Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008072.1 Hibiscus syriacus cultivar Beakdansim tig00110570_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: 1263316
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 5
Found at i:363927 original size:20 final size:20
Alignment explanation
Indices: 363902--363939 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
363892 TCTAGGTTCG
363902 AATATCGATATTGGATGAAC
1 AATATCGATATTGGATGAAC
363922 AATATCGATATTGGATGA
1 AATATCGATATTGGATGA
363940 TTGGGACAAA
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:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (20 bp):
AATATCGATATTGGATGAAC
Found at i:366359 original size:15 final size:15
Alignment explanation
Indices: 366336--366411 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
366326 ATGATTATGC
*
366336 ATAACGTCACCATAT
1 ATAATGTCACCATAT
366351 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
* * **
366365 ATAGTGGCAAAACTA-
1 ATAATGTCACCA-TAT
*
366380 AAAATTGTCACCATAT
1 ATAA-TGTCACCATAT
366396 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
366410 AT
1 AT
366412 CGTTTTGTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
14 14 0.30
15 23 0.50
16 9 0.20
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (15 bp):
ATAATGTCACCATAT
Found at i:376429 original size:37 final size:37
Alignment explanation
Indices: 376356--376430 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
376346 GTTGGAAAAT
* *
376356 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
376393 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
376430 A
1 A
376431 AGATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:378067 original size:2 final size:2
Alignment explanation
Indices: 378060--378106 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
378050 TTAATCATTA
378060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378102 AT AT A
1 AT AT A
378107 ATGATATAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:394513 original size:30 final size:30
Alignment explanation
Indices: 394472--394532 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
394462 GACAAGAAGG
394472 TGCCATATTTTCCCATTTAATTCTCAAGTA
1 TGCCATATTTTCCCATTTAATTCTCAAGTA
*
394502 TGCCATGTTTTCCCATTTAATTCTCAAGTA
1 TGCCATATTTTCCCATTTAATTCTCAAGTA
394532 T
1 T
394533 ACTAAGGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (30 bp):
TGCCATATTTTCCCATTTAATTCTCAAGTA
Found at i:402692 original size:29 final size:28
Alignment explanation
Indices: 402658--402745 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 28
402648 GATGCATTTA
*
402658 TGATTCTACATGAGATTATATTCTGGTCC
1 TGATTCTGCATGAGATTATATTCT-GTCC
* * *
402687 TGATTCTGGATGGGATTATATCTCTGCCC
1 TGATTCTGCATGAGATTATAT-TCTGTCC
*
402716 TGATTCTGCATGAGATTATATCCTTGTCC
1 TGATTCTGCATGAGATTATATTC-TGTCC
402745 T
1 T
402746 ATTTATGTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.02
29 45 0.92
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (28 bp):
TGATTCTGCATGAGATTATATTCTGTCC
Found at i:405572 original size:29 final size:29
Alignment explanation
Indices: 405538--405618 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
405528 TGATGCATTT
* *
405538 ATGATTCTACATGAGATTATAT-TCTGGTC
1 ATGATTCTGCATGAGATTATATCTCT-GCC
*
405567 ATGATTCTGCATGGGATTATATCTCTGCC
1 ATGATTCTGCATGAGATTATATCTCTGCC
* *
405596 CTGATTCTGTATGAGATTATATC
1 ATGATTCTGCATGAGATTATATC
405619 ATTGTCCTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 42 0.93
30 3 0.07
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (29 bp):
ATGATTCTGCATGAGATTATATCTCTGCC
Found at i:407137 original size:3 final size:3
Alignment explanation
Indices: 407131--407219 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
407121 TTTTTATCCA
* *
407131 TAT TAT TAA TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
407179 TAC TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
407220 AATATATATT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:407142 original size:9 final size:9
Alignment explanation
Indices: 407130--407231 Score: 107
Period size: 9 Copynumber: 11.1 Consensus size: 9
407120 TTTTTTATCC
407130 ATATTATTA
1 ATATTATTA
407139 ATATTATTA
1 ATATTATTA
407148 ATATTATTA
1 ATATTATTA
*
407157 TTATTATTA
1 ATATTATTA
*
407166 TTATTATTA
1 ATATTATTA
* *
407175 TTATTACTA
1 ATATTATTA
*
407184 TTATTATTA
1 ATATTATTA
*
407193 TTATTATT-
1 ATATTATTA
407201 ATCATTATTA
1 AT-ATTATTA
*
407211 TTATTATTAA
1 ATATTATT-A
407221 ATATATATTA
1 ATAT-TATTA
407231 A
1 A
407232 ATATATATAA
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
8 1 0.01
9 71 0.86
10 7 0.08
11 4 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTATTA
Found at i:407231 original size:11 final size:11
Alignment explanation
Indices: 407215--407244 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
407205 TTATTATTAT
407215 TATTAAATATA
1 TATTAAATATA
407226 TATTAAATATA
1 TATTAAATATA
407237 TA-TAAATA
1 TATTAAATA
407245 ATAATTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:409337 original size:18 final size:18
Alignment explanation
Indices: 409314--409354 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
409304 TTCTTTCAAA
409314 TTTTTTAT-TACTTATTAT
1 TTTTTTATATA-TTATTAT
409332 TTTTTTATATATTATTAT
1 TTTTTTATATATTATTAT
409350 TTTTT
1 TTTTT
409355 ATTTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTATATATTATTAT
Found at i:409362 original size:18 final size:18
Alignment explanation
Indices: 409313--409362 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
409303 TTTCTTTCAA
409313 ATTTTTTA--TTACTTATT
1 ATTTTTTATTTTA-TTATT
*
409330 ATTTTTT-TATATATTATT
1 ATTTTTTAT-TTTATTATT
409348 ATTTTTTATTTTATT
1 ATTTTTTATTTTATT
409363 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 7 0.26
18 17 0.63
19 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTATTTTATTATT
Found at i:410794 original size:15 final size:14
Alignment explanation
Indices: 410769--410810 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
410759 TTTTCATGCA
410769 TACAT-TTGCATTT
1 TACATCTTGCATTT
410782 TACATCCTTGCATTT
1 TACAT-CTTGCATTT
* *
410797 TTCATTTTGCATTT
1 TACATCTTGCATTT
410811 ATACTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (14 bp):
TACATCTTGCATTT
Found at i:416477 original size:83 final size:83
Alignment explanation
Indices: 416338--416649 Score: 509
Period size: 83 Copynumber: 3.7 Consensus size: 83
416328 AAACATTAAC
416338 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
416403 AGAATCAATCATTGAATT
66 AGAATCAATCATTGAATT
416421 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
* *
416486 AAAATAAATCATTGAATT
66 AGAATCAATCATTGAATT
*
416504 TGGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
*
416569 AGAACCAATCATTGAATT
66 AGAATCAATCATTGAATT
** * * *
416587 TGGAAGAAT-AAGGATACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTTATCTGGTT
1 TGGAAG-ATGAA-TTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
416650 TGGTAAGAAC
Statistics
Matches: 214, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
83 168 0.79
84 4 0.02
85 42 0.20
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.37
Consensus pattern (83 bp):
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAC
AGAATCAATCATTGAATT
Found at i:417237 original size:113 final size:113
Alignment explanation
Indices: 417034--417592 Score: 967
Period size: 113 Copynumber: 5.0 Consensus size: 113
417024 CAAAGATTCA
* ** *
417034 AATCTATCATTTGAAAGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
417099 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
417147 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
417212 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
417260 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
417325 AGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
417373 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
417438 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * * *
417486 AATTCATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
417550 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
417593 GCATAATTCT
Statistics
Matches: 429, Mismatches: 17, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
112 70 0.16
113 359 0.84
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGAGGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:417919 original size:3 final size:3
Alignment explanation
Indices: 417913--418006 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
417903 TTTTTATCCA
* *
417913 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
417960 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
418007 AATATATATT
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 82 0.98
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:418018 original size:11 final size:11
Alignment explanation
Indices: 418002--418031 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
417992 TTATTATTAT
418002 TATTAAATATA
1 TATTAAATATA
418013 TATTAAATATA
1 TATTAAATATA
418024 TA-TAAATA
1 TATTAAATA
418032 ATAATTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:419425 original size:20 final size:21
Alignment explanation
Indices: 419396--419436 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
419386 TTTATTTTTA
419396 TTTTATTATATGAATAAATAT
1 TTTTATTATATGAATAAATAT
**
419417 TTTTA-TATATTCATAAATAT
1 TTTTATTATATGAATAAATAT
419437 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTATTATATGAATAAATAT
Found at i:424667 original size:27 final size:29
Alignment explanation
Indices: 424637--424695 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
424627 TTTTGAAAGT
**
424637 TATAAAATAGTTATTA-AATTTATT-AAA
1 TATAAAATAACTATTAGAATTTATTGAAA
*
424664 TATAAAATAACTATTAGATTTTATTGAAA
1 TATAAAATAACTATTAGAATTTATTGAAA
424693 TAT
1 TAT
424696 TATAAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 14 0.52
28 7 0.26
29 6 0.22
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (29 bp):
TATAAAATAACTATTAGAATTTATTGAAA
Found at i:427957 original size:6 final size:6
Alignment explanation
Indices: 427947--427993 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
427937 GGCACCGGCG
* *
427947 ATGGGG ATGGGG ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATGGG
1 ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATGGG
427994 TGTGATGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.17, C:0.11, G:0.55, T:0.17
Consensus pattern (6 bp):
ATGGGC
Found at i:454598 original size:15 final size:14
Alignment explanation
Indices: 454570--454597 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
454560 CATTGCCAAC
454570 TCTTTTAAAAAAAA
1 TCTTTTAAAAAAAA
454584 TCTTTTAAAAAAAA
1 TCTTTTAAAAAAAA
454598 ACCTTTAGAA
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:0.00, T:0.36
Consensus pattern (14 bp):
TCTTTTAAAAAAAA
Found at i:461410 original size:9 final size:8
Alignment explanation
Indices: 461394--461502 Score: 59
Period size: 8 Copynumber: 12.9 Consensus size: 8
461384 AAATAAAAGA
461394 GAAAAAAT
1 GAAAAAAT
461402 GAGAAAAAT
1 GA-AAAAAT
461411 GAAAAATGAT
1 GAAAAA--AT
*
461421 GGAAAAAACG
1 -GAAAAAA-T
461431 GAAAGAAA-
1 GAAA-AAAT
461439 -AAAAGAAT
1 GAAAA-AAT
461447 -AAAAAAT
1 GAAAAAAT
461454 GGAAAAGGGAA-
1 -GAAAA---AAT
461465 GAAAAAAT
1 GAAAAAAT
461473 G-AAAAAT
1 GAAAAAAT
461480 GAAAAAA-
1 GAAAAAAT
461487 GAGAAAAAT
1 GA-AAAAAT
461496 GAAAAAA
1 GAAAAAA
461503 AAAGAAATAA
Statistics
Matches: 83, Mismatches: 1, Indels: 34
0.70 0.01 0.29
Matches are distributed among these distances:
6 1 0.01
7 19 0.23
8 26 0.31
9 19 0.23
10 10 0.12
11 6 0.07
12 2 0.02
ACGTcount: A:0.71, C:0.01, G:0.20, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:461503 original size:17 final size:16
Alignment explanation
Indices: 461466--461509 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
461456 AAAAGGGAAG
*
461466 AAAAAATGAAAAATGA
1 AAAAAAAGAAAAATGA
*
461482 AAAAAGAGAAAAATGAA
1 AAAAAAAGAAAAATG-A
461499 AAAAAAAGAAA
1 AAAAAAAGAAA
461510 TAAAAGGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (16 bp):
AAAAAAAGAAAAATGA
Found at i:462964 original size:55 final size:55
Alignment explanation
Indices: 462773--463181 Score: 421
Period size: 55 Copynumber: 7.6 Consensus size: 55
462763 GTTGAAGATT
* *
462773 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCGTTGAAGATTGTTC
*
462824 GA-TTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTT-CTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCGTTGAAGATTGTTC
* *
462875 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCGTTGAAGATTGTTC
* * *
462930 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACACGTT-TTATTAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCGT-TGAAGATTGTTC
* * * **
462985 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATT-TTCC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCGTTGAAGATTGTT-C
* * **
463040 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACG-TTCGTTGAAGATTGTTC
* * ** * * ** *
463096 AAG-TCTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCCGAAGATTGTTT
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACACGTTCGTTGAAGATTGTTC
* *
463151 GAG-TCTTATACTCCCTGAAAGAATAGGGAGC
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGC
463182 ATACCCGCCA
Statistics
Matches: 316, Mismatches: 30, Indels: 20
0.86 0.08 0.05
Matches are distributed among these distances:
50 1 0.00
51 94 0.30
52 1 0.00
54 5 0.02
55 170 0.54
56 43 0.14
57 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTCGTTGAAGATTGTTC
Found at i:463147 original size:166 final size:160
Alignment explanation
Indices: 462778--463181 Score: 413
Period size: 166 Copynumber: 2.5 Consensus size: 160
462768 AGATTGAGTC
* * * * * ** *
462778 CTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGATTC----CTATACTCTC
1 CTATACTCCCTGAAGGAATAGAGAGCAGACACGTTTGACGAAGATTG-TTCGAGTCTATACTCCC
* * *
462839 TGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGA
65 TGAAAGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGA
* *
462904 GCGGACAAGTTCGTTGAAGATTGTTCGAGTT
130 GCGGACAAGTTCATTGAAGATTGTTCAAGTT
* * * **
462935 CTATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATTAAGATTGTTCGAGTTCTATACTCCC
1 CTATACTCCCTGAAGGAATAGAGAGCAGACACGTTTGACGAAGATTGTTCGAG-TCTATACTCCC
* ** * *
463000 TGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTTTCCGAGTTCTATACTCTCTGAAGGAATA
65 TGAAAGAATAGGGAGCGGACAAGTTCATTGAAGA--TT--GAGTCCTATACTCTCTGAAGGAATA
** *
463065 GAGAGCGGACCCGTTTTATTGAAGATTGTTCAAG-T
126 GAGAGCGGACAAG-TTCATTGAAGATTGTTCAAGTT
** * * *
463100 CTTATACTCCCTGACTGAATAGGGAGCAGACACGTTTGCCGAAGATTGTTTGAGTCTTATACTCC
1 C-TATACTCCCTGAAGGAATAGAGAGCAGACACGTTTGACGAAGATTGTTCGAGTC-TATACTCC
463165 CTGAAAGAATAGGGAGC
64 CTGAAAGAATAGGGAGC
463182 ATACCCGCCA
Statistics
Matches: 205, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
156 3 0.01
157 41 0.20
161 38 0.19
163 2 0.01
165 38 0.19
166 83 0.40
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (160 bp):
CTATACTCCCTGAAGGAATAGAGAGCAGACACGTTTGACGAAGATTGTTCGAGTCTATACTCCCT
GAAAGAATAGGGAGCGGACAAGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAG
CGGACAAGTTCATTGAAGATTGTTCAAGTT
Found at i:466833 original size:2 final size:2
Alignment explanation
Indices: 466826--466887 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
466816 TTTACACTGC
466826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466868 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
466888 GCGCGTGTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:469935 original size:21 final size:21
Alignment explanation
Indices: 469893--469936 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
469883 ACTTACGATG
* *
469893 CTAACTTGGTAGTTTACAGTA
1 CTAACGTGGTAGTCTACAGTA
* *
469914 CTAACGTGGTGGTCTACGGTA
1 CTAACGTGGTAGTCTACAGTA
469935 CT
1 CT
469937 GATGTGACAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (21 bp):
CTAACGTGGTAGTCTACAGTA
Found at i:485036 original size:9 final size:8
Alignment explanation
Indices: 485005--485033 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
484995 ATTGAACTTG
485005 AAAAATTA
1 AAAAATTA
485013 AAAAATTA
1 AAAAATTA
485021 AAAAATTA
1 AAAAATTA
485029 AAAAA
1 AAAAA
485034 ATTTGATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATTA
Found at i:487394 original size:16 final size:16
Alignment explanation
Indices: 487367--487409 Score: 77
Period size: 16 Copynumber: 2.6 Consensus size: 16
487357 CAACATAATA
487367 GTGACTAAAATAAATGC
1 GTGAC-AAAATAAATGC
487384 GTGACAAAATAAATGC
1 GTGACAAAATAAATGC
487400 GTGACAAAAT
1 GTGACAAAAT
487410 TAAAGGCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.21
Consensus pattern (16 bp):
GTGACAAAATAAATGC
Found at i:488613 original size:12 final size:10
Alignment explanation
Indices: 488588--488635 Score: 57
Period size: 9 Copynumber: 5.1 Consensus size: 10
488578 TTGTAATCTG
488588 TAATAATAAA
1 TAATAATAAA
*
488598 TAATAAT-AT
1 TAATAATAAA
488607 TAATAAT-AA
1 TAATAATAAA
488616 TAA-AATAAA
1 TAATAATAAA
*
488625 TAAAAATAAA
1 TAATAATAAA
488635 T
1 T
488636 CCAAACTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 3 0.09
9 17 0.50
10 14 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAATAATAAA
Found at i:488616 original size:15 final size:15
Alignment explanation
Indices: 488591--488634 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
488581 TAATCTGTAA
*
488591 TAATAAATAATAATAT
1 TAAT-AATAATAAAAT
488607 TAATAATAATAAAAT
1 TAATAATAATAAAAT
* *
488622 AAATAAAAATAAA
1 TAATAATAATAAA
488635 TCCAAACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATAATAATAAAAT
Found at i:493439 original size:25 final size:25
Alignment explanation
Indices: 493388--493441 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
493378 TGATACATAC
* * *
493388 ATATTATCATTTTAAGTAACATGTT
1 ATATCATCATTTTAAATAACATATT
**
493413 ATATCATCATTTTAAATAATGTATT
1 ATATCATCATTTTAAATAACATATT
493438 ATAT
1 ATAT
493442 TTTACGTCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (25 bp):
ATATCATCATTTTAAATAACATATT
Found at i:509166 original size:3 final size:3
Alignment explanation
Indices: 509158--509186 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
509148 AATCAGGGGA
509158 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
509187 AAGCAAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:516301 original size:3 final size:3
Alignment explanation
Indices: 516293--516342 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
516283 ACATGTAAAT
* **
516293 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
516340 TAA
1 TAA
516343 ATATTAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:516857 original size:20 final size:21
Alignment explanation
Indices: 516832--516872 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
516822 GATTTTGATA
*
516832 AAAATT-GTCTCAAGGGAAAC
1 AAAATTCGTCTCAAGAGAAAC
*
516852 AAAATTCGTTTCAAGAGAAAC
1 AAAATTCGTCTCAAGAGAAAC
516873 GATCTCAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAATTCGTCTCAAGAGAAAC
Found at i:517112 original size:66 final size:63
Alignment explanation
Indices: 516938--517116 Score: 171
Period size: 66 Copynumber: 2.8 Consensus size: 63
516928 CAAAAGCAAC
* * * * *
516938 TGTCTCGAAAGAGACAAAATTCGTTTCAAAGGAAA-TAACCCAAAGATGGCATTTAAAGGGAAT
1 TGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGCATTTAAAGGGAAT
* ** * * ** * *
517001 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAAGATCGGTGTTTCATGGGAA
1 TGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GGCATTTAAAGGG-A
517066 AT
62 AT
517068 TGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 TGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
517117 TTTGTTTTGT
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
62 2 0.02
63 15 0.16
64 12 0.13
65 9 0.10
66 34 0.37
67 20 0.22
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (63 bp):
TGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGCATTTAAAGGGAAT
Found at i:517445 original size:15 final size:15
Alignment explanation
Indices: 517421--517464 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
517411 AAGATGATCT
*
517421 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
517436 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
517451 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
517465 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:517734 original size:15 final size:15
Alignment explanation
Indices: 517710--517753 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
517700 AAGATGATTT
*
517710 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
517725 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
517740 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
517754 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:517903 original size:289 final size:289
Alignment explanation
Indices: 517313--517996 Score: 1187
Period size: 289 Copynumber: 2.4 Consensus size: 289
517303 GTATCTTAGT
* **
517313 GAGACAAAATTTTGTTTCCAAA-GAAATAGGCTCAAAGA-TTTTTCTTCAAAAGAAATTGTTTTA
1 GAGACAAAATTTTGTTT-CAAAGGAAACAAACTCAAAGATTTTTTC-TCAAAAGAAATTGTTTTA
517376 AGGGATAAAACATTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAATGTTT
64 AGGGATAAAACATTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAATGTTT
517441 CAAGAGAAAATGTTTCAAGTGAAACGACTCAAAATGGTTTTATTTCAAGAGAAACAAACTCAAAG
129 CAAGAGAAAATGTTTCAAGTGAAACGACTCAAAATGGTTTTATTTCAAGAGAAACAAACTCAAAG
*
517506 ATTTTGTATTTCTAGAGAAACTGCCTCAAGGGAGTCAAAATTTGTTTTAATAAAAACAATCTCAA
194 ATTTTGTATTTCTAGAGAAACTGCCTCAAGGGAGTCAAAATTTATTTTAATAAAAACAATCTCAA
517571 AGGTGGGTAGTTTTAAAAGAAATTGTCTCGA
259 AGGTGGGTAGTTTTAAAAGAAATTGTCTCGA
517602 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTTTTAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTTTTAAG
*
517667 GGATAAAACATTGTTTCCAGAGAAACAAACTCAAAGATGATTTTGTTTTAAGAGAAAATGTTTCA
66 GGATAAAACATTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAATGTTTCA
517732 AGAGAAAATGTTTCAAGTGAAACGACTCAAAAATGGTTTTATTTCAAGAGAAACAAACTCAAAGA
131 AGAGAAAATGTTTCAAGTGAAACGACTC-AAAATGGTTTTATTTCAAGAGAAACAAACTCAAAGA
517797 TTTTGTATTTCTAGAGAAACTGCCTCAAGGGAGTCAAAATTTATTTTAATAAAAACAATCTCAAA
195 TTTTGTATTTCTAGAGAAACTGCCTCAAGGGAGTCAAAATTTATTTTAATAAAAACAATCTCAAA
517862 GGTGGGTAGTTTTAAAAGAAATTGTCTCGA
260 GGTGGGTAGTTTTAAAAGAAATTGTCTCGA
* *
517892 GAGAC-AAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAG
1 GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTTTTAAG
* * * *
517956 AGAGACAAAA-ATTTGTTTCCAAAGAAATATACTCAAAGATG
66 -G-GATAAAACA-TTGTTTCCAGAGAAACAAACTCAAAGATG
517997 GATTACATCT
Statistics
Matches: 378, Mismatches: 11, Indels: 10
0.95 0.03 0.03
Matches are distributed among these distances:
288 4 0.01
289 199 0.53
290 143 0.38
291 32 0.08
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (289 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTTTTAAG
GGATAAAACATTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAATGTTTCA
AGAGAAAATGTTTCAAGTGAAACGACTCAAAATGGTTTTATTTCAAGAGAAACAAACTCAAAGAT
TTTGTATTTCTAGAGAAACTGCCTCAAGGGAGTCAAAATTTATTTTAATAAAAACAATCTCAAAG
GTGGGTAGTTTTAAAAGAAATTGTCTCGA
Found at i:518091 original size:118 final size:119
Alignment explanation
Indices: 517899--518114 Score: 303
Period size: 118 Copynumber: 1.8 Consensus size: 119
517889 CGAGAGACAA
*
517899 ATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAA
1 ATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAACTGTCTCAAGAGAGACAA
*
517964 AAATTTGTTTCCAAAGAAATATACTCAAAGATGGATTACATCTTAAGTGAGACG
66 AAATTTGTTTCCAAAGAAATAAACTCAAAGATGGATTACATCTTAAGTGAGACG
* * * **
518018 ATTTT-TTTCAAAGGAGACAATCTCAAAGGTTGGTTTT-TCATTAGAAACTGTCTCAAGAGAGAC
1 ATTTTGTTTCAAAGGAAACAAACTCAAAGATT--TTTTCTCAAAAGAAACTGTCTCAAGAGAGAC
* **
518081 -ACAATTTGTTTTTAAAGAAATAAACTCAAAGATG
64 AAAAATTTGTTTCCAAAGAAATAAACTCAAAGATG
518115 ATTTTGTTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
118 53 0.62
119 28 0.33
120 4 0.05
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (119 bp):
ATTTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTCTCAAAAGAAACTGTCTCAAGAGAGACAA
AAATTTGTTTCCAAAGAAATAAACTCAAAGATGGATTACATCTTAAGTGAGACG
Found at i:518138 original size:30 final size:28
Alignment explanation
Indices: 518104--518168 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
518094 AAAGAAATAA
518104 ACTCAAAGATGATTTTGTTAAGA-GAAACAG
1 ACTCAAAGAT-ATTTTGTTAA-ATG-AACAG
* *
518134 ACTCAAAGATTTTTTTTTAAATGAACAG
1 ACTCAAAGATATTTTGTTAAATGAACAG
518162 ACTCAAA
1 ACTCAAA
518169 AATTTGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 13 0.41
29 9 0.28
30 10 0.31
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (28 bp):
ACTCAAAGATATTTTGTTAAATGAACAG
Found at i:518320 original size:30 final size:30
Alignment explanation
Indices: 518258--518319 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
518248 GAGACAAAAA
*
518258 TTTGTTTCCAAAGAAACAGACTCAAAGATT
1 TTTGTTTCAAAAGAAACAGACTCAAAGATT
518288 TTTGTTTCAAAAGAAAC-GACTCAAAGATT
1 TTTGTTTCAAAAGAAACAGACTCAAAGATT
518317 TTT
1 TTT
518320 TCACGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (30 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGATT
Found at i:518340 original size:91 final size:94
Alignment explanation
Indices: 518210--518379 Score: 258
Period size: 91 Copynumber: 1.8 Consensus size: 94
518200 AAGAAAAATA
* *
518210 GACTCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAAA-TTTGTTTCCAAAGAAA
1 GACTCAAAGATTTTTTCTC-AAAGAAATTGTCTCAAGAGAGA-AAAAACTTTATTTCAAAAGAAA
518274 CAGACTCAAAGATTTTTGTTTCAAAAGAAAC
64 CAGACTCAAAGATTTTTGTTTCAAAAGAAAC
* *
518305 GACTCAAAGA-TTTTT-TC-ACGAAATTGTCTCAAGAGAGAAAAAACTTTATTTCAAAAGAAATA
1 GACTCAAAGATTTTTTCTCAAAGAAATTGTCTCAAGAGAGAAAAAACTTTATTTCAAAAGAAACA
518367 GACTCAAAGATTT
66 GACTCAAAGATTT
518380 GTTCAAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
90 5 0.07
91 48 0.69
93 2 0.03
94 5 0.07
95 10 0.14
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (94 bp):
GACTCAAAGATTTTTTCTCAAAGAAATTGTCTCAAGAGAGAAAAAACTTTATTTCAAAAGAAACA
GACTCAAAGATTTTTGTTTCAAAAGAAAC
Found at i:518411 original size:91 final size:91
Alignment explanation
Indices: 518233--518411 Score: 243
Period size: 91 Copynumber: 2.0 Consensus size: 91
518223 TTTCTCAAAA
* * *****
518233 GAAATTGTCTCAAGAGAGACAAAAATTTGTTTCCAAAGAAACAGACTCAAAGATTTTTGTTTCAA
1 GAAATTGTCTCAAGAGAGACAAAAATTTATTTCAAAAGAAACAGACTCAAAGATTTTTCAAAAAA
*
518298 AAGAAACGACTCAAAGATTTTTTCAC
66 AAGAAACAACTCAAAGATTTTTTCAC
*
518324 GAAATTGTCTCAAGAGAGA-AAAAACTTTATTTCAAAAGAAATAGACTCAAAGATTTGTTCAAAA
1 GAAATTGTCTCAAGAGAGACAAAAA-TTTATTTCAAAAGAAACAGACTCAAAGATTT-TTCAAAA
*
518388 AAAAGAAATAACTCAAAGATTTTT
64 AAAAGAAACAACTCAAAGATTTTT
518412 ATTTAAAAGG
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
90 5 0.07
91 47 0.62
92 24 0.32
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (91 bp):
GAAATTGTCTCAAGAGAGACAAAAATTTATTTCAAAAGAAACAGACTCAAAGATTTTTCAAAAAA
AAGAAACAACTCAAAGATTTTTTCAC
Found at i:518843 original size:103 final size:103
Alignment explanation
Indices: 518612--518915 Score: 382
Period size: 104 Copynumber: 2.9 Consensus size: 103
518602 CATCTTTGAA
* * * * * * *
518612 AATCTCAAGTGATATTAATTTTGTTTTAAAT-ACAACAACTTTGAAATTTGTATT-ATGAGGGAA
1 AATCTCAAGTGAGATTAATTTTGTTTTAAGTGA-AGCAAATTCGAAATTTGTATTCA-AAGGAAA
*
518675 AATGTCTCAAGCAAGACGAAATTTGTTTTGAAAGAAACAAC
64 AATGTCTCAAGCGAGACGAAATTTGTTTT-AAAGAAACAAC
* * *
518716 AATCTCAATTGAGATTAATATTGTTTTAAGTGAAGCAAATTCAAAATTTGTATCTCAAAGGAAAA
1 AATCTCAAGTGAGATTAATTTTGTTTTAAGTGAAGCAAATTCGAAATTTGTAT-TCAAAGGAAAA
* * *
518781 ATGTCTAAAGCGAGATGAAGTTTGTTTT-AAGAAACAAC
65 ATGTCTCAAGCGAGACGAAATTTGTTTTAAAGAAACAAC
*
518819 AATCTCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTCGAAATTTGTATATCAAAGGAAAA
1 AATCTCAAGTGAGATTAATTTTGTTTTAAGTGAAGCAAATTCGAAATTTGTAT-TCAAAGG-AAA
518884 AATGTCTCAAGCGAGAC-ACAATTTGTTTTAAA
64 AATGTCTCAAGCGAGACGA-AATTTGTTTTAAA
518916 TTTCTCAAAA
Statistics
Matches: 172, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
103 67 0.39
104 70 0.41
105 34 0.20
106 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (103 bp):
AATCTCAAGTGAGATTAATTTTGTTTTAAGTGAAGCAAATTCGAAATTTGTATTCAAAGGAAAAA
TGTCTCAAGCGAGACGAAATTTGTTTTAAAGAAACAAC
Found at i:523102 original size:32 final size:32
Alignment explanation
Indices: 523055--523116 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
523045 GAAAAAAAAG
* *
523055 ACACAAACAACAGAAAATAAATAAGTTAGTGC
1 ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
* *
523087 ACACAAAGAAAAGAAAAGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAGAAATAAGTTAGT
523117 ACAGGTAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATAAGTTAGTGC
Found at i:526796 original size:3 final size:3
Alignment explanation
Indices: 526788--526834 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
526778 ACATGTAAAT
* **
526788 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
526835 ATATTAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:534321 original size:17 final size:17
Alignment explanation
Indices: 534299--534333 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
534289 GTCCTGTTTC
534299 CAATATTTGACTATGTG
1 CAATATTTGACTATGTG
534316 CAATATTTGACTATGTG
1 CAATATTTGACTATGTG
534333 C
1 C
534334 GTCATGCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (17 bp):
CAATATTTGACTATGTG
Found at i:540462 original size:12 final size:12
Alignment explanation
Indices: 540445--540479 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
540435 ATAACTAATA
540445 ATATTAAATATT
1 ATATTAAATATT
*
540457 ATATTAAATA-A
1 ATATTAAATATT
540468 ATATTAAATATT
1 ATATTAAATATT
540480 TTATGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATTAAATATT
Found at i:543750 original size:124 final size:124
Alignment explanation
Indices: 543567--544164 Score: 1080
Period size: 124 Copynumber: 4.8 Consensus size: 124
543557 CTATAATCGG
543567 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
*
543632 CATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAG-ATATCAGTACCTATTAT
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTAT
543690 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
543755 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTAT
543816 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCA-TATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
543880 TCATTG-CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTA-TAT
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTAT
*
543939 TTCACTATTCATATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
544004 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTA-
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTAT
544063 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATA--TT
544128 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
64 ATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
544165 ATAACTTAAA
Statistics
Matches: 464, Mismatches: 3, Indels: 13
0.97 0.01 0.03
Matches are distributed among these distances:
122 15 0.03
123 84 0.18
124 237 0.51
125 28 0.06
126 100 0.22
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (124 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTAT
Found at i:544605 original size:32 final size:33
Alignment explanation
Indices: 544546--544642 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 33
544536 AAATTTAATG
*
544546 TTAAATTTCGAATACTA-TAATTATATTTTAAAT
1 TTAAATTTCGAATA-TATTATTTATATTTTAAAT
* * *
544579 TTAAATTT-GAATATATTATTTTTATTTTTATT
1 TTAAATTTCGAATATATTATTTATATTTTAAAT
* *
544611 TTAAATTTCGAATA-ATAAATTTGTATTTTAAA
1 TTAAATTTCGAATATAT-TATTTATATTTTAAA
544643 AACATTTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
31 2 0.04
32 27 0.51
33 24 0.45
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TTAAATTTCGAATATATTATTTATATTTTAAAT
Found at i:544638 original size:33 final size:34
Alignment explanation
Indices: 544546--544642 Score: 112
Period size: 33 Copynumber: 3.0 Consensus size: 34
544536 AAATTTAATG
*
544546 TTAAATTTCGAATACTATAA-TTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
544579 TTAAATTT-GAAT-ATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
544611 TTAAATTTCGAATAATA-AATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
544643 AACATTTATC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
31 4 0.08
32 22 0.42
33 23 0.44
34 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:545247 original size:21 final size:21
Alignment explanation
Indices: 545159--545252 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
545149 TATGGTATAA
*
545159 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
545180 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
545201 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
545222 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
545243 AACCCTGCGG
1 AACCCTGCGG
545253 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:545282 original size:21 final size:21
Alignment explanation
Indices: 545256--545303 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
545246 CCTGCGGAGA
*
545256 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
545277 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
545298 GGGCAT
1 TGGCAT
545304 TACCCCTGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:547060 original size:31 final size:31
Alignment explanation
Indices: 546990--547060 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
546980 AATTCTAAAT
* * *
546990 AAATAATAATTATATAAATATTATTTTAATA
1 AAATAATAATTACATAAATATTAATATAATA
*
547021 AAAAAATAATTTACATAAATATTAATATAA-A
1 AAATAATAA-TTACATAAATATTAATATAATA
*
547052 AACTAATAA
1 AAATAATAA
547061 CTATTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (31 bp):
AAATAATAATTACATAAATATTAATATAATA
Found at i:553642 original size:288 final size:293
Alignment explanation
Indices: 553217--553802 Score: 1092
Period size: 288 Copynumber: 2.0 Consensus size: 293
553207 ACCCACATGA
553217 TCTTGTTTTATGAAAAGAAAAGAAAAAGTGAACTGGAAGAGATGATTGTTGTGTGCAGCAACACA
1 TCTTGTTTTATGAAAAGAAAAGAAAAAGTGAACTGGAAGAGATGATTGTTGTGTGCAGCAACACA
553282 AGCGTTATATAGCTGGGAAATTGCGTTTGTATCTGAAAACAAAATGAAAAAGGAAAGAGAGAGAA
66 AGCGTTATATAGCTGGGAAATTGCGTTTGTATCTGAAAACAAAATGAAAAAGGAAAGAGAGAGAA
553347 GGGAGGGCTTTTGATGGTAATGATGGCACAAGGACTCATGATTAC-TGGGAGCAGCAATAGAAGA
131 GGGAGGGCTTTTGATGGTAATGATGGCACAAGGACTCATGATTACTTGGGAGCAGCAATAGAAGA
553411 AAACAAGGAAAATAC-AAATAAAATAAAA-AAAAT-AAAGGGAGTTTCTTTCTTTCTTCTTCTAT
196 AAACAAGGAAAATACAAAATAAAATAAAATAAAATAAAAGGGAGTTTCTTTCTTTCTTCTTCTAT
553473 GTTTATGGAATGGATGTACGA-TACTAATAAAT
261 GTTTATGGAATGGATGTACGATTACTAATAAAT
553505 TCTTGTTTTATGAAAAGAAAAGAAAAAGTGAACTGGAAGAGATGATTGTTGTGTGCAGCAACACA
1 TCTTGTTTTATGAAAAGAAAAGAAAAAGTGAACTGGAAGAGATGATTGTTGTGTGCAGCAACACA
553570 AGCGTTATATAGCTGGGAAATTGCGTTTGTATCTGAAAACAAAATGAAAAAGGAAAGAGAGAGAA
66 AGCGTTATATAGCTGGGAAATTGCGTTTGTATCTGAAAACAAAATGAAAAAGGAAAGAGAGAGAA
553635 GGGAGGGCTTTTGATGGTAATGATGGCACAAGGACTCATGATTACTTGGGAGCAGCAATAGAAGA
131 GGGAGGGCTTTTGATGGTAATGATGGCACAAGGACTCATGATTACTTGGGAGCAGCAATAGAAGA
553700 AAACAAGGAAAATACAAAATAAAATAAAATAAAATAAAATAAAAGGGAGTTTCTTTCTTTCTTCT
196 AAACAAGGAAAATAC-----AAAATAAAATAAAATAAAATAAAAGGGAGTTTCTTTCTTTCTTCT
553765 TCTATGTTTATGGAATGGATGTACGATTACTAATAAAT
256 TCTATGTTTATGGAATGGATGTACGATTACTAATAAAT
553803 ATGATCGAGT
Statistics
Matches: 288, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
288 175 0.61
289 34 0.12
295 13 0.05
296 5 0.02
297 50 0.17
298 11 0.04
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (293 bp):
TCTTGTTTTATGAAAAGAAAAGAAAAAGTGAACTGGAAGAGATGATTGTTGTGTGCAGCAACACA
AGCGTTATATAGCTGGGAAATTGCGTTTGTATCTGAAAACAAAATGAAAAAGGAAAGAGAGAGAA
GGGAGGGCTTTTGATGGTAATGATGGCACAAGGACTCATGATTACTTGGGAGCAGCAATAGAAGA
AAACAAGGAAAATACAAAATAAAATAAAATAAAATAAAAGGGAGTTTCTTTCTTTCTTCTTCTAT
GTTTATGGAATGGATGTACGATTACTAATAAAT
Found at i:553725 original size:5 final size:5
Alignment explanation
Indices: 553715--553743 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
553705 AGGAAAATAC
553715 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
553744 GGGAGTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:554428 original size:19 final size:19
Alignment explanation
Indices: 554406--554442 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
554396 ATAATTTATA
554406 TAAAATACAAAAGAATGTT
1 TAAAATACAAAAGAATGTT
*
554425 TAAAATATAAAAGAATGT
1 TAAAATACAAAAGAATGT
554443 AAAACTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.11, T:0.27
Consensus pattern (19 bp):
TAAAATACAAAAGAATGTT
Found at i:571311 original size:19 final size:20
Alignment explanation
Indices: 571272--571311 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
571262 TTTCAAAACT
*
571272 TATTTTAAAAATTAGAATTA
1 TATTTTAAAAATTAAAATTA
*
571292 TATTTT-AAATTTAAAATTA
1 TATTTTAAAAATTAAAATTA
571311 T
1 T
571312 TAAACAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTTAAAAATTAAAATTA
Found at i:571461 original size:22 final size:21
Alignment explanation
Indices: 571416--571480 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
571406 TTAATTTTAC
*
571416 AAATATAATTATAATTAAATAAA
1 AAAT-TAATTATAATTTAA-AAA
571439 AAATTAATTATAACTTTAAAAA
1 AAATTAATTATAA-TTTAAAAA
* * *
571461 ATATT-TTTATAATTTTAAAA
1 AAATTAATTATAATTTAAAAA
571481 CTGAGTTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.19
21 6 0.16
22 16 0.43
23 8 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTAATTATAATTTAAAAA
Found at i:579488 original size:5 final size:5
Alignment explanation
Indices: 579438--579489 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
579428 ATATAAATAT
* * * *
579438 TTTAA CTTAA TTAAA TTAAA TTAAAA TTTAA -TTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TTTAA TTTAA TTTAA TTTAA
579488 TT
1 TT
579490 CTTTTCAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 4 0.10
5 32 0.78
6 5 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (5 bp):
TTTAA
Found at i:582528 original size:18 final size:16
Alignment explanation
Indices: 582489--582528 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
582479 AAGAATAAAT
582489 AATTATAAAAAAAAAA
1 AATTATAAAAAAAAAA
*
582505 ACTTATAAAAAATAAAA
1 AATTATAAAAAA-AAAA
582522 GAATTAT
1 -AATTAT
582529 GGACATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (16 bp):
AATTATAAAAAAAAAA
Found at i:582747 original size:108 final size:110
Alignment explanation
Indices: 582570--582770 Score: 345
Period size: 108 Copynumber: 1.8 Consensus size: 110
582560 ATTATCATCA
*
582570 AAGATTATTAAAGAATCAATTAATAAAATTAAAAATGAAAAAAAATAAATTTATCAACATCTAAA
1 AAGACTATTAAAGAATCAATTAATAAAATTAAAAATG-AAAAAAATAAATTTATCAACATCTAAA
582635 ATAAAAAATAAATTTA-TTGATGGTAAAAGAATTGTTATTATTCCCT
65 ATAAAAAATAAATTTATTTG-TGGTAAAAGAATTGTTATTATTCCCT
*
582681 AAGACTATTAAAGAATCAATTAATAAAA-TAAAAATG-ATAAAATAAATTTATCAACATCTAAAA
1 AAGACTATTAAAGAATCAATTAATAAAATTAAAAATGAAAAAAATAAATTTATCAACATCTAAAA
582744 TAAAAAATAAATTTATTTGTGGTAAAA
66 TAAAAAATAAATTTATTTGTGGTAAAA
582771 ATATATTATT
Statistics
Matches: 87, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
108 49 0.56
109 3 0.03
110 8 0.09
111 27 0.31
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (110 bp):
AAGACTATTAAAGAATCAATTAATAAAATTAAAAATGAAAAAAATAAATTTATCAACATCTAAAA
TAAAAAATAAATTTATTTGTGGTAAAAGAATTGTTATTATTCCCT
Found at i:583139 original size:6 final size:6
Alignment explanation
Indices: 583128--583184 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
583118 CCACGTAGTT
* * *
583128 GAGACG GAGACG GAGACG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG
1 GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG GAGAAG
*
583176 GGGAAG GAG
1 GAGAAG GAG
583185 CTAGAGATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.42, C:0.05, G:0.53, T:0.00
Consensus pattern (6 bp):
GAGAAG
Found at i:587431 original size:18 final size:18
Alignment explanation
Indices: 587405--587451 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
587395 TTCTGACTCC
* *
587405 TCGTTGTCATCATCGTCG
1 TCGTCGTCATCATCGTCA
*
587423 TCGTCGTCACCATCGTCA
1 TCGTCGTCATCATCGTCA
587441 TCGTCGTCATC
1 TCGTCGTCATC
587452 GTCCTGAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.34, G:0.19, T:0.34
Consensus pattern (18 bp):
TCGTCGTCATCATCGTCA
Found at i:587447 original size:9 final size:9
Alignment explanation
Indices: 587405--587454 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
587395 TTCTGACTCC
*
587405 TCGTTGTCA
1 TCGTCGTCA
* *
587414 TCATCGTCG
1 TCGTCGTCA
587423 TCGTCGTCA
1 TCGTCGTCA
* *
587432 CCATCGTCA
1 TCGTCGTCA
587441 TCGTCGTCA
1 TCGTCGTCA
587450 TCGTC
1 TCGTC
587455 CTGAGCAGGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (9 bp):
TCGTCGTCA
Found at i:587819 original size:18 final size:18
Alignment explanation
Indices: 587793--587832 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
587783 AAAGGCGATG
*
587793 GCGGTATCATATATGGTT
1 GCGGCATCATATATGGTT
587811 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGTT
587829 GCGG
1 GCGG
587833 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (18 bp):
GCGGCATCATATATGGTT
Found at i:589449 original size:111 final size:111
Alignment explanation
Indices: 589317--589538 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
589307 ATTACAAAAA
* * *
589317 TTAATTCTTAATTTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * * *
589382 AATTAAAACGTTAAAATGTTACCGTATCGGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTGACCGTATCAGCAAAGTGTAGAGATAT
589428 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
589493 AATTAAAACGTTAAAATGTGACCGTATCAGCAAATTGTAGAGATAT
66 AATTAAAACGTTAAAATGTGACCGTATCAGCAAAGTGTAGAGATAT
589539 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTGACCGTATCAGCAAAGTGTAGAGATAT
Found at i:589641 original size:17 final size:17
Alignment explanation
Indices: 589590--589644 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 17
589580 CTGTAAAAGA
*
589590 ATTATATTAGT-AAAAT
1 ATTATAATAGTAAAAAT
*
589606 ATTA-AATA--AAACAAA
1 ATTATAATAGTAAA-AAT
589621 ATTATAATAGTAAAAAT
1 ATTATAATAGTAAAAAT
589638 ATTATAA
1 ATTATAA
589645 AATATACCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 8 0.26
17 9 0.29
18 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
ATTATAATAGTAAAAAT
Found at i:589689 original size:20 final size:19
Alignment explanation
Indices: 589661--589699 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
589651 CCTTAAAAAG
*
589661 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
589681 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
589700 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:603258 original size:4 final size:4
Alignment explanation
Indices: 603249--603280 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
603239 TCTTCTTGTT
603249 TTTG TTTG TTTG TTTG TTTG TTTG TTGTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TT-TG TTT
603281 AAACTGTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (4 bp):
TTTG
Found at i:605561 original size:5 final size:5
Alignment explanation
Indices: 605553--605602 Score: 100
Period size: 5 Copynumber: 10.0 Consensus size: 5
605543 GGAAAAGGCC
605553 AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG
1 AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG
605603 CCTAGTACAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
AAATG
Found at i:605733 original size:74 final size:74
Alignment explanation
Indices: 605609--605766 Score: 235
Period size: 74 Copynumber: 2.1 Consensus size: 74
605599 AATGCCTAGT
* **
605609 ACAGAAAACACAGACAAAAGAAAGTACTTCTAACTCTCAGCAATACAACACAGATTTACTTGTTC
1 ACAGAAAACACAGACAAAAGAAAGTACTTCAAACTCAAAGCAATACAACACAGATTTACTTGTTC
*
605674 AAGAATCGA
66 AAGAATCAA
** * * *
605683 ACAGAAAACACAGTGAAAAGAAAGTACTTCAAACTCAAAGCTATATAACACTGATTTACTTGTTC
1 ACAGAAAACACAGACAAAAGAAAGTACTTCAAACTCAAAGCAATACAACACAGATTTACTTGTTC
605748 AAGAATCAA
66 AAGAATCAA
605757 ACAGAAAACA
1 ACAGAAAACA
605767 AAGATTAGCT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.48, C:0.20, G:0.12, T:0.20
Consensus pattern (74 bp):
ACAGAAAACACAGACAAAAGAAAGTACTTCAAACTCAAAGCAATACAACACAGATTTACTTGTTC
AAGAATCAA
Found at i:610104 original size:18 final size:18
Alignment explanation
Indices: 610065--610105 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
610055 GAGCCACATT
* * *
610065 TGTTGCTGTTGATGTTGT
1 TGTTGCTGATGATGATGA
610083 TGTTGCTGATGATGATGA
1 TGTTGCTGATGATGATGA
610101 TGTTG
1 TGTTG
610106 TTGAAAGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.34, T:0.49
Consensus pattern (18 bp):
TGTTGCTGATGATGATGA
Found at i:611047 original size:10 final size:10
Alignment explanation
Indices: 610998--611047 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
610988 CCGACTCCCC
610998 ATTATATAT-
1 ATTATATATA
611007 A-TATATATA
1 ATTATATATA
* *
611016 TTTATATATTT
1 ATTATATA-TA
*
611027 TTTATATATA
1 ATTATATATA
611037 ATTATATATA
1 ATTATATATA
611047 A
1 A
611048 AATTTTTCGG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 17 0.50
11 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTATATATA
Found at i:611053 original size:25 final size:27
Alignment explanation
Indices: 611002--611054 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
610992 CTCCCCATTA
* * *
611002 TATATATATATATATTTATATATTTTT
1 TATATATATATATATATATAAAATTTT
611029 TATATATA-AT-TATATATAAAATTTT
1 TATATATATATATATATATAAAATTTT
611054 T
1 T
611055 CGGGTTCAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.57
26 2 0.09
27 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATATATATATATATATATAAAATTTT
Found at i:612323 original size:19 final size:19
Alignment explanation
Indices: 612296--612335 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
612286 TCAGGGTATA
612296 ATTTATTT-CTGGGAGTAAT
1 ATTTATTTCCTGGGAG-AAT
*
612315 ATTTTTTTCCTGGGAGAAT
1 ATTTATTTCCTGGGAGAAT
612334 AT
1 AT
612336 ACCCACGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (19 bp):
ATTTATTTCCTGGGAGAAT
Found at i:615023 original size:15 final size:15
Alignment explanation
Indices: 615003--615033 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
614993 CAACAAATAG
615003 AATTTTTATATAAAT
1 AATTTTTATATAAAT
615018 AATTTTTATATAAAT
1 AATTTTTATATAAAT
615033 A
1 A
615034 TGTAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:617389 original size:11 final size:12
Alignment explanation
Indices: 617359--617412 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
617349 GTTATTTAAA
617359 CGGGTATTGGGC
1 CGGGTATTGGGC
*
617371 CGGGTATTGGGT
1 CGGGTATTGGGC
617383 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
617394 CGGGAATCGGGC
1 CGGGTATTGGGC
617406 CGGGTAT
1 CGGGTAT
617413 ATATATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.11, C:0.17, G:0.48, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:617417 original size:2 final size:2
Alignment explanation
Indices: 617410--617519 Score: 95
Period size: 2 Copynumber: 57.5 Consensus size: 2
617400 TCGGGCCGGG
* * * * *
617410 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA TA TA TA TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
617451 TA TT TA AA T- TA AA TT TA T- TA -A TA T- 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
*
617489 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
617520 TTTTAATATT
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
1 5 0.06
2 80 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:617561 original size:13 final size:13
Alignment explanation
Indices: 617531--617579 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
617521 TTTAATATTT
*
617531 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
617543 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
617556 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
617569 ATCGGGGCGGG
1 ATCGGGGCGGG
617580 GATTACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:617579 original size:26 final size:25
Alignment explanation
Indices: 617531--617579 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
617521 TTTAATATTT
*
617531 ATCGGGTCGGGTATCGGGGCGGGTA
1 ATCGGGGCGGGTATCGGGGCGGGTA
617556 ATCGGGGCGGGTAATCGGGGCGGG
1 ATCGGGGCGGGT-ATCGGGGCGGG
617580 GATTACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (25 bp):
ATCGGGGCGGGTATCGGGGCGGGTA
Found at i:621923 original size:13 final size:13
Alignment explanation
Indices: 621879--621910 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
621869 TTTAATATTT
621879 ATCGGGGCGGATA
1 ATCGGGGCGGATA
*
621892 ATCGGGGCGGGTA
1 ATCGGGGCGGATA
621905 ATCGGG
1 ATCGGG
621911 TAATCGGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.50, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGATA
Found at i:621967 original size:6 final size:6
Alignment explanation
Indices: 621956--621980 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
621946 AAATGGGTTT
621956 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
621981 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:622551 original size:24 final size:24
Alignment explanation
Indices: 622519--622583 Score: 98
Period size: 23 Copynumber: 2.8 Consensus size: 24
622509 ACAAGGAATA
622519 TGCCACAAGAGCAGAGAAAAAGTG
1 TGCCACAAGAGCAGAGAAAAAGTG
*
622543 TGCCACAAGAGAAGAG-AAAAGTG
1 TGCCACAAGAGCAGAGAAAAAGTG
622566 TGCCACAAG-GACAGAGAA
1 TGCCACAAGAG-CAGAGAA
622584 TCTTATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.03
23 20 0.54
24 16 0.43
ACGTcount: A:0.46, C:0.17, G:0.29, T:0.08
Consensus pattern (24 bp):
TGCCACAAGAGCAGAGAAAAAGTG
Found at i:624873 original size:46 final size:46
Alignment explanation
Indices: 624817--624904 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
624807 TTAACAGGTA
*
624817 CCTGTCTATTGTGGTAATAATGCAAAACTATGTTGCAGCATCTGGT
1 CCTGTCTATTGTGATAATAATGCAAAACTATGTTGCAGCATCTGGT
* *
624863 CCTGTTTATTGTGATAATAATGCAAAACTATGTTGCTGCATC
1 CCTGTCTATTGTGATAATAATGCAAAACTATGTTGCAGCATC
624905 CTATTGTCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (46 bp):
CCTGTCTATTGTGATAATAATGCAAAACTATGTTGCAGCATCTGGT
Found at i:630676 original size:18 final size:17
Alignment explanation
Indices: 630653--630691 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
630643 AGAGAACTGA
630653 AATCTATGAAGGAATTAG
1 AATCTAT-AAGGAATTAG
* *
630671 AATCTATCAGGAATTTG
1 AATCTATAAGGAATTAG
630688 AATC
1 AATC
630692 CAATTCCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (17 bp):
AATCTATAAGGAATTAG
Found at i:648487 original size:35 final size:35
Alignment explanation
Indices: 648419--648516 Score: 124
Period size: 35 Copynumber: 2.7 Consensus size: 35
648409 AACACCTACC
* *
648419 AAACTTTGAAAAACCATTTTTCAAAGAAGCATTTACT
1 AAACTTTG-AAAACTA-TTTTCAAAGAAACATTTACT
648456 AAACTTTGAAAACTATTTTCAAAGAAACATTTACT
1 AAACTTTGAAAACTATTTTCAAAGAAACATTTACT
* *
648491 AAACTTTAAAAATCATTTTTTCAAAG
1 AAACTTTGAAAA-C-TATTTTCAAAG
648517 TTGGTTGCCA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
35 30 0.55
36 7 0.13
37 18 0.33
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (35 bp):
AAACTTTGAAAACTATTTTCAAAGAAACATTTACT
Found at i:654782 original size:14 final size:14
Alignment explanation
Indices: 654763--654790 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
654753 ATGTAAACTG
654763 AACATAAATAAATA
1 AACATAAATAAATA
654777 AACATAAATAAATA
1 AACATAAATAAATA
654791 TTTATTCTAT
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:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AACATAAATAAATA
Found at i:654923 original size:368 final size:366
Alignment explanation
Indices: 654246--654983 Score: 1335
Period size: 368 Copynumber: 2.0 Consensus size: 366
654236 ATTAACAAAA
654246 AAGCTTTAAACATTCATCAACTTTCGCTCATGGACATATTTATAAATATATTTATTTAATATTAA
1 AAGCTTTAAACATTCATCAACTTTCGCTCATGGACATATTTAT-AATATATTTATTTAATATTAA
654311 TGACTATATTAATTTAATATTTAAATATGTATAATTTTAAAAATATAAATACTAAATATAATTTT
65 TGACTATATTAATTTAATATTTAAATATGTATAATTTTAAAAATATAAATACTAAATATAATTTT
654376 AAACTTAATAATAAATGTAAACTGAACATAAATAATTAAATAAATTCTATTCTAAACTCAAACTC
130 AAACTTAATAATAAATGTAAACTGAACATAAATAATTAAATAAATTCTATTCT-AACTCAAACTC
654441 ATCTTTTACTGCCTACAGAATAGACGCTTGGTCTGATGATGGCCCGACCGGGTCTGAAAAAAATG
194 ATCTTTTACTGCCTACAGAATAGACGCTTGGTCTGATGATGGCCCGACCGGGTCTGAAAAAAATG
654506 CGTCGAAATTCGGCCCGAATCGGTCGTGTAGCTTCCATTTATATATGCAATCTCGTGAACCTTCC
259 CGTCGAAATTCGGCCCGAATCGGTCGTGTAGCTTCCATTTATATATGCAATCTCGTGAACCTTCC
654571 ATTCATAAGCCATCGCCCTGTTCCAATTATCTCCAACATCAAC
324 ATTCATAAGCCATCGCCCTGTTCCAATTATCTCCAACATCAAC
654614 AAGCTTTAAACATTCATCAACTTTCGCTCATGGACATATTTAT-A-A-A-TTATTTAATATTAAT
1 AAGCTTTAAACATTCATCAACTTTCGCTCATGGACATATTTATAATATATTTATTTAATATTAAT
654675 GACTATATTAATTTAATATTTAAATATGTATAATTTTAAAAATATAAATACTAAATATAATTTTA
66 GACTATATTAATTTAATATTTAAATATGTATAATTTTAAAAATATAAATACTAAATATAATTTTA
*
654740 AACTTAATAATAAATGTAAACTGAACATAAATAAATAAACATAAATAAATATTTATTCT-A-TCA
131 AACTTAATAATAAATGTAAACTGAACATAAAT-AAT-----TAAATAAAT-TCTATTCTAACTCA
654803 AACTCATCTATTTACTGCCTACAGAATAGACGCTTGGTCTGATGATGGCCCGACCGGGTCTGAAA
189 AACTCATCT-TTTACTGCCTACAGAATAGACGCTTGGTCTGATGATGGCCCGACCGGGTCTGAAA
654868 AAAATGCGTCGAAATTCGGCCCGAATCGGTCGTGTAGCTTCCATTTATATATGCAATCTCGTGAA
253 AAAATGCGTCGAAATTCGGCCCGAATCGGTCGTGTAGCTTCCATTTATATATGCAATCTCGTGAA
654933 CCTTCCATTCATAAGCCATCGCCCTGTTCCAATTATCTCCAACATCAAC
318 CCTTCCATTCATAAGCCATCGCCCTGTTCCAATTATCTCCAACATCAAC
654982 AA
1 AA
654984 TAACAGCGAC
Statistics
Matches: 361, Mismatches: 1, Indels: 16
0.96 0.00 0.04
Matches are distributed among these distances:
363 112 0.31
364 4 0.01
365 1 0.00
366 1 0.00
367 12 0.03
368 215 0.60
369 9 0.02
370 7 0.02
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (366 bp):
AAGCTTTAAACATTCATCAACTTTCGCTCATGGACATATTTATAATATATTTATTTAATATTAAT
GACTATATTAATTTAATATTTAAATATGTATAATTTTAAAAATATAAATACTAAATATAATTTTA
AACTTAATAATAAATGTAAACTGAACATAAATAATTAAATAAATTCTATTCTAACTCAAACTCAT
CTTTTACTGCCTACAGAATAGACGCTTGGTCTGATGATGGCCCGACCGGGTCTGAAAAAAATGCG
TCGAAATTCGGCCCGAATCGGTCGTGTAGCTTCCATTTATATATGCAATCTCGTGAACCTTCCAT
TCATAAGCCATCGCCCTGTTCCAATTATCTCCAACATCAAC
Found at i:663064 original size:27 final size:28
Alignment explanation
Indices: 663034--663094 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
663024 AATTTATCAT
663034 ATTAC-TTAAAACATGTCAAAATATATA
1 ATTACGTTAAAACATGTCAAAATATATA
* *
663061 ATTACTGTTCATACATGTCAAAATATATA
1 ATTAC-GTTAAAACATGTCAAAATATATA
663090 ATTAC
1 ATTAC
663095 AAGTAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
29 25 0.83
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (28 bp):
ATTACGTTAAAACATGTCAAAATATATA
Found at i:663474 original size:22 final size:22
Alignment explanation
Indices: 663446--663487 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
663436 TTGAAAATTT
*
663446 TAATTATTCAAATAATATAAGA
1 TAATTATACAAATAATATAAGA
*
663468 TAATTATACAGATAATATAA
1 TAATTATACAAATAATATAA
663488 TTAGTCGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (22 bp):
TAATTATACAAATAATATAAGA
Found at i:668323 original size:12 final size:12
Alignment explanation
Indices: 668285--668377 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
668275 ATTTCTGACT
668285 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
668297 TG-ATACATGACC
1 TGAATTC-TGTTC
668309 TGAATTCTGTTC
1 TGAATTCTGTTC
* * *
668321 TGATTTTTGATC
1 TGAATTCTGTTC
*
668333 TGGATTCTGTTC
1 TGAATTCTGTTC
668345 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
* * *
668357 TGGATTATGTTT
1 TGAATTCTGTTC
*
668369 TGATTTCTG
1 TGAATTCTG
668378 ATATCTCCGT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 5 0.08
12 49 0.83
13 5 0.08
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.49
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:668339 original size:24 final size:24
Alignment explanation
Indices: 668288--668379 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
668278 TCTGACTTGA
* *
668288 ATTCTGTTCTGATA-CATGACCTGA
1 ATTCTGTTCTGATATC-TGATCTGG
* *
668312 ATTCTGTTCTGATTTTTGATCTGG
1 ATTCTGTTCTGATATCTGATCTGG
*
668336 ATTCTGTTCTGATATCTGTTCTGG
1 ATTCTGTTCTGATATCTGATCTGG
* * *
668360 ATTATGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGAT
668380 ATCTCCGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.50
Consensus pattern (24 bp):
ATTCTGTTCTGATATCTGATCTGG
Found at i:668373 original size:48 final size:49
Alignment explanation
Indices: 668271--668379 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 49
668261 AAATATTTTA
*
668271 TTTGATTTCTGA-CTTGAATTCTGTTCTGATACATGACCTGAATTCTGT
1 TTTGATTTCTGATCTTGAATTCTGTTCTGATACATGACCTGAATTATGT
* * * ** *
668319 TCTGATTTTTGATC-TGGATTCTGTTCTGATATC-TGTTCTGGATTATGT
1 TTTGATTTCTGATCTTGAATTCTGTTCTGATA-CATGACCTGAATTATGT
668367 TTTGATTTCTGAT
1 TTTGATTTCTGAT
668380 ATCTCCGTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
48 48 0.96
49 2 0.04
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.50
Consensus pattern (49 bp):
TTTGATTTCTGATCTTGAATTCTGTTCTGATACATGACCTGAATTATGT
Found at i:670979 original size:3 final size:3
Alignment explanation
Indices: 670971--670996 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
670961 CTTCTACTCT
670971 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
670997 GTATAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:671387 original size:11 final size:12
Alignment explanation
Indices: 671359--671404 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
671349 TATTACAAAC
*
671359 AAATAAATAATG
1 AAATAAATAATA
671371 AAATAAAT-ATA
1 AAATAAATAATA
671382 AAAT-AATAATA
1 AAATAAATAATA
**
671393 CTATAAATAATA
1 AAATAAATAATA
671405 TTTAAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 11 0.38
12 15 0.52
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:671434 original size:21 final size:21
Alignment explanation
Indices: 671392--671453 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
671382 AAATAATAAT
*
671392 ACTATAA-ATAATATTT-AAAA
1 ACTATAATAT-ATTTTTAAAAA
*
671412 ACTATATTATATTTTTAAAAA
1 ACTATAATATATTTTTAAAAA
*
671433 ACTATAATATGTTTTTAAAAA
1 ACTATAATATATTTTTAAAAA
671454 TTATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 11 0.31
21 25 0.69
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (21 bp):
ACTATAATATATTTTTAAAAA
Found at i:671442 original size:19 final size:20
Alignment explanation
Indices: 671408--671464 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
671398 AATAATATTT
671408 AAAAACTATATTATATTTTTA
1 AAAAACTATA-TATATTTTTA
*
671429 AAAAACTATA-ATATGTTTTT
1 AAAAACTATATATAT-TTTTA
*
671449 AAAAATTATATATATT
1 AAAAACTATATATATT
671465 ATATGCGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.12
20 14 0.44
21 14 0.44
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (20 bp):
AAAAACTATATATATTTTTA
Found at i:671463 original size:21 final size:20
Alignment explanation
Indices: 671405--671464 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
671395 ATAAATAATA
671405 TTTAAAAACTATATTATATTT
1 TTTAAAAACTATA-TATATTT
*
671426 TTAAAAAACTATA-ATATGTT
1 TTTAAAAACTATATATAT-TT
*
671446 TTTAAAAATTATATATATT
1 TTTAAAAACTATATATATT
671465 ATATGCGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 4 0.12
20 14 0.41
21 16 0.47
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAAAAACTATATATATTT
Found at i:671545 original size:22 final size:21
Alignment explanation
Indices: 671489--671572 Score: 89
Period size: 22 Copynumber: 3.8 Consensus size: 21
671479 AAACTGCTTT
*
671489 AAAT-ATATATATATTTTAAA
1 AAATCATATATATATTTTCAA
*
671509 AAATTATATATTATATGTTTTCAA
1 AAATCATATA-TATA--TTTTCAA
671533 AAATCATACTATATATTTTCAA
1 AAATCATA-TATATATTTTCAA
*
671555 AAATTATATATATTATTT
1 AAATCATATATA-TATTT
671573 ATTTTTGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
20 4 0.07
21 9 0.16
22 23 0.42
24 17 0.31
25 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (21 bp):
AAATCATATATATATTTTCAA
Found at i:676919 original size:29 final size:31
Alignment explanation
Indices: 676886--676945 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
676876 AAATGTGAAC
*
676886 TTAAACTTATAAAATTTT-AAGAGAC-AAAT
1 TTAAACTCATAAAATTTTAAAGAGACGAAAT
676915 TTAAACTCATAAAATTTTAAAGAGACGAAAT
1 TTAAACTCATAAAATTTTAAAGAGACGAAAT
676946 AGATTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 17 0.61
30 7 0.25
31 4 0.14
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (31 bp):
TTAAACTCATAAAATTTTAAAGAGACGAAAT
Found at i:678716 original size:42 final size:42
Alignment explanation
Indices: 678621--678744 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 42
678611 GCTCCCATTT
* * * *
678621 TTTTATCTTTATAATT-AGGCCTCTAGTTTTTTGAATCTCATCT
1 TTTTAACTTTATAATTGA-GCCCCTA-TTTTTTTAATCTCATCA
*
678664 TTTTACCTTTATAATTGATGCCCCTATTTTTTTAATCTCA-CA
1 TTTTAACTTTATAATTGA-GCCCCTATTTTTTTAATCTCATCA
* *
678706 TTTTAACTTTATAACTGAGCCCTTATGTTTTTTCAATCT
1 TTTTAACTTTATAATTGAGCCCCTAT-TTTTTT-AATCT
678745 TACTTTCTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 7 0.10
42 23 0.33
43 33 0.47
44 7 0.10
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.52
Consensus pattern (42 bp):
TTTTAACTTTATAATTGAGCCCCTATTTTTTTAATCTCATCA
Found at i:678899 original size:45 final size:43
Alignment explanation
Indices: 678780--678906 Score: 116
Period size: 45 Copynumber: 2.9 Consensus size: 43
678770 ATTGAGGCCT
* * * * *
678780 CTAAGTTTTTTCAATCTCAATTTGTACCTATATAATTAAATCC
1 CTAATTTTTTTCAATATCACTTTCTACCTTTATAATTAAATCC
* *
678823 CTAATTTTTTT-AATCA-CACATTTTTAACTTTATAATTGAGAA-CC
1 CTAATTTTTTTCAAT-ATCAC-TTTCTACCTTTATAATT-A-AATCC
*
678867 TTAAATTTTTTTCAATATCACTTTCTACCTTTATAATTAA
1 CT-AATTTTTTTCAATATCACTTTCTACCTTTATAATTAA
678907 GGCCCCTAAG
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
42 5 0.07
43 25 0.37
44 5 0.07
45 27 0.40
46 6 0.09
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (43 bp):
CTAATTTTTTTCAATATCACTTTCTACCTTTATAATTAAATCC
Found at i:682351 original size:39 final size:37
Alignment explanation
Indices: 682274--682553 Score: 195
Period size: 38 Copynumber: 7.6 Consensus size: 37
682264 TGAAACTACG
* * * *
682274 TATATAATATATAGTTTTTAATA-GTTTT-TAAAAT-
1 TATATAATATATAGTTTTAAAAACATTTTGGAAAATA
*
682308 TATATAATATATAGTTTTAAAAAAACATTTTAGAAAATA
1 TATATAATATATAGTTTT--AAAAACATTTTGGAAAATA
* *
682347 TATATAATATATAATTTTTAAAATCA-TTTGGAAAACT-
1 TATATAATATAT-AGTTTTAAAAACATTTTGGAAAA-TA
* * *
682384 TATATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATA-ATATATAG-TTTTAAAAACATTTTGGAAAATA
* * *
682423 TATAT-AT-TATAGTTTTGAAAGCATTTT-GAAAACA
1 TATATAATATATAGTTTTAAAAACATTTTGGAAAATA
* * * *
682457 TTTATATTATATAGTTTTTAAAACATTTTGGGAAAATT
1 TATATAATATATAGTTTTAAAAACATTTT-GGAAAATA
* * * *
682495 TATATAATCT-T--TTTTGAAAACATGTTGGAAAACA
1 TATATAATATATAGTTTTAAAAACATTTTGGAAAATA
* *
682529 TTCGTATATTATATAGTTTTAAAAA
1 -T-ATATAATATATAGTTTTAAAAA
682554 AAAAAAAACA
Statistics
Matches: 196, Mismatches: 30, Indels: 35
0.75 0.11 0.13
Matches are distributed among these distances:
34 35 0.18
35 29 0.15
36 32 0.16
37 23 0.12
38 39 0.20
39 33 0.17
40 5 0.03
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAACATTTTGGAAAATA
Found at i:682375 original size:38 final size:37
Alignment explanation
Indices: 682274--682526 Score: 177
Period size: 34 Copynumber: 6.9 Consensus size: 37
682264 TGAAACTACG
* * * *
682274 TATATAATATATAGTTTTTAATA-GTTTT-TAAAAT-
1 TATATAATATATAATTTTTAAAACATTTTGGAAAATA
* * *
682308 TATATAATATATAGTTTTAAAAAAACATTTTAGAAAATA
1 TATATAATATATAATTTT--TAAAACATTTTGGAAAATA
682347 TATATAATATATAATTTTTAAAATCA-TTTGGAAAACT-
1 TATATAATATATAATTTTTAAAA-CATTTTGGAAAA-TA
* * *
682384 TATATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATA-ATATATAATTTTT-AAAACATTTTGGAAAATA
* * * *
682423 TATAT-AT-TATAGTTTTGAAAGCATTTT-GAAAACA
1 TATATAATATATAATTTTTAAAACATTTTGGAAAATA
* * * *
682457 TTTATATTATATAGTTTTTAAAACATTTTGGGAAAATT
1 TATATAATATATAATTTTTAAAACATTTT-GGAAAATA
* * *
682495 TATATAATCT-T--TTTTGAAAACATGTTGGAAAA
1 TATATAATATATAATTTTTAAAACATTTTGGAAAA
682527 CATTCGTATA
Statistics
Matches: 181, Mismatches: 23, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
34 35 0.19
35 23 0.13
36 30 0.17
37 25 0.14
38 34 0.19
39 34 0.19
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TATATAATATATAATTTTTAAAACATTTTGGAAAATA
Found at i:682416 original size:12 final size:12
Alignment explanation
Indices: 682399--682423 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
682389 ATATATATAG
682399 TTTTTGAAAACA
1 TTTTTGAAAACA
682411 TTTTTGAAAACA
1 TTTTTGAAAACA
682423 T
1 T
682424 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:682463 original size:36 final size:36
Alignment explanation
Indices: 682329--682541 Score: 161
Period size: 36 Copynumber: 5.8 Consensus size: 36
682319 TAGTTTTAAA
* * * *
682329 AAAACATTTTAGAAAATATATATA-ATATATAATTTTT
1 AAAACATTTT-GAAAACATTTATATAT-TATAGTTTTG
*
682366 AAAATCATTTGGAAAAC-TTATATATATATATAGTTTTTG
1 AAAA-CATTTTGAAAACATT-TATATAT-TATAG-TTTTG
682405 AAAACATTTTTGAAAACA--TATATATTATAGTTTTG
1 AAAACA-TTTTGAAAACATTTATATATTATAGTTTTG
* *
682440 AAAGCATTTTGAAAACATTTATAT-TATATAGTTTTT
1 AAAACATTTTGAAAACATTTATATAT-TATAGTTTTG
* * * *
682476 AAAACATTTTGGGAAA-ATTTATATAATCT-TTTTTG
1 AAAACATTTT-GAAAACATTTATATATTATAGTTTTG
* **
682511 AAAACATGTTGGAAAACATTCGTATATTATA
1 AAAACAT-TTTGAAAACATTTATATATTATA
682542 TAGTTTTAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
34 11 0.08
35 26 0.18
36 50 0.35
37 24 0.17
38 14 0.10
39 17 0.12
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (36 bp):
AAAACATTTTGAAAACATTTATATATTATAGTTTTG
Found at i:682525 original size:34 final size:34
Alignment explanation
Indices: 682329--682526 Score: 139
Period size: 35 Copynumber: 5.5 Consensus size: 34
682319 TAGTTTTAAA
* * *
682329 AAAACATTTTAGAAAATATATATAATATATAATTTTT
1 AAAACATTTTGGAAAATTTATATAATAT-T--TTTTG
682366 AAAATCA-TTTGGAAAACTTATATATATATATAGTTTTTG
1 AAAA-CATTTTGGAAAA-TT-TATATA-ATAT--TTTTTG
* ** * *
682405 AAAACATTTTTGAAAACATATATATTATAGTTTTG
1 AAAACATTTTGGAAAATTTATATAATAT-TTTTTG
* * *
682440 AAAGCATTTTGAAAACATTTATATTATATAGTTTTT-
1 AAAACATTTTGGAAA-ATTTATA-TA-ATATTTTTTG
*
682476 AAAACATTTTGGGAAAATTTATATAATCTTTTTTG
1 AAAACATTTT-GGAAAATTTATATAATATTTTTTG
*
682511 AAAACATGTTGGAAAA
1 AAAACATTTTGGAAAA
682527 CATTCGTATA
Statistics
Matches: 127, Mismatches: 23, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
34 13 0.10
35 28 0.22
36 24 0.19
37 28 0.22
38 7 0.06
39 22 0.17
40 4 0.03
41 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAACATTTTGGAAAATTTATATAATATTTTTTG
Found at i:682622 original size:3 final size:3
Alignment explanation
Indices: 682614--682651 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
682604 TGTATATATA
682614 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
682652 TTCATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:688204 original size:248 final size:249
Alignment explanation
Indices: 687718--688844 Score: 1560
Period size: 248 Copynumber: 4.5 Consensus size: 249
687708 ACTATTTGTA
687718 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGTCACCAAAG
1 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAG
* * ** * * * * *
687783 ACCCTCGAGTTCGACTACGTTCAGCTTCGAA-GGCACATCATTTGCAGTATAACTTAAGTCAAGA
63 ACCCTTGAGTTCGATTACACTCAGCTTC-AAGGGCATATCATTTACAGCATAACTCAAGGCAAGA
* * *
687847 AGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTA
127 AGGGTTATCTGCCAACAAAAGACCCTTAAGTTCGACTACACTCAGCTTCAACGGCATATCATTTA
* *
687912 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTAC
192 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTGCGACTAC
*
687970 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACC
1 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
* * * *
688035 CTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAACATAACTCAAGGCTAGAAGGG
66 CTTGAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCAAGAAGGG
** * * * *
688100 TTATCTGTTAACAAAAGACCTTTGAGTTTGACTACGCTCAGC-TCAACGGCATATCATTTACAGC
131 TTATCTGCCAACAAAAGACCCTTAAGTTCGACTACACTCAGCTTCAACGGCATATCATTTACAGC
* *
688164 ATAACTCAAGGCTAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTAC
196 ATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTGCGACTAC
* * *
688218 GCTCGGCTCTAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
* * ** * * * * *
688283 CTCGAGTTCGACTACGTTCAGCTTCGAA-GGCACATCATTTGCAGTATAACTTAAGTCAAGAAGG
66 CTTGAGTTCGATTACACTCAGCTTC-AAGGGCATATCATTTACAGCATAACTCAAGGCAAGAAGG
* * * *
688347 GTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTTCAG
130 GTTATCTGCCAACAAAAGACCCTTAAGTTCGACTACACTCAGCTTCAACGGCATATCATTTACAG
* *
688412 CATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTAC
195 CATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTGCGACTAC
*
688467 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACC
1 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
* * *
688532 CTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGG
66 CTTGAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCAAGAAGGG
** * * * *
688597 TTATCTGTTAACAAAAGACCTTTGAGTTTGACTACGCTCAGC-TCAACGGCATATCATTTACAGC
131 TTATCTGCCAACAAAAGACCCTTAAGTTCGACTACACTCAGCTTCAACGGCATATCATTTACAGC
* *
688661 ATAACTCAAGGCTAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTAC
196 ATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTGCGACTAC
* * * *
688715 GCTCGGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
* * * * * * * *
688780 CCTGGGTTCGATTACACTCAACTTCGAGGTCATATCAGTTACAACATAGCTCAAGGCAAGAAGGG
66 CTTGAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCAAGAAGGG
688845 CTATTTGTCA
Statistics
Matches: 767, Mismatches: 104, Indels: 12
0.87 0.12 0.01
Matches are distributed among these distances:
248 403 0.53
249 309 0.40
252 55 0.07
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (249 bp):
GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
CTTGAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCAAGAAGGG
TTATCTGCCAACAAAAGACCCTTAAGTTCGACTACACTCAGCTTCAACGGCATATCATTTACAGC
ATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTGCGACTAC
Found at i:688844 original size:497 final size:497
Alignment explanation
Indices: 687718--688780 Score: 2045
Period size: 497 Copynumber: 2.1 Consensus size: 497
687708 ACTATTTGTA
* * *
687718 GCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGTCACCAAAG
1 GCTCGGCTCTAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAG
687783 ACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAA
63 ACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAA
687848 GGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTAC
128 GGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTAC
687913 AGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCT
193 AGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCT
687978 CCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACCCTTAAGTT
258 CCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACCCTTAAGTT
688043 CGATTACACTCAGCTTCAAGGGCATAACATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGT
323 CGATTACACTCAGCTTCAAGGGCATAACATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGT
688108 TAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCATATCATTTACAGCATAACTCAA
388 TAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCATATCATTTACAGCATAACTCAA
688173 GGCTAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTAC
453 GGCTAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTAC
688218 GCTCGGCTCTAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1 GCTCGGCTCTAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
688283 CTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGG
66 CTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGG
*
688348 TTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTTCAGC
131 TTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGC
688413 ATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCA
196 ATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCA
688478 AGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACCCTTAAGTTCGA
261 AGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACCCTTAAGTTCGA
*
688543 TTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAA
326 TTACACTCAGCTTCAAGGGCATAACATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTTAA
688608 CAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCATATCATTTACAGCATAACTCAAGGC
391 CAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCATATCATTTACAGCATAACTCAAGGC
688673 TAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTAC
456 TAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTAC
*
688715 GCTCGGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
1 GCTCGGCTCTAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
688780 C
66 C
688781 CTGGGTTCGA
Statistics
Matches: 557, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
497 504 0.90
500 53 0.10
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (497 bp):
GCTCGGCTCTAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGG
TTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGC
ATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCA
AGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAAAGACCCTTAAGTTCGA
TTACACTCAGCTTCAAGGGCATAACATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTTAA
CAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCATATCATTTACAGCATAACTCAAGGC
TAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTAC
Found at i:689550 original size:37 final size:37
Alignment explanation
Indices: 689444--689670 Score: 204
Period size: 39 Copynumber: 6.2 Consensus size: 37
689434 TGAAACTACG
* * *
689444 TATATAATATATAGTTTTTAATA-GTTTT--TAAAT-
1 TATATAATATATAGTTTTTAAAACATTTTGGAAAATA
* *
689477 TATATAATATATAGTTTTAAAAAAACATTTTAGAAAATA
1 TATATAATATATAGTTTT--TAAAACATTTTGGAAAATA
*
689516 TATATAATATATAATTTTTAAAATCA-TTTGGAAAACT-
1 TATATAATATATAGTTTTTAAAA-CATTTTGGAAAA-TA
* *
689553 TATATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATA-ATATATAGTTTTT-AAAACATTTTGGAAAATA
* * *
689592 TATAT-AT-TATAGTTTTGAAAGCATTTT-GAAAACA
1 TATATAATATATAGTTTTTAAAACATTTTGGAAAATA
* *
689626 TTTAT-ATATATAGTTTTTAAAACATTTTGGGAAAATT
1 TATATAATATATAGTTTTTAAAACATTTT-GGAAAATA
689663 TATATAAT
1 TATATAAT
689671 CTTTTTGAAA
Statistics
Matches: 160, Mismatches: 18, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
33 18 0.11
34 13 0.08
35 30 0.19
36 13 0.08
37 29 0.18
38 23 0.14
39 34 0.21
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAACATTTTGGAAAATA
Found at i:689585 original size:12 final size:12
Alignment explanation
Indices: 689568--689592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
689558 ATATATATAG
689568 TTTTTGAAAACA
1 TTTTTGAAAACA
689580 TTTTTGAAAACA
1 TTTTTGAAAACA
689592 T
1 T
689593 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:689608 original size:35 final size:36
Alignment explanation
Indices: 689477--689720 Score: 210
Period size: 39 Copynumber: 6.6 Consensus size: 36
689467 GTTTTTAAAT
* * *
689477 TATATAATATATAGTTTTAAAAAAACATTTTAGAAAATA
1 TATAT-ATATATAGTTTT--GAAAACATTTTGGAAAACA
* *
689516 TATATAATATATAATTTTTAAAATCA-TTTGGAAAACTTA
1 TATAT-ATATATAGTTTTGAAAA-CATTTTGGAAAAC--A
*
689555 TATATATATATAGTTTTTGAAAACATTTTTGAAAACA
1 TATATATATATAG-TTTTGAAAACATTTTGGAAAACA
*
689592 TATATAT-TATAGTTTTGAAAGCATTTT-GAAAACA
1 TATATATATATAGTTTTGAAAACATTTTGGAAAACA
* * *
689626 TTTATATATATAGTTTTTAAAACATTTTGGGAAA-A
1 TATATATATATAGTTTTGAAAACATTTTGGAAAACA
* ** *
689661 TTTATATA-ATCTTTTTGAAAACATGTTGGAAAACA
1 TATATATATATAGTTTTGAAAACATTTTGGAAAACA
* *
689696 TTCGTATATTATATAGTTTTAAAAA
1 -T-ATATA-TATATAGTTTTGAAAA
689721 AAAAAAAAAC
Statistics
Matches: 172, Mismatches: 21, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
34 33 0.19
35 42 0.24
36 10 0.06
37 24 0.14
38 13 0.08
39 50 0.29
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.43
Consensus pattern (36 bp):
TATATATATATAGTTTTGAAAACATTTTGGAAAACA
Found at i:689643 original size:71 final size:69
Alignment explanation
Indices: 689483--689720 Score: 226
Period size: 73 Copynumber: 3.2 Consensus size: 69
689473 AAATTATATA
*
689483 ATATATAGTTTTAAAAAAACATTTTAGAAAATATATATAATATATAATTTTT-AAAATCATTTGG
1 ATATATAGTTTT--TAAAACATTTTAGAAAA-ATATAT-AT-TAT-ATTTTTGAAAA-CATTTGG
*
689547 AAAACTTATATAT
59 AAAAC--ATTTAT
* * * *
689560 ATATATAGTTTTTGAAAACATTTTTGAAAACATATATATTATAGTTTTGAAAGCATTTTGAAAAC
1 ATATATAGTTTTT-AAAACATTTTAGAAAA-ATATATATTATATTTTTGAAAACATTTGGAAAAC
689625 ATTTAT
64 ATTTAT
* * * * *
689631 ATATATAGTTTTTAAAACATTTTGGGAAAATTTATATAATCTTTTTGAAAACATGTTGGAAAACA
1 ATATATAGTTTTTAAAACATTTTAGAAAAATATATATTATATTTTTGAAAACAT-TTGGAAAACA
689696 TTCGTAT
65 TT--TAT
*
689703 ATTATATAGTTTTAAAAA
1 A-TATATAGTTTTTAAAA
689721 AAAAAAAAAC
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
69 20 0.14
70 25 0.18
71 18 0.13
72 4 0.03
73 31 0.22
74 6 0.04
75 2 0.01
76 21 0.15
77 12 0.09
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (69 bp):
ATATATAGTTTTTAAAACATTTTAGAAAAATATATATTATATTTTTGAAAACATTTGGAAAACAT
TTAT
Found at i:689790 original size:3 final size:3
Alignment explanation
Indices: 689782--689816 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
689772 TGTATATATA
689782 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
689817 TTTCATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:689801 original size:16 final size:16
Alignment explanation
Indices: 689782--689813 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
689772 TGTATATATA
689782 TATTATTATTATTATT
1 TATTATTATTATTATT
689798 TATTATTATTATTATT
1 TATTATTATTATTATT
689814 ATTTTTCATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTATTATTATTATT
Found at i:691364 original size:20 final size:20
Alignment explanation
Indices: 691331--691374 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
691321 GGAATGTAAG
*
691331 ATTATTAGTAGAAATAAAAA
1 ATTATCAGTAGAAATAAAAA
*
691351 ATTATCAGTGGAAATAAAAA
1 ATTATCAGTAGAAATAAAAA
691371 ATTA
1 ATTA
691375 CCAGATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (20 bp):
ATTATCAGTAGAAATAAAAA
Found at i:691605 original size:32 final size:32
Alignment explanation
Indices: 691520--691605 Score: 88
Period size: 36 Copynumber: 2.6 Consensus size: 32
691510 TTGTATAATA
691520 TTAC-AAATTATAAAATATTTATATATTTTCTT
1 TTACAAAATTA-AAAATATTTATATATTTTCTT
691552 TTA-AAAATTAAATTCATAATATTTATATAATTTT-TT
1 TTACAAAATT-AA---A-AATATTTATAT-ATTTTCTT
691588 TTACAAAATTAAAAATAT
1 TTACAAAATTAAAAATAT
691606 AAAAAATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
32 14 0.30
33 2 0.04
35 1 0.02
36 18 0.39
37 11 0.24
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (32 bp):
TTACAAAATTAAAAATATTTATATATTTTCTT
Done.