Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008270.1 Hibiscus syriacus cultivar Beakdansim tig00110927_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: 726180
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:191370 original size:2 final size:2
Alignment explanation
Indices: 191365--191413 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
191355 AATCTTTCTT
191365 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
191407 TA TA TA T
1 TA TA TA T
191414 CATTTTTCGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:195621 original size:15 final size:16
Alignment explanation
Indices: 195598--195631 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
195588 TTTGAAATAA
*
195598 ATATTTATTTATTA-T
1 ATATATATTTATTACT
195613 ATATATATTTATTACT
1 ATATATATTTATTACT
195629 ATA
1 ATA
195632 AAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATATATATTTATTACT
Found at i:197020 original size:3 final size:3
Alignment explanation
Indices: 197012--197069 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
197002 TTAATATATT
* * *
197012 TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
197060 TAA TAA TAA T
1 TAA TAA TAA T
197070 CAATTAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:197903 original size:114 final size:114
Alignment explanation
Indices: 197389--198392 Score: 1516
Period size: 114 Copynumber: 8.8 Consensus size: 114
197379 GATAGAATTA
* * *
197389 TTGAACAAGTTCTTCT-ATTATGAA-CTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTTATTAT
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * ** * * * *
197452 GAACTCTAC-CTGGCAATGTTGATACATCAA-ATGATGAATTCAAGAAAAAGG
63 GAAC-CTTCTCTGGAAATGTCAATCCATCAATTTGATGAATTCAGGTAAAAGG
* *
197503 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
*
197568 GAA-C-TCTCTGGAAAAG-CTAATCCATCAATTTGATGAATTCAGGTAAAAGG
63 GAACCTTCTCTGGAAATGTC-AATCCATCAATTTGATGAATTCAGGTAAAAGG
197618 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
197683 CCTTCTCTGGAAAAG-CTAAT-CATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGTC-AATCCATCAATTTGATGAATTCAGGTAAAAGG
197731 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
197796 CCTTCTCTGGAAATGTCAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGTCAATCCATCAATTTGATGAATTCAGGTAAAAGG
197845 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * ** * * * * *
197910 CTCTAC-CTGGCAATGTTGATACATCAA-ATGATGAATTCAAGCAAAATG
66 C-CTTCTCTGGAAATGTCAATCCATCAATTTGATGAATTCAGGTAAAAGG
* *
197958 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
*
198023 GAA-C-TCTCTGGAAAAG-CTAATCCATCAATTTGATGAATTCAGGTAAAAGG
63 GAACCTTCTCTGGAAATGTC-AATCCATCAATTTGATGAATTCAGGTAAAAGG
198073 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
198138 CCTTCTCTGGAAAAG-CTAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGTC-AATCCATCAATTTGATGAATTCAGGTAAAAGG
198187 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
198252 CCTTCTCTGGAAATGTCAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAATGTCAATCCATCAATTTGATGAATTCAGGTAAAAGG
198301 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
198366 CCTTCTCTGGAAATGTCAATCCATCAA
66 CCTTCTCTGGAAATGTCAATCCATCAA
198393 ATGATAGATT
Statistics
Matches: 833, Mismatches: 38, Indels: 38
0.92 0.04 0.04
Matches are distributed among these distances:
112 38 0.05
113 175 0.21
114 426 0.51
115 135 0.16
116 59 0.07
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (114 bp):
TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CCTTCTCTGGAAATGTCAATCCATCAATTTGATGAATTCAGGTAAAAGG
Found at i:199395 original size:160 final size:164
Alignment explanation
Indices: 199131--199514 Score: 652
Period size: 160 Copynumber: 2.4 Consensus size: 164
199121 GTAGTTCTTA
* *
199131 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
*
199196 ATTCAATGATTGGTTCAACCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 ATTCAATGATTGGTTCAACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
199261 A-ACATTCATCTTCTAAATTC-A-A-TGGTTCTG
131 AGACATTCATCTTCCAAATTCAAGATTGGTTCTG
199291 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
**
199356 ATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
66 ATTCAATGATTGGTTC-AACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
199420 GAGTACATTCATCTTCCAAATTCAATGATTGGTTCTG
130 GAG-ACATTCATCTTCCAAATTCAA-GATTGGTTCTG
199457 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
199515 TTTTCAGTTA
Statistics
Matches: 211, Mismatches: 6, Indels: 8
0.94 0.03 0.04
Matches are distributed among these distances:
160 123 0.58
161 2 0.01
162 18 0.09
163 1 0.00
165 1 0.00
166 66 0.31
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (164 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
ATTCAATGATTGGTTCAACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
AGACATTCATCTTCCAAATTCAAGATTGGTTCTG
Found at i:199402 original size:83 final size:83
Alignment explanation
Indices: 199131--199514 Score: 606
Period size: 83 Copynumber: 4.7 Consensus size: 83
199121 GTAGTTCTTA
* *
199131 CCAAACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
**
199196 ATTCAATGATTGGTTCAA
66 ATTCAATGATTGGTTCTG
*
199214 CCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTA-T-G-AACATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA-ATTCATCTTCTA
199276 AATTC-A--A-TGGTTCTG
65 AATTCAATGATTGGTTCTG
199291 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
199356 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
199374 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGTACATTCATCTTCC
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCT
199437 AAATTCAATGATTGGTTCTG
64 AAATTCAATGATTGGTTCTG
199457 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
199515 TTTTCAGTTA
Statistics
Matches: 278, Mismatches: 11, Indels: 24
0.89 0.04 0.08
Matches are distributed among these distances:
77 50 0.18
78 2 0.01
79 18 0.06
80 6 0.02
81 17 0.06
82 6 0.02
83 175 0.63
84 4 0.01
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
ATTCAATGATTGGTTCTG
Found at i:200302 original size:19 final size:16
Alignment explanation
Indices: 200278--200320 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
200268 TTCATAGAAG
200278 AATAAATTAAAATTTCGAA
1 AATAAATT-AAATTTC--A
*
200297 AATAAATTGAATTTCA
1 AATAAATTAAATTTCA
200313 AATAAATT
1 AATAAATT
200321 GAACTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
18 6 0.26
19 8 0.35
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (16 bp):
AATAAATTAAATTTCA
Found at i:200331 original size:16 final size:16
Alignment explanation
Indices: 200296--200332 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
200286 AAAATTTCGA
*
200296 AAATAAATTGAATTTC
1 AAATAAATTGAACTTC
*
200312 AAATAAATTGAACTTG
1 AAATAAATTGAACTTC
200328 AAATA
1 AAATA
200333 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (16 bp):
AAATAAATTGAACTTC
Found at i:200680 original size:14 final size:14
Alignment explanation
Indices: 200648--200719 Score: 74
Period size: 14 Copynumber: 4.9 Consensus size: 14
200638 ACCTTGACCC
*
200648 CTTTTTTTTTTTCTCT
1 CTTTCTTTTTTT-T-T
200664 CTTTCTTTTTTTTT
1 CTTTCTTTTTTTTT
*
200678 CTTTTTTTTTATTTT
1 CTTTCTTTTT-TTTT
*
200693 CTTTC-TTTTCTTT
1 CTTTCTTTTTTTTT
200706 CTTCTCTTTTTTTT
1 CTT-TCTTTTTTTT
200720 CTTCAAGCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.12
14 16 0.33
15 15 0.31
16 11 0.23
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTCTTTTTTTTT
Found at i:200693 original size:33 final size:32
Alignment explanation
Indices: 200649--200719 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
200639 CCTTGACCCC
* *
200649 TTTTTTTTTTTCTCTC-TTTCTTTTTTTTTCTT
1 TTTTTTTTTTTCTCTCTTTTC-TTTCTTCTCTT
*
200681 TTTTTTTATTTTCTTTCTTTTCTTTCTTCTCTT
1 TTTTTTT-TTTTCTCTCTTTTCTTTCTTCTCTT
200714 TTTTTT
1 TTTTTT
200720 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.21
33 23 0.68
34 4 0.12
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.83
Consensus pattern (32 bp):
TTTTTTTTTTTCTCTCTTTTCTTTCTTCTCTT
Found at i:212080 original size:14 final size:15
Alignment explanation
Indices: 212061--212089 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
212051 AATAAATATT
212061 TATTTATTA-TATAA
1 TATTTATTACTATAA
212075 TATTTATTACTATAA
1 TATTTATTACTATAA
212090 AAATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTATTACTATAA
Found at i:212094 original size:18 final size:18
Alignment explanation
Indices: 212054--212098 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
212044 TATTTGAAAT
*
212054 AAATATTTATTTATTATA
1 AAATATTTATTTACTATA
*
212072 TAATATTTA-TTACTATAA
1 AAATATTTATTTACTAT-A
212090 AAATATTTA
1 AAATATTTA
212099 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATTTATTTACTATA
Found at i:213475 original size:3 final size:3
Alignment explanation
Indices: 213467--213536 Score: 113
Period size: 3 Copynumber: 23.3 Consensus size: 3
213457 TTAATATATT
* *
213467 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
213515 TAA TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
213537 CAATTAATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:213488 original size:18 final size:18
Alignment explanation
Indices: 213458--213536 Score: 124
Period size: 18 Copynumber: 4.4 Consensus size: 18
213448 TATATGTATT
213458 TAATATATT-TAATAATAA
1 TAATA-ATTATAATAATAA
* *
213476 TAATGATAATAATAATAA
1 TAATAATTATAATAATAA
213494 TAATAATTATAATAATAA
1 TAATAATTATAATAATAA
213512 TAATAATTATAATAATAA
1 TAATAATTATAATAATAA
213530 TAATAAT
1 TAATAAT
213537 CAATTAATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
17 2 0.04
18 54 0.96
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
TAATAATTATAATAATAA
Found at i:214523 original size:18 final size:18
Alignment explanation
Indices: 214500--214537 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
214490 ATTATGCATA
214500 ATCATCATTTATAATTTT
1 ATCATCATTTATAATTTT
214518 ATCATCATTTATAATTTT
1 ATCATCATTTATAATTTT
214536 AT
1 AT
214538 TAGGTAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (18 bp):
ATCATCATTTATAATTTT
Found at i:218366 original size:14 final size:14
Alignment explanation
Indices: 218347--218401 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
218337 GTTCGTGAAT
218347 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
218361 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
*
218375 G-T---TTATGTTT
1 GTTCGGTTATGTTC
218385 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
218399 GTT
1 GTT
218402 TATGTTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.07, C:0.11, G:0.27, T:0.55
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:218421 original size:24 final size:24
Alignment explanation
Indices: 218345--218408 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
218335 ACGTTCGTGA
*
218345 ATGTTCGGTTATGTTCGTTCGGTT
1 ATGTTCGTTTATGTTCGTTCGGTT
*
218369 ATGTTCGTTTATGTTTGTTCGGTT
1 ATGTTCGTTTATGTTCGTTCGGTT
218393 ATGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
218409 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.09, C:0.11, G:0.25, T:0.55
Consensus pattern (24 bp):
ATGTTCGTTTATGTTCGTTCGGTT
Found at i:219479 original size:16 final size:16
Alignment explanation
Indices: 219458--219508 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
219448 GTCTCCAACG
219458 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
** *
219474 TTTATGTTTTTGTTCG
1 TTTATGTTCGTGTTCA
219490 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
219504 TTTAT
1 TTTAT
219509 TAAATGAACG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 5 0.17
15 2 0.07
16 22 0.76
ACGTcount: A:0.12, C:0.08, G:0.16, T:0.65
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:220133 original size:14 final size:14
Alignment explanation
Indices: 220114--220141 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
220104 ACAAGTATAT
220114 TGAAAACTGAAAAG
1 TGAAAACTGAAAAG
220128 TGAAAACTGAAAAG
1 TGAAAACTGAAAAG
220142 AAAGAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAACTGAAAAG
Found at i:220780 original size:13 final size:12
Alignment explanation
Indices: 220753--220790 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
220743 ACTTTAATTC
220753 TTAATTCTT--T
1 TTAATTCTTAAT
220763 TTAATTCTTTAAT
1 TTAATTC-TTAAT
220776 TTAATTCTTAAT
1 TTAATTCTTAAT
220788 TTA
1 TTA
220791 GATAGTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 8 0.32
13 8 0.32
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (12 bp):
TTAATTCTTAAT
Found at i:224307 original size:18 final size:18
Alignment explanation
Indices: 224284--224319 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
224274 TATTGGATGT
224284 TGAATTCAAGTTCAAGGG
1 TGAATTCAAGTTCAAGGG
224302 TGAATTCAAGTTCAAGGG
1 TGAATTCAAGTTCAAGGG
224320 AGATCAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (18 bp):
TGAATTCAAGTTCAAGGG
Found at i:226364 original size:12 final size:12
Alignment explanation
Indices: 226346--226381 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
226336 TATATATGTT
226346 CATGTGATATGA
1 CATGTGATATGA
*
226358 TATGTGATATGA
1 CATGTGATATGA
*
226370 CCTGTGATATGA
1 CATGTGATATGA
226382 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:234568 original size:31 final size:31
Alignment explanation
Indices: 234505--234574 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
234495 GGCTTTACGT
*
234505 CCCCGAGATAAATCTTGTGTAGGCCCTATGG
1 CCCCGAGATAAATCTTGTGTAGGCCCCATGG
** *
234536 CCCCGAGATTCATCTTAG-GTAGGCCCCGTGG
1 CCCCGAGATAAATCTT-GTGTAGGCCCCATGG
*
234567 CCTCGAGA
1 CCCCGAGA
234575 ACTTCCTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (31 bp):
CCCCGAGATAAATCTTGTGTAGGCCCCATGG
Found at i:237670 original size:23 final size:23
Alignment explanation
Indices: 237598--237661 Score: 128
Period size: 23 Copynumber: 2.8 Consensus size: 23
237588 AAATATTCAA
237598 ATAAAATCCTAAATAATAGAAAG
1 ATAAAATCCTAAATAATAGAAAG
237621 ATAAAATCCTAAATAATAGAAAG
1 ATAAAATCCTAAATAATAGAAAG
237644 ATAAAATCCTAAATAATA
1 ATAAAATCCTAAATAATA
237662 AGTTGATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.23
Consensus pattern (23 bp):
ATAAAATCCTAAATAATAGAAAG
Found at i:243115 original size:40 final size:40
Alignment explanation
Indices: 243070--243149 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
243060 GTCGTCATTT
243070 TTTTAACAAAAAAGATAAATTTGAAACATATGAATAGTCG
1 TTTTAACAAAAAAGATAAATTTGAAACATATGAATAGTCG
* *
243110 TTTTAACAAAAATGATAAATTTGGAACATATGAATAGTCG
1 TTTTAACAAAAAAGATAAATTTGAAACATATGAATAGTCG
243150 AGTTATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.31
Consensus pattern (40 bp):
TTTTAACAAAAAAGATAAATTTGAAACATATGAATAGTCG
Found at i:254752 original size:15 final size:14
Alignment explanation
Indices: 254727--254893 Score: 72
Period size: 15 Copynumber: 11.3 Consensus size: 14
254717 AAAGACAATG
*
254727 AAGATAAATAAACTA
1 AAGA-AAATAAAATA
254742 AAGAAACATAAAATA
1 AAGAAA-ATAAAATA
*
254757 AAGAAAATAAAAAAA
1 AAGAAAAT-AAAATA
*
254772 AATGAAAA-AAAAAA
1 AA-GAAAATAAAATA
* *
254786 AAAAAAAGACATAA-A
1 AAGAAAATA-A-AATA
* *
254801 AATAAAATAAAGGTAA
1 AAGAAAATAAA-AT-A
*
254817 AAAACTAAATAAAATA
1 AAGA--AAATAAAATA
* *
254833 AAGAACATAAAAAACA
1 AAGAA-A-ATAAAATA
*
254849 AAAAAAATAAAA-A
1 AAGAAAATAAAATA
*
254862 AAAAAAATAAAATA
1 AAGAAAATAAAATA
*
254876 AA-ATAATCAAAATA
1 AAGAAAAT-AAAATA
254890 AAGA
1 AAGA
254894 TAACGAGCAA
Statistics
Matches: 122, Mismatches: 14, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
13 22 0.18
14 31 0.25
15 36 0.30
16 25 0.20
17 1 0.01
18 7 0.06
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (14 bp):
AAGAAAATAAAATA
Found at i:254763 original size:9 final size:9
Alignment explanation
Indices: 254751--254877 Score: 50
Period size: 9 Copynumber: 13.9 Consensus size: 9
254741 AAAGAAACAT
254751 AAAATAAAG
1 AAAATAAAG
254760 AAAATAAA-
1 AAAATAAAG
*
254768 AAAA-AATG
1 AAAATAAAG
* *
254776 AAAAAAAAA
1 AAAATAAAG
*
254785 AAAAAAAAG
1 AAAATAAAG
*
254794 ACATAA-AAAT
1 A-A-AATAAAG
254804 AAAATAAAGG
1 AAAATAAA-G
*
254814 TAAAAAACTAAAT
1 ---AAAA-TAAAG
254827 AAAATAAAG
1 AAAATAAAG
*
254836 AACATAAA-
1 AAAATAAAG
254844 AAACA-AAA-
1 AAA-ATAAAG
*
254852 AAAATAAAA
1 AAAATAAAG
* *
254861 AAAAAAAAT
1 AAAATAAAG
254870 AAAATAAA
1 AAAATAAA
254878 ATAATCAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.03
8 21 0.23
9 49 0.53
10 9 0.10
11 2 0.02
13 4 0.04
14 4 0.04
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.11
Consensus pattern (9 bp):
AAAATAAAG
Found at i:254781 original size:18 final size:17
Alignment explanation
Indices: 254760--254878 Score: 71
Period size: 19 Copynumber: 6.5 Consensus size: 17
254750 TAAAATAAAG
254760 AAAATAAAAAAAAATGAAA
1 AAAATAAAAAAAAA-G-AA
*
254779 AAAAAAAAAAAAAAGACATA
1 AAAATAAAAAAAAAG--A-A
* *
254799 AAAATAAAATAAAGGTAA
1 AAAATAAAAAAAAAG-AA
*
254817 AAAACTAAATAAAATAA-AG
1 AAAA-TAAA-AAAA-AAGAA
* *
254836 AACATAAAAAACAA-AA
1 AAAATAAAAAAAAAGAA
*
254852 AAAATAAAAAAAAAAAA
1 AAAATAAAAAAAAAGAA
254869 TAAAATAAAA
1 -AAAATAAAA
254879 TAATCAAAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
16 15 0.19
17 5 0.06
18 19 0.24
19 23 0.29
20 16 0.20
21 1 0.01
ACGTcount: A:0.82, C:0.03, G:0.04, T:0.11
Consensus pattern (17 bp):
AAAATAAAAAAAAAGAA
Found at i:254792 original size:10 final size:10
Alignment explanation
Indices: 254751--254881 Score: 83
Period size: 10 Copynumber: 12.7 Consensus size: 10
254741 AAAGAAACAT
*
254751 AAAAT-AAAG
1 AAAATAAAAA
254760 AAAATAAAAA
1 AAAATAAAAA
254770 AAAATGAAAAA
1 AAAAT-AAAAA
*
254781 AAAAAAAAAA
1 AAAATAAAAA
254791 AAGACATAAAAA
1 AA-A-ATAAAAA
254803 TAAAATAAAGGTAA
1 -AAAATAAA---AA
*
254817 AAAACT-AAAT
1 AAAA-TAAAAA
*
254827 AAAAT-AAAG
1 AAAATAAAAA
*
254836 AACATAAAAA
1 AAAATAAAAA
254846 ACAAA-AAAAA
1 A-AAATAAAAA
*
254856 TAAA-AAAAA
1 AAAATAAAAA
*
254865 AAAATAAAAT
1 AAAATAAAAA
254875 AAAATAA
1 AAAATAA
254882 TCAAAATAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 23
0.74 0.08 0.17
Matches are distributed among these distances:
9 24 0.24
10 40 0.40
11 17 0.17
12 7 0.07
13 8 0.08
14 3 0.03
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.11
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:254792 original size:73 final size:74
Alignment explanation
Indices: 254713--254868 Score: 187
Period size: 76 Copynumber: 2.1 Consensus size: 74
254703 AACATGTTAG
* *
254713 AAAAAAAGACAATGAAGAT-AAATAAA-CTAAAGAAAC-ATAAAATAAAGAAAATAAAAAA-AAA
1 AAAAAAAGAC-ATAAAAATAAAATAAAGCTAAA-AAACAATAAAATAAAGAAAATAAAAAACAAA
254774 TGAAAAA-AAAAA
64 --AAAAATAAAAA
* *
254786 AAAAAAAGACATAAAAATAAAATAAAGGTAAAAAACTAAATAAAATAAAGAACATAAAAAACAAA
1 AAAAAAAGACATAAAAATAAAATAAAGCTAAAAAAC--AATAAAATAAAGAAAATAAAAAACAAA
254851 AAAAATAAAAA
64 AAAAATAAAAA
254862 AAAAAAA
1 AAAAAAA
254869 TAAAATAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
72 6 0.08
73 21 0.29
74 4 0.06
75 5 0.07
76 33 0.46
77 3 0.04
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.11
Consensus pattern (74 bp):
AAAAAAAGACATAAAAATAAAATAAAGCTAAAAAACAATAAAATAAAGAAAATAAAAAACAAAAA
AAATAAAAA
Found at i:254913 original size:5 final size:5
Alignment explanation
Indices: 254749--254881 Score: 67
Period size: 5 Copynumber: 25.8 Consensus size: 5
254739 CTAAAGAAAC
* * * * *
254749 ATAAA AT-AA AGAAA ATAAA AAAAA ATGAAA AAAAA AAAAA AAAAGA CATAAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA ATAAA ATAA-A -AT-AAA
* * * * *
254802 ATAAA ATAAA GGTAAA AAACTAA ATAAA AT-AA AGAAC ATAAA AAACAA
1 ATAAA ATAAA -ATAAA ATA--AA ATAAA ATAAA ATAAA ATAAA ATA-AA
*
254850 AAAAA ATAAA A-AAA A-AAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
254882 TCAAAATAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 22
0.73 0.12 0.16
Matches are distributed among these distances:
4 14 0.14
5 63 0.62
6 16 0.16
7 6 0.06
8 2 0.02
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (5 bp):
ATAAA
Found at i:255008 original size:6 final size:6
Alignment explanation
Indices: 254959--255065 Score: 62
Period size: 6 Copynumber: 18.3 Consensus size: 6
254949 TAACAAGAGG
* * * * *
254959 AAAATA AAAATG AAAATA AATATA TAAATA AAACT- AATATA AAAAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * * * *
255005 AAAATA AGAA-A AGAATA AAAA-G AAAAGA AAAA-A CAAATA AAATAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA-ATA
255051 AAAATAA AAAATA AA
1 AAAAT-A AAAATA AA
255066 TATATGGAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
5 21 0.28
6 44 0.58
7 11 0.14
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:255010 original size:5 final size:5
Alignment explanation
Indices: 254959--255065 Score: 56
Period size: 5 Copynumber: 19.6 Consensus size: 5
254949 TAACAAGAGG
*
254959 AAAAT AAAAAT GAAAAT AAATAT ATAAAT AAAACT AATAT AAAAAT AAAAT
1 AAAAT -AAAAT -AAAAT AAA-AT A-AAAT AAAA-T AAAAT -AAAAT AAAAT
* * * *
255010 AAGAA- AAGAAT AAAAAG AAAAG AAAAA ACAAAT AAAAT AAAA- AAATAA
1 AA-AAT AA-AAT -AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAA-AT
255058 AAAAT AAA
1 AAAAT AAA
255066 TATATGGAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
4 3 0.04
5 42 0.50
6 35 0.42
7 4 0.05
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:255016 original size:8 final size:7
Alignment explanation
Indices: 254984--255065 Score: 53
Period size: 7 Copynumber: 11.0 Consensus size: 7
254974 ATAAATATAT
254984 AAATAAA
1 AAATAAA
254991 ACTAATATAA
1 A--AATA-AA
255001 AAATAAA
1 AAATAAA
*
255008 ATAAGAAA
1 A-AATAAA
255016 AGAATAAA
1 A-AATAAA
255024 AAGA-AAA
1 AA-ATAAA
255031 GAAA-AAA
1 -AAATAAA
255038 CAAATAAA
1 -AAATAAA
*
255046 ATA-AAA
1 AAATAAA
255052 AAATAAA
1 AAATAAA
255059 AAATAAA
1 AAATAAA
255066 TATATGGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
6 5 0.08
7 27 0.44
8 22 0.36
9 4 0.07
10 3 0.05
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.13
Consensus pattern (7 bp):
AAATAAA
Found at i:255022 original size:22 final size:20
Alignment explanation
Indices: 254997--255065 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 20
254987 TAAAACTAAT
*
254997 ATAAAAATAAAATAAGAAAAGA
1 ATAAAAATAAAA-AA-AAAAAA
*
255019 ATAAAAAGAAAAGAAAAAACAA
1 ATAAAAATAAAA-AAAAAA-AA
255041 AT-AAAATAAAAAAATAAAAA
1 ATAAAAATAAAAAAA-AAAAA
255061 ATAAA
1 ATAAA
255066 TATATGGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.17
21 17 0.43
22 16 0.40
ACGTcount: A:0.81, C:0.01, G:0.06, T:0.12
Consensus pattern (20 bp):
ATAAAAATAAAAAAAAAAAA
Found at i:255841 original size:20 final size:20
Alignment explanation
Indices: 255813--255860 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
255803 TTTTTAATAT
* *
255813 TTTATATATTTTAACTTAAA
1 TTTACATATTTTAAATTAAA
*
255833 TTTACATA--TTAAATTAAT
1 TTTACATATTTTAAATTAAA
255851 TTTACATATT
1 TTTACATATT
255861 AATATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 16 0.70
20 7 0.30
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTACATATTTTAAATTAAA
Found at i:255849 original size:18 final size:18
Alignment explanation
Indices: 255823--255869 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
255813 TTTATATATT
*
255823 TTAACTTAAATTTACATA
1 TTAAATTAAATTTACATA
*
255841 TTAAATTAATTTTACATA
1 TTAAATTAAATTTACATA
255859 TTAATATTAAA
1 TTAA-ATTAAA
255870 AATTATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATTAAATTTACATA
Found at i:255952 original size:29 final size:29
Alignment explanation
Indices: 255879--255952 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
255869 AAATTATTTT
* *
255879 TTATCTTAACTTATTAAATATATTTTATTC
1 TTATCTTAACTTA-AAAATATATTTTAATC
* * *
255909 TTTTCATAACCTAAAAATATATTTTAATC
1 TTATCTTAACTTAAAAATATATTTTAATC
*
255938 TTATCTTAAATTAAA
1 TTATCTTAACTTAAA
255953 TATTTATATT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (29 bp):
TTATCTTAACTTAAAAATATATTTTAATC
Found at i:256018 original size:30 final size:30
Alignment explanation
Indices: 255985--256337 Score: 155
Period size: 30 Copynumber: 12.1 Consensus size: 30
255975 TATTTTAAAT
* *
255985 TTAAGATAAAAATATAATATATTTTTTTAT
1 TTAAGATAAAAATATAATATATTTTTTAAG
* * *
256015 TTAATATAAAAATAAAAAATA-TTTTT-AG
1 TTAAGATAAAAATATAATATATTTTTTAAG
*
256043 TT-A-A-AATAA-AT-ATATA-TTTTTAAG
1 TTAAGATAAAAATATAATATATTTTTTAAG
* * *
256067 TTAAGATAATAATAAAATATATGTTTTAAG
1 TTAAGATAAAAATATAATATATTTTTTAAG
* ** *
256097 TTAAAATAAAAA-ATAATTATATTTAATAAT
1 TTAAGATAAAAATATAA-TATATTTTTTAAG
* * ** ** *
256127 TTAAGGTAAGAATGGAATATATTTAATAAT
1 TTAAGATAAAAATATAATATATTTTTTAAG
* * **
256157 TTAAGTTAAAAATATAATTTATGTAATT-AG
1 TTAAGATAAAAATATAATATAT-TTTTTAAG
* *
256187 TTAAAATAAGAAATAAAATATA-TTTTTAA-
1 TTAAGATAA-AAATATAATATATTTTTTAAG
* * *
256216 TATAACATAAAGACTAAAATATA-TTTTTAAG
1 T-TAAGATAAA-AATATAATATATTTTTTAAG
* * *
256247 TTAAAATAAGAATA-AA-ATA-TTTTTAGG
1 TTAAGATAAAAATATAATATATTTTTTAAG
* * * * * ** *
256274 TTAAAACAATAATAAAATATGTTTAATAAA
1 TTAAGATAAAAATATAATATATTTTTTAAG
* *
256304 TTAATATAAAAATAAAATATA-TTTTTAATG
1 TTAAGATAAAAATATAATATATTTTTTAA-G
256334 TTAA
1 TTAA
256338 AATGTAAAAT
Statistics
Matches: 249, Mismatches: 55, Indels: 38
0.73 0.16 0.11
Matches are distributed among these distances:
23 9 0.04
24 5 0.02
25 5 0.02
26 2 0.01
27 28 0.11
28 8 0.03
29 28 0.11
30 148 0.59
31 16 0.06
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (30 bp):
TTAAGATAAAAATATAATATATTTTTTAAG
Found at i:256040 original size:28 final size:30
Alignment explanation
Indices: 255983--256058 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 30
255973 ACTATTTTAA
* * *
255983 ATTTAAGATAAAAATATAATATATTTTTTT
1 ATTTAAAATAAAAATATAATAAATATTTTT
*
256013 ATTTAATATAAAAATA-AA-AAATATTTTT
1 ATTTAAAATAAAAATATAATAAATATTTTT
* *
256041 AGTTAAAATAAATATATA
1 ATTTAAAATAAAAATATA
256059 TTTTTAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 21 0.54
29 3 0.08
30 15 0.38
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
ATTTAAAATAAAAATATAATAAATATTTTT
Found at i:256059 original size:23 final size:23
Alignment explanation
Indices: 256023--256111 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 23
256013 ATTTAATATA
256023 AAAATAAAAAATATTTTT-AGTT
1 AAAATAAAAAATATTTTTAAGTT
*
256045 AAAATAAATATATATTTTTAAGTT
1 AAAATAAA-AAATATTTTTAAGTT
256069 AAGATAATAATAAAATATATGTTTTAAGTT
1 -A-A-AAT-A-AAAA-ATAT-TTTTAAGTT
256099 AAAATAAAAAATA
1 AAAATAAAAAATA
256112 ATTATATTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
22 8 0.14
23 9 0.16
24 7 0.12
25 5 0.09
26 2 0.04
27 6 0.11
28 3 0.05
29 7 0.12
30 9 0.16
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (23 bp):
AAAATAAAAAATATTTTTAAGTT
Found at i:256063 original size:24 final size:22
Alignment explanation
Indices: 256023--256111 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 22
256013 ATTTAATATA
*
256023 AAAATAAAAAATATTTTTAGTT
1 AAAATAAAAAATATTTTAAGTT
*
256045 AAAATAAATATATATTTTTAAGTT
1 AAAATAAA-AAATA-TTTTAAGTT
256069 AAGATAATAATAAAATATATGTTTTAAGTT
1 -A-A-AAT-A-AAAA-ATA--TTTTAAGTT
256099 AAAATAAAAAATA
1 AAAATAAAAAATA
256112 ATTATATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
22 8 0.15
23 4 0.07
24 11 0.20
25 5 0.09
26 2 0.04
27 6 0.11
28 3 0.06
29 6 0.11
30 9 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (22 bp):
AAAATAAAAAATATTTTAAGTT
Found at i:256081 original size:52 final size:53
Alignment explanation
Indices: 255984--256106 Score: 151
Period size: 52 Copynumber: 2.3 Consensus size: 53
255974 CTATTTTAAA
* * * *
255984 TTTAAGATAAAAATATAATATATTTTTTTATTTAATATAAAAATAAAAAATAT-T
1 TTTAAG-TTAAAATA-AATATATTTTTTAAGTTAAGATAAAAATAAAAAATATGT
* *
256038 TTT-AGTTAAAATAAATATATATTTTTAAGTTAAGATAATAATAAAATATATGT
1 TTTAAGTTAAAATAAATATAT-TTTTTAAGTTAAGATAAAAATAAAAAATATGT
256091 TTTAAGTTAAAATAAA
1 TTTAAGTTAAAATAAA
256107 AAATAATTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
51 7 0.12
52 32 0.53
53 6 0.10
54 15 0.25
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (53 bp):
TTTAAGTTAAAATAAATATATTTTTTAAGTTAAGATAAAAATAAAAAATATGT
Found at i:256579 original size:16 final size:16
Alignment explanation
Indices: 256558--256592 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
256548 TCACCGTGGG
* *
256558 AAAAATATATTAAATT
1 AAAAATAAATTAAAAT
256574 AAAAATAAATTAAAAT
1 AAAAATAAATTAAAAT
256590 AAA
1 AAA
256593 GTTAATTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATAAATTAAAAT
Found at i:257655 original size:28 final size:28
Alignment explanation
Indices: 257615--257699 Score: 152
Period size: 28 Copynumber: 3.0 Consensus size: 28
257605 TGATGGTTGT
257615 AAGTATTATTCGAATAAATTTTTATTTA
1 AAGTATTATTCGAATAAATTTTTATTTA
257643 AAGTATTATTCGAATAAATTTTTATTTA
1 AAGTATTATTCGAATAAATTTTTATTTA
257671 AAGTATTATTCGAATAAATATTTTTATTT
1 AAGTATTATTCGAAT-AA-ATTTTTATTT
257700 TATCTCGTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 43 0.78
29 2 0.04
30 10 0.18
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.51
Consensus pattern (28 bp):
AAGTATTATTCGAATAAATTTTTATTTA
Found at i:257667 original size:16 final size:16
Alignment explanation
Indices: 257620--257668 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
257610 GTTGTAAGTA
257620 TTATTCGAATAAATTT
1 TTATTCGAATAAATTT
* *
257636 TTATT----TAAAGTA
1 TTATTCGAATAAATTT
257648 TTATTCGAATAAATTT
1 TTATTCGAATAAATTT
257664 TTATT
1 TTATT
257669 TAAAGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 10 0.40
16 15 0.60
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (16 bp):
TTATTCGAATAAATTT
Found at i:258242 original size:34 final size:34
Alignment explanation
Indices: 258199--258263 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
258189 TTTAATTGAT
258199 AAAAATATTGTTAATATATTTACAATTTTTATAA
1 AAAAATATTGTTAATATATTTACAATTTTTATAA
*
258233 AAAAATATTGTTAATATATTTACATTTTTTA
1 AAAAATATTGTTAATATATTTACAATTTTTA
258264 CAAGGTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (34 bp):
AAAAATATTGTTAATATATTTACAATTTTTATAA
Found at i:258451 original size:33 final size:32
Alignment explanation
Indices: 258412--258477 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
258402 TAAAAATGTT
258412 AAAAAATATTGTTAATATATTTACATTTTTATA
1 AAAAAATATTGTTAATATATTTA-ATTTTTATA
258445 AAAAAATATTGTTAATATATTTAATTTTTATA
1 AAAAAATATTGTTAATATATTTAATTTTTATA
258477 A
1 A
258478 CTTTAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (32 bp):
AAAAAATATTGTTAATATATTTAATTTTTATA
Found at i:260863 original size:26 final size:27
Alignment explanation
Indices: 260834--260915 Score: 102
Period size: 23 Copynumber: 3.2 Consensus size: 27
260824 TGTTGATGTT
* *
260834 ATATTTCAATGAATGTG-ATTATGTCA
1 ATATTTCAATGAATGTGAATAATATCA
*
260860 ATATTTGAATGAATGTGAATAATATCA
1 ATATTTCAATGAATGTGAATAATATCA
260887 ATATTTC--T--ATGTGAATAATATCA
1 ATATTTCAATGAATGTGAATAATATCA
260910 ATATTT
1 ATATTT
260916 TATTTAATGT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 21 0.41
25 1 0.02
26 16 0.31
27 13 0.25
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (27 bp):
ATATTTCAATGAATGTGAATAATATCA
Found at i:263132 original size:23 final size:23
Alignment explanation
Indices: 263106--263154 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
263096 ATAAAGAACC
*
263106 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
263129 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
263152 AAA
1 AAA
263155 CCAACTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:267005 original size:11 final size:11
Alignment explanation
Indices: 266989--267013 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
266979 AAAATGGTAA
266989 AAACAGTAAAT
1 AAACAGTAAAT
267000 AAACAGTAAAT
1 AAACAGTAAAT
267011 AAA
1 AAA
267014 ATGAAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (11 bp):
AAACAGTAAAT
Found at i:267531 original size:23 final size:23
Alignment explanation
Indices: 267505--267553 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
267495 ATAAAGAATC
*
267505 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
267528 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
267551 AAA
1 AAA
267554 CCAACTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:270564 original size:30 final size:29
Alignment explanation
Indices: 270495--270592 Score: 119
Period size: 29 Copynumber: 3.3 Consensus size: 29
270485 TATCTTATCA
**
270495 TTAAAAATATATATTTTATTATTACCTTAAC
1 TTAAAAA-ATATATTTTATT-TTATATTAAC
*
270526 TT-AAAAATATATTTTATTCTTATTTTAAC
1 TTAAAAAATATATTTTATT-TTATATTAAC
*
270555 TTAAAAAATATATTTAATTTT-TATTAAC
1 TTAAAAAATATATTTTATTTTATATTAAC
270583 TTAAAAAATA
1 TTAAAAAATA
270593 AAATATACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.26
29 24 0.39
30 19 0.31
31 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAAAAAATATATTTTATTTTATATTAAC
Found at i:270608 original size:27 final size:27
Alignment explanation
Indices: 270548--270624 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
270538 TTTATTCTTA
* *
270548 TTTTAACTTAAAAAAT-ATATTTAATTT
1 TTTTAACTTAAAAAATAAAATATAA-TT
270575 TTATTAACTTAAAAAATAAAATATACA-T
1 TT-TTAACTTAAAAAATAAAATATA-ATT
*
270603 TTTTAAGTT-AAAAATAAGAATA
1 TTTTAACTTAAAAAATAA-AATA
270625 AAATATATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
26 8 0.19
27 12 0.28
28 17 0.40
29 5 0.12
30 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (27 bp):
TTTTAACTTAAAAAATAAAATATAATT
Found at i:270649 original size:30 final size:32
Alignment explanation
Indices: 270589--270662 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 32
270579 TAACTTAAAA
*
270589 AATAAAATATACATTTTTAAGTTAAAAATAAG
1 AATAAAATATATATTTTTAAGTTAAAAATAAG
270621 AATAAAATATATA-TTTTATA-TT-AAAATAAG
1 AATAAAATATATATTTTTA-AGTTAAAAATAAG
* *
270651 GATAAATTATAT
1 AATAAAATATAT
270663 TTAATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 18 0.47
31 7 0.18
32 13 0.34
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (32 bp):
AATAAAATATATATTTTTAAGTTAAAAATAAG
Found at i:270722 original size:30 final size:30
Alignment explanation
Indices: 270658--270722 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
270648 AAGGATAAAT
* * *
270658 TATATTTAATAATTTAATGTGAGACTAGAG
1 TATATTTAATAATTTAATGTAAGAATAGAA
*
270688 TATATTTAATAATTTAA-GTTAAGAATATAA
1 TATATTTAATAATTTAATG-TAAGAATAGAA
270718 TATAT
1 TATAT
270723 GTAGTAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (30 bp):
TATATTTAATAATTTAATGTAAGAATAGAA
Found at i:270806 original size:29 final size:30
Alignment explanation
Indices: 270728--270835 Score: 123
Period size: 31 Copynumber: 3.7 Consensus size: 30
270718 TATATGTAGT
* *
270728 AAGTTAAAATAAAAATAAGATATACTTTTAA
1 AAGTTAAGATAAAAATAAAATATACTTTT-A
270759 AAGTTAAGATAAAAATAAAATATACTTTT-
1 AAGTTAAGATAAAAATAAAATATACTTTTA
* * * *
270788 ATGTTAGGATAAGATTAAAATATA--TTTA
1 AAGTTAAGATAAAAATAAAATATACTTTTA
*
270816 AAGTTAAAATAAAAATAAAA
1 AAGTTAAGATAAAAATAAAA
270836 AAAAAATTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
27 3 0.05
28 15 0.23
29 20 0.31
31 27 0.42
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.32
Consensus pattern (30 bp):
AAGTTAAGATAAAAATAAAATATACTTTTA
Found at i:270828 original size:57 final size:57
Alignment explanation
Indices: 270754--270910 Score: 165
Period size: 57 Copynumber: 2.7 Consensus size: 57
270744 AAGATATACT
* * * * * *
270754 TTTAAAAGTTAAGATAAAAATAAAATATACTTTTATGTTAGGATAAGATTAAAATATA
1 TTTAAAAGTTAAAATAAAAATAAAA-ATAATTTTATGTTAAGACAAGACTAAAATAGA
* *
270812 TTT-AAAGTTAAAATAAAAATAAAAAAAAAATTTA-GATTAAGACAAGACTAAAATAGA
1 TTTAAAAGTTAAAATAAAAAT-AAAAATAATTTTATG-TTAAGACAAGACTAAAATAGA
* *
270869 TTTAATAATTTAAAATAAAAATAAAAATATTTTTAATGTTAA
1 TTTAA-AAGTTAAAATAAAAATAAAAATAATTTT-ATGTTAA
270911 TATGTGAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
56 1 0.01
57 42 0.52
58 17 0.21
59 20 0.25
60 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.34
Consensus pattern (57 bp):
TTTAAAAGTTAAAATAAAAATAAAAATAATTTTATGTTAAGACAAGACTAAAATAGA
Found at i:275920 original size:31 final size:31
Alignment explanation
Indices: 275877--275943 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
275867 ATTTGTACAC
* * *
275877 TTTTGGTTACTTACGTTATCCTTTTATTAAG
1 TTTTGGTCACTTACATTATCATTTTATTAAG
275908 TTTTGGTCACTTACATTATCATTTTATTAAG
1 TTTTGGTCACTTACATTATCATTTTATTAAG
275939 TTTTG
1 TTTTG
275944 ATCTCTTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (31 bp):
TTTTGGTCACTTACATTATCATTTTATTAAG
Found at i:276721 original size:31 final size:31
Alignment explanation
Indices: 276683--276747 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
276673 ACCTCATTTC
* *
276683 TAAGTGACCAAAACTTAATAAAACGTTAACG
1 TAAGTGACCAAAACTTAATAAAACGATAAAG
276714 TAAGTGACCAAAACTTAATAAAACGATAAAG
1 TAAGTGACCAAAACTTAATAAAACGATAAAG
276745 TAA
1 TAA
276748 ATGGTCAAAC
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:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACGATAAAG
Found at i:276945 original size:31 final size:31
Alignment explanation
Indices: 276910--276968 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
276900 CATATAAAAT
* *
276910 AAAATAAAATGAAAGTGACCAGATCTTAATC
1 AAAATAAAACGAAAGTGACCAAATCTTAATC
* * *
276941 AAAATGAAACGACAGTGATCAAATCTTA
1 AAAATAAAACGAAAGTGACCAAATCTTA
276969 TGTTTTTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.22
Consensus pattern (31 bp):
AAAATAAAACGAAAGTGACCAAATCTTAATC
Found at i:287554 original size:38 final size:38
Alignment explanation
Indices: 287493--287586 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 38
287483 AGGGATTATC
* * * * *
287493 AGTGGTCCTTTGGGATAAACAGTGGTCCTTTGGAACAT
1 AGTGGTCCTTCGGAACAATCAGTGGTCCTTCGGAACAT
*
287531 AGTGGGT-CTTCGGAACAATCAGTGGTCCTTCGGGACAT
1 AGT-GGTCCTTCGGAACAATCAGTGGTCCTTCGGAACAT
*
287569 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGAACAA
287587 ATATTCAGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 3 0.06
38 41 0.87
39 3 0.06
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCGGAACAATCAGTGGTCCTTCGGAACAT
Found at i:287561 original size:20 final size:20
Alignment explanation
Indices: 287490--287586 Score: 96
Period size: 18 Copynumber: 5.0 Consensus size: 20
287480 TCGAGGGATT
* *
287490 ATCAGTGGTCCTTTGGGATA
1 ATCAGTGGTCCTTCGGGACA
* * *
287510 AACAGTGGTCCTTTGGAAC-
1 ATCAGTGGTCCTTCGGGACA
*
287529 AT-AGTGGGT-CTTCGGAACA
1 ATCAGT-GGTCCTTCGGGACA
287548 ATCAGTGGTCCTTCGGGAC-
1 ATCAGTGGTCCTTCGGGACA
287567 AT-AGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGGGACA
287586 A
1 A
287587 ATATTCAGTG
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 27 0.41
19 12 0.18
20 27 0.41
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (20 bp):
ATCAGTGGTCCTTCGGGACA
Found at i:287870 original size:14 final size:15
Alignment explanation
Indices: 287845--287873 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
287835 AATATAGTTG
287845 CTGATGTATATGTTA
1 CTGATGTATATGTTA
287860 CTGATGT-TATGTTA
1 CTGATGTATATGTTA
287874 AGATATAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
CTGATGTATATGTTA
Found at i:287967 original size:4 final size:4
Alignment explanation
Indices: 287960--288065 Score: 189
Period size: 4 Copynumber: 27.0 Consensus size: 4
287950 TGATAATGAC
287960 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
288008 ATGT ATGT A--T ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
288054 ATGT ATGT ATGT
1 ATGT ATGT ATGT
288066 GTATTTGTAC
Statistics
Matches: 98, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
4 96 0.98
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:296750 original size:23 final size:19
Alignment explanation
Indices: 296708--296811 Score: 95
Period size: 19 Copynumber: 5.2 Consensus size: 19
296698 ATAGGGTAGA
*
296708 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATTCCCCC-T--AG
296730 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCC--T--AG
296753 GGGAA-CTGATTCCCCCTAG
1 GGGAATC-GATTCCCCCTAG
*
296772 GGGAACCGATTCCCCCTAG
1 GGGAATCGATTCCCCCTAG
*
296791 GGGAATCGATACCCCCT-G
1 GGGAATCGATTCCCCCTAG
296809 GGG
1 GGG
296812 TTCTGGTTTT
Statistics
Matches: 76, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
18 4 0.05
19 34 0.45
20 1 0.01
21 1 0.01
22 16 0.21
23 20 0.26
ACGTcount: A:0.22, C:0.30, G:0.29, T:0.19
Consensus pattern (19 bp):
GGGAATCGATTCCCCCTAG
Found at i:299546 original size:20 final size:20
Alignment explanation
Indices: 299521--299573 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
299511 TTTACACTTA
299521 GGGAACCGATTCCTCATGAG
1 GGGAACCGATTCCTCATGAG
299541 GGGAACCGATTCCTCATGAG
1 GGGAACCGATTCCTCATGAG
*
299561 GGGTACCGATTCC
1 GGGAACCGATTCC
299574 CCTACGTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (20 bp):
GGGAACCGATTCCTCATGAG
Found at i:300869 original size:20 final size:20
Alignment explanation
Indices: 300846--300883 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
300836 AAGGGATTAT
300846 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
300866 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
300884 TAGTCGGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:300901 original size:31 final size:31
Alignment explanation
Indices: 300856--300918 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
300846 CAGTGGTCCT
* *
300856 TCGGGACAAACAGTGGTCCTTCGGGACATAG
1 TCGGAACAAACAGTGGTCCTTCGAGACATAG
*
300887 TCGGAACAATCAGTGGTCCTTCGAGACATAG
1 TCGGAACAAACAGTGGTCCTTCGAGACATAG
300918 T
1 T
300919 GGTCCTTCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (31 bp):
TCGGAACAAACAGTGGTCCTTCGAGACATAG
Found at i:307745 original size:321 final size:321
Alignment explanation
Indices: 307163--307803 Score: 1282
Period size: 321 Copynumber: 2.0 Consensus size: 321
307153 TGAAATCAAG
307163 TTGGCAGACTTTGGAATGGCAAAACATGTATGTTACGTAATCTCATATTGGGGATGGTGGATGTA
1 TTGGCAGACTTTGGAATGGCAAAACATGTATGTTACGTAATCTCATATTGGGGATGGTGGATGTA
307228 GTTCTATTCCTTAAGCTACAATATCTCTCAAAAAATAGTTGTGGCTATGATTTTAACTATCTACT
66 GTTCTATTCCTTAAGCTACAATATCTCTCAAAAAATAGTTGTGGCTATGATTTTAACTATCTACT
307293 AAACGGTGCTGATAGGATGCTGCTTTTGTTGCACAGAAAATTGTGTGTTCTGTAGAATTTTTTCC
131 AAACGGTGCTGATAGGATGCTGCTTTTGTTGCACAGAAAATTGTGTGTTCTGTAGAATTTTTTCC
307358 CTTTAGATGATACCTAAAACTCTAATTTAACTTGAAAGCTGATATTTTCTTATTTATTCTTTTCT
196 CTTTAGATGATACCTAAAACTCTAATTTAACTTGAAAGCTGATATTTTCTTATTTATTCTTTTCT
307423 TCCTTTTTCAGAACTGAATGTTGTTTTCAGGCTGAAAATATGACTTTGATGTAAATTTAAA
261 TCCTTTTTCAGAACTGAATGTTGTTTTCAGGCTGAAAATATGACTTTGATGTAAATTTAAA
307484 TTGGCAGACTTTGGAATGGCAAAACATGTATGTTACGTAATCTCATATTGGGGATGGTGGATGTA
1 TTGGCAGACTTTGGAATGGCAAAACATGTATGTTACGTAATCTCATATTGGGGATGGTGGATGTA
307549 GTTCTATTCCTTAAGCTACAATATCTCTCAAAAAATAGTTGTGGCTATGATTTTAACTATCTACT
66 GTTCTATTCCTTAAGCTACAATATCTCTCAAAAAATAGTTGTGGCTATGATTTTAACTATCTACT
307614 AAACGGTGCTGATAGGATGCTGCTTTTGTTGCACAGAAAATTGTGTGTTCTGTAGAATTTTTTCC
131 AAACGGTGCTGATAGGATGCTGCTTTTGTTGCACAGAAAATTGTGTGTTCTGTAGAATTTTTTCC
307679 CTTTAGATGATACCTAAAACTCTAATTTAACTTGAAAGCTGATATTTTCTTATTTATTCTTTTCT
196 CTTTAGATGATACCTAAAACTCTAATTTAACTTGAAAGCTGATATTTTCTTATTTATTCTTTTCT
307744 TCCTTTTTCAGAACTGAATGTTGTTTTCAGGCTGAAAATATGACTTTGATGTAAATTTAA
261 TCCTTTTTCAGAACTGAATGTTGTTTTCAGGCTGAAAATATGACTTTGATGTAAATTTAA
307804 CAAATTAGTT
Statistics
Matches: 320, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
321 320 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (321 bp):
TTGGCAGACTTTGGAATGGCAAAACATGTATGTTACGTAATCTCATATTGGGGATGGTGGATGTA
GTTCTATTCCTTAAGCTACAATATCTCTCAAAAAATAGTTGTGGCTATGATTTTAACTATCTACT
AAACGGTGCTGATAGGATGCTGCTTTTGTTGCACAGAAAATTGTGTGTTCTGTAGAATTTTTTCC
CTTTAGATGATACCTAAAACTCTAATTTAACTTGAAAGCTGATATTTTCTTATTTATTCTTTTCT
TCCTTTTTCAGAACTGAATGTTGTTTTCAGGCTGAAAATATGACTTTGATGTAAATTTAAA
Found at i:308759 original size:21 final size:21
Alignment explanation
Indices: 308733--308775 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
308723 TTATACTGCA
308733 CAAAGAGAAACCCATAGAAAC
1 CAAAGAGAAACCCATAGAAAC
**
308754 CAAAGAGAAACCTTTAGAAAC
1 CAAAGAGAAACCCATAGAAAC
308775 C
1 C
308776 TAGTATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.23, G:0.14, T:0.09
Consensus pattern (21 bp):
CAAAGAGAAACCCATAGAAAC
Found at i:310420 original size:112 final size:112
Alignment explanation
Indices: 310205--310666 Score: 764
Period size: 112 Copynumber: 4.1 Consensus size: 112
310195 TTGTTGGCTT
* * * *
310205 GTGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAGGT-AAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
310269 GGTTTATAAATGAAAAAACAGGTAAAGCGCTATCGGATATATTGAAA
66 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
310316 GTGTCGATACTTTATAAAAATGTATAGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
**
310381 GGTTTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAA
66 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
310428 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
310493 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
310540 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAACAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
310605 GATTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
310652 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
310667 TATAAGTATC
Statistics
Matches: 329, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
111 45 0.14
112 284 0.86
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:310915 original size:181 final size:181
Alignment explanation
Indices: 310537--310991 Score: 698
Period size: 181 Copynumber: 2.5 Consensus size: 181
310527 GGATATATTG
*
310537 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAACAA-ATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAA-AATATGACAA
* ** * * *
310601 AACCGATTTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTA
65 AACCG-TATCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTA
** * * *
310666 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
129 TTATAAGTATCGACACTTTTAAAATTTAAAAGAAAAGAAGTTATAGCACCAAT
* * *
310719 AAAGTGTTGATACTTTATAAAAATGTATTGATCCATAATAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
* *
310784 ACCAGTCTCGAAATGATAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGT-TCGATACTTTAT
66 ACC-GTATCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
310848 TATAAGTATCGACACTTTTAAAATTTAAAAGAAAAGAAGTTATAGCACCAAT
130 TATAAGTATCGACACTTTTAAAATTTAAAAGAAAAGAAGTTATAGCACCAAT
310900 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
*
310965 ATCGGTATCGAAATGACAAAACCGGTA
66 A-CCGTATCGAAATGACAAAACCGGTA
310992 GTAAAAAAGT
Statistics
Matches: 248, Mismatches: 22, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
181 145 0.58
182 102 0.41
183 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (181 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
ACCGTATCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATT
ATAAGTATCGACACTTTTAAAATTTAAAAGAAAAGAAGTTATAGCACCAAT
Found at i:311660 original size:23 final size:23
Alignment explanation
Indices: 311631--311678 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
311621 AAATAGGTCA
*
311631 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
* *
311654 ATATAAGTGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
311677 AT
1 AT
311679 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:312163 original size:20 final size:20
Alignment explanation
Indices: 312140--312177 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
312130 GTAAATTACT
312140 TAATAATATTTTAAATAAAA
1 TAATAATATTTTAAATAAAA
*
312160 TAATAATATTTTTAATAA
1 TAATAATATTTTAAATAA
312178 TTTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAATATTTTAAATAAAA
Found at i:313084 original size:2 final size:2
Alignment explanation
Indices: 313077--313106 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
313067 AAATAATTAT
313077 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
313107 TAATAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:314086 original size:31 final size:30
Alignment explanation
Indices: 314043--314112 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 30
314033 TCCAACAGTT
* *
314043 ATGTCAGGGACCATATTGCAAATAGACTAA
1 ATGTTAGGGACCATATTGCAAACAGACTAA
314073 ATGTTGAGGGACCATATTGCAAACAGACTAA
1 ATGTT-AGGGACCATATTGCAAACAGACTAA
314104 ATGTTAGGG
1 ATGTTAGGG
314113 GATTATATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 8 0.22
31 29 0.78
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (30 bp):
ATGTTAGGGACCATATTGCAAACAGACTAA
Found at i:315118 original size:31 final size:31
Alignment explanation
Indices: 315047--315110 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
315037 TTACGTCGGT
315047 GACCATATTGCAAACAGAATAAATGTTGAGG
1 GACCATATTGCAAACAGAATAAATGTTGAGG
*
315078 GACCATATTGCAAACAGAATAAATGTTGGGG
1 GACCATATTGCAAACAGAATAAATGTTGAGG
315109 GA
1 GA
315111 TTGTATTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (31 bp):
GACCATATTGCAAACAGAATAAATGTTGAGG
Found at i:315248 original size:13 final size:12
Alignment explanation
Indices: 315213--315275 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
315203 AATAAACTAT
315213 TTATAATTAATA
1 TTATAATTAATA
315225 TTAAAATAATTATATA
1 TT---ATAATTA-ATA
315241 TTATAATTAATA
1 TTATAATTAATA
*
315253 TTA-ATATTAA-C
1 TTATA-ATTAATA
315264 TTAT-ATTAATA
1 TTATAATTAATA
315275 T
1 T
315276 AATCTAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
10 5 0.12
11 5 0.12
12 13 0.31
13 7 0.17
15 7 0.17
16 5 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATAATTAATA
Found at i:315268 original size:28 final size:27
Alignment explanation
Indices: 315193--315356 Score: 94
Period size: 28 Copynumber: 6.1 Consensus size: 27
315183 TTTACCCTAA
*
315193 AATTTATATTAATA-AAC-TAT-TTAT
1 AATTAATATTAATATAACTTATATTAT
* *
315217 AATTAATATTAAAATAATTATATATTAT
1 AATTAATATTAATATAACT-TATATTAT
315245 AATTAATATTAATATTAACTTATA-T-T
1 AATTAATATTAATA-TAACTTATATTAT
* * * *
315271 AATATAAT-CTAGT-TTA-TAAT-TTAT
1 AAT-TAATATTAATATAACTTATATTAT
**
315295 AATTAATATTAATATAAAATATAGTCTAT
1 AATTAATATTAATATAACTTATA-T-TAT
*
315324 AAAATTAATATTAATATAAACTATATGTTAT
1 --AATTAATATTAATAT-AACT-TATATTAT
315355 AA
1 AA
315357 ATTATATAGT
Statistics
Matches: 105, Mismatches: 17, Indels: 31
0.69 0.11 0.20
Matches are distributed among these distances:
23 8 0.08
24 21 0.20
25 4 0.04
26 9 0.09
27 8 0.08
28 22 0.21
29 9 0.09
31 18 0.17
32 3 0.03
33 3 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (27 bp):
AATTAATATTAATATAACTTATATTAT
Found at i:315271 original size:16 final size:16
Alignment explanation
Indices: 315213--315275 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
315203 AATAAACTAT
315213 TTATAATTAATATTAAA
1 TTAT-ATTAATATTAAA
*
315230 ATA-ATTATATATTATAA
1 TTATATTA-ATATTA-AA
*
315247 TTAATATTAATATTAAC
1 TT-ATATTAATATTAAA
315264 TTATATTAATAT
1 TTATATTAATAT
315276 AATCTAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.10
16 16 0.41
17 8 0.21
18 7 0.18
19 4 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATATTAATATTAAA
Found at i:315333 original size:31 final size:31
Alignment explanation
Indices: 315295--315357 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
315285 TATAATTTAT
315295 AATTAATATTAATATAAAATATA-GTCTATAA
1 AATTAATATTAATATAAAATATATGT-TATAA
*
315326 AATTAATATTAATATAAACTATATGTTATAA
1 AATTAATATTAATATAAAATATATGTTATAA
315357 A
1 A
315358 TTATATAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATATGTTATAA
Found at i:315347 original size:24 final size:25
Alignment explanation
Indices: 315302--315348 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
315292 TATAATTAAT
**
315302 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
315327 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
315349 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:315377 original size:81 final size:77
Alignment explanation
Indices: 315211--315366 Score: 179
Period size: 78 Copynumber: 1.9 Consensus size: 77
315201 TTAATAAACT
* * *
315211 ATTTATAATTAATATTAAAATAATTATATATTATAATTAATATTAATATTAACTTATATTAATAT
1 ATTTATAATTAATATTAAAATAATAATATATTATAATTAATATTAATATAAACTTATATTAAAAT
*
315276 AATCTAGTTTATA
66 AATATAG-TTATA
* *
315289 ATTTATAATTAATATTAATATAA-AATATAGTCTATAAAATTAATATTAATATAAACTATATGTT
1 ATTTATAATTAATATTAAAATAATAATATA-T-TAT--AATTAATATTAATATAAACT-TATATT
*
315353 ATAAATTATATAGT
61 A-AAATAATATAGT
315367 ATGGTTTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
77 5 0.08
78 23 0.35
79 3 0.05
81 19 0.29
82 7 0.11
83 8 0.12
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (77 bp):
ATTTATAATTAATATTAAAATAATAATATATTATAATTAATATTAATATAAACTTATATTAAAAT
AATATAGTTATA
Found at i:315437 original size:15 final size:15
Alignment explanation
Indices: 315414--315471 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
315404 GTTTATAAAC
*
315414 TATATATTATATTAA
1 TATAAATTATATTAA
315429 TATAAATTATAGTTAA
1 TATAAATTATA-TTAA
* *
315445 GAT-AATTAACATTAA
1 TATAAATT-ATATTAA
*
315460 TATAAACTATAT
1 TATAAATTATAT
315472 AGTACATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 23 0.68
16 11 0.32
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (15 bp):
TATAAATTATATTAA
Found at i:315493 original size:20 final size:21
Alignment explanation
Indices: 315453--315494 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
315443 AAGATAATTA
315453 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
315475 ACATTAATATAAA-ATATAGT
1 ACATTAATATAAACATATAGT
315495 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:315637 original size:22 final size:21
Alignment explanation
Indices: 315609--315697 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 21
315599 AAATAGATTG
315609 TATATATACATATACTATAGG-
1 TATATATA-ATATACTATAGGT
*
315630 T-TATAT-ATATA-TATAGTT
1 TATATATAATATACTATAGGT
*
315648 TATATATAATATAC-ATAGTT
1 TATATATAATATACTATAGGT
* * *
315668 TATACATACATGTACTATAAGT
1 TATATATA-ATATACTATAGGT
*
315690 TACATATA
1 TATATATA
315698 TAGTTTACAT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 5 0.09
18 6 0.11
19 5 0.09
20 23 0.42
21 6 0.11
22 10 0.18
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (21 bp):
TATATATAATATACTATAGGT
Found at i:315642 original size:15 final size:15
Alignment explanation
Indices: 315618--315660 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 15
315608 GTATATATAC
315618 ATATACTATAGGTTATAT
1 ATATA-TATA-GTT-TAT
315636 ATATATATAGTTTAT
1 ATATATATAGTTTAT
315651 ATATAATATA
1 ATAT-ATATA
315661 CATAGTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 4 0.17
18 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (15 bp):
ATATATATAGTTTAT
Found at i:315684 original size:59 final size:61
Alignment explanation
Indices: 315577--315699 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 61
315567 TATAGGTTAC
* * * *
315577 ATATATAGTTTATGTAACATATAAATAGATTGTATATATACATATACTATAGGTTATATAT
1 ATATATAGTTTATATAACATATAAATAGATTGTATACATACATATACTATAAGTTACATAT
* *
315638 ATATATAGTTTATATATA-ATATACATAG-TT-TATACATACATGTACTATAAGTTACATAT
1 ATATATAGTTTATATA-ACATATAAATAGATTGTATACATACATATACTATAAGTTACATAT
315697 ATA
1 ATA
315700 GTTTACATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
59 28 0.51
60 2 0.04
61 24 0.44
62 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (61 bp):
ATATATAGTTTATATAACATATAAATAGATTGTATACATACATATACTATAAGTTACATAT
Found at i:315697 original size:37 final size:36
Alignment explanation
Indices: 315662--315732 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 36
315652 TATAATATAC
*
315662 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
315697 ATAGTTTACATGTATACATATACTATAGGTTACATA
1 ATAGTTTA-ATACATACATATACTATAAGTTACATA
315733 GATTAACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 7 0.23
37 23 0.77
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:315795 original size:14 final size:14
Alignment explanation
Indices: 315756--315823 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 14
315746 TTATGCATGG
315756 TGTTTAGGGTTT-A
1 TGTTTAGGGTTTAA
* **
315769 GGTTTAGTATTTAA
1 TGTTTAGGGTTTAA
*
315783 TGTTTAGGGTTTAG
1 TGTTTAGGGTTTAA
** *
315797 CATTTAGGATTTAA
1 TGTTTAGGGTTTAA
*
315811 TATTTAGGGTTTA
1 TGTTTAGGGTTTA
315824 GAGTATATAT
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
13 9 0.22
14 32 0.78
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.50
Consensus pattern (14 bp):
TGTTTAGGGTTTAA
Found at i:315795 original size:21 final size:20
Alignment explanation
Indices: 315764--315802 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
315754 GGTGTTTAGG
*
315764 GTTTAGGTTTAGTATTTAAT
1 GTTTAGGTTTAGCATTTAAT
315784 GTTTAGGGTTTAGCATTTA
1 GTTTA-GGTTTAGCATTTA
315803 GGATTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (20 bp):
GTTTAGGTTTAGCATTTAAT
Found at i:315809 original size:21 final size:19
Alignment explanation
Indices: 315758--315809 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
315748 ATGCATGGTG
*
315758 TTTAGGGTTTAGGTTTAGTA
1 TTTA-GGTTTAGGTTTAGCA
*
315778 TTTAATGTTTAGGGTTTAGCA
1 TTT-AGGTTTA-GGTTTAGCA
315799 TTTAGGATTTA
1 TTTAGG-TTTA
315810 ATATTTAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (19 bp):
TTTAGGTTTAGGTTTAGCA
Found at i:315811 original size:28 final size:27
Alignment explanation
Indices: 315756--315825 Score: 104
Period size: 28 Copynumber: 2.6 Consensus size: 27
315746 TTATGCATGG
* *
315756 TGTTTAGGGTTTAGGTTTAGTATTTAA
1 TGTTTAGGGTTTAGATTTAGGATTTAA
315783 TGTTTAGGGTTTAGCATTTAGGATTTAA
1 TGTTTAGGGTTTAG-ATTTAGGATTTAA
*
315811 TATTTAGGGTTTAGA
1 TGTTTAGGGTTTAGA
315826 GTATATATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 15 0.38
28 24 0.62
ACGTcount: A:0.24, C:0.01, G:0.26, T:0.49
Consensus pattern (27 bp):
TGTTTAGGGTTTAGATTTAGGATTTAA
Found at i:315967 original size:20 final size:20
Alignment explanation
Indices: 315944--316024 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
315934 TATATATATG
315944 TAGTTTATATATACTATACA
1 TAGTTTATATATACTATACA
* *
315964 TAGTTTATACATACATGTACTA
1 TAGTTTATATATAC-TATAC-A
* * *
315986 TAAGTTACATATATAGTTTACA
1 T-AGTT-TATATATACTATACA
*
316008 T-GTGTATATATACTATA
1 TAGTTTATATATACTATA
316025 GGTTACATAG
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
19 10 0.21
20 15 0.32
21 4 0.09
22 4 0.09
23 8 0.17
24 6 0.13
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (20 bp):
TAGTTTATATATACTATACA
Found at i:316082 original size:20 final size:21
Alignment explanation
Indices: 316059--316116 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
316049 ATACATGGTG
*
316059 TTTAGGGTTTA-GGTTTAGTA
1 TTTAAGGTTTAGGGTTTAGTA
* **
316079 TTTAATGTTTAGGGTTTAGGG
1 TTTAAGGTTTAGGGTTTAGTA
**
316100 TTTAACATTTAGGGTTT
1 TTTAAGGTTTAGGGTTT
316117 TTATTACTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.50
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTAGTA
Found at i:316096 original size:21 final size:21
Alignment explanation
Indices: 316065--316116 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
316055 GGTGTTTAGG
* *
316065 GTTTA-GGTTTAGTATTTAAT
1 GTTTAGGGTTTAGGATTTAAC
*
316085 GTTTAGGGTTTAGGGTTTAAC
1 GTTTAGGGTTTAGGATTTAAC
*
316106 ATTTAGGGTTT
1 GTTTAGGGTTT
316117 TTATTACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.50
Consensus pattern (21 bp):
GTTTAGGGTTTAGGATTTAAC
Found at i:316464 original size:22 final size:21
Alignment explanation
Indices: 316412--316464 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
316402 TAGGGTTTTA
316412 TAAAC-TATATACTTTATATT
1 TAAACTTATATACTTTATATT
*
316432 ATATACTTATATACTTTATATT
1 -TAAACTTATATACTTTATATT
316454 TAAAC-TATATA
1 TAAACTTATATA
316465 AACTATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 8 0.28
22 15 0.52
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAACTTATATACTTTATATT
Found at i:316562 original size:49 final size:48
Alignment explanation
Indices: 316439--316562 Score: 158
Period size: 49 Copynumber: 2.5 Consensus size: 48
316429 ATTATATACT
* * * *
316439 TATATACTTTATATTTAAACTATATAAACTATATAATTTATACATGGTA
1 TATATAATTTATATTTATACTA-ATAAACAATATAATTTATACATAGTA
* *
316488 TATATAATTTATAGTTTATATTAATAAACAATATAATTTATACGTAGTA
1 TATATAATTTATA-TTTATACTAATAAACAATATAATTTATACATAGTA
*
316537 TATATAATTTATAATTATACATAATA
1 TATATAATTTATATTTATAC-TAATA
316563 TATAAATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
48 5 0.08
49 53 0.82
50 7 0.11
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (48 bp):
TATATAATTTATATTTATACTAATAAACAATATAATTTATACATAGTA
Found at i:316602 original size:21 final size:22
Alignment explanation
Indices: 316556--316614 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
316546 TATAATTATA
*
316556 CATA-ATATATAAATATAAGTT
1 CATATATATTTAAATATAAGTT
*
316577 -GTATATATTTAAATATAA-TT
1 CATATATATTTAAATATAAGTT
*
316597 CATATATAATTTATATAT
1 CATATAT-ATTTAAATAT
316615 TAACTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 18 0.58
22 9 0.29
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (22 bp):
CATATATATTTAAATATAAGTT
Found at i:316611 original size:9 final size:10
Alignment explanation
Indices: 316535--316718 Score: 57
Period size: 11 Copynumber: 17.8 Consensus size: 10
316525 TTATACGTAG
316535 TATATATAA-
1 TATATATAAT
316544 T-T-TATAAT
1 TATATATAAT
*
316552 TATACATAAT
1 TATATATAAT
316562 ATATAAATATAAGT
1 -TAT--ATATAA-T
* *
316576 TGTATATATT
1 TATATATAAT
*
316586 TAAATATAAT
1 TATATATAAT
316596 TCATATATAAT
1 T-ATATATAAT
316607 T-TATAT-AT
1 TATATATAAT
316615 TAACTATATAAT
1 T-A-TATATAAT
316627 T-TATATTAAT
1 TATATA-TAAT
* *
316637 AAACTATATAGTT
1 -TA-TATATA-AT
*
316650 TATATATACAC
1 TATATATA-AT
316661 TATATAGT--T
1 TATATA-TAAT
316670 TATAT-TAAT
1 TATATATAAT
* *
316679 AAACTATATAGT
1 -TA-TATATAAT
316691 T-TATATAA-
1 TATATATAAT
316699 TATATATATAT
1 TATATATA-AT
316710 ATATATATA
1 -TATATATA
316719 GTTGTTTCAA
Statistics
Matches: 129, Mismatches: 19, Indels: 51
0.65 0.10 0.26
Matches are distributed among these distances:
7 6 0.05
8 6 0.05
9 29 0.22
10 20 0.16
11 37 0.29
12 18 0.14
13 12 0.09
14 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (10 bp):
TATATATAAT
Found at i:316614 original size:22 final size:22
Alignment explanation
Indices: 316536--316718 Score: 97
Period size: 20 Copynumber: 8.8 Consensus size: 22
316526 TATACGTAGT
*
316536 ATATATAATTTATA-ATTATAC
1 ATATATAATTTATATATAATAC
* * *
316557 ATA-AT-ATATAAATATAAGT-T
1 ATATATAATTTATATATAA-TAC
* * *
316577 GTATAT-ATTTAAATATAATTC
1 ATATATAATTTATATATAATAC
*
316598 ATATATAATTTATATATTA-AC
1 ATATATAATTTATATATAATAC
*
316619 -TATATAATTTATAT-TAATAA
1 ATATATAATTTATATATAATAC
* *
316639 ACTATATAGTTTATATAT-ACAC
1 A-TATATAATTTATATATAATAC
* *
316661 -TATATAGTTTATAT-TAATAA
1 ATATATAATTTATATATAATAC
* *
316681 ACTATAT-AGTT-TATATAATAT
1 A-TATATAATTTATATATAATAC
*
316702 ATATAT-ATATATATATA
1 ATATATAATTTATATATA
316719 GTTGTTTCAA
Statistics
Matches: 125, Mismatches: 23, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
19 8 0.06
20 49 0.39
21 37 0.30
22 30 0.24
23 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (22 bp):
ATATATAATTTATATATAATAC
Found at i:316622 original size:20 final size:20
Alignment explanation
Indices: 316599--316718 Score: 127
Period size: 20 Copynumber: 5.8 Consensus size: 20
316589 ATATAATTCA
* *
316599 TATATAATTTATATATTAAC
1 TATATAGTTTATATATAAAC
*
316619 TATATAATTTATATTAATAAAC
1 TATATAGTTTATA-T-ATAAAC
*
316641 TATATAGTTTATATATACAC
1 TATATAGTTTATATATAAAC
316661 TATATAGTTTATATTAATAAAC
1 TATATAGTTTATA-T-ATAAAC
*
316683 TATATAGTTTATATAATATA-
1 TATATAGTTTATAT-ATAAAC
*
316703 TATATA-TATATATATA
1 TATATAGTTTATATATA
316719 GTTGTTTCAA
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.03
19 6 0.07
20 37 0.41
21 9 0.10
22 35 0.39
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (20 bp):
TATATAGTTTATATATAAAC
Found at i:316696 original size:42 final size:42
Alignment explanation
Indices: 316599--316697 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
316589 ATATAATTCA
*
316599 TATATAATTTATATATTAACTATATAATTTATATTAATAAAC
1 TATATAGTTTATATATTAACTATATAATTTATATTAATAAAC
*
316641 TATATAGTTTATATA-TACACTATATAGTTTATATTAATAAAC
1 TATATAGTTTATATATTA-ACTATATAATTTATATTAATAAAC
316683 TATATAGTTTATATA
1 TATATAGTTTATATA
316698 ATATATATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
41 2 0.04
42 52 0.96
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (42 bp):
TATATAGTTTATATATTAACTATATAATTTATATTAATAAAC
Found at i:316707 original size:42 final size:41
Alignment explanation
Indices: 316497--316715 Score: 159
Period size: 42 Copynumber: 5.3 Consensus size: 41
316487 ATATATAATT
* *
316497 TATAGTTTATATTAATAAACAATATAATTTATACGTAGTATATA
1 TATA-TTTATATTAATAAACTATATAATTTATA--TAATATATA
* *
316541 TA-ATTTATAATT-ATACATAATATATAA---ATATAAGT-TGTA
1 TATATTTAT-ATTAATA-A-ACTATATAATTTATATAA-TATATA
* ** *
316580 TATATTTAAATATAATTCA-TATATAATTTATATATTA-ACTA
1 TATATTTATAT-TAATAAACTATATAATTTATATAATATA-TA
* *
316621 TATAATTTATATTAATAAACTATATAGTTTATAT-ATACACTA
1 TAT-ATTTATATTAATAAACTATATAATTTATATAATATA-TA
*
316663 TATAGTTTATATTAATAAACTATATAGTTTATATAATATATA
1 TATA-TTTATATTAATAAACTATATAATTTATATAATATATA
*
316705 TATATATATAT
1 TATATTTATAT
316716 ATAGTTGTTT
Statistics
Matches: 142, Mismatches: 16, Indels: 37
0.73 0.08 0.19
Matches are distributed among these distances:
38 7 0.05
39 10 0.07
40 8 0.06
41 29 0.20
42 70 0.49
43 9 0.06
44 9 0.06
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (41 bp):
TATATTTATATTAATAAACTATATAATTTATATAATATATA
Found at i:319481 original size:31 final size:31
Alignment explanation
Indices: 319446--319511 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
319436 CAATTACGTC
*
319446 GGGACTATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
* *
319477 GGGACCATATTGCAAATGGACTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGA
319508 GGGA
1 GGGA
319512 TTATTTACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:320360 original size:31 final size:31
Alignment explanation
Indices: 320302--320368 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
320292 TGCAATACAA
*
320302 TCCCCCAACATTTAGTTCGTTTGCAATATGG
1 TCCCCCAACATTTAGTTCGTTTACAATATGG
*
320333 TCCCTCAACATTTAG-TCTGTTTACAATATGG
1 TCCCCCAACATTTAGTTC-GTTTACAATATGG
320364 TCCCC
1 TCCCC
320369 GACATAACTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAGTTCGTTTACAATATGG
Found at i:322232 original size:263 final size:263
Alignment explanation
Indices: 321765--322290 Score: 989
Period size: 263 Copynumber: 2.0 Consensus size: 263
321755 ACCTTCAATT
321765 CCATTCCTTTGCAAAACTGTTAAAGGAGCATTTGGGTATGCTGTCAACAACATTGTCCTATAGAA
1 CCATTCCTTTGCAAAACTGTTAAAGGAGCATTTGGGTATGCTGTCAACAACATTGTCCTATAGAA
321830 AGCTAAAGGATACTTTTTCGTTTTATTTTGCTTCTTGAAATACTCGGTAAAGATTTGTCTTTTTT
66 AGCTAAAGGATACTTTTTCGTTTTATTTTGCTTCTTGAAATACTCGGTAAAGATTTGTCTTTTTT
* * *
321895 TCTCTCATATTTTGGGCATGTAGGTAATTGGTACCCGAGTATTTCCAACTTGGAAAAGTGTATGA
131 CCTCTCATATTTTGGGCATGTAGGTAATTGGCACCCGAGTATTTCCAACATGGAAAAGTGTATGA
*
321960 TAAAACTGATGTTTATGCTTTTGGGGTTGTCTTGTTGGAGCTAATAACCGGACGAAAACCAATCG
196 TAAAACTGATGTTTATGCTTTTGGGGTTGTCTTGTTAGAGCTAATAACCGGACGAAAACCAATCG
322025 AGG
261 AGG
322028 CCATTCCTTTGCAAAACTGTTAAAGGAGCATTTGGGTATGCTGTCAACAACATTGTCCTATAGAA
1 CCATTCCTTTGCAAAACTGTTAAAGGAGCATTTGGGTATGCTGTCAACAACATTGTCCTATAGAA
*
322093 AGCTAAAGGATACTTTTTCGTTTTATTTTGCTTCTTGACATACTCGGTAAAGATTTGTCTTTTTT
66 AGCTAAAGGATACTTTTTCGTTTTATTTTGCTTCTTGAAATACTCGGTAAAGATTTGTCTTTTTT
*
322158 CCTCTCATATTTTGGGCATGTAGGTACTTGGCACCCGAGTATTTCCAACATGGAAAAGTGTATGA
131 CCTCTCATATTTTGGGCATGTAGGTAATTGGCACCCGAGTATTTCCAACATGGAAAAGTGTATGA
*
322223 TAAAACTGATGTTTATGCTTTTGGGGTTGTCTTGTTAGAGCTGATAACCGGACGAAAACCAATCG
196 TAAAACTGATGTTTATGCTTTTGGGGTTGTCTTGTTAGAGCTAATAACCGGACGAAAACCAATCG
322288 AGG
261 AGG
322291 TAAGACGGCC
Statistics
Matches: 256, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
263 256 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (263 bp):
CCATTCCTTTGCAAAACTGTTAAAGGAGCATTTGGGTATGCTGTCAACAACATTGTCCTATAGAA
AGCTAAAGGATACTTTTTCGTTTTATTTTGCTTCTTGAAATACTCGGTAAAGATTTGTCTTTTTT
CCTCTCATATTTTGGGCATGTAGGTAATTGGCACCCGAGTATTTCCAACATGGAAAAGTGTATGA
TAAAACTGATGTTTATGCTTTTGGGGTTGTCTTGTTAGAGCTAATAACCGGACGAAAACCAATCG
AGG
Found at i:323412 original size:13 final size:13
Alignment explanation
Indices: 323393--323430 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
323383 TAATTTAGTG
323393 ATTATAAATAA-A
1 ATTATAAATAAGA
323405 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
323420 ATTATAAATAA
1 ATTATAAATAA
323431 TATAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:323490 original size:18 final size:19
Alignment explanation
Indices: 323410--323493 Score: 59
Period size: 19 Copynumber: 4.5 Consensus size: 19
323400 ATAAAATTTA
*
323410 TAATAT-AAGAATTATAAA
1 TAATATAAAGAATTATAAT
* **
323428 TAATATAAATAATTGGAAT
1 TAATATAAAGAATTATAAT
*
323447 TAATATAAA-AATCA-AATTT
1 TAATATAAAGAATTATAA--T
*
323466 ATAATATACA-AATTATAAT
1 -TAATATAAAGAATTATAAT
323485 TAATATAAA
1 TAATATAAA
323494 AACTAAATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
17 2 0.04
18 17 0.33
19 19 0.37
20 12 0.23
21 2 0.04
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
TAATATAAAGAATTATAAT
Found at i:323684 original size:16 final size:16
Alignment explanation
Indices: 323650--323684 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
323640 TGAGTCAATC
*
323650 ACATGTCAGGTTCATA
1 ACATGTCAGGTTCAAA
*
323666 ACATGTCAGGTTGAAA
1 ACATGTCAGGTTCAAA
323682 ACA
1 ACA
323685 AGTCGGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (16 bp):
ACATGTCAGGTTCAAA
Found at i:324458 original size:59 final size:59
Alignment explanation
Indices: 324382--324912 Score: 794
Period size: 59 Copynumber: 9.0 Consensus size: 59
324372 TATTTCCCAA
* * * * * *
324382 ATGGGAATTCATACACTTCGTATGAATTCCTTATCATTTTAGCACAC-AAGGTGTCCAAT
1 ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAA-GTGCCCTAT
** * * * *
324441 ACAGAAATTCATACACTTAGTATGATATTTCTTATCATTTTAGCACACTAAGTGCCCTAT
1 ATGGAAATTCATACACTTAGTATGA-ATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
* *
324501 ATGGAAATTCATACACTTGGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCTTAT
1 ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
*
324560 ATGGAAAATTCATACACTTAATATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
1 ATGG-AAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
* * * *
324620 ATGGAAATTCATACACTTGGTATGAATTCATTCTCATGTTAGCGCACGAAGGGCCCTAT
1 ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
* * *
324679 ATGGTAATTCATACACTTAGTATGAATTCATTCTCATGTCAGCACACGAAGTGCCCTAT
1 ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
*
324738 ATGGAAATTCATAAACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
1 ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
*
324797 ATGGAAATTCATAAACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
1 ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
* *
324856 ATGGAAATTTATACACTTAGTATGAATTCCTTTTCATGTTAGCACACGAAGTGCCCT
1 ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
324913 TCTGGTAAAC
Statistics
Matches: 434, Mismatches: 35, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
59 326 0.75
60 106 0.24
61 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (59 bp):
ATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTAT
Found at i:325229 original size:20 final size:22
Alignment explanation
Indices: 325204--325256 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
325194 TTGGTTCCTC
325204 AGTATCGATACT-CCC-ACAAT
1 AGTATCGATACTACCCTACAAT
*
325224 AGTATCGATACTACCCTACTAT
1 AGTATCGATACTACCCTACAAT
*
325246 GGTATCGATAC
1 AGTATCGATAC
325257 CCCCTTCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 3 0.10
22 14 0.48
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (22 bp):
AGTATCGATACTACCCTACAAT
Found at i:331591 original size:59 final size:59
Alignment explanation
Indices: 331394--331751 Score: 518
Period size: 59 Copynumber: 6.1 Consensus size: 59
331384 CAAATTATTT
* * * * * *
331394 CCTAAATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCATACAAGGTGT
1 CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
* ** * * * *
331453 CCAATACAGAAATTCATACACTTAGTATGATATTTCTTATCATTTTAGCACACTAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGA-ATTCCTTCTCATGTTAGCACACAAAGTGC
* * * *
331513 CCTATATGGAAATTAATACACTTAGTATGAATTCCTTCTCATGTTAGCAAACGAAGTTC
1 CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
*
331572 CCTATATGAAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
*
331631 CCTATATGGAAATTCTTACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
* *
331690 CCTATATGGAAATTCATACACTTAGTATGAATTCATTCTCATGTTAGCACACAAAGTTC
1 CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
331749 CCT
1 CCT
331752 TCTGGTAATC
Statistics
Matches: 269, Mismatches: 29, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
59 219 0.81
60 50 0.19
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.34
Consensus pattern (59 bp):
CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACAAAGTGC
Found at i:332097 original size:20 final size:20
Alignment explanation
Indices: 332072--332109 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
332062 ATAGTTCCTC
*
332072 AGTATCAATACTCCCATAAT
1 AGTATCAATACTACCATAAT
*
332092 AGTATCGATACTACCATA
1 AGTATCAATACTACCATA
332110 CTATGGTATC
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:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (20 bp):
AGTATCAATACTACCATAAT
Found at i:332224 original size:22 final size:22
Alignment explanation
Indices: 332167--332238 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
332157 ATGTGCTCCA
*
332167 GTATCGATA-CCCTA-ACCATG
1 GTATCGATACCCCTATACTATG
**
332187 GTATCGATACTACTATACTATG
1 GTATCGATACCCCTATACTATG
332209 GTATCGATACCCC--TA-TATG
1 GTATCGATACCCCTATACTATG
332228 GTATCGATACC
1 GTATCGATACC
332239 AAAATTAGCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.33
20 11 0.24
21 3 0.07
22 16 0.36
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (22 bp):
GTATCGATACCCCTATACTATG
Found at i:332273 original size:95 final size:93
Alignment explanation
Indices: 332093--332295 Score: 293
Period size: 95 Copynumber: 2.2 Consensus size: 93
332083 TCCCATAATA
332093 GTATCGATACTACCATACTATGGTATCGATACCCCCTTACAGTACGATACCAAAATTAGATTCGA
1 GTATCGATACTACCATACTATGGTATCGATACCCCCTTACAGTACGATACCAAAATTAGATTCGA
332158 TGTGCTCCAGTATCGATACCCTAACCATG
66 TGT-CTCCAGTATCGATACCCTAACCATG
* ** *
332187 GTATCGATACTACTATACTATGGTATCGATA-CCCCTATATGGTATCGATACCAAAATTAGCTTC
1 GTATCGATACTACCATACTATGGTATCGATACCCCCT-TACAGTA-CGATACCAAAATTAGATTC
* *
332251 GATGT-TACCTGATATCGATACCCTTACCATG
64 GATGTCT-CCAG-TATCGATACCCTAACCATG
332282 GTATCGATACTACC
1 GTATCGATACTACC
332296 TCATTCAATA
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
93 6 0.06
94 38 0.39
95 54 0.55
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (93 bp):
GTATCGATACTACCATACTATGGTATCGATACCCCCTTACAGTACGATACCAAAATTAGATTCGA
TGTCTCCAGTATCGATACCCTAACCATG
Found at i:339112 original size:16 final size:16
Alignment explanation
Indices: 339093--339126 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
339083 CAATATACGA
339093 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
339109 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
339125 AT
1 AT
339127 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:339204 original size:14 final size:16
Alignment explanation
Indices: 339168--339204 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
339158 TATTAATGTA
339168 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
339185 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
339200 T-AATA
1 TGAATA
339205 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:339738 original size:21 final size:23
Alignment explanation
Indices: 339693--339739 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
339683 GTGTCACCAA
339693 TAACATATATCATGATCATGTGT
1 TAACATATATCATGATCATGTGT
* *
339716 TAACATATGTCA-GATCCTG-GT
1 TAACATATATCATGATCATGTGT
339737 TAA
1 TAA
339740 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (23 bp):
TAACATATATCATGATCATGTGT
Done.