Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold192
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: 2196177
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 12544 characters in sequence are not A, C, G, or T
File 9 of 14
Found at i:1290622 original size:14 final size:14
Alignment explanation
Indices: 1290605--1290631 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1290595 TTTTCCTCTC
1290605 TTTTTGTATTCTTT
1 TTTTTGTATTCTTT
1290619 TTTTTGTATTCTT
1 TTTTTGTATTCTT
1290632 GAAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTTTGTATTCTTT
Found at i:1295086 original size:24 final size:24
Alignment explanation
Indices: 1295033--1295096 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
1295023 TTTATTATAT
* *
1295033 TATTCAATAAAAT-AAAAAAATAA
1 TATTTAATAAATTAAAAAAAATAA
* *
1295056 TATTTAATTAAGTTAAAAAAAATTA
1 TATTTAA-TAAATTAAAAAAAATAA
1295081 TA-TTAATAAATTAAAA
1 TATTTAATAAATTAAAA
1295097 TATTAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 15 0.44
24 8 0.24
25 11 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
TATTTAATAAATTAAAAAAAATAA
Found at i:1295367 original size:130 final size:129
Alignment explanation
Indices: 1295199--1295445 Score: 374
Period size: 130 Copynumber: 1.9 Consensus size: 129
1295189 AATTATTATG
*
1295199 TTTTTTAATTTAAAATTTTTATTTTTTAAAAAATATAATAATTAATATTTTAATTTATTAATGTA
1 TTTTTTAATTTAAAATTTTTATTTTTTAAAAAACATAATAATTAATATTTTAATTTATTAATGTA
* *
1295264 AA-TTTTTTAGACTTAATTAAATATTTTTATTTTATTAAATAA-TAATAATAATAAACCTTTTTT
66 AATTTTTTTAAACTTAATTAAATA---TTATTTTATTAAAAAATTAATAATAATAAACCTTTTTT
1295327 TA
128 TA
* * * *
1295329 TTTTTT-ATTTAAATTTTTTTTATTTTTAAAAAACATAATAATTAATGTTTTAATTTGTTAATGT
1 TTTTTTAATTTAAAATTTTTAT-TTTTTAAAAAACATAATAATTAATATTTTAATTTATTAATGT
1295393 AAATTTTTTTAAACTTAATTAAATATTATTTTATTAAAAAATTAATAATAATA
65 AAATTTTTTTAAACTTAATTAAATATTATTTTATTAAAAAATTAATAATAATA
1295446 GTTTTTAAAT
Statistics
Matches: 107, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
128 15 0.14
129 24 0.22
130 48 0.45
131 20 0.19
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (129 bp):
TTTTTTAATTTAAAATTTTTATTTTTTAAAAAACATAATAATTAATATTTTAATTTATTAATGTA
AATTTTTTTAAACTTAATTAAATATTATTTTATTAAAAAATTAATAATAATAAACCTTTTTTTA
Found at i:1296321 original size:99 final size:101
Alignment explanation
Indices: 1296121--1296322 Score: 268
Period size: 99 Copynumber: 2.0 Consensus size: 101
1296111 AACAACTATT
1296121 TTTTCGATGTAATATTAACAAGAATTATAAACTAATTATATATCTATTATTTAATTTTTAATTAG
1 TTTTCGATGTAATATTAACAAGAATTATAAACTAATTATATA-CTATTATTTAATTTTTAATTAG
* *
1296186 TATAAATTTCAATAATTTCAATGATAGTAGAAGAATA
65 TATAAAGTTCAATAATTTCAATGATAGTAAAAGAATA
* * * * *
1296223 TTTT-GATGTAATATTAATAAGAATTATAAAGTAATTATATA-TATTTTTTAGTTTTTAATATCG
1 TTTTCGATGTAATATTAACAAGAATTATAAACTAATTATATACTATTATTTAATTTTTAAT-TAG
* *
1296286 -ATAAAGTTCATTAA-TTCTAATGATGGTAAAAGAATA
65 TATAAAGTTCAATAATTTC-AATGATAGTAAAAGAATA
1296322 T
1 T
1296323 AGAATACCTT
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
98 3 0.03
99 45 0.51
100 2 0.02
101 35 0.39
102 4 0.04
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (101 bp):
TTTTCGATGTAATATTAACAAGAATTATAAACTAATTATATACTATTATTTAATTTTTAATTAGT
ATAAAGTTCAATAATTTCAATGATAGTAAAAGAATA
Found at i:1299294 original size:29 final size:30
Alignment explanation
Indices: 1299241--1299298 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1299231 GTTTAGAGAT
* *
1299241 TTTTATTTATTTTTTATTGTTTTTAAATTG
1 TTTTATTTATTTTTCATTGTATTTAAATTG
1299271 TTTTATTTA-TTTTCATTGTATTTAAATT
1 TTTTATTTATTTTTCATTGTATTTAAATT
1299299 ACATAGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (30 bp):
TTTTATTTATTTTTCATTGTATTTAAATTG
Found at i:1303636 original size:22 final size:22
Alignment explanation
Indices: 1303609--1303653 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1303599 TTTATAAAGG
1303609 AAATCTTATCAAAGAAGAAGAA
1 AAATCTTATCAAAGAAGAAGAA
* *
1303631 AAATCTTATTAAAGAAGAGGAA
1 AAATCTTATCAAAGAAGAAGAA
1303653 A
1 A
1303654 TTCAGTGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.20
Consensus pattern (22 bp):
AAATCTTATCAAAGAAGAAGAA
Found at i:1304928 original size:21 final size:21
Alignment explanation
Indices: 1304902--1304957 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1304892 AATAAGTAAA
*
1304902 TGTATCGATACATTTA-CTGTT
1 TGTATCGATACATTTATCT-AT
*
1304923 TGTATCAATACA-TTATCTAT
1 TGTATCGATACATTTATCTAT
1304943 TGTATCGATACATTT
1 TGTATCGATACATTT
1304958 TGGGTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATTTATCTAT
Found at i:1308479 original size:53 final size:52
Alignment explanation
Indices: 1308382--1308488 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 52
1308372 CCTTGGAAGC
*
1308382 CATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATA
1 CATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATA
*
1308434 CATTTTATAATGTATCGATACATCTAGGGCAAATTTGCCTGCATGTATCGATA
1 CATTTAATAATGTATCGATACATCT-GGGCAAATTTGCCTGCATGTATCGATA
1308487 CA
1 CA
1308489 AAGATCAGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
52 23 0.44
53 29 0.56
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATA
Found at i:1308501 original size:53 final size:52
Alignment explanation
Indices: 1308388--1308508 Score: 181
Period size: 53 Copynumber: 2.3 Consensus size: 52
1308378 AAGCCATTTA
***
1308388 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTT
1 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAG
*
1308440 ATAATGTATCGATACATCTAGGGCAAATTTGCCTGCATGTATCGATACA-AAG
1 ATAGTGTATCGATACATCT-GGGCAAATTTGCCTGCATGTATCGATACATAAG
1308492 ATCAGTGTATCGATACA
1 AT-AGTGTATCGATACA
1308509 ATGTATCGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
52 20 0.32
53 42 0.68
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (52 bp):
ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAG
Found at i:1308515 original size:13 final size:13
Alignment explanation
Indices: 1308497--1308521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1308487 CAAAGATCAG
1308497 TGTATCGATACAA
1 TGTATCGATACAA
1308510 TGTATCGATACA
1 TGTATCGATACA
1308522 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1308599 original size:33 final size:33
Alignment explanation
Indices: 1308562--1308628 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1308552 AGTAGCTTAA
1308562 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1308595 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1308628 A
1 A
1308629 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1308602 original size:13 final size:13
Alignment explanation
Indices: 1308584--1308608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1308574 CAAAAAAATA
1308584 TGTATCGATACAT
1 TGTATCGATACAT
1308597 TGTATCGATACA
1 TGTATCGATACA
1308609 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1309537 original size:67 final size:68
Alignment explanation
Indices: 1309415--1309541 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 68
1309405 ATTGGGTTTT
* * *
1309415 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
1309480 AGA
66 AGA
* * *
1309483 AAAG-TGATAAAGATGCCAATATGTTGATTCACA-GCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCA-AGGCCAACAATATTGGACTTAAAGATGA
1309542 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
67 47 0.90
68 5 0.10
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:1309595 original size:55 final size:52
Alignment explanation
Indices: 1309491--1310055 Score: 442
Period size: 49 Copynumber: 11.6 Consensus size: 52
1309481 GAAAAGTGAT
* * * * * **
1309491 AAAGATGCCAATATGTTGATTCACA-GCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCA-AGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
1309545 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
1309598 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
1309641 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACACT-AGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGA-ACTTAAAGATGGA
* * *
1309691 --AGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * **
1309739 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
1309787 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-ATGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
1309836 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
1309885 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
1309931 ---GGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
1309978 --AGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
*
1310026 -AAGGTGCCAATATGCTGATTCAGGGCCAGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGC
1310056 AATATTGGGC
Statistics
Matches: 442, Mismatches: 44, Indels: 55
0.82 0.08 0.10
Matches are distributed among these distances:
43 73 0.17
44 1 0.00
45 1 0.00
46 6 0.01
47 2 0.00
48 89 0.20
49 187 0.42
51 2 0.00
52 34 0.08
53 6 0.01
54 6 0.01
55 35 0.08
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:1310063 original size:49 final size:49
Alignment explanation
Indices: 1309554--1310055 Score: 672
Period size: 49 Copynumber: 10.5 Consensus size: 49
1309544 AAAAGGATGT
*
1309554 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
1309606 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1309649 CAATGTGCTGATTCAAGGCCAGCTACACTAGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1309697 TAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1309746 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1309795 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1309844 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1309893 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AT---GGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1309936 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1309984 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1310033 CAATATGCTGATTCAGGGCCAGC
1 CAATGTGCTGATTCAAGGCCAGC
1310056 AATATTGGGC
Statistics
Matches: 397, Mismatches: 40, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
43 75 0.19
45 1 0.00
46 3 0.01
47 1 0.00
48 91 0.23
49 194 0.49
52 32 0.08
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1310215 original size:35 final size:34
Alignment explanation
Indices: 1310151--1310218 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
1310141 TAACTTTTGG
* * *
1310151 GCTTAAAAAGGAAAAGAGTGCTATAGAGTTGTGA
1 GCTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGA
*
1310185 GCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTG
1 GCTTA-AAAAGAAAAAGAGTGCCACAGAGTTGTG
1310219 GACTTTGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 5 0.17
35 24 0.83
ACGTcount: A:0.40, C:0.10, G:0.29, T:0.21
Consensus pattern (34 bp):
GCTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGA
Found at i:1310321 original size:28 final size:29
Alignment explanation
Indices: 1310198--1310367 Score: 175
Period size: 30 Copynumber: 5.9 Consensus size: 29
1310188 TACAAAAGAA
* * * * *
1310198 AAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAGGGTGCCACTGACTTGTGGGCTTTTG
* * * **
1310227 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAGGGTGCCACTGACTTGTGGGCTTTTG
*
1310256 AAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 -AAAGGGTGCCACTGACTTGTGGGCTTTTG
*
1310285 -AAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTTG
*
1310313 -AAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTTG
*
1310341 AAAAGGGTGCCACTAACTTGTGGGCTT
1 -AAAGGGTGCCACTGACTTGTGGGCTT
1310368 AAAAAGAAAA
Statistics
Matches: 120, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
27 21 0.17
28 32 0.27
29 24 0.20
30 43 0.36
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.29
Consensus pattern (29 bp):
AAAGGGTGCCACTGACTTGTGGGCTTTTG
Found at i:1310403 original size:34 final size:33
Alignment explanation
Indices: 1310358--1311151 Score: 614
Period size: 34 Copynumber: 25.2 Consensus size: 33
1310348 TGCCACTAAC
1310358 TTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTT-AAAAGAAAAAGAGTGCCACGGAG
* *
1310392 TCGTGGACTTAAAAG-----G-GTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* *
1310419 TTGTGGGCTT----TAAAAAGAGTGCCACGAAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* *
1310448 TCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTAAAA-GAAAAAGAGTGCCACGGAG
* *
1310482 TTGTGGGCTTTAAA-AAGAAG-GTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* * * *
1310513 TCGTTGGACTTAAAAGGAAAAAAGGGTGCCACGAAG
1 TTG-TGGGCTTAAAA-G-AAAAAGAGTGCCACGGAG
* *
1310549 TCGTGGACTTAAAAG-----G-GTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
*
1310576 TTGTGGGCTT----TAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
*
1310605 TTGTGGACTTAAAAGGAAAAA-AGGTGCCACGGAG
1 TTGTGGGCTTAAAA-GAAAAAGA-GTGCCACGGAG
* *
1310639 TTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAG
1 TTGTGGGCTTAAAA-GAAAAAGAGTGCCACGGAG
** * *
1310673 TTGTGGGCTTTGAA-AAGAAG-GTGCCACGCAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
*
1310704 TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTA-AAAGAAAAAGAGTGCCACGGAG
*
1310738 TTGTGGGCTTAAACG-----G-GTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* *
1310765 TTGTGGGCTTAAAAGGAAAAGAGTGCCACGTAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* * *
1310798 TTGTGGGCTTTAAAGGAAAAAAGGGTGCCACGAAG
1 TTGTGGGC-TTAAAAG-AAAAAGAGTGCCACGGAG
* *
1310833 TCGTGGACTTAAAAG-----G-GTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
*
1310860 TTGTGGGCTT----TAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* *
1310889 TTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAG
1 TTGTGGGCTTAAAA-GAAAAAGAGTGCCACGGAG
* * *
1310923 TTGTGGACTTAAAAGGAAAAAGGGTGTCACGGAG
1 TTGTGGGCTTAAAA-GAAAAAGAGTGCCACGGAG
** * *
1310957 TTGTGGGCTTTGAA-AAGAAG-GTGCCACGCAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
*
1310988 TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTA-AAAGAAAAAGAGTGCCACGGAG
* *
1311022 TTGTGGGCTTAAACG-----G-GTGCCACAGAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* *
1311049 TTGTGGGCTTAAAAGGAAAAGAGTGCCACGTAG
1 TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
* *
1311082 TTGTGGGCTT---TGAAAAGGAGGTGCCACGGAG
1 TTGTGGGCTTAAAAGAAAAAGA-GTGCCACGGAG
* *
1311113 TTGTGGACTTTGAAAGAAAAAG-GTGCCACGGAG
1 TTGTGGGC-TTAAAAGAAAAAGAGTGCCACGGAG
*
1311146 TCGTGG
1 TTGTGG
1311152 ACTTTAATGC
Statistics
Matches: 617, Mismatches: 78, Indels: 131
0.75 0.09 0.16
Matches are distributed among these distances:
27 104 0.17
28 8 0.01
29 58 0.09
30 6 0.01
31 69 0.11
32 30 0.05
33 75 0.12
34 211 0.34
35 43 0.07
36 13 0.02
ACGTcount: A:0.31, C:0.14, G:0.35, T:0.20
Consensus pattern (33 bp):
TTGTGGGCTTAAAAGAAAAAGAGTGCCACGGAG
Found at i:1310475 original size:63 final size:63
Alignment explanation
Indices: 1310402--1311034 Score: 541
Period size: 65 Copynumber: 9.9 Consensus size: 63
1310392 TCGTGGACTT
* * *
1310402 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGAAGTCGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
*
1310465 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTCGTTGGACTTAAAAGG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG-A-GTGCCACGGAGTTG-TGGACTTAAAAGG
1310530 AA
63 -A
* * * * * * *
1310532 AAAAGGGTGCCACGAAGTCGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGGCTT-----TA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1310588 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGGTGCCACGGAGTTGTGGACTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTT--TA--AAAAGA-GTGCCACGGAGTTGTGGACTTAAAA
1310653 GGA
61 GGA
* * * * *
1310656 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAGTTGTGGGCTTAGAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG-A-GTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1310721 AAAAGAGTGCCACGGAGTTGTGGGC-TT-AAACGGGTGCCACGGAGTTGTGGGCTTAAAAGG-
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
1310781 AAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACGAAGTCGTGGACTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTT------AAAAAGAGTGCCACGGAGTTGTGGACTTAAA
1310846 A-G-
60 AGGA
1310848 ----G-GTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * * * * **
1310906 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGTCACGGAGTTGTGGGCTTTGAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTT-----TAAAAAGAGTGCCACGGAGTTGTGGACTTAAAA
1310971 --A
61 GGA
* * * *
1310972 AGAAG-GTGCCACGCAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTT-----TAAAAAGAGTGCCACGGAGTTGTGGACTTAAA
1311035 CGGGTGCCAC
Statistics
Matches: 478, Mismatches: 55, Indels: 72
0.79 0.09 0.12
Matches are distributed among these distances:
56 52 0.11
57 2 0.00
60 24 0.05
61 27 0.06
62 32 0.07
63 91 0.19
64 7 0.01
65 120 0.25
66 20 0.04
67 23 0.05
68 80 0.17
ACGTcount: A:0.31, C:0.14, G:0.35, T:0.20
Consensus pattern (63 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1310842 original size:284 final size:284
Alignment explanation
Indices: 1310358--1311092 Score: 1134
Period size: 284 Copynumber: 2.6 Consensus size: 284
1310348 TGCCACTAAC
* * * * * *
1310358 TTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTCGTGGAC-TT-AAAAG--GGTGCCACGGAG
1 TTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAG
* * * * *
1310419 TTGTGGGCTT-----TAAAAAGAGTGCCACGAAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACG
66 TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AAACG-----G-GTGCCACG
* * * * *
1310479 GAGTTGTGGGCTTTAAAA--AGAAG-GTGCCACGGAGTCGTTGGACTTAAAAGGAAAAAAGGGTG
124 GAGTTGTGGGC-TTAAAAGGAAAAGAGTGCCACGTAGTTG-TGGGCTTTAAAGGAAAAAAGGGTG
1310541 CCACGAAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGT
187 CCACGAAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGT
1310606 TGTGGACTTAAAAGGAAAAAAGGTGCCACGGAG
252 TGTGGACTTAAAAGGAAAAAAGGTGCCACGGAG
1310639 TTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAG
1 TTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAG
1310704 TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGGAGTTGT
66 TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGGAGTTGT
1310769 GGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACGAAGT
131 GGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACGAAGT
1310834 CGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTT
196 CGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTT
*
1310899 AAAAGGAAAAAGGGTGCCACGGAG
261 AAAAGGAAAAAAGGTGCCACGGAG
*
1310923 TTGTGGACTTAAAAGGAAAAAGGGTGTCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAG
1 TTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAG
*
1310988 TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACAGAGTTGT
66 TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGGAGTTGT
1311053 GGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTT
131 GGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTT
1311093 GAAAAGGAGG
Statistics
Matches: 423, Mismatches: 19, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
281 37 0.09
282 8 0.02
283 24 0.06
284 292 0.69
285 33 0.08
289 4 0.01
290 25 0.06
ACGTcount: A:0.31, C:0.14, G:0.35, T:0.20
Consensus pattern (284 bp):
TTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAG
TTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGGTGCCACGGAGTTGT
GGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACGAAGT
CGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTTGTGGACTT
AAAAGGAAAAAAGGTGCCACGGAG
Found at i:1310916 original size:125 final size:124
Alignment explanation
Indices: 1310402--1311155 Score: 657
Period size: 125 Copynumber: 5.9 Consensus size: 124
1310392 TCGTGGACTT
* * * *
1310402 AAAAGGGTGCCACGGAGTTGTGGGCTTT-AAAAAGAGTGCCACGAAGTCGTGGACTTAAAAGGAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGGGTGCCACGAAGTTGTGGGCTT-TAA--AA
* *
1310466 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTCGTTGGACTTAAAAGGA
63 AGAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG-AGGTGCCACGGAGTTG-TGGACTTAAAAGG-
1310531 A
124 A
* * * *
1310532 AAAAGGGTGCCACGAAGTCGTGGAC-TT--AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGGGTGCCACGAAGTTGTGGGCTTTAAAAAGA
* * *
1310594 -GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
66 GGTGCCACGGAGTTGTGGGCTT--TA--AAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1310656 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGCAGTTGTGGGCTTAGAAGGA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAA-AGGGTGCCACGAAGTTGTGGGCTT-TAA--A
* * *
1310721 AAAAGAGTGCCACGGAGTTGTGGGC-TT-AAACG-GGTGCCACGGAGTTGTGGGCTTAAAAGG-
62 AAGAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
1310781 AAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACGAAGTCGTGGAC-TT-A
1 AAAAGGGTGCCACGGAGTTGTGGGCTTT----G-AAAAAGGGTGCCACGAAGTTGTGGGCTTTAA
1310844 AAAG-GGTGCCACGGAGTTGTGGGCTTTAAAAAGA-GTGCCACGGAGTTGTGGACTTAAAAGGA
61 AAAGAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * * *
1310906 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGTCACGGAGTTGTGGGCTTTGAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTT----TGAAAAAGGGTGCCACGAAGTTGTGGGCTTTAAA
* * * *
1310971 AAGAAGGTGCCACGCAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT----
62 AAG-AGGTGCCACGGAGTTGTGGGCTT-TAA--AAAGAG-GTGCCACGGAGTTGTGGACTTAAAA
1311032 ---
122 GGA
* * * * * *
1311032 AAACGGGTGCCACAGAGTTGTGGGCTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTGAAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTT---TGAAAAAGGGTGCCACGAAGTTGTGGGCTTT-AAA
* * * *
1311097 AGGAGGTGCCACGGAGTTGTGGACTTTGAAAGAAAAAGGTGCCACGGAGTCGTGGACTT
62 AAGAGGTGCCACGGAGTTGTGGGCTTT--AA-AAAGAGGTGCCACGGAGTTGTGGACTT
1311156 TAATGCCACT
Statistics
Matches: 524, Mismatches: 62, Indels: 82
0.78 0.09 0.12
Matches are distributed among these distances:
122 19 0.04
123 23 0.04
124 97 0.19
125 130 0.25
126 78 0.15
127 12 0.02
128 67 0.13
129 25 0.05
130 26 0.05
131 8 0.02
132 1 0.00
133 38 0.07
ACGTcount: A:0.31, C:0.14, G:0.35, T:0.20
Consensus pattern (124 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGGGTGCCACGAAGTTGTGGGCTTTAAAAAGA
GGTGCCACGGAGTTGTGGGCTTTAAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1311283 original size:62 final size:61
Alignment explanation
Indices: 1311186--1311614 Score: 449
Period size: 62 Copynumber: 6.9 Consensus size: 61
1311176 CTTAAAAGGG
* * * * *
1311186 ATGCCACTGAATTGTGGACTTTTAGGACAAA-ATGCCACTGAGTCGTGGGCTTT-GAGA-AAA
1 ATGCCACTGAGTCGTGGACTTTGAAGA-AAAGATGCCACTGAGTCGTGGACTTTAG-GACAAA
* * * * *
1311246 GATTGCCACTGAGTCATGGACTTT-AAGAAGGAGATGCCACTGAATTGTGAACTTTAGGACAAA
1 -A-TGCCACTGAGTCGTGGACTTTGAAGAA-AAGATGCCACTGAGTCGTGGACTTTAGGACAAA
* * * * *
1311309 ATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAAGGTGCCACGGAATCGTGGACTTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTT--GAAG-AAAAGATGCCACTGAGTCGTGGACTTTAGGACAAA
* * *
1311373 ATGCCACTGATTCGTGGGCTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTT-GAGACAAA
1 ATGCCACTGAGTCGTGGACTTTGAAGAAAA-GATGCCACTGAGTCGTGGACTTTAG-GACAAA
* *
1311435 ATGCCACTGAGTCGTGGACTTTGAGAAGAAAAAGGTGCCACGGAGTCGTGGACTTTAGGACAAA
1 ATGCCACTGAGTCGTGGACTTT--GAAG-AAAAGATGCCACTGAGTCGTGGACTTTAGGACAAA
* * *
1311499 ATGCCACTGATTCGTGGGCTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTT-GAGACAAA
1 ATGCCACTGAGTCGTGGACTTTGAAGAAAA-GATGCCACTGAGTCGTGGACTTTAG-GACAAA
*
1311561 ATGCCACTGAGTCGTGGACTTTG-AGAAGAGATTGCCACTGAGTCGTGGACTTTA
1 ATGCCACTGAGTCGTGGACTTTGAAGAAAAGA-TGCCACTGAGTCGTGGACTTTA
1311615 AAAAGGTATT
Statistics
Matches: 312, Mismatches: 37, Indels: 37
0.81 0.10 0.10
Matches are distributed among these distances:
60 3 0.01
61 58 0.19
62 139 0.45
63 4 0.01
64 101 0.32
65 7 0.02
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (61 bp):
ATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTAGGACAAA
Found at i:1311364 original size:64 final size:64
Alignment explanation
Indices: 1311278--1311589 Score: 401
Period size: 64 Copynumber: 4.9 Consensus size: 64
1311268 TTAAGAAGGA
* * *
1311278 GATGCCACTGAATTGTGAACTTTAGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAAAG
1 GATGCCAC-GAATCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGGCTTTGAGAAGAAAAAG
*
1311343 G-TGCCACGGAATCGTGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTT--GAAG-AAAAG
1 GATGCCAC-GAATCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGGCTTTGAGAAGAAAAAG
* *
1311404 GATGCCACTAAGTCGTGGACTTT-GAGACAAAATGCCACTGAGTCGTGGACTTTGAGAAGAAAAA
1 GATGCCACGAA-TCGTGGACTTTAG-GACAAAATGCCACTGAGTCGTGGGCTTTGAGAAGAAAAA
1311468 G
64 G
* *
1311469 G-TGCCACGGAGTCGTGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTT--GAAG-AAAAG
1 GATGCCAC-GAATCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGGCTTTGAGAAGAAAAAG
* *
1311530 GATGCCACTAAGTCGTGGACTTT-GAGACAAAATGCCACTGAGTCGTGGACTTTGAGAAGA
1 GATGCCACGAA-TCGTGGACTTTAG-GACAAAATGCCACTGAGTCGTGGGCTTTGAGAAGA
1311590 GATTGCCACT
Statistics
Matches: 217, Mismatches: 16, Indels: 28
0.83 0.06 0.11
Matches are distributed among these distances:
61 17 0.08
62 94 0.43
64 97 0.45
65 9 0.04
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
GATGCCACGAATCGTGGACTTTAGGACAAAATGCCACTGAGTCGTGGGCTTTGAGAAGAAAAAG
Found at i:1311408 original size:126 final size:126
Alignment explanation
Indices: 1311278--1311589 Score: 547
Period size: 126 Copynumber: 2.5 Consensus size: 126
1311268 TTAAGAAGGA
* * * *
1311278 GATGCCACTGAA-TTGTGAACTTT-AGGACAAAATGCCATTGAGTCGTGGGCTTTGAGAAGAAAA
1 GATGCCACT-AAGTCGTGGACTTTGA-GACAAAATGCCACTGAGTCGTGGACTTTGAGAAGAAAA
1311341 AGGTGCCACGGAATCGTGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAAGAAAAG
64 AGGTGCCACGGAATCGTGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAAGAAAAG
1311404 GATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTGAGAAGAAAAAG
1 GATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTGAGAAGAAAAAG
*
1311469 GTGCCACGGAGTCGTGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAAGAAAAG
66 GTGCCACGGAATCGTGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAAGAAAAG
1311530 GATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTGAGAAGA
1 GATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTGAGAAGA
1311590 GATTGCCACT
Statistics
Matches: 179, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
125 2 0.01
126 176 0.98
127 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (126 bp):
GATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTGAGAAGAAAAAG
GTGCCACGGAATCGTGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAAGAAAAG
Found at i:1312558 original size:16 final size:16
Alignment explanation
Indices: 1312535--1312577 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1312525 GGGTTTTTCC
*
1312535 TCTTTTTTGTTTTTTTTT
1 TCTTTTTTG--TTTTGTT
1312553 TCTTTTTTGTTTTGTT
1 TCTTTTTTGTTTTGTT
1312569 TCTTTTTTG
1 TCTTTTTTG
1312578 GAAAAGAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.62
18 9 0.38
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (16 bp):
TCTTTTTTGTTTTGTT
Found at i:1319818 original size:52 final size:52
Alignment explanation
Indices: 1319732--1319856 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
1319722 ATATGAAAAG
*
1319732 TTGCTTGCATGTATCGATACATTTAATAGAGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGAGTATCGATACATCTGGGCAAAT
* *
1319784 TTGCCTGCATGCATCGATACATTTTATA-ATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAGA-GTATCGATACATCTGGGCAAAT
1319836 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1319857 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 1 0.01
52 67 0.99
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAGAGTATCGATACATCTGGGCAAAT
Found at i:1319869 original size:52 final size:51
Alignment explanation
Indices: 1319732--1319876 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 51
1319722 ATATGAAAAG
* *
1319732 TTGCTTGCATGTATCGATACATTTAATAGAGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
1319784 TTGCCTGCATGCATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1319836 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1319877 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1319883 original size:13 final size:13
Alignment explanation
Indices: 1319865--1319889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319855 CAAAGATCAG
1319865 TGTATCGATACAA
1 TGTATCGATACAA
1319878 TGTATCGATACA
1 TGTATCGATACA
1319890 TTTGAGTAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1319967 original size:33 final size:33
Alignment explanation
Indices: 1319930--1319996 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1319920 AGTAGCTTAA
1319930 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1319963 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1319996 A
1 A
1319997 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1319970 original size:13 final size:13
Alignment explanation
Indices: 1319952--1319976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319942 CAAAAAAATA
1319952 TGTATCGATACAT
1 TGTATCGATACAT
1319965 TGTATCGATACA
1 TGTATCGATACA
1319977 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1321803 original size:20 final size:20
Alignment explanation
Indices: 1321777--1321838 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
1321767 ACTGCCAGTT
1321777 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAATTGA
1321796 TCCATGTATCGATACAA-TGA
1 T-CATGTATCGATACAATTGA
*
1321816 TCATGTATCGATACAATTTA
1 TCATGTATCGATACAATTGA
1321836 TCA
1 TCA
1321839 ATACAAAGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (20 bp):
TCATGTATCGATACAATTGA
Found at i:1321822 original size:19 final size:18
Alignment explanation
Indices: 1321777--1321832 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 18
1321767 ACTGCCAGTT
1321777 TCATGTATCGATACAATTG
1 TCATGTATCGATACAA-TG
1321796 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
1321815 ATCATGTATCGATACAAT
1 -TCATGTATCGATACAAT
1321833 TTATCAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 19 0.54
20 16 0.46
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:1322317 original size:45 final size:45
Alignment explanation
Indices: 1322253--1322345 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
1322243 TTGGGCAGCA
1322253 TTTATAAACTTACCAATTCGTATGGCCTTGTATGCAATCATTTTC
1 TTTATAAACTTACCAATTCGTATGGCCTTGTATGCAATCATTTTC
*
1322298 TTTATAAACTTACCAATTCGTATGGGCTTGTATGCAATCATTTTC
1 TTTATAAACTTACCAATTCGTATGGCCTTGTATGCAATCATTTTC
1322343 TTT
1 TTT
1322346 GTATCAACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.44
Consensus pattern (45 bp):
TTTATAAACTTACCAATTCGTATGGCCTTGTATGCAATCATTTTC
Found at i:1324293 original size:21 final size:21
Alignment explanation
Indices: 1324252--1324293 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1324242 CATTTTTGTT
*
1324252 AGTGATTTTGATGAAAAATGA
1 AGTGATTTTGAAGAAAAATGA
*
1324273 AGTGA-TTTGAAGTAAAGATGA
1 AGTGATTTTGAAG-AAAAATGA
1324294 TGAAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (21 bp):
AGTGATTTTGAAGAAAAATGA
Found at i:1324441 original size:13 final size:13
Alignment explanation
Indices: 1324423--1324449 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1324413 ATAGTAACCC
1324423 ATGTATCGATACA
1 ATGTATCGATACA
1324436 ATGTATCGATACA
1 ATGTATCGATACA
1324449 A
1 A
1324450 GGAATGTTGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1330638 original size:20 final size:20
Alignment explanation
Indices: 1330613--1330666 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1330603 GTTGCAAGCA
*
1330613 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATCT-ACC
1330633 ATGTATCGATACAATCTACC
1 ATGTATCGATACAATCTACC
1330653 ATGTATCGATACAA
1 ATGTATCGATACAA
1330667 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATCTACC
Found at i:1330740 original size:19 final size:20
Alignment explanation
Indices: 1330695--1330750 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1330685 CTGCCAGTTT
*
1330695 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATC
*
1330715 CATGTATCCATACAATGAT-
1 CATGTATCGATACAATGATC
*
1330734 TATGTATCGATACAATG
1 CATGTATCGATACAATG
1330751 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATGATC
Found at i:1330753 original size:13 final size:13
Alignment explanation
Indices: 1330735--1330761 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1330725 TACAATGATT
1330735 ATGTATCGATACA
1 ATGTATCGATACA
1330748 ATGTATCGATACA
1 ATGTATCGATACA
1330761 A
1 A
1330762 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1330777 original size:33 final size:32
Alignment explanation
Indices: 1330716--1330779 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1330706 ACAATTATCC
* *
1330716 ATGTATCCATACAATGATTATGTATCGATACA
1 ATGTATCCATACAAAGATAATGTATCGATACA
*
1330748 ATGTATCGATACAAAGCATAATGTATCGATAC
1 ATGTATCCATACAAAG-ATAATGTATCGATAC
1330780 TTCTGGGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (32 bp):
ATGTATCCATACAAAGATAATGTATCGATACA
Found at i:1338601 original size:28 final size:28
Alignment explanation
Indices: 1338492--1338604 Score: 129
Period size: 28 Copynumber: 4.1 Consensus size: 28
1338482 TTTTTTCTAA
** **
1338492 AAGTCCATGACTCCATGGCACCCTTTCA
1 AAGTCCACAACTCCATGGCACCCTTTTT
* *
1338520 AAGTCCACAACTCCGTGGCACCC-CTTT
1 AAGTCCACAACTCCATGGCACCCTTTTT
* * *
1338547 AAGTCTACAACTTCGTGGCACCCTTTTT
1 AAGTCCACAACTCCATGGCACCCTTTTT
*
1338575 AAGTCCACAACTCTATGGCACCCTTTTT
1 AAGTCCACAACTCCATGGCACCCTTTTT
1338603 AA
1 AA
1338605 AGTTCATAAC
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
27 22 0.31
28 49 0.69
ACGTcount: A:0.25, C:0.34, G:0.13, T:0.28
Consensus pattern (28 bp):
AAGTCCACAACTCCATGGCACCCTTTTT
Found at i:1338807 original size:31 final size:31
Alignment explanation
Indices: 1338660--1339505 Score: 623
Period size: 31 Copynumber: 26.6 Consensus size: 31
1338650 GTGGTGTCTT
*
1338660 TTTCTAAAGCCCACACAAGTCTATGGCAACCC
1 TTTCTAAAGCCCACACAAGTCGATGGCAA-CC
* *
1338692 TCCTCTAAAGCCCACACAAGT-TAGTGGCAACC
1 T-TTCTAAAGCCCACACAAGTCGA-TGGCAACC
* *
1338724 TTTTCTCTAAAGCCCACACAAGTCAATGGTAACCAC
1 --TT-TCTAAAGCCCACACAAGTCGATGGCAA-C-C
** * *
1338760 CCTCTAAAGCCTACACAAGTCGATGGCAATC
1 TTTCTAAAGCCCACACAAGTCGATGGCAACC
* * *
1338791 TTTTTAAAGCCCACACAAGTTGATGGCACCC
1 TTTCTAAAGCCCACACAAGTCGATGGCAACC
* *
1338822 TTCTCTAAAGCCCACACAAGTTGATGGCACCC
1 TT-TCTAAAGCCCACACAAGTCGATGGCAACC
* *
1338854 TTCTCTAAAGCCCACACAAGTCGGTGGCAATC
1 TT-TCTAAAGCCCACACAAGTCGATGGCAACC
*
1338886 TTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 TTTCTAAAGCCCACACAAGTCGATGGCAACC
* *
1338917 TCTTCTCAAAGCTCATACAAGTCGATGGCAATCC
1 T-TTCT-AAAGCCCACACAAGTCGATGGCAA-CC
* * * *
1338951 -TTCTAAAGCCTACACAAATTGGTGGCAACC
1 TTTCTAAAGCCCACACAAGTCGATGGCAACC
* *
1338981 TTTCTCTAAAGCCCACATAAGT-TAGTGGCAATCC
1 -TT-TCTAAAGCCCACACAAGTCGA-TGGCAA-CC
* * **
1339015 -TTCTAAAGCCCACACAAGTTGGTGGCGCCC
1 TTTCTAAAGCCCACACAAGTCGATGGCAACC
* *
1339045 TTCTCTAAAGCCCACATAAGTCGATGGCATCCC
1 TT-TCTAAAGCCCACACAAGTCGATGGCA-ACC
* *
1339078 TTT-TAAAGCCCACACAAGT-TAGTGGCACCCC
1 TTTCTAAAGCCCACACAAGTCGA-TGGCA-ACC
*
1339109 TTT-TCAAAGCCCACACAAGTCGATGGCAA-T
1 TTTCT-AAAGCCCACACAAGTCGATGGCAACC
1339139 TCTTCTAAAGCCCACACAAGTC-AGTGGCAACCC
1 T-TTCTAAAGCCCACACAAGTCGA-TGGCAA-CC
* * *
1339172 TTT-TAAAGCCCACATAAGT-TAGTGGCAAACT
1 TTTCTAAAGCCCACACAAGTCGA-TGGC-AACC
* *
1339203 TTCTCTAAAACCCACACAAGTC-AGTGGCAA-T
1 TT-TCTAAAGCCCACACAAGTCGA-TGGCAACC
* * * *
1339234 TCTTCTAAAGTCCACACAAGTTGGTGGCACCC
1 T-TTCTAAAGCCCACACAAGTCGATGGCAACC
*
1339266 TTCTCTAAAGCCCACACAAGT-TAGTGGCAATCC
1 TT-TCTAAAGCCCACACAAGTCGA-TGGCAA-CC
* *
1339299 -TTCTAAAGCCCACACAACTTGATGGCAACCC
1 TTTCTAAAGCCCACACAAGTCGATGGCAA-CC
*
1339330 TTT-TAAAGCCCACACAAGT-TAGTGGCAACC
1 TTTCTAAAGCCCACACAAGTCGA-TGGCAACC
* * * *
1339360 TTTCTCTAAAGCCTACACAAGTTGGTTGCAATCC
1 -TT-TCTAAAGCCCACACAAGTCGATGGCAA-CC
* *
1339394 TTT-TAAAGCCCACACAAGTCGGTGGCACCC
1 TTTCTAAAGCCCACACAAGTCGATGGCAACC
* * * * *
1339424 ATTCTCAAAGCTCACACAAGTTGGTGGCACCC
1 TTTCT-AAAGCCCACACAAGTCGATGGCAACC
* * * *
1339456 TTTCTCAAAGCTCACACAAGTTGGTGGCACCCC
1 TTTCT-AAAGCCCACACAAGTCGATGGCA-ACC
*
1339489 TTT-TCAAGCCCACACAA
1 TTTCTAAAGCCCACACAA
1339506 ATTGGTGGCA
Statistics
Matches: 677, Mismatches: 86, Indels: 103
0.78 0.10 0.12
Matches are distributed among these distances:
30 14 0.02
31 276 0.41
32 207 0.31
33 147 0.22
34 30 0.04
35 2 0.00
36 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (31 bp):
TTTCTAAAGCCCACACAAGTCGATGGCAACC
Found at i:1338863 original size:64 final size:63
Alignment explanation
Indices: 1338662--1339532 Score: 646
Period size: 64 Copynumber: 13.7 Consensus size: 63
1338652 GGTGTCTTTT
*
1338662 TCTAAAGCCCACACAAGTCT-ATGGCAACCCTCCTCTAAAGCCCACACAAGTT-AGTGGCAACCT
1 TCTAAAGCCCACACAAGT-TGATGGC-ACCCT-TTCTAAAGCCCACACAAGTTGA-TGGC-ACC-
*
1338725 TTTC
60 CTTC
** * ** * * **
1338729 TCTAAAGCCCACACAAGTCAATGGTAACCACCCTCTAAAGCCTACACAAGTCGATGGCAATCTT-
1 TCTAAAGCCCACACAAGTTGATGG-CACC-CTTTCTAAAGCCCACACAAGTTGATGGCACCCTTC
*
1338793 TTTAAAGCCCACACAAGTTGATGGCACCCTTCTCTAAAGCCCACACAAGTTGATGGCACCCTTC
1 TCTAAAGCCCACACAAGTTGATGGCACCCTT-TCTAAAGCCCACACAAGTTGATGGCACCCTTC
* * ** * *
1338857 TCTAAAGCCCACACAAGTCGGTGGCAATCTTTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTC
1 TCTAAAGCCCACACAAGTTGATGGCACCCTTTCTAAAGCCCACACAAGTTGATGGC-ACC-CTTC
* * * * * * * *
1338922 TC-AAAGCTCATACAAGTCGATGGCAATCC-TTCTAAAGCCTACACAAATTGGTGGCAACCTTTC
1 TCTAAAGCCCACACAAGTTGATGGC-ACCCTTTCTAAAGCCCACACAAGTTGATGGC-ACCCTTC
* * * *
1338985 TCTAAAGCCCACATAAGTT-AGTGGCAATCC-TTCTAAAGCCCACACAAGTTGGTGGCGCCCTTC
1 TCTAAAGCCCACACAAGTTGA-TGGC-ACCCTTTCTAAAGCCCACACAAGTTGATGGCACCCTTC
* *
1339048 TCTAAAGCCCACATAAGTCGATGGCATCCCTTT-TAAAGCCCACACAAGTT-AGTGGCACCCCTT
1 TCTAAAGCCCACACAAGTTGATGGCA-CCCTTTCTAAAGCCCACACAAGTTGA-TGGCA-CCCTT
*
1339111 T
63 C
* ** *
1339112 TC-AAAGCCCACACAAGTCGATGGCA-ATTCTTCTAAAGCCCACACAAG-TCAGTGGCAACCCTT
1 TCTAAAGCCCACACAAGTTGATGGCACCCT-TTCTAAAGCCCACACAAGTTGA-TGGC-ACCCTT
1339174 -
63 C
* * * * * *
1339174 T-TAAAGCCCACATAAGTT-AGTGGCAAACTTTCTCTAAAACCCACACAAG-TCAGTGGCA--AT
1 TCTAAAGCCCACACAAGTTGA-TGGC-ACCCTT-TCTAAAGCCCACACAAGTTGA-TGGCACCCT
1339234 TC
62 TC
* * *
1339236 TTCTAAAGTCCACACAAGTTGGTGGCACCCTTCTCTAAAGCCCACACAAGTT-AGTGGCAATCC-
1 -TCTAAAGCCCACACAAGTTGATGGCACCCTT-TCTAAAGCCCACACAAGTTGA-TGGC-ACCCT
1339299 T-
62 TC
* *
1339300 TCTAAAGCCCACACAACTTGATGGCAACCCTTT-TAAAGCCCACACAAGTT-AGTGGCAACCTTT
1 TCTAAAGCCCACACAAGTTGATGGC-ACCCTTTCTAAAGCCCACACAAGTTGA-TGGC-ACCCTT
1339363 C
63 C
* * * * * *
1339364 TCTAAAGCCTACACAAGTTGGTTGCAATCCTTT-TAAAGCCCACACAAGTCGGTGGCACCCATTC
1 TCTAAAGCCCACACAAGTTGATGGC-ACCCTTTCTAAAGCCCACACAAGTTGATGGCACCC-TTC
* * * *
1339428 TC-AAAGCTCACACAAGTTGGTGGCACCCTTTCTCAAAGCTCACACAAGTTGGTGGCACCCCTT-
1 TCTAAAGCCCACACAAGTTGATGGCACCCTTTCT-AAAGCCCACACAAGTTGATGGCA-CCCTTC
* * * * *
1339491 T-TCAAGCCCACACAAATTGGTGGCAGCAC-TTCTAAAGTCCAC
1 TCTAAAGCCCACACAAGTTGATGGCA-CCCTTTCTAAAGCCCAC
1339533 GTAAGTCAGT
Statistics
Matches: 674, Mismatches: 87, Indels: 91
0.79 0.10 0.11
Matches are distributed among these distances:
61 4 0.01
62 63 0.09
63 260 0.39
64 283 0.42
65 14 0.02
66 1 0.00
67 47 0.07
68 2 0.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (63 bp):
TCTAAAGCCCACACAAGTTGATGGCACCCTTTCTAAAGCCCACACAAGTTGATGGCACCCTTC
Found at i:1338882 original size:95 final size:95
Alignment explanation
Indices: 1338662--1339515 Score: 765
Period size: 95 Copynumber: 8.9 Consensus size: 95
1338652 GGTGTCTTTT
** * * *
1338662 TCTAAAGCCCACACAAGTCTATGGCAACCCTCCTCTAAAGCCCACACAAGTTAGTGGCAACCTTT
1 TCTAAAGCCCACACAAGTCGGTGGCAA-CCT-TTTTAAAGCCCACACAAGTTAGTGGCAACC-CT
** * *
1338727 TCTCTAAAGCCCACACAAGTCAATGGTAACCAC-CC
63 T-TCTAAAGCCCACACAAGTTGATGG-CACC-CTTC
* * *
1338762 TCTAAAGCCTACACAAGTCGATGGCAATCTTTTTAAAGCCCACACAAGTT-GATGGC-ACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTAAAGCCCACACAAGTTAG-TGGCAACCCTT-
1338825 TCTAAAGCCCACACAAGTTGATGGCACCCTTC
64 TCTAAAGCCCACACAAGTTGATGGCACCCTTC
* * **
1338857 TCTAAAGCCCACACAAGTCGGTGGCAATCTTTCTAAAGCCCACACAAGTCGGTGGCAA-CCTCTT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTAAAGCCCACACAAGTTAGTGGCAACCCT-TT
* * * *
1338921 CTCAAAGCTCATACAAGTCGATGGCAATCC-T-
65 CT-AAAGCCCACACAAGTTGATGGC-ACCCTTC
* * * * *
1338952 TCTAAAGCCTACACAAATTGGTGGCAACCTTTCTCTAAAGCCCACATAAGTTAGTGGCAATCC-T
1 TCTAAAGCCCACACAAGTCGGTGGCAACCTTT-T-TAAAGCCCACACAAGTTAGTGGCAACCCTT
* *
1339016 TCTAAAGCCCACACAAGTTGGTGGCGCCCTTC
64 TCTAAAGCCCACACAAGTTGATGGCACCCTTC
* * * * *
1339048 TCTAAAGCCCACATAAGTCGATGGCATCCCTTTTAAAGCCCACACAAGTTAGTGGCACCCCTTT-
1 TCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTAAAGCCCACACAAGTTAGTGGCAACCCTTTC
* *
1339112 TCAAAGCCCACACAAGTCGATGGCA--ATTC
66 T-AAAGCCCACACAAGTTGATGGCACCCTTC
* * * * *
1339141 TTCTAAAGCCCACACAAGTCAGTGGCAACCCTTTTAAAGCCCACATAAGTTAGTGGCAAACTTTC
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTAAAGCCCACACAAGTTAGTGGCAACCCTT-
* * *
1339206 TCTAAAACCCACACAAG-TCAGTGGCA--ATTC
64 TCTAAAGCCCACACAAGTTGA-TGGCACCCTTC
* * * * *
1339236 TTCTAAAGTCCACACAAGTTGGTGGCACCCTTCTCTAAAGCCCACACAAGTTAGTGGCAATCC-T
1 -TCTAAAGCCCACACAAGTCGGTGGCAACCTT-TTTAAAGCCCACACAAGTTAGTGGCAACCCTT
*
1339300 TCTAAAGCCCACACAACTTGATGGCAACCCTT-
64 TCTAAAGCCCACACAAGTTGATGGC-ACCCTTC
** * * * *
1339332 T-TAAAGCCCACACAAGTTAGTGGCAACCTTTCTCTAAAGCCTACACAAGTTGGTTGCAATCCTT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCTTT-T-TAAAGCCCACACAAGTTAGTGGCAACCCTT
* *
1339396 T-TAAAGCCCACACAAGTCGGTGGCACCCATTC
64 TCTAAAGCCCACACAAGTTGATGGCACCC-TTC
* * * * * * *
1339428 TC-AAAGCTCACACAAGTTGGTGGCACCCTTTCTCAAAGCTCACACAAGTTGGTGGCACCCCTTT
1 TCTAAAGCCCACACAAGTCGGTGGCAACCTTT-TTAAAGCCCACACAAGTTAGTGGCAACCCTTT
* * *
1339492 -TCAAGCCCACACAAATTGGTGGCA
65 CTAAAGCCCACACAAGTTGATGGCA
1339516 GCACTTCTAA
Statistics
Matches: 633, Mismatches: 92, Indels: 63
0.80 0.12 0.08
Matches are distributed among these distances:
93 4 0.01
94 134 0.21
95 278 0.44
96 135 0.21
97 31 0.05
98 24 0.04
99 2 0.00
100 25 0.04
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (95 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTAAAGCCCACACAAGTTAGTGGCAACCCTTTC
TAAAGCCCACACAAGTTGATGGCACCCTTC
Found at i:1339557 original size:31 final size:32
Alignment explanation
Indices: 1339519--1339588 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
1339509 GGTGGCAGCA
** *
1339519 CTTCTAAAGTCCACGTAAGTCAGTAGTAA-TC
1 CTTCTAAAGTCCACACAAGTCAGTAGTAACCC
*
1339550 CTTCTAAAGTCCACACAAGTCAGTGGTAACCC
1 CTTCTAAAGTCCACACAAGTCAGTAGTAACCC
1339582 CTTCTAA
1 CTTCTAA
1339589 GCCTAATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 26 0.76
32 8 0.24
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (32 bp):
CTTCTAAAGTCCACACAAGTCAGTAGTAACCC
Found at i:1339799 original size:52 final size:52
Alignment explanation
Indices: 1339715--1339837 Score: 131
Period size: 52 Copynumber: 2.4 Consensus size: 52
1339705 ATGCCGTTGG
* * ** * *
1339715 CCTTGAATCAGCACATTAGAACCCTTGTCATTTGTAAG-TCCATTGTTGTTAA
1 CCTTGAATCAGCATATTGGAACCCTTACCATTTGTAAGCT-CAATGTCGTTAA
* * * *
1339767 CCTTGAATCAGCATATTGGTACCTTTACCATTTTTAAGCTCAATGTCGTTGA
1 CCTTGAATCAGCATATTGGAACCCTTACCATTTGTAAGCTCAATGTCGTTAA
*
1339819 CCTTGAATCAGTATATTGG
1 CCTTGAATCAGCATATTGG
1339838 CCTTCTTCTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 58 0.98
53 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (52 bp):
CCTTGAATCAGCATATTGGAACCCTTACCATTTGTAAGCTCAATGTCGTTAA
Found at i:1340070 original size:61 final size:61
Alignment explanation
Indices: 1339957--1340074 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 61
1339947 GGCATTTTTG
* **
1339957 TCATCTTTAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCATATTTATCATTCTTC
1 TCATCTTCAAGCCCAATATCACTGGCCTTGAATCAGCATATCAGCATATTTATCATTCTTC
* **
1340018 TCATCTTCAAGCTCAATATCAC-GGGGTGTGAATCAGCATATCAGCACT-TTTATCATT
1 TCATCTTCAAGCCCAATATCACTGGCCT-TGAATCAGCATATCAGCA-TATTTATCATT
1340075 TTTCGCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 3 0.06
61 45 0.92
62 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (61 bp):
TCATCTTCAAGCCCAATATCACTGGCCTTGAATCAGCATATCAGCATATTTATCATTCTTC
Found at i:1341518 original size:13 final size:13
Alignment explanation
Indices: 1341500--1341525 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1341490 CAATTTTTTG
1341500 TGTATCGATACAT
1 TGTATCGATACAT
1341513 TGTATCGATACAT
1 TGTATCGATACAT
1341526 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1343880 original size:21 final size:21
Alignment explanation
Indices: 1343856--1343902 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1343846 TTTGATGCTG
1343856 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1343876 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1343897 ATTTTG
1 ATTTTG
1343903 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1344041 original size:13 final size:13
Alignment explanation
Indices: 1344023--1344061 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1344013 ATAATCACCC
*
1344023 TGTATCGATACAG
1 TGTATCGATACAA
1344036 TGTATCGATACAA
1 TGTATCGATACAA
1344049 TGTATCGATACAA
1 TGTATCGATACAA
1344062 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1344072 original size:20 final size:20
Alignment explanation
Indices: 1344047--1344125 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1344037 GTATCGATAC
1344047 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1344067 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1344092 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1344112 CATGTATCGATACA
1 AATGTATCGATACA
1344126 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1346169 original size:16 final size:16
Alignment explanation
Indices: 1346135--1346172 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1346125 CATCGATTTC
*
1346135 TTTTGGAGCTTCTTCA
1 TTTTGGAGCTTCCTCA
1346151 TTTT-GAGCTTCCTCA
1 TTTTGGAGCTTCCTCA
*
1346166 ATTTGGA
1 TTTTGGA
1346173 CATTTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (16 bp):
TTTTGGAGCTTCCTCA
Found at i:1348004 original size:21 final size:21
Alignment explanation
Indices: 1347975--1348019 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1347965 AAGTTTTCAT
*
1347975 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1347995 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1348017 TTT
1 TTT
1348020 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1350771 original size:21 final size:21
Alignment explanation
Indices: 1350724--1350779 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
1350714 TATAAATAAT
*
1350724 AAATGTATCGATACATAGGTG
1 AAATGTATCGATACATAGCTG
1350745 -AATGTATCGATACAT-GCCTG
1 AAATGTATCGATACATAG-CTG
1350765 AAATGTATCGATACA
1 AAATGTATCGATACA
1350780 AAACCAACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.53
21 14 0.44
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (21 bp):
AAATGTATCGATACATAGCTG
Found at i:1350872 original size:20 final size:21
Alignment explanation
Indices: 1350824--1350879 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1350814 TATATAACTA
1350824 AATGTATCGATACATTTACTC
1 AATGTATCGATACATTTACTC
** *
1350845 TTTGTATCGATACATTT-TTC
1 AATGTATCGATACATTTACTC
1350865 AATGTATCGATACAT
1 AATGTATCGATACAT
1350880 GCAGGCAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTACTC
Found at i:1353765 original size:2 final size:2
Alignment explanation
Indices: 1353758--1353801 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1353748 ACCTAGATTT
1353758 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1353800 TA
1 TA
1353802 ATTCATGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1354603 original size:18 final size:18
Alignment explanation
Indices: 1354580--1354614 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1354570 GTGTTATTCA
* *
1354580 AAAAAAATTTTAAAAAAG
1 AAAAAAAGTGTAAAAAAG
1354598 AAAAAAAGTGTAAAAAA
1 AAAAAAAGTGTAAAAAA
1354615 AAATGTGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (18 bp):
AAAAAAAGTGTAAAAAAG
Found at i:1356246 original size:6 final size:6
Alignment explanation
Indices: 1356235--1356259 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1356225 ATTTCAGTTA
1356235 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
1356260 TTTATAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:1358941 original size:23 final size:22
Alignment explanation
Indices: 1358915--1358975 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 22
1358905 TAATTATAAT
1358915 TATCATATTGATTTAATGTTTGG
1 TATCAT-TTGATTTAATGTTTGG
1358938 TATCGCATTTGATTTAATGTTTGG
1 TAT--CATTTGATTTAATGTTTGG
1358962 TATCGCATTTGATT
1 TAT--CATTTGATT
1358976 GATAGGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.08
24 30 0.83
25 3 0.08
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (22 bp):
TATCATTTGATTTAATGTTTGG
Found at i:1358953 original size:24 final size:24
Alignment explanation
Indices: 1358922--1358975 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1358912 AATTATCATA
1358922 TTGATTTAATGTTTGGTATCGCAT
1 TTGATTTAATGTTTGGTATCGCAT
1358946 TTGATTTAATGTTTGGTATCGCAT
1 TTGATTTAATGTTTGGTATCGCAT
1358970 TTGATT
1 TTGATT
1358976 GATAGGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.52
Consensus pattern (24 bp):
TTGATTTAATGTTTGGTATCGCAT
Found at i:1365371 original size:33 final size:33
Alignment explanation
Indices: 1365334--1365400 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1365324 TTCAACGATT
1365334 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1365367 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1365400 T
1 T
1365401 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1365372 original size:13 final size:13
Alignment explanation
Indices: 1365354--1365378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1365344 CATAAAATGT
1365354 TGTATCGATACAA
1 TGTATCGATACAA
1365367 TGTATCGATACA
1 TGTATCGATACA
1365379 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1365459 original size:13 final size:13
Alignment explanation
Indices: 1365441--1365465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1365431 ATTACTCAAA
1365441 TGTATCGATACAT
1 TGTATCGATACAT
1365454 TGTATCGATACA
1 TGTATCGATACA
1365466 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1365529 original size:51 final size:52
Alignment explanation
Indices: 1365474--1365589 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
1365464 CACTGATCTT
*
1365474 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1365525 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1365577 TGTATCGATACAT
1 TGTATCGATACAT
1365590 ACAAGCAACT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 19 0.31
52 43 0.69
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1368928 original size:2 final size:2
Alignment explanation
Indices: 1368921--1368958 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1368911 GTTTCACTCC
* *
1368921 AT AT AT AT AT TT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368959 CTTTATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1371777 original size:15 final size:16
Alignment explanation
Indices: 1371734--1371770 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1371724 TTTGATTCTT
1371734 TGAAAAA-GAAAAAAA
1 TGAAAAATGAAAAAAA
1371749 TGAAAAATGAAAAAAA
1 TGAAAAATGAAAAAAA
*
1371765 TTAAAA
1 TGAAAA
1371771 TTAAAAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
TGAAAAATGAAAAAAA
Found at i:1371800 original size:39 final size:38
Alignment explanation
Indices: 1371742--1371824 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
1371732 TTTGAAAAAG
*
1371742 AAAAAAATGAAAAATGAAAAAAATTAAAATTAAAAAGAGA
1 AAAAAAAAGAAAAATGAAAAAAATTAAAA--AAAAAGAGA
* * *
1371782 AAAAAAAAGAAAGA-GAAAAAAATTGAAAAAAAAGTGA
1 AAAAAAAAGAAAAATGAAAAAAATTAAAAAAAAAGAGA
1371819 AAAAAA
1 AAAAAA
1371825 GAAAATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 14 0.36
39 13 0.33
40 12 0.31
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (38 bp):
AAAAAAAAGAAAAATGAAAAAAATTAAAAAAAAAGAGA
Found at i:1375171 original size:52 final size:51
Alignment explanation
Indices: 1375087--1375199 Score: 127
Period size: 52 Copynumber: 2.2 Consensus size: 51
1375077 ATTTGCTTGC
* * ** *
1375087 ATGTATCGATACAGTAAAGAATATATCGATACATTTAAGTCAAAAACATAGA
1 ATGTATCGATAAAATAAAGAATATATAAATACATTTAAGTC-AAAACACAGA
* * ** *
1375139 ATGTATCGATAAAATGAAGAATGTATAAATACATTTGGGTCAAAACCCAGA
1 ATGTATCGATAAAATAAAGAATATATAAATACATTTAAGTCAAAACACAGA
1375190 ATGTATCGAT
1 ATGTATCGAT
1375200 CTAATAAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 18 0.35
52 33 0.65
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (51 bp):
ATGTATCGATAAAATAAAGAATATATAAATACATTTAAGTCAAAACACAGA
Found at i:1377976 original size:167 final size:166
Alignment explanation
Indices: 1377802--1378133 Score: 425
Period size: 166 Copynumber: 2.0 Consensus size: 166
1377792 TCTCATATTT
* ** * * *
1377802 TTTGAAATACGGTATTTTCTACTCCATAAATTTTTTCAACGGGATTTTTCTTAGTTTTTAATTTT
1 TTTGAAATACAGTATTTTAAAATCCAT-AAGTTTTTCAACGGGATTTTTCTTAGTTTATAATTTT
1377867 TAAAATTCATAAAATATCATCATTTGA-TTCATATTAAATCAGTTCTAAAAAATTAATTCATTTT
65 TAAAATTCATAAAATATCATCATTT-ATTTCATATTAAATCAGTTCTAAAAAATTAATTCATTTT
*
1377931 CATGAG-TTTTTGATTTTTTTCCTTGAAATTCTCTTTTC
129 CATGAGTTTTTTAATTTTTTT-CTTGAAATTCTCTTTTC
* * * * **** *
1377969 TTTGAAATACATTGTTTTAAAATTCATGAGTTTTTGGGGGGGATTTTTCTTGGTTTATAATTTTT
1 TTTGAAATACAGTATTTTAAAATCCATAAGTTTTTCAACGGGATTTTTCTTAGTTTATAATTTTT
* * * * *
1378034 AAAATTCATCAAATATCATTATTTATTTCATATTAAATCAGTTTTCAAAAATTATTTCATTTTCA
66 AAAATTCATAAAATATCATCATTTATTTCATATTAAATCAGTTCTAAAAAATTAATTCATTTTCA
*
1378099 TGAGTTTTTTAATTTTTTTCTTGAAATTCTTTTTT
131 TGAGTTTTTTAATTTTTTTCTTGAAATTCTCTTTT
1378134 TTCAAAAAAC
Statistics
Matches: 141, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
165 1 0.01
166 107 0.76
167 33 0.23
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (166 bp):
TTTGAAATACAGTATTTTAAAATCCATAAGTTTTTCAACGGGATTTTTCTTAGTTTATAATTTTT
AAAATTCATAAAATATCATCATTTATTTCATATTAAATCAGTTCTAAAAAATTAATTCATTTTCA
TGAGTTTTTTAATTTTTTTCTTGAAATTCTCTTTTC
Found at i:1378798 original size:13 final size:13
Alignment explanation
Indices: 1378776--1378823 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
1378766 TGATCAGCTG
1378776 GAAAAA-AAAAGA
1 GAAAAAGAAAAGA
1378788 GAAAAAGAAAAGA
1 GAAAAAGAAAAGA
1378801 -AAAAAGAAAA-A
1 GAAAAAGAAAAGA
*
1378812 AATAAAAGAAAA
1 GA-AAAAGAAAA
1378824 TAGGTAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.03
12 17 0.52
13 15 0.45
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
GAAAAAGAAAAGA
Found at i:1378803 original size:18 final size:18
Alignment explanation
Indices: 1378776--1378811 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1378766 TGATCAGCTG
*
1378776 GAAAAAAAAAGAGAAAAA
1 GAAAAAAAAAAAGAAAAA
*
1378794 GAAAAGAAAAAAGAAAAA
1 GAAAAAAAAAAAGAAAAA
1378812 AATAAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAAAGAAAAA
Found at i:1378805 original size:20 final size:20
Alignment explanation
Indices: 1378780--1378823 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1378770 CAGCTGGAAA
*
1378780 AAAAAAGAGAAAAAGAAAAG
1 AAAAAAGAAAAAAAGAAAAG
*
1378800 AAAAAAGAAAAAAATAAAAG
1 AAAAAAGAAAAAAAGAAAAG
1378820 AAAA
1 AAAA
1378824 TAGGTAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAAGAAAAAAAGAAAAG
Found at i:1379890 original size:155 final size:156
Alignment explanation
Indices: 1379610--1379991 Score: 525
Period size: 155 Copynumber: 2.4 Consensus size: 156
1379600 CATATTAATT
* * * * **
1379610 ATTTTTTAATCTTTTATATTTCTATGGG-GTCTGTAGGGGTATAAAAGAATATAAAAACTTTTTT
1 ATTTTTTAATCTTTTATATTCCTATGGGAG-CCGTAGGGGTATAAAAG-ATTTCAAAACTTTTCG
* * * *
1379674 TATCTTTTCGGGTTCCCATTAAGTTACGAAAAGGCATTTTTCAAAAATAAATAAATTAAATTAAC
64 TATCCTTTCAGGTTCCCATTAAGGTACGAAAAGACATTTTTCAAAAATAAATAAATTAAATTAAC
*
1379739 ACTTGCAAAATTGAAATAAATATCAATC
129 ACTTGCAAAATTGAAATAAATATCAACC
1379767 -TTTTTTAATCTTTTATATTCCTATGGGAGCCGTAGGGGTATAAAAGATTTCAAAACTTTTCGTA
1 ATTTTTTAATCTTTTATATTCCTATGGGAGCCGTAGGGGTATAAAAGATTTCAAAACTTTTCGTA
* * * *
1379831 TCCTTTCAGGTTTCCATTAAGGTATGAAATGATATTTTTCAAAAATAAATAAATTAAATTAACAC
66 TCCTTTCAGGTTCCCATTAAGGTACGAAAAGACATTTTTCAAAAATAAATAAATTAAATTAACAC
* * *
1379896 TTTCATAATTGAAATAAATATTAACC
131 TTGCAAAATTGAAATAAATATCAACC
* * * *
1379922 ATTTTTTAATCTTTTATACTCTTATGAGGATCCGTAGGTGTATAAAAGATTTCAAAACTTTTCGT
1 ATTTTTTAATCTTTTATATTCCTATG-GGAGCCGTAGGGGTATAAAAGATTTCAAAACTTTTCGT
1379987 ATCCT
65 ATCCT
1379992 CACGATTTTT
Statistics
Matches: 200, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
155 93 0.47
156 65 0.32
157 42 0.21
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (156 bp):
ATTTTTTAATCTTTTATATTCCTATGGGAGCCGTAGGGGTATAAAAGATTTCAAAACTTTTCGTA
TCCTTTCAGGTTCCCATTAAGGTACGAAAAGACATTTTTCAAAAATAAATAAATTAAATTAACAC
TTGCAAAATTGAAATAAATATCAACC
Found at i:1383709 original size:23 final size:23
Alignment explanation
Indices: 1383665--1383727 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
1383655 TTTATATAAA
** *
1383665 ATAATATTTTTATCTTTTATTTT
1 ATAATATTTTTATAATTTAATTT
1383688 ATAAT-TTTTTATAATTTAATTT
1 ATAATATTTTTATAATTTAATTT
1383710 A-AATATTTTATATAATTT
1 ATAATATTTT-TATAATTT
1383728 TATAAATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.09
22 19 0.54
23 13 0.37
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATAATATTTTTATAATTTAATTT
Found at i:1384335 original size:2 final size:2
Alignment explanation
Indices: 1384328--1384369 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1384318 AGCGATTATT
* *
1384328 AG AG AG AG AG AG AG AG AG AG TG TG AG AG AG AG A- ATG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG
1384370 CATTAGTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.48, T:0.07
Consensus pattern (2 bp):
AG
Found at i:1384511 original size:2 final size:2
Alignment explanation
Indices: 1384504--1384547 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1384494 ATGTAGATAG
1384504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1384546 AT
1 AT
1384548 GCAATTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1385347 original size:10 final size:12
Alignment explanation
Indices: 1385313--1385349 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1385303 AAAAAGAGAA
1385313 AAAGAGAAAAAT
1 AAAGAGAAAAAT
1385325 AAAGAGAAAAAT
1 AAAGAGAAAAAT
1385337 AAAG-G-AAAAT
1 AAAGAGAAAAAT
1385347 AAA
1 AAA
1385350 AGGTTTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 8 0.32
11 1 0.04
12 16 0.64
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAGAGAAAAAT
Found at i:1390664 original size:3 final size:3
Alignment explanation
Indices: 1390656--1390699 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1390646 TTTGACCTGA
1390656 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1390700 AGGGAGGGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1390841 original size:3 final size:3
Alignment explanation
Indices: 1390826--1390855 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1390816 TCAACCCATA
*
1390826 ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1390856 TAGTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1396539 original size:19 final size:19
Alignment explanation
Indices: 1396515--1396551 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1396505 TCTCCTCTCC
*
1396515 CTTTCATTAAACTCCACAG
1 CTTTCATCAAACTCCACAG
1396534 CTTTCATCAAACTCCACA
1 CTTTCATCAAACTCCACA
1396552 ACTTCCATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.30
Consensus pattern (19 bp):
CTTTCATCAAACTCCACAG
Found at i:1396560 original size:19 final size:19
Alignment explanation
Indices: 1396523--1396560 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1396513 CCCTTTCATT
* *
1396523 AAACTCCACAGCTTTCATC
1 AAACTCCACAACTTCCATC
1396542 AAACTCCACAACTTCCATC
1 AAACTCCACAACTTCCATC
1396561 TGAAAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.39, G:0.03, T:0.24
Consensus pattern (19 bp):
AAACTCCACAACTTCCATC
Found at i:1400129 original size:28 final size:28
Alignment explanation
Indices: 1400064--1400138 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
1400054 GTAATAAAGT
1400064 CGAGGTTGGAGTATCCCCTCGAAAATAA
1 CGAGGTTGGAGTATCCCCTCGAAAATAA
* *
1400092 CG-GGACTGGAGTAT-CCC-CGATGATATAA
1 CGAGG-TTGGAGTATCCCCTCGA--AAATAA
*
1400120 CGAGGTTGGAGTACCCCCT
1 CGAGGTTGGAGTATCCCCT
1400139 ATTATGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
26 3 0.08
27 5 0.14
28 24 0.65
29 5 0.14
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (28 bp):
CGAGGTTGGAGTATCCCCTCGAAAATAA
Found at i:1400260 original size:51 final size:51
Alignment explanation
Indices: 1400203--1400380 Score: 161
Period size: 51 Copynumber: 3.5 Consensus size: 51
1400193 AAATAACTGG
* * *
1400203 GTTAGAGTATCCCCAATTATGAAAAATTGGTGTTTTGAAAATAAAGTCGGA
1 GTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTGAAAATAAAATCGGA
* *
1400254 GTTAGAGTATCCTCGA-T-TGCAATAAATCGATGCTTTT-AAAA-AAAATCGGA
1 GTTAGAGTATCCCCGATTATG-AA-AAATTGATG-TTTTGAAAATAAAATCGGA
* * * ** *
1400304 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGGAACCAGGA
1 GTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTGAAAATAAAATC-GGA
* *
1400356 -TTGGAGTATCCCCGA-GATGAAAAAT
1 GTTAGAGTATCCCCGATTATGAAAAAT
1400381 CTAGAAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 17
0.76 0.11 0.12
Matches are distributed among these distances:
49 6 0.06
50 44 0.42
51 46 0.44
52 8 0.08
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (51 bp):
GTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTGAAAATAAAATCGGA
Found at i:1402732 original size:20 final size:21
Alignment explanation
Indices: 1402707--1402765 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
1402697 AAAATGCGTG
*
1402707 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATGTAGA
* *
1402727 AATGTATCGATATAATG-AGC
1 AATGTATCGATACAATGTAGA
1402747 AATGTATCGATACAATGTA
1 AATGTATCGATACAATGTA
1402766 TCGATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (21 bp):
AATGTATCGATACAATGTAGA
Found at i:1402762 original size:13 final size:13
Alignment explanation
Indices: 1402746--1402776 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1402736 ATATAATGAG
1402746 CAATGTATCGATA
1 CAATGTATCGATA
1402759 CAATGTATCGATA
1 CAATGTATCGATA
*
1402772 TAATG
1 CAATG
1402777 AGAAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1402769 original size:33 final size:33
Alignment explanation
Indices: 1402727--1402796 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
1402717 TACATTGTAA
*
1402727 AATGTATCGATATAATGAGCAATGTATCGATAC
1 AATGTATCGATATAATGAGAAATGTATCGATAC
1402760 AATGTATCGATATAATGAGAAATGTATCGATAC
1 AATGTATCGATATAATGAGAAATGTATCGATAC
1402793 AATG
1 AATG
1402797 CGAAATGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (33 bp):
AATGTATCGATATAATGAGAAATGTATCGATAC
Found at i:1402769 original size:53 final size:53
Alignment explanation
Indices: 1402707--1402814 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
1402697 AAAATGCGTG
* * *
1402707 AATGTATCGATACATTGTA-AAATGTATCGATATAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATG-AGAAATGTATCGATACAATGAGAAATGTATCGATAC
* * *
1402760 AATGTATCGATATAATGAGAAATGTATCGATACAATGCGAAATGTATCGGTAC
1 AATGTATCGATACAATGAGAAATGTATCGATACAATGAGAAATGTATCGATAC
1402813 AA
1 AA
1402815 CATCTGGGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 1 0.02
53 47 0.98
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (53 bp):
AATGTATCGATACAATGAGAAATGTATCGATACAATGAGAAATGTATCGATAC
Found at i:1402785 original size:20 final size:20
Alignment explanation
Indices: 1402760--1402814 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1402750 GTATCGATAC
*
1402760 AATGTATCGATATAATGAGA
1 AATGTATCGATACAATGAGA
*
1402780 AATGTATCGATACAATGCGA
1 AATGTATCGATACAATGAGA
*
1402800 AATGTATCGGTACAA
1 AATGTATCGATACAA
1402815 CATCTGGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:1402879 original size:13 final size:13
Alignment explanation
Indices: 1402832--1402861 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1402822 GTAAACCCAG
*
1402832 AATGTATCGATAT
1 AATGTATCGATAC
1402845 AATGTATCGATAC
1 AATGTATCGATAC
1402858 AATG
1 AATG
1402862 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1403675 original size:42 final size:42
Alignment explanation
Indices: 1403622--1403950 Score: 316
Period size: 42 Copynumber: 7.6 Consensus size: 42
1403612 GAAAACGAAA
1403622 TGCGTCCTGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAG
1 TGCGTCCTGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAG
* * * * * * *
1403664 TGCATCATGCTCTTTGAGGAAAAAAGAGAAAATAAGGGAATGAAG
1 TGCGTCCTGCTCTTTGAGGATAAAAGA-AAGAGAA--AAATAAAG
* * * *
1403709 TGTGTCTTGCTCTTTGAGGATAAAGGAAAGAGGAAAATAAAG
1 TGCGTCCTGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAG
** *
1403751 TGTATCCTGCTCTTTGAGGATAAAAGAGAAAAGAAGAGAATAAAG
1 TGCGTCCTGCTCTTTGAGGATAAAAGA-AAGAGAA-A-AATAAAG
* * * *
1403796 TGCGTCCTACTCTTTGAGGATAAAGGAAAGAGGAAAATAAAA
1 TGCGTCCTGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAG
* * * * *
1403838 TGCATCCTGCTCTTTGAGGACAAAAGAGAAAAGAAGGGAATGAAG
1 TGCGTCCTGCTCTTTGAGGATAAAAGA-AAGAGAA--AAATAAAG
* * * *
1403883 TGTGTCATGTTCTTTGAAGATAAAAGAAAGAGAAAAATAAAG
1 TGCGTCCTGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAG
*
1403925 TGCGTCCTACTCTTTGAGGACTAAAA
1 TGCGTCCTGCTCTTTGAGGA-TAAAA
1403951 AGTGCCACCA
Statistics
Matches: 225, Mismatches: 52, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
42 104 0.46
43 21 0.09
44 16 0.07
45 84 0.37
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (42 bp):
TGCGTCCTGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAG
Found at i:1403776 original size:87 final size:87
Alignment explanation
Indices: 1403629--1403950 Score: 455
Period size: 87 Copynumber: 3.7 Consensus size: 87
1403619 AAATGCGTCC
* *
1403629 TGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAGTGCATCATGCTCTTTGAGGAAAAAAGAGAA
1 TGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAGTGCATCCTGCTCTTTGAGGATAAAAGAGAA
* *
1403694 AATAAGGGAATGAAGTGTGTCT
66 AAGAAGGGAATGAAGTGTGTCA
* * *
1403716 TGCTCTTTGAGGATAAAGGAAAGAGGAAAATAAAGTGTATCCTGCTCTTTGAGGATAAAAGAGAA
1 TGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAGTGCATCCTGCTCTTTGAGGATAAAAGAGAA
* * * *
1403781 AAGAAGAGAATAAAGTGCGTCC
66 AAGAAGGGAATGAAGTGTGTCA
* * * * *
1403803 TACTCTTTGAGGATAAAGGAAAGAGGAAAATAAAATGCATCCTGCTCTTTGAGGACAAAAGAGAA
1 TGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAGTGCATCCTGCTCTTTGAGGATAAAAGAGAA
1403868 AAGAAGGGAATGAAGTGTGTCA
66 AAGAAGGGAATGAAGTGTGTCA
* * * *
1403890 TGTTCTTTGAAGATAAAAGAAAGAGAAAAATAAAGTGCGTCCTACTCTTTGAGGACTAAAA
1 TGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAGTGCATCCTGCTCTTTGAGGA-TAAAA
1403951 AGTGCCACCA
Statistics
Matches: 207, Mismatches: 27, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
87 203 0.98
88 4 0.02
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.23
Consensus pattern (87 bp):
TGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAGTGCATCCTGCTCTTTGAGGATAAAAGAGAA
AAGAAGGGAATGAAGTGTGTCA
Found at i:1403835 original size:174 final size:175
Alignment explanation
Indices: 1403622--1403950 Score: 516
Period size: 174 Copynumber: 1.9 Consensus size: 175
1403612 GAAAACGAAA
* *
1403622 TGCGTCCTGCTCTTTGAGGATAAAAGAAAGAGAAAAATAAAGTGCATCATGCTCTTTGAGGAAAA
1 TGCGTCCTACTCTTTGAGGATAAAAGAAAGAGAAAAATAAAATGCATCATGCTCTTTGAGGAAAA
* * * * *
1403687 AAGAGAAAATAAGGGAATGAAGTGTGTCTTGCTCTTTGAGGATAAAGGAAAGAGGAAAATAAAGT
66 AAGAGAAAAGAAGGGAATGAAGTGTGTCATGCTCTTTGAAGATAAAAGAAAGAGAAAAATAAAGT
* *
1403752 GTATCCTGCTCTTTGAGGA-TAAAAGAGAAAAGAAGAGAATAAAG
131 GCATCCTACTCTTTGAGGACTAAAAGAGAAAAGAAGAGAATAAAG
* * * *
1403796 TGCGTCCTACTCTTTGAGGATAAAGGAAAGAGGAAAATAAAATGCATCCTGCTCTTTGAGGACAA
1 TGCGTCCTACTCTTTGAGGATAAAAGAAAGAGAAAAATAAAATGCATCATGCTCTTTGAGGAAAA
*
1403861 AAGAGAAAAGAAGGGAATGAAGTGTGTCATGTTCTTTGAAGATAAAAGAAAGAGAAAAATAAAGT
66 AAGAGAAAAGAAGGGAATGAAGTGTGTCATGCTCTTTGAAGATAAAAGAAAGAGAAAAATAAAGT
*
1403926 GCGTCCTACTCTTTGAGGACTAAAA
131 GCATCCTACTCTTTGAGGACTAAAA
1403951 AGTGCCACCA
Statistics
Matches: 139, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
174 134 0.96
175 5 0.04
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (175 bp):
TGCGTCCTACTCTTTGAGGATAAAAGAAAGAGAAAAATAAAATGCATCATGCTCTTTGAGGAAAA
AAGAGAAAAGAAGGGAATGAAGTGTGTCATGCTCTTTGAAGATAAAAGAAAGAGAAAAATAAAGT
GCATCCTACTCTTTGAGGACTAAAAGAGAAAAGAAGAGAATAAAG
Found at i:1404010 original size:61 final size:60
Alignment explanation
Indices: 1403929--1404403 Score: 556
Period size: 61 Copynumber: 7.9 Consensus size: 60
1403919 ATAAAGTGCG
* *
1403929 TCCTACTCTTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAGGCA
* * *
1403990 TTCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGAAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAGGCA
* * * *
1404051 TCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAGGCA
* * * *
1404112 TCCTGCTCTTTGAGGACTGAAAAATGTCACTAACTTGTGTGGTCTTTAAAAGGAGAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAGGCA
* * * * *
1404173 TCCTACTCTTTGAGGACTGGAAAATGCCACCAGCTTGTGTAGGCTTTGAAAGGCGAAA-GCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAGGCA
* * *
1404234 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAGCTTGTGTGGACTTT-----GAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCA
*
1404289 TCCTGCTCTTTGAGGACT-AGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGCA
* *
1404350 TCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACT-GAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGG
1404404 CATCCTACTC
Statistics
Matches: 364, Mismatches: 33, Indels: 33
0.85 0.08 0.08
Matches are distributed among these distances:
54 4 0.01
55 46 0.13
59 2 0.01
60 7 0.02
61 257 0.71
62 45 0.12
63 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGCA
Found at i:1404186 original size:183 final size:174
Alignment explanation
Indices: 1403929--1404403 Score: 630
Period size: 183 Copynumber: 2.6 Consensus size: 174
1403919 ATAAAGTGCG
* * *
1403929 TCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAGGCGTTCT
1 TCCTGCTCTTTGAGGACTAAAAA-TGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGCGTCCT
1403994 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAA-GAGAAAGCATCCTGCT
64 GCTCTTTGAGGACTAAAA-GTGCCACCAACTTGTGTGGGCTTTG-AAAGGAGAAAGCATCCTGCT
*
1404058 CTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAGCA
127 CTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGACTTTG-AA--AG---GCA
* * * *
1404112 TCCTGCTCTTTGAGGACTGAAAAATGTCACTAACTTGTGTGGTCTTTAAAAGGAGAAAGCATCCT
1 TCCTGCTCTTTGAGGACT-AAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGCGTCCT
* * * *
1404177 ACTCTTTGAGGACTGGAAAA-TGCCACCAGCTTGTGTAGGCTTTGAAAGGCGAAAGCATCCTGCT
64 GCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAGCATCCTGCT
* *
1404241 CTTTGAGGACTGGAAAATGCCACCAGCTTGTGTGGACTTTGAAAGGCA
127 CTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGACTTTGAAAGGCA
1404289 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTA-AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GCGTCCT
* *
1404354 GCTTTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
64 GCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
1404404 CATCCTACTC
Statistics
Matches: 260, Mismatches: 24, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
176 4 0.02
177 75 0.29
178 26 0.10
180 2 0.01
182 12 0.05
183 132 0.51
184 5 0.02
185 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (174 bp):
TCCTGCTCTTTGAGGACTAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGCGTCCTGC
TCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAGCATCCTGCTCTTT
AAGGACTGGAAAATGCCACCAACTTGTGTGGACTTTGAAAGGCA
Found at i:1404277 original size:27 final size:27
Alignment explanation
Indices: 1404247--1404330 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
1404237 TGCTCTTTGA
*
1404247 GGACTGGAAAATGCCACCAGCTTGTGT
1 GGACTAGAAAATGCCACCAGCTTGTGT
* * * * *
1404274 GGACTTTG-AAA-GGCATCCTGCTCTTTGA
1 GGAC-TAGAAAATGCCA-CCAGCT-TGTGT
*
1404302 GGACTAGAAAATGCCACCAACTTGTGT
1 GGACTAGAAAATGCCACCAGCTTGTGT
1404329 GG
1 GG
1404331 GCTTTAAAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
26 3 0.07
27 19 0.46
28 16 0.39
29 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (27 bp):
GGACTAGAAAATGCCACCAGCTTGTGT
Found at i:1404306 original size:28 final size:28
Alignment explanation
Indices: 1404227--1404306 Score: 69
Period size: 27 Copynumber: 2.9 Consensus size: 28
1404217 TTTGAAAGGC
1404227 GAAA-GCATCCTGCTCTTTGAGGAC-TG
1 GAAAGGCATCCTGCTCTTTGAGGACTTG
* * * * *
1404253 GAAAATGCCA-CCAGCT-TGTGTGGACTTT
1 G-AAA-GGCATCCTGCTCTTTGAGGACTTG
1404281 GAAAGGCATCCTGCTCTTTGAGGACT
1 GAAAGGCATCCTGCTCTTTGAGGACT
1404307 AGAAAATGCC
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
26 4 0.10
27 18 0.46
28 15 0.38
29 2 0.05
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (28 bp):
GAAAGGCATCCTGCTCTTTGAGGACTTG
Found at i:1404312 original size:55 final size:55
Alignment explanation
Indices: 1404227--1404421 Score: 248
Period size: 55 Copynumber: 3.4 Consensus size: 55
1404217 TTTGAAAGGC
* * *
1404227 GAAA-GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAGCTTGTGTGGACTTT
1 GAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
1404281 GAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
1 GAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* *
1404336 AAAAGGAAAAGGCGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 -----G-AAAGGCATCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT
* * *
1404398 AAAAGGCATCCTACTCTTTAAGGA
1 GAAAGGCATCCTGCTCTTTGAGGA
1404422 TTAAAGGCCG
Statistics
Matches: 123, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
54 4 0.03
55 47 0.38
56 19 0.15
60 1 0.01
61 29 0.24
62 23 0.19
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (55 bp):
GAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:1404499 original size:94 final size:95
Alignment explanation
Indices: 1404347--1404520 Score: 278
Period size: 94 Copynumber: 1.8 Consensus size: 95
1404337 AAAGGAAAAG
* *
1404347 GCGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTAC
1 GCGTCCTGCTCTTTGAAGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTAC
*
1404412 TCTTTAAGGATTAAAGGCCGAAAGGAGAGA
66 TCTTTAAGGACTAAAGGCCGAAAGGAGAGA
* * *
1404442 GCGTCCTGCTCTTTGAAGACTAG-GAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCTTGC
1 GCGTCCTGCTCTTTGAAGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTAC
*
1404506 TCTTTGAGGACTAAA
66 TCTTTAAGGACTAAA
1404521 AAATGCCACC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 51 0.71
95 21 0.29
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (95 bp):
GCGTCCTGCTCTTTGAAGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTAC
TCTTTAAGGACTAAAGGCCGAAAGGAGAGA
Found at i:1404532 original size:55 final size:55
Alignment explanation
Indices: 1404442--1404631 Score: 229
Period size: 55 Copynumber: 3.5 Consensus size: 55
1404432 AAAGGAGAGA
* * ** *
1404442 GCGTCCTGCTCTTTGAAGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCGTCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
* * * *
1404497 GCATCTTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGCGAGCTTTGAAAG
1 GCGTCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
** *
1404552 GCGT-TCTGCTCTTTGAGGACTAAAGGGTACCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCT-TGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
* * *
1404607 GTGTCCTACTCTTTGAGGACTAAAA
1 GCGTCTTGCTCTTTGAGGACTAAAA
1404632 GTGAAAGGAG
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
54 1 0.01
55 112 0.99
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (55 bp):
GCGTCTTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:1405729 original size:10 final size:9
Alignment explanation
Indices: 1405716--1405767 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
1405706 TTTTCTCTCT
1405716 TTTTTCTTTG
1 TTTTT-TTTG
1405726 TTTTGTTTT-
1 TTTT-TTTTG
*
1405735 TTTTTCTTG
1 TTTTTTTTG
*
1405744 TTTTTTGT-
1 TTTTTTTTG
1405752 TTTTTTTTG
1 TTTTTTTTG
1405761 TTTTTTT
1 TTTTTTT
1405768 GAAAAAGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 10 0.29
9 17 0.49
10 7 0.20
11 1 0.03
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.87
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1405740 original size:30 final size:30
Alignment explanation
Indices: 1405701--1405767 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1405691 AAGCAGGTTC
*
1405701 TTTTCTTTTCTCTCTTTTTT-CTTTGTTTTG
1 TTTTTTTTTCT-TCTTTTTTGCTTTGTTTTG
* * *
1405731 TTTTTTTTTCTTGTTTTTTGTTTTTTTTTG
1 TTTTTTTTTCTTCTTTTTTGCTTTGTTTTG
1405761 TTTTTTT
1 TTTTTTT
1405768 GAAAAAGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (30 bp):
TTTTTTTTTCTTCTTTTTTGCTTTGTTTTG
Found at i:1405765 original size:18 final size:18
Alignment explanation
Indices: 1405715--1405768 Score: 67
Period size: 17 Copynumber: 3.0 Consensus size: 18
1405705 CTTTTCTCTC
1405715 TTTTTTCTTTGTTTTGTTT-
1 TTTTTT-TTTGTTTT-TTTG
*
1405734 TTTTTTCTTG-TTTTTTG
1 TTTTTTTTTGTTTTTTTG
1405751 TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTGTTTTTTTG
1405769 AAAAAGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 10 0.32
19 6 0.19
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTTG
Found at i:1405767 original size:20 final size:20
Alignment explanation
Indices: 1405715--1405759 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1405705 CTTTTCTCTC
*
1405715 TTTTTTCTT-TGTTTTGTTT
1 TTTTTTCTTGTTTTTTGTTT
1405734 TTTTTTCTTGTTTTTTGTTT
1 TTTTTTCTTGTTTTTTGTTT
1405754 TTTTTT
1 TTTTTT
1405760 GTTTTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (20 bp):
TTTTTTCTTGTTTTTTGTTT
Found at i:1409201 original size:51 final size:48
Alignment explanation
Indices: 1409121--1409215 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 48
1409111 GTATCCCCTC
*
1409121 GAAAATAAAAAGGTTGGAGTATCCCTGATTAT-AGAAAATTGGTATTTT
1 GAAAATAAAAAGGTTGGAGTATCCATGATTATGA-AAAATTGGTATTTT
* *
1409169 GAAAATAAAATCAGAGTTTGAGTATCCATGATTGTGAAAAATTGGTA
1 GAAAATAAAA--AG-GTTGGAGTATCCATGATTATGAAAAATTGGTA
1409216 ATAAAGTCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
48 10 0.25
50 2 0.05
51 27 0.68
52 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (48 bp):
GAAAATAAAAAGGTTGGAGTATCCATGATTATGAAAAATTGGTATTTT
Found at i:1409318 original size:51 final size:51
Alignment explanation
Indices: 1409259--1409398 Score: 138
Period size: 51 Copynumber: 2.7 Consensus size: 51
1409249 AACGGGACTG
* * * * *
1409259 GAGTATCCCCAATTGTGAAAAATTGGTGTTTTGAAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGAGAAAAATTGATGTTTTGAAAATAAAACCAGAGTTA
* * ** * * *
1409310 GAGTATCCCTGATTGCGGTAAATCGATGCTTTT-AAAAAAAAACCAGAGTTG
1 GAGTATCCCCGATTGAGAAAAATTGATG-TTTTGAAAATAAAACCAGAGTTA
* *
1409361 GAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAAT
1 GAGTATCCCCGATTGAGAAAAATTGATGTTTTGAAAAT
1409399 GGAACCGGGA
Statistics
Matches: 68, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
50 4 0.06
51 60 0.88
52 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGAGAAAAATTGATGTTTTGAAAATAAAACCAGAGTTA
Found at i:1411762 original size:20 final size:20
Alignment explanation
Indices: 1411718--1411812 Score: 138
Period size: 20 Copynumber: 4.7 Consensus size: 20
1411708 AAAATGCCTG
*
1411718 AATGTATCGATACATTGTAAA
1 AATGTATCGATACAATGT-AA
1411739 AATGTATCGATACAATGTAA
1 AATGTATCGATACAATGTAA
1411759 AATGTATCGATACAATG-AGA
1 AATGTATCGATACAATGTA-A
* *
1411779 AATGTATCGATATAATGCAA
1 AATGTATCGATACAATGTAA
1411799 AATGTATCGATACA
1 AATGTATCGATACA
1411813 TCTGGGTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
19 1 0.01
20 50 0.72
21 18 0.26
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGTAA
Found at i:1412452 original size:23 final size:24
Alignment explanation
Indices: 1412406--1412465 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
1412396 ATTATATGAC
* *
1412406 ATAAACATGATATAAAAAAATAAT
1 ATAAATATAATATAAAAAAATAAT
*
1412430 -TAAAATATAATAT-AAAAATTAAT
1 AT-AAATATAATATAAAAAAATAAT
*
1412453 ATGAATATAATAT
1 ATAAATATAATAT
1412466 GAATAGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (24 bp):
ATAAATATAATATAAAAAAATAAT
Found at i:1412759 original size:20 final size:19
Alignment explanation
Indices: 1412736--1412795 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
1412726 AAAAATTTTA
1412736 AATATTAAATATATAATTAT
1 AATA-TAAATATATAATTAT
*
1412756 AATAGTAAATATGT-ATTA-
1 AATA-TAAATATATAATTAT
* *
1412774 AATAT-AATAAATATTTAT
1 AATATAAATATATAATTAT
1412792 AATA
1 AATA
1412796 ATATATATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 5 0.15
17 4 0.12
18 8 0.24
19 4 0.12
20 12 0.36
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATATAAATATATAATTAT
Found at i:1412786 original size:27 final size:27
Alignment explanation
Indices: 1412715--1412786 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 27
1412705 TCCGGTCAAT
**
1412715 TGTATTAAA-ATAA-AAATTTTAAATA
1 TGTATTAAATATAATAAATAGTAAATA
1412740 T-TA--AATATATAATTATAATAGTAAATA
1 TGTATTAA-ATATAA-TA-AATAGTAAATA
1412767 TGTATTAAATATAATAAATA
1 TGTATTAAATATAATAAATA
1412787 TTTATAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
22 2 0.05
23 1 0.03
24 6 0.16
25 1 0.03
26 1 0.03
27 14 0.38
28 4 0.11
29 6 0.16
30 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
TGTATTAAATATAATAAATAGTAAATA
Found at i:1412801 original size:23 final size:23
Alignment explanation
Indices: 1412747--1412802 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 23
1412737 ATATTAAATA
* *
1412747 TATAATTATA-ATAGTAAATATG
1 TATAATAATATATAATAAATATG
*
1412769 TAT--TAA-ATATAATAAATATT
1 TATAATAATATATAATAAATATG
1412789 TATAATAATATATA
1 TATAATAATATATA
1412803 TTTGATTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.04
20 15 0.56
22 6 0.22
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TATAATAATATATAATAAATATG
Found at i:1413854 original size:24 final size:24
Alignment explanation
Indices: 1413825--1413882 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1413815 ATCAATGTGT
* * *
1413825 AAATCAAGTTGAATCGTAAGGAGA
1 AAATCAAGGTAAACCGTAAGGAGA
*
1413849 AAATCAAGGTAAACCGTAGGGAGA
1 AAATCAAGGTAAACCGTAAGGAGA
1413873 AAATCAAGGT
1 AAATCAAGGT
1413883 GGATCAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.26, T:0.17
Consensus pattern (24 bp):
AAATCAAGGTAAACCGTAAGGAGA
Found at i:1416101 original size:18 final size:17
Alignment explanation
Indices: 1416071--1416105 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1416061 TATTTGGTGC
*
1416071 ATTGTATTGATTTATAT
1 ATTGTATTAATTTATAT
1416088 ATTGTCATTAATTTATAT
1 ATTGT-ATTAATTTATAT
1416106 TTTGATACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (17 bp):
ATTGTATTAATTTATAT
Found at i:1418034 original size:2 final size:2
Alignment explanation
Indices: 1418023--1418066 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1418013 TGTCTAGTAC
1418023 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1418064 TA T
1 TA T
1418067 TAATTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1421872 original size:13 final size:13
Alignment explanation
Indices: 1421850--1421882 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1421840 ATCGATACAA
1421850 AATATCAATGTATC
1 AATAT-AATGTATC
1421864 AATATAATGTATC
1 AATATAATGTATC
1421877 AATATA
1 AATATA
1421883 TTTGAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (13 bp):
AATATAATGTATC
Found at i:1424662 original size:23 final size:23
Alignment explanation
Indices: 1424636--1424684 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1424626 TCATCTTAGG
1424636 TAAAATGCTAAATACCATAATGA
1 TAAAATGCTAAATACCATAATGA
1424659 TAAAATGCTAAATACCATAATGA
1 TAAAATGCTAAATACCATAATGA
1424682 TAA
1 TAA
1424685 GAGAAGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (23 bp):
TAAAATGCTAAATACCATAATGA
Found at i:1425143 original size:27 final size:27
Alignment explanation
Indices: 1425113--1425165 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1425103 TATATCTTCA
*
1425113 AAGAGTTA-TGTCTCTTTATGATTTATT
1 AAGAG-TAGTGTCTCTTGATGATTTATT
*
1425140 AAGAGTAGTGTCTCTTGATTATTTAT
1 AAGAGTAGTGTCTCTTGATGATTTAT
1425166 CAAGTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.26, C:0.08, G:0.17, T:0.49
Consensus pattern (27 bp):
AAGAGTAGTGTCTCTTGATGATTTATT
Found at i:1426023 original size:2 final size:2
Alignment explanation
Indices: 1426016--1426100 Score: 77
Period size: 2 Copynumber: 43.0 Consensus size: 2
1426006 AAAATAATTT
* * *
1426016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA CA -A CCA CCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA
* **
1426058 CA CC T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1426099 TA
1 TA
1426101 AATTACAACC
Statistics
Matches: 76, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
1 3 0.04
2 69 0.91
3 4 0.05
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1426628 original size:3 final size:3
Alignment explanation
Indices: 1426620--1426668 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1426610 AATTATTGCT
1426620 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1426668 T
1 T
1426669 ACAATATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1428989 original size:26 final size:28
Alignment explanation
Indices: 1428934--1428997 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
1428924 AAAATGATTA
1428934 AATAATTAGAAAAAATAAATACATACAT
1 AATAATTAGAAAAAATAAATACATACAT
1428962 AATAATTAGAAAGTAAATAAACTA-ATA-A-
1 AATAATTAGAAA--AAATAAA-TACATACAT
1428990 AATAATTA
1 AATAATTA
1428998 TATTTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
28 20 0.61
29 1 0.03
30 10 0.30
31 2 0.06
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (28 bp):
AATAATTAGAAAAAATAAATACATACAT
Found at i:1431393 original size:20 final size:20
Alignment explanation
Indices: 1431370--1431493 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
1431360 AAGTACCCAG
1431370 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* *
1431390 ATGTATCGATACA-TTATGA
1 ATGTATCGATACATTTTTCA
* * *
1431409 ATATATCGATAAATTCTTCA
1 ATGTATCGATACATTTTTCA
1431429 ATGTATCGATACATTCTGTCTTTTTACCTA
1 ATGTATCGATACA-------TTTTT--C-A
1431459 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1431480 ATGTATCGATACAT
1 ATGTATCGATACAT
1431494 CTAGTTAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
19 15 0.18
20 41 0.50
21 1 0.01
22 1 0.01
24 5 0.06
27 4 0.05
29 1 0.01
30 1 0.01
31 13 0.16
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1435042 original size:41 final size:41
Alignment explanation
Indices: 1434926--1435092 Score: 142
Period size: 41 Copynumber: 4.1 Consensus size: 41
1434916 TTCTTACACT
* ** * * *
1434926 AAACGCCACTAAAGTTTTCCTATTAGCT-GCGTTTTTAATAT
1 AAACGCCACTAAATTTTTCAAATTAG-TGGCGTTTATAGTAA
** * ** *
1434967 AAACATCACTAATTTTTTTCAAA-TAGCAGTGTTTAGT-GTAA
1 AAACGCCACTAA-ATTTTTCAAATTAGTGGCGTTTA-TAGTAA
* *
1435008 AAACGCCACTAAATTTTTCATATTAGTGGCGTTTATATTAA
1 AAACGCCACTAAATTTTTCAAATTAGTGGCGTTTATAGTAA
* *
1435049 AAACGCCACTAAATTTTTTAAATTAGTGGCGTTTATATTAA
1 AAACGCCACTAAATTTTTCAAATTAGTGGCGTTTATAGTAA
1435090 AAA
1 AAA
1435093 TGTCGCTAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
40 9 0.09
41 84 0.84
42 7 0.07
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (41 bp):
AAACGCCACTAAATTTTTCAAATTAGTGGCGTTTATAGTAA
Done.