Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 160 of 186
Found at i:53249917 original size:39 final size:41
Alignment explanation
Indices: 53249822--53249939 Score: 140
Period size: 39 Copynumber: 3.0 Consensus size: 41
53249812 TTGAATGATG
* *
53249822 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGA-T-ACTAATA
* *
53249861 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAATA
53249901 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAT
53249940 CAGATGGATA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
39 45 0.65
40 12 0.17
41 11 0.16
42 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:53250727 original size:40 final size:40
Alignment explanation
Indices: 53250672--53250750 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
53250662 AATATGCGTG
*
53250672 GGAATGCGTATCCACTGAAGCTACCATGTGTAAGAGGTTA
1 GGAATGCATATCCACTGAAGCTACCATGTGTAAGAGGTTA
53250712 GGAATGCATATCCACTGAAGCTACCATGTGTAAGAGGTT
1 GGAATGCATATCCACTGAAGCTACCATGTGTAAGAGGTT
53250751 TGAGGATGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (40 bp):
GGAATGCATATCCACTGAAGCTACCATGTGTAAGAGGTTA
Found at i:53268143 original size:27 final size:27
Alignment explanation
Indices: 53268112--53268289 Score: 166
Period size: 27 Copynumber: 6.6 Consensus size: 27
53268102 ATATTGAGTC
* *
53268112 CGCACACTCAGTGCTATATGATCAACT
1 CGCACACTTAGTGCTACATGATCAACT
* * *
53268139 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATGATCAACT
53268166 CGCACACTTAGTGCTACAT-AGTCAAACT
1 CGCACACTTAGTGCTACATGA-TC-AACT
** * *
53268194 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATGATCAACT
**
53268221 CGCACACTTAGTGC-ATCAT-ATTCATTT
1 CGCACACTTAGTGCTA-CATGA-TCAACT
* *
53268248 CGCACACTTAGTGCAACAT-AGTCAAAT
1 CGCACACTTAGTGCTACATGA-TCAACT
53268275 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53268290 GTACAATTTA
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.01
27 103 0.81
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATGATCAACT
Found at i:53268251 original size:82 final size:81
Alignment explanation
Indices: 53268133--53268288 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53268123 TGCTATATGA
* *
53268133 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53268198 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53268215 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53268279 CACTTAGTGC
65 CACTTAGTGC
53268289 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:53271897 original size:94 final size:94
Alignment explanation
Indices: 53271774--53271953 Score: 342
Period size: 94 Copynumber: 1.9 Consensus size: 94
53271764 TGACACTCGG
53271774 CCATGGATGCATCATTCTTGGTTGATGTTTGATGTTGTGGTGATGAGGCATGAGGATGAGTTAAG
1 CCATGGATGCATCATTCTTGGTTGATGTTTGATGTTGTGGTGATGAGGCATGAGGATGAGTTAAG
53271839 ATTCGGCCTAGGTGGAGGTTGGCACTTGA
66 ATTCGGCCTAGGTGGAGGTTGGCACTTGA
* *
53271868 CCATGGATGCATCATTCTTGGTTGGTGTTTGATGTTGTGGTGATGAGGTATGAGGATGAGTTAAG
1 CCATGGATGCATCATTCTTGGTTGATGTTTGATGTTGTGGTGATGAGGCATGAGGATGAGTTAAG
53271933 ATTCGGCCTAGGTGGAGGTTG
66 ATTCGGCCTAGGTGGAGGTTG
53271954 TGTTAATGCC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (94 bp):
CCATGGATGCATCATTCTTGGTTGATGTTTGATGTTGTGGTGATGAGGCATGAGGATGAGTTAAG
ATTCGGCCTAGGTGGAGGTTGGCACTTGA
Found at i:53272370 original size:61 final size:61
Alignment explanation
Indices: 53272276--53272395 Score: 206
Period size: 61 Copynumber: 2.0 Consensus size: 61
53272266 TGTATTAAGT
* *
53272276 GTTGAAATCGGCCCCAAAATAGACATGCATATTCGGCCAAGGGGGAA-AAATTAGCTAAAA
1 GTTGAAATCGACCCCAAAATAGACATGCATATTCGGCCAAGGGGAAAGAAATTAGCTAAAA
53272336 GTTGAAATCGACCCCAAAAATAGACATGCATATTCGGCCAAGGGGAAAGAAATTAGCTAA
1 GTTGAAATCGACCCC-AAAATAGACATGCATATTCGGCCAAGGGGAAAGAAATTAGCTAA
53272396 TATGTTGTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 14 0.25
61 31 0.55
62 11 0.20
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (61 bp):
GTTGAAATCGACCCCAAAATAGACATGCATATTCGGCCAAGGGGAAAGAAATTAGCTAAAA
Found at i:53272835 original size:40 final size:40
Alignment explanation
Indices: 53272785--53273007 Score: 186
Period size: 40 Copynumber: 5.6 Consensus size: 40
53272775 TTGAATGCTG
* *
53272785 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTGAATAAA
* * * *
53272825 TCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTGAATAAA
* * *
53272865 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTG-TTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAG-TGAATAAA
* * * *
53272905 TCCGAGTTAAGTCCCGAAGGCATTCGTGCGAGTTG-TTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAG-TGAATAAA
* * ** * *
53272945 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTGAATAAA
* *
53272984 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53273008 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 1 0.01
39 33 0.20
40 119 0.74
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTGAATAAA
Found at i:53272922 original size:80 final size:79
Alignment explanation
Indices: 53272785--53273007 Score: 252
Period size: 80 Copynumber: 2.8 Consensus size: 79
53272775 TTGAATGCTG
* * * * * * *
53272785 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCG-GACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGAG-CTAAG-TCCCGAAGGCAT
53272848 TCGTGCGAGTTATTAAA
63 TCGTGCGAGTTATTAAA
** * *
53272865 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGAGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGAGCTAAGTCCCGAAGGCATTC
*
53272930 GTGCGAGTTGTTAAA
65 GTGCGAGTTATTAAA
* * * *
53272945 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGAGCTAAGTCCCGAAGGCATT
53273008 TGAACGAGGA
Statistics
Matches: 123, Mismatches: 17, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
79 33 0.27
80 85 0.69
81 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGAGCTAAGTCCCGAAGGCATTCG
TGCGAGTTATTAAA
Found at i:53274320 original size:2 final size:2
Alignment explanation
Indices: 53274315--53274495 Score: 317
Period size: 2 Copynumber: 90.5 Consensus size: 2
53274305 CATATATATA
53274315 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
53274357 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
53274399 TG TG TC TG TC TG TC TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
53274441 TG TG TG TG TG TG TG TG TG TC TC TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
53274483 TG TG TG TG TG TG T
1 TG TG TG TG TG TG T
53274496 ATACATGTTC
Statistics
Matches: 171, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 171 1.00
ACGTcount: A:0.00, C:0.03, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:53278695 original size:6 final size:6
Alignment explanation
Indices: 53278677--53278857 Score: 122
Period size: 6 Copynumber: 29.3 Consensus size: 6
53278667 AAGAAACATT
* *
53278677 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * *
53278726 ATCAAA ATCAAA ATCAGA ATTAGGTA A-CAGA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCA-G-A
* * * *
53278777 A-CAGA ATCAGA ATCAAA ACCAGA ATCAAA ATTAGGTA A-CAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
*
53278825 ATCAGT ATCAGGTA A-CAGA ATCAGA ATCAGA AT
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
53278858 GTGAATGCAA
Statistics
Matches: 140, Mismatches: 18, Indels: 34
0.73 0.09 0.18
Matches are distributed among these distances:
5 10 0.07
6 110 0.79
7 13 0.09
8 7 0.05
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:53278698 original size:18 final size:18
Alignment explanation
Indices: 53278677--53278857 Score: 122
Period size: 19 Copynumber: 9.8 Consensus size: 18
53278667 AAGAAACATT
53278677 ATCAGAA-CTAGAATCAGA
1 ATCAGAATC-AGAATCAGA
53278695 ATCAGAATCAGAATCAG-
1 ATCAGAATCAGAATCAGA
* * *
53278712 GTGACAGAATCAAAATCAAA
1 AT--CAGAATCAGAATCAGA
* *
53278732 ATCAAAATCAGAATTAGGTA
1 ATCAGAATCAGAATCA-G-A
*
53278752 A-CAGAATCAGAATCAGT
1 ATCAGAATCAGAATCAGA
53278769 ATCAGGTAA-CAGAATCAGA
1 ATCA-G-AATCAGAATCAGA
* * *
53278788 ATCAAAACCAGAATCAAA
1 ATCAGAATCAGAATCAGA
*
53278806 ATTAGGTAA-CAGAATCAGA
1 ATCA-G-AATCAGAATCAGA
*
53278825 ATCAGTATCAGGTAA-CAGA
1 ATCAGAATCA-G-AATCAGA
53278844 ATCAGAATCAGAAT
1 ATCAGAATCAGAAT
53278858 GTGAATGCAA
Statistics
Matches: 127, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
17 7 0.06
18 45 0.35
19 66 0.52
20 9 0.07
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (18 bp):
ATCAGAATCAGAATCAGA
Found at i:53278722 original size:25 final size:25
Alignment explanation
Indices: 53278688--53278857 Score: 122
Period size: 25 Copynumber: 6.8 Consensus size: 25
53278678 TCAGAACTAG
53278688 AATCAGAATCAGAATCAGAATCAGGT
1 AATCAGAATCAGAATCAGAATCA-GT
* * * *
53278714 GA-CAGAATCAAAATCAAAATCA-A
1 AATCAGAATCAGAATCAGAATCAGT
*
53278737 AATCAGAATTAGGTAA-CAGAATCAG-
1 AATCAGAATCA-G-AATCAGAATCAGT
*
53278762 AATCAGTATCAGGTAA-CAGAATCAG-
1 AATCAGAATCA-G-AATCAGAATCAGT
* * * *
53278787 AATCAAAACCAGAATCAAAATTAGGT
1 AATCAGAATCAGAATCAGAATCA-GT
*
53278813 AA-CAGAATCAGAATCAGTATCAGGT
1 AATCAGAATCAGAATCAGAATCA-GT
53278838 AA-CAGAATCAGAATCAGAAT
1 AATCAGAATCAGAATCAGAAT
53278858 GTGAATGCAA
Statistics
Matches: 116, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
23 3 0.03
24 14 0.12
25 94 0.81
26 5 0.04
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.18
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGAATCAGT
Found at i:53278729 original size:37 final size:37
Alignment explanation
Indices: 53278688--53278857 Score: 126
Period size: 37 Copynumber: 4.2 Consensus size: 37
53278678 TCAGAACTAG
*
53278688 AATCAGAATCAGAATCAGAATCAGGTGACAGAATCAA
1 AATCAGAATCAGAATCAGAATCAGGTAACAGAATCAA
* * * *
53278725 AATCAAAATCAAAATCAGAATTAGGTAACAGAATCAG
1 AATCAGAATCAGAATCAGAATCAGGTAACAGAATCAA
* *
53278762 AATCAGTATCAGGTAA-CAGAATCAGAATCAAAACCAGAATCAAA
1 AATCAGAATCA-G-AATCAGAATCAG-GT---AA-CAGAATC-AA
* *
53278806 ATTAGGTAACAGAATCAGAATCAGTATCAGGTAACAGAATCAG
1 A--A--T--CAGAATCAGAATCAGAATCAGGTAACAGAATCAA
53278849 AATCAGAAT
1 AATCAGAAT
53278858 GTGAATGCAA
Statistics
Matches: 103, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
37 47 0.46
38 8 0.08
39 4 0.04
41 1 0.01
42 2 0.02
43 9 0.09
44 9 0.09
45 2 0.02
46 1 0.01
48 4 0.04
49 9 0.09
50 7 0.07
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.18
Consensus pattern (37 bp):
AATCAGAATCAGAATCAGAATCAGGTAACAGAATCAA
Found at i:53278773 original size:62 final size:62
Alignment explanation
Indices: 53278691--53278853 Score: 272
Period size: 62 Copynumber: 2.6 Consensus size: 62
53278681 GAACTAGAAT
* * * * *
53278691 CAGAATCAGAATCAGAATCAGGTGACAGAATCAAAATCAAAATCAAAATCAGAATTAGGTAA
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAAAACCAAAATCAAAATTAGGTAA
*
53278753 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAAAACCAGAATCAAAATTAGGTAA
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAAAACCAAAATCAAAATTAGGTAA
53278815 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCA
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCA
53278854 GAATGTGAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 95 1.00
ACGTcount: A:0.50, C:0.16, G:0.17, T:0.18
Consensus pattern (62 bp):
CAGAATCAGAATCAGTATCAGGTAACAGAATCAGAATCAAAACCAAAATCAAAATTAGGTAA
Found at i:53279391 original size:27 final size:28
Alignment explanation
Indices: 53279361--53279419 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
53279351 AGCACCCTAG
53279361 GGGTAAAAT-GGTAATTTTACCCCACAA
1 GGGTAAAATCGGTAATTTTACCCCACAA
** * *
53279388 GGGT-ATCTCGGTAATTTTACCCTACAG
1 GGGTAAAATCGGTAATTTTACCCCACAA
53279415 GGGTA
1 GGGTA
53279420 TTTCAGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (28 bp):
GGGTAAAATCGGTAATTTTACCCCACAA
Found at i:53279420 original size:27 final size:27
Alignment explanation
Indices: 53279370--53279621 Score: 269
Period size: 27 Copynumber: 9.3 Consensus size: 27
53279360 GGGGTAAAAT
* * *
53279370 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAGGGGTATTTC
53279397 GGTAATTTTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
* * *
53279424 AGTAATTCTACCCTACAGGGATATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
* * *
53279451 -ATTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
* * * *
53279478 GATAATTCTACCTTACAGGGGTATTTT
1 GGTAATTTTACCCTACAGGGGTATTTC
* *
53279505 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTTTACCCTACAGGGGTATTTC
53279532 GGT-ATTTCTACCCTACAGGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
**
53279559 GGT-ATTTCTACCCTACAAAGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
*
53279586 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GGTAATTT-TACCCTACAGGGGTATTTC
*
53279613 GATAATTTT
1 GGTAATTTT
53279622 GTAAATCGAG
Statistics
Matches: 195, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
26 7 0.04
27 179 0.92
28 9 0.05
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACCCTACAGGGGTATTTC
Found at i:53279513 original size:81 final size:80
Alignment explanation
Indices: 53279374--53279612 Score: 318
Period size: 81 Copynumber: 3.0 Consensus size: 80
53279364 TAAAATGGTA
* * *
53279374 ATTT-TACCCCACAAGGGTATCTCGGTAATTTTACCCTACAGGGGTATTTCAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
*
53279438 ACAGGGATATTTCATT
66 ACAGGG-TATTTCAGT
* * *
53279454 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCTTACAGGGGTATTTTAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
*
53279519 ACAGGGGTATTTCGGT
66 ACA-GGGTATTTCAGT
* * ** * *
53279535 ATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAAGGTATTTCGGTATTTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
53279600 ACAAGGGTATTTC
66 AC-AGGGTATTTC
53279613 GATAATTTTG
Statistics
Matches: 139, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
80 4 0.03
81 131 0.94
82 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (80 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
ACAGGGTATTTCAGT
Found at i:53279633 original size:27 final size:27
Alignment explanation
Indices: 53279603--53280058 Score: 173
Period size: 27 Copynumber: 16.9 Consensus size: 27
53279593 CTACCCTACA
**
53279603 AGGGTATTTCGATAATTTTGTAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
*** * * *
53279630 AGGGTAAAACGGTAATTCTGTA-AATTAG
1 AGGGTATTTCGATAATT-T-TACAAATCG
* *
53279658 -GGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCGATAATTTTACAAATCG
* **
53279684 AGGGTATTTCAATAATTTTACAGGTCG
1 AGGGTATTTCGATAATTTTACAAATCG
*
53279711 AGGGTATTTC-AGTAATTTCACAAATC-
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * *
53279737 AGGGGTATTTTGGTAATTTTACAAA-CT
1 A-GGGTATTTCGATAATTTTACAAATCG
* *
53279764 AGGGGTATTTTGATAATTTTACAAA-CC
1 A-GGGTATTTCGATAATTTTACAAATCG
* * *
53279791 AGGGGTATTTTGGTAATTTTACAAA-CC
1 A-GGGTATTTCGATAATTTTACAAATCG
* * * *
53279818 AGGGGTATTTTGGTAATTTTACAAACCA
1 A-GGGTATTTCGATAATTTTACAAATCG
* * ** * *
53279846 AGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
53279873 AGAGTATTTTGGTAATTTTACAAA-CC
1 AGGGTATTTCGATAATTTTACAAATCG
* * * * * *
53279899 AGGGGTATTTTGGTGATTTTATAAACCA
1 A-GGGTATTTCGATAATTTTACAAATCG
* *
53279927 AGGGTATTT-TAGTAATTTTACAAA-CC
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * * *
53279953 AGGGGTATTTTGGTAATTTTATAAA-CTA
1 A-GGGTATTTCGATAATTTTACAAATC-G
* * *
53279981 AGGGTA-TTCTAGTAATTTTACAAACCA
1 AGGGTATTTCGA-TAATTTTACAAATCG
* * ** * *
53280008 AGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTCGATAATTTTACAAATCG
* *
53280035 AGGGTATTTTGGTAATTTTACAAA
1 AGGGTATTTCGATAATTTTACAAA
53280059 CCAGGGGTAT
Statistics
Matches: 354, Mismatches: 55, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.01
26 17 0.05
27 321 0.91
28 13 0.04
29 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:53279712 original size:81 final size:80
Alignment explanation
Indices: 53279603--53279864 Score: 213
Period size: 81 Copynumber: 3.2 Consensus size: 80
53279593 CTACCCTACA
** * ** *
53279603 AGGGTATTTCGATAATTTTGTAAATCGAGGGTAAAACGGTAA-TTCTGTAAATTAGGGGTACTTT
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTAAAACAGTAATTTC-ACAAATCAGGGGTACTTT
*
53279667 GGTAATTTTACAAGTCG
65 GGTAATTTTACAA-ACG
* ** *** *
53279684 AGGGTATTTCAATAATTTTACAGGTCGAGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTG
1 AGGGTATTTCGATAATTTTACAAATCGAGGGTAAAACAGTAATTTCACAAATCAGGGGTACTTTG
*
53279749 GTAATTTTACAAACT
66 GTAATTTTACAAACG
* * ***** * * *
53279764 AGGGGTATTTTGATAATTTTACAAA-CCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTT
1 A-GGGTATTTCGATAATTTTACAAATCGA-GGGTAAAACAGTAATTTCACAAATCAGGGGTACTT
*
53279828 TGGTAATTTTACAAACCA
64 TGGTAATTTTACAAA-CG
* *
53279846 AGGGTATTTTGGTAATTTT
1 AGGGTATTTCGATAATTTT
53279865 GTAAACCAAG
Statistics
Matches: 151, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
80 4 0.03
81 142 0.94
82 5 0.03
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (80 bp):
AGGGTATTTCGATAATTTTACAAATCGAGGGTAAAACAGTAATTTCACAAATCAGGGGTACTTTG
GTAATTTTACAAACG
Found at i:53280059 original size:27 final size:27
Alignment explanation
Indices: 53279658--53280133 Score: 583
Period size: 27 Copynumber: 17.6 Consensus size: 27
53279648 TGTAAATTAG
* ** *
53279658 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
*** *** *
53279685 GGGTATTTCAATAATTTTACAGGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
** * * *
53279712 GGGTATTTCAGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53279739 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53279766 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
53279793 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
53279820 GGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
53279847 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53279874 GAGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53279901 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53279928 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53279955 GGGTATTTTGGTAATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53279982 GGGTATTCTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
53280009 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
53280036 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
53280063 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
53280090 TGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
53280117 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
53280134 GGTAAAGTAA
Statistics
Matches: 390, Mismatches: 59, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 390 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:53286467 original size:13 final size:13
Alignment explanation
Indices: 53286449--53286474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53286439 TAAGTATCGA
53286449 TGTTTGGCTAAAG
1 TGTTTGGCTAAAG
53286462 TGTTTGGCTAAAG
1 TGTTTGGCTAAAG
53286475 CATTTCCAAT
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:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
TGTTTGGCTAAAG
Found at i:53289944 original size:12 final size:12
Alignment explanation
Indices: 53289927--53289953 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53289917 AAACTCTGAG
53289927 ATATCACTTTTC
1 ATATCACTTTTC
53289939 ATATCACTTTTC
1 ATATCACTTTTC
53289951 ATA
1 ATA
53289954 CCATTCCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATCACTTTTC
Found at i:53301174 original size:41 final size:43
Alignment explanation
Indices: 53301128--53301219 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 43
53301118 ACCGGCACGA
* * *
53301128 AGCCTGCTAGACTTTAAGTCTAA-ACTCA-TTCACCGGCATT-T
1 AGCCTGCTAGACTTGAAGCCCAATA-TCATTTCACCGGCATTAT
* *
53301169 CGCCTGCTAGGCTTGAAGCCCAATATCATTTCACCGGCATTAT
1 AGCCTGCTAGACTTGAAGCCCAATATCATTTCACCGGCATTAT
53301212 AGCCTGCT
1 AGCCTGCT
53301220 GGCCCGAAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
41 21 0.50
42 13 0.31
43 8 0.19
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (43 bp):
AGCCTGCTAGACTTGAAGCCCAATATCATTTCACCGGCATTAT
Found at i:53301433 original size:28 final size:28
Alignment explanation
Indices: 53301402--53301468 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
53301392 TTGATATTTT
53301402 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
* *
53301430 GCACACTAAATGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
53301458 GTACACTAAGT
1 GCACACTAAGT
53301469 ACCATATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:53308077 original size:43 final size:45
Alignment explanation
Indices: 53308002--53308131 Score: 135
Period size: 44 Copynumber: 3.0 Consensus size: 45
53307992 GTCTAAACTC
* *
53308002 ATTCACCGGCATT-TTGCCTGCTAGGCTTGAAGCCCGATATCA-T
1 ATTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATT
* *
53308045 -TTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCTATAAT-ATT
1 ATTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGAT-ATCATT
* * * *
53308089 ATTCACCAGC-TTAAAGCTTGCTAGGCTCAAAGCCCGAATATCA
1 ATTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCG-ATATCA
53308132 CCATTATAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
42 12 0.17
43 22 0.31
44 26 0.37
45 11 0.15
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (45 bp):
ATTCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATCATT
Found at i:53308281 original size:28 final size:28
Alignment explanation
Indices: 53308250--53308321 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
53308240 TTGATATTTT
*
53308250 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
53308278 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
53308306 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
53308322 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:53309919 original size:23 final size:25
Alignment explanation
Indices: 53309893--53309942 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
53309883 TTCATGAAGA
*
53309893 AATTAAAGC-ATAAA-TCATGATAC
1 AATTAAAGCAATAAACACATGATAC
* *
53309916 AATTTAGGCAATAAACACATGATAC
1 AATTAAAGCAATAAACACATGATAC
53309941 AA
1 AA
53309943 CATCACATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 5 0.23
25 10 0.45
ACGTcount: A:0.52, C:0.14, G:0.10, T:0.24
Consensus pattern (25 bp):
AATTAAAGCAATAAACACATGATAC
Found at i:53313175 original size:27 final size:27
Alignment explanation
Indices: 53313082--53313181 Score: 146
Period size: 27 Copynumber: 3.7 Consensus size: 27
53313072 AGGGGTGGTG
* *
53313082 CCTATCTGATATGCGGCACCAGTGACC
1 CCTATCTAATAGGCGGCACCAGTGACC
* *
53313109 CCTATCTAATAGACGGCACCAATGACC
1 CCTATCTAATAGGCGGCACCAGTGACC
*
53313136 CCTATCTAATAGGCGACACCAGTGACC
1 CCTATCTAATAGGCGGCACCAGTGACC
*
53313163 CCTATCTAATAGGCAGCAC
1 CCTATCTAATAGGCGGCAC
53313182 TACTATTAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (27 bp):
CCTATCTAATAGGCGGCACCAGTGACC
Found at i:53315971 original size:54 final size:54
Alignment explanation
Indices: 53315889--53316051 Score: 317
Period size: 54 Copynumber: 3.0 Consensus size: 54
53315879 TCGATACATA
53315889 ACCTCATTGACCCGTCCTTCTTTTTCACAAAAAGCACTGGAGCACCCCATGGTG
1 ACCTCATTGACCCGTCCTTCTTTTTCACAAAAAGCACTGGAGCACCCCATGGTG
*
53315943 ACCTCATTGACCCGTCTTTCTTTTTCACAAAAAGCACTGGAGCACCCCATGGTG
1 ACCTCATTGACCCGTCCTTCTTTTTCACAAAAAGCACTGGAGCACCCCATGGTG
53315997 ACCTCATTGACCCGTCCTTCTTTTTCACAAAAAGCACTGGAGCACCCCATGGTG
1 ACCTCATTGACCCGTCCTTCTTTTTCACAAAAAGCACTGGAGCACCCCATGGTG
53316051 A
1 A
53316052 GTAACTCGGT
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 107 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.26
Consensus pattern (54 bp):
ACCTCATTGACCCGTCCTTCTTTTTCACAAAAAGCACTGGAGCACCCCATGGTG
Found at i:53319658 original size:47 final size:46
Alignment explanation
Indices: 53319415--53319677 Score: 162
Period size: 47 Copynumber: 5.6 Consensus size: 46
53319405 ATAAATTGCA
* * *
53319415 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGCGTGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATATCT--GTGCC
* * * * *
53319465 AATGCATGTCCTAGACATGTCTTACACTAGCA--CA-ACTCT-TAACT
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATA-TCTGT-GCC
** * ** *
53319509 GATGTGTGTCCTAGACACATCTTACACTGGCTATCTC-TGTC-GATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-A-CTCATATCTG-TGCC
* * * *
53319556 GATGCATGTCCCAGACATGCCTTACTCTGGCACTCATCTCTGTGTC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATATCTGTGCC
* *
53319602 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATATCTGT-GCC
* * *
53319650 GAAGCATGTCTCAAACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
53319678 AGCGCACAAA
Statistics
Matches: 166, Mismatches: 33, Indels: 32
0.72 0.14 0.14
Matches are distributed among these distances:
43 1 0.01
44 27 0.16
45 5 0.03
46 25 0.15
47 57 0.34
48 35 0.21
49 13 0.08
50 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACTCATATCTGTGCC
Found at i:53322009 original size:48 final size:47
Alignment explanation
Indices: 53321941--53322080 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 47
53321931 TATGTAATCC
* * *
53321941 AATGTACCTAATTTAAATTACAAAGTTTGTTCATCGTTTTAATGTTGT
1 AATGTATCTAATTTATATTACAAAGTTTGTTCA-AGTTTTAATGTTGT
53321989 AATGTATCTAATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGT
1 AATGTATCTAATTTATATTACAAAGTTTGTT-CAAGTTTTAATGTTGT
**
53322037 AATGTATCTAATTTATGACCACAAAGTTTGTTCCAAGTTTTAAT
1 AATGTATCTAATTTAT-ATTACAAAGTTTGTT-CAAGTTTTAAT
53322081 ATTTCAATTA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
48 58 0.68
49 27 0.32
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (47 bp):
AATGTATCTAATTTATATTACAAAGTTTGTTCAAGTTTTAATGTTGT
Found at i:53322433 original size:33 final size:33
Alignment explanation
Indices: 53322357--53322451 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
53322347 CGATGAACTT
* *
53322357 GAGCCGGGAGGAGTGGAGTACTGTGGTGGATAC
1 GAGCCGGGAGGAGTGGAGTACTGCGGTGGATAA
*
53322390 GAGCCGGGAGGAGTGGAGTAATGCGGTGGATATA
1 GAGCCGGGAGGAGTGGAGTACTGCGGTGGATA-A
* **
53322424 G-GCCTGGAGGAGTGTTGTACTGCGGTGG
1 GAGCCGGGAGGAGTGGAGTACTGCGGTGG
53322452 TACTAGATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.20, C:0.12, G:0.48, T:0.20
Consensus pattern (33 bp):
GAGCCGGGAGGAGTGGAGTACTGCGGTGGATAA
Found at i:53323078 original size:14 final size:14
Alignment explanation
Indices: 53323059--53323093 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
53323049 CAAATTACAT
53323059 GTTAGAATAGTATC
1 GTTAGAATAGTATC
53323073 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
53323087 ATTAGAA
1 GTTAGAA
53323094 AATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:53324652 original size:27 final size:27
Alignment explanation
Indices: 53324614--53324686 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
53324604 TTTATCTCGT
53324614 AAATTCCAACTCAATGGTCCCATTCAC
1 AAATTCCAACTCAATGGTCCCATTCAC
53324641 AAATTCCAACTCAATGGTCCCATTCAC
1 AAATTCCAACTCAATGGTCCCATTCAC
*
53324668 AAATTCCATCTCAATGGTC
1 AAATTCCAACTCAATGGTC
53324687 TCATCTTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.27
Consensus pattern (27 bp):
AAATTCCAACTCAATGGTCCCATTCAC
Found at i:53324807 original size:49 final size:49
Alignment explanation
Indices: 53324743--53324910 Score: 300
Period size: 49 Copynumber: 3.4 Consensus size: 49
53324733 ACATGCCAAG
53324743 TAAATTACATAAAAAAATAAATCTAATAAACCTAAAACACATATGACAAA
1 TAAATTACAT-AAAAAATAAATCTAATAAACCTAAAACACATATGACAAA
* *
53324793 TAAATTACATAAAAATTAAATCTAATAAACCTAAAACACACATGACAAA
1 TAAATTACATAAAAAATAAATCTAATAAACCTAAAACACATATGACAAA
*
53324842 TAAATTACATAAAAAATAAATCTAGTAAACCTAAAACACATATGACAAA
1 TAAATTACATAAAAAATAAATCTAATAAACCTAAAACACATATGACAAA
53324891 TAAATTACATAAAAAATAAA
1 TAAATTACATAAAAAATAAA
53324911 ACATTCTTTC
Statistics
Matches: 113, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 103 0.91
50 10 0.09
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (49 bp):
TAAATTACATAAAAAATAAATCTAATAAACCTAAAACACATATGACAAA
Found at i:53325222 original size:29 final size:30
Alignment explanation
Indices: 53325189--53325245 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53325179 ACCTCTTAAT
* *
53325189 TAATTTTTT-TCAAATCCTAAACACAACCC
1 TAATTTTTTCTCAAAACCCAAACACAACCC
53325218 TAATTTTTTCTCAAAACCCAAACACAAC
1 TAATTTTTTCTCAAAACCCAAACACAAC
53325246 TTCTTCTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATTTTTTCTCAAAACCCAAACACAACCC
Found at i:53326298 original size:31 final size:30
Alignment explanation
Indices: 53326194--53326309 Score: 107
Period size: 31 Copynumber: 3.9 Consensus size: 30
53326184 TTAATATAAT
* *
53326194 ATTTTGTACCTGAACTTGACATTTTTTCCTA
1 ATTTGGTACCTAAACTTGACA-TTTTTCCTA
* *
53326225 ATTTGGTATCTAAATTTG---TTTTATCC-A
1 ATTTGGTACCTAAACTTGACATTTT-TCCTA
53326252 ATTTGGTA-CTCAAACTTGACACTTTTTCCTA
1 ATTTGGTACCT-AAACTTGACA-TTTTTCCTA
* *
53326283 ATATGGTACCTAAACTTGACTTTTTTC
1 ATTTGGTACCTAAACTTGACATTTTTC
53326310 TTAAGTTGAT
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
26 2 0.03
27 19 0.27
28 3 0.04
30 9 0.13
31 35 0.50
32 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.47
Consensus pattern (30 bp):
ATTTGGTACCTAAACTTGACATTTTTCCTA
Found at i:53328479 original size:79 final size:79
Alignment explanation
Indices: 53328385--53328537 Score: 297
Period size: 79 Copynumber: 1.9 Consensus size: 79
53328375 ATTTTAATCA
53328385 CCTCGGAATTTTCTCTTCTCTTTATACTATATTTAAACCTTCTCTTCTGGAGCCAATCAGAATTT
1 CCTCGGAATTTTCTCTTCTCTTTATACTATATTTAAACCTTCTCTTCTGGAGCCAATCAGAATTT
53328450 TGAGGTTTTTTTTT
66 TGAGGTTTTTTTTT
*
53328464 CCTCGGAATTTTCTCTTCTTTTTATACTATATTTAAACCTTCTCTTCTGGAGCCAATCAGAATTT
1 CCTCGGAATTTTCTCTTCTCTTTATACTATATTTAAACCTTCTCTTCTGGAGCCAATCAGAATTT
53328529 TGAGGTTTT
66 TGAGGTTTT
53328538 GTGGGGGGGG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (79 bp):
CCTCGGAATTTTCTCTTCTCTTTATACTATATTTAAACCTTCTCTTCTGGAGCCAATCAGAATTT
TGAGGTTTTTTTTT
Found at i:53330341 original size:14 final size:14
Alignment explanation
Indices: 53330314--53330346 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53330304 CAGAGCAGAC
53330314 CTTCCCAAACATGG
1 CTTCCCAAACATGG
53330328 CTTCACCAAA-ATGG
1 CTTC-CCAAACATGG
53330342 CTTCC
1 CTTCC
53330347 ATTCACTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.06
14 12 0.67
15 5 0.28
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.24
Consensus pattern (14 bp):
CTTCCCAAACATGG
Found at i:53333307 original size:22 final size:25
Alignment explanation
Indices: 53333275--53333330 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 25
53333265 CAATTGCTAA
* *
53333275 ATATATATTAATAT-ATACAATATT
1 ATATAGATTAATATAATAAAATATT
53333299 -T-TAGATTAATATAATAAAATATT
1 ATATAGATTAATATAATAAAATATT
53333322 ATATAGATT
1 ATATAGATT
53333331 TAAAATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 1 0.04
25 6 0.22
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATAGATTAATATAATAAAATATT
Found at i:53337864 original size:29 final size:29
Alignment explanation
Indices: 53337857--53338655 Score: 1598
Period size: 29 Copynumber: 27.6 Consensus size: 29
53337847 ATATGATATG
53337857 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53337886 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53337915 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53337944 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53337973 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338002 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338031 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338060 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338089 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338118 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338147 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338176 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338205 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338234 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338263 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338292 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338321 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338350 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338379 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338408 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338437 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338466 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338495 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338524 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338553 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338582 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338611 CACATGATATGTATGATATGTATGATATG
1 CACATGATATGTATGATATGTATGATATG
53338640 CACATGATATGTATGA
1 CACATGATATGTATGA
53338656 AATGCACATG
Statistics
Matches: 770, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 770 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.38
Consensus pattern (29 bp):
CACATGATATGTATGATATGTATGATATG
Found at i:53338759 original size:26 final size:26
Alignment explanation
Indices: 53338717--53338904 Score: 258
Period size: 26 Copynumber: 7.3 Consensus size: 26
53338707 GAGGAAGTGC
53338717 AAAAGGGC-TATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
53338742 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
53338768 AAAAGGGCTTATGCCCCAGTGTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
53338794 AAAAGGGCTTATGCCGCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
53338820 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
53338846 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
53338872 AAAAGGGCTT-TGCCCTAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
53338895 AAAAGAGGCT
1 AAAAG-GGCT
53338905 AGGCCTCCAG
Statistics
Matches: 144, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.03
24 7 0.05
25 15 0.10
26 117 0.81
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:53338794 original size:52 final size:52
Alignment explanation
Indices: 53338717--53338904 Score: 312
Period size: 52 Copynumber: 3.7 Consensus size: 52
53338707 GAGGAAGTGC
53338717 AAAAGGGC-TATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
* *
53338768 AAAAGGGCTTATGCCCCAGTGTATTGAAAAGGGCTTATGCCGCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
53338820 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
53338872 AAAAGGGCTT-TGCCCTAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
53338905 AGGCCTCCAG
Statistics
Matches: 130, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
49 5 0.04
50 9 0.07
51 15 0.12
52 101 0.78
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:53346555 original size:21 final size:20
Alignment explanation
Indices: 53346529--53346568 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
53346519 GCATTACGGT
53346529 AAGTTGGGCCTCAAGGGGCTG
1 AAGTTGGGCC-CAAGGGGCTG
*
53346550 AAGTTGGGCCCAATGGGCT
1 AAGTTGGGCCCAAGGGGCT
53346569 TTCGGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (20 bp):
AAGTTGGGCCCAAGGGGCTG
Found at i:53346945 original size:20 final size:21
Alignment explanation
Indices: 53346910--53346966 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
53346900 TTGATAGTGG
53346910 GATATGATAT--ACATGA-AT
1 GATATGATATGCACATGATAT
53346928 GATATGATATGCACATGATAT
1 GATATGATATGCACATGATAT
*
53346949 G-TATGAAATGCACATGAT
1 GATATGATATGCACATGAT
53346967 GTAATCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 10 0.29
20 22 0.63
21 3 0.09
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (21 bp):
GATATGATATGCACATGATAT
Found at i:53347058 original size:26 final size:26
Alignment explanation
Indices: 53347016--53347094 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 26
53347006 GAGGAAGTGC
53347016 AAAAGGGC-TATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
53347041 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
53347067 AAAAGGGCTT-TGCCCTAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
53347090 AAAAG
1 AAAAG
53347095 AAGCTAGGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 5 0.10
24 3 0.06
25 15 0.31
26 25 0.52
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:53347340 original size:7 final size:7
Alignment explanation
Indices: 53347328--53347369 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
53347318 GGCCCAGTGT
53347328 TATGAAA
1 TATGAAA
53347335 TATGAAA
1 TATGAAA
53347342 TATGAAA
1 TATGAAA
53347349 TATGAAA
1 TATGAAA
53347356 TATGAAA
1 TATGAAA
53347363 TATGAAA
1 TATGAAA
53347370 AGACTTCGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
TATGAAA
Found at i:53352138 original size:10 final size:10
Alignment explanation
Indices: 53352123--53352151 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
53352113 GTTTTACACT
53352123 TAGGAGAGCA
1 TAGGAGAGCA
53352133 TAGGAGAGCA
1 TAGGAGAGCA
53352143 TAGGAGAGC
1 TAGGAGAGC
53352152 GAAAGGAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.41, T:0.10
Consensus pattern (10 bp):
TAGGAGAGCA
Found at i:53365151 original size:47 final size:47
Alignment explanation
Indices: 53365097--53365334 Score: 343
Period size: 47 Copynumber: 5.1 Consensus size: 47
53365087 TTAGGATTTT
** * * *
53365097 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
53365144 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53365191 ATGTGATGAATGCGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53365238 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
53365285 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
53365332 ATG
1 ATG
53365335 CGAAACGTGT
Statistics
Matches: 175, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
47 172 0.98
48 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:53365172 original size:25 final size:25
Alignment explanation
Indices: 53365144--53365269 Score: 92
Period size: 25 Copynumber: 5.3 Consensus size: 25
53365134 CGAATGGCAA
*
53365144 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
* *
53365169 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-CGAACAT-GCATAT
53365191 ATGTGATGAATGCGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
* *
53365216 ATGTGAT-AAGGCCG-A-ATGGC-CA-
1 ATGTGATGAATG-CGAACAT-GCATAT
*
53365238 ATGTGATGAATGTGAACATGCATAT
1 ATGTGATGAATGCGAACATGCATAT
53365263 ATGTGAT
1 ATGTGAT
53365270 AAGGCAGAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
22 17 0.22
23 18 0.23
24 18 0.23
25 24 0.31
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (25 bp):
ATGTGATGAATGCGAACATGCATAT
Found at i:53365197 original size:22 final size:22
Alignment explanation
Indices: 53365169--53365244 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
53365159 ACATGCATAT
53365169 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
53365191 ATGTGATGAATG-CGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
53365215 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
53365238 ATGTGAT
1 ATGTGAT
53365245 GAATGTGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
22 16 0.37
23 9 0.21
24 9 0.21
25 9 0.21
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:53365291 original size:22 final size:22
Alignment explanation
Indices: 53365169--53365291 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
53365159 ACATGCATAT
*
53365169 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
* *
53365191 ATGTGATGAATGC-GAACAT-GCATA
1 ATGTGAT-AAGGCAG-A-ATGGC-CA
*
53365215 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
*
53365238 ATGTGATGAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
53365262 TATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
53365285 ATGTGAT
1 ATGTGAT
53365292 GAACGTGGAA
Statistics
Matches: 78, Mismatches: 7, Indels: 32
0.67 0.06 0.27
Matches are distributed among these distances:
22 23 0.29
23 20 0.26
24 19 0.24
25 16 0.21
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:53365361 original size:46 final size:46
Alignment explanation
Indices: 53365308--53365398 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
53365298 GGAAGTGTAT
* *
53365308 ATATGTGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
53365354 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
53365399 TGTATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:53370717 original size:42 final size:42
Alignment explanation
Indices: 53370568--53370724 Score: 134
Period size: 42 Copynumber: 3.6 Consensus size: 42
53370558 GGGTCCCAAA
*** * * * *
53370568 GCCATGTCCCAGACATGGTCTTACGTGGGACCACATATCGAT
1 GCCATGTCCCAGACATGGTCTTATACGAGACCTCGTACCGAT
* * * * *
53370610 GCCATATCCCAGATATGGTCTTATACGAAGTCTCGAATCAGTGCCGAC
1 GCCATGTCCCAGACATGGTCTTATACG-AGAC-C---TC-GTACCGAT
* *
53370658 GCCATGCCCCAAACATGGTCTTATACGAGACCTCGTACCGAT
1 GCCATGTCCCAGACATGGTCTTATACGAGACCTCGTACCGAT
53370700 GCCATGTCCCAGACATGGTCTTATA
1 GCCATGTCCCAGACATGGTCTTATA
53370725 GAAATCACTT
Statistics
Matches: 88, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
42 51 0.58
43 4 0.05
44 1 0.01
46 1 0.01
47 4 0.05
48 27 0.31
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24
Consensus pattern (42 bp):
GCCATGTCCCAGACATGGTCTTATACGAGACCTCGTACCGAT
Found at i:53370826 original size:48 final size:48
Alignment explanation
Indices: 53370695--53370826 Score: 126
Period size: 48 Copynumber: 2.8 Consensus size: 48
53370685 AGACCTCGTA
**
53370695 CCGATGCCATGTCCCAGACATGGTC-TT-ATAGAAATCACTTATTGATG
1 CCGATGCCATGTCCCAGACATGGTCTTTCAT-GGGATCACTTATTGATG
* * * * * ** *
53370742 CCGAAGCCATATCCCTGATATGGTCTTACACAGGATC-GTGTATTGATG
1 CCGATGCCATGTCCCAGACATGGTCTTTCATGGGATCACT-TATTGATG
*
53370790 CTGATGCCATGTCCCAGACATGGTCTTTCATGGGATC
1 CCGATGCCATGTCCCAGACATGGTCTTTCATGGGATC
53370827 TCGTTAATCA
Statistics
Matches: 64, Mismatches: 18, Indels: 5
0.74 0.21 0.06
Matches are distributed among these distances:
47 22 0.34
48 41 0.64
49 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTTCATGGGATCACTTATTGATG
Found at i:53372294 original size:36 final size:36
Alignment explanation
Indices: 53372253--53372324 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
53372243 ATTGCATGGT
53372253 GTGCCATTATTTATCATTTTAGATTGGGATCTGAGG
1 GTGCCATTATTTATCATTTTAGATTGGGATCTGAGG
*
53372289 GTGCCATTATTTATCATTTTAGATTGGGATTTGAGG
1 GTGCCATTATTTATCATTTTAGATTGGGATCTGAGG
53372325 TTTACCTCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (36 bp):
GTGCCATTATTTATCATTTTAGATTGGGATCTGAGG
Found at i:53390911 original size:29 final size:28
Alignment explanation
Indices: 53390875--53390952 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
53390865 TCATGAGATT
53390875 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
53390905 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
53390932 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
53390953 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:53391170 original size:174 final size:174
Alignment explanation
Indices: 53390905--53392102 Score: 2342
Period size: 174 Copynumber: 6.9 Consensus size: 174
53390895 AAATTGTACA
* * *
53390905 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
53390970 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53391035 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
53391079 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
53391144 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53391209 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
53391253 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
53391318 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53391383 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
53391427 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
53391492 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53391557 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
53391601 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
53391666 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53391731 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
53391775 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
53391840 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53391905 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
53391949 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
53392014 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
53392079 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
53392103 ACCTTGAGTT
Statistics
Matches: 1018, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 1018 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:53400487 original size:25 final size:25
Alignment explanation
Indices: 53400430--53400487 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
53400420 CACAAACGCA
*
53400430 GCTATTTATGAGCGTCCTAATATAG
1 GCTATTTGTGAGCGTCCTAATATAG
* * *
53400455 GCTTTTTGTGAGCTTCCTGATAT-G
1 GCTATTTGTGAGCGTCCTAATATAG
53400479 GCTCATTTG
1 GCT-ATTTG
53400488 AACTTCCTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.41
Consensus pattern (25 bp):
GCTATTTGTGAGCGTCCTAATATAG
Found at i:53401497 original size:59 final size:59
Alignment explanation
Indices: 53401423--53401540 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
53401413 ATGTATAAGA
* *
53401423 TTGGTTTTGGTTTGGTTTTAACATATTTAATTGGTTGGTATATGTCTGCAAGTATTAAT
1 TTGGTTTTGGCTTGGTTTTAACATATTTAATTGGTTGGTATATGTATGCAAGTATTAAT
*
53401482 TTGGTTTTGGCTTGGTTTTAACATCTTTAATTGGTTGGTATATGTATGCAAGTATTAAT
1 TTGGTTTTGGCTTGGTTTTAACATATTTAATTGGTTGGTATATGTATGCAAGTATTAAT
53401541 GTAGGTACAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (59 bp):
TTGGTTTTGGCTTGGTTTTAACATATTTAATTGGTTGGTATATGTATGCAAGTATTAAT
Found at i:53403450 original size:27 final size:27
Alignment explanation
Indices: 53403419--53403603 Score: 244
Period size: 27 Copynumber: 6.9 Consensus size: 27
53403409 GAATACTTTA
* *
53403419 GTTTACAAAATTACCAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTG
*
53403446 GTTTACAAAATTACCAAAATACCCCTG
1 GTTTATAAAATTACCAAAATACCCCTG
* *
53403473 GTTTGTAAAATTACCAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTG
*
53403500 GTTTATAAAATTACCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTG
* *
53403527 GTTTGTAAAATTACCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTG
* *
53403554 GTTTGTAAAATTACCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTG
* * * *
53403581 ATTTGTGAAATTACTAAAATACC
1 GTTTATAAAATTACCAAAATACC
53403604 TTCGACCTTT
Statistics
Matches: 147, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 147 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (27 bp):
GTTTATAAAATTACCAAAATACCCCTG
Found at i:53403491 original size:54 final size:54
Alignment explanation
Indices: 53403425--53403676 Score: 294
Period size: 54 Copynumber: 4.7 Consensus size: 54
53403415 TTTAGTTTAC
* *
53403425 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGT
53403479 AAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGT
* * * *
53403533 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGT
* * ** *** **
53403587 GAAATTACTAAAATA-CCTTCGACCTT-TAAAATTATTGAAATA-CCCTGAACTTGT
1 AAAATTACCAAAATACCCTT-G-GTTTATAAAATTACCAAAATACCCCT-AGTTTGT
* * *
53403641 AAAATTACCAAAGTACCCTTGATTTATAGAATTACC
1 AAAATTACCAAAATACCCTTGGTTTATAAAATTACC
53403677 GTTTTACCCT
Statistics
Matches: 169, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
53 9 0.05
54 154 0.91
55 6 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGT
Found at i:53403558 original size:81 final size:80
Alignment explanation
Indices: 53403420--53403676 Score: 273
Period size: 81 Copynumber: 3.2 Consensus size: 80
53403410 AATACTTTAG
* * * * *
53403420 TTTACAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATT
1 TTTATAAAATTACCAAAATACCCCTAGTTT-TAAAATTACCAAAATACCCCTAGTTTGTAAAATT
*
53403485 ACCAAAATACCCTTGG
65 ACCAAAATACCCTTGA
53403501 TTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATT
1 TTTATAAAATTACCAAAATACCCCTAGTTT-TAAAATTACCAAAATACCCCTAGTTTGTAAAATT
* *
53403566 ACCAAAATACCCCTAA
65 ACCAAAATACCCTTGA
* * * * * ** *** **
53403582 TTTGTGAAATTACTAAAATACCTTCGACCTTTAAAATTATTGAAATA-CCCTGAACTTGTAAAAT
1 TTTATAAAATTACCAAAATACC-CCTAGTTTTAAAATTACCAAAATACCCCT-AGTTTGTAAAAT
*
53403646 TACCAAAGTACCCTTGA
64 TACCAAAATACCCTTGA
*
53403663 TTTATAGAATTACC
1 TTTATAAAATTACC
53403677 GTTTTACCCT
Statistics
Matches: 146, Mismatches: 28, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
80 4 0.03
81 138 0.95
82 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.32
Consensus pattern (80 bp):
TTTATAAAATTACCAAAATACCCCTAGTTTTAAAATTACCAAAATACCCCTAGTTTGTAAAATTA
CCAAAATACCCTTGA
Found at i:53403673 original size:27 final size:27
Alignment explanation
Indices: 53403425--53403676 Score: 235
Period size: 27 Copynumber: 9.3 Consensus size: 27
53403415 TTTAGTTTAC
* * **
53403425 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCTGATTTGT
*
53403452 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* * *
53403479 AAAATTACCAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTGATTTGT
53403506 AAAATTACCAAAATACCCCT-AGTTTGT
1 AAAATTACCAAAATACCCCTGA-TTTGT
53403533 AAAATTACCAAAATACCCCT-AGTTTGT
1 AAAATTACCAAAATACCCCTGA-TTTGT
*
53403560 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTGATTTGT
* * * *
53403587 GAAATTACTAAAATA-CCTTCGACCTT-T
1 AAAATTACCAAAATACCCCT-GA-TTTGT
*** *
53403614 AAAATTATTGAAATA-CCCTGAACTTGT
1 AAAATTACCAAAATACCCCTG-ATTTGT
* * *
53403641 AAAATTACCAAAGTACCCTTGATTTAT
1 AAAATTACCAAAATACCCCTGATTTGT
*
53403668 AGAATTACC
1 AAAATTACC
53403677 GTTTTACCCT
Statistics
Matches: 193, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.04
27 179 0.93
28 7 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGATTTGT
Found at i:53403736 original size:27 final size:27
Alignment explanation
Indices: 53403704--53403823 Score: 154
Period size: 27 Copynumber: 4.4 Consensus size: 27
53403694 CAAAATTTAT
53403704 CGAAATACCCTTGTAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
*
53403731 CGAAATACCCCTGTAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATAC
*
53403758 CGAAATA-CCTCTGTAGGGTAGAATTAC
1 CGAAATACCCT-TGTAGGGTAGAAATAC
* * *
53403785 TGAAATACTCC-TGTAAGGTAGAATTAC
1 CGAAATAC-CCTTGTAGGGTAGAAATAC
*
53403812 CGAGATACCCTT
1 CGAAATACCCTT
53403824 ATGGGGTAAC
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
26 4 0.05
27 76 0.93
29 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
CGAAATACCCTTGTAGGGTAGAAATAC
Found at i:53403774 original size:54 final size:54
Alignment explanation
Indices: 53403704--53403823 Score: 170
Period size: 54 Copynumber: 2.2 Consensus size: 54
53403694 CAAAATTTAT
*
53403704 CGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAAATAC
1 CGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAAGGTAGAAATAC
* * * *
53403758 CGAAATA-CCTCTGTAGGGTAGAATTACTGAAATACTCCTGTAAGGTAGAATTAC
1 CGAAATACCCT-TGTAGGGTAGAAATACCGAAATACCCCTGTAAGGTAGAAATAC
*
53403812 CGAGATACCCTT
1 CGAAATACCCTT
53403824 ATGGGGTAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
53 3 0.05
54 52 0.90
55 3 0.05
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (54 bp):
CGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAAGGTAGAAATAC
Found at i:53404128 original size:27 final size:26
Alignment explanation
Indices: 53404084--53404135 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
53404074 CTCGATACAA
*
53404084 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
53404111 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
53404136 GCAGCCTCGT
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:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:53404200 original size:33 final size:32
Alignment explanation
Indices: 53404151--53404214 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
53404141 CTCGTTGCAA
* *
53404151 TCTGGTGGCTTCGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
53404184 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
53404215 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:53404228 original size:27 final size:26
Alignment explanation
Indices: 53404176--53404235 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
53404166 ACATATATAT
*
53404176 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
53404202 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
53404229 ATATCTG
1 ATATCTG
53404236 GCAGTCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:53407533 original size:40 final size:42
Alignment explanation
Indices: 53407464--53407545 Score: 150
Period size: 40 Copynumber: 2.0 Consensus size: 42
53407454 AGAAAATGTA
53407464 AAGATTGAAAACAAAAAAAAATTTTCTATGTTACCTCCACAC
1 AAGATTGAAAACAAAAAAAAATTTTCTATGTTACCTCCACAC
53407506 AAGATTGAAAAC-AAAAAAAA-TTTCTATGTTACCTCCACAC
1 AAGATTGAAAACAAAAAAAAATTTTCTATGTTACCTCCACAC
53407546 TTTAGTTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 20 0.50
41 8 0.20
42 12 0.30
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.26
Consensus pattern (42 bp):
AAGATTGAAAACAAAAAAAAATTTTCTATGTTACCTCCACAC
Found at i:53413162 original size:52 final size:52
Alignment explanation
Indices: 53413096--53413200 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
53413086 GTGTAAATTC
*
53413096 ATTTTGAGATGATTCAGTTATGTACATAAA-CCCATGTTTCTTAAATGCTTGA
1 ATTTCGAGATGATTCAG-TATGTACATAAAGCCCATGTTTCTTAAATGCTTGA
53413148 ATTTCGAGATGATTCAGTATGTACATAAAGCCCATGTTTCTTAAATGCTTGA
1 ATTTCGAGATGATTCAGTATGTACATAAAGCCCATGTTTCTTAAATGCTTGA
53413200 A
1 A
53413201 ACGATGAATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 12 0.24
52 39 0.76
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (52 bp):
ATTTCGAGATGATTCAGTATGTACATAAAGCCCATGTTTCTTAAATGCTTGA
Found at i:53420742 original size:40 final size:40
Alignment explanation
Indices: 53420684--53420915 Score: 315
Period size: 40 Copynumber: 5.8 Consensus size: 40
53420674 ATTTGAATGA
*
53420684 TATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
53420724 TATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
53420764 TATCCGGGTTAAGACCAGAAGGCATTTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
* *
53420804 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * *
53420844 TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTT
* * *
53420884 TACCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCT
53420916 TATGGTTATA
Statistics
Matches: 176, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 173 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTT
Found at i:53429196 original size:40 final size:40
Alignment explanation
Indices: 53429137--53429388 Score: 312
Period size: 40 Copynumber: 6.3 Consensus size: 40
53429127 CATTTGAATG
* *
53429137 ATATCCGGGCTATGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
53429177 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
53429217 TTATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
53429257 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
53429297 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
53429337 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
53429377 ATATCC-GGCTAA
1 ATATCCGGGCTAA
53429389 ATTCCGAAGA
Statistics
Matches: 190, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 7 0.04
40 180 0.95
41 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:53435218 original size:46 final size:46
Alignment explanation
Indices: 53435168--53435343 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 46
53435158 TATTTGGGCA
*
53435168 TCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATACGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
*** * * *
53435214 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-AC-TAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATACGAATG
* *
53435259 CATCCGACCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
* **
53435307 CCCGGGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53435344 GCGTGTTACA
Statistics
Matches: 107, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
45 2 0.02
46 69 0.64
47 34 0.32
48 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATG
Found at i:53435323 original size:93 final size:93
Alignment explanation
Indices: 53435164--53435335 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
53435154 AGGATATTTG
* *
53435164 GGCATCCGAACTCGTTGAGTTGAGTCCGATTTCACTTATGGATACGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGCCCGAACTCGTTGAG
53435229 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * **
53435257 GGCATCCGACCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGGGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGCCCGAACTCGTTGAG
53435322 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
53435336 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAATGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:53439623 original size:4 final size:4
Alignment explanation
Indices: 53439614--53439644 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
53439604 CCATAGCTGA
53439614 TCAC TCAC TCAC TCAC TCAC TCAC TCAC TCA
1 TCAC TCAC TCAC TCAC TCAC TCAC TCAC TCA
53439645 TCTTCTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
TCAC
Found at i:53443819 original size:20 final size:20
Alignment explanation
Indices: 53443751--53443820 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
53443741 CAATCAATTA
53443751 AAAAAAT-TTAAAATTAT-T
1 AAAAAATATTAAAATTATAT
* *
53443769 AAAACATATTAAAATTTTAT
1 AAAAAATATTAAAATTATAT
* *
53443789 AAAAATGTATTAAAATTCTAT
1 AAAAA-ATATTAAAATTATAT
53443810 AAAAAATATTA
1 AAAAAATATTA
53443821 GATTAAACCC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.14
19 9 0.21
20 10 0.23
21 18 0.42
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAAATATTAAAATTATAT
Found at i:53444167 original size:18 final size:21
Alignment explanation
Indices: 53444131--53444168 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
53444121 ATGAGTACAC
53444131 ATTTAATATATCTTGACTTTT
1 ATTTAATATATCTTGACTTTT
53444152 ATTT-ATATAT-TT-ACTTT
1 ATTTAATATATCTTGACTTT
53444169 AATTAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 2 0.12
20 6 0.35
21 4 0.24
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (21 bp):
ATTTAATATATCTTGACTTTT
Found at i:53449081 original size:31 final size:33
Alignment explanation
Indices: 53449021--53449082 Score: 85
Period size: 31 Copynumber: 1.9 Consensus size: 33
53449011 AGAATAAGCT
53449021 TGAAATTGTTAATATAATTTGGTTAGTTTAAAA
1 TGAAATTGTTAATATAATTTGGTTAGTTTAAAA
*
53449054 TGAAA-TGTTTATAT-ATTTGAGTT-GTTTAA
1 TGAAATTGTTAATATAATTTG-GTTAGTTTAA
53449083 TTGCTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 11 0.41
32 11 0.41
33 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (33 bp):
TGAAATTGTTAATATAATTTGGTTAGTTTAAAA
Found at i:53452253 original size:23 final size:24
Alignment explanation
Indices: 53452194--53452255 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
53452184 ATTTGATATA
*
53452194 TATTTTCTTTTTTGA-TTTCTTGC
1 TATTTTCTTTTTTAATTTTCTTGC
* *
53452217 T-TTTTGTTTATTTAATTTTCTT-T
1 TATTTTCTTT-TTTAATTTTCTTGC
53452240 TATTTTCTTTTTTAAT
1 TATTTTCTTTTTTAAT
53452256 ATTTTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 7 0.22
23 12 0.38
24 13 0.41
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (24 bp):
TATTTTCTTTTTTAATTTTCTTGC
Found at i:53457808 original size:46 final size:46
Alignment explanation
Indices: 53457756--53457937 Score: 220
Period size: 46 Copynumber: 4.0 Consensus size: 46
53457746 AGTGTACTCT
* * *
53457756 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGTAAC
1 CTGACATAAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
53457802 CTGATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAAC
1 CTGACATAAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
53457848 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATAAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
53457894 ATGACAGAAAACGAGTAAGACCATAGTTGAAAAATACTATGGCA
1 CTGACATAAAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
53457938 TCATGTCGAA
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 120 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGACATAAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:53461929 original size:46 final size:46
Alignment explanation
Indices: 53461879--53461970 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
53461869 TTGATAGTTT
53461879 TTTTTTGTCTC-GAAAGTGATCACTAC-AACTCTCTCTACTAGACAAG
1 TTTTTTGTC-CAGAAAGTGATCACTACTAA-TCTCTCTACTAGACAAG
* * *
53461925 TTTTTTGTCCAGGAAGTGATTACTACTAATGTCTCTACTAGACAAG
1 TTTTTTGTCCAGAAAGTGATCACTACTAATCTCTCTACTAGACAAG
53461971 AGTTAAGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
45 1 0.02
46 38 0.93
47 2 0.05
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (46 bp):
TTTTTTGTCCAGAAAGTGATCACTACTAATCTCTCTACTAGACAAG
Found at i:53466750 original size:40 final size:40
Alignment explanation
Indices: 53466695--53466776 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
53466685 GTGAACAAGA
53466695 GCAATCACCAGCTTTGAGGAGTTGTCTACACTCTTCATTG
1 GCAATCACCAGCTTTGAGGAGTTGTCTACACTCTTCATTG
53466735 GCAATCACCAGCTTTGAGGAGTTGTCTACACTCTTCATTG
1 GCAATCACCAGCTTTGAGGAGTTGTCTACACTCTTCATTG
53466775 GC
1 GC
53466777 CCCTTCTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (40 bp):
GCAATCACCAGCTTTGAGGAGTTGTCTACACTCTTCATTG
Found at i:53471748 original size:24 final size:24
Alignment explanation
Indices: 53471719--53471767 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
53471709 CACATTACAA
53471719 ACAAACACAACATTCAATTAACAT
1 ACAAACACAACATTCAATTAACAT
53471743 ACAAACACAACATTCAATTAACAT
1 ACAAACACAACATTCAATTAACAT
53471767 A
1 A
53471768 ATTACATGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.20
Consensus pattern (24 bp):
ACAAACACAACATTCAATTAACAT
Found at i:53474614 original size:12 final size:12
Alignment explanation
Indices: 53474597--53474633 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
53474587 TAAAATGAAT
53474597 GATGACACGGGC
1 GATGACACGGGC
53474609 GATGACACGGGC
1 GATGACACGGGC
53474621 GATGACACGGGC
1 GATGACACGGGC
53474633 G
1 G
53474634 TGTCTAGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.43, T:0.08
Consensus pattern (12 bp):
GATGACACGGGC
Found at i:53474667 original size:13 final size:13
Alignment explanation
Indices: 53474649--53474673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53474639 AGGCCGTATG
53474649 AGGGACACGGGCC
1 AGGGACACGGGCC
53474662 AGGGACACGGGC
1 AGGGACACGGGC
53474674 GTGTGCTTGG
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:0.24, C:0.28, G:0.48, T:0.00
Consensus pattern (13 bp):
AGGGACACGGGCC
Found at i:53476717 original size:40 final size:39
Alignment explanation
Indices: 53476619--53476841 Score: 241
Period size: 40 Copynumber: 5.6 Consensus size: 39
53476609 TCCTCGTTCA
* * * * *
53476619 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
53476658 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
53476697 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* *
53476737 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
* * * * * *
53476777 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCAC
* *
53476818 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53476842 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
Found at i:53476841 original size:120 final size:119
Alignment explanation
Indices: 53476619--53476841 Score: 272
Period size: 120 Copynumber: 1.9 Consensus size: 119
53476609 TCCTCGTTCA
* * * *
53476619 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
53476684 TAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
66 TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
53476738 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* *
53476802 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
53476842 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
119 37 0.43
120 44 0.51
121 6 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:53478145 original size:48 final size:48
Alignment explanation
Indices: 53478075--53478172 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 48
53478065 CACTACTCAT
53478075 TAGGGGGGGGAATTTGACATGCAAGTCCCCCCTTT-GTCCACATGCAC
1 TAGGGGGGGGAATTTGACATGCAAGTCCCCCCTTTCGTCCACATGCAC
** *
53478122 TAGGGAGGGGGAATTTGACATGCAAGTCCCCTTTTTCTTCCACATGCAC
1 TAGGG-GGGGGAATTTGACATGCAAGTCCCCCCTTTCGTCCACATGCAC
53478171 TA
1 TA
53478173 ATAGGTCCTC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 5 0.11
48 28 0.61
49 13 0.28
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.27
Consensus pattern (48 bp):
TAGGGGGGGGAATTTGACATGCAAGTCCCCCCTTTCGTCCACATGCAC
Found at i:53484678 original size:40 final size:40
Alignment explanation
Indices: 53484580--53484842 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
53484570 TCCTCGTTCA
* * * ** *
53484580 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
53484619 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
53484659 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
53484699 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
53484739 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
53484779 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
53484819 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
53484843 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:53495704 original size:48 final size:46
Alignment explanation
Indices: 53495630--53495749 Score: 125
Period size: 48 Copynumber: 2.6 Consensus size: 46
53495620 TGTCTTCGAC
** * *
53495630 ATGGACTTACATGAATTATTCCTGTCTCC-AATGCTATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAT-CCATATA-A-ATAAT
* * * *
53495678 ATGGGCTTACATGGCTCATTCTTGTCTCCAAATCCATATAACTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAATCCATATAAATAAT
*
53495724 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
53495750 CTGTCCTATC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
46 26 0.43
47 1 0.02
48 30 0.50
49 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAATCCATATAAATAAT
Found at i:53502153 original size:20 final size:20
Alignment explanation
Indices: 53502124--53502168 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
53502114 AGCACATGTA
* *
53502124 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAAATT
*
53502144 TTCATCAAATTTTACAAATT
1 TTCATAAAATTTTACAAATT
53502164 TTCAT
1 TTCAT
53502169 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAAATT
Found at i:53502766 original size:12 final size:12
Alignment explanation
Indices: 53502749--53502775 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53502739 TCACACGACA
53502749 TACCTACCATAT
1 TACCTACCATAT
53502761 TACCTACCATAT
1 TACCTACCATAT
53502773 TAC
1 TAC
53502776 AGACCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (12 bp):
TACCTACCATAT
Found at i:53505809 original size:13 final size:13
Alignment explanation
Indices: 53505791--53505816 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53505781 TTGGATCTGT
53505791 ACCAAAACAATCA
1 ACCAAAACAATCA
53505804 ACCAAAACAATCA
1 ACCAAAACAATCA
53505817 TGAAACATAT
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:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:53506948 original size:44 final size:43
Alignment explanation
Indices: 53506850--53506977 Score: 143
Period size: 44 Copynumber: 3.0 Consensus size: 43
53506840 CTCGTACAAC
* ** *
53506850 GCCAACGTCCCAGACGTGGTCTTACATGTAACCACATATCGAT
1 GCCAACGTCCCAAACGTGGTCTTACACATAATCACATATCGAT
* * *
53506893 GCC-ACTATCCCATACAG-GGTCTTACACATAAATCACAAATCGAT
1 GCCAAC-GTCCCAAAC-GTGGTCTTACACAT-AATCACATATCGAT
*
53506937 GCCAACGTCCCAAACGTGGTCTTACACAGAATCACATATCG
1 GCCAACGTCCCAAACGTGGTCTTACACATAATCACATATCG
53506978 GAACCCTATA
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
42 2 0.03
43 32 0.46
44 34 0.49
45 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCAACGTCCCAAACGTGGTCTTACACATAATCACATATCGAT
Found at i:53510717 original size:118 final size:118
Alignment explanation
Indices: 53510502--53510740 Score: 451
Period size: 118 Copynumber: 2.0 Consensus size: 118
53510492 ATGGTAGATA
53510502 AGTGCCTTGTGTCTGAGTTCTAGTAATGATAACGAAATAAAAATGTGTTATGATTTGTGGACTTA
1 AGTGCCTTGTGTCTGAGTTCTAGTAATGATAACGAAATAAAAATGTGTTATGATTTGTGGACTTA
53510567 TGTGCATGATTATTCGGATGATAACCGAGCTAAGACCCGAAGGCATTTGTGCG
66 TGTGCATGATTATTCGGATGATAACCGAGCTAAGACCCGAAGGCATTTGTGCG
53510620 AGTGCCTTGTGTCTGAGTTCTAGTAATGATAACGAAATAAAAATGTGTTATGATTTGTGGACTTA
1 AGTGCCTTGTGTCTGAGTTCTAGTAATGATAACGAAATAAAAATGTGTTATGATTTGTGGACTTA
* * *
53510685 TGTGCATGATTATTCGGATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCG
66 TGTGCATGATTATTCGGATGATAACCGAGCTAAGACCCGAAGGCATTTGTGCG
53510738 AGT
1 AGT
53510741 TGCTGTATCC
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (118 bp):
AGTGCCTTGTGTCTGAGTTCTAGTAATGATAACGAAATAAAAATGTGTTATGATTTGTGGACTTA
TGTGCATGATTATTCGGATGATAACCGAGCTAAGACCCGAAGGCATTTGTGCG
Found at i:53510762 original size:40 final size:40
Alignment explanation
Indices: 53510704--53510805 Score: 154
Period size: 40 Copynumber: 2.6 Consensus size: 40
53510694 TTATTCGGAT
53510704 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGC
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGC
* * *
53510744 TGTATCCGGGCTAGGACCCGAAGGCATTTGTGCGAGTTGT
1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGC
53510784 TATATCC-GGCTAA-ATCCCGAAG
1 TATATCCGGGCTAAGA-CCCGAAG
53510806 ATACTTGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
38 1 0.02
39 12 0.21
40 43 0.77
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGC
Found at i:53511074 original size:22 final size:22
Alignment explanation
Indices: 53511031--53511074 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53511021 GAAAATGTGC
* *
53511031 ATATATGAAGTTATTCATTTAG
1 ATATATGAAGTTATACACTTAG
53511053 ATATATGAATGTTATAC-CTTAG
1 ATATATGAA-GTTATACACTTAG
53511075 CCGAAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATATGAAGTTATACACTTAG
Found at i:53521417 original size:37 final size:37
Alignment explanation
Indices: 53521376--53521463 Score: 167
Period size: 37 Copynumber: 2.4 Consensus size: 37
53521366 AACATAGACA
53521376 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
1 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
*
53521413 TGTATGTTTGGCCACATGAATAAGTACATAAGTTATG
1 TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
53521450 TGTATGTTCGGCCA
1 TGTATGTTCGGCCA
53521464 TAGGTAGCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (37 bp):
TGTATGTTCGGCCACATGAATAAGTACATAAGTTATG
Found at i:53522164 original size:39 final size:40
Alignment explanation
Indices: 53522062--53522246 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
53522052 TCGAATGATG
* * * *
53522062 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
53522101 ATCCGGACTAAGAT-GCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
53522142 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
53522181 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
53522220 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
53522247 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:53522268 original size:79 final size:79
Alignment explanation
Indices: 53522116--53522279 Score: 199
Period size: 79 Copynumber: 2.1 Consensus size: 79
53522106 GACTAAGATG
* * **
53522116 CGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 CGAAGGCATTTGTACGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
*
53522181 TCCGGGTTAAGTCC
66 TCCGGGTTAAATCC
* *
53522195 CGAAGGCATTTGTACGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CGAAGGCATTTGTACGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CT
* *
53522258 ATATCC-GGTTAAATTC
63 AAATCCGGGTTAAATCC
53522274 CGAAGG
1 CGAAGG
53522280 TACGTGATTC
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CGAAGGCATTTGTACGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
TCCGGGTTAAATCC
Found at i:53532201 original size:47 final size:47
Alignment explanation
Indices: 53532132--53532352 Score: 182
Period size: 47 Copynumber: 4.6 Consensus size: 47
53532122 GTAGAATGCC
53532132 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-CATCAAGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCACATCAAGTT
* * * * *
53532179 GATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCGAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ACATC-AAGTT
* * * ***
53532228 GATGCCATGTCCTAAACATGGTCTTACACTAGCTCTCACATCTCCTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACATCAAGTT
* * * * * *
53532275 GCAGATGCCATGTCCCAAACATGATCCTACACTGGCTCTCATAAT-ATGGTC
1 ---GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-CATCA-AGTT
53532326 GATG-CAT-TCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
53532353 AGCACACAAT
Statistics
Matches: 139, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
45 8 0.06
46 11 0.08
47 37 0.27
48 11 0.08
49 35 0.25
50 34 0.24
51 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACATCAAGTT
Found at i:53534872 original size:18 final size:18
Alignment explanation
Indices: 53534833--53534877 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
53534823 TTCATAGTTT
53534833 TATCGATACCTTTTTTGA
1 TATCGATACCTTTTTTGA
*
53534851 TATCAATACCTTTTTT-A
1 TATCGATACCTTTTTTGA
53534868 GTATCGATAC
1 -TATCGATAC
53534878 AAAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (18 bp):
TATCGATACCTTTTTTGA
Found at i:53535871 original size:33 final size:32
Alignment explanation
Indices: 53535832--53536135 Score: 171
Period size: 33 Copynumber: 9.6 Consensus size: 32
53535822 TAAAATATTT
53535832 AAAATATTTTAATATAATTTAATATAAAACTAA
1 AAAATATTTTAATATAATTTAATATAAAA-TAA
53535865 AAAATATTTTAATATAA--T--T-TAAAAT--
1 AAAATATTTTAATATAATTTAATATAAAATAA
53535890 AAAATATTTTAATAT-ATTTAATATAAGAAT-A
1 AAAATATTTTAATATAATTTAATATAA-AATAA
** ** * * * *
53535921 ATTATATTAAAATGTTATTAAATTATAAAAATATTT
1 AAAATATTTTAATATAATTTAA-TAT-AAAATA--A
*
53535957 GAAATATTTTAATATAATTTAATATAAAACTAA
1 AAAATATTTTAATATAATTTAATATAAAA-TAA
*
53535990 AAAATATTTTAACATAA--T--T-TAAAAT--
1 AAAATATTTTAATATAATTTAATATAAAATAA
*
53536015 AAAATATTTTAATAT-ACTTAATATAAAAATAA
1 AAAATATTTTAATATAATTTAATAT-AAAATAA
* * * *
53536047 ATATATTAATTTT-TTATTAAATT-ATA-AAAATATTT
1 A-A-AAT-ATTTTAATA-TAATTTAATATAAAATA--A
*
53536082 GAAATATTTTAATATAATTTAATATAAAACTAAA
1 AAAATATTTTAATATAATTTAATATAAAA-T-AA
*
53536116 AAAATATTTTAATATGATTT
1 AAAATATTTTAATATAATTT
53536136 TAAATAATAT
Statistics
Matches: 207, Mismatches: 30, Indels: 67
0.68 0.10 0.22
Matches are distributed among these distances:
24 2 0.01
25 29 0.14
26 2 0.01
27 2 0.01
28 12 0.06
29 6 0.03
30 8 0.04
31 12 0.06
32 16 0.08
33 52 0.25
34 33 0.16
35 15 0.07
36 18 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (32 bp):
AAAATATTTTAATATAATTTAATATAAAATAA
Found at i:53535893 original size:25 final size:24
Alignment explanation
Indices: 53535865--53535920 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 24
53535855 ATAAAACTAA
53535865 AAAATATTTTAATATAATTTAAAAT
1 AAAATATTTTAATAT-ATTTAAAAT
*
53535890 AAAATATTTTAATATATTTAATAT
1 AAAATATTTTAATATATTTAAAAT
53535914 AAGAATA
1 AA-AATA
53535921 ATTATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAATATTTTAATATATTTAAAAT
Found at i:53535898 original size:67 final size:66
Alignment explanation
Indices: 53535818--53536155 Score: 291
Period size: 67 Copynumber: 5.3 Consensus size: 66
53535808 AAAAAATATA
53535818 AAAATAAAATATTTAAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAAT
1 AAAATAAAATATTT-AAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAAT
53535883 TT
65 TT
* * ** ** * *
53535885 AAAATAAAATATTTTAATATATTTAATATAA--GAATA-ATTA-TATTAAA-ATGTT-AT-TAAA
1 AAAATAAAATATTTAAATAT-TTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAAT
53535943 TT
65 TT
* *
53535945 -ATA-AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAACATAAT
1 AAAATAAAATATTT-AAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAAT
53536008 TT
65 TT
* * ** *
53536010 AAAATAAAATATTTTAATATACTTAATATAA---AA-AT-AAA-TATATTAAT-TTTTTAT-TAA
1 AAAATAAAATATTTAAATAT-TTTAATATAATTTAATATAAAACTA-AAAAATATTTTAATATAA
*
53536067 ATT
64 TTT
* *
53536070 -ATA-AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAAATATTTTAATATGA
1 AAAATAAAATATTT-AAATATTTTAATATAATTTAATATAAAACT-AAAAAATATTTTAATATAA
53536133 TTT
64 TTT
* * *
53536136 TAAATAATATATTTTAATAT
1 AAAATAAAATATTTAAATAT
53536156 AAAAATAATT
Statistics
Matches: 209, Mismatches: 37, Indels: 50
0.71 0.12 0.17
Matches are distributed among these distances:
58 37 0.18
59 14 0.07
60 14 0.07
61 13 0.06
62 18 0.09
63 14 0.07
64 10 0.05
65 16 0.08
66 16 0.08
67 49 0.23
68 8 0.04
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (66 bp):
AAAATAAAATATTTAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAATT
T
Found at i:53535963 original size:125 final size:125
Alignment explanation
Indices: 53535823--53536156 Score: 560
Period size: 125 Copynumber: 2.7 Consensus size: 125
53535813 ATATAAAAAT
*
53535823 AAAATATTTAAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAATTTAAA
1 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAATTTAAA
* * *
53535888 ATAAAATATTTTAATATATTTAATATAAGAATAATTATATTAAAATGTTATTAAATTATA
66 ATAAAATATTTTAATATACTTAATATAAAAATAAATATATTAAAATGTTATTAAATTATA
*
53535948 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAACATAATTTAAA
1 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAATTTAAA
** *
53536013 ATAAAATATTTTAATATACTTAATATAAAAATAAATATATTAATTTTTTATTAAATTATA
66 ATAAAATATTTTAATATACTTAATATAAAAATAAATATATTAAAATGTTATTAAATTATA
* *
53536073 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAAATATTTTAATATGATTTTA
1 AAAATATTTGAAATATTTTAATATAATTTAATATAAAACT-AAAAAATATTTTAATATAATTTAA
*
53536138 AATAATATATTTTAATATA
65 AATAAAATATTTTAATATA
53536157 AAAATAATTG
Statistics
Matches: 196, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
125 157 0.80
126 39 0.20
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (125 bp):
AAAATATTTGAAATATTTTAATATAATTTAATATAAAACTAAAAAATATTTTAATATAATTTAAA
ATAAAATATTTTAATATACTTAATATAAAAATAAATATATTAAAATGTTATTAAATTATA
Found at i:53536043 original size:25 final size:26
Alignment explanation
Indices: 53535989--53536045 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
53535979 TATAAAACTA
*
53535989 AAAAATATTTTAACATAATTTAAAAT
1 AAAAATATTTTAACATAACTTAAAAT
* *
53536015 -AAAATATTTTAATAT-ACTTAATAT
1 AAAAATATTTTAACATAACTTAAAAT
53536039 AAAAATA
1 AAAAATA
53536046 AATATATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAAATATTTTAACATAACTTAAAAT
Found at i:53536145 original size:15 final size:15
Alignment explanation
Indices: 53536125--53536157 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
53536115 AAAAATATTT
53536125 TAATATGATTTTAA-A
1 TAATAT-ATTTTAATA
53536140 TAATATATTTTAATA
1 TAATATATTTTAATA
53536155 TAA
1 TAA
53536158 AAATAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TAATATATTTTAATA
Found at i:53537663 original size:18 final size:19
Alignment explanation
Indices: 53537626--53537666 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
53537616 CATACAGCAA
* *
53537626 TTGTAGTAACGAAATTTAT
1 TTGTAGTAAAGAAATATAT
53537645 TTGTAG-AAAGAAATATAT
1 TTGTAGTAAAGAAATATAT
53537663 TTGT
1 TTGT
53537667 CTAAAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.41
Consensus pattern (19 bp):
TTGTAGTAAAGAAATATAT
Found at i:53540387 original size:30 final size:30
Alignment explanation
Indices: 53540351--53540410 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53540341 TAATTTCTGA
53540351 AACAGATTTTGCCCCTAAAAGATTGTTTAT
1 AACAGATTTTGCCCCTAAAAGATTGTTTAT
53540381 AACAGATTTTGCCCCTAAAAGATTGTTTAT
1 AACAGATTTTGCCCCTAAAAGATTGTTTAT
53540411 CTCTAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (30 bp):
AACAGATTTTGCCCCTAAAAGATTGTTTAT
Found at i:53540756 original size:30 final size:30
Alignment explanation
Indices: 53540722--53540778 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
53540712 ATTATACATG
53540722 ATTTTAATTGGTATAATAATAAATTTAGCC
1 ATTTTAATTGGTATAATAATAAATTTAGCC
*
53540752 ATTTTGATTGGTATAATAATAAATTTA
1 ATTTTAATTGGTATAATAATAAATTTA
53540779 ACCCTCATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.46
Consensus pattern (30 bp):
ATTTTAATTGGTATAATAATAAATTTAGCC
Found at i:53541518 original size:38 final size:38
Alignment explanation
Indices: 53541473--53541559 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
53541463 ATACATATAT
* *
53541473 TAATAATTATATTAAGAATGTTATTAAATTA-TATTTAA
1 TAATAATTATATTAA-AATATGATTAAATTATTATTTAA
* * *
53541511 TAATAATTATGTTAAAATATGGTTAAATTATTTTTTAA
1 TAATAATTATATTAAAATATGATTAAATTATTATTTAA
53541549 TAA-AA-TATATT
1 TAATAATTATATT
53541560 TAACAATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
36 5 0.12
37 14 0.33
38 23 0.55
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (38 bp):
TAATAATTATATTAAAATATGATTAAATTATTATTTAA
Found at i:53541768 original size:16 final size:16
Alignment explanation
Indices: 53541748--53541818 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
53541738 TGAATTACTT
*
53541748 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCA
*
53541764 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
*
53541780 ATCACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
53541796 ATTACAGCCCTATTCA
1 ATTACAGCTCTATTCA
53541812 ATTACAG
1 ATTACAG
53541819 TGAACCAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:53544738 original size:101 final size:101
Alignment explanation
Indices: 53544604--53544819 Score: 288
Period size: 101 Copynumber: 2.1 Consensus size: 101
53544594 CATGGCCTTG
* * * * ** *
53544604 CCATAGTCTTACGTTCATAGTGCCCTAACCCAGTTATGGTCTTATCACCAGAATGTCATAGCCCA
1 CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATGATCTTATCACCAGAATCCCATAACCCA
*
53544669 ACTATGGTCTTAGATATAAACAATGCCATAGTCCAA
66 ACTATGGTCTTACATATAAACAATGCCATAGTCCAA
* * *
53544705 CCATGGTCTTATGTCCATAGTGCCATAACCCAGTTATGATCTTATCATCAGAATCCCATAACCTA
1 CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATGATCTTATCACCAGAATCCCATAACCCA
* * * * *
53544770 GCTATGGTCTTACATATATACACTGTCATGGTCCAA
66 ACTATGGTCTTACATATAAACAATGCCATAGTCCAA
53544806 CCATGGTCTTACGT
1 CCATGGTCTTACGT
53544820 TTGAATAATT
Statistics
Matches: 98, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (101 bp):
CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATGATCTTATCACCAGAATCCCATAACCCA
ACTATGGTCTTACATATAAACAATGCCATAGTCCAA
Found at i:53553187 original size:32 final size:32
Alignment explanation
Indices: 53553150--53553216 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
53553140 GCTATGTATA
*
53553150 TATATTTTATG-AAATTTTTAT-ATTTTATATTT
1 TATATTTT-TGTAAATTTTTATAATTTT-TAATT
*
53553182 TATATTTTTGTATATTTTTATAATTTTTAATT
1 TATATTTTTGTAAATTTTTATAATTTTTAATT
53553214 TAT
1 TAT
53553217 TTGTTGACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.06
32 24 0.77
33 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (32 bp):
TATATTTTTGTAAATTTTTATAATTTTTAATT
Found at i:53553197 original size:10 final size:10
Alignment explanation
Indices: 53553146--53553210 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
53553136 TCCCGCTATG
53553146 TATATATATTT
1 TATATAT-TTT
*
53553157 TATGAAATTTT
1 TAT-ATATTTT
*
53553168 TATATTTTATAT
1 TATATATT-T-T
*
53553180 TTTATATTTT
1 TATATATTTT
*
53553190 TGTATATTTT
1 TATATATTTT
53553200 TATA-ATTTT
1 TATATATTTT
53553209 TA
1 TA
53553211 ATTTATTTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
9 7 0.16
10 16 0.36
11 11 0.25
12 10 0.23
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (10 bp):
TATATATTTT
Found at i:53553200 original size:25 final size:24
Alignment explanation
Indices: 53553150--53553208 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
53553140 GCTATGTATA
53553150 TATATTTTATGAAATTTTTATATTT
1 TATATTTTAT-AAATTTTTATATTT
*
53553175 TATATTTTAT-ATTTTTGTATATTTT
1 TATATTTTATAAATTTT-TATA-TTT
53553200 TATAATTTT
1 TAT-ATTTT
53553209 TAATTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.17
24 4 0.13
25 16 0.53
26 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
TATATTTTATAAATTTTTATATTT
Found at i:53553207 original size:9 final size:8
Alignment explanation
Indices: 53553163--53553214 Score: 56
Period size: 7 Copynumber: 6.5 Consensus size: 8
53553153 ATTTTATGAA
53553163 ATTTTTAT
1 ATTTTTAT
53553171 A-TTTTAT
1 ATTTTTAT
53553178 A-TTTTAT
1 ATTTTTAT
53553185 ATTTTTGTAT
1 A-TTTT-TAT
53553195 ATTTTTAT
1 ATTTTTAT
53553203 AATTTTTA-
1 -ATTTTTAT
53553211 ATTT
1 ATTT
53553215 ATTTGTTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
7 18 0.45
8 4 0.10
9 14 0.35
10 4 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
ATTTTTAT
Found at i:53553648 original size:13 final size:13
Alignment explanation
Indices: 53553630--53553655 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53553620 TAGAGTCTCC
53553630 CACTCATTTGTAA
1 CACTCATTTGTAA
53553643 CACTCATTTGTAA
1 CACTCATTTGTAA
53553656 TCATCCATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CACTCATTTGTAA
Done.