Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold56
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: 1793205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 19648 characters in sequence are not A, C, G, or T
File 9 of 11
Found at i:1419789 original size:14 final size:15
Alignment explanation
Indices: 1419767--1419804 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1419757 AGAAAACTAG
1419767 AAAAG-AAAAAG-AA
1 AAAAGAAAAAAGAAA
1419780 AAAAGAAAAAAGAAA
1 AAAAGAAAAAAGAAA
1419795 AAAAGAAAAA
1 AAAAGAAAAA
1419805 GAAGAGAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.22
14 6 0.26
15 12 0.52
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAA
Found at i:1419807 original size:6 final size:7
Alignment explanation
Indices: 1419767--1419804 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
1419757 AGAAAACTAG
1419767 AAAAG-A
1 AAAAGAA
1419773 AAAAGAA
1 AAAAGAA
1419780 AAAAGAA
1 AAAAGAA
1419787 AAAAGAAA
1 AAAAG-AA
1419795 AAAAGAA
1 AAAAGAA
1419802 AAA
1 AAA
1419805 GAAGAGAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 5 0.17
7 18 0.60
8 7 0.23
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1420402 original size:30 final size:30
Alignment explanation
Indices: 1420368--1420461 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
1420358 TTCACGTATA
*
1420368 TTAGGGATTATTATGCAATTTTCATGCATT
1 TTAGGGAATATTATGCAATTTTCATGCATT
* *
1420398 TTA-GGACCAT-TTA-GAACATTTTCCAT-C-TC
1 TTAGGGA--ATATTATGCA-ATTTT-CATGCATT
1420427 TTAGGGAATATTATGCAATTTTCATGCATT
1 TTAGGGAATATTATGCAATTTTCATGCATT
1420457 TTAGG
1 TTAGG
1420462 ACCATTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
28 5 0.10
29 18 0.36
30 23 0.46
31 4 0.08
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (30 bp):
TTAGGGAATATTATGCAATTTTCATGCATT
Found at i:1420432 original size:59 final size:58
Alignment explanation
Indices: 1420368--1420688 Score: 305
Period size: 59 Copynumber: 5.5 Consensus size: 58
1420358 TTCACGTATA
* * * *
1420368 TTAGGGATTATTATGCAATTTTCATGCATTTTAGGACCATTTAGAACATTTTCCAT-CT
1 TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTT-CATGAT
* * *
1420426 CTTAGGGAATATTATGCAATTTTCATGCATTTTAGGACCATTTAAAACATTTTC-TGTCTT
1 -TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTTCATG--AT
*
1420486 TTAAGGACTATTAT-CTAATTTTCATGCATTTTAAGG-CCATTTAAAATAATTTTCATGAT
1 TTAGGGACTATTATGC-AATTTTCATGCATTTT-AGGACCATTTAAAA-AATTTTCATGAT
* ** * * * *
1420545 ATAAAGACTTTTATGTAATTTTCATGTATTTTAGGATCATTTAGAAAAATTTTCATGAT
1 TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTA-AAAAATTTTCATGAT
* * *** * *
1420604 TTAGGGACTCTTATGCAA-TTACATGCATTTTAGGGTTATTTAAAATA-TTTCATGCT
1 TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTTCATGAT
* *
1420660 TT-GGGACTGTTATGCAGTTTTCATGCATT
1 TTAGGGACTATTATGCAATTTTCATGCATT
1420689 AAGGGCTATT
Statistics
Matches: 224, Mismatches: 27, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
55 13 0.06
56 20 0.09
57 5 0.02
58 25 0.11
59 146 0.65
60 13 0.06
61 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (58 bp):
TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTTCATGAT
Found at i:1420478 original size:30 final size:30
Alignment explanation
Indices: 1420385--1420542 Score: 93
Period size: 30 Copynumber: 5.3 Consensus size: 30
1420375 TTATTATGCA
*
1420385 ATTTTCATGCATTTTAGGACCATTTAGAAC
1 ATTTTCATGCATTTTAGGACCATTTAAAAC
* **
1420415 ATTTTCCAT-C-TCTTAGGGA--ATATT-ATGC
1 ATTTT-CATGCATTTTA-GGACCAT-TTAAAAC
1420443 AATTTTCATGCATTTTAGGACCATTTAAAAC
1 -ATTTTCATGCATTTTAGGACCATTTAAAAC
* **
1420474 ATTTTC-TGTC-TTTTAAGGACTA-TTATCTA-
1 ATTTTCATG-CATTTT-AGGACCATTTA-AAAC
*
1420503 ATTTTCATGCATTTTAAGG-CCATTTAAAATA
1 ATTTTCATGCATTTT-AGGACCATTTAAAA-C
1420534 ATTTTCATG
1 ATTTTCATG
1420543 ATATAAAGAC
Statistics
Matches: 98, Mismatches: 13, Indels: 33
0.68 0.09 0.23
Matches are distributed among these distances:
28 6 0.06
29 34 0.35
30 42 0.43
31 16 0.16
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (30 bp):
ATTTTCATGCATTTTAGGACCATTTAAAAC
Found at i:1420699 original size:55 final size:55
Alignment explanation
Indices: 1420590--1420700 Score: 136
Period size: 55 Copynumber: 2.0 Consensus size: 55
1420580 ATCATTTAGA
* *
1420590 AAAATTTTCATGATTTAGGGACTCTTATGCAATTACATGCATTTTAGGGTTATTT
1 AAAATTTTCATGATTTAGGGACTCTTATGCAATTACATGCATTTAAGGGCTATTT
* * * *
1420645 AAAATATTTCATGCTTT-GGGACTGTTATGCAGTTTTCATGCA-TTAAGGGCTATTT
1 AAAAT-TTTCATGATTTAGGGACTCTTATGCA-ATTACATGCATTTAAGGGCTATTT
1420700 A
1 A
1420701 GATTACTTCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
55 30 0.62
56 18 0.38
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (55 bp):
AAAATTTTCATGATTTAGGGACTCTTATGCAATTACATGCATTTAAGGGCTATTT
Found at i:1420990 original size:59 final size:59
Alignment explanation
Indices: 1420886--1420997 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
1420876 GTCTTTAGGG
* *
1420886 TCATGTGAAAACTTTCATGTCGAAACATGTCCATTAGGGTCATTTAGGTAAAACTACGA
1 TCATGTGAAAACTTTCATGTCAAAACATGTCCATTAAGGTCATTTAGGTAAAACTACGA
* * ** ** *
1420945 TCATTTGAGAACTTTCATGTCAAAACATGTTTATTAATTTTATTTAGGTAAAA
1 TCATGTGAAAACTTTCATGTCAAAACATGTCCATTAAGGTCATTTAGGTAAAA
1420998 GTCCATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (59 bp):
TCATGTGAAAACTTTCATGTCAAAACATGTCCATTAAGGTCATTTAGGTAAAACTACGA
Found at i:1423035 original size:2 final size:2
Alignment explanation
Indices: 1423028--1423055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1423018 ATTTCTATTT
1423028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1423056 CTACCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1423838 original size:25 final size:25
Alignment explanation
Indices: 1423809--1423893 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
1423799 AAATTCATCA
1423809 AAATGGATGCAAACAAAGCTTTCAT
1 AAATGGATGCAAACAAAGCTTTCAT
** **
1423834 AAATGG-TGATCTTAATGAAA-AATTCAT
1 AAATGGATG--C--AAACAAAGCTTTCAT
1423861 CAAAATGGATGCAAACAAAGCTTTCAT
1 --AAATGGATGCAAACAAAGCTTTCAT
1423888 AAATGG
1 AAATGG
1423894 TGATCTTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 16
0.65 0.12 0.24
Matches are distributed among these distances:
24 2 0.05
25 12 0.27
26 6 0.14
27 10 0.23
28 6 0.14
29 6 0.14
30 2 0.05
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (25 bp):
AAATGGATGCAAACAAAGCTTTCAT
Found at i:1423873 original size:54 final size:54
Alignment explanation
Indices: 1423797--1423908 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
1423787 TTAATAATAT
1423797 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
1 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
*
1423851 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAGTG
1 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
1423905 AAAA
1 AAAA
1423909 GGTTTATATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (54 bp):
AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
Found at i:1423886 original size:27 final size:27
Alignment explanation
Indices: 1423802--1423887 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1423792 AATATAAAAA
1423802 TTCATCAAAATGGATGCAAACAAAGCT
1 TTCATCAAAATGGATGCAAACAAAGCT
** **
1423829 TTCAT--AAATGG-TGATCTTAATGAAA-AA
1 TTCATCAAAATGGATG--C--AAACAAAGCT
1423856 TTCATCAAAATGGATGCAAACAAAGCT
1 TTCATCAAAATGGATGCAAACAAAGCT
1423883 TTCAT
1 TTCAT
1423888 AAATGGTGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 2 0.05
25 6 0.14
26 6 0.14
27 15 0.35
28 6 0.14
29 6 0.14
30 2 0.05
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (27 bp):
TTCATCAAAATGGATGCAAACAAAGCT
Found at i:1425267 original size:13 final size:13
Alignment explanation
Indices: 1425249--1425273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1425239 ATATTGGACA
1425249 GTATCGATACATT
1 GTATCGATACATT
1425262 GTATCGATACAT
1 GTATCGATACAT
1425274 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1425286 original size:20 final size:21
Alignment explanation
Indices: 1425261--1425313 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1425251 ATCGATACAT
*
1425261 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
1425281 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
1425302 TGTATCGATACA
1 TGTATCGATACA
1425314 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:1425390 original size:32 final size:33
Alignment explanation
Indices: 1425354--1425421 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1425344 CCTTAACTGC
*
1425354 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
* *
1425386 TTGTATCGATACATCCCAAAATGTATTGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
1425419 TTG
1 TTG
1425422 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:1425392 original size:13 final size:13
Alignment explanation
Indices: 1425374--1425399 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1425364 ACACACAATA
1425374 TGTATCGATACAT
1 TGTATCGATACAT
1425387 TGTATCGATACAT
1 TGTATCGATACAT
1425400 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1432067 original size:21 final size:20
Alignment explanation
Indices: 1432023--1432074 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1432013 CCTCTAGGCA
* *
1432023 GCACCCACCAGGTCGCGACTG
1 GCACCC-CCAGGTCGCAACGG
1432044 GCACCCCCAGGTCGCAATCGG
1 GCACCCCCAGGTCGCAA-CGG
1432065 GCAGCCCCCA
1 GCA-CCCCCA
1432075 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 11 0.41
22 6 0.22
ACGTcount: A:0.19, C:0.46, G:0.27, T:0.08
Consensus pattern (20 bp):
GCACCCCCAGGTCGCAACGG
Found at i:1434815 original size:20 final size:20
Alignment explanation
Indices: 1434760--1434815 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1434750 CAAAACCCTG
*
1434760 AAATGTATCGATACACCTTC
1 AAATGTATCGATACATCTTC
1434780 AAATGTATCGATACATCTTGC
1 AAATGTATCGATACATCTT-C
*
1434801 ACA-GTATCGATACAT
1 AAATGTATCGATACAT
1434816 TGTATCGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATCTTC
Found at i:1434822 original size:13 final size:13
Alignment explanation
Indices: 1434804--1434828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1434794 ATCTTGCACA
1434804 GTATCGATACATT
1 GTATCGATACATT
1434817 GTATCGATACAT
1 GTATCGATACAT
1434829 GACCAAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1434953 original size:20 final size:20
Alignment explanation
Indices: 1434910--1434961 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1434900 CTTAACTGTT
*
1434910 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
1434929 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1434949 TGTATCGATACAT
1 TGTATCGATACAT
1434962 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1443485 original size:14 final size:16
Alignment explanation
Indices: 1443466--1443506 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
1443456 TTGTTAATAA
1443466 TAAAATTTTAATT-AT
1 TAAAATTTTAATTAAT
*
1443481 T-AAATGTTAATTGAAT
1 TAAAATTTTAATT-AAT
1443497 TAAAATTTTA
1 TAAAATTTTA
1443507 CTAGCACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 3 0.14
17 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TAAAATTTTAATTAAT
Found at i:1445154 original size:16 final size:15
Alignment explanation
Indices: 1445135--1445194 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
1445125 CTCAAATCCA
*
1445135 AAATGATCTGAACTTG
1 AAATGATC-GAACTAG
**
1445151 AAATGATACGAACCCG
1 AAATGAT-CGAACTAG
1445167 AAATGATCCGAACTAG
1 AAATGAT-CGAACTAG
*
1445183 AAATGCTCGAAC
1 AAATGATCGAAC
1445195 AATTAATCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 5 0.14
16 31 0.84
17 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (15 bp):
AAATGATCGAACTAG
Found at i:1446088 original size:16 final size:16
Alignment explanation
Indices: 1446046--1446096 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1446036 CCCAAATCCG
*
1446046 AAATGACCCGAACCTA
1 AAATGACCTGAACCTA
** * *
1446062 AAACAATCTGAACCCA
1 AAATGACCTGAACCTA
1446078 AAATGACCTGAACCTA
1 AAATGACCTGAACCTA
1446094 AAA
1 AAA
1446097 CGACTCAAAC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.49, C:0.27, G:0.10, T:0.14
Consensus pattern (16 bp):
AAATGACCTGAACCTA
Found at i:1449289 original size:20 final size:20
Alignment explanation
Indices: 1449264--1449313 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1449254 AAATTCCCAG
*
1449264 ATGTATCGATACAAAGATTA
1 ATGTATCGATACAAAGAATA
**
1449284 ATGTATCGATACATTGAATA
1 ATGTATCGATACAAAGAATA
1449304 ATGTATCGAT
1 ATGTATCGAT
1449314 TCATTTCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAAAGAATA
Found at i:1453231 original size:19 final size:19
Alignment explanation
Indices: 1453187--1453274 Score: 89
Period size: 19 Copynumber: 4.9 Consensus size: 19
1453177 CTGCCAGTTT
* **
1453187 CATGTATAGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1453207 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1453226 CATGTATCGATAC-----A
1 CATGTATCGATACAATGAA
*
1453240 -ATGTATCGATACAAAGAA
1 CATGTATCGATACAATGAA
1453258 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1453275 TATCGATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
13 12 0.21
14 1 0.02
18 1 0.02
19 30 0.52
20 14 0.24
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1453245 original size:13 final size:13
Alignment explanation
Indices: 1453227--1453282 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
1453217 TACAATGAAC
1453227 ATGTATCGATACA
1 ATGTATCGATACA
1453240 ATGTATCGATACA
1 ATGTATCGATACA
1453253 A---A--GA-AC-
1 ATGTATCGATACA
1453259 ATGTATCGATACA
1 ATGTATCGATACA
1453272 ATGTATCGATA
1 ATGTATCGATA
1453283 TAAAGCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
6 1 0.03
7 2 0.06
8 2 0.06
9 1 0.03
10 1 0.03
11 2 0.06
12 2 0.06
13 25 0.69
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1453249 original size:32 final size:32
Alignment explanation
Indices: 1453208--1453304 Score: 142
Period size: 32 Copynumber: 3.0 Consensus size: 32
1453198 ACAATTGTCC
*
1453208 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
1453240 ATGTATCGATACAAAGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
* *
1453272 ATGTATCGATATAAAGCATA-ATGTATTGATACA
1 ATGTATCGATACAAAG-A-ACATGTATCGATACA
1453305 TCTGGGTGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
32 46 0.77
33 13 0.22
34 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1457913 original size:19 final size:20
Alignment explanation
Indices: 1457891--1457937 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1457881 ATAAAATTTT
*
1457891 AAAAAAATACA-TAAAAATA
1 AAAAAAATAAAGTAAAAATA
* *
1457910 AAAAAATTAAAGTAAAATTA
1 AAAAAAATAAAGTAAAAATA
1457930 AAAAAAAT
1 AAAAAAAT
1457938 GGAGTTGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAAATAAAGTAAAAATA
Found at i:1461912 original size:2 final size:2
Alignment explanation
Indices: 1461905--1461946 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1461895 AATGGGAAGA
1461905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1461947 TGTCACGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1462527 original size:1 final size:1
Alignment explanation
Indices: 1462521--1462547 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1462511 CCTAGCCCCG
1462521 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1462548 ATGTTTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1466987 original size:59 final size:57
Alignment explanation
Indices: 1466915--1467209 Score: 193
Period size: 59 Copynumber: 5.0 Consensus size: 57
1466905 ATGGAAGTAA
*
1466915 TCTAAATGACCCTAAAATGCATAAAAATTACATAATAGTCCCTAAGACATGAAATATAT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTAA-ACATGAAA-ATAT
* * *** **
1466974 TTTAAATGACCCTAAAATACA-GGTAATTGCATAATAGTCTTTAAACAATGAAAAATAT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTAAAC-ATG-AAAATAT
* * * * * * *
1467032 TCTAAATGATCTTAAAATGCATAGAAATTGCATAAAAGACCTTACAATATGGAAAATAT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTA-AACAT-GAAAATAT
* * * * * * **
1467091 TCGAAATGGCCTTGAAATGCTTAAAAATTGGATAA-ATGTCCCTCGGACATGAAAA-ATT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATA-GTCCCT-AAACATGAAAATA-T
* * ** *
1467149 TCTAAAT-AGTCCTAAAATGCATCAAAATTATATAATAGTCCGTAATATGCATGAAAATAT
1 TCTAAATGA-CCCTAAAATGCATAAAAATTGCATAATAGTCCCTAA-A--CATGAAAATAT
1467209 T
1 T
1467210 ATGAAAAAAT
Statistics
Matches: 180, Mismatches: 42, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
57 3 0.02
58 79 0.44
59 84 0.47
60 13 0.07
61 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (57 bp):
TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTAAACATGAAAATAT
Found at i:1467175 original size:29 final size:31
Alignment explanation
Indices: 1467143--1467211 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
1467133 TCGGACATGA
*
1467143 AAAATTTCTA-AATAGTCC-TAAAATGCATC
1 AAAATTTATATAATAGTCCGTAAAATGCATC
* *
1467172 AAAA-TTATATAATAGTCCGTAATATGCATG
1 AAAATTTATATAATAGTCCGTAAAATGCATC
1467202 AAAATATTAT
1 AAAAT-TTAT
1467212 GAAAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 4 0.12
29 12 0.36
30 13 0.39
32 4 0.12
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (31 bp):
AAAATTTATATAATAGTCCGTAAAATGCATC
Found at i:1468465 original size:79 final size:79
Alignment explanation
Indices: 1468283--1468741 Score: 465
Period size: 78 Copynumber: 5.9 Consensus size: 79
1468273 TATTCTTTTA
* * * * *
1468283 GAGTA-TCTCCTCGAAAATAATGGGGTTAGAGTATCTCCGATGGTGAAAAATCAGTG-TTTGGAA
1 GAGTATTC-CCTCGAAAATAATGGGGTTGGAGTATCCCCGATGATGAAAAATCAATGTTTTAGAA
* *
1468346 ATAAAATC-GAGATTA
65 ATAAAATCAG-GGTTG
* * *
1468361 GAGTA-TCCCGTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATGTTTTAGAA
1 GAGTATTCCC-TCGAAAATAATGGGGTTGGAGTATCCCCGATGATGAAAAATCAATGTTTTAGAA
*
1468425 ATAAAATCAAGGTTG
65 ATAAAATCAGGGTTG
* * *
1468440 GAGTATTCCCTCGAAAATAATGGGGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAGAAA
1 GAGTATTCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGATGAAAAATCAATGTTTTAGAAA
* * *
1468505 TAGAA-CCGGGATTA
66 TAAAATCAGGG-TTG
**
1468519 GAGTATTCCCTCGAAAATAATGGGGTTGGAGTAT-CCCGATGATGAAAAATTGATGTTTTAGAAA
1 GAGTATTCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGATGAAAAATCAATGTTTTAGAAA
*
1468583 TAAAATTAGGGTTG
66 TAAAATCAGGGTTG
* * * * * *
1468597 GAGTATCCCCTCGAAATTAATGAGGTTAGAGTATCCCCGATGGTGAAAAATCAGTGTTTT-GAAA
1 GAGTATTCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGATGAAAAATCAATGTTTTAGAAA
*
1468661 -ATAAACCAGGGTTG
66 TA-AAATCAGGGTTG
* * * ** *
1468675 AAGTATCCCCTC-AGAAATAACGGGGTTGGAGCT-TCCCCGAT-AGTG-AAAATCGGTATTTTAG
1 GAGTATTCCCTCGA-AAATAATGGGGTTGGAG-TATCCCCGATGA-TGAAAAATCAATGTTTTAG
1468736 AAATAA
63 AAATAA
1468742 CACCGAGGTT
Statistics
Matches: 324, Mismatches: 44, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
77 16 0.05
78 165 0.51
79 139 0.43
80 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
GAGTATTCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATGATGAAAAATCAATGTTTTAGAAA
TAAAATCAGGGTTG
Found at i:1468575 original size:157 final size:154
Alignment explanation
Indices: 1468283--1468741 Score: 522
Period size: 157 Copynumber: 2.9 Consensus size: 154
1468273 TATTCTTTTA
*
1468283 GAGTA-TCTCCTCGAAAATAATGGGGTTAGAGTATCTCCGATGGTGAAAAATCAGTGTTTGGAAA
1 GAGTATTC-CCTCGAAAATAATGGGGTTAGAGTATC-CCGATGGTGAAAAATCA-TGTTTTGAAA
* * * *
1468347 TAAAATCGAGATTAGAGTA-TCCCGTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
63 T-AAACCGGGATTAGAGTATTCCC-TCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAA
1468411 TCAATGTTTTAGAAATAAAATCAAGGTTG
126 TCAATGTTTTAGAAATAAAATCAAGGTTG
* **
1468440 GAGTATTCCCTCGAAAATAATGGGGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAGAAA
1 GAGTATTCCCTCGAAAATAATGGGGTTAGAGTATCCC-GATGGTGAAAAATC-ATGTTTT-GAAA
*
1468505 TAGAACCGGGATTAGAGTATTCCCTCGAAAATAATGGGGTTGGAGTAT-CCCGATGATGAAAAAT
63 TA-AACCGGGATTAGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAAT
** * *
1468569 TGATGTTTTAGAAATAAAATTAGGGTTG
127 CAATGTTTTAGAAATAAAATCAAGGTTG
* * *
1468597 GAGTATCCCCTCGAAATTAATGAGGTTAGAGTATCCCCGATGGTGAAAAATCAGTGTTTTGAAAA
1 GAGTATTCCCTCGAAAATAATGGGGTTAGAGTAT-CCCGATGGTGAAAAATCA-TGTTTTG-AAA
*
1468662 TAAACCAGGG-TT-GAAGTATCCCCTC-AGAAATAACGGGGTTGGAGCT-TCCCCGAT-AGTG-A
63 TAAACC-GGGATTAG-AGTATTCCCTCGA-AAATAACGGGGTTGGAG-TATCCCCGATGA-TGAA
** *
1468721 AAATCGGTATTTTAGAAATAA
123 AAATCAATGTTTTAGAAATAA
1468742 CACCGAGGTT
Statistics
Matches: 263, Mismatches: 24, Indels: 31
0.83 0.08 0.10
Matches are distributed among these distances:
155 2 0.01
156 57 0.22
157 153 0.58
158 47 0.18
159 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (154 bp):
GAGTATTCCCTCGAAAATAATGGGGTTAGAGTATCCCGATGGTGAAAAATCATGTTTTGAAATAA
ACCGGGATTAGAGTATTCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATCAAT
GTTTTAGAAATAAAATCAAGGTTG
Found at i:1472111 original size:23 final size:22
Alignment explanation
Indices: 1472085--1472134 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1472075 ATGTATCGAT
1472085 ACATTACGTATTTACTTTGAAAA
1 ACATTACGTATTTAC-TTGAAAA
** *
1472108 ACATTATTTATTTGCTTGAAAA
1 ACATTACGTATTTACTTGAAAA
1472130 ACATT
1 ACATT
1472135 TAATCATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (22 bp):
ACATTACGTATTTACTTGAAAA
Found at i:1473270 original size:19 final size:17
Alignment explanation
Indices: 1473240--1473274 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1473230 TTGAAGGAAA
1473240 TCTTTTTTTTTTCTTTT
1 TCTTTTTTTTTTCTTTT
1473257 TCTTTTTTGGTTTTCTTT
1 TCTTTTTT--TTTTCTTT
1473275 AGTTGAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TCTTTTTTTTTTCTTTT
Found at i:1473827 original size:20 final size:21
Alignment explanation
Indices: 1473781--1473833 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1473771 AAAAGCTGAT
* *
1473781 AATGTATTGATACATCATGCA
1 AATGTATCGATACATCAAGCA
1473802 AATGTATCGATACATCAAGC-
1 AATGTATCGATACATCAAGCA
1473822 AATGTATCGATA
1 AATGTATCGATA
1473834 AATTTGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
AATGTATCGATACATCAAGCA
Found at i:1474999 original size:76 final size:76
Alignment explanation
Indices: 1474855--1475000 Score: 179
Period size: 76 Copynumber: 1.9 Consensus size: 76
1474845 TTTTAGTTAG
* * * * *
1474855 AATCGGGCTTTTAAGACTATTTTGATAACTTTGATTCAAAATTAGGCCTTTAAGCTATTTCAATA
1 AATCGAGCCTTTAAGACTATTTTGATAACTTTGATACAAAATCAGGCCTTTAAGCTATTTCAAGA
1474920 ATTTTTGTCAA
66 ATTTTTGTCAA
* * **
1474931 AATCGAGCCTTTAAGACTATTTTGATAATTTTGGATAC-AAATCAGG-TTTTAAGGCTATTTTGA
1 AATCGAGCCTTTAAGACTATTTTGATAACTTT-GATACAAAATCAGGCCTTTAA-GCTATTTCAA
1474994 GAATTTT
64 GAATTTT
1475001 GGCTTAAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
75 5 0.08
76 50 0.85
77 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (76 bp):
AATCGAGCCTTTAAGACTATTTTGATAACTTTGATACAAAATCAGGCCTTTAAGCTATTTCAAGA
ATTTTTGTCAA
Found at i:1475069 original size:38 final size:37
Alignment explanation
Indices: 1474845--1475058 Score: 135
Period size: 38 Copynumber: 5.6 Consensus size: 37
1474835 TTTTGGCACT
* * * *
1474845 TTTTAGTTAGAATCGGGCTTTTAAGACTATTTTGATAA
1 TTTTGGTTAAAATCGGG-TTTTAAGGCTATTTTGGTAA
* * * ** ***
1474883 CTTTGATTCAAAATTAGGCCTTTAA-GCTATTTCAATAA
1 TTTTGGTT-AAAA-TCGGGTTTTAAGGCTATTTTGGTAA
* * ** * *
1474921 TTTTTGTCAAAATCGAGCCTTTAAGACTATTTTGATAA
1 TTTTGGTTAAAATCG-GGTTTTAAGGCTATTTTGGTAA
* *
1474959 TTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAG-AA
1 TTTTGGTTA-AAATCGGGTTTTAAGGCTATTTTG-GTAA
* *
1474997 TTTTGGCTTAAAATTGGATTTTTAAGGCTATTTTGGTAA
1 TTTTGG-TTAAAATCGG-GTTTTAAGGCTATTTTGGTAA
1475036 TTTTGAGTTAAAATCGGGTTTTA
1 TTTTG-GTTAAAATCGGGTTTTA
1475059 GAGTCATTTT
Statistics
Matches: 134, Mismatches: 32, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
36 2 0.01
37 12 0.09
38 69 0.51
39 47 0.35
40 4 0.03
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (37 bp):
TTTTGGTTAAAATCGGGTTTTAAGGCTATTTTGGTAA
Found at i:1475087 original size:77 final size:77
Alignment explanation
Indices: 1474863--1475096 Score: 176
Period size: 77 Copynumber: 3.1 Consensus size: 77
1474853 AGAATCGGGC
* * * * ** * *
1474863 TTTTAAGACTATTTTGATAACTTT-GATTCAAAATTAGGCCTTTAA-GCTATTTCAATAATTTTT
1 TTTTAAGACTATTTTGATAATTTTGGATAC-AAATCAGG-TTTTAAGGCTATTTTGAGAATTTTA
* *
1474926 G-TCAAAA-TCGAGC
64 GCTCAAAATTGGA-T
* *
1474939 CTTTAAGACTATTTTGATAATTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAGAATTTTGGC
1 TTTTAAGACTATTTTGATAATTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAGAATTTTAGC
*
1475004 TTAAAATTGGAT
66 TCAAAATTGGAT
* * * * * * *
1475016 TTTTAAGGCTATTTTGGTAATTTTGAGTTA-AAATCGGGTTTTAGAGTC-ATTTTGCTGATTTTT
1 TTTTAAGACTATTTTGATAATTTTG-GATACAAATCAGGTTTTA-AGGCTATTTTG-AGAATTTT
*
1475079 AG-TCAAAATTGGGT
63 AGCTCAAAATTGGAT
1475093 TTTT
1 TTTT
1475097 GTAAGTACTA
Statistics
Matches: 128, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
75 5 0.04
76 44 0.34
77 63 0.49
78 16 0.12
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (77 bp):
TTTTAAGACTATTTTGATAATTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAGAATTTTAGC
TCAAAATTGGAT
Found at i:1475660 original size:20 final size:20
Alignment explanation
Indices: 1475616--1475686 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
1475606 TTCTACAATT
*
1475616 TGTATCGATACA-ACAAGTTAA
1 TGTATCGATACATA-AA-TAAA
*
1475637 TGTATCGATACATAAATGAA
1 TGTATCGATACATAAATAAA
*
1475657 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAAATAAA
1475677 TGTATC-ATAC
1 TGTATCGATAC
1475687 CAGACAATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 4 0.09
20 27 0.59
21 14 0.30
22 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAATAAA
Found at i:1475859 original size:12 final size:12
Alignment explanation
Indices: 1475844--1475868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1475834 CTTCAAAATA
1475844 TCGATACATGCT
1 TCGATACATGCT
1475856 TCGATACATGCT
1 TCGATACATGCT
1475868 T
1 T
1475869 GCAATGTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGATACATGCT
Found at i:1480132 original size:52 final size:52
Alignment explanation
Indices: 1480054--1480254 Score: 332
Period size: 52 Copynumber: 3.9 Consensus size: 52
1480044 CGAAATATGA
*
1480054 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
1480106 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
* *
1480158 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
1480210 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
1480255 ATGTATCGAT
Statistics
Matches: 141, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
51 2 0.01
52 139 0.99
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:1480261 original size:13 final size:13
Alignment explanation
Indices: 1480243--1480267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1480233 CAAAGATCAG
1480243 TGTATCGATACAA
1 TGTATCGATACAA
1480256 TGTATCGATACA
1 TGTATCGATACA
1480268 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1480349 original size:13 final size:13
Alignment explanation
Indices: 1480331--1480355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1480321 AAAAAAAACA
1480331 TGTATCGATACAT
1 TGTATCGATACAT
1480344 TGTATCGATACA
1 TGTATCGATACA
1480356 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1480454 original size:21 final size:21
Alignment explanation
Indices: 1480413--1480454 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1480403 GTTGGGACCT
*
1480413 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1480434 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1480455 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1486533 original size:14 final size:13
Alignment explanation
Indices: 1486516--1486588 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 13
1486506 AAAGAAAAGG
*
1486516 AGAAAAAGGAATAA
1 AGAAAAA-GAAGAA
1486530 AGAAAGAAGAAGAA
1 AGAAA-AAGAAGAA
1486544 AGAAAAA-AA-AA
1 AGAAAAAGAAGAA
*
1486555 GGAAAAATGGAA-AA
1 AGAAAAA--GAAGAA
*
1486569 AAAAAAAGAAGAAA
1 AGAAAAAGAAG-AA
1486583 AGAAAA
1 AGAAAA
1486589 TAGGGTGGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
11 8 0.17
12 5 0.10
13 2 0.04
14 31 0.65
15 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (13 bp):
AGAAAAAGAAGAA
Found at i:1486540 original size:21 final size:20
Alignment explanation
Indices: 1486505--1486588 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
1486495 AGCAAACCAG
*
1486505 AAAAGAAAAGGAGAAAAAGGA
1 AAAAG-AAAGAAGAAAAAGGA
1486526 ATAAAGAAAGAAGAAGAAA-GA
1 A-AAAGAAAGAAGAA-AAAGGA
*
1486547 AAAA-AAA-AGGAAAAATGGA
1 AAAAGAAAGAAGAAAAA-GGA
* *
1486566 AAAA-AAAAAAGAAGAAAAGA
1 AAAAGAAAGAAGAA-AAAGGA
1486586 AAA
1 AAA
1486589 TAGGGTGGCC
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
17 3 0.06
18 4 0.08
19 12 0.23
20 12 0.23
21 15 0.28
22 7 0.13
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAAGAAAGAAGAAAAAGGA
Found at i:1486556 original size:41 final size:39
Alignment explanation
Indices: 1486503--1486588 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 39
1486493 ACAGCAAACC
* *
1486503 AGAAAAGAAAAGGAGAAAAAGGAATAAAGAAAGAAGAAG-AA
1 AGAAAAAAAAAGGA-AAAAAGGAA-AAA-AAAAAAGAAGAAA
*
1486544 AGAAAAAAAAAGGAAAAATGGAAAAAAAAAAAGAAGAAA
1 AGAAAAAAAAAGGAAAAAAGGAAAAAAAAAAAGAAGAAA
1486583 AGAAAA
1 AGAAAA
1486589 TAGGGTGGCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
38 9 0.22
39 11 0.27
40 8 0.20
41 13 0.32
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (39 bp):
AGAAAAAAAAAGGAAAAAAGGAAAAAAAAAAAGAAGAAA
Found at i:1487375 original size:109 final size:110
Alignment explanation
Indices: 1487248--1487623 Score: 377
Period size: 109 Copynumber: 3.5 Consensus size: 110
1487238 ATCTAAAATC
** * ** **
1487248 ATAAAGTAGA-GTACGAACACTTTTTTATATAGGAT-ATTTATTTTTTATATTAGTTACATAAAT
1 ATAAAGT-GACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAAT
* * * *
1487311 TCGAGCACTAAAAGATTGACCTTGGAATAGGTCATTGTCTAGGGTA
65 TCGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
* *
1487357 ATAAAGTGACGTATGAACA-TCCTTTATATAAGATAATTCATTTTTTGCATTAGTTATGTAAATT
1 ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAATT
* * * * * *
1487421 TGGGTATTAAAGGATTGGCCTTGAAATAGGTCATTATCTAGAGTC
66 CGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
* ** *
1487466 ATAAAGTGACGTAGGAATGC-CCTTTATATAGAATAATTCATTTTTTGCATTAGTTATGTAAATT
1 ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAATT
* * * ** * * *
1487530 CGAGCACCAAGGGATTGACCTCGAAATATATCATTATCTATAATC
66 CGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
* * * * *
1487575 ATAAAGTGGCGTACGAACACT-TTTTACATA-AATAATTCATTTTTCGCAT
1 ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCAT
1487624 AAAATACATA
Statistics
Matches: 220, Mismatches: 43, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
108 32 0.15
109 188 0.85
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (110 bp):
ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAATT
CGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
Found at i:1490272 original size:16 final size:16
Alignment explanation
Indices: 1490235--1490301 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
1490225 GATTTATTTA
*
1490235 GGTTCAAATTTTTTCG
1 GGTTCGAATTTTTTCG
1490251 GGTTCGAATCTTTTT-G
1 GGTTCGAAT-TTTTTCG
*
1490267 GGTTCG-ACTTTTTCG
1 GGTTCGAATTTTTTCG
* * *
1490282 AGTTCGAACTTATTCG
1 GGTTCGAATTTTTTCG
1490298 GGTT
1 GGTT
1490302 TGGGTTTAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.12
15 7 0.16
16 26 0.60
17 5 0.12
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (16 bp):
GGTTCGAATTTTTTCG
Found at i:1491648 original size:16 final size:16
Alignment explanation
Indices: 1491639--1491696 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
1491629 GTTCGGGTTC
1491639 TTTCGAGTTCGAGCTT
1 TTTCGAGTTCGAGCTT
* *
1491655 TTTTGAGTTCGAACTT
1 TTTCGAGTTCGAGCTT
* *
1491671 TTTCGAGTTCGGGCTA
1 TTTCGAGTTCGAGCTT
1491687 TTTCGAGTTC
1 TTTCGAGTTC
1491697 TGATAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (16 bp):
TTTCGAGTTCGAGCTT
Found at i:1494246 original size:68 final size:67
Alignment explanation
Indices: 1494126--1494317 Score: 204
Period size: 68 Copynumber: 2.8 Consensus size: 67
1494116 TTTGATCATC
* * * * * * * *
1494126 ATCTCAACATATTACCAAATGACAAGAAGTCACCTATACTAGTAAACAACCTCAAAAGACTAATT
1 ATCTCAACATATAAGCAAATGAC-ATAAGTCACCTATGCTAATAAGCGACCTCAAAAGACTAATC
1494191 GAT
65 GAT
* * * * * * *
1494194 ATCTTAGCATATAAGTAAATGACACTAAGTCACCTATGTTAATAAGCGACCTCAAAGGTCTGATC
1 ATCTCAACATATAAGCAAATGACA-TAAGTCACCTATGCTAATAAGCGACCTCAAAAGACTAATC
1494259 GAT
65 GAT
* *
1494262 ATCTCAACATATAAGCAAGTGATATCAAGTCACCTATGCTAATAAGCGACCTCAAA
1 ATCTCAACATATAAGCAAATGACAT-AAGTCACCTATGCTAATAAGCGACCTCAAA
1494318 TATTTGATCA
Statistics
Matches: 101, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
67 2 0.02
68 99 0.98
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.25
Consensus pattern (67 bp):
ATCTCAACATATAAGCAAATGACATAAGTCACCTATGCTAATAAGCGACCTCAAAAGACTAATCG
AT
Found at i:1494326 original size:68 final size:68
Alignment explanation
Indices: 1494118--1494370 Score: 202
Period size: 68 Copynumber: 3.7 Consensus size: 68
1494108 GTTAAAAGTT
* * * * ** * * * *
1494118 TGATCATCATCTCAACATATTACCAAATGACAAGAAGTCACCTATACTAGTAAACAACCTCAAAA
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTC-AAA
1494183 GA-C
65 GATC
* ** * * * * * * *
1494186 TAATTGATATCTTAGCATATAAGTAAATGACACTAAGTCACCTATGTTAATAAGCGACCTCAAAG
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTCAAAG
*
1494251 GTC
66 ATC
* * * * *
1494254 TGATCGATATCTCAACATATAAGCAAGTGATATCAAGTCACCTATGCTAATAAGCGACCTCAAAT
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTCAAAG
*
1494319 ATT
66 ATC
* * * * *
1494322 TGATCAACATCTTAGCATATAAGTAAGTGACACCAAGTTACTTATGCTA
1 TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTA
1494371 GTGAAAAAGC
Statistics
Matches: 144, Mismatches: 40, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
67 4 0.03
68 140 0.97
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (68 bp):
TGATCAACATCTCAACATATAAGCAAGTGACACCAAGTCACCTATGCTAATAAGCGACCTCAAAG
ATC
Found at i:1494893 original size:39 final size:39
Alignment explanation
Indices: 1494781--1494900 Score: 127
Period size: 38 Copynumber: 3.1 Consensus size: 39
1494771 TAAGTACCTA
* * * * *
1494781 TAAAAACTCAGTTTTGACTAAAAATCACCAAAATAGCTC
1 TAAAAACTAAGTTTTAACTCAAAATTACCAAAATAGCTT
*
1494820 T-AAAACTCAGTTTTAACTCAAAATTACCAAAATAGCTT
1 TAAAAACTAAGTTTTAACTCAAAATTACCAAAATAGCTT
* * * *
1494858 TAAAAATCTAATTTTTACCT-AAAATTATCAAAATAGCCT
1 TAAAAA-CTAAGTTTTAACTCAAAATTACCAAAATAGCTT
1494897 TAAA
1 TAAA
1494901 GGCTCGATTT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 34 0.49
39 26 0.37
40 10 0.14
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (39 bp):
TAAAAACTAAGTTTTAACTCAAAATTACCAAAATAGCTT
Found at i:1494911 original size:39 final size:39
Alignment explanation
Indices: 1494839--1495076 Score: 123
Period size: 39 Copynumber: 6.2 Consensus size: 39
1494829 GTTTTAACTC
* * *** * * *
1494839 AAAATTACCAAAATAGCTTTAAAAATCTAATTTTTACCT
1 AAAATTATCAAAATAGCCTTAAAGGCCTGATTTTGACAT
*
1494878 AAAATTATCAAAATAGCCTTAAAGG-CTCGATTTTGACAA
1 AAAATTATCAAAATAGCCTTAAAGGCCT-GATTTTGACAT
* *
1494917 AAAATTATTAAAATAGCC-AAAAGGCCTGATTTTGA-AT
1 AAAATTATCAAAATAGCCTTAAAGGCCTGATTTTGACAT
* * * ** *** *
1494954 CAAAGTTACCAAAATAGCCTTAAAAGCCCAATTCAAACCAA
1 -AAAATTATCAAAATAGCCTTAAAGGCCTGATTTTGA-CAT
* * *
1494995 AAAATT-CCAAAATAACCTGAAAGGCCT-AGTTTTGAACA-
1 AAAATTATCAAAATAGCCTTAAAGGCCTGA-TTTTG-ACAT
* * * *
1495033 AAAATT-TACAAAATAGCCCTAAAAGCTTGGTTTTGAC-T
1 AAAATTAT-CAAAATAGCCTTAAAGGCCTGATTTTGACAT
1495071 AAAATT
1 AAAATT
1495077 TGATTTTGAC
Statistics
Matches: 151, Mismatches: 37, Indels: 23
0.72 0.18 0.11
Matches are distributed among these distances:
37 1 0.01
38 45 0.30
39 98 0.65
40 6 0.04
41 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (39 bp):
AAAATTATCAAAATAGCCTTAAAGGCCTGATTTTGACAT
Found at i:1496480 original size:7 final size:7
Alignment explanation
Indices: 1496468--1496506 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
1496458 AGAAAACTAG
1496468 AAAAGAA
1 AAAAGAA
1496475 AAAAGAA
1 AAAAGAA
1496482 AAAAGAA
1 AAAAGAA
1496489 AAAAGAAA
1 AAAAG-AA
1496497 AAAAGAA
1 AAAAGAA
1496504 AAA
1 AAA
1496507 GAAGAGAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:1497105 original size:30 final size:30
Alignment explanation
Indices: 1497071--1497164 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
1497061 TTCACGTATA
*
1497071 TTAGGGATTATTATGCAATTTTCATGCATT
1 TTAGGGAATATTATGCAATTTTCATGCATT
* *
1497101 TTA-GGACCAT-TTA-GAACATTTTCCAT-C-TC
1 TTAGGGA--ATATTATGCA-ATTTT-CATGCATT
1497130 TTAGGGAATATTATGCAATTTTCATGCATT
1 TTAGGGAATATTATGCAATTTTCATGCATT
1497160 TTAGG
1 TTAGG
1497165 ACCATTTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
28 5 0.10
29 18 0.36
30 23 0.46
31 4 0.08
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (30 bp):
TTAGGGAATATTATGCAATTTTCATGCATT
Found at i:1497181 original size:30 final size:30
Alignment explanation
Indices: 1497088--1497245 Score: 93
Period size: 30 Copynumber: 5.3 Consensus size: 30
1497078 TTATTATGCA
*
1497088 ATTTTCATGCATTTTAGGACCATTTAGAAC
1 ATTTTCATGCATTTTAGGACCATTTAAAAC
* **
1497118 ATTTTCCAT-C-TCTTAGGGA--ATATT-ATGC
1 ATTTT-CATGCATTTTA-GGACCAT-TTAAAAC
1497146 AATTTTCATGCATTTTAGGACCATTTAAAAC
1 -ATTTTCATGCATTTTAGGACCATTTAAAAC
* **
1497177 ATTTTC-TGTC-TTTTAAGGACTA-TTATCTA-
1 ATTTTCATG-CATTTT-AGGACCATTTA-AAAC
*
1497206 ATTTTCATGCATTTTAAGG-CCATTTAAAATA
1 ATTTTCATGCATTTT-AGGACCATTTAAAA-C
1497237 ATTTTCATG
1 ATTTTCATG
1497246 ATATAAAGAC
Statistics
Matches: 98, Mismatches: 13, Indels: 33
0.68 0.09 0.23
Matches are distributed among these distances:
28 6 0.06
29 34 0.35
30 42 0.43
31 16 0.16
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (30 bp):
ATTTTCATGCATTTTAGGACCATTTAAAAC
Found at i:1497321 original size:59 final size:58
Alignment explanation
Indices: 1497071--1497391 Score: 296
Period size: 59 Copynumber: 5.5 Consensus size: 58
1497061 TTCACGTATA
* * * *
1497071 TTAGGGATTATTATGCAATTTTCATGCATTTTAGGACCATTTAGAACATTTTCCAT-CT
1 TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTT-CATGAT
* * *
1497129 CTTAGGGAATATTATGCAATTTTCATGCATTTTAGGACCATTTAAAACATTTTC-TGTCTT
1 -TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTTCATG--AT
*
1497189 TTAAGGACTATTAT-CTAATTTTCATGCATTTTAAGG-CCATTTAAAATAATTTTCATGAT
1 TTAGGGACTATTATGC-AATTTTCATGCATTTT-AGGACCATTTAAAA-AATTTTCATGAT
* ** * * * *
1497248 ATAAAGACTTTTATGTAATTTTCATGTATTTTAGGATCATTTAGAAAAATTTTCATGAT
1 TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTA-AAAAATTTTCATGAT
* * * *** * *
1497307 TTAGGGACTCTTATGCAA-TTACACGCATTTTAGGGTTATTTAAAATA-TTTCATGCT
1 TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTTCATGAT
* *
1497363 TT-GGGACTGTTATGCAGTTTTCATGCATT
1 TTAGGGACTATTATGCAATTTTCATGCATT
1497392 AAGGGCTATT
Statistics
Matches: 222, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
55 13 0.06
56 19 0.09
57 5 0.02
58 24 0.11
59 146 0.66
60 13 0.06
61 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (58 bp):
TTAGGGACTATTATGCAATTTTCATGCATTTTAGGACCATTTAAAAAATTTTCATGAT
Found at i:1497402 original size:55 final size:55
Alignment explanation
Indices: 1497293--1497403 Score: 127
Period size: 55 Copynumber: 2.0 Consensus size: 55
1497283 ATCATTTAGA
* *
1497293 AAAATTTTCATGATTTAGGGACTCTTATGCAATTACACGCATTTTAGGGTTATTT
1 AAAATTTTCATGATTTAGGGACTCTTATGCAATTACACGCATTTAAGGGCTATTT
* * * * *
1497348 AAAATATTTCATGCTTT-GGGACTGTTATGCAGTTTTCATGCA-TTAAGGGCTATTT
1 AAAAT-TTTCATGATTTAGGGACTCTTATGCA-ATTACACGCATTTAAGGGCTATTT
1497403 A
1 A
1497404 GATTACTTCC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
55 30 0.64
56 17 0.36
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (55 bp):
AAAATTTTCATGATTTAGGGACTCTTATGCAATTACACGCATTTAAGGGCTATTT
Found at i:1497694 original size:59 final size:59
Alignment explanation
Indices: 1497590--1497701 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
1497580 GTCTTTAGGG
* *
1497590 TCATGTGAAAACTTTCATGTCGAAACATGTCCATTAGGGTCATTTAGGTAAAACTACGA
1 TCATGTGAAAACTTTCATGTCAAAACATGTCCATTAAGGTCATTTAGGTAAAACTACGA
* * ** ** *
1497649 TCATTTGAGAACTTTCATGTCAAAACATGTTTATTAATTTTATTTAGGTAAAA
1 TCATGTGAAAACTTTCATGTCAAAACATGTCCATTAAGGTCATTTAGGTAAAA
1497702 GTCCATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (59 bp):
TCATGTGAAAACTTTCATGTCAAAACATGTCCATTAAGGTCATTTAGGTAAAACTACGA
Found at i:1499739 original size:2 final size:2
Alignment explanation
Indices: 1499732--1499769 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1499722 ATTTCTATTT
1499732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1499770 CCTTTTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1500548 original size:25 final size:25
Alignment explanation
Indices: 1500519--1500603 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
1500509 AAATTCATCA
1500519 AAATGGATGCAAACAAAGCTTTCAT
1 AAATGGATGCAAACAAAGCTTTCAT
** **
1500544 AAATGG-TGATCTTAATGAAA-AATTCAT
1 AAATGGATG--C--AAACAAAGCTTTCAT
1500571 CAAAATGGATGCAAACAAAGCTTTCAT
1 --AAATGGATGCAAACAAAGCTTTCAT
1500598 AAATGG
1 AAATGG
1500604 TGATCTTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 16
0.65 0.12 0.24
Matches are distributed among these distances:
24 2 0.05
25 12 0.27
26 6 0.14
27 10 0.23
28 6 0.14
29 6 0.14
30 2 0.05
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (25 bp):
AAATGGATGCAAACAAAGCTTTCAT
Found at i:1500583 original size:54 final size:54
Alignment explanation
Indices: 1500507--1500618 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
1500497 TTAATAATAT
1500507 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
1 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
*
1500561 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAGTG
1 AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
1500615 AAAA
1 AAAA
1500619 GGTTTATATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (54 bp):
AAAAATTCATCAAAATGGATGCAAACAAAGCTTTCATAAATGGTGATCTTAATG
Found at i:1500596 original size:27 final size:27
Alignment explanation
Indices: 1500512--1500597 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1500502 AATATAAAAA
1500512 TTCATCAAAATGGATGCAAACAAAGCT
1 TTCATCAAAATGGATGCAAACAAAGCT
** **
1500539 TTCAT--AAATGG-TGATCTTAATGAAA-AA
1 TTCATCAAAATGGATG--C--AAACAAAGCT
1500566 TTCATCAAAATGGATGCAAACAAAGCT
1 TTCATCAAAATGGATGCAAACAAAGCT
1500593 TTCAT
1 TTCAT
1500598 AAATGGTGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 2 0.05
25 6 0.14
26 6 0.14
27 15 0.35
28 6 0.14
29 6 0.14
30 2 0.05
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (27 bp):
TTCATCAAAATGGATGCAAACAAAGCT
Found at i:1501976 original size:13 final size:13
Alignment explanation
Indices: 1501958--1501982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1501948 ATATTGGACA
1501958 GTATCGATACATT
1 GTATCGATACATT
1501971 GTATCGATACAT
1 GTATCGATACAT
1501983 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1501995 original size:20 final size:21
Alignment explanation
Indices: 1501970--1502022 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1501960 ATCGATACAT
*
1501970 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
1501990 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
1502011 TGTATCGATACA
1 TGTATCGATACA
1502023 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:1502099 original size:32 final size:33
Alignment explanation
Indices: 1502063--1502130 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1502053 CCTTAACTGT
*
1502063 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
* *
1502095 TTGTATCGATACATCCCAAAATGTATTGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
1502128 TTG
1 TTG
1502131 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:1502101 original size:13 final size:13
Alignment explanation
Indices: 1502083--1502108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1502073 ACACACAATA
1502083 TGTATCGATACAT
1 TGTATCGATACAT
1502096 TGTATCGATACAT
1 TGTATCGATACAT
1502109 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1508290 original size:13 final size:13
Alignment explanation
Indices: 1508272--1508309 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1508262 CAGTATTCTC
*
1508272 TGTATCGATACAT
1 TGTATCGATACAG
1508285 TGTATCGATACAG
1 TGTATCGATACAG
1508298 TGTATCGATACA
1 TGTATCGATACA
1508310 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1508788 original size:21 final size:20
Alignment explanation
Indices: 1508744--1508795 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1508734 CCTCTAGGCA
* *
1508744 GCACCCACCAGGTCGCGACTG
1 GCACCC-CCAGGTCGCAACGG
1508765 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAA-CGG
1508786 GCAGCCCCCA
1 GCA-CCCCCA
1508796 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 11 0.41
22 6 0.22
ACGTcount: A:0.19, C:0.48, G:0.27, T:0.06
Consensus pattern (20 bp):
GCACCCCCAGGTCGCAACGG
Found at i:1510747 original size:20 final size:20
Alignment explanation
Indices: 1510692--1510747 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1510682 CAAAACCCTG
*
1510692 AAATGTATCGATACACCTTC
1 AAATGTATCGATACATCTTC
1510712 AAATGTATCGATACATCTTGC
1 AAATGTATCGATACATCTT-C
*
1510733 ACA-GTATCGATACAT
1 AAATGTATCGATACAT
1510748 TGTATCGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATCTTC
Found at i:1510754 original size:13 final size:13
Alignment explanation
Indices: 1510736--1510760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1510726 ATCTTGCACA
1510736 GTATCGATACATT
1 GTATCGATACATT
1510749 GTATCGATACAT
1 GTATCGATACAT
1510761 GACCAAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1510885 original size:20 final size:20
Alignment explanation
Indices: 1510842--1510893 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1510832 CTTAACTGTT
*
1510842 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
1510861 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1510881 TGTATCGATACAT
1 TGTATCGATACAT
1510894 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1517080 original size:27 final size:27
Alignment explanation
Indices: 1517042--1517096 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1517032 CTATGAAGGT
1517042 TTCAAGTGGTAAAGTGTGTTTTGAGAA
1 TTCAAGTGGTAAAGTGTGTTTTGAGAA
1517069 TTCAAGTGGTAAAGTGTGTTTTGAGAA
1 TTCAAGTGGTAAAGTGTGTTTTGAGAA
1517096 T
1 T
1517097 GTGTTTAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (27 bp):
TTCAAGTGGTAAAGTGTGTTTTGAGAA
Found at i:1519461 original size:14 final size:16
Alignment explanation
Indices: 1519442--1519482 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
1519432 TTGTTAATAA
1519442 TAAAATTTTAATT-AT
1 TAAAATTTTAATTAAT
*
1519457 T-AAATGTTAATTGAAT
1 TAAAATTTTAATT-AAT
1519473 TAAAATTTTA
1 TAAAATTTTA
1519483 CTAGCACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 3 0.14
17 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TAAAATTTTAATTAAT
Found at i:1521126 original size:16 final size:15
Alignment explanation
Indices: 1521107--1521166 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
1521097 CTCAAATCCA
*
1521107 AAATGATCTGAACTTG
1 AAATGATC-GAACCTG
1521123 AAATGATACGAACCTG
1 AAATGAT-CGAACCTG
* *
1521139 AAATGATCCGAATCAG
1 AAATGAT-CGAACCTG
*
1521155 AAATGCTCGAAC
1 AAATGATCGAAC
1521167 AATTAATCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 4 0.11
16 32 0.86
17 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (15 bp):
AAATGATCGAACCTG
Found at i:1522053 original size:16 final size:16
Alignment explanation
Indices: 1522011--1522061 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1522001 CCCAAATCCG
*
1522011 AAATGACCCGAACCTA
1 AAATGACCTGAACCTA
** * *
1522027 AAACAATCTGAACCCA
1 AAATGACCTGAACCTA
1522043 AAATGACCTGAACCTA
1 AAATGACCTGAACCTA
1522059 AAA
1 AAA
1522062 CGACTCAAAC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.49, C:0.27, G:0.10, T:0.14
Consensus pattern (16 bp):
AAATGACCTGAACCTA
Found at i:1525255 original size:20 final size:20
Alignment explanation
Indices: 1525230--1525279 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1525220 AAATTCCCAG
*
1525230 ATGTATCGATACAAAGATTA
1 ATGTATCGATACAAAGAATA
**
1525250 ATGTATCGATACATTGAATA
1 ATGTATCGATACAAAGAATA
1525270 ATGTATCGAT
1 ATGTATCGAT
1525280 TCATTTCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAAAGAATA
Found at i:1528012 original size:23 final size:25
Alignment explanation
Indices: 1527985--1528040 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
1527975 TTTTATTCGA
*
1527985 GTTGTGTTTAAGTTATT-TTTT-GT
1 GTTGTGTTTAAGTTATTATTTTCAT
* * *
1528008 GTTGTATTTTATTTATTATTTTCAT
1 GTTGTGTTTAAGTTATTATTTTCAT
1528033 GTTGTGTT
1 GTTGTGTT
1528041 GGAGTCTATG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 14 0.54
24 4 0.15
25 8 0.31
ACGTcount: A:0.14, C:0.02, G:0.18, T:0.66
Consensus pattern (25 bp):
GTTGTGTTTAAGTTATTATTTTCAT
Found at i:1529194 original size:19 final size:19
Alignment explanation
Indices: 1529150--1529237 Score: 89
Period size: 19 Copynumber: 4.9 Consensus size: 19
1529140 CTGCCAGTTT
* **
1529150 CATGTATAGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1529170 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1529189 CATGTATCGATAC-----A
1 CATGTATCGATACAATGAA
*
1529203 -ATGTATCGATACAAAGAA
1 CATGTATCGATACAATGAA
1529221 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1529238 TATCGATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
13 12 0.21
14 1 0.02
18 1 0.02
19 30 0.52
20 14 0.24
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1529208 original size:13 final size:13
Alignment explanation
Indices: 1529190--1529245 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
1529180 TACAATGAAC
1529190 ATGTATCGATACA
1 ATGTATCGATACA
1529203 ATGTATCGATACA
1 ATGTATCGATACA
1529216 A---A--GA-AC-
1 ATGTATCGATACA
1529222 ATGTATCGATACA
1 ATGTATCGATACA
1529235 ATGTATCGATA
1 ATGTATCGATA
1529246 TAAAGCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
6 1 0.03
7 2 0.06
8 2 0.06
9 1 0.03
10 1 0.03
11 2 0.06
12 2 0.06
13 25 0.69
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1529212 original size:32 final size:32
Alignment explanation
Indices: 1529171--1529267 Score: 142
Period size: 32 Copynumber: 3.0 Consensus size: 32
1529161 ACAATTGTCC
*
1529171 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
1529203 ATGTATCGATACAAAGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
* *
1529235 ATGTATCGATATAAAGCATA-ATGTATTGATACA
1 ATGTATCGATACAAAG-A-ACATGTATCGATACA
1529268 TCTGGGTGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
32 46 0.77
33 13 0.22
34 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1532524 original size:11 final size:11
Alignment explanation
Indices: 1532508--1532532 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1532498 TAAGAGTATT
1532508 TTTTATAAATA
1 TTTTATAAATA
1532519 TTTTATAAATA
1 TTTTATAAATA
1532530 TTT
1 TTT
1532533 CATTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:1533873 original size:20 final size:19
Alignment explanation
Indices: 1533838--1533884 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1533828 TATAAAATTT
*
1533838 TAAAAAAA-TACATAAAAA
1 TAAAAAAATTAAATAAAAA
*
1533856 TAAAAAAATTAAAGTAAAAT
1 TAAAAAAATTAAA-TAAAAA
1533876 TAAAAAAAT
1 TAAAAAAAT
1533885 GGAGTTGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 3 0.12
20 14 0.56
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
TAAAAAAATTAAATAAAAA
Found at i:1537851 original size:2 final size:2
Alignment explanation
Indices: 1537844--1537871 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1537834 AATGGGAAGA
1537844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1537872 TGTCACGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1538489 original size:1 final size:1
Alignment explanation
Indices: 1538483--1538507 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1538473 CCTAGCCCCG
1538483 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1538508 ATGTTTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1542947 original size:59 final size:57
Alignment explanation
Indices: 1542875--1543169 Score: 193
Period size: 59 Copynumber: 5.0 Consensus size: 57
1542865 ATGGAAGTAA
*
1542875 TCTAAATGACCCTAAAATGCATAAAAATTACATAATAGTCCCTAAGACATGAAATATAT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTAA-ACATGAAA-ATAT
* * *** **
1542934 TTTAAATGACCCTAAAATACA-GGTAATTGCATAATAGTCTTTAAACAATGAAAAATAT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTAAAC-ATG-AAAATAT
* * * * * * *
1542992 TCTAAATGATCTTAAAATGCATAGAAATTGCATAAAAGACCTTACAATATGGAAAATAT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTA-AACAT-GAAAATAT
* * * * * * **
1543051 TCGAAATGGCCTTGAAATGCTTAAAAATTGGATAA-ATGTCCCTCGGACATGAAAA-ATT
1 TCTAAATGACCCTAAAATGCATAAAAATTGCATAATA-GTCCCT-AAACATGAAAATA-T
* * ** *
1543109 TCTAAAT-AGTCCTAAAATGCATCAAAATTATATAATAGTCCGTAATATGCATGAAAATAT
1 TCTAAATGA-CCCTAAAATGCATAAAAATTGCATAATAGTCCCTAA-A--CATGAAAATAT
1543169 T
1 T
1543170 ATGAAAAAAT
Statistics
Matches: 180, Mismatches: 42, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
57 3 0.02
58 79 0.44
59 84 0.47
60 13 0.07
61 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (57 bp):
TCTAAATGACCCTAAAATGCATAAAAATTGCATAATAGTCCCTAAACATGAAAATAT
Found at i:1543135 original size:29 final size:31
Alignment explanation
Indices: 1543103--1543171 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
1543093 TCGGACATGA
*
1543103 AAAATTTCTA-AATAGTCC-TAAAATGCATC
1 AAAATTTATATAATAGTCCGTAAAATGCATC
* *
1543132 AAAA-TTATATAATAGTCCGTAATATGCATG
1 AAAATTTATATAATAGTCCGTAAAATGCATC
1543162 AAAATATTAT
1 AAAAT-TTAT
1543172 GAAAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 4 0.12
29 12 0.36
30 13 0.39
32 4 0.12
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (31 bp):
AAAATTTATATAATAGTCCGTAAAATGCATC
Found at i:1544345 original size:79 final size:78
Alignment explanation
Indices: 1544256--1544644 Score: 374
Period size: 78 Copynumber: 5.0 Consensus size: 78
1544246 TATCTCCGCG
* *
1544256 AAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATCAATGTTTTAGAAATAAAATCAAGGTT
1 AAAATAACGGGGTTGGAGTATC-CCGATGATGAAAAATCAATGTTTTAGAAATAAAACCAAGGTT
*
1544321 GGAGTATTCCCTCA
65 GGAGTATCCCCTCA
* * * * *
1544335 AAAATAACGGGGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAGAAATAGAACCGAGATT
1 AAAATAACGGGGTTGGAGTATCCC-GATGATGAAAAATCAATGTTTTAGAAATAAAACCAAGGTT
* * *
1544400 AGAGTATTCCCTCG
65 GGAGTATCCCCTCA
* ** * ** *
1544414 AAAATAATGGGGTTGGAGTATCCCGATGATGAAAAATTGATGTTTTAGAAATAGAATTAGGGTTG
1 AAAATAACGGGGTTGGAGTATCCCGATGATGAAAAATCAATGTTTTAGAAATAAAACCAAGGTTG
*
1544479 GAGTATCCCCTCG
66 GAGTATCCCCTCA
* * * * * * *
1544492 AAATTAATGAGGTTAGAGTATCCCCGATGGTGAAAAATCAGTGTTTT-GAAA-ATAAACCAGGGT
1 AAAATAACGGGGTTGGAGTAT-CCCGATGATGAAAAATCAATGTTTTAGAAATA-AAACCAAGGT
*
1544555 TGAAGTATCCCCTCA
64 TGGAGTATCCCCTCA
* ** * * *
1544570 GAAATAACGGGGTTGGAGCT-TCCCCGAT-AGTG-AAAATCGGTATTTTAGAAATAACACCGAGG
1 AAAATAACGGGGTTGGAG-TAT-CCCGATGA-TGAAAAATCAATGTTTTAGAAATAAAACCAAGG
*
1544632 TTGAAGTATCCCC
63 TTGGAGTATCCCC
1544645 GAGATGAAAA
Statistics
Matches: 263, Mismatches: 40, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
77 13 0.05
78 135 0.51
79 115 0.44
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (78 bp):
AAAATAACGGGGTTGGAGTATCCCGATGATGAAAAATCAATGTTTTAGAAATAAAACCAAGGTTG
GAGTATCCCCTCA
Found at i:1544490 original size:78 final size:78
Alignment explanation
Indices: 1544243--1544622 Score: 389
Period size: 79 Copynumber: 4.8 Consensus size: 78
1544233 TATTCTTTTA
* * * *
1544243 GAGTATCTCCGCGAAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATCAATGTTTTAGAAA
1 GAGTATCCCCTCGAAAATAACGGGGTTGGAGTATC-CCGATGATGAAAAATCGATGTTTTAGAAA
* *
1544308 TAAAATCAAGGTTG
65 TAGAATCAGGGTTG
* * *
1544322 GAGTATTCCCTCAAAAATAACGGGGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTAGAAA
1 GAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC-GATGATGAAAAATCGATGTTTTAGAAA
* * *
1544387 TAGAA-CCGAGATTA
65 TAGAATCAG-GGTTG
* * *
1544401 GAGTATTCCCTCGAAAATAATGGGGTTGGAGTATCCCGATGATGAAAAATTGATGTTTTAGAAAT
1 GAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCGATGATGAAAAATCGATGTTTTAGAAAT
*
1544466 AGAATTAGGGTTG
66 AGAATCAGGGTTG
* * * * *
1544479 GAGTATCCCCTCGAAATTAATGAGGTTAGAGTATCCCCGATGGTGAAAAATC-AGTGTTTT-GAA
1 GAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT-CCCGATGATGAAAAATCGA-TGTTTTAG-A
*
1544542 AATA-AACCAGGGTTG
63 AATAGAATCAGGGTTG
* * *
1544557 AAGTATCCCCTC-AGAAATAACGGGGTTGGAGCT-TCCCCGAT-AGTG-AAAATCGGTATTTTAG
1 GAGTATCCCCTCGA-AAATAACGGGGTTGGAG-TAT-CCCGATGA-TGAAAAATCGATGTTTTAG
1544618 AAATA
62 AAATA
1544623 ACACCGAGGT
Statistics
Matches: 256, Mismatches: 34, Indels: 24
0.82 0.11 0.08
Matches are distributed among these distances:
77 17 0.07
78 112 0.44
79 127 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (78 bp):
GAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCGATGATGAAAAATCGATGTTTTAGAAAT
AGAATCAGGGTTG
Found at i:1544527 original size:157 final size:157
Alignment explanation
Indices: 1544240--1544644 Score: 407
Period size: 157 Copynumber: 2.6 Consensus size: 157
1544230 GAATATTCTT
*
1544240 TTAGAGTATCTCCGCGAAAATAACGGGGTTGGAGTATCTCCGATTATGAAAAATCAATGTTTTAG
1 TTAGAGTATCTCCGCGAAAATAACGGGGTTGGAGTATCTCCGATGATGAAAAATCAATGTTTTAG
* * * * *
1544305 AAATAAAATCAAGGTTGGAGTATTCCCTCAAAAATAACGGGGTTGGAGTATCCCTGATTATGAAA
66 AAATAAAATCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGATGAAA
1544370 AATC-GATGTTTTAGAAATAGAACCGAGA
131 AATCAG-TGTTTT-GAAATAGAACCGAGA
* * **
1544398 TTAGAGTAT-TCCCTCGAAAATAATGGGGTTGGAGTATC-CCGATGATGAAAAATTGATGTTTTA
1 TTAGAGTATCT-CCGCGAAAATAACGGGGTTGGAGTATCTCCGATGATGAAAAATCAATGTTTTA
* * * * * * *
1544461 GAAATAGAATTAGGGTTGGAGTATCCCCTCGAAATTAATGAGGTTAGAGTATCCCCGATGGTGAA
65 GAAATAAAATCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGATGAA
*
1544526 AAATCAGTGTTTTGAAAATA-AACC-AGGG
130 AAATCAGTGTTTTG-AAATAGAACCGA-GA
* * * ** *
1544554 TT-GAAGTATCCCCTC-AGAAATAACGGGGTTGGAGCT-TCCCCGAT-AGTG-AAAATCGGTATT
1 TTAG-AGTATCTCCGCGA-AAATAACGGGGTTGGAG-TATCTCCGATGA-TGAAAAATCAATGTT
* * * *
1544614 TTAGAAATAACACCGAGGTTGAAGTATCCCC
62 TTAGAAATAAAATCAAGGTTGGAGTATCCCC
1544645 GAGATGAAAA
Statistics
Matches: 207, Mismatches: 30, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
155 3 0.01
156 69 0.33
157 100 0.48
158 35 0.17
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (157 bp):
TTAGAGTATCTCCGCGAAAATAACGGGGTTGGAGTATCTCCGATGATGAAAAATCAATGTTTTAG
AAATAAAATCAAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGATGAAA
AATCAGTGTTTTGAAATAGAACCGAGA
Found at i:1549152 original size:19 final size:18
Alignment explanation
Indices: 1549121--1549156 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1549111 TTGAAGGAAC
*
1549121 TCTTTTTTTTTTTCTTTT
1 TCTTTTTTGTTTTCTTTT
1549139 TCTTTTTTGGTTTTCTTT
1 TCTTTTTT-GTTTTCTTT
1549157 AGTTGAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (18 bp):
TCTTTTTTGTTTTCTTTT
Found at i:1549709 original size:20 final size:21
Alignment explanation
Indices: 1549663--1549715 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1549653 AAAAGCTGAT
* *
1549663 AATGTATTGATACATCATGCA
1 AATGTATCGATACATCAAGCA
1549684 AATGTATCGATACATCAAGC-
1 AATGTATCGATACATCAAGCA
1549704 AATGTATCGATA
1 AATGTATCGATA
1549716 AATTTGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
AATGTATCGATACATCAAGCA
Found at i:1550882 original size:76 final size:76
Alignment explanation
Indices: 1550738--1550883 Score: 179
Period size: 76 Copynumber: 1.9 Consensus size: 76
1550728 TTTTAGTTAG
* * * * *
1550738 AATCGGGCTTTTAAGACTATTTTGATAACTTTGATTCAAAATTAGGCCTTTAAGCTATTTCAATA
1 AATCGAGCCTTTAAGACTATTTTGATAACTTTGATACAAAATCAGGCCTTTAAGCTATTTCAAGA
1550803 ATTTTTGTCAA
66 ATTTTTGTCAA
* * **
1550814 AATCGAGCCTTTAAGACTATTTTGATAATTTTGGATAC-AAATCAGG-TTTTAAGGCTATTTTGA
1 AATCGAGCCTTTAAGACTATTTTGATAACTTT-GATACAAAATCAGGCCTTTAA-GCTATTTCAA
1550877 GAATTTT
64 GAATTTT
1550884 GGCTTAAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
75 5 0.08
76 50 0.85
77 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (76 bp):
AATCGAGCCTTTAAGACTATTTTGATAACTTTGATACAAAATCAGGCCTTTAAGCTATTTCAAGA
ATTTTTGTCAA
Found at i:1550952 original size:38 final size:37
Alignment explanation
Indices: 1550728--1550941 Score: 135
Period size: 38 Copynumber: 5.6 Consensus size: 37
1550718 TTTTGGCACT
* * * *
1550728 TTTTAGTTAGAATCGGGCTTTTAAGACTATTTTGATAA
1 TTTTGGTTAAAATCGGG-TTTTAAGGCTATTTTGGTAA
* * * ** ***
1550766 CTTTGATTCAAAATTAGGCCTTTAA-GCTATTTCAATAA
1 TTTTGGTT-AAAA-TCGGGTTTTAAGGCTATTTTGGTAA
* * ** * *
1550804 TTTTTGTCAAAATCGAGCCTTTAAGACTATTTTGATAA
1 TTTTGGTTAAAATCG-GGTTTTAAGGCTATTTTGGTAA
* *
1550842 TTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAG-AA
1 TTTTGGTTA-AAATCGGGTTTTAAGGCTATTTTG-GTAA
* *
1550880 TTTTGGCTTAAAATTGGATTTTTAAGGCTATTTTGGTAA
1 TTTTGG-TTAAAATCGG-GTTTTAAGGCTATTTTGGTAA
1550919 TTTTGAGTTAAAATCGGGTTTTA
1 TTTTG-GTTAAAATCGGGTTTTA
1550942 GAGTCATTTT
Statistics
Matches: 134, Mismatches: 32, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
36 2 0.01
37 12 0.09
38 69 0.51
39 47 0.35
40 4 0.03
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (37 bp):
TTTTGGTTAAAATCGGGTTTTAAGGCTATTTTGGTAA
Found at i:1550970 original size:77 final size:77
Alignment explanation
Indices: 1550746--1550979 Score: 176
Period size: 77 Copynumber: 3.1 Consensus size: 77
1550736 AGAATCGGGC
* * * * ** * *
1550746 TTTTAAGACTATTTTGATAACTTT-GATTCAAAATTAGGCCTTTAA-GCTATTTCAATAATTTTT
1 TTTTAAGACTATTTTGATAATTTTGGATAC-AAATCAGG-TTTTAAGGCTATTTTGAGAATTTTA
* *
1550809 G-TCAAAA-TCGAGC
64 GCTCAAAATTGGA-T
* *
1550822 CTTTAAGACTATTTTGATAATTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAGAATTTTGGC
1 TTTTAAGACTATTTTGATAATTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAGAATTTTAGC
*
1550887 TTAAAATTGGAT
66 TCAAAATTGGAT
* * * * * * *
1550899 TTTTAAGGCTATTTTGGTAATTTTGAGTTA-AAATCGGGTTTTAGAGTC-ATTTTGCTGATTTTT
1 TTTTAAGACTATTTTGATAATTTTG-GATACAAATCAGGTTTTA-AGGCTATTTTG-AGAATTTT
*
1550962 AG-TCAAAATTGGGT
63 AGCTCAAAATTGGAT
1550976 TTTT
1 TTTT
1550980 GTAAGTACTA
Statistics
Matches: 128, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
75 5 0.04
76 44 0.34
77 63 0.49
78 16 0.12
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (77 bp):
TTTTAAGACTATTTTGATAATTTTGGATACAAATCAGGTTTTAAGGCTATTTTGAGAATTTTAGC
TCAAAATTGGAT
Found at i:1551543 original size:20 final size:20
Alignment explanation
Indices: 1551499--1551569 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
1551489 TTCTACAATT
*
1551499 TGTATCGATACA-ACAAGTTAA
1 TGTATCGATACATA-AA-TAAA
*
1551520 TGTATCGATACATAAATGAA
1 TGTATCGATACATAAATAAA
*
1551540 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAAATAAA
1551560 TGTATC-ATAC
1 TGTATCGATAC
1551570 CAGACAATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 4 0.09
20 27 0.59
21 14 0.30
22 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAATAAA
Found at i:1551742 original size:12 final size:12
Alignment explanation
Indices: 1551727--1551751 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1551717 CTTCAAAATA
1551727 TCGATACATGCT
1 TCGATACATGCT
1551739 TCGATACATGCT
1 TCGATACATGCT
1551751 T
1 T
1551752 GCAATGTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGATACATGCT
Found at i:1558791 original size:37 final size:42
Alignment explanation
Indices: 1558717--1558801 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 42
1558707 ACAGCAAACC
*
1558717 AGAAAAGAAAAGGAGAAAAAGGAATAAAGAAAGAAGAAG-AA
1 AGAAAAGAAAAGGAGAAAAAGGAATAAAGAAAAAAGAAGAAA
*
1558758 AGAAAA-AAAAGGA-AAAATGGAA-AAA-AAAAAAGAAGAAA
1 AGAAAAGAAAAGGAGAAAAAGGAATAAAGAAAAAAGAAGAAA
1558796 AGAAAA
1 AGAAAA
1558802 TAGGGTGGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
37 9 0.22
38 11 0.27
39 8 0.20
40 7 0.17
41 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.02
Consensus pattern (42 bp):
AGAAAAGAAAAGGAGAAAAAGGAATAAAGAAAAAAGAAGAAA
Found at i:1558800 original size:20 final size:20
Alignment explanation
Indices: 1558742--1558801 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 20
1558732 AAAAAGGAAT
1558742 AAAGAAAGAAGAAGAAAGAAAAA
1 AAAG-AAGAA-AAGAAA-AAAAA
*
1558765 AAAGGAA-AAATGGAAAAAAAA
1 AAA-GAAGAAA-AGAAAAAAAA
1558786 AAAGAAGAAAAGAAAA
1 AAAGAAGAAAAGAAAA
1558802 TAGGGTGGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
20 8 0.25
21 12 0.38
22 6 0.19
23 5 0.16
24 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAGAAGAAAAGAAAAAAAA
Found at i:1559586 original size:109 final size:110
Alignment explanation
Indices: 1559459--1559834 Score: 377
Period size: 109 Copynumber: 3.5 Consensus size: 110
1559449 ATCTAAAATC
** * ** **
1559459 ATAAAGTAGA-GTACGAACACTTTTTTATATAGGAT-ATTTATTTTTTATATTAGTTACATAAAT
1 ATAAAGT-GACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAAT
* * * *
1559522 TCGAGCACTAAAAGATTGACCTTGGAATAGGTCATTGTCTAGGGTA
65 TCGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
* *
1559568 ATAAAGTGACGTATGAACA-TCCTTTATATAAGATAATTCATTTTTTGCATTAGTTATGTAAATT
1 ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAATT
* * * * * *
1559632 TGGGTATTAAAGGATTGGCCTTGAAATAGGTCATTATCTAGAGTC
66 CGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
* ** *
1559677 ATAAAGTGACGTAGGAATGC-CCTTTATATAGAATAATTCATTTTTTGCATTAGTTATGTAAATT
1 ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAATT
* * * ** * * *
1559741 CGAGCACCAAGGGATTGACCTCGAAATATATCATTATCTATAATC
66 CGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
* * * * *
1559786 ATAAAGTGACGTACGAGCACT-TTTTACATA-AATAATTCATTTTTCGCAT
1 ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCAT
1559835 AAAATACATA
Statistics
Matches: 220, Mismatches: 43, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
108 32 0.15
109 188 0.85
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (110 bp):
ATAAAGTGACGTACGAACACTCCTTTATATAGGATAATTCATTTTTTGCATTAGTTATGTAAATT
CGAGCACTAAAGGATTGACCTTGAAATAGGTCATTATCTAGAGTA
Found at i:1562452 original size:16 final size:16
Alignment explanation
Indices: 1562433--1562483 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1562423 GATTTATTTA
*
1562433 GGTTTGAATTTTTTCG
1 GGTTCGAATTTTTTCG
*
1562449 GGTTCGACTTTTTT-G
1 GGTTCGAATTTTTTCG
* * *
1562464 AGTTCGAACTTATTCG
1 GGTTCGAATTTTTTCG
1562480 GGTT
1 GGTT
1562484 TGGGTTTAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.14, C:0.12, G:0.25, T:0.49
Consensus pattern (16 bp):
GGTTCGAATTTTTTCG
Found at i:1562855 original size:9 final size:10
Alignment explanation
Indices: 1562840--1562883 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 10
1562830 TAAGTAAATT
1562840 AATATTTAAA
1 AATATTTAAA
1562850 AA-ATTTAAA
1 AATATTTAAA
1562859 ATATATTTAATA
1 A-ATATTTAA-A
1562871 TAATATTTAAA
1 -AATATTTAAA
1562882 AA
1 AA
1562884 CCCATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.27
10 5 0.17
11 7 0.23
12 9 0.30
13 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTTAAA
Found at i:1562882 original size:23 final size:20
Alignment explanation
Indices: 1562841--1562882 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 20
1562831 AAGTAAATTA
1562841 ATATTTAAAAAATTTAAAAT
1 ATATTTAAAAAATTTAAAAT
1562861 ATATTTAATATAATATTTAAAA
1 ATATTTAA-A-AA-ATTTAAAA
1562883 ACCCATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 2 0.11
23 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTTAAAAAATTTAAAAT
Found at i:1563862 original size:16 final size:16
Alignment explanation
Indices: 1563839--1563879 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1563829 GTTCGGGTTC
*
1563839 TTTCGAGTTCGAGCTT
1 TTTCGAGTTCGAACTT
*
1563855 TTTTGAGTTCGAACTT
1 TTTCGAGTTCGAACTT
1563871 TTTCGAGTT
1 TTTCGAGTT
1563880 TGGGCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.49
Consensus pattern (16 bp):
TTTCGAGTTCGAACTT
Found at i:1566431 original size:25 final size:24
Alignment explanation
Indices: 1566403--1566454 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 24
1566393 CTGAAACTCT
1566403 GATTACAGCAGTTAATATAATCCAA
1 GATTACAGCAGTTAATATAA-CCAA
1566428 GATTACAGCAGTTAATATAACCAA
1 GATTACAGCAGTTAATATAACCAA
1566452 GAT
1 GAT
1566455 CCAGAGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.27
Consensus pattern (24 bp):
GATTACAGCAGTTAATATAACCAA
Found at i:1566593 original size:21 final size:21
Alignment explanation
Indices: 1566567--1566608 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1566557 TACTTGTGGG
*
1566567 GTTGACTTACAATAGCTTCTT
1 GTTGACTTAAAATAGCTTCTT
1566588 GTTGACTTAAAATAGCTTCTT
1 GTTGACTTAAAATAGCTTCTT
1566609 CCTCACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (21 bp):
GTTGACTTAAAATAGCTTCTT
Found at i:1566620 original size:21 final size:21
Alignment explanation
Indices: 1566577--1566622 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1566567 GTTGACTTAC
** * *
1566577 AATAGCTTCTTGTTGACTTAA
1 AATAGCTTCTTCCTCACTAAA
1566598 AATAGCTTCTTCCTCACTAAA
1 AATAGCTTCTTCCTCACTAAA
1566619 AATA
1 AATA
1566623 ACAGAGAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (21 bp):
AATAGCTTCTTCCTCACTAAA
Found at i:1579290 original size:32 final size:33
Alignment explanation
Indices: 1579247--1579308 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
1579237 TAGCCAAACT
**
1579247 TGTATCAATACACCAAGTA-TGTATCGATATAA
1 TGTATCAATACACCAAAAATTGTATCGATATAA
*
1579279 TGTATCGATACACCAAAAATTGTATCGATA
1 TGTATCAATACACCAAAAATTGTATCGATA
1579309 CATTGGCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (33 bp):
TGTATCAATACACCAAAAATTGTATCGATATAA
Found at i:1579367 original size:19 final size:20
Alignment explanation
Indices: 1579343--1579382 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1579333 GGCTATATTT
1579343 TCAAAAA-TGTATCGATACA
1 TCAAAAATTGTATCGATACA
1579362 TCAAAAATTGTATCGATACA
1 TCAAAAATTGTATCGATACA
1579382 T
1 T
1579383 TTACATGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
TCAAAAATTGTATCGATACA
Found at i:1581125 original size:13 final size:13
Alignment explanation
Indices: 1581107--1581132 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1581097 CAATTTTTTG
1581107 TGTATCGATACAT
1 TGTATCGATACAT
1581120 TGTATCGATACAT
1 TGTATCGATACAT
1581133 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1581144 original size:32 final size:33
Alignment explanation
Indices: 1581087--1581148 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1581077 TACAAGCCAA
**
1581087 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1581120 TGTATCGATAC-ATACTTTGTGTATCGATA
1 TGTATCGATACAATACTTTGTGTATCGATA
1581149 TAAGTTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1583729 original size:13 final size:13
Alignment explanation
Indices: 1583690--1583731 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1583680 TATAATCCCC
1583690 TTGTATCGATACA
1 TTGTATCGATACA
*
1583703 GTGTATCGATACA
1 TTGTATCGATACA
1583716 TTGTATCGATACA
1 TTGTATCGATACA
1583729 TTG
1 TTG
1583732 AATTTCCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1589809 original size:13 final size:13
Alignment explanation
Indices: 1589791--1589816 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1589781 CAATTTTTGG
1589791 TGTATCGATACAT
1 TGTATCGATACAT
1589804 TGTATCGATACAT
1 TGTATCGATACAT
1589817 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1589813 original size:33 final size:32
Alignment explanation
Indices: 1589771--1589834 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1589761 TACAAGCCAA
*
1589771 TGTATCGATACA-ATTTTTGGTGTATCGATACAT
1 TGTATCGATACATA-CTTT-GTGTATCGATACAT
1589804 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
1589835 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 15 0.52
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:1589831 original size:32 final size:33
Alignment explanation
Indices: 1589771--1589834 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1589761 TACAAGCCAA
*
1589771 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATCTTTGGTGTATCGATACAT
1589804 TGTATCGATAC-ATACTTT-GTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTGTATCGATACA
1589835 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCGATACAT
Found at i:1595329 original size:13 final size:13
Alignment explanation
Indices: 1595311--1595335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1595301 CATTTTTCTT
1595311 TGTATCGATACAC
1 TGTATCGATACAC
1595324 TGTATCGATACA
1 TGTATCGATACA
1595336 GGGGGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1595480 original size:21 final size:20
Alignment explanation
Indices: 1595456--1595502 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1595446 AAATCTTTTG
1595456 CAAAATACTT-ATTTTTCACTT
1 CAAAATACTTCATTTTTCA--T
* *
1595477 CAAATTACTTCGTTTTTCAT
1 CAAAATACTTCATTTTTCAT
1595497 CAAAAT
1 CAAAAT
1595503 CAGCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (20 bp):
CAAAATACTTCATTTTTCAT
Found at i:1597171 original size:23 final size:23
Alignment explanation
Indices: 1597115--1597175 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1597105 GGAGAAAATA
**
1597115 GATATGTGTGCAAATAAATTTTT
1 GATATGTGTGTGAATAAATTTTT
1597138 GATATGTGTGTGAATAAATTTTT
1 GATATGTGTGTGAATAAATTTTT
1597161 GATATGTGTGTGAAT
1 GATATGTGTGTGAAT
1597176 TACTTAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.44
Consensus pattern (23 bp):
GATATGTGTGTGAATAAATTTTT
Done.