Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 4 of 77
Found at i:478079 original size:16 final size:15
Alignment explanation
Indices: 478032--478136 Score: 54
Period size: 16 Copynumber: 6.9 Consensus size: 15
478022 TAATTTTTAC
478032 AAAAAAATAAAACA-A
1 AAAAAAATAAAA-ATA
* **
478047 AAAAAATTAAAGCTA
1 AAAAAAATAAAAATA
478062 AAAAAAACTAAAAATA
1 AAAAAAA-TAAAAATA
* *** *
478078 AAATGAGCCAAAACTA
1 AAA-AAAATAAAAATA
*
478094 AAAGAAAATATAAAT-
1 AAA-AAAATAAAAATA
*
478109 -CAAAAATAAAAATA
1 AAAAAAATAAAAATA
478123 AAATAAAATAAAAA
1 AAA-AAAATAAAAA
478137 CCTTGCAAAA
Statistics
Matches: 63, Mismatches: 21, Indels: 11
0.66 0.22 0.12
Matches are distributed among these distances:
13 10 0.16
14 1 0.02
15 18 0.29
16 33 0.52
17 1 0.02
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:478462 original size:31 final size:31
Alignment explanation
Indices: 478427--478494 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
478417 CTTGTGTTCT
478427 TAAAAAAA-ACCAATATTTTCCCAGAAATCCC
1 TAAAAAAATACCAA-ATTTTCCCAGAAATCCC
*
478458 TAAAAAAATCCCAAATTTTCCCAGAAATCCC
1 TAAAAAAATACCAAATTTTCCCAGAAATCCC
478489 -AAAAAA
1 TAAAAAA
478495 TTCACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 6 0.17
31 25 0.71
32 4 0.11
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (31 bp):
TAAAAAAATACCAAATTTTCCCAGAAATCCC
Found at i:478908 original size:3 final size:3
Alignment explanation
Indices: 478902--478937 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
478892 GAATAAAAAG
*
478902 AAT AAT AAT AAT AAT AAT AAT AA- AAT GAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
478938 TCATGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:479042 original size:25 final size:23
Alignment explanation
Indices: 478989--479042 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
478979 GTAACATTAT
*
478989 ACTATAATATTATACCATAACAC
1 ACTATAATATTATAACATAACAC
*
479012 ATTATAATATATAATAACAT-ACTAC
1 ACTATAATAT-T-ATAACATAAC-AC
479037 ACTATA
1 ACTATA
479043 GTAATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 9 0.36
24 3 0.12
25 13 0.52
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (23 bp):
ACTATAATATTATAACATAACAC
Found at i:479163 original size:18 final size:18
Alignment explanation
Indices: 479142--479190 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
479132 TAATTAATTA
*
479142 TAATTAATCAATAAAAAT
1 TAATTAATAAATAAAAAT
*
479160 TAATT-ATAAATTATAAAT
1 TAATTAATAAA-TAAAAAT
479178 TAATTAATAAATA
1 TAATTAATAAATA
479191 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 18 0.67
19 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTAATAAATAAAAAT
Found at i:480531 original size:18 final size:17
Alignment explanation
Indices: 480508--480558 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
480498 ATGGGTTGCT
*
480508 TTTTCATTTTTCTTTTAA
1 TTTTCATTTTTATTTT-A
**
480526 TTTTCAGTTTAGATTTTA
1 TTTTCA-TTTTTATTTTA
480544 TTTTCATTTTTATTT
1 TTTTCATTTTTATTT
480559 CCTTTTTCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 7 0.26
18 13 0.48
19 7 0.26
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTCATTTTTATTTTA
Found at i:481557 original size:12 final size:12
Alignment explanation
Indices: 481540--481580 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
481530 CTCCAAGGTT
481540 TTTTTTTGTTGC
1 TTTTTTTGTTGC
481552 TTTTTTTGTT--
1 TTTTTTTGTTGC
481562 TTTCTTTATGTTGC
1 TTT-TTT-TGTTGC
481576 TTTTT
1 TTTTT
481581 CGTCGAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 3 0.12
11 3 0.12
12 14 0.56
13 2 0.08
14 3 0.12
ACGTcount: A:0.02, C:0.07, G:0.12, T:0.78
Consensus pattern (12 bp):
TTTTTTTGTTGC
Found at i:481575 original size:24 final size:22
Alignment explanation
Indices: 481537--481580 Score: 70
Period size: 24 Copynumber: 1.9 Consensus size: 22
481527 GTCCTCCAAG
481537 GTTTTTTTTTGTTGCTTTTTTT
1 GTTTTTTTTTGTTGCTTTTTTT
481559 GTTTTTCTTTATGTTGCTTTTT
1 GTTTTT-TTT-TGTTGCTTTTT
481581 CGTCGAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.02, C:0.07, G:0.14, T:0.77
Consensus pattern (22 bp):
GTTTTTTTTTGTTGCTTTTTTT
Found at i:488941 original size:84 final size:84
Alignment explanation
Indices: 488831--489005 Score: 318
Period size: 84 Copynumber: 2.1 Consensus size: 84
488821 ATAAATTTTC
488831 AATTTT-ATCAAATGATTGGAGGATTTAAATTTCTAAGCTAAATCTTACTAAACTATTGGAAGAT
1 AATTTTCATCAAATGATTGGAGGATTTAAATTTCTAAGCTAAATCTTACTAAACTATTGGAAGAT
488895 TTAATGATAATTTTTTTAA
66 TTAATGATAATTTTTTTAA
488914 AATTTTCAT-AAATAGATTGGAGGATTTAAATTTCTAAGCTAAATCTTACTAAACTATTGGAAGA
1 AATTTTCATCAAAT-GATTGGAGGATTTAAATTTCTAAGCTAAATCTTACTAAACTATTGGAAGA
488978 TTTAATGATAATTTTTTTAA
65 TTTAATGATAATTTTTTTAA
488998 ATATTTTC
1 A-ATTTTC
489006 GCAAATGGGT
Statistics
Matches: 89, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
83 10 0.11
84 73 0.82
85 6 0.07
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.43
Consensus pattern (84 bp):
AATTTTCATCAAATGATTGGAGGATTTAAATTTCTAAGCTAAATCTTACTAAACTATTGGAAGAT
TTAATGATAATTTTTTTAA
Found at i:488980 original size:40 final size:40
Alignment explanation
Indices: 488845--488982 Score: 122
Period size: 40 Copynumber: 3.4 Consensus size: 40
488835 TTATCAAATG
*
488845 ATTGGAGGATTTAAATTTCTAAGCTAAATCTTACTAAACT
1 ATTGGAAGATTTAAATTTCTAAGCTAAATCTTACTAAACT
*** *
488885 ATTGGAAGATTTAATGATAATT-T-TTTTAAAAT-TTTCATAAA-T
1 ATTGGAAGATTTAA--AT--TTCTAAGCT-AAATCTTAC-TAAACT
*
488927 AGATTGGAGGATTTAAATTTCTAAGCTAAATCTTACTAAACT
1 --ATTGGAAGATTTAAATTTCTAAGCTAAATCTTACTAAACT
488969 ATTGGAAGATTTAA
1 ATTGGAAGATTTAA
488983 TGATAATTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
40 28 0.37
41 9 0.12
42 14 0.19
43 9 0.12
44 15 0.20
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (40 bp):
ATTGGAAGATTTAAATTTCTAAGCTAAATCTTACTAAACT
Found at i:492084 original size:15 final size:15
Alignment explanation
Indices: 492066--492095 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
492056 AATAATAATG
*
492066 AAAAAATGAAAAAAA
1 AAAAAAGGAAAAAAA
492081 AAAAAAGGAAAAAAA
1 AAAAAAGGAAAAAAA
492096 TGAGAAAGAT
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:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAAAAGGAAAAAAA
Found at i:493636 original size:2 final size:2
Alignment explanation
Indices: 493629--493655 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
493619 GATGAGCCTT
493629 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
493656 TCAAAGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:493869 original size:44 final size:44
Alignment explanation
Indices: 493816--493919 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 44
493806 TTCAATTATG
*
493816 AATCTTTGAATCACTTGCGAATCTTTGAATCTTAAATTATTGCA
1 AATCTTTGAATCACTTGCGAATCTTTGAATCTTAAATTATTACA
** * * * *
493860 AATCTTTGAATCGTTTGCGAATTTTTGAATTTTAAATTTTTACG
1 AATCTTTGAATCACTTGCGAATCTTTGAATCTTAAATTATTACA
*
493904 AATC-TTAAATCACTTG
1 AATCTTTGAATCACTTG
493920 TAAATATTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 9 0.18
44 41 0.82
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (44 bp):
AATCTTTGAATCACTTGCGAATCTTTGAATCTTAAATTATTACA
Found at i:493970 original size:18 final size:18
Alignment explanation
Indices: 493949--493997 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
493939 ATCTTTAATT
493949 TTTTACGAATCTTTGAAC
1 TTTTACGAATCTTTGAAC
** *
493967 TTTTGTGAATCTTTGATC
1 TTTTACGAATCTTTGAAC
* *
493985 TCTTACAAATCTT
1 TTTTACGAATCTT
493998 GTAAATCTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.10, T:0.49
Consensus pattern (18 bp):
TTTTACGAATCTTTGAAC
Found at i:494057 original size:79 final size:78
Alignment explanation
Indices: 493916--494073 Score: 176
Period size: 79 Copynumber: 2.0 Consensus size: 78
493906 TCTTAAATCA
* * **
493916 CTTGTAAATATTGAAACTTACAAATCTTTAATTTTTTACGAATCTTTGAACTTTTGTGAATCTTT
1 CTTGTAAATATTGAAACTTACAAATCTTTAATTTTGTA-GAATCTTTGAACTCTTGCAAATC-TT
493981 G-ATCTCTTACAAAT
64 GAATCTCTTACAAAT
* * ** *
493995 CTTGTAAATCTTTAAACTTATGAATCTTTGAACTTTTGT-GAATCTTTGATCTCTTGCAAATCTT
1 CTTGTAAATATTGAAACTTACAAATCTTT-AA-TTTTGTAGAATCTTTGAACTCTTGCAAATCTT
*
494059 GAATCTTTTACAAAT
64 GAATCTCTTACAAAT
494074 TTAAATCTCT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
78 3 0.05
79 56 0.85
80 2 0.03
81 5 0.08
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (78 bp):
CTTGTAAATATTGAAACTTACAAATCTTTAATTTTGTAGAATCTTTGAACTCTTGCAAATCTTGA
ATCTCTTACAAAT
Found at i:494118 original size:71 final size:71
Alignment explanation
Indices: 494039--494188 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 71
494029 TTTGTGAATC
* *
494039 TTTG-ATCTCTTGCAAATCTTGAATCTTTTACAAA-TTTAAATCTCTTGCAAATCTTGAATCTTT
1 TTTGAATCTCTTGCAAATCTTGAATATTTTACAAATTTTAAATCT-TTGCAAATCTTGAATCTCT
494102 TACAAAT
65 TACAAAT
* * * * * *
494109 TTTGAATCTCTTGTAAATCTTGAATATTTTGCAAATTTTGAATCTTTGCGAGTTTTGAATCTCTT
1 TTTGAATCTCTTGCAAATCTTGAATATTTTACAAATTTTAAATCTTTGCAAATCTTGAATCTCTT
*
494174 GCAAAT
66 ACAAAT
*
494180 CTTGAATCT
1 TTTGAATCT
494189 TTTATGAACC
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
70 4 0.06
71 56 0.82
72 8 0.12
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (71 bp):
TTTGAATCTCTTGCAAATCTTGAATATTTTACAAATTTTAAATCTTTGCAAATCTTGAATCTCTT
ACAAAT
Found at i:494168 original size:53 final size:54
Alignment explanation
Indices: 494051--494191 Score: 160
Period size: 53 Copynumber: 2.6 Consensus size: 54
494041 TGATCTCTTG
* * * * * *
494051 CAAATCTTGAATCTTTTACAAAT-TTAAATCTCTTGCAAATCTTGAATCTTTTA
1 CAAATTTTGAATCTCTTGCAAATCTTGAATATTTTGCAAATCTTGAATCTTTTA
* * *
494104 CAAATTTTGAATCTCTTGTAAATCTTGAATATTTTGCAAATTTTGAATC-TTTG
1 CAAATTTTGAATCTCTTGCAAATCTTGAATATTTTGCAAATCTTGAATCTTTTA
* * *
494157 CGAGTTTTGAATCTCTTGCAAATCTTGAATCTTTT
1 CAAATTTTGAATCTCTTGCAAATCTTGAATATTTT
494192 ATGAACCTTG
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 53 0.72
54 21 0.28
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (54 bp):
CAAATTTTGAATCTCTTGCAAATCTTGAATATTTTGCAAATCTTGAATCTTTTA
Found at i:494190 original size:35 final size:36
Alignment explanation
Indices: 494039--494188 Score: 189
Period size: 35 Copynumber: 4.2 Consensus size: 36
494029 TTTGTGAATC
494039 TTTG-ATCTCTTGCAAATCTTGAATCTTTTACAAA-
1 TTTGAATCTCTTGCAAATCTTGAATCTTTTACAAAT
*
494073 TTTAAATCTCTTGCAAATCTTGAATCTTTTACAAAT
1 TTTGAATCTCTTGCAAATCTTGAATCTTTTACAAAT
* * *
494109 TTTGAATCTCTTGTAAATCTTGAATATTTTGCAAAT
1 TTTGAATCTCTTGCAAATCTTGAATCTTTTACAAAT
* * * * *
494145 TTTGAATCT-TTGCGAGTTTTGAATCTCTTGCAAAT
1 TTTGAATCTCTTGCAAATCTTGAATCTTTTACAAAT
*
494180 CTTGAATCT
1 TTTGAATCT
494189 TTTATGAACC
Statistics
Matches: 102, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
34 3 0.03
35 58 0.57
36 41 0.40
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (36 bp):
TTTGAATCTCTTGCAAATCTTGAATCTTTTACAAAT
Found at i:494202 original size:71 final size:72
Alignment explanation
Indices: 494056--494222 Score: 178
Period size: 71 Copynumber: 2.3 Consensus size: 72
494046 TCTTGCAAAT
* * * *
494056 CTTGAATCTTTTACAAA-TTTAAATCTCTTGCAAATCTTGAATCTTTTACAAATTTTGAATCTCT
1 CTTGAATCTTTTGCAAATTTTGAATCTCTTGCAAATCTTGAATCTCTTACAAATCTTGAATCTCT
* *
494120 TGTAAAT
66 TATAAAC
* * * * * *
494127 CTTGAATATTTTGCAAATTTTGAATCT-TTGCGAGTTTTGAATCTCTTGCAAATCTTGAATCTTT
1 CTTGAATCTTTTGCAAATTTTGAATCTCTTGCAAATCTTGAATCTCTTACAAATCTTGAATCTCT
*
494191 TATGAAC
66 TATAAAC
*
494198 CTTGAA-CTTTTGTAAATCTTTGAAT
1 CTTGAATCTTTTGCAAAT-TTTGAAT
494223 TCAATTTATT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
70 9 0.11
71 62 0.78
72 8 0.10
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (72 bp):
CTTGAATCTTTTGCAAATTTTGAATCTCTTGCAAATCTTGAATCTCTTACAAATCTTGAATCTCT
TATAAAC
Found at i:494203 original size:53 final size:52
Alignment explanation
Indices: 494108--494207 Score: 128
Period size: 53 Copynumber: 1.9 Consensus size: 52
494098 CTTTTACAAA
* * **
494108 TTTTGAATCTCTTGTAAATCTTGAATATTTTGCAAATTTTGAATCTTTGCGAG
1 TTTTGAATCTCTTGCAAATCTTGAATATTTTACAAACCTTGAA-CTTTGCGAG
* **
494161 TTTTGAATCTCTTGCAAATCTTGAATCTTTTATGAACCTTGAACTTT
1 TTTTGAATCTCTTGCAAATCTTGAATATTTTACAAACCTTGAACTTT
494208 TGTAAATCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
52 4 0.10
53 36 0.90
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (52 bp):
TTTTGAATCTCTTGCAAATCTTGAATATTTTACAAACCTTGAACTTTGCGAG
Found at i:494220 original size:18 final size:19
Alignment explanation
Indices: 494017--494281 Score: 157
Period size: 18 Copynumber: 14.4 Consensus size: 19
494007 TAAACTTATG
**
494017 AATCTTTGAA-CTTTTGTG
1 AATCTTTGAATCTTTTGCA
*
494035 AATCTTTG-ATCTCTTGCA
1 AATCTTTGAATCTTTTGCA
*
494053 AATC-TTGAATCTTTTACA
1 AATCTTTGAATCTTTTGCA
* *
494071 AA--TTTAAATCTCTTGCA
1 AATCTTTGAATCTTTTGCA
*
494088 AATC-TTGAATCTTTTACA
1 AATCTTTGAATCTTTTGCA
* *
494106 AAT-TTTGAATCTCTTGTA
1 AATCTTTGAATCTTTTGCA
*
494124 AATC-TTGAATATTTTGCA
1 AATCTTTGAATCTTTTGCA
*
494142 AAT-TTTGAATC-TTTGCG
1 AATCTTTGAATCTTTTGCA
* *
494159 AGT-TTTGAATCTCTTGCA
1 AATCTTTGAATCTTTTGCA
***
494177 AATC-TTGAATCTTTTATG
1 AATCTTTGAATCTTTTGCA
* *
494195 AA-CCTTGAA-CTTTTGTA
1 AATCTTTGAATCTTTTGCA
494212 AATCTTTGAATTCAATTTATTTGCA
1 AATCTTTGAA-TC----T-TTTGCA
*
494237 AATCTTTGAA-CTTTTGGGA
1 AATCTTTGAATCTTTT-GCA
*
494256 GAATC-TTGAATGTTTTGCA
1 -AATCTTTGAATCTTTTGCA
*
494275 AGTCTTT
1 AATCTTT
494282 AAATTCAAAT
Statistics
Matches: 189, Mismatches: 35, Indels: 45
0.70 0.13 0.17
Matches are distributed among these distances:
17 41 0.22
18 110 0.58
19 12 0.06
20 9 0.05
23 1 0.01
24 1 0.01
25 15 0.08
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (19 bp):
AATCTTTGAATCTTTTGCA
Found at i:496440 original size:19 final size:19
Alignment explanation
Indices: 496397--496442 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
496387 ATAATTTTTC
496397 AATTAAAATGATAAAATAT
1 AATTAAAATGATAAAATAT
*
496416 ATATTAAAAT-ATAAAAATTT
1 A-ATTAAAATGAT-AAAATAT
496436 AATTAAA
1 AATTAAA
496443 TTTATAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTAAAATGATAAAATAT
Found at i:497317 original size:15 final size:15
Alignment explanation
Indices: 497294--497327 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
497284 GGTTTTGTTA
* *
497294 ATTTTAAATTAAATT
1 ATTTAAAATCAAATT
497309 ATTTAAAATCAAATT
1 ATTTAAAATCAAATT
497324 ATTT
1 ATTT
497328 TATTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAAATCAAATT
Found at i:497699 original size:24 final size:24
Alignment explanation
Indices: 497666--497745 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
497656 TAAAATTCTT
*
497666 TTAAAA-TAATTTTTATTAATTGA
1 TTAAAATTAATTTTAATTAATTGA
* *
497689 TTAAAATTAATTTTAATTGATTAA
1 TTAAAATTAATTTTAATTAATTGA
* *
497713 TT-AAATTAA-ATTAATTAACTCGA
1 TTAAAATTAATTTTAATTAA-TTGA
497736 TTAAAATTAA
1 TTAAAATTAA
497746 ATTATGAACG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 7 0.15
23 17 0.36
24 23 0.49
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (24 bp):
TTAAAATTAATTTTAATTAATTGA
Found at i:498019 original size:14 final size:14
Alignment explanation
Indices: 498002--498033 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
497992 TTTATTATTT
*
498002 TTATTAAATTAAAA
1 TTATTAAAATAAAA
498016 TTATTAAAATAAAA
1 TTATTAAAATAAAA
498030 TTAT
1 TTAT
498034 AATTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATTAAAATAAAA
Found at i:503559 original size:119 final size:119
Alignment explanation
Indices: 503348--503587 Score: 408
Period size: 119 Copynumber: 2.0 Consensus size: 119
503338 GTAGATGACA
* * *
503348 AACTGCAAATTATGATGGTTTCTTAAAGGATTGTAAAATATACGTCTTCAATTTAAACCCATTAA
1 AACTGCAAATTAAGATGATTTCTTAAAGGATTGTAAAATATACATCTTCAATTTAAACCCATTAA
503413 GGCTCGATTTTCACGCTTGTATAGAGGATGAATGCCCTGCATGTCTGACCTTGG
66 GGCTCGATTTTCACGCTTGTATAGAGGATGAATGCCCTGCATGTCTGACCTTGG
* * *
503467 AACTGCAAATTAAGATGATTTCTTAAAGGATTGTAAAATATATATGTTCAATTTAAATCCATTAA
1 AACTGCAAATTAAGATGATTTCTTAAAGGATTGTAAAATATACATCTTCAATTTAAACCCATTAA
* *
503532 GGCTTGATTTTCACGCTTGTATAGAGGATGAATGCCCTGCATGTTTGACCTTGG
66 GGCTCGATTTTCACGCTTGTATAGAGGATGAATGCCCTGCATGTCTGACCTTGG
503586 AA
1 AA
503588 TTTATAAGGA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 113 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (119 bp):
AACTGCAAATTAAGATGATTTCTTAAAGGATTGTAAAATATACATCTTCAATTTAAACCCATTAA
GGCTCGATTTTCACGCTTGTATAGAGGATGAATGCCCTGCATGTCTGACCTTGG
Found at i:509641 original size:2 final size:2
Alignment explanation
Indices: 509634--509665 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
509624 ACAATCATAC
*
509634 AT AT AT AT AA 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
509666 TAGTTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:509838 original size:21 final size:21
Alignment explanation
Indices: 509814--509908 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 21
509804 TATCATTTTG
509814 ATTTTAATAACTTTTGATAAA
1 ATTTTAATAACTTTTGATAAA
** **
509835 ATTTTAGGAACTTTTGATTCA
1 ATTTTAATAACTTTTGATAAA
** *
509856 ATTTTGGTAA-TCATTGATAAA
1 ATTTTAATAACT-TTTGATAAA
* * **
509877 ATTTTTATAATCTCTTGATGTA
1 ATTTTAATAA-CTTTTGATAAA
509899 ATTTTAATAA
1 ATTTTAATAA
509909 TTAACCTTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
20 1 0.02
21 39 0.70
22 15 0.27
23 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (21 bp):
ATTTTAATAACTTTTGATAAA
Found at i:509838 original size:27 final size:26
Alignment explanation
Indices: 509788--509839 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
509778 AGATAAGTTA
* **
509788 ATTTTGATAATTTTGATATCATTTTG
1 ATTTTAATAATTTTGATAAAATTTTG
509814 ATTTTAATAACTTTTGATAAAATTTT
1 ATTTTAATAA-TTTTGATAAAATTTT
509840 AGGAACTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.56
Consensus pattern (26 bp):
ATTTTAATAATTTTGATAAAATTTTG
Found at i:510256 original size:22 final size:22
Alignment explanation
Indices: 510231--510272 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
510221 GTTATTATTG
* * *
510231 ATTTATTATTATGTTATCAACT
1 ATTTACTATTAAGCTATCAACT
510253 ATTTACTATTAAGCTATCAA
1 ATTTACTATTAAGCTATCAA
510273 ATCTTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAGCTATCAACT
Found at i:510302 original size:22 final size:22
Alignment explanation
Indices: 510289--510349 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
510279 AAATTAGCAT
*
510289 TAATTTATTGTTAATTTATGAA
1 TAATTTATTGTTAAATTATGAA
** * *
510311 TAATTTATTACTAACTTATAAA
1 TAATTTATTGTTAAATTATGAA
* *
510333 TAATTTACTATTAAATT
1 TAATTTATTGTTAAATT
510350 GTTAATGATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (22 bp):
TAATTTATTGTTAAATTATGAA
Found at i:510360 original size:22 final size:22
Alignment explanation
Indices: 510299--510431 Score: 99
Period size: 22 Copynumber: 6.0 Consensus size: 22
510289 TAATTTATTG
* * * *
510299 TTAATTTATGAATAATTTATTA
1 TTAAATTATTAATGATTTACTA
* * * *
510321 CTAACTTATAAATAATTTACTA
1 TTAAATTATTAATGATTTACTA
* *
510343 TTAAATTGTTAATGATTTGCTA
1 TTAAATTATTAATGATTTACTA
* *
510365 TTAAGTTATTAATGATTTATTA
1 TTAAATTATTAATGATTTACTA
*
510387 -TAAAGTTA-TAACTAATTTACTA
1 TTAAA-TTATTAA-TGATTTACTA
* *
510409 TTAATTTATCAATGATTTACTA
1 TTAAATTATTAATGATTTACTA
510431 T
1 T
510432 AAAGCTATCA
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
21 6 0.07
22 76 0.87
23 5 0.06
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (22 bp):
TTAAATTATTAATGATTTACTA
Found at i:510383 original size:66 final size:66
Alignment explanation
Indices: 510299--510452 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 66
510289 TAATTTATTG
* * * * * *
510299 TTAATTTATGAATAATTTATTACT-AACTTATAAATAATTTACTATTAAATTGTTAATGATTTGC
1 TTAAGTTATCAATGATTTATTA-TAAACTTATAAATAATTTACTATTAAATTATCAATGATTTAC
510363 TA
65 TA
* * * *
510365 TTAAGTTATTAATGATTTATTATAAAGTTATAACTAATTTACTATTAATTTATCAATGATTTACT
1 TTAAGTTATCAATGATTTATTATAAACTTATAAATAATTTACTATTAAATTATCAATGATTTACT
510430 A
66 A
* * *
510431 TAAAGCTATCAATGATTAATTA
1 TTAAGTTATCAATGATTTATTA
510453 ATTTTCTACT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 1 0.01
66 73 0.99
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (66 bp):
TTAAGTTATCAATGATTTATTATAAACTTATAAATAATTTACTATTAAATTATCAATGATTTACT
A
Found at i:510440 original size:22 final size:22
Alignment explanation
Indices: 510326--510447 Score: 104
Period size: 22 Copynumber: 5.5 Consensus size: 22
510316 TATTACTAAC
* *
510326 TTATAAATAATTTACTATTAAA-
1 TTATCAATGATTTACTA-TAAAG
* * * *
510348 TTGTTAATGATTTGCTATTAAG
1 TTATCAATGATTTACTATAAAG
* *
510370 TTATTAATGATTTATTATAAAG
1 TTATCAATGATTTACTATAAAG
* * *
510392 TTAT-AACTAATTTACTATTAAT
1 TTATCAA-TGATTTACTATAAAG
510414 TTATCAATGATTTACTATAAAG
1 TTATCAATGATTTACTATAAAG
*
510436 CTATCAATGATT
1 TTATCAATGATT
510448 AATTAATTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
21 5 0.06
22 73 0.91
23 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (22 bp):
TTATCAATGATTTACTATAAAG
Found at i:510493 original size:22 final size:22
Alignment explanation
Indices: 510449--510502 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
510439 TCAATGATTA
* *
510449 ATTAATTTTCTACTAAATTATC
1 ATTAATTTACTACTAAATAATC
* *
510471 ATTAATTTACTATTAAGTAATC
1 ATTAATTTACTACTAAATAATC
*
510493 AATAATTTAC
1 ATTAATTTAC
510503 ATATAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTAATTTACTACTAAATAATC
Found at i:510660 original size:21 final size:22
Alignment explanation
Indices: 510634--510687 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
510624 TAATATTCAT
510634 TATTAAGTTATC-ACTAATTTA-
1 TATTAAGTTATCTA-TAATTTAC
*
510655 TATTAAATTATCTATAATTTAC
1 TATTAAGTTATCTATAATTTAC
510677 TATTAAGTTAT
1 TATTAAGTTAT
510688 TTAACTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (22 bp):
TATTAAGTTATCTATAATTTAC
Found at i:510696 original size:16 final size:15
Alignment explanation
Indices: 510671--510704 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
510661 ATTATCTATA
*
510671 ATTTACTATTAAGTT
1 ATTTACTATTAAATT
510686 ATTTAACTATTAAATT
1 ATTT-ACTATTAAATT
510702 ATT
1 ATT
510705 GATGATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTACTATTAAATT
Found at i:510874 original size:22 final size:22
Alignment explanation
Indices: 510848--510902 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
510838 ATTGATTTAC
510848 TATTAAGTTATTACTAATTGAT
1 TATTAAGTTATTACTAATTGAT
* * *
510870 TATTAAGTTATTATTGATTTAT
1 TATTAAGTTATTACTAATTGAT
*
510892 TATTAAATTAT
1 TATTAAGTTAT
510903 CAATGGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
TATTAAGTTATTACTAATTGAT
Found at i:510882 original size:11 final size:11
Alignment explanation
Indices: 510848--510902 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
510838 ATTGATTTAC
510848 TATTAAGTTAT
1 TATTAAGTTAT
*
510859 TACTAA-TTGAT
1 TATTAAGTT-AT
510870 TATTAAGTTAT
1 TATTAAGTTAT
* *
510881 TATTGATTTAT
1 TATTAAGTTAT
*
510892 TATTAAATTAT
1 TATTAAGTTAT
510903 CAATGGTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 2 0.06
11 32 0.89
12 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (11 bp):
TATTAAGTTAT
Found at i:510912 original size:22 final size:22
Alignment explanation
Indices: 510840--510926 Score: 57
Period size: 22 Copynumber: 4.0 Consensus size: 22
510830 AAACTAAAAT
* * * *
510840 TGATTTACTATTAAGTTATTAC
1 TGATTTATTATTAAATTATCAA
* * * * *
510862 TAATTGATTATTAAGTTATTAT
1 TGATTTATTATTAAATTATCAA
510884 TGATTTATTATTAAATTATCAA
1 TGATTTATTATTAAATTATCAA
* ** *
510906 TGGTTTAAAACTAAATTATCA
1 TGATTTATTATTAAATTATCA
510927 CTTTTTTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (22 bp):
TGATTTATTATTAAATTATCAA
Found at i:513653 original size:14 final size:15
Alignment explanation
Indices: 513634--513677 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
513624 TTAATTTTTC
*
513634 TTTTATTTTAAAAA-
1 TTTTATTATAAAAAT
513648 TTTTATTATACATAAAT
1 TTTTATTATA-A-AAAT
513665 TTTTATTATAAAA
1 TTTTATTATAAAA
513678 TATTAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 9 0.35
15 3 0.12
16 4 0.15
17 10 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTATTATAAAAAT
Found at i:514195 original size:19 final size:18
Alignment explanation
Indices: 514171--514206 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
514161 ACTTCTTTTA
*
514171 TCTAATTATAAAATAAAAC
1 TCTAATAATAAAA-AAAAC
514190 TCTAATAATAAAAAAAA
1 TCTAATAATAAAAAAAA
514207 TTCATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (18 bp):
TCTAATAATAAAAAAAAC
Found at i:514506 original size:2 final size:2
Alignment explanation
Indices: 514499--514525 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
514489 TAATTGGATG
514499 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 A
514526 AGTTATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:515625 original size:13 final size:14
Alignment explanation
Indices: 515589--515625 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
515579 AAATTTATTA
*
515589 TTTAT-TAACAAAT
1 TTTATATAATAAAT
515602 TTTATATAATAAAT
1 TTTATATAATAAAT
515616 TTTATA-AATA
1 TTTATATAATA
515626 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTATATAATAAAT
Found at i:520295 original size:17 final size:17
Alignment explanation
Indices: 520270--520303 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
520260 GATCTGGGAG
520270 TTTTATCTTTCCTTATT
1 TTTTATCTTTCCTTATT
* *
520287 TTTTTTCTTTTCTTATT
1 TTTTATCTTTCCTTATT
520304 AAATCAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATCTTTCCTTATT
Found at i:523459 original size:4 final size:4
Alignment explanation
Indices: 523450--523477 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
523440 CTGGAGATTC
523450 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
523478 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:525439 original size:26 final size:26
Alignment explanation
Indices: 525405--525455 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
525395 ATATAAGTTA
* * *
525405 AAAAAATATTTATTCCTAATTTTTTT
1 AAAAAATATTAATTCATAATATTTTT
525431 AAAAAATATTAATTCATAATATTTT
1 AAAAAATATTAATTCATAATATTTT
525456 CATCTAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (26 bp):
AAAAAATATTAATTCATAATATTTTT
Found at i:526206 original size:62 final size:60
Alignment explanation
Indices: 526070--526462 Score: 220
Period size: 62 Copynumber: 6.3 Consensus size: 60
526060 TAATCCATGA
* * * * * * **
526070 ATTATTCAAGCTATTTTTAGCCAGAAACGCCTTCAATAATCTCAT-TTAATATTTTGTAAGGG
1 ATTATTCAAGGTGTTTTTAGTCAAAAACACCTTCAATAATC-CATCATAA-AAATTG-AAGGG
* *
526132 ATTATTTAAGGTGTTTTCTAGTTAAAAACACCTTCAATAATCCATCATAAAAATTGAAGGG
1 ATTATTCAAGGTGTTTT-TAGTCAAAAACACCTTCAATAATCCATCATAAAAATTGAAGGG
* * * * * * *** *
526193 AATTATTCAAGGTGTTTTTGGTCATAAACACTTTGACTAATCCCAT-TTAATTTTTTCTAAGGG
1 -ATTATTCAAGGTGTTTTTAGTCAAAAACACCTTCAATAAT-CCATCATAA-AAATT-GAAGGG
* * * * ** *
526256 ATTATTCAAGGTGTTTTCTCA--CAAAAACGCCTTGAACAATCTAAAAAAAAAATAAATGAAAGG
1 ATTATTCAAGGTGTTTT-T-AGTCAAAAACACCTTCAATAATCCATCATAAAAAT---TG-AAGG
526319 AG
60 -G
* * ** *
526321 ATTATTGAAGGTGTTTTTTGTCAAAAATGCCTTCAATAATCTTATC-TAAAAAATTGGAAGGG
1 ATTATTCAAGGTGTTTTTAGTCAAAAACACCTTCAATAATC-CATCAT-AAAAATT-GAAGGG
* * * *
526383 ATTATTCAAGGTATTTTTTTTGTAAAAAACACCTTCAATAATCCACTCATAAAAATTTAAGGGG
1 ATTATTCAAGG--TGTTTTTAGTCAAAAACACCTTCAATAATCCA-TCATAAAAATTGAA-GGG
*
526447 ATTATTCAAAGTGTTT
1 ATTATTCAAGGTGTTT
526463 CTGGTCGAAA
Statistics
Matches: 254, Mismatches: 53, Indels: 48
0.72 0.15 0.14
Matches are distributed among these distances:
61 28 0.11
62 91 0.36
63 37 0.15
64 55 0.22
65 35 0.14
66 8 0.03
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (60 bp):
ATTATTCAAGGTGTTTTTAGTCAAAAACACCTTCAATAATCCATCATAAAAATTGAAGGG
Found at i:526437 original size:64 final size:64
Alignment explanation
Indices: 526334--526455 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
526324 ATTGAAGGTG
* ** *
526334 TTTTTTGTCAAAAATGCCTTCAATAATCTTATCTAAAAAATTGGAA-GGGATTATTCAAGGTATT
1 TTTTTTGTAAAAAACACCTTCAATAATCTCATCTAAAAAATT-GAAGGGGATTATTCAAGGTATT
*
526398 TTTTTTGTAAAAAACACCTTCAATAATC-CA-CTCATAAAAATTTAAGGGGATTATTCAA
1 TTTTTTGTAAAAAACACCTTCAATAATCTCATCT-A-AAAAATTGAAGGGGATTATTCAA
526456 AGTGTTTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 2 0.04
63 4 0.08
64 44 0.88
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (64 bp):
TTTTTTGTAAAAAACACCTTCAATAATCTCATCTAAAAAATTGAAGGGGATTATTCAAGGTATT
Found at i:529986 original size:23 final size:20
Alignment explanation
Indices: 529948--529990 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
529938 ACGGTAGAAT
*
529948 GAATAAAATATATATAATAAA
1 GAATAAAAAATATAT-ATAAA
529969 GAATAAAAAATACCTATATAAA
1 GAATAAAAAATA--TATATAAA
529991 AAAATATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 5 0.26
23 3 0.16
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (20 bp):
GAATAAAAAATATATATAAA
Found at i:531004 original size:22 final size:22
Alignment explanation
Indices: 530970--531013 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
530960 GTTTTTGGCC
*
530970 AAAAATACTTTTAATAATCTAG
1 AAAAATACCTTTAATAATCTAG
*
530992 AAAAATGCCTTTAATAATCTAG
1 AAAAATACCTTTAATAATCTAG
531014 GAATTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAAATACCTTTAATAATCTAG
Found at i:533809 original size:73 final size:73
Alignment explanation
Indices: 533688--533846 Score: 219
Period size: 73 Copynumber: 2.2 Consensus size: 73
533678 TACAGTGAAA
* *
533688 AGCTCGAGCTCGTGCTCAACTCCTAACTCATAGCTCAATACTCAACTCGAACTCAATCGAGTTTC
1 AGCTCGAGCTCGAGCTCAACTCCTAACTCACAGCTCAATACTCAACTCGAACTCAATCGAGTTTC
533753 ATTTTCTT
66 ATTTTCTT
* * ** * ** *
533761 AGCTCGAGCTCGAGCTCGACTCCTAATTCACAGCTTGATACTCGACTCGAACTTGATCGAGTTTT
1 AGCTCGAGCTCGAGCTCAACTCCTAACTCACAGCTCAATACTCAACTCGAACTCAATCGAGTTTC
*
533826 ATTTTTTT
66 ATTTTCTT
533834 AGCTCGAGCTCGA
1 AGCTCGAGCTCGA
533847 TTCGTGATCA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (73 bp):
AGCTCGAGCTCGAGCTCAACTCCTAACTCACAGCTCAATACTCAACTCGAACTCAATCGAGTTTC
ATTTTCTT
Found at i:539798 original size:55 final size:55
Alignment explanation
Indices: 539729--539866 Score: 179
Period size: 55 Copynumber: 2.5 Consensus size: 55
539719 ATATAATAAA
* *
539729 AAAATTAAAACATATAAGTTTATACTGACAATCTTTAACCGTCGGTAAATGTAAG
1 AAAATTAAAACATATAAGTTTATACTGACAATCTCTAACCGTCGGTAAAGGTAAG
* * **
539784 AAAATTAAAGCATATAA-TTATATACTGACAATCTCTAACCGTTGGTTTAGGTAAG
1 AAAATTAAAACATATAAGTT-TATACTGACAATCTCTAACCGTCGGTAAAGGTAAG
* * *
539839 AAAATTAAAAAACACAAGTTTATACTGA
1 AAAATTAAAACATATAAGTTTATACTGA
539867 TAAATGCTAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
54 2 0.03
55 67 0.94
56 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (55 bp):
AAAATTAAAACATATAAGTTTATACTGACAATCTCTAACCGTCGGTAAAGGTAAG
Found at i:540892 original size:7 final size:7
Alignment explanation
Indices: 540880--540910 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
540870 TTTATTTCTT
540880 TTTTATA
1 TTTTATA
540887 TTTTATA
1 TTTTATA
540894 TTTTATA
1 TTTTATA
*
540901 TTTTACA
1 TTTTATA
540908 TTT
1 TTT
540911 ATTTGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:542618 original size:12 final size:14
Alignment explanation
Indices: 542590--542621 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
542580 ATCATCAAAA
542590 AATTTTATTTAATT
1 AATTTTATTTAATT
542604 AATTTTA-TT-ATT
1 AATTTTATTTAATT
542616 AATTTT
1 AATTTT
542622 TAAAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 2 0.11
14 7 0.39
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AATTTTATTTAATT
Found at i:547876 original size:15 final size:15
Alignment explanation
Indices: 547856--547895 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
547846 CTAGAGAGAG
547856 AAGAAGAGAAAAAGA
1 AAGAAGAGAAAAAGA
*
547871 AAGAAGAGAAAGAGA
1 AAGAAGAGAAAAAGA
547886 AAGAAGAGAA
1 AAGAAGAGAA
547896 GGAAAATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAAAAGA
Found at i:548449 original size:14 final size:14
Alignment explanation
Indices: 548430--548456 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
548420 TATTTTTAAT
548430 CAAAAAATAAAAAA
1 CAAAAAATAAAAAA
548444 CAAAAAATAAAAA
1 CAAAAAATAAAAA
548457 TTTTTTTAAT
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:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (14 bp):
CAAAAAATAAAAAA
Found at i:549391 original size:12 final size:12
Alignment explanation
Indices: 549374--549398 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
549364 TGATCAAAAT
549374 TGCTTATGTGGA
1 TGCTTATGTGGA
549386 TGCTTATGTGGA
1 TGCTTATGTGGA
549398 T
1 T
549399 AATCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (12 bp):
TGCTTATGTGGA
Found at i:549674 original size:28 final size:27
Alignment explanation
Indices: 549643--549729 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 27
549633 TTTTGTCAAA
549643 TAATTCTATTTAATAAATTATTTAAATT
1 TAATT-TATTTAATAAATTATTTAAATT
549671 TAATATT-TTTAGAT-AATTATTTAAATT
1 TAAT-TTATTTA-ATAAATTATTTAAATT
* * *
549698 CAATAATATTTAATAGATTATTTAAATT
1 TAAT-TTATTTAATAAATTATTTAAATT
549726 TAAT
1 TAAT
549730 ACTTTTAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
27 24 0.47
28 26 0.51
29 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TAATTTATTTAATAAATTATTTAAATT
Found at i:549688 original size:27 final size:27
Alignment explanation
Indices: 549658--549741 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
549648 CTATTTAATA
549658 AATTATTTAAATTTAATATTTTTAGAT
1 AATTATTTAAATTTAATATTTTTAGAT
* *
549685 AATTATTTAAATTCAATAATATTTA-AT
1 AATTATTTAAATTTAAT-ATTTTTAGAT
*
549712 AGATTATTTAAATTTAATACTTTTAGAT
1 A-ATTATTTAAATTTAATATTTTTAGAT
549740 AA
1 AA
549742 GTTAATGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 25 0.51
28 24 0.49
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (27 bp):
AATTATTTAAATTTAATATTTTTAGAT
Found at i:549730 original size:28 final size:27
Alignment explanation
Indices: 549649--549730 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 27
549639 CAAATAATTC
549649 TATTTAATAAATTATTTAAATTTAAT-A
1 TATTTAAT-AATTATTTAAATTTAATAA
* *
549676 TTTTTAGATAATTATTTAAATTCAATAA
1 TATTTA-ATAATTATTTAAATTTAATAA
549704 TATTTAATAGATTATTTAAATTTAATA
1 TATTTAATA-ATTATTTAAATTTAATA
549731 CTTTTAGATA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 24 0.50
28 24 0.50
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (27 bp):
TATTTAATAATTATTTAAATTTAATAA
Found at i:551130 original size:20 final size:20
Alignment explanation
Indices: 551105--551144 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
551095 TGTAGACACC
551105 CAATTGGGTCC-GGCCCAAAT
1 CAATTGGG-CCTGGCCCAAAT
551125 CAATTGGGCCTGGCCCAAAT
1 CAATTGGGCCTGGCCCAAAT
551145 GGGTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (20 bp):
CAATTGGGCCTGGCCCAAAT
Found at i:551234 original size:16 final size:19
Alignment explanation
Indices: 551213--551261 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
551203 TTTTATGTAT
551213 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
551230 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
551248 TGTATATATTTATT
1 TGTAT-TATTTATT
551262 TATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:551337 original size:15 final size:18
Alignment explanation
Indices: 551317--551356 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 18
551307 TATATATATA
551317 TATTTTTA-TC-TTTTT-
1 TATTTTTATTCATTTTTG
551332 TA-TTTTATTCATTTTTG
1 TATTTTTATTCATTTTTG
551349 TATTTTTA
1 TATTTTTA
551357 CTTATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.24
15 4 0.19
16 5 0.24
17 2 0.10
18 5 0.24
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (18 bp):
TATTTTTATTCATTTTTG
Found at i:552313 original size:11 final size:10
Alignment explanation
Indices: 552280--552383 Score: 67
Period size: 10 Copynumber: 10.4 Consensus size: 10
552270 TTTAGATTAG
*
552280 ATTTATTTAAT
1 ATTTATTT-TT
*
552291 ATTTTTTCTTT
1 ATTTATT-TTT
552302 ATCTTATTTTT
1 AT-TTATTTTT
552313 ATTT-TTTTT
1 ATTTATTTTT
*
552322 -TTTACTTTT
1 ATTTATTTTT
*
552331 CTTTAATTTTT
1 ATTT-ATTTTT
552342 -TTTAATTTTT
1 ATTT-ATTTTT
*
552352 ATTTATTTTC
1 ATTTATTTTT
552362 ACTTT-TTTTT
1 A-TTTATTTTT
552372 A-TTA-TTTT
1 ATTTATTTTT
552380 ATTT
1 ATTT
552384 TCTTTAAAGA
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
8 10 0.13
9 11 0.14
10 26 0.34
11 25 0.32
12 5 0.06
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:552323 original size:28 final size:28
Alignment explanation
Indices: 552292--552389 Score: 69
Period size: 28 Copynumber: 3.4 Consensus size: 28
552282 TTATTTAATA
552292 TTTTTTCTTTATCTTATTTTTATTTTTT
1 TTTTTTCTTTATCTTATTTTTATTTTTT
*
552320 TTTTTACTTT-TCTTTAATTTTT-TTTAATTT
1 TTTTTTCTTTATC-TT-ATTTTTATTT--TTT
* *
552350 TTATTTAT-TTTCA-CTTTTTTTTATTATTT
1 TT-TTT-TCTTT-ATCTTATTTTTATTTTTT
*
552379 TATTTTCTTTA
1 TTTTTTCTTTA
552390 AAGAAAAATC
Statistics
Matches: 55, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
27 4 0.07
28 20 0.36
29 10 0.18
30 10 0.18
31 10 0.18
32 1 0.02
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTTTCTTTATCTTATTTTTATTTTTT
Found at i:552335 original size:22 final size:23
Alignment explanation
Indices: 552285--552344 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
552275 ATTAGATTTA
552285 TTTAATATTTTTTCTTTATCTTATT
1 TTTAAT-TTTTTT-TTTATCTTATT
*
552310 TTTATTTTTTTTTTTA-CTT-TT
1 TTTAATTTTTTTTTTATCTTATT
552331 CTTTAATTTTTTTT
1 -TTTAATTTTTTTT
552345 AATTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 2 0.06
22 15 0.47
23 4 0.12
24 6 0.19
25 5 0.16
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTAATTTTTTTTTTATCTTATT
Found at i:552344 original size:23 final size:24
Alignment explanation
Indices: 552285--552384 Score: 73
Period size: 23 Copynumber: 4.1 Consensus size: 24
552275 ATTAGATTTA
*
552285 TTTAATATTTTTTCTTTATCTTATT
1 TTTAAT-TTTTTTTTTTATCTTATT
552310 TTT-ATTTTTTTTTTTA-CTT-TT
1 TTTAATTTTTTTTTTTATCTTATT
552331 CTTTAATTTTTTTTAATTTTTAT-TTATT
1 -TTTAA--TTTTTT--TTTTTATCTTATT
* * * *
552359 TTCACTTTTTTTTATTATTTTATT
1 TTTAATTTTTTTTTTTATCTTATT
552383 TT
1 TT
552385 CTTTAAAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
21 2 0.03
22 6 0.10
23 17 0.27
24 9 0.15
25 15 0.24
27 11 0.18
28 2 0.03
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTAATTTTTTTTTTTATCTTATT
Found at i:552461 original size:61 final size:61
Alignment explanation
Indices: 552395--552557 Score: 239
Period size: 62 Copynumber: 2.8 Consensus size: 61
552385 CTTTAAAGAA
*
552395 AAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGG
1 AAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
552456 AAATCAAAATTTCAAAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAG
1 AAATCAAAATTTC-CAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
*
552518 AAAT--AAATTT-C--AAAAAATA-TTTTGGGGAAAAGTTGAAAGT
1 AAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGT
552558 TTAGGGAAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
55 19 0.20
56 8 0.08
60 6 0.06
61 13 0.14
62 49 0.52
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (61 bp):
AAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
Found at i:552618 original size:199 final size:194
Alignment explanation
Indices: 552380--552754 Score: 578
Period size: 199 Copynumber: 1.9 Consensus size: 194
552370 TTATTATTTT
*
552380 ATTTTCTTTAAAGAAAAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCA
1 ATTTTCTTAAAAGAAAAAT-AAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCA
*
552445 ATTTTCCTTGGAAATCAAAATTTCAAAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATT
65 ATTTTCCTTAGAAAT--AAATTTC---AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATT
552510 TTCCTT-AGAAAT-AAATTT-CAAAAAATATTTTGGGGAAAAGTTGAAAGTTTAGGGAAAGTGAA
125 TTCCTTGA-AAATCAAATTTCCAAAAAATATTTTGGGGAAAAGTTGAAAGTTTAGGGAAAGTGAA
552572 GTATCA
189 GTATCA
552578 ATTTTCCTTAAAAGAAAAAT-AAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTAT
1 ATTTT-CTTAAAAGAAAAATAAAATTTCC--AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTAT
* **
552642 CAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
63 CAATTTTCCTTAGAAATAAATTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTC
552707 CTTGAAAATCGAAATTTCCAAAAAATATTTTGGGGAAAAGTTGAAAGT
128 CTTGAAAATC-AAATTTCCAAAAAATATTTTGGGGAAAAGTTGAAAGT
552755 ATCAATTTTC
Statistics
Matches: 165, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
194 45 0.27
195 1 0.01
196 6 0.04
197 45 0.27
198 5 0.03
199 63 0.38
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.33
Consensus pattern (194 bp):
ATTTTCTTAAAAGAAAAATAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA
TTTTCCTTAGAAATAAATTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTT
GAAAATCAAATTTCCAAAAAATATTTTGGGGAAAAGTTGAAAGTTTAGGGAAAGTGAAGTATCA
Found at i:552630 original size:137 final size:138
Alignment explanation
Indices: 552421--552696 Score: 438
Period size: 137 Copynumber: 2.0 Consensus size: 138
552411 AAAAAATATT
* *
552421 TTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAATTTCAAAAAAAAAATATTTTT
1 TTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAAATTTCAAAAAAAAAATATTTTT
552486 AAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTT-CAAAAAATA-TTTTGGGGAAAA
66 AAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGGGAAAA
552549 GTTGAAAG
131 GTTGAAAG
552557 TTTAGGG-AAAG-TG-AAGTATCAATTTTCCTTAAAAGAAA-AATAAATTTCCAAAAAAAAAATA
1 TTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AGAAATAA-AAATTT-CAAAAAAAAAATA
*
552618 TTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGG
61 TTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGG
552683 GAAAAGTTGAAAG
126 GAAAAGTTGAAAG
552696 T
1 T
552697 ATCAATTTTC
Statistics
Matches: 130, Mismatches: 3, Indels: 11
0.90 0.02 0.08
Matches are distributed among these distances:
133 17 0.13
134 2 0.02
135 5 0.04
136 17 0.13
137 59 0.45
138 9 0.07
139 21 0.16
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (138 bp):
TTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAAATTTCAAAAAAAAAATATTTTT
AAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAATATTTTTGGGGAAAA
GTTGAAAG
Found at i:552686 original size:57 final size:58
Alignment explanation
Indices: 552610--552765 Score: 264
Period size: 57 Copynumber: 2.7 Consensus size: 58
552600 ATTTCCAAAA
*
552610 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-AAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATCAAATTTCC
552667 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTCC
552726 AAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
552766 CTGCAAAAAA
Statistics
Matches: 95, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
57 46 0.48
58 33 0.35
59 16 0.17
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (58 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTCC
Found at i:556254 original size:11 final size:11
Alignment explanation
Indices: 556240--556272 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
556230 AAAAGGTCTC
556240 AAAAATAAAAA
1 AAAAATAAAAA
556251 AAAAAT-AAAA
1 AAAAATAAAAA
556261 AAAAATAAAAA
1 AAAAATAAAAA
556272 A
1 A
556273 TGCCACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:556260 original size:9 final size:10
Alignment explanation
Indices: 556240--556272 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
556230 AAAAGGTCTC
556240 AAAAATAAAAA
1 AAAAAT-AAAA
556251 AAAAATAAAA
1 AAAAATAAAA
556261 AAAAATAAAA
1 AAAAATAAAA
556271 AA
1 AA
556273 TGCCACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:556604 original size:9 final size:9
Alignment explanation
Indices: 556599--556663 Score: 68
Period size: 8 Copynumber: 7.8 Consensus size: 9
556589 GATAAAAGAA
*
556599 AAAAAAAAG
1 AAAAAAATG
556608 AAAAAAA-G
1 AAAAAAATG
*
556616 GAAAAAATG
1 AAAAAAATG
*
556625 -AGAAAATG
1 AAAAAAATG
556633 -AAAAAATG
1 AAAAAAATG
556641 AAAAAAATG
1 AAAAAAATG
556650 -AAAAAAT-
1 AAAAAAATG
556657 AAAAAAA
1 AAAAAAA
556664 GAGATCCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
8 34 0.68
9 16 0.32
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
AAAAAAATG
Found at i:556630 original size:25 final size:24
Alignment explanation
Indices: 556601--556665 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 24
556591 TAAAAGAAAA
*
556601 AAAAAAGAAAAAAAGGAAAAAATG
1 AAAAAAGAAAAAAAGAAAAAAATG
* *
556625 AGAAAATGAAAAAATGAAAAAAATG
1 A-AAAAAGAAAAAAAGAAAAAAATG
*
556650 AAAAAATAAAAAAAGA
1 AAAAAAGAAAAAAAGA
556666 GATCCAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (24 bp):
AAAAAAGAAAAAAAGAAAAAAATG
Found at i:558005 original size:42 final size:40
Alignment explanation
Indices: 557846--558815 Score: 767
Period size: 41 Copynumber: 24.0 Consensus size: 40
557836 GTCTAGGAGT
*
557846 ATTTACTTTTCCAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
557886 ATTTAC-TTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCA
557926 ATTTA-TTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
557966 ATTTACTTTTCAAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTC-AAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
558008 ATTTA-TTTTCCAAAGTTCGTTGCCTCTGTTTAGAGGATCA
1 ATTTACTTTT-CAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
558048 ATTTACTTTTCAAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTC-AAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
558090 ATTTACTTTTTCAAAGTTCGTTGCCTTTGTTTAGAGGAGCA
1 ATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
* ** * * * ***
558131 ATTTATTTTTCAAAGTTCCGGAGCAATTTATTT--TTCA--A
1 ATTTACTTTTCAAAGTT-CGTTGC-CTCTGTTTAGAGGAGCA
* * * * * ** * **
558169 AGTTCCGTTGC----CTC--TG--T-T-TAGAGGAGCAATTTA
1 ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTA-GAG-GA-GCA
* *** * * * *
558202 TTTTTCAAAGTTC--CGTT-G-T-CTCTGT-TTAGAGGAGCA--A
1 -ATTT-ACTTTTCAAAGTTCGTTGC-CTCTGTT-TA-GAGGAGCA
* *** ** * * *
558239 TTTACTTTTCAAAAGTCGT-GGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAGT--TCGTTGCCTCTGTTTAGAGGAGCA
*
558280 ATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
* *
558321 ATTTACTTTTCCAAAG-TCATGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTTC--GTTGCCTCTGTTTAGAGGAGCA
558363 ATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
* * *
558404 ATTTACTTTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGTA
1 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
558446 ATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
*
558487 ATTTACTTTTCCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
558529 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
*
558570 ATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
558611 ATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAGAGGAGCA
558652 ATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
558693 ATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
* * *
558734 A-TTACTTTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGTA
1 ATTTACTTTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
558775 ATTTACTTTTCAAAAG-TCGTGGTGCCTCTGTTTAGAGGAGC
1 ATTTACTTTTC-AAAGTTCGT--TGCCTCTGTTTAGAGGAGC
558816 TTTGGTAAAA
Statistics
Matches: 792, Mismatches: 73, Indels: 128
0.80 0.07 0.13
Matches are distributed among these distances:
26 1 0.00
27 1 0.00
28 1 0.00
30 1 0.00
31 1 0.00
33 2 0.00
34 3 0.00
35 3 0.00
36 3 0.00
37 5 0.01
38 8 0.01
39 24 0.03
40 149 0.19
41 345 0.44
42 223 0.28
43 21 0.03
44 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (40 bp):
ATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCA
Found at i:558159 original size:25 final size:25
Alignment explanation
Indices: 558125--558175 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
558115 TTTGTTTAGA
558125 GGAGCAATTTATTTTTCAAAGTTCC
1 GGAGCAATTTATTTTTCAAAGTTCC
558150 GGAGCAATTTATTTTTCAAAGTTCC
1 GGAGCAATTTATTTTTCAAAGTTCC
558175 G
1 G
558176 TTGCCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (25 bp):
GGAGCAATTTATTTTTCAAAGTTCC
Found at i:558190 original size:66 final size:66
Alignment explanation
Indices: 558084--558216 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
558074 TCTGTTTAGA
*
558084 GGAGCAATTTACTTTTTCAAAGTTCGTTGCCTTTGTTTAGAGGAGCAATTTATTTTTCAAAGTTC
1 GGAGCAATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTC
558149 C
66 C
558150 GGAGCAATTTA-TTTTTCAAAGTTCCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTT
1 GGAGCAATTTACTTTTTCAAAGTT-CGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTT
558214 CC
65 CC
558216 G
1 G
558217 TTGTCTCTGT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 12 0.18
66 53 0.82
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (66 bp):
GGAGCAATTTACTTTTTCAAAGTTCGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTC
C
Found at i:558207 original size:41 final size:40
Alignment explanation
Indices: 558150--558815 Score: 903
Period size: 41 Copynumber: 16.1 Consensus size: 40
558140 TCAAAGTTCC
*
558150 GGAGCAATTTATTTTTCAAAGTTCCGT-TGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAG-T-CGTGTGCCTCTGTTTAGA
* *
558191 GGAGCAATTTATTTTTCAAAGTTCCGT-TGTCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAG-T-CGTGTGCCTCTGTTTAGA
* *
558232 GGAGCAATTTACTTTTCAAAAGTCGTGGTACCTCTGTTGAGA
1 GGAGCAATTTACTTTTC-AAAGTCGT-GTGCCTCTGTTTAGA
*
558274 GGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGA
* *
558315 GGAGCAATTTACTTTTCCAAAGTCATGGTACCTCTGTTTAGA
1 GGAGCAATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGA
558357 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGA
* *
558398 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGA
1 GGAGCAATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGA
*
558440 GGAGTAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGA
*
558481 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGA
1 GGAGCAATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGA
558523 GGAGCAATTTACTTTTTCAAAGTTCGT-TGCCTCTGTTTAGA
1 GGAGCAATTTAC-TTTTCAAAG-TCGTGTGCCTCTGTTTAGA
*
558564 GGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGA
558605 GGAGCAATTTACTTTTCAAAGTTTCGT-TGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAG--TCGTGTGCCTCTGTTTAGA
558646 GGAGCAATTTACTTTTTCAAAGTTCGT-TGCCTCTGTTTAGA
1 GGAGCAATTTAC-TTTTCAAAG-TCGTGTGCCTCTGTTTAGA
558687 GGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGA
* *
558728 GGAGCAA-TTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGA
1 GGAGCAATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGA
*
558769 GGAGTAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTACTTTTC-AAAGTCGT-GTGCCTCTGTTTAGA
558811 GGAGC
1 GGAGC
558816 TTTGGTAAAA
Statistics
Matches: 578, Mismatches: 29, Indels: 35
0.90 0.05 0.05
Matches are distributed among these distances:
39 8 0.01
40 28 0.05
41 338 0.58
42 192 0.33
43 12 0.02
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (40 bp):
GGAGCAATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGA
Found at i:558294 original size:83 final size:82
Alignment explanation
Indices: 558150--558815 Score: 992
Period size: 83 Copynumber: 8.1 Consensus size: 82
558140 TCAAAGTTCC
* * *
558150 GGAGCAATTTA-TTTTTCAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAG
1 GGAGCAATTTACTTTTCCAAAG-T-CGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG
*
558212 TTCCGT-TGTCTCTGTTTAGA
64 -T-CGTGTGCCTCTGTTTAGA
* * *
558232 GGAGCAATTTACTTTTCAAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTC
1 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
558297 GTGGTGCCTCTGTTTAGA
66 GT-GTGCCTCTGTTTAGA
*
558315 GGAGCAATTTACTTTTCCAAAGTCATGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
1 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
558380 GTGGTGCCTCTGTTTAGA
66 GT-GTGCCTCTGTTTAGA
* *
558398 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGTAATTTACTTTTCAAAGTC
1 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
558463 GTGGTGCCTCTGTTTAGA
66 GT-GTGCCTCTGTTTAGA
558481 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGT
1 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTAC-TTTTCAAAG-
558546 TCGT-TGCCTCTGTTTAGA
64 TCGTGTGCCTCTGTTTAGA
*
558564 GGAGCAATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTT
1 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG--
558628 TCGT-TGCCTCTGTTTAGA
64 TCGTGTGCCTCTGTTTAGA
* *
558646 GGAGCAATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
1 GGAGCAATTTACTTTTCCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
558709 CGTGGTGCCTCTGTTTAGA
65 CGT-GTGCCTCTGTTTAGA
* *
558728 GGAGCAA-TTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGTAATTTACTTTTCAAAAGT
1 GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTC-AAAGT
558792 CGTGGTGCCTCTGTTTAGA
65 CGT-GTGCCTCTGTTTAGA
558811 GGAGC
1 GGAGC
558816 TTTGGTAAAA
Statistics
Matches: 547, Mismatches: 22, Indels: 29
0.91 0.04 0.05
Matches are distributed among these distances:
80 8 0.01
81 28 0.05
82 168 0.31
83 326 0.60
84 13 0.02
85 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (82 bp):
GGAGCAATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
GTGTGCCTCTGTTTAGA
Found at i:558840 original size:9 final size:9
Alignment explanation
Indices: 558828--558954 Score: 183
Period size: 9 Copynumber: 14.6 Consensus size: 9
558818 TGGTAAAAAG
558828 AAAAAAACA
1 AAAAAAACA
558837 AAAAAAAC-
1 AAAAAAACA
558845 AAAAAAACA
1 AAAAAAACA
*
558854 AAAAAAAAA
1 AAAAAAACA
558863 AAAAAAAC-
1 AAAAAAACA
558871 AAAAAAACA
1 AAAAAAACA
558880 AAAAAAACA
1 AAAAAAACA
558889 AAAAAAAC-
1 AAAAAAACA
558897 AAAAAAAC-
1 AAAAAAACA
*
558905 AAAAAAACC
1 AAAAAAACA
558914 AAAAAAAC-
1 AAAAAAACA
*
558922 CAAAAAACA
1 AAAAAAACA
558931 AAAAAAACA
1 AAAAAAACA
558940 AAAAAAACCA
1 AAAAAAA-CA
558950 AAAAA
1 AAAAA
558955 TGTTGAGTTG
Statistics
Matches: 109, Mismatches: 4, Indels: 9
0.89 0.03 0.07
Matches are distributed among these distances:
8 39 0.36
9 63 0.58
10 7 0.06
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:558848 original size:17 final size:17
Alignment explanation
Indices: 558822--558954 Score: 180
Period size: 17 Copynumber: 7.7 Consensus size: 17
558812 GAGCTTTGGT
*
558822 AAAAAGAAAAAAACAAA
1 AAAAACAAAAAAACAAA
558839 AAAAACAAAAAAACAAA
1 AAAAACAAAAAAACAAA
*
558856 AAAAA-AAAAAAAAACAA
1 AAAAACAAAAAAACA-AA
558873 AAAAACAAAAAAAACAAA
1 AAAAAC-AAAAAAACAAA
558891 AAAAACAAAAAAACAAA
1 AAAAACAAAAAAACAAA
* *
558908 AAAACCAAAAAAAC-CA
1 AAAAACAAAAAAACAAA
558924 AAAAACAAAAAAAACAAA
1 AAAAAC-AAAAAAACAAA
558942 AAAAACCAAAAAA
1 AAAAA-CAAAAAA
558955 TGTTGAGTTG
Statistics
Matches: 103, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.14
17 60 0.58
18 20 0.19
19 9 0.09
ACGTcount: A:0.87, C:0.12, G:0.01, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAACAAA
Found at i:558858 original size:26 final size:26
Alignment explanation
Indices: 558828--558954 Score: 211
Period size: 26 Copynumber: 4.9 Consensus size: 26
558818 TGGTAAAAAG
558828 AAAAAAACAAAAAAAACAAAAAAACA
1 AAAAAAACAAAAAAAACAAAAAAACA
*
558854 AAAAAAAAAAAAAAAACAAAAAAACA
1 AAAAAAACAAAAAAAACAAAAAAACA
558880 AAAAAAACAAAAAAAACAAAAAAAC-
1 AAAAAAACAAAAAAAACAAAAAAACA
* *
558905 AAAAAAACCAAAAAAACCAAAAAACA
1 AAAAAAACAAAAAAAACAAAAAAACA
*
558931 AAAAAAACAAAAAAAACCAAAAAA
1 AAAAAAACAAAAAAAACAAAAAAA
558955 TGTTGAGTTG
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 23 0.24
26 72 0.76
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (26 bp):
AAAAAAACAAAAAAAACAAAAAAACA
Found at i:558954 original size:1 final size:1
Alignment explanation
Indices: 558822--558946 Score: 115
Period size: 1 Copynumber: 125.0 Consensus size: 1
558812 GAGCTTTGGT
* * * * * *
558822 AAAAAGAAAAAAACAAAAAAAACAAAAAAACAAAAAAAAAAAAAAAAACAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * ** ** * *
558887 CAAAAAAAACAAAAAAACAAAAAAACCAAAAAAACCAAAAAACAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
558947 CCAAAAAATG
Statistics
Matches: 98, Mismatches: 26, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 98 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:559068 original size:20 final size:20
Alignment explanation
Indices: 559043--559082 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
559033 TGTAGACACC
559043 CAATTGGGTCC-GGCCCAAAT
1 CAATTGGG-CCTGGCCCAAAT
559063 CAATTGGGCCTGGCCCAAAT
1 CAATTGGGCCTGGCCCAAAT
559083 GGGTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (20 bp):
CAATTGGGCCTGGCCCAAAT
Found at i:559164 original size:12 final size:12
Alignment explanation
Indices: 559144--559233 Score: 55
Period size: 12 Copynumber: 7.4 Consensus size: 12
559134 CTTTTGTATT
*
559144 TTATGTATTGTA
1 TTATTTATTGTA
*
559156 TTATTTATTATTA
1 TTATTTATT-GTA
559169 TTA-TTA-TGTA
1 TTATTTATTGTA
*
559179 TTA-ATATATGTA
1 TTATTTAT-TGTA
559191 TATATTTATT-TA
1 T-TATTTATTGTA
559203 TTTATTT-TTGTTA
1 -TTATTTATTG-TA
*
559216 ATATTTATGTGTA
1 TTATTTAT-TGTA
559229 TTATT
1 TTATT
559234 ATTTATGTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
10 7 0.11
11 3 0.05
12 28 0.46
13 18 0.30
14 5 0.08
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (12 bp):
TTATTTATTGTA
Found at i:559173 original size:16 final size:16
Alignment explanation
Indices: 559154--559257 Score: 51
Period size: 16 Copynumber: 6.6 Consensus size: 16
559144 TTATGTATTG
559154 TATTATTTATTATTAT
1 TATTATTTATTATTAT
* *
559170 TATTATGTATTAATA-
1 TATTATTTATTATTAT
*
559185 TATGTATATA-T-TTA-
1 TAT-TATTTATTATTAT
* *
559199 T-TTATTTATTTTTGT
1 TATTATTTATTATTAT
* *
559214 TAATATTTATGT-GTAT
1 TATTATTTAT-TATTAT
559230 TATTATTTATGTATATAT
1 TATTATTTAT-TAT-TAT
559248 ATATT-TTTAT
1 -TATTATTTAT
559258 CTTTTTTATT
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
12 5 0.07
13 2 0.03
14 5 0.07
15 5 0.07
16 38 0.56
17 1 0.01
18 8 0.12
19 4 0.06
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (16 bp):
TATTATTTATTATTAT
Found at i:559207 original size:60 final size:62
Alignment explanation
Indices: 559143--559268 Score: 136
Period size: 64 Copynumber: 2.0 Consensus size: 62
559133 TCTTTTGTAT
*
559143 TTTATGTATTG-TATTATTTA-T-TATTATTA-TTATGTAT-TAATATATGTATATATTTATTTA
1 TTTAT-TATTGTTAATATTTAGTGTATTATTATTTATGTATAT-ATATATGTATATATTT-TTTA
* * * *
559203 TTTATTTTTGTTAATATTTATGTGTATTATTATTTATGTATATATATATTTTTATCTTTTTTA
1 TTTATTATTGTTAATATTTA-GTGTATTATTATTTATGTATATATATATGTATATATTTTTTA
559266 TTT
1 TTT
559269 TATTCATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
59 4 0.07
60 13 0.24
62 1 0.02
63 15 0.27
64 21 0.38
65 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.65
Consensus pattern (62 bp):
TTTATTATTGTTAATATTTAGTGTATTATTATTTATGTATATATATATGTATATATTTTTTA
Found at i:560164 original size:5 final size:5
Alignment explanation
Indices: 560154--560179 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
560144 TTTCTTCCTT
560154 GAGCC GAGCC GAGCC GAGCC GAGCC G
1 GAGCC GAGCC GAGCC GAGCC GAGCC G
560180 CTCCAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.42, T:0.00
Consensus pattern (5 bp):
GAGCC
Found at i:560245 original size:11 final size:10
Alignment explanation
Indices: 560242--560313 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
560232 TTATCTTATT
*
560242 TTTATTTTTT
1 TTTATTTTTA
* *
560252 TTTACTTTTC
1 TTTATTTTTA
560262 TTTAATTTTT-
1 TTT-ATTTTTA
*
560272 TTAATTTTTA
1 TTTATTTTTA
*
560282 TTTATTTTCA
1 TTTATTTTTA
*
560292 CTTTTTTTTTA
1 -TTTATTTTTA
560303 -TTA-TTTTA
1 TTTATTTTTA
560311 TTT
1 TTT
560314 TCTTTAAAGA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
8 5 0.10
9 10 0.20
10 21 0.43
11 13 0.27
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:560255 original size:10 final size:10
Alignment explanation
Indices: 560222--560289 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
560212 ATTTATTTAA
560222 TATTTTTTCTT
1 TATTTTTT-TT
*
560233 TATCTTATTTT
1 TAT-TTTTTTT
560244 TATTTTTTTT
1 TATTTTTTTT
* *
560254 TACTTTTCTT
1 TATTTTTTTT
*
560264 TAATTTTTTT
1 TATTTTTTTT
* *
560274 AATTTTTATT
1 TATTTTTTTT
560284 TATTTT
1 TATTTT
560290 CACTTTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
10 34 0.74
11 8 0.17
12 4 0.09
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:560280 original size:36 final size:35
Alignment explanation
Indices: 560232--560314 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 35
560222 TATTTTTTCT
* * *
560232 TTATCTTATTTTTATTTTTTTTTACTTTTCTTTAA
1 TTATTTTATTTTTATTTATTTTCACTTTTCTTTAA
* * *
560267 TTTTTTTAATTTTTATTTATTTTCACTTTTTTTTTA
1 TTATTTT-ATTTTTATTTATTTTCACTTTTCTTTAA
560303 TTATTTTATTTT
1 TTATTTTATTTT
560315 CTTTAAAGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 10 0.25
36 30 0.75
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (35 bp):
TTATTTTATTTTTATTTATTTTCACTTTTCTTTAA
Found at i:560296 original size:24 final size:25
Alignment explanation
Indices: 560269--560315 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
560259 TTCTTTAATT
560269 TTTTTAATTT-TTA-TTTATTTTCAC
1 TTTTT-ATTTATTATTTTATTTTCAC
*
560293 TTTTTTTTTATTATTTTATTTTC
1 TTTTTATTTATTATTTTATTTTC
560316 TTTAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 8 0.40
25 9 0.45
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTATTTATTATTTTATTTTCAC
Found at i:560551 original size:57 final size:57
Alignment explanation
Indices: 560331--560858 Score: 684
Period size: 57 Copynumber: 8.9 Consensus size: 57
560321 AGAAAAATCA
*
560331 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 AAATTTCC--AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* * *
560390 AAAATTTCAAAAAAGAGGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAAT
1 -AAATTTCCAAAAA-A-TATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
560450 CAAAATTTCAAAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 --AAATTTC---CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
560512 AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
560569 AAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
1 AAATTTC-CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAAT
560632 AAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTCC----AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
560693 AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
560750 AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT
1 AAATTTC--CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
*
560809 CGAAATTTCCAAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 --AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
560859 CTGCAAAAAA
Statistics
Matches: 423, Mismatches: 22, Indels: 48
0.86 0.04 0.10
Matches are distributed among these distances:
57 107 0.25
58 78 0.18
59 55 0.13
60 52 0.12
61 29 0.07
62 39 0.09
63 14 0.03
64 6 0.01
66 43 0.10
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (57 bp):
AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:560675 original size:181 final size:177
Alignment explanation
Indices: 560331--560858 Score: 795
Period size: 181 Copynumber: 3.0 Consensus size: 177
560321 AGAAAAATCA
* * *
560331 AAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATT
1 AAATTTCC--AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT-AAATT
** *
560396 TCAAAAAAGAGGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTG-GAAATCAAAATTT-
63 TCAAAAAA-AATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAAT--AAATTTC
*
560458 CAAAAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
124 CAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
560512 AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCA
1 AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCA
560577 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCAA
66 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT----GAAAAATAAATTTCCAA
560642 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
127 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
560693 AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCA
1 AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTC-
560758 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTG-AAAATCGAAATTTCC---
65 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAAT--AAATTTCCAAA
*
560819 -AAAAAATA-TTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
128 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
560859 CTGCAAAAAA
Statistics
Matches: 329, Mismatches: 8, Indels: 27
0.90 0.02 0.07
Matches are distributed among these distances:
174 31 0.09
175 8 0.02
177 40 0.12
178 15 0.05
179 54 0.16
180 6 0.02
181 126 0.38
182 49 0.15
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (177 bp):
AAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTCA
AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAATAAATTTCCAAAAAA
AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:561442 original size:18 final size:18
Alignment explanation
Indices: 561421--561455 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
561411 TTTTCTTGAA
561421 TTTTGAAAAAAAAATAAC
1 TTTTGAAAAAAAAATAAC
*
561439 TTTTGAAAATAAAATAA
1 TTTTGAAAAAAAAATAA
561456 GAGATCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
TTTTGAAAAAAAAATAAC
Found at i:561935 original size:104 final size:104
Alignment explanation
Indices: 561767--562072 Score: 320
Period size: 104 Copynumber: 2.9 Consensus size: 104
561757 CATTCGAAAG
* * * *
561767 TCTTACAAATCTCAACATCTTTAAATGCTTCTCGTAT-AAGAGGTATTGAAAA-TTTAAAATTTT
1 TCTTACAAATCTCTACATCTTTGAATGCTTCTCATATCAA-AGGTATT-AAAACTTTAAAAATTT
* *
561830 AAAATGTTTTGCTCAAAAGTCTTATAGATTATGTTCAG-AGA
64 AAAATGTTTTGCTCAAAAGTCTTAAAGATTATG-CCAGAAGA
* * * *
561871 TCTTACAACTCTCTATATCTTTGAATGCTCCTCATGTCAAAGGTATTAAAACTTTAAAAATTTAA
1 TCTTACAAATCTCTACATCTTTGAATGCTTCTCATATCAAAGGTATTAAAACTTTAAAAATTTAA
* * * *
561936 AATATTTTG-TCAAGATGTCTTAAAGATTATGCCTGAAGG
66 AATGTTTTGCTCAA-AAGTCTTAAAGATTATGCCAGAAGA
* * * *
561975 TCTTACAAATC-CTAACATCTTTGAATGCTTATCATATCAAAAGCATTGAAACTTTAAAAATTTA
1 TCTTACAAATCTCT-ACATCTTTGAATGCTTCTCATATCAAAGGTATTAAAACTTTAAAAATTTA
* *
562039 AAATAG-TTTGC-CTAAAAATCTTACAGATTATGCC
65 AAAT-GTTTTGCTC-AAAAGTCTTAAAGATTATGCC
562073 TGTCATAACA
Statistics
Matches: 168, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
103 12 0.07
104 152 0.90
105 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (104 bp):
TCTTACAAATCTCTACATCTTTGAATGCTTCTCATATCAAAGGTATTAAAACTTTAAAAATTTAA
AATGTTTTGCTCAAAAGTCTTAAAGATTATGCCAGAAGA
Found at i:562920 original size:18 final size:17
Alignment explanation
Indices: 562893--562926 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
562883 TGAATAAAAT
*
562893 AATAATTAAAATAATAAC
1 AATAAGTAAAA-AATAAC
562911 AATAAGTAAAAAATAA
1 AATAAGTAAAAAATAA
562927 ATAAAAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AATAAGTAAAAAATAAC
Found at i:562929 original size:21 final size:18
Alignment explanation
Indices: 562878--562941 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 18
562868 TTCAATTTTT
562878 AAAAATGAATAAAATAATA
1 AAAAAT-AATAAAATAATA
562897 ATTAAAATAATAACAATAAGTA
1 A--AAAATAATAA-AATAA-TA
*
562919 AAAAATAAATAAAAGAATA
1 AAAAAT-AATAAAATAATA
562938 AAAA
1 AAAA
562942 TCCAAAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 7 0.18
20 14 0.36
21 15 0.38
22 3 0.08
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (18 bp):
AAAAATAATAAAATAATA
Found at i:562948 original size:25 final size:25
Alignment explanation
Indices: 562920--562974 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
562910 CAATAAGTAA
*
562920 AAAAT-AAATA-AAAGAATAAAAATCC
1 AAAATAAAATAGAAAAAAT-AAAAT-C
562945 AAAATAAAATAGAAAAAATAAAATC
1 AAAATAAAATAGAAAAAATAAAATC
562970 AAAAT
1 AAAAT
562975 CAACAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 11 0.41
26 10 0.37
27 6 0.22
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAATAAAATAGAAAAAATAAAATC
Found at i:568075 original size:24 final size:25
Alignment explanation
Indices: 568032--568094 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 25
568022 AAATTTTTCC
568032 AAACCCTAAAATTCCAAAA-CTATG
1 AAACCCTAAAATTCCAAAACCTATG
*** *
568056 AAACCCTAAAATTTTGAAACCTTTG
1 AAACCCTAAAATTCCAAAACCTATG
*
568081 AAAACCTAAAATTC
1 AAACCCTAAAATTC
568095 TCTAAACCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 16 0.50
25 16 0.50
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (25 bp):
AAACCCTAAAATTCCAAAACCTATG
Found at i:568125 original size:24 final size:25
Alignment explanation
Indices: 568081--568140 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
568071 GAAACCTTTG
* *
568081 AAAACCT-AAAATTCTCTAAACCCT
1 AAAACCTCAAAAATCTCAAAACCCT
*
568105 AAAACCTCAAAAATCT-AAAACTCT
1 AAAACCTCAAAAATCTCAAAACCCT
*
568129 AAAAACTCAAAA
1 AAAACCTCAAAA
568141 CCCTTAAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (25 bp):
AAAACCTCAAAAATCTCAAAACCCT
Found at i:568149 original size:24 final size:24
Alignment explanation
Indices: 568097--568156 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
568087 TAAAATTCTC
* *
568097 TAAACCCTAAAACCTCAAAAATCT
1 TAAACCCTAAAAACTCAAAAACCT
* * *
568121 AAAACTCTAAAAACTCAAAACCCT
1 TAAACCCTAAAAACTCAAAAACCT
568145 TAAACCCCTAAA
1 TAAA-CCCTAAA
568157 GTTTGAAACC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (24 bp):
TAAACCCTAAAAACTCAAAAACCT
Found at i:569172 original size:21 final size:21
Alignment explanation
Indices: 569148--569202 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
569138 TCTTAAACCC
*
569148 AATTTTATTTTTATAGAC-CAA
1 AATTTT-TTTTTATAAACTCAA
*
569169 AATTATCTTTTTTATAAACTTAA
1 AATT-T-TTTTTTATAAACTCAA
569192 AATTTTTTTTT
1 AATTTTTTTTT
569203 GCTTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 10 0.34
22 12 0.41
23 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTTTTTTTTATAAACTCAA
Found at i:570259 original size:150 final size:147
Alignment explanation
Indices: 569940--570262 Score: 339
Period size: 150 Copynumber: 2.2 Consensus size: 147
569930 AAAAGCCATG
*
569940 TGTCTTTTTTTCTTTGCTTTTTCTTTTTTAGAAACATTTGACTTCAACTTTAACATTTTACTTTC
1 TGTCTTTTTTTCTTTTCTTTTTCTTTTTTAGAAACATTTGACTTCAACTTTAACATTTTACTTTC
* * * *
570005 TTAAATTTTATCATCTTTTTACTTGGGATTCTAGCTAATGCTTTATTCATTTTTTGTCCCAAACT
66 TTAAATTCTATCATCTTTTTACTTGAGATTCTAACTAATGCTTCATTCATTTTTTGTCCCAAACT
*
570070 CTCATATCTAAGGAGTA
131 CTCATATCTAAGGAGCA
* ** * * * * *
570087 TGCCTTCCTTTCTTTGTATTTTTCTTTTTTTTGGAAACATTTGACTTTAATTTTAGCATTTTACT
1 TGTCTTTTTTTCTTT-TCTTTTTC--TTTTTTAGAAACATTTGACTTCAACTTTAACATTTTACT
** * * **
570152 TTCTTGGATTCTATC-TTTTTTTTCTTGAGATTCTAACTGAA-GCTTCATTCATTTTTT-TCTTA
63 TTCTTAAATTCTATCATCTTTTTACTTGAGATTCTAACT-AATGCTTCATTCATTTTTTGTCCCA
* * * * *
570214 GACTCTCATCTTTGAGGTGCA
127 AACTCTCATATCTAAGGAGCA
570235 TGTCTTTTTTTCCTTATTCTTTTT-TTTT
1 TGTCTTTTTTT-CTT-TTCTTTTTCTTTT
570263 AACTTTTGAC
Statistics
Matches: 141, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
146 4 0.03
147 12 0.09
148 32 0.23
149 43 0.30
150 50 0.35
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.55
Consensus pattern (147 bp):
TGTCTTTTTTTCTTTTCTTTTTCTTTTTTAGAAACATTTGACTTCAACTTTAACATTTTACTTTC
TTAAATTCTATCATCTTTTTACTTGAGATTCTAACTAATGCTTCATTCATTTTTTGTCCCAAACT
CTCATATCTAAGGAGCA
Found at i:578250 original size:48 final size:48
Alignment explanation
Indices: 578196--578297 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 48
578186 AAAAAACAAA
*
578196 AAAAAAAAGAGAATTTCTAAATAGACCCAAATGGTGAAAAATTTAGAAAT
1 AAAAAAAA-A-AATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAAT
* *
578246 AAAAAAAAAAATTTCTAAATTGGCCCAAATAGTGAAAAATTTAGAAAT
1 AAAAAAAAAAATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAAT
578294 AAAA
1 AAAA
578298 CTTGTAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
48 40 0.82
49 1 0.02
50 8 0.16
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (48 bp):
AAAAAAAAAAATTTCTAAATAGACCCAAATAGTGAAAAATTTAGAAAT
Found at i:589548 original size:33 final size:30
Alignment explanation
Indices: 589511--589580 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
589501 ATAAAATATT
589511 ATAATTAAATATTATATCTATATAATCAATAAA
1 ATAATTAAATATTATAT-TAT-TAAT-AATAAA
* * *
589544 ATAATCAATTATTATATTATTAATAATTAA
1 ATAATTAAATATTATATTATTAATAATAAA
*
589574 TTAATTA
1 ATAATTA
589581 TAATTTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 10 0.31
31 4 0.12
32 3 0.09
33 15 0.47
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (30 bp):
ATAATTAAATATTATATTATTAATAATAAA
Found at i:589580 original size:15 final size:16
Alignment explanation
Indices: 589562--589595 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
589552 TTATTATATT
589562 ATTAATAA-TTAATTA
1 ATTAATAATTTAATTA
589577 ATT-ATAATTTAATTA
1 ATTAATAATTTAATTA
589592 ATTA
1 ATTA
589596 TTCAAATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATAATTTAATTA
Found at i:590330 original size:31 final size:31
Alignment explanation
Indices: 590273--590335 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
590263 ATATTATAAT
*
590273 TTATATAGTTATATTATATTTTATATAAAAA
1 TTATATAGTTATATTATATTTAATATAAAAA
590304 TTATATA-TTATCATT-TATATTAATATAAAAA
1 TTATATAGTTAT-ATTATAT-TTAATATAAAAA
590335 T
1 T
590336 ATAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (31 bp):
TTATATAGTTATATTATATTTAATATAAAAA
Found at i:590984 original size:2 final size:2
Alignment explanation
Indices: 590946--590970 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
590936 CAATCTCTAA
590946 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 A
590971 ATTTTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:594889 original size:14 final size:14
Alignment explanation
Indices: 594849--594895 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
594839 TATAGAAACA
594849 ATAT-TAAACATAT
1 ATATATAAACATAT
** * *
594862 ATGCATATATATAT
1 ATATATAAACATAT
594876 ATATATAAACATAT
1 ATATATAAACATAT
594890 ATATAT
1 ATATAT
594896 TGCAAAAACA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
13 2 0.08
14 23 0.92
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (14 bp):
ATATATAAACATAT
Found at i:595280 original size:14 final size:14
Alignment explanation
Indices: 595263--595298 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
595253 AACAAAAAAA
595263 AAAAAGAATGAAAT
1 AAAAAGAATGAAAT
595277 AAAAAGAA--AAAT
1 AAAAAGAATGAAAT
595289 AAAAA-AATGA
1 AAAAAGAATGA
595299 GTAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.10
12 9 0.45
13 1 0.05
14 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (14 bp):
AAAAAGAATGAAAT
Found at i:596145 original size:56 final size:56
Alignment explanation
Indices: 596038--596150 Score: 140
Period size: 56 Copynumber: 2.0 Consensus size: 56
596028 AAATTAAAAA
* * * *
596038 TATTTTTTTTAATTTCTAAATTTTTCACCATTTGGACCTATTTAGAGATTTTTTTT
1 TATTTTTTTTAATCTCTAAATTTTTCACCATTTGGACCAATATAGAAATTTTTTTT
* *
596094 TATTTTTTTTTATCTCTAAA-TTTTCTACCATTTTGG-TCAATATAGAAATTTTTTTT
1 TATTTTTTTTAATCTCTAAATTTTTC-ACCA-TTTGGACCAATATAGAAATTTTTTTT
596150 T
1 T
596151 CGAAATTTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
55 5 0.10
56 39 0.80
57 5 0.10
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.59
Consensus pattern (56 bp):
TATTTTTTTTAATCTCTAAATTTTTCACCATTTGGACCAATATAGAAATTTTTTTT
Found at i:596206 original size:106 final size:104
Alignment explanation
Indices: 596015--596208 Score: 225
Period size: 106 Copynumber: 1.8 Consensus size: 104
596005 CTAATTATTA
596015 TACCATTTAGGTCAAATTAAAAATATTTTTTTTAATTTCTAAATTTTTCACCATTTGGACCTATT
1 TACCATTTAGGTCAAATTAAAAATATTTTTTTTAATTTCTAAATTTTTCACCATTTGGACCTATT
* * ** *
596080 TAGAGATTTTTTTTTATTTTTTTTTATCTCTAAATTTTC
66 TAAAAAAATTTTATTATTTTTTTTTATCTCTAAATTTTC
* * * *
596119 TACCATTTTGGTC-AATATAGAAAT-TTTTTTTTCGAAATTTCTAAATTTTTCATCATTTTGG-T
1 TACCATTTAGGTCAAAT-TAAAAATATTTTTTTT---AATTTCTAAATTTTTCACCA-TTTGGAC
596181 CTATTTAAAAAAAATTTTATT-TTTTTTT
61 CTATTT-AAAAAAATTTTATTATTTTTTT
596209 AAAAGAAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
103 11 0.15
104 18 0.24
106 32 0.43
107 14 0.19
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (104 bp):
TACCATTTAGGTCAAATTAAAAATATTTTTTTTAATTTCTAAATTTTTCACCATTTGGACCTATT
TAAAAAAATTTTATTATTTTTTTTTATCTCTAAATTTTC
Found at i:597229 original size:21 final size:21
Alignment explanation
Indices: 597205--597259 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
597195 TTTCTAATTA
597205 TTTTCTGCTTGTGAT-TTTTTT
1 TTTTCTGCTTGTG-TGTTTTTT
* *
597226 TTTTCTGTTTTTGTGTTTTTT
1 TTTTCTGCTTGTGTGTTTTTT
*
597247 TTGTCT-CTTGTGT
1 TTTTCTGCTTGTGT
597260 TCATACCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.02, C:0.09, G:0.16, T:0.73
Consensus pattern (21 bp):
TTTTCTGCTTGTGTGTTTTTT
Found at i:597244 original size:18 final size:18
Alignment explanation
Indices: 597223--597260 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
597213 TTGTGATTTT
*
597223 TTTTTTTCTGT-TTTTGTG
1 TTTTTTT-TGTCTCTTGTG
597241 TTTTTTTTGTCTCTTGTG
1 TTTTTTTTGTCTCTTGTG
597259 TT
1 TT
597261 CATACCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (18 bp):
TTTTTTTTGTCTCTTGTG
Found at i:597725 original size:11 final size:10
Alignment explanation
Indices: 597697--597755 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 10
597687 CTTCTCTTAC
597697 TTTTATTTTT
1 TTTTATTTTT
*
597707 TTGTT-TTTCT
1 TT-TTATTTTT
597717 TTTTATTTTGT
1 TTTTATTTT-T
597728 TTTTATTTTTT
1 TTTTA-TTTTT
597739 TTTTCATTTTT
1 TTTT-ATTTTT
597750 TGTTTA
1 T-TTTA
597756 AAATTAAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 2 0.05
10 11 0.27
11 20 0.49
12 8 0.20
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.83
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:597742 original size:17 final size:17
Alignment explanation
Indices: 597702--597742 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
597692 CTTACTTTTA
*
597702 TTTTTTTGTTTTTCTTT
1 TTTTTTTGTTTTTATTT
*
597719 TTATTTTGTTTTTATTT
1 TTTTTTTGTTTTTATTT
597736 TTTTTTT
1 TTTTTTT
597743 CATTTTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.05, C:0.02, G:0.05, T:0.88
Consensus pattern (17 bp):
TTTTTTTGTTTTTATTT
Found at i:597750 original size:12 final size:11
Alignment explanation
Indices: 597702--597755 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
597692 CTTACTTTTA
*
597702 TTTTTTTGTTT
1 TTTTTTTATTT
597713 TTCTTTTTATTT
1 TT-TTTTTATTT
*
597725 TGTTTTTATTT
1 TTTTTTTATTT
597736 TTTTTTTCATTT
1 TTTTTTT-ATTT
*
597748 TTTGTTTA
1 TTTTTTTA
597756 AAATTAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.07, C:0.04, G:0.06, T:0.83
Consensus pattern (11 bp):
TTTTTTTATTT
Done.