Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2453
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: 44981
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:950 original size:13 final size:13
Alignment explanation
Indices: 932--957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
922 TACAGTAAGT
932 ATGTATCGATACA
1 ATGTATCGATACA
945 ATGTATCGATACA
1 ATGTATCGATACA
958 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2707 original size:8 final size:8
Alignment explanation
Indices: 2694--2737 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
2684 TATACTAAAA
2694 ACATATAT
1 ACATATAT
2702 ACATATAT
1 ACATATAT
*
2710 AAATATAT
1 ACATATAT
*
2718 AAATATAT
1 ACATATAT
2726 ATCATACTAT
1 A-CATA-TAT
2736 AC
1 AC
2738 CATTAAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 24 0.75
9 4 0.12
10 4 0.12
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (8 bp):
ACATATAT
Found at i:7999 original size:15 final size:15
Alignment explanation
Indices: 7979--8010 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7969 ATTTTAATTA
7979 TTTAATATATTATAT
1 TTTAATATATTATAT
7994 TTTAATATATTATAT
1 TTTAATATATTATAT
8009 TT
1 TT
8011 AAAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATATATTATAT
Found at i:8075 original size:36 final size:38
Alignment explanation
Indices: 8012--8084 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 38
8002 ATTATATTTA
8012 AAATATTTAAAAATAATAATGTAATAAT-TAA-ATAAT
1 AAATATTTAAAAATAATAATGTAATAATATAATATAAT
*
8048 AAATATTTAATAAT-AT-ATAGTATATAATATAATATAA
1 AAATATTTAAAAATAATAAT-GTA-ATAATATAATATAA
8085 AATACTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 2 0.06
35 5 0.16
36 18 0.56
37 3 0.09
38 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (38 bp):
AAATATTTAAAAATAATAATGTAATAATATAATATAAT
Found at i:9503 original size:20 final size:21
Alignment explanation
Indices: 9478--9530 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
9468 TACAAGCCAA
* *
9478 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
9498 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
9518 TGTATCGATACAA
1 TGTATCGATACAA
9531 ATTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:9535 original size:19 final size:19
Alignment explanation
Indices: 9478--9536 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
9468 TACAAGCCAA
* *
9478 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-ATTTGG
*
9498 TGTATCGATACATACTTTGG
1 TGTATCGATACA-AATTTGG
9518 TGTATCGATACAAATTTGG
1 TGTATCGATACAAATTTGG
9537 CTACTGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAAATTTGG
Found at i:11642 original size:21 final size:20
Alignment explanation
Indices: 11613--11653 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11603 GGCTAGTATG
*
11613 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
11634 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
11654 AGTGGTGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.10, C:0.32, G:0.41, T:0.17
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:12114 original size:13 final size:13
Alignment explanation
Indices: 12096--12120 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12086 ATAATCCCCC
12096 TGTATCGATACAG
1 TGTATCGATACAG
12109 TGTATCGATACA
1 TGTATCGATACA
12121 TTGAATTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:12656 original size:13 final size:13
Alignment explanation
Indices: 12638--12662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12628 CATAAAGTGT
12638 TGTATCGATACAA
1 TGTATCGATACAA
12651 TGTATCGATACA
1 TGTATCGATACA
12663 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12744 original size:13 final size:13
Alignment explanation
Indices: 12726--12750 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12716 ATCACTTAAA
12726 TGTATCGATACAT
1 TGTATCGATACAT
12739 TGTATCGATACA
1 TGTATCGATACA
12751 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16309 original size:20 final size:21
Alignment explanation
Indices: 16284--16336 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
16274 TACAAGCCAA
* *
16284 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
16304 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
16324 TGTATCGATACAA
1 TGTATCGATACAA
16337 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:16341 original size:19 final size:19
Alignment explanation
Indices: 16284--16342 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
16274 TACAAGCCAA
* *
16284 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
16304 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
16324 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
16343 CTACTGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:17598 original size:28 final size:28
Alignment explanation
Indices: 17558--17629 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
17548 GAAAAAAAAT
* ** *
17558 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
17586 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
17614 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
17630 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:17680 original size:52 final size:52
Alignment explanation
Indices: 17618--17899 Score: 279
Period size: 52 Copynumber: 5.4 Consensus size: 52
17608 AAATAACGAG
*
17618 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * * * *
17670 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCA-TTTTGAAAATAAAACCGG-
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
* * * * * *
17721 GATTGGAGTATCCCTGATTGTGGAAAAATTAGTGTTTTAGTG--ATAAAACCGGG
1 G-TTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
*
17774 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
17828 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
*
17879 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
17900 GAGAATTGAG
Statistics
Matches: 188, Mismatches: 30, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
51 39 0.21
52 93 0.49
53 28 0.15
54 28 0.15
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:17890 original size:105 final size:104
Alignment explanation
Indices: 17622--17904 Score: 281
Period size: 105 Copynumber: 2.7 Consensus size: 104
17612 AACGAGGTTG
* * * * *
17622 GAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA
1 GAGTATCCCCGATTATAGAAAAATTAGT-GTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGA
* *
17686 -T-TAAAGGAAAATTGGCATTTTGAAAATAAAACCGGGATTG
65 TTGTGAA-G-AAATTGGCATTTTGAAAATAAAACCGGGATTA
* * * ** * *
17726 GAGTATCCCTGATTGTGGAAAAATTAGTGTTTT-AGTGATAAAACCGGGGTTGGAGTATCCCCGA
1 GAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGGAGTTGGAGTATCCCCGA
** * *
17790 TTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATC-GGAGTTA
65 TTGTGAAGAAATT-G-GCATTTTGAAAATAAAACCGGGA-TTA
*
17832 GAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGAT
1 GAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGAT
*
17896 TGTGGAGAA
66 TGTGAAGAA
17905 TTGAGAAACT
Statistics
Matches: 147, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
104 48 0.33
105 63 0.43
106 36 0.24
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.31
Consensus pattern (104 bp):
GAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGAT
TGTGAAGAAATTGGCATTTTGAAAATAAAACCGGGATTA
Found at i:20279 original size:13 final size:13
Alignment explanation
Indices: 20261--20286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20251 ACAAAGATCC
20261 ATGTATCGATACA
1 ATGTATCGATACA
20274 ATGTATCGATACA
1 ATGTATCGATACA
20287 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20282 original size:33 final size:33
Alignment explanation
Indices: 20240--20306 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
20230 AAAATTTCCA
***
20240 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
20273 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
20306 A
1 A
20307 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:20441 original size:21 final size:21
Alignment explanation
Indices: 20417--20494 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
20407 CATTTGTAGG
20417 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
20438 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
20459 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
20480 ATGTATCGATACATT
1 ATGTATCGATACATT
20495 TGGATAATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:21339 original size:59 final size:59
Alignment explanation
Indices: 21194--22527 Score: 1687
Period size: 59 Copynumber: 23.0 Consensus size: 59
21184 GTGGGCTTTG
21194 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA
* * * *
21255 AAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
21314 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
21373 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* *
21432 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * ** *
21491 AAAGGCATCCCGCTCTTTGAGGACTGGAAAATGCCACCAACCTGTGTGGGCTTT-----A
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* **
21546 AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* *
21601 AAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA
* * * * * * *
21662 AAAAGCATCATGCTCTTTGAGGATTAAAGGTGCCACCGACTTGGGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
21721 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * *
21780 AAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* *
21839 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * *
21898 AAAGGAGTCCCGCTCTTTGAGGACTGGAA-GTGCCACCAACTTGTGTGGTCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* *
21957 AAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* ** *
22016 AAAGGCGTCCCGCTCTTTGAGGACTGGAAAATGCCACCAACCTGTGTGGGCTTT-----A
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* **
22071 AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
*
22126 AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA
** * * *
22187 AAAATCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* *
22246 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * *
22305 AAATGTGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG-
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* * * **
22361 --AGGTGTCCTGCTCTCTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* **
22414 AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
* ** * *
22469 AAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
22528 GTGTCCTGCT
Statistics
Matches: 1164, Mismatches: 83, Indels: 54
0.89 0.06 0.04
Matches are distributed among these distances:
53 1 0.00
54 20 0.02
55 333 0.29
57 3 0.00
58 3 0.00
59 607 0.52
60 132 0.11
61 65 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (59 bp):
AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
Found at i:21901 original size:407 final size:404
Alignment explanation
Indices: 21146--22471 Score: 1896
Period size: 407 Copynumber: 3.3 Consensus size: 404
21136 ATAAAGTGTA
* * * * *
21146 TCCTGCTCATTGAGGAGTAAAAAGTGCCATCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
*
21211 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
65 TGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
* * * *
21276 GACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGA
129 GATTAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGA
*
21341 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGC
194 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGC
21406 CACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAA
259 CACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAA
* *
21471 CTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGGAAAATGCCACCAACCTGT
324 CTTGTGTGGGCTTTAAAAGAAAAGG-ATCCCGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGT
21536 GTGGGCTTTAAAAGGTG
388 GTGGGCTTTAAAAGGTG
*
21553 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
*
21618 TGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCATGCTCTTTGA
65 TGAGGACTGAAAA--TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGA
*
21682 GGATTAAAGGTGCCACCGACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG
128 GGATTAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTG
*
21747 AAGGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTG
193 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTG
*
21812 CCACCAACTTGTGTAGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCA
258 CCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCA
21877 ACTTGTGTGGGCTTTAAAAGAAAAGGAGTCCCGCTCTTTGAGGACTGG-AAGTGCCACCAACTTG
323 ACTTGTGTGGGCTTTAAAAGAAAAGGA-TCCCGCTCTTTGAGGACTGGAAAGTGCCACCAACTTG
*
21941 TGTGGTCTTTAAAAGAAAAG-G
387 TGTGGGCTTTAAAAG----GTG
* ** *
21962 CATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCC
1 --TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCGTCCT
* **
22027 GCTCTTTGAGGACTGGAAAATGCCACCAACCTGTGTGGGCTTT-AAAAG-----GTGTCCTGCTC
59 GCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTC
* * * *
22086 TTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTG
123 TTTGAGGA-T-TAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTG
** * *
22145 AGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAATCATCCTGCTCTTTGAGGA
186 AGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCCGCTCTTTGAGGA
* *
22210 CT-AAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAA
249 CTGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAA
* *
22274 GGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAATGTG-TCCCGCTCTTTGAGGACT-GAAGGTG
313 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAA-G-GATCCCGCTCTTTGAGGACTGGAAAGTG
*
22337 CCACCAACTTGTGTGGGCTTTAAGAGGTG
376 CCACCAACTTGTGTGGGCTTTAAAAGGTG
* * *
22366 TCCTGCTCTCTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTT
22431 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAA
65 TGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAA
22472 GGTGTCCTGC
Statistics
Matches: 838, Mismatches: 53, Indels: 64
0.88 0.06 0.07
Matches are distributed among these distances:
398 51 0.06
399 4 0.00
402 15 0.02
403 27 0.03
404 1 0.00
405 25 0.03
406 63 0.08
407 505 0.60
408 5 0.01
409 18 0.02
410 49 0.06
411 20 0.02
414 6 0.01
415 45 0.05
417 4 0.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (404 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTT
GAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGA
TTAAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGAAG
GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAAGTGCCA
CCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACT
TGTGTGGGCTTTAAAAGAAAAGGATCCCGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTG
GGCTTTAAAAGGTG
Found at i:22015 original size:525 final size:525
Alignment explanation
Indices: 21194--22527 Score: 2178
Period size: 525 Copynumber: 2.6 Consensus size: 525
21184 GTGGGCTTTG
*
21194 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGTCTTT-AAAAGAAAAA
* * * *
21259 GCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCGTCC
64 GCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC
*
21324 CGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCT
129 CGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGAGTCCCGCTCT
21389 TTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAG
194 TTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAG
21453 GACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGG
258 GACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGG
21518 AAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCAC
323 AAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCAC
21583 CAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGT
388 CAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGT
* *
21648 GGGCTTTGAAAAGAAAAAGCATCATGCTCTTTGAGGATTAAAGGTGCCACCGACTTGGGTGGGCT
453 GGGCTTTGAAAAGAAAAAGCATCATGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCT
21713 TTAAAAGA
518 TTAAAAGA
*
21721 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAAGGC
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAAAGC
* * *
21786 GTCCCGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAGGCATCCCG
66 GTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
21851 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGAGTCCCGCTCTTT
131 CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGAGTCCCGCTCTTT
*
21916 GAGGACTGGAAGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGAC
196 GAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGAC
*
21981 TGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGGAAA
261 TGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGGAAA
22046 ATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
326 ATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
*
22111 CTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGG
391 CTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGG
* *
22176 CTTTGAAAAGAAAAATCATCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCTTTA
456 CTTTGAAAAGAAAAAGCATCATGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCTTTA
22241 AAAGA
521 AAAGA
* * *
22246 AAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAATGT
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAAAGC
* *
22311 GTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTGTCCTG
66 GTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
* * ** * *
22371 CTCTCTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTT
131 CTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGAGTCCCGCTCTT
* ** *
22431 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTGCTCTTTGAGG
195 TGAGGACTGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGG
** * *
22491 ACTGGAAAATGCCACCAACTTATGTGGGCTTTGAAAG
259 ACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
22528 GTGTCCTGCT
Statistics
Matches: 763, Mismatches: 40, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
512 22 0.03
513 30 0.04
516 25 0.03
517 25 0.03
520 18 0.02
521 26 0.03
523 3 0.00
525 559 0.73
526 29 0.04
527 26 0.03
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (525 bp):
AAAGGCGTCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGTCTTTAAAAGAAAAAGC
GTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCG
CTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGAGTCCCGCTCTTT
GAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGAC
TGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCCGCTCTTTGAGGACTGGAAA
ATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
CTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGG
CTTTGAAAAGAAAAAGCATCATGCTCTTTGAGGACTAAAGGTGCCACCAACTTGGGTGGGCTTTA
AAAGA
Found at i:22443 original size:27 final size:27
Alignment explanation
Indices: 22413--22498 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
22403 TGTGGGCTTT
22413 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
22440 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
22468 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
22495 GAAA
1 GAAA
22499 ATGCCACCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:23565 original size:12 final size:12
Alignment explanation
Indices: 23542--23595 Score: 74
Period size: 12 Copynumber: 4.4 Consensus size: 12
23532 TTTTTCTTTG
*
23542 TTTTGTTTTTTT
1 TTTTGCTTTTTT
23554 GTTTTG-TTTTTT
1 -TTTTGCTTTTTT
23566 TTTTGCTTTTTT
1 TTTTGCTTTTTT
23578 TTTTGCTCTTTTT
1 TTTTGCT-TTTTT
23591 TTTTG
1 TTTTG
23596 AAGAGAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.13
12 19 0.49
13 15 0.38
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (12 bp):
TTTTGCTTTTTT
Found at i:23576 original size:18 final size:17
Alignment explanation
Indices: 23532--23595 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
23522 CTTTTCTCTC
*
23532 TTTTTCTTTGTTTTGTT
1 TTTTTTTTTGTTTTGTT
23549 TTTTTGTTTTGTTTT-TT
1 TTTTT-TTTTGTTTTGTT
* *
23566 TTTTGCTTTTTTTTTTGCTC
1 TTTT--TTTTTGTTTTG-TT
23586 TTTTTTTTTG
1 TTTTTTTTTG
23596 AAGAGAAGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
17 11 0.29
18 21 0.55
19 1 0.03
20 5 0.13
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTGTTTTGTT
Found at i:23590 original size:15 final size:14
Alignment explanation
Indices: 23517--23594 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
23507 AAGCAGGTTC
* *
23517 TTTTTCTTTTCTCT
1 TTTTTTTTTTGTCT
* *
23531 CTTTTTCTTTGT-T
1 TTTTTTTTTTGTCT
*
23544 TTGTTTTTTTGT-T
1 TTTTTTTTTTGTCT
*
23557 TTGTTTTTTTTTTGC-
1 TT-TTTTTTTTGT-CT
23572 TTTTTTTTTTGCTCT
1 TTTTTTTTTTG-TCT
23587 TTTTTTTT
1 TTTTTTTT
23595 GAAGAGAAGG
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
13 13 0.27
14 25 0.51
15 11 0.22
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTGTCT
Found at i:29971 original size:11 final size:11
Alignment explanation
Indices: 29955--29981 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
29945 CGTCAAGATT
29955 AACATAAAAGA
1 AACATAAAAGA
29966 AACATAAAAGA
1 AACATAAAAGA
29977 AACAT
1 AACAT
29982 GTTAATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.11
Consensus pattern (11 bp):
AACATAAAAGA
Found at i:32480 original size:52 final size:52
Alignment explanation
Indices: 32399--32519 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
32389 GAAAATTTAT
* *
32399 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
32451 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
32503 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
32520 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:32532 original size:52 final size:51
Alignment explanation
Indices: 32399--32539 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
32389 GAAAATTTAT
*
32399 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
32451 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
32503 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
32540 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:32546 original size:13 final size:13
Alignment explanation
Indices: 32528--32552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32518 CAAAGATCAG
32528 TGTATCGATACAA
1 TGTATCGATACAA
32541 TGTATCGATACA
1 TGTATCGATACA
32553 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:32634 original size:13 final size:13
Alignment explanation
Indices: 32616--32640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32606 CAAAAAAATA
32616 TGTATCGATACAT
1 TGTATCGATACAT
32629 TGTATCGATACA
1 TGTATCGATACA
32641 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:32636 original size:33 final size:33
Alignment explanation
Indices: 32594--32660 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
32584 AGTAGCTTAA
32594 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
32627 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
32660 A
1 A
32661 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:33628 original size:22 final size:22
Alignment explanation
Indices: 33603--33671 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
33593 ATGCTGATTC
33603 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * * *
33625 AAGGTGCCA-ATGTGTT-GA-TTC
1 AA-G-GCCAGCTATATTGGACTTA
*
33646 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
33668 AAGG
1 AAGG
33672 TGAAGGTGCC
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.18
22 10 0.30
23 5 0.15
24 4 0.12
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:33697 original size:49 final size:49
Alignment explanation
Indices: 33537--34602 Score: 1470
Period size: 49 Copynumber: 21.7 Consensus size: 49
33527 AAAAGGATGT
*
33537 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
33589 CGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
33632 CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
33681 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
33730 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
33779 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
33828 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
33877 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
33928 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
33977 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGTG-GGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
34025 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
34074 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
34123 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
34172 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
34223 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
34272 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGTG-GGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
34320 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
34369 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
34418 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
34467 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
34518 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
34567 CAATGTGCTGAGTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
34603 GAGGGGTTGC
Statistics
Matches: 894, Mismatches: 100, Indels: 43
0.86 0.10 0.04
Matches are distributed among these distances:
43 38 0.04
48 101 0.11
49 589 0.66
51 120 0.13
52 46 0.05
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:34124 original size:295 final size:295
Alignment explanation
Indices: 33532--34602 Score: 1807
Period size: 295 Copynumber: 3.6 Consensus size: 295
33522 GATGAAAAAG
* * * * * * *
33532 GATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGC
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G--AAGGTGCCAATGTGC
* * * *
33597 TGATTCAAGGCCAGCTATATTGGAC-T----T---AAAGGTGCCAATGTGTTGATTCAAGGCCAG
63 TGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
* * *
33654 CTACATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
128 CTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAT
* * * * * * * * *
33719 GATGATGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAATGGTGAAGGTGCCAATG
193 GGTG-GGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATG
*
33784 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAT
257 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
*
33823 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
33888 GTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
66 GTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
33953 TATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGT
131 TATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGT
34018 GGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCT
196 GGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCT
34083 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
261 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
34118 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
34183 GTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
66 GTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
34248 TATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGT
131 TATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGT
34313 GGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCT
196 GGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCT
34378 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
261 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
34413 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
1 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
34478 GTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
66 GTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
* *
34543 TATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTATATTGGGCTTA
131 TATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
34603 GAGGGGTTGC
Statistics
Matches: 744, Mismatches: 28, Indels: 12
0.95 0.04 0.02
Matches are distributed among these distances:
288 36 0.05
289 1 0.00
290 1 0.00
291 40 0.05
293 1 0.00
295 572 0.77
296 93 0.12
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (295 bp):
GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGA
GTCAAGGCCAGCTACATTGGACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
TATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGT
GGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCT
GAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
Found at i:34646 original size:33 final size:34
Alignment explanation
Indices: 34606--34702 Score: 166
Period size: 33 Copynumber: 3.0 Consensus size: 34
34596 GGGCTTAGAG
34606 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
34640 -GGTTGCCACCGACTTGTGTGGGCTTTGG--GAA
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
34671 GGGTTGCCACCGACTTGTGTGGGCTTT-GAAGA
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAGA
34703 GGGAAAAAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
31 4 0.07
32 26 0.43
33 30 0.50
ACGTcount: A:0.15, C:0.19, G:0.38, T:0.28
Consensus pattern (34 bp):
GGGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:34681 original size:32 final size:32
Alignment explanation
Indices: 34606--34698 Score: 161
Period size: 32 Copynumber: 2.9 Consensus size: 32
34596 GGGCTTAGAG
34606 GGGTTGCCACCGACTTGTGTGGGCTTT-GGAA
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGGAA
34637 GAAGGTTGCCACCGACTTGTGTGGGCTTTGGGAA
1 G--GGTTGCCACCGACTTGTGTGGGCTTTGGGAA
34671 GGGTTGCCACCGACTTGTGTGGGCTTTG
1 GGGTTGCCACCGACTTGTGTGGGCTTTG
34699 AAGAGGGAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
31 1 0.02
32 27 0.46
33 26 0.44
34 5 0.08
ACGTcount: A:0.13, C:0.19, G:0.39, T:0.29
Consensus pattern (32 bp):
GGGTTGCCACCGACTTGTGTGGGCTTTGGGAA
Found at i:34729 original size:37 final size:35
Alignment explanation
Indices: 34688--35280 Score: 382
Period size: 34 Copynumber: 17.3 Consensus size: 35
34678 CACCGACTTG
34688 TGTGGGCTTTGAAGAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTGAA-A-GGAAAAAGAGTGCCACGGAGT
**
34725 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTTG-AAA-GGAAAAAGAGTGCCACGGAGT
* **
34762 TGTAGGTGCCACAGAGTTG-TGGGCTTTAAAAAGAGTGCCACGGAGT
1 TGT-GG-G---C---TTTGAAAGG----AAAAAGAGTGCCACGGAGT
* * *
34808 CGTGGGCTTTGAAAAGAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
* **
34842 TGTGGGCTTTGAAAAGACGAAG-GTGCCACGGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
*
34876 TGTGGGCTTT-AAAGG-AAAAG-GTGCCACAGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
*
34908 TGTGGGCTTT-AAA-GAAAAA-A-TGCCACTGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
* * **
34939 CGTGGACGTTAAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGC-TTTGAAA-GGAAAAAGAGTGCCACGGAGT
*
34976 TGTGGGCTTT-AAAAGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
35009 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTG-AAA-GGAAAAAGAGTGCCACGGAGT
* *
35046 TGTGGACTTT-AAACAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTGAAA-GGAAAAAGAGTGCCACGGAGT
* *
35080 TGTGGAC-TT-AAAGATGAAAAA-AGTGCCACGGAAT
1 TGTGGGCTTTGAAAG--GAAAAAGAGTGCCACGGAGT
*
35114 TGTGGGCTTT-------AAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
* *
35142 TGTGGAC-TT-AAAGATGAAAAA-AGTGCCACGGAAT
1 TGTGGGCTTTGAAAG--GAAAAAGAGTGCCACGGAGT
*
35176 TGTGGGCTTT-AAA-GAAAAA-A-TGCCACTGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
* * * *
35207 CGTGGACTTTG--A-GACAAA-A-TGCCACTGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
* *
35237 TGTGGACTTT-AAA-GAAAAAGA-TGCCACTGAGT
1 TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
* *
35269 CGTGGACTTTGA
1 TGTGGGCTTTGA
35281 GCAGAGATTG
Statistics
Matches: 462, Mismatches: 49, Indels: 94
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.01
28 17 0.04
30 27 0.06
31 39 0.08
32 61 0.13
33 36 0.08
34 119 0.26
35 38 0.08
36 9 0.02
37 72 0.16
38 7 0.02
39 2 0.00
41 1 0.00
42 3 0.01
44 1 0.00
45 5 0.01
46 19 0.04
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.21
Consensus pattern (35 bp):
TGTGGGCTTTGAAAGGAAAAAGAGTGCCACGGAGT
Found at i:34839 original size:34 final size:33
Alignment explanation
Indices: 34765--35341 Score: 439
Period size: 34 Copynumber: 17.7 Consensus size: 33
34755 ACAAAGTTGT
* * *
34765 AGGTGCCACAGAGTTGTGGGCTTT--AA-AAAG
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* * *
34795 A-GTGCCACGGAGTCGTGGGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGACTTT-AAAAGAAAA
* **
34828 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGACGA
1 AGGTGCCACGGAGTTGTGGACTTT-AAAAGAAAA
* *
34862 AGGTGCCACGGAGTTGTGGGCTTT-AAAGGAAA
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* *
34894 AGGTGCCACAGAGTTGTGGGCTTT-AAAGAAAA
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* * * *
34926 A-ATGCCACTGAGTCGTGGACGTTAAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGAC-TTTAAAA--GAAAA
*
34961 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 AG-GTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* *
34995 AAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGACTTT-AAAA--GAAAA
35031 AGAGTGCCACGGAGTTGTGGACTTTAAACAGAAAA
1 AG-GTGCCACGGAGTTGTGGACTTTAAA-AGAAAA
35066 AGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAA
1 AGGTGCCACGGAGTTGTGGACTTTAAA-A-GAAAA
* * *
35100 AAGTGCCACGGAATTGTGGGCTTTAAAAG----
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
35129 -GGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAA
1 AGGTGCCACGGAGTTGTGGACTTTAAA-A-GAAAA
* * *
35162 AAGTGCCACGGAATTGTGGGCTTT-AAAGAAAA
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* * * *
35194 A-ATGCCACTGAGTCGTGGACTTT--GAGACAAA
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGA-AAA
*
35225 A--TGCCACTGAGTTGTGGACTTT-AAAGAAAA
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* * * * * *
35255 AGATGCCACTGAGTCGTGGACTTT--GAG-CAG
1 AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* * *
35285 AGATTGCCACTGAGTCGTGGACTTT-AAAGAAAA
1 AG-GTGCCACGGAGTTGTGGACTTTAAAAGAAAA
* * *
35318 AGATGCCACTGAGTCGTGGACTTT
1 AGGTGCCACGGAGTTGTGGACTTT
35342 GAGCAGAGAT
Statistics
Matches: 463, Mismatches: 51, Indels: 64
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.01
28 18 0.04
29 21 0.05
30 31 0.07
31 62 0.13
32 89 0.19
33 39 0.08
34 126 0.27
35 20 0.04
36 15 0.03
37 37 0.08
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (33 bp):
AGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
Found at i:35137 original size:62 final size:62
Alignment explanation
Indices: 34767--35188 Score: 307
Period size: 62 Copynumber: 6.4 Consensus size: 62
34757 AAAGTTGTAG
* * * * * *
34767 GTGCCACAGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTTGAAA-A-GAAGAAG
1 GTGCCACGGAATTGTGGGCTTTAAAAAG-GTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAAA
* *
34830 GTGCCACGGAGTTGTGGGCTTTGAAAAGACGAAGGTGCCACGGAGTTGTGGGCTTTAAAG--G-A
1 GTGCCACGGAATTGTGGGCTTT---AA-A--AAGGTGCCACGGAGTTGTGGAC-TTAAAGATGAA
*
34892 AAAG
59 AAAA
* * ** * * * *
34896 GTGCCACAGAGTTGTGGGCTTTAAAGAAAAAATGCCACTGAGTCGTGGACGTTAAAAAGGGAAAA
1 GTGCCACGGAATTGTGGGCTTT--A-AAAAGGTGCCACGGAGTTGTGGAC-TTAAAGA-TGAAAA
34961 AGA
61 A-A
* * * *
34964 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAA-AGGGA
1 GTGCCACGGAATTGTGGGCTTT-----AAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAGA-TGA
35028 AAAAGA
58 AAAA-A
* *
35034 GTGCCACGGAGTTGTGGACTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAA
1 GTGCCACGGAATTGTGGGCTTT------AAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAA
35099 AAA
60 AAA
*
35102 GTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
1 GTGCCACGGAATTGTGGGCTTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
35164 GTGCCACGGAATTGTGGGCTTTAAA
1 GTGCCACGGAATTGTGGGCTTTAAA
35189 GAAAAAATGC
Statistics
Matches: 313, Mismatches: 27, Indels: 39
0.83 0.07 0.10
Matches are distributed among these distances:
62 64 0.20
63 43 0.14
65 4 0.01
66 29 0.09
67 9 0.03
68 63 0.20
69 12 0.04
70 57 0.18
71 32 0.10
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (62 bp):
GTGCCACGGAATTGTGGGCTTTAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
Found at i:35281 original size:62 final size:62
Alignment explanation
Indices: 35035--35372 Score: 303
Period size: 62 Copynumber: 5.3 Consensus size: 62
35025 GGAAAAAGAG
* * * * *
35035 TGCCACGGAGTTGTGGACTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAA
1 TGCCACGGAGTTGTGGACTTT-AA-AGAAAAAGATGCCACTGAGTCGTGGACTT--TGA-GACAA
35100 AA
61 AA
* * * * * * * *
35102 GTGCCACGGAATTGTGGGCTTT----AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA
1 -TGCCACGGAGTTGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTT--TGA-GACAAA
35163 A
62 A
* *
35164 GTGCCACGGAATTGTGGGCTTTAAAGAAAAA-ATGCCACTGAGTCGTGGACTTTGAGACAAAA
1 -TGCCACGGAGTTGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
35226 TGCCACTGAGTTGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACGGAGTTGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
* * *
35289 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACGGAGTTGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
* *
35352 TGCCACTGAGTCGTGGACTTT
1 TGCCACGGAGTTGTGGACTTT
35373 TTTTTTTTTT
Statistics
Matches: 249, Mismatches: 14, Indels: 19
0.88 0.05 0.07
Matches are distributed among these distances:
61 29 0.12
62 93 0.37
63 86 0.35
65 18 0.07
66 4 0.02
68 19 0.08
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (62 bp):
TGCCACGGAGTTGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:35314 original size:63 final size:63
Alignment explanation
Indices: 35177--35372 Score: 335
Period size: 63 Copynumber: 3.1 Consensus size: 63
35167 CCACGGAATT
* * *
35177 GTGGGCTTTAAAGAAAAA-ATGCCACTGAGTCGTGGACTTTGAGACA-A-AATGCCACTGAGTT
1 GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAG-CAGAGATTGCCACTGAGTC
35238 GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTC
1 GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTC
35301 GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTC
1 GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTC
35364 GTGGACTTT
1 GTGGACTTT
35373 TTTTTTTTTT
Statistics
Matches: 129, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
61 19 0.15
62 26 0.20
63 84 0.65
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (63 bp):
GTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTC
Found at i:35359 original size:31 final size:31
Alignment explanation
Indices: 35195--35372 Score: 236
Period size: 31 Copynumber: 5.7 Consensus size: 31
35185 TAAAGAAAAA
35195 ATGCCACTGAGTCGTGGACTTTGAGACAAA-
1 ATGCCACTGAGTCGTGGACTTTGAGACAAAG
* * *
35225 ATGCCACTGAGTTGTGGACTTTAAAGAAAAAG
1 ATGCCACTGAGTCGTGGACTTT-GAGACAAAG
*
35257 ATGCCACTGAGTCGTGGACTTTGAG-CAGAG
1 ATGCCACTGAGTCGTGGACTTTGAGACAAAG
* *
35287 ATTGCCACTGAGTCGTGGACTTTAAAGAAAAAG
1 A-TGCCACTGAGTCGTGGACTTT-GAGACAAAG
*
35320 ATGCCACTGAGTCGTGGACTTTGAG-CAGAG
1 ATGCCACTGAGTCGTGGACTTTGAGACAAAG
35350 ATTGCCACTGAGTCGTGGACTTT
1 A-TGCCACTGAGTCGTGGACTTT
35373 TTTTTTTTTT
Statistics
Matches: 129, Mismatches: 13, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
30 29 0.22
31 52 0.40
32 44 0.34
33 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (31 bp):
ATGCCACTGAGTCGTGGACTTTGAGACAAAG
Found at i:36361 original size:17 final size:16
Alignment explanation
Indices: 36329--36359 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36319 TTTCCTCTCT
*
36329 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
36345 TTTTGTTTCTTTTTT
1 TTTTGTTTCTTTTTT
36360 TGGAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:41141 original size:11 final size:11
Alignment explanation
Indices: 41125--41151 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41115 CGTCAAGATT
41125 AACATAAAAGA
1 AACATAAAAGA
41136 AACATAAAAGA
1 AACATAAAAGA
41147 AACAT
1 AACAT
41152 GTTAATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.11
Consensus pattern (11 bp):
AACATAAAAGA
Found at i:43650 original size:52 final size:52
Alignment explanation
Indices: 43569--43689 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
43559 GAAAATTTAT
* *
43569 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
43621 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
43673 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
43690 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:43702 original size:52 final size:51
Alignment explanation
Indices: 43569--43709 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
43559 GAAAATTTAT
*
43569 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
43621 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
43673 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
43710 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:43716 original size:13 final size:13
Alignment explanation
Indices: 43698--43722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43688 CAAAGATCAG
43698 TGTATCGATACAA
1 TGTATCGATACAA
43711 TGTATCGATACA
1 TGTATCGATACA
43723 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:43804 original size:13 final size:13
Alignment explanation
Indices: 43786--43810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43776 CAAAAAAATA
43786 TGTATCGATACAT
1 TGTATCGATACAT
43799 TGTATCGATACA
1 TGTATCGATACA
43811 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:43806 original size:33 final size:33
Alignment explanation
Indices: 43764--43830 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
43754 AGTAGCTTAA
43764 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
43797 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
43830 A
1 A
43831 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Done.