Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold13
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: 2744999
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.26
Warning! 506982 characters in sequence are not A, C, G, or T
File 15 of 15
Found at i:2705303 original size:20 final size:20
Alignment explanation
Indices: 2705280--2705354 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
2705270 AAAAAGACAG
2705280 AATGTATCGATACATT-AAA
1 AATGTATCGATACATTCAAA
*
2705299 GAATGTATCGATACATTCATA
1 -AATGTATCGATACATTCAAA
* *
2705320 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
*
2705340 AATGTATCGAGACAT
1 AATGTATCGATACAT
2705355 CTAGGTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 46 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:2710732 original size:19 final size:19
Alignment explanation
Indices: 2710710--2710747 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2710700 CTGCTATGGT
*
2710710 CTAGTTTTGGGGTAAGGAA
1 CTAGTTTTGAGGTAAGGAA
*
2710729 CTAGTTTTGAGTTAAGGAA
1 CTAGTTTTGAGGTAAGGAA
2710748 GAAGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (19 bp):
CTAGTTTTGAGGTAAGGAA
Found at i:2710769 original size:21 final size:22
Alignment explanation
Indices: 2710743--2710784 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
2710733 TTTTGAGTTA
2710743 AGGAAGAAGAA-AAAAAAGAAG
1 AGGAAGAAGAAGAAAAAAGAAG
2710764 AGGAAGAAGAAGAAAAAAGAA
1 AGGAAGAAGAAGAAAAAAGAA
2710785 AAAAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AGGAAGAAGAAGAAAAAAGAAG
Found at i:2714371 original size:52 final size:52
Alignment explanation
Indices: 2714225--2714353 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2714215 CGAAATATGA
2714225 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
2714277 AACTTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
2714329 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2714354 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:2714434 original size:19 final size:18
Alignment explanation
Indices: 2714410--2714505 Score: 86
Period size: 13 Copynumber: 5.7 Consensus size: 18
2714400 GCTTACATTA
2714410 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
2714429 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
2714442 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
2714461 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
2714474 TATCGATACAACACTTTATG
1 TATCGATACAA-AC-TTATG
2714494 TATCGATACAAA
1 TATCGATACAAA
2714506 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 26
0.71 0.00 0.29
Matches are distributed among these distances:
13 22 0.34
14 2 0.03
16 4 0.06
18 1 0.02
19 22 0.34
20 13 0.20
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:2714446 original size:32 final size:32
Alignment explanation
Indices: 2714403--2714503 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
2714393 GGCAGTAGCT
* *
2714403 TACATTATATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
2714435 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
2714467 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
2714500 TACA
1 TACA
2714504 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 51 0.77
33 15 0.23
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:2716025 original size:25 final size:26
Alignment explanation
Indices: 2715992--2716051 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
2715982 CGGCATTTGT
*
2715992 AGGGATACTCCAATC-CATCCTTCGA
1 AGGGATACTCCAACCTCATCCTTCGA
* *
2716017 GGGGATACTCCAACCTCGTCCTTCGA
1 AGGGATACTCCAACCTCATCCTTCGA
2716043 AGGGATACT
1 AGGGATACT
2716052 GAAACTCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (26 bp):
AGGGATACTCCAACCTCATCCTTCGA
Found at i:2718412 original size:26 final size:25
Alignment explanation
Indices: 2718351--2718399 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
2718341 CATTTATATG
* *
2718351 GATACTCCAACCCTGTCTTCCGAAA
1 GATACTCCAACCCTATCCTCCGAAA
2718376 GTATACTCCAACCCTATCCTCCGA
1 G-ATACTCCAACCCTATCCTCCGA
2718400 GGAGATACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.27, C:0.39, G:0.10, T:0.24
Consensus pattern (25 bp):
GATACTCCAACCCTATCCTCCGAAA
Found at i:2719261 original size:14 final size:14
Alignment explanation
Indices: 2719242--2719268 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2719232 ACATTATGCT
2719242 TTGTATCGATACAA
1 TTGTATCGATACAA
2719256 TTGTATCGATACA
1 TTGTATCGATACA
2719269 TGTTCATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TTGTATCGATACAA
Found at i:2719266 original size:34 final size:33
Alignment explanation
Indices: 2719223--2719287 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
2719213 CTCACCCAGA
*
2719223 TGTATCGATACAT-TATGCTTTGTATCGATACAAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAAT
2719257 TGTATCGATACATGTTCATTGTATCGATACA
1 TGTATCGATACATGTTCATTGTATCGATACA
2719288 TGGACAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 14 0.48
34 14 0.48
35 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATGTTCATTGTATCGATACAAT
Found at i:2719299 original size:20 final size:20
Alignment explanation
Indices: 2719252--2719308 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
2719242 TTGTATCGAT
*
2719252 ACAATTGTATCGATACATGT
1 ACAATTGTATCGATACATGG
*
2719272 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
2719291 ACAATTGTATCGATACAT
1 ACAATTGTATCGATACAT
2719309 AAAATTGGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:2720497 original size:62 final size:62
Alignment explanation
Indices: 2720392--2720530 Score: 181
Period size: 62 Copynumber: 2.2 Consensus size: 62
2720382 ATTTGCTTTT
* * * * *
2720392 GTAACCCTCCGTATATGCATGGCAAGACCTTCCAAGATATAATTTACCTATGTCTCTCGTGA
1 GTAACCCTCCGCATATGCATGGCAAAACCTTCCAAGATATAATTTACCAACGTCTCTCATGA
* * *
2720454 GTAACCCTCCGCATA-GTCATGGCAAAACCTTCCGAGGTGTAATTTACCAACGTCTCTCATGA
1 GTAACCCTCCGCATATG-CATGGCAAAACCTTCCAAGATATAATTTACCAACGTCTCTCATGA
*
2720516 GTAACCCTCCACATA
1 GTAACCCTCCGCATA
2720531 AGGAAGTACA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
61 1 0.01
62 66 0.99
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (62 bp):
GTAACCCTCCGCATATGCATGGCAAAACCTTCCAAGATATAATTTACCAACGTCTCTCATGA
Found at i:2721328 original size:18 final size:18
Alignment explanation
Indices: 2721305--2721343 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2721295 TTATTTATTA
2721305 TAAGACTAATTAATTAAT
1 TAAGACTAATTAATTAAT
2721323 TAAGACTAATTAATTAAT
1 TAAGACTAATTAATTAAT
2721341 TAA
1 TAA
2721344 TTAAAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAGACTAATTAATTAAT
Found at i:2721973 original size:18 final size:17
Alignment explanation
Indices: 2721951--2721991 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
2721941 AGAAAAGACC
*
2721951 AAAGAAGGAAGAAAGAA
1 AAAGAAGAAAGAAAGAA
2721968 ACAAGAAGAAAGAAAGAA
1 A-AAGAAGAAAGAAAGAA
2721986 AAAGAA
1 AAAGAA
2721992 AAAAAAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAGAAAGAA
Found at i:2721975 original size:14 final size:14
Alignment explanation
Indices: 2721959--2722016 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
2721949 CCAAAGAAGG
*
2721959 AAGAAAGAAACAAG
1 AAGAAAGAAACAAA
*
2721973 AAGAAAGAAAGAAA
1 AAGAAAGAAACAAA
2721987 AAGAAA-AAA-AAA
1 AAGAAAGAAACAAA
2721999 AAGGAAAGAAGACAAA
1 AA-GAAAGAA-ACAAA
2722015 AA
1 AA
2722017 AAAAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
12 5 0.13
13 7 0.18
14 20 0.53
15 1 0.03
16 5 0.13
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAACAAA
Found at i:2722008 original size:23 final size:24
Alignment explanation
Indices: 2721958--2722025 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 24
2721948 ACCAAAGAAG
*
2721958 GAAGAAAGAAACAAGAAGAAA-GAAA
1 GAAGAAAGAAA-AA-AAAAAAGGAAA
2721983 GAA-AAAGAAAAAAAAAAAGGAAA
1 GAAGAAAGAAAAAAAAAAAGGAAA
2722006 GAAGACAA-AAAAAAAAAAAG
1 GAAGA-AAGAAAAAAAAAAAG
2722026 AGGAGAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 5 0.13
23 9 0.23
24 20 0.51
25 5 0.13
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (24 bp):
GAAGAAAGAAAAAAAAAAAGGAAA
Found at i:2722019 original size:26 final size:27
Alignment explanation
Indices: 2721975--2722029 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2721965 GAAACAAGAA
2721975 GAAAGAAAGAAAAAGAAAAAAAAAAAG
1 GAAAGAAAGAAAAAGAAAAAAAAAAAG
*
2722002 GAAAG-AAGACAAAA-AAAAAAAAAGAG
1 GAAAGAAAGA-AAAAGAAAAAAAAAAAG
2722028 GA
1 GA
2722030 GAAAGGCTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (27 bp):
GAAAGAAAGAAAAAGAAAAAAAAAAAG
Found at i:2722378 original size:4 final size:4
Alignment explanation
Indices: 2722369--2722394 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2722359 TGTTATTGAG
2722369 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
2722395 TTGTTGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2728714 original size:19 final size:19
Alignment explanation
Indices: 2728695--2728732 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2728685 TTAATAATAA
*
2728695 TATTTATATATTTGTTTAAT
1 TATTTA-ATATTTATTTAAT
2728715 TATTTAATATTTATTTAA
1 TATTTAATATTTATTTAA
2728733 GCTAATTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TATTTAATATTTATTTAAT
Found at i:2729331 original size:23 final size:22
Alignment explanation
Indices: 2729287--2729331 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2729277 TATAATAATT
*
2729287 TTATAAATTTTTAAATATATAA
1 TTATAAATTTTTAAATAAATAA
*
2729309 TTATATATTTTATAAATAAATAA
1 TTATAAATTTT-TAAATAAATAA
2729332 AATTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATAAATTTTTAAATAAATAA
Found at i:2729882 original size:19 final size:16
Alignment explanation
Indices: 2729860--2729903 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
2729850 TAATAGCAAA
2729860 AAAAATTATAATGATAAT
1 AAAAATTATAATG--AAT
*
2729878 CAAAAAATATAATGAAT
1 -AAAAATTATAATGAAT
2729895 AAAAATTAT
1 AAAAATTAT
2729904 CATTTTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 3 0.13
19 12 0.52
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAAATTATAATGAAT
Found at i:2729973 original size:15 final size:16
Alignment explanation
Indices: 2729944--2729973 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2729934 TCGTACTTCT
2729944 CTATAACTAGTATTAG
1 CTATAACTAGTATTAG
2729960 CTATAACT-GTATTA
1 CTATAACTAGTATTA
2729974 CACGTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (16 bp):
CTATAACTAGTATTAG
Found at i:2730696 original size:15 final size:15
Alignment explanation
Indices: 2730676--2730704 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2730666 TTACTTGATA
2730676 AAAATAATATAATAC
1 AAAATAATATAATAC
2730691 AAAATAATATAATA
1 AAAATAATATAATA
2730705 AATAAACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAATATAATAC
Found at i:2731121 original size:6 final size:6
Alignment explanation
Indices: 2731112--2731141 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2731102 AAAAAGCTAT
*
2731112 ATTAAA ATTAAA ATTAAA ATTAAA GTTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
2731142 TTACAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (6 bp):
ATTAAA
Found at i:2731284 original size:3 final size:3
Alignment explanation
Indices: 2731278--2731326 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
2731268 CAGCATCTTA
* * *
2731278 AGG AGG AGG AGG AGG AGG CGG CGG AGG CA-G AGG TGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG -AGG AGG AGG AGG AGG AGG
2731323 AGG A
1 AGG A
2731327 AGAGAAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.63, T:0.02
Consensus pattern (3 bp):
AGG
Found at i:2735340 original size:84 final size:84
Alignment explanation
Indices: 2735196--2735364 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 84
2735186 TTTTCTTTGC
* **
2735196 ATCTGACAAGCAAAATTATGATAAATGGATAAAAGCATACAAAAGTTACCTTCTCCTTTCCTTAG
1 ATCTGACAAGCAAAATTATGACAAATAAATAAAAGCATACAAAAGTTACCTTCTCCTTTCCTTAG
*
2735261 CTGGGTTTGCAGAATTAGA
66 CCGGGTTTGCAGAATTAGA
* *
2735280 ATCTGACAAGCAAAATTATGACAAA-AAATTAAGAGCATACAAAAGTTACCTTCTCTTTTCCTTA
1 ATCTGACAAGCAAAATTATGACAAATAAA-TAAAAGCATACAAAAGTTACCTTCTCCTTTCCTTA
2735344 GCCGGGTTTGCAGAATTAGA
65 GCCGGGTTTGCAGAATTAGA
2735364 A
1 A
2735365 CAAGGAAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
83 1 0.01
84 77 0.99
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (84 bp):
ATCTGACAAGCAAAATTATGACAAATAAATAAAAGCATACAAAAGTTACCTTCTCCTTTCCTTAG
CCGGGTTTGCAGAATTAGA
Found at i:2741623 original size:13 final size:13
Alignment explanation
Indices: 2741605--2741629 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2741595 GTATTTATAT
2741605 ATATTAATATAAG
1 ATATTAATATAAG
2741618 ATATTAATATAA
1 ATATTAATATAA
2741630 AATGTATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATTAATATAAG
Found at i:2743409 original size:22 final size:21
Alignment explanation
Indices: 2743342--2743410 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
2743332 TATCAAAGGA
*
2743342 AGAGA-AATAAAATGAGGGAAG
1 AGAGAGAATAAAA-GAGGAAAG
* *
2743363 AGAGAGGAA-AATAGAGAAGAAG
1 AGAGA-GAATAAAAGAGGA-AAG
2743385 AGAGAGAATAAAAGAGGAAATG
1 AGAGAGAATAAAAGAGGAAA-G
2743407 AGAG
1 AGAG
2743411 GTGGAAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
21 13 0.34
22 23 0.61
23 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.07
Consensus pattern (21 bp):
AGAGAGAATAAAAGAGGAAAG
Found at i:2743472 original size:17 final size:17
Alignment explanation
Indices: 2743450--2743540 Score: 64
Period size: 17 Copynumber: 5.3 Consensus size: 17
2743440 GGTGAATGGA
2743450 AAAAAAAAGGAAGAGAG
1 AAAAAAAAGGAAGAGAG
*
2743467 -AAAAAAAGGAAG-GGG
1 AAAAAAAAGGAAGAGAG
* * *
2743482 AAAAATAAAGGAGGAAAAA
1 AAAAA-AAAGGAAG-AGAG
2743501 AAAAGAAAAGG-AGAGAG
1 AAAA-AAAAGGAAGAGAG
*
2743518 AAAATGAAAGAGAAGAG-G
1 AAAA-AAAAG-GAAGAGAG
2743536 AAAAA
1 AAAAA
2743541 GAACACATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
15 2 0.04
16 16 0.29
17 17 0.30
18 7 0.12
19 13 0.23
20 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGGAAGAGAG
Found at i:2743486 original size:16 final size:15
Alignment explanation
Indices: 2743450--2743505 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
2743440 GGTGAATGGA
*
2743450 AAAAAAAAGGAAGAG
1 AAAAAAAAGGAAGGG
2743465 AGAAAAAAAGGAAGGGG
1 A-AAAAAAAGGAA-GGG
*
2743482 AAAAATAAAGG-AGGA
1 AAAAA-AAAGGAAGGG
2743497 AAAAAAAAG
1 AAAAAAAAG
2743506 AAAAGGAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 4 0.11
15 8 0.22
16 16 0.44
17 8 0.22
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.02
Consensus pattern (15 bp):
AAAAAAAAGGAAGGG
Found at i:2743631 original size:21 final size:21
Alignment explanation
Indices: 2743607--2743657 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2743597 GCCAACGACC
*
2743607 GAAAATAAAGAAAAAGAAGAA
1 GAAAATAAAGAAAAAGAAAAA
* * *
2743628 GAAAAAAAAGATAAATAAAAA
1 GAAAATAAAGAAAAAGAAAAA
*
2743649 TAAAATAAA
1 GAAAATAAA
2743658 AATAATACAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (21 bp):
GAAAATAAAGAAAAAGAAAAA
Found at i:2743662 original size:21 final size:21
Alignment explanation
Indices: 2743629--2743670 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2743619 AAAGAAGAAG
2743629 AAAAAAAAGATAAATA-AAAAT
1 AAAAAAAAGAT-AATACAAAAT
2743650 AAAATAAAA-ATAATACAAAAT
1 AAAA-AAAAGATAATACAAAAT
2743671 TAAGAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAAAAAGATAATACAAAAT
Found at i:2744703 original size:22 final size:19
Alignment explanation
Indices: 2744673--2744714 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2744663 TATTATTATC
2744673 TAAATTTAATAATAAAATATA
1 TAAATTTAAT-ATAAAA-ATA
2744694 TAAATATTAATATAAAAATA
1 TAAAT-TTAATATAAAAATA
2744714 T
1 T
2744715 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATATAAAAATA
Found at i:2744758 original size:15 final size:16
Alignment explanation
Indices: 2744734--2744771 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2744724 TTATTAATAT
2744734 AAAT-AAATTAAA-TC
1 AAATAAAATTAAATTC
*
2744748 AAATAAAATTAAATTT
1 AAATAAAATTAAATTC
2744764 AAATAAAA
1 AAATAAAA
2744772 AATTCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 8 0.38
16 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAAAATTAAATTC
Done.