Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 58 of 373
Found at i:17479820 original size:570 final size:571
Alignment explanation
Indices: 17478718--17479860 Score: 2073
Period size: 570 Copynumber: 2.0 Consensus size: 571
17478708 GTTAGTGTGA
17478718 ACAACATAGATGCCGAATATCAAATAGGCATTTTAGGCTTATAAATAGCTTACTTGTTTATTGTA
1 ACAACATAGATGCCGAATATC-AATAGGCATTTTAGGCTTATAAATAGCTTACTTGTTTATTGTA
*
17478783 AAAGGTTTACAGAATTGATCAATTAAACTTAATAGAACTTTTGTTCTGTGAGGTTACCTCCTCTC
65 AAAGGTTTACAGAATTGATCAATTAAACTTAATAGAACTTTTGTTCTGTAAGGTTACCTCCTCTC
* * *
17478848 TTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGTGTCAATCCGAACTCCATTG
130 TTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGCGTCAATCCAAACTCAATTG
* *
17478913 AACTTATCACCGAATCGTGTGGCGTTCAACCATATTTTATACCTTTGGTTCTTACCTCTATATAG
195 AACTTATCACCAAACCGTGTGGCGTTCAACCATATTTTATACCTTTGGTTCTTACCTCTATATAG
*
17478978 GTATTGGGTCAAGGTTCGCTTCTATCCTTCCACAAATTTCACCTTAAGCAATATAAGACTCGGGC
260 GTATTGGGTCAAGGTTCGCTTCTATCCTTCCACAAATTTCACCTTAAGCAATATAAAACTCGGGC
17479043 AATACTTTTTAGTATTGAACATTCTTGACGTTAAGTTTTATTTTCCATCTCCATCAATTACCTTT
325 AATACTTTTTAGTATTGAACATTCTTGACGTTAAGTTTTATTTTCCATCTCCATCAATTACCTTT
17479108 TTCTAACCTACCTTGTTTCTATTCTAAACCGAATTTATCAACACCAAACCACTCATCTAAACCCT
390 TTCTAACCTACCTTGTTTCTATTCTAAACCGAATTTATCAACACCAAACCACTCATCTAAACCCT
17479173 CTCAAAGCTTCCGCAACCCTTAGCCTAAATCACCCAATTTTGACAACTCCAACTACTCCTCGTAG
455 CTCAAAGCTTCCGCAACCCTTAGCCTAAATCACCCAATTTTGACAACTCCAACTACTCCTCGTAG
* *
17479238 ACGATCGGGCAACTTTGTGAAACGACTCGGTTAACCTGGGCCGGATCACATC
520 ACGATCGGGCAACTTTGTGAAACGACTCGATTAACCTAGGCCGGATCACATC
*
17479290 ACAACATATATGCCGAATATC-ATAGGCATTTTAGGCTTATAAATAGCTTACTTG-TTATTGTAA
1 ACAACATAGATGCCGAATATCAATAGGCATTTTAGGCTTATAAATAGCTTACTTGTTTATTGTAA
*
17479353 AAGG-TTACAGAATTTGAT-TATTAAACTTAATAGAACTTTTGTTCTTGTAAGGTTACCTCCTCT
66 AAGGTTTACAGAA-TTGATCAATTAAACTTAATAGAACTTTTGTTC-TGTAAGGTTACCTCCTCT
*
17479416 CTTC-TTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGCGTCCATCCAAACTCAATT
129 CTTCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGCGTCAATCCAAACTCAATT
17479480 GAACTTATCACCAAACCGGTGTGGCGTTCAACCATATTTTTATACCTTTGGTTCTTACCTCTATA
194 GAACTTATCACCAAACC-GTGTGGCGTTCAACCATA-TTTTATACCTTTGGTTCTTACCTCTATA
17479545 TAGGTATTGGGTCAAGGTTCGCTTCTATCCTT-CATCAAATTTCACCTTAAGCAATATAAAACTC
257 TAGGTATTGGGTCAAGGTTCGCTTCTATCCTTCCA-CAAATTTCACCTTAAGCAATATAAAACTC
17479609 GGGCAATACTTTTTAGTATTGAACATTCTTGACGTTAAGTTTTATTTTCCATCTCCATCAATTAC
321 GGGCAATACTTTTTAGTATTGAACATTCTTGACGTTAAGTTTTATTTTCCATCTCCATCAATTAC
*
17479674 CTTTTTCTAACCTACCTTGTTTCTATTCTAAATCGAATTTATCAACACCAAACCACTCATCTAAA
386 CTTTTTCTAACCTACCTTGTTTCTATTCTAAACCGAATTTATCAACACCAAACCACTCATCTAAA
17479739 CCCTCTCAAAGCTTCCGCAACCCTTAGCCTAAATCACCCAATTTTGACAACTCCAACTACTCCTC
451 CCCTCTCAAAGCTTCCGCAACCCTTAGCCTAAATCACCCAATTTTGACAACTCCAACTACTCCTC
17479804 GTAGACGATCGGGCAACTTTGTGAAACGACTCGATTAACCTAGGCCGGATCACATC
516 GTAGACGATCGGGCAACTTTGTGAAACGACTCGATTAACCTAGGCCGGATCACATC
17479860 A
1 A
17479861 TCAAGGCTTC
Statistics
Matches: 553, Mismatches: 13, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
568 104 0.19
569 59 0.11
570 370 0.67
572 20 0.04
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (571 bp):
ACAACATAGATGCCGAATATCAATAGGCATTTTAGGCTTATAAATAGCTTACTTGTTTATTGTAA
AAGGTTTACAGAATTGATCAATTAAACTTAATAGAACTTTTGTTCTGTAAGGTTACCTCCTCTCT
TCTTTCGTTCGAGTCTCGAAGCGACTTATCTAGCTTGCTAGTGGCGTCAATCCAAACTCAATTGA
ACTTATCACCAAACCGTGTGGCGTTCAACCATATTTTATACCTTTGGTTCTTACCTCTATATAGG
TATTGGGTCAAGGTTCGCTTCTATCCTTCCACAAATTTCACCTTAAGCAATATAAAACTCGGGCA
ATACTTTTTAGTATTGAACATTCTTGACGTTAAGTTTTATTTTCCATCTCCATCAATTACCTTTT
TCTAACCTACCTTGTTTCTATTCTAAACCGAATTTATCAACACCAAACCACTCATCTAAACCCTC
TCAAAGCTTCCGCAACCCTTAGCCTAAATCACCCAATTTTGACAACTCCAACTACTCCTCGTAGA
CGATCGGGCAACTTTGTGAAACGACTCGATTAACCTAGGCCGGATCACATC
Found at i:17481871 original size:30 final size:30
Alignment explanation
Indices: 17481785--17481872 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
17481775 CTACCTCATA
17481785 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
17481815 TTCAGCTTAGGAGTTTAGCCTCAGCTCAAC
1 TTTAGCTCACGAGCTAAACCTTAGCTCAAC
*
17481845 TTTAGCTCACGAGCTAAAACTTAGCTCA
1 TTTAGCTCACGAGCTAAACCTTAGCTCA
17481873 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (30 bp):
TTTAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:17483609 original size:12 final size:12
Alignment explanation
Indices: 17483592--17483627 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
17483582 AAAGGAGAAG
17483592 AAATTCAGAAAA
1 AAATTCAGAAAA
17483604 AAATTCA-AAAA
1 AAATTCAGAAAA
17483615 AAA-TC-GAAAA
1 AAATTCAGAAAA
17483625 AAA
1 AAA
17483628 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.39
11 7 0.30
12 7 0.30
ACGTcount: A:0.72, C:0.08, G:0.06, T:0.14
Consensus pattern (12 bp):
AAATTCAGAAAA
Found at i:17483634 original size:21 final size:22
Alignment explanation
Indices: 17483578--17483637 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
17483568 ATTGGATTTA
* * *
17483578 AAAAAAAGGAGAAGAAATTCAG
1 AAAAAAAGGAAAAAAAAATCAG
***
17483600 AAAAAAATTCAAAAAAAATC-G
1 AAAAAAAGGAAAAAAAAATCAG
17483621 AAAAAAAGGAAAAAAAA
1 AAAAAAAGGAAAAAAAA
17483638 GTGACAAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.73, C:0.05, G:0.13, T:0.08
Consensus pattern (22 bp):
AAAAAAAGGAAAAAAAAATCAG
Found at i:17484578 original size:5 final size:5
Alignment explanation
Indices: 17484559--17484631 Score: 60
Period size: 5 Copynumber: 14.0 Consensus size: 5
17484549 ACATTCTTGT
* * *
17484559 AAAGA GAAAGC AAAGA AAAGA AAAGA AAAGA AAA-A GCAAGA GAAGAA
1 AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA -AAAGA AAAG-A
17484606 AAAGA AAATGA AATA-A AAAGA AAAGA
1 AAAGA AAA-GA AA-AGA AAAGA AAAGA
17484632 GAGGCAAGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
4 2 0.04
5 40 0.71
6 13 0.23
7 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:17484696 original size:12 final size:12
Alignment explanation
Indices: 17484679--17484708 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
17484669 TTGAGAGAAC
17484679 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17484691 TTGAAAAAGCCT
1 TTGAAAAAGCCT
17484703 TTGAAA
1 TTGAAA
17484709 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:17486844 original size:22 final size:20
Alignment explanation
Indices: 17486812--17486860 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
17486802 GCCGAATTTA
17486812 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
17486835 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
17486855 TGAACA
1 TGAACA
17486861 CCTAGATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:17487711 original size:23 final size:22
Alignment explanation
Indices: 17487685--17487737 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17487675 TTGATAGTGA
*
17487685 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
17487708 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
17487730 AAAAGAAA
1 AAAAGAAA
17487738 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:17490520 original size:19 final size:19
Alignment explanation
Indices: 17490498--17490580 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 19
17490488 TCACTTTCAA
17490498 CTCACGAGCTAAACTTTAG
1 CTCACGAGCTAAACTTTAG
* *
17490517 CTCAACTTCAGCTTAAGAGTTTAG
1 CTC-AC--GAGC-TAA-ACTTTAG
* *
17490541 C-CTC-AGCTCAACTTTAG
1 CTCACGAGCTAAACTTTAG
17490558 CTCACGAGCTAAAGC-TTAG
1 CTCACGAGCTAAA-CTTTAG
17490577 CTCA
1 CTCA
17490581 TTTTAGTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
17 7 0.14
18 4 0.08
19 20 0.41
20 3 0.06
22 4 0.08
23 4 0.08
24 7 0.14
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (19 bp):
CTCACGAGCTAAACTTTAG
Found at i:17490579 original size:30 final size:30
Alignment explanation
Indices: 17490484--17490580 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
17490474 AGCTCACTCC
*
17490484 TAGCTC-ACTTTCAACTCACGAGCTAAA-CTT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGC-T
* * * **
17490514 TAGCTCAACTTCAGCTTAAGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
17490544 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
17490574 TAGCTCA
1 TAGCTCA
17490581 TTTTAGTTAA
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
29 2 0.04
30 40 0.80
31 8 0.16
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:17494417 original size:21 final size:21
Alignment explanation
Indices: 17494391--17494447 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
17494381 TTGGTATTTG
17494391 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
17494412 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
17494433 GGTATTTGGTACGAA
1 GG-AATTGGTACGAA
17494448 TCGGTAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.32, C:0.04, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:17494422 original size:11 final size:11
Alignment explanation
Indices: 17494402--17494434 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
17494392 GAATTGGTAC
17494402 GAAATGGTATG
1 GAAATGGTATG
*
17494413 GAATTGGTAT-
1 GAAATGGTATG
17494423 GAAATGGTATG
1 GAAATGGTATG
17494434 G
1 G
17494435 TATTTGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:17503165 original size:31 final size:28
Alignment explanation
Indices: 17503121--17503194 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 28
17503111 CTCGCAAGAC
*
17503121 TTTTCACTTTTTTTTAACTTGATTTTTT
1 TTTTCACTTTTTTTTAACTCGATTTTTT
**
17503149 TTTGGTCACCTTTTTTTTTGCTCGATTTTTT
1 TTT--TCA-CTTTTTTTTAACTCGATTTTTT
17503180 TTTTCACTTTTTTTT
1 TTTTCACTTTTTTTT
17503195 GAATTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.30
29 3 0.08
30 3 0.08
31 22 0.55
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (28 bp):
TTTTCACTTTTTTTTAACTCGATTTTTT
Found at i:17503177 original size:15 final size:15
Alignment explanation
Indices: 17503141--17503182 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
17503131 TTTTTAACTT
*
17503141 GATTTTTTTTTGGTC
1 GATTTTTTTTTGCTC
17503156 -ACCTTTTTTTTTGCTC
1 GA--TTTTTTTTTGCTC
17503172 GATTTTTTTTT
1 GATTTTTTTTT
17503183 TCACTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 1 0.04
15 9 0.39
16 12 0.52
17 1 0.04
ACGTcount: A:0.07, C:0.12, G:0.12, T:0.69
Consensus pattern (15 bp):
GATTTTTTTTTGCTC
Found at i:17503218 original size:24 final size:24
Alignment explanation
Indices: 17503173--17503218 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
17503163 TTTTTGCTCG
* ***
17503173 ATTTTTTTTTTCACTTTTTTTTGA
1 ATTTTTTTTTTCAATCAATTTTGA
17503197 ATTTTTTTTTTCAATCAATTTT
1 ATTTTTTTTTTCAATCAATTTT
17503219 TTTTTCGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTTTTTTCAATCAATTTTGA
Found at i:17503230 original size:14 final size:14
Alignment explanation
Indices: 17503187--17503238 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 14
17503177 TTTTTTTCAC
*
17503187 TTTTTTTT-GAATT
1 TTTTTTTTCGAAAT
*
17503200 TTTTTTTTCAATCAAT
1 TTTTTTTTCGA--AAT
17503216 TTTTTTTTCGAAAT
1 TTTTTTTTCGAAAT
17503230 TTTCTTTTT
1 TTT-TTTTT
17503239 TTTTTGTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 8 0.25
14 7 0.22
15 5 0.16
16 12 0.38
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (14 bp):
TTTTTTTTCGAAAT
Found at i:17507023 original size:21 final size:21
Alignment explanation
Indices: 17506974--17507040 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
17506964 CCTCTTTGAA
* * *
17506974 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
17506997 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
17507018 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
17507039 CC
1 CC
17507041 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:17513720 original size:23 final size:22
Alignment explanation
Indices: 17513669--17513720 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17513659 CCTCGTCTTT
*
17513669 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
17513691 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
17513714 TTCTTTT
1 TTCTTTT
17513721 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:17513735 original size:18 final size:18
Alignment explanation
Indices: 17513714--17513752 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17513704 TTTCTTCAAC
* *
17513714 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
17513732 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
17513750 TTC
1 TTC
17513753 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:17516994 original size:21 final size:20
Alignment explanation
Indices: 17516951--17517017 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
17516941 AAGAAAAAAA
**
17516951 GAAATGAAAGAAAAAGAGTGT
1 GAAA-GAAAGAAAAAGAAAGT
17516972 GAAAGAAAGCAAAAAGAAAGT
1 GAAAGAAAG-AAAAAGAAAGT
*
17516993 GAGAA-AAAGAAAAACGAAATT
1 GA-AAGAAAGAAAAA-GAAAGT
17517014 GAAA
1 GAAA
17517018 AAAAAATTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 12 0.30
21 26 0.65
22 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.24, T:0.09
Consensus pattern (20 bp):
GAAAGAAAGAAAAAGAAAGT
Found at i:17517065 original size:6 final size:6
Alignment explanation
Indices: 17517044--17517087 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
17517034 AGAGAAAATT
** * *
17517044 GAAAAA GAAAGT GAAAAA GAAAAA GAGAAG GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GA
17517088 GATCGAGAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:17517088 original size:18 final size:19
Alignment explanation
Indices: 17517044--17517089 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
17517034 AGAGAAAATT
17517044 GAAAAAGA-AAGTGAAAAA
1 GAAAAAGAGAAGTGAAAAA
17517062 GAAAAAGAGAAG-GAAAAA
1 GAAAAAGAGAAGTGAAAAA
17517080 GAAAAAGAGA
1 GAAAAAGAGA
17517090 TCGAGAGTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (19 bp):
GAAAAAGAGAAGTGAAAAA
Found at i:17517133 original size:19 final size:18
Alignment explanation
Indices: 17517099--17517137 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
17517089 ATCGAGAGTG
17517099 AAAAAAAATGTGAGAAGA
1 AAAAAAAATGTGAGAAGA
17517117 AAAAGAAAAT-TGAAGAAGA
1 AAAA-AAAATGTG-AGAAGA
17517136 AA
1 AA
17517138 TTGAGTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (18 bp):
AAAAAAAATGTGAGAAGA
Found at i:17517250 original size:22 final size:21
Alignment explanation
Indices: 17517225--17517287 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
17517215 GAAAGATCCT
17517225 AAACGAACAGATCTGAAAATTA
1 AAAC-AACAGATCTGAAAATTA
* *
17517247 AAACAA-AGAAC--AAGATT-
1 AAACAACAGATCTGAAAATTA
17517264 AAACTAATCAGATCTGAAAATTA
1 AAAC-AA-CAGATCTGAAAATTA
17517287 A
1 A
17517288 GATCCCCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 11
0.67 0.09 0.24
Matches are distributed among these distances:
17 4 0.13
18 7 0.23
20 8 0.26
21 2 0.06
22 9 0.29
23 1 0.03
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.19
Consensus pattern (21 bp):
AAACAACAGATCTGAAAATTA
Found at i:17520204 original size:22 final size:22
Alignment explanation
Indices: 17520153--17520218 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
17520143 GGTATTTGGG
* *
17520153 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
17520174 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
17520196 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
17520219 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:17525884 original size:17 final size:17
Alignment explanation
Indices: 17525859--17525910 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
17525849 TCTCTTTTCA
*
17525859 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
17525876 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
17525893 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
17525910 T
1 T
17525911 CGCTCTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.77
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:17528523 original size:22 final size:22
Alignment explanation
Indices: 17528472--17528537 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
17528462 GGTATTTGGG
* *
17528472 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
17528493 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
17528515 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
17528538 TCAAAAGGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:17530570 original size:14 final size:14
Alignment explanation
Indices: 17530553--17530604 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
17530543 AAAAAAAATC
17530553 AAAAAAAAATTTCG
1 AAAAAAAAATTTCG
17530567 AAAAAAAAATTT-G
1 AAAAAAAAATTTCG
*
17530580 ATTGAAAAAAAAATTC-
1 A---AAAAAAAATTTCG
17530596 AAAAAAAAA
1 AAAAAAAAA
17530605 GTGAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
13 10 0.30
14 12 0.36
16 11 0.33
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAAAAAAATTTCG
Found at i:17530625 original size:24 final size:23
Alignment explanation
Indices: 17530585--17530639 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
17530575 ATTTGATTGA
**
17530585 AAAAAAAATTCAAAAAAAAAGTG
1 AAAAAAAATTCAAAAAAAAAAAG
17530608 AAAAAAAA-TCGAACAAAAAAAAAG
1 AAAAAAAATTC-AA-AAAAAAAAAG
17530632 AAAAAAAA
1 AAAAAAAA
17530640 GGTGAGCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 10 0.36
24 16 0.57
ACGTcount: A:0.80, C:0.05, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAAAAAATTCAAAAAAAAAAAG
Found at i:17531687 original size:12 final size:12
Alignment explanation
Indices: 17531675--17531792 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
17531665 GAAAGAGATT
*
17531675 GAAAAAGAAATT
1 GAAAAAGAAATA
17531687 G--AAAGAAA-A
1 GAAAAAGAAATA
*
17531696 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
17531707 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
17531720 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
17531732 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
17531744 GAAAAAGTGAGA
1 GAAAAAGAAATA
17531756 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
17531767 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
17531783 GAAAAAGAAA
1 GAAAAAGAAA
17531793 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:17531718 original size:18 final size:18
Alignment explanation
Indices: 17531692--17531795 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
17531682 AAATTGAAAG
*
17531692 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
17531710 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
17531728 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
17531746 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
17531764 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
17531785 AAAAGAAAAAG
1 AAAAGAAAAAG
17531796 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:17531720 original size:6 final size:6
Alignment explanation
Indices: 17531688--17531795 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
17531678 AAAGAAATTG
* * ** *
17531688 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
17531735 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
17531786 AAAGAA AAAG
1 AAAGAA AAAG
17531796 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:17531777 original size:14 final size:13
Alignment explanation
Indices: 17531756--17531793 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
17531746 AAAAGTGAGA
17531756 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
17531768 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
17531783 GAAAAAGAAAA
1 GAAAAAGAAAA
17531794 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:17531807 original size:21 final size:21
Alignment explanation
Indices: 17531757--17531807 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
17531747 AAAGTGAGAG
*
17531757 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
17531778 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
17531799 AAAAAGAAA
1 AAAAAGAAA
17531808 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:17531847 original size:33 final size:33
Alignment explanation
Indices: 17531810--17531872 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17531800 AAAAGAAATT
17531810 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
17531843 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
17531873 GTAAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:17536298 original size:6 final size:6
Alignment explanation
Indices: 17536261--17536335 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
17536251 GATCTCGATC
* * ** **
17536261 TCTTTT TCCTTT TCTTTT TCTTTT GCACTT TCTTTT TCAATT TCATTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TC-TTTT
*
17536310 TCTTTT TCTCATTC TCTTTT TCTTTT
1 TCTTTT TCT--TTT TCTTTT TCTTTT
17536336 GTTTCTTTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
6 43 0.83
7 4 0.08
8 5 0.10
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (6 bp):
TCTTTT
Found at i:17536311 original size:19 final size:20
Alignment explanation
Indices: 17536289--17536335 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
17536279 TCTTTTGCAC
17536289 TTTCTTTTTC-AATT-TCATT
1 TTTCTTTTTCTAATTCTC-TT
*
17536308 TTTCTTTTTCTCATTCTCTT
1 TTTCTTTTTCTAATTCTCTT
17536328 TTTCTTTT
1 TTTCTTTT
17536336 GTTTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
20 13 0.52
21 2 0.08
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCTTTTTCTAATTCTCTT
Found at i:17536763 original size:30 final size:30
Alignment explanation
Indices: 17536729--17536816 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
17536719 CTAGTTCATA
*
17536729 TTCAGCTCACGAGCTAAACCTTAGCTCAGC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
17536759 TTCAGCTTAGGAGTTTAATCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
17536789 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
17536817 TTTTAGTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:17538447 original size:12 final size:12
Alignment explanation
Indices: 17538430--17538473 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 12
17538420 TTATACAAGT
17538430 AAAAAAAATTC-
1 AAAAAAAATTCA
17538441 -AAAAAAATTCA
1 AAAAAAAATTCA
17538452 AAAAAAAATTCGA
1 AAAAAAAATTC-A
17538465 AAAGAAAAA
1 AAA-AAAAA
17538474 AAATCTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.34
12 10 0.34
13 4 0.14
14 5 0.17
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:17538476 original size:22 final size:21
Alignment explanation
Indices: 17538430--17538476 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
17538420 TTATACAAGT
*
17538430 AAAAAAAATTCAAAAAAATTCA
1 AAAAAAAATTCAAAAAAA-TAA
* *
17538452 AAAAAAAATTCGAAAAGA-AA
1 AAAAAAAATTCAAAAAAATAA
17538472 AAAAA
1 AAAAA
17538477 TCTGAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 6 0.27
22 16 0.73
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (21 bp):
AAAAAAAATTCAAAAAAATAA
Found at i:17538483 original size:17 final size:16
Alignment explanation
Indices: 17538451--17538488 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
17538441 AAAAAAATTC
17538451 AAAAAAAAATTCGAAA
1 AAAAAAAAATTCGAAA
17538467 AGAAAAAAAA-TCTGAAA
1 A-AAAAAAAATTC-GAAA
17538484 AAAAA
1 AAAAA
17538489 GTGTTTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (16 bp):
AAAAAAAAATTCGAAA
Found at i:17539418 original size:21 final size:20
Alignment explanation
Indices: 17539384--17539451 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
17539374 ACATTCTTGT
17539384 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
17539405 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
17539426 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
17539447 AAAGA
1 AAAGA
17539452 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:17539419 original size:6 final size:5
Alignment explanation
Indices: 17539395--17539451 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
17539385 AAGAGAAAAC
*
17539395 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
17539442 AAAGA AAAGA
1 AAAGA AAAGA
17539452 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:17539426 original size:15 final size:14
Alignment explanation
Indices: 17539395--17539451 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
17539385 AAGAGAAAAC
17539395 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
17539411 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
17539426 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
17539442 AAAGAAAAGA
1 AAAGAAAAGA
17539452 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:17539566 original size:30 final size:30
Alignment explanation
Indices: 17539532--17539612 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
17539522 TGTGAAAAGC
*
17539532 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAG-AAAAGAAATATGAGAGTG
* * *
17539562 AAAAAGAGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAGAAATATGAGAGTG
*
17539592 AAAAAGAAGATA-AAAAGAAAT
1 AAAAAGAA-AAAGAAAAGAAAT
17539613 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 8 0.19
30 33 0.79
31 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.21, T:0.11
Consensus pattern (30 bp):
AAAAAGAAAAAGAAAAGAAATATGAGAGTG
Found at i:17539586 original size:24 final size:24
Alignment explanation
Indices: 17539537--17539583 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17539527 AAAGCAAAAA
*
17539537 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
17539561 GAAAAAGAGAACGAAAA-GAAATT
1 GAAAAAGAAAAAGAAAATGAAATT
17539584 TGAGAGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:17541720 original size:30 final size:30
Alignment explanation
Indices: 17541686--17541783 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
17541676 AGCTCACTCC
17541686 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
17541716 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * * *
17541746 CAGCTCA-ACTTTAGCTCATGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
17541776 TAGCTCAT
1 TAGCTCAT
17541784 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:17543687 original size:6 final size:6
Alignment explanation
Indices: 17543654--17543684 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
17543644 AAGTAAATAA
*
17543654 ATAAAT ATAAAT ATAAAT ATAAAT AAAAAT A
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT A
17543685 AAACTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
ATAAAT
Found at i:17544847 original size:30 final size:30
Alignment explanation
Indices: 17544813--17544909 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17544803 AGCTCACTCC
17544813 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17544843 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17544873 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17544903 TAGCTCA
1 TAGCTCA
17544910 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17546539 original size:23 final size:24
Alignment explanation
Indices: 17546509--17546557 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
17546499 AGGTTCGTAA
*
17546509 CGAAAAAAAAAT-TCAAAAAAAAT
1 CGAAAAAAAAATGACAAAAAAAAT
*
17546532 CG-AAAAAAAGTGACAAAAAAAAT
1 CGAAAAAAAAATGACAAAAAAAAT
17546555 CGA
1 CGA
17546558 GTTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.69, C:0.10, G:0.10, T:0.10
Consensus pattern (24 bp):
CGAAAAAAAAATGACAAAAAAAAT
Found at i:17547487 original size:5 final size:5
Alignment explanation
Indices: 17547477--17547538 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
17547467 AAGAGAAAAC
* *
17547477 AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAGA AAAGA AAA-GA
17547524 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
17547539 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 35 0.73
6 10 0.21
7 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:17547507 original size:26 final size:26
Alignment explanation
Indices: 17547477--17547538 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
17547467 AAGAGAAAAC
17547477 AAAGAAAAGAAAAGAAAAAGAAA-AA
1 AAAGAAAAGAAAAGAAAAAGAAATAA
* * *
17547502 GCAAGAGAAGAAAAGAAAATGAAATAA
1 -AAAGAAAAGAAAAGAAAAAGAAATAA
17547529 AAAGAAAAGA
1 AAAGAAAAGA
17547539 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (26 bp):
AAAGAAAAGAAAAGAAAAAGAAATAA
Found at i:17547539 original size:31 final size:30
Alignment explanation
Indices: 17547465--17547540 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
17547455 TACATTCTTG
* *
17547465 TAAAGAGAAAACA-AAGAAAAGAAAAGAAA
1 TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
17547494 -AAGAAA-AAGCAAGAGAAGAAAAGAAAATGAAA
1 TAA-AAAGAA--AAGAGAAGAAAAGAAAA-GAAA
17547526 TAAAAAGAAAAGAGA
1 TAAAAAGAAAAGAGA
17547541 GGCAAGAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
28 4 0.11
29 2 0.05
30 3 0.08
31 18 0.47
32 7 0.18
33 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.04
Consensus pattern (30 bp):
TAAAAAGAAAAGAGAAGAAAAGAAAAGAAA
Found at i:17549816 original size:30 final size:30
Alignment explanation
Indices: 17549782--17549878 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
17549772 AGCTCACTCC
17549782 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
17549812 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
17549842 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
17549872 TAGCTCA
1 TAGCTCA
17549879 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:17551605 original size:10 final size:10
Alignment explanation
Indices: 17551590--17551627 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
17551580 GCTCGTTTCC
*
17551590 AGCTCACTCG
1 AGCTCAATCG
17551600 AGCTCAAATC-
1 AGCTC-AATCG
17551610 AGCTCAATCG
1 AGCTCAATCG
17551620 AGCTCAAT
1 AGCTCAAT
17551628 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 4 0.16
10 18 0.72
11 3 0.12
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:17551614 original size:20 final size:20
Alignment explanation
Indices: 17551589--17551626 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17551579 AGCTCGTTTC
*
17551589 CAGCTCACTCGAGCTCAAAT
1 CAGCTCAATCGAGCTCAAAT
17551609 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
17551627 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAAT
Found at i:17551633 original size:20 final size:20
Alignment explanation
Indices: 17551590--17551650 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
17551580 GCTCGTTTCC
* * *
17551590 AGCTCACTCGAGCTCAAATC
1 AGCTCAATCGAGCTCAATTT
17551610 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
17551630 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
17551650 A
1 A
17551651 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:17551644 original size:11 final size:10
Alignment explanation
Indices: 17551600--17551646 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
17551590 AGCTCACTCG
*
17551600 AGCTCAAATC
1 AGCTCAATTC
17551610 AGCTCAA-TC
1 AGCTCAATTC
*
17551619 GAGCTCAATTT
1 -AGCTCAATTC
17551630 AGCTACAATTC
1 AGCT-CAATTC
17551641 AGCTCA
1 AGCTCA
17551647 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:17552146 original size:13 final size:13
Alignment explanation
Indices: 17552128--17552152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17552118 GTATTGATCA
17552128 TGTGTTCACACCT
1 TGTGTTCACACCT
17552141 TGTGTTCACACC
1 TGTGTTCACACC
17552153 ATGATGACCT
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:17567224 original size:24 final size:25
Alignment explanation
Indices: 17567171--17567224 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
17567161 AACAAATTCT
* *
17567171 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
17567196 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
17567219 TTTTTT
1 TTTTTT
17567225 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:17569499 original size:12 final size:13
Alignment explanation
Indices: 17569476--17569501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17569466 CTAGACCATA
17569476 TGCAATTTTTTTT
1 TGCAATTTTTTTT
17569489 TGCAATTTTTTTT
1 TGCAATTTTTTTT
17569502 CCTTCTTTTT
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:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
TGCAATTTTTTTT
Found at i:17569554 original size:12 final size:13
Alignment explanation
Indices: 17569521--17569554 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
17569511 TTTTTTCGGA
17569521 TTTTTTTTTGAAAC
1 TTTTTTTTT-AAAC
17569535 TTTTTTTTT-AAC
1 TTTTTTTTTAAAC
17569547 TTTTTTTT
1 TTTTTTTT
17569555 CGAAGCTACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTAAAC
Found at i:17571511 original size:5 final size:5
Alignment explanation
Indices: 17571501--17571556 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
17571491 CTCTTGTCTC
*
17571501 TCTTT TCTTT T-TATT TCTTTT TCTTT T-TCT TCTTT TGCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-CTTT TCTTT
17571547 TCTTT TCTTT
1 TCTTT TCTTT
17571557 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 30 0.68
6 9 0.20
7 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:17571521 original size:15 final size:14
Alignment explanation
Indices: 17571501--17571563 Score: 72
Period size: 16 Copynumber: 4.2 Consensus size: 14
17571491 CTCTTGTCTC
17571501 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
17571516 TCTTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
17571531 TCTTTTGCTTTTCTTT
1 TCTTTT-CTTTT-TTT
*
17571547 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
17571561 TCT
1 TCT
17571564 CTTTACAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.24
15 14 0.33
16 18 0.43
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:17571546 original size:11 final size:10
Alignment explanation
Indices: 17571501--17571556 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 10
17571491 CTCTTGTCTC
17571501 TCTTTTCTTT
1 TCTTTTCTTT
17571511 T-TATTTCTTTT
1 TCT-TTTC-TTT
*
17571522 TCTTTT-TCT
1 TCTTTTCTTT
17571531 TCTTTTGCTTT
1 TCTTTT-CTTT
17571542 TCTTTTCTTT
1 TCTTTTCTTT
17571552 TCTTT
1 TCTTT
17571557 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 9 0.23
10 14 0.36
11 15 0.38
12 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (10 bp):
TCTTTTCTTT
Found at i:17572314 original size:16 final size:16
Alignment explanation
Indices: 17572293--17572324 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17572283 TAATGTGTTT
17572293 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
17572309 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
17572325 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:17572506 original size:45 final size:45
Alignment explanation
Indices: 17572438--17572701 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
17572428 AAGAGGTGGA
** * * *
17572438 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
17572483 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
17572528 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
17572573 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
17572618 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * * *
17572663 CAACATCATTCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
17572702 CCATGGCCGA
Statistics
Matches: 204, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 204 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:17576147 original size:16 final size:16
Alignment explanation
Indices: 17576126--17576157 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17576116 TAATGTGTTT
17576126 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
17576142 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
17576158 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:17576339 original size:45 final size:45
Alignment explanation
Indices: 17576271--17576534 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
17576261 AAGAGGTGGA
** * * *
17576271 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
17576316 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
*
17576361 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
17576406 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* *
17576451 CAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
* * * * *
17576496 CAACATCATTCATAATTTAAGGAACAAATTGAGGAAGCA
1 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCA
17576535 CCATGGCCGA
Statistics
Matches: 204, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 204 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGAC
Found at i:17577265 original size:20 final size:20
Alignment explanation
Indices: 17577240--17577294 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
17577230 TGTGGTTCAA
* *
17577240 CTCATTCAAGCTTAAGTTAG
1 CTCATTCAAGCTCAAGTCAG
**
17577260 CTCATTCGTGCTCAAGTCAG
1 CTCATTCAAGCTCAAGTCAG
17577280 CTCATTCAAGCTCAA
1 CTCATTCAAGCTCAA
17577295 TTTAACTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (20 bp):
CTCATTCAAGCTCAAGTCAG
Found at i:17579790 original size:11 final size:12
Alignment explanation
Indices: 17579774--17579828 Score: 80
Period size: 11 Copynumber: 4.8 Consensus size: 12
17579764 CATAAATCAC
17579774 TTTTTTTTC-AA
1 TTTTTTTTCGAA
17579785 TTTTTTTT-GAA
1 TTTTTTTTCGAA
17579796 TTTTTTTTCGAA
1 TTTTTTTTCGAA
17579808 -TTTTTTTCGAA
1 TTTTTTTTCGAA
*
17579819 ATTTTTTTCG
1 TTTTTTTTCG
17579829 GTTTTTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
11 29 0.71
12 12 0.29
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:17579809 original size:23 final size:23
Alignment explanation
Indices: 17579774--17579837 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
17579764 CATAAATCAC
*
17579774 TTTTTTTTC-AATTTTTTTTGAA
1 TTTTTTTTCGAATTTTTTTCGAA
17579796 TTTTTTTTCGAATTTTTTTCGAA
1 TTTTTTTTCGAATTTTTTTCGAA
* *
17579819 ATTTTTTTCG-GTTTTTTTC
1 TTTTTTTTCGAATTTTTTTC
17579838 AAACTTGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 17 0.45
23 21 0.55
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.70
Consensus pattern (23 bp):
TTTTTTTTCGAATTTTTTTCGAA
Found at i:17579828 original size:12 final size:11
Alignment explanation
Indices: 17579775--17579837 Score: 76
Period size: 12 Copynumber: 5.7 Consensus size: 11
17579765 ATAAATCACT
17579775 TTTTTTTC-AA
1 TTTTTTTCGAA
*
17579785 TTTTTTTTGAA
1 TTTTTTTCGAA
17579796 TTTTTTTTCGAA
1 -TTTTTTTCGAA
17579808 TTTTTTTCGAAA
1 TTTTTTTCG-AA
*
17579820 TTTTTTTCG-G
1 TTTTTTTCGAA
17579830 TTTTTTTC
1 TTTTTTTC
17579838 AAACTTGTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
10 15 0.32
11 11 0.23
12 21 0.45
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.70
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:17579834 original size:11 final size:11
Alignment explanation
Indices: 17579774--17579836 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
17579764 CATAAATCAC
*
17579774 TTTTTTTTCAA
1 TTTTTTTTCGA
17579785 TTTTTTTT-GAA
1 TTTTTTTTCG-A
17579796 TTTTTTTTCGA
1 TTTTTTTTCGA
*
17579807 ATTTTTTTCGAA
1 TTTTTTTTCG-A
* *
17579819 ATTTTTTTCGG
1 TTTTTTTTCGA
17579830 TTTTTTT
1 TTTTTTT
17579837 CAAACTTGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
11 33 0.73
12 12 0.27
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.71
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:17585133 original size:13 final size:13
Alignment explanation
Indices: 17585115--17585139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17585105 TGGTCATCAT
17585115 GGTGTGAACACAA
1 GGTGTGAACACAA
17585128 GGTGTGAACACA
1 GGTGTGAACACA
17585140 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:17587349 original size:27 final size:30
Alignment explanation
Indices: 17587271--17587356 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
17587261 TTTTCTCTCG
*
17587271 TTTCTTCTTCAA-CATCTTTTTCTTTTTCAAT
1 TTTCTTCTT-AATC-TCATTTTCTTTTTCAAT
* *
17587302 TTTTTTCTTAATCTCAATTTCTTTTTCAAT
1 TTTCTTCTTAATCTCATTTTCTTTTTCAAT
*
17587332 TTTCTT-TT-CT-TCATTTTCTTTTTCA
1 TTTCTTCTTAATCTCATTTTCTTTTTCA
17587357 CTCACTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 14 0.29
28 1 0.02
29 2 0.04
30 22 0.46
31 9 0.19
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTCTTCTTAATCTCATTTTCTTTTTCAAT
Found at i:17588237 original size:29 final size:28
Alignment explanation
Indices: 17588205--17588275 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 28
17588195 GCAAGACTTT
**
17588205 TCACTTTTTTTTTAACTTGATTTTTTTGG
1 TCACTTTTTTTTTAACTCAATTTTTTT-G
** *
17588234 TCACCTTTTTTTTTTGCTCAATTTTTTTT
1 TCA-CTTTTTTTTTAACTCAATTTTTTTG
17588263 TCACTTTTTTTTT
1 TCACTTTTTTTTT
17588276 GAATATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.28
29 6 0.17
30 20 0.56
ACGTcount: A:0.11, C:0.14, G:0.06, T:0.69
Consensus pattern (28 bp):
TCACTTTTTTTTTAACTCAATTTTTTTG
Found at i:17588258 original size:16 final size:17
Alignment explanation
Indices: 17588225--17588263 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17588215 TTTAACTTGA
* *
17588225 TTTTTTTGGTCACCTTT
1 TTTTTTTGCTCACATTT
17588242 TTTTTTTGCTCA-ATTT
1 TTTTTTTGCTCACATTT
17588258 TTTTTT
1 TTTTTT
17588264 CACTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.72
Consensus pattern (17 bp):
TTTTTTTGCTCACATTT
Found at i:17588270 original size:12 final size:12
Alignment explanation
Indices: 17588241--17588293 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 12
17588231 TGGTCACCTT
17588241 TTTTTTTTGCTCAA
1 TTTTTTTT--TCAA
*
17588255 TTTTTTTTTCAC
1 TTTTTTTTTCAA
*
17588267 TTTTTTTTTGAATA
1 TTTTTTTTT-CA-A
17588281 TTTTTTTTTCAA
1 TTTTTTTTTCAA
17588293 T
1 T
17588294 CAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 14 0.42
13 2 0.06
14 17 0.52
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:17588284 original size:14 final size:14
Alignment explanation
Indices: 17588267--17588318 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
17588257 TTTTTTTCAC
17588267 TTTTTTTTTGAATA
1 TTTTTTTTTGAATA
*
17588281 TTTTTTTTTCAATCAA
1 TTTTTTTTTGAAT--A
17588297 TTTTTTTTTTCGAAT-
1 -TTTTTTTTT-GAATA
17588312 TTTTTTT
1 TTTTTTT
17588319 GATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 19 0.59
16 1 0.03
17 9 0.28
18 3 0.09
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTGAATA
Found at i:17588285 original size:42 final size:41
Alignment explanation
Indices: 17588239--17588329 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 41
17588229 TTTGGTCACC
*
17588239 TTTTTTTTTTGC--TCAA-TTTTTTTTTC-ACTTTTTTTTTGAA
1 TTTTTTTTTT-CAATCAATTTTTTTTTTCGA-ATTTTTTTTG-A
17588279 TATTTTTTTTTCAATCAATTTTTTTTTTCGAATTTTTTTTGA
1 T-TTTTTTTTTCAATCAATTTTTTTTTTCGAATTTTTTTTGA
17588321 TTTTTTTTT
1 TTTTTTTTT
17588330 GTTACTCCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
40 2 0.04
41 17 0.38
42 6 0.13
43 19 0.42
44 1 0.02
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (41 bp):
TTTTTTTTTTCAATCAATTTTTTTTTTCGAATTTTTTTTGA
Found at i:17589205 original size:27 final size:27
Alignment explanation
Indices: 17589175--17589324 Score: 176
Period size: 27 Copynumber: 5.5 Consensus size: 27
17589165 GATCACATCA
* *
17589175 CACACTTAGTGCTACGTAATCAAATCG
1 CACACTTAGTGCTACATAGTCAAATCG
17589202 CACACTTAGTGCTACATAGTCAAACTCG
1 CACACTTAGTGCTACATAGTCAAA-TCG
** * *
17589230 CACACTTAGTGCCGCATGGTCAATTCG
1 CACACTTAGTGCTACATAGTCAAATCG
* **
17589257 CACACTTAGTGC-ATCATATTCATTTCG
1 CACACTTAGTGCTA-CATAGTCAAATCG
* *
17589284 CACACTTAGTGCAACATAGTCATATCG
1 CACACTTAGTGCTACATAGTCAAATCG
17589311 CACACTTAGTGCTA
1 CACACTTAGTGCTA
17589325 TACAATTTAA
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
27 83 0.78
28 24 0.22
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CACACTTAGTGCTACATAGTCAAATCG
Found at i:17589888 original size:13 final size:13
Alignment explanation
Indices: 17589870--17589894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17589860 TACTAAATTT
17589870 TCATGGATTCAAG
1 TCATGGATTCAAG
17589883 TCATGGATTCAA
1 TCATGGATTCAA
17589895 TATACCATCA
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:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:17597208 original size:27 final size:27
Alignment explanation
Indices: 17597178--17597356 Score: 173
Period size: 27 Copynumber: 6.6 Consensus size: 27
17597168 ATATTGAGCC
* *
17597178 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
17597205 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
17597232 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
17597260 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* * **
17597287 TGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
17597314 CGCACACTTAGTGCAACATAGTCATA-T
1 CGCACACTTAGTGCTACATAATCA-ACT
17597341 CGCACACTTAGTGCTA
1 CGCACACTTAGTGCTA
17597357 TACAATTTAA
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:17597920 original size:13 final size:13
Alignment explanation
Indices: 17597902--17597926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17597892 TACTAAATTT
17597902 TCATGGATTCAAG
1 TCATGGATTCAAG
17597915 TCATGGATTCAA
1 TCATGGATTCAA
17597927 TATACCATCA
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:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:17598699 original size:23 final size:24
Alignment explanation
Indices: 17598668--17598714 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17598658 TCCTCCCTTA
17598668 TTTTATTCA-TCCTTTT-TTTTCT
1 TTTTATTCACTCCTTTTATTTTCT
*
17598690 TTTTAATTCACTTCTTTTATTTTCT
1 TTTT-ATTCACTCCTTTTATTTTCT
17598715 AATCTACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 5 0.24
24 6 0.29
25 6 0.29
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTATTCACTCCTTTTATTTTCT
Found at i:17601999 original size:28 final size:28
Alignment explanation
Indices: 17601931--17602026 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
17601921 TCGATGTCTC
* * * * * *
17601931 GCACACTATGTACCATACTCGATACCTA
1 GCACACTAAGTGCCATCCTGGATACTTT
* * * **
17601959 GCACGCTAAGTGCTATTCTGGATGTTTT
1 GCACACTAAGTGCCATCCTGGATACTTT
*
17601987 GCACACTAAGTGCCATCCTTGATACTTT
1 GCACACTAAGTGCCATCCTGGATACTTT
17602015 GCACACTAAGTG
1 GCACACTAAGTG
17602027 TCATTTATAT
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (28 bp):
GCACACTAAGTGCCATCCTGGATACTTT
Found at i:17611263 original size:9 final size:9
Alignment explanation
Indices: 17611251--17611299 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
17611241 TAATTTTAAT
17611251 AATTTTTTA
1 AATTTTTTA
17611260 AATTTTTTA
1 AATTTTTTA
17611269 AATTTTTTAA
1 AATTTTTT-A
*
17611279 AATTTTTTT
1 AATTTTTTA
17611288 AA-TTTTTA
1 AATTTTTTA
17611296 AATT
1 AATT
17611300 ATTCATTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 7 0.19
9 20 0.56
10 9 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AATTTTTTA
Found at i:17614653 original size:19 final size:19
Alignment explanation
Indices: 17614629--17614677 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
17614619 AATATATATA
17614629 TTTGAATTTTAAAAACTAT
1 TTTGAATTTTAAAAACTAT
* * *
17614648 TTTGAAAATTTGAAAATTAT
1 TTTG-AATTTTAAAAACTAT
17614668 TTTGAATTTT
1 TTTGAATTTT
17614678 TTTTTTGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTGAATTTTAAAAACTAT
Found at i:17614817 original size:19 final size:19
Alignment explanation
Indices: 17614794--17614836 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
17614784 TGAATTGTGA
17614794 AATTCAACTTGAATTGAAT
1 AATTCAACTTGAATTGAAT
* * * *
17614813 TATTCGAGTTGACTTGAAT
1 AATTCAACTTGAATTGAAT
17614832 AATTC
1 AATTC
17614837 GAATAACTCA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (19 bp):
AATTCAACTTGAATTGAAT
Found at i:17614837 original size:19 final size:19
Alignment explanation
Indices: 17614802--17614838 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17614792 GAAATTCAAC
*
17614802 TTGAATTGAATTATTCGAG
1 TTGAATTGAATAATTCGAG
*
17614821 TTGACTTGAATAATTCGA
1 TTGAATTGAATAATTCGA
17614839 ATAACTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (19 bp):
TTGAATTGAATAATTCGAG
Found at i:17620702 original size:19 final size:20
Alignment explanation
Indices: 17620678--17620715 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17620668 GGTACCACCA
17620678 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
17620697 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
17620716 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:17621011 original size:46 final size:46
Alignment explanation
Indices: 17620944--17621065 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
17620934 CGCCCCTAAG
* * *
17620944 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
* *
17620990 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
17621036 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
17621066 TGCTCAACCA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
Found at i:17621084 original size:46 final size:45
Alignment explanation
Indices: 17620942--17621084 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 45
17620932 CCCGCCCCTA
* ** *
17620942 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
* ** **
17620987 AAATGAACTCGGACTCAACTCAACGAGTTCGGACATT-TGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
*
17621033 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTC-ACCATCCT
17621080 AGTGA
1 AGTGA
17621085 CATGTCACTT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
46 78 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCCT
Found at i:17621522 original size:30 final size:30
Alignment explanation
Indices: 17621488--17621547 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
17621478 ATTTAATACG
17621488 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
17621518 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
17621548 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:17625645 original size:28 final size:28
Alignment explanation
Indices: 17625605--17625661 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
17625595 ATGAATTCAC
17625605 CAGTGTTCATTCAAGGTAAAGGGTTTAA
1 CAGTGTTCATTCAAGGTAAAGGGTTTAA
*
17625633 CAGTGTTCATTCAGGGTAAAGGGTTTAA
1 CAGTGTTCATTCAAGGTAAAGGGTTTAA
17625661 C
1 C
17625662 CGTTTGGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (28 bp):
CAGTGTTCATTCAAGGTAAAGGGTTTAA
Found at i:17636806 original size:7 final size:7
Alignment explanation
Indices: 17636794--17636827 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
17636784 TAATAATGCC
17636794 GATAAAT
1 GATAAAT
17636801 GATAAAT
1 GATAAAT
17636808 GATAAAT
1 GATAAAT
17636815 GATAAAT
1 GATAAAT
17636822 GATAAA
1 GATAAA
17636828 AATGTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (7 bp):
GATAAAT
Found at i:17637178 original size:57 final size:58
Alignment explanation
Indices: 17637046--17637187 Score: 157
Period size: 57 Copynumber: 2.5 Consensus size: 58
17637036 CTCATTACAG
* * **
17637046 AATGGATTTAGCTTGGACAGGTAATCCTGATATAAGTCCTCTCGAGCATATGTTAGGG
1 AATGGATTTAGCTTGGACAGGTAATCCAGATATAAGTCCTCTAGAGCATATGTTAGAA
* * *
17637104 ATTGGATTTAGCCTGGACGGGTAATCCAGAT-TAAGCTCCT-TAGAGCATATGTCATA-AA
1 AATGGATTTAGCTTGGACAGGTAATCCAGATATAAG-TCCTCTAGAGCATATGT--TAGAA
*
17637162 AAT-GATTTAGCTTGGACTGGTAATCC
1 AATGGATTTAGCTTGGACAGGTAATCC
17637188 TATTGTATAC
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
57 36 0.51
58 33 0.46
59 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (58 bp):
AATGGATTTAGCTTGGACAGGTAATCCAGATATAAGTCCTCTAGAGCATATGTTAGAA
Found at i:17638907 original size:25 final size:25
Alignment explanation
Indices: 17638877--17638959 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
17638867 TGTAAACGGT
* *
17638877 AAGCTCCTCCAAGCTGAATAATGGG
1 AAGCTCATGCAAGCTGAATAATGGG
** * *
17638902 AAGCTCATGTGAGCTGAGTAATAGG
1 AAGCTCATGCAAGCTGAATAATGGG
* * *
17638927 AAGCTAATGCAAGCTGAATAACGAG
1 AAGCTCATGCAAGCTGAATAATGGG
17638952 AAGCTCAT
1 AAGCTCAT
17638960 TCGAGCTAAG
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (25 bp):
AAGCTCATGCAAGCTGAATAATGGG
Found at i:17638981 original size:50 final size:50
Alignment explanation
Indices: 17638886--17638981 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
17638876 TAAGCTCCTC
* * * *
17638886 CAAGCTGAATAATGGGAAGCTCATGTGAGCTGAGTAATAGGAAGCTAATG
1 CAAGCTGAATAACGAGAAGCTCATGTGAGCTAAGTAATAGAAAGCTAATG
17638936 CAAGCTGAATAACGAGAAGCTCAT-TCGAGCTAAGT-ATCAGAAAGCT
1 CAAGCTGAATAACGAGAAGCTCATGT-GAGCTAAGTAAT-AGAAAGCT
17638982 CATGAAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
49 3 0.08
50 37 0.93
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.21
Consensus pattern (50 bp):
CAAGCTGAATAACGAGAAGCTCATGTGAGCTAAGTAATAGAAAGCTAATG
Found at i:17643495 original size:41 final size:41
Alignment explanation
Indices: 17643434--17643531 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
17643424 ACAGGCCTGG
*
17643434 TCACACAAGCTGTCAATCAAGATGTAGCTACACGGTGCTGC
1 TCACACAAGCTGTCAATCAAGACGTAGCTACACGGTGCTGC
* *
17643475 TCACACAAGCTGTCAGTCAAGGCGTAGCTACACGGTGCTGC
1 TCACACAAGCTGTCAATCAAGACGTAGCTACACGGTGCTGC
17643516 TCACACAAGCTGTCAA
1 TCACACAAGCTGTCAA
17643532 GTATCCGCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (41 bp):
TCACACAAGCTGTCAATCAAGACGTAGCTACACGGTGCTGC
Found at i:17649592 original size:112 final size:110
Alignment explanation
Indices: 17649398--17649677 Score: 422
Period size: 110 Copynumber: 2.6 Consensus size: 110
17649388 TCAATAAATC
* * * *
17649398 AAAAAAATTACATT-ATAACAAATCACAATACACATTAAACT-AA-ACAAATAATTTATAACCTA
1 AAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTTATAACCTA
* *
17649460 ATCATAAATTACTAATAAAATAACTTTAATATAATTTAAAAAAACAA
66 ATCATAAATTACTAAAAAAATAACTTTAAAATAA-TTAAAAAAAC-A
* * * *
17649507 AAAAAAACTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTCATAAGCTA
1 AAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTTATAACCTA
17649572 ATCATAAATTACTAAAAAAATAACTTTAAAATAATTAAAAAAACA
66 ATCATAAATTACTAAAAAAATAACTTTAAAATAATTAAAAAAACA
*
17649617 AAAAAAATTACATTCATAAAAAATTACAATAAACACTAAACTAAACACAAAAAATTTATAA
1 AAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTTATAA
17649678 TAATTACTAA
Statistics
Matches: 155, Mismatches: 13, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
109 13 0.08
110 82 0.53
111 12 0.08
112 48 0.31
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (110 bp):
AAAAAAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTTATAACCTA
ATCATAAATTACTAAAAAAATAACTTTAAAATAATTAAAAAAACA
Found at i:17649723 original size:110 final size:110
Alignment explanation
Indices: 17649398--17649725 Score: 290
Period size: 110 Copynumber: 3.0 Consensus size: 110
17649388 TCAATAAATC
* * * * * *
17649398 AAAAAAATTACATT-ATAACAAATCACAATACACATTAAACT-AA-ACAAATAATTTATAACCTA
1 AAAAAAACTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTCATAA-CTA
* ** * * * * * *
17649460 ATCATAAATTACTAATAAAATAACTTTAATATAATTTAAAAAAACAA
65 ATCAAAAAAAACTAAAAAAATAAATTAAAAACAA-ATAAAAAAACAA
*
17649507 AAAAAAACTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTCATAAGCTA
1 AAAAAAACTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTCATAA-CTA
* ** * * * *
17649572 ATCATAAATTACTAAAAAAATAACTTTAAAATAATTAAAAAAAC-A
65 ATCAAAAAAAACTAAAAAAATAAATTAAAAACAAATAAAAAAACAA
* * *
17649617 AAAAAAATTACATTCATAAAAAATTACAATAAACACTAAACTAAACACAAAAAATTTATAA-TAA
1 AAAAAAACTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTCATAACTAA
** *
17649681 TTACTAAAAAAAACT-TTACAATAAATTAAAAACAACATAAAAAAA
66 -T-C-AAAAAAAACTAAAAAAATAAATTAAAAACAA-ATAAAAAAA
17649726 TAACTAATCC
Statistics
Matches: 189, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
108 3 0.02
109 14 0.07
110 97 0.51
111 27 0.14
112 48 0.25
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (110 bp):
AAAAAAACTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAAAAATTCATAACTAA
TCAAAAAAAACTAAAAAAATAAATTAAAAACAAATAAAAAAACAA
Found at i:17653881 original size:46 final size:46
Alignment explanation
Indices: 17653787--17653903 Score: 170
Period size: 46 Copynumber: 2.6 Consensus size: 46
17653777 GTGCCAATGC
*
17653787 CATGTCCCAGACATGGTCTTACACT---TATAAATCTCGAGCCGATG
1 CATGTCCTAGACAT-GTCTTACACTAGCTATAAATCTCGAGCCGATG
*
17653831 CATGTCCTAGACATGTCTTACACTAGCT-TACATCTCGAGGCCGATG
1 CATGTCCTAGACATGTCTTACACTAGCTATAAATCTCGA-GCCGATG
17653877 CATGTCCTAGACATGTCTTACACTAGC
1 CATGTCCTAGACATGTCTTACACTAGC
17653904 ACTCGTCTCA
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
43 10 0.15
44 13 0.19
45 9 0.13
46 35 0.52
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCTAGACATGTCTTACACTAGCTATAAATCTCGAGCCGATG
Found at i:17653920 original size:46 final size:45
Alignment explanation
Indices: 17653824--17653997 Score: 147
Period size: 46 Copynumber: 3.8 Consensus size: 45
17653814 TAAATCTCGA
* * * * *
17653824 GCCGATGCATGTCCTAGACATGTCTTACACTAGCTTACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCCT-CGTCTCAAT
*
17653870 GCCGATGCATGTCCTAGACATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-CTCGTCTCAAT
* * * *
17653916 GCCGATGCCGTGTCCCAAACATGGTCTTACA-TTGGCTC-TCGT-AATGT
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCCTCGTC-TCAA--T
* *
17653963 GGCTGACGCATGTCCCAGACATGTCTTACACTAGC
1 -GCCGATGCATGTCCCAGACATGTCTTACACTAGC
17653998 TCACACAAGT
Statistics
Matches: 105, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
45 4 0.04
46 59 0.56
47 29 0.28
48 13 0.12
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCCTCGTCTCAAT
Found at i:17660048 original size:13 final size:13
Alignment explanation
Indices: 17660030--17660062 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
17660020 GGACACACGC
17660030 CCGTGTGGCCAGG
1 CCGTGTGGCCAGG
17660043 CCGTGTGGCCAGG
1 CCGTGTGGCCAGG
17660056 CCGTGTG
1 CCGTGTG
17660063 TCTCACATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.06, C:0.30, G:0.45, T:0.18
Consensus pattern (13 bp):
CCGTGTGGCCAGG
Found at i:17681491 original size:46 final size:46
Alignment explanation
Indices: 17681408--17681618 Score: 205
Period size: 46 Copynumber: 4.5 Consensus size: 46
17681398 AGGTCGATAC
* * *
17681408 CATGTCCCAAACATGGTCTTACACTGACTATCATCTCGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTCGTAGCCGATG
* *
17681455 CATGTCCCAGACATGTCTTACACTGGCT-TACGTCTCG-AGGTCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCGTA-GCCGATG
* * *
17681501 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATA-CCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATCTC-GTAGCCGATG
* * * * * *
17681547 CCATGTCTCAAACATAATCTTACACTGGCTCTCATAAT-GTGGTCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCGTAGCCGATG
17681595 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
17681619 AGCCAACAAT
Statistics
Matches: 136, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.01
46 72 0.53
47 39 0.29
48 22 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATCTCGTAGCCGATG
Found at i:17681575 original size:94 final size:92
Alignment explanation
Indices: 17681387--17681621 Score: 255
Period size: 94 Copynumber: 2.5 Consensus size: 92
17681377 GTCTTCACAA
* * * *
17681387 GCTCACATCTC-AGGTCGATACCATGTCCCAAACATGGTCTTACACT-GACTATCATCTCGTAGC
1 GCTCTCATCTCGAGGTCGAT-GCATGTCCCAGACAT-GTCTTACACTAG-CTATCATCTCATAGC
* *
17681450 CGATGCATGTCCCAGACATGTCTTACACTG
63 CGATGCATGTCCCAAACATATCTTACACTG
* * *
17681480 GCT-TACGTCTCGAGGTCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATA-CC
1 GCTCT-CATCTCGAGGTCGATGCATGTCCCAGACATGTCTTACACTAGCTATCATCTC-ATAGCC
*
17681543 GATGCCATGTCTCAAACATAATCTTACACTG
64 GATG-CATGTCCCAAACAT-ATCTTACACTG
* *
17681574 GCTCTCATAAT-GTGGTCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCTCTCAT-CTCGAGGTCGATGCATGTCCCAGACATGTCTTACACTAGC
17681622 CAACAATAAC
Statistics
Matches: 121, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
92 24 0.20
93 36 0.30
94 59 0.49
95 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (92 bp):
GCTCTCATCTCGAGGTCGATGCATGTCCCAGACATGTCTTACACTAGCTATCATCTCATAGCCGA
TGCATGTCCCAAACATATCTTACACTG
Found at i:17689107 original size:47 final size:46
Alignment explanation
Indices: 17689037--17689256 Score: 225
Period size: 47 Copynumber: 4.7 Consensus size: 46
17689027 TAAGGTGCCA
* *
17689037 ATGCCATGTCCTAGACATAGTCTTACACTGGCTTACATCTCAAGTTG
1 ATGCCATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCAAGTCG
* * * *
17689084 ATGCCATGTCCCAAACATGGTCTTACACTGAC-TATCATCTCGTAGCCG
1 ATGCCATGTCCCAGACAT-GTCTTACACTGGCTTA-CATCTC-AAGTCG
* * *
17689132 ATG-CATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGTCG
1 ATGCCATGTCCCAGACATGTCTTACACTGGCTTACATC-TCAAGTCG
*
17689178 ATG-CATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCAA-TACCG
1 ATGCCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCAAGT--CG
*
17689224 ATGCCATGTCCTAGACATGATCTTACACTGGCT
1 ATGCCATGTCCCAGACATG-TCTTACACTGGCT
17689257 CTCATAATGT
Statistics
Matches: 144, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 58 0.40
47 65 0.45
48 18 0.12
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.30
Consensus pattern (46 bp):
ATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAAGTCG
Found at i:17689180 original size:46 final size:46
Alignment explanation
Indices: 17689041--17689298 Score: 211
Period size: 46 Copynumber: 5.5 Consensus size: 46
17689031 GTGCCAATGC
* * * **
17689041 CATGTCCTAGACATAGTCTTACACTGGCTTACATC-TCAAGTTGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTTGAGGCCGATG
* * *
17689087 CCATGTCCCAAACATGGTCTTACACTGAC-TATCATCTCGTA-GCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTTA-CATCTTG-AGGCCGATG
* *
17689135 CATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGTCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTTGAGGCCGATG
* ** **
17689181 CATGTCCCAGACATGTCTTACACTAGCTCT-CATCTCAATACCGATG
1 CATGTCCCAGACATGTCTTACACTGGCT-TACATCTTGAGGCCGATG
* ** *
17689227 CCATGTCCTAGACATGATCTTACACTGGCTCT-CATAATGTGGCCGATG
1 -CATGTCCCAGACATG-TCTTACACTGGCT-TACATCTTGAGGCCGATG
* *
17689275 CAAGTCCCGGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
17689299 AGCCAACAAT
Statistics
Matches: 171, Mismatches: 32, Indels: 17
0.78 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 71 0.42
47 70 0.41
48 28 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATCTTGAGGCCGATG
Found at i:17689282 original size:94 final size:92
Alignment explanation
Indices: 17689041--17689301 Score: 260
Period size: 94 Copynumber: 2.8 Consensus size: 92
17689031 GTGCCAATGC
* * * * ** * *
17689041 CATGTCCTAGACATAGTCTTACACTGGCTTACAT-CTCAAGTTGATGCCATGTCCCAAACATGGT
1 CATGTCCCAGACAT-GTCTTACACTGGCTTACATAATGAGGCCGATG-CAAGTCCCAGACAT-GT
*
17689105 CTTACACT-GACTATCATCTCGTAGCCGATG
63 CTTACACTAG-CTATCATCTCATAGCCGATG
* ** * *
17689135 CATGTCCCAGACATGTCTTACACTGGCTTACGTCTTGAGGTCGATGCATGTCCCAGACATGTCTT
1 CATGTCCCAGACATGTCTTACACTGGCTTACATAATGAGGCCGATGCAAGTCCCAGACATGTCTT
*
17689200 ACACTAGCTCTCATCTCAATA-CCGATG
66 ACACTAGCTATCATCTC-ATAGCCGATG
* * *
17689227 CCATGTCCTAGACATGATCTTACACTGGCTCT-CATAATGTGGCCGATGCAAGTCCCGGACATGT
1 -CATGTCCCAGACATG-TCTTACACTGGCT-TACATAATGAGGCCGATGCAAGTCCCAGACATGT
17689291 CTTACACTAGC
63 CTTACACTAGC
17689302 CAACAATTCC
Statistics
Matches: 144, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
92 25 0.17
93 48 0.33
94 70 0.49
95 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (92 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATAATGAGGCCGATGCAAGTCCCAGACATGTCTT
ACACTAGCTATCATCTCATAGCCGATG
Found at i:17689293 original size:140 final size:140
Alignment explanation
Indices: 17689041--17689298 Score: 344
Period size: 140 Copynumber: 1.8 Consensus size: 140
17689031 GTGCCAATGC
* * * *
17689041 CATGTCCTAGACATAGTCTTACACTGGCTTACATCTCAAGTTGATGCCATGTCCCAAACATGGTC
1 CATGTCCCAGACATAGTCTTACACTAGCTTACATCTCAAGTCGATGCCATGTCCCAAACATGATC
* *
17689106 TTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTT
66 TTACACTGACTATCATATCGTAGCCGATGCAAGTCCCAGACATGTCTTACACTGGCTTACGTCTT
17689171 GAGGTCGATG
131 GAGGTCGATG
* *
17689181 CATGTCCCAGACAT-GTCTTACACTAGCTCT-CATCTCAA-TACCGATGCCATGTCCTAGACATG
1 CATGTCCCAGACATAGTCTTACACTAGCT-TACATCTCAAGT--CGATGCCATGTCCCAAACATG
* * * *
17689243 ATCTTACACTGGCTCTCATAAT-GTGGCCGATGCAAGTCCCGGACATGTCTTACACT
63 ATCTTACACTGACTATCAT-ATCGTAGCCGATGCAAGTCCCAGACATGTCTTACACT
17689299 AGCCAACAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
138 1 0.01
139 21 0.21
140 79 0.77
141 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (140 bp):
CATGTCCCAGACATAGTCTTACACTAGCTTACATCTCAAGTCGATGCCATGTCCCAAACATGATC
TTACACTGACTATCATATCGTAGCCGATGCAAGTCCCAGACATGTCTTACACTGGCTTACGTCTT
GAGGTCGATG
Found at i:17700846 original size:60 final size:59
Alignment explanation
Indices: 17700770--17700906 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
17700760 AACTATGTTA
* *
17700770 ATATGGGCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * *
17700830 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
17700890 ATATGGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
17700907 GTTAACGCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 1 0.01
60 52 0.76
61 15 0.22
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:17701578 original size:16 final size:17
Alignment explanation
Indices: 17701546--17701578 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17701536 CATCAAGAAG
17701546 GGTTTTCAATGAAAACAT
1 GGTTTTCAA-GAAAACAT
17701564 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
17701579 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAT
Found at i:17702886 original size:26 final size:24
Alignment explanation
Indices: 17702857--17702908 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
17702847 TTTACTCATG
*
17702857 TTGTTTGAAGTTTTTTAATTTTAATT
1 TTGTTTCAAGTTTTTT--TTTTAATT
17702883 TTGTTTCAAGTTTTTTTTTTAATT
1 TTGTTTCAAGTTTTTTTTTTAATT
17702907 TT
1 TT
17702909 AATTTTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.40
26 15 0.60
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (24 bp):
TTGTTTCAAGTTTTTTTTTTAATT
Found at i:17702955 original size:23 final size:21
Alignment explanation
Indices: 17702929--17702991 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 21
17702919 TTTTAATTAA
17702929 TTTAATTCATGTTGTTTAAATTT
1 TTTAATTCATG-T-TTTAAATTT
*
17702952 TTTAATAAACATGTTTTAAATTT
1 TTTAAT--TCATGTTTTAAATTT
*
17702975 TTCTAATTTAT-TTTTAA
1 TT-TAATTCATGTTTTAA
17702992 TTCATAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 6 0.18
22 2 0.06
23 17 0.50
24 5 0.15
25 4 0.12
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTAATTCATGTTTTAAATTT
Found at i:17708559 original size:13 final size:13
Alignment explanation
Indices: 17708527--17708552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17708517 TATGTTATAC
17708527 ATATCAACACATA
1 ATATCAACACATA
17708540 ATATCAACACATA
1 ATATCAACACATA
17708553 TGTTCAATTA
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:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
ATATCAACACATA
Found at i:17709557 original size:26 final size:27
Alignment explanation
Indices: 17709521--17709574 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
17709511 GAAGCTCTGG
17709521 AGAGCCATTAATAAGGAAGCTCA-GAA
1 AGAGCCATTAATAAGGAAGCTCACGAA
* **
17709547 AGAGCCTTTAATTGGGAAGCTCACGAA
1 AGAGCCATTAATAAGGAAGCTCACGAA
17709574 A
1 A
17709575 AGTTATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.19
Consensus pattern (27 bp):
AGAGCCATTAATAAGGAAGCTCACGAA
Found at i:17717264 original size:5 final size:5
Alignment explanation
Indices: 17717254--17717278 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
17717244 ATATCTTGTA
17717254 TGATT TGATT TGATT TGATT TGATT
1 TGATT TGATT TGATT TGATT TGATT
17717279 ATGTAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TGATT
Found at i:17721829 original size:15 final size:15
Alignment explanation
Indices: 17721809--17721842 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17721799 TAATTATTTT
*
17721809 AATATAAAATAAATA
1 AATATAAAATAAACA
*
17721824 AATATAAACTAAACA
1 AATATAAAATAAACA
17721839 AATA
1 AATA
17721843 GTGACCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AATATAAAATAAACA
Done.