Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008854.1 Hibiscus syriacus cultivar Beakdansim tig00112071_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: 279653
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2979 original size:36 final size:36
Alignment explanation
Indices: 2937--3012 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2927 GTTATAGCTA
*
2937 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2973 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3009 AAAA
1 AAAA
3013 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:9002 original size:29 final size:30
Alignment explanation
Indices: 8969--9025 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
8959 TTGCTTTTTA
8969 AGTTTAGTGCCTAACGTT-TATTCCGTTCT
1 AGTTTAGTGCCTAACGTTGTATTCCGTTCT
* * *
8998 AGTTTGGTGTCTAACGTTGTATTTCGTT
1 AGTTTAGTGCCTAACGTTGTATTCCGTT
9026 ATTCAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (30 bp):
AGTTTAGTGCCTAACGTTGTATTCCGTTCT
Found at i:9935 original size:21 final size:21
Alignment explanation
Indices: 9906--9949 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9896 ATAATAAAAG
*
9906 TTTAAATTTT-TGTTGTGGAAA
1 TTTAAATTTTATG-TATGGAAA
*
9927 TTTATATTTTATGTATGGAAA
1 TTTAAATTTTATGTATGGAAA
9948 TT
1 TT
9950 GCATGTTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTAAATTTTATGTATGGAAA
Found at i:12087 original size:31 final size:31
Alignment explanation
Indices: 12049--12113 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
12039 GAACCGAGAC
*
12049 AAAGGTTGGGCACCAAAGTGGAAAACAATTT
1 AAAGGTTGGGCACCAAAGTGAAAAACAATTT
*
12080 AAAGGTTGGGCACCAAATTGAAAAACAATTT
1 AAAGGTTGGGCACCAAAGTGAAAAACAATTT
12111 AAA
1 AAA
12114 TTGGAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (31 bp):
AAAGGTTGGGCACCAAAGTGAAAAACAATTT
Found at i:13750 original size:15 final size:15
Alignment explanation
Indices: 13732--13762 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13722 TGTTTAACAA
13732 ACAAATCAAATAACC
1 ACAAATCAAATAACC
*
13747 ACAAGTCAAATAACC
1 ACAAATCAAATAACC
13762 A
1 A
13763 ATATTCATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.26, G:0.03, T:0.13
Consensus pattern (15 bp):
ACAAATCAAATAACC
Found at i:14967 original size:36 final size:36
Alignment explanation
Indices: 14893--14969 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
14883 CTTCATTGAC
* * *
14893 ACAAATTTTATCTCACTTGAAATAATTTCTCTTTAA
1 ACAAATTTTATCTCACTCGAAATAATTTCACTTCAA
*
14929 ACAAATTTTCATCTCACTCGAGATAATTTCAC-TCAA
1 ACAAATTTT-ATCTCACTCGAAATAATTTCACTTCAA
14965 ACAAA
1 ACAAA
14970 AACTGTAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 17 0.47
37 19 0.53
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (36 bp):
ACAAATTTTATCTCACTCGAAATAATTTCACTTCAA
Found at i:26272 original size:3 final size:3
Alignment explanation
Indices: 26213--26256 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
26203 TTGTCAGTTT
*
26213 TTA TTA TTAA TTA -TA TATA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TT-A TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
26257 CTTACATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:26274 original size:9 final size:9
Alignment explanation
Indices: 26217--26305 Score: 51
Period size: 9 Copynumber: 9.7 Consensus size: 9
26207 CAGTTTTTAT
*
26217 TATTAATTA
1 TATTTATTA
*
26226 TATATATTA
1 TATTTATTA
26235 T-TGTTATTA
1 TAT-TTATTA
26244 T-TATTATTA
1 TAT-TTATTA
*
26253 TTATCTTA-CA
1 -TAT-TTATTA
26263 TATTTATTA
1 TATTTATTA
* *
26272 TATATAATA
1 TATTTATTA
26281 TA-TTATTA
1 TATTTATTA
26289 TATTATATTTA
1 TATT-TA-TTA
26300 TATTTA
1 TATTTA
26306 CAAATACTAC
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
8 10 0.16
9 35 0.56
10 6 0.10
11 11 0.18
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
TATTTATTA
Found at i:26294 original size:25 final size:25
Alignment explanation
Indices: 26214--26294 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
26204 TGTCAGTTTT
*
26214 TATTATTA-AT-TATATATATTATTGT
1 TATTATTATATATA-ATATATTATT-A
* * *
26239 TATTATTAT-TATTATTATCTTA-CA
1 TATTATTATATA-TAATATATTATTA
26263 TATTTATTATATATAATATATTATTA
1 TA-TTATTATATATAATATATTATTA
26289 TATTAT
1 TATTAT
26295 ATTTATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
24 2 0.05
25 28 0.65
26 11 0.26
27 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.59
Consensus pattern (25 bp):
TATTATTATATATAATATATTATTA
Found at i:29078 original size:3 final size:3
Alignment explanation
Indices: 29070--29102 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29060 TTCACTTCAC
29070 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29103 TAAATCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32435 original size:32 final size:32
Alignment explanation
Indices: 32363--32438 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
32353 GTTAAATCAC
* * *
32363 TTCAAGTTGCTTTCGGTTCTGGTTAATTTCTG
1 TTCAGGTTGCTTTCAGTTCGGGTTAATTTCTG
32395 TT-ATGGTTGCTTTCAGTTCGGGTTAATTT-TG
1 TTCA-GGTTGCTTTCAGTTCGGGTTAATTTCTG
32426 ATTCAGGTTGCTT
1 -TTCAGGTTGCTT
32439 CTAAACATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
31 3 0.08
32 34 0.89
33 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.24, T:0.50
Consensus pattern (32 bp):
TTCAGGTTGCTTTCAGTTCGGGTTAATTTCTG
Found at i:32730 original size:16 final size:16
Alignment explanation
Indices: 32709--32760 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
32699 ATTTGCTTTA
*
32709 CTTTCAGTTCGGGTTG
1 CTTTCAATTCGGGTTG
*
32725 CTTTCAATTCGGGTTA
1 CTTTCAATTCGGGTTG
* * *
32741 ATTTCGATTCAGGTTG
1 CTTTCAATTCGGGTTG
32757 CTTT
1 CTTT
32761 TGGTTCGAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.13, C:0.17, G:0.23, T:0.46
Consensus pattern (16 bp):
CTTTCAATTCGGGTTG
Found at i:34543 original size:42 final size:43
Alignment explanation
Indices: 34456--34555 Score: 130
Period size: 42 Copynumber: 2.3 Consensus size: 43
34446 TATTGGAATC
* *
34456 TTCCTACTTATTACCTAAGATTATGTTAGAGCTATTACCAGCTT
1 TTCCAACTTATTACCTAAAATTA-GTTAGAGCTATTACCAGCTT
* * *
34500 TTCCAACTTATTCCCTAAAATTA-TTGGAGCTATTACCATCTT
1 TTCCAACTTATTACCTAAAATTAGTTAGAGCTATTACCAGCTT
34542 TTCCAACTTTATTA
1 TTCCAAC-TTATTA
34556 AAAAATTGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
42 24 0.49
43 5 0.10
44 20 0.41
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (43 bp):
TTCCAACTTATTACCTAAAATTAGTTAGAGCTATTACCAGCTT
Found at i:37968 original size:24 final size:24
Alignment explanation
Indices: 37936--37988 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
37926 TTCTTTCGCC
37936 TCAATTGAGCTCAAATTTTAGGCT
1 TCAATTGAGCTCAAATTTTAGGCT
*
37960 TCAATTGAGCTCAAATTTTATGCT
1 TCAATTGAGCTCAAATTTTAGGCT
37984 TCAAT
1 TCAAT
37989 CGAACTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (24 bp):
TCAATTGAGCTCAAATTTTAGGCT
Found at i:38253 original size:30 final size:30
Alignment explanation
Indices: 38219--38275 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
38209 GCAGTTCAAA
*
38219 CCGGTTTTGCCAGTTTTCAGCCGGTTCACC
1 CCGGTTTTCCCAGTTTTCAGCCGGTTCACC
38249 CCGGTTTTCCCAGTTTTCAGCCGGTTC
1 CCGGTTTTCCCAGTTTTCAGCCGGTTC
38276 TTTACCGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.09, C:0.33, G:0.23, T:0.35
Consensus pattern (30 bp):
CCGGTTTTCCCAGTTTTCAGCCGGTTCACC
Found at i:38423 original size:14 final size:14
Alignment explanation
Indices: 38406--38442 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
38396 ATAATAATAA
38406 TAATAATATAAATC
1 TAATAATATAAATC
38420 TAATAATATAAATC
1 TAATAATATAAATC
38434 TAATAATAT
1 TAATAATAT
38443 TTATTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATAATATAAATC
Found at i:38427 original size:3 final size:3
Alignment explanation
Indices: 38387--38413 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
38377 AATAACATTG
38387 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
38414 TAAATCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51416 original size:12 final size:12
Alignment explanation
Indices: 51401--51427 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
51391 ATGTTTTTTC
51401 TTTGATTTATTT
1 TTTGATTTATTT
51413 TTTGATTTATTT
1 TTTGATTTATTT
51425 TTT
1 TTT
51428 TTATTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTGATTTATTT
Found at i:51426 original size:29 final size:29
Alignment explanation
Indices: 51394--51467 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
51384 TTTAAATATG
*
51394 TTTTTTCTTTGATTTATTTTTTGAT-TTATT
1 TTTTTTCTTTCATTTA-TTTTT-ATCTTATT
* * *
51424 TTTTTTATTTTATCTATTTTTATCTTATT
1 TTTTTTCTTTCATTTATTTTTATCTTATT
*
51453 TTATTTCTTTCATTT
1 TTTTTTCTTTCATTT
51468 CTTTGATTCG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.06
29 21 0.58
30 13 0.36
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.76
Consensus pattern (29 bp):
TTTTTTCTTTCATTTATTTTTATCTTATT
Found at i:51436 original size:5 final size:5
Alignment explanation
Indices: 51418--51584 Score: 58
Period size: 5 Copynumber: 32.2 Consensus size: 5
51408 TATTTTTTGA
* * * *
51418 TTTAT TTT-T TTTAT TTTA- TCTATT TTTAT CTTAT TTTA- TTTCT TTCA-
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT
* * * * * *
51465 TTTCT TTGAT TCGTTAT TTTTT TTTTT TTTTT TTTACATT TTTAGT TTGA-
1 TTTAT TTTAT T--TTAT TTTAT TTTAT TTTAT TTT--A-T TTTA-T TTTAT
* * * *
51515 TTTA- TTTAA TATAT CTTTAT TTTAT TTTAT TTTAT TTTCCT TTTTT ATTTAT
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT -TTTAT
51567 TATTAT TATTAT TTTAT T
1 T-TTAT T-TTAT TTTAT T
51585 AATTATTTAA
Statistics
Matches: 124, Mismatches: 23, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
4 19 0.15
5 66 0.53
6 31 0.25
7 4 0.03
8 4 0.03
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:51583 original size:21 final size:20
Alignment explanation
Indices: 51515--51591 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 20
51505 TTTAGTTTGA
*
51515 TTTATTTAATA-TATCTTTAT
1 TTTATTTATTATTAT-TTTAT
*
51535 TTTATTTTATT-TTATTTTCCTTT
1 TTTA-TTTATTATTA-TTT--TAT
51558 TTTATTTATTATTATTATTAT
1 TTTATTTATTATTATT-TTAT
*
51579 TTTATTAATTATT
1 TTTATTTATTATT
51592 TAACATTGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
20 4 0.09
21 23 0.50
22 9 0.20
23 10 0.22
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTATTATTATTTTAT
Found at i:54389 original size:99 final size:99
Alignment explanation
Indices: 54270--54467 Score: 308
Period size: 99 Copynumber: 2.0 Consensus size: 99
54260 TTATAATATC
*
54270 ATATATATACAATAAAGCTTGAGTTGTCCCTCTATA-GCAATTGGTTAAACACCCCGACTTTATG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTAAAACACCCCGACTTTATG
* *
54334 GATAAGATTCATCTAGCCTGATAAAGGTGATTATA
65 GATAAGATTCAGCTAACCTGATAAAGGTGATTATA
* * * *
54369 ATATCTATACAATAAAGCTTGAGTTGTCCCTCTAAGGTAATTGGTAAAACACCTCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTAAAACACCCCGACTTTATGG
*
54434 ATAAGATTCAGCTAACCTGATAAAGGTGTTTATA
66 ATAAGATTCAGCTAACCTGATAAAGGTGATTATA
54468 TATTGAGTTG
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 1 0.01
99 89 0.99
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAGGCAATTGGTAAAACACCCCGACTTTATGG
ATAAGATTCAGCTAACCTGATAAAGGTGATTATA
Found at i:55793 original size:84 final size:84
Alignment explanation
Indices: 55642--56400 Score: 693
Period size: 84 Copynumber: 8.9 Consensus size: 84
55632 AACTATTGAT
* * * * **
55642 AGCATAACTCAAGGCAAAAAGGGTTATCTATCC-AC-CAAGTTCTTCGAGTTCGATTACACTCAG
1 AGCATAACTCAAGGCGAGAAGGGTTATCT-GCCAACAAAAGACCTTCGAGTTCGATTACACTCAG
*
55705 CTCAAAGGCGCATCATTTGC
65 CTCAAAGGCACATCATTTGC
* * * * *
55725 AGCATAGCTCAAGTCGAGAAGGGTTATCGGCCAACAAAAAACCTTCAAGTTCGATTACACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
*
55790 TCAAAGGCACATCTAATTTAC
66 TCAAAGGCACATC--ATTTGC
* * * * *
55811 AGCATAACTCAAGGTGAGAAGGTTTATTTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
*
55875 TCAAAGACACATCATTTGC
66 TCAAAGGCACATCATTTGC
* * *
55894 AGAATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
*
55959 TCAAAGGCACATTATTTGC
66 TCAAAGGCACATCATTTGC
* * * * *
55978 AGCATAGCTCAAGGTGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCAATTATACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
*
56043 TCAAAGGCGCATCATTTGC
66 TCAAAGGCACATCATTTGC
* * *
56062 AGCATAACTCAAGGCGAGAAGAGTTATCTGCCAACAAAAAACCTTCGAGTTCGATTATACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
* **
56127 TCAAAGTCACATCATTTAA
66 TCAAAGGCACATCATTTGC
* * * * * *
56146 AACATAACTCAAGGCGAGAATGGTTATCAGTCAAC-CAAGACCTTCGAGTTTAACATCATACTCA
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAG----------T--TCG
* ** * *
56210 ATTACACTCTGCTCAAAGAAATATCAAATTTAC
54 ATTACACTCAGCTCAAAGGCACATCA--TTTGC
* * * ** * * * * **
56243 AACATAACTCAAGGTGAGAAGGGCTATCTATCATC-CAACACCCTCGAGTTTAATTACACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
** * *
56307 TCTGAGGCACCTCAAATTTAC
66 TCAAAGGCACATC--ATTTGC
* * * * * *
56328 AGCATAGCTCAAGGAGAGAAGGGTTATTTGTCAAC-CAAGACCCTCGAGTTCGATTACACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
*
56392 TCAAGGGCA
66 TCAAAGGCA
56401 TGTCAAATTT
Statistics
Matches: 559, Mismatches: 96, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
82 2 0.00
83 70 0.13
84 261 0.47
85 123 0.22
86 33 0.06
87 2 0.00
93 1 0.00
95 23 0.04
97 44 0.08
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (84 bp):
AGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGC
TCAAAGGCACATCATTTGC
Found at i:55929 original size:169 final size:168
Alignment explanation
Indices: 55642--56395 Score: 778
Period size: 168 Copynumber: 4.4 Consensus size: 168
55632 AACTATTGAT
* * * * **
55642 AGCATAACTCAAGGCAAAAAGGGTTATCTATCCACCAAGTTCTTCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCT
* * * * * * * *
55707 CAAAGGCGCATCATTTGCAGCATAGCTCAAGTCGAGAAGGGTTATCGGCCAACAAAAAACCTTCA
66 CAAAGACACATCATTTGCAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAAACCTTCG
55772 AGTTCGATTACACTCAGCTCAAAGGCACATCTAATTTAC
131 AGTTCGATTACACTCAGCTCAAAGGCACATCT-ATTTAC
* * *
55811 AGCATAACTCAAGGTGAGAAGGTTTATTTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCT
* *
55876 CAAAGACACATCATTTGCAGAATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCG
66 CAAAGACACATCATTTGCAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAAACCTTCG
*
55941 AGTTCGATTACACTCAGCTCAAAGGCACAT-TATTTGC
131 AGTTCGATTACACTCAGCTCAAAGGCACATCTATTTAC
* * ** * * *
55978 AGCATAGCTCAAGGTGAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCAATTATACTCAGC
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCAGC
* * * * *
56043 TCAAAGGCGCATCATTTGCAGCATAACTCAAGGCGAGAAGAGTTATCTGCCAACAAAAAACCTTC
65 TCAAAGACACATCATTTGCAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAAACCTTC
* * *
56108 GAGTTCGATTATACTCAGCTCAAAGTCACATC-ATTTAA
130 GAGTTCGATTACACTCAGCTCAAAGGCACATCTATTTAC
* * * *
56146 AACATAACTCAAGGCGAGAATGGTTATCAGTCAACCAAGACCTTCGAGTTTAACATCATACTCAA
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAG----------T--TCGA
* * * * * **
56211 TTACACTCTGCTCAAAGAAATATCAAATTTACA-ACATAACTCAAGGTGAGAAGGGCTATCTATC
54 TTACACTCAGCTCAAAGACACATC--ATTTGCAGA-ATAACTCAAGGCGAGAAGGGCTATCTGCC
* * * * ** ** * *
56275 ATC-CAACACCCTCGAGTTTAATTACACTCAGCTCTGAGGCACCTCAAATTTAC
116 AACAAAAAACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC-TATTTAC
* * * *
56328 AGCATAGCTCAAGGAGAGAAGGGTTATTTGTCAACCAAGACCCTCGAGTTCGATTACACTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCT
56393 CAA
66 CAA
56396 GGGCATGTCA
Statistics
Matches: 487, Mismatches: 79, Indels: 37
0.81 0.13 0.06
Matches are distributed among these distances:
167 47 0.10
168 146 0.30
169 143 0.29
170 17 0.03
172 1 0.00
177 1 0.00
179 22 0.05
180 32 0.07
181 32 0.07
182 46 0.09
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (168 bp):
AGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCT
CAAAGACACATCATTTGCAGAATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAAACCTTCG
AGTTCGATTACACTCAGCTCAAAGGCACATCTATTTAC
Found at i:56419 original size:85 final size:85
Alignment explanation
Indices: 56207--56420 Score: 250
Period size: 85 Copynumber: 2.5 Consensus size: 85
56197 AACATCATAC
* * ** * * *
56207 TCAATTACACTCTGCTCAAAGAAATATCAAATTTACAACATAACTCAAGGTGAGAAGGGCTATCT
1 TCAATTACACTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGAGAGAAGGGCTATCT
*
56272 ATCATCCAACACCCTCGAGT
66 ATCAACCAACACCCTCGAGT
* * ** * *
56292 TTAATTACACTCAGCTC-TGAGGCACCTCAAATTTACAGCATAGCTCAAGGAGAGAAGGGTTATT
1 TCAATTACACTCAGCTCAAG-GGCATATCAAATTTACAGCATAGCTCAAGGAGAGAAGGGCTATC
* *
56356 TGTCAACCAAGACCCTCGAGT
65 TATCAACCAACACCCTCGAGT
* *
56377 TCGATTACACTCAGCTCAAGGGCATGTCAAATTTACAGCATAGC
1 TCAATTACACTCAGCTCAAGGGCATATCAAATTTACAGCATAGC
56421 ATAATTCAAG
Statistics
Matches: 106, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
85 105 0.99
86 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (85 bp):
TCAATTACACTCAGCTCAAGGGCATATCAAATTTACAGCATAGCTCAAGGAGAGAAGGGCTATCT
ATCAACCAACACCCTCGAGT
Found at i:56445 original size:85 final size:85
Alignment explanation
Indices: 56233--56478 Score: 219
Period size: 85 Copynumber: 2.9 Consensus size: 85
56223 CAAAGAAATA
* * ** ** * * * *
56233 TCAAATTTACAACATAACTCAAGGTGAGAAGGGCTATCTATCATCCAACACCCTCGAGTTTAATT
1 TCAAATTTACAGCATAGCTCAAGCAGAGAAAAGCTATCTGTCAACCAAAACCCTCGAGTTTGATT
*
56298 ACACTCAGCTCTGAGGCACC
66 ACACTCAGCTCAGAGGCACC
* ** * * * *
56318 TCAAATTTACAGCATAGCTCAAGGAGAGAAGGGTTATTTGTCAACCAAGACCCTCGAGTTCGATT
1 TCAAATTTACAGCATAGCTCAAGCAGAGAAAAGCTATCTGTCAACCAAAACCCTCGAGTTTGATT
**
56383 ACACTCAGCTCA-AGGGCATG
66 ACACTCAGCTCAGA-GGCACC
* * *
56403 TCAAATTTACAGCATAGCAT-AATTCA-AGAAAAGCTATCTGTCAACAAAAACCTTCGAGTTTGA
1 TCAAATTTACAGCATAGC-TCAA-GCAGAGAAAAGCTATCTGTCAACCAAAACCCTCGAGTTTGA
* *
56466 TTCCATTCAGCTC
64 TTACACTCAGCTC
56479 GATGACACAT
Statistics
Matches: 133, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
84 1 0.01
85 130 0.98
86 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (85 bp):
TCAAATTTACAGCATAGCTCAAGCAGAGAAAAGCTATCTGTCAACCAAAACCCTCGAGTTTGATT
ACACTCAGCTCAGAGGCACC
Found at i:58147 original size:18 final size:18
Alignment explanation
Indices: 58095--58151 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
58085 GGCCTCTTAT
* *
58095 TTTATTTATTTTAATTTA
1 TTTACTTATTTTATTTTA
* *
58113 TTTAGTTACTATT-TTTTA
1 TTTACTTA-TTTTATTTTA
58131 TTTACTTATTTTATTTTA
1 TTTACTTATTTTATTTTA
58149 TTT
1 TTT
58152 TGTAGACACC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 3 0.09
18 26 0.81
19 3 0.09
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTACTTATTTTATTTTA
Found at i:58302 original size:31 final size:31
Alignment explanation
Indices: 58246--58304 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
58236 TATTACTTCA
58246 TTTTCATTATTATTTTATATCCTTTTAATTT
1 TTTTCATTATTATTTTATATCCTTTTAATTT
*
58277 TTTTTATTATT-TTATTATTAT-CTTTTAA
1 TTTTCATTATTATT-TTA-TATCCTTTTAA
58305 AAAAAACCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 20 0.80
32 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (31 bp):
TTTTCATTATTATTTTATATCCTTTTAATTT
Found at i:61411 original size:10 final size:10
Alignment explanation
Indices: 61398--61482 Score: 66
Period size: 10 Copynumber: 8.1 Consensus size: 10
61388 ACAAAAAGGA
61398 AAAAAAGAAG
1 AAAAAAGAAG
61408 AAAAAAGAAG
1 AAAAAAGAAG
61418 AAAAAAGCAAAG
1 AAAAAAG--AAG
* *
61430 AGAAAATAA-
1 AAAAAAGAAG
*
61439 AAAAGAGAA-
1 AAAAAAGAAG
*
61448 ACAAAAATAAAG
1 A-AAAAA-GAAG
61460 AAAAAAGTGAAG
1 AAAAAA--GAAG
61472 AAAAAAGAAG
1 AAAAAAGAAG
61482 A
1 A
61483 CAATACGCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
9 7 0.11
10 28 0.46
11 7 0.11
12 19 0.31
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:61423 original size:12 final size:12
Alignment explanation
Indices: 61397--61482 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 12
61387 AACAAAAAGG
61397 AAAAAAAGAAGA
1 AAAAAAAGAAGA
61409 AAAAAGAAGAA-A
1 AAAAA-AAGAAGA
61421 AAAGCAAAGAGAA-A
1 AAA--AAA-AGAAGA
61435 ATAAAAAAG-AGA
1 A-AAAAAAGAAGA
*
61447 AACAAAAATAAAGA
1 AA-AAAAA-GAAGA
**
61461 AAAAAGTGAAGA
1 AAAAAAAGAAGA
61473 AAAAAGAAGA
1 AAAAA-AAGA
61483 CAATACGCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 2 0.03
12 27 0.47
13 14 0.24
14 13 0.22
15 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.03
Consensus pattern (12 bp):
AAAAAAAGAAGA
Found at i:61454 original size:14 final size:13
Alignment explanation
Indices: 61408--61465 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
61398 AAAAAAGAAG
61408 AAAAAAGAAGAAAA
1 AAAAAAG-AGAAAA
*
61422 AAGCAAAGAGAAAA
1 AA-AAAAGAGAAAA
61436 TAAAAAAGAGAAACA
1 -AAAAAAGAGAAA-A
61451 AAAATAA-AGAAAA
1 AAAA-AAGAGAAAA
61464 AA
1 AA
61466 GTGAAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 3 0.08
14 26 0.68
15 9 0.24
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:65511 original size:18 final size:17
Alignment explanation
Indices: 65450--65511 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 17
65440 ATTAAGGCCT
65450 CTTATTTTATTTA-TT-
1 CTTATTTTATTTATTTA
* *
65465 -TTAATTTATTTAGTTA
1 CTTATTTTATTTATTTA
65481 C-TA-TTT-TTTATTTA
1 CTTATTTTATTTATTTA
65495 CTTATTTTATTTCATTT
1 CTTATTTTATTT-ATTT
65512 TGTAGACACC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
14 19 0.50
15 7 0.18
16 5 0.13
17 3 0.08
18 4 0.11
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (17 bp):
CTTATTTTATTTATTTA
Found at i:65565 original size:3 final size:3
Alignment explanation
Indices: 65559--65584 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
65549 TTTATTTACT
65559 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
65585 TTTTTCCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:65625 original size:25 final size:23
Alignment explanation
Indices: 65597--65662 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
65587 TTTCCTCTCT
*
65597 TTTTATTACTTCTTTTTCATTATTA
1 TTTTATTA-TTCTTTTT-AATATTA
* *
65622 TTTTTTTA-TCCTTTTAATATTA
1 TTTTATTATTCTTTTTAATATTA
*
65644 TTTTATTATTATCTTTTAA
1 TTTTATTATTCT-TTTTAA
65663 AAAATCCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
22 13 0.39
23 7 0.21
24 6 0.18
25 7 0.21
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTATTATTCTTTTTAATATTA
Found at i:79448 original size:36 final size:37
Alignment explanation
Indices: 79368--79450 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
79358 TCAAAAAAAA
* * *
79368 TTTCAAGGGAGATTATCTCAAGCGAGATGATATTTTG
1 TTTCAAGAGAGACTATCTCAAGCGAGATGATAATTTG
*
79405 TTTCAAGAGAGACTATCTCAAGTGAGATGA-AATTTG
1 TTTCAAGAGAGACTATCTCAAGCGAGATGATAATTTG
79441 TTTCAAGAGA
1 TTTCAAGAGA
79451 ATCAATATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.33
Consensus pattern (37 bp):
TTTCAAGAGAGACTATCTCAAGCGAGATGATAATTTG
Found at i:79462 original size:36 final size:36
Alignment explanation
Indices: 79385--79475 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 36
79375 GGAGATTATC
* * * *
79385 TCAAGCGAGATGATATTTTGTTTCAAGAGAGACTATC
1 TCAAGTGAGATGA-AATTTGTTTCAAGAGAGACAATA
79422 TCAAGTGAGATGAAATTTGTTTCAAGAGA-ATCAATA
1 TCAAGTGAGATGAAATTTGTTTCAAGAGAGA-CAATA
* *
79458 TCAAGTGCGATAAAATTT
1 TCAAGTGAGATGAAATTT
79476 TTGTTTTGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.02
36 34 0.72
37 12 0.26
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (36 bp):
TCAAGTGAGATGAAATTTGTTTCAAGAGAGACAATA
Found at i:79521 original size:29 final size:28
Alignment explanation
Indices: 79474--79553 Score: 128
Period size: 27 Copynumber: 2.9 Consensus size: 28
79464 GCGATAAAAT
*
79474 TTTTGTTTTGAG-GAAATGATCTTGCAA
1 TTTTGTTTTTAGTGAAATGATCTTGCAA
79501 TTCTTGTTTTTAGTGAAATGATCTTGCAA
1 TT-TTGTTTTTAGTGAAATGATCTTGCAA
79530 TTTT-TTTTTAGTGAAATGATCTTG
1 TTTTGTTTTTAGTGAAATGATCTTG
79554 ATATTTTTGT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
27 22 0.44
28 11 0.22
29 17 0.34
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (28 bp):
TTTTGTTTTTAGTGAAATGATCTTGCAA
Found at i:79560 original size:26 final size:27
Alignment explanation
Indices: 79471--79561 Score: 123
Period size: 27 Copynumber: 3.3 Consensus size: 27
79461 AGTGCGATAA
79471 AATTTTTGTTTTGAG-GAAATGATCTTGC
1 AATTTTT-TTTT-AGTGAAATGATCTTGC
79499 AATTCTTGTTTTTAGTGAAATGATCTTGC
1 AATT-TT-TTTTTAGTGAAATGATCTTGC
79528 AATTTTTTTTTAGTGAAATGATCTTG-
1 AATTTTTTTTTAGTGAAATGATCTTGC
79554 ATATTTTT
1 A-ATTTTT
79562 GTTTCGTGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
26 1 0.02
27 26 0.44
28 8 0.14
29 23 0.39
30 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (27 bp):
AATTTTTTTTTAGTGAAATGATCTTGC
Found at i:79581 original size:56 final size:57
Alignment explanation
Indices: 79471--79582 Score: 126
Period size: 56 Copynumber: 2.0 Consensus size: 57
79461 AGTGCGATAA
* *
79471 AATTTTTGTTTTGAGGAAATGATCTTGCAATTCTTGTTTTTAGTGAAATGATCTTGC
1 AATTTTTGTTTTGAGGAAATGATCTTGCAATTCTTGTTTGTAGTAAAATGATCTTGC
*
79528 AATTTTT-TTTT-AGTGAAATGATCTTG-ATATTTTTGTTTCGT-GTAAAACT-ATCTTG
1 AATTTTTGTTTTGAG-GAAATGATCTTGCA-ATTCTTGTTT-GTAGTAAAA-TGATCTTG
79583 AGCAAGATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
55 3 0.06
56 36 0.75
57 9 0.19
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (57 bp):
AATTTTTGTTTTGAGGAAATGATCTTGCAATTCTTGTTTGTAGTAAAATGATCTTGC
Found at i:81480 original size:12 final size:12
Alignment explanation
Indices: 81463--81488 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
81453 TATTTGGTCC
81463 ACCTTATTTCAT
1 ACCTTATTTCAT
81475 ACCTTATTTCAT
1 ACCTTATTTCAT
81487 AC
1 AC
81489 GGACTTGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (12 bp):
ACCTTATTTCAT
Found at i:88480 original size:21 final size:21
Alignment explanation
Indices: 88447--88613 Score: 153
Period size: 21 Copynumber: 7.8 Consensus size: 21
88437 TTGCGATAGA
*
88447 CCAAGTTCGCGTTACGATTTATT
1 CCAAGTT--CGTTGCGATTTATT
*
88470 CCAAGTTCGTTGCGA--TAGT
1 CCAAGTTCGTTGCGATTTATT
*
88489 CGAAGTTTGCGTTGCGATTTATT
1 CCAAG-TT-CGTTGCGATTTATT
*
88512 CCAAATTCGTTGCGATTTATT
1 CCAAGTTCGTTGCGATTTATT
* *
88533 CCAAATTCGTTGCGA--TAGT
1 CCAAGTTCGTTGCGATTTATT
*
88552 CGAAGTTCGCGTTGCGATTTATT
1 CCAAGTT--CGTTGCGATTTATT
*
88575 CCAAATTCGTTGCGATTTATT
1 CCAAGTTCGTTGCGATTTATT
*
88596 CCAAATTTGCGTTGCGAT
1 CC-AAGTT-CGTTGCGAT
88614 AGTCCAAAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
19 15 0.12
20 2 0.02
21 68 0.56
22 6 0.05
23 30 0.25
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (21 bp):
CCAAGTTCGTTGCGATTTATT
Found at i:88528 original size:63 final size:63
Alignment explanation
Indices: 88456--88617 Score: 279
Period size: 63 Copynumber: 2.5 Consensus size: 63
88446 ACCAAGTTCG
* * *
88456 CGTTACGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
88519 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
88582 CGTTGCGATTTATTCCAAATTTGCGTTGCGATAGTC
1 CGTTGCGATTTATTCCAAA-TT-CGTTGCGATAGTC
88618 CAAAATTGCA
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
63 79 0.84
64 2 0.02
65 13 0.14
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (63 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:88620 original size:42 final size:42
Alignment explanation
Indices: 88437--88626 Score: 149
Period size: 42 Copynumber: 4.5 Consensus size: 42
88427 CATATTCGCA
* * * *
88437 TTGCGATAGACCAAGTTCGCGTTACGATTTATTCC-AAGTTCG
1 TTGCGATAGTCCAAATT-GCGTTGCGATTTATTCCAAATTTCG
* *
88479 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAA-TTCG
1 TTGCGATAGTCCAA-ATTGCGTTGCGATTTATTCCAAATTTCG
* * * * *
88521 TTGCGATTTATTCCAAATT-CGTTGCGA--TAGTCGAAGTTCGCG
1 TTGCGA--TAGTCCAAATTGCGTTGCGATTTATTCCAAATT-TCG
*
88563 TTGCGATTTATTCCAAATT-CGTTGCGATTTATTCCAAATTTGCG
1 TTGCGA--TAGTCCAAATTGCGTTGCGATTTATTCCAAATTT-CG
88607 TTGCGATAGTCCAAAATTGC
1 TTGCGATAGTCC-AAATTGC
88627 AACGACGGTA
Statistics
Matches: 121, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
40 6 0.05
41 1 0.01
42 80 0.66
43 11 0.09
44 23 0.19
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAATTGCGTTGCGATTTATTCCAAATTTCG
Found at i:89227 original size:5 final size:5
Alignment explanation
Indices: 89217--89246 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
89207 TCCATCTCGT
89217 CCGTC CCGTC CCGTC CCGTC CCGTC CCGTC
1 CCGTC CCGTC CCGTC CCGTC CCGTC CCGTC
89247 TCTCGGGTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
CCGTC
Found at i:89273 original size:6 final size:6
Alignment explanation
Indices: 89252--89294 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
89242 CCGTCTCTCG
89252 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
89295 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:89403 original size:21 final size:21
Alignment explanation
Indices: 89384--89487 Score: 156
Period size: 21 Copynumber: 5.0 Consensus size: 21
89374 CATTGCGATT
*
89384 TTGGACTATCGTAATGCGATA-
1 TTGGACTATCGCAATGCGA-AC
* *
89405 GTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
89426 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
89447 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
89468 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAATGCGAA
89488 TATTAAATCG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
20 1 0.01
21 74 0.99
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:89430 original size:42 final size:42
Alignment explanation
Indices: 89384--89487 Score: 174
Period size: 42 Copynumber: 2.5 Consensus size: 42
89374 CATTGCGATT
*
89384 TTGGACTATCGTAATGCGATA-GTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGA-ACGTCGACTATCGCAATGCGAAC
*
89426 TTGGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAACGTCGACTATCGCAATGCGAAC
89468 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAATGCGAA
89488 TATTAAATCG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (42 bp):
TTGGACTATCGCAATGCGAACGTCGACTATCGCAATGCGAAC
Found at i:89527 original size:21 final size:21
Alignment explanation
Indices: 89503--89671 Score: 195
Period size: 21 Copynumber: 8.1 Consensus size: 21
89493 AATCGCAATA
89503 CGATAGTCGAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
* *
89524 CGATAGTCG-ACTATCGTATTG
1 CGATAGTCGAAGT-TCGCATTG
*
89545 CGAT-TTAC-ATA-TT-GCATTG
1 CGATAGT-CGA-AGTTCGCATTG
*
89564 CGATAGTCCAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
*
89585 CGATAGTCGAAGTTCGCAATG
1 CGATAGTCGAAGTTCGCATTG
*
89606 CGATAGTCTAAGTTCGCATTG
1 CGATAGTCGAAGTTCGCATTG
*
89627 CGATAGTCGAAGTTCGCGTTG
1 CGATAGTCGAAGTTCGCATTG
* *
89648 CGATAGTCAAAGTTCGCGTTG
1 CGATAGTCGAAGTTCGCATTG
89669 CGA
1 CGA
89672 ATCTGGAAAC
Statistics
Matches: 128, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.09
20 8 0.06
21 108 0.84
22 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
CGATAGTCGAAGTTCGCATTG
Found at i:89536 original size:61 final size:61
Alignment explanation
Indices: 89471--89655 Score: 214
Period size: 61 Copynumber: 3.0 Consensus size: 61
89461 TGCGAACTTG
* *
89471 GACTATCGCAATGCGAATATTAA-ATCGCAATACGATAGTCGAAGTTCGCATTGCGATAGTC
1 GACTATCGCAATGCG-ATATTAAGATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTC
* * * * *
89532 GACTATCGTATTGCGAT-TTACATATTGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 GACTATCGCAATGCGATATTA-AGATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTC
* * *
89593 GAAGT-TCGCAATGCGATAGTCTAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTC
1 G-ACTATCGCAATGCGATA-T-TAAGATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTC
89656 AAAGTTCGCG
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 3 0.03
60 3 0.03
61 58 0.56
62 2 0.02
63 36 0.35
64 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (61 bp):
GACTATCGCAATGCGATATTAAGATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTC
Found at i:95431 original size:10 final size:10
Alignment explanation
Indices: 95418--95445 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
95408 AAAATAATAC
95418 AAAACAAACA
1 AAAACAAACA
95428 AAAACAAACA
1 AAAACAAACA
95438 AAAACAAA
1 AAAACAAA
95446 ATATTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAACA
Found at i:106275 original size:23 final size:21
Alignment explanation
Indices: 106223--106282 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 21
106213 TTTTGGTGCA
*
106223 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
106243 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
106264 GAAGGGGAACCGATTCCCC
1 G-A-GGGAACCGATTCCCC
106283 TAGGGGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 15 0.43
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:106711 original size:26 final size:25
Alignment explanation
Indices: 106669--106720 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
106659 AGAATTTTCC
106669 AAAAAAAATTTTAAA-TTTCGAAATT
1 AAAAAAAATTTTAAATTTTC-AAATT
*
106694 AAAAAAAATTTGTTAATTTTCAAATT
1 AAAAAAAATTT-TAAATTTTCAAATT
106720 A
1 A
106721 TCGTGTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 11 0.46
26 9 0.38
27 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
AAAAAAAATTTTAAATTTTCAAATT
Found at i:114266 original size:36 final size:34
Alignment explanation
Indices: 114218--114342 Score: 114
Period size: 35 Copynumber: 3.7 Consensus size: 34
114208 GATCTGTTCC
*
114218 TGCTTCAGTACTCTTTTGTGAAGGTTGGATTTGCAT
1 TGCTTCACTACTCTTTTGTGAAGG-TGGA-TTGCAT
* *
114254 TGCTTCACTACTCTTTCGTGAAGGTCGA----AT
1 TGCTTCACTACTCTTTTGTGAAGGTGGATTGCAT
* * ** *
114284 TACTTTACTACTCTGATGTAAAGGCTGGATTGCAT
1 TGCTTCACTACTCTTTTGTGAAGG-TGGATTGCAT
*
114319 TGTTTCACTACTCTTTTGTGAAGG
1 TGCTTCACTACTCTTTTGTGAAGG
114343 CTGAATGATT
Statistics
Matches: 68, Mismatches: 16, Indels: 11
0.72 0.17 0.12
Matches are distributed among these distances:
30 20 0.29
31 3 0.04
35 23 0.34
36 22 0.32
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (34 bp):
TGCTTCACTACTCTTTTGTGAAGGTGGATTGCAT
Found at i:127514 original size:20 final size:20
Alignment explanation
Indices: 127485--127527 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
127475 ATTCCACCAC
127485 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
127505 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
127525 ATG
1 ATG
127528 AGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:127817 original size:22 final size:24
Alignment explanation
Indices: 127791--127834 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
127781 TTGTAAGTAC
127791 TATTCGAAT-AAAAT-TTTATTCG
1 TATTCGAATAAAAATCTTTATTCG
127813 TATTCGAATAAAAATCTTTATT
1 TATTCGAATAAAAATCTTTATT
127835 TTATCTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (24 bp):
TATTCGAATAAAAATCTTTATTCG
Found at i:128178 original size:22 final size:24
Alignment explanation
Indices: 128153--128231 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
128143 TATAAATGCT
* *
128153 AAAAAAATA-TAATTATAATGAAA
1 AAAAAAATATTTATTATAATGAGA
128176 AAATAATAATATTTATTATAATGATGA
1 AAA-AA-AATATTTATTATAATGA-GA
*
128203 AAAATAATATTTATTATAATGACGA
1 AAAAAAATATTTATTATAATGA-GA
128228 AAAA
1 AAAA
128232 TAATGACACC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.06
24 2 0.04
25 27 0.56
26 12 0.25
27 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.33
Consensus pattern (24 bp):
AAAAAAATATTTATTATAATGAGA
Found at i:128208 original size:25 final size:25
Alignment explanation
Indices: 128164--128235 Score: 108
Period size: 25 Copynumber: 2.8 Consensus size: 25
128154 AAAAAATATA
*
128164 ATTATAATGAAAAAATAATAATATTT
1 ATTATAATGAAGAAA-AATAATATTT
*
128190 ATTATAATGATGAAAAATAATATTT
1 ATTATAATGAAGAAAAATAATATTT
*
128215 ATTATAATGACGAAAAATAAT
1 ATTATAATGAAGAAAAATAAT
128236 GACACCATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 30 0.70
26 13 0.30
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (25 bp):
ATTATAATGAAGAAAAATAATATTT
Found at i:133669 original size:93 final size:93
Alignment explanation
Indices: 133571--133759 Score: 240
Period size: 94 Copynumber: 2.0 Consensus size: 93
133561 AAATTACACG
* * * *
133571 AAAA-TTTAAATTTAACTTACCAAACCACTCAAATACAG-TTTGATATGTAAAATCAAAATAAAT
1 AAAATTTTAAACTAAACTTACCAAACCACTCAAATA-AGATTTAATATGTAAAATAAAAATAAAT
* *
133634 AGTCTAATTCATTTATATTTA-CAATAAAAA
65 AGTCT-AGTAATTTATA-TTACCAATAAAAA
* * *
133664 AAAATTTTAAACTAAACTTACCAAACCACTCAAATATGATTTAATCTGTAAAATAAAAATAATTA
1 AAAATTTTAAACTAAACTTACCAAACCACTCAAATAAGATTTAATATGTAAAATAAAAATAAATA
133729 GTCTAGTAATTTATATTACTCAATAAAAA
66 GTCTAGTAATTTATATTAC-CAATAAAAA
133758 AA
1 AA
133760 TAATGTAATA
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
92 3 0.04
93 14 0.17
94 66 0.80
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (93 bp):
AAAATTTTAAACTAAACTTACCAAACCACTCAAATAAGATTTAATATGTAAAATAAAAATAAATA
GTCTAGTAATTTATATTACCAATAAAAA
Found at i:133944 original size:311 final size:303
Alignment explanation
Indices: 133351--133975 Score: 842
Period size: 311 Copynumber: 2.0 Consensus size: 303
133341 TAAAAATAGA
* * *
133351 AATAAAACAAGAAAATTTAAACAAAACTTACCAAACCACTCAAATACGATTTAATTTTTAAAATC
1 AATAAAA-AAGAAAATTTAAACAAAACTTACCAAACCACTCAAATACGATTTAATCTGTAAAATA
*
133416 AAAATAAATAGTCCAATAATTTATATTACTCTATAAAAAATAATTTAAACTAAACTTACCAAACT
65 AAAATAAATAGTCCAATAATTTATATTACTCTAAAAAAAATAATTTAAACTAAACTTACCAAACT
* * *
133481 ACTCAAATACAACTTAATATGTAAAATTAAAATATATAGTGTAATAATTATAAGTTAAATTAAAA
130 ACTCAAATACAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAAGTTAAATT-AAA
* * * *
133546 ACAAAATTATACTAAAAATTACACGAAAATTTAAATTTAACTTACCAAACCACTCAAATACAGTT
194 ACAAAATTACACTAAAAATTAAACGAAAATTTAAATTAAACTTACCAAACCACTCAAATACAATT
* * *
133611 TGATATGTAAAATCAAAATAAATAGTCTAATTCATTTATATTTAC
259 TCATATGTAAAATCAAAATAAATAATCTAATTAATTTATATTTAC
* * *
133656 AATAAAAAA-AAATTTTAAACTAAACTTACCAAACCACTCAAATATGATTTAATCTGTAAAATAA
1 AATAAAAAAGAAAATTTAAACAAAACTTACCAAACCACTCAAATACGATTTAATCTGTAAAATAA
* * * *
133720 AAATAATTAGTCTAGTAATTTATATTACTCAATAAAAAAATAATGTAATAATTTAAACTACACTT
66 AAATAAATAGTCCAATAATTTATATTACTC--T---AAAA-AA---AATAATTTAAACTAAACTT
** * *
133785 ACCAATTTTTACTCAATTACAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAATT
122 ACCAA--ACTACTCAAATACAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAAGT
*
133850 TAAATT-AAA-AAAATTACACTAAAAATTAAACGAAAATTTAAATTAAACTTACCAAACCACTCG
185 TAAATTAAAACAAAATTACACTAAAAATTAAACGAAAATTTAAATTAAACTTACCAAACCACTCA
* * *
133913 AATACAATTTCATCTGTAAAATCAAAATAAATAATTTAATTAATTTATATTTAT
250 AATACAATTTCATATGTAAAATCAAAATAAATAATCTAATTAATTTATATTTAC
*
133967 ATTAAAAAA
1 AATAAAAAA
133976 TTAAAAATGA
Statistics
Matches: 279, Mismatches: 30, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
303 76 0.27
304 2 0.01
305 8 0.03
308 3 0.01
309 2 0.01
311 105 0.38
312 26 0.09
314 57 0.20
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (303 bp):
AATAAAAAAGAAAATTTAAACAAAACTTACCAAACCACTCAAATACGATTTAATCTGTAAAATAA
AAATAAATAGTCCAATAATTTATATTACTCTAAAAAAAATAATTTAAACTAAACTTACCAAACTA
CTCAAATACAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAAGTTAAATTAAAAC
AAAATTACACTAAAAATTAAACGAAAATTTAAATTAAACTTACCAAACCACTCAAATACAATTTC
ATATGTAAAATCAAAATAAATAATCTAATTAATTTATATTTAC
Found at i:154879 original size:83 final size:83
Alignment explanation
Indices: 154730--155000 Score: 357
Period size: 83 Copynumber: 3.3 Consensus size: 83
154720 ACGACATTTG
* * * * *
154730 TGCCACAATAGATGAACCCTATTATGACATTTATATAAAAATACTGCTAAAGTATTACTATGTTG
1 TGCCACTATAGATGAACCCTATTATGGCATTTATATAAAAATGCCGCTAAAGTATTACTCTGTTG
154795 CGGTGTTTGTTGAAAAAA
66 CGGTGTTTGTTGAAAAAA
** * * * * *
154813 CACCACTATAGATGAACCCTATTATGGCGTTTATATAAAAACGCCGCTAAATTACTACTCTATTG
1 TGCCACTATAGATGAACCCTATTATGGCATTTATATAAAAATGCCGCTAAAGTATTACTCTGTTG
* *
154878 CGGCGTTAGTTGAAAAAA
66 CGGTGTTTGTTGAAAAAA
* * * *
154896 TGCCACCATAGATGAACCCTATTATGGCATTTGTAT-AAAATGCCACGAAAGTATTACTCTGTTG
1 TGCCACTATAGATGAACCCTATTATGGCATTTATATAAAAATGCCGCTAAAGTATTACTCTGTTG
*
154960 CGATGTTTGTTG-AAAAA
66 CGGTGTTTGTTGAAAAAA
154977 TGCCACTATAGATGAACCCTATTA
1 TGCCACTATAGATGAACCCTATTA
155001 CGACCGCTAA
Statistics
Matches: 159, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
81 28 0.18
82 31 0.19
83 100 0.63
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (83 bp):
TGCCACTATAGATGAACCCTATTATGGCATTTATATAAAAATGCCGCTAAAGTATTACTCTGTTG
CGGTGTTTGTTGAAAAAA
Found at i:159559 original size:10 final size:11
Alignment explanation
Indices: 159531--159558 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
159521 AAACGAGAGA
159531 GAAAAAACGTC
1 GAAAAAACGTC
159542 GAAAAAACGTC
1 GAAAAAACGTC
159553 GAAAAA
1 GAAAAA
159559 CTAGAGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.14, G:0.18, T:0.07
Consensus pattern (11 bp):
GAAAAAACGTC
Found at i:159950 original size:35 final size:34
Alignment explanation
Indices: 159910--159980 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 34
159900 TGGATGCTAT
*
159910 TTATAATAAGACATGTCACTTGGTGAATAGACTTA
1 TTATAATAAGACATATCACTTGGTGAAT-GACTTA
*
159945 TTATAATAAGTCATATCACTTGGTGAATGACTTA
1 TTATAATAAGACATATCACTTGGTGAATGACTTA
159979 TT
1 TT
159981 TTTAGTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 8 0.24
35 26 0.76
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (34 bp):
TTATAATAAGACATATCACTTGGTGAATGACTTA
Found at i:160500 original size:3 final size:3
Alignment explanation
Indices: 160494--160518 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
160484 ATAATAATAT
160494 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
160519 CTCGGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:161871 original size:21 final size:21
Alignment explanation
Indices: 161842--161889 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
161832 AAAACCAATG
*
161842 GTATTGGTACCTCTCAAGGGA
1 GTATCGGTACCTCTCAAGGGA
*
161863 GTATCGGTACCTCTCAAGGGG
1 GTATCGGTACCTCTCAAGGGA
161884 GTATCG
1 GTATCG
161890 ATACTACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (21 bp):
GTATCGGTACCTCTCAAGGGA
Found at i:162263 original size:17 final size:18
Alignment explanation
Indices: 162243--162282 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
162233 TTATATTCGA
162243 ATAA-TTGAATCGAATAT
1 ATAATTTGAATCGAATAT
*
162260 ATAATTTTGAATTGAATAT
1 ATAA-TTTGAATCGAATAT
162279 ATAA
1 ATAA
162283 AATCTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
19 16 0.80
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (18 bp):
ATAATTTGAATCGAATAT
Found at i:164165 original size:12 final size:12
Alignment explanation
Indices: 164148--164172 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
164138 CTAATGGGTA
164148 ATTTTGAAAACT
1 ATTTTGAAAACT
164160 ATTTTGAAAACT
1 ATTTTGAAAACT
164172 A
1 A
164173 AGTTTGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTTGAAAACT
Found at i:164700 original size:23 final size:19
Alignment explanation
Indices: 164651--164693 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
164641 AAACAAGACT
*
164651 AGGGGTATCGATACCATCG
1 AGGGGTATCGATACCATCA
164670 AGGGGTATCGATACACATTCA
1 AGGGGTATCGATAC-CA-TCA
164691 AGG
1 AGG
164694 AGGGTATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 2 0.10
21 5 0.24
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (19 bp):
AGGGGTATCGATACCATCA
Found at i:169822 original size:22 final size:20
Alignment explanation
Indices: 169778--169822 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
169768 CAAATAATTG
* *
169778 AATCGAATATATAATTTTGA
1 AATCGAATATATAATCTTAA
169798 AATCGAATATATAAAATCTTAA
1 AATCGAATATAT--AATCTTAA
169820 AAT
1 AAT
169823 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
AATCGAATATATAATCTTAA
Found at i:172968 original size:54 final size:54
Alignment explanation
Indices: 172879--173172 Score: 417
Period size: 54 Copynumber: 5.4 Consensus size: 54
172869 ATGTTACATT
* * * *
172879 TTACTGTATTGTCACTATGTGAGCACCCCACGTAATTCATAACGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
* * * * *
172933 TTATCGTATTGGAACTATGTGTACACCCCATGTAATTTATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
**
172987 TTACCGTATTGGCACTATGTGTGCACCCCCACAAAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCA-CCCCACGTAATTCATAATGAGTTTATGAA
* *
173042 TTACCGTATTGGCACTATGTGTGTACTCCACGTAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
* * *
173096 TTACCATATTGGCACTATGTGTGCACCCCACGTAATTCATAATGATTTTGTGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
* *
173150 TTACCGTATCGACACTATGTGTG
1 TTACCGTATTGGCACTATGTGTG
173173 TAAAACCACA
Statistics
Matches: 211, Mismatches: 28, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
54 162 0.77
55 49 0.23
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (54 bp):
TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
Found at i:173168 original size:163 final size:163
Alignment explanation
Indices: 172879--173172 Score: 444
Period size: 163 Copynumber: 1.8 Consensus size: 163
172869 ATGTTACATT
* * * *
172879 TTACTGTATTGTCACTATGTGAGCACCCCACGTAATTCATAACGAGTTTATGAATTATCGTATTG
1 TTACCGTATTGGCACTATGTGAGCACCCCACGTAATTCATAACGAGTTTATGAATTACCATATTG
* * * *
172944 GAACTATGTGTACACCCCATGTAATTTATAATGAGTTTATGAATTACCGTATTGGCACTATGTGT
66 GAACTATGTGTACACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATCGACACTATGTGT
173009 GCACCCCCACAAAATTCATAATGAGTTTATGAA
131 GCACCCCCACAAAATTCATAATGAGTTTATGAA
* * * *
173042 TTACCGTATTGGCACTATGTGTGTACTCCACGTAATTCATAATGAGTTTATGAATTACCATATTG
1 TTACCGTATTGGCACTATGTGAGCACCCCACGTAATTCATAACGAGTTTATGAATTACCATATTG
* * * *
173107 GCACTATGTGTGCACCCCACGTAATTCATAATGATTTTGTGAATTACCGTATCGACACTATGTGT
66 GAACTATGTGTACACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATCGACACTATGTGT
173172 G
131 G
173173 TAAAACCACA
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
163 115 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (163 bp):
TTACCGTATTGGCACTATGTGAGCACCCCACGTAATTCATAACGAGTTTATGAATTACCATATTG
GAACTATGTGTACACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATCGACACTATGTGT
GCACCCCCACAAAATTCATAATGAGTTTATGAA
Found at i:173187 original size:109 final size:108
Alignment explanation
Indices: 172885--173198 Score: 409
Period size: 109 Copynumber: 2.9 Consensus size: 108
172875 CATTTTACTG
* * * * *
172885 TATTGTCACTATGTGAGCACCCCACGTAATTCATAACGAGTTTATGAATTATCGTATTGGA-ACT
1 TATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAATTACCGTA-TCGACACT
* *
172949 A--TGTGTACACCCCATGTAATTTATAATGAGTTTATGAATTACCG
65 ATGTGTGTACACCACA--TAATTTATAATGAGTTTATGAATTACCA
** * *
172993 TATTGGCACTATGTGTGCACCCCCACAAAATTCATAATGAGTTTATGAATTACCGTATTGGCACT
1 TATTGGCACTATGTGTGCA-CCCCACGTAATTCATAATGAGTTTATGAATTACCGTATCGACACT
* * *
173058 ATGTGTGTACTCCACGTAATTCATAATGAGTTTATGAATTACCA
65 ATGTGTGTACACCACATAATTTATAATGAGTTTATGAATTACCA
* *
173102 TATTGGCACTATGTGTGCACCCCACGTAATTCATAATGATTTTGTGAATTACCGTATCGACACTA
1 TATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATCGACACTA
*
173167 TGTGTGTAAAACCACATAATTTATAATGAGTT
66 TGTGTGT-ACACCACATAATTTATAATGAGTT
173199 GTAATATCAC
Statistics
Matches: 178, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
108 66 0.37
109 102 0.57
111 10 0.06
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (108 bp):
TATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAATTACCGTATCGACACTA
TGTGTGTACACCACATAATTTATAATGAGTTTATGAATTACCA
Found at i:178091 original size:21 final size:21
Alignment explanation
Indices: 178066--178106 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
178056 CCTGATTTAA
*
178066 TGAAAGAAATGGAAGATAATG
1 TGAAAGAAATCGAAGATAATG
**
178087 TGAAAGTTATCGAAGATAAT
1 TGAAAGAAATCGAAGATAAT
178107 CTTAAGATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (21 bp):
TGAAAGAAATCGAAGATAATG
Found at i:179988 original size:54 final size:54
Alignment explanation
Indices: 179918--180263 Score: 559
Period size: 54 Copynumber: 6.4 Consensus size: 54
179908 ATGTTACATT
*
179918 TTACCGTATTAGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
*
179972 TTACTGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
180026 TTACCGTATTGGCACTATGTGTGCACCCCAC-TAAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGT-AATTCATAATGAGTTTATGAA
*
180080 TTACCGTATTGGCACTATGTATGCACCCCACGTAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
* * *
180134 TTATCGTATTAGCACTATGTGTGCACCCCACATAATTCATAATGAGTTTATGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
* * * *
180188 TTACGGTATTGGCACTATGTGTGCACCACATGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
* * *
180242 TTATCGTATCGACACTATGTGT
1 TTACCGTATTGGCACTATGTGT
180264 ACAAAATCGC
Statistics
Matches: 271, Mismatches: 19, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
53 1 0.00
54 269 0.99
55 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (54 bp):
TTACCGTATTGGCACTATGTGTGCACCCCACGTAATTCATAATGAGTTTATGAA
Found at i:181425 original size:3 final size:3
Alignment explanation
Indices: 181417--181455 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
181407 GTTCGATTAT
181417 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
181456 TGATCATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:181943 original size:2 final size:2
Alignment explanation
Indices: 181936--181973 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
181926 GTAAAATTTA
181936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
181974 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203208 original size:13 final size:11
Alignment explanation
Indices: 203170--203216 Score: 87
Period size: 11 Copynumber: 4.4 Consensus size: 11
203160 GTTTGATGCT
203170 TTCTCT-TTGA
1 TTCTCTCTTGA
203180 TTCTCTCTTGA
1 TTCTCTCTTGA
203191 TTCTCTCTTGA
1 TTCTCTCTTGA
203202 TTCTCTCTTGA
1 TTCTCTCTTGA
203213 TTCT
1 TTCT
203217 AGTTGCTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 6 0.17
11 30 0.83
ACGTcount: A:0.09, C:0.26, G:0.09, T:0.57
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:206303 original size:23 final size:22
Alignment explanation
Indices: 206273--206353 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
206263 GCATGACCCT
206273 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
206295 CGTGCATCGGTGCATCA-GCAA-G
1 -GTGCATCGATGCA-CATTCAAGG
* *
206317 ATGAATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
206340 GATGCATCGATGCA
1 G-TGCATCGATGCA
206354 TCGATGCACT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
20 2 0.04
21 11 0.24
22 3 0.07
23 16 0.36
24 13 0.29
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:212282 original size:45 final size:46
Alignment explanation
Indices: 212194--212284 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
212184 TTGAAAAAGC
* *
212194 CTGAGTGCATCGATGCATGGTCTTGTGCATCAATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCA
*
212240 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCA
212285 TTCGATGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCA
Found at i:212332 original size:20 final size:20
Alignment explanation
Indices: 212304--212341 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
212294 CAAGAAATTA
212304 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
212324 ATTGGTGCATCGGTGCAT
1 ATTGATGCATCGATGCAT
212342 ACCCTTGAAA
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:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:214253 original size:21 final size:21
Alignment explanation
Indices: 214227--214268 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
214217 CCAGAATGGG
*
214227 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
214248 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
214269 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:214464 original size:29 final size:31
Alignment explanation
Indices: 214432--214491 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
214422 AAATTTTGAA
*
214432 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
214461 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
214492 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:225520 original size:42 final size:42
Alignment explanation
Indices: 225339--225795 Score: 430
Period size: 42 Copynumber: 11.0 Consensus size: 42
225329 AGATCAATCA
* * * *
225339 TAATTTTA-AAGAATAGT-GATAATCTCAAAAATGGTATTCA
1 TAATTTTATAAGAATAGTAGATAATCCCAAAAGTGTTATTCG
* * * * * *
225379 TAATTTTAGAATAATAGCAGATAA-CCCAAAA-AGTTGTTCA
1 TAATTTTATAAGAATAGTAGATAATCCCAAAAGTGTTATTCG
* * *
225419 TAATTTTATAAGAGTAGTAGATAA-CCTCAAAAAATGTTATTCT
1 TAATTTTATAAGAATAGTAGATAATCC-C-AAAAGTGTTATTCG
* * ** * * *
225462 TAATTTTAAAAAAATAGTAGATTTTTCTAAAAGTGTTATTGG
1 TAATTTTATAAGAATAGTAGATAATCCCAAAAGTGTTATTCG
* * * *
225504 TAATTCTATAAGAATAGTAAATAATCTCAAAAGTGTTGTTCG
1 TAATTTTATAAGAATAGTAGATAATCCCAAAAGTGTTATTCG
* * *
225546 TAATTTTATGAGAATAGTATATAA-CTCCAACAGTGTTATT-G
1 TAATTTTATAAGAATAGTAGATAATC-CCAAAAGTGTTATTCG
* * *
225587 ATAATTTTATAAGAATAGTAGACAATCCCAAAAGTGTTGTTCA
1 -TAATTTTATAAGAATAGTAGATAATCCCAAAAGTGTTATTCG
* * *
225630 TAATTTTATAGGAATAATAGATAA-CCCTAAAAGTGTTATTGG
1 TAATTTTATAAGAATAGTAGATAATCCC-AAAAGTGTTATTCG
* * * *
225672 TAATTTTATAAAAATAGTA-TTAAATCCCAAAAATGTTGTTCG
1 TAATTTTATAAGAATAGTAGAT-AATCCCAAAAGTGTTATTCG
* *
225714 TAATCTTATAAGAATAGTAGATAATCCCAAAAGTGTTGTTCG
1 TAATTTTATAAGAATAGTAGATAATCCCAAAAGTGTTATTCG
225756 TAATTTTATAAGAATAGTAGATAA-CCCTAAAAGTGTTATT
1 TAATTTTATAAGAATAGTAGATAATCCC-AAAAGTGTTATT
225796 ATAAAAATAG
Statistics
Matches: 337, Mismatches: 65, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
40 36 0.11
41 23 0.07
42 247 0.73
43 30 0.09
44 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (42 bp):
TAATTTTATAAGAATAGTAGATAATCCCAAAAGTGTTATTCG
Found at i:225805 original size:33 final size:32
Alignment explanation
Indices: 225761--225822 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
225751 GTTCGTAATT
*
225761 TTATAAGAATAGTAGATAA-CCCTAAAAGTGTTA
1 TTATAAAAATAG-AGATAATCCC-AAAAGTGTTA
*
225794 TTATAAAAATAGATATAATCCCAAAAGTG
1 TTATAAAAATAGAGATAATCCCAAAAGTG
225823 ATGTTTAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (32 bp):
TTATAAAAATAGAGATAATCCCAAAAGTGTTA
Found at i:231880 original size:16 final size:17
Alignment explanation
Indices: 231859--231897 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
231849 ATTTTCTTTC
231859 ATTATTTAAGTATTA-T
1 ATTATTTAAGTATTATT
* *
231875 ATTATTTTATTATTATT
1 ATTATTTAAGTATTATT
231892 ATTATT
1 ATTATT
231898 ATTATTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTATTTAAGTATTATT
Found at i:231887 original size:3 final size:3
Alignment explanation
Indices: 231869--231903 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
231859 ATTATTTAAG
231869 TAT TA- TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
231904 TGAATTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:232426 original size:16 final size:17
Alignment explanation
Indices: 232402--232439 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
232392 ATTTCAAAGT
232402 TATAATTATATA-AAAA
1 TATAATTATATATAAAA
*
232418 TATATTTATATATAAAA
1 TATAATTATATATAAAA
232435 TATAA
1 TATAA
232440 ATAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATTATATATAAAA
Found at i:232653 original size:134 final size:133
Alignment explanation
Indices: 232410--232663 Score: 309
Period size: 134 Copynumber: 1.9 Consensus size: 133
232400 GTTATAATTA
* * *
232410 TATAAAAATATATTTATATATAAAATATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAT
1 TATAAAAATATAATAATATATAAAATAAAAATAAAATATTTATTTATTTAGAAATATCAGAAAAT
* * * *
232475 GACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACA
66 GACATCCAGGTGCCTTAAGACAGCTCCTTTCTTTAATATT-AAAAATAAATAAATAATTAAAACA
232540 TTTT
130 TTTT
* **
232544 TATAAAAATAATAATAATATAT-AATTAAAAATAGGATATTTATTTATTTA-AACATATCAGAAA
1 TATAAAAAT-ATAATAATATATAAAATAAAAATAAAATATTTATTTATTTAGAA-ATATCAGAAA
* ** *
232607 ATGGACATCCAGTTGTTTTAAGACTGC-CCTTTC-TTAATATTGAAAAATAAATAAATA
64 AT-GACATCCAGGTGCCTTAAGACAGCTCCTTTCTTTAATATT-AAAAATAAATAAATA
232664 TCAAAATATG
Statistics
Matches: 102, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
133 24 0.24
134 50 0.49
135 28 0.27
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (133 bp):
TATAAAAATATAATAATATATAAAATAAAAATAAAATATTTATTTATTTAGAAATATCAGAAAAT
GACATCCAGGTGCCTTAAGACAGCTCCTTTCTTTAATATTAAAAATAAATAAATAATTAAAACAT
TTT
Found at i:234471 original size:76 final size:76
Alignment explanation
Indices: 234340--235055 Score: 1261
Period size: 76 Copynumber: 9.4 Consensus size: 76
234330 ATGAAATATT
* *
234340 GAAATCATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCC
1 GAAA-CATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCC
*
234405 AAAGGCTTTTTG
65 GAAGGCTTTTTG
* * * *
234417 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGTTCCTG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
234482 AAGGCTTTTTG
66 AAGGCTTTTTG
*
234493 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
234558 AAGGCTTTTTG
66 AAGGCTTTTTG
*
234569 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
234634 AAGGCTTTTTG
66 AAGGCTTTTTG
*
234645 GAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
*
234710 AAGGCTATTTG
66 AAGGCTTTTTG
* *
234721 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAATCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
*
234786 AAGGCTATTTG
66 AAGGCTTTTTG
*
234797 GAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
234862 AAGGCTTTTTG
66 AAGGCTTTTTG
*
234873 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATTAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
234938 AAGGCTTTTTG
66 AAGGCTTTTTG
234949 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
235014 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
235025 GAAACATCATGCACTGTAAGACTTACAGATG
1 GAAACATCATGCACTGCAGGACTTACAGATG
235056 TGAGAAATAG
Statistics
Matches: 617, Mismatches: 22, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
76 613 0.99
77 4 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:235333 original size:166 final size:166
Alignment explanation
Indices: 235059--235380 Score: 558
Period size: 166 Copynumber: 1.9 Consensus size: 166
235049 ACAGATGTGA
235059 GAAATAGTTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTT
1 GAAATAGTTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCA-TTTTT
**
235124 AGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTA-TTTTTCAAAATAACATGTTGA
65 AGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTCAAAATAACATGTTGA
*
235188 TTGGGTAACATGCCCCAATCTCAAGAAAAGGTTGTTG
130 TTGGGTAACATGCCCCAATCGCAAGAAAAGGTTGTTG
235225 GAAATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCA-TTT
1 GAAATAGTTTACTAAGT--AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
**
235289 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTTGAAATAACATGTTG
64 TAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTCAAAATAACATGTTG
235354 ATTGGGTAACATGCCCCAATCGCAAGA
129 ATTGGGTAACATGCCCCAATCGCAAGA
235381 TAATGCTCAT
Statistics
Matches: 148, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
166 62 0.42
167 44 0.30
168 42 0.28
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (166 bp):
GAAATAGTTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTCAAAATAACATGTTGAT
TGGGTAACATGCCCCAATCGCAAGAAAAGGTTGTTG
Found at i:235920 original size:22 final size:22
Alignment explanation
Indices: 235895--235949 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
235885 AATAAAGCTT
235895 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
235917 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
235939 TCATCTTTGAA
1 TCATCTTTGAA
235950 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:238690 original size:114 final size:113
Alignment explanation
Indices: 238490--238712 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 113
238480 AGATTATCAT
* ** *
238490 CAAATTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTAAGGGTTCATACCAAACCAAATCAGATAACTCA
* *
238555 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATCTCTACTATGAG
66 AAGAACACTTCCAGAAAATGCTATTGGGCCT-CTTATCTCTACTATGAG
* *
238604 CAAATTCATCTTTTAAATCCAATGATTGGTTTAAGGGTTCCTACCAAACCAAATCAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTAAGGGTTCATACCAAACCAAATCAGATAACTCA
*
238669 AAGAACACTTCCAGAAAATGCTATTGGGCCTCTTATTTCTACTA
66 AAGAACACTTCCAGAAAATGCTATTGGGCCTCTTATCTCTACTA
238713 CGAGAACATG
Statistics
Matches: 100, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 12 0.12
114 88 0.88
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (113 bp):
CAAATTCATCTTTCAAATCCAATGATTGGTTTAAGGGTTCATACCAAACCAAATCAGATAACTCA
AAGAACACTTCCAGAAAATGCTATTGGGCCTCTTATCTCTACTATGAG
Found at i:245549 original size:26 final size:25
Alignment explanation
Indices: 245524--245571 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
245514 AACATTAATA
245524 AAATA-ATATAAATATTATGAAAAAT
1 AAATATATATAAA-ATTATGAAAAAT
* *
245549 ATATATATATAAAATTTTGAAAA
1 AAATATATATAAAATTATGAAAA
245572 GAAAGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
AAATATATATAAAATTATGAAAAAT
Found at i:246064 original size:16 final size:17
Alignment explanation
Indices: 246040--246077 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
246030 ATTTCAAAGT
246040 TATAATTATATA-AAAA
1 TATAATTATATATAAAA
*
246056 TATATTTATATATAAAA
1 TATAATTATATATAAAA
246073 TATAA
1 TATAA
246078 ATAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAATTATATATAAAA
Found at i:247842 original size:15 final size:15
Alignment explanation
Indices: 247822--247874 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
247812 ATAATATATT
247822 TAATAAAAAAAATAA
1 TAATAAAAAAAATAA
*
247837 TAATAATAAAAATAA
1 TAATAAAAAAAATAA
**
247852 T--TTTAAAAAATAA
1 TAATAAAAAAAATAA
247865 -AATAAAAAAA
1 TAATAAAAAAA
247875 TCAATGTCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 9 0.30
14 6 0.20
15 15 0.50
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
TAATAAAAAAAATAA
Found at i:247873 original size:12 final size:13
Alignment explanation
Indices: 247822--247873 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 13
247812 ATAATATATT
247822 TAATAA-AAAAAA
1 TAATAATAAAAAA
247834 TAATAATAATAAAAA
1 TAATAAT-A-AAAAA
**
247849 TAATTTTAAAAAA
1 TAATAATAAAAAA
247862 TAA-AATAAAAAA
1 TAATAATAAAAAA
247874 ATCAATGTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 13 0.39
13 8 0.24
14 2 0.06
15 10 0.30
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
TAATAATAAAAAA
Found at i:250763 original size:9 final size:9
Alignment explanation
Indices: 250741--250821 Score: 55
Period size: 9 Copynumber: 9.4 Consensus size: 9
250731 ATATTAAAGG
250741 ATAA-AAAA
1 ATAATAAAA
*
250749 ATAATAAAG
1 ATAATAAAA
250758 ATAATAAAA
1 ATAATAAAA
*
250767 AT-A-AATA
1 ATAATAAAA
*
250774 ATAATAATA
1 ATAATAAAA
*
250783 ATAACAAAA
1 ATAATAAAA
**
250792 ATGGTAAAA
1 ATAATAAAA
250801 A-AATAAAGA
1 ATAATAAA-A
*
250810 GTAA-AAAA
1 ATAATAAAA
250818 ATAA
1 ATAA
250822 ACTAAGAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
7 5 0.09
8 14 0.25
9 35 0.62
10 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (9 bp):
ATAATAAAA
Found at i:250773 original size:19 final size:18
Alignment explanation
Indices: 250729--250821 Score: 70
Period size: 18 Copynumber: 5.3 Consensus size: 18
250719 AAGTCAACAG
*
250729 AAATATTAAAGGATAA-AA
1 AAATAATAAA-GATAATAA
250747 AAATAATAAAGATAATAA
1 AAATAATAAAGATAATAA
*
250765 AAATAA-ATA-ATAATAA
1 AAATAATAAAGATAATAA
* * * **
250781 TAATAACAAAAATGGTAA
1 AAATAATAAAGATAATAA
250799 AAA-AATAAAGAGTAA-AA
1 AAATAATAAAGA-TAATAA
250816 AAATAA
1 AAATAA
250822 ACTAAGAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
16 12 0.20
17 20 0.34
18 27 0.46
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (18 bp):
AAATAATAAAGATAATAA
Found at i:250775 original size:22 final size:21
Alignment explanation
Indices: 250743--250793 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
250733 ATTAAAGGAT
250743 AAAAAAATAATAA-AGATAATA
1 AAAAAAATAATAATA-ATAATA
250764 AAAATAAATAATAATAATAATA
1 AAAA-AAATAATAATAATAATA
*
250786 ACAAAAAT
1 AAAAAAAT
250794 GGTAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
22 18 0.67
23 1 0.04
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAAAATAATAATAATAATA
Found at i:250870 original size:13 final size:13
Alignment explanation
Indices: 250741--250872 Score: 65
Period size: 15 Copynumber: 9.5 Consensus size: 13
250731 ATATTAAAGG
250741 ATAAAAAAAT--A
1 ATAAAAAAATAAA
*
250752 ATAAAGATAATAAAA
1 ATAAA-AAAAT-AAA
250767 ATAAATAATAATAATA
1 ATAAA-AA-AATAA-A
*
250783 ATAACAAAAAT--G
1 ATAA-AAAAATAAA
*
250795 GTAAAAAAATAAA
1 ATAAAAAAATAAA
250808 GAGTAAAAAAATAAA
1 -A-TAAAAAAATAAA
*
250823 CTAAGAAAATATTAAA
1 ATAA-AAAA-A-TAAA
**
250839 ATTAAAAAACGAAA
1 A-TAAAAAAATAAA
*
250853 TTAAAAAAATAAA
1 ATAAAAAAATAAA
250866 ATAAAAA
1 ATAAAAA
250873 TGTTAAATTT
Statistics
Matches: 91, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
11 11 0.12
12 7 0.08
13 19 0.21
14 7 0.08
15 25 0.27
16 18 0.20
17 4 0.04
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:252174 original size:36 final size:36
Alignment explanation
Indices: 252046--252298 Score: 164
Period size: 37 Copynumber: 6.9 Consensus size: 36
252036 TAATAAATTA
* * * * *
252046 AAAAATTATTTTTTAAAACTATATATTATATGTTTTTT
1 AAAAAGTA-TTTTCAAAACTATATAATATAT-ATTTTC
* **
252084 AAAAAATATTTTCAAAACCCTATAATATATATTTTC
1 AAAAAGTATTTTCAAAACTATATAATATATATTTTC
* *
252120 AAATAAAGTAATTT-AAAACTATATAATAT-TTTTTTC
1 -AA-AAAGTATTTTCAAAACTATATAATATATATTTTC
252156 AAAAAGTATTTTCCAAAACTATAT--TATATATTTTC
1 AAAAAGTATTTT-CAAAACTATATAATATATATTTTC
* *
252191 --AAATTATTTTAAAAAACTATATATTATATATATTATTTC
1 AAAAAGTATTTT-CAAAACTATATA--ATATATA-T-TTTC
* *
252230 AAAATGGT-TTTT-AAAACTATATATTATATATTTTTC
1 AAAA-AGTATTTTCAAAACTATATAATATATA-TTTTC
* * *
252266 GAAAA-TAATTTTTAAAAACTATATATTATATAT
1 AAAAAGT-A-TTTTCAAAACTATATAATATATAT
252299 GTATGTTTTC
Statistics
Matches: 175, Mismatches: 22, Indels: 37
0.75 0.09 0.16
Matches are distributed among these distances:
33 19 0.11
34 13 0.07
35 8 0.05
36 27 0.15
37 52 0.30
38 34 0.19
39 15 0.09
41 6 0.03
42 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (36 bp):
AAAAAGTATTTTCAAAACTATATAATATATATTTTC
Found at i:252185 original size:71 final size:72
Alignment explanation
Indices: 252057--252194 Score: 201
Period size: 71 Copynumber: 1.9 Consensus size: 72
252047 AAAATTATTT
252057 TTTAAAACTATATATTATATGTTTTTTAAAAAATATTTTCAAAACCCTATAATATATATTTTCAA
1 TTTAAAACTATATA-TATATGTTTTTTAAAAAATATTTTCAAAA-CCTATAATATATATTTTCAA
252122 ATAAAGTAA
64 ATAAAGTAA
* *
252131 TTTAAAACTATATA-ATAT-TTTTTTCAAAAAGTATTTTCCAAAA-CTATATTATATATTTTCAA
1 TTTAAAACTATATATATATGTTTTTT-AAAAAATATTTT-CAAAACCTATAATATATATTTTCAA
252193 AT
64 AT
252195 TATTTTAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
71 26 0.43
72 15 0.25
73 5 0.08
74 14 0.23
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (72 bp):
TTTAAAACTATATATATATGTTTTTTAAAAAATATTTTCAAAACCTATAATATATATTTTCAAAT
AAAGTAA
Found at i:252207 original size:33 final size:34
Alignment explanation
Indices: 252080--252298 Score: 99
Period size: 36 Copynumber: 6.0 Consensus size: 34
252070 ATTATATGTT
* * ** *
252080 TTTTAAAAAATATTTTCAAAACCCTATAATATATA
1 TTTTCAAAAGTATTTT-AAAAAACTATATTATATA
* * *
252115 TTTTCAAATAAAGTAATTT--AAAACTATATAATATTT
1 TTTTC--A-AAAGTATTTTAAAAAACTATATTATA-TA
**
252151 TTTTCAAAAAGTATTTTCCAAAACTATATTATATA
1 TTTTC-AAAAGTATTTTAAAAAACTATATTATATA
*
252186 TTTTC-AAATTATTTTAAAAAACTATATATTATATATA
1 TTTTCAAAAGTATTTTAAAAAAC--TATA-T-TATATA
*
252223 TTATTTCAAAATGGT-TTTTAAAACTA-TATATTATATA
1 -T-TTTCAAAA--GTATTTTAAAA-AACTATATTATATA
*
252260 TTTTTCGAAAA-TAATTTTTAAAAACTATATATTATATA
1 -TTTTC-AAAAGT-ATTTTAAAAAAC--TATATTATATA
252298 T
1 T
252299 GTATGTTTTC
Statistics
Matches: 144, Mismatches: 18, Indels: 42
0.71 0.09 0.21
Matches are distributed among these distances:
33 14 0.10
34 10 0.07
35 27 0.19
36 31 0.22
37 20 0.14
38 21 0.15
39 8 0.06
40 3 0.02
41 8 0.06
42 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (34 bp):
TTTTCAAAAGTATTTTAAAAAACTATATTATATA
Found at i:252372 original size:38 final size:38
Alignment explanation
Indices: 252325--252544 Score: 260
Period size: 38 Copynumber: 6.0 Consensus size: 38
252315 ATATAACATG
252325 TTTTC-AAAATGTTTTCAAAAACTATATAATATATATA
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATATA
* * *
252362 TTTTCAAAAATGTTATCAAAAATTATATATTATATATA
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATATA
*
252400 TTTT-AAAAATGTTTTCAAAAAACTATATATTATATATA
1 TTTTCAAAAATGTTTTC-AAAAACTATATAATATATATA
* * * *
252438 TTTTCAAAAACGTTTTCAAAAATTATATATTATATATG
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATATA
*
252476 TTTTC--AAAT-TTTT-TAAAAC--TATAATATATATA
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATATA
**
252508 TTTTCGAAAACCGTTTTC-AAAACTATATAATATATAT
1 TTTTC-AAAAATGTTTTCAAAAACTATATAATATATAT
252545 TTTCAATTAC
Statistics
Matches: 158, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
32 16 0.10
34 4 0.03
35 6 0.04
36 12 0.08
37 16 0.10
38 93 0.59
39 11 0.07
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
TTTTCAAAAATGTTTTCAAAAACTATATAATATATATA
Found at i:252432 original size:138 final size:140
Alignment explanation
Indices: 252164--252436 Score: 351
Period size: 139 Copynumber: 2.0 Consensus size: 140
252154 TCAAAAAGTA
* * * *
252164 TTTTCCAAAACTATATTATATATTTTCAAATTATTTTAAAAAACTATATATTATATATATTATTT
1 TTTTCCAAAACTATATAACATATTTTCAAAATATTTTAAAAAACTATATAATATATATATTATTT
** * *
252229 CAAAATGGTTTTTAAAACTATATATTATATATTTTTCGAAAATAATTTTTAAAAACTATATATTA
66 CAAAATGGTTTCAAAAACTATATATTATATATTTTTCAAAAATAATTTTAAAAAACTATATATTA
252294 TATATGTATG
131 TATATGTATG
* * *
252304 TTTT-CAAAACTATATAACATGTTTTCAAAATGTTTTCAAAAACTATATAATATATATA-T-TTT
1 TTTTCCAAAACTATATAACATATTTTCAAAATATTTTAAAAAACTATATAATATATATATTATTT
* *
252366 CAAAAAT-GTTATCAAAAATTATATATTATATATATTTT-AAAAAT-GTTTTCAAAAAACTATAT
66 C-AAAATGGTT-TCAAAAACTATATATTATATAT-TTTTCAAAAATAATTTT-AAAAAACTATAT
252428 ATTATATAT
127 ATTATATAT
252437 ATTTTCAAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
137 11 0.09
138 50 0.43
139 51 0.44
140 4 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (140 bp):
TTTTCCAAAACTATATAACATATTTTCAAAATATTTTAAAAAACTATATAATATATATATTATTT
CAAAATGGTTTCAAAAACTATATATTATATATTTTTCAAAAATAATTTTAAAAAACTATATATTA
TATATGTATG
Found at i:253741 original size:88 final size:85
Alignment explanation
Indices: 253504--253909 Score: 478
Period size: 88 Copynumber: 4.7 Consensus size: 85
253494 TATGTCATCA
* * * *
253504 AGCTGAATGGAATCGAACTCGATAATTTTTTATATTGATAGATAGCCCTCCTCGCCTTGAGCTAT
1 AGCTGAATGTAATCGAACTCG--AAGTTTTT-TGTTGATAGATAGCCCTTCTCGCCTTGAGCTAT
** *
253569 GCTGTAAATTTGGCATGCCTTTG
63 GCTGTAAATTTGATATGCCCTTG
* * *
253592 AGCTGAATGTAACCGAACTCGAAG--GTTTGTTGATATATAGCCCTTCTCGCCTTGAGCTATGCT
1 AGCTGAATGTAATCGAACTCGAAGTTTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGCT
*
253655 ATAAATTTGATATGCCCTTG
66 GTAAATTTGATATGCCCTTG
* *
253675 AGCTGAATGTAATCGAACTCGAATGTTTTTTTTGTTGACAGATAGCCCTTCTCGCCTT-ATGTTA
1 AGCTGAATGTAATCGAACTCGAA-G--TTTTTTGTTGATAGATAGCCCTTCTCGCCTTGA-GCTA
*
253739 TGCTGTGAATTTGATATGCCCTTG
62 TGCTGTAAATTTGATATGCCCTTG
* * *
253763 AGCTGAATGTAATCGAACTTGAAGGCTTTTTGTTGATAGATAGCCCTTCTCACCTTGAGCTATGC
1 AGCTGAATGTAATCGAACTCGAA-GTTTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGC
* **
253828 TGTGAATTTG-GCTGCCCTTG
65 TGTAAATTTGATATGCCCTTG
* * * * * *
253848 AGCTGAATGGAATCGAACTCAAAGGTTTTTGTTGACAGATATCCCTTCTTGCCTTGAGCTAT
1 AGCTGAATGTAATCGAACTCGAAGTTTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTAT
253910 ATTGTAATAG
Statistics
Matches: 277, Mismatches: 34, Indels: 18
0.84 0.10 0.05
Matches are distributed among these distances:
83 71 0.26
84 37 0.13
85 28 0.10
86 46 0.17
87 2 0.01
88 93 0.34
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (85 bp):
AGCTGAATGTAATCGAACTCGAAGTTTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGCTATGCT
GTAAATTTGATATGCCCTTG
Found at i:259319 original size:17 final size:17
Alignment explanation
Indices: 259293--259371 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 17
259283 AAGTTAAAAT
*
259293 AAATATTAAAGGATAA-A
1 AAATAATAAA-GATAATA
259310 AAATAATAAAGATAATA
1 AAATAATAAAGATAATA
*
259327 AAAAAAT-AA-A-AATA
1 AAATAATAAAGATAATA
*
259341 AAGATAATAAAAATAAATTA
1 AA-ATAATAAAGAT-AA-TA
259361 ATAATAATAAA
1 A-AATAATAAA
259372 AAAAACAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
14 6 0.12
15 5 0.10
16 9 0.18
17 17 0.33
19 2 0.04
20 11 0.22
21 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATAATAAAGATAATA
Found at i:259326 original size:9 final size:8
Alignment explanation
Indices: 259305--259429 Score: 63
Period size: 8 Copynumber: 16.2 Consensus size: 8
259295 ATATTAAAGG
259305 ATAA-AAA
1 ATAATAAA
259312 ATAATAAA
1 ATAATAAA
259320 GATAATAAA
1 -ATAATAAA
*
259329 AAAAT-AA
1 ATAATAAA
259336 A-AATAAA
1 ATAATAAA
259343 GATAAT-AA
1 -ATAATAAA
259351 A-AATAAA
1 ATAATAAA
*
259358 TTAATAATA
1 ATAATAA-A
259367 ATAA-AAA
1 ATAATAAA
*
259374 A-AACAAA
1 ATAATAAA
259381 A-AAGTAAA
1 ATAA-TAAA
259389 A-AAT-AA
1 ATAATAAA
* *
259395 AGAGTAAA
1 ATAATAAA
*
259403 AAAATAAA
1 ATAATAAA
*
259411 ACTAAGAAA
1 A-TAATAAA
*
259420 ATATTAAA
1 ATAATAAA
259428 AT
1 AT
259430 TAAAAAACGA
Statistics
Matches: 94, Mismatches: 11, Indels: 25
0.72 0.08 0.19
Matches are distributed among these distances:
6 11 0.12
7 23 0.24
8 39 0.41
9 21 0.22
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (8 bp):
ATAATAAA
Found at i:259330 original size:20 final size:20
Alignment explanation
Indices: 259307--259375 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 20
259297 ATTAAAGGAT
259307 AAAAAATAATAAAGATAATA
1 AAAAAATAATAAAGATAATA
259327 AAAAAATAAAAATAAAGATAATA
1 AAAAAAT---AATAAAGATAATA
*
259350 AAAATAA-ATTAATA-ATAATA
1 AAAA-AATAATAA-AGATAATA
259370 AAAAAA
1 AAAAAA
259376 ACAAAAAAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
19 2 0.05
20 21 0.49
21 1 0.02
23 17 0.40
24 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (20 bp):
AAAAAATAATAAAGATAATA
Found at i:259342 original size:14 final size:14
Alignment explanation
Indices: 259323--259461 Score: 93
Period size: 14 Copynumber: 9.6 Consensus size: 14
259313 TAATAAAGAT
259323 AATAAAAAAATAAA
1 AATAAAAAAATAAA
*
259337 AATAAAGATAATAAA
1 AATAAA-AAAATAAA
** *
259352 AATAAATTAATAAT
1 AATAAAAAAATAAA
259366 AATAAAAAAA-ACAA
1 AATAAAAAAATA-AA
*
259380 AAAAGTAAAAAATAAA
1 AATA--AAAAAATAAA
*
259396 GAGTAAAAAAATAAA
1 -AATAAAAAAATAAA
* *
259411 ACTAAGAAAATATTAA
1 AATAA-AAAA-ATAAA
* **
259427 AATTAAAAAACGAA
1 AATAAAAAAATAAA
*
259441 ATTAAAAAAAT-AA
1 AATAAAAAAATAAA
259454 AATAAAAA
1 AATAAAAA
259462 TGTTAAATTT
Statistics
Matches: 98, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
13 10 0.10
14 39 0.40
15 31 0.32
16 15 0.15
17 3 0.03
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:259351 original size:15 final size:14
Alignment explanation
Indices: 259334--259461 Score: 60
Period size: 15 Copynumber: 9.2 Consensus size: 14
259324 ATAAAAAAAT
259334 AAAAATAAAGATAA
1 AAAAATAAAGATAA
*
259348 TAAAAATAAA-TTAA
1 -AAAAATAAAGATAA
*
259362 TAATAATAAA-A-AA
1 -AAAAATAAAGATAA
259375 AACAAA-AAAG-T-A
1 AA-AAATAAAGATAA
259387 AAAAATAAAGAGTAA
1 AAAAATAAAGA-TAA
259402 AAAAATAAA-ACTAA
1 AAAAATAAAGA-TAA
259416 GAAAATATTAAA-ATTAA
1 -AAAA-A-TAAAGA-TAA
** *
259433 AAAACGAAA-TTAA
1 AAAAATAAAGATAA
259446 AAAAATAAA-ATAA
1 AAAAATAAAGATAA
259459 AAA
1 AAA
259462 TGTTAAATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
11 3 0.03
12 12 0.13
13 20 0.22
14 20 0.22
15 23 0.25
16 5 0.05
17 8 0.09
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (14 bp):
AAAAATAAAGATAA
Found at i:259363 original size:23 final size:23
Alignment explanation
Indices: 259310--259376 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
259300 AAAGGATAAA
259310 AAATAATAAAGATAATAAAAAAAT
1 AAATAATAAAGATAAT-AAAAAAT
259334 AAA-AATAAAGATAAT-AAAAAT
1 AAATAATAAAGATAATAAAAAAT
259355 AAATTAATAATA-ATAA-AAAAAA
1 AAA-TAATAA-AGATAATAAAAAA
259377 CAAAAAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
21 9 0.23
23 26 0.67
24 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (23 bp):
AAATAATAAAGATAATAAAAAAT
Found at i:259382 original size:52 final size:53
Alignment explanation
Indices: 259311--259410 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
259301 AAGGATAAAA
* * *
259311 AATAATAAAGATAATAAAAAAAT-AAAAATAAAGA-TAATAAAAATAAATTAAT
1 AATAATAAAAAAAACAAAAAAATAAAAAATAAAGAGTAA-AAAAATAAATTAAT
*
259363 AATAATAAAAAAAACAAAAAAGTAAAAAATAAAGAGTAAAAAAATAAA
1 AATAATAAAAAAAACAAAAAAATAAAAAATAAAGAGTAAAAAAATAAA
259411 ACTAAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 19 0.45
53 20 0.48
54 3 0.07
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (53 bp):
AATAATAAAAAAAACAAAAAAATAAAAAATAAAGAGTAAAAAAATAAATTAAT
Found at i:259435 original size:53 final size:52
Alignment explanation
Indices: 259311--259436 Score: 130
Period size: 53 Copynumber: 2.4 Consensus size: 52
259301 AAGGATAAAA
* * * *
259311 AATAATAAAGATAATAAAAAAATAAAAATAAAGATAATAAAAATAAATTAAT
1 AATAATAAAAAAAATAAAAAAATAAAAATAAAGATAATAAAAATAAACTAAG
* *
259363 AATAATAAAAAAAACAAAAAAGTAAAAAATAAAGAGTAA-AAAAATAAAACTAAG
1 AATAATAAAAAAAATAAAAAAAT-AAAAATAAAGA-TAATAAAAAT-AAACTAAG
** *
259417 AA-AATATTAAAATTAAAAAA
1 AATAATAAAAAAAATAAAAAA
259437 CGAAATTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
52 19 0.31
53 31 0.51
54 11 0.18
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (52 bp):
AATAATAAAAAAAATAAAAAAATAAAAATAAAGATAATAAAAATAAACTAAG
Found at i:259550 original size:23 final size:23
Alignment explanation
Indices: 259524--259567 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
259514 TAAAATACCA
259524 AAATAG-AAAAATAAATAATAAGT
1 AAATAGAAAAAAT-AATAATAAGT
*
259547 AAATATAAAAAATAATAATAA
1 AAATAGAAAAAATAATAATAA
259568 AAAAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATAGAAAAAATAATAATAAGT
Found at i:260870 original size:39 final size:39
Alignment explanation
Indices: 260656--261239 Score: 424
Period size: 39 Copynumber: 15.6 Consensus size: 39
260646 TAATAAATAA
* *
260656 TTTTTT-AAAACTATATATTATATGTT-TTTTAGAAAATG
1 TTTTTTAAAAACTATATATTATATATTATTTT-CAAAATG
* *
260694 --TTTTCAAAACCA-ATA--ATATA-TATTTTC--AAT-
1 TTTTTTAAAAACTATATATTATATATTATTTTCAAAATG
260724 TTTTTT-AAAAC--TATA-TA-ATA-TATTTTCAAAAATG
1 TTTTTTAAAAACTATATATTATATATTATTTTC-AAAATG
** *
260758 -TTTTCCAAAACTATAT-TTATATA-T-TTTTCAAAATA
1 TTTTTTAAAAACTATATATTATATATTATTTTCAAAATG
*
260793 TTTTTAAAAAACTATATATTATATATATATTTTCAAAATG
1 TTTTTTAAAAACTATATATTATATAT-TATTTTCAAAATG
* *
260833 TTTTTTAAAAACCATATATTATATATTTTTTTCAAAATG
1 TTTTTTAAAAACTATATATTATATATTATTTTCAAAATG
*
260872 TTTTTTAAAAACTATATATTATATATATGTTTTCAAAATG
1 TTTTTTAAAAACTATATATTATATAT-TATTTTCAAAATG
260912 -TTTTTAAAAACTATATATTATATA-TATGATTTCAAAATG
1 TTTTTTAAAAACTATATATTATATATTAT--TTTCAAAATG
* * * *
260951 --TTTTCAAAACTATCTAATATGTATGT-TTTT-AAAATG
1 TTTTTTAAAAACTATATATTATATAT-TATTTTCAAAATG
* *
260987 -TTTTCAAAAACTATATAATATATA-TATTTTCAAAAAT-
1 TTTTTTAAAAACTATATATTATATATTATTTTC-AAAATG
* * *
261024 ATTTTTAAAAACTATATTTTATATATATATATTTTAAAAATG
1 TTTTTTAAAAACTATA-TAT-TATATAT-TATTTTCAAAATG
* * **
261066 -TTTTAAAAAACTATATATTATTTA-TATTTTCAAAAAC
1 TTTTTTAAAAACTATATATTATATATTATTTTCAAAATG
* *
261103 TTTTTCAAAAACTATATATTATATA-TGTTTTCAAAA--
1 TTTTTTAAAAACTATATATTATATATTATTTTCAAAATG
* * * * *
261139 -TTTTTCAAAACTATAGAATATATATATTTTTTTGAAAACCG
1 TTTTTTAAAAACTATA-TAT-TATATATTATTTTCAAAA-TG
261180 --TTTT-AAAACTATATA--ATATA-TATTTTCAAAAACTG
1 TTTTTTAAAAACTATATATTATATATTATTTTC-AAAA-TG
* *
261215 ATTTTTAAAAAAGTATATATTATAT
1 -TTTTTTAAAAACTATATATTATAT
261240 GTTTTCGAAA
Statistics
Matches: 451, Mismatches: 46, Indels: 95
0.76 0.08 0.16
Matches are distributed among these distances:
30 13 0.03
31 9 0.02
32 4 0.01
33 8 0.02
34 18 0.04
35 30 0.07
36 43 0.10
37 57 0.13
38 83 0.18
39 98 0.22
40 59 0.13
41 23 0.05
42 6 0.01
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (39 bp):
TTTTTTAAAAACTATATATTATATATTATTTTCAAAATG
Found at i:260985 original size:154 final size:150
Alignment explanation
Indices: 260735--261239 Score: 521
Period size: 154 Copynumber: 3.3 Consensus size: 150
260725 TTTTTAAAAC
**
260735 TATATAATATATTTTCAAAAATGTTTTCCAAAACTATAT-TTATATAT-TTTTCAAAATATTTTT
1 TATAT-ATATATTTTCAAAAATGTTTTTAAAAACTATATATTATATATATTTTC-AAA-ATTTTT
* * *
260798 AAAAAACTATATATTATATATATATTTTCAAAATGTTTTTTAAAAACCATATATTATATATTTTT
63 -CAAAACTATATA--ATATATATGTTTTCAAAATG-TTTTTAAAAACTATATATTATATATTTTT
260863 TTCAAAATGTTTTTTAAAAACTATATAT
124 TTCAAAATG-TTTTTAAAAACTATATAT
*
260891 TATATATATGTTTTC-AAAATGTTTTTAAAAACTATATATTATATATATGATTTCAAAATGTTTT
1 TATATATATATTTTCAAAAATGTTTTTAAAAACTATATATTATATATAT--TTTCAAAAT-TTTT
* * * * * *
260955 CAAAACTATCTAATATGTATGTTTTTAAAATGTTTTCAAAAACTATATAATATATA-TATTTTCA
63 CAAAACTATATAATATATATGTTTTCAAAATGTTTTTAAAAACTATATATTATATATTTTTTTC-
* *
261019 AAAATATTTTTAAAAACTATATTT
127 AAAATGTTTTTAAAAACTATATAT
* * *
261043 TATATATATATATTTTAAAAATGTTTTAAAAAACTATATATTATTTATATTTTCAAAAACTTTTT
1 TATATATATAT-TTTCAAAAATGTTTTTAAAAACTATATATTATATATATTTTC-AAAA-TTTTT
* * *
261108 CAAAAACTATATATTATATATGTTTTCAAAA--TTTTTCAAAACTATAGAATATATATATTTTTT
63 C-AAAACTATATAATATATATGTTTTCAAAATGTTTTTAAAAACTATA-TAT-TATATATTTTTT
* *
261171 TGAAAACCG-TTTT-AAAAC--TATA-
125 TCAAAA-TGTTTTTAAAAACTATATAT
*
261193 TA-ATATATATTTTCAAAAACTGATTTTTAAAAAAGTATATATTATAT
1 TATATATATATTTTCAAAAA-TG-TTTTT-AAAAACTATATATTATAT
261240 GTTTTCGAAA
Statistics
Matches: 296, Mismatches: 35, Indels: 41
0.80 0.09 0.11
Matches are distributed among these distances:
148 8 0.03
149 10 0.03
150 6 0.02
151 19 0.06
152 50 0.17
153 44 0.15
154 108 0.36
155 22 0.07
156 18 0.06
157 7 0.02
158 4 0.01
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (150 bp):
TATATATATATTTTCAAAAATGTTTTTAAAAACTATATATTATATATATTTTCAAAATTTTTCAA
AACTATATAATATATATGTTTTCAAAATGTTTTTAAAAACTATATATTATATATTTTTTTCAAAA
TGTTTTTAAAAACTATATAT
Found at i:261298 original size:74 final size:73
Alignment explanation
Indices: 261156--261300 Score: 170
Period size: 74 Copynumber: 2.0 Consensus size: 73
261146 AAACTATAGA
* * * * * *
261156 ATATATATATTTTTTTGAAAACCGTTTTAAAACTATATAATATATATTTTCAAAAACTGATTTTT
1 ATATATATATGTTTTCGAAAACCGTTTTAAAACTATATAATATATATTTACAAAAACTAACTTAT
261221 AAAAAAGT
66 AAAAAAGT
*
261229 ATATATTATATGTTTTCGAAAACCGTTTTCTAAAAACTATA-AA-A-ATATTTACAAAAATTAAC
1 ATATA-TATATGTTTTCGAAAACCG-TTT-T-AAAACTATATAATATATATTTACAAAAACTAAC
261291 TTATAAAAAA
62 TTATAAAAAA
261301 ATTCCGGATG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
73 5 0.08
74 40 0.66
75 4 0.07
76 3 0.05
77 9 0.15
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (73 bp):
ATATATATATGTTTTCGAAAACCGTTTTAAAACTATATAATATATATTTACAAAAACTAACTTAT
AAAAAAGT
Found at i:270352 original size:20 final size:21
Alignment explanation
Indices: 270298--270360 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
270288 GATTCCCCTG
270298 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
270322 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
270342 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
270361 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:273660 original size:22 final size:21
Alignment explanation
Indices: 273634--273680 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
273624 AAGGTCAAAA
*
273634 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
273656 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
273676 ATCAA
1 ATCAA
273681 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:277961 original size:58 final size:58
Alignment explanation
Indices: 277890--278006 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
277880 AACGACAACC
* * *
277890 AAAATTTTTAACCAATAAACATCAATTACTATTTAACAAAGTATGGCAGAATGGTACA
1 AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
277948 AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
1 AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
278006 A
1 A
278007 CACCTCCCCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (58 bp):
AAAATTTTCAACCAATAAACATCAATTACTATTTAACAAAGTATGGAAGAATGATACA
Done.