Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001736.1 Hibiscus syriacus cultivar Beakdansim tig00003507_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: 1778036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:566243 original size:31 final size:32
Alignment explanation
Indices: 566194--566256 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
566184 AATCAATTTT
566194 AAATATTAAAGTAAAACAAAA-TTAAATTAAG
1 AAATATTAAAGTAAAACAAAACTTAAATTAAG
566225 AAATA-TAAAGTAAGAACAAAACTTTAAATTAA
1 AAATATTAAAGTAA-AACAAAAC-TTAAATTAA
566257 AAGGATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 8 0.28
31 12 0.41
33 9 0.31
ACGTcount: A:0.63, C:0.05, G:0.06, T:0.25
Consensus pattern (32 bp):
AAATATTAAAGTAAAACAAAACTTAAATTAAG
Found at i:567865 original size:73 final size:72
Alignment explanation
Indices: 567747--567896 Score: 248
Period size: 73 Copynumber: 2.1 Consensus size: 72
567737 TATGTTGTAG
* *
567747 ATTAAAAATATTATATTTAAATTATATTTATTACTATGATATTTGAAATATATAAACTTAAACTA
1 ATTAAAAATATTATATTTAAACTATATTTAATACTATGATATTTGAAATATATAAACTTAAACTA
567812 TAATAAA
66 TAATAAA
*
567819 ATTAAAAATATT-TCATTTTATACTATATTTAATACTATGATATTTGAAATATATAAACTTAAAC
1 ATTAAAAATATTAT-A-TTTAAACTATATTTAATACTATGATATTTGAAATATATAAACTTAAAC
567883 TATAATAAA
64 TATAATAAA
567892 ATTAA
1 ATTAA
567897 GCTCAAAAAC
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
71 1 0.01
72 13 0.18
73 59 0.81
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (72 bp):
ATTAAAAATATTATATTTAAACTATATTTAATACTATGATATTTGAAATATATAAACTTAAACTA
TAATAAA
Found at i:574992 original size:21 final size:21
Alignment explanation
Indices: 574936--575000 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
574926 TAATGAATCG
*
574936 ATCTCTCGAGGAAAAGGATCA
1 ATCTCTCGACGAAAAGGATCA
* * *
574957 ATCCCTTGACCAAAAGGATCA
1 ATCTCTCGACGAAAAGGATCA
* *
574978 ATCTCTCGATGAAAATGATCA
1 ATCTCTCGACGAAAAGGATCA
574999 AT
1 AT
575001 TCATTCCCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCTCTCGACGAAAAGGATCA
Found at i:576400 original size:8 final size:8
Alignment explanation
Indices: 576389--576419 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
576379 AAGAAGAAAA
576389 ATGAATGG
1 ATGAATGG
576397 ATGAATGG
1 ATGAATGG
*
576405 ATGAATGA
1 ATGAATGG
576413 ATGAATG
1 ATGAATG
576420 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (8 bp):
ATGAATGG
Found at i:578131 original size:13 final size:13
Alignment explanation
Indices: 578113--578137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
578103 GTGGTCTGAC
578113 AACATCACATAAT
1 AACATCACATAAT
578126 AACATCACATAA
1 AACATCACATAA
578138 ATTCTATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (13 bp):
AACATCACATAAT
Found at i:579906 original size:17 final size:17
Alignment explanation
Indices: 579884--579916 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
579874 CCTAAAATTT
579884 TACAAAGTTTATACTTG
1 TACAAAGTTTATACTTG
579901 TACAAAGTTTATACTT
1 TACAAAGTTTATACTT
579917 TAGCCAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (17 bp):
TACAAAGTTTATACTTG
Found at i:581089 original size:21 final size:21
Alignment explanation
Indices: 581065--581110 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
581055 GGTAAAAAAA
*
581065 GAATTAAAGCATAAATTGAAG
1 GAATTAAAGCACAAATTGAAG
581086 GAATTAAAGCACAAATTGAAG
1 GAATTAAAGCACAAATTGAAG
581107 GAAT
1 GAAT
581111 AAGGAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.22
Consensus pattern (21 bp):
GAATTAAAGCACAAATTGAAG
Found at i:582683 original size:16 final size:16
Alignment explanation
Indices: 582664--582694 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
582654 CCGCTAACTT
582664 TTCTAACAACTAATTG
1 TTCTAACAACTAATTG
*
582680 TTCTAACCACTAATT
1 TTCTAACAACTAATT
582695 ACTATTAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (16 bp):
TTCTAACAACTAATTG
Found at i:589613 original size:55 final size:55
Alignment explanation
Indices: 589541--590154 Score: 802
Period size: 55 Copynumber: 11.1 Consensus size: 55
589531 CTTTTTAGGG
* * * **
589541 GTTTCTTGAT-ATTTTTAAATGAATTTTGAAAGAAGA-TAAGTCTAATTTTTGGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAA-ACTAAGTCTGATTTTCAGAA
* * *
589595 GTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
* * ** ** * *
589650 GTTTCTTAATGATTTTTAAATAAGGTTTTTTAAAGAAGTTAAGTCCAATTTTCGGAT
1 GTTTCTTGATGATTTTTAAATGA-G-TTTTTAAAGAAACTAAGTCTGATTTTCAGAA
* * *
589707 GTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
589762 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
* * * *
589817 GTTTCTTTATGATTTTAAAATGAGTTTTTAAAGAAACTAAGTCTTATTTTGAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
589872 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
* * * *
589927 GTTTCTTTATGATTTTAAAATGAGTTTTTAAAGAAACTAAGTCTTATTTTGAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
* * * *
589982 GTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTATGATTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
* * * * * *
590037 GTTTCTTTACGA-TTTTAAATTACTTTTTAAAGAAACTAAGTATGATTTTAAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
* * * *
590091 GTTTCTTGACGATTTTCAAATGAGTTTTATAAAGAAACTAAGTATGGTTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTT-TAAAGAAACTAAGTCTGATTTTCAGAA
590147 GTTTCTTG
1 GTTTCTTG
590155 TCATGATGAA
Statistics
Matches: 491, Mismatches: 63, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
54 59 0.12
55 354 0.72
56 35 0.07
57 43 0.09
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (55 bp):
GTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAGTCTGATTTTCAGAA
Found at i:590707 original size:200 final size:199
Alignment explanation
Indices: 590361--590785 Score: 588
Period size: 200 Copynumber: 2.1 Consensus size: 199
590351 TCCATCAGGC
*
590361 CATCCATAAGACCTTCGGGCATGATGTTTTCACATGATTTTAAAGAAAAATAAGAAAGCAATTTC
1 CATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAAAGAAAAATAAGAAAGCAATTTC
* **
590426 CAAAGTTTCTCATTTAAATCTTTTCTAAAATTTTATTTTTGAAAAGTAAGAAAATGATTTCCAAA
66 CAAAATTTCTCATTTAAATCTTTTCTAAAATTTTATTTTTGAAAAGTAAGAAAACAATTTCCAAA
* *
590491 GTTTCTTACTTAGTAAGTCCTTCGGGTCATCAATAAGTCTTCTGAGCAAGGTGTTTAAATCCTTC
131 GTTTCTTACTTAGTAAGTCCTTCAGGCCATCAATAAGTCTTCTGAGCAAGGTGTTTAAATCCTTC
590556 GGGT
196 GGGT
* * * *
590560 CATCCATAAGACCTTTGGGCAGGATGTTTTCACATGATTTT-CA-AAAAATAAGAAATCGATTTC
1 CATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAAAGAAAAATAAGAAAGCAATTTC
590623 CAAAATTTCTCATTTAAATCTTTTCTGAAAATTGATT-TTTCTTGAAAAGTAAGAAAACAATTTC
66 CAAAATTTCTCATTTAAATCTTTTCT-AAAATT--TTATTT-TTGAAAAGTAAGAAAACAATTTC
* * * ***
590687 CAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGTCTT-TCGAGCATGATGCCCAAAT
127 CAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAATAAGTCTTCT-GAGCAAGGTGTTTAAAT
* *
590751 CTTTCGTGT
191 CCTTCGGGT
* **
590760 CGTCTGTAAGACCTTCGGGCAGGATG
1 CATCCATAAGACCTTCGGGCAGGATG
590786 AAACAAGTCA
Statistics
Matches: 199, Mismatches: 22, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
197 43 0.22
198 7 0.04
199 43 0.22
200 106 0.53
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (199 bp):
CATCCATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAAAGAAAAATAAGAAAGCAATTTC
CAAAATTTCTCATTTAAATCTTTTCTAAAATTTTATTTTTGAAAAGTAAGAAAACAATTTCCAAA
GTTTCTTACTTAGTAAGTCCTTCAGGCCATCAATAAGTCTTCTGAGCAAGGTGTTTAAATCCTTC
GGGT
Found at i:590803 original size:3 final size:3
Alignment explanation
Indices: 590795--590862 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
590785 GAAACAAGTC
590795 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
590843 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
590863 ATTCTTAGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:592462 original size:103 final size:101
Alignment explanation
Indices: 592381--592566 Score: 259
Period size: 102 Copynumber: 1.8 Consensus size: 101
592371 TATTATTGCT
**
592381 TATTAA-TATTTGAATTATTATACGACCTTGTGGTGACCCAATCCGGGGTATGATCCACATTATT
1 TATTAATTATTTGAATTATTATACGACCTTGTGCCGACCCAAT-CGGGGTATGATCCACATTATT
592445 ATGGTCC-AGACTCTATTAACTCCTAACTGTTAATTTA
65 ATGGTCCGA-ACTCTATTAACTCCTAACTGTTAATTTA
* ** * *
592482 TATTAATTTGTTTGAATTATTATACGACCTTGTGCCGACCTGATCTGGGTGTGATCCACATTATT
1 TATTAA-TTATTTGAATTATTATACGACCTTGTGCCGACCCAATCGGGGTATGATCCACATTATT
*
592547 ATGGTCCGAACTCTACTAAC
65 ATGGTCCGAACTCTATTAAC
592567 ATTTCTAACA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
101 6 0.08
102 36 0.49
103 32 0.43
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (101 bp):
TATTAATTATTTGAATTATTATACGACCTTGTGCCGACCCAATCGGGGTATGATCCACATTATTA
TGGTCCGAACTCTATTAACTCCTAACTGTTAATTTA
Found at i:600654 original size:15 final size:15
Alignment explanation
Indices: 600634--600663 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
600624 ATCGATTCTG
600634 ATGCGAAAAATGACC
1 ATGCGAAAAATGACC
*
600649 ATGCGAAAATTGACC
1 ATGCGAAAAATGACC
600664 GTGCAACTGC
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:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (15 bp):
ATGCGAAAAATGACC
Found at i:604911 original size:13 final size:13
Alignment explanation
Indices: 604893--604917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
604883 AGTCCATTAC
604893 TAATCCAACTTTT
1 TAATCCAACTTTT
604906 TAATCCAACTTT
1 TAATCCAACTTT
604918 GAAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATCCAACTTTT
Found at i:610483 original size:25 final size:25
Alignment explanation
Indices: 610455--610512 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
610445 TTAAGTTAAT
610455 TAGTAATACTTTATACATAAATAGA
1 TAGTAATACTTTATACATAAATAGA
610480 TAGTAATACTTTATACATAAATAGA
1 TAGTAATACTTTATACATAAATAGA
610505 TAGTAATA
1 TAGTAATA
610513 ATGTAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (25 bp):
TAGTAATACTTTATACATAAATAGA
Found at i:613651 original size:23 final size:23
Alignment explanation
Indices: 613625--613695 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
613615 TAATAAAATA
613625 ATAAATTATTGTTGAATTTTTAT
1 ATAAATTATTGTTGAATTTTTAT
* * *
613648 ATAAATAATT-TT---TATTTAA
1 ATAAATTATTGTTGAATTTTTAT
* * *
613667 ATATATTATCGATGAATTTTTAT
1 ATAAATTATTGTTGAATTTTTAT
613690 ATAAAT
1 ATAAAT
613696 AATTTTATTT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
19 12 0.35
20 1 0.03
22 2 0.06
23 19 0.56
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (23 bp):
ATAAATTATTGTTGAATTTTTAT
Found at i:613659 original size:15 final size:15
Alignment explanation
Indices: 613639--613710 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 15
613629 ATTATTGTTG
613639 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
613654 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* **
613669 -A--TAT-TATCGAT
1 AATTTTTATATAAAT
613680 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
613696 AA-TTTTATTTAAAT
1 AATTTTTATATAAAT
613710 A
1 A
613711 TTTAGAATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 11
0.68 0.14 0.17
Matches are distributed among these distances:
11 4 0.09
12 2 0.05
13 1 0.02
14 13 0.30
15 18 0.42
16 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:620126 original size:14 final size:14
Alignment explanation
Indices: 620103--620147 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
620093 TATAAGTGTG
620103 ATTC-TTATTATTC
1 ATTCATTATTATTC
620116 ATTCATTATTATTC
1 ATTCATTATTATTC
* *
620130 GTTCATTATTTTTC
1 ATTCATTATTATTC
620144 ATTC
1 ATTC
620148 GTTCGTTAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 4 0.14
14 24 0.86
ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTCATTATTATTC
Found at i:620136 original size:18 final size:18
Alignment explanation
Indices: 620113--620151 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
620103 ATTCTTATTA
620113 TTCATTCATTATT-ATTCG
1 TTCATT-ATTATTCATTCG
*
620131 TTCATTATTTTTCATTCG
1 TTCATTATTATTCATTCG
620149 TTC
1 TTC
620152 GTTAGGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (18 bp):
TTCATTATTATTCATTCG
Found at i:621801 original size:2 final size:2
Alignment explanation
Indices: 621794--621831 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
621784 CGTTTGGAGG
621794 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
621832 GCATATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:626461 original size:2 final size:2
Alignment explanation
Indices: 626448--626478 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
626438 TTATTTATCA
*
626448 AT AT AT AC 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
626479 GCCTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:629797 original size:23 final size:23
Alignment explanation
Indices: 629738--629803 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
629728 TAAGAATAAT
* *
629738 TATGTCTTCGTGACATATTTATC
1 TATGTCTTTGTGACATGTTTATC
* *
629761 TATG-CTTTTATGACACGTTTATC
1 TATGTC-TTTGTGACATGTTTATC
*
629784 TCTGTCTTTGTGACATGTTT
1 TATGTCTTTGTGACATGTTT
629804 TTATATGCCT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.50
Consensus pattern (23 bp):
TATGTCTTTGTGACATGTTTATC
Found at i:633003 original size:19 final size:19
Alignment explanation
Indices: 632979--633048 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 19
632969 GAGAATATGA
*
632979 TTTCCAACCTAAAACTTGT
1 TTTCCAACCTAAAACTAGT
**
632998 TTTCCAAATTAAAA-TCAGGT
1 TTTCCAACCTAAAACT-A-GT
*
633018 TTT-CAA-CTCAAAACTAGA
1 TTTCCAACCT-AAAACTAGT
633036 TTTCCAACCTAAA
1 TTTCCAACCTAAA
633049 GCCCGTTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 6 0.15
19 26 0.65
20 8 0.20
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.33
Consensus pattern (19 bp):
TTTCCAACCTAAAACTAGT
Found at i:633078 original size:38 final size:38
Alignment explanation
Indices: 633036--633114 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
633026 CAAAACTAGA
* *
633036 TTTCCAACCTAAAGCCC-GTTTTCTAAACTAAAATCAGG
1 TTTCCAACCTAAAACCCATTTTTC-AAACTAAAATCAGG
* * **
633074 TTTCCAGCTTAAAACTTATTTTTCAAACTAAAATCAGG
1 TTTCCAACCTAAAACCCATTTTTCAAACTAAAATCAGG
633112 TTT
1 TTT
633115 TTAACATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 29 0.85
39 5 0.15
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (38 bp):
TTTCCAACCTAAAACCCATTTTTCAAACTAAAATCAGG
Found at i:633088 original size:57 final size:57
Alignment explanation
Indices: 632977--633089 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
632967 CGGAGAATAT
** * *
632977 GATTTCCAACCTAAAACTTGTTTTCCAAATTAAAATCAGGTTTTCAACTCAAAACTA
1 GATTTCCAACCTAAAACCCGTTTTCCAAACTAAAATCAGGTTTCCAACTCAAAACTA
* * * *
633034 GATTTCCAACCTAAAGCCCGTTTTCTAAACTAAAATCAGGTTTCCAGCTTAAAACT
1 GATTTCCAACCTAAAACCCGTTTTCCAAACTAAAATCAGGTTTCCAACTCAAAACT
633090 TATTTTTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (57 bp):
GATTTCCAACCTAAAACCCGTTTTCCAAACTAAAATCAGGTTTCCAACTCAAAACTA
Found at i:633115 original size:19 final size:19
Alignment explanation
Indices: 632996--633115 Score: 52
Period size: 19 Copynumber: 6.3 Consensus size: 19
632986 CCTAAAACTT
*
632996 GTTTTCCAAATTAAAATCAG
1 GTTTT-CAAACTAAAATCAG
633016 GTTTTC-AACTCAAAA-CTAG
1 GTTTTCAAACT-AAAATC-AG
* * * * **
633035 ATTTCCAACCT-AAAGCCC
1 GTTTTCAAACTAAAATCAG
633053 GTTTTCTAAACTAAAATCAG
1 GTTTTC-AAACTAAAATCAG
* * *
633073 G-TTTCCAGCTTAAAACTTA-
1 GTTTTCAAAC-TAAAA-TCAG
*
633092 TTTTTCAAACTAAAATCAG
1 GTTTTCAAACTAAAATCAG
633111 GTTTT
1 GTTTT
633116 TAACATAAAA
Statistics
Matches: 70, Mismatches: 20, Indels: 21
0.63 0.18 0.19
Matches are distributed among these distances:
18 15 0.21
19 34 0.49
20 21 0.30
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (19 bp):
GTTTTCAAACTAAAATCAG
Found at i:638439 original size:82 final size:81
Alignment explanation
Indices: 638343--638505 Score: 317
Period size: 82 Copynumber: 2.0 Consensus size: 81
638333 CATGAGTAGA
638343 AATCTTTCAAATCGTAAATTCGTTCATACCTCCCATCATAAAAGTTTCAAACTTTAATACAAAAA
1 AATCTTTCAAATCGTAAATTCGTTCATACCTCCCATCATAAAAGTTTCAAAC-TTAATACAAAAA
638408 TCAAATGTGCCCTACAT
65 TCAAATGTGCCCTACAT
638425 AATCTTTCAAATCGTAAATTCGTTCATACCTCCCATCATAAAAGTTTCAAACTTAATACAAAAAT
1 AATCTTTCAAATCGTAAATTCGTTCATACCTCCCATCATAAAAGTTTCAAACTTAATACAAAAAT
638490 CAAATGTGCCCTACAT
66 CAAATGTGCCCTACAT
638506 GCCCCCTAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 29 0.36
82 52 0.64
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.31
Consensus pattern (81 bp):
AATCTTTCAAATCGTAAATTCGTTCATACCTCCCATCATAAAAGTTTCAAACTTAATACAAAAAT
CAAATGTGCCCTACAT
Found at i:640385 original size:2 final size:2
Alignment explanation
Indices: 640378--640403 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
640368 TGATTCAATC
640378 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
640404 CATTTACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:641452 original size:19 final size:19
Alignment explanation
Indices: 641428--641465 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
641418 CGGTTCAGTC
*
641428 CAGACTGGCCCAACTGATT
1 CAGACTGGCCCAACCGATT
*
641447 CAGACTGGTCCAACCGATT
1 CAGACTGGCCCAACCGATT
641466 TAGAGCAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (19 bp):
CAGACTGGCCCAACCGATT
Found at i:645764 original size:29 final size:29
Alignment explanation
Indices: 645722--645788 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
645712 GCTCGACAGC
645722 TTGGTCCAGACTGGCCCAATCGGTTCAGA
1 TTGGTCCAGACTGGCCCAATCGGTTCAGA
645751 TTGGTCCAGACTGGCCCAATCGGTTCAGA
1 TTGGTCCAGACTGGCCCAATCGGTTCAGA
* *
645780 CTAGTCCAG
1 TTGGTCCAG
645789 CCAGTCAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.21, C:0.28, G:0.27, T:0.24
Consensus pattern (29 bp):
TTGGTCCAGACTGGCCCAATCGGTTCAGA
Found at i:649878 original size:69 final size:69
Alignment explanation
Indices: 649767--649979 Score: 250
Period size: 69 Copynumber: 3.1 Consensus size: 69
649757 ATTTTAAACA
* * *
649767 TAATCCATCGAGGCTCCCGTGTGAGTCATCC-GAAATAAATATGATTAGGTGTTCCCATGCGAGT
1 TAATCCATCGAGGCTCTCGTGCGAGTCA-CCTGGAATAAATATGATTAGGTGTTCCCATGCGAGT
*
649831 CATTC
65 CACTC
* ** *
649836 TAATCCATCGGGGCTCTCGTGCGAGTCACCTGGAATAAATATGATTAGGTACTCCCATACGAGTC
1 TAATCCATCGAGGCTCTCGTGCGAGTCACCTGGAATAAATATGATTAGGTGTTCCCATGCGAGTC
649901 ACTC
66 ACTC
* * * * * ** *
649905 TAATCCTTCGAGACTCTCGTACGAGACA-CTCGGAATAAATATAATTAGGTGTTCCTGTGCGAGA
1 TAATCCATCGAGGCTCTCGTGCGAGTCACCT-GGAATAAATATGATTAGGTGTTCCCATGCGAGT
649969 CACTC
65 CACTC
649974 TAATCC
1 TAATCC
649980 TTCGGGAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
68 4 0.03
69 118 0.97
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (69 bp):
TAATCCATCGAGGCTCTCGTGCGAGTCACCTGGAATAAATATGATTAGGTGTTCCCATGCGAGTC
ACTC
Found at i:654082 original size:26 final size:26
Alignment explanation
Indices: 654052--654101 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
654042 AAAACAATTT
*
654052 TAAAGTGA-AATAAAACATAAATTTCA
1 TAAAGT-ATAATAAAAAATAAATTTCA
*
654078 TAAAGTATTATAAAAAATAAATTT
1 TAAAGTATAATAAAAAATAAATTT
654102 GTAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (26 bp):
TAAAGTATAATAAAAAATAAATTTCA
Found at i:654292 original size:17 final size:16
Alignment explanation
Indices: 654256--654307 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 16
654246 ATTCGTACAT
*
654256 ATTTCAGTACTTCATTTC
1 ATTTCA-TA-TTCTTTTC
654274 ATTTCCATATTCTTTTC
1 ATTT-CATATTCTTTTC
*
654291 A-TTCATATTCTTGTC
1 ATTTCATATTCTTTTC
654306 AT
1 AT
654308 AACTTTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 12 0.40
16 2 0.07
17 8 0.27
18 6 0.20
19 2 0.07
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (16 bp):
ATTTCATATTCTTTTC
Found at i:656176 original size:17 final size:17
Alignment explanation
Indices: 656154--656187 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
656144 CCGGTCTGAC
656154 CCGACCCGACCCATTGA
1 CCGACCCGACCCATTGA
*
656171 CCGACCCGACCCGTTGA
1 CCGACCCGACCCATTGA
656188 TCTGACCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.12
Consensus pattern (17 bp):
CCGACCCGACCCATTGA
Found at i:656178 original size:22 final size:24
Alignment explanation
Indices: 656149--656211 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 24
656139 CTTGACCGGT
656149 CTGACCCGACCCGACCCAT-TGAC
1 CTGACCCGACCCGACCCATCTGAC
***
656172 C-GACCCGACCCG-TTGATCTGAC
1 CTGACCCGACCCGACCCATCTGAC
656194 CTGACCCGACCCGACCCA
1 CTGACCCGACCCGACCCA
656212 GTGATATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 2 0.06
22 16 0.52
23 12 0.39
24 1 0.03
ACGTcount: A:0.21, C:0.48, G:0.19, T:0.13
Consensus pattern (24 bp):
CTGACCCGACCCGACCCATCTGAC
Found at i:656277 original size:29 final size:27
Alignment explanation
Indices: 656212--656308 Score: 113
Period size: 29 Copynumber: 3.4 Consensus size: 27
656202 ACCCGACCCA
*
656212 GTGATATTTTGGGAATTATTTTAAAAAT
1 GTGATATTTT-GGAATTATTTTAAAAAG
* *
656240 GTGACATTTTAGGAATTATTTGTAAAACG
1 GTGATATTTT-GGAATTATTT-TAAAAAG
656269 GTGATATTTTGGTAATTATTTTTAATAAAG
1 GTGATATTTTGG-AATTA-TTTTAA-AAAG
656299 GTGATATTTT
1 GTGATATTTT
656309 TGTAATTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 21 0.36
29 22 0.37
30 16 0.27
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (27 bp):
GTGATATTTTGGAATTATTTTAAAAAG
Found at i:663620 original size:29 final size:28
Alignment explanation
Indices: 663578--663733 Score: 170
Period size: 29 Copynumber: 5.4 Consensus size: 28
663568 ACCCGACCCA
*
663578 GTGACATTTTGGGAATTATTTTGAAAAAG
1 GTGATATTTTGGGAATTATTTT-AAAAAG
* * *
663607 GTGATATATTGGGATTTCTTTTGAAAAAG
1 GTGATATTTTGGGAATTATTTT-AAAAAG
* * *
663636 GTGACATTCTGGGAATTATTTATAAAATG
1 GTGATATTTTGGGAATTATTT-TAAAAAG
663665 GTGATATTTTGGGAATTATTTATAAAACA-
1 GTGATATTTTGGGAATTATTT-TAAAA-AG
*
663694 GTGATATTTTGGTAATTATTTTTAATAAAG
1 GTGATATTTTGGGAATTA-TTTTAA-AAAG
663724 GTGATATTTT
1 GTGATATTTT
663734 TGTAATTTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
29 92 0.85
30 16 0.15
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (28 bp):
GTGATATTTTGGGAATTATTTTAAAAAG
Found at i:666474 original size:28 final size:28
Alignment explanation
Indices: 666442--666500 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
666432 ATAATTTTAA
*
666442 TAATCACACAAGCCTTAGAATTAAACTC
1 TAATCACACAAGCCTAAGAATTAAACTC
666470 TAATCACACAAGCCTAAGAATTAAACTC
1 TAATCACACAAGCCTAAGAATTAAACTC
666498 TAA
1 TAA
666501 CATAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.24
Consensus pattern (28 bp):
TAATCACACAAGCCTAAGAATTAAACTC
Found at i:671977 original size:24 final size:24
Alignment explanation
Indices: 671948--671997 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
671938 AATACATGAC
671948 AATATAACATGTTGAAATTTAACA
1 AATATAACATGTTGAAATTTAACA
*
671972 AATATAACATGTTGAAATTTGACA
1 AATATAACATGTTGAAATTTAACA
671996 AA
1 AA
671998 ATCGGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (24 bp):
AATATAACATGTTGAAATTTAACA
Found at i:672215 original size:20 final size:20
Alignment explanation
Indices: 672187--672224 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
672177 AATATAACAT
672187 GTTTAAATTTGACAAAACTG
1 GTTTAAATTTGACAAAACTG
*
672207 GTTTCAATTTGACAAAAC
1 GTTTAAATTTGACAAAAC
672225 CAAGTTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
GTTTAAATTTGACAAAACTG
Found at i:672373 original size:191 final size:196
Alignment explanation
Indices: 671972--672503 Score: 611
Period size: 191 Copynumber: 2.7 Consensus size: 196
671962 AAATTTAACA
* *
671972 AATATAACATGTTGAAATTTGACAAAA-TCGGTTTCAATTTGATAAAATCGGTAAAGAGCTACCG
1 AATATAACATGTTGAAATTTGACAAAACT-GGTTTCAATTTGACAAAA-C-G--AAGAGCTACCA
*
672036 GAATTGTTGAAATATGTATCGATACTTTTATAAGTATATGTACCAAAGTATCGAAGTATCGATAC
61 GAATGGTTGAAATATGTATCGATACTTTTATAAGTATATGTACCAAAGTATC--AG--T-GATAC
** * * *
672101 TTTAGGAATTTAAAAGAATTGCAATAATAGCGGCTATAAAGTGTCGATATCTTAGACACATGTAT
121 TTTAGGAATTTAAAAGAATAACAATAATAGCGCCTATAAAGTATCGATACCTTAGACACATGTAT
672166 CAATACATGAC
186 CAATACATGAC
* * *
672177 AATATAACATGTTTAAATTTGACAAAACTGGTTTCAATTTGACAAAAC-CA-AGTTACCAGAATG
1 AATATAACATGTTGAAATTTGACAAAACTGGTTTCAATTTGACAAAACGAAGAGCTACCAGAATG
* * *
672240 GTTGAAATTTGTATCGATTCTTTTATAAGTATATGTATCAAAGTATC-G-G-TACTTTAGGAATT
66 GTTGAAATATGTATCGATACTTTTATAAGTATATGTACCAAAGTATCAGTGATACTTTAGGAATT
* *
672302 TAAAAGAATAACAGTAATAGCGCCTATAAAGTATCGATACCTTAGACACATGTATCGATACATGA
131 TAAAAGAATAACAATAATAGCGCCTATAAAGTATCGATACCTTAGACACATGTATCAATACATGA
672367 C
196 C
* * * * **
672368 AATATAACAGGTTGAAATTTGACAAAACCGATTTCAATTTGACAAAACTGGTAAAGCGCTACTGG
1 AATATAACATGTTGAAATTTGACAAAACTGGTTTCAATTTGACAAAAC--G--AAGAGCTACCAG
* * ** *
672433 AATTGTTG-AA-A-GTATTGATACGCTTATAAGTATATGTACCATAGTATCA--G-TACTTTAGG
62 AATGGTTGAAATATGTATCGATACTTTTATAAGTATATGTACCAAAGTATCAGTGATACTTTAGG
672492 AATTTAAAAGAA
127 AATTTAAAAGAA
672504 ATGAAAAAAG
Statistics
Matches: 286, Mismatches: 33, Indels: 27
0.83 0.10 0.08
Matches are distributed among these distances:
191 116 0.41
192 1 0.00
194 53 0.19
196 4 0.01
197 12 0.04
199 54 0.19
200 1 0.00
204 1 0.00
205 43 0.15
206 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.32
Consensus pattern (196 bp):
AATATAACATGTTGAAATTTGACAAAACTGGTTTCAATTTGACAAAACGAAGAGCTACCAGAATG
GTTGAAATATGTATCGATACTTTTATAAGTATATGTACCAAAGTATCAGTGATACTTTAGGAATT
TAAAAGAATAACAATAATAGCGCCTATAAAGTATCGATACCTTAGACACATGTATCAATACATGA
C
Found at i:674248 original size:199 final size:199
Alignment explanation
Indices: 673903--674267 Score: 624
Period size: 199 Copynumber: 1.8 Consensus size: 199
673893 TTATTTACTT
*
673903 GCGTAAATACCAAGTATCAATACTTTTATATAGGTATGGATATTTTTATTCCAGTATGCTTCTCA
1 GCGTAAATACCAAGTATCAATACTTTTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCA
* * *
673968 AACAATTTGCACGCAAAATGTATCGATACACATATCTAAAGTATCGATACTTGGAATTTCAAAAC
66 AACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCAATACTTCGAATTTCAAAAC
*
674033 TTATTACTTAAAAGTAATAAGTTAATTAACAATGTAAATGGTAAAAATCTATTGGTATATTGATA
131 TTATTACTTAAAAGTAATAAGTAAATTAACAATGTAAATGGTAAAAATCTATTGGTATATTGATA
674098 ATAG
196 ATAG
*
674102 GCGTAAATACCAAGTATCAATACTTTTATATAGGTATGGATACTTTTATTTCAGTATGCTTCTCA
1 GCGTAAATACCAAGTATCAATACTTTTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCA
*
674167 AACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCAATACTTCTAATTT-AGAAA
66 AACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCAATACTTCGAATTTCA-AAA
* * *
674231 CTTATTACTTTAAAGTAATAGGTAAATTAACGATGTA
130 CTTATTACTTAAAAGTAATAAGTAAATTAACAATGTA
674268 CACGGTAAGC
Statistics
Matches: 155, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
198 1 0.01
199 154 0.99
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (199 bp):
GCGTAAATACCAAGTATCAATACTTTTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCA
AACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCAATACTTCGAATTTCAAAAC
TTATTACTTAAAAGTAATAAGTAAATTAACAATGTAAATGGTAAAAATCTATTGGTATATTGATA
ATAG
Found at i:674435 original size:131 final size:131
Alignment explanation
Indices: 674186--674532 Score: 463
Period size: 131 Copynumber: 2.7 Consensus size: 131
674176 CACGCAAAAT
* * *
674186 GTATCGATACACATATATAAAGTATCAATACTTCTAATTT-AGAAA-CTTATTACTTTAAAGTAA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCA-AAATC-TATTACTTTAAAGTAA
* * * *
674249 TAGGTAAATTAACGATGTACACGGTAAGCGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTC
64 TAGGTAAATTAACAATGTACACGGTAAGCGTTTCTACCGATACAATGAAAATAGGCGTAAATGTA
674314 CAA
129 CAA
*
674317 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCAAAATCTATTACTTTAAAGTAAAA
1 GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCAAAATCTATTACTTTAAAGTAATA
* *
674382 GGTAAATTAACAATGTATATGGTTAA-CGTTTCTACCGATACAAT-AAAAGTAGGCGTAAATGTA
66 GGTAAATTAACAATGTACACGG-TAAGCGTTTCTACCGATACAATGAAAA-TAGGCGTAAATGTA
674445 CAA
129 CAA
* * * * *
674448 GTATCAATACT-GTCATAT-AAGTATCGATACTTATAATTTCGAAATATATTATTTTAAAGTAAT
1 GTATCGATACTCAT-ATATAAAGTATCGATACTTATAATTTCAAAATCTATTACTTTAAAGTAAT
*
674511 AGGTAAATTAACAGTGTACACG
65 AGGTAAATTAACAATGTACACG
674533 ATAATATGTT
Statistics
Matches: 192, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
130 65 0.34
131 122 0.64
132 5 0.03
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (131 bp):
GTATCGATACTCATATATAAAGTATCGATACTTATAATTTCAAAATCTATTACTTTAAAGTAATA
GGTAAATTAACAATGTACACGGTAAGCGTTTCTACCGATACAATGAAAATAGGCGTAAATGTACA
A
Found at i:676027 original size:52 final size:52
Alignment explanation
Indices: 675949--676054 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 52
675939 GGATCATGCA
*
675949 TGGATCTGGTGTGCAGTAACTCTCAACATTCTCCCTGCTTTCTCAACCTTCT
1 TGGATCTGGTATGCAGTAACTCTCAACATTCTCCCTGCTTTCTCAACCTTCT
* * * *
676001 TGGATCTGTTATGCAGTAACTCTCAACATTTTCTCTGTTTTCTCAACCTTCT
1 TGGATCTGGTATGCAGTAACTCTCAACATTCTCCCTGCTTTCTCAACCTTCT
676053 TG
1 TG
676055 ATGAAAAGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (52 bp):
TGGATCTGGTATGCAGTAACTCTCAACATTCTCCCTGCTTTCTCAACCTTCT
Found at i:676109 original size:35 final size:35
Alignment explanation
Indices: 676069--676280 Score: 289
Period size: 35 Copynumber: 6.0 Consensus size: 35
676059 AAAGATGAAA
**
676069 ACTTGAATCGAAAGTGTTGATGCTTCCTTCCGTTC
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
* * * *
676104 ACTTGAATCGAAAGTGTCGGTGCTTCCTTTCATTC
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
**
676139 TTTTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
1 -ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
*
676175 ACTTGAATCGAAAGTGCCGATGCTTCATTCCGTTC
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
* * *
676210 ATTTGAATCGAAAGTACCGATGCTTCATTCCGTTC
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
* *
676245 ACTTGAATTGAAAGTGCCGATGCTTCCATCCGTTC
1 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
676280 A
1 A
676281 AACTCTAAAT
Statistics
Matches: 156, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 127 0.81
36 29 0.19
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (35 bp):
ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
Found at i:692987 original size:31 final size:31
Alignment explanation
Indices: 692949--693049 Score: 157
Period size: 31 Copynumber: 3.3 Consensus size: 31
692939 TGAACACAGG
692949 TCGGGTTCGGTTATCATATTATCCCTTAAAT
1 TCGGGTTCGGTTATCATATTATCCCTTAAAT
*
692980 TCGGGTTCGGTTATCATATTATCTCTTAAAT
1 TCGGGTTCGGTTATCATATTATCCCTTAAAT
* * * *
693011 TTGGGTTTGATTTTCATATTATCCCTTAAAT
1 TCGGGTTCGGTTATCATATTATCCCTTAAAT
693042 TCGGGTTC
1 TCGGGTTC
693050 AGGTCGTTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (31 bp):
TCGGGTTCGGTTATCATATTATCCCTTAAAT
Found at i:694991 original size:30 final size:30
Alignment explanation
Indices: 694916--694984 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
694906 AAACGAAAAC
694916 ATCCCAAAAGTATTATTTTATATCTAATTT
1 ATCCCAAAAGTATTATTTTATATCTAATTT
694946 ATCCCAAAAGTATTATTTTATATCTAATTT
1 ATCCCAAAAGTATTATTTTATATCTAATTT
694976 ATCCCAAAA
1 ATCCCAAAA
694985 ACATTATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (30 bp):
ATCCCAAAAGTATTATTTTATATCTAATTT
Found at i:695746 original size:5 final size:5
Alignment explanation
Indices: 695736--695782 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
695726 AAACATTATG
*
695736 AAAAT AAAAT --AAT AATAAT AAAAT -AAAT AAGAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
695783 ATATAATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 3 0.08
4 4 0.11
5 24 0.67
6 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:695757 original size:14 final size:14
Alignment explanation
Indices: 695738--695789 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
695728 ACATTATGAA
695738 AATAAAATAATAAT
1 AATAAAATAATAAT
695752 AATAAAATAAATAA-
1 AATAAAAT-AATAAT
*
695766 GATAAAATAA-AAT
1 AATAAAATAATAAT
695779 AA-AAATATAAT
1 AATAAA-ATAAT
695790 GATTTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 5 0.16
13 7 0.22
14 15 0.47
15 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AATAAAATAATAAT
Found at i:695760 original size:19 final size:20
Alignment explanation
Indices: 695736--695782 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
695726 AAACATTATG
695736 AAAATAAAAT-A-ATAATAAT
1 AAAATAAAATAAGATAA-AAT
695755 AAAAT-AAATAAGATAAAAT
1 AAAATAAAATAAGATAAAAT
695774 AAAATAAAA
1 AAAATAAAA
695783 ATATAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.16
19 14 0.56
20 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAATAAAATAAGATAAAAT
Found at i:695940 original size:2 final size:2
Alignment explanation
Indices: 695933--695958 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
695923 TTTTGAGTGG
695933 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
695959 AGGGAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:696068 original size:2 final size:2
Alignment explanation
Indices: 696061--696092 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
696051 CTATTAAGTA
696061 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
696093 GACATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:696929 original size:32 final size:32
Alignment explanation
Indices: 696893--697045 Score: 118
Period size: 32 Copynumber: 5.2 Consensus size: 32
696883 TATCCTTGCG
*
696893 ACGAACCTGAACCAGCATCGCGGCTCCTCGAC
1 ACGAACCTGAACCAGCGTCGCGGCTCCTCGAC
* *
696925 ACGAACCTGAACTAGCGTCGTGGCTCCTCG--
1 ACGAACCTGAACCAGCGTCGCGGCTCCTCGAC
* * *
696955 --GTA-C-GAACCAGCGTTGCGGCTTCTC-A-
1 ACGAACCTGAACCAGCGTCGCGGCTCCTCGAC
*
696981 AC--A-C-GAACCA--GTCGCGGCTCTTCGAC
1 ACGAACCTGAACCAGCGTCGCGGCTCCTCGAC
* * *
697007 ACAAACCTGAACCAACGTCGCGGCTCCTCCAC
1 ACGAACCTGAACCAGCGTCGCGGCTCCTCGAC
697039 ACGAACC
1 ACGAACC
697046 AGCGTCGTGG
Statistics
Matches: 96, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
24 10 0.10
25 1 0.01
26 27 0.28
27 1 0.01
28 3 0.03
29 1 0.01
30 6 0.06
32 47 0.49
ACGTcount: A:0.24, C:0.38, G:0.22, T:0.16
Consensus pattern (32 bp):
ACGAACCTGAACCAGCGTCGCGGCTCCTCGAC
Found at i:697006 original size:82 final size:83
Alignment explanation
Indices: 696901--697068 Score: 212
Period size: 82 Copynumber: 2.0 Consensus size: 83
696891 CGACGAACCT
* * * * ***
696901 GAACCAGCATCGCGGCTCCTCGACACGAACCTGAACTAGCGTCGTGGCTCCTCGGTACGAACCAG
1 GAACCAG-ATCGCGGCTCCTCGACACAAACCTGAACCAACGTCGCGGCTCCTCCACACGAACCAG
* *
696966 CGTTGCGGCTTCTCAACAC
65 CGTCGCGGCTCCTCAACAC
*
696985 GAACCAG-TCGCGGCTCTTCGACACAAACCTGAACCAACGTCGCGGCTCCTCCACACGAACCAGC
1 GAACCAGATCGCGGCTCCTCGACACAAACCTGAACCAACGTCGCGGCTCCTCCACACGAACCAGC
* *
697049 GTCGTGGCTCCTCCACAC
66 GTCGCGGCTCCTCAACAC
697067 GA
1 GA
697069 TAGTAATAGA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
82 65 0.90
84 7 0.10
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.16
Consensus pattern (83 bp):
GAACCAGATCGCGGCTCCTCGACACAAACCTGAACCAACGTCGCGGCTCCTCCACACGAACCAGC
GTCGCGGCTCCTCAACAC
Found at i:697051 original size:26 final size:26
Alignment explanation
Indices: 696901--697068 Score: 106
Period size: 26 Copynumber: 6.1 Consensus size: 26
696891 CGACGAACCT
*
696901 GAACCAGCATCGCGGCTCCTCGACACGAACC
1 GAACCAGCGTCGCGGCTCCTC--CAC--A-C
* * ***
696932 TGAACTAGCGTCGTGGCTCCTCGGTAC
1 -GAACCAGCGTCGCGGCTCCTCCACAC
* * *
696959 GAACCAGCGTTGCGGCTTCTCAACAC
1 GAACCAGCGTCGCGGCTCCTCCACAC
*
696985 GAACCA--GTCGCGGCTCTTCGACACAAACC
1 GAACCAGCGTCGCGGCTCCTC--CAC--A-C
*
697014 TGAACCAACGTCGCGGCTCCTCCACAC
1 -GAACCAGCGTCGCGGCTCCTCCACAC
*
697041 GAACCAGCGTCGTGGCTCCTCCACAC
1 GAACCAGCGTCGCGGCTCCTCCACAC
697067 GA
1 GA
697069 TAGTAATAGA
Statistics
Matches: 108, Mismatches: 20, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
24 10 0.09
26 53 0.49
27 2 0.02
28 3 0.03
29 1 0.01
30 9 0.08
32 30 0.28
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.16
Consensus pattern (26 bp):
GAACCAGCGTCGCGGCTCCTCCACAC
Found at i:698169 original size:20 final size:21
Alignment explanation
Indices: 698144--698185 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
698134 TGATCCAATT
698144 TATTGTCAAG-AAAAATTGAA
1 TATTGTCAAGCAAAAATTGAA
* *
698164 TATTGTGAAGCACAAATTGAA
1 TATTGTCAAGCAAAAATTGAA
698185 T
1 T
698186 TCTCTCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (21 bp):
TATTGTCAAGCAAAAATTGAA
Found at i:698997 original size:42 final size:42
Alignment explanation
Indices: 698945--699085 Score: 172
Period size: 42 Copynumber: 3.5 Consensus size: 42
698935 GATGTTGATT
* * *
698945 TTATTTAGACTTATTAGTGTTATGGTGTTGTTTATTTTAGAC
1 TTATTGAGACTTAATAGTGTTATGGTGTTATTTATTTTAGAC
* *
698987 TTATTGAGACTTAATGGTGTTATGTTGTTATTTATTTTAGAC
1 TTATTGAGACTTAATAGTGTTATGGTGTTATTTATTTTAGAC
699029 TTATTGAGAC-T--TA-----ATGGTGTTATTTATTTTAGAC
1 TTATTGAGACTTAATAGTGTTATGGTGTTATTTATTTTAGAC
*
699063 TTATTGAGACTTAATGGTGTTAT
1 TTATTGAGACTTAATAGTGTTAT
699086 TTATTTACTT
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
34 30 0.36
35 1 0.01
37 1 0.01
39 1 0.01
41 1 0.01
42 49 0.59
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (42 bp):
TTATTGAGACTTAATAGTGTTATGGTGTTATTTATTTTAGAC
Found at i:699052 original size:34 final size:34
Alignment explanation
Indices: 699012--699091 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
699002 GGTGTTATGT
699012 TGTTATTTATTTTAGACTTATTGAGACTTAATGG
1 TGTTATTTATTTTAGACTTATTGAGACTTAATGG
699046 TGTTATTTATTTTAGACTTATTGAGACTTAATGG
1 TGTTATTTATTTTAGACTTATTGAGACTTAATGG
699080 TGTTATTTATTT
1 TGTTATTTATTT
699092 ACTTGTTTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (34 bp):
TGTTATTTATTTTAGACTTATTGAGACTTAATGG
Found at i:699058 original size:76 final size:72
Alignment explanation
Indices: 698936--699085 Score: 228
Period size: 76 Copynumber: 2.0 Consensus size: 72
698926 AATATTATTG
** *
698936 ATGTTGATTTTATTTAGACTTATTAGTGTTATGGTGTTGTTTATTTTAGACTTATTGAGACTTAA
1 ATGTTGATTTTATTTAGACTTATTAGACTTATGGTGTTATTTATTTTAGACTTATTGAGACTTAA
699001 TGGTGTT
66 TGGTGTT
*
699008 ATGTTGTTATTTATTTTAGACTTATTGAGACTTAATGGTGTTATTTATTTTAGACTTATTGAGAC
1 ATGTTGAT-TTTA-TTTAGACTTATT-AGACTT-ATGGTGTTATTTATTTTAGACTTATTGAGAC
699073 TTAATGGTGTT
62 TTAATGGTGTT
699084 AT
1 AT
699086 TTATTTACTT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
72 7 0.10
73 4 0.06
74 12 0.17
75 4 0.06
76 43 0.61
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (72 bp):
ATGTTGATTTTATTTAGACTTATTAGACTTATGGTGTTATTTATTTTAGACTTATTGAGACTTAA
TGGTGTT
Found at i:700879 original size:3 final size:3
Alignment explanation
Indices: 700871--700951 Score: 135
Period size: 3 Copynumber: 26.7 Consensus size: 3
700861 AAATAAAGAT
700871 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
700919 TAA TAA TAA TAAA TAT TAA TAT TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA
700952 TATATTTAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 70 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:701241 original size:31 final size:31
Alignment explanation
Indices: 701198--701276 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 31
701188 ATAACGGTGG
*
701198 AGTGACCATTTTGTTACGAAT-AGATAACGTT
1 AGTGACCATTTTGTTACAAATCA-ATAACGTT
*
701229 AGTGACCGTTTTGTTACAAATCAATAACGTT
1 AGTGACCATTTTGTTACAAATCAATAACGTT
*
701260 AGTGACCAATTTGTTAC
1 AGTGACCATTTTGTTAC
701277 TTTTGAAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCAATAACGTT
Found at i:719375 original size:22 final size:21
Alignment explanation
Indices: 719350--719443 Score: 54
Period size: 21 Copynumber: 4.5 Consensus size: 21
719340 AATAAAACAT
719350 TAAAAAAATAATATATAATTTA
1 TAAAAAAATAATAT-TAATTTA
*
719372 TAAAAGTAAAT--TATTTATTTA
1 TAAAA--AAATAATATTAATTTA
* *
719393 -AAAATAAT-ATATATAATTAA
1 TAAAAAAATAATAT-TAATTTA
* *
719413 TAAAAGTAA-AATATTTATTTA
1 TAAAA-AAATAATATTAATTTA
*
719434 TTAAAAAATA
1 TAAAAAAATA
719444 TCAGAAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
18 3 0.05
19 3 0.05
20 11 0.20
21 20 0.36
22 15 0.27
24 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAAAATAATATTAATTTA
Found at i:719376 original size:19 final size:18
Alignment explanation
Indices: 719353--719405 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
719343 AAAACATTAA
719353 AAAAATAATATATAATTT
1 AAAAATAATATATAATTT
*
719371 ATAAAAGTAA-ATTATTTATTT
1 A-AAAA-TAATA-TA-TAATTT
719392 AAAAATAATATATA
1 AAAAATAATATATA
719406 TAATTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 10 0.36
21 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAAATAATATATAATTT
Found at i:719395 original size:41 final size:41
Alignment explanation
Indices: 719349--719443 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
719339 TAATAAAACA
* *
719349 TTAAAAAAATAATATATAATTTATAAAAGTAAATTATTTAT
1 TTAAAAAAATAATATATAATTAATAAAAGTAAAATATTTAT
719390 TTAAAAATAAT-ATATATAATTAATAAAAGTAAAATATTTAT
1 TTAAAAA-AATAATATATAATTAATAAAAGTAAAATATTTAT
719431 TTATTAAAAAATA
1 TTA--AAAAAATA
719444 TCAGAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
41 38 0.79
42 6 0.12
43 4 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (41 bp):
TTAAAAAAATAATATATAATTAATAAAAGTAAAATATTTAT
Found at i:719412 original size:19 final size:19
Alignment explanation
Indices: 719348--719412 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
719338 TTAATAAAAC
719348 ATTAAAAA-AATAATATATA
1 ATTAAAAATAAT-ATATATA
*
719367 ATTTATAAAAGTAA-ATTATTTA
1 A-TTA-AAAA-TAATA-TATATA
*
719389 TTTAAAAATAATATATATA
1 ATTAAAAATAATATATATA
719408 ATTAA
1 ATTAA
719413 TAAAAGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
19 13 0.36
20 8 0.22
21 8 0.22
22 5 0.14
23 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTAAAAATAATATATATA
Found at i:720983 original size:3 final size:3
Alignment explanation
Indices: 720975--721040 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
720965 ATATTTATTA
* * * **
720975 AAT AAT AAT AAT AAT -AT ATAT TAT ATAT AAT GAT AAT GAT AAT TTT
1 AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT
721021 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
721041 AATGAAATGA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 2 0.04
3 43 0.86
4 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:724771 original size:3 final size:3
Alignment explanation
Indices: 724763--724815 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
724753 TATTTTTAAA
* * *
724763 ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT AAAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
724809 ATT ATT A
1 ATT ATT A
724816 CAGGCCCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:724803 original size:16 final size:16
Alignment explanation
Indices: 724771--724815 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
724761 AAATTATTAT
724771 TATTATTATTA-TAAA
1 TATTATTATTATTAAA
724786 TATTATTATTATTAAA
1 TATTATTATTATTAAA
724802 TATTATTATTATTA
1 TATTATTATTATTA
724816 CAGGCCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATTATTATTAAA
Found at i:725076 original size:22 final size:22
Alignment explanation
Indices: 725050--725129 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
725040 TCAACCACTC
725050 CAACTGCTCCGCCGCCTCCAGT
1 CAACTGCTCCGCCGCCTCCAGT
*
725072 CAACTGCTCTGCCGCCTCCAGT
1 CAACTGCTCCGCCGCCTCCAGT
* * * *
725094 CAACTGCTCTGCTGTCTCCATT
1 CAACTGCTCCGCCGCCTCCAGT
**
725116 CAACCACTCCGCCG
1 CAACTGCTCCGCCG
725130 TTATGTCCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.15, C:0.46, G:0.16, T:0.23
Consensus pattern (22 bp):
CAACTGCTCCGCCGCCTCCAGT
Found at i:726358 original size:25 final size:25
Alignment explanation
Indices: 726288--726359 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
726278 TTTTATTACT
*
726288 TTTTAATTTAATTTTA-TATCT-TTAA
1 TTTT-ATTTTATTTTATTAT-TATTAA
* *
726313 TTTT-CTTTATTTTAATCATTATTAA
1 TTTTATTTTATTTT-ATTATTATTAA
726338 TTTTATTTTATTTTATTATTAT
1 TTTTATTTTATTTTATTATTAT
726360 CCCTTTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
23 7 0.18
24 2 0.05
25 21 0.55
26 8 0.21
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTTATTTTATTTTATTATTATTAA
Found at i:726765 original size:3 final size:3
Alignment explanation
Indices: 726759--726843 Score: 115
Period size: 3 Copynumber: 29.3 Consensus size: 3
726749 TCCTTTTTAT
*
726759 TTA TTA TTT TTA TTA -TA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
726805 TTA -TA TTA TTA TTA ATA -TA TTA TTA TTA TTA TTAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
726844 GTTTTTCTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
2 8 0.11
3 63 0.85
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:726777 original size:14 final size:14
Alignment explanation
Indices: 726759--726836 Score: 117
Period size: 14 Copynumber: 5.7 Consensus size: 14
726749 TCCTTTTTAT
726759 TTATTATT-T-TTA
1 TTATTATTATATTA
726771 TTA-TATTATTATTA
1 TTATTATTA-TATTA
726785 TTATTATTATATTA
1 TTATTATTATATTA
726799 TTATTATTATATTA
1 TTATTATTATATTA
*
726813 TTATTAATATATTA
1 TTATTATTATATTA
726827 TTATTATTAT
1 TTATTATTAT
726837 TAATTATGTT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.07
12 3 0.05
13 1 0.02
14 47 0.78
15 5 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:726781 original size:17 final size:17
Alignment explanation
Indices: 726755--726843 Score: 118
Period size: 17 Copynumber: 5.5 Consensus size: 17
726745 TTTTTCCTTT
*
726755 TTAT-TTATTATTTTTA
1 TTATATTATTATTATTA
726771 TTATATTATTATTATTA
1 TTATATTATTATTATTA
726788 TTAT-TATATTATTATTA
1 TTATAT-TATTATTATTA
726805 TTATATTATTATTA--A
1 TTATATTATTATTATTA
726820 -TATATTATTATTATTA
1 TTATATTATTATTATTA
726836 TTA-ATTAT
1 TTATATTAT
726844 GTTTTTCTTG
Statistics
Matches: 66, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
14 13 0.20
15 1 0.02
16 11 0.17
17 40 0.61
18 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTATTATTATTA
Found at i:727625 original size:18 final size:18
Alignment explanation
Indices: 727602--727639 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
727592 TCTTTTCAAA
727602 ATTTTT-ATATATACTTAT
1 ATTTTTCATA-ATACTTAT
*
727620 ATTTTTCATAATATTTAT
1 ATTTTTCATAATACTTAT
727638 AT
1 AT
727640 GTATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTCATAATACTTAT
Found at i:727653 original size:28 final size:28
Alignment explanation
Indices: 727594--727680 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
727584 TAATTCTTTC
* * *
727594 TTTTCAAAATTTTTATATATA-CTTATAT
1 TTTTCATAATATTTATATATATTTTAT-T
*
727622 TTTTCATAATATTTATATGTATTTTATT
1 TTTTCATAATATTTATATATATTTTATT
* *
727650 TTTT-ATTAATATTTTTATTTTATTTTATT
1 TTTTCA-TAATATTTATA-TATATTTTATT
727679 TT
1 TT
727681 CAAGTATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.02
28 33 0.66
29 16 0.32
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (28 bp):
TTTTCATAATATTTATATATATTTTATT
Found at i:737654 original size:112 final size:112
Alignment explanation
Indices: 737452--737677 Score: 443
Period size: 112 Copynumber: 2.0 Consensus size: 112
737442 GGTCATCTGT
737452 AAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTCCAGTGCAGGATGTTT
1 AAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTCCAGTGCAGGATGTTT
737517 TCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTTAATCTTA
66 TCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTTAATCTTA
737564 AAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTCCAGTGCAGGATGTTT
1 AAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTCCAGTGCAGGATGTTT
*
737629 TCAAATGAGATTTTAAGAAATTGATTTTCAAAGGTTTCTTAATCTTA
66 TCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTTAATCTTA
737676 AA
1 AA
737678 TCCTTCGGGT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (112 bp):
AAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCATAAGACCTCCAGTGCAGGATGTTT
TCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTTAATCTTA
Found at i:737787 original size:243 final size:243
Alignment explanation
Indices: 737356--737794 Score: 806
Period size: 243 Copynumber: 1.8 Consensus size: 243
737346 CTATTTCCCA
737356 CATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAATTGATTTTCAAAGGT
1 CATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAATTGATTTTCAAAGGT
737421 TCCTTAATCTTAAATCCTTCAGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
66 TCCTTAATCTTAAATCCTTCAGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
*
737486 CCATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAACTGATTTTCAAAGG
131 CCATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATAAGATTTTAAGAAACTGATTTTCAAAGG
737551 TTTCTTAATCTTAAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
196 TTTCTTAATCTTAAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
737599 CATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAATTGATTTTCAAAGGT
1 CATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAATTGATTTTCAAAGGT
* * *
737664 TTCTTAATCTTAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTTAGGG
66 TCCTTAATCTTAAATCCTTCAGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
* * * *
737729 CTATCTATATGACCTCCAGTGCAGGATGTTTTCAAATAAGATTTTAAGAAATTGATTTTCAAAGG
131 CCATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATAAGATTTTAAGAAACTGATTTTCAAAGG
737794 T
196 T
737795 CTTAAATCCT
Statistics
Matches: 188, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 188 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (243 bp):
CATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATGAGATTTTAAGAAATTGATTTTCAAAGGT
TCCTTAATCTTAAATCCTTCAGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGG
CCATCCATAAGACCTCCAGTGCAGGATGTTTTCAAATAAGATTTTAAGAAACTGATTTTCAAAGG
TTTCTTAATCTTAAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
Found at i:738030 original size:3 final size:3
Alignment explanation
Indices: 737995--738072 Score: 70
Period size: 3 Copynumber: 26.3 Consensus size: 3
737985 GTAGACACTA
* ** * * *
737995 ATT ATT -TT ATT -TT ATT TTT AAA ATT AGT ATT ATT ATT ATT ATA AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
738041 ATT ATT ATT ATT ATT AAAT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT A
738073 CAGGCCCAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
2 4 0.07
3 52 0.90
4 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:738317 original size:22 final size:22
Alignment explanation
Indices: 738286--738341 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
738276 TCAACCACTC
*
738286 CAACTGCTCCG-TCGCCTCCATT
1 CAACTACTCCGCT-GCCTCCATT
*
738308 CAACTACTCCGCTGTCTCCATT
1 CAACTACTCCGCTGCCTCCATT
*
738330 CAACCACTCCGC
1 CAACTACTCCGC
738342 CGTTATGTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.46, G:0.11, T:0.25
Consensus pattern (22 bp):
CAACTACTCCGCTGCCTCCATT
Found at i:739977 original size:3 final size:3
Alignment explanation
Indices: 739971--740033 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
739961 TCCTTTTTAT
* *
739971 TTA TTA TTT TTA TTA TTA -TA TTA TTA ATA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
740017 ATA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
740034 ATTTTTTTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 6 0.11
3 47 0.89
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:739992 original size:14 final size:14
Alignment explanation
Indices: 739975--740039 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
739965 TTTTATTTAT
739975 TATTTTTATTATTA
1 TATTTTTATTATTA
*
739989 TATTATTAATATATTA
1 TATT-TTTAT-TATTA
* *
740005 TTATTATTATTAATA
1 -TATTTTTATTATTA
*
740020 TATTATTATTATTA
1 TATTTTTATTATTA
740034 -ATTTTT
1 TATTTTT
740040 TTCTTAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
13 5 0.12
14 17 0.40
15 8 0.19
16 8 0.19
17 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTTATTATTA
Found at i:739994 original size:20 final size:20
Alignment explanation
Indices: 739971--740033 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
739961 TCCTTTTTAT
739971 TTATTATT-TT-TATTATTA
1 TTATTATTATTATATTATTA
*
739989 -TATTATTAATATATTATTA
1 TTATTATTATTATATTATTA
*
740008 TTATTATTAATATATTATTA
1 TTATTATTATTATATTATTA
740028 TTATTA
1 TTATTA
740034 ATTTTTTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
17 7 0.17
18 1 0.02
19 8 0.20
20 25 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTATTATTATATTATTA
Found at i:740034 original size:17 final size:17
Alignment explanation
Indices: 739972--740035 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
739962 CCTTTTTATT
* *
739972 TATTATTTTTATTATTA
1 TATTATTATTATTAATA
*
739989 TATTATTAATA-T-AT-
1 TATTATTATTATTAATA
740003 TATTATTATTATTAATA
1 TATTATTATTATTAATA
740020 TATTATTATTATTAAT
1 TATTATTATTATTAAT
740036 TTTTTTCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.25
15 2 0.05
16 3 0.08
17 25 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTATTATTAATA
Found at i:740253 original size:2 final size:2
Alignment explanation
Indices: 740246--740284 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
740236 AAACCTAAGC
*
740246 AT AT AT AT AT AT AT AT AT AC 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
740285 CTTTAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:742677 original size:25 final size:25
Alignment explanation
Indices: 742648--742697 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
742638 ATCCTGATGC
742648 GATAATTTTAATTATTTCCCAATGT
1 GATAATTTTAATTATTTCCCAATGT
742673 GATAATTTTAATTATTTCCCAATGT
1 GATAATTTTAATTATTTCCCAATGT
742698 TAACATGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (25 bp):
GATAATTTTAATTATTTCCCAATGT
Found at i:744286 original size:46 final size:46
Alignment explanation
Indices: 744219--744310 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
744209 CAACTTTCTC
744219 ACTTATATGTTTCTTATTCTACTTATTTTCTATTCAATCGGATGGT
1 ACTTATATGTTTCTTATTCTACTTATTTTCTATTCAATCGGATGGT
744265 ACTTATATGTTTCTTATTCTACTTATTTTCTATTCAATCGGATGGT
1 ACTTATATGTTTCTTATTCTACTTATTTTCTATTCAATCGGATGGT
744311 GGCACGTGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (46 bp):
ACTTATATGTTTCTTATTCTACTTATTTTCTATTCAATCGGATGGT
Found at i:754522 original size:26 final size:26
Alignment explanation
Indices: 754480--754529 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
754470 ATAAAAAGGT
*
754480 AAGAAATAAATAAATTAAATTAAAATG
1 AAGAAATAAACAAATTAAA-TAAAATG
754507 AAGAAA-AAACAAATTAAATAAAA
1 AAGAAATAAACAAATTAAATAAAA
754530 GATAAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (26 bp):
AAGAAATAAACAAATTAAATAAAATG
Found at i:754621 original size:26 final size:25
Alignment explanation
Indices: 754551--754623 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
754541 GAAAGCAAAG
* *
754551 ATAAAATAGTAAGTAATATAAAAAATAT
1 ATAAAATAATAA-TAA-A-AAAAAATAA
* * *
754579 ATAAAAAAAGAAGAAAAAACAAATAA
1 ATAAAATAATAATAAAAAA-AAATAA
754605 ATAAAATAATAATAAAAAA
1 ATAAAATAATAATAAAAAA
754624 GTAAAAATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 3 0.08
26 22 0.61
27 2 0.06
28 9 0.25
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (25 bp):
ATAAAATAATAATAAAAAAAAATAA
Found at i:754769 original size:20 final size:19
Alignment explanation
Indices: 754744--754790 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
754734 CTAAAAAAAT
754744 AAAAATATATACTAAA-GTAA
1 AAAAATATATA--AAATGTAA
**
754764 AAAAATGCATAAAATGTAA
1 AAAAATATATAAAATGTAA
754783 AAAAATAT
1 AAAAATAT
754791 TATATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.14
19 10 0.45
20 9 0.41
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (19 bp):
AAAAATATATAAAATGTAA
Found at i:755394 original size:34 final size:34
Alignment explanation
Indices: 755356--755466 Score: 153
Period size: 34 Copynumber: 3.4 Consensus size: 34
755346 AAGGTCTTGG
*
755356 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
755390 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
755424 GTTTC------AACAATTTCAAAGGTTTTTTTCGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTT-GT
*
755453 GTTTCAAGATAAAC
1 GTTTCAAGAGAAAC
755467 TGTCTCAAGG
Statistics
Matches: 69, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
28 21 0.30
29 7 0.10
34 38 0.55
35 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (34 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
Found at i:755581 original size:37 final size:36
Alignment explanation
Indices: 755519--755771 Score: 234
Period size: 36 Copynumber: 7.1 Consensus size: 36
755509 CAAAGATTGG
* * *
755519 TGTTTCAAGAGAAAATGTTTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
755556 TGTTTCAAGGGAAATTGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
755592 TGTTTAAAGAGAAACTGTATCAAGAGAGGCAAAACCT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* * ** * *
755629 AGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
755665 TGTTTCAAGGAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT
755694 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
755730 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
755767 TGTTT
1 TGTTT
755772 TGGGTAAGTT
Statistics
Matches: 173, Mismatches: 32, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.10
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 1 0.01
36 79 0.46
37 67 0.39
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:756065 original size:116 final size:116
Alignment explanation
Indices: 755876--756085 Score: 332
Period size: 116 Copynumber: 1.8 Consensus size: 116
755866 GTTGGTGGGT
*
755876 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTTGCGAAGTTGAGCCTTGAA
1 ACGATTCCCTTCGTCGTAAAGTTGAAACCGTGGATGGCCCCTTCGTTGCGAAGTTGAGCCTTGAA
* *
755941 TTGGATATCCTTCGCCATGAAGTTGAAATCCAATGAATGTTTCTGGTAAGC
66 TTGAATATCCTTCGCCATGAAGTTAAAATCCAATGAATGTTTCTGGTAAGC
* * *
755992 ACGATTCCCTTCGTCGTAAAGTTGAAATCGTGGATGGCCCCTTTGTTGTGAAGTTGAGCCTT-AA
1 ACGATTCCCTTCGTCGTAAAGTTGAAACCGTGGATGGCCCCTTCGTTGCGAAGTTGAGCCTTGAA
**
756056 CTTGAATATCCTTCGCTGTGAAGTTAAAAT
66 -TTGAATATCCTTCGCCATGAAGTTAAAAT
756086 TGACTCTGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
115 2 0.02
116 83 0.98
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (116 bp):
ACGATTCCCTTCGTCGTAAAGTTGAAACCGTGGATGGCCCCTTCGTTGCGAAGTTGAGCCTTGAA
TTGAATATCCTTCGCCATGAAGTTAAAATCCAATGAATGTTTCTGGTAAGC
Found at i:757528 original size:14 final size:13
Alignment explanation
Indices: 757500--757557 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
757490 TTTTCTTCAC
757500 TTTTTTCT-TTATT
1 TTTTTTCTCTT-TT
757513 TTTGTTTCTCTTTT
1 TTT-TTTCTCTTTT
757527 TTATTTTCTCTTTGCT
1 TT-TTTTCTCTTT--T
*
757543 TTTTATCTCTTTT
1 TTTTTTCTCTTTT
757556 TT
1 TT
757558 CCTTTTTGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 6 0.15
14 18 0.46
15 12 0.31
16 3 0.08
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTTTCTCTTTT
Found at i:761241 original size:62 final size:63
Alignment explanation
Indices: 761151--761271 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 63
761141 AACCTCGACA
* *
761151 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGT-T-CATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGT-AACTGTGTACATATGTTCCGTAGAACATAGGTAT
* * *
761213 ACTGTCCATATGTCTCGAA-AGACATAGGTAATTGTGTACATATGTTCCGTAGAACATAG
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAACTGTGTACATATGTTCCGTAGAACATAG
761272 ATAAACCCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
61 6 0.12
62 25 0.49
63 20 0.39
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (63 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAACTGTGTACATATGTTCCGTAGAACATAGGTAT
Found at i:761270 original size:32 final size:31
Alignment explanation
Indices: 761151--761271 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
761141 AACCTCGACA
* * * * * *
761151 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 ACTGTACATATGTTCCGTAGAACATAGGTAT
* *
761182 ACTGTTCATATGTTCCTTAGAACATAGGTAT
1 ACTGTACATATGTTCCGTAGAACATAGGTAT
* *
761213 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTACATATGTTC-CGTAGA-ACATAGGT-AT
**
761245 TGTGTACATATGTTCCGTAGAACATAG
1 ACTGTACATATGTTCCGTAGAACATAG
761272 ATAAACCCTC
Statistics
Matches: 71, Mismatches: 14, Indels: 9
0.76 0.15 0.10
Matches are distributed among these distances:
30 4 0.06
31 44 0.62
32 19 0.27
33 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (31 bp):
ACTGTACATATGTTCCGTAGAACATAGGTAT
Found at i:761711 original size:24 final size:23
Alignment explanation
Indices: 761669--761721 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
761659 CATAGTTATG
*
761669 TATCATATTACATAATTTAACTTA
1 TATCATATTACATAATTT-ACATA
*
761693 TATCATATTATCAT-GTTTACATA
1 TATCATATTA-CATAATTTACATA
761716 TATCAT
1 TATCAT
761722 GGATACTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 10 0.38
24 13 0.50
25 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (23 bp):
TATCATATTACATAATTTACATA
Found at i:765218 original size:12 final size:14
Alignment explanation
Indices: 765190--765221 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
765180 CACACATACA
765190 TCATATCCTATAAC
1 TCATATCCTATAAC
765204 TCATATCC-A-AAC
1 TCATATCCTATAAC
765216 TCATAT
1 TCATAT
765222 ATCAGTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (14 bp):
TCATATCCTATAAC
Found at i:765491 original size:31 final size:32
Alignment explanation
Indices: 765454--765543 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
765444 AGGTAAACTA
*
765454 TCCATATGTTCCTTAGAACATAGGT-ATGAT-
1 TCCATATGTTCCATAGAACATAGGTAATGATG
* * *
765484 TCTCATATGTCTCGAAAG-ACATAGGTAATTATG
1 TC-CATATGT-TCCATAGAACATAGGTAATGATG
*
765517 TCCATATGTTCCATAGAACATATGTAA
1 TCCATATGTTCCATAGAACATAGGTAA
765544 ACCCTCGACT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
30 2 0.04
31 20 0.42
32 24 0.50
33 2 0.04
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (32 bp):
TCCATATGTTCCATAGAACATAGGTAATGATG
Found at i:765960 original size:37 final size:37
Alignment explanation
Indices: 765899--765971 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
765889 ACATAATCTC
** * *
765899 TATCATATATACATTCTTTCACTTATCTCATAGTTATG
1 TATCATATATACATAATTTAACTTATATCATA-TTATG
765937 TATCATAT-TACATAATTTAACTTATATCATATTAT
1 TATCATATATACATAATTTAACTTATATCATATTAT
765972 CATGTGTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 4 0.13
37 19 0.61
38 8 0.26
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.48
Consensus pattern (37 bp):
TATCATATATACATAATTTAACTTATATCATATTATG
Found at i:767455 original size:26 final size:26
Alignment explanation
Indices: 767413--767462 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
767403 ATAAAAAGGT
*
767413 AAGAAATAAATAAATTAAATTAAAATG
1 AAGAAATAAACAAATTAAA-TAAAATG
767440 AAGAAA-AAACAAATTAAATAAAA
1 AAGAAATAAACAAATTAAATAAAA
767463 GATAAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (26 bp):
AAGAAATAAACAAATTAAATAAAATG
Found at i:767623 original size:77 final size:77
Alignment explanation
Indices: 767542--767732 Score: 178
Period size: 77 Copynumber: 2.4 Consensus size: 77
767532 AGAAAAACAA
767542 ATAAATAAAATAATAATAAAAGTAAAAATAATATATATATATATATATA-AT-TAAAACATAAAA
1 ATAAATAAAATAATAATAAAAGTAAAAATAATATATATATATATATATATATGTAAAACAT-AAA
*
767605 AATAGTAAATATAT
65 AATA-AAAATATAT
* * * ***
767619 ATAAAT-TAATAA-AACAGATAA-TAAAAAATAACATATATATATATATATATATGTAATTTATA
1 ATAAATAAAATAATAATA-A-AAGT-AAAAATAATATATATATATATATATATATGTAAAACATA
767681 AAAATAAAAATATAT
63 AAAATAAAAATATAT
* *
767696 ACTAAAGTAAAAAAATGCATAAAATGTAAAAA-AATAT
1 A-TAAA-TAAAATAAT-AATAAAA-GTAAAAATAATAT
767733 TACATGAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
75 3 0.03
76 7 0.08
77 42 0.47
78 13 0.14
79 6 0.07
80 10 0.11
81 6 0.07
82 3 0.03
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (77 bp):
ATAAATAAAATAATAATAAAAGTAAAAATAATATATATATATATATATATATGTAAAACATAAAA
ATAAAAATATAT
Found at i:767711 original size:20 final size:19
Alignment explanation
Indices: 767686--767732 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
767676 TTATAAAAAT
767686 AAAAATATATACTAAA-GTAA
1 AAAAATATATA--AAATGTAA
**
767706 AAAAATGCATAAAATGTAA
1 AAAAATATATAAAATGTAA
767725 AAAAATAT
1 AAAAATAT
767733 TACATGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 3 0.14
19 10 0.45
20 9 0.41
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (19 bp):
AAAAATATATAAAATGTAA
Found at i:768191 original size:13 final size:13
Alignment explanation
Indices: 768175--768208 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
768165 TAAATCGTGT
768175 GTTACAATAGTAA
1 GTTACAATAGTAA
768188 GTTACAATAGTAA
1 GTTACAATAGTAA
768201 GTTACAAT
1 GTTACAAT
768209 GGCTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (13 bp):
GTTACAATAGTAA
Found at i:768284 original size:37 final size:37
Alignment explanation
Indices: 768232--768378 Score: 258
Period size: 37 Copynumber: 4.0 Consensus size: 37
768222 GCTTGTGGAA
*
768232 CCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
768269 CCTATTTTTAAGAGTTTGAATCCTAGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
768306 CCTATTTTTAGGAGTTTGAATCCTTGTAAAACTCTAT
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
*
768343 CCTATTTTTAGGAGTTTGAATCCTACTAAAACTCTA
1 CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
768379 ATGTTTGTTT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (37 bp):
CCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTAT
Found at i:774254 original size:32 final size:34
Alignment explanation
Indices: 774173--774259 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 34
774163 TGACTTCCCC
* *
774173 ATTTT-CGATGCCAAACATTTGTTGAAAACCTCC
1 ATTTTGCGGTGCCAAACATTTGTTGAAAACCTCA
* *
774206 ATTTTG-AGTGCCAAACATTTGTTTAAAA-C-CA
1 ATTTTGCGGTGCCAAACATTTGTTGAAAACCTCA
774237 ATTTTGCGGTGCCAAACATTTGT
1 ATTTTGCGGTGCCAAACATTTGT
774260 CTTGACTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.15
32 16 0.34
33 24 0.51
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.36
Consensus pattern (34 bp):
ATTTTGCGGTGCCAAACATTTGTTGAAAACCTCA
Found at i:785807 original size:20 final size:20
Alignment explanation
Indices: 785782--785819 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
785772 TGGGTTTGAG
785782 TATCGATACTAGATGAACAA
1 TATCGATACTAGATGAACAA
*
785802 TATCGATACTGGATGAAC
1 TATCGATACTAGATGAAC
785820 TAGGATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (20 bp):
TATCGATACTAGATGAACAA
Found at i:796949 original size:8 final size:8
Alignment explanation
Indices: 796938--796977 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
796928 CCGTTTACCC
796938 GACCCGTT
1 GACCCGTT
796946 GACCC---
1 GACCCGTT
796951 GACCCGTT
1 GACCCGTT
796959 GA-CCGTT
1 GACCCGTT
796966 GACCCGTT
1 GACCCGTT
796974 GACC
1 GACC
796978 AGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:796956 original size:18 final size:18
Alignment explanation
Indices: 796898--796943 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
796888 ACCGGTCACA
796898 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
796916 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
796934 ACCCGACCCG
1 ACCCGACCCG
796944 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.52, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:796971 original size:15 final size:13
Alignment explanation
Indices: 796920--796977 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
796910 CCGTTGACCC
796920 GACCCGACCCGTT
1 GACCCGACCCGTT
*
796933 TACCCGACCCGTT
1 GACCCGACCCGTT
796946 GACCCGACCCGTT
1 GACCCGACCCGTT
*
796959 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
796974 GACC
1 GACC
796978 AGAGTTGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 28 0.70
15 12 0.30
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:796996 original size:20 final size:18
Alignment explanation
Indices: 796951--796998 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 18
796941 CCGTTGACCC
796951 GACCCGTTGACC---GTT
1 GACCCGTTGACCAGAGTT
796966 GACCCGTTGACCAGAGTT
1 GACCCGTTGACCAGAGTT
796984 GACCACTGTTGACCA
1 GACC-C-GTTGACCA
796999 AAACTTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.43
18 7 0.25
19 1 0.04
20 8 0.29
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (18 bp):
GACCCGTTGACCAGAGTT
Found at i:799469 original size:48 final size:48
Alignment explanation
Indices: 799417--799548 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
799407 AATATTTTAC
*
799417 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
799465 CTGA-TATCTGACATAGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
799513 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
799549 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:799555 original size:24 final size:24
Alignment explanation
Indices: 799434--799548 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
799424 TCGATTTGAT
799434 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
799458 TTCTGATCTGATA-TCTGACATAGA
1 TTCTGATCTGATACT-TGACATGGA
*
799482 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
799506 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
799529 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
799549 CTGATTTATA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:799565 original size:24 final size:24
Alignment explanation
Indices: 799485--799557 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
799475 ACATAGATTC
* * *
799485 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
799509 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
799533 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
799557 T
1 T
799558 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:801742 original size:8 final size:8
Alignment explanation
Indices: 801729--801768 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
801719 AACCCGACCC
801729 GACCCGTT
1 GACCCGTT
801737 GACCC---
1 GACCCGTT
801742 GACCCGTT
1 GACCCGTT
801750 GA-CCGTT
1 GACCCGTT
801757 GACCCGTT
1 GACCCGTT
801765 GACC
1 GACC
801769 AGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:801762 original size:15 final size:13
Alignment explanation
Indices: 801724--801768 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
801714 GTCACAACCC
801724 GACCCGACCCGTT
1 GACCCGACCCGTT
801737 GACCCGACCCGTT
1 GACCCGACCCGTT
*
801750 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
801765 GACC
1 GACC
801769 AGAGTTGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.16, C:0.42, G:0.24, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:801787 original size:20 final size:18
Alignment explanation
Indices: 801742--801789 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 18
801732 CCGTTGACCC
801742 GACCCGTTGACC---GTT
1 GACCCGTTGACCAGAGTT
801757 GACCCGTTGACCAGAGTT
1 GACCCGTTGACCAGAGTT
801775 GACCACTGTTGACCA
1 GACC-C-GTTGACCA
801790 AAACTTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.43
18 7 0.25
19 1 0.04
20 8 0.29
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (18 bp):
GACCCGTTGACCAGAGTT
Found at i:804260 original size:48 final size:48
Alignment explanation
Indices: 804208--804339 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
804198 AATATTTTAC
*
804208 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
804256 CTGA-TATCTGACATAGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
804304 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
804340 CTGATTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:804346 original size:24 final size:24
Alignment explanation
Indices: 804225--804339 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
804215 TCGATTTGAT
804225 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
804249 TTCTGATCTGATA-TCTGACATAGA
1 TTCTGATCTGATACT-TGACATGGA
*
804273 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
804297 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
804320 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
804340 CTGATTTATA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:804356 original size:24 final size:24
Alignment explanation
Indices: 804276--804348 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
804266 ACATAGATTC
* * *
804276 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
804300 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
804324 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
804348 T
1 T
804349 ATTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:805280 original size:21 final size:21
Alignment explanation
Indices: 805256--805376 Score: 113
Period size: 21 Copynumber: 5.8 Consensus size: 21
805246 ATATAAAATT
*
805256 TGTCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACGTATA
* *
805277 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACGTATA
*
805298 TGTCCC-AGAGGACTACGTATA
1 TGTCCCGA-AGGACCACGTATA
* *
805319 TGTCCC-AGAGGACTATGTATA
1 TGTCCCGA-AGGACCACGTATA
* *
805340 TATCCCCG-AGGACTACGTATA
1 TGT-CCCGAAGGACCACGTATA
*
805361 TGTCCCAAAGGACCAC
1 TGTCCCGAAGGACCAC
805377 TCCTTAAGGA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
20 4 0.05
21 79 0.92
22 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACGTATA
Done.