Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008822.1 Hibiscus syriacus cultivar Beakdansim tig00111990_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: 699754
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:346834 original size:38 final size:39
Alignment explanation
Indices: 346795--346874 Score: 99
Period size: 44 Copynumber: 1.9 Consensus size: 39
346785 ATCTGTTAGG
*
346795 AATTG-GAATCCAATTCCATATTCTGTTTGGTTGGCAGGA
1 AATTGAGAATCCAATTCCATATTCT-TTTGGTTCGCAGGA
346834 AATTGAATTAGAATCCAATTCCATATTCTTTTGGTTCGCAG
1 AATTG----AGAATCCAATTCCATATTCTTTTGGTTCGCAG
346875 ACATGTCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
39 5 0.14
43 11 0.31
44 19 0.54
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (39 bp):
AATTGAGAATCCAATTCCATATTCTTTTGGTTCGCAGGA
Found at i:347569 original size:205 final size:199
Alignment explanation
Indices: 347174--347539 Score: 551
Period size: 204 Copynumber: 1.8 Consensus size: 199
347164 CCGACCCGAA
* *
347174 ATAATAAAAAAATTATTTTTATTCAATAAAAATAGTTACTTAATTGAAAAAAAATATATATAGAG
1 ATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATATATAGAG
*
347239 AGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTGGGGTCGGGTCA
66 AGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT---GTC-GG--A
****
347304 GGTCGGGCATTTTTCACCCTAAACCCGAACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGA
125 GGTCGGGCATTTTTCACCCTAAACCCGAACCCGACCCGACCAAAATAAAAAACCACCCGACCCGA
347369 CCGACCAAAT
190 CCGACCAAAT
* *
347379 ATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGTAAAAAAAT-TATATATAG
1 ATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATATATAGAG
347443 AGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT-TC-G-GGTCGG
66 AGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTGTCGGAGGTCGG
* *
347505 GTATTTTTCACCCTAAACCCGAACTCGACCCGACC
131 GCATTTTTCACCCTAAACCCGAACCCGACCCGACC
347540 CGAATATCAT
Statistics
Matches: 154, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
195 39 0.25
198 1 0.01
200 2 0.01
204 60 0.39
205 52 0.34
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (199 bp):
ATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATATATAGAG
AGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTGTCGGAGGTCGG
GCATTTTTCACCCTAAACCCGAACCCGACCCGACCAAAATAAAAAACCACCCGACCCGACCGACC
AAAT
Found at i:347725 original size:261 final size:257
Alignment explanation
Indices: 347362--347925 Score: 929
Period size: 261 Copynumber: 2.2 Consensus size: 257
347352 AGTTTCACCC
*
347362 GACCCGA-CCGA-CCAAATATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTG
1 GACCCGACCCGACCCGAA-ATAAT-AAAAAATTATTTTTATTCAAT-AAAACAGTGACTTAATTG
347425 TAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATAT
63 TAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATAT
*
347490 ATATTTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCATACTTA
128 ATATTTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTA
*
347555 A-AAAACCGACCCGACTCGACCAAAATAAAGTTTCACCCGAACCTACCCGAATATATGAATTAGA
193 AGAAAACCGACCCGACCCGACCAAAATAAAGTTTCACCCG-----ACCCGAATATATGAATTAGA
347619 AATCT
253 AATCT
*
347624 GACCCGACCCGACCCGAAATAATAAAAATATTATTTTTATTCAATAAAACAGTTACTTAATTG-A
1 GACCCGACCCGACCCGAAATAATAAAAA-ATTATTTTTATTCAATAAAACAGTGACTTAATTGTA
347688 AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
65 AAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
* * *
347753 ATTTTTGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACTCGACCTGAATATCACACTTAAG
130 ATTTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAG
* *
347818 AAAACCGACTCTACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATCT
195 AAAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATCT
*
347881 GACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
1 GACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATA
347926 TATGAATAAG
Statistics
Matches: 288, Mismatches: 10, Indels: 14
0.92 0.03 0.04
Matches are distributed among these distances:
256 16 0.06
257 53 0.18
261 126 0.44
262 64 0.22
263 25 0.09
264 4 0.01
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (257 bp):
GACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAACAGTGACTTAATTGTAA
AAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATA
TTTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAGA
AAACCGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATCT
Found at i:352250 original size:21 final size:21
Alignment explanation
Indices: 352209--352256 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
352199 AGAAGTATTA
352209 ATACTCTTATCCCGAGTACCG
1 ATACTCTTATCCCGAGTACCG
*
352230 ATACTCTTATCCTGAGTACCG
1 ATACTCTTATCCCGAGTACCG
*
352251 ACACTC
1 ATACTC
352257 CATGGTCTGG
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:0.25, C:0.33, G:0.12, T:0.29
Consensus pattern (21 bp):
ATACTCTTATCCCGAGTACCG
Found at i:366440 original size:21 final size:23
Alignment explanation
Indices: 366416--366467 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
366406 AGGAAATCGA
366416 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAATGGGAACCGAT
**
366437 TCCCCCTTTGAATGGGAACCGAT
1 TCCCCCCATGAATGGGAACCGAT
366460 TCCCCCCA
1 TCCCCCCA
366468 CACGGGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.19
Consensus pattern (23 bp):
TCCCCCCATGAATGGGAACCGAT
Found at i:366933 original size:2 final size:2
Alignment explanation
Indices: 366926--366964 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
366916 TTATGAAAAC
366926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
366965 TGTTTCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:374616 original size:20 final size:20
Alignment explanation
Indices: 374555--374622 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
374545 CAGTATACAA
374555 TATCGATATCGCATGAATAG
1 TATCGATATCGCATGAATAG
* * *
374575 TA-CTGATATTGTTCTTG--CAG
1 TATC-GATATCG--CATGAATAG
374595 TATCGATATCGCATGAATAG
1 TATCGATATCGCATGAATAG
374615 TATCGATA
1 TATCGATA
374623 CCCAAGGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 3 0.08
19 1 0.03
20 28 0.78
21 1 0.03
22 3 0.08
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
TATCGATATCGCATGAATAG
Found at i:379421 original size:2 final size:2
Alignment explanation
Indices: 379412--379447 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
379402 TATTTTTTGT
379412 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
379448 TTCTTGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:379666 original size:21 final size:21
Alignment explanation
Indices: 379627--379672 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
379617 TTTATTTTCT
*
379627 TTTAATTTTTTAGTTTGTTTA
1 TTTAATTTTTTAGTGTGTTTA
*
379648 TTTAATTATTTTA-TGTGTTTG
1 TTTAATT-TTTTAGTGTGTTTA
379669 TTTA
1 TTTA
379673 CCTACTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.70
Consensus pattern (21 bp):
TTTAATTTTTTAGTGTGTTTA
Found at i:391325 original size:60 final size:58
Alignment explanation
Indices: 391257--391385 Score: 174
Period size: 55 Copynumber: 2.2 Consensus size: 58
391247 CGACACAAAT
*
391257 GATATCCAACTCAAAGCCAATTTGGTGAAACAAAGATTGGGTTTCAACTTCACGACGAAG
1 GATATCCAACTCAAA-CCAATTTGGTGAAACAAA-ATTGGATTTCAACTTCACGACGAAG
* **
391317 GATATCCAAC-C--ACCAATTTGGTGAAGCAAAATTGGATTTCAACTTCACGGTGAAG
1 GATATCCAACTCAAACCAATTTGGTGAAACAAAATTGGATTTCAACTTCACGACGAAG
*
391372 GATATCCAATTCAA
1 GATATCCAACTCAA
391386 GGCTCAACTT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
55 31 0.51
56 18 0.30
57 1 0.02
59 1 0.02
60 10 0.16
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (58 bp):
GATATCCAACTCAAACCAATTTGGTGAAACAAAATTGGATTTCAACTTCACGACGAAG
Found at i:391642 original size:124 final size:121
Alignment explanation
Indices: 391351--391650 Score: 359
Period size: 121 Copynumber: 2.5 Consensus size: 121
391341 AGCAAAATTG
** * * **
391351 GATTTCAACTTCACGGTGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGAAGCCATCCA
* * * * * * *
391416 CGATTTCAACTTCATGACGAAGGATATCATACCTACAAGCAGCAATGCAACCCTTG
66 CGATTTCAACTTCACGACGAAGGATATCATACCCACAAGAAACAATACAACCATTA
*
391472 GATTTCAACTTCACGACGAAGGATATCCAATTCTAAGCTCAACTTCACAACGAAGAAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGAAGCCATCCA
* * * * *
391537 TGATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGAAAC-ATACAACTTAAGATTA
66 CGATTTCAACTTCACGACGAAGGATATCATACCCACAAGAAACAATACAAC----CATTA
* * *
391596 GATTTCAACTTCACGACGGAGGATATTCAATTCAAAGCTCAACTTCACAGCGAAG
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAG
391651 GAGCTTTCCA
Statistics
Matches: 152, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
120 6 0.04
121 93 0.61
124 53 0.35
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (121 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGAAGCCATCCA
CGATTTCAACTTCACGACGAAGGATATCATACCCACAAGAAACAATACAACCATTA
Found at i:393498 original size:2 final size:2
Alignment explanation
Indices: 393493--393543 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
393483 TATTTTTTAT
393493 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
393535 TA TA TA TA T
1 TA TA TA TA T
393544 TTCTTGTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:395581 original size:25 final size:25
Alignment explanation
Indices: 395553--395608 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
395543 AATTTTCTGA
* *
395553 CAGCTTTATTTTTTTTTTGAAAAGT
1 CAGCTTGATTTTATTTTTGAAAAGT
* *
395578 CAGCTTGGTTTTATTTTTGACAAGT
1 CAGCTTGATTTTATTTTTGAAAAGT
*
395603 TAGCTT
1 CAGCTT
395609 AAAAGGTTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (25 bp):
CAGCTTGATTTTATTTTTGAAAAGT
Found at i:399255 original size:21 final size:21
Alignment explanation
Indices: 399231--399279 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
399221 AGGTTGCTAT
399231 GTTGGTAATGGATATCTTACA
1 GTTGGTAATGGATATCTTACA
399252 GTTGGTAATGGATATCTTACA
1 GTTGGTAATGGATATCTTACA
399273 GTTGGTA
1 GTTGGTA
399280 GAGCGCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.39
Consensus pattern (21 bp):
GTTGGTAATGGATATCTTACA
Found at i:424929 original size:24 final size:24
Alignment explanation
Indices: 424909--424963 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
424899 GAACGTTCGG
424909 TTATGTTCGTTTATATGCGTTCAA
1 TTATGTTCGTTTATATGCGTTCAA
* *
424933 TTATGTTCGTTTATGTGCGTTCAT
1 TTATGTTCGTTTATATGCGTTCAA
424957 TTATGTT
1 TTATGTT
424964 TAACATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.55
Consensus pattern (24 bp):
TTATGTTCGTTTATATGCGTTCAA
Found at i:429058 original size:16 final size:16
Alignment explanation
Indices: 429037--429102 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
429027 GTCTCCAACG
429037 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
429053 TTTATGTTTGTGTTC-
1 TTTATGTTCGTGTTCA
*
429068 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
429084 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
429098 TTTAT
1 TTTAT
429103 TAAATGAACG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
14 5 0.11
15 16 0.35
16 25 0.54
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.62
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:429185 original size:16 final size:16
Alignment explanation
Indices: 429164--429195 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
429154 AAAAACAATT
429164 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
429180 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
429196 CTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:441146 original size:77 final size:79
Alignment explanation
Indices: 441047--441195 Score: 196
Period size: 77 Copynumber: 1.9 Consensus size: 79
441037 TTAATAAAAA
* **
441047 TCTTATTTAATTAATTCAAATTAAATATCCATT-AAAGACTTATAATCTGAATTACA-ATCTTTA
1 TCTTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCAAAATTACATATCTTTA
441110 ATGTTTATTTAAAT
66 ATGTTTATTTAAAT
* * * * *
441124 TCTTATTTAATT-ATTCTGAATTAAATATAGATTAAAAGAGTTATAATCAAAATTACATTTTTTT
1 TCTTATTTAATTAATTC-AAATTAAATATACATTAAAAGACTTATAATCAAAATTACATATCTTT
441188 AATGTTTA
65 AATGTTTA
441196 CTTACTATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
76 4 0.07
77 25 0.41
78 20 0.33
79 12 0.20
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.46
Consensus pattern (79 bp):
TCTTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCAAAATTACATATCTTTA
ATGTTTATTTAAAT
Found at i:441963 original size:30 final size:29
Alignment explanation
Indices: 441863--441981 Score: 78
Period size: 30 Copynumber: 3.9 Consensus size: 29
441853 CACCATGAGC
*
441863 AATGT-TTGTGTTCATTTATTTATTTTTG
1 AATGTGTTCTGTTCATTTATTTATTTTTG
* * * * **
441891 AAGGTGTTCGGTTCGTGTTCGTTTAAATTTTCA
1 AATGTGTTCTGTTCAT-TT-ATTT--ATTTTTG
441924 ATATCGTGTTCATGTTCATTTATTTATTTTTG
1 A-AT-GTGTTC-TGTTCATTTATTTATTTTTG
* *
441956 AATGTGTTTGTGTTCGTTTATTTATT
1 AATGTG-TTCTGTTCATTTATTTATT
441982 GTTCACAAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
28 4 0.06
29 7 0.10
30 20 0.30
31 7 0.10
32 6 0.09
33 6 0.09
34 4 0.06
35 8 0.12
36 5 0.07
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.57
Consensus pattern (29 bp):
AATGTGTTCTGTTCATTTATTTATTTTTG
Found at i:442000 original size:23 final size:23
Alignment explanation
Indices: 441971--442043 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
441961 GTTTGTGTTC
441971 GTTTATTTATTGTTCACAAACAT
1 GTTTATTTATTGTTCACAAACAT
* ** * *
441994 GTTTATTTAATAATCGCAAGCAT
1 GTTTATTTATTGTTCACAAACAT
* *
442017 GTTCATTTATATGTTCACGAACAT
1 GTTTATTTAT-TGTTCACAAACAT
442041 GTT
1 GTT
442044 CGTTTAGCGT
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 26 0.70
24 11 0.30
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (23 bp):
GTTTATTTATTGTTCACAAACAT
Found at i:442353 original size:12 final size:12
Alignment explanation
Indices: 442336--442403 Score: 59
Period size: 12 Copynumber: 5.7 Consensus size: 12
442326 AACATAGATG
442336 AACGAGTTGATA
1 AACGAGTTGATA
442348 AACGAGCTTG-TA
1 AACGAG-TTGATA
*
442360 AACAAGCTT-ATA
1 AACGAG-TTGATA
* *
442372 AACAAGCTGATA
1 AACGAGTTGATA
*
442384 AACGAGTTCATA
1 AACGAGTTGATA
*
442396 AATGAGTT
1 AACGAGTT
442404 TGTTCGTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
11 1 0.02
12 43 0.91
13 3 0.06
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (12 bp):
AACGAGTTGATA
Found at i:444039 original size:112 final size:112
Alignment explanation
Indices: 443842--444066 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
443832 ATTTGATTAC
443842 AACTTTAGGGACCTATATTATATATATTCAAGAGTCTTAATAGGAAAGTCAACTATACAAGAAAT
1 AACTTTAGGGACCTATATTATATATATTCAAGAGTCTTAATAGGAAAGTCAACTATACAAGAAAT
443907 ATGGAAACACTTATAAGTTAGCCTATAAATTTGACACAAATTTGTAA
66 ATGGAAACACTTATAAGTTAGCCTATAAATTTGACACAAATTTGTAA
443954 AACTTTAGGGACCTATATTATATATATTCAAGAGTCTTAATAGGAAAGTCAACTATACAAGAAAT
1 AACTTTAGGGACCTATATTATATATATTCAAGAGTCTTAATAGGAAAGTCAACTATACAAGAAAT
444019 ATGGAAACACTTATAAGTTAGCCTATAAATTTGACACAAATTTGTAA
66 ATGGAAACACTTATAAGTTAGCCTATAAATTTGACACAAATTTGTAA
444066 A
1 A
444067 CAATCTGTCC
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (112 bp):
AACTTTAGGGACCTATATTATATATATTCAAGAGTCTTAATAGGAAAGTCAACTATACAAGAAAT
ATGGAAACACTTATAAGTTAGCCTATAAATTTGACACAAATTTGTAA
Found at i:445380 original size:18 final size:16
Alignment explanation
Indices: 445357--445407 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 16
445347 TATGTATATA
445357 TATTTTATATCATTATTT
1 TATTTTAT-TCATT-TTT
*
445375 TATTTTATTTTATTTTT
1 TATTTTA-TTCATTTTT
445392 TA-TTTATTCATTTTT
1 TATTTTATTCATTTTT
445407 T
1 T
445408 GGGTTTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 9 0.30
16 4 0.13
17 5 0.17
18 11 0.37
19 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TATTTTATTCATTTTT
Found at i:445406 original size:16 final size:17
Alignment explanation
Indices: 445357--445407 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
445347 TATGTATATA
*
445357 TATTTTATATCATTATTT
1 TATTTTAT-TCATTTTTT
*
445375 TATTTTATT-TTATTTTT
1 TATTTTATTCAT-TTTTT
445392 TA-TTTATTCATTTTTT
1 TATTTTATTCATTTTTT
445408 GGGTTTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 12 0.43
17 8 0.29
18 8 0.29
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTTATTCATTTTTT
Found at i:445491 original size:18 final size:16
Alignment explanation
Indices: 445468--445530 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 16
445458 ATATTTATAC
445468 ATATATGTTTTTATTATT
1 ATATAT-TTTTTATT-TT
*
445486 ATATATATTTTATTTT
1 ATATATTTTTTATTTT
*
445502 ATTTATCTTATTTATTTT
1 ATATAT-TT-TTTATTTT
*
445520 TTATATTTTTT
1 ATATATTTTTT
445531 TACTATTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 10 0.26
17 10 0.26
18 18 0.47
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
ATATATTTTTTATTTT
Found at i:445521 original size:25 final size:26
Alignment explanation
Indices: 445484--445532 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
445474 GTTTTTATTA
445484 TTATATATATTTTAT-TTTATTTATC
1 TTATATATATTTTATATTTATTTATC
* * *
445509 TTATTTATTTTTTATATTTTTTTA
1 TTATATATATTTTATATTTATTTA
445533 CTATTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TTATATATATTTTATATTTATTTATC
Found at i:445537 original size:20 final size:21
Alignment explanation
Indices: 445514--445552 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
445504 TTATCTTATT
*
445514 TATTTTTTA-TATTTTTTTAC
1 TATTTTTCATTATTTTTTTAC
445534 TATTTTTCATTATTTTTTT
1 TATTTTTCATTATTTTTTT
445553 CCTAACGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TATTTTTCATTATTTTTTTAC
Found at i:445550 original size:11 final size:10
Alignment explanation
Indices: 445475--445551 Score: 52
Period size: 10 Copynumber: 7.5 Consensus size: 10
445465 TACATATATG
445475 TTTTTATTAT
1 TTTTTATTAT
* *
445485 TATATA-TAT
1 TTTTTATTAT
445494 TTTATT-TTAT
1 TTT-TTATTAT
445504 TTATCTTATTTAT
1 TT-T-TTA-TTAT
445517 TTTTTA-TATT
1 TTTTTATTA-T
*
445527 TTTTTACTAT
1 TTTTTATTAT
*
445537 TTTTCATTAT
1 TTTTTATTAT
445547 TTTTT
1 TTTTT
445552 TCCTAACGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
9 7 0.13
10 30 0.58
11 8 0.15
12 1 0.02
13 6 0.12
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:445566 original size:2 final size:2
Alignment explanation
Indices: 445561--445603 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
445551 TTCCTAACGT
445561 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
445603 T
1 T
445604 TTGTTTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:445893 original size:5 final size:5
Alignment explanation
Indices: 445861--446029 Score: 53
Period size: 5 Copynumber: 32.0 Consensus size: 5
445851 TATATATATA
* * * *
445861 TTATT TT-TT TATAATT TTATTT TCTATT TTATT TTCTT TTGTT TCAGT
1 TTATT TTATT T-T-ATT TTA-TT T-TATT TTATT TTATT TTATT TTATT
* *
445909 TT-TT TTAGTT TTATT TGATT CCATT-TT TTATT TTCATT TTCATC TTATT
1 TTATT TTA-TT TTATT TTATT ---TTATT TTATT TT-ATT TT-ATT TTATT
* * * * * *
445958 CTATT TTACT TTA-T TTCTT TTATT ATT-TT TCT-TT TTACT TTACT TTACT
1 TTATT TTATT TTATT TTATT TTATT -TTATT T-TATT TTATT TTATT TTATT
446007 TTACTT TTATTTT TTATT TTATT
1 TTA-TT TTA--TT TTATT TTATT
446030 ATTTATTATT
Statistics
Matches: 127, Mismatches: 19, Indels: 36
0.70 0.10 0.20
Matches are distributed among these distances:
4 13 0.10
5 73 0.57
6 28 0.22
7 12 0.09
8 1 0.01
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:446061 original size:38 final size:37
Alignment explanation
Indices: 445975--446081 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 37
445965 ACTTTATTTC
* *
445975 TTTTATTATTTTTCTTTTTACTTTACTTTACTTTACTTTTA
1 TTTT-TTATTTTACTTTTTA-TTTA-TTTA-TCTACTTTTA
446016 TTTTTTATTTTA-TTATTTA-TTATTTATCTACTTTTA
1 TTTTTTATTTTACTT-TTTATTTATTTATCTACTTTTA
446052 GGTTTTTTATTTTACTTTTTATTTATTTAT
1 --TTTTTTATTTTACTTTTTATTTATTTAT
446082 TGGAGTAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
36 9 0.15
37 4 0.07
38 19 0.32
39 12 0.20
40 11 0.19
41 4 0.07
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (37 bp):
TTTTTTATTTTACTTTTTATTTATTTATCTACTTTTA
Found at i:449163 original size:13 final size:13
Alignment explanation
Indices: 449163--449205 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
449153 CCGTTGACCC
449163 GACCCGACCCGTT
1 GACCCGACCCGTT
449176 GACCCGACCCGTT
1 GACCCGACCCGTT
*
449189 GACTCGACCCGTT
1 GACCCGACCCGTT
449202 GACC
1 GACC
449206 GTTAACCCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:449199 original size:18 final size:18
Alignment explanation
Indices: 449141--449186 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
449131 ACCGGTCACA
449141 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
449159 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
449177 ACCCGACCCG
1 ACCCGACCCG
449187 TTGACTCGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.52, G:0.22, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:451777 original size:24 final size:24
Alignment explanation
Indices: 451715--451784 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 24
451705 AATTTAGTTA
*
451715 TGATACCTGACCTGGATTCTGATC
1 TGATACATGACCTGGATTCTGATC
* *
451739 TGATA-TTGACATGGATTCTGATC
1 TGATACATGACCTGGATTCTGATC
451762 TGATACATGACCTGGATTCTGAT
1 TGATACATGACCTGGATTCTGAT
451785 ATAATACTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (24 bp):
TGATACATGACCTGGATTCTGATC
Found at i:451791 original size:24 final size:24
Alignment explanation
Indices: 451715--451796 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
451705 AATTTAGTTA
*
451715 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
451739 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
451762 TGATACATGACCTGGATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
*
451786 TAATACTTGAC
1 TGATACTTGAC
451797 TTGAATTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.42
24 29 0.58
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:451921 original size:35 final size:35
Alignment explanation
Indices: 451874--451948 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
451864 TAGAGGAAGG
*
451874 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
451909 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
451944 TTACT
1 TTACT
451949 ATTCGTGACG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.09, C:0.29, G:0.28, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
Found at i:453929 original size:13 final size:13
Alignment explanation
Indices: 453911--453953 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
453901 GTCACAACCC
453911 GACCCGACCCGTT
1 GACCCGACCCGTT
453924 GACCCGACCCGTT
1 GACCCGACCCGTT
*
453937 GACTCGACCCGTT
1 GACCCGACCCGTT
453950 GACC
1 GACC
453954 GTTGACCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:456468 original size:24 final size:24
Alignment explanation
Indices: 456441--456531 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
456431 TCAAATTTGA
* *
456441 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
456465 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
456488 ATTATGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
*
456512 ATTCTGATATAATACTTGAC
1 ATTCTGATATGATACTTGAC
456532 TTGAATTATG
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 20 0.36
24 35 0.64
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:456654 original size:33 final size:35
Alignment explanation
Indices: 456609--456681 Score: 123
Period size: 34 Copynumber: 2.1 Consensus size: 35
456599 TGGAGGAAGA
*
456609 TTACTTGGAGGCTC-TCGGCTTTGTGCTCA-GGCC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
456642 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
456677 TTACT
1 TTACT
456682 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
33 13 0.35
34 15 0.41
35 9 0.24
ACGTcount: A:0.11, C:0.27, G:0.27, T:0.34
Consensus pattern (35 bp):
TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
Found at i:459370 original size:93 final size:93
Alignment explanation
Indices: 459204--459399 Score: 293
Period size: 93 Copynumber: 2.1 Consensus size: 93
459194 AAATTATAAT
* * * *
459204 ATTATATATACAATAAAGTTTGAACTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATT
1 ATTATA-ATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGATTTATG
459269 GATAAGATTCAACTAGCCTGATAAAGGTC
65 GATAAGATTCAACTAGCCTGATAAAGGTC
** * *
459298 ATTATAATACAATAAAGCTTGAGTTGTCCCTTTAAAGTAATTGGTTAAACGCCCCAGATTTATGG
1 ATTATAATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGATTTATGG
* *
459363 ATAAGATTCAGCTAGCCTGATAAAGGTG
66 ATAAGATTCAACTAGCCTGATAAAGGTC
459391 ATTATAATA
1 ATTATAATA
459400 TTGAGCTGTC
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 86 0.93
94 6 0.07
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (93 bp):
ATTATAATACAATAAAGCTTGAACTGTCCCTCTAAAGCAATTGGTTAAACGCCCCAGATTTATGG
ATAAGATTCAACTAGCCTGATAAAGGTC
Found at i:460815 original size:85 final size:85
Alignment explanation
Indices: 460585--461335 Score: 869
Period size: 85 Copynumber: 8.8 Consensus size: 85
460575 TAAAGGAACT
* * *
460585 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTTTCAACTAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
*
460650 TCAGCTCAAAGACATATCAA
66 TCAGCTCAAAGGCATATCAA
* * * * * *
460670 ATTTACAACATAACT-AAGGCGAGAAGGGTTATATATCAATAAAGACCTTCGAGTTTGATTACAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
*
460734 TTAGCTCAAAGGCATATCAA
66 TCAGCTCAAAGGCATATCAA
* * * * * *
460754 ATTTGCAGCATAGCTTAAGGCTAGAAGGGCTATATGTCAACCAAAACGTTCGAGTTCGATTACAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
*
460819 TCAGCTC-AAGGAAATATCAA
66 TCAGCTCAAAGG-CATATCAA
* * * * * *
460839 ATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGATTTCGATTACAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
**
460904 TCAGCTCAAAGTTATATCAA
66 TCAGCTCAAAGGCATATCAA
* * * * * * * *
460924 ATTTATAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACCAAAACCATCGAATTCGATTGCAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
460989 CCATCTCAAAGGTATATCAA
66 TCAGCTCAAAGGCATATCAA
* * * * * * *
461009 GTTTACAACATAAATCAAGGTGATAAGGGTTATATGTCAACAAAAACCTTCGAGTTCGATTATAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
*
461074 TCAGCTCAAAGGCATATAAA
66 TCAGCTCAAAGGCATATCAA
* * * * *
461094 ATTTACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAATAAAAACCTTCAAGTTCGATTACAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
*
461159 TCAGCTCAAGGGCATATCAA
66 TCAGCTCAAAGGCATATCAA
* * * * * *
461179 ATTTATAGCATAACTCAAGGCGAGAAGGGTTATTTGTCAACAAATACCTTCGAGTTTGATTCCAT
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
461244 TTAGCTCAAGGGCATGTCAA
66 TCAGCTCAAAGGCATATCAA
* * * ** *
461264 ATTTACAGCATAGCTTAAGTCGAGAAAAGCTATATGTCAACAAAAA-CTATCGAGTTCGATTCCA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCT-TCGAGTTCGATTACA
461328 TTCAGCTC
65 TTCAGCTC
461336 GATGACACAT
Statistics
Matches: 557, Mismatches: 105, Indels: 8
0.83 0.16 0.01
Matches are distributed among these distances:
84 78 0.14
85 476 0.85
86 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (85 bp):
ATTTACAGCATAACTCAAGGCGAGAAGGGCTATATGTCAACAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAAGGCATATCAA
Found at i:460943 original size:170 final size:170
Alignment explanation
Indices: 460585--461335 Score: 961
Period size: 170 Copynumber: 4.4 Consensus size: 170
460575 TAAAGGAACT
* * * *
460585 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTTTCAACTAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTTAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
460650 TCAGCTCAAAGACATATCAAATTTACAACATAACT-AAGGCGAGAAGGGTTATATATCAATAAAG
66 TCAGCTCAAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATATGTCAACAAAG
*
460714 ACCTTCGAGTTTGATTACATTTAGCTCAAAGGCATATCAA
131 ACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATCAA
* * * * *
460754 ATTTGCAGCATAGCTTAAGGCTAGAAGGGCTATATGTCAACCAAAACGTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTTAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
460819 TCAGCTCAAGGAAATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAATAAAG
66 TCAGCTCAAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATATGTCAACAAAG
**
460884 ACCTTCGA-TTTCGATTACATTCAGCTCAAAGTTATATCAA
131 ACCTTCGAGTTT-GATTACATTCAGCTCAAAGGCATATCAA
* * * * * * *
460924 ATTTATAGCATAACTTAAGGCGAGAAAGGCTATCTGTCAACCAAAACCATCGAATTCGATTGCAT
1 ATTTACAGCATAGCTTAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * * * * * *
460989 CCATCTCAAAGG-TATATCAAGTTTACAACATAAATCAAGGTGATAAGGGTTATATGTCAACAAA
66 TCAGCTC-AAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATATGTCAACAAA
* * * *
461053 AACCTTCGAGTTCGATTATATTCAGCTCAAAGGCATATAAA
130 GACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATCAA
* * * *
461094 ATTTACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAATAAAAACCTTCAAGTTCGATTACAT
1 ATTTACAGCATAGCTTAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * * * *
461159 TCAGCTCAAGGGCATATCAAATTTATAGCATAACTCAAGGCGAGAAGGGTTATTTGTCAACAAAT
66 TCAGCTCAAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATATGTCAACAAAG
* * * *
461224 ACCTTCGAGTTTGATTCCATTTAGCTCAAGGGCATGTCAA
131 ACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATCAA
* ** * *
461264 ATTTACAGCATAGCTTAAGTCGAGAAAAGCTATATGTCAACAAAAA-CTATCGAGTTCGATTCCA
1 ATTTACAGCATAGCTTAAGGCGAGAAGGGCTATCTGTCAACAAAAACCT-TCGAGTTCGATTACA
461328 TTCAGCTC
65 TTCAGCTC
461336 GATGACACAT
Statistics
Matches: 498, Mismatches: 78, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
169 99 0.20
170 393 0.79
171 6 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (170 bp):
ATTTACAGCATAGCTTAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATATGTCAACAAAG
ACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATCAA
Found at i:464735 original size:17 final size:18
Alignment explanation
Indices: 464710--464774 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 18
464700 TTTTATACCA
*
464710 TTATTTTATTTTATTT-T
1 TTATATTATTTTATTTAT
464727 TTATATTA-TTTATTTAT
1 TTATATTATTTTATTTAT
464744 TTATTTCATTTATTTTATTTAT
1 TTA--T-A-TTATTTTATTTAT
464766 TTAT-TTATT
1 TTATATTATT
464775 CATTTTTTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
16 7 0.17
17 16 0.39
19 1 0.02
20 2 0.05
21 3 0.07
22 12 0.29
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATATTATTTTATTTAT
Found at i:464741 original size:4 final size:4
Alignment explanation
Indices: 464714--464779 Score: 80
Period size: 4 Copynumber: 15.8 Consensus size: 4
464704 ATACCATTAT
464714 TTTA TTTTA TTT- TTTA TATTA TTTA TTTA TTTA TTTCA TTTA TTTTA
1 TTTA -TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTT-A TTTA -TTTA
*
464761 TTTA TTTA TTTA TTCA TTT
1 TTTA TTTA TTTA TTTA TTT
464780 TTTGGGTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
3 3 0.05
4 36 0.65
5 16 0.29
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:464940 original size:2 final size:2
Alignment explanation
Indices: 464935--464965 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
464925 TTCCTAACGT
464935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
464966 CATAATGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:465260 original size:25 final size:24
Alignment explanation
Indices: 465239--465287 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
465229 TTCGTTTTCT
* *
465239 TTTGTTTCTATTTTTTTAGTTTTA
1 TTTGATTCCATTTTTTTAGTTTTA
465263 TTTGATTCCA-TTTTTTA-TTTTA
1 TTTGATTCCATTTTTTTAGTTTTA
465285 TTT
1 TTT
465288 TCATTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 8 0.35
23 7 0.30
24 8 0.35
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.73
Consensus pattern (24 bp):
TTTGATTCCATTTTTTTAGTTTTA
Found at i:465285 original size:5 final size:5
Alignment explanation
Indices: 465275--465336 Score: 65
Period size: 5 Copynumber: 12.4 Consensus size: 5
465265 TGATTCCATT
* * *
465275 TTTTA TTTTA TTTTCA TTTTCA TCTTA TTCTA TTTTA TTTTA -TTTA ATTTA
1 TTTTA TTTTA TTTT-A TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
465326 -TTTA TTTTA TT
1 TTTTA TTTTA TT
465337 ATTTTTCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 8 0.16
5 32 0.64
6 10 0.20
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:465325 original size:9 final size:9
Alignment explanation
Indices: 465276--465341 Score: 62
Period size: 9 Copynumber: 6.9 Consensus size: 9
465266 GATTCCATTT
465276 TTTATTTTA
1 TTTATTTTA
465285 TTTTCATTTTCA
1 -TTT-ATTTT-A
*
465297 TCTTATTCTA
1 T-TTATTTTA
465307 TTTTATTTTA
1 -TTTATTTTA
*
465317 TTTAATTTA
1 TTTATTTTA
465326 TTTATTTTA
1 TTTATTTTA
465335 -TTATTTT
1 TTTATTTT
465342 TCTTTTTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
8 7 0.15
9 16 0.33
10 11 0.23
11 11 0.23
12 3 0.06
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:465365 original size:54 final size:55
Alignment explanation
Indices: 465215--465367 Score: 127
Period size: 54 Copynumber: 2.8 Consensus size: 55
465205 ATTTTATAAT
* * * *
465215 TTTATTTT-CTATTTTTCGTTTTCTTTTGTTTCTATTTTTTTAGTTTTATTTGATTCCA
1 TTTATTTTATTATTTTTCATTTTCTTTT-TTTC--CTTTTTTA-TTTTATTTAATTCCA
* * * * *
465273 -TT-TTTTATTTTATTTTCATTTTCATCTTATT-CTATTTTATTTTATTTAATT-TA
1 TTTATTTTATTAT-TTTTCATTTTC-TTTTTTTCCTTTTTTATTTTATTTAATTCCA
*
465326 TTTATTTTATTATTTTTCTTTTTCTTTTTTTCCTTTTTTATT
1 TTTATTTTATTATTTTTCATTTTCTTTTTTTCCTTTTTTATT
465368 ATTTAGCTAC
Statistics
Matches: 75, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
53 6 0.08
54 32 0.43
55 14 0.19
56 4 0.05
57 4 0.05
58 12 0.16
59 3 0.04
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (55 bp):
TTTATTTTATTATTTTTCATTTTCTTTTTTTCCTTTTTTATTTTATTTAATTCCA
Found at i:466647 original size:16 final size:16
Alignment explanation
Indices: 466626--466656 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
466616 AAATTAAAAA
466626 ATATTAAATATTAAAC
1 ATATTAAATATTAAAC
*
466642 ATATTATATATTAAA
1 ATATTAAATATTAAA
466657 TACATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTAAATATTAAAC
Found at i:467528 original size:21 final size:21
Alignment explanation
Indices: 467502--467554 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
467492 GTTTCCAGAT
467502 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
467523 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
467544 TCGCAATGCGA
1 TCGCAACGCGA
467555 TTTACATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:467615 original size:42 final size:40
Alignment explanation
Indices: 467563--467846 Score: 361
Period size: 42 Copynumber: 6.9 Consensus size: 40
467553 GATTTACATA
* * *
467563 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATT--CGTTGCGATAGTCGAAG
*
467605 TTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
467645 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTCGAAG
* **
467687 TTCGCGTTGCGATTTTCCAAATTATTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
* * * *
467727 TTGGCGTTGCGATTTTTCAAATTCGTTGCGTTAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
* * *
467767 TTCGCATTGCGATTTATTCAAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTCGAAG
*
467809 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTC
467847 CAAAATCGCA
Statistics
Matches: 217, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 99 0.46
42 118 0.54
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (40 bp):
TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:467700 original size:82 final size:82
Alignment explanation
Indices: 467588--467846 Score: 414
Period size: 82 Copynumber: 3.2 Consensus size: 82
467578 TCCAAGTTCG
467588 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
467653 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
** *
467670 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTATTTGCGATAGTCGAAGTTGGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
467735 GCGATTT-TT-CAAATT
66 GCGATTTATTCCAAATT
* * * * *
467750 CGTTGCGTTAGTCGAAGTTCGCATTGCGATTTATTCAAAATTCGTTGCGATAGTCCAAGTTCGCA
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
467815 TTGCGATTTATTCCAAATT
64 TTGCGATTTATTCCAAATT
467834 CGTTGCGATAGTC
1 CGTTGCGATAGTC
467847 CAAAATCGCA
Statistics
Matches: 161, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
80 33 0.20
81 4 0.02
82 104 0.65
83 2 0.01
84 18 0.11
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATT
Found at i:467728 original size:122 final size:124
Alignment explanation
Indices: 467589--467846 Score: 421
Period size: 122 Copynumber: 2.1 Consensus size: 124
467579 CCAAGTTCGC
*
467589 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTG
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCATTG
* * *
467654 CGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTA
66 CGATTTATTCAAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTA
* * * *
467711 TTTGCGATAGTCGAAGTTGGCGTTGCGATTTTTCAAATTCGTTGCGTTAGTCGAAGTTCGCATTG
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCATTG
*
467776 CGATTTATTCAAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTC
66 CGATTTATTCAAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTA
467835 GTTGCGATAGTC
1 GTTGCGATAGTC
467847 CAAAATCGCA
Statistics
Matches: 124, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
122 102 0.82
123 2 0.02
124 20 0.16
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (124 bp):
GTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCATTG
CGATTTATTCAAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTA
Found at i:467849 original size:42 final size:42
Alignment explanation
Indices: 467588--467846 Score: 404
Period size: 40 Copynumber: 6.3 Consensus size: 42
467578 TCCAAGTTCG
467588 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
467628 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
467670 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
** *
467710 ATTTGCGATAGTCGAAGTTGGCGTTGCGATTT-TT-CAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
467750 CGTTGCGTTAGTCGAAGTTCGCATTGCGATTTATTCAAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
467792 CGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
467834 CGTTGCGATAGTC
1 CGTTGCGATAGTC
467847 CAAAATCGCA
Statistics
Matches: 202, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
40 97 0.48
41 10 0.05
42 95 0.47
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:468309 original size:41 final size:41
Alignment explanation
Indices: 468252--468333 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
468242 TACAATTGGG
468252 AACATAATCTGATCCCAAAGACTCACTTCTTCCTTCAAGCC
1 AACATAATCTGATCCCAAAGACTCACTTCTTCCTTCAAGCC
468293 AACATAATCTGATCCCAAAGACTCACTTCTTCCTTCAAGCC
1 AACATAATCTGATCCCAAAGACTCACTTCTTCCTTCAAGCC
468334 CTATTCTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (41 bp):
AACATAATCTGATCCCAAAGACTCACTTCTTCCTTCAAGCC
Found at i:470696 original size:42 final size:41
Alignment explanation
Indices: 470659--470743 Score: 77
Period size: 40 Copynumber: 2.0 Consensus size: 41
470649 ATATTTTATT
470659 TTTATATACATGTGTTATTAGTATTTTATTATTTA-TTTA-T
1 TTTATATACATGTGTTATTA-TATTTTATTATTTATTTTATT
* * *
470699 TTTATTTATATGT-TATATTATATATATATATATTTTATTTTATT
1 TTTATATACATGTGT-TATTATAT-TTTAT-TA-TTTATTTTATT
470743 T
1 T
470744 CTTAATATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
39 4 0.11
40 20 0.56
41 2 0.06
42 4 0.11
43 4 0.11
44 2 0.06
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (41 bp):
TTTATATACATGTGTTATTATATTTTATTATTTATTTTATT
Found at i:470701 original size:16 final size:16
Alignment explanation
Indices: 470680--470737 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
470670 GTGTTATTAG
*
470680 TATTTTATTATTTATT
1 TATTTTATTATATATT
470696 TATTTTATT-TATATGT
1 TATTTTATTATATAT-T
* *
470712 TATATTATATATATATA
1 TATTTTAT-TATATATT
470729 TATTTTATT
1 TATTTTATT
470738 TTATTTCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 4 0.11
16 18 0.51
17 8 0.23
18 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TATTTTATTATATATT
Found at i:471038 original size:14 final size:15
Alignment explanation
Indices: 471009--471045 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
470999 TTGTTAGTTA
*
471009 TTTATTTTTCTCTTC
1 TTTATTTTACTCTTC
471024 TTTATTTTACT-TTC
1 TTTATTTTACTCTTC
471038 TTTATTTT
1 TTTATTTT
471046 CAATTTATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTACTCTTC
Found at i:474230 original size:21 final size:21
Alignment explanation
Indices: 474204--474243 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
474194 ATACTTTGCA
474204 TTTTATATATTT-CATGTTTAC
1 TTTTATAT-TTTCCATGTTTAC
474225 TTTTATATTTTCCATGTTT
1 TTTTATATTTTCCATGTTT
474244 TTACATTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTATATTTTCCATGTTTAC
Found at i:481359 original size:14 final size:15
Alignment explanation
Indices: 481333--481376 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
481323 ATCTTAAGTC
* *
481333 GAAAAAGGGAAAAAG
1 GAAAAAGAGAAAAAA
481348 GAAAAAGA-AAAAAA
1 GAAAAAGAGAAAAAA
*
481362 TAAAAAGAGAAAAAA
1 GAAAAAGAGAAAAAA
481377 ACGTTTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
GAAAAAGAGAAAAAA
Found at i:481437 original size:16 final size:15
Alignment explanation
Indices: 481416--481458 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
481406 CCTAAATTGA
*
481416 AAAAAGGAAAAAAGAG
1 AAAAA-GAAAAAAAAG
481432 AAAAAGAACAAAAAAG
1 AAAAAGAA-AAAAAAG
481448 AAAAAGAAAAA
1 AAAAAGAAAAA
481459 TAAGGTGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:481458 original size:81 final size:80
Alignment explanation
Indices: 481300--481458 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 80
481290 AGTACTTCGC
* * * *
481300 TTAGGATGAAAACCCGAAAGGGCATCTTAAGTCGAAAAAGGGAAAAAGGAAAAAGAAAAAAATAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCGAAAAAGGAAAAAAGGAAAAAGAAAAAAATAA
481365 AAAGAGAAAAAAACGT
66 AAAGAG-AAAAAACGT
*
481381 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGGAAAAAAGAGAAAAAGAACAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATCG-AAAAAGGAAAAAAG-GAAAAAGAA-AAAAA
481446 -AGAAAA-AGAAAAA
63 TA-AAAAGAGAAAAA
481459 TAAGGTGGGT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
81 30 0.43
82 18 0.26
83 12 0.17
84 9 0.13
ACGTcount: A:0.60, C:0.09, G:0.21, T:0.09
Consensus pattern (80 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATCGAAAAAGGAAAAAAGGAAAAAGAAAAAAATAA
AAAGAGAAAAAACGT
Found at i:482764 original size:110 final size:110
Alignment explanation
Indices: 482564--482821 Score: 294
Period size: 110 Copynumber: 2.4 Consensus size: 110
482554 GCTTCTCAAT
* * *
482564 TTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* * * * *
482629 CGATGAAGGGGCGGTTGATTGTCAACCAACAACTTTTCAGTTTCA
66 CGACGAAGGGGCGGCTGACTATCAACAAACAACTTTTCAGTTTCA
* * * *
482674 TTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
*
482739 C-AGCGAAGGGGCGGCTGACTATCAACAAACAA-TTTCCCAG-TTC-
66 CGA-CGAAGGGGCGGCTGACTATCAACAAACAACTTT-TCAGTTTCA
* * ** *
482782 -T-AGAACCAATTTCAACTTCACGACGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAGACTC
482822 GGAGTAATAC
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
106 32 0.25
107 1 0.01
109 7 0.06
110 86 0.68
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACAAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CGACGAAGGGGCGGCTGACTATCAACAAACAACTTTTCAGTTTCA
Found at i:484847 original size:2 final size:2
Alignment explanation
Indices: 484835--484866 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
484825 ATTTATATGT
484835 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
484867 GTATTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:485172 original size:14 final size:15
Alignment explanation
Indices: 485143--485179 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
485133 TTGTTAGTTA
*
485143 TTTATTTTTCTCTTC
1 TTTATTTTACTCTTC
485158 TTTATTTTACT-TTC
1 TTTATTTTACTCTTC
485172 TTTATTTT
1 TTTATTTT
485180 CAATTTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTACTCTTC
Found at i:495965 original size:21 final size:21
Alignment explanation
Indices: 495941--495980 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
495931 TTTATTTTAT
495941 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
495962 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
495981 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:496032 original size:33 final size:32
Alignment explanation
Indices: 495975--496071 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 32
495965 TTTGTTTCAA
495975 TTATCGAACTT-GAAG-TTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
496005 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAG-TTTTAAGTATTTGAAT
* *
496038 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGT-TTTAAGTATTTGAAT
496071 T
1 T
496072 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.18
31 4 0.07
32 1 0.02
33 45 0.74
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (32 bp):
TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
Found at i:496327 original size:21 final size:21
Alignment explanation
Indices: 496301--496357 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
496291 TGGAGCGTGG
*
496301 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
* *
496322 GGGAATCGATTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
496343 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
496358 AAGTGTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:496552 original size:14 final size:14
Alignment explanation
Indices: 496522--496575 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
496512 ATCTAGAATA
*
496522 TTAAAATCGGTTTTT
1 TTAAAACCGG-TTTT
*
496537 TTATAACCGGTTTT
1 TTAAAACCGGTTTT
496551 TTAAAAAACCGGTTTT
1 TT--AAAACCGGTTTT
496567 TTAAAACCG
1 TTAAAACCG
496576 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 13 0.38
15 8 0.24
16 13 0.38
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (14 bp):
TTAAAACCGGTTTT
Found at i:496560 original size:16 final size:16
Alignment explanation
Indices: 496541--496572 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
496531 GTTTTTTTAT
496541 AACCGGTTTTTTAAAA
1 AACCGGTTTTTTAAAA
496557 AACCGGTTTTTTAAAA
1 AACCGGTTTTTTAAAA
496573 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
AACCGGTTTTTTAAAA
Found at i:496692 original size:15 final size:17
Alignment explanation
Indices: 496666--496697 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
496656 TTCTATGAGA
496666 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
496682 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
496698 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:502804 original size:57 final size:57
Alignment explanation
Indices: 502743--502860 Score: 218
Period size: 57 Copynumber: 2.1 Consensus size: 57
502733 TATCACGAAA
*
502743 AATTAACTATGTTCAATCAATCAAATCTATCATTGAATTTTATTTGAACATATTATT
1 AATTAACTATGTTCAATCAATCAAATCTATCATTGAACTTTATTTGAACATATTATT
*
502800 AATTAACTATGTTCAATCAATCAAATCTATTATTGAACTTTATTTGAACATATTATT
1 AATTAACTATGTTCAATCAATCAAATCTATCATTGAACTTTATTTGAACATATTATT
502857 AATT
1 AATT
502861 TTCTCTAAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (57 bp):
AATTAACTATGTTCAATCAATCAAATCTATCATTGAACTTTATTTGAACATATTATT
Found at i:512708 original size:23 final size:23
Alignment explanation
Indices: 512681--512725 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
512671 CGAAAAACAC
*
512681 ATAGAATTGTCCATAAGGACCAT
1 ATAGAATTGCCCATAAGGACCAT
*
512704 ATAGAATTGCCCCTAAGGACCA
1 ATAGAATTGCCCATAAGGACCA
512726 CATATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (23 bp):
ATAGAATTGCCCATAAGGACCAT
Found at i:519034 original size:21 final size:21
Alignment explanation
Indices: 519010--519072 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
519000 CTAGTCGTTG
*
519010 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
**
519031 CAG-CAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
519051 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
519072 C
1 C
519073 TAATTGCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.43
21 19 0.54
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.21
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:519140 original size:22 final size:22
Alignment explanation
Indices: 519094--519171 Score: 108
Period size: 22 Copynumber: 3.6 Consensus size: 22
519084 GGTGTTTGAT
519094 TGCATGGATGCAC---TGCATGG
1 TGCATGGATGCACTAGTGCA-GG
**
519114 TGCATCCATGCACTAGTGCAGG
1 TGCATGGATGCACTAGTGCAGG
519136 TGCATGGATGCACTAGTGCAGG
1 TGCATGGATGCACTAGTGCAGG
519158 TGCATGGATGCACT
1 TGCATGGATGCACT
519172 GCAGGGATGC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.22
22 36 0.71
23 4 0.08
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (22 bp):
TGCATGGATGCACTAGTGCAGG
Found at i:519213 original size:21 final size:21
Alignment explanation
Indices: 519160--519213 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
519150 AGTGCAGGTG
*
519160 CATGGATGCACTGCAGGGATG
1 CATGGATGCACTGCAGGGATA
* *
519181 CATAGATACACTGCAAGGG-TA
1 CATGGATGCACTGC-AGGGATA
519202 CATGGATGCACT
1 CATGGATGCACT
519214 TTGACACCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
CATGGATGCACTGCAGGGATA
Found at i:519314 original size:29 final size:29
Alignment explanation
Indices: 519293--519350 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
519283 AAACTTTGAA
519293 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
519322 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
519351 TGCCTGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:519340 original size:30 final size:30
Alignment explanation
Indices: 519293--519352 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
519283 AAACTTTGAA
519293 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
519322 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
519353 CCTGAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:520626 original size:20 final size:19
Alignment explanation
Indices: 520590--520636 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
520580 CTAAATCCTT
*
520590 TTTCAAAATTTCATTTTGCC
1 TTTCAAAATCTCATTTTG-C
*
520610 TTTCAAAATCT-ATTTTTGT
1 TTTCAAAATCTCA-TTTTGC
520629 TTTCAAAA
1 TTTCAAAA
520637 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:521961 original size:20 final size:20
Alignment explanation
Indices: 521932--522005 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
521922 GTAGCCTTCG
*
521932 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
**
521952 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
* *
521973 TGCATCGATGCACAGAAGAA
1 TGCATCGATGCACAGCAGGA
521993 TGCATCGATGCAC
1 TGCATCGATGCAC
522006 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 28 0.61
21 18 0.39
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:521969 original size:41 final size:41
Alignment explanation
Indices: 521924--522005 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
521914 TAGCCATTGT
* * *
521924 AGCCTTCG-TGCATGGATGCACAGCAGGATGCATCGATGCAC
1 AGCCTT-GATGCATCGATGCACAGAAGAATGCATCGATGCAC
521965 AGCCTTGATGCATCGATGCACAGAAGAATGCATCGATGCAC
1 AGCCTTGATGCATCGATGCACAGAAGAATGCATCGATGCAC
522006 TAATTGCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.20
Consensus pattern (41 bp):
AGCCTTGATGCATCGATGCACAGAAGAATGCATCGATGCAC
Found at i:521976 original size:21 final size:21
Alignment explanation
Indices: 521924--521987 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
521914 TAGCCATTGT
*
521924 AGCCTTCG-TGCATGGATGCAC
1 AGCCTT-GATGCATCGATGCAC
**
521945 AG-CAGGATGCATCGATGCAC
1 AGCCTTGATGCATCGATGCAC
521965 AGCCTTGATGCATCGATGCAC
1 AGCCTTGATGCATCGATGCAC
521986 AG
1 AG
521988 AAGAATGCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 20 0.56
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.20
Consensus pattern (21 bp):
AGCCTTGATGCATCGATGCAC
Found at i:522126 original size:21 final size:21
Alignment explanation
Indices: 522026--522124 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
522016 CGGTGTTTGA
*
522026 GTGCATGGATGCACTGTA-TG
1 GTGCATGGATGCACTGTAGGG
* *
522046 GTGCATCGATGCACTAGT-GCAG
1 GTGCATGGATGCACT-GTAG-GG
*
522068 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGTAGGG
* *
522089 ATGCATGGATGCACTTTAGGG
1 GTGCATGGATGCACTGTAGGG
522110 GTGCATGGATGCACT
1 GTGCATGGATGCACT
522125 TTGATACCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 14 0.21
21 36 0.55
22 16 0.24
ACGTcount: A:0.21, C:0.18, G:0.35, T:0.25
Consensus pattern (21 bp):
GTGCATGGATGCACTGTAGGG
Found at i:522225 original size:29 final size:30
Alignment explanation
Indices: 522193--522261 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
522183 GAAACCTTTT
*
522193 AAAAC-TTTAAATAAATTCAA-TTAAGTTCA
1 AAAACATTT-AATAAATTCAATTTAAGTCCA
**
522222 AAAACATTTTGTAAATTCAATTTAAGTCCA
1 AAAACATTTAATAAATTCAATTTAAGTCCA
522252 AAAACCATTT
1 AAAA-CATTT
522262 TGCCTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.41
30 15 0.44
31 5 0.15
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAACATTTAATAAATTCAATTTAAGTCCA
Found at i:522254 original size:30 final size:30
Alignment explanation
Indices: 522204--522263 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
522194 AAACTTTAAA
*
522204 TAAATTCAATTAAGTTCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
522233 TAAATTCAATTTAAGTCCAAAAACCATTTTG
1 TAAATTCAA-TTAAGTCCAAAAACCATTTTG
522264 CCTTAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 12 0.43
31 7 0.25
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:526842 original size:6 final size:6
Alignment explanation
Indices: 526825--526910 Score: 70
Period size: 6 Copynumber: 14.2 Consensus size: 6
526815 TAATTGGACC
* *
526825 TAAAAA TGAAAA TAAAAA TAAAAA T--AAA -AAAAA TAAAAA TAGAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
* * *
526870 TAGAAA TAGAAA TAGAAA TAAATAAA TAAATAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA T-AA-AAA T-AA-AAA TAAAAA T
526911 GTATATATTT
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
4 3 0.04
5 3 0.04
6 50 0.70
7 3 0.04
8 12 0.17
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:526848 original size:18 final size:18
Alignment explanation
Indices: 526825--526891 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
526815 TAATTGGACC
526825 TAAAAAT-GAAAATAAAAA
1 TAAAAATAG-AAATAAAAA
526843 TAAAAAT--AAA-AAAAA
1 TAAAAATAGAAATAAAAA
*
526858 TAAAAATAGAAATAGAAA
1 TAAAAATAGAAATAAAAA
*
526876 TAGAAATAGAAATAAA
1 TAAAAATAGAAATAAA
526892 TAAATAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
15 12 0.28
16 3 0.07
17 3 0.07
18 25 0.58
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (18 bp):
TAAAAATAGAAATAAAAA
Found at i:526910 original size:18 final size:16
Alignment explanation
Indices: 526834--526910 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 16
526824 CTAAAAATGA
526834 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
526850 AAA-AAAAATAAAAAT
1 AAATAAAAATAAAAAT
* *
526865 AGAAATAGAAATAGAAATAG
1 --AAATAAAAATA-AAA-AT
*
526885 AAATAAATAA-ATAAAT
1 AAATAAA-AATAAAAAT
526901 AAATAAAAAT
1 AAATAAAAAT
526911 GTATATATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
15 14 0.29
16 11 0.22
17 5 0.10
18 13 0.27
19 5 0.10
20 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:527057 original size:27 final size:29
Alignment explanation
Indices: 527009--527071 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 29
526999 TATATACTAT
* **
527009 ATATATTTTCAAAAATGTTTTTTTAAACC
1 ATATATTTTCAAAAACGTTTTTCAAAACC
* *
527038 ATATATTTT-TAAAACG-TTTTCAAAACT
1 ATATATTTTCAAAAACGTTTTTCAAAACC
527065 ATATATT
1 ATATATT
527072 ATATACTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 15 0.52
28 5 0.17
29 9 0.31
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.48
Consensus pattern (29 bp):
ATATATTTTCAAAAACGTTTTTCAAAACC
Found at i:527220 original size:36 final size:36
Alignment explanation
Indices: 527038--527226 Score: 213
Period size: 38 Copynumber: 5.2 Consensus size: 36
527028 TTTTTAAACC
* *
527038 ATATATTTT-TAAAACGTTTTCAAAACTATATAT-T
1 ATATATTTTCAAAAATGTTTTCAAAACTATATATAT
* * *
527072 ATATACTTT-AAAAATATTTTCAAAATTATATATTAT
1 ATATATTTTCAAAAATGTTTTCAAAACTATATA-TAT
*
527108 ATATATTTTCAAAAATGTTTTCAAAATTATATATTAT
1 ATATATTTTCAAAAATGTTTTCAAAACTATATA-TAT
* *
527145 ATATATTTTCGAACAATATTTTCAAAACTATATACTAT
1 ATATATTTTC-AAAAATGTTTTCAAAACTATATA-TAT
* *
527183 ATATATTTTTCAAAAACGTATTCAAAACTATATTATAT
1 ATATA-TTTTCAAAAATGTTTTCAAAACTATA-TATAT
527221 ATATAT
1 ATATAT
527227 ATATATATAT
Statistics
Matches: 134, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.20
35 1 0.01
36 9 0.07
37 37 0.28
38 53 0.40
39 7 0.05
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (36 bp):
ATATATTTTCAAAAATGTTTTCAAAACTATATATAT
Found at i:527594 original size:3 final size:3
Alignment explanation
Indices: 527577--527654 Score: 97
Period size: 3 Copynumber: 26.0 Consensus size: 3
527567 TTGAAAAAAC
* *
527577 ATT ATT AATT A-T ATT ATT ATT ATA ATT AATT A-A ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
*
527622 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
527655 TAATACATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 3 0.05
3 56 0.86
4 6 0.09
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:533099 original size:24 final size:23
Alignment explanation
Indices: 533072--533155 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 23
533062 CCGACTTGAG
* *
533072 TTCTGTTCTGATACAGTACCTGAA
1 TTCTGTTCTGATACTG-ATCTGAA
* * *
533096 TTCTGTTATGATTTCTGATCTGGA
1 TTCTGTTCTGA-TACTGATCTGAA
533120 TTCTGTTCTGATATCTGATCTGAA
1 TTCTGTTCTGATA-CTGATCTGAA
*
533144 TTCTGTTTTGAT
1 TTCTGTTCTGAT
533156 TTCTGATATC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 1 0.02
24 45 0.92
25 3 0.06
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (23 bp):
TTCTGTTCTGATACTGATCTGAA
Found at i:533111 original size:12 final size:12
Alignment explanation
Indices: 533091--533160 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
533081 GATACAGTAC
*
533091 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
533103 ATGATTTCTGAT
1 CTGATTTCTGTT
533115 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
533127 CTGATATCTGAT
1 CTGATTTCTGTT
*
533139 CTGAATTCTGTT
1 CTGATTTCTGTT
*
533151 TTGATTTCTG
1 CTGATTTCTG
533161 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:533160 original size:24 final size:24
Alignment explanation
Indices: 533091--533162 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
533081 GATACAGTAC
533091 CTGAATTCTGTTATGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
533115 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
*
533139 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
533163 ATCTCCGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:534962 original size:148 final size:150
Alignment explanation
Indices: 534779--535079 Score: 498
Period size: 148 Copynumber: 2.0 Consensus size: 150
534769 CGGATCGGGT
* * * *
534779 TTTTTGTAAGTGTGATATTCGGATCGGGTTCGGGTTTAGGGTGAAAAAAACCGTACCGAGACGAA
1 TTTTTGTAAGTGTGATATTCGGATCGAGTTCGGGTTTAAGGTGAAAAAAACCGGACCGACACGAA
*
534844 AATATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTTATTAAAT-AAAATATTTTTTTA
66 AATATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTTATTAAATAAAAATACTTTTTTA
534908 TTATTTCGGGTCGGGTCGGA
131 TTATTTCGGGTCGGGTCGGA
* *
534928 TTTTT-TAAGTGTGATATTCGGGTCGAGTTCGGGTTTAAGGTGAAAAAAACCGGACCGACCCGAA
1 TTTTTGTAAGTGTGATATTCGGATCGAGTTCGGGTTTAAGGTGAAAAAAACCGGACCGACACGAA
* * *
534992 AATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATACTTTTTTA
66 AATATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTTATTAAATAAAAATACTTTTTTA
535057 TTATTTCGGGTCGGGTCGGA
131 TTATTTCGGGTCGGGTCGGA
535077 TTT
1 TTT
535080 CTAATTCATA
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
148 100 0.71
149 41 0.29
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (150 bp):
TTTTTGTAAGTGTGATATTCGGATCGAGTTCGGGTTTAAGGTGAAAAAAACCGGACCGACACGAA
AATATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTTATTAAATAAAAATACTTTTTTA
TTATTTCGGGTCGGGTCGGA
Found at i:535158 original size:27 final size:28
Alignment explanation
Indices: 535128--535190 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
535118 TTTTGTTCGG
535128 TCGGGTCGGG-TTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
535155 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
535183 TCGGGTCG
1 TCGGGTCG
535191 AGTCGGGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.29
28 25 0.71
ACGTcount: A:0.13, C:0.10, G:0.35, T:0.43
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:535338 original size:27 final size:28
Alignment explanation
Indices: 535306--535370 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
535296 AACTTTATTT
535306 TATTCGGGTCGGG-TTTTTTAAGTGTGA
1 TATTCGGGTCGGGTTTTTTTAAGTGTGA
535333 TATTCGGGTCGGGTTTTTTTAAGTGTGA
1 TATTCGGGTCGGGTTTTTTTAAGTGTGA
535361 TATTCGGGTC
1 TATTCGGGTC
535371 AGGTCGGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 13 0.35
28 24 0.65
ACGTcount: A:0.14, C:0.09, G:0.32, T:0.45
Consensus pattern (28 bp):
TATTCGGGTCGGGTTTTTTTAAGTGTGA
Found at i:535369 original size:181 final size:188
Alignment explanation
Indices: 535062--535434 Score: 562
Period size: 181 Copynumber: 2.0 Consensus size: 188
535052 TTTTATTATT
** * *
535062 TCGGGTCGGGTCGGATTTCTAATTCATATATTTGGGTTGGGTCGGATGAAATTTTATTTTGTTCG
1 TCGGGTCGGGTCGGATTTCTAATTCATATA-TT--GTCAGGTCGGATGAAACTTTATTTTGAT--
535127 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGATATTC-G-GGTC
61 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGAGGTC
*
535190 GAGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCG-AAAATATATATAATTCGGG
126 GAGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAAAAATATATAATTCGGG
535252 TCGGGTCGGGTCGGATTTCTAATTCATATA-T-TCAGGTCGGATGAAACTTTATTTT-AT-TCGG
1 TCGGGTCGGGTCGGATTTCTAATTCATATATTGTCAGGTCGGATGAAACTTTATTTTGATGTCGG
*
535313 GTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGG
66 GTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGATATTC-GG--AGGTCGA
*
535378 GTCGGGTTCGGGTTTAGGGTGAAAAAACCCGGACCGACCCGAAAAAAATATATAATT
128 GTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAAAAATATATAATT
535435 TTACCTTATA
Statistics
Matches: 170, Mismatches: 7, Indels: 15
0.89 0.04 0.08
Matches are distributed among these distances:
181 57 0.34
183 1 0.01
184 1 0.01
185 21 0.12
186 45 0.26
187 14 0.08
188 1 0.01
190 30 0.18
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (188 bp):
TCGGGTCGGGTCGGATTTCTAATTCATATATTGTCAGGTCGGATGAAACTTTATTTTGATGTCGG
GTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGAGGTCGAGTC
GGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAAAAATATATAATTCGGG
Found at i:535959 original size:18 final size:16
Alignment explanation
Indices: 535916--535960 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
535906 TATGGAATTG
535916 GATTTCAATTCCTACA
1 GATTTCAATTCCTACA
535932 GA-TTCAAATTCCTTCACA
1 GATTTC-AATTCC-T-ACA
535950 GATTTCAATTC
1 GATTTCAATTC
535961 TCTCATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.12
16 8 0.32
17 1 0.04
18 10 0.40
19 3 0.12
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (16 bp):
GATTTCAATTCCTACA
Found at i:540372 original size:18 final size:17
Alignment explanation
Indices: 540349--540383 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
540339 AATAACACTA
*
540349 TAAATAATTTTATAATTT
1 TAAATAATATT-TAATTT
540367 TAAATAATATTTAATTT
1 TAAATAATATTTAATTT
540384 ATTCAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATAATATTTAATTT
Found at i:548140 original size:24 final size:24
Alignment explanation
Indices: 548113--548184 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
548103 GTAAACGGAG
548113 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
548137 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATTC
*
548161 AGATCAG-AATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
548184 A
1 A
548185 GGTAACGTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 14 0.34
24 27 0.66
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:548144 original size:12 final size:12
Alignment explanation
Indices: 548117--548184 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
548107 ACGGAGATAT
*
548117 CAGAAATCAAAA
1 CAGAATTCAAAA
* *
548129 CAGAATTCATAT
1 CAGAATTCAAAA
*
548141 CAG-ATATCAGAA
1 CAGAAT-TCAAAA
* * *
548153 CAGAATCCAGAT
1 CAGAATTCAAAA
548165 CAGAA-TCAAAA
1 CAGAATTCAAAA
548176 CAGAATTCA
1 CAGAATTCA
548185 GGTAACGTAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
11 10 0.23
12 31 0.72
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.12, T:0.18
Consensus pattern (12 bp):
CAGAATTCAAAA
Found at i:549332 original size:17 final size:18
Alignment explanation
Indices: 549304--549337 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
549294 TGCCATCCGG
549304 TCTTATTATTTAATTCAA
1 TCTTATTATTTAATTCAA
*
549322 TCTTA-TATTTACTTCA
1 TCTTATTATTTAATTCA
549338 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTATTATTTAATTCAA
Found at i:550657 original size:13 final size:13
Alignment explanation
Indices: 550639--550681 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
550629 GTCGGTCAAT
550639 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
550652 GGTCAACGGTTCG
1 GGTCAACGGGTCG
*
550665 GGTCAACAGGTCG
1 GGTCAACGGGTCG
550678 GGTC
1 GGTC
550682 GGGTCGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.16, C:0.23, G:0.42, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:552750 original size:24 final size:23
Alignment explanation
Indices: 552710--552816 Score: 110
Period size: 24 Copynumber: 4.6 Consensus size: 23
552700 GGTAAACGGG
*
552710 ATATCAGAATCAAAACAGAATTC
1 ATATCAGAATCAGAACAGAATTC
*
552733 ATATCAGATATCAGAACAGAATCC
1 ATATCAGA-ATCAGAACAGAATTC
*
552757 AGATCAGAATCAGAACAGAATTC
1 ATATCAGAATCAGAACAGAATTC
* * *
552780 AGGTAAC-GTATCAGAACATAATTC
1 A--TATCAGAATCAGAACAGAATTC
*
552804 AT-TCGGAATCAGA
1 ATATCAGAATCAGA
552817 TAAAATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
21 1 0.01
22 8 0.11
23 23 0.33
24 36 0.51
25 2 0.03
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (23 bp):
ATATCAGAATCAGAACAGAATTC
Found at i:552752 original size:12 final size:11
Alignment explanation
Indices: 552714--552777 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
552704 AACGGGATAT
*
552714 CAGAATCAAAA
1 CAGAATCAGAA
* *
552725 CAGAATTCATAT
1 CAGAA-TCAGAA
552737 CAGATATCAGAA
1 CAGA-ATCAGAA
*
552749 CAGAATCCAGAT
1 CAGAAT-CAGAA
552761 CAGAATCAGAA
1 CAGAATCAGAA
552772 CAGAAT
1 CAGAAT
552778 TCAGGTAACG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 17 0.39
12 26 0.59
13 1 0.02
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (11 bp):
CAGAATCAGAA
Found at i:554106 original size:18 final size:18
Alignment explanation
Indices: 554085--554120 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
554075 ATGCCATCCG
*
554085 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
554103 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
554121 GTTTTTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:555411 original size:18 final size:19
Alignment explanation
Indices: 555383--555423 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
555373 GCCGGTCAAC
555383 GGTTCGGGTCAACAGGTCG
1 GGTTCGGGTCAACAGGTCG
*
555402 GGTT-GGGTCAACGGGTCG
1 GGTTCGGGTCAACAGGTCG
555420 GGTT
1 GGTT
555424 AACGGGTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.12, C:0.17, G:0.46, T:0.24
Consensus pattern (19 bp):
GGTTCGGGTCAACAGGTCG
Found at i:555414 original size:31 final size:31
Alignment explanation
Indices: 555376--555440 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
555366 GGTCAACGCC
* * *
555376 GGTCAACGGTTCGGGTCAACAGGTCGGGTTG
1 GGTCAACGGGTCGGGTCAACAGGTCAGGTCG
* *
555407 GGTCAACGGGTCGGGTTAACGGGTCAGGTCG
1 GGTCAACGGGTCGGGTCAACAGGTCAGGTCG
555438 GGT
1 GGT
555441 TGGGTTATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.18, G:0.45, T:0.22
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACAGGTCAGGTCG
Found at i:560065 original size:81 final size:81
Alignment explanation
Indices: 559980--560132 Score: 245
Period size: 81 Copynumber: 1.9 Consensus size: 81
559970 ACCCAAAAGC
* * * *
559980 ATTTAGCCTTTCATCTAACT-TGCATGATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTA
1 ATTTAACCTTTCATCTAACTGT-CATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTA
560044 ATCTTTTACTTAAAGGT
65 ATCTTTTACTTAAAGGT
*
560061 ATTTAACCTTTCATCTAACTGTCATAATTGATACATTTCTGCCAAATGCACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGTCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAA
560126 TCTTTTA
66 TCTTTTA
560133 TTTAGAACAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 65 0.98
82 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTGTCATAATTGACACATTTCTGCCAAATGCACAACTAGGCCATTAA
TCTTTTACTTAAAGGT
Found at i:560532 original size:46 final size:46
Alignment explanation
Indices: 560478--560628 Score: 223
Period size: 46 Copynumber: 3.3 Consensus size: 46
560468 TTATTCGTTA
560478 ATTTCATTTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGC
* * *
560524 ATTTCATTTATGGC-TTTCTTTCATGCCTTAATGTATCATTTCATGA
1 ATTTCATTTATGGCATCT-TTTCATGCCTTAATGCATCATTTCATGC
* * * *
560570 ATTTTATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGC
560616 ATTTCATTTATGG
1 ATTTCATTTATGG
560629 ATTCATTTTA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
45 2 0.02
46 88 0.97
47 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (46 bp):
ATTTCATTTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGC
Found at i:565808 original size:46 final size:46
Alignment explanation
Indices: 565754--565904 Score: 223
Period size: 46 Copynumber: 3.3 Consensus size: 46
565744 TTATTCGTCA
* *
565754 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGT
1 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
* * *
565800 ATTTCATTTATGTCAT-ATTTTCATGCCTTAAAGCATCATTTCATGC
1 ATTTCATTTATGGCATCA-TTTCATGCCTTAATGCATCCTTTCATGC
* *
565846 ATTTTATTTATGGTATCATTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
565892 ATTTCATTTATGG
1 ATTTCATTTATGG
565905 ATTCGTTATA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
46 91 0.99
47 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.47
Consensus pattern (46 bp):
ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
Found at i:566702 original size:22 final size:21
Alignment explanation
Indices: 566649--566699 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
566639 GATACCCATA
*
566649 CCCGGATTTACCATTTTTCAG
1 CCCGGTTTTACCATTTTTCAG
*
566670 CCCGGTTTTACCATTTTTTAG
1 CCCGGTTTTACCATTTTTCAG
*
566691 CCCAGTTTT
1 CCCGGTTTT
566700 TACTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (21 bp):
CCCGGTTTTACCATTTTTCAG
Found at i:570059 original size:40 final size:40
Alignment explanation
Indices: 570004--570125 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
569994 TGCAGGTTTA
570004 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
570044 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
570084 TAATACACTTCGGTGTATATGCTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
570124 TA
1 TA
570126 GCACTACAGG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:576411 original size:40 final size:40
Alignment explanation
Indices: 576356--576477 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
576346 TGCAGGTTTA
*
576356 TAATACACTTCGGTGTATATGGTGGGCACGGCATTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACATTATGTG
*
576396 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACATTATGTG
* *
576436 TAATACACTTCGGTGTATATGGTGGGCACGACCTTTTGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACATTATGTG
576476 TA
1 TA
576478 GCACTACGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACATTATGTG
Found at i:576675 original size:47 final size:45
Alignment explanation
Indices: 576581--576706 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
576571 GTAACCATGC
* * *
576581 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * * *
576625 AAATAAGCTTACGAGATTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
576672 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
576707 AGATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.16
46 1 0.01
47 37 0.53
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:580297 original size:19 final size:19
Alignment explanation
Indices: 580273--580311 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
580263 GTAATCATCG
580273 ATGGTTCTCCTAACCCTCC
1 ATGGTTCTCCTAACCCTCC
580292 ATGGTTCTCCTAACCCTCC
1 ATGGTTCTCCTAACCCTCC
580311 A
1 A
580312 AGAAACCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.41, G:0.10, T:0.31
Consensus pattern (19 bp):
ATGGTTCTCCTAACCCTCC
Found at i:580794 original size:18 final size:18
Alignment explanation
Indices: 580771--580811 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
580761 AGACTCCAAA
580771 AGAAGAAAGAAGAAAAA-G
1 AGAAGAAAG-AGAAAAAGG
*
580789 AGAAGAACGAGAAAAAGG
1 AGAAGAAAGAGAAAAAGG
580807 AGAAG
1 AGAAG
580812 GTGAGAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAGAAAAAGG
Found at i:586503 original size:22 final size:22
Alignment explanation
Indices: 586451--586503 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
586441 TTAGCAATGA
*
586451 TACTAAAGTGCCTTGGCATCAT
1 TACTAAAGTGCATTGGCATCAT
** * **
586473 TACGGAAGTGCATTTGCATTGT
1 TACTAAAGTGCATTGGCATCAT
586495 TACTAAAGT
1 TACTAAAGT
586504 ATCTTAGCAC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (22 bp):
TACTAAAGTGCATTGGCATCAT
Done.