Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019415.1 Corchorus olitorius cultivar O-4 contig19448, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 115215
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9060 original size:4 final size:4
Alignment explanation
Indices: 9051--9075 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9041 ACAAGATGGG
9051 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
9076 AGAGGCGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:10419 original size:198 final size:198
Alignment explanation
Indices: 10081--10480 Score: 800
Period size: 198 Copynumber: 2.0 Consensus size: 198
10071 ATATGCTCTT
10081 CTACCCTCCCAAACCCTACTATCTCAGCCTTCTACTTTCTACATAAGTGTCTCAGATTGTAGATC
1 CTACCCTCCCAAACCCTACTATCTCAGCCTTCTACTTTCTACATAAGTGTCTCAGATTGTAGATC
10146 ATTTTTAGCATTTACAGTTCAAAACTTGGAACTAGAATAGAAGATCATATACCTGCCCCATTTGT
66 ATTTTTAGCATTTACAGTTCAAAACTTGGAACTAGAATAGAAGATCATATACCTGCCCCATTTGT
10211 ATCAACAAGTTTTTCCTTGGGTAACAAGATTACAGGGAACTGCGTCACTTTCCCATCCTCAGCAA
131 ATCAACAAGTTTTTCCTTGGGTAACAAGATTACAGGGAACTGCGTCACTTTCCCATCCTCAGCAA
10276 CAA
196 CAA
10279 CTACCCTCCCAAACCCTACTATCTCAGCCTTCTACTTTCTACATAAGTGTCTCAGATTGTAGATC
1 CTACCCTCCCAAACCCTACTATCTCAGCCTTCTACTTTCTACATAAGTGTCTCAGATTGTAGATC
10344 ATTTTTAGCATTTACAGTTCAAAACTTGGAACTAGAATAGAAGATCATATACCTGCCCCATTTGT
66 ATTTTTAGCATTTACAGTTCAAAACTTGGAACTAGAATAGAAGATCATATACCTGCCCCATTTGT
10409 ATCAACAAGTTTTTCCTTGGGTAACAAGATTACAGGGAACTGCGTCACTTTCCCATCCTCAGCAA
131 ATCAACAAGTTTTTCCTTGGGTAACAAGATTACAGGGAACTGCGTCACTTTCCCATCCTCAGCAA
10474 CAA
196 CAA
10477 CTAC
1 CTAC
10481 TGGATCTGCA
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 202 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (198 bp):
CTACCCTCCCAAACCCTACTATCTCAGCCTTCTACTTTCTACATAAGTGTCTCAGATTGTAGATC
ATTTTTAGCATTTACAGTTCAAAACTTGGAACTAGAATAGAAGATCATATACCTGCCCCATTTGT
ATCAACAAGTTTTTCCTTGGGTAACAAGATTACAGGGAACTGCGTCACTTTCCCATCCTCAGCAA
CAA
Found at i:22348 original size:2 final size:2
Alignment explanation
Indices: 22343--22373 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22333 ATGTAATTGC
22343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22374 CCCCTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26674 original size:45 final size:44
Alignment explanation
Indices: 26610--26699 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 44
26600 GATGATCGAT
* *
26610 ATCCAAAATGGACGTTCAAGGGCAAAAGGAAAGCAACTGTCCCAA
1 ATCCAAAATGGAAGTTCAAGGGCAAAA-AAAAGCAACTGTCCCAA
26655 ATCCAAAATGGAAGTTCAAGGGCAAAAAAAAGCAACTGTCCCAA
1 ATCCAAAATGGAAGTTCAAGGGCAAAAAAAAGCAACTGTCCCAA
26699 A
1 A
26700 CAAGATAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 17 0.40
45 26 0.60
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (44 bp):
ATCCAAAATGGAAGTTCAAGGGCAAAAAAAAGCAACTGTCCCAA
Found at i:27012 original size:12 final size:12
Alignment explanation
Indices: 26997--27021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
26987 TTCTTCTTCG
26997 TTTTTTTTTTTA
1 TTTTTTTTTTTA
27009 TTTTTTTTTTTA
1 TTTTTTTTTTTA
27021 T
1 T
27022 GGGCTAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:29195 original size:63 final size:63
Alignment explanation
Indices: 29122--29370 Score: 471
Period size: 63 Copynumber: 4.0 Consensus size: 63
29112 TGGATCTGGC
*
29122 TCAGAGCATGGTGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
*
29185 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGCGAGAGCCACTTGTAAT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
29248 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
*
29311 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGTCTCGGAAGAAGTGAGAGCCACTTGT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGT
29371 GACAATCAGC
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 182 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.19
Consensus pattern (63 bp):
TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
Found at i:31419 original size:75 final size:74
Alignment explanation
Indices: 31293--31709 Score: 475
Period size: 75 Copynumber: 5.5 Consensus size: 74
31283 ACCTCCTACA
* * * * * *
31293 TCAGCCCTGCATGGAAGGATGCCTAATCAGCAAATAGCAAATAACCCTCCGGCAATCTCACCAAA
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAAA
* *
31358 TCTACATGCG
66 CCTACAT-TG
** *
31368 TCAGCCTTGCTTGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAGA
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAAA
**
31433 CCCGCACTTG
66 CCTACA-TTG
* *
31443 TCACCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATGATCTTCCGGCAATTTCACCAGA
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCA-A
*
31508 CCCATAC-TTG
65 ACC-TACATTG
*
31518 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAACCTTCCGGCAATTTCACCAGA
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCA-A
*
31583 CCCATAC-TTG
65 ACC-TACATTG
* * *
31593 TCAGCCTTGCAAGGAAGTATGCCTAATCAGCAGCAACTAGCACATAATCTTCCGACAATTTCA-C
1 TCAGCCTTGCAAGGAAGGATGCCTAAT---CAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
*
31657 AAGATCC-GCACTTG
63 AA-A-CCTACA-TTG
*
31671 TCAGCCTTGCAAGGAAGGATGTCC-AATCAGCAATTAGCA
1 TCAGCCTTGCAAGGAAGGATG-CCTAATCAGCAACTAGCA
31710 CATACTCAAC
Statistics
Matches: 301, Mismatches: 30, Indels: 22
0.85 0.08 0.06
Matches are distributed among these distances:
75 233 0.77
76 5 0.02
77 3 0.01
78 58 0.19
79 2 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (74 bp):
TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAAA
CCTACATTG
Found at i:31576 original size:150 final size:149
Alignment explanation
Indices: 31300--31709 Score: 536
Period size: 150 Copynumber: 2.7 Consensus size: 149
31290 ACATCAGCCC
* * * * * *
31300 TGCATGGAAGGATGCCTAATCAGCAAATAGCAAATAACCCTCCGGCAATCTCACCA-AATCTACA
1 TGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAGAACCTAC-
* ** *
31364 TGCGTCAGCCTTGCTTGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCAC
65 T-TGTCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAACCTTCCGGCAATTTCAC
*
31429 CAGACCCGCACTTGTCACCCT
129 CAGACCCACACTTGTCACCCT
* *
31450 TGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATGATCTTCCGGCAATTTCACCAGACCCATAC
1 TGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAGAACC-TAC
31515 TTGTCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAACCTTCCGGCAATTTCACC
65 TTGTCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAACCTTCCGGCAATTTCACC
* *
31580 AGACCCATACTTGTCAGCCT
130 AGACCCACACTTGTCACCCT
* * * * *
31600 TGCAAGGAAGTATGCCTAATCAGCAGCAACTAGCACATAATCTTCCGACAATTTCACAAGATCCG
1 TGCAAGGAAGGATGCCTAAT---CAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAGAACC-
* *
31665 CACTTGTCAGCCTTGCAAGGAAGGATGTCC-AATCAGCAATTAGCA
62 TACTTGTCAGCCTTGCAAGGAAGGATG-CCTAATCAGCAACTAGCA
31710 CATACTCAAC
Statistics
Matches: 230, Mismatches: 24, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
150 146 0.63
151 3 0.01
152 3 0.01
153 76 0.33
154 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (149 bp):
TGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAATCTTCCGGCAATTTCACCAGAACCTACT
TGTCAGCCTTGCAAGGAAGGATGCCTAATCAGCAACTAGCAAATAACCTTCCGGCAATTTCACCA
GACCCACACTTGTCACCCT
Found at i:35554 original size:17 final size:17
Alignment explanation
Indices: 35532--35564 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35522 CTTATTTCCC
35532 TTTCGAATTATTTTTAT
1 TTTCGAATTATTTTTAT
*
35549 TTTCGAATTTTTTTTA
1 TTTCGAATTATTTTTA
35565 GTTATTGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTCGAATTATTTTTAT
Found at i:37511 original size:13 final size:12
Alignment explanation
Indices: 37478--37538 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 12
37468 TGGATTAATT
37478 TTATTACTAT-TA
1 TTATTA-TATATA
37490 TTATTATATATA
1 TTATTATATATA
37502 TTATT-TATATA
1 TTATTATATATA
*
37513 TGA-TATATATGAA
1 TTATTATATAT--A
37526 TTA-TATATATA
1 TTATTATATATA
37537 TT
1 TT
37539 GTCAATAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
10 1 0.02
11 19 0.44
12 13 0.30
13 10 0.23
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (12 bp):
TTATTATATATA
Found at i:41496 original size:18 final size:18
Alignment explanation
Indices: 41458--41496 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41448 AAGTGGGTTG
* *
41458 TTTTTGTTTTTGTTTTAT
1 TTTTTGTTTTCGTTTCAT
*
41476 TTTTTGTTTTCGTTTCCT
1 TTTTTGTTTTCGTTTCAT
41494 TTT
1 TTT
41497 CCTGAAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.08, G:0.10, T:0.79
Consensus pattern (18 bp):
TTTTTGTTTTCGTTTCAT
Found at i:42136 original size:34 final size:36
Alignment explanation
Indices: 42093--42164 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 36
42083 AATATTAAGA
*
42093 GTTCATAAAGTGTTGAACTC-TTTTTTT-TTTTTCG
1 GTTCATAAAGTGCTGAACTCTTTTTTTTCTTTTTCG
42127 GTTCATAAAGTGCTGAACTCTTTTTTTTCTTTTTCG
1 GTTCATAAAGTGCTGAACTCTTTTTTTTCTTTTTCG
42163 GT
1 GT
42165 AAGGCTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 19 0.54
35 7 0.20
36 9 0.26
ACGTcount: A:0.17, C:0.14, G:0.15, T:0.54
Consensus pattern (36 bp):
GTTCATAAAGTGCTGAACTCTTTTTTTTCTTTTTCG
Found at i:43305 original size:32 final size:32
Alignment explanation
Indices: 43268--43328 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
43258 TCCACCGCGG
**
43268 ATATATTATATAATTTACG-ATATAATATATAT
1 ATATATTATAT-ATACACGTATATAATATATAT
43300 ATATATTATATATACACGTATATAATATA
1 ATATATTATATATACACGTATATAATATA
43329 ACACAAGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (32 bp):
ATATATTATATATACACGTATATAATATATAT
Found at i:43975 original size:2 final size:2
Alignment explanation
Indices: 43970--44011 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
43960 AGTGGGTGTG
43970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44012 ATTTTTGCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45046 original size:2 final size:2
Alignment explanation
Indices: 45039--45081 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
45029 ATACCCAACC
45039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45081 A
1 A
45082 AAAGAGCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49131 original size:20 final size:19
Alignment explanation
Indices: 49106--49144 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
49096 TATGATGTTT
49106 AAATTAAATTGCCTTAAAAA
1 AAATTAAATTGCC-TAAAAA
49126 AAATTAAATTGCCTAAAAA
1 AAATTAAATTGCCTAAAAA
49145 GTACGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATTAAATTGCCTAAAAA
Found at i:49801 original size:2 final size:2
Alignment explanation
Indices: 49794--49838 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
49784 AGCAATGTAG
49794 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49836 TA T
1 TA T
49839 GTGGGCTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53234 original size:48 final size:48
Alignment explanation
Indices: 53163--53311 Score: 280
Period size: 48 Copynumber: 3.1 Consensus size: 48
53153 TAGTCCCACA
*
53163 AATCAGTGGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCAG
1 AATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCAG
53211 AATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCAG
1 AATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCAG
53259 AATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCAG
1 AATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCAG
*
53307 CATCA
1 AATCA
53312 ACATTTCGGT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 99 1.00
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (48 bp):
AATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCAG
Found at i:58696 original size:15 final size:13
Alignment explanation
Indices: 58673--58710 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
58663 GGTTTTATTG
58673 TTTTTTT-TTTTT
1 TTTTTTTCTTTTT
* *
58685 CTTTTCTCTTTTT
1 TTTTTTTCTTTTT
58698 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
58711 GGCACAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:59446 original size:22 final size:22
Alignment explanation
Indices: 59404--59446 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59394 TTTTTTTGTT
* *
59404 TTTTGTTTTTGTTTCGTTTTCG
1 TTTTGTTTTTGTTGCGCTTTCG
59426 TTTTGTTTTTGTTGCGCTTTC
1 TTTTGTTTTTGTTGCGCTTTC
59447 AATTTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.19, T:0.70
Consensus pattern (22 bp):
TTTTGTTTTTGTTGCGCTTTCG
Found at i:61414 original size:29 final size:29
Alignment explanation
Indices: 61379--61434 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
61369 AAAATTAGAA
* * *
61379 GATGTCGGTTATGTTATGTCAGATTAAAG
1 GATGTCGGTGATATTACGTCAGATTAAAG
*
61408 GATGTCGGTGATATTACGTCATATTAA
1 GATGTCGGTGATATTACGTCAGATTAA
61435 TTTGTCGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.38
Consensus pattern (29 bp):
GATGTCGGTGATATTACGTCAGATTAAAG
Found at i:73687 original size:26 final size:26
Alignment explanation
Indices: 73633--73690 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
73623 CCGAATACAT
* *
73633 TGACATGCAAGGGAGAGCTTCGAGAG
1 TGACATGCAAGGGAGAGCGTCAAGAG
* *
73659 TGACATGCAAGGGAGAGGGTCAAGTG
1 TGACATGCAAGGGAGAGCGTCAAGAG
73685 TGACAT
1 TGACAT
73691 TGTGAGCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.38, T:0.17
Consensus pattern (26 bp):
TGACATGCAAGGGAGAGCGTCAAGAG
Found at i:82506 original size:123 final size:123
Alignment explanation
Indices: 82282--82526 Score: 368
Period size: 123 Copynumber: 2.0 Consensus size: 123
82272 AGCAAAATTG
*
82282 TCCTAAATTTGGAAAATTCAGGGGGCAAATAGTCCTATTAGGCCTATAATTCAGGGGGCAAAAAG
1 TCCTAAATTTGGAAAATTCAGGGGGCAAATAGTCCTATTAGACCTATAATTCAGGGGGCAAAAAG
* *
82347 TTAATAAGCCAATTTTCTTGTCACCCTTTTAATTCATAGGACTAATGGGGAAATTGAT
66 TTAATAAACCAATTTTCTTGTCACCCTTTGAATTCATAGGACTAATGGGGAAATTGAT
* * * * *
82405 TCCTGAATTTGGAAAGTTCAGGGGGCAAATTGTCCT-TTAGACTTATAATTCA-GGGGTAAAAAG
1 TCCTAAATTTGGAAAATTCAGGGGGCAAATAGTCCTATTAGACCTATAATTCAGGGGGCAAAAA-
* *
82468 GTTAATAAACCAATTTTTCTTGTCATCCTTTGAATTCATATGACTAATGGGGAAATTGA
65 GTTAATAAACCAA-TTTTCTTGTCACCCTTTGAATTCATAGGACTAATGGGGAAATTGA
82527 ACTTGAACTT
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
121 9 0.08
122 26 0.24
123 75 0.68
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (123 bp):
TCCTAAATTTGGAAAATTCAGGGGGCAAATAGTCCTATTAGACCTATAATTCAGGGGGCAAAAAG
TTAATAAACCAATTTTCTTGTCACCCTTTGAATTCATAGGACTAATGGGGAAATTGAT
Found at i:87017 original size:3 final size:3
Alignment explanation
Indices: 87009--87034 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
86999 TTAGTGTAAA
87009 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
87035 ATTTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:87852 original size:50 final size:49
Alignment explanation
Indices: 87777--87872 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 49
87767 AATGATTCTT
*
87777 ATCTAAAAAAAAATTATGATCAAGTTTTGACTAAACTAGAAACCCAGAA
1 ATCTAAAAAAAAATTATGATAAAGTTTTGACTAAACTAGAAACCCAGAA
87826 ATCTAAAAAAAAAATTATGATAAAGTTTTGACTAAACTAGAAACCCA
1 ATCT-AAAAAAAAATTATGATAAAGTTTTGACTAAACTAGAAACCCA
87873 AAACCTTATA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 4 0.09
50 41 0.91
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (49 bp):
ATCTAAAAAAAAATTATGATAAAGTTTTGACTAAACTAGAAACCCAGAA
Found at i:89587 original size:2 final size:2
Alignment explanation
Indices: 89580--89617 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
89570 AGAAATGAAA
89580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89618 TATGAGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91719 original size:22 final size:21
Alignment explanation
Indices: 91694--91739 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
91684 AATTAAATTA
* *
91694 AATTAATTTACATATCATATAT
1 AATTAAATTAAATATCATA-AT
*
91716 AATTAAATTAAATTTCATAAT
1 AATTAAATTAAATATCATAAT
91737 AAT
1 AAT
91740 GCATGAGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAAATTAAATATCATAAT
Found at i:94045 original size:196 final size:196
Alignment explanation
Indices: 93686--94140 Score: 705
Period size: 196 Copynumber: 2.3 Consensus size: 196
93676 AGTTGTTGAG
* * * * *
93686 TGACTTGAATTTTAATGATCCGGCCAAATTAGTGATCCGAATTGACTGATTAATTGGGAGCTCGA
1 TGACTTAAATTTTGATGATCCGGCCAAATTAGTGACCCGAATTGAC----TAATTAGGAGCTCAA
*
93751 CTTGAATGGAAATTTTCATGGAGTTCTATGGTGGAAGCGGAGGGCAAGGACCATAGGTCACATTA
62 CTTGAATCGAAATTTTCATGGAGTTCTATGGTGGAAGCGGAGGGCAAGGACCATAGGTCACATTA
*
93816 ACCGGACCAGTACTTAAATCACTAGTATTCTTTAATTTTATCACTTTTAATTCTCTGTCTGATTC
127 ACCGGACCAGTACTTAAATCACTAGTATTCTTTAATCTTATCACTTTTAATTCTCTGTCTGATTC
93881 ACTAA
192 ACTAA
*
93886 TGACTTAAATTTTGATGATTCGGCCAAATTAGTGACCCGAATTGACTAATTAGGAGCTCAACTTG
1 TGACTTAAATTTTGATGATCCGGCCAAATTAGTGACCCGAATTGACTAATTAGGAGCTCAACTTG
* *
93951 AA-CGAAATTTTTCATGGAGTTCTATGGTGGAAGCGGAGGGCAAGGACCATAGGTCATATTAATC
66 AATCGAAA-TTTTCATGGAGTTCTATGGTGGAAGCGGAGGGCAAGGACCATAGGTCACATTAACC
* * * *
94015 GGACCAGTACTTAGATCACTAGTGTTCTTTAATCTTCTCACTTTTAATTCTCTGTTTGATTCACT
130 GGACCAGTACTTAAATCACTAGTATTCTTTAATCTTATCACTTTTAATTCTCTGTCTGATTCACT
*
94080 AG
195 AA
* *
94082 TGACTTAAAATTTGATGATCCGGCCAAATTAGTAACCCGAATTGACTAATTAGGAGCTC
1 TGACTTAAATTTTGATGATCCGGCCAAATTAGTGACCCGAATTGACTAATTAGGAGCTC
94141 GACCATGGAA
Statistics
Matches: 236, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
195 4 0.02
196 190 0.81
200 42 0.18
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (196 bp):
TGACTTAAATTTTGATGATCCGGCCAAATTAGTGACCCGAATTGACTAATTAGGAGCTCAACTTG
AATCGAAATTTTCATGGAGTTCTATGGTGGAAGCGGAGGGCAAGGACCATAGGTCACATTAACCG
GACCAGTACTTAAATCACTAGTATTCTTTAATCTTATCACTTTTAATTCTCTGTCTGATTCACTA
A
Found at i:101830 original size:54 final size:54
Alignment explanation
Indices: 101721--101921 Score: 330
Period size: 54 Copynumber: 3.6 Consensus size: 54
101711 CTCTAGTTTC
*
101721 TCTCTTCGTTTGCTGGTTCTTTTCTTTCTTTTTCTTGTTCGACGTTTCTCCCATTT
1 TCTCTTCGTTTGCTGGTTCTTTTC-TTC-CTTTCTTGTTCGACGTTTCTCCCATTT
101777 TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCTCCCATTT
1 TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCTCCCATTT
*
101831 TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCACCCATTTTT
1 TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCTCCCA--TTT
* *
101887 TCTCTTCGTTTGCTGTTTCTTTTCTTTCTTTCTTG
1 TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTG
101922 ATTTCCTCAC
Statistics
Matches: 139, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
54 76 0.55
55 3 0.02
56 60 0.43
ACGTcount: A:0.03, C:0.26, G:0.12, T:0.58
Consensus pattern (54 bp):
TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCTCCCATTT
Found at i:101850 original size:27 final size:27
Alignment explanation
Indices: 101766--101850 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
101756 TGTTCGACGT
101766 TTCTCCCATTTTCTCTTCGTTTGCTGG
1 TTCTCCCATTTTCTCTTCGTTTGCTGG
** * *
101793 TTCTTTTC-TTCCTT-TCTT-GTTCGAC-GT
1 TTC-TCCCATT--TTCTCTTCGTTTG-CTGG
101820 TTCTCCCATTTTCTCTTCGTTTGCTGG
1 TTCTCCCATTTTCTCTTCGTTTGCTGG
101847 TTCT
1 TTCT
101851 TTTCTTCCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 2 0.05
26 7 0.17
27 24 0.57
28 7 0.17
29 2 0.05
ACGTcount: A:0.04, C:0.28, G:0.13, T:0.55
Consensus pattern (27 bp):
TTCTCCCATTTTCTCTTCGTTTGCTGG
Found at i:101851 original size:110 final size:109
Alignment explanation
Indices: 101721--101921 Score: 332
Period size: 110 Copynumber: 1.8 Consensus size: 109
101711 CTCTAGTTTC
* *
101721 TCTCTTCGTTTGCTGGTTCTTTTCTTTCTTTTTCTTGTTCGACGTTTCTCCCA-TTTTCTCTTCG
1 TCTCTTCGTTTGCTGGTTCTTTTC-TTC-CTTTCTTGTTCGACGTTTCACCCATTTTTCTCTTCG
101785 TTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCTCCCATTT
64 TTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCTCCCATTT
101831 TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCACCCATTTTTTCTCTTCGT
1 TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCACCCA-TTTTTCTCTTCGT
* *
101896 TTGCTGTTTCTTTTCTTTCTTTCTTG
65 TTGCTGGTTCTTTTCTTCCTTTCTTG
101922 ATTTCCTCAC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
108 22 0.26
109 3 0.04
110 60 0.71
ACGTcount: A:0.03, C:0.26, G:0.12, T:0.58
Consensus pattern (109 bp):
TCTCTTCGTTTGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCACCCATTTTTCTCTTCGTT
TGCTGGTTCTTTTCTTCCTTTCTTGTTCGACGTTTCTCCCATTT
Found at i:102457 original size:18 final size:18
Alignment explanation
Indices: 102434--102480 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
102424 GTGGGTAATG
102434 CCCAGAATTTTCCAAACC
1 CCCAGAATTTTCCAAACC
* * *
102452 CCCAGAATTATGCAATCC
1 CCCAGAATTTTCCAAACC
*
102470 TCCAGAATTTT
1 CCCAGAATTTT
102481 TATAAAAACC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.28
Consensus pattern (18 bp):
CCCAGAATTTTCCAAACC
Found at i:102630 original size:99 final size:101
Alignment explanation
Indices: 102393--102663 Score: 456
Period size: 99 Copynumber: 2.7 Consensus size: 101
102383 CCCATTCTCT
*
102393 GAACCAGAACTTACCGGAGAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCCAGA
1 GAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCCAGA
* *
102458 ATTATGCAATCCTCCAGAATTTTTATAAAAACCTCCA
66 ATTTTGCAATCCTCCA-AATTTTGATAAAAACCTCCA
* *
102495 GAACCAGAACTTACCGGAAAACCGTGCTGATATGGGTAATGCCCAGAATTTTCCAAACCCCCAGA
1 GAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCCAGA
* *
102560 ATTTTGTAATCCT-C-AATTTTGATCAAAACCTCCA
66 ATTTTGCAATCCTCCAAATTTTGATAAAAACCTCCA
102594 GAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCCAGA
1 GAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCCAGA
102659 ATTTT
66 ATTTT
102664 CATCAAAACC
Statistics
Matches: 160, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
99 86 0.54
101 1 0.01
102 73 0.46
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (101 bp):
GAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCCAGA
ATTTTGCAATCCTCCAAATTTTGATAAAAACCTCCA
Found at i:102692 original size:84 final size:84
Alignment explanation
Indices: 102574--102747 Score: 330
Period size: 84 Copynumber: 2.1 Consensus size: 84
102564 TGTAATCCTC
*
102574 AATTTTGATCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCA
1 AATTTTCATCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCA
*
102639 GAATTTTCCAAACCCCCAG
66 GAATTTTCCAAACCCCCAA
102658 AATTTTCATCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCA
1 AATTTTCATCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCA
102723 GAATTTTCCAAACCCCCAA
66 GAATTTTCCAAACCCCCAA
102742 AATTTT
1 AATTTT
102748 GTAAACCTCC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (84 bp):
AATTTTCATCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCA
GAATTTTCCAAACCCCCAA
Found at i:102718 original size:183 final size:187
Alignment explanation
Indices: 102452--102857 Score: 622
Period size: 183 Copynumber: 2.2 Consensus size: 187
102442 TTTCCAAACC
* * * * *
102452 CCCAGAATTATGCAATCCTCCAGAATTTTTATAAAAACCTCCAGAACCAGAACTTACCGGAAAAC
1 CCCAGAATTTTCCAAACCCCCAGAATTTTCATAAAAACCTCCAGAACCAGAACTTACCGGAAAAC
* * *
102517 CGTGCTGATATGGGTAATGCCCAGAATTTTCCAAACCCCCAGAATTTTGTAATCCT-C-AATTTT
66 CATGCTGATATGGGTAATGCCCAGAATTTTCCAAACCCCCAAAATTTTGTAAACCTCCAAATTTT
102580 G-A-TCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATG
131 GAAGTCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATG
*
102635 CCCAGAATTTTCCAAACCCCCAGAATTTTCATCAAAACCTCCAGAACCAGAACTTACCGGAAAAC
1 CCCAGAATTTTCCAAACCCCCAGAATTTTCATAAAAACCTCCAGAACCAGAACTTACCGGAAAAC
*
102700 CATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCCAAAATTTTGTAAACCTCCAAAATTT
66 CATGCTGATATGGGTAATGCCCAGAATTTTCCAAACCCCCAAAATTTTGTAAACCTCC-AAATTT
102765 TGATCAAAAGTTCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATG
130 TG-----AAG-TCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATG
*
102829 CCCAGAATTTTCCAAACCCCCAAAATTTT
1 CCCAGAATTTTCCAAACCCCCAGAATTTT
102858 GCAAACCTCC
Statistics
Matches: 201, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
183 111 0.55
184 1 0.00
186 7 0.03
192 1 0.00
194 81 0.40
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (187 bp):
CCCAGAATTTTCCAAACCCCCAGAATTTTCATAAAAACCTCCAGAACCAGAACTTACCGGAAAAC
CATGCTGATATGGGTAATGCCCAGAATTTTCCAAACCCCCAAAATTTTGTAAACCTCCAAATTTT
GAAGTCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATG
Found at i:102745 original size:18 final size:18
Alignment explanation
Indices: 102719--102765 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
102709 GTGGGTAATG
*
102719 CCCAGAATTTTCCAAACC
1 CCCAAAATTTTCCAAACC
**
102737 CCCAAAATTTTGTAAACC
1 CCCAAAATTTTCCAAACC
*
102755 TCCAAAATTTT
1 CCCAAAATTTT
102766 GATCAAAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (18 bp):
CCCAAAATTTTCCAAACC
Found at i:102766 original size:18 final size:18
Alignment explanation
Indices: 102732--102766 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
102722 AGAATTTTCC
102732 AAACCCCCAAAATTTTGT
1 AAACCCCCAAAATTTTGT
*
102750 AAACCTCCAAAATTTTG
1 AAACCCCCAAAATTTTG
102767 ATCAAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.29
Consensus pattern (18 bp):
AAACCCCCAAAATTTTGT
Found at i:102838 original size:110 final size:110
Alignment explanation
Indices: 102666--102883 Score: 418
Period size: 110 Copynumber: 2.0 Consensus size: 110
102656 AGAATTTTCA
102666 TCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTC
1 TCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTC
* *
102731 CAAACCCCCAAAATTTTGTAAACCTCCAAAATTTTGATCAAAAGT
66 CAAACCCCCAAAATTTTGCAAACCTCCAAAATTTTCATCAAAAGT
102776 TCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTC
1 TCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTC
102841 CAAACCCCCAAAATTTTGCAAACCTCCAAAATTTTCATCAAAA
66 CAAACCCCCAAAATTTTGCAAACCTCCAAAATTTTCATCAAAA
102884 CGTCCAGAAT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 106 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.23
Consensus pattern (110 bp):
TCAAAACCTCCAGAACCAGAACTTACCGGAAAACCATGCTGATGTGGGTAATGCCCAGAATTTTC
CAAACCCCCAAAATTTTGCAAACCTCCAAAATTTTCATCAAAAGT
Found at i:102855 original size:18 final size:18
Alignment explanation
Indices: 102829--102876 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
102819 GTGGGTAATG
*
102829 CCCAGAATTTTCCAAACC
1 CCCAAAATTTTCCAAACC
*
102847 CCCAAAATTTTGCAAACC
1 CCCAAAATTTTCCAAACC
*
102865 TCCAAAATTTTC
1 CCCAAAATTTTC
102877 ATCAAAACGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (18 bp):
CCCAAAATTTTCCAAACC
Found at i:102889 original size:21 final size:21
Alignment explanation
Indices: 102860--102901 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
102850 AAAATTTTGC
102860 AAACCTCCAAAATTTTCATCA
1 AAACCTCCAAAATTTTCATCA
* *
102881 AAACGTCCAGAATTTTCATCA
1 AAACCTCCAAAATTTTCATCA
102902 TCCCAATGAC
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:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (21 bp):
AAACCTCCAAAATTTTCATCA
Found at i:103427 original size:53 final size:53
Alignment explanation
Indices: 103347--103454 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
103337 CTCTATAGGA
*
103347 GTAGATGTGAAATGGTTGTATATGGAGCAAACCATTCCATTTGTTCTTTAGAT
1 GTAGATGTGAAATGGTTGTATATGGAGCAAACCATTCCATTTGTTCTTTAAAT
* *
103400 GTAGATGTGATATGGTTGTATATGGAGCAAGCCATTCCATTTGTTCTTTAAAT
1 GTAGATGTGAAATGGTTGTATATGGAGCAAACCATTCCATTTGTTCTTTAAAT
103453 GT
1 GT
103455 GAATTTTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (53 bp):
GTAGATGTGAAATGGTTGTATATGGAGCAAACCATTCCATTTGTTCTTTAAAT
Found at i:104489 original size:38 final size:38
Alignment explanation
Indices: 104429--104505 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
104419 CTTATAAAAT
* * ** *
104429 TTTGAGCTAGTGTTGTTAAATTTTGGGTTTAATTTTAG
1 TTTGAGCTAGTCTTATTAAATTTTAAGTTCAATTTTAG
* *
104467 TTTGAGTTAGTCTTATTGAATTTTAAGTTCAATTTTAG
1 TTTGAGCTAGTCTTATTAAATTTTAAGTTCAATTTTAG
104505 T
1 T
104506 CCAAATTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.23, C:0.04, G:0.19, T:0.53
Consensus pattern (38 bp):
TTTGAGCTAGTCTTATTAAATTTTAAGTTCAATTTTAG
Found at i:107292 original size:323 final size:318
Alignment explanation
Indices: 106477--108850 Score: 1466
Period size: 323 Copynumber: 7.2 Consensus size: 318
106467 GTACAATATA
* * * * ** *
106477 TATATATTTTT-TAAATATT-TTGCAAAAAATTGAGAAAAACTTTTCGAATTAGTTTTTAGCCGA
1 TATATATTTTTCTGAATATTGTGGCAAAAAATTGTGAAAAACCTTTCGGGTCAGTTTTTAGCCGA
*
106540 AATCGTGTACTAACCATCACGGTTTTTGGCATAAAAACGCGTTTCGGACCCCAGTCTTCAGTTTT
66 AATCGTGTACTAACCATCACGGTTTTTGG-ATAAAAACGCGTTTCGG-CCCC-GACTT-AGTTTT
* *
106605 GCATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCAGTCACAA
127 GCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAA
*
106670 TGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCAATTTAATTAGAAATAAATTC
192 TGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTC
* *
106735 AGAAAAAAAA-GAAAAACGATATTTGAAGCGTGAAAACCCTTCAATGTTTTTGGCGTTGAAT
257 AGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAATCTTTTTGGCGTTGAAT
* * * *
106796 TATTTATTATTTTTGAGTATTGTGGCAAACAAATTAG-GAAAAACCCTTCGGGTCAAATTTTGCA
1 TATATATT-TTTCTGAATATTGTGGCAAA-AAATT-GTGAAAAACCTTTCGGGTC--A----G--
* * * * * ** * * *
106860 AAATTTTAGCCAAAATCGTGTACTGAGCATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCTC
55 --TTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGATAAAAACGCGTTTC-G-GCCCC
* * * * * * **
106925 GGCTCAATTTTGCATAATTTTT-GCCGCAAAGACTCCTTGAAATATCTATATTCATCGAATGAAA
116 GACTTAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
* * * * *
106989 TTTCAGCCACATTGTATATAAGAATTTGTTTTTAC-ATGCATCT-AAT-TCTTGTTTCGATTTAA
180 TCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGA-GCATCTCAATCT-TTGTTTCGATTTAA
* * *
107051 TTA-ATAATTAATTCAGGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAAT
243 TTAGA-AATAAATTCA-GAAAAAA-AA-GGAAAAACGATATTAGAAGCGTGAAAA-CCCTTCAAT
*
107115 CTTTTTGGCTTTGAAT
303 CTTTTTGGCGTTGAAT
* *
107131 TATATATTTTTCTGAATATT-TTGCAAAAAATTGTGAAAAAACTTTTCGGGTCAGTTTTTAGCCG
1 TATATATTTTTCTGAATATTGTGGCAAAAAATTGTG-AAAAACCTTTCGGGTCAGTTTTTAGCCG
* *
107195 AAATCGTGTACTAACCATCGCGGTTTTTGGTTAAAAACGCGTTTCATGGCCCCGACTTAGTTTTG
65 AAATCGTGTACTAACCATCACGGTTTTTGGATAAAAACGCGTTTC--GGCCCCGACTTAGTTTTG
* ** * *
107260 AATGATTTTTGGCAGAAAGACTTGTAGAAATATCTATATTCATCTAACCAGATCTCAGCCACAAT
128 CATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAAT
* * * * * *
107325 GGATTTAAGGATTTGATTTTACGAGTATCTGAATCTTTATTTTGATTTAATTAGAAATAAATTCC
193 GGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCA
*
107390 G-AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAAT
258 GAAAAAAAAGGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAA-TCTTTTTGGCGTTGAAT
* * *
107452 TATATATTTTTTCTGAGTATTGTGGCAAAAAAATTATGGAAAAACCTTTCGGGTCAATTTTT-G-
1 TATATA-TTTTTCTGAATATTGTGGC-AAAAAATTGT-GAAAAACCTTTCGGGTCAGTTTTTAGC
* * * * ** *** *** * *
107515 CAAAAT--TTTAGCCGAA--ATC-GGGTACTTTT-TTTTCCAACG-AAATCGTG----TAC-TAA
63 CGAAATCGTGTA--CTAACCATCACGGT--TTTTGGATAAAAACGCGTTTCG-GCCCCGACTTAG
* * * * * * * * **** * *** * *
107568 CTAT-CATGGTTTTTGGGCTA-AAA-ACGCGTTCCGGAGT-CCCGGCTTAAT-TTTGCATGATTT
123 TTTTGCATGATTTTT-GGC-AGAAAGACTCCTT--GAAATATCTATATTCATCTAACCA-AATCT
** * * * ** * * * * * * *
107628 TTGGCATAA-AGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCAGTCACGTTGTATATA
183 CAGCCACAATGGA-T--TT-AAGGATTTGTTTTTA-CG-AGC--ATCTCAAT--CTTTGT-T-T-
* ** **
107692 AGGATTTGTTTTTATGAGCATATGAATCTTATTTTGATTTAATTAGAAATTTATGCGGAAAAAAA
235 -CGA-TT-TAATTA-GA--A-AT-AA----ATTCAGA---AA--A-AAA---A---GG-AAAA--
* * * * *
107757 TGGAAAAACGATATTAGAAGCATGGACAGCCCGTCAATTTTTTTGGCGTTGAAT
273 -------ACGATATTAGAAGCGT-GAAAACCCTTCAATCTTTTTGGCGTTGAAT
* * * * * * *
107811 TATATATTTTTTCTAAATATT-TTGCAAAAAATTGAGAATAACTTTTCGAGTTAGTTTTTAGCCG
1 TATATA-TTTTTCTGAATATTGTGGCAAAAAATTGTGAAAAACCTTTCGGGTCAGTTTTTAGCCG
* * * * *
107875 AAATCGTGCACTAACCCTTCACGGTTTTTGGCTAAAAA-ACGTTTCGGGCCCCGGCTTAGTTTTG
65 AAATCGTGTACTAA-CCATCACGGTTTTTGGATAAAAACGCGTTTC-GGCCCCGACTTAGTTTTG
* * * ** *
107939 TATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTAAATTCATCTAATTAAATCTCAGTCACAAT
128 CATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAAT
*
108004 GGATTTAAGGATTT-TTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCG
193 GGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCA
* * * *
108068 GAAAAAAAAGGGAAAACGATATTAGAAGCGTGAAAAACCTTCAATTTTTGTTTGGCGTTAAAT
258 GAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAA-TCTT-TTTGGCGTTGAAT
* * * * *
108131 TATATATTTTTTTTTTCTGAGTATTGTGGCAAAAAGTTTATAAAAAAACTTTTCGGGTCAGTTTT
1 TATATA-----TTTTTCTGAATATTGTGGCAAAAA-ATTGT-GAAAAACCTTTCGGGTCAGTTTT
* * * ** * * **
108196 T-G-CAAAATTTTAACG-GAAACTTGTGTACGTTAACGGTTTTTGGCTAAAAACGCGTTAAGGAG
59 TAGCCGAAA---T--CGTG-TAC---T-AACCATCACGGTTTTTGGATAAAAACGCGTT-TCG-G
* * * * * *
108258 TCCTGGCTCAATTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCAAAC
112 CCCCGACTTAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAAC
* * * *
108322 CAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACTAGCATCTGAATC-TTGTTTCGATTT
176 CAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTT
* *****
108386 AATTAGAAATTAATTCAGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAGGTAGT-ACAT
241 AATTAGAAATAAATTCAGAAAAAA-AA-GGAAAAACGATATTAGAAGCGTGAAAACCCTTCA-AT
*
108450 TTTTTTGGCGTTGAAT
303 CTTTTTGGCGTTGAAT
* * * * *
108466 TATATATTTTTTCTGAATATT-TGGCAAAAAATTGAGAAAAAACTTTTCTGATTAGTTTTTAGCC
1 TATATA-TTTTTCTGAATATTGTGGCAAAAAATTGTG-AAAAACCTTTCGGGTCAGTTTTTAGCC
* * * * * * *
108530 AAAATCGTGTACTAACTATTACTGTTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGACTCATTTT
64 GAAATCGTGTACTAACCATCAC-GGTTTTTGGATAAAAACGCGTTTC--GGCCCCGACTTAGTTT
* * * * *
108595 TGCATGATTTTTCGTAGAAAGAATCCTTGAAATATCTACATTCATCTAACCAAATCTCAGCCAAA
126 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
* *
108660 ATAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATT
191 ATGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATT
* *
108725 CGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAAT
256 CAGAAAAAAAA-GGAAAAACGATATTAGAAGCGTG-AAAACCCTTCAATCTTTTTGGCGTTGAAT
* * * * * * *
108790 TATTTATTCTTTC-AAAGTAATGTGGCAAAAAATTGAGAAAAAACCCTTCGGCTCAATTTTT
1 TATATATT-TTTCTGAA-TATTGTGGCAAAAAATTGTG-AAAAACCTTTCGGGTCAGTTTTT
108851 GCAAAATTTT
Statistics
Matches: 1581, Mismatches: 312, Indels: 318
0.72 0.14 0.14
Matches are distributed among these distances:
312 17 0.01
313 25 0.02
314 6 0.00
315 2 0.00
316 8 0.01
317 3 0.00
318 11 0.01
319 31 0.02
320 68 0.04
321 37 0.02
322 41 0.03
323 306 0.19
324 146 0.09
325 50 0.03
326 9 0.01
327 24 0.02
328 9 0.01
329 30 0.02
330 46 0.03
331 112 0.07
332 27 0.02
333 81 0.05
334 43 0.03
335 164 0.10
336 26 0.02
337 31 0.02
338 2 0.00
341 7 0.00
343 1 0.00
344 3 0.00
345 2 0.00
346 2 0.00
347 2 0.00
349 2 0.00
350 6 0.00
351 6 0.00
352 2 0.00
354 1 0.00
355 1 0.00
356 24 0.02
357 9 0.01
358 18 0.01
359 36 0.02
360 32 0.02
361 11 0.01
362 8 0.01
363 5 0.00
364 2 0.00
365 5 0.00
366 24 0.02
367 17 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (318 bp):
TATATATTTTTCTGAATATTGTGGCAAAAAATTGTGAAAAACCTTTCGGGTCAGTTTTTAGCCGA
AATCGTGTACTAACCATCACGGTTTTTGGATAAAAACGCGTTTCGGCCCCGACTTAGTTTTGCAT
GATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGA
TTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCAGAA
AAAAAAGGAAAAACGATATTAGAAGCGTGAAAACCCTTCAATCTTTTTGGCGTTGAAT
Found at i:108207 original size:683 final size:682
Alignment explanation
Indices: 106872--108933 Score: 1902
Period size: 683 Copynumber: 3.1 Consensus size: 682
106862 ATTTTAGCCA
* *
106872 AAATCGTGTACTGAGC-ATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCTCGGCTCAATTTT
1 AAATCGTGTACT-AACTATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTT
* * ** *
106936 GCATAATTTTTGCCGCAAAGACTCCTTGAAATATCTATATTCATCGAATGAAATTTCAGCCACAT
65 GCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAT
* *
107001 TGTATATAAGAATTTGTTTTTACATGCATCT-AATTCTTGTTTCGATTTAATTA-ATAATTAATT
130 TGTATATAAGGATTTGTTTTTATA-GCATCTGAA-TCTTGTTTCGATTTAATTAGA-AATTAATT
* * *
107064 CAGGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGCTTTGA
192 CAGG-AAAAATAATGGAAAAACGATATTAGAAGCGTGGAAAGGCCGTCAATTTTTTTGGCGTTGA
* * *
107129 ATTATATA-TTTTTCTGAATATTTTGCAAAAAATTGTGAAAAAACTTTTCGGGTCAGTTTTTAGC
256 ATTATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAACTTTTCGAGTTAGTTTTTAGC
* * * *
107193 CGAAATCGTGTACTAA-CCATCGCGGTTTTTGGTTAAAAACGCGTTTCATGGCCCCGACTTAGTT
321 CGAAATCGTGTACTAACCCTTCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCCCGACTTAGTT
** * * *
107257 TTGAATGATTTTTGGCAGAAAGACTTGTAGAAATATCTATATTCATCTAACCAGATCTCAGCCAC
385 TTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGCCAC
* * * *
107322 AATGGATTTAAGGATTTGATTTTACGAGTATCTGAATCTTTATTTTGATTTAATTAGAAATAAAT
450 AATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAAT
*
107387 TCCG-AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAA
515 TCGGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTT-AA
* *
107451 TTATATA---TTTTTTCTGAGTATTGTGGCAAAAAAATTATGGAAAAACCTTTCGGGTCAATTTT
579 TTATATATTTTTTTTTCTGAGTATTGTGGCAAAAAATTTATGAAAAAACCTTTCGGGTCAATTTT
107513 TGCAAAATTTTAGCCGAAATCGGGTACTTTTTTTTCCAAC
644 TGCAAAATTTTAG-CGAAATCGGGTACTTTTTTTTCCAAC
* * * *
107553 GAAATCGTGTACTAACTATCATGGTTTTTGGGCTAAAAACGCGTTCCGGAGTCCCGGCTTAATTT
1 -AAATCGTGTACTAACTATCACGATTTTT-GCCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTT
** * * *
107618 TGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGTACCAAATCTCAGTCACG
64 TGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACA
* * * * *
107683 TTGTATATAAGGATTTGTTTTTATGAGCATATGAATCTTATTTTGATTTAATTAGAAATTTATGC
129 TTGTATATAAGGATTTGTTTTTAT-AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC
* * *
107748 -GGAAAAA-AATGGAAAAACGATATTAGAAGCATGGACAGCCCGTCAATTTTTTTGGCGTTGAAT
193 AGGAAAAATAATGGAAAAACGATATTAGAAGCGTGGAAAGGCCGTCAATTTTTTTGGCGTTGAAT
* *
107811 TATATATTTTTTCTAAATATTTTGCAAAAAATTGAG-AATAACTTTTCGAGTTAGTTTTTAGCCG
258 TATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAACTTTTCGAGTTAGTTTTTAGCCG
* * *
107875 AAATCGTGCACTAACCCTTCACGGTTTTTGGCTAAAAA-ACGTTTCGGGCCCCGGCTTAGTTTTG
323 AAATCGTGTACTAACCCTTCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGACTTAGTTTTG
* * ** *
107939 TATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTAAATTCATCTAATTAAATCTCAGTCACAAT
388 AATGATTTTTGGCAGAAAGACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGCCACAAT
*
108004 GGATTTAAGGATTT-TTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCG
453 GGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCG
*
108068 GAAAAAAAAGGGAAAACGATATTAGAAGCGTGAAAAA-CCTTCAATTTTTGTTTGGCGTTAAATT
518 GAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTT-TTTGGCGTT-AATT
* * * *
108132 ATATATTTTTTTTTTCTGAGTATTGTGGCAAAAAGTTTATAAAAAAACTTTTCGGGTCAGTTTTT
581 ATATA-TTTTTTTTTCTGAGTATTGTGGCAAAAAATTTATGAAAAAACCTTTCGGGTCAATTTTT
108197 GCAAAATTTT-----AA-C-GG-A-----------AAC
645 GCAAAATTTTAGCGAAATCGGGTACTTTTTTTTCCAAC
* * * ** *
108216 ---TTGTGTACGT---TA--ACGGTTTTTGGCTAAAAACGCGTTAAGGAGTCCTGGCTCAATTTT
1 AAATCGTGTAC-TAACTATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCCCGG--C-----T
* ** * ** * * * *
108273 GCATGATTTTTGGCGCAAAGACTCCTT---G-AAATATCTATATTCATCAA-A-CCAAATCTCAG
58 -CA--A-TTTT---GC-ATGA-TTTTTGGCGCAAAGA-CT-CCTTGA--AATATCTATAT-TCAT
* **** * * * * * * * * ** * ** **
108332 CCACATTGGATATAAG-GA-TTTGTTTTTACTAGCATCTGAATCT-T-GTTTC-G-AT-TTAATT
109 CGA-ACCAAATCTCAGCCACATTGTATATA--AGGATTTGTTTTTATAGCATCTGAATCTTGTTT
* * * * *
108390 AGAAATTAATTCAGAAA--AAATAATGGAAAAA-C----------GATATTAGAAGCGT-GAAAG
171 CG-ATTTAATT-AGAAATTAATTCA-GGAAAAATAATGGAAAAACGATATTAGAAGCGTGGAAAG
** *
108441 GTAGT-ACATTTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTGGCAAAAAATTGAGAAA
233 GCCGTCA-ATTTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAA
* ** *
108505 AAACTTTTCTGA-TTAGTTTTTAGCCAAAATCGTGTACTAACTATT-ACTGTTTTTTGGCTAAAA
297 AAACTTTTC-GAGTTAGTTTTTAGCCGAAATCGTGTACTAACCCTTCAC-GGTTTTTGGCTAAAA
* * * * * *
108568 ACGCGTTTCGAGGCCCCGACTCATTTTTGCATGATTTTTCGTAGAAAGAATCCTTGAAATATCTA
360 ACGCGTTTCG-GGCCCCGACTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTA
* * *
108633 CATTCATCTAACCAAATCTCAGCCAAAATAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
424 AATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
108698 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
489 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAA
* * ** *
108763 AACCCTTCAA-TTTTTTTGGCGTTGAA-T-TAT-TTATTCTTTCAAAGTAATGTGGCAAAAAATT
553 AACCCTTCAATTTTTTTTGGCGTT-AATTATATATTTTTTTTTCTGAGTATTGTGGCAAAAAATT
* * * * *
108824 GA-GAAAAAACCCTTCGGCTCAATTTTTGCAAAATTTTAGTCGAAATTGTGTACTTTTTTTTTTG
617 TATGAAAAAACCTTTCGGGTCAATTTTTGCAAAATTTTAG-CGAAATCGGGTAC--TTTTTTTT-
108888 CCAAC
678 CCAAC
* * *
108893 AAAATCTTGTACTTACCATCACGATTTTTGCCTAAAAACGC
1 -AAATCGTGTACTAACTATCACGATTTTTGCCTAAAAACGC
108934 ATTTCTGAGT
Statistics
Matches: 1137, Mismatches: 160, Indels: 163
0.78 0.11 0.11
Matches are distributed among these distances:
654 55 0.05
655 94 0.08
656 68 0.06
657 14 0.01
658 84 0.07
659 76 0.07
660 34 0.03
661 8 0.01
662 2 0.00
663 4 0.00
664 8 0.01
665 13 0.01
666 17 0.01
667 4 0.00
668 16 0.01
669 10 0.01
670 19 0.02
674 1 0.00
675 2 0.00
676 1 0.00
677 5 0.00
678 57 0.05
679 138 0.12
680 101 0.09
681 60 0.05
682 24 0.02
683 199 0.18
684 4 0.00
685 19 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (682 bp):
AAATCGTGTACTAACTATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTG
CATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATT
GTATATAAGGATTTGTTTTTATAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGG
AAAAATAATGGAAAAACGATATTAGAAGCGTGGAAAGGCCGTCAATTTTTTTGGCGTTGAATTAT
ATATTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAACTTTTCGAGTTAGTTTTTAGCCGAAA
TCGTGTACTAACCCTTCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGACTTAGTTTTGAAT
GATTTTTGGCAGAAAGACTCCTTGAAATATCTAAATTCATCTAACCAAATCTCAGCCACAATGGA
TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAA
AAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTAATTATATA
TTTTTTTTTCTGAGTATTGTGGCAAAAAATTTATGAAAAAACCTTTCGGGTCAATTTTTGCAAAA
TTTTAGCGAAATCGGGTACTTTTTTTTCCAAC
Found at i:108833 original size:654 final size:650
Alignment explanation
Indices: 106475--108861 Score: 3011
Period size: 654 Copynumber: 3.6 Consensus size: 650
106465 GGGTACAATA
106475 TATATATATTTTT-TAAATATTTTGCAAAAAATTGAGAAAAACTTTTCGAATTAGTTTTTAGCCG
1 TATATAT-TTTTTCTAAATATTTTGCAAAAAATTGAGAAAAACTTTTCG-ATTAGTTTTTAGCCG
* *
106539 AAATCGTGTACTAACCATCACGGTTTTTGGCATAAAAACGCGTTTCGGACCCCAGTCTTCAGTTT
64 AAATCGTGTACTAACCATCACGGTTTTTGGC-TAAAAACGCGTTTCGGGCCCC-GAC-TCAGTTT
*
106604 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCAGTCACA
126 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCAGCCACA
*
106669 ATGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCAATTTAATTAGAAATAAATT
191 ATGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATT
* * *
106734 CAGAAAAAAAA-GAAAAACGATATTTGAAGCGTG-AAAACCCTTCAA-TGTTTTTGGCGTTGAAT
256 CGGAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAAT
* *
106796 TATTTATTATTTT-TGAGTATTGTGGCAAACAAATTA-GGAAAAACCCTTCGGGTCAAATTTTGC
321 TATTTATT-TTTTCTGAGTATTGTGGCAAA-AAATTATGAAAAAACCCTTCGGGTCAATTTTTGC
* * * * * * *
106859 AAAATTTTAGC-CAAAATCGTGTACTGAGCATCACGATTTTTGCCTAAAAACGCGTTCCGGAGT-
384 AAAATTTTAACGGAAACTCGTGTAC---G-TTAACGGTTTTTGGCTAAAAACGCGTTCCGGAGTC
* * **
106922 CTCGGCTCAATTTTGCATAATTTTTGCCGCAAAGACTCCTTGAAATATCTATATTCATCGAATGA
445 CT-GGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCA
* *
106987 AATTTCAGCCACATTGTATATAAGAATTTGTTTTTAC-ATGCATCT-AATTCTTGTTTCGATTTA
509 AATCTCAGCCACATTGTATATAAGGATTTGTTTTTACTA-GCATCTGAA-TCTTGTTTCGATTTA
107050 ATTA-ATAATTAATTCAGGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAA
572 ATTAGA-AATTAATTCA-GAAAAAATAATGGAAAAACGATATTAGAAGCGTG-AAAGGCCGTCAA
* *
107114 TCTTTTTGGCTTTGAAT
634 TTTTTTTGGCGTTGAAT
* * * *
107131 TATATA-TTTTTCTGAATATTTTGCAAAAAATTGTGAAAAAACTTTTCGGGTCAGTTTTTAGCCG
1 TATATATTTTTTCTAAATATTTTGCAAAAAATTGAG-AAAAACTTTTC-GATTAGTTTTTAGCCG
* * * *
107195 AAATCGTGTACTAACCATCGCGGTTTTTGGTTAAAAACGCGTTTCATGGCCCCGACTTAGTTTTG
64 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCCCGACTCAGTTTTG
* ** * * *
107260 AATGATTTTTGGCAGAAAGACTTGTAGAAATATCTATATTCATCTAACCAGATCTCAGCCACAAT
128 CATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCAGCCACAAT
* * * * * *
107325 GGATTTAAGGATTTGATTTTACGAGTATCTGAATCTTTATTTTGATTTAATTAGAAATAAATTCC
193 GGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCG
107390 G-AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTA
258 GAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTA
* * *
107454 TATATTTTTTCTGAGTATTGTGGCAAAAAAATTATGGAAAAACCTTTCGGGTCAATTTTTGCAAA
323 TTTATTTTTTCTGAGTATTGTGGC-AAAAAATTATGAAAAAACCCTTCGGGTCAATTTTTGCAAA
*
107519 ATTTTAGCCGAAATCGGGTACTTTTTTTTCCAACGAAATCGTGTAC-TAACTATCATGGTTTTTG
387 ATTTT------AA-C-GG-A-----------AAC----TCGTGTACGT---TA--ACGGTTTTT-
* * **
107583 GGCTAAAAACGCGTTCCGGAGTCCCGGCTTAATTTTGCATGATTTTTGGCATAAAGACTCCTTGA
422 GGCTAAAAACGCGTTCCGGAGTCCTGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGA
* * *
107648 AATATCTATATTCATCGTACCAAATCTCAGTCACGTTGTATATAAGGATTTGTTTTTA-TGAGCA
487 AATATCTATATTCATCGAACCAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTACT-AGCA
* * * * * *
107712 TATGAATCTTATTTTGATTTAATTAGAAATTTATGC-GGAAAAA-AATGGAAAAACGATATTAGA
551 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAATGGAAAAACGATATTAGA
* * *
107775 AGCATGGACAGCCCGTCAATTTTTTTGGCGTTGAAT
616 AGCGT-GAAAGGCCGTCAATTTTTTTGGCGTTGAAT
*
107811 TATATATTTTTTCTAAATATTTTGCAAAAAATTGAGAATAACTTTTCGAGTTAGTTTTTAGCCGA
1 TATATATTTTTTCTAAATATTTTGCAAAAAATTGAGAAAAACTTTTCGA-TTAGTTTTTAGCCGA
* * * * * *
107876 AATCGTGCACTAACCCTTCACGGTTTTTGGCTAAAAA-ACGTTTCGGGCCCCGGCTTAGTTTTGT
65 AATCGTGTACTAA-CCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGACTCAGTTTTGC
* ** *
107940 ATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTAAATTCATCTAATTAAATCTCAGTCACAATG
129 ATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCAGCCACAATG
108005 GATTTAAGGATTT-TTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCGG
194 GATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCGG
* *
108069 AAAAAAAAGGGAAAACGATATTAGAAGCGTGAAAAA-CCTTCAATTTTTGTTTGGCGTTAAATTA
259 AAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTT-TTTGGCGTT-GA--A
* * * ** *
108133 TATATTTTTTTTTTCTGAGTATTGTGGCAAAAAGTTTATAAAAAAACTTTTCGGGTCAGTTTTTG
320 T-TATTTATTTTTTCTGAGTATTGTGGCAAAAA-ATTATGAAAAAACCCTTCGGGTCAATTTTTG
* **
108198 CAAAATTTTAACGGAAACTTGTGTACGTTAACGGTTTTTGGCTAAAAACGCGTTAAGGAGTCCTG
383 CAAAATTTTAACGGAAACTCGTGTACGTTAACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCTG
*
108263 GCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATC
448 GCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATC
*
108328 TCAGCCACATTGGATATAAGGATTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAGA
513 TCAGCCACATTGTATATAAGGATTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAGA
**
108393 AATTAATTCAGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAGGTAGT-ACATTTTTTTG
578 AATTAATTCAGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAGGCCGTCA-ATTTTTTTG
108457 GCGTTGAAT
642 GCGTTGAAT
* * *
108466 TATATATTTTTTCTGAATATTTGGCAAAAAATTGAGAAAAAACTTTTCTGATTAGTTTTTAGCCA
1 TATATATTTTTTCTAAATATTTTGCAAAAAATTGAG-AAAAACTTTTC-GATTAGTTTTTAGCCG
* * * *
108531 AAATCGTGTACTAACTATTACTGTTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGACTCATTTTT
64 AAATCGTGTACTAACCATCAC-GGTTTTTGGCTAAAAACGCGTTTCG-GGCCCCGACTCAGTTTT
* * * * * *
108596 GCATGATTTTTCGTAGAAAGAATCCTTGAAATATCTACATTCATCTAACCAAATCTCAGCCAAAA
127 GCATGATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCAGCCACAA
* *
108661 TAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTC
192 TGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTC
108726 GGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTTTGGCGTTGAAT
257 GGAAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAAT
* ** * *
108790 TATTTATTCTTTCAAAGTAATGTGGCAAAAAATTGA-GAAAAAACCCTTCGGCTCAATTTTTGCA
321 TATTTATTTTTTCTGAGTATTGTGGCAAAAAATT-ATGAAAAAACCCTTCGGGTCAATTTTTGCA
108854 AAATTTTA
385 AAATTTTA
108862 GTCGAAATTG
Statistics
Matches: 1500, Mismatches: 160, Indels: 144
0.83 0.09 0.08
Matches are distributed among these distances:
653 7 0.00
654 332 0.22
655 157 0.10
656 183 0.12
657 48 0.03
658 84 0.06
659 74 0.05
660 32 0.02
661 7 0.00
663 4 0.00
664 1 0.00
667 1 0.00
674 1 0.00
675 2 0.00
676 1 0.00
677 2 0.00
678 59 0.04
679 130 0.09
680 99 0.07
681 54 0.04
682 22 0.01
683 195 0.13
684 5 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (650 bp):
TATATATTTTTTCTAAATATTTTGCAAAAAATTGAGAAAAACTTTTCGATTAGTTTTTAGCCGAA
ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGACTCAGTTTTGCAT
GATTTTTGGCAGAAAGACTCCTTGAAATAGCTATATTCATCTAACCAAATCTCAGCCACAATGGA
TTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAA
AAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTATTT
ATTTTTTCTGAGTATTGTGGCAAAAAATTATGAAAAAACCCTTCGGGTCAATTTTTGCAAAATTT
TAACGGAAACTCGTGTACGTTAACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCTGGCTCAATT
TTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCAC
ATTGTATATAAGGATTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
CAGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAGGCCGTCAATTTTTTTGGCGTTGAAT
Found at i:110986 original size:30 final size:31
Alignment explanation
Indices: 110950--111018 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 31
110940 ACTGTGCTAA
110950 TTGTTGTTGCT-GTTGTTGGAGTATTTGCTG
1 TTGTTGTTGCTAGTTGTTGGAGTATTTGCTG
*
110980 TTGTTG-TACTAGTTGTTGGAGTATTTGCTG
1 TTGTTGTTGCTAGTTGTTGGAGTATTTGCTG
*
111010 TTGCTGTTG
1 TTGTTGTTG
111019 TGCTTGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 30 0.88
31 1 0.03
ACGTcount: A:0.09, C:0.07, G:0.32, T:0.52
Consensus pattern (31 bp):
TTGTTGTTGCTAGTTGTTGGAGTATTTGCTG
Found at i:111011 original size:15 final size:15
Alignment explanation
Indices: 110963--111012 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
110953 TTGTTGCTGT
110963 TGTTGGAGTATTTGC
1 TGTTGGAGTATTTGC
** * * *
110978 TGTTGTTGTACTAGT
1 TGTTGGAGTATTTGC
110993 TGTTGGAGTATTTGC
1 TGTTGGAGTATTTGC
111008 TGTTG
1 TGTTG
111013 CTGTTGTGCT
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.12, C:0.06, G:0.32, T:0.50
Consensus pattern (15 bp):
TGTTGGAGTATTTGC
Found at i:112472 original size:18 final size:18
Alignment explanation
Indices: 112449--112487 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
112439 GTAACTTCAC
112449 TTTACATAATTATTGTTT
1 TTTACATAATTATTGTTT
112467 TTTACATAATTATTGTTT
1 TTTACATAATTATTGTTT
112485 TTT
1 TTT
112488 TATAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTACATAATTATTGTTT
Found at i:112809 original size:107 final size:107
Alignment explanation
Indices: 112623--112834 Score: 334
Period size: 107 Copynumber: 2.0 Consensus size: 107
112613 CAATTATTGT
*
112623 CGGGTACGGTTTGGAGGAACCTAATCGTAACTAGACATATTAAAAGGTCGGGCTATCCACCAAAA
1 CGGGTACGGTTTGGAGGAACCTAATCGTAACTAGAAATATTAAAAGGTCGGGCTATCCACCAAAA
112688 CCCGTAAGCCCACCTGATATTTAGGAGGACTTAGACAACAGA
66 CCCGTAAGCCCACCTGATATTTAGGAGGACTTAGACAACAGA
* * * * *
112730 CGGGTCCGGTTTGGAGGAACCTAATCGTAACTAGAAATTTTCAAGGGTCGGGCTATCCACCAAAG
1 CGGGTACGGTTTGGAGGAACCTAATCGTAACTAGAAATATTAAAAGGTCGGGCTATCCACCAAAA
* * * *
112795 TCCGTCAGTCCACCTGATATTTAGGAGGACTTGGACAACA
66 CCCGTAAGCCCACCTGATATTTAGGAGGACTTAGACAACA
112835 TAATGAAGTC
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 95 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (107 bp):
CGGGTACGGTTTGGAGGAACCTAATCGTAACTAGAAATATTAAAAGGTCGGGCTATCCACCAAAA
CCCGTAAGCCCACCTGATATTTAGGAGGACTTAGACAACAGA
Found at i:113073 original size:31 final size:31
Alignment explanation
Indices: 113038--113099 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
113028 TGTTAGAAAA
113038 AATAAGGATATAATAGACGTTTCAAAAGTTT
1 AATAAGGATATAATAGACGTTTCAAAAGTTT
* *
113069 AATAAGGGTATAATAGGCGTTTCAAAAGTTT
1 AATAAGGATATAATAGACGTTTCAAAAGTTT
113100 TACAAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (31 bp):
AATAAGGATATAATAGACGTTTCAAAAGTTT
Done.