Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 177 of 290
Found at i:57419502 original size:37 final size:37
Alignment explanation
Indices: 57419449--57419549 Score: 175
Period size: 37 Copynumber: 2.7 Consensus size: 37
57419439 CGAATAGTCC
* *
57419449 CCACACGTAGTTATCGGGTCTTACCCGGGCAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
57419486 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
57419523 CCACACGTAGTCATCGGGTCTTACCCG
1 CCACACGTAGTCATCGGGTCTTACCCG
57419550 AAATATATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:57419750 original size:48 final size:48
Alignment explanation
Indices: 57419692--57419789 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
57419682 ATATACACAC
* *
57419692 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTCCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
57419740 ATCTCATACATGTTCCACATTAGCCATTCGGCTTTACCACGTATACAT
1 ATCTCATACATATTCCACACTAGCCATTCGGCTTTACCACATATACAT
57419788 AT
1 AT
57419790 ATATTTATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.34
Consensus pattern (48 bp):
ATCTCATACATATTCCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:57425189 original size:27 final size:26
Alignment explanation
Indices: 57425149--57425260 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
57425139 AGGAAGCGTC
*
57425149 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
57425176 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
57425203 CTGATGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
57425231 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
57425257 CTGG
1 CTGG
57425261 CAGCCATGCA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.69
28 16 0.22
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:57425253 original size:54 final size:54
Alignment explanation
Indices: 57425153--57425259 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
57425143 AGCGTCCTGG
*
57425153 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCTGA
1 TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTGA
* * *
57425207 TGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTCTG
1 TGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTCTG
57425260 GCAGCCATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 30 0.62
55 18 0.38
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (54 bp):
TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTGA
Found at i:57428678 original size:70 final size:70
Alignment explanation
Indices: 57428560--57428695 Score: 245
Period size: 70 Copynumber: 1.9 Consensus size: 70
57428550 TTGCATGCCC
*
57428560 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTTCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
57428625 TATTG
66 TATTG
* *
57428630 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
57428695 T
66 T
57428696 GATTTAATTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TATTG
Found at i:57430632 original size:21 final size:18
Alignment explanation
Indices: 57430590--57430634 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
57430580 TTTTTCAAAC
57430590 TCTTTTTCAAATCCTCTT
1 TCTTTTTCAAATCCTCTT
*
57430608 TCTTTTATCACATCACTCATT
1 TCTTTT-TCAAATC-CTC-TT
57430629 TCTTTT
1 TCTTTT
57430635 GTACTCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTTTTCAAATCCTCTT
Found at i:57430768 original size:15 final size:16
Alignment explanation
Indices: 57430743--57430774 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
57430733 TATCTCACAC
57430743 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
57430759 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
57430774 T
1 T
57430775 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:57431650 original size:17 final size:17
Alignment explanation
Indices: 57431628--57431670 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
57431618 AATCACTCTT
*
57431628 TTTTTTTTCAATTTCG-A
1 TTTTTTTT-AATTCCGAA
57431645 TTTTTTTTAATTCCGAA
1 TTTTTTTTAATTCCGAA
57431662 TTTCTTTTT
1 TTT-TTTTT
57431671 TTCTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 12 0.52
18 5 0.22
ACGTcount: A:0.16, C:0.12, G:0.05, T:0.67
Consensus pattern (17 bp):
TTTTTTTTAATTCCGAA
Found at i:57431748 original size:13 final size:12
Alignment explanation
Indices: 57431730--57431786 Score: 71
Period size: 13 Copynumber: 4.7 Consensus size: 12
57431720 GAATACAAAC
57431730 TTTTTTTTTTGAA
1 TTTTTTTTTTG-A
57431743 TTTTTTTTTTGA
1 TTTTTTTTTTGA
*
57431755 TTTTTTTTTTCAA
1 TTTTTTTTTT-GA
*
57431768 GTTTTTTTTT-A
1 TTTTTTTTTTGA
57431779 TTTTTTTT
1 TTTTTTTT
57431787 ACAATACCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 8 0.20
12 11 0.28
13 21 0.52
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTGA
Found at i:57431758 original size:25 final size:24
Alignment explanation
Indices: 57431730--57431786 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 24
57431720 GAATACAAAC
* *
57431730 TTTTTTTTTTGAATTTTTTTTTTGA
1 TTTTTTTTTTCAAGTTTTTTTTT-A
57431755 TTTTTTTTTTCAAGTTTTTTTTTA
1 TTTTTTTTTTCAAGTTTTTTTTTA
57431779 TTTTTTTT
1 TTTTTTTT
57431787 ACAATACCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.11, C:0.02, G:0.05, T:0.82
Consensus pattern (24 bp):
TTTTTTTTTTCAAGTTTTTTTTTA
Found at i:57433048 original size:70 final size:70
Alignment explanation
Indices: 57432930--57433066 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
57432920 TTGCATGCCC
*
57432930 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTTCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
57432995 TGTTG
66 TGTTG
* *
57433000 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
57433065 TG
66 TG
57433067 ATTTAATTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:57434065 original size:21 final size:20
Alignment explanation
Indices: 57434039--57434078 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
57434029 ACTAGCTCAA
*
57434039 TGAGCTAGCTTTGTGTTGAAT
1 TGAGCT-GCTTTGAGTTGAAT
*
57434060 TGAGCTTCTTTGAGTTGAA
1 TGAGCTGCTTTGAGTTGAA
57434079 ATGAACTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (20 bp):
TGAGCTGCTTTGAGTTGAAT
Found at i:57436047 original size:14 final size:14
Alignment explanation
Indices: 57436028--57436058 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
57436018 CTATTTGAAC
57436028 CTTTCTTAACCTTT
1 CTTTCTTAACCTTT
*
57436042 CTTTCTTAGCCTTT
1 CTTTCTTAACCTTT
57436056 CTT
1 CTT
57436059 CAACTATCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.29, G:0.03, T:0.58
Consensus pattern (14 bp):
CTTTCTTAACCTTT
Found at i:57437838 original size:27 final size:27
Alignment explanation
Indices: 57437757--57437908 Score: 120
Period size: 27 Copynumber: 5.8 Consensus size: 27
57437747 TTAGTTTACC
* * *
57437757 AAATTACTGAAATACCC-CCAGTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
57437783 AAATTACC-AAAGTA--C-CGGTTTATA
1 AAATTACCGAAA-TACCCTCGATTTGTA
* *
57437807 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
57437834 AAATTACCGAAATACCCT-AAGTTTGCA
1 AAATTACCGAAATACCCTCGA-TTTGTA
* *
57437861 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
57437888 AAATTATC-AAAGTACCCTCGA
1 AAATTACCGAAA-TACCCTCGA
57437909 ATTACAAAAT
Statistics
Matches: 101, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
24 16 0.16
25 6 0.06
26 14 0.14
27 64 0.63
28 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:57437904 original size:54 final size:53
Alignment explanation
Indices: 57437748--57437920 Score: 174
Period size: 54 Copynumber: 3.3 Consensus size: 53
57437738 TAGAATACTT
* * *
57437748 TAGTTTACCAAATTACTGAAATACCC-CCAGTTGTAAAATTACCAAAGTA-CC
1 TAGTTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCC
* * ** * *
57437799 -GGTTTATAAAATTACCCAAATATCCTCGATTTGTAAAATTACCGAAA-TACCC
1 TAGTTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTACC-AAAGTACCC
* *
57437851 TAAGTTTGCAAAATTACTGAAATACCCTCGACTTGTAAAATTATCAAAGTACCC
1 T-AGTTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCC
* *
57437905 TCGAATTACAAAATTA
1 TAG-TTTACAAAATTA
57437921 ATGTTTTACC
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
50 19 0.20
51 17 0.18
52 5 0.05
53 4 0.04
54 51 0.53
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (53 bp):
TAGTTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCC
Found at i:57437917 original size:27 final size:27
Alignment explanation
Indices: 57437806--57438084 Score: 79
Period size: 27 Copynumber: 10.3 Consensus size: 27
57437796 ACCGGTTTAT
* * * **
57437806 AAAATTACCCAAATATCCTCGATTTGT
1 AAAATTACTCAAATACCCTCGAATTAC
*
57437833 AAAATTAC-CGAAATACCCT--AAGTTTGC
1 AAAATTACTC-AAATACCCTCGAA--TTAC
* * **
57437860 AAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACTCAAATACCCTCGAATTAC
57437887 AAAATTA-TCAAAGTACCCTCGAATTAC
1 AAAATTACTCAAA-TACCCTCGAATTAC
* **** *
57437914 AAAATTAATGTTTTACCCTCGATTTAC
1 AAAATTACTCAAATACCCTCGAATTAC
* * ** * * * *
57437941 AGAATTA-TTATTTTACCTTTGATTTAT
1 AAAATTACTCA-AATACCCTCGAATTAC
** *
57437968 AAAATTAC-CATTTTACCCTCGATTTAC
1 AAAATTACTCA-AATACCCTCGAATTAC
*** *
57437995 AAAATTA-TCGTTTTACCCTCGATTTAC
1 AAAATTACTC-AAATACCCTCGAATTAC
** *
57438022 AAAATTACT-ATTTTACCCTCGATTTAC
1 AAAATTACTCA-AATACCCTCGAATTAC
**** *
57438049 AAAATTACTGTTTTACCCTCGATTTAC
1 AAAATTACTCAAATACCCTCGAATTAC
57438076 AAAATTACT
1 AAAATTACT
57438085 ATTTTACCCT
Statistics
Matches: 208, Mismatches: 29, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
25 1 0.00
26 6 0.03
27 198 0.95
28 2 0.01
29 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.37
Consensus pattern (27 bp):
AAAATTACTCAAATACCCTCGAATTAC
Found at i:57438089 original size:27 final size:27
Alignment explanation
Indices: 57437900--57438198 Score: 393
Period size: 27 Copynumber: 11.1 Consensus size: 27
57437890 ATTATCAAAG
* *
57437900 TACCCTCGAATTACAAAATTAATGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
57437927 TACCCTCGATTTACAGAATTATTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * * **
57437954 TACCTTTGATTTATAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTT
57437981 TACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
*
57438008 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
57438035 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
57438062 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
57438089 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
57438116 TACCCTCGATTGACAGAATTATTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
57438143 TACCCTCTATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
57438170 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
57438197 TA
1 TA
57438199 TCGGAGCTGC
Statistics
Matches: 237, Mismatches: 33, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
27 236 1.00
28 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:57442870 original size:16 final size:17
Alignment explanation
Indices: 57442851--57442887 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
57442841 AGAAAGTTGT
*
57442851 AAAAAAATAA-AAGAAG
1 AAAAAAATAAGAAAAAG
57442867 AAAAAAATAAGAAAAAG
1 AAAAAAATAAGAAAAAG
57442884 AAAA
1 AAAA
57442888 CAAAAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAATAAGAAAAAG
Found at i:57446602 original size:30 final size:30
Alignment explanation
Indices: 57446517--57446613 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
57446507 TAAACTAAAA
* *
57446517 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
57446547 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
57446577 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
57446606 ATGAGCTA
1 -TGAGCTA
57446614 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:57448787 original size:30 final size:30
Alignment explanation
Indices: 57448716--57448798 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
57448706 CTTTTGTTTC
* *
57448716 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
57448747 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
57448776 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
57448799 TCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:57448798 original size:18 final size:18
Alignment explanation
Indices: 57448749--57448804 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
57448739 CACTCTCAAA
* *
57448749 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
57448766 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
57448784 TTTCATTTTCTTTTTTCTT
1 TTTCATTTTC-ATTTTCTT
57448803 TT
1 TT
57448805 CAAAGGAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:57448805 original size:12 final size:12
Alignment explanation
Indices: 57448774--57448798 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57448764 TTTTTCAATC
57448774 TCATTTTCTTTT
1 TCATTTTCTTTT
57448786 TCATTTTCTTTT
1 TCATTTTCTTTT
57448798 T
1 T
57448799 TCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:57448877 original size:5 final size:5
Alignment explanation
Indices: 57448867--57448923 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57448857 CTCTTGCCTC
*
57448867 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
57448914 TCTTT TCTTT
1 TCTTT TCTTT
57448924 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:57448907 original size:15 final size:14
Alignment explanation
Indices: 57448867--57448923 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57448857 CTCTTGCCTC
*
57448867 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
57448882 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
57448897 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
57448914 TCTTTTCTTT
1 TCTTTTCTTT
57448924 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:57448924 original size:21 final size:21
Alignment explanation
Indices: 57448867--57448934 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
57448857 CTCTTGCCTC
* *
57448867 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
57448888 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
57448909 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
57448929 CTCTTT
1 -TCTTT
57448935 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:57449871 original size:18 final size:17
Alignment explanation
Indices: 57449844--57449882 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
57449834 CATTAAACAC
*
57449844 TTTTTTTTCAGATTTTT
1 TTTTTTTTCAAATTTTT
57449861 TTTTCTTTTCAAATTTTT
1 TTTT-TTTTCAAATTTTT
57449879 TTTT
1 TTTT
57449883 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTTTTCAAATTTTT
Found at i:57449877 original size:17 final size:17
Alignment explanation
Indices: 57449844--57449882 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
57449834 CATTAAACAC
*
57449844 TTTTTTTTCAGATTTTT
1 TTTTTTTTCAGAATTTT
57449861 TTTTCTTTTCA-AATTTT
1 TTTT-TTTTCAGAATTTT
57449878 TTTTT
1 TTTTT
57449883 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 13 0.65
18 6 0.30
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTTTTCAGAATTTT
Found at i:57449881 original size:12 final size:12
Alignment explanation
Indices: 57449861--57449904 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
57449851 TCAGATTTTT
*
57449861 TTTTCTTTTCAAA
1 TTTT-TTTTCGAA
*
57449874 TTTTTTTTTGAA
1 TTTTTTTTCGAA
*
57449886 TTTTTTTCCGAA
1 TTTTTTTTCGAA
57449898 TTTTTTT
1 TTTTTTT
57449905 GACTTGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:57451711 original size:30 final size:30
Alignment explanation
Indices: 57451624--57451722 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 30
57451614 TAAACTAAAA
* *
57451624 TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAACTGAAGT
* * * * *
57451654 TGAGCTGAGGCTAAACTCCT-AAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAA-CTGAAGT
57451684 TGAGCTAAGGTTTAGCTCGTGAACTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAACTGAAGT
57451713 ATGAGCTAAG
1 -TGAGCTAAG
57451723 AGTGAGCTCG
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
29 2 0.04
30 50 0.93
31 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAACTGAAGT
Found at i:57453283 original size:13 final size:13
Alignment explanation
Indices: 57453265--57453289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57453255 TAACCTACAA
57453265 AATTAAATAACAT
1 AATTAAATAACAT
57453278 AATTAAATAACA
1 AATTAAATAACA
57453290 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:57453569 original size:20 final size:21
Alignment explanation
Indices: 57453514--57453562 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
57453504 AAAAAGGAAT
* *
57453514 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAAATC
57453535 GAGCTCAAACGAGCTAAAAT-
1 GAGCTCAAACGAGCTAAAATC
57453555 GAGCTCAA
1 GAGCTCAA
57453563 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.16
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAAATC
Found at i:57457270 original size:23 final size:22
Alignment explanation
Indices: 57457218--57457270 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
57457208 TCCACGTCTT
*
57457218 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
57457240 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
57457263 TTTCTTTT
1 TTTCTTTT
57457271 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:57462117 original size:27 final size:27
Alignment explanation
Indices: 57462079--57462132 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
57462069 TAAGTGCATG
57462079 TATGGTGGCTGTCTCCTAACTTTCCAA
1 TATGGTGGCTGTCTCCTAACTTTCCAA
57462106 TATGGTGGCTGTCTCCTAACTTTCCAA
1 TATGGTGGCTGTCTCCTAACTTTCCAA
57462133 GGCACTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (27 bp):
TATGGTGGCTGTCTCCTAACTTTCCAA
Found at i:57464216 original size:21 final size:20
Alignment explanation
Indices: 57464182--57464249 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
57464172 ACATTTTTGT
57464182 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
57464203 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
57464224 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
57464245 AAAGA
1 AAAGA
57464250 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:57464217 original size:6 final size:5
Alignment explanation
Indices: 57464193--57464249 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57464183 AAGAGAAAAC
*
57464193 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
57464240 AAAGA AAAGA
1 AAAGA AAAGA
57464250 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:57464224 original size:15 final size:14
Alignment explanation
Indices: 57464193--57464249 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
57464183 AAGAGAAAAC
57464193 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
57464209 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
57464224 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
57464240 AAAGAAAAGA
1 AAAGAAAAGA
57464250 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:57464353 original size:30 final size:31
Alignment explanation
Indices: 57464319--57464400 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
57464309 TTTGAAAAGC
* *
57464319 AAAAAGAAAATGAAAAAGAAA-GTGAGATTG
1 AAAAAGAAAATGAAAAAGAAATCTGAGAGTG
* *
57464349 AAAAAGAGAACG-AAAAGAAATCTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATCTGAGAGTG
*
57464379 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
57464401 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.63, C:0.02, G:0.23, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATCTGAGAGTG
Found at i:57466708 original size:30 final size:30
Alignment explanation
Indices: 57466611--57466709 Score: 85
Period size: 30 Copynumber: 3.3 Consensus size: 30
57466601 CGAGCTCACT
* *
57466611 CTTAGCTC-ACTTTCAACTCACGAGCTAAAC
1 CTTAGCTCAACTTT-AGCTCACGAGCTAAAG
* * * **
57466641 CTTAGCTCAACTTCAGCTTAGGAG-TTTAG
1 CTTAGCTCAACTTTAGCTCACGAGCTAAAG
*
57466670 CCTCAGCTCAACTTTAGCTCACGAGCTAAAG
1 -CTTAGCTCAACTTTAGCTCACGAGCTAAAG
*
57466701 GTTAGCTCA
1 CTTAGCTCA
57466710 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
29 2 0.04
30 42 0.82
31 7 0.14
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
CTTAGCTCAACTTTAGCTCACGAGCTAAAG
Found at i:57468187 original size:9 final size:10
Alignment explanation
Indices: 57468160--57468186 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
57468150 TCACATCACT
57468160 TTTTTTTTAA
1 TTTTTTTTAA
57468170 TTTTTTTTAA
1 TTTTTTTTAA
57468180 TTTTTTT
1 TTTTTTT
57468187 ACTTATGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:57474589 original size:15 final size:13
Alignment explanation
Indices: 57474551--57474592 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
57474541 ACCTATTGTA
*
57474551 AAAAGAAAATGAG
1 AAAAGAAAAAGAG
57474564 AAAAGAAAAAGATG
1 AAAAGAAAAAGA-G
57474578 AAAAGCAAAAAGAG
1 AAAAG-AAAAAGAG
57474592 A
1 A
57474593 TCAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 8 0.31
15 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.05
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:57474603 original size:15 final size:15
Alignment explanation
Indices: 57474564--57474607 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
57474554 AGAAAATGAG
*
57474564 AAAAGAAAA-AGATG
1 AAAAGAAAAGAGATC
57474578 AAAAGCAAAAAGAGATC
1 AAAAG--AAAAGAGATC
57474595 AAAAGAAAAGAGA
1 AAAAGAAAAGAGA
57474608 GGCAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 4 0.15
17 9 0.35
ACGTcount: A:0.70, C:0.05, G:0.20, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAGAGATC
Found at i:57474721 original size:12 final size:12
Alignment explanation
Indices: 57474701--57474743 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
57474691 GAGAGGAAAC
*
57474701 AAAATGAGATTG
1 AAAAAGAGATTG
57474713 AAAAAGAGATTG
1 AAAAAGAGATTG
*
57474725 AAAAAGAGAATG
1 AAAAAGAGATTG
57474737 AAAAAGA
1 AAAAAGA
57474744 AAAGAGTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:57476446 original size:20 final size:20
Alignment explanation
Indices: 57476421--57476475 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
57476411 ACGAGTTAAA
* *
57476421 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
57476441 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
57476461 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
57476476 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:57477781 original size:13 final size:13
Alignment explanation
Indices: 57477763--57477787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57477753 TAACCTACAA
57477763 AATTAAATAACAT
1 AATTAAATAACAT
57477776 AATTAAATAACA
1 AATTAAATAACA
57477788 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:57480098 original size:68 final size:68
Alignment explanation
Indices: 57480019--57480155 Score: 184
Period size: 68 Copynumber: 2.0 Consensus size: 68
57480009 GATAATTTAA
* * *
57480019 TTTGTCCAGCCGCATGACATAAATTACATTGGTTTGAATGCTGCCGAATTTAATGTGTCTTAACC
1 TTTGTCCAGCCGCATGACATAAATTAAATTGGTTTGAATACTACCGAATTTAATGTGTCTTAACC
57480084 CTT
66 CTT
* * *** * *
57480087 TTTGTTCAGCCGCATGACATGAATTAAATTGGTTTTTCTACTACCGATTTTAATGTGTTTTAACC
1 TTTGTCCAGCCGCATGACATAAATTAAATTGGTTTGAATACTACCGAATTTAATGTGTCTTAACC
57480152 CTT
66 CTT
57480155 T
1 T
57480156 AATTGCTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (68 bp):
TTTGTCCAGCCGCATGACATAAATTAAATTGGTTTGAATACTACCGAATTTAATGTGTCTTAACC
CTT
Found at i:57482513 original size:18 final size:17
Alignment explanation
Indices: 57482490--57482529 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
57482480 TTAGAACCCA
57482490 AAATTAATGTGTCTAAAT
1 AAATTAATGTG-CTAAAT
57482508 AAATTAATGTGCTAAAT
1 AAATTAATGTGCTAAAT
*
57482525 TAATT
1 AAATT
57482530 TGTGTGTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (17 bp):
AAATTAATGTGCTAAAT
Found at i:57485992 original size:13 final size:13
Alignment explanation
Indices: 57485974--57485998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57485964 TAACCTACAA
57485974 AATTAAATAACAT
1 AATTAAATAACAT
57485987 AATTAAATAACA
1 AATTAAATAACA
57485999 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:57488381 original size:30 final size:29
Alignment explanation
Indices: 57488326--57488389 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
57488316 TTTTTCAATT
* *
57488326 TCTTTTTCACTCTCAAATTTCTTTTCGTTC
1 TCTTTTTCAATCTCAAATCTCTTTTC-TTC
*
57488356 TCTTTTTCAATCTC-AATCTCATTTTCTTT
1 TCTTTTTCAATCTCAAATCTC-TTTTCTTC
57488385 TCTTT
1 TCTTT
57488390 ATTTTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (29 bp):
TCTTTTTCAATCTCAAATCTCTTTTCTTC
Found at i:57488404 original size:19 final size:20
Alignment explanation
Indices: 57488380--57488420 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
57488370 AATCTCATTT
57488380 TCTTTTCTTTATTT-TTCTC
1 TCTTTTCTTTATTTCTTCTC
*
57488399 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTATTTCTTCTC
57488419 TC
1 TC
57488421 GATTTCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTATTTCTTCTC
Found at i:57490595 original size:13 final size:13
Alignment explanation
Indices: 57490577--57490601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57490567 TAACCTACAA
57490577 AATTAAATAACAT
1 AATTAAATAACAT
57490590 AATTAAATAACA
1 AATTAAATAACA
57490602 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:57491253 original size:30 final size:30
Alignment explanation
Indices: 57491158--57491254 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
57491148 AGCCCACTCC
* *
57491158 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
57491188 TAGCTCAACTTCAGCTTATGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
* *
57491218 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
57491248 TAGCTCA
1 TAGCTCA
57491255 TTTTTGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:57493543 original size:30 final size:31
Alignment explanation
Indices: 57493509--57493605 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
57493499 AGCTCACTCC
*
57493509 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
57493539 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
57493569 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
57493599 TAGCTCA
1 TAGCTCA
57493606 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:57495472 original size:16 final size:14
Alignment explanation
Indices: 57495425--57495480 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 14
57495415 AGAGAAAATG
57495425 AAGAAAAGAAAAGAAA
1 AAGAAAAG--AAGAAA
57495441 AAGCAAAAGAAGAAA
1 AAG-AAAAGAAGAAA
57495456 AAGAAAATGAAGTAAA
1 AAGAAAA-GAAG-AAA
57495472 AAGAAAAGA
1 AAGAAAAGA
57495481 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.11
15 15 0.41
16 13 0.35
17 5 0.14
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (14 bp):
AAGAAAAGAAGAAA
Found at i:57495583 original size:30 final size:31
Alignment explanation
Indices: 57495549--57495630 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
57495539 TTTGAAAAGA
* *
57495549 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAGAAGAAAAAGAAATATGAGAGTG
* *
57495579 AAAAAG-AGAACAAAAAGAAATTTGAGAGTG
1 AAAAAGAAGAAGAAAAAGAAATATGAGAGTG
*
57495609 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAGAAGAAAAAGAAAT
57495631 TGAAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.27
30 19 0.43
31 13 0.30
ACGTcount: A:0.67, C:0.01, G:0.21, T:0.11
Consensus pattern (31 bp):
AAAAAGAAGAAGAAAAAGAAATATGAGAGTG
Found at i:57497577 original size:15 final size:15
Alignment explanation
Indices: 57497557--57497604 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
57497547 TCAAAGATAG
57497557 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
57497572 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
57497586 GTTTATGGATATAAA
1 GTTTATGGATATGAA
57497601 GTTT
1 GTTT
57497605 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:57497620 original size:29 final size:29
Alignment explanation
Indices: 57497551--57497610 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
57497541 AAGGATTCAA
* *
57497551 AGATAGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
57497580 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
57497609 AG
1 AG
57497611 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:57498630 original size:14 final size:14
Alignment explanation
Indices: 57498588--57498632 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
57498578 TTAAAGAAGC
57498588 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
57498602 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
57498615 AACTCATTTAATTA
1 AACTCATTAAATTA
57498629 AACT
1 AACT
57498633 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:57500090 original size:68 final size:66
Alignment explanation
Indices: 57500018--57500200 Score: 244
Period size: 67 Copynumber: 2.7 Consensus size: 66
57500008 CATCATGTGT
* * *
57500018 ACAAGAAGGCTAC-GAGATACTATATAGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCAT
1 ACAAG-AGGCTACGGAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGATACGAGATGTATCCCAT
57500082 GTAG
63 GTAG
57500086 ACAAG-GAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATG
1 ACAAGAG-GCTACG-GAGAGATAAATGTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATG
57500150 TAG
64 TAG
* *
57500153 ACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGAT
1 ACAAGAG-GCTACG-GAGAGATAAATGTAGCTAGGTCACATGTGTGAT
57500201 TCCAAGTGAA
Statistics
Matches: 106, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
66 1 0.01
67 51 0.48
68 49 0.46
69 5 0.05
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (66 bp):
ACAAGAGGCTACGGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATGTA
G
Found at i:57500128 original size:67 final size:68
Alignment explanation
Indices: 57500044--57500200 Score: 280
Period size: 67 Copynumber: 2.3 Consensus size: 68
57500034 ATACTATATA
*
57500044 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAG-GAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
57500108 AAT
66 AAT
57500111 GTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
57500176 AAT
66 AAT
* *
57500179 GTAGCTAGGTCGCATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
57500201 TCCAAGTGAA
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 46 0.53
68 40 0.47
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (68 bp):
GTAGCTAGGTCACATGTGTGATACGAGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
AAT
Found at i:57507592 original size:68 final size:66
Alignment explanation
Indices: 57507511--57507728 Score: 232
Period size: 68 Copynumber: 3.3 Consensus size: 66
57507501 CATCATGTGT
* * *
57507511 ACAAGA-AGGCTACGAGATACTATATAGTAGCTAGGTCACATGTGTTATACGGAATGTATCCCAT
1 ACAAGAGA-GCTACGAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGATACGGAATGTATCCCAT
57507575 GTAG
63 GTAG
* *
57507579 ACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATATGGGATGTATCCCATG
1 ACAAGAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGAATGTATCCCATG
57507644 TAG
64 TAG
* * * *
57507647 ACAAGAGAGCTACGTGAGAGATAAAT-T-GCTAGGTCGCATGAGTGATTC-CAA-GTGA-CACCA
1 ACAAGAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGAATGT-ATC-CCA
57507707 TGTAG
62 TGTAG
57507712 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
57507729 TAAATCGGCT
Statistics
Matches: 134, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
63 4 0.03
64 3 0.02
65 23 0.17
66 17 0.13
67 1 0.01
68 76 0.57
69 5 0.04
70 5 0.04
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (66 bp):
ACAAGAGAGCTACGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGAATGTATCCCATGTA
G
Found at i:57507762 original size:62 final size:63
Alignment explanation
Indices: 57507571--57507784 Score: 195
Period size: 68 Copynumber: 3.3 Consensus size: 63
57507561 GGAATGTATC
* * ***
57507571 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATA-TGGGATG
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG--GCTAGGTCGCATGAGTGATACCAAG-TG
57507635 TATC-
60 TA-CA
* *
57507639 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATTGCTAGGTCGCATGAGTGATTCCAAGTG-AC
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATGGCTAGGTCGCATGAGTGATACCAAGTGTAC
57507703 A
63 A
* * *
57507704 CCATGTAGACAAGAGAGCTAC-GAGATAAATCGGCTAGGTCGCATGAGTGGTACTAAGTGTTCA
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GGCTAGGTCGCATGAGTGATACCAAGTGTACA
57507767 CCATGT-GTACAAGAGAGC
1 CCATGTAG-ACAAGAGAGC
57507785 CGAATTAAAT
Statistics
Matches: 129, Mismatches: 12, Indels: 15
0.83 0.08 0.10
Matches are distributed among these distances:
61 9 0.07
62 25 0.19
63 18 0.14
64 1 0.01
65 22 0.17
66 19 0.15
67 1 0.01
68 34 0.26
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (63 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGGCTAGGTCGCATGAGTGATACCAAGTGTACA
Found at i:57509652 original size:10 final size:10
Alignment explanation
Indices: 57509637--57509663 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
57509627 TAAGTTGAAG
57509637 TTGAGCTGAT
1 TTGAGCTGAT
57509647 TTGAGCTGAT
1 TTGAGCTGAT
57509657 TTGAGCT
1 TTGAGCT
57509664 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:57510019 original size:20 final size:20
Alignment explanation
Indices: 57509996--57510049 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
57509986 AGTTTTACCC
*
57509996 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
57510016 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
57510036 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
57510050 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:57510031 original size:30 final size:30
Alignment explanation
Indices: 57509996--57510069 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
57509986 AGTTTTACCC
57509996 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
57510026 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
57510056 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
57510070 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:57510059 original size:20 final size:20
Alignment explanation
Indices: 57509996--57510060 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
57509986 AGTTTTACCC
* * * *
57509996 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
57510016 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
57510035 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
57510056 AGCTC
1 AGCTC
57510061 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:57511723 original size:10 final size:10
Alignment explanation
Indices: 57511710--57511748 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
57511700 AAAAAGGAGC
57511710 AAAAAAGAAA
1 AAAAAAGAAA
57511720 AAAAAAGTAAA
1 AAAAAAG-AAA
57511731 AAAAGAAGAAA
1 AAAA-AAGAAA
57511742 AAAAAAG
1 AAAAAAG
57511749 TGAAAAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 14 0.52
12 3 0.11
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:57511747 original size:22 final size:21
Alignment explanation
Indices: 57511710--57511754 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
57511700 AAAAAGGAGC
57511710 AAAAAAGAAAAAAAAAGTAAA
1 AAAAAAGAAAAAAAAAGTAAA
*
57511731 AAAAGAAGAAAAAAAAAGTGAA
1 AAAA-AAGAAAAAAAAAGTAAA
57511753 AA
1 AA
57511755 GTCTTGCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAGTAAA
Found at i:57512785 original size:6 final size:6
Alignment explanation
Indices: 57512765--57512859 Score: 50
Period size: 6 Copynumber: 15.7 Consensus size: 6
57512755 AAAGAAATTG
* ** * **
57512765 AAAG-A AAACAA AAAGAA AAAGAA ATTGCA AAAGAA AAAGAA ATCGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * * *
57512812 AAAGTG AGAG-A AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
57512860 CGAAAAAAGA
Statistics
Matches: 64, Mismatches: 21, Indels: 9
0.68 0.22 0.10
Matches are distributed among these distances:
5 6 0.09
6 47 0.73
7 7 0.11
8 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:57512814 original size:18 final size:18
Alignment explanation
Indices: 57512765--57512815 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
57512755 AAAGAAATTG
*
57512765 AAAGAAAAC-AAAAAGAA
1 AAAGAAATCGAAAAAGAA
* *
57512782 AAAGAAATTGCAAAAGAA
1 AAAGAAATCGAAAAAGAA
57512800 AAAGAAATCGAAAAAG
1 AAAGAAATCGAAAAAG
57512816 TGAGAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.06
Consensus pattern (18 bp):
AAAGAAATCGAAAAAGAA
Found at i:57512839 original size:14 final size:14
Alignment explanation
Indices: 57512819--57512857 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
57512809 GAAAAAGTGA
57512819 GAGAAAAGAAAA-T
1 GAGAAAAGAAAATT
57512832 GAAGAAAAGAAAATT
1 G-AGAAAAGAAAATT
57512847 GA-AAAAGAAAA
1 GAGAAAAGAAAA
57512858 AGCGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.42
14 12 0.50
15 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (14 bp):
GAGAAAAGAAAATT
Found at i:57512911 original size:33 final size:33
Alignment explanation
Indices: 57512874--57512936 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
57512864 AAAAGAAATT
57512874 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
57512907 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
57512937 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:57514733 original size:20 final size:20
Alignment explanation
Indices: 57514710--57514763 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
57514700 AGTTTTTCCC
*
57514710 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
57514730 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
57514750 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
57514764 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:57514745 original size:30 final size:30
Alignment explanation
Indices: 57514710--57514783 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
57514700 AGTTTTTCCC
57514710 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
57514740 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
57514770 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
57514784 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:57514773 original size:20 final size:20
Alignment explanation
Indices: 57514710--57514774 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
57514700 AGTTTTTCCC
* * * *
57514710 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
57514730 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
57514749 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
57514770 AGCTC
1 AGCTC
57514775 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:57519579 original size:23 final size:22
Alignment explanation
Indices: 57519528--57519579 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
57519518 CCTCGTCTTT
*
57519528 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
57519550 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
57519573 TTCTTTT
1 TTCTTTT
57519580 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:57532998 original size:30 final size:31
Alignment explanation
Indices: 57532962--57533058 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
57532952 TGCTCACTCC
*
57532962 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
57532992 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
57533022 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
57533052 TAGCTCA
1 TAGCTCA
57533059 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:57533561 original size:13 final size:13
Alignment explanation
Indices: 57533543--57533567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57533533 GTATTGATCA
57533543 TGTGTTCACACCT
1 TGTGTTCACACCT
57533556 TGTGTTCACACC
1 TGTGTTCACACC
57533568 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:57539520 original size:10 final size:11
Alignment explanation
Indices: 57539481--57539534 Score: 63
Period size: 11 Copynumber: 4.6 Consensus size: 11
57539471 TACAAGTTTG
*
57539481 AAAAAAAAATC
1 AAAAAAAATTC
57539492 GAAAAAAAATTTTC
1 -AAAAAAAA--TTC
57539506 AAAAAAAATTC
1 AAAAAAAATTC
*
57539517 AAAAAAAATTG
1 AAAAAAAATTC
57539528 AAAAAAA
1 AAAAAAA
57539535 GTGATTTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
11 20 0.53
12 8 0.21
13 8 0.21
14 2 0.05
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.17
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:57539533 original size:24 final size:24
Alignment explanation
Indices: 57539481--57539534 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
57539471 TACAAGTTTG
**
57539481 AAAAAAAAATCGAAAAAAAATTTTC
1 AAAAAAAAATCGAAAAAAAA-TTGA
*
57539506 AAAAAAAATTC-AAAAAAAATTGA
1 AAAAAAAAATCGAAAAAAAATTGA
57539529 AAAAAA
1 AAAAAA
57539535 GTGATTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 8 0.31
24 8 0.31
25 10 0.38
ACGTcount: A:0.74, C:0.06, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAAAAATCGAAAAAAAATTGA
Found at i:57540470 original size:12 final size:11
Alignment explanation
Indices: 57540449--57540502 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
57540439 AAGAGAACAA
57540449 AAAAAGAAAAG
1 AAAAAGAAAAG
57540460 AAAAAGCAAAAG
1 AAAAAG-AAAAG
*
57540472 -AAGA-AAAAG
1 AAAAAGAAAAG
* *
57540481 AAAATG-AAAT
1 AAAAAGAAAAG
57540491 AAAAAGAAAAG
1 AAAAAGAAAAG
57540502 A
1 A
57540503 GAGGCAAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 5 0.15
10 10 0.30
11 13 0.39
12 5 0.15
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.04
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:57540477 original size:15 final size:14
Alignment explanation
Indices: 57540457--57540502 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
57540447 AAAAAAAGAA
57540457 AAGAAAAAGCAAAAG
1 AAGAAAAAG-AAAAG
57540472 AAGAAAAAGAAAATG
1 AAGAAAAAGAAAA-G
*
57540487 AAATAAAAAGAAAAG
1 -AAGAAAAAGAAAAG
57540502 A
1 A
57540503 GAGGCAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 12 0.43
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:57540481 original size:21 final size:20
Alignment explanation
Indices: 57540446--57540502 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
57540436 GTAAAGAGAA
57540446 CAAAAAAAGAAAAGAAAAAG
1 CAAAAAAAGAAAAGAAAAAG
* *
57540466 CAAAAGAAGAAAAAGAAAATG
1 CAAAAAAAG-AAAAGAAAAAG
*
57540487 AAATAAAAAGAAAAGA
1 CAA-AAAAAGAAAAGA
57540503 GAGGCAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 8 0.26
21 18 0.58
22 5 0.16
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (20 bp):
CAAAAAAAGAAAAGAAAAAG
Found at i:57542216 original size:24 final size:23
Alignment explanation
Indices: 57542162--57542239 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
57542152 GGATAATTAA
**
57542162 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
57542185 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
57542209 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
57542230 GAAATAGTAT
1 GAAATGGTAT
57542240 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:57542224 original size:21 final size:21
Alignment explanation
Indices: 57542198--57542264 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
57542188 TTGGTATTTG
57542198 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
57542219 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
57542240 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
57542263 GG
1 GG
57542265 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:57546534 original size:17 final size:17
Alignment explanation
Indices: 57546509--57546564 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
57546499 TCTCTTTTCA
*
57546509 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
57546526 TTCTTTTTTTTT-ATCATTT
1 TTCTTTTTTTTTGA--A-TT
* *
57546545 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
57546562 TTC
1 TTC
57546565 AGTCTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 16 0.50
18 2 0.06
19 13 0.41
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:57548709 original size:1 final size:1
Alignment explanation
Indices: 57548703--57548729 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
57548693 ATTTTGGAAA
57548703 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
57548730 ACGGATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:57548791 original size:13 final size:14
Alignment explanation
Indices: 57548772--57548813 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
57548762 AAACCGTATG
57548772 CAATTTTTTTTTTT
1 CAATTTTTTTTTTT
57548786 -AATTTTTTTTTTTT
1 CAA-TTTTTTTTTTT
57548800 CAATTTTTTTTTTT
1 CAATTTTTTTTTTT
57548814 TTTGAACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (14 bp):
CAATTTTTTTTTTT
Found at i:57548794 original size:14 final size:15
Alignment explanation
Indices: 57548775--57548814 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
57548765 CCGTATGCAA
57548775 TTTTTTTTTTT-AAT
1 TTTTTTTTTTTCAAT
57548789 TTTTTTTTTTTCAAT
1 TTTTTTTTTTTCAAT
57548804 TTTTTTTTTTT
1 TTTTTTTTTTT
57548815 TTGAACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTCAAT
Found at i:57548795 original size:15 final size:16
Alignment explanation
Indices: 57548775--57548834 Score: 86
Period size: 17 Copynumber: 3.8 Consensus size: 16
57548765 CCGTATGCAA
57548775 TTTTTTTTTTTAA-TT
1 TTTTTTTTTTTAACTT
* *
57548790 TTTTTTTTTTCAATTT
1 TTTTTTTTTTTAACTT
57548806 TTTTTTTTTTTGAACTT
1 TTTTTTTTTTT-AACTT
57548823 TTTTTTTTTTTA
1 TTTTTTTTTTTA
57548835 CGCACCTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.30
16 13 0.32
17 15 0.38
ACGTcount: A:0.12, C:0.03, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTAACTT
Found at i:57549149 original size:24 final size:23
Alignment explanation
Indices: 57549095--57549172 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
57549085 GGATAATTAA
**
57549095 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
57549118 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
57549142 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
57549163 GAAATAGTAT
1 GAAATGGTAT
57549173 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:57549157 original size:21 final size:21
Alignment explanation
Indices: 57549131--57549197 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
57549121 TTGGTATTTG
57549131 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
57549152 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
57549173 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
57549196 GG
1 GG
57549198 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:57554667 original size:22 final size:21
Alignment explanation
Indices: 57554636--57554680 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57554626 TTATGTCTAA
*
57554636 ATTTAATTATTGCTTTTAAATT
1 ATTTAATTATT-ATTTTAAATT
*
57554658 ATTTAGTTATTATTTTAAATT
1 ATTTAATTATTATTTTAAATT
57554679 AT
1 AT
57554681 AATTATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
ATTTAATTATTATTTTAAATT
Found at i:57554721 original size:13 final size:13
Alignment explanation
Indices: 57554703--57554728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57554693 AGTTGTGTGC
57554703 TATTTAATTATGT
1 TATTTAATTATGT
57554716 TATTTAATTATGT
1 TATTTAATTATGT
57554729 AGGTTAGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTAATTATGT
Found at i:57557119 original size:15 final size:17
Alignment explanation
Indices: 57557094--57557135 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
57557084 AAAGAAAGTC
57557094 AAAATGAAAATG-AA-AG
1 AAAA-GAAAATGAAAGAG
57557110 AAAAGAAAATGAAAGAG
1 AAAAGAAAATGAAAGAG
57557127 AAAAGAAAA
1 AAAAGAAAA
57557136 AGAATTGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (17 bp):
AAAAGAAAATGAAAGAG
Found at i:57560209 original size:15 final size:16
Alignment explanation
Indices: 57560189--57560220 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
57560179 ATTATATGAA
57560189 TAATTATA-TTTTATT
1 TAATTATATTTTTATT
57560204 TAATTATATTTTTATT
1 TAATTATATTTTTATT
57560220 T
1 T
57560221 CTTTGTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTATATTTTTATT
Found at i:57565248 original size:40 final size:40
Alignment explanation
Indices: 57565169--57565345 Score: 207
Period size: 40 Copynumber: 4.5 Consensus size: 40
57565159 CGGATGATAA
* * * ** *
57565169 CCGGACTAAGATCCGAAGGTATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT
* * *
57565209 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTG-TTATAT
* *
57565249 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT
*
57565289 CTGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT
57565329 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
57565346 ATGCTTGGGT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 98 0.84
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT
Found at i:57565307 original size:80 final size:80
Alignment explanation
Indices: 57565169--57565345 Score: 243
Period size: 80 Copynumber: 2.2 Consensus size: 80
57565159 CGGATGATAA
* * * * *
57565169 CCGGACTAAGATCCGAAGGTATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
*
57565234 TGCTAG-TGATTATAT
66 TGCGAGTTG-TTATAT
* *
57565249 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCTGGGCTAAGACCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
57565314 TGCGAGTTGTTATAT
66 TGCGAGTTGTTATAT
57565329 CC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
57565346 ATGCTTGGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
78 1 0.01
79 13 0.15
80 71 0.82
81 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
TGCGAGTTGTTATAT
Found at i:57569171 original size:20 final size:20
Alignment explanation
Indices: 57569126--57569173 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
57569116 AGTAAGCTCG
57569126 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
** * *
57569146 AATGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
57569166 GTTGAGCT
1 GTTGAGCT
57569174 GGACGGAGCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:57571942 original size:20 final size:20
Alignment explanation
Indices: 57571917--57571971 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
57571907 ACGAGTTAAA
* *
57571917 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
57571937 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
57571957 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
57571972 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:57573024 original size:42 final size:42
Alignment explanation
Indices: 57572962--57573058 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
57572952 AGATTATGAG
* * * *
57572962 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAATAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
57573004 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
57573046 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
57573059 AAAGAAAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.15
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:57573077 original size:6 final size:6
Alignment explanation
Indices: 57573068--57573099 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
57573058 AAAAGAAAAA
*
57573068 GAGATT GAGAGT GAGAGT GAGAGT GAGAGT GA
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GA
57573100 AAAAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.47, T:0.19
Consensus pattern (6 bp):
GAGAGT
Found at i:57573112 original size:18 final size:18
Alignment explanation
Indices: 57573091--57573160 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 18
57573081 AGAGTGAGAG
57573091 TGAGAGTGAAAAAGAAAA
1 TGAGAGTGAAAAAGAAAA
* * **
57573109 TGAGATTGAGATTGAAAA
1 TGAGAGTGAAAAAGAAAA
* * ***
57573127 AGAGAATGAAAAAGAGTT
1 TGAGAGTGAAAAAGAAAA
*
57573145 TGAGAGAGAAAAAGAA
1 TGAGAGTGAAAAAGAA
57573161 TGTGAACAAG
Statistics
Matches: 36, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.16
Consensus pattern (18 bp):
TGAGAGTGAAAAAGAAAA
Found at i:57573112 original size:24 final size:24
Alignment explanation
Indices: 57573085--57573135 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
57573075 AGAGTGAGAG
57573085 TGAGAGTGAGAGTGAAAAAGAAAA
1 TGAGAGTGAGAGTGAAAAAGAAAA
* * *
57573109 TGAGATTGAGATTGAAAAAGAGAA
1 TGAGAGTGAGAGTGAAAAAGAAAA
57573133 TGA
1 TGA
57573136 AAAAGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.18
Consensus pattern (24 bp):
TGAGAGTGAGAGTGAAAAAGAAAA
Found at i:57573147 original size:24 final size:24
Alignment explanation
Indices: 57573092--57573156 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
57573082 GAGTGAGAGT
* * **
57573092 GAGAGTGAAAAAGAAAATGAGATT
1 GAGATTGAAAAAGAAAATGAAAAA
*
57573116 GAGATTGAAAAAGAGAATGAAAAA
1 GAGATTGAAAAAGAAAATGAAAAA
* * *
57573140 GAGTTTGAGAGAGAAAA
1 GAGATTGAAAAAGAAAA
57573157 AGAATGTGAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.15
Consensus pattern (24 bp):
GAGATTGAAAAAGAAAATGAAAAA
Found at i:57573149 original size:36 final size:36
Alignment explanation
Indices: 57573053--57573150 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 36
57573043 CAAAGAAATG
* * *
57573053 AAAGAAAAAGAAAAAGAGATTGAGAGTGAGAGTGAG
1 AAAGAGAATGAAAAAGAGATTGAGAGTGAGAGTGAA
** * * * * *
57573089 AGTGAGAGTGAAAAAGAAAATGAGATTGAGATTGAA
1 AAAGAGAATGAAAAAGAGATTGAGAGTGAGAGTGAA
*
57573125 AAAGAGAATGAAAAAGAGTTTGAGAG
1 AAAGAGAATGAAAAAGAGATTGAGAG
57573151 AGAAAAAGAA
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.32, T:0.15
Consensus pattern (36 bp):
AAAGAGAATGAAAAAGAGATTGAGAGTGAGAGTGAA
Found at i:57573189 original size:18 final size:19
Alignment explanation
Indices: 57573153--57573191 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57573143 TTTGAGAGAG
*
57573153 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
57573172 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
57573190 AA
1 AA
57573192 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:57577289 original size:17 final size:19
Alignment explanation
Indices: 57577262--57577299 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57577252 TAGAAGTGAA
*
57577262 TGGATAGGTTT-GAATAAG
1 TGGATAGGTTTCAAATAAG
57577280 TGGA-AGGTTTCAAATAAG
1 TGGATAGGTTTCAAATAAG
57577298 TG
1 TG
57577300 TAAGAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (19 bp):
TGGATAGGTTTCAAATAAG
Found at i:57578201 original size:15 final size:16
Alignment explanation
Indices: 57578176--57578207 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
57578166 ACCTACAAAG
57578176 AAATAAAAATATAATT
1 AAATAAAAATATAATT
57578192 AAAT-AAAATATAATT
1 AAATAAAAATATAATT
57578207 A
1 A
57578208 TTCATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAAAAATATAATT
Found at i:57578450 original size:21 final size:21
Alignment explanation
Indices: 57578426--57578473 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
57578416 AAAAGAAATG
*
57578426 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTAAAATCA
* *
57578447 AGCTCAAACGAGCTGAAATGA
1 AGCTCAAACGAGCTAAAATCA
57578468 A-CTCAA
1 AGCTCAA
57578474 GTGAGCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.15
Consensus pattern (21 bp):
AGCTCAAACGAGCTAAAATCA
Found at i:57579582 original size:21 final size:22
Alignment explanation
Indices: 57579546--57579597 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
57579536 TCACAACTCT
57579546 TTTTCTTTTCTCTTTCATTTTC-
1 TTTTC-TTTCTCTTTCATTTTCA
*
57579568 TTTTCTTTCTTTTTCATTTTCA
1 TTTTCTTTCTCTTTCATTTTCA
*
57579590 CTTTCTTT
1 TTTTCTTT
57579598 TTCCACTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCTTTCTCTTTCATTTTCA
Found at i:57581656 original size:30 final size:30
Alignment explanation
Indices: 57581620--57581680 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
57581610 CAGGTTCGAC
57581620 AAAGAACACGGTTGACACAACTAGAATGCT
1 AAAGAACACGGTTGACACAACTAGAATGCT
57581650 AAAGAACACGGTTGACACAACTAGAATGCT
1 AAAGAACACGGTTGACACAACTAGAATGCT
57581680 A
1 A
57581681 GGAACGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (30 bp):
AAAGAACACGGTTGACACAACTAGAATGCT
Found at i:57586499 original size:46 final size:46
Alignment explanation
Indices: 57586449--57586624 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
57586439 TGGTTGAGCA
57586449 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
57586495 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
57586540 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
57586588 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
57586625 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:57586605 original size:93 final size:93
Alignment explanation
Indices: 57586446--57586617 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
57586436 GGATGGTTGA
* *
57586446 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
57586511 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
57586539 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
57586604 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
57586618 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:57589208 original size:11 final size:10
Alignment explanation
Indices: 57589184--57589228 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
57589174 AAAAGAAATG
57589184 AGCTAAAACA
1 AGCTAAAACA
57589194 AGCTAAAATCA
1 AGCTAAAA-CA
* *
57589205 AGCTCAAACG
1 AGCTAAAACA
*
57589215 AGCTGAAACA
1 AGCTAAAACA
57589225 AGCT
1 AGCT
57589229 CAAGTGAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (10 bp):
AGCTAAAACA
Found at i:57589240 original size:20 final size:20
Alignment explanation
Indices: 57589184--57589231 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
57589174 AAAAGAAATG
* * *
57589184 AGCTAAAACAAGCTAAAATCA
1 AGCTCAAACGAGCTGAAA-CA
57589205 AGCTCAAACGAGCTGAAACA
1 AGCTCAAACGAGCTGAAACA
57589225 AGCTCAA
1 AGCTCAA
57589232 GTGAGCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (20 bp):
AGCTCAAACGAGCTGAAACA
Found at i:57590776 original size:114 final size:114
Alignment explanation
Indices: 57590560--57590785 Score: 285
Period size: 114 Copynumber: 2.0 Consensus size: 114
57590550 AACTTCTTGT
* * * * *
57590560 TTAAGCCTACTTTCTATCTATTTTTAGCCTTCTTCGAAATAAGTCAAGATTTACCCAATTTATCG
1 TTAAGCCTACTTTCTATCCATTTTTAGCCTTCTTCAAAACAAGCCAAGACTTACCCAATTTATCG
* * * **
57590625 ATAGGGCAACTATAACGACTCGATTCATCACTGAGGTGAGATCGTATCA
66 ATAGGGCAACTATAACAACTCAAATCATCACCAAGGTGAGATCGTATCA
* * *
57590674 TTAAGCCTACTTTCTATCCATTTTTAGCCTTTTTCAAAACGAGCCAAGACTTACCTAATTTATCG
1 TTAAGCCTACTTTCTATCCATTTTTAGCCTTCTTCAAAACAAGCCAAGACTTACCCAATTTATCG
* *
57590739 ATCGGGCAACTCAT-ACAACTCAAATCACTC-CCAAGGTGAGTTCGTAT
66 ATAGGGCAACT-ATAACAACTCAAATCA-TCACCAAGGTGAGATCGTAT
57590786 TAGAAGTCCA
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
114 91 0.96
115 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (114 bp):
TTAAGCCTACTTTCTATCCATTTTTAGCCTTCTTCAAAACAAGCCAAGACTTACCCAATTTATCG
ATAGGGCAACTATAACAACTCAAATCATCACCAAGGTGAGATCGTATCA
Found at i:57594588 original size:46 final size:46
Alignment explanation
Indices: 57594521--57594696 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
57594511 TGTAACCCGC
* *
57594521 CCATAAGCGAACTCAGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
57594567 CCATAAGTGAACTCAGACTCAACTCAAGGAGCTCGGATACCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGG--A-C--GTTCGCAT
* * * *
57594617 -C-TCA-CGAACTTAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
57594660 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA
57594697 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 3 0.03
46 61 0.58
47 25 0.24
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:57594657 original size:93 final size:93
Alignment explanation
Indices: 57594528--57594697 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 93
57594518 CGCCCATAAG
* * *
57594528 CGAACTCAGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
57594593 AGGAGCTCGGATACCTAGTTACATCTCA
66 ACGAGCTCGGATACCTAGTTACATCTCA
* * *
57594621 CGAACTTAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
57594686 ACGAGTTCGGAT
66 ACGAGCTCGGAT
57594698 GCCCAAATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATACCTAGTTACATCTCA
Found at i:57598372 original size:30 final size:30
Alignment explanation
Indices: 57598327--57598386 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
57598317 ATTTAATACG
*
57598327 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
57598357 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
57598387 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:57603675 original size:33 final size:34
Alignment explanation
Indices: 57603627--57603692 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
57603617 ATCACTCTCC
*
57603627 CTCATTTAAATGCCG-TCCATTGCATGTGGAACAT
1 CTCATTTAAATGCCGTTCCA-TGCATGTAGAACAT
*
57603661 CTCA-TTAATTGCCGTTCCATGCATGTAGAACA
1 CTCATTTAAATGCCGTTCCATGCATGTAGAACA
57603693 ACATCTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (34 bp):
CTCATTTAAATGCCGTTCCATGCATGTAGAACAT
Done.