Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012152.1 Kokia drynarioides strain JFW-HI SEQ_127151, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 458257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 84 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:8485 original size:21 final size:19
Alignment explanation
Indices: 8453--8495 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
8443 AGTTGTTAGG
*
8453 TTATTTTTCTTTTAAAAGT
1 TTATTTTTCTTTGAAAAGT
*
8472 TTATGTTTTCCTTTGAACAGT
1 TTAT-TTTT-CTTTGAAAAGT
8493 TTA
1 TTA
8496 CTACTCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (19 bp):
TTATTTTTCTTTGAAAAGT
Found at i:17305 original size:32 final size:32
Alignment explanation
Indices: 17261--17325 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
17251 CTAGTGATAG
17261 TAAGCTTCGATTGTATTCTTTAATCCTTTTTT
1 TAAGCTTCGATTGTATTCTTTAATCCTTTTTT
*
17293 TAAGCTTTGATTGTATTCTTTAATCCTTTTTT
1 TAAGCTTCGATTGTATTCTTTAATCCTTTTTT
17325 T
1 T
17326 TATGCTGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.58
Consensus pattern (32 bp):
TAAGCTTCGATTGTATTCTTTAATCCTTTTTT
Found at i:25793 original size:15 final size:15
Alignment explanation
Indices: 25773--25801 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25763 TGTTGTTATA
25773 AGGCTCAACCTGATG
1 AGGCTCAACCTGATG
25788 AGGCTCAACCTGAT
1 AGGCTCAACCTGAT
25802 TCGAGCTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (15 bp):
AGGCTCAACCTGATG
Found at i:26622 original size:38 final size:38
Alignment explanation
Indices: 26568--26644 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
26558 GCCAAGGGAG
*
26568 AACACTCCGCTGCAGGTTTAGAGAAATCATCTAGCCAA
1 AACACTCCGCTACAGGTTTAGAGAAATCATCTAGCCAA
26606 AACACTCCGCTACAGGTTTAGAGAAATCATCTAGCCAA
1 AACACTCCGCTACAGGTTTAGAGAAATCATCTAGCCAA
26644 A
1 A
26645 GGCTGTCACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (38 bp):
AACACTCCGCTACAGGTTTAGAGAAATCATCTAGCCAA
Found at i:26798 original size:24 final size:25
Alignment explanation
Indices: 26764--26810 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
26754 TCAGTCACTT
26764 GAAAAAGGAAAATG-AGAAAAAATAA
1 GAAAAAGGAAAA-GAAGAAAAAATAA
26789 GAAAAA-GAAAAGAAGAAAAAAT
1 GAAAAAGGAAAAGAAGAAAAAAT
26811 GTTTGCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.05
24 14 0.67
25 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (25 bp):
GAAAAAGGAAAAGAAGAAAAAATAA
Found at i:30876 original size:21 final size:21
Alignment explanation
Indices: 30850--30920 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
30840 TACAAACCAT
*
30850 CACATATCTGCCAATAATGGC
1 CACATATTTGCCAATAATGGC
* *
30871 CACATAATTTTG-TAGATATATTGC
1 CACAT-A-TTTGCCA-ATA-ATGGC
*
30895 CACAAATTTGCCAATAATGGC
1 CACATATTTGCCAATAATGGC
30916 CACAT
1 CACAT
30921 TTTCTACCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
21 13 0.34
22 9 0.24
23 8 0.21
24 8 0.21
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (21 bp):
CACATATTTGCCAATAATGGC
Found at i:32314 original size:16 final size:16
Alignment explanation
Indices: 32293--32323 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32283 AATTAAACTA
32293 AATGCAAATGATCCTT
1 AATGCAAATGATCCTT
*
32309 AATGCAAATTATCCT
1 AATGCAAATGATCCT
32324 AAGTATGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (16 bp):
AATGCAAATGATCCTT
Found at i:37457 original size:18 final size:19
Alignment explanation
Indices: 37424--37459 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
37414 ACAAACAAAA
*
37424 AAATTAGAATACAAAAATT
1 AAATTAGAAAACAAAAATT
37443 AAATTA-AAAACAAAAAT
1 AAATTAGAAAACAAAAAT
37460 ATTAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (19 bp):
AAATTAGAAAACAAAAATT
Found at i:37477 original size:20 final size:19
Alignment explanation
Indices: 37431--37477 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
37421 AAAAAATTAG
* *
37431 AATACAAAAATTAAATTAA
1 AATAAAAAAATTAAAATAA
37450 AA-ACAAAAATATTAAAATAA
1 AATA-AAAAA-ATTAAAATAA
37470 AATAAAAA
1 AATAAAAA
37478 TGGCTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 1 0.04
19 6 0.26
20 15 0.65
21 1 0.04
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (19 bp):
AATAAAAAAATTAAAATAA
Found at i:41560 original size:16 final size:16
Alignment explanation
Indices: 41539--41595 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
41529 TCAATGCATG
41539 AACACAATGAAATGTA
1 AACACAATGAAATGTA
* *
41555 AACACAA-AAACATGCATG
1 AACACAATGAA-ATG--TA
41573 AACACAATGAAATGTA
1 AACACAATGAAATGTA
41589 AACACAA
1 AACACAA
41596 AAACATGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 2 0.06
16 18 0.55
18 11 0.33
19 2 0.06
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.14
Consensus pattern (16 bp):
AACACAATGAAATGTA
Found at i:41575 original size:34 final size:34
Alignment explanation
Indices: 41532--41610 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
41522 ATTGTCCTCA
41532 ATGCATGAACACAATGAAATGTAAACACAAAAAC
1 ATGCATGAACACAATGAAATGTAAACACAAAAAC
41566 ATGCATGAACACAATGAAATGTAAACACAAAAAC
1 ATGCATGAACACAATGAAATGTAAACACAAAAAC
41600 ATGCATGAACA
1 ATGCATGAACA
41611 AACAAACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (34 bp):
ATGCATGAACACAATGAAATGTAAACACAAAAAC
Found at i:41578 original size:18 final size:18
Alignment explanation
Indices: 41555--41610 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
41545 ATGAAATGTA
41555 AACACAAAAACATGCATG
1 AACACAAAAACATGCATG
* *
41573 AACACAATGAA-ATG--TA
1 AACACAA-AAACATGCATG
41589 AACACAAAAACATGCATG
1 AACACAAAAACATGCATG
41607 AACA
1 AACA
41611 AACAAACACA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 2 0.07
16 11 0.37
18 15 0.50
19 2 0.07
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.12
Consensus pattern (18 bp):
AACACAAAAACATGCATG
Found at i:53247 original size:20 final size:20
Alignment explanation
Indices: 53222--53339 Score: 155
Period size: 20 Copynumber: 5.9 Consensus size: 20
53212 GTATGCAAAT
*
53222 TTTGCACTTTGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* * *
53242 TTTGCACTTCGATGCCCTTA
1 TTTGCACTTCGGTGCCCCTG
* *
53262 TTTGCACTTCGGTGCCCTTA
1 TTTGCACTTCGGTGCCCCTG
53282 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* *
53302 CTTGCACTTCGATGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
*
53322 TTTGCACTTTGGTGCCCC
1 TTTGCACTTCGGTGCCCC
53340 AATTAATACA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.08, C:0.33, G:0.21, T:0.37
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:53315 original size:60 final size:60
Alignment explanation
Indices: 53222--53338 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
53212 GTATGCAAAT
* * *
53222 TTTGCACTTTGGTGCCCCTGTTTGCACTTCGATGCCCTTATTTGCACTTCGGTGCCCTTA
1 TTTGCACTTCGGTGCCCCTGCTTGCACTTCGATGCCCCTATTTGCACTTCGGTGCCCTTA
* *
53282 TTTGCACTTCGGTGCCCCTGCTTGCACTTCGATGCCCCTGTTTGCACTTTGGTGCCC
1 TTTGCACTTCGGTGCCCCTGCTTGCACTTCGATGCCCCTATTTGCACTTCGGTGCCC
53339 CAATTAATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.09, C:0.32, G:0.21, T:0.38
Consensus pattern (60 bp):
TTTGCACTTCGGTGCCCCTGCTTGCACTTCGATGCCCCTATTTGCACTTCGGTGCCCTTA
Found at i:53949 original size:71 final size:71
Alignment explanation
Indices: 53828--54052 Score: 254
Period size: 71 Copynumber: 3.2 Consensus size: 71
53818 TGAATTTTGA
* ** * *
53828 TACTAACTTGAGTTGTTTTGGAACAACTCTATGAAGTACCA-GTAGAAGTTCAGGGGAAAAGGTA
1 TACTAACTTGAGTTGTTTCGGAACAACTCTACAAAGTA-TAGGTAGAAGTTCAGGGGAAAAGATA
*
53892 TCTTGGC
65 ACTTGGC
* * *
53899 TACTGACTTGAGTTGTTTCGGATCAACTCTACAAAGTATAGGTAGAAGTTCAGGGGAAAAGATAC
1 TACTAACTTGAGTTGTTTCGGAACAACTCTACAAAGTATAGGTAGAAGTTCAGGGGAAAAGATAA
*
53964 CTTGGT
66 CTTGGC
* * * * * ** * *
53970 TACTAACTTAAGTTGTTTCGAAACAACTCAACAAAGTATCGATAGTTGTTTAGGAGAAAAGATAA
1 TACTAACTTGAGTTGTTTCGGAACAACTCTACAAAGTATAGGTAGAAGTTCAGGGGAAAAGATAA
54035 CTTGGC
66 CTTGGC
*
54041 TACTGACTTGAG
1 TACTAACTTGAG
54053 AGGTTTCAGT
Statistics
Matches: 129, Mismatches: 24, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
70 1 0.01
71 128 0.99
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (71 bp):
TACTAACTTGAGTTGTTTCGGAACAACTCTACAAAGTATAGGTAGAAGTTCAGGGGAAAAGATAA
CTTGGC
Found at i:55374 original size:27 final size:27
Alignment explanation
Indices: 55344--55432 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
55334 AATGGTATTC
* *
55344 ATGATGAACTCTGAAGGAACAATATGT
1 ATGATGAACTATGAAGAAACAATATGT
* *
55371 ATGATGAACTTTGAAGAAAAAATATGT
1 ATGATGAACTATGAAGAAACAATATGT
* * *
55398 ATGACGAACTATAAAGAAACAATATCT
1 ATGATGAACTATGAAGAAACAATATGT
55425 ATGATGAA
1 ATGATGAA
55433 TTTTAAAGGA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (27 bp):
ATGATGAACTATGAAGAAACAATATGT
Found at i:57764 original size:28 final size:29
Alignment explanation
Indices: 57718--57782 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
57708 ACTTTTTATT
* *
57718 ATTTTTAATATAATTTTATAATATTTAGA
1 ATTTTTAAGATAAATTTATAATATTTAGA
* *
57747 ATTTTTAAGA-AAATTTATAATTTTTATA
1 ATTTTTAAGATAAATTTATAATATTTAGA
57775 ATCTTTTA
1 AT-TTTTA
57783 CTTTTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTTAAGATAAATTTATAATATTTAGA
Found at i:57781 original size:10 final size:9
Alignment explanation
Indices: 57663--57782 Score: 53
Period size: 9 Copynumber: 12.6 Consensus size: 9
57653 TTTGTATATC
57663 TTTTATAAT
1 TTTTATAAT
57672 TTTTATAACT
1 TTTTATAA-T
**
57682 TTAAATAAT
1 TTTTATAAT
**
57691 TAATATAAT
1 TTTTATAAT
*
57700 TATATGT-TACT
1 T-T-T-TATAAT
*
57711 TTTTATTAT
1 TTTTATAAT
*
57720 TTTTAATATAA
1 TTTT-ATA-AT
57731 TTTTATAAT
1 TTTTATAAT
* *
57740 ATTTAGAAT
1 TTTTATAAT
* *
57749 TTTTAAGAAA
1 TTTT-ATAAT
*
57759 ATTTATAAT
1 TTTTATAAT
57768 TTTTATAAT
1 TTTTATAAT
57777 CTTTTA
1 -TTTTA
57783 CTTTTTTTTC
Statistics
Matches: 82, Mismatches: 20, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
8 1 0.01
9 46 0.56
10 25 0.30
11 9 0.11
12 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (9 bp):
TTTTATAAT
Found at i:59542 original size:11 final size:12
Alignment explanation
Indices: 59517--59546 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
59507 CTTTCTTTCG
59517 TTTTATTTCATT
1 TTTTATTTCATT
59529 TTTTATTTCATT
1 TTTTATTTCATT
59541 TTTTAT
1 TTTTAT
59547 GTCCTTTAAT
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:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTCATT
Found at i:64530 original size:12 final size:11
Alignment explanation
Indices: 64508--64542 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
64498 TTGTTATTGC
64508 ATTTTTCTTTT
1 ATTTTTCTTTT
64519 ATTTTTCATTTT
1 ATTTTTC-TTTT
64531 ATTTTTGCTTTT
1 ATTTTT-CTTTT
64543 GATGTGTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 14 0.64
13 1 0.05
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.77
Consensus pattern (11 bp):
ATTTTTCTTTT
Found at i:72426 original size:128 final size:128
Alignment explanation
Indices: 72276--72534 Score: 518
Period size: 128 Copynumber: 2.0 Consensus size: 128
72266 GCATAAATAC
72276 TTGGTCCTAAACGGATGGGAGACCTTTAATAGCTACTATTCGAACCATTCTTTTTAATCACTACT
1 TTGGTCCTAAACGGATGGGAGACCTTTAATAGCTACTATTCGAACCATTCTTTTTAATCACTACT
72341 ATAGCTGATTGTGGGCAGAACTACGTCAGATTCAAACCGAATTTCAATAAAATTTAAGTTTAA
66 ATAGCTGATTGTGGGCAGAACTACGTCAGATTCAAACCGAATTTCAATAAAATTTAAGTTTAA
72404 TTGGTCCTAAACGGATGGGAGACCTTTAATAGCTACTATTCGAACCATTCTTTTTAATCACTACT
1 TTGGTCCTAAACGGATGGGAGACCTTTAATAGCTACTATTCGAACCATTCTTTTTAATCACTACT
72469 ATAGCTGATTGTGGGCAGAACTACGTCAGATTCAAACCGAATTTCAATAAAATTTAAGTTTAA
66 ATAGCTGATTGTGGGCAGAACTACGTCAGATTCAAACCGAATTTCAATAAAATTTAAGTTTAA
72532 TTG
1 TTG
72535 CTAAATCCGA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 131 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (128 bp):
TTGGTCCTAAACGGATGGGAGACCTTTAATAGCTACTATTCGAACCATTCTTTTTAATCACTACT
ATAGCTGATTGTGGGCAGAACTACGTCAGATTCAAACCGAATTTCAATAAAATTTAAGTTTAA
Found at i:72873 original size:19 final size:19
Alignment explanation
Indices: 72833--72879 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
72823 TATAATATTT
* *
72833 AAATAATATTAAAAAAATA
1 AAATAATAATAAAAAAACA
*
72852 AAATAATAATAAAAACACA
1 AAATAATAATAAAAAAACA
*
72871 AAAAAATAA
1 AAATAATAA
72880 CATCCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATAATAATAAAAAAACA
Found at i:72913 original size:21 final size:21
Alignment explanation
Indices: 72851--72913 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
72841 TTAAAAAAAT
* * *
72851 AAAATAATAATAAAAACACAAA
1 AAAATAACAATCAAAACA-ACA
* *
72873 AAAATAAC-ATCCAAATAACA
1 AAAATAACAATCAAAACAACA
72893 AAAATAACAATCAAAACAACA
1 AAAATAACAATCAAAACAACA
72914 TTAAAAACAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 10 0.30
21 16 0.48
22 7 0.21
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (21 bp):
AAAATAACAATCAAAACAACA
Found at i:72973 original size:53 final size:53
Alignment explanation
Indices: 72851--72984 Score: 148
Period size: 53 Copynumber: 2.5 Consensus size: 53
72841 TTAAAAAAAT
* * *
72851 AAAATAATAATAAAAACACAAAAAAATAACATCCAAATAACAAAAATAACAATC
1 AAAACAATAATAAAAACACAAAAAAATAACA-CAAAATAACAAAAACAACAATC
* * *
72905 AAAACAACATTAAAAACAACAAAAATAATAACA-AAAAT-ACGAAAACAACAATC
1 AAAACAATAATAAAAAC-ACAAAAA-AATAACACAAAATAACAAAAACAACAATC
* *
72958 AAAACAATAAAAAAAAC-CAAAACAATA
1 AAAACAATAATAAAAACACAAAAAAATA
72985 TAAAACAACA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
50 4 0.06
51 5 0.07
53 27 0.40
54 18 0.26
55 7 0.10
56 7 0.10
ACGTcount: A:0.72, C:0.16, G:0.01, T:0.12
Consensus pattern (53 bp):
AAAACAATAATAAAAACACAAAAAAATAACACAAAATAACAAAAACAACAATC
Found at i:72998 original size:20 final size:19
Alignment explanation
Indices: 72946--72999 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 19
72936 CAAAAATACG
72946 AAAACAACAATCAAAACAATA
1 AAAACAAC-A-CAAAACAATA
*
72967 AAAAAAAC-CAAAACAATA
1 AAAACAACACAAAACAATA
72985 TAAAACAACACAAAA
1 -AAAACAACACAAAA
73000 ACAGCAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 10 0.34
19 7 0.24
20 5 0.17
21 7 0.24
ACGTcount: A:0.74, C:0.19, G:0.00, T:0.07
Consensus pattern (19 bp):
AAAACAACACAAAACAATA
Found at i:72999 original size:27 final size:26
Alignment explanation
Indices: 72966--73042 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 26
72956 TCAAAACAAT
72966 AAAAAAAACCAAAACAATATAAAACA
1 AAAAAAAACCAAAACAATATAAAACA
* *
72992 ACACAAAAACAGCAAAA-AATA-AAAATA
1 A-A-AAAAA-ACCAAAACAATATAAAACA
73019 AAAAAAATCACCAAAACAATATAA
1 AAAAAAA--ACCAAAACAATATAA
73043 TTTTTTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
25 5 0.12
26 9 0.21
27 11 0.26
28 11 0.26
29 6 0.14
ACGTcount: A:0.74, C:0.16, G:0.01, T:0.09
Consensus pattern (26 bp):
AAAAAAAACCAAAACAATATAAAACA
Found at i:76932 original size:15 final size:15
Alignment explanation
Indices: 76892--76921 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
76882 AATTATTAAT
*
76892 AAATATAATTTTTTA
1 AAATCTAATTTTTTA
76907 AAATCTAATTTTTTA
1 AAATCTAATTTTTTA
76922 TCATTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATCTAATTTTTTA
Found at i:81460 original size:22 final size:20
Alignment explanation
Indices: 81393--81469 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
81383 TTTTGATGTG
* * *
81393 TTAAAATGATTTTGACTTAG
1 TTAAAATCATTTTAACTTAT
* *
81413 TTGAAATCATTTTGACTTAT
1 TTAAAATCATTTTAACTTAT
81433 TTAAAATCATTTTAACTTGATT
1 TTAAAATCATTTTAACTT-A-T
*
81455 TTAAAATTATTTTAA
1 TTAAAATCATTTTAA
81470 AATTTTCTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 33 0.67
21 1 0.02
22 15 0.31
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.49
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTAT
Found at i:81473 original size:11 final size:11
Alignment explanation
Indices: 81432--81473 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
81422 TTTTGACTTA
*
81432 TTTAAAATCAT
1 TTTAAAATTAT
*
81443 TTT-AACTTGAT
1 TTTAAAATT-AT
81454 TTTAAAATTAT
1 TTTAAAATTAT
81465 TTTAAAATT
1 TTTAAAATT
81474 TTCTAAGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 3 0.12
11 19 0.73
12 4 0.15
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (11 bp):
TTTAAAATTAT
Found at i:83666 original size:20 final size:20
Alignment explanation
Indices: 83638--83692 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
83628 AACCCCCGTG
* **
83638 GTATCGATATTTTTATACGA
1 GTATTGATATTTTTATAAAA
83658 GTATTGATATTTTTATAAAA
1 GTATTGATATTTTTATAAAA
*
83678 GTATTGATAATTTTA
1 GTATTGATATTTTTA
83693 AATCGGTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (20 bp):
GTATTGATATTTTTATAAAA
Found at i:86384 original size:26 final size:26
Alignment explanation
Indices: 86351--86416 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
86341 TCATACGAGC
*
86351 CCAG-TCAGGATATCGCTATTACAAG
1 CCAGTTCAGTATATCGCTATTACAAG
* *
86376 CCAGTTCAGTATATCGCTCTTACGAG
1 CCAGTTCAGTATATCGCTATTACAAG
*
86402 CAAGTTCAGTATATC
1 CCAGTTCAGTATATC
86417 CTCAGAGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 4 0.11
26 32 0.89
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (26 bp):
CCAGTTCAGTATATCGCTATTACAAG
Found at i:86687 original size:47 final size:47
Alignment explanation
Indices: 86618--86714 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
86608 TGTCCTATTA
86618 TTCACAAAGTCCATATGTGTCATATACCATATCCATTTCAATTAACT
1 TTCACAAAGTCCATATGTGTCATATACCATATCCATTTCAATTAACT
*
86665 TTCACGAAGTCCATATGTGTCATATACCATATCCATTTCAATTAACT
1 TTCACAAAGTCCATATGTGTCATATACCATATCCATTTCAATTAACT
86712 TTC
1 TTC
86715 TTCACATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (47 bp):
TTCACAAAGTCCATATGTGTCATATACCATATCCATTTCAATTAACT
Found at i:98253 original size:21 final size:21
Alignment explanation
Indices: 98227--98268 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
98217 TTTTATGAAA
* *
98227 TTCTCTTACTTGTTTCGGTAG
1 TTCTCTTACTTATATCGGTAG
*
98248 TTCTCTTGCTTATATCGGTAG
1 TTCTCTTACTTATATCGGTAG
98269 AAGTTCCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50
Consensus pattern (21 bp):
TTCTCTTACTTATATCGGTAG
Found at i:119170 original size:2 final size:2
Alignment explanation
Indices: 119160--119195 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
119150 AAACGAAAAC
119160 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
119196 GTTAGCCCTC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:119938 original size:15 final size:15
Alignment explanation
Indices: 119918--119972 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
119908 TATCATAAAT
119918 TTTTTTAAATATTTA
1 TTTTTTAAATATTTA
*
119933 TTTTTT---TAATT-
1 TTTTTTAAATATTTA
119944 TTTTTTAAATATTTA
1 TTTTTTAAATATTTA
*
119959 TTTTTTTAATATTT
1 TTTTTTAAATATTT
119973 TACTATACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
14 4 0.12
15 19 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTAAATATTTA
Found at i:119946 original size:26 final size:26
Alignment explanation
Indices: 119917--119973 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
119907 TTATCATAAA
119917 TTTTTTTAAATATTTATTTTTTTAAT
1 TTTTTTTAAATATTTATTTTTTTAAT
119943 TTTTTTTAAATATTTATTTTTTTAAT
1 TTTTTTTAAATATTTATTTTTTTAAT
*
119969 ATTTT
1 TTTTT
119974 ACTATACTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTTTTAAATATTTATTTTTTTAAT
Found at i:120201 original size:31 final size:31
Alignment explanation
Indices: 120143--120203 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
120133 ACTGATCAGT
* * **
120143 CCAACCCATTGACATTTTGATGGTTTTCATC
1 CCAACCAATTGACATTTTAATAATTTTCATC
120174 CCAACCAATTGACATTTTAATAATTTTCAT
1 CCAACCAATTGACATTTTAATAATTTTCAT
120204 GAGACTCCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (31 bp):
CCAACCAATTGACATTTTAATAATTTTCATC
Found at i:124830 original size:16 final size:17
Alignment explanation
Indices: 124811--124855 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
124801 CGGGATTTCC
124811 TTCTTTTTCTCTCC-CT
1 TTCTTTTTCTCTCCTCT
*
124827 TTCTTTCTC-CTTCCTCT
1 TTCTTTTTCTC-TCCTCT
124844 TT-TTTTTCTCTC
1 TTCTTTTTCTCTC
124856 TTTTTCGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.04
16 18 0.75
17 5 0.21
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCTTTTTCTCTCCTCT
Found at i:128740 original size:26 final size:26
Alignment explanation
Indices: 128700--128751 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
128690 ATGAATTTGG
*
128700 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
128726 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
128752 TGGTTTAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:128928 original size:16 final size:16
Alignment explanation
Indices: 128907--129001 Score: 97
Period size: 16 Copynumber: 6.1 Consensus size: 16
128897 CGATTCATGA
128907 TTTAAGGTTTAAGGTT
1 TTTAAGGTTTAAGGTT
*
128923 TTTAAGGTTTAATGTT
1 TTTAAGGTTTAAGGTT
**
128939 TTT-AGGTTTTGGGTT
1 TTTAAGGTTTAAGGTT
**
128954 TTTTGGGTTTAAGGTT
1 TTTAAGGTTTAAGGTT
*
128970 TTTAGGGTATT-AGG-T
1 TTTAAGGT-TTAAGGTT
*
128985 TTTAAGGTTTAGGGTT
1 TTTAAGGTTTAAGGTT
129001 T
1 T
129002 AGGACTTAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
14 2 0.03
15 22 0.34
16 39 0.60
17 2 0.03
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (16 bp):
TTTAAGGTTTAAGGTT
Found at i:128946 original size:31 final size:30
Alignment explanation
Indices: 128911--129001 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 30
128901 TCATGATTTA
*
128911 AGGTTTAAGGTTTTTAAGGTTTAATGTTTTT
1 AGGTTT-AGGTTTTTAAGGTTTAAGGTTTTT
* **
128942 AGGTTTTGGGTTTTTTGGGTTTAAGGTTTTT
1 AGG-TTTAGGTTTTTAAGGTTTAAGGTTTTT
*
128973 AGGGTATTAGG-TTTTAAGGTTTAGGGTTT
1 A-GGT-TTAGGTTTTTAAGGTTTAAGGTTT
129002 AGGACTTAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
31 40 0.82
32 9 0.18
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.53
Consensus pattern (30 bp):
AGGTTTAGGTTTTTAAGGTTTAAGGTTTTT
Found at i:128963 original size:47 final size:47
Alignment explanation
Indices: 128912--129001 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
128902 CATGATTTAA
* * *
128912 GGTTTAAGGTTTTTAAGGT-TTAATGTTTTTAGGTTTTGGGTTTTTTG
1 GGTTTAAGGTTTTTAAGGTATT-AGGTTTTAAGGTTTAGGGTTTTTTG
*
128959 GGTTTAAGGTTTTTAGGGTATTAGGTTTTAAGGTTTAGGGTTT
1 GGTTTAAGGTTTTTAAGGTATTAGGTTTTAAGGTTTAGGGTTT
129002 AGGACTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
47 36 0.95
48 2 0.05
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (47 bp):
GGTTTAAGGTTTTTAAGGTATTAGGTTTTAAGGTTTAGGGTTTTTTG
Found at i:128987 original size:15 final size:14
Alignment explanation
Indices: 128938--129021 Score: 55
Period size: 15 Copynumber: 5.9 Consensus size: 14
128928 GGTTTAATGT
* *
128938 TTTTAGGTTTTGGG
1 TTTTAGGGTTTAGG
*
128952 TTTTTTGGGTTTAAGG
1 -TTTTAGGGTTT-AGG
128968 TTTTTAGGGTATTAGG
1 -TTTTAGGGT-TTAGG
*
128984 TTTTAAGGTTTAGG
1 TTTTAGGGTTTAGG
* **
128998 GTTTAGGACTTA-G
1 TTTTAGGGTTTAGG
129011 -TTTAGGGTTTA
1 TTTTAGGGTTTA
129022 ATTTATGCAC
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 13 0.23
15 17 0.30
16 14 0.25
17 2 0.04
ACGTcount: A:0.17, C:0.01, G:0.31, T:0.51
Consensus pattern (14 bp):
TTTTAGGGTTTAGG
Found at i:132073 original size:47 final size:47
Alignment explanation
Indices: 132014--132108 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
132004 TGATTTTTAT
* * *
132014 GATTTTTTACCAATATAATATCAAAAT-AATAATTATATGCCAAAATG
1 GATTATTTACCAAAATAATA-CAAAATAAATAATTATATACCAAAATG
*
132061 GATTATTTACCAAAATAATACAAAATAAATATTTATATACCAAAATG
1 GATTATTTACCAAAATAATACAAAATAAATAATTATATACCAAAATG
132108 G
1 G
132109 TATCCCCACC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 6 0.14
47 37 0.86
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (47 bp):
GATTATTTACCAAAATAATACAAAATAAATAATTATATACCAAAATG
Found at i:132237 original size:47 final size:47
Alignment explanation
Indices: 132151--132301 Score: 234
Period size: 47 Copynumber: 3.3 Consensus size: 47
132141 GAGATACCAA
132151 TTTAG-ATATAAATATTTA-TTTGTACCATTTTGGTAAATAACCCAT
1 TTTAGTATATAAATATTTATTTTGTACCATTTTGGTAAATAACCCAT
* *
132196 TTTAGTATATAAATATTTATTTTGAACCATTTTGATAAATAACCCAT
1 TTTAGTATATAAATATTTATTTTGTACCATTTTGGTAAATAACCCAT
* * *
132243 TTTGGTATATAAATATTTATTGTGTACCATTTTGGTAAATAACTCAT
1 TTTAGTATATAAATATTTATTTTGTACCATTTTGGTAAATAACCCAT
*
132290 TTTGGTATATAA
1 TTTAGTATATAA
132302 TTTATTATGT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
45 5 0.05
46 13 0.13
47 79 0.81
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (47 bp):
TTTAGTATATAAATATTTATTTTGTACCATTTTGGTAAATAACCCAT
Found at i:141228 original size:28 final size:28
Alignment explanation
Indices: 141146--141228 Score: 112
Period size: 28 Copynumber: 3.0 Consensus size: 28
141136 GTAAGCAGAC
* * *
141146 CAAAGCTCTACCCGAGCTATAAACAGGT
1 CAAAGCTCTACCTGAGCTATAAATAGAT
141174 CAAAGCTCTACCTGAGCTATAAATAGAT
1 CAAAGCTCTACCTGAGCTATAAATAGAT
* * *
141202 CAAAGCTTTACTTGAGCTATAATTAGA
1 CAAAGCTCTACCTGAGCTATAAATAGA
141229 GTATCGCTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (28 bp):
CAAAGCTCTACCTGAGCTATAAATAGAT
Found at i:149317 original size:18 final size:18
Alignment explanation
Indices: 149296--149357 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
149286 CTCCATAGAA
149296 TCTTCCTTAGGATCTTCT
1 TCTTCCTTAGGATCTTCT
* *
149314 TCTTCCTCAGGATCCTCT
1 TCTTCCTTAGGATCTTCT
*
149332 TCTTCTTCTTGAGGATTTTCT
1 TCTTC--CTT-AGGATCTTCT
149353 TCTTC
1 TCTTC
149358 TTCTTCTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.58
20 2 0.06
21 13 0.36
ACGTcount: A:0.10, C:0.29, G:0.11, T:0.50
Consensus pattern (18 bp):
TCTTCCTTAGGATCTTCT
Found at i:149361 original size:21 final size:21
Alignment explanation
Indices: 149308--149363 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
149298 TTCCTTAGGA
*
149308 TCTTCTTCTTCCTCAGGATCC
1 TCTTCTTCTTCTTCAGGATCC
* **
149329 TCTTCTTCTTCTTGAGGATTT
1 TCTTCTTCTTCTTCAGGATCC
149350 TCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
149364 TTCAGCTTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.07, C:0.30, G:0.09, T:0.54
Consensus pattern (21 bp):
TCTTCTTCTTCTTCAGGATCC
Found at i:150839 original size:15 final size:15
Alignment explanation
Indices: 150801--150839 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
150791 AATTTTGAAG
150801 AAATAAAAATAAATA
1 AAATAAAAATAAATA
*
150816 ACATAAAAATAAATA
1 AAATAAAAATAAATA
150831 AAATGAAAA
1 AAAT-AAAA
150840 CTTTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAAAATAAATA
Found at i:155022 original size:21 final size:21
Alignment explanation
Indices: 154996--155035 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
154986 AACATTCACC
*
154996 GGTTCTGGTGAAA-TTGGTTCT
1 GGTTCTAGT-AAAGTTGGTTCT
155017 GGTTCTAGTAAAGTTGGTT
1 GGTTCTAGTAAAGTTGGTT
155036 TTGATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.17, C:0.07, G:0.33, T:0.42
Consensus pattern (21 bp):
GGTTCTAGTAAAGTTGGTTCT
Found at i:157399 original size:15 final size:15
Alignment explanation
Indices: 157349--157399 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
157339 CATTATGCCC
157349 ATTTTATTTATTCATTT
1 ATTTT-TTTA-TCATTT
*
157366 A-TTTTTTATTATTTT
1 ATTTTTTTATCA-TTT
*
157381 ATTTTTTTATCATTG
1 ATTTTTTTATCATTT
157396 ATTT
1 ATTT
157400 AAATATGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 12 0.41
17 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (15 bp):
ATTTTTTTATCATTT
Found at i:157952 original size:109 final size:110
Alignment explanation
Indices: 157746--157945 Score: 296
Period size: 109 Copynumber: 1.8 Consensus size: 110
157736 GGCAATGTAA
* ** *
157746 TTTTATTTTAGGGGACTCGAGAAATTATGTCCTAACGTGTTGTGTATGATTTTTTTCTTTGAACC
1 TTTTATTTTAGGGAACTCGAGAAATTATGTCCTAACGTACTGGGTATGA-TTTTTTCTTTGAACC
*
157811 TAAGTAATTGGATATCCTATTTAAAACTGATAAATATTCAATGTTC
65 TAAGTAATTGAATATCCTATTTAAAACTGATAAATATTCAATGTTC
* * *
157857 TTTTATTTTAGGGAACTTGATAAATTGTG-CCTTAACGTACTGGGTATGA-TTTTTCTTTGAACC
1 TTTTATTTTAGGGAACTCGAGAAATTATGTCC-TAACGTACTGGGTATGATTTTTTCTTTGAACC
157920 TAAGTAATTGAATATCCTATTTAAAA
65 TAAGTAATTGAATATCCTATTTAAAA
157946 TCGATAAGTG
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
109 39 0.49
110 2 0.03
111 39 0.49
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (110 bp):
TTTTATTTTAGGGAACTCGAGAAATTATGTCCTAACGTACTGGGTATGATTTTTTCTTTGAACCT
AAGTAATTGAATATCCTATTTAAAACTGATAAATATTCAATGTTC
Found at i:160704 original size:27 final size:27
Alignment explanation
Indices: 160674--160729 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
160664 GATTTTGAAG
* *
160674 ATAACTAAGAAGGTAAGTTGCCTCTGA
1 ATAACCAAGAAGGTAACTTGCCTCTGA
*
160701 ATAACCAAGAATGTAACTTGCCTCTGA
1 ATAACCAAGAAGGTAACTTGCCTCTGA
160728 AT
1 AT
160730 CTACTATGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (27 bp):
ATAACCAAGAAGGTAACTTGCCTCTGA
Found at i:162096 original size:8 final size:9
Alignment explanation
Indices: 162082--162125 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
162072 TTCACCCCAA
162082 AAAAAAAAG
1 AAAAAAAAG
*
162091 -AAAAAAGG
1 AAAAAAAAG
162099 AAAAAAGAAG
1 AAAAAA-AAG
162109 ATAAAAAAAG
1 A-AAAAAAAG
162119 AAAAAAA
1 AAAAAAA
162126 TGAGAGGTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 7 0.23
9 11 0.37
10 7 0.23
11 5 0.17
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:163111 original size:48 final size:48
Alignment explanation
Indices: 163050--163281 Score: 184
Period size: 48 Copynumber: 4.8 Consensus size: 48
163040 AACATTGGCG
* * * *
163050 AATCTTTATCTCCCTGAAGTTGTAGTGAAGCGGATTAAACTAATAGCA
1 AATCTTTATCTTCCTGAAGTTGCAGTGAAGCAGATTAAACTAATACCA
* * * * * * *
163098 AATCTTTATCTCCCTGTAGTTGTAGTGGAGCAAGA-TGAACTCACACCA
1 AATCTTTATCTTCCTGAAGTTGCAGTGAAGC-AGATTAAACTAATACCA
** * * * *
163146 AAT-TCAATCTTCTTAAAGTTGCAGTGAAGCAGATTAAAAC-AGTAGCA
1 AATCTTTATCTTCCTGAAGTTGCAGTGAAGCAGATT-AAACTAATACCA
* * *
163193 AATCTTTATCTTCCTGAAGTTGCAGTGGAGCAAGATAAAACTACAAATCCA
1 AATCTTTATCTTCCTGAAGTTGCAGTGAAGC-AGATTAAACTA-ATA-CCA
* * *
163244 AATC-CTATCTTCCTGAAGTTACAGTGAAGCGGATTAAA
1 AATCTTTATCTTCCTGAAGTTGCAGTGAAGCAGATTAAA
163282 ATTATTGTAG
Statistics
Matches: 142, Mismatches: 34, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
46 3 0.02
47 26 0.18
48 70 0.49
49 13 0.09
50 24 0.17
51 6 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (48 bp):
AATCTTTATCTTCCTGAAGTTGCAGTGAAGCAGATTAAACTAATACCA
Found at i:163282 original size:98 final size:96
Alignment explanation
Indices: 163056--163322 Score: 295
Period size: 95 Copynumber: 2.8 Consensus size: 96
163046 GGCGAATCTT
* * *
163056 TATCTCCCTGAAGTTGTAGTGAAGCGGATT-AAACTAATAGCAAATCTTTATCTCCCTGTAGTTG
1 TATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACTAATAGCAAATCTTTATCTCCCTGAAGTTG
* * * *
163120 TAGTGGAGCAAGATGAACTCACACCAAATTC
66 CAGTGGAGCAAGATAAACTCAAACCAAATCC
* * * * * *
163151 AATCTTCTTAAAGTTGCAGTGAAGCAGATTAAAAC-AGTAGCAAATCTTTATCTTCCTGAAGTTG
1 TATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACTAATAGCAAATCTTTATCTCCCTGAAGTTG
163215 CAGTGGAGCAAGATAAAACTACAAATCCAAATCC
66 CAGTGGAGCAAGAT-AAACT-CAAA-CCAAATCC
* * * ** **
163249 TATCTTCCTGAAGTTACAGTGAAGCGGATTAAAATTATTGTAGCGGATCTCAATCTCCCTGAAGT
1 TATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACTA--ATAGCAAATCTTTATCTCCCTGAAGT
163314 TGCAGTGGA
64 TGCAGTGGA
163323 ATAGAGTGAA
Statistics
Matches: 141, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
95 63 0.45
96 8 0.06
97 3 0.02
98 36 0.26
99 1 0.01
101 30 0.21
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (96 bp):
TATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACTAATAGCAAATCTTTATCTCCCTGAAGTTG
CAGTGGAGCAAGATAAACTCAAACCAAATCC
Found at i:163514 original size:42 final size:42
Alignment explanation
Indices: 163383--163919 Score: 346
Period size: 39 Copynumber: 13.1 Consensus size: 42
163373 AAAATTGAAG
* * *
163383 CCATCTAATCTTTTACCCTAACCAGAGGGAAGATAT-AAGCCA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAGAT-TGAAGACA
* * * *
163425 -CATCCAATCTCTTATCCC-GACCATG-TGGTAGATTGAAG---
1 CCATCCAATCTTTTA-CCCTAACCA-GAGGGCAGATTGAAGACA
* *
163463 TCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGAAGACA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
* * *
163505 CCATCCAATCTCTTACCTTGACCATG-GGGCAGATTG-A-A-A
1 CCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACA
*
163544 CCATTCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
* * **
163586 CCATCCAATGTCTTACCCCGACCATG-GGGCAGATTGAAG---
1 CCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACA
* * *
163625 CCATCCAATCTATTACCCTAACTAGATGGCAGATTGAAGACA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
* ** * * * *
163667 CCATCCAATCTCTTACCCCGATC-GTGGGGCAAATT-AA-A-G
1 CCATCCAATCTTTTACCCTAACCAG-AGGGCAGATTGAAGACA
* *
163706 CCATCCAATCTTTTACCCTAACCAGAGGGTAGATTGAAGCCA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
* *
163748 CCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCA
1 CCATCCAATCTTTTA-CCCTAA--CCAGA-GGGCAGATTGAAGACA
*
163794 CCATCCAATC--TTA---T-------GGGCAGATTGAAGCCA
1 CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
* * * *
163824 CCATCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTAAAGCCA
1 CCATCCAATCTTTTA-CCCTAA-CCAGA-GGGCAGATTGAAGACA
* *
163869 CTATCCAATCTTTTACCTCTAAATCAAGAGGGGCAGATTGAAG-CTA
1 CCATCCAATCTTTTACC-CT-AA-CCAGA-GGGCAGATTGAAGAC-A
163915 CCATC
1 CCATC
163920 TCATAGAAGC
Statistics
Matches: 393, Mismatches: 56, Indels: 88
0.73 0.10 0.16
Matches are distributed among these distances:
30 26 0.07
32 3 0.01
36 1 0.00
38 6 0.02
39 115 0.29
40 8 0.02
41 30 0.08
42 106 0.27
43 8 0.02
44 5 0.01
45 35 0.09
46 50 0.13
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
CCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACA
Found at i:163542 original size:81 final size:81
Alignment explanation
Indices: 163344--163766 Score: 580
Period size: 81 Copynumber: 5.2 Consensus size: 81
163334 TTACATCATC
** * * *
163344 CCATCCAATCTCTTACAACGACCATGGGGAAAATTGAAGCCATCTAATCTTTTACCCTAACCAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
* *
163409 GGGAAGATAT-AAGCCA
66 GGGCAGAT-TGAAGACA
* * * * *
163425 -CATCCAATCTCTTATCCCGACCATGTGGTAGATTGAAGTCATCCAATCTTTTACCCTAACTAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
163489 GGGCAGATTGAAGACA
66 GGGCAGATTGAAGACA
** * *
163505 CCATCCAATCTCTTACCTTGACCATGGGGCAGATTGAAACCATTCAATCTTTTACCCTAACCAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
163570 GGGCAGATTGAAGACA
66 GGGCAGATTGAAGACA
* * *
163586 CCATCCAATGTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTATTACCCTAACTAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
*
163651 TGGCAGATTGAAGACA
66 GGGCAGATTGAAGACA
* * * *
163667 CCATCCAATCTCTTACCCCGATCGTGGGGCAAATTAAAGCCATCCAATCTTTTACCCTAACCAGA
1 CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
* *
163732 GGGTAGATTGAAGCCA
66 GGGCAGATTGAAGACA
*
163748 CCATCCAATCTTTTACCCC
1 CCATCCAATCTCTTACCCC
163767 TAAGTCAAGA
Statistics
Matches: 301, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
79 1 0.00
80 67 0.22
81 233 0.77
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (81 bp):
CCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACCAGA
GGGCAGATTGAAGACA
Found at i:163814 original size:30 final size:30
Alignment explanation
Indices: 163778--163835 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
163768 AAGTCAAGAG
163778 GGGCAGATTGAAGCCACCATCCAATCTTAT
1 GGGCAGATTGAAGCCACCATCCAATCTTAT
163808 GGGCAGATTGAAGCCACCATCCAATCTT
1 GGGCAGATTGAAGCCACCATCCAATCTT
163836 TTACCCCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (30 bp):
GGGCAGATTGAAGCCACCATCCAATCTTAT
Found at i:163831 original size:76 final size:75
Alignment explanation
Indices: 163736--163880 Score: 254
Period size: 76 Copynumber: 1.9 Consensus size: 75
163726 ACCAGAGGGT
* *
163736 AGATTGAAGCCACCATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCCACCATCCA
1 AGATTGAAGCCACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAAATTAAAGCCACCATCCA
163801 ATCTTATGGGC
65 ATCTTATGGGC
*
163812 AGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTAAAGCCACTATCCAA
1 AGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTAAAGCCACCATCCAA
163877 TCTT
66 TCTT
163881 TTACCTCTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
75 32 0.48
76 34 0.52
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (75 bp):
AGATTGAAGCCACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAAATTAAAGCCACCATCCAA
TCTTATGGGC
Found at i:163875 original size:45 final size:46
Alignment explanation
Indices: 163808--163919 Score: 172
Period size: 45 Copynumber: 2.5 Consensus size: 46
163798 CCAATCTTAT
163808 GGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT-AATCAAGAG
1 GGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCAAGAG
* * * *
163853 GGGCAAATTAAAGCCACTATCCAATCTTTTACCTCTAAATCAAGAG
1 GGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCAAGAG
*
163899 GGGCAGATTGAAGCTACCATC
1 GGGCAGATTGAAGCCACCATC
163920 TCATAGAAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
45 32 0.55
46 26 0.45
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (46 bp):
GGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAATCAAGAG
Found at i:165918 original size:109 final size:110
Alignment explanation
Indices: 165713--165924 Score: 313
Period size: 109 Copynumber: 1.9 Consensus size: 110
165703 ACGATGTTTT
* * *
165713 TTTTATTTTAGGAGACTCGAGGAATTGTGCCCTAACATGCTGGGTATGATTTTTTCTTTGAATCT
1 TTTTATTTTAGGAGACTCGAGAAATTGTGCCCTAACATACTGGGTATGATTTTTTCTTTGAACCT
*
165778 AAGTAATTAGATATCCTATTTAAAATTGATAAATGTTCAATGTTC
66 AAGTAATTAGATATCCTATTTAAAATCGATAAATGTTCAATGTTC
* * *
165823 TTTTATTTTAGG-GAACTCGAGAAATTTTGTCCTAACGTACTGGGTATGA-TTTTTCTTTGAACC
1 TTTTATTTTAGGAG-ACTCGAGAAATTGTGCCCTAACATACTGGGTATGATTTTTTCTTTGAACC
*
165886 TAAGTAATT-GAATATCCTATTTAAAATCGATAAGTGTTC
65 TAAGTAATTAG-ATATCCTATTTAAAATCGATAAATGTTC
165925 TTTATTTTCG
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
108 1 0.01
109 49 0.53
110 42 0.46
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (110 bp):
TTTTATTTTAGGAGACTCGAGAAATTGTGCCCTAACATACTGGGTATGATTTTTTCTTTGAACCT
AAGTAATTAGATATCCTATTTAAAATCGATAAATGTTCAATGTTC
Found at i:168181 original size:26 final size:26
Alignment explanation
Indices: 168144--168197 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
168134 ATTCTGGGTG
* *
168144 CAATTCTGGACACGTTCATGCAGCGA
1 CAATTCTAGACACGTTCATGCAGAGA
*
168170 CAATTCTAGACATGTTCATGCAGAGA
1 CAATTCTAGACACGTTCATGCAGAGA
168196 CA
1 CA
168198 TTCCTGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (26 bp):
CAATTCTAGACACGTTCATGCAGAGA
Found at i:168228 original size:37 final size:38
Alignment explanation
Indices: 168201--168274 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
168191 AGAGACATTC
* *
168201 CTGGGTGCAA-TTGAAGAATACTTATGCAATGATAGTT
1 CTGGATGCAATTTGAAGAATACTTATGCAATGACAGTT
* * *
168238 CTGGATGCAATTTGAAGAATATTTATGTAGTGACAGT
1 CTGGATGCAATTTGAAGAATACTTATGCAATGACAGT
168275 CTTGGGCGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 9 0.29
38 22 0.71
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.34
Consensus pattern (38 bp):
CTGGATGCAATTTGAAGAATACTTATGCAATGACAGTT
Found at i:171747 original size:16 final size:16
Alignment explanation
Indices: 171726--171756 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
171716 ATAATCTGAA
171726 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
171742 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
171757 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:172585 original size:26 final size:26
Alignment explanation
Indices: 172556--172608 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
172546 TTCTAGGTGA
*
172556 AATTATGTACATGTTCATGCAGCGAC
1 AATTATGGACATGTTCATGCAGCGAC
* *
172582 AATTCTGGACATGTTCATGTAGCGAC
1 AATTATGGACATGTTCATGCAGCGAC
172608 A
1 A
172609 TTCCTGGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (26 bp):
AATTATGGACATGTTCATGCAGCGAC
Found at i:172794 original size:37 final size:37
Alignment explanation
Indices: 172712--172795 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 37
172702 AAAATATTCT
* * * *
172712 TGCAGTGACAGTTTTGGGTGCAATTTGGAAGTGCTCA
1 TGCAGCGACAATTTTGGGCGCAATTTAGAAGTGCTCA
**
172749 TGTGGCGACAATTTTGGGCGCAATTTAGAAGTGCTCA
1 TGCAGCGACAATTTTGGGCGCAATTTAGAAGTGCTCA
172786 TGCAGCGACA
1 TGCAGCGACA
172796 TTAGTAGTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (37 bp):
TGCAGCGACAATTTTGGGCGCAATTTAGAAGTGCTCA
Found at i:176800 original size:28 final size:28
Alignment explanation
Indices: 176760--176816 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
176750 TACAGTCATC
* * *
176760 AATAGGTCAAAGCTCTACCCGAGCTATA
1 AATAGATCAAAGCGCTACCCGAACTATA
*
176788 AATAGATCAAAGCGCTACCCTAACTATA
1 AATAGATCAAAGCGCTACCCGAACTATA
176816 A
1 A
176817 GCAGAGTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (28 bp):
AATAGATCAAAGCGCTACCCGAACTATA
Found at i:178697 original size:22 final size:23
Alignment explanation
Indices: 178669--178720 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
178659 ACAATGGCAG
*
178669 AAGGAAAGTGTTTCAACTGC-GA
1 AAGGAAAGTGTTCCAACTGCTGA
178691 AAGGAAAGTGTTCCAACTGCTGA
1 AAGGAAAGTGTTCCAACTGCTGA
178714 AA-GAAAG
1 AAGGAAAG
178721 GTCACATGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.19
Consensus pattern (23 bp):
AAGGAAAGTGTTCCAACTGCTGA
Found at i:179385 original size:11 final size:11
Alignment explanation
Indices: 179369--179393 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
179359 TATTTTTGAA
179369 AAATCTTTTAT
1 AAATCTTTTAT
179380 AAATCTTTTAT
1 AAATCTTTTAT
179391 AAA
1 AAA
179394 AACCAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATCTTTTAT
Found at i:181545 original size:26 final size:26
Alignment explanation
Indices: 181425--181700 Score: 175
Period size: 26 Copynumber: 10.9 Consensus size: 26
181415 AATAAATTTA
* * *
181425 GCTCATACGAGCCCAGT-TAGTAAATC
1 GCTCTTACGAG-CCAGTACAGTATATC
181451 GCTCTTACGAGCCAGTACAGTATATC
1 GCTCTTACGAGCCAGTACAGTATATC
*
181477 GCTCTTACGAGCCAGTTCAGTATATC
1 GCTCTTACGAGCCAGTACAGTATATC
* * * * *
181503 GCTCTTCCGATCTAGTACAATTTATC
1 GCTCTTACGAGCCAGTACAGTATATC
* *
181529 GCTCTTTCGAGCCAGTACAGTATCTTC
1 GCTCTTACGAGCCAGTACAGTAT-ATC
* *
181556 AAG-TCTCT-C-A---A-TA-A--ATTTA
1 --GCTCT-TACGAGCCAGTACAGTATATC
* *
181575 GCTC-AACGAGCCCAGT-CAGTAAATC
1 GCTCTTACGAG-CCAGTACAGTATATC
* *
181600 GCTCTTACGAGCTAGTATAGTATATC
1 GCTCTTACGAGCCAGTACAGTATATC
* * *
181626 ACTCTTACGAGCCAGTTCAGTATATT
1 GCTCTTACGAGCCAGTACAGTATATC
* *
181652 GCTCTTCCGAGCCAGTACAGTTTATC
1 GCTCTTACGAGCCAGTACAGTATATC
* *
181678 ACTCTT-CTAAGCCAGTACAGTAT
1 GCTCTTAC-GAGCCAGTACAGTAT
181701 CTTTAAGTCT
Statistics
Matches: 193, Mismatches: 38, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
17 2 0.01
18 3 0.02
19 2 0.01
20 2 0.01
22 2 0.01
23 4 0.02
24 1 0.01
25 16 0.08
26 152 0.79
27 3 0.02
28 4 0.02
29 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (26 bp):
GCTCTTACGAGCCAGTACAGTATATC
Found at i:181676 original size:149 final size:149
Alignment explanation
Indices: 181401--181771 Score: 557
Period size: 149 Copynumber: 2.5 Consensus size: 149
181391 CCAAACGATC
* *
181401 TCTTCAAGACTCCTAATAAATTTAGCTCATACGAGCCCAGTTAGTAAATCGCTCTTACGAGCCAG
1 TCTTCAAGTCTCC-AATAAATTTAGCTCATACGAGCCCAGTAAGTAAATCGCTCTTACGAGCCAG
* * * *
181466 TACAGTATATCGCTCTTACGAGCCAGTTCAGTATATCGCTCTTCCGATCTAGTACAATTTATCGC
65 TACAGTATATCACTCTTACGAGCCAGTTCAGTATATCGCTCTTCCGAGCCAGTACAATTTATCAC
*
181531 TCTT-TCGAGCCAGTACAGTA
130 TCTTCT-AAGCCAGTACAGTA
* *
181551 TCTTCAAGTCTCTCAATAAATTTAGCTCA-ACGAGCCCAGTCAGTAAATCGCTCTTACGAGCTAG
1 TCTTCAAGTCTC-CAATAAATTTAGCTCATACGAGCCCAGTAAGTAAATCGCTCTTACGAGCCAG
* * *
181615 TATAGTATATCACTCTTACGAGCCAGTTCAGTATATTGCTCTTCCGAGCCAGTACAGTTTATCAC
65 TACAGTATATCACTCTTACGAGCCAGTTCAGTATATCGCTCTTCCGAGCCAGTACAATTTATCAC
181680 TCTTCTAAGCCAGTACAGTA
130 TCTTCTAAGCCAGTACAGTA
* * *
181700 TCTTTAAGTCTCCCAGTAAATTTAGCTCATACGAGCCCAATAAGTAAATCGCTCTTACGAGCCAG
1 TCTTCAAGTCT-CCAATAAATTTAGCTCATACGAGCCCAGTAAGTAAATCGCTCTTACGAGCCAG
181765 TACAGTA
65 TACAGTA
181772 ATTCCTCAGA
Statistics
Matches: 200, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
149 133 0.67
150 66 0.33
151 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (149 bp):
TCTTCAAGTCTCCAATAAATTTAGCTCATACGAGCCCAGTAAGTAAATCGCTCTTACGAGCCAGT
ACAGTATATCACTCTTACGAGCCAGTTCAGTATATCGCTCTTCCGAGCCAGTACAATTTATCACT
CTTCTAAGCCAGTACAGTA
Found at i:203911 original size:24 final size:24
Alignment explanation
Indices: 203884--204006 Score: 75
Period size: 24 Copynumber: 5.1 Consensus size: 24
203874 TTTCAGAAAT
*
203884 TTAGCTAAAACGAGCCTAGAATGG
1 TTAGCTAAAACGAGCCCAGAATGG
***
203908 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTAAAACGAGCCCAGAATGG
*** ** *
203932 TTAGCTCTTATTAACCCAGAATGG
1 TTAGCTAAAACGAGCCCAGAATGG
* *** *
203956 TTAACTCTTACGAGCCTAGAATGG
1 TTAGCTAAAACGAGCCCAGAATGG
* ***
203980 TTAGTTCTTACGAGCCCAGAATGG
1 TTAGCTAAAACGAGCCCAGAATGG
204004 TTA
1 TTA
204007 ACTAGTATAC
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
TTAGCTAAAACGAGCCCAGAATGG
Found at i:203953 original size:48 final size:48
Alignment explanation
Indices: 203901--204009 Score: 164
Period size: 48 Copynumber: 2.3 Consensus size: 48
203891 AAACGAGCCT
* **
203901 AGAATGGTTAGCTCTTACGAGCCCAGAATGGTTAGCTCTTATTAACCC
1 AGAATGGTTAACTCTTACGAGCCCAGAATGGTTAGCTCTTACGAACCC
* * *
203949 AGAATGGTTAACTCTTACGAGCCTAGAATGGTTAGTTCTTACGAGCCC
1 AGAATGGTTAACTCTTACGAGCCCAGAATGGTTAGCTCTTACGAACCC
203997 AGAATGGTTAACT
1 AGAATGGTTAACT
204010 AGTATACGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (48 bp):
AGAATGGTTAACTCTTACGAGCCCAGAATGGTTAGCTCTTACGAACCC
Found at i:207031 original size:15 final size:17
Alignment explanation
Indices: 206999--207057 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 17
206989 TGTGGTTAAT
206999 GAAGAAGAAGAGAAAAGA
1 GAAGAAGAAGAG-AAAGA
207017 GAAGAAGAAG-G-AAGA
1 GAAGAAGAAGAGAAAGA
* *
207032 GAAG-ACAAG-GAAAAA
1 GAAGAAGAAGAGAAAGA
*
207047 GAAAAAGAAGA
1 GAAGAAGAAGA
207058 AGAAGTTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 5 0.15
15 14 0.41
16 4 0.12
17 1 0.03
18 10 0.29
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAGAGAAAGA
Found at i:207061 original size:12 final size:12
Alignment explanation
Indices: 207003--207061 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
206993 GTTAATGAAG
207003 AAGAAG-AGAAA
1 AAGAAGAAGAAA
*
207014 AGAGAAGAAGAAGG
1 A-AGAAGAAGAA-A
*
207028 AAG-AGAAGACA
1 AAGAAGAAGAAA
* *
207039 AGGAAAAAGAAA
1 AAGAAGAAGAAA
207051 AAGAAGAAGAA
1 AAGAAGAAGAA
207062 GTTGTTCTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
11 3 0.08
12 26 0.72
13 6 0.17
14 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.31, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:207987 original size:2 final size:2
Alignment explanation
Indices: 207975--208011 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
207965 CCTCAGTCGC
207975 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
208012 ATAAATGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:223900 original size:7 final size:7
Alignment explanation
Indices: 223882--223913 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
223872 TTTATTAACA
223882 TAAAAAT
1 TAAAAAT
223889 T-AAAAT
1 TAAAAAT
223895 TAAAAAT
1 TAAAAAT
223902 TAAAAAT
1 TAAAAAT
223909 TAAAA
1 TAAAA
223914 GAAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAAAT
Found at i:232576 original size:24 final size:27
Alignment explanation
Indices: 232544--232600 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
232534 TGTGAGAGAT
232544 ATTAATCTAAG-T-AA-TCAAAACTAA
1 ATTAATCTAAGTTAAATTCAAAACTAA
*
232568 ATTAATCTAAGTTAAATTTAAAACTAA
1 ATTAATCTAAGTTAAATTCAAAACTAA
232595 ATTAAT
1 ATTAAT
232601 ATTCCTATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 11 0.38
25 1 0.03
26 2 0.07
27 15 0.52
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (27 bp):
ATTAATCTAAGTTAAATTCAAAACTAA
Found at i:233227 original size:17 final size:18
Alignment explanation
Indices: 233205--233241 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
233195 GGCCTATAAC
*
233205 AATATGAACATG-AATTA
1 AATATGAACAAGCAATTA
233222 AATATGAACAAGCAATTA
1 AATATGAACAAGCAATTA
233240 AA
1 AA
233242 CACAATCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.08, G:0.11, T:0.24
Consensus pattern (18 bp):
AATATGAACAAGCAATTA
Found at i:236091 original size:3 final size:3
Alignment explanation
Indices: 236083--236114 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
236073 TTTCACAGGA
236083 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
236115 AGCTTGTTGT
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:237706 original size:19 final size:18
Alignment explanation
Indices: 237682--237718 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
237672 AATTTTTGAA
237682 AAATAAATATCATAAAAAT
1 AAATAAATA-CATAAAAAT
*
237701 AAATAAATACATGAAAAT
1 AAATAAATACATAAAAAT
237719 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATAAATACATAAAAAT
Found at i:245873 original size:551 final size:550
Alignment explanation
Indices: 244830--245932 Score: 1589
Period size: 551 Copynumber: 2.0 Consensus size: 550
244820 TAAATTAGAG
* * * * *
244830 CTCAAGGTATTACCTTGACTTTTAAAATATGTTTATTTTGGTGACGCTTTTACTTTGCATGTGAT
1 CTCAAGGTACTACCTTGACATTTAAAATATGTTTATTTAGGTGACGCTTCTACTTTGCATATGAT
* * * * *
244895 TATTTCACCACAACTAACTGAGAAGCAGGAAGACCGATTGATTAAAGTGCTGAAGCAATTTACGA
66 TATTTCACCACAACTAACTGAGAAGCAAGAAGACCAATTGATTAAAGTGCTGAAACAATTCAAGA
* *
244960 AGGCTAATGGATGGACATAGCTAACATTCGTGGTATAAGTCCATCCGTATGCATGCACAAGATCA
131 AAGCTAATGGATGGACATAGCTAACATTCGTGGTATAAGTCCATCCGTACGCATGCACAAGATCA
* * * * * * *
245025 TCCTTTAAGATGATAAGAAAGCATCAATTTATGGAAAATGGAGACTAAACCCCATTATGAAGGAT
196 ACCTTGAAGATGACAAGAAAGCAACAATTGACGGAAAATGAAGACTAAACCCCATTATGAAGGAT
*
245090 GTAGTCAAGAAGGAAATTATCAAGTGGTTAGATGCGGGTATAATCTATCCCATCTTAAACAGTTC
261 GTAGTCAAGAAGGAAATTATCAAGTGGTTAGATGCGGGTATAATCTATCCCATCTCAAACAGTTC
* * * *
245155 ATGGGTTAGTCCTGTCCAATGCGTGCCAAAGAAAGGAGGTATTATGGTCGTAAAGAATGAAAACA
326 ATGGGTTAGTCCTGTCCAATACATGCCAAACAAAGGAGGTATTACGGTCGTAAAGAATGAAAACA
* * * *
245220 ACGAGTTAATATCGACTAGAATAGTTACGGGATGGCGAATTTGTATCGACTACCGAAAATTGAAC
391 ACGAGTTAATACCGACTAGAATAGTTACGGGATGGCAAATTTGCATCAACTACCGAAAATTGAAC
* * * ** *
245285 AAAGCGAATAGGAAACATCACTTTCCTTTATCGTTCTTGGATCAGATGCTGGATAGACTTGTAGG
456 AAAGCGAATAGGAAACATAACTTTCCTTTACCGTTCTTGGATCAGATGCTAGATAGACTCATAAG
*
245350 GTGAGACTATTACTATTTTCTAGACGGGTA
521 GCGAGACTATTACTATTTTCTAGACGGGTA
* * *
245380 CTCAAGGTACTACCTTCG-CATTTGAAATATGTTTATTTAGGTGACTCTTCTACTTTGCCTATGA
1 CTCAAGGTACTACCTT-GACATTTAAAATATGTTTATTTAGGTGACGCTTCTACTTTGCATATGA
* * * * *
245444 TTATTTTAGCACAATTAACTGAGAAGCAAGAAGACCAATTTATTAAAGTGTTGAAACAATTCAAG
65 TTATTTCACCACAACTAACTGAGAAGCAAGAAGACCAATTGATTAAAGTGCTGAAACAATTCAAG
* * * *
245509 AAAGCTATTGGATGGGCCATAGTTAACATTTGTGGTATAAGTCCATCCGTACGCATGCACAAGAT
130 AAAGCTAATGGAT-GGACATAGCTAACATTCGTGGTATAAGTCCATCCGTACGCATGCACAAGAT
* * ** *
245574 CAACCTTGAAGATGACAAGAAAGCAACAATTGACGGACAATGAAGACTGAACCCTGTTGTGAAGG
194 CAACCTTGAAGATGACAAGAAAGCAACAATTGACGGAAAATGAAGACTAAACCCCATTATGAAGG
* *
245639 ATGTAGTCAAGAA-GACAATTATCAAGTGGTTAGATGTGGGTATAATCTATCCCATCTCAGACAG
259 ATGTAGTCAAGAAGGA-AATTATCAAGTGGTTAGATGCGGGTATAATCTATCCCATCTCAAACAG
* * *
245703 TTCATGGGTTAGTCCTGTCTAGTACATGCCAAACAAAGGAGGTATTACGGTTGTAAAGAATGAAA
323 TTCATGGGTTAGTCCTGTCCAATACATGCCAAACAAAGGAGGTATTACGGTCGTAAAGAATGAAA
* *
245768 ACAACGATTTAATACCGACTAGAATGGTTACGGGATGGCAAATTTGCATCAACTACCGAAAATTG
388 ACAACGAGTTAATACCGACTAGAATAGTTACGGGATGGCAAATTTGCATCAACTACCGAAAATTG
* * * *
245833 AACAAAGCGACTTGGAAAGATAACTTTCCTTTGCCGTTCTTGGATCAGATGCTAGATAGACTCAT
453 AACAAAGCGAATAGGAAACATAACTTTCCTTTACCGTTCTTGGATCAGATGCTAGATAGACTCAT
*
245898 AAGGCGAGACTATTACTATTTTCTAGATGGGTA
518 AAGGCGAGACTATTACTATTTTCTAGACGGGTA
245931 CT
1 CT
245933 TAGGGTACAA
Statistics
Matches: 486, Mismatches: 64, Indels: 5
0.88 0.12 0.01
Matches are distributed among these distances:
550 122 0.25
551 364 0.75
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (550 bp):
CTCAAGGTACTACCTTGACATTTAAAATATGTTTATTTAGGTGACGCTTCTACTTTGCATATGAT
TATTTCACCACAACTAACTGAGAAGCAAGAAGACCAATTGATTAAAGTGCTGAAACAATTCAAGA
AAGCTAATGGATGGACATAGCTAACATTCGTGGTATAAGTCCATCCGTACGCATGCACAAGATCA
ACCTTGAAGATGACAAGAAAGCAACAATTGACGGAAAATGAAGACTAAACCCCATTATGAAGGAT
GTAGTCAAGAAGGAAATTATCAAGTGGTTAGATGCGGGTATAATCTATCCCATCTCAAACAGTTC
ATGGGTTAGTCCTGTCCAATACATGCCAAACAAAGGAGGTATTACGGTCGTAAAGAATGAAAACA
ACGAGTTAATACCGACTAGAATAGTTACGGGATGGCAAATTTGCATCAACTACCGAAAATTGAAC
AAAGCGAATAGGAAACATAACTTTCCTTTACCGTTCTTGGATCAGATGCTAGATAGACTCATAAG
GCGAGACTATTACTATTTTCTAGACGGGTA
Found at i:250282 original size:18 final size:18
Alignment explanation
Indices: 250261--250301 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
250251 AGATCTTTTA
250261 GAAGAA-AAGGATCCTAAG
1 GAAGAAGAA-GATCCTAAG
*
250279 GAAGAAGAAGATCTTAAG
1 GAAGAAGAAGATCCTAAG
250297 GAAGA
1 GAAGA
250302 TCTTGTGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.51, C:0.07, G:0.29, T:0.12
Consensus pattern (18 bp):
GAAGAAGAAGATCCTAAG
Found at i:265313 original size:56 final size:56
Alignment explanation
Indices: 265252--265371 Score: 206
Period size: 56 Copynumber: 2.2 Consensus size: 56
265242 TTCCTTTCTA
*
265252 ATTATTTTCCCAAATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
1 ATTATTTTCCCAAATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
* *
265308 ATTATTTTTCCAGATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
1 ATTATTTTCCCAAATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
265364 ATT-TTTTC
1 ATTATTTTC
265372 TTTTTTTCCG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 4 0.07
56 56 0.93
ACGTcount: A:0.21, C:0.30, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTTTCCCAAATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTC
Found at i:272232 original size:22 final size:23
Alignment explanation
Indices: 272202--272250 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
272192 ATTTTGTTCA
*
272202 ATTTTAATTT-TTAT-TCAAAAAC
1 ATTTCAATTTGTTATGTC-AAAAC
272224 ATTTCAATTTGTTATGTCAAAAC
1 ATTTCAATTTGTTATGTCAAAAC
272247 ATTT
1 ATTT
272251 TATCAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 9 0.38
23 13 0.54
24 2 0.08
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTCAATTTGTTATGTCAAAAC
Found at i:272308 original size:13 final size:14
Alignment explanation
Indices: 272277--272309 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
272267 GTTTAACAAT
272277 TAAAAATGATTTTC
1 TAAAAATGATTTTC
*
272291 GAAAAATGA-TTTC
1 TAAAAATGATTTTC
272304 TAAAAA
1 TAAAAA
272310 ATAACTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (14 bp):
TAAAAATGATTTTC
Found at i:276391 original size:21 final size:21
Alignment explanation
Indices: 276365--276425 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 21
276355 TTTAAAAATC
276365 TAAAATTATGAAAAAATT-ATT
1 TAAAATTAT-AAAAAATTCATT
276386 TAAAA-T-TAAAAAATTCATT
1 TAAAATTATAAAAAATTCATT
*
276405 TTAAATATATAAAAAAATTCA
1 TAAAAT-TAT-AAAAAATTCA
276426 AAATTCAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 1 0.03
21 6 0.18
22 1 0.03
23 10 0.29
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAATTATAAAAAATTCATT
Found at i:276407 original size:20 final size:22
Alignment explanation
Indices: 276367--276425 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
276357 TAAAAATCTA
*
276367 AAAT-TATGAAAAAATT-ATTT
1 AAATATATAAAAAAATTCATTT
276387 AAA-AT-T-AAAAAATTCATTTT
1 AAATATATAAAAAAATTCA-TTT
276407 AAATATATAAAAAAATTCA
1 AAATATATAAAAAAATTCA
276426 AAATTCAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 10 0.30
21 2 0.06
22 1 0.03
23 10 0.30
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (22 bp):
AAATATATAAAAAAATTCATTT
Found at i:278890 original size:84 final size:84
Alignment explanation
Indices: 278768--278989 Score: 327
Period size: 84 Copynumber: 2.6 Consensus size: 84
278758 AATGTATTTA
* * * * *
278768 TTACTGATATACCTTTTTCATCGATACCCTTACGGATATCCCTTTTCATAGATACCCTTACGGAT
1 TTACAGATAT-CCCTTTTCATTGATATCCTTACGGATATCCCTTTTCATTGATACCCTTACGGAT
278833 ATCTCTTTTCGTTGACATCC
65 ATCTCTTTTCGTTGACATCC
* * * *
278853 TTACAGATATCCCTTTTCATTGACATCCTTACAGATATCCCTTTTCATTGACATCCTTACGGATA
1 TTACAGATATCCCTTTTCATTGATATCCTTACGGATATCCCTTTTCATTGATACCCTTACGGATA
*
278918 TCTCTTTTCGTTGACATCT
66 TCTCTTTTCGTTGACATCC
* *
278937 TTACGGATATCCCTTTTCTTTGATATCCTTACGGATATCCCTTTTCATTGATA
1 TTACAGATATCCCTTTTCATTGATATCCTTACGGATATCCCTTTTCATTGATA
278990 TCAATAATAC
Statistics
Matches: 122, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 113 0.93
85 9 0.07
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (84 bp):
TTACAGATATCCCTTTTCATTGATATCCTTACGGATATCCCTTTTCATTGATACCCTTACGGATA
TCTCTTTTCGTTGACATCC
Found at i:278991 original size:28 final size:28
Alignment explanation
Indices: 278768--278987 Score: 278
Period size: 28 Copynumber: 7.8 Consensus size: 28
278758 AATGTATTTA
* * * * *
278768 TTACTGATATACCTTTTTCATCGATACCC
1 TTACGGATAT-CCCTTTTCATTGACATCC
* * *
278797 TTACGGATATCCCTTTTCATAGATACCC
1 TTACGGATATCCCTTTTCATTGACATCC
* *
278825 TTACGGATATCTCTTTTCGTTGACATCC
1 TTACGGATATCCCTTTTCATTGACATCC
*
278853 TTACAGATATCCCTTTTCATTGACATCC
1 TTACGGATATCCCTTTTCATTGACATCC
*
278881 TTACAGATATCCCTTTTCATTGACATCC
1 TTACGGATATCCCTTTTCATTGACATCC
* * *
278909 TTACGGATATCTCTTTTCGTTGACATCT
1 TTACGGATATCCCTTTTCATTGACATCC
* *
278937 TTACGGATATCCCTTTTCTTTGATATCC
1 TTACGGATATCCCTTTTCATTGACATCC
278965 TTACGGATATCCCTTTTCATTGA
1 TTACGGATATCCCTTTTCATTGA
278988 TATCAATAAT
Statistics
Matches: 171, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 162 0.95
29 9 0.05
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (28 bp):
TTACGGATATCCCTTTTCATTGACATCC
Found at i:283964 original size:11 final size:11
Alignment explanation
Indices: 283948--284023 Score: 78
Period size: 11 Copynumber: 7.6 Consensus size: 11
283938 GATGATGATT
283948 ATAATTTTAAA
1 ATAATTTTAAA
283959 ATAATTTT--A
1 ATAATTTTAAA
283968 ATAATTTT---
1 ATAATTTTAAA
283976 AT-ATTTTAAA
1 ATAATTTTAAA
*
283986 TTAATTTTAAA
1 ATAATTTTAAA
283997 ATAATTTT--A
1 ATAATTTTAAA
284006 ATAATTTTAAA
1 ATAATTTTAAA
*
284017 ATCATTT
1 ATAATTT
284024 ACTGACGTGA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
7 5 0.09
8 2 0.04
9 18 0.32
10 1 0.02
11 30 0.54
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:283972 original size:9 final size:9
Alignment explanation
Indices: 283948--284015 Score: 68
Period size: 9 Copynumber: 7.1 Consensus size: 9
283938 GATGATGATT
283948 ATAATTTTAAA
1 ATAATTTT--A
283959 ATAATTTTA
1 ATAATTTTA
283968 ATAATTTT-
1 ATAATTTTA
283976 AT-ATTTTAA
1 ATAATTTT-A
283985 ATTAATTTTAAA
1 A-TAATTTT--A
283997 ATAATTTTA
1 ATAATTTTA
284006 ATAATTTTA
1 ATAATTTTA
284015 A
1 A
284016 AATCATTTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 21 0.40
10 1 0.02
11 20 0.38
12 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATAATTTTA
Found at i:283973 original size:20 final size:20
Alignment explanation
Indices: 283948--284023 Score: 97
Period size: 20 Copynumber: 3.9 Consensus size: 20
283938 GATGATGATT
283948 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
283968 ATAATTTT---AT-ATTTTAA
1 ATAATTTTAAAATAATTTT-A
283985 ATTAATTTTAAAATAATTTTA
1 A-TAATTTTAAAATAATTTTA
*
284006 ATAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
284024 ACTGACGTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.10
17 4 0.08
18 7 0.14
20 24 0.49
21 4 0.08
22 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:285942 original size:25 final size:23
Alignment explanation
Indices: 285900--285946 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
285890 AGCAATTTGA
285900 TTTTCATTTTTTTATTTATCTAAT
1 TTTTCATTTTTTTATTTA-CTAAT
*
285924 TTTTTATTTTTTTATTTTACTAA
1 TTTTCATTTTTTTA-TTTACTAA
285947 CTAATTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTCATTTTTTTATTTACTAAT
Found at i:292722 original size:18 final size:18
Alignment explanation
Indices: 292685--292723 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
292675 AAACTTCAAG
*
292685 AAATGACTAAAAACATAA
1 AAATGACTAAAAACAGAA
* *
292703 AAATTACTAAAAACGGAA
1 AAATGACTAAAAACAGAA
292721 AAA
1 AAA
292724 AATTACTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (18 bp):
AAATGACTAAAAACAGAA
Found at i:295507 original size:3 final size:3
Alignment explanation
Indices: 295499--295528 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
295489 AGGAAAAGTT
295499 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
295529 AGATATCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:296259 original size:28 final size:28
Alignment explanation
Indices: 296219--296474 Score: 291
Period size: 28 Copynumber: 9.1 Consensus size: 28
296209 ACTAGTTACT
*
296219 ATATCCATAAGGATATCGAA-GAAAAGGG
1 ATATCCGTAAGGATATC-AATGAAAAGGG
* *
296247 ATATCCGTAAGGATGTCAAAGAAAAGGG
1 ATATCCGTAAGGATATCAATGAAAAGGG
* *
296275 ATATTCGTAAGGATGTCAATGAAAAGGG
1 ATATCCGTAAGGATATCAATGAAAAGGG
*
296303 ATATCCGTAAGGATGTCAATGAAAAGGG
1 ATATCCGTAAGGATATCAATGAAAAGGG
* * *
296331 ATATCCATAAGGATGTCAACGAAAAGGG
1 ATATCCGTAAGGATATCAATGAAAAGGG
* *
296359 ATATCCATAAGGATATCAACGAAAAGGG
1 ATATCCGTAAGGATATCAATGAAAAGGG
*
296387 ATATTCGTAAGGATATCAATGAAAAGGG
1 ATATCCGTAAGGATATCAATGAAAAGGG
* * ** *
296415 ATATCCGCAAGGGTATTGATGAAAAGGAT
1 ATATCCGTAAGGATATCAATGAAAAGG-G
* *
296444 ATATCTGTAAGGA-ATACATTTGAAAAGGG
1 ATATCCGTAAGGATAT-CA-ATGAAAAGGG
296473 AT
1 AT
296475 GTTCGCAATG
Statistics
Matches: 200, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
27 2 0.01
28 178 0.89
29 12 0.06
30 8 0.04
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (28 bp):
ATATCCGTAAGGATATCAATGAAAAGGG
Found at i:297736 original size:18 final size:18
Alignment explanation
Indices: 297713--297750 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
297703 TGGGATAGAA
*
297713 GAGTTTTGAGGAACAGCT
1 GAGTTTCGAGGAACAGCT
297731 GAGTTTCGAGGAACAGCT
1 GAGTTTCGAGGAACAGCT
297749 GA
1 GA
297751 AGATGACCTC
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:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (18 bp):
GAGTTTCGAGGAACAGCT
Found at i:309653 original size:27 final size:26
Alignment explanation
Indices: 309612--309671 Score: 102
Period size: 27 Copynumber: 2.3 Consensus size: 26
309602 ACAAAAGTCT
*
309612 TTTACAAAGAAAAGGATGGTGGACAA
1 TTTACAAAGAAAAGGATAGTGGACAA
309638 TTTCACAAAGAAAAGGATAGTGGACAA
1 TTT-ACAAAGAAAAGGATAGTGGACAA
309665 TTTACAA
1 TTTACAA
309672 GGGAAGCTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 7 0.22
27 25 0.78
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.22
Consensus pattern (26 bp):
TTTACAAAGAAAAGGATAGTGGACAA
Found at i:309871 original size:46 final size:46
Alignment explanation
Indices: 309810--309927 Score: 155
Period size: 46 Copynumber: 2.5 Consensus size: 46
309800 TTTGAAGTCC
*
309810 GCATAGTACAGGGATAAGTATGATATCTCTTCATCTTTTTGAAGCTG
1 GCAT-GTATAGGGATAAGTATGATATCTCTTCATCTTTTTGAAGCTG
* *
309857 GCATGTATAGGGATAAGTATGACATCTCTTCTTCTTTTTGAAGCTG
1 GCATGTATAGGGATAAGTATGATATCTCTTCATCTTTTTGAAGCTG
* * ** *
309903 ACACGTATATTGATAAGGATGATAT
1 GCATGTATAGGGATAAGTATGATAT
309928 TTTGTCGGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
46 58 0.94
47 4 0.06
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (46 bp):
GCATGTATAGGGATAAGTATGATATCTCTTCATCTTTTTGAAGCTG
Found at i:310078 original size:30 final size:31
Alignment explanation
Indices: 310042--310099 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
310032 GGCACTTTTA
*
310042 TTGTC-TTTCATGTGGT-GTATTCCACGTGTT
1 TTGTCTTTTCACGTGGTGGT-TTCCACGTGTT
310072 TTGTCTTTTCACGTGGTGGTTTCCACGT
1 TTGTCTTTTCACGTGGTGGTTTCCACGT
310100 ATCTAGTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 5 0.20
31 18 0.72
32 2 0.08
ACGTcount: A:0.09, C:0.19, G:0.24, T:0.48
Consensus pattern (31 bp):
TTGTCTTTTCACGTGGTGGTTTCCACGTGTT
Found at i:310109 original size:31 final size:31
Alignment explanation
Indices: 310047--310109 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
310037 TTTTATTGTC
* * * *
310047 TTTCATGTGGTGTATTCCACGTGTTTTGTCT
1 TTTCACGTGGTGTATTCCACGTATCTAGTCT
310078 TTTCACGTGGTGGT-TTCCACGTATCTAGTCT
1 TTTCACGTGGT-GTATTCCACGTATCTAGTCT
310109 T
1 T
310110 CCTAGATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (31 bp):
TTTCACGTGGTGTATTCCACGTATCTAGTCT
Found at i:310479 original size:13 final size:13
Alignment explanation
Indices: 310441--310469 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
310431 AAAATTATTC
310441 TGGCACTTGTCAA
1 TGGCACTTGTCAA
310454 TGGCACTTGTCAA
1 TGGCACTTGTCAA
310467 TGG
1 TGG
310470 ATTTTGTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (13 bp):
TGGCACTTGTCAA
Found at i:316262 original size:21 final size:20
Alignment explanation
Indices: 316238--316286 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
316228 ATAAGAGCAA
316238 AAATAAAAGGCTAAG-TGAAG
1 AAATAAAA-GCTAAGCTGAAG
*
316258 TAAATGAAAAGCTTAGCTGAAG
1 -AAAT-AAAAGCTAAGCTGAAG
316280 AAATAAA
1 AAATAAA
316287 TTGTTTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (20 bp):
AAATAAAAGCTAAGCTGAAG
Found at i:321468 original size:18 final size:19
Alignment explanation
Indices: 321445--321490 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
321435 AACATAATAT
321445 CTTCAACATCT-CTTTTTA
1 CTTCAACATCTACTTTTTA
*
321463 CTTCAACAT-TACTTTTTC
1 CTTCAACATCTACTTTTTA
321481 CTTCAACATC
1 CTTCAACATC
321491 CAAATTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.46
Consensus pattern (19 bp):
CTTCAACATCTACTTTTTA
Found at i:325558 original size:21 final size:21
Alignment explanation
Indices: 325532--325572 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
325522 TTTGCCTCGA
*
325532 CTTCTT-TTCCTTCCTCTTGTT
1 CTTCTTCTT-CTTCCACTTGTT
325553 CTTCTTCTTCTTCCACTTGT
1 CTTCTTCTTCTTCCACTTGT
325573 ATTTCCTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.02, C:0.34, G:0.05, T:0.59
Consensus pattern (21 bp):
CTTCTTCTTCTTCCACTTGTT
Found at i:335592 original size:25 final size:25
Alignment explanation
Indices: 335555--335603 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
335545 TAATTATTTC
*
335555 ATTAAAAATTTGGGTTTATTTAATT
1 ATTAAAAATTTGGGTTAATTTAATT
335580 ATTAAATAA-TTGGGTTAATTTAAT
1 ATTAAA-AATTTGGGTTAATTTAAT
335604 ACTTTGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (25 bp):
ATTAAAAATTTGGGTTAATTTAATT
Found at i:341760 original size:25 final size:25
Alignment explanation
Indices: 341721--341771 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
341711 ATAAATTATT
*
341721 TCATTAATAATTTGGGTTTATTTAA
1 TCATTAATAATTTGGGTTAATTTAA
341746 TCATTAAATAA-TTGGGTTAATTTAA
1 TCATT-AATAATTTGGGTTAATTTAA
341771 T
1 T
341772 ACTTTGATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (25 bp):
TCATTAATAATTTGGGTTAATTTAA
Found at i:351349 original size:20 final size:20
Alignment explanation
Indices: 351333--351375 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
351323 ATTAAAATGT
*
351333 AAAAATTAAATTAAAAACAA
1 AAAAATTAAATTAAAAATAA
*
351353 AAAAATTAAAATAAAAATAA
1 AAAAATTAAATTAAAAATAA
351373 AAA
1 AAA
351376 TGGTTGAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAAATTAAATTAAAAATAA
Found at i:353059 original size:26 final size:25
Alignment explanation
Indices: 353030--353127 Score: 97
Period size: 26 Copynumber: 3.8 Consensus size: 25
353020 CGTTACTCTG
*
353030 TCTGGACTCGAATGAGCTAAATTTTA
1 TCTGG-CTCGAATGAGCTAAAATTTA
* *
353056 TCTGTGCTCAAATGAGCTAAAATTTG
1 TCTG-GCTCGAATGAGCTAAAATTTA
* * *
353082 TCTAGGCTCGAATAAGCTAAACTCTA
1 TCT-GGCTCGAATGAGCTAAAATTTA
*
353108 TCTGGGCTCGTATGAGCTAA
1 TCT-GGCTCGAATGAGCTAA
353128 TCTCTTTCTA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 57 0.97
27 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (25 bp):
TCTGGCTCGAATGAGCTAAAATTTA
Found at i:353132 original size:26 final size:26
Alignment explanation
Indices: 353036--353158 Score: 95
Period size: 26 Copynumber: 4.7 Consensus size: 26
353026 TCTGTCTGGA
* * *
353036 CTCGAATGAGCTAAATTTTATCT-GTG
1 CTCGTATGAGCTAAACTCTATCTAG-G
** * * *
353062 CTCAAATGAGCTAAAATTTGTCTAGG
1 CTCGTATGAGCTAAACTCTATCTAGG
* * *
353088 CTCGAATAAGCTAAACTCTATCTGGG
1 CTCGTATGAGCTAAACTCTATCTAGG
* *
353114 CTCGTATGAGCTAATCTCTTTCTAGG
1 CTCGTATGAGCTAAACTCTATCTAGG
* *
353140 CTCATATGAGCTAACCTCT
1 CTCGTATGAGCTAAACTCT
353159 GTTCTAGCTT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 79 0.99
27 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (26 bp):
CTCGTATGAGCTAAACTCTATCTAGG
Found at i:353152 original size:52 final size:52
Alignment explanation
Indices: 353028--353158 Score: 133
Period size: 52 Copynumber: 2.5 Consensus size: 52
353018 AGCGTTACTC
* * *
353028 TGTCT-GGACTCGAATGAGCTAAATTTTATCTGTGCTCAAATGAGCTAAAATT
1 TGTCTAGG-CTCGAATGAGCTAAACTCTATCTGGGCTCAAATGAGCTAAAATT
* ** **
353080 TGTCTAGGCTCGAATAAGCTAAACTCTATCTGGGCTCGTATGAGCTAATCTCT
1 TGTCTAGGCTCGAATGAGCTAAACTCTATCTGGGCTCAAATGAGCTAAAAT-T
*
353133 T-TCTAGGCTC-ATATGAGCTAACCTCT
1 TGTCTAGGCTCGA-ATGAGCTAAACTCT
353159 GTTCTAGCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
51 1 0.02
52 61 0.92
53 4 0.06
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (52 bp):
TGTCTAGGCTCGAATGAGCTAAACTCTATCTGGGCTCAAATGAGCTAAAATT
Found at i:359973 original size:26 final size:26
Alignment explanation
Indices: 359934--360025 Score: 121
Period size: 26 Copynumber: 3.5 Consensus size: 26
359924 GAAATAAATG
359934 AGCAAGCTTCGAGCCAGTGTGTATTT
1 AGCAAGCTTCGAGCCAGTGTGTATTT
*
359960 AGCAAGCTTTGAGCCAGTGTGTATTT
1 AGCAAGCTTCGAGCCAGTGTGTATTT
* * * *
359986 AGCATGCTTCAAGCCAATGTATATTT
1 AGCAAGCTTCGAGCCAGTGTGTATTT
* *
360012 AGTAGGCTTCGAGC
1 AGCAAGCTTCGAGC
360026 TGATTAATGT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (26 bp):
AGCAAGCTTCGAGCCAGTGTGTATTT
Found at i:360074 original size:25 final size:26
Alignment explanation
Indices: 360009--360077 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
359999 CCAATGTATA
* * *
360009 TTTAGTAGGCTTCGAGCTGATTAATG
1 TTTAGCAGGCTTTGAGCTGATGAATG
* *
360035 TTTAGCAGGCCTTGAGCTGGTGAATG
1 TTTAGCAGGCTTTGAGCTGATGAATG
360061 -TTAGCAGGCTTTGAGCT
1 TTTAGCAGGCTTTGAGCT
360078 AGTTAAAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.35
Consensus pattern (26 bp):
TTTAGCAGGCTTTGAGCTGATGAATG
Found at i:362489 original size:26 final size:26
Alignment explanation
Indices: 362460--362538 Score: 117
Period size: 26 Copynumber: 3.0 Consensus size: 26
362450 AGCGTTACTT
362460 TGTCTAGGCTCGA-ATGAGCTAAACTC
1 TGTCTAGGCTC-ATATGAGCTAAACTC
362486 TGTCTAGGCTCATATGAGCTAATA-TC
1 TGTCTAGGCTCATATGAGCTAA-ACTC
*
362512 TGTCTAGGCTCATACGAGCTAAACTC
1 TGTCTAGGCTCATATGAGCTAAACTC
362538 T
1 T
362539 ATTCTGGCTC
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
25 2 0.04
26 46 0.94
27 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (26 bp):
TGTCTAGGCTCATATGAGCTAAACTC
Found at i:365754 original size:123 final size:122
Alignment explanation
Indices: 365536--365902 Score: 515
Period size: 123 Copynumber: 3.0 Consensus size: 122
365526 TAGTATTTAC
* * * *
365536 TGAATATT-AAAACATGGAAGTTATTATCCTTTTGCAAAGGATATAATATTTTTATAAGCCTTTC
1 TGAATATTAAAAACAT-GAAGTTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTTC
* * * *
365600 ATATATTTGTTTAAA-AGAATATTTCCATTTTAATATGAGATATTATATAAAAGGAAAT
65 ATATATTTCTCTAAAGA-AATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAAT
** *
365658 TGAATATTAAAAACATCGAAGTTAATATCCTTTTGGAAATTATATAATATTTTAATAAACCTTCC
1 TGAATATTAAAAACAT-GAAGTTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTTC
*
365723 ATAGATTTCTCTAAAGAAATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAAT
65 ATATATTTCTCTAAAGAAATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAAT
* * * *
365781 TGAATATTAAAAACATGTAAGTTAATATTCTTTTGGAAAGGATATAATGTATTAATAAACCTTTA
1 TGAATATTAAAAACATG-AAGTTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTTC
*
365846 ATATATTTCTCTAAATG-AATACTTCCATTTTAATATGAGATATTAAATAAAAAGAAA
65 ATATATTTCTCTAAA-GAAATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAA
365903 AGATAGCATA
Statistics
Matches: 219, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
122 9 0.04
123 208 0.95
124 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (122 bp):
TGAATATTAAAAACATGAAGTTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTTCA
TATATTTCTCTAAAGAAATATTTCCATTTTAATATGAGATATTAAATAAAAAGAAAT
Found at i:370110 original size:18 final size:18
Alignment explanation
Indices: 370083--370118 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
370073 ACCCTCTTAT
370083 TAAACATAAAAATGAAAA
1 TAAACATAAAAATGAAAA
* *
370101 TAAACTTAAAATTGAAAA
1 TAAACATAAAAATGAAAA
370119 CAAAATTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (18 bp):
TAAACATAAAAATGAAAA
Found at i:382307 original size:15 final size:15
Alignment explanation
Indices: 382266--382307 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
382256 AACCAAATTT
382266 AAAAAA-ATAAAATA
1 AAAAAATATAAAATA
* **
382280 AAAATATGGAAAATA
1 AAAAAATATAAAATA
382295 AAAAAATATAAAA
1 AAAAAATATAAAA
382308 AATCATATTT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (15 bp):
AAAAAATATAAAATA
Found at i:388236 original size:19 final size:21
Alignment explanation
Indices: 388212--388250 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
388202 ATCGAATCTC
388212 ATTAATGAA-T-AAGGAAAGA
1 ATTAATGAATTCAAGGAAAGA
*
388231 ATTAATTAATTCAAGGAAAG
1 ATTAATGAATTCAAGGAAAG
388251 GGATCGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.26
Consensus pattern (21 bp):
ATTAATGAATTCAAGGAAAGA
Done.