Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 121 of 199
Found at i:40056520 original size:21 final size:21
Alignment explanation
Indices: 40056496--40056547 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40056486 TTAATCACTT
*
40056496 TAATATTAAACTA-ATATAATA
1 TAATATTAAACAAGATA-AATA
* *
40056517 TAATATTTATCAAGATAAATA
1 TAATATTAAACAAGATAAATA
40056538 TAATATTAAA
1 TAATATTAAA
40056548 TATAATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATATTAAACAAGATAAATA
Found at i:40056549 original size:12 final size:12
Alignment explanation
Indices: 40056532--40056560 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40056522 TTTATCAAGA
40056532 TAAATATAATAT
1 TAAATATAATAT
40056544 TAAATATAATAT
1 TAAATATAATAT
40056556 TAAAT
1 TAAAT
40056561 CTTATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATATAATAT
Found at i:40056659 original size:25 final size:27
Alignment explanation
Indices: 40056604--40056659 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
40056594 TAAGCATTAA
*
40056604 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAATTTAATATTAAGAAAATCACT
* *
40056631 -TTAATTTTAA-ATTAATAAAAT-ACT
1 ATTAAATTTAATATTAAGAAAATCACT
40056655 ATTAA
1 ATTAA
40056660 GATAACTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTAAATTTAATATTAAGAAAATCACT
Found at i:40057979 original size:12 final size:11
Alignment explanation
Indices: 40057959--40058015 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
40057949 CGCCACAAGT
40057959 GAATTAATTCA
1 GAATTAATTCA
*
40057970 CGAATGAATTCA
1 -GAATTAATTCA
40057982 GAATTAATTCA
1 GAATTAATTCA
** *
40057993 CGAACGAATTTA
1 -GAATTAATTCA
40058005 GAATTAATTCA
1 GAATTAATTCA
40058016 TCTTGGATCT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
11 18 0.50
12 18 0.50
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (11 bp):
GAATTAATTCA
Found at i:40057989 original size:23 final size:23
Alignment explanation
Indices: 40057959--40058015 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
40057949 CGCCACAAGT
*
40057959 GAATTAATTCACGAATGAATTCA
1 GAATTAATTCACGAACGAATTCA
*
40057982 GAATTAATTCACGAACGAATTTA
1 GAATTAATTCACGAACGAATTCA
40058005 GAATTAATTCA
1 GAATTAATTCA
40058016 TCTTGGATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (23 bp):
GAATTAATTCACGAACGAATTCA
Found at i:40059130 original size:20 final size:20
Alignment explanation
Indices: 40059106--40059157 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
40059096 TCGAAATGCT
*
40059106 AACAGAGGCATTAAAGCGCA
1 AACAGAGGCATCAAAGCGCA
* *
40059126 TACAGAGGCATCAAAGTGCA
1 AACAGAGGCATCAAAGCGCA
*
40059146 AACAAAGGCATC
1 AACAGAGGCATC
40059158 GTGTAACAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
AACAGAGGCATCAAAGCGCA
Found at i:40059865 original size:24 final size:24
Alignment explanation
Indices: 40059794--40059919 Score: 118
Period size: 22 Copynumber: 5.3 Consensus size: 24
40059784 CACTAATGAA
* *
40059794 CAGAGAGCACTAAAGTGCT-ATA-
1 CAGAGAGCACTAACGTGCTAAAAT
*
40059816 CAGAGAGCAC-ATATGTGCT-AAA-
1 CAGAGAGCACTA-ACGTGCTAAAAT
*
40059838 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACTAACGTGCTAAAAT
* * * *
40059862 CAGAGAGCACCAACGTACTAGTAGT
1 CAGAGAGCACTAACGTGCTA-AAAT
40059887 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCTAA-AAT
40059912 CAGAGAGC
1 CAGAGAGC
40059920 GCGCTAAAGT
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
21 1 0.01
22 34 0.40
23 3 0.04
24 17 0.20
25 30 0.35
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.17
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTAAAAT
Found at i:40059895 original size:25 final size:25
Alignment explanation
Indices: 40059838--40059919 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
40059828 ATGTGCTAAA
** *
40059838 CAGAGAGCACTGACGTGCTAA-AAT
1 CAGAGAGCACCAACGTACTAATAAT
* *
40059862 CAGAGAGCACCAACGTACTAGTAGT
1 CAGAGAGCACCAACGTACTAATAAT
* *
40059887 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACCAACGTACTAATAAT
40059912 CAGAGAGC
1 CAGAGAGC
40059920 GCGCTAAAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
24 17 0.35
25 31 0.65
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACGTACTAATAAT
Found at i:40061024 original size:13 final size:13
Alignment explanation
Indices: 40061006--40061045 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
40060996 TTGTTTTATG
40061006 TATATAATAATAA
1 TATATAATAATAA
40061019 TATAT-ATAATAA
1 TATATAATAATAA
40061031 TAATATAAT-ATAA
1 T-ATATAATAATAA
40061044 TA
1 TA
40061046 ACTTACTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.36
13 14 0.56
14 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATAATAATAA
Found at i:40061032 original size:18 final size:16
Alignment explanation
Indices: 40061007--40061046 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
40060997 TGTTTTATGT
40061007 ATATAATAATAATAT-
1 ATATAATAATAATATA
40061022 ATATAATAATAATATA
1 ATATAATAATAATATA
40061038 ATATAATAA
1 ATATAATAA
40061047 CTTACTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:40061040 original size:5 final size:5
Alignment explanation
Indices: 40061007--40061045 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
40060997 TGTTTTATGT
40061007 ATATA ATAATA ATAT- ATATA ATAATA ATATA ATATA ATA
1 ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATA
40061046 ACTTACTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.13
5 17 0.55
6 10 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:40062266 original size:9 final size:9
Alignment explanation
Indices: 40062209--40062266 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
40062199 TTTGGTTAAA
*
40062209 AATTAACTG
1 AATTAACCG
40062218 AATTAACCG
1 AATTAACCG
* *
40062227 AATTCACTG
1 AATTAACCG
*
40062236 AATTACCCG
1 AATTAACCG
*
40062245 AATTAATCG
1 AATTAACCG
*
40062254 AATTAACCA
1 AATTAACCG
40062263 AATT
1 AATT
40062267 GAATCACTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:40062423 original size:13 final size:13
Alignment explanation
Indices: 40062407--40062431 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40062397 AATTTTTATG
40062407 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
40062420 ATTGGGTTGGGT
1 ATTGGGTTGGGT
40062432 TGGATACTTG
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:40062431 original size:18 final size:19
Alignment explanation
Indices: 40062408--40062455 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
40062398 ATTTTTATGA
40062408 TTGGGTTGGGTAATTGGG-
1 TTGGGTTGGGTAATTGGGT
* *
40062426 TTGGGTTGGATACTTGGGT
1 TTGGGTTGGGTAATTGGGT
*
40062445 TTGGATTGGGT
1 TTGGGTTGGGT
40062456 TTAGGTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.10, C:0.02, G:0.46, T:0.42
Consensus pattern (19 bp):
TTGGGTTGGGTAATTGGGT
Found at i:40067979 original size:23 final size:22
Alignment explanation
Indices: 40067927--40067979 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40067917 TCCACGTCTT
*
40067927 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40067949 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40067972 TTTCTTTT
1 TTTCTTTT
40067980 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40070349 original size:40 final size:40
Alignment explanation
Indices: 40070294--40070525 Score: 324
Period size: 40 Copynumber: 5.8 Consensus size: 40
40070284 ATTTGAATGA
*
40070294 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
*
40070334 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
*
40070374 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
40070414 GATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * * *
40070455 -ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * *
40070495 G-CCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 GATCCGGGCTAAGACCCGAAGGCATTTGTGCT
40070526 TGTGGTAATA
Statistics
Matches: 180, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 175 0.97
41 5 0.03
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.26
Consensus pattern (40 bp):
GATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
Found at i:40070537 original size:80 final size:80
Alignment explanation
Indices: 40070295--40070553 Score: 319
Period size: 80 Copynumber: 3.2 Consensus size: 80
40070285 TTTGAATGAG
*
40070295 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCATT
* *
40070360 TGTGCTAGTGAT-TT
66 TGTGCTAGTGGTAAT
40070374 GATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCAT
1 -ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCAT
* *
40070439 TTGTGCGAGTTG-ATAT
65 TTGTGCTAGTGGTA-AT
* * * * * * * *
40070455 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATG-CCCGGGTTAAGACCCGAAGGCAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGATTTGATCCGGGCTAAGACCCGAAGGCAT
*
40070519 TTGTGCTTGTGGTAAT
65 TTGTGCTAGTGGTAAT
* *
40070535 ATCC-GGCTAAATTCCGAAG
1 ATCCGGGCTAAGTCCCGAAG
40070554 AAACTTGGGT
Statistics
Matches: 156, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
79 12 0.08
80 137 0.88
81 7 0.04
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTTGATCCGGGCTAAGACCCGAAGGCATT
TGTGCTAGTGGTAAT
Found at i:40102997 original size:18 final size:18
Alignment explanation
Indices: 40102976--40103015 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40102966 GATTGAGAGT
* * *
40102976 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
40102994 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
40103012 GAAA
1 GAAA
40103016 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:40106416 original size:13 final size:13
Alignment explanation
Indices: 40106398--40106433 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
40106388 GATATCAAGT
40106398 TGAAAAAAAATTG
1 TGAAAAAAAATTG
40106411 TGAAAAAAAATTG
1 TGAAAAAAAATTG
40106424 TGAAAAAAAA
1 TGAAAAAAAA
40106434 GAAGAAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (13 bp):
TGAAAAAAAATTG
Found at i:40107390 original size:16 final size:18
Alignment explanation
Indices: 40107369--40107414 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
40107359 AAAAGAAACC
40107369 GAAAAAGAAAAAA-ATT-
1 GAAAAAGAAAAAAGATTG
40107385 GAAAAAGAGAAAAAGATTG
1 GAAAAAGA-AAAAAGATTG
*
40107404 GAGAAAGAAAA
1 GAAAAAGAAAA
40107415 GAAAGAGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 8 0.31
17 5 0.19
18 6 0.23
19 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAAAAGATTG
Found at i:40107395 original size:18 final size:17
Alignment explanation
Indices: 40107370--40107414 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
40107360 AAAGAAACCG
40107370 AAAAAGAAAAAAATTGA
1 AAAAAGAAAAAAATTGA
* *
40107387 AAAAGAGAAAAAGATTGG
1 AAAA-AGAAAAAAATTGA
*
40107405 AGAAAGAAAA
1 AAAAAGAAAA
40107415 GAAAGAGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (17 bp):
AAAAAGAAAAAAATTGA
Found at i:40116311 original size:41 final size:41
Alignment explanation
Indices: 40116246--40116331 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
40116236 TTTAATTAGG
* *
40116246 TGTTTTAAATATGTCTGGAGGAATTTAATGCTGCCACTACA
1 TGTTATAAATATGTCTGGACGAATTTAATGCTGCCACTACA
*
40116287 TGTTATAAATATGTCTGGACGAATTTAATGCTGCTACTACA
1 TGTTATAAATATGTCTGGACGAATTTAATGCTGCCACTACA
40116328 TGTT
1 TGTT
40116332 TGGCCGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
TGTTATAAATATGTCTGGACGAATTTAATGCTGCCACTACA
Found at i:40120362 original size:13 final size:13
Alignment explanation
Indices: 40120341--40120375 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40120331 ATAAGTTGCT
* *
40120341 GTTAGTTAAATTA
1 GTTAATTAAATAA
40120354 GTTAATTAAATAA
1 GTTAATTAAATAA
40120367 GTTAATTAA
1 GTTAATTAA
40120376 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:40123103 original size:12 final size:12
Alignment explanation
Indices: 40123086--40123112 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40123076 GACGTCAAGC
40123086 CAAGGTGAGTAT
1 CAAGGTGAGTAT
40123098 CAAGGTGAGTAT
1 CAAGGTGAGTAT
40123110 CAA
1 CAA
40123113 ATTGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (12 bp):
CAAGGTGAGTAT
Found at i:40140084 original size:52 final size:52
Alignment explanation
Indices: 40140001--40140101 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
40139991 TAAGGAAAAG
* *
40140001 TAATGGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAACAA
40140053 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAA
40140102 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGATTGAAGCTCAAACAA
Found at i:40146353 original size:46 final size:46
Alignment explanation
Indices: 40146300--40146393 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 46
40146290 CAAAGAAAAG
**
40146300 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGGATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAAAACCTTGGGATATGATGA
*
40146346 ACCTCGACCCACTATCAATGATGATAAAAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAAAACCTTGGGATATGATGA
40146392 AC
1 AC
40146394 GCCACACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 43 0.98
47 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAAAACCTTGGGATATGATGA
Found at i:40149122 original size:46 final size:47
Alignment explanation
Indices: 40148867--40149336 Score: 768
Period size: 47 Copynumber: 10.1 Consensus size: 47
40148857 GAAATGATAG
*
40148867 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40148914 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40148961 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
40149008 TAAGGCCAAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40149055 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40149101 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA-GTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40149147 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40149193 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40149240 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
40149286 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40149333 TAAG
1 TAAG
40149337 TCCCGAAGGG
Statistics
Matches: 403, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
45 3 0.01
46 168 0.42
47 232 0.58
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40149509 original size:36 final size:37
Alignment explanation
Indices: 40149455--40149531 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40149445 CCGAGCTCTA
* *
40149455 AAGA-CCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40149490 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40149527 AAGAC
1 AAGAC
40149532 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 4 0.11
36 15 0.41
37 18 0.49
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40155017 original size:19 final size:19
Alignment explanation
Indices: 40154993--40155030 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
40154983 TTGAAGGCAA
40154993 AGCCCAAT-AAGCAAATTCC
1 AGCCCAATCAAG-AAATTCC
40155012 AGCCCAATCAAGAAATTCC
1 AGCCCAATCAAGAAATTCC
40155031 TACATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (19 bp):
AGCCCAATCAAGAAATTCC
Found at i:40158737 original size:23 final size:22
Alignment explanation
Indices: 40158686--40158737 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
40158676 CCTCGTCTTT
*
40158686 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
40158708 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
40158731 TTCTTTT
1 TTCTTTT
40158738 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:40163310 original size:27 final size:26
Alignment explanation
Indices: 40163280--40163363 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 26
40163270 TGATTCAAAA
* *
40163280 CTATATATTAAGTCCGCACACTCAGTG
1 CTATATATCAACT-CGCACACTCAGTG
*
40163307 CTATATAATCAACTCGCACACTTAGTG
1 CTATAT-ATCAACTCGCACACTCAGTG
*
40163334 CTATATAATCAAACTCGCACACTTAGTG
1 CTATAT-ATC-AACTCGCACACTCAGTG
40163362 CT
1 CT
40163364 GTACAATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 28 0.54
28 24 0.46
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (26 bp):
CTATATATCAACTCGCACACTCAGTG
Found at i:40163357 original size:28 final size:28
Alignment explanation
Indices: 40163294--40163391 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
40163284 ATATTAAGTC
*
40163294 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40163321 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40163349 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40163378 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40163392 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40171231 original size:28 final size:28
Alignment explanation
Indices: 40171169--40171265 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 28
40171159 TATTAAGTCT
*
40171169 GCACACTCAGTGCTATATAATC-AACTC
1 GCACACTTAGTGCTATATAATCAAACTC
40171196 GCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTC
* * * *
40171224 GCACACTTAGTGCTGTACAATTTAAACCC
1 GCACACTTAGTGCTATATAA-TCAAACTC
40171253 GCACACTTAGTGC
1 GCACACTTAGTGC
40171266 CAATCTCATG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.33
28 23 0.37
29 19 0.30
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
GCACACTTAGTGCTATATAATCAAACTC
Found at i:40178851 original size:18 final size:18
Alignment explanation
Indices: 40178830--40178869 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40178820 GATTGAGAGT
* * *
40178830 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
40178848 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
40178866 GAAA
1 GAAA
40178870 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:40183818 original size:27 final size:28
Alignment explanation
Indices: 40183734--40183829 Score: 131
Period size: 27 Copynumber: 3.4 Consensus size: 28
40183724 CATGAGATTG
* * * *
40183734 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
40183763 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40183791 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40183818 GCACTGAGTGTG
1 GCACTAAGTGTG
40183830 TGGACTTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.35
28 22 0.35
29 18 0.29
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40183842 original size:27 final size:27
Alignment explanation
Indices: 40183762--40183844 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
40183752 TAAATTGTAC
* *
40183762 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
40183790 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
* *
40183817 AGCACTGAGTGTGTGGACTT-AATATAT
1 AGCACTAAGTGTG-CGACTTGAATATAT
40183844 A
1 A
40183845 TTTTTGAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 29 0.59
28 20 0.41
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:40183844 original size:29 final size:27
Alignment explanation
Indices: 40183734--40183845 Score: 89
Period size: 28 Copynumber: 4.0 Consensus size: 27
40183724 CATGAGATTG
** * *
40183734 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
40183763 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
40183791 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
* *
40183818 GCACTGAGTGTGTGGACTTAATATATAT
1 GCACTAAGTGTG-CGACTTAAT-TATAT
40183846 TTTTGAATCA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.31
28 28 0.39
29 21 0.30
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.34
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:40200510 original size:19 final size:19
Alignment explanation
Indices: 40200486--40200522 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40200476 TAAGTATGTA
40200486 GGAATTT-CTTGATTGGGCT
1 GGAATTTACTT-ATTGGGCT
40200505 GGAATTTACTTATTGGGC
1 GGAATTTACTTATTGGGC
40200523 CTTGCCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (19 bp):
GGAATTTACTTATTGGGCT
Found at i:40201347 original size:22 final size:21
Alignment explanation
Indices: 40201315--40201378 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
40201305 TTGGTATTTA
40201315 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
40201336 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
40201358 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
40201379 AGGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40205489 original size:14 final size:15
Alignment explanation
Indices: 40205467--40205495 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40205457 AACTTTTCAC
40205467 TCAT-TTTTTCTTTT
1 TCATCTTTTTCTTTT
40205481 TCATCTTTTTCTTTT
1 TCATCTTTTTCTTTT
40205496 CTCGCTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (15 bp):
TCATCTTTTTCTTTT
Found at i:40205540 original size:18 final size:18
Alignment explanation
Indices: 40205517--40205572 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
40205507 TTCATTCTAT
40205517 TTTTTTGAATTTTCTTTC
1 TTTTTTGAATTTTCTTTC
*
40205535 TTTTTT-CATTTT-TTT-
1 TTTTTTGAATTTTCTTTC
* *
40205550 TTCTTTTGTATTTTCGTTC
1 TT-TTTTGAATTTTCTTTC
40205569 TTTT
1 TTTT
40205573 CTTTTTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 2 0.06
16 7 0.23
17 10 0.32
18 10 0.32
19 2 0.06
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTTTGAATTTTCTTTC
Found at i:40207790 original size:18 final size:18
Alignment explanation
Indices: 40207767--40207808 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40207757 TTTTTTTCTT
*
40207767 TTTTTTCAATTATTTTGA
1 TTTTTTAAATTATTTTGA
* *
40207785 TTTTTTAAATTTTTTTTA
1 TTTTTTAAATTATTTTGA
40207803 TTTTTT
1 TTTTTT
40207809 TTTCACGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTTTAAATTATTTTGA
Found at i:40208147 original size:22 final size:21
Alignment explanation
Indices: 40208115--40208156 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
40208105 TTGGTATTTA
40208115 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
40208136 GGAAGTTGGTACGAAATGGTA
1 GGAA-TTGGTACGAAATGGTA
40208157 ATGGTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.26
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40209274 original size:29 final size:31
Alignment explanation
Indices: 40209212--40209276 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
40209202 AGCAAAAATT
*
40209212 AATTGAGCTGAATTTGTAAGTATTTGAGCTA
1 AATTGAGCTGAATTTGTAACTATTTGAGCTA
40209243 AATTGAGCTG-ATTTG-AACTCA-TTGAGCTA
1 AATTGAGCTGAATTTGTAACT-ATTTGAGCTA
40209272 AATTG
1 AATTG
40209277 GAAGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.50
30 6 0.19
31 10 0.31
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (31 bp):
AATTGAGCTGAATTTGTAACTATTTGAGCTA
Found at i:40210523 original size:23 final size:22
Alignment explanation
Indices: 40210471--40210523 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
40210461 TCCTTGTCTT
*
40210471 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
40210493 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
40210516 TTTCTTTT
1 TTTCTTTT
40210524 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40210533 original size:31 final size:31
Alignment explanation
Indices: 40210497--40210555 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
40210487 TTCTAACTTA
* *
40210497 TTTTCTCTTCTTTCTTCA-ATTTCTTTTTCAC
1 TTTTCTCTTCTGT-TTCACATTCCTTTTTCAC
*
40210528 TTTTCTTTTCTGTTTCACATTCCTTTTT
1 TTTTCTCTTCTGTTTCACATTCCTTTTT
40210556 ACTCTCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.08, C:0.24, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTTCTCTTCTGTTTCACATTCCTTTTTCAC
Found at i:40210553 original size:18 final size:18
Alignment explanation
Indices: 40210516--40210554 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40210506 CTTTCTTCAA
* * *
40210516 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
40210534 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
40210552 TTT
1 TTT
40210555 TACTCTCAAT
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:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:40213025 original size:19 final size:19
Alignment explanation
Indices: 40213001--40213037 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40212991 TAAGTATGTA
40213001 GGAATTT-CTTGATTGGGCT
1 GGAATTTGCTT-ATTGGGCT
40213020 GGAATTTGCTTATTGGGC
1 GGAATTTGCTTATTGGGC
40213038 CTTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (19 bp):
GGAATTTGCTTATTGGGCT
Found at i:40673433 original size:79 final size:82
Alignment explanation
Indices: 40673322--40673506 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
40673312 GCTACTCGTT
* *
40673322 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40673385 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
40673402 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40673465 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
40673482 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40673507 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40673506 original size:40 final size:40
Alignment explanation
Indices: 40673303--40673506 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
40673293 CGGAATTTAA
** *
40673303 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40673343 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40673383 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40673422 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40673462 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40673502 CCGGA
1 CCGGA
40673507 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40681323 original size:79 final size:82
Alignment explanation
Indices: 40681212--40681396 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
40681202 GCTACTCGTT
* * *
40681212 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40681275 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
40681292 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40681355 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
40681372 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40681397 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40681396 original size:40 final size:40
Alignment explanation
Indices: 40681193--40681396 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
40681183 CGAAATTTAA
** *
40681193 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40681233 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
40681273 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40681312 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40681352 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40681392 CCGGA
1 CCGGA
40681397 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40683842 original size:13 final size:12
Alignment explanation
Indices: 40683824--40683872 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
40683814 AAATTGAGAG
40683824 AAAAGAACATTGA
1 AAAAGAA-ATTGA
40683837 AAAAGAAATTG-
1 AAAAGAAATTGA
*
40683848 -AAATAAA-TGA
1 AAAAGAAATTGA
*
40683858 AAAAGAAAATGA
1 AAAAGAAATTGA
40683870 AAA
1 AAA
40683873 TGATGAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 2 0.06
10 6 0.19
11 6 0.19
12 10 0.32
13 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:40688579 original size:12 final size:12
Alignment explanation
Indices: 40688562--40688645 Score: 78
Period size: 12 Copynumber: 6.6 Consensus size: 12
40688552 GTATTGGATT
40688562 AAAAAAAAGTGA
1 AAAAAAAAGTGA
40688574 AAAAAAAAGTGA
1 AAAAAAAAGTGA
* *
40688586 AAAAAAATCGAGCA
1 AAAAAAA-AGTG-A
*
40688600 AAAAAAAGAGAGA
1 AAAAAAA-AGTGA
*
40688613 GAAGAAAAAATTGA
1 -AA-AAAAAAGTGA
*
40688627 AAAAAAAATTGA
1 AAAAAAAAGTGA
40688639 AAAAAAA
1 AAAAAAA
40688646 GAAGAAGAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
12 36 0.58
13 5 0.08
14 16 0.26
15 5 0.08
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAAAAAGTGA
Found at i:40688644 original size:41 final size:41
Alignment explanation
Indices: 40688576--40688654 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
40688566 AAAAGTGAAA
*
40688576 AAAAAAGTGAAAAAAAATCGAGCAAAAAA-AAGAGAGAGAAG
1 AAAAAAGTGAAAAAAAATCGAGAAAAAAAGAAGA-AGAGAAG
* *
40688617 AAAAAATTGAAAAAAAAATTGA-AAAAAAAGAAGAAGAG
1 AAAAAAGTG-AAAAAAAATCGAGAAAAAAAGAAGAAGAG
40688655 GATTTCGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 18 0.55
42 15 0.45
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.08
Consensus pattern (41 bp):
AAAAAAGTGAAAAAAAATCGAGAAAAAAAGAAGAAGAGAAG
Found at i:40693781 original size:22 final size:23
Alignment explanation
Indices: 40693753--40693795 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
40693743 AAAGACGAAA
*
40693753 GAAAAAGAACAAGAAA-AAAATT
1 GAAAAAGAAAAAGAAAGAAAATT
40693775 GAAAAAGAAAAAGAAAGAAAA
1 GAAAAAGAAAAAGAAAGAAAA
40693796 ATAGAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (23 bp):
GAAAAAGAAAAAGAAAGAAAATT
Found at i:40693791 original size:10 final size:10
Alignment explanation
Indices: 40693778--40693818 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
40693768 AAAAATTGAA
40693778 AAAGAAAAAG
1 AAAGAAAAAG
*
40693788 AAAGAAAAAT
1 AAAGAAAAAG
*
40693798 AGAGAAAAAG
1 AAAGAAAAAG
40693808 AAAGGAAAAAG
1 AAA-GAAAAAG
40693819 TGAAAATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:40693794 original size:16 final size:15
Alignment explanation
Indices: 40693749--40693810 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
40693739 TGGAAAAGAC
*
40693749 GAAAGAAAAAGAACAA
1 GAAA-AAAAAGAAAAA
*
40693765 GAAAAAAATTGAAAAA
1 GAAAAAAA-AGAAAAA
40693781 GAAAAAGAAAGAAAAA
1 GAAAAA-AAAGAAAAA
* *
40693797 TAGAGAAAAAGAAA
1 GA-AAAAAAAGAAA
40693811 GGAAAAAGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.11
16 29 0.76
17 5 0.13
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.05
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:40693804 original size:26 final size:28
Alignment explanation
Indices: 40693750--40693810 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
40693740 GGAAAAGACG
**
40693750 AAAGAAAAAGAACAAGAAAAAAATTGAA
1 AAAGAAAAAGAACAAGAAAAAAAGAGAA
*
40693778 AAAGAAAAAG-A-AAGAAAAATAGAGAA
1 AAAGAAAAAGAACAAGAAAAAAAGAGAA
40693804 AAAGAAA
1 AAAGAAA
40693811 GGAAAAAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 19 0.63
27 1 0.03
28 10 0.33
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (28 bp):
AAAGAAAAAGAACAAGAAAAAAAGAGAA
Found at i:40697919 original size:33 final size:33
Alignment explanation
Indices: 40697881--40697948 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
40697871 TTTGAACATC
* *
40697881 ATTAATATACATCT-TTAATTAATATCCTGCATT
1 ATTAATATACATATCTTAATT-ATATCATGCATT
*
40697914 ATTAATCTACATATCTTAATTATATCATGCATT
1 ATTAATATACATATCTTAATTATATCATGCATT
40697947 AT
1 AT
40697949 GTAACTCCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.46
Consensus pattern (33 bp):
ATTAATATACATATCTTAATTATATCATGCATT
Found at i:40698549 original size:46 final size:46
Alignment explanation
Indices: 40698479--40698571 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
40698469 GGTTTAAAAG
*
40698479 ACCTCGACCCACTATCAAGAATGATAGGAACGTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
* *
40698525 ACCTCGACCCACTATCAAGGATGATAGGAACCTTGGTGTATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
40698571 A
1 A
40698572 GGCCACACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:40699238 original size:21 final size:23
Alignment explanation
Indices: 40699194--40699243 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
40699184 AAATCTGCAA
40699194 TAAACACATTAAAATGAGCTTAT
1 TAAACACATTAAAATGAGCTTAT
40699217 TAAACACA-TATAAAT-A-CTTAT
1 TAAACACATTA-AAATGAGCTTAT
40699238 TAAACA
1 TAAACA
40699244 TAACACACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.42
22 3 0.12
23 12 0.46
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (23 bp):
TAAACACATTAAAATGAGCTTAT
Found at i:40702113 original size:54 final size:54
Alignment explanation
Indices: 40702075--40702275 Score: 366
Period size: 54 Copynumber: 3.7 Consensus size: 54
40702065 AGCTAAGTTT
* * *
40702075 AACTTAATTAACTAAGATGAGTAATTTATTTCAGCAACTTAATTAACTAAAATG
1 AACTCAATTAACTAAGATGAGTAATTTATTCCAGCAACTTAATTAACTAAGATG
40702129 AACTCAATTAACTAAGATGAGTAATTTATTCCAGCAACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATGAGTAATTTATTCCAGCAACTTAATTAACTAAGATG
40702183 AACTCAATTAACTAAGATGAGTAATTTATTCCAGCAACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATGAGTAATTTATTCCAGCAACTTAATTAACTAAGATG
*
40702237 AGCTCAATTAACTAAGATGAGTAATTTATTCCAGCAACT
1 AACTCAATTAACTAAGATGAGTAATTTATTCCAGCAACT
40702276 AAATACTTAT
Statistics
Matches: 143, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 143 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (54 bp):
AACTCAATTAACTAAGATGAGTAATTTATTCCAGCAACTTAATTAACTAAGATG
Found at i:40702137 original size:19 final size:19
Alignment explanation
Indices: 40702110--40702148 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40702100 TTATTTCAGC
*
40702110 AACTTAATTAACTAAAATG
1 AACTCAATTAACTAAAATG
*
40702129 AACTCAATTAACTAAGATG
1 AACTCAATTAACTAAAATG
40702148 A
1 A
40702149 GTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAAATG
Found at i:40702257 original size:19 final size:19
Alignment explanation
Indices: 40702115--40702257 Score: 81
Period size: 19 Copynumber: 7.8 Consensus size: 19
40702105 TCAGCAACTT
* *
40702115 AATTAACTAAAATGAACTC
1 AATTAACTAAGATGAGCTC
40702134 AATTAACTAAGATGAG-T-
1 AATTAACTAAGATGAGCTC
* * * *
40702151 AATTTATTCCAGCA--A-CTT
1 AATTAACT-AAG-ATGAGCTC
*
40702169 AATTAACTAAGATGAACTC
1 AATTAACTAAGATGAGCTC
40702188 AATTAACTAAGATGAG-T-
1 AATTAACTAAGATGAGCTC
* * * *
40702205 AATTTATTCCAGCA--A-CTT
1 AATTAACT-AAG-ATGAGCTC
40702223 AATTAACTAAGATGAGCTC
1 AATTAACTAAGATGAGCTC
40702242 AATTAACTAAGATGAG
1 AATTAACTAAGATGAG
40702258 TAATTTATTC
Statistics
Matches: 93, Mismatches: 17, Indels: 28
0.67 0.12 0.20
Matches are distributed among these distances:
16 2 0.02
17 20 0.22
18 20 0.22
19 51 0.55
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (19 bp):
AATTAACTAAGATGAGCTC
Found at i:40706327 original size:106 final size:106
Alignment explanation
Indices: 40706116--40706431 Score: 519
Period size: 106 Copynumber: 3.0 Consensus size: 106
40706106 CTTTGAAGTT
* * * * *
40706116 TTAAGAGGATATTTGGC-ATTTAGTCGAACGAG-AATCGAAACCCAGCAGGTTAGGGCACGTTTT
1 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
40706179 CTCGATTTTCCAAAAGCGAAATATTGCCTTATTTAGAAAATC
66 CTCGATTTTCC-AAAGCGAAATATTGCCTTATTTAGAAAATC
* *
40706221 TTAAAAGGATACTTGACTATTTGGTCGAACGAGAAATCGAAACCCAGCATGTTAGGGCACGTTTC
1 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
*
40706286 CTCGATTTTCCAAAGCGAAATATTGCCTTAGTTAGAAAATC
66 CTCGATTTTCCAAAGCGAAATATTGCCTTATTTAGAAAATC
40706327 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
1 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
*
40706392 CTCGATTTTCCAAACGTGAAATATTGCCTTATTTAGAAAA
66 CTCGATTTTCCAAA-GCGAAATATTGCCTTATTTAGAAAA
40706432 ACCTTCTTTT
Statistics
Matches: 197, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
105 14 0.07
106 120 0.61
107 63 0.32
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (106 bp):
TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
CTCGATTTTCCAAAGCGAAATATTGCCTTATTTAGAAAATC
Found at i:40709024 original size:132 final size:132
Alignment explanation
Indices: 40708790--40709332 Score: 718
Period size: 132 Copynumber: 4.1 Consensus size: 132
40708780 AGATCTGTGG
* * *
40708790 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTATCTTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCATCGATCCACTTCCTACCA
* * * *
40708855 ATATAGGAAGACAGAACCTGCTATCTTTGATCAACTTCACGCCAATAAATGAAGACAAGATCGGC
66 ATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
40708920 TT
131 TT
*
40708922 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCATCGATCCACTTCCTACCA
* *
40708987 ATATAGGAAGACAGGACCTACTATCTTGGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
66 ATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
*
40709052 AT
131 TT
* *
40709054 TCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCATCATCGATCCACTTCCTACCA
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCATCGATCCACTTCCTACCA
* * * *
40709119 ACATAGGAAGACAGGACCTGCAATCTTTGATCTACTTCATGCCAATACATGAAGA-AAGATCTAC
66 ATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
40709183 TT
131 TT
* * * *
40709185 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-ATCATCGATCCACTTC-CTAC
* * * * * * * * * *
40709250 CAGTAT-GGTAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGAC
64 CAATATAGG-AAGACAGGACCTGCTATCTTTGATCTACTTCAC-GCCAATACATGAAGACAAGAT
40709312 CTG-TT
127 CTGCTT
*
40709317 ATCTTTGATCTACTTC
1 -TCTTCGATCTACTTC
40709333 ATGCCAATAC
Statistics
Matches: 365, Mismatches: 40, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
131 50 0.14
132 277 0.76
133 38 0.10
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (132 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCATCGATCCACTTCCTACCA
ATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
TT
Found at i:40709224 original size:176 final size:177
Alignment explanation
Indices: 40709037--40709362 Score: 564
Period size: 176 Copynumber: 1.8 Consensus size: 177
40709027 GCCAATACAT
40709037 GAAGACAAGATCTGCATTCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCATCAT
1 GAAGACAAGATCTGCATTCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCATCAT
40709102 CGATCCACTTCCTACCAACATAGGAAGACAGGACCTGCAATCTTTGATCTACTTCATGCCAATAC
66 CGATCCACTTCCTACCAACATAGGAAGACAGGACCTGCAATCTTTGATCTACTTCATGCCAATAC
40709167 ATGAAGA-AAGATCTACTTTCTTCGATCTACTTCGCCACCAGTATGG
131 ATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAGTATGG
* * * * *
40709213 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGTAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGCATTCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCATCAT
* **
40709278 CGATCCACTTCCTACCAATATAGGAAGACAGGACCTGTTATCTTTGATCTACTTCATGCCAATAC
66 CGATCCACTTCCTACCAACATAGGAAGACAGGACCTGCAATCTTTGATCTACTTCATGCCAATAC
*
40709343 ATGAAGACAAGATCTGCTTT
131 ATGAAGACAAGATCTACTTT
40709363 AATGACTTCA
Statistics
Matches: 140, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
176 129 0.92
177 11 0.08
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (177 bp):
GAAGACAAGATCTGCATTCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCATCAT
CGATCCACTTCCTACCAACATAGGAAGACAGGACCTGCAATCTTTGATCTACTTCATGCCAATAC
ATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAGTATGG
Found at i:40720988 original size:107 final size:107
Alignment explanation
Indices: 40720794--40721112 Score: 557
Period size: 107 Copynumber: 3.0 Consensus size: 107
40720784 CTTTGAAGTT
* * * * * *
40720794 TTAAGAGGATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCATGTTTT
1 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
*
40720859 CTCGATTTTCCAAACGCAAAATATTGCCTTATTTAGAAAATC
66 CTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAATC
40720901 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
1 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
**
40720966 CTCGATTTTCCAAACGCGAAATATTTTCTTATTTAGAAAATC
66 CTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAATC
40721008 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
1 TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
40721073 CTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAA
66 CTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAA
40721113 ACCTTCTTTT
Statistics
Matches: 201, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 201 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (107 bp):
TTAAAAGGATACTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
CTCGATTTTCCAAACGCGAAATATTGCCTTATTTAGAAAATC
Found at i:40722963 original size:10 final size:10
Alignment explanation
Indices: 40722948--40722992 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
40722938 AGTCATTGTG
40722948 AAAAAAATTC
1 AAAAAAATTC
40722958 AAAAAAA-TC
1 AAAAAAATTC
*
40722967 AAAAAAATTT
1 AAAAAAATTC
40722977 AAAAAAATT-
1 AAAAAAATTC
40722986 AAAAAAA
1 AAAAAAA
40722993 GAGTTTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:40722972 original size:19 final size:19
Alignment explanation
Indices: 40722948--40722992 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
40722938 AGTCATTGTG
40722948 AAAAAAATTCAAAAAAATC
1 AAAAAAATTCAAAAAAATC
* *
40722967 AAAAAAATTTAAAAAAATT
1 AAAAAAATTCAAAAAAATC
40722986 AAAAAAA
1 AAAAAAA
40722993 GAGTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAAATTCAAAAAAATC
Found at i:40722992 original size:9 final size:9
Alignment explanation
Indices: 40722948--40722992 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
40722938 AGTCATTGTG
40722948 AAAAAAATT
1 AAAAAAATT
*
40722957 CAAAAAAATC
1 -AAAAAAATT
40722967 AAAAAAATTT
1 AAAAAAA-TT
40722977 AAAAAAATT
1 AAAAAAATT
40722986 AAAAAAA
1 AAAAAAA
40722993 GAGTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAAAAATT
Found at i:40724287 original size:30 final size:32
Alignment explanation
Indices: 40724226--40724289 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
40724216 AAGAGATTGA
*
40724226 AAAAGAAAAAGAGCCTGAAAAGAAATTGAGTG
1 AAAAGAAAAAGAGCCTGAAAAGAAATCGAGTG
*
40724258 AAAA-AAAAA-AGTCTGTAAAAGAAA-CGAGTG
1 AAAAGAAAAAGAGCCTG-AAAAGAAATCGAGTG
40724288 AA
1 AA
40724290 GAGAGTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 12 0.41
31 13 0.45
32 4 0.14
ACGTcount: A:0.59, C:0.06, G:0.22, T:0.12
Consensus pattern (32 bp):
AAAAGAAAAAGAGCCTGAAAAGAAATCGAGTG
Found at i:40726298 original size:29 final size:29
Alignment explanation
Indices: 40726260--40726326 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
40726250 TTTGAAATGC
40726260 AAACTTAACTAACATGAAAGATACATAATT
1 AAAC-TAACTAACATGAAAGATACATAATT
40726290 AAACTAACTAACATGAAAGATACATAATT
1 AAACTAACTAACATGAAAGATACATAATT
40726319 AAACTAAC
1 AAACTAAC
40726327 ATGACTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 33 0.89
30 4 0.11
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (29 bp):
AAACTAACTAACATGAAAGATACATAATT
Found at i:40727076 original size:17 final size:17
Alignment explanation
Indices: 40727054--40727121 Score: 91
Period size: 17 Copynumber: 3.8 Consensus size: 17
40727044 TAAATTGAGT
40727054 TCATCTTAGTTAATTAC
1 TCATCTTAGTTAATTAC
*
40727071 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATT-A-C
*
40727090 TCATCTTAGTTAATAAC
1 TCATCTTAGTTAATTAC
40727107 TCATCTTAGATTAAT
1 TCATCTTAG-TTAAT
40727122 AAATGAGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
17 24 0.53
18 7 0.16
19 14 0.31
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.46
Consensus pattern (17 bp):
TCATCTTAGTTAATTAC
Found at i:40727087 original size:36 final size:37
Alignment explanation
Indices: 40727046--40727121 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 37
40727036 TTTGTTAATA
*
40727046 AATTGAGTTCATCTTAGTTAATTACTCATCTTAG-TT
1 AATTGAGTTCATCTTAGTTAATAACTCATCTTAGATT
40727082 AATTGAGTTCATCTTAGTTAATAACTCATCTTAGATT
1 AATTGAGTTCATCTTAGTTAATAACTCATCTTAGATT
40727119 AAT
1 AAT
40727122 AAATGAGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 33 0.87
37 5 0.13
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (37 bp):
AATTGAGTTCATCTTAGTTAATAACTCATCTTAGATT
Found at i:40727095 original size:19 final size:19
Alignment explanation
Indices: 40727046--40727103 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 19
40727036 TTTGTTAATA
40727046 AATTGAGTTCATCTTAGTT
1 AATTGAGTTCATCTTAGTT
*
40727065 AATT-A-CTCATCTTAGTT
1 AATTGAGTTCATCTTAGTT
40727082 AATTGAGTTCATCTTAGTT
1 AATTGAGTTCATCTTAGTT
40727101 AAT
1 AAT
40727104 AACTCATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 15 0.43
18 2 0.06
19 18 0.51
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (19 bp):
AATTGAGTTCATCTTAGTT
Found at i:40728734 original size:52 final size:55
Alignment explanation
Indices: 40728665--40728801 Score: 124
Period size: 55 Copynumber: 2.5 Consensus size: 55
40728655 AAAATATAAT
* * *
40728665 TTAAT-TTGTATGAAACTAAGACATAATTAAAAT-GTCTAA-CT-TAAGACATGTA
1 TTAATGTTGTACG-AACTAAGACATAATTAAAATAATCTAAGATATAAGACATGTA
* * * *
40728717 TTAATGTTGTACGAACTAGGACACAA-TAAAATAATTTAAGATACTCAGACATGTA
1 TTAATGTTGTACGAACTAAGACATAATTAAAATAATCTAAGATA-TAAGACATGTA
* *
40728772 TTAATGCTGTACGAAAT-AGAACATAATTAA
1 TTAATGTTGTACGAACTAAG-ACATAATTAA
40728802 TAGTTATTAA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
51 6 0.09
52 20 0.30
53 7 0.10
54 1 0.01
55 30 0.45
56 3 0.04
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (55 bp):
TTAATGTTGTACGAACTAAGACATAATTAAAATAATCTAAGATATAAGACATGTA
Found at i:40733086 original size:40 final size:40
Alignment explanation
Indices: 40733042--40733227 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
40733032 GCTCCTCGTT
*
40733042 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
40733082 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
40733122 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
40733162 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
40733203 CAAA-GCCTTCGGGAGTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40733228 CATCATTCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.02
40 114 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40737894 original size:19 final size:19
Alignment explanation
Indices: 40737870--40737906 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40737860 TAAGTATGTA
40737870 GGAATTT-CTTGATTGGGCT
1 GGAATTTACTT-ATTGGGCT
40737889 GGAATTTACTTATTGGGC
1 GGAATTTACTTATTGGGC
40737907 CTTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (19 bp):
GGAATTTACTTATTGGGCT
Found at i:40738731 original size:22 final size:21
Alignment explanation
Indices: 40738699--40738762 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
40738689 TTGGTATTTA
40738699 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
40738720 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
40738742 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
40738763 AGGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40742929 original size:18 final size:18
Alignment explanation
Indices: 40742902--40742954 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
40742892 CATTCTATTT
*
40742902 TTTTGAATTTTCTTTCTC
1 TTTTGTATTTTCTTTCTC
40742920 TTTT-TCATTTTTCTTT-TC
1 TTTTGT-A-TTTTCTTTCTC
*
40742938 TTTTGTATTTTCGTTCT
1 TTTTGTATTTTCTTTCT
40742955 TTTCTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.24
18 13 0.45
19 9 0.31
ACGTcount: A:0.08, C:0.15, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTTGTATTTTCTTTCTC
Found at i:40745179 original size:11 final size:10
Alignment explanation
Indices: 40745154--40745208 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
40745144 GTATACAATT
*
40745154 TTTTTTTC-T
1 TTTTTTTCAA
40745163 TTTTTTTCAA
1 TTTTTTTCAA
* * *
40745173 TTATTTTGAT
1 TTTTTTTCAA
40745183 TTTTTTTCAA
1 TTTTTTTCAA
*
40745193 TTTTTTT-TA
1 TTTTTTTCAA
40745202 TTTTTTT
1 TTTTTTT
40745209 TTCACGAGTC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
9 16 0.43
10 21 0.57
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:40745185 original size:20 final size:20
Alignment explanation
Indices: 40745162--40745209 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
40745152 TTTTTTTTTC
40745162 TTTTTTTTCAATTATTTTGA
1 TTTTTTTTCAATTATTTTGA
* *
40745182 TTTTTTTTCAATTTTTTTTA
1 TTTTTTTTCAATTATTTTGA
40745202 TTTTTTTT
1 TTTTTTTT
40745210 TCACGAGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTTTTCAATTATTTTGA
Found at i:40745210 original size:21 final size:21
Alignment explanation
Indices: 40745149--40745212 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
40745139 AGACCGTATA
40745149 CAATTTTTTTT-TCTTTTTTTT
1 CAATTTTTTTTAT-TTTTTTTT
* *
40745170 CAATTATTTTGA-TTTTTTTT
1 CAATTTTTTTTATTTTTTTTT
40745190 CAATTTTTTTTATTTTTTTTT
1 CAATTTTTTTTATTTTTTTTT
40745211 CA
1 CA
40745213 CGAGTCTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 18 0.49
21 19 0.51
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (21 bp):
CAATTTTTTTTATTTTTTTTT
Found at i:40745550 original size:22 final size:22
Alignment explanation
Indices: 40745518--40745577 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
40745508 TATTTAGGAA
*
40745518 TTGGTATGAAATGGTATAGAAG
1 TTGGTACGAAATGGTATAGAAG
* * *
40745540 TTGGTACGAAATGGTATGGTAT
1 TTGGTACGAAATGGTATAGAAG
*
40745562 TTGGTACGAATTGGTA
1 TTGGTACGAAATGGTA
40745578 ATGGTTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (22 bp):
TTGGTACGAAATGGTATAGAAG
Found at i:40746698 original size:29 final size:31
Alignment explanation
Indices: 40746636--40746700 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
40746626 AGCAAAAATT
*
40746636 AATTGAGCTGAATTTGTAAGTATTTGAGCTA
1 AATTGAGCTGAATTTGTAACTATTTGAGCTA
40746667 AATTGAGCTG-ATTTG-AACTCA-TTGAGCTA
1 AATTGAGCTGAATTTGTAACT-ATTTGAGCTA
40746696 AATTG
1 AATTG
40746701 GAAGTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.50
30 6 0.19
31 10 0.31
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (31 bp):
AATTGAGCTGAATTTGTAACTATTTGAGCTA
Found at i:40747949 original size:23 final size:22
Alignment explanation
Indices: 40747897--40747949 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
40747887 TCCTTGTCTT
*
40747897 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
* *
40747919 CTTATTTTCTCTTCTTTCTTC-AA
1 TTTCTTTTCT-TTCTTT-TTCTAA
40747942 TTTCTTTT
1 TTTCTTTT
40747950 TCACTTTTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 7 0.29
23 14 0.58
24 3 0.12
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40747959 original size:31 final size:31
Alignment explanation
Indices: 40747923--40747981 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
40747913 TTCTAACTTA
* *
40747923 TTTTCTCTTCTTTCTTCA-ATTTCTTTTTCAC
1 TTTTCTCTTCTGT-TTCACATTCCTTTTTCAC
*
40747954 TTTTCTTTTCTGTTTCACATTCCTTTTT
1 TTTTCTCTTCTGTTTCACATTCCTTTTT
40747982 ACTCTCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.08, C:0.24, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTTCTCTTCTGTTTCACATTCCTTTTTCAC
Found at i:40747979 original size:18 final size:18
Alignment explanation
Indices: 40747942--40747980 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40747932 CTTTCTTCAA
* * *
40747942 TTTCTTTTTCACTTTTCT
1 TTTCTGTTTCACATTCCT
40747960 TTTCTGTTTCACATTCCT
1 TTTCTGTTTCACATTCCT
40747978 TTT
1 TTT
40747981 TACTCTCAAT
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:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTCTGTTTCACATTCCT
Found at i:40750459 original size:19 final size:19
Alignment explanation
Indices: 40750435--40750471 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40750425 TAAGTATGTA
40750435 GGAATTT-CTTGATTGGGCT
1 GGAATTTGCTT-ATTGGGCT
40750454 GGAATTTGCTTATTGGGC
1 GGAATTTGCTTATTGGGC
40750472 CTTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (19 bp):
GGAATTTGCTTATTGGGCT
Found at i:40751200 original size:11 final size:11
Alignment explanation
Indices: 40751170--40751203 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
40751160 GAAGAGCCAT
40751170 ATGGTGTGAAC
1 ATGGTGTGAAC
*
40751181 ATGG-CTGAAC
1 ATGGTGTGAAC
40751191 ATGGTGTGAAC
1 ATGGTGTGAAC
40751202 AT
1 AT
40751204 CTTTATGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.26
Consensus pattern (11 bp):
ATGGTGTGAAC
Found at i:40753692 original size:21 final size:21
Alignment explanation
Indices: 40753663--40753703 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40753653 TCTCTCTCAC
*
40753663 TTTCCTTTTCGTCATTTTCAT
1 TTTCATTTTCGTCATTTTCAT
* *
40753684 TTTCATTTTCTTCTTTTTCA
1 TTTCATTTTCGTCATTTTCA
40753704 CTTGTACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTCATTTTCGTCATTTTCAT
Found at i:40762567 original size:31 final size:32
Alignment explanation
Indices: 40762522--40762588 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
40762512 ACATGCATGC
*
40762522 ACCTTGCTAAAATGAATCTCCA-A-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-CCACACATTCGGCCA
*
40762554 ACCTTG-TTAAATGATCCCACACATTCGGCCA
1 ACCTTGCTAAAATGATCCCACACATTCGGCCA
40762585 ACCT
1 ACCT
40762589 ATATAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 18 0.58
32 6 0.19
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCCCACACATTCGGCCA
Found at i:40762920 original size:30 final size:30
Alignment explanation
Indices: 40762862--40762920 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
40762852 TTGAAAATGT
* *
40762862 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
40762892 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
40762921 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:40766577 original size:37 final size:36
Alignment explanation
Indices: 40766527--40766604 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 36
40766517 TTATTACGAA
* *
40766527 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACA-GAAGTCATCGG
*
40766564 GTCTTACCCGGACAAAATTCCCACAGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACAGAAGTCATCGG
40766600 GTCTT
1 GTCTT
40766605 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 14 0.38
37 21 0.57
38 2 0.05
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (36 bp):
GTCTTACCCGGACAAAATTCCCACAGAAGTCATCGG
Found at i:40766841 original size:47 final size:47
Alignment explanation
Indices: 40766723--40767375 Score: 1087
Period size: 47 Copynumber: 13.7 Consensus size: 47
40766713 CCCTTCGGGA
* * * * *
40766723 CTTATCACATTTATTACACTTTCACATCCATCACGTTGGCCA-TCGGC
1 CTTATCACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40766770 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40766817 CTTATCACATGTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40766864 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40766911 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40766960 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40767007 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40767054 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40767103 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40767152 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40767199 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40767246 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40767295 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40767341 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
40767376 AGAATCCTAA
Statistics
Matches: 583, Mismatches: 15, Indels: 17
0.95 0.02 0.03
Matches are distributed among these distances:
45 1 0.00
46 58 0.10
47 335 0.57
49 189 0.32
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40766955 original size:96 final size:94
Alignment explanation
Indices: 40766723--40767375 Score: 1087
Period size: 96 Copynumber: 6.9 Consensus size: 94
40766713 CCCTTCGGGA
* * * * * * *
40766723 CTTATCACATTTATTACACTTTCACATCCATCACGTTGGCCA-TCGGCCCTGTCACATATATACA
1 CTTATCACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
40766787 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATCGGCCATTAGGC
*
40766817 CTTATCACATGTATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
40766882 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
40766911 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
40766976 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
40767007 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
40767072 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
40767103 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
40767168 ACTTTCACATTCATCGCATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
40767199 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
40767264 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
40767295 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTTATCACATATATGCA-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
40767358 TGTTCACATCCATCACAT
66 T-TTCACATTCATCACAT
40767376 AGAATCCTAA
Statistics
Matches: 535, Mismatches: 14, Indels: 21
0.94 0.02 0.04
Matches are distributed among these distances:
92 1 0.00
93 48 0.09
94 162 0.30
95 10 0.02
96 267 0.50
98 47 0.09
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:40766979 original size:143 final size:144
Alignment explanation
Indices: 40766723--40767354 Score: 1091
Period size: 143 Copynumber: 4.4 Consensus size: 144
40766713 CCCTTCGGGA
* * * * * * *
40766723 CTTATCACATTTATTACACTTTCACATCCATCACGTTGGCCA-TCGGCCCTGTCAC--ATATATA
1 CTTATCACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
*
40766785 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATGTATACACTTTCACATTCATCA
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCA
40766849 CATCGGCCATTAGGC
130 CATCGGCCATTAGGC
40766864 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
40766929 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATACACTTTCACATTCATCAC
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCAC
40766993 ATCGGCCATTAGGC
131 ATCGGCCATTAGGC
40767007 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
40767072 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACTTTCACATTCATCA
40767137 CATCGGCCATTAGGC
130 CATCGGCCATTAGGC
*
40767152 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
*
40767215 ACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACTTTCACATTCATCA
40767280 CATCGGCCATTAGGC
130 CATCGGCCATTAGGC
40767295 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA-GCCTTATCACATATAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
40767355 GCATGTTCAC
Statistics
Matches: 473, Mismatches: 11, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
140 25 0.05
141 22 0.05
142 10 0.02
143 319 0.67
144 4 0.01
145 93 0.20
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (144 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCAC
ATCGGCCATTAGGC
Found at i:40775900 original size:80 final size:82
Alignment explanation
Indices: 40775788--40775973 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 82
40775778 GCTCCTCGTT
* *
40775788 CAAATGCCTTCGAGACATAGCCC-GATTATAGTAACTCGCACAAATACCTTCAGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATACCTTC-GGATCTTAACCC
* *
40775851 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * * **
40775868 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATACCTTCGGATCTTAACCCG
* *
40775932 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
*
40775949 CAAA-GCCTTCGGGAGTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40775974 CATCATTCAA
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
79 3 0.03
80 75 0.83
81 12 0.13
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATACCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40775920 original size:40 final size:40
Alignment explanation
Indices: 40775788--40775973 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
40775778 GCTCCTCGTT
* * *
40775788 CAAATGCCTTCGAGACATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
* *
40775828 CAAATACCTTCAGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
40775868 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
40775908 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
40775949 CAAA-GCCTTCGGGAGTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40775974 CATCATTCAA
Statistics
Matches: 125, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
39 3 0.02
40 107 0.86
41 15 0.12
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:40781359 original size:50 final size:50
Alignment explanation
Indices: 40781170--40781362 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
40781160 GATAATAACA
* * * * ** *
40781170 TGCCAAAGCCATGTCCCAGACATGGCCTTACATGAGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCT-CTCATCTCGG
* ** *
40781221 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
40781271 TGCCAATGCCATGTCCAAAACATAGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
*
40781321 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
40781363 TTACCCCAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 92 0.75
51 31 0.25
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40781478 original size:13 final size:13
Alignment explanation
Indices: 40781457--40781486 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40781447 GCTTAGATCA
40781457 TCATCAAATAAAT
1 TCATCAAATAAAT
*
40781470 TCATGAAATAAAT
1 TCATCAAATAAAT
40781483 TCAT
1 TCAT
40781487 TGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:40786710 original size:27 final size:27
Alignment explanation
Indices: 40786680--40786750 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 27
40786670 AATAAGTGAG
* *
40786680 GAAAAAGGAAAAGGAGAAGA-GAAAAAT
1 GAAAAAGGAAAAGAAGAAAATG-AAAAT
** *
40786707 GAAAGTGAAAAAGAAGAAAATGAAAAT
1 GAAAAAGGAAAAGAAGAAAATGAAAAT
40786734 GAAAAAGGCGAAAAGAA
1 GAAAAA-G-GAAAAGAA
40786751 AAGCGAGAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
27 24 0.73
28 2 0.06
29 7 0.21
ACGTcount: A:0.66, C:0.01, G:0.27, T:0.06
Consensus pattern (27 bp):
GAAAAAGGAAAAGAAGAAAATGAAAAT
Found at i:40796908 original size:50 final size:50
Alignment explanation
Indices: 40796786--40796978 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 50
40796776 GATAATAACA
* * ** *
40796786 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* **
40796837 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
40796887 TGCCAATGCCACGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
40796937 TGCCAATGTCATGTCCCAGACATGGTCTTATATGAGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40796979 TTACCCCAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 90 0.73
51 33 0.27
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40797094 original size:13 final size:13
Alignment explanation
Indices: 40797073--40797102 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40797063 GCTTGGATCA
40797073 TCATCAAATAAAT
1 TCATCAAATAAAT
*
40797086 TCATGAAATAAAT
1 TCATCAAATAAAT
40797099 TCAT
1 TCAT
40797103 TGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:40798806 original size:10 final size:9
Alignment explanation
Indices: 40798793--40798820 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
40798783 ACAAAAATTC
40798793 AAAAAAAAT
1 AAAAAAAAT
40798802 AAAAAAAAT
1 AAAAAAAAT
40798811 AAAAAAAAT
1 AAAAAAAAT
40798820 A
1 A
40798821 CGAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:40798814 original size:17 final size:17
Alignment explanation
Indices: 40798793--40798837 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
40798783 ACAAAAATTC
40798793 AAAAAAAATAAAAAAAAT
1 AAAAAAAAT-AAAAAAAT
** *
40798811 AAAAAAAATACGAATAT
1 AAAAAAAATAAAAAAAT
40798828 AAAAAAAATA
1 AAAAAAAATA
40798838 TAGTGAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.13
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAT
Found at i:40799695 original size:6 final size:6
Alignment explanation
Indices: 40799676--40799724 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
40799666 ATAAAATTGA
* * **
40799676 AAAAAG AAATAG AAAAAG AAAAGG AAAAAG AAAAAG AAATCG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
40799724 A
1 A
40799725 GTGTGAGCCC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:40801639 original size:11 final size:11
Alignment explanation
Indices: 40801623--40801648 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40801613 TTTTTGTGTC
40801623 TTTAATTATGT
1 TTTAATTATGT
40801634 TTTAATTATGT
1 TTTAATTATGT
40801645 TTTA
1 TTTA
40801649 GTTTGTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
TTTAATTATGT
Found at i:40803556 original size:22 final size:22
Alignment explanation
Indices: 40803526--40803569 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40803516 TTTGGTATTT
40803526 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
40803548 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
40803570 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:40807746 original size:28 final size:27
Alignment explanation
Indices: 40807685--40807748 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
40807675 TATTAATTAT
* *
40807685 TGTAATAATTTAAGACATATTAAACAC
1 TGTAATAAATTAAAACATATTAAACAC
*
40807712 TCATAATAAATTAAAACATAATTAAA-AC
1 T-GTAATAAATTAAAACAT-ATTAAACAC
40807740 ATGTAATAA
1 -TGTAATAA
40807749 GCTGACAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
27 1 0.03
28 22 0.73
29 7 0.23
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (27 bp):
TGTAATAAATTAAAACATATTAAACAC
Found at i:40807900 original size:20 final size:20
Alignment explanation
Indices: 40807856--40807904 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
40807846 ACGAGCTTAT
* *
40807856 TGAGCTGAATTGAGCTGGTG
1 TGAGCTGAATTGAGCTCGAG
* *
40807876 GGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
40807896 TGAGCTGAA
1 TGAGCTGAA
40807905 CCGCATGGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.39, T:0.24
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40809677 original size:18 final size:18
Alignment explanation
Indices: 40809656--40809701 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
40809646 TTTTCACTCA
*
40809656 CTTTTGTAATTTCCTTTT
1 CTTTTGCAATTTCCTTTT
*
40809674 CTTTTGCAATTTCTTTTT
1 CTTTTGCAATTTCCTTTT
*
40809692 CTTTTTCAAT
1 CTTTTGCAAT
40809702 GTCTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.17, G:0.04, T:0.65
Consensus pattern (18 bp):
CTTTTGCAATTTCCTTTT
Found at i:40809706 original size:18 final size:18
Alignment explanation
Indices: 40809656--40809709 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
40809646 TTTTCACTCA
* * *
40809656 CTTTTGTAATTTCCTTTT
1 CTTTTGCAATGTCTTTTT
*
40809674 CTTTTGCAATTTCTTTTT
1 CTTTTGCAATGTCTTTTT
*
40809692 CTTTTTCAATGTCTTTTT
1 CTTTTGCAATGTCTTTTT
40809710 ATTTCATTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.11, C:0.17, G:0.06, T:0.67
Consensus pattern (18 bp):
CTTTTGCAATGTCTTTTT
Found at i:40811276 original size:28 final size:27
Alignment explanation
Indices: 40811235--40811301 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
40811225 TTTTGTGATA
* * *
40811235 AATGTGTTTTATTTTATTACATGTTATT
1 AATGTGTCTAATTTTATTACATGCT-TT
40811263 AATGTGTCTAATTTTATTACATGCTTT
1 AATGTGTCTAATTTTATTACATGCTTT
40811290 AATGATGTCTAA
1 AATG-TGTCTAA
40811302 GTCATAGTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.52
Consensus pattern (27 bp):
AATGTGTCTAATTTTATTACATGCTTT
Found at i:40813633 original size:12 final size:12
Alignment explanation
Indices: 40813616--40813640 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40813606 AAAATTTGAT
40813616 TTCAATGTGTAA
1 TTCAATGTGTAA
40813628 TTCAATGTGTAA
1 TTCAATGTGTAA
40813640 T
1 T
40813641 GTAGGGTGGC
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:40817488 original size:12 final size:12
Alignment explanation
Indices: 40817471--40817495 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40817461 AAAATCTGAT
40817471 TTCAATGTGTAA
1 TTCAATGTGTAA
40817483 TTCAATGTGTAA
1 TTCAATGTGTAA
40817495 T
1 T
40817496 GTAGGGTGGC
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:40818223 original size:14 final size:14
Alignment explanation
Indices: 40818204--40818231 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40818194 ATACATTGAC
40818204 TAGATTCATGCATG
1 TAGATTCATGCATG
40818218 TAGATTCATGCATG
1 TAGATTCATGCATG
40818232 GGAATATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TAGATTCATGCATG
Found at i:40830737 original size:40 final size:40
Alignment explanation
Indices: 40830678--40830889 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
40830668 CATTTGAATG
* * *
40830678 ATATCCGGGCTAAGTCCCGAAGGAAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
40830718 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
40830758 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * * * * *
40830798 TTATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
40830838 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
40830878 ATATCC-GGCTAA
1 ATATCCGGGCTAA
40830890 ATTCCGAAGA
Statistics
Matches: 139, Mismatches: 31, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
39 8 0.06
40 129 0.93
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Done.