Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012730.1 Corchorus capsularis cultivar CVL-1 contig12751, 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: 110939
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2934 original size:16 final size:16
Alignment explanation
Indices: 2762--2937 Score: 69
Period size: 16 Copynumber: 11.1 Consensus size: 16
2752 GGTAATCAAG
2762 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
* *
2778 GGAAGTAATTAGTAAA
1 AGAAGTAATCAGTAAA
** * *
2794 AGGGGCAA-AAGTAAA
1 AGAAGTAATCAGTAAA
*
2809 AGAAGAAATCAGTAAA
1 AGAAGTAATCAGTAAA
* ** *
2825 AGTAAAAGAACAAAAGCAAA
1 AG---AAGTA-ATCAGTAAA
*
2845 AGAAGTAATCCG-AAA
1 AGAAGTAATCAGTAAA
* *
2860 A-ATGGTAATC---AAG
1 AGA-AGTAATCAGTAAA
* * *
2873 AGAAGTAACCCGTAGA
1 AGAAGTAATCAGTAAA
2889 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
* * *
2905 ATGGAGCAA-AAGTAAA
1 A-GAAGTAATCAGTAAA
2921 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
2937 A
1 A
2938 TGGTAATTAA
Statistics
Matches: 115, Mismatches: 33, Indels: 24
0.67 0.19 0.14
Matches are distributed among these distances:
13 8 0.07
14 2 0.02
15 26 0.23
16 57 0.50
17 9 0.08
19 5 0.04
20 8 0.07
ACGTcount: A:0.56, C:0.08, G:0.22, T:0.15
Consensus pattern (16 bp):
AGAAGTAATCAGTAAA
Found at i:2995 original size:14 final size:15
Alignment explanation
Indices: 2963--2995 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2953 AGAGTGAAAT
2963 AGTAATCAGTAGAAG
1 AGTAATCAGTAGAAG
2978 -GTAATCAGTA-AAG
1 AGTAATCAGTAGAAG
2991 AGTAA
1 AGTAA
2996 AATAGTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.21
Consensus pattern (15 bp):
AGTAATCAGTAGAAG
Found at i:2999 original size:36 final size:35
Alignment explanation
Indices: 2949--3038 Score: 135
Period size: 36 Copynumber: 2.5 Consensus size: 35
2939 GGTAATTAAG
* * *
2949 AGTAAGAGTGAAATAGTAATCAGTAGAAGGTAATC
1 AGTAAGAGTAAAATAGTAATCAGTAAAAGATAATC
2984 AGTAAAGAGTAAAATAGTAATCAGTAAAAGATAATC
1 AGT-AAGAGTAAAATAGTAATCAGTAAAAGATAATC
*
3020 AGTAAGAGTAAAACAGTAA
1 AGTAAGAGTAAAATAGTAA
3039 CCAGGAAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 18 0.36
36 32 0.64
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (35 bp):
AGTAAGAGTAAAATAGTAATCAGTAAAAGATAATC
Found at i:3020 original size:14 final size:15
Alignment explanation
Indices: 2991--3024 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2981 ATCAGTAAAG
*
2991 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
3006 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
3020 AGTAA
1 AGTAA
3025 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:3086 original size:21 final size:20
Alignment explanation
Indices: 3062--3108 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
3052 AGTGTTCATT
3062 AGTAAGAGTCAAATA-GTAATC
1 AGTAAGAGT-AAA-AGGTAATC
*
3083 AGTAAAGAGTAAAAGGTGATC
1 AGT-AAGAGTAAAAGGTAATC
3104 AGTAA
1 AGTAA
3109 TTCAAAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 14 0.61
22 6 0.26
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.21
Consensus pattern (20 bp):
AGTAAGAGTAAAAGGTAATC
Found at i:3185 original size:29 final size:28
Alignment explanation
Indices: 3160--3222 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
3150 GTAAAAAGTG
3160 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
* *
3188 GTAATTAGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
*
3215 ATAA-AAAT
1 GTAATAAAT
3223 GATAAAAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.07
27 17 0.57
28 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.19, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:4491 original size:17 final size:18
Alignment explanation
Indices: 4469--4502 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4459 AGCAACTAAT
*
4469 TTCTTT-GCTTTTCATTG
1 TTCTTTCGCTTTGCATTG
4486 TTCTTTCGCTTTGCATT
1 TTCTTTCGCTTTGCATT
4503 TTGCATCCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.06, C:0.21, G:0.12, T:0.62
Consensus pattern (18 bp):
TTCTTTCGCTTTGCATTG
Found at i:11670 original size:27 final size:27
Alignment explanation
Indices: 11578--11648 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
11568 TCACCTAGGG
11578 GGGCATTTTGGTCATTTTTCACGCTAA
1 GGGCATTTTGGTCATTTTTCACGCTAA
11605 GGGCATTTTGGTCATTTTTCACGCTAA
1 GGGCATTTTGGTCATTTTTCACGCTAA
11632 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
11649 GCACATTTAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTTCACGCTAA
Found at i:17301 original size:18 final size:18
Alignment explanation
Indices: 17287--17322 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17277 ATCAGCATAT
17287 GACATTACATTAGCATTC
1 GACATTACATTAGCATTC
* *
17305 GACATTGCATTATCATTC
1 GACATTACATTAGCATTC
17323 TAACCCGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (18 bp):
GACATTACATTAGCATTC
Found at i:17446 original size:35 final size:35
Alignment explanation
Indices: 17394--17521 Score: 136
Period size: 35 Copynumber: 3.7 Consensus size: 35
17384 GTTGGGATCG
*
17394 GATGACTCGGTGTAGCATCCTT-AAAATCGGAATCA
1 GATGACTCGGTGAAGCAT-CTTCAAAATCGGAATCA
* * **
17429 GTTGACTCGGTGAAGCATCTTCAAAGTTTGAATCA
1 GATGACTCGGTGAAGCATCTTCAAAATCGGAATCA
* * *
17464 GATGACTCGGTGAAGCGTCTTCAAAGTTC-GACTCA
1 GATGACTCGGTGAAGCATCTTCAAA-ATCGGAATCA
17499 GATGACTCGGT-ATAGCATCTTCA
1 GATGACTCGGTGA-AGCATCTTCA
17522 GATATTAGGA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
34 4 0.05
35 74 0.94
36 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (35 bp):
GATGACTCGGTGAAGCATCTTCAAAATCGGAATCA
Found at i:18652 original size:8 final size:9
Alignment explanation
Indices: 18637--18677 Score: 54
Period size: 8 Copynumber: 5.0 Consensus size: 9
18627 GTGGGATAAA
18637 AGAGAGAGT
1 AGAGAGAGT
18646 A-AGAGAG-
1 AGAGAGAGT
18653 AGAGAGAGT
1 AGAGAGAGT
18662 A-AGAGAG-
1 AGAGAGAGT
18669 AGAGAGAGT
1 AGAGAGAGT
18678 GACTTACCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 2 0.07
8 24 0.86
9 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (9 bp):
AGAGAGAGT
Found at i:18658 original size:16 final size:16
Alignment explanation
Indices: 18637--18677 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
18627 GTGGGATAAA
18637 AGAGAGAGTAAGAGAG
1 AGAGAGAGTAAGAGAG
18653 AGAGAGAGTAAGAGAG
1 AGAGAGAGTAAGAGAG
18669 AGAGAGAGT
1 AGAGAGAGT
18678 GACTTACCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (16 bp):
AGAGAGAGTAAGAGAG
Found at i:20357 original size:34 final size:36
Alignment explanation
Indices: 20318--20412 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 36
20308 AGCTAATATC
20318 AATCAGTAAATCAGTAATTAAGT-AA-AAAGAGATT
1 AATCAGTAAATCAGTAATTAAGTCAAGAAAGAGATT
** *
20352 AATCAGT-AATTTGATAATTAAGAGTCAAGGTAAGAGATT
1 AATCAGTAAATCAG-TAATT-A-AGTCAA-GAAAGAGATT
20391 AATCAGTAAAGTCAGTAATTAA
1 AATCAGTAAA-TCAGTAATTAA
20413 AGAGTCAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
33 4 0.08
34 12 0.25
35 1 0.02
36 3 0.06
37 2 0.04
38 1 0.02
39 16 0.33
40 7 0.15
41 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (36 bp):
AATCAGTAAATCAGTAATTAAGTCAAGAAAGAGATT
Found at i:20553 original size:111 final size:112
Alignment explanation
Indices: 20425--20631 Score: 346
Period size: 111 Copynumber: 1.9 Consensus size: 112
20415 AGTCAAAGTA
*
20425 AAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGTAATCAGTA-AAGGAAGTAATCAGTAAAA
1 AAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGTAACCAGTAGAA-GAAGTAATCAGTAAAA
*
20489 -GGGGCAAAAGTAAAAGAAGAAATCAGTAAAAGTAAAAGAACAAAAGC
65 TGGAGCAAAAGTAAAAGAAGAAATCAGTAAAAGTAAAAGAACAAAAGC
* *
20536 AAAAGAAGTAATCAGAAAAATGGTAATCAAGAGAAGTAACCCGTAGAAGAAGTAATCAGTAAAAT
1 AAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGTAACCAGTAGAAGAAGTAATCAGTAAAAT
*
20601 GGAGCAAAAGTAAAAGAAGTAATCAGTAAAA
66 GGAGCAAAAGTAAAAGAAGAAATCAGTAAAA
20632 TGGTAATTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
111 58 0.65
112 31 0.35
ACGTcount: A:0.57, C:0.08, G:0.21, T:0.14
Consensus pattern (112 bp):
AAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGTAACCAGTAGAAGAAGTAATCAGTAAAAT
GGAGCAAAAGTAAAAGAAGAAATCAGTAAAAGTAAAAGAACAAAAGC
Found at i:20628 original size:16 final size:16
Alignment explanation
Indices: 20456--20631 Score: 87
Period size: 16 Copynumber: 11.1 Consensus size: 16
20446 GGTAATCAAG
20456 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
*
20472 GGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
** * *
20488 AGGGGCAA-AAGTAAA
1 AGAAGTAATCAGTAAA
*
20503 AGAAGAAATCAGTAAA
1 AGAAGTAATCAGTAAA
* ** *
20519 AGTAAAAGAACAAAAGCAAA
1 AG---AAGTA-ATCAGTAAA
20539 AGAAGTAATCAG-AAA
1 AGAAGTAATCAGTAAA
* *
20554 A-ATGGTAATC---AAG
1 AGA-AGTAATCAGTAAA
* * *
20567 AGAAGTAACCCGTAGA
1 AGAAGTAATCAGTAAA
20583 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
* * *
20599 ATGGAGCAA-AAGTAAA
1 A-GAAGTAATCAGTAAA
20615 AGAAGTAATCAGTAAA
1 AGAAGTAATCAGTAAA
20631 A
1 A
20632 TGGTAATTAA
Statistics
Matches: 117, Mismatches: 31, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
13 8 0.07
14 2 0.02
15 26 0.22
16 59 0.50
17 9 0.08
19 5 0.04
20 8 0.07
ACGTcount: A:0.56, C:0.08, G:0.22, T:0.14
Consensus pattern (16 bp):
AGAAGTAATCAGTAAA
Found at i:20675 original size:14 final size:15
Alignment explanation
Indices: 20640--20675 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
20630 AATGGTAATT
20640 AAGAGTAATCAGTAG
1 AAGAGTAATCAGTAG
20655 AAG-GTAATCAGTA-
1 AAGAGTAATCAGTAG
20668 AAGAGTAA
1 AAGAGTAA
20676 AATAGTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 14 0.70
15 3 0.15
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (15 bp):
AAGAGTAATCAGTAG
Found at i:20699 original size:36 final size:35
Alignment explanation
Indices: 20643--20725 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 35
20633 GGTAATTAAG
* * *
20643 AGTAATCAGTAGAAGGTAATCAGTAAAGAGTAAAAT
1 AGTAATCAGTAAAAGATAATCAGT-AAGAGTAAAAC
20679 AGTAATCAGTAAAAGATAATCAGTAAGAGTAAAAC
1 AGTAATCAGTAAAAGATAATCAGTAAGAGTAAAAC
*
20714 AGTAACCAGTAA
1 AGTAATCAGTAA
20726 GAGCAAAGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 21 0.49
36 22 0.51
ACGTcount: A:0.52, C:0.08, G:0.19, T:0.20
Consensus pattern (35 bp):
AGTAATCAGTAAAAGATAATCAGTAAGAGTAAAAC
Found at i:20700 original size:14 final size:15
Alignment explanation
Indices: 20671--20704 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20661 ATCAGTAAAG
*
20671 AGTAAAATAGTAATC
1 AGTAAAAGAGTAATC
20686 AGTAAAAGA-TAATC
1 AGTAAAAGAGTAATC
20700 AGTAA
1 AGTAA
20705 GAGTAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:20723 original size:21 final size:21
Alignment explanation
Indices: 20686--20776 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
20676 AATAGTAATC
*
20686 AGTAAAAGA-TAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
* *
20706 AGTAAAACAGTAACCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
* * * *
20727 AGCAAAGTGGTAATTAGTAAG
1 AGTAAAATAGTAATCAGTAAG
*
20748 AGTCAAATAGTAATCAGTAAAG
1 AGTAAAATAGTAATCAGT-AAG
20770 AGTAAAA
1 AGTAAAA
20777 GGTGATCAGT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 8 0.15
21 38 0.69
22 9 0.16
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.20
Consensus pattern (21 bp):
AGTAAAATAGTAATCAGTAAG
Found at i:20725 original size:42 final size:41
Alignment explanation
Indices: 20686--20788 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
20676 AATAGTAATC
*
20686 AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAG
1 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
* * * * * *
20727 AGCAAAGTGGTAATTAGTAAGAGTCAAATAGTAATCAGTAAAG
1 AGTAAA-AGGTAATCAGTAAGAGTAAAACAGTAACCAGT-AAG
*
20770 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
20789 TTCAAAGAGT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 5 0.10
42 36 0.73
43 8 0.16
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.20
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
Found at i:24747 original size:3 final size:3
Alignment explanation
Indices: 24741--24782 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
24731 AAAAAAACTG
*
24741 ATA ATA ATA AGTA ATA ACA ATA A-A A-A ATA ATA ATA ATA ATA A
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
24783 CAATTTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:29330 original size:35 final size:35
Alignment explanation
Indices: 29278--29405 Score: 138
Period size: 35 Copynumber: 3.7 Consensus size: 35
29268 GTTGGGATCG
*
29278 GATGACTCGGTGTAGCATCCTT-AAAATCGGAATCA
1 GATGACTCGGTGAAGCAT-CTTCAAAATCGGAATCA
* **
29313 G-TGGACTCGGTGAAGCATCTTCAAAGTTTGAATCA
1 GAT-GACTCGGTGAAGCATCTTCAAAATCGGAATCA
* *
29348 GATGACTCGGTGAAGCGTCTTCAAAATTC-GACTCA
1 GATGACTCGGTGAAGCATCTTCAAAA-TCGGAATCA
29383 GATGACTCGGT-ATAGCATCTTCA
1 GATGACTCGGTGA-AGCATCTTCA
29406 GATATTAGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
34 5 0.06
35 72 0.91
36 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (35 bp):
GATGACTCGGTGAAGCATCTTCAAAATCGGAATCA
Found at i:36503 original size:18 final size:18
Alignment explanation
Indices: 36477--36511 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36467 GTTAAGATTT
36477 GAAGAAAAAGCAAAAAAA
1 GAAGAAAAAGCAAAAAAA
* *
36495 GAAGGAAAAGGAAAAAA
1 GAAGAAAAAGCAAAAAA
36512 TAAAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (18 bp):
GAAGAAAAAGCAAAAAAA
Found at i:36508 original size:25 final size:25
Alignment explanation
Indices: 36480--36528 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
36470 AAGATTTGAA
*
36480 GAAAAAGCAAAAAAAGAA-GGAAAAG
1 GAAAAAACAAAAAAA-AATGGAAAAG
*
36505 GAAAAAATAAAAAAAAATGGAAAA
1 GAAAAAACAAAAAAAAATGGAAAA
36529 ATCAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (25 bp):
GAAAAAACAAAAAAAAATGGAAAAG
Found at i:49610 original size:7 final size:6
Alignment explanation
Indices: 49595--49707 Score: 69
Period size: 6 Copynumber: 18.8 Consensus size: 6
49585 TATTTGCACG
* * *
49595 TTTTTC TTTTTC -CTTTC -TTTTC TTCTTT- TTTCTC TTCTTC -TTTT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTTTC
*
49639 TTTTTC TCTTTTC TTTTTCC TCCTTTT- TTTATC ATTTTTTC TTTTTC
1 TTTTTC T-TTTTC TTTTT-C T--TTTTC TTTTTC --TTTTTC TTTTTC
*
49686 TTCTTC -TTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTT
49708 TCTAAGACCT
Statistics
Matches: 84, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
5 24 0.29
6 39 0.46
7 12 0.14
8 5 0.06
9 4 0.05
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:49626 original size:20 final size:18
Alignment explanation
Indices: 49595--49656 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 18
49585 TATTTGCACG
*
49595 TTTTTCTTTTTCCTTTCT
1 TTTTTTTTTTTCCTTTCT
49613 TTTCTTCTTTTTT-CTCTTCT
1 TTT-TT-TTTTTTCCT-TTCT
*
49633 TCTTTTTTTTTCTCTTTTCT
1 T-TTTTTTTTT-TCCTTTCT
49653 TTTT
1 TTTT
49657 CCTCCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
18 3 0.08
19 12 0.33
20 18 0.50
21 3 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTTTCCTTTCT
Found at i:49632 original size:15 final size:15
Alignment explanation
Indices: 49608--49640 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
49598 TTCTTTTTCC
*
49608 TTTCTTTTCTTCTTT
1 TTTCTCTTCTTCTTT
49623 TTTCTCTTCTTCTTT
1 TTTCTCTTCTTCTTT
49638 TTT
1 TTT
49641 TTTCTCTTTT
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:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTCTTCTTCTTT
Found at i:49635 original size:18 final size:17
Alignment explanation
Indices: 49610--49708 Score: 82
Period size: 17 Copynumber: 5.8 Consensus size: 17
49600 CTTTTTCCTT
49610 TCTTTTCTTCTTTTTTC
1 TCTTTTCTTCTTTTTTC
*
49627 TCTTCTTCTTTTTTTTTC
1 TCTT-TTCTTCTTTTTTC
**
49645 TCTTTTCTT-TTTCCTC
1 TCTTTTCTTCTTTTTTC
*
49661 -CTTTTTTTATCATTTTTTC
1 TC-TTTTCT-TC-TTTTTTC
49680 T-TTTTCTTCTTCTTTTC
1 TCTTTTCTTCTT-TTTTC
49697 T-TTTTCTT-TTTT
1 TCTTTTCTTCTTTT
49709 CTAAGACCTA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
15 3 0.04
16 14 0.21
17 25 0.37
18 21 0.31
19 5 0.07
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTTCTTCTTTTTTC
Found at i:49655 original size:12 final size:12
Alignment explanation
Indices: 49596--49706 Score: 68
Period size: 13 Copynumber: 8.8 Consensus size: 12
49586 ATTTGCACGT
49596 TTTTCTTTT-TC
1 TTTTCTTTTCTC
*
49607 CTTTCTTTTCTTC
1 TTTTCTTTTC-TC
*
49620 TTTTTTCTCTTCTTC
1 --TTTTCTTTTC-TC
*
49635 TTTTTTTTTCTC
1 TTTTCTTTTCTC
49647 TTTTCTTTTTCCTCC
1 TTTTC-TTTT-CT-C
*
49662 TTTT-TTTATCATT
1 TTTTCTTT-TC-TC
49675 TTTTCTTTT-TC
1 TTTTCTTTTCTC
49686 TTCTTCTTTTCT-
1 TT-TTCTTTTCTC
49698 TTTTCTTTT
1 TTTTCTTTT
49707 TTCTAAGACC
Statistics
Matches: 80, Mismatches: 8, Indels: 24
0.71 0.07 0.21
Matches are distributed among these distances:
11 18 0.22
12 15 0.19
13 24 0.30
14 7 0.09
15 16 0.20
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTCTC
Found at i:49687 original size:51 final size:51
Alignment explanation
Indices: 49595--49707 Score: 137
Period size: 51 Copynumber: 2.2 Consensus size: 51
49585 TATTTGCACG
*
49595 TTTTTCTTTTTCCTTTCTTTTCTTCTTTTTTCTCTTCTTCTT-TTTTTTTC
1 TTTTTCTTTTTCCTTTCTTTTCTTCTTTTTTCTCTTCTTCTTCTTCTTTTC
49645 TCTTTTCTTTTTCCTCCTT-TTTT-TATCATTTTTTCT-TT-TTCTTCTTCTTTTC
1 T-TTTTCTTTTTCCT--TTCTTTTCT-TC-TTTTTTCTCTTCTTCTTCTTCTTTTC
49697 TTTTTCTTTTT
1 TTTTTCTTTTT
49708 TCTAAGACCT
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
50 1 0.02
51 29 0.52
52 16 0.29
53 10 0.18
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (51 bp):
TTTTTCTTTTTCCTTTCTTTTCTTCTTTTTTCTCTTCTTCTTCTTCTTTTC
Found at i:49695 original size:27 final size:26
Alignment explanation
Indices: 49595--49707 Score: 103
Period size: 26 Copynumber: 4.4 Consensus size: 26
49585 TATTTGCACG
*
49595 TTTTTCTTTTTCCT-TTCTTTTCTTCT
1 TTTTTCTTTTTCTTCTTCTTTT-TTCT
* *
49621 TTTTTC-TCTTCTTCTTTTTTTTTCT
1 TTTTTCTTTTTCTTCTTCTTTTTTCT
* *
49646 CTTTTCTTTTTCCTCCTT-TTTTTATCAT
1 TTTTTCTTTTT-CTTCTTCTTTTT-TC-T
49674 TTTTTCTTTTTCTTCTTC--TTTTC-
1 TTTTTCTTTTTCTTCTTCTTTTTTCT
49697 TTTTTCTTTTT
1 TTTTTCTTTTT
49708 TCTAAGACCT
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
23 11 0.15
25 16 0.22
26 23 0.32
27 12 0.16
28 11 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTTCTTTTTCTTCTTCTTTTTTCT
Found at i:49818 original size:47 final size:47
Alignment explanation
Indices: 49761--49979 Score: 357
Period size: 47 Copynumber: 4.7 Consensus size: 47
49751 GAAACCTGTT
* * *
49761 GACCAACTTTGGTCACTAAATTGAAAACTCGCGTGGAAGCGAGAGAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
* * *
49808 GACCATCTTTGGTCACTAAATTGAAAGCCCGCGTGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
*
49855 GACCATCTTTGGTCACTAGATTGAAAACTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
* *
49902 GACCATCTTTCGTCACCAAATTGAAAACTCGCATGGAAGCGAGAAAA
1 GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
49949 GACCATCTTTGGTCACTAAATTGAAAACTCG
1 GACCATCTTTGGTCACTAAATTGAAAACTCG
49980 AAGTGAGACA
Statistics
Matches: 159, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 159 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (47 bp):
GACCATCTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAAAA
Found at i:50240 original size:69 final size:69
Alignment explanation
Indices: 50102--50465 Score: 351
Period size: 69 Copynumber: 5.3 Consensus size: 69
50092 CTCACTGAAC
* ** * * ** * *
50102 TTGGCTTATGGAAAAGCCCCTAAATGCTTGGATGGAGCCAAATCTTAAACT-ATCTCGCGTGGAA
1 TTGGCTTATGGAAAAGCCTCT-CTTGCCTGGATGGAACCAAGGCTTGAACTGA-CTCGTGTGGAA
*
50166 GCGAGT
64 ACGAGT
*
50172 TTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCGAA-G-TTGGATCTGACTCGTGTGGAA
1 TTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACC-AAGGCTT-GAACTGACTCGTGTGGAA
50235 ACGAGT
64 ACGAGT
* * * ** *** * * *
50241 TTGGCTTGTGGGAAAGCCACTGAATATTTGGATGGAACCAAGGCTTAAACT-ATCTCGCGTCGAA
1 TTGGCTTATGGAAAAGCCTCT-CTTGCCTGGATGGAACCAAGGCTTGAACTGA-CTCGTGTGGAA
*
50305 GCGAGT
64 ACGAGT
* * *
50311 TTGGCTTATGGAAAAGCCTCTCTTGCTTGGATGGAACCAAGGCTT-AACTGACTCGTATTGAAAC
1 TTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAAC
50375 GAGT
66 GAGT
* * * * *
50379 TTGGCTTATGGAAAATCCTATCTTGCCTGGATGGAACCAAAGCTGGATCTGACTCGTGTGGAAAC
1 TTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAAC
50444 GAGT
66 GAGT
*
50448 TTGGCTTGTGGAAAAGCC
1 TTGGCTTATGGAAAAGCC
50466 GAAGCATTCG
Statistics
Matches: 241, Mismatches: 44, Indels: 19
0.79 0.14 0.06
Matches are distributed among these distances:
68 59 0.24
69 109 0.45
70 71 0.29
71 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (69 bp):
TTGGCTTATGGAAAAGCCTCTCTTGCCTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAAC
GAGT
Found at i:50745 original size:29 final size:29
Alignment explanation
Indices: 50708--50768 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
50698 TTGCCCCAGA
*
50708 TCTGTCTTGAATAGTATGCTTTGAAAAAT
1 TCTGACTTGAATAGTATGCTTTGAAAAAT
*
50737 TCTGACTTGAATAGTATGCTTTGAAAGAT
1 TCTGACTTGAATAGTATGCTTTGAAAAAT
50766 TCT
1 TCT
50769 TTTACTGATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (29 bp):
TCTGACTTGAATAGTATGCTTTGAAAAAT
Found at i:51411 original size:17 final size:18
Alignment explanation
Indices: 51389--51430 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
51379 CTAGAGCCTC
51389 TTTTCTTCATTCTCTTT-
1 TTTTCTTCATTCTCTTTA
* *
51406 TTTTCTT-TTTCTTTTTA
1 TTTTCTTCATTCTCTTTA
51423 TTTTCTTC
1 TTTTCTTC
51431 TTTTTCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTTCATTCTCTTTA
Found at i:51776 original size:26 final size:27
Alignment explanation
Indices: 51745--51798 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
51735 AACTTCACTC
*
51745 TTCCTTTCACTTT-TATTTTCAATTTT
1 TTCCTTTCACTTTCAATTTTCAATTTT
*
51771 TTCCTTTCACTTTCAATTTTCACTTTT
1 TTCCTTTCACTTTCAATTTTCAATTTT
51798 T
1 T
51799 CCTCCGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (27 bp):
TTCCTTTCACTTTCAATTTTCAATTTT
Found at i:52296 original size:298 final size:298
Alignment explanation
Indices: 51755--52356 Score: 1177
Period size: 298 Copynumber: 2.0 Consensus size: 298
51745 TTCCTTTCAC
51755 TTTTATTTTCAATTTTTTCCTTTCACTTTCAATTTTCACTTTTTCCTCCGCATTTTTCTTTTTTA
1 TTTT-TTTTCAATTTTTTCCTTTCACTTTCAATTTTCACTTTTTCCTCCGCATTTTTCTTTTTTA
51820 TTTCCTTCCCTTCTTCATCTGACTTTTGATTTGAATTTATTGATGGAGTGGACTCAATGCCTCTT
65 TTTCCTTCCCTTCTTCATCTGACTTTTGATTTGAATTTATTGATGGAGTGGACTCAATGCCTCTT
*
51885 TCTGAACTCTACTCATTACTATTGGGATGCCCCATTTGAACATTGAGTGCAAACCCTTCCTCTCG
130 TCTGAACTCTACTCATTACTATTGGGATGCCCCATTTGAACATTGAGTCCAAACCCTTCCTCTCG
51950 AGGCTAATCCTTCTTCACCTTTGCCCCCCAGTGTGGAGGGTGATCCTCGATTAGGGTTCATTGAA
195 AGGCTAATCCTTCTTCACCTTTGCCCCCCAGTGTGGAGGGTGATCCTCGATTAGGGTTCATTGAA
52015 AAGAAATTAATTAGACTCAAAGGGGGACAACAATGGATA
260 AAGAAATTAATTAGACTCAAAGGGGGACAACAATGGATA
52054 TTTTTTTTCAATTTTTTCCTTTCACTTTCAATTTTCACTTTTTCCTCCGCATTTTTCTTTTTTAT
1 TTTTTTTTCAATTTTTTCCTTTCACTTTCAATTTTCACTTTTTCCTCCGCATTTTTCTTTTTTAT
52119 TTCCTTCCCTTCTTCATCTGACTTTTGATTTGAATTTATTGATGGAGTGGACTCAATGCCTCTTT
66 TTCCTTCCCTTCTTCATCTGACTTTTGATTTGAATTTATTGATGGAGTGGACTCAATGCCTCTTT
52184 CTGAACTCTACTCATTACTATTGGGATGCCCCATTTGAACATTGAGTCCAAACCCTTCCTCTCGA
131 CTGAACTCTACTCATTACTATTGGGATGCCCCATTTGAACATTGAGTCCAAACCCTTCCTCTCGA
52249 GGCTAATCCTTCTTCACCTTTGCCCCCCAGTGTGGAGGGTGATCCTCGATTAGGGTTCATTGAAA
196 GGCTAATCCTTCTTCACCTTTGCCCCCCAGTGTGGAGGGTGATCCTCGATTAGGGTTCATTGAAA
*
52314 AGAAATTAATTAGGCTCAAAGGGGGACAACAATGGATA
261 AGAAATTAATTAGACTCAAAGGGGGACAACAATGGATA
52352 TTTTT
1 TTTTT
52357 CTGCAAGTGA
Statistics
Matches: 301, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
298 297 0.99
299 4 0.01
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (298 bp):
TTTTTTTTCAATTTTTTCCTTTCACTTTCAATTTTCACTTTTTCCTCCGCATTTTTCTTTTTTAT
TTCCTTCCCTTCTTCATCTGACTTTTGATTTGAATTTATTGATGGAGTGGACTCAATGCCTCTTT
CTGAACTCTACTCATTACTATTGGGATGCCCCATTTGAACATTGAGTCCAAACCCTTCCTCTCGA
GGCTAATCCTTCTTCACCTTTGCCCCCCAGTGTGGAGGGTGATCCTCGATTAGGGTTCATTGAAA
AGAAATTAATTAGACTCAAAGGGGGACAACAATGGATA
Found at i:52572 original size:45 final size:45
Alignment explanation
Indices: 52508--52611 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
52498 TATGTTTTTT
* *
52508 TTTTTGAAAAACCATTTTATTAACACCTTTTGAAAACCATTACTC
1 TTTTTGAAAAACCATTTTATGAACACCTTTTGAAAACCATGACTC
*
52553 TTTTTGAAAAACCATTTTATGAACACCTTTTGAAATCCATGACTC
1 TTTTTGAAAAACCATTTTATGAACACCTTTTGAAAACCATGACTC
52598 TTTTTG-AAAACCAT
1 TTTTTGAAAAACCAT
52612 CATTGCTTCT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 8 0.14
45 48 0.86
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (45 bp):
TTTTTGAAAAACCATTTTATGAACACCTTTTGAAAACCATGACTC
Found at i:52652 original size:20 final size:20
Alignment explanation
Indices: 52629--52684 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
52619 TCTTCTCTTT
52629 TTCTTTTTTCTCTTTTATC-C
1 TTCTTTTTTCTCTTTT-TCTC
*
52649 TTCTTCTTTCTCTTTTTCTC
1 TTCTTTTTTCTCTTTTTCTC
52669 TTCTTTTTT-TCTTTTT
1 TTCTTTTTTCTCTTTTT
52685 TTTTATGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (20 bp):
TTCTTTTTTCTCTTTTTCTC
Found at i:52687 original size:11 final size:11
Alignment explanation
Indices: 52632--52688 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 11
52622 TCTCTTTTTC
52632 TTTTTTC-TCT
1 TTTTTTCTTCT
* *
52642 TTTATCCTTC-
1 TTTTTTCTTCT
*
52652 TTCTTTC-TCT
1 TTTTTTCTTCT
*
52662 TTTTCTCTTCT
1 TTTTTTCTTCT
52673 TTTTTTCTT-T
1 TTTTTTCTTCT
52683 TTTTTT
1 TTTTTT
52689 ATGGGAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
9 2 0.06
10 21 0.58
11 13 0.36
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:58085 original size:24 final size:25
Alignment explanation
Indices: 58060--58112 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
58050 ATCAATCAAG
*
58060 AAACCCAAAGACTAAAAGTGAAAGA
1 AAACCAAAAGACTAAAAGTGAAAGA
* * *
58085 AAATCAAAAGGCTAAAAGTGAAATA
1 AAACCAAAAGACTAAAAGTGAAAGA
58110 AAA
1 AAA
58113 GGCCACATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.62, C:0.11, G:0.15, T:0.11
Consensus pattern (25 bp):
AAACCAAAAGACTAAAAGTGAAAGA
Found at i:58222 original size:22 final size:23
Alignment explanation
Indices: 58176--58222 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
58166 AAAGAAACTT
58176 AAGAATTATTCTAAAAAGGAGGA
1 AAGAATTATTCTAAAAAGGAGGA
*
58199 AAGAATTATTCTAAAGA-GAGGA
1 AAGAATTATTCTAAAAAGGAGGA
58221 AA
1 AA
58223 TGATTCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.21
Consensus pattern (23 bp):
AAGAATTATTCTAAAAAGGAGGA
Found at i:58560 original size:8 final size:8
Alignment explanation
Indices: 58544--58619 Score: 82
Period size: 8 Copynumber: 9.5 Consensus size: 8
58534 ATTGAGGTAC
*
58544 TGAAGAAT
1 TGAATAAT
58552 TGAATAAT
1 TGAATAAT
*
58560 TGAGTAAT
1 TGAATAAT
58568 TGAATAAT
1 TGAATAAT
*
58576 TGAAGAAT
1 TGAATAAT
58584 TGAATAAT
1 TGAATAAT
**
58592 TGAGGAAT
1 TGAATAAT
58600 TGAA-ACAT
1 TGAATA-AT
*
58608 GGAATAAT
1 TGAATAAT
58616 TGAA
1 TGAA
58620 GAAAGACCAC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
7 1 0.02
8 54 0.96
9 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.21, T:0.30
Consensus pattern (8 bp):
TGAATAAT
Found at i:58560 original size:24 final size:23
Alignment explanation
Indices: 58529--58622 Score: 73
Period size: 24 Copynumber: 4.0 Consensus size: 23
58519 CATTTTGAAA
58529 TGAAAATTGAGGT-ACTGAAGAAT
1 TGAAAATTGA-GTAACTGAAGAAT
* *
58552 TGAATAATTGAGTAATTGAATAAT
1 TGAA-AATTGAGTAACTGAAGAAT
* * *
58576 TGAAGAATTGAATAATTGAGGAAT
1 TGAA-AATTGAGTAACTGAAGAAT
* * *
58600 TGAAACATGGAATAATTGAAGAA
1 TGAAA-ATTGAGTAACTGAAGAA
58623 AGACCACCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.12
24 53 0.88
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (23 bp):
TGAAAATTGAGTAACTGAAGAAT
Found at i:58769 original size:8 final size:7
Alignment explanation
Indices: 58758--59050 Score: 83
Period size: 8 Copynumber: 40.0 Consensus size: 7
58748 AAAATGAAGC
58758 ATTGAAGA
1 ATTGAA-A
58766 ATTG-AA
1 ATTGAAA
*
58772 ATTGAAGC
1 ATTGAA-A
*
58780 GTTGAAA
1 ATTGAAA
58787 TATTG-AA
1 -ATTGAAA
58794 ATTG-AA
1 ATTGAAA
58800 ATTGAAA
1 ATTGAAA
*
58807 CATTGAGGA
1 -ATTGA-AA
58816 ATTG-AA
1 ATTGAAA
*
58822 TTTGAAGA
1 ATTGAA-A
58830 ATTG-AA
1 ATTGAAA
*
58836 ATTGAAGC
1 ATTGAA-A
*
58844 GTTGAAA
1 ATTGAAA
58851 TATTG-AA
1 -ATTGAAA
58858 ATTGAAA
1 ATTGAAA
58865 CATTG-AA
1 -ATTGAAA
* *
58872 TTATGGAA
1 AT-TGAAA
58880 ATTGAAGA
1 ATTGAA-A
58888 ATTGAAA
1 ATTGAAA
*
58895 CATTGAAGT
1 -ATTGAA-A
*
58904 ACT-AAA
1 ATTGAAA
*
58910 ATTGAATC
1 ATTGAA-A
58918 ATTGAAGA
1 ATTGAA-A
*
58926 ATTG-CA
1 ATTGAAA
58932 ATTGAAA
1 ATTGAAA
58939 CATTGAAGA
1 -ATTGAA-A
58948 ATTG-AA
1 ATTGAAA
* *
58954 GTTGAAGC
1 ATTGAA-A
* *
58962 ATCGGAAT
1 AT-TGAAA
58970 ATTG-AA
1 ATTGAAA
58976 ATTGAAA
1 ATTGAAA
*
58983 CATTGATGA
1 -ATTGA-AA
58992 ATTG-AA
1 ATTGAAA
*
58998 TTTGAAGA
1 ATTGAA-A
59006 ATTGAAA
1 ATTGAAA
59013 TATTG-AA
1 -ATTGAAA
59020 ATTGAAA
1 ATTGAAA
59027 CATT-AAGGA
1 -ATTGAA--A
59036 ATTGAAGA
1 ATTGAA-A
59044 ATTGAAA
1 ATTGAAA
59051 CTGAAGCATT
Statistics
Matches: 213, Mismatches: 35, Indels: 75
0.66 0.11 0.23
Matches are distributed among these distances:
6 53 0.25
7 40 0.19
8 111 0.52
9 9 0.04
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.30
Consensus pattern (7 bp):
ATTGAAA
Found at i:58777 original size:14 final size:14
Alignment explanation
Indices: 58758--59013 Score: 92
Period size: 14 Copynumber: 17.1 Consensus size: 14
58748 AAAATGAAGC
58758 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
**
58772 ATTGAAGCGTTGAAA
1 ATTGAAGAATTG-AA
58787 TATTGAAATTGAAATTGAAA
1 -ATTG-AA--G-AATTG-AA
*
58807 CATTGAGGAATTGAA
1 -ATTGAAGAATTGAA
*
58822 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
**
58836 ATTGAAGCGTTGAAA
1 ATTGAAGAATTG-AA
58851 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
** *
58865 CATTGAATTATGGAA
1 -ATTGAAGAATTGAA
58880 ATTGAAGAATTGAAA
1 ATTGAAGAATTG-AA
* * *
58895 CATTGAAGTACTAAA
1 -ATTGAAGAATTGAA
**
58910 ATTGAATCATTGAAGA
1 ATTGAAGAATTG-A-A
*
58926 ATTG--CAATTGAAA
1 ATTGAAGAATTG-AA
58939 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
* * *
58954 GTTGAAGCATCGGAA
1 ATTGAAGAAT-TGAA
58969 TATTG-A-AATTGAAA
1 -ATTGAAGAATTG-AA
*
58983 CATTGATGAATTGAA
1 -ATTGAAGAATTGAA
*
58998 TTTGAAGAATTGAA
1 ATTGAAGAATTGAA
59012 AT
1 AT
59014 ATTGAAATTG
Statistics
Matches: 180, Mismatches: 40, Indels: 44
0.68 0.15 0.17
Matches are distributed among these distances:
13 2 0.01
14 97 0.54
15 23 0.13
16 43 0.24
17 3 0.02
19 2 0.01
20 10 0.06
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:58784 original size:22 final size:22
Alignment explanation
Indices: 58752--58901 Score: 141
Period size: 22 Copynumber: 6.9 Consensus size: 22
58742 TGGAATAAAA
58752 TGAAGCATTGAAGA-ATTGAAAT
1 TGAAGCATTGAA-ATATTGAAAT
*
58774 TGAAGCGTTGAAATATTGAAAT
1 TGAAGCATTGAAATATTGAAAT
*
58796 TGAA--ATTGAAACATTGAGGAAT
1 TGAAGCATTGAAATATTGA--AAT
*
58818 TGAA--TTTGAAGA-ATTGAAAT
1 TGAAGCATTGAA-ATATTGAAAT
*
58838 TGAAGCGTTGAAATATTGAAAT
1 TGAAGCATTGAAATATTGAAAT
* * *
58860 TGAAACATTGAATTATGGAAAT
1 TGAAGCATTGAAATATTGAAAT
* *
58882 TGAAGAATTGAAACATTGAA
1 TGAAGCATTGAAATATTGAA
58902 GTACTAAAAT
Statistics
Matches: 107, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
20 18 0.17
21 2 0.02
22 86 0.80
23 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (22 bp):
TGAAGCATTGAAATATTGAAAT
Found at i:58786 original size:100 final size:99
Alignment explanation
Indices: 58573--58792 Score: 220
Period size: 100 Copynumber: 2.2 Consensus size: 99
58563 GTAATTGAAT
* * * * * * * * *
58573 AATTGAAGAATTG-AATAATTGAGGAATT-GAAACATGGAATAATTGAAGAAAGACCACCTTGGA
1 AATTGAAGAATTGAAAT-ATTGACGACTTAAAAAAATAGAAGAATTGAAGAAAAACCACCCTCGA
*
58636 TCATTGAAGTAAATGGAAGCATTGAATGGTTGGAG
65 TCATTGAAGTAAATGGAAGCATTGAATGATTGGAG
58671 AATTGAAGAATTGAAATTATTGACGACTTAAAAAAATAGAAGAATTGAAGAAAAACCACCCTCGA
1 AATTGAAGAATTGAAA-TATTGACGACTTAAAAAAATAGAAGAATTGAAGAAAAACCACCCTCGA
58736 TCATTCTGGAA-TAAAAT-GAAGCATTGAA-GAATT-GA-
65 TCA-T-T-GAAGT-AAATGGAAGCATTGAATG-ATTGGAG
**
58771 AATTGAAGCGTTGAAATATTGA
1 AATTGAAGAATTGAAATATTGA
58793 AATTGAAATT
Statistics
Matches: 102, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
98 13 0.13
99 17 0.17
100 46 0.45
101 4 0.04
102 15 0.15
103 7 0.07
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (99 bp):
AATTGAAGAATTGAAATATTGACGACTTAAAAAAATAGAAGAATTGAAGAAAAACCACCCTCGAT
CATTGAAGTAAATGGAAGCATTGAATGATTGGAG
Found at i:58835 original size:30 final size:30
Alignment explanation
Indices: 58799--59019 Score: 122
Period size: 30 Copynumber: 7.5 Consensus size: 30
58789 TTGAAATTGA
*
58799 AATTGAAACATTGAGGAATTGAATTTGAAG
1 AATTGAAACATTGAAGAATTGAATTTGAAG
**
58829 AATTG-AA-ATTGAAGCGTTGAAATATTG-A-
1 AATTGAAACATTGAAGAATTG-AAT-TTGAAG
** * *
58857 AATTGAAACATTGAATTATGGAAATTGAAG
1 AATTGAAACATTGAAGAATTGAATTTGAAG
* * * * *
58887 AATTGAAACATTGAAGTACTAAAATTGAAT
1 AATTGAAACATTGAAGAATTGAATTTGAAG
* * *
58917 CATTGAAGA-ATTG--CAATTGAAACATTGAAG
1 AATTGAA-ACATTGAAGAATTG-AA-TTTGAAG
* * *
58947 AATTG-AA-GTTGAAGCATCGGAATATTG-A-
1 AATTGAAACATTGAAGAAT-TGAAT-TTGAAG
*
58975 AATTGAAACATTGATGAATTGAATTTGAAG
1 AATTGAAACATTGAAGAATTGAATTTGAAG
*
59005 AATTGAAATATTGAA
1 AATTGAAACATTGAA
59020 ATTGAAACAT
Statistics
Matches: 143, Mismatches: 31, Indels: 34
0.69 0.15 0.16
Matches are distributed among these distances:
28 31 0.22
29 22 0.15
30 88 0.62
31 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (30 bp):
AATTGAAACATTGAAGAATTGAATTTGAAG
Found at i:58849 original size:44 final size:42
Alignment explanation
Indices: 58788--59041 Score: 208
Period size: 44 Copynumber: 5.8 Consensus size: 42
58778 GCGTTGAAAT
* *
58788 ATTGAAATTGAAATTGAAACATTGAGGAATTGAATTTGAAGA
1 ATTGAAATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
* * **
58830 ATTGAAATTGAAGCGTTGAAATATTG-A-AATTGAAACATTGAATT
1 ATTGAAATTGAA--ATTGAAACATTGAAGAATTG-AA-ATTGAAGA
* * * * **
58874 ATGGAAATTGAAGAATTGAAACATTGAAGTACTAAAATTGAATC
1 ATTGAAATTG-A-AATTGAAACATTGAAGAATTGAAATTGAAGA
* * *
58918 ATTGAAGAATTGCAATTGAAACATTGAAGAATTGAAGTTGAAGC
1 ATTG-A-AATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
* * *
58962 ATCGGAATATTGAAATTGAAACATTGATGAATTGAATTTGAAGA
1 AT-TGAA-ATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
59006 ATTGAAATATTGAAATTGAAACATT-AAGGAATTGAA
1 ATTG-AA-ATTGAAATTGAAACATTGAA-GAATTGAA
59042 GAATTGAAAC
Statistics
Matches: 171, Mismatches: 27, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
42 17 0.10
43 5 0.03
44 135 0.79
45 6 0.04
46 8 0.05
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (42 bp):
ATTGAAATTGAAATTGAAACATTGAAGAATTGAAATTGAAGA
Found at i:58856 original size:36 final size:35
Alignment explanation
Indices: 58788--58945 Score: 92
Period size: 36 Copynumber: 4.4 Consensus size: 35
58778 GCGTTGAAAT
*
58788 ATTG-AAATTGAAATTGAAACATTGAGGAATTGAA
1 ATTGAAAATTGAAATTGAAACATTGAGAAATTGAA
* * *
58822 TTTGAAGAATTGAAATTGAAGCGTTGA-AATATTGAA
1 ATTGAA-AATTGAAATTGAAACATTGAGAA-ATTGAA
* *
58858 ATTGAAACATTGAATTATGGAA-ATTGA-AGAATTGAAA
1 ATTGAAA-ATTGAAAT-TGAAACATTGAGA-AATTG-AA
* * * * *
58895 CATTGAAGTACTAAAATTGAATCATTGA-AGAATTGCA
1 -ATTGAA-AATTGAAATTGAAACATTGAGA-AATTGAA
58932 ATTGAAACATTGAA
1 ATTGAAA-ATTGAA
58946 GAATTGAAGT
Statistics
Matches: 94, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
34 3 0.03
35 3 0.03
36 55 0.59
37 10 0.11
38 23 0.24
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (35 bp):
ATTGAAAATTGAAATTGAAACATTGAGAAATTGAA
Found at i:58949 original size:22 final size:22
Alignment explanation
Indices: 58781--59051 Score: 163
Period size: 22 Copynumber: 12.3 Consensus size: 22
58771 AATTGAAGCG
*
58781 TTGAAATATTG-A-AATTGAAA
1 TTGAAACATTGAAGAATTGAAA
* *
58801 TTGAAACATTGAGGAATTGAAT
1 TTGAAACATTGAAGAATTGAAA
*
58823 TTGAAGA-ATTG-A-AATTGAAGCG
1 TTGAA-ACATTGAAGAATTGAA--A
*
58845 TTGAAATATTG-A-AATTGAAACA
1 TTGAAACATTGAAGAATTG-AA-A
** *
58867 TTGAATTA-TGGA-AATTGAAGAA
1 TTGAAACATTGAAGAATTG-A-AA
* * *
58889 TTGAAACATTGAAGTACTAAAA
1 TTGAAACATTGAAGAATTGAAA
* *
58911 TTGAATCATTGAAGAATTGCAA
1 TTGAAACATTGAAGAATTGAAA
*
58933 TTGAAACATTGAAGAATTGAAG
1 TTGAAACATTGAAGAATTGAAA
* * *
58955 TTGAAGCATCGGAA-TATTGAAA
1 TTGAAACAT-TGAAGAATTGAAA
* *
58977 TTGAAACATTGATGAATTGAAT
1 TTGAAACATTGAAGAATTGAAA
58999 TTGAAGA-ATTGAA-ATATTGAAA
1 TTGAA-ACATTGAAGA-ATTGAAA
59021 TTGAAACATT-AAGGAATTGAAGAA
1 TTGAAACATTGAA-GAATTG-A-AA
59045 TTGAAAC
1 TTGAAAC
59052 TGAAGCATTA
Statistics
Matches: 199, Mismatches: 32, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
20 17 0.09
21 9 0.05
22 148 0.74
23 14 0.07
24 11 0.06
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (22 bp):
TTGAAACATTGAAGAATTGAAA
Found at i:59022 original size:14 final size:13
Alignment explanation
Indices: 58758--59055 Score: 86
Period size: 14 Copynumber: 20.5 Consensus size: 13
58748 AAAATGAAGC
58758 ATTGAAGAATTGAA
1 ATTGAA-AATTGAA
**
58772 ATTGAAGCGTTGAAA
1 ATTGAA-AATTG-AA
58787 TATTG-AAATTGAA
1 -ATTGAAAATTGAA
58800 ATTGAAACATTGAGGA
1 ATTGAAA-ATTGA--A
*
58816 ATTG-AATTTGAAGA
1 ATTGAAAATTG-A-A
58830 ATTG-AAATTGAA
1 ATTGAAAATTGAA
*
58842 GCGTTGAAATATTGAA
1 --ATTGAAA-ATTGAA
58858 ATTGAAACATTGAA
1 ATTGAAA-ATTGAA
* *
58872 TTATGGAAATTGAAGA
1 AT-TGAAAATTG-A-A
58888 ATTGAAACATTGAA
1 ATTGAAA-ATTGAA
*
58902 GTACT-AAAATTGAA
1 --ATTGAAAATTGAA
*
58916 TCATTGAAGAATTGCA
1 --ATTGAA-AATTGAA
58932 ATTGAAACATTGAAGA
1 ATTGAAA-ATTG-A-A
*
58948 ATTG-AAGTTGAA
1 ATTGAAAATTGAA
* *
58960 GCATCGGAATATTGAA
1 --AT-TGAAAATTGAA
58976 ATTGAAACATTGATGA
1 ATTGAAA-ATTGA--A
*
58992 ATTG-AATTTGAAGA
1 ATTGAAAATTG-A-A
59006 ATTGAAATATTGAA
1 ATTGAAA-ATTGAA
*
59020 ATTGAAACATTAAGGA
1 ATTGAAA-ATT--GAA
59036 ATTGAAGAATTGAA
1 ATTGAA-AATTGAA
*
59050 ACTGAA
1 ATTGAA
59056 GCATTAAAGA
Statistics
Matches: 218, Mismatches: 31, Indels: 70
0.68 0.10 0.22
Matches are distributed among these distances:
12 6 0.03
13 10 0.05
14 110 0.50
15 32 0.15
16 59 0.27
17 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (13 bp):
ATTGAAAATTGAA
Found at i:59038 original size:30 final size:30
Alignment explanation
Indices: 59004--59062 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
58994 TGAATTTGAA
*
59004 GAATTGAA-ATATTGAAATTGAAACATTAAG
1 GAATTGAAGA-ATTGAAACTGAAACATTAAG
*
59034 GAATTGAAGAATTGAAACTGAAGCATTAA
1 GAATTGAAGAATTGAAACTGAAACATTAA
59063 AGATTTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (30 bp):
GAATTGAAGAATTGAAACTGAAACATTAAG
Found at i:59216 original size:24 final size:24
Alignment explanation
Indices: 59177--59250 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
59167 CACCCTGGGT
*
59177 CATTGAAGTGAATTGAAGATTTGAAG
1 CATTG-AGT-AATTGAAGAATTGAAG
*
59203 CATTGAGTAATTGAATAATTGAAG
1 CATTGAGTAATTGAAGAATTGAAG
* * **
59227 CAATAAGTAATCAAAGAATTGAAG
1 CATTGAGTAATTGAAGAATTGAAG
59251 AAATAATTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
24 33 0.80
25 3 0.07
26 5 0.12
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (24 bp):
CATTGAGTAATTGAAGAATTGAAG
Found at i:59273 original size:16 final size:16
Alignment explanation
Indices: 59252--59295 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
59242 GAATTGAAGA
59252 AATAATTGAA-ATATTG
1 AATAATTGAAGAT-TTG
59268 AATAATTGAAGATTTG
1 AATAATTGAAGATTTG
*
59284 AATAATTAAAGA
1 AATAATTGAAGA
59296 GTCGAAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 24 0.92
17 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (16 bp):
AATAATTGAAGATTTG
Found at i:59295 original size:52 final size:53
Alignment explanation
Indices: 59212--59324 Score: 124
Period size: 52 Copynumber: 2.2 Consensus size: 53
59202 GCATTGAGTA
*
59212 ATTGAATAATTGAAGCAATAAGTAATCAAAGAATTGAAGAAAT-AATTGAAAT
1 ATTGAATAATTGAAGCAATAAGTAATCAAAGAATCGAAGAAATAAATTGAAAT
* * * * *
59264 ATTGAATAATTGAAG-ATTTGAA-TAATTAAAGAGTCGAAGAGATAAATTGAAGT
1 ATTGAATAATTGAAGCA-AT-AAGTAATCAAAGAATCGAAGAAATAAATTGAAAT
*
59317 GTTGAATA
1 ATTGAATA
59325 GTTAAAGAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
51 1 0.02
52 33 0.65
53 17 0.33
ACGTcount: A:0.50, C:0.03, G:0.19, T:0.29
Consensus pattern (53 bp):
ATTGAATAATTGAAGCAATAAGTAATCAAAGAATCGAAGAAATAAATTGAAAT
Found at i:59312 original size:37 final size:37
Alignment explanation
Indices: 59271--59364 Score: 145
Period size: 37 Copynumber: 2.5 Consensus size: 37
59261 AATATTGAAT
59271 AATTGAAGAT-TTGAATAATTAAAGAGTCGAAGAGATA
1 AATTGAAG-TGTTGAATAATTAAAGAGTCGAAGAGATA
*
59308 AATTGAAGTGTTGAATAGTTAAAGAGTCGAAGAGATA
1 AATTGAAGTGTTGAATAATTAAAGAGTCGAAGAGATA
* *
59345 AATTGAAGTATTGAAGAATT
1 AATTGAAGTGTTGAATAATT
59365 GAATGATGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 1 0.02
37 51 0.98
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (37 bp):
AATTGAAGTGTTGAATAATTAAAGAGTCGAAGAGATA
Found at i:59364 original size:16 final size:16
Alignment explanation
Indices: 59345--59391 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
59335 CGAAGAGATA
59345 AATTGAAGTATTGAAG
1 AATTGAAGTATTGAAG
*
59361 AATTGAA-TGATGGAAG
1 AATTGAAGT-ATTGAAG
* *
59377 ATTTGAAGCATTGAA
1 AATTGAAGTATTGAA
59392 TAGTTGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.30
Consensus pattern (16 bp):
AATTGAAGTATTGAAG
Found at i:59400 original size:24 final size:25
Alignment explanation
Indices: 59346--59401 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
59336 GAAGAGATAA
59346 ATTGAAG-TATTGAAGAATTGAATG
1 ATTGAAGATATTGAAGAATTGAATG
* *
59370 ATGGAAGAT-TTGAAGCATTGAAT-
1 ATTGAAGATATTGAAGAATTGAATG
59393 AGTTGAAGA
1 A-TTGAAGA
59402 AAGAGATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 25 0.93
25 1 0.04
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.30
Consensus pattern (25 bp):
ATTGAAGATATTGAAGAATTGAATG
Found at i:59443 original size:16 final size:16
Alignment explanation
Indices: 59422--59465 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
59412 TTTGATATAA
*
59422 ATTGAAGCATTGAAGG
1 ATTGAAGAATTGAAGG
59438 ATTGAAGAATTGAAGTTG
1 ATTGAAGAATTGAAG--G
59456 ATTGAA-AATT
1 ATTGAAGAATT
59466 AATTCGGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 14 0.56
17 4 0.16
18 7 0.28
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.32
Consensus pattern (16 bp):
ATTGAAGAATTGAAGG
Found at i:59633 original size:17 final size:17
Alignment explanation
Indices: 59611--59645 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
59601 TTCATGATGC
59611 AATGCAAAATGCATGAT
1 AATGCAAAATGCATGAT
* *
59628 AATGCAATATGTATGAT
1 AATGCAAAATGCATGAT
59645 A
1 A
59646 TGTTTTGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (17 bp):
AATGCAAAATGCATGAT
Found at i:60411 original size:17 final size:16
Alignment explanation
Indices: 60386--60431 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
60376 TCTTTTCCAT
60386 TCATTTTTTCATTTTC
1 TCATTTTTTCATTTTC
* *
60402 TCATTTTTTTTATTTTT
1 TCA-TTTTTTCATTTTC
60419 TCATTTTTTCATT
1 TCATTTTTTCATT
60432 CATTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (16 bp):
TCATTTTTTCATTTTC
Found at i:60416 original size:25 final size:25
Alignment explanation
Indices: 60388--60447 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
60378 TTTTCCATTC
**
60388 ATTTTTTCATTTTCTCATTTTTTTT
1 ATTTTTTCATTTTCTCATTCATTTT
*
60413 ATTTTTTCATTTTTTCATTCATTTT
1 ATTTTTTCATTTTCTCATTCATTTT
60438 -TTTTTTCATT
1 ATTTTTTCATT
60448 GCACTTGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.13, C:0.12, G:0.00, T:0.75
Consensus pattern (25 bp):
ATTTTTTCATTTTCTCATTCATTTT
Found at i:60417 original size:7 final size:8
Alignment explanation
Indices: 60385--60431 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
60375 CTCTTTTCCA
60385 TTCATTTT
1 TTCATTTT
60393 TTCATTTT
1 TTCATTTT
*
60401 CTCATTTTT
1 TTCA-TTTT
*
60410 TTTATTTT
1 TTCATTTT
60418 TTCATTTT
1 TTCATTTT
60426 TTCATT
1 TTCATT
60432 CATTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 28 0.82
9 6 0.18
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCATTTT
Found at i:60445 original size:12 final size:12
Alignment explanation
Indices: 60409--60447 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
60399 TTCTCATTTT
60409 TTTTATTTTTTCA
1 TTTT-TTTTTTCA
**
60422 TTTTTTCATTCA
1 TTTTTTTTTTCA
60434 TTTTTTTTTTCA
1 TTTTTTTTTTCA
60446 TT
1 TT
60448 GCACTTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:61155 original size:33 final size:33
Alignment explanation
Indices: 61118--61182 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
61108 TTATTTTTTT
* *
61118 TTTTGAAAAACATTTTTGAAAATCATGACTCTC
1 TTTTGAAAAACATTTTTGAAAACCACGACTCTC
*
61151 TTTTGAAAAATATTTTTGAAAACCACGACTCT
1 TTTTGAAAAACATTTTTGAAAACCACGACTCT
61183 ACTATTCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (33 bp):
TTTTGAAAAACATTTTTGAAAACCACGACTCTC
Found at i:65366 original size:39 final size:39
Alignment explanation
Indices: 65312--65714 Score: 472
Period size: 39 Copynumber: 10.8 Consensus size: 39
65302 GCCTATACTT
* *
65312 AAGACTGACTAACTTAATTTCAAGGAAATTAGGTAAACG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
*
65351 AAGACTGACTGACTTAATTTCAAGGAAATTACGTAAAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
*
65390 AAGACTGACTGACTCAATTTCAAGGAAATTAGGTAAAAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGT-AAAAG
65430 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
* *
65469 AAGACTAACTGACTTAATTTCAAGGGAATTAGGTAAAAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGT-AAAAG
*
65509 AAGA-T---TGATTTAATTTCAAGGAAATTAGGTAAAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
65544 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
* * * *
65583 CATACT-A--G-CTTAGTTTCAAGGAAACTAGGT-AAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
* *
65617 AA-A-AGACTGGCTTAATTTCAAGGAAATTAGGT-AAAG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
* * *
65653 ATA-A---ACTGGC-TAGTTTCAAGGAAACTAGGT-AAAG
1 A-AGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
65687 AA-A--GACT-AGCTTAATTTCAAGGAAATTA
1 AAGACTGACTGA-CTTAATTTCAAGGAAATTA
65715 AGTAGAATAA
Statistics
Matches: 326, Mismatches: 24, Indels: 32
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.01
34 32 0.10
35 51 0.16
36 50 0.15
37 2 0.01
38 1 0.00
39 139 0.43
40 47 0.14
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.26
Consensus pattern (39 bp):
AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAG
Found at i:65460 original size:79 final size:77
Alignment explanation
Indices: 65312--65714 Score: 473
Period size: 79 Copynumber: 5.4 Consensus size: 77
65302 GCCTATACTT
* *
65312 AAGACTGACTAACTTAATTTCAAGGAAATTAGGT-AAACGAAGACTGACTGACTTAATTTCAAGG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACT-A-TGACTTAATTTCAAGG
*
65376 AAATTACGTAAAAG
64 AAATTAGGTAAAAG
*
65390 AAGACTGACTGACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGG
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACT-A-TGACTTAATTTCAAGG
65455 AAATTAGGTAAAAG
64 AAATTAGGTAAAAG
* * *
65469 AAGACTAACTGACTTAATTTCAAGGGAATTAGGTAAAAAGAAGA-T-TGATTTAATTTCAAGGAA
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTATGACTTAATTTCAAGGAA
65532 ATTAGGTAAAAG
66 ATTAGGTAAAAG
* * *
65544 AAGACTGACTGACTTAATTTCAAGGAAATTAGGT-AAAAGCATACTA-G-CTTAGTTTCAAGGAA
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTATGACTTAATTTCAAGGAA
*
65606 ACTAGGT-AAAG
66 ATTAGGTAAAAG
* * * * * *
65617 AA-A-AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGATAA-AC--TGGC-TAGTTTCAAGGAA
1 AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTATGACTTAATTTCAAGGAA
*
65676 ACTAGGT-AAAG
66 ATTAGGTAAAAG
65687 AA-A--GACT-AGCTTAATTTCAAGGAAATTA
1 AAGACTGACTGA-CTTAATTTCAAGGAAATTA
65715 AGTAGAATAA
Statistics
Matches: 297, Mismatches: 21, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
69 23 0.08
70 28 0.09
71 30 0.10
72 5 0.02
73 6 0.02
74 26 0.09
75 63 0.21
78 33 0.11
79 83 0.28
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.26
Consensus pattern (77 bp):
AAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTATGACTTAATTTCAAGGAA
ATTAGGTAAAAG
Found at i:65788 original size:32 final size:32
Alignment explanation
Indices: 65695--65780 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
65685 AGAAAGACTA
* * *
65695 GCTTAATTTCAAGGAAATTAAGTAGAATAAGTG
1 GCTTAA-TTCAGGGTAATTAAGTAGAATAAGAG
65728 GCTTAATTCAGGGTAATTAAGTAGAATAAGAG
1 GCTTAATTCAGGGTAATTAAGTAGAATAAGAG
65760 GCTTAATTCAGGGTAATTAAG
1 GCTTAATTCAGGGTAATTAAG
65781 CATAATAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
32 44 0.88
33 6 0.12
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (32 bp):
GCTTAATTCAGGGTAATTAAGTAGAATAAGAG
Found at i:69194 original size:11 final size:11
Alignment explanation
Indices: 69178--69207 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
69168 ATGAGGTTTT
69178 AAAAAAAAAGA
1 AAAAAAAAAGA
69189 AAAAAAAAAGA
1 AAAAAAAAAGA
69200 AGAAAAAA
1 A-AAAAAA
69208 GAGAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:69214 original size:14 final size:14
Alignment explanation
Indices: 69178--69218 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
69168 ATGAGGTTTT
69178 AAAAAAA-AAGAAA
1 AAAAAAAGAAGAAA
69191 AAAAAAAGAAGAAA
1 AAAAAAAGAAGAAA
* *
69205 AAAGAGAGAAGAAA
1 AAAAAAAGAAGAAA
69219 GGTTTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAGAAA
Found at i:70047 original size:6 final size:6
Alignment explanation
Indices: 70036--70106 Score: 76
Period size: 6 Copynumber: 12.2 Consensus size: 6
70026 GACAAGTCGC
*
70036 AAAGAA AAAGAA AAAGAA AAGAAAA AAAGAA AAAGAA AAAG-- AAAGAA
1 AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA
* * *
70083 AAA-AA AAGGAA CAAGAA GAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
70107 GAAAAAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
6 41 0.76
7 5 0.09
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:70074 original size:24 final size:25
Alignment explanation
Indices: 70036--70113 Score: 104
Period size: 25 Copynumber: 3.1 Consensus size: 25
70026 GACAAGTCGC
70036 AAAGAAAAAGAAAAAGAAAAGAAAA
1 AAAGAAAAAGAAAAAGAAAAGAAAA
*
70061 AAAGAAAAAGAAAAAGAAAGAAAAAA
1 AAAGAAAAAGAAAAAGAAA-AGAAAA
* *
70087 AAAGGAACAAGAAGAAG-AAAGAAAA
1 AAA-GAAAAAGAAAAAGAAAAGAAAA
70112 AA
1 AA
70114 TAACAACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
25 26 0.55
26 10 0.21
27 11 0.23
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAGAAAAAGAAAAAGAAAAGAAAA
Found at i:70098 original size:27 final size:26
Alignment explanation
Indices: 70036--70113 Score: 113
Period size: 27 Copynumber: 3.0 Consensus size: 26
70026 GACAAGTCGC
*
70036 AAAGAAAAAGAAAAAGAAA-AGAAAA
1 AAAGAAAAAGAAAAAGAAAGAAAAAA
70061 AAAGAAAAAGAAAAAGAAAGAAAAAA
1 AAAGAAAAAGAAAAAGAAAGAAAAAA
* *
70087 AAAGGAACAAGAAGAAGAAAGAAAAAA
1 AAA-GAAAAAGAAAAAGAAAGAAAAAA
70114 TAACAACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
25 19 0.40
26 8 0.17
27 21 0.44
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAGAAAAAGAAAGAAAAAA
Found at i:71802 original size:43 final size:43
Alignment explanation
Indices: 71754--71853 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
71744 AGTCTTCCGC
* * * * *
71754 GTCTCAGGGCATACTCCCAGTGTTTCAGGGCAGACTTTCAAAT
1 GTCTCAGGGCAGACTCCCAGCGTCTCAAGGCAGACTTCCAAAT
**
71797 GTCTCAGGGCAGACTTTCAGCGTCTCAAGGCAGACTTCCAAAT
1 GTCTCAGGGCAGACTCCCAGCGTCTCAAGGCAGACTTCCAAAT
*
71840 GGT-TGAGGGCAGAC
1 -GTCTCAGGGCAGAC
71854 CTTCCAAGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 46 0.96
44 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (43 bp):
GTCTCAGGGCAGACTCCCAGCGTCTCAAGGCAGACTTCCAAAT
Found at i:71806 original size:22 final size:22
Alignment explanation
Indices: 71778--71853 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
71768 TCCCAGTGTT
71778 TCAGGGCAGACTTTCAAATGTC
1 TCAGGGCAGACTTTCAAATGTC
**
71800 TCAGGGCAGACTTTC-AGCGTC
1 TCAGGGCAGACTTTCAAATGTC
* *
71821 TCAAGGCAGACTTCCAAATGGT-
1 TCAGGGCAGACTTTCAAAT-GTC
*
71843 TGAGGGCAGAC
1 TCAGGGCAGAC
71854 CTTCCAAGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.39
22 25 0.57
23 2 0.05
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (22 bp):
TCAGGGCAGACTTTCAAATGTC
Found at i:71823 original size:21 final size:21
Alignment explanation
Indices: 71752--71833 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
71742 GCAGTCTTCC
* **
71752 GCGTCTCAGGGCATACTCCCA
1 GCGTCTCAGGGCAGACTTTCA
* *
71773 GTGTTTCAGGGCAGACTTTCAA
1 GCGTCTCAGGGCAGACTTTC-A
**
71795 ATGTCTCAGGGCAGACTTTCA
1 GCGTCTCAGGGCAGACTTTCA
*
71816 GCGTCTCAAGGCAGACTT
1 GCGTCTCAGGGCAGACTT
71834 CCAAATGGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 31 0.62
22 19 0.38
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.26
Consensus pattern (21 bp):
GCGTCTCAGGGCAGACTTTCA
Found at i:73424 original size:49 final size:49
Alignment explanation
Indices: 73351--73494 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
73341 CAGTGTGATT
*
73351 AAAGAAAATTAAGAGAAGTAAATCTTAATTCAGTGAAAATAAGGAACATA
1 AAAG-AAATTAAGAGAAGTAAATCTTAATTCAGTGAAATTAAGGAACATA
73401 AAAGAAATTAAGAGAAGTAAATCTTAATTCAGTGAAATTAAGGAACATA
1 AAAGAAATTAAGAGAAGTAAATCTTAATTCAGTGAAATTAAGGAACATA
* * * * *
73450 AAGGGAATTAAGAGAATTGAATCTTAATTCAATGAAATTAAGGAA
1 AAAGAAATTAAGAGAAGTAAATCTTAATTCAGTGAAATTAAGGAA
73495 ATTAAGAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 84 0.95
50 4 0.05
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (49 bp):
AAAGAAATTAAGAGAAGTAAATCTTAATTCAGTGAAATTAAGGAACATA
Found at i:76429 original size:39 final size:39
Alignment explanation
Indices: 76385--76477 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
76375 GGACTTAAGG
76385 AAATTAAGTAAAAAGTAGTTAAAGGACTTAATTTCAAGA
1 AAATTAAGTAAAAAGTAGTTAAAGGACTTAATTTCAAGA
*
76424 AAATTAAGTAAAAAGTAGTTAAAGGACTTAATTTCAAGG
1 AAATTAAGTAAAAAGTAGTTAAAGGACTTAATTTCAAGA
*
76463 AAATTAGGTAAAAAG
1 AAATTAAGTAAAAAG
76478 AAGACTGACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (39 bp):
AAATTAAGTAAAAAGTAGTTAAAGGACTTAATTTCAAGA
Found at i:76527 original size:39 final size:39
Alignment explanation
Indices: 76448--76986 Score: 832
Period size: 39 Copynumber: 13.9 Consensus size: 39
76438 GTAGTTAAAG
76448 GACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGT-AAAAGAAGACTGACT
*
76488 GACATAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
76527 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
76566 GACTGACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACT
1 GACT---T-AATTTCAAGGAAATTAGGT-AAAAGAAGACTGACT
76610 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
76649 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
**
76688 GACCCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGT-AAAAGAAGACTGACT
*
76728 GACTTAATTT-GAGGAAATTAGGTAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
* *
76766 GACTTAATTTCAAGGGAATTAGGT-AAA-AAGAAT-ACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
76802 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
76841 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
76880 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTG---
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
* * *
76916 G-CTTAGTTTCAAGGAAACTAGGTAAAA-AA-A-AGACT
1 GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
*
76951 GGCTTAATTTCAAGGAAATTAGGT-AAAGATAGACTG
1 GACTTAATTTCAAGGAAATTAGGTAAAAGA-AGACTG
76987 GCTAGTTTCA
Statistics
Matches: 463, Mismatches: 18, Indels: 37
0.89 0.03 0.07
Matches are distributed among these distances:
32 1 0.00
33 1 0.00
34 2 0.00
35 28 0.06
36 48 0.10
37 9 0.02
38 34 0.07
39 235 0.51
40 65 0.14
41 1 0.00
42 1 0.00
43 19 0.04
44 19 0.04
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (39 bp):
GACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACT
Found at i:76624 original size:122 final size:121
Alignment explanation
Indices: 76448--76986 Score: 818
Period size: 122 Copynumber: 4.6 Consensus size: 121
76438 GTAGTTAAAG
* *
76448 GACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACATAATTTCAAGGAAATTAGGTA
1 GACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
76513 AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGACTGACT
66 AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGA-TGACT
76570 GACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
1 GACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
76635 AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGAC---TGACT
66 AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATGACT
* *
76688 GACCCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTT-GAGGAAATTAGGTA
1 GACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
*
76752 AAAGAAGACTGACTGACTTAATTTCAAGGGAATTAGGT-AAA-AAGA---AT-ACT
66 AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATGACT
*
76802 GACTTAATTTCAAGGAAATTAGGT-AAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
1 GACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
76866 AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTG--G-CT
66 AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATGACT
* * *
76919 ---T-AGTTTCAAGGAAACTAGGTAAAAA-AA-A--GACTGGCTTAATTTCAAGGAAATTAGGT-
1 GACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
76975 AAAGATAGACTG
66 AAAGA-AGACTG
76987 GCTAGTTTCA
Statistics
Matches: 395, Mismatches: 12, Indels: 32
0.90 0.03 0.07
Matches are distributed among these distances:
109 5 0.01
110 33 0.08
112 1 0.00
113 44 0.11
114 80 0.20
115 8 0.02
116 7 0.02
117 52 0.13
118 54 0.14
122 111 0.28
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (121 bp):
GACTCAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTA
AAAGAAGACTGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGATGACT
Found at i:77080 original size:32 final size:33
Alignment explanation
Indices: 76882--77082 Score: 91
Period size: 35 Copynumber: 5.9 Consensus size: 33
76872 GACTGACTGA
* * * *
76882 CTTAATTTCAAGGAAATTAGGTAAAAGAAGACTGG
1 CTTAATTTCAAGGAAATTAAGCAGAATAAG--TGG
* * * * * *
76917 CTTAGTTTCAAGGAAACTAGGTAAAAAAAAGACTGG
1 CTTAATTTCAAGGAAATTAAG-CAGAATAAG--TGG
* * * *
76953 CTTAATTTCAAGGAAATTAGGTAAAGATAGACTGG
1 CTTAATTTCAAGGAAATTAAGCAGA-ATA-AGTGG
* * * * * * *
76988 C-TAGTTTCAAGGAAACTAGGTAAAGAAAAACTAG
1 CTTAATTTCAAGGAAATTAAG--CAGAATAAGTGG
* *
77022 CTTAATTTCACGGAAATTAAGTAGAATAAGTGG
1 CTTAATTTCAAGGAAATTAAGCAGAATAAGTGG
*
77055 CTTAA-TTCAAGGTAATTAAGCAGAATAA
1 CTTAATTTCAAGGAAATTAAGCAGAATAA
77083 AAGAACTTAA
Statistics
Matches: 134, Mismatches: 26, Indels: 15
0.77 0.15 0.09
Matches are distributed among these distances:
32 20 0.15
33 13 0.10
34 22 0.16
35 43 0.32
36 35 0.26
37 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (33 bp):
CTTAATTTCAAGGAAATTAAGCAGAATAAGTGG
Found at i:79563 original size:15 final size:15
Alignment explanation
Indices: 79543--79576 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
79533 ATTGGATTTA
79543 TTATTACTAA-TTGTT
1 TTATTA-TAACTTGTT
79558 TTATTATAACTTGTT
1 TTATTATAACTTGTT
79573 TTAT
1 TTAT
79577 AAGTTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.62
Consensus pattern (15 bp):
TTATTATAACTTGTT
Found at i:80261 original size:21 final size:21
Alignment explanation
Indices: 80231--80271 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
80221 CTAAAAACAA
*
80231 GACAAGTCCTGCCCAAGACTC
1 GACAACTCCTGCCCAAGACTC
* *
80252 GACAACTCCTGTCCAGGACT
1 GACAACTCCTGCCCAAGACT
80272 TGGTCTGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.37, G:0.20, T:0.17
Consensus pattern (21 bp):
GACAACTCCTGCCCAAGACTC
Found at i:82040 original size:45 final size:45
Alignment explanation
Indices: 81982--82067 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
81972 AAGATCTCAA
* * *
81982 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACAC
* *
82027 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
82068 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:82061 original size:22 final size:22
Alignment explanation
Indices: 81938--82518 Score: 154
Period size: 22 Copynumber: 27.0 Consensus size: 22
81928 TAAACTTTCT
*
81938 TATGAAATTTT-ATGAACCTCCT
1 TATGAAATTTTGAT-AACCTCCA
* * *
81960 TA-AAGAATTTTGA-AGATCTCAA
1 TATGA-AATTTTGATA-ACCTCCA
*
81982 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
**
82005 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
82026 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
82049 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* * * * *
82071 TATAAAAATTTAAAAACTTCCA
1 TATGAAATTTTGATAACCTCCA
82093 TATG-AATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
* *
82114 CTTTAAAATTTTGATAA--TCACA
1 -TATGAAATTTTGATAACCTC-CA
*
82136 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
* *
82159 TATGAAATTTTGATAAATCTTTC-
1 TATGAAATTTTGAT-AA-CCTCCA
* * *
82182 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * *
82205 TAT-AAATTTTTGATAACTTTCT
1 TATGAAA-TTTTGATAACCTCCA
*
82227 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* * * *
82244 TA-CAAATTTTGACAAGCTCCT
1 TATGAAATTTTGATAACCTCCA
**
82265 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* *
82286 TTATGAAATTTTGTTAATCTACC-
1 -TATGAAATTTTGATAACCT-CCA
* * *
82309 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
*
82331 TATGAAATTTTG-TAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
82352 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* * *
82373 CTATTAAAATTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
* *
82396 TATGAAATTTTGAT-ATCTTCA
1 TATGAAATTTTGATAACCTCCA
* *
82417 -CTG-AATTTTGATATCCTCC-
1 TATGAAATTTTGATAACCTCCA
* *
82436 T-TG-AATTTTGGTATCCTTCC-
1 TATGAAATTTTGATAACC-TCCA
*
82456 TA--AAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
* * * *
82475 TCATAAAAGTTTAATAACCATAC-
1 T-ATGAAATTTTGATAACC-TCCA
82498 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
82519 CTAAAAATAC
Statistics
Matches: 411, Mismatches: 100, Indels: 97
0.68 0.16 0.16
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
18 4 0.01
19 25 0.06
20 24 0.06
21 37 0.09
22 235 0.57
23 66 0.16
24 8 0.02
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:82425 original size:19 final size:19
Alignment explanation
Indices: 82401--82467 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
82391 CTTCATATGA
*
82401 AATTTTGATATCTTCAC-TG
1 AATTTTGATATCCTC-CTTG
82420 AATTTTGATATCCTCCTTG
1 AATTTTGATATCCTCCTTG
* **
82439 AATTTTGGTATCCTTCCTAA
1 AATTTTGATATCC-TCCTTG
82459 AATTTTGAT
1 AATTTTGAT
82468 TACTCCATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 1 0.02
19 28 0.68
20 12 0.29
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.48
Consensus pattern (19 bp):
AATTTTGATATCCTCCTTG
Found at i:82645 original size:66 final size:65
Alignment explanation
Indices: 82556--82768 Score: 184
Period size: 66 Copynumber: 3.2 Consensus size: 65
82546 AATAAGATTT
* * * * * ** *
82556 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATCTTTATAAAATTTTATTGACCCCTCT
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATAAAATTTGA-TAACAACACT
82621 A
65 A
* * *
82622 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTTT-TAAAATTGTGATAACAACAC
1 TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATC-TTTATAAAATT-TGATAACAACAC
82686 TA
64 TA
*
82688 TGAAATTTTGATAATCTTCA-TAT-AAATTTTGATAATCATATCTTTATGAAATTTCGATAATC-
1 TGAAATTTTGATAATC-TCATTATGAAATTTTGATAA-C--ATCTTTATAAAATTT-GATAA-CA
*
82750 ACTCTA
60 ACACTA
*
82756 TGAGA-TTTGATAA
1 TGAAATTTTGATAA
82769 CCTTCTATCA
Statistics
Matches: 121, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
65 11 0.09
66 68 0.56
67 19 0.16
68 22 0.18
69 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (65 bp):
TGAAATTTTGATAATCTCATTATGAAATTTTGATAACATCTTTATAAAATTTGATAACAACACTA
Found at i:82672 original size:44 final size:43
Alignment explanation
Indices: 82624--82749 Score: 114
Period size: 44 Copynumber: 2.8 Consensus size: 43
82614 CCCCTCTATG
* * *
82624 AAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTT-TTA-
1 AAATTTTGATAATCACACTATGAAATTTTGATAA--TC-TTCATAT
*
82668 AAATTGTGATAA-CAACACTATGAAATTTTGATAATCTTCATAT
1 AAATTTTGATAATC-ACACTATGAAATTTTGATAATCTTCATAT
* *
82711 AAATTTTGATAATCATATCTTTATGAAATTTCGATAATC
1 AAATTTTGATAATCACA-C--TATGAAATTTTGATAATC
82750 ACTCTATGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
41 2 0.03
42 4 0.06
43 14 0.21
44 31 0.46
46 17 0.25
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (43 bp):
AAATTTTGATAATCACACTATGAAATTTTGATAATCTTCATAT
Found at i:82728 original size:18 final size:19
Alignment explanation
Indices: 82690--82728 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
82680 CAACACTATG
82690 AAATTTTGATAATCTTCATAT
1 AAATTTTGATAA--TTCATAT
82711 AAATTTTGATAA-TCATAT
1 AAATTTTGATAATTCATAT
82729 CTTTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
21 12 0.67
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
AAATTTTGATAATTCATAT
Found at i:82837 original size:22 final size:22
Alignment explanation
Indices: 82556--82918 Score: 98
Period size: 22 Copynumber: 16.3 Consensus size: 22
82546 AATAAGATTT
* *
82556 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
82578 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* * *
82600 TAAAATTTT-ATTGACCCCTC-TA
1 TGAAATTTTGA-T-AACCTTCATA
* *
82622 TGAAATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
82644 TGTAATTTTGATAACC-TCGTTT
1 TGAAATTTTGATAACCTTC-ATA
* * **
82666 TAAAATTGTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
82688 TGAAATTTTGATAATCTTCATA
1 TGAAATTTTGATAACCTTCATA
* *
82710 T-AAATTTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-CCT-TC-ATA
*
82734 TGAAATTTCGATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
82756 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
82776 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
82801 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
82824 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
82846 TAAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCTTCATA
* *
82868 TGAAGTATT-AGTAACCTTC-TAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
82890 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
82912 TGAAATT
1 TGAAATT
82919 CGTATAACCT
Statistics
Matches: 252, Mismatches: 53, Indels: 72
0.67 0.14 0.19
Matches are distributed among these distances:
19 1 0.00
20 9 0.04
21 40 0.16
22 155 0.62
23 11 0.04
24 6 0.02
25 19 0.08
26 6 0.02
27 5 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:83054 original size:46 final size:43
Alignment explanation
Indices: 82989--83142 Score: 130
Period size: 44 Copynumber: 3.5 Consensus size: 43
82979 AATTAACCAC
*** *
82989 CCTATGAAATTTCAATAACCAAACTAAGAAATTTTAATAACTTGA
1 CCTATGAAATTTTGGTAACCACACTAAGAAATTTTAATAAC-T-A
* * **
83034 TCCTATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTA
1 -CCTATGAAATTTTGGTAACCACACTAAGAAATTTTAATAACTA
** *
83078 CACTATGAAATTTTGGTAACCACAC-AATGAAATTTTGGTAACCA
1 C-CTATGAAATTTTGGTAACCACACTAA-GAAATTTTAATAACTA
* *
83122 CACTATGGAATTTTGATAACC
1 C-CTATGAAATTTTGGTAACC
83143 TCCTCATGGA
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.02
44 57 0.61
45 1 0.01
46 33 0.35
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (43 bp):
CCTATGAAATTTTGGTAACCACACTAAGAAATTTTAATAACTA
Found at i:83064 original size:22 final size:22
Alignment explanation
Indices: 83036--83142 Score: 169
Period size: 22 Copynumber: 4.9 Consensus size: 22
83026 TAACTTGATC
*
83036 CTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGGTAACCACA
*
83058 CTATGAAATTTTGGTAACTACA
1 CTATGAAATTTTGGTAACCACA
83080 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
83102 CAATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
83124 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
83143 TCCTCATGGA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 78 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:83091 original size:68 final size:66
Alignment explanation
Indices: 82982--83142 Score: 171
Period size: 68 Copynumber: 2.4 Consensus size: 66
82972 TTGTGATAAT
* ** * *
82982 TAACCACCCTATGAAATTTCAATAACCAAACTAAGAAATTTTAATAACTTGATC-CTATGAAATT
1 TAACCACACTATGAAATTTTGATAACCAAACTAAGAAATTTTAATAAC--CA-CACAATGAAATT
83046 TTGG
63 TTGG
* * * * * **
83050 TAACCACTCTATGAAATTTTGGTAACTACACTATGAAATTTTGGTAACCACACAATGAAATTTTG
1 TAACCACACTATGAAATTTTGATAACCAAACTAAGAAATTTTAATAACCACACAATGAAATTTTG
83115 G
66 G
*
83116 TAACCACACTATGGAATTTTGATAACC
1 TAACCACACTATGAAATTTTGATAACC
83143 TCCTCATGGA
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 1 0.01
66 37 0.48
68 39 0.51
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (66 bp):
TAACCACACTATGAAATTTTGATAACCAAACTAAGAAATTTTAATAACCACACAATGAAATTTTG
G
Found at i:83151 original size:22 final size:22
Alignment explanation
Indices: 83036--83165 Score: 118
Period size: 22 Copynumber: 5.9 Consensus size: 22
83026 TAACTTGATC
* * *
83036 CTATGAAATTTTGGTAACCACT
1 CTATGGAATTTTGATAACCACA
* * *
83058 CTATGAAATTTTGGTAACTACA
1 CTATGGAATTTTGATAACCACA
* *
83080 CTATGAAATTTTGGTAACCACA
1 CTATGGAATTTTGATAACCACA
* * *
83102 CAATGAAATTTTGGTAACCACA
1 CTATGGAATTTTGATAACCACA
*
83124 CTATGGAATTTTGATAACCTC-
1 CTATGGAATTTTGATAACCACA
* *
83145 CTCATGGAATTATAATAACCA
1 CT-ATGGAATTTTGATAACCA
83166 AAGTAAAATA
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
21 2 0.02
22 94 0.98
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (22 bp):
CTATGGAATTTTGATAACCACA
Found at i:83164 original size:66 final size:66
Alignment explanation
Indices: 83038--83165 Score: 161
Period size: 66 Copynumber: 1.9 Consensus size: 66
83028 ACTTGATCCT
* * * **
83038 ATGAAATTTTGGTAACCACTCTATGAAATTTTGGTAACTACACTATGAAATTTTGGTAACCACAC
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTACACTATGAAATTATAATAACCACAC
83103 A
66 A
* *
83104 ATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCT-C-CTCATGGAATTATAATAACCA
1 ATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-CTACACT-ATGAAATTATAATAACCA
83166 AAGTAAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 2 0.04
66 49 0.92
67 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (66 bp):
ATGAAATTTTGGTAACCACACTATGAAATTTTGATAACTACACTATGAAATTATAATAACCACAC
A
Found at i:83292 original size:31 final size:31
Alignment explanation
Indices: 83247--83314 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
83237 TTTAGTAATG
*
83247 ACAATTTAGAAATATGTTTTAAAAAAAAGGGT
1 ACAA-TTAAAAATATGTTTTAAAAAAAAGGGT
*
83279 ACAATTAAAAATATGTTTTAAAAATAAGGGT
1 ACAATTAAAAATATGTTTTAAAAAAAAGGGT
83310 ACAAT
1 ACAAT
83315 CGGAAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (31 bp):
ACAATTAAAAATATGTTTTAAAAAAAAGGGT
Found at i:89928 original size:6 final size:6
Alignment explanation
Indices: 89919--89947 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
89909 AAAGAAAAAG
89919 GGAGAC GGAGAC GGAGAC GGAGAC GGAGA
1 GGAGAC GGAGAC GGAGAC GGAGAC GGAGA
89948 GAGACCAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAGAC
Found at i:90638 original size:17 final size:17
Alignment explanation
Indices: 90616--90649 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
90606 AAGGAAAAAC
90616 TGAAAAAGAAAGAGCTT
1 TGAAAAAGAAAGAGCTT
90633 TGAAAAAGAAAGAGCTT
1 TGAAAAAGAAAGAGCTT
90650 GGAACGATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (17 bp):
TGAAAAAGAAAGAGCTT
Found at i:93457 original size:21 final size:22
Alignment explanation
Indices: 93431--93488 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
93421 CTTTCTGCAT
*
93431 ATGATTCTTAATTTTCCTTTGA
1 ATGATTCTTAATTATCCTTTGA
** **
93453 A-GATTGATAATTATGTTTTGA
1 ATGATTCTTAATTATCCTTTGA
93474 ATGATTCTTAATTAT
1 ATGATTCTTAATTAT
93489 TTCTTTATCA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (22 bp):
ATGATTCTTAATTATCCTTTGA
Found at i:95033 original size:2 final size:2
Alignment explanation
Indices: 95026--95056 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
95016 TTAATACCAG
95026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
95057 ATGTTGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:110020 original size:19 final size:18
Alignment explanation
Indices: 109987--110022 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
109977 TTGAAATAAT
109987 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
110005 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
110023 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.