Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold625
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: 78406
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:501 original size:18 final size:19
Alignment explanation
Indices: 450--502 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
440 ATAATATTAA
*
450 GTAAAATTATTTATTAAAT
1 GTAAAATTTTTTATTAAAT
*
469 GT--AATTTTTGAATTAAAT
1 GTAAAATTTTT-TATTAAAT
487 -TAAAATTTTTTATTAA
1 GTAAAATTTTTTATTAA
503 TTTTTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 7 0.25
18 12 0.43
19 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
GTAAAATTTTTTATTAAAT
Found at i:2685 original size:15 final size:15
Alignment explanation
Indices: 2665--2694 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2655 ATTTTGGTGC
2665 ATAAACTTTACCTGG
1 ATAAACTTTACCTGG
2680 ATAAACTTTACCTGG
1 ATAAACTTTACCTGG
2695 GTTCATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
ATAAACTTTACCTGG
Found at i:6376 original size:8 final size:8
Alignment explanation
Indices: 6363--6415 Score: 60
Period size: 7 Copynumber: 7.0 Consensus size: 8
6353 AAAATAAAAA
6363 TAAATATT
1 TAAATATT
6371 TAAATATT
1 TAAATATT
6379 T-AA-ATT
1 TAAATATT
6385 TAAAT-TT
1 TAAATATT
6392 TAAAT-TT
1 TAAATATT
*
6399 TAAATTTAT
1 TAAATAT-T
6408 TAAATATT
1 TAAATATT
6416 ATTTTTTATG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 4 0.10
7 18 0.45
8 11 0.28
9 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TAAATATT
Found at i:6395 original size:7 final size:7
Alignment explanation
Indices: 6363--6405 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
6353 AAAATAAAAA
6363 TAAATATT
1 TAAAT-TT
6371 TAAATATT
1 TAAAT-TT
6379 TAAA-TT
1 TAAATTT
6385 TAAATTT
1 TAAATTT
6392 TAAATTT
1 TAAATTT
6399 TAAATTT
1 TAAATTT
6406 ATTAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.18
7 16 0.47
8 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TAAATTT
Found at i:7131 original size:31 final size:31
Alignment explanation
Indices: 7097--7156 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
7087 TTAAGATTGA
* *
7097 TTTTAAATTTTATAAATATTAGATATAATTAT
1 TTTTAAA-TTTAAAAATATTAGACATAATTAT
7129 TTTTAAATTTAAAAATATTAGACATAAT
1 TTTTAAATTTAAAAATATTAGACATAAT
7157 CACTCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTTAAATTTAAAAATATTAGACATAATTAT
Found at i:7167 original size:31 final size:31
Alignment explanation
Indices: 7100--7171 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
7090 AGATTGATTT
* * * * **
7100 TAAATTTTATAAATATTAGATATAATTATTTT
1 TAAA-TTTAAAAATATTAGACATAATCACTCA
7132 TAAATTTAAAAATATTAGACATAATCACTCA
1 TAAATTTAAAAATATTAGACATAATCACTCA
7163 TAAATTTAA
1 TAAATTTAA
7172 TTGTCATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (31 bp):
TAAATTTAAAAATATTAGACATAATCACTCA
Found at i:7321 original size:16 final size:15
Alignment explanation
Indices: 7289--7322 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
7279 ATAAAATTTA
*
7289 TTTAATTTAATATAT
1 TTTAATTTAAAATAT
7304 TTTAATTTAAAAATAT
1 TTTAATTT-AAAATAT
7320 TTT
1 TTT
7323 TTATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAATTTAAAATAT
Found at i:7717 original size:10 final size:9
Alignment explanation
Indices: 7692--7721 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
7682 CTTTCTCTCT
7692 TTTATTTTC
1 TTTATTTTC
7701 TTTATTTTC
1 TTTATTTTC
7710 TTTCATTTTC
1 TTT-ATTTTC
7720 TT
1 TT
7722 CTTGAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTC
Found at i:9157 original size:68 final size:70
Alignment explanation
Indices: 9077--9214 Score: 208
Period size: 68 Copynumber: 2.0 Consensus size: 70
9067 AATATCCTTC
* * * *
9077 ATTAAATAGTTTAGAAACAAAGATTTTAGTAATTGTGAACTTC-TT-TTTTTGACTTATTTTTTT
1 ATTAAATAGTTTAGAAACAAAGATGTTAATAATTGTAAACTTCTTTATTTTTGAATTATTTTTTT
9140 GGTCT
66 GGTCT
*
9145 ATTAAATAGTTTAGCAACAAAGATGTTAATAATTGTAAACTTCTTTTATTTTTGAATTATTTTTT
1 ATTAAATAGTTTAGAAACAAAGATGTTAATAATTGTAAACTTC-TTTATTTTTGAATTATTTTTT
9210 TGGTC
65 TGGTC
9215 ATGTTAAGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
68 39 0.63
70 2 0.03
71 21 0.34
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.49
Consensus pattern (70 bp):
ATTAAATAGTTTAGAAACAAAGATGTTAATAATTGTAAACTTCTTTATTTTTGAATTATTTTTTT
GGTCT
Found at i:10471 original size:20 final size:20
Alignment explanation
Indices: 10439--10488 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
10429 TCAAATGATC
*
10439 AAAATAAAAATAAATCAAAT
1 AAAATAAACATAAATCAAAT
* * *
10459 AAATTAAACATAAGTTAAAT
1 AAAATAAACATAAATCAAAT
10479 AAAATAAACA
1 AAAATAAACA
10489 AGTTTATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAATAAACATAAATCAAAT
Found at i:10546 original size:27 final size:27
Alignment explanation
Indices: 10494--10546 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
10484 AAACAAGTTT
* *
10494 ATAAATAATTCATAAGTAATGCATTTC
1 ATAAATAACTCATAAATAATGCATTTC
10521 ATAAATAACTCATAAATCAATG-ATTT
1 ATAAATAACTCATAAAT-AATGCATTT
10547 TTATTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (27 bp):
ATAAATAACTCATAAATAATGCATTTC
Found at i:13364 original size:35 final size:35
Alignment explanation
Indices: 13318--13384 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
13308 AAAAAATAAA
* *
13318 ATAACATTTAGTTGCATTCCT-TTTGTATAACATAT
1 ATAACATTTAGTTAC-TTCCTCTTTGTACAACATAT
13353 ATAACATTTAGTTACTTCCTCTTTGTACAACA
1 ATAACATTTAGTTACTTCCTCTTTGTACAACA
13385 CAAGAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 5 0.17
35 24 0.83
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.43
Consensus pattern (35 bp):
ATAACATTTAGTTACTTCCTCTTTGTACAACATAT
Found at i:15819 original size:28 final size:27
Alignment explanation
Indices: 15778--15858 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
15768 AAGTAAAAAC
* *
15778 AGGGATTAGAGTATCCTCTTGGAGATGG
1 AGGG-TTAGAGTATCCTCTCGAAGATGG
*
15806 AAGGGTTAGAGTATCCCCTCGAAGATGG
1 -AGGGTTAGAGTATCCTCTCGAAGATGG
*
15834 AGGAGTTGGAGTATCCT-T-GAAGATG
1 AGG-GTTAGAGTATCCTCTCGAAGATG
15859 AAAATTTTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.15
27 4 0.09
28 31 0.67
29 4 0.09
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.26
Consensus pattern (27 bp):
AGGGTTAGAGTATCCTCTCGAAGATGG
Found at i:16061 original size:79 final size:77
Alignment explanation
Indices: 15854--16061 Score: 195
Period size: 79 Copynumber: 2.6 Consensus size: 77
15844 GTATCCTTGA
* * * * * * * *
15854 AGATGAAAATTTTAGTGTTTTAGAAGTAAAAACATGGTTGGAATATCCCCTCAGATATGGTGGGG
1 AGATGAAAAATTCAGTGTTTTAGAAGTAAAAAC-GGGTTCGAATAT-CCCTCAAAGATGATGAGG
*
15919 TTGGAGTATCACAG
64 TTGGAATATCACAG
* * * * * *
15933 AGATGAAAAATTCTA-TATTTTAGAAATAAAAATAGGGTTCGAGTGTCCCTCAAAGATTATGAGG
1 AGATGAAAAATTC-AGTGTTTTAGAAGTAAAAA-CGGGTTCGAATATCCCTCAAAGATGATGAGG
*
15997 TTGGAATATCCTCAG
64 TTGGAATAT-CACAG
16012 AGATGAAAAATTCAGTGTTTTAGAAGTAAAAACGGGATT-GAACTATCCCT
1 AGATGAAAAATTCAGTGTTTTAGAAGTAAAAACGGG-TTCGAA-TATCCCT
16062 TCTGAGATGG
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
78 27 0.26
79 74 0.73
80 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.30
Consensus pattern (77 bp):
AGATGAAAAATTCAGTGTTTTAGAAGTAAAAACGGGTTCGAATATCCCTCAAAGATGATGAGGTT
GGAATATCACAG
Found at i:18255 original size:1 final size:1
Alignment explanation
Indices: 18249--18348 Score: 83
Period size: 1 Copynumber: 100.0 Consensus size: 1
18239 AAATCTTCAC
* * ** * * * *
18249 TTTTTTTTTTGTTTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTCTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * *
18314 TTTTCCTTTTTTTTTGTTTTGTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18349 CCAATTGCCA
Statistics
Matches: 77, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:18296 original size:37 final size:38
Alignment explanation
Indices: 18249--18348 Score: 168
Period size: 37 Copynumber: 2.7 Consensus size: 38
18239 AAATCTTCAC
18249 TTTTTT-TTTTGTTTTTTTTTTTTTTTCTTTTTCC-TT
1 TTTTTTGTTTTGTTTTTTTTTTTTTTTCTTTTTCCTTT
*
18285 TTTTTTGTTTTGTTTTTTTCTTTTTTTCTTTTTCCTTT
1 TTTTTTGTTTTGTTTTTTTTTTTTTTTCTTTTTCCTTT
*
18323 TTTTTTGTTTTGTTTTTTTTCTTTTT
1 TTTTTTGTTTTGTTTTTTTTTTTTTT
18349 CCAATTGCCA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 6 0.10
37 27 0.46
38 26 0.44
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (38 bp):
TTTTTTGTTTTGTTTTTTTTTTTTTTTCTTTTTCCTTT
Found at i:23832 original size:79 final size:81
Alignment explanation
Indices: 23694--23844 Score: 207
Period size: 79 Copynumber: 1.9 Consensus size: 81
23684 TAACCTATCA
* * ** * *
23694 GTAGGGCTGGAGTATCCACAGAGATAAAAAAATTCGGTGTTTTAGAAGTAAAAATGAGGTTAGAG
1 GTAGGGCTAGAGTATCCACAAAGATAAAAAAATTCAATGTTTTAAAAGTAAAAACGAGGTTAGAG
*
23759 TGTCCCCTCAAAGATT
66 TATCCCCTCAAAGATT
* *
23775 GTAGGGTTAGAGTATCC-CAAAGAT-AAAAAATTTAATGTTTTAAAAGTAAAAACGAGGTTAGAG
1 GTAGGGCTAGAGTATCCACAAAGATAAAAAAATTCAATGTTTTAAAAGTAAAAACGAGGTTAGAG
23838 TATCCCC
66 TATCCCC
23845 AGAGATAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 40 0.66
80 6 0.10
81 15 0.25
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (81 bp):
GTAGGGCTAGAGTATCCACAAAGATAAAAAAATTCAATGTTTTAAAAGTAAAAACGAGGTTAGAG
TATCCCCTCAAAGATT
Found at i:23838 original size:51 final size:52
Alignment explanation
Indices: 23779--23885 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
23769 AAGATTGTAG
23779 GGTTAGAGTAT-CCCAAAGATAAAAAATTTAATG-TTTTAAAAGTAAAAACGA
1 GGTTAGAGTATCCCCAAAGAT-AAAAATTTAATGTTTTTAAAAGTAAAAACGA
* ** *
23830 GGTTAGAGTATCCCCAGAGATAAAAATTTGGTGTTTTTAAAAGTGAAAACGA
1 GGTTAGAGTATCCCCAAAGATAAAAATTTAATGTTTTTAAAAGTAAAAACGA
23882 GGTT
1 GGTT
23886 GGAATACCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
51 21 0.42
52 29 0.58
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (52 bp):
GGTTAGAGTATCCCCAAAGATAAAAATTTAATGTTTTTAAAAGTAAAAACGA
Found at i:29003 original size:28 final size:28
Alignment explanation
Indices: 28904--30289 Score: 1051
Period size: 28 Copynumber: 48.6 Consensus size: 28
28894 TAAAAAAAAT
*
28904 GGTGCCACTAACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
* **
28935 AGTTGCCACCAACTCGTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
*
28967 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
28995 GGTACCACTAACTTGTGGG-TTTGAAAAT
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * * *
29023 GTTACCACCGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
29051 GATGCCACTAACTTGTGGGCTTTAAAAAG
1 GGTGCCACTGACTTGTGGGCTTT-GAAAG
* *
29080 GGTTGCCACCGACTCGTGGAGGCTTTGAAAG
1 GG-TGCCACTGACTTGT-G-GGCTTTGAAAG
*
29111 GATGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
29139 GGTACCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * * *
29168 TGTTGCCACCGACTCGTGGGCTTTAAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
*
29197 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
29226 GGTTGCCACCGACTCGTGTAGGCTTTGAAAAG
1 GG-TGCCACTGACT--TGTGGGCTTTG-AAAG
* *
29258 AGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
29286 GGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
29314 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
29343 TGTTGCCACCGACTCGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
29372 GATGCCACTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
29401 GGTTGCCACCGACTCGTGTGGGCTTTGCAAAG
1 GG-TGCCACTGACT--TGTGGGCTTTG-AAAG
* *
29433 AGTGCCACTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
29462 GGTTGCCACCGACTCGTGTGGGCTTTGCAAAG
1 GG-TGCCACTGACT--TGTGGGCTTTG-AAAG
* *
29494 AGTGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
29522 GGTGCCACTGATTTGTGGGCTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
29550 GGTGCCACTGACTTTTGGG-TTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
29577 GGTGCCACTGATTTGTGGGCTCTGAAATG
1 GGTGCCACTGACTTGTGGGCTTTGAAA-G
* *
29606 GGTTGCCACCGACTTGTGGGCTTTAAAAG
1 GG-TGCCACTGACTTGTGGGCTTTGAAAG
*
29635 GGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
29663 GGTGCCACTGATTTATGGGCTTTGAAATG
1 GGTGCCACTGACTTGTGGGCTTTGAAA-G
* *
29692 GGTTGCCACCGACTTGTGTGGGCTTTAAAAG
1 GG-TGCCACTGAC-T-TGTGGGCTTTGAAAG
**
29723 GGTGCCACTGACTTGTGGGCTTAAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * ** *
29751 GATGCCAC-GAAGTTGTGAAC-TTAAAAG
1 GGTGCCACTG-ACTTGTGGGCTTTGAAAG
* * *
29778 GGTGCCA-TGGAGTTGTGGACTTTAAAAG
1 GGTGCCACT-GACTTGTGGGCTTTGAAAG
* * *
29806 GGTGCCACGGAGTTGTGGACTTT-AAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * ** *
29833 GGTGCCACGGAGTTGTGAAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
29860 TGTGCCACAGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
29888 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
29916 GGTGCCA-TGGAGTTGTGGACTTTAAAAG
1 GGTGCCACT-GACTTGTGGGCTTTGAAAG
* * * *
29944 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
29972 GGTGCCAC-GAAGTTGTGGACTTTAAAAG
1 GGTGCCACTG-ACTTGTGGGCTTTGAAAG
* * * * *
30000 GGTCCCACGGAGTTGTGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
30027 GGTGCCACGGAGTTGTGGACTTT-AAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
30054 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
30082 GGTGTCACAGAATTGTGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
30109 GATGCCACGGAGTTGTGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * * *
30136 GATGCCACGGAGTTATGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
30163 GGTGCCACTGAGTTATGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
30190 GGTGCCACTGAGTGGTGGAC-TTAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
30217 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
30245 GGTGCCACGGAGTTGTGGACTTT-AAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
30272 GGTGCCACGGAGTTGTGG
1 GGTGCCACTGACTTGTGG
30290 ACTGAAAAGA
Statistics
Matches: 1180, Mismatches: 131, Indels: 91
0.84 0.09 0.06
Matches are distributed among these distances:
26 2 0.00
27 292 0.25
28 522 0.44
29 94 0.08
30 129 0.11
31 48 0.04
32 93 0.08
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:29042 original size:56 final size:57
Alignment explanation
Indices: 28920--29767 Score: 435
Period size: 58 Copynumber: 14.5 Consensus size: 57
28910 ACTAACTTGT
* * * * *
28920 GTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAAAAGAG-TGCCACTGACTT
1 GTGGGCTTTG-AAAG-GATGCCACTAACT--TGTGGGCTTTGAAAAG-GTTACCACCGACTC
* * *
28981 GTGGGCTTTGAAAGGGTACCACTAACTTGTGGG-TTTGAAAATGTTACCACCGACTC
1 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
* *
29037 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTAAAAAGGGTTGCCACCGACTC
1 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA-GGTTACCACCGACTC
* * * *
29095 GTGGAGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGGTACCACTGACTT
1 GT-G-GGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
* ** * * * * *
29153 GTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTT-AAAAGGATGCCACTGACTT
1 GTGGGCTTTG-AAAG-GATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
* ** * * * *
29211 GTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTAGGCTTTGAAAAGAG-TGCCACTGACTT
1 GTGGGCTTTG-AAA-GGATGCCACTAACT--TGTGGGCTTTGAAAAG-GTTACCACCGACTC
* * * * * * * *
29272 ATGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTG-AAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
* ** * * * ** *
29328 GTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTG-AAAGGATGCCACTAACTT
1 GTGGGCTTTG-AAAG-GATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
* ** * * ** *
29386 GTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGCAAAGAG-TGCCACTAACTT
1 GTGGGCTTTG-AAA-GGATGCCACTAACT--TGTGGGCTTTGAAAAG-GTTACCACCGACTC
* ** * * ** *
29447 GTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGCAAAGAG-TGCCACTAACTT
1 GTGGGCTTTG-AAA-GGATGCCACTAACT--TGTGGGCTTTGAAAAG-GTTACCACCGACTC
* * * * * * *
29508 GTGGGCTTTGAAAGGGTGCCACTGATTTGTGGGCTTT-AAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
* * * * * * * *
29564 TTGGG-TTTGAAAGGGTGCCACTGATTTGTGGGCTCTGAAATGGGTTGCCACCGACTT
1 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAA-AGGTTACCACCGACTC
* * * * * * * * *
29621 GTGGGCTTTAAAAGGGTGCCACTGACTTATGGGCTTTG-AAAGGGTGCCACTGATTT
1 GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
* * ** * * * *
29677 ATGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT-AAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAA--GGATGCCACTAAC-T-TGTGGGCTTTGAAAAGGTTACCACCGACTC
** * *
29737 GTGGGCTTAAAAAGGATGCCACGAAGTTGTG
1 GTGGGCTTTGAAAGGATGCCACTAACTTGTG
29768 AACTTAAAAG
Statistics
Matches: 688, Mismatches: 69, Indels: 65
0.84 0.08 0.08
Matches are distributed among these distances:
55 33 0.05
56 129 0.19
57 61 0.09
58 203 0.30
59 40 0.06
60 97 0.14
61 123 0.18
62 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (57 bp):
GTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAGGTTACCACCGACTC
Found at i:29575 original size:291 final size:289
Alignment explanation
Indices: 28899--30085 Score: 1070
Period size: 291 Copynumber: 4.1 Consensus size: 289
28889 TTTTTTAAAA
* *
28899 AAAATGGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGTGGGCTTTGAA
1 AAAA-GGTGCCACTAAC-T-TGTGGGCTTTGAAAAG-GGTGCCACCGACTCGTGTGGGCTTTGAA
* * * * *
28964 AAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTAACTTGTGGG-TTTGAAAATGTTAC
62 AAGAGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGTTGC
* * * * *
29028 CACCGACTCGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTAAAAAGGGTTGCCACCGA
126 CACCGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTT-GAAA-GGATGCCACTGA
* * * *
29092 CTCGTGGAGGCTTTG-AAA-GGATGCCACTGACT-TGTGGGCTTTGAAAGGGTACCACTGACTTG
189 CTTGT-G-GGCTTTGAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAGGGTGCCACTGACTTG
*
29154 TGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTT
252 TGGGCTTTGAAAAGGGTTGCCACCGACTCGTGGGCTTT
* *
29192 AAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTAGGCTTTGAAAA
1 AAAAGG-TGCCACTAACTTGTGGGCTTTGAAAAGGG-TGCCACCGACTCGTGTGGGCTTTGAAAA
* *
29257 GAGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGATGCCAC
64 GAGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGTTGCCAC
* * * * *
29322 TGACTTGTGGGCTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTAACTTG
129 CGACTTGTGGGCTTTGAAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
* *
29387 TGGGCTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGCAAAGAGTGCCACTAACTTGTGGG
193 TGGGCTTTGAAAAGGGTTGCCACCGACT-GTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGG
29452 CTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTT
256 CTTTGAAAAGGGTTGCCACCGACTC--GTGGGCTTT
* * *
29488 GCAAAGAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGA-T-TTGTGGGCTTT-AAAA
1 -AAAAG-GTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACCGACTCGTGTGGGCTTTGAAAA
* * * *
29549 GGGTGCCACTGACTTTTGGG-TTTGAAAGGGTGCCACTGATTTGTGGGCTCTGAAATGGGTTGCC
64 GAGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA--GGTTGCC
* * * *
29613 ACCGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGATTT
127 ACCGACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTT
* * *
29677 ATGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG
192 GTGGGCTTTGAAAAGGGTTGCCACCGAC-TGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
* * * * **
29742 C-TT-AAAAAGGATGCCA-CGAAGTTGTGAAC-TT
256 CTTTGAAAAGGGTTGCCACCG-ACTCGTGGGCTTT
* * * * * *
29773 AAAAGGGTGCCA-TGGAGTTGTGGACTTT-AAAAGGGTGCCACGGAGT--TGTGGACTTT--AAA
1 AAAA-GGTGCCACT-AACTTGTGGGCTTTGAAAAGGGTGCCACCGACTCGTGTGGGCTTTGAAAA
* * * * ** * * * * * * *
29832 GGGTGCCACGGAGTTGTGAAC-TTAAAAGTGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCAC
64 GAGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGTTGCCAC
* * * * * * * * * *
29896 GGAGTTGTGGACTTT-AAAAGGGTGCCA-TGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTG
129 CGACTTGTGGGCTTTGAAAAGGATGCCACT-GACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
* * * * * * * *
29959 TGGACTTT-AAAAGGG-TGCCA-CGA-AGTTGTGGACTTTAAAAGGGTCCCACGGAGTTGTGGAC
193 TGGGCTTTGAAAAGGGTTGCCACCGACTG-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
30020 -TT-AAAAGGG-TGCCACGGAGTTGTGGACTTT
257 TTTGAAAAGGGTTGCCACCGACTCGTGGGCTTT
* ** * *
30050 AAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGGGTG
1 AAAAGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTG
30086 TCACAGAATT
Statistics
Matches: 766, Mismatches: 100, Indels: 73
0.82 0.11 0.08
Matches are distributed among these distances:
276 45 0.06
277 44 0.06
278 3 0.00
279 5 0.01
280 7 0.01
281 66 0.09
283 46 0.06
284 43 0.06
285 4 0.01
286 4 0.01
287 2 0.00
288 13 0.02
289 9 0.01
290 27 0.04
291 238 0.31
292 42 0.05
293 74 0.10
294 45 0.06
295 8 0.01
296 15 0.02
297 25 0.03
298 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (289 bp):
AAAAGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACCGACTCGTGTGGGCTTTGAAAAGA
GTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACCG
ACTTGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGG
GCTTTGAAAAGGGTTGCCACCGACTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
AAAAGGGTTGCCACCGACTCGTGGGCTTT
Found at i:29784 original size:27 final size:27
Alignment explanation
Indices: 29518--30352 Score: 898
Period size: 27 Copynumber: 30.1 Consensus size: 27
29508 GTGGGCTTTG
* * *
29518 AAAGGGTGCCACTGATTTGTGGGCTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* * * ** *
29546 AAAGGGTGCCACTGACTTTTGGGTTTG
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* * *
29573 AAAGGGTGCCACTGATTTGTGGGCTCTGA
1 AAAGGGTGCCACGGAGTTGTGGACT-T-A
* * * *
29602 AATGGGTTGCCACCGACTTGTGGGCTTTA
1 AAAGGG-TGCCACGGAGTTGTGGAC-TTA
* * * * *
29631 AAAGGGTGCCACTGACTTATGGGCTTTG
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* * * *
29659 AAAGGGTGCCACTGATTTATGGGCTTTGA
1 AAAGGGTGCCACGGAGTTGTGGAC-TT-A
* * * *
29688 AATGGGTTGCCACCGACTTGTGTGGGCTTTA
1 AAAGGG-TGCCACGGA-GT-TGTGGAC-TTA
* * *
29719 AAAGGGTGCCACTGACTTGTGGGCTTAA
1 AAAGGGTGCCACGGAGTTGTGGACTT-A
* * *
29747 AAAGGATGCCACGAAGTTGTGAACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
29774 AAAGGGTGCCATGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
*
29802 AAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
29829 AAAGGGTGCCACGGAGTTGTGAACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
29856 AAAGTGTGCCACAGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
29884 AAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
*
29912 AAAGGGTGCCATGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
29940 AAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
*
29968 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
*
29996 AAAGGGTCCCACGGAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
30023 AAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAGGGTGCCACGGAGTTGTGGACTTA
30050 AAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
* * *
30078 AAAGGGTGTCACAGAATTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
30105 AAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
30132 AAAGGATGCCACGGAGTTATGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
30159 AAAGGGTGCCACTGAGTTATGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
* *
30186 AAAGGGTGCCACTGAGTGGTGGACTTA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
*
30213 AAAAGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
30241 AAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAGGGTGCCACGGAGTTGTGGAC-TTA
*
30269 AAA-GGTGCCACGGAGTTGTGGACTGA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
** * *
30295 AAAGAATGCCACGGAGTTGTAGACTGA
1 AAAGGGTGCCACGGAGTTGTGGACTTA
** *
30322 AAAGAATGCCACGGAGTTGTGGACTTT
1 AAAGGGTGCCACGGAGTTGTGGACTTA
30349 AAAG
1 AAAG
30353 AGGTCACAGT
Statistics
Matches: 720, Mismatches: 73, Indels: 29
0.88 0.09 0.04
Matches are distributed among these distances:
26 5 0.01
27 338 0.47
28 309 0.43
29 17 0.02
30 33 0.05
31 9 0.01
32 9 0.01
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (27 bp):
AAAGGGTGCCACGGAGTTGTGGACTTA
Found at i:30290 original size:55 final size:55
Alignment explanation
Indices: 29102--30351 Score: 949
Period size: 55 Copynumber: 22.1 Consensus size: 55
29092 CTCGTGGAGG
* * * * * * * * *
29102 CTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTGTGGG
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGGTGCCACTGAGTTGTGGA
* * * * * * *
29158 CTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTAAAAGGATGCCACTGACTTGTGGG
1 CTTT-AAAAG-GGTGCCACGGAGTTGTGGACTTTAAAAGG-TGCCACTGAGTTGTGGA
* * * * *
29216 CTTTGAAAAGGGTTGCCACCGACTCGTGTAGG-CTTTGAAAAGAGTGCCACTGACTTATGGG
1 CTTT-AAAAGGG-TGCCACGGAGT--TGT-GGACTTT-AAAAG-GTGCCACTGAGTTGTGGA
* * * * * * * *
29277 CTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGG
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG-TGCCACTGAGTTGTGGA
* * * * * * * * *
29333 CTTTGAAAAGTGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTAACTTGTGGG
1 CTTT-AAAAG-GGTGCCACGGAGTTGTGGACTTTAAAAGG-TGCCACTGAGTTGTGGA
* * * * * * *
29391 CTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGCAAAGAGTGCCACTAACTTGTGGG
1 CTTT-AAAAGGG-TGCCACGGAGT--TGTGGACTTT-AAAAG-GTGCCACTGAGTTGTGGA
* * * * * * *
29452 CTTTGAAAAGGGTTGCCACCGACTCGTGTGGGCTTTGCAAAGAGTGCCACTAACTTGTGGG
1 CTTT-AAAAGGG-TGCCACGGAGT--TGTGGACTTT-AAAAG-GTGCCACTGAGTTGTGGA
* * * * * *
29513 CTTTGAAAGGGTGCCACTGATTTGTGGGCTTTAAAAGGGTGCCACTGACTTTTGG-
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTGCCACTGAGTTGTGGA
* * * * * * * * * *
29568 GTTTGAAAGGGTGCCACTGATTTGTGGGCTCTGAAATGGGTTGCCACCGACTTGTGGG
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACT-TTAAA-AGG-TGCCACTGAGTTGTGGA
* * * * * * * *
29626 CTTTAAAAGGGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGATTTATGGG
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGGTGCCACTGAGTTGTGGA
* * * * * *
29682 CTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGG
1 CTTT-AAAAGGG-TGCCACGGA-GT-TGTGGACTTTAAAA-GGTGCCACTGAGTTGTGGA
* * * *
29742 CTTAAAAAGGATGCCACGAAGTTGTGAAC-TTAAAAGGGTGCCA-TGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTGCCACT-GAGTTGTGGA
* * *
29797 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGAA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACTGAGTTGTGGA
* * *
29852 C-TTAAAAGTGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTGCCACTGAGTTGTGGA
* *
29907 CTTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTGCCACTGAGTTGTGGA
* * *
29963 CTTTAAAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGGTCCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTGCCACTGAGTTGTGGA
* *
30019 C-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACTGAGTTGTGGA
* * * *
30073 CTTTAAAAGGGTGTCACAGAATTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG-TGCCACTGAGTTGTGGA
* * *
30128 C-TTAAAAGGATGCCACGGAGTTATGGAC-TTAAAAGGGTGCCACTGAGTTATGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GGTGCCACTGAGTTGTGGA
* * * *
30182 C-TTAAAAGGGTGCCACTGAGTGGTGGACTTAAAAAGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACTGAGTTGTGGA
*
30236 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACTGAGTTGTGGA
* ** * * * *
30291 C-TGAAAAGAATGCCACGGAGTTGTAGAC-TGAAAAGAATGCCACGGAGTTGTGGA
1 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG-GTGCCACTGAGTTGTGGA
30345 CTTTAAA
1 CTTTAAA
30352 GAGGTCACAG
Statistics
Matches: 1046, Mismatches: 107, Indels: 83
0.85 0.09 0.07
Matches are distributed among these distances:
53 6 0.01
54 184 0.18
55 249 0.24
56 187 0.18
57 57 0.05
58 164 0.16
59 28 0.03
60 56 0.05
61 113 0.11
62 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (55 bp):
CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGTGCCACTGAGTTGTGGA
Found at i:31654 original size:16 final size:16
Alignment explanation
Indices: 31635--31678 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
31625 TCCCTTTTTA
31635 TTTTGCTTTTGCACTT
1 TTTTGCTTTTGCACTT
* *
31651 TTTTTCTTTT-CATTT
1 TTTTGCTTTTGCACTT
31666 TTTGTGCTTTTGC
1 TTT-TGCTTTTGC
31679 TTTTGACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.05, C:0.16, G:0.11, T:0.68
Consensus pattern (16 bp):
TTTTGCTTTTGCACTT
Found at i:38746 original size:20 final size:19
Alignment explanation
Indices: 38717--38791 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
38707 AAAAAGACAT
38717 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
38736 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
38757 CATGTATCGATATATTGAA
1 AATGTATCGATACATTGAA
38776 AATTGTATCGATACAT
1 AA-TGTATCGATACAT
38792 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:38774 original size:40 final size:39
Alignment explanation
Indices: 38714--38791 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 39
38704 GGTAAAAAGA
38714 CATAATGTATCGATACATTGAAGAA-TATATCGATACATT
1 CATAATGTATCGATACATTGAA-AATTATATCGATACATT
* *
38753 CATACATGTATCGATATATTGAAAATTGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAATTATATCGATACAT
38792 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
39 6 0.17
40 29 0.83
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAATTATATCGATACATT
Found at i:40175 original size:21 final size:21
Alignment explanation
Indices: 40150--40204 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
40140 ACAATAAGTG
* *
40150 ATGTATTGATACATTGCAAGC
1 ATGTATCGATACATTACAAGC
*
40171 ATGTATCGATATATTACAAGC
1 ATGTATCGATACATTACAAGC
40192 ATGTATCGATACA
1 ATGTATCGATACA
40205 ATTTTTCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTACAAGC
Found at i:45004 original size:20 final size:21
Alignment explanation
Indices: 44971--45009 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
44961 AATATTTTAT
* *
44971 AAAGTATTTTAAATGATTTGC
1 AAAGTATTTGAAATCATTTGC
44992 AAAG-ATTTGAAATCATTT
1 AAAGTATTTGAAATCATTT
45010 AGTTTGAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (21 bp):
AAAGTATTTGAAATCATTTGC
Found at i:49389 original size:16 final size:16
Alignment explanation
Indices: 49368--49398 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
49358 ATTTTAACTA
49368 GATGTATCGATACATT
1 GATGTATCGATACATT
49384 GATGTATCGATACAT
1 GATGTATCGATACAT
49399 CTGGGCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (16 bp):
GATGTATCGATACATT
Found at i:49438 original size:20 final size:20
Alignment explanation
Indices: 49413--49489 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
49403 GCAAAAGGAT
*
49413 AGAATGTATTGATACATTGA
1 AGAATGTATCGATACATTGA
*
49433 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
49453 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
49473 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
49490 CTGGGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:50477 original size:28 final size:28
Alignment explanation
Indices: 50358--51548 Score: 1463
Period size: 28 Copynumber: 41.8 Consensus size: 28
50348 TGTGCCATTA
* *
50358 ACTTGTGTAGGCTTTGAAAAGAGTTGCCACCG
1 ACTTGTG--GGCTTTG-AAAG-GATGCCACTG
* *
50390 ACTCGTGTGGGCTTTGAAAAGAGTTACCACT-
1 ACT--TGTGGGCTTTG-AAAG-GATGCCACTG
* * *
50421 AGCTTGTGGGCTTCGAAAAGAGTGCCACTA
1 A-CTTGTGGGCTTTGAAAGGA-TGCCACTG
* *
50451 ACTTGTGGGCTTTGAAAGGGTGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
50479 ACTTGTGGGCTTTGAAAAGAGTGCTATTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
*
50508 ACTTGTGGGCTTTGAAAAGG-TGCCACTA
1 ACTTGTGGGCTTTG-AAAGGATGCCACTG
* *
50536 ACTTGTGGGCTTTGAAAAGAGTGTCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
*
50565 ACTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
** * *
50593 ACTTGTGGGCTTTGAAAAAATGCTACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
50621 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
* * *
50650 ACTTGTGGGCTTTAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
50678 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
*
50707 ACTTGTGGGCTTTGAAAGGTTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
50735 ACTTGCATGGGTTTTGAAAGGGTGCCACTG
1 ACTTG--TGGGCTTTGAAAGGATGCCACTG
* *
50765 ACTTATGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * * *
50793 ACTTGTGGGCTCTGAAAAGATGCAATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
50821 ACTTGTAGGCTTTGAAAAGAGTTACCACTG
1 ACTTGTGGGCTTTG-AAAG-GATGCCACTG
*
50851 A-TTCATGGGCTTTGAAAGGATGCCACTG
1 ACTT-GTGGGCTTTGAAAGGATGCCACTG
*
50879 ACTTGTGGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
50907 ACTTGTGGGCTTTGAAA-GAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
50935 ACTTGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
50963 ACTTGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
50991 ACTTGTGGGCTTTGAAAAGAGTTGCCACTA
1 ACTTGTGGGCTTTG-AAAG-GATGCCACTG
** *
51021 ACTTGTGGGCTTTGAAAAAATGCCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
51049 ACTTGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
51077 CCTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
51105 ACTTGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
51133 ACTTGTGGGCTTTGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
51161 ACTTGTGGGCTTTGAAAAGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
**
51189 ACTTGTGGGCTTTGAAAAAATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
51217 ACTTGTAGGCTTCGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
51245 ACTTGTGGGCTTTGAACGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
51273 ACTTATGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
51301 ACTTGTGGGCTTTGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
51329 ACTTGTGGGCTTTGAAATGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * * *
51357 ACTTATGGGCTTTGAAAATAGTTGCCATTG
1 ACTTGTGGGCTTTG-AAA-GGATGCCACTG
* * *
51387 ACTCGTGGGCTTTGAAAGGATGGCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
51415 ACTTGTGGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
51443 ACTTGTGGGCTTTGAAAGGGTGCCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
51471 ACTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
51499 ACTTGTGGGCTTTAAAAGGGTGCCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
51527 ACTTGTGGGCTTTGAAAAGATG
1 ACTTGTGGGCTTTGAAAGGATG
51549 AACATTCTAG
Statistics
Matches: 1016, Mismatches: 120, Indels: 50
0.86 0.10 0.04
Matches are distributed among these distances:
27 6 0.01
28 741 0.73
29 142 0.14
30 97 0.10
31 1 0.00
32 25 0.02
34 4 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAAGGATGCCACTG
Found at i:50698 original size:142 final size:142
Alignment explanation
Indices: 50349--51546 Score: 1481
Period size: 142 Copynumber: 8.4 Consensus size: 142
50339 TAAAAAAAAT
* * * *
50349 GTGCCATTAACTTGTGTAGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGT
1 GTGCCACTGACTTGTG--GGCTTT-AAAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGAG-
* * * * * *
50414 TACCACT-AGCTTGTGGGCTTCGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACT
59 TGCCACTGA-CTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGATGCCACT
50478 AACTTGTGGGCTTTGAAAAGA
122 AACTTGTGGGCTTTGAAAAGA
* * * *
50499 GTGCTATTGACTTGTGGGCTTTGAAAA-GGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGTCAC
1 GTGCCACTGACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
* * *
50563 TGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAAATGCTACTAACTTGTG
65 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTG
50628 GGCTTTGAAAAGA
130 GGCTTTGAAAAGA
*
50641 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT
* * * * * *
50706 GACTTGTGGGCTTTGAAAGGTTGCCACTGACTTGCATGGGTTTTGAAAGGGTGCCACTGACTTAT
66 GACTTGTGGGCTTTGAAAGGATGCCACTGACTTG--TGGGCTTTGAAAAGATGCCACTAACTTGT
*
50771 GGGCTTTG-AAAGG
129 GGGCTTTGAAAAGA
* * * * * *
50784 GTGCCACTGACTTGTGGGCTCTGAAAA-GATGCAATTGACTTGTAGGCTTTGAAAAGAGTTACCA
1 GTGCCACTGACTTGTGGGCT-TTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCA
* *
50848 CTGA-TTCATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTG
64 CTGACTT-GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTG
50912 TGGGCTTTG-AAAGA
128 TGGGCTTTGAAAAGA
* * *
50926 GTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACT
1 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT
* * * * *
50990 GACTTGTGGGCTTTGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAAATGCCATTGACTTGT
66 GACTTGTGGGCTTTG-AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGT
*
51055 GGGCTTTGAAAGGA
129 GGGCTTTGAAAAGA
* * *
51069 -TGCCACTGCCTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACT
1 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT
*
51132 GACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGG
66 GACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGG
51197 GCTTTGAAAA-A
131 GCTTTGAAAAGA
* * * * * *
51208 ATGCCACTGACTTGTAGGCTTCGAAAA-GATGCCACTGACTTGTGGGCTTTG-AACGGGTGCCAC
1 GTGCCACTGACTTGTGGGCTT-TAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
* *
51271 TGACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTG
65 TGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTG
*
51336 GGCTTTGAAATGA
130 GGCTTTGAAAAGA
* * * * * * *
51349 -TGCCACTGACTTATGGGCTTTGAAAATAGTTGCCATTGACTCGTGGGCTTTGAAAGGA-TGGCA
1 GTGCCACTGACTTGTGGGCTTT-AAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
* * * * * *
51412 TTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGT
64 CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGT
*
51477 GGGCTTTG-AAAGG
129 GGGCTTTGAAAAGA
*
51490 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCATTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
51547 TGAACATTCT
Statistics
Matches: 929, Mismatches: 98, Indels: 52
0.86 0.09 0.05
Matches are distributed among these distances:
139 4 0.00
140 235 0.25
141 28 0.03
142 458 0.49
143 80 0.09
144 89 0.10
146 10 0.01
148 11 0.01
150 14 0.02
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (142 bp):
GTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT
GACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGG
GCTTTGAAAAGA
Found at i:52798 original size:8 final size:7
Alignment explanation
Indices: 52761--52810 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
52751 GACACCTTTC
52761 TGTTTTT
1 TGTTTTT
52768 TGTTATTT
1 TGTT-TTT
52776 T-TTTCTT
1 TGTTT-TT
*
52783 GGTTTTT
1 TGTTTTT
52790 TGCTTTTT
1 TG-TTTTT
52798 TGTTTTT
1 TGTTTTT
52805 T-TTTTT
1 TGTTTTT
52811 ATGAAGGACG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
6 6 0.16
7 17 0.46
8 14 0.38
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (7 bp):
TGTTTTT
Found at i:68320 original size:20 final size:21
Alignment explanation
Indices: 68297--68353 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
68287 CTGGACATGT
68297 TAAAAAAA-CATGAAACATAA
1 TAAAAAAAGCATGAAACATAA
68317 TAAAAAAAAATGCATGAAACATAA
1 T--AAAAAAA-GCATGAAACATAA
*
68341 TAAAAAATGCATG
1 TAAAAAAAGCATG
68354 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 5 0.16
22 13 0.41
24 13 0.41
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (21 bp):
TAAAAAAAGCATGAAACATAA
Found at i:68324 original size:21 final size:23
Alignment explanation
Indices: 68298--68347 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
68288 TGGACATGTT
68298 AAAAAAA-CATGAAACATAATAA
1 AAAAAAAGCATGAAACATAATAA
68320 AAAAAAATGCATGAAACATAATAA
1 AAAAAAA-GCATGAAACATAATAA
68344 AAAA
1 AAAA
68348 TGCATGGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 7 0.27
24 19 0.73
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAAAAGCATGAAACATAATAA
Found at i:68348 original size:21 final size:21
Alignment explanation
Indices: 68297--68353 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 21
68287 CTGGACATGT
*
68297 TAAAAAA-ACATGAAACATAA
1 TAAAAAATGCATGAAACATAA
68317 TAAAAAAAAATGCATGAAACATAA
1 T---AAAAAATGCATGAAACATAA
68341 TAAAAAATGCATG
1 TAAAAAATGCATG
68354 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.38
23 6 0.19
24 13 0.41
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (21 bp):
TAAAAAATGCATGAAACATAA
Found at i:69311 original size:20 final size:20
Alignment explanation
Indices: 69264--69338 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
69254 AAAAAGACAT
*
69264 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
69283 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
69304 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
69324 AATGTATCGATACAT
1 AATGTATCGATACAT
69339 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:69332 original size:40 final size:39
Alignment explanation
Indices: 69261--69338 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
69251 GGTAAAAAGA
* *
69261 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
69300 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
69339 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:70289 original size:20 final size:20
Alignment explanation
Indices: 70264--70388 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
70254 TTTTAACTAG
70264 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
70284 ATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* *
70315 ATGTATCGATAAATTGAAGA
1 ATGTATCGATACATTGAAAA
* * * *
70335 ATGTATCAATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
70355 ATGTATCGATAAATTGAAAA
1 ATGTATCGATACATTGAAAA
70375 ATGTATCGATACAT
1 ATGTATCGATACAT
70389 CTAGGTACTT
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
20 57 0.71
21 1 0.01
22 1 0.01
23 2 0.03
28 2 0.03
29 1 0.01
30 2 0.03
31 14 0.17
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:74656 original size:217 final size:216
Alignment explanation
Indices: 74332--74738 Score: 669
Period size: 217 Copynumber: 1.9 Consensus size: 216
74322 TTTCTTCTCT
*
74332 TGATCTCGCTCTTTTCTTTCTTCGTCATTAAATTAAAAAAAAAAAAGTTTGTTTTTCATTTAATA
1 TGATCTCGCTCTTTTCTTTCTTCGTCATTAAATTAAAAAAAAAAAAGTTTGTCTTTCATTTAATA
* *
74397 GATGGTAATAATTTTCTTTCAAAAACGTAATAAATGCTTGAAGG-TTTTTTTTTTTTTTCATAAA
66 GATGATAATAATTTTCTTTCAAAAACGTAATAAATACTTGAAGGTTTTTTTTTTTTTTTCATAAA
*
74461 -GGATTTTGCCAGTCAATAAACAAAGCATTTGTCTCATTATATATAAAA-ATAAAATCATTTGAT
131 GGGATTTTCCCAGTCAATAAACAAAGCATTTGTCTCATTATATATAAAATATAAAATCATTTGAT
74524 TAGATGGTAATAATTTTCTTG
196 TAGATGGTAATAATTTTCTTG
* *
74545 TGATCTCTCTCTTTTCTTTCTTTCTTCATTAAATTAAAAAAAAAAACAAAGTTTG-CTTTCATTT
1 TGATCTCGCTCTTTTCTTTC-TTCGTCATTAAATT--AAAAAAAAA-AAAGTTTGTCTTTCATTT
* *
74609 GATTAGATGATAATAATTTTCTTTCAAAAATGTAATAAATACTTGAAGGTTTTTTTTTTTTTTTC
62 -AATAGATGATAATAATTTTCTTTCAAAAACGTAATAAATACTTGAAGGTTTTTTTTTTTTTTTC
74674 ATAAAGGGATTTTCCCAGTCAATAAACAAAGCATTTGTCTCATTATATATAAAATATAAAATCAT
126 ATAAAGGGATTTTCCCAGTCAATAAACAAAGCATTTGTCTCATTATATATAAAATATAAAATCAT
74739 ATTAACAGGT
Statistics
Matches: 178, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
213 19 0.11
214 13 0.07
216 17 0.10
217 52 0.29
218 20 0.11
219 47 0.26
220 10 0.06
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (216 bp):
TGATCTCGCTCTTTTCTTTCTTCGTCATTAAATTAAAAAAAAAAAAGTTTGTCTTTCATTTAATA
GATGATAATAATTTTCTTTCAAAAACGTAATAAATACTTGAAGGTTTTTTTTTTTTTTTCATAAA
GGGATTTTCCCAGTCAATAAACAAAGCATTTGTCTCATTATATATAAAATATAAAATCATTTGAT
TAGATGGTAATAATTTTCTTG
Done.