Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold26
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: 1656043
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 334368 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:1526229 original size:20 final size:20
Alignment explanation
Indices: 1526204--1526280 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
1526194 ATCGATACAT
1526204 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
1526224 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
1526249 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
1526269 TGTATCGATACA
1 TGTATCGATACA
1526281 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:1528309 original size:15 final size:15
Alignment explanation
Indices: 1528289--1528319 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1528279 ATTTCGTTTG
*
1528289 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1528304 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1528319 G
1 G
1528320 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1532400 original size:13 final size:13
Alignment explanation
Indices: 1532382--1532407 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1532372 CAATTTTTTG
1532382 TGTATCGATACAT
1 TGTATCGATACAT
1532395 TGTATCGATACAT
1 TGTATCGATACAT
1532408 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1532492 original size:20 final size:20
Alignment explanation
Indices: 1532467--1532539 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1532457 CAACTTTTTT
1532467 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1532487 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1532508 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1532528 ATGTATCGATAC
1 ATGTATCGATAC
1532540 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1532505 original size:41 final size:41
Alignment explanation
Indices: 1532446--1532539 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1532436 CTGCCAAGAA
*
1532446 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1532487 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1532528 ATGTATCGATAC
1 ATGTATCGATAC
1532540 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1532521 original size:21 final size:21
Alignment explanation
Indices: 1532446--1532521 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1532436 CTGCCAAGAA
* *
1532446 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1532467 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1532487 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1532508 ATGTATCGATACAT
1 ATGTATCGATACAT
1532522 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1533900 original size:63 final size:61
Alignment explanation
Indices: 1533826--1533947 Score: 190
Period size: 63 Copynumber: 2.0 Consensus size: 61
1533816 TTTTTACAAT
*
1533826 TTGTATCGATACATTATTCACTGTATCGATACATTCTAGGTTTTACCCAGATGTATCGATATA
1 TTGTATCGATACATTATTCACTGTATCGATACATTC--GGGTTTACCCAGATGTATCGATATA
* * *
1533889 TTGTATCGATACATTGTTCATTGTATTGATACATTCGGGTTTACCCAGATGTATCGATA
1 TTGTATCGATACATTATTCACTGTATCGATACATTCGGGTTTACCCAGATGTATCGATA
1533948 CATTTTACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 22 0.40
63 33 0.60
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (61 bp):
TTGTATCGATACATTATTCACTGTATCGATACATTCGGGTTTACCCAGATGTATCGATATA
Found at i:1536330 original size:53 final size:51
Alignment explanation
Indices: 1536273--1536447 Score: 197
Period size: 51 Copynumber: 3.4 Consensus size: 51
1536263 ATTTTTAATC
* * *
1536273 TCGGGGATACTCCAACCCCGATTTTATCTCCAAAACATCAATTTTTTTCATAA
1 TCGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAA--TTTTTCACAA
* * * *
1536326 TCGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTCCACAA
1 TCGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAA
* * * * *
1536377 TTGGGGATACTCTAACTCCGATTTTATTTTTTAAACATCAATTTTTCACAA
1 TCGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAA
** *
1536428 TCGATGATACTTCAACCCCG
1 TCGGGGATACTCCAACCCCG
1536448 TTATTTCCAT
Statistics
Matches: 100, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
51 64 0.64
53 36 0.36
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (51 bp):
TCGGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAA
Found at i:1536503 original size:79 final size:78
Alignment explanation
Indices: 1536400--1536601 Score: 237
Period size: 79 Copynumber: 2.6 Consensus size: 78
1536390 AACTCCGATT
* * * *
1536400 TTATTTTTTAAACATCAATTTTTCACAATCGATGATACTTCAACCCCGTTA-TTTCCATGAGGAT
1 TTATTTCTAAAACAT-AAATTTTCACAATCGAGGATACTTCAACCCCGTTATTTTCCA-GAGGAT
1536464 ACTTCAACCCC-GACC
64 ACTTCAACCCCAG-CC
* * * * *
1536479 TTATTTCTAAAGCATAAAATTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATA
1 TTATTTCTAAAACAT-AAATTTTCACAATCGAGGATACTTCAACCCCGTTATTTTCCAGAGGATA
**
1536544 CTTCAACCCCAGTT
65 CTTCAACCCCAGCC
*
1536558 TTATTTCTAAAACATCAATTTTCCACAATCGAGGATACTTCAAC
1 TTATTTCTAAAACATAAATTTT-CACAATCGAGGATACTTCAAC
1536602 TCCAATTTTA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
78 6 0.06
79 92 0.88
80 6 0.06
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34
Consensus pattern (78 bp):
TTATTTCTAAAACATAAATTTTCACAATCGAGGATACTTCAACCCCGTTATTTTCCAGAGGATAC
TTCAACCCCAGCC
Found at i:1536600 original size:51 final size:52
Alignment explanation
Indices: 1536539--1536648 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 52
1536529 ATTTTCGAGG
* * *
1536539 GGATACTTCAACCCCAGTTTTATTTCTAAAAC-ATCAATTTTCCACAATCGA
1 GGATACTTCAACCCCAATTTTATTTCCAAAACAACCAATTTTCCACAATCGA
* * *
1536590 GGATACTTCAACTCCAATTTTATTTCCAAAACAACCAATTTTTCACAATCGG
1 GGATACTTCAACCCCAATTTTATTTCCAAAACAACCAATTTTCCACAATCGA
1536642 GGATACT
1 GGATACT
1536649 CCAATCCCGT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 29 0.56
52 23 0.44
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.33
Consensus pattern (52 bp):
GGATACTTCAACCCCAATTTTATTTCCAAAACAACCAATTTTCCACAATCGA
Found at i:1536817 original size:79 final size:78
Alignment explanation
Indices: 1536736--1537000 Score: 220
Period size: 79 Copynumber: 3.4 Consensus size: 78
1536726 AAATATTAAT
* **
1536736 TTTTC-ACAATCGGGAATACTCCAACCCTGCTATTTTCACGGGGATACTCCAACCCCGACCTTAT
1 TTTTCTACAATCGGGAATACTCCAACCCTGCTATTTTCA-GGGGATACTCCAACCTCGATTTTAT
1536800 TTCTATAGCATCGA
65 TTCTATAGCATCGA
* * * * * *
1536814 TTTTCTACAATTGGGGATGCTCTAA-CCT-CGTAATTTTTGAGGGAATACTCCAACCTCGATTTT
1 TTTTCTACAATCGGGAATACTCCAACCCTGC-T-A-TTTTCAGGGGATACTCCAACCTCGATTTT
* *
1536877 A-TTCTCATAACACCGA
63 ATTTCT-ATAGCATCGA
* * * *
1536893 TTTTCTATAATCAGGG-ATACTCTAACCCTGTTATTTCCAAGGGGATACTCCAACCTCGATTTTA
1 TTTTCTACAATC-GGGAATACTCCAACCCTGCTATTTTC-AGGGGATACTCCAACCTCGATTTTA
* *
1536957 TTT-TTTAGAACATAGA
64 TTTCTATAG--CATCGA
* *
1536973 TTTT-TCATAATCGGGAATATTCCAACCC
1 TTTTCT-ACAATCGGGAATACTCCAACCC
1537001 CGTTGTTATC
Statistics
Matches: 149, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
77 1 0.01
78 18 0.12
79 92 0.62
80 38 0.26
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (78 bp):
TTTTCTACAATCGGGAATACTCCAACCCTGCTATTTTCAGGGGATACTCCAACCTCGATTTTATT
TCTATAGCATCGA
Found at i:1549428 original size:6 final size:6
Alignment explanation
Indices: 1549417--1549452 Score: 51
Period size: 5 Copynumber: 6.5 Consensus size: 6
1549407 TTTTTTTAAA
1549417 AAAAAC AAAAAC AAAAA- AAAAAC -AAAAC -AAAAC AAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAA
1549453 GAAAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.54
6 13 0.46
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:1549436 original size:10 final size:10
Alignment explanation
Indices: 1549414--1549469 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
1549404 TCTTTTTTTT
*
1549414 AAAAA-AAAC
1 AAAAACAAAA
1549423 AAAAACAAAAA
1 AAAAAC-AAAA
1549434 AAAAACAAAA
1 AAAAACAAAA
*
1549444 CAAAACAAAGA
1 AAAAACAAA-A
* *
1549455 AAAAAGAGAA
1 AAAAACAAAA
1549465 AAAAA
1 AAAAA
1549470 GAACTTGCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
9 5 0.13
10 18 0.46
11 16 0.41
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:1549436 original size:17 final size:16
Alignment explanation
Indices: 1549414--1549448 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
1549404 TCTTTTTTTT
1549414 AAAAAAAACAAAAACAA
1 AAAAAAAAC-AAAACAA
1549431 AAAAAAAACAAAACAA
1 AAAAAAAACAAAACAA
1549447 AA
1 AA
1549449 CAAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAACAA
Found at i:1549448 original size:21 final size:21
Alignment explanation
Indices: 1549414--1549459 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1549404 TCTTTTTTTT
1549414 AAAAAAAACAAAAACAAAAAA
1 AAAAAAAACAAAAACAAAAAA
*
1549435 AAAACAAAAC-AAAACAAAGAA
1 AAAA-AAAACAAAAACAAAAAA
1549456 AAAA
1 AAAA
1549460 GAGAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAACAAAAAA
Found at i:1549464 original size:9 final size:8
Alignment explanation
Indices: 1549414--1549472 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 8
1549404 TCTTTTTTTT
1549414 AAAAAAA-
1 AAAAAAAG
* *
1549421 ACAAAAAC
1 AAAAAAAG
1549429 AAAAAAA-
1 AAAAAAAG
*
1549436 AAACAAAAC
1 AAA-AAAAG
1549445 AAAACAAAG
1 AAAA-AAAG
1549454 AAAAAAGAG
1 AAAAAA-AG
1549463 AAAAAAAG
1 AAAAAAAG
1549471 AA
1 AA
1549473 CTTGCTTAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
7 9 0.20
8 17 0.39
9 18 0.41
ACGTcount: A:0.85, C:0.08, G:0.07, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1549469 original size:21 final size:20
Alignment explanation
Indices: 1549414--1549469 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
1549404 TCTTTTTTTT
*
1549414 AAAAAA-AACAAAAACAAAA
1 AAAAAACAAAAAAAACAAAA
1549433 AAAAAACAAAACAAAACAAAGA
1 AAAAAACAAAA-AAAACAAA-A
*
1549455 AAAAAGAGAAAAAAA
1 AAAAA-ACAAAAAAA
1549470 GAACTTGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 3 0.10
21 8 0.26
22 9 0.29
23 5 0.16
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAACAAAAAAAACAAAA
Found at i:1550601 original size:61 final size:62
Alignment explanation
Indices: 1550501--1550914 Score: 505
Period size: 61 Copynumber: 6.9 Consensus size: 62
1550491 CTCAAAGAGC
* * * *
1550501 CCTTTTAAAGCCCACATAAATTAGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* *
1550562 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAACGAGCAGGACGCCTTTG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1550623 CCTTTCAAAGCCCATACAAAGCTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACAC-AAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * ***
1550686 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAGGAGCAGGATGCCTACG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1550747 CCTTTCAAAG-CC-CACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCC-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
1550805 -C----AAAGCCCACACAAGCTGGTGGTAC-CTTCTAGTCCTCAAGGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1550861 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCCCAAGGAGCAGGAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGAC
1550915 CTATTTCATT
Statistics
Matches: 307, Mismatches: 33, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
53 4 0.01
54 2 0.01
55 36 0.12
56 3 0.01
57 2 0.01
58 5 0.02
59 36 0.12
60 2 0.01
61 141 0.46
62 37 0.12
63 39 0.13
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (62 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1550752 original size:124 final size:121
Alignment explanation
Indices: 1550501--1550914 Score: 529
Period size: 124 Copynumber: 3.4 Consensus size: 121
1550491 CTCAAAGAGC
* * * *
1550501 CCTTTTAAAGCCCACATAAATTAGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1 CCTTTCAAAGCCCA-ACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
*
1550566 TTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAACGAGCAGGACGCCTTTG
65 TTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTG
* *
1550623 CCTTTCAAAGCCCATACAAAGCTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC
1 CCTTTCAAAGCCCA-AC-AAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC
* **
1550688 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGATGCCTACG
63 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTG
** * *
1550747 CCTTTCAAAGCCC-ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCC-TTT-C---
1 CCTTTCAAAGCCCAACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* * * *
1550806 -AAAGCCCACACAAGCTGGTGGTAC-CTTCTAGTCCTCAAGGAGCAGGACGCCTTTT
66 TAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAGGAGCAGGACGCCTTTG
* * *
1550861 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCCCAAGGAGCAGGAC
1 CCTTTCAAAGCCCA-ACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGAC
1550915 CTATTTCATT
Statistics
Matches: 258, Mismatches: 29, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
113 3 0.01
114 56 0.22
116 33 0.13
118 1 0.00
119 3 0.01
120 25 0.10
121 11 0.04
122 16 0.06
123 10 0.04
124 100 0.39
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (121 bp):
CCTTTCAAAGCCCAACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
TAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCAGGACGCCTTTG
Found at i:1551641 original size:13 final size:13
Alignment explanation
Indices: 1551623--1551671 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1551613 GATACATTTT
1551623 CATTGTATCGATA
1 CATTGTATCGATA
1551636 CATTGT-TC---A
1 CATTGTATCGATA
1551645 --TTGTATCGATA
1 CATTGTATCGATA
1551656 CATTGTATCGATA
1 CATTGTATCGATA
1551669 CAT
1 CAT
1551672 CCTGGGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 4 0.13
8 2 0.07
9 1 0.03
11 1 0.03
12 2 0.07
13 20 0.67
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1551661 original size:20 final size:19
Alignment explanation
Indices: 1551589--1551659 Score: 106
Period size: 20 Copynumber: 3.6 Consensus size: 19
1551579 TACCCAGATA
* *
1551589 TATCGATACATTTCCCACTG
1 TATCGATACATTT-TCATTG
1551609 TATCGATACATTTTCATTG
1 TATCGATACATTTTCATTG
1551628 TATCGATACATTGTTCATTG
1 TATCGATACATT-TTCATTG
1551648 TATCGATACATT
1 TATCGATACATT
1551660 GTATCGATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (19 bp):
TATCGATACATTTTCATTG
Found at i:1554075 original size:52 final size:53
Alignment explanation
Indices: 1554018--1554124 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 53
1554008 AATTTCTAGA
* * *
1554018 TTTTTCAT-CTCGAGGATACTCCAACCCCGGTTTTATCTCCAAAACATCAATT
1 TTTTTCATAATCGAGGATACTCCAACCCCAGTTTTATCTCCAAAACACCAATT
* * * **
1554070 TTTTTCATAATCGGGGATACTCTAACCCCAGTTTTATTTTTAAAACACCAATT
1 TTTTTCATAATCGAGGATACTCCAACCCCAGTTTTATCTCCAAAACACCAATT
1554123 TT
1 TT
1554125 CCACAATCGG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
52 8 0.17
53 38 0.83
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.38
Consensus pattern (53 bp):
TTTTTCATAATCGAGGATACTCCAACCCCAGTTTTATCTCCAAAACACCAATT
Found at i:1554088 original size:53 final size:50
Alignment explanation
Indices: 1554031--1554200 Score: 180
Period size: 50 Copynumber: 3.3 Consensus size: 50
1554021 TTCATCTCGA
* * *
1554031 GGATACTCCAACCCCGGTTTTATCTCCAAAACATCAATTTTTTTCATAATCGG
1 GGATACTCCAACCCCGGTTTTATTTTCAAAACA-CAA--TTTTTCACAATCGG
* * * *
1554084 GGATACTCTAACCCCAGTTTTATTTTTAAAACACCAATTTTCCACAATCGG
1 GGATACTCCAACCCCGGTTTTATTTTCAAAACA-CAATTTTTCACAATCGG
* * *
1554135 GG-TACTCCAACTCTGATTTTATTTTCAAAACACTAATTTTTCACAATCGG
1 GGATACTCCAACCCCGGTTTTATTTTCAAAACAC-AATTTTTCACAATCGG
* *
1554185 TGATACGCCAACCCCG
1 GGATACTCCAACCCCG
1554201 TTATTTCCAC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.01
50 40 0.42
51 24 0.25
53 31 0.32
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (50 bp):
GGATACTCCAACCCCGGTTTTATTTTCAAAACACAATTTTTCACAATCGG
Found at i:1554349 original size:79 final size:79
Alignment explanation
Indices: 1554133--1554746 Score: 320
Period size: 79 Copynumber: 7.8 Consensus size: 79
1554123 TTCCACAATC
* * * * *
1554133 GGGG-TACTCCAACTCTGATTTTATTT-TCAAAACACTAATTTTTCACAATC-GGTGATACGCCA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTCCACAATCAGG-GATACTCCA
*
1554195 ACCCCGTTA-TTTCCA
64 ACCCCGTTATTTTCGA
* * * ** * *
1554210 CAGAGATACTCTAACCCCGGCTTTATTTCTAAAGCATCAATTTTCCACAATC-GAGGATACTCCA
1 -GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCAG-GGATACTCCA
1554274 ACCCCGTTATTTTCGA
64 ACCCCGTTATTTTCGA
* *
1554290 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTTCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
* * *
1554355 TCCGATTTTATTTCCA
66 CCCG-TTAT-TTTCGA
* * ** * * ** *
1554371 ----A-A--ACAA--CCAATTTT-TCACAATCAGGGATACTCCAACCCTGTTGT-TTC-ATCGGG
1 GGGGATACTCCAACCCCGATTTTATTTC--T-A---AAACACCAA---T-TT-TCCACAATCAGG
* *
1554424 GATACTCCAACCCCCTTATTTCCGA
55 GATACTCCAACCCCGTTATTTTCGA
* * * ** *
1554449 GAGGATACTCCAACCCCGACTTTA-TTCTTAAAATATTAATTTTTCACAATCAGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTC-TAAAACACCAATTTTCCACAATCAGGGATACTCCAA
*
1554513 CCCCGCTATTTTC-A
65 CCCCGTTATTTTCGA
* * ** * * * * * * *
1554527 CGAGGACACTCCAACCCC-AGCCTTATTTCTATAGCATCGATTTTCCATAATCGGGGATGCTCCA
1 -GGGGATACTCCAACCCCGA-TTTTATTTCTAAAACACCAATTTTCCACAATCAGGGATACTCCA
*
1554591 ACCCCGTTATTTTTGA
64 ACCCCGTTATTTTCGA
* * * *
1554607 GGGGATACTCCAACCCTGATTTTA-TTCTCAAAACACCGATTTTCTATAAAT-AGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTCCA-CAATCAGGGATACTCCA
* *
1554670 ACCCTGTTATTTTCAA
64 ACCCCGTTATTTTCGA
* * * * *
1554686 GGGGATACTCCAACCCTGATTTTATTTTTTAAAACATCGATTTTCCATAATC-GGCGATACT
1 GGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACCAATTTTCCACAATCAGG-GATACT
1554747 TTAGCCCTAT
Statistics
Matches: 405, Mismatches: 90, Indels: 80
0.70 0.16 0.14
Matches are distributed among these distances:
71 2 0.00
72 7 0.02
73 1 0.00
74 4 0.01
76 1 0.00
77 9 0.02
78 15 0.04
79 280 0.69
80 56 0.14
81 11 0.03
82 6 0.01
83 1 0.00
85 4 0.01
86 1 0.00
87 7 0.02
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:1554360 original size:51 final size:52
Alignment explanation
Indices: 1554292--1554408 Score: 182
Period size: 51 Copynumber: 2.3 Consensus size: 52
1554282 ATTTTCGAGG
*
1554292 GGATACTCCAACCCCGATTTTATTTCTAAAAC-ACCAATTTTCCACAATCAA
1 GGATACTCCAACCCCGATTTTATTTCCAAAACAACCAATTTTCCACAATCAA
* * * *
1554343 GGATACTTCAACTCCGATTTTATTTCCAAAACAACCAATTTTTCACAATCAG
1 GGATACTCCAACCCCGATTTTATTTCCAAAACAACCAATTTTCCACAATCAA
1554395 GGATACTCCAACCC
1 GGATACTCCAACCC
1554409 TGTTGTTTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 29 0.50
52 29 0.50
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (52 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACAACCAATTTTCCACAATCAA
Found at i:1554445 original size:28 final size:27
Alignment explanation
Indices: 1554393--1554465 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
1554383 TTTCACAATC
** *
1554393 AGGGATACTCCAACCCTGTTGTTTCATCG
1 AGGGATACTCCAACCCCCTTATTTC--CG
1554422 -GGGATACTCCAACCCCCTTATTTCCG
1 AGGGATACTCCAACCCCCTTATTTCCG
1554448 AGAGGATACTCCAACCCC
1 AG-GGATACTCCAACCCC
1554466 GACTTTATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 36 0.92
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (27 bp):
AGGGATACTCCAACCCCCTTATTTCCG
Found at i:1554711 original size:158 final size:159
Alignment explanation
Indices: 1554418--1554746 Score: 378
Period size: 158 Copynumber: 2.1 Consensus size: 159
1554408 CTGTTGTTTC
* *
1554418 ATCGGGGATACTCCAACCCCCTTATTTCCGAGAGGATACTCCAACCCCGACTTTATTCTTAAAAT
1 ATCGGGGATACTCCAACCCCCTTATTTCCGAGAGGATACTCCAACCCCGACTTTATTCTCAAAAC
** * *
1554483 ATTAATTTTTCACAATCAGGGATACTCCAACCCCGCTATTTTCACGAGGACACTCCAACCCCAGC
66 ACCAATTTTTCAAAATCAGGGATACTCCAACCCCGCTATTTTCAAGAGGACACTCCAACCCCAGC
* *
1554548 CTTA-TTTCTATAGCATCGATTTTCCATA
131 CTTATTTTCTAAAACATCGATTTTCCATA
* * ** * * *
1554576 ATCGGGGATGCTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTGATTTTATTCTCAAAAC
1 ATCGGGGATACTCCAACCCCCTTATTTCCGAGAGGATACTCCAACCCCGACTTTATTCTCAAAAC
* * * * * *
1554641 ACCGA-TTTTCTATAAAT-AGGGATACTCCAACCCTGTTATTTTCAAGGGGATACTCCAA-CCCT
66 ACCAATTTTTC-A-AAATCAGGGATACTCCAACCCCGCTATTTTCAAGAGGACACTCCAACCCCA
** *
1554703 GATTTTATTTTTTAAAACATCGATTTTCCATA
129 G-CCTTATTTTCTAAAACATCGATTTTCCATA
*
1554735 ATCGGCGATACT
1 ATCGGGGATACT
1554747 TTAGCCCTAT
Statistics
Matches: 141, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
157 9 0.06
158 98 0.70
159 34 0.24
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (159 bp):
ATCGGGGATACTCCAACCCCCTTATTTCCGAGAGGATACTCCAACCCCGACTTTATTCTCAAAAC
ACCAATTTTTCAAAATCAGGGATACTCCAACCCCGCTATTTTCAAGAGGACACTCCAACCCCAGC
CTTATTTTCTAAAACATCGATTTTCCATA
Found at i:1561199 original size:20 final size:20
Alignment explanation
Indices: 1561176--1561248 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1561166 ACAACTCAAA
1561176 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1561196 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1561217 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1561237 GTATCGATACAT
1 GTATCGATACAT
1561249 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1561227 original size:41 final size:42
Alignment explanation
Indices: 1561176--1561270 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
1561166 ACAACTCAAA
*
1561176 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1561217 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1561259 GTATCGATACAT
1 GTATCGATACAT
1561271 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:1561327 original size:13 final size:13
Alignment explanation
Indices: 1561309--1561334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1561299 TACAGCAAGT
1561309 ATGTATCGATACA
1 ATGTATCGATACA
1561322 ATGTATCGATACA
1 ATGTATCGATACA
1561335 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1566183 original size:21 final size:22
Alignment explanation
Indices: 1566137--1566183 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1566127 CAAAAAAAAA
1566137 AAAAAGAGAAAAAGCAAAGAAT
1 AAAAAGAGAAAAAGCAAAGAAT
1566159 -AAAAGA-ATAAAAG-AAAGAAT
1 AAAAAGAGA-AAAAGCAAAGAAT
1566179 AAAAA
1 AAAAA
1566184 AACCATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (22 bp):
AAAAAGAGAAAAAGCAAAGAAT
Found at i:1567165 original size:20 final size:19
Alignment explanation
Indices: 1567142--1567190 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1567132 CACATTCAGA
* *
1567142 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CAT
*
1567162 TGTATCGATATATGATCAT
1 TGTATCGATACATGATCAT
1567181 TGTATCGATA
1 TGTATCGATA
1567191 TATGCACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:1567185 original size:19 final size:20
Alignment explanation
Indices: 1567142--1567194 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1567132 CACATTCAGA
* * *
1567142 TGTATCGATACATTATGCTT
1 TGTATCGATATATGATGCAT
1567162 TGTATCGATATATGAT-CAT
1 TGTATCGATATATGATGCAT
1567181 TGTATCGATATATG
1 TGTATCGATATATG
1567195 CACAATTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (20 bp):
TGTATCGATATATGATGCAT
Found at i:1568899 original size:15 final size:15
Alignment explanation
Indices: 1568879--1568913 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1568869 AACCATCAAA
1568879 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
1568894 GATGATGATGATAAT
1 GATGATGAAGATAAT
1568909 GATGA
1 GATGA
1568914 AGTTGACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:1572154 original size:20 final size:21
Alignment explanation
Indices: 1572129--1572170 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1572119 GAAATTTTCC
*
1572129 ATGATGTATCGATACAT-TGA
1 ATGATGTATCAATACATCTGA
1572149 ATGATGTATCAATACATCTGA
1 ATGATGTATCAATACATCTGA
1572170 A
1 A
1572171 AAAACCCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (21 bp):
ATGATGTATCAATACATCTGA
Found at i:1574721 original size:13 final size:13
Alignment explanation
Indices: 1574703--1574729 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1574693 ATATTATGCT
1574703 TTGTATCGATACA
1 TTGTATCGATACA
1574716 TTGTATCGATACA
1 TTGTATCGATACA
1574729 T
1 T
1574730 GATCAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1574741 original size:19 final size:19
Alignment explanation
Indices: 1574717--1574789 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
1574707 ATCGATACAT
1574717 TGTATCGATACATGATCAA
1 TGTATCGATACATGATCAA
*
1574736 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAA
1574755 TGTATCGATACATGCA-CAA
1 TGTATCGATACATG-ATCAA
1574774 TTGTATCGATACATGA
1 -TGTATCGATACATGA
1574790 AACTAGCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 35 0.70
20 15 0.30
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGATCAA
Found at i:1574765 original size:38 final size:39
Alignment explanation
Indices: 1574714--1574789 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
1574704 TGTATCGATA
1574714 CATTGTATCGATACATG-ATCAA-TGTATCGATACATGAT
1 CATTGTATCGATACATGCA-CAATTGTATCGATACATGAT
1574752 CATTGTATCGATACATGCACAATTGTATCGATACATGA
1 CATTGTATCGATACATGCACAATTGTATCGATACATGA
1574790 AACTAGCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
38 20 0.56
39 16 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (39 bp):
CATTGTATCGATACATGCACAATTGTATCGATACATGAT
Found at i:1574856 original size:13 final size:13
Alignment explanation
Indices: 1574838--1574862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1574828 CATGGCACAT
1574838 TGTATCGATACAA
1 TGTATCGATACAA
1574851 TGTATCGATACA
1 TGTATCGATACA
1574863 CGAATAATTG
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:1577429 original size:24 final size:24
Alignment explanation
Indices: 1577402--1577448 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1577392 GGGAAGATCT
*
1577402 AAACAAGCACCTTAAGAAGTTTCC
1 AAACAAACACCTTAAGAAGTTTCC
*
1577426 AAACAAACACCTTAAGGAGTTTC
1 AAACAAACACCTTAAGAAGTTTC
1577449 ATGTAGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (24 bp):
AAACAAACACCTTAAGAAGTTTCC
Found at i:1582311 original size:49 final size:50
Alignment explanation
Indices: 1582239--1582358 Score: 156
Period size: 49 Copynumber: 2.4 Consensus size: 50
1582229 TCAAAAGAAG
* *
1582239 TTTTGTACCTACCATTAAAATCAATCT-AAATCAACTCTTTTAAGGTTA-A
1 TTTTGTACCTATCATTAAAATCAA-CTAAAATCAACTATTTTAAGGTTAGA
* ** *
1582288 TTTTGTACCTATCATCAAAATCAACTAAAATTGAGTATTTTAAGGTTAGA
1 TTTTGTACCTATCATTAAAATCAACTAAAATCAACTATTTTAAGGTTAGA
1582338 -TTTGTACCTATCATTAAAATC
1 TTTTGTACCTATCATTAAAATC
1582359 GAGTTTTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
48 2 0.03
49 59 0.95
50 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (50 bp):
TTTTGTACCTATCATTAAAATCAACTAAAATCAACTATTTTAAGGTTAGA
Found at i:1582418 original size:49 final size:49
Alignment explanation
Indices: 1582353--1582495 Score: 164
Period size: 49 Copynumber: 2.9 Consensus size: 49
1582343 ACCTATCATT
* *
1582353 AAAATCGAGTTTTTTAGGGTTGGTTTTGTATTTTTTATCAAAAT-TAAT-
1 AAAATCGAGTTTTTTAGGGTTAGTTTTGTATTTTTTGTCAAAATCT-ATC
* * * *
1582401 AAAAGTTGAGTTTTTTAGGGTTTGTTTTATACTTTTTGTCAAAATCTATC
1 AAAA-TCGAGTTTTTTAGGGTTAGTTTTGTATTTTTTGTCAAAATCTATC
* *
1582451 AAAATCGTGTTTTTTTGGGGGTTAGTTTTGTATTTTTTGTCAAAA
1 AAAATCGAG-TTTTTT-AGGGTTAGTTTTGTATTTTTTGTCAAAA
1582496 CTGACATAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
48 4 0.05
49 40 0.51
50 11 0.14
51 24 0.30
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (49 bp):
AAAATCGAGTTTTTTAGGGTTAGTTTTGTATTTTTTGTCAAAATCTATC
Found at i:1589720 original size:142 final size:141
Alignment explanation
Indices: 1589281--1589768 Score: 637
Period size: 140 Copynumber: 3.5 Consensus size: 141
1589271 TAAAATTTTT
* * * *
1589281 TATACCCATACGGAAAACTATGAGAATATTAAAAATTTTGAAAAATTAAGATAATAA-TTTTATT
1 TATACCCCTACGGAAAACCATAAGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATT
* * ** *
1589345 TAATTTTTAA-TTTTAAAAAAATTTATTTTATACCTTAATGGAGAAC-GAAAAAGATATGAAATA
66 TAATTTTTAATTTTTAAAAAAA-TCATTTTGTACCTTAATGGAGAACTG-AAAAGATAAAAAATG
1589408 TTTTGAAGATTTC
129 TTTTGAAGATTTC
* * * *
1589421 TATACCCTTACGGAAAACCATAGGAATA-TAAGAAATCTTGAGAAAGTAAGAT-ATAATTTTTAT
1 TATACCCCTACGGAAAACCATAAGAATATTAA-AAATCTTGAAAAATTAAGATAATAATTTTTAT
* * * *
1589484 TTAATTTTTAATTTTTAAAAAATTCATTTTGTACCTTAATGGAGAAATGAAAATATAAAAAAAG-
65 TTAATTTTTAATTTTTAAAAAAATCATTTTGTACCTTAATGGAGAACTGAAAAGATAAAAAATGT
1589548 TTTGAAGATTTC
130 TTTGAAGATTTC
* *
1589560 TATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATT
1 TATACCCCTACGGAAAACCATAAGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATT
* * *
1589625 TAATTTTTAATTTTTAAGAAAAATCATTTCGTACTTTAATGGAGAACTGAAAAGATACAAAATGT
66 TAATTTTTAATTTTTAA-AAAAATCATTTTGTACCTTAATGGAGAACTGAAAAGATAAAAAATGT
*
1589690 TTTGAAGATTTT
130 TTTGAAGATTTC
** * * * *
1589702 TATACCCCTACAAAAAACCATAGGAATGTTAAAAATCTTGAGAAATTAAGATAATAATTTTCATT
1 TATACCCCTACGGAAAACCATAAGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATT
1589767 TA
66 TA
1589769 GTGATAAAAT
Statistics
Matches: 302, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
139 62 0.21
140 120 0.40
141 50 0.17
142 70 0.23
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (141 bp):
TATACCCCTACGGAAAACCATAAGAATATTAAAAATCTTGAAAAATTAAGATAATAATTTTTATT
TAATTTTTAATTTTTAAAAAAATCATTTTGTACCTTAATGGAGAACTGAAAAGATAAAAAATGTT
TTGAAGATTTC
Found at i:1590682 original size:21 final size:21
Alignment explanation
Indices: 1590658--1590703 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1590648 CTTTGCTTGA
1590658 TTTTCCTAT-TTTTTTATCTTT
1 TTTTCCT-TGTTTTTTATCTTT
* *
1590679 TTTTTCTTGTTTTTTCTCTTT
1 TTTTCCTTGTTTTTTATCTTT
1590700 TTTT
1 TTTT
1590704 TCTCTCCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCCTTGTTTTTTATCTTT
Found at i:1590704 original size:21 final size:21
Alignment explanation
Indices: 1590667--1590706 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1590657 ATTTTCCTAT
1590667 TTTTTTATCTTTTTTTTCTTG
1 TTTTTTATCTTTTTTTTCTTG
*
1590688 TTTTTTCTCTTTTTTTTCT
1 TTTTTTATCTTTTTTTTCT
1590707 CTCCCTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (21 bp):
TTTTTTATCTTTTTTTTCTTG
Found at i:1590705 original size:11 final size:11
Alignment explanation
Indices: 1590666--1590708 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
1590656 GATTTTCCTA
*
1590666 TTTTTTTATCT
1 TTTTTTTCTCT
1590677 TTTTTTTCT-T
1 TTTTTTTCTCT
*
1590687 GTTTTTTCTCT
1 TTTTTTTCTCT
1590698 TTTTTTTCTCT
1 TTTTTTTCTCT
1590709 CCCTTTTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:1591423 original size:165 final size:166
Alignment explanation
Indices: 1591194--1591573 Score: 441
Period size: 165 Copynumber: 2.3 Consensus size: 166
1591184 CAATATACAT
* * * * *
1591194 AAAAAATTAAAAA-TTCATG-AAATAAATTGAAATTTTT-AAAACTGATTCAATGGGAGTTTAAT
1 AAAAAATAAAAAACTT-ATGAAAATAAA-TG-AATTTTTCAAAACTGATTTAAAGAGAGTCTAAT
* * * *
1591256 GACAACATTAGATGAATTTTGAAAATTTTAAA-TCGA-AGAAAGTCCCCCCGAAAACATTTATGG
63 GACAACATTAGACGAATTTTAAAAATTTTAAACT-GAGA-AAAATCCCCCCAAAAACATTTATGG
* * ** *
1591319 GATAGAAAATTCAATTTTTCGAAAA-A-GAGGCATTTCAAGG
126 AATAGAAAATTCAATTTTACGAAAACAGGA-AAATTTCAAGA
*
1591359 AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTTATTTAAAGAGAGTCTAATGAC
1 AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTGATTTAAAGAGAGTCTAATGAC
* **
1591424 AATATTAGACGAATTTTAAAAATTTTAAACTGAGAAAAATCTTCCCAAAAACATTTATGGAATAG
66 AACATTAGACGAATTTTAAAAATTTTAAACTGAGAAAAATCCCCCCAAAAACATTTATGGAATAG
*** *
1591489 AAAATTTGGTTTTACGAAAACAGGAAAATTTTAAGA
131 AAAATTCAATTTTACGAAAACAGGAAAATTTCAAGA
* *
1591525 AAAAAATGAAAAACTTATGAAAATGAATGAATTTTTCAAAACTGATTTA
1 AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTGATTTA
1591574 CTATAAATTA
Statistics
Matches: 183, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
164 7 0.04
165 109 0.60
166 65 0.36
167 2 0.01
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (166 bp):
AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTGATTTAAAGAGAGTCTAATGAC
AACATTAGACGAATTTTAAAAATTTTAAACTGAGAAAAATCCCCCCAAAAACATTTATGGAATAG
AAAATTCAATTTTACGAAAACAGGAAAATTTCAAGA
Found at i:1591606 original size:166 final size:165
Alignment explanation
Indices: 1591194--1591658 Score: 433
Period size: 166 Copynumber: 2.8 Consensus size: 165
1591184 CAATATACAT
* * * * * *
1591194 AAAAAATTAAAAA-TTCATG-AAATAAATTGAAATTTTT-AAAACTGATTCAATGGGAGTTTAAT
1 AAAAAATAAAAAACTT-ATGAAAATAAA-TG-AATTTTTCAAAACTGATTTAAAGAGAATCTAAT
* * * *
1591256 GACAACATTAGATGAATTTTGAAAATTTTAAA-TCGA-AGAAAGTCCCCCCGAAAACATTTATGG
63 GACAATATTAGATGAATTTTAAAAATTTTAAACT-GAGA-AAAATCCCCCCAAAAACATTTATGG
* * ** *
1591319 GATAGAAAATTCAATTTTTCGAAAAAGAGGCATTTCAAGG
126 AATAGAAAATTCAATTTTACGAAAAAGAGAAATTTCAAGA
* *
1591359 AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTTATTTAAAGAGAGTCTAATGAC
1 AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTGATTTAAAGAGAATCTAATGAC
* **
1591424 AATATTAGACGAATTTTAAAAATTTTAAACTGAGAAAAATCTTCCCAAAAACATTTATGGAATAG
66 AATATTAGATGAATTTTAAAAATTTTAAACTGAGAAAAATCCCCCCAAAAACATTTATGGAATAG
*** *
1591489 AAAATTTGGTTTTACGAAAACAG-GAAAATTTTAAGA
131 AAAATTCAATTTTACGAAAA-AGAG-AAATTTCAAGA
* * * *
1591525 AAAAAATGAAAAACTTATGAAAATGAATGAATTTTTCAAAACTGATTTACTATA-AAT-TACATG
1 AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTGATTTA-AAGAGAATCTA-ATG
** * * ** * ** * * *
1591588 ATGATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCACCCTGAAAATATTTACGGAGT
64 ACAATATTAGATGAATTTTAAAAATTTTAAACTGAGAAAAATCCCCCCAAAAACATTTATGGAAT
1591653 AGAAAA
129 AGAAAA
1591659 CTCTGTATTT
Statistics
Matches: 249, Mismatches: 42, Indels: 17
0.81 0.14 0.06
Matches are distributed among these distances:
164 7 0.03
165 112 0.45
166 128 0.51
167 2 0.01
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (165 bp):
AAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTGATTTAAAGAGAATCTAATGAC
AATATTAGATGAATTTTAAAAATTTTAAACTGAGAAAAATCCCCCCAAAAACATTTATGGAATAG
AAAATTCAATTTTACGAAAAAGAGAAATTTCAAGA
Found at i:1591705 original size:166 final size:164
Alignment explanation
Indices: 1591350--1591975 Score: 465
Period size: 166 Copynumber: 3.8 Consensus size: 164
1591340 AAAAAGAGGC
* * *
1591350 ATTTCAAGGAAAAAATAAAAAACTTATGAAAATAAATGAATTTTTCAAAACTTATTTA-AAGAGA
1 ATTTCAAAGAAAAAATAAAAAACTTATGAAAAT-AATGAATTTTTCAAAACTGATTTACTAGA-A
* * * * ** *
1591414 GTCTAATGACAATATTAGACGAATTTTAAAAATTTTAAACTGAGAAAAATCTTCCC-AAAAACAT
64 AT-TAATGACAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATC-TCCCTAAAAAAAT
* * * * *
1591478 TTATGGAATAGAAAA-TTTGGT-TTTACGAAAACAGGAAA
127 TTACGGAGTAGAAAACTCT-GTATTT-CGAAAACAAGAGA
* * *
1591516 ATTT-TAAGAAAAAAATGAAAAACTTATGAAAATGAATGAATTTTTCAAAACTGATTTACTATAA
1 ATTTCAAAG-AAAAAATAAAAAACTTATGAAAAT-AATGAATTTTTCAAAACTGATTTACTAGAA
** * * *
1591580 ATTACATGATGATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCACCCTGAAAATATT
64 ATTA-ATGACAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCTCCCTAAAAAAATT
*
1591645 TACGGAGTAGAAAACTCTGTATTTCAAAAACAAGAGA
128 TACGGAGTAGAAAACTCTGTATTTCGAAAACAAGAGA
* ** *** * *
1591682 ATTTCAAAGAAAACAAT-AAAAACTCACAAAAATTAA--AAAAATTCAAAACTGATTAAAC-AGT
1 ATTTCAAAGAAAA-AATAAAAAACTTATGAAAA-TAATGAATTTTTCAAAACTGATT-TACTAGA
* * * * * * * * *
1591743 GATTAGATAATAATA-TTGAATGAATTGTAAAAATT-TTAATC-TGATGAAATCTTCCTAAAAAA
63 AATTA-ATGACAATATTTG-ATGAATTTTAAAAATTATAAACCAAGA-AAAATCTCCCTAAAAAA
* * *
1591805 ATTTACGAAGAAGAAAACTCCGTATTTCGAAAACAAGAAGA
125 ATTTACGGAGTAGAAAACTCTGTATTTCGAAAACAAG-AGA
* * * * *
1591846 A-TTCTAAGAGAAAAAT-AGAAA-TTCATGGAACAA-AATAAATTTTTCAAAACTGATTTAATGG
1 ATTTCAAAGA-AAAAATAAAAAACTT-AT-GAA-AATAATGAATTTTTCAAAACTGATTTACTAG
* * * * *
1591907 CAATTAAATGACAATATTTAATGAATTTTAAAAATTATAAACCAAGAAAAATCTTCTTAGAAAAA
62 AAATT-AATGACAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCTCCCTAAAAAAA
1591972 TTTA
126 TTTA
1591976 TAGAGCGGAA
Statistics
Matches: 362, Mismatches: 74, Indels: 48
0.75 0.15 0.10
Matches are distributed among these distances:
162 3 0.01
163 69 0.19
164 52 0.14
165 52 0.14
166 170 0.47
167 16 0.04
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (164 bp):
ATTTCAAAGAAAAAATAAAAAACTTATGAAAATAATGAATTTTTCAAAACTGATTTACTAGAAAT
TAATGACAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCTCCCTAAAAAAATTTAC
GGAGTAGAAAACTCTGTATTTCGAAAACAAGAGA
Found at i:1593206 original size:15 final size:15
Alignment explanation
Indices: 1593188--1593218 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1593178 TTGATGGAAA
1593188 AATCTAAAGCACTTG
1 AATCTAAAGCACTTG
*
1593203 AATCTAAAGCATTTG
1 AATCTAAAGCACTTG
1593218 A
1 A
1593219 TTTTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (15 bp):
AATCTAAAGCACTTG
Found at i:1593520 original size:110 final size:109
Alignment explanation
Indices: 1593391--1593630 Score: 322
Period size: 110 Copynumber: 2.2 Consensus size: 109
1593381 AAAATGTTTG
1593391 GTGGTATATCCAAAGCTTTTAATGGTGGTAA-TTGGAATAATTGTCAAAA-TATTTGGTGGTATA
1 GTGGTATATCCAAAGCTTTTAATGGTGGTAACTT-GAATAATTGT-AAAATTATTTGGTGGTATA
* *
1593454 TCCAAAACTTCTAGTGGTGGTAATCTAAAAAATTTTCAAAGTCTTTA
64 TCCAAAACTTCTAGTGGTAGTAA-CCAAAAAATTTTCAAAGTCTTTA
* ** * * *
1593501 GTGGTATATCCAAAACTTTTGGTGTTGGTAACTTGAATAATTGTAAAATTCTTTGGTGGTGTATC
1 GTGGTATATCCAAAGCTTTTAATGGTGGTAACTTGAATAATTGTAAAATTATTTGGTGGTATATC
* * * * *
1593566 CAAAGCTTCTTGTGGTAGTAACCGAAAAATTTTCAAAGTTTTTG
66 CAAAACTTCTAGTGGTAGTAACCAAAAAATTTTCAAAGTCTTTA
1593610 GTGGTATATCCAAAGCTTTTA
1 GTGGTATATCCAAAGCTTTTA
1593631 GTAGTAGTAA
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
109 42 0.37
110 69 0.61
111 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (109 bp):
GTGGTATATCCAAAGCTTTTAATGGTGGTAACTTGAATAATTGTAAAATTATTTGGTGGTATATC
CAAAACTTCTAGTGGTAGTAACCAAAAAATTTTCAAAGTCTTTA
Found at i:1593620 original size:54 final size:54
Alignment explanation
Indices: 1593387--1593661 Score: 268
Period size: 55 Copynumber: 5.0 Consensus size: 54
1593377 TAAAAAAATG
* * * * * *
1593387 TTTGGTGGTATATCCAAAGCTTTTAATGGTGGTAATTGGAATAATTGTCAAAATA
1 TTTGGTGGTATATCCAAAGCTTTTAGTGGTGGTAACT-GAAAAATTTTCAAAGTT
* * * *
1593442 TTTGGTGGTATATCCAAAACTTCTAGTGGTGGTAATCTAAAAAATTTTCAAAGTC
1 TTTGGTGGTATATCCAAAGCTTTTAGTGGTGGTAA-CTGAAAAATTTTCAAAGTT
* * * * * * *
1593497 TTTAGTGGTATATCCAAAACTTTTGGTGTTGGTAACTTGAATAATTGT-AAAATT
1 TTTGGTGGTATATCCAAAGCTTTTAGTGGTGGTAAC-TGAAAAATTTTCAAAGTT
* * *
1593551 CTTTGGTGGTGTATCCAAAGCTTCTT-GTGGTAGTAACCGAAAAATTTTCAAAGTT
1 -TTTGGTGGTATATCCAAAGCTT-TTAGTGGTGGTAACTGAAAAATTTTCAAAGTT
* * *
1593606 TTTGGTGGTATATCCAAAGCTTTTAGTAGTAGTAA-TAAAAAATTTTTCAAAGTT
1 TTTGGTGGTATATCCAAAGCTTTTAGTGGTGGTAACTGAAAAA-TTTTCAAAGTT
1593660 TT
1 TT
1593662 CAATGTTATA
Statistics
Matches: 182, Mismatches: 31, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
53 7 0.04
54 56 0.31
55 116 0.64
56 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (54 bp):
TTTGGTGGTATATCCAAAGCTTTTAGTGGTGGTAACTGAAAAATTTTCAAAGTT
Found at i:1593672 original size:54 final size:54
Alignment explanation
Indices: 1593557--1593672 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 54
1593547 AATTCTTTGG
* * * ***
1593557 TGGTGTATCCAAAGCTTCTTGTGGTAGTAACCGAAAAATTTTCAAAGTTTTTGG
1 TGGTATATCCAAAGCTTCTTGTAGTAGTAACCAAAAAATTTTCAAAGTTTTCAA
*
1593611 TGGTATATCCAAAGCTT-TTAGTAGTAGTAA-TAAAAAATTTTTCAAAGTTTTCAA
1 TGGTATATCCAAAGCTTCTT-GTAGTAGTAACCAAAAAA-TTTTCAAAGTTTTCAA
*
1593665 TGTTATAT
1 TGGTATAT
1593673 TCTAACCTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
53 7 0.13
54 45 0.87
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (54 bp):
TGGTATATCCAAAGCTTCTTGTAGTAGTAACCAAAAAATTTTCAAAGTTTTCAA
Found at i:1594661 original size:32 final size:33
Alignment explanation
Indices: 1594620--1594687 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1594610 GTAGCTAAAC
**
1594620 TTGTATCGATACA-CATAGTATGTATCAATACA
1 TTGTATCGATACACCATAAAATGTATCAATACA
*
1594652 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCAATACA
1594685 TTG
1 TTG
1594688 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:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCAATACA
Found at i:1594966 original size:33 final size:31
Alignment explanation
Indices: 1594929--1594992 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
1594919 TTTTCAAAGA
*
1594929 TCAAAGTGTTTTATATTTTTCAAGAGCT-TTTGT
1 TCAAAGTGTTAT-TA-TTTTCAA-AGCTCTTTGT
*
1594962 TCAAATTGTTATTATTTTCAAAGCTCTTTGT
1 TCAAAGTGTTATTATTTTCAAAGCTCTTTGT
1594993 ATTTGATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.14
31 12 0.43
32 2 0.07
33 10 0.36
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (31 bp):
TCAAAGTGTTATTATTTTCAAAGCTCTTTGT
Found at i:1598959 original size:28 final size:28
Alignment explanation
Indices: 1598908--1598979 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
1598898 AAAATCAGGA
*** * *
1598908 TTGGAGTATCCCCTCGGAAGTAACGGGG
1 TTGGAGTATCCCCGATGAAATAACGAGG
1598936 TTGGAGTATCCCCGATGAAATAACGAGG
1 TTGGAGTATCCCCGATGAAATAACGAGG
* *
1598964 TTAGAGTATCCTCGAT
1 TTGGAGTATCCCCGAT
1598980 TGTGAAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (28 bp):
TTGGAGTATCCCCGATGAAATAACGAGG
Found at i:1601405 original size:13 final size:13
Alignment explanation
Indices: 1601387--1601412 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1601377 ACAAAGATCC
1601387 ATGTATCGATACA
1 ATGTATCGATACA
1601400 ATGTATCGATACA
1 ATGTATCGATACA
1601413 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1601408 original size:33 final size:33
Alignment explanation
Indices: 1601366--1601432 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1601356 AAAATTTCCA
***
1601366 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1601399 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1601432 A
1 A
1601433 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1601492 original size:13 final size:13
Alignment explanation
Indices: 1601474--1601498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1601464 ACAATACTTA
1601474 TGTATCGATACAT
1 TGTATCGATACAT
1601487 TGTATCGATACA
1 TGTATCGATACA
1601499 AAACTTATGT
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:1604653 original size:52 final size:52
Alignment explanation
Indices: 1604583--1604703 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1604573 GAAAATTTAT
*
1604583 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1604635 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1604687 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1604704 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1604716 original size:52 final size:51
Alignment explanation
Indices: 1604583--1604723 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1604573 GAAAATTTAT
1604583 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1604635 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1604687 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1604724 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1604730 original size:13 final size:13
Alignment explanation
Indices: 1604712--1604736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1604702 CAAAGATCAG
1604712 TGTATCGATACAA
1 TGTATCGATACAA
1604725 TGTATCGATACA
1 TGTATCGATACA
1604737 TGTGAGTAAT
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:1604819 original size:13 final size:13
Alignment explanation
Indices: 1604801--1604825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1604791 CAAAAAAATA
1604801 TGTATCGATACAT
1 TGTATCGATACAT
1604814 TGTATCGATACA
1 TGTATCGATACA
1604826 ACATTTTATG
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:1604821 original size:33 final size:33
Alignment explanation
Indices: 1604779--1604845 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1604769 AGTAGCTTAA
1604779 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1604812 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1604845 A
1 A
1604846 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1605797 original size:175 final size:170
Alignment explanation
Indices: 1605423--1605803 Score: 439
Period size: 169 Copynumber: 2.2 Consensus size: 170
1605413 CCATTGTGCA
* * * *
1605423 GATTCAAGGCCTGCCACACTGGACTTAAAGATGATGAGGATGAAGAGCGATGAAAGGACCAATAT
1 GATTCAAGGCCAGCCACATTGGACTTAAAGATGAAGAGGATGAAAAGCGATGAAAGGACCAATAT
*
1605488 GTTGATTCACGGCCAACGATATTGGGTTTAAAGACGAGAAAAAGGATAAAAGAGCCAATATGCGG
66 GTTGATTCACGGCCAACGATATTGGGCTTAAAGACGAGAAAAAGGATAAAAGAGCCAATATGCGG
* * * *
1605553 CTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCT
131 CCAGCGACATTGAACTTAAAGATAAAGGTGCCAATATGCT
* * *
1605593 GATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGA-GAAAAGTGAT-AAA-GATGCCAAT
1 GATTCAAGGCCAGCCACATTGGACTTAAAGATGAAGAGGATGAAAAGCGATGAAAGGA--CCAAT
* * * * **
1605655 ATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGTCAATGTGCTGAT-
64 ATGTTGATTCACGGCCAACGATATTGGGCTTAAAGACGA-GAAAAAGGA--TAAAAGAGCCAATA
* *
1605719 T-CAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCT
126 TGC--GGCCAGCGACATTGAACTTAAAGAT---AAAGGTGCCAATATGCT
* *
1605768 GATTCAAGGCCAGCTATATTGGACTTAAAGATGAAG
1 GATTCAAGGCCAGCCACATTGGACTTAAAGATGAAG
1605804 GTGCCAATGT
Statistics
Matches: 179, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
167 2 0.01
168 3 0.02
169 50 0.28
170 45 0.25
171 1 0.01
172 29 0.16
175 49 0.27
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (170 bp):
GATTCAAGGCCAGCCACATTGGACTTAAAGATGAAGAGGATGAAAAGCGATGAAAGGACCAATAT
GTTGATTCACGGCCAACGATATTGGGCTTAAAGACGAGAAAAAGGATAAAAGAGCCAATATGCGG
CCAGCGACATTGAACTTAAAGATAAAGGTGCCAATATGCT
Found at i:1606197 original size:295 final size:292
Alignment explanation
Indices: 1605643--1606971 Score: 1970
Period size: 295 Copynumber: 4.5 Consensus size: 292
1605633 GAAAAGTGAT
* * * * * *
1605643 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGATGAAAAAGGATGTC
1 AAAG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-GATG---AAGG-TGCC
* * *
1605708 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATTC
58 AATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTC
1605773 AAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
123 AAGGCCAGCTATATTGGACTT--A-A--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
*
1605838 GACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A-AAGGTG
183 GACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTG
1605901 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
248 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
1605946 AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
* *
1606011 GAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAAAAGTGCCAATATGCTGATTCAAGGCCAG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
*
1606075 CTATATTGGGCTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
131 CTATATTGGACTTAA-----AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
1606140 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A-AAGGTGCCAATGT
191 GAT-AAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAATGT
*
1606203 GCTGAGTCAAGGCCAGCAACATTGGACTTAAAGATAAA
255 GCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
* * *
1606241 AAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCT
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
*
1606306 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
1606371 CTATATTGGACTT-AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAA
131 CTATATTGGACTTAAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAA
* * *
1606435 AAAAGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATGAAGGTGCCGATGTGC
196 AAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A-GAAGGTGCCAATGTGC
1606500 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
257 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
* * *
1606536 AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGCCAATGTGCT
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1606601 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
* *
1606666 CGATATTGGACTT-AAAGGTGCCAATGTGCTGAGTCAAAGCCAGCTACATTGGACTTAAAGATAA
131 CTATATTGGACTTAAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAA
*
1606730 AAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGC
196 AAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA---GAAGGTGCCAATGTGC
*
1606795 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAA
257 TGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAA
* *
1606832 AAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCT
1 AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
* *
1606891 GAGTCAAGGCCAGCTACATTGGACTTAAAG-TTG--AAGATGCCAATATGCTGATTCAAGGCCAG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
* *
1606953 CTATATTGGGCTTAGAAGG
131 CTATATTGGACTTAAAAGG
1606972 GTTGCCACCG
Statistics
Matches: 961, Mismatches: 50, Indels: 45
0.91 0.05 0.04
Matches are distributed among these distances:
287 39 0.04
288 4 0.00
289 43 0.04
290 94 0.10
291 1 0.00
292 1 0.00
293 2 0.00
294 93 0.10
295 554 0.58
296 86 0.09
299 4 0.00
300 1 0.00
301 2 0.00
302 33 0.03
303 4 0.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (292 bp):
AAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
CTATATTGGACTTAAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAA
AAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAG
TCAAGGCCAGCTACATTGGACTTAAAGATAAA
Found at i:1606278 original size:195 final size:194
Alignment explanation
Indices: 1605707--1606971 Score: 1884
Period size: 195 Copynumber: 6.5 Consensus size: 194
1605697 AAAAGGATGT
* * *
1605707 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATT
1605772 CAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATT
65 CAAGGCCAGCTATATTGGACTT--A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATT
1605837 GGACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A---AAG
126 GGACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAGTGAAG
1605898 GTGC
191 GTGC
* *
1605902 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTC
1605967 AAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
66 AAGGCCAGCTATATTGGACTT--A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
*
1606032 GACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAA
127 GACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA--GTGAA
1606097 GGTGC
190 GGTGC
1606102 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATT
* *
1606167 CAAGGCCAGCGATATTGGACTT-A-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCAACATTGGAC
65 CAAGGCCAGCTATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
*
1606230 TTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGT
130 TTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-GTGAAGGT
*
1606295 GT
193 GC
*
1606297 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATT
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATT
1606362 CAAGGCCAGCTATATTGGACTT-A-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
65 CAAGGCCAGCTATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
*
1606425 TTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATGAAGGT
130 TTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AAG-TGAAGGT
1606490 GC
193 GC
* * *
1606492 CGATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTC
*
1606557 AAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
66 AAGGCCAGCTATATTGGACTTAA----GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
* * *
1606622 GACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A---AAG
127 GACTTAAAGAT-AAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAGTGAAG
1606683 GTGC
191 GTGC
* * *
1606687 CAATGTGCTGAGTCAAAGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTC
* *
1606752 AAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAGCTACATTG
66 AAGGCCAGCTATATTGGACTT-AA---GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTG
* * *
1606817 GACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT-A---AAG
127 GACTTAAAGAT-AAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAGTGAAG
1606878 GTGC
191 GTGC
* *
1606882 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGTTG--AAGATGCCAATATGCTGATTC
1 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTC
*
1606945 AAGGCCAGCTATATTGGGCTT-AGAAGG
66 AAGGCCAGCTATATTGGACTTAAGAAGG
1606972 GTTGCCACCG
Statistics
Matches: 1011, Mismatches: 42, Indels: 41
0.92 0.04 0.04
Matches are distributed among these distances:
188 5 0.00
191 1 0.00
193 38 0.04
194 183 0.18
195 599 0.59
196 4 0.00
197 1 0.00
199 1 0.00
200 96 0.09
201 83 0.08
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (194 bp):
CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTC
AAGGCCAGCTATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
TAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAGTGAAGGTGC
Found at i:1606627 original size:490 final size:490
Alignment explanation
Indices: 1605698--1606966 Score: 2319
Period size: 490 Copynumber: 2.6 Consensus size: 490
1605688 AGATGATGAA
* * * * * *
1605698 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCGAT
1 AAAGG-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAAAAGTGCCAAT
* * *
1605763 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
64 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCTGAGTCAAGGCC
* * *
1605828 AGCTACATTGGACTTAAAGAT-AAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
129 AGCTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGAC
1605892 TTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAAT
194 TTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAAT
1605957 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
259 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
1606022 AGCTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCT
324 AGCTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCT
1606087 TAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGT
389 TAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGT
1606152 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
454 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
1606189 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCAACATTGGACTTAAAGATAAAAAAGTGCCAATAT
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
1606254 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAG
66 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAG
1606319 CTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT
131 CTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT
1606384 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
196 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
* *
1606449 GCTGATTCAAGGCTAGCTATATTGGACTTAAAGATGAAGGTGCCGATGTGCTGAGTCAAGGCCAG
261 GCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAG
1606514 CTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
326 CTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1606579 ATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
391 ATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1606644 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT
456 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
1606679 AAAGGTGCCAATGTGCTGAGTCAAAGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
1 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
1606744 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAG
66 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAG
1606809 CTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT
131 CTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT
** *
1606874 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAG-TTGAAGA-TGCCAATAT
196 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
*
1606937 GCTGATTCAAGGCCAGCTATATTGGGCTTA
261 GCTGATTCAAGGCCAGCTATATTGGACTTA
1606967 GAAGGGTTGC
Statistics
Matches: 755, Mismatches: 22, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
488 37 0.05
489 98 0.13
490 615 0.81
491 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (490 bp):
AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGTCAATGTGCTGAGTCAAGGCCAG
CTACATTGGACTTAAAGATGGAAAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT
AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAAAGTGCCAATAT
GCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAG
CTACATTGGACTTAAAGATAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
ATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
CAATATGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:1607010 original size:33 final size:35
Alignment explanation
Indices: 1606966--1607035 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
1606956 TATTGGGCTT
1606966 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
1607000 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
1607034 AG
1 AG
1607036 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:1607078 original size:34 final size:33
Alignment explanation
Indices: 1607040--1607983 Score: 621
Period size: 34 Copynumber: 28.6 Consensus size: 33
1607030 AGGAAGGGAG
*
1607040 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAA-GGAA
* *
1607074 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAG--GAA
* * * *
1607111 AAAGGTGCCACGGAGTTGTGGACTTACAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTA-AAAGGAA
*
1607145 AAA-AGTGCCACGGAGTTATGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
**
1607176 ---G-TGCCACGGAGTTGTGGGCTTAGGAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
*
1607205 AAAGAGTGCCACGGAGTTGTGGGCTT-TAA--AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
1607236 AGAG-TGCCACGGAGTCGTGGGCTTTGAAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * * * *
1607269 GAAGGTGCCATGGAGCTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
1607303 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
*
1607333 --AG-TGCCACGGAGTCGTGGGCTTTAAACA-GAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAA-AGGAA
*
1607364 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
* *
1607400 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
1607435 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
1607465 --AG-TGCCACGGAGTCGTGGTCTTTGAAAAGAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAG-GAA
*
1607498 AAAGAGTGTCACGGAGTTGTGGGCTTTAAACA-GAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAA-AGGAA
*
1607533 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
*
1607569 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAA-GAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
1607603 AAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
* **
1607637 AAAGGTGCCACGGAGTTGTGGGCTTAAGCGG--
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
1607668 ---G-TGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAA-AGGAA
* *
1607698 AAA-AGTGCCACAGAATTGTGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
1607729 ---G-TGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAA-AGGAA
* *
1607759 AAA-AGTGCCACGGAATTGTGGGCTTTAAA-GAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * * *
1607791 AAA-ATGCCACTGAGTTATGGACTTTGAGAGGAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAG-GAA
1607826 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACA-GAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAA-AGGAA
* * *
1607861 AAAGGTGCCACGGTGTTGTGGGCTTTGATAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-A-AAAGGAA
*
1607897 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
1607932 AAAGGTGCCACGGAGTTGTGGGCTTCAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
1607964 AAA-ATGCCACTGAGTCGTGG
1 AAAGATGCCACGGAGTTGTGG
1607984 ACTTTGAGAC
Statistics
Matches: 741, Mismatches: 94, Indels: 153
0.75 0.10 0.15
Matches are distributed among these distances:
27 97 0.13
28 14 0.02
29 22 0.03
30 2 0.00
31 34 0.05
32 20 0.03
33 63 0.09
34 260 0.35
35 64 0.09
36 62 0.08
37 103 0.14
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:1607095 original size:71 final size:68
Alignment explanation
Indices: 1607020--1607956 Score: 803
Period size: 71 Copynumber: 14.1 Consensus size: 68
1607010 CACCGACTTG
* * * * *
1607020 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTA-AAAGAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAA--GAAAAAGAGTGCCA
*
1607085 CAGAGT
63 CGGAGT
* * *
1607091 TGTGGGCTTTAAAAGAAAAAAAAGGTGCCACGGAGTTGTGGACTTACAGATGAAAAA-AGTGCCA
1 TGTGGGCTTTAAAAG-AGAAAAAGGTGCCACGGAGTTGTGGGCTTA-A-AAGAAAAAGAGTGCCA
1607155 CGGAGT
63 CGGAGT
* * *
1607161 TATGGGC-TT-AAA-AG-----GGTGCCACGGAGTTGTGGGCTTAGGAGGAAAAAGAGTGCCACG
1 TGTGGGCTTTAAAAGAGAAAAAGGTGCCACGGAGTTGTGGGCTTA-AAAGAAAAAGAGTGCCACG
1607218 GAGT
65 GAGT
* * *
1607222 TGTGGGCTTTAAAA-AG----A-GTGCCACGGAGTCGTGGGCTTTGAAAAGAAGAAG-GTGCCAT
1 TGTGGGCTTTAAAAGAGAAAAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGAAAAAGAGTGCCAC
*
1607280 GGAGC
64 GGAGT
* *
1607285 TGTGGGCTTTAAAA-AGAAGAAGGTGCCACGGAGTTGTGGGCTT------TAAAGAGTGCCACGG
1 TGTGGGCTTTAAAAGAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACGG
1607343 AGT
66 AGT
* *
1607346 CGTGGGCTTT-AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAAGAGAAAAAGGTGCCACGGAGTTGTGGGC-TT-AAAA--GAAAAAGAGTGCC
*
1607410 ACAGAGT
62 ACGGAGT
* *
1607417 TGTGGGCTTTAAAA-AGAAGAAGGTGCCACGGAGTTGTGGGCTT------TAAAGAGTGCCACGG
1 TGTGGGCTTTAAAAGAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACGG
1607475 AGT
66 AGT
* * *
1607478 CGTGGTCTTTGAAAAGAGAAAAAGAGTGTCACGGAGTTGTGGGCTTTAAACAGAAAAAG-GTGCC
1 TGTGGGCTTT-AAAAGAGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAA-AGAAAAAGAGTGCC
1607542 ACGGAGT
62 ACGGAGT
* *
1607549 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAG-GTGCCA
1 TGTGGGCTTT-AAAAGAGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGAAAAAGAGTGCCA
*
1607613 CAGAGT
63 CGGAGT
* *
1607619 TGTGGGCTTTAAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTT--AAG----CGGGTGCCACGG
1 TGTGGGCTTTAAAAGAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACGG
1607677 AGT
66 AGT
* * * *
1607680 TGTGGAC-TT-AAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTAAAAG-----G-GTGCCACG
1 TGTGGGCTTTAAAAGA-GAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACG
1607737 GAGT
65 GAGT
* * * * *
1607741 TGTGGAC-TT-AAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAGAAAAA-A-TGCCACT
1 TGTGGGCTTTAAAAGA-GAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACG
1607802 GAGT
65 GAGT
* * * *
1607806 TATGGACTTTGAGAGGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAG-GTGCC
1 TGTGGGCTTT-AAAAGAGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAA-AGAAAAAGAGTGCC
*
1607870 ACGGTGT
62 ACGGAGT
* *
1607877 TGTGGGCTTTGATAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCC
1 TGTGGGCTTT-AAAAGAGAAAAAG-GTGCCACGGAGTTGTGGGC-TT-AAAAGAAAAAGAGTGCC
1607941 ACGGAGT
62 ACGGAGT
1607948 TGTGGGCTT
1 TGTGGGCTT
1607957 CAAAGAAAAA
Statistics
Matches: 739, Mismatches: 69, Indels: 116
0.80 0.07 0.13
Matches are distributed among these distances:
59 3 0.00
60 17 0.02
61 210 0.28
62 9 0.01
63 59 0.08
64 30 0.04
65 19 0.03
66 5 0.01
67 27 0.04
68 49 0.07
69 10 0.01
70 59 0.08
71 230 0.31
72 11 0.01
73 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (68 bp):
TGTGGGCTTTAAAAGAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGAGTGCCACGG
AGT
Found at i:1607213 original size:61 final size:63
Alignment explanation
Indices: 1607108--1607459 Score: 233
Period size: 61 Copynumber: 5.4 Consensus size: 63
1607098 TTTAAAAGAA
* * *
1607108 AAAAAAGGTGCCACGGAGTTGTGGACTTACAGATGAAAAAAGTGCCACGGAGTTATGGGC-TT
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTACAGAGGAAAAAAGTGCCACGGAGTTATGGGCTTT
* *
1607170 -AAAAGGGTGCCACGGAGTTGTGGGCTTA-GGAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTACAGAGGAAAAA-AGTGCCACGGAGTTATGGGCTTT
* * ** * * * * * * *
1607232 AAAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAAGAAGGTGCCATGGAGCTGTGGGCTTT
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTACAGAGGAAAAAAGTGCCACGGAGTTATGGGCTTT
**
1607295 AAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTA-A-A-G-----AGTGCCACGGAGTCGTGGG
1 --AAA-AAG--GGTGCCACGGAGTTGTGGGC-TTACAGAGGAAAAAAGTGCCACGGAGTTATGGG
1607352 CTTT
60 CTTT
* * * *
1607356 AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA-AAAGGGAAAAAGAGTGCCACAGAGTTGT
1 ----A-AAAAGGGTGCCACGGAGTTGTGGGC-TT-ACAGA-GGAAAAA-AGTGCCACGGAGTTAT
1607420 GGGCTTT
57 GGGCTTT
1607427 AAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTT
1 --AAA-AAG--GGTGCCACGGAGTTGTGGGCTT
1607460 TAAAGAGTGC
Statistics
Matches: 236, Mismatches: 28, Indels: 44
0.77 0.09 0.14
Matches are distributed among these distances:
60 8 0.03
61 87 0.37
62 4 0.02
63 50 0.21
64 8 0.03
65 4 0.02
66 4 0.02
67 1 0.00
68 21 0.09
69 6 0.03
70 2 0.01
71 41 0.17
ACGTcount: A:0.30, C:0.14, G:0.36, T:0.20
Consensus pattern (63 bp):
AAAAAGGGTGCCACGGAGTTGTGGGCTTACAGAGGAAAAAAGTGCCACGGAGTTATGGGCTTT
Found at i:1607345 original size:27 final size:27
Alignment explanation
Indices: 1607307--1607358 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1607297 AAAGAAGAAG
*
1607307 GTGCCACGGAGTTGTGGGCTTTAAAGA
1 GTGCCACGGAGTCGTGGGCTTTAAAGA
1607334 GTGCCACGGAGTCGTGGGCTTTAAA
1 GTGCCACGGAGTCGTGGGCTTTAAA
1607359 CAGAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.37, T:0.25
Consensus pattern (27 bp):
GTGCCACGGAGTCGTGGGCTTTAAAGA
Found at i:1609657 original size:55 final size:55
Alignment explanation
Indices: 1609573--1609973 Score: 614
Period size: 55 Copynumber: 7.3 Consensus size: 55
1609563 AAAGTGTATT
* * *
1609573 CTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTC
1 CTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
*
1609628 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTC
1 CTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTC
1609683 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
* *
1609738 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTCTGGGCTTTGAGAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
* *
1609793 CTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1609848 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
1 CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
* * * *
1609903 CTGCTCTTTGAGGAC-CGAAAGGTGCCACTAATTTGTGTGGGCTTT-AAGAGGTGTC
1 CTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTC
1609958 CTGCTCTTTGAGGACT
1 CTGCTCTTTGAGGACT
1609974 AAAAAGCGGA
Statistics
Matches: 322, Mismatches: 17, Indels: 13
0.91 0.05 0.04
Matches are distributed among these distances:
54 8 0.02
55 308 0.96
56 6 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (55 bp):
CTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTC
Found at i:1609758 original size:27 final size:27
Alignment explanation
Indices: 1609618--1609758 Score: 65
Period size: 28 Copynumber: 5.1 Consensus size: 27
1609608 TGTGGGCTTT
*
1609618 GAAAGGCGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
** * * * *
1609644 GAAAGGTG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
1609672 TAAGAGGTGTCCTGCTCTTTGAGGACTG
1 GAA-AGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1609700 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1609728 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
1609755 GAAA
1 GAAA
1609759 ATGCCACCAA
Statistics
Matches: 77, Mismatches: 28, Indels: 19
0.62 0.23 0.15
Matches are distributed among these distances:
25 6 0.08
26 15 0.19
27 17 0.22
28 20 0.26
29 13 0.17
30 6 0.08
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1610958 original size:7 final size:6
Alignment explanation
Indices: 1610939--1611027 Score: 50
Period size: 6 Copynumber: 15.3 Consensus size: 6
1610929 CTTAAGCAGG
* *
1610939 TTCTTT TTCTTT TCTCTTT TT-TTCT TTGTTT TGT-TTT TT-TTGT TT-TGT
1 TTCTTT TTCTTT T-TCTTT TTCTT-T TTCTTT T-TCTTT TTCTT-T TTCTTT
*
1610987 TT-TTT TTCTTT TT-TTT TTGCTCT TT-TTT TTCTTT TT-TTT TT
1 TTCTTT TTCTTT TTCTTT TT-CTTT TTCTTT TTCTTT TTCTTT TT
1611028 TTGAAGAGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 19
0.75 0.04 0.20
Matches are distributed among these distances:
5 26 0.37
6 31 0.44
7 13 0.19
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:1610959 original size:1 final size:1
Alignment explanation
Indices: 1610955--1611029 Score: 60
Period size: 1 Copynumber: 75.0 Consensus size: 1
1610945 TTCTTTTCTC
* * * * * * ** * *
1610955 TTTTTTTCTTTGTTTTGTTTTTTTTGTTTTGTTTTTTTTCTTTTTTTTTTGCTCTTTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1611020 TTTTTTTTTT
1 TTTTTTTTTT
1611030 GAAGAGAAGG
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.87
Consensus pattern (1 bp):
T
Found at i:1610978 original size:32 final size:32
Alignment explanation
Indices: 1610942--1611030 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
1610932 AAGCAGGTTC
1610942 TTTTTCTTTTCTCTTTTTTTCTTTGTTTTGTTT
1 TTTTTCTTTTCT-TTTTTTTCTTTGTTTTGTTT
* *
1610975 TTTTTGTTTTGTTTTTTTTCTTT-TTTT-TTT
1 TTTTTCTTTTCTTTTTTTTCTTTGTTTTGTTT
*
1611005 GCTCTTTT-TTTTCTTTTTTTTTTTTG
1 --T-TTTTCTTTTCTTTTTTTTCTTTG
1611031 AAGAGAAGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
30 3 0.06
31 4 0.08
32 27 0.56
33 14 0.29
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (32 bp):
TTTTTCTTTTCTTTTTTTTCTTTGTTTTGTTT
Found at i:1610993 original size:23 final size:22
Alignment explanation
Indices: 1610942--1611029 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 22
1610932 AAGCAGGTTC
1610942 TTTTTCTTTTCTCTTTTTTTCTTT
1 TTTTTCTTTT-T-TTTTTTTCTTT
* * *
1610966 GTTTTGTTTTTTTTGTTTTGTTT
1 TTTTTCTTTTTTTT-TTTTCTTT
*
1610989 TTTTTCTTTTTTTTTTGCTCTTT
1 TTTTTCTTTTTTTTTT-TTCTTT
1611012 TTTTTCTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTTT
1611030 GAAGAGAAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
22 6 0.11
23 40 0.74
24 8 0.15
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (22 bp):
TTTTTCTTTTTTTTTTTTCTTT
Found at i:1611010 original size:14 final size:13
Alignment explanation
Indices: 1610940--1611030 Score: 82
Period size: 14 Copynumber: 7.0 Consensus size: 13
1610930 TTAAGCAGGT
* *
1610940 TCTTTTTCTTTTC
1 TCTTTTTTTTTTG
1610953 TCTTTTTTTCTTTG
1 TCTTTTTTT-TTTG
*
1610967 TTTTGTTTTTTTTG
1 TCTT-TTTTTTTTG
1610981 T-TTTGTTTTTTT-
1 TCTTT-TTTTTTTG
1610993 TCTTTTTTTTTTG
1 TCTTTTTTTTTTG
*
1611006 CTCTTTTTTTTCT-
1 -TCTTTTTTTTTTG
1611019 T-TTTTTTTTTTG
1 TCTTTTTTTTTTG
1611031 AAGAGAAGGT
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.14
12 10 0.15
13 20 0.30
14 22 0.33
15 5 0.08
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.84
Consensus pattern (13 bp):
TCTTTTTTTTTTG
Found at i:1614212 original size:8 final size:8
Alignment explanation
Indices: 1614195--1614226 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1614185 ATTTGATTAA
1614195 ATTTTGTG
1 ATTTTGTG
*
1614203 ATTTTATG
1 ATTTTGTG
1614211 ATTTTGTG
1 ATTTTGTG
1614219 ATTTTGTG
1 ATTTTGTG
1614227 TTGAATGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1614454 original size:12 final size:13
Alignment explanation
Indices: 1614430--1614467 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1614420 ACATAATTCT
1614430 TTGTATCGATACA
1 TTGTATCGATACA
1614443 TTGTAT-GATACA
1 TTGTATCGATACA
*
1614455 CTGTATCGATACA
1 TTGTATCGATACA
1614468 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1615153 original size:54 final size:54
Alignment explanation
Indices: 1615085--1615203 Score: 229
Period size: 54 Copynumber: 2.2 Consensus size: 54
1615075 GAATCCGCAA
*
1615085 AACCAAACCTTCTTCGAAGGTTGTTTCCGAACATAAGCCAACCTCGACCATTTC
1 AACCGAACCTTCTTCGAAGGTTGTTTCCGAACATAAGCCAACCTCGACCATTTC
1615139 AACCGAACCTTCTTCGAAGGTTGTTTCCGAACATAAGCCAACCTCGACCATTTC
1 AACCGAACCTTCTTCGAAGGTTGTTTCCGAACATAAGCCAACCTCGACCATTTC
1615193 AACCGAACCTT
1 AACCGAACCTT
1615204 TTCCCGGTTG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.25
Consensus pattern (54 bp):
AACCGAACCTTCTTCGAAGGTTGTTTCCGAACATAAGCCAACCTCGACCATTTC
Found at i:1617074 original size:13 final size:13
Alignment explanation
Indices: 1617056--1617080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1617046 ACACATAGTA
1617056 TGTATCGATACAT
1 TGTATCGATACAT
1617069 TGTATCGATACA
1 TGTATCGATACA
1617081 CCATAAAATG
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:1617077 original size:32 final size:33
Alignment explanation
Indices: 1617036--1617103 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1617026 GTAGCTAAAC
**
1617036 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1617068 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1617101 TTG
1 TTG
1617104 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:1622444 original size:18 final size:18
Alignment explanation
Indices: 1622400--1622451 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1622390 TTCTTTAATC
1622400 ATTTTCTTTA-ATATA-G
1 ATTTTCTTTATATATATG
* *
1622416 TTTCTTTTTTATATATATG
1 ATT-TTCTTTATATATATG
1622435 ATTTTCTTTATATATAT
1 ATTTTCTTTATATATAT
1622452 TTAATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 18 0.62
19 3 0.10
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (18 bp):
ATTTTCTTTATATATATG
Found at i:1622977 original size:13 final size:13
Alignment explanation
Indices: 1622959--1622984 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1622949 TTTTACAATT
1622959 TGTATCGATACAA
1 TGTATCGATACAA
1622972 TGTATCGATACAA
1 TGTATCGATACAA
1622985 AACTACTCTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1625408 original size:27 final size:27
Alignment explanation
Indices: 1625378--1625443 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
1625368 TATCATCATC
1625378 GGGGGCACTCCAACCTCATTCCTCCGA
1 GGGGGCACTCCAACCTCATTCCTCCGA
*
1625405 GGGGGCACTCCAACCTCATTTCTCCGA
1 GGGGGCACTCCAACCTCATTCCTCCGA
*
1625432 GGGGACACTCCA
1 GGGGGCACTCCA
1625444 TCCCCGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.38, G:0.24, T:0.18
Consensus pattern (27 bp):
GGGGGCACTCCAACCTCATTCCTCCGA
Found at i:1637049 original size:39 final size:39
Alignment explanation
Indices: 1636920--1637068 Score: 126
Period size: 39 Copynumber: 3.8 Consensus size: 39
1636910 AAAATAGAGT
* * * *
1636920 CTTTTAAGTTTAGTTTTGTACCTTCGATTGAGATTGAGC
1 CTTTTTAGTTTAGTTTTATACCTTCTATCGAGATTGAGC
* * * * *
1636959 CTTTTAAAGTTTAGTTTCATACTTTTTGTCGA-AGTTGAG-
1 CTTTT-TAGTTTAGTTTTATACCTTCTATCGAGA-TTGAGC
*
1636998 -TTTATTAGGTTTAGTTTTATACCTTCTATTGAGATCT-AGC
1 CTTT-TTA-GTTTAGTTTTATACCTTCTATCGAGAT-TGAGC
*
1637038 CTTTTTAGTTTAGTTTCATACCTTCTATCGA
1 CTTTTTAGTTTAGTTTTATACCTTCTATCGA
1637069 AACCAAGCCT
Statistics
Matches: 87, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
38 4 0.05
39 51 0.59
40 29 0.33
41 3 0.03
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.49
Consensus pattern (39 bp):
CTTTTTAGTTTAGTTTTATACCTTCTATCGAGATTGAGC
Found at i:1637101 original size:79 final size:78
Alignment explanation
Indices: 1637000--1637405 Score: 308
Period size: 79 Copynumber: 5.2 Consensus size: 78
1636990 AAGTTGAGTT
* *
1637000 TATTAGGTTTAGTTTTATACCTTCTATTGAGATCTAGCCTTTTTAGTTTAGTTTCATACCTTCTA
1 TATTAGGTTTAGTTTCATACCTTCTATTAAGATCTAGCCTTTTTAGTTTAGTTTCATACCTTCTA
* *
1637065 TCGAAACCAAGCC
66 TCAAAACCAAGTC
* ** * ** * * *
1637078 TATTAGGTTTAGTTTTCAGACCTTCTATCCAGA-C-CG-AATCTAAGTTTAGTTTCATACCTGCC
1 TATTAGGTTTAG-TTTCATACCTTCTATTAAGATCTAGCCTTTTTAGTTTAGTTTCATACCT-TC
1637140 T-TCAAAACCAAGTAC
64 TATCAAAACCAAGT-C
* * * * * * *
1637155 -AATAGG-TTAGTTTCATACCTTTTGTTGAGAGT-AATCCTTTTTAAGTTTAGTTTTATACCTTC
1 TATTAGGTTTAGTTTCATACCTTCTATTAAGA-TCTAGCCTTTTT-AGTTTAGTTTCATACCTTC
* *
1637217 CATCAAAACCAAGTT
64 TATCAAAACCAAGTC
* * * * * *
1637232 TGTTAGGTTTAGTTTCATACTTTTTGTTAAGA-CTGAGTCTTTTTAAGTTTAGTTTCATACCTTT
1 TATTAGGTTTAGTTTCATACCTTCTATTAAGATCT-AGCCTTTTT-AGTTTAGTTTCATACCTTC
* **
1637296 TGTTGAAACCAAGTC
64 TATCAAAACCAAGTC
* * * * *
1637311 TATTAGGTTTAGTTTCATACCTTCTATCAAAATCGAGCCTATTAAGTTTAGTTTCATA-CTATCT
1 TATTAGGTTTAGTTTCATACCTTCTATTAAGATCTAGCCTTTTTAGTTTAGTTTCATACCT-TCT
* * *
1637375 GTCAAAACGAAATC
65 ATCAAAACCAAGTC
* *
1637389 CATTAGTTTTAGTTTCA
1 TATTAGGTTTAGTTTCA
1637406 CAGCTTTTGT
Statistics
Matches: 254, Mismatches: 59, Indels: 30
0.74 0.17 0.09
Matches are distributed among these distances:
74 15 0.06
75 4 0.02
76 34 0.13
77 9 0.04
78 86 0.34
79 105 0.41
80 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.42
Consensus pattern (78 bp):
TATTAGGTTTAGTTTCATACCTTCTATTAAGATCTAGCCTTTTTAGTTTAGTTTCATACCTTCTA
TCAAAACCAAGTC
Found at i:1637380 original size:39 final size:39
Alignment explanation
Indices: 1637035--1637436 Score: 178
Period size: 39 Copynumber: 10.3 Consensus size: 39
1637025 ATTGAGATCT
* * * *
1637035 AGCCTTTTTAGTTTAGTTTCATACCTTCTATCGAAACCA
1 AGCCTATTAAGTTTAGTTTCATACCTTCTGTCAAAACCA
* * * * *
1637074 AGCCTATTAGGTTTAGTTTTCAGACCTTCTATCCAGACCGA
1 AGCCTATTAAGTTTAG-TTTCATACCTTCTGTCAAAACC-A
* *
1637115 A---T-CTAAGTTTAGTTTCATACCTGCCT-TCAAAACCA
1 AGCCTATTAAGTTTAGTTTCATACCT-TCTGTCAAAACCA
** * * ** * **
1637150 AG--TACAATAGGTTAGTTTCATACCTTTTGTTGAGAGTA
1 AGCCTATTA-AGTTTAGTTTCATACCTTCTGTCAAAACCA
* * * **
1637188 ATCCTTTTTAAGTTTAGTTTTATACCTTCCATCAAAACCA
1 AGCC-TATTAAGTTTAGTTTCATACCTTCTGTCAAAACCA
** * * * * * * **
1637228 AGTTTGTTAGGTTTAGTTTCATACTTTTTGTTAAGACTG
1 AGCCTATTAAGTTTAGTTTCATACCTTCTGTCAAAACCA
* * * **
1637267 AGTCTTTTTAAGTTTAGTTTCATACCTTTTGTTGAAACCA
1 AG-CCTATTAAGTTTAGTTTCATACCTTCTGTCAAAACCA
* * * * *
1637307 AGTCTATTAGGTTTAGTTTCATACCTTCTATCAAAATCG
1 AGCCTATTAAGTTTAGTTTCATACCTTCTGTCAAAACCA
*
1637346 AGCCTATTAAGTTTAGTTTCATA-CTATCTGTCAAAACGAA
1 AGCCTATTAAGTTTAGTTTCATACCT-TCTGTCAAAAC-CA
* * * *
1637386 ATCC-ATT-AGTTTTAGTTTCACAGCTTTTGTCAAAACCGA
1 AGCCTATTAAG-TTTAGTTTCATACCTTCTGTCAAAACC-A
*
1637425 ACCCT-TTAAGTT
1 AGCCTATTAAGTT
1637437 CAATTTTGTA
Statistics
Matches: 267, Mismatches: 78, Indels: 36
0.70 0.20 0.09
Matches are distributed among these distances:
35 2 0.01
36 16 0.06
37 13 0.05
38 26 0.10
39 128 0.48
40 78 0.29
41 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (39 bp):
AGCCTATTAAGTTTAGTTTCATACCTTCTGTCAAAACCA
Found at i:1639392 original size:22 final size:22
Alignment explanation
Indices: 1639370--1639446 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 22
1639360 AACATAACTC
1639370 CCCTTTAATTAAAAATTTTC-T
1 CCCTTTAATTAAAAATTTTCTT
*
1639391 CCCTATTAATAAAAAAATTTTCTT
1 CCCT-TTAAT-TAAAAATTTTCTT
1639415 CCCTTTAA-T-AAAA-TTTCTT
1 CCCTTTAATTAAAAATTTTCTT
1639434 CCCTTT--TTAAAAA
1 CCCTTTAATTAAAAA
1639447 ATATCTCTCC
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.02
19 16 0.33
20 4 0.08
21 4 0.08
22 5 0.10
23 14 0.29
24 5 0.10
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.44
Consensus pattern (22 bp):
CCCTTTAATTAAAAATTTTCTT
Found at i:1639406 original size:23 final size:23
Alignment explanation
Indices: 1639370--1639427 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1639360 AACATAACTC
*
1639370 CCCTTTAAT-TAAAAATTTTC-T
1 CCCTTTAATAAAAAAATTTTCTT
1639391 CCCTATTAATAAAAAAATTTTCTT
1 CCCT-TTAATAAAAAAATTTTCTT
1639415 CCCTTTAATAAAA
1 CCCTTTAATAAAA
1639428 TTTCTTCCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 19 0.58
24 5 0.15
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (23 bp):
CCCTTTAATAAAAAAATTTTCTT
Found at i:1642889 original size:13 final size:13
Alignment explanation
Indices: 1642871--1642896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1642861 TACACAAAGT
1642871 ATGTATCGATACA
1 ATGTATCGATACA
1642884 ATGTATCGATACA
1 ATGTATCGATACA
1642897 CCAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1642894 original size:32 final size:33
Alignment explanation
Indices: 1642853--1642916 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1642843 TAGCCAAACT
**
1642853 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
1642885 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
1642917 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:1646197 original size:276 final size:276
Alignment explanation
Indices: 1645704--1646256 Score: 1061
Period size: 276 Copynumber: 2.0 Consensus size: 276
1645694 TGTAACCTTT
*
1645704 GGCGACAATTCGAAAGGAAAAATTGAAGGAATCGGCACCATTGGTAACATCTCTTCATTTTGCAT
1 GGCGACAATTCGAAAGGAAAAATCGAAGGAATCGGCACCATTGGTAACATCTCTTCATTTTGCAT
*
1645769 TGAAAGTGTCTTATATGTCAATGGTCTTAAGCACAACCTCCTTAGTATTAGTCAATTATGTGACA
66 TGAAAGTGTCTTATATGTCAATGGTCTTAAGCACAACATCCTTAGTATTAGTCAATTATGTGACA
*
1645834 AAGGCATGAAGGTAGTTTTTGAATCACAAAACTGTCACGTAATTGATGTTTGTAATAATAAAACA
131 AAGGCATGAAGGTAGTTTTTGAACCACAAAACTGTCACGTAATTGATGTTTGTAATAATAAAACA
*
1645899 ATTTTCTTAGGCCATAGAGAAGGGAACATTTATGTTGTACATTTAGATGTTTTAAGTTCTCAAAA
196 ATTTTCTTAGGCCATAGAGAAGGGAACATTTATGTTGTACATCTAGATGTTTTAAGTTCTCAAAA
1645964 CGTATGTTTTGTTGCC
261 CGTATGTTTTGTTGCC
1645980 GGCGACAATTCGAAAGGAAAAATCGAAGGAATCGGCACCATTGGTAACATCTCTTCATTTTGCAT
1 GGCGACAATTCGAAAGGAAAAATCGAAGGAATCGGCACCATTGGTAACATCTCTTCATTTTGCAT
1646045 TGAAAGTGTCTTATATGTCAATGGTCTTAAGCACAACATCCTTAGTATTAGTCAATTATGTGACA
66 TGAAAGTGTCTTATATGTCAATGGTCTTAAGCACAACATCCTTAGTATTAGTCAATTATGTGACA
1646110 AAGGCATGAAGGTAGTTTTTGAACCACAAAACTGTCACGTAATTGATGTTTGTAATAATAAAACA
131 AAGGCATGAAGGTAGTTTTTGAACCACAAAACTGTCACGTAATTGATGTTTGTAATAATAAAACA
*
1646175 ATTTTCTTAGGCCATAGAGAAGGGAACATTTATGTTGTACATCTAGGTGTTTTAAGTTCTCAAAA
196 ATTTTCTTAGGCCATAGAGAAGGGAACATTTATGTTGTACATCTAGATGTTTTAAGTTCTCAAAA
1646240 CGTATGTTTTGTTGCC
261 CGTATGTTTTGTTGCC
1646256 G
1 G
1646257 ACAACAAGGA
Statistics
Matches: 272, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
276 272 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (276 bp):
GGCGACAATTCGAAAGGAAAAATCGAAGGAATCGGCACCATTGGTAACATCTCTTCATTTTGCAT
TGAAAGTGTCTTATATGTCAATGGTCTTAAGCACAACATCCTTAGTATTAGTCAATTATGTGACA
AAGGCATGAAGGTAGTTTTTGAACCACAAAACTGTCACGTAATTGATGTTTGTAATAATAAAACA
ATTTTCTTAGGCCATAGAGAAGGGAACATTTATGTTGTACATCTAGATGTTTTAAGTTCTCAAAA
CGTATGTTTTGTTGCC
Found at i:1649370 original size:13 final size:13
Alignment explanation
Indices: 1649352--1649390 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1649342 ACATCTTTCT
1649352 TTGTATCGATACA
1 TTGTATCGATACA
1649365 TTGTATCGATACA
1 TTGTATCGATACA
*
1649378 CTGTATCGATACA
1 TTGTATCGATACA
1649391 GGGGATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1649536 original size:21 final size:20
Alignment explanation
Indices: 1649512--1649558 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
1649502 AAATCTTTTG
*
1649512 CAAAATAC-TTGTTTTTCACT
1 CAAAATACATCGTTTTTCA-T
*
1649532 ACAAATTACATCGTTTTTCAT
1 -CAAAATACATCGTTTTTCAT
1649553 CAAAAT
1 CAAAAT
1649559 CACCTTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 8 0.36
22 9 0.41
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (20 bp):
CAAAATACATCGTTTTTCAT
Found at i:1651229 original size:29 final size:27
Alignment explanation
Indices: 1651187--1651252 Score: 107
Period size: 29 Copynumber: 2.4 Consensus size: 27
1651177 AAATAAATTT
1651187 TTTATGATTAATTAAGGGGGAGATAAGTG
1 TTTATGATTAATTAA-GGGGAGAT-AGTG
1651216 TTTATGATTAATTAAGGGGAGATAGTG
1 TTTATGATTAATTAAGGGGAGATAGTG
1651243 -TTATGATTAA
1 TTTATGATTAA
1651253 GGGGAGAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
26 10 0.27
27 4 0.11
28 8 0.22
29 15 0.41
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (27 bp):
TTTATGATTAATTAAGGGGAGATAGTG
Found at i:1651932 original size:13 final size:13
Alignment explanation
Indices: 1651914--1651939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1651904 TACACAAAGT
1651914 ATGTATCGATACA
1 ATGTATCGATACA
1651927 ATGTATCGATACA
1 ATGTATCGATACA
1651940 CCAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1651937 original size:32 final size:33
Alignment explanation
Indices: 1651896--1651959 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1651886 TAGCCAAACT
**
1651896 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAATGTATCGATACAA
1651928 TGTATCGATACACCAAAAAATGTATCGATACA
1 TGTATCGATACACCAAAAAATGTATCGATACA
1651960 TTAGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTATCGATACACCAAAAAATGTATCGATACAA
Found at i:1654752 original size:17 final size:16
Alignment explanation
Indices: 1654716--1654755 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1654706 CGTACAACGT
1654716 AAAATCTGTAATTATA
1 AAAATCTGTAATTATA
* *
1654732 AAAATTTGTAATTCGTA
1 AAAATCTGTAATT-ATA
1654749 AAAATCT
1 AAAATCT
1654756 ATGATTCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (16 bp):
AAAATCTGTAATTATA
Found at i:1654762 original size:17 final size:17
Alignment explanation
Indices: 1654742--1654797 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
1654732 AAAATTTGTA
*
1654742 ATTCGTAAAAATCTATG
1 ATTCCTAAAAATCTATG
*
1654759 ATTCCTAAAAAATTTATG
1 ATTCCT-AAAAATCTATG
* *
1654777 ATTCTTTGAAAATCTATG
1 ATTC-CTAAAAATCTATG
1654795 ATT
1 ATT
1654798 GATGCTGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.16
18 26 0.81
19 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (17 bp):
ATTCCTAAAAATCTATG
Found at i:1654769 original size:18 final size:18
Alignment explanation
Indices: 1654748--1654797 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1654738 TGTAATTCGT
1654748 AAAAATCTATGATTCCTA
1 AAAAATCTATGATTCCTA
* * *
1654766 AAAAATTTATGATTCTTT
1 AAAAATCTATGATTCCTA
*
1654784 GAAAATCTATGATT
1 AAAAATCTATGATT
1654798 GATGCTGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (18 bp):
AAAAATCTATGATTCCTA
Found at i:1655187 original size:20 final size:21
Alignment explanation
Indices: 1655126--1655187 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
1655116 AAGCAGATAA
1655126 TCTTTAAAAAAAATTAAATAGTT
1 TCTTTAAAAAAAATT-AATA-TT
*
1655149 T-TTTCAAAAAAA-TATATATT
1 TCTTTAAAAAAAATTA-ATATT
1655169 TCTTT-AAAAAAATTAATAT
1 TCTTTAAAAAAAATTAATAT
1655188 ATAAAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 15 0.43
21 9 0.26
22 10 0.29
23 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (21 bp):
TCTTTAAAAAAAATTAATATT
Found at i:1655187 original size:22 final size:23
Alignment explanation
Indices: 1655126--1655189 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
1655116 AAGCAGATAA
1655126 TCTTTAAAAAAAATTAA-ATAGTT
1 TCTTTAAAAAAAATTAATATA-TT
*
1655149 T-TTTCAAAAAAA-T-ATATATT
1 TCTTTAAAAAAAATTAATATATT
1655169 TCTTT-AAAAAAATTAATATAT
1 TCTTTAAAAAAAATTAATATAT
1655190 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 11 0.31
21 8 0.22
22 16 0.44
23 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (23 bp):
TCTTTAAAAAAAATTAATATATT
Found at i:1655930 original size:198 final size:201
Alignment explanation
Indices: 1655579--1655985 Score: 597
Period size: 198 Copynumber: 2.0 Consensus size: 201
1655569 CTCCTCTCTC
* * * *
1655579 AAATTTAGGGAATTATTATATTCTTTCTATTCCATAAATATTGTCCTGATTTGCCTTTAGTGACC
1 AAATTTAAGGAATTATTATATTCTTTCTATTCCATAAATATTATACTGATTTGCC--T-CTGACC
** * * *
1655644 ATTTTTTTAACTTTGACTTTGTTTTAATTTAAATATATTAATTAAAATATAAAAAAATTTCATGA
63 AACTTTTTAACTTTGACTTTATTTTAATTGAAATATATTAATTAAAATATAAAAAAATTTAATGA
* ** *
1655709 GGGGATCTTTTTAAATATTTTTCACAAAAATTAATTTAATAAAATATTTAAAATA-AAATTATCA
128 AGCAATATTTTTAAATATTTTTCACAAAAATTAATTTAATAAAATATTTAAAATATAAATTATCA
*
1655773 AAGTTGAAA
193 AAATTGAAA
*
1655782 AAATTTAAGGAATTATTATATTCTTTCTATTTCATAAATATTATACTGATTTGCC-CT-ACCAAC
1 AAATTTAAGGAATTATTATATTCTTTCTATTCCATAAATATTATACTGATTTGCCTCTGACCAAC
*
1655845 TTTTTAACTTTGACTTTATTTTAATTGAAATATATTAATTAAAATATGAAAAAATTTTAATGAAG
66 TTTTTAACTTTGACTTTATTTTAATTGAAATATATTAATTAAAATAT-AAAAAAATTTAATGAAG
*
1655910 CAATATTTTTTAAT-TTTTTCACAAAAATTAATTTAATAAAATATTTAAAATATAAATTATCAAA
130 CAATATTTTTAAATATTTTTCACAAAAATTAATTTAATAAAATATTTAAAATATAAATTATCAAA
1655974 ATTGAAA
195 ATTGAAA
1655981 AAATT
1 AAATT
1655986 GACTGCAAAA
Statistics
Matches: 185, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
198 87 0.47
199 47 0.25
203 51 0.28
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (201 bp):
AAATTTAAGGAATTATTATATTCTTTCTATTCCATAAATATTATACTGATTTGCCTCTGACCAAC
TTTTTAACTTTGACTTTATTTTAATTGAAATATATTAATTAAAATATAAAAAAATTTAATGAAGC
AATATTTTTAAATATTTTTCACAAAAATTAATTTAATAAAATATTTAAAATATAAATTATCAAAA
TTGAAA
Done.