Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 109 of 199
Found at i:33180688 original size:43 final size:43
Alignment explanation
Indices: 33180583--33180894 Score: 315
Period size: 43 Copynumber: 7.3 Consensus size: 43
33180573 AGATTATGTT
** * *
33180583 TTTAGCGGCGTTT-TGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
33180624 TTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAATGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * **
33180667 TATATCGGCGTTTGTGATAAAAGCACCGCTAAATATCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
33180710 TTTAGTGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
33180753 TTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * *
33180796 TTTAGCGGCGTTTGTGGGGAAAGCACCGTTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * *
33180839 TTTAGCAGCATTTGTG-GAAAAACCGCCGCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGAG-AAAAGCGCCGCTAAAGGTCTTGGTC
*
33180882 TTTAGCGCCGTTT
1 TTTAGCGGCGTTT
33180895 TTTCCGGCGC
Statistics
Matches: 229, Mismatches: 39, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
41 12 0.05
42 20 0.09
43 197 0.86
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:33180785 original size:129 final size:129
Alignment explanation
Indices: 33180602--33180894 Score: 363
Period size: 129 Copynumber: 2.3 Consensus size: 129
33180592 GTTTTGCTAG
* * * *
33180602 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGTGTTTGTGATAAAAGCGCCGCTAAATGTCATGGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGT
* * * * ** *
33180666 CTATATCGGCGTTTGTGATAAAAGCACCGCTAAATATCTTGGTCTTTAGTGGCATTTGTGGGAA
66 CTATAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTCTTTAGCAGCATTTGTGGAAA
* * * *
33180730 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGGTCTTGGT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGT
* * * * *
33180795 CTTTAGCGGCGTTTGTGGGGAAAGCACCGTTAAAGGTCATGGTCTTTAGCAGCATTTGTGGAAA
66 CTATAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTCTTTAGCAGCATTTGTGGAAA
* * * *
33180859 AACCGCCGCTAAAGATCATGGTCTTTAGCGCCGTTT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
33180895 TTTCCGGCGC
Statistics
Matches: 140, Mismatches: 24, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
128 16 0.11
129 124 0.89
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (129 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGT
CTATAGCGGCGTTTGTGAGAAAAGCACCGCTAAAGATCATGGTCTTTAGCAGCATTTGTGGAAA
Found at i:33180963 original size:21 final size:22
Alignment explanation
Indices: 33180937--33180981 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
33180927 TTTAGCGGCG
*
33180937 CTAAAAA-GCGCCGCTAAAGGC
1 CTAAAAAGGCGCCGCTAAAAGC
33180958 CTAAAAAGGCGCCGCTAAAAGC
1 CTAAAAAGGCGCCGCTAAAAGC
33180980 CT
1 CT
33180982 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.38, C:0.29, G:0.22, T:0.11
Consensus pattern (22 bp):
CTAAAAAGGCGCCGCTAAAAGC
Found at i:33185330 original size:18 final size:18
Alignment explanation
Indices: 33185288--33185330 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
33185278 AAAGAAGAAA
33185288 ATTT-TATTAAATTTAAT
1 ATTTATATTAAATTTAAT
**
33185305 ATAAATATTAAATTTAAT
1 ATTTATATTAAATTTAAT
33185323 ATTTATAT
1 ATTTATAT
33185331 AATAACCCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATATTAAATTTAAT
Found at i:33185694 original size:21 final size:20
Alignment explanation
Indices: 33185650--33185703 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
33185640 AAAATTCAAA
*
33185650 AAAATTATAAAAATTAGTTTT
1 AAAATTAT-AAAATTAGTTGT
*
33185671 AAAATTATAAAATTGGTTGGT
1 AAAATTATAAAATTAGTT-GT
33185692 -AAATTAATAAAA
1 AAAATT-ATAAAA
33185704 AGTAAGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (20 bp):
AAAATTATAAAATTAGTTGT
Found at i:33189796 original size:44 final size:45
Alignment explanation
Indices: 33189717--33189848 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 45
33189707 ACTTCCAATT
* * **
33189717 CCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGT-G
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTCG
** *
33189761 CCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGT-----CG
*
33189811 CCATGTCCCAGACATGGTCTTACATGAGACCTCTCATA
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
33189849 ATCCCAATGA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
44 36 0.51
50 35 0.49
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (45 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTCG
Found at i:33189871 original size:56 final size:50
Alignment explanation
Indices: 33189659--33189892 Score: 162
Period size: 50 Copynumber: 4.7 Consensus size: 50
33189649 TGATAATAAC
* * * *
33189659 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGA--TGT-TTCCTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
* * * * * **
33189706 TACTTCCAATTCCATATCCCAGATATGGTCTTACATGGGAGTTCTCAT----
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
** ** * *
33189754 AT--CGGTGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
* *
33189802 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCCCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTC---ATCCC---G
33189858 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
33189893 GGATCTCTTT
Statistics
Matches: 143, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
44 33 0.23
46 1 0.01
47 1 0.01
48 2 0.01
49 31 0.22
50 34 0.24
51 2 0.01
52 1 0.01
53 4 0.03
56 34 0.24
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCCCG
Found at i:33192769 original size:61 final size:61
Alignment explanation
Indices: 33192674--33192795 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
33192664 CCATTTTCAA
33192674 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
1 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
33192735 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
1 AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
33192796 GAACCTTCAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (61 bp):
AATATTTTGGATTTTGATATTCTTGGAAATCAATTTGCATAAATGAAGGTATCTTACGATT
Found at i:33197612 original size:20 final size:19
Alignment explanation
Indices: 33197571--33197614 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
33197561 CTTTAAAACA
* **
33197571 AATATATAATTATTCATTT
1 AATATATAACTATTCAAAT
33197590 AATACTATAACTATTCAAAT
1 AATA-TATAACTATTCAAAT
33197610 AATAT
1 AATAT
33197615 TATTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATATAACTATTCAAAT
Found at i:33201648 original size:21 final size:20
Alignment explanation
Indices: 33201624--33201678 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
33201614 AAATAAAATA
33201624 TTTTATATTTAAATATTATTC
1 TTTTATA-TTAAATATTATTC
**
33201645 TTTTGATAGAAAATATTATTC
1 TTTT-ATATTAAATATTATTC
*
33201666 TTTAATATTAAAT
1 TTTTATATTAAAT
33201679 TGATGTGGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTATATTAAATATTATTC
Found at i:33205198 original size:12 final size:13
Alignment explanation
Indices: 33205181--33205209 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33205171 ATTTTAATTT
33205181 CTTTAA-TTTTAA
1 CTTTAATTTTTAA
33205193 CTTTAATTTTTAA
1 CTTTAATTTTTAA
33205206 CTTT
1 CTTT
33205210 TTACTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTAATTTTTAA
Found at i:33208046 original size:10 final size:11
Alignment explanation
Indices: 33208007--33208059 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
33207997 ATCTACTTCT
33208007 AAAAATTATAA
1 AAAAATTATAA
*
33208018 AAAAATCTATGTGA
1 AAAAAT-TA--TAA
33208032 AAAAATTATAA
1 AAAAATTATAA
*
33208043 AAAAA-CATAA
1 AAAAATTATAA
33208053 AAAAATT
1 AAAAATT
33208060 TGGAAAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 9 0.26
11 13 0.38
12 2 0.06
13 2 0.06
14 8 0.24
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:33212608 original size:21 final size:20
Alignment explanation
Indices: 33212555--33212609 Score: 101
Period size: 20 Copynumber: 2.7 Consensus size: 20
33212545 TTCTAAGCAG
33212555 TGCAAAGTTATTCTTTCCTT
1 TGCAAAGTTATTCTTTCCTT
33212575 TGCAAAGTTATTCTTTCCTT
1 TGCAAAGTTATTCTTTCCTT
33212595 TGCAAAGTTTATTCT
1 TGCAAAG-TTATTCT
33212610 ATTTCCTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 27 0.79
21 7 0.21
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (20 bp):
TGCAAAGTTATTCTTTCCTT
Found at i:33212992 original size:23 final size:24
Alignment explanation
Indices: 33212966--33213018 Score: 99
Period size: 23 Copynumber: 2.2 Consensus size: 24
33212956 CAAAGTAAAC
33212966 ATCAATTCATTCAAGCAATACCT-
1 ATCAATTCATTCAAGCAATACCTA
33212989 ATCAATTCATTCAAGCAATACCTA
1 ATCAATTCATTCAAGCAATACCTA
33213013 ATCAAT
1 ATCAAT
33213019 ACCTAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.30
Consensus pattern (24 bp):
ATCAATTCATTCAAGCAATACCTA
Found at i:33213616 original size:21 final size:21
Alignment explanation
Indices: 33213590--33213631 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33213580 GAACACGCCG
*
33213590 ACAGAAGCTCATGAGAGCTGA
1 ACAGAAGCTCATAAGAGCTGA
* *
33213611 ACAGAATCTCGTAAGAGCTGA
1 ACAGAAGCTCATAAGAGCTGA
33213632 TCTACCGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (21 bp):
ACAGAAGCTCATAAGAGCTGA
Found at i:33222088 original size:22 final size:23
Alignment explanation
Indices: 33222047--33222098 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
33222037 TTAAATATTA
*
33222047 TTAAAAATATAACCATTACAAAT
1 TTAAATATATAACCATTACAAAT
*
33222070 TTAAATATATAA-CATTACATAT
1 TTAAATATATAACCATTACAAAT
33222092 TTAAATA
1 TTAAATA
33222099 AATCCTAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAATATATAACCATTACAAAT
Found at i:33223496 original size:147 final size:148
Alignment explanation
Indices: 33223254--33223557 Score: 520
Period size: 147 Copynumber: 2.0 Consensus size: 148
33223244 GAGGAGGAAG
* *
33223254 AGGAAGAGGTGGGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGTAAGGGAGAGGAAG
1 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
*
33223319 ATTGTGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTT-GAAGATGAAGACAAGGATTATG
66 ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTAGAAGATGAAGACAAGGATTATG
33223383 AGGAGGAAGAAGAAGAAA
131 AGGAGGAAGAAGAAGAAA
33223401 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
1 AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
* * * *
33223466 ATTGCGGATAAAAAATCTGTCAAGCGGGAAAGCTTGTCTGTTGAAGAAGATGAAGACAAGGATTA
66 ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTT--AGAAGATGAAGACAAGGATTA
33223531 TGAGGAGGAAGAAGAAGAAA
129 TGAGGAGGAAGAAGAAGAAA
33223551 AGGAAGA
1 AGGAAGA
33223558 TGATGATGAG
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
147 100 0.68
150 47 0.32
ACGTcount: A:0.40, C:0.06, G:0.36, T:0.18
Consensus pattern (148 bp):
AGGAAGAGGTGAGAGAGGTTGTTAGGTTGAAAAGAGAACGGATATCTTCGGAAAGGGAGAGGAAG
ATTGCGGATAAAAAATCTGTAAAGCAGGAAACCGTGTCTGTTAGAAGATGAAGACAAGGATTATG
AGGAGGAAGAAGAAGAAA
Found at i:33223603 original size:36 final size:36
Alignment explanation
Indices: 33223562--33223678 Score: 153
Period size: 36 Copynumber: 3.2 Consensus size: 36
33223552 GGAAGATGAT
* * ** *
33223562 GATGAGGAGTTCACTCCAGATTTAGAAGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
* *
33223598 GATGAGGAATTTACTCTGGATGAAGAGGATTGTTTG
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
* *
33223634 GATGAAGAATTCACTCCGGATGAAGAGGATTGTTTA
1 GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
33223670 GATGAGGAA
1 GATGAGGAA
33223679 GAGGAATTGA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 69 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.30
Consensus pattern (36 bp):
GATGAGGAATTCACTCCGGATGAAGAGGATTGTTTG
Found at i:33226176 original size:33 final size:33
Alignment explanation
Indices: 33226134--33226198 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
33226124 AGTCAATTTT
33226134 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
1 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
33226167 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTT
1 CTGCTTCTCAGTGCTGATTGCTTTTACTGCTT
33226199 GAGTTCTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.09, C:0.26, G:0.18, T:0.46
Consensus pattern (33 bp):
CTGCTTCTCAGTGCTGATTGCTTTTACTGCTTC
Found at i:33226188 original size:17 final size:17
Alignment explanation
Indices: 33226135--33226189 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
33226125 GTCAATTTTC
33226135 TGCTTCTCAGTGCTGAT
1 TGCTTCTCAGTGCTGAT
* * ***
33226152 TGCTT-TTACTGCTTCC
1 TGCTTCTCAGTGCTGAT
33226168 TGCTTCTCAGTGCTGAT
1 TGCTTCTCAGTGCTGAT
33226185 TGCTT
1 TGCTT
33226190 TTACTGCTTG
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.09, C:0.25, G:0.20, T:0.45
Consensus pattern (17 bp):
TGCTTCTCAGTGCTGAT
Found at i:33231362 original size:18 final size:17
Alignment explanation
Indices: 33231329--33231370 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
33231319 AGCTTCTCAG
* *
33231329 AAATACTTTTGGGATAA
1 AAATATTTTTGAGATAA
33231346 AAAGTATTTTTGAGATAA
1 AAA-TATTTTTGAGATAA
33231364 AAATATT
1 AAATATT
33231371 GTTAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (17 bp):
AAATATTTTTGAGATAA
Found at i:33233559 original size:15 final size:15
Alignment explanation
Indices: 33233515--33233561 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
33233505 AAAAGTATGT
*
33233515 ATAAAATCTAAAAAA
1 ATAAAATTTAAAAAA
*
33233530 ATATAAA-TTATAAAA
1 ATA-AAATTTAAAAAA
33233545 ATAAAATTTACAAAAA
1 ATAAAATTTA-AAAAA
33233561 A
1 A
33233562 ATTACGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.12
15 15 0.58
16 8 0.31
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAATTTAAAAAA
Found at i:33233654 original size:17 final size:18
Alignment explanation
Indices: 33233612--33233654 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
33233602 TTATTACAAA
*
33233612 AAAATTAT-AAAAATTGT
1 AAAATTATAAAAAAATGT
*
33233629 AAAAATATAAAAAAATGT
1 AAAATTATAAAAAAATGT
33233647 -AAATTATA
1 AAAATTATA
33233655 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATTATAAAAAAATGT
Found at i:33233655 original size:19 final size:18
Alignment explanation
Indices: 33233611--33233649 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33233601 ATTATTACAA
*
33233611 AAAAAT-TATAAAAATTGT
1 AAAAATATA-AAAAAATGT
33233629 AAAAATATAAAAAAATGT
1 AAAAATATAAAAAAATGT
33233647 AAA
1 AAA
33233650 TTATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAAAATGT
Found at i:33233673 original size:24 final size:22
Alignment explanation
Indices: 33233652--33233702 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
33233642 AATGTAAATT
*
33233652 ATATTTTTTAAAAAATTTTAAA
1 ATATTTTTTAAAAAATTCTAAA
* *
33233674 ATTTTTTTTATAAAATTCTAAA
1 ATATTTTTTAAAAAATTCTAAA
33233696 ACTATTT
1 A-TATTT
33233703 AAATTTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTTTTTAAAAAATTCTAAA
Found at i:33234077 original size:7 final size:7
Alignment explanation
Indices: 33234042--33234080 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
33234032 TATTTAAATA
33234042 TTTAATAT
1 TTTAAT-T
*
33234050 TATAATT
1 TTTAATT
*
33234057 TTTTATT
1 TTTAATT
33234064 TTTAATT
1 TTTAATT
33234071 TTTAATT
1 TTTAATT
33234078 TTT
1 TTT
33234081 TTAAACGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTAATT
Found at i:33236095 original size:29 final size:29
Alignment explanation
Indices: 33236063--33236119 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
33236053 ACTCACTACA
*
33236063 TTGTATTTAAACAAGCCCTTAACATATTC
1 TTGTAGTTAAACAAGCCCTTAACATATTC
* *
33236092 TTGTAGTTAAATAAGCCCTTAACTTATT
1 TTGTAGTTAAACAAGCCCTTAACATATT
33236120 ATTTTTACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (29 bp):
TTGTAGTTAAACAAGCCCTTAACATATTC
Found at i:33237123 original size:20 final size:20
Alignment explanation
Indices: 33237100--33237140 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
33237090 CTTAAACAAA
*
33237100 TTAAGATTTATTTAA-TTAAT
1 TTAAG-TTTAATTAACTTAAT
33237120 TTAAGTTTAATTAACTTAAT
1 TTAAGTTTAATTAACTTAAT
33237140 T
1 T
33237141 AACAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAAGTTTAATTAACTTAAT
Found at i:33237735 original size:49 final size:50
Alignment explanation
Indices: 33237663--33237792 Score: 183
Period size: 49 Copynumber: 2.6 Consensus size: 50
33237653 TGCCTTAGGT
* * *
33237663 TGAAAATCATCATTGTCGGGCTATCCGAGATGA-TAGGATAAGTAAATTG
1 TGAAAACCATCATTTTCGGGCTATCCGTGATGAGTAGGATAAGTAAATTG
** *
33237712 TGAAAACCATTGTTTTCGGGCTATCTGTGAT-AGTAGGATAAGTAAATTG
1 TGAAAACCATCATTTTCGGGCTATCCGTGATGAGTAGGATAAGTAAATTG
*
33237761 TGAAAACCATCATTTTCAGGCTATCCGTGATG
1 TGAAAACCATCATTTTCGGGCTATCCGTGATG
33237793 GTAAAATGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.01
49 68 0.99
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (50 bp):
TGAAAACCATCATTTTCGGGCTATCCGTGATGAGTAGGATAAGTAAATTG
Found at i:33237877 original size:23 final size:23
Alignment explanation
Indices: 33237850--33237896 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
33237840 TGATAATGTA
*
33237850 TTGTATAGTGCGAACCATTGTTG
1 TTGTATAGTGCGAACCATCGTTG
33237873 TTGTATAGTGCGAACCATCGTTG
1 TTGTATAGTGCGAACCATCGTTG
33237896 T
1 T
33237897 CGGGCCACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (23 bp):
TTGTATAGTGCGAACCATCGTTG
Found at i:33240226 original size:29 final size:29
Alignment explanation
Indices: 33240192--33240250 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
33240182 TCCACCTTGA
* * * *
33240192 CACGAATTCTCAATGAATAAGTTCTTCAT
1 CACGAACTCTCAACGAACAAGTTCTCCAT
33240221 CACGAACTCTCAACGAACAAGTTCTCCAT
1 CACGAACTCTCAACGAACAAGTTCTCCAT
33240250 C
1 C
33240251 TATTCCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27
Consensus pattern (29 bp):
CACGAACTCTCAACGAACAAGTTCTCCAT
Found at i:33244179 original size:5 final size:6
Alignment explanation
Indices: 33244166--33244190 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33244156 ATCACAAAGT
33244166 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
33244191 GAACACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:33244754 original size:14 final size:14
Alignment explanation
Indices: 33244735--33244763 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
33244725 AGTTAACCCC
33244735 ACAAAAATTTGAAT
1 ACAAAAATTTGAAT
33244749 ACAAAAATTTGAAT
1 ACAAAAATTTGAAT
33244763 A
1 A
33244764 GGATTCACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
ACAAAAATTTGAAT
Found at i:33245192 original size:32 final size:32
Alignment explanation
Indices: 33245156--33245216 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
33245146 TTTTTAGAGG
* * *
33245156 TTGATTAATGCAAATCCTTAAAGAAATTAGAA
1 TTGATTAATACAAACCCCTAAAGAAATTAGAA
*
33245188 TTGATTAATACAAACCCCTGAAGAAATTA
1 TTGATTAATACAAACCCCTAAAGAAATTA
33245217 AGGTTGAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (32 bp):
TTGATTAATACAAACCCCTAAAGAAATTAGAA
Found at i:33246749 original size:4 final size:4
Alignment explanation
Indices: 33246742--33246971 Score: 451
Period size: 4 Copynumber: 57.5 Consensus size: 4
33246732 GTTAAAATAA
*
33246742 ATGT ATGT GTGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
33246790 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
33246838 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
33246886 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
33246934 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
33246972 NNNNNNNNNN
Statistics
Matches: 224, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 224 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:33253807 original size:5 final size:5
Alignment explanation
Indices: 33253797--33253822 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
33253787 TGAGCATTCG
33253797 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
33253823 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:33254312 original size:17 final size:17
Alignment explanation
Indices: 33254270--33254316 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
33254260 AATTCAATTT
33254270 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
33254286 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
33254304 TAATATAAATAAT
1 TAATATAAATAAT
33254317 ATAAAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 13 0.48
18 8 0.30
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:33254947 original size:9 final size:9
Alignment explanation
Indices: 33254930--33254960 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33254920 TCGAGTTGAT
33254930 TCGAATAAC
1 TCGAATAAC
*
33254939 TCGATTAAC
1 TCGAATAAC
33254948 TCGAATAAC
1 TCGAATAAC
33254957 TCGA
1 TCGA
33254961 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:33262483 original size:42 final size:42
Alignment explanation
Indices: 33262344--33262500 Score: 129
Period size: 42 Copynumber: 3.7 Consensus size: 42
33262334 TCGTGTTTAC
* * * **
33262344 TTTCCGTTTAGCTCTCACTAGCTTCTATTCAACTCA-TATAAG
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAAC-CATTATGGG
**** * *
33262386 TTTCTGTTTAGCTCTTTTAAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACCATTATGGG
* * * *
33262428 TTT-TCGCTCAGCTCTTACGAGCTTCCGTTCAACCATTATGGG
1 TTTCT-GTTTAGCTCTCACGAGCTTCTGTTCAACCATTATGGG
* *
33262470 TTTCTGTTTAGCTCTCATGAGCTTTTGTTCA
1 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCA
33262501 GCCTTTGGGC
Statistics
Matches: 88, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
41 2 0.02
42 85 0.97
43 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACCATTATGGG
Found at i:33270011 original size:42 final size:42
Alignment explanation
Indices: 33269912--33270068 Score: 147
Period size: 42 Copynumber: 3.7 Consensus size: 42
33269902 TCATGTTTAC
* * * * * *
33269912 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* * * * *
33269954 TTT-TCGTTTAACTCTTTTGAGCTTCTGTTTACCCCTTATGGG
1 TTTCT-GTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* *
33269996 TTTCTGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* *
33270038 TTTTTGTTTAGCT-TTCATGAGCTTCTGTTCA
1 TTTCTGTTCAGCTCTT-ATGAGCTTCTGTTCA
33270069 GGCTTCAGGC
Statistics
Matches: 92, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 3 0.03
42 88 0.96
43 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
Found at i:33270012 original size:21 final size:21
Alignment explanation
Indices: 33269913--33270069 Score: 84
Period size: 21 Copynumber: 7.5 Consensus size: 21
33269903 CATGTTTACT
* * *
33269913 TTCTGTTTAGCTCTCACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* *
33269934 TTCTGTTCAACTCATATGAG-
1 TTCTGTTCAGCTCTTATGAGC
* * * *
33269954 TTTTCGTTTAACTCTTTTGAGC
1 TTCT-GTTCAGCTCTTATGAGC
* * * * *
33269976 TTCTGTTTACCCCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGC
*
33269997 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * * *
33270018 TTCCGTTCAACCCTTATGGGT
1 TTCTGTTCAGCTCTTATGAGC
* *
33270039 TTTTGTTTAGCT-TTCATGAGC
1 TTCTGTTCAGCTCTT-ATGAGC
33270060 TTCTGTTCAG
1 TTCTGTTCAG
33270070 GCTTCAGGCT
Statistics
Matches: 97, Mismatches: 36, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
20 5 0.05
21 89 0.92
22 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:33270059 original size:84 final size:84
Alignment explanation
Indices: 33269912--33270066 Score: 213
Period size: 84 Copynumber: 1.8 Consensus size: 84
33269902 TCATGTTTAC
* * * *
33269912 TTTCTGTTTAGCTCTCACGAGCTTCTGTTCAACTCATATGAGTTTTCGTTTAACTCTTTTGAGCT
1 TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCGTTTAACTCTTATGAGCT
33269977 TCTGTTTACCCCTTATGGG
66 TCTGTTTACCCCTTATGGG
* * * * *
33269996 TTTCTGTTCAGCTCTTACGAGCTTCCGTTCAACCCTTATGGGTTTTTGTTTAGCT-TTCATGAGC
1 TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCGTTTAACTCTT-ATGAGC
33270060 TTCTGTT
65 TTCTGTT
33270067 CAGGCTTCAG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.03
84 59 0.97
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (84 bp):
TTTCTGTTCAGCTCTCACGAGCTTCCGTTCAACCCATATGAGTTTTCGTTTAACTCTTATGAGCT
TCTGTTTACCCCTTATGGG
Found at i:33272508 original size:50 final size:50
Alignment explanation
Indices: 33272386--33272632 Score: 182
Period size: 50 Copynumber: 4.8 Consensus size: 50
33272376 GATAATAACA
* * ** * * **
33272386 TGCCAAAGTCATGTCCCAGAAATGGTCTTACATGGGATGTTTC-T-TGTAC
1 TGCCAATGCCATGTCCCA-AAATGGTCTTACATGGGACCTCTCATATATGG
* * **
33272435 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-TGG
1 TGCCAATGCCATGTCCCA-AAATGGTCTTACATGGGACCTCTCATATATGG
* *
33272485 TG-CACATGCCATGTCCCAAATATGGTCTTACGA-GGGACCTCTCATCT-CGG
1 TGCCA-ATGCCATGTCCCAAA-ATGGTCTTAC-ATGGGACCTCTCATATATGG
* * *
33272535 TGTCAACGCCATGTCCCAGAAATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCA-AAATGGTCTTACATGGGACCTCTCAT-A--T--ATGG
*
33272591 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAAA-ATGGTCTTACATGGGACCTCT
33272633 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
49 40 0.25
50 75 0.47
51 6 0.04
53 1 0.01
55 2 0.01
56 37 0.23
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAAATGGTCTTACATGGGACCTCTCATATATGG
Found at i:33279568 original size:49 final size:50
Alignment explanation
Indices: 33279455--33279651 Score: 209
Period size: 56 Copynumber: 3.8 Consensus size: 50
33279445 TTTTTTGTAC
* **
33279455 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
* * *
33279505 TGTCC-ATGCCATGTCCCAGATATGGTCTTAC-GGGGACCTCTCATCTTGG
1 TG-CCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
* * *
33279554 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
33279610 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCT
33279652 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
48 2 0.02
49 39 0.32
50 39 0.32
51 2 0.02
53 1 0.01
56 40 0.33
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCGG
Found at i:33279621 original size:56 final size:50
Alignment explanation
Indices: 33279418--33279651 Score: 208
Period size: 49 Copynumber: 4.6 Consensus size: 50
33279408 CCAAAGCTAG
* * *
33279418 GTCCCAGACATGGTCTTACATGGGA--TGT-TTTTTGTACTGCCAATGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG-A-TGCCAATGCCAT
* * ** * * *
33279467 ATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGTCC-ATGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGATG-CCAATGCCAT
* * * *
33279517 GTCCCAGATATGGTCTTAC-GGGGACCTCTCATCTTGGTGCCAACGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGATGCCAATGCCAT
33279566 GTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATGCCAT
1 GTCCCAGACATGGTCTTACATGGGACCTCTCAT---CT---TGATGCCAATGCCAT
* *
33279622 GTCCCAAACATGGTCTTACATGGGATCTCT
1 GTCCCAGACATGGTCTTACATGGGACCTCT
33279652 TTACCCAAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
48 2 0.01
49 62 0.41
50 39 0.25
51 4 0.03
52 3 0.02
53 2 0.01
56 41 0.27
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
GTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGATGCCAATGCCAT
Found at i:33288641 original size:13 final size:13
Alignment explanation
Indices: 33288625--33288650 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33288615 CCAATCCATC
33288625 CCTCAACTCCAGT
1 CCTCAACTCCAGT
33288638 CCTCAACTCCAGT
1 CCTCAACTCCAGT
33288651 GCTGCAACAT
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:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
CCTCAACTCCAGT
Found at i:33292590 original size:6 final size:6
Alignment explanation
Indices: 33292581--33292610 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
33292571 TTTTCTTTCC
33292581 CATTTT CATTTT CATTTT CATTTT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
33292611 GGAGAAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
CATTTT
Found at i:33297711 original size:13 final size:13
Alignment explanation
Indices: 33297693--33297717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33297683 TGATATACCA
33297693 AAAAAAAGTTCTC
1 AAAAAAAGTTCTC
33297706 AAAAAAAGTTCT
1 AAAAAAAGTTCT
33297718 TTCTATTCTT
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAAAGTTCTC
Found at i:33302585 original size:43 final size:43
Alignment explanation
Indices: 33302519--33302647 Score: 176
Period size: 43 Copynumber: 3.0 Consensus size: 43
33302509 ATAGGATTTC
33302519 CGATATGTG-TTATCATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATTA-CATGTAAGACCACGTCTGGGACGTTGGCAT
* *
33302562 CGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGA-TATGTGATTACATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
33302605 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
33302648 TGTACGAGTT
Statistics
Matches: 76, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
42 3 0.04
43 67 0.88
44 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (43 bp):
CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:33303567 original size:46 final size:47
Alignment explanation
Indices: 33303492--33303751 Score: 416
Period size: 47 Copynumber: 5.6 Consensus size: 47
33303482 ATGAGTTGAA
* *
33303492 CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
33303539 CCAATTTGTTACATA-ATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
* * *
33303585 CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAAAGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
33303632 CCAATTTGTTACATA-ATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
33303678 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
** ** *
33303725 CCAAACTGTTTTATATATGCTGACCAA
1 CCAATTTGTTACATATATGCTGTCCAA
33303752 ATTCATGAAT
Statistics
Matches: 198, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 88 0.44
47 110 0.56
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:33303603 original size:93 final size:93
Alignment explanation
Indices: 33303492--33303728 Score: 447
Period size: 93 Copynumber: 2.5 Consensus size: 93
33303482 ATGAGTTGAA
33303492 CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATG
1 CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATG
33303557 CTGTCCAATTTTGATGCTTAAATGCTGC
66 CTGTCCAATTTTGATGCTTAAATGCTGC
*
33303585 CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAAAGCTGCCCAATTTGTTACATAATG
1 CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATG
33303650 CTGTCCAATTTTGATGCTTAAATGCTGC
66 CTGTCCAATTTTGATGCTTAAATGCTGC
* *
33303678 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAA
1 CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAA
33303729 ACTGTTTTAT
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 140 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (93 bp):
CCAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATG
CTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:33304070 original size:2 final size:2
Alignment explanation
Indices: 33304063--33304087 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33304053 AAGAGCATGT
33304063 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
33304088 TCGAATGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33310530 original size:43 final size:42
Alignment explanation
Indices: 33310463--33310592 Score: 167
Period size: 43 Copynumber: 3.0 Consensus size: 42
33310453 CATAGGATTT
33310463 TCGATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
33310506 TCGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCA
1 TCGA-TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* *
33310549 TCGATATGTGATTACATGTAAGACCACGTCTGAGACGTTGGCA
1 TCGATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
33310592 T
1 T
33310593 TGTCGAGTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
42 3 0.04
43 68 0.88
44 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (42 bp):
TCGATATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:33311509 original size:46 final size:47
Alignment explanation
Indices: 33311436--33311694 Score: 414
Period size: 47 Copynumber: 5.6 Consensus size: 47
33311426 TGAGTTGAAT
* *
33311436 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
33311483 CAATTTGTTACATA-ATGCTGTCCAATTTTGATGCTTAAATGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
* * *
33311529 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAAAGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
33311576 CAATTTGTTACATA-ATGCTGTCCAATTTTGATGCTTAAATGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
33311622 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
1 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
** ** *
33311669 CAAACTGTTTTATATATGCTGACCAA
1 CAATTTGTTACATATATGCTGTCCAA
33311695 ATTCATGAAT
Statistics
Matches: 197, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 88 0.45
47 109 0.55
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (47 bp):
CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCC
Found at i:33311536 original size:93 final size:93
Alignment explanation
Indices: 33311436--33311671 Score: 445
Period size: 93 Copynumber: 2.5 Consensus size: 93
33311426 TGAGTTGAAT
33311436 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATGC
1 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATGC
33311501 TGTCCAATTTTGATGCTTAAATGCTGCC
66 TGTCCAATTTTGATGCTTAAATGCTGCC
*
33311529 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAAAGCTGCCCAATTTGTTACATAATGC
1 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATGC
33311594 TGTCCAATTTTGATGCTTAAATGCTGCC
66 TGTCCAATTTTGATGCTTAAATGCTGCC
* *
33311622 CAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAA
1 CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAA
33311672 ACTGTTTTAT
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 139 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (93 bp):
CAATTTATTACATATATGCTGTCCAATTTTGATGCATAAATGCTGCCCAATTTGTTACATAATGC
TGTCCAATTTTGATGCTTAAATGCTGCC
Found at i:33312013 original size:2 final size:2
Alignment explanation
Indices: 33312006--33312046 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
33311996 AAGAGCATGT
33312006 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33312047 TCGAATGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33312993 original size:9 final size:8
Alignment explanation
Indices: 33312976--33313000 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
33312966 TTTAATTCTG
33312976 TTATTTTT
1 TTATTTTT
33312984 TTATTTTT
1 TTATTTTT
33312992 TTATTTTT
1 TTATTTTT
33313000 T
1 T
33313001 CAAGAACGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:33316109 original size:17 final size:16
Alignment explanation
Indices: 33316072--33316139 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
33316062 CAACCCAATT
*
33316072 TTTATTTTTATTATTTA
1 TTTATTTTT-TTCTTTA
33316089 -TTATTTTTTTCTTTA
1 TTTATTTTTTTCTTTA
* *
33316104 CTTTATTTATTACTTTA
1 -TTTATTTTTTTCTTTA
* *
33316121 TTTTATTTTATTATTTA
1 -TTTATTTTTTTCTTTA
33316138 TT
1 TT
33316140 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.15
16 10 0.24
17 25 0.61
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTTTTTCTTTA
Found at i:33316118 original size:12 final size:12
Alignment explanation
Indices: 33316082--33316147 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
33316072 TTTATTTTTA
33316082 TTATTTATTA-T
1 TTATTTATTACT
* *
33316093 TTTTTTCTTTACT
1 TTATTT-ATTACT
33316106 TTATTTATTACT
1 TTATTTATTACT
*
33316118 TTATTTTATT-TT
1 TTA-TTTATTACT
33316130 ATTATTTATTAC-
1 -TTATTTATTACT
33316142 TTATTT
1 TTATTT
33316148 GGATATTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
11 11 0.25
12 18 0.41
13 15 0.34
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTTATTACT
Found at i:33316461 original size:25 final size:25
Alignment explanation
Indices: 33316415--33316466 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
33316405 CTGTAATTTT
* *
33316415 TTGCTGTGATTGGTTATTGTTGCTG
1 TTGCTGTGATTGATTATTGTTGATG
*
33316440 TTGCTGTGATT-ATTTTTGGTTGATG
1 TTGCTGTGATTGATTATT-GTTGATG
33316465 TT
1 TT
33316467 ACTGCTTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.10, C:0.06, G:0.29, T:0.56
Consensus pattern (25 bp):
TTGCTGTGATTGATTATTGTTGATG
Found at i:33317184 original size:101 final size:100
Alignment explanation
Indices: 33316994--33317182 Score: 254
Period size: 101 Copynumber: 1.8 Consensus size: 100
33316984 AAGAACATGT
* * *
33316994 TGGGCTGAGTAACCAGGGTGGGGTGCTTGGCTGTCATCTCTTTTCGCATCAAAAGGTTCGATGTG
1 TGGGCTGAGTAACCAGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATG
* *
33317059 TTCTTAAGAAAAAATTATAATAAATTAGGAGTCTGC
66 TCCTAAAGAAAAAA-TATAATAAATTAGGAGTCTGC
* *
33317095 TGGGCTGAGTAACCGGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATA
1 TGGGCTGAGTAACCAGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTC-G-ATA
33317160 T-TCCTAAAGCATAAAAAATATAA
64 TGTCCTAAAG---AAAAAATATAA
33317183 ATAATAAATA
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
101 55 0.72
102 7 0.09
103 3 0.04
104 5 0.07
105 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (100 bp):
TGGGCTGAGTAACCAGGGTGGGGTACTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATG
TCCTAAAGAAAAAATATAATAAATTAGGAGTCTGC
Found at i:33323366 original size:15 final size:14
Alignment explanation
Indices: 33323341--33323376 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
33323331 GACTCTATTT
*
33323341 TAATTATATTAGGA
1 TAATTATATTAAGA
33323355 TAATTGATATTAAGA
1 TAATT-ATATTAAGA
33323370 TAATTAT
1 TAATTAT
33323377 TAAGGATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATTATATTAAGA
Found at i:33326864 original size:13 final size:14
Alignment explanation
Indices: 33326848--33326934 Score: 51
Period size: 13 Copynumber: 6.5 Consensus size: 14
33326838 AGATGAATAA
33326848 ATGAAAT-GATTAT
1 ATGAAATAGATTAT
* *
33326861 ATG-AATCGGTTAT
1 ATGAAATAGATTAT
*
33326874 ATGGAAGTAGA-TAT
1 AT-GAAATAGATTAT
*
33326888 ATGAAAT-GGTTAT
1 ATGAAATAGATTAT
* *
33326901 ATG-AATCGGTTAT
1 ATGAAATAGATTAT
*
33326914 ATGGAACTAGA-TAT
1 AT-GAAATAGATTAT
33326928 ATGAAAT
1 ATGAAAT
33326935 GAAACATTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
12 7 0.12
13 32 0.56
14 12 0.21
15 6 0.11
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (14 bp):
ATGAAATAGATTAT
Found at i:33326903 original size:40 final size:40
Alignment explanation
Indices: 33326848--33326936 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
33326838 AGATGAATAA
*
33326848 ATGAAATGATTATATGAATCGGTTATATGGAAGTAGATAT
1 ATGAAATGATTATATGAATCGGTTATATGGAACTAGATAT
*
33326888 ATGAAATGGTTATATGAATCGGTTATATGGAACTAGATAT
1 ATGAAATGATTATATGAATCGGTTATATGGAACTAGATAT
33326928 ATGAAATGA
1 ATGAAATGA
33326937 AACATTGGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (40 bp):
ATGAAATGATTATATGAATCGGTTATATGGAACTAGATAT
Found at i:33330629 original size:28 final size:28
Alignment explanation
Indices: 33330597--33330652 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
33330587 CCCTTTTTAC
*
33330597 GATTTAGTTTTTTTCACCTAATTAACCA
1 GATTTAGTCTTTTTCACCTAATTAACCA
33330625 GATTTAGTCTTTTTCACCTAATTAACCA
1 GATTTAGTCTTTTTCACCTAATTAACCA
33330653 TTTAAACTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.45
Consensus pattern (28 bp):
GATTTAGTCTTTTTCACCTAATTAACCA
Found at i:33330708 original size:75 final size:75
Alignment explanation
Indices: 33330618--33330771 Score: 299
Period size: 75 Copynumber: 2.1 Consensus size: 75
33330608 TTTCACCTAA
33330618 TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
1 TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
33330683 TAATACGACC
66 TAATACGACC
*
33330693 TTAACCAGATTTAGTCTTTTTCTCCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
1 TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
33330758 TAATACGACC
66 TAATACGACC
33330768 TTAA
1 TTAA
33330772 TATAATCCCA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (75 bp):
TTAACCAGATTTAGTCTTTTTCACCTAATTAACCATTTAAACTTCAAAATTTCTCAACGAAACTT
TAATACGACC
Found at i:33333300 original size:6 final size:6
Alignment explanation
Indices: 33333289--33333319 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
33333279 AAGCCTTCCT
33333289 TTTTTC TTTTTC TTTTTC TTTTT- TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
33333320 CATTTTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:33333728 original size:76 final size:76
Alignment explanation
Indices: 33333648--33333798 Score: 284
Period size: 76 Copynumber: 2.0 Consensus size: 76
33333638 AAGATTACTT
*
33333648 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAATATGATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
33333713 ACAAACAATTA
66 ACAAACAATTA
*
33333724 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATTATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
33333789 ACAAACAATT
66 ACAAACAATT
33333799 CTGGCAAACC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.33
Consensus pattern (76 bp):
ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
ACAAACAATTA
Found at i:33335102 original size:8 final size:8
Alignment explanation
Indices: 33335089--33335121 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
33335079 AGTAAGCACT
33335089 GTGGAGTC
1 GTGGAGTC
33335097 GTGGAGTC
1 GTGGAGTC
33335105 GTGGA--C
1 GTGGAGTC
33335111 GTGGAGTC
1 GTGGAGTC
33335119 GTG
1 GTG
33335122 AATCGGTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.26
8 17 0.74
ACGTcount: A:0.12, C:0.12, G:0.52, T:0.24
Consensus pattern (8 bp):
GTGGAGTC
Found at i:33342069 original size:17 final size:17
Alignment explanation
Indices: 33342021--33342072 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
33342011 AATTTAAGGT
33342021 TTTTTTAATATTTTT-TA
1 TTTTTTAA-ATTTTTATA
* *
33342038 -ATTTTAAATCATTTATA
1 TTTTTTAAAT-TTTTATA
33342055 TTTTTTAAATTTTTATA
1 TTTTTTAAATTTTTATA
33342072 T
1 T
33342073 ATTATTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 9 0.32
18 8 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTAAATTTTTATA
Found at i:33342142 original size:50 final size:50
Alignment explanation
Indices: 33342048--33342142 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
33342038 ATTTTAAATC
* * * * *
33342048 ATTTATATTTTTTAAATTTTTATATATTATTTTGACCTTTTAAAATTTAT
1 ATTTATATATTTTAAATTTTTATAAATTACTTTAAACTTTTAAAATTTAT
33342098 ATTTATATATTTTAGAA-TTTTATAAATT-CTTTAAACTTTATAAAA
1 ATTTATATATTTTA-AATTTTTATAAATTACTTTAAACTTT-TAAAA
33342143 AAAATTTGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
49 8 0.21
50 28 0.74
51 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (50 bp):
ATTTATATATTTTAAATTTTTATAAATTACTTTAAACTTTTAAAATTTAT
Found at i:33343770 original size:25 final size:25
Alignment explanation
Indices: 33343742--33343820 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
33343732 GATAATCAAT
*
33343742 TTAAGGATCCCTTGATGGATTTGAA
1 TTAAGAATCCCTTGATGGATTTGAA
* * *
33343767 TTAATAATCCCTTAAAGGATTTGAA
1 TTAAGAATCCCTTGATGGATTTGAA
* * *
33343792 TCAAGAATCCCCTGATGGATTTGAG
1 TTAAGAATCCCTTGATGGATTTGAA
33343817 TTAA
1 TTAA
33343821 TGATATTGTT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (25 bp):
TTAAGAATCCCTTGATGGATTTGAA
Found at i:33344980 original size:31 final size:31
Alignment explanation
Indices: 33344944--33345006 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
33344934 AAATAATGGC
33344944 AGGACATATGATAATATTATTAACTCAGAAG
1 AGGACATATGATAATATTATTAACTCAGAAG
33344975 AGGACATATGATAATATTATTAACTCAGAAG
1 AGGACATATGATAATATTATTAACTCAGAAG
33345006 A
1 A
33345007 TGTACATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (31 bp):
AGGACATATGATAATATTATTAACTCAGAAG
Found at i:33349541 original size:23 final size:23
Alignment explanation
Indices: 33349515--33349558 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
33349505 TCATATTATA
33349515 CAATTAAAACAATTCATCTTGTG
1 CAATTAAAACAATTCATCTTGTG
33349538 CAATTAAAACAATTCATCTTG
1 CAATTAAAACAATTCATCTTG
33349559 CTAATGCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (23 bp):
CAATTAAAACAATTCATCTTGTG
Found at i:33360045 original size:21 final size:21
Alignment explanation
Indices: 33360007--33360046 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33359997 CCTCTTTTTT
*
33360007 TATGTATTCCGGCTTGTCCAG
1 TATGTATTCCGGCATGTCCAG
33360028 TATGTA-TCCGGGCATGTCC
1 TATGTATTCC-GGCATGTCC
33360047 GACGAGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGTATTCCGGCATGTCCAG
Found at i:33364716 original size:21 final size:21
Alignment explanation
Indices: 33364690--33364745 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
33364680 AATAGCGGTG
*
33364690 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
33364711 GCGGTGAAATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
33364732 GCGATGAGATTAGA
1 GCGGTGAGATTAGA
33364746 AACAATGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:33364966 original size:17 final size:18
Alignment explanation
Indices: 33364944--33364984 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
33364934 TATTTTAATG
*
33364944 AATTATATAATTA-ATTA
1 AATTATATAATTAGATAA
*
33364961 AATTAT-TTATTAGATAA
1 AATTATATAATTAGATAA
33364978 AATTATA
1 AATTATA
33364985 ATTTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATTATATAATTAGATAA
Found at i:33368312 original size:39 final size:39
Alignment explanation
Indices: 33368258--33368338 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
33368248 ATGCAATCGA
33368258 TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
* *
33368297 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
33368336 TTT
1 TTT
33368339 TCACTTTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (39 bp):
TTTGTTCATCTTTAAAGCTTTACTTGAACTACTGTTCTC
Found at i:33368729 original size:30 final size:30
Alignment explanation
Indices: 33368648--33369308 Score: 1071
Period size: 30 Copynumber: 22.2 Consensus size: 30
33368638 GAATAAACTG
33368648 AATACACTACATATATATTTTTTATTTTTAA
1 AATACACTACATATAT-TTTTTTATTTTTAA
*
33368679 AATACACTAAATATATTTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTTATTTTTAA
33368710 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33368740 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33368769 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33368798 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33368827 AATACACTACATATATATATTTTTTATTTTTAA
1 AATACACTAC--ATATAT-TTTTTTATTTTTAA
*
33368860 AGTACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33368889 AATACACTACATATA--TTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
33368917 AATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33368947 AATACACTACATATA--TTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33368975 AATACACTACATATATATTTTTTTTATTTTTAA
1 AATACACTAC--ATATA-TTTTTTTATTTTTAA
33369008 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
33369038 AATACACTAC--ATATTTTTTTATTTTTTA
1 AATACACTACATATATTTTTTTATTTTTAA
*
33369066 AATATACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33369096 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
33369126 AATACACTACATATA-GTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33369155 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33369185 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33369214 AATACACTAC--ATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
33369242 AATACACTACATATATTTCTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
* *
33369272 AATACATTACATATATATTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
33369302 AATACAC
1 AATACAC
33369309 AAATACAATG
Statistics
Matches: 597, Mismatches: 15, Indels: 37
0.92 0.02 0.06
Matches are distributed among these distances:
27 3 0.01
28 101 0.17
29 162 0.27
30 227 0.38
31 57 0.10
32 1 0.00
33 46 0.08
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (30 bp):
AATACACTACATATATTTTTTTATTTTTAA
Found at i:33368796 original size:58 final size:58
Alignment explanation
Indices: 33368648--33369308 Score: 1060
Period size: 58 Copynumber: 11.1 Consensus size: 58
33368638 GAATAAACTG
*
33368648 AATACACTACATATATATTTTTTATTTTTAAAATACACTAAATATATTTTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTATTTTTAAAATACACTACATATA--TTTTTTATTTTTAA
33368710 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
33368769 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
33368827 AATACACTACATATATATATTTTTTATTTTTAAAGTACACTACATATATTTTTTATTTTTAA
1 AATACACTAC----ATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
33368889 AATACACTACATATA-TTTTTATTTTTAAAATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATAT-TTTTTATTTTTAA
33368947 AATACACTACATATA-TTTTTATTTTTAAAATACACTACATATATATTTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTAC--ATATA--TTTTTTATTTTTAA
*
33369008 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATAT-TTTTTTATTTTTTA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
33369066 AATATACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
*
33369126 AATACACTACATATAGTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
33369185 AATACACTACATATATTTTTTATTTTTAAAATACACTACATAT-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
33369242 AATACACTACATATATTTCTTTATTTTTAAAATACATTACATATATATTTTTATTTTTAA
1 AATACACTACATATATTT-TTTATTTTTAAAATACACTACATATAT-TTTTTATTTTTAA
33369302 AATACAC
1 AATACAC
33369309 AAATACAATG
Statistics
Matches: 572, Mismatches: 10, Indels: 36
0.93 0.02 0.06
Matches are distributed among these distances:
57 60 0.10
58 189 0.33
59 115 0.20
60 57 0.10
61 60 0.10
62 68 0.12
63 23 0.04
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (58 bp):
AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
Found at i:33369402 original size:43 final size:43
Alignment explanation
Indices: 33369354--33369486 Score: 212
Period size: 43 Copynumber: 3.0 Consensus size: 43
33369344 CTTCTATCGA
* *
33369354 TTCCCCTTTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCAT
1 TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCCATTCCCAT
*
33369397 TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCTATTCCCAT
1 TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCCATTCCCAT
*
33369440 TTCCCCTCTTCCATCGATTCCCCTCCTCCCATTTCCCATTCCCAT
1 TTCCCCTCTTCCATCG--TGCCCTCCTCCCATTTCCCATTCCCAT
33369485 TT
1 TT
33369487 ACGGTTACTT
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 56 0.67
45 27 0.33
ACGTcount: A:0.10, C:0.50, G:0.04, T:0.37
Consensus pattern (43 bp):
TTCCCCTCTTCCATCGTGCCCTCCTCCCATTTCCCATTCCCAT
Found at i:33370936 original size:19 final size:19
Alignment explanation
Indices: 33370914--33370972 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 19
33370904 CTATTTTCGA
33370914 GTTCCTTTCACTTTTTTCT
1 GTTCCTTTCACTTTTTTCT
* * *
33370933 GTT-C--TAACTATTTTCGA
1 GTTCCTTTCACTTTTTTC-T
33370950 GTTCCTTTCACTTTTTTCT
1 GTTCCTTTCACTTTTTTCT
33370969 GTTC
1 GTTC
33370973 TAACTTTGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 9 0.30
17 3 0.10
18 2 0.07
19 7 0.23
20 9 0.30
ACGTcount: A:0.10, C:0.24, G:0.08, T:0.58
Consensus pattern (19 bp):
GTTCCTTTCACTTTTTTCT
Found at i:33370950 original size:36 final size:36
Alignment explanation
Indices: 33370903--33370977 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
33370893 CCTTTGAGGT
33370903 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
1 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
33370939 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
1 ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
33370975 ACT
1 ACT
33370978 TTGAATCTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.55
Consensus pattern (36 bp):
ACTATTTTCGAGTTCCTTTCACTTTTTTCTGTTCTA
Found at i:33371320 original size:19 final size:19
Alignment explanation
Indices: 33371292--33371362 Score: 106
Period size: 19 Copynumber: 3.6 Consensus size: 19
33371282 TTCGAGGATC
*
33371292 TGCAACCTTAGATATGATA
1 TGCAATCTTAGATATGATA
33371311 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATG--ATA
33371332 TGCAATCTTAGATATGATA
1 TGCAATCTTAGATATGATA
*
33371351 TGTAATCTTAGA
1 TGCAATCTTAGA
33371363 AGATATGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 29 0.60
21 19 0.40
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
TGCAATCTTAGATATGATA
Found at i:33371334 original size:21 final size:21
Alignment explanation
Indices: 33371292--33371351 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
33371282 TTCGAGGATC
*
33371292 TGCAACCTTAGATATG--ATA
1 TGCAATCTTAGATATGATATA
33371311 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGATATA
33371332 TGCAATCTTAGATATGATAT
1 TGCAATCTTAGATATGATAT
33371352 GTAATCTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 15 0.39
21 23 0.61
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGCAATCTTAGATATGATATA
Found at i:33371381 original size:23 final size:22
Alignment explanation
Indices: 33371301--33371385 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
33371291 CTGCAACCTT
*
33371301 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
33371322 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
33371341 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
33371363 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
33371386 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:33371395 original size:22 final size:23
Alignment explanation
Indices: 33371351--33371395 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
33371341 AGATATGATA
*
33371351 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
33371374 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
33371396 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:33371831 original size:18 final size:19
Alignment explanation
Indices: 33371806--33371851 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
33371796 GTTTTTAGTC
*
33371806 TATT-TTATTAATTTTAT-
1 TATTATTATTAATATTATA
*
33371823 TTTTATTATT-ATATTATA
1 TATTATTATTAATATTATA
33371841 TATTATTATTA
1 TATTATTATTA
33371852 TACCTACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATTATTAATATTATA
Found at i:33378261 original size:6 final size:6
Alignment explanation
Indices: 33378250--33378282 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
33378240 CATTCTCAAA
33378250 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
33378283 TAAATAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:33378527 original size:44 final size:44
Alignment explanation
Indices: 33378479--33378705 Score: 136
Period size: 44 Copynumber: 5.2 Consensus size: 44
33378469 AGACACCAGC
*
33378479 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAATTAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* **** * * ** * * *
33378523 CTTGCCTTCCTGCACCGACAGCGAAGCA-GATCGAAGTCACCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAAT-AGCAGAT
* *
33378567 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
* **** * * * ** * * * *
33378611 CTTGCCTTCCTGCACCGACAGCGAATCAGATCGAAGACACCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAGCAGAT
*
33378655 CTTGCCTCCCTGGGTTGCAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
33378699 CTTGCCT
1 CTTGCCT
33378706 TCTTGCACCG
Statistics
Matches: 121, Mismatches: 56, Indels: 12
0.64 0.30 0.06
Matches are distributed among these distances:
43 28 0.23
44 65 0.54
45 28 0.23
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:33378923 original size:44 final size:44
Alignment explanation
Indices: 33378523--33378930 Score: 141
Period size: 44 Copynumber: 9.3 Consensus size: 44
33378513 ATTAGCAGAT
*
33378523 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
* **** * * * * * ** *
33378567 CTTGCCTCCCTGGGTTG-CAGCGGAGCAG-GCTAAAAATAGTAGAT
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATC-GAAGACACCAG-C
*
33378611 CTTGCCTTCCTGCACCGACAGCGAATCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
* **** * * * ** * * * *
33378655 CTTGCCTCCCTGGGTTG-CAGCGGAGTAGGTTAAAAATAGCAGAT
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAG-C
* ** * *
33378699 CTTGCCTTCTTGCACCGACAATGAAGCAGATCGAAGTCACCAAC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
**** * * * * * * *
33378743 CTTGCC-TCCTTGGGTTG-CAGCGGAGCAG-GCTAAAAATAGCAGAT
1 CTTGCCTTCC-TGCACCGACAGCGAAGCAGATC-GAAGACACCAG-C
* *
33378787 ATTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
* **** * * * * *
33378831 CTTGCCTCCCTGTGTTG-CAGC-AGAGCAG-GCTGAAAATAGCAGAT
1 CTTGCCTTCCTGCACCGACAGCGA-AGCAGATC-GAAGACACCAG-C
*
33378875 CTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
*
33378919 CTTGCCTCCCTG
1 CTTGCCTTCCTG
33378931 GGTTACAGCG
Statistics
Matches: 230, Mismatches: 116, Indels: 36
0.60 0.30 0.09
Matches are distributed among these distances:
42 4 0.02
43 63 0.27
44 94 0.41
45 65 0.28
46 4 0.02
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (44 bp):
CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:33379040 original size:88 final size:88
Alignment explanation
Indices: 33378421--33379007 Score: 886
Period size: 88 Copynumber: 6.7 Consensus size: 88
33378411 AGCAGATTAG
* * * * * * *
33378421 TAAAGATAACAGATCTTGCCTTCCTGTACTGGCAGCGAAACAGATCAAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
33378486 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* *
33378509 TAAAATTAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGTCACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
33378574 CCCTGGGTTGCAGCGGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGT
* *
33378597 TAAAAATAGTAGATCTTGCCTTCCTGCACCGACAGCGAATCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
*
33378662 CCCTGGGTTGCAGCGGAGTAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* ** * *
33378685 TAAAAATAGCAGATCTTGCCTTCTTGCACCGACAATGAAGCAGATCGAAGTCACCAACCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
33378750 CCTTGGGTTGCAGCGGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGT
* *
33378773 TAAAAATAGCAGATATTGCCTTCCTGCACCAACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
33378838 CCCTGTGTTGCAGCAGAGCAGGC
66 CCCTGGGTTGCAGCGGAGCAGGT
* *
33378861 TGAAAATAGCAGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* *
33378926 CCCTGGGTTACAGCGGAGCAAGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * *
33378949 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATTGATGACCCCAGCC
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
33379008 CTATCTCCCT
Statistics
Matches: 449, Mismatches: 50, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 449 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:33379073 original size:44 final size:44
Alignment explanation
Indices: 33379007--33379344 Score: 455
Period size: 44 Copynumber: 7.7 Consensus size: 44
33378997 TGACCCCAGC
*
33379007 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
33379051 CCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
33379095 CCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
33379139 CCTATCTCCTTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
33379183 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * ** *
33379227 TCTATTTCCCTGGGCAGCAGTGGAATAAATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGA-AT
* *
33379271 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATGGTGAAA
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
33379315 CTTATCTCCCTGAG-CAGTAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
33379345 GGAAAATAGC
Statistics
Matches: 257, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
43 1 0.00
44 254 0.99
45 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:33379744 original size:44 final size:44
Alignment explanation
Indices: 33379651--33379758 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
33379641 ATGACAAATT
* *
33379651 TTATCTCCCTAAAGTTGCAATGAAACAGATTAAAGCCGATAATC
1 TTATCTCCCTAAAGTTGCAGTGAAACAGATTAAAACCGATAATC
* * * * * *
33379695 CTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC-TTGGATC
1 TTATCTCCCTAAAGTTGCAGTGAAACAGATTAAAACCGAT-AATC
*
33379739 TTATCTCTCTAAAGTTGCAG
1 TTATCTCCCTAAAGTTGCAG
33379759 AGAGCAGAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 1 0.02
44 51 0.98
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
TTATCTCCCTAAAGTTGCAGTGAAACAGATTAAAACCGATAATC
Found at i:33380221 original size:20 final size:21
Alignment explanation
Indices: 33380189--33380240 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
33380179 CTTCGAGGAT
33380189 ATGCAATCTTAGATATGATAA
1 ATGCAATCTTAGATATGATAA
33380210 ATGCAA-CTTAGATATGAT--
1 ATGCAATCTTAGATATGATAA
*
33380228 ATGTAATCTTAGA
1 ATGCAATCTTAGA
33380241 AGATATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.17
19 6 0.21
20 12 0.41
21 6 0.21
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
ATGCAATCTTAGATATGATAA
Found at i:33380247 original size:22 final size:23
Alignment explanation
Indices: 33380219--33380263 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
33380209 AATGCAACTT
33380219 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
33380241 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
33380264 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:33380273 original size:22 final size:23
Alignment explanation
Indices: 33380229--33380273 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
33380219 AGATATGATA
*
33380229 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
33380252 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
33380274 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:33380478 original size:21 final size:19
Alignment explanation
Indices: 33380441--33380479 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
33380431 ACTGTTTTCT
*
33380441 TTTTTTCCTTTTTCGATTA
1 TTTTTTACTTTTTCGATTA
33380460 TTTTTTACTTATTTACGATT
1 TTTTTTACTT-TTT-CGATT
33380480 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTTACTTTTTCGATTA
Found at i:33380712 original size:15 final size:15
Alignment explanation
Indices: 33380683--33380738 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
33380673 GTTTTTAGTC
*
33380683 TATT-TTATTAATTT
1 TATTATTATTATTTT
*
33380697 TGTTATTATTATTTT
1 TATTATTATTATTTT
*
33380712 TATTGTTA-TATTTT
1 TATTATTATTATTTT
33380726 ATATTATTATTAT
1 -TATTATTATTAT
33380739 ACCTACATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.26
15 22 0.65
16 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (15 bp):
TATTATTATTATTTT
Found at i:33382682 original size:21 final size:21
Alignment explanation
Indices: 33382641--33382725 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
33382631 CCAAGAACAA
*
33382641 AGCAAAAAAGAGAGGAGAAACC
1 AGCAAAAACGAG-GGAGAAACC
*
33382663 AGCAAAAACGAGGGACAAACC
1 AGCAAAAACGAGGGAGAAACC
* * *
33382684 AGTAAGAACAAGGGAGAAACC
1 AGCAAAAACGAGGGAGAAACC
* *
33382705 AGCAAGAACTAGGGGAGAAAC
1 AGCAAAAACGA-GGGAGAAAC
33382726 TGTTATTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 34 0.63
22 20 0.37
ACGTcount: A:0.53, C:0.16, G:0.28, T:0.02
Consensus pattern (21 bp):
AGCAAAAACGAGGGAGAAACC
Found at i:33386978 original size:26 final size:26
Alignment explanation
Indices: 33386949--33387001 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
33386939 ATCGGTTTTA
33386949 TCTGTAAGTTGAATCCACCATAATAG
1 TCTGTAAGTTGAATCCACCATAATAG
*
33386975 TCTGTAAGTTGAATTCACCATAATAG
1 TCTGTAAGTTGAATCCACCATAATAG
33387001 T
1 T
33387002 AATTTGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (26 bp):
TCTGTAAGTTGAATCCACCATAATAG
Found at i:33390506 original size:18 final size:19
Alignment explanation
Indices: 33390471--33390530 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
33390461 GTGACCCTTA
33390471 TTTTC-AAAATTTTCCTAT
1 TTTTCTAAAATTTTCCTAT
33390489 TTTTCTAAAATTTT-CTAT
1 TTTTCTAAAATTTTCCTAT
*
33390507 TTTGTTTAAAATTTGTCCCTAT
1 TTT-TCTAAAATTT-T-CCTAT
33390529 TT
1 TT
33390531 GTTCCCGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 12 0.33
19 17 0.47
20 1 0.03
22 6 0.17
ACGTcount: A:0.25, C:0.13, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTCTAAAATTTTCCTAT
Found at i:33394086 original size:2 final size:2
Alignment explanation
Indices: 33394079--33394108 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33394069 GTATAATAAC
33394079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33394109 CGATTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33396316 original size:13 final size:13
Alignment explanation
Indices: 33396298--33396327 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33396288 TGACGAGATG
33396298 CAAAAGTGCAAGC
1 CAAAAGTGCAAGC
*
33396311 CAAAAGTTCAAGC
1 CAAAAGTGCAAGC
33396324 CAAA
1 CAAA
33396328 TGGGGGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (13 bp):
CAAAAGTGCAAGC
Found at i:33402634 original size:23 final size:23
Alignment explanation
Indices: 33402607--33402760 Score: 172
Period size: 23 Copynumber: 6.8 Consensus size: 23
33402597 GGCTTTGCCG
33402607 ATCAGGCACTTTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
33402630 ATCAGGCACTTTATGTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTA-C
*
33402654 -TTAGGCACTTTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
*
33402676 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAC
* * ** *
33402699 TTCAGGCACCTCGTGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAC
* * * *
33402722 TTCAGGCACCTTGTGTGTC--AT
1 ATCAGGCACTTTATGTGTCGTAC
33402743 ATCAGGCAC-TTATGTGTC
1 ATCAGGCACTTTATGTGTC
33402761 ATATACTGAT
Statistics
Matches: 119, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
20 8 0.07
21 10 0.08
22 1 0.01
23 99 0.83
24 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAC
Found at i:33402663 original size:46 final size:46
Alignment explanation
Indices: 33402610--33402760 Score: 193
Period size: 46 Copynumber: 3.3 Consensus size: 46
33402600 TTTGCCGATC
33402610 AGGCACTTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
1 AGGCACTTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
33402656 AGGCACTTTATGTGTCGTACATCAGGCACTTTATGTGTCGTAT-TT
1 AGGCACTTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
* ** ** * * *
33402701 CAGGCACCTCGTGTGTCGTATTTCAGGCACCTTGTGTGTCATATC--
1 -AGGCACTTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
33402746 AGGCAC-TTATGTGTC
1 AGGCACTTTATGTGTC
33402761 ATATACTGAT
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
43 7 0.08
44 6 0.06
45 2 0.02
46 78 0.84
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (46 bp):
AGGCACTTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
Found at i:33402718 original size:69 final size:67
Alignment explanation
Indices: 33402607--33402760 Score: 195
Period size: 69 Copynumber: 2.3 Consensus size: 67
33402597 GGCTTTGCCG
* * *
33402607 ATCAGGCACTTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT-AGGCACTTTATGTGT
1 ATCAGGCACTTTATGTGTCGTACATCAGGCACCTCATGTGTCGTAT-TTCAGGCACCTTATGTGT
33402671 CGTAC
65 C--AC
** * *
33402676 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTATTTCAGGCACCTTGTGTGTC
1 ATCAGGCACTTTATGTGTCGTACATCAGGCACCTCATGTGTCGTATTTCAGGCACCTTATGTGTC
*
33402741 AT
66 AC
33402743 ATCAGGCAC-TTATGTGTC
1 ATCAGGCACTTTATGTGTC
33402761 ATATACTGAT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
66 9 0.12
67 10 0.13
68 2 0.03
69 55 0.72
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (67 bp):
ATCAGGCACTTTATGTGTCGTACATCAGGCACCTCATGTGTCGTATTTCAGGCACCTTATGTGTC
AC
Found at i:33405460 original size:28 final size:27
Alignment explanation
Indices: 33405423--33405477 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
33405413 GGTTAAATAG
* *
33405423 TTTAGGTACCAGTTCTAACAAAAA-AAAA
1 TTTAGATACCAATT-TAA-AAAAACAAAA
33405451 TTTAGATACCAATTTAAAAAAACAAAA
1 TTTAGATACCAATTTAAAAAAACAAAA
33405478 CTAGTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 12 0.50
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (27 bp):
TTTAGATACCAATTTAAAAAAACAAAA
Found at i:33406768 original size:19 final size:17
Alignment explanation
Indices: 33406746--33406786 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
33406736 TACTTTAGAC
33406746 TTTTTTCATTTTCTATATA
1 TTTTTTCATTTTCT-TA-A
*
33406765 TTTTTTTATTTTCTTAA
1 TTTTTTCATTTTCTTAA
33406782 TTTTT
1 TTTTT
33406787 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCATTTTCTTAA
Found at i:33415822 original size:28 final size:27
Alignment explanation
Indices: 33415791--33415844 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
33415781 ACAATTTGGA
33415791 ATTTGTAAT-AATTTTATAATTATTTTAC
1 ATTTGTAATAAATTTTA-AATT-TTTTAC
*
33415819 ATTTTTAATAAATTTTAAATTTTTTA
1 ATTTGTAATAAATTTTAAATTTTTTA
33415845 TTTTAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 5 0.21
28 12 0.50
29 7 0.29
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTTGTAATAAATTTTAAATTTTTTAC
Found at i:33418996 original size:3 final size:3
Alignment explanation
Indices: 33418988--33419030 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
33418978 TAAATTTGAC
*
33418988 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
33419031 TTCCTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:33419154 original size:7 final size:7
Alignment explanation
Indices: 33419142--33419167 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33419132 ATTATATCAT
33419142 TTTATTA
1 TTTATTA
33419149 TTTATTA
1 TTTATTA
33419156 TTTATTA
1 TTTATTA
33419163 TTTAT
1 TTTAT
33419168 GTCCTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:33419223 original size:14 final size:14
Alignment explanation
Indices: 33419206--33419246 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
33419196 TTACTATATT
33419206 TTATTTATATTTAC
1 TTATTTATATTTAC
*
33419220 TTATTTATATTTTTC
1 TTATTTATA-TTTAC
33419235 TTATTATATATT
1 TTATT-TATATT
33419247 ATTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 9 0.38
15 11 0.46
16 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTTATATTTAC
Found at i:33419246 original size:16 final size:15
Alignment explanation
Indices: 33419206--33419246 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
33419196 TTACTATATT
33419206 TTATTTATA-TTTAC
1 TTATTTATATTTTAC
*
33419220 TTATTTATATTTTTC
1 TTATTTATATTTTAC
33419235 TTATTATATATT
1 TTATT-TATATT
33419247 ATTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
15 9 0.38
16 6 0.25
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTATATTTTAC
Found at i:33419250 original size:10 final size:10
Alignment explanation
Indices: 33419235--33419268 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
33419225 TATATTTTTC
33419235 TTATTATATA
1 TTATTATATA
33419245 TTATTATATAA
1 TTATTATAT-A
33419256 TTATTTATATA
1 TTA-TTATATA
33419267 TT
1 TT
33419269 TTTTTCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 7 0.32
12 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTATATA
Found at i:33427330 original size:14 final size:14
Alignment explanation
Indices: 33427308--33427341 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
33427298 ACTACACAAT
33427308 TAATAACATGATTA
1 TAATAACATGATTA
*
33427322 TAATGACATGATTA
1 TAATAACATGATTA
*
33427336 AAATAA
1 TAATAA
33427342 TATAACTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (14 bp):
TAATAACATGATTA
Found at i:33427711 original size:27 final size:27
Alignment explanation
Indices: 33427672--33427731 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
33427662 TATTATGCTT
33427672 TGTTGCCCAACAAAGCTCACAGTACAA
1 TGTTGCCCAACAAAGCTCACAGTACAA
*
33427699 TGTTGCCCGACAAAGCTCACAGTACAA
1 TGTTGCCCAACAAAGCTCACAGTACAA
33427726 TGTTGC
1 TGTTGC
33427732 TAATACTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (27 bp):
TGTTGCCCAACAAAGCTCACAGTACAA
Found at i:33428711 original size:2 final size:2
Alignment explanation
Indices: 33428704--33428738 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
33428694 CTTTATTATC
* *
33428704 AT AT AT AT AT AT AT AT AT AT AT AA AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33428739 GAGGGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:33429125 original size:21 final size:22
Alignment explanation
Indices: 33429099--33429143 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
33429089 ATGATTCGAC
33429099 TTATTTTT-AATTAAGTGCTAT
1 TTATTTTTAAATTAAGTGCTAT
33429120 TTATTTTTAAATTAAGTGCTAT
1 TTATTTTTAAATTAAGTGCTAT
33429142 TT
1 TT
33429144 TTCTATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (22 bp):
TTATTTTTAAATTAAGTGCTAT
Found at i:33429688 original size:111 final size:109
Alignment explanation
Indices: 33429487--33430619 Score: 1115
Period size: 111 Copynumber: 10.2 Consensus size: 109
33429477 TATACAGGGG
* * * *
33429487 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTATGT-AA-TTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * *
33429550 CATTTTGAGTTGTCATTGGCTGGCACCAGTATAC-AAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* * *******
33429593 AAAAAACGAAAATTTTGGTGGTGGCCTGGCAATGGTCGGCACCACCTTTATGTAAAAAAAAAAAT
1 AAAAAA--AAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-AAATTTTTTTT
* *
33429658 TTACATTTTGGGTTGTCATTGGTCGGCACCAGTATAC-AAAAAATTC
63 TTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* * *
33429704 AAAAAAAAAAATTTTTTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATG-CAATTTTTTT
1 --AAAAAAAAA--TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTT
* *
33429768 TTTACATTTTGGGCTGTCATTAGCCGGCACCAGTATACAAAAAAATT-
62 TTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* * *
33429815 AAAAAAAAA-TTTTGGTGGTGGCTTGGTAATAGCCGGCACCACCTTTATGTAAATTGGTTTTTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA--------TTT
**
33429879 TTTTTTTACATTTTGGGCTGTCATTGGCCAACACCAGTATACGAAAACAATTC
58 TTTTTTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAA-AATTC
***** *
33429932 AAAATTTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * ** *
33429997 CATTTTGGGCTATAATTGGTTGGCACCAGTATACAAAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
*** * * * *
33430041 --AAAATTTTTTTTTGAGGTGGCCTGGCAATGGCCTGCACCACCTTTAAGT-AATTTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * * *
33430103 CATTTTGGACTGTCATTGGCTGACACTAGTATACGAAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
***** * * * **
33430147 AAAATTTTTTTTTTGGTGGTGGCTTGGCAATGGACAGCATGACCTTTATGTAAATTTTTTTTTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA--TTTTTTTTT
* * *
33430212 TACATTTTGGGCTATCATTGGCAGGCACCAGTATACGAAAAAGTT-
64 TACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* *
33430257 AAAAAAAAAATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTATTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT----AAATTTTTTT
* * *
33430322 TTTACATTTTGGGCTGTCATTGGCCTGCACTAGTATATGAAAAAAATT-
62 TTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACG-AAAAAATTC
** * ******
33430370 AAAAAAAAATTTTTCATGGTGGCCTGGCAATGGCCGGCACCACTTTTATGTAAA-AAAAAATTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * *
33430434 CATTTTGGGCTATCATTGGCCGGCATCAATATACGAAAAAATTC
66 CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
* *
33430478 AAAAAAAATTTTTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATG-AAATTTTTTTTT
1 AAAAAAAA--ATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA----TTTTT
* *
33430542 CTTTTTACATTTTGGGCTGTCATTGGCCGGTACCAGTATACGAAAAAATTGA
60 -TTTTTACATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATT-C
*
33430594 AAAAAAAAACTTTTAGGTGGTGGCCT
1 AAAAAAAAA-TTTTTGGTGGTGGCCT
33430620 AAAAATTGCC
Statistics
Matches: 846, Mismatches: 138, Indels: 77
0.80 0.13 0.07
Matches are distributed among these distances:
106 90 0.11
107 53 0.06
108 120 0.14
109 22 0.03
110 122 0.14
111 132 0.16
112 48 0.06
113 97 0.11
114 3 0.00
115 103 0.12
116 12 0.01
117 4 0.00
118 40 0.05
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (109 bp):
AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
CATTTTGGGCTGTCATTGGCCGGCACCAGTATACGAAAAAATTC
Done.