Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 26
Found at i:2347118 original size:106 final size:106
Alignment explanation
Indices: 2346659--2347129 Score: 674
Period size: 106 Copynumber: 4.4 Consensus size: 106
2346649 CACATCCACG
* * * * *
2346659 ATTTCAACTCCACAACGGAGGATATCGCGCCACCCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATATTG-G--ACTCGAAACAACACAAGTTCAACTTCACAACGAA
*
2346724 GGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
63 GGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
* *
2346768 ATTTCAACTTCACAGCGAATGATATTGGACTC-AAGACAACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAA-ACAACACAAGTTCAACTTCACAACGAAGG
* * *
2346832 GATGGCTGGTTGTCAACAAACAATTTCCCAATTTTAGAGCCA
65 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
** * *
2346874 ATTTCAACTTCACAACGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAACACAAGTTCAACTTCACAACGAAGGG
*
2346939 ACGGCTGGTTGTCAACAAACAATTTCTCAATTTCAGAACCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
*
2346980 ATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAACACAAGTTCAAATTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAACACAAGTTCAACTTCACAACGAAGGG
* *
2347045 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAACCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
*** * * *
2347086 ATTTCAACTTCATGGCGGAGGATATTGGACTCGGAACAATACAA
1 ATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAACACAA
2347130 CCTACTTGGA
Statistics
Matches: 327, Mismatches: 33, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
105 1 0.00
106 302 0.92
107 1 0.00
108 1 0.00
109 22 0.07
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAACCA
Found at i:2348505 original size:62 final size:58
Alignment explanation
Indices: 2348437--2348589 Score: 152
Period size: 60 Copynumber: 2.6 Consensus size: 58
2348427 AATTTTCTTC
* * *
2348437 TTATTTTATTTAATATTACATTATAGTATATATTTGATATTACTCTATTATATTATTA-TTAT
1 TTATTTTATTTAATGTTA-ATTATA-TATATATAT-ATATCA-T-TATTATATTATTATTTAT
* * * *
2348499 TTATTTTCTTT--TGTT-GTTATATATATACATATATCATTATTATTTTATTATTTAT
1 TTATTTTATTTAATGTTAATTATATATATATATATATCATTATTATATTATTATTTAT
2348554 TTATTTTATTTATATGTTATATTATATATATATATA
1 TTATTTTATTTA-ATGTTA-ATTATATATATATATA
2348590 CATATATATT
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
54 12 0.16
55 15 0.20
56 5 0.07
57 7 0.09
58 9 0.12
60 17 0.23
62 10 0.13
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (58 bp):
TTATTTTATTTAATGTTAATTATATATATATATATATCATTATTATATTATTATTTAT
Found at i:2348585 original size:54 final size:54
Alignment explanation
Indices: 2348482--2348600 Score: 145
Period size: 55 Copynumber: 2.2 Consensus size: 54
2348472 GATATTACTC
* *
2348482 TATTATATTATTATTATTTATTTTCTTTTGTTGTTATATATATACATATATCAT
1 TATTATATTATTATTATTTATTTTATTTTGATGTTATATATATACATATATCAT
* *
2348536 TATTATTTTATTATTTATTTATTTTATTTAT-ATGTTATATTATATATATATATACA-
1 TATTATATTATTA-TTATTTATTTTATTT-TGATGTTATA-TATATACATATAT-CAT
2348592 TA-TATATTA
1 TATTATATTA
2348601 CGTTATTTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
54 12 0.21
55 27 0.48
56 15 0.27
57 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (54 bp):
TATTATATTATTATTATTTATTTTATTTTGATGTTATATATATACATATATCAT
Found at i:2350334 original size:21 final size:21
Alignment explanation
Indices: 2350243--2350361 Score: 107
Period size: 21 Copynumber: 5.7 Consensus size: 21
2350233 GATGCACCTA
* *
2350243 TCATCGTTCAAGAGACGCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
2350264 -CTATCATTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
*
2350285 TCATC-ATCGAAGAGGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
2350306 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
* *
2350327 TCATCGTTCAAGAGGTCCCGC
1 TCATCGTTCAAGAGGCCCCTC
* *
2350348 CCGTCGTTCAAGAG
1 TCATCGTTCAAGAG
2350362 CCCGATTCAC
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.04
21 73 0.92
22 3 0.04
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:2350340 original size:42 final size:42
Alignment explanation
Indices: 2350243--2350361 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
2350233 GATGCACCTA
* * * *
2350243 TCATCGTTCAAGAGACGCCTCCTATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTC
* * *
2350285 TCATC-ATCGAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCGTTC-AAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTC
* * *
2350327 TCATCGTTCAAGAGGTCCCGCCCGTCGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAG
2350362 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 59 0.94
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.21
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTC
Found at i:2352010 original size:20 final size:20
Alignment explanation
Indices: 2351919--2352003 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
2351909 AATGTACGCT
2351919 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
** *
2351939 TTCGCATTGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
** *
2351959 TTCGCAACGTTAAAGTTAAA
1 TTCGCAACGCGAAAGTCAAA
2351979 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
2351999 TTCGC
1 TTCGC
2352004 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:2354632 original size:24 final size:24
Alignment explanation
Indices: 2354598--2354651 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2354588 CTGAAACATC
2354598 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2354622 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2354646 ATCAAA
1 ATCAAA
2354652 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2354665 original size:24 final size:24
Alignment explanation
Indices: 2354598--2354665 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2354588 CTGAAACATC
* * *
2354598 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2354622 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2354646 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2354666 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2354869 original size:18 final size:18
Alignment explanation
Indices: 2354842--2354879 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2354832 AAATTGTGGT
2354842 GGAACCATTAAATTTTGA
1 GGAACCATTAAATTTTGA
*
2354860 GGAACTATTAAATTTTGA
1 GGAACCATTAAATTTTGA
2354878 GG
1 GG
2354880 TTGATAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (18 bp):
GGAACCATTAAATTTTGA
Found at i:2355628 original size:19 final size:20
Alignment explanation
Indices: 2355604--2355733 Score: 85
Period size: 19 Copynumber: 6.6 Consensus size: 20
2355594 AACTAAAACC
2355604 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
2355623 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* * *
2355643 AGTTGCGAATTTAAAATTC-
1 TGTTGCGAAATTGAAATTCG
* *
2355662 AGTTGCGAATTTGAAATT--
1 TGTTGCGAAATTGAAATTCG
2355680 TAGTTGC-AAATTTGAAATTCAG
1 T-GTTGCGAAA-TTGAAATTC-G
* *
2355702 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAAATTGAAATTC-G
*
2355722 TGTTGCAAAATT
1 TGTTGCGAAATT
2355734 AACTTCTGCA
Statistics
Matches: 89, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
18 6 0.07
19 37 0.42
20 32 0.36
21 11 0.12
22 3 0.03
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:2355657 original size:39 final size:39
Alignment explanation
Indices: 2355605--2355712 Score: 121
Period size: 38 Copynumber: 2.8 Consensus size: 39
2355595 ACTAAAACCT
*
2355605 GTTGCGAAATT-AAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTAAAATTCGTGTTGCGAATTCG-AAATCGA
* * **
2355644 GTTGCGAATTTAAAATTC-AGTTGCGAATTTGAAATTTA
1 GTTGCGAATTTAAAATTCGTGTTGCGAATTCGAAATCGA
* *
2355682 GTTGCAAATTTGAAATTCAGTGTTGCGAATT
1 GTTGCGAATTTAAAATTC-GTGTTGCGAATT
2355713 TGACTTCTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
38 21 0.36
39 21 0.36
40 16 0.28
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.36
Consensus pattern (39 bp):
GTTGCGAATTTAAAATTCGTGTTGCGAATTCGAAATCGA
Found at i:2355733 original size:21 final size:20
Alignment explanation
Indices: 2355682--2355741 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
2355672 TTGAAATTTA
* *
2355682 GTTGCAAATTTGAAATTCAGT
1 GTTGCAAATTTG-ACTTCTGT
*
2355703 GTTGCGAATTTGACTTCTGT
1 GTTGCAAATTTGACTTCTGT
* *
2355723 GTTGCAAAATTAACTTCTG
1 GTTGCAAATTTGACTTCTG
2355742 CATTGCGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (20 bp):
GTTGCAAATTTGACTTCTGT
Found at i:2357027 original size:27 final size:27
Alignment explanation
Indices: 2356995--2357091 Score: 140
Period size: 27 Copynumber: 3.6 Consensus size: 27
2356985 GCTATAAAAT
*
2356995 TTTGTCCCAAAAGACCTATGTACTGTA
1 TTTGTCCCGAAAGACCTATGTACTGTA
* *
2357022 TTTGTCCCGAAGGACTTATGTACTGTA
1 TTTGTCCCGAAAGACCTATGTACTGTA
* *
2357049 TTTGTCCCGAATGACCTATTTACTGTA
1 TTTGTCCCGAAAGACCTATGTACTGTA
*
2357076 TTTGTCCCGAATGACC
1 TTTGTCCCGAAAGACC
2357092 ACTCCTTAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (27 bp):
TTTGTCCCGAAAGACCTATGTACTGTA
Found at i:2364334 original size:31 final size:30
Alignment explanation
Indices: 2364299--2364400 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
2364289 ATTTTTTTAA
* *
2364299 AATTTAATTTCTAAACTTTAGATGAAATATC
1 AATTTAA-CTCTAAATTTTAGATGAAATATC
*
2364330 AATTTAAC-CTTAAATTTTAGATGAAATACC
1 AATTTAACTC-TAAATTTTAGATGAAATATC
* *
2364360 AA-TGAGACCCTAAATTTTAGATGAAATATC
1 AATTTA-ACTCTAAATTTTAGATGAAATATC
*
2364390 AATTTGACTCT
1 AATTTAACTCT
2364401 TCGGTCACCA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
29 3 0.05
30 47 0.80
31 9 0.15
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (30 bp):
AATTTAACTCTAAATTTTAGATGAAATATC
Found at i:2364351 original size:30 final size:31
Alignment explanation
Indices: 2364309--2364394 Score: 122
Period size: 30 Copynumber: 2.8 Consensus size: 31
2364299 AATTTAATTT
*
2364309 CTAAACTTTAGATGAAATATCAATTTA-ACC
1 CTAAATTTTAGATGAAATATCAATTTAGACC
* * *
2364339 TTAAATTTTAGATGAAATACCAA-TGAGACC
1 CTAAATTTTAGATGAAATATCAATTTAGACC
2364369 CTAAATTTTAGATGAAATATCAATTT
1 CTAAATTTTAGATGAAATATCAATTT
2364395 GACTCTTCGG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 2 0.04
30 44 0.94
31 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (31 bp):
CTAAATTTTAGATGAAATATCAATTTAGACC
Found at i:2364663 original size:38 final size:38
Alignment explanation
Indices: 2364614--2364693 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
2364604 TCATTAATAT
2364614 TCATTTAAAAATAAATTCACCAAAAATATAAATCTATA
1 TCATTTAAAAATAAATTCACCAAAAATATAAATCTATA
2364652 TCATTTAAAAATAAATTCACCAAAAATATAAATCTATA
1 TCATTTAAAAATAAATTCACCAAAAATATAAATCTATA
2364690 TCAT
1 TCAT
2364694 AATCAAATCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.33
Consensus pattern (38 bp):
TCATTTAAAAATAAATTCACCAAAAATATAAATCTATA
Found at i:2370305 original size:2 final size:2
Alignment explanation
Indices: 2370298--2370336 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2370288 TATCCTTCAA
2370298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2370337 CTACTAGCTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2374223 original size:20 final size:20
Alignment explanation
Indices: 2374200--2374238 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2374190 TAGGAGACAT
2374200 CCATAAAAA-ATCCTAAAAAA
1 CCATAAAAATA-CCTAAAAAA
*
2374220 CCATCAAAATACCTAAAAA
1 CCATAAAAATACCTAAAAA
2374239 GCATCTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (20 bp):
CCATAAAAATACCTAAAAAA
Found at i:2379466 original size:2 final size:2
Alignment explanation
Indices: 2379459--2379543 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
2379449 CTTATTTAGA
2379459 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
2379501 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
2379543 A
1 A
2379544 GAACATATTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2379856 original size:2 final size:2
Alignment explanation
Indices: 2379849--2379876 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2379839 TGCCTGCCTC
2379849 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
2379877 TTAAAACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2384465 original size:43 final size:43
Alignment explanation
Indices: 2384391--2384611 Score: 180
Period size: 43 Copynumber: 5.2 Consensus size: 43
2384381 TGAGAACAAA
* * * * * *
2384391 AAACGCCGCAATAGGTCAAGATTTATCGCGGCATTTTTGGAAC
1 AAACGCCGCAAAAAGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
2384434 AAACGCCGCTAAATGTCGATATCTATAGCGGCGCTTTAT-GAAC
1 AAACGCCGCAAAAAGTCGAGATCTATAGCGGCG-TTTTTGGAAC
* * * * **
2384477 AAATGCTGCAAAAAGTAGAGATATATAGCGGCGTTTTTTCTAA-
1 AAACGCCGCAAAAAGTCGAGATCTATAGCGGCG-TTTTTGGAAC
* * * *
2384520 AAACGCCGTAAAAGGT-TAGTTCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAAGTCGAGATCTATAGCGGCGTTTTTGGA-AC
* * *
2384563 AAACACCGCAAAAGGTC-AGATCTATAGCGACGTTTTTGGAAC
1 AAACGCCGCAAAAAGTCGAGATCTATAGCGGCGTTTTTGGAAC
2384605 AAACGCC
1 AAACGCC
2384612 ACCAAATATG
Statistics
Matches: 140, Mismatches: 33, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
41 6 0.04
42 22 0.16
43 106 0.76
44 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAAGTCGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:2385178 original size:20 final size:20
Alignment explanation
Indices: 2385153--2385207 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2385143 ATACTACGCT
*
2385153 AAAATGAGAATATTCATTTA
1 AAAATGAGAAAATTCATTTA
*
2385173 AAAATGATAAAATTCATTTA
1 AAAATGAGAAAATTCATTTA
*
2385193 AAAATGATAAAATTC
1 AAAATGAGAAAATTC
2385208 CAAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (20 bp):
AAAATGAGAAAATTCATTTA
Found at i:2389046 original size:2 final size:2
Alignment explanation
Indices: 2389039--2389078 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2389029 AAATGGATGG
2389039 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
2389079 TATGCATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2390018 original size:12 final size:12
Alignment explanation
Indices: 2390003--2390059 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
2389993 AATTTTGTTA
2390003 TGATTTCTGCTC
1 TGATTTCTGCTC
2390015 TGATTTCTGCTC
1 TGATTTCTGCTC
* * *
2390027 TGAATTCTGTTA
1 TGATTTCTGCTC
*
2390039 TGATTTCTACTC
1 TGATTTCTGCTC
2390051 TGATTTCTG
1 TGATTTCTG
2390060 ATATCTCCGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.51
Consensus pattern (12 bp):
TGATTTCTGCTC
Found at i:2390019 original size:36 final size:36
Alignment explanation
Indices: 2389979--2390056 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
2389969 ATATTTTATT
* * * *
2389979 TGATTTATGTTTTGAATTTTGTTATGATTTCTGCTC
1 TGATTTATGCTCTGAATTCTGTTATGATTTCTACTC
*
2390015 TGATTTCTGCTCTGAATTCTGTTATGATTTCTACTC
1 TGATTTATGCTCTGAATTCTGTTATGATTTCTACTC
2390051 TGATTT
1 TGATTT
2390057 CTGATATCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.55
Consensus pattern (36 bp):
TGATTTATGCTCTGAATTCTGTTATGATTTCTACTC
Found at i:2390057 original size:36 final size:36
Alignment explanation
Indices: 2389991--2390059 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
2389981 ATTTATGTTT
* *
2389991 TGAATTTTGTTATGATTTCTGCTCTGATTTCTGCTC
1 TGAATTCTGTTATGATTTCTACTCTGATTTCTGCTC
2390027 TGAATTCTGTTATGATTTCTACTCTGATTTCTG
1 TGAATTCTGTTATGATTTCTACTCTGATTTCTG
2390060 ATATCTCCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (36 bp):
TGAATTCTGTTATGATTTCTACTCTGATTTCTGCTC
Found at i:2391495 original size:60 final size:59
Alignment explanation
Indices: 2391422--2391545 Score: 203
Period size: 60 Copynumber: 2.1 Consensus size: 59
2391412 TTCTATTTGA
*
2391422 AGTTTTATTCTTACTAGATAAGATTCCAACTATGAAAACCCCAACTAAAACAATCTAATC
1 AGTTTTAGTCTTACTAGATAAGATTCCAACTATGAAAA-CCCAACTAAAACAATCTAATC
* * *
2391482 AGTTTTAGTCTTACTATATAAGATTCTAACTATGAAAACCCAACTGAAACAATCTAATC
1 AGTTTTAGTCTTACTAGATAAGATTCCAACTATGAAAACCCAACTAAAACAATCTAATC
2391541 AGTTT
1 AGTTT
2391546 GCTTATTACT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 25 0.42
60 35 0.58
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (59 bp):
AGTTTTAGTCTTACTAGATAAGATTCCAACTATGAAAACCCAACTAAAACAATCTAATC
Found at i:2391555 original size:59 final size:60
Alignment explanation
Indices: 2391432--2391562 Score: 192
Period size: 59 Copynumber: 2.2 Consensus size: 60
2391422 AGTTTTATTC
* *
2391432 TTACTAGATAAGATTCCAACTATGAAAACCCCAACTAAAACAATCTAATCAGTTTTAGTC
1 TTACTAGATAAGATTCCAACTATGAAAACCCCAACTAAAACAATCTAATCAGTTTGAGTA
* * * **
2391492 TTACTATATAAGATTCTAACTATGAAAA-CCCAACTGAAACAATCTAATCAGTTTGCTTA
1 TTACTAGATAAGATTCCAACTATGAAAACCCCAACTAAAACAATCTAATCAGTTTGAGTA
2391551 TTACTAGATAAG
1 TTACTAGATAAG
2391563 GATCATCGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 37 0.59
60 26 0.41
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (60 bp):
TTACTAGATAAGATTCCAACTATGAAAACCCCAACTAAAACAATCTAATCAGTTTGAGTA
Found at i:2392027 original size:6 final size:6
Alignment explanation
Indices: 2392016--2392043 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2392006 CAAAGCCACG
2392016 AAATCA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAAT
2392044 AACAACAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCA
Found at i:2392355 original size:41 final size:41
Alignment explanation
Indices: 2392310--2392567 Score: 293
Period size: 41 Copynumber: 6.3 Consensus size: 41
2392300 TTGTAAACAC
* *
2392310 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTATGTATAT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
** * *
2392351 AAACGCCACTAAAGTATAATTATATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * ** *
2392392 AAACACCACTAAAGTACAATTATATAGCAACATTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
2392433 AAATGCCACTAAAGTACGAGTCTATAGCGGAGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
2392474 AAACACCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
2392515 AAACGCCACTAAAGTACTACTTTGTTGCGGCGTTTGT-TGAAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT--AA
2392557 AAACGCCACTA
1 AAACGCCACTA
2392568 TGGATAAACC
Statistics
Matches: 185, Mismatches: 30, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
40 1 0.01
41 171 0.92
42 13 0.07
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:2392558 original size:123 final size:124
Alignment explanation
Indices: 2392297--2392531 Score: 339
Period size: 123 Copynumber: 1.9 Consensus size: 124
2392287 AAATTTGCGG
* * *
2392297 CATTTGTA-AACACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTATGTATATAAACGCCACT
1 CATTTGTATAA-A-AAACGCCACTAAAGTACGAGTCTATAGCGGAGTATGTATAAAAACACCACT
* *
2392361 AAAGTATAATTATATAGCGGCGTTTGTATAAAAACACCACTAAAGTACAATTATATAGCAA
64 AAAGTACAAGTATATAGCGGCGTTTGTATAAAAACACCACTAAAGTACAATTATATAGCAA
* *
2392422 CATTTGTAT-AAAAATGCCACTAAAGTACGAGTCTATAGCGGAGTTTGTATAAAAACACCACTAA
1 CATTTGTATAAAAAACGCCACTAAAGTACGAGTCTATAGCGGAGTATGTATAAAAACACCACTAA
* * * *
2392486 AGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAC
66 AGTACAAGTATATAGCGGCGTTTGTATAAAAACACCACTAAAGTAC
2392532 TACTTTGTTG
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
123 88 0.90
124 1 0.01
125 9 0.09
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (124 bp):
CATTTGTATAAAAAACGCCACTAAAGTACGAGTCTATAGCGGAGTATGTATAAAAACACCACTAA
AGTACAAGTATATAGCGGCGTTTGTATAAAAACACCACTAAAGTACAATTATATAGCAA
Found at i:2396733 original size:16 final size:16
Alignment explanation
Indices: 2396674--2396733 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 16
2396664 AGCACCTCAT
*
2396674 TATATATTTACATAT-
1 TATATATATACATATA
*
2396689 T-TATATATACACATA
1 TATATATATACATATA
*
2396704 TA-AT-TAT--ATTTA
1 TATATATATACATATA
2396716 TATATATATACATATA
1 TATATATATACATATA
2396732 TA
1 TA
2396734 AAATAAAACG
Statistics
Matches: 34, Mismatches: 5, Indels: 11
0.68 0.10 0.22
Matches are distributed among these distances:
12 5 0.15
13 2 0.06
14 17 0.50
15 4 0.12
16 6 0.18
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATATACATATA
Found at i:2406677 original size:20 final size:21
Alignment explanation
Indices: 2406638--2406698 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
2406628 TTTTTGTGCA
* *
2406638 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCTTT
*
2406658 GAGGGAACCGATTCCTCCTTT
1 GAGGGAACCGATTCCCCCTTT
2406679 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
2406699 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:2406707 original size:21 final size:21
Alignment explanation
Indices: 2406681--2406720 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2406671 CCTCCTTTGA
*
2406681 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2406702 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2406721 TGGGGTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2410290 original size:23 final size:21
Alignment explanation
Indices: 2410239--2410298 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
2410229 AGGGTGTCAA
*
2410239 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
2410260 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
*
2410282 TAGTGCATCGATGCACC
1 -AGTGCATCCATGCACC
2410299 ATGTAGTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.47
22 1 0.03
23 17 0.50
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:2410765 original size:34 final size:32
Alignment explanation
Indices: 2410726--2410795 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2410716 TTTTGTAAAG
*
2410726 GGGAAAGGTTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* *
2410760 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
2410792 GGGA
1 GGGA
2410796 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:2413421 original size:18 final size:19
Alignment explanation
Indices: 2413388--2413433 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 19
2413378 AAGTTTGGTT
2413388 TGAAAAATTCAATTTCTTAA
1 TGAAAAA-TCAATTTCTTAA
2413408 TGAAAAAT-AATTTCTTAA
1 TGAAAAATCAATTTCTTAA
2413426 TGAAAAAT
1 TGAAAAAT
2413434 GGGGAGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.69
19 1 0.04
20 7 0.27
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (19 bp):
TGAAAAATCAATTTCTTAA
Found at i:2413500 original size:19 final size:19
Alignment explanation
Indices: 2413476--2413530 Score: 92
Period size: 21 Copynumber: 2.8 Consensus size: 19
2413466 AATTGGTAAA
2413476 AATTGATATCTTTTTTAAC
1 AATTGATATCTTTTTTAAC
2413495 AATTGATATCCTTTTGTTAAC
1 AATTGATAT-CTTTT-TTAAC
2413516 AATTGATATCTTTTT
1 AATTGATATCTTTTT
2413531 CATTAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.29
20 10 0.29
21 14 0.41
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (19 bp):
AATTGATATCTTTTTTAAC
Found at i:2413804 original size:23 final size:21
Alignment explanation
Indices: 2413753--2413831 Score: 72
Period size: 21 Copynumber: 3.7 Consensus size: 21
2413743 AGGGTGTCAA
*
2413753 AGTGCATCCATACACCCCTAC
1 AGTGCATCCATGCACCCCTAC
2413774 AGTGCATCCATGCACCTTCC-AC
1 AGTGCATCCATGCACC--CCTAC
* * **
2413796 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTAC
2413817 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
2413832 TCCATTTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 14 0.30
21 15 0.32
22 3 0.06
23 15 0.32
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:2414406 original size:46 final size:46
Alignment explanation
Indices: 2414353--2414446 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
2414343 ACAAATTGGT
2414353 GAATTTGTTAGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGATGTA
1 GAATTTGTTAGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGATGTA
2414399 GAATTTGTTAGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGATGTA
1 GAATTTGTTAGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGATGTA
2414445 GA
1 GA
2414447 CTTGGTTGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.30
Consensus pattern (46 bp):
GAATTTGTTAGAAAATCCTTGGTGAGGAGCTAAGGTAGTGGATGTA
Found at i:2414654 original size:22 final size:22
Alignment explanation
Indices: 2414606--2414670 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2414596 TTCTAATTAG
* *
2414606 CATTCAGACGAATTTCAATCAA
1 CATTCAGACTAATTCCAATCAA
*
2414628 CATTCAGACTAATTCCAGTCATA
1 CATTCAGACTAATTCCAATCA-A
* *
2414651 -ATTCATACTAA-TCTAATCAA
1 CATTCAGACTAATTCCAATCAA
2414671 TGGTAAAGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 1 0.03
21 6 0.17
22 28 0.78
23 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (22 bp):
CATTCAGACTAATTCCAATCAA
Found at i:2414831 original size:57 final size:57
Alignment explanation
Indices: 2414768--2414882 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 57
2414758 ATACATTTAT
* *
2414768 ATGCTTGCTGAAATTTATGAAAATTAATCAAAAAGCAATAAATGTAAAAGGAGTAGC
1 ATGCTTGCTGAAATTCATGAAAACTAATCAAAAAGCAATAAATGTAAAAGGAGTAGC
* * *
2414825 ATGCTTGCTGAAATTCATGAAAACTAATGAAAAAGCAGTAAATGTAAAAGTAGTAGC
1 ATGCTTGCTGAAATTCATGAAAACTAATCAAAAAGCAATAAATGTAAAAGGAGTAGC
2414882 A
1 A
2414883 CCCTAAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (57 bp):
ATGCTTGCTGAAATTCATGAAAACTAATCAAAAAGCAATAAATGTAAAAGGAGTAGC
Found at i:2415523 original size:22 final size:22
Alignment explanation
Indices: 2415483--2415524 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2415473 AAAGACAAAT
*
2415483 AAAATAAAAAGTCATAATTATG
1 AAAATAAAAAATCATAATTATG
2415505 AAAATAAAATAATCA-AATTA
1 AAAATAAAA-AATCATAATTA
2415525 AATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAATAAAAAATCATAATTATG
Found at i:2415674 original size:2 final size:2
Alignment explanation
Indices: 2415667--2415697 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2415657 ATTTTGAATA
2415667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2415698 ATAAACTCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2416691 original size:14 final size:14
Alignment explanation
Indices: 2416672--2416698 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2416662 TAAATAATAA
2416672 TTAAAATATTTAAT
1 TTAAAATATTTAAT
2416686 TTAAAATATTTAA
1 TTAAAATATTTAA
2416699 ACACGAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAAATATTTAAT
Found at i:2417188 original size:25 final size:25
Alignment explanation
Indices: 2417159--2417208 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2417149 AAAATACATG
*
2417159 TATAAATGACTAAAAAGAAATAAAA
1 TATAAATGACAAAAAAGAAATAAAA
* *
2417184 TATAAATGCCAAAAAATAAATAAAA
1 TATAAATGACAAAAAAGAAATAAAA
2417209 ACATGCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (25 bp):
TATAAATGACAAAAAAGAAATAAAA
Found at i:2418508 original size:3 final size:3
Alignment explanation
Indices: 2418500--2418562 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
2418490 ATTTGGCCTG
* * * * * *
2418500 TAA TAA TAA TAT TAT TTA TAA TAA TAA TAA TAA TAT TTA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2418548 TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
2418563 AATGAAAACA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2418526 original size:21 final size:21
Alignment explanation
Indices: 2418500--2418555 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
2418490 ATTTGGCCTG
*
2418500 TAATAATAATATTATTTATAA
1 TAATAATAATAATATTTATAA
2418521 TAATAATAATAATATTTATAA
1 TAATAATAATAATATTTATAA
* *
2418542 AAATAATTATAATA
1 TAATAATAATAATA
2418556 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATAATAATAATATTTATAA
Found at i:2418774 original size:45 final size:45
Alignment explanation
Indices: 2418713--2419641 Score: 1750
Period size: 45 Copynumber: 20.6 Consensus size: 45
2418703 AGGTCTCGAA
* *
2418713 AACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2418758 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2418803 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2418848 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2418893 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAC
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2418938 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2418983 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2419028 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2419073 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAC
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2419118 AACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2419163 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
* *
2419208 AACATCATGCACTGAAGGGATTACAGATGACCCGAAGGTTTTGAA
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2419253 AACATCATGCACTGAAGGGCTTACAGATGGCCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2419298 AACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2419343 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2419388 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2419433 AACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2419478 AACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2419523 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
*
2419568 AACATCATGTACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
1 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
2419613 AACATCATGCACTGAAGGGCTTACAGATG
1 AACATCATGCACTGAAGGGCTTACAGATG
2419642 TGGGAAATAG
Statistics
Matches: 864, Mismatches: 20, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 864 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (45 bp):
AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAT
Found at i:2419469 original size:20 final size:20
Alignment explanation
Indices: 2419444--2419515 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
2419434 ACATCATGCA
2419444 CTGAAGGGCTTACAGATGAC
1 CTGAAGGGCTTACAGATGAC
* * *
2419464 CTGAAGGTTTTGATAACATCATG-C
1 CTGAAGG----GCTTACA-GATGAC
2419488 ACTGAAGGGCTTACAGATGAC
1 -CTGAAGGGCTTACAGATGAC
2419509 CTGAAGG
1 CTGAAGG
2419516 TTTTGATAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 17 0.44
21 6 0.15
24 6 0.15
25 10 0.26
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.24
Consensus pattern (20 bp):
CTGAAGGGCTTACAGATGAC
Found at i:2420445 original size:22 final size:22
Alignment explanation
Indices: 2420301--2420443 Score: 232
Period size: 22 Copynumber: 6.5 Consensus size: 22
2420291 AATAAAGCTT
* *
2420301 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
2420323 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2420345 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
2420367 TTATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2420389 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
2420411 TTATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2420433 TCATCTTTGAA
1 TCATCTTTGAA
2420444 AATATTAGAT
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 112 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:2424983 original size:12 final size:11
Alignment explanation
Indices: 2424968--2425016 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
2424958 TTTTGATTCA
2424968 TTTTTTTCCTTC
1 TTTTTTT-CTTC
*
2424980 TTTTTTTCTTT
1 TTTTTTTCTTC
2424991 TTTCTTTTCTTC
1 TTT-TTTTCTTC
*
2425003 TTCTTCTTCTTC
1 TT-TTTTTCTTC
2425015 TT
1 TT
2425017 CAAGTATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 6 0.19
12 25 0.78
13 1 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:2428963 original size:25 final size:25
Alignment explanation
Indices: 2428933--2428982 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2428923 AAAATACATG
*
2428933 TATAAATGACTAAAAATAAATAAAA
1 TATAAATGACAAAAAATAAATAAAA
**
2428958 TATAAATTCCAAAAAATAAATAAAA
1 TATAAATGACAAAAAATAAATAAAA
2428983 ACATGCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (25 bp):
TATAAATGACAAAAAATAAATAAAA
Found at i:2430302 original size:3 final size:3
Alignment explanation
Indices: 2430296--2430350 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
2430286 AATATTGTTT
* * *
2430296 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTT ATA AAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2430344 ATA ATA A
1 ATA ATA A
2430351 AATGAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2430315 original size:30 final size:30
Alignment explanation
Indices: 2430279--2430350 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2430269 TTTTGGCCTG
* * *
2430279 TAATAATAATATTGTTTATAATAATAATAA
1 TAATAATAATAATATTTATAAAAATAATAA
2430309 TAATAATAATAATATTTATAAAAATAATAA
1 TAATAATAATAATATTTATAAAAATAATAA
2430339 TAATAATAATAA
1 TAATAATAATAA
2430351 AATGAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TAATAATAATAATATTTATAAAAATAATAA
Found at i:2430358 original size:27 final size:27
Alignment explanation
Indices: 2430298--2430359 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
2430288 TATTGTTTAT
* *
2430298 AATAATAATAATAATAATAATAATATT
1 AATAAAAATAATAATAATAATAATATA
*
2430325 TATAAAAATAATAATAATAATAATA-A
1 AATAAAAATAATAATAATAATAATATA
2430351 AATGAAAAA
1 AAT-AAAAA
2430360 AATTAGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
AATAAAAATAATAATAATAATAATATA
Found at i:2431613 original size:27 final size:25
Alignment explanation
Indices: 2431581--2431631 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
2431571 TATAAACGGG
2431581 AAACAGAAAATAAATAAATAACAAAAA
1 AAACAGAAAATAAAT-AATAA-AAAAA
*
2431608 AAACAGAAACTAAATAATAAAAAA
1 AAACAGAAAATAAATAATAAAAAA
2431632 GAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 14 0.61
ACGTcount: A:0.76, C:0.08, G:0.04, T:0.12
Consensus pattern (25 bp):
AAACAGAAAATAAATAATAAAAAAA
Found at i:2431665 original size:27 final size:27
Alignment explanation
Indices: 2431581--2431666 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 27
2431571 TATAAACGGG
* *
2431581 AAACAGAAAATAAATAAATAACA-AAAA
1 AAACAGAAAAAAAATAAA-AAAATAAAA
2431608 AAACAGAAACTAAATAATAAAAAAGAAATAAAA
1 AAACAGAAA--AAA-AAT--AAAA-AAATAAAA
* *
2431641 AAACAGAAAACAAATAAAAATATAAA
1 AAACAGAAAAAAAATAAAAAAATAAA
2431667 TAAATATAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
27 15 0.31
28 4 0.08
29 2 0.04
30 6 0.12
31 3 0.06
32 5 0.10
33 13 0.27
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.12
Consensus pattern (27 bp):
AAACAGAAAAAAAATAAAAAAATAAAA
Found at i:2431800 original size:16 final size:15
Alignment explanation
Indices: 2431763--2431880 Score: 62
Period size: 16 Copynumber: 7.3 Consensus size: 15
2431753 GAACTTATAA
2431763 AAAAACAAATAGAAAAT
1 AAAAACAAAT--AAAAT
2431780 AAAAACAAATAAAAT
1 AAAAACAAATAAAAT
*
2431795 AGAAAACAGA-AAAAT
1 A-AAAACAAATAAAAT
*
2431810 AAAAA-AATATAATGTATAC
1 AAAAACAA-ATAA---A-AT
* *
2431829 AGAAAATAAATAAAAA
1 A-AAAACAAATAAAAT
*
2431845 AGAAAACAAA-AAATT
1 A-AAAACAAATAAAAT
*
2431860 AAAAACATATAAAATT
1 AAAAACAAATAAAA-T
2431876 AAAAA
1 AAAAA
2431881 AAAACATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
13 1 0.01
14 12 0.15
15 21 0.26
16 23 0.28
17 11 0.14
18 1 0.01
19 2 0.02
20 8 0.10
21 2 0.02
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (15 bp):
AAAAACAAATAAAAT
Found at i:2431815 original size:22 final size:20
Alignment explanation
Indices: 2431761--2431921 Score: 63
Period size: 22 Copynumber: 7.2 Consensus size: 20
2431751 TTGAACTTAT
* *
2431761 AAAAAAACAAATAGAAAATA
1 AAAAAAAAAAATAGAAAACA
2431781 AAAACAAATAAAATAGAAAACAGA
1 AAAA-AAA-AAAATAGAAAAC--A
*
2431805 AAAATAAAAAAATATAATGTATACA
1 AAAA-AAAAAAATAGAA---A-ACA
*
2431830 GAAAATAAATAAAAAAGAAAACA
1 -AAAA-AAA-AAAATAGAAAACA
* *
2431853 AAAAATTAAAAACATATAAAATTA
1 AAAAA--AAAAA-ATAGAAAA-CA
* *
2431877 AAAAAAAACATATAAAAAAC-
1 AAAAAAAA-AAATAGAAAACA
* * *
2431897 AAAAAAACAATTAGAAAATA
1 AAAAAAAAAAATAGAAAACA
2431917 AAAAA
1 AAAAA
2431922 CAAATAATAA
Statistics
Matches: 108, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
19 7 0.06
20 16 0.15
21 4 0.04
22 27 0.25
23 20 0.19
24 15 0.14
25 1 0.01
26 9 0.08
27 9 0.08
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (20 bp):
AAAAAAAAAAATAGAAAACA
Found at i:2431892 original size:50 final size:49
Alignment explanation
Indices: 2431775--2431919 Score: 136
Period size: 50 Copynumber: 2.9 Consensus size: 49
2431765 AAACAAATAG
* *
2431775 AAAATAAAAACAAATAAAATAGAAAACAGAAAAA-TAAAAAAATATAATGT
1 AAAA-AAAAACAAATAAAAAAGAAAACA-AAAAATTAAAAAAATAAAATGT
* * *
2431825 ATACAGAAAATAAATAAAAAAGAAAACAAAAAATTAAAAACATATAAAAT-T
1 A-AAAAAAAACAAATAAAAAAGAAAACAAAAAATTAAAAA-A-ATAAAATGT
* * * *
2431876 AAAAAAAAACATATAAAAAACAAAA-AAACAATT-AGAAAATAAAA
1 AAAAAAAAACAAATAAAAAAGAAAACAAAAAATTAAAAAAATAAAA
2431920 AACAAATAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
46 6 0.08
47 1 0.01
48 3 0.04
49 12 0.15
50 46 0.58
51 5 0.06
52 6 0.08
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (49 bp):
AAAAAAAAACAAATAAAAAAGAAAACAAAAAATTAAAAAAATAAAATGT
Found at i:2431900 original size:18 final size:18
Alignment explanation
Indices: 2431860--2431935 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
2431850 ACAAAAAATT
*
2431860 AAAAACATATAAAATTAAAA
1 AAAAACATATAAAA--AACA
2431880 AAAAACATATAAAAAACAA
1 AAAAACATATAAAAAAC-A
* *
2431899 AAAAACA-ATTAGAAAATA
1 AAAAACATA-TAAAAAACA
* *
2431917 AAAAACAAATAATAAACA
1 AAAAACATATAAAAAACA
2431935 A
1 A
2431936 TGGTTTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 18 0.38
19 15 0.32
20 14 0.30
ACGTcount: A:0.76, C:0.08, G:0.01, T:0.14
Consensus pattern (18 bp):
AAAAACATATAAAAAACA
Found at i:2431900 original size:19 final size:18
Alignment explanation
Indices: 2431860--2431928 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
2431850 ACAAAAAATT
2431860 AAAAACATATAAAATTAAAA
1 AAAAACATATAAAA--AAAA
2431880 AAAAACATATAAAAAACAA
1 AAAAACATATAAAAAA-AA
* *
2431899 AAAAACA-ATTAGAAAATA
1 AAAAACATA-TAAAAAAAA
*
2431917 AAAAACAAATAA
1 AAAAACATATAA
2431929 TAAACAATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
18 13 0.30
19 16 0.37
20 14 0.33
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.14
Consensus pattern (18 bp):
AAAAACATATAAAAAAAA
Found at i:2432120 original size:2 final size:2
Alignment explanation
Indices: 2432113--2432156 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2432103 GTTAGAACAT
2432113 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
2432155 TA
1 TA
2432157 GCAAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2432801 original size:25 final size:23
Alignment explanation
Indices: 2432773--2432858 Score: 77
Period size: 25 Copynumber: 3.6 Consensus size: 23
2432763 ATAGAAAACG
*
2432773 AAAAGAAATAAAAAACAAGTAATAA
1 AAAACAAATAAAAAACAA-T-ATAA
*
2432798 AAAACAAATACAAAAGAGAATATAA
1 AAAACAAATA-AAAA-ACAATATAA
*
2432823 AAAACAAATACAAAACAGA-ATATA
1 AAAACAAATAAAAAACA-ATATA-A
2432847 AAAACAAA-AAAA
1 AAAACAAATAAAA
2432859 TATATAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
23 8 0.15
24 13 0.25
25 23 0.44
26 5 0.10
27 3 0.06
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAACAAATAAAAAACAATATAA
Found at i:2432812 original size:12 final size:11
Alignment explanation
Indices: 2432773--2432858 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
2432763 ATAGAAAACG
*
2432773 AAAAGAAATAA
1 AAAACAAATAA
2432784 AAAACAAGTAATAA
1 AAAAC-A--AATAA
2432798 AAAACAAATACA
1 AAAACAAATA-A
*
2432810 AAAGAGAATATAA
1 AAA-ACAA-ATAA
*
2432823 AAAACAAATAC
1 AAAACAAATAA
2432834 AAAACAGAATATA
1 AAAACA-AATA-A
2432847 AAAACAAA-AA
1 AAAACAAATAA
2432857 AA
1 AA
2432859 TATATAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
10 3 0.05
11 18 0.29
12 14 0.23
13 14 0.23
14 13 0.21
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAACAAATAA
Found at i:2432862 original size:16 final size:18
Alignment explanation
Indices: 2432842--2432877 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2432832 ACAAAACAGA
2432842 ATATAAAAACAAA-AAAAT
1 ATATAAAAA-AAAGAAAAT
2432860 ATATAAAAAAAAGAAAAT
1 ATATAAAAAAAAGAAAAT
2432878 TTTAACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
ATATAAAAAAAAGAAAAT
Found at i:2433297 original size:16 final size:17
Alignment explanation
Indices: 2433278--2433309 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2433268 ATAGAACTAT
2433278 AGAAGA-TGAGGATTCG
1 AGAAGATTGAGGATTCG
2433294 AGAAGATTGAGGATTC
1 AGAAGATTGAGGATTC
2433310 TAGAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.22
Consensus pattern (17 bp):
AGAAGATTGAGGATTCG
Found at i:2434243 original size:65 final size:64
Alignment explanation
Indices: 2434140--2434298 Score: 178
Period size: 65 Copynumber: 2.5 Consensus size: 64
2434130 AATTAAATTG
* * * *
2434140 AACATCAAATGCATTTCATGCATCGATGCACATACCATGCACCAATGCACTGAG-GATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACAGACCATGCACCAATGCACTCAGCGATTTTA--A
2434204 A
64 A
* * * * * *
2434205 AACATCGAATGCATTTGATGCATCGATGCACCGGCCATGCATCGATGCACTCTGCTATTTTAAA
1 AACATCGAATGCATTTGATGCATCGATGCACAGACCATGCACCAATGCACTCAGCGATTTTAAA
* *
2434269 TA-ATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
2434299 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 27 0.33
64 3 0.04
65 45 0.56
66 6 0.07
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACAGACCATGCACCAATGCACTCAGCGATTTTAAA
Found at i:2434298 original size:17 final size:19
Alignment explanation
Indices: 2434271--2434318 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
2434261 ATTTTAAATA
2434271 ATCGAATGCACT-TGA-TGC
1 ATCG-ATGCACTCTGAGTGC
*
2434289 ATCGATGCACTCTTAGTGC
1 ATCGATGCACTCTGAGTGC
*
2434308 ACCGATGCACT
1 ATCGATGCACT
2434319 AAGGGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (19 bp):
ATCGATGCACTCTGAGTGC
Found at i:2453488 original size:15 final size:15
Alignment explanation
Indices: 2453465--2453494 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2453455 TATGTATATG
*
2453465 TATTTTATACTTATA
1 TATTATATACTTATA
2453480 TATTATATACTTATA
1 TATTATATACTTATA
2453495 ACTATAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATATACTTATA
Found at i:2453543 original size:56 final size:56
Alignment explanation
Indices: 2453478--2453584 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 56
2453468 TTTATACTTA
* * *
2453478 TATATTATATAC-TTATAACTATAATGTATA-TTTATATTATATATATATATATAAAC
1 TATAGTATATACTTTAT-A-TATAAAGTATAGTTTATATAATATATATATATATAAAC
* *
2453534 TATAGTATATAGTTTATATATAAAGTATAGTTTATATAATTTATATATATA
1 TATAGTATATACTTTATATATAAAGTATAGTTTATATAATATATATATATA
2453585 GTTTATATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
55 10 0.23
56 30 0.68
57 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (56 bp):
TATAGTATATACTTTATATATAAAGTATAGTTTATATAATATATATATATATAAAC
Found at i:2453569 original size:27 final size:27
Alignment explanation
Indices: 2453514--2453602 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
2453504 TATATTTATA
* *
2453514 TTATATA-TATATATATAAACTATAG-
1 TTATATAGTTTATATATAAAGTATAGT
2453539 -TATATAGTTTATATATAAAGTATAGT
1 TTATATAGTTTATATATAAAGTATAGT
* * *
2453565 TTATATAATTTATATATATAGTTTA-T
1 TTATATAGTTTATATATAAAGTATAGT
*
2453591 ATATATAGTTTA
1 TTATATAGTTTA
2453603 CACATAGTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
24 6 0.11
25 16 0.30
26 11 0.20
27 21 0.39
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (27 bp):
TTATATAGTTTATATATAAAGTATAGT
Found at i:2453615 original size:20 final size:20
Alignment explanation
Indices: 2453590--2453636 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2453580 ATATAGTTTA
2453590 TATATATAGTTTACACATAG
1 TATATATAGTTTACACATAG
* * *
2453610 TATATATGGTTTATATATAG
1 TATATATAGTTTACACATAG
*
2453630 TTTATAT
1 TATATAT
2453637 CAATAAACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (20 bp):
TATATATAGTTTACACATAG
Found at i:2453616 original size:2 final size:2
Alignment explanation
Indices: 2453381--2453597 Score: 123
Period size: 2 Copynumber: 108.0 Consensus size: 2
2453371 ACTTTCTACT
2453381 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
* * * *
2453423 TA TA TA TA TA T- TA TA CT- TA TT TA -A TT TA GTCC TA TG TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -T-A TA TA TA TA
* *
2453463 TG TA T- TT TA TA CT- TA TA TA T- TA TA TA CT- TA TA -A CTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* * *
2453501 -A TG TA TA TT TA TA T- TA TA TA TA TA TA TA TA AA CTA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA
* * * *
2453543 TA GTT TA TA TA TA AA GTA TA GTT TA TA TA -A TT 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
*
2453585 GTT TA TA TA TA TA
1 -TA TA TA TA TA TA
2453598 GTTTACACAT
Statistics
Matches: 165, Mismatches: 27, Indels: 46
0.69 0.11 0.19
Matches are distributed among these distances:
1 11 0.07
2 141 0.85
3 13 0.08
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2453624 original size:11 final size:11
Alignment explanation
Indices: 2453559--2453751 Score: 97
Period size: 11 Copynumber: 18.2 Consensus size: 11
2453549 ATATATAAAG
2453559 TATAGTTTATA
1 TATAGTTTATA
*
2453570 TA-ATTTATATA
1 TATAGTT-TATA
2453581 TATAGTTTATATA
1 TATAG-TT-TATA
*
2453594 TATAGTTTACA
1 TATAGTTTATA
*
2453605 CATAG--TATA
1 TATAGTTTATA
*
2453614 TATGGTTTATA
1 TATAGTTTATA
2453625 TATAGTTTATA
1 TATAGTTTATA
**
2453636 TCA-A-TAAACTA
1 T-ATAGTTTA-TA
*
2453647 TATAATTTATA
1 TATAGTTTATA
* *
2453658 CATAGTCTATA
1 TATAGTTTATA
2453669 TA-A--TT-TA
1 TATAGTTTATA
2453676 TA-A--TTATA
1 TATAGTTTATA
*
2453684 TATAGTATATA
1 TATAGTTTATA
* **
2453695 AATA-TAAACTA
1 TATAGTTTA-TA
*
2453706 TACAGTTTATA
1 TATAGTTTATA
*
2453717 TATAGTTCATA
1 TATAGTTTATA
2453728 TATAGTTTATA
1 TATAGTTTATA
*
2453739 TATAATTTATA
1 TATAGTTTATA
2453750 TA
1 TA
2453752 GTTTATTAGT
Statistics
Matches: 139, Mismatches: 28, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
7 7 0.05
8 5 0.04
9 7 0.05
10 10 0.07
11 90 0.65
12 8 0.06
13 12 0.09
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (11 bp):
TATAGTTTATA
Found at i:2453703 original size:59 final size:61
Alignment explanation
Indices: 2453620--2453738 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 61
2453610 TATATATGGT
* * *
2453620 TTATATATAGTTTATATCAATAAACTATATAATTTATACATAG-TC-TATATAATTTATAA
1 TTATATATAGTATATATAAATAAACTATACAATTTATACATAGTTCATATATAATTTATAA
* * *
2453679 TTATATATAGTATATA-AATATAAACTATACAGTTTATATATAGTTCATATATAGTTTATA
1 TTATATATAGTATATATAA-ATAAACTATACAATTTATACATAGTTCATATATAATTTATA
2453739 TATAATTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
58 1 0.02
59 36 0.71
60 2 0.04
61 12 0.24
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (61 bp):
TTATATATAGTATATATAAATAAACTATACAATTTATACATAGTTCATATATAATTTATAA
Found at i:2453719 original size:20 final size:20
Alignment explanation
Indices: 2453623--2453757 Score: 96
Period size: 20 Copynumber: 6.6 Consensus size: 20
2453613 ATATGGTTTA
*
2453623 TATATAGTTTATATCAATAAAC
1 TATATAGTTTATAT--ATAATC
* * *
2453645 TATATAATTTATACATAGTC
1 TATATAGTTTATATATAATC
* *
2453665 TATATAATTTATA-AT--TA
1 TATATAGTTTATATATAATC
* *
2453682 TATATAGTATATAAATATAAAC
1 TATATAGT-T-TATATATAATC
* *
2453704 TATACAGTTTATATATAGTTC
1 TATATAGTTTATATATA-ATC
*
2453725 ATATATAGTTTATATATAATT
1 -TATATAGTTTATATATAATC
2453746 TATATAGTTTAT
1 TATATAGTTTAT
2453758 TAGTTTACAT
Statistics
Matches: 90, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
17 8 0.09
18 1 0.01
19 5 0.06
20 38 0.42
21 3 0.03
22 35 0.39
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
TATATAGTTTATATATAATC
Found at i:2453828 original size:20 final size:20
Alignment explanation
Indices: 2453510--2453836 Score: 117
Period size: 22 Copynumber: 15.8 Consensus size: 20
2453500 AATGTATATT
*
2453510 TATATTATATATA-TATATA
1 TATATTATATATAGTTTATA
*
2453529 TAAACTATAGTATATAGTTTATA
1 TATA-T-TA-TATATAGTTTATA
2453552 TATA--A-AGTATAGTTTATA
1 TATATTATA-TATAGTTTATA
*
2453570 TAATTTATATATATAGTTTATATA
1 T-ATAT-TATATATAG-TT-TATA
* * *
2453594 TATAGTTTACACATAGTATATA
1 TATA--TTATATATAGTTTATA
*
2453616 TGGT-TTATATATAGTTTATA
1 T-ATATTATATATAGTTTATA
* *
2453636 TCA-ATAAACTATATAATTTATA
1 T-ATAT-TA-TATATAGTTTATA
* * * *
2453658 CATAGTCTATATA-ATT-TA
1 TATATTATATATAGTTTATA
*
2453676 TA-ATTATATATAGTATATA
1 TATATTATATATAGTTTATA
* * *
2453695 AATATAAACTATACAGTTTATA
1 TATAT-TA-TATATAGTTTATA
2453717 TATAGTTCATATATAGTTTATA
1 TATA-TT-ATATATAGTTTATA
2453739 TATAATT-TATATAGTTTAT-
1 TAT-ATTATATATAGTTTATA
*
2453758 TAGT-TTACATATATAGTTCATA
1 TA-TATT--ATATATAGTTTATA
* * *
2453780 TGTA--A-ACTATAATTTATT
1 TATATTATA-TATAGTTTATA
*
2453798 TAGTTTGTATATATAGTTTATA
1 TA-TAT-TATATATAGTTTATA
*
2453820 TATATTATATATGGTTT
1 TATATTATATATAGTTT
2453837 TTTATTAGGG
Statistics
Matches: 225, Mismatches: 44, Indels: 77
0.65 0.13 0.22
Matches are distributed among these distances:
17 10 0.04
18 28 0.12
19 14 0.06
20 48 0.21
21 19 0.08
22 74 0.33
23 19 0.08
24 12 0.05
25 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.48
Consensus pattern (20 bp):
TATATTATATATAGTTTATA
Found at i:2454485 original size:2 final size:2
Alignment explanation
Indices: 2454480--2454714 Score: 73
Period size: 2 Copynumber: 117.0 Consensus size: 2
2454470 ATTATTTAAC
* * * *
2454480 TA TA TA TA GTA TA AA TA -A TT TA TA -A T- TA TA CA TA GTA TA TG
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
2454521 TA TA AA TA TA AA CTA TA TA CTT TA TA TA TA AA T- 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 TA TA
* *
2454563 TA TA TA TA TA GTA TA TA TA GTT TA TA TT TA TA T- TA T- 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
* * * *
2454605 CTA TA TA TA AA AA CTA TA TA GTT TA T- TA -A TA TA AA T- TA TA
1 -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2454645 TA GTT TA TA TA TA GA -A CTA TA TA TA AA CTA TA TA GTT TA TA TT
1 TA -TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA
*
2454688 TA TA TA TA TA CTA TG TA TA -A T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
2454715 GTTTATTAAT
Statistics
Matches: 169, Mismatches: 37, Indels: 54
0.65 0.14 0.21
Matches are distributed among these distances:
1 13 0.08
2 137 0.81
3 19 0.11
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2454550 original size:11 final size:10
Alignment explanation
Indices: 2454534--2454613 Score: 56
Period size: 11 Copynumber: 7.6 Consensus size: 10
2454524 AAATATAAAC
2454534 TATATACTTTA
1 TATATA-TTTA
*
2454545 TATATAAATTA
1 TATAT-ATTTA
2454556 TATATA-TTA
1 TATATATTTA
*
2454565 TATATATAGTA
1 TATATAT-TTA
2454576 TATATAGTTTA
1 TATATA-TTTA
*
2454587 TATTTATATTA
1 TATATAT-TTA
*
2454598 T-TATATACTA
1 TATATAT-TTA
2454608 TATATA
1 TATATA
2454614 AAAACTATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 9 0.16
10 10 0.18
11 36 0.63
12 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (10 bp):
TATATATTTA
Found at i:2454594 original size:85 final size:87
Alignment explanation
Indices: 2454480--2454657 Score: 229
Period size: 85 Copynumber: 2.1 Consensus size: 87
2454470 ATTATTTAAC
* *
2454480 TATATATAGTATAAATAATTTATAATTATACATAGTATAT-GTATAAATATAAACTATATACTTT
1 TATATATAGTATAAATAATTTATAATTATA-ATAGTATATACTATAAATAAAAACTATATACTTT
2454544 A-T-ATATAAATTATATA-TATTA
65 ATTAATATAAATTATATAGT-TTA
* * * * * * *
2454565 TATATATAGTATATATAGTTTATATTTATATTATTATATACTATATATAAAAACTATATAGTTTA
1 TATATATAGTATAAATAATTTATAATTATAATAGTATATACTATAAATAAAAACTATATACTTTA
2454630 TTAATATAAATTATATAGTTTA
66 TTAATATAAATTATATAGTTTA
2454652 TATATA
1 TATATA
2454658 GAACTATATA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
84 7 0.09
85 48 0.60
86 1 0.01
87 23 0.29
88 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (87 bp):
TATATATAGTATAAATAATTTATAATTATAATAGTATATACTATAAATAAAAACTATATACTTTA
TTAATATAAATTATATAGTTTA
Found at i:2454668 original size:65 final size:65
Alignment explanation
Indices: 2454534--2454738 Score: 170
Period size: 65 Copynumber: 3.1 Consensus size: 65
2454524 AAATATAAAC
* * * * * *
2454534 TATATACTTTATATATAAATTATATATATTATATATATAGTATATATAGTTTATATTTATATTAT
1 TATATACTATATATAAAAATTATATATATTATATATATAATATATATAGTTTATATATAAACTAT
*
2454599 TATATACTATATATAAAAACTATATAGT-TTAT-TAATATAA-ATTATATAGTTTATATATAGAA
1 TATATACTATATATAAAAATTATATA-TATTATAT-ATATAATA-TATATAGTTTATATATA-AA
2454661 CTAT
62 CTAT
* ** * *
2454665 ATATAAACTATATAGTTTATATT-TATATATATACTATGTATAAT-TATATAGTTTATTAATATA
1 -TATATACTATATA-TAAAAATTATATATAT-TA-TATATATAATATATATAGTTTA-T-ATATA
2454728 AACTA-
60 AACTAT
2454733 TATATA
1 TATATA
2454739 AACCATATAG
Statistics
Matches: 113, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
64 2 0.02
65 48 0.42
66 6 0.05
67 22 0.19
68 17 0.15
69 12 0.11
70 6 0.05
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (65 bp):
TATATACTATATATAAAAATTATATATATTATATATATAATATATATAGTTTATATATAAACTAT
Found at i:2454673 original size:11 final size:12
Alignment explanation
Indices: 2454650--2454678 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2454640 TTATATAGTT
2454650 TATATATAGAAC
1 TATATATAGAAC
2454662 TATATATA-AAC
1 TATATATAGAAC
2454673 TATATA
1 TATATA
2454679 GTTTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (12 bp):
TATATATAGAAC
Found at i:2454713 original size:36 final size:37
Alignment explanation
Indices: 2454643--2454783 Score: 145
Period size: 36 Copynumber: 3.9 Consensus size: 37
2454633 ATATAAATTA
2454643 TATAGTTTATATATAGAACTATATATAAACTATATAGTT
1 TATA-TTTATATATA-AACTATATATAAACTATATAGTT
* * *
2454682 TATATTTATATATATACTATGTAT-AATTATATAG-T
1 TATATTTATATATAAACTATATATAAACTATATAGTT
*
2454717 T-TA-TTA-ATATAAACTATATATAAACCATATAGTT
1 TATATTTATATATAAACTATATATAAACTATATAGTT
*
2454751 TAT-TCTTATATACT--ACTATGTATAAACTATATA
1 TATAT-TTATATA-TAAACTATATATAAACTATATA
2454784 TATTATGTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
32 13 0.15
33 11 0.13
34 4 0.05
35 3 0.03
36 29 0.34
37 11 0.13
38 11 0.13
39 4 0.05
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATTTATATATAAACTATATATAAACTATATAGTT
Found at i:2454782 original size:69 final size:69
Alignment explanation
Indices: 2454634--2454783 Score: 218
Period size: 69 Copynumber: 2.2 Consensus size: 69
2454624 AGTTTATTAA
*
2454634 TATAAATTATATAGTTTATATATAGAACTATATATAAACTATATAGTTTATATTTATATATATAC
1 TATAAATTATATAGTTTATATATAGAACTATATATAAACCATATAGTTTATATTTATATATATAC
2454699 TATG
66 TATG
*
2454703 TAT-AATTATATAGTTTATTAATATA-AACTATATATAAACCATATAGTTTAT-TCTTATATA-C
1 TATAAATTATATAGTTTA-T-ATATAGAACTATATATAAACCATATAGTTTATAT-TTATATATA
2454764 TACTATG
63 TACTATG
*
2454771 TATAAACTATATA
1 TATAAATTATATA
2454784 TATTATGTAT
Statistics
Matches: 74, Mismatches: 3, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
68 25 0.34
69 44 0.59
70 5 0.07
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (69 bp):
TATAAATTATATAGTTTATATATAGAACTATATATAAACCATATAGTTTATATTTATATATATAC
TATG
Found at i:2454792 original size:20 final size:21
Alignment explanation
Indices: 2454757--2454803 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
2454747 AGTTTATTCT
2454757 TATATACTACTATGTATAAAC
1 TATATACTACTATGTATAAAC
* *
2454778 TATATA-TATTATGTATAAAT
1 TATATACTACTATGTATAAAC
2454798 TATATA
1 TATATA
2454804 GTTTATCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (21 bp):
TATATACTACTATGTATAAAC
Found at i:2454814 original size:20 final size:20
Alignment explanation
Indices: 2454757--2454814 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2454747 AGTTTATTCT
* *
2454757 TATATACTACTATGTATAAAC
1 TATATA-TATTATCTATAAAC
* *
2454778 TATATATATTATGTATAAAT
1 TATATATATTATCTATAAAC
2454798 TATATAGT-TTATCTATA
1 TATATA-TATTATCTATA
2454815 TTATATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.79
21 7 0.21
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (20 bp):
TATATATATTATCTATAAAC
Found at i:2454855 original size:26 final size:26
Alignment explanation
Indices: 2454796--2454851 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
2454786 TTATGTATAA
2454796 ATTATATAGTTTATCTATATTATATT
1 ATTATATAGTTTATCTATATTATATT
2454822 ATTATATAGTTT-T-TATA-TATATT
1 ATTATATAGTTTATCTATATTATATT
*
2454845 AATATAT
1 ATTATAT
2454852 TATAATTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 12 0.41
24 4 0.14
25 1 0.03
26 12 0.41
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (26 bp):
ATTATATAGTTTATCTATATTATATT
Found at i:2459176 original size:19 final size:21
Alignment explanation
Indices: 2459146--2459184 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2459136 TTTTAAAGGT
2459146 AAATTAGATTAGT-GTGTTAC
1 AAATTAGATTAGTAGTGTTAC
2459166 AAATT-GATTAGTAGTGTTA
1 AAATTAGATTAGTAGTGTTA
2459185 TTAAATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (21 bp):
AAATTAGATTAGTAGTGTTAC
Found at i:2459306 original size:23 final size:23
Alignment explanation
Indices: 2459239--2459306 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2459229 TCACGTATGG
* *
2459239 TGTTTGTGAATATTAAATGAACA
1 TGTTTGTGAATGTTAAATGAATA
*
2459262 TGTTTGTGAATGTCAAATGAATA
1 TGTTTGTGAATGTTAAATGAATA
* *
2459285 TGTTTGTGAACGTTAAACGAAT
1 TGTTTGTGAATGTTAAATGAAT
2459307 TAAAACATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
TGTTTGTGAATGTTAAATGAATA
Found at i:2462015 original size:22 final size:19
Alignment explanation
Indices: 2461975--2462018 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
2461965 TGAATAGACT
*
2461975 TAATTTAATAAAAATTAAA
1 TAATTTAATAAAAAATAAA
2461994 TAATATTAATATAACAAATAAA
1 TAAT-TTAATA-AA-AAATAAA
2462016 TAA
1 TAA
2462019 AATATTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 2 0.10
22 9 0.43
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATTTAATAAAAAATAAA
Found at i:2464359 original size:39 final size:37
Alignment explanation
Indices: 2464305--2464560 Score: 200
Period size: 38 Copynumber: 6.8 Consensus size: 37
2464295 TGCTAATGGT
*
2464305 TTTTGAAATAGATATATAATATAAAGTTTTTTTAAAAGCA
1 TTTTGAAA-ATATATATAATATAAAG-TTTTTTAAAA-CA
* * *
2464345 TTTTGAAAACATATATATTATATAGTTTTTTTAAAAAAACA
1 TTTTGAAAATATATATAATATAAAG-TTTTTT---AAAACA
* **
2464386 TTTTGGAAATATATATAATAT--AGTTTTGGAAAACA
1 TTTTGAAAATATATATAATATAAAGTTTTTTAAAACA
* * ** *
2464421 TTTTAAAAATATATATATTATATGGTTTTTAAAAACA
1 TTTTGAAAATATATATAATATAAAGTTTTTTAAAACA
* *
2464458 TTTTGAAAAATATATATAATATATAGTTTTTTAAAACG
1 TTTTG-AAAATATATATAATATAAAGTTTTTTAAAACA
* * *
2464496 TTTTGAAAA-CTATATAATATATAA--TTTTGAAAATA
1 TTTTGAAAATATATATAATATA-AAGTTTTTTAAAACA
* *
2464531 TTTTTTTAAAA-ATATATAATATATAGTTTT
1 --TTTTGAAAATATATATAATATAAAGTTTT
2464561 AAAATGTTAT
Statistics
Matches: 178, Mismatches: 27, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
35 32 0.18
36 12 0.07
37 39 0.22
38 40 0.22
39 23 0.13
40 8 0.04
41 20 0.11
42 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATAAAGTTTTTTAAAACA
Found at i:2464546 original size:73 final size:74
Alignment explanation
Indices: 2464316--2464621 Score: 232
Period size: 73 Copynumber: 4.1 Consensus size: 74
2464306 TTTGAAATAG
* * *
2464316 ATATATAATATAAAGTTTTTTTAAAAGCATTTTGAAAACATATATATTATATAGTTTTTTTAAAA
1 ATATATAATATATAG-TTTTTTAAAA-CATTTTGAAAAC-TATATAATATATA--ATTTTTAAAA
* * ** *
2464381 AAACATTTTGGAAAT
61 TAA-TTTTTAAAAAC
** * **
2464396 ATATAT-A-ATATAGTTTTGGAAAACATTTT-AAAAATATATATATTATATGGTTTTTAAAA-AC
1 ATATATAATATATAGTTTTTTAAAACATTTTGAAAACTATATA-A-TATATAATTTTTAAAATA-
* *
2464457 ATTTTGAAAAAT
63 ATTTTTAAAAAC
* * *
2464469 ATATATAATATATAGTTTTTTAAAACGTTTTGAAAACTATATAATATATAATTTTGAAAATATTT
1 ATATATAATATATAGTTTTTTAAAACATTTTGAAAACTATATAATATATAATTTTTAAAATAATT
*
2464534 TTTTAAAA-
66 TTTAAAAAC
** * * * *
2464542 ATATATAATATATAG--TTTTAAAATGTTATTTGAAAA-TATATATTATATGATTTTAAAAATAT
1 ATATATAATATATAGTTTTTTAAAA-CAT-TTTGAAAACTATATAATATATAATTTTTAAAATAA
2464604 TTTTTAAAAAC
64 TTTTTAAAAAC
2464615 ATATATA
1 ATATATA
2464622 TAGCATATGA
Statistics
Matches: 189, Mismatches: 27, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
71 8 0.04
72 33 0.17
73 44 0.23
74 38 0.20
75 25 0.13
76 21 0.11
77 8 0.04
78 5 0.03
79 1 0.01
80 6 0.03
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (74 bp):
ATATATAATATATAGTTTTTTAAAACATTTTGAAAACTATATAATATATAATTTTTAAAATAATT
TTTAAAAAC
Found at i:2464578 original size:35 final size:35
Alignment explanation
Indices: 2464386--2464644 Score: 141
Period size: 36 Copynumber: 7.0 Consensus size: 35
2464376 TAAAAAAACA
* * **
2464386 TTTTGGAAATATAT-ATAATATAGTTTTGGAAAA-CA
1 TTTTGAAAATATATAAT-ATATAGTTTT-TAAAATGT
* * ***
2464421 TTTTAAAAATATATATATTATATGGTTTTTAAAAACA
1 TTTTGAAAATATATA-A-TATATAGTTTTTAAAATGT
*
2464458 TTTTGAAAAATATATATAATATATAGTTTTTTAAAACG-
1 TTTTG--AAA-ATATATAATATATAG-TTTTTAAAATGT
* * *
2464496 TTTTGAAAACTATATAATATATAATTTTGAAAATATTT
1 TTTTGAAAA-TATATAATATATAGTTTT-TAAA-ATGT
*
2464534 TTTTAAAAATATATAATATATAG-TTTTAAAATGT
1 TTTTGAAAATATATAATATATAGTTTTTAAAATGT
* * *
2464568 TATTTGAAAATATATATTATAT-GATTTTAAAAATATT
1 T-TTTGAAAATATATAATATATAG-TTTTTAAAAT-GT
* * *
2464605 TTTTAAAAACATATATATAGCATATGATTTTTAAAATGT
1 TTTTGAAAATATATA-ATA-TATA-G-TTTTTAAAATGT
2464644 T
1 T
2464645 CTTTTTTATT
Statistics
Matches: 178, Mismatches: 26, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
34 5 0.03
35 38 0.21
36 46 0.26
37 34 0.19
38 22 0.12
39 15 0.08
40 18 0.10
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (35 bp):
TTTTGAAAATATATAATATATAGTTTTTAAAATGT
Found at i:2465701 original size:19 final size:18
Alignment explanation
Indices: 2465657--2465712 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
2465647 TGTTTTATTC
* * *
2465657 TTATTCTTATTTATTTAT
1 TTATTATTATATATGTAT
2465675 TTATTTATTATATATGTAT
1 TTA-TTATTATATATGTAT
2465694 GTTATTATTAT-TAT-TAT
1 -TTATTATTATATATGTAT
2465711 TT
1 TT
2465713 CCTTTTTGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 3 0.09
18 6 0.18
19 19 0.58
20 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.68
Consensus pattern (18 bp):
TTATTATTATATATGTAT
Found at i:2465826 original size:23 final size:22
Alignment explanation
Indices: 2465800--2465859 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
2465790 GTTTTATTTA
*
2465800 TTTTTATTTATTTTACTTTTACT
1 TTTTTATTTATTTTA-TCTTACT
* *
2465823 TTTTTATTTTCTTTTATCTTATT
1 TTTTTA-TTTATTTTATCTTACT
2465846 TATTTTATTTATTT
1 T-TTTTATTTATTT
2465860 ATTTGTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTATTTATTTTATCTTACT
Found at i:2465828 original size:19 final size:20
Alignment explanation
Indices: 2465803--2465863 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 20
2465793 TTATTTATTT
2465803 TTATTTATTTTACTTTTA-C
1 TTATTTATTTTACTTTTATC
*
2465822 TTTTTTATTTT-CTTTTATC
1 TTATTTATTTTACTTTTATC
2465841 TTATTTATTTTA--TTTAT-
1 TTATTTATTTTACTTTTATC
2465858 TTATTT
1 TTATTT
2465864 GTTGTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 6 0.16
18 11 0.29
19 21 0.55
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (20 bp):
TTATTTATTTTACTTTTATC
Found at i:2465832 original size:5 final size:5
Alignment explanation
Indices: 2465783--2465863 Score: 59
Period size: 5 Copynumber: 17.2 Consensus size: 5
2465773 AGGATATTTA
* *
2465783 TTATT TTGTT TTA-T TTATT TT-TAT TTATT TTACTT TTA-C TT-TT TTATT
1 TTATT TTATT TTATT TTATT TTAT-T TTATT TTA-TT TTATT TTATT TTATT
* *
2465831 TTCTT TTATC TTA-T TTATT TTA-T TTA-T TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT T
2465864 GTTGTTTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
4 20 0.33
5 34 0.57
6 6 0.10
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:2470083 original size:84 final size:83
Alignment explanation
Indices: 2469912--2470564 Score: 763
Period size: 84 Copynumber: 7.8 Consensus size: 83
2469902 TATCGACAGT
* * * * *
2469912 ATAACTCAAGGCGAGAAGGGTTATCTGTCAGCC-AAGACCTTCGAGTTAGATTACACTCAGCTCA
1 ATAACTCAAGGCAAGAAGGGTTATCTGCCA-CCAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
2469976 AAGGCACATAATTTGCAGT
65 AAGGCACATCATTTGCAGC
* * *
2469995 ATAACTCAAGGCAAGAAGGGCTATCTGCCACCAAAAGACCTTCGAGTTCGACTACGCTCACCTCC
1 ATAACTCAAGGCAAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCC
*
2470060 AAGGCATATCATTTGCAGC
65 AAGGCACATCATTTGCAGC
* * * *
2470079 ATAACTCAAGGCTAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC
1 ATAACTCAAGGCAAGAAGGGTTATCTGC-CACCAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* * *
2470144 AAGGCATATAATTTGCAAC
65 AAGGCACATCATTTGCAGC
* * * * *
2470163 ATAGCTCAAGGCAAGAAGGGTTATTTGCCACCAAAAGACCTTTGAGGTCGACTACGCTCAGCTCC
1 ATAACTCAAGGCAAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
2470228 AAAGCACATCATTTACAGC
65 AAGGCACATCATTTGCAGC
* * *
2470247 ATAACTCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCA
1 ATAACTCAAGGCAAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCC
*
2470312 AAGGCACAACATTTGCAGC
65 AAGGCACATCATTTGCAGC
* * * * * * *
2470331 ATAGCTTAAGTCAAGAAGGGTTATCTTCCAACTAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 ATAACTCAAGGCAAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCC
* *
2470396 AAGGCACGTCATTTACAGC
65 AAGGCACATCATTTGCAGC
* * * * *
2470415 ATAACTCAAGGCGATAAAGGTTATCTGTCAACC-AAGACCTTCGAGTTCGATTACACTCAGCTCC
1 ATAACTCAAGGCAAGAAGGGTTATCTG-CCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCC
2470479 AAGGCACATCATTTGCAGC
65 AAGGCACATCATTTGCAGC
* * * * * * * *
2470498 ATAGCTCAAGGCGAGAAGGGTTATCTGCAAACAAAAACCTTCGAGTTCGATTCCATTCAGCT-CA
1 ATAACTCAAGGCAAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCA
2470562 AGG
66 AGG
2470565 GCATGACAAA
Statistics
Matches: 494, Mismatches: 69, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
82 11 0.02
83 127 0.26
84 349 0.71
85 7 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (83 bp):
ATAACTCAAGGCAAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCA
AGGCACATCATTTGCAGC
Found at i:2470194 original size:168 final size:167
Alignment explanation
Indices: 2469907--2470547 Score: 869
Period size: 168 Copynumber: 3.8 Consensus size: 167
2469897 GAAACTATCG
* * * *
2469907 ACAGTATAACTCAAGGCGAGAAGGGTTATCTGTCAGCCAAGACCTTCGAGTTAGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGACTACACTCAG
* * * *
2469972 CTCAAAGGCACATAATTTGCAGTATAACTCAAGGCAAGAAGGGCTATCTGCCACCAAAAGACCTT
66 CTCAAAGGCACATAATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTT
* *
2470037 CGAGTTCGACTACGCTCACCTCCAAGGCATATCATTT
131 CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
2470074 GCAGCATAACTCAAGGCTAGAAGGGTTATCTG-CTAACCAAAGACCTTCGAGTTCGACTACGCTC
1 ACAGCATAACTCAAGGCGAGAAGGGTTATCTGTC-AACC-AAGACCTTCGAGTTCGACTACACTC
* * * *
2470138 AGCTTC-AAGGCATATAATTTGCAACATAGCTCAAGGCAAGAAGGGTTATTTGCCACCAAAAGAC
64 AGC-TCAAAGGCACATAATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGAC
* * *
2470202 CTTTGAGGTCGACTACGCTCAGCTCCAAAGCACATCATTT
128 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
2470242 ACAGCATAACTCAAGGCTAGAAGGGTTATCT-TCCAACCAAAGACCTTCGAGTTCGACTACACTC
1 ACAGCATAACTCAAGGCGAGAAGGGTTATCTGT-CAACC-AAGACCTTCGAGTTCGACTACACTC
* * * *
2470306 AGCTCAAAGGCACA-ACATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTTCCAACTAAAGAC
64 AGCTCAAAGGCACATA-ATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGAC
* * * *
2470370 CTTCGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTT
128 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * *
2470410 ACAGCATAACTCAAGGCGATAAAGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGACTACACTCAG
* * * *
2470475 CTCCAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCTGCAAACAAAA-ACCTT
66 CTCAAAGGCACATAATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTT
2470539 CGAGTTCGA
131 CGAGTTCGA
2470548 TTCCATTCAG
Statistics
Matches: 418, Mismatches: 47, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
166 15 0.04
167 111 0.27
168 288 0.69
169 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (167 bp):
ACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGACTACACTCAG
CTCAAAGGCACATAATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTT
CGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
Found at i:2471223 original size:39 final size:37
Alignment explanation
Indices: 2471169--2471473 Score: 264
Period size: 39 Copynumber: 8.1 Consensus size: 37
2471159 TGCTAATGGT
* *
2471169 TTTTGAAATAGATATATAATATATAGTTTTTTTAAAAGCA
1 TTTTGAAA-ATATATATAATATATAG--TTTTTAAAAACA
* *
2471209 TTTTGAAAACATATATATTATATAGTTTTTTGAAAAAACA
1 TTTTGAAAATATATATAATATATAG-TTTTT--AAAAACA
* **
2471249 TTTTGGAAATATATAT-A-ATATAGTTTTCGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
*
2471284 TTTTAAAAATATATATAATATATAGTTTTTAAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTT-AAAAACA
* *
2471322 TTTTGAAAAATATATATAATATATAGTTTTTTAAAACG
1 TTTTG-AAAATATATATAATATATAGTTTTTAAAAACA
* * * **
2471360 TTTTGAAAA-CTATATAATATATAATTTTGAAAATATT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAA-ACA
* ***
2471397 TTTTAAAAATATATATATAATATATAG-TTTTAAAATGT
1 TTTT-GAAA-ATATATATAATATATAGTTTTTAAAAACA
* *
2471435 TATTTGAAAATATATATTATAT-TA--TTTTAAAAATA
1 T-TTTGAAAATATATATAATATATAGTTTTTAAAAACA
2471470 TTTT
1 TTTT
2471474 TTTAAAAACA
Statistics
Matches: 222, Mismatches: 32, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
34 3 0.01
35 29 0.13
36 23 0.10
37 35 0.16
38 40 0.18
39 51 0.23
40 41 0.18
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
Found at i:2471261 original size:75 final size:76
Alignment explanation
Indices: 2471169--2471420 Score: 266
Period size: 75 Copynumber: 3.3 Consensus size: 76
2471159 TGCTAATGGT
*
2471169 TTTTGAAATAGATATATA-ATATATAGTTTTTTTAAAAGCATTTTGAAAACATATATATTATATA
1 TTTTGAAA-A-ATATATATA-ATATAGTTTTTTTAAAA-CATTTTGAAAACATATATAATATATA
2471233 GTTTTTTGAAAAAACA
62 GTTTTTT-AAAAAACA
* ** * *
2471249 TTTTG-GAAATATATATAATATAG-TTTTCGAAAACATTTTAAAAATATATATAATATATAG-TT
1 TTTTGAAAAATATATATAATATAGTTTTTTTAAAACATTTTGAAAACATATATAATATATAGTTT
2471311 TTTAAAAAACA
66 TTTAAAAAACA
* *
2471322 TTTTGAAAAATATATATAATATA-TAGTTTTTTAAAACGTTTTGAAAAC-TATATAATATATA-A
1 TTTTGAAAAATATATATAATATAGT--TTTTTTAAAACATTTTGAAAACATATATAATATATAGT
* * **
2471384 TTTTGAAAATATT
64 TTTTTAAAAAACA
*
2471397 TTTTAAAAATATATATATAATATA
1 TTTTGAAAA-ATATATATAATATA
2471421 TAGTTTTAAA
Statistics
Matches: 148, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
73 13 0.09
74 21 0.14
75 54 0.36
76 39 0.26
77 13 0.09
78 2 0.01
79 1 0.01
80 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (76 bp):
TTTTGAAAAATATATATAATATAGTTTTTTTAAAACATTTTGAAAACATATATAATATATAGTTT
TTTAAAAAACA
Found at i:2471411 original size:76 final size:75
Alignment explanation
Indices: 2471180--2471508 Score: 287
Period size: 76 Copynumber: 4.3 Consensus size: 75
2471170 TTTGAAATAG
* *
2471180 ATATATAATATATAGTTTTTTTAAAAGCATTTTGAAAACATATATATTATATAGTTTTTTGAAAA
1 ATATATAATATATAG-TTTTTTAAAA-CATTTTGAAAAC-TATATAATATATA--ATTTTGAAAA
**
2471245 AACATTTT-GGAAAT
61 AACATTTTAAAAAAT
** * * * *
2471259 ATATAT-A-ATATAGTTTTCGAAAACATTTTAAAAATATATATAATATATAGTTTTTAAAAAACA
1 ATATATAATATATAGTTTTTTAAAACATTTTGAAAA-CTATATAATATATAATTTTGAAAAAACA
*
2471322 TTTTGAAAAAT
65 TTTTAAAAAAT
* * **
2471333 ATATATAATATATAGTTTTTTAAAACGTTTTGAAAACTATATAATATATAATTTTGAAAATATTT
1 ATATATAATATATAGTTTTTTAAAACATTTTGAAAACTATATAATATATAATTTTGAAAAAACAT
2471398 TTTAAAAATAT
66 TTTAAAAA-AT
** * *
2471409 ATATATAATATATAG--TTTTAAAATGTTATTTGAAAA-TATATATTATATTATTTT-AAAAATA
1 ATATATAATATATAGTTTTTTAAAA-CAT-TTTGAAAACTATATAATATATAATTTTGAAAAA-A
**
2471470 TTTTTTTAAAAACAT
63 -CATTTTAAAAA-AT
* *
2471485 ATATATAGTATAT-GATTTTTAAAA
1 ATATATAATATATAGTTTTTTAAAA
2471509 TATTCTTTTT
Statistics
Matches: 212, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
73 16 0.08
74 22 0.10
75 72 0.34
76 81 0.38
77 14 0.07
78 1 0.00
79 6 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (75 bp):
ATATATAATATATAGTTTTTTAAAACATTTTGAAAACTATATAATATATAATTTTGAAAAAACAT
TTTAAAAAAT
Found at i:2471489 original size:41 final size:39
Alignment explanation
Indices: 2471370--2471518 Score: 139
Period size: 39 Copynumber: 3.8 Consensus size: 39
2471360 TTTTGAAAAC
*
2471370 TATATAATATATAATTTTGAAAATA-TTTTTTAAAAATATA
1 TATATAATATATTATTTT-AAAATATTTTTTTAAAAA-ATA
* * *
2471410 TATATAATATA-TAGTTTTAAAAT-GTTATTT-GAAAATA
1 TATATAATATATTA-TTTTAAAATATTTTTTTAAAAAATA
2471447 TATAT--TATATTATTTTAAAAATATTTTTTTAAAAACATA
1 TATATAATATATTATTTT-AAAATATTTTTTTAAAAA-ATA
* *
2471486 TATATAGTATATGATTTTTAAAATATTCTTTTT
1 TATATAATATATTA-TTTTAAAATATT-TTTTT
2471519 TATTTTTTTA
Statistics
Matches: 91, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
35 8 0.09
36 7 0.08
37 13 0.14
38 6 0.07
39 19 0.21
40 15 0.16
41 14 0.15
42 9 0.10
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (39 bp):
TATATAATATATTATTTTAAAATATTTTTTTAAAAAATA
Found at i:2471534 original size:4 final size:4
Alignment explanation
Indices: 2471517--2471566 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
2471507 AATATTCTTT
*
2471517 TTTA TTTT TTTA TTTA TTTA -TTA -TTA TTTA TTTA -TT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2471561 TTTA TT
1 TTTA TT
2471567 ATTCATTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 10 0.24
4 31 0.76
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2471545 original size:14 final size:14
Alignment explanation
Indices: 2471517--2471574 Score: 84
Period size: 14 Copynumber: 4.2 Consensus size: 14
2471507 AATATTCTTT
2471517 TTTATTT-TT-TTA
1 TTTATTTATTATTA
2471529 TTTATTTATTATTA
1 TTTATTTATTATTA
*
2471543 TTTATTTATTTTTA
1 TTTATTTATTATTA
2471557 TTTATTTATTATTCA
1 TTTATTTATTATT-A
2471572 TTT
1 TTT
2471575 CTTTTTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
12 7 0.17
13 2 0.05
14 28 0.68
15 4 0.10
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTATTATTA
Found at i:2471546 original size:18 final size:18
Alignment explanation
Indices: 2471517--2471566 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
2471507 AATATTCTTT
2471517 TTTATT-TT-TTTATTTA
1 TTTATTATTATTTATTTA
2471533 TTTATTATTATTTATTTA
1 TTTATTATTATTTATTTA
2471551 TTT-TTATTTATTTATT
1 TTTATTA-TTATTTATT
2471567 ATTCATTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.19
17 5 0.16
18 20 0.65
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTATTATTTATTTA
Found at i:2472627 original size:19 final size:18
Alignment explanation
Indices: 2472583--2472638 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
2472573 TGTTTTATTC
* * *
2472583 TTATTTTTATTTATTTAT
1 TTATTATTATATATGTAT
2472601 TTATTTATTATATATGTAT
1 TTA-TTATTATATATGTAT
2472620 GTTATTATTAT-TAT-TAT
1 -TTATTATTATATATGTAT
2472637 TT
1 TT
2472639 CTTTTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 3 0.09
18 6 0.18
19 19 0.58
20 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
TTATTATTATATATGTAT
Found at i:2472717 original size:31 final size:31
Alignment explanation
Indices: 2472681--2472739 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2472671 TTTACTTCTT
2472681 TTATTTCATT-TTTTGGTTTTATTT-TTTTAGG
1 TTATTT-ATTATTTT-GTTTTATTTATTTTAGG
2472712 TTATTTATTATTTTGTTTTATTTATTTT
1 TTATTTATTATTTTGTTTTATTTATTTT
2472740 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (31 bp):
TTATTTATTATTTTGTTTTATTTATTTTAGG
Found at i:2472720 original size:17 final size:17
Alignment explanation
Indices: 2472698--2472741 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2472688 ATTTTTTGGT
2472698 TTTATTTTTTTAG-GTTA
1 TTTATTTTTTT-GTGTTA
* *
2472715 TTTATTATTTTGTTTTA
1 TTTATTTTTTTGTGTTA
2472732 TTTATTTTTT
1 TTTATTTTTT
2472742 ATTTATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (17 bp):
TTTATTTTTTTGTGTTA
Found at i:2472738 original size:21 final size:19
Alignment explanation
Indices: 2472697--2472798 Score: 84
Period size: 20 Copynumber: 5.1 Consensus size: 19
2472687 CATTTTTTGG
*
2472697 TTTTA-TTTTTTTAGGTTAT
1 TTTTATTTTTTTTA-TTTAT
2472716 TTATTATTTTGTTTTATTTATT
1 TT-TTATTTT-TTTTATTTA-T
2472738 TTTTATTTATTTTT-TTTACT
1 TTTTATTT-TTTTTATTTA-T
2472758 TTTTATTTTCTTTTATCTTA-
1 TTTTATTTT-TTTTAT-TTAT
* *
2472778 TTTTCTTTTATTTATTTAT
1 TTTTATTTTTTTTATTTAT
2472797 TT
1 TT
2472799 GTTGTTTTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
18 3 0.04
19 10 0.14
20 28 0.40
21 17 0.24
22 12 0.17
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTATTTTTTTTATTTAT
Found at i:2472744 original size:41 final size:42
Alignment explanation
Indices: 2472697--2472790 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 42
2472687 CATTTTTTGG
*
2472697 TTTTATTT-TTTTAGGTTA-TTTATTATTTTGTTTTAT-TTATT
1 TTTTATTTATTTT-GGTTACTTT-TTATTTTCTTTTATCTTATT
**
2472738 TTTTATTTATTTTTTTTACTTTTTATTTTCTTTTATCTTATT
1 TTTTATTTATTTTGGTTACTTTTTATTTTCTTTTATCTTATT
*
2472780 TTCT-TTTATTT
1 TTTTATTTATTT
2472791 ATTTATTTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 31 0.67
42 15 0.33
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.78
Consensus pattern (42 bp):
TTTTATTTATTTTGGTTACTTTTTATTTTCTTTTATCTTATT
Found at i:2472771 original size:5 final size:5
Alignment explanation
Indices: 2472719--2472798 Score: 60
Period size: 5 Copynumber: 16.2 Consensus size: 5
2472709 AGGTTATTTA
* *
2472719 TTATT TTGTT TTA-T TTATT TTTTAT TTATT TT-TT TTACTTT TTATT
1 TTATT TTATT TTATT TTATT TTAT-T TTATT TTATT TTA--TT TTATT
* * *
2472765 TTCTT TTATC TTATT TTCTT TTA-T TTA-T TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT T
2472799 GTTGTTTTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 16 0.27
5 34 0.58
6 4 0.07
7 5 0.08
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:2472806 original size:106 final size:108
Alignment explanation
Indices: 2472587--2472799 Score: 244
Period size: 108 Copynumber: 2.0 Consensus size: 108
2472577 TTATTCTTAT
* *
2472587 TTTTATTTATTTATTTATTTATTATATATGTATGTTATTATTATTATTATTTCTTTTTTTTCTCT
1 TTTTATTTATTTAGTTATTTATTATATATGTATGTTATTATTATTATTATTTATTTTTTTTCTCT
*
2472652 TTATATTATTTTACATCTTTTTACTTCTTTTATTTCATTTTTTGG
66 TTATATTATTTTA-ATCTTATTA-TTCTTTTATTTCATTTTTTGG
* *
2472697 TTTTATTTTTTTAGGTTATTTATTAT-TTTGT-T-TTATTTATT-TT-TTATTTATTTTTTTTAC
1 TTTTATTTATTTA-GTTATTTATTATATATGTATGTTA-TTATTATTATTATTTATTTTTTTT-C
* * *
2472757 TTTTTATTTTCTTTT-ATCTTATT-TTCTTTTATTT-ATTTATTTG
63 TCTTTATATTATTTTAATCTTATTATTCTTTTATTTCATTT-TTTG
2472800 TTGTTTTTAC
Statistics
Matches: 91, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
103 4 0.04
104 15 0.16
106 7 0.08
107 14 0.15
108 18 0.20
109 6 0.07
110 16 0.18
111 11 0.12
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (108 bp):
TTTTATTTATTTAGTTATTTATTATATATGTATGTTATTATTATTATTATTTATTTTTTTTCTCT
TTATATTATTTTAATCTTATTATTCTTTTATTTCATTTTTTGG
Found at i:2472815 original size:108 final size:110
Alignment explanation
Indices: 2472601--2472815 Score: 237
Period size: 107 Copynumber: 2.0 Consensus size: 110
2472591 ATTTATTTAT
*
2472601 TTATTTATTATATATGTATGTTATTATTATTATTATTTCTTTTTTTTCTCTTTATATTATTTTAC
1 TTATTTATTATATATGTATGTTATTATTATTATTATTTATTTTTTTTCTCTTTATATTATTTTA-
* *
2472666 ATCTTTTTACTTCTTTTATTTCATTTTTTGGTTTTATTTTTTTAGG
65 ATCTTTTTACTTCTTTTATTTCATTTGTTGGTTTTACTTTTTTAGG
* * * *
2472712 TTATTTATTAT-TTTGT-T-TTATTTATT-TT-TTATTTATTTTTTTTACTTTTTATTTTCTTTT
1 TTATTTATTATATATGTATGTTA-TTATTATTATTATTTATTTTTTTT-CTCTTTATATTATTTT
* * * *
2472772 -ATCTTATTTTCTTTTATTTATTT-ATTTGTTGTTTTTACCTTTTT
64 AATCTT-TTTACTTCT-TTTATTTCATTTGTTGGTTTTACTTTTTT
2472816 GATTTATTAT
Statistics
Matches: 89, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
106 5 0.06
107 38 0.43
108 25 0.28
109 6 0.07
110 4 0.04
111 11 0.12
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.73
Consensus pattern (110 bp):
TTATTTATTATATATGTATGTTATTATTATTATTATTTATTTTTTTTCTCTTTATATTATTTTAA
TCTTTTTACTTCTTTTATTTCATTTGTTGGTTTTACTTTTTTAGG
Found at i:2477418 original size:64 final size:64
Alignment explanation
Indices: 2477341--2477468 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
2477331 TTAAAATCAT
2477341 ACGTAATATTTAATTTAGATTTCAAATTGATATACAACCGTTAAAAACTTAATGACAGCGAGAC
1 ACGTAATATTTAATTTAGATTTCAAATTGATATACAACCGTTAAAAACTTAATGACAGCGAGAC
*
2477405 ACGTAATATTTAATTTAGATTTCAAATTGATATACAACTGTTAAAAACTTAATGACAGCGAGAC
1 ACGTAATATTTAATTTAGATTTCAAATTGATATACAACCGTTAAAAACTTAATGACAGCGAGAC
2477469 GTGAAATTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (64 bp):
ACGTAATATTTAATTTAGATTTCAAATTGATATACAACCGTTAAAAACTTAATGACAGCGAGAC
Found at i:2478781 original size:17 final size:17
Alignment explanation
Indices: 2478759--2478800 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2478749 AAAAAATGAG
* *
2478759 AAAATTATATATTTTTA
1 AAAATTATAAATTATTA
2478776 AAAATTATAAATTATTA
1 AAAATTATAAATTATTA
2478793 AAATATTA
1 AAA-ATTA
2478801 AAAAATTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTATAAATTATTA
Found at i:2480452 original size:31 final size:31
Alignment explanation
Indices: 2480417--2480477 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
2480407 TATAACAAAG
*
2480417 AATAATTTAGATTTTAAGTTAGATACTTACA
1 AATAATATAGATTTTAAGTTAGATACTTACA
2480448 AATAATATAGATTTTAAGTTAGATACTTAC
1 AATAATATAGATTTTAAGTTAGATACTTAC
2480478 CTACCCTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
AATAATATAGATTTTAAGTTAGATACTTACA
Found at i:2484419 original size:2 final size:2
Alignment explanation
Indices: 2484412--2484470 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2484402 ATTAATTAAT
2484412 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
2484454 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2484471 GATTCCATAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.