Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008322.1 Hibiscus syriacus cultivar Beakdansim tig00111025_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 456513
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:3490 original size:39 final size:37
Alignment explanation
Indices: 3437--3564 Score: 117
Period size: 35 Copynumber: 3.5 Consensus size: 37
3427 ACATATATAC
* **
3437 ACATATATATTATATAGTTTACAAATTGTTTTTGAAAAT
1 ACATATATAATATATAGTTTA-AAA-CATTTTTGAAAAT
3476 ACATATATAATATATAGTTTAAAACATTTTTGAAAAT
1 ACATATATAATATATAGTTTAAAACATTTTTGAAAAT
* *
3513 --ATGTAT-AT-TATAGTTTTTAAAATATTTTTGAAAAT
1 ACATATATAATATATAG--TTTAAAACATTTTTGAAAAT
*
3548 ---TACATAATATATAGTTT
1 ACATATATAATATATAGTTT
3565 TTGAAAGCGT
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
33 5 0.06
34 8 0.10
35 26 0.33
36 5 0.06
37 11 0.14
38 3 0.04
39 20 0.26
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
ACATATATAATATATAGTTTAAAACATTTTTGAAAAT
Found at i:3664 original size:15 final size:16
Alignment explanation
Indices: 3644--3673 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3634 TTAAAAACCA
3644 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
3659 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
3674 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:5459 original size:31 final size:31
Alignment explanation
Indices: 5421--5574 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
5411 GGGTCGAGGG
5421 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
5452 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
5483 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
5514 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
5545 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
5575 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:8552 original size:21 final size:21
Alignment explanation
Indices: 8526--8570 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8516 GATTTCTGGG
* *
8526 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
8547 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
8568 CAA
1 CAA
8571 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:9474 original size:31 final size:31
Alignment explanation
Indices: 9436--9589 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
9426 GGGTCGAGGG
9436 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
9467 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
9498 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
9529 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
9560 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
9590 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:12358 original size:21 final size:21
Alignment explanation
Indices: 12334--12374 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12324 TTTAATAGAT
12334 TTTCTT-ATAATTATATATATA
1 TTTCTTCAT-ATTATATATATA
*
12355 TTTCTTCATATTTTATATAT
1 TTTCTTCATATTATATATAT
12375 GATATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTCTTCATATTATATATATA
Found at i:12985 original size:26 final size:26
Alignment explanation
Indices: 12949--13011 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
12939 GCATTAAGGA
*
12949 AACGAAGACTAATTAATAAAGTTGGC
1 AACGTAGACTAATTAATAAAGTTGGC
12975 AACGTAGACTAATTAATAAAGTTGGC
1 AACGTAGACTAATTAATAAAGTTGGC
13001 AACGTAGACTA
1 AACGTAGACTA
13012 CAAACATTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (26 bp):
AACGTAGACTAATTAATAAAGTTGGC
Found at i:14483 original size:3 final size:3
Alignment explanation
Indices: 14464--14532 Score: 86
Period size: 3 Copynumber: 22.3 Consensus size: 3
14454 AGCCCCTGCA
**
14464 AAT AAT AA- AAT TTT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
14511 AAT AAT AAAT AAAT AAAT AAT A
1 AAT AAT -AAT -AAT -AAT AAT A
14533 TTTTTTAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.03
3 47 0.78
4 11 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:14818 original size:23 final size:23
Alignment explanation
Indices: 14792--14839 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
14782 TATAAGTACA
*
14792 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
14815 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
14838 AT
1 AT
14840 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:15607 original size:23 final size:23
Alignment explanation
Indices: 15581--15653 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
15571 GACACTTACA
*
15581 ATATAACCACTACCTATTACATT
1 ATATAACGACTACCTATTACATT
*
15604 ATATAAACGA-TACATATTACATT
1 ATAT-AACGACTACCTATTACATT
* * *
15627 ATATAAGGGCTACCTATTACATC
1 ATATAACGACTACCTATTACATT
15650 ATAT
1 ATAT
15654 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
22 3 0.07
23 35 0.83
24 4 0.10
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAACGACTACCTATTACATT
Found at i:16054 original size:25 final size:25
Alignment explanation
Indices: 15997--16062 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
15987 CACTCAAAAG
*
15997 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
16022 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
16047 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
16063 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:19172 original size:182 final size:183
Alignment explanation
Indices: 18561--19224 Score: 1258
Period size: 183 Copynumber: 3.6 Consensus size: 183
18551 ACACATTTTA
*
18561 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAAACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
18626 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
18691 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
*
18744 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATACA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
18809 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
18874 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
18927 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
18992 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
19057 TGTAAATGTCGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
131 TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
19109 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
1 GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
* * * **
19174 ACCGGTATATTTATACCGGTTATATTGCAAATTTACCTATTTTATTATAAT
66 ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
19225 ATGTTGAAAG
Statistics
Matches: 473, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
182 148 0.31
183 325 0.69
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (183 bp):
GACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAA
ACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
TGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATG
Found at i:20433 original size:3 final size:3
Alignment explanation
Indices: 20425--20499 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
20415 ACTTGTTTGG
* * * ** * *
20425 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
20473 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
20500 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:20442 original size:12 final size:12
Alignment explanation
Indices: 20429--20511 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
20419 GTTTGGATCA
*
20429 TCATCTTCATCA
1 TCATCTTCATCG
* * *
20441 TCATCATCGTCA
1 TCATCTTCATCG
20453 TCATCTTCATCG
1 TCATCTTCATCG
* *
20465 CCAGCTTCATCG
1 TCATCTTCATCG
*
20477 TCATCATCATCG
1 TCATCTTCATCG
20489 TCATCTTCATCG
1 TCATCTTCATCG
*
20501 TCAGCTTCATC
1 TCATCTTCATC
20512 TTCTGCGACC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:20473 original size:36 final size:36
Alignment explanation
Indices: 20433--20511 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
20423 GGATCATCAT
*
20433 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
20469 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
20505 CTTCATC
1 CTTCATC
20512 TTCTGCGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:20512 original size:18 final size:18
Alignment explanation
Indices: 20453--20514 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
20443 ATCATCGTCA
*
20453 TCATCTTCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
* * * *
20471 TCATCGTCATCATCATCG
1 TCATCTTCATCGTCAGCT
20489 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGTCAGCT
20507 TCATCTTC
1 TCATCTTC
20515 TGCGACCGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:20514 original size:6 final size:6
Alignment explanation
Indices: 20429--20514 Score: 64
Period size: 6 Copynumber: 14.3 Consensus size: 6
20419 GTTTGGATCA
* * * * * * * *
20429 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
20477 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
20515 TGCGACCGCT
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.20, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:22766 original size:197 final size:198
Alignment explanation
Indices: 21953--23032 Score: 2062
Period size: 197 Copynumber: 5.5 Consensus size: 198
21943 TTTAAATTAG
* *
21953 TATCGACACAAACTCTATTAGTGTCGACACATTATTTAGATATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
22018 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
22083 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA-
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
22147 ACAA
196 A-AA
22151 TATCGACACAAACTATATTA--GTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
22214 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
22279 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
22344 AAA
196 AAA
*
22347 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
22412 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
22477 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
22542 AAA
196 AAA
*
22545 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
22610 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
22674 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
22739 AAA
196 AAA
22742 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
22807 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
22872 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
22936 AAA
196 AAA
*
22939 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
23004 ATTGTACCGGTTAGATTGAAAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
23033 CCTTTTGGCC
Statistics
Matches: 871, Mismatches: 7, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
196 193 0.22
197 349 0.40
198 329 0.38
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
AAA
Found at i:23203 original size:19 final size:19
Alignment explanation
Indices: 23157--23205 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
23147 TTATATTCAC
*
23157 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
23176 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
23195 ATACAAAATTA
1 ATACAAAATTA
23206 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:25032 original size:33 final size:33
Alignment explanation
Indices: 24995--25060 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
24985 CATCTTAATA
*
24995 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
25028 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
25061 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:25134 original size:21 final size:21
Alignment explanation
Indices: 25094--25158 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
25084 CCCCTTATGC
* *
25094 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
25115 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
25136 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
25157 CT
1 CT
25159 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:27405 original size:17 final size:18
Alignment explanation
Indices: 27383--27425 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
27373 ATATATCCGG
27383 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
27400 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
27420 TATCAT
1 TATCAT
27426 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:27443 original size:20 final size:19
Alignment explanation
Indices: 27388--27434 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
27378 TCCGGTATCA
27388 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
27407 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
27428 TTTTACC
1 TTTTACC
27435 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:27582 original size:20 final size:20
Alignment explanation
Indices: 27556--27601 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
27546 CACTTTTAAA
27556 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
27575 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
27596 TTTACC
1 TTTACC
27602 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:32540 original size:34 final size:34
Alignment explanation
Indices: 32497--32564 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
32487 CTGGTTCAAG
32497 CTATCAAAGTTATTTGCATAGTGAAAAACTTACC
1 CTATCAAAGTTATTTGCATAGTGAAAAACTTACC
32531 CTATCAAAGTTATTTGCATAGTGAAAAACTTACC
1 CTATCAAAGTTATTTGCATAGTGAAAAACTTACC
32565 TGTATAAGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (34 bp):
CTATCAAAGTTATTTGCATAGTGAAAAACTTACC
Found at i:33694 original size:55 final size:55
Alignment explanation
Indices: 33622--33731 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
33612 ACCAGCCTTT
** * *
33622 GCTTTCTCAACTCAATAATGGAACACTGGAGCAACATCAACAACAAAGAACACCA
1 GCTTTCTCAACTCAATAATGGAACACTACAGAAACATCAACAACAAAGAAAACCA
33677 GCTTTCTCAACAT-AATAATGGAACACTACAGAAACATCAACAACAAAGAAAACCA
1 GCTTTCTCAAC-TCAATAATGGAACACTACAGAAACATCAACAACAAAGAAAACCA
33732 AGAGGTAAGC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 49 0.98
56 1 0.02
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.16
Consensus pattern (55 bp):
GCTTTCTCAACTCAATAATGGAACACTACAGAAACATCAACAACAAAGAAAACCA
Found at i:33922 original size:18 final size:19
Alignment explanation
Indices: 33886--33924 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33876 AGCTCCATAT
**
33886 AAAGAAAAAAAATTCAACA
1 AAAGAAAAAAAATAAAACA
33905 AAAG-AAAAAAATAAAACA
1 AAAGAAAAAAAATAAAACA
33923 AA
1 AA
33925 GGGTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.79, C:0.08, G:0.05, T:0.08
Consensus pattern (19 bp):
AAAGAAAAAAAATAAAACA
Found at i:35280 original size:24 final size:25
Alignment explanation
Indices: 35252--35313 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
35242 AATTCAACCC
35252 AATTTTAAAAAAA-TCATTAGATTT
1 AATTTTAAAAAAATTCATTAGATTT
*
35276 AATTTTAAAAAAATTCATTTGATTT
1 AATTTTAAAAAAATTCATTAGATTT
*
35301 AATTTTTAAAAAA
1 AATTTTAAAAAAA
35314 GTAAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 13 0.37
25 22 0.63
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (25 bp):
AATTTTAAAAAAATTCATTAGATTT
Found at i:36578 original size:9 final size:9
Alignment explanation
Indices: 36564--36624 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
36554 CAGCTGGAAA
36564 ACCGGTTTG
1 ACCGGTTTG
36573 ACCGGTTTTG
1 ACCGG-TTTG
*
36583 AACTGGTTTTG
1 -ACCGG-TTTG
36594 ACCGGTTTG
1 ACCGGTTTG
*
36603 ACCGGTCTG
1 ACCGGTTTG
*
36612 AACCGGTCTG
1 -ACCGGTTTG
36622 ACC
1 ACC
36625 CAACCCGACC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
9 20 0.43
10 17 0.37
11 9 0.20
ACGTcount: A:0.15, C:0.25, G:0.30, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:48372 original size:24 final size:24
Alignment explanation
Indices: 48345--48391 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
48335 TAAATTTTTA
*
48345 TATAAAATTTAAAAAAAATAAAAT
1 TATAAAATTTAAAAAAAAGAAAAT
* * *
48369 TATATATTTTTAAAAAAAGAAAA
1 TATAAAATTTAAAAAAAAGAAAA
48392 CACACAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
TATAAAATTTAAAAAAAAGAAAAT
Found at i:63702 original size:59 final size:59
Alignment explanation
Indices: 63610--63728 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 59
63600 TATGACCCAA
*
63610 ATAGCAAGCCATAAAACTATTAATGCTGGTTCTTATTCAATGAATATGA-AAACTTTTCT
1 ATAGCAAGCCATAAAACTATTAATGCTGGTTCTTATTCAACGAATATGACAAA-TTTTCT
* *
63669 ATAGCAAGCCGTAAAACTATTAATGCTGGTTCTTCTTCAACGAATATGACAAATTTTCT
1 ATAGCAAGCCATAAAACTATTAATGCTGGTTCTTATTCAACGAATATGACAAATTTTCT
63728 A
1 A
63729 CTGACAAGCA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 53 0.95
60 3 0.05
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (59 bp):
ATAGCAAGCCATAAAACTATTAATGCTGGTTCTTATTCAACGAATATGACAAATTTTCT
Found at i:65780 original size:17 final size:17
Alignment explanation
Indices: 65758--65791 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
65748 CTTAAACTTG
*
65758 AAATTTGTAGTTTTAAT
1 AAATTTGTAATTTTAAT
*
65775 AAATTTTTAATTTTAAT
1 AAATTTGTAATTTTAAT
65792 CTTAACTCAA
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:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
AAATTTGTAATTTTAAT
Found at i:66595 original size:83 final size:82
Alignment explanation
Indices: 66508--67031 Score: 531
Period size: 83 Copynumber: 6.3 Consensus size: 82
66498 TTTTTATACA
* * * * * * *
66508 AAACGTCGCGACAAAGTAGTACTTTAG-TGGATCTTGTATAAAAATGTCGTAATAGGGTTTATCT
1 AAACGCCGCAACAGAGTAGTACTTTAGCAGG-T-TTGTATAAAAATGCCGCAATAGGGTTCATCT
*
66572 ATAGTGTCATTTTTTCAAC
64 ATAGTGGCATTTTTTCAAC
* * * **
66591 AAACGCCGCAACAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGCTACAATA-GGTT-ATAC-
1 AAACGCCGCAACAGAGTAGTACTTTAGCAG-GTTTGTATAAAAATGCCGCAATAGGGTTCAT-CT
* * *
66653 ATAGTGGC-GTTTCTCAAT
64 ATAGTGGCATTTTTTCAAC
** *
66671 AAACGCCGTGACAGAGTAGTACTTTAGCGGCGTTTGTAT-AAAATGCCGCAATAGGGTTCATCTA
1 AAACGCCGCAACAGAGTAGTACTTTAGCAG-GTTTGTATAAAAATGCCGCAATAGGGTTCATCTA
*
66735 TAGTGGCATTTTTTAAAC
65 TAGTGGCATTTTTTCAAC
* ** **
66753 AAACGCCGCAAAAGAGTAGTACTTTAGTGGTGTTTGTATAAAAATGTTGCAATAGGGTTCATCTA
1 AAACGCCGCAACAGAGTAGTACTTTAGCAG-GTTTGTATAAAAATGCCGCAATAGGGTTCATCTA
66818 TAGTGGCATTTTTTCAAC
65 TAGTGGCATTTTTTCAAC
* * * * * * * *
66836 AAAAGCCGCAAAATAGTAGTACTTTAGCAGCGTTTTTATACAAATGACGTAATAGGGTTCATTTA
1 AAACGCCGCAACAGAGTAGTACTTTAGCAG-GTTTGTATAAAAATGCCGCAATAGGGTTCATCTA
*
66901 TAGTGGCGTTTTTTTCAAC
65 TAGTGGC-ATTTTTTCAAC
* * * * *
66920 AAATGCCACAACAGAGTAGTACTTTAGCGGGTTTTTTTATACAAACT-CCGCAATAGGGTTCATC
1 AAACGCCGCAACAGAGTAGTACTTTAGCAGG--TTTGTATA-AAAATGCCGCAATAGGGTTCATC
*
66984 TATAGTGGCATTTTTTAAAC
63 TATAGTGGCATTTTTTCAAC
*
67004 AAACGCCGCAACAGAGTAGTTCTTTAGC
1 AAACGCCGCAACAGAGTAGTACTTTAGC
67032 GGCCTTGTTT
Statistics
Matches: 367, Mismatches: 62, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
79 10 0.03
80 47 0.13
81 19 0.05
82 45 0.12
83 140 0.38
84 71 0.19
85 32 0.09
86 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (82 bp):
AAACGCCGCAACAGAGTAGTACTTTAGCAGGTTTGTATAAAAATGCCGCAATAGGGTTCATCTAT
AGTGGCATTTTTTCAAC
Found at i:66781 original size:42 final size:41
Alignment explanation
Indices: 66581--67057 Score: 158
Period size: 41 Copynumber: 11.6 Consensus size: 41
66571 TATAGTGTCA
* * **
66581 TTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGC
1 TTTTTTAAACAAACGCCGCAATAGAGTAGTACTTTAGTGGC
* * ** *
66622 GTTTTTATACAAACGCTACAATAG-GTTA-TAC-ATAGTGGC
1 TTTTTTAAACAAACGCCGCAATAGAG-TAGTACTTTAGTGGC
* * * * ** * *
66661 GTTTCTCAATAAACGCCGTGACAGAGTAGTACTTTAGCGGC
1 TTTTTTAAACAAACGCCGCAATAGAGTAGTACTTTAGTGGC
* * * * * *
66702 GTTTGTATA-AAATGCCGCAATAGGGT--TCATCTATAGTGGC
1 TTTTTTAAACAAACGCCGCAATAGAGTAGT-A-CTTTAGTGGC
*
66742 ATTTTTTAAACAAACGCCGCAAAAGAGTAGTACTTTAGTGG-
1 -TTTTTTAAACAAACGCCGCAATAGAGTAGTACTTTAGTGGC
* * ** * *
66783 TGTTTGTATAA-AAATGTTGCAATAGGGT--TCATCTATAGTGGC
1 T-TTTTTA-AACAAACGCCGCAATAGAGTAGT-A-CTTTAGTGGC
* * * * **
66825 ATTTTTTCAACAAAAGCCGCAAAATAGTAGTACTTTAGCAGC
1 -TTTTTTAAACAAACGCCGCAATAGAGTAGTACTTTAGTGGC
* * * * * * *
66867 GTTTTTATACAAATGACGTAATAGGGT--TCATTTATAGTGGC
1 TTTTTTAAACAAACGCCGCAATAGAGTAGT-ACTT-TAGTGGC
* * * * * *
66908 GTTTTTTTCAACAAATGCCACAACAGAGTAGTACTTTAGCGGGT
1 --TTTTTTAAACAAACGCCGCAATAGAGTAGTACTTTAG-TGGC
* * * *
66952 TTTTTTATACAAACTCCGCAATAGGGT--TCATCTATAGTGGC
1 TTTTTTAAACAAACGCCGCAATAGAGTAGT-A-CTTTAGTGGC
* * *
66993 ATTTTTTAAACAAACGCCGCAACAGAGTAGTTCTTTAGCGGCC
1 -TTTTTTAAACAAACGCCGCAATAGAGTAGTACTTTAGTGG-C
*
67036 TTGTTTT--ACAAACGTCGCAATA
1 TT-TTTTAAACAAACGCCGCAATA
67058 ATTTGGTATG
Statistics
Matches: 306, Mismatches: 97, Indels: 66
0.65 0.21 0.14
Matches are distributed among these distances:
38 1 0.00
39 25 0.08
40 34 0.11
41 104 0.34
42 103 0.34
43 30 0.10
44 8 0.03
45 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (41 bp):
TTTTTTAAACAAACGCCGCAATAGAGTAGTACTTTAGTGGC
Found at i:66808 original size:162 final size:165
Alignment explanation
Indices: 66508--67034 Score: 546
Period size: 162 Copynumber: 3.2 Consensus size: 165
66498 TTTTTATACA
* * * * *
66508 AAACGTCGCGACAAAGTAGTACTTTAGTGG-ATCTTGTATAAAAATGTCGTAATAGGGTTTATCT
1 AAACGCCGCGACAAAGTAGTACTTTAGCGGCGT-TTGTAT-AAAATGACGTAATAGGGTTCATCT
* * *
66572 ATAGTGTCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGCGTTTTTATACAAACG
64 ATAGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGCGTTTGTATAAAAACG
*
66637 CTACAATA-GGTT-ATAC-ATAGTGGC-GTTTCTCAAT
129 CTACAATAGGGTTCAT-CTATAGTGGCAGTTTCTCAAC
* * * *
66671 AAACGCCGTGACAGAGTAGTACTTTAGCGGCGTTTGTATAAAATGCCGCAATAGGGTTCATCTAT
1 AAACGCCGCGACAAAGTAGTACTTTAGCGGCGTTTGTATAAAATGACGTAATAGGGTTCATCTAT
* * ** * * *
66736 AGTGGCATTTTTTAAACAAACGCCGCAAAAGAGTAGTACTTTAGTGGTGTTTGTATAAAAATGTT
66 AGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGCGTTTGTATAAAAACGCT
* * *
66801 GCAATAGGGTTCATCTATAGTGGCATTTTTTCAAC
131 ACAATAGGGTTCATCTATAGTGGCAGTTTCTCAAC
* * * * *
66836 AAAAGCCGC-AAAATAGTAGTACTTTAGCAGCGTTTTTATACAAATGACGTAATAGGGTTCATTT
1 AAACGCCGCGACAA-AGTAGTACTTTAGCGGCGTTTGTATA-AAATGACGTAATAGGGTTCATCT
* * * * * *
66900 ATAGTGGCGTTTTTTTCAACAAATGCCACAACAGAGTAGTACTTTAGC-GGGTTTTTTTATACAA
64 ATAGTGGC-ATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGCG--TTTGTATAAAA
* ** * * *
66964 ACTCCGCAATAGGGTTCATCTATAGTGGCATTTTTTAAAC
126 ACGCTACAATAGGGTTCATCTATAGTGGCAGTTTCTCAAC
* * *
67004 AAACGCCGCAACAGAGTAGTTCTTTAGCGGC
1 AAACGCCGCGACAAAGTAGTACTTTAGCGGC
67035 CTTGTTTTAC
Statistics
Matches: 303, Mismatches: 50, Indels: 17
0.82 0.14 0.05
Matches are distributed among these distances:
162 83 0.27
163 37 0.12
164 13 0.04
165 38 0.13
166 30 0.10
167 33 0.11
168 67 0.22
169 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (165 bp):
AAACGCCGCGACAAAGTAGTACTTTAGCGGCGTTTGTATAAAATGACGTAATAGGGTTCATCTAT
AGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGCGTTTGTATAAAAACGCT
ACAATAGGGTTCATCTATAGTGGCAGTTTCTCAAC
Found at i:66846 original size:245 final size:248
Alignment explanation
Indices: 66522--67030 Score: 710
Period size: 245 Copynumber: 2.1 Consensus size: 248
66512 GTCGCGACAA
* * *
66522 AGTAGTACTTTAGTGGATCTTGTATAAAAATGTCGTAATAGGGTTTATCTATAGTGTCATTTTTT
1 AGTAGTACTTTAGTGGATCTTGTATAAAAATGTCGCAATAGGGTTCATCTATAGTGGCATTTTTT
* *
66587 CAACAAACGCCGCAACAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGCTAC-AATA-GGTT-
66 CAACAAAAGCCGCAAAAGAGTAGTACTTTAGCAGCGTTTTTATACAAACG--ACGAATAGGGTTC
* ***
66649 ATACATAGTGGCG-TTTCTCAATAAACGCCGTGACAGAGTAGTACTTTAGCGGCG-TTTGTATA-
129 ATACATAGTGGCGTTTTCTCAACAAACGCCACAACAGAGTAGTACTTTAGCGG-GTTTTGTATAC
66711 AAA-TGCCGCAATAGGGTTCATCTATAGTGGCATTTTTTAAACAAACGCCGCAAAAG
193 AAACT-CCGCAATAGGGTTCATCTATAGTGGCATTTTTTAAACAAACGCCGCAAAAG
* *
66767 AGTAGTACTTTAGTGG-TGTTTGTATAAAAATGTTGCAATAGGGTTCATCTATAGTGGCATTTTT
1 AGTAGTACTTTAGTGGAT-CTTGTATAAAAATGTCGCAATAGGGTTCATCTATAGTGGCATTTTT
* *
66831 TCAACAAAAGCCGCAAAATAGTAGTACTTTAGCAGCGTTTTTATACAAATGACGTAATAGGGTTC
65 TCAACAAAAGCCGCAAAAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGACG-AATAGGGTTC
** * * *
66896 ATTTATAGTGGCGTTTTTTTCAACAAATGCCACAACAGAGTAGTACTTTAGCGGGTTTTTTTATA
129 ATACATAGTGGCG-TTTTCTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGG-TTTTGTATA
*
66961 CAAACTCCGCAATAGGGTTCATCTATAGTGGCATTTTTTAAACAAACGCCGCAACAG
192 CAAACTCCGCAATAGGGTTCATCTATAGTGGCATTTTTTAAACAAACGCCGCAAAAG
*
67018 AGTAGTTCTTTAG
1 AGTAGTACTTTAG
67031 CGGCCTTGTT
Statistics
Matches: 233, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
243 2 0.01
244 1 0.00
245 108 0.46
246 4 0.02
247 11 0.05
248 1 0.00
249 33 0.14
250 7 0.03
251 65 0.28
252 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (248 bp):
AGTAGTACTTTAGTGGATCTTGTATAAAAATGTCGCAATAGGGTTCATCTATAGTGGCATTTTTT
CAACAAAAGCCGCAAAAGAGTAGTACTTTAGCAGCGTTTTTATACAAACGACGAATAGGGTTCAT
ACATAGTGGCGTTTTCTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGGTTTTGTATACAAA
CTCCGCAATAGGGTTCATCTATAGTGGCATTTTTTAAACAAACGCCGCAAAAG
Found at i:73528 original size:31 final size:30
Alignment explanation
Indices: 73490--73583 Score: 111
Period size: 31 Copynumber: 3.0 Consensus size: 30
73480 AATTCATTTC
73490 ATATTTTATCTAAAGTTTAAGGGTCAAATT
1 ATATTTTATCTAAAGTTTAAGGGTCAAATT
73520 GATATTTTATCTAAAGTTTATA-GGTCAAATT
1 -ATATTTTATCTAAAGTTTA-AGGGTCAAATT
* *
73551 AGTATTTCATCTAAA-TTAAAGGGTGCCAAATT
1 A-TATTTTATCTAAAGTTTAAGGGT--CAAATT
73583 A
1 A
73584 AAAATTAACT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.12
31 40 0.71
32 8 0.14
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (30 bp):
ATATTTTATCTAAAGTTTAAGGGTCAAATT
Found at i:75121 original size:215 final size:215
Alignment explanation
Indices: 74750--75183 Score: 868
Period size: 215 Copynumber: 2.0 Consensus size: 215
74740 CAAGTAGACA
74750 TGAAATAAACTCAATACAAGGGGATAATCTTTGGATTAAGTTAGCAAAAACCCGACGAAGTATCA
1 TGAAATAAACTCAATACAAGGGGATAATCTTTGGATTAAGTTAGCAAAAACCCGACGAAGTATCA
74815 ATAAAGGACCAAATGGAATAAACAACATAATAAGATTAGGCAAGTTGTCATCTTGCTAATGGATC
66 ATAAAGGACCAAATGGAATAAACAACATAATAAGATTAGGCAAGTTGTCATCTTGCTAATGGATC
74880 ACAGTCACCTTATACTCAATAATGGCGTCGCCGGTAGTGAAATTCGCGTAGTAAGTCTTAAGCTT
131 ACAGTCACCTTATACTCAATAATGGCGTCGCCGGTAGTGAAATTCGCGTAGTAAGTCTTAAGCTT
74945 AGCGTACCCCTGCGCCATTC
196 AGCGTACCCCTGCGCCATTC
74965 TGAAATAAACTCAATACAAGGGGATAATCTTTGGATTAAGTTAGCAAAAACCCGACGAAGTATCA
1 TGAAATAAACTCAATACAAGGGGATAATCTTTGGATTAAGTTAGCAAAAACCCGACGAAGTATCA
75030 ATAAAGGACCAAATGGAATAAACAACATAATAAGATTAGGCAAGTTGTCATCTTGCTAATGGATC
66 ATAAAGGACCAAATGGAATAAACAACATAATAAGATTAGGCAAGTTGTCATCTTGCTAATGGATC
75095 ACAGTCACCTTATACTCAATAATGGCGTCGCCGGTAGTGAAATTCGCGTAGTAAGTCTTAAGCTT
131 ACAGTCACCTTATACTCAATAATGGCGTCGCCGGTAGTGAAATTCGCGTAGTAAGTCTTAAGCTT
75160 AGCGTACCCCTGCGCCATTC
196 AGCGTACCCCTGCGCCATTC
75180 TGAA
1 TGAA
75184 CTTTGCCCTC
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
215 219 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (215 bp):
TGAAATAAACTCAATACAAGGGGATAATCTTTGGATTAAGTTAGCAAAAACCCGACGAAGTATCA
ATAAAGGACCAAATGGAATAAACAACATAATAAGATTAGGCAAGTTGTCATCTTGCTAATGGATC
ACAGTCACCTTATACTCAATAATGGCGTCGCCGGTAGTGAAATTCGCGTAGTAAGTCTTAAGCTT
AGCGTACCCCTGCGCCATTC
Found at i:77151 original size:2 final size:2
Alignment explanation
Indices: 77144--77172 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
77134 AATATTAATA
77144 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77173 TTTATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83205 original size:35 final size:36
Alignment explanation
Indices: 83120--83238 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
83110 ATCCCATTAT
* *
83120 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
83156 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
83192 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
83227 CAATTTTTCAAA
1 C-ATTTTTCAAA
83239 TTTGGTTGCC
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 14 0.18
37 28 0.37
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:83582 original size:12 final size:12
Alignment explanation
Indices: 83565--83589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
83555 GATAGCACTT
83565 TGACTGTCACAA
1 TGACTGTCACAA
83577 TGACTGTCACAA
1 TGACTGTCACAA
83589 T
1 T
83590 ACAAGACATT
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:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TGACTGTCACAA
Found at i:87813 original size:36 final size:37
Alignment explanation
Indices: 87744--87862 Score: 154
Period size: 36 Copynumber: 3.3 Consensus size: 37
87734 TCTCATTGTC
* * *
87744 ATTTTTC-AACAAATATATACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAATATTTACCAAACTTTGAAAAACA
* * *
87780 ATTTTTCAAAGAAACATTTACCAAA-TTTTAAAAACC
1 ATTTTTCAAAGAAATATTTACCAAACTTTGAAAAACA
*
87816 A-TTTTCAAAGAAATATTTACCAAACTTTGAAAACCA
1 ATTTTTCAAAGAAATATTTACCAAACTTTGAAAAACA
87852 ATTTTTCAAAG
1 ATTTTTCAAAG
87863 TTGGTTGCCA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
35 22 0.31
36 26 0.37
37 23 0.32
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (37 bp):
ATTTTTCAAAGAAATATTTACCAAACTTTGAAAAACA
Found at i:87827 original size:35 final size:36
Alignment explanation
Indices: 87743--87862 Score: 136
Period size: 35 Copynumber: 3.3 Consensus size: 36
87733 ATCTCATTGT
* * * *
87743 CATTTTTC-AACAAATATATACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAA-TTTTAAAAAC
*
87779 TATTTTTCAAAGAAACATTTACCAAATTTTAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAATTTTAAAAAC
* * *
87815 CA-TTTTCAAAGAAATATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAATTTTAAAAAC
87850 CAATTTTTCAAAG
1 C-ATTTTTCAAAG
87863 TTGGTTGCCA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 31 0.43
36 18 0.25
37 23 0.32
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAATTTTAAAAAC
Found at i:96678 original size:29 final size:27
Alignment explanation
Indices: 96645--96712 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
96635 CATGTATCAT
*
96645 ATTTAGGATTTAGGTTTCAGAGATTTAGA
1 ATTTAGGATTTAGATTT-AGAGA-TTAGA
* *
96674 ATTTAGAAATTTTGATTTAGAGATTAGA
1 ATTTAG-GATTTAGATTTAGAGATTAGA
*
96702 ATTTACGATTT
1 ATTTAGGATTT
96713 TATATTTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 4 0.12
28 10 0.30
29 11 0.33
30 8 0.24
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTTAGGATTTAGATTTAGAGATTAGA
Found at i:96705 original size:14 final size:15
Alignment explanation
Indices: 96645--96706 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
96635 CATGTATCAT
96645 ATTTAG-GATTTAG-
1 ATTTAGAGATTTAGA
*
96658 GTTTCAGAGATTTAGA
1 ATTT-AGAGATTTAGA
* *
96674 ATTTAGAAATTTTG-
1 ATTTAGAGATTTAGA
96688 ATTTAGAGA-TTAGA
1 ATTTAGAGATTTAGA
96702 ATTTA
1 ATTTA
96707 CGATTTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
13 6 0.15
14 15 0.38
15 15 0.38
16 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (15 bp):
ATTTAGAGATTTAGA
Found at i:97272 original size:29 final size:32
Alignment explanation
Indices: 97229--97295 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
97219 ACTTTCAAGA
* *
97229 GTTATAAAATAATCATT-AATTTATT-AAATT
1 GTTACAAAATAATCATTAAATCTATTAAAATT
97259 GTTACAAAAT-ATCATTAAATCTATTAAAATT
1 GTTACAAAATAATCATTAAATCTATTAAAATT
97290 -TTACAA
1 GTTACAA
97296 TTATTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 6 0.18
30 22 0.67
31 5 0.15
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (32 bp):
GTTACAAAATAATCATTAAATCTATTAAAATT
Found at i:98424 original size:75 final size:76
Alignment explanation
Indices: 98300--98449 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 76
98290 CATAATTTTG
* * *
98300 TTTGGATTAATATATAATTGTGATTTCTTTACTTGTCGGTTGAACTGGTTGATTGAGTTTAATTC
1 TTTGGAGTAATATATAATTGTGAATTCTTTACTTGTCGATTGAACTGGTTGATTGAGTTTAATTC
98365 AATTAGTATTA
66 AATTAGTATTA
98376 TTTGGAGTAATATATAATTGTGAATT-TTTACTTGTCGATTGAACTGGTTGATTGAGTTTAATTC
1 TTTGGAGTAATATATAATTGTGAATTCTTTACTTGTCGATTGAACTGGTTGATTGAGTTTAATTC
98440 AATTAGTATT
66 AATTAGTATT
98450 TGTCATTGGT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 47 0.66
76 24 0.34
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (76 bp):
TTTGGAGTAATATATAATTGTGAATTCTTTACTTGTCGATTGAACTGGTTGATTGAGTTTAATTC
AATTAGTATTA
Found at i:98839 original size:20 final size:20
Alignment explanation
Indices: 98816--98856 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
98806 TTGTGCCAAC
98816 ACTCATTATGTATATATATT
1 ACTCATTATGTATATATATT
98836 ACTCATTATGTATATATATT
1 ACTCATTATGTATATATATT
98856 A
1 A
98857 TGTAAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (20 bp):
ACTCATTATGTATATATATT
Found at i:100204 original size:70 final size:71
Alignment explanation
Indices: 100121--100310 Score: 274
Period size: 70 Copynumber: 2.7 Consensus size: 71
100111 GTGAGGTTTC
* *
100121 GGCTTATAAATCGGAATCGGCGGCGGAAGCGGCTTCTTATAAACCGGAACTGGATGAGGCTTAT-
1 GGCTTGTAAATCGGAAACGGCGGCGGAAGCGGCTTCTTATAAACCGGAACTGGATGAGGCTTATA
*
100185 ACTGGA
66 ACCGGA
*
100191 GGCTTGTAAATCGGAACCGGCGGCGGAAGCGGCTTCTTATAAACCGGAACTGGATGAGGCTTATA
1 GGCTTGTAAATCGGAAACGGCGGCGGAAGCGGCTTCTTATAAACCGGAACTGGATGAGGCTTAT-
100256 AACCGGA
65 AACCGGA
* * * * * *
100263 GGCTTGTAGACCGGAAACGGCGGTGGTAGCGGCTTCTTGTAAATCGGA
1 GGCTTGTAAATCGGAAACGGCGGCGGAAGCGGCTTCTTATAAACCGGA
100311 GGGTGAGGGT
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 62 0.57
72 46 0.43
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (71 bp):
GGCTTGTAAATCGGAAACGGCGGCGGAAGCGGCTTCTTATAAACCGGAACTGGATGAGGCTTATA
ACCGGA
Found at i:100240 original size:33 final size:33
Alignment explanation
Indices: 100123--100240 Score: 85
Period size: 33 Copynumber: 3.5 Consensus size: 33
100113 GAGGTTTCGG
* *
100123 CTTATAAATCGGAATCGGCGGCGGAAGCGGCTT
1 CTTATAAACCGGAACCGGCGGCGGAAGCGGCTT
* * ** ***
100156 CTTATAAACCGGAACTGGATGAGGCTTATA-CTGGAGG
1 CTTATAAACCGGAAC-CG--GCGGCGGA-AGC-GGCTT
* *
100193 CTTGTAAATCGGAACCGGCGGCGGAAGCGGCTT
1 CTTATAAACCGGAACCGGCGGCGGAAGCGGCTT
100226 CTTATAAACCGGAAC
1 CTTATAAACCGGAAC
100241 TGGATGAGGC
Statistics
Matches: 59, Mismatches: 20, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
33 29 0.49
34 7 0.12
36 7 0.12
37 16 0.27
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (33 bp):
CTTATAAACCGGAACCGGCGGCGGAAGCGGCTT
Found at i:102261 original size:23 final size:23
Alignment explanation
Indices: 102234--102279 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
102224 ATTTACGACG
102234 GACTTTTCAAATAGAATTTAAAC
1 GACTTTTCAAATAGAATTTAAAC
102257 GACTTTTCAAATAGAATTTAAAC
1 GACTTTTCAAATAGAATTTAAAC
102280 ATTTACAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (23 bp):
GACTTTTCAAATAGAATTTAAAC
Found at i:103436 original size:3 final size:3
Alignment explanation
Indices: 103428--103470 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
103418 GGGGATAGTT
103428 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
103471 GGGTAAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:108963 original size:12 final size:12
Alignment explanation
Indices: 108946--108970 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
108936 TTTTTCACAT
108946 GAAGATAATGAG
1 GAAGATAATGAG
108958 GAAGATAATGAG
1 GAAGATAATGAG
108970 G
1 G
108971 GTGACGGTGG
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GAAGATAATGAG
Found at i:110551 original size:20 final size:20
Alignment explanation
Indices: 110528--110614 Score: 59
Period size: 20 Copynumber: 4.2 Consensus size: 20
110518 ATTTTAAAAG
110528 TTATTAAATGATCATAAATT
1 TTATTAAATGATCATAAATT
* * *
110548 TTATTGAATGGTTATAAAATAT
1 TTATTAAATGATCAT-AAAT-T
* * *
110570 TTATTAAATTTATTA-AAATA
1 TTATTAAA-TGATCATAAATT
* *
110590 TTATAAAATAATCATTAAATT
1 TTATTAAATGATCA-TAAATT
110611 TTAT
1 TTAT
110615 AAAGTTATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
19 4 0.08
20 19 0.37
21 16 0.31
22 8 0.16
23 4 0.08
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (20 bp):
TTATTAAATGATCATAAATT
Found at i:110582 original size:31 final size:31
Alignment explanation
Indices: 110559--110628 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
110549 TATTGAATGG
* *
110559 TTATAAAATATTTATTAAATTTATTAAAATA
1 TTATAAAATAATCATTAAATTTATTAAAATA
*
110590 TTATAAAATAATCATTAAATTT-TATAAAGTTA
1 TTATAAAATAATCATTAAATTTAT-TAAA-ATA
110622 TTATAAA
1 TTATAAA
110629 TTATTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 24 0.71
32 9 0.26
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
TTATAAAATAATCATTAAATTTATTAAAATA
Found at i:110625 original size:11 final size:10
Alignment explanation
Indices: 110559--110634 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 10
110549 TATTGAATGG
*
110559 TTATAAAATA
1 TTATAAATTA
110569 TTTATTAAATTTA
1 -TTA-TAAA-TTA
110582 TTA-AAA-TA
1 TTATAAATTA
*
110590 TTATAAAATAA
1 TTAT-AAATTA
*
110601 TCATTAAATT-
1 TTA-TAAATTA
110611 TTATAAAGTTA
1 TTATAAA-TTA
110622 TTATAAATTA
1 TTATAAATTA
110632 TTA
1 TTA
110635 ATTTTTATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
8 5 0.10
9 4 0.08
10 16 0.31
11 17 0.33
12 8 0.15
13 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (10 bp):
TTATAAATTA
Found at i:120168 original size:2 final size:2
Alignment explanation
Indices: 120088--120157 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
120078 TGCTTCAGAT
120088 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
120130 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
120158 CAAGCATATA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128881 original size:18 final size:18
Alignment explanation
Indices: 128832--128882 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
128822 TGAAAACTAA
* *
128832 AAAAAATAAAAGAAAAAT
1 AAAAAATGAAATAAAAAT
*
128850 AAAAAATGATATAAAAAT
1 AAAAAATGAAATAAAAAT
128868 AAATAAAT-AAATAAA
1 AAA-AAATGAAATAAA
128883 CAACAAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAAAATGAAATAAAAAT
Found at i:130163 original size:42 final size:42
Alignment explanation
Indices: 130104--130189 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
130094 GCCTGGGGTA
130104 TCCCAGACAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
1 TCCCAGACAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
*
130146 TCCCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
1 TCCCAGACAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
130188 TC
1 TC
130190 TATTTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.36
Consensus pattern (42 bp):
TCCCAGACAACCCCTCAAAATTGTAACTTAGTGTTAATTTTT
Found at i:130285 original size:82 final size:82
Alignment explanation
Indices: 130148--130309 Score: 306
Period size: 82 Copynumber: 2.0 Consensus size: 82
130138 TAATTTTTTC
* *
130148 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATTTTTTCTATTTTTTTAATTAATATAATTG
1 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
130213 CTACCCCTAATATTACT
66 CTACCCCTAATATTACT
130230 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
1 CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
130295 CTACCCCTAATATTA
66 CTACCCCTAATATTA
130310 TGTGTAAATG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (82 bp):
CCAGGCAACCCCTCAAAATTGTAACTTAGTGTTAATATTTTCTATTTTTTTAATTAATACAATTG
CTACCCCTAATATTACT
Found at i:133685 original size:18 final size:18
Alignment explanation
Indices: 133662--133707 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
133652 AATAAGTTTG
133662 ACAAGTTTGACCGATTTA
1 ACAAGTTTGACCGATTTA
133680 ACAAGTTTGACCGATTTA
1 ACAAGTTTGACCGATTTA
133698 ACAAGTTTGA
1 ACAAGTTTGA
133708 TATGCAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (18 bp):
ACAAGTTTGACCGATTTA
Found at i:137442 original size:17 final size:19
Alignment explanation
Indices: 137409--137443 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
137399 TAAAGTTTTT
137409 ATCTCAATTATTTATATTC
1 ATCTCAATTATTTATATTC
137428 ATCT-AATTA-TTATATT
1 ATCTCAATTATTTATATT
137444 TTCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (19 bp):
ATCTCAATTATTTATATTC
Found at i:138626 original size:18 final size:19
Alignment explanation
Indices: 138589--138626 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
138579 GTTTTTTTTA
*
138589 TCATATTCAGTATGTCATT
1 TCATATTCAGGATGTCATT
*
138608 TCATTTTCAGGAT-TCATT
1 TCATATTCAGGATGTCATT
138626 T
1 T
138627 ACTGTACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.50
Consensus pattern (19 bp):
TCATATTCAGGATGTCATT
Found at i:139701 original size:94 final size:94
Alignment explanation
Indices: 139540--139727 Score: 313
Period size: 94 Copynumber: 2.0 Consensus size: 94
139530 AATTGTTACT
** * *
139540 ACTTGCAAACCTTTAGTTCTGCGAGTGTTTATATAAGTGAATATATTACTCATGTGAACATTTAA
1 ACTTGCAAACCTTTAGTTCCACAAGTGTTTATATAAGTGAATATATTACTCATGCGAACATTTAA
* *
139605 GAATGCAAATATAAGATCCATGTAAGTTC
66 GAATACAAATATAAGATCCATGCAAGTTC
*
139634 ACTTGCAAACCTTTAGTTCCACAAGTGTTTGTATAAGTGAATATATTACTCATGCGAACATTTAA
1 ACTTGCAAACCTTTAGTTCCACAAGTGTTTATATAAGTGAATATATTACTCATGCGAACATTTAA
139699 GAATACAAATATAAGATCCATGCAAGTTC
66 GAATACAAATATAAGATCCATGCAAGTTC
139728 TCAGACACAT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (94 bp):
ACTTGCAAACCTTTAGTTCCACAAGTGTTTATATAAGTGAATATATTACTCATGCGAACATTTAA
GAATACAAATATAAGATCCATGCAAGTTC
Found at i:142446 original size:20 final size:20
Alignment explanation
Indices: 142418--142463 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
142408 TCCATAAAAT
*
142418 ACAATTATTAGGAACACTTG
1 ACAACTATTAGGAACACTTG
142438 ACAACTATTAGGAACACTTG
1 ACAACTATTAGGAACACTTG
142458 ACAACT
1 ACAACT
142464 TTCTTGTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (20 bp):
ACAACTATTAGGAACACTTG
Found at i:143740 original size:18 final size:18
Alignment explanation
Indices: 143717--143769 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
143707 TTGGTACATA
143717 TAAATAAATAAATAATAT
1 TAAATAAATAAATAATAT
143735 TAAATACAATAAA-AATAT
1 TAAATA-AATAAATAATAT
* *
143753 GATATAAATACAATAAT
1 TAAATAAATA-AATAAT
143770 TCAAATTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAATAAATAAATAATAT
Found at i:143763 original size:22 final size:20
Alignment explanation
Indices: 143714--143768 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
143704 TTTTTGGTAC
*
143714 ATATAAATA-AATAAATAAT
1 ATATAAATACAATAAAAAAT
143733 AT-TAAATACAATAAAAATAT
1 ATATAAATACAATAAAAA-AT
143753 GATATAAATACAATAA
1 -ATATAAATACAATAA
143769 TTCAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 6 0.19
19 9 0.29
20 2 0.06
21 2 0.06
22 12 0.39
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
ATATAAATACAATAAAAAAT
Found at i:158675 original size:33 final size:33
Alignment explanation
Indices: 158616--158680 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
158606 TGCCCCCTCG
* **
158616 ATCCTGGGTTCATCCTCTTCTCTAGATAACTCA
1 ATCCTGGGGTCATCCTCACCTCTAGATAACTCA
*
158649 ATCCTGGGGTCATCCATCACCT-TAGATGACTC
1 ATCCTGGGGTCATCC-TCACCTCTAGATAACTC
158681 GACTCCCCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (33 bp):
ATCCTGGGGTCATCCTCACCTCTAGATAACTCA
Found at i:162705 original size:2 final size:2
Alignment explanation
Indices: 162698--162742 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
162688 TTTTCAAAAT
162698 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
162740 TA T
1 TA T
162743 TAATAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:164017 original size:33 final size:33
Alignment explanation
Indices: 163976--164075 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
163966 AAAATGCTTC
163976 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
164009 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
* * *
164042 AGTTTTAGTGTTTTAATAAGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
164075 G
1 G
164076 ATTTATTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
Found at i:164154 original size:20 final size:17
Alignment explanation
Indices: 164127--164176 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
164117 AGGGCCTACA
164127 AAAATAATAAAAT-AAT
1 AAAATAATAAAATAAAT
164143 AATAATAATAATAAATAAAT
1 AA-AATAAT-A-AAATAAAT
164163 AAATATAATAAAAT
1 AAA-ATAATAAAAT
164177 GTTTTTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 5 0.17
19 6 0.21
20 10 0.34
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATAATAAAATAAAT
Found at i:164828 original size:85 final size:85
Alignment explanation
Indices: 164523--165047 Score: 626
Period size: 84 Copynumber: 6.3 Consensus size: 85
164513 AATGGAATCA
* * * * * * * **
164523 AACTCGAAGGTC-TTTGG-TGACAGATAACCCTTATAGCCTTGAGTTGTGTTGTAAATGATGTGC
1 AACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTG-
* * *
164586 CCTCGAAGCTGAGTGTAATCG
65 CCTTGGAGCTGAGTGTAGTCG
* *
164607 AACTCGAGGGTC---T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
1 AACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
164667 CTTGGAGCTGAGTGTAGTCG
66 CTTGGAGCTGAGTGTAGTCG
* * *
164687 AACTCGAAGGT-TTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGC
1 AACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
*
164751 CTTGGAGCTGAGTGTAGTTG
66 CTTGGAGCTGAGTGTAGTCG
*
164771 AACTCGAAGGTCTTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
1 AACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
* *
164836 CTTGAAGCTGAGCGTAGTCG
66 CTTGGAGCTGAGTGTAGTCG
* * * *
164856 AACTCGAAGGT-ATTTGGTTGGCAAATAACCCTTCTCAACTTAAGTTATGCTACAAATGATATGC
1 AACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
164920 CTTGGAGCTGAGTGTAGTC-
66 CTTGGAGCTGAGTGTAGTCG
* * *
164939 AATCTCGAAGGCCTTTTGGTTGGCAGATAACCCTTCTCGACTTAA-TCTATAC-AGCAAATGTTG
1 AA-CTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT-TATGCTA-CAAATGATG
* * *
165002 TGCCTTTGAGCTGAGCGTAATCG
63 TGCCTTGGAGCTGAGTGTAGTCG
* *
165025 AACTTGAAGGTC-TTTGGTGGGCA
1 AACTCGAAGGTCTTTTGGTTGGCA
165048 CAATTCCCTT
Statistics
Matches: 382, Mismatches: 47, Indels: 24
0.84 0.10 0.05
Matches are distributed among these distances:
80 28 0.07
81 35 0.09
82 2 0.01
83 2 0.01
84 169 0.44
85 144 0.38
86 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (85 bp):
AACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGC
CTTGGAGCTGAGTGTAGTCG
Found at i:164832 original size:169 final size:169
Alignment explanation
Indices: 164620--165047 Score: 655
Period size: 169 Copynumber: 2.5 Consensus size: 169
164610 TCGAGGGTCT
*
164620 TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGTGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * * * *
164685 CGAACTCGAAGGTTTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
66 CGAACTCGAAGGTATTTGGTTGGCAAATAACCCTTCTCAACTTAAGTTATGCTACAAATGATATG
* *
164750 CCTTGGAGCTGAGTGTAGTTGAA-CTCGAAGGTCTTTTGG
131 CCTTGGAGCTGAGTGTAG-TCAATCTCGAAGGCCTTTTGG
*
164789 TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGAAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGT
164854 CGAACTCGAAGGTATTTGGTTGGCAAATAACCCTTCTCAACTTAAGTTATGCTACAAATGATATG
66 CGAACTCGAAGGTATTTGGTTGGCAAATAACCCTTCTCAACTTAAGTTATGCTACAAATGATATG
164919 CCTTGGAGCTGAGTGTAGTCAATCTCGAAGGCCTTTTGG
131 CCTTGGAGCTGAGTGTAGTCAATCTCGAAGGCCTTTTGG
* * * *
164958 TTGGCAGATAACCCTTCTCGACTTAA-TCTATAC-AGCAAATGTTGTGCCTTTGAGCTGAGCGTA
1 TTGGCAGATAGCCCTTCTCGACTTAAGT-TATGCTA-CAAATGATGTGCCTTGGAGCTGAGCGTA
* * * *
165021 ATCGAACTTGAAGGTCTTTGGTGGGCA
64 GTCGAACTCGAAGGTATTTGGTTGGCA
165048 CAATTCCCTT
Statistics
Matches: 238, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
168 5 0.02
169 233 0.98
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (169 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTATTTGGTTGGCAAATAACCCTTCTCAACTTAAGTTATGCTACAAATGATATG
CCTTGGAGCTGAGTGTAGTCAATCTCGAAGGCCTTTTGG
Found at i:165368 original size:110 final size:110
Alignment explanation
Indices: 165159--165569 Score: 564
Period size: 110 Copynumber: 3.8 Consensus size: 110
165149 ATATGTTGCT
* * ** *
165159 TCGAGGCCAATATCATTCGCCGTGAAGTTGAAATTGACTC----TGAAACTGGAAAA-TTGTTTG
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTG
* *
165219 TTGACAGCCAGTCTCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
165265 TCGAGTCCAATATCATTTGTTGTGAAGTTAAAATTGCCTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
165330 TGACAGTCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * * * * *
165375 TTGAGACCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAAT-AAAATGAAAAAGTTTTTTG
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTG-AAAAGTTGTTTG
*
165439 TTGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* *
165485 TCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGG
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
165550 TGACAGTCAGTCACCCCTTC
66 TGACAGTCAGTCGCCCCTTC
165570 TGTAACATCC
Statistics
Matches: 267, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
106 34 0.13
109 10 0.04
110 218 0.82
111 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:165543 original size:220 final size:216
Alignment explanation
Indices: 165152--165569 Score: 622
Period size: 220 Copynumber: 1.9 Consensus size: 216
165142 CAAACATATA
* * *
165152 TGTTGCTTCGAGGCCAATATCATTCGCCGTGAAGTTGAAATTGACTCTGAAACTGGAAAATTGTT
1 TGTTGCTTCGAGACCAATATCATTCGCCGTGAAGTTGAAATTGACTCTGAAAATGAAAAATTGTT
* *
165217 TGTTGACAGCCAGTCTCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATT
66 TGTTGACAGCCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATT
* * * * *
165282 TGTTGTGAAGTTAAAATTGCCTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGCCGCCCC
131 CGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGGTGACAGTCAGCCACCCC
165347 TTCGTTGTGAAGTTGAGCTTG
196 TTCGTTGTGAAGTTGAGCTTG
* ** *
165368 TGTTGTCTT-GAGACCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATAAAATGAAAAAG
1 TGTTG-CTTCGAGACCAATATCATTCGCCGTGAAGTTGAAATTGACTCT---GAAAATGAAAAA-
* *
165432 TTTTTTGTTGACAGTCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
61 TTGTTTGTTGACAGCCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
* *
165497 TCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGGTGACAGTCAGTC
126 TCATTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGGTGACAGTCAGCC
165562 ACCCCTTC
191 ACCCCTTC
165570 TGTAACATCC
Statistics
Matches: 179, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
216 40 0.22
217 3 0.02
219 9 0.05
220 127 0.71
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (216 bp):
TGTTGCTTCGAGACCAATATCATTCGCCGTGAAGTTGAAATTGACTCTGAAAATGAAAAATTGTT
TGTTGACAGCCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATT
CGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGGTGACAGTCAGCCACCCC
TTCGTTGTGAAGTTGAGCTTG
Found at i:167610 original size:2 final size:2
Alignment explanation
Indices: 167603--167642 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
167593 GAACATGTGA
167603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
167643 GATAAGACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:167927 original size:18 final size:18
Alignment explanation
Indices: 167904--167977 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
167894 AGGGATTATC
167904 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
167922 AGTGGTTCTTCGGAAAAAAT
1 AGTGGTCCTTCGG--GACAT
167942 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
167961 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
167978 AATATTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 28 0.61
19 3 0.07
20 3 0.07
21 12 0.26
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:171257 original size:13 final size:13
Alignment explanation
Indices: 171239--171263 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
171229 TTCTCCAGAA
171239 CTTCTTCTTCCTT
1 CTTCTTCTTCCTT
171252 CTTCTTCTTCCT
1 CTTCTTCTTCCT
171264 CTCCTCCCGT
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:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
CTTCTTCTTCCTT
Found at i:173054 original size:2 final size:2
Alignment explanation
Indices: 173047--173083 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
173037 AGGAAAGATA
173047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
173084 GGAAGATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:173452 original size:18 final size:19
Alignment explanation
Indices: 173426--173483 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 19
173416 TCGAGGGATT
173426 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* *
173445 AT-AGTGGTTCTTCGGAAC
1 ATCAGTGGTCCTTCGGGAC
173463 AATCAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCCTTCGGGAC
173483 A
1 A
173484 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.42
19 5 0.15
20 14 0.42
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:173472 original size:20 final size:20
Alignment explanation
Indices: 173426--173484 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
173416 TCGAGGGATT
173426 ATCAGTGGTCCTTCGGGAC-
1 ATCAGTGGTCCTTCGGGACA
* *
173445 AT-AGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACA
173464 ATCAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCGGGACA
173484 A
1 A
173485 ATATTCAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.41
19 4 0.12
20 16 0.47
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCAGTGGTCCTTCGGGACA
Found at i:178064 original size:6 final size:6
Alignment explanation
Indices: 178053--178130 Score: 50
Period size: 6 Copynumber: 12.7 Consensus size: 6
178043 TGTTGGATTG
* * * * *
178053 TAAAAA TAAAAA TAAACA TGAGAAAA TAATAA TAAAAAA TTAATA TAATAA
1 TAAAAA TAAAAA TAAAAA T-A-AAAA TAAAAA T-AAAAA TAAAAA TAAAAA
** *
178104 TATTAA TAAAAA TGAAAA -AAAAA TAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAA
178131 TAAATGTATA
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
5 4 0.07
6 39 0.72
7 7 0.13
8 4 0.07
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (6 bp):
TAAAAA
Found at i:178200 original size:21 final size:22
Alignment explanation
Indices: 178185--178232 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
178175 TAAAATTAGG
178185 AGAAAATAAA-AAAAAATATAA
1 AGAAAATAAATAAAAAATATAA
*
178206 AGTAAATAAATAAAAAATA-AA
1 AGAAAATAAATAAAAAATATAA
*
178227 ATAAAA
1 AGAAAA
178233 AGAATAAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (22 bp):
AGAAAATAAATAAAAAATATAA
Found at i:178239 original size:21 final size:22
Alignment explanation
Indices: 178187--178239 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
178177 AAATTAGGAG
178187 AAAATAAA-AAAAAATATAAAGT
1 AAAA-AAATAAAAAATATAAAGT
*
178209 AAATAAATAAAAAATA-AAA-T
1 AAAAAAATAAAAAATATAAAGT
178229 AAAAAGAATAA
1 AAAAA-AATAA
178240 GTCAAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.19
21 11 0.41
22 11 0.41
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAAAAATAAAAAATATAAAGT
Found at i:178246 original size:25 final size:25
Alignment explanation
Indices: 178188--178236 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
178178 AATTAGGAGA
*
178188 AAAT-AAAAAAAAATATAAAGTAAAT
1 AAATAAAAAAAAAATAAAAAG-AAAT
178213 AAATAAAAAATAAAATAAAAAGAA
1 AAATAAAAAA-AAAATAAAAAGAA
178237 TAAGTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 7 0.33
27 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (25 bp):
AAATAAAAAAAAAATAAAAAGAAAT
Found at i:178559 original size:33 final size:33
Alignment explanation
Indices: 178507--178588 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
178497 GTCCTAATTG
178507 GACTCAAAATAC-TTCGGTTTTAGTGTTTCAATAA
1 GACTC-AAATACGTT-GGTTTTAGTGTTTCAATAA
* *
178541 GACTCAAATACGTTGGTTTTAGTGTTTTAATAT
1 GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
178574 GACTCAAATACGTTG
1 GACTCAAATACGTTG
178589 ATTTATTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 38 0.84
34 7 0.16
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (33 bp):
GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
Found at i:178677 original size:20 final size:21
Alignment explanation
Indices: 178641--178689 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 21
178631 AGGCCTACAA
178641 AAATAAAATAATAATAATAAT
1 AAATAAAATAATAATAATAAT
178662 AAAT-AAAT-A-AAT-ATAAT
1 AAATAAAATAATAATAATAAT
178679 ATAATAAAATA
1 A-AATAAAATA
178690 TTTTTGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.24
18 6 0.24
19 5 0.20
20 4 0.16
21 4 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAAATAATAATAATAAT
Found at i:180060 original size:24 final size:23
Alignment explanation
Indices: 180020--180081 Score: 97
Period size: 24 Copynumber: 2.7 Consensus size: 23
180010 TACTGTATGG
*
180020 TAAACCAGAATGGCAGCAGCAGC
1 TAAACCAGAATGGCAGCAACAGC
180043 TAAACCAGAAATGGCAGCAACAGC
1 TAAACCAG-AATGGCAGCAACAGC
*
180067 AAAACCAGAATGGCA
1 TAAACCAGAATGGCA
180082 ACAATAAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 15 0.42
24 21 0.58
ACGTcount: A:0.45, C:0.24, G:0.23, T:0.08
Consensus pattern (23 bp):
TAAACCAGAATGGCAGCAACAGC
Found at i:181017 original size:28 final size:28
Alignment explanation
Indices: 180973--181026 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
180963 CTAATTATTT
180973 ATTATATATTTAGAAT-AATTGTATTTTA
1 ATTATATATTTAGAATAAATT-TATTTTA
*
181001 ATTATATTTATTA-AATAAATTTATTT
1 ATTATATAT-TTAGAATAAATTTATTT
181027 ATTTCGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
ATTATATATTTAGAATAAATTTATTTTA
Found at i:181795 original size:19 final size:20
Alignment explanation
Indices: 181749--181796 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
181739 TTAAATTTTT
181749 TAAATTAAA-ATTAAATTAA
1 TAAATTAAATATTAAATTAA
* * *
181768 TATACTAAATA-TATATTAA
1 TAAATTAAATATTAAATTAA
181787 TAAATTAAAT
1 TAAATTAAAT
181797 TTATTATCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTAAATATTAAATTAA
Found at i:188975 original size:36 final size:38
Alignment explanation
Indices: 188935--189014 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 38
188925 TATTAATAAA
188935 TAATAAATAATAAAA-A-ATTAACTAAT-ATATTATTTT
1 TAATAAATAATAAAATATATTAACTAATAATATTA-TTT
*
188971 TAATAAATAATAAAATATTATTAATTAATAATATTATTT
1 TAATAAATAATAAAATA-TATTAACTAATAATATTATTT
189010 TAATA
1 TAATA
189015 CCAAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 15 0.38
37 1 0.03
39 17 0.44
40 6 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (38 bp):
TAATAAATAATAAAATATATTAACTAATAATATTATTT
Found at i:189012 original size:18 final size:18
Alignment explanation
Indices: 188952--189013 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 18
188942 TAATAAAAAA
*
188952 TTAACTAAT-ATATTATTT
1 TTAATTAATAATATTA-TT
* *
188970 TTAATAAATAATAAAATATT
1 TTAATTAATAAT--ATTATT
188990 ATTAATTAATAATATTATT
1 -TTAATTAATAATATTATT
189009 TTAAT
1 TTAAT
189014 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 12 0.34
19 7 0.20
20 2 0.06
21 14 0.40
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTAATAATATTATT
Found at i:189357 original size:42 final size:42
Alignment explanation
Indices: 189200--189574 Score: 430
Period size: 41 Copynumber: 9.0 Consensus size: 42
189190 CAAAATACTA
* * *
189200 TACTTTAGTGGCGTTTGT-ATA-AAAACGCCGCTAAAGA-ATCG
1 TACTTTTGTGGCGTTT-TAATACCAAACGCCGCTATAGACA-CG
* * * * *
189241 TAATGTAGTGGCGTTTTTATA-CAAACGCCGCTATAAACTA-G
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAC-ACG
* *
189282 TA-TTTTAGTGGCGTTTTTATA-CAAACGCTGCTATAGACACG
1 TACTTTT-GTGGCGTTTTAATACCAAACGCCGCTATAGACACG
* * *
189323 TACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCA
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
* *
189365 TACTTTAGTGGCATTTT--TACACAAACGCCGCTATAGACACG
1 TACTTTTGTGGCGTTTTAATAC-CAAACGCCGCTATAGACACG
*
189406 TACTTTTGTGGCGTTTTAATACCAAATGCCGCTATAGACACG
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
* **
189448 TACTTTTGTGGCGTTTTAATACCAAATGCCGCTATAGATTCG
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
*
189490 TACTTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACG
1 TACTTTTGTGGCGTTTTAATAC-CAAACGCCGCTATAGACACG
*
189531 TACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACACG
1 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
189573 TA
1 TA
189575 AAAAAACGTT
Statistics
Matches: 291, Mismatches: 30, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
40 10 0.03
41 143 0.49
42 132 0.45
43 6 0.02
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (42 bp):
TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACG
Found at i:189382 original size:83 final size:83
Alignment explanation
Indices: 189199--189574 Score: 440
Period size: 83 Copynumber: 4.5 Consensus size: 83
189189 GCAAAATACT
* * * * * *
189199 ATACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-
1 ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACA-CGTACTTTAGTGGCGTTTTAATAC
189262 CAAACGCCGCTATA-A-AC
65 CAAACGCCGCTATAGACAC
* * *
189279 TAGTATTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACACGTACTTTTGTGGCGTTTTAATA
1 -A-TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATA
* *
189344 CCAAACGACGCTATAGACTC
64 CCAAACGCCGCTATAGACAC
* * *
189364 ATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
1 ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
*
189429 AAATGCCGCTATAGACAC
66 AAACGCCGCTATAGACAC
* * * * **
189447 GTACTTTTGTGGCGTTTTAATACCAAATGCCGCTATAGATTCGTACTTTAGTGGCGTTTT--TAC
1 ATACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATAC
189510 ACAAACGCCGCTATAGACAC
65 -CAAACGCCGCTATAGACAC
* * *
189530 GTACTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACACGTA
1 ATACTTTAGTGGCGTTTTTAT-ACAAACGCCGCTATAGACACGTA
189575 AAAAAACGTT
Statistics
Matches: 256, Mismatches: 31, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
81 1 0.00
82 54 0.21
83 164 0.64
84 36 0.14
85 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (83 bp):
ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
AAACGCCGCTATAGACAC
Found at i:189481 original size:125 final size:124
Alignment explanation
Indices: 189246--189574 Score: 518
Period size: 125 Copynumber: 2.6 Consensus size: 124
189236 AATCGTAATG
* * *
189246 TAGTGGCGTTTTTATACAAACGCCGCTATAAACTA-GTA-TTTTAGTGGCGTTTTTATACAAACG
1 TAGTGGCGTTTTTACACAAACGCCGCTATAGAC-ACGTACTTTT-GTGGCGTTTTAATACAAACG
*
189309 CTGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTT
64 CCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTT
* *
189370 TAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAATGC
1 TAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATA-CAAACGC
* * * *
189435 CGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAATGCCGCTATAGATTCGTACTT
65 CGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTT
189495 TAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAACAAACGC
1 TAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAAT-ACAAACGC
189560 CGCTATAGACACGTA
65 CGCTATAGACACGTA
189575 AAAAAACGTT
Statistics
Matches: 189, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
123 1 0.01
124 46 0.24
125 141 0.75
126 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (124 bp):
TAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACAAACGCC
GCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTT
Found at i:193988 original size:21 final size:21
Alignment explanation
Indices: 193946--194004 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
193936 TGATTTATTA
**
193946 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
193967 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
* *
193988 TTATCGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
194005 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:194204 original size:43 final size:42
Alignment explanation
Indices: 194157--194424 Score: 331
Period size: 43 Copynumber: 6.3 Consensus size: 42
194147 ACAAGATCTT
* * *
194157 TTGCGGTGTTTGTGGGAAAAAAGCCGCTAAATATTAAGACCTA
1 TTGCGGCGTTTGT-GGAAAAAAGCCGCTAAATATCAACACCTA
*
194200 TTGCGGCGTTTGTGGACAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGA-AAAAAGCCGCTAAATATCAACACCTA
*
194243 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGGAAAAAA-GCCGCTAAATATCAACACCTA
* *
194286 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTG-TGGAAAAAAGCCGCTAAATATCAACACCTA
* *
194329 TTGCGGCGTTTGTTGG-AAAAAGCCACCAAATATCAACACCTA
1 TTGCGGCGTTTG-TGGAAAAAAGCCGCTAAATATCAACACCTA
** * * ***
194371 TTGCGGCGTTTGTCCAACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTGGAA-AAAAGCCGCTAAATATCAACACCTA
194414 TTGCGGCGTTT
1 TTGCGGCGTTT
194425 TTTGTTACCA
Statistics
Matches: 200, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.00
42 42 0.21
43 149 0.75
44 8 0.04
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (42 bp):
TTGCGGCGTTTGTGGAAAAAAGCCGCTAAATATCAACACCTA
Found at i:194263 original size:86 final size:84
Alignment explanation
Indices: 194132--194424 Score: 365
Period size: 86 Copynumber: 3.4 Consensus size: 84
194122 TTTGTATCTT
* * * * * * *
194132 AAAACGCCGCTATATA-CAAGATCTTTTGCGGTGTTTGTGGGAAAAAAGCCGCTAAATATTAAGA
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-GGAAAAAAGCCGCTAAATATCAACA
194196 CCTATTGCGGCGTTTGTGGA
65 CCTATTGCGGCGTTTGTGGA
*
194216 CAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAAC
1 -AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGAAAAAA-GCCGCTAAATATCAAC
194281 ACCTATTGCGGCGTTTGTTGGA
64 ACCTATTGCGGCGTTTG-TGGA
* * *
194303 AAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTTGG-AAAAAGCCACCAAATATCAACA
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTG-TGGAAAAAAGCCGCTAAATATCAACA
**
194367 CCTATTGCGGCGTTTGTCCA
65 CCTATTGCGGCGTTTGTGGA
* ***
194387 ACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTT
1 A-AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
194425 TTTGTTACCA
Statistics
Matches: 184, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
84 3 0.02
85 84 0.46
86 90 0.49
87 7 0.04
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (84 bp):
AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGAAAAAAGCCGCTAAATATCAACAC
CTATTGCGGCGTTTGTGGA
Found at i:197865 original size:2 final size:2
Alignment explanation
Indices: 197858--197885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
197848 TTATAATTCT
197858 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
197886 AGTAGAATAA
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):
TA
Found at i:199048 original size:20 final size:19
Alignment explanation
Indices: 199022--199080 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
199012 ATCGATCCAC
* *
199022 AATGATATAACAGGTAAAA
1 AATGATAAAACCGGTAAAA
*
199041 ATATGATAAAACCGGTATCAA
1 A-ATGATAAAACCGGTA-AAA
199062 AATGATAAAACCGGTAAAA
1 AATGATAAAACCGGTAAAA
199081 CGCTACCGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.20
Consensus pattern (19 bp):
AATGATAAAACCGGTAAAA
Found at i:199054 original size:179 final size:180
Alignment explanation
Indices: 198643--199113 Score: 703
Period size: 179 Copynumber: 2.6 Consensus size: 180
198633 GATCCAAATT
* * * * * **
198643 AAAAATATATCGATCTACAACGATATAACAGGTAAAACTATGACAAAACCGTTATTGAAATGATA
1 AAAAATATATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGATA
* * * * * *
198708 AAACCGGTAAAGCGGTATCGGATATATTTAAAGTGTCGGTACTTTAATATAATGATCGACACTTC
66 AAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
198773 GTTAATTTAAAAGAGAAGCAGTTTTAGCACCTGTAAAGTGTCGATGCTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCACC--TAAAGTGTCGATACTTTAA
* *
198825 AAAAATGTATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGATG
1 AAAAATATATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGATA
* *
198890 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
198954 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCC-AAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCACCTAAAGTGTCGATACTTTAA
* *
199003 AAAAAAATTATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATA-TATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGAT
199068 AAAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGATACTTT
199114 TGTAAGTACG
Statistics
Matches: 264, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
178 22 0.08
179 100 0.38
181 46 0.17
182 96 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (180 bp):
AAAAATATATCGATCCACAATGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGATA
AAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCACCTAAAGTGTCGATACTTTAA
Found at i:201227 original size:15 final size:15
Alignment explanation
Indices: 201207--201239 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
201197 TGGTTGTATT
*
201207 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
201222 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
201237 GGG
1 GGG
201240 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:201348 original size:21 final size:21
Alignment explanation
Indices: 201322--201386 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
201312 AAGACAATCA
*
201322 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
201343 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* * *
201364 AGAGTCAAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
201385 AG
1 AG
201387 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:201462 original size:33 final size:33
Alignment explanation
Indices: 201420--201485 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
201410 AAATATATGG
*
201420 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
201453 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
201486 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:201711 original size:33 final size:33
Alignment explanation
Indices: 201673--201760 Score: 131
Period size: 33 Copynumber: 2.7 Consensus size: 33
201663 AAAATATGAA
*
201673 GAAGAAAAGAGGGAGGAGGAAGAAGAAGATATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
201706 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
* * * *
201739 AAAGAAATGAGGAAGAAGGAAG
1 GAAGAAAAGAGGGAGGAGGAAG
201761 TCGATGTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
Found at i:203333 original size:19 final size:19
Alignment explanation
Indices: 203309--203357 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
203299 AATGTAGGTT
203309 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
203328 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
203347 TAATTTTGTAT
1 TAATTTTGTAT
203358 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:204043 original size:200 final size:200
Alignment explanation
Indices: 203586--204571 Score: 1751
Period size: 200 Copynumber: 4.9 Consensus size: 200
203576 AATTTACAAT
* * *
203586 ATGGCAAACAGGGTGCAATCATAAAGTGTCGATCCATATATAAAAAGTGTCGATTCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
203651 CGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
203716 ATGAGAGAATAGGTGTAATATA--TATCGACACTTTTTAATTTTATGTTGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
*
203779 AATAA
196 AATGA
* *
203784 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATAAATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
203849 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
203914 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
203979 AATGA
196 AATGA
*
203984 ATGGCAAACAGGGTGCAACCATAAAGTATCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
204049 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACTGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
204114 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
204179 AATGA
196 AATGA
* *
204184 ATGACAATCAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
204249 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
204314 ATGAGAGAATAGGTGTAATATATGTATCAATACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
204379 AATGA
196 AATGA
* * * *
204384 ATGGCAATCAAGGTGCAACCATAAAGTGTTGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
204449 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
204514 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTTATTTTGTGTCGATACTATT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
204572 TTAAATATCG
Statistics
Matches: 758, Mismatches: 28, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
198 146 0.19
200 612 0.81
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:210558 original size:21 final size:20
Alignment explanation
Indices: 210534--210650 Score: 132
Period size: 21 Copynumber: 5.8 Consensus size: 20
210524 CATATTCACA
210534 TTGCGATAG-TCCAAGTTCG
1 TTGCGATAGCTCCAAGTTCG
** *
210553 CATTGCGAT-TTTCCAAATTCG
1 --TTGCGATAGCTCCAAGTTCG
210574 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
210595 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
210616 TTGTGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
210637 TTGCGATAG-TCCAA
1 TTGCGATAGCTCCAA
210651 AATCGCAACG
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
19 12 0.14
21 74 0.86
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
TTGCGATAGCTCCAAGTTCG
Found at i:210610 original size:42 final size:42
Alignment explanation
Indices: 210534--210647 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 42
210524 CATATTCACA
*
210534 TTGCGATAG--TCCAAGTTCGCATTGCGAT--TTTCCAAATTCG
1 TTGCGATAGTCTCCAAGTTCG--TTGCGATAGTCTCCAAATTCG
*
210574 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCG
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCG
*
210616 TTGTGATAGTCTCCAAGTTCGTTGCGATAGTC
1 TTGCGATAGTCTCCAAGTTCGTTGCGATAGTC
210648 CAAAATCGCA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
40 16 0.24
42 51 0.76
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCG
Found at i:210751 original size:6 final size:6
Alignment explanation
Indices: 210740--210766 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
210730 GACACGTATT
210740 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
210767 CGAGACGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:211993 original size:21 final size:21
Alignment explanation
Indices: 211771--211989 Score: 320
Period size: 21 Copynumber: 10.5 Consensus size: 21
211761 TGCGATTTTG
*
211771 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
211792 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
211813 GACTGTCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* *
211834 GACTGTCGTAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
211855 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
211876 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
211897 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
211918 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
211939 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
211960 -A-AATCGCAATGCGAACTT-G-
1 GACTATCGCAA--CGAACTTGGA
211979 GACTATCGCAA
1 GACTATCGCAA
211990 TGCGCGATTT
Statistics
Matches: 181, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
19 7 0.04
20 3 0.02
21 171 0.94
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:212916 original size:23 final size:23
Alignment explanation
Indices: 212857--212916 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
212847 CTTGTTAAAA
*
212857 ACCTATTTTATTATATAAGCGTT
1 ACCTAATTTATTATATAAGCGTT
* *
212880 ATCT-ATTACATTATATAAGCGTT
1 ACCTAATT-TATTATATAAGCGTT
*
212903 ACCTAATTTGTTAT
1 ACCTAATTTATTAT
212917 TGTACTTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 2 0.07
23 24 0.83
24 3 0.10
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (23 bp):
ACCTAATTTATTATATAAGCGTT
Found at i:212941 original size:87 final size:87
Alignment explanation
Indices: 212782--212942 Score: 259
Period size: 87 Copynumber: 1.9 Consensus size: 87
212772 AAATAGGTCA
*
212782 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTTATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
**
212847 CTTGTTAAAAACCTATTTTATT
66 CCGGTTAAAAACCTATTTTATT
* * * *
212869 ATATAAGCGTTATCTATTACATTATATAAGCGTTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
212934 CCGGTTAAA
66 CCGGTTAAA
212943 TAATATAACA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAAAACCTATTTTATT
Found at i:221821 original size:17 final size:17
Alignment explanation
Indices: 221791--221824 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
221781 GATAGTCTTC
*
221791 ATTACAATGGATGAAGA
1 ATTACAATGCATGAAGA
*
221808 ATTACAATTCATGAAGA
1 ATTACAATGCATGAAGA
221825 TAATAGAAGA
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:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (17 bp):
ATTACAATGCATGAAGA
Found at i:223915 original size:29 final size:30
Alignment explanation
Indices: 223874--223937 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
223864 GAGCAGAAAT
* * *
223874 TAAATGTCGAAAATGAGTAATTGAAAATAA
1 TAAATGTCGAAAAAGAGCAATTGAAAACAA
223904 TAAATG-CGAAAAAGAGCAATTGAAAACAA
1 TAAATGTCGAAAAAGAGCAATTGAAAACAA
223933 TAAAT
1 TAAAT
223938 AATGTCGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (30 bp):
TAAATGTCGAAAAAGAGCAATTGAAAACAA
Found at i:223991 original size:3 final size:3
Alignment explanation
Indices: 223975--224033 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
223965 TTTATAAAAA
223975 TAT T-T TAT TA- TAT TAT TATT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA-T TAT
*
224020 T-T TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT
224034 ATGCCCCACA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
2 6 0.12
3 37 0.76
4 6 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:223998 original size:15 final size:15
Alignment explanation
Indices: 223978--224035 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
223968 ATAAAAATAT
223978 TTTATTATATTATTA
1 TTTATTATATTATTA
223993 TTTATTATTATTATTA
1 TTTATTA-TATTATTA
*
224009 TTATTATTTATTTTATTA
1 -T-TTA-TTATATTATTA
224027 TTT-TTATAT
1 TTTATTATAT
224036 GCCCCACACT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 5 0.14
15 7 0.19
16 10 0.27
17 2 0.05
18 10 0.27
19 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:224693 original size:16 final size:15
Alignment explanation
Indices: 224674--224769 Score: 51
Period size: 16 Copynumber: 6.4 Consensus size: 15
224664 ATTTTAGCAT
224674 TTTTTAGTATTATTTA
1 TTTTTAGTATT-TTTA
224690 -TTTTATGT-TTTTTA
1 TTTTTA-GTATTTTTA
*
224704 CTTTTTATTATTTTTA
1 -TTTTTAGTATTTTTA
224720 -TTTTA-T-TTTATTA
1 TTTTTAGTATTT-TTA
* * **
224733 CTTTTAGAATTTAACA
1 TTTTTAGTATTT-TTA
224749 TTTTTTA-TATTTTTA
1 -TTTTTAGTATTTTTA
224764 TTTTTA
1 TTTTTA
224770 TTTAATATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
12 3 0.05
13 4 0.06
14 20 0.32
15 9 0.14
16 22 0.35
17 5 0.08
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTTAGTATTTTTA
Found at i:224744 original size:28 final size:30
Alignment explanation
Indices: 224674--224737 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 30
224664 ATTTTAGCAT
*
224674 TTTTTAGTATTATTTATTTTATGTTTTTTAC
1 TTTTTAGTATT-TTTATTTTATGTTTATTAC
*
224705 TTTTTATTATTTTTATTTTAT-TTTATTAC
1 TTTTTAGTATTTTTATTTTATGTTTATTAC
224734 TTTT
1 TTTT
224738 AGAATTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 11 0.35
30 10 0.32
31 10 0.32
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (30 bp):
TTTTTAGTATTTTTATTTTATGTTTATTAC
Found at i:226835 original size:15 final size:15
Alignment explanation
Indices: 226815--226844 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
226805 TTATCACCTT
226815 TCGTAGTCCACTGTC
1 TCGTAGTCCACTGTC
226830 TCGTAGTCCACTGTC
1 TCGTAGTCCACTGTC
226845 ACCGCTCGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.33, G:0.20, T:0.33
Consensus pattern (15 bp):
TCGTAGTCCACTGTC
Done.