Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold629
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: 578285
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 5
Found at i:419735 original size:44 final size:43
Alignment explanation
Indices: 419683--419926 Score: 235
Period size: 44 Copynumber: 5.6 Consensus size: 43
419673 GAGAGAGGCA
**
419683 AATTTGACTAAAGTGGTAACCATACGTCAAATCAGAATGAAAAG
1 AATTTGACTAGGGTGGTAACCATACGTCAAATCAGAA-GAAAAG
* * * *
419727 AATCTGACTAGGGTGGTAACCATA-GCCAGA-CA-AAAAAAAGG
1 AATTTGACTAGGGTGGTAACCATACGTCAAATCAGAAGAAAA-G
** * *
419768 CAGATTTGACTAGGGCAGTAACCATATGTCAAATCGAAAAGAAAAG
1 -A-ATTTGACTAGGGTGGTAACCATACGTCAAATC-AGAAGAAAAG
* * * * *
419814 AATCTGACTAGGGTGGTAACCATATGTCAGA-CAGGAGAAAGG
1 AATTTGACTAGGGTGGTAACCATACGTCAAATCAGAAGAAAAG
419856 TAGATTTGACTAGGGTGGTAACCATACGTCAAATCAGAATGAAAAG
1 -A-ATTTGACTAGGGTGGTAACCATACGTCAAATCAGAA-GAAAAG
* *
419902 AATTTGACTAAGTTGGTAACCATAC
1 AATTTGACTAGGGTGGTAACCATAC
419927 ATCAGATAAG
Statistics
Matches: 163, Mismatches: 26, Indels: 22
0.77 0.12 0.10
Matches are distributed among these distances:
40 4 0.02
41 3 0.02
42 10 0.06
43 26 0.16
44 100 0.61
45 7 0.04
46 7 0.04
47 6 0.04
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (43 bp):
AATTTGACTAGGGTGGTAACCATACGTCAAATCAGAAGAAAAG
Found at i:419887 original size:88 final size:88
Alignment explanation
Indices: 419654--419925 Score: 368
Period size: 88 Copynumber: 3.1 Consensus size: 88
419644 CGTTACGACA
* * * **
419654 GTAACCATATGTCAGACATGAGAGAGGCAAATTTGACTAAAGTGGTAACCATACGTCAAATCAGA
1 GTAACCATATGTCAGACAAGAGAAAGGCAGATTTGACTAGGGTGGTAACCATACGTCAAATCAGA
419719 ATGAAAAGAATCTGACTAGGGTG
66 ATGAAAAGAATCTGACTAGGGTG
* * * ** *
419742 GTAACCATA-GCCAGACAAAAAAAAGGCAGATTTGACTAGGGCAGTAACCATATGTCAAATC-GA
1 GTAACCATATGTCAGACAAGAGAAAGGCAGATTTGACTAGGGTGGTAACCATACGTCAAATCAG-
*
419805 AAAGAAAAGAATCTGACTAGGGTG
65 AATGAAAAGAATCTGACTAGGGTG
* *
419829 GTAACCATATGTCAGACAGGAGAAAGGTAGATTTGACTAGGGTGGTAACCATACGTCAAATCAGA
1 GTAACCATATGTCAGACAAGAGAAAGGCAGATTTGACTAGGGTGGTAACCATACGTCAAATCAGA
* * *
419894 ATGAAAAGAATTTGACTAAGTTG
66 ATGAAAAGAATCTGACTAGGGTG
419917 GTAACCATA
1 GTAACCATA
419926 CATCAGATAA
Statistics
Matches: 157, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
86 1 0.01
87 73 0.46
88 82 0.52
89 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (88 bp):
GTAACCATATGTCAGACAAGAGAAAGGCAGATTTGACTAGGGTGGTAACCATACGTCAAATCAGA
ATGAAAAGAATCTGACTAGGGTG
Found at i:420000 original size:48 final size:47
Alignment explanation
Indices: 419944--420196 Score: 267
Period size: 48 Copynumber: 5.3 Consensus size: 47
419934 AAGAAAGAGG
*
419944 AGAGTTTGACCAGGCCTTAACACCAATACAGTCAAATGAGGGATGAAA
1 AGAGTTTGACCAGGCC-TAACACCAATACAGTCAAATAAGGGATGAAA
* * * * * * *
419992 AGAGTTTGACTAGATCTTAACACAAATATAGTCAAACAAAGGATGAAA
1 AGAGTTTGACCAG-GCCTAACACCAATACAGTCAAATAAGGGATGAAA
* * *
420040 AGAGTTTGACTAGGCCCTAACACCAATACATTCAAACAAAGGG-TGAAA
1 AGAGTTTGACCAGG-CCTAACACCAATACAGTCAAA-TAAGGGATGAAA
* *
420088 AGAGTTTGACCAGGGCCTAACACCAATACAGTCAAATGAGAGATGAAA
1 AGAGTTTGACCA-GGCCTAACACCAATACAGTCAAATAAGGGATGAAA
* ** * *
420136 ATAGTTTGACCAGGTCCTAAGGCCAATATAGTCAAAT-AGAGAATGAAA
1 AGAGTTTGACCAGG-CCTAACACCAATACAGTCAAATAAG-GGATGAAA
420184 AGAGTTTGACCAG
1 AGAGTTTGACCAG
420197 ATACAATCAA
Statistics
Matches: 171, Mismatches: 27, Indels: 14
0.81 0.13 0.07
Matches are distributed among these distances:
47 7 0.04
48 157 0.92
49 7 0.04
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (47 bp):
AGAGTTTGACCAGGCCTAACACCAATACAGTCAAATAAGGGATGAAA
Found at i:421801 original size:28 final size:28
Alignment explanation
Indices: 421761--421832 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
421751 AAAAAAAAAT
* ** *
421761 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
421789 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
421817 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
421833 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:421883 original size:52 final size:50
Alignment explanation
Indices: 421820--422157 Score: 166
Period size: 52 Copynumber: 6.4 Consensus size: 50
421810 GAAATAACGA
* * * *
421820 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACCG
** * *
421871 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCG
1 G-GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACCG
* * * **
421923 GGATTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGG
1 GG-TTGGAGTATCCCCGATTGT-GAAAAATTGGAGTTTTGA-AAATAAAACC-G
* * ** ** * *
421976 GGTTAGAGTATCCCC--TCG-GAAATAACAGGGTTGGAGTATCCCCGATGAT-TAACGG
1 GGTTGGAGTATCCCCGATTGTG-AA-AA-A---TTGGAGT-T--TTGAAAATAAAACCG
* * *
422031 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGGAG--TTTTGAAAATAAAACCG
* * * * *
422084 GAGTTAGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCG
1 G-GTTGGAGTATCCCCGATTGTGA-AAAATTGGAGTTTTGAAAATAAAACCG
*
422135 GAGTTGGAATATCCCCGATTGTG
1 G-GTTGGAGTATCCCCGATTGTG
422158 GAGAATTGAG
Statistics
Matches: 219, Mismatches: 43, Indels: 49
0.70 0.14 0.16
Matches are distributed among these distances:
48 1 0.00
49 2 0.01
50 4 0.02
51 39 0.18
52 86 0.39
53 30 0.14
54 25 0.11
55 17 0.08
56 4 0.02
57 9 0.04
58 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACCG
Found at i:422015 original size:28 final size:27
Alignment explanation
Indices: 421975--422047 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
421965 GATAAAACCG
* **
421975 GGGTTAGAGTATCCCCTCGGAAATAACA
1 GGGTTGGAGTATCCCCGAGG-AATAACA
* * *
422003 GGGTTGGAGTATCCCCGATGATTAACG
1 GGGTTGGAGTATCCCCGAGGAATAACA
422030 GGGTTGGAGTATCCCCGA
1 GGGTTGGAGTATCCCCGA
422048 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAATAACA
Found at i:422062 original size:212 final size:212
Alignment explanation
Indices: 421769--422159 Score: 617
Period size: 212 Copynumber: 1.8 Consensus size: 212
421759 ATCGGGATTG
* * *
421769 GAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCT
1 GAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCC
*
421834 CGATTGTGAAAAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAA
66 CGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAA-GAA
* *
421898 AATTGGCGTTTTGAAAATAAAACCGG-GATTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT
130 AATTAGCGTTTTGAAAATAAAACCGGAG-TTAGAATATCCCCGATTGTGGAAAAATTAGTGTTTT
421962 AGCGATAAAACCGGGGTTA
194 AGCGATAAAACCGGGGTTA
* *
421981 GAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCC
1 GAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCC
* *
422045 CGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAA
66 CGATTGTGAA-AAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGAA
* * *
422110 AATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
130 AATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGA
422160 GAATTGAGAA
Statistics
Matches: 163, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 29 0.18
212 94 0.58
213 40 0.25
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
GAGTATCCCCTCGGAAATAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCC
CGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGAAA
ATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAG
CGATAAAACCGGGGTTA
Found at i:422132 original size:51 final size:53
Alignment explanation
Indices: 422036--422154 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
422026 AACGGGGTTG
* * *
422036 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
422090 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
422141 GAATATCCCCGATT
1 GAGTATCCCCGATT
422155 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:424490 original size:13 final size:13
Alignment explanation
Indices: 424472--424497 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
424462 ACAAAGATCC
424472 ATGTATCGATACA
1 ATGTATCGATACA
424485 ATGTATCGATACA
1 ATGTATCGATACA
424498 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:424493 original size:33 final size:33
Alignment explanation
Indices: 424451--424517 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
424441 AAAATTTCCA
***
424451 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
424484 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
424517 A
1 A
424518 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:424561 original size:19 final size:18
Alignment explanation
Indices: 424537--424604 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
424527 CAGTAGCTAA
424537 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
424556 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
424571 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
424588 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
424605 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:424577 original size:13 final size:13
Alignment explanation
Indices: 424559--424583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
424549 ACAATACTTA
424559 TGTATCGATACAT
1 TGTATCGATACAT
424572 TGTATCGATACA
1 TGTATCGATACA
424584 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:424581 original size:32 final size:32
Alignment explanation
Indices: 424540--424602 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
424530 TAGCTAATTA
*
424540 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
424572 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
424603 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:424684 original size:21 final size:21
Alignment explanation
Indices: 424660--424716 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
424650 CATTTGTAGG
424660 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
424681 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
424702 ATGTATCGATACATT
1 ATGTATCGATACATT
424717 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:428408 original size:43 final size:43
Alignment explanation
Indices: 428344--428446 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
428334 GATACAATTC
428344 TTCATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGT
1 TTCATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGT
*
428387 TTCATGTATCGATACAGACAGTGGTAGGGTAGCTACTGCCAGT
1 TTCATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGT
428430 TTCATGTATCGATACAA
1 TTCATGTATCGATACAA
428447 TTATGCATGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (43 bp):
TTCATGTATCGATACAAACAGTGGTAGGGTAGCTACTGCCAGT
Found at i:428476 original size:19 final size:19
Alignment explanation
Indices: 428431--428487 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
428421 ACTGCCAGTT
*
428431 TCATGTATCGATACAATTA
1 TCATGTATCGATACAATGA
428450 TGCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
428470 TCATGTAT-GCATACAATG
1 TCATGTATCG-ATACAATG
428488 TATCGATACA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 1 0.03
19 16 0.46
20 18 0.51
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:429566 original size:19 final size:19
Alignment explanation
Indices: 429527--429629 Score: 146
Period size: 19 Copynumber: 5.7 Consensus size: 19
429517 TTTCAACGAT
429527 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
429547 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
429566 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
429585 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
429599 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
429617 TTGTATCGATACA
1 TTGTATCGATACA
429630 ATGTAAGCTA
Statistics
Matches: 77, Mismatches: 0, Indels: 13
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.14
15 2 0.03
17 2 0.03
19 48 0.62
20 14 0.18
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:429604 original size:13 final size:13
Alignment explanation
Indices: 429586--429610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
429576 ACATAAGTGT
429586 TGTATCGATACAA
1 TGTATCGATACAA
429599 TGTATCGATACA
1 TGTATCGATACA
429611 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:429608 original size:32 final size:32
Alignment explanation
Indices: 429528--429634 Score: 142
Period size: 32 Copynumber: 3.1 Consensus size: 32
429518 TTCAACGATT
429528 TGTATCGATACATAAAGTGTTGTATCGATACATAA
1 TGTATCGATACAT-AAGTGTTGTATCGATAC--AA
429563 GTGTTGTATCGATACATAAGTGTTGTATCGATACAA
1 ----TGTATCGATACATAAGTGTTGTATCGATACAA
*
429599 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
429631 TGTA
1 TGTA
429635 AGCTACTGCA
Statistics
Matches: 67, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
32 35 0.52
36 2 0.03
38 17 0.25
39 13 0.19
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:429690 original size:13 final size:13
Alignment explanation
Indices: 429672--429696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
429662 ATTACTCAAA
429672 TGTATCGATACAT
1 TGTATCGATACAT
429685 TGTATCGATACA
1 TGTATCGATACA
429697 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:429749 original size:52 final size:52
Alignment explanation
Indices: 429705--429833 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
429695 CACTGATCTT
429705 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
429757 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
429809 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
429834 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:440794 original size:13 final size:13
Alignment explanation
Indices: 440776--440800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
440766 CAATTCTTCA
440776 TGTATCGATACAT
1 TGTATCGATACAT
440789 TGTATCGATACA
1 TGTATCGATACA
440801 ATGTGCCATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:440798 original size:33 final size:33
Alignment explanation
Indices: 440756--440818 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
440746 CTTGAGTCAA
440756 TGTATCGATACAAT-T-CTTCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
440789 TGTATCGATACAATGTGCCATGTATCGATA
1 TGTATCGATACAATGTGCCATGTATCGATA
440819 TAAACAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:440911 original size:28 final size:28
Alignment explanation
Indices: 440878--440936 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
440868 TGCATGTAAA
440878 AGACAAGTTATATACAAAACAGGTTCAG
1 AGACAAGTTATATACAAAACAGGTTCAG
440906 AGACAAGTTATATACAAAACAGGTTCAG
1 AGACAAGTTATATACAAAACAGGTTCAG
440934 AGA
1 AGA
440937 TGAAGACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (28 bp):
AGACAAGTTATATACAAAACAGGTTCAG
Found at i:443607 original size:155 final size:156
Alignment explanation
Indices: 443294--443820 Score: 405
Period size: 156 Copynumber: 3.4 Consensus size: 156
443284 AAAAATTATG
* * *
443294 AAAATGCCCTTAGGAGATAACTTCGATGCAAAAGTACTTGATACCCCTAAAGGACTTAAAAAGGA
1 AAAATGCCCTTAGGAGATAACTTCGACGTAAAAGTACCTGATACCCCTAAAGGACTTAAAAAGGA
* *
443359 TTATAGATGAGACAAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAACCCAGTGACAACA
66 TTAAAAATGAGACAAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAACCCAGTGACAACA
*
443424 TAGGACTCAGTTCTTAAAAATTT-CC
131 TAGGACTCAGTTCTTAAAAATTTACA
* * * * *
443449 AAAATGCCCTTAAGG-GATATCTTCGACGTAAAAGTGCCTGATATCCTTAAAGGACTTAAGAAGG
1 AAAATGCCCTT-AGGAGATAACTTCGACGTAAAAGTACCTGATACCCCTAAAGGACTTAAAAAGG
* ** * * ** * **
443513 ATTACAAAATGGGATGAACCTA-CCTAAATACCCTCCATT-GGCATTTAAAGTGGACCTGGTGAC
65 ATTA-AAAATGAGACAAACCTATCCTAAATACCCACC-TTCGGCA-TAAAAACGAACCCAGTGAC
* ** *
443576 AACTTAGGACTTGGTTC-TAGACAA-TTACA
127 AACATAGGACTCAGTTCTTA-AAAATTTACA
* * * ** * *
443605 AAAATGCCCTTAGGAGATACCTTTGACATAAAAGTACCTGGCACCTCTAAAAGACTTAAAAAGGC
1 AAAATGCCCTTAGGAGATAACTTCGACGTAAAAGTACCTGATACCCCTAAAGGACTTAAAAAGG-
* * * * ** * * ** *
443670 CA-TAGAAA-G-GATAAAACTATCCTAAATACCCACTTTCAACGT-GAAA-GTAGACCTGGTGAT
65 -ATTAAAAATGAGACAAACCTATCCTAAATACCCACCTTCGGCATAAAAACG-A-ACCCAGTGAC
* * *
443730 AACCTAAGACTCAATT-TTAAGAAA-TTACA
127 AACATAGGACTCAGTTCTTAA-AAATTTACA
* * * * **
443759 AAAATACCCTTAGGGGATACCTTCGACGTAAAAGTACCCGATATACCTAAAGGACTTAAAAA
1 AAAATGCCCTTAGGAGATAACTTCGACGTAAAAGTACCTGATACCCCTAAAGGACTTAAAAA
443821 AATTTGGATG
Statistics
Matches: 292, Mismatches: 65, Indels: 31
0.75 0.17 0.08
Matches are distributed among these distances:
152 1 0.00
153 3 0.01
154 91 0.31
155 94 0.32
156 100 0.34
157 2 0.01
158 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (156 bp):
AAAATGCCCTTAGGAGATAACTTCGACGTAAAAGTACCTGATACCCCTAAAGGACTTAAAAAGGA
TTAAAAATGAGACAAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAACCCAGTGACAACA
TAGGACTCAGTTCTTAAAAATTTACA
Found at i:444399 original size:167 final size:164
Alignment explanation
Indices: 444093--444509 Score: 525
Period size: 167 Copynumber: 2.5 Consensus size: 164
444083 TGGAATTTTG
* * * *
444093 AAAAGATACG-AAATTTTTTGAAATCTTTTATATCCCTACAGACCTTCATAGGAATATAAAAGAT
1 AAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACGGACCCTCATAGGAATATAAAAGA-
* * *** * *
444157 TTAAAAAGAAGGATTCAAAATTTATCTTGGTTATGAAAGTGTTGATTTAATATAATTTTATTTGT
65 TT-AAAA-AATGATT-AATATTTATCTCAATTATGAAAGTGTTAATTTAATATAATTTTATTTAT
444222 TATCAAAAAATACCATTTCGTACCTTAATGGAAACCCA
127 TATCAAAAAATACCATTTCGTACCTTAATGGAAACCCA
* * *
444260 AAAAGATATGAAAAGTTTTTGAAATCTTTTATACCCCTGCGGACCCTCATAGGAATATAAAATAT
1 AAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACGGACCCTCATAGGAATATAAAAGAT
* *
444325 TAAAAAATGATTAATATTTAT-TACAATTATGAAAGTGTTAATTTAATTTTA-TTTATTTATTCA
66 TAAAAAATGATTAATATTTATCT-CAATTATGAAAGTGTTAATTTAATATAATTTTATTTATT-A
* * * *
444388 TTTTTAAAAAATACCATTTTGTACCTTAATGGAAGCCCG
129 ---TCAAAAAATACCATTTCGTACCTTAATGGAAACCCA
*
444427 AAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACGGACCCCCATAGGAATATAAAAGAT
1 AAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACGGACCCTCATAGGAATATAAAAGAT
* *
444492 TGAATAATGATTAATATT
66 TAAAAAATGATTAATATT
444510 AAATTTTACC
Statistics
Matches: 218, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
163 10 0.05
164 31 0.14
165 6 0.03
166 4 0.02
167 120 0.55
168 47 0.22
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (164 bp):
AAAAGATACGAAAAGTTTTTGAAATCTTTTATACCCCTACGGACCCTCATAGGAATATAAAAGAT
TAAAAAATGATTAATATTTATCTCAATTATGAAAGTGTTAATTTAATATAATTTTATTTATTATC
AAAAAATACCATTTCGTACCTTAATGGAAACCCA
Found at i:447010 original size:10 final size:11
Alignment explanation
Indices: 446988--447016 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
446978 GAAGTTTTTA
446988 TGAAAAATGTT
1 TGAAAAATGTT
446999 TGAAAAAT-TT
1 TGAAAAATGTT
447009 TGAAAAAT
1 TGAAAAAT
447017 CATCTATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (11 bp):
TGAAAAATGTT
Found at i:448822 original size:45 final size:45
Alignment explanation
Indices: 448773--448860 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
448763 AAGGCCAGCT
*
448773 ACATTGGGCCAATAAAGGTGCTAATATGATGATTCAATGCCAGTG
1 ACATTAGGCCAATAAAGGTGCTAATATGATGATTCAATGCCAGTG
448818 ACATTAGGCCAATAAAGGTGCTAATATGATGATTCAATGCCAG
1 ACATTAGGCCAATAAAGGTGCTAATATGATGATTCAATGCCAG
448861 CGATATCGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (45 bp):
ACATTAGGCCAATAAAGGTGCTAATATGATGATTCAATGCCAGTG
Found at i:449031 original size:28 final size:28
Alignment explanation
Indices: 448986--449544 Score: 600
Period size: 28 Copynumber: 19.6 Consensus size: 28
448976 GTTGCCACCA
*
448986 ACTTGTGTGAGCTTTGAAAGGGTGCCACCG
1 ACTTGTG-G-GCTTTGAAAGGGTGCCACTG
* *
449016 ACTTGTGGGCTTTGAAAAGGTATGCCACCG
1 ACTTGTGGGCTTTG-AAAGG-GTGCCACTG
*
449046 ACTTGTGGGCTTTGAAAGGGTATGCCACCG
1 ACTTGTGGGCTTTGAAAGGG--TGCCACTG
*
449076 ACTTGTGGGCTTTGAAAAGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
449104 ACTTGTGGGCTTTGAAAAGGTGCCACCG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
*
449132 ACTTGTGGGCTTTGAAAGGGTATGCCACTA
1 ACTTGTGGGCTTTGAAAGGG--TGCCACTG
*
449162 ACTTGTAGGCTTTGGAAA-GGTGCCACTG
1 ACTTGTGGGCTTT-GAAAGGGTGCCACTG
* *
449190 ACTTGTGGGCTTTGAAGGGGTACCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* * *
449218 ACTTGTGGGATTTGAAAAGGTGCCACTA
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
449246 ACTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
449274 ACTTGTAGGCTTTGGAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* * *
449302 ATTTGTGTGGGCTTTGAAAGGATACCACTG
1 A-CT-TGTGGGCTTTGAAAGGGTGCCACTG
* * *
449332 ACTTGTGGTCTTTTG-AAGAGATGCCACTA
1 ACTTGTGGGC-TTTGAAAG-GGTGCCACTG
* * * *
449361 ACTTATGGGCTTTGAAAAGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
449389 ACTTGTGGGCTTTGAAAGTGTGTCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* * *
449417 ACTTGTAGGCTTTGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* * **
449445 ATTTGTGGGCTTTGAAAAGACGCCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* ***
449473 ACCTGTGGGCTTTGAAAAAATGCCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
449501 ACTTGTGGGCTTTGAAAGGATGTCACTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACTG
* *
449529 ACCTATGGGCTTTGAA
1 ACTTGTGGGCTTTGAA
449545 GAGATAAACG
Statistics
Matches: 457, Mismatches: 59, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.01
28 317 0.69
29 35 0.08
30 98 0.21
31 4 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAAGGGTGCCACTG
Found at i:450811 original size:13 final size:12
Alignment explanation
Indices: 450793--450846 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
450783 TCTAGGACCC
*
450793 TTTTTTGTTTGT
1 TTTTTTTTTTGT
450805 TTTTTTTTTCTGT
1 TTTTTTTTT-TGT
450818 TTTTTTTTTAT-T
1 TTTTTTTTT-TGT
*
450830 TTTTTTGTTTTCT
1 TTTTTT-TTTTGT
450843 TTTT
1 TTTT
450847 GTACGAAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
12 16 0.43
13 21 0.57
ACGTcount: A:0.02, C:0.04, G:0.07, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTTGT
Found at i:450833 original size:20 final size:20
Alignment explanation
Indices: 450804--450846 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
450794 TTTTTGTTTG
450804 TTTTTTTTTTCTGTTTT-TT
1 TTTTTTTTTTCTGTTTTCTT
*
450823 TTTTATTTTTTTTGTTTTCTT
1 TTTT-TTTTTTCTGTTTTCTT
450844 TTT
1 TTT
450847 GTACGAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.02, C:0.05, G:0.05, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTCTGTTTTCTT
Found at i:450845 original size:11 final size:10
Alignment explanation
Indices: 450806--450848 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
450796 TTTGTTTGTT
450806 TTTTTTTTCTG
1 TTTTTTTT-TG
450817 TTTTTTTTT-
1 TTTTTTTTTG
450826 TATTTTTTTTG
1 T-TTTTTTTTG
450837 TTTTCTTTTTG
1 TTTT-TTTTTG
450848 T
1 T
450849 ACGAAGGACG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 1 0.03
10 12 0.41
11 16 0.55
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:454247 original size:13 final size:13
Alignment explanation
Indices: 454229--454254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
454219 CAATTTTTTG
454229 TGTATCGATACAT
1 TGTATCGATACAT
454242 TGTATCGATACAT
1 TGTATCGATACAT
454255 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:454340 original size:20 final size:20
Alignment explanation
Indices: 454315--454387 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
454305 ATCTTTTTTT
454315 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
454335 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
454356 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
454376 ATGTATCGATAC
1 ATGTATCGATAC
454388 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:454366 original size:41 final size:42
Alignment explanation
Indices: 454293--454387 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
454283 CTGCCAAGAA
*
454293 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
454335 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
454376 ATGTATCGATAC
1 ATGTATCGATAC
454388 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:455025 original size:16 final size:16
Alignment explanation
Indices: 454994--455039 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
454984 CTCTCCTTTG
454994 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
455012 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
455028 TCTCCCCCTTAA
1 TCTCCCCCTTAA
455040 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:456863 original size:13 final size:13
Alignment explanation
Indices: 456845--456883 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
456835 ATAATCACCC
*
456845 TGTATCGATACAG
1 TGTATCGATACAA
456858 TGTATCGATACAA
1 TGTATCGATACAA
456871 TGTATCGATACAA
1 TGTATCGATACAA
456884 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:456894 original size:20 final size:20
Alignment explanation
Indices: 456869--456947 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
456859 GTATCGATAC
456869 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
456889 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
456914 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
456933 ACATGTATCGATACA
1 A-ATGTATCGATACA
456948 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:459001 original size:15 final size:15
Alignment explanation
Indices: 458965--459002 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
458955 TACATCAATT
* *
458965 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
458980 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
458995 TCATTTTG
1 TCATTTTG
459003 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:463082 original size:13 final size:13
Alignment explanation
Indices: 463064--463089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
463054 CAATTTTTTG
463064 TGTATCGATACAT
1 TGTATCGATACAT
463077 TGTATCGATACAT
1 TGTATCGATACAT
463090 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:463175 original size:20 final size:20
Alignment explanation
Indices: 463150--463222 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
463140 ATCTTTTTTT
463150 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
463170 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
463191 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
463211 ATGTATCGATAC
1 ATGTATCGATAC
463223 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:463201 original size:41 final size:42
Alignment explanation
Indices: 463128--463222 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
463118 CTGCCAAGAA
*
463128 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
463170 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
463211 ATGTATCGATAC
1 ATGTATCGATAC
463223 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:474281 original size:52 final size:52
Alignment explanation
Indices: 474084--474264 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
474074 CAAAATATGA
* * *
474084 AAATTCGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
474136 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
474188 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
474240 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
474265 AAGATCAGTG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:474364 original size:19 final size:18
Alignment explanation
Indices: 474340--474437 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
474330 TAGCTTACAT
474340 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
474359 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
474372 TGTATCGAAACAACACTTA
1 TGTATCGATACAA-ACTTA
474391 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
474404 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
474424 TGTATCGATACAAA
1 TGTATCGATACAAA
474438 TCGTTGAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.36
20 13 0.20
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:474376 original size:32 final size:32
Alignment explanation
Indices: 474335--474435 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
474325 GGCAGTAGCT
*
474335 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
474367 TACATTGTATCGAAACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
474399 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
474432 TACA
1 TACA
474436 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 50 0.77
33 15 0.23
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:474377 original size:13 final size:13
Alignment explanation
Indices: 474359--474415 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
474349 ACAAAACTTA
474359 TGTATCGATACAT
1 TGTATCGATACAT
*
474372 TGTATCGAAACAACACTT
1 TGTATCG--A-TACA--T
474390 ATGTATCGATACAT
1 -TGTATCGATACAT
474404 TGTATCGATACA
1 TGTATCGATACA
474416 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 19 0.53
14 1 0.03
15 1 0.03
16 6 0.17
17 1 0.03
18 1 0.03
19 7 0.19
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:475107 original size:48 final size:48
Alignment explanation
Indices: 475043--475380 Score: 336
Period size: 48 Copynumber: 6.9 Consensus size: 48
475033 GTTAGACTTG
* * * * *
475043 AAGGTGACAATGTGCTGATTCAAGGCCGGCGACATTGGTCTTAAAGAC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
* **
475091 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
* * * * * * * *
475139 GAGGTACCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTATAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-C
* *
475188 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA---GAC
* * ** * *
475239 AAAAGCGCCAATATGAGGATTCAAGGCCAACGATATTGGACTTAAAGATG
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-C
* * * **
475289 AA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAAACTTAAAGAC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
* *
475336 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
475381 AGAAGACGCC
Statistics
Matches: 233, Mismatches: 50, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
47 2 0.01
48 151 0.65
49 40 0.17
52 40 0.17
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (48 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAC
Found at i:475457 original size:28 final size:28
Alignment explanation
Indices: 475400--475551 Score: 182
Period size: 28 Copynumber: 5.3 Consensus size: 28
475390 CACCAACTTG
*
475400 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
* *
475429 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
475457 TGTGGGCTTTTAAAGATTGCTACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
475485 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
475513 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
475543 TGTGGGCTT
1 TGTGGGCTT
475552 AAAAGGAAAA
Statistics
Matches: 108, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
27 3 0.03
28 70 0.65
29 11 0.10
30 24 0.22
ACGTcount: A:0.18, C:0.16, G:0.29, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:475536 original size:30 final size:30
Alignment explanation
Indices: 475426--475770 Score: 235
Period size: 30 Copynumber: 11.6 Consensus size: 30
475416 GTTTGCATCA
* *
475426 ACTTGTGTGCTTTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** *
475454 ACTTGTGGGCTTTT--AAAGATTGCTACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
475482 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
475510 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * * *
475540 ACTTGTGGGCTTAAAAGGAAAAAGAGTGCTACGG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACTG
* * ** * *
475574 AGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGG
1 ACTTGTGGGCTT----TTG-AAAAGGGTGCCACTG
* * * * *
475609 AGTTGTGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
**
475638 ACTTGTGGGCTTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
475668 ATTTGTGGGC-TTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * *
475695 ACTTGTGGAC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* * *
475724 ACTTGTGGGCTTTGGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
475754 ACTTGTGGGCTTTTGAA
1 ACTTGTGGGCTTTTGAA
475771 GGGTGAGGAA
Statistics
Matches: 264, Mismatches: 41, Indels: 22
0.81 0.13 0.07
Matches are distributed among these distances:
27 24 0.09
28 64 0.24
29 45 0.17
30 79 0.30
31 1 0.00
33 1 0.00
34 21 0.08
35 29 0.11
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
Found at i:475554 original size:84 final size:84
Alignment explanation
Indices: 475400--475556 Score: 203
Period size: 84 Copynumber: 1.8 Consensus size: 84
475390 CACCAACTTG
* * *
475400 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTGGGC-
475465 TTTAAAGATTGCTACTGACT
65 TTTAAAGATTGCTACTGACT
*
475485 TGTGGGCTTTT-AAAGG-TTGCCA-CTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTG
1 TGTGGGCTTTTGAAAGGTTTG-CATC-AACTTGTGGGCTTTTG--AAGGGTGCCACTAACTTGTG
*
475547 GGCTTAAAAG
62 GGCTTTAAAG
475557 GAAAAAGAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
83 4 0.06
84 21 0.33
85 17 0.27
86 21 0.33
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (84 bp):
TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTGGGCT
TTAAAGATTGCTACTGACT
Found at i:475580 original size:34 final size:35
Alignment explanation
Indices: 475542--475616 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
475532 TGCCACTAAC
* *
475542 TTGTGGGCTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
*
475576 TTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
475611 TTGTGG
1 TTGTGG
475617 ACTTTGGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.21
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
Found at i:475750 original size:86 final size:87
Alignment explanation
Indices: 475601--475772 Score: 265
Period size: 86 Copynumber: 2.0 Consensus size: 87
475591 AGAAAAAGAG
* * * *
475601 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCAC
1 TGCCACGGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCAC
*
475666 TGATTTGTGGGC-TTTGAAGGT
66 TGACTTGTGGGCTTTTGAAGGT
* * *
475687 TGCCACTGACTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGGAAAAAGATGCCAC
1 TGCCACGGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCAC
475752 TGACTTGTGGGCTTTTGAAGG
66 TGACTTGTGGGCTTTTGAAGG
475773 GTGAGGAATG
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 69 0.90
87 8 0.10
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (87 bp):
TGCCACGGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCAC
TGACTTGTGGGCTTTTGAAGGT
Found at i:486995 original size:20 final size:20
Alignment explanation
Indices: 486943--486997 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
486933 CATCTTTTTC
*
486943 ATGTATCGATACATTGCAAT
1 ATGTATCGATACTTTGCAAT
486963 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-T
*
486983 GTGTATCGATACTTT
1 ATGTATCGATACTTT
486998 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAT
Found at i:487632 original size:21 final size:21
Alignment explanation
Indices: 487591--487634 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
487581 CTCCCCTTTA
* *
487591 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
487612 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
487633 TC
1 TC
487635 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:489446 original size:13 final size:13
Alignment explanation
Indices: 489428--489466 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
489418 ATAATCACCC
489428 TGTATCAATACAA
1 TGTATCAATACAA
489441 TGTATCAATACAA
1 TGTATCAATACAA
*
489454 TGTATCGATACAA
1 TGTATCAATACAA
489467 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (13 bp):
TGTATCAATACAA
Found at i:493427 original size:21 final size:21
Alignment explanation
Indices: 493380--493424 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
493370 AAGTTTTCAT
493380 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
493400 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
493422 TTT
1 TTT
493425 CATCTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:500168 original size:20 final size:20
Alignment explanation
Indices: 500143--500190 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
500133 TGGAGGTGCT
**
500143 AAACATGCTGTAAATGCATG
1 AAACATGCTCAAAATGCATG
500163 AAACATAGCTCAAAATGCATG
1 AAACAT-GCTCAAAATGCATG
*
500184 AATCATG
1 AAACATG
500191 GGCTGTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AAACATGCTCAAAATGCATG
Found at i:501220 original size:104 final size:104
Alignment explanation
Indices: 501029--501230 Score: 334
Period size: 104 Copynumber: 1.9 Consensus size: 104
501019 CGAAATATGA
*
501029 AAATTCGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGTAAATTTGCCTGCA
1 AAATTCGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
***
501094 TGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
66 TGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
* *
501133 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATATATCTGGGCAAATTTGCCTGCA
1 AAATTCGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
501198 TGTATCGATACA-AAGATCAGTGTATCGATACAT
66 TGTATCGATACATAAGAT-AGTGTATCGATACAT
501231 TTAAGTAATG
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 2 0.02
104 89 0.98
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (104 bp):
AAATTCGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
TGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
Found at i:501227 original size:52 final size:52
Alignment explanation
Indices: 501029--501209 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
501019 CGAAATATGA
* *
501029 AAATTCGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
501081 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
501133 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
501185 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
501210 AAGATCAGTG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:501296 original size:19 final size:18
Alignment explanation
Indices: 501272--501369 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
501262 TAGCTTACAT
501272 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
501291 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
501304 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
501323 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
501336 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
501356 TGTATCGATACAAA
1 TGTATCGATACAAA
501370 TCATTGAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:501308 original size:32 final size:32
Alignment explanation
Indices: 501267--501367 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
501257 GGCAGTAGCT
*
501267 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
501299 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
501331 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
501364 TACA
1 TACA
501368 AATCATTGAA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 52 0.78
33 15 0.22
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:501309 original size:13 final size:13
Alignment explanation
Indices: 501291--501347 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
501281 ACAAAACTTA
501291 TGTATCGATACAT
1 TGTATCGATACAT
501304 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
501322 ATGTATCGATACAT
1 -TGTATCGATACAT
501336 TGTATCGATACA
1 TGTATCGATACA
501348 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:501446 original size:21 final size:21
Alignment explanation
Indices: 501405--501446 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
501395 GTTGGGACCT
*
501405 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
501426 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
501447 CAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:503777 original size:10 final size:11
Alignment explanation
Indices: 503755--503783 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
503745 AAAGTTTTTA
503755 TGAAAAATGTT
1 TGAAAAATGTT
503766 TGAAAAAT-TT
1 TGAAAAATGTT
503776 TGAAAAAT
1 TGAAAAAT
503784 CATCTAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (11 bp):
TGAAAAATGTT
Found at i:505500 original size:20 final size:20
Alignment explanation
Indices: 505474--505620 Score: 78
Period size: 20 Copynumber: 6.8 Consensus size: 20
505464 GAATGTATTC
* *
505474 AATGTATCAATACATTCATA
1 AATGTATCGATACATTCAAA
* *
505494 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
*
505514 AATGTATCGATACATCTGGGTAAAAAAA
1 AATGTATCGATACA--T---T---CAAA
* * * *
505542 TAGAATGTATCAACACATTGAAT
1 -A-A-TGTATCGATACATTCAAA
*
505565 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
505585 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
*
505605 AATGTATCAATACATT
1 AATGTATCGATACATT
505621 TGGGTAAAAA
Statistics
Matches: 96, Mismatches: 20, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
20 73 0.76
21 1 0.01
22 2 0.02
23 2 0.02
25 1 0.01
26 1 0.01
28 3 0.03
29 2 0.02
30 1 0.01
31 10 0.10
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:506814 original size:165 final size:162
Alignment explanation
Indices: 506600--507207 Score: 670
Period size: 165 Copynumber: 3.7 Consensus size: 162
506590 AAACTCAATT
506600 TTTCGAAAAAAATGAGAATTTCAAGAAAAGAATTCAAAAACTCATGAAAATGAATTAATTTTTAA
1 TTTCGAAAAAAA--AGAATTTCAAGAAAA-AATTCAAAAACTCATGAAAATGAATTAATTTTTAA
** *
506665 AAACTGATTTAATATAAAATAAATAATGTTATTTTATGAATTTTAAAAATTAAAAACCAAGAAAT
63 AAACTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAA-
*
506730 ATTCTCCCAAAAAAATTACGAAGTCGAAAACAACGTA
127 A-TCTCCCAAAAAAATTACGAAGTAGAAAACAACGTA
* * *
506767 TTTCGGAAAAAGAAGAATTTTAAGGAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAA
1 TTTC-GAAAAAAAAGAATTTCAAGAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAA
* * * * * *
506832 ACTGATTTAATATGAAATAAATAATGATATTTTATTAATTTTAAAAACTAAAAA-CAGAGAGAA-
65 ACTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCA-AGAAAAT
**** * *
506895 CTCCC-TCCGAATTACGAAGTAAAAAATAACGTA
129 CTCCCAAAAAAATTACGAAGTAGAAAACAACGTA
** * * * * *
506928 TTTTAAAAAAAAAGAATTTTAAGGAAAAAATTTAAAAACTCATGAAGATGAGTTAATTTTTCAAA
1 TTTCGAAAAAAAAGAATTTCAA-GAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAA
* * *
506993 ATTGATTTATTA-AAAATAAATAATAATATTTGAT-AGATTTTAAAAATTAGAAACCAAGAAAAA
65 ACTGATTTAATATAAAATAAATAATAATATTTGATGA-ATTTTAAAAATTAAAAACCAAG-AAAA
* * ** *
507056 TCCCCTCGAAAAAATTTACGGAAG-AGAAAACTCCGTT
128 TCTCC-C-AAAAAAATTAC-GAAGTAGAAAACAACGTA
* * * * * *
507093 TTTCGAAAAGAAAATAATTTCAAGAAAAAAATTTAAAAACTTATGAAAGTGAATAAATTTTTTAA
1 TTTCGAAAA-AAAAGAATTTCAAG-AAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAA
*
507158 AACTGATTTATTATAAAATAAATAATAATATTTGATGAATTTTAAAAATT
64 AACTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATT
507208 TTAACTAATG
Statistics
Matches: 373, Mismatches: 53, Indels: 30
0.82 0.12 0.07
Matches are distributed among these distances:
159 1 0.00
160 52 0.14
161 76 0.20
162 8 0.02
163 1 0.00
164 3 0.01
165 112 0.30
166 74 0.20
167 38 0.10
168 8 0.02
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (162 bp):
TTTCGAAAAAAAAGAATTTCAAGAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAA
CTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAATCT
CCCAAAAAAATTACGAAGTAGAAAACAACGTA
Found at i:507179 original size:327 final size:327
Alignment explanation
Indices: 506605--507205 Score: 793
Period size: 327 Copynumber: 1.8 Consensus size: 327
506595 CAATTTTTCG
*
506605 AAAAAAATGAGAATTTCAAGAAAAGAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAACT
1 AAAAAAATAAGAATTTCAAGAAAAGAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAACT
** * * *
506670 GATTTAATATAAAATAAATAATGTTATTTTATGAATTTTAAAAATTAAAAACCAAGAAATATTCT
66 GATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAATAATCC
* * * *
506735 CCCAAAAAAATTACGAAGTCGAAAACAACGTATTTCGGAAAAAGAAGAATTTTAAGGAAAAATTC
131 CCCAAAAAAATTACGAAGTAGAAAACAACGTATTTCGGAAAAAAAAGAATTTCAAGAAAAAATTC
* * * *
506800 AAAAACTCATGAAAATGAATTAATTTTTAAAAACTGATTTAATATGAAATAAATAATGATATTTT
196 AAAAACTCATGAAAATGAATAAATTTTTAAAAACTGATTTAATATAAAATAAATAATAATATTTG
*
506865 ATTAATTTTAAAAACTAAAAACAGAGAGAACTCCCTCCGAATTACGAAGTAAAAAATAACGTATT
261 ATGAATTTTAAAAACTAAAAACAGAGAGAACTCCCTCCGAATTACGAAGTAAAAAATAACGTATT
506930 TT
326 TT
* * * * * *
506932 AAAAAAA-AAGAATTTTAAGGAAAA-AATTTAAAAACTCATGAAGATGAGTTAATTTTTCAAAAT
1 AAAAAAATAAGAATTTCAA-GAAAAGAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAAC
* *
506995 TGATTTATTA-AAAATAAATAATAATATTTGAT-AGATTTTAAAAATTAGAAACCAAGAAA-AAT
65 TGATTTAATATAAAATAAATAATAATATTTGATGA-ATTTTAAAAATTAAAAACCAAGAAATAAT
* ** * *
507057 CCCCTCGAAAAAATTTACGGAAG-AGAAAACTCCGTTTTTC-GAAAAGAAAATAATTTCAAGAAA
129 CCCC-C-AAAAAAATTAC-GAAGTAGAAAACAACGTATTTCGGAAAA-AAAAGAATTTCAAG-AA
* * * * *
507120 AAAATTTAAAAACTTATGAAAGTGAATAAATTTTTTAAAACTGATTTATTATAAAATAAATAATA
189 AAAATTCAAAAACTCATGAAAATGAATAAATTTTTAAAAACTGATTTAATATAAAATAAATAATA
507185 ATATTTGATGAATTTTAAAAA
254 ATATTTGATGAATTTTAAAAA
507206 TTTTAACTAA
Statistics
Matches: 234, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
324 6 0.03
325 49 0.21
326 86 0.37
327 93 0.40
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (327 bp):
AAAAAAATAAGAATTTCAAGAAAAGAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAACT
GATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAATAATCC
CCCAAAAAAATTACGAAGTAGAAAACAACGTATTTCGGAAAAAAAAGAATTTCAAGAAAAAATTC
AAAAACTCATGAAAATGAATAAATTTTTAAAAACTGATTTAATATAAAATAAATAATAATATTTG
ATGAATTTTAAAAACTAAAAACAGAGAGAACTCCCTCCGAATTACGAAGTAAAAAATAACGTATT
TT
Found at i:507280 original size:166 final size:162
Alignment explanation
Indices: 506606--507280 Score: 629
Period size: 165 Copynumber: 4.1 Consensus size: 162
506596 AATTTTTCGA
*
506606 AAAAAATG-AGAATTTCAAGAAAAGAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAACT
1 AAAAAA-GAAGAATTTCAAGAAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAACT
** * *
506670 GATTTAATATAAAATAAATAATGTTATTTTATGAATTTTAAAAATTAAAAACCAAGAAATATTCT
65 GATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAA-ATCCT
* * **
506735 CCCAAAAAAATTACGAAGTCGAAAACAACGTATTT
129 CTCAAAAAATTTACGAAGAAGAAAAC-ACGTATTT
* * *
506770 CGGAAAAAGAAGAATTTTAAG-GAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAAC
1 --AAAAAAGAAGAATTTCAAGAAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAAC
* * * * * *
506834 TGATTTAATATGAAATAAATAATGATATTTTATTAATTTTAAAAACTAAAAA-CAGAGAGAACTC
64 TGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCA-AGA-AAATC
** *
506898 C-CTC--CGAA-TTACGAAGTAA-AAAATAACGTATTTT
127 CTCTCAAAAAATTTACGAAG-AAGAAAA-CACGTA-TTT
* * * * * * * *
506932 AAAAAAAAAGAATTTTAAGGAAAAAATTTAAAAACTCATGAAGATGAGTTAATTTTTCAAAATTG
1 AAAAAAGAAGAATTTCAAGAAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAACTG
* * *
506997 ATTTATTA-AAAATAAATAATAATATTTGAT-AGATTTTAAAAATTAGAAACCAAGAAAAATCCC
66 ATTTAATATAAAATAAATAATAATATTTGATGA-ATTTTAAAAATTAAAAACCAAG-AAAATCCT
* *
507060 CTCGAAAAAATTTACGGAAG-AGAAAACTCCGTTTTT
129 CTC-AAAAAATTTAC-GAAGAAGAAAAC-ACGTATTT
* * * * * *
507096 CGAAAAGAA-AATAATTTCAAGAAAAAAATTTAAAAACTTATGAAAGTGAATAAATTTTTTAAAA
1 --AAAA-AAGAAGAATTTCAAGAAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAA
* ** *
507160 CTGATTTATTATAAAATAAATAATAATATTTGATGAATTTTAAAAATT-TTAACTAATGAAAATC
63 CTGATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAA-GAAAATC
* *
507224 CTCTCAAAAAATTTACAAAGAAGAAAATCTCGTAATTT
127 CTCTCAAAAAATTTACGAAGAAGAAAA-CACGT-ATTT
*
507262 AAAAATAGGAGAAATTTCA
1 AAAAA-AGAAG-AATTTCA
507281 TAAGAAAATC
Statistics
Matches: 424, Mismatches: 55, Indels: 60
0.79 0.10 0.11
Matches are distributed among these distances:
159 1 0.00
160 58 0.14
161 69 0.16
162 5 0.01
163 1 0.00
164 18 0.04
165 127 0.30
166 107 0.25
167 37 0.09
168 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.30
Consensus pattern (162 bp):
AAAAAAGAAGAATTTCAAGAAAAAAATTCAAAAACTCATGAAAATGAATTAATTTTTAAAAACTG
ATTTAATATAAAATAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAATCCTCT
CAAAAAATTTACGAAGAAGAAAACACGTATTT
Found at i:513422 original size:20 final size:20
Alignment explanation
Indices: 513387--513440 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
513377 TTCTACAACT
* * *
513387 TGTATCAATAACATAAGTTAA
1 TGTATCGAT-ACATAACTGAA
*
513408 TGTATTGATACATAACTGAA
1 TGTATCGATACATAACTGAA
513428 TGTATCGATACAT
1 TGTATCGATACAT
513441 GCTTGAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAACTGAA
Found at i:513447 original size:20 final size:21
Alignment explanation
Indices: 513406--513455 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
513396 AACATAAGTT
*
513406 AATGTATTGATACATAACTG-
1 AATGTATCGATACATAACTGA
*
513426 AATGTATCGATACAT-GCTTGA
1 AATGTATCGATACATAAC-TGA
513447 AATGTATCG
1 AATGTATCG
513456 GTACTAGGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.62
21 9 0.35
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATAACTGA
Found at i:518872 original size:14 final size:15
Alignment explanation
Indices: 518834--518876 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
518824 AACTTATAAT
518834 AAATTTATAATA-ACC
1 AAATTTATAATATA-C
518849 AAATTTTATAATATA-
1 AAA-TTTATAATATAC
518864 AAATTTATAATAT
1 AAATTTATAATAT
518877 TTTATATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.38
15 6 0.23
16 9 0.35
17 1 0.04
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTATAATATAC
Found at i:521160 original size:21 final size:21
Alignment explanation
Indices: 521136--521195 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
521126 TCTTAGCAGC
521136 CCATATT-TGTGCATTTTTATG
1 CCATATTCTGTGCATTTTT-TG
*
521157 CCATGTTCTGTGCATTTTTTG
1 CCATATTCTGTGCATTTTTTG
* **
521178 CCATGTTCCATGCATTTT
1 CCATATTCTGTGCATTTT
521196 GACATGTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 24 0.69
22 11 0.31
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (21 bp):
CCATATTCTGTGCATTTTTTG
Found at i:521168 original size:22 final size:21
Alignment explanation
Indices: 521143--521195 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
521133 AGCCCATATT
521143 TGTGCATTTTTATGCCATGTTC
1 TGTGCATTTTT-TGCCATGTTC
521165 TGTGCATTTTTTGCCATGTTC
1 TGTGCATTTTTTGCCATGTTC
**
521186 CATGCATTTT
1 TGTGCATTTT
521196 GACATGTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.51
Consensus pattern (21 bp):
TGTGCATTTTTTGCCATGTTC
Found at i:522105 original size:34 final size:35
Alignment explanation
Indices: 522067--522133 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
522057 CCTTACAACA
522067 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
522101 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
522134 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:522630 original size:13 final size:13
Alignment explanation
Indices: 522612--522637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
522602 CTATTTATGA
522612 TGTATCGATACAC
1 TGTATCGATACAC
522625 TGTATCGATACAC
1 TGTATCGATACAC
522638 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:522775 original size:22 final size:22
Alignment explanation
Indices: 522720--522775 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
522710 ACAGTGACCT
522720 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
522742 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
522763 ATGAACAGTGATG
1 ATGAACAGTGATG
522776 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:522782 original size:10 final size:10
Alignment explanation
Indices: 522763--522793 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
522753 GTATCGATAC
522763 ATGAACAGTG
1 ATGAACAGTG
*
522773 ATGAATAGTG
1 ATGAACAGTG
522783 ATGAACAGTG
1 ATGAACAGTG
522793 A
1 A
522794 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:522933 original size:20 final size:20
Alignment explanation
Indices: 522870--522940 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
522860 GCCAATGACC
**
522870 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
522890 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
522910 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
522930 TGTATCGATAC
1 TGTATCGATAC
522941 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:523006 original size:21 final size:21
Alignment explanation
Indices: 522980--523020 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
522970 GTCAACCTTG
522980 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
523001 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
523021 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:525253 original size:2 final size:2
Alignment explanation
Indices: 525246--525273 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
525236 TACATGCGTG
525246 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
525274 TACACATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:527137 original size:17 final size:18
Alignment explanation
Indices: 527090--527137 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
527080 TAGTTTTATT
*
527090 ATATTATATATGTATATTA
1 ATATT-TATATGTATATGA
*
527109 ACA-TTATATGTATATGA
1 ATATTTATATGTATATGA
527126 ATATTTAT-TGTA
1 ATATTTATATGTA
527138 ATATACGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 18 0.72
18 5 0.20
19 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (18 bp):
ATATTTATATGTATATGA
Found at i:528153 original size:2 final size:2
Alignment explanation
Indices: 528146--528194 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
528136 TTCAGCTTCT
528146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
528188 TA TA TA T
1 TA TA TA T
528195 CGACCCCTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:529934 original size:13 final size:13
Alignment explanation
Indices: 529918--529944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
529908 AAGCTTTTAC
529918 TTATATATATATA
1 TTATATATATATA
529931 TTATATATATATA
1 TTATATATATATA
529944 T
1 T
529945 AATGACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:530699 original size:11 final size:11
Alignment explanation
Indices: 530663--530700 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
530653 CCTGTCAACA
530663 ATATAGACTAT
1 ATATAGACTAT
*
530674 ATATATA-TAT
1 ATATAGACTAT
530684 AATATAGACTAT
1 -ATATAGACTAT
530696 ATATA
1 ATATA
530701 CAAGACATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (11 bp):
ATATAGACTAT
Found at i:532953 original size:13 final size:13
Alignment explanation
Indices: 532937--532961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
532927 TATAAAATAA
532937 TATTGTAAATATG
1 TATTGTAAATATG
532950 TATTGTAAATAT
1 TATTGTAAATAT
532962 ATTATAATAT
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TATTGTAAATATG
Found at i:533054 original size:20 final size:22
Alignment explanation
Indices: 533031--533076 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
533021 ATGTATATGG
*
533031 ATATTTA-TTATAATA-TACAT
1 ATATTTACGTATAATATTACAT
*
533051 ATATTTACGTATATTATTACAT
1 ATATTTACGTATAATATTACAT
533073 ATAT
1 ATAT
533077 ATTTACTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
ATATTTACGTATAATATTACAT
Found at i:537397 original size:13 final size:13
Alignment explanation
Indices: 537379--537405 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
537369 ACATGCTGCT
537379 TTGTATCGATACA
1 TTGTATCGATACA
537392 TTGTATCGATACA
1 TTGTATCGATACA
537405 T
1 T
537406 GAAACTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:537472 original size:13 final size:13
Alignment explanation
Indices: 537451--537482 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
537441 CGATACATGG
*
537451 TACAATGTATCGA
1 TACATTGTATCGA
537464 TACATTGTATCGA
1 TACATTGTATCGA
537477 TACATT
1 TACATT
537483 AAGAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:540485 original size:51 final size:51
Alignment explanation
Indices: 540420--540537 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
540410 TGAAAATAAT
* *
540420 GGGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAAAAATAAGGTC
1 GGGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAAAAATAAAGCC
* * **
540471 GGGGTT-GAGGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAGCC
1 GGGGTTGGA-GTATCCCTAATTATGAGAAATCAATATTTTAAAAATAAAGCC
540522 GGGGTTGGAGTATCCC
1 GGGGTTGGAGTATCCC
540538 CTTGGAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 55 0.93
52 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAAAAATAAAGCC
Found at i:540561 original size:28 final size:27
Alignment explanation
Indices: 540524--540594 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
540514 ATAAAGCCGG
540524 GGTTGGAGTATCCCCTTG-GAAATAACTA
1 GGTTGGAGTATCCCC-TGAGAAATAAC-A
*
540552 GGTTGGAGTAT-CCCTGATGAAATAACG
1 GGTTGGAGTATCCCCTGA-GAAATAACA
540579 GGTTTGGAGTATCCCC
1 GG-TTGGAGTATCCCC
540595 GATTGTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 2 0.05
27 5 0.13
28 28 0.74
29 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (27 bp):
GGTTGGAGTATCCCCTGAGAAATAACA
Found at i:540694 original size:51 final size:51
Alignment explanation
Indices: 540578--540695 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
540568 ATGAAATAAC
* *
540578 GGGTTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCG
1 GGGTTT-GAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCG
* * * * * *
540630 GAG-CTGAAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCG
1 GGGTTTG-AGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCG
540681 GGGTTTGAGTATCCC
1 GGGTTTGAGTATCCC
540696 TTCGAAAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
50 1 0.02
51 48 0.91
52 4 0.08
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.31
Consensus pattern (51 bp):
GGGTTTGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCG
Found at i:540770 original size:79 final size:76
Alignment explanation
Indices: 540664--540850 Score: 259
Period size: 79 Copynumber: 2.4 Consensus size: 76
540654 AGAATTGGTG
* * *
540664 TTTTAGAAATAAAACCGGGGTTTGAGTATCCCTTCGAAAATAACGGGATTGGAGTATCCTCGATT
1 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCTTCGAAAATAACGGGATCGGAGTATCCCCG---
540729 ATGAAAAATTGATA
63 ATGAAAAATTGATA
*
540743 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTCGGAGTATCCCCGATG
1 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCTTCGAAAATAACGGGATCGGAGTATCCCCGATG
* *
540808 AAAAATTGGTG
66 AAAAATTGATA
* *
540819 TTTT-GAAAATAAAATCGGAGTTGGAGTATCCC
1 TTTTAG-AAATAAAACCGGGGTTGGAGTATCCC
540851 CGATTGCGGT
Statistics
Matches: 99, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
75 1 0.01
76 40 0.40
79 58 0.59
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (76 bp):
TTTTAGAAATAAAACCGGGGTTGGAGTATCCCTTCGAAAATAACGGGATCGGAGTATCCCCGATG
AAAAATTGATA
Found at i:540930 original size:51 final size:49
Alignment explanation
Indices: 540793--540965 Score: 161
Period size: 51 Copynumber: 3.4 Consensus size: 49
540783 TAACGGGGTC
* *
540793 GGAGTATCCCCGA-TGAAAAATTGGTGTTTTGAAAATAAAATCGGAGTT
1 GGAGTATCCCCGATTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTT
** * *
540841 GGAGTATCCCCGATTGCGGTAAATTGATGCTTTAGAAATAAAATCGGAGTT
1 GGAGTATCCCCGATT--GAAAAATTGATGTTTTGGAAATAAAATCGGAGTT
* * ** **
540892 GGGGTATCCCCGATTAAGAAAAATTAATGTTTTGGAAATGGAA-CCAAGATT
1 GGAGTATCCCCGATT--GAAAAATTGATGTTTTGGAAATAAAATCGGAG-TT
*
540943 GGAGTATCCCCGAGATGAAAAAT
1 GGAGTATCCCCGA-TTGAAAAAT
540966 ATAGAAATTT
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
48 13 0.13
49 1 0.01
50 10 0.10
51 75 0.75
52 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (49 bp):
GGAGTATCCCCGATTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTT
Found at i:543329 original size:33 final size:32
Alignment explanation
Indices: 543276--543338 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
543266 TTGTAAAATG
543276 TATCGATACAATAAGTAATGTATCAATACAATA
1 TATCGATACAATAAG-AATGTATCAATACAATA
*
543309 TATCGATACAATGCAA-AATGTATCGATACA
1 TATCGATACAAT--AAGAATGTATCAATACA
543339 TCTGGGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 25 0.93
35 2 0.07
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (32 bp):
TATCGATACAATAAGAATGTATCAATACAATA
Found at i:543334 original size:20 final size:18
Alignment explanation
Indices: 543252--543338 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 18
543242 AAAATGCCTG
*
543252 AATGTATCGATACATTGTAA
1 AATGTATCGATACA--ATAA
543272 AATGTATCGATACAATAA
1 AATGTATCGATACAATAA
*
543290 GTAATGTATCAATACAAT--
1 --AATGTATCGATACAATAA
543308 -A--TATCGATACAATGCAA
1 AATGTATCGATACAAT--AA
543325 AATGTATCGATACA
1 AATGTATCGATACA
543339 TCTGGGTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
13 11 0.20
15 1 0.02
18 4 0.07
20 39 0.71
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (18 bp):
AATGTATCGATACAATAA
Found at i:543400 original size:20 final size:20
Alignment explanation
Indices: 543377--543444 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
543367 ACAAAGATCG
543377 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
543397 ATGTATCGATAC-------A
1 ATGTATCGATACATTGAATA
543410 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
543430 ATGTATCGATACATT
1 ATGTATCGATACATT
543445 TCCTTCGCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.32
20 28 0.68
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:543414 original size:13 final size:13
Alignment explanation
Indices: 543396--543422 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
543386 TACATTGAAT
543396 AATGTATCGATAC
1 AATGTATCGATAC
543409 AATGTATCGATAC
1 AATGTATCGATAC
543422 A
1 A
543423 TTGAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:543419 original size:33 final size:33
Alignment explanation
Indices: 543377--543442 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
543367 ACAAAGATCG
543377 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACATTGAATAATGTATCGATACA
543410 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACATTGAATAATGTATCGATACA
543443 TTTCCTTCGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACATTGAATAATGTATCGATACA
Found at i:544201 original size:40 final size:40
Alignment explanation
Indices: 544157--544257 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 40
544147 GTCCCACTTT
* * *
544157 TTGAGGACAAAGGAAAAAAGAATGAAATAG-GTCTTGCTCC
1 TTGAGGACAAAGGAAAAAAAAAAGAAA-AGTGTCCTGCTCC
* *
544197 TTGAGGACAAAGGAAGAGAAAAAAAGGAAAGTGTCCTGCTTC
1 TTGAGGACAAAGGAA-A-AAAAAAAGAAAAGTGTCCTGCTCC
544239 TTGAGGACAAAGTGAAAAA
1 TTGAGGACAAAG-GAAAAA
544258 TAGTACGTCC
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 15 0.29
41 5 0.10
42 29 0.56
43 3 0.06
ACGTcount: A:0.45, C:0.11, G:0.27, T:0.18
Consensus pattern (40 bp):
TTGAGGACAAAGGAAAAAAAAAAGAAAAGTGTCCTGCTCC
Found at i:544320 original size:42 final size:41
Alignment explanation
Indices: 544273--544371 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
544263 CGTCCCATTT
*
544273 TTTGAGGACAAAGGAAAAAG-GGAAACGAAATATG-TCCTGCTC
1 TTTGAGGACAAA--AAAAAGAGGAAAAGAAA-ATGATCCTGCTC
* * *
544315 TTTGAGGACGAAAAAAAGAGGAAAATAAAGTGCATCCTGCTC
1 TTTGAGGACAAAAAAAAGAGGAAAAGAAAATG-ATCCTGCTC
*
544357 TTTGAGGACTAAAAA
1 TTTGAGGACAAAAAA
544372 GTGCCACCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 8 0.16
41 8 0.16
42 33 0.67
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.20
Consensus pattern (41 bp):
TTTGAGGACAAAAAAAAGAGGAAAAGAAAATGATCCTGCTC
Found at i:544550 original size:55 final size:55
Alignment explanation
Indices: 544471--544936 Score: 485
Period size: 55 Copynumber: 8.3 Consensus size: 55
544461 AGAGAAAGCT
* * * *
544471 TCCTACTCTTTGAGGATTGGAAAATGCCACCAATTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
544526 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
544581 TCCTACTCTTTGAGGACTGGAAAATGCCACAAACTTGTGTGGGCTTT-AAGAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
544636 TCCTGCTCTTTGAGGACT-AGAAAATGCCACCAACTTGTGTGGCCTTTAAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
* ** * *
544697 TCTTGCTCTTTGAGGACT-AGAGGATGCCACCAA-TTCGTATGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTT-GTGTGGGCTTTGAAAGGCG
* ** * * * * *
544752 TCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTCTATGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
544807 TCCTGCTCTTTGAGGA-TAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT---GAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * ** * * *
544864 TCCTACTTTTTGAGGACTGAAAGGTGTCACCAAGTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
544919 TCCTGCTTTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
544937 AAATGGTGAA
Statistics
Matches: 347, Mismatches: 48, Indels: 32
0.81 0.11 0.07
Matches are distributed among these distances:
54 3 0.01
55 250 0.72
56 3 0.01
57 43 0.12
58 1 0.00
60 2 0.01
61 43 0.12
62 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:544706 original size:171 final size:163
Alignment explanation
Indices: 544349--544936 Score: 622
Period size: 171 Copynumber: 3.4 Consensus size: 163
544339 ATAAAGTGCA
*
544349 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTAAAAA-TGCCACCAACTTGTGTGGGCTTT------GAAAGGCGTCCT
* * * *
544414 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCTTCCTACTC
59 ACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT---AAGAG---GCGTCCTGCTC
* *
544479 TTTGAGGATTGGAAAATGCCACCAATTTGTGTGGGCTTTGAAAGGCG
118 TTTGAGGA-TAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
544526 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCGTCCTACTCT
1 TCCTGCTCTTTGAGGACT-AAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCGTCCTACTCT
* *
544590 TTGAGGACTGGAAAATGCCACAAACTTGTGTGGGCTTTAAGAGGCGTCCTGCTCTTTGAGGACTA
64 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCGTCCTGCTCTTTGAGGA-TA
* *
544655 GAAAATGCCACCAACTTGTGTGGCCTTTAAAAAGAAAAGGTG
128 GAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
* ** * *
544697 TCTTGCTCTTTGAGGACTAGAGGATGCCACCAA-TTCGTATGGGCTTTGAAAGGCATCCTACTCT
1 TCCTGCTCTTTGAGGACTA-AAAATGCCACCAACTT-GTGTGGGCTTTGAAAGGCGTCCTACTCT
* * * * *
544761 TTGAGGACTGGGAAGTGCCACCAACTTCTATGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATAA
64 TTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCGTCCTGCTCTTTGAGGAT--
*
544826 AAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
127 -AGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * ** * * * * *
544864 TCCTACTTTTTGAGGACTGAAAGGTGTCACCAAGTTGTGTGGGCTTTGAAAGGTGTCCTGCTTTT
1 TCCTGCTCTTTGAGGACT-AAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTACTCTT
544929 TGAGGACT
65 TGAGGACT
544937 AAATGGTGAA
Statistics
Matches: 357, Mismatches: 38, Indels: 42
0.82 0.09 0.10
Matches are distributed among these distances:
165 44 0.12
167 63 0.18
168 9 0.03
170 7 0.02
171 160 0.45
172 2 0.01
173 27 0.08
177 40 0.11
178 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (163 bp):
TCCTGCTCTTTGAGGACTAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTACTCTTT
GAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGCGTCCTGCTCTTTGAGGATAGAA
AATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:544710 original size:226 final size:225
Alignment explanation
Indices: 544349--544910 Score: 673
Period size: 226 Copynumber: 2.4 Consensus size: 225
544339 ATAAAGTGCA
*
544349 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTAAAAA-TGCCACCAACTTGTGTGGGCTTT--AAA-G--AGGCGTCCT
* **
544414 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAAGCTTCCTACTC
60 GCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAAGCTTCCTACTC
* * * * * *
544479 TTTGAGGATTGGAAAATGCCACCAATTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACT
124 TTTGAGGACTAGAAAATGCCACCAATTCGTATGGGCTTTGAAAGGCATCCTACTCTTTGAGGACT
* * *
544544 GAAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCG
189 GAAAAATGCCACCAACTTCTATGGGCTTTAAAAGGCG
* * *
544581 TCCTACTCTTTGAGGACTGGAAAATGCCACAAACTTGTGTGGGCTTT-AAGAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACT-AAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCT
* * * * *
544645 TTGAGGACTAGAAAATGCCACCAACTTGTGTGGCCTTTAAAAAGA-AAAGGTGTCTTGCTCTTTG
65 TTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAAGCT-TCCTACTCTTTG
** **
544709 AGGACTAGAGGATGCCACCAATTCGTATGGGCTTTGAAAGGCATCCTACTCTTTGAGGACTGGGA
128 AGGACTAGAAAATGCCACCAATTCGTATGGGCTTTGAAAGGCATCCTACTCTTTGAGGACTGAAA
* *
544774 AGTGCCACCAACTTCTATGGGCTTTAAAAGGTG
193 AATGCCACCAACTTCTATGGGCTTTAAAAGGCG
* *
544807 TCCTGCTCTTTGAGGA-TAAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCGTCCTAC
1 TCCTGCTCTTTGAGGACT----AAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGC
* * *
544870 TTTTTGAGGACTGAAAGGTGTCACCAAGTTGTGTGGGCTTT
62 TCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT
544911 GAAAGGTGTC
Statistics
Matches: 285, Mismatches: 38, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
225 6 0.02
226 161 0.56
227 4 0.01
228 68 0.24
229 4 0.01
232 38 0.13
233 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (225 bp):
TCCTGCTCTTTGAGGACTAAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTT
TGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAAGCTTCCTACTCTTTGAGG
ACTAGAAAATGCCACCAATTCGTATGGGCTTTGAAAGGCATCCTACTCTTTGAGGACTGAAAAAT
GCCACCAACTTCTATGGGCTTTAAAAGGCG
Found at i:546018 original size:1 final size:1
Alignment explanation
Indices: 546012--546083 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
546002 AAGAAGATTC
* * * * * * * * *
546012 TTTTTTTTTTCTTTTTTCTTTGTTTTGTTTTGTTTTTTTTGTTTTTTTATTTTTTTTGTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
546077 TGTTTTT
1 TTTTTTT
546084 CTTTGAAAAA
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:546042 original size:26 final size:25
Alignment explanation
Indices: 546012--546088 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 25
546002 AAGAAGATTC
*
546012 TTTTTT-TTTTCTTTTTTCTTTGTT
1 TTTTTTGTTTTTTTTTTTCTTTGTT
* *
546036 TTGTTTTGTTTTTTTTGTTTTTTTATT
1 TT-TTTTGTTTTTTTT-TTTCTTTGTT
546063 TTTTTTGTTGTTTTTGTTTTTCTTTG
1 TTTTTTG-T-TTTTT-TTTTTCTTTG
546089 AAAAAGAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 2 0.05
25 4 0.10
26 12 0.29
27 11 0.26
28 11 0.26
29 2 0.05
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.84
Consensus pattern (25 bp):
TTTTTTGTTTTTTTTTTTCTTTGTT
Found at i:546047 original size:19 final size:18
Alignment explanation
Indices: 546009--546088 Score: 76
Period size: 19 Copynumber: 4.4 Consensus size: 18
545999 CTTAAGAAGA
*
546009 TTCTTT-TTTTTTTCTTTT
1 TTCTTTGTTTTTTT-TGTT
546027 TTCTTTGTTTTGTTTTGTT
1 TTCTTTGTTTT-TTTTGTT
*
546046 TTTTTTGTTTTTTTAT-TT
1 TTCTTTGTTTTTTT-TGTT
*
546064 TT-TTTGTTGTTTTTGTTT
1 TTCTTTGTTTTTTTTG-TT
546082 TTCTTTG
1 TTCTTTG
546089 AAAAAGAATG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
16 1 0.02
17 10 0.19
18 17 0.32
19 22 0.42
20 3 0.06
ACGTcount: A:0.01, C:0.05, G:0.10, T:0.84
Consensus pattern (18 bp):
TTCTTTGTTTTTTTTGTT
Found at i:546051 original size:31 final size:31
Alignment explanation
Indices: 546012--546087 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
546002 AAGAAGATTC
*
546012 TTTTTTTTTTCTTTTTTCTTTGTTTTGTT-T
1 TTTTTTTTTTCTTTTTTATTTGTTTTGTTGT
*
546042 TGTTTTTTTTGT-TTTTTTATTTTTTTTGTTGT
1 T-TTTTTTTT-TCTTTTTTATTTGTTTTGTTGT
*
546074 TTTTGTTTTTCTTT
1 TTTTTTTTTTCTTT
546088 GAAAAAGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 2 0.05
31 34 0.87
32 3 0.08
ACGTcount: A:0.01, C:0.04, G:0.09, T:0.86
Consensus pattern (31 bp):
TTTTTTTTTTCTTTTTTATTTGTTTTGTTGT
Found at i:558855 original size:106 final size:104
Alignment explanation
Indices: 558685--558890 Score: 261
Period size: 106 Copynumber: 2.0 Consensus size: 104
558675 CTCCTCAGAA
* * * * * **
558685 ATAACGGGGTTGGAGTATCCCCGATGAAAAATTAGTATTTTGGAAATAAAATTGGGGTTAGAGTA
1 ATAACAGGGTTGGAGTATCCCCGATAAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTA
**
558750 TCCCCTTGGAAATAACGGGATTGGAGTATCCCCGATGAC
66 TCCCCTCAGAAATAACGGGATTGGAGTATCCCCGATGAC
* *
558789 ATAACAGGGTTGGAGTA-CCCCGATTATAAAAAATCAATATTTTAGATATAAAACCGGGGTTGGA
1 ATAACAGGGTTGGAGTATCCCCG---ATAAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGA
* *
558853 GTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGA
63 GTATCCCCTCAGAAATAACGGGATTGGAGTATCCCCGA
558891 GATAAAAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
103 5 0.06
104 16 0.19
106 65 0.76
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (104 bp):
ATAACAGGGTTGGAGTATCCCCGATAAAAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTA
TCCCCTCAGAAATAACGGGATTGGAGTATCCCCGATGAC
Found at i:558899 original size:78 final size:78
Alignment explanation
Indices: 558795--558938 Score: 191
Period size: 78 Copynumber: 1.8 Consensus size: 78
558785 TGACATAACA
* * * *
558795 GGGTTGGAGTACCCCGATTATAAAAAATCAATATTTTAGATATAAAACCGGGGTTGGAGTATCCC
1 GGGTTGGAGTACCCCGATGATAAAAAATCAATATTTTAGAAATAAAACCGGGATTGAAGTATCCC
558860 CTCAGAAATAATG
66 CTCAGAAATAATG
** * * *
558873 GGGTTGGAGTATCCCCGA-GATAAAAAATTGATGTTTTGGAAATGAAACCGGGATTGAAGTATCC
1 GGGTTGGAGTA-CCCCGATGATAAAAAATCAATATTTTAGAAATAAAACCGGGATTGAAGTATCC
558937 CC
65 CC
558939 GAGATGAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 50 0.89
79 6 0.11
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (78 bp):
GGGTTGGAGTACCCCGATGATAAAAAATCAATATTTTAGAAATAAAACCGGGATTGAAGTATCCC
CTCAGAAATAATG
Found at i:565748 original size:41 final size:40
Alignment explanation
Indices: 565703--565795 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 40
565693 ATTCTTACAA
*
565703 AAGGGGGAAAAGATAATTGTTTAAGAGGAAGAATTTTTTTT
1 AAGGGGGAAAAGATAATTGTTTAAGAGGAAGAA-TTCTTTT
* * *
565744 AAGGGGGAGAAGATAATTGTTTAAGGGGGAGAATTCTTTT
1 AAGGGGGAAAAGATAATTGTTTAAGAGGAAGAATTCTTTT
565784 AAGGGGAGAAAA
1 AAGGGG-GAAAA
565796 ATGAAAACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 12 0.26
41 34 0.74
ACGTcount: A:0.39, C:0.01, G:0.32, T:0.28
Consensus pattern (40 bp):
AAGGGGGAAAAGATAATTGTTTAAGAGGAAGAATTCTTTT
Found at i:565766 original size:22 final size:22
Alignment explanation
Indices: 565703--565776 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
565693 ATTCTTACAA
*
565703 AAGGGGGAAAAGATAATTGTTT
1 AAGGGGGAGAAGATAATTGTTT
* * * *
565725 AAGAGGAAG-A-AT-TTTTTTT
1 AAGGGGGAGAAGATAATTGTTT
565744 AAGGGGGAGAAGATAATTGTTT
1 AAGGGGGAGAAGATAATTGTTT
565766 AAGGGGGAGAA
1 AAGGGGGAGAA
565777 TTCTTTTAAG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 12 0.30
20 3 0.08
21 3 0.08
22 22 0.55
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.27
Consensus pattern (22 bp):
AAGGGGGAGAAGATAATTGTTT
Found at i:566450 original size:33 final size:32
Alignment explanation
Indices: 566408--566471 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 32
566398 CTATCACTAT
566408 TTGTATCGATACATG-GTACAATGTATCGATAAA
1 TTGTATCGATACATGAG-A-AATGTATCGATAAA
566441 TTGTATCGATACATGAAGAAATGTATCGATA
1 TTGTATCGATACATG-AGAAATGTATCGATA
566472 CATAGCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATAAA
Found at i:567776 original size:12 final size:11
Alignment explanation
Indices: 567750--567777 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
567740 TTGCGCATTG
567750 AAAAATAATTT
1 AAAAATAATTT
567761 AAAAATAATTT
1 AAAAATAATTT
567772 AAAAAT
1 AAAAAT
567778 CCAAAGGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATAATTT
Found at i:568547 original size:20 final size:19
Alignment explanation
Indices: 568522--568592 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
568512 ACCCTGAAAA
568522 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
568542 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
568561 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
568582 GTATCGATACA
1 GTATCGATACA
568593 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:568645 original size:53 final size:53
Alignment explanation
Indices: 568562--568698 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
568552 AAATTGCATA
568562 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
568616 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
568669 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
568699 TTGGAAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:568741 original size:10 final size:10
Alignment explanation
Indices: 568722--568752 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
568712 AATCTCATTT
568722 TCACTGTTCA
1 TCACTGTTCA
*
568732 TCACTATTCA
1 TCACTGTTCA
568742 TCACTGTTCA
1 TCACTGTTCA
568752 T
1 T
568753 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:568800 original size:23 final size:22
Alignment explanation
Indices: 568731--568809 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
568721 TTCACTGTTC
*
568731 ATCACTATTCATCACTGTTCATGT
1 ATCACTATTCA-CACT-TTCACGT
*
568755 ATCGA-TA--CATCACTTTCATGT
1 ATC-ACTATTCA-CACTTTCACGT
*
568776 ATCACTGTTCACACTGTTCACGT
1 ATCACTATTCACACT-TTCACGT
568799 ATCACTATTCA
1 ATCACTATTCA
568810 TGTATCGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 1 0.02
21 11 0.23
22 11 0.23
23 18 0.38
24 5 0.11
25 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.38
Consensus pattern (22 bp):
ATCACTATTCACACTTTCACGT
Found at i:569410 original size:34 final size:35
Alignment explanation
Indices: 569347--569413 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
569337 CTAAGTGATT
569347 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
569383 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
569414 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:571325 original size:13 final size:13
Alignment explanation
Indices: 571306--571344 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
571296 ACTATTTATG
571306 ATGTATCGATACA
1 ATGTATCGATACA
* *
571319 CTGTATCAATACA
1 ATGTATCGATACA
571332 ATGTATCGATACA
1 ATGTATCGATACA
571345 TGAATAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:571442 original size:10 final size:10
Alignment explanation
Indices: 571423--571453 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
571413 GTATCGATAC
571423 ATGAACAGTG
1 ATGAACAGTG
*
571433 ATGAATAGTG
1 ATGAACAGTG
571443 ATGAACAGTG
1 ATGAACAGTG
571453 A
1 A
571454 AAAATGAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Done.