Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 5 of 163
Found at i:1322985 original size:9 final size:9
Alignment explanation
Indices: 1322971--1323010 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1322961 AAACCCTAAG
1322971 CCCTAAAAA
1 CCCTAAAAA
*
1322980 CCCT--AAG
1 CCCTAAAAA
1322987 CCCTAAAAA
1 CCCTAAAAA
1322996 CCCT-AAAA
1 CCCTAAAAA
1323004 CCCTAAA
1 CCCTAAA
1323011 CCCTAGACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
7 6 0.23
8 8 0.31
9 12 0.46
ACGTcount: A:0.47, C:0.38, G:0.03, T:0.12
Consensus pattern (9 bp):
CCCTAAAAA
Found at i:1324053 original size:17 final size:17
Alignment explanation
Indices: 1324031--1324065 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1324021 GCAAAAAACA
1324031 GTACATGTGATGGTATT
1 GTACATGTGATGGTATT
1324048 GTACATGTGATGGTATT
1 GTACATGTGATGGTATT
1324065 G
1 G
1324066 CAGCCAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.31, T:0.40
Consensus pattern (17 bp):
GTACATGTGATGGTATT
Found at i:1324747 original size:14 final size:14
Alignment explanation
Indices: 1324728--1324761 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1324718 ATTTCATTTT
**
1324728 ATATTAATTGTATA
1 ATATTAATTAAATA
1324742 ATATTAATTAAATA
1 ATATTAATTAAATA
1324756 ATATTA
1 ATATTA
1324762 TAATTGGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATATTAATTAAATA
Found at i:1328507 original size:31 final size:31
Alignment explanation
Indices: 1328469--1328532 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1328459 CCCCTAGACA
1328469 CCAATCCGGGATATCCCTAGAATGGGATATC
1 CCAATCCGGGATATCCCTAGAATGGGATATC
*
1328500 CCAATCCGGGATATCCCTGGAATGGGATATC
1 CCAATCCGGGATATCCCTAGAATGGGATATC
1328531 CC
1 CC
1328533 TGGTTGGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (31 bp):
CCAATCCGGGATATCCCTAGAATGGGATATC
Found at i:1328512 original size:15 final size:15
Alignment explanation
Indices: 1328469--1328516 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
1328459 CCCCTAGACA
1328469 CCAATCCGGGATATC
1 CCAATCCGGGATATC
1328484 CCTAGAAT--GGGATATC
1 CC---AATCCGGGATATC
1328500 CCAATCCGGGATATC
1 CCAATCCGGGATATC
1328515 CC
1 CC
1328517 TGGAATGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.11
15 12 0.43
16 10 0.36
18 3 0.11
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (15 bp):
CCAATCCGGGATATC
Found at i:1328535 original size:16 final size:16
Alignment explanation
Indices: 1328476--1328535 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
1328466 ACACCAATCC
*
1328476 GGGATATCCCTAGAAT
1 GGGATATCCCTGGAAT
1328492 GGGATATCCC---AAT
1 GGGATATCCCTGGAAT
1328505 CCGGGATATCCCTGGAAT
1 --GGGATATCCCTGGAAT
1328523 GGGATATCCCTGG
1 GGGATATCCCTGG
1328536 TTGGAATAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
13 3 0.08
15 10 0.26
16 23 0.59
18 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.23
Consensus pattern (16 bp):
GGGATATCCCTGGAAT
Found at i:1329099 original size:13 final size:14
Alignment explanation
Indices: 1329053--1329091 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
1329043 ATTGTAGGGG
*
1329053 ATTCAAGAATGGTA
1 ATTCAAAAATGGTA
1329067 ATTCAAAAATGGTA
1 ATTCAAAAATGGTA
1329081 ATTCAAAAATG
1 ATTCAAAAATG
1329092 TAAATCAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (14 bp):
ATTCAAAAATGGTA
Found at i:1332414 original size:24 final size:24
Alignment explanation
Indices: 1332387--1332438 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1332377 CTATGGAAAG
*
1332387 AAATAATAAAGAT-TATATGCTAAT
1 AAATAACAAAGATAT-TATGCTAAT
* *
1332411 AAATAACAAATATATTATGTTAAT
1 AAATAACAAAGATATTATGCTAAT
1332435 AAAT
1 AAAT
1332439 TCTAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATAACAAAGATATTATGCTAAT
Found at i:1340937 original size:100 final size:101
Alignment explanation
Indices: 1340810--1341010 Score: 395
Period size: 100 Copynumber: 2.0 Consensus size: 101
1340800 TTAGGATAGA
1340810 ATTCGTAAACTTTGAAAGATAACTTTGTTATATTCTAATATATTTATATAAATTTGATACAAATT
1 ATTCGTAAACTTTGAAAGATAACTTTGTTATATTCTAATATATTTATATAAATTTGATACAAATT
1340875 CTTAATATTATGAGTAATTATTCTTAAATATTTACT
66 CTTAATATTATGAGTAATTATTCTTAAATATTTACT
1340911 ATTCGTAAAC-TTGAAAGATAACTTTGTTATATTCTAATATATTTATATAAATTTGATACAAATT
1 ATTCGTAAACTTTGAAAGATAACTTTGTTATATTCTAATATATTTATATAAATTTGATACAAATT
1340975 CTTAATATTATGAGTAATTATTCTTAAATATTTACT
66 CTTAATATTATGAGTAATTATTCTTAAATATTTACT
1341011 TTTAAAATTG
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 90 0.90
101 10 0.10
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (101 bp):
ATTCGTAAACTTTGAAAGATAACTTTGTTATATTCTAATATATTTATATAAATTTGATACAAATT
CTTAATATTATGAGTAATTATTCTTAAATATTTACT
Found at i:1345814 original size:23 final size:23
Alignment explanation
Indices: 1345771--1345813 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1345761 TTAATTATAC
*
1345771 CTTTTAATTATTTTTTTAAAATT
1 CTTTTAATTATTTTTTAAAAATT
1345794 CTTTTAATT-TTTTTTAAAAA
1 CTTTTAATTATTTTTTAAAAA
1345814 AATCTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (23 bp):
CTTTTAATTATTTTTTAAAAATT
Found at i:1364403 original size:20 final size:20
Alignment explanation
Indices: 1364378--1364419 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1364368 CTAACTCAGA
1364378 ATTGAGTATGTAAAGCATAT
1 ATTGAGTATGTAAAGCATAT
1364398 ATTGAGTATGTAAAGCATAT
1 ATTGAGTATGTAAAGCATAT
1364418 AT
1 AT
1364420 AAAGAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (20 bp):
ATTGAGTATGTAAAGCATAT
Found at i:1382898 original size:26 final size:27
Alignment explanation
Indices: 1382842--1382906 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
1382832 AGCACACATC
* * *
1382842 TAAGAGTTGAAAAAATAAACATAAATT
1 TAAGAGTTGAAAAAACAAAAATAAATG
1382869 TAAGAGTTGAAAAAGACAAAAAT-AA-G
1 TAAGAGTTGAAAAA-ACAAAAATAAATG
1382895 TAAGAGTT-AAAA
1 TAAGAGTTGAAAA
1382907 TAAGCGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.12
26 8 0.24
27 16 0.47
28 6 0.18
ACGTcount: A:0.60, C:0.03, G:0.15, T:0.22
Consensus pattern (27 bp):
TAAGAGTTGAAAAAACAAAAATAAATG
Found at i:1383387 original size:38 final size:40
Alignment explanation
Indices: 1383314--1383390 Score: 104
Period size: 38 Copynumber: 1.9 Consensus size: 40
1383304 TTGAAATTTA
*
1383314 AAATTTTAAAATAAATAAATGAGATACAATTAAAATACTAT
1 AAATTTTAAAATAAATAAA-GAGATACAATAAAAATACTAT
* *
1383355 AAATTTTAAAA-AATTAAA-AGTTACAATAAAAATACT
1 AAATTTTAAAATAAATAAAGAGATACAATAAAAATACT
1383391 TTTAAACCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 16 0.48
40 6 0.18
41 11 0.33
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (40 bp):
AAATTTTAAAATAAATAAAGAGATACAATAAAAATACTAT
Found at i:1385393 original size:24 final size:22
Alignment explanation
Indices: 1385349--1385394 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1385339 TGGATAAAAA
*
1385349 TTAATTTTAAATATATTTAATG
1 TTAAATTTAAATATATTTAATG
1385371 TTAAATTTAAATTAATATTTAATG
1 TTAAATTTAAA-T-ATATTTAATG
1385395 CAAAAAGTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAAATTTAAATATATTTAATG
Found at i:1387999 original size:19 final size:20
Alignment explanation
Indices: 1387970--1388007 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1387960 ACCAAAAATT
1387970 TATTTTAAAAATAAAAAAAG
1 TATTTTAAAAATAAAAAAAG
1387990 TATTTT-AAAATAAAAAAA
1 TATTTTAAAAATAAAAAAA
1388008 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAAAG
Found at i:1390425 original size:154 final size:154
Alignment explanation
Indices: 1390198--1390490 Score: 397
Period size: 154 Copynumber: 1.9 Consensus size: 154
1390188 GAATTAAAGC
* * * * *
1390198 TATTAAATTTAAGTAACCAATTTATAAGTTTATAATGTTTTAAACTCGTATTAGAATACATTCTT
1 TATTAAATTCAAGTAACCAATTTATAAGTTTATAACGTTTCAAACTCATAGTAGAATACATTCTT
* * * * * *
1390263 TCACATGATTAATTATAAAGTTTATAAATCTAATAAGCTCAATTAATCAATATGAGCTACCAAAT
66 TAACATGATAAATTATAAAGTTAATAAATCTAACAAACTCAATTAATCAATACGAGCTACCAAAT
*
1390328 TAAATTAATCAATTAATCACGAGT
131 GAAATTAATCAATTAATCACGAGT
* * * * *
1390352 TATTAAATTCAAGTGATCAATTTTTAAGTTTATAACGTTTCAAACTCATAGTAGAATATATTTTT
1 TATTAAATTCAAGTAACCAATTTATAAGTTTATAACGTTTCAAACTCATAGTAGAATACATTCTT
* * * *
1390417 TAATATGATAAATTATAAAGTTAATAAATTTAACAAACTCAATTAATCAATACGAGTTATCAAAT
66 TAACATGATAAATTATAAAGTTAATAAATCTAACAAACTCAATTAATCAATACGAGCTACCAAAT
1390482 GAAATTAAT
131 GAAATTAAT
1390491 TTATAATGAA
Statistics
Matches: 118, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
154 118 1.00
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (154 bp):
TATTAAATTCAAGTAACCAATTTATAAGTTTATAACGTTTCAAACTCATAGTAGAATACATTCTT
TAACATGATAAATTATAAAGTTAATAAATCTAACAAACTCAATTAATCAATACGAGCTACCAAAT
GAAATTAATCAATTAATCACGAGT
Found at i:1400344 original size:18 final size:18
Alignment explanation
Indices: 1400321--1400355 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1400311 CTTGGAGCGA
1400321 CGGGAGAAGGAAAGAGAG
1 CGGGAGAAGGAAAGAGAG
*
1400339 CGGGAGAAGGAGAGAGA
1 CGGGAGAAGGAAAGAGA
1400356 ACGAGAGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.51, T:0.00
Consensus pattern (18 bp):
CGGGAGAAGGAAAGAGAG
Found at i:1402541 original size:15 final size:15
Alignment explanation
Indices: 1402521--1402549 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1402511 CAGTTTCCTT
1402521 TTATTATCTACACTG
1 TTATTATCTACACTG
1402536 TTATTATCTACACT
1 TTATTATCTACACT
1402550 ATAAGGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.48
Consensus pattern (15 bp):
TTATTATCTACACTG
Found at i:1406150 original size:45 final size:45
Alignment explanation
Indices: 1406094--1406181 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
1406084 ATGATTGTGA
*
1406094 CCAAGGAAGAAACTACCACAGATCAAGTTGAGGAGCCAAAGATGG
1 CCAAGGAAGAAACTAACACAGATCAAGTTGAGGAGCCAAAGATGG
* *** *
1406139 CCAATGAAGAAACTAACGTTGATCATGTTGAGGAGCCAAAGAT
1 CCAAGGAAGAAACTAACACAGATCAAGTTGAGGAGCCAAAGAT
1406182 AAAAGATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (45 bp):
CCAAGGAAGAAACTAACACAGATCAAGTTGAGGAGCCAAAGATGG
Found at i:1409731 original size:2 final size:2
Alignment explanation
Indices: 1409726--1409752 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1409716 TATTAATTTG
1409726 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1409753 GGGCTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1410995 original size:3 final size:3
Alignment explanation
Indices: 1410987--1411016 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1410977 TAAATACCAA
1410987 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1411017 CCTTGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:1433608 original size:9 final size:9
Alignment explanation
Indices: 1433591--1433636 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
1433581 TGAGTTTTCG
1433591 AATTCGAAT
1 AATTCGAAT
*
1433600 AACTCGAAT
1 AATTCGAAT
1433609 AATTCGAAT
1 AATTCGAAT
1433618 AATTCGAAT
1 AATTCGAAT
1433627 AATTCGAAT
1 AATTCGAAT
1433636 A
1 A
1433637 TGANNNNNNN
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1436889 original size:18 final size:16
Alignment explanation
Indices: 1436847--1436895 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
1436837 AATTTTTTTA
1436847 AAAATAATAAAAATTT
1 AAAATAATAAAAATTT
*
1436863 ATAAA-AATATAAACTATT
1 A-AAATAATA-AAAAT-TT
1436881 AAAATAATAAAAATT
1 AAAATAATAAAAATT
1436896 ATATTTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATAATAAAAATTT
Found at i:1440783 original size:171 final size:172
Alignment explanation
Indices: 1440483--1440793 Score: 491
Period size: 171 Copynumber: 1.8 Consensus size: 172
1440473 GACACGAGAA
* * * * *
1440483 TGTATCGAATCATATATCCAACAGCATAAGCTTTGAGGTCATCCAAGCTCGGTTTTTAACATGAC
1 TGTATCAAACCATATATCCAACAACATAAGCTTTGAGGTCATCCAAGCTCGGTTTCTAACACGAC
* * * *
1440548 AATGAATTAGACATGGGTATGTTCGAGTAACTTAAGCAACTAATCACACTCGAGATATGTTCAAC
66 AATGAATTAGACACGGGTATGTTCGAGTAACATAAGCAACGAATCACACTCGAGATACGTTCAAC
1440613 AACATAAGCATGGACCTGAAAAGTTTTTATGTCGAGTGTATG
131 AACATAAGCATGGACCTGAAAAGTTTTTATGTCGAGTGTATG
* * *
1440655 TGTATCAAACCATATATCCAACAACATAAGCTTTTAGGTCATCCATGCTC-GTTTCTAACGCGAC
1 TGTATCAAACCATATATCCAACAACATAAGCTTTGAGGTCATCCAAGCTCGGTTTCTAACACGAC
1440719 AATGAATTAGACACGGGTATGTT-GAAGTAACATAAGCAACGAATCACACTCGAGATACGTTCAA
66 AATGAATTAGACACGGGTATGTTCG-AGTAACATAAGCAACGAATCACACTCGAGATACGTTCAA
1440783 CAACATAAGCA
130 CAACATAAGCA
1440794 ACCATCCATG
Statistics
Matches: 126, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
170 1 0.01
171 80 0.63
172 45 0.36
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (172 bp):
TGTATCAAACCATATATCCAACAACATAAGCTTTGAGGTCATCCAAGCTCGGTTTCTAACACGAC
AATGAATTAGACACGGGTATGTTCGAGTAACATAAGCAACGAATCACACTCGAGATACGTTCAAC
AACATAAGCATGGACCTGAAAAGTTTTTATGTCGAGTGTATG
Found at i:1451197 original size:46 final size:46
Alignment explanation
Indices: 1451130--1451268 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
1451120 TCATTGCTAT
* * *
1451130 AACTCAGTATGGCTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * *
1451176 AACTCAGTATGGTTTTCTTCACTGAAACACCATACATACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1451222 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1451268 A
1 A
1451269 CTTTGCCATG
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:1453525 original size:111 final size:113
Alignment explanation
Indices: 1453317--1453534 Score: 262
Period size: 111 Copynumber: 1.9 Consensus size: 113
1453307 GCTTTAACCC
* * * * *
1453317 TATATCAAATAAAAAAAAACTAAAAATTGACAAAATACTTTGAGGACTGATTTAGATAACGTTGA
1 TATATAAAATAAAAAAAAACTAAAAATTGACAAAATACTTTGAGGACTAAATTAGAAAACGTTAA
* * *
1453382 GATTGAACCATAGTTCAGGGATGTGTGGTGCAAATAATAAAACTATAA
66 GATTGAACCATAGTTCAGGGACGTATGATGCAAATAATAAAACTATAA
* *
1453430 TATATAAAAT-AAAAAAAACT-AAAATTGACACAATACTTTGAGGACTAAATTA-AAAGATGTTA
1 TATATAAAATAAAAAAAAACTAAAAATTGACAAAATACTTTGAGGACTAAATTAGAAA-ACGTTA
* ** * * *
1453492 AGTTTGAGTCATAGTTGAGGGGCGTATGATGCAATTAATAAAA
65 AGATTGAACCATAGTTCAGGGACGTATGATGCAAATAATAAAA
1453535 ATATCGGTTT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
110 2 0.02
111 67 0.76
112 10 0.11
113 9 0.10
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (113 bp):
TATATAAAATAAAAAAAAACTAAAAATTGACAAAATACTTTGAGGACTAAATTAGAAAACGTTAA
GATTGAACCATAGTTCAGGGACGTATGATGCAAATAATAAAACTATAA
Found at i:1456156 original size:2 final size:2
Alignment explanation
Indices: 1456151--1456200 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1456141 ACTCTTTATA
1456151 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1456193 TG TG TG TG
1 TG TG TG TG
1456201 ATATTATATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1457228 original size:27 final size:29
Alignment explanation
Indices: 1457197--1457255 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
1457187 TAGAGTTTCA
*
1457197 CGTATAT-AATTGCAC-TAAATTAAAATT
1 CGTATATAAATTGCACATAAATCAAAATT
1457224 CGTATATACAATTGCACATTAAATCAAAATT
1 CGTATATA-AATTGCACA-TAAATCAAAATT
1457255 C
1 C
1457256 ATGTGTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
29 8 0.30
31 12 0.44
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (29 bp):
CGTATATAAATTGCACATAAATCAAAATT
Found at i:1464948 original size:28 final size:31
Alignment explanation
Indices: 1464881--1464949 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1464871 GCCACAAAAT
* *
1464881 ATTATTTAATAAAAAAGTACTAACGATTTTA
1 ATTATTAAATAAAAAAGTACAAACGATTTTA
1464912 ATTATTAAATAAAAAA-TACAAAC-A-TTTA
1 ATTATTAAATAAAAAAGTACAAACGATTTTA
*
1464940 ATTTTTAAAT
1 ATTATTAAAT
1464950 TTTAAGTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 13 0.37
29 1 0.03
30 6 0.17
31 15 0.43
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (31 bp):
ATTATTAAATAAAAAAGTACAAACGATTTTA
Found at i:1478569 original size:21 final size:21
Alignment explanation
Indices: 1478545--1478588 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1478535 GAAGTCTGAC
1478545 GTTCAAAGTTTAGGGTTTAGG
1 GTTCAAAGTTTAGGGTTTAGG
* *
1478566 GTTCTAAGTTTGGGGTTTAGG
1 GTTCAAAGTTTAGGGTTTAGG
1478587 GT
1 GT
1478589 AAAAGTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.05, G:0.36, T:0.41
Consensus pattern (21 bp):
GTTCAAAGTTTAGGGTTTAGG
Found at i:1481931 original size:17 final size:18
Alignment explanation
Indices: 1481909--1481948 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1481899 TTAATTATTC
*
1481909 TTTATTTATTTGAAAAT-
1 TTTATTTATTTAAAAATA
*
1481926 TTTATTTTTTTAAAAATA
1 TTTATTTATTTAAAAATA
1481944 TTTAT
1 TTTAT
1481949 GAAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATTTATTTAAAAATA
Found at i:1484358 original size:101 final size:101
Alignment explanation
Indices: 1484136--1484359 Score: 288
Period size: 101 Copynumber: 2.2 Consensus size: 101
1484126 AATTGACGGA
* * * * *
1484136 TAAGACCATGGTTGGACCATGACAATGTTTATATGTAAGACCATAGCTGGGCTATGGAATTTTAG
1 TAAGACCATGGCTGGACCATGACAATATTTATAAGTAAGACCACAGCTGGGCTATGGAATTTGAG
**
1484201 TGAAAAGACCATAACTGAGTTATGACACTTTGAACG
66 TGAAAAGACCATAACTGAGTTATGACACTACGAACG
* * * *
1484237 TAAGACCATGGCTGAACCATGACAGTATTTATAAGTAAGACCACAGCTGGGCTGTGGCATTCTGA
1 TAAGACCATGGCTGGACCATGACAATATTTATAAGTAAGACCACAGCTGGGCTATGGAATT-TGA
* * *
1484302 -TGATAAGACCATAACTGGGTTATGACACTACGAATG
65 GTGAAAAGACCATAACTGAGTTATGACACTACGAACG
* *
1484338 TAAGATCATGGCTGGGCCATGA
1 TAAGACCATGGCTGGACCATGA
1484360 AAATGCATGT
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
101 103 0.98
102 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (101 bp):
TAAGACCATGGCTGGACCATGACAATATTTATAAGTAAGACCACAGCTGGGCTATGGAATTTGAG
TGAAAAGACCATAACTGAGTTATGACACTACGAACG
Found at i:1497614 original size:16 final size:16
Alignment explanation
Indices: 1497583--1497616 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1497573 ACCCTTCTTT
* *
1497583 TACATATATGTCTATA
1 TACATATATATATATA
1497599 TACATATATATATATA
1 TACATATATATATATA
1497615 TA
1 TA
1497617 TATTTCCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (16 bp):
TACATATATATATATA
Found at i:1503353 original size:56 final size:56
Alignment explanation
Indices: 1503286--1503454 Score: 275
Period size: 56 Copynumber: 3.0 Consensus size: 56
1503276 TGGTAACTAC
*
1503286 TATTATCGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
1 TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
1503342 TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
1 TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
* * *
1503398 TATTATTATTATTTTTTCTTGGTTATATATGTTAAAGACACTATGTTAGAATGTTTG
1 TATTATTGTTA---TTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTG
1503455 CTTAAGAACT
Statistics
Matches: 106, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
56 65 0.61
59 41 0.39
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.49
Consensus pattern (56 bp):
TATTATTGTTATTTCATGGTTATATATGTTAAAGACGCTATGTTAGAATGTTTGAT
Found at i:1509184 original size:32 final size:27
Alignment explanation
Indices: 1509114--1509173 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
1509104 TTGATTGTTT
1509114 CTTGCTGTCCAAGCAAAGCTTTAGCAG
1 CTTGCTGTCCAAGCAAAGCTTTAGCAG
1509141 CTTGCTGTCCAAGCAAAGCTTTAGCAG
1 CTTGCTGTCCAAGCAAAGCTTTAGCAG
1509168 CTTGCT
1 CTTGCT
1509174 ACTGCCTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (27 bp):
CTTGCTGTCCAAGCAAAGCTTTAGCAG
Found at i:1514514 original size:109 final size:109
Alignment explanation
Indices: 1514323--1514540 Score: 409
Period size: 109 Copynumber: 2.0 Consensus size: 109
1514313 CTAGTATAGG
*
1514323 GGAAATGTCAAGGAGGACAGGTAGTGGCATTGGCCACCTTAAAATGAGAAAATTGCATTTTTTAC
1 GGAAATGTCAAGGAGGACAGGTAGTGGCATTAGCCACCTTAAAATGAGAAAATTGCATTTTTTAC
1514388 CCTCTAATACATGGTAAATTACACTTTGTCCCCTCAAATATGAT
66 CCTCTAATACATGGTAAATTACACTTTGTCCCCTCAAATATGAT
* *
1514432 GGAAATGTCAAGGAGGACAGGTAGTGGCCTTAGCCATCTTAAAATGAGAAAATTGCATTTTTTAC
1 GGAAATGTCAAGGAGGACAGGTAGTGGCATTAGCCACCTTAAAATGAGAAAATTGCATTTTTTAC
1514497 CCTCTAATACATGGTAAATTACACTTTGTCCCCTCAAATATGAT
66 CCTCTAATACATGGTAAATTACACTTTGTCCCCTCAAATATGAT
1514541 AAAATTTTGA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (109 bp):
GGAAATGTCAAGGAGGACAGGTAGTGGCATTAGCCACCTTAAAATGAGAAAATTGCATTTTTTAC
CCTCTAATACATGGTAAATTACACTTTGTCCCCTCAAATATGAT
Found at i:1516692 original size:15 final size:16
Alignment explanation
Indices: 1516672--1516702 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1516662 GAAATTTTAA
1516672 AACCCAAAGT-AACCC
1 AACCCAAAGTCAACCC
1516687 AACCCAAAGTCAACCC
1 AACCCAAAGTCAACCC
1516703 GAAATCAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.42, G:0.06, T:0.06
Consensus pattern (16 bp):
AACCCAAAGTCAACCC
Found at i:1520392 original size:31 final size:31
Alignment explanation
Indices: 1520357--1520423 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1520347 GAAAACCTTA
* * * *
1520357 AAGTTTAAGCCCCAATGTGAGAATAATTGTC
1 AAGTTCAAACCCCAATATGAGAACAATTGTC
*
1520388 AAGTTCAAACCTCAATATGAGAACAATTGTC
1 AAGTTCAAACCCCAATATGAGAACAATTGTC
1520419 AAGTT
1 AAGTT
1520424 GAAGGGTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (31 bp):
AAGTTCAAACCCCAATATGAGAACAATTGTC
Found at i:1524889 original size:15 final size:15
Alignment explanation
Indices: 1524869--1524900 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1524859 CTGCGACAAA
*
1524869 GACAACGACAACGAC
1 GACAACGACAAAGAC
1524884 GACAACGACAAAGAC
1 GACAACGACAAAGAC
1524899 GA
1 GA
1524901 GCTACTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.28, G:0.22, T:0.00
Consensus pattern (15 bp):
GACAACGACAAAGAC
Found at i:1532415 original size:4 final size:4
Alignment explanation
Indices: 1532406--1532430 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1532396 GAGGGCTAAA
1532406 TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT T
1532431 TTATTTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:1552916 original size:54 final size:54
Alignment explanation
Indices: 1552834--1552945 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
1552824 ATCCCTGCAC
1552834 GTCAACTATAGGTACACGTGGCACGCCACATGTAACTGTCTAGTTATTCCATCA
1 GTCAACTATAGGTACACGTGGCACGCCACATGTAACTGTCTAGTTATTCCATCA
1552888 GTCAACTATAGGTACACGTGGCACGCCACATGTAACTGTCTAGTTATTCCATCA
1 GTCAACTATAGGTACACGTGGCACGCCACATGTAACTGTCTAGTTATTCCATCA
1552942 GTCA
1 GTCA
1552946 GGATGAAGTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (54 bp):
GTCAACTATAGGTACACGTGGCACGCCACATGTAACTGTCTAGTTATTCCATCA
Found at i:1562378 original size:29 final size:29
Alignment explanation
Indices: 1562335--1562399 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1562325 TTGGCCTCAC
* * * *
1562335 TTGATTCTTTTTAATAGTATAGGGACTAAA
1 TTGA-TCTATTTAATAATAGAGAGACTAAA
*
1562365 TTGATCTATTTAATAATAGAGAGACTAAT
1 TTGATCTATTTAATAATAGAGAGACTAAA
1562394 TTGATC
1 TTGATC
1562400 AATTCCCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (29 bp):
TTGATCTATTTAATAATAGAGAGACTAAA
Found at i:1565927 original size:25 final size:28
Alignment explanation
Indices: 1565880--1565933 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
1565870 TTAAGATGCT
1565880 TATATATAAAATTTTACTAAATA-AAAA
1 TATATATAAAATTTTACTAAATATAAAA
* *
1565907 TATATAT-AAA-TTTATTGAATATAAAA
1 TATATATAAAATTTTACTAAATATAAAA
1565933 T
1 T
1565934 TGAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 8 0.33
27 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
TATATATAAAATTTTACTAAATATAAAA
Found at i:1566926 original size:108 final size:108
Alignment explanation
Indices: 1566737--1566938 Score: 307
Period size: 108 Copynumber: 1.9 Consensus size: 108
1566727 TGGATTAAGA
* * * *
1566737 TTTAAGAGAATATTTGGCTATTTGGTTAAACGAAAAAAATCGGAACCCAGCACATTAGGGCACGT
1 TTTAAAAGAATATTTGGCTATTTGATCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
1566802 TTCTTCGAATTTCCAAACGCAAAATATTATCTTAATTTGAAAT
66 TTCTTCGAATCTCCAAACGCAAAACATTATCTTAATTTGAAAT
* * *
1566845 TTTAAAAGGATATTTGGCTATTTGATCGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGAATATTTGGCTATTTGATCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
1566910 TT-TCTCGAATCTCCAAACGCAAAACATTA
66 TTCT-TCGAATCTCCAAACGCAAAACATTA
1566939 CCTTTATTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
107 1 0.01
108 83 0.99
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (108 bp):
TTTAAAAGAATATTTGGCTATTTGATCAAACGAAAAAAATCGAAACCCAGCACATTAGGGCACGT
TTCTTCGAATCTCCAAACGCAAAACATTATCTTAATTTGAAAT
Found at i:1567653 original size:15 final size:15
Alignment explanation
Indices: 1567627--1567662 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1567617 AATATAAAGA
1567627 ACATAT-AAATATGT
1 ACATATAAAATATGT
*
1567641 ATATATAAAATATGT
1 ACATATAAAATATGT
1567656 ACATATA
1 ACATATA
1567663 TACGTAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
ACATATAAAATATGT
Found at i:1567966 original size:3 final size:3
Alignment explanation
Indices: 1567946--1568002 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
1567936 AAAATAAAAC
*
1567946 TAA TAAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1567992 TAA TAA TAA TA
1 TAA TAA TAA TA
1568003 TCAAATTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1569143 original size:27 final size:28
Alignment explanation
Indices: 1569095--1569149 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1569085 GTTTTGGGCC
*
1569095 TGTTGGGTATTTGGGCTTGGTT-TAATT
1 TGTTGGGTACTTGGGCTTGGTTGTAATT
*
1569122 TGTTGGGT-CTTGGGTTTGGGTTGTAATT
1 TGTTGGGTACTTGGGCTT-GGTTGTAATT
1569150 GGGTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.09, C:0.04, G:0.36, T:0.51
Consensus pattern (28 bp):
TGTTGGGTACTTGGGCTTGGTTGTAATT
Found at i:1577546 original size:20 final size:20
Alignment explanation
Indices: 1577508--1577544 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1577498 ATTAGGGCTT
1577508 GAATTAGATAATTAGTTTCC
1 GAATTAGATAATTAGTTTCC
*
1577528 GAATTTGATAATT-GTTT
1 GAATTAGATAATTAGTTT
1577545 TCATATTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (20 bp):
GAATTAGATAATTAGTTTCC
Found at i:1587635 original size:276 final size:278
Alignment explanation
Indices: 1586985--1587923 Score: 925
Period size: 276 Copynumber: 3.4 Consensus size: 278
1586975 AAAATTTCTA
* * * * ** * * * *
1586985 TTTTTATATATGTAGATTAAAGTATTTACCTTTCGGTTTTTCATTCCGTTTGTCCTCTGAACTTG
1 TTTTTAGATGTGTAGATTAAGGTCTTTACCTTTCGGTTCATCATTACGTTTTTCCTCCGAACCTG
* ** * * * **
1587050 TTGTTGTATCTGAAATAAAAACAG----ATAAA-AAATAAATCATTTAATTATTTTATCTAGTGA
66 TAGCCGTACCTAAAATAAAAA-AGATAAATAAATAAATAAATCATTTAATTATTTTCTCCGGTGA
* * * *
1587110 TATTATATTAAACTGATTCGTTTAAAAAATATTTATTTTAATAATTTCATCTTCACCTAGTTAAA
130 TATCATATTAAACTGATTTGTTTAAAATATGTTTATTTTAATAATTTCATCTTCACCTAGTTAAA
*
1587175 CCATTTTTATTTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTC-AAATTATTAAT-A
195 CCATTTTTA-TTTTTGA-TT-ATATGCAAT-TGGTATGAGAATTTTAATTCAAAATT-TT-ATCA
** **
1587238 ATGTAAATTCGATTAAAATTTTTTAT
254 ATGT-AATTCGGCTAAAATAATTTAT
* * * *
1587264 TTTTTAGACT-TGTATG-TAAAAGTTTTTACCTTTCGGTTCATCATTACGTTTTTCCTTCGAACC
1 TTTTTAGA-TGTGTA-GATTAAGGTCTTTACCTTTCGGTTCATCATTACGTTTTTCCTCCGAACC
* * * *
1587327 TGAAGTCGTACCTAAAAT---AAA-A-ACAT--ATAAATAAATCATTTAATTGTTTTCTCCGGTG
64 TGTAGCCGTACCTAAAATAAAAAAGATAAATAAATAAATAAATCATTTAATTATTTTCTCCGGTG
* *
1587385 ATATCATATTAAACCGATTTGTTTAAAATATGTTTATTTTAATAATTTCATCTTCACCTACTTAA
129 ATATCATATTAAACTGATTTGTTTAAAATATGTTTATTTTAATAATTTCATCTTCACCTAGTTAA
*
1587450 ACCATTTTTATTTTT-A-T-TATGCAATGTGGTATGAGAATTTTAATTCAAAATTTTATCAGTGT
194 ACCATTTTTATTTTTGATTATATGCAAT-TGGTATGAGAATTTTAATTCAAAATTTTATCAATGT
*
1587512 -ATTCGGCTAAAATGATTTAT
258 AATTCGGCTAAAATAATTTAT
* * * *
1587532 TTTTTAGATGTGTAGATTAAGGTCTTTACCTTTCGATTCTTCTTTAAGTTTTTCCTCCGAACCTG
1 TTTTTAGATGTGTAGATTAAGGTCTTTACCTTTCGGTTCATCATTACGTTTTTCCTCCGAACCTG
* *
1587597 TTGCCATACCTAAAATAAAAATAGATAAATAAATAAATAAATCATTTAATTATTTTCT-CGAGTG
66 TAGCCGTACCTAAAATAAAAA-AGATAAATAAATAAATAAATCATTTAATTATTTTCTCCG-GTG
* * *
1587661 ATATCATATTAAACTGATTTGTTTAGAATATGCTCTTTTTCTTCTAATAATTTCATCTTCACCTG
129 ATATCATATTAAACTGATTTGTTTAAAATATG---TTTAT-TT-TAATAATTTCATCTTCACCTA
** *
1587726 GTTAAAGCTTTTTTTTTTTTTTTTGATTTTATATGCAATT-GTATGAGAATTTTAATTCAAAATT
189 GTTAAA-C---CATTTTTATTTTTGA--TTATATGCAATTGGTATGAGAATTTTAATTCAAAATT
* *
1587790 TTAACAATGTAAATTCAGCTAAAATAATTTA-
248 TTATCAATGT-AATTCGGCTAAAATAATTTAT
* * * * **
1587821 TTTTTAGACGTGTAGATTAAGGTCTTTACCTTTTGGTTCCTCATTACGTTTTTCTTCTAAACCTG
1 TTTTTAGATGTGTAGATTAAGGTCTTTACCTTTCGGTTCATCATTACGTTTTTCCTCCGAACCTG
* * *
1587886 TAGCCGTATCTAAAATAAAAACGAATAAGTAAATAAAT
66 TAGCCGTACCTAAAATAAAAAAG-ATAAATAAATAAAT
1587924 TAATAAATCA
Statistics
Matches: 552, Mismatches: 72, Indels: 62
0.80 0.10 0.09
Matches are distributed among these distances:
267 2 0.00
268 81 0.15
269 2 0.00
270 33 0.06
271 7 0.01
272 2 0.00
273 1 0.00
274 4 0.01
275 9 0.02
276 155 0.28
277 2 0.00
279 66 0.12
280 4 0.01
281 25 0.05
282 1 0.00
285 10 0.02
286 1 0.00
288 33 0.06
289 89 0.16
290 25 0.05
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (278 bp):
TTTTTAGATGTGTAGATTAAGGTCTTTACCTTTCGGTTCATCATTACGTTTTTCCTCCGAACCTG
TAGCCGTACCTAAAATAAAAAAGATAAATAAATAAATAAATCATTTAATTATTTTCTCCGGTGAT
ATCATATTAAACTGATTTGTTTAAAATATGTTTATTTTAATAATTTCATCTTCACCTAGTTAAAC
CATTTTTATTTTTGATTATATGCAATTGGTATGAGAATTTTAATTCAAAATTTTATCAATGTAAT
TCGGCTAAAATAATTTAT
Found at i:1588178 original size:304 final size:289
Alignment explanation
Indices: 1587789--1588383 Score: 750
Period size: 304 Copynumber: 2.0 Consensus size: 289
1587779 AATTCAAAAT
1587789 TTTAACAATGTAAATTCAGCTAAAATAATTTATTTTTAGACGTGTAGATTAAGGTCTTTACCTTT
1 TTTAACAATGTAAATTCAGCTAAAATAATTTATTTTTAGACGTGTAGATTAAGGTCTTTACCTTT
* * *
1587854 TGGTTCCTCATTACGTTTTTCTTCTAAACCTGTAGCCGTATCTAAAATAAAAACGAATAAGTAAA
66 CGGTTCCTCATTACGTTTTTCTTCTAAACCTGTAGCCGAACCTAAAATAAAAACG-----G---A
1587919 TAAATTAATAAATCATTCAATCATTTTCTCTAACAATGTAAATTTGGCTAAAATAATAT-TTTTT
123 T--A--AATAAATCATTCAATCATTTTCTCTAACAATGTAAATTTGGCTAAAATAATATATTTTT
* * ** ** *
1587983 TAGAGGTGTAGGTTAAGCA-TTTACCTTTTGGTTCTTCATTACGTTTTTCTTTTGTA-TCTGTAG
184 TAGACGTGTAGATTAA-CATTTTACCTTTCAGTTCTTCATTACGTTTTTCTTCCGAACT-TGTAG
1588046 TCGTACCTAAA-ATAAAAACGGATAAATAAATCATTCAATTATTTTC
247 TCGTACCTAAAGA-AAAAA---ATAAATAAATCATTCAATTATTTTC
* * *
1588092 TTTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGTTTAAGG-CATTTGCCT
1 TTTAACAATGTAAATTCAGCTAAAATAATTTA-TTTTTAGACGTGTAGATTAAGGTC-TTTACCT
* * * * *
1588156 TTCGGTTCTTCATTACGTTTTTCTTTTGAACTTGTAGTCGAACCTAAAATAAAAACGGATAAATA
64 TTCGGTTCCTCATTACGTTTTTCTTCTAAACCTGTAGCCGAACCTAAAATAAAAACGGATAAATA
* *
1588221 AATCATTCAATTATTTTCTCTAACAATGTAAATTTGGCTAAAATAATTTATTTTTTAGACGTGTA
129 AATCATTCAATCATTTTCTCTAACAATGTAAATTTGGCTAAAATAATATATTTTTTAGACGTGTA
*
1588286 GATTAATATTTTTACCTTTCAGTTCTTCATTACGTTTTTCTTCCGAACTTGTAGTCGTACCTAAA
194 GATTAACA-TTTTACCTTTCAGTTCTTCATTACGTTTTTCTTCCGAACTTGTAGTCGTACCTAAA
* * *
1588351 GAGATAAATAAATAAATCGTTCAATTATTTTC
258 GAAAAAAATAAATAAATCATTCAATTATTTTC
1588383 T
1 T
1588384 CTAGTGATAT
Statistics
Matches: 261, Mismatches: 24, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
291 25 0.10
292 52 0.20
293 19 0.07
294 52 0.20
295 2 0.01
296 2 0.01
299 1 0.00
303 32 0.12
304 76 0.29
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (289 bp):
TTTAACAATGTAAATTCAGCTAAAATAATTTATTTTTAGACGTGTAGATTAAGGTCTTTACCTTT
CGGTTCCTCATTACGTTTTTCTTCTAAACCTGTAGCCGAACCTAAAATAAAAACGGATAAATAAA
TCATTCAATCATTTTCTCTAACAATGTAAATTTGGCTAAAATAATATATTTTTTAGACGTGTAGA
TTAACATTTTACCTTTCAGTTCTTCATTACGTTTTTCTTCCGAACTTGTAGTCGTACCTAAAGAA
AAAAATAAATAAATCATTCAATTATTTTC
Found at i:1588192 original size:147 final size:146
Alignment explanation
Indices: 1587925--1588386 Score: 641
Period size: 147 Copynumber: 3.2 Consensus size: 146
1587915 TAAATAAATT
* * * *
1587925 AATAAATCATTCAATCATTTTCTCTAACAATGTAAATTTGGCTAAAATAATAT-TTTTTTAGAGG
1 AATAAATCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACG
* * *
1587989 TGTAGGTTAA-GCATTTACCTTTTGGTTCTTCATTACGTTTTTCTTTTGTA-TCTGTAGTCGTAC
66 TGTAGATTAAGGC-TTTACCTTTCGGTTCTTCATTACGTTTTTCTTTTGAACT-TGTAGTCGTAC
1588052 CTAAAATAAAAACGGATA
129 CTAAAATAAAAACGGATA
*
1588070 AATAAATCATTCAATTATTTTCTTTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACG
1 AATAAATCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACG
* * *
1588135 TGTAGTTTAAGGCATTTGCCTTTCGGTTCTTCATTACGTTTTTCTTTTGAACTTGTAGTCGAACC
66 TGTAGATTAAGGC-TTTACCTTTCGGTTCTTCATTACGTTTTTCTTTTGAACTTGTAGTCGTACC
1588200 TAAAATAAAAACGGATA
130 TAAAATAAAAACGGATA
*
1588217 AATAAATCATTCAATTATTTTCTCTAACAATGTAAATTTGGCTAAAATAATTTATTTTTTAGACG
1 AATAAATCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACG
*** * **
1588282 TGTAGATTAATATTTTTACCTTTCAGTTCTTCATTACGTTTTTCTTCCGAACTTGTAGTCGTACC
66 TGTAGATTAA-GGCTTTACCTTTCGGTTCTTCATTACGTTTTTCTTTTGAACTTGTAGTCGTACC
* *
1588347 TAAAGA-GATAA---ATA
130 TAAA-ATAAAAACGGATA
*
1588361 AATAAATCGTTCAATTATTTTCTCTA
1 AATAAATCATTCAATTATTTTCTCTA
1588387 GTGATATCAT
Statistics
Matches: 288, Mismatches: 24, Indels: 11
0.89 0.07 0.03
Matches are distributed among these distances:
144 28 0.10
145 49 0.17
146 19 0.07
147 190 0.66
148 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (146 bp):
AATAAATCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACG
TGTAGATTAAGGCTTTACCTTTCGGTTCTTCATTACGTTTTTCTTTTGAACTTGTAGTCGTACCT
AAAATAAAAACGGATA
Found at i:1588740 original size:574 final size:548
Alignment explanation
Indices: 1587951--1589221 Score: 1675
Period size: 574 Copynumber: 2.3 Consensus size: 548
1587941 ATTTTCTCTA
* * * * *
1587951 ACAATGTAAATTTGGCTAAAATAATAT-TTTTTTAGAGGTGTAGGTTAA-G-CATTTACCTTTTG
1 ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGATTAAGGTC-TTTACCTTTCG
* * * *
1588013 GTTCTTCATTACGTTTTTCTTTTGTATCTGTAGTCGTACCTAAAATAAAAACGGATAAAT---AA
65 GTTCTTCATTAGGTTTTTCTTTTGAACCTGTAGTCGTACCTAAAATAAAAACAGATAAATAAAAA
*
1588075 ATCATTCAATTATTTTCTTTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAG
130 ATCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAG
* * * * *
1588140 TTTAAGGCATTTGCCTTTCGGTTCTTCATTACGTTTTTCTTTTGAACTTGTAGTCGAACCTAAAA
195 GTTAAGGCATTTACCTTTCAGTTCTTCATTACGTTTTTCTTTTGAACCTGTAGTCGAACCAAAAA
*
1588205 TAAAAACGGATAAATAAATCATTCAATTATTTTCTCTAACAATGTAAATTTGGCTAAAATAATTT
260 TAAAAACGGATAAATAAATCATTCAATTATTTTCTCTAAC------AA-----C---------GT
* * *
1588270 ATTTTTTAGACGTGTAGATTAATATTTTTACCTTTCAGTTCTTCATTACGTTTTTCTTCCGAACT
305 A------A-A-GTGTAGATTAAGATTTTTACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACC
* *
1588335 TGTAGTCGTACCT-AAAGA-GATAAATAAATAAATCGTTCAATTATTTTCTCTAGTGATATCATA
362 TGTAGTCGTACCTAAAAAAGGATAAATAAATAAATCGTTCAATTATTTTCTCTAGTAATATCATA
* ** * *
1588398 TTAAATAATCAATTAAATATGTTGTTTTTAAATAATTTCAGCTTTACCTAGTTAAAACATTTTTA
427 TTAAACAATCAATTAAATATAATCTTTTTAAATAATTTCAGCTTCACCTAGTTAAAACATTTTTA
1588463 ATTTCA-TTTTTGATTTAATATGTAACATGATATGAGAATTTTAATTCAAATTTTTG
492 ATTTCATTTTTTGATTTAATATGTAACATGATATGAGAATTTTAATTCAAATTTTTG
* *
1588519 ACAATATAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTCTTTACCTTTCGG
1 ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGATTAAGGTCTTTACCTTTCGG
* *
1588584 TTCCTCATTAGGTTTTTCTTTTGAACCTGTAGTCGTATCTAAAATAAAAACAGATAAATAAACAA
66 TTCTTCATTAGGTTTTTCTTTTGAACCTGTAGTCGTACCTAAAATAAAAACAGATAAATAAA-AA
1588649 ATCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAG
130 ATCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAG
* * *
1588714 GTTAAGGTC-TTTACCTTTCAGTTCTTCATTACGTTTTTCTTTTGTACCTGTAGTCGTATCAAAA
195 GTTAAGG-CATTTACCTTTCAGTTCTTCATTACGTTTTTCTTTTGAACCTGTAGTCGAACCAAAA
* *
1588778 ATAAAAACGGGTAAATAAATCATTCAATTATTTTCTCTAACAACGTAAAGTGTAGATTAAGGTTT
259 ATAAAAACGGATAAATAAATCATTCAATTATTTTCTCTAACAACGTAAAGTGTAGATTAAGATTT
1588843 TTACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACCTGTAGTCGTACCTAAAAAATGGATAAA
324 TTACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACCTGTAGTCGTACCTAAAAAA-GGATAAA
* *
1588908 TAAATAAATCGTTCAATTATTTTCTCTAGTAATATCATATTAAACAATTAGTTAAATATAATCTT
388 TAAATAAATCGTTCAATTATTTTCTCTAGTAATATCATATTAAACAATCAATTAAATATAATCTT
* * *
1588973 TTTAAATAATTTCATCTTCACCTAGTTAAAACATTTTTAATTTTATTTTTTGATTTAATGTGTAA
453 TTTAAATAATTTCAGCTTCACCTAGTTAAAACATTTTTAATTTCATTTTTTGATTTAATATGTAA
*
1589038 TATGATATGAGAATTTTAATTCAAATTTTTG
518 CATGATATGAGAATTTTAATTCAAATTTTTG
* * *
1589069 ACAATGTTAATTCGGCTACAATAATTTATTTTTTATACGTGTAGATTAAGGTCTTTACCTTTCGG
1 ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGATTAAGGTCTTTACCTTTCGG
* * * *
1589134 TTCTTCATT-GAGTTTTTCCTTCGAACCTGTCA-TCGTACCTAAAAAATAATAATAGATAAATAA
66 TTCTTCATTAG-GTTTTTCTTTTGAACCTGT-AGTCGTACCT--AAAATAAAAACAGATAAATAA
* *
1589197 ATAAATTATTTAATTATTTTCTCTA
127 A-AAATCATTCAATTATTTTCTCTA
1589222 GTGATATCAT
Statistics
Matches: 632, Mismatches: 55, Indels: 48
0.86 0.07 0.07
Matches are distributed among these distances:
546 63 0.10
547 5 0.01
548 1 0.00
549 107 0.17
550 140 0.22
551 1 0.00
552 41 0.06
554 2 0.00
563 1 0.00
568 26 0.04
569 18 0.03
570 65 0.10
571 1 0.00
574 160 0.25
575 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (548 bp):
ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGATTAAGGTCTTTACCTTTCGG
TTCTTCATTAGGTTTTTCTTTTGAACCTGTAGTCGTACCTAAAATAAAAACAGATAAATAAAAAA
TCATTCAATTATTTTCTCTAACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGG
TTAAGGCATTTACCTTTCAGTTCTTCATTACGTTTTTCTTTTGAACCTGTAGTCGAACCAAAAAT
AAAAACGGATAAATAAATCATTCAATTATTTTCTCTAACAACGTAAAGTGTAGATTAAGATTTTT
ACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACCTGTAGTCGTACCTAAAAAAGGATAAATAA
ATAAATCGTTCAATTATTTTCTCTAGTAATATCATATTAAACAATCAATTAAATATAATCTTTTT
AAATAATTTCAGCTTCACCTAGTTAAAACATTTTTAATTTCATTTTTTGATTTAATATGTAACAT
GATATGAGAATTTTAATTCAAATTTTTG
Found at i:1588793 original size:151 final size:147
Alignment explanation
Indices: 1588519--1588826 Score: 481
Period size: 151 Copynumber: 2.1 Consensus size: 147
1588509 CAAATTTTTG
* *
1588519 ACAATATAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTCTTTACCTTTCGG
1 ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTCTTTACCTTTCAG
* *
1588584 TTCCTCATTAGGTTTTTCTTTTGAACCTGTAGTCGTATCTAAAATAAAAACAGATAAATAAACAA
66 TTCCTCATTACGTTTTTCTTTTGAACCTGTAGTCGTATCAAAAATAAAAACAGATAAAT----AA
1588649 ATCATTCAATTATTTTCTCTA
127 ATCATTCAATTATTTTCTCTA
* *
1588670 ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGGTTAAGGTCTTTACCTTTCAG
1 ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTCTTTACCTTTCAG
* * * *
1588735 TTCTTCATTACGTTTTTCTTTTGTACCTGTAGTCGTATCAAAAATAAAAACGGGTAAATAAATCA
66 TTCCTCATTACGTTTTTCTTTTGAACCTGTAGTCGTATCAAAAATAAAAACAGATAAATAAATCA
1588800 TTCAATTATTTTCTCTA
131 TTCAATTATTTTCTCTA
*
1588817 ACAACGTAAA
1 ACAATGTAAA
1588827 GTGTAGATTA
Statistics
Matches: 146, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
147 32 0.22
151 114 0.78
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (147 bp):
ACAATGTAAATTCGGCTAAAATAATTTATTTTTTAGACATGTAGATTAAGGTCTTTACCTTTCAG
TTCCTCATTACGTTTTTCTTTTGAACCTGTAGTCGTATCAAAAATAAAAACAGATAAATAAATCA
TTCAATTATTTTCTCTA
Found at i:1588923 original size:119 final size:116
Alignment explanation
Indices: 1588708--1588935 Score: 305
Period size: 119 Copynumber: 1.9 Consensus size: 116
1588698 TTTTTTAGAC
* * ** *
1588708 GTGTAGGTTAAGGTCTTTACCTTTCAGTTCTTCATTACGTTTTTCTTTTGTACCTGTAGTCGTAT
1 GTGTAGATTAAGGTCTTTACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACCTGTAGTCGTAT
*
1588773 CAAAAATAAAAACGGGTAAATAAATCATTCAATTATTTTCTCTAACAACGTAAA
66 AAAAAATAAAAA---GTAAATAAATCATTCAATTATTTTCTCTAACAACGTAAA
*
1588827 GTGTAGATTAAGGTTTTTACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACCTGTAGTCGTAC
1 GTGTAGATTAAGGTCTTTACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACCTGTAGTCGTA-
* *
1588892 CTAAAAAATGGATAAA-TAAATAAATCGTTCAATTATTTTCTCTA
65 -TAAAAAAT--AAAAAGTAAATAAATCATTCAATTATTTTCTCTA
1588936 GTAATATCAT
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
119 85 0.89
121 7 0.07
123 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (116 bp):
GTGTAGATTAAGGTCTTTACCTTTCAGTTCTTCATTACATTTTTCTTCCGAACCTGTAGTCGTAT
AAAAAATAAAAAGTAAATAAATCATTCAATTATTTTCTCTAACAACGTAAA
Found at i:1589578 original size:286 final size:281
Alignment explanation
Indices: 1588828--1589827 Score: 1122
Period size: 286 Copynumber: 3.6 Consensus size: 281
1588818 CAACGTAAAG
* * * * *
1588828 TGTAGATTAAGGTTTTTACCTTTCAGTTCTTCATTACATTTTT-CTTCCGAACCTGTAGTCGTAC
1 TGTAGGTTAAGGTCTTTACCTTTCGGTTCTTCATTACGTTTTTCCTT-CGAACCTGTTGTCGTAC
** * * *
1588892 CT---A-AAAAATGGATAAATAAATAAATCGTTCAATTATTTTCTCTAGTAATATCATATTAAAC
65 CTAAAATAAAAACAGATAAATAAATAAATCATTTAATTATTTTCTCCAGTAATATCATATTAAAC
* * * * * *
1588953 -AATTAG-TT-AAATATAATCTTTTTAAATAATTTCATCTTCACCTAGTTAAAACATTTTTAATT
130 TGATTTGTTTAAAATAT-GTTTTTTTTAATAATTTCATCTTCACCTAGTT-AAACAATTTT--TT
* * *
1589015 TTATTTTTTGATTTAATGTGTAATATGATATGAGAATTTTAATTC-AAATTTTTGACAATGTTAA
191 TT-TTTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAAATTTTTAACAATG-TAA
* * * *
1589079 TTCGGCTACAATAATTTATTTTTTATACG
254 CTCGACTAAAATAATTTATTTTTTAT-CA
* **
1589108 TGTAGATTAAGGTCTTTACCTTTCGGTTCTTCATTGA-GTTTTTCCTTCGAACCTGTCATCGTAC
1 TGTAGGTTAAGGTCTTTACCTTTCGGTTCTTCATT-ACGTTTTTCCTTCGAACCTGTTGTCGTAC
* * * * *
1589172 CTAAAAAATAATAATAGATAAATAAATAAATTATTTAATTATTTTCTCTAGTGATATCATATTAA
65 CT--AAAATAAAAACAGATAAATAAATAAATCATTTAATTATTTTCTCCAGTAATATCATATTAA
*
1589237 ACTGATTTGTTGAAAATATGTTTTTTTTAATAATTTCATCTTCACCTAGTTAAACAATTTTTGTT
128 ACTGATTTGTTTAAAATATGTTTTTTTTAATAATTTCATCTTCACCTAGTTAAACAATTTTT-TT
* *
1589302 TTTGTTTTCGTTTTAATATGCAATATGATAAGAGAATTTTAATTCAAAATTTTTAACAATGTAAA
192 TTT-TTTT-GATTTAATATGCAATATGATATGAGAATTTTAATTCAAAATTTTTAACAATGT--A
1589367 ACT-GACTAAAATAATTTATTTTTTAGTCA
253 ACTCGACTAAAATAATTTATTTTTTA-TCA
** * * * *
1589396 TGTAGGTTAAAATTTTTACCTTTCGGTTCATCATTACGTTTTTCCTTTGAACCTGTTGTCGCACC
1 TGTAGGTTAAGGTCTTTACCTTTCGGTTCTTCATTACGTTTTTCCTTCGAACCTGTTGTCGTACC
*
1589461 TAAAATAAAAACAGATAAATAAATAAATCATTTAATTATTTTCTCCACTAATATCATATTAAACT
66 TAAAATAAAAACAGATAAATAAATAAATCATTTAATTATTTTCTCCAGTAATATCATATTAAACT
* * * *
1589526 GATTTGTTTAAAACATGTTTTTTTTTATAATTTCATCTTCACCTGGTTAAACAA---TTTTTATT
131 GATTTGTTTAAAATATGTTTTTTTTAATAATTTCATCTTCACCTAGTTAAACAATTTTTTTTTTT
* *
1589588 TTTGATTTAGTATGCAATATGAGATGAGAATTTTAATTCAAAA-TTTTAACAATGTAACTTCGAC
196 TTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAAATTTTTAACAATGTAAC-TCGAC
*
1589652 TAAAATAATTTATTTTTTACACA
260 TAAAATAATTTATTTTTTA-TCA
* * *
1589675 TGTAGGTTAAGGTCTTTACCTTTCGGTTCTTCATTAAGTTTTTTCTTCGAATCTGTTG-CAGTAC
1 TGTAGGTTAAGGTCTTTACCTTTCGGTTCTTCATTACGTTTTTCCTTCGAACCTGTTGTC-GTAC
* * * * * * * *
1589739 CTAAAATAAAAAC----AAACAAATAAATCATTTAATTACTTTATCCAATGATATCAAATTAGAT
65 CTAAAATAAAAACAGATAAATAAATAAATCATTTAATTATTTTCTCCAGTAATATCATATTAAAC
* * *
1589800 TGATTTGTTCAAAAAATGTTTATTTTAA
130 TGATTTGTTTAAAATATGTTTTTTTTAA
1589828 CCATTTTTGT
Statistics
Matches: 624, Mismatches: 74, Indels: 49
0.84 0.10 0.07
Matches are distributed among these distances:
275 64 0.10
277 3 0.00
278 2 0.00
279 102 0.16
280 91 0.15
281 8 0.01
282 4 0.01
283 2 0.00
285 4 0.01
286 167 0.27
287 47 0.08
288 120 0.19
289 10 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (281 bp):
TGTAGGTTAAGGTCTTTACCTTTCGGTTCTTCATTACGTTTTTCCTTCGAACCTGTTGTCGTACC
TAAAATAAAAACAGATAAATAAATAAATCATTTAATTATTTTCTCCAGTAATATCATATTAAACT
GATTTGTTTAAAATATGTTTTTTTTAATAATTTCATCTTCACCTAGTTAAACAATTTTTTTTTTT
TTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAAATTTTTAACAATGTAACTCGACT
AAAATAATTTATTTTTTATCA
Found at i:1591124 original size:280 final size:278
Alignment explanation
Indices: 1590611--1591127 Score: 777
Period size: 280 Copynumber: 1.8 Consensus size: 278
1590601 TTTTTATTTA
* *
1590611 AAAATAAATAAATAAATAAATAATTTAATTACTTTATCCAGTGATATCATATTAAATTGATTTGT
1 AAAATAAACAAATAAATAAATAATTTAATTACTTTATCCAGTGATATCATATTAAACTGATTTGT
1590676 TTAAAAAATGTTTATTTTAATAATTTCATCTTCACCTACTTAAACCATTTTTTTTAATTTTTGAT
66 TTAAAAAATGTTTATTTTAATAATTTCATCTTCACCTACTTAAACCATTTTTTTTAATTTTTGAT
* * * *
1590741 TTAATACGCAATATGATATGAGAATTTTAATTCAAATTTTTAACAATGTAAATTCGACTAAAATA
131 TTAATACGCAATATCATATGAAAATTTTAATTCAAATTTTTAACAATCTAAATTCAACTAAAATA
* * * *
1590806 ATTTATTTTTTTTAAATGTATAGGTTAAAGTTTTTACCTTTCGGTTCATCCTTTCGTTTTTCCTT
196 ATTTA-TTTCTTTAAACGTATAGATTAAAGTCTTTACCTTTCGGTTCATCCTTTCGTTTTTCCTT
1590871 GTAACCTGTAGTCGTACCT
260 GTAACCTGTAGTCGTACCT
* * *
1590890 AAAATAAAACAAATAAATAAATCATTTAATTATTTTCTCCAGTGATATCATATTAAACTGATTTG
1 AAAAT-AAACAAATAAATAAATAATTTAATTACTTTATCCAGTGATATCATATTAAACTGATTTG
* * * * *
1590955 TTTAAAATATGTTTATTTTAATATTTTCATCTTCACCTAGTTAAACTATTTTTATTTTTATTTTT
65 TTTAAAAAATGTTTATTTTAATAATTTCATCTTCACCTACTTAAACCA-TTTT-TTTTAATTTTT
*
1591020 GATTTAATATC-CAATATCATATGAAAATTTTAATTCAATTTTTTAACAATCTAAATTCAACTAA
128 GATTTAATA-CGCAATATCATATGAAAATTTTAATTCAAATTTTTAACAATCTAAATTCAACTAA
* * *
1591084 AATAATTTA-TTCTTTAGACGTGTAGATTAAGGTCTTTACCTTTC
192 AATAATTTATTTCTTTAAACGTATAGATTAAAGTCTTTACCTTTC
1591128 AATTCCTCAT
Statistics
Matches: 212, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
279 5 0.02
280 126 0.59
281 4 0.02
282 76 0.36
283 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (278 bp):
AAAATAAACAAATAAATAAATAATTTAATTACTTTATCCAGTGATATCATATTAAACTGATTTGT
TTAAAAAATGTTTATTTTAATAATTTCATCTTCACCTACTTAAACCATTTTTTTTAATTTTTGAT
TTAATACGCAATATCATATGAAAATTTTAATTCAAATTTTTAACAATCTAAATTCAACTAAAATA
ATTTATTTCTTTAAACGTATAGATTAAAGTCTTTACCTTTCGGTTCATCCTTTCGTTTTTCCTTG
TAACCTGTAGTCGTACCT
Found at i:1591346 original size:155 final size:155
Alignment explanation
Indices: 1591063--1591688 Score: 763
Period size: 155 Copynumber: 4.0 Consensus size: 155
1591053 TTCAATTTTT
* ** *
1591063 TAACAATCTAAATTCAACTAAAATAATTTATTCTTTAGACGTGTAGATTAAGGTCTTTACCTTTC
1 TAACAATGTAAATTCGGCTAAAATAATTTATTCTTTAGACGTGTAGATTAAAGTCTTTACCTTTC
* * * * * **
1591128 AATTCCTCATTACGTTTTTCTTCCGAACTTGTAGTCATACCTGAAATAAAAACGAATGGATAAAT
66 AGTTCCTCATTACGTTTTTCTTCCGAACCTGTAGTCGTACCTAAAATAAAAACGGATAAATAAAT
*
1591193 AAATAAATCATTCAAATATTTTCTC
131 AAATAAATCATTCAATTATTTTCTC
* * * * *
1591218 TAACAATATAAATTCGGCTAAAATAATGTATTCTTTAGATGTGTAGATTAAAGCCTTTACCTTTT
1 TAACAATGTAAATTCGGCTAAAATAATTTATTCTTTAGACGTGTAGATTAAAGTCTTTACCTTTC
** * *
1591283 AGTTGTTGATTACGTTTTTCTTCCGAACCTATAGTCGTACCTAAAATAAAAACGGATAAATAAAT
66 AGTTCCTCATTACGTTTTTCTTCCGAACCTGTAGTCGTACCTAAAATAAAAACGGATAAATAAAT
*
1591348 AAGTAAATCATTCAATTATTTTCTC
131 AAATAAATCATTCAATTATTTTCTC
* * * *
1591373 TAACAATGTAAATTTGGCTAAAATAATTTAATT-ATTGGACATGTAGATT-AAGTTCTTTACCTT
1 TAACAATGTAAATTCGGCTAAAATAATTT-ATTCTTTAGACGTGTAGATTAAAG-TCTTTACCTT
** * * * * * *
1591436 TTTGTTCTTCGTTGCGTTTTCCTTCCGAACTTGTAGTTGTACCTAAAATAAAAACGGACAACTAA
64 TCAGTTCCTCATTACGTTTTTCTTCCGAACCTGTAGTCGTACCTAAAATAAAAACGG---A-TAA
1591501 ATAAATAAATAAATCATTCAATTATTTTCTC
125 ATAAATAAATAAATCATTCAATTATTTTCTC
* * * * *
1591532 TAACAATGTAAAATT-GGCTAAAATAAATTATTTTTTATACTTGTAGATTAAGGTCTTTACCTTT
1 TAACAATGT-AAATTCGGCTAAAATAATTTATTCTTTAGACGTGTAGATTAAAGTCTTTACCTTT
* * * * *
1591596 CGGTTCCTCATTACATTTTTCTTCCGAACCTGTAGTCTTGCCTAAAATAAAAATGGATAAATAAA
65 CAGTTCCTCATTACGTTTTTCTTCCGAACCTGTAGTCGTACCTAAAATAAAAACGGATAAATAAA
*
1591661 TAAGTAAATCATTCAATTATTTTCTC
130 TAAATAAATCATTCAATTATTTTCTC
1591687 TA
1 TA
1591689 GTGATACCAT
Statistics
Matches: 404, Mismatches: 58, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
154 3 0.01
155 264 0.65
156 4 0.01
158 4 0.01
159 122 0.30
160 7 0.02
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (155 bp):
TAACAATGTAAATTCGGCTAAAATAATTTATTCTTTAGACGTGTAGATTAAAGTCTTTACCTTTC
AGTTCCTCATTACGTTTTTCTTCCGAACCTGTAGTCGTACCTAAAATAAAAACGGATAAATAAAT
AAATAAATCATTCAATTATTTTCTC
Found at i:1591642 original size:314 final size:310
Alignment explanation
Indices: 1591080--1591688 Score: 830
Period size: 314 Copynumber: 2.0 Consensus size: 310
1591070 CTAAATTCAA
* *
1591080 CTAAAATAATTTATTCTTTAGACGTGTAGATTAAGGTCTTTACCTTTCAATTCCTCATTACGTTT
1 CTAAAATAATTTATTCATTAGACATGTAGATTAAGGTCTTTACCTTTCAATTCCTCATTACGTTT
* * **
1591145 TTCTTCCGAACTTGTAGTCATACCTGAAATAAAAACGAATGGATAAATAAATAAATCATTCAAAT
66 TCCTTCCGAACTTGTAGTCATACCTAAAATAAAAACGAATAAATAAATAAATAAATCATTCAAAT
1591210 ATTTTCTCTAACAATATAAATTCGGCTAAAATAATGTATTCTTTAGATGTGTAGATTAAAGCCTT
131 ATTTTCTCTAACAATATAAATTCGGCTAAAATAATGTATTCTTTAGATGTGTAGATTAAAGCCTT
* ** * *
1591275 TACCTTTTAGTTGTTGATTACGTTTTTCTTCCGAACCTATAGTCGTACCTAAAATAAAAACGGAT
196 TACCTTTCAGTTCCTCATTACATTTTTCTTCCGAACCTATAGTCGTACCTAAAATAAAAACGGAT
1591340 AAATAAATAAGTAAATCATTCAATTATTTTCTCTAACAATGTAAATTTGG
261 AAATAAATAAGTAAATCATTCAATTATTTTCTCTAACAATGTAAATTTGG
* * *** * * *
1591390 CTAAAATAATTTAATT-ATTGGACATGTAGATTAAGTTCTTTACCTTTTTGTTCTTCGTTGCGTT
1 CTAAAATAATTT-ATTCATTAGACATGTAGATTAAGGTCTTTACCTTTCAATTCCTCATTACGTT
**
1591454 TTCCTTCCGAACTTGTAGTTGTACCTAAAATAAAAACGGACAACTAAATAAATAAATAAATCATT
65 TTCCTTCCGAACTTGTAGTCATACCTAAAATAAAAAC-G--AA-TAAATAAATAAATAAATCATT
* * * *
1591519 CAATTATTTTCTCTAACAATGTAAAATT-GGCTAAAATAAAT-TATTTTTTATACT-TGTAGATT
126 CAAATATTTTCTCTAACAATAT-AAATTCGGCTAAAAT-AATGTATTCTTTAGA-TGTGTAGATT
* * * * * *
1591581 AAGGTCTTTACCTTTCGGTTCCTCATTACATTTTTCTTCCGAACCTGTAGTCTTGCCTAAAATAA
188 AAAGCCTTTACCTTTCAGTTCCTCATTACATTTTTCTTCCGAACCTATAGTCGTACCTAAAATAA
*
1591646 AAATGGATAAATAAATAAGTAAATCATTCAATTATTTTCTCTA
253 AAACGGATAAATAAATAAGTAAATCATTCAATTATTTTCTCTA
1591689 GTGATACCAT
Statistics
Matches: 259, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
310 83 0.32
311 4 0.02
313 2 0.01
314 161 0.62
315 9 0.03
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (310 bp):
CTAAAATAATTTATTCATTAGACATGTAGATTAAGGTCTTTACCTTTCAATTCCTCATTACGTTT
TCCTTCCGAACTTGTAGTCATACCTAAAATAAAAACGAATAAATAAATAAATAAATCATTCAAAT
ATTTTCTCTAACAATATAAATTCGGCTAAAATAATGTATTCTTTAGATGTGTAGATTAAAGCCTT
TACCTTTCAGTTCCTCATTACATTTTTCTTCCGAACCTATAGTCGTACCTAAAATAAAAACGGAT
AAATAAATAAGTAAATCATTCAATTATTTTCTCTAACAATGTAAATTTGG
Found at i:1592088 original size:271 final size:273
Alignment explanation
Indices: 1591735--1592246 Score: 769
Period size: 271 Copynumber: 1.9 Consensus size: 273
1591725 TTTTGATTTA
*
1591735 AAACATTTTTCTTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAATTTTTAACAA
1 AAACATTTTTATTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAATTTTTAACAA
* * * * * *
1591800 TGTATATTCGGCTAAAATAATTTATTTTTTAGACGTGTAGATTAAAGTATTTACCTTTTGGTTCT
66 TATAAATTCGGCTAAAATAATTTATTTTTTAGACATATAGATTAAAGTATTTACCTTTCGATTCT
* * *
1591865 TCATTACGTTTTTTCTCCAAACCTGTAGTCATACCTAAAAT-AA-AAATAAA-AAATTATTTAAT
131 TCATTACGTTTTTCCTCCAAACCTGTAGTCATACCTAAAATAAACAAACAAATAAATCATTTAAT
** *
1591927 TATTTTCTGCAGTGATATCATATTAAACTGATTTGTCTAAAATATGTTTTTTTTTAAATAATTTC
196 TATTTTCCCCAGTGACATCATATTAAACTGATTTGTCTAAAATATGTTTTTTTTTAAATAATTTC
1591992 ATCTTCACTGGTT
261 ATCTTCACTGGTT
* *
1592005 AAACAATTTTTATTTTTTATTTAATATGTAATATGATATGAGAATTTTAATTCAAATTTTTAACA
1 AAAC-ATTTTTATTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAATTTTTAACA
* *
1592070 ATATAAATTCGGCTAAAATAATTTATTTTTTAGACATATAGATTAGAGTTTTTACCTTTCGATTC
65 ATATAAATTCGGCTAAAATAATTTATTTTTTAGACATATAGATTAAAGTATTTACCTTTCGATTC
* * *
1592135 TTCATTACGTTTTTCCTCCAAATCTGTTGTCGTACCTAAAATAGAAACAAACAAATAAATCATTT
130 TTCATTACGTTTTTCCTCCAAACCTGTAGTCATACCTAAAAT--AAACAAACAAATAAATCATTT
* * *
1592200 AATTATTTTCCCCAGTGGCATTATATTAAACTGATTTGTTTAAAATA
193 AATTATTTTCCCCAGTGACATCATATTAAACTGATTTGTCTAAAATA
1592247 AATAAATTAT
Statistics
Matches: 213, Mismatches: 23, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
270 4 0.02
271 152 0.71
274 2 0.01
275 6 0.03
276 49 0.23
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (273 bp):
AAACATTTTTATTTTTGATTTAATATGCAATATGATATGAGAATTTTAATTCAAATTTTTAACAA
TATAAATTCGGCTAAAATAATTTATTTTTTAGACATATAGATTAAAGTATTTACCTTTCGATTCT
TCATTACGTTTTTCCTCCAAACCTGTAGTCATACCTAAAATAAACAAACAAATAAATCATTTAAT
TATTTTCCCCAGTGACATCATATTAAACTGATTTGTCTAAAATATGTTTTTTTTTAAATAATTTC
ATCTTCACTGGTT
Found at i:1598267 original size:9 final size:9
Alignment explanation
Indices: 1598253--1598284 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1598243 GTAGTGATTC
1598253 AATTCGGTT
1 AATTCGGTT
*
1598262 AATTCGGGT
1 AATTCGGTT
1598271 AATTCGGTT
1 AATTCGGTT
1598280 AATTC
1 AATTC
1598285 TTAACCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:1608243 original size:4 final size:4
Alignment explanation
Indices: 1608234--1608259 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1608224 AGAAACCCCA
1608234 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
1608260 CTTCTTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:1609238 original size:21 final size:22
Alignment explanation
Indices: 1609201--1609242 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1609191 GCAGAGGGAG
*
1609201 TGGAGGCCGGGGACGGCGGAAA
1 TGGAGGCCGGAGACGGCGGAAA
1609223 TGGAGG-CGGAGACGGCGGAA
1 TGGAGGCCGGAGACGGCGGAA
1609243 GCGGTGGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.24, C:0.17, G:0.55, T:0.05
Consensus pattern (22 bp):
TGGAGGCCGGAGACGGCGGAAA
Found at i:1609251 original size:21 final size:21
Alignment explanation
Indices: 1609202--1609252 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1609192 CAGAGGGAGT
* *
1609202 GGAGGCCGGGGACGGCGGAAAT
1 GGAGG-CGGAGACGGCGGAAAC
*
1609224 GGAGGCGGAGACGGCGGAAGC
1 GGAGGCGGAGACGGCGGAAAC
*
1609245 GGTGGCGG
1 GGAGGCGG
1609253 CGGAGGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.20, C:0.18, G:0.59, T:0.04
Consensus pattern (21 bp):
GGAGGCGGAGACGGCGGAAAC
Found at i:1619506 original size:14 final size:14
Alignment explanation
Indices: 1619480--1619518 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1619470 TATTTTTTGT
1619480 CATTTTAAATTTTAA
1 CATTTT-AATTTTAA
*
1619495 GATTTTAATTTTAA
1 CATTTTAATTTTAA
*
1619509 CATTTCAATT
1 CATTTTAATT
1619519 AAAACTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (14 bp):
CATTTTAATTTTAA
Found at i:1619570 original size:15 final size:15
Alignment explanation
Indices: 1619526--1619572 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1619516 ATTAAAACTT
*
1619526 TATTTATTCTTAATA
1 TATTTATTATTAATA
*
1619541 TAATTTTTTATTAATA
1 T-ATTTATTATTAATA
*
1619557 TATTTATTAATAATA
1 TATTTATTATTAATA
1619572 T
1 T
1619573 TTTCACCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTATTATTAATA
Found at i:1629176 original size:93 final size:93
Alignment explanation
Indices: 1629010--1629191 Score: 231
Period size: 93 Copynumber: 2.0 Consensus size: 93
1629000 AAATTAAGAG
* * **
1629010 GGAGAAAATTAGGGAAAAGCCTTCGCAAGATTCTGAATCCTTGGAAATTAAAGTCAAGAATGAGG
1 GGAGAAAATTAGGGAAAAGCCTTCGCAAGATTCTGAATCCCTAGAAATTAAAACCAAGAATGAGG
* *
1629075 AGTTGATTTCTGATGAGAAACCTCGTGT
66 AATCGATTTCTGATGAGAAACCTCGTGT
* * * * *
1629103 GGAGAAAATTAGGGAAAAGTCTTCGCAAGATTTTGAATCCCTAGAAGTTAAAACCGAGAGTG-GA
1 GGAGAAAATTAGGGAAAAGCCTTCGCAAGATTCTGAATCCCTAGAAATTAAAACCAAGAATGAG-
* *
1629167 GAATCGATTTCTTATGGGAAACCTC
65 GAATCGATTTCTGATGAGAAACCTC
1629192 ATAGGCAGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
92 1 0.01
93 74 0.99
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (93 bp):
GGAGAAAATTAGGGAAAAGCCTTCGCAAGATTCTGAATCCCTAGAAATTAAAACCAAGAATGAGG
AATCGATTTCTGATGAGAAACCTCGTGT
Found at i:1631411 original size:16 final size:15
Alignment explanation
Indices: 1631392--1631422 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1631382 TTTTTTATGG
1631392 TTAAATTAATTTAAAT
1 TTAAATTAA-TTAAAT
1631408 TTAAATTAATTAAAT
1 TTAAATTAATTAAAT
1631423 AAAAGATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAATTAATTAAAT
Found at i:1641322 original size:16 final size:17
Alignment explanation
Indices: 1641301--1641347 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
1641291 TTTATTTAGC
*
1641301 AATAAAATTAAA-TAAA
1 AATAAAAATAAATTAAA
1641317 AATAAAAATAAATTAAA
1 AATAAAAATAAATTAAA
*
1641334 AAGAAAAA-AAATTA
1 AATAAAAATAAATTA
1641348 GTGTTGGGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AATAAAAATAAATTAAA
Found at i:1646232 original size:123 final size:124
Alignment explanation
Indices: 1646012--1646259 Score: 489
Period size: 123 Copynumber: 2.0 Consensus size: 124
1646002 AAAATTCGAG
1646012 TATCATATAAAAATATATATAATTCTTTTGTTAGCAAACTTCAAATTTTAACTTTTTTTTTCTTT
1 TATCATATAAAAATATATATAATTCTTTTGTTAGCAAACTTCAAATTTTAACTTTTTTTTTCTTT
1646077 ATTTATTTATTACTTTGCTAGATCTCTCTATATGTCTCTTTTTCTTGGGGAGCTTTTTC
66 ATTTATTTATTACTTTGCTAGATCTCTCTATATGTCTCTTTTTCTTGGGGAGCTTTTTC
1646136 TATCATAT-AAAATATATATAATTCTTTTGTTAGCAAACTTCAAATTTTAACTTTTTTTTTCTTT
1 TATCATATAAAAATATATATAATTCTTTTGTTAGCAAACTTCAAATTTTAACTTTTTTTTTCTTT
1646200 ATTTATTTATTACTTTGCTAGATCTCTCTATATGTCTCTTTTTCTTGGGGAGCTTTTTC
66 ATTTATTTATTACTTTGCTAGATCTCTCTATATGTCTCTTTTTCTTGGGGAGCTTTTTC
1646259 T
1 T
1646260 CTTTTTTAAT
Statistics
Matches: 124, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
123 116 0.94
124 8 0.06
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.54
Consensus pattern (124 bp):
TATCATATAAAAATATATATAATTCTTTTGTTAGCAAACTTCAAATTTTAACTTTTTTTTTCTTT
ATTTATTTATTACTTTGCTAGATCTCTCTATATGTCTCTTTTTCTTGGGGAGCTTTTTC
Found at i:1646871 original size:23 final size:23
Alignment explanation
Indices: 1646828--1646887 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1646818 ATTTCATGCT
*
1646828 TTTTTTATGAACTTTTTA-TTTTTA
1 TTTTTT-TGAA-TTTTAATTTTTTA
*
1646852 TTTTTTTGAATTTTGAATTTTTTT
1 TTTTTTTGAATTTT-AATTTTTTA
1646876 TATTTTTTGAAT
1 T-TTTTTTGAAT
1646888 ACTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 4 0.13
23 5 0.16
24 12 0.39
25 10 0.32
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTTTTGAATTTTAATTTTTTA
Found at i:1647346 original size:5 final size:5
Alignment explanation
Indices: 1647332--1647368 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1647322 ATTTTTAAGT
*
1647332 TTATA ATATA TTATA TTATA TTATA TT-TA -TATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1647369 GTAATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
3 1 0.04
4 4 0.14
5 23 0.82
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:1657708 original size:31 final size:31
Alignment explanation
Indices: 1657647--1657709 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1657637 AACAACCCGG
*
1657647 TGACTTAAATAAAAACTGTCAAATAGTTCAA
1 TGACTTAAATAAAAACTGTCAAATAATTCAA
* * **
1657678 TGACTTAAATGAAAACTTTTGAATAATTCAA
1 TGACTTAAATAAAAACTGTCAAATAATTCAA
1657709 T
1 T
1657710 AACAATTCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTGTCAAATAATTCAA
Found at i:1677141 original size:3 final size:3
Alignment explanation
Indices: 1677133--1677159 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1677123 TACACGGAAA
1677133 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1677160 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1679968 original size:29 final size:29
Alignment explanation
Indices: 1679927--1679984 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1679917 TTATAGTGAC
*
1679927 TGGATCAAATTAGTCCCTCTATTATTAAA
1 TGGATCAAATTAGTCCCTCTACTATTAAA
* *
1679956 TGGATCAATTTAGTCCCTGTACTATTAAA
1 TGGATCAAATTAGTCCCTCTACTATTAAA
1679985 AAGAATCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (29 bp):
TGGATCAAATTAGTCCCTCTACTATTAAA
Found at i:1680201 original size:29 final size:30
Alignment explanation
Indices: 1680146--1680210 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
1680136 TTGGCCTTAT
* *
1680146 TTGATTCATTTTAATAGTACATAGACTAAA
1 TTGATCCATTTTAATAGTACAGAGACTAAA
* * *
1680176 TTGATCCA-TTTAATAGTAGAGGGACTAAT
1 TTGATCCATTTTAATAGTACAGAGACTAAA
1680205 TTGATC
1 TTGATC
1680211 AAGCACCTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (30 bp):
TTGATCCATTTTAATAGTACAGAGACTAAA
Found at i:1684276 original size:42 final size:42
Alignment explanation
Indices: 1684213--1684385 Score: 339
Period size: 42 Copynumber: 4.1 Consensus size: 42
1684203 AGCATCCGGT
1684213 AAAA-GTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1 AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1684254 AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1 AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1684296 AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1 AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1684338 AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1 AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
1684380 AAAATG
1 AAAATG
1684386 ATTGTTAAAA
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
41 4 0.03
42 127 0.97
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (42 bp):
AAAATGTATGCCACATTTCACATTCTTATTGGTGTTGGGATG
Found at i:1692967 original size:31 final size:31
Alignment explanation
Indices: 1692932--1693003 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
1692922 TAGTGAATAA
*
1692932 TTAAGTCAAATTAAATCAGATAATTAGTTAC
1 TTAAGTCAAATTAAATCAGATAACTAGTTAC
*
1692963 TTAAGTCAAATTAAATCAGATAACTAGTTGC
1 TTAAGTCAAATTAAATCAGATAACTAGTTAC
1692994 TTAAGTCAAA
1 TTAAGTCAAA
1693004 ATCCATCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (31 bp):
TTAAGTCAAATTAAATCAGATAACTAGTTAC
Found at i:1698817 original size:2 final size:2
Alignment explanation
Indices: 1698810--1698852 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1698800 GTGATTGATT
1698810 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1698852 A
1 A
1698853 AATGTTAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1705476 original size:168 final size:165
Alignment explanation
Indices: 1705104--1705578 Score: 486
Period size: 168 Copynumber: 2.9 Consensus size: 165
1705094 ATACTATTCA
* *
1705104 TTTACGTGTAAAATATCAGTTTTTCTTATACCCATTTCATGAATTTTG-TCT-TGTGAATGTATG
1 TTTACGTGTAAAATATCAATTTTTCTAATACCCATTTCATGAA-TTTGATCTCT-TGAATGTATG
* * *
1705167 TGAAGAAGCCATTAGTTA--TT--TG-T-TTTAGAATTAGGTGCAACTATGCAATGTAGTCAATG
64 TGAAGAAGCCCTTAGTTATTTTAGTGTTATTTTGAATTATGTGCAA-TATGCAATGTAGTCAATG
* * * *
1705226 TGTTTGTAAAAAGTATTGACGGAAAGTGTTTCTATGCG
128 TGTTTGTAAAAAGTATTAACAGAAAGTGGTTCTATGAG
** * *
1705264 TTTACGCATAAAATGTC-ATTTTCTCTAATACCCATTTTATGAATTTGATCTCTTGAATGTATGT
1 TTTACGTGTAAAATATCAATTTT-TCTAATACCCATTTCATGAATTTGATCTCTTGAATGTATGT
*
1705328 TAAGAAGCCCTTAGTTATTTTAGCTCGTTATTTTGAATTATGTGCAGATATGCAATGTAGTCAAT
65 GAAGAAGCCCTTAGTTATTTTAG-T-GTTATTTTGAATTATGTGCA-ATATGCAATGTAGTCAAT
* * *
1705393 GTGTTTGTAAAAAGTATTAACAGACAGTGGTTCTATTAT
127 GTGTTTGTAAAAAGTATTAACAGAAAGTGGTTCTATGAG
* * * * * * *
1705432 TTTACGTGTAAAATCTCAATTTTTGTGATGCCCGTTTCATGAATTTTATCTCTTGGATGTATGTG
1 TTTACGTGTAAAATATCAATTTTTCTAATACCCATTTCATGAATTTGATCTCTTGAATGTATGTG
* * * * *
1705497 AAGAA-CCCGTTAGTCTTTTGTTTAGGTGTTATTTTGAATTGGATAT-AAAAATGGAATGTAGTC
66 AAGAAGCCC-TTAG--TTAT-TTTA-GTGTTATTTTGAATT--ATGTGCAATATGCAATGTAGTC
1705560 AATGTGTTTGTAAAAAGTA
124 AATGTGTTTGTAAAAAGTA
1705579 CCAGCAGAAA
Statistics
Matches: 262, Mismatches: 33, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
159 8 0.03
160 61 0.23
161 1 0.00
162 2 0.01
165 1 0.00
166 1 0.00
167 4 0.02
168 120 0.46
169 6 0.02
170 48 0.18
171 6 0.02
172 4 0.02
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (165 bp):
TTTACGTGTAAAATATCAATTTTTCTAATACCCATTTCATGAATTTGATCTCTTGAATGTATGTG
AAGAAGCCCTTAGTTATTTTAGTGTTATTTTGAATTATGTGCAATATGCAATGTAGTCAATGTGT
TTGTAAAAAGTATTAACAGAAAGTGGTTCTATGAG
Found at i:1723475 original size:16 final size:16
Alignment explanation
Indices: 1723450--1723480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1723440 TGCAGCAACA
*
1723450 ATTGTGTGTTGGTGAC
1 ATTGTATGTTGGTGAC
1723466 ATTGTATGTTGGTGA
1 ATTGTATGTTGGTGA
1723481 AAATTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.35, T:0.45
Consensus pattern (16 bp):
ATTGTATGTTGGTGAC
Found at i:1728026 original size:29 final size:29
Alignment explanation
Indices: 1727935--1728030 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
1727925 TTTGTTATCC
1727935 CAACTATGAAAAATTATAAAATGGTCATT
1 CAACTATGAAAAATTATAAAATGGTCATT
* * ** * *** *
1727964 CGACTATTAGTAACTTTCTTTTATGGTCACT
1 CAACTA-T-GAAAAATTATAAAATGGTCATT
*
1727995 CAACTATGAAAAATTATAACATGGTCATT
1 CAACTATGAAAAATTATAAAATGGTCATT
1728024 CAACTAT
1 CAACTAT
1728031 TCAATTTTGT
Statistics
Matches: 47, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
29 26 0.55
30 2 0.04
31 19 0.40
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (29 bp):
CAACTATGAAAAATTATAAAATGGTCATT
Found at i:1738153 original size:12 final size:12
Alignment explanation
Indices: 1738123--1738159 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
1738113 ATTTTTAATA
1738123 ATTTATAATTTTT
1 ATTTA-AATTTTT
1738136 ATTTTAAATTTTT
1 A-TTTAAATTTTT
1738149 ATTTAAATTTT
1 ATTTAAATTTT
1738160 GACATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 9 0.39
14 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTAAATTTTT
Found at i:1739012 original size:14 final size:14
Alignment explanation
Indices: 1738990--1739020 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1738980 GGCCTAGCCC
1738990 TTTTAAAATATTTT
1 TTTTAAAATATTTT
*
1739004 TTTTTAAATATTTT
1 TTTTAAAATATTTT
1739018 TTT
1 TTT
1739021 GGTGTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTAAAATATTTT
Found at i:1740125 original size:57 final size:57
Alignment explanation
Indices: 1740037--1740151 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
1740027 GGCCTTGTTT
1740037 ATCCATGGGAGACCTTTCAAGGTTTATTTTCCCCCTTTTCCTTTTTTTTTAAACTAA
1 ATCCATGGGAGACCTTTCAAGGTTTATTTTCCCCCTTTTCCTTTTTTTTTAAACTAA
1740094 ATCCATGGGAGACCTTTCAAGGTTTATTTTCCCCCTTTTCCTTTTTTTTTAAACTAA
1 ATCCATGGGAGACCTTTCAAGGTTTATTTTCCCCCTTTTCCTTTTTTTTTAAACTAA
1740151 A
1 A
1740152 AATTGATTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (57 bp):
ATCCATGGGAGACCTTTCAAGGTTTATTTTCCCCCTTTTCCTTTTTTTTTAAACTAA
Found at i:1742185 original size:59 final size:61
Alignment explanation
Indices: 1742122--1742341 Score: 282
Period size: 68 Copynumber: 3.4 Consensus size: 61
1742112 TCAAGTTTGT
* *
1742122 TTTACTAATCAAATGTTAGATTTTGTTAC-A-ACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAATACAATTAATACAGTTAATAATTTGATAAA
1742181 TTTACTAATCAAATGTTAGATTTTATTACAAAAATTAATACAATTAATACAGTTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTAC-------AATACAATTAATACAGTTAATAATTTGAT
1742246 AAA
59 AAA
1742249 TTTACTAATCAAATGTTAGATTTTATTACAAAAATTAATACAATTAATACAGTTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTAC-------AATACAATTAATACAGTTAATAATTTGAT
1742314 AAA
59 AAA
1742317 TTTACTAATCAAATGTTAGATTTTA
1 TTTACTAATCAAATGTTAGATTTTA
1742342 ATTGGGCCCA
Statistics
Matches: 150, Mismatches: 2, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
59 28 0.19
67 1 0.01
68 121 0.81
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (61 bp):
TTTACTAATCAAATGTTAGATTTTATTACAATACAATTAATACAGTTAATAATTTGATAAA
Found at i:1742229 original size:68 final size:68
Alignment explanation
Indices: 1742152--1742341 Score: 371
Period size: 68 Copynumber: 2.8 Consensus size: 68
1742142 TTTTGTTACA
*
1742152 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
1 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
1742217 AAT
66 AAT
1742220 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
1 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
1742285 AAT
66 AAT
1742288 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTA
1 ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTA
1742342 ATTGGGCCCA
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 121 1.00
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (68 bp):
ACAATTAATACAGTTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAAAAATT
AAT
Found at i:1749834 original size:13 final size:13
Alignment explanation
Indices: 1749816--1749840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1749806 TTAAGAAAGT
1749816 AAAAATTAAAATA
1 AAAAATTAAAATA
1749829 AAAAATTAAAAT
1 AAAAATTAAAAT
1749841 TGTCGCGATC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:1752152 original size:55 final size:54
Alignment explanation
Indices: 1752064--1752236 Score: 237
Period size: 55 Copynumber: 3.2 Consensus size: 54
1752054 TGACACACTC
*
1752064 TTTTTTTCATTCAGTCTCATTTA-TTTAAATTTTTTTTCCTACATCTAACACCGT
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTTTTTTTCCTACATCTAACACC-T
1752118 TTTTTTTCATTCAATCTCATTTATTTTAAA--TTTTTTCCTACATCTAACACCCTTT
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTTTTTTTCCTACATCTAACA-CC--T
* * * *
1752173 TTTTTTTCATTTAATCTCATTTATTTCAGATTTTTTTT-CTACATCTAACACCC
1 TTTTTTTCATTCAATCTCATTTATTTTAAATTTTTTTTCCTACATCTAACACCT
1752226 TTTTTTTCATT
1 TTTTTTTCATT
1752237 TTCGTTTCTA
Statistics
Matches: 108, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
53 30 0.28
54 24 0.22
55 36 0.33
56 12 0.11
57 6 0.06
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.56
Consensus pattern (54 bp):
TTTTTTTCATTCAATCTCATTTATTTTAAATTTTTTTTCCTACATCTAACACCT
Found at i:1753052 original size:120 final size:115
Alignment explanation
Indices: 1752820--1753034 Score: 335
Period size: 113 Copynumber: 1.8 Consensus size: 115
1752810 TTTTTCTCCC
1752820 AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAATGTTTTTTTTTTTTACTTTTTTCGT
1 AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACC-AAAA----TTTTTTTTTTACTTTTTTCGT
* *
1752885 ATACTGATACCTGCTATTGACACAAAAAAAGTAAAAAAATATTTTTTTTCCACAA
61 ATACTGATACCTGATACTGACACAAAAAAAGTAAAAAAATATTTTTTTTCCACAA
1752940 AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACC-AAA-TTTTTTTTTACTTTTTTCGTATACT
1 AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACT
*
1753003 GATACCTGATACTGACACGAAAAAATGTAAAA
66 GATACCTGATACTGACAC-AAAAAAAGTAAAA
1753035 TTTTTTTTTA
Statistics
Matches: 91, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
113 41 0.45
114 12 0.13
118 3 0.03
120 35 0.38
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (115 bp):
AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACT
GATACCTGATACTGACACAAAAAAAGTAAAAAAATATTTTTTTTCCACAA
Found at i:1753297 original size:56 final size:57
Alignment explanation
Indices: 1753172--1753310 Score: 185
Period size: 56 Copynumber: 2.4 Consensus size: 57
1753162 TTTTTTACTC
* * * *
1753172 TACTGGGTGCTGGCCATTGACAGGCCCAGCACCCAAAATTTTTTTTTCCTTTTTTTCG
1 TACTGGATGCCGGCCATTGACA-GACTAGCACCCAAAATTTTTTTTTCCTTTTTTTCG
*
1753230 TACTGGATGCCGGCCATTGATAGACTAGCACCCAAAA-TTTTTTTT-CTTTTTTTCG
1 TACTGGATGCCGGCCATTGACAGACTAGCACCCAAAATTTTTTTTTCCTTTTTTTCG
1753285 TACTCTGG-TGCCGGCCATTGACAGAC
1 TA--CTGGATGCCGGCCATTGACAGAC
1753311 CAAAACTCGA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
55 12 0.16
56 25 0.34
57 17 0.23
58 19 0.26
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (57 bp):
TACTGGATGCCGGCCATTGACAGACTAGCACCCAAAATTTTTTTTTCCTTTTTTTCG
Found at i:1753327 original size:56 final size:56
Alignment explanation
Indices: 1753172--1753328 Score: 156
Period size: 56 Copynumber: 2.8 Consensus size: 56
1753162 TTTTTTACTC
* * * **
1753172 TACTGGGTGCTGGCCATTGACAGGCCCAGCACCCAAAATTTTTTTTTCCTTTTTTTCG
1 TACTGGATGCCGGCCATTGACA-GACCAAAACCC-AAATTTTTTTTTCCTTTTTTTCG
* * ** *
1753230 TACTGGATGCCGGCCATTGATAGACTAGCACCCAAAATTTTTTTT-CTTTTTTTCG
1 TACTGGATGCCGGCCATTGACAGACCAAAACCCAAATTTTTTTTTCCTTTTTTTCG
* *
1753285 TACTCTGG-TGCCGGCCATTGACAGACCAAAACTCGAATTTTTTT
1 TA--CTGGATGCCGGCCATTGACAGACCAAAACCCAAATTTTTTT
1753329 CCTGTATCTT
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
55 12 0.14
56 40 0.48
57 13 0.15
58 19 0.23
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (56 bp):
TACTGGATGCCGGCCATTGACAGACCAAAACCCAAATTTTTTTTTCCTTTTTTTCG
Found at i:1755867 original size:2 final size:2
Alignment explanation
Indices: 1755862--1755892 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1755852 ATATATATAT
*
1755862 AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1755893 ATTGCATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1760827 original size:39 final size:39
Alignment explanation
Indices: 1760784--1760867 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
1760774 TAGGTATACG
1760784 CTAGAAATATGTCCTATGTGTAAAGGCAAAATCTGCATA
1 CTAGAAATATGTCCTATGTGTAAAGGCAAAATCTGCATA
*
1760823 CTAGAAATATGTCCTGTGTGTAAAGGCAAAATCTGCATA
1 CTAGAAATATGTCCTATGTGTAAAGGCAAAATCTGCATA
*
1760862 CCAGAA
1 CTAGAA
1760868 TGTAAACTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (39 bp):
CTAGAAATATGTCCTATGTGTAAAGGCAAAATCTGCATA
Found at i:1763466 original size:186 final size:186
Alignment explanation
Indices: 1763152--1763524 Score: 710
Period size: 186 Copynumber: 2.0 Consensus size: 186
1763142 GGGTTAGGAT
1763152 AAAAATCTTAAATCTGAGCTCTCCTCGTACATGAAAAGATAAAAAAAAGGATACAGAACTTAAAG
1 AAAAATCTTAAATCTGAGCTCTCCTCGTACATGAAAAGATAAAAAAAAGGATACAGAACTTAAAG
* *
1763217 ATTGCCAAGGTCCCAAGGACTCATGTTTAATATAGGGTTCTATAGATACAAACTACAATTGTTAA
66 ATTGCCAAGGTACCAAGGACTCATGTTTAATATAGGGTTCTACAGATACAAACTACAATTGTTAA
1763282 AATTGAAGTAAAAATCATAAACTCAAAGAATGTACTTAAATTAACAAAGCTAGAAA
131 AATTGAAGTAAAAATCATAAACTCAAAGAATGTACTTAAATTAACAAAGCTAGAAA
1763338 AAAAATCTTAAATCTGAGCTCTCCTCGTACATGAAAAGATAAAAAAAAGGATACAGAACTTAAAG
1 AAAAATCTTAAATCTGAGCTCTCCTCGTACATGAAAAGATAAAAAAAAGGATACAGAACTTAAAG
*
1763403 ATTGCCAGGGTACCAAGGACTCATGTTTAATATAGGGTTCTACAGATACAAACTACAATTGTTAA
66 ATTGCCAAGGTACCAAGGACTCATGTTTAATATAGGGTTCTACAGATACAAACTACAATTGTTAA
*
1763468 AATTGAAGTAAAAATCATAACCTCAAAGAATGTACTTAAATTAACAAAGCTAGAAA
131 AATTGAAGTAAAAATCATAAACTCAAAGAATGTACTTAAATTAACAAAGCTAGAAA
1763524 A
1 A
1763525 CACCCACGCA
Statistics
Matches: 183, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
186 183 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (186 bp):
AAAAATCTTAAATCTGAGCTCTCCTCGTACATGAAAAGATAAAAAAAAGGATACAGAACTTAAAG
ATTGCCAAGGTACCAAGGACTCATGTTTAATATAGGGTTCTACAGATACAAACTACAATTGTTAA
AATTGAAGTAAAAATCATAAACTCAAAGAATGTACTTAAATTAACAAAGCTAGAAA
Found at i:1763941 original size:132 final size:131
Alignment explanation
Indices: 1763758--1764025 Score: 436
Period size: 132 Copynumber: 2.0 Consensus size: 131
1763748 AAGAGTATTA
1763758 AAACAGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATCATG-AA-ATAGAAAT
1 AAACAGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATCATGAAATATAGAAAT
*
1763821 AT-AATACTACACGATAAAATAAACCA-CTGAAAGCTTTATTTAACATATAGTTATTAAAATCAA
66 ATCAA-ACT--ACGATAAAATAAACCATC-GAAAGCTTCATTTAACATATAGTTA-TAAAATCAA
1763884 AAGCAG
126 AAGCAG
*
1763890 AAACAGTAAATTATACTGGTCGGCTTCCATTAATAAACATTTGTAGAATCATGAAAATATAGAAA
1 AAACAGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATCATG-AAATATAGAAA
1763955 TATCAAACTACGATAAAATAAACCATCGAAAGCTTCATTTAACATATAGTTATAAAATCAAAAGC
65 TATCAAACTACGATAAAATAAACCATCGAAAGCTTCATTTAACATATAGTTATAAAATCAAAAGC
1764020 AG
130 AG
1764022 AAAC
1 AAAC
1764026 TATGATCTGA
Statistics
Matches: 129, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
132 71 0.55
133 40 0.31
134 3 0.02
135 13 0.10
136 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (131 bp):
AAACAGTAAATTATACTGGTCAGCTTCCATTAATAAACATTTGTAGAATCATGAAATATAGAAAT
ATCAAACTACGATAAAATAAACCATCGAAAGCTTCATTTAACATATAGTTATAAAATCAAAAGCA
G
Found at i:1773118 original size:9 final size:9
Alignment explanation
Indices: 1773104--1773134 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1773094 ATTTATACGT
1773104 TTTTAATAA
1 TTTTAATAA
1773113 TTTTAATAA
1 TTTTAATAA
*
1773122 TTTTAATGA
1 TTTTAATAA
1773131 TTTT
1 TTTT
1773135 TCTTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTAATAA
Found at i:1773323 original size:17 final size:17
Alignment explanation
Indices: 1773301--1773338 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1773291 NNNNNNNTAT
1773301 TTATATTAAATT-TAAAA
1 TTATATTAAATTAT-AAA
*
1773318 TTATATTATATTATAAA
1 TTATATTAAATTATAAA
1773335 TTAT
1 TTAT
1773339 TTTTGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATTAAATTATAAA
Found at i:1773565 original size:16 final size:16
Alignment explanation
Indices: 1773544--1773579 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1773534 TATGGAAAGC
*
1773544 AAATTATTTTTTCTTT
1 AAATTATTTGTTCTTT
1773560 AAATTATTTGTTCTTT
1 AAATTATTTGTTCTTT
1773576 AAAT
1 AAAT
1773580 GTGTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
AAATTATTTGTTCTTT
Found at i:1777608 original size:30 final size:30
Alignment explanation
Indices: 1777574--1777633 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1777564 ACTTAACAAG
1777574 CAAATACCTCTAAAAAAATAACAAAATTAA
1 CAAATACCTCTAAAAAAATAACAAAATTAA
* * * *
1777604 CAAATGCCTTTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAAAAATAACAAAATTAA
1777634 TAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAAAAATAACAAAATTAA
Found at i:1777636 original size:12 final size:12
Alignment explanation
Indices: 1777614--1777642 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1777604 CAAATGCCTT
1777614 TAAAA-TAATAA
1 TAAAATTAATAA
1777625 TAAAATTAATAA
1 TAAAATTAATAA
1777637 TAAAAT
1 TAAAAT
1777643 AATTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:1780622 original size:31 final size:31
Alignment explanation
Indices: 1780587--1780661 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
1780577 CAACCCAATA
*
1780587 ACTTAAATAAAAACTTTCGAATAGTTC-AGT
1 ACTTAAATAAAAACTTTCGAATAGTTCAAAT
* *
1780617 GACTTAGATAAAAACTTTTGAATAGTTCAAAT
1 -ACTTAAATAAAAACTTTCGAATAGTTCAAAT
1780649 ACTTAAATAAAAA
1 ACTTAAATAAAAA
1780662 GGCCCCATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 37 0.95
32 2 0.05
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCGAATAGTTCAAAT
Found at i:1784519 original size:20 final size:20
Alignment explanation
Indices: 1784477--1784519 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1784467 TGAAAAAACT
* *
1784477 AAATTGATATAAAGTTATTA
1 AAATTAATATAAAGTTATAA
1784497 AAATTAATAT-AAGTTTATAA
1 AAATTAATATAAAG-TTATAA
1784517 AAA
1 AAA
1784520 CTATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
AAATTAATATAAAGTTATAA
Found at i:1784708 original size:33 final size:33
Alignment explanation
Indices: 1784645--1784709 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1784635 ATTTCGCTGC
* *
1784645 TTAATTAATTTTATTTATTTATTTCCTTATTAA
1 TTAATTAATTTTATTTATTTACTTACTTATTAA
*
1784678 TTAATTAATTTTATTTATTTACTTATTTATTA
1 TTAATTAATTTTATTTATTTACTTACTTATTA
1784710 GCACTGTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (33 bp):
TTAATTAATTTTATTTATTTACTTACTTATTAA
Found at i:1787343 original size:210 final size:209
Alignment explanation
Indices: 1786972--1787390 Score: 766
Period size: 210 Copynumber: 2.0 Consensus size: 209
1786962 GATGTGCAAG
1786972 CTAAGCAGCACTTAGTGTGTATTTTCTTTTGAATAATGGTAACGTGATAGATTTGGGAGATGAAC
1 CTAAGCAGCACTTAGTGTGTATTTTCTTTTGAATAATGGTAACGTGATAGATTTGGGAGATGAAC
*
1787037 TGTTTATGCTTTGACATTTGCTTTTTTAACTGTTGGGAGCTTAAATTTCATTTCATTCACTGAAC
66 TGTTTATGCTTTGACATTTGCTTTTTTAACTGTTGGGAGCTTAAATTTCATTTCATTCAATGAAC
* *
1787102 TTGAGAATCTTTTTCTTTCTTTTTCGCTTTTGTTTGTTGCTTTCATATGTGATCCGTGGAGGTTT
131 TTCAGAATCTTTTTCTTTCTTTTTCGCTTTTGTTTGTTGCTTTCACATGTGAT-CGTGGAGGTTT
1787167 TGGTATTATTGTGTA
195 TGGTATTATTGTGTA
*
1787182 CTAAGCGGCACTTAGTGTGTATTTTCTTTTGAATAATGGTAACGTGATAGATTTGGGAGATGAAC
1 CTAAGCAGCACTTAGTGTGTATTTTCTTTTGAATAATGGTAACGTGATAGATTTGGGAGATGAAC
1787247 TGTTTATGCTTTGACATTTGCTTTTTTAACTGTTGGGAGCTTAAATTTCATTTCATTCAATGAAC
66 TGTTTATGCTTTGACATTTGCTTTTTTAACTGTTGGGAGCTTAAATTTCATTTCATTCAATGAAC
* * *
1787312 TTCAGAATCTTTTTCTTTCTTTTTTGCTTTTGTTTGTTGCTTTCGCATGTGATCGTGGAGTTTTT
131 TTCAGAATCTTTTTCTTTCTTTTTCGCTTTTGTTTGTTGCTTTCACATGTGATCGTGGAGGTTTT
1787377 GGTATTATTGTGTA
196 GGTATTATTGTGTA
1787391 TAGCTTTGTG
Statistics
Matches: 202, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
209 25 0.12
210 177 0.88
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.47
Consensus pattern (209 bp):
CTAAGCAGCACTTAGTGTGTATTTTCTTTTGAATAATGGTAACGTGATAGATTTGGGAGATGAAC
TGTTTATGCTTTGACATTTGCTTTTTTAACTGTTGGGAGCTTAAATTTCATTTCATTCAATGAAC
TTCAGAATCTTTTTCTTTCTTTTTCGCTTTTGTTTGTTGCTTTCACATGTGATCGTGGAGGTTTT
GGTATTATTGTGTA
Found at i:1789746 original size:36 final size:36
Alignment explanation
Indices: 1789670--1789759 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
1789660 CGACCCCTCG
* ** *
1789670 GACT-GGAGCAAACTATCCGAAGCTATTGGCACTGCC
1 GACTGGGA-CAAACTGTCCGAAGCTATCAGCACCGCC
* *
1789706 GACTGGGACAAACTGTCCGAAGCTCTCAGCACCGCT
1 GACTGGGACAAACTGTCCGAAGCTATCAGCACCGCC
*
1789742 GACTGGAACAAACTGTCC
1 GACTGGGACAAACTGTCC
1789760 AAAGTTTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
36 43 0.93
37 3 0.07
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (36 bp):
GACTGGGACAAACTGTCCGAAGCTATCAGCACCGCC
Found at i:1791805 original size:78 final size:79
Alignment explanation
Indices: 1791701--1791859 Score: 311
Period size: 78 Copynumber: 2.0 Consensus size: 79
1791691 TTTTTTAACA
1791701 TATTAATAATTAAAAATAATTAATCCATAGATCGCACTGAAAATAAATTTTTTATAAATTAAATA
1 TATTAATAATTAAAAATAATTAATCCATAGATCGCACTGAAAATAAATTTTTTATAAATTAAATA
1791766 AAAAAAGTATACGT
66 AAAAAAGTATACGT
1791780 TATTAATAATT-AAAATAATTAATCCATAGATCGCACTGAAAATAAATTTTTTATAAATTAAATA
1 TATTAATAATTAAAAATAATTAATCCATAGATCGCACTGAAAATAAATTTTTTATAAATTAAATA
1791844 AAAAAAGTATACGT
66 AAAAAAGTATACGT
1791858 TA
1 TA
1791860 ATGTGATGTT
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 69 0.86
79 11 0.14
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (79 bp):
TATTAATAATTAAAAATAATTAATCCATAGATCGCACTGAAAATAAATTTTTTATAAATTAAATA
AAAAAAGTATACGT
Found at i:1798583 original size:19 final size:20
Alignment explanation
Indices: 1798549--1798587 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1798539 ATTAATATAG
1798549 GTTAAATATTTGAGATTTAT
1 GTTAAATATTTGAGATTTAT
*
1798569 GTTAAA-ATTTTAGATTTAT
1 GTTAAATATTTGAGATTTAT
1798588 CGTAACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
GTTAAATATTTGAGATTTAT
Found at i:1799062 original size:18 final size:20
Alignment explanation
Indices: 1799023--1799063 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1799013 AGAATATTAT
*
1799023 AATAAAATAAATTGGGAAAA
1 AATAAAATAAATTGGAAAAA
1799043 AATAAAA-AAA-TGGAAAAA
1 AATAAAATAAATTGGAAAAA
1799061 AAT
1 AAT
1799064 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 3 0.15
20 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (20 bp):
AATAAAATAAATTGGAAAAA
Found at i:1805722 original size:20 final size:20
Alignment explanation
Indices: 1805684--1805722 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1805674 GAATATTCTA
*
1805684 TGGATAATATAATTTAAATT
1 TGGATAATATAATTCAAATT
1805704 TGGATAATA-ATATTCAAAT
1 TGGATAATATA-ATTCAAAT
1805723 AATAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (20 bp):
TGGATAATATAATTCAAATT
Found at i:1808133 original size:20 final size:20
Alignment explanation
Indices: 1808095--1808133 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1808085 GAATATTCTA
*
1808095 TGGATAATATAATTTAAATT
1 TGGATAATATAATTCAAATT
1808115 TGGATAATA-ATATTCAAAT
1 TGGATAATATA-ATTCAAAT
1808134 AATAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (20 bp):
TGGATAATATAATTCAAATT
Found at i:1828127 original size:13 final size:15
Alignment explanation
Indices: 1828097--1828128 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1828087 ATATTTCATG
1828097 CATTTCATCAATAAT
1 CATTTCATCAATAAT
1828112 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
1828125 CATT
1 CATT
1828129 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:1828644 original size:6 final size:6
Alignment explanation
Indices: 1828615--1828657 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
1828605 CCAAACACAC
*
1828615 CAGTATA CAGTAA TCAGTAA CAGTAG CAGTAA CAGTAA CAGTA
1 CAGTA-A CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
1828658 TTCAACACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 22 0.67
7 11 0.33
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (6 bp):
CAGTAA
Found at i:1828652 original size:18 final size:19
Alignment explanation
Indices: 1828622--1828657 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1828612 CACCAGTATA
1828622 CAGTAATCAGTAACAGTAG
1 CAGTAATCAGTAACAGTAG
1828641 CAGTAA-CAGTAACAGTA
1 CAGTAATCAGTAACAGTA
1828658 TTCAACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (19 bp):
CAGTAATCAGTAACAGTAG
Found at i:1828763 original size:45 final size:45
Alignment explanation
Indices: 1828635--1828775 Score: 194
Period size: 45 Copynumber: 3.1 Consensus size: 45
1828625 TAATCAGTAA
* *
1828635 CAGTAGCAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
* *
1828680 CTGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
* * * *
1828725 CAGTAATCAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCTTAAT
1 CAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
1828770 CAGTAA
1 CAGTAA
1828776 GCCGGTAAAT
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 61 0.72
46 24 0.28
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTGAAT
Found at i:1832793 original size:2 final size:2
Alignment explanation
Indices: 1832786--1832818 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1832776 AACAAAACTC
*
1832786 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1832819 GGAGAGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1835931 original size:23 final size:23
Alignment explanation
Indices: 1835903--1835949 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1835893 ATAAAGACTG
1835903 AAATTTACCCATTTAATTATTGA
1 AAATTTACCCATTTAATTATTGA
1835926 AAATTTACCCATTTAATTATTGA
1 AAATTTACCCATTTAATTATTGA
1835949 A
1 A
1835950 GGACTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATTTACCCATTTAATTATTGA
Found at i:1837846 original size:257 final size:258
Alignment explanation
Indices: 1837381--1837895 Score: 1023
Period size: 257 Copynumber: 2.0 Consensus size: 258
1837371 AGTTCAAATA
1837381 ATGTAGAATTTTTTATTTTATTTTTCATGTTTCTATTATAAAAATTAGGTACTAAACATGTTTTT
1 ATGTAGAATTTTTTATTTTATTTTTCATGTTTCTATTATAAAAATTAGGTACTAAACATGTTTTT
1837446 GTATTTTCATTATTGAAAACAATTTTTATTTTTTTATTTTTATTTATCGAACACGTTTTCTAATT
66 GTATTTTCATTATTGAAAACAATTTTTATTTTTTTATTTTTATTTATCGAACACGTTTTCTAATT
1837511 TTTAAAATAAAATAGAAAATAAAAAGAAAAAAATTTCAAAAACTAGAGCCCATAATCAATTATAG
131 TTTAAAATAAAATAGAAAATAAAAAGAAAAAAATTTCAAAAACTAGAGCCCATAATCAATTATAG
1837576 GGTTGTTAACAGAATGACCAATACAGAAAAAAAGAAAAAAAGAAATGACTTCAACTGTAACTC
196 GGTTGTTAACAGAATGACCAATACAGAAAAAAAGAAAAAAAGAAATGACTTCAACTGTAACTC
1837639 ATGTAGAA-TTTTTATTTTATTTTTCATGTTTCTATTATAAAAATTAGGTACTAAACATGTTTTT
1 ATGTAGAATTTTTTATTTTATTTTTCATGTTTCTATTATAAAAATTAGGTACTAAACATGTTTTT
1837703 GTATTTTCATTATTGAAAACAATTTTTATTTTTTTATTTTTATTTATCGAACACGTTTTCTAATT
66 GTATTTTCATTATTGAAAACAATTTTTATTTTTTTATTTTTATTTATCGAACACGTTTTCTAATT
1837768 TTTAAAATAAAATAGAAAATAAAAAGAAAAAAATTTCAAAAACTAGAGCCCATAATCAATTATAG
131 TTTAAAATAAAATAGAAAATAAAAAGAAAAAAATTTCAAAAACTAGAGCCCATAATCAATTATAG
1837833 GGTTGTTAACAGAATGACCAATACAGAAAAAAAGAAAAAAAGAAATGACTTCAACTGTAACTC
196 GGTTGTTAACAGAATGACCAATACAGAAAAAAAGAAAAAAAGAAATGACTTCAACTGTAACTC
1837896 TATATAACTG
Statistics
Matches: 257, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
257 249 0.97
258 8 0.03
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (258 bp):
ATGTAGAATTTTTTATTTTATTTTTCATGTTTCTATTATAAAAATTAGGTACTAAACATGTTTTT
GTATTTTCATTATTGAAAACAATTTTTATTTTTTTATTTTTATTTATCGAACACGTTTTCTAATT
TTTAAAATAAAATAGAAAATAAAAAGAAAAAAATTTCAAAAACTAGAGCCCATAATCAATTATAG
GGTTGTTAACAGAATGACCAATACAGAAAAAAAGAAAAAAAGAAATGACTTCAACTGTAACTC
Found at i:1840475 original size:30 final size:30
Alignment explanation
Indices: 1840414--1840476 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1840404 ATCATTATAT
* *
1840414 TTTTTAGAATGACTAAATTAAAATTTGTCA
1 TTTTTAGAATGACTAAACTAAAATTTATCA
* *
1840444 TTTTTAGGATG-CTAAACTATAATTTTATCA
1 TTTTTAGAATGACTAAACTA-AAATTTATCA
1840474 TTT
1 TTT
1840477 ATTAACTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (30 bp):
TTTTTAGAATGACTAAACTAAAATTTATCA
Found at i:1842485 original size:68 final size:69
Alignment explanation
Indices: 1842344--1842486 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 69
1842334 ATGATTTATG
* * **
1842344 AATATGATCTTTACTCTCTTTTTTTTCGATACAATATTAGGGATAGAAGATGAGGTAATATGATT
1 AATATAATCTCTACTCTCTTTTTTTTCGATACAATATTAGGGATAGAAGATGAGGTAATACCATT
*
1842409 CATG
66 CATA
* * *
1842413 AATATAATCTCTACTCTCTTTTTTTT-GATATAATATTAAGGG-TAGAATAT-AGGGTAATACCT
1 AATATAATCTCTACTCTCTTTTTTTTCGATACAATATT-AGGGATAGAAGATGA-GGTAATACCA
*
1842475 TTCGTA
64 TTCATA
1842481 AATATA
1 AATATA
1842487 GAAAATAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
67 1 0.02
68 34 0.54
69 28 0.44
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (69 bp):
AATATAATCTCTACTCTCTTTTTTTTCGATACAATATTAGGGATAGAAGATGAGGTAATACCATT
CATA
Found at i:1854630 original size:21 final size:21
Alignment explanation
Indices: 1854606--1854648 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1854596 TTGTATTGTT
*
1854606 AAAATATTAACTTGTATAAAA
1 AAAATATGAACTTGTATAAAA
* *
1854627 AAAATATGAATTTGTGTAAAA
1 AAAATATGAACTTGTATAAAA
1854648 A
1 A
1854649 TTTTACCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAATATGAACTTGTATAAAA
Done.