Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 57 of 150
Found at i:17157803 original size:17 final size:18
Alignment explanation
Indices: 17157783--17157816 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17157773 TTTTTGGGGG
17157783 GGATTGT-TTTTGGTTTC
1 GGATTGTATTTTGGTTTC
*
17157800 GGATTTTATTTTGGTTT
1 GGATTGTATTTTGGTTT
17157817 TCTAGCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.03, G:0.26, T:0.62
Consensus pattern (18 bp):
GGATTGTATTTTGGTTTC
Found at i:17159843 original size:20 final size:20
Alignment explanation
Indices: 17159814--17159852 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17159804 CGACATGTAT
*
17159814 TATCTATTAAGGCTTATCTA
1 TATCTATTAAGCCTTATCTA
*
17159834 TATCTTTTAAGCCTTATCT
1 TATCTATTAAGCCTTATCT
17159853 TATGGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (20 bp):
TATCTATTAAGCCTTATCTA
Found at i:17163658 original size:22 final size:24
Alignment explanation
Indices: 17163625--17163669 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
17163615 GTATAAATTT
*
17163625 AAAATTTTTATT-ATTTATTTATC
1 AAAATTTTTATTGATTTAATTATC
17163648 AAAA-TTTTATTGATTTAATTAT
1 AAAATTTTTATTGATTTAATTAT
17163670 ATAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
AAAATTTTTATTGATTTAATTATC
Found at i:17164412 original size:13 final size:13
Alignment explanation
Indices: 17164394--17164420 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17164384 GAGCTAGGTC
17164394 AGGCAAGAGTTTA
1 AGGCAAGAGTTTA
17164407 AGGCAAGAGTTTA
1 AGGCAAGAGTTTA
17164420 A
1 A
17164421 CATTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.22
Consensus pattern (13 bp):
AGGCAAGAGTTTA
Found at i:17165121 original size:3 final size:3
Alignment explanation
Indices: 17165113--17165139 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17165103 AATTACACAA
17165113 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
17165140 TAGAGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17173660 original size:27 final size:25
Alignment explanation
Indices: 17173629--17173696 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
17173619 CATCTTGACC
17173629 CACAACTTGTGTGAGCAAACCCATATT
1 CACAACTTGTGTGAGC-AA-CCATATT
* * **
17173656 CACAACTCGTGCGAGC-ATTATATT
1 CACAACTTGTGTGAGCAACCATATT
*
17173680 CACAACTTATGTGAGCA
1 CACAACTTGTGTGAGCA
17173697 TTTCTATCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
24 18 0.55
25 1 0.03
27 14 0.42
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (25 bp):
CACAACTTGTGTGAGCAACCATATT
Found at i:17173695 original size:24 final size:24
Alignment explanation
Indices: 17173651--17173698 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17173641 GAGCAAACCC
*
17173651 ATATTCACAACTCGTGCGAGCATT
1 ATATTCACAACTCATGCGAGCATT
* *
17173675 ATATTCACAACTTATGTGAGCATT
1 ATATTCACAACTCATGCGAGCATT
17173699 TCTATCCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (24 bp):
ATATTCACAACTCATGCGAGCATT
Found at i:17177714 original size:21 final size:21
Alignment explanation
Indices: 17177689--17177729 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17177679 TACTGCATTT
*
17177689 ATCCATGACAT-AGATAAATTC
1 ATCCATAACATAAG-TAAATTC
17177710 ATCCATAACATAAGTAAATT
1 ATCCATAACATAAGTAAATT
17177730 TCTCACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.29
Consensus pattern (21 bp):
ATCCATAACATAAGTAAATTC
Found at i:17179352 original size:44 final size:45
Alignment explanation
Indices: 17179303--17179392 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
17179293 TCGGTTGTGT
*
17179303 TAGAGAAGAAACCAAAAAGATGATAATATTTAAGCCTTTT-TTTC
1 TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
17179347 TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
1 TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
17179392 T
1 T
17179393 TTTAATTTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 39 0.89
45 5 0.11
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (45 bp):
TAGAGAAGAAACAAAAAAGATGATAATATTTAAGCCTTTTGTTTC
Found at i:17180736 original size:97 final size:97
Alignment explanation
Indices: 17180570--17180762 Score: 341
Period size: 97 Copynumber: 2.0 Consensus size: 97
17180560 TAGCTTTGAT
* *
17180570 TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAGGGTTACTACCAATCAGGGAGGTTG
1 TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
*
17180635 AATTTGCTATTGAATTGGCATCGGGAACTTCC
66 AATTTGCTATTGAATTGGCATCGAGAACTTCC
*
17180667 TGTTCATGAATTTGCTGATGTTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
1 TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
*
17180732 AATTTGCTATTGAATTGGCATCTAGAACTTC
66 AATTTGCTATTGAATTGGCATCGAGAACTTC
17180763 TCCAATATTG
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 91 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (97 bp):
TGTTCATGAATTTGCTGATATTTTCCCAAAAGAATTGCCAAGGTTACCACCAATCAGGGAGGTTG
AATTTGCTATTGAATTGGCATCGAGAACTTCC
Found at i:17186127 original size:28 final size:28
Alignment explanation
Indices: 17186076--17186136 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
17186066 TATGAATGCT
*
17186076 ATGAAATATGTTTGAATAAGGTGTTTAA
1 ATGAAATATGTTTGAATAAGGTGTATAA
** *
17186104 ATGAAATATTGTTTGTTTAA-GTGTATAT
1 ATGAAATA-TGTTTGAATAAGGTGTATAA
17186132 ATGAA
1 ATGAA
17186137 TGCTAGATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.43
Consensus pattern (28 bp):
ATGAAATATGTTTGAATAAGGTGTATAA
Found at i:17187154 original size:22 final size:24
Alignment explanation
Indices: 17187124--17187168 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
17187114 AGCACCCGCT
*
17187124 AAAACCCAATATT-TT-TTTTATA
1 AAAAACCAATATTGTTGTTTTATA
17187146 AAAAACCAATATTGTTGTTTTAT
1 AAAAACCAATATTGTTGTTTTAT
17187169 GATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 2 0.10
24 6 0.30
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (24 bp):
AAAAACCAATATTGTTGTTTTATA
Found at i:17187580 original size:5 final size:5
Alignment explanation
Indices: 17187572--17187606 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
17187562 TAAATAATTA
17187572 AAAAT AAAATT AAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT AAA
17187607 CCCAATTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:17187582 original size:12 final size:12
Alignment explanation
Indices: 17187567--17187603 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
17187557 TAAATTAAAT
17187567 AATTAAAAATAA
1 AATTAAAAATAA
17187579 AATTAAAAATAA
1 AATTAAAAATAA
17187591 AA-T-AAAATAA
1 AATTAAAAATAA
17187601 AAT
1 AAT
17187604 AAACCCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
12 14 0.58
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATTAAAAATAA
Found at i:17191618 original size:342 final size:342
Alignment explanation
Indices: 17190993--17191670 Score: 1230
Period size: 342 Copynumber: 2.0 Consensus size: 342
17190983 TCGTAAATCT
* *
17190993 TCAAGAAAACATCCTAAAATTTCATAGATTTCATCATCTTCCCCACGTTGTAACGCTGGGGTTTG
1 TCAAGAAAACATCCTAAAAGTTCATAGATTTCATCATCTTCCCCACATTGTAACGCTGGGGTTTG
* *
17191058 TGCAAGTGTACACAGTCGTTATCAAGTCATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
66 TGCAAGTGTACACAATCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
17191123 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
131 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
17191188 TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
196 TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
*
17191253 AAGGATGCAAACTATATGAATGAAATAGATTTTAGTAAAATTAAACACAATTTGCAACAATTATA
261 AAGGATGCAAACTATATGAATGAAATAGATTTCAGTAAAATTAAACACAATTTGCAACAATTATA
*
17191318 ATATAAATAAAACTAGG
326 ACATAAATAAAACTAGG
*
17191335 TCAAGAAAACATCCTAAAAGTTCATAGATTTCATCATCTTCCCCACATTGTAACGTTGGGGTTTG
1 TCAAGAAAACATCCTAAAAGTTCATAGATTTCATCATCTTCCCCACATTGTAACGCTGGGGTTTG
* *
17191400 TGCAAGTGTACACAATCGTTATCAAGTAATAAGTAAGTATTGAGTTATCGTCTCTACAGGGATTG
66 TGCAAGTGTACACAATCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
17191465 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
131 TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
* *
17191530 TAGTTGAGAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAGATTATCCT
196 TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
* * *
17191595 AAGTATGCAAACTATATGAATGAAATAGATTTCAGTAAAATTAAATACAATTTGCAACAGTTATA
261 AAGGATGCAAACTATATGAATGAAATAGATTTCAGTAAAATTAAACACAATTTGCAACAATTATA
17191660 ACATAAATAAA
326 ACATAAATAAA
17191671 CTACGACAAT
Statistics
Matches: 322, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
342 322 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (342 bp):
TCAAGAAAACATCCTAAAAGTTCATAGATTTCATCATCTTCCCCACATTGTAACGCTGGGGTTTG
TGCAAGTGTACACAATCGTTATCAAGTAATAAGTAAGTATTGAGTTATCATCTCCACAGGGATTG
TATTTGTGCTAAGTCACTTAATTTGTAAAATTATATTAACAATTTGGTAAATAAAAAACACAATA
TAGTTGAAAAGTGGTGATTAAAATATATTAAACTAAATGCAATGATCCCTAATGCAAATTATCCT
AAGGATGCAAACTATATGAATGAAATAGATTTCAGTAAAATTAAACACAATTTGCAACAATTATA
ACATAAATAAAACTAGG
Found at i:17192421 original size:19 final size:19
Alignment explanation
Indices: 17192397--17192434 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
17192387 CTAAAAAATT
17192397 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
17192416 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
17192435 GGATGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:17195531 original size:28 final size:28
Alignment explanation
Indices: 17195486--17195574 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
17195476 AACACGATAG
* *
17195486 AAAATAATAGCCTTTGTGGCGAATCGTA
1 AAAAGAATAACCTTTGTGGCGAATCGTA
* * *
17195514 AAAAGAATAACCTCTGTGGAGAATTGTA
1 AAAAGAATAACCTTTGTGGCGAATCGTA
* * *
17195542 AAAAGAA-AAGCCTTTATGGCGGATCATA
1 AAAAGAATAA-CCTTTGTGGCGAATCGTA
17195570 AAAAG
1 AAAAG
17195575 GAAAGCTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 2 0.04
28 47 0.96
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (28 bp):
AAAAGAATAACCTTTGTGGCGAATCGTA
Found at i:17196983 original size:31 final size:31
Alignment explanation
Indices: 17196945--17197010 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
17196935 TTTTTTTTGT
17196945 TTAATTTGATACCTAAACTTGATACATTTTC
1 TTAATTTGATACCTAAACTTGATACATTTTC
* * **
17196976 TTAATTTGGTATCTAAACTTGATATTTTTTC
1 TTAATTTGATACCTAAACTTGATACATTTTC
17197007 TTAA
1 TTAA
17197011 GTTGGTACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (31 bp):
TTAATTTGATACCTAAACTTGATACATTTTC
Found at i:17197016 original size:31 final size:31
Alignment explanation
Indices: 17196957--17197017 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
17196947 AATTTGATAC
*
17196957 CTAAACTTGATACATTTTCTTAATTTGGTAT
1 CTAAACTTGATACATTTTCTTAAGTTGGTAT
**
17196988 CTAAACTTGATATTTTTTCTTAAGTTGGTA
1 CTAAACTTGATACATTTTCTTAAGTTGGTA
17197018 CTTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (31 bp):
CTAAACTTGATACATTTTCTTAAGTTGGTAT
Found at i:17197584 original size:59 final size:59
Alignment explanation
Indices: 17197480--17197623 Score: 175
Period size: 59 Copynumber: 2.4 Consensus size: 59
17197470 ATTTAATAAA
* * * * *
17197480 TTTAGGTACTAAATTAGGAAAACATGTCAAGTTCAACTATCAAATTGGGCCCAAAAAAGT
1 TTTA-GTACCAAATTAAGAAAAAATGTCAAGTTCAACTATCAAATTGGGCCAAAAAAAAT
* *
17197540 TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAAGTA-CTAAATTGGGCTAAAAAAAAT
1 TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAACTATC-AAATTGGGCCAAAAAAAAT
* *
17197599 TTAAATACCAAATTAA-AAAAAATGT
1 TTTAGTACCAAATTAAGAAAAAATGT
17197624 TAAGATCAGT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 10 0.14
59 60 0.81
60 4 0.05
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (59 bp):
TTTAGTACCAAATTAAGAAAAAATGTCAAGTTCAACTATCAAATTGGGCCAAAAAAAAT
Found at i:17198175 original size:21 final size:19
Alignment explanation
Indices: 17198124--17198200 Score: 127
Period size: 19 Copynumber: 3.9 Consensus size: 19
17198114 ATAATTTTCA
17198124 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
17198143 ATGATGTGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
17198162 ATGATATATGCAATCTTAGAT
1 ATG--ATATGCAATCTTAGAT
17198183 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
17198201 AGATATGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 36 0.67
21 18 0.33
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:17198222 original size:23 final size:22
Alignment explanation
Indices: 17198124--17198223 Score: 90
Period size: 19 Copynumber: 4.8 Consensus size: 22
17198114 ATAATTTTCA
17198124 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
* *
17198143 ATGATGTGCAATCTTAG-ATAT
1 ATGATATGCAATCTTAGAAGAT
17198164 GAT-ATATGCAATCTT---AGAT
1 -ATGATATGCAATCTTAGAAGAT
17198183 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
17198205 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
17198224 GATTTAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.03
19 29 0.43
21 14 0.21
22 10 0.15
23 12 0.18
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:17202991 original size:6 final size:6
Alignment explanation
Indices: 17202982--17203009 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17202972 ATCAAAATCA
17202982 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
17203010 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:17203921 original size:47 final size:46
Alignment explanation
Indices: 17203852--17203940 Score: 142
Period size: 47 Copynumber: 1.9 Consensus size: 46
17203842 AGGAGAAGGG
* * *
17203852 ACCAAGGTGAAAACCTGCAAAGGGCGCTTTGAGTTTCAAAAAAAAAT
1 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAG-TCCAAAAAAAAAT
17203899 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAA
1 ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAA
17203941 TAAAAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 8 0.21
47 31 0.79
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (46 bp):
ACCAAGGTGAAAACCCGCAAAGGGCACTTTGAGTCCAAAAAAAAAT
Found at i:17205366 original size:45 final size:45
Alignment explanation
Indices: 17205187--17205368 Score: 283
Period size: 45 Copynumber: 4.0 Consensus size: 45
17205177 CAGATCAGTA
*
17205187 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCA
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
* * *
17205232 AAAATAGCAGATCTTGTCTTCCTATATTGGTAGCAAAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
* * *
17205277 AAGATAACGGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
* *
17205322 AAAACAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATCG
1 AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
17205367 AA
1 AA
17205369 GACAGAAGTA
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 122 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (45 bp):
AAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCG
Found at i:17205523 original size:44 final size:44
Alignment explanation
Indices: 17205473--17205582 Score: 175
Period size: 44 Copynumber: 2.5 Consensus size: 44
17205463 ATCCAGTCTC
* * * *
17205473 ATCTCCCCGAGGTTGCAGTGGAACAGATTGAATAAGCCAATCTT
1 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
17205517 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
1 ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
*
17205561 ATCTCCCTGAAGTTGCAGTGGA
1 ATCTCCCTGAGGTTGCAGTGGA
17205583 GTGGATCAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (44 bp):
ATCTCCCTGAGGTTGCAGTGGAACAGATTGAAGAAACCAATCCT
Found at i:17206170 original size:21 final size:19
Alignment explanation
Indices: 17206124--17206198 Score: 132
Period size: 19 Copynumber: 3.8 Consensus size: 19
17206114 AATCTTCAAG
17206124 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
17206143 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
17206162 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
17206183 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
17206199 AGATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
19 35 0.65
21 19 0.35
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:17206220 original size:23 final size:22
Alignment explanation
Indices: 17206124--17206221 Score: 95
Period size: 19 Copynumber: 4.7 Consensus size: 22
17206114 AATCTTCAAG
17206124 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
17206143 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
17206165 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
17206183 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
17206205 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
17206222 GATTTAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.03
19 28 0.42
21 15 0.22
22 10 0.15
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:17212923 original size:58 final size:58
Alignment explanation
Indices: 17212794--17212926 Score: 196
Period size: 58 Copynumber: 2.3 Consensus size: 58
17212784 ATTTATAAGA
* * * *
17212794 TAGTCCTTAACGGACTTCCCAACGCTAGATAGTCCTAACGAACATCCTCTTCATTCGT
1 TAGTCCTTAGCGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
* *
17212852 TAGTCCTTGGCGGACTTCCCAACCCTAGATAATCATAACGGACATCCTCTTCATTCGT
1 TAGTCCTTAGCGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
17212910 TAGT-CTCTAGCGGACTT
1 TAGTCCT-TAGCGGACTT
17212927 TATAGAACAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 2 0.03
58 65 0.97
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (58 bp):
TAGTCCTTAGCGGACTTCCCAACCCTAGATAATCATAACGAACATCCTCTTCATTCGT
Found at i:17217551 original size:21 final size:21
Alignment explanation
Indices: 17217526--17217578 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
17217516 AGCGGTGGCG
*
17217526 GTGAGATTAGTTACTGTAGTA
1 GTGAGATTAGATACTGTAGTA
* *
17217547 GTGAGATTGGATACTGTAG-C
1 GTGAGATTAGATACTGTAGTA
17217567 GATGAGATTAGA
1 G-TGAGATTAGA
17217579 AACAATGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGTA
Found at i:17219554 original size:15 final size:16
Alignment explanation
Indices: 17219534--17219567 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17219524 AAAAGCATAG
17219534 CATAAAAA-TATCAAA
1 CATAAAAAGTATCAAA
*
17219549 CATAAAAAGTATCATA
1 CATAAAAAGTATCAAA
17219565 CAT
1 CAT
17219568 TAGTTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (16 bp):
CATAAAAAGTATCAAA
Found at i:17221546 original size:30 final size:30
Alignment explanation
Indices: 17221510--17222463 Score: 1553
Period size: 29 Copynumber: 32.3 Consensus size: 30
17221500 GAATAAATCG
*
17221510 AATACACTATATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17221540 AATACACTACATATATTTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTTATTTTTAA
17221571 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17221600 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17221629 ACTACACTACATATATATTTTTTATTTTTAA
1 AATACACTACATATAT-TTTTTTATTTTTAA
17221660 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17221689 AATACACTACATATATATTTTTTAGTTTTAA
1 AATACACTACATATAT-TTTTTTATTTTTAA
17221720 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17221749 AATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17221779 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17221809 AATACACTAC--ATA-----TT-TTTTT-A
1 AATACACTACATATATTTTTTTATTTTTAA
17221830 AATACACTACATATATATTTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTTATTTTTAA
*
17221862 AATACACTATATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17221891 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17221920 AATACACTACAAATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17221950 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17221979 AATGCACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17222008 AATACACTAAATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222037 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222067 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
17222097 AATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222127 AATACACTACATATA-TTTTTTA-TTTTATA
1 AATACACTACATATATTTTTTTATTTTTA-A
17222156 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222186 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222215 AATACACTACATATATTTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTTATTTTTAA
*
17222246 AATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222276 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222305 AATACACTACATATATATATTTTTTATTTTTAA
1 AATACACTAC--ATATAT-TTTTTTATTTTTAA
17222338 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222367 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222397 AATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222427 AATACACTACATATA--TTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
17222455 AATACACTA
1 AATACACTA
17222464 ATACAGTGCA
Statistics
Matches: 876, Mismatches: 19, Indels: 60
0.92 0.02 0.06
Matches are distributed among these distances:
21 11 0.01
22 5 0.01
23 2 0.00
25 3 0.00
28 30 0.03
29 356 0.41
30 300 0.34
31 135 0.15
32 10 0.01
33 24 0.03
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (30 bp):
AATACACTACATATATTTTTTTATTTTTAA
Found at i:17221605 original size:60 final size:58
Alignment explanation
Indices: 17221510--17222463 Score: 1535
Period size: 60 Copynumber: 16.2 Consensus size: 58
17221500 GAATAAATCG
*
17221510 AATACACTATATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATA--TTTTTTATTTTTAA
17221571 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
17221629 ACTACACTACATATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
17221689 AATACACTACATATATATTTTTTAGTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTAC--ATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
17221749 AATACACTACATATATATTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATAT-TTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
** * * *
17221809 AATACACTACATAT-TTTTTTA--AATACACTACA-TATATAT-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
17221862 AATACACTATATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
*
17221920 AATACACTACAAATATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
* *
17221979 AATGCACTACATATATTTTTTATTTTTAAAATACACTAAATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
17222037 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
17222097 AATACACTACATATATATTTTTATTTTTAAAATACACTACATATATTTTTTA-TTTTATA
1 AATACACTACATATAT-TTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTA-A
17222156 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
17222215 AATACACTACATATATTTTTTTTATTTTTAAAATACACTACATATATATTTTTATTTTTAA
1 AATACACTACATATA--TTTTTTATTTTTAAAATACACTACATATAT-TTTTTATTTTTAA
17222276 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATATATTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTAC----ATATATTTTTTATTTTTAA
17222338 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAA
1 AATACACTACATATATTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAA
17222397 AATACACTACATATATTTTTTTATTTTTAAAATACACTACATATA-TTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
17222455 AATACACTA
1 AATACACTA
17222464 ATACAGTGCA
Statistics
Matches: 846, Mismatches: 23, Indels: 51
0.92 0.03 0.06
Matches are distributed among these distances:
53 27 0.03
54 7 0.01
55 6 0.01
56 14 0.02
57 6 0.01
58 150 0.18
59 240 0.28
60 296 0.35
61 42 0.05
62 52 0.06
63 6 0.01
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (58 bp):
AATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAA
Found at i:17221845 original size:23 final size:22
Alignment explanation
Indices: 17221800--17221851 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
17221790 TATATTTTTT
*
17221800 TATTTTTAAAATACACTACATA
1 TATTTTTTAAATACACTACATA
17221822 T-TTTTTTAAATACACTACATA
1 TATTTTTTAAATACACTACATA
17221843 TATATTTTT
1 TAT-TTTTT
17221852 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 20 0.74
22 2 0.07
23 5 0.19
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTTTTAAATACACTACATA
Found at i:17222477 original size:27 final size:28
Alignment explanation
Indices: 17222419--17222477 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
17222409 ATATTTTTTT
* * ***
17222419 ATTTTTAAAATACACTACATATATTTTT
1 ATTTTTAAAATACACTACATACAGTGCA
17222447 ATTTTTAAAATACACTA-ATACAGTGCA
1 ATTTTTAAAATACACTACATACAGTGCA
17222474 ATTT
1 ATTT
17222478 CCCCATTCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (28 bp):
ATTTTTAAAATACACTACATACAGTGCA
Found at i:17222550 original size:13 final size:13
Alignment explanation
Indices: 17222532--17222556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17222522 CCGTGCCCTC
17222532 CTCCCATTTCCCA
1 CTCCCATTTCCCA
17222545 CTCCCATTTCCC
1 CTCCCATTTCCC
17222557 CTCTTCCACC
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:0.12, C:0.56, G:0.00, T:0.32
Consensus pattern (13 bp):
CTCCCATTTCCCA
Found at i:17225010 original size:22 final size:22
Alignment explanation
Indices: 17224991--17225076 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
17224981 ACCAAGAACA
17224991 AAGCAAAAAAGAGGGGAGAAAC
1 AAGCAAAAAAGAGGGGAGAAAC
* * *
17225013 CAGCAAAAACGAGGGG-CAAAC
1 AAGCAAAAAAGAGGGGAGAAAC
* *
17225034 CAGCAAGAACA-A-GGGAGAAAC
1 AAGCAA-AAAAGAGGGGAGAAAC
* * *
17225055 CAGCAAGAACGAGGGGAGAAAC
1 AAGCAAAAAAGAGGGGAGAAAC
17225077 TGCTGTTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 4 0.08
21 22 0.43
22 25 0.49
ACGTcount: A:0.51, C:0.17, G:0.31, T:0.00
Consensus pattern (22 bp):
AAGCAAAAAAGAGGGGAGAAAC
Found at i:17225033 original size:21 final size:20
Alignment explanation
Indices: 17224992--17225071 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 20
17224982 CCAAGAACAA
*
17224992 AGCAAAAAAGAGGGGAGAAACC
1 AGCAAAAACGA-GGG-GAAACC
17225014 AGCAAAAACGAGGGGCAAACC
1 AGCAAAAACGAGGGG-AAACC
* *
17225035 AGCAAGAACAAGGGAGAAACC
1 AGCAAAAACGAGGG-GAAACC
*
17225056 AGCAAGAACGAGGGGA
1 AGCAAAAACGAGGGGA
17225072 GAAACTGCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.06
21 38 0.73
22 11 0.21
ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00
Consensus pattern (20 bp):
AGCAAAAACGAGGGGAAACC
Found at i:17229573 original size:16 final size:16
Alignment explanation
Indices: 17229554--17229585 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17229544 AAAAAAAAGA
17229554 AAGTACCTGAAGAAGG
1 AAGTACCTGAAGAAGG
17229570 AAGTACCTGAAGAAGG
1 AAGTACCTGAAGAAGG
17229586 TAAACTTGTT
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:0.44, C:0.12, G:0.31, T:0.12
Consensus pattern (16 bp):
AAGTACCTGAAGAAGG
Found at i:17231461 original size:51 final size:52
Alignment explanation
Indices: 17231358--17231461 Score: 165
Period size: 51 Copynumber: 2.0 Consensus size: 52
17231348 CGCTATCTTG
*
17231358 GAATTGAGTGAAATTGCATTTTGTGTTTTTTTATTGAAAAATGATAAATTAAT
1 GAATTGAGTGAAATTGCATTTTGTG-TTTTTTATTGAAAAATAATAAATTAAT
**
17231411 GAATTGAGTGAAATTTTATTTTGTG-TTTTTATTGAAAAATAATAAATTAAT
1 GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATAATAAATTAAT
17231462 CTTATAAGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
51 25 0.52
53 23 0.48
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (52 bp):
GAATTGAGTGAAATTGCATTTTGTGTTTTTTATTGAAAAATAATAAATTAAT
Found at i:17231481 original size:24 final size:23
Alignment explanation
Indices: 17231454--17231500 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
17231444 GAAAAATAAT
17231454 AAATTAATCTTATAAGTTAGAAAA
1 AAATTAATCTTATAAGTTA-AAAA
* * *
17231478 AAATTATTTTTTTAAGTTAAAAA
1 AAATTAATCTTATAAGTTAAAAA
17231501 TGTTATCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (23 bp):
AAATTAATCTTATAAGTTAAAAA
Found at i:17232428 original size:18 final size:18
Alignment explanation
Indices: 17232401--17232436 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17232391 AAGTTACATC
17232401 GAGTACTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
*
17232419 GAGTATTTTGTTAGTAAT
1 GAGTACTTTGTTAGTAAT
17232437 ATGTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (18 bp):
GAGTACTTTGTTAGTAAT
Found at i:17232692 original size:22 final size:21
Alignment explanation
Indices: 17232667--17232714 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17232657 CTCTTAAAAG
17232667 CAAAGAAGAACGGCTATCGTTT
1 CAAA-AAGAACGGCTATCGTTT
***
17232689 CAAAATTTACGGCTATCGTTT
1 CAAAAAGAACGGCTATCGTTT
17232710 CAAAA
1 CAAAA
17232715 TTTTTTTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (21 bp):
CAAAAAGAACGGCTATCGTTT
Found at i:17232700 original size:21 final size:21
Alignment explanation
Indices: 17232676--17232717 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17232666 GCAAAGAAGA
17232676 ACGGCTATCGTTTCAAAATTT
1 ACGGCTATCGTTTCAAAATTT
17232697 ACGGCTATCGTTTCAAAATTT
1 ACGGCTATCGTTTCAAAATTT
17232718 TTTTCACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (21 bp):
ACGGCTATCGTTTCAAAATTT
Found at i:17234208 original size:13 final size:13
Alignment explanation
Indices: 17234190--17234253 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
17234180 ACACTCAAAT
17234190 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
17234203 TTCTCAAAAACAC
1 TTCTCAAAAGCAC
*
17234216 TTTTCAAAAGCAC
1 TTCTCAAAAGCAC
17234229 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
17234242 TTCTCAAAAGCA
1 TTCTCAAAAGCA
17234254 ATAAAGAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.25
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:17237743 original size:41 final size:41
Alignment explanation
Indices: 17237627--17237782 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
17237617 ACAACGGTTA
* * *
17237627 TCTGATTCACA-ACACTGGCACGAAGCCTACTAGGCCCAAGG
1 TCTGATTC-CATACACTGACACGAAGCCTGCTAGGCTCAAGG
* * * * * * * *
17237668 TCTAATTTCATACACCGGCACAAATCCTGATAGGCTTAAGG
1 TCTGATTCCATACACTGACACGAAGCCTGCTAGGCTCAAGG
* *
17237709 TCTGATTCCATACACTGACACGAAGCTTGCTAGGCTGAAGG
1 TCTGATTCCATACACTGACACGAAGCCTGCTAGGCTCAAGG
* * *
17237750 CCTGATTTCATACACT-AGCTCGAAGCCTGCTAG
1 TCTGATTCCATACACTGA-CACGAAGCCTGCTAG
17237783 ATTCAAAACC
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 3 0.03
41 88 0.97
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
TCTGATTCCATACACTGACACGAAGCCTGCTAGGCTCAAGG
Found at i:17252574 original size:21 final size:22
Alignment explanation
Indices: 17252542--17252597 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
17252532 ACTGTTGTTG
*
17252542 AGAAGAAAGTTGCTT-CTGTAGA
1 AGAAG-AAGTTGCTTGCTGAAGA
*
17252564 AGAGGAAGTTG-TTGCTGAAGA
1 AGAAGAAGTTGCTTGCTGAAGA
17252585 AGAAGAAGTTGCT
1 AGAAGAAGTTGCT
17252598 GAAAATGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 22 0.76
22 5 0.17
ACGTcount: A:0.36, C:0.07, G:0.32, T:0.25
Consensus pattern (22 bp):
AGAAGAAGTTGCTTGCTGAAGA
Found at i:17252914 original size:15 final size:14
Alignment explanation
Indices: 17252894--17252924 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17252884 CTTAAAAGAT
*
17252894 AAAAAAGGGAGGAG
1 AAAAAAAGGAGGAG
17252908 AAAAAAAGGAGGAG
1 AAAAAAAGGAGGAG
17252922 AAA
1 AAA
17252925 GAAACATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AAAAAAAGGAGGAG
Found at i:17253061 original size:17 final size:17
Alignment explanation
Indices: 17253039--17253072 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17253029 GATAAATATA
* *
17253039 TATTGTGATTGCATTTT
1 TATTGTCATTACATTTT
17253056 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
17253073 CATGTTAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:17257619 original size:62 final size:59
Alignment explanation
Indices: 17257507--17257705 Score: 145
Period size: 68 Copynumber: 3.2 Consensus size: 59
17257497 ATCACTTTAG
* * ** * *
17257507 TATTAAATTAATATAATATTTATTAAGATAAATGTTAGATTTAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
17257566 TATTAAAATAATAGAATGTTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAAATAATAGAATATTTAT-T--AAGATAAACATTAAATTAAATTTAATATT---A-AAT-
17257631 ACTT
58 -C-T
* * * * *
17257635 TAATTTTAAATTAATAAAATA-CTATTAAGATAAATATTAAATTTAATTTAATATTAAA-C-
1 T-A--TTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
17257694 -ATTAAAATAATA
1 TATTAAAATAATA
17257706 TTATCTTTGG
Statistics
Matches: 113, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
55 10 0.09
57 1 0.01
59 20 0.18
60 1 0.01
61 1 0.01
62 25 0.22
64 2 0.02
65 2 0.02
66 3 0.03
68 28 0.25
69 2 0.02
70 2 0.02
71 3 0.03
72 13 0.12
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:17257662 original size:25 final size:27
Alignment explanation
Indices: 17257607--17257662 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
17257597 TAAACATTAA
*
17257607 ATTAAATTTAATATTAAGATAATCACT
1 ATTAAATTTAATATTAAGAAAATCACT
* *
17257634 -TTAATTTTAA-ATTAATAAAAT-ACT
1 ATTAAATTTAATATTAAGAAAATCACT
17257658 ATTAA
1 ATTAA
17257663 GATAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 3 0.12
25 13 0.52
26 9 0.36
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTAAATTTAATATTAAGAAAATCACT
Found at i:17260426 original size:13 final size:13
Alignment explanation
Indices: 17260408--17260440 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
17260398 CGAGATAATC
17260408 GGAATTGAAGCTT
1 GGAATTGAAGCTT
*
17260421 GGAATTAAAGCTT
1 GGAATTGAAGCTT
17260434 GGAATTG
1 GGAATTG
17260441 CCTAGTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (13 bp):
GGAATTGAAGCTT
Found at i:17266388 original size:33 final size:33
Alignment explanation
Indices: 17266350--17266415 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17266340 GAGTAAGTTC
17266350 GTAAATATTATTATTTAATATTTACGAGTAGAA
1 GTAAATATTATTATTTAATATTTACGAGTAGAA
17266383 GTAAATATTATTATTTAATATTTACGAGTAGAA
1 GTAAATATTATTATTTAATATTTACGAGTAGAA
17266416 TATGGTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (33 bp):
GTAAATATTATTATTTAATATTTACGAGTAGAA
Found at i:17272750 original size:30 final size:30
Alignment explanation
Indices: 17272714--17272774 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
17272704 TGACTTGGGT
17272714 CACATGCCCATGTGTGTTACCT-GTGTGTGA
1 CACATGCCCATGTGTGTT-CCTCGTGTGTGA
*
17272744 CACATGCCCATGTGTGTTGCTCGTGTGTGA
1 CACATGCCCATGTGTGTTCCTCGTGTGTGA
17272774 C
1 C
17272775 TATCTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.15, C:0.25, G:0.28, T:0.33
Consensus pattern (30 bp):
CACATGCCCATGTGTGTTCCTCGTGTGTGA
Found at i:17272795 original size:8 final size:8
Alignment explanation
Indices: 17272782--17272814 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
17272772 GACTATCTTT
17272782 TTCTTTTC
1 TTCTTTTC
*
17272790 TTCTTTAC
1 TTCTTTTC
17272798 TT-TTTTC
1 TTCTTTTC
17272805 TTCTTTTC
1 TTCTTTTC
17272813 TT
1 TT
17272815 TGTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:17272805 original size:15 final size:15
Alignment explanation
Indices: 17272785--17272815 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17272775 TATCTTTTTC
17272785 TTTTCTTCTTTACTT
1 TTTTCTTCTTTACTT
*
17272800 TTTTCTTCTTTTCTT
1 TTTTCTTCTTTACTT
17272815 T
1 T
17272816 GTTAAATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTCTTTACTT
Found at i:17276548 original size:42 final size:42
Alignment explanation
Indices: 17276499--17276690 Score: 196
Period size: 42 Copynumber: 4.6 Consensus size: 42
17276489 CGGCTTTATA
* * *
17276499 CTTCAGTTTAGCCGATGATGCACTTATGTACCAATATATTCG
1 CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
*
17276541 CTTCAGTTTAGCTGATGATGAACTTATGTGCCAGTATATTCG
1 CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
* *
17276583 CTT-TGTTTTAGCTAATGATGCACTTATGTGCCAGTATAATT-G
1 CTTCAG-TTTAGCTGATGATGCACTTATGTGCCAGTAT-ATTCG
* *
17276625 CCTC-GACTT-GTCTGATGATGCACTTATGTGCCAGTATATTTC-
1 CTTCAG-TTTAG-CTGATGATGCACTTATGTGCCAGTATA-TTCG
* * **
17276667 CTTCGGTTTATCCAATGATGCACT
1 CTTCAGTTTAGCTGATGATGCACT
17276691 GTGGTGCTAG
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.02
42 119 0.94
43 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (42 bp):
CTTCAGTTTAGCTGATGATGCACTTATGTGCCAGTATATTCG
Found at i:17276604 original size:84 final size:84
Alignment explanation
Indices: 17276499--17276690 Score: 221
Period size: 84 Copynumber: 2.3 Consensus size: 84
17276489 CGGCTTTATA
* * * *
17276499 CTTCAGTTTAGCCGATGATGCACTTATGTACCAATAT-ATTCGCTTC-AGTT-TAGCTGATGATG
1 CTTCGGTTTAGCCAATGATGCACTTATGTACCAATATAATT-GCCTCGACTTGT--CTGATGATG
17276561 AACTTATGTGCCAGTATA-TTC
63 AACTTATGTGCCAGTATATTTC
* * * * * *
17276582 GCTTTGTTTTAGCTAATGATGCACTTATGTGCCAGTATAATTGCCTCGACTTGTCTGATGATGCA
1 -CTTCGGTTTAGCCAATGATGCACTTATGTACCAATATAATTGCCTCGACTTGTCTGATGATGAA
17276647 CTTATGTGCCAGTATATTTC
65 CTTATGTGCCAGTATATTTC
*
17276667 CTTCGGTTTATCCAATGATGCACT
1 CTTCGGTTTAGCCAATGATGCACT
17276691 GTGGTGCTAG
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
84 80 0.89
85 9 0.10
86 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (84 bp):
CTTCGGTTTAGCCAATGATGCACTTATGTACCAATATAATTGCCTCGACTTGTCTGATGATGAAC
TTATGTGCCAGTATATTTC
Found at i:17282475 original size:19 final size:19
Alignment explanation
Indices: 17282433--17282475 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17282423 CCACAGAATA
*
17282433 TTTTTTCTTTTTTTCTCAT
1 TTTTTTCTATTTTTCTCAT
*
17282452 ATTTTTCTATTTTTC-CAT
1 TTTTTTCTATTTTTCTCAT
17282470 TTTTTT
1 TTTTTT
17282476 AATATTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTCTATTTTTCTCAT
Found at i:17283799 original size:17 final size:19
Alignment explanation
Indices: 17283777--17283818 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
17283767 AATAAATAAG
17283777 ATAAAT-AAAA-TAGAATA
1 ATAAATCAAAACTAGAATA
*
17283794 ATAAATCAAAACTTATAATA
1 ATAAATCAAAAC-TAGAATA
17283814 ATAAA
1 ATAAA
17283819 GAAGACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 4 0.19
20 11 0.52
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
ATAAATCAAAACTAGAATA
Found at i:17291488 original size:23 final size:23
Alignment explanation
Indices: 17291446--17291489 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
17291436 GATTTAAACA
*
17291446 TTCATATTTATATTATTAAAATT
1 TTCATATTTATAATATTAAAATT
17291469 TTCATATTTTATAATA-TAAAA
1 TTCATA-TTTATAATATTAAAA
17291490 CATTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTCATATTTATAATATTAAAATT
Found at i:17291608 original size:17 final size:17
Alignment explanation
Indices: 17291588--17291628 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17291578 ATTTAAAATT
*
17291588 TAAAATTATTATTAATG
1 TAAAATTATTATTAATA
* *
17291605 TAAATTTATTATTTATA
1 TAAAATTATTATTAATA
17291622 TAAAATT
1 TAAAATT
17291629 TTAATATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAAATTATTATTAATA
Found at i:17291629 original size:18 final size:18
Alignment explanation
Indices: 17291588--17291642 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
17291578 ATTTAAAATT
*
17291588 TAAAA-TTATTATTAATG
1 TAAAATTTATTATTAATA
*
17291605 T-AAATTTATTATTTATA
1 TAAAATTTATTATTAATA
*
17291622 TAAAATTTTAATATTAA-A
1 TAAAA-TTTATTATTAATA
17291640 TAA
1 TAA
17291643 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 7 0.23
19 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAAATTTATTATTAATA
Found at i:17292229 original size:65 final size:65
Alignment explanation
Indices: 17292144--17292270 Score: 209
Period size: 65 Copynumber: 2.0 Consensus size: 65
17292134 TATCGATGTT
*
17292144 TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTGATAAATTATATATACA
1 TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTAATAAATTATATATACA
* * * *
17292209 TTTAAATATTTTTTACATATATATTTATAGTCTTATTTTTAGTTTCTTAATAAATTATATAT
1 TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTAATAAATTATATAT
17292271 TATTTTGGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.55
Consensus pattern (65 bp):
TTTAAATATTTTTCACATATATATTTATAATCTAATTTTTAATTTCTTAATAAATTATATATACA
Found at i:17298036 original size:22 final size:22
Alignment explanation
Indices: 17298011--17298054 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17298001 TAGTCATATA
17298011 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* *
17298033 ATAAATTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
17298055 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:17298084 original size:72 final size:75
Alignment explanation
Indices: 17298008--17298169 Score: 172
Period size: 72 Copynumber: 2.2 Consensus size: 75
17297998 ATTTAGTCAT
* * * * *
17298008 ATAATAAATTATT-AATATAATAAATATAAATTATTATT-TTAATAAATTATTTAATAT-TTCAA
1 ATAATAAATT-TTAAAAATAATAAATATAAATAATT-TTATTAACAAATTATTGAAAATATTCAA
17298070 -TTT-TATTTTA
64 TTTTATATTTTA
* * * *
17298080 ATAATAAATTTTAAAAATAATAATTTTAAATAATTTTATTCACATATTATTGAAAATATTCAATT
1 ATAATAAATTTTAAAAATAATAAATATAAATAATTTTATTAACAAATTATTGAAAATATTCAATT
17298145 TTAATATTTTA
66 TT-ATATTTTA
17298156 ATAATAAATATTTA
1 ATAATAAAT-TTTA
17298170 TTACAATTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
71 4 0.05
72 42 0.57
73 5 0.07
74 3 0.04
76 16 0.22
77 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (75 bp):
ATAATAAATTTTAAAAATAATAAATATAAATAATTTTATTAACAAATTATTGAAAATATTCAATT
TTATATTTTA
Found at i:17298106 original size:15 final size:16
Alignment explanation
Indices: 17298079--17298109 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17298069 ATTTTATTTT
17298079 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
17298095 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
17298110 TAATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:17298167 original size:15 final size:15
Alignment explanation
Indices: 17298147--17298203 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
17298137 ATTCAATTTT
17298147 AATATTTTAATAATA
1 AATATTTTAATAATA
*
17298162 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
17298181 AATATATTAATAATA
1 AATATTTTAATAATA
*
17298196 AATGTTTT
1 AATATTTT
17298204 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:17305253 original size:24 final size:24
Alignment explanation
Indices: 17305226--17305284 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 24
17305216 AGAAGATGCT
*
17305226 CCAAAAGCAGGAGTGCTTGAACCC
1 CCAAAAGCAGGAGTACTTGAACCC
* *
17305250 CCAAAAGCA-GA--ACTTGAAGCT
1 CCAAAAGCAGGAGTACTTGAACCC
17305271 CCAAAAGCAGGAGT
1 CCAAAAGCAGGAGT
17305285 TGTGGAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 16 0.55
22 2 0.07
23 2 0.07
24 9 0.31
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.12
Consensus pattern (24 bp):
CCAAAAGCAGGAGTACTTGAACCC
Found at i:17305432 original size:24 final size:24
Alignment explanation
Indices: 17305405--17305554 Score: 176
Period size: 24 Copynumber: 6.2 Consensus size: 24
17305395 TTCCAGTTGA
* *
17305405 ACCAAATGCAGGGGTGCTCGTGGC
1 ACCAAACGCAGGGGTGCTTGTGGC
*
17305429 ACCAAACGCGGGGGTGCTTGTGGC
1 ACCAAACGCAGGGGTGCTTGTGGC
* * *
17305453 ACCAAAAGCAGGGGTACTTGAGGC
1 ACCAAACGCAGGGGTGCTTGTGGC
17305477 ACCAAACGCAGGGGTGCTTGTGGC
1 ACCAAACGCAGGGGTGCTTGTGGC
* * *
17305501 ACCGAAAC-CTGGAGTGCTTGAGGC
1 ACC-AAACGCAGGGGTGCTTGTGGC
* * *
17305525 GCCAAACGCAAGGGTGCTTGTCGC
1 ACCAAACGCAGGGGTGCTTGTGGC
17305549 ACCAAA
1 ACCAAA
17305555 AGCCGGGCTA
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.04
24 96 0.92
25 4 0.04
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (24 bp):
ACCAAACGCAGGGGTGCTTGTGGC
Found at i:17305578 original size:48 final size:47
Alignment explanation
Indices: 17305426--17305584 Score: 176
Period size: 48 Copynumber: 3.3 Consensus size: 47
17305416 GGGTGCTCGT
* *
17305426 GGCACCAAACGCGGGGGTGCTTGTGGCACCAAAAGCAGGGGTACTTGA
1 GGCACCAAACGCAGGGGTGCTTGTGGCACCAAAAGC-CGGGTACTTGA
* *
17305474 GGCACCAAACGCAGGGGTGCTTGTGGCACCGAAA-CCTGGAGTGCTTGA
1 GGCACCAAACGCAGGGGTGCTTGTGGCACCAAAAGCC-GG-GTACTTGA
* * * * *
17305522 GGCGCCAAACGCAAGGGTGCTTGTCGCACCAAAAGCCGGGCTACTAGT
1 GGCACCAAACGCAGGGGTGCTTGTGGCACCAAAAGCCGGG-TACTTGA
* *
17305570 GGAACCAAAGGCAGG
1 GGCACCAAACGCAGG
17305585 ACTAGAACCA
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.04
48 86 0.93
49 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.35, T:0.14
Consensus pattern (47 bp):
GGCACCAAACGCAGGGGTGCTTGTGGCACCAAAAGCCGGGTACTTGA
Found at i:17309036 original size:15 final size:16
Alignment explanation
Indices: 17309016--17309052 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
17309006 ACAAAATCAA
17309016 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
17309031 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
17309047 ATAAAA
1 ATAAAA
17309053 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:17309659 original size:19 final size:19
Alignment explanation
Indices: 17309628--17309800 Score: 120
Period size: 19 Copynumber: 8.6 Consensus size: 19
17309618 AAAATTAATT
17309628 ATAAAATAATTACAATATTC
1 ATAAAA-AATTACAATATTC
17309648 ATAAAAAATTACAATATTC
1 ATAAAAAATTACAATATTC
*
17309667 ATACAAAAAATTACACTATTC
1 AT--AAAAAATTACAATATTC
* * *
17309688 ATACAAAA-TACTA-ATCC
1 ATAAAAAATTACAATATTC
*
17309705 A-AAACTATAAATACAAAATTAGTT-
1 ATAAA--A-AATTAC--AA-TA-TTC
17309729 ATAAAATAATTACAATATTC
1 ATAAAA-AATTACAATATTC
* *
17309749 ATACAAAATTATAATATTC
1 ATAAAAAATTACAATATTC
*
17309768 ATACAAAAAGTTACAATATAC
1 ATA-AAAAA-TTACAATATTC
*
17309789 ATACAAAATTAC
1 ATAAAAAATTAC
17309801 CCATTGGCGC
Statistics
Matches: 123, Mismatches: 15, Indels: 31
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.02
17 4 0.03
18 4 0.03
19 43 0.35
20 24 0.20
21 32 0.26
22 1 0.01
23 7 0.06
24 2 0.02
25 4 0.03
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.30
Consensus pattern (19 bp):
ATAAAAAATTACAATATTC
Found at i:17309674 original size:21 final size:21
Alignment explanation
Indices: 17309630--17309796 Score: 120
Period size: 21 Copynumber: 8.2 Consensus size: 21
17309620 AATTAATTAT
17309630 AAAATAATTACAATATTCAT--
1 AAAA-AATTACAATATTCATAC
17309650 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
17309671 AAAAAATTACACTATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
17309692 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * *
17309710 TATAAA-TACAAAATT-AGTTAT
1 AAAAAATTACAATATTCA--TAC
17309731 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
*
17309753 --AAAATTATAATATTCATAC
1 AAAAAATTACAATATTCATAC
* *
17309772 AAAAAGTTACAATATACATAC
1 AAAAAATTACAATATTCATAC
17309793 AAAA
1 AAAA
17309797 TTACCCATTG
Statistics
Matches: 116, Mismatches: 18, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
17 3 0.03
18 6 0.05
19 36 0.31
20 13 0.11
21 45 0.39
22 4 0.03
23 8 0.07
24 1 0.01
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.29
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:17309731 original size:101 final size:101
Alignment explanation
Indices: 17309572--17309797 Score: 389
Period size: 101 Copynumber: 2.2 Consensus size: 101
17309562 ACAAAATTAC
17309572 AAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAA
1 AAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAA
17309637 TTACAATATTCATAAAAAATTACAATATTCATACAA
66 TTACAATATTCATAAAAAATTACAATATTCATACAA
* * *
17309673 AAAATTACACTATTCATACAAAATACTAATCCAAAACTATAAATACAAAATTAGTTATAAAATAA
1 AAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAA
* *
17309738 TTACAATATTCATACAAAATTATAATATTCATACAA
66 TTACAATATTCATAAAAAATTACAATATTCATACAA
* *
17309774 AAAGTTACAATATACATACAAAAT
1 AAAATTACAATATTCATACAAAAT
17309798 TACCCATTGG
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 117 1.00
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.30
Consensus pattern (101 bp):
AAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAAATTAATTATAAAATAA
TTACAATATTCATAAAAAATTACAATATTCATACAA
Found at i:17311758 original size:123 final size:123
Alignment explanation
Indices: 17311432--17311805 Score: 518
Period size: 126 Copynumber: 3.0 Consensus size: 123
17311422 AGGTTTTTAA
** *
17311432 GTCATGGAAGAAATAATTTCGAGTTGACGTTTCTGATA-AAATAGTATAAAATCGCTTCTAGCAG
1 GTCATGGAAGAAATAATTT--TTTTGACGTTTCTGA-ACAAATAATATAAAATCGCTTCTAGCAG
* * *
17311496 GATTCTATTTGAGAAGAATTTGTGAAATCGCGCCCTTGTGGACGCGCTTTTGCTATAGTAG
63 GATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
* *
17311557 GTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAACAAATAATATAAAATCACTTCTAGCAG
1 GTCATGGAAGAAAT-A--ATTTTTTTGACGTTTCTGAACAAATAATATAAAATCGCTTCTAGCAG
* * *
17311622 GATGCTATTTGAGAAGAATTTGTGAAATCGCGGCCTCGT-CAGCGTGCTTTTGCTACAGTAG
63 GATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAG
* * *
17311683 GTCATGTAAGAAATAATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCGTTTCTAGCAGGAT
1 GTCATGGAAGAAATAATTTTTTTGACGTTTCTGAACAAATAATATAAAATCGCTTCTAGCAGGAT
* * *
17311748 GCTATTTGAGAAGAATTTGTTAAATCGTGCCCTCGTGGACACGCTTTTGCTACAGTAG
66 GCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
17311806 CATGTTTGGG
Statistics
Matches: 221, Mismatches: 22, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
123 97 0.44
124 1 0.00
125 16 0.07
126 103 0.47
128 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (123 bp):
GTCATGGAAGAAATAATTTTTTTGACGTTTCTGAACAAATAATATAAAATCGCTTCTAGCAGGAT
GCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
Found at i:17314958 original size:23 final size:23
Alignment explanation
Indices: 17314931--17315411 Score: 408
Period size: 23 Copynumber: 19.6 Consensus size: 23
17314921 TTAGGGTTAG
17314931 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17314954 GGTTAGGGTTTTTAATTAATTTAGGTTAA
1 GGTTAGGGTTTTTAATTAA---A--TT-A
**
17314983 GGTTAGGGTTTTTAAGTT-AA-GG
1 GGTTAGGGTTTTTAA-TTAAATTA
17315005 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
* *
17315028 GGTTAAGGTTAGGGTTT--TTAAGTTAA
1 GGTTAGGGTT----TTTAATTAAATT-A
17315054 GGGTTTAGGGTTTTTAAGTT-AATTA
1 -GG-TTAGGGTTTTTAA-TTAAATTA
17315079 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
17315102 GGTTAGGGTTTTCAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17315125 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
17315148 GGTTAGGGTTTTCAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17315171 GGTTAGGGTTTTTAATTAAATTAGATTA
1 GGTTAGGGTTTTTAATT--A--A-ATTA
17315199 GAGTTAGGGTTTTTAATTAAATTA
1 G-GTTAGGGTTTTTAATTAAATTA
17315223 GGTTAGGGTTAGGGTTT--TT-AATTAA
1 GGTTAGGGTT----TTTAATTAAATT-A
17315248 GGGGTTAGGGTTTTTAATTAAATTA
1 --GGTTAGGGTTTTTAATTAAATTA
*
17315273 GGTTAGGGCTAGGGTTTTTAATT-AA--G
1 GG-T-----TAGGGTTTTTAATTAAATTA
17315299 GGTTTAGGGTTTTTAATTAAATTAAGTTA
1 GG-TTAGGGTTTTTAATT--A--AA-TTA
17315328 GGGTTAGGGTTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
*
17315352 GGTTAGGGTTTTTAATTAATTTA
1 GGTTAGGGTTTTTAATTAAATTA
****
17315375 GGTTAGGGTTTAGGGTTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
17315398 GGTTAGGGTTTTTA
1 GGTTAGGGTTTTTA
17315412 TTACATCAAA
Statistics
Matches: 384, Mismatches: 23, Indels: 102
0.75 0.05 0.20
Matches are distributed among these distances:
21 16 0.04
22 19 0.05
23 193 0.50
24 18 0.05
25 17 0.04
26 16 0.04
27 23 0.06
28 16 0.04
29 62 0.16
30 4 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:17315023 original size:21 final size:22
Alignment explanation
Indices: 17314983--17315023 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17314973 TTTAGGTTAA
17314983 GGTTAGGGTTTTTAAGTTAAGG
1 GGTTAGGGTTTTTAAGTTAAGG
17315005 GGTTAGGGTTTTTAA-TTAA
1 GGTTAGGGTTTTTAAGTTAA
17315024 ATTAGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (22 bp):
GGTTAGGGTTTTTAAGTTAAGG
Found at i:17315254 original size:21 final size:21
Alignment explanation
Indices: 17315228--17315318 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 21
17315218 AATTAGGTTA
17315228 GGGTTAGGGTTTTTAATTAAG
1 GGGTTAGGGTTTTTAATTAAG
*
17315249 GGGTTAGGGTTTTTAATTAAATT
1 GGGTTAGGGTTTTTAATT-AA-G
*
17315272 AGGTTAGGGCTAGGGTTTTTAATTAAG
1 GGGTT------AGGGTTTTTAATTAAG
*
17315299 GGTTTAGGGTTTTTAATTAA
1 GGGTTAGGGTTTTTAATTAA
17315319 ATTAAGTTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
21 33 0.58
22 2 0.04
23 4 0.07
27 3 0.05
28 2 0.04
29 13 0.23
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (21 bp):
GGGTTAGGGTTTTTAATTAAG
Found at i:17315435 original size:25 final size:25
Alignment explanation
Indices: 17315407--17315499 Score: 159
Period size: 25 Copynumber: 3.7 Consensus size: 25
17315397 AGGTTAGGGT
17315407 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
17315432 TTTTATTACATCAAATAAACTCCTA
1 TTTTATTACATCAAATAAACTTCTA
*
17315457 TTTTATTAGATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
17315482 TTTTAGTACATCAAATAA
1 TTTTATTACATCAAATAA
17315500 TATCAAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.42
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:17315536 original size:44 final size:45
Alignment explanation
Indices: 17315467--17315553 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 45
17315457 TTTTATTAGA
*
17315467 TCAAATAAACTTCTATTTTAGTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTAGTACATAAAATAATATCAAAATAAC
* **
17315512 TCAAA-AAATTTCTATTTTTTTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTAGTACATAAAATAATATCAAAATA
17315554 TTTGTACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
44 33 0.87
45 5 0.13
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.37
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTAGTACATAAAATAATATCAAAATAAC
Found at i:17316660 original size:7 final size:7
Alignment explanation
Indices: 17316650--17316674 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17316640 TTATATACAT
17316650 AATACTA
1 AATACTA
17316657 AATACTA
1 AATACTA
17316664 AATACTA
1 AATACTA
17316671 AATA
1 AATA
17316675 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:17317877 original size:22 final size:22
Alignment explanation
Indices: 17317852--17317907 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
17317842 AAATATGGAT
17317852 TTGAGAGAATTTTGGAAAGAAA
1 TTGAGAGAATTTTGGAAAGAAA
*
17317874 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAAGAAA
17317896 TTGAGAGGAATT
1 TTGAGA-GAATT
17317908 GAGAGGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 27 0.84
23 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAAGAAA
Found at i:17317924 original size:12 final size:11
Alignment explanation
Indices: 17317890--17317924 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
17317880 GAATTTTGGA
17317890 AGGAAATTGAG
1 AGGAAATTGAG
17317901 AGG-AATTGAG
1 AGGAAATTGAG
17317911 AGGAAATATGAG
1 AGGAAAT-TGAG
17317923 AG
1 AG
17317925 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:17321027 original size:16 final size:16
Alignment explanation
Indices: 17321006--17321039 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
17320996 ACAGTTCCAT
*
17321006 CATTAGTGTTATATTA
1 CATTAGTGTCATATTA
17321022 CATTAGTGTCATATTA
1 CATTAGTGTCATATTA
17321038 CA
1 CA
17321040 CTTACTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (16 bp):
CATTAGTGTCATATTA
Found at i:17324386 original size:102 final size:102
Alignment explanation
Indices: 17324210--17324405 Score: 293
Period size: 102 Copynumber: 1.9 Consensus size: 102
17324200 TTGAAAGAAC
* * * * *
17324210 GAGTTTATGTTTTTAAGCTATTTTGAACCCTGAAAATGAAAATAATCCATTCAACCATAGTGAAT
1 GAGTTTATGTTTTTAAGCTATTTTGAACCCCGAAAATAAAAATAAACCATTCAACCACAGTGAAC
17324275 ATGTTGAGTTGTGAAATACTAAATATTTTTTGGAAAT
66 ATGTTGAGTTGTGAAATACTAAATATTTTTTGGAAAT
* * ***
17324312 GAGTTTATGTTTTTAAGTTGTTTTGAACCCCGAAAATAAAAATAAACCATTCGGTCACAGTGAAC
1 GAGTTTATGTTTTTAAGCTATTTTGAACCCCGAAAATAAAAATAAACCATTCAACCACAGTGAAC
*
17324377 ATGTTGAGTTGTGAAATATTAAATATTTT
66 ATGTTGAGTTGTGAAATACTAAATATTTT
17324406 CTGAAAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 83 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (102 bp):
GAGTTTATGTTTTTAAGCTATTTTGAACCCCGAAAATAAAAATAAACCATTCAACCACAGTGAAC
ATGTTGAGTTGTGAAATACTAAATATTTTTTGGAAAT
Found at i:17325715 original size:26 final size:22
Alignment explanation
Indices: 17325653--17325705 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
17325643 TTATTGGTTA
*
17325653 TTAGTACGTTAAACATGAGAGC
1 TTAGTACGTGAAACATGAGAGC
17325675 TTAGTACGTGAAACATGAGAGC
1 TTAGTACGTGAAACATGAGAGC
17325697 TTAGTACGT
1 TTAGTACGT
17325706 ACTATCAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (22 bp):
TTAGTACGTGAAACATGAGAGC
Found at i:17330667 original size:46 final size:43
Alignment explanation
Indices: 17330594--17330697 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 43
17330584 TACTATGTGA
*
17330594 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
17330637 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
17330683 ACCGTGTATCTATTA
1 ACCG-GTATC-ATTA
17330698 TTATTCCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
43 5 0.10
44 11 0.22
45 2 0.04
46 27 0.53
47 6 0.12
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:17330837 original size:16 final size:16
Alignment explanation
Indices: 17330816--17330847 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17330806 TGATTGAAAG
*
17330816 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
17330832 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
17330848 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:17343565 original size:13 final size:13
Alignment explanation
Indices: 17343547--17343571 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17343537 TTGAATAAAA
17343547 GGTAAAAGTTTAG
1 GGTAAAAGTTTAG
17343560 GGTAAAAGTTTA
1 GGTAAAAGTTTA
17343572 AAATATCATT
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:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (13 bp):
GGTAAAAGTTTAG
Found at i:17344167 original size:54 final size:51
Alignment explanation
Indices: 17344093--17344202 Score: 132
Period size: 54 Copynumber: 2.1 Consensus size: 51
17344083 ATACGAAACG
* *
17344093 GTTATATGAAATGGTTATATAAAGTAG-ATGTACAAAATGATCATATGAATCA
1 GTTATATGAAATAGTTATATAAAGT-GTATATACAAAATGATCATATGAAT-A
* * *
17344145 GTTATATGGAAAATAGTTATATAAAGTGTTTATACAAAATGTTGATATGAATA
1 GTTATAT-G-AAATAGTTATATAAAGTGTATATACAAAATGATCATATGAATA
17344198 GTTAT
1 GTTAT
17344203 GAAAAAAGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
52 7 0.14
53 8 0.16
54 35 0.70
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (51 bp):
GTTATATGAAATAGTTATATAAAGTGTATATACAAAATGATCATATGAATA
Found at i:17344231 original size:13 final size:13
Alignment explanation
Indices: 17344213--17344237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17344203 GAAAAAAGGG
17344213 ACATTTGAAATGA
1 ACATTTGAAATGA
17344226 ACATTTGAAATG
1 ACATTTGAAATG
17344238 CTAAATGAAA
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
ACATTTGAAATGA
Found at i:17361618 original size:27 final size:28
Alignment explanation
Indices: 17361563--17361627 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 28
17361553 ATAAAAAATA
* *
17361563 ACCAGAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
17361591 ACCAAAATATTATAA-ATTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
17361618 ACCAAAATAT
1 ACCAAAATAT
17361628 ACCAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACATTTTTTTATTT
Found at i:17361654 original size:15 final size:15
Alignment explanation
Indices: 17361635--17361664 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
17361625 TATACCAAAA
17361635 AAAAACAAAAACCTGC
1 AAAAA-AAAAACCTGC
17361651 AAAAAAAAAACCTG
1 AAAAAAAAAACCTG
17361665 TGGCGGCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAACCTGC
Found at i:17361695 original size:27 final size:26
Alignment explanation
Indices: 17361665--17361718 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
17361655 AAAAAACCTG
17361665 TGGCGGCACCAAAGGTGCCAAAGAGAT
1 TGGCGGCACCAAAGGTGCCAAAG-GAT
*
17361692 TGGCGGCACCAATGGTGCCAAAGGAT
1 TGGCGGCACCAAAGGTGCCAAAGGAT
17361718 T
1 T
17361719 AAAATGTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.30, C:0.22, G:0.33, T:0.15
Consensus pattern (26 bp):
TGGCGGCACCAAAGGTGCCAAAGGAT
Found at i:17362645 original size:27 final size:26
Alignment explanation
Indices: 17362608--17362661 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 26
17362598 GTTACATTTT
17362608 AATCCTTTGGCACCATTGGTGCCGCC
1 AATCCTTTGGCACCATTGGTGCCGCC
*
17362634 AATCTCTTTGGCACCTTTGGTGCCGCC
1 AATC-CTTTGGCACCATTGGTGCCGCC
17362661 A
1 A
17362662 CAGATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.15, C:0.33, G:0.22, T:0.30
Consensus pattern (26 bp):
AATCCTTTGGCACCATTGGTGCCGCC
Found at i:17363101 original size:21 final size:22
Alignment explanation
Indices: 17363067--17363107 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
17363057 TCAAATTGTG
17363067 CATTAAAACCTATTAATTTTTA
1 CATTAAAACCTATTAATTTTTA
*
17363089 CATTAAAA-TTATTAATTTT
1 CATTAAAACCTATTAATTTT
17363108 ACTTGACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (22 bp):
CATTAAAACCTATTAATTTTTA
Found at i:17376294 original size:27 final size:29
Alignment explanation
Indices: 17376231--17376298 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 29
17376221 AAAATCCTTC
** *
17376231 AAACCCTAAACATTAATTTATTTTTTTAA
1 AAACCCTAAACCCTAATTTATTTTCTTAA
17376260 AAACCCTAAACCCT-ATTTA-TTTCTTAA
1 AAACCCTAAACCCTAATTTATTTTCTTAA
17376287 AAACCCTAAACC
1 AAACCCTAAACC
17376299 AGCGTCGCCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 19 0.53
28 5 0.14
29 12 0.33
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (29 bp):
AAACCCTAAACCCTAATTTATTTTCTTAA
Found at i:17376625 original size:14 final size:15
Alignment explanation
Indices: 17376600--17376628 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17376590 AACTGTCATC
17376600 TATTTACATTTATCT
1 TATTTACATTTATCT
17376615 TATTTAC-TTTATCT
1 TATTTACATTTATCT
17376629 AGCTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTACATTTATCT
Found at i:17377202 original size:123 final size:116
Alignment explanation
Indices: 17376906--17377324 Score: 476
Period size: 114 Copynumber: 3.6 Consensus size: 116
17376896 GTTTATTTGT
* * * * * *
17376906 AAGCGCCGCAAAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAATTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAATGCACCGTTTGGTCTTGAGGTAGATTAGAGTTAGTGGC
* * * * *
17376971 GTTTACGG-GAA-A-ACGCCGCTAAAGAACAGTATTAGCGGCGTTTTACAAA
66 GCTT-GGGAGAACATACGCCGCTAAAGCACAGTATTAGCGGCATTTTACAAG
*
17377020 AAGCGCCGCAAAAGATCTTAACCAAAATGCACCGTTTGGTCTTGAGGTAGATTAGAGTTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAATGCACCGTTTGGTCTTGAGGTAGATTAGAGTTAGTGGC
17377085 GCTTGGGAGAACACGCCGCTTACGCCGCTAAAGCACAGTATTAGCGGCATTTTACAAG
66 GCTTGGGAGAACA-------TACGCCGCTAAAGCACAGTATTAGCGGCATTTTACAAG
*
17377143 AAGCGCCGCAAAATATCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAGAGTTAGTGGC
1 AAGCGCCGCAAAATATCTTAACCAAAATGCACCGTTTGGTCTTGAGGTAGATTAGAGTTAGTGGC
* * ** * *
17377208 GTTTGGGAGAACAT--GCTGCTAAAGCACAGTATTAGCGGCGCCTGT-C-TG
66 GCTTGGGAGAACATACGCCGCTAAAGCACAGTATTAGCGGC-ATTTTACAAG
* * * *
17377256 AACGCGCTGCAAAATATCTT-ACCTAAAATGCAGCGTTTAGTCTTGAGGTAGATTAGAATTAGTG
1 AA-GCGCCGCAAAATATCTTAACC-AAAATGCACCGTTTGGTCTTGAGGTAGATTAGAGTTAGTG
17377320 GCGCT
64 GCGCT
17377325 AGGAAAAACG
Statistics
Matches: 266, Mismatches: 26, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
113 8 0.03
114 145 0.55
115 3 0.01
116 1 0.00
123 109 0.41
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (116 bp):
AAGCGCCGCAAAATATCTTAACCAAAATGCACCGTTTGGTCTTGAGGTAGATTAGAGTTAGTGGC
GCTTGGGAGAACATACGCCGCTAAAGCACAGTATTAGCGGCATTTTACAAG
Found at i:17378123 original size:13 final size:14
Alignment explanation
Indices: 17378088--17378124 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
17378078 ATAAGGTAAT
17378088 TTAGGGGTTAGTAG
1 TTAGGGGTTAGTAG
*
17378102 TTAGGGGTTAGTGG
1 TTAGGGGTTAGTAG
17378116 TT-GGGGTTA
1 TTAGGGGTTA
17378125 AAGGTTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.16, C:0.00, G:0.46, T:0.38
Consensus pattern (14 bp):
TTAGGGGTTAGTAG
Found at i:17380128 original size:28 final size:29
Alignment explanation
Indices: 17380070--17380129 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
17380060 TACCAATTTA
*
17380070 TTTTGTTTAGGGTATTAAGCAGTAAATAT
1 TTTTGTTTAGGGTATTAAGCAGTAAACAT
17380099 TTTTGTTTAGGGTATTAAGCAGT-AACAT
1 TTTTGTTTAGGGTATTAAGCAGTAAACAT
17380127 TTT
1 TTT
17380130 GACAAGTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (29 bp):
TTTTGTTTAGGGTATTAAGCAGTAAACAT
Found at i:17381678 original size:15 final size:16
Alignment explanation
Indices: 17381641--17381684 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
17381631 TATAAATATT
*
17381641 TATATACATTTTTAATA
1 TATATA-ATTTTTAAAA
17381658 TATAT-ATTTTTAAAA
1 TATATAATTTTTAAAA
*
17381673 TCTATAATTTTT
1 TATATAATTTTT
17381685 TCAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 6 0.25
17 5 0.21
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATTTTTAAAA
Found at i:17381827 original size:12 final size:12
Alignment explanation
Indices: 17381812--17381836 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17381802 TATATAGAAT
17381812 CTTATATAATAA
1 CTTATATAATAA
17381824 CTTATATAATAA
1 CTTATATAATAA
17381836 C
1 C
17381837 ATAATACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (12 bp):
CTTATATAATAA
Found at i:17381862 original size:9 final size:9
Alignment explanation
Indices: 17381850--17382000 Score: 107
Period size: 9 Copynumber: 16.8 Consensus size: 9
17381840 ATACATGGCC
17381850 TACATAACT
1 TACATAACT
17381859 TACATAACT
1 TACATAACT
* *
17381868 TACATTATT
1 TACATAACT
*
17381877 TAGATAA--
1 TACATAACT
* *
17381884 TACATAGCC
1 TACATAACT
17381893 TACATAACTT
1 TACATAAC-T
*
17381903 ATATATAAACT
1 -TACAT-AACT
*
17381914 TACATAAAT
1 TACATAACT
*
17381923 TAAATAACT
1 TACATAACT
17381932 TACATAACT
1 TACATAACT
*
17381941 CACATAA--
1 TACATAACT
*
17381948 TACACAACT
1 TACATAACT
17381957 TACATAACT
1 TACATAACT
17381966 TACATAA--
1 TACATAACT
*
17381973 TACAGAACTT
1 TACATAAC-T
17381983 AGTACATAACT
1 --TACATAACT
17381994 TACATAA
1 TACATAA
17382001 TACATAAAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
7 16 0.15
9 74 0.67
10 4 0.04
11 6 0.05
12 10 0.09
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:17388313 original size:28 final size:28
Alignment explanation
Indices: 17388257--17388319 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
17388247 TTAATTCCAG
* *
17388257 GGTT-AGGGTTTAGGGTTTGTTGTTCAA
1 GGTTAAGGGTTAAGGGTTTGTGGTTCAA
*
17388284 GGTTAAGGGTTAAGGG-TTGATGGTTTAA
1 GGTTAAGGGTTAAGGGTTTG-TGGTTCAA
*
17388312 GGGTAAGG
1 GGTTAAGG
17388320 ATATGATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.21, C:0.02, G:0.41, T:0.37
Consensus pattern (28 bp):
GGTTAAGGGTTAAGGGTTTGTGGTTCAA
Found at i:17397384 original size:19 final size:19
Alignment explanation
Indices: 17397334--17397389 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
17397324 AACTAATGTA
*
17397334 AATTATGTTTATATTTTAATT
1 AATTATGTTTA-A-TTAAATT
* *
17397355 -ATTAAGGTTAATTAAATT
1 AATTATGTTTAATTAAATT
17397373 AATTATGTTTAATTAAA
1 AATTATGTTTAATTAAA
17397390 GGTTAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 6 0.21
19 15 0.52
20 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
AATTATGTTTAATTAAATT
Found at i:17402550 original size:41 final size:41
Alignment explanation
Indices: 17402406--17402565 Score: 114
Period size: 41 Copynumber: 3.9 Consensus size: 41
17402396 TCAATATTAG
* * * *
17402406 CGCCGCTAATGCTGAGACCTTTAACGGCGTTTTTGACTATA
1 CGCCGCTAATGCTGGGACTTTTATCGGCGTTTTTGAGTATA
* * *
17402447 CGCCGCTAATGATAGGG--TTTTTTGCGGCATTTTT-A-TAATA
1 CGCCGCTAATGCT-GGGACTTTTAT-CGGCGTTTTTGAGT-ATA
* * **
17402487 GCGCCGCAAATTCTATGACTTTTATCGGCGTTTTTGAGTATA
1 -CGCCGCTAATGCTGGGACTTTTATCGGCGTTTTTGAGTATA
* * *
17402529 CGCCGCTAATGGTGGGTCTTTTAGT-GGCGTTTGTGAG
1 CGCCGCTAATGCTGGGACTTTTA-TCGGCGTTTTTGAG
17402566 AAACCGCCAG
Statistics
Matches: 90, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
39 1 0.01
40 8 0.09
41 68 0.76
42 12 0.13
43 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (41 bp):
CGCCGCTAATGCTGGGACTTTTATCGGCGTTTTTGAGTATA
Found at i:17402657 original size:124 final size:123
Alignment explanation
Indices: 17402485--17402850 Score: 350
Period size: 124 Copynumber: 3.0 Consensus size: 123
17402475 ATTTTTATAA
* *
17402485 TAGCGCCGCAAA--TTCTATGACTTTTATCGGCGTTTTTGA-GTATACGCCGCTAATGGTGG-GT
1 TAGCGCCGCAAATGTTCT-T-ACTTTTACCGGCGTTTTT-ATGTATGCGCCGCTAATGGTGGAG-
* *
17402546 CTTTTAGTGGCGTTTGTGAG-AAACCGCCAGTAATGTTACA-ATATTTATCGGCGTTTTCTAGT-
62 CTTTTAGTGGCGTTTGTG-GTAAACCGCCACTAATGTTA-AGATATTTAGCGGCG-TTTCTA-TC
*
17402608 G
123 C
* * *
17402609 TAGCGCCGCAAATGTTCTTACCTTTACCGGCGTTTTTATGTTTGCGCCGCTAATGGTGGAGGTTT
1 TAGCGCCGCAAATGTTCTTACTTTTACCGGCGTTTTTATGTATGCGCCGCTAATGGTGGAGCTTT
* * * *
17402674 TAGTGGCGTTTTTGGTCAATCGCCACTAATGTTAAGGTATTTAGCGGCGTTTCTATCC
66 TAGTGGCGTTTGTGGTAAACCGCCACTAATGTTAAGATATTTAGCGGCGTTTCTATCC
* * * * * * * * *
17402732 TAGCGCCGCTAATGTTGTGAATTTTACTGGCGTTTTTATGTATGCGCCGCTATTGGTTGGGGGTG
1 TAGCGCCGCAAATGTTCTTACTTTTACCGGCGTTTTTATGTATGCGCCGCTAATGG-TGGAGCTT
* * * * * *
17402797 GTAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTAGTGGCGTTT
65 TTAGTGGCGT-TTGTGGTAAACCGCCACTAATGTTAAGATATTTAGCGGCGTTT
17402851 GGTTTTAAAG
Statistics
Matches: 209, Mismatches: 24, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
122 1 0.00
123 57 0.27
124 103 0.49
125 44 0.21
126 4 0.02
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.37
Consensus pattern (123 bp):
TAGCGCCGCAAATGTTCTTACTTTTACCGGCGTTTTTATGTATGCGCCGCTAATGGTGGAGCTTT
TAGTGGCGTTTGTGGTAAACCGCCACTAATGTTAAGATATTTAGCGGCGTTTCTATCC
Found at i:17402682 original size:41 final size:41
Alignment explanation
Indices: 17402637--17402811 Score: 117
Period size: 41 Copynumber: 4.2 Consensus size: 41
17402627 TACCTTTACC
*
17402637 GGCGTTTTTATGTTTGCGCCGCTAATGGTGGAGGTTTTAGT
1 GGCGTTTTTATGTATGCGCCGCTAATGGTGGAGGTTTTAGT
* * ** *
17402678 GGCGTTTTT-GGTCAAT-CGCCACTAAT-GTTAAGGTATTTAGC
1 GGCGTTTTTATGT--ATGCGCCGCTAATGGTGGAGGT-TTTAGT
* * * * *
17402719 GGCGTTTCTATCCTA-GCGCCGCTAATGTTGTGA-ATTTTACT
1 GGCGTTTTTAT-GTATGCGCCGCTAATGGTG-GAGGTTTTAGT
* * **
17402760 GGCGTTTTTATGTATGCGCCGCTATTGGTTGGGGGTGGTAGT
1 GGCGTTTTTATGTATGCGCCGCTAATGG-TGGAGGTTTTAGT
17402802 GGCGTGTTTT
1 GGCGT-TTTT
17402812 GGTCAATCGC
Statistics
Matches: 97, Mismatches: 25, Indels: 22
0.67 0.17 0.15
Matches are distributed among these distances:
40 10 0.10
41 67 0.69
42 14 0.14
43 6 0.06
ACGTcount: A:0.14, C:0.15, G:0.31, T:0.39
Consensus pattern (41 bp):
GGCGTTTTTATGTATGCGCCGCTAATGGTGGAGGTTTTAGT
Found at i:17402889 original size:125 final size:122
Alignment explanation
Indices: 17402631--17402891 Score: 333
Period size: 125 Copynumber: 2.1 Consensus size: 122
17402621 TGTTCTTACC
* **
17402631 TTTACCGGCGTTTTTATGTTTGCGCCGCTAATGGTGGAGGTTTTAGTGGCGTTTTTGGTCAATCG
1 TTTA-CGGCGTTTTTATGTATGCGCCGCTAATGGTGGAGGTGGTAGTGGCGTTTTTGGTCAATCG
** * *
17402696 CCACTAATGTTAAGGTATTTAGCGGCGTTTCTATCCTAGCGCCGCTAATGTTGTGAAT
65 CCACTAATGTTAAGGTATTTAGCGGCGTTTCTATCAAAGCGCCGCTAAGGTTGGGAAT
* *
17402754 TTTACTGGCGTTTTTATGTATGCGCCGCTATTGGTTGGGGGTGGTAGTGGCGTGTTTTGGTCAAT
1 TTTAC-GGCGTTTTTATGTATGCGCCGCTAATGG-TGGAGGTGGTAGTGGCGT-TTTTGGTCAAT
* * * * **
17402819 CGCCACTAATGTTAAGGTATTTAGTGGCGTTTGGTTTTAAAGCGCCGCTAAGGTTGGGTTT
63 CGCCACTAATGTTAAGGTATTTAGCGGCGTTT-CTATCAAAGCGCCGCTAAGGTTGGGAAT
*
17402880 TTTGCGGCGTTT
1 TTTACGGCGTTT
17402892 ATTGGTAAGC
Statistics
Matches: 118, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
122 1 0.01
123 30 0.25
124 15 0.13
125 49 0.42
126 23 0.19
ACGTcount: A:0.15, C:0.16, G:0.30, T:0.39
Consensus pattern (122 bp):
TTTACGGCGTTTTTATGTATGCGCCGCTAATGGTGGAGGTGGTAGTGGCGTTTTTGGTCAATCGC
CACTAATGTTAAGGTATTTAGCGGCGTTTCTATCAAAGCGCCGCTAAGGTTGGGAAT
Found at i:17403920 original size:7 final size:7
Alignment explanation
Indices: 17403908--17404068 Score: 60
Period size: 7 Copynumber: 22.7 Consensus size: 7
17403898 GGATTAAGGT
17403908 TTAGGGG
1 TTAGGGG
17403915 TTAGGGG
1 TTAGGGG
17403922 TTAGGGG
1 TTAGGGG
*
17403929 TTAGGGA
1 TTAGGGG
* *
17403936 TTTGGGA
1 TTAGGGG
* *
17403943 TTTGGGA
1 TTAGGGG
17403950 TCT-GGGG
1 T-TAGGGG
17403957 TT-GGTGG
1 TTAGG-GG
*
17403964 TTTGGGG
1 TTAGGGG
*
17403971 TTTGGGG
1 TTAGGGG
* **
17403978 TTTGTGAT
1 TTAG-GGG
17403986 TTA-GGG
1 TTAGGGG
* *
17403992 TTTGGGA
1 TTAGGGG
* *
17403999 TTAAGGT
1 TTAGGGG
17404006 TTAGGGG
1 TTAGGGG
*
17404013 TTAGGGAC
1 TTAGGG-G
17404021 TTAGGGG
1 TTAGGGG
**
17404028 TTAGGTAT
1 TTAGG-GG
17404036 TTA-GGG
1 TTAGGGG
*
17404042 TTCGGGG
1 TTAGGGG
* *
17404049 TTTGGGAT
1 TTAGGG-G
17404057 TTAGGGG
1 TTAGGGG
17404064 TTAGG
1 TTAGG
17404069 TACTCAAGTT
Statistics
Matches: 119, Mismatches: 26, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
6 8 0.07
7 91 0.76
8 20 0.17
ACGTcount: A:0.14, C:0.02, G:0.47, T:0.37
Consensus pattern (7 bp):
TTAGGGG
Found at i:17404039 original size:15 final size:15
Alignment explanation
Indices: 17403907--17404041 Score: 72
Period size: 14 Copynumber: 9.5 Consensus size: 15
17403897 GGGATTAAGG
17403907 TTTAGGGGTTAGGG-
1 TTTAGGGGTTAGGGA
*
17403921 GTTAGGGGTTAGGGA
1 TTTAGGGGTTAGGGA
* *
17403936 TTT-GGGATTTGGGA
1 TTTAGGGGTTAGGGA
* *
17403950 TCT-GGGGTT-GGTGG
1 TTTAGGGGTTAGG-GA
* *
17403964 TTT-GGGGTTTGGGG
1 TTTAGGGGTTAGGGA
**
17403978 TTT-GTGATTTAGGG-
1 TTTAG-GGGTTAGGGA
* *
17403992 TTT-GGGATTAAGG-
1 TTTAGGGGTTAGGGA
17404005 TTTAGGGGTTAGGGA
1 TTTAGGGGTTAGGGA
* *
17404020 CTTAGGGGTTAGGTA
1 TTTAGGGGTTAGGGA
17404035 TTTAGGG
1 TTTAGGG
17404042 TTCGGGGTTT
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
13 11 0.11
14 56 0.58
15 29 0.30
ACGTcount: A:0.14, C:0.01, G:0.47, T:0.38
Consensus pattern (15 bp):
TTTAGGGGTTAGGGA
Found at i:17404571 original size:16 final size:17
Alignment explanation
Indices: 17404544--17404579 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17404534 GTATACTTAG
*
17404544 TAATTAAAAGATACAAT
1 TAATTAAAAGATAAAAT
17404561 TAATT-AAAGATAAAAT
1 TAATTAAAAGATAAAAT
17404577 TAA
1 TAA
17404580 GAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
TAATTAAAAGATAAAAT
Found at i:17404780 original size:11 final size:11
Alignment explanation
Indices: 17404766--17404814 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
17404756 CACTTAGCCA
17404766 AAATTCCCCCC
1 AAATTCCCCCC
* *
17404777 AAATTATCCCCA
1 AAATT-CCCCCC
17404789 AAATTCCCCCC
1 AAATTCCCCCC
*
17404800 AAATTTTCCCCC
1 AAA-TTCCCCCC
17404812 AAA
1 AAA
17404815 AATCCCCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 12 0.39
12 19 0.61
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (11 bp):
AAATTCCCCCC
Found at i:17404787 original size:12 final size:12
Alignment explanation
Indices: 17404772--17404824 Score: 56
Period size: 11 Copynumber: 4.6 Consensus size: 12
17404762 GCCAAAATTC
17404772 CCCCCAAATTAT
1 CCCCCAAATTAT
* *
17404784 CCCCAAAATT-C
1 CCCCCAAATTAT
*
17404795 CCCCCAAATTTT
1 CCCCCAAATTAT
*
17404807 CCCCCAAA-AAT
1 CCCCCAAATTAT
17404818 CCCCCAA
1 CCCCCAA
17404825 TTCTAGAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 17 0.50
12 17 0.50
ACGTcount: A:0.34, C:0.47, G:0.00, T:0.19
Consensus pattern (12 bp):
CCCCCAAATTAT
Found at i:17404824 original size:23 final size:23
Alignment explanation
Indices: 17404763--17404822 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
17404753 CAACACTTAG
17404763 CCAAAATTCCCCCCAAATTATCC
1 CCAAAATTCCCCCCAAATTATCC
*
17404786 CCAAAATTCCCCCCAAATTTTCCC
1 CCAAAATTCCCCCCAAATTAT-CC
*
17404810 CCAAAAATCCCCC
1 CCAAAATTCCCCC
17404823 AATTCTAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (23 bp):
CCAAAATTCCCCCCAAATTATCC
Found at i:17405238 original size:12 final size:12
Alignment explanation
Indices: 17405221--17405246 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17405211 AGTTTGAAAC
17405221 TGTTCATAATTT
1 TGTTCATAATTT
17405233 TGTTCATAATTT
1 TGTTCATAATTT
17405245 TG
1 TG
17405247 ACTATCCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.58
Consensus pattern (12 bp):
TGTTCATAATTT
Found at i:17405310 original size:12 final size:12
Alignment explanation
Indices: 17405295--17405334 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
17405285 TGTAATACTG
17405295 TTTGTTCATAAT
1 TTTGTTCATAAT
17405307 TTTGTT-ACTAAT
1 TTTGTTCA-TAAT
*
17405319 TTTGTTCATAAG
1 TTTGTTCATAAT
17405331 TTTG
1 TTTG
17405335 AAACTGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (12 bp):
TTTGTTCATAAT
Found at i:17406873 original size:24 final size:24
Alignment explanation
Indices: 17406846--17406945 Score: 75
Period size: 24 Copynumber: 4.2 Consensus size: 24
17406836 TTGTACATGT
17406846 TATTTTTCTAAATATTAACATCTA
1 TATTTTTCTAAATATTAACATCTA
* *
17406870 TA-TTTTC--AATAATAA-ATTTTA
1 TATTTTTCTAAATATTAACA-TCTA
* ** * *
17406891 TAATTTTAGAAATAATTGTACATGT-
1 TATTTTTCTAAAT-ATT-AACATCTA
17406916 TATTTTTCTAAATATTAACATCTA
1 TATTTTTCTAAATATTAACATCTA
17406940 TATTTT
1 TATTTT
17406946 CAATAATTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
20 1 0.02
21 12 0.21
22 4 0.07
23 10 0.18
24 14 0.25
25 12 0.21
26 3 0.05
27 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (24 bp):
TATTTTTCTAAATATTAACATCTA
Done.