Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 66 of 325
Found at i:20440620 original size:19 final size:18
Alignment explanation
Indices: 20440576--20440623 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
20440566 GTTATATGTC
*
20440576 TAATTAGGTTTTATTTAGG
1 TAATTA-GTTTAATTTAGG
20440595 TGAAATTAGTTTAATTTAGAG
1 T--AATTAGTTTAATTTAG-G
20440616 TAATTAGT
1 TAATTAGT
20440624 AAAAAGGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 8 0.32
20 10 0.40
21 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (18 bp):
TAATTAGTTTAATTTAGG
Found at i:20440988 original size:26 final size:25
Alignment explanation
Indices: 20440959--20441042 Score: 123
Period size: 26 Copynumber: 3.2 Consensus size: 25
20440949 TGGTACAAAT
*
20440959 TGATATTAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTC-A
20440985 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
20441011 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
20441037 TGATAA
1 TGATAA
20441043 GAATTTCATG
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
26 51 0.94
27 3 0.06
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:20442702 original size:27 final size:27
Alignment explanation
Indices: 20442661--20442773 Score: 111
Period size: 27 Copynumber: 4.2 Consensus size: 27
20442651 GAGGAAGCGT
*
20442661 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
20442688 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * * *
20442715 TCTGGTCGCTCTGCCTCGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
20442743 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
20442769 TCTGG
1 TCTGG
20442774 CAGCCATGCT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
26 5 0.07
27 53 0.75
28 13 0.18
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:20445847 original size:3 final size:3
Alignment explanation
Indices: 20445833--20445898 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
20445823 TTCTTAGATT
* * * * * *
20445833 TTA TTAA TTA TTA TTG TTA ATA TTA ATA TTA ATA TTA ATA TTA ATA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
20445879 ATA ATA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
20445899 TGATTTAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:20445860 original size:6 final size:6
Alignment explanation
Indices: 20445834--20445898 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
20445824 TCTTAGATTT
* * *
20445834 TATTAA TTATTAT TGTTAA TATTAA TATTAA TATTAA TATTAA TAATAA
1 TATTAA -TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
* *
20445883 TATTAT TATTAT TATT
1 TATTAA TATTAA TATT
20445899 TGATTTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
6 46 0.90
7 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
TATTAA
Found at i:20447320 original size:27 final size:27
Alignment explanation
Indices: 20447282--20447377 Score: 106
Period size: 27 Copynumber: 3.4 Consensus size: 27
20447272 ATGCCTTAAG
20447282 GGTGTGTTTGGGAGGATATGA-TATACC
1 GGTGTGTTTGGGAGGATAT-ATTATACC
* *
20447309 GGTGTGTTTGGGAGGCTATATTATACT
1 GGTGTGTTTGGGAGGATATATTATACC
*
20447336 GGTGTGTTAT-GGAGGATTTATATTATTCC
1 GGTGTGTT-TGGGAGGA--TATATTATACC
20447365 TGGTGTGTTTGGG
1 -GGTGTGTTTGGG
20447378 TTGGATATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.02
27 36 0.62
28 1 0.02
29 10 0.17
30 10 0.17
ACGTcount: A:0.18, C:0.06, G:0.35, T:0.41
Consensus pattern (27 bp):
GGTGTGTTTGGGAGGATATATTATACC
Found at i:20450843 original size:25 final size:25
Alignment explanation
Indices: 20450815--20450864 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20450805 TCCACGACTA
20450815 GTAAGCTGAATCTTTTAACAAAAAT
1 GTAAGCTGAATCTTTTAACAAAAAT
*
20450840 GTAAGCTGAATCTTTTAACAGAAAT
1 GTAAGCTGAATCTTTTAACAAAAAT
20450865 ATCATACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (25 bp):
GTAAGCTGAATCTTTTAACAAAAAT
Found at i:20454763 original size:21 final size:20
Alignment explanation
Indices: 20454739--20454782 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
20454729 TTAAAATATG
20454739 AATTTATTAATATATATAATA
1 AATTTATTAATATATATAA-A
*
20454760 AATTTATTAATATATGTAAA
1 AATTTATTAATATATATAAA
20454780 AAT
1 AAT
20454783 AGCTTTTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATTTATTAATATATATAAA
Found at i:20454879 original size:19 final size:20
Alignment explanation
Indices: 20454855--20454900 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
20454845 CATCCAAACA
20454855 CCAGAAAAGTAAACCATT-T
1 CCAGAAAAGTAAACCATTCT
*
20454874 CCAGAAAAGTAAATCATTCT
1 CCAGAAAAGTAAACCATTCT
20454894 CCAGAAA
1 CCAGAAA
20454901 TGATTTTTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.48, C:0.22, G:0.11, T:0.20
Consensus pattern (20 bp):
CCAGAAAAGTAAACCATTCT
Found at i:20459756 original size:26 final size:25
Alignment explanation
Indices: 20459713--20459788 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 25
20459703 TCATATCAAA
*
20459713 ATTTTCATATATCTAGAACATATATC
1 ATTTTCATAT-TTTAGAACATATATC
20459739 ATTTTCATATTTTGAGAACATATATC
1 ATTTTCATATTTT-AGAACATATATC
*
20459765 ATTTTCATATTTTCAGAACGTATA
1 ATTTTCATATTTT-AGAACATATA
20459789 ACATATCAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 2 0.04
26 44 0.96
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (25 bp):
ATTTTCATATTTTAGAACATATATC
Found at i:20466382 original size:16 final size:16
Alignment explanation
Indices: 20466357--20466387 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20466347 GACAAATCCC
*
20466357 GAAATGCCGAAAAGCT
1 GAAATACCGAAAAGCT
20466373 GAAATACCGAAAAGC
1 GAAATACCGAAAAGC
20466388 CAAAAGTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.23, T:0.10
Consensus pattern (16 bp):
GAAATACCGAAAAGCT
Found at i:20466637 original size:28 final size:28
Alignment explanation
Indices: 20466604--20466703 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 28
20466594 ATTGCATGAC
* * *
20466604 TATGAATGTGATTGAGCCTGACGGGCTA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
20466632 TATGAAAGTGATTGGGTCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
20466660 TATGAGTGTGATTGGGCCCGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
20466688 TTTGAATGAGATTGGG
1 TATGAATGTGATTGGG
20466704 TCTAAAGGGG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.23, C:0.12, G:0.36, T:0.29
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:20471013 original size:16 final size:16
Alignment explanation
Indices: 20470992--20471025 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20470982 TCGACAAATC
*
20470992 CCGAAATGCCGAAAAG
1 CCGAAATACCGAAAAG
20471008 CCGAAATACCGAAAAG
1 CCGAAATACCGAAAAG
20471024 CC
1 CC
20471026 AGAAGTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.29, G:0.21, T:0.06
Consensus pattern (16 bp):
CCGAAATACCGAAAAG
Found at i:20471545 original size:26 final size:26
Alignment explanation
Indices: 20471516--20471597 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
20471506 TGGTACAAAT
* *
20471516 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATATTCCA
20471542 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
20471568 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
20471594 TGAT
1 TGAT
20471598 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:20474283 original size:28 final size:28
Alignment explanation
Indices: 20474251--20474314 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
20474241 GGAGCTACAG
*
20474251 ATTGGGCCTGACGGGCCATATGAAAGTT
1 ATTGGGCCTGACGGGCCATATGAAAGTA
* *
20474279 ATTGGGCCTGATGGGCCATATGAATGTA
1 ATTGGGCCTGACGGGCCATATGAAAGTA
20474307 ATTGGGCC
1 ATTGGGCC
20474315 CAATAGGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (28 bp):
ATTGGGCCTGACGGGCCATATGAAAGTA
Found at i:20474323 original size:28 final size:28
Alignment explanation
Indices: 20474264--20474331 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
20474254 GGGCCTGACG
* * ** *
20474264 GGCCATATGAAAGTTATTGGGCCTGATG
1 GGCCATATGAATGTAATTGGGCCCAATA
20474292 GGCCATATGAATGTAATTGGGCCCAATA
1 GGCCATATGAATGTAATTGGGCCCAATA
20474320 GGCCATATGAAT
1 GGCCATATGAAT
20474332 AAGATTGGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (28 bp):
GGCCATATGAATGTAATTGGGCCCAATA
Found at i:20478895 original size:35 final size:35
Alignment explanation
Indices: 20478856--20478930 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
20478846 ACGACCATAC
20478856 AAAGCCTCATAAGGTGCCATTTTGATACTCGACTG
1 AAAGCCTCATAAGGTGCCATTTTGATACTCGACTG
20478891 AAAGCCTCATAAGGTGCCATTTTGATACTCGACTG
1 AAAGCCTCATAAGGTGCCATTTTGATACTCGACTG
20478926 AAAGC
1 AAAGC
20478931 TGTTATTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (35 bp):
AAAGCCTCATAAGGTGCCATTTTGATACTCGACTG
Found at i:20485145 original size:47 final size:47
Alignment explanation
Indices: 20485091--20485183 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
20485081 CCCAGACAGG
20485091 TTCTTACTCGTACACATATATCAGAATCACATATTGATGCAATGGTT
1 TTCTTACTCGTACACATATATCAGAATCACATATTGATGCAATGGTT
*
20485138 TTCTTACTCGTACACATATATCAGAATCACATATTGATGCCATGGT
1 TTCTTACTCGTACACATATATCAGAATCACATATTGATGCAATGGT
20485184 CTTACTCACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (47 bp):
TTCTTACTCGTACACATATATCAGAATCACATATTGATGCAATGGTT
Found at i:20485209 original size:44 final size:45
Alignment explanation
Indices: 20485089--20485202 Score: 176
Period size: 47 Copynumber: 2.5 Consensus size: 45
20485079 GTCCCAGACA
20485089 GGTTCTTACTCGTACACATATATCAGAATCACATATTGATGCAAT
1 GGTTCTTACTCGTACACATATATCAGAATCACATATTGATGCAAT
*
20485134 GGTTTTCTTACTCGTACACATATATCAGAATCACATATTGATGCCAT
1 GG--TTCTTACTCGTACACATATATCAGAATCACATATTGATGCAAT
**
20485181 GG-TCTTACTCACACACATATAT
1 GGTTCTTACTCGTACACATATAT
20485203 AGGAATCTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
44 18 0.28
45 2 0.03
47 44 0.69
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (45 bp):
GGTTCTTACTCGTACACATATATCAGAATCACATATTGATGCAAT
Found at i:20492433 original size:15 final size:17
Alignment explanation
Indices: 20492415--20492446 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20492405 TAGCATAATT
20492415 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
20492430 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
20492447 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:20497780 original size:37 final size:37
Alignment explanation
Indices: 20497730--20497801 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
20497720 TTTAGCTCGA
*
20497730 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGGC
1 ATAATCTCCACACGTAGCCATCGGGTCTTACCCGGGC
20497767 ATAATCTCCACACGTAGCCATCGGGTCTTACCCGG
1 ATAATCTCCACACGTAGCCATCGGGTCTTACCCGG
20497802 AATATATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (37 bp):
ATAATCTCCACACGTAGCCATCGGGTCTTACCCGGGC
Found at i:20497995 original size:48 final size:48
Alignment explanation
Indices: 20497935--20498040 Score: 158
Period size: 48 Copynumber: 2.2 Consensus size: 48
20497925 CGGCCACAAT
* * *
20497935 ATATACAGATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGACATTCGGCTTTACCAC
*
20497983 ATATACATATCTCATACATATTTCACACTAGACATTTGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGACATTCGGCTTTACCAC
* *
20498031 ACATATATAT
1 ATATACATAT
20498041 ATTTATCTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.35
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACACTAGACATTCGGCTTTACCAC
Found at i:20506166 original size:14 final size:13
Alignment explanation
Indices: 20506143--20506174 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
20506133 GGGATATCAA
20506143 AACAATAATTAAG
1 AACAATAATTAAG
20506156 AACACATAATTAAG
1 AACA-ATAATTAAG
20506170 AACAA
1 AACAA
20506175 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:20507206 original size:45 final size:45
Alignment explanation
Indices: 20507137--20507223 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
20507127 TATCTAATCT
20507137 GAACTCATTGAGTTGTGGTATGAGTTCGTGATATATGTGACAACC
1 GAACTCATTGAGTTGTGGTATGAGTTCGTGATATATGTGACAACC
* *
20507182 GAACTCATTGAGTTGTGGTTTGAGTTTGTGATATATGTGACA
1 GAACTCATTGAGTTGTGGTATGAGTTCGTGATATATGTGACA
20507224 CATGTTTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.37
Consensus pattern (45 bp):
GAACTCATTGAGTTGTGGTATGAGTTCGTGATATATGTGACAACC
Found at i:20510659 original size:5 final size:6
Alignment explanation
Indices: 20510644--20510673 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20510634 ATCTTGTGGC
20510644 AAAAAG AAAAAG AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
20510674 TGGTAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:20510665 original size:11 final size:11
Alignment explanation
Indices: 20510644--20510673 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
20510634 ATCTTGTGGC
20510644 AAAAAGAAAAAG
1 AAAAAG-AAAAG
20510656 AAAAAGAAAAG
1 AAAAAGAAAAG
20510667 AAAAAGA
1 AAAAAGA
20510674 TGGTAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:20520019 original size:13 final size:14
Alignment explanation
Indices: 20520001--20520029 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20519991 TGAGTTGAGT
20520001 TTATGGCAT-AATG
1 TTATGGCATAAATG
20520014 TTATGGCATAAATG
1 TTATGGCATAAATG
20520028 TT
1 TT
20520030 GTATGGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (14 bp):
TTATGGCATAAATG
Found at i:20530468 original size:17 final size:17
Alignment explanation
Indices: 20530446--20530479 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20530436 AAAGATAAAA
20530446 CATTAGTAACAAAAACT
1 CATTAGTAACAAAAACT
*
20530463 CATTAGTAACGAAAACT
1 CATTAGTAACAAAAACT
20530480 GAGTATCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (17 bp):
CATTAGTAACAAAAACT
Found at i:20530923 original size:16 final size:18
Alignment explanation
Indices: 20530898--20530930 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20530888 TTTTATTTTT
20530898 AAAAATTATATT-TATTG
1 AAAAATTATATTATATTG
20530915 AAAAA-TATATTATATT
1 AAAAATTATATTATATT
20530931 CAAGACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AAAAATTATATTATATTG
Found at i:20545888 original size:39 final size:39
Alignment explanation
Indices: 20545845--20546058 Score: 284
Period size: 39 Copynumber: 5.4 Consensus size: 39
20545835 TCTTAAATTA
20545845 TGAATGTTATGTGATTATACAAGTATTGTAATATATGCT
1 TGAATGTTATGTGATTATACAAGTATTGTAATATATGCT
*
20545884 TGAATGTTATGAGATTATACAAGTATTGTGATAATATATGCT
1 TGAATGTTATGTGATTATACAAGTA-T-TG-TAATATATGCT
* *
20545926 TTAATGTTATGTGATTATACGAGTATTGTAATATATGCT
1 TGAATGTTATGTGATTATACAAGTATTGTAATATATGCT
* *
20545965 TGAATGTTATGAGATTATACAAGTATTGTGATATATGCT
1 TGAATGTTATGTGATTATACAAGTATTGTAATATATGCT
* *** * *
20546004 TAAATGTTATGTGATTATTTGAGCATTGTGATATATGCT
1 TGAATGTTATGTGATTATACAAGTATTGTAATATATGCT
* *
20546043 TGTATGTTAGGTGATT
1 TGAATGTTATGTGATT
20546059 TATGTGTAAT
Statistics
Matches: 155, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 116 0.75
40 3 0.02
41 3 0.02
42 33 0.21
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (39 bp):
TGAATGTTATGTGATTATACAAGTATTGTAATATATGCT
Found at i:20545937 original size:81 final size:78
Alignment explanation
Indices: 20545847--20546051 Score: 320
Period size: 81 Copynumber: 2.6 Consensus size: 78
20545837 TTAAATTATG
*
20545847 AATGTTATGTGATTATACAAGTATTGTAATATATGCTTGAATGTTATGAGATTATACAAGTATTG
1 AATGTTATGTGATTATACGAGTATTGTAATATATGCTTGAATGTTATGAGATTATACAAGTATTG
*
20545912 TGATAATATATGCTTT
66 TG---ATATATGCTTA
20545928 AATGTTATGTGATTATACGAGTATTGTAATATATGCTTGAATGTTATGAGATTATACAAGTATTG
1 AATGTTATGTGATTATACGAGTATTGTAATATATGCTTGAATGTTATGAGATTATACAAGTATTG
20545993 TGATATATGCTTA
66 TGATATATGCTTA
** * * *
20546006 AATGTTATGTGATTATTTGAGCATTGTGATATATGCTTGTATGTTA
1 AATGTTATGTGATTATACGAGTATTGTAATATATGCTTGAATGTTA
20546052 GGTGATTTAT
Statistics
Matches: 117, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
78 51 0.44
81 66 0.56
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (78 bp):
AATGTTATGTGATTATACGAGTATTGTAATATATGCTTGAATGTTATGAGATTATACAAGTATTG
TGATATATGCTTA
Found at i:20547428 original size:7 final size:7
Alignment explanation
Indices: 20547387--20547510 Score: 54
Period size: 7 Copynumber: 17.4 Consensus size: 7
20547377 TTAGTTATCA
*
20547387 TTATAGT
1 TTATGGT
*
20547394 TTAGGGT
1 TTATGGT
20547401 TTATGGT
1 TTATGGT
* *
20547408 ATAGGGT
1 TTATGGT
*
20547415 GTATGGT
1 TTATGGT
20547422 TTATGGT
1 TTATGGT
* *
20547429 TTAAGCT
1 TTATGGT
*
20547436 TTAAGAGTT
1 TTATG-G-T
20547445 ATTAT--T
1 -TTATGGT
*
20547451 TTAAGGT
1 TTATGGT
* *
20547458 TTATCGA
1 TTATGGT
*
20547465 TTATGGA
1 TTATGGT
20547472 TTATGGGT
1 TTAT-GGT
* *
20547480 TTAGGGA
1 TTATGGT
*
20547487 TTATGGC
1 TTATGGT
20547494 TTATGGT
1 TTATGGT
*
20547501 TTATGAT
1 TTATGGT
20547508 TTA
1 TTA
20547511 AGGGTTGGGG
Statistics
Matches: 87, Mismatches: 24, Indels: 12
0.71 0.20 0.10
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 74 0.85
8 5 0.06
9 1 0.01
10 3 0.03
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (7 bp):
TTATGGT
Found at i:20547480 original size:22 final size:20
Alignment explanation
Indices: 20547455--20547508 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
20547445 ATTATTTTAA
20547455 GGTTTATCGATTATGGATTAT
1 GGTTTAT-GATTATGGATTAT
* *
20547476 GGGTTTAGGGATTATGGCTTAT
1 -GGTTTA-TGATTATGGATTAT
20547498 GGTTTATGATT
1 GGTTTATGATT
20547509 TAAGGGTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 18 0.64
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.46
Consensus pattern (20 bp):
GGTTTATGATTATGGATTAT
Found at i:20547589 original size:21 final size:22
Alignment explanation
Indices: 20547536--20547590 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
20547526 TGGTCAGGGG
* *
20547536 TTTAGGGTTTATGGTTTTATGG
1 TTTAGAGTTTATGGTTTTATGA
* *
20547558 TTTATATTTTAT-GTTTTATGA
1 TTTAGAGTTTATGGTTTTATGA
20547579 TTTAGAGTTTAT
1 TTTAGAGTTTAT
20547591 AGGGATACGG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (22 bp):
TTTAGAGTTTATGGTTTTATGA
Found at i:20548008 original size:21 final size:21
Alignment explanation
Indices: 20547984--20548030 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
20547974 TTAGGGTGTA
*
20547984 GGTTTATTG-TCTATGATTTAG
1 GGTTTA-TGATCTAAGATTTAG
20548005 GGTTTATGATCTAAGATTTAG
1 GGTTTATGATCTAAGATTTAG
20548026 GGTTT
1 GGTTT
20548031 GGTGTTTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49
Consensus pattern (21 bp):
GGTTTATGATCTAAGATTTAG
Found at i:20548052 original size:28 final size:28
Alignment explanation
Indices: 20548021--20548081 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
20548011 TGATCTAAGA
*
20548021 TTTAGGGTTTGGTGTTTGGAGATCATGG
1 TTTAAGGTTTGGTGTTTGGAGATCATGG
** *
20548049 TTTAATTTTTGGTGTTTGGAGATTATGG
1 TTTAAGGTTTGGTGTTTGGAGATCATGG
20548077 TTTAA
1 TTTAA
20548082 TTGTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.49
Consensus pattern (28 bp):
TTTAAGGTTTGGTGTTTGGAGATCATGG
Found at i:20548082 original size:28 final size:28
Alignment explanation
Indices: 20548028--20548083 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
20548018 AGATTTAGGG
20548028 TTTGGTGTTTGGAGATCATGGTTTAATT
1 TTTGGTGTTTGGAGATCATGGTTTAATT
*
20548056 TTTGGTGTTTGGAGATTATGGTTTAATT
1 TTTGGTGTTTGGAGATCATGGTTTAATT
20548084 GTATATATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.52
Consensus pattern (28 bp):
TTTGGTGTTTGGAGATCATGGTTTAATT
Found at i:20551194 original size:37 final size:37
Alignment explanation
Indices: 20551144--20551217 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
20551134 TTAGACGTCT
20551144 TACGTAGGTGTATAACTCCATTGCATGATTTTTGAGG
1 TACGTAGGTGTATAACTCCATTGCATGATTTTTGAGG
20551181 TACGTAGGTGTATAACTCCATTGCATGATTTTTGAGG
1 TACGTAGGTGTATAACTCCATTGCATGATTTTTGAGG
20551218 GACTTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (37 bp):
TACGTAGGTGTATAACTCCATTGCATGATTTTTGAGG
Found at i:20554746 original size:24 final size:24
Alignment explanation
Indices: 20554648--20554747 Score: 155
Period size: 24 Copynumber: 4.2 Consensus size: 24
20554638 AATCTGTCAA
*
20554648 GAGAGGATTTAGGAGTTGATAAGA
1 GAGAGGATTTAGGAGTTGATAAGG
*
20554672 GATAGGATTTAGGAGTTGATAAGG
1 GAGAGGATTTAGGAGTTGATAAGG
* *
20554696 GATAGGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGTTGATAAGG
*
20554720 GAGAGGATTTAGGAGTTGATTAGG
1 GAGAGGATTTAGGAGTTGATAAGG
20554744 GAGA
1 GAGA
20554748 ACAGTGTTGG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.34, C:0.01, G:0.39, T:0.26
Consensus pattern (24 bp):
GAGAGGATTTAGGAGTTGATAAGG
Found at i:20555735 original size:16 final size:15
Alignment explanation
Indices: 20555709--20555739 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
20555699 ACTAGATCGG
20555709 TAAAAGCTGAAAAGC
1 TAAAAGCTGAAAAGC
20555724 TAAAATGCTGAAAAGC
1 TAAAA-GCTGAAAAGC
20555740 CAGCATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (15 bp):
TAAAAGCTGAAAAGC
Found at i:20556745 original size:6 final size:6
Alignment explanation
Indices: 20556727--20556820 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
20556717 AAGAAACATT
* *
20556727 ATCAGA A-CTAGA ATCAGA ATTAGA ATCAGA ATCAGA ATCAGA ATTAG-
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * *
20556774 GTGACAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 AT--CAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
20556821 GTGAATGCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.06
6 58 0.83
7 6 0.09
8 2 0.03
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:20556751 original size:18 final size:18
Alignment explanation
Indices: 20556727--20556820 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 18
20556717 AAGAAACATT
20556727 ATCAGAA-CTAGAATCAGA
1 ATCAGAATC-AGAATCAGA
*
20556745 ATTAGAATCAGAATCAGA
1 ATCAGAATCAGAATCAGA
* *
20556763 ATCAGAATTAG-GTGACAGA
1 ATCAGAATCAGAAT--CAGA
*
20556782 ATCAGAATCAGTATCAGGTA
1 ATCAGAATCAGAATCA-G-A
*
20556802 A-CAGAATCAAAATCAGA
1 ATCAGAATCAGAATCAGA
20556819 AT
1 AT
20556821 GTGAATGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.05
18 27 0.44
19 28 0.46
20 3 0.05
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (18 bp):
ATCAGAATCAGAATCAGA
Found at i:20556787 original size:25 final size:25
Alignment explanation
Indices: 20556736--20556820 Score: 111
Period size: 25 Copynumber: 3.4 Consensus size: 25
20556726 TATCAGAACT
20556736 AGAATCAGAATTA-G-AATCAGAATC
1 AGAATCAGAATTAGGTAA-CAGAATC
*
20556760 AGAATCAGAATTAGGTGACAGAATC
1 AGAATCAGAATTAGGTAACAGAATC
* *
20556785 AGAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATTAGGTAACAGAATC
*
20556810 AAAATCAGAAT
1 AGAATCAGAAT
20556821 GTGAATGCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
24 13 0.25
25 39 0.74
26 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (25 bp):
AGAATCAGAATTAGGTAACAGAATC
Found at i:20557099 original size:27 final size:26
Alignment explanation
Indices: 20557051--20557102 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
20557041 GCGAGGCTAC
*
20557051 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
20557077 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
20557103 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:20557368 original size:27 final size:27
Alignment explanation
Indices: 20557338--20557775 Score: 536
Period size: 27 Copynumber: 16.2 Consensus size: 27
20557328 TAACACCCTA
* *
20557338 AGGGTAAAATGGTAATTTTATAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
** * *
20557365 AGGGTAAAACGGTAATTCTGTAAATTG
1 AGGGTAAAATAGTAATTTTGTAAATCG
*
20557392 AGGGTAAAACAGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
*
20557419 AGGGTAAAATAATAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
*
20557446 AGGGTAAAATAGTAATTTTGTCAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* * *
20557473 AGGGTAAAA-CGATAATTCTGTAAATGG
1 AGGGTAAAATAG-TAATTTTGTAAATCG
* *
20557500 AGGGTAAAACAGTAATTTTATAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* * *
20557527 AGGGTAAAACAGTAATTCTGTAAATTG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* *
20557554 AGGGTAAAACAGTAATTTTGCAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* * *
20557581 AGGGTAAAATAATAATTCTATAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* *
20557608 AGGGTAAAATAGTAATTCTGTCAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* * *
20557635 AGGGTAAAATGGTAATTCTATAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
20557662 AGGGTAAAATAGTAATTTTGTAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* ** * *
20557689 AGAGTAAAACGGTAATTTTATAAATTG
1 AGGGTAAAATAGTAATTTTGTAAATCG
*
20557716 AGGGTAAAATAGTAATTCTGTAAATCG
1 AGGGTAAAATAGTAATTTTGTAAATCG
* * *
20557743 AGGGTAAAACAGTAATTTTGTAATTCA
1 AGGGTAAAATAGTAATTTTGTAAATCG
20557770 AGGGTA
1 AGGGTA
20557776 CTTTGATAAT
Statistics
Matches: 355, Mismatches: 54, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 1 0.00
27 353 0.99
28 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (27 bp):
AGGGTAAAATAGTAATTTTGTAAATCG
Found at i:20557800 original size:27 final size:26
Alignment explanation
Indices: 20557770--20557900 Score: 145
Period size: 27 Copynumber: 4.8 Consensus size: 26
20557760 TTGTAATTCA
* *
20557770 AGGGTACTTTGATAATTTTACAAGTCG
1 AGGGTA-TTTGGTAATTTTACAAATCG
* *
20557797 AGGGTATTTCAGTAATTTTACAAATTG
1 AGGGTATTT-GGTAATTTTACAAATCG
*
20557824 ATGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTT-GGTAATTTTACAAATCG
* *
20557851 AGGATATTTGGGTAATTTTATAAATCG
1 AGGGTATTT-GGTAATTTTACAAATCG
*
20557878 GGGGTACTTTGGTAATTTTACAA
1 AGGGTA-TTTGGTAATTTTACAA
20557901 CTGGGGATAT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.03
27 82 0.93
28 3 0.03
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (26 bp):
AGGGTATTTGGTAATTTTACAAATCG
Found at i:20557810 original size:54 final size:54
Alignment explanation
Indices: 20557737--20557926 Score: 163
Period size: 54 Copynumber: 3.5 Consensus size: 54
20557727 GTAATTCTGT
*** * *
20557737 AAATCGAGGGTAAAACAGTAATTTTGTAATTCAAGGGTACTTTGATAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTGTAATTCGAGGGTACTTTGGTAATTTTAC
* ** *
20557791 AAGTCGAGGGTATTTCAGTAATTTTACAAATT-GATGGTA-TTTCGGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTT-GTAATTCGAGGGTACTTT-GGTAATTTTAC
* ** * * *
20557845 AAATCGAGGATATTTGGGTAATTTTATAAATCGGGGGTACTTTGGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTGTAATTCGAGGGTACTTTGGTAATTTTAC
* * *
20557899 AACT-G-GGGATATTTCATTAATTTGGTAA
1 AAATCGAGGG-TATTTCAGTAATTTTGTAA
20557927 ACTAAAGTAT
Statistics
Matches: 106, Mismatches: 25, Indels: 11
0.75 0.18 0.08
Matches are distributed among these distances:
52 2 0.02
53 21 0.20
54 76 0.72
55 7 0.07
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.38
Consensus pattern (54 bp):
AAATCGAGGGTATTTCAGTAATTTTGTAATTCGAGGGTACTTTGGTAATTTTAC
Found at i:20559478 original size:30 final size:32
Alignment explanation
Indices: 20559410--20559485 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
20559400 ATAGAAGTTT
* * **
20559410 TGTTATTTATATAAAATACATATGATTTTTGG
1 TGTTATATATATAAAATACATATGATGTGGGG
*
20559442 TGTTATATATATAAAATATATATGA-GTGGGG
1 TGTTATATATATAAAATACATATGATGTGGGG
20559473 T-TTATAATATATA
1 TGTTAT-ATATATA
20559486 TATGTGTGCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 4 0.11
31 11 0.29
32 23 0.61
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.46
Consensus pattern (32 bp):
TGTTATATATATAAAATACATATGATGTGGGG
Found at i:20559517 original size:32 final size:32
Alignment explanation
Indices: 20559476--20559538 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
20559466 AGTGGGGTTT
*
20559476 ATAATATATATATGTGTGCATGGGTGTTATAA
1 ATAATATATATATGGGTGCATGGGTGTTATAA
*
20559508 ATAATATATATTTGGGTGCATGGGTGTTATA
1 ATAATATATATATGGGTGCATGGGTGTTATA
20559539 TGTATAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (32 bp):
ATAATATATATATGGGTGCATGGGTGTTATAA
Found at i:20560602 original size:17 final size:17
Alignment explanation
Indices: 20560580--20560654 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
20560570 TTATGATGGA
20560580 GCATGAACTATTATTTT
1 GCATGAACTATTATTTT
* * *
20560597 GCATGAATTGTTATTTG
1 GCATGAACTATTATTTT
** *
20560614 GTGTGAACTGA-TATTTC
1 GCATGAACT-ATTATTTT
**
20560631 ATATGAACTATTATTTTT
1 GCATGAACTATTA-TTTT
20560649 GCATGA
1 GCATGA
20560655 GCTGTCATTT
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
16 1 0.02
17 34 0.81
18 7 0.17
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.45
Consensus pattern (17 bp):
GCATGAACTATTATTTT
Found at i:20560665 original size:52 final size:51
Alignment explanation
Indices: 20560582--20560690 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 51
20560572 ATGATGGAGC
* * **
20560582 ATGAACTATTATTTTGCATGAATTGTTATTTGGTGTGAACTGATATTTCAT
1 ATGAACTATTATTTTGCATGAACTGTCATTTGGTAAGAACTGATATTTCAT
* *
20560633 ATGAACTATTATTTTTGCATGAGCTGTCATTTGGTAAGAACTGTTATTTCAT
1 ATGAACTATTA-TTTTGCATGAACTGTCATTTGGTAAGAACTGATATTTCAT
20560685 ATGAAC
1 ATGAAC
20560691 AAATGTTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 11 0.22
52 40 0.78
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.44
Consensus pattern (51 bp):
ATGAACTATTATTTTGCATGAACTGTCATTTGGTAAGAACTGATATTTCAT
Found at i:20560690 original size:17 final size:17
Alignment explanation
Indices: 20560617--20560690 Score: 51
Period size: 17 Copynumber: 4.3 Consensus size: 17
20560607 TTATTTGGTG
*
20560617 TGAACTGATATTTCATA
1 TGAACTGTTATTTCATA
* *
20560634 TGAACTATTATTT-TTGCA
1 TGAACTGTTATTTCAT--A
* * **
20560652 TGAGCTGTCATTTGGTA
1 TGAACTGTTATTTCATA
*
20560669 AGAACTGTTATTTCATA
1 TGAACTGTTATTTCATA
20560686 TGAAC
1 TGAAC
20560691 AAATGTTTTA
Statistics
Matches: 41, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
16 1 0.02
17 28 0.68
18 11 0.27
19 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (17 bp):
TGAACTGTTATTTCATA
Found at i:20561171 original size:16 final size:16
Alignment explanation
Indices: 20561150--20561182 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20561140 CATTGCATTA
20561150 GATAGATGATTGAATG
1 GATAGATGATTGAATG
20561166 GATAGATGATTGAATG
1 GATAGATGATTGAATG
20561182 G
1 G
20561183 TGGATTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (16 bp):
GATAGATGATTGAATG
Found at i:20564129 original size:19 final size:20
Alignment explanation
Indices: 20564107--20564150 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20564097 CTTTTCTTAC
*
20564107 TTTTAC-TTTTCTTTCATGA
1 TTTTACATTTTCTTGCATGA
*
20564126 TTTTACATTTTCTTGCATGG
1 TTTTACATTTTCTTGCATGA
20564146 TTTTA
1 TTTTA
20564151 GTATATCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTTACATTTTCTTGCATGA
Found at i:20567292 original size:255 final size:255
Alignment explanation
Indices: 20566841--20567335 Score: 954
Period size: 255 Copynumber: 1.9 Consensus size: 255
20566831 GAAATAACTG
20566841 GTATTATGTCTCGTTTATTGATGTATGCACTCGTTTTACATGGATATATCTGCTTCGACAAAAGT
1 GTATTATGTCTCGTTTATTGATGTATGCACTCGTTTTACATGGATATATCTGCTTCGACAAAAGT
20566906 CTCAGGCTATGCAGTGTTTTGTTCAGTTTCAGCAACTTGTTAAAACTCAGTTTGGAAAGATGATT
66 CTCAGGCTATGCAGTGTTTTGTTCAGTTTCAGCAACTTGTTAAAACTCAGTTTGGAAAGATGATT
20566971 AAACAATTTTAAAGTGATTAGGGCGGAGAGTATCGAGCCTTCACATTTGTTCTAGCTTTGCAAGG
131 AAACAATTTTAAAGTGATTAGGGCGGAGAGTATCGAGCCTTCACATTTGTTCTAGCTTTGCAAGG
**
20567036 GATAGTTCATCGATTGACGTGTCCACGTACTTTTGAAAAAAATGGTTCATCGATTGACTT
196 GATAGTTCATCGATTGACGTGTCCACGTACTTCCGAAAAAAATGGTTCATCGATTGACTT
20567096 GTATTATGTCTCGTTTATTGATGTATGCACTCGTTTTACATGGATATATCTGCTTCGACAAAAGT
1 GTATTATGTCTCGTTTATTGATGTATGCACTCGTTTTACATGGATATATCTGCTTCGACAAAAGT
20567161 CTCAGGCTATGCAGTGTTTTGTTCAGTTTCAGCAACTTGTTAAAACTCAGTTTGGAAAGATGATT
66 CTCAGGCTATGCAGTGTTTTGTTCAGTTTCAGCAACTTGTTAAAACTCAGTTTGGAAAGATGATT
* *
20567226 AAACAATTTTAAAGTGATTGGGGCGGAGAGTATCGAGGCTTCACATTTGTTCTAGCTTTGCAAGG
131 AAACAATTTTAAAGTGATTAGGGCGGAGAGTATCGAGCCTTCACATTTGTTCTAGCTTTGCAAGG
20567291 GATAGTTCATCGATTGACGTGTCCACGTACTTCCGAAAAAAATGG
196 GATAGTTCATCGATTGACGTGTCCACGTACTTCCGAAAAAAATGG
20567336 AGTGGCTGAA
Statistics
Matches: 236, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
255 236 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (255 bp):
GTATTATGTCTCGTTTATTGATGTATGCACTCGTTTTACATGGATATATCTGCTTCGACAAAAGT
CTCAGGCTATGCAGTGTTTTGTTCAGTTTCAGCAACTTGTTAAAACTCAGTTTGGAAAGATGATT
AAACAATTTTAAAGTGATTAGGGCGGAGAGTATCGAGCCTTCACATTTGTTCTAGCTTTGCAAGG
GATAGTTCATCGATTGACGTGTCCACGTACTTCCGAAAAAAATGGTTCATCGATTGACTT
Found at i:20578395 original size:50 final size:50
Alignment explanation
Indices: 20578222--20578608 Score: 283
Period size: 50 Copynumber: 7.7 Consensus size: 50
20578212 TGAGAACACA
* * *** ** * *
20578222 TGTGTGGTACTATGTGCAGGCTACTATGTGTTTAAGATAGTTTTAGGTCGCC
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-G-GATAGGTCACG
* * * ** * *
20578274 TGTGTAGTACTAAGTGCAGGGTACTATGCGTACCCGATAGTTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-GGATAGGTCACG
* * * * *
20578325 TGTGTAGTACTAAGTGCAGGCTACTATATGTATCAAATGGTTAGGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGATAGGTCACG
* * * * * *
20578375 TGTGTAGTACTAAGTGCAGGCTACCACGTGTACCGGATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGATAGGTCACG
* * * * ** * *
20578425 TGTGTTGTACTAAGTACAGGCTACTATGCGTACCCG-TTAACTTTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGA--TAGGTCACG
* * * *
20578476 TGTGTAGTACTAAGTGCAGGCTACTACT-TTTATCAGATGGATAAGTGACG
1 TGTGTAGTACTAAGTGCAGGCTACTA-TGTGTACCAGATGGATAGGTCACG
* * * * *
20578526 TGTGTAGTACGAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGATAGGTCACG
* * *
20578576 TGTGTAGTACTGAGTGTAGGCTACTATGCGTAC
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTAC
20578609 TAGAGAGCTT
Statistics
Matches: 260, Mismatches: 70, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
49 3 0.01
50 150 0.58
51 72 0.28
52 35 0.13
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGATAGGTCACG
Found at i:20578494 original size:151 final size:151
Alignment explanation
Indices: 20578265--20578608 Score: 503
Period size: 151 Copynumber: 2.3 Consensus size: 151
20578255 AAGATAGTTT
* * *
20578265 TAGGTCGCCTGTGTAGTACTAAGTGCAGGGTACTATGCGTACCCGATAGTTTCGATCACGTGTGT
1 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATACTTTCGATCACGTGTGT
* * * *
20578330 AGTACTAAGTGCAGGCTACTA-TATGTATCAAATGGTTAGGTCATGTGTGTAGTACTAAGTGCAG
66 AGTACTAAGTGCAGGCTACTACT-TGTATCAAATGGATAAGTCACGTGTGTAGTACGAAGTGCAG
*
20578394 GCTACCACGTGTACCGGATTGA
130 GCTACCACGTGTACCAGATTGA
* * *
20578416 TAGGTCGCATGTGTTGTACTAAGTACAGGCTACTATGCGTACCCGTTAACTTT-GATCACGTGTG
1 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAT-ACTTTCGATCACGTGTG
* * *
20578480 TAGTACTAAGTGCAGGCTACTACTTTTATCAGATGGATAAGTGACGTGTGTAGTACGAAGTGCAG
65 TAGTACTAAGTGCAGGCTACTACTTGTATCAAATGGATAAGTCACGTGTGTAGTACGAAGTGCAG
*
20578545 GCTACTACGTGTACCAGATTGA
130 GCTACCACGTGTACCAGATTGA
* *
20578567 TAGGTCGCATGTGTAGTACTGAGTGTAGGCTACTATGCGTAC
1 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTAC
20578609 TAGAGAGCTT
Statistics
Matches: 172, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
151 167 0.97
152 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (151 bp):
TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATACTTTCGATCACGTGTGT
AGTACTAAGTGCAGGCTACTACTTGTATCAAATGGATAAGTCACGTGTGTAGTACGAAGTGCAGG
CTACCACGTGTACCAGATTGA
Found at i:20578559 original size:101 final size:101
Alignment explanation
Indices: 20578374--20578559 Score: 239
Period size: 101 Copynumber: 1.8 Consensus size: 101
20578364 GTTAGGTCAT
* * * * *
20578374 GTGTGTAGTACTAAGTGCAGGCTACCACGTGTACCGGATTGATAGGTCGCATGTGTTGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACCACGTGTACCAGATGGATAAGTCGCATGTGTAGTACGAAG
*
20578439 TACAGGCTACTATGCGTACCCGTTAACTTTGATCAC
66 TACAGGCTACTACGCGTACCCGTTAACTTTGATCAC
* * * * *
20578475 GTGTGTAGTACTAAGTGCAGGCTACTACTTTTATCAGATGGATAAGT-GACGTGTGTAGTACGAA
1 GTGTGTAGTACTAAGTGCAGGCTACCACGTGTACCAGATGGATAAGTCG-CATGTGTAGTACGAA
* *
20578539 GTGCAGGCTACTACGTGTACC
65 GTACAGGCTACTACGCGTACC
20578560 AGATTGATAG
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
100 1 0.01
101 70 0.99
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (101 bp):
GTGTGTAGTACTAAGTGCAGGCTACCACGTGTACCAGATGGATAAGTCGCATGTGTAGTACGAAG
TACAGGCTACTACGCGTACCCGTTAACTTTGATCAC
Found at i:20579483 original size:180 final size:180
Alignment explanation
Indices: 20579171--20579525 Score: 507
Period size: 180 Copynumber: 2.0 Consensus size: 180
20579161 TCCGAGATCT
* *
20579171 GTACCATGAGATAAATAATCTTTAGTGAAGAAAGATCGGAACTGTCAGATAGTGAAATAGGGGTA
1 GTACCATGAGATAAATAATCTTTAGTGAAGAAAGATCAGAACAGTCAGATAGTGAAATAGGGGTA
** *
20579236 TCTTTAATGAATAAAATGTACTAATTGGCTAAACCAAAAATTCTTAAAAGTTTATGGGAATAATA
66 AATTTAATGAATAAAATGTACTAATTGGCTAAACCAAAAATTCTTAAAAGTTTATGGGAAGAATA
* * * * *
20579301 TATGTGAGTCTCATTTCTGGTAAAATTATCGGTTCTTAATTTGGAGTCCC
131 TATATGAATCTCATTTCTGGGAAAATTAACGGATCTTAATTTGGAGTCCC
* * * **
20579351 GTACCATGAGATAAATAATTTTTAGTGAAGAGAGGTCAGAACAGTTGGATAGTGAAAT-GAGGGT
1 GTACCATGAGATAAATAATCTTTAGTGAAGAAAGATCAGAACAGTCAGATAGTGAAATAG-GGGT
* * *
20579415 AAATTTAATGAATAAATTGTACTAATTGGCTAAACCAAAAATT-TTGAAAATTTTATGGTAAGAA
65 AAATTTAATGAATAAAATGTACTAATTGGCTAAACCAAAAATTCTT-AAAAGTTTATGGGAAGAA
*
20579479 TATATATGAATCTCGTTTCTGGGAAAATTAACGGATCTTAATTTGGA
129 TATATATGAATCTCATTTCTGGGAAAATTAACGGATCTTAATTTGGA
20579526 TTTCTGTAGC
Statistics
Matches: 154, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
179 3 0.02
180 151 0.98
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (180 bp):
GTACCATGAGATAAATAATCTTTAGTGAAGAAAGATCAGAACAGTCAGATAGTGAAATAGGGGTA
AATTTAATGAATAAAATGTACTAATTGGCTAAACCAAAAATTCTTAAAAGTTTATGGGAAGAATA
TATATGAATCTCATTTCTGGGAAAATTAACGGATCTTAATTTGGAGTCCC
Found at i:20579735 original size:36 final size:36
Alignment explanation
Indices: 20579683--20579755 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
20579673 CTTTATGCTT
20579683 ACTCTCTTTCCATTCCTTTGTCTTATAGTGTCACCA
1 ACTCTCTTTCCATTCCTTTGTCTTATAGTGTCACCA
*
20579719 ACTCTCTTTCCTTTCCTTTGTCTTATAGTGTCACCA
1 ACTCTCTTTCCATTCCTTTGTCTTATAGTGTCACCA
20579755 A
1 A
20579756 GCCAGCTCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.16, C:0.30, G:0.08, T:0.45
Consensus pattern (36 bp):
ACTCTCTTTCCATTCCTTTGTCTTATAGTGTCACCA
Found at i:20596772 original size:24 final size:24
Alignment explanation
Indices: 20596744--20596795 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
20596734 TTAGTAGGTC
* *
20596744 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
20596768 AAATATATTATACTAATATATACT
1 AAATAAACTATACTAATAAATACT
20596792 AAAT
1 AAAT
20596796 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:20607716 original size:39 final size:39
Alignment explanation
Indices: 20607672--20607752 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
20607662 ATTATATTAT
20607672 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
* *
20607711 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC
1 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
20607750 CAG
1 CAG
20607753 TGTCTTGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (39 bp):
CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
Found at i:20609754 original size:10 final size:9
Alignment explanation
Indices: 20609739--20609764 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20609729 TAATACCGAG
20609739 TTTTTTTAT
1 TTTTTTTAT
20609748 TTTTTTTAT
1 TTTTTTTAT
20609757 TTTTTTTA
1 TTTTTTTA
20609765 AGAATAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:20610880 original size:5 final size:5
Alignment explanation
Indices: 20610870--20610967 Score: 74
Period size: 6 Copynumber: 18.2 Consensus size: 5
20610860 TATGTCTTTC
*
20610870 AAAAT AAAAT AATAAT AAAATT GAAAT AAAAAT CAAAAT CAAAAT AAAAAT
1 AAAAT AAAAT AA-AAT AAAA-T AAAAT -AAAAT -AAAAT -AAAAT -AAAAT
* *
20610921 AAAAAT AAAGT -AAAG AAAAT AAAAAT AAGAAT -AAAT AAAAT AAAAT
1 -AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT
20610967 A
1 A
20610968 GGAGGATTCA
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
4 5 0.06
5 30 0.38
6 43 0.55
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20610914 original size:18 final size:17
Alignment explanation
Indices: 20610868--20610934 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
20610858 GATATGTCTT
*
20610868 TCAAAATAAAATAATAA
1 TCAAAATAAAATAAAAA
*
20610885 T-AAAATTGAAATAAAAA
1 TCAAAA-TAAAATAAAAA
20610902 TCAAAATCAAAATAAAAA
1 TCAAAAT-AAAATAAAAA
* *
20610920 TAAAAATAAAGTAAA
1 TCAAAATAAAATAAA
20610935 GAAAATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
16 4 0.10
17 19 0.45
18 19 0.45
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (17 bp):
TCAAAATAAAATAAAAA
Found at i:20610941 original size:20 final size:21
Alignment explanation
Indices: 20610916--20610965 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
20610906 AATCAAAATA
*
20610916 AAAATAAAAATAA-AGTAAAG
1 AAAATAAAAATAAGAATAAAG
*
20610936 AAAATAAAAATAAGAATAAAT
1 AAAATAAAAATAAGAATAAAG
20610957 AAAATAAAA
1 AAAATAAAA
20610966 TAGGAGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (21 bp):
AAAATAAAAATAAGAATAAAG
Found at i:20610965 original size:26 final size:25
Alignment explanation
Indices: 20610871--20610967 Score: 88
Period size: 26 Copynumber: 3.6 Consensus size: 25
20610861 ATGTCTTTCA
* *
20610871 AAATAAAATAATAATAAAATTGAAATAA
1 AAATAAAATAA-AATAAAAAT-AAA-AT
20610899 AAATCAAAATCAAAATAAAAATAAAAAT
1 AAAT-AAAAT-AAAATAAAAAT-AAAAT
*
20610927 AAAGT-AAAGAAAATAAAAATAAGAAT
1 AAA-TAAAATAAAATAAAAATAA-AAT
20610953 AAATAAAATAAAATA
1 AAATAAAATAAAATA
20610968 GGAGGATTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
25 3 0.05
26 26 0.44
27 3 0.05
28 8 0.14
29 17 0.29
30 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (25 bp):
AAATAAAATAAAATAAAAATAAAAT
Found at i:20620223 original size:40 final size:40
Alignment explanation
Indices: 20620168--20620382 Score: 297
Period size: 40 Copynumber: 5.3 Consensus size: 40
20620158 TATTCGGATG
20620168 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
20620208 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
20620251 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
20620291 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
20620331 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
20620371 ATATCC-GGCTAA
1 ATATCCGGGCTAA
20620383 ATCCTATCTT
Statistics
Matches: 158, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 6 0.04
40 114 0.72
41 1 0.01
43 37 0.23
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:20620311 original size:83 final size:80
Alignment explanation
Indices: 20620172--20620382 Score: 293
Period size: 83 Copynumber: 2.6 Consensus size: 80
20620162 CGGATGATAT
* **
20620172 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
20620237 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
20620255 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
20620320 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* *
20620335 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAA
20620383 ATCCTATCTT
Statistics
Matches: 119, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
79 8 0.07
80 45 0.38
81 2 0.02
83 64 0.54
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:20627702 original size:15 final size:15
Alignment explanation
Indices: 20627682--20627711 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20627672 ACAAACAGAT
20627682 GTCTTCATTTAAGCC
1 GTCTTCATTTAAGCC
20627697 GTCTTCATTTAAGCC
1 GTCTTCATTTAAGCC
20627712 ATTTTCGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (15 bp):
GTCTTCATTTAAGCC
Found at i:20629907 original size:50 final size:51
Alignment explanation
Indices: 20629789--20629924 Score: 206
Period size: 50 Copynumber: 2.7 Consensus size: 51
20629779 CTGGTACGCA
* **
20629789 TAGTAGCCTGCACTTAGTACTACACATGCGA-CT-AACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACCAGTCTAATACACG
* *
20629838 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACCAGTCTAATACACG
20629888 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCAC
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTCAC
20629925 AATAGATCAT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
49 29 0.37
50 46 0.59
51 3 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTCACCAGTCTAATACACG
Found at i:20633043 original size:43 final size:42
Alignment explanation
Indices: 20632977--20633131 Score: 170
Period size: 43 Copynumber: 3.6 Consensus size: 42
20632967 AGCTCGTACA
*
20632977 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGTAATCAAATA-CG
* * * *
20633020 ATGCCACTTTCCCAGATAGGGTCTTACATGAAATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATACG
* **
20633062 ATGCCAATGTCCCAGACATGGTCTTACATGTAAATCATAAGCCG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGT-AATCA-AATACG
*
20633106 ATGCCAACGTCCCAGAC-GTGGTCTTA
1 ATGCCAATGTCCCAGACAG-GGTCTTA
20633132 AACTAAATCA
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
42 28 0.30
43 38 0.40
44 28 0.30
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATACG
Found at i:20634251 original size:13 final size:13
Alignment explanation
Indices: 20634233--20634257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20634223 CACAAACGAT
20634233 AAAATTTTCACAC
1 AAAATTTTCACAC
20634246 AAAATTTTCACA
1 AAAATTTTCACA
20634258 GACATTAATT
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:20635108 original size:17 final size:17
Alignment explanation
Indices: 20635088--20635161 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
20635078 TTATGATAAA
20635088 GCATGAACTGTTATTTT
1 GCATGAACTGTTATTTT
*
20635105 GCATGAATTGTTA-TTT
1 GCATGAACTGTTATTTT
* * *
20635121 GATATGAACTGATATTTC
1 G-CATGAACTGTTATTTT
** * *
20635139 ATATGAACTATTATGTT
1 GCATGAACTGTTATTTT
20635156 GCATGA
1 GCATGA
20635162 GTTGTCATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
16 4 0.09
17 37 0.86
18 2 0.05
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (17 bp):
GCATGAACTGTTATTTT
Found at i:20635188 original size:51 final size:51
Alignment explanation
Indices: 20635090--20635197 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
20635080 ATGATAAAGC
* * * * *
20635090 ATGAACTGTTATTTTGCATGAATTGTTATTTGATATGAACTGATATTTCAT
1 ATGAACTATTATGTTGCATGAATTGTCATTTGATAAGAACTAATATTTCAT
* *
20635141 ATGAACTATTATGTTGCATGAGTTGTCATTTGGTAAGAAC-AATTATTTCAT
1 ATGAACTATTATGTTGCATGAATTGTCATTTGATAAGAACTAA-TATTTCAT
*
20635192 AGGAAC
1 ATGAAC
20635198 AGATGTTTGG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.02
51 47 0.98
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (51 bp):
ATGAACTATTATGTTGCATGAATTGTCATTTGATAAGAACTAATATTTCAT
Found at i:20648640 original size:56 final size:57
Alignment explanation
Indices: 20648574--20648689 Score: 139
Period size: 58 Copynumber: 2.0 Consensus size: 57
20648564 ACCCCTACGT
* * *
20648574 ACATGCATATGGCCCA-CTTGG-CCTATCTC-ATTCATATGGCCCATTAGGCCCAATTC
1 ACATGCATATGGCCCATC-AGGCCCAAT-TCAATTCATATGGCCCATTAGGCCCAAATC
* *
20648630 ACATTCATATGGCCCATCAGGCCCAATTCATATTCATATGGCCTATTAGGCCCAAATC
1 ACATGCATATGGCCCATCAGGCCCAATTCA-ATTCATATGGCCCATTAGGCCCAAATC
20648688 AC
1 AC
20648690 CTTTATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
56 19 0.37
57 5 0.10
58 27 0.53
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.28
Consensus pattern (57 bp):
ACATGCATATGGCCCATCAGGCCCAATTCAATTCATATGGCCCATTAGGCCCAAATC
Found at i:20648643 original size:29 final size:29
Alignment explanation
Indices: 20648602--20648689 Score: 140
Period size: 29 Copynumber: 3.0 Consensus size: 29
20648592 TGGCCTATCT
20648602 CATTCATATGGCCCATTAGGCCCAATTCA
1 CATTCATATGGCCCATTAGGCCCAATTCA
*
20648631 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCCATTAGGCCCAATTCA
* * *
20648660 TATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCCCATTAGGCCCAATTCA
20648689 C
1 C
20648690 CTTTATAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
CATTCATATGGCCCATTAGGCCCAATTCA
Found at i:20653126 original size:28 final size:29
Alignment explanation
Indices: 20652977--20653111 Score: 145
Period size: 29 Copynumber: 4.8 Consensus size: 29
20652967 ACCCCTACGT
*
20652977 ACATGCATATGGCCCACTT-GGCCC-A-TC
1 ACATTCATATGGCCCA-TTAGGCCCAATTC
* *
20653004 -TATTCATATGGCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
*
20653032 ACATTCATATGGCCCATTAGGTCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* * *
20653061 ATATTCATAT-GCCTATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* *
20653089 ACCTTTATATGGCCCATTAGGCC
1 ACATTCATATGGCCCATTAGGCC
20653112 TAGATCACCT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.01
26 18 0.20
27 1 0.01
28 24 0.27
29 45 0.51
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAATTC
Found at i:20654507 original size:17 final size:17
Alignment explanation
Indices: 20654471--20654506 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20654461 ACTAAAAAAA
*
20654471 TTTGGGATTTCGGGATT
1 TTTGGGATTTCAGGATT
20654488 TTTGGG-TTTCAGGATT
1 TTTGGGATTTCAGGATT
20654504 TTT
1 TTT
20654507 TTTGGGGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.11, C:0.06, G:0.31, T:0.53
Consensus pattern (17 bp):
TTTGGGATTTCAGGATT
Found at i:20656295 original size:43 final size:42
Alignment explanation
Indices: 20656214--20656297 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
20656204 GAATCGTACA
*
20656214 ATGCCAATGTCCCAACGTGGTCTTACATGTAGCTACATATCG
1 ATGCCAATGTCCCAACGTGGTCTTACATGTAACTACATATCG
* *
20656256 ATGCCACTGTCCCAGACAG-GGTCTTACTTGTAAAC-ACATATC
1 ATGCCAATGTCCCA-AC-GTGGTCTTACATGT-AACTACATATC
20656298 AGAAACACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 13 0.36
43 20 0.56
44 3 0.08
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAACGTGGTCTTACATGTAACTACATATCG
Found at i:20656305 original size:13 final size:13
Alignment explanation
Indices: 20656287--20656311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20656277 TCTTACTTGT
20656287 AAACACATATCAG
1 AAACACATATCAG
20656300 AAACACATATCA
1 AAACACATATCA
20656312 ATGCCATGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.24, G:0.04, T:0.16
Consensus pattern (13 bp):
AAACACATATCAG
Found at i:20659697 original size:53 final size:54
Alignment explanation
Indices: 20659616--20659823 Score: 215
Period size: 53 Copynumber: 3.9 Consensus size: 54
20659606 TTTTCTTTTT
* * * *
20659616 GAACTTACCATTGCTATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * *
20659669 GAACTTACCAATGCTATGCCTTGGCATGGTCTTACATGAG-A-CCTTTTCCTTATA
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTATCC-TTGCCTTATA
* * * * * *
20659723 GTAACTCATCAATACCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * *
20659778 GAACTTATCAATGCCATGCCTTGGCATGGTCTTGCATGATATCCTT
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
20659824 ATCTTACCAA
Statistics
Matches: 129, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.02
53 43 0.33
54 41 0.32
55 41 0.32
56 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:20660049 original size:44 final size:44
Alignment explanation
Indices: 20659968--20660054 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
20659958 GTATCCTTAA
* * *
20659968 CCATCAATTCCTCCTTAAATGTCATGTTATGAACATGGACTTTT
1 CCATCAATTCCTCCTTAAATGCCATGGTATCAACATGGACTTTT
* *
20660012 CCATCAATTCTTCCTTAATTGCCATGGTA-CAACCATGGACTTT
1 CCATCAATTCCTCCTTAAATGCCATGGTATCAA-CATGGACTTT
20660055 GAGATATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 2 0.05
44 35 0.95
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.37
Consensus pattern (44 bp):
CCATCAATTCCTCCTTAAATGCCATGGTATCAACATGGACTTTT
Found at i:20660619 original size:31 final size:30
Alignment explanation
Indices: 20660584--20660641 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
20660574 AAAACTCAAA
20660584 CTTTGGAAAAATTACAATTTTGCCCCTAAAC
1 CTTT-GAAAAATTACAATTTTGCCCCTAAAC
*
20660615 CTTTGCAAAATTACAATTTTGCCCCTA
1 CTTTGAAAAATTACAATTTTGCCCCTA
20660642 GGATCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (30 bp):
CTTTGAAAAATTACAATTTTGCCCCTAAAC
Found at i:20668911 original size:13 final size:13
Alignment explanation
Indices: 20668893--20668918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20668883 CGTGTTGATG
20668893 CACACGGCCATGT
1 CACACGGCCATGT
20668906 CACACGGCCATGT
1 CACACGGCCATGT
20668919 TCTGCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
CACACGGCCATGT
Found at i:20674317 original size:24 final size:25
Alignment explanation
Indices: 20674290--20674368 Score: 92
Period size: 24 Copynumber: 3.3 Consensus size: 25
20674280 CACTCGGCGA
*
20674290 TGGTGGTACATCCTCATGTGGA-TG
1 TGGTGGTACATCATCATGTGGACTG
* *
20674314 TGGTAGTACAACATCATGT-GACTG
1 TGGTGGTACATCATCATGTGGACTG
* *
20674338 TGGTGGTACATCTTCATGT-GACTA
1 TGGTGGTACATCATCATGTGGACTG
20674362 TGGTGGT
1 TGGTGGT
20674369 GTCAGCATTG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.04
24 45 0.96
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.34
Consensus pattern (25 bp):
TGGTGGTACATCATCATGTGGACTG
Found at i:20678492 original size:9 final size:9
Alignment explanation
Indices: 20678474--20678662 Score: 225
Period size: 9 Copynumber: 20.6 Consensus size: 9
20678464 TATTTATGTA
20678474 TTATGTAAG
1 TTATGTAAG
*
20678483 TTATGCAAG
1 TTATGTAAG
*
20678492 TCATGTAAG
1 TTATGTAAG
*
20678501 TTATGATATATAT
1 TTATG---TA-AG
20678514 TTATGTAAG
1 TTATGTAAG
20678523 TTATGTAAG
1 TTATGTAAG
*
20678532 CTATGTAAG
1 TTATGTAAG
*
20678541 TTATGGAAG
1 TTATGTAAG
20678550 TTATGTAAG
1 TTATGTAAG
*
20678559 CTATGTAAG
1 TTATGTAAG
*
20678568 TTATATAAG
1 TTATGTAAG
20678577 TTATGTAAG
1 TTATGTAAG
*
20678586 TTATATAAG
1 TTATGTAAG
20678595 TTATGTAAG
1 TTATGTAAG
20678604 TTATGTAAG
1 TTATGTAAG
*
20678613 CTATGTAAG
1 TTATGTAAG
* *
20678622 TTTTATAAG
1 TTATGTAAG
*
20678631 TTATATAAG
1 TTATGTAAG
*
20678640 CTATGTAAG
1 TTATGTAAG
20678649 TTATGTAAG
1 TTATGTAAG
20678658 TTATG
1 TTATG
20678663 GTTATATTTT
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
9 142 0.93
10 2 0.01
12 2 0.01
13 6 0.04
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20681745 original size:34 final size:34
Alignment explanation
Indices: 20681706--20681770 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
20681696 CCCTATACCT
*
20681706 TAAACTCTAAACCCTAAACTCC-AACCACTAATCC
1 TAAACTCTAAACCCTAAA-TCCTAAACACTAATCC
*
20681740 TAAACTTTAAACCCTAAATCCTAAACACTAA
1 TAAACTCTAAACCCTAAATCCTAAACACTAA
20681771 AACCATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (34 bp):
TAAACTCTAAACCCTAAATCCTAAACACTAATCC
Found at i:20690278 original size:43 final size:43
Alignment explanation
Indices: 20690217--20690375 Score: 143
Period size: 43 Copynumber: 3.7 Consensus size: 43
20690207 TAAGCTCGTA
*
20690217 CAATGCCAACT-TCCCAGACATGGTCTTACATGTAATCTAATAT
1 CAATG-CAACTGTCCCAGACATGGTCTTACACGTAATCTAATAT
* * *
20690260 CAATGCTACTGTCCCAGACAGGGTCTTACACGAAATC--ATAT
1 CAATGCAACTGTCCCAGACATGGTCTTACACGTAATCTAATAT
*
20690301 ACGATGCCAA-TGTCCCA-AGCATGGTCTTACACGTAAATCATAA-AT
1 -CAATG-CAACTGTCCCAGA-CATGGTCTTACACGT-AATC-TAATAT
**
20690346 CAATGCCAACT-TCCCAGATGTGGTCTTACA
1 CAATG-CAACTGTCCCAGACATGGTCTTACA
20690376 TGATAACACA
Statistics
Matches: 95, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
41 5 0.05
42 28 0.29
43 34 0.36
44 23 0.24
45 4 0.04
46 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
CAATGCAACTGTCCCAGACATGGTCTTACACGTAATCTAATAT
Found at i:20691360 original size:20 final size:20
Alignment explanation
Indices: 20691309--20691360 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
20691299 ATTTATTTCT
* *
20691309 TATTAATATACATTTTACTA
1 TATTAATATACCTTTAACTA
*
20691329 TATTAATATACCTTTAAGTA
1 TATTAATATACCTTTAACTA
20691349 TATTAATATACC
1 TATTAATATACC
20691361 ATATAACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (20 bp):
TATTAATATACCTTTAACTA
Found at i:20692920 original size:39 final size:39
Alignment explanation
Indices: 20692877--20692965 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
20692867 ATTCACTTTT
* * *
20692877 AAGCATATATCACATTACACATATAATTACATAATGTTG
1 AAGCATATATCACAATACACATATAATCACATAATGTTC
* *
20692916 AAGCACATATCACAATACTCATATAATCACATAATGTTC
1 AAGCATATATCACAATACACATATAATCACATAATGTTC
20692955 AAGCATATATC
1 AAGCATATATC
20692966 GATATACTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (39 bp):
AAGCATATATCACAATACACATATAATCACATAATGTTC
Found at i:20692973 original size:39 final size:38
Alignment explanation
Indices: 20692877--20692975 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 38
20692867 ATTCACTTTT
* * * *
20692877 AAGCATATATCACATTACACATATAATTACATAATGTTG
1 AAGCATATATCA-AATACTCATATAATCACATAATGTTC
*
20692916 AAGCACATATCACAATACTCATATAATCACATAATGTTC
1 AAGCATATATCA-AATACTCATATAATCACATAATGTTC
*
20692955 AAGCATATATCGATATACTCA
1 AAGCATATATC-AAATACTCA
20692976 AAAACATGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
39 51 0.98
40 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.30
Consensus pattern (38 bp):
AAGCATATATCAAATACTCATATAATCACATAATGTTC
Found at i:20698247 original size:3 final size:3
Alignment explanation
Indices: 20698239--20698270 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
20698229 TGTATTGAAG
*
20698239 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20698271 AGAACAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:20704002 original size:26 final size:26
Alignment explanation
Indices: 20703973--20704028 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
20703963 TGATACAAAT
* *
20703973 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATATTCCA
20703999 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATATTCCA
20704025 TGAT
1 TGAT
20704029 GGGAATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATATTCCA
Found at i:20711857 original size:10 final size:10
Alignment explanation
Indices: 20711842--20711866 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20711832 CCATAATTTA
20711842 TGATACAAAT
1 TGATACAAAT
20711852 TGATACAAAT
1 TGATACAAAT
20711862 TGATA
1 TGATA
20711867 ATGGGTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (10 bp):
TGATACAAAT
Found at i:20711901 original size:26 final size:25
Alignment explanation
Indices: 20711862--20711969 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 25
20711852 TGATACAAAT
20711862 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTTCCA
*
20711888 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGG-TTAGGTAAATGTTCCA
20711914 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATG-GTTAGGTAAATGTTCCA
20711940 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGG-TTAGGTAAATGTTCCA
20711966 TGAT
1 TGAT
20711970 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
25 3 0.04
26 73 0.95
27 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37
Consensus pattern (25 bp):
TGATAATGGTTAGGTAAATGTTCCA
Found at i:20711919 original size:52 final size:52
Alignment explanation
Indices: 20711862--20711969 Score: 189
Period size: 52 Copynumber: 2.1 Consensus size: 52
20711852 TGATACAAAT
20711862 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* * *
20711914 TGATAATGTGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
20711966 TGAT
1 TGAT
20711970 GGGAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:20715368 original size:30 final size:31
Alignment explanation
Indices: 20715288--20715370 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
20715278 TCAGTCTCGA
20715288 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
20715318 CATATCACTGGGCAGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
20715349 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
20715371 ACTGTAAGCG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.34
31 33 0.66
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:20715610 original size:24 final size:25
Alignment explanation
Indices: 20715583--20715634 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
20715573 GCCTAGCCTC
20715583 TTTTAAT-AACTGAGGAAAAGCCCT
1 TTTTAATAAACTGAGGAAAAGCCCT
* * * *
20715607 TTTTGATAAATTGGGGCAAAGCCCT
1 TTTTAATAAACTGAGGAAAAGCCCT
20715632 TTT
1 TTT
20715635 CGGTAAGCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (25 bp):
TTTTAATAAACTGAGGAAAAGCCCT
Found at i:20715631 original size:25 final size:25
Alignment explanation
Indices: 20715590--20715659 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
20715580 CTCTTTTAAT
* * *
20715590 AACTGAGGAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
20715615 AATTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
20715640 AGCTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
20715660 AGCACTTCCT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:20716498 original size:27 final size:27
Alignment explanation
Indices: 20716468--20716532 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
20716458 GGGCATATTC
*
20716468 GTCATTTTACCATACAGGGGTAGTACG
1 GTCATTTTACCATACAGAGGTAGTACG
* * **
20716495 GTCACTTTACCCTACAGAGGTTTTACG
1 GTCATTTTACCATACAGAGGTAGTACG
*
20716522 GTCTTTTTACC
1 GTCATTTTACC
20716533 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGAGGTAGTACG
Found at i:20716606 original size:27 final size:28
Alignment explanation
Indices: 20716576--20716772 Score: 104
Period size: 27 Copynumber: 7.2 Consensus size: 28
20716566 GGGTGTTTTG
*
20716576 GTAAATTTACAAACCAAGGGTATTTC-A
1 GTAATTTTACAAACCAAGGGTATTTCTA
** * *
20716603 GTAATTTTTTAAACTAATGGTATTTCTA
1 GTAATTTTACAAACCAAGGGTATTTCTA
*
20716631 -TAATTTTTAGAAAGCCAAGGGTATTTCTA
1 GTAA-TTTTACAAA-CCAAGGGTATTTCTA
** ** * *
20716660 -TAATTTTGTAAGTCAGGGGTATTT-TG
1 GTAATTTTACAAACCAAGGGTATTTCTA
*** *
20716686 GTAATTTTACAAATTGAGGGTATTTCGA
1 GTAATTTTACAAACCAAGGGTATTTCTA
* * * *
20716714 -TAACTTCACAAACC-AGTGATATTT-TG
1 GTAATTTTACAAACCAAG-GGTATTTCTA
* * *
20716740 GTAATTTTACAAACTAGGGGTATTT-TG
1 GTAATTTTACAAACCAAGGGTATTTCTA
20716767 GTAATT
1 GTAATT
20716773 CTACCCTATA
Statistics
Matches: 127, Mismatches: 35, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
26 3 0.02
27 93 0.73
28 15 0.12
29 16 0.13
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (28 bp):
GTAATTTTACAAACCAAGGGTATTTCTA
Found at i:20716812 original size:27 final size:27
Alignment explanation
Indices: 20716674--20716812 Score: 95
Period size: 27 Copynumber: 5.1 Consensus size: 27
20716664 TTTGTAAGTC
* *
20716674 AGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGGTATTTTGGTAATTTCAC-AATCG
* * * * *
20716702 A-GGGTATTTCGATAACTTCACAAACC
1 AGGGGTATTTTGGTAATTTCACAATCG
* * * * *
20716728 AGTGATATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTCACAATCG
* *
20716755 AGGGGTATTTTGGTAATTCTACCCTAT--
1 AGGGGTATTTTGGTAATT-T-CACAATCG
*
20716782 AGGGGTATTTTAGTAATTTCACAATCG
1 AGGGGTATTTTGGTAATTTCACAATCG
20716809 AGGG
1 AGGG
20716813 TAAAACGGTA
Statistics
Matches: 83, Mismatches: 23, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
25 4 0.05
26 4 0.05
27 71 0.86
28 2 0.02
29 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTCACAATCG
Found at i:20716823 original size:26 final size:26
Alignment explanation
Indices: 20716794--20716844 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
20716784 GGGTATTTTA
20716794 GTAATTT-CACAATCGAGGGTAAAACG
1 GTAATTTGCA-AATCGAGGGTAAAACG
*
20716820 GTAATTTGTAAATCGAGGGTAAAAC
1 GTAATTTGCAAATCGAGGGTAAAAC
20716845 AGTGATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (26 bp):
GTAATTTGCAAATCGAGGGTAAAACG
Found at i:20716866 original size:27 final size:26
Alignment explanation
Indices: 20716804--20716867 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
20716794 GTAATTTCAC
* *
20716804 AATCGAGGGTAAAACGGTAATTTGTA
1 AATCGAGGGTAAAACAGTAATTTATA
*
20716830 AATCGAGGGTAAAACAGTGATTCTATA
1 AATCGAGGGTAAAACAGTAATT-TATA
*
20716857 AATTGAGGGTA
1 AATCGAGGGTA
20716868 CTTTGGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 20 0.61
27 13 0.39
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.27
Consensus pattern (26 bp):
AATCGAGGGTAAAACAGTAATTTATA
Found at i:20719310 original size:24 final size:25
Alignment explanation
Indices: 20719278--20719354 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 25
20719268 GCCTAGCTTC
* *
20719278 TTTTAAT-AACTATGGCAAATCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
* *
20719302 TTTTGATAAACTGGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
*** * *
20719327 TTTCGGTAAACTGGGGCATAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
20719352 TTT
1 TTT
20719355 AGCAGTTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 6 0.13
25 39 0.87
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (25 bp):
TTTTAATAAACTAGGGCAAAGCCCT
Found at i:20719319 original size:25 final size:25
Alignment explanation
Indices: 20719291--20719354 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
20719281 TAATAACTAT
* *
20719291 GGCAAATCCCTTTTTGATAAACTGG
1 GGCAAAGCCCTTTTCGATAAACTGG
*
20719316 GGCAAAGCCCTTTTCGGTAAACTGG
1 GGCAAAGCCCTTTTCGATAAACTGG
*
20719341 GGCATAGCCCTTTT
1 GGCAAAGCCCTTTT
20719355 AGCAGTTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (25 bp):
GGCAAAGCCCTTTTCGATAAACTGG
Found at i:20720328 original size:29 final size:27
Alignment explanation
Indices: 20720257--20720354 Score: 117
Period size: 27 Copynumber: 3.6 Consensus size: 27
20720247 GTAAATCTAC
*
20720257 AAACCAAGGGTATTTCAATAATTTTGT
1 AAACCAAGGGTATTTCTATAATTTTGT
*
20720284 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCTATAATTTTGT
*
20720310 AGGAAGTCAAGGGTATTTCTATAATTTTGT
1 A--AA-CCAAGGGTATTTCTATAATTTTGT
* *
20720340 AAATCAGGGGTATTT
1 AAACCAAGGGTATTT
20720355 TGGTAATTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
26 2 0.03
27 34 0.55
28 4 0.06
29 20 0.32
30 2 0.03
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:20720361 original size:27 final size:27
Alignment explanation
Indices: 20720345--20720476 Score: 142
Period size: 27 Copynumber: 4.9 Consensus size: 27
20720335 TTTGTAAATC
20720345 AGGGGTATTTTGGTAATTTTACAAA-T
1 AGGGGTATTTTGGTAATTTTACAAACT
* * *
20720371 TGAGGGTATTTCGGTAATTTCACAAACT
1 AG-GGGTATTTTGGTAATTTTACAAACT
*
20720399 AGTGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
* * **
20720426 AGGGGTATTTTAGTAATTCTACCCTA-T
1 AGGGGTATTTTGGTAATTTTA-CAAACT
* *
20720453 AGGGGTATTTTAGTAATTTCACAA
1 AGGGGTATTTTGGTAATTTTACAA
20720477 TCGAGGGTAA
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.02
27 81 0.93
28 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:20720494 original size:26 final size:26
Alignment explanation
Indices: 20720465--20720515 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
20720455 GGGTATTTTA
20720465 GTAATTT-CACAATCGAGGGTAAAACG
1 GTAATTTGCA-AATCGAGGGTAAAACG
*
20720491 GTAATTTGTAAATCGAGGGTAAAAC
1 GTAATTTGCAAATCGAGGGTAAAAC
20720516 AATGATTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (26 bp):
GTAATTTGCAAATCGAGGGTAAAACG
Found at i:20720537 original size:27 final size:26
Alignment explanation
Indices: 20720475--20720538 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
20720465 GTAATTTCAC
** *
20720475 AATCGAGGGTAAAACGGTAATTTGTA
1 AATCGAGGGTAAAACAATAATTTATA
*
20720501 AATCGAGGGTAAAACAATGATTCTATA
1 AATCGAGGGTAAAACAATAATT-TATA
20720528 AATCGAGGGTA
1 AATCGAGGGTA
20720539 CTTTGGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (26 bp):
AATCGAGGGTAAAACAATAATTTATA
Found at i:20731883 original size:29 final size:29
Alignment explanation
Indices: 20731850--20731939 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
20731840 TCTTATTGAC
20731850 TAAGGTTGGCCTAATGATCTTAAGTGAGA
1 TAAGGTTGGCCTAATGATCTTAAGTGAGA
* ** * * *
20731879 TAAGG--GG-GTGAATCCTCTCTTATTGA-C
1 TAAGGTTGGCCT-AATGATCT-TAAGTGAGA
20731906 TAAGGTTGGCCTAATGATCTTAAGTGAGA
1 TAAGGTTGGCCTAATGATCTTAAGTGAGA
20731935 TAAGG
1 TAAGG
20731940 GGGTGAATTA
Statistics
Matches: 43, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 1 0.02
27 13 0.30
28 10 0.23
29 18 0.42
30 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (29 bp):
TAAGGTTGGCCTAATGATCTTAAGTGAGA
Found at i:20731921 original size:56 final size:56
Alignment explanation
Indices: 20731835--20731947 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
20731825 TTGTAAGTAT
20731835 TCCTCTCTTATTGACTAAGGTTGGCCTAATGATCTTAAGTGAGATAAGGGGGTGAA
1 TCCTCTCTTATTGACTAAGGTTGGCCTAATGATCTTAAGTGAGATAAGGGGGTGAA
20731891 TCCTCTCTTATTGACTAAGGTTGGCCTAATGATCTTAAGTGAGATAAGGGGGTGAA
1 TCCTCTCTTATTGACTAAGGTTGGCCTAATGATCTTAAGTGAGATAAGGGGGTGAA
20731947 T
1 T
20731948 TATGTTGGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (56 bp):
TCCTCTCTTATTGACTAAGGTTGGCCTAATGATCTTAAGTGAGATAAGGGGGTGAA
Found at i:20731926 original size:27 final size:27
Alignment explanation
Indices: 20731840--20731927 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
20731830 AGTATTCCTC
20731840 TCTTATTGACTAAGGTTGGCCTAATGA
1 TCTTATTGACTAAGGTTGGCCTAATGA
* * * **
20731867 TCTTAAGTGAGATAAGG--GG-GTGAATCCTC
1 TCTT-ATTGA-CTAAGGTTGGCCT-AAT--GA
20731896 TCTTATTGACTAAGGTTGGCCTAATGA
1 TCTTATTGACTAAGGTTGGCCTAATGA
20731923 TCTTA
1 TCTTA
20731928 AGTGAGATAA
Statistics
Matches: 43, Mismatches: 10, Indels: 16
0.62 0.14 0.23
Matches are distributed among these distances:
26 1 0.02
27 19 0.44
28 8 0.19
29 14 0.33
30 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (27 bp):
TCTTATTGACTAAGGTTGGCCTAATGA
Found at i:20732225 original size:16 final size:16
Alignment explanation
Indices: 20732204--20732246 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
20732194 GTAGATCGAC
*
20732204 AAAAGCCGAAATGCTG
1 AAAAGCCGAAAAGCTG
* *
20732220 AAAAGCCAAAAAGTTG
1 AAAAGCCGAAAAGCTG
20732236 AAAAGCCGAAA
1 AAAAGCCGAAA
20732247 GTTTGGCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.16, G:0.21, T:0.09
Consensus pattern (16 bp):
AAAAGCCGAAAAGCTG
Found at i:20732288 original size:19 final size:19
Alignment explanation
Indices: 20732266--20732303 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20732256 TGGTAGTCTT
*
20732266 GCGAGTGCATGGACTTTGG
1 GCGAGTCCATGGACTTTGG
*
20732285 GCGATTCCATGGACTTTGG
1 GCGAGTCCATGGACTTTGG
20732304 TTGTGAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.37, T:0.29
Consensus pattern (19 bp):
GCGAGTCCATGGACTTTGG
Found at i:20732505 original size:29 final size:29
Alignment explanation
Indices: 20732423--20732569 Score: 160
Period size: 28 Copynumber: 5.1 Consensus size: 29
20732413 GTGAGCATGA
20732423 ATAT-AATGTGATTTGGG-CTGGATGGGCC
1 ATATAAATGTGATTTGGGCCT-GATGGGCC
* *
20732451 ATATAAATGAGA-TTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
* *
20732479 ATATAAAGGTGATTTGGCCCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
* *
20732508 ATATGAAATGTGAATTGGGGCTGATGGGCC
1 ATAT-AAATGTGATTTGGGCCTGATGGGCC
* *
20732538 ATATAAATGAGA-TTGGGCC-AAGTGGGCC
1 ATATAAATGTGATTTGGGCCTGA-TGGGCC
20732566 ATAT
1 ATAT
20732570 GCATGTATGT
Statistics
Matches: 101, Mismatches: 13, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
27 1 0.01
28 42 0.42
29 33 0.33
30 25 0.25
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.27
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTGATGGGCC
Found at i:20740784 original size:22 final size:21
Alignment explanation
Indices: 20740759--20740823 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
20740749 GTAACTACGT
20740759 TTGGCACACAACCATAATCAGG
1 TTGGCACA-AACCATAATCAGG
*
20740781 TTGGCACAGAACCAT-ATGTAGG
1 TTGGCACA-AACCATAAT-CAGG
*
20740803 TTGGCGCAAAGCCATAATCAG
1 TTGGCACAAA-CCATAATCAG
20740824 AATAATTAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 4 0.11
22 30 0.83
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
TTGGCACAAACCATAATCAGG
Found at i:20741293 original size:27 final size:27
Alignment explanation
Indices: 20741262--20741611 Score: 231
Period size: 27 Copynumber: 13.0 Consensus size: 27
20741252 TTGATAAATC
*
20741262 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * *
20741289 TACAAACCAATGGTATTTCTGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
** *
20741316 TTGAAAGTCAAGGGTATTTCTGTAATTT
1 TACAAA-TCAAGGGTATTTCAGTAATTT
* * * * *
20741344 TATAAATTAGGGGTATTTCTGTAAATT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * **
20741371 TCCAAATCAATGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
**
20741398 TACAAATTGAGGGTATTTCAGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * ** *
20741425 TGCAAGTTGAGGATATTTC-GATAATTT
1 TACAAATCAAGGGTATTTCAG-TAATTT
* *
20741452 TATAAGTCAAGGGTATTTCAGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* * * *
20741479 TGCAAGTCGAGGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* ** * * **
20741506 TATAGGTCGATGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCAGTAATTT
* **
20741533 TACAAAT-TAGGGTTATTTTGGTAATTT
1 TACAAATCAAGGG-TATTTCAGTAATTT
** *
20741560 T-GTATTCCAAGGGTATTT-AGTAATTT
1 TACAAAT-CAAGGGTATTTCAGTAATTT
** *
20741586 TGTAAACCAAGGGTATTTCAGTAATT
1 TACAAATCAAGGGTATTTCAGTAATT
20741612 CTACCCTACA
Statistics
Matches: 259, Mismatches: 56, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
26 25 0.10
27 206 0.80
28 28 0.11
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCAGTAATTT
Found at i:20741508 original size:54 final size:54
Alignment explanation
Indices: 20741264--20741611 Score: 281
Period size: 54 Copynumber: 6.4 Consensus size: 54
20741254 GATAAATCTA
* * * * * *
20741264 CAAACCAAGGGTATTTCAGTAATTTTACAAACCAATGGTATTTCTGTAATTTTTG
1 CAAATCAAGGGTATTTCGGTAATTTTATAAATCAAGGGTATTTCAGTAA-TTTTG
* * * * * *
20741319 -AAAGTCAAGGGTATTTCTGTAATTTTATAAATTAGGGGTATTTCTGTAAATTTC
1 CAAA-TCAAGGGTATTTCGGTAATTTTATAAATCAAGGGTATTTCAGTAATTTTG
* * * **
20741373 CAAATCAATGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTTG
1 CAAATCAAGGGTATTTCGGTAATTTTATAAATCAAGGGTATTTCAGTAATTTTG
* ** * * *
20741427 CAAGTTGAGGATATTTCGATAATTTTATAAGTCAAGGGTATTTCAGTAATTTTG
1 CAAATCAAGGGTATTTCGGTAATTTTATAAATCAAGGGTATTTCAGTAATTTTG
* * ** * * ** *
20741481 CAAGTCGAGGGTATTTCGGTAATTTTATAGGTCGATGGTATTTTGGTAATTTTA
1 CAAATCAAGGGTATTTCGGTAATTTTATAAATCAAGGGTATTTCAGTAATTTTG
* * * *
20741535 CAAAT-TAGGGTTATTTTGGTAATTTTGT-ATTCCAAGGGTATTT-AGTAATTTTG
1 CAAATCAAGGG-TATTTCGGTAATTTTATAAAT-CAAGGGTATTTCAGTAATTTTG
* * *
20741588 TAAACCAAGGGTATTTCAGTAATT
1 CAAATCAAGGGTATTTCGGTAATT
20741612 CTACCCTACA
Statistics
Matches: 235, Mismatches: 53, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
53 27 0.11
54 167 0.71
55 41 0.17
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.42
Consensus pattern (54 bp):
CAAATCAAGGGTATTTCGGTAATTTTATAAATCAAGGGTATTTCAGTAATTTTG
Done.