Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 131 of 318
Found at i:40065409 original size:15 final size:14
Alignment explanation
Indices: 40065369--40065425 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
40065359 CTCTTGCCTC
*
40065369 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
40065384 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
40065399 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
40065416 TCTTTTCTTT
1 TCTTTTCTTT
40065426 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:40065426 original size:21 final size:21
Alignment explanation
Indices: 40065369--40065436 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
40065359 CTCTTGCCTC
* *
40065369 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
40065390 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
40065411 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
40065431 CTCTTT
1 -TCTTT
40065437 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:40068797 original size:28 final size:27
Alignment explanation
Indices: 40068750--40068854 Score: 115
Period size: 27 Copynumber: 3.8 Consensus size: 27
40068740 TGCAAGAACT
* * *
40068750 GATAATGTGACAGAGTCACCAGATATA
1 GATAATGTGGCAGAGCCACCAGATACA
*
40068777 GATAATCGTGGCAGAACCACCAGA-ACA
1 GATAAT-GTGGCAGAGCCACCAGATACA
40068804 GATATATGTGGCAGAGCCACCAGAT-CA
1 GATA-ATGTGGCAGAGCCACCAGATACA
*
40068831 GATAATTTGTGGCATAGCCACCAG
1 GATAA--TGTGGCAGAGCCACCAG
40068855 GACGCTTCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.01
27 34 0.51
28 32 0.48
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
GATAATGTGGCAGAGCCACCAGATACA
Found at i:40068827 original size:55 final size:54
Alignment explanation
Indices: 40068744--40068854 Score: 134
Period size: 55 Copynumber: 2.0 Consensus size: 54
40068734 CATGGCTGCA
* * *
40068744 AGAACTGATAATGTGACAGAGTCACCAGATATAGATAA-TCGTGGCAGAACCACC
1 AGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATTCGTGGCAGAACCACC
* * * *
40068798 AGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTTGTGGCATAGCCACC
1 AGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAACCACC
40068853 AG
1 AG
40068855 GACGCTTCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
54 15 0.31
55 33 0.69
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (54 bp):
AGAACAGATAATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAACCACC
Found at i:40073513 original size:27 final size:27
Alignment explanation
Indices: 40073474--40073541 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
40073464 AGCATGGCTG
* **
40073474 CCAGAACTGATAAT-GTGACAGAGTCA
1 CCAGAACAGATAATCGTGACAGAACCA
*
40073500 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAATCGTGACAGAACCA
40073528 CCAGAACAGATAAT
1 CCAGAACAGATAAT
40073542 TTGTGGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.14
27 17 0.47
28 14 0.39
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATCGTGACAGAACCA
Found at i:40073529 original size:28 final size:28
Alignment explanation
Indices: 40073498--40073559 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
40073488 GTGACAGAGT
40073498 CACCAGATACAGATAA-TCGTGGCAGAAC
1 CACCAGA-ACAGATAATTCGTGGCAGAAC
* * *
40073526 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTCGTGGCAGAAC
40073554 CACCAG
1 CACCAG
40073560 GACGCTTCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (28 bp):
CACCAGAACAGATAATTCGTGGCAGAAC
Found at i:40074994 original size:24 final size:24
Alignment explanation
Indices: 40074967--40075013 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40074957 CTAGATTTCC
**
40074967 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
40074991 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
40075014 CTCCTGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:40075563 original size:30 final size:30
Alignment explanation
Indices: 40075529--40075625 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
40075519 TAAACTAAAA
*
40075529 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
40075559 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
40075589 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
40075619 TGAGCTA
1 TGAGCTA
40075626 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:40088532 original size:26 final size:22
Alignment explanation
Indices: 40088487--40088531 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
40088477 GAGTGATAAA
40088487 TACAATGTATGTTCATCTTTCT
1 TACAATGTATGTTCATCTTTCT
40088509 TACAATGTATGTTCATCTTTCT
1 TACAATGTATGTTCATCTTTCT
40088531 T
1 T
40088532 TTCCCCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (22 bp):
TACAATGTATGTTCATCTTTCT
Found at i:40090217 original size:43 final size:42
Alignment explanation
Indices: 40090129--40090293 Score: 156
Period size: 43 Copynumber: 3.9 Consensus size: 42
40090119 AATGTGATAT
* * * *
40090129 TCGGGCCTC-AGCCTAGCAAGCTTTAA-GCTGGTGAATAATATTA
1 TCGGGCTTCAAGCCTAGCAGGCTATAATGC-GGTG-A-AATAATA
*
40090172 TCGGGCTTCAAGCCTAGCAGGCTATAATGTCGGTGAGATAATA
1 TCGGGCTTCAAGCCTAGCAGGCTATAATG-CGGTGAAATAATA
** *
40090215 TCGGGCTTCGGGCCTAGCAGGCTATAATGCTGGTGAAATGATA
1 TCGGGCTTCAAGCCTAGCAGGCTATAATGC-GGTGAAATAATA
* * *
40090258 TCAGGCTTCAAGCCTAGTAGGCGA-AATGCCGGTGAA
1 TCGGGCTTCAAGCCTAGCAGGCTATAATG-CGGTGAA
40090294 TGAGTTCAGA
Statistics
Matches: 103, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
42 11 0.11
43 70 0.68
44 16 0.16
45 5 0.05
46 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (42 bp):
TCGGGCTTCAAGCCTAGCAGGCTATAATGCGGTGAAATAATA
Found at i:40090374 original size:40 final size:41
Alignment explanation
Indices: 40090175--40090373 Score: 138
Period size: 43 Copynumber: 4.8 Consensus size: 41
40090165 AATATTATCG
* *
40090175 GGCTTCAAGCCTAGCAGGCTATAATG-TCGGTGAGAT-AATATCG
1 GGCTTAAAGCCTAGCAGGCTA-AATGCT-GGTGA-ATGAAT-TCA
***
40090218 GGCTTCGGGCCTAGCAGGCTATAATGCTGGTGAAATG-ATATCA
1 GGCTTAAAGCCTAGCAGGCTA-AATGCTGGTG-AATGAAT-TCA
* * * * *
40090261 GGCTTCAAGCCTAGTAGGCGAAATGCCGGTGAATGAGTTCA
1 GGCTTAAAGCCTAGCAGGCTAAATGCTGGTGAATGAATTCA
* * ***
40090302 GACTTAAAGTCTAGCAGGCTTCGTG-TCGGTG-ATGAATTCA
1 GGCTTAAAGCCTAGCAGGCTAAATGCT-GGTGAATGAATTCA
* *
40090342 GGTTTAAAACCTAGCAGGCTAAATGCTGGTGA
1 GGCTTAAAGCCTAGCAGGCTAAATGCTGGTGA
40090374 TTTGATAAAA
Statistics
Matches: 123, Mismatches: 26, Indels: 16
0.75 0.16 0.10
Matches are distributed among these distances:
40 30 0.24
41 29 0.24
42 10 0.08
43 52 0.42
44 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (41 bp):
GGCTTAAAGCCTAGCAGGCTAAATGCTGGTGAATGAATTCA
Found at i:40093036 original size:20 final size:21
Alignment explanation
Indices: 40093010--40093055 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
40093000 ATTGTGATAA
*
40093010 ATTCACTTATGTTTTGTTGAC
1 ATTCACTTATGTTTTGCTGAC
40093031 -TTCACTTATGTTTTGCTGAC
1 ATTCACTTATGTTTTGCTGAC
40093051 ATTCA
1 ATTCA
40093056 TAGGAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (21 bp):
ATTCACTTATGTTTTGCTGAC
Found at i:40101567 original size:74 final size:74
Alignment explanation
Indices: 40101486--40101633 Score: 278
Period size: 74 Copynumber: 2.0 Consensus size: 74
40101476 ATTCCAATAC
40101486 AAAACATTTTAATCTATCACATATCTTTTATTTTCTACCATCAAACAAAAAAAATCACAAGCTTT
1 AAAACATTTTAATCTATCACATATCTTTTATTTTCTACCATCAAACAAAAAAAATCACAAGCTTT
40101551 CAACAATGG
66 CAACAATGG
* *
40101560 AAAACATTTTAATCTATCACATATCTTTTATTTTCTACCATCAAACAACAAAAATCACCAGCTTT
1 AAAACATTTTAATCTATCACATATCTTTTATTTTCTACCATCAAACAAAAAAAATCACAAGCTTT
40101625 CAACAATGG
66 CAACAATGG
40101634 CATAACTCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (74 bp):
AAAACATTTTAATCTATCACATATCTTTTATTTTCTACCATCAAACAAAAAAAATCACAAGCTTT
CAACAATGG
Found at i:40102146 original size:13 final size:13
Alignment explanation
Indices: 40102130--40102155 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40102120 TAATAAACAC
40102130 AAAAAATATTTTT
1 AAAAAATATTTTT
40102143 AAAAAATATTTTT
1 AAAAAATATTTTT
40102156 CTGACTCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAAATATTTTT
Found at i:40110208 original size:30 final size:30
Alignment explanation
Indices: 40110137--40110219 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
40110127 CTTTTGTTTC
* *
40110137 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
40110168 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
40110197 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
40110220 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:40110219 original size:18 final size:18
Alignment explanation
Indices: 40110170--40110225 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
40110160 CACTCTCAAA
* *
40110170 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
40110187 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
40110205 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
40110224 TT
1 TT
40110226 CAAAGACTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:40110226 original size:12 final size:12
Alignment explanation
Indices: 40110195--40110219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40110185 TTTTTCAATC
40110195 TCATTTTCTTTT
1 TCATTTTCTTTT
40110207 TCATTTTCTTTT
1 TCATTTTCTTTT
40110219 T
1 T
40110220 GCTTTTCAAA
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:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:40110237 original size:12 final size:12
Alignment explanation
Indices: 40110222--40110252 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
40110212 TTCTTTTTGC
40110222 TTTTCAAAGACT
1 TTTTCAAAGACT
*
40110234 TTTTCAAAGGCT
1 TTTTCAAAGACT
40110246 TTTTCAA
1 TTTTCAA
40110253 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:40110310 original size:5 final size:5
Alignment explanation
Indices: 40110300--40110356 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
40110290 CTCTTGCCTC
*
40110300 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
40110347 TCTTT TCTTT
1 TCTTT TCTTT
40110357 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:40110340 original size:15 final size:14
Alignment explanation
Indices: 40110300--40110356 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
40110290 CTCTTGCCTC
*
40110300 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
40110315 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
40110330 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
40110347 TCTTTTCTTT
1 TCTTTTCTTT
40110357 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:40110357 original size:21 final size:21
Alignment explanation
Indices: 40110300--40110367 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
40110290 CTCTTGCCTC
* *
40110300 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
40110321 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
40110342 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
40110362 CTCTTT
1 -TCTTT
40110368 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:40111510 original size:10 final size:10
Alignment explanation
Indices: 40111497--40111526 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
40111487 TTTCTATACT
40111497 TTTTTTTTTC
1 TTTTTTTTTC
40111507 -TTTTTTTTC
1 TTTTTTTTTC
40111516 TTTTTTTTTC
1 TTTTTTTTTC
40111526 T
1 T
40111527 GACCCTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:40111512 original size:9 final size:9
Alignment explanation
Indices: 40111498--40111523 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40111488 TTCTATACTT
40111498 TTTTTTTTC
1 TTTTTTTTC
40111507 TTTTTTTTC
1 TTTTTTTTC
40111516 TTTTTTTT
1 TTTTTTTT
40111524 TCTGACCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:40113086 original size:30 final size:30
Alignment explanation
Indices: 40113000--40113097 Score: 88
Period size: 30 Copynumber: 3.3 Consensus size: 30
40112990 TTAAACTAAA
* * *
40113000 ATGAGCTAAGCTTTAGCTCGTGACCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
40113030 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
40113060 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
40113090 ATGAGCTA
1 ATGAGCTA
40113098 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:40124346 original size:10 final size:10
Alignment explanation
Indices: 40124331--40124376 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
40124321 TCACTTTTTC
40124331 TTTTTTTGAT
1 TTTTTTTGAT
*
40124341 TTTTTTCGAT
1 TTTTTTTGAT
40124351 TTTTTTTCGAT
1 TTTTTTT-GAT
40124362 TTTTTTT--T
1 TTTTTTTGAT
40124370 TTTTTTT
1 TTTTTTT
40124377 TAACTTGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 8 0.24
10 15 0.45
11 10 0.30
ACGTcount: A:0.07, C:0.04, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTTTTTGAT
Found at i:40124369 original size:12 final size:11
Alignment explanation
Indices: 40124331--40124368 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
40124321 TCACTTTTTC
40124331 TTTTTTT-GA-
1 TTTTTTTCGAT
40124340 TTTTTTTCGAT
1 TTTTTTTCGAT
40124351 TTTTTTTCGAT
1 TTTTTTTCGAT
40124362 TTTTTTT
1 TTTTTTT
40124369 TTTTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 18 0.67
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTTTTCGAT
Found at i:40124778 original size:14 final size:14
Alignment explanation
Indices: 40124731--40124778 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
40124721 GTACGAATGG
*
40124731 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
40124745 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
40124759 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
40124773 ATTGGT
1 AATGGT
40124779 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:40125796 original size:19 final size:19
Alignment explanation
Indices: 40125759--40125798 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
40125749 CGTGAGCTGA
*
40125759 TAATGAGCTGGTTCTGAGC
1 TAATGAGCTGGTTCGGAGC
40125778 TAATGAGCTGGTGT-GGAGC
1 TAATGAGCTGGT-TCGGAGC
40125797 TA
1 TA
40125799 CATGGGAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.30
Consensus pattern (19 bp):
TAATGAGCTGGTTCGGAGC
Found at i:40131421 original size:40 final size:39
Alignment explanation
Indices: 40131377--40131502 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
40131367 GGGACTCAAC
*
40131377 CCGGATTTAGTAGCTTGCTCGAAAGCCTTCGGATCTTAGT
1 CCGGATTTAGTA-CTTGCACGAAAGCCTTCGGATCTTAGT
* * * *
40131417 CCGGATTTAGTAACTCGCACGTATGCCGTCGGATCTTAGT
1 CCGGATTTAGT-ACTTGCACGAAAGCCTTCGGATCTTAGT
*
40131457 CCGGATTTAGTCACTTAGCAC-AAAGCCTTCGGGA-CTTAGC
1 CCGGATTTAGT-ACTT-GCACGAAAGCCTTC-GGATCTTAGT
40131497 CCGGAT
1 CCGGAT
40131503 ATCATTCGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 64 0.89
41 8 0.11
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (39 bp):
CCGGATTTAGTACTTGCACGAAAGCCTTCGGATCTTAGT
Found at i:40131461 original size:80 final size:80
Alignment explanation
Indices: 40131316--40131502 Score: 204
Period size: 80 Copynumber: 2.3 Consensus size: 80
40131306 GCTACACATT
* * *
40131316 CAAATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACGAATGCCTTCGGGACTCAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCGTCGGGACTCAACCCG
*
40131380 GATTTAGT-AGCTT-GCT
64 GATTTAGTCA-CTTAGCA
* * * **
40131396 CGAAAGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACGTATGCCGTC-GGATCTTAGTCC
1 C-AAAGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGA-CTCAACCC
40131459 GGATTTAGTCACTTAGCA
63 GGATTTAGTCACTTAGCA
40131477 CAAAGCCTTCGGGACTTAGCCCGGAT
1 CAAAGCCTTCGGGACTTAGCCCGGAT
40131503 ATCATTCGAA
Statistics
Matches: 90, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 6 0.07
80 72 0.80
81 12 0.13
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGACTCAACCCGGA
TTTAGTCACTTAGCA
Found at i:40139495 original size:40 final size:39
Alignment explanation
Indices: 40139451--40139576 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 39
40139441 GGGACTCAAC
*
40139451 CCGGATTTAGTAGCTTGCTCGAAAGCCTTCGGATCTTAGT
1 CCGGATTTAGTA-CTTGCACGAAAGCCTTCGGATCTTAGT
* * * *
40139491 CCGGATTTAGTAACTCGCACGTATGCCGTCGGATCTTAGT
1 CCGGATTTAGT-ACTTGCACGAAAGCCTTCGGATCTTAGT
*
40139531 CCGGATTTAGTCACTTAGCAC-AAAGCCTTCGGGA-CTTAGC
1 CCGGATTTAGT-ACTT-GCACGAAAGCCTTC-GGATCTTAGT
40139571 CCGGAT
1 CCGGAT
40139577 ATCATTCGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 64 0.89
41 8 0.11
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (39 bp):
CCGGATTTAGTACTTGCACGAAAGCCTTCGGATCTTAGT
Found at i:40139535 original size:80 final size:80
Alignment explanation
Indices: 40139390--40139576 Score: 204
Period size: 80 Copynumber: 2.3 Consensus size: 80
40139380 GCTACACATT
* * *
40139390 CAAATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACGAATGCCTTCGGGACTCAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCGTCGGGACTCAACCCG
*
40139454 GATTTAGT-AGCTT-GCT
64 GATTTAGTCA-CTTAGCA
* * * **
40139470 CGAAAGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACGTATGCCGTC-GGATCTTAGTCC
1 C-AAAGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGA-CTCAACCC
40139533 GGATTTAGTCACTTAGCA
63 GGATTTAGTCACTTAGCA
40139551 CAAAGCCTTCGGGACTTAGCCCGGAT
1 CAAAGCCTTCGGGACTTAGCCCGGAT
40139577 ATCATTCGAA
Statistics
Matches: 90, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 6 0.07
80 72 0.80
81 12 0.13
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGACTCAACCCGGA
TTTAGTCACTTAGCA
Found at i:40145315 original size:40 final size:40
Alignment explanation
Indices: 40145232--40145384 Score: 143
Period size: 40 Copynumber: 3.8 Consensus size: 40
40145222 TCGAATGATG
* *
40145232 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAA
* **
40145272 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTCCCAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTGACCAAA
* **
40145312 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCT-ATTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TGACCA-AA
* * *
40145353 -CCGGGCTATGTCCCGAAGGCTTTTGAGCGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
40145385 CGCTATATCC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.02
40 81 0.86
41 11 0.12
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAA
Found at i:40147807 original size:25 final size:25
Alignment explanation
Indices: 40147779--40147871 Score: 114
Period size: 25 Copynumber: 3.7 Consensus size: 25
40147769 GAATCAGAAT
40147779 CAGAATCAAAATCAAAATTAGGTGA
1 CAGAATCAAAATCAAAATTAGGTGA
*
40147804 CAGAATCAGAATCAAAATTAGGTGA
1 CAGAATCAAAATCAAAATTAGGTGA
* * ** * *
40147829 CAGAATTAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAAAATTAGGTGA
*
40147854 TAGAATCAAAATCAAAAT
1 CAGAATCAAAATCAAAAT
40147872 GTGAATGCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.22
Consensus pattern (25 bp):
CAGAATCAAAATCAAAATTAGGTGA
Found at i:40148830 original size:27 final size:26
Alignment explanation
Indices: 40148800--40148916 Score: 92
Period size: 27 Copynumber: 4.4 Consensus size: 26
40148790 ATCGGTAGTC
* *
40148800 CTACCCTGCAGGGGTATTTTAGTAATT
1 CTACCCTACAGGGG-ATTTCAGTAATT
* *
40148827 CTACCCTACAGGGGATTTCGGTATTT
1 CTACCCTACAGGGGATTTCAGTAATT
* * *
40148853 CTACCCAACAAGGGTATTTC-GATATTT
1 CTACCCTAC-AGGGGATTTCAG-TAATT
* * * *
40148880 CTACCCTACAAAGGTATTTCGGTATTT
1 CTACCCTAC-AGGGGATTTCAGTAATT
40148907 CTACCCTACA
1 CTACCCTACA
40148917 AAGGTATTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
26 19 0.24
27 59 0.75
28 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (26 bp):
CTACCCTACAGGGGATTTCAGTAATT
Found at i:40148917 original size:27 final size:27
Alignment explanation
Indices: 40148825--40148926 Score: 152
Period size: 27 Copynumber: 3.8 Consensus size: 27
40148815 ATTTTAGTAA
* *
40148825 TTCTACCCTAC-AGGGGATTTCGGTAT
1 TTCTACCCTACAAAGGTATTTCGGTAT
* * *
40148851 TTCTACCCAACAAGGGTATTTCGATAT
1 TTCTACCCTACAAAGGTATTTCGGTAT
40148878 TTCTACCCTACAAAGGTATTTCGGTAT
1 TTCTACCCTACAAAGGTATTTCGGTAT
40148905 TTCTACCCTACAAAGGTATTTC
1 TTCTACCCTACAAAGGTATTTC
40148927 AATAATTTTG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
26 10 0.14
27 59 0.86
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (27 bp):
TTCTACCCTACAAAGGTATTTCGGTAT
Found at i:40149014 original size:81 final size:81
Alignment explanation
Indices: 40148919--40149074 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 81
40148909 ACCCTACAAA
** * *
40148919 GGTATTTCAATAATTTTGTAAATCGAGGGTAAAAT-AGTAA-TTCTATAAATCGGGGGTACTTTG
1 GGTATTTCAATAATTTTACAAATCGAGGGT-AAATCAGTAATTTC-ACAAATCAGGGGTACTTTG
40148982 GTAATTTTACAAGTTGAG
64 GTAATTTTACAAGTTGAG
* ** ** *
40149000 GGTATTTCAGTAATTTTACAGGTCGAGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGGT
1 GGTATTTCAATAATTTTACAAATCGAGGGTAAATCAGTAATTTCACAAATCAGGGGTACTTTGGT
40149065 AATTTTACAA
66 AATTTTACAA
40149075 ACTAAGGGTA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
80 2 0.03
81 58 0.92
82 3 0.05
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (81 bp):
GGTATTTCAATAATTTTACAAATCGAGGGTAAATCAGTAATTTCACAAATCAGGGGTACTTTGGT
AATTTTACAAGTTGAG
Found at i:40149083 original size:54 final size:53
Alignment explanation
Indices: 40149025--40149181 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 53
40149015 TTACAGGTCG
* *
40149025 AGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACTA
1 AGGGTATTTTAGTAATTT-ACAAATCAGGGGTATTTTGGTAATTTTACAAACCA
* * * *
40149079 AGGGTATTTTGGTAGTTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
1 AGGGTATTTTAGTA-ATTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCA
*
40149133 AGGGTATTTTAGTAATTTACAAATCAGGGGTATTTTGGTAATTCTACAA
1 AGGGTATTTTAGTAATTTACAAATCAGGGGTATTTTGGTAATTTTACAA
40149182 CTTATCCACT
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 31 0.34
54 57 0.63
55 3 0.03
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (53 bp):
AGGGTATTTTAGTAATTTACAAATCAGGGGTATTTTGGTAATTTTACAAACCA
Found at i:40149102 original size:27 final size:27
Alignment explanation
Indices: 40148972--40149181 Score: 197
Period size: 27 Copynumber: 7.8 Consensus size: 27
40148962 TATAAATCGG
* ****
40148972 GGGTACTTTGGTAATTTTACAAGTTGA
1 GGGTATTTTGGTAATTTTACAAACCAA
** *** *
40148999 GGGTATTTCAGTAATTTTACAGGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
** * * *
40149026 GGGTATTTCAGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
40149053 GGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
40149080 GGGTATTTTGGTAGTTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
40149107 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
40149134 GGGTATTTTAGTAA-TTTACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
40149160 GGGTATTTTGGTAATTCTACAA
1 GGGTATTTTGGTAATTTTACAA
40149182 CTTATCCACT
Statistics
Matches: 154, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
26 22 0.14
27 132 0.86
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:40151535 original size:27 final size:27
Alignment explanation
Indices: 40151503--40151709 Score: 274
Period size: 27 Copynumber: 7.7 Consensus size: 27
40151493 CACGAGGGGC
*
40151503 AAAATAGTAATTCTGTAAATCGAGGGT
1 AAAACAGTAATTCTGTAAATCGAGGGT
*
40151530 AAAATAGTAATTCTGTAAATCGAGGGT
1 AAAACAGTAATTCTGTAAATCGAGGGT
*
40151557 AAAA-AGGTCATTCTGTAAATCGAGGGT
1 AAAACA-GTAATTCTGTAAATCGAGGGT
*
40151584 AAAA-AGGTCATTCTGTAAATCGAGGGT
1 AAAACA-GTAATTCTGTAAATCGAGGGT
* *
40151611 AAAATAGTAATTCTGTCAATCGAGGGT
1 AAAACAGTAATTCTGTAAATCGAGGGT
* * * *
40151638 AAAACGGTAATTCTATAAATTGAAGGT
1 AAAACAGTAATTCTGTAAATCGAGGGT
40151665 AAAACAGTAATTCTGTAAATCGAGGGT
1 AAAACAGTAATTCTGTAAATCGAGGGT
* *
40151692 AAAACGGTAATTTTGTAA
1 AAAACAGTAATTCTGTAA
40151710 TTTGGGGGTA
Statistics
Matches: 163, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
26 1 0.01
27 161 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (27 bp):
AAAACAGTAATTCTGTAAATCGAGGGT
Found at i:40151742 original size:54 final size:54
Alignment explanation
Indices: 40151681--40151873 Score: 201
Period size: 54 Copynumber: 3.6 Consensus size: 54
40151671 GTAATTCTGT
*** **
40151681 AAATCGAGGGTAAAACGGTAATTTTGTAATTTGGGGGTACTTTGATAATTTTAC
1 AAATCGAGGGTATTTCGGTAATTTTGTAAACTGGGGGTACTTTGATAATTTTAC
* ** * *
40151735 AAGTCGAGGGTATTTCAATAATTTTGCAAACTGAGGGTA-TTTCGATAATTTTAC
1 AAATCGAGGGTATTTCGGTAATTTTGTAAACTGGGGGTACTTT-GATAATTTTAC
* * * *
40151789 AAATCGAGGATATTTGGGTAATTTTATAAACTGGGGGTACTTTGGTAATTTTAC
1 AAATCGAGGGTATTTCGGTAATTTTGTAAACTGGGGGTACTTTGATAATTTTAC
* * * *
40151843 AACTAG-GGGTATTTCAGTAATTTGGTAAACT
1 AAATCGAGGGTATTTCGGTAATTTTGTAAACT
40151874 AAAGTATTCT
Statistics
Matches: 111, Mismatches: 26, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
53 23 0.21
54 85 0.77
55 3 0.03
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (54 bp):
AAATCGAGGGTATTTCGGTAATTTTGTAAACTGGGGGTACTTTGATAATTTTAC
Found at i:40151745 original size:27 final size:27
Alignment explanation
Indices: 40151715--40151865 Score: 118
Period size: 27 Copynumber: 5.6 Consensus size: 27
40151705 TGTAATTTGG
*
40151715 GGGTACTTT-GATAATTTTAC-AAGTCGA
1 GGGTA-TTTCGATAATTTTACAAACT-GA
* *
40151742 GGGTATTTCAATAATTTTGCAAACTGA
1 GGGTATTTCGATAATTTTACAAACTGA
40151769 GGGTATTTCGATAATTTTACAAA-TCGA
1 GGGTATTTCGATAATTTTACAAACT-GA
* * * * *
40151796 GGATATTTGGGTAATTTTATAAACTGG
1 GGGTATTTCGATAATTTTACAAACTGA
*
40151823 GGGTACTTT-GGTAATTTTAC-AACT-A
1 GGGTA-TTTCGATAATTTTACAAACTGA
40151848 GGGGTATTTC-AGTAATTT
1 -GGGTATTTCGA-TAATTT
40151866 GGTAAACTAA
Statistics
Matches: 102, Mismatches: 14, Indels: 17
0.77 0.11 0.13
Matches are distributed among these distances:
25 3 0.03
26 19 0.19
27 73 0.72
28 7 0.07
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAACTGA
Found at i:40151784 original size:108 final size:107
Alignment explanation
Indices: 40151672--40151865 Score: 244
Period size: 108 Copynumber: 1.8 Consensus size: 107
40151662 GGTAAAACAG
** * * **
40151672 TAATTCTGTAAATCGAGGGTAAAACGGTAATTTTGTAATTTGGGGGTACTTTGATAATTTTACAA
1 TAATTCTACAAATCGAGGATAAAACGGTAATTTTATAAACTGGGGGTACTTTGATAATTTTACAA
* *
40151737 GTCGAGGGTATTTCAATAATTTTGCAAACTGAGGGTATTTCGA
66 CTAG-GGGTATTTCAATAATTTTGCAAACTGAGGGTATTTCGA
* **** *
40151780 TAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAACTGGGGGTACTTTGGTAATTTTACAA
1 TAATTCTACAAATCGAGGATAAAACGGTAATTTTATAAACTGGGGGTACTTTGATAATTTTACAA
*
40151845 CTAGGGGTATTTCAGTAATTT
66 CTAGGGGTATTTCAATAATTT
40151866 GGTAAACTAA
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
107 16 0.23
108 55 0.77
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (107 bp):
TAATTCTACAAATCGAGGATAAAACGGTAATTTTATAAACTGGGGGTACTTTGATAATTTTACAA
CTAGGGGTATTTCAATAATTTTGCAAACTGAGGGTATTTCGA
Found at i:40152578 original size:53 final size:55
Alignment explanation
Indices: 40152493--40152727 Score: 334
Period size: 55 Copynumber: 4.3 Consensus size: 55
40152483 TTTTTGATGT
* *
40152493 CTTGACATGGTCTTACATGGTATCTTTTCCTTAT-G-AACTCACCAATGCCATGC
1 CTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCACCAATGCCATGC
* * *
40152546 CTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCCATGT
1 CTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCACCAATGCCATGC
* * *
40152601 CTTGACATGGTCTTACATGGTATCTTTGCCTTAT-G-AACTCACCAATGCCATGC
1 CTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCACCAATGCCATGC
* * * *
40152654 CTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGTCATGT
1 CTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCACCAATGCCATGC
40152709 CTTGACATGGTCTTACATG
1 CTTGACATGGTCTTACATG
40152728 ATATCCTTAT
Statistics
Matches: 159, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
53 77 0.48
54 3 0.02
55 79 0.50
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (55 bp):
CTTGACATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCACCAATGCCATGC
Found at i:40152612 original size:55 final size:53
Alignment explanation
Indices: 40152489--40152727 Score: 334
Period size: 53 Copynumber: 4.4 Consensus size: 53
40152479 AAGCTTTTTG
* *
40152489 ATGTCTTGACATGGTCTTACATGGTATCTTTTCCTTATGAACTCACCAATGCC
1 ATGTCTTGACATGGTCTTACATGGGACCTTTTCCTTATGAACTCACCAATGCC
* * *
40152542 ATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCC
1 ATGTCTTGACATGGTCTTACATGGGACCTTTTCCTTAT-G-AACTCACCAATGCC
* * *
40152597 ATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAACTCACCAATGCC
1 ATGTCTTGACATGGTCTTACATGGGACCTTTTCCTTATGAACTCACCAATGCC
* * * *
40152650 ATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGTC
1 ATGTCTTGACATGGTCTTACATGGGACCTTTTCCTTAT-G-AACTCACCAATGCC
40152705 ATGTCTTGACATGGTCTTACATG
1 ATGTCTTGACATGGTCTTACATG
40152728 ATATCCTTAT
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 80 0.49
54 3 0.02
55 79 0.49
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
ATGTCTTGACATGGTCTTACATGGGACCTTTTCCTTATGAACTCACCAATGCC
Found at i:40152678 original size:108 final size:108
Alignment explanation
Indices: 40152489--40152732 Score: 461
Period size: 108 Copynumber: 2.3 Consensus size: 108
40152479 AAGCTTTTTG
*
40152489 ATGTCTTGACATGGTCTTACATGGTATCTTTTCCTTATGAACTCACCAATGCCATGCCTTGGCAT
1 ATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAACTCACCAATGCCATGCCTTGGCAT
40152554 GGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCC
66 GGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCC
40152597 ATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAACTCACCAATGCCATGCCTTGGCAT
1 ATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAACTCACCAATGCCATGCCTTGGCAT
*
40152662 GGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGTC
66 GGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCC
*
40152705 ATGTCTTGACATGGTCTTACATGATATC
1 ATGTCTTGACATGGTCTTACATGGTATC
40152733 CTTATCTTAC
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 133 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (108 bp):
ATGTCTTGACATGGTCTTACATGGTATCTTTGCCTTATGAACTCACCAATGCCATGCCTTGGCAT
GGTCTTACATGGGACCTTTTCCTTATAGTAACTCATCAATGCC
Found at i:40152766 original size:47 final size:47
Alignment explanation
Indices: 40152713--40152835 Score: 203
Period size: 47 Copynumber: 2.6 Consensus size: 47
40152703 TCATGTCTTG
*
40152713 ACATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAA
1 ACATGGTCTTACATGATATCCTTGTCTTACCAAATGCCATGTTCCAA
*
40152760 ACATGGTCTTACATGGA-ATCCTTGTCTTACCAAATGCCATGTTCGAA
1 ACATGGTCTTACAT-GATATCCTTGTCTTACCAAATGCCATGTTCCAA
*
40152807 ACATGGTCTTACATGGTATCCTTGTCTTA
1 ACATGGTCTTACATGATATCCTTGTCTTA
40152836 GTGCCAATGC
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
46 1 0.01
47 68 0.96
48 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.35
Consensus pattern (47 bp):
ACATGGTCTTACATGATATCCTTGTCTTACCAAATGCCATGTTCCAA
Found at i:40159922 original size:48 final size:48
Alignment explanation
Indices: 40159791--40160016 Score: 218
Period size: 48 Copynumber: 4.8 Consensus size: 48
40159781 GTTATGTACA
* *
40159791 ATCCCATGTAAGACCATGTCTGGGACATGG--TCTCGCATCGATATGTA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCAT-TGGCATCGATATGTG
**** *
40159838 ATTTGGTGTAAGACCATAGT-TGGG-C-T---ATCGGCATCGATATGTG
1 ATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATGTG
* ** **
40159881 ATCCCATGTAAGACTATGTCTGGGACATGGCATTGGCATCGACCTACG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
**
40159929 ATCCCATGTAAGACCATGTCTGGGACATGATATTGGCATCGATATGTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
* *
40159977 ATCCCATGTAAGACCATATCCT-GGATATGGCATTGGCATC
1 ATCCCATGTAAGACCATGT-CTGGGACATGGCATTGGCATC
40160017 CTACCATGTG
Statistics
Matches: 142, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
42 2 0.01
43 28 0.20
44 2 0.01
45 2 0.01
46 1 0.01
47 17 0.12
48 88 0.62
49 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (48 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
Found at i:40161297 original size:76 final size:76
Alignment explanation
Indices: 40161209--40161364 Score: 260
Period size: 76 Copynumber: 2.1 Consensus size: 76
40161199 CGGCCTAAGC
*
40161209 ACACGAGCATGTGTCTTGGAC-GTGTGACCCTAATTGTATTGATGACGTCATAAATAGAGAGTTA
1 ACACGAGCATGTGTCTTGG-CTGTGTGACCCTAATTGTATTGATGACATCATAAATAGAGAGTTA
40161273 CACGAATTGAGG
65 CACGAATTGAGG
*
40161285 ACACGAGTATGTGTCTTGGCTGTGTGACCCTAATTGTATTGATGACATCATAAATAGAGAGTTAC
1 ACACGAGCATGTGTCTTGGCTGTGTGACCCTAATTGTATTGATGACATCATAAATAGAGAGTTAC
**
40161350 ACGGGTTGAGG
66 ACGAATTGAGG
40161361 ACAC
1 ACAC
40161365 AGGCGTGTCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
75 1 0.01
76 74 0.99
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (76 bp):
ACACGAGCATGTGTCTTGGCTGTGTGACCCTAATTGTATTGATGACATCATAAATAGAGAGTTAC
ACGAATTGAGG
Found at i:40170615 original size:48 final size:48
Alignment explanation
Indices: 40170499--40170620 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
40170489 GGGCTATCGA
* * * *
40170499 CATCGATATGTGATCCCATGTAAAACCATGTTTTGGTCATGGCATTGG
1 CATCGATATGTGATCCCATGTAAAACCATGTCTAGGACATGACATTGG
** ** *
40170547 CATCGACCTACGATCCCATGTAAGACCATGTCTAGGACATGACATTGG
1 CATCGATATGTGATCCCATGTAAAACCATGTCTAGGACATGACATTGG
* *
40170595 CATCGATATGTGGTCTCATGTAAAAC
1 CATCGATATGTGATCCCATGTAAAAC
40170621 TATATCTGTA
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (48 bp):
CATCGATATGTGATCCCATGTAAAACCATGTCTAGGACATGACATTGG
Found at i:40175553 original size:40 final size:40
Alignment explanation
Indices: 40175460--40175677 Score: 276
Period size: 40 Copynumber: 5.7 Consensus size: 40
40175450 CTAACGGGGT
* * *
40175460 TAAGT-CCGAAGACATTTGTGCTAGTGA-TAATTCC--GC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
40175496 TAAGTCCC-AAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
40175535 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
40175575 TAAGT-CCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* * *
40175614 TAAGTCCCGAAGGCATTTGTGCTAGTGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
* *
40175654 TAAGACCCG-AGGC-CTTGTGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCGAGT
40175678 GGTTATATCC
Statistics
Matches: 166, Mismatches: 8, Indels: 14
0.88 0.04 0.07
Matches are distributed among these distances:
36 21 0.13
37 9 0.05
38 11 0.07
39 50 0.30
40 75 0.45
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:40175588 original size:79 final size:79
Alignment explanation
Indices: 40175460--40175702 Score: 304
Period size: 79 Copynumber: 3.2 Consensus size: 79
40175450 CTAACGGGGT
*
40175460 TAAGT-CCGAAGACATTTGTGCTAGTGA-TAATTCC--GCTAAGTCCCAAGGCATTTGTGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCAAGGCATTTGTGCGAGT
40175521 TACTA-ATTCCGGGC
66 TACTATA-TCCGGGC
* * *
40175535 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCGAAGGCATTTGTGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCAAGGCATTTGTGCGAGT
40175600 TACTATATCCGGGC
66 TACTATATCCGGGC
* * * *
40175614 TAAGTCCCGAAGGCATTTGTGCTAGTGAC-CATATCCGGGCTAAGACCCGAGGC-CTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-TCCGGGCTAAGTCCCAAGGCATTTGTGCGAG
***
40175677 TGGTTATATCC-GGC
65 TTACTATATCCGGGC
*
40175691 TAAATCCCGAAG
1 TAAGTCCCGAAG
40175703 ATACTTGGGT
Statistics
Matches: 147, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
75 5 0.03
76 19 0.13
77 21 0.14
78 19 0.13
79 82 0.56
80 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (79 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCAAGGCATTTGTGCGAGT
TACTATATCCGGGC
Found at i:40180304 original size:13 final size:13
Alignment explanation
Indices: 40180286--40180312 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40180276 GCGATGAATG
40180286 TACACTTGTCTGT
1 TACACTTGTCTGT
40180299 TACACTTGTCTGT
1 TACACTTGTCTGT
40180312 T
1 T
40180313 CTATCCGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (13 bp):
TACACTTGTCTGT
Found at i:40182640 original size:40 final size:41
Alignment explanation
Indices: 40182515--40182642 Score: 167
Period size: 40 Copynumber: 3.2 Consensus size: 41
40182505 ATGCTGGAAA
* *
40182515 TTATATCCGGGTTAAGACCCGAAGGCATT-GTGCTAC--GG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGACGTGG
* * *
40182553 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGACGTGG
*
40182593 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGACGTGG
40182633 TTATATCCGG
1 TTATATCCGG
40182643 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
38 26 0.34
39 6 0.08
40 44 0.58
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (41 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGACGTGG
Found at i:40187598 original size:40 final size:40
Alignment explanation
Indices: 40187542--40187732 Score: 213
Period size: 40 Copynumber: 4.8 Consensus size: 40
40187532 CATGAGCATT
* * *
40187542 TGAATGATACCCGGGCTAAGTCCCGAAGGCATTTATGCCAG
1 TGAAT-ATATCCGGGCTAAGACCCGAAGGCATTTATGCAAG
* *
40187583 TGAATATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
1 TGAATATATCCGGGCTAAGACCCGAAGGCATTTATGCAAG
* ** *
40187623 TGATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG
1 TGAATATATCCGGGCTAAGACCCGAAGGCATTTATGCAAG
* *
40187663 TTG-TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAG
1 -TGAATATATCCGGGCTAAGACCCGAAGGCATTTATGCAAG
* ** * *
40187703 TTACCAAATCCGGGTTAAGACCCGAAGGCA
1 TGAATATATCCGGGCTAAGACCCGAAGGCA
40187733 ATTGCGCTTG
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 126 0.94
41 7 0.05
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TGAATATATCCGGGCTAAGACCCGAAGGCATTTATGCAAG
Found at i:40187754 original size:40 final size:40
Alignment explanation
Indices: 40187552--40187759 Score: 206
Period size: 40 Copynumber: 5.2 Consensus size: 40
40187542 TGAATGATAC
* * * * *
40187552 CCGGGCTAAGTCCCGAAGGCATTTATGCCAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
40187592 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
40187632 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * * ** *
40187672 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * * *
40187712 CCGGGTTAAGACCCGAAGGCAATTGCGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
40187752 CC-GGCTAA
1 CCGGGCTAA
40187760 ATTTCGAAGA
Statistics
Matches: 141, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
39 8 0.06
40 129 0.91
41 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:40189668 original size:40 final size:39
Alignment explanation
Indices: 40189503--40189686 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
40189493 AAATTGAATG
* * *
40189503 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40189543 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40189583 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40189623 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40189662 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40189687 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:40189711 original size:80 final size:81
Alignment explanation
Indices: 40189543--40189731 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
40189533 GCTGGAAATT
* * * *
40189543 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
40189608 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
40189624 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
40189687 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
40189703 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
40189732 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:40195117 original size:40 final size:39
Alignment explanation
Indices: 40194952--40195135 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
40194942 AAATTGAATG
* * *
40194952 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40194992 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40195032 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40195072 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40195111 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40195136 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:40195160 original size:80 final size:81
Alignment explanation
Indices: 40194992--40195180 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
40194982 GCTGGAAATT
* * * *
40194992 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
40195057 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
40195073 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
40195136 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
40195152 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
40195181 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:40203235 original size:40 final size:39
Alignment explanation
Indices: 40203070--40203253 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
40203060 AAATTGAATG
* * *
40203070 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
40203110 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
40203150 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
40203190 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
40203229 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
40203254 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:40203278 original size:80 final size:81
Alignment explanation
Indices: 40203110--40203298 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
40203100 GCTGGAAATT
* * * *
40203110 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
40203175 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
40203191 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
40203254 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
40203270 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
40203299 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:40204766 original size:40 final size:40
Alignment explanation
Indices: 40204697--40204890 Score: 273
Period size: 40 Copynumber: 4.8 Consensus size: 40
40204687 GGTGTTACAG
* * *
40204697 ACCCGAAGGCAATTGTGCTAG-TGACTATATCCGGGCTAAT
1 ACCCGAAGGCATTTGTGCAAGTTG-TTATATCCGGGCTAAT
*
40204737 ACCCAAAGGCATTTGTGCAAGTTGTTATATCCGGGCTAAT
1 ACCCGAAGGCATTTGTGCAAGTTGTTATATCCGGGCTAAT
40204777 ACCCGAAGGCATTTGTGCAAGTTGTTATATCCGGGCTAAT
1 ACCCGAAGGCATTTGTGCAAGTTGTTATATCCGGGCTAAT
* *
40204817 ACCCGAAGGCATTTGTGCAAGTCGTTATATCCGGGCTAAG
1 ACCCGAAGGCATTTGTGCAAGTTGTTATATCCGGGCTAAT
* * ** *
40204857 ACCCGAGGGCATTCGTGCGTGTGGTTATATCCGG
1 ACCCGAAGGCATTTGTGCAAGTTGTTATATCCGG
40204891 TTGTATTCCG
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 139 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ACCCGAAGGCATTTGTGCAAGTTGTTATATCCGGGCTAAT
Found at i:40206349 original size:46 final size:46
Alignment explanation
Indices: 40206275--40206495 Score: 370
Period size: 46 Copynumber: 4.8 Consensus size: 46
40206265 GGGTGTTACA
* ** *
40206275 GTATCTTTCAACCATGGCCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
40206321 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
* *
40206367 GTATCTTTCAACCATGGTTTTATACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
* *
40206413 GTATCTTTCAACCATGGTTTTACACATTTCACATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
40206459 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
40206496 AGAGCACACT
Statistics
Matches: 165, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 165 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
Found at i:40206385 original size:25 final size:25
Alignment explanation
Indices: 40206357--40206431 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
40206347 TTTCATATCA
40206357 GGTTGCCATGGTATCTTTCAACCAT
1 GGTTGCCATGGTATCTTTCAACCAT
*
40206382 GGTT----T--TATACATTTCATATCA-
1 GGTTGCCATGGTAT-C-TTTCA-ACCAT
40206403 GGTTGCCATGGTATCTTTCAACCAT
1 GGTTGCCATGGTATCTTTCAACCAT
40206428 GGTT
1 GGTT
40206432 TTACACATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 20
0.63 0.03 0.33
Matches are distributed among these distances:
19 3 0.08
20 1 0.03
21 10 0.26
22 3 0.08
24 3 0.08
25 14 0.37
26 1 0.03
27 3 0.08
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (25 bp):
GGTTGCCATGGTATCTTTCAACCAT
Found at i:40213769 original size:37 final size:37
Alignment explanation
Indices: 40213717--40213813 Score: 176
Period size: 37 Copynumber: 2.6 Consensus size: 37
40213707 TTATTACGAA
*
40213717 GTCTTACCCGGACATAATCTCTACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
40213754 GTCTTACCCGAACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
40213791 GTCTTACCCGGACATAATCTCCA
1 GTCTTACCCGGACATAATCTCCA
40213814 AGTTTCATGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:40213924 original size:48 final size:48
Alignment explanation
Indices: 40213848--40214566 Score: 1132
Period size: 48 Copynumber: 15.0 Consensus size: 48
40213838 GTTACAACAC
* * *
40213848 TCACATTAGCCATTCGGCTTTACCACATATTCTTATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* ** *
40213896 TCACATTCGCCATTCGGCTTTATGACATATACATATCTCATATATACT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
40213944 TCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
40213992 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
40214040 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
40214088 TCACATTAGCCATTCGGCTCTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * *
40214136 TCACATTAGCCATTCGGCTTTACGACATAGACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
40214184 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * * *
40214232 TCACATTCGCCATTCGGCTTTACCACATCTACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
40214280 TCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
40214328 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * * *
40214376 TCACATTCGCCATTCGGCTTTACCACATCTACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
40214424 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
40214472 TCACATTACCCATTCGGCTTTACCACATATACATATCTTATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * *
40214520 TCACATTAGCCATTCGGCTTTACCACATACACATATCACACATATAT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
40214567 ATATTTATCT
Statistics
Matches: 617, Mismatches: 54, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 617 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (48 bp):
TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
Found at i:40215791 original size:2 final size:2
Alignment explanation
Indices: 40215784--40215815 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40215774 CCATTGCCGA
40215784 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
40215816 CATCAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40217607 original size:79 final size:81
Alignment explanation
Indices: 40217480--40217663 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
40217470 ACGACTCGCT
** * *
40217480 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCCGAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCCGAATGCCTTC-GGATCCTAACCCG
* *
40217543 GGTTTAGTAACTT-GCA
65 GATATAGTAACTTAGCA
* **
40217559 CAAATGCCTTCGGG-CTTAGCCCGGATT-TATTAACTCGCACGAATGCCTTCGGATCCTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGC-CGAATGCCTTCGGATCCTAACCCG
*
40217622 GATATAGTCACTTAGCA
65 GATATAGTAACTTAGCA
40217639 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40217664 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 20 0.22
79 52 0.58
80 18 0.20
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCCGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:40217663 original size:40 final size:39
Alignment explanation
Indices: 40217473--40217663 Score: 154
Period size: 39 Copynumber: 4.8 Consensus size: 39
40217463 GGATATAACG
* ** * *
40217473 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
40217513 ACTCGC-CGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
40217552 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
40217591 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
40217631 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
40217664 CATCATTCGA
Statistics
Matches: 120, Mismatches: 23, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
38 2 0.02
39 58 0.48
40 52 0.43
41 8 0.07
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:40236244 original size:34 final size:33
Alignment explanation
Indices: 40236173--40236254 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 33
40236163 TTGATGGCTG
*
40236173 TACTGAACTGGGCTAAGGCCCACACTGTTAATAC
1 TACTGAA-TGGGCTAAGGCCCACACTGTAAATAC
*
40236207 TACTGTAATGGGCTAAGGCCCACACTG-AAATTGC
1 TACTG-AATGGGCTAAGGCCCACACTGTAAA-TAC
40236241 TACTGATATGGGCT
1 TACTGA-ATGGGCT
40236255 TAAGCCAGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 3 0.07
34 38 0.88
35 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (33 bp):
TACTGAATGGGCTAAGGCCCACACTGTAAATAC
Found at i:40238983 original size:46 final size:46
Alignment explanation
Indices: 40238816--40238990 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
40238806 ATGTAACCGC
* * *
40238816 CCATAAGTGAACTCGGACT-AACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * *
40238861 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* *
40238911 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
40238954 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40238991 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 20 0.18
46 44 0.40
47 29 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:40238990 original size:93 final size:92
Alignment explanation
Indices: 40238824--40238994 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 92
40238814 GCCCATAAGT
* *
40238824 GAACTCGGACTAACTCAACGAGCTCGGGCATTCGCATCCATGAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
40238889 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* *
40238916 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACT-AACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40238981 CGAGTTCGGATGCC
65 CGAGTTCGGATGCC
40238995 CAAATATCCA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 11 0.15
93 63 0.85
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40241409 original size:30 final size:30
Alignment explanation
Indices: 40241365--40241453 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
40241355 CAAAGATAAC
40241365 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
40241394 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
40241424 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
40241454 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:40241413 original size:15 final size:15
Alignment explanation
Indices: 40241365--40241444 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
40241355 CAAAGATAAC
*
40241365 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
40241379 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
40241394 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
40241409 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
40241424 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
40241439 AAGAAA
1 AAGAAA
40241445 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:40241453 original size:15 final size:15
Alignment explanation
Indices: 40241376--40241453 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
40241366 AGAAAACCGA
40241376 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
40241391 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
40241405 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
40241420 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
40241436 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
40241451 ATA
1 ATA
40241454 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:40244452 original size:47 final size:49
Alignment explanation
Indices: 40244342--40244520 Score: 180
Period size: 45 Copynumber: 3.8 Consensus size: 49
40244332 TGTAACCCGC
* * * **
40244342 CCATAAGTGAACTCGGACTTAACTCAACGAGCTCGG--G-CA-TCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
* *
40244387 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACAT
* * *
40244437 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
*
40244480 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC
40244521 CAAATATCCA
Statistics
Matches: 112, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
43 6 0.05
44 2 0.02
45 35 0.31
46 29 0.26
47 30 0.27
48 3 0.03
49 3 0.03
50 4 0.04
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
Found at i:40244508 original size:93 final size:92
Alignment explanation
Indices: 40244350--40244520 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 92
40244340 GCCCATAAGT
* * *
40244350 GAACTCGGACTTAACTCAACGAGCTCGGGCATCGCATCCATGAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
40244415 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* *
40244442 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACA-TCGCATCCATAAGTGAACTCGGACTCAACTCAA
40244507 CGAGTTCGGATGCC
65 CGAGTTCGGATGCC
40244521 CAAATATCCA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 28 0.38
93 45 0.62
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40256472 original size:39 final size:38
Alignment explanation
Indices: 40256386--40256485 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 38
40256376 AAAATCCTTG
* *
40256386 TTATAATTATTGTAATTATAATTTATGATCGAATTTTA
1 TTATAATTATTTTAATTATAATTTATGATCGAATGTTA
* *
40256424 TTATAATTATTTTAATTGTAATTTTTCGATC-AATCGTTA
1 TTATAATTATTTTAATTATAATTTAT-GATCGAAT-GTTA
* *
40256463 TTATAATTATGTTAATTTTAATT
1 TTATAATTATTTTAATTATAATT
40256486 ATTATATTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
38 26 0.48
39 28 0.52
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (38 bp):
TTATAATTATTTTAATTATAATTTATGATCGAATGTTA
Found at i:40258653 original size:21 final size:21
Alignment explanation
Indices: 40258628--40258677 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
40258618 TCTTTAATGG
40258628 GAATCATAATAAAAATCCACT
1 GAATCATAATAAAAATCCACT
40258649 GAATCATAATAAAAATCCACT
1 GAATCATAATAAAAATCCACT
40258670 -ATATCATA
1 GA-ATCATA
40258678 TTGTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.52, C:0.18, G:0.04, T:0.26
Consensus pattern (21 bp):
GAATCATAATAAAAATCCACT
Found at i:40262516 original size:41 final size:41
Alignment explanation
Indices: 40262454--40262603 Score: 203
Period size: 41 Copynumber: 3.7 Consensus size: 41
40262444 TCGGGGTTTA
*
40262454 AATCCGAGCTTGATCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
*
40262495 AATCTGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
40262536 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
40262576 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
40262604 TGAGTCAGCG
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 31 0.34
41 60 0.66
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:40265738 original size:19 final size:20
Alignment explanation
Indices: 40265710--40265756 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
40265700 AAGAACATGT
40265710 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
40265731 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
40265750 TATATAT
1 TATATAT
40265757 ACTTACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:40269779 original size:131 final size:131
Alignment explanation
Indices: 40269530--40269767 Score: 307
Period size: 131 Copynumber: 1.8 Consensus size: 131
40269520 AATTTAGAAA
* *
40269530 ACATGAGTAAAATTTTAAAAGAACATTCGATTATTTTGAACAAACAAAAAATTACAACCCAACAC
1 ACATGAGTAAAATTCTAAAAGAACATTCGATTATTTTGAACAAACAAAAAATCACAACCCAACAC
*
40269595 GATAAGACACGATTCTCCAAATTGCCAAACATTAAATATTACTTTCATTTTAAAGAGTTTTTAAA
66 GATAAGACACGATTCTCCAAATTGCCAAACATCAAATATTACTTTCATTTTAAAGAGTTTTTAAA
40269660 G
131 G
* ** * * * * *
40269661 ACATGAGTAAAATTCTAAAGGAATGTTCGATTGTTTTGAACAAGCGAGAAAATCGCAACCTAACA
1 ACATGAGTAAAATTCTAAAAGAACATTCGATTATTTTGAACAAAC-AAAAAATCACAACCCAACA
* * * * * *
40269726 CTATAGGGCACGATTCT-CAAATTGCCGAACATCGAGTATTAC
65 CGATAAGACACGATTCTCCAAATTGCCAAACATCAAATATTAC
40269768 CTTTGTTTTA
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
131 60 0.67
132 29 0.33
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (131 bp):
ACATGAGTAAAATTCTAAAAGAACATTCGATTATTTTGAACAAACAAAAAATCACAACCCAACAC
GATAAGACACGATTCTCCAAATTGCCAAACATCAAATATTACTTTCATTTTAAAGAGTTTTTAAA
G
Found at i:40270128 original size:15 final size:16
Alignment explanation
Indices: 40270110--40270139 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40270100 TATATGAAAT
40270110 AATATA-AAAACAATC
1 AATATACAAAACAATC
40270125 AATATACAAAACAAT
1 AATATACAAAACAAT
40270140 ATAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (16 bp):
AATATACAAAACAATC
Found at i:40270140 original size:27 final size:26
Alignment explanation
Indices: 40270092--40270146 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
40270082 AATAATATGC
** *
40270092 AACAATAATATATGAAATAATATAAA
1 AACAATAATATACAAAACAATATAAA
40270118 AACAATCAATATACAAAACAATATAAA
1 AACAAT-AATATACAAAACAATATAAA
40270145 AA
1 AA
40270147 TTAAGAGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (26 bp):
AACAATAATATACAAAACAATATAAA
Found at i:40270516 original size:15 final size:16
Alignment explanation
Indices: 40270498--40270527 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40270488 TATATGGAAT
40270498 AATATA-AAAACAATC
1 AATATACAAAACAATC
40270513 AATATACAAAACAAT
1 AATATACAAAACAAT
40270528 ATAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (16 bp):
AATATACAAAACAATC
Found at i:40270559 original size:388 final size:389
Alignment explanation
Indices: 40269842--40270629 Score: 1427
Period size: 388 Copynumber: 2.0 Consensus size: 389
40269832 TGAAATAAAA
*
40269842 TGAAATAATTGATTTTTAAGAGTTAGAAATTACAAAGCGATATTTGTAAATCAACAAAAAAATAA
1 TGAAATAATTGATTTTTAAGAGTTAAAAATTACAAAGCGATATTTGTAAATCAACAAAAAAATAA
*
40269907 AAACATAGGATAACATGCATACTTAAAACGCAATAATGGATGAATGAAGATAATATATATCTTAT
66 AAACATAGGATAACATGCATACTTAAAACACAATAATGGATGAATGAAGATAATATATATCTTAT
40269972 TTAATCGATTAACAAAATAAACAATTAAATATAACTAGCCTAAAAAAATATAACCCAATTTACAA
131 TTAATCGATTAACAAAATAAACAATTAAATATAACTAGCCTAAAAAAATATAACCCAATTTACAA
*
40270037 ATATGGGTGAACAACAATTAATTTAATAAAACAAAAAAAGGGATAAATAATATGCAACAATAATA
196 ATATGGGTGAACAACAATTAATTTAATAAAACAAAAAAAGGGATAAACAATATGCAACAATAATA
40270102 TATGAAATAATATAAAAACAATCAATATACAAAACAATATAAAAATTAAGAGTCAATATAATGTA
261 TATGAAATAATATAAAAACAATCAATATACAAAACAATATAAAAATTAAGAGTCAATATAATGTA
40270167 AAAACGAAT-AAAAAAACATTAAATATATGAAAAAATTTAAAATGAACCATACATACTAAGGTT
326 AAAACGAATAAAAAAAACATTAAATATATGAAAAAATTTAAAATGAACCATACATACTAAGGTT
* *
40270230 TGAAATAATTGATTTTTAAGAGTTAAAAATTACAAAGCGATATTTGTAAATCTACAAAAAAGTAA
1 TGAAATAATTGATTTTTAAGAGTTAAAAATTACAAAGCGATATTTGTAAATCAACAAAAAAATAA
* *
40270295 AAACGTAGGATAACATGCATA-TGTAAAATACAATAATGGATGAATGAAGATAATATATATCTTA
66 AAACATAGGATAACATGCATACT-TAAAACACAATAATGGATGAATGAAGATAATATATATCTTA
* *
40270359 TTTAATCGATTAACAAAATAAACAATTAAATATAACTAGCCTAAAAAAGTATAACCCAATTTGCA
130 TTTAATCGATTAACAAAATAAACAATTAAATATAACTAGCCTAAAAAAATATAACCCAATTTACA
*
40270424 AATATGGGTGAACAACAATTGATTTAATAAAACAAAAAAAGGGATAAACAATATGCAACAATAAT
195 AATATGGGTGAACAACAATTAATTTAATAAAACAAAAAAAGGGATAAACAATATGCAACAATAAT
* * *
40270489 ATATGGAATAATATAAAAACAATCAATATACAAAACAATATAAAAATTAGGAGTCAATATAATTT
260 ATATGAAATAATATAAAAACAATCAATATACAAAACAATATAAAAATTAAGAGTCAATATAATGT
40270554 AAAAACGAATAAAAAAAAACATTAAATATATGAAAAAATTTAAAATGAACCATACATACTAAGGT
325 AAAAACGAAT-AAAAAAAACATTAAATATATGAAAAAATTTAAAATGAACCATACATACTAAGGT
40270619 T
389 T
40270620 TGAAATAATT
1 TGAAATAATT
40270630 TTTTTTTTAA
Statistics
Matches: 384, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
387 1 0.00
388 319 0.83
390 64 0.17
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (389 bp):
TGAAATAATTGATTTTTAAGAGTTAAAAATTACAAAGCGATATTTGTAAATCAACAAAAAAATAA
AAACATAGGATAACATGCATACTTAAAACACAATAATGGATGAATGAAGATAATATATATCTTAT
TTAATCGATTAACAAAATAAACAATTAAATATAACTAGCCTAAAAAAATATAACCCAATTTACAA
ATATGGGTGAACAACAATTAATTTAATAAAACAAAAAAAGGGATAAACAATATGCAACAATAATA
TATGAAATAATATAAAAACAATCAATATACAAAACAATATAAAAATTAAGAGTCAATATAATGTA
AAAACGAATAAAAAAAACATTAAATATATGAAAAAATTTAAAATGAACCATACATACTAAGGTT
Found at i:40273108 original size:35 final size:35
Alignment explanation
Indices: 40273069--40273142 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
40273059 CAAAATCAAT
40273069 TTCCGACACTATTGAAAAACAAGTTGTTACAAACC
1 TTCCGACACTATTGAAAAACAAGTTGTTACAAACC
*
40273104 TTCCGACACTATTGAAAAACGAGTTGTTACAAACC
1 TTCCGACACTATTGAAAAACAAGTTGTTACAAACC
40273139 TTCC
1 TTCC
40273143 AACCTTATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (35 bp):
TTCCGACACTATTGAAAAACAAGTTGTTACAAACC
Found at i:40273722 original size:23 final size:23
Alignment explanation
Indices: 40273669--40273724 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
40273659 AAATAATTTT
40273669 AATTTAATAAAATACTATAATTAC
1 AATTTAA-AAAATACTATAATTAC
*
40273693 ACA-TTAAAAAATAAGTATAATT-C
1 A-ATTTAAAAAAT-ACTATAATTAC
40273716 AATTTAAAA
1 AATTTAAAA
40273725 TTATTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.04
23 13 0.46
24 13 0.46
25 1 0.04
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (23 bp):
AATTTAAAAAATACTATAATTAC
Found at i:40273883 original size:24 final size:21
Alignment explanation
Indices: 40273855--40273908 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
40273845 TTATAATTTT
40273855 TAATTATTTGTTACAAATAATTA
1 TAATTATTT-TT-CAAATAATTA
* * *
40273878 TAAATTAATTTTGAAATTATTA
1 T-AATTATTTTTCAAATAATTA
40273900 TAATTATTT
1 TAATTATTT
40273909 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.27
22 9 0.35
23 3 0.12
24 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
TAATTATTTTTCAAATAATTA
Found at i:40282214 original size:19 final size:18
Alignment explanation
Indices: 40282184--40282222 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
40282174 TGTCCATTAA
40282184 AGGTAGTTTATTATGGTATG
1 AGGTAGTTTATT-TGGT-TG
40282204 AGGTA-TTTATTTGGTTG
1 AGGTAGTTTATTTGGTTG
40282221 AG
1 AG
40282223 ATATGTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 6 0.32
20 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (18 bp):
AGGTAGTTTATTTGGTTG
Found at i:40284239 original size:22 final size:22
Alignment explanation
Indices: 40284213--40284256 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40284203 GAAAATGATC
*
40284213 AAAATTAATCAAAATTTATTAT
1 AAAATTAATCAAAATTCATTAT
*
40284235 AAAATTAATTAAAATTCATTAT
1 AAAATTAATCAAAATTCATTAT
40284257 GTTAATAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAATCAAAATTCATTAT
Found at i:40286617 original size:50 final size:52
Alignment explanation
Indices: 40286554--40286671 Score: 168
Period size: 50 Copynumber: 2.3 Consensus size: 52
40286544 TAATAAAGTT
* * *
40286554 ATGCATTATGTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAATTATGAC
1 ATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTAAGAC
* *
40286604 ATGCTTTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTAAGTC
1 ATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTAAGAC
*
40286656 ATGCATTAAGTAACTC
1 ATGCATTATGTAACTC
40286672 ATTTGTTCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 25 0.42
51 11 0.19
52 23 0.39
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (52 bp):
ATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCACCATTAAATTAAGAC
Found at i:40297830 original size:48 final size:48
Alignment explanation
Indices: 40297759--40298036 Score: 274
Period size: 48 Copynumber: 6.0 Consensus size: 48
40297749 CATAAGGGTT
40297759 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
*
40297807 ATATGAGATTCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* * *** *
40297855 ATATAAGATCCCATGTAAGGCCAAACCTGGGATATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* ** * *
40297903 ATATGTGATTTCATGTAATACCGTGTCTGGGACATGGCA-T----T-G
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
** *
40297945 ATATGAGATATCGTGTAAGACCATAG-CTGGG-C-T---ATTGGCATCG
1 ATATGAGATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCG
* * * *
40297988 ATATGTGTGATCCCATATAAGACCATATCTGGGATATGGCATTGGCATC
1 ATA--TGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
40298037 TTACTATGTG
Statistics
Matches: 184, Mismatches: 31, Indels: 28
0.76 0.13 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
42 26 0.14
43 6 0.03
45 21 0.11
47 2 0.01
48 116 0.63
50 9 0.05
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (48 bp):
ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
Found at i:40300730 original size:40 final size:41
Alignment explanation
Indices: 40300686--40300872 Score: 156
Period size: 40 Copynumber: 4.7 Consensus size: 41
40300676 GCTACTCGTT
*
40300686 CAAATGCCTTCGGGACATAGCCCGG-TTATAGCAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGCAACTAGCA
* * * *
40300726 CAAATGCCTTCGGGACCTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGCAACTAGCA
** * *
40300766 CCCATGCCTTCGGG-CTTAGCCCGGGATTA-A-TAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGATTATAGCAACTAGCA
* *
40300805 CAAAGGCCTTC-GGATCTTAGTCCGGA-TATAGTC-ACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTATAG-CAAC-TAGCA
* * *
40300846 CAAAAGCCTTCGGCACTTAGCTCGGAT
1 CAAATGCCTTCGGGACTTAGCCCGGAT
40300873 ATCATTCGAA
Statistics
Matches: 118, Mismatches: 18, Indels: 20
0.76 0.12 0.13
Matches are distributed among these distances:
38 4 0.03
39 27 0.23
40 60 0.51
41 25 0.21
42 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGCAACTAGCA
Found at i:40301587 original size:2 final size:2
Alignment explanation
Indices: 40301580--40301607 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40301570 ATGTGCAAAC
40301580 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
40301608 GTGTGTGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40305575 original size:28 final size:27
Alignment explanation
Indices: 40305512--40305581 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
40305502 ATAGTGAGTC
40305512 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
40305539 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
40305567 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40305582 GTACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:40310046 original size:40 final size:41
Alignment explanation
Indices: 40310002--40310188 Score: 190
Period size: 40 Copynumber: 4.7 Consensus size: 41
40309992 GCTACTCGTT
*
40310002 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTAGCA
* * *
40310042 CAAATGCCTTCGGGACCTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTAGCA
** *
40310082 CCCATGCCTTCGGG-CTTAGCCCGGGATTA-A-TAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGATTATAGTAACTAGCA
* * * *
40310121 CAAAGGCCTTC-GGATCTTAGTCCAGA-TATAGTCACTGAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTATAGTAACT-AGCA
*
40310162 CAAAAGCCTTCGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAGCCCGGAT
40310189 ATCATTCGAA
Statistics
Matches: 120, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
38 4 0.03
39 26 0.22
40 63 0.52
41 24 0.20
42 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.22
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTAGCA
Found at i:40313100 original size:3 final size:3
Alignment explanation
Indices: 40313092--40313152 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
40313082 CTCTGTGGGA
*
40313092 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
40313140 TCT TCT TCT TCT T
1 TCT TCT TCT TCT T
40313153 TAGGATCCTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:40314482 original size:16 final size:16
Alignment explanation
Indices: 40314461--40314492 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40314451 AGTGTAACGC
40314461 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
40314477 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
40314493 TCCTGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.38, G:0.06, T:0.06
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:40315906 original size:58 final size:57
Alignment explanation
Indices: 40315841--40315949 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
40315831 AATGTGACTA
* * * *
40315841 GGCCTAATGTGCCATATAAATGTGGTTTGGGCCTAATGGGCCATATACAGGTGATTTG
1 GGCCTAATGGGCCATATAAATAT-GATTGGGCCTAATGGGCCAGATACAGGTGATTTG
* * *
40315899 GGCCTAATGGGCCATATGAATATGATTGGGCTTAATGGGCCAGATATAGGT
1 GGCCTAATGGGCCATATAAATATGATTGGGCCTAATGGGCCAGATACAGGT
40315950 ATGTGAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 24 0.55
58 20 0.45
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (57 bp):
GGCCTAATGGGCCATATAAATATGATTGGGCCTAATGGGCCAGATACAGGTGATTTG
Found at i:40315936 original size:28 final size:28
Alignment explanation
Indices: 40315826--40315940 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
40315816 GTGAGCATGA
* * *
40315826 ATATGAATGTGACTAGGCCTAATGTGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
* *
40315854 ATATAAATGTGGTTTGGGCCTAATGGGCC
1 ATATGAATGT-GATTGGGCCTAATGGGCC
*
40315883 ATAT-ACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGA-TTGGGCCTAATGGGCC
* *
40315912 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
40315940 A
1 A
40315941 GATATAGGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 27 0.37
29 45 0.62
30 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:40317474 original size:20 final size:20
Alignment explanation
Indices: 40317414--40317476 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
40317404 TGTAAAGTTG
*
40317414 ATAATAATTAATTTATATT-
1 ATAATAATTATTTTATATTA
*
40317433 ATAATAAATATAATTATATATTA
1 ATAAT-AAT-T-ATTTTATATTA
*
40317456 ATAATAATTATTTTTTATTA
1 ATAATAATTATTTTATATTA
40317476 A
1 A
40317477 ACTAAAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 5 0.14
20 13 0.36
21 2 0.06
22 11 0.31
23 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATAATTATTTTATATTA
Found at i:40318026 original size:18 final size:18
Alignment explanation
Indices: 40318003--40318037 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40317993 AAATGGGCCG
40318003 GATCAACGTGATTTTAAT
1 GATCAACGTGATTTTAAT
40318021 GATCAACGTGATTTTAA
1 GATCAACGTGATTTTAA
40318038 CTTACCTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (18 bp):
GATCAACGTGATTTTAAT
Found at i:40319374 original size:48 final size:48
Alignment explanation
Indices: 40319304--40319535 Score: 356
Period size: 48 Copynumber: 4.8 Consensus size: 48
40319294 CATAAGGGTT
*
40319304 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCT
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
40319352 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
40319400 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* *** * *
40319448 ATATAAGATCCCATGTAAGACCACACCTGGGATATGGCATTCGCATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* ** * *
40319496 ATATGTGATTTCATGCAATACCATGTCTGGGACATGGCAT
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCAT
40319536 CGATATGAGA
Statistics
Matches: 167, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 167 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (48 bp):
ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
Found at i:40323021 original size:11 final size:11
Alignment explanation
Indices: 40322992--40323026 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
40322982 ATTAAAACAA
40322992 ACATATTAAAC
1 ACATATTAAAC
40323003 ACAT-TTAAAC
1 ACATATTAAAC
*
40323013 ACTTATTAAAC
1 ACATATTAAAC
40323024 ACA
1 ACA
40323027 AAACACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (11 bp):
ACATATTAAAC
Found at i:40323021 original size:21 final size:22
Alignment explanation
Indices: 40322976--40323026 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
40322966 ACTTGCAATC
40322976 AAACACATTAAAACAAACATATT
1 AAACACATTAAAAC-AACATATT
* *
40322999 AAACACATTTAAAC-ACTTATT
1 AAACACATTAAAACAACATATT
40323020 AAACACA
1 AAACACA
40323027 AAACACATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 13 0.50
23 13 0.50
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACACATTAAAACAACATATT
Found at i:40323041 original size:9 final size:9
Alignment explanation
Indices: 40322990--40323045 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
40322980 ACATTAAAAC
*
40322990 AAACATATT
1 AAACACATT
40322999 AAACACATTT
1 AAACACA-TT
40323009 AAACACTTATT
1 AAACAC--ATT
40323020 AAACACA--
1 AAACACATT
40323027 AAACACATT
1 AAACACATT
40323036 AAACAC-TT
1 AAACACATT
40323044 AA
1 AA
40323046 CTTAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
7 7 0.17
8 4 0.10
9 13 0.32
10 8 0.20
11 8 0.20
12 1 0.02
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (9 bp):
AAACACATT
Found at i:40326534 original size:94 final size:94
Alignment explanation
Indices: 40326288--40326606 Score: 273
Period size: 94 Copynumber: 3.4 Consensus size: 94
40326278 TGGGATATAT
* * *
40326288 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCATA-TACGCGTGCTGATGCATGTC
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTA--TG-GCTGATGCATGTC
* * * * *
40326352 CCAAACATGTCTTACACTAGTAC-AACTCT-TA
63 ACAGACATGTCTTACACTAGCACTCA-TCTGGA
* * * * * *
40326383 -GCCGATG-CGTGTCCCAAACA-CGTCTTACACTAGCTAT-ATCTGTCGA-GG-TCGATGCATGT
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT-AGT--ATGGCT-GATGCATGT
* * * * *
40326442 CATAGACATGTCTTATATTGGCACTCATCT--C
62 CACAGACATGTCTTACACTAGCACTCATCTGGA
*
40326473 TGTGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCC
1 TGT-C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCA
* *
40326538 CAGACATGTCTTACACTAGCCCTCGTCTGGA
64 CAGACATGTCTTACACTAGCACTCATCTGGA
40326569 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
1 TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCT
40326607 TTCAAATCAC
Statistics
Matches: 177, Mismatches: 31, Indels: 33
0.73 0.13 0.14
Matches are distributed among these distances:
90 1 0.01
91 33 0.19
92 16 0.09
93 17 0.10
94 85 0.48
95 20 0.11
96 5 0.03
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (94 bp):
TGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTGATGCATGTCACA
GACATGTCTTACACTAGCACTCATCTGGA
Found at i:40326535 original size:47 final size:46
Alignment explanation
Indices: 40326292--40326606 Score: 164
Period size: 47 Copynumber: 6.7 Consensus size: 46
40326282 ATATATTGTC
* * *
40326292 GATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCATA-TACGCGTGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATAGTA--TG-GCT
* * * * * *
40326342 GATGCATGTCCCAAACATGTCTTACACTAG-TA-CA-ACTCTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCATAGT-ATGGCT
* * * * *
40326386 GATGCGTGTCCCAAACACGTCTTACACTAGCTAT-ATCTGTCGA-GG-T
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCAT-AGT--ATGGCT
** * * * *
40326432 CGATGCATGTCATAGACATGTCTTATATTGGC-ACTCAT-CTCTGTGCT
1 -GATGCATGTCCCAGACATGTCTTACACTGGCTA-TCATAGTATG-GCT
40326479 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATAGTATGGCT
* ** * * * *
40326527 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTGGATGTC-
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCAT-AGTATGGCT
40326573 GATGCCATGTCCCAGACATGGTCTTACACTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT
40326607 TTCAAATCAC
Statistics
Matches: 205, Mismatches: 40, Indels: 42
0.71 0.14 0.15
Matches are distributed among these distances:
44 30 0.15
45 5 0.02
46 29 0.14
47 73 0.36
48 47 0.23
49 17 0.08
50 4 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTATCATAGTATGGCT
Found at i:40326582 original size:141 final size:137
Alignment explanation
Indices: 40326289--40326598 Score: 302
Period size: 141 Copynumber: 2.2 Consensus size: 137
40326279 GGGATATATT
* * * ** * *
40326289 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGTTCTCATATACGCGTGCTGATGCATGTCCC
1 GTCGATG-CATGTCACAGACATGGTCTTATATTGGCACTCATCT-C-TGTGCTGATGCATGTCCC
* * *
40326354 AAACATGTCTTACACTAGTACAACTCTTAGCCGATGCGTGTCCCAAACACGTCTTACACTAGCTA
63 AAACATGTCTTACACTAGTACAACTCATAGCCGATGCATGTCCCAAACACGTCTTACACTAGCCA
40326419 TATCTGTCGAG
128 TATCTG-CGAG
* *
40326430 GTCGATGCATGTCATAGACAT-GTCTTATATTGGCACTCATCTCTGTGCTGATGCCATGTCCCAG
1 GTCGATGCATGTCACAGACATGGTCTTATATTGGCACTCATCTCTGTGCTGATG-CATGTCCCAA
* * * * * *
40326494 ACATGGTCTTACACTGGCTATCATAGT-ATGGCTGATGCATGTCCCAGACATGTCTTACACTAGC
65 ACAT-GTCTTACACTAG-TA-CA-ACTCATAGCCGATGCATGTCCCAAACACGTCTTACACTAGC
* * *
40326558 CCTCGTCTG-GAT
126 CAT-ATCTGCGAG
*
40326570 GTCGATGCCATGTCCCAGACATGGTCTTA
1 GTCGATG-CATGTCACAGACATGGTCTTA
40326599 CACTGGCTTT
Statistics
Matches: 138, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
137 9 0.07
138 14 0.10
139 27 0.20
140 23 0.17
141 53 0.38
142 12 0.09
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (137 bp):
GTCGATGCATGTCACAGACATGGTCTTATATTGGCACTCATCTCTGTGCTGATGCATGTCCCAAA
CATGTCTTACACTAGTACAACTCATAGCCGATGCATGTCCCAAACACGTCTTACACTAGCCATAT
CTGCGAG
Found at i:40330880 original size:40 final size:40
Alignment explanation
Indices: 40330820--40331006 Score: 266
Period size: 40 Copynumber: 4.7 Consensus size: 40
40330810 CAATTGAGGA
* * * *
40330820 TTATATCCGGGTTAAGTCCCGAAGGCATTCATGCGGGATG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
40330860 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
40330900 CTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
** *
40330940 CCATTTCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
** * *
40330980 TTACATCCGGGCTAAATCCCGAAGGCA
1 TTATTTCCGGGTTAAGTCCCGAAGGCA
40331007 ATTGGGTTGG
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 134 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (40 bp):
TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:40332441 original size:48 final size:48
Alignment explanation
Indices: 40332381--40332561 Score: 238
Period size: 48 Copynumber: 3.8 Consensus size: 48
40332371 CATTAGGGTT
* * *
40332381 ATATGAGATCCCATGTAAGACCATGTCTTGGACATGGCATTAGCACCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* *
40332429 ATATGATATCCCATGTAAGACCATGTCTGGGACATGGCATTGGTATCG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
* * *
40332477 ATATGAGATCCCATGT-AGCACAATATCTGGGATATGGCATTGGCATCG
1 ATATGAGATCCCATGTAAG-ACCATGTCTGGGACATGGCATTGGCATCG
* ** *
40332525 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATGG
1 ATATGAGATCCCATGTAAGACCATGTCTGGGACATGG
40332562 GATCGATATG
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
47 2 0.02
48 110 0.96
49 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (48 bp):
ATATGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
Found at i:40333992 original size:53 final size:53
Alignment explanation
Indices: 40333923--40334128 Score: 232
Period size: 53 Copynumber: 3.8 Consensus size: 53
40333913 TTCCTTTTTA
* * * *
40333923 AACTTACCATTTCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
* * * * *
40333976 AACTCACCATTGCCATGCCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G
** * * * * * *
40334030 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTCTA
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
*
40334084 AACTTACCAATGCCATGCCTTGACATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
40334129 AAACCGTAAT
Statistics
Matches: 124, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
53 83 0.67
54 1 0.01
55 40 0.32
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
Found at i:40335507 original size:24 final size:23
Alignment explanation
Indices: 40335480--40335588 Score: 137
Period size: 24 Copynumber: 4.6 Consensus size: 23
40335470 ACCAAACGTT
* **
40335480 GCACACATAGTGCTTATTATGTTC
1 GCACACATAGTGCTTAGTA-AATC
*
40335504 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATC
40335528 GCACACATAGTGCTATAGTAAATC
1 GCACACATAGTGCT-TAGTAAATC
*
40335552 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATC
40335576 GCACACATAGTGC
1 GCACACATAGTGC
40335589 ATTTGAGATT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
23 2 0.03
24 68 0.89
25 6 0.08
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (23 bp):
GCACACATAGTGCTTAGTAAATC
Found at i:40335536 original size:48 final size:48
Alignment explanation
Indices: 40335480--40335588 Score: 175
Period size: 48 Copynumber: 2.3 Consensus size: 48
40335470 ACCAAACGTT
* **
40335480 GCACACATAGTGCT-TATTATGTTCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCTATAGTA-AATCGCACACATAGTGCCATAGTAAATC
40335528 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
40335576 GCACACATAGTGC
1 GCACACATAGTGC
40335589 ATTTGAGATT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 53 0.93
49 4 0.07
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (48 bp):
GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
Found at i:40350590 original size:40 final size:40
Alignment explanation
Indices: 40350545--40350712 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
40350535 CGGAATATAA
* *
40350545 CCGGATATAACCA-TGTGCACAAATGGCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
40350585 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40350625 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
40350665 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
40350705 CCGGATAT
1 CCGGATAT
40350713 CATTCAATTT
Statistics
Matches: 102, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 101 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40362328 original size:27 final size:27
Alignment explanation
Indices: 40362290--40362403 Score: 151
Period size: 27 Copynumber: 4.2 Consensus size: 27
40362280 AGCATGGCTG
* * *
40362290 CCAGAACAGATA-TTGTGACAGAGTCA
1 CCAGAAAAGATATTTGTGGCAGAGCCA
40362316 CCAGATAAAGATA-TTGTGGCAGAGCCA
1 CCAGA-AAAGATATTTGTGGCAGAGCCA
* *
40362343 CAAGAACAGATATTTGTGGCAGAGCCA
1 CCAGAAAAGATATTTGTGGCAGAGCCA
40362370 CCAGAAATAGATATTTGTGGCAGAGCCA
1 CCAGAAA-AGATATTTGTGGCAGAGCCA
40362398 CCAGAA
1 CCAGAA
40362404 CGCTTCCTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.14
27 41 0.53
28 26 0.33
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (27 bp):
CCAGAAAAGATATTTGTGGCAGAGCCA
Found at i:40362373 original size:54 final size:54
Alignment explanation
Indices: 40362292--40362404 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 54
40362282 CATGGCTGCC
*
40362292 AGAACAGATATTGTGACAGAGTCACCAGATAA-AGATA-TTGTGGCAGAGCCACA
1 AGAACAGATATTGTGACAGAGCCACCAGA-AATAGATATTTGTGGCAGAGCCACA
* *
40362345 AGAACAGATATTTGTGGCAGAGCCACCAGAAATAGATATTTGTGGCAGAGCCACC
1 AGAACAGATA-TTGTGACAGAGCCACCAGAAATAGATATTTGTGGCAGAGCCACA
40362400 AGAAC
1 AGAAC
40362405 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
53 12 0.22
54 22 0.41
55 20 0.37
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (54 bp):
AGAACAGATATTGTGACAGAGCCACCAGAAATAGATATTTGTGGCAGAGCCACA
Found at i:40365365 original size:46 final size:43
Alignment explanation
Indices: 40365286--40365398 Score: 111
Period size: 44 Copynumber: 2.5 Consensus size: 43
40365276 AGAGCTAGTG
* * *
40365286 TAAGACATGTTCGGACATGCATCGGCCTCGAGATGTAAGCCATTA
1 TAAGACATGTCCGGACATGCATCAGCCTCGAGATGT--GCCAGTA
* * *
40365331 TAAGACATGTCCAGGACATGCATCAG-CTATGAGATGTGCTAGTG
1 TAAGACATGTCC-GGACATGCATCAGCCT-CGAGATGTGCCAGTA
*
40365375 TAAGACATGTCTGGGACATGCATC
1 TAAGACATGTC-CGGACATGCATC
40365399 GACACAGATA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
44 26 0.45
45 13 0.22
46 19 0.33
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (43 bp):
TAAGACATGTCCGGACATGCATCAGCCTCGAGATGTGCCAGTA
Done.