Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 112 of 135
Found at i:41146808 original size:25 final size:25
Alignment explanation
Indices: 41146754--41146808 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
41146744 AAACATTAAA
*
41146754 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
41146779 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
41146803 TATTAA
1 T-TTAA
41146809 GATAGGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:41147254 original size:9 final size:9
Alignment explanation
Indices: 41147234--41147264 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
41147224 AAAATATCAT
41147234 ATTAATTTTA
1 ATTAA-TTTA
41147244 ATTAATTTA
1 ATTAATTTA
41147253 ATTAATTTA
1 ATTAATTTA
41147262 ATT
1 ATT
41147265 TTACTTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:41148437 original size:15 final size:15
Alignment explanation
Indices: 41148413--41148444 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41148403 TATACATGCA
*
41148413 AAATATAAAAGACAT
1 AAATACAAAAGACAT
41148428 AAATACAAAAGACAT
1 AAATACAAAAGACAT
41148443 AA
1 AA
41148445 TAATGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:41150888 original size:17 final size:16
Alignment explanation
Indices: 41150857--41150892 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
41150847 GTGATTTTTT
41150857 AGAAAAAAAAAAAGAA
1 AGAAAAAAAAAAAGAA
*
41150873 AGAAAGAAAGAAAAGAA
1 AGAAA-AAAAAAAAGAA
41150890 AGA
1 AGA
41150893 TAGGATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAAGAA
Found at i:41151644 original size:31 final size:31
Alignment explanation
Indices: 41151608--41151677 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
41151598 TAAACTTAGT
* * *
41151608 AATTCAGTGACTTAAATAAAAAATTTTAAAC
1 AATTCAATGACTTAAATAAAAAATTTCAAAA
* *
41151639 AATTCAATGATTTAAATAAAAACTTTCAAAA
1 AATTCAATGACTTAAATAAAAAATTTCAAAA
41151670 AATTCAAT
1 AATTCAAT
41151678 AACTATTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (31 bp):
AATTCAATGACTTAAATAAAAAATTTCAAAA
Found at i:41152049 original size:21 final size:20
Alignment explanation
Indices: 41152025--41152082 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
41152015 TGACAAATAC
41152025 AATTATATTGATAAAATTAAT
1 AATTATATTG-TAAAATTAAT
* *
41152046 AATTAGATTGTTAAAA-TATT
1 AATTATATTG-TAAAATTAAT
*
41152066 AATCATA-TGTAAAATTA
1 AATTATATTGTAAAATTA
41152083 CTTTAGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
20 8 0.26
21 14 0.45
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
AATTATATTGTAAAATTAAT
Found at i:41160150 original size:28 final size:28
Alignment explanation
Indices: 41160118--41160243 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
41160108 TTTAATAAGT
* * *
41160118 TCGCACACTTAGTG-TTCAATAATCAAAC
1 TCGCACACTTAGTGCTT-TACAATTAAAC
* *
41160146 TCGCACACTTAGTGCTTTGCCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41160174 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
41160202 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
41160230 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41160244 TCGAAAGTCA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
28 87 0.98
29 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:41162755 original size:36 final size:37
Alignment explanation
Indices: 41162709--41162800 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
41162699 GCCTCCAGTT
* *
41162709 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
* *
41162745 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCACTTTCAAG
*
41162783 TCA-ATATTCATTTCAATT
1 TCACA-ATTCAATTCAATT
41162801 CCACACATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
36 13 0.28
37 23 0.49
38 11 0.23
ACGTcount: A:0.32, C:0.23, G:0.01, T:0.45
Consensus pattern (37 bp):
TCACAATTCAATTCAATTTCACTTTTCCACTTTCAAG
Found at i:41162801 original size:36 final size:35
Alignment explanation
Indices: 41162709--41162801 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 35
41162699 GCCTCCAGTT
* *
41162709 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAA-TTCACTTTTCCACTTTCAA
*
41162745 TCACAATTCAATTCAAAATTCACTTTTCCATTTTCAA
1 TCACAATTCAATTC--AATTCACTTTTCCACTTTCAA
*
41162782 GTCA-ATATTCATTTCAATTC
1 -TCACA-ATTCAATTCAATTC
41162802 CACACATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
36 18 0.37
37 18 0.37
38 13 0.27
ACGTcount: A:0.31, C:0.24, G:0.01, T:0.44
Consensus pattern (35 bp):
TCACAATTCAATTCAATTCACTTTTCCACTTTCAA
Found at i:41163023 original size:3 final size:3
Alignment explanation
Indices: 41163015--41163044 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41163005 TAGCTACGAA
41163015 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41163045 TTACACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41166692 original size:165 final size:166
Alignment explanation
Indices: 41166436--41166766 Score: 655
Period size: 165 Copynumber: 2.0 Consensus size: 166
41166426 CTATTGCGCT
41166436 TTATTCAAAAGAACTTCTATTTTATTAAAAATAAAAAAAATAATTTAATATAAAAATATTAAAAA
1 TTATTCAAAAGAACTTCTATTTTATTAAAAATAAAAAAAATAATTTAATATAAAAATATTAAAAA
41166501 CAACTTTCATTTTATTAAATGAAACAATATAAAAATAGTTTTTACAAATATATTAAAAAATCAAT
66 CAACTTTCATTTTATTAAATGAAACAATATAAAAATAGTTTTTACAAATATATTAAAAAATCAAT
41166566 GTATGTGCCGGTCGAAATCATTGCCACATGGGGGTG
131 GTATGTGCCGGTCGAAATCATTGCCACATGGGGGTG
41166602 TTATTCAAAA-AACTTCTATTTTATTAAAAATAAAAAAAATAATTTAATATAAAAATATTAAAAA
1 TTATTCAAAAGAACTTCTATTTTATTAAAAATAAAAAAAATAATTTAATATAAAAATATTAAAAA
41166666 CAACTTTCATTTTATTAAATGAAACAATATAAAAATAGTTTTTACAAATATATTAAAAAATCAAT
66 CAACTTTCATTTTATTAAATGAAACAATATAAAAATAGTTTTTACAAATATATTAAAAAATCAAT
41166731 GTATGTGCCGGTCGAAATCATTGCCACATGGGGGTG
131 GTATGTGCCGGTCGAAATCATTGCCACATGGGGGTG
41166767 GTCGACGATT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 155 0.94
166 10 0.06
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (166 bp):
TTATTCAAAAGAACTTCTATTTTATTAAAAATAAAAAAAATAATTTAATATAAAAATATTAAAAA
CAACTTTCATTTTATTAAATGAAACAATATAAAAATAGTTTTTACAAATATATTAAAAAATCAAT
GTATGTGCCGGTCGAAATCATTGCCACATGGGGGTG
Found at i:41169236 original size:17 final size:17
Alignment explanation
Indices: 41169211--41169257 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
41169201 ATCGTTTTTA
*
41169211 TTTTAATCATTTTAATT
1 TTTTAATCAATTTAATT
*
41169228 TTTTTATCAATTTAATT
1 TTTTAATCAATTTAATT
*
41169245 AATTTAAT-AATTT
1 -TTTTAATCAATTT
41169258 CAATAATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATCAATTTAATT
Found at i:41171421 original size:28 final size:29
Alignment explanation
Indices: 41171370--41171432 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 29
41171360 GTTCAAATAA
41171370 CAAATTGGGCACAAAAAAAGTTTA-AGTAC
1 CAAATTGGGCACAAAAAAAGTTTAGA-TAC
41171399 CAAATTGGGC-CAAAAAAAGTTTAGATAC
1 CAAATTGGGCACAAAAAAAGTTTAGATAC
41171427 CAAATT
1 CAAATT
41171433 ATAAAAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (29 bp):
CAAATTGGGCACAAAAAAAGTTTAGATAC
Found at i:41171713 original size:93 final size:93
Alignment explanation
Indices: 41171567--41171756 Score: 226
Period size: 93 Copynumber: 2.0 Consensus size: 93
41171557 CTTAAATCTC
* * * * * *
41171567 AAATAATCCAAGCTTAAAAGTGGTCAAAATCTAAAATGATTTGAACACATAATGGCTTGA-CTTG
1 AAATAATCCAAACTTAAAAGTGATCAAAATCTAAAATAATTTAAACACATAATGACTTGATC-AG
* *
41171631 AAAATCCTGAATCCT-AAACAATAAACCCA
65 AAAAACCTAAAT-CTAAAACAATAAACCCA
*
41171660 AAATAATCCAAACTTTGAAAA-TGATCAAAATCTAAAATAATTTAAAC-CGTAATGACTTGATCA
1 AAATAATCCAAAC-TT-AAAAGTGATCAAAATCTAAAATAATTTAAACACATAATGACTTGATCA
*
41171723 GAAAAACCTAAATTTAAAACAATAAACCCA
64 GAAAAACCTAAATCTAAAACAATAAACCCA
41171753 AAAT
1 AAAT
41171757 CACCCTAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
92 1 0.01
93 52 0.63
94 26 0.31
95 4 0.05
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (93 bp):
AAATAATCCAAACTTAAAAGTGATCAAAATCTAAAATAATTTAAACACATAATGACTTGATCAGA
AAAACCTAAATCTAAAACAATAAACCCA
Found at i:41173745 original size:22 final size:23
Alignment explanation
Indices: 41173713--41173767 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
41173703 TGGTATCTAT
41173713 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
41173735 AAATCATATCTTCTAAGATTAC-
1 AAATCAAATCTTCTAAGATTACA
*
41173757 ATATCAAATCT
1 AAATCAAATCT
41173768 ACGATTGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:41178858 original size:22 final size:21
Alignment explanation
Indices: 41178828--41178885 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
41178818 AAATGGTATC
41178828 TACAAATCAAATCTCTAAGAT
1 TACAAATCAAATCTCTAAGAT
*
41178849 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCAAATC-TCTAAGAT
*
41178872 TACATATCAAATCT
1 TACAAATCAAATCT
41178886 ACGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.12
22 17 0.53
23 11 0.34
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (21 bp):
TACAAATCAAATCTCTAAGAT
Found at i:41181639 original size:24 final size:24
Alignment explanation
Indices: 41181607--41181657 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
41181597 TTCAGTGCTT
*
41181607 CCCATTAATTGCTCTTCGGAGCCA
1 CCCATTAATTGCTCTTCGAAGCCA
*
41181631 CCCATTAATTGCTCTTCGAAGCTA
1 CCCATTAATTGCTCTTCGAAGCCA
41181655 CCC
1 CCC
41181658 GTTATAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (24 bp):
CCCATTAATTGCTCTTCGAAGCCA
Found at i:41181729 original size:24 final size:24
Alignment explanation
Indices: 41181697--41181759 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
41181687 TATTGCCCGG
41181697 ATAAGCTTCCCGTTACAAGGCTCA
1 ATAAGCTTCCCGTTACAAGGCTCA
41181721 ATAAGCTTCCCGTTACAAGGCTCA
1 ATAAGCTTCCCGTTACAAGGCTCA
41181745 ATAAGCTTCCCGTTA
1 ATAAGCTTCCCGTTA
41181760 TAGTGCTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (24 bp):
ATAAGCTTCCCGTTACAAGGCTCA
Found at i:41185763 original size:13 final size:13
Alignment explanation
Indices: 41185745--41185769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41185735 CTGGTTCAGT
41185745 GTCAATTTAGATG
1 GTCAATTTAGATG
41185758 GTCAATTTAGAT
1 GTCAATTTAGAT
41185770 TAGAAAGATT
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:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
GTCAATTTAGATG
Found at i:41186708 original size:24 final size:24
Alignment explanation
Indices: 41186680--41186732 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
41186670 ATTAGTAAGG
* *
41186680 TAAATAAACTATGCTAATAAATGC
1 TAAATAAACTATACTAATAAATAC
* *
41186704 TAAATATATTATACTAATAAATAC
1 TAAATAAACTATACTAATAAATAC
41186728 TAAAT
1 TAAAT
41186733 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
TAAATAAACTATACTAATAAATAC
Found at i:41189674 original size:22 final size:21
Alignment explanation
Indices: 41189634--41189675 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41189624 AAAATTTTAT
* *
41189634 AAAAATATTAAAGTTTATGAA
1 AAAAATATTAAAATATATGAA
41189655 AAAAATATTAAACATATATGA
1 AAAAATATTAAA-ATATATGA
41189676 TAAATATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (21 bp):
AAAAATATTAAAATATATGAA
Found at i:41195014 original size:58 final size:59
Alignment explanation
Indices: 41194942--41195058 Score: 157
Period size: 58 Copynumber: 2.0 Consensus size: 59
41194932 CCCAATATGA
* * *
41194942 GAACAAGTACCAAGTTCAGGGACTAACTTG-GAAAAAAAAAGTTCA-AGCCTCAATGTGG
1 GAACAAGTACCAAGTTAAGGAACTAACTTGACAAAAAAAAAGTTCAGA-CCTCAATGTGG
* *
41195000 GAACAATTATCAAGTTAAGGAACTAACTTGACCAAAAAAAAAGTTCAGACCTCAATGTG
1 GAACAAGTACCAAGTTAAGGAACTAACTTGA-CAAAAAAAAAGTTCAGACCTCAATGTG
41195059 AGAATTATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
58 26 0.51
60 24 0.47
61 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.21
Consensus pattern (59 bp):
GAACAAGTACCAAGTTAAGGAACTAACTTGACAAAAAAAAAGTTCAGACCTCAATGTGG
Found at i:41196310 original size:27 final size:27
Alignment explanation
Indices: 41196280--41196332 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
41196270 TCTAGTAATT
41196280 TATCTATATTGTAATAAAATACTAGTA
1 TATCTATATTGTAATAAAATACTAGTA
41196307 TATCTATATTGTAATAAAATACTAGT
1 TATCTATATTGTAATAAAATACTAGT
41196333 TTGATCAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (27 bp):
TATCTATATTGTAATAAAATACTAGTA
Found at i:41198916 original size:5 final size:5
Alignment explanation
Indices: 41198900--41198934 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
41198890 GCAAAGGTTT
*
41198900 TTTTG TTTTTG TATTG TTTTG TTTTG TTTTG TTTT
1 TTTTG -TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
41198935 AATGTGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:41204779 original size:18 final size:18
Alignment explanation
Indices: 41204756--41204790 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41204746 ACACCAGTAC
*
41204756 CTGCTATCAACTAACTAA
1 CTGCTAACAACTAACTAA
41204774 CTGCTAACAACTAACTA
1 CTGCTAACAACTAACTA
41204791 TAACAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.29, G:0.06, T:0.26
Consensus pattern (18 bp):
CTGCTAACAACTAACTAA
Found at i:41209852 original size:6 final size:6
Alignment explanation
Indices: 41209841--41209879 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
41209831 GTTGTGGGTC
*
41209841 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGGCT GAG
1 GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAGCCT GAG
41209880 ATTGAGTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.18, C:0.28, G:0.38, T:0.15
Consensus pattern (6 bp):
GAGCCT
Found at i:41209953 original size:6 final size:6
Alignment explanation
Indices: 41209942--41209971 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
41209932 TGCAACCCTG
41209942 TTACCA TTACCA TTACCA TTACCA TTACCA
1 TTACCA TTACCA TTACCA TTACCA TTACCA
41209972 AGCGATGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
TTACCA
Found at i:41216422 original size:50 final size:50
Alignment explanation
Indices: 41216312--41216490 Score: 148
Period size: 50 Copynumber: 3.6 Consensus size: 50
41216302 GGTAAAGAGA
* * * **
41216312 TCCCATGTAAGACCATGTCTGTGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
41216362 TGCCC-CGTAAGACTATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 T-CCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * * ** ** * * *
41216412 TCCCATGTAAGACCATATTTGGGATATTACATTAGCA-CTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
*
41216460 ATCCCATGCAAGACCATGTCTGGGACATGGC
1 -TCCCATGTAAGACCATGTCTGGGACATGGC
41216491 TTTGGCATGT
Statistics
Matches: 100, Mismatches: 26, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
48 3 0.03
49 32 0.32
50 62 0.62
51 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:41217076 original size:42 final size:42
Alignment explanation
Indices: 41217017--41217100 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
41217007 TTGCTAAAGA
41217017 ATGATGTGTAAATATGTGACAATGTTTAGCTATTAAAATGGC
1 ATGATGTGTAAATATGTGACAATGTTTAGCTATTAAAATGGC
41217059 ATGATGTGTAAATATGTGACAATGTTTAGCTATTAAAATGGC
1 ATGATGTGTAAATATGTGACAATGTTTAGCTATTAAAATGGC
41217101 TAAGTAAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (42 bp):
ATGATGTGTAAATATGTGACAATGTTTAGCTATTAAAATGGC
Found at i:41222818 original size:50 final size:50
Alignment explanation
Indices: 41222753--41222937 Score: 149
Period size: 50 Copynumber: 3.6 Consensus size: 50
41222743 TAATGTCATA
* * ** * *
41222753 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCTC-ATGCCATG
1 TCCCAGACATAGTCTTACATGGGACCTCTCATATCAGTGC-CAACGCCATG
* ** *
41222803 TCCCTGACATAGTCTTACGGGGGACCTCTCATCTCAGTGCCAACGCCATG
1 TCCCAGACATAGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATG
* * *
41222853 TCCCAGACATGGTCTTACATGAGG-CCTCTCATAATCTCAATGATGCCAATGTCATG
1 TCCCAGACATAGTCTTACATG-GGACCTCTCAT-A--TC-A-G-TGCCAACGCCATG
* *
41222909 TCCCAGACATGGTCTTACATGGGATCTCT
1 TCCCAGACATAGTCTTACATGGGACCTCT
41222938 TTATCCAAAT
Statistics
Matches: 108, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
49 1 0.01
50 63 0.58
51 2 0.02
53 2 0.02
54 1 0.01
55 3 0.03
56 36 0.33
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
TCCCAGACATAGTCTTACATGGGACCTCTCATATCAGTGCCAACGCCATG
Found at i:41225620 original size:63 final size:62
Alignment explanation
Indices: 41225546--41225677 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 62
41225536 TTTGGAGTTT
41225546 TGATTATCAATTCAGCTGTTTGAATCAACTTAAGTTAATTCTCCTTTATGTTGTTTGATTGA
1 TGATTATCAATTCAGCTGTTTGAATCAACTTAAGTTAATTCTCCTTTATGTTGTTTGATTGA
*
41225608 TGACTTATCAATTCAGCTGTTTGAATCAACTTAAGTTAATTCTTCTTTATGTTGTTTGATTGA
1 TGA-TTATCAATTCAGCTGTTTGAATCAACTTAAGTTAATTCTCCTTTATGTTGTTTGATTGA
41225671 TGATTAT
1 TGATTAT
41225678 ATTTATATGC
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 7 0.10
63 61 0.90
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (62 bp):
TGATTATCAATTCAGCTGTTTGAATCAACTTAAGTTAATTCTCCTTTATGTTGTTTGATTGA
Found at i:41234850 original size:46 final size:46
Alignment explanation
Indices: 41234779--41235619 Score: 1007
Period size: 46 Copynumber: 17.8 Consensus size: 46
41234769 CTTCAACCTC
* *
41234779 CTCCGCTGCCAAATACAAGAAGACAAGATCTACTATCTACGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* * * *
41234825 CTCTGCTGCCAAATACAGGAAGACAAGATCTGTTATCTTCAATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* * * * *
41234871 CTTCGCTGCCAAATACAGGAAGATAATATCTGCTATCTTCAATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* * * * *
41234917 CTCCGTTGCCAAATACAGGAAGATAATATCTGCTATCTTCAATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* * * * *
41234963 CTCCGTTGCCAAATATAGAAAGACAAGATCTGCTATCTACTATTTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* * * * *
41235009 CTCCGCTACCAAATACAGGAATATAAGATATGCTATCTACTATCTACTATCTA
1 CTCCGCTGCCAAATACAGG-----AAGACAAG--ATCTGCTATCTACGATCTA
* *
41235062 CTCCTCTGCCAAATACAGGAAGATAAGATCTGCTATCTACTATCTACGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTG-------CTATCTACGATCTA
*
41235115 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTATGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* *
41235161 CTCCGCTGCCAAATACAGGAAGACAAGATCTCCTATCTATGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
*
41235207 CTCTGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTACGA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCT---A
* * * * *
41235256 TCTACTTCTCTGCCAAATACAGGAAAATAAGATCTGCTATCTATGATTTA
1 -CT-C--CGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
*
41235306 CTCCGCTGCCAAATACAGGAAGACAAGATCTACTATCTACGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* * * *
41235352 CTTCGCTGCCAAATACAGGAAGATAAGATCTGCCATCTTCGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
*
41235398 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTATGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
* *
41235444 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATTTATGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
*
41235490 CTCCGCTGCCAAATACAGGAAGACAAGAGCTGCTATCTACGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
** * * **
41235536 CTTTGCTGCCAAATACAGGAAGATAAGATCTGCTATATTTGATCTA
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
**
41235582 CTCCGCTGCCAAATACAAAAAGACAAGATCTGCTATCT
1 CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCT
41235620 TTAATCTGCT
Statistics
Matches: 695, Mismatches: 79, Indels: 42
0.85 0.10 0.05
Matches are distributed among these distances:
46 561 0.81
48 8 0.01
49 3 0.00
50 3 0.00
51 7 0.01
53 113 0.16
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (46 bp):
CTCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTACGATCTA
Found at i:41237146 original size:13 final size:12
Alignment explanation
Indices: 41237121--41237187 Score: 73
Period size: 13 Copynumber: 5.4 Consensus size: 12
41237111 AGGCCTCTCA
41237121 TTTTTCTTTTTCT
1 TTTTTC-TTTTCT
41237134 TCTTTTCTTTTCT
1 T-TTTTCTTTTCT
41237147 TTTTTCCTTTTCT
1 TTTTT-CTTTTCT
*
41237160 TTTTTCTTTCCT
1 TTTTTCTTTTCT
* *
41237172 TCTTT-TTTTGT
1 TTTTTCTTTTCT
41237183 TTTTT
1 TTTTT
41237188 TTAATATTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
11 8 0.17
12 14 0.30
13 20 0.43
14 5 0.11
ACGTcount: A:0.00, C:0.18, G:0.01, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTCT
Found at i:41237179 original size:17 final size:16
Alignment explanation
Indices: 41237138--41237185 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
41237128 TTTTCTTCTT
*
41237138 TTCTTTTCTTTTTTCC
1 TTCTTTTTTTTTTTCC
41237154 TT-TTCTTTTTTCTTTCC
1 TTCTT-TTTTTT-TTTCC
41237171 TTCTTTTTTTGTTTT
1 TTCTTTTTTT-TTTT
41237186 TTTTAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.07
16 7 0.26
17 15 0.56
18 3 0.11
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTTTTTCC
Found at i:41237198 original size:38 final size:39
Alignment explanation
Indices: 41237121--41237199 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 39
41237111 AGGCCTCTCA
* ** *
41237121 TTTTTCTTTTTCTTCTTTTCTTTTCTTTTTTCCTTTTCT
1 TTTTTCTTTTCCTTCTTTTCTTTTCTTTTTTAATATTCT
*
41237160 TTTTTC-TTTCCTTCTTTT-TTTGTTTTTTTTAATATTCT
1 TTTTTCTTTTCCTTCTTTTCTTT-TCTTTTTTAATATTCT
41237198 TT
1 TT
41237200 GATTGAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 3 0.09
38 25 0.74
39 6 0.18
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.78
Consensus pattern (39 bp):
TTTTTCTTTTCCTTCTTTTCTTTTCTTTTTTAATATTCT
Found at i:41237577 original size:7 final size:7
Alignment explanation
Indices: 41237565--41237598 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
41237555 TTTCTTCTCC
41237565 TTTTTTA
1 TTTTTTA
41237572 TTTTTTA
1 TTTTTTA
*
41237579 TTTTTTG
1 TTTTTTA
41237586 TTTTTTA
1 TTTTTTA
41237593 TTTTTT
1 TTTTTT
41237599 TTGCTCCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:41238625 original size:13 final size:13
Alignment explanation
Indices: 41238607--41238643 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
41238597 TCATATCTGA
41238607 GAATGGGGCTTAT
1 GAATGGGGCTTAT
*
41238620 GAATGGGGTTTAT
1 GAATGGGGCTTAT
41238633 GAATGGGGCTT
1 GAATGGGGCTT
41238644 TCAAAGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.05, G:0.41, T:0.32
Consensus pattern (13 bp):
GAATGGGGCTTAT
Found at i:41239834 original size:8 final size:9
Alignment explanation
Indices: 41239816--41239840 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41239806 CAAATATTTT
41239816 AAAAATAAA
1 AAAAATAAA
41239825 AAAAATAAA
1 AAAAATAAA
41239834 AAAAATA
1 AAAAATA
41239841 TATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:41242091 original size:14 final size:15
Alignment explanation
Indices: 41242063--41242091 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41242053 GATACGATAG
41242063 TATGAGCATAAATAA
1 TATGAGCATAAATAA
41242078 TATGAGCA-AAATAA
1 TATGAGCATAAATAA
41242092 AATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (15 bp):
TATGAGCATAAATAA
Found at i:41242400 original size:42 final size:43
Alignment explanation
Indices: 41242353--41242443 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 43
41242343 ATAAAAATAT
41242353 AAAAATAAAAGTAATAACAGTATTAAACA-TAA-TAA-TT-ATAGC
1 AAAAAT-AAA-TAATAACAGTATTAAA-ATTAATTAATTTAATAGC
* *
41242395 AAAAAT-AATGATAACATTATTAAAATTAATTAATTTAATAGC
1 AAAAATAAATAATAACAGTATTAAAATTAATTAATTTAATAGC
41242437 AAAAATA
1 AAAAATA
41242444 TAACAAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
38 1 0.02
39 17 0.40
40 5 0.12
41 2 0.05
42 17 0.40
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (43 bp):
AAAAATAAATAATAACAGTATTAAAATTAATTAATTTAATAGC
Found at i:41242416 original size:39 final size:42
Alignment explanation
Indices: 41242366--41242443 Score: 110
Period size: 39 Copynumber: 1.9 Consensus size: 42
41242356 AATAAAAGTA
41242366 ATAACAGTATTAAACA-TAA-TAA-TT-ATAGCAAAAATAATG
1 ATAACAGTATTAAA-ATTAATTAATTTAATAGCAAAAATAATG
*
41242405 ATAACATTATTAAAATTAATTAATTTAATAGCAAAAATA
1 ATAACAGTATTAAAATTAATTAATTTAATAGCAAAAATA
41242444 TAACAAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
38 1 0.03
39 16 0.47
40 3 0.09
41 2 0.06
42 12 0.35
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.32
Consensus pattern (42 bp):
ATAACAGTATTAAAATTAATTAATTTAATAGCAAAAATAATG
Found at i:41246639 original size:6 final size:6
Alignment explanation
Indices: 41246628--41246658 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
41246618 TTAATATTTT
*
41246628 AATATA AATATA AATATA AATATA TATATA A
1 AATATA AATATA AATATA AATATA AATATA A
41246659 TAATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:41251524 original size:17 final size:17
Alignment explanation
Indices: 41251500--41251537 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41251490 TTTAAAAACT
* *
41251500 AATT-TTTTTTAAAATA
1 AATTATTTTATAAAAAA
41251516 AATTATTTTATAAAAAA
1 AATTATTTTATAAAAAA
41251533 AATTA
1 AATTA
41251538 AAGAATCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTATTTTATAAAAAA
Found at i:41253726 original size:22 final size:23
Alignment explanation
Indices: 41253673--41253728 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
41253663 CCCGTTTTTA
* * *
41253673 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
41253696 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
41253718 ATTAAAATTAA
1 ATTAAAATTAA
41253729 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:41253741 original size:16 final size:16
Alignment explanation
Indices: 41253704--41253743 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
41253694 TTAATAAAAT
* *
41253704 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
41253720 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
41253736 TAAAATTA
1 TAAAATTA
41253744 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:41253824 original size:25 final size:27
Alignment explanation
Indices: 41253796--41253846 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
41253786 AAATAAACTT
*
41253796 AAAATAAAAAAACTA-TT-ATATTTTA
1 AAAATAAAAAAAATATTTAATATTTTA
41253821 AAAATAAAAAAAATATTTAATATTTT
1 AAAATAAAAAAAATATTTAATATTTT
41253847 TCGGGCCCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.61
26 2 0.09
27 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATAAAAAAAATATTTAATATTTTA
Found at i:41256782 original size:18 final size:18
Alignment explanation
Indices: 41256754--41256789 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
41256744 AAATAGATTA
41256754 AAAATTTTAAAACATAAAT
1 AAAATTTTAAAA-ATAAAT
41256773 AAAA-TTTAAAAATAAAT
1 AAAATTTTAAAAATAAAT
41256790 TATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTTTAAAAATAAAT
Found at i:41256787 original size:13 final size:13
Alignment explanation
Indices: 41256769--41256809 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
41256759 TTTAAAACAT
41256769 AAATAAAATTTAA
1 AAATAAAATTTAA
41256782 AAAT-AAA-TTATA
1 AAATAAAATTTA-A
*
41256794 AAATAAAATATAA
1 AAATAAAATTTAA
41256807 AAA
1 AAA
41256810 ACTATTAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 3 0.12
12 8 0.33
13 11 0.46
14 2 0.08
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAAATTTAA
Found at i:41256794 original size:20 final size:20
Alignment explanation
Indices: 41256741--41256797 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
41256731 ATATATATAA
*
41256741 TAAAAATAGATTA-AAAATTT
1 TAAAAATAAATTATAAAA-TT
41256761 TAAAACAT-AA--ATAAAATT
1 TAAAA-ATAAATTATAAAATT
41256779 TAAAAATAAATTATAAAAT
1 TAAAAATAAATTATAAAAT
41256798 AAAATATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 2 0.06
18 10 0.32
19 4 0.13
20 13 0.42
21 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAATAAATTATAAAATT
Found at i:41256796 original size:12 final size:12
Alignment explanation
Indices: 41256769--41256808 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
41256759 TTTAAAACAT
*
41256769 AAATAAAATTTAA
1 AAATAAAATAT-A
*
41256782 AAATAAATTATA
1 AAATAAAATATA
41256794 AAATAAAATATA
1 AAATAAAATATA
41256806 AAA
1 AAA
41256809 AACTATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAATAAAATATA
Found at i:41259603 original size:41 final size:41
Alignment explanation
Indices: 41259558--41259660 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
41259548 GTGATAATCG
* * * ** *
41259558 GGCTTTATGCCTAGCAAGCTTTATGTCGGTGAATTATATCA
1 GGCTTTACGCCTAGCAGGCTTAATGTCGGTGAACCATAACA
* *
41259599 GGCTTTACGCCTAGTAGGCTTAATGTCGGTGTACCATAACA
1 GGCTTTACGCCTAGCAGGCTTAATGTCGGTGAACCATAACA
41259640 GGCTTTACGCCTAGCAGGCTT
1 GGCTTTACGCCTAGCAGGCTT
41259661 CGTGCCGGTG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.32
Consensus pattern (41 bp):
GGCTTTACGCCTAGCAGGCTTAATGTCGGTGAACCATAACA
Found at i:41259670 original size:41 final size:41
Alignment explanation
Indices: 41259558--41259677 Score: 123
Period size: 41 Copynumber: 2.9 Consensus size: 41
41259548 GTGATAATCG
* * * * * ** *
41259558 GGCTTTATGCCTAGCAAGCTTTATGTCGGTGAATTATATCA
1 GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTACCATAACA
* *
41259599 GGCTTTACGCCTAGTAGGCTTAATGTCGGTGTACCATAACA
1 GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTACCATAACA
** *
41259640 GGCTTTACGCCTAGCAGGCTTCGTGCCGGTGTATCATA
1 GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTACCATA
41259678 TTAAGATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (41 bp):
GGCTTTACGCCTAGCAGGCTTAATGCCGGTGTACCATAACA
Found at i:41263107 original size:42 final size:41
Alignment explanation
Indices: 41263057--41263179 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
41263047 AAGTTTCCGT
*
41263057 TCAACCCTAATGGGTTTCTGTTCAGCTCTGTTGAGCTTCAGT
1 TCAACCCTAATGGGTTTCTGTTCAGCTCT-TTGAGCTTCAGC
* * * * * *
41263099 TTAACCCTATTAGGTTTCCGTTCAGCTCTTACGAGCTTCTGC
1 TCAACCCTAATGGGTTTCTGTTCAGCTCTT-TGAGCTTCAGC
* * * *
41263141 TCAACCCTTATGGATTTCTGTTTAGCTCTCATGAGCTTC
1 TCAACCCTAATGGGTTTCTGTTCAGCTCT-TTGAGCTTC
41263180 TGTTCAGCCT
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.98
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (41 bp):
TCAACCCTAATGGGTTTCTGTTCAGCTCTTTGAGCTTCAGC
Found at i:41267789 original size:246 final size:246
Alignment explanation
Indices: 41267350--41267825 Score: 691
Period size: 246 Copynumber: 1.9 Consensus size: 246
41267340 GCCCGTCTCT
* * * * *
41267350 ATGCTCGTGTAACTCTCTGACTTAGGTCACACGACCAAGTCACACACCCGTGTACTAGGTCGTGT
1 ATGCCCGTGTAACTCTCTAACTTAGGTCACACGACCAAGTCACACACCCGTGCACTAGGCCGTAT
* * * * * * *
41267415 GTTATGAAATTAAGGTGCAAGGGTCACACGGCCAAGTCACACTCCCGTGTGCTAGGCCGTGTGCA
66 GTTATGAAAATAAGGTGCAAGGGTCACACAGCCAAGCCACACGCCCGTGTCCTAGGCCGTGCGAA
41267480 AAAACCTGAACATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACACGACCAGACCACATGCCC
131 AAAACCTGAACATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACACGACCAGACCACATGCCC
* *
41267545 ATGTGCTTGGCCGTGTGTCACACACGGCTGAGACAGTCCCAACCCGTGTTC
196 ATGTGCTAGGCCATGTGTCACACACGGCTGAGACAGTCCCAACCCGTGTTC
* * * * * * *
41267596 ATGCCCGTGTAACTCTCTAATTTGGGTCACATGGCCAAGTCACACGCCTGTGCGCTAGGCCGTAT
1 ATGCCCGTGTAACTCTCTAACTTAGGTCACACGACCAAGTCACACACCCGTGCACTAGGCCGTAT
* *
41267661 GTTATGAAAATAAGGTGCATGGGTCACACAGCCAAGCCACACGCCCGTGTCCTAGTCCGTGCGAA
66 GTTATGAAAATAAGGTGCAAGGGTCACACAGCCAAGCCACACGCCCGTGTCCTAGGCCGTGCGAA
* * * *
41267726 AAAACCTGAGCATTTTGTTTCTAAATTTTAAGGATGCAGTGGACACATGACCAGACCACATGCCC
131 AAAACCTGAACATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACACGACCAGACCACATGCCC
* *
41267791 ATGTGCTAGGCCATGTGTTACACATGGCTGAGACA
196 ATGTGCTAGGCCATGTGTCACACACGGCTGAGACA
41267826 CACACCCGTG
Statistics
Matches: 201, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
246 201 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (246 bp):
ATGCCCGTGTAACTCTCTAACTTAGGTCACACGACCAAGTCACACACCCGTGCACTAGGCCGTAT
GTTATGAAAATAAGGTGCAAGGGTCACACAGCCAAGCCACACGCCCGTGTCCTAGGCCGTGCGAA
AAAACCTGAACATTCTGTTTCTAAATTTTAAGGATGCAGAGGACACACGACCAGACCACATGCCC
ATGTGCTAGGCCATGTGTCACACACGGCTGAGACAGTCCCAACCCGTGTTC
Found at i:41268672 original size:42 final size:42
Alignment explanation
Indices: 41268615--41268726 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
41268605 CTGAAGGCTG
* * * *
41268615 AACAAAAGCACATAAGTGCTAAACAGAAACCCATAAGGATTG
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGATTA
* * * * *
41268657 AACGGAAGCTCATAAGAGCTTAACGGAAACCTATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGATTA
* *
41268699 AACAGAAGCTCAAAAGAGCTGAAC-GAAA
1 AACAGAAGCTCATAAGAGCTAAACAGAAA
41268727 ACTCATATGA
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
41 4 0.07
42 54 0.93
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAGGATTA
Found at i:41268681 original size:21 final size:21
Alignment explanation
Indices: 41268625--41268741 Score: 62
Period size: 21 Copynumber: 5.6 Consensus size: 21
41268615 AACAAAAGCA
* * * *
41268625 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTTAACGGAAACT
* *
41268646 CATAAG-GATTGAACGGAAGCT
1 CATAAGAGCTT-AACGGAAACT
41268667 CATAAGAGCTTAACGGAAAC-
1 CATAAGAGCTTAACGGAAACT
* * *
41268687 CTATAAG-GGTTAAACAGAAGCT
1 C-ATAAGAGCTT-AACGGAAACT
* * *
41268709 CAAAAGAGCTGAACGAAAACT
1 CATAAGAGCTTAACGGAAACT
*
41268730 CATATGAG-TTAA
1 CATAAGAGCTTAA
41268742 ACAAAAACTC
Statistics
Matches: 71, Mismatches: 19, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
20 9 0.13
21 56 0.79
22 6 0.08
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (21 bp):
CATAAGAGCTTAACGGAAACT
Found at i:41268741 original size:42 final size:42
Alignment explanation
Indices: 41268661--41268744 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
41268651 GGATTGAACG
* * * *
41268661 GAAGCTCATAAGAGCTTAACGGAAACCTATAAGGGTTAAACA
1 GAAGCTCAAAAGAGCTGAACGAAAACCTATAAGAGTTAAACA
*
41268703 GAAGCTCAAAAGAGCTGAACGAAAA-CTCATATGAGTTAAACA
1 GAAGCTCAAAAGAGCTGAACGAAAACCT-ATAAGAGTTAAACA
41268745 AAAACTCGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (42 bp):
GAAGCTCAAAAGAGCTGAACGAAAACCTATAAGAGTTAAACA
Found at i:41270576 original size:3 final size:3
Alignment explanation
Indices: 41270570--41270627 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
41270560 TTTTAACTGT
41270570 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41270618 TTA TTA TTA T
1 TTA TTA TTA T
41270628 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41270783 original size:22 final size:22
Alignment explanation
Indices: 41270755--41270797 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41270745 TTGCGGCACT
* *
41270755 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
41270777 AAAAAGCACCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
41270798 GTTATGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:41272836 original size:9 final size:9
Alignment explanation
Indices: 41272822--41272861 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
41272812 GATCAAGTAA
41272822 AATTAAATT
1 AATTAAATT
41272831 AATTAAATT
1 AATTAAATT
* *
41272840 AATCAGATT
1 AATTAAATT
41272849 AATTAAAATT
1 AATT-AAATT
41272859 AAT
1 AAT
41272862 ATGATAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:41273646 original size:318 final size:318
Alignment explanation
Indices: 41273066--41273701 Score: 1247
Period size: 318 Copynumber: 2.0 Consensus size: 318
41273056 GTCATTATTA
41273066 ACCCGGACCAAACCGACAGCAGTCAAATCAGCTCAAGGTGTCGTAAGGGTATCGCACTTGCATCA
1 ACCCGGACCAAACCGACAGCAGTCAAATCAGCTCAAGGTGTCGTAAGGGTATCGCACTTGCATCA
41273131 CCGGACAGGGTGGTGCCGGTGGCTGCGATGGTGGTGTCCTGGTGACCGACGGCTGTTGGTCATCG
66 CCGGACAGGGTGGTGCCGGTGGCTGCGATGGTGGTGTCCTGGTGACCGACGGCTGTTGGTCATCG
41273196 GTGGTTGAGTAGTGGAAATGTTACACTTCTACTATGACTTTACCAGAAATTTTGATTTCAGATTA
131 GTGGTTGAGTAGTGGAAATGTTACACTTCTACTATGACTTTACCAGAAATTTTGATTTCAGATTA
*
41273261 ATTATTTCAAAAATAATATTATTTTAATAGTTTAACATTAAATTTAATTTAATACTTAATCGTAT
196 ATTATTTCAAAAATAATATTATTTTAATAGTTTAACATTAAATTTAATTTAATACTTAATAGTAT
41273326 TTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATCTAATATTAATT
261 TTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATCTAATATTAATT
41273384 ACCCGGACCAAACCGACAGCAGTCAAATCAGCTCAAGGTGTCGTAAGGGTATCGCACTTGCATCA
1 ACCCGGACCAAACCGACAGCAGTCAAATCAGCTCAAGGTGTCGTAAGGGTATCGCACTTGCATCA
41273449 CCGGACAGGGTGGTGCCGGTGGCTGCGATGGTGGTGTCCTGGTGACCGACGGCTGTTGGTCATCG
66 CCGGACAGGGTGGTGCCGGTGGCTGCGATGGTGGTGTCCTGGTGACCGACGGCTGTTGGTCATCG
41273514 GTGGTTGAGTAGTGGAAATGTTACACTTCTACTATGACTTTACCAGAAATTTTGATTTCAGATTA
131 GTGGTTGAGTAGTGGAAATGTTACACTTCTACTATGACTTTACCAGAAATTTTGATTTCAGATTA
41273579 ATTATTTCAAAAATAATATTATTTTAATAGTTTAACATTAAATTTAAATTTAATAC-TAATAGTA
196 ATTATTTCAAAAATAATATTATTTTAATAGTTTAACATTAAATTT-AATTTAATACTTAATAGTA
41273643 TTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATCTAATATTAATT
260 TTTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATCTAATATTAATT
41273702 TAATATTAAA
Statistics
Matches: 316, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
318 306 0.97
319 10 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (318 bp):
ACCCGGACCAAACCGACAGCAGTCAAATCAGCTCAAGGTGTCGTAAGGGTATCGCACTTGCATCA
CCGGACAGGGTGGTGCCGGTGGCTGCGATGGTGGTGTCCTGGTGACCGACGGCTGTTGGTCATCG
GTGGTTGAGTAGTGGAAATGTTACACTTCTACTATGACTTTACCAGAAATTTTGATTTCAGATTA
ATTATTTCAAAAATAATATTATTTTAATAGTTTAACATTAAATTTAATTTAATACTTAATAGTAT
TTTATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTTAATCTAATATTAATT
Found at i:41273670 original size:20 final size:18
Alignment explanation
Indices: 41273646--41273699 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
41273636 AATAGTATTT
41273646 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
41273664 GTGATT-ATCTTAATATTAAA
1 -T-ATTAAT-TTAATATTAAA
*
41273684 T-TTAATCTAATATTAA
1 TATTAATTTAATATTAA
41273700 TTTAATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 11 0.35
18 2 0.06
19 4 0.13
20 14 0.45
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:41273676 original size:25 final size:24
Alignment explanation
Indices: 41273625--41273713 Score: 83
Period size: 25 Copynumber: 3.7 Consensus size: 24
41273615 ATTAAATTTA
* *
41273625 AATTTAATACTAATAGTATTTTATT
1 AATTTAATATTAA-AGTATTATATT
*
41273650 AATTTAATATTAAAGTGATTATCTT
1 AATTTAATATTAAAGT-ATTATATT
* * *
41273675 AATATTAA-ATTTAA-TCTAATATT
1 AAT-TTAATATTAAAGTATTATATT
41273698 AATTTAATATTAAAGT
1 AATTTAATATTAAAGT
41273714 GAATAAGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
22 4 0.08
23 13 0.25
24 5 0.10
25 26 0.50
26 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (24 bp):
AATTTAATATTAAAGTATTATATT
Found at i:41273696 original size:17 final size:16
Alignment explanation
Indices: 41273674--41273705 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
41273664 GTGATTATCT
41273674 TAATATTAAATTTAATC
1 TAATATT-AATTTAATC
41273691 TAATATTAATTTAAT
1 TAATATTAATTTAAT
41273706 ATTAAAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATATTAATTTAATC
Found at i:41276350 original size:2 final size:2
Alignment explanation
Indices: 41276343--41276379 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41276333 ATATGGTTTC
41276343 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41276380 GTTTGGGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41285484 original size:13 final size:13
Alignment explanation
Indices: 41285466--41285509 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
41285456 TTTTGCTATC
41285466 TTATTTCTACCTT
1 TTATTTCTACCTT
*
41285479 TTATTT-TA--TC
1 TTATTTCTACCTT
41285489 TTATTTCTACCTT
1 TTATTTCTACCTT
41285502 TTATTTCT
1 TTATTTCT
41285510 CTATGGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 2 0.08
13 15 0.58
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTCTACCTT
Found at i:41285489 original size:23 final size:23
Alignment explanation
Indices: 41285462--41285507 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41285452 TCACTTTTGC
41285462 TATCTTATTTCTACCTTTTATTT
1 TATCTTATTTCTACCTTTTATTT
41285485 TATCTTATTTCTACCTTTTATTT
1 TATCTTATTTCTACCTTTTATTT
41285508 CTCTATGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (23 bp):
TATCTTATTTCTACCTTTTATTT
Found at i:41288005 original size:24 final size:24
Alignment explanation
Indices: 41287978--41288036 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
41287968 TCACAAGCTC
41287978 AAATGATTTGAAAATGAGAAAATA
1 AAATGATTTGAAAATGAGAAAATA
* **
41288002 AAATGATTTGGAAATGAGAATGTA
1 AAATGATTTGAAAATGAGAAAATA
*
41288026 AAATGAGTTGA
1 AAATGATTTGA
41288037 TATGATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (24 bp):
AAATGATTTGAAAATGAGAAAATA
Found at i:41288851 original size:21 final size:22
Alignment explanation
Indices: 41288821--41288869 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
41288811 ATAAATTATA
* *
41288821 TATTTGTTAG-TTTTATATTTT
1 TATTTTTTAGTTTTTATAGTTT
41288842 TATTTTTTAGTTTTTATAGTTT
1 TATTTTTTAGTTTTTATAGTTT
41288864 TATTTT
1 TATTTT
41288870 ATTTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.73
Consensus pattern (22 bp):
TATTTTTTAGTTTTTATAGTTT
Found at i:41299235 original size:21 final size:21
Alignment explanation
Indices: 41299194--41299251 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
41299184 TATATATATA
*
41299194 TATATATTATAGTTTT-TAGTTT
1 TATAT-TTATA-TTTTACAGTTT
41299216 TATATTTATATTTTACAGTTT
1 TATATTTATATTTTACAGTTT
41299237 TATAATTT-TATTTTA
1 TAT-ATTTATATTTTA
41299252 TTTAATAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 4 0.12
21 20 0.61
22 9 0.27
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TATATTTATATTTTACAGTTT
Found at i:41299235 original size:28 final size:29
Alignment explanation
Indices: 41299188--41299252 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
41299178 TTCTTTTATA
* * *
41299188 TATATATATATATTATAGTTTT-TAGTTT
1 TATATTTATATATTACAGTTTTATAATTT
*
41299216 TATATTTATATTTTACAGTTTTATAATTT
1 TATATTTATATATTACAGTTTTATAATTT
41299245 TAT-TTTAT
1 TATATTTAT
41299253 TTAATAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 24 0.75
29 8 0.25
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (29 bp):
TATATTTATATATTACAGTTTTATAATTT
Found at i:41300386 original size:19 final size:19
Alignment explanation
Indices: 41300346--41300388 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41300336 CCCTTTATTA
* *
41300346 AATTTATTTACTTTATTTT
1 AATTTATATAATTTATTTT
41300365 AATTTATATAATTT-TTTAT
1 AATTTATATAATTTATTT-T
41300384 AATTT
1 AATTT
41300389 TATTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTATATAATTTATTTT
Found at i:41303547 original size:15 final size:15
Alignment explanation
Indices: 41303527--41303561 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
41303517 GGCCGTATGA
*
41303527 TAGTTGGGCTAGGTG
1 TAGTTGGGCTAGGCG
41303542 TAGTTGGGCTAGGCG
1 TAGTTGGGCTAGGCG
41303557 TAGTT
1 TAGTT
41303562 TGGGTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.43, T:0.34
Consensus pattern (15 bp):
TAGTTGGGCTAGGCG
Found at i:41304245 original size:132 final size:132
Alignment explanation
Indices: 41304089--41304520 Score: 627
Period size: 132 Copynumber: 3.3 Consensus size: 132
41304079 TGCTATTTTT
* * *
41304089 AACCTACTCCACTGCTG-CTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCT-CATACAT
1 AACCTATTCCACTGCTGTCT-AGGGAGATAGGACTGGCGGCTTAAATCTGCTTCCCTAC-TACCT
* * *
41304152 TGGGAAGATAATATTCATCGTCTTTGATATGTTCCACTACTGTTTAAGGAGACATGATCTACAAT
64 TGGGAAGATAAGATTCATCGTCTTTGATCTGTTCCACTACTGTTTAGGGAGACATGATCTACAAT
41304217 CTTC
129 CTTC
* *
41304221 AACCTATTCCACTGCTGTCTAGGGAGATAGGACTGGCGGCTTAAATCTGCTTCCTTACTACCGTG
1 AACCTATTCCACTGCTGTCTAGGGAGATAGGACTGGCGGCTTAAATCTGCTTCCCTACTACCTTG
* * * *
41304286 AGAAGATAAGATTCATCGTTTTTGATCTGTTCTACTACTGTTCAGGGAGACATGATCTACAATCT
66 GGAAGATAAGATTCATCGTCTTTGATCTGTTCCACTACTGTTTAGGGAGACATGATCTACAATCT
41304351 TC
131 TC
* * * *
41304353 AACCTATTCCACTGCTGTCCAGGGAGATAGGACTGACGACTTAAATCTACTTCCCTACTACCTTG
1 AACCTATTCCACTGCTGTCTAGGGAGATAGGACTGGCGGCTTAAATCTGCTTCCCTACTACCTTG
* * *
41304418 GGAAGATAAGATTCA-CTGTCTTTGATCTGTTCCGCTATTATTTAGGGAGACATGATCTACAATC
66 GGAAGATAAGATTCATC-GTCTTTGATCTGTTCCACTACTGTTTAGGGAGACATGATCTACAATC
41304482 TTC
130 TTC
* *
41304485 AACTTATTCCACTGCTGTCAAGGGAGATAGGACTGG
1 AACCTATTCCACTGCTGTCTAGGGAGATAGGACTGG
41304521 TATCTTCGAT
Statistics
Matches: 269, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
131 1 0.00
132 265 0.99
133 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (132 bp):
AACCTATTCCACTGCTGTCTAGGGAGATAGGACTGGCGGCTTAAATCTGCTTCCCTACTACCTTG
GGAAGATAAGATTCATCGTCTTTGATCTGTTCCACTACTGTTTAGGGAGACATGATCTACAATCT
TC
Found at i:41304583 original size:88 final size:88
Alignment explanation
Indices: 41304523--41305180 Score: 1005
Period size: 88 Copynumber: 7.5 Consensus size: 88
41304513 AGGACTGGTA
* * * *
41304523 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAATATCTGCTATTTTCAACCTATTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
41304588 TGCTCAAGGAGACAAGGCT-GGTA
66 TGCTCAGGGAGACAAGGCTAGG-G
*
41304611 TCTTCGATCTACTTTGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
41304676 TGCTCAGGGAGACAAGCCTGGGG
66 TGCTCAGGGAGACAAGGCTAGGG
* * *
41304699 TCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATTTTCAACCTAATCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
*
41304764 TGCTCAAGGAGACAAGGCTAGGG
66 TGCTCAGGGAGACAAGGCTAGGG
* * * *
41304787 TCTTCGATCTACTTCGCTGCCAATACAGAAAGATAAGATCTGCTATTTTTAACCTACTCCACTGG
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
41304852 TGCTCAGGGAGACAAGGCTAGGG
66 TGCTCAGGGAGACAAGGCTAGGG
* * *
41304875 TCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATTTGCTATTTTTAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
41304940 TGCTTAGGGAGACAAGGCT-GGTA
66 TGCTCAGGGAGACAAGGCTAGG-G
* * * *
41304963 TATTCGATCTACTTCGCTGCCAATACAGGAAGACAAAATCTGCTATTTTTAACTTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
41305028 TGCTCAGGGAGACAAGGCTAGGG
66 TGCTCAGGGAGACAAGGCTAGGG
* * *
41305051 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAAATCTGCTATTTTTAACTTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
41305116 TGCTCAGGGAGACAAGGCTAGGG
66 TGCTCAGGGAGACAAGGCTAGGG
* *
41305139 TCTTCGATCTACTTCGCTGGCAATACAGGAAGACAATATCTG
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG
41305181 TTTAGGATTA
Statistics
Matches: 527, Mismatches: 40, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
87 2 0.00
88 521 0.99
89 4 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
TGCTCAGGGAGACAAGGCTAGGG
Found at i:41304589 original size:264 final size:264
Alignment explanation
Indices: 41304089--41304601 Score: 605
Period size: 264 Copynumber: 1.9 Consensus size: 264
41304079 TGCTATTTTT
** * *
41304089 AACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTCATACATTG
1 AACCTACTCCACTGCTGCTCAGGGAGATAGGACTGACGACTTAAATCTACTTCCCTCATACATTG
* *
41304154 GGAAGATAATATTCATCGTCTTTGATATGTTCCACTACTGTTTAAGGAGACATGATCTACAATCT
66 GGAAGATAAGATTCATCGTCTTTGATATGTTCCACTACTATTTAAGGAGACATGATCTACAATCT
* * *
41304219 TCAACCTATTCCACTGCTGTCTAGGGAGATAGGACTGGCGGCTTAAATCTGCTTCCTTACTACCG
131 TCAACCTATTCCACTGCTGTCAAGGGAGATAGGACTGGCAGCTTAAATCTACTTCCTTACTACCG
* * * * * * * *
41304284 TGAGAAGATAAGATTCATCGTTTTTGATCTGTTCTACTACTGTTCAGGGAGACATGATCTACAAT
196 AGAGAAGACAAGATTCATCGTTTTTAACCTATTCCACTACTGCTCAAGGAGACATGATCTACAAT
41304349 CTTC
261 CTTC
* *
41304353 AACCTATTCCACTGCTG-TCCAGGGAGATAGGACTGACGACTTAAATCTACTTCCCT-ACTACCT
1 AACCTACTCCACTGCTGCT-CAGGGAGATAGGACTGACGACTTAAATCTACTTCCCTCA-TACAT
* * * *
41304416 TGGGAAGATAAGATTCA-CTGTCTTTGATCTGTTCCGCTATTATTTAGGGAGACATGATCTACAA
64 TGGGAAGATAAGATTCATC-GTCTTTGATATGTTCCACTACTATTTAAGGAGACATGATCTACAA
* * * **
41304480 TCTTCAACTTATTCCACTGCTGTCAAGGGAGATAGGACTGGTATCTTCGATCTACTTCGC-TACC
128 TCTTCAACCTATTCCACTGCTGTCAAGGGAGATAGGACTGGCAGCTTAAATCTACTTC-CTTA-C
*
41304544 AATA-C-AG-GAAGACAATA-TC-T-GCTATTTTCAACCTATTCCACTACTGCTCAAGGAGACA
191 --TACCGAGAGAAGACAAGATTCATCG-T-TTTT-AACCTATTCCACTACTGCTCAAGGAGACA
41304602 AGGCTGGTAT
Statistics
Matches: 210, Mismatches: 29, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
261 1 0.00
262 2 0.01
263 9 0.04
264 192 0.91
265 3 0.01
266 1 0.00
267 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (264 bp):
AACCTACTCCACTGCTGCTCAGGGAGATAGGACTGACGACTTAAATCTACTTCCCTCATACATTG
GGAAGATAAGATTCATCGTCTTTGATATGTTCCACTACTATTTAAGGAGACATGATCTACAATCT
TCAACCTATTCCACTGCTGTCAAGGGAGATAGGACTGGCAGCTTAAATCTACTTCCTTACTACCG
AGAGAAGACAAGATTCATCGTTTTTAACCTATTCCACTACTGCTCAAGGAGACATGATCTACAAT
CTTC
Found at i:41305646 original size:55 final size:55
Alignment explanation
Indices: 41305576--41305687 Score: 163
Period size: 55 Copynumber: 2.0 Consensus size: 55
41305566 TTTAAAAAAA
* *
41305576 TTTAATCGTGCCTATCTGACAGACGCGAATCAATT-TTTATATTAAAAAATATTTT
1 TTTAATCGCGCCTATCTAACAGACGCGAATCAATTATTTATATT-AAAAATATTTT
* **
41305631 TTTAATCGCGGCTATCTAACAGGTGCGAATCAATTATTTATATTAAAAATATTTT
1 TTTAATCGCGCCTATCTAACAGACGCGAATCAATTATTTATATTAAAAATATTTT
41305686 TT
1 TT
41305688 GTTTAAATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 43 0.84
56 8 0.16
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (55 bp):
TTTAATCGCGCCTATCTAACAGACGCGAATCAATTATTTATATTAAAAATATTTT
Found at i:41306616 original size:108 final size:106
Alignment explanation
Indices: 41306314--41306633 Score: 381
Period size: 106 Copynumber: 3.0 Consensus size: 106
41306304 ACGACGTGGA
* *
41306314 TTAAAA-TTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
1 TTAAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
* * *
41306378 CACGTTCTCTCGAATTTCCAAACGCAAAACATTACCTTGTT
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
** * * * * *
41306419 TTAAAATTTCGAAAGGATATTTGACTATTTGGCCAAACGAGTAATCGAAACCCAACACGTTAGGG
1 TTAAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
* * * * **
41306484 CACGTTTTTTCGAATTTCCGAACGCGAAATATGGTCTTATT
66 CACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
* * *
41306525 TTGAAAGTTTTAAAAGGGTATTTGGCTATTTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAT
1 TT-AAAATTTTAAAAGGATATTTGGCTA-TTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAG
* * * * *
41306590 GGTACATTTTCTCGATTTTCTAAACGCAAAACATTACCTTATT
64 GGCACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
41306633 T
1 T
41306634 AGAAAAATTT
Statistics
Matches: 173, Mismatches: 39, Indels: 3
0.80 0.18 0.01
Matches are distributed among these distances:
105 6 0.03
106 83 0.48
107 20 0.12
108 64 0.37
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (106 bp):
TTAAAATTTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGG
CACGTTTTCTCGAATTTCCAAACGCAAAACATGACCTTATT
Found at i:41307166 original size:31 final size:30
Alignment explanation
Indices: 41307121--41307178 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
41307111 ATAAAGTTTA
*
41307121 AAATAAAGATATAAATAAGCAAAAAAAAACT
1 AAATAAAGAAATAAATAAG-AAAAAAAAACT
* *
41307152 AAATAAATAAATAAATAAGATAAAAAA
1 AAATAAAGAAATAAATAAGAAAAAAAA
41307179 GGGTTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (30 bp):
AAATAAAGAAATAAATAAGAAAAAAAAACT
Found at i:41311617 original size:27 final size:27
Alignment explanation
Indices: 41311553--41311637 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
41311543 GCTGTGGGCC
*
41311553 CCACCATTGGCGCCTCTCA-ACATGGCA
1 CCACCATTGGCGCCTCTCAGATA-GGCA
* * * *
41311580 CAACTAGTGGCGCCTCTCAGATAGGCT
1 CCACCATTGGCGCCTCTCAGATAGGCA
*
41311607 CCACCATTGGCGCCTCTGAGATAGGCA
1 CCACCATTGGCGCCTCTCAGATAGGCA
41311634 CCAC
1 CCAC
41311638 TACTCTTGTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 45 0.96
28 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.19
Consensus pattern (27 bp):
CCACCATTGGCGCCTCTCAGATAGGCA
Found at i:41313354 original size:31 final size:31
Alignment explanation
Indices: 41313318--41313376 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
41313308 TAATGATTAC
41313318 TGAACTACTCGAAAGTTTTCATTTAAGTCAT
1 TGAACTACTCGAAAGTTTTCATTTAAGTCAT
** *
41313349 TGAACTTGTCGAAAGTTTTTATTTAAGT
1 TGAACTACTCGAAAGTTTTCATTTAAGT
41313377 GGGCTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (31 bp):
TGAACTACTCGAAAGTTTTCATTTAAGTCAT
Found at i:41315676 original size:140 final size:140
Alignment explanation
Indices: 41315424--41315705 Score: 564
Period size: 140 Copynumber: 2.0 Consensus size: 140
41315414 TTTAAAATCT
41315424 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
1 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
41315489 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
66 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
41315554 AATTTGGGTG
131 AATTTGGGTG
41315564 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
1 GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
41315629 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
66 AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
41315694 AATTTGGGTG
131 AATTTGGGTG
41315704 GG
1 GG
41315706 AAATATTTCC
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 142 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.35
Consensus pattern (140 bp):
GGTATTTGGTTTCATCGACGAAGAAAAAGGGCTTGGTTTCTATGAGTGGAAATATGGTCCCCGTA
AAATCGTTTTCGGTTCGATTCGGTTTTATAAAGTAAGATAAAAAGCGTTGGTTCGGTTCGGTTTT
AATTTGGGTG
Found at i:41318637 original size:17 final size:18
Alignment explanation
Indices: 41318615--41318655 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41318605 GTCTTTATAC
*
41318615 TTTACAAATT-TTAAATT
1 TTTACAAATTCTTAAAGT
*
41318632 TTTACAAATTCTTTAAGT
1 TTTACAAATTCTTAAAGT
41318650 TTTACA
1 TTTACA
41318656 TATCATCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTACAAATTCTTAAAGT
Found at i:41323829 original size:3 final size:3
Alignment explanation
Indices: 41323823--41323847 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41323813 CATAATAAAA
41323823 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
41323848 AGAGATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:41339767 original size:186 final size:187
Alignment explanation
Indices: 41339504--41339880 Score: 747
Period size: 186 Copynumber: 2.0 Consensus size: 187
41339494 AATAAAAAAT
41339504 TAATAAAAATATAAAAACAAATAATAATCTATTATATAAAGATTTTTCAAAGAGAAATGAAATTG
1 TAATAAAAATATAAAAACAAATAATAATCTATTATATAAAGATTTTTCAAAGAGAAATGAAATTG
41339569 AATATCATATATGAGAATTACTTTTTTAAAAAACATTAATTTAATTAATTAAATTTATTTAATAC
66 AATATCATATATGAGAATTACTTTTTTAAAAAACATTAATTTAATTAATTAAATTTATTTAATAC
41339634 TATTTGAAAATAACATATTAATAATTTTATTGTAGTTTATTTTTTCTTCTCTTTCCA
131 TATTTGAAAATAACATATTAATAATTTTATTGTAGTTTATTTTTTCTTCTCTTTCCA
41339691 TAATAAAAATAT-AAAACAAATAATAATCTATTATATAAAGATTTTTCAAAGAGAAATGAAATTG
1 TAATAAAAATATAAAAACAAATAATAATCTATTATATAAAGATTTTTCAAAGAGAAATGAAATTG
41339755 AATATCATATATGAGAATTACTTTTTTAAAAAACATTAATTTAATTAATTAAATTTATTTAATAC
66 AATATCATATATGAGAATTACTTTTTTAAAAAACATTAATTTAATTAATTAAATTTATTTAATAC
41339820 TATTTGAAAATAACATATTAATAATTTTATTGTAGTTTATTTTTTCTTCTCTTTCCA
131 TATTTGAAAATAACATATTAATAATTTTATTGTAGTTTATTTTTTCTTCTCTTTCCA
41339877 TAAT
1 TAAT
41339881 TTGTGGGTGC
Statistics
Matches: 190, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
186 178 0.94
187 12 0.06
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (187 bp):
TAATAAAAATATAAAAACAAATAATAATCTATTATATAAAGATTTTTCAAAGAGAAATGAAATTG
AATATCATATATGAGAATTACTTTTTTAAAAAACATTAATTTAATTAATTAAATTTATTTAATAC
TATTTGAAAATAACATATTAATAATTTTATTGTAGTTTATTTTTTCTTCTCTTTCCA
Found at i:41340472 original size:10 final size:10
Alignment explanation
Indices: 41340454--41340513 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
41340444 CTATTTAGAT
*
41340454 TTATTAAAAA
1 TTATAAAAAA
*
41340464 TTAGAAAAAA
1 TTATAAAAAA
*
41340474 ATAT-AAAAA
1 TTATAAAAAA
*
41340483 TTGTAAAAAAA
1 TTAT-AAAAAA
41340494 TTATAAAAAA
1 TTATAAAAAA
41340504 TTATAAAAAA
1 TTATAAAAAA
41340514 ATTTTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 7 0.17
10 26 0.63
11 8 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:41340502 original size:21 final size:21
Alignment explanation
Indices: 41340454--41340543 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
41340444 CTATTTAGAT
* *
41340454 TTATTAAAAATTAGAAAAAAA
1 TTATAAAAAATTATAAAAAAA
*
41340475 -TAT-AAAAATTGTAAAAAAA
1 TTATAAAAAATTATAAAAAAA
41340494 TTATAAAAAATTATAAAAAAA
1 TTATAAAAAATTATAAAAAAA
* **
41340515 TT-TTAAATTTTATAAAAAAAA
1 TTATAAAAAATTAT-AAAAAAA
41340536 TTATAAAA
1 TTATAAAA
41340544 TACATCAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
19 14 0.24
20 14 0.24
21 26 0.45
22 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TTATAAAAAATTATAAAAAAA
Found at i:41340521 original size:11 final size:11
Alignment explanation
Indices: 41340459--41340543 Score: 74
Period size: 11 Copynumber: 8.2 Consensus size: 11
41340449 TAGATTTATT
*
41340459 AAAAATTAGAA
1 AAAAATTATAA
41340470 AAAAA-TAT--
1 AAAAATTATAA
*
41340478 AAAAATTGTAA
1 AAAAATTATAA
41340489 AAAAATTAT-A
1 AAAAATTATAA
41340499 AAAAATTATAA
1 AAAAATTATAA
*
41340510 AAAAATT-T-T
1 AAAAATTATAA
**
41340519 AAATTTTATAAA
1 AAAAATTAT-AA
41340531 AAAAATTATAA
1 AAAAATTATAA
41340542 AA
1 AA
41340544 TACATCAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
8 5 0.09
9 7 0.12
10 14 0.24
11 25 0.43
12 7 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:41340759 original size:19 final size:18
Alignment explanation
Indices: 41340735--41340799 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
41340725 GTACGATAAT
41340735 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTAC-AA
* *
41340754 TTTTAT-ATTTCTTTATATT
1 TTTTATAATTT-TTTACA-A
41340773 TTTTATAATTTTCTTACAA
1 TTTTATAATTTT-TTACAA
*
41340792 CTTTATAA
1 TTTTATAA
41340800 AACTTATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 5 0.14
19 24 0.65
20 8 0.22
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTTTACAA
Found at i:41343482 original size:89 final size:87
Alignment explanation
Indices: 41343370--41343559 Score: 246
Period size: 89 Copynumber: 2.2 Consensus size: 87
41343360 TTTTTTCTTT
* * *
41343370 AAAAAGCAATTAAG-TCCC-CT-TTTTTT-CACTCAATT-GAGCACTTAAACTTTTAAAATGCAT
1 AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGA-CACCTAAACTTTCAAAATGCAT
* *
41343430 CAAAAAGGCCCTCAAACTTCTTCAA
65 CAAAAA-ACCCTCAAAATTCTTC-A
* *
41343455 AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGATACCTGAACTTTCAAAATGCATC
1 AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGACACCTAAACTTTCAAAATGCATC
*
41343520 AAAAAACCCTCAAAATTTTTCA
66 AAAAAACCCTCAAAATTCTTCA
41343542 AAAAAGCAATTAAGCCCC
1 AAAAAGCAATTAAGCCCC
41343560 TACTCTTATT
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
85 14 0.15
86 3 0.03
87 21 0.23
88 19 0.21
89 33 0.36
90 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.28
Consensus pattern (87 bp):
AAAAAGCAATTAAGCCCCCGCTCTTTTTTCCACTCAATTGGACACCTAAACTTTCAAAATGCATC
AAAAAACCCTCAAAATTCTTCA
Found at i:41348954 original size:47 final size:46
Alignment explanation
Indices: 41348793--41348957 Score: 177
Period size: 47 Copynumber: 3.5 Consensus size: 46
41348783 GCTTGACCGA
* * * * *
41348793 TGGTTTATCCACAACGTATTTTACTCGGCATTCACCTGTTCGACTAG
1 TGGTTTATCCACAACATATTTTAGTC-ACAATCACCTGCTCGACTAG
* * * *
41348840 TGGTTTGTCCACAACATATCTTAATCGACAATCATCTGCTCGACTAG
1 TGGTTTATCCACAACATATTTTAGTC-ACAATCACCTGCTCGACTAG
* * *
41348887 TGGTTTATCCACAACATATTTTAGTCATCAGTCACCTGCTCTACCAG
1 TGGTTTATCCACAACATATTTTAGTCA-CAATCACCTGCTCGACTAG
* *
41348934 TGGTATATCCACAACGTATTTTAG
1 TGGTTTATCCACAACATATTTTAG
41348958 CAGCTTTTAT
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
46 1 0.01
47 99 0.99
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (46 bp):
TGGTTTATCCACAACATATTTTAGTCACAATCACCTGCTCGACTAG
Found at i:41352121 original size:24 final size:24
Alignment explanation
Indices: 41352079--41352130 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
41352069 AATCAAAATC
** *
41352079 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
41352103 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
41352127 AAAT
1 AAAT
41352131 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41356471 original size:23 final size:24
Alignment explanation
Indices: 41356423--41356473 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41356413 AGTCAAAGTC
* *
41356423 AAATATATTATGTTAATAAATGCT
1 AAATATATTATCTTAATAAATACT
41356447 AAATATATTATCTT-ATAAATACT
1 AAATATATTATCTTAATAAATACT
41356470 AAAT
1 AAAT
41356474 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATATTATCTTAATAAATACT
Found at i:41357347 original size:2 final size:2
Alignment explanation
Indices: 41357340--41357365 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41357330 CATACCATAT
41357340 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
41357366 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:41357370 original size:2 final size:2
Alignment explanation
Indices: 41357365--41357389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41357355 ACACACACAC
41357365 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41357390 CACCACCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41359525 original size:31 final size:31
Alignment explanation
Indices: 41359490--41359552 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
41359480 ATTTAACCAC
41359490 TAAGTTTTCATTTTACGCGATTAAGCCCTTT
1 TAAGTTTTCATTTTACGCGATTAAGCCCTTT
*
41359521 TAAGTTTTCATTTTACTCGATTAAGCCCTTT
1 TAAGTTTTCATTTTACGCGATTAAGCCCTTT
41359552 T
1 T
41359553 CTCAAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (31 bp):
TAAGTTTTCATTTTACGCGATTAAGCCCTTT
Found at i:41359614 original size:14 final size:15
Alignment explanation
Indices: 41359595--41359623 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41359585 TCACGAAACT
41359595 TTCACACAT-ATAAA
1 TTCACACATAATAAA
41359609 TTCACACATAATAAA
1 TTCACACATAATAAA
41359624 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:41365800 original size:31 final size:31
Alignment explanation
Indices: 41365756--41365819 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
41365746 ATCACTCAAC
*
41365756 TTCAAAAGGTTTTAAAATAA-TCATTGAACTA
1 TTCAAAAAGTTTT-AAATAAGTCATTGAACTA
* **
41365787 TTCAAAAATTTTTATTTAAGTCATTGAACTA
1 TTCAAAAAGTTTTAAATAAGTCATTGAACTA
41365818 TT
1 TT
41365820 AAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (31 bp):
TTCAAAAAGTTTTAAATAAGTCATTGAACTA
Found at i:41365873 original size:2 final size:2
Alignment explanation
Indices: 41365866--41365897 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
41365856 ACTATTTATC
41365866 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41365898 TGGCCATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41365881 original size:12 final size:12
Alignment explanation
Indices: 41365866--41365897 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41365856 ACTATTTATC
41365866 ATATATATATAT
1 ATATATATATAT
41365878 ATATATA-ATAT
1 ATATATATATAT
41365889 A-ATATATAT
1 ATATATATAT
41365898 TGGCCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 7 0.37
12 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATATAT
Found at i:41370353 original size:14 final size:14
Alignment explanation
Indices: 41370299--41370355 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
41370289 AATGGTCAAA
41370299 TTATAGTTTTAATCCTT
1 TTATA-TTTTAAT-C-T
41370316 TTATATTTTCAA-CT
1 TTATATTTT-AATCT
* *
41370330 TTAAAATTTAATCT
1 TTATATTTTAATCT
41370344 TTATATTTTAAT
1 TTATATTTTAAT
41370356 TTTTGACATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
13 2 0.06
14 20 0.59
15 1 0.03
16 4 0.12
17 7 0.21
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.58
Consensus pattern (14 bp):
TTATATTTTAATCT
Found at i:41373242 original size:20 final size:20
Alignment explanation
Indices: 41373206--41373243 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41373196 CTTAATTAGT
*
41373206 TTATAAAATTTAAAAAAGCA
1 TTATAAAATGTAAAAAAGCA
41373226 TTAT-AAATGTAACAAAAG
1 TTATAAAATGTAA-AAAAG
41373244 GAAATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (20 bp):
TTATAAAATGTAAAAAAGCA
Found at i:41375216 original size:167 final size:164
Alignment explanation
Indices: 41374478--41375289 Score: 773
Period size: 167 Copynumber: 4.9 Consensus size: 164
41374468 TTCGAAATTG
* * * * * *
41374478 TTGTGTCAAATCTTTTGAATTTTGAATTCTTCGCGTAGTTTAATCTGATCTAAATCTCGGAAGCG
1 TTGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTAAATCTCAGAAGCG
* * * *
41374543 TCGTGAGTTCGTTCGTTTGCTCAGATTTGTATTTCTCAAATTGAATTTATGTTTGTTATAGATTG
65 -C-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTG
**
41374608 GATTTAGATTTCTCCTTTAAGTGTTGATCTGCTCAGAAAT
128 GATTTAGA-TTCT--TTTTTGTGTTGATCTGCTCAGAAAT
* * * * *
41374648 TGATGTGTCAAATCTTTTGAATTCTGAATTATTCGCGTAGTGGT-ATCTGATCTGAATCTCTG-A
1 T--TGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGT-GTCATCTGATCTAAATCTCAGAA
* * * *
41374711 TC-TTGAGTTCGTTGGTTTG-T---A-----A-TTCTCGAACTGAATTTATGTTTGTTACAGATT
62 GCGCTGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATT
* *
41374765 GGATTTAGATTATTTTTTACATGTT-ACTCTGCTCAGAAATT
127 GGATTTAGATTCTTTTTT--GTGTTGA-TCTGCTCAGAAA-T
* *
41374806 GTTGTGTCAAATCATTTTGAA---T---TATTCGA-GTAGAGTCATCTGATCTAAATCTCGGAA-
1 -TTGTGTCAAAT-ATTTTGAATTTTGAATATTC-ACGTAGTGTCATCTGATCTAAATCTCAGAAG
*
41374863 -G-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTTTCGAATTGAATTTATGTTTGTTACAGATTG
63 CGCTGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTG
41374926 GATTTAGATTATCTTCTTTTG-GTTGATCTGCTCAGAAAT
128 GATTTAGA-T-TCTT-TTTTGTGTTGATCTGCTCAGAAAT
* * *
41374965 TGTCGTGTCAAATCTTTTGAATTTTGAATTATTCGCGTAGTGTCATCTGATCTAATTCTCAGAAG
1 T-T-GTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTAAATCTCAGAAG
* * * * * *
41375030 CGTCGTGAGTTCCTTGGTTTGCTCGGATTTGTATTTCTCTATTTGAATTTATGTTTGTTACGGAT
63 CG-C-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGAT
*
41375095 TGGATTTAGCTTCTTTTTATGTGTTGATCTGCTCAGAAA-
126 TGGATTTAGATTCTTTTT-TGTGTTGATCTGCTCAGAAAT
41375134 TTGTGTCAAATATTTTGAATTTTGAACTATTCACGTAGTGTCATCTGATC-AGAATCTCAGAAGC
1 TTGTGTCAAATATTTTGAATTTTGAA-TATTCACGTAGTGTCATCTGATCTA-AATCTCAGAAGC
* * *
41375198 GACTTGGGCTCGTTGGTTTGCTCAGATTTGTATATCTCGAAATGAATTTATGTTTGTTACAGATT
64 G-C-TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATT
* **
41375263 GGACTT-GGGT-TTTTTTGTGTTGATCTG
127 GGATTTAGATTCTTTTTTGTGTTGATCTG
41375290 GTCAATTCTG
Statistics
Matches: 541, Mismatches: 56, Indels: 96
0.78 0.08 0.14
Matches are distributed among these distances:
150 17 0.03
151 26 0.05
152 1 0.00
154 1 0.00
155 4 0.01
156 1 0.00
157 29 0.05
158 47 0.09
159 12 0.02
160 63 0.12
161 2 0.00
162 4 0.01
163 4 0.01
164 13 0.02
165 5 0.01
166 33 0.06
167 116 0.21
168 20 0.04
169 7 0.01
170 19 0.04
171 64 0.12
172 52 0.10
173 1 0.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (164 bp):
TTGTGTCAAATATTTTGAATTTTGAATATTCACGTAGTGTCATCTGATCTAAATCTCAGAAGCGC
TGAGCTCGTTGGTTTGCTCAGATTTGTATTTCTCGAATTGAATTTATGTTTGTTACAGATTGGAT
TTAGATTCTTTTTTGTGTTGATCTGCTCAGAAAT
Found at i:41378689 original size:3 final size:3
Alignment explanation
Indices: 41378681--41378757 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
41378671 TTGTGGAGTT
41378681 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41378729 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41378758 TATATTTNNN
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41382741 original size:21 final size:21
Alignment explanation
Indices: 41382717--41382759 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41382707 ACCTTTTCTG
*
41382717 AAGTTAAAAGTCAAAACCATT
1 AAGTTAAAAGGCAAAACCATT
*
41382738 AAGTTAAAAGGCAAATCCATT
1 AAGTTAAAAGGCAAAACCATT
41382759 A
1 A
41382760 TATTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACCATT
Found at i:41383089 original size:16 final size:17
Alignment explanation
Indices: 41383068--41383106 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41383058 AGTTGAAAAA
41383068 AGATAAAAAAAT-TATT
1 AGATAAAAAAATATATT
*
41383084 AGATAAAATAATATATT
1 AGATAAAAAAATATATT
41383101 A-ATAAA
1 AGATAAA
41383107 GTTGTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (17 bp):
AGATAAAAAAATATATT
Found at i:41405096 original size:50 final size:50
Alignment explanation
Indices: 41405034--41405615 Score: 497
Period size: 50 Copynumber: 11.6 Consensus size: 50
41405024 CGTAACTTTT
* * *
41405034 GGAAGTAAGATTCG-TCATTGTGGCTTTAATCTTTTTAACTACAATGTCGG
1 GGAAGCAAGATTCGCT-GTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * ** ** * *
41405084 GGAAGCATGATTCACTGTTGTGGCTTTAATCTATTCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* *
41405134 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * ** ** * *
41405184 GGAAGCATGATTCGCTGTTGTGGCCTTAATCTATTCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * * *
41405234 TGAGGCAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGA
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * ** ** * *
41405284 GGAAGCAAGATTTGCCGTTGTGGCTTTAATCTCTTCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * *
41405334 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGTAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * * ** * * *
41405384 GGAAGCATGATTCGCTGTTATGGTTTTAATCTGTTCCACTGCATTGCCTG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * *
41405434 GGAGGCAAGATTCACTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* * * * ** * *
41405484 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGC-ATCGCCTGA
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAAT-GTC-GG
* * *
41405535 GG-AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
* *
41405584 GGAAGCAAGATTC-ATCGATGTGGCTTTAATCT
1 GGAAGCAAGATTCGCT-GTTGTGGCTTTAATCT
41405616 GTTCGACTGC
Statistics
Matches: 402, Mismatches: 124, Indels: 12
0.75 0.23 0.02
Matches are distributed among these distances:
49 6 0.01
50 390 0.97
51 6 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (50 bp):
GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
Found at i:41405207 original size:100 final size:100
Alignment explanation
Indices: 41405034--41405651 Score: 819
Period size: 100 Copynumber: 6.2 Consensus size: 100
41405024 CGTAACTTTT
* * * * *
41405034 GGAAGTAAGATTCG-TCATTGTGGCTTTAATCTTTTTAACTACAATGTCGGGGAAGCATGATTCA
1 GGAAGTAAGATTCGCT-GTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCG
*
41405098 CTGTTGTGGCTTTAATCTATTCCACTGCACCGCCTG
65 CTGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
41405134 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* *
41405199 TGTTGTGGCCTTAATCTATTCCACTGCACCGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
* * * * * * * *
41405234 TGAGGCAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGAGGAAGCAAGATTTGC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* *
41405299 CGTTGTGGCTTTAATCTCTTCCACTGCACCGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
* * *
41405334 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGTAATGTCGGGGAAGCATGATTCGC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* * **
41405399 TGTTATGGTTTTAATCTGTTCCACTGCATTGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
* * * * *
41405434 GGAGGCAAGATTCACTGTTGTAGCTTTAATCTTTTTAACCGCAATGTCGGGGAAGCAAGATTCAC
1 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
* * *
41405499 CGATGTGGCTTTAATCTGTTCCACTGCATCGCCTG
66 TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
41405534 AGG-AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTC-
1 -GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCG
* * * * *
41405597 ATCGATGTGGCTTTAATCTGTTCGACTGCAGCGCCAG
65 CT-GTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
41405634 GGAAATAAGATTCGCTGT
1 GGAAGTAAGATTCGCTGT
41405652 CTTCACCGAT
Statistics
Matches: 458, Mismatches: 56, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
99 2 0.00
100 453 0.99
101 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (100 bp):
GGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGC
TGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
Found at i:41409742 original size:47 final size:47
Alignment explanation
Indices: 41409681--41409770 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
41409671 TCATTTTTCA
* * *
41409681 TTTTTTGGATTCAAAGTGCCCTTTGAGGATTTTCACTTTGATCATTT
1 TTTTTTGGACTCAAAGCGCCCTTTGAGGATTTTCACCTTGATCATTT
* *
41409728 TTTTTTGGACTCAAAGCGCCCTTTGTGGGTTTTCACCTTGATC
1 TTTTTTGGACTCAAAGCGCCCTTTGAGGATTTTCACCTTGATC
41409771 CTTTCTCTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.46
Consensus pattern (47 bp):
TTTTTTGGACTCAAAGCGCCCTTTGAGGATTTTCACCTTGATCATTT
Found at i:41420434 original size:14 final size:13
Alignment explanation
Indices: 41420411--41420454 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
41420401 CCTGCGGTAG
*
41420411 GGTTTTGGGTTATT
1 GGTTTAGGGTT-TT
*
41420425 GGTTTAGGGTTTAG
1 GGTTTAGGGTTT-T
41420439 GGTTTAGGGTTTT
1 GGTTTAGGGTTTT
41420452 GGT
1 GGT
41420455 ATTTTTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (13 bp):
GGTTTAGGGTTTT
Found at i:41420435 original size:7 final size:7
Alignment explanation
Indices: 41420425--41420450 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41420415 TTGGGTTATT
41420425 GGTTTAG
1 GGTTTAG
41420432 GGTTTAG
1 GGTTTAG
41420439 GGTTTAG
1 GGTTTAG
41420446 GGTTT
1 GGTTT
41420451 TGGTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:41420449 original size:21 final size:21
Alignment explanation
Indices: 41420408--41420450 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41420398 TCTCCTGCGG
* *
41420408 TAGGGTTTTGGGTTATTGGTT
1 TAGGGTTTAGGGTTATGGGTT
41420429 TAGGGTTTAGGGTT-TAGGGTT
1 TAGGGTTTAGGGTTAT-GGGTT
41420450 T
1 T
41420451 TGGTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.49
Consensus pattern (21 bp):
TAGGGTTTAGGGTTATGGGTT
Found at i:41420718 original size:46 final size:46
Alignment explanation
Indices: 41420668--41420836 Score: 132
Period size: 46 Copynumber: 3.6 Consensus size: 46
41420658 GTTTTTAAGG
*
41420668 AAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
1 AAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
* * ** * * *
41420714 AAAAAAATTGAAAATCATATTAGGATTTAAAGTTA--AGAGT-TTTTAATA
1 --AAAAATT--AAAT-AAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
* * *
41420762 AAAAATTAAATAAATTAGAGTTCAGGGTTACTTGAGTAAATTAATT
1 AAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
*
41420808 ATAAATTTATAATAAATTA--GTTTAGGGTT
1 A-AAAATTA-AATAAATTAGGGTTTAGGGTT
41420837 TAGTGTTTAG
Statistics
Matches: 93, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
43 13 0.14
44 4 0.04
45 4 0.04
46 22 0.24
47 6 0.06
48 21 0.23
49 4 0.04
50 4 0.04
51 15 0.16
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (46 bp):
AAAAATTAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATT
Found at i:41420759 original size:94 final size:92
Alignment explanation
Indices: 41420573--41420881 Score: 328
Period size: 86 Copynumber: 3.3 Consensus size: 92
41420563 GTGTATATTA
*
41420573 TTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTTAATT-AAAAATTT
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAA-TTTAATTAAAAAATTT
*
41420637 AAAAATCAAATTAGGA--T-AAG---GG
65 AAAAATCATATTAGGATTTAAAGTTAGG
* * *
41420659 TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAATTG
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTTA
41420724 AAAATCATATTAGGATTTAAAGTTAAGAG
66 AAAATCATATTAGGATTTAAAGTT-AG-G
* * * * * * *
41420753 TTTTTAATAAAAAATTAAATAAATTAGAGTTCAGGGTTACTTGAGTAAATTAATTATAAATTTAT
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATT-T
* * **
41420818 AATAAATTAGT-TTAGGGTTTAGTGTTTAGGG
65 AA-AAATCA-TATTAGGATTTAAAG-TTA-GG
*
41420849 TTTTTAAGTAAAAACTCAAATAAATTAGGGTTT
1 TTTTTAAG-AAAAAATCAAATAAATTAGGGTTT
41420882 GGGATTTACG
Statistics
Matches: 184, Mismatches: 24, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
85 7 0.04
86 67 0.36
88 1 0.01
89 3 0.02
93 1 0.01
94 55 0.30
95 2 0.01
96 24 0.13
97 24 0.13
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (92 bp):
TTTTTAAGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTTA
AAAATCATATTAGGATTTAAAGTTAGG
Found at i:41421199 original size:125 final size:126
Alignment explanation
Indices: 41420924--41421346 Score: 722
Period size: 126 Copynumber: 3.4 Consensus size: 126
41420914 TAATTTAAAG
* * * *
41420924 AAGCTCGCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATTTCAAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
41420989 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* *
41421050 AAGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTACTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
*
41421115 CTGAGCAAACAGTGTC-AAAATGCTTTAAGCAGGATGTTTTGTCAGCAGAAGTACTGAAAA
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
**
41421175 AAGCTTTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
* *
41421240 TTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAG
66 CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
*
41421301 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTACCTCCTGAAAAAA
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAA
41421347 GCTCCTACGT
Statistics
Matches: 278, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 118 0.42
126 160 0.58
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
CTGAGCAAACAGTGTCAAAAATGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:41423677 original size:41 final size:41
Alignment explanation
Indices: 41423627--41423714 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
41423617 GGCTTAGCAC
* * *
41423627 CTAGAAGGCTTATTGCCAGTGAAACAATTCAGACTTTATGT
1 CTAGCAGGCTTACTGCCAGTGAAACAATTCAGACTATATGT
* *
41423668 CTAGCAGGCTTACTGCCGGTGAAACATTTCAGACTATATGT
1 CTAGCAGGCTTACTGCCAGTGAAACAATTCAGACTATATGT
41423709 CTAGCA
1 CTAGCA
41423715 AGCTAAGTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (41 bp):
CTAGCAGGCTTACTGCCAGTGAAACAATTCAGACTATATGT
Found at i:41423726 original size:41 final size:41
Alignment explanation
Indices: 41423640--41423726 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
41423630 GAAGGCTTAT
* * * *
41423640 TGCCAGTGAAACAATTCAGACTTTATGTCTAGCAGGCTTAC
1 TGCCGGTGAAACAATTCAGACTATATGTCTAGCAAGCTAAC
* *
41423681 TGCCGGTGAAACATTTCAGACTATATGTCTAGCAAGCTAAG
1 TGCCGGTGAAACAATTCAGACTATATGTCTAGCAAGCTAAC
41423722 TGCCG
1 TGCCG
41423727 ATGTATTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (41 bp):
TGCCGGTGAAACAATTCAGACTATATGTCTAGCAAGCTAAC
Found at i:41426134 original size:70 final size:70
Alignment explanation
Indices: 41425921--41426251 Score: 281
Period size: 72 Copynumber: 4.6 Consensus size: 70
41425911 ACCGATGGTA
* * * * * * * * *
41425921 TGAGATCCGACATATGTTGCGAATTCTCTCAAGCTTGTGAGAGCAGAATGGAATCTTTCTTT-GC
1 TGAGATCTGGCATATGTTGC--ATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATC
41425985 TGATGGCT
64 TG-TGGCT
* * * * *
41425993 TGAGATC-GGACATATGTTACGAATTCTTTAAAGCTTGTGTGAGCAGCATCGAACCATTCTTTAT
1 TGAGATCTGG-CATATGTT--GCATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTAT
41426057 -TGATGGCT
63 CTG-TGGCT
* * * * *
41426065 TGAGATCTGGCATATGTTGCATTCTCTGAAGTTTGTGTAAGCATCGTGGAATCATTCTTCATCTG
1 TGAGATCTGGCATATGTTGCATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATCTG
41426130 TGGCT
66 TGGCT
* **
41426135 TGAGATTTAACATATGTTGCGGATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATC
1 TGAGATCTGGCATATGTTGC--ATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATC
*
41426200 GGTGGCT
64 TGTGGCT
*** * * *
41426207 TGAGATCCAACACATGTTATGGATTCTCTGAAGCTTGTGTGAGCA
1 TGAGATCTGGCATATG-T-TGCATTCTCTGAAGTTTGTGTGAGCA
41426252 ACACCCAATA
Statistics
Matches: 215, Mismatches: 34, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
70 56 0.26
71 3 0.01
72 150 0.70
73 3 0.01
74 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (70 bp):
TGAGATCTGGCATATGTTGCATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCTTTATCTG
TGGCT
Found at i:41426224 original size:142 final size:144
Alignment explanation
Indices: 41425988--41426251 Score: 352
Period size: 142 Copynumber: 1.8 Consensus size: 144
41425978 TCTTTGCTGA
* *
41425988 TGGCTTGAGATCGGACATATGTTACGAATTCTTTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
1 TGGCTTGAGATCGAACATATGTTACGAATTCTCTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
* *** * *
41426053 TTATTGATGGCTTGAGATCTGGCATATG-T-TGCATTCTCTGAAGTTTGTGTAAGCATCGTGGAA
66 TTATCGATGGCTTGAGATCCAACACATGTTATGCATTCTCTGAAGCTTGTGTAAGCATCGTGGAA
41426116 TCATTCTTCATCTG
131 TCATTCTTCATCTG
** * * * * *
41426130 TGGCTTGAGATTTAACATATGTTGCGGATTCTCTGAAGTTTGTGTGAGCAGCATCGAATCATTCT
1 TGGCTTGAGATCGAACATATGTTACGAATTCTCTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
* * *
41426195 TTATCGGTGGCTTGAGATCCAACACATGTTATGGATTCTCTGAAGCTTGTGTGAGCA
66 TTATCGATGGCTTGAGATCCAACACATGTTATGCATTCTCTGAAGCTTGTGTAAGCA
41426252 ACACCCAATA
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
142 78 0.76
143 1 0.01
144 23 0.23
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (144 bp):
TGGCTTGAGATCGAACATATGTTACGAATTCTCTAAAGCTTGTGTGAGCAGCATCGAACCATTCT
TTATCGATGGCTTGAGATCCAACACATGTTATGCATTCTCTGAAGCTTGTGTAAGCATCGTGGAA
TCATTCTTCATCTG
Found at i:41429177 original size:27 final size:27
Alignment explanation
Indices: 41429116--41429170 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
41429106 AATTGATAAA
41429116 TATAGAACATGGCCACGGGTTGTTTGT
1 TATAGAACATGGCCACGGGTTGTTTGT
41429143 TATAGAACATGGCCACGGGTTGTTTGT
1 TATAGAACATGGCCACGGGTTGTTTGT
41429170 T
1 T
41429171 CTCGAACGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.35
Consensus pattern (27 bp):
TATAGAACATGGCCACGGGTTGTTTGT
Done.