Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1138
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: 87355
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2755 original size:17 final size:17
Alignment explanation
Indices: 2733--2766 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2723 ATGGAATAGT
2733 GTTTTTCTTTGTTTTTG
1 GTTTTTCTTTGTTTTTG
* *
2750 GTTTTTTTTTTTTTTTG
1 GTTTTTCTTTGTTTTTG
2767 CTAAAGGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (17 bp):
GTTTTTCTTTGTTTTTG
Found at i:3318 original size:13 final size:13
Alignment explanation
Indices: 3300--3325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3290 ACAAAGATCC
3300 ATGTATCGATACA
1 ATGTATCGATACA
3313 ATGTATCGATACA
1 ATGTATCGATACA
3326 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:3321 original size:33 final size:33
Alignment explanation
Indices: 3279--3345 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3269 AAAATTTCCA
***
3279 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3312 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3345 A
1 A
3346 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:9742 original size:99 final size:98
Alignment explanation
Indices: 9573--9772 Score: 348
Period size: 99 Copynumber: 2.0 Consensus size: 98
9563 GAGGCAAAAA
*
9573 ATGATAATAAAAAAAATGAAACTAACACCATATACAAGCTAACAAATCACATTCCTTCTTCACAT
1 ATGATAATAAAAAAAAGGAAACTAACACCATATACAAGCTAACAAATCACATTCCTTCTTCACAT
9638 AATTAAATAAACTTG-AAACATGATGAACATAC
66 AATTAAATAAACTTGAAAACATGATGAACATAC
* *
9670 ATGATAATAAAAAAAAAAGGTAACTAACACCATATATAAGCTAACAAATCACATTCCTTCTTCAC
1 ATGATAAT--AAAAAAAAGGAAACTAACACCATATACAAGCTAACAAATCACATTCCTTCTTCAC
9735 ATAATTAAATAAACTTGAAAACATGATGAACATAC
64 ATAATTAAATAAACTTGAAAACATGATGAACATAC
9770 ATG
1 ATG
9773 CTGATATATA
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 8 0.08
99 69 0.71
100 20 0.21
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (98 bp):
ATGATAATAAAAAAAAGGAAACTAACACCATATACAAGCTAACAAATCACATTCCTTCTTCACAT
AATTAAATAAACTTGAAAACATGATGAACATAC
Found at i:10394 original size:20 final size:21
Alignment explanation
Indices: 10360--10399 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10350 TTATGCATAA
10360 TATTTTTTCACTTTT-ATTTT
1 TATTTTTTCACTTTTGATTTT
* *
10380 TATTTTTTGATTTTTGATTT
1 TATTTTTTCACTTTTGATTT
10400 CTACTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (21 bp):
TATTTTTTCACTTTTGATTTT
Found at i:11107 original size:21 final size:21
Alignment explanation
Indices: 11081--11135 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
11071 ATTCTATAAT
* *
11081 TTGTATCGATACATTAAGTTA
1 TTGTATCGATACATTAAATGA
*
11102 TTGTATCAATACA-TAAATGA
1 TTGTATCGATACATTAAATGA
*
11122 ATGTATCGATACAT
1 TTGTATCGATACAT
11136 GCTTGTAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (21 bp):
TTGTATCGATACATTAAATGA
Found at i:19213 original size:22 final size:23
Alignment explanation
Indices: 19188--19232 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
19178 ATTCTTATTA
*
19188 ATTAAGCAAATATTG-ATGAATG
1 ATTAAGAAAATATTGAATGAATG
* *
19210 ATTATGAAAATGTTGAATGAATG
1 ATTAAGAAAATATTGAATGAATG
19233 CCATGAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.33
Consensus pattern (23 bp):
ATTAAGAAAATATTGAATGAATG
Found at i:24246 original size:5 final size:5
Alignment explanation
Indices: 24238--24266 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
24228 TTGCTTTTGT
24238 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
24267 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:24641 original size:22 final size:22
Alignment explanation
Indices: 24609--24664 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
24599 GGAGGCTGCT
* *
24609 GAGCTGCTGGAGGTTGTCGTGG
1 GAGCTGCTGGAGGCTATCGTGG
*
24631 GAGCTGTTGGAGGCTATCGTGG
1 GAGCTGCTGGAGGCTATCGTGG
*
24653 AAGCTGCTGGAG
1 GAGCTGCTGGAG
24665 CTGCTGGAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.46, T:0.25
Consensus pattern (22 bp):
GAGCTGCTGGAGGCTATCGTGG
Found at i:24726 original size:80 final size:82
Alignment explanation
Indices: 24631--24784 Score: 206
Period size: 85 Copynumber: 1.9 Consensus size: 82
24621 GTTGTCGTGG
* *
24631 GAGCTGTTGGAGGCTATCGT-GGA-AG-CTGCTGGAGCTGCTGGAAGTTACTATGGGAGTTGTGG
1 GAGCTGCTGGAGGCTATCGTAGGAGAGCCTGCTGGAGCTGCTGGAAGTTACTAT-GGAGCTGTGG
24693 GAGCTACTCAGGATTGCT
65 GAGCTACTCAGGATTGCT
* * * *
24711 GAGCTGCTGGAGGCTATCGTAGGAGTTGCTCTGCTGGAGCTGTTGGAAGTTGCTGTGGAGCTGTG
1 GAGCTGCTGGAGGCTATCGTAGGAG-AGC-CTGCTGGAGCTGCTGGAAGTTACTATGGAGCTGTG
24776 GGAGCTACT
64 GGAGCTACT
24785 GAAAGTTACT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
80 19 0.30
81 3 0.05
83 1 0.02
84 17 0.27
85 23 0.37
ACGTcount: A:0.17, C:0.16, G:0.40, T:0.28
Consensus pattern (82 bp):
GAGCTGCTGGAGGCTATCGTAGGAGAGCCTGCTGGAGCTGCTGGAAGTTACTATGGAGCTGTGGG
AGCTACTCAGGATTGCT
Found at i:24780 original size:30 final size:31
Alignment explanation
Indices: 24746--24814 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
24736 TTGCTCTGCT
* * *
24746 GGAGCTGTTGGAAGTTGCTGT-GGAGCTGTG
1 GGAGCTGCTGAAAGTTACTGTGGGAGCTGTG
*
24776 GGAGCTACTGAAAGTTACTGTGGGAGCTGTG
1 GGAGCTGCTGAAAGTTACTGTGGGAGCTGTG
*
24807 GGGGCTGC
1 GGAGCTGC
24815 CGGTGGTTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.16, C:0.13, G:0.45, T:0.26
Consensus pattern (31 bp):
GGAGCTGCTGAAAGTTACTGTGGGAGCTGTG
Found at i:25217 original size:10 final size:10
Alignment explanation
Indices: 25202--25235 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
25192 ATGCTGTCCG
25202 TTATTTATTA
1 TTATTTATTA
25212 TTATTT-TTA
1 TTATTTATTA
25221 TTTATTTATTA
1 -TTATTTATTA
25232 TTAT
1 TTAT
25236 ATTTTTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.14
10 16 0.73
11 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTTATTA
Found at i:25227 original size:20 final size:21
Alignment explanation
Indices: 25202--25240 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
25192 ATGCTGTCCG
25202 TTATTTATTATTAT-TTTTAT
1 TTATTTATTATTATATTTTAT
25222 TTATTTATTATTATATTTT
1 TTATTTATTATTATATTTT
25241 TTGCAGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTATTATTATATTTTAT
Found at i:25557 original size:43 final size:41
Alignment explanation
Indices: 25495--25576 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 41
25485 CAATTTCATG
* * * *
25495 CATGAATGCATGCATTGCCACCTAATTGATTTAGGTGGCAA
1 CATGAATGCATGCAATGCCACCTAAGTCAATTAGGTGGCAA
25536 CATGCAATGCAATGCAATGCCACCTAAGTCAATTAGGTGGC
1 CATG-AATGC-ATGCAATGCCACCTAAGTCAATTAGGTGGC
25577 TACAAATCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.11
42 5 0.14
43 26 0.74
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (41 bp):
CATGAATGCATGCAATGCCACCTAAGTCAATTAGGTGGCAA
Found at i:26080 original size:22 final size:22
Alignment explanation
Indices: 26052--26106 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
26042 AAATATATTT
26052 TTCTCAAATTTTAGTTTTCGTG
1 TTCTCAAATTTTAGTTTTCGTG
26074 TTCTCAAATTTTAGTTTTCGTG
1 TTCTCAAATTTTAGTTTTCGTG
*
26096 TTTTCAAATTT
1 TTCTCAAATTT
26107 CTCTCACGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (22 bp):
TTCTCAAATTTTAGTTTTCGTG
Found at i:26428 original size:131 final size:130
Alignment explanation
Indices: 26266--26500 Score: 375
Period size: 131 Copynumber: 1.8 Consensus size: 130
26256 TGCTAAATTG
* *
26266 TTTTTATCTCAGGGATACTCCAACCCTAACATCAAAAG-GAGTACTCCAACCCCCATTTTC-CTT
1 TTTTTATCTCACGGATACTCCAACCCCAACATCAAAAGAG-GTACTCCAACCCCCATTTTCACTT
26329 TCTAAAACACCAAAATTTTCATCTTCGAGGATACTCCAACCTCTTTTCTACTTCCAAAACATTGA
65 T-TAAAACACCAAAATTTTCATCTTCGAGGATACTCCAACCTCTTTTCTACTTCCAAAACATTGA
26394 AT
129 AT
* **
26396 TTTTTATCTCTACGGATACTCTAACCCCAACATCAAAAGAGGTACTCCAACCCTTATTTTCACTT
1 TTTTTATCTC-ACGGATACTCCAACCCCAACATCAAAAGAGGTACTCCAACCCCCATTTTCACTT
*
26461 TTAAAACACTAAAATTTTCATCTTCGAGGATACTCCAACC
65 TTAAAACACCAAAATTTTCATCTTCGAGGATACTCCAACC
26501 CCACCATCTC
Statistics
Matches: 96, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
130 10 0.10
131 81 0.84
132 5 0.05
ACGTcount: A:0.32, C:0.29, G:0.08, T:0.32
Consensus pattern (130 bp):
TTTTTATCTCACGGATACTCCAACCCCAACATCAAAAGAGGTACTCCAACCCCCATTTTCACTTT
TAAAACACCAAAATTTTCATCTTCGAGGATACTCCAACCTCTTTTCTACTTCCAAAACATTGAAT
Found at i:26492 original size:79 final size:79
Alignment explanation
Indices: 26355--26746 Score: 250
Period size: 79 Copynumber: 4.9 Consensus size: 79
26345 TTTCATCTTC
* * * * *
26355 GAGGATACTCCAA-CCTC-TTTTCTACTTCCAAAACATTGAATTTTTTATCTCTAC-GGATACTC
1 GAGG-TACTCCAACCCTCATTTTC-ACTTTCAAAACACTAAAATTTTCATCT-T-CGGGATACTC
*
26417 TAACCCCAACATC-AAAA
62 CAACCCCAACATCTAAAA
* *
26434 GAGGTACTCCAACCCTTATTTTCACTTTTAAAACACTAAAATTTTCATCTTCGAGGATACTCCAA
1 GAGGTACTCCAACCCTCATTTTCACTTTCAAAACACTAAAATTTTCATCTTCG-GGATACTCCAA
* **
26499 CCCCACCATCTCTAA
65 CCCCAACATCTAAAA
* * *
26514 GGGGATACTCCAACCC-CA-TTTCTAC-TTCAAAAC-GTAAAATTTTTCATCTCCGGGGATACTC
1 GAGG-TACTCCAACCCTCATTTTC-ACTTTCAAAACACTAAAA-TTTTCATCTTC-GGGATACTC
* ** ***
26575 TAATTCC-ACTATCTCCGA
62 CAACCCCAAC-ATCTAAAA
* * * * * *
26593 GAGATGCTCCAACCCTAATTTT-ACTTCCAAAACA-TCAAATTTTTCATCTTTGGGAATACTCCA
1 GAGGTACTCCAACCCTCATTTTCACTTTCAAAACACT-AAAATTTTCATCTTCGGG-ATACTCCA
* *
26656 ACTCTAACATC-AAAA
64 ACCCCAACATCTAAAA
* * * * * * * *
26671 GGGGTACTCTAACCCCCATTTTCACTTTTAAAACACCAAAATTTTCATCTCTAGGGATACTTCGA
1 GAGGTACTCCAACCCTCATTTTCACTTTCAAAACACTAAAATTTTCATCT-TCGGGATACTCCAA
*
26736 CCCCACCATCT
65 CCCCAACATCT
26747 CCAAGGAGAT
Statistics
Matches: 240, Mismatches: 52, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
77 1 0.00
78 47 0.20
79 155 0.65
80 26 0.11
81 11 0.05
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (79 bp):
GAGGTACTCCAACCCTCATTTTCACTTTCAAAACACTAAAATTTTCATCTTCGGGATACTCCAAC
CCCAACATCTAAAA
Found at i:26637 original size:158 final size:159
Alignment explanation
Indices: 26357--26976 Score: 447
Period size: 158 Copynumber: 3.9 Consensus size: 159
26347 TCATCTTCGA
* * ** * *
26357 GGATACTCCAACCTCTTTTCTACTTCCAAAACATTGAATTTTTTATCTCTACGGATACTCT-AAC
1 GGATACTCCAACCCCATTT-TACTT-CAAAACATAAAATTTTTCATCTCTAGGGATACTCTCAAC
* * * * ** *
26421 CCCAACA--TCAAAAGAGGTA-CTCCAACCCTTATTTTCACTTTTAAAACA-CTAAAATTTTCAT
64 CCCACCATCTCCAAGGAGATAGCTCCAACCC-TATTTT-ACTTCCAAAACATC-AAATTTTTCAT
26482 CTTCGAGGATACTCCAACCCCACCATCTCTAAGG
126 CTTCGAGGATACTCCAACCCCACCATCTCTAAGG
* ** **
26516 GGATACTCCAACCCCATTTCTACTTCAAAACGTAAAATTTTTCATCTCCGGGGATACTCT-AATT
1 GGATACTCCAACCCCATTT-TACTTCAAAACATAAAATTTTTCATCTCTAGGGATACTCTCAACC
* *
26580 CCACTATCTCCGA-GAGAT-GCTCCAACCCTAATTTTACTTCCAAAACATCAAATTTTTCATCTT
65 CCACCATCTCCAAGGAGATAGCTCCAACCCT-ATTTTACTTCCAAAACATCAAATTTTTCATCTT
* * * * **
26643 TG-GGAATACTCCAACTCTAACATC-AAAAGG
129 CGAGG-ATACTCCAACCCCACCATCTCTAAGG
* * * *
26673 GG-TACTCTAACCCCCATTTTCACTTTTAAAACACCAAAA-TTTTCATCTCTAGGGATACT-TCG
1 GGATACTCCAA-CCCCATTTT-AC-TTCAAAACA-TAAAATTTTTCATCTCTAGGGATACTCTCA
* * * *
26735 ACCCCACCATCTCCAAGGAGATAG-TACAACTCTA-TCTACTTCCAAAACGTCAAATTTTTCATC
62 ACCCCACCATCTCCAAGGAGATAGCTCCAACCCTATTTTACTTCCAAAACATCAAATTTTTCATC
* *
26798 -TCTGAGGATACTCTAATCCCACCATCTCTGAA-G
127 TTC-GAGGATACTCCAACCCCACCATCTCT-AAGG
* ** * *
26831 GGATACTCCAACCCTATTTTTAAATCTAAAACATCAAATTTTTTATCTCTAGGGATACTC-CAAC
1 GGATACTCCAACCCCA-TTTTACTTC-AAAACATAAAATTTTTCATCTCTAGGGATACTCTCAAC
** * * * * * * **
26895 CTTACCATCTCTGAAAG-GATA-CTCTAACCTTGTTTTTACTTTCAAAACATTGAATTTTT-ATC
64 CCCACCATCTC-CAAGGAGATAGCTCCAACCCT-ATTTTACTTCCAAAACATCAAATTTTTCATC
* *
26957 TTTG-GGATACTCTAACCCCA
127 TTCGAGGATACTCCAACCCCA
26977 TTTTTTACTT
Statistics
Matches: 361, Mismatches: 73, Indels: 55
0.74 0.15 0.11
Matches are distributed among these distances:
156 9 0.02
157 65 0.18
158 184 0.51
159 78 0.22
160 25 0.07
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.32
Consensus pattern (159 bp):
GGATACTCCAACCCCATTTTACTTCAAAACATAAAATTTTTCATCTCTAGGGATACTCTCAACCC
CACCATCTCCAAGGAGATAGCTCCAACCCTATTTTACTTCCAAAACATCAAATTTTTCATCTTCG
AGGATACTCCAACCCCACCATCTCTAAGG
Found at i:26798 original size:78 final size:80
Alignment explanation
Indices: 26700--26917 Score: 196
Period size: 80 Copynumber: 2.8 Consensus size: 80
26690 TTTCACTTTT
* * * *
26700 AAAACACCAAAATTTTCATCTCTAGGGATACTTC-GACCCCACCATCTC-CAAGGAGATAGTACA
1 AAAACATCAAATTTTTCATCTCTAGGGATACTTCTAACCCCACCATCTCTCAAGG-GATACTACA
* **
26763 ACTCTA-TCTACTTCC
65 ACCCTATTCTAAATCC
* * * *
26778 AAAACGTCAAATTTTTCATCTCT-GAGGATAC-TCTAATCCCACCATCTCTGAAGGGATACTCCA
1 AAAACATCAAATTTTTCATCTCTAG-GGATACTTCTAACCCCACCATCTCTCAAGGGATACTACA
* *
26841 ACCCTATTTTTAAATCT
65 ACCCTA-TTCTAAATCC
* * ** * *
26858 AAAACATCAAATTTTTTATCTCTAGGGATAC-TCCAACCTTACCATCTCTGAAAGGATACT
1 AAAACATCAAATTTTTCATCTCTAGGGATACTTCTAACCCCACCATCTCTCAAGGGATACT
26918 CTAACCTTGT
Statistics
Matches: 114, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
77 3 0.03
78 50 0.44
79 4 0.04
80 56 0.49
81 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (80 bp):
AAAACATCAAATTTTTCATCTCTAGGGATACTTCTAACCCCACCATCTCTCAAGGGATACTACAA
CCCTATTCTAAATCC
Found at i:26842 original size:237 final size:236
Alignment explanation
Indices: 26348--26895 Score: 676
Period size: 237 Copynumber: 2.3 Consensus size: 236
26338 CCAAAATTTT
* ** *
26348 CATCTTCGA-GGATACTCCAACCTCT-TTTCTACTTCCAAAACATTGAATTTTTTATCTCTACGG
1 CATCTCCGAGGGATACTCCAACC-CTATTT-TACTTCCAAAACATCAAATTTTTTATCTCTAGGG
* ** *
26411 ATACTCTAACCCCAACATCAAAAGAGGTACTCCAACCCTTATTTTCACTTTTAAAACACTAAAAT
64 ATACTCCAACCCCAACATCAAAAGAGGTACTCCAACCCCCATTTTCACTTTTAAAACACCAAAAT
* * * * *
26476 TTTCATCTTCGAGGATACTCCAACCCCACCATCTCTAAGGGGATACTCCAACCCCATTTCTACTT
129 TTTCATCTTAGAGGATACTCCAACCCCACCATCTCCAAGGAGATACTACAACCCCATATCTACTT
* *
26541 CAAAACGTAAAATTTTTCATCTCCGGGGATACTCTAATTCCAC
194 CAAAACGTAAAATTTTTCATCTCCGAGGATACTCTAATCCCAC
* * * * *
26584 TATCTCCGAGAGATGCTCCAACCCTAATTTTACTTCCAAAACATCAAATTTTTCATCT-TTGGGA
1 CATCTCCGAGGGATACTCCAACCCT-ATTTTACTTCCAAAACATCAAATTTTTTATCTCTAGGG-
* * * *
26648 ATACTCCAACTCTAACATCAAAAGGGGTACTCTAACCCCCATTTTCACTTTTAAAACACCAAAAT
64 ATACTCCAACCCCAACATCAAAAGAGGTACTCCAACCCCCATTTTCACTTTTAAAACACCAAAAT
* * * *
26713 TTTCATCTCTAG-GGATACTTCGACCCCACCATCTCCAAGGAGATAGTACAA-CTC-TATCTACT
129 TTTCATCT-TAGAGGATACTCCAACCCCACCATCTCCAAGGAGATACTACAACCCCATATCTACT
* *
26775 TCCAAAACGTCAAATTTTTCATCTCTGAGGATACTCTAATCCCAC
193 T-CAAAACGTAAAATTTTTCATCTCCGAGGATACTCTAATCCCAC
* ** *
26820 CATCTCTGAAGGGATACTCCAACCCTATTTTTAAATCTAAAACATCAAATTTTTTATCTCTAGGG
1 CATCTCCG-AGGGATACTCCAACCCTA-TTTTACTTCCAAAACATCAAATTTTTTATCTCTAGGG
26885 ATACTCCAACC
64 ATACTCCAACC
26896 TTACCATCTC
Statistics
Matches: 263, Mismatches: 40, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
235 8 0.03
236 60 0.23
237 186 0.71
238 9 0.03
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (236 bp):
CATCTCCGAGGGATACTCCAACCCTATTTTACTTCCAAAACATCAAATTTTTTATCTCTAGGGAT
ACTCCAACCCCAACATCAAAAGAGGTACTCCAACCCCCATTTTCACTTTTAAAACACCAAAATTT
TCATCTTAGAGGATACTCCAACCCCACCATCTCCAAGGAGATACTACAACCCCATATCTACTTCA
AAACGTAAAATTTTTCATCTCCGAGGATACTCTAATCCCAC
Found at i:27027 original size:53 final size:51
Alignment explanation
Indices: 26927--27027 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 51
26917 TCTAACCTTG
* * *
26927 TTTTTACTTTCAAAACATTGAATTTTTATCTTTGGGATACTCTAACCCCAT
1 TTTTTACTTCCAAAACATCGAATTTTTATCTTTGGGATACTCCAACCCCAT
* *
26978 TTTTTACTTCCACAATATCGAATTCTTTATCTTTGGGGATACTCCAACCC
1 TTTTTACTTCCAAAACATCGAATT-TTTATCTTT-GGGATACTCCAACCC
27028 TACCATCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 20 0.47
52 9 0.21
53 14 0.33
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (51 bp):
TTTTTACTTCCAAAACATCGAATTTTTATCTTTGGGATACTCCAACCCCAT
Found at i:28133 original size:13 final size:13
Alignment explanation
Indices: 28115--28140 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28105 TACACCAAGT
28115 ATGTATCGATACA
1 ATGTATCGATACA
28128 ATGTATCGATACA
1 ATGTATCGATACA
28141 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:28138 original size:32 final size:33
Alignment explanation
Indices: 28097--28160 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
28087 TAGCCAAACT
* **
28097 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
28129 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
28161 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:30389 original size:21 final size:21
Alignment explanation
Indices: 30356--30400 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30346 TTGCAAGTTG
*
30356 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
30378 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
30398 AAA
1 AAA
30401 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:32224 original size:15 final size:15
Alignment explanation
Indices: 32204--32234 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32194 TAAAAATGTC
*
32204 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
32219 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
32234 C
1 C
32235 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:34331 original size:13 final size:13
Alignment explanation
Indices: 34313--34338 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34303 ACATTTTTCT
34313 TTGTATCGATACA
1 TTGTATCGATACA
34326 TTGTATCGATACA
1 TTGTATCGATACA
34339 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:34502 original size:20 final size:20
Alignment explanation
Indices: 34459--34504 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
34449 AAATCTTTTG
34459 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
34480 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
34500 CAAAA
1 CAAAA
34505 CAGCATCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:36910 original size:13 final size:13
Alignment explanation
Indices: 36892--36917 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36882 TACACCAAGT
36892 ATGTATCGATACA
1 ATGTATCGATACA
36905 ATGTATCGATACA
1 ATGTATCGATACA
36918 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:36915 original size:32 final size:33
Alignment explanation
Indices: 36874--36937 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
36864 TTGCCAAACT
* **
36874 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
36906 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
36938 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:44293 original size:20 final size:21
Alignment explanation
Indices: 44263--44317 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
44253 TTGCCAAGGA
*
44263 AATGTATCGATACATTTA-TC
1 AATGCATCGATACATTTATTC
* *
44283 ATTGCATCGATATA-TTATTC
1 AATGCATCGATACATTTATTC
*
44303 AATGTATCGATACAT
1 AATGCATCGATACAT
44318 GCAGGCAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (21 bp):
AATGCATCGATACATTTATTC
Found at i:46710 original size:27 final size:27
Alignment explanation
Indices: 46679--46734 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
46669 ATACCAAATT
46679 TTATTCATCAG-GGATACTCCAACCCCA
1 TTATTC-TCAGAGGATACTCCAACCCCA
*
46706 TTATTCTGAGAGGATACTCCAACCCCA
1 TTATTCTCAGAGGATACTCCAACCCCA
46733 TT
1 TT
46735 TTTAAACTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.29
Consensus pattern (27 bp):
TTATTCTCAGAGGATACTCCAACCCCA
Found at i:57587 original size:19 final size:19
Alignment explanation
Indices: 57563--57624 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
57553 TTTTGAACTT
57563 CAAACAATTTGTATCGATA
1 CAAACAATTTGTATCGATA
**
57582 CAAACAGAAAATGTATCGATA
1 CAAAC--AATTTGTATCGATA
* *
57603 CATA-AGTGTTGTATCGATA
1 CAAACAAT-TTGTATCGATA
57622 CAA
1 CAA
57625 TGTATCGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.03
19 17 0.52
21 15 0.45
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (19 bp):
CAAACAATTTGTATCGATA
Found at i:57630 original size:13 final size:13
Alignment explanation
Indices: 57612--57636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57602 ACATAAGTGT
57612 TGTATCGATACAA
1 TGTATCGATACAA
57625 TGTATCGATACA
1 TGTATCGATACA
57637 TAAGTTTTGT
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:57632 original size:32 final size:32
Alignment explanation
Indices: 57591--57663 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
57581 ACAAACAGAA
57591 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
* *
57623 AATGTATCGATACATAAGTTTTGTATTGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
57655 ATTGTATCG
1 AATGTATCG
57664 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:57706 original size:21 final size:21
Alignment explanation
Indices: 57680--57721 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
57670 AGCTACTGCC
57680 AAGGAAATGTATCAATACATT
1 AAGGAAATGTATCAATACATT
*
57701 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCAATACATT
57722 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCAATACATT
Found at i:57726 original size:13 final size:13
Alignment explanation
Indices: 57708--57733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57698 ATTAAGGAAA
57708 TGTATCGATACAT
1 TGTATCGATACAT
57721 TGTATCGATACAT
1 TGTATCGATACAT
57734 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:60159 original size:52 final size:52
Alignment explanation
Indices: 60092--60227 Score: 191
Period size: 52 Copynumber: 2.6 Consensus size: 52
60082 TTAAGTTTCT
* * * * *
60092 CAATTTTTCATAATCGGGGGTACTCCAACTCCGGTTTTATTTCTAAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
60144 TAATTTTCCACAATCGGGGATAGTCCAACCCCGATTTTATTTCCAAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
*
60196 CAATTTTTCACAATCGGAGATACTCCAACCCC
1 CAATTTTTCACAATCGGGGATACTCCAACCCC
60228 ATTAATCATC
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (52 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:60238 original size:27 final size:28
Alignment explanation
Indices: 60208--60281 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 28
60198 ATTTTTCACA
60208 ATCGGAGATACTCCAACCCCATTA-ATC
1 ATCGGAGATACTCCAACCCCATTATATC
* *
60235 ATCGGGGATACTCCAACCCCATTATTTC
1 ATCGGAGATACTCCAACCCCATTATATC
* *
60263 CTAGGAGATACTCCAACCC
1 ATCGGAGATACTCCAACCC
60282 TGGCTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.23
Consensus pattern (28 bp):
ATCGGAGATACTCCAACCCCATTATATC
Found at i:60318 original size:79 final size:76
Alignment explanation
Indices: 60235--60488 Score: 296
Period size: 79 Copynumber: 3.2 Consensus size: 76
60225 CCCATTAATC
* *
60235 ATCGGGGATACTCCAACCCCATTATTTCCTAGGAGATACTCCAACCCTGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTT-CTAGGGGATACTCCAACCC-GG-TTTATTCCTAAAAT
60300 ATTGATTTCTTATA
63 ATTGATTTCTTATA
*
60314 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTA-TTTCTAGGGGATACTCCAA-CCCGG-TTTATTCCTAAAAT
* *
60379 ATTGATTTCTCACA
63 ATTGATTTCTTATA
* *
60393 ATCGGAGATACTCCAACCCCGTTCTTTCTGAGGGGATACTCCAATCCCGGTTTCATTTCC-AAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCT-AGGGGATACTCCAA-CCCGGTTT-A-TTCCTAAAA
* **
60457 CATCAATTTCTCT-TA
62 TATTGATTTCT-TATA
*
60472 ATCGGGGATACTTCAAC
1 ATCGGGGATACTCCAAC
60489 TCCGATTTTA
Statistics
Matches: 152, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
78 7 0.05
79 135 0.89
80 10 0.07
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (76 bp):
ATCGGGGATACTCCAACCCCGTTATTTCTAGGGGATACTCCAACCCGGTTTATTCCTAAAATATT
GATTTCTTATA
Found at i:60502 original size:51 final size:50
Alignment explanation
Indices: 60424--60590 Score: 183
Period size: 51 Copynumber: 3.3 Consensus size: 50
60414 TTCTTTCTGA
* * * *
60424 GGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTCTCTTAATC
1 GGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTT-TCATAATC
* * *
60475 GGGGATACTTCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAATC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTT-CATAATC
* * * *
60526 GGGGATACTCCAACTCTGATTTTATTTTCAAAGCACCAACTTTTCACAATC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA-TTTTCATAATC
*
60577 GGGGATATTCCAAC
1 GGGGATACTCCAAC
60591 CCCGTTATTT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.01
51 92 0.94
52 5 0.05
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCATAATC
Found at i:60710 original size:27 final size:28
Alignment explanation
Indices: 60643--60724 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
60633 TAAAAGATCA
*
60643 ATTATTCATC-GGGGATACTCCAACCCC
1 ATTAATCATCAGGGGATACTCCAACCCC
* *
60670 GTTAATCATCA-GGGATACTCCAACCTC
1 ATTAATCATCAGGGGATACTCCAACCCC
**
60697 ATT-ATTTTCGAGGGGATACTCCAACCCC
1 ATTAATCATC-AGGGGATACTCCAACCCC
60725 CGGCTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
26 4 0.09
27 26 0.58
28 15 0.33
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (28 bp):
ATTAATCATCAGGGGATACTCCAACCCC
Found at i:60842 original size:79 final size:79
Alignment explanation
Indices: 60681--61039 Score: 452
Period size: 79 Copynumber: 4.5 Consensus size: 79
60671 TTAATCATCA
* *
60681 GGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAAT-AT
1 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAA-CCCCGGCTTTATT-TTAAAATCAT
* *
60745 TGATTTCTCATAATCG
64 CGATTTCTCACAATCG
* * *
60761 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT-ATT
1 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTT-TAAAATCATC
* *
60825 AATTTCTCATAATCG
65 GATTTCTCACAATCG
* * *** * * *
60840 GGGATACTCAAACCCCGTTATCCCCGAGGGGATACTTCAACCCCGGTTTTATTTTCAAATCATCG
1 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTTAAAATCATCG
*
60905 ATTTTTCACAATCG
66 ATTTCTCACAATCG
* * * * *
60919 GGGATACTCCAACCCCTTTATTTTCAAGGGGATACTCCAACCTCGGTTTTATTTTCAAATCATCG
1 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTTAAAATCATCG
*
60984 ATTTTTCACAATCG
66 ATTTCTCACAATCG
*
60998 GGGATACTCCAACCCCATTATTTTCAAGGGGATACTCCAACC
1 GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACC
61040 TCGTTACTAT
Statistics
Matches: 253, Mismatches: 24, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
78 5 0.02
79 211 0.83
80 37 0.15
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTTAAAATCATCG
ATTTCTCACAATCG
Found at i:73412 original size:15 final size:14
Alignment explanation
Indices: 73392--73468 Score: 70
Period size: 15 Copynumber: 5.4 Consensus size: 14
73382 TCTCTTCTAA
73392 AAAAAAAACAAAAG
1 AAAAAAAACAAAAG
73406 CAAAAAATAA-AAAA-
1 -AAAAAA-AACAAAAG
*
73420 ATAAAAAAACAAAAA
1 A-AAAAAAACAAAAG
73435 AAAACAAAAC-AAAG
1 AAAA-AAAACAAAAG
*
73449 AAAAAAAGAGAAAAG
1 AAAAAAA-ACAAAAG
73464 AAAAA
1 AAAAA
73469 GAACCTGCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
13 6 0.11
14 20 0.38
15 25 0.47
16 2 0.04
ACGTcount: A:0.84, C:0.06, G:0.06, T:0.03
Consensus pattern (14 bp):
AAAAAAAACAAAAG
Found at i:73456 original size:8 final size:8
Alignment explanation
Indices: 73390--73468 Score: 54
Period size: 8 Copynumber: 9.6 Consensus size: 8
73380 ATTCTCTTCT
73390 AAAAAAA-
1 AAAAAAAG
73397 AAACAAAAG
1 AAA-AAAAG
* *
73406 CAAAAAAT
1 AAAAAAAG
*
73414 AAAAAAATA
1 AAAAAAA-G
*
73423 AAAAAACAA
1 AAAAAA-AG
*
73432 AAAAAAAC
1 AAAAAAAG
73440 AAAACAAAG
1 AAAA-AAAG
73449 AAAAAAAG
1 AAAAAAAG
*
73457 -AGAAAAG
1 AAAAAAAG
73464 AAAAA
1 AAAAA
73469 GAACCTGCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
7 9 0.16
8 26 0.45
9 22 0.38
10 1 0.02
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:73468 original size:1 final size:1
Alignment explanation
Indices: 73390--73455 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
73380 ATTCTCTTCT
* ** * * * * * *
73390 AAAAAAAAAACAAAAGCAAAAAATAAAAAAATAAAAAAACAAAAAAAAACAAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
73455 A
1 A
73456 GAGAAAAGAA
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:74607 original size:55 final size:55
Alignment explanation
Indices: 74521--74767 Score: 223
Period size: 55 Copynumber: 4.4 Consensus size: 55
74511 TTCAGCCTTT
* * *
74521 AGTCCTCAAAGAGA-AGGACGCCTTTCGAAGCCCACACGAGTTGGTGGCATTTTCC
1 AGTCCTCAAA-AAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
74576 AGTCCTCAAAAAATAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTT--
1 AGTCCTCAAAAAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCC
* * * *
74631 AGTCCTCAAAGAGCAGGACGCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
1 AGTCCTCAAAAAACAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * * * *
74691 TAGTCCTTAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCT
1 -AGTCCTCAAAAAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
74747 AGTCCTCAAAGAGCAGGACGC
1 AGTCCTCAAAAAACAGGACGC
74768 TCTCTCTTTT
Statistics
Matches: 165, Mismatches: 14, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
54 2 0.01
55 108 0.65
56 3 0.02
57 4 0.02
58 2 0.01
61 46 0.28
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (55 bp):
AGTCCTCAAAAAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:74695 original size:61 final size:59
Alignment explanation
Indices: 74596--74777 Score: 241
Period size: 55 Copynumber: 3.1 Consensus size: 59
74586 AAATAGGACG
* * *
74596 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTAGTCCTCAAAGAGCAGGACGC-TTCT
*
74657 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTTAAAGAGCAGGACG-----
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTT-CTAGTCCTCAAAGAGCAGGACGCTTCT
74712 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGC-TCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTCTAGTCCTCAAAGAGCAGGACGCTTCT
74771 CTCTTTT
1 C-CTTTT
74778 CACCCTTTAG
Statistics
Matches: 109, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
55 51 0.47
56 2 0.02
59 1 0.01
60 8 0.07
61 47 0.43
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (59 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAGTCCTCAAAGAGCAGGACGCTTCT
Found at i:74716 original size:116 final size:115
Alignment explanation
Indices: 74548--74777 Score: 338
Period size: 116 Copynumber: 2.0 Consensus size: 115
74538 ACGCCTTTCG
* * *
74548 AAGCCCACACGAGTTGGTGGCATTTTCCAGTCCTCAAAAAATAGGACGCCTTTCAAAGCCCACAC
1 AAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAAAACAGGACGCCTTTCAAAGCCCACAC
*
74613 AAGCTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGACGCTTTCTCCTTTTA
66 AAGCTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCTCTCT-CTTTTA
* * * *
74664 AAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTTAAAGAGCAGGACGCCTTTTAAAGCCCACA
1 AAGCCCACACAAGTTGGTGGCATCTTCC-AGTCCTCAAAAAACAGGACGCCTTTCAAAGCCCACA
*
74728 CAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCTTTT
65 CAAGCTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCTTTT
74778 CACCCTTTAG
Statistics
Matches: 103, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
115 13 0.13
116 90 0.87
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (115 bp):
AAGCCCACACAAGTTGGTGGCATCTTCCAGTCCTCAAAAAACAGGACGCCTTTCAAAGCCCACAC
AAGCTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCTCTCTCTTTTA
Found at i:74853 original size:94 final size:94
Alignment explanation
Indices: 74691--74861 Score: 272
Period size: 94 Copynumber: 1.8 Consensus size: 94
74681 TGGCACTTCC
* * **
74691 TAGTCCTTAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCTAGTCCTCAA
74756 AGAGCAGGACGCTCTCTCTTTTCACCCTT
66 AGAGCAGGACGCTCTCTCTTTTCACCCTT
* *
74785 TAGTCCTCAGAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCC-CTCAGTCCTCG
1 TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCT-AGTCCTCA
74849 AAGAGCAGGACGC
65 AAGAGCAGGACGC
74862 CTGTTTCTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 2 0.03
94 68 0.97
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.22
Consensus pattern (94 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCCTCTAGTCCTCAA
AGAGCAGGACGCTCTCTCTTTTCACCCTT
Found at i:74919 original size:156 final size:150
Alignment explanation
Indices: 74628--74968 Score: 409
Period size: 156 Copynumber: 2.2 Consensus size: 150
74618 GGTGGCACCT
* *
74628 TTTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTA
1 TTTAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCACTCCCTA
*
74693 GTCCTTAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAG
60 GTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAG
* *
74758 AGCAGGACGCTCTCTCTTTTCAC-C-C
125 AGCAGGACGCACTCTATTTTC-CTCTC
*
74783 TTTAGTCCTCAGAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCAC-CCCTCAGTCCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTCCCT-AGTCCT
* * *
74847 CGAAGAGCAGGACGCCTGTTTCTTTTCAAAGCCCACACAAGTTGGTGGCTCTTTGTAGTCCTCAA
65 CAAAGAGCAGGACG-C-----CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAA
* *
74912 AGAGCAGGACTCACTTTATTTTCCTCTC
123 AGAGCAGGACGCACTCTATTTTCCTCTC
* *
74940 TTTTGTCCTCAAAGAGCAGGACGCATTTC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTC
74969 GTTTTCTTTT
Statistics
Matches: 162, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
148 3 0.02
149 47 0.29
150 1 0.01
155 28 0.17
156 56 0.35
157 27 0.17
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (150 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTCCCTAGTCCTC
AAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGG
ACGCACTCTATTTTCCTCTC
Found at i:75001 original size:43 final size:43
Alignment explanation
Indices: 74904--75070 Score: 164
Period size: 43 Copynumber: 3.8 Consensus size: 43
74894 GCTCTTTGTA
* * *
74904 GTCCTCAAAGAGCAGGACTCACTTT-ATTTTC---CTCTCTTTT
1 GTCCTCAAAGAGCAGGACGCA-TTTCATTTTCTTTTTCTCCTTT
*
74944 GTCCTCAAAGAGCAGGACGCATTTCGTTTTCTTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTCATTTTCTTTTTCTCCTTT
* * *
74987 GTCCTCAAAGAGCAGGACGCTCTTTTATTTCCTTCTTT-TCCCTTCT
1 GTCCTCAAAGAGCAGGACGC-ATTTCATTTTCTT-TTTCT-CCTT-T
*
75033 AGTCCTCAAAGAGCAGGACACATTTCATTTTTCTTTTT
1 -GTCCTCAAAGAGCAGGACGCATTTCA-TTTTCTTTTT
75071 TCTTTTTTCC
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
39 3 0.03
40 25 0.24
43 27 0.26
44 10 0.10
45 7 0.07
46 8 0.08
47 25 0.24
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.41
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCATTTCATTTTCTTTTTCTCCTTT
Found at i:75820 original size:19 final size:19
Alignment explanation
Indices: 75796--75857 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
75786 TTTTGAACTT
75796 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
75815 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
*
75836 CATA-AGTGTTGTATCGATA
1 CAAACAGT-TTGTATCGATA
75855 CAA
1 CAA
75858 TGTATCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:75863 original size:13 final size:13
Alignment explanation
Indices: 75845--75901 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
75835 ACATAAGTGT
75845 TGTATCGATACAA
1 TGTATCGATACAA
75858 TGTATCGATACATAA
1 TGTATCGATAC--AA
75873 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
75890 TGTATCGATACA
1 TGTATCGATACA
75902 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:75865 original size:32 final size:32
Alignment explanation
Indices: 75824--75928 Score: 201
Period size: 32 Copynumber: 3.3 Consensus size: 32
75814 ACAAACAGAA
75824 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
75856 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
75888 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
75920 AATGTATCG
1 AATGTATCG
75929 CTACGAAGCT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:75882 original size:19 final size:18
Alignment explanation
Indices: 75826--75920 Score: 93
Period size: 19 Copynumber: 5.7 Consensus size: 18
75816 AAACAGAAAA
75826 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
75845 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
75858 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
75877 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
75890 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
75909 TGTATCGATACA
1 TGTATCGATACA
75921 ATGTATCGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 34 0.53
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:75971 original size:21 final size:21
Alignment explanation
Indices: 75945--75986 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
75935 AGCTACTGCC
*
75945 AAGGAACTATATCGATACATT
1 AAGGAAATATATCGATACATT
*
75966 AAGGAAATGTATCGATACATT
1 AAGGAAATATATCGATACATT
75987 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AAGGAAATATATCGATACATT
Found at i:75991 original size:13 final size:13
Alignment explanation
Indices: 75973--75998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
75963 ATTAAGGAAA
75973 TGTATCGATACAT
1 TGTATCGATACAT
75986 TGTATCGATACAT
1 TGTATCGATACAT
75999 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:78490 original size:52 final size:52
Alignment explanation
Indices: 78355--78491 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 52
78345 TTAAGTTTCT
* * ** * *
78355 CAATTTTTCATAATCGGGGGTACTCCAATGCCAGTTTTATTTCTAAAAACAG
1 CAATTTTTCACAATCGGGGATACTCCAACCCCAGTTTTATTTCCAAAAACAC
* *
78407 TAATTTTCCACAATCGGGGATACTCCAACCCC-GATTTTATTTCCAAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCAG-TTTTATTTCCAAAAACAC
*
78459 CAATTTTTCACAATCGAGGATACTCCAACCCCA
1 CAATTTTTCACAATCGGGGATACTCCAACCCCA
78492 TTAATCATTG
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
51 1 0.01
52 71 0.99
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (52 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCAGTTTTATTTCCAAAAACAC
Found at i:78541 original size:28 final size:27
Alignment explanation
Indices: 78476--78541 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
78466 TCACAATCGA
*
78476 GGATACTCCAACCCCATTAATCATTGG
1 GGATACTCCAACCCCATTAATCATAGG
*
78503 GGATACTCCAACCCCATTATTTTC-TAGG
1 GGATACTCCAACCCCATTA--ATCATAGG
78531 GGATACTCCAA
1 GGATACTCCAA
78542 GCCCGGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 19 0.54
28 14 0.40
29 2 0.06
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
GGATACTCCAACCCCATTAATCATAGG
Found at i:78584 original size:79 final size:78
Alignment explanation
Indices: 78501--78751 Score: 335
Period size: 79 Copynumber: 3.2 Consensus size: 78
78491 ATTAATCATT
* *
78501 GGGGATACTCCAACCCCATTATTTTCTAGGGGATACTCCAAGCCCGGCTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTCTAGGGGATACTCCAACCCCGG-TTTATTCCTAAAATATT
78566 GATTTCTCATAATC
65 GATTTCTCATAATC
* *
78580 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTTCTAGGGGATACTCCAACCCCG-GTTTATTCCTAAAATATT
*
78645 GATTTCTCACAATC
65 GATTTCTCATAATC
* * *
78659 GGGGATACTCCAACCCCGTTA-TTTCTGAAGGGATACTCCAATCCCGGTTTCATTTCC-AAAACA
1 GGGGATACTCCAACCCCGTTATTTTCT-AGGGGATACTCCAACCCCGGTTT-A-TTCCTAAAATA
** *
78722 TCAATTTCTCTTAATC
63 TTGATTTCTCATAATC
*
78738 GGGGACACTCCAAC
1 GGGGATACTCCAAC
78752 TCCGATTTTA
Statistics
Matches: 153, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
78 7 0.05
79 142 0.93
80 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGTTATTTTCTAGGGGATACTCCAACCCCGGTTTATTCCTAAAATATTG
ATTTCTCATAATC
Found at i:78765 original size:51 final size:51
Alignment explanation
Indices: 78688--78853 Score: 167
Period size: 51 Copynumber: 3.3 Consensus size: 51
78678 TATTTCTGAA
* * *
78688 GGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAA-TTTCTCTTAATCG
1 GGGATACTCCAACT-CCGATTTTATTTCCAAAACATCAATTTTC-CATAATCG
* * * *
78739 GGGACACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTCCATAATCG
* * * * *
78790 GGGATACTCCAACTCTGATTTTATTTCCAAAGCATCGACTTTT-CACAATCC
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACATC-AATTTTCCATAATCG
*
78841 GGGATATTCCAAC
1 GGGATACTCCAAC
78854 CCCATTATTT
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
51 86 0.91
52 9 0.09
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTCCATAATCG
Found at i:78976 original size:181 final size:183
Alignment explanation
Indices: 78577--79105 Score: 535
Period size: 181 Copynumber: 2.9 Consensus size: 183
78567 ATTTCTCATA
* *
78577 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTCCTAAAAT
* *
78642 ATTGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCTGAAGGGATACTCCAATCCCGGT
66 A-TGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGT
* * * *
78707 TTCATTTCCAAAACATCAATTTCTCTTAATCGGGGACACTCCAACTCCGATTTTAT
130 TTTATTTCTAAAACATCAATTTCTC-T-ATCGGGGACACTCCAACTCCCATTTAAT
* **** * *** * * *
78763 TTCTAAAACAC-CCATTTTCCA-TA--ATC--GGGGATACTCCAACTCTGATTTTATTTCC-AAA
1 ATCGGGGATACTCCAACCT-CATTATTTTCGAGGGGATACTCCAACCCCGATTTTA-TTCCTAAA
** * * * *
78821 GCATCGACTTT-TCACAATCCGGGATATTCCAACCCCATTATTTCTGAGGGGACACTCCAACCCC
64 ATAT-GA-TTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCC
*
78885 GGTTTTATTTCTAAAACATCAAATTT-TC-ATC-GGGATACTCCAAC-CCCA-TTAAT
127 GGTTTTATTTCTAAAACATC-AATTTCTCTATCGGGGACACTCCAACTCCCATTTAAT
**
78938 CATCGGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAA
1 -ATCGGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAA-CCCCGATTTTATTCCTAAA
* * *
79003 ATATTAATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCG
64 ATA-TGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCG
* * *
79068 GCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGA
128 GTTTTATTTCTAAAACATCAATTTCTC-T-ATCGGGGA
79106 TACTAAACCC
Statistics
Matches: 269, Mismatches: 53, Indels: 42
0.74 0.15 0.12
Matches are distributed among these distances:
175 4 0.01
176 10 0.04
177 18 0.07
178 3 0.01
179 2 0.01
180 1 0.00
181 120 0.45
182 90 0.33
183 3 0.01
185 8 0.03
186 10 0.04
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (183 bp):
ATCGGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCCCGATTTTATTCCTAAAAT
ATGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTT
TTATTTCTAAAACATCAATTTCTCTATCGGGGACACTCCAACTCCCATTTAAT
Found at i:78982 original size:28 final size:27
Alignment explanation
Indices: 78911--78986 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
78901 CATCAAATTT
78911 TCATC-GGGATACTCCAACCCCATTAA
1 TCATCGGGGATACTCCAACCCCATTAA
*
78937 TCATCGGGGATACTCCAACCTCATT-A
1 TCATCGGGGATACTCCAACCCCATTAA
**
78963 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
78987 CGGCTTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.21
27 18 0.42
28 16 0.37
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCATTAA
Found at i:79105 original size:79 final size:79
Alignment explanation
Indices: 78939--79254 Score: 372
Period size: 79 Copynumber: 4.0 Consensus size: 79
78929 CCCATTAATC
* *
78939 ATCGGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAA-CCCCGGCTTTATTTCTAAAA
79004 TATTAATTTCTCATA
65 TATTAATTTCTCATA
* *
79019 ATTGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCATTATTTTC-GAGGGGATACTCCAACCCCGGCTTTATTTCTAAAA
79083 TATTAATTTCTCATA
65 TATTAATTTCTCATA
* * *** * *
79098 ATCGGGGATACT-AAACCCCGTTATCCCCGAGGGGATACTCCAACCCCGGTTTTATTT-TCAAAT
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
** * *
79161 CATCGATTTTTCACA
66 -ATTAATTTCTCATA
* * * *
79176 ATCGGGGATACTCCAACCCTATTATTTTCAAGGGGATACTCCAACCCC-G-TTACTATCTCCAAA
1 ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCTT--TATTTCTAAA
79239 ATATTAAATTTCTCAT
64 ATATT-AATTTCTCAT
79255 TGGGAAATAT
Statistics
Matches: 199, Mismatches: 29, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
77 7 0.04
78 61 0.31
79 84 0.42
80 47 0.24
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAT
ATTAATTTCTCATA
Found at i:79186 original size:157 final size:158
Alignment explanation
Indices: 78967--79254 Score: 379
Period size: 157 Copynumber: 1.8 Consensus size: 158
78957 TCATTATTTT
* * *
78967 CGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAATATTAATTTCTCATAATTGGGGATACTC
1 CGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAATATCAATTTCTCACAATCGGGGATACTC
* * * *
79032 CAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGGCTT-TATTTCTAAAATATT-AATTTCT
66 CAACCCCATTATTTTC-AAGGGGATACTCCAACCCC-G-TTATATCTCCAAAATATTAAATTTCT
79094 CATAATCGGGGATACTAAACCCCGTTATCCC
128 CATAATCGGGGATACTAAACCCCGTTATCCC
* * * * *
79125 CGAGGGGATACTCCAA-CCCCGGTTTTATT-TTCAAATCATCGATTTTTCACAATCGGGGATACT
1 CGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAAT-ATCAATTTCTCACAATCGGGGATACT
*
79188 CCAACCCTATTATTTTCAAGGGGATACTCCAACCCCGTTACTATCTCCAAAATATTAAATTTCTC
65 CCAACCCCATTATTTTCAAGGGGATACTCCAACCCCGTTA-TATCTCCAAAATATTAAATTTCTC
79253 AT
129 AT
79255 TGGGAAATAT
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
155 2 0.02
156 6 0.05
157 74 0.66
158 30 0.27
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (158 bp):
CGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAATATCAATTTCTCACAATCGGGGATACTC
CAACCCCATTATTTTCAAGGGGATACTCCAACCCCGTTATATCTCCAAAATATTAAATTTCTCAT
AATCGGGGATACTAAACCCCGTTATCCC
Found at i:82661 original size:21 final size:21
Alignment explanation
Indices: 82616--82662 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
82606 TCAATTTCAA
* *
82616 CAGGAAACAAGAGCCAACATT
1 CAGGAAACAAGAGACAACATC
82637 CAGGAAACAAG-GACAAGCATC
1 CAGGAAACAAGAGACAA-CATC
82658 CAGGA
1 CAGGA
82663 TTTAGGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.47, C:0.23, G:0.23, T:0.06
Consensus pattern (21 bp):
CAGGAAACAAGAGACAACATC
Done.