Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 178 of 206
Found at i:54241952 original size:12 final size:12
Alignment explanation
Indices: 54241935--54241959 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54241925 AGTGATAACA
54241935 TTGAACGTTAAT
1 TTGAACGTTAAT
54241947 TTGAACGTTAAT
1 TTGAACGTTAAT
54241959 T
1 T
54241960 CGAAAGGTTA
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTGAACGTTAAT
Found at i:54242999 original size:27 final size:28
Alignment explanation
Indices: 54242956--54243017 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
54242946 AAACACTATT
* *
54242956 AAAA-ATAATAGAAAATACAA-AATTTA
1 AAAATATAATAGAAAATAAAATAATATA
* *
54242982 AAAATATAATATATAATAAAATAATATA
1 AAAATATAATAGAAAATAAAATAATATA
54243010 AATAATAT
1 AA-AATAT
54243018 TTTTGAAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 7 0.24
29 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
AAAATATAATAGAAAATAAAATAATATA
Found at i:54245434 original size:33 final size:33
Alignment explanation
Indices: 54245392--54245459 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
54245382 GTATACAAGT
*
54245392 TGAGACCGTGGCCATCCCTAGGTTCCTGGGAGC
1 TGAGACCGTGGCCATCCCTAGGTTCCTGCGAGC
* *
54245425 TGAGACCGTGGCCATCCCTGGGTTCTTGCGAGC
1 TGAGACCGTGGCCATCCCTAGGTTCCTGCGAGC
54245458 TG
1 TG
54245460 GATCTGCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.13, C:0.29, G:0.34, T:0.24
Consensus pattern (33 bp):
TGAGACCGTGGCCATCCCTAGGTTCCTGCGAGC
Found at i:54248519 original size:57 final size:56
Alignment explanation
Indices: 54248388--54248527 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 56
54248378 CCACGAGCCG
* * *
54248388 TTTTAGGCTTAGGAAATTTTCTAAAATAATCGGCTGGAAATATCAATCTGCAAACTA
1 TTTTAGACTT-GGAAATTTTCTAAAATAATCAGCTGGAAATATCAATCCGCAAACTA
* * * * ** *
54248445 TTTTAGATTTGGAAAATTTTCTAAAATAATCAGCTGGGAGTATTAATCCGTGAGCTA
1 TTTTAGACTTGG-AAATTTTCTAAAATAATCAGCTGGAAATATCAATCCGCAAACTA
* *
54248502 TTTTATACTTGAGAAATTTTCAAAAA
1 TTTTAGACTTG-GAAATTTTCTAAAA
54248528 AAATTGACTG
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
56 2 0.03
57 65 0.96
58 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (56 bp):
TTTTAGACTTGGAAATTTTCTAAAATAATCAGCTGGAAATATCAATCCGCAAACTA
Found at i:54249270 original size:69 final size:69
Alignment explanation
Indices: 54248569--54249291 Score: 624
Period size: 69 Copynumber: 10.4 Consensus size: 69
54248559 TTTTAAGGGT
* * * *
54248569 TGCGGTTTTGATCCTGCGAGCCTAAATTTGACAGCTGGGAG-TTTGTAACTCTCGCTAACTATGT
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTG---CTCTCGCTAACTATGT
54248633 TGGAGGC
63 TGGAGGC
* ** * * * * * * *
54248640 TACAATTTTAATCCCGCGAGCCTTATTATGATAGCTGGGAGCTTTACTCTTGCTAACTGTATTGG
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
*
54248705 AGGA
66 AGGC
* * * * ** *
54248709 TACAGTTTTAATCCTGCAAGCCTTAGTATGACAACTAAGAGCATTGCTCTCGCTAACTATGTTGG
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
54248774 AGGC
66 AGGC
* * * * * * *
54248778 TACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTCGTTAACTGTGTTAG
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
*
54248843 AGGT
66 AGGC
* * *
54248847 TGTGGTTTTAATCCTGCGAGCCTTTA-TATGATAGTTGGGAGCTTTGCTCTTC-CTAACTATGTT
1 TGCGGTTTTAATCCTGCGAGCC-TTAGTATGACAGCTGGGAGCTTTGCTC-TCGCTAACTATGTT
54248910 GGAGGC
64 GGAGGC
* * * * *
54248916 TTCGGTTTTAATCCTGTGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTTGCTAACCATATTGG
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
*
54248981 AGGT
66 AGGC
** * * * * ** * ** *
54248985 TATGATTTTTCATCCTACAAATCTTATTATGACAATTGGGAGCTTTGCTCTCACTAACTATGTTG
1 TGCG-GTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTG
*
54249050 GGGGC
65 GAGGC
* ** ** * * *
54249055 CGCGACTTTAATCCTATGAGCCTTAGTATGATAACTGGGAGCTTTGCTCTCGCTGACTATGTTGG
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
54249120 AGGC
66 AGGC
* * * * * * * *
54249124 TCCGATTTTAATCTTACGAGTCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGG
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
54249189 AGGC
66 AGGC
* * * * * ** * *
54249193 TGCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAACTTTACTCTTACTAACTGTGTTAG
1 TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
*
54249258 AGGT
66 AGGC
* * * *
54249262 TGTGGTTTTTTATCCTACGATCCTTAGTAT
1 TGCGG-TTTTAATCCTGCGAGCCTTAGTAT
54249292 TCACAGGATA
Statistics
Matches: 524, Mismatches: 121, Indels: 15
0.79 0.18 0.02
Matches are distributed among these distances:
68 4 0.01
69 410 0.78
70 75 0.14
71 32 0.06
72 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (69 bp):
TGCGGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGG
AGGC
Found at i:54249279 original size:277 final size:277
Alignment explanation
Indices: 54248574--54249291 Score: 778
Period size: 277 Copynumber: 2.6 Consensus size: 277
54248564 AGGGTTGCGG
* * * * *
54248574 TTTTGATCCTGCGAGCCTAAATTTGACAGCTGGGAG-TTTGTAACTCTCGCTAACTATGTTGGAG
1 TTTTAATCCTACGAGCCTTAATATGATAGCTGGGAGCTTTG---CTCTCGCTAACTATGTTGGAG
* * * *
54248638 GCTACAATTTTAATCCCGCGAGCCTTATTATGATAGCTGGGAGCTTTACTCTTGCTAACTGTATT
63 GCTACAGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTACTCTTGCTAACTGTATT
* ** * * *
54248703 GGAGGATACAG-TTTTAATCCTGCAAGCCTTAGTATGACAACTAAGAGCATTGCTCTCGCTAACT
128 GGAGGTTATGGTTTTTAATCCTACAAACCTTAGTATGACAACTAAGAGCATTGCTCTCACTAACT
* * * ** *
54248767 ATGTTGGAGGCTACAGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAGCTTTGCTCTCGTT
193 ATGTTGGAGGCCACAGCTTTAATCCTACAAGCCTTAGTATGACAACTGGGAGCTTTGCTCTCGCT
* * ** *
54248832 AACTGTGTTAGAGGTTGTGG
258 AACTATGTTAGAGGCTCCGA
* * *
54248852 TTTTAATCCTGCGAGCCTTTATATGATAGTTGGGAGCTTTGCTCTTC-CTAACTATGTTGGAGGC
1 TTTTAATCCTACGAGCCTTAATATGATAGCTGGGAGCTTTGCTC-TCGCTAACTATGTTGGAGGC
* * * * **
54248916 TTCGGTTTTAATCCTGTGAGCCTTAGTATGACAGCTGGGAGCTTTGCTCTTGCTAACCATATTGG
65 TACAGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTACTCTTGCTAACTGTATTGG
* * * * * ** *
54248981 AGGTTATGATTTTTCATCCTACAAATCTTATTATGACAATTGGGAGCTTTGCTCTCACTAACTAT
130 AGGTTATGGTTTTTAATCCTACAAACCTTAGTATGACAACTAAGAGCATTGCTCTCACTAACTAT
* * ** * *
54249046 GTTGGGGGCCGC-GACTTTAATCCTATGAGCCTTAGTATGATAACTGGGAGCTTTGCTCTCGCTG
195 GTTGGAGGCCACAG-CTTTAATCCTACAAGCCTTAGTATGACAACTGGGAGCTTTGCTCTCGCTA
*
54249110 ACTATGTTGGAGGCTCCGA
259 ACTATGTTAGAGGCTCCGA
* * *
54249129 TTTTAATCTTACGAGTCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCT
1 TTTTAATCCTACGAGCCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGGAGGCT
* * * * * * * *
54249194 GCTGTTTTAATCCTGCAAGCCTTAGTATGACAGTTGGGAACTTTACTCTTACTAACTGTGTTAGA
66 ACAGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTACTCTTGCTAACTGTATTGGA
* * * *
54249259 GGTTGTGGTTTTTTATCCTACGATCCTTAGTAT
131 GGTTATGGTTTTTAATCCTACAAACCTTAGTAT
54249292 TCACAGGATA
Statistics
Matches: 362, Mismatches: 73, Indels: 11
0.81 0.16 0.02
Matches are distributed among these distances:
276 83 0.23
277 245 0.68
278 30 0.08
279 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (277 bp):
TTTTAATCCTACGAGCCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAACTATGTTGGAGGCT
ACAGTTTTAATCCTGCGAGCCTTAGTATGACAGCTGGGAGCTTTACTCTTGCTAACTGTATTGGA
GGTTATGGTTTTTAATCCTACAAACCTTAGTATGACAACTAAGAGCATTGCTCTCACTAACTATG
TTGGAGGCCACAGCTTTAATCCTACAAGCCTTAGTATGACAACTGGGAGCTTTGCTCTCGCTAAC
TATGTTAGAGGCTCCGA
Found at i:54257029 original size:38 final size:38
Alignment explanation
Indices: 54256945--54257057 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
54256935 TCCCTATCCA
*
54256945 TACTTCAAATCTGTCTTATTTTTTAGAC--AATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
* * *
54256981 TACTTTAAATCTATCTCATCTTTTAGACTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
* *
54257019 TACTTCAAATCTGTCTCATTTTTTAAATTTAATATTTT
1 TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
54257057 T
1 T
54257058 TGTTCAAGCT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 24 0.36
38 42 0.64
ACGTcount: A:0.28, C:0.14, G:0.04, T:0.54
Consensus pattern (38 bp):
TACTTCAAATCTGTCTCATTTTTTAGACTTAATATTTT
Found at i:54261720 original size:10 final size:12
Alignment explanation
Indices: 54261707--54261746 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
54261697 AATATGTAAT
54261707 TATATA-ATA-A
1 TATATATATATA
54261717 TATATATATATA
1 TATATATATATA
54261729 TATATATAT-TA
1 TATATATATATA
*
54261740 CATATAT
1 TATATAT
54261747 CATTATGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 6 0.22
11 11 0.41
12 10 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATATATA
Found at i:54261721 original size:2 final size:2
Alignment explanation
Indices: 54261707--54261746 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
54261697 AATATGTAAT
*
54261707 TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA TA T- TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54261746 T
1 T
54261747 CATTATGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:54261732 original size:22 final size:19
Alignment explanation
Indices: 54261691--54261734 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
54261681 ATAAAATCAA
*
54261691 ATAATAAATATGTAATTAT
1 ATAATAAATATATAATTAT
54261710 ATAATAATATATATATATATAT
1 ATAATAA-ATATATA-AT-TAT
54261732 ATA
1 ATA
54261735 TATTACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 2 0.10
22 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAATAAATATATAATTAT
Found at i:54265007 original size:25 final size:25
Alignment explanation
Indices: 54264971--54265102 Score: 128
Period size: 25 Copynumber: 5.3 Consensus size: 25
54264961 CGTAAACAGA
* * *
54264971 AAGCTCAAGAGAGTC-ATTAATTGGG
1 AAGCTCATGAGAGCCAATT-ATCGGG
*
54264996 AAGCTCATGAGAGCCAATTATCGAG
1 AAGCTCATGAGAGCCAATTATCGGG
*
54265021 AAGCTCCA-GAGAGCC-ATTAATCAGG
1 AAGCT-CATGAGAGCCAATT-ATCGGG
*
54265046 AAGCTCATGAGAGCCAATTATTGGG
1 AAGCTCATGAGAGCCAATTATCGGG
* *
54265071 AAGCTCGTGAGAGCCAAATAGT-GGG
1 AAGCTCATGAGAGCCAATTA-TCGGG
54265096 AAGCTCA
1 AAGCTCA
54265103 AAAGAGATGC
Statistics
Matches: 90, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
24 5 0.06
25 76 0.84
26 9 0.10
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (25 bp):
AAGCTCATGAGAGCCAATTATCGGG
Found at i:54265032 original size:50 final size:50
Alignment explanation
Indices: 54264971--54265086 Score: 160
Period size: 50 Copynumber: 2.3 Consensus size: 50
54264961 CGTAAACAGA
* **
54264971 AAGCTCAAGAGAGTCATTAATTGGGAAGCTCATGAGAGCCAATTATCGAG
1 AAGCTCAAGAGAGCCATTAATCAGGAAGCTCATGAGAGCCAATTATCGAG
* * *
54265021 AAGCTCCAGAGAGCCATTAATCAGGAAGCTCATGAGAGCCAATTATTGGG
1 AAGCTCAAGAGAGCCATTAATCAGGAAGCTCATGAGAGCCAATTATCGAG
**
54265071 AAGCTCGTGAGAGCCA
1 AAGCTCAAGAGAGCCA
54265087 AATAGTGGGA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (50 bp):
AAGCTCAAGAGAGCCATTAATCAGGAAGCTCATGAGAGCCAATTATCGAG
Found at i:54265098 original size:50 final size:49
Alignment explanation
Indices: 54264971--54265102 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 49
54264961 CGTAAACAGA
* * *
54264971 AAGCTCAAGAGAGTCATTAATTGGGAAGCTCATGAGAGCCAATTATCGAG
1 AAGCTCCAGAGAGCCAATAA-TGGGAAGCTCATGAGAGCCAATTATCGAG
* * * *
54265021 AAGCTCCAGAGAGCCATTAATCAGGAAGCTCATGAGAGCCAATTATTGGG
1 AAGCTCCAGAGAGCCAATAAT-GGGAAGCTCATGAGAGCCAATTATCGAG
** *
54265071 AAGCTCGTGAGAGCCAAATAGTGGGAAGCTCA
1 AAGCTCCAGAGAGCC-AATAATGGGAAGCTCA
54265103 AAAGAGATGC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 65 0.93
51 4 0.06
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (49 bp):
AAGCTCCAGAGAGCCAATAATGGGAAGCTCATGAGAGCCAATTATCGAG
Found at i:54265901 original size:69 final size:69
Alignment explanation
Indices: 54265822--54265956 Score: 175
Period size: 69 Copynumber: 2.0 Consensus size: 69
54265812 TCTTTTTCTT
* * *
54265822 GTCTTTTCTTGCAGGGAATATTTCCTGTTCACACATCA-TCTCTT-CAAGGGGATCTTTCTTGTT
1 GTCTTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTCT-TTGC-AGGGAATCTTTCCTGTT
54265885 CACCTC
64 CACCTC
* * **
54265891 GTCTTTTCTTGTAGAGAATCTTTCCTGTTCATGCATCATTCTTTGCAGGGAATCTTTCCTGTTCA
1 GTCTTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTCTTTGCAGGGAATCTTTCCTGTTCA
54265956 C
66 C
54265957 AAATCTTTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
69 53 0.93
70 4 0.07
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.42
Consensus pattern (69 bp):
GTCTTTTCTTGCAGAGAATATTTCCTGTTCACACATCATTCTTTGCAGGGAATCTTTCCTGTTCA
CCTC
Found at i:54265971 original size:34 final size:34
Alignment explanation
Indices: 54265823--54265971 Score: 140
Period size: 34 Copynumber: 4.4 Consensus size: 34
54265813 CTTTTTCTTG
*
54265823 TCTTTTCTTGCAGGGAATATTTCCTGTTCACACA
1 TCTTTTCTTGCAGGGAATCTTTCCTGTTCACACA
* * * * * *
54265857 TCATCTCTT-CAAGGGGATCTTTCTTGTTCACCTCG
1 TCTTTTCTTGC-AGGGAATCTTTCCTGTTCA-CACA
* * **
54265892 TCTTTTCTTGTAGAGAATCTTTCCTGTTCATGCA
1 TCTTTTCTTGCAGGGAATCTTTCCTGTTCACACA
* *
54265926 TC-ATTCTTTGCAGGGAATCTTTCCTGTTCACAAA
1 TCTTTTC-TTGCAGGGAATCTTTCCTGTTCACACA
54265960 TCTTTTCTTGCA
1 TCTTTTCTTGCA
54265972 TCATTTTTTC
Statistics
Matches: 87, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
33 4 0.05
34 55 0.63
35 28 0.32
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (34 bp):
TCTTTTCTTGCAGGGAATCTTTCCTGTTCACACA
Found at i:54268929 original size:21 final size:23
Alignment explanation
Indices: 54268905--54268947 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
54268895 TTAATTTTTT
*
54268905 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
*
54268926 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
54268948 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:54273707 original size:22 final size:20
Alignment explanation
Indices: 54273681--54273720 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
54273671 GAAATAAAAA
54273681 ATATGTATATAGATATATATAG
1 ATATGTATAT-GAT-TATATAG
54273703 ATATGTATATGATTATAT
1 ATATGTATATGATTATAT
54273721 GCTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (20 bp):
ATATGTATATGATTATATAG
Found at i:54274090 original size:14 final size:12
Alignment explanation
Indices: 54274060--54274114 Score: 67
Period size: 12 Copynumber: 4.5 Consensus size: 12
54274050 TGTTCATTTA
*
54274060 TTCATCAAGTCT
1 TTCATCAAGTTT
*
54274072 TTCATCATGTGTTT
1 TTCATCA--AGTTT
54274086 TTCATCAAGTTT
1 TTCATCAAGTTT
54274098 TTCATCAAG-TT
1 TTCATCAAGTTT
54274109 TTCATC
1 TTCATC
54274115 TTCTAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
11 8 0.21
12 20 0.53
14 10 0.26
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (12 bp):
TTCATCAAGTTT
Found at i:54274110 original size:23 final size:25
Alignment explanation
Indices: 54274060--54274114 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
54274050 TGTTCATTTA
*
54274060 TTCATCAAGTCTTTCATCATGTGTTT
1 TTCATCAAGTCTTTCATCA-GAGTTT
*
54274086 TTCATCAAGTTTTTCATCA-AG-TT
1 TTCATCAAGTCTTTCATCAGAGTTT
54274109 TTCATC
1 TTCATC
54274115 TTCTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
24 1 0.04
26 18 0.67
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (25 bp):
TTCATCAAGTCTTTCATCAGAGTTT
Found at i:54280329 original size:11 final size:12
Alignment explanation
Indices: 54280301--54280333 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
54280291 TTCACCATGT
54280301 GTTTTTCATCAA
1 GTTTTTCATCAA
54280313 GTTTTTCATCAA
1 GTTTTTCATCAA
54280325 G-TTTTCATC
1 GTTTTTCATC
54280334 TTCTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (12 bp):
GTTTTTCATCAA
Found at i:54281600 original size:3 final size:3
Alignment explanation
Indices: 54281586--54281635 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
54281576 AAATTGAAAT
*
54281586 ATA ATA ACA ATA ATA ATA ATA A-A ATA ATA GCATA AT- ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA
54281630 ATA ATA
1 ATA ATA
54281636 TTGAGGAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 31 0.77
5 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:54281622 original size:16 final size:14
Alignment explanation
Indices: 54281586--54281635 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 14
54281576 AAATTGAAAT
54281586 ATAATAACAATAATA
1 ATAATAA-AATAATA
54281601 ATAATAAAATAATA
1 ATAATAAAATAATA
*
54281615 GCATAATATAATAAT-
1 --ATAATAAAATAATA
54281630 ATAATA
1 ATAATA
54281636 TTGAGGAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 6 0.19
14 7 0.22
15 7 0.22
16 12 0.38
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAATAAAATAATA
Found at i:54282423 original size:15 final size:16
Alignment explanation
Indices: 54282403--54282433 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54282393 AAAAAAACTA
54282403 ATTTCT-GTTTTTTTT
1 ATTTCTCGTTTTTTTT
54282418 ATTTCTCGTTTTTTTT
1 ATTTCTCGTTTTTTTT
54282434 TTTGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (16 bp):
ATTTCTCGTTTTTTTT
Found at i:54282434 original size:19 final size:19
Alignment explanation
Indices: 54282410--54282456 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
54282400 CTAATTTCTG
54282410 TTTTTTTTATTTCTCGTTT
1 TTTTTTTTATTTCTCGTTT
* * *
54282429 TTTTTTTTGTTTTTTGTTT
1 TTTTTTTTATTTCTCGTTT
54282448 TTTTTTTTA
1 TTTTTTTTA
54282457 AATCCACCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.04, C:0.04, G:0.06, T:0.85
Consensus pattern (19 bp):
TTTTTTTTATTTCTCGTTT
Found at i:54295778 original size:18 final size:17
Alignment explanation
Indices: 54295757--54295791 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54295747 TTATTATTAA
*
54295757 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
54295775 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
54295792 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:54295898 original size:18 final size:17
Alignment explanation
Indices: 54295875--54295911 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
54295865 AATTATTATT
54295875 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
54295891 AAATATATGATTTAATA
1 AAATATATGATTTAATA
54295908 AAAT
1 AAAT
54295912 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:54295970 original size:61 final size:61
Alignment explanation
Indices: 54295785--54295972 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
54295775 ATATAATTTA
*
54295785 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * * * * ** * * *
54295846 ATAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TT
1 ATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
54295904 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
54295966 ATAAAAT
1 ATAAAAT
54295973 ATAATTTGAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 1 0.01
59 35 0.36
60 18 0.19
61 42 0.43
62 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:54296018 original size:18 final size:17
Alignment explanation
Indices: 54295995--54296031 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
54295985 AATTATTATT
54295995 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
54296011 AAATATATGATTTAATA
1 AAATATATGATTTAATA
54296028 AAAT
1 AAAT
54296032 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:54296041 original size:120 final size:120
Alignment explanation
Indices: 54295737--54296032 Score: 558
Period size: 120 Copynumber: 2.5 Consensus size: 120
54295727 TTAATCATAT
*
54295737 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
*
54295802 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
54295857 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
54295922 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
54295977 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
54296033 TAAAATAATT
Statistics
Matches: 173, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
120 171 0.99
121 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:54300356 original size:23 final size:23
Alignment explanation
Indices: 54300299--54300370 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
54300289 ACTCACTAAA
*
54300299 AAATCAAGAACAATCTCCAACAGAC
1 AAATCAAGAACAATATCCAA-A-AC
* *
54300324 -TATCAA-AACAATTTCCAAAAC
1 AAATCAAGAACAATATCCAAAAC
54300345 AAATCAAGAACAATAT-CAAAAC
1 AAATCAAGAACAATATCCAAAAC
54300367 AAAT
1 AAAT
54300371 GCAACAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 2 0.05
22 16 0.39
23 18 0.44
24 5 0.12
ACGTcount: A:0.57, C:0.22, G:0.04, T:0.17
Consensus pattern (23 bp):
AAATCAAGAACAATATCCAAAAC
Found at i:54300362 original size:12 final size:11
Alignment explanation
Indices: 54300324--54300368 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
54300314 TCCAACAGAC
54300324 TATCAAAACAA
1 TATCAAAACAA
*
54300335 TTTCCAAAACAA
1 TAT-CAAAACAA
54300347 -ATCAAGAACAA
1 TATCAA-AACAA
54300358 TATCAAAACAA
1 TATCAAAACAA
54300369 ATGCAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 3 0.10
11 13 0.45
12 13 0.45
ACGTcount: A:0.60, C:0.20, G:0.02, T:0.18
Consensus pattern (11 bp):
TATCAAAACAA
Found at i:54300385 original size:107 final size:107
Alignment explanation
Indices: 54300268--54300728 Score: 832
Period size: 107 Copynumber: 4.3 Consensus size: 107
54300258 ACTATACTTG
* *
54300268 CAATTTCCAGTTTCATCTTCTACTCACTAAAAAATCAAGAACAATCTCCAACAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
*
54300333 AATTTCCAAAACAAATCAAGAACAATATCAAAACAAATGCAA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
*
54300375 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAGTTTCCAACAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
*
54300440 AATTTCCATAACAAATCAAGAACAATATCAAAACAAATGCAA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
*
54300482 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
* * *
54300547 AATTGCCAGAACAAATCAAGAACAATACCAAAACAAATGTAA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
*
54300589 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
54300654 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
54300696 CAATTTCCAGTTTCATCTTCTACTCACTAACAA
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAA
54300729 CGAGAAGCTA
Statistics
Matches: 341, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 341 1.00
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.24
Consensus pattern (107 bp):
CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAACAGACTATCAAAAC
AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
Found at i:54300463 original size:23 final size:22
Alignment explanation
Indices: 54300401--54300465 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
54300391 CTTCTACTCA
*
54300401 CTAACAAATCAAGAACAGTTTC
1 CTAACAAATCAAGAACAATTTC
54300423 C-AACAGACTATCAA-AACAATTTC
1 CTAACA-A--ATCAAGAACAATTTC
54300446 CATAACAAATCAAGAACAAT
1 C-TAACAAATCAAGAACAAT
54300466 ATCAAAACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 15 0.42
24 6 0.17
25 4 0.11
ACGTcount: A:0.51, C:0.23, G:0.06, T:0.20
Consensus pattern (22 bp):
CTAACAAATCAAGAACAATTTC
Found at i:54300474 original size:22 final size:22
Alignment explanation
Indices: 54300432--54300477 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54300422 CCAACAGACT
* *
54300432 ATCAAAACAATTTCCATAACAA
1 ATCAAAACAATATCCAAAACAA
54300454 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
54300476 AT
1 AT
54300478 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.20
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:54300570 original size:23 final size:24
Alignment explanation
Indices: 54300510--54300572 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
54300500 TCTACTCACT
*
54300510 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTGCCAGC
*
54300534 AGAC-TATCAA-AACAATTGCCAG-
1 A-ACAAATCAAGAACAATTGCCAGC
54300556 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
54300573 ACCAAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 17 0.52
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.22, G:0.10, T:0.16
Consensus pattern (24 bp):
AACAAATCAAGAACAATTGCCAGC
Found at i:54300581 original size:22 final size:22
Alignment explanation
Indices: 54300539--54300584 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54300529 CCAGCAGACT
* *
54300539 ATCAAAACAATTGCCAGAACAA
1 ATCAAAACAATTACCAAAACAA
54300561 ATCAAGAACAA-TACCAAAACAA
1 ATCAA-AACAATTACCAAAACAA
54300583 AT
1 AT
54300585 GTAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.59, C:0.22, G:0.07, T:0.13
Consensus pattern (22 bp):
ATCAAAACAATTACCAAAACAA
Found at i:54300677 original size:23 final size:24
Alignment explanation
Indices: 54300617--54300679 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
54300607 TCTACTCACT
54300617 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTTCCAGC
*
54300641 AGAC-TATCAA-AACAATTTCCAG-
1 A-ACAAATCAAGAACAATTTCCAGC
54300663 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
54300680 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 18 0.53
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCCAGC
Found at i:54300688 original size:22 final size:22
Alignment explanation
Indices: 54300646--54300691 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54300636 CCAGCAGACT
* *
54300646 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
54300668 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
54300690 AT
1 AT
54300692 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:54300832 original size:19 final size:18
Alignment explanation
Indices: 54300790--54300834 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
54300780 GTGAACTCTT
*
54300790 TCAAAAAACGGCAGACTA
1 TCAAAAAACAGCAGACTA
*
54300808 TCAAAAAACAGCATACTA
1 TCAAAAAACAGCAGACTA
54300826 TCAAAAAAC
1 TCAAAAAAC
54300835 TGTCTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.22, G:0.09, T:0.13
Consensus pattern (18 bp):
TCAAAAAACAGCAGACTA
Found at i:54313632 original size:93 final size:93
Alignment explanation
Indices: 54313473--54313648 Score: 307
Period size: 93 Copynumber: 1.9 Consensus size: 93
54313463 AGAATCAGTA
*
54313473 ATTTCTTTGACAGAAGTTATAAGCAACTCGGCTCATTCAATAAGTTCTGCTACACCAGAAAATGA
1 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
54313538 ATGCATGAATCCTGAATCTGATTTCACG
66 ATGCATGAATCCTGAATCTGATTTCACG
* **
54313566 ATTTCTTTGACTGAAGTTATAAGCAACTCGACTCATTTGATAAGTTCTGCTACACCAGAAAATGA
1 ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
*
54313631 ATGCATGTATCCTGAATC
66 ATGCATGAATCCTGAATC
54313649 CGGTTTCGCT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (93 bp):
ATTTCTTTGACAGAAGTTATAAGCAACTCGACTCATTCAATAAGTTCTGCTACACCAGAAAATGA
ATGCATGAATCCTGAATCTGATTTCACG
Found at i:54320654 original size:22 final size:22
Alignment explanation
Indices: 54320619--54320660 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54320609 TATTTTAGTT
* *
54320619 TACAGATATTAAGTTTATTTTC
1 TACAGAAATAAAGTTTATTTTC
54320641 TACAGAAATAAAGTTTATTT
1 TACAGAAATAAAGTTTATTT
54320661 AGTTTATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (22 bp):
TACAGAAATAAAGTTTATTTTC
Found at i:54323016 original size:17 final size:18
Alignment explanation
Indices: 54322984--54323017 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54322974 ATTTTCTTTT
54322984 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
54323002 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
54323018 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:54326805 original size:37 final size:38
Alignment explanation
Indices: 54326755--54326834 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
54326745 ATATTCACAT
* *
54326755 TTCAAATTTCACTTTTTCACTTTC-AGTCACA-ATTCGA
1 TTCAAAATTCACTTTTCCACTTTCAAGTCA-ATATTCGA
*
54326792 TTCAAAATTCACTTTTCCATTTTCAAGTCAATATTCGA
1 TTCAAAATTCACTTTTCCACTTTCAAGTCAATATTCGA
*
54326830 CTCAA
1 TTCAA
54326835 TTCCACACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 22 0.59
38 15 0.41
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (38 bp):
TTCAAAATTCACTTTTCCACTTTCAAGTCAATATTCGA
Found at i:54326908 original size:16 final size:16
Alignment explanation
Indices: 54326887--54326917 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54326877 AAATAATAAT
*
54326887 ACTTACCATATATATC
1 ACTTACCATACATATC
54326903 ACTTACCATACATAT
1 ACTTACCATACATAT
54326918 AAATTTAAAT
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:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
ACTTACCATACATATC
Found at i:54327629 original size:3 final size:3
Alignment explanation
Indices: 54327621--54327673 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
54327611 ATGTATTAGT
* * *
54327621 TAA TAA TAA TAA TAA TAA TAA CAA AAA TACA TTA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
54327666 TAA TAA TA
1 TAA TAA TA
54327674 TTTAATTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:54327826 original size:15 final size:15
Alignment explanation
Indices: 54327806--54327838 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54327796 TTCATAATAT
54327806 AATAATTAG-AATACA
1 AATAATT-GTAATACA
54327821 AATAATTGTAATACA
1 AATAATTGTAATACA
54327836 AAT
1 AAT
54327839 GTATATACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (15 bp):
AATAATTGTAATACA
Found at i:54330802 original size:51 final size:51
Alignment explanation
Indices: 54330718--54330913 Score: 234
Period size: 51 Copynumber: 3.8 Consensus size: 51
54330708 TATGATCAAT
* *
54330718 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACTAATA
1 GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAA-A
* * * *
54330770 TC-ATCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA
1 GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAA
54330820 GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAA
1 GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-AA
* *** * * * *
54330872 -ATATCTTATACTCATAGTATCCTACACATAGTACTACACATG
1 GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATG
54330914 AGTTCACATG
Statistics
Matches: 124, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
50 2 0.02
51 119 0.96
52 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.26
Consensus pattern (51 bp):
GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAA
Found at i:54330890 original size:102 final size:102
Alignment explanation
Indices: 54330718--54330911 Score: 284
Period size: 102 Copynumber: 1.9 Consensus size: 102
54330708 TATGATCAAT
*
54330718 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACTAATATCATCCGGTACAC
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACTAATATCATCCGATACAC
* *
54330783 GTAGTAGCCTGCACATAGTACTACACACGTGACCAAA
66 ATAGTAGCCTACACATAGTACTACACACGTGACCAAA
* **
54330820 GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAA-AT-ATCTTATAC
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGA-C-TAATATCATCCGATAC
* *
54330883 TCATAGTATCCTACACATAGTACTACACA
64 ACATAGTAGCCTACACATAGTACTACACA
54330912 TGAGTTCACA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
102 76 0.93
103 3 0.04
104 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (102 bp):
GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACTAATATCATCCGATACAC
ATAGTAGCCTACACATAGTACTACACACGTGACCAAA
Found at i:54349885 original size:18 final size:18
Alignment explanation
Indices: 54349862--54349900 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54349852 CTATTCAAAT
*
54349862 ATTTATTATTGGAATTT-A
1 ATTTATT-TTGAAATTTGA
54349880 ATTTATTTTGAAATTTGA
1 ATTTATTTTGAAATTTGA
54349898 ATT
1 ATT
54349901 CACATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (18 bp):
ATTTATTTTGAAATTTGA
Found at i:54350789 original size:17 final size:16
Alignment explanation
Indices: 54350761--54350798 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
54350751 TTGAATCGAT
54350761 TTTTTTATTTTTAATATA
1 TTTTTTATTTTT-ATA-A
54350779 TTTTTTA-TTTTATAA
1 TTTTTTATTTTTATAA
54350794 TTTTT
1 TTTTT
54350799 AACAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 3 0.15
17 4 0.20
18 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTATAA
Found at i:54352779 original size:16 final size:17
Alignment explanation
Indices: 54352758--54352789 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54352748 TAATTGGGGA
54352758 AAAAGTAT-AATTTTGC
1 AAAAGTATGAATTTTGC
54352774 AAAAGTATGAATTTTG
1 AAAAGTATGAATTTTG
54352790 GACCGAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.38
Consensus pattern (17 bp):
AAAAGTATGAATTTTGC
Found at i:54358368 original size:375 final size:375
Alignment explanation
Indices: 54357678--54358432 Score: 1474
Period size: 375 Copynumber: 2.0 Consensus size: 375
54357668 TGGTGAAATG
54357678 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
1 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
54357743 ATCATTTAAAACGGACTCTTAAAAGTAGTACAAAACATTACAACTTAAATATTTGATAAAATAGA
66 ATCATTTAAAACGGACTCTTAAAAGTAGTACAAAACATTACAACTTAAATATTTGATAAAATAGA
*
54357808 CATATTCGCGACATATAATATTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTAT
131 CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTAT
54357873 GCATAACATCGCACTACGATCAACCATCTTGGCACATTCCTGGTTTGGTCATTTCTAGCGAACTA
196 GCATAACATCGCACTACGATCAACCATCTTGGCACATTCCTGGTTTGGTCATTTCTAGCGAACTA
54357938 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
261 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
*
54358003 CCAATTTTACCTTTAAACGATGATGTTGAACTCCTTGACTTAAGAATTCT
326 CCAATTTTACCTTTAAACGATGATGCTGAACTCCTTGACTTAAGAATTCT
54358053 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
1 ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
54358118 ATCATTTAAAACGGACTCTTAAAAGTAGTACAAAACATTACAACTTAAATATTTGATAAAATAGA
66 ATCATTTAAAACGGACTCTTAAAAGTAGTACAAAACATTACAACTTAAATATTTGATAAAATAGA
54358183 CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTAT
131 CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTAT
*
54358248 GCATAACATCGCACTACGATCAACCATCTTGGCACATTCCTGGTTTGGTCCTTTCTAGCGAACTA
196 GCATAACATCGCACTACGATCAACCATCTTGGCACATTCCTGGTTTGGTCATTTCTAGCGAACTA
54358313 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
261 GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
54358378 CCAATTTTACCTTTAAACGATGATGCTGAACTCCTTGACTTAAGAATTCT
326 CCAATTTTACCTTTAAACGATGATGCTGAACTCCTTGACTTAAGAATTCT
*
54358428 CTACT
1 ATACT
54358433 TCTTTTTAGA
Statistics
Matches: 376, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
375 376 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (375 bp):
ATACTAGATGTACTTTTTATTTATTTTAAAAAAATTCTAAGTCAAATGATTTGAATGAAATGTTT
ATCATTTAAAACGGACTCTTAAAAGTAGTACAAAACATTACAACTTAAATATTTGATAAAATAGA
CATATTCGCGACATATAATACTATTCACCATTTGAAAACATATTCTAAAAAATGTCCCCCTGTAT
GCATAACATCGCACTACGATCAACCATCTTGGCACATTCCTGGTTTGGTCATTTCTAGCGAACTA
GTTCAACTCAAGAACTTGTATTACAAATAAAATCCATAAGTTCAATGGAACTTAATGAGTCTCAA
CCAATTTTACCTTTAAACGATGATGCTGAACTCCTTGACTTAAGAATTCT
Found at i:54359074 original size:25 final size:25
Alignment explanation
Indices: 54359013--54359089 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 25
54359003 TACGTCATAT
* *
54359013 AGGCTTTACAGGTAAACTGCCACAA
1 AGGCTTTACAAGTAAATTGCCACAA
**
54359038 AGGCTTCCCAAGTAAATTGCCACAA
1 AGGCTTTACAAGTAAATTGCCACAA
* * *
54359063 AGGCTTTACAAGTGACTCGCCACAA
1 AGGCTTTACAAGTAAATTGCCACAA
54359088 AG
1 AG
54359090 ACACACATAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (25 bp):
AGGCTTTACAAGTAAATTGCCACAA
Found at i:54359971 original size:152 final size:152
Alignment explanation
Indices: 54359723--54360015 Score: 532
Period size: 152 Copynumber: 1.9 Consensus size: 152
54359713 AATCTAGTAG
*
54359723 TAGTAACTGCGTACAAGATCATGAAAATTCTATTAGAATCTTCATTAATAGATAGTTTACTAACG
1 TAGTAACTACGTACAAGATCATGAAAATTCTATTAGAATCTTCATTAATAGATAGTTTACTAACG
*
54359788 TTTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACGTTTCA
66 TTTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCA
*
54359853 GTATCCTTACTTCATTAATAGA
131 ATATCCTTACTTCATTAATAGA
*
54359875 TAGTAACTACGTACAAGATCATGAAATTTCTATTAGAATCTTCATTAATAGATAGTTTACTAACG
1 TAGTAACTACGTACAAGATCATGAAAATTCTATTAGAATCTTCATTAATAGATAGTTTACTAACG
* *
54359940 TTTCAACTACATGCAACCCCTATGTATGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCA
66 TTTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCA
54360005 ATATCCTTACT
131 ATATCCTTACT
54360016 CATCAACAAT
Statistics
Matches: 135, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 135 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (152 bp):
TAGTAACTACGTACAAGATCATGAAAATTCTATTAGAATCTTCATTAATAGATAGTTTACTAACG
TTTCAACTACATGCAACCCCTATGCAGGGCCTTTCACTCACACTCTACTTTTCTTACACCTTTCA
ATATCCTTACTTCATTAATAGA
Found at i:54364456 original size:24 final size:23
Alignment explanation
Indices: 54364415--54364482 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
54364405 CTCATCTTCT
* *
54364415 TCATCTTCACCTCGACCCTTGTAC
1 TCATCTTCATCTCCACCCTTGT-C
* *
54364439 TCATCTTCATTTCCACCCTCGTC
1 TCATCTTCATCTCCACCCTTGTC
*
54364462 TACATCTTCATCTCCAGCCTT
1 T-CATCTTCATCTCCACCCTT
54364483 TGTTTTGTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
23 2 0.06
24 34 0.94
ACGTcount: A:0.16, C:0.41, G:0.06, T:0.37
Consensus pattern (23 bp):
TCATCTTCATCTCCACCCTTGTC
Found at i:54365970 original size:15 final size:16
Alignment explanation
Indices: 54365950--54365980 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
54365940 TTTTAAGAAT
54365950 TAAAAAAT-AATAAAA
1 TAAAAAATAAATAAAA
54365965 TAAAAAATAAATAAAA
1 TAAAAAATAAATAAAA
54365981 CGAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAAATAAATAAAA
Found at i:54371704 original size:18 final size:18
Alignment explanation
Indices: 54371681--54371717 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54371671 GAGGAGGAGC
54371681 AAGCGGA-GATGGCGAAGA
1 AAGCGGAGGA-GGCGAAGA
54371699 AAGCGGAGGAGGCGAAGA
1 AAGCGGAGGAGGCGAAGA
54371717 A
1 A
54371718 GAGACAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.41, C:0.11, G:0.46, T:0.03
Consensus pattern (18 bp):
AAGCGGAGGAGGCGAAGA
Found at i:54376499 original size:2 final size:2
Alignment explanation
Indices: 54376492--54376519 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54376482 AGTTTAGCCA
54376492 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54376520 TTGAATTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54381513 original size:15 final size:15
Alignment explanation
Indices: 54381471--54381516 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
54381461 TTTAAATTTT
54381471 ATTTAAAAT-AA-AA
1 ATTTAAAATAAATAA
* *
54381484 ACTTAAAAAATAATAA
1 ATTTAAAATA-AATAA
54381500 ATTTAAAATAAATAA
1 ATTTAAAATAAATAA
54381515 AT
1 AT
54381517 ATAAGCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.27
15 9 0.35
16 10 0.38
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTTAAAATAAATAA
Found at i:54389704 original size:20 final size:21
Alignment explanation
Indices: 54389666--54389705 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
54389656 CTTTTAATAT
54389666 ATAAAAGTTATTAAAAAAATC
1 ATAAAAGTTATTAAAAAAATC
54389687 ATAAAA-TTA-TAAACAAAAT
1 ATAAAAGTTATTAAA-AAAAT
54389706 TTATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (21 bp):
ATAAAAGTTATTAAAAAAATC
Found at i:54389706 original size:12 final size:12
Alignment explanation
Indices: 54389689--54389727 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
54389679 AAAAAATCAT
54389689 AAAA-TTATAAA
1 AAAAGTTATAAA
*
54389700 CAAAATTTATAAA
1 -AAAAGTTATAAA
54389713 AAAAGTTATAAA
1 AAAAGTTATAAA
54389725 AAA
1 AAA
54389728 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 18 0.72
13 7 0.28
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (12 bp):
AAAAGTTATAAA
Found at i:54389711 original size:21 final size:21
Alignment explanation
Indices: 54389665--54389713 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
54389655 CCTTTTAATA
54389665 TATAAAAGTTATTAAAAAAAT
1 TATAAAAGTTATTAAAAAAAT
*
54389686 CATAAAA-TTA-TAAACAAAATT
1 TATAAAAGTTATTAAA-AAAA-T
54389707 TATAAAA
1 TATAAAA
54389714 AAAGTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 7 0.29
21 13 0.54
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (21 bp):
TATAAAAGTTATTAAAAAAAT
Found at i:54400111 original size:15 final size:15
Alignment explanation
Indices: 54400093--54400125 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
54400083 TTATACAATT
54400093 TTAATT-TGATAAATA
1 TTAATTATGAT-AATA
54400108 TTAATTATGATAATA
1 TTAATTATGATAATA
54400123 TTA
1 TTA
54400126 TTAAGCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TTAATTATGATAATA
Found at i:54401897 original size:22 final size:20
Alignment explanation
Indices: 54401872--54401919 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
54401862 TTTTAATCAT
54401872 AAATTCCTAAAATCCTAATTAA
1 AAATTCCTAAAAT-CTAA-TAA
* * *
54401894 AAATTACTCAACTCTAATAA
1 AAATTCCTAAAATCTAATAA
54401914 AAATTC
1 AAATTC
54401920 TATCTTCACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTCCTAAAATCTAATAA
Found at i:54408369 original size:25 final size:25
Alignment explanation
Indices: 54408344--54408452 Score: 75
Period size: 25 Copynumber: 4.4 Consensus size: 25
54408334 TGGGTATGCC
54408344 CATACGAGCATGTAATTGGGAAGC-
1 CATACGAGCATGTAATTGGGAAGCT
* *
54408368 CCTTCTGAGTCATGTAA-TGGGAAGCT
1 CATAC-GAG-CATGTAATTGGGAAGCT
** * *
54408394 CATGTGAG-TTGTATAATGGGAAGCT
1 CATACGAGCATGTA-ATTGGGAAGCT
*
54408419 CTTACGAGCCAAT-T-ATTGGGAAGCT
1 CATACGAG-C-ATGTAATTGGGAAGCT
54408444 CATACGAGC
1 CATACGAGC
54408453 CATAAACGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
23 4 0.06
24 5 0.08
25 45 0.69
26 9 0.14
27 1 0.02
28 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (25 bp):
CATACGAGCATGTAATTGGGAAGCT
Found at i:54409674 original size:15 final size:15
Alignment explanation
Indices: 54409650--54409681 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
54409640 TATGCATGTA
*
54409650 AAATATAAAAGACAT
1 AAATACAAAAGACAT
54409665 AAATACAAAAGACAT
1 AAATACAAAAGACAT
54409680 AA
1 AA
54409682 TAGTTGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:54413902 original size:25 final size:23
Alignment explanation
Indices: 54413864--54413911 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
54413854 TCTAAACAAT
**
54413864 ATCAAAATTTATATTTATAATCAAA
1 ATCAAAATAAATATTT-T-ATCAAA
54413889 ATCAAAATAAATATTTTATCAAA
1 ATCAAAATAAATATTTTATCAAA
54413912 GTTCAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 14 0.67
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (23 bp):
ATCAAAATAAATATTTTATCAAA
Found at i:54423174 original size:3 final size:3
Alignment explanation
Indices: 54423162--54423199 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
54423152 GCGCATGGAT
54423162 ATA A-A ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT
54423200 GATACAAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:54423190 original size:16 final size:16
Alignment explanation
Indices: 54423169--54423199 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
54423159 GATATAAAAT
54423169 AATAATAATAATAATA
1 AATAATAATAATAATA
54423185 AATAATAATAATAAT
1 AATAATAATAATAAT
54423200 GATACAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:54423684 original size:23 final size:24
Alignment explanation
Indices: 54423654--54423700 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
54423644 AAATTAAATC
54423654 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
54423677 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
54423701 AAGATTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:54423700 original size:24 final size:23
Alignment explanation
Indices: 54423654--54423719 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 23
54423644 AAATTAAATC
* *
54423654 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGCAATATCATATCT
54423677 TCTAAGATTGCATATATCATA---
1 TCTAAGATTGCA-ATATCATATCT
54423698 TCTAAGATTGC-ATATCATATCT
1 TCTAAGATTGCAATATCATATCT
54423720 AAGATTACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 8 0.22
21 11 0.30
23 11 0.30
24 7 0.19
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
TCTAAGATTGCAATATCATATCT
Found at i:54423703 original size:21 final size:21
Alignment explanation
Indices: 54423677--54423731 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
54423667 AATCATATCT
54423677 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
54423698 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
54423717 TCTAAGATTACATAT
1 TCTAAGATTGCATAT
54423732 CCTTGAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:54424159 original size:44 final size:44
Alignment explanation
Indices: 54424061--54424431 Score: 216
Period size: 44 Copynumber: 8.6 Consensus size: 44
54424051 CTTGAGTCTA
* * * *
54424061 CTCCACTGCAACTTCAGGGAGATAAGACCCGAT-G---TGATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGATCTG-TGGTTTTAATCTG
* * *
54424102 CTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCTG
* *
54424146 CTCCACTGCAACTTCAGGGAGAT-AGAAT-TATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAG-ATCT-GTGGTTTTAATCTG
* * *** * *
54424190 CTCCACTGCATCTTCAGGGAAATAAGAT-TCGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGT-TTTAATCTG
* *
54424235 C-CTCACTGCAACTTCA-GGAGGATAAGA-CT-TGATTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGATCTGTGGTT--TTAATCTG
* * * * ***
54424279 CTCCACTGAAACTTCAGGAAGATAAGA-C--TAGATGCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCTG
* * ** * *
54424320 CT-CTCTGTAACTTCAAAGAGATAAGATCTGTGATTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCTG
* * *
54424363 CTCCACTGCAACTTCAGGGAGATAGGAT-TATTGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATCT-GTGGTTTTAATCTG
* *
54424407 CTCCACTGCAACTTTAGGAAGATAA
1 CTCCACTGCAACTTCAGGGAGATAA
54424432 TATTCGCCAT
Statistics
Matches: 250, Mismatches: 60, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
40 20 0.08
41 35 0.14
42 1 0.00
43 16 0.06
44 146 0.58
45 32 0.13
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATCTG
Found at i:54424439 original size:217 final size:219
Alignment explanation
Indices: 54424022--54424450 Score: 666
Period size: 217 Copynumber: 2.0 Consensus size: 219
54424012 CAGAGAGATA
* * * * * *
54424022 TGCAATTTCAGGGGGATAAGACTTGCTTTCTTGAGTCTACTCCACTGCAACTTCAGGGAGATAAG
1 TGCAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGAAACTTCAGGAAGATAAG
* * * *
54424087 ACCCGATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCAC
66 ACCAGATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCGCTCCAC
*
54424152 TGCAACTTCAGGGAGATAGAATTATTGGCTTTAATCTGCTCCACTGCATCTTCAGGGAAATAAGA
131 TGCAACTTCAGGGAGATAGAATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGA
54424217 TTCGCCATCTTCAGTCTGCCTCAC
196 TTCGCCATCTTCAGTCTGCCTCAC
*
54424241 TGCAACTTCAGGAGGATAAGACTTGATTACTT-AGTCTGCTCCACTGAAACTTCAGGAAGATAAG
1 TGCAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGAAACTTCAGGAAGATAAG
* * *
54424305 ACTAGATGCGATCTGCTCT-CTGTAACTTCAAAGAGATAAGATCTGTGATTTTAATCCGCTCCAC
66 ACCAGATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCGCTCCAC
* * *
54424369 TGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTTA-GGAAGATAAT
131 TGCAACTTCAGGGAGATAGAATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAA-ATAAG
54424433 ATTCGCCATCTTCAGTCT
195 ATTCGCCATCTTCAGTCT
54424451 TTTAAATTGC
Statistics
Matches: 191, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
216 4 0.02
217 115 0.60
218 44 0.23
219 28 0.15
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (219 bp):
TGCAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGAAACTTCAGGAAGATAAG
ACCAGATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCGCTCCAC
TGCAACTTCAGGGAGATAGAATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGA
TTCGCCATCTTCAGTCTGCCTCAC
Found at i:54424579 original size:100 final size:100
Alignment explanation
Indices: 54424442--54424650 Score: 269
Period size: 100 Copynumber: 2.1 Consensus size: 100
54424432 TATTCGCCAT
* * * *
54424442 CTTCAGTCTTTTAAATTGCAATGTTAGGGAAATAAGATTCGCTATCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTAGGGAAACAAGATCCGCCATCGTAGCTTCAATCTGTTCCA
* *
54424507 CTACACCGCTAG-GGAAGTAAGATTCACCGTTGCGG
66 CTACACCGCCAGAGG-AGTAAGATTCACCGTCGCGG
* * *
54424542 CTTCAATCTTTTTAATTGCAATGTT-GGTGAAACAAGATCCGCCGTCGTAGCTTCAATTTGTTCC
1 CTTCAATCTTTTAAATTGCAATGTTAGG-GAAACAAGATCCGCCATCGTAGCTTCAATCTGTTCC
* * *
54424606 ATTACACTGCCAGAGGAGTAAGATTCACCGTCGTGG
65 ACTACACCGCCAGAGGAGTAAGATTCACCGTCGCGG
*
54424642 TTTCAATCT
1 CTTCAATCT
54424651 GCTCCACTGT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
99 2 0.02
100 90 0.96
101 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTTAGGGAAACAAGATCCGCCATCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGAGGAGTAAGATTCACCGTCGCGG
Found at i:54424788 original size:50 final size:50
Alignment explanation
Indices: 54424728--54424822 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
54424718 TTCAAGCCTT
* * *
54424728 AACGCTAGGGAGATAAGATTCGCCGTCGTGGCTTCAATCTGTTCCGCTAC
1 AACGCCAGGGAAATAAGATTCGCCATCGTGGCTTCAATCTGTTCCGCTAC
* * * *
54424778 AACGCCAGGGAAATAAGATTCGTCATTGTGGCTTTAATCTTTTCC
1 AACGCCAGGGAAATAAGATTCGCCATCGTGGCTTCAATCTGTTCC
54424823 ATTGCAACGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (50 bp):
AACGCCAGGGAAATAAGATTCGCCATCGTGGCTTCAATCTGTTCCGCTAC
Found at i:54431113 original size:24 final size:24
Alignment explanation
Indices: 54431007--54431138 Score: 180
Period size: 25 Copynumber: 5.5 Consensus size: 24
54430997 ATACAGAACA
* *
54431007 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
***
54431030 AA-A-CAGAGAGCACTGCCGTGCT
1 AATATCAGAGAGCACCAACGTGCT
54431052 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
54431077 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
54431102 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
54431126 AATATCAGAGAGC
1 AATATCAGAGAGC
54431139 GCGCTAAAGT
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
22 16 0.16
23 4 0.04
24 38 0.39
25 40 0.41
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:54431119 original size:49 final size:50
Alignment explanation
Indices: 54431006--54431138 Score: 179
Period size: 49 Copynumber: 2.8 Consensus size: 50
54430996 TATACAGAAC
* * ***
54431006 AAATA-CAGAGAGCACAAATGTGCT-A-AA-CAGAGAGCACTGCCGTGCT
1 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
54431052 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
1 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
54431102 -AATATCAGAGAGCACCAACGTGCTAAT-ATCAGAGAGC
1 AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGC
54431139 GCGCTAAAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
46 5 0.06
47 17 0.22
48 11 0.14
49 29 0.37
50 16 0.21
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.16
Consensus pattern (50 bp):
AAATATCAGAGAGCACCAACGTGCTAATAATCAGAGAGCACCAACGTGCT
Found at i:54432299 original size:5 final size:5
Alignment explanation
Indices: 54432285--54432354 Score: 63
Period size: 5 Copynumber: 13.6 Consensus size: 5
54432275 TGTTTTATGT
* *
54432285 ATATA TATATA ATATA ATATA ATATA TTAATA ATATA ATATA A-A-A ACATA
1 ATATA -ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA
*
54432335 ATCATTA CTATA ATATA ATA
1 AT-A-TA ATATA ATATA ATA
54432355 ATATTTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 36 0.67
6 11 0.20
7 3 0.06
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:54432309 original size:21 final size:21
Alignment explanation
Indices: 54432284--54432327 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
54432274 TTGTTTTATG
54432284 TATATATATATAATATAATATAA
1 TATAT-TA-ATAATATAATATAA
54432307 TATATTAATAATATAATATAA
1 TATATTAATAATATAATATAA
54432328 AAACATAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.67
22 2 0.10
23 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATTAATAATATAATATAA
Found at i:54432317 original size:16 final size:17
Alignment explanation
Indices: 54432284--54432326 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
54432274 TTGTTTTATG
54432284 TATATATATATAATATAA
1 TATA-ATATATAATATAA
*
54432302 TATAATATATTA-ATAA
1 TATAATATATAATATAA
54432318 TATAATATA
1 TATAATATA
54432327 AAAACATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 13 0.54
17 7 0.29
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATAATATATAATATAA
Found at i:54432336 original size:21 final size:21
Alignment explanation
Indices: 54432293--54432357 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
54432283 GTATATATAT
* *
54432293 ATAATATAATATAATATATTA
1 ATAATATAATATAATAAAATA
54432314 ATAATATAATATAA-AAACATA
1 ATAATATAATATAATAAA-ATA
* * *
54432335 ATCAT-TACTATAATATAATA
1 ATAATATAATATAATAAAATA
54432355 ATA
1 ATA
54432358 TTTTTTTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATATAATATAATAAAATA
Found at i:54436041 original size:23 final size:22
Alignment explanation
Indices: 54436011--54436061 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
54436001 AATAAAAACA
*
54436011 AAAACATATGTATAAAATATAT
1 AAAACATACGTATAAAATATAT
**
54436033 ATAAACATACGTATACTATATAT
1 A-AAACATACGTATAAAATATAT
54436056 AAAACA
1 AAAACA
54436062 ATATATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAACATACGTATAAAATATAT
Found at i:54436106 original size:3 final size:3
Alignment explanation
Indices: 54436098--54436130 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
54436088 GCGCATGAAT
*
54436098 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54436131 CAAGATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:54436629 original size:21 final size:21
Alignment explanation
Indices: 54436603--54436657 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
54436593 AATCATATTT
*
54436603 TCTAAGATTGCATATATTATA
1 TCTAAGATTGCATATATCATA
54436624 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
54436643 TCTAAGATTACATAT
1 TCTAAGATTGCATAT
54436658 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:54446557 original size:7 final size:7
Alignment explanation
Indices: 54446545--54446572 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
54446535 CCCTCAAACT
54446545 TAAAAAA
1 TAAAAAA
54446552 TAAAAAA
1 TAAAAAA
54446559 TAAAAAA
1 TAAAAAA
54446566 TAAAAAA
1 TAAAAAA
54446573 AAAGCAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:54446755 original size:90 final size:90
Alignment explanation
Indices: 54446568--54446776 Score: 234
Period size: 91 Copynumber: 2.3 Consensus size: 90
54446558 ATAAAAAATA
* **
54446568 AAAAAAAAGCAATTAAGCTCTTGTTTTTTCTTACACTCAATTGGGTACTTGAACCTTTAAATTGC
1 AAAAAAAAGCAATTAAGCCCTTGTTTTTTCTTACACTCAATTGAATACTTGAACCTTTAAATTGC
* *
54446633 ATAAAAATTGCCCTCAATTTTTTTTC
66 ATAAAAATTGCCATCAA-TCTTTTTC
* *
54446659 -AAAAAAAGCAAATAAGCCCTTGCTTTTTTTTTTA-ACTCAATTGAATACTTGAA-CTGTTGAAA
1 AAAAAAAAGCAATTAAGCCCTTG--TTTTTTCTTACACTCAATTGAATACTTGAACCT-TT-AAA
54446721 -TGCATCAAAAA-TGCCATCAGA-CTTTTTC
62 TTGCAT-AAAAATTGCCATCA-ATCTTTTTC
*
54446749 AAAAAAAAGCAATTAAACCCTT-TTTTTT
1 AAAAAAAAGCAATTAAGCCCTTGTTTTTT
54446777 GCACTCAATT
Statistics
Matches: 102, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
88 6 0.06
90 28 0.27
91 50 0.49
92 18 0.18
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (90 bp):
AAAAAAAAGCAATTAAGCCCTTGTTTTTTCTTACACTCAATTGAATACTTGAACCTTTAAATTGC
ATAAAAATTGCCATCAATCTTTTTC
Found at i:54446959 original size:20 final size:20
Alignment explanation
Indices: 54446934--54447016 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
54446924 AAATTTTAAT
*
54446934 AAAAAATATATAAAATCGTA
1 AAAAAATATATAAAATCATA
* * **
54446954 AAAAAATATAAAAAACCGGA
1 AAAAAATATATAAAATCATA
***
54446974 AAATTTTATA-AAAATCAT-
1 AAAAAATATATAAAATCATA
54446992 AAAAAAT-TATAAAATGCATA
1 AAAAAATATATAAAAT-CATA
54447012 AAAAA
1 AAAAA
54447017 TTCCCTTTAA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
17 2 0.04
18 9 0.19
19 8 0.17
20 29 0.60
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAAATATATAAAATCATA
Found at i:54447005 original size:29 final size:28
Alignment explanation
Indices: 54446932--54447016 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 28
54446922 TTAAATTTTA
54446932 ATAAAAAATATATAAAATCGTAAAAAAAT
1 ATAAAAAAT-TATAAAATCGTAAAAAAAT
**** ** *
54446961 ATAAAAAACCGGAAAATTTTATAAAAAT
1 ATAAAAAATTATAAAATCGTAAAAAAAT
*
54446989 CATAAAAAATTATAAAATGCATAAAAAA
1 -ATAAAAAATTATAAAAT-CGTAAAAAA
54447017 TTCCCTTTAA
Statistics
Matches: 40, Mismatches: 14, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
28 13 0.32
29 21 0.52
30 6 0.15
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.24
Consensus pattern (28 bp):
ATAAAAAATTATAAAATCGTAAAAAAAT
Found at i:54447018 original size:19 final size:19
Alignment explanation
Indices: 54446932--54447018 Score: 70
Period size: 19 Copynumber: 4.5 Consensus size: 19
54446922 TTAAATTTTA
54446932 ATAAAAAA-TATATAAAATC
1 ATAAAAAATTATA-AAAATC
* * *
54446951 GTAAAAAAATATAAAAAACC
1 ATAAAAAATTAT-AAAAATC
** **
54446971 GGAAAATTTTATAAAAATC
1 ATAAAAAATTATAAAAATC
54446990 ATAAAAAATTAT-AAAATGC
1 ATAAAAAATTATAAAAAT-C
54447009 ATAAAAAATT
1 ATAAAAAATT
54447019 CCCTTTAACC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
18 5 0.09
19 32 0.59
20 16 0.30
21 1 0.02
ACGTcount: A:0.64, C:0.06, G:0.05, T:0.25
Consensus pattern (19 bp):
ATAAAAAATTATAAAAATC
Found at i:54447647 original size:92 final size:92
Alignment explanation
Indices: 54447524--54447731 Score: 249
Period size: 93 Copynumber: 2.3 Consensus size: 92
54447514 TAAGGTACTT
** * * * *
54447524 AATTGAGTGCAAAAAAAAAAAGTAGGGGCTTAATTACTTT-TTTGAAACAGTTTGAGGGCCTTTT
1 AATTGAGTGCAAAAAAAAAAAAAAGGAGCTTAATTACTTTCTTTAAAAAAGTTTGAGGGCCCTTT
* *
54447588 TAATACA-TTTAGACAGTTCAAGTACCC
66 TAATACATTTTA-AAAGTTCAAATACCC
* **
54447615 AATTGGGTGCAAAAAAAAAAGAAAAGGAGCTTAATTGTTTTCTTTAAAAAAGTTTGAGGGCCCTT
1 AATTGAGTGCAAAAAAAAAA-AAAAGGAGCTTAATTACTTTCTTTAAAAAAGTTTGAGGGCCCTT
* * *
54447680 TTGATGCATTTTAAAAGTTCAAATACCT
65 TTAATACATTTTAAAAGTTCAAATACCC
*
54447708 AATTGAGTGCAAAAAAAGAAAAAA
1 AATTGAGTGCAAAAAAAAAAAAAA
54447732 TTTGAGGGCT
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
91 19 0.19
92 19 0.19
93 56 0.57
94 4 0.04
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (92 bp):
AATTGAGTGCAAAAAAAAAAAAAAGGAGCTTAATTACTTTCTTTAAAAAAGTTTGAGGGCCCTTT
TAATACATTTTAAAAGTTCAAATACCC
Found at i:54448211 original size:27 final size:25
Alignment explanation
Indices: 54448164--54448243 Score: 90
Period size: 25 Copynumber: 3.1 Consensus size: 25
54448154 AACTAGCAAG
* *
54448164 TTTAATTAAATTTAAATTTAAATAA
1 TTTAATAAAATTTATATTTAAATAA
54448189 TTTAATAAAAATAATT-TATTTAAATAA
1 TTTAAT-AAAAT--TTATATTTAAATAA
* *
54448216 CTTAATTAAATTTATATTTAAATAA
1 TTTAATAAAATTTATATTTAAATAA
54448241 TTT
1 TTT
54448244 TGTGGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.04
25 19 0.41
26 8 0.17
27 15 0.33
28 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTAATAAAATTTATATTTAAATAA
Found at i:54452772 original size:6 final size:6
Alignment explanation
Indices: 54452761--54452785 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54452751 GTATTATTCA
54452761 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
54452786 TTGTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:54453868 original size:17 final size:17
Alignment explanation
Indices: 54453842--54453880 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
54453832 AATAAACAAT
54453842 TAAA-TAAATT-GGAAA
1 TAAATTAAATTGGGAAA
54453857 TATAATTAAATTGGGAAA
1 TA-AATTAAATTGGGAAA
54453875 TAAATT
1 TAAATT
54453881 CGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 2 0.10
17 10 0.48
18 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.13, T:0.33
Consensus pattern (17 bp):
TAAATTAAATTGGGAAA
Found at i:54457709 original size:23 final size:22
Alignment explanation
Indices: 54457666--54457709 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
54457656 TTCTAAGTCG
54457666 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
54457689 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
54457710 TTCGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:54457818 original size:45 final size:45
Alignment explanation
Indices: 54457754--54457847 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
54457744 AACAGATACT
* * *
54457754 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCGATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
*
54457799 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
54457844 CGGT
1 CGGT
54457848 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:54457911 original size:51 final size:51
Alignment explanation
Indices: 54457849--54457989 Score: 185
Period size: 51 Copynumber: 2.8 Consensus size: 51
54457839 ATGTTCGGTT
* *
54457849 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATA
* * * *
54457900 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCGATA
* * *
54457951 CGCATAGTAGCCTACACATAGTACTACACACATGACCAT
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
54457990 CACTTTCACT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.03
51 73 0.95
52 2 0.03
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATA
Found at i:54461014 original size:25 final size:25
Alignment explanation
Indices: 54460986--54461073 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
54460976 CAAGCATATA
* *
54460986 AACGGGAAGCTCATGTGAGTTGCAT
1 AACGGGAAGCTCATCTGAGCTGCAT
* * * *
54461011 AACGAGAAGCTTATCTGGGCTGTAT
1 AACGGGAAGCTCATCTGAGCTGCAT
**
54461036 AACGGGAAGCTCATAAGAGC--CAT
1 AACGGGAAGCTCATCTGAGCTGCAT
54461059 AATCGGGAAGCTCAT
1 AA-CGGGAAGCTCAT
54461074 ACGAGCCAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
23 4 0.08
24 12 0.24
25 34 0.68
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (25 bp):
AACGGGAAGCTCATCTGAGCTGCAT
Found at i:54461067 original size:24 final size:23
Alignment explanation
Indices: 54461034--54461094 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 23
54461024 TCTGGGCTGT
54461034 ATAACGGGAAGCTCATAAGAGCC
1 ATAACGGGAAGCTCATAAGAGCC
*
54461057 ATAATCGGGAAGCTCATACGAGCC
1 ATAA-CGGGAAGCTCATAAGAGCC
*
54461081 AATAACGGGTAGCT
1 -ATAACGGGAAGCT
54461095 GCGAAGAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 4 0.12
24 26 0.76
25 4 0.12
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.16
Consensus pattern (23 bp):
ATAACGGGAAGCTCATAAGAGCC
Found at i:54461119 original size:73 final size:71
Alignment explanation
Indices: 54461040--54461240 Score: 163
Period size: 73 Copynumber: 2.7 Consensus size: 71
54461030 CTGTATAACG
* *
54461040 GGAAGCTCATAAGAGCCATAATCGGGAAGCTCATACGAGCCAATAACGGGTAGCTGCGAAGAGCC
1 GGAAGCTCA-AAGAGCCATAATCGGGAAGCTCA-ACGAGCCAATAACGGGAAGCTCCGAAGAGCC
54461105 ATTAATTGA
64 ATT-ATTGA
** * * * * * *
54461114 -GAAGCTCCGGATAGCCATCTATCGGGAAGTTCAAGCGAGCC-ATATCAGGAAGCTCCGAAGTGC
1 GGAAGCT-CAAAGAGCCAT-AATCGGGAAGCTCAA-CGAGCCAATAACGGGAAGCTCCGAAGAGC
*
54461177 CATTATTTA
63 CATTATTGA
* *
54461186 GGAAGCTAACAAAGAGCCTTTAATCGGGAAGCTCAAGAAGAGCCATATAACGGGA
1 GGAAGCT--CAAAGAGCC-ATAATCGGGAAGCTC-A-ACGAGCCA-ATAACGGGA
54461241 CACTCATAAA
Statistics
Matches: 96, Mismatches: 21, Indels: 17
0.72 0.16 0.13
Matches are distributed among these distances:
72 4 0.04
73 41 0.43
74 36 0.38
75 7 0.07
76 1 0.01
77 7 0.07
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (71 bp):
GGAAGCTCAAAGAGCCATAATCGGGAAGCTCAACGAGCCAATAACGGGAAGCTCCGAAGAGCCAT
TATTGA
Found at i:54461345 original size:25 final size:25
Alignment explanation
Indices: 54461313--54461376 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
54461303 GAAGAGCTAT
*
54461313 TAACGGGAAGCTCGCAAGAATAATA
1 TAACGGGAAGCTCGCAAGAACAATA
*
54461338 TAACGGGAAGCTCACAAGAACAATA
1 TAACGGGAAGCTCGCAAGAACAATA
54461363 TAACGGGAAGCTCG
1 TAACGGGAAGCTCG
54461377 AGAGGGCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCGCAAGAACAATA
Found at i:54466075 original size:23 final size:23
Alignment explanation
Indices: 54466049--54466170 Score: 190
Period size: 23 Copynumber: 5.3 Consensus size: 23
54466039 AGAAGTGCAA
54466049 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54466072 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54466095 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
54466118 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
54466141 CACTGAAACGTAGCCGAAGCTAA
1 CACTGATATGTAGCCGAAGCTAC
54466164 CACTGAT
1 CACTGAT
54466171 CAATAACACT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 89 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:54466116 original size:46 final size:46
Alignment explanation
Indices: 54466049--54466168 Score: 213
Period size: 46 Copynumber: 2.6 Consensus size: 46
54466039 AGAAGTGCAA
*
54466049 CACTGATATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
54466095 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
* *
54466141 CACTGAAACGTAGCCGAAGCTAACACTG
1 CACTGAAATGTAGCCGAAGCTACCACTG
54466169 ATCAATAACA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
Found at i:54470557 original size:2 final size:2
Alignment explanation
Indices: 54470550--54470574 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54470540 ACATATGATC
54470550 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
54470575 AGTTGATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54470839 original size:79 final size:75
Alignment explanation
Indices: 54470708--54470909 Score: 182
Period size: 75 Copynumber: 2.6 Consensus size: 75
54470698 AATCTCACTT
* * *
54470708 AAACTTATATAATTA-TCATACCTAAATTCAATACATAAACATGTACATATATAAGTTTGTATAT
1 AAACTTATATAA-TAGTCATACCTAAATTCAACACATAAACATATACAAATAT-A--TT-TATAT
54470772 ATTC-GAGA-CTCACAC
61 -TTCTGA-ACCTCACAC
* * *
54470787 ACACTTATATAATAGTCATACCTAAATTTAACACA-AGAACATATTCAAATATATTTATATTTCT
1 AAACTTATATAATAGTCATACCTAAATTCAACACATA-AACATATACAAATATATTTATATTTCT
* *
54470851 GAACCTCATAT
65 GAACCTCACAC
* *
54470862 AAACTTATATAAAAGTCATACCTAAACTCAA-A-ATAATAACATATACAA
1 AAACTTATATAATAGTCATACCTAAATTCAACACAT-A-AACATATACAA
54470910 TTGTATTTGC
Statistics
Matches: 103, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
73 1 0.01
74 5 0.05
75 50 0.49
76 2 0.02
78 4 0.04
79 41 0.40
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (75 bp):
AAACTTATATAATAGTCATACCTAAATTCAACACATAAACATATACAAATATATTTATATTTCTG
AACCTCACAC
Found at i:54470882 original size:75 final size:75
Alignment explanation
Indices: 54470789--54470983 Score: 219
Period size: 75 Copynumber: 2.6 Consensus size: 75
54470779 ACTCACACAC
* * * * * * **
54470789 ACTTATATAATAGTCATACCTAAATTTAACACAAGAACATATTCAAATATATTTATATTTCTGAA
1 ACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTACATTTCCAAA
54470854 CCTCATATAA
66 CCTCATATAA
* * * * *
54470864 ACTTATATAAAAGTCATACCTAAACTCAAAATAATAACATATACAATTGTATTTGCATTTCCAAA
1 ACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTACATTTCCAAA
**
54470929 TTTCATATAA
66 CCTCATATAA
* * * *
54470939 ACTTACATAAAAATCATACCCAAACTCAATACAAGAACATATACA
1 ACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACA
54470984 TGTAAATATA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
75 99 1.00
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.32
Consensus pattern (75 bp):
ACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTACATTTCCAAA
CCTCATATAA
Found at i:54471408 original size:2 final size:2
Alignment explanation
Indices: 54471401--54471435 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54471391 GATATACATG
54471401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54471436 TAATTTCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54472394 original size:13 final size:13
Alignment explanation
Indices: 54472376--54472400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54472366 TCAAACGATC
54472376 AAATTTTCACACG
1 AAATTTTCACACG
54472389 AAATTTTCACAC
1 AAATTTTCACAC
54472401 ATATAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:54480678 original size:13 final size:13
Alignment explanation
Indices: 54480657--54480733 Score: 118
Period size: 13 Copynumber: 5.9 Consensus size: 13
54480647 ACACTCAAAT
54480657 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
54480670 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
*
54480683 TTCTCAAAAGCCC
1 TTCTCAAAAGCAC
*
54480696 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
*
54480709 TTCTCAAAAGCCC
1 TTCTCAAAAGCAC
54480722 TTCTCAAAAGCA
1 TTCTCAAAAGCA
54480734 ATGAAGAACT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 56 1.00
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.23
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:54480686 original size:26 final size:26
Alignment explanation
Indices: 54480657--54480733 Score: 136
Period size: 26 Copynumber: 3.0 Consensus size: 26
54480647 ACACTCAAAT
*
54480657 TTCTCAAAAGCACTTCTGAAAAGCAC
1 TTCTCAAAAGCCCTTCTGAAAAGCAC
54480683 TTCTCAAAAGCCCTTCTGAAAAGCAC
1 TTCTCAAAAGCCCTTCTGAAAAGCAC
*
54480709 TTCTCAAAAGCCCTTCTCAAAAGCA
1 TTCTCAAAAGCCCTTCTGAAAAGCA
54480734 ATGAAGAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.23
Consensus pattern (26 bp):
TTCTCAAAAGCCCTTCTGAAAAGCAC
Found at i:54485254 original size:2 final size:2
Alignment explanation
Indices: 54485242--54485271 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
54485232 CATATCCGTT
*
54485242 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54485272 ATTACTAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:54485907 original size:79 final size:75
Alignment explanation
Indices: 54485776--54485985 Score: 194
Period size: 75 Copynumber: 2.7 Consensus size: 75
54485766 AATCTCACTT
* * *
54485776 AAACTTATATAATTA-TCATACCTAAATTCAATACATAAACATGTACATATATAAGTTTGTATAT
1 AAACTTATATAA-TAGTCATACCTAAATTCAACACATAAACATATACAAATAT-A--TT-TATAT
**
54485840 CTTC-GAGTCTCATAC
61 -TTCTGAACCTCATAC
* * * *
54485855 ACACTTATATAATAGTCATACCTAAATTTAACGCA-AGAACATATTCAAATATATTTATATTTCT
1 AAACTTATATAATAGTCATACCTAAATTCAACACATA-AACATATACAAATATATTTATATTTCT
*
54485919 GAACCTCATAT
65 GAACCTCATAC
* * * *
54485930 AAACTTATATAAAAGTCATACCTAAACTCAAAACA-ATAACATATACAATTATATTT
1 AAACTTATATAATAGTCATACCTAAATTCAACACATA-AACATATACAAATATATTT
54485986 GCATTTCCAA
Statistics
Matches: 109, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
74 3 0.03
75 60 0.55
76 2 0.02
78 4 0.04
79 40 0.37
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.35
Consensus pattern (75 bp):
AAACTTATATAATAGTCATACCTAAATTCAACACATAAACATATACAAATATATTTATATTTCTG
AACCTCATAC
Found at i:54485947 original size:75 final size:75
Alignment explanation
Indices: 54485848--54486051 Score: 228
Period size: 75 Copynumber: 2.7 Consensus size: 75
54485838 ATCTTCGAGT
* * * * * ** * *
54485848 CTCATACACACTTATATAATAGTCATACCTAAATTTAACGCAAGAACATATTCAAATATATTTAT
1 CTCATATAAACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTAC
**
54485913 ATTTCTGAAC
66 ATTTCCAAAC
* * *
54485923 CTCATATAAACTTATATAAAAGTCATACCTAAACTCAAAACAATAACATATACAATTATATTTGC
1 CTCATATAAACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTAC
*
54485988 ATTTCCAAAT
66 ATTTCCAAAC
* * * * *
54485998 TTCATATAAACTTACATAAAAATCATACCCAAACTCAATACAAGAACATATACA
1 CTCATATAAACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACA
54486052 TGTAAATATA
Statistics
Matches: 108, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 108 1.00
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (75 bp):
CTCATATAAACTTATATAAAAGTCATACCTAAACTCAAAACAAGAACATATACAAATATATTTAC
ATTTCCAAAC
Found at i:54487354 original size:13 final size:13
Alignment explanation
Indices: 54487336--54487360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54487326 TCAAACGATC
54487336 AAATTTTCACACG
1 AAATTTTCACACG
54487349 AAATTTTCACAC
1 AAATTTTCACAC
54487361 ATATAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:54489453 original size:26 final size:26
Alignment explanation
Indices: 54489372--54489464 Score: 70
Period size: 26 Copynumber: 3.7 Consensus size: 26
54489362 ATAGCTATAT
*
54489372 ATCAGGAAG-TC-CAAGCGAGCCA-T-
1 ATCAGGAAGCTCACAA-AGAGCCATTA
* *
54489395 ATCAAGAAGCTC-CGAAGAGCCATTA
1 ATCAGGAAGCTCACAAAGAGCCATTA
* *
54489420 ATCAGGAATCTCACAAAGAGCCTTTA
1 ATCAGGAAGCTCACAAAGAGCCATTA
** *
54489446 ATTGGGAAGCTCACGAAGA
1 ATCAGGAAGCTCACAAAGA
54489465 ACCGTATATC
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
23 14 0.25
24 5 0.09
25 10 0.18
26 26 0.47
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
ATCAGGAAGCTCACAAAGAGCCATTA
Found at i:54489959 original size:5 final size:5
Alignment explanation
Indices: 54489930--54489973 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
54489920 TAAATTTAGG
* *
54489930 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCA
54489974 CATCTTAGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:54491237 original size:25 final size:26
Alignment explanation
Indices: 54491209--54491258 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
54491199 GAAATATTAT
54491209 TATTTT-AATCAAGAATTATT-TTAAC
1 TATTTTCAA-CAAGAATTATTCTTAAC
54491234 TATTTTCAACAAGAATTATTCTTAA
1 TATTTTCAACAAGAATTATTCTTAA
54491259 ATAATAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (26 bp):
TATTTTCAACAAGAATTATTCTTAAC
Found at i:54491332 original size:14 final size:15
Alignment explanation
Indices: 54491299--54491332 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54491289 AACTGAAATC
*
54491299 CTATTTTAAACCTAA
1 CTATTCTAAACCTAA
54491314 CTATTCTAAACCT-A
1 CTATTCTAAACCTAA
54491328 CTATT
1 CTATT
54491333 GTTTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (15 bp):
CTATTCTAAACCTAA
Found at i:54497776 original size:24 final size:24
Alignment explanation
Indices: 54497722--54497769 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
54497712 CTTTTCCTAT
*
54497722 AATATT-TTTTTTTACTTTAAAAA
1 AATATTATTATTTTACTTTAAAAA
*
54497745 AATATTATTATTTTATTTTAAAAA
1 AATATTATTATTTTACTTTAAAAA
54497769 A
1 A
54497770 TGTTTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATTATTATTTTACTTTAAAAA
Found at i:54497965 original size:3 final size:3
Alignment explanation
Indices: 54497957--54498017 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
54497947 CCGAACGCCC
*
54497957 AAG AAG AAG AAG ACG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
54498004 AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AA
54498018 TTTATTAATG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.66, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Done.