Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008259.1 Hibiscus syriacus cultivar Beakdansim tig00110912_pilon, 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: 2373650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:4225 original size:23 final size:23
Alignment explanation
Indices: 4195--4246 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
4185 TGAAAGGGAT
*
4195 GCTGCAGTTCGGCAAACATTGCA
1 GCTGCAGTTCGGCAAACATTGAA
4218 GCTGCAGTTCGGCAAACATTGAA
1 GCTGCAGTTCGGCAAACATTGAA
4241 GCTGCA
1 GCTGCA
4247 ACAAGACCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (23 bp):
GCTGCAGTTCGGCAAACATTGAA
Found at i:7980 original size:8 final size:8
Alignment explanation
Indices: 7967--8010 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
7957 CTATTTTTTC
7967 AAAAAACA
1 AAAAAACA
7975 AAAAAAGGCA
1 AAAAAA--CA
7985 AAAAAA-A
1 AAAAAACA
7992 AAAAAACA
1 AAAAAACA
*
8000 AAAAACCA
1 AAAAAACA
8008 AAA
1 AAA
8011 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
7 7 0.22
8 17 0.53
10 8 0.25
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:8964 original size:22 final size:22
Alignment explanation
Indices: 8936--8988 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
8926 TAAATGAGCT
8936 CATAAACGAGTTTGTTCGTGAA
1 CATAAACGAGTTTGTTCGTGAA
8958 CATAAACGAGTTTGTTCGTGAA
1 CATAAACGAGTTTGTTCGTGAA
*
8980 AATAAACGA
1 CATAAACGA
8989 ACTGAACACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (22 bp):
CATAAACGAGTTTGTTCGTGAA
Found at i:19732 original size:23 final size:23
Alignment explanation
Indices: 19702--19753 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
19692 TGAAAGGGAT
*
19702 GCTGCAGTTCGGCAAACATTGCA
1 GCTGCAGTTCGGCAAACATTGAA
19725 GCTGCAGTTCGGCAAACATTGAA
1 GCTGCAGTTCGGCAAACATTGAA
19748 GCTGCA
1 GCTGCA
19754 ACAAGACCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (23 bp):
GCTGCAGTTCGGCAAACATTGAA
Found at i:21344 original size:21 final size:23
Alignment explanation
Indices: 21308--21349 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
21298 TTTAATTATC
*
21308 ACAAATATTTTTTA-GGTAAATT
1 ACAAATATTATTTAGGGTAAATT
21330 ACAAAT-TTATTTAGGGTAAA
1 ACAAATATTATTTAGGGTAAA
21350 CTATGAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (23 bp):
ACAAATATTATTTAGGGTAAATT
Found at i:23510 original size:10 final size:8
Alignment explanation
Indices: 23489--23531 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
23479 CTATTTTTTT
23489 CAAAAAAA
1 CAAAAAAA
23497 CAAAAAAA
1 CAAAAAAA
23505 GGCAAAAAAA
1 --CAAAAAAA
*
23515 AAACAAAAA
1 CAA-AAAAA
23524 CAAAAAAA
1 CAAAAAAA
23532 AAACCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 15 0.50
9 7 0.23
10 8 0.27
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:23527 original size:17 final size:18
Alignment explanation
Indices: 23489--23554 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
23479 CTATTTTTTT
**
23489 CAAAAAAACAAA-AAAAGG
1 CAAAAAAA-AAACAAAATA
23507 CAAAAAAAAAACAAAA-A
1 CAAAAAAAAAACAAAATA
*
23524 CAAAAAAAAAACCAAAATTT
1 CAAAAAAAAAA-CAAAA-TA
23544 CAAAAAAAAAA
1 CAAAAAAAAAA
23555 AAATTGCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 14 0.33
18 17 0.40
20 11 0.26
ACGTcount: A:0.80, C:0.12, G:0.03, T:0.05
Consensus pattern (18 bp):
CAAAAAAAAAACAAAATA
Found at i:23532 original size:21 final size:21
Alignment explanation
Indices: 23490--23534 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
23480 TATTTTTTTC
**
23490 AAAAAAACAAAAAAAGGCAAA
1 AAAAAAACAAAAAAAGAAAAA
*
23511 AAAAAAACAAAAACA-AAAAA
1 AAAAAAACAAAAAAAGAAAAA
23531 AAAA
1 AAAA
23535 CCAAAATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAAAAAAGAAAAA
Found at i:23557 original size:17 final size:17
Alignment explanation
Indices: 23489--23564 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
23479 CTATTTTTTT
**
23489 CAAAAAAACAAAAAAAGG
1 CAAAAAAA-AAAAAATTG
**
23507 CAAAAAAAAAACAAA-AA
1 CAAAAAAAAAA-AAATTG
*
23524 CAAAAAAAAAACCAAAATTT
1 C-AAAAAAAAA--AAAATTG
23544 CAAAAAAAAAAAAATTG
1 CAAAAAAAAAAAAATTG
23561 CAAA
1 CAAA
23565 CGAAGGTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
17 14 0.29
18 20 0.42
19 12 0.25
20 2 0.04
ACGTcount: A:0.78, C:0.12, G:0.04, T:0.07
Consensus pattern (17 bp):
CAAAAAAAAAAAAATTG
Found at i:26029 original size:21 final size:23
Alignment explanation
Indices: 25993--26034 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
25983 TTTAATTATC
*
25993 ACAAATATTTTTTA-GGTAAATT
1 ACAAATATTATTTAGGGTAAATT
26015 ACAAAT-TTATTTAGGGTAAA
1 ACAAATATTATTTAGGGTAAA
26035 CTATGAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (23 bp):
ACAAATATTATTTAGGGTAAATT
Found at i:28019 original size:20 final size:20
Alignment explanation
Indices: 27994--28031 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27984 TTCTGGGCAA
*
27994 GTGCATCGATGCATTAAGGG
1 GTGCATCGATGCACTAAGGG
*
28014 GTGCATCGTTGCACTAAG
1 GTGCATCGATGCACTAAG
28032 ATAAATTTTG
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:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (20 bp):
GTGCATCGATGCACTAAGGG
Found at i:28928 original size:62 final size:62
Alignment explanation
Indices: 28829--28953 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
28819 AAGGGTTAGG
* * *
28829 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACTTATGTTCTTCGGGA-CATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACTTAGGTTCTTCGGAATC-TATGGATT
*
28891 GTTTACCTATGTTCTTCGGTACATATGGACTGATTACTTAGGTTCTTCGGAATCTATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACTTAGGTTCTTCGGAATCTATGGATT
28953 G
1 G
28954 GTCCTTTGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 57 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACTTAGGTTCTTCGGAATCTATGGATT
Found at i:28950 original size:31 final size:31
Alignment explanation
Indices: 28829--28940 Score: 170
Period size: 31 Copynumber: 3.6 Consensus size: 31
28819 AAGGGTTAGG
*
28829 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACTTATGTTCTTCGGGACATATGGACT
*
28860 GTTTACTTATGTTCTTCGGGACATATGGATT
1 GTTTACTTATGTTCTTCGGGACATATGGACT
* *
28891 GTTTACCTATGTTCTTCGGTACATATGGACT
1 GTTTACTTATGTTCTTCGGGACATATGGACT
* *
28922 GATTACTTAGGTTCTTCGG
1 GTTTACTTATGTTCTTCGG
28941 AATCTATGGA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (31 bp):
GTTTACTTATGTTCTTCGGGACATATGGACT
Found at i:32058 original size:23 final size:23
Alignment explanation
Indices: 32024--32091 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
32014 AACCTTATAT
32024 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
32047 GGCACTAT-GGTGCAATTCTACGT
1 GGCACT-TCGGTGCATTTCTACGC
*
32070 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
32092 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:38735 original size:21 final size:21
Alignment explanation
Indices: 38709--38748 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38699 CCCCCTTTGA
*
38709 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
38730 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
38749 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:43471 original size:2 final size:2
Alignment explanation
Indices: 43464--43491 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43454 ATATGTCACT
43464 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
43492 CTTGAAATTG
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):
TA
Found at i:54896 original size:46 final size:47
Alignment explanation
Indices: 54839--54933 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 47
54829 AACCCTCGCT
* * *
54839 GACTTAGAATTTTTTATTA-AAAAATGTATCTGTAGTACTAAACTGC
1 GACTTAAAATTTTTTATTATAAAAAGGTATCCGTAGTACTAAACTGC
*
54885 GACTTAAAATTTTTTTTTATTAAAAAGGTATCCGTAGTACTAAACTGC
1 GACTTAAAATTTTTTATTA-TAAAAAGGTATCCGTAGTACTAAACTGC
54933 G
1 G
54934 CTATGTGCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 17 0.40
48 26 0.60
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39
Consensus pattern (47 bp):
GACTTAAAATTTTTTATTATAAAAAGGTATCCGTAGTACTAAACTGC
Found at i:59489 original size:20 final size:20
Alignment explanation
Indices: 59466--59536 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
59456 TCTGAAACTT
*
59466 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
**
59486 AAAATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
59506 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
59525 AAAATCGCAACG
1 AAAATCGCAACG
59537 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 13 0.31
20 29 0.69
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:59635 original size:11 final size:11
Alignment explanation
Indices: 59619--59649 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
59609 ACTTCAACCA
59619 AAAGACAAAAC
1 AAAGACAAAAC
59630 AAAGACAAAAC
1 AAAGACAAAAC
59641 AAAGACAAA
1 AAAGACAAA
59650 TACTAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.16, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAGACAAAAC
Found at i:59913 original size:22 final size:22
Alignment explanation
Indices: 59883--59944 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
59873 TGACCGTAAA
59883 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
59905 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGAGAC
* *
59927 TGCTTTTGTCGGAGATGG
1 TGATTTCGTCGGAGATGG
59945 GGATGGATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.13, G:0.39, T:0.29
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:60152 original size:20 final size:20
Alignment explanation
Indices: 60127--60177 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
60117 GCTATGTAAA
60127 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
60147 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
60167 TAGCATTGCGA
1 TCGCATTGCGA
60178 ATTAGGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:60200 original size:21 final size:21
Alignment explanation
Indices: 60174--60219 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
60164 TATTAGCATT
60174 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
60195 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
60216 GCGA
1 GCGA
60220 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:60291 original size:19 final size:19
Alignment explanation
Indices: 60267--60317 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
60257 CGATACCGGA
*
60267 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
60286 GATCGCATTGCGAATTATC
1 GATCGCATTGCGAATTATC
*
60305 GATCGTATTGCGA
1 GATCGCATTGCGA
60318 TTTAGTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:62338 original size:22 final size:24
Alignment explanation
Indices: 62297--62359 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 24
62287 CTATTAACGA
62297 AAATAAAAA-ATA-AGTGAAATAAAT
1 AAATAAAAATATATA-T-AAATAAAT
*
62321 AAAT-AAAATA-ATATAAATAACT
1 AAATAAAAATATATATAAATAAAT
*
62343 AACTAAAAATATATATA
1 AAATAAAAATATATATA
62360 TTATACGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 10 0.30
23 12 0.36
24 11 0.33
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (24 bp):
AAATAAAAATATATATAAATAAAT
Found at i:62397 original size:37 final size:34
Alignment explanation
Indices: 62354--62623 Score: 227
Period size: 37 Copynumber: 7.5 Consensus size: 34
62344 ACTAAAAATA
* * *
62354 TATATATTATACGTTTTCGAAACCTTTTTATAAAAAC
1 TATATAATATACGTTTTC-AAA-ATTTTT-TCAAAAC
* * * *
62391 TATATATTATACATTTTCAAATTTATTTTAAAAAC
1 TATATAATATACGTTTTCAAAATT-TTTTCAAAAC
* * *
62426 TATATACTA-AAGTTTTTAAAATTGTTTTCAAAAC
1 TATATAATATACGTTTTCAAAATT-TTTTCAAAAC
*
62460 TATATAATATACATTTTCAAAAATTGTTTTTCAAAAC
1 TATATAATATACGTTTTC-AAAA-T-TTTTTCAAAAC
*
62497 TATATAATATACGTTTTAAAAATGTGTTTTCAAAAC
1 TATATAATATACGTTTTCAAAAT-T-TTTTCAAAAC
62533 TATATAATATACGTTTTCAAAAATTGTTTTTCAAAAC
1 TATATAATATACGTTTTC-AAAA-T-TTTTTCAAAAC
* * * *
62570 TATAAAATATATGTTTTTAAAAATGTGTTTTCAAAAT
1 TATATAATATACG-TTTTCAAAAT-T-TTTTCAAAAC
* *
62607 TATTTAATATATGTTTT
1 TATATAATATACGTTTT
62624 AAACCATATT
Statistics
Matches: 201, Mismatches: 22, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
34 27 0.13
35 25 0.12
36 48 0.24
37 93 0.46
38 8 0.04
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.46
Consensus pattern (34 bp):
TATATAATATACGTTTTCAAAATTTTTTCAAAAC
Found at i:62544 original size:73 final size:73
Alignment explanation
Indices: 62386--62617 Score: 321
Period size: 73 Copynumber: 3.2 Consensus size: 73
62376 CCTTTTTATA
* * * *
62386 AAAACTATATATTATACATTTTC--AAATT-TATTTTAAAAACTATATACTA-AAGTTTTTAAAA
1 AAAACTATATAATATACATTTTCAAAAATTGT-TTTTCAAAACTATATAATATAAGTTTTAAAAA
62447 T-TGTTTTC
65 TGTGTTTTC
*
62455 AAAACTATATAATATACATTTTCAAAAATTGTTTTTCAAAACTATATAATATACGTTTTAAAAAT
1 AAAACTATATAATATACATTTTCAAAAATTGTTTTTCAAAACTATATAATATAAGTTTTAAAAAT
62520 GTGTTTTC
66 GTGTTTTC
* * *
62528 AAAACTATATAATATACGTTTTCAAAAATTGTTTTTCAAAACTATAAAATATATGTTTTTAAAAA
1 AAAACTATATAATATACATTTTCAAAAATTGTTTTTCAAAACTATATAATATAAG-TTTTAAAAA
62593 TGTGTTTTC
65 TGTGTTTTC
* *
62602 AAAATTATTTAATATA
1 AAAACTATATAATATA
62618 TGTTTTAAAC
Statistics
Matches: 147, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
69 22 0.15
71 22 0.15
72 12 0.08
73 59 0.40
74 32 0.22
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (73 bp):
AAAACTATATAATATACATTTTCAAAAATTGTTTTTCAAAACTATATAATATAAGTTTTAAAAAT
GTGTTTTC
Found at i:62625 original size:36 final size:35
Alignment explanation
Indices: 62386--62626 Score: 277
Period size: 37 Copynumber: 6.7 Consensus size: 35
62376 CCTTTTTATA
* * * * * *
62386 AAAACTATATATTATACATTTTCAAATTTATTTTA
1 AAAACTATATAATATACGTTTTAAAAATTGTTTTC
* * *
62421 AAAACTATATACTA-AAGTTTTTAAAATTGTTTTC
1 AAAACTATATAATATACGTTTTAAAAATTGTTTTC
*
62455 AAAACTATATAATATACATTTTCAAAAATTGTTTTTC
1 AAAACTATATAATATACGTTTT-AAAAATTG-TTTTC
62492 AAAACTATATAATATACGTTTTAAAAATGTGTTTTC
1 AAAACTATATAATATACGTTTTAAAAAT-TGTTTTC
62528 AAAACTATATAATATACGTTTTCAAAAATTGTTTTTC
1 AAAACTATATAATATACGTTTT-AAAAATTG-TTTTC
* *
62565 AAAACTATAAAATATATGTTTTTAAAAATGTGTTTTC
1 AAAACTATATAATATACG-TTTTAAAAAT-TGTTTTC
* * *
62602 AAAATTATTTAATATATGTTTTAAA
1 AAAACTATATAATATACGTTTTAAA
62627 CCATATTATA
Statistics
Matches: 181, Mismatches: 17, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
34 27 0.15
35 18 0.10
36 49 0.27
37 81 0.45
38 6 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (35 bp):
AAAACTATATAATATACGTTTTAAAAATTGTTTTC
Found at i:65378 original size:101 final size:100
Alignment explanation
Indices: 65203--65504 Score: 412
Period size: 99 Copynumber: 3.0 Consensus size: 100
65193 GGATAACTCA
* * ** *
65203 ATATTATAATCACCTTTATCATGCTAGCTGAATCTTATCCATAAAGACGGGACACTAAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGG-CGTTTAACCAATT
* * *
65268 GCTCTAGAGGTATAACTCAAACTTTATTGTATATAT
65 GCTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
** *
65304 ATATTATAATCACCTTTATCAGGCTAGCAAAATCTTATCCATAAAGCCAGGGTGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCC-GGGCGTTTAACCAATT
* *
65369 GTTCTAGAGGGACAACTCAAGCTTT-TT-TGTATAT
65 GCTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
* *
65403 ATATTATACTCACCTTTATCAGGATAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCC-GGGCGTTTAACCAATT
*
65468 ACTCTAGAGGGACAACTCAAGCTTTATTGTATA-AT
65 GCTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
65503 AT
1 AT
65505 TATAATATGG
Statistics
Matches: 176, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
99 88 0.50
100 8 0.05
101 77 0.44
102 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (100 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGCGTTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTTTATTGTATATAT
Found at i:71063 original size:36 final size:36
Alignment explanation
Indices: 70934--71196 Score: 250
Period size: 37 Copynumber: 7.3 Consensus size: 36
70924 TGTATAAATA
* * * *
70934 TATATATTATACGTTTTC-AAAATCTTTTTATAAAAAC
1 TATATAATATACATTTTCAAAAAT-TGTTT-TCAAAAC
* * *
70971 TATATATTATACATTTTC-AAAATTATTTTAAAAAC
1 TATATAATATACATTTTCAAAAATTGTTTTCAAAAC
* ***
71006 TATAT-A-CTA-ATTTTTTTAAATTGTTTTCAAAAC
1 TATATAATATACATTTTCAAAAATTGTTTTCAAAAC
*
71039 TATATAATATACATTTTCAAAAATTGTTTTTCAAAAT
1 TATATAATATACATTTTCAAAAATTG-TTTTCAAAAC
* *
71076 TATATAATATGCGTTTTCAAAAATGTGTTTTCAAAAC
1 TATATAATATACATTTTCAAAAAT-TGTTTTCAAAAC
*
71113 TATATAATATACATTTTCAAAAATTGTTTTTCAAAAT
1 TATATAATATACATTTTCAAAAATTG-TTTTCAAAAC
** * *
71150 TATATAATATATGTTTT-AAAAATGTGTATTCAAAAT
1 TATATAATATACATTTTCAAAAAT-TGTTTTCAAAAC
*
71186 TATATAGTATA
1 TATATAATATA
71197 TGTTTTTAAA
Statistics
Matches: 195, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
32 5 0.03
33 21 0.11
34 1 0.01
35 14 0.07
36 42 0.22
37 110 0.56
38 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATAATATACATTTTCAAAAATTGTTTTCAAAAC
Found at i:71148 original size:74 final size:73
Alignment explanation
Indices: 70929--71196 Score: 312
Period size: 74 Copynumber: 3.7 Consensus size: 73
70919 ATATATGTAT
* * * * * *
70929 AAATATATATATTATACGTTTTCAAAATCTTTTTATAAAAACTATATATTATACATTTTC-AAAA
1 AAAT-TATATAATATACGTTTTAAAAATGTGTTT-TCAAAACTATATAATATACATTTTCAAAAA
* *
70993 TT-ATTTTAA
64 TTGTTTTTCA
* * * **
71002 AAACTATATACTA-A-TTTTTTTAAAT-TGTTTTCAAAACTATATAATATACATTTTCAAAAATT
1 AAATTATATAATATACGTTTTAAAAATGTGTTTTCAAAACTATATAATATACATTTTCAAAAATT
71064 GTTTTTCA
66 GTTTTTCA
*
71072 AAATTATATAATATGCGTTTTCAAAAATGTGTTTTCAAAACTATATAATATACATTTTCAAAAAT
1 AAATTATATAATATACGTTTT-AAAAATGTGTTTTCAAAACTATATAATATACATTTTCAAAAAT
71137 TGTTTTTCA
65 TGTTTTTCA
* * * *
71146 AAATTATATAATATATGTTTTAAAAATGTGTATTCAAAATTATATAGTATA
1 AAATTATATAATATACGTTTTAAAAATGTGTTTTCAAAACTATATAATATA
71197 TGTTTTTAAA
Statistics
Matches: 168, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
68 23 0.14
69 10 0.06
70 24 0.14
71 1 0.01
72 12 0.07
73 34 0.20
74 64 0.38
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (73 bp):
AAATTATATAATATACGTTTTAAAAATGTGTTTTCAAAACTATATAATATACATTTTCAAAAATT
GTTTTTCA
Found at i:76711 original size:20 final size:20
Alignment explanation
Indices: 76686--76723 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
76676 CACATGTTAA
76686 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
76706 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
76724 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:84815 original size:22 final size:21
Alignment explanation
Indices: 84773--84812 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
84763 GAGTTTGTTT
*
84773 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
84794 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
84813 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:86865 original size:45 final size:46
Alignment explanation
Indices: 86777--86866 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
86767 TGAAAGAGCC
* * *
86777 TGAGTGCATCGATGCATGGTCTTTTGCATCGATGCATCAAATGCAA
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAA
*
86823 TGAGTGTATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
86867 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (46 bp):
TGAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCAA
Found at i:87342 original size:18 final size:18
Alignment explanation
Indices: 87296--87345 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
87286 GGGTCTACGC
*
87296 GGTCCTTCGGAACACAGT
1 GGTCCTTCGGGACACAGT
87314 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
87332 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
87346 AATTTCATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (18 bp):
GGTCCTTCGGGACACAGT
Found at i:90894 original size:20 final size:20
Alignment explanation
Indices: 90869--90906 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
90859 CACATGTTAA
90869 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
90889 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
90907 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:91393 original size:2 final size:2
Alignment explanation
Indices: 91388--91433 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
91378 TATATATATA
91388 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
91430 TG TG
1 TG TG
91434 AATAAGATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:91715 original size:18 final size:18
Alignment explanation
Indices: 91692--91759 Score: 118
Period size: 18 Copynumber: 3.8 Consensus size: 18
91682 GGGTCTACGC
91692 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
91710 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
* *
91728 GGTCCTTCGAGACATAGT
1 GGTCCTTCGGGACACAGT
91746 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
91760 AATTTCATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (18 bp):
GGTCCTTCGGGACACAGT
Found at i:96023 original size:23 final size:23
Alignment explanation
Indices: 95993--96036 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
95983 GTCGAGGGTT
*
95993 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCATTCGGGACAAAC
96016 CTATGTGGTCATTCGGGACAA
1 CTATGTGGTCATTCGGGACAA
96037 TTATATAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAC
Found at i:98051 original size:19 final size:18
Alignment explanation
Indices: 98027--98063 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
98017 TAGGGGTGTA
98027 TTCGGTTCGGTTCGAGTTT
1 TTCGGTTCGGTTCG-GTTT
98046 TTCGGTTCGGTTCGGTTT
1 TTCGGTTCGGTTCGGTTT
98064 ATCAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.03, C:0.16, G:0.32, T:0.49
Consensus pattern (18 bp):
TTCGGTTCGGTTCGGTTT
Found at i:98897 original size:20 final size:20
Alignment explanation
Indices: 98874--98937 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
98864 TAGTATTTAG
98874 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
98894 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
98914 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
98933 TTAAA
1 ATAAA
98938 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:98907 original size:19 final size:20
Alignment explanation
Indices: 98883--98932 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
98873 GATAAATTTA
*
98883 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
98902 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
98923 TT-ATAATTTT
1 TTAATAATTTT
98933 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:98935 original size:31 final size:30
Alignment explanation
Indices: 98850--98936 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
98840 TTCGATAATA
* *
98850 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
98881 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
98912 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
98937 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:99717 original size:31 final size:31
Alignment explanation
Indices: 99659--99726 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
99649 TCAATAAAGT
**
99659 TTAAAAAATTATAAAATACTTTTTAAATTTA
1 TTAAAAAATTATAAAATACTTAATAAATTTA
*
99690 TTAAAAGATTATAAAATTA-TTAATAAATTTA
1 TTAAAAAATTATAAAA-TACTTAATAAATTTA
99721 TCTAAA
1 T-TAAA
99727 TACTATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATACTTAATAAATTTA
Found at i:102466 original size:20 final size:21
Alignment explanation
Indices: 102441--102492 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
102431 AATTGACTTA
* *
102441 GTATCGATACTGAGGTGGA-G
1 GTATCGATACTGAAGAGGACG
*
102461 GTATCGATAC-CAAGAGGACG
1 GTATCGATACTGAAGAGGACG
102481 GTATCGATACTG
1 GTATCGATACTG
102493 TTGTTGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.29, C:0.15, G:0.33, T:0.23
Consensus pattern (21 bp):
GTATCGATACTGAAGAGGACG
Found at i:107131 original size:30 final size:30
Alignment explanation
Indices: 107097--107174 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
107087 ATTCAAAAAA
*
107097 AATAATATTTGCTT-ACTTTCATCT-TTATTT
1 AATAAGATTTG-TTCACTTTCAT-TATTATTT
107127 AATAAGATTTGTTCACTTTCATTATTATTT
1 AATAAGATTTGTTCACTTTCATTATTATTT
* *
107157 AATTAAGATGTGATCACT
1 AA-TAAGATTTGTTCACT
107175 GAGGGTTAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.07
30 26 0.62
31 13 0.31
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.50
Consensus pattern (30 bp):
AATAAGATTTGTTCACTTTCATTATTATTT
Found at i:108549 original size:111 final size:104
Alignment explanation
Indices: 108395--108704 Score: 333
Period size: 103 Copynumber: 2.9 Consensus size: 104
108385 TTAATGGTTA
* * * *
108395 AAGAAAAAAATC-GATTAATTCGGTTCAGTTAATCAAACCAAAATTTATTTGAAAATTATTAACC
1 AAGAAAAAATTCAG-TTTATTCAGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACC
* *
108459 AAACCGAATTAACCGATTTTTCTTAAAATTATTAATCGAATTAATCG
65 AAACCGAATTAA---A---TT-TGAAAATTATTAACCGAATTAATCG
* * * *
108506 AA-ACAAAAATTCAG-TTAGTTTAGTTCGGTTAATCGAATCAAAATTTATTTGAAAATTATTAAT
1 AAGA-AAAAATTCAGTTTA-TTCAGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAAC
** *
108569 CAAACTAAATT-AATTTGAAAATTATTAACCGGATTAATCG
64 CAAACCGAATTAAATTTGAAAATTATTAACCGAATTAATCG
* * * *
108609 AAGAAAAAATTCAGTTTATTCGGCTCGGCTAATCAAACCAAAATTTATTTGAAAATTATTAACCG
1 AAGAAAAAATTCAGTTTATTCAGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACCA
*
108674 AACCGAATT-AATTTGAAAATGATTAACCGAA
66 AACCGAATTAAATTTGAAAATTATTAACCGAA
108705 CCGAATTAAC
Statistics
Matches: 169, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
103 100 0.59
104 6 0.04
107 1 0.01
110 4 0.02
111 57 0.34
112 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (104 bp):
AAGAAAAAATTCAGTTTATTCAGTTCGGTTAATCAAACCAAAATTTATTTGAAAATTATTAACCA
AACCGAATTAAATTTGAAAATTATTAACCGAATTAATCG
Found at i:108682 original size:29 final size:29
Alignment explanation
Indices: 108650--108713 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
108640 ATCAAACCAA
* *
108650 AATTTATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATGATTAACCGAACCG
108679 AATTAATTTGAAAATGATTAACCGAACCG
1 AATTAATTTGAAAATGATTAACCGAACCG
108708 AATTAA
1 AATTAA
108714 CCAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.31
Consensus pattern (29 bp):
AATTAATTTGAAAATGATTAACCGAACCG
Found at i:108840 original size:106 final size:105
Alignment explanation
Indices: 108695--109116 Score: 248
Period size: 109 Copynumber: 3.9 Consensus size: 105
108685 TTTGAAAATG
* * **
108695 ATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGA-ATTAATCGA-TGCAAAAATT
1 ATTAACCGAACCGAATAAACCAATTTTTTTAAATTATTAAT-GAGATTAAT-AATTAAAAAAATT
* *
108758 CTGTTAATTTGGTTCGGTTAATAATTTTCAAATTAATTTAGTT
64 CGGTTAA-TTGGTTCGGTTAATAATTTTCAAATAAATTTAGTT
* * ** *
108801 ATTAATCGAACCGAATAAATCAA-TTTTTTGCATTGATTAATTAGATTAATAATTAAAAAAATTC
1 ATTAACCGAACCGAATAAACCAATTTTTTTAAATT-ATTAATGAGATTAATAATTAAAAAAATTC
* * * *
108865 GGTTAATTGGTTTGTTTAATAATTTTCATATAAATTTTGGTT
65 GGTTAATTGGTTCGGTTAATAATTTTCAAATAAA-TTTAGTT
* * * * **** * * *
108907 CGATCAACCAAACCGAATTAACAAAAAAATTT-CATCTATTAATTCA-ATTAGTAATTTAAAAAA
1 --ATTAACCGAACCGAATAAACCAATTTTTTTAAAT-TATTAA-TGAGATTAATAA-TTAAAAAA
* * * * *
108970 AATCGATTAATTCAGTTCGGTTAATAATTTTCAAATACATTTTGGTT
61 ATTCGGTTAATT-GGTTCGGTTAATAATTTTCAAATA-AATTTAGTT
* * * * ** *
109017 GATTAACCGAACCAAATTAACTGAATTTTTTCT---TCGATTAATTCGGTTAATAATTTTTAAAA
1 -ATTAACCGAACCGAATAAAC-CAATTTTTT-TAAAT-TATTAATGAGATTAATAA---TTAAAA
* *
109079 AAATTCAGTTAGTTCGGTTCGGTTAATAATTTTCAAAT
59 AAATTCGGTTAATT-GGTTCGGTTAATAATTTTCAAAT
109117 TAGATTAGTT
Statistics
Matches: 248, Mismatches: 51, Indels: 29
0.76 0.16 0.09
Matches are distributed among these distances:
105 35 0.14
106 52 0.21
108 33 0.13
109 55 0.22
110 31 0.12
111 42 0.17
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (105 bp):
ATTAACCGAACCGAATAAACCAATTTTTTTAAATTATTAATGAGATTAATAATTAAAAAAATTCG
GTTAATTGGTTCGGTTAATAATTTTCAAATAAATTTAGTT
Found at i:109112 original size:111 final size:107
Alignment explanation
Indices: 108751--109116 Score: 357
Period size: 109 Copynumber: 3.4 Consensus size: 107
108741 TAATCGATGC
* * *
108751 AAAAATTCTGTTAATTTGGTTCGGTTAATAATTTTCAAATTAA-TTTAGTT-ATTAATCGAACCG
1 AAAAATTC-GTTAATTCGGTTCGGTTAATAATTTTCAAA-TAATTTTGGTTGATTAACCGAACCG
* * *
108814 AA-TAAATCAATTTTTTGCATT-GATTAATTAGATTAATAA-TTAA
64 AATTAACTAAATTTTTT-C-TTCGATTAATTCGATTAATAATTTAA
* * * * *
108857 AAAAATTCGGTTAATT-GGTTTGTTTAATAATTTTCATATAAATTTTGGTTCGATCAACCAAACC
1 AAAAATTC-GTTAATTCGGTTCGGTTAATAATTTTCAAAT-AATTTTGGTT-GATTAACCGAACC
* *** * * * *
108921 GAATTAACAAAAAAATTTCATCTATTAATTCAATTAGTAATTTAA
63 GAATTAACTAAATTTTTTCTTCGATTAATTCGATTAATAATTTAA
* * *
108966 AAAAAATCGATTAATTCAGTTCGGTTAATAATTTTCAAATACATTTTGGTTGATTAACCGAACCA
1 AAAAATTCG-TTAATTCGGTTCGGTTAATAATTTTCAAATA-ATTTTGGTTGATTAACCGAACCG
* *
109031 AATTAACTGAATTTTTTCTTCGATTAATTCGGTTAATAATTTTTAA
64 AATTAACTAAATTTTTTCTTCGATTAATTCGATTAATAA--TTTAA
*
109077 AAAAATTCAGTTAGTTCGGTTCGGTTAATAATTTTCAAAT
1 AAAAATTC-GTTAATTCGGTTCGGTTAATAATTTTCAAAT
109117 TAGATTAGTT
Statistics
Matches: 207, Mismatches: 40, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
104 1 0.00
105 21 0.10
106 21 0.10
107 1 0.00
108 28 0.14
109 66 0.32
110 28 0.14
111 40 0.19
112 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (107 bp):
AAAAATTCGTTAATTCGGTTCGGTTAATAATTTTCAAATAATTTTGGTTGATTAACCGAACCGAA
TTAACTAAATTTTTTCTTCGATTAATTCGATTAATAATTTAA
Found at i:118307 original size:33 final size:33
Alignment explanation
Indices: 118234--118373 Score: 113
Period size: 32 Copynumber: 4.3 Consensus size: 33
118224 TTGTGTCATG
* * * * *
118234 TCATCACTTTTGAGTGATGTGGCATATAATACA
1 TCATCACTTTTGGGTGACGTGACACATAACACA
*
118267 TCATCACTTTTGGGTGAGGTGACACATAACACA
1 TCATCACTTTTGGGTGACGTGACACATAACACA
* * * * *
118300 CCGTCAC-TTTGGATGACATGACACATGACACA
1 TCATCACTTTTGGGTGACGTGACACATAACACA
* * * * **
118332 TCATCAC-TTCGGGTGATGTGGCACACAACATG
1 TCATCACTTTTGGGTGACGTGACACATAACACA
118364 TCATCACTTT
1 TCATCACTTT
118374 GGATGATTTG
Statistics
Matches: 84, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
32 49 0.58
33 35 0.42
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (33 bp):
TCATCACTTTTGGGTGACGTGACACATAACACA
Found at i:118386 original size:64 final size:64
Alignment explanation
Indices: 118230--118417 Score: 180
Period size: 64 Copynumber: 2.9 Consensus size: 64
118220 TTAATTGTGT
* * * * * * *
118230 CATGTCATCACTTTTGAGTGATGTGGCATATAATACATCATCACTTTTGGGTGAGGTGACACATA
1 CATGTCATCACTTTGGA-TGATATGACATATAATACATCATCAC-TTCGGGTGACGTGGCACACA
118295 A
64 A
*** * * * * * *
118296 CACACCGTCACTTTGGATGACATGACACATGACACATCATCACTTCGGGTGATGTGGCACACAA
1 CATGTCATCACTTTGGATGATATGACATATAATACATCATCACTTCGGGTGACGTGGCACACAA
* * *
118360 CATGTCATCACTTTGGATGATTTGACATA-AATACATTATCAGTTCGGGTGACGTGGCA
1 CATGTCATCACTTTGGATGATATGACATATAATACATCATCACTTCGGGTGACGTGGCA
118418 GAGGTCACAT
Statistics
Matches: 95, Mismatches: 27, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
63 24 0.25
64 39 0.41
65 20 0.21
66 12 0.13
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (64 bp):
CATGTCATCACTTTGGATGATATGACATATAATACATCATCACTTCGGGTGACGTGGCACACAA
Found at i:119627 original size:18 final size:18
Alignment explanation
Indices: 119604--119641 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
119594 AAAAATAAAA
119604 AACTCTCAAACTTC-CAAT
1 AACTCTCAAA-TTCACAAT
*
119622 AACTCTTAAATTCACAAT
1 AACTCTCAAATTCACAAT
119640 AA
1 AA
119642 AACACTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (18 bp):
AACTCTCAAATTCACAAT
Found at i:119681 original size:39 final size:39
Alignment explanation
Indices: 119597--119712 Score: 135
Period size: 39 Copynumber: 2.9 Consensus size: 39
119587 TATACTAAAA
* * *
119597 AATAAAAAACTCTCAAACTTCCAATA-ACTCTTAAATTCAC
1 AATAAAACACTCT--AACTCCCAAGAGACTCTTAAATTCAC
* * *
119637 AATAAAACACTCTAACTCCCAAGAGATTCTTTAATTCAT
1 AATAAAACACTCTAACTCCCAAGAGACTCTTAAATTCAC
* *
119676 AATAAAACACTCTAACTCTCAAGTGACTCTTAAATTC
1 AATAAAACACTCTAACTCCCAAGAGACTCTTAAATTC
119713 CCCCTTAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 9 0.14
39 44 0.68
40 12 0.18
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.29
Consensus pattern (39 bp):
AATAAAACACTCTAACTCCCAAGAGACTCTTAAATTCAC
Found at i:127171 original size:8 final size:8
Alignment explanation
Indices: 127158--127408 Score: 168
Period size: 7 Copynumber: 32.6 Consensus size: 8
127148 TATTTCTCAT
127158 TTTTTTCA
1 TTTTTTCA
127166 TTTTTTCA
1 TTTTTTCA
127174 -TTTTTCA
1 TTTTTTCA
127181 -TTTTTCTA
1 TTTTTTC-A
*
127189 TTTCTTC-
1 TTTTTTCA
127196 TTTTTTCA
1 TTTTTTCA
*
127204 CTTTTTC-
1 TTTTTTCA
127211 TTTTTT-A
1 TTTTTTCA
127218 -TTTTTCA
1 TTTTTTCA
127225 TTTTTCTTCA
1 -TTTT-TTCA
*
127235 TTTCTTCA
1 TTTTTTCA
127243 TTTTTTTCA
1 -TTTTTTCA
127252 TTTTTTTCA
1 -TTTTTTCA
127261 -TTTTTCA
1 TTTTTTCA
127268 TTTTTCTTCA
1 -TTTT-TTCA
127278 -TTTTTCA
1 TTTTTTCA
127285 -TTTTTCA
1 TTTTTTCA
127292 -TTTTTCA
1 TTTTTTCA
127299 -TTTTTCA
1 TTTTTTCA
127306 ---TTTCA
1 TTTTTTCA
127311 -TTTTTCA
1 TTTTTTCA
127318 TTTTTTTC-
1 -TTTTTTCA
127326 TTTTCTTC-
1 TTTT-TTCA
*
127334 -TTTTTCC
1 TTTTTTCA
* *
127341 CTTTTTCT
1 TTTTTTCA
127349 TTTTTTC-
1 TTTTTTCA
*
127356 TTTTTTCC
1 TTTTTTCA
*
127364 TTTTCTTCC
1 TTTT-TTCA
127373 TTTTTTC-
1 TTTTTTCA
127380 --TTTTCA
1 TTTTTTCA
127386 TTTTTTCA
1 TTTTTTCA
127394 TCATTTTTCA
1 T--TTTTTCA
127404 TTTTT
1 TTTTT
127409 CTTCAAGCGA
Statistics
Matches: 209, Mismatches: 8, Indels: 52
0.78 0.03 0.19
Matches are distributed among these distances:
5 10 0.05
6 8 0.04
7 76 0.36
8 55 0.26
9 44 0.21
10 16 0.08
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:127209 original size:31 final size:30
Alignment explanation
Indices: 127166--127309 Score: 137
Period size: 31 Copynumber: 4.9 Consensus size: 30
127156 ATTTTTTTCA
127166 TTTTTTCATTTTTCATTTTTCTATTTCTTC
1 TTTTTTCATTTTTCATTTTTCTATTTCTTC
127196 TTTTTTCACTTTTTC-TTTTT-TATTT-TTC
1 TTTTTTCA-TTTTTCATTTTTCTATTTCTTC
*
127224 ATTTTTCTTCATTTCTTCA--TTT-T-TTTCAT-
1 --TTTT-TTCATTT-TTCATTTTTCTATTTCTTC
127253 TTTTTTCATTTTTCATTTTTCTTCATTT-TTC
1 TTTTTTCATTTTTCATTTTTC-T-ATTTCTTC
*
127284 ATTTTTCATTTTTCATTTTTC-ATTTC
1 TTTTTTCATTTTTCATTTTTCTATTTC
127310 ATTTTTCATT
Statistics
Matches: 96, Mismatches: 3, Indels: 31
0.74 0.02 0.24
Matches are distributed among these distances:
25 4 0.04
26 7 0.07
27 7 0.07
28 7 0.07
29 9 0.09
30 26 0.27
31 36 0.38
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTTTCATTTTTCATTTTTCTATTTCTTC
Found at i:127209 original size:38 final size:39
Alignment explanation
Indices: 127158--127408 Score: 189
Period size: 38 Copynumber: 6.3 Consensus size: 39
127148 TATTTCTCAT
127158 TTTTTTCATTTTTTCATTTTTCATTTTTC-TATTTCTTC
1 TTTTTTCATTTTTTCATTTTTCATTTTTCATATTTCTTC
* * *
127196 TTTTTTCACTTTTTC-TTTTTTATTTTTCATTTTTCTTC
1 TTTTTTCATTTTTTCATTTTTCATTTTTCATATTTCTTC
* *
127234 ATTTCTTCATTTTTTTCATTTTTTTCATTTTTCATTTTTCTTC
1 -TTTTTTCA-TTTTTTCA--TTTTTCATTTTTCATATTTCTTC
*
127277 ATTTTTCA-TTTTTCATTTTTCATTTTTCATTTCATTT-TTC
1 TTTTTTCATTTTTTCATTTTTCATTTTTCA--T-ATTTCTTC
* *
127317 ATTTTTTTC-TTTTCTTC-TTTTTCCCTTTTTC-T-TTTTTTC
1 --TTTTTTCATTTT-TTCATTTTT-CATTTTTCATATTTCTTC
* * * *
127356 TTTTTTCCTTTTCTTCCTTTTT--TCTTTTCATTTTTTCATC
1 TTTTTTCATTTT-TTCATTTTTCAT-TTTTCA-TATTTCTTC
*
127396 ATTTTTCATTTTT
1 TTTTTTCATTTTT
127409 CTTCAAGCGA
Statistics
Matches: 177, Mismatches: 15, Indels: 41
0.76 0.06 0.18
Matches are distributed among these distances:
36 1 0.01
37 24 0.14
38 47 0.27
39 17 0.10
40 33 0.19
41 3 0.02
42 20 0.11
43 32 0.18
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (39 bp):
TTTTTTCATTTTTTCATTTTTCATTTTTCATATTTCTTC
Found at i:127326 original size:87 final size:86
Alignment explanation
Indices: 127143--127327 Score: 245
Period size: 87 Copynumber: 2.1 Consensus size: 86
127133 CTTGAACCCC
*
127143 CATTTTATTTC-TCATTTTTTTCATTTTTTCATTTTTCATTTTTCTATTTCTTCTTTTTTCACTT
1 CATTTT-TTTCTTCATTTTTTTCATTTTTTCATTTTTCATTTTTCTATTTCTTCATTTTTCACTT
*
127207 TTTCTTTTTTATTTTTCATTTTT
65 TTTCTTTTTCA-TTTTCATTTTT
**
127230 C-TTCATTTCTTCATTTTTTTCATTTTTTTCATTTTTCATTTTTCTTCATTT-TTCATTTTTCA-
1 CATTTTTTTCTTCATTTTTTTCA-TTTTTTCATTTTTCATTTTTC-T-ATTTCTTCATTTTTCAC
127292 TTTTTCATTTTTCA-TTTCATTTTT
63 TTTTTC-TTTTTCATTTTCATTTTT
127316 CATTTTTTTCTT
1 CATTTTTTTCTT
127328 TTCTTCTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
85 4 0.05
86 25 0.29
87 36 0.42
88 17 0.20
89 4 0.05
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (86 bp):
CATTTTTTTCTTCATTTTTTTCATTTTTTCATTTTTCATTTTTCTATTTCTTCATTTTTCACTTT
TTCTTTTTCATTTTCATTTTT
Found at i:127346 original size:74 final size:73
Alignment explanation
Indices: 127145--127413 Score: 226
Period size: 74 Copynumber: 3.7 Consensus size: 73
127135 TGAACCCCCA
*
127145 TTTT-ATTTCTCA-TTTT-TTTCATTTTTTCA--TTTTTCA-TTT-TTCTATTTCTTC--TTTT-
1 TTTTCATTTTTCATTTTTCTTTCA-TTTTTCATTTTTTTCATTTTCTTC-ATTT-TTCATTTTTC
127200 TTCACTTTTTCT
63 TTCA-TTTTTCT
* *
127212 TTTTTATTTTTCATTTTTC-TTCATTTCTTCATTTTTTTCATTTTTTTCATTTTTCATTTTTCTT
1 TTTTCATTTTTCATTTTTCTTTCATTT-TTCATTTTTTTCATTTTCTTCATTTTTCATTTTTCTT
127276 CATTTTTCAT
65 CATTTTTC-T
*
127286 TTTTCATTTTTCATTTTTCATTTCATTTTTCATTTTTTTC-TTTTCTTC-TTTTTCCCTTTTTCT
1 TTTTCATTTTTCATTTTTC-TTTCATTTTTCATTTTTTTCATTTTCTTCATTTTT-CATTTTTCT
127349 T--TTTTTCTT
64 TCATTTTTC-T
* * *
127358 TTTTCCTTTTCTTCCTTTTTTCTTTTCATTTTTTCATCATTTTTCATTTTTCTTCA
1 TTTT-CATTT-TT-CATTTTTC-TTTCA-TTTTTCAT-TTTTTTCA-TTTTCTTCA
127414 AGCGAAATAT
Statistics
Matches: 170, Mismatches: 9, Indels: 33
0.80 0.04 0.16
Matches are distributed among these distances:
67 4 0.02
68 10 0.06
69 12 0.07
71 10 0.06
72 18 0.11
73 22 0.13
74 41 0.24
75 24 0.14
76 15 0.09
77 6 0.04
79 8 0.05
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (73 bp):
TTTTCATTTTTCATTTTTCTTTCATTTTTCATTTTTTTCATTTTCTTCATTTTTCATTTTTCTTC
ATTTTTCT
Found at i:127372 original size:9 final size:8
Alignment explanation
Indices: 127311--127383 Score: 64
Period size: 8 Copynumber: 9.4 Consensus size: 8
127301 TTTCATTTCA
*
127311 TTTTTCAT
1 TTTTTCCT
*
127319 TTTTTTCT
1 TTTTTCCT
127327 TTTCTT-C-
1 TTT-TTCCT
*
127334 TTTTTCCC
1 TTTTTCCT
127342 TTTTT-CT
1 TTTTTCCT
*
127349 TTTTTTCT
1 TTTTTCCT
127357 TTTTTCCT
1 TTTTTCCT
127365 TTTCTTCCT
1 TTT-TTCCT
127374 TTTTT-CT
1 TTTTTCCT
127381 TTT
1 TTT
127384 CATTTTTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
6 2 0.04
7 15 0.27
8 29 0.52
9 10 0.18
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCCT
Found at i:127391 original size:95 final size:94
Alignment explanation
Indices: 127154--127394 Score: 241
Period size: 95 Copynumber: 2.5 Consensus size: 94
127144 ATTTTATTTC
*
127154 TCATTTTTTTCATTTTTTCA--TTT-TTCATTTTTCTATTTCTTC-TTTTTTCACTTTTTCTTTT
1 TCATTTTTTTCA-TTTTTCACTTTTCTTCATTTTTC-A-TT-TTCATTTTTTCA-TTTTTCTATT
*
127215 TTATTTTTCATTTTTCTTCATTTCTTCATTTTTT
61 TCATTTTTCATTTTTCTTCATTTCTTCATTTTTT
*
127249 TCATTTTTTTCATTTTTCATTTTTCTTCATTTTTCATTTTTCA-TTTTTCATTTTTC-ATTTCAT
1 TCATTTTTTTCATTTTTCACTTTTCTTCATTTTTCA-TTTTCATTTTTTCATTTTTCTATTTCAT
* *
127312 TTTTCATTTTT-TTCTTTTCTTCTTTTTCCCTTTT
65 TTTTCATTTTTCTTCATTTCTTC--ATT---TTTT
* *
127346 TC-TTTTTTTCTTTTTTC-CTTTTCTTCCTTTTTTC-TTTTCATTTTTTCAT
1 TCATTTTTTTCATTTTTCACTTTTCTT-CATTTTTCATTTTCATTTTTTCAT
127395 CATTTTTCAT
Statistics
Matches: 128, Mismatches: 7, Indels: 22
0.82 0.04 0.14
Matches are distributed among these distances:
92 10 0.08
93 16 0.12
94 21 0.16
95 37 0.29
96 28 0.22
97 16 0.12
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.73
Consensus pattern (94 bp):
TCATTTTTTTCATTTTTCACTTTTCTTCATTTTTCATTTTCATTTTTTCATTTTTCTATTTCATT
TTTCATTTTTCTTCATTTCTTCATTTTTT
Found at i:137130 original size:45 final size:45
Alignment explanation
Indices: 137063--137233 Score: 288
Period size: 45 Copynumber: 3.8 Consensus size: 45
137053 TGTTATTCAC
*
137063 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
1 AAAAATAAA-CCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
* *
137109 AAAAATAAACCTAACCTCATGATATCTAATTCGCATGCTTGTTTG
1 AAAAATAAACCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
*
137154 AAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTGTTCG
1 AAAAATAAACCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
*
137199 AAAAATAAACCTAACCGCATGATATCTAGTTCGCA
1 AAAAATAAACCTAACCGCATGATATCTAATTCGCA
137234 AGCATTTATT
Statistics
Matches: 119, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 111 0.93
46 8 0.07
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (45 bp):
AAAAATAAACCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
Found at i:139924 original size:42 final size:42
Alignment explanation
Indices: 139867--139946 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
139857 GTTCCTTTTG
* *
139867 TTTTTTTGCTCTCGGTTAATTTCTCCTCTTCTCTGTGTTCGT
1 TTTTTTTGCTCTCGGTTAATTTCCCCTCTTCGCTGTGTTCGT
139909 TTTTTTTGCTCTCGGTTAATTTCCCCTCTTCGCTGTGT
1 TTTTTTTGCTCTCGGTTAATTTCCCCTCTTCGCTGTGT
139947 GATTTCTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.05, C:0.25, G:0.15, T:0.55
Consensus pattern (42 bp):
TTTTTTTGCTCTCGGTTAATTTCCCCTCTTCGCTGTGTTCGT
Found at i:149484 original size:131 final size:131
Alignment explanation
Indices: 149277--149566 Score: 402
Period size: 131 Copynumber: 2.3 Consensus size: 131
149267 TACTTTGTTT
* *
149277 TCGTAACTCTCTCAAAGCA---G-T-AGTTA-AAG-TTACCATAGAATTCGCCCTTTCAATTTAA
1 TCGTAACTCTCTCAAAGCACTTGTTAAGTTACCAGCTTACCATAGAATTCACCC-TTCAATTTAA
* * * *
149335 ACAACATTTTACAGAGGTGGGAATAAATACTAAATAGGAGGTCGGTGAATGCTATGCTACTCTGC
65 ACAACATTTTACAGAGGTGAGAATAAATACTAAATAGGAAGTCGGTAAATGCAATGCTACTCTGC
149400 TG
130 TG
149402 TCGTAACT-TGCTCAAAGCACTTGTTAAAGTTACCAGCTTACCATAGAATTCACCC-TCAATTTA
1 TCGTAACTCT-CTCAAAGCACTTGTT-AAGTTACCAGCTTACCATAGAATTCACCCTTCAATTTA
*
149465 AAC-ACTATTTTACAGAGGTGAGAATAAATACTAAATAGGAAGTTGGTAAATGCAATGCTACTCT
64 AACAAC-ATTTTACAGAGGTGAGAATAAATACTAAATAGGAAGTCGGTAAATGCAATGCTACTCT
149529 GCTG
128 GCTG
*
149533 TCGTAGCTCTCTCAAAGCACTTGTTAAGTTACCA
1 TCGTAACTCTCTCAAAGCACTTGTTAAGTTACCA
149567 AAGAATTTAA
Statistics
Matches: 146, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
124 1 0.01
125 17 0.12
128 1 0.01
129 1 0.01
130 11 0.08
131 95 0.65
132 3 0.02
133 17 0.12
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (131 bp):
TCGTAACTCTCTCAAAGCACTTGTTAAGTTACCAGCTTACCATAGAATTCACCCTTCAATTTAAA
CAACATTTTACAGAGGTGAGAATAAATACTAAATAGGAAGTCGGTAAATGCAATGCTACTCTGCT
G
Found at i:151164 original size:280 final size:280
Alignment explanation
Indices: 150657--151186 Score: 749
Period size: 280 Copynumber: 1.9 Consensus size: 280
150647 TTCTTTTTCC
* ** * *
150657 TTTATTTTCAATAGATAAAAGTTCTTTTATAACTAAGAATCTTTCTGCAGGCCATTTACAATTGG
1 TTTATTTTCAATAGATAAAAGTTCTTTTATAACTAACAATCTCACTGCAGGACATCTACAATTGG
* * * *
150722 AAATATTTGATAACCTTTCTAAATTGCAAGTATTAAACTTGGACGGAAACCAGATTCCTGGTAGC
66 AAATATTTGATAACCTTTCTAAATTGCAACTATTAAACTTGGAAGGAAACCAAATTCCTAGTAGC
* * * *
150787 TTTCCCAGTAGCTTGTACAAATGAAAAGAGTTGAGGTATTTATCATTTTGGAACAACTATATGGA
131 ATTCCCAGTAGCTTATACAAATGAAAAGAATTGAGGTATTTATCATTTTCGAACAACTATATGGA
* * *
150852 AGGAAGTATACCTATAGAAATCAAATATTTGACAATGATCCAATCTTTGTATCTTCATCAGAACA
196 AGGAAATATACCAATAGAAATCAAAAATTTGACAATGATCCAATCTTTGTATCTTCATCAGAACA
150917 ATCTTTGCATTTCGTTCTCT
261 ATCTTTGCATTTCGTTCTCT
* * * *
150937 TTTATTTTCATTAGATAAAAGTTGTTTTATAACTAACAATCTCACTGCATGACATCTAGAATTGG
1 TTTATTTTCAATAGATAAAAGTTCTTTTATAACTAACAATCTCACTGCAGGACATCTACAATTGG
* * * * *
151002 GAATATTTGATAACCTTTCTAAATTGTAACTATTAAACTTGTATAGG-AATCAAATTTCTAGTAG
66 AAATATTTGATAACCTTTCTAAATTGCAACTATTAAACTTGGA-AGGAAACCAAATTCCTAGTAG
* * *
151066 CATTCCCAGTAGCTTATACAAGTGCAAAGAATTGAGGTATTTATCATTTTCGAACAACTCTATGG
130 CATTCCCAGTAGCTTATACAAATGAAAAGAATTGAGGTATTTATCATTTTCGAACAACTATATGG
* **
151131 AAGGAAATATACCAATAGAAAT-AAGAAATTTGACGATTCTCCAATCTTTGTATCTT
195 AAGGAAATATACCAATAGAAATCAA-AAATTTGACAATGATCCAATCTTTGTATCTT
151187 GATTACAACA
Statistics
Matches: 217, Mismatches: 31, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
279 2 0.01
280 213 0.98
281 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (280 bp):
TTTATTTTCAATAGATAAAAGTTCTTTTATAACTAACAATCTCACTGCAGGACATCTACAATTGG
AAATATTTGATAACCTTTCTAAATTGCAACTATTAAACTTGGAAGGAAACCAAATTCCTAGTAGC
ATTCCCAGTAGCTTATACAAATGAAAAGAATTGAGGTATTTATCATTTTCGAACAACTATATGGA
AGGAAATATACCAATAGAAATCAAAAATTTGACAATGATCCAATCTTTGTATCTTCATCAGAACA
ATCTTTGCATTTCGTTCTCT
Found at i:151890 original size:41 final size:39
Alignment explanation
Indices: 151829--151965 Score: 121
Period size: 41 Copynumber: 3.4 Consensus size: 39
151819 GATGCATTTC
*
151829 CTAAAGTACGAGTCTTTAGTGGTGTTTGTATAAAAATGCCA
1 CTAAAGTACGAGTCTATAGTGG-GTTTGTATAAAAA-GCCA
*** * *
151870 CTAAAGTACGAGTCTATAGTGGCCCTGCATAAAAACACCA
1 CTAAAGTACGAGTCTATAGTGGGTTTGTATAAAAA-GCCA
* * * *
151910 CTAACGTATGAGTTTATAGTTGCGTTTGTATACAAAAGCCA
1 CTAAAGTACGAGTCTATAG-TGGGTTTGTATA-AAAAGCCA
* *
151951 CTATAGTAAGAGTCT
1 CTAAAGTACGAGTCT
151966 TTTGCGACGT
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
40 28 0.38
41 42 0.57
42 4 0.05
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (39 bp):
CTAAAGTACGAGTCTATAGTGGGTTTGTATAAAAAGCCA
Found at i:151913 original size:40 final size:41
Alignment explanation
Indices: 151829--151929 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 41
151819 GATGCATTTC
* *** * **
151829 CTAAAGTACGAGTCTTTAGTGGTGTTTGTATAAAAATGCCA
1 CTAAAGTACGAGTCTATAGTGGTCCCTGCATAAAAACACCA
151870 CTAAAGTACGAGTCTATAGTGG-CCCTGCATAAAAACACCA
1 CTAAAGTACGAGTCTATAGTGGTCCCTGCATAAAAACACCA
* * *
151910 CTAACGTATGAGTTTATAGT
1 CTAAAGTACGAGTCTATAGT
151930 TGCGTTTGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 29 0.58
41 21 0.42
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (41 bp):
CTAAAGTACGAGTCTATAGTGGTCCCTGCATAAAAACACCA
Found at i:152198 original size:82 final size:83
Alignment explanation
Indices: 152112--152359 Score: 250
Period size: 83 Copynumber: 3.0 Consensus size: 83
152102 TGCATCTAAG
* * * ** *
152112 GTACTACTCTATTGCGGTGTTTGTCGAAAAAAATACCACTATAGA-TAATCCTATTGGGGCATCT
1 GTACTACTCTATTGCGGTGTTTGTTG-AAAAAATGCCACTATAGATTAACCCTATTACGACATCT
*
152176 -TATAAAAATGTCGATAAA
65 GTATAAAAACGTCGATAAA
* * * * * *
152194 GTACTACTTTATTG-TGTCATTTTTTGAAAAAATGCCACTATATATTAACCCTATTACGACATTT
1 GTACTACTCTATTGCGGT-GTTTGTTGAAAAAATGCCACTATAGATTAACCCTATTACGACATCT
* *
152258 GTATAACAACGTCGCTAAA
65 GTATAAAAACGTCGATAAA
* * * * * *
152277 GTATTACTCTGTTGCGATGTTTGTTGAAAAAATGCCACTATAGATTAACCCTATTACAACGTTTG
1 GTACTACTCTATTGCGGTGTTTGTTGAAAAAATGCCACTATAGATTAACCCTATTACGACATCTG
* *
152342 TATAAAAACATCGCTAAA
66 TATAAAAACGTCGATAAA
152360 TTTACCATTT
Statistics
Matches: 135, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
81 18 0.13
82 32 0.24
83 84 0.62
84 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (83 bp):
GTACTACTCTATTGCGGTGTTTGTTGAAAAAATGCCACTATAGATTAACCCTATTACGACATCTG
TATAAAAACGTCGATAAA
Found at i:152468 original size:46 final size:46
Alignment explanation
Indices: 152401--152495 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
152391 GACGTTATAT
*
152401 GTTTAAAGTTAGTAACGTTTACTCTCAAAACGCCGCTAAAAATACC
1 GTTTAAAGTTAGTAACATTTACTCTCAAAACGCCGCTAAAAATACC
152447 GTTTAAAGTTAGTAACATTTACTCTCAAAACGCCGCTAAAAATACC
1 GTTTAAAGTTAGTAACATTTACTCTCAAAACGCCGCTAAAAATACC
152493 GTT
1 GTT
152496 GTAGAATAGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (46 bp):
GTTTAAAGTTAGTAACATTTACTCTCAAAACGCCGCTAAAAATACC
Found at i:153541 original size:39 final size:39
Alignment explanation
Indices: 153470--153580 Score: 170
Period size: 39 Copynumber: 2.9 Consensus size: 39
153460 TTTATACTAA
* * *
153470 AAAACTCTCCAACTTCCAAGA-ACTCTTAAATTCACAAT
1 AAAACACTCTAACTCCCAAGAGACTCTTAAATTCACAAT
*
153508 AAAACACTCTAACTCCCAAGAGACTCTTTAATTCACAAT
1 AAAACACTCTAACTCCCAAGAGACTCTTAAATTCACAAT
*
153547 AAAACACTCTAACTCCCAAAAGACTCTTAAATTC
1 AAAACACTCTAACTCCCAAGAGACTCTTAAATTC
153581 CCCCTTAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
38 18 0.27
39 48 0.73
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (39 bp):
AAAACACTCTAACTCCCAAGAGACTCTTAAATTCACAAT
Found at i:156265 original size:60 final size:61
Alignment explanation
Indices: 156143--156279 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 61
156133 GTATATATAT
* ** * *
156143 ATAGTTTG-AGATGAAATTGAAATGTTCAAAAAATTTGGGGACTAATTTATAATGAAGCTC
1 ATAGTTTGAAGATGAAATTGAAATGCTCAAAAAATTTAAGAACTAATTTAGAATGAAGCTC
* * * * *
156203 ATAGTTTGAAGGTGAAATTGAAATGCTC-AAAAGTTTAAGAATTAATTTAGAATGATGGTC
1 ATAGTTTGAAGATGAAATTGAAATGCTCAAAAAATTTAAGAACTAATTTAGAATGAAGCTC
* *
156263 ATAATTTAAAGATGAAA
1 ATAGTTTGAAGATGAAA
156280 CTGGAATATT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
60 46 0.73
61 17 0.27
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (61 bp):
ATAGTTTGAAGATGAAATTGAAATGCTCAAAAAATTTAAGAACTAATTTAGAATGAAGCTC
Found at i:156678 original size:12 final size:13
Alignment explanation
Indices: 156661--156689 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
156651 GAATTAGGAA
156661 AAAATATAATCT-
1 AAAATATAATCTG
156673 AAAATATAATCTG
1 AAAATATAATCTG
156686 AAAA
1 AAAA
156690 AAAAAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (13 bp):
AAAATATAATCTG
Found at i:161907 original size:26 final size:27
Alignment explanation
Indices: 161868--161918 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
161858 ATTTATAATA
**
161868 ATAAATTTTTTATAATTT-AAAAAATT
1 ATAAATTTCATATAATTTGAAAAAATT
*
161894 ATAAATTTCATATATTTTGAAAAAA
1 ATAAATTTCATATAATTTGAAAAAA
161919 GTATTTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
ATAAATTTCATATAATTTGAAAAAATT
Found at i:162341 original size:340 final size:337
Alignment explanation
Indices: 161868--162694 Score: 1392
Period size: 340 Copynumber: 2.5 Consensus size: 337
161858 ATTTATAATA
* * **
161868 ATAAATTTTTTATAATTTAAAAAATTATAAATTTCATATA-TTTTGAAAAAAGTATTTTCTTTTA
1 ATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTACCTTTTA
* *
161932 AAATTAATTG-TTAAAAA-ATATAAAATATTAAAATAAACTTTTAATTACAATTAAGTGATCAAA
66 AAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTAAGGGATCAAA
* * * *
161995 TGAATTATTATTCATTAATTTTTATTTTTTAGCAACAGTTAATAATGTTTATTTATTTTTAATAA
131 TGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAACAATGTTTATTCATTTTTAATAA
**
162060 AATTATTTTGATTTTTGCATTAAAATTACACAATACGTATAATCTAGTATA-AGAAAACTTTGAG
196 AATTATTTAAATTTTTGCATTAAAATTACACAATACGTATAATCTAGTATATA-AAAACTTTGAG
* *
162124 GGTAAGTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTACAAAAT
260 GGTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTTACAAAAT
162189 GATGATGATGATG
325 GATGATGATGATG
*
162202 ATAAATATTTTATAATTTTAAAAATTATAAATTTCATATATTTTTTGAAAAAATTATTACCTTTT
1 ATAAATATTTTATAATTTAAAAAATTATAAATTTCATATA-TTTTTGAAAAAATTATTACCTTTT
*
162267 AAAATTAATTGTTTAAAAATATAAAAAAAGTATTAAAATAAACTTTTAATTACAATTGAGGGATC
65 AAAATTAATTGTTTAAAAATAT-AAAAAA-TATTAAAATAAACTTTTAATTACAATTAAGGGATC
162332 AAATGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAACAATGTTTATTCATTTTTAA
128 AAATGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAACAATGTTTATTCATTTTTAA
*
162397 TAAAATTATTTAAATTTTTGCATTAAAATTACACAATACTTATAATCTAGTATATAAAAACTTTG
193 TAAAATTATTTAAATTTTTGCATTAAAATTACACAATACGTATAATCTAGTATATAAAAACTTTG
162462 AGGGTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTTACAAA
258 AGGGTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTTACAAA
162527 ATGATGATGATGATG
323 ATGATGATGATGATG
* *
162542 ATAAATATTTTATAATTTAAAAAATTATAAAATTCATATATTTTTGAAAAAATTATTGCCTTTTA
1 ATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTACCTTTTA
* *
162607 AAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTTAGGGATTAAA
66 AAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTAAGGGATCAAA
*
162672 TGAATTATTATTCAATAATTTTT
131 TGAATTATTATTCATTAATTTTT
162695 TCAAAATATA
Statistics
Matches: 463, Mismatches: 23, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
334 38 0.08
336 31 0.07
337 65 0.14
338 8 0.02
339 50 0.11
340 270 0.58
341 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (337 bp):
ATAAATATTTTATAATTTAAAAAATTATAAATTTCATATATTTTTGAAAAAATTATTACCTTTTA
AAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTAAGGGATCAAA
TGAATTATTATTCATTAATTTTTAATTTTTAACAACAGTTAACAATGTTTATTCATTTTTAATAA
AATTATTTAAATTTTTGCATTAAAATTACACAATACGTATAATCTAGTATATAAAAACTTTGAGG
GTAAATATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTATTTTACAAAATG
ATGATGATGATG
Found at i:169389 original size:24 final size:24
Alignment explanation
Indices: 169355--169405 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
169345 CGTTCGGTAA
169355 TATGTTCGTTTAAGTTCGTTCATT
1 TATGTTCGTTTAAGTTCGTTCATT
* * *
169379 TATGTTTGTTTATGTTCGTTCGTT
1 TATGTTCGTTTAAGTTCGTTCATT
169403 TAT
1 TAT
169406 ATTCAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.10, G:0.18, T:0.59
Consensus pattern (24 bp):
TATGTTCGTTTAAGTTCGTTCATT
Found at i:169405 original size:14 final size:14
Alignment explanation
Indices: 169358--169405 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
169348 TCGGTAATAT
*
169358 GTTCGTTTAAGTTC
1 GTTCGTTTATGTTC
*
169372 GTTCATTTATG-T-
1 GTTCGTTTATGTTC
169384 -TT-GTTTATGTTC
1 GTTCGTTTATGTTC
169396 GTTCGTTTAT
1 GTTCGTTTAT
169406 ATTCAACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
10 6 0.22
11 3 0.11
13 3 0.11
14 15 0.56
ACGTcount: A:0.12, C:0.10, G:0.19, T:0.58
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:172912 original size:6 final size:6
Alignment explanation
Indices: 172901--172925 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
172891 ATTAATGACT
172901 AACTAA AACTAA AACTAA AACTAA A
1 AACTAA AACTAA AACTAA AACTAA A
172926 GAACTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AACTAA
Found at i:174752 original size:19 final size:17
Alignment explanation
Indices: 174730--174773 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
174720 TAATATCTAA
174730 TATAATATGCAATACTATT
1 TATAATATGCAAT--TATT
*
174749 TATAACATGCAATTATT
1 TATAATATGCAATTATT
174766 TA-AATATG
1 TATAATATG
174774 AACTATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 6 0.26
19 12 0.52
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (17 bp):
TATAATATGCAATTATT
Found at i:177413 original size:25 final size:24
Alignment explanation
Indices: 177365--177425 Score: 95
Period size: 25 Copynumber: 2.5 Consensus size: 24
177355 AATATTTATC
**
177365 TTCAAGATAATTTTAAATTAAATA
1 TTCAAGATAATTCGAAATTAAATA
177389 TTCAAGATAATTCCGAAATTAAATA
1 TTCAAGATAATT-CGAAATTAAATA
177414 TTCAAGATAATT
1 TTCAAGATAATT
177426 TTGTCCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 12 0.35
25 22 0.65
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (24 bp):
TTCAAGATAATTCGAAATTAAATA
Found at i:180832 original size:23 final size:23
Alignment explanation
Indices: 180806--180851 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
180796 CACCACAGCT
*
180806 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
180829 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
180852 TATAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:181117 original size:31 final size:30
Alignment explanation
Indices: 181073--181132 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
181063 TAATGTATAG
181073 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
181103 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
181133 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:182103 original size:10 final size:10
Alignment explanation
Indices: 182088--182122 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
182078 AACTTTGTCT
182088 AGAAGAAGAA
1 AGAAGAAGAA
*
182098 AGAAGAATAA
1 AGAAGAAGAA
182108 AGAAGAAGAA
1 AGAAGAAGAA
182118 GAGAA
1 -AGAA
182123 ATCTGGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (10 bp):
AGAAGAAGAA
Found at i:187749 original size:23 final size:23
Alignment explanation
Indices: 187694--187749 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
187684 TAAATGTACT
*
187694 GAAGTGCCACGTAGAATTGCACC
1 GAAGTGCCATGTAGAATTGCACC
187717 GAAGTGCCATGTAGAATTGCACC
1 GAAGTGCCATGTAGAATTGCACC
*
187740 GTAGTGCCAT
1 GAAGTGCCAT
187750 ATAAGATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (23 bp):
GAAGTGCCATGTAGAATTGCACC
Found at i:188004 original size:30 final size:31
Alignment explanation
Indices: 187965--188025 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
187955 ATTTATAATG
*
187965 TATAGACATATAAT-TTCCAT-ACCTTTATCA
1 TATAAACATATAATGTTCCATCA-CTTTATCA
*
187995 TATAAACATATCATGTTCCATCACTTTATCA
1 TATAAACATATAATGTTCCATCACTTTATCA
188026 CATAGCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 12 0.44
31 14 0.52
32 1 0.04
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (31 bp):
TATAAACATATAATGTTCCATCACTTTATCA
Found at i:189042 original size:10 final size:10
Alignment explanation
Indices: 189027--189053 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
189017 AGCTTTGTCT
189027 AGAAGAAGAA
1 AGAAGAAGAA
189037 AGAAGAAGAA
1 AGAAGAAGAA
189047 AGAAGAA
1 AGAAGAA
189054 TAAGAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AGAAGAAGAA
Found at i:194077 original size:18 final size:18
Alignment explanation
Indices: 194050--194093 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
194040 TTAGGATAAT
*
194050 GAAAAGAAAGTAATGAAA
1 GAAAAGAAAGCAATGAAA
* *
194068 GAAAATAAAGCGATGAAA
1 GAAAAGAAAGCAATGAAA
194086 GAAAAGAA
1 GAAAAGAA
194094 CTTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (18 bp):
GAAAAGAAAGCAATGAAA
Found at i:201995 original size:34 final size:32
Alignment explanation
Indices: 201931--202018 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 32
201921 AATTTTAATT
* * * * *
201931 TTTTTAATTTTTTTATTTAATTTTTGATTTAC
1 TTTTTAAATTTTTTAATAAATTTTTAATTTAA
201963 TTTTTAAATTTTTTAATAAATTTTATCAATTTAA
1 TTTTTAAATTTTTTAATAAATTTT-T-AATTTAA
* *
201997 TTTTTAAAATTTTAAATAAATT
1 TTTTTAAATTTTTTAATAAATT
202019 ATTTTTTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 21 0.45
33 1 0.02
34 25 0.53
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (32 bp):
TTTTTAAATTTTTTAATAAATTTTTAATTTAA
Found at i:206470 original size:20 final size:20
Alignment explanation
Indices: 206441--206479 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
206431 CTCTCATTTT
* *
206441 TGCATCTTTGCATTTGTATG
1 TGCATATTTGCATTAGTATG
206461 TGCATATTTGCATTAGTAT
1 TGCATATTTGCATTAGTAT
206480 ATACACATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (20 bp):
TGCATATTTGCATTAGTATG
Found at i:207705 original size:12 final size:12
Alignment explanation
Indices: 207683--207785 Score: 100
Period size: 12 Copynumber: 8.0 Consensus size: 12
207673 CAAATCAAAG
207683 CAAAGGAAAAAAA
1 CAAA-GAAAAAAA
207696 CAAAGAAAAAAA
1 CAAAGAAAAAAA
207708 CAAAGAGAAAAAA
1 CAAAGA-AAAAAA
*
207721 GAAAAGAAAAAAA
1 -CAAAGAAAAAAA
207734 CAAAGAGAAAAAAA
1 C-AA-AGAAAAAAA
*
207748 GAAAAGAGAAAAAA
1 -CAAAGA-AAAAAA
*
207762 CAAA-AGAAAAAG
1 CAAAGA-AAAAAA
207774 CAAAGAAAAAAA
1 CAAAGAAAAAAA
207786 AGACTAGAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
12 30 0.39
13 25 0.32
14 22 0.29
ACGTcount: A:0.80, C:0.06, G:0.15, T:0.00
Consensus pattern (12 bp):
CAAAGAAAAAAA
Found at i:207716 original size:14 final size:13
Alignment explanation
Indices: 207683--207785 Score: 115
Period size: 14 Copynumber: 8.0 Consensus size: 13
207673 CAAATCAAAG
*
207683 CAAAGGAAAAAAA
1 CAAAAGAAAAAAA
207696 C-AAAGAAAAAAA
1 CAAAAGAAAAAAA
207708 C-AAAGAGAAAAAA
1 CAAAAGA-AAAAAA
*
207721 GAAAAGAAAAAAA
1 CAAAAGAAAAAAA
207734 CAAAGAGAAAAAAA
1 CAAA-AGAAAAAAA
*
207748 GAAAAGAGAAAAAA
1 CAAAAGA-AAAAAA
*
207762 CAAAAG-AAAAAG
1 CAAAAGAAAAAAA
207774 C-AAAGAAAAAAA
1 CAAAAGAAAAAAA
207786 AGACTAGAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
11 4 0.05
12 27 0.35
13 19 0.24
14 28 0.36
ACGTcount: A:0.80, C:0.06, G:0.15, T:0.00
Consensus pattern (13 bp):
CAAAAGAAAAAAA
Found at i:207726 original size:26 final size:26
Alignment explanation
Indices: 207683--207785 Score: 142
Period size: 26 Copynumber: 4.0 Consensus size: 26
207673 CAAATCAAAG
207683 CAAAG-GAAAAAA-ACAAAGAAAAAAA
1 CAAAGAGAAAAAAGA-AAAGAAAAAAA
207708 CAAAGAGAAAAAAGAAAAGAAAAAAA
1 CAAAGAGAAAAAAGAAAAGAAAAAAA
207734 CAAAGAGAAAAAAAGAAAAGAGAAAAAA
1 CAAAGAG-AAAAAAGAAAAGA-AAAAAA
*
207762 CAAA-AG-AAAAAGCAAAGAAAAAAA
1 CAAAGAGAAAAAAGAAAAGAAAAAAA
207786 AGACTAGAAG
Statistics
Matches: 73, Mismatches: 1, Indels: 9
0.88 0.01 0.11
Matches are distributed among these distances:
24 6 0.08
25 16 0.22
26 25 0.34
27 16 0.22
28 10 0.14
ACGTcount: A:0.80, C:0.06, G:0.15, T:0.00
Consensus pattern (26 bp):
CAAAGAGAAAAAAGAAAAGAAAAAAA
Found at i:207758 original size:41 final size:40
Alignment explanation
Indices: 207690--207788 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 40
207680 AAGCAAAGGA
* *
207690 AAAAAAC-AA-AGAAAAAAA-CAAAGAGAAAAAAGAAAAG
1 AAAAAACAAAGAGAAAAAAAGAAAAGAGAAAAAACAAAAG
207727 AAAAAAACAAAGAGAAAAAAAGAAAAGAGAAAAAACAAAAG
1 -AAAAAACAAAGAGAAAAAAAGAAAAGAGAAAAAACAAAAG
*
207768 AAAAAGCAAAGA-AAAAAAAGA
1 AAAAAACAAAGAGAAAAAAAGA
207789 CTAGAAGCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
38 7 0.13
39 11 0.20
40 20 0.36
41 17 0.31
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (40 bp):
AAAAAACAAAGAGAAAAAAAGAAAAGAGAAAAAACAAAAG
Found at i:207794 original size:25 final size:25
Alignment explanation
Indices: 207683--207786 Score: 104
Period size: 25 Copynumber: 4.0 Consensus size: 25
207673 CAAATCAAAG
* *
207683 CAAAGGAAAAAAACAAAG-AAAAAAA
1 CAAAAGAAAAAGA-AAAGAAAAAAAA
207708 CAAAGAGAAAAAAGAAAAG-AAAAAAA
1 CAAA-AG-AAAAAGAAAAGAAAAAAAA
*
207734 CAAAGAGAAAAAAAGAAAAGAGAAAAAA
1 CAAA-AG--AAAAAGAAAAGAAAAAAAA
*
207762 CAAAAGAAAAAGCAAAGAAAAAAAA
1 CAAAAGAAAAAGAAAAGAAAAAAAA
207787 GACTAGAAGC
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
25 21 0.30
26 19 0.27
27 20 0.29
28 10 0.14
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (25 bp):
CAAAAGAAAAAGAAAAGAAAAAAAA
Found at i:209008 original size:74 final size:75
Alignment explanation
Indices: 208921--209402 Score: 329
Period size: 76 Copynumber: 6.4 Consensus size: 75
208911 AGTTTTATTA
* **
208921 AAAACAAATTTTGTCTCGCTTGAGACAGTCTTATTT-AATACTG-AG-GATTT-ATCTCACTTGA
1 AAAACAAATTTTGTCTCGCTTGAGACAGTCTTATTTGAA-A--GAAGACATTTCATCTCACTCAA
*
208982 GATTGTTTTTCTT
63 GATTGCTTTTCTT
* * * * *
208995 AAAACAAACTTTGTCTCGCTTGAGACAATTTTATTTGAAAGAAGACATTTCATTTGACTCAAGAT
1 AAAACAAATTTTGTCTCGCTTGAGACAGTCTTATTTGAAAGAAGACATTTCATCTCACTCAAGAT
209060 TGCTTTTCTT
66 TGCTTTTCTT
* * * ** * * * *
209070 AAAACAAGATTTTGTCTCCCTTGAGACAGTTTTTACTCAAAACAAGACATTTCTTTTCACTACAT
1 AAAACAA-ATTTTGTCTCGCTTGAGACAG-TCTTATTTGAAAGAAGACATTTCATCTCACT-CAA
*
209135 G-TT--TTTTTTT
63 GATTGCTTTTCTT
* * * ** * *
209145 AAAACAAGA-TTTGTCTCGCTTGAGACAATTTTTACTCAAAAGAATACATTTCATTTCACTCAAG
1 AAAACAA-ATTTTGTCTCGCTTGAGAC-AGTCTTATTTGAAAGAAGACATTTCATCTCACTCAAG
* *
209209 ATTGTTTTTCTC
64 ATTGCTTTTCTT
* * * * * * * *
209221 AAAATAGACTTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAATACATTTCATTTCACT-ACAG
1 AAAACAAATTTTGTCTCGCTTGAGACAG-TCTTATTTGAAAGAAGACATTTCATCTCACTCA-AG
**
209285 ATTATTTTTCTT
64 ATTGCTTTTCTT
* * * *** * *
209297 AAAACAAGA-TTTATCTCGCTTGAGATAGTTTTTACCCGAAACAAGA-ATATTCATTTCACTCAA
1 AAAACAA-ATTTTGTCTCGCTTGAGACAG-TCTTATTTGAAAGAAGACAT-TTCATCTCACTCAA
*
209360 GATTGTTTTTCTT
63 GATTGCTTTTCTT
*
209373 AAAACCAAATTTTGTCTCTCTTGAGACAGT
1 AAAA-CAAATTTTGTCTCGCTTGAGACAGT
209403 TTCCCTGAAA
Statistics
Matches: 344, Mismatches: 45, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
72 1 0.00
73 5 0.01
74 84 0.24
75 49 0.14
76 154 0.45
77 48 0.14
78 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (75 bp):
AAAACAAATTTTGTCTCGCTTGAGACAGTCTTATTTGAAAGAAGACATTTCATCTCACTCAAGAT
TGCTTTTCTT
Found at i:209263 original size:76 final size:76
Alignment explanation
Indices: 208981--209404 Score: 515
Period size: 76 Copynumber: 5.6 Consensus size: 76
208971 ATCTCACTTG
* * *
208981 AGATTGTTTTTCTTAAAACAA-ACTTTGTCTCGCTTGAGACA-ATTTTATTTGAAAGAAGACATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATT
*
209044 TCATTTGACTCA
65 TCATTTCACTCA
* * * *
209056 AGATTGCTTTTCTTAAAACAAGATTTTGTCTCCCTTGAGACAGTTTTTACTCAAAACAAGACATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATT
*
209121 TCTTTTCACTACA
65 TCATTTCACT-CA
* * * *
209134 TG-TT-TTTTT-TTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCAAAAGAATACATTT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATTT
209196 CATTTCACTCA
66 CATTTCACTCA
* * *
209207 AGATTGTTTTTCTCAAAA-TAGACTTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAATACATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATT
209271 TCATTTCACT-A
65 TCATTTCACTCA
* * * * *
209282 CAGATTATTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTTTACCCGAAACAAGA-ATA
1 -AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACAT-
209346 TTCATTTCACTCA
64 TTCATTTCACTCA
*
209359 AGATTGTTTTTCTTAAAACCAA-ATTTTGTCTCTCTTGAGACAGTTT
1 AGATTGTTTTTCTTAAAA-CAAGA-TTTGTCTCGCTTGAGACAGTTT
209405 CCCTGAAACA
Statistics
Matches: 302, Mismatches: 34, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
73 3 0.01
74 48 0.16
75 42 0.14
76 153 0.51
77 53 0.18
78 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAAGACATTT
CATTTCACTCA
Found at i:209321 original size:226 final size:229
Alignment explanation
Indices: 208981--209400 Score: 577
Period size: 226 Copynumber: 1.8 Consensus size: 229
208971 ATCTCACTTG
* * *
208981 AGATTGTTTTTCTTAAAACAAACTTTGTCTCGCTTGAGACAATTTTATTTGAAAGAAGACATTTC
1 AGATTGTTTTTCTCAAAACAAACTTTGTCTCGCTTGAGACAATTTTACTCGAAAGAAGACATTTC
* * * *
209046 ATTTGACTCAAGATTGCTTTTCTTAAAACAAGATTTTGTCTCCCTTGAGACAGTTTTTACTCAAA
66 ATTTCACTCAAGATTACTTTTCTTAAAACAAGATTTTATCTCCCTTGAGACAGTTTTTACCCAAA
* *
209111 ACAAGACAT-TTCTTTTCACTACATG-TT-TTTTT-TTAAAA-CAAGA-TTTGTCTCGCTTGAGA
131 ACAAGA-ATATTCATTTCACT-CAAGATTGTTTTTCTTAAAACCAA-ATTTTGTCTCGCTTGAGA
209170 CAATTTTTACTCAAAAGAATACATTTCATTTCACTCA
193 CAATTTTTACTCAAAAGAATACATTTCATTTCACTCA
* * * *
209207 AGATTGTTTTTCTCAAAATAGACTTTGTCTCGCTTGAGACAGTTTTTACTCGAAAGAATACATTT
1 AGATTGTTTTTCTCAAAACAAACTTTGTCTCGCTTGAGACA-ATTTTACTCGAAAGAAGACATTT
* * * *
209272 CATTTCACT-ACAGATTATTTTTCTTAAAACAAGA-TTTATCTCGCTTGAGATAGTTTTTACCCG
65 CATTTCACTCA-AGATTACTTTTCTTAAAACAAGATTTTATCTCCCTTGAGACAGTTTTTACCCA
*
209335 AAACAAGAATATTCATTTCACTCAAGATTGTTTTTCTTAAAACCAAATTTTGTCTCTCTTGAGAC
129 AAACAAGAATATTCATTTCACTCAAGATTGTTTTTCTTAAAACCAAATTTTGTCTCGCTTGAGAC
209400 A
194 A
209401 GTTTCCCTGA
Statistics
Matches: 168, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
225 5 0.03
226 83 0.49
227 53 0.32
228 7 0.04
229 20 0.12
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (229 bp):
AGATTGTTTTTCTCAAAACAAACTTTGTCTCGCTTGAGACAATTTTACTCGAAAGAAGACATTTC
ATTTCACTCAAGATTACTTTTCTTAAAACAAGATTTTATCTCCCTTGAGACAGTTTTTACCCAAA
ACAAGAATATTCATTTCACTCAAGATTGTTTTTCTTAAAACCAAATTTTGTCTCGCTTGAGACAA
TTTTTACTCAAAAGAATACATTTCATTTCACTCA
Found at i:209356 original size:152 final size:151
Alignment explanation
Indices: 208981--209404 Score: 554
Period size: 150 Copynumber: 2.8 Consensus size: 151
208971 ATCTCACTTG
* * *
208981 AGATTGTTTTTCTTAAAACAA-ACTTTGTCTCGCTTGAGACAATTTTATTTGAAAGAAGACATTT
1 AGATT-TTTTTCTTAAAACAAGA-TTTGTCTCGCTTGAGACATTTTTACTCGAAAGAAGACATTT
* *
209045 CATTTGACTCAAGATTGCTTTTCTTAAAACAAGATTTTGTCTCCCTTGAGACAGTTTTTACTCAA
64 CATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTTGTCTCCCTTGAGACAGTTTTTACTCAA
*
209110 AACAAGACATTTCTTTTCACTAC
129 AACAAGACATTTCATTTCACTAC
* *
209133 ATG-TTTTTTT-TTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCAAAAGAATACATTT
1 A-GATTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC-ATTTTTACTCGAAAGAAGACATTT
* * * * *
209196 CATTTCACTCAAGATTGTTTTTCTCAAAA-TAGACTTTGTCTCGCTTGAGACAGTTTTTACTCGA
64 CATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTTGTCTCCCTTGAGACAGTTTTTACTCAA
* *
209260 AAGAATACATTTCATTTCACTAC
129 AACAAGACATTTCATTTCACTAC
* * * *
209283 AGATTATTTTTCTTAAAACAAGATTTATCTCGCTTGAGATAGTTTTTACCCGAAACAAGA-ATAT
1 AGATT-TTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACA-TTTTTACTCGAAAGAAGACAT-T
*
209347 TCATTTCACTCAAGATTGTTTTTCTTAAAACCAA-ATTTTGTCTCTCTTGAGACAGTTT
63 TCATTTCACTCAAGATTGTTTTTCTTAAAA-CAAGATTTTGTCTCCCTTGAGACAGTTT
209405 CCCTGAAACA
Statistics
Matches: 237, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
149 1 0.00
150 80 0.34
151 59 0.25
152 73 0.31
153 23 0.10
154 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (151 bp):
AGATTTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACATTTTTACTCGAAAGAAGACATTTCA
TTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTTGTCTCCCTTGAGACAGTTTTTACTCAAAA
CAAGACATTTCATTTCACTAC
Found at i:209431 original size:35 final size:36
Alignment explanation
Indices: 209378--209450 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 36
209368 TTCTTAAAAC
*
209378 CAAATTTTGTCTCTCTTGAGACAGTTTC-CCTGAAA
1 CAAATTTTGTCTCCCTTGAGACAGTTTCTCCTGAAA
* * *
209413 CAAATTTTGTTTCCCTTGAGTCAGTTTCTCTTGAAA
1 CAAATTTTGTCTCCCTTGAGACAGTTTCTCCTGAAA
209449 CA
1 CA
209451 TAAACTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (36 bp):
CAAATTTTGTCTCCCTTGAGACAGTTTCTCCTGAAA
Found at i:209539 original size:101 final size:101
Alignment explanation
Indices: 209378--209652 Score: 383
Period size: 101 Copynumber: 2.7 Consensus size: 101
209368 TTCTTAAAAC
* * *
209378 CAAATTTTGTCTCTCTTGAGACAGTTTCCC-TGAAACAAATTTTGTTTCCCTTGAGTCAGTTTCT
1 CAAATTTTGTATCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
*
209442 CTTGAAACATAAACTTTGAAAATGTTTCCCTTTAAA
66 CTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAA
* * * *
209478 CAAATTTTGTATCTCTTGAGATAATTTCCGTTGAAACAAATTTTGTCTCCCTTGATACAGTTTCT
1 CAAATTTTGTATCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
*
209543 CTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAA
66 CTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAA
* * * * * *
209579 CGAATTTTGTCTCTATTGAGACAGTTTCCCTTGAAACGAAA-TTTGTCTCTCTTGAAACATTTTC
1 CAAATTTTGTATCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTC
*
209643 GCTTGAAACA
65 TCTTGAAACA
209653 AATTTTGTCT
Statistics
Matches: 154, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
100 26 0.17
101 125 0.81
102 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (101 bp):
CAAATTTTGTATCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
CTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAA
Found at i:209548 original size:36 final size:35
Alignment explanation
Indices: 209465--209551 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 35
209455 CTTTGAAAAT
* * *
209465 GTTTCCCTTTAAACAAATTTTGTATCTCTTGAGATA
1 GTTT-CCTTGAAACAAATTTTGTATCCCTTGAGACA
* * *
209501 ATTTCCGTTGAAACAAATTTTGTCTCCCTTGATACA
1 GTTTCC-TTGAAACAAATTTTGTATCCCTTGAGACA
209537 GTTTCTCTTGAAACA
1 GTTTC-CTTGAAACA
209552 TAAACTTTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
35 2 0.05
36 39 0.93
37 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (35 bp):
GTTTCCTTGAAACAAATTTTGTATCCCTTGAGACA
Found at i:209613 original size:36 final size:36
Alignment explanation
Indices: 209566--209687 Score: 172
Period size: 36 Copynumber: 3.4 Consensus size: 36
209556 CTTTGAAAAC
*
209566 GTTTCCCTTGAAACGAATTTTGTCTCTATTGAGACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
* *
209602 GTTTCCCTTGAAACGAAATTTGTCTCTCTTGAAACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
* * * *
209638 TTTTCGCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
*
209674 GTTTCTCTTGAAAC
1 GTTTCCCTTGAAAC
209688 ATAAACTTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 75 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACA
Found at i:209630 original size:137 final size:135
Alignment explanation
Indices: 209465--210091 Score: 594
Period size: 137 Copynumber: 4.6 Consensus size: 135
209455 CTTTGAAAAT
* *
209465 GTTTCCCTTTAAACAAATTTTGTATCTCTTGAGATAATTTCCGTTGAAACAAATTTTGTCTCCCT
1 GTTTCCCTTGAAACAAA-TTTGTCTCTCTTGAGA-AATTTCCGTTGAAACAAATTTTGTCTCCCT
* * *
209530 TGATACAGTTTCTCTTGAAACATAAACTTTGAAAACGTTTCCCTTGAAACGAATTTTGTCTCTAT
64 TGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAACGAATTTTGTCTCTCT
209595 TGAGACA
129 TGAGACA
*
209602 GTTTCCCTTGAAACGAAATTTGTCTCTCTTGA-AACATTTTCGCTTGAAACAAATTTTGTCTCCC
1 GTTTCCCTTGAAAC-AAATTTGTCTCTCTTGAGAA-ATTTCCG-TTGAAACAAATTTTGTCTCCC
*
209666 TTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAATGAATTTTGTCTCTC
63 TTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAACGAATTTTGTCTCTC
209731 TTGAGACA
128 TTGAGACA
* * * ** ** *
209739 GTTTCCATTGAAAC--A--TAT-ACT-TTGA-AAACGTTTCATTTGAAATGAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAATTTGTCTCTCTTGAGAAA--TTTCCGTTGAAACAAATTTTGTCTCCCT
* * * *
209797 TGAGACAGTTTCGCTTGAAAC--AAA-TTT-----TGTCTCCCTTGAGATA-GATTCTCTTGAAA
64 TGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGA-A-ACGAAT-T-TTG--T
*
209853 CATAAACT-TTGA-AAA
123 C-T---CTCTTGAGACA
* * * *
209868 TGTTTCCCTTGAAATGAAATTTATTTCTCTTGAGACAGTTTGCC-TTGAAACAAATTTTGTCTCC
1 -GTTTCCCTTGAAA-CAAATTTGTCTCTCTTGAGA-AATTT-CCGTTGAAACAAATTTTGTCTCC
* * *
209932 CTTGAGACAGTTT-TCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAGCGAACTTTGTCACT
62 CTTGAGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAACGAATTTTGTCTCT
209996 CTTGAGACA
127 CTTGAGACA
* * * * * *
210005 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTGGAAACGAATTTTGTCTCTCT
1 GTTTCCCTTGAAACAAA-TTTGTCTCTCTTGAGA-AATTTCCGTTGAAACAAATTTTGTCTCCCT
*
210070 TGAGACAGTTTCCCTTGAAACA
64 TGAGACAGTTTCTCTTGAAACA
210092 AATTTTGTGT
Statistics
Matches: 404, Mismatches: 46, Indels: 80
0.76 0.09 0.15
Matches are distributed among these distances:
122 11 0.03
123 4 0.01
124 2 0.00
125 3 0.01
127 4 0.01
128 4 0.01
129 3 0.01
130 61 0.15
131 7 0.02
132 2 0.00
133 1 0.00
134 1 0.00
135 11 0.03
136 82 0.20
137 177 0.44
138 8 0.02
139 5 0.01
141 3 0.01
142 1 0.00
143 3 0.01
144 11 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (135 bp):
GTTTCCCTTGAAACAAATTTGTCTCTCTTGAGAAATTTCCGTTGAAACAAATTTTGTCTCCCTTG
AGACAGTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAACGAATTTTGTCTCTCTTG
AGACA
Found at i:209734 original size:65 final size:64
Alignment explanation
Indices: 209630--209818 Score: 263
Period size: 65 Copynumber: 2.9 Consensus size: 64
209620 TTTGTCTCTC
* ** *
209630 TTGAAACAT-TTTCGCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGAAA-ATGTTTCACTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTC-CTTGAAACATAAAC
209694 T
64 T
* *
209695 TTGAAAATGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACATATACT
1 TTGAAAATGTTTCACTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCC-TTGAAACATAAACT
* *
209760 TTGAAAACGTTTCATTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCGCTTGAAACA
1 TTGAAAATGTTTCACTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTC-CTTGAAACA
209819 AATTTTGTCT
Statistics
Matches: 113, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
64 3 0.03
65 109 0.96
66 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (64 bp):
TTGAAAATGTTTCACTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCTTGAAACATAAACT
Found at i:209750 original size:36 final size:36
Alignment explanation
Indices: 209703--209837 Score: 101
Period size: 36 Copynumber: 3.9 Consensus size: 36
209693 CTTTGAAAAT
*
209703 GTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACA
1 GTTTCCATTGAAATGAATTTTGTCTCTCTTGAGACA
* * * *
209739 GTTTCCATTGAAA--CA---TAT-ACT-TTGA-AAA
1 GTTTCCATTGAAATGAATTTTGTCTCTCTTGAGACA
209767 CGTTT-CATTTGAAATGAATTTTGTCTCTCTTGAGACA
1 -GTTTCCA-TTGAAATGAATTTTGTCTCTCTTGAGACA
** *
209804 GTTTCGC-TTGAAACAAATTTTGTCTCCCTTGAGA
1 GTTTC-CATTGAAATGAATTTTGTCTCTCTTGAGA
209838 TAGATTCTCT
Statistics
Matches: 75, Mismatches: 12, Indels: 24
0.68 0.11 0.22
Matches are distributed among these distances:
28 4 0.05
29 14 0.19
30 2 0.03
31 3 0.04
34 3 0.04
35 2 0.03
36 44 0.59
37 2 0.03
38 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (36 bp):
GTTTCCATTGAAATGAATTTTGTCTCTCTTGAGACA
Found at i:209808 original size:101 final size:100
Alignment explanation
Indices: 209703--210046 Score: 472
Period size: 101 Copynumber: 3.4 Consensus size: 100
209693 CTTTGAAAAT
** * * * *
209703 GTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCATTGAAACATATACTTTGAAAAC
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCC-TTGAAACATAAACTTTGAAAAT
** *
209768 GTTTCATTTGAAATGAATTTTGTCTCTCTTGAGACA
65 GTTTCCCTTGAAATGAAATTTGTCTCTCTTGAGACA
* *
209804 GTTTCGCTTGAAACAAATTTTGTCTCCCTTGAGATAGATTCTCTTGAAACATAAACTTTGAAAAT
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTC-CTTGAAACATAAACTTTGAAAAT
* *
209869 GTTTCCCTTGAAATGAAATTTATTTCTCTTGAGACA
65 GTTTCCCTTGAAATGAAATTTGTCTCTCTTGAGACA
* * *
209905 GTTTGCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTTCTTGAAACATAAACTTTGAAAATG
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCTTGAAACATAAACTTTGAAAATG
** * *
209970 TTTCCCTTGAAGCGAACTTTGTCACTCTTGAGACA
66 TTTCCCTTGAAATGAAATTTGTCTCTCTTGAGACA
* *
210005 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCC
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCC
210047 CTGGAAACGA
Statistics
Matches: 213, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
100 90 0.42
101 122 0.57
102 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (100 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCCTTGAAACATAAACTTTGAAAATG
TTTCCCTTGAAATGAAATTTGTCTCTCTTGAGACA
Found at i:209850 original size:36 final size:36
Alignment explanation
Indices: 209783--209854 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
209773 ATTTGAAATG
* *
209783 AATTTTGTCTCTCTTGAGACAGTTTCGCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGATTCGCTTGAAACA
* *
209819 AATTTTGTCTCCCTTGAGATAGATTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGATTCGCTTGAAACA
209855 TAAACTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (36 bp):
AATTTTGTCTCCCTTGAGACAGATTCGCTTGAAACA
Found at i:209899 original size:166 final size:166
Alignment explanation
Indices: 209609--209919 Score: 525
Period size: 166 Copynumber: 1.9 Consensus size: 166
209599 ACAGTTTCCC
*
209609 TTGAAACGAAATTTGTCTCTCTTGAAACATTTTCGCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 TTGAAACGAAATTTGTCTCTCTTGAAACAGTTTCGCTTGAAACAAATTTTGTCTCCCTTGAGACA
* * *
209674 GTTTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACA
66 GATTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAATGAAATTTATCTCTCTTGAGACA
209739 GTTT-CCATTGAAACATATACTTTGAAAACGTTTCAT
131 GTTTGCC-TTGAAACATATACTTTGAAAACGTTTCAT
* * * *
209775 TTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCGCTTGAAACAAATTTTGTCTCCCTTGAGATA
1 TTGAAACGAAATTTGTCTCTCTTGAAACAGTTTCGCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
209840 GATTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAATGAAATTTATTTCTCTTGAGACA
66 GATTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAATGAAATTTATCTCTCTTGAGACA
209905 GTTTGCCTTGAAACA
131 GTTTGCCTTGAAACA
209920 AATTTTGTCT
Statistics
Matches: 135, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
166 133 0.99
167 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (166 bp):
TTGAAACGAAATTTGTCTCTCTTGAAACAGTTTCGCTTGAAACAAATTTTGTCTCCCTTGAGACA
GATTCTCTTGAAACATAAACTTTGAAAATGTTTCCCTTGAAATGAAATTTATCTCTCTTGAGACA
GTTTGCCTTGAAACATATACTTTGAAAACGTTTCAT
Found at i:210027 original size:36 final size:36
Alignment explanation
Indices: 209969--210374 Score: 344
Period size: 36 Copynumber: 11.4 Consensus size: 36
209959 CTTTGAAAAT
* * * *
209969 GTTTCCCTTGAAGCGAACTTTGTCACTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
210005 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
210041 GTTTCCCTGGAAACGAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
210077 GTTTCCCTTGAAACAAATTTTGTGTCACTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * ***
210113 GTTTCTCTTGAAACACATAACTTTGAGAACT-TTGAGA-A
1 GTTTCCCTTG-AA-ACA-AATTTTG-TCTCTCTTGAGACA
** *
210151 CGTTTCCCTTGAAATGAATTTTGTCTCTTTTGAGACA
1 -GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
210188 GTTCCCCTT-AAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * ** * **
210223 ATTTTCCTTGAAACGAATTTCATATCTCTTGAGATT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
210259 GTTTCCCTTGAAACAAACTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* ** ** * *
210295 GTTTCTCTTGAAAC----CCT-AATCT-TTGAGTCT
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
**
210325 GTTTCCCTTGAAACATGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
210361 GTTTCTCTTGAAAC
1 GTTTCCCTTGAAAC
210375 CATTAACCCT
Statistics
Matches: 289, Mismatches: 67, Indels: 28
0.75 0.17 0.07
Matches are distributed among these distances:
30 19 0.07
31 2 0.01
32 1 0.00
34 1 0.00
35 34 0.12
36 200 0.69
37 4 0.01
38 6 0.02
39 21 0.07
40 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:210265 original size:182 final size:183
Alignment explanation
Indices: 209957--210321 Score: 500
Period size: 182 Copynumber: 2.0 Consensus size: 183
209947 TTGAAACATA
* * *
209957 AACTTTGAAAATGTTTCCCTTGAAGCGAACTTTGTCACTCTTGAGACAATTTCCCTTGAAACAAA
1 AACTTTGAAAACGTTTCCCTTGAAACGAACTTTGTCACTCTTGAGACAATTCCCCTTGAAACAAA
* * ** *
210022 TTTTGTCTCTCTTGAGATAGTTTCCCTGGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
66 TTTTGTCTCTCTTGAGACAATTTCCCTGGAAACGAATTTCATATCTCTTGAGACAGTTTCCCTTG
* * *
210087 AAACAAATTTTGTGTCACTTGAGATAGTTTCTCTTGAAACACATAA-CTTTGAG
131 AAACAAACTTTGTCTCACTTGAGACAGTTTCTCTTGAAAC-CATAATCTTTGAG
* * * * * *
210140 AACTTTGAGAACGTTTCCCTTGAAATGAATTTTGTCTCTTTTGAGACAGTTCCCCTT-AAACAAA
1 AACTTTGAAAACGTTTCCCTTGAAACGAACTTTGTCACTCTTGAGACAATTCCCCTTGAAACAAA
* * **
210204 TTTTGTCTCTCTTGAGACAATTTTCCTTGAAACGAATTTCATATCTCTTGAGATTGTTTCCCTTG
66 TTTTGTCTCTCTTGAGACAATTTCCCTGGAAACGAATTTCATATCTCTTGAGACAGTTTCCCTTG
* *
210269 AAACAAACTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACCCTAATCTTTGAG
131 AAACAAACTTTGTCTCACTTGAGACAGTTTCTCTTGAAACCATAATCTTTGAG
210322 TCTGTTTCCC
Statistics
Matches: 158, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
181 4 0.03
182 106 0.67
183 48 0.30
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (183 bp):
AACTTTGAAAACGTTTCCCTTGAAACGAACTTTGTCACTCTTGAGACAATTCCCCTTGAAACAAA
TTTTGTCTCTCTTGAGACAATTTCCCTGGAAACGAATTTCATATCTCTTGAGACAGTTTCCCTTG
AAACAAACTTTGTCTCACTTGAGACAGTTTCTCTTGAAACCATAATCTTTGAG
Found at i:211713 original size:5 final size:5
Alignment explanation
Indices: 211703--211727 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
211693 TATGGAGTTT
211703 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
211728 GTCATTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:213396 original size:36 final size:36
Alignment explanation
Indices: 213268--213389 Score: 151
Period size: 36 Copynumber: 3.5 Consensus size: 36
213258 TTTTTTTATT
* * *
213268 TAAAATTCAAATTCCAGCCTTATTTTCAGC-A--AA
1 TAAAATTCAAATTCCAACCTTATCTTCAACAACTAA
* *
213301 TAAAAGTCAAATTCCAACCCTATCTTCAACAACTAA
1 TAAAATTCAAATTCCAACCTTATCTTCAACAACTAA
* *
213337 TAAAATTCAAATCCCAACCTTATCTTCATCAACTAA
1 TAAAATTCAAATTCCAACCTTATCTTCAACAACTAA
*
213373 TCAAATTCAAATTCCAA
1 TAAAATTCAAATTCCAA
213390 TATTATCATC
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
33 25 0.33
34 1 0.01
36 49 0.65
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (36 bp):
TAAAATTCAAATTCCAACCTTATCTTCAACAACTAA
Found at i:223889 original size:8 final size:8
Alignment explanation
Indices: 223876--223900 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
223866 ACTTATTATT
223876 AAGAATGG
1 AAGAATGG
223884 AAGAATGG
1 AAGAATGG
223892 AAGAATGG
1 AAGAATGG
223900 A
1 A
223901 GGGGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (8 bp):
AAGAATGG
Found at i:224799 original size:53 final size:53
Alignment explanation
Indices: 224715--224826 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 53
224705 GTATACTTTT
* * ** *
224715 GGCACTATGTGTTCACCCATGGTATTGATAATGAGTTTATGAATTACCATTTC
1 GGCACTATATGTGCACCCATGAAATTCATAATGAGTTTATGAATTACCATTTC
* * *
224768 GGCACTATATGTGCATCCATGAAATTCATAATGAGTTTGTGAATTTCCATTTC
1 GGCACTATATGTGCACCCATGAAATTCATAATGAGTTTATGAATTACCATTTC
*
224821 GACACT
1 GGCACT
224827 TAGGTACAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
GGCACTATATGTGCACCCATGAAATTCATAATGAGTTTATGAATTACCATTTC
Found at i:233325 original size:24 final size:24
Alignment explanation
Indices: 233298--233347 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
233288 ATAAAGAACC
233298 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
233322 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
233346 AA
1 AA
233348 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:234488 original size:2 final size:2
Alignment explanation
Indices: 234481--234510 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
234471 CTTACTACAA
234481 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
234511 TTTTTTCACT
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:238320 original size:12 final size:12
Alignment explanation
Indices: 238300--238329 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
238290 AGGAAAATGG
238300 TAAAAAAATAAA
1 TAAAAAAATAAA
*
238312 TAAATAAATAAA
1 TAAAAAAATAAA
238324 TAAAAA
1 TAAAAA
238330 GAAGATAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:238840 original size:24 final size:24
Alignment explanation
Indices: 238813--238862 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
238803 ATAAAGAACC
238813 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
238837 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
238861 AA
1 AA
238863 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:242067 original size:53 final size:53
Alignment explanation
Indices: 242002--242163 Score: 227
Period size: 53 Copynumber: 3.1 Consensus size: 53
241992 TACTTTTGAC
242002 ACTATGTGTGCACTCATGGTTTTCATAATGAGTTTATGAATTACCATTTCGGA
1 ACTATGTGTGCACTCATGGTTTTCATAATGAGTTTATGAATTACCATTTCGGA
*
242055 ACTATGTGTGCACTCATGGTTTTCATAATGAGTTTATGAATTACCATTTCGAA
1 ACTATGTGTGCACTCATGGTTTTCATAATGAGTTTATGAATTACCATTTCGGA
* ** ** * * *
242108 ACTATTTGTGCA-TCCACAGAATTGATAATGAGTTTGTGAATTGCCATTTCGGA
1 ACTATGTGTGCACT-CATGGTTTTCATAATGAGTTTATGAATTACCATTTCGGA
242161 ACT
1 ACT
242164 TAGGTGCAAC
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 1 0.01
53 97 0.99
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (53 bp):
ACTATGTGTGCACTCATGGTTTTCATAATGAGTTTATGAATTACCATTTCGGA
Found at i:243012 original size:31 final size:30
Alignment explanation
Indices: 242941--243031 Score: 103
Period size: 31 Copynumber: 3.0 Consensus size: 30
242931 CCCGAAGGAC
* *
242941 CTATCCATATGTTCCAGAGAACATAGGT-AA
1 CTATCCATATGTCCCAAAG-ACATAGGTAAA
* * *
242971 CTGTCTATATGTCCCTAAAGACATAAGTAAA
1 CTATCCATATGTCCC-AAAGACATAGGTAAA
243002 CTATCCATATGTCTCCAAAGACATAGGTAA
1 CTATCCATATGTC-CCAAAGACATAGGTAA
243032 CCCTTGACTC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
30 19 0.38
31 29 0.58
32 2 0.04
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (30 bp):
CTATCCATATGTCCCAAAGACATAGGTAAA
Found at i:243104 original size:22 final size:22
Alignment explanation
Indices: 243079--243121 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
243069 TCATATCATG
243079 TAACATGGGCATTCTCTTCTAA
1 TAACATGGGCATTCTCTTCTAA
**
243101 TAACATGTTCATTCTCTTCTA
1 TAACATGGGCATTCTCTTCTA
243122 TCACATACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (22 bp):
TAACATGGGCATTCTCTTCTAA
Found at i:243186 original size:15 final size:17
Alignment explanation
Indices: 243161--243192 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
243151 ATCTCATATT
243161 ATATAACATGT-ATCAC
1 ATATAACATGTAATCAC
243177 ATAT-ACATGTAATCAC
1 ATATAACATGTAATCAC
243193 GCATATCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (17 bp):
ATATAACATGTAATCAC
Done.