT
1 AATATAATTAATAT
2217522 A
1 A
2217523 TATTATATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
10 3 0.06
11 4 0.08
12 1 0.02
13 13 0.25
14 22 0.43
15 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (14 bp):
AATATAATTAATAT
Found at i:2217556 original size:17 final size:19
Alignment explanation
Indices: 2217534--2217577 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2217524 ATTATATTTT
2217534 TATTTAA-AA-CTTTAATA
1 TATTTAATAATCTTTAATA
* *
2217551 TATTTAATAATTTTTATTA
1 TATTTAATAATCTTTAATA
2217570 TATTTAAT
1 TATTTAAT
2217578 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 2 0.09
19 14 0.61
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTAATAATCTTTAATA
Found at i:2218485 original size:21 final size:20
Alignment explanation
Indices: 2218447--2218501 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
2218437 AAATAATTTG
2218447 ATATATTTATATTATTATATT
1 ATAT-TTTATATTATTATATT
*
2218468 ATATTTTATAATTTTTATATT
1 ATATTTTAT-ATTATTATATT
2218489 ATA-TTTATATTAT
1 ATATTTTATATTAT
2218502 ATAATCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTTTATATTATTATATT
Found at i:2218497 original size:11 final size:11
Alignment explanation
Indices: 2218448--2218503 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
2218438 AATAATTTGA
2218448 TATATTTATA-
1 TATATTTATAT
2218458 T-TA-TTATAT
1 TATATTTATAT
2218467 TATATTT-TAT
1 TATATTTATAT
* *
2218477 AATTTTTATAT
1 TATATTTATAT
2218488 TATATTTATAT
1 TATATTTATAT
2218499 TATAT
1 TATAT
2218504 AATCATATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 5 0.13
9 3 0.08
10 11 0.29
11 19 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:2219457 original size:3 final size:3
Alignment explanation
Indices: 2219442--2219485 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2219432 AATGCTTAAT
*
2219442 TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2219486 GCAATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2220253 original size:22 final size:22
Alignment explanation
Indices: 2220209--2220253 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2220199 ATAATTATTA
*
2220209 ATTATTACTTTTAATATATATT
1 ATTATTACTTTTAATATAAATT
*
2220231 ATTATTA-TTATTATTATAAATT
1 ATTATTACTT-TTAATATAAATT
2220253 A
1 A
2220254 AATATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTACTTTTAATATAAATT
Found at i:2220746 original size:2 final size:2
Alignment explanation
Indices: 2220739--2220767 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2220729 CAAGCTCTTT
2220739 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 T
2220768 TATCTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2220787 original size:15 final size:15
Alignment explanation
Indices: 2220763--2220797 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2220753 TATATATATA
2220763 TATATTATCTTATCT
1 TATATTATCTTATCT
* *
2220778 TATCTTATCTTATAT
1 TATATTATCTTATCT
2220793 TATAT
1 TATAT
2220798 GTGGTGTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTATCTTATCT
Found at i:2221852 original size:2 final size:2
Alignment explanation
Indices: 2221836--2221878 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2221826 TCATTAGTTT
* *
2221836 TA TA TA CA TA CA 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
2221878 T
1 T
2221879 GATACAGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2222818 original size:3 final size:3
Alignment explanation
Indices: 2222810--2222841 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2222800 TTTTGCTTCT
2222810 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2222842 TGACATTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2231225 original size:2 final size:2
Alignment explanation
Indices: 2231218--2231252 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2231208 TGTAATTTAT
*
2231218 TA TA TA TA TA TA TA TA TA TG 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 T
2231253 TATGACAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2231446 original size:21 final size:22
Alignment explanation
Indices: 2231421--2231464 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2231411 ACTATTTTAA
*
2231421 ATTCAAAAATTAAT-TTAATTT
1 ATTCAAAAATTAATAATAATTT
* *
2231442 ATTCATATATTAATAATAATTT
1 ATTCAAAAATTAATAATAATTT
2231464 A
1 A
2231465 AAAATTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTCAAAAATTAATAATAATTT
Found at i:2235916 original size:2 final size:2
Alignment explanation
Indices: 2235909--2235934 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2235899 ATCAGTGACT
2235909 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
2235935 AACTGTCAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2238387 original size:22 final size:23
Alignment explanation
Indices: 2238362--2238417 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
2238352 TTATGTTAAT
2238362 AATTTATTTAAATA-AAAATAAA
1 AATTTATTTAAATATAAAATAAA
* *
2238384 AATTTATATAAATATATAATAAA
1 AATTTATTTAAATATAAAATAAA
* *
2238407 ATTTTACTTAA
1 AATTTATTTAA
2238418 TGTAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTTATTTAAATATAAAATAAA
Found at i:2238412 original size:23 final size:22
Alignment explanation
Indices: 2238362--2238412 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2238352 TTATGTTAAT
*
2238362 AATTTATTTAAATAAAAATAAA
1 AATTTATATAAATAAAAATAAA
*
2238384 AATTTATATAAATATATAATAAA
1 AATTTATATAAATA-AAAATAAA
*
2238407 ATTTTA
1 AATTTA
2238413 CTTAATGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTTATATAAATAAAAATAAA
Found at i:2239222 original size:21 final size:22
Alignment explanation
Indices: 2239197--2239238 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2239187 TAATATGATT
2239197 ATATT-TCTTAAAATTTTAAAA
1 ATATTATCTTAAAATTTTAAAA
*
2239218 ATATTACTTTTAAAATTTTAA
1 ATATTA-TCTTAAAATTTTAA
2239239 TTTTATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTATCTTAAAATTTTAAAA
Found at i:2239842 original size:6 final size:6
Alignment explanation
Indices: 2239831--2239870 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
2239821 CAACCAGAAC
* *
2239831 AAGAGG AAGAGG AAGAGG AAGAGG AAGAAG AAGAAG AAGA
1 AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGAGG AAGA
2239871 AAATGACCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:2239854 original size:18 final size:18
Alignment explanation
Indices: 2239826--2239870 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2239816 AAGAACAACC
* *
2239826 AGAACAAGAGGAAGAGGA
1 AGAAGAAGAGGAAGAAGA
*
2239844 AGAGGAAGAGGAAGAAGA
1 AGAAGAAGAGGAAGAAGA
2239862 AGAAGAAGA
1 AGAAGAAGA
2239871 AAATGACCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.40, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAGGAAGAAGA
Found at i:2242565 original size:48 final size:48
Alignment explanation
Indices: 2242512--2242604 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
2242502 AAAAAGTCGT
* * *
2242512 CTTTTTTGACATCAATAAGGGTGATTTTTGTTGATTAAAGAGAGTCAC
1 CTTTTTTGACATCAATAAGGGTGACTTTTGTTGACTAAAAAGAGTCAC
*
2242560 CTTTTTTGACATCAATAAGGGTGGCTTTTGTTGACTAAAAAGAGT
1 CTTTTTTGACATCAATAAGGGTGACTTTTGTTGACTAAAAAGAGT
2242605 TGCCCACCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.39
Consensus pattern (48 bp):
CTTTTTTGACATCAATAAGGGTGACTTTTGTTGACTAAAAAGAGTCAC
Found at i:2245852 original size:16 final size:15
Alignment explanation
Indices: 2245831--2245861 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2245821 GAGCTCAGTT
2245831 AAATTTAAGTTATAAA
1 AAATTTAAGTT-TAAA
2245847 AAATTTAAGTTTAAA
1 AAATTTAAGTTTAAA
2245862 TTTAATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
AAATTTAAGTTTAAA
Found at i:2245864 original size:12 final size:12
Alignment explanation
Indices: 2245847--2245897 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
2245837 AAGTTATAAA
2245847 AAATTTAAGTTT-
1 AAATTTAA-TTTG
2245859 AAATTTAATTTG
1 AAATTTAATTTG
*
2245871 AAATTTTAATCTCG
1 AAA-TTTAAT-TTG
*
2245885 AAATTTGATTTG
1 AAATTTAATTTG
2245897 A
1 A
2245898 GTTTTACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 14 0.42
13 11 0.33
14 5 0.15
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (12 bp):
AAATTTAATTTG
Found at i:2246104 original size:22 final size:21
Alignment explanation
Indices: 2246073--2246120 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2246063 AAATAAAAAA
*
2246073 TTAAATTAAAT-TTATAAATTAT
1 TTAAAATAAATATT-TAAA-TAT
2246095 TTAAAATAAATATTTAAATAT
1 TTAAAATAAATATTTAAATAT
2246116 TTAAA
1 TTAAA
2246121 TGGAGTTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 14 0.58
23 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAAATAAATATTTAAATAT
Found at i:2248113 original size:20 final size:22
Alignment explanation
Indices: 2248089--2248148 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2248079 TATATCACTT
*
2248089 TAATTATAAAAATATATTTAAA
1 TAATTATAAAAATATATATAAA
* *
2248111 -ATTTATATAATATATATATAAA
1 TAATTATA-AAAATATATATAAA
*
2248133 TAATTATATAAATATA
1 TAATTATAAAAATATA
2248149 AAATAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 6 0.20
22 18 0.60
23 6 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTATAAAAATATATATAAA
Found at i:2248149 original size:52 final size:53
Alignment explanation
Indices: 2248044--2248151 Score: 123
Period size: 52 Copynumber: 2.1 Consensus size: 53
2248034 ACAAATAATT
* * *
2248044 AAAATATAATATAAAATATCATATATATATATATATATATCACTTTAATTATA
1 AAAATATAATATAAAATATCATATATATATATATAAATATCACTATAAATATA
* * *
2248097 AAAATAT-ATTTAAAAT-TTATATAATATATATATAAATAATTA-TATAAATATA
1 AAAATATAATATAAAATATCATAT-ATATATATATAAAT-ATCACTATAAATATA
2248149 AAA
1 AAA
2248152 TAATTAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
51 5 0.11
52 32 0.68
53 10 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (53 bp):
AAAATATAATATAAAATATCATATATATATATATAAATATCACTATAAATATA
Found at i:2248250 original size:25 final size:25
Alignment explanation
Indices: 2248216--2248263 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2248206 TAAATTTAAT
*
2248216 TAAATTAAAA-TTATTATTTAAATAA
1 TAAAATAAAATTTA-TATTTAAATAA
2248241 TAAAATAAAATTTATATTTAAAT
1 TAAAATAAAATTTATATTTAAAT
2248264 TTAATTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAAATAAAATTTATATTTAAATAA
Found at i:2248273 original size:25 final size:25
Alignment explanation
Indices: 2248206--2248283 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 25
2248196 ATAATTTAAA
2248206 TAAATTTAATTAAATTAAAA-TTATTATT
1 TAAATTTAATT--A-TAAAATTTA-TATT
* *
2248234 TAAATAATAA-AATAAAATTTATATT
1 TAAAT-TTAATTATAAAATTTATATT
*
2248259 TAAATTTAATTATAAATATTAATAT
1 TAAATTTAATTATAAA-ATTTATAT
2248284 AAAAATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 3 0.07
25 19 0.46
26 11 0.27
28 5 0.12
29 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAATTTAATTATAAAATTTATATT
Found at i:2248280 original size:13 final size:11
Alignment explanation
Indices: 2248172--2248286 Score: 50
Period size: 12 Copynumber: 10.6 Consensus size: 11
2248162 GATTGTGTCC
2248172 ATATAAATTTAA
1 ATATAAATTT-A
*
2248184 ATAAAAATTT-
1 ATATAAATTTA
2248194 -TCAT-AATTTA
1 AT-ATAAATTTA
2248204 A-ATAAATTTA
1 ATATAAATTTA
2248214 AT-TAAA-TTA
1 ATATAAATTTA
* *
2248223 AAATTATTATTTA
1 ATA-TA-AATTTA
**
2248236 A-AT-AATAAA
1 ATATAAATTTA
2248245 ATA-AAATTTA
1 ATATAAATTTA
*
2248255 TATTTAAATTTA
1 -ATATAAATTTA
2248267 ATTATAAATATTA
1 A-TATAAAT-TTA
2248280 ATATAAA
1 ATATAAA
2248287 AATAAAATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 30
0.65 0.09 0.25
Matches are distributed among these distances:
9 16 0.21
10 17 0.22
11 6 0.08
12 30 0.39
13 8 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATAAATTTA
Found at i:2248299 original size:38 final size:37
Alignment explanation
Indices: 2248234--2248339 Score: 97
Period size: 38 Copynumber: 2.7 Consensus size: 37
2248224 AATTATTATT
* *
2248234 TAAATAATAAAATAAAATTTATATTTAAATTTAATTATAAATA
1 TAAAT-ATAAAATAAAA--AAT-TTTAAATTTAACT-T-AATA
* *
2248277 TTAATATAAAA-ATAAAATTTTAAATTTAACTTAATA
1 TAAATATAAAATAAAAAATTTTAAATTTAACTTAATA
*
2248313 TAAATTTAAAATTAAAAAATTTTAAAT
1 TAAATATAAAA-TAAAAAATTTTAAAT
2248340 CATTTCAACT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
36 13 0.24
37 1 0.02
38 25 0.46
39 2 0.04
41 3 0.06
42 6 0.11
43 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (37 bp):
TAAATATAAAATAAAAAATTTTAAATTTAACTTAATA
Found at i:2248332 original size:43 final size:43
Alignment explanation
Indices: 2248242--2248330 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
2248232 TTTAAATAAT
* * *
2248242 AAAATAAAATTTATATTTAAATTTAATTATAAATATTAATATA
1 AAAATAAAATTTAAATTTAAACTTAATTATAAATATTAAAATA
2248285 AAAATAAAATTTTAAATTT-AACTTAA-TATAAAT-TTAAAATTA
1 AAAATAAAA-TTTAAATTTAAACTTAATTATAAATATTAAAA-TA
2248327 AAAA
1 AAAA
2248331 ATTTTAAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 5 0.12
42 13 0.32
43 15 0.37
44 8 0.20
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (43 bp):
AAAATAAAATTTAAATTTAAACTTAATTATAAATATTAAAATA
Found at i:2249093 original size:78 final size:75
Alignment explanation
Indices: 2249011--2249164 Score: 209
Period size: 75 Copynumber: 2.0 Consensus size: 75
2249001 ATTAATCTAA
*
2249011 ATAAGATATTTTGTTACAACAACAACGATAAATTTAATCTCATCAAATTAGATTTTATTTAAAAA
1 ATAAGATATTTTGTT--AAC-ACAACGATAAACTTAATCTCATCAAATTAGATTTTATTTAAAAA
2249076 CTTATATTGATAT
63 CTTATATTGATAT
* * * * * * *
2249089 ATAAGATATTTTGTTATCACAATGATAAGCTTAATCTTATTAAATTAGATTTTGTTTAATAACTT
1 ATAAGATATTTTGTTAACACAACGATAAACTTAATCTCATCAAATTAGATTTTATTTAAAAACTT
2249154 ATATTGATAT
66 ATATTGATAT
2249164 A
1 A
2249165 AAATTAAGCA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
75 51 0.75
76 2 0.03
78 15 0.22
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (75 bp):
ATAAGATATTTTGTTAACACAACGATAAACTTAATCTCATCAAATTAGATTTTATTTAAAAACTT
ATATTGATAT
Found at i:2249626 original size:2 final size:2
Alignment explanation
Indices: 2249621--2249654 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2249611 GTGTGTGTTA
2249621 AT AT 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
2249655 TTTAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2250671 original size:21 final size:21
Alignment explanation
Indices: 2250620--2250674 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2250610 TATTTTTATT
*
2250620 TAAATA-TAATTATAAAATATA
1 TAAATATTAA-TATAAAATAAA
2250641 TAAATATTAATATAAAA-AAA
1 TAAATATTAATATAAAATAAA
*
2250661 TAAATTTTTAATAT
1 TAAA-TATTAATAT
2250675 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.20
21 21 0.70
22 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAATAAA
Found at i:2251015 original size:14 final size:15
Alignment explanation
Indices: 2250979--2251040 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
2250969 TTAATTACAT
*
2250979 AATAATTTAAATTAA
1 AATAATTTAAATAAA
*
2250994 ATTAATTTAAATAAA
1 AATAATTTAAATAAA
*
2251009 AAT-ATTTAAATTTAA
1 AATAATTTAAA-TAAA
* *
2251024 TATAATTTTAATAAA
1 AATAATTTAAATAAA
2251039 AA
1 AA
2251041 ATATTAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 7 0.19
15 24 0.65
16 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAATTTAAATAAA
Found at i:2251037 original size:30 final size:30
Alignment explanation
Indices: 2250983--2251045 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
2250973 TTACATAATA
2250983 ATTTAAATTAAATTAATTTAAAT-AAAAAT
1 ATTTAAATTAAATTAATTTAAATAAAAAAT
* *
2251012 ATTTAAATTTAATATAATTTTAATAAAAAAT
1 ATTTAAATTAAAT-TAATTTAAATAAAAAAT
2251043 ATT
1 ATT
2251046 AAAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.40
30 9 0.30
31 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATTTAAATTAAATTAATTTAAATAAAAAAT
Found at i:2251048 original size:30 final size:29
Alignment explanation
Indices: 2250949--2251048 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 29
2250939 ATTATTTTTA
2250949 AAAAATATTAAATTATAATATTAA--TTACAT
1 AAAAATATTAAATT-TAATA-TAATTTTA-AT
* * *
2250979 AATAAT-TTAAATTAAAT-TAATTTAAAT
1 AAAAATATTAAATTTAATATAATTTTAAT
2251006 AAAAATATTTAAATTTAATATAATTTTAAT
1 AAAAATA-TTAAATTTAATATAATTTTAAT
2251036 AAAAAATATTAAA
1 -AAAAATATTAAA
2251049 AATAATAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 3 0.05
27 7 0.12
28 5 0.09
29 17 0.29
30 19 0.33
31 7 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAATATTAAATTTAATATAATTTTAAT
Found at i:2251055 original size:30 final size:30
Alignment explanation
Indices: 2250996--2251055 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2250986 TAAATTAAAT
**
2250996 TAATTTAAATAAAAATATTTAAATTTAATA
1 TAATTTAAATAAAAATATTTAAAAATAATA
*
2251026 TAATTTTAATAAAAA-ATATTAAAAATAATA
1 TAATTTAAATAAAAATAT-TTAAAAATAATA
2251056 ATTCGATTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TAATTTAAATAAAAATATTTAAAAATAATA
Found at i:2251441 original size:35 final size:34
Alignment explanation
Indices: 2251331--2251443 Score: 108
Period size: 35 Copynumber: 3.2 Consensus size: 34
2251321 AAATTTTTAG
2251331 TTTTATAATATAT-TATATTAAATTAAATATTAA
1 TTTTATAATATATATATATTAAATTAAATATTAA
*
2251364 TTTTTATTTAAT-TA-AT-TGATTTAATATTAAAAAAATTAA
1 -TTTTA--TAATATATATAT-A-TTAA-ATT--AAATATTAA
2251403 TTTTATAATATATATCATATTAAATTAAATATTAA
1 TTTTATAATATATAT-ATATTAAATTAAATATTAA
2251438 TTTTAT
1 TTTTAT
2251444 TTAATTAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 23
0.72 0.02 0.26
Matches are distributed among these distances:
34 6 0.09
35 18 0.28
36 12 0.18
37 8 0.12
38 11 0.17
39 9 0.14
40 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (34 bp):
TTTTATAATATATATATATTAAATTAAATATTAA
Found at i:2251719 original size:23 final size:23
Alignment explanation
Indices: 2251673--2251720 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2251663 TAATATTTAT
*
2251673 AAATAAATTTAAATAAAATATAA
1 AAATAAATTTAAACAAAATATAA
*
2251696 AAATATATTTAAACAACAAT-TAA
1 AAATAAATTTAAACAA-AATATAA
2251719 AA
1 AA
2251721 TTAATCTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATAAATTTAAACAAAATATAA
Found at i:2255187 original size:1 final size:1
Alignment explanation
Indices: 2255183--2255207 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2255173 CCGAATGAAA
2255183 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
2255208 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2258997 original size:1 final size:1
Alignment explanation
Indices: 2258991--2259015 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2258981 CATCTACCAC
2258991 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2259016 CAGAAGTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2261637 original size:20 final size:19
Alignment explanation
Indices: 2261614--2261663 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2261604 TTATAATAAA
2261614 TAAAAAATAATTAAAGATAT
1 TAAAAAATAATTAAA-ATAT
* *
2261634 TAAAAACATTATTTAAATAT
1 TAAAAA-ATAATTAAAATAT
2261654 TAATAAAATA
1 TAA-AAAATA
2261664 TTATATGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAAATAATTAAAATAT
Found at i:2261887 original size:9 final size:9
Alignment explanation
Indices: 2261875--2261945 Score: 58
Period size: 9 Copynumber: 8.0 Consensus size: 9
2261865 CGTAATTTTC
2261875 TATAAATTT
1 TATAAATTT
*
2261884 TATATA-TT
1 TATAAATTT
2261892 TAT-AATTT
1 TATAAATTT
2261900 TATAAATTTT
1 TATAAA-TTT
2261910 TATAAATTT
1 TATAAATTT
**
2261919 CTA-AAACAT
1 -TATAAATTT
* *
2261928 AACAAATTT
1 TATAAATTT
2261937 TATAAATTT
1 TATAAATTT
2261946 CTCATTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
7 1 0.02
8 11 0.23
9 25 0.52
10 11 0.23
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (9 bp):
TATAAATTT
Found at i:2261983 original size:3 final size:3
Alignment explanation
Indices: 2261969--2262017 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
2261959 AAACGGTGTA
2261969 ATT ATT -TT 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
2262016 AT
1 AT
2262018 AAAAAGCCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2267124 original size:61 final size:61
Alignment explanation
Indices: 2267029--2267148 Score: 213
Period size: 61 Copynumber: 2.0 Consensus size: 61
2267019 AGATTAAGAC
*
2267029 ATGGAGATGGCAAGACAAATATAGGGACTGTCAAAACATAAAAACGTTGCTATATTTGCAA
1 ATGGAGATGGCAAGACAAATATAGGGACGGTCAAAACATAAAAACGTTGCTATATTTGCAA
* *
2267090 ATGGAGATGGCGAGACAAATATAGGGAGGGTCAAAACATAAAAACGTTGCTATATTTGC
1 ATGGAGATGGCAAGACAAATATAGGGACGGTCAAAACATAAAAACGTTGCTATATTTGC
2267149 CGTTATGCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (61 bp):
ATGGAGATGGCAAGACAAATATAGGGACGGTCAAAACATAAAAACGTTGCTATATTTGCAA
Found at i:2269304 original size:18 final size:18
Alignment explanation
Indices: 2269283--2269320 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2269273 TGAAGAGTAC
2269283 TGGCCGACTAGTAGTAGT
1 TGGCCGACTAGTAGTAGT
*
2269301 TGGCCGACTGGTAGTAGT
1 TGGCCGACTAGTAGTAGT
2269319 TG
1 TG
2269321 TTGTATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.16, G:0.37, T:0.29
Consensus pattern (18 bp):
TGGCCGACTAGTAGTAGT
Found at i:2269814 original size:35 final size:34
Alignment explanation
Indices: 2269740--2269823 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 34
2269730 TATAAAATTT
* *
2269740 AATTATAATTAAA-AATATATTTTAATATGTTTAT
1 AATTA-AATTAAATAATATATTTTAATATATTTAA
* * *
2269774 TATTAAATTAAATAATTTTATTTTTATATATTTAA
1 AATTAAATTAAATAA-TATATTTTAATATATTTAA
*
2269809 AATTAAAATAAATAA
1 AATTAAATTAAATAA
2269824 AATAAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
33 7 0.17
34 6 0.15
35 28 0.68
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
AATTAAATTAAATAATATATTTTAATATATTTAA
Found at i:2270231 original size:2 final size:2
Alignment explanation
Indices: 2270224--2270264 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2270214 ATTTGTTGTT
2270224 TA TA 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 TA TA T
2270265 TATGAAGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2270345 original size:68 final size:68
Alignment explanation
Indices: 2270246--2270372 Score: 227
Period size: 68 Copynumber: 1.9 Consensus size: 68
2270236 TATATATATA
2270246 TATATATATATATATATATTATGAAGTTAAGGTTGAATTCAGAACCTGATCAAAGAATTATATTT
1 TATATATATATATATATATTATGAAGTTAAGGTTGAATTCAGAACCTGATCAAAGAATTATATTT
2270311 GTT
66 GTT
* * *
2270314 TATATATATATATATATATTGTGAAGTTAAGGTTGAATTCAGAACCTGATTAAATAATT
1 TATATATATATATATATATTATGAAGTTAAGGTTGAATTCAGAACCTGATCAAAGAATT
2270373 CCATGTGCCA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (68 bp):
TATATATATATATATATATTATGAAGTTAAGGTTGAATTCAGAACCTGATCAAAGAATTATATTT
GTT
Found at i:2271333 original size:2 final size:2
Alignment explanation
Indices: 2271326--2271351 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2271316 CAAGCAGGAG
2271326 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
2271352 TAATTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2271421 original size:21 final size:20
Alignment explanation
Indices: 2271384--2271423 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2271374 TGAATATTTT
2271384 AAATTATTTTATATATTTAA
1 AAATTATTTTATATATTTAA
*
2271404 AAATTATATTTTTATATTTA
1 AAATTAT-TTTATATATTTA
2271424 TATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTATTTTATATATTTAA
Found at i:2274500 original size:14 final size:15
Alignment explanation
Indices: 2274483--2274520 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2274473 TATAATTATT
2274483 TTTAATAAA-TAATA
1 TTTAATAAATTAATA
2274497 TTTAATAAATTTAATA
1 TTTAATAAA-TTAATA
2274513 TTCTAATA
1 TT-TAATA
2274521 TTTATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
16 7 0.33
17 5 0.24
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAATAAATTAATA
Found at i:2275609 original size:18 final size:18
Alignment explanation
Indices: 2275586--2275655 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
2275576 TTTTGATACT
2275586 CTTTTGCTGCTGCTGTTG
1 CTTTTGCTGCTGCTGTTG
*
2275604 CTTTTGTTGCTTCCTATGCTGTT-
1 C--TT-TTGC-TGC--TGCTGTTG
2275627 CTTTTGCTGCTGCTGTTG
1 CTTTTGCTGCTGCTGTTG
*
2275645 CTTTTGTTGCT
1 CTTTTGCTGCT
2275656 TCCTATGCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
17 7 0.17
18 11 0.26
19 2 0.05
20 6 0.14
21 6 0.14
22 2 0.05
23 1 0.02
24 7 0.17
ACGTcount: A:0.01, C:0.21, G:0.23, T:0.54
Consensus pattern (18 bp):
CTTTTGCTGCTGCTGTTG
Found at i:2275642 original size:41 final size:41
Alignment explanation
Indices: 2275585--2275669 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
2275575 CTTTTGATAC
2275585 TCTTTTGCTGCTGCTGTTGCTTTTGTTGCTTCCTATGCTGT
1 TCTTTTGCTGCTGCTGTTGCTTTTGTTGCTTCCTATGCTGT
2275626 TCTTTTGCTGCTGCTGTTGCTTTTGTTGCTTCCTATGCTGT
1 TCTTTTGCTGCTGCTGTTGCTTTTGTTGCTTCCTATGCTGT
2275667 TCT
1 TCT
2275670 GAATTTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.02, C:0.22, G:0.21, T:0.54
Consensus pattern (41 bp):
TCTTTTGCTGCTGCTGTTGCTTTTGTTGCTTCCTATGCTGT
Found at i:2275664 original size:18 final size:18
Alignment explanation
Indices: 2275602--2275664 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
2275592 CTGCTGCTGT
2275602 TGCTTTTGTTGCTTCCTA
1 TGCTTTTGTTGCTTCCTA
* * *
2275620 TGCTGTTCTTTTGCTGCTGCTGT
1 TGCT-TT-TGTTGCT--TCCT-A
2275643 TGCTTTTGTTGCTTCCTA
1 TGCTTTTGTTGCTTCCTA
2275661 TGCT
1 TGCT
2275665 GTTCTGAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 8 0.24
19 5 0.15
20 6 0.18
21 6 0.18
22 5 0.15
23 4 0.12
ACGTcount: A:0.03, C:0.22, G:0.21, T:0.54
Consensus pattern (18 bp):
TGCTTTTGTTGCTTCCTA
Found at i:2277079 original size:2 final size:2
Alignment explanation
Indices: 2277068--2277134 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
2277058 GGAGCACACT
2277068 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2277109 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
2277135 AACTTGGTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2279071 original size:28 final size:31
Alignment explanation
Indices: 2279021--2279088 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 31
2279011 CGTGTATTTC
2279021 TATTATATTATAATCATATTTAAAATATTT-TA
1 TATT-TATTATAA-CATATTTAAAATATTTATA
2279053 TATTTATTATAA-AT-TTTAAAATATTTATA
1 TATTTATTATAACATATTTAAAATATTTATA
2279082 TATTTAT
1 TATTTAT
2279089 ATCATATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
28 12 0.34
29 11 0.31
31 8 0.23
32 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTTATTATAACATATTTAAAATATTTATA
Found at i:2281241 original size:2 final size:2
Alignment explanation
Indices: 2281236--2281261 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2281226 AAATCACTCC
2281236 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2281262 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2281266 original size:2 final size:2
Alignment explanation
Indices: 2281261--2281293 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2281251 TCTCTCTCTC
2281261 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 T
2281294 GTCCATATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2282699 original size:3 final size:3
Alignment explanation
Indices: 2282691--2282729 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2282681 TATTTCCAAC
2282691 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2282730 CAACAATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2283525 original size:3 final size:3
Alignment explanation
Indices: 2283517--2283560 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
2283507 ATAGAAAATC
2283517 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2283561 CTATATCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2283804 original size:21 final size:24
Alignment explanation
Indices: 2283774--2283819 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
2283764 AGATAATAAA
2283774 ATTTAAA-TTTAAAA-AATT-TAT
1 ATTTAAATTTTAAAATAATTATAT
*
2283795 ATTTATATTTTAAAATAATTATAT
1 ATTTAAATTTTAAAATAATTATAT
2283819 A
1 A
2283820 AAACAACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 7 0.33
23 4 0.19
24 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAAATTTTAAAATAATTATAT
Found at i:2284311 original size:16 final size:16
Alignment explanation
Indices: 2284267--2284298 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2284257 ATTAAAAAAT
*
2284267 ATATATATATAATATA
1 ATATAAATATAATATA
2284283 ATATAAATATAATATA
1 ATATAAATATAATATA
2284299 TTATTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAAATATAATATA
Found at i:2288231 original size:15 final size:14
Alignment explanation
Indices: 2288211--2288242 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
2288201 AATCTGCCTG
2288211 TTTTTTTTTCCTTCT
1 TTTTTTTTTCC-TCT
2288226 TTTTTTTTTCCTCT
1 TTTTTTTTTCCTCT
2288240 TTT
1 TTT
2288243 GTACAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTCCTCT
Found at i:2289480 original size:2 final size:2
Alignment explanation
Indices: 2289473--2289512 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2289463 ACTCCGACTC
*
2289473 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2289513 TCTATAACCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2289845 original size:20 final size:20
Alignment explanation
Indices: 2289822--2289862 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2289812 TAATATTTGA
2289822 TAAATATAAATTT-TAAATTT
1 TAAA-ATAAATTTATAAATTT
*
2289842 TAAAATAATTTTATAAATTT
1 TAAAATAAATTTATAAATTT
2289862 T
1 T
2289863 TTTTTCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATAAATTTATAAATTT
Found at i:2290747 original size:3 final size:3
Alignment explanation
Indices: 2290739--2290772 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2290729 GGATTAGTTG
2290739 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2290773 CATCCGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2293168 original size:2 final size:2
Alignment explanation
Indices: 2293161--2293189 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2293151 GATGTCAAAT
2293161 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 T
2293190 GAACAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2293765 original size:6 final size:6
Alignment explanation
Indices: 2293754--2293784 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2293744 TGATTTTTTT
2293754 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA A
2293785 ATTTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTAAA
Found at i:2294091 original size:19 final size:18
Alignment explanation
Indices: 2294066--2294119 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
2294056 TCAATATTAC
2294066 ATTATAATATATATTATTT
1 ATTATAATATATATT-TTT
* *
2294085 TTTATAATTTCATAGATTTTT
1 ATTATAA--T-ATATATTTTT
2294106 ATTATAATATATAT
1 ATTATAATATATAT
2294120 CTAGTATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
18 5 0.18
19 7 0.25
21 10 0.36
22 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
ATTATAATATATATTTTT
Found at i:2294278 original size:18 final size:17
Alignment explanation
Indices: 2294247--2294280 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2294237 TTAAAAAGAT
*
2294247 TTTATTTTTTATTTAAG
1 TTTATTTTTAATTTAAG
2294264 TTTATTTTTAAATTTAA
1 TTTATTTTT-AATTTAA
2294281 TAATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTATTTTTAATTTAAG
Found at i:2300303 original size:24 final size:23
Alignment explanation
Indices: 2300268--2300312 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2300258 ATTTTATATT
* *
2300268 TAATTATTTATTAATTTATTTATA
1 TAATTATATATT-ATATATTTATA
2300292 TAATTATATATTATATATTTA
1 TAATTATATATTATATATTTA
2300313 CGTTTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATTATATATTATATATTTATA
Found at i:2302868 original size:2 final size:2
Alignment explanation
Indices: 2302861--2302885 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2302851 CTTAGTCCCC
2302861 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
2302886 GCTCGAATGC
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:2302908 original size:3 final size:3
Alignment explanation
Indices: 2302900--2302926 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2302890 GAATGCAGTA
2302900 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
2302927 CTGTACATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2305341 original size:2 final size:2
Alignment explanation
Indices: 2305334--2305363 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2305324 TTGAAGTATG
2305334 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
2305364 TAAAGTTCTA
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):
AT
Found at i:2305700 original size:10 final size:10
Alignment explanation
Indices: 2305657--2305717 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
2305647 ATTTTGATAC
*
2305657 ATATTTAAAT
1 ATATTTAAAA
*
2305667 ATA-ATAAAA
1 ATATTTAAAA
*
2305676 ATTATTTTTAAA
1 A-TA-TTTAAAA
*
2305688 ATATATAAAA
1 ATATTTAAAA
2305698 ATATTTTAAAA
1 ATA-TTTAAAA
2305709 ATATTTAAA
1 ATATTTAAA
2305718 TTAAACGCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
9 5 0.12
10 19 0.47
11 11 0.28
12 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATTTAAAA
Found at i:2305702 original size:21 final size:22
Alignment explanation
Indices: 2305663--2305717 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
2305653 ATACATATTT
*
2305663 AAATATAATAAAAATTATTTTTA
1 AAATAT-ATAAAAATTATTTTAA
2305686 AAATATATAAAAA-TATTTTAA
1 AAATATATAAAAATTATTTTAA
*
2305707 AAATATTTAAA
1 AAATATATAAA
2305718 TTAAACGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 17 0.57
22 7 0.23
23 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATATAAAAATTATTTTAA
Found at i:2305709 original size:11 final size:11
Alignment explanation
Indices: 2305671--2305714 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2305661 TTAAATATAA
2305671 TAAAAATTATTT
1 TAAAAA-TATTT
* *
2305683 TTAAAATA-TA
1 TAAAAATATTT
2305693 TAAAAATATTT
1 TAAAAATATTT
2305704 TAAAAATATTT
1 TAAAAATATTT
2305715 AAATTAAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.30
11 14 0.52
12 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:2311883 original size:59 final size:58
Alignment explanation
Indices: 2311785--2311900 Score: 205
Period size: 59 Copynumber: 2.0 Consensus size: 58
2311775 CTAAATATGG
*
2311785 CATGCTTATAATGGTTCAGATACACATACCATATACTACCAAAGGTATATATACATGT
1 CATGCTTATAATGGTTCAGATACACATACCATATACTACCAAAGGCATATATACATGT
*
2311843 CATGCCTTATAATGGTTCAGATACACATACCATATTCTACCAAAGGCATATATACATG
1 CATG-CTTATAATGGTTCAGATACACATACCATATACTACCAAAGGCATATATACATG
2311901 CCATACATAG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 4 0.07
59 51 0.93
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (58 bp):
CATGCTTATAATGGTTCAGATACACATACCATATACTACCAAAGGCATATATACATGT
Found at i:2311994 original size:22 final size:22
Alignment explanation
Indices: 2311966--2312010 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2311956 TAATTTTGGC
2311966 ATTAATACACATACCATATACG
1 ATTAATACACATACCATATACG
2311988 ATTAATACACATACCATATACG
1 ATTAATACACATACCATATACG
2312010 A
1 A
2312011 CCATATATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (22 bp):
ATTAATACACATACCATATACG
Found at i:2317898 original size:60 final size:60
Alignment explanation
Indices: 2317827--2317983 Score: 215
Period size: 60 Copynumber: 2.6 Consensus size: 60
2317817 TTAATACATC
* * * * *
2317827 TTCCATATATGGATTCTCTCCTTGTAAAGATACTTATATTAAGGAATATTAGGACATCTT
1 TTCCGTATATGGATTCTTTCCTTGTAAAGATACCTATATTAAGAAATATCAGGACATCTT
* * * *
2317887 TTCCGTATATGGATTATTTCCTTGTAAAGATGCCTATATTAATAAATATCAGGATATCTT
1 TTCCGTATATGGATTCTTTCCTTGTAAAGATACCTATATTAAGAAATATCAGGACATCTT
* *
2317947 TTCCGTATATAGATTCTTTCCTTGTAAAGATGCCTAT
1 TTCCGTATATGGATTCTTTCCTTGTAAAGATACCTAT
2317984 TTTGAGAATT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 86 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (60 bp):
TTCCGTATATGGATTCTTTCCTTGTAAAGATACCTATATTAAGAAATATCAGGACATCTT
Found at i:2325246 original size:2 final size:2
Alignment explanation
Indices: 2325239--2325266 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2325229 TTTTCTGAGA
2325239 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
2325267 GTCTGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2330463 original size:33 final size:33
Alignment explanation
Indices: 2330380--2330465 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 33
2330370 TATAATAATT
* *
2330380 ATATTTAATATATTTTTTATTTATATAAATTTTA
1 ATATTTAA-ATACTTTTTATATATATAAATTTTA
*
2330414 ATATGTT-AATACTTTTTATCATATA-AAATTTATG
1 ATAT-TTAAATACTTTTTAT-ATATATAAATTT-TA
*
2330448 ATATTTAAATATTTTTTA
1 ATATTTAAATACTTTTTA
2330466 AAAATATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
33 18 0.41
34 24 0.55
35 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (33 bp):
ATATTTAAATACTTTTTATATATATAAATTTTA
Found at i:2331252 original size:18 final size:18
Alignment explanation
Indices: 2331226--2331262 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2331216 GATTGTAACG
2331226 TTTTCATAATTTTTAAAT
1 TTTTCATAATTTTTAAAT
* *
2331244 TTTTTATAATTTTTTAAT
1 TTTTCATAATTTTTAAAT
2331262 T
1 T
2331263 AAATTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCATAATTTTTAAAT
Found at i:2331287 original size:17 final size:17
Alignment explanation
Indices: 2331246--2331303 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
2331236 TTTTAAATTT
2331246 TTTATAAT-TT-TTTAA
1 TTTATAATATTATTTAA
*
2331261 TTAAATTAATATTATTTAA
1 TT-TA-TAATATTATTTAA
2331280 TTTATAATATTAATTTAA
1 TTTATAATATT-ATTTAA
2331298 -TTATAA
1 TTTATAA
2331304 GCTTAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
15 2 0.06
16 1 0.03
17 17 0.47
18 9 0.25
19 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATAATATTATTTAA
Found at i:2331309 original size:17 final size:18
Alignment explanation
Indices: 2331274--2331311 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2331264 AATTAATATT
*
2331274 ATTTAATTTATAATATTA
1 ATTTAATTTATAAGATTA
*
2331292 ATTTAA-TTATAAGCTTA
1 ATTTAATTTATAAGATTA
2331309 ATT
1 ATT
2331312 ATTAATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAATTTATAAGATTA
Found at i:2332019 original size:21 final size:21
Alignment explanation
Indices: 2331969--2332038 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
2331959 TTAAAAAATT
2331969 ATATTAA-ATAATTTTA-AT-
1 ATATTAATATAATTTTAGATA
*
2331987 AT-TTACATATAATTTTGGATA
1 ATATTA-ATATAATTTTAGATA
*
2332008 ATATTAATATAATTTTAGATG
1 ATATTAATATAATTTTAGATA
*
2332029 ACATTAATAT
1 ATATTAATAT
2332039 GATAGATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 8 0.19
20 2 0.05
21 24 0.56
22 3 0.07
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (21 bp):
ATATTAATATAATTTTAGATA
Found at i:2333160 original size:14 final size:13
Alignment explanation
Indices: 2333135--2333159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2333125 AAAGCTACTG
2333135 CCCATTAAAAAAC
1 CCCATTAAAAAAC
2333148 CCCATTAAAAAA
1 CCCATTAAAAAA
2333160 AAAAGACTAT
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:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
CCCATTAAAAAAC
Found at i:2333473 original size:23 final size:23
Alignment explanation
Indices: 2333430--2333473 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2333420 TAAATTATTA
* *
2333430 TTTAAAAATAAAATTATATTTAT
1 TTTAAAAATAAAATAAAATTTAT
2333453 TTTAAATAA-AAAATAAAATTT
1 TTTAAA-AATAAAATAAAATTT
2333474 TGAATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAAATAAAATAAAATTTAT
Found at i:2334317 original size:28 final size:29
Alignment explanation
Indices: 2334257--2334317 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
2334247 CTTTCAACAC
2334257 AATATTTTAAAATAATAAAATATATAAAA
1 AATATTTTAAAATAATAAAATATATAAAA
* *
2334286 AATATTTTAAATTAA-AAATTA-ATAAATA
1 AATATTTTAAAATAATAAAATATATAAA-A
2334314 AATA
1 AATA
2334318 ATATAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 10 0.34
29 14 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AATATTTTAAAATAATAAAATATATAAAA
Found at i:2334339 original size:17 final size:17
Alignment explanation
Indices: 2334280--2334342 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
2334270 AATAAAATAT
*
2334280 ATAAAAA-ATATTTTAA
1 ATAAAAATATAATTTAA
2334296 ATTAAAAAT-TAA--TAA
1 A-TAAAAATATAATTTAA
2334311 ATAAATAATATAATTTAA
1 ATAAA-AATATAATTTAA
2334329 ATAAAAATATAATT
1 ATAAAAATATAATT
2334343 ACATTTTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
14 4 0.10
15 7 0.17
16 4 0.10
17 17 0.43
18 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAAAATATAATTTAA
Found at i:2338205 original size:2 final size:2
Alignment explanation
Indices: 2338198--2338223 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2338188 TCTATATTTA
2338198 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
2338224 GGAGATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2338300 original size:34 final size:35
Alignment explanation
Indices: 2338228--2338300 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
2338218 ATATATGGAG
* * *
2338228 ATATAATTTTTAAAAAATATTATATATATTTATAT
1 ATATAAATTTTAAAAAATATTATATAAATATATAT
*
2338263 ATATAAATTTT-AAAAATATTA-ATTAAATATATTT
1 ATATAAATTTTAAAAAATATTATA-TAAATATATAT
2338297 ATAT
1 ATAT
2338301 CGAATATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 1 0.03
34 22 0.67
35 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATATAAATTTTAAAAAATATTATATAAATATATAT
Found at i:2338300 original size:36 final size:35
Alignment explanation
Indices: 2338228--2338300 Score: 101
Period size: 38 Copynumber: 2.0 Consensus size: 35
2338218 ATATATGGAG
* *
2338228 ATATAATTTTTAAAAAATATTATATATATTTATAT
1 ATATAAATTTTAAAAAATATTAAATATATTTATAT
2338263 ATATAAATTTTAAAAATATTAATTAAATATATTTATAT
1 ATATAAATTTTAAAAA-A-T-ATTAAATATATTTATAT
2338301 CGAATATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 15 0.45
36 1 0.03
37 1 0.03
38 16 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATATAAATTTTAAAAAATATTAAATATATTTATAT
Found at i:2338884 original size:6 final size:6
Alignment explanation
Indices: 2338867--2338895 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2338857 TATGTTTAAT
2338867 TATTTA TA-TTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA
2338896 CATAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:2340377 original size:23 final size:24
Alignment explanation
Indices: 2340333--2340388 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
2340323 TAATATTTTC
2340333 ATTTTGATATTATTAAACATAAAT
1 ATTTTGATATTATTAAACATAAAT
*
2340357 ATTTTTATATT-TTAATA-ATAAAT
1 ATTTTGATATTATTAA-ACATAAAT
*
2340380 -TATTGATAT
1 ATTTTGATAT
2340389 AAAATAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.25
23 10 0.36
24 11 0.39
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTTGATATTATTAAACATAAAT
Done.