Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 122 of 211
Found at i:38673723 original size:4 final size:4
Alignment explanation
Indices: 38673707--38673758 Score: 79
Period size: 4 Copynumber: 13.0 Consensus size: 4
38673697 AAATAAAAAG
*
38673707 GAAA GAGAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA GGAA GAAA
1 GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
38673755 GAAA
1 GAAA
38673759 ATGAGAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
3 3 0.07
4 38 0.84
5 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:38675805 original size:13 final size:13
Alignment explanation
Indices: 38675771--38675980 Score: 114
Period size: 13 Copynumber: 15.8 Consensus size: 13
38675761 AACCAGTGTT
*
38675771 CCATTTCATATAT
1 CCATTTCATATAA
*
38675784 CTATTTTCATATAA
1 CCA-TTTCATATAA
38675798 CCGA-TTCATATAA
1 CC-ATTTCATATAA
38675811 CCATTTCATAT-A
1 CCATTTCATATAA
*
38675823 TCATTTTTCATATAA
1 CCA--TTTCATATAA
* *
38675838 TCGA-TTCGTATAA
1 -CCATTTCATATAA
*
38675851 CCATTTCATA-CA
1 CCATTTCATATAA
* *
38675863 TCATTTTTAATATAA
1 CCA--TTTCATATAA
* *
38675878 CTTATTT-GTATAA
1 C-CATTTCATATAA
38675891 CCATTTCATAT-A
1 CCATTTCATATAA
*
38675903 TCATTTTTCATATAA
1 CCA--TTTCATATAA
38675918 CCGA-TTCATATAA
1 CC-ATTTCATATAA
38675931 CCATTTCATAT-A
1 CCATTTCATATAA
* *
38675943 TCATTCTTCACATAA
1 CCA-T-TTCATATAA
38675958 CCGA-TTCATATAA
1 CC-ATTTCATATAA
38675971 CCATTTCATA
1 CCATTTCATA
38675981 AATCATTCTT
Statistics
Matches: 150, Mismatches: 24, Indels: 46
0.68 0.11 0.21
Matches are distributed among these distances:
12 21 0.14
13 77 0.51
14 41 0.27
15 7 0.05
16 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (13 bp):
CCATTTCATATAA
Found at i:38675832 original size:27 final size:27
Alignment explanation
Indices: 38675802--38675929 Score: 81
Period size: 27 Copynumber: 4.8 Consensus size: 27
38675792 ATATAACCGA
38675802 TTCATATAACCATTTCATATATCATTT
1 TTCATATAACCATTTCATATATCATTT
* * *
38675829 TTCATATAATCGA-TTCGTATAACCA--T
1 TTCATATAA-CCATTTCATAT-ATCATTT
* * * *
38675855 TTCATA-CATCATTT-TTAATATAACTTAT
1 TTCATATAACCATTTCAT-ATATCA-TT-T
*
38675883 TT-GTATAACCATTTCATATATCATTT
1 TTCATATAACCATTTCATATATCATTT
38675909 TTCATATAACCGA-TTCATATA
1 TTCATATAACC-ATTTCATATA
38675930 ACCATTTCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 24
0.65 0.13 0.21
Matches are distributed among these distances:
24 4 0.05
25 5 0.07
26 10 0.14
27 34 0.46
28 20 0.27
29 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.45
Consensus pattern (27 bp):
TTCATATAACCATTTCATATATCATTT
Found at i:38675986 original size:120 final size:120
Alignment explanation
Indices: 38675771--38675987 Score: 373
Period size: 120 Copynumber: 1.8 Consensus size: 120
38675761 AACCAGTGTT
* *
38675771 CCATTTCATATATCTATTTTCATATAACCGATTCATATAACCATTTCATATATCATTTTTCATAT
1 CCATTTCATATATCTATTTTCATATAACCGATTCATATAACCATTTCATATATCATTCTTCACAT
* * *
38675836 AATCGATTCGTATAACCATTTCATACATCATTTTTAATATAACTTATTTGTATAA
66 AACCGATTCATATAACCATTTCATAAATCATTTTTAATATAACTTATTTGTATAA
38675891 CCATTTCATATATC-ATTTTTCATATAACCGATTCATATAACCATTTCATATATCATTCTTCACA
1 CCATTTCATATATCTA-TTTTCATATAACCGATTCATATAACCATTTCATATATCATTCTTCACA
38675955 TAACCGATTCATATAACCATTTCATAAATCATT
65 TAACCGATTCATATAACCATTTCATAAATCATT
38675988 CTTCACCCGA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
119 1 0.01
120 90 0.99
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.43
Consensus pattern (120 bp):
CCATTTCATATATCTATTTTCATATAACCGATTCATATAACCATTTCATATATCATTCTTCACAT
AACCGATTCATATAACCATTTCATAAATCATTTTTAATATAACTTATTTGTATAA
Found at i:38675993 original size:40 final size:40
Alignment explanation
Indices: 38675771--38675992 Score: 320
Period size: 40 Copynumber: 5.5 Consensus size: 40
38675761 AACCAGTGTT
38675771 CCATTTCATATATC-TATTTTCATATAACCGATTCATATAA
1 CCATTTCATATATCAT-TTTTCATATAACCGATTCATATAA
* *
38675811 CCATTTCATATATCATTTTTCATATAATCGATTCGTATAA
1 CCATTTCATATATCATTTTTCATATAACCGATTCATATAA
* * ** **
38675851 CCATTTCATACATCATTTTTAATATAACTTATTTGTATAA
1 CCATTTCATATATCATTTTTCATATAACCGATTCATATAA
38675891 CCATTTCATATATCATTTTTCATATAACCGATTCATATAA
1 CCATTTCATATATCATTTTTCATATAACCGATTCATATAA
* *
38675931 CCATTTCATATATCATTCTTCACATAACCGATTCATATAA
1 CCATTTCATATATCATTTTTCATATAACCGATTCATATAA
* *
38675971 CCATTTCATAAATCATTCTTCA
1 CCATTTCATATATCATTTTTCA
38675993 CCCGATGAAC
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 163 0.99
41 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.43
Consensus pattern (40 bp):
CCATTTCATATATCATTTTTCATATAACCGATTCATATAA
Found at i:38678113 original size:17 final size:17
Alignment explanation
Indices: 38678091--38678124 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38678081 ATAGTCAATC
38678091 GGAAGCTTGTTCGAGTT
1 GGAAGCTTGTTCGAGTT
*
38678108 GGAAGCTTGTTGGAGTT
1 GGAAGCTTGTTCGAGTT
38678125 ATATCACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.38, T:0.35
Consensus pattern (17 bp):
GGAAGCTTGTTCGAGTT
Found at i:38678320 original size:71 final size:71
Alignment explanation
Indices: 38678240--38678381 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
38678230 CCAATGTGTT
* *
38678240 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTTTTATGTGTCTGTGGC
1 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATGTGGC
38678305 CTTATA
66 CTTATA
38678311 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATGTGGC
1 TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATGTGGC
38678376 CTTATA
66 CTTATA
38678382 ATGGTTGAAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (71 bp):
TTGACTTGAGAATTTGGTATTTTGAATGTTTGAAATGGTTGAATACATTGTTATGTGTATGTGGC
CTTATA
Found at i:38689414 original size:40 final size:38
Alignment explanation
Indices: 38689370--38689490 Score: 97
Period size: 40 Copynumber: 3.2 Consensus size: 38
38689360 CAGTCTACCT
*
38689370 GACTAGTGCAGAGCACACCATTATATCTGTCAGTTTATCC
1 GACTAGTGCAG-GCACA-CATTATATCTGTCAATTTATCC
* * *
38689410 GACTAGCGCTAGGCACA-ACT-T-TC-GTCAATTTATCT
1 GACTAGTGC-AGGCACACATTATATCTGTCAATTTATCC
* * * *
38689445 GACTAGTGCTGGGCACAACATTATATTTTTCAATTTATCT
1 GACTAGTGC-AGGCAC-ACATTATATCTGTCAATTTATCC
38689485 GACTAG
1 GACTAG
38689491 CGCTGGGTGC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
35 24 0.36
36 3 0.05
37 3 0.05
38 3 0.05
39 1 0.02
40 30 0.45
41 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (38 bp):
GACTAGTGCAGGCACACATTATATCTGTCAATTTATCC
Found at i:38689482 original size:75 final size:76
Alignment explanation
Indices: 38689368--38689532 Score: 197
Period size: 75 Copynumber: 2.2 Consensus size: 76
38689358 GTCAGTCTAC
* * * * *
38689368 CTGACTAGTGCAGAGCACACCATTATATCTGTCAGTTTATCCGACTAGCGCTAGGCACAACT-TT
1 CTGACTAGTGCTGGGCACAACATTATATCTGTCAATTTATCCGACTAGCGCTAGGCACAAATCTT
*
38689432 CGTCAATTTAT
66 CATCAATTTAT
* * * * **
38689443 CTGACTAGTGCTGGGCACAACATTATATTTTTCAATTTATCTGACTAGCGCTGGGTGCAAATCTT
1 CTGACTAGTGCTGGGCACAACATTATATCTGTCAATTTATCCGACTAGCGCTAGGCACAAATCTT
*
38689508 CATCAGTTTAT
66 CATCAATTTAT
*
38689519 TTGACTAGTGCTGG
1 CTGACTAGTGCTGG
38689533 TCGCAAATCT
Statistics
Matches: 75, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
75 51 0.68
76 24 0.32
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (76 bp):
CTGACTAGTGCTGGGCACAACATTATATCTGTCAATTTATCCGACTAGCGCTAGGCACAAATCTT
CATCAATTTAT
Found at i:38694957 original size:53 final size:53
Alignment explanation
Indices: 38694877--38694983 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
38694867 GAAGGAGGAA
38694877 TAGGAACACAAGCTGAGCTACGAAGAATAATCGAATTTATCTTTTAGTTTCTT
1 TAGGAACACAAGCTGAGCTACGAAGAATAATCGAATTTATCTTTTAGTTTCTT
38694930 TAGGAACACAAGCTGAGCTACGAAGAATAATCGAATTTATCTTTTAGTTTCTT
1 TAGGAACACAAGCTGAGCTACGAAGAATAATCGAATTTATCTTTTAGTTTCTT
38694983 T
1 T
38694984 CCCTTTTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (53 bp):
TAGGAACACAAGCTGAGCTACGAAGAATAATCGAATTTATCTTTTAGTTTCTT
Found at i:38695646 original size:51 final size:51
Alignment explanation
Indices: 38695570--38695671 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
38695560 ATAAATAAAC
38695570 TGTTTTCTAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTT
1 TGTTTTCTAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTT
38695621 TGTTTTCTAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTT
1 TGTTTTCTAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTT
38695672 AGTCAAGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (51 bp):
TGTTTTCTAATAATGTCCTAAGAATAATATGATTATTCTTAAAAGATCCTT
Found at i:38696910 original size:13 final size:13
Alignment explanation
Indices: 38696892--38696916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38696882 ATAAACATTC
38696892 GGTTAGGATCCTT
1 GGTTAGGATCCTT
38696905 GGTTAGGATCCT
1 GGTTAGGATCCT
38696917 CACACATGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (13 bp):
GGTTAGGATCCTT
Found at i:38705745 original size:27 final size:27
Alignment explanation
Indices: 38705713--38705766 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
38705703 ATACTAATAA
*
38705713 AATATAATATCTTAATATTTTGATACT
1 AATATAATATCATAATATTTTGATACT
38705740 AATATAATATCATAATATTTTGATACT
1 AATATAATATCATAATATTTTGATACT
38705767 TATCTTCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (27 bp):
AATATAATATCATAATATTTTGATACT
Found at i:38708683 original size:28 final size:28
Alignment explanation
Indices: 38708651--38708736 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 28
38708641 CTTTAATCCC
* *
38708651 TAACGGATATTCCACCCAAGATAGTCTT
1 TAACGGACATTCCACTCAAGATAGTCTT
* *
38708679 TAAC-GAGCATTCCACTTAAGATAGTCCT
1 TAACGGA-CATTCCACTCAAGATAGTCTT
* * * *
38708707 TGATGGACATTCCATTGAAGATAGTCTT
1 TAACGGACATTCCACTCAAGATAGTCTT
38708735 TA
1 TA
38708737 GCGAACTTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
27 2 0.04
28 42 0.91
29 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (28 bp):
TAACGGACATTCCACTCAAGATAGTCTT
Found at i:38710137 original size:28 final size:28
Alignment explanation
Indices: 38710105--38710175 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
38710095 TACTTAATGG
38710105 AAAGGACA-CATTTGTAGCAACCTCTATT
1 AAAGGA-AGCATTTGTAGCAACCTCTATT
* * * *
38710133 AAAGGAAGCATTTGTGGCAATCTTTGTT
1 AAAGGAAGCATTTGTAGCAACCTCTATT
38710161 AAAGGAAAGC-TTTGT
1 AAAGG-AAGCATTTGT
38710176 GGCTATCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.03
28 32 0.86
29 4 0.11
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (28 bp):
AAAGGAAGCATTTGTAGCAACCTCTATT
Found at i:38710978 original size:18 final size:19
Alignment explanation
Indices: 38710957--38710994 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38710947 TTAGAGGTAG
38710957 AATAAGT-GGAGTA-ATGTA
1 AATAAGTAGGA-TATATGTA
38710975 AATAAGTAGGATATATGTA
1 AATAAGTAGGATATATGTA
38710994 A
1 A
38710995 TTGTAAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
AATAAGTAGGATATATGTA
Found at i:38711673 original size:33 final size:33
Alignment explanation
Indices: 38711636--38711732 Score: 90
Period size: 35 Copynumber: 2.8 Consensus size: 33
38711626 GTCAGGAAAC
* *
38711636 CATTTTCATGGTGTTGCTCC-AGAGCCTGTAAA
1 CATTTTCATGGTGTCGCTCCAAGAGCCAGTAAA
* *
38711668 TCA-TTTCTATAGTATCGCTCCATAGAGCCAGTAAA
1 -CATTTTC-ATGGTGTCGCTCCA-AGAGCCAGTAAA
*
38711703 CTATTTTCATGGTGTCGCTCCGTAGAGCCA
1 C-ATTTTCATGGTGTCGCTCC-AAGAGCCA
38711733 ATAGATTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
32 4 0.08
33 12 0.24
34 1 0.02
35 30 0.59
36 4 0.08
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (33 bp):
CATTTTCATGGTGTCGCTCCAAGAGCCAGTAAA
Found at i:38713798 original size:21 final size:19
Alignment explanation
Indices: 38713766--38713833 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
38713756 TGTCAATATC
38713766 TAATTATAAATATTTAATTA
1 TAATT-TAAATATTTAATTA
* *
38713786 TTATATTTAAATACTTAAATA
1 -TA-ATTTAAATATTTAATTA
*
38713807 TAATTTATATATTTTAATTA
1 TAATTTAAATA-TTTAATTA
38713827 -AATTTAA
1 TAATTTAA
38713834 TAAATAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 14 0.36
20 8 0.21
21 14 0.36
22 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATTTAAATATTTAATTA
Found at i:38713871 original size:29 final size:26
Alignment explanation
Indices: 38713839--38713901 Score: 65
Period size: 30 Copynumber: 2.2 Consensus size: 26
38713829 TTTAATAAAT
38713839 AAATAATATT-TATTATTTAAAAATATTTA
1 AAATAATATTATA-TA-TT-AAAATA-TTA
38713868 AAATTAATATTATATATTAAAATATTA
1 AAA-TAATATTATATATTAAAATATTA
38713895 ACAATAA
1 A-AATAA
38713902 GTTATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
27 7 0.23
28 8 0.26
29 5 0.16
30 9 0.29
31 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATAATATTATATATTAAAATATTA
Found at i:38727463 original size:68 final size:68
Alignment explanation
Indices: 38727354--38727493 Score: 253
Period size: 68 Copynumber: 2.1 Consensus size: 68
38727344 GTATAGGACC
*
38727354 TCTTTATAATGGTAGTTCTTGTATGTGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
1 TCTTTATAATGGTAGTTCTTGTATGAGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
38727419 ATG
66 ATG
* *
38727422 TCTTTATAATGGTAGTTCTTGTATGAGTTAATGATCAAATTGGTATGAATATGCTTTTGGAGTTT
1 TCTTTATAATGGTAGTTCTTGTATGAGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
38727487 ATG
66 ATG
38727490 TCTT
1 TCTT
38727494 GTTTGATGGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (68 bp):
TCTTTATAATGGTAGTTCTTGTATGAGTTAAGGATCAAATTGGCATGAATATGCTTTTGGAGTTT
ATG
Found at i:38728908 original size:51 final size:51
Alignment explanation
Indices: 38728839--38728946 Score: 182
Period size: 51 Copynumber: 2.1 Consensus size: 51
38728829 AATATTATTC
*
38728839 CAATATTTGATAGTACAAAATTAGTTGAAAGCT-TCAGAAGAGTTAATATAT
1 CAATATTTGATAGTACAAAATTAGTTGAAAGCTCT-AGAAGAGCTAATATAT
*
38728890 CAATATTTGGTAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAATATAT
1 CAATATTTGATAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAATATAT
38728941 CAATAT
1 CAATAT
38728947 CTAAAAATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
51 53 0.98
52 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (51 bp):
CAATATTTGATAGTACAAAATTAGTTGAAAGCTCTAGAAGAGCTAATATAT
Found at i:38732069 original size:26 final size:26
Alignment explanation
Indices: 38732011--38732080 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 26
38732001 ATTCATGGGC
*
38732011 AAATGACTGAAATACCCTCGATGGGTA
1 AAATGAC-GAAATACCCTCGAAGGGTA
38732038 AAATGATCGAAATACCCT-GAAGGGTA
1 AAATGA-CGAAATACCCTCGAAGGGTA
38732064 AAATGACCGAAATACCC
1 AAATGA-CGAAATACCC
38732081 CTATAATGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.57
27 16 0.40
28 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (26 bp):
AAATGACGAAATACCCTCGAAGGGTA
Found at i:38732091 original size:27 final size:26
Alignment explanation
Indices: 38732011--38732097 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 26
38732001 ATTCATGGGC
* **
38732011 AAATGACTGAAATACCCTCGATGGGTA
1 AAATGACCGAAATACCCT-GAAAGGTA
* *
38732038 AAATGATCGAAATACCCTGAAGGGTA
1 AAATGACCGAAATACCCTGAAAGGTA
*
38732064 AAATGACCGAAATACCCCT-ATAATGTA
1 AAATGACCGAAATA-CCCTGA-AAGGTA
38732091 AAATGAC
1 AAATGAC
38732098 TGTTATACTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.40
27 31 0.60
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (26 bp):
AAATGACCGAAATACCCTGAAAGGTA
Found at i:38732303 original size:26 final size:26
Alignment explanation
Indices: 38732274--38732348 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 26
38732264 TTGCCACATA
* *
38732274 TACTGTTACTGGTAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
*
38732300 TACTATTACTGGCAGCTTTGCTACGT
1 TACTATTACTGGCAGCTTTGCTGCGT
* *
38732326 CATTATTACTGGCAGCTTTGCTG
1 TACTATTACTGGCAGCTTTGCTG
38732349 TGATATTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGT
Found at i:38732496 original size:28 final size:28
Alignment explanation
Indices: 38732456--38732517 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
38732446 ACTACATTGT
38732456 ACTGTTACGGTATTAAGCTAAGGCCCAC
1 ACTGTTACGGTATTAAGCTAAGGCCCAC
* ** *
38732484 ACTGTTACTGTATTGGGTTAAGGCCCAC
1 ACTGTTACGGTATTAAGCTAAGGCCCAC
38732512 ACTGTT
1 ACTGTT
38732518 GCTGCATAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (28 bp):
ACTGTTACGGTATTAAGCTAAGGCCCAC
Found at i:38732529 original size:28 final size:28
Alignment explanation
Indices: 38732474--38732552 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
38732464 GGTATTAAGC
* *
38732474 TAAGGCCCACACTGTTACTGTATTGGGT
1 TAAGGCCCACACTGTTACTGCATAGGGT
*
38732502 TAAGGCCCACACTGTTGCTGCATAGGGT
1 TAAGGCCCACACTGTTACTGCATAGGGT
* * *
38732530 TCAGGCCCAGACTGCTACTGCAT
1 TAAGGCCCACACTGTTACTGCAT
38732553 GTTGTATACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (28 bp):
TAAGGCCCACACTGTTACTGCATAGGGT
Found at i:38737125 original size:34 final size:33
Alignment explanation
Indices: 38737052--38737163 Score: 122
Period size: 34 Copynumber: 3.4 Consensus size: 33
38737042 GATTTAGTGT
*
38737052 TATTTTTTAAAAATTAATTAAA-TTAGGGTTTA-
1 TATTTTTAAAAAATTAATTAAATTTA-GGTTTAG
*
38737084 -AGGTTTTAAATAAATTAATTAAATTTAGGTTTAG
1 TA-TTTTTAAA-AAATTAATTAAATTTAGGTTTAG
**
38737118 TATTTTTAAGAAAATTAATTAAATTTCTGTTTAG
1 TATTTTTAA-AAAATTAATTAAATTTAGGTTTAG
*
38737152 TTTTTTTAAAAA
1 TATTTTTAAAAA
38737164 TAATATTGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
31 1 0.01
32 6 0.09
33 21 0.31
34 38 0.56
35 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.49
Consensus pattern (33 bp):
TATTTTTAAAAAATTAATTAAATTTAGGTTTAG
Found at i:38737374 original size:126 final size:126
Alignment explanation
Indices: 38737224--38737869 Score: 1046
Period size: 126 Copynumber: 5.1 Consensus size: 126
38737214 GATTTTGATT
38737224 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* *
38737289 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTC
* * *
38737350 ATTTTCTTCAGTAGTTCCTGAAAAAATAATTTTGAGACGACGGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * * *
38737415 ACGCTTCAAGCAGGATACACTATCAACAAAATTACTGAAAAGAGCTCCCATGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTC
38737476 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
*
38737541 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGA-TGAAAAAAGCTCCCATGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCATGTGGACGCTC
* *
38737602 TTTTTCTACAGTAGTTCCTG-AAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * * * * *
38737666 ATGCTTCAAGAAGGATGCACTGTTAGCAAAATTACTGAAAATAGCTCCCACGTGGACACTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTC
*** *
38737727 TTTTTCTACAGTAGTTCCT-AAAAAGATAATTTTGAGAAGAAATTTCTGAAAAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAA-ATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAA
*
38737791 AATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTC
38737853 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
38737870 ATGTTTGGCC
Statistics
Matches: 484, Mismatches: 32, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
124 1 0.00
125 117 0.24
126 365 0.75
127 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTC
Found at i:38737800 original size:251 final size:252
Alignment explanation
Indices: 38737224--38737869 Score: 1055
Period size: 251 Copynumber: 2.6 Consensus size: 252
38737214 GATTTTGATT
38737224 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
* * *
38737289 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCACACGTGGACGCTCATTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTCTTTT
* *
38737354 TCTTCAGTAGTTCCTGAAAAAATAATTTTGAGACGACGGTTCTGAACAAATAGTGTCAAAAACGC
131 TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGC
* * *
38737419 TTCAAGCAGGATACACTATCAACAAAATTACTGAAAAGAGCTCCCATGTGGACGCTC
196 TTCAAGAAGGATACACTATCAACAAAATTACTGAAAAGAGCTCCCACGTGGACACTC
38737476 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
*
38737541 ACGCTTCAAGCAGGATGCACTATCAGCAAAATTGA-TGAAAAAAGCTCCCATGTGGACGCTCTTT
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCATGTGGACGCTCTTT
* * *
38737605 TTCTACAGTAGTTCCTG-AAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAATG
130 TTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACG
* * * * *
38737669 CTTCAAGAAGGATGCACTGTTAGCAAAATTACTGAAAATAGCTCCCACGTGGACACTC
195 CTTCAAGAAGGATACACTATCAACAAAATTACTGAAAAGAGCTCCCACGTGGACACTC
*** *
38737727 TTTTTCTACAGTAGTTCCT-AAAAAGATAATTTTGAGAAGAAATTTCTGAAAAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAA-ATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAA
*
38737791 AATGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTCTTT
65 AACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTCTTT
38737856 TTCTACAGTAGTTC
130 TTCTACAGTAGTTC
38737870 ATGTTTGGCC
Statistics
Matches: 368, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
250 6 0.02
251 222 0.60
252 139 0.38
253 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (252 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACGCTCTTTT
TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGC
TTCAAGAAGGATACACTATCAACAAAATTACTGAAAAGAGCTCCCACGTGGACACTC
Found at i:38740883 original size:24 final size:23
Alignment explanation
Indices: 38740827--38740883 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
38740817 AAGAACTTCT
38740827 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAATA
38740850 ATTTACTATT-AAAATATTAAAAATGA
1 ATTT--TATTAAAAATA-TAAAAAT-A
*
38740876 CTTTTATT
1 ATTTTATT
38740884 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 11 0.38
26 4 0.14
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAATA
Found at i:38743131 original size:30 final size:30
Alignment explanation
Indices: 38743077--38743141 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
38743067 ATTAATTAAA
*
38743077 GAGAGCTTTGAGAAATTTAAGGAGAAGTTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
**
38743107 GAGAGCTTTGAGAAATTTCGGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
*
38743137 TAGAG
1 GAGAG
38743142 TTTTTTGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.05, G:0.31, T:0.29
Consensus pattern (30 bp):
GAGAGCTTTGAGAAATTTAAGGAGAAATTT
Found at i:38743966 original size:22 final size:22
Alignment explanation
Indices: 38743938--38743989 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
38743928 TGGGCATCGA
*
38743938 AAATTGACCA-AATAAACCAATT
1 AAATTGAACATAA-AAACCAATT
* *
38743960 AAATTGAACATGAAAATCAATT
1 AAATTGAACATAAAAACCAATT
38743982 AAATTGAA
1 AAATTGAA
38743990 AAATCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.25
Consensus pattern (22 bp):
AAATTGAACATAAAAACCAATT
Found at i:38743992 original size:17 final size:17
Alignment explanation
Indices: 38743972--38744009 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
38743962 ATTGAACATG
*
38743972 AAAATC-AATTAAATTGA
1 AAAATCGAA-TAAACTGA
38743989 AAAATCGAATAAACTGA
1 AAAATCGAATAAACTGA
38744006 AAAA
1 AAAA
38744010 ATTCAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAATCGAATAAACTGA
Found at i:38746885 original size:19 final size:20
Alignment explanation
Indices: 38746863--38746921 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 20
38746853 ATACTTGCGT
38746863 ACAAAAG-GCATCCTAGTGC
1 ACAAAAGCGCATCCTAGTGC
*
38746882 AC-AAAGCGCATACT-G-GC
1 ACAAAAGCGCATCCTAGTGC
*
38746899 ACACAAAGTGCATCCTAGTGC
1 ACA-AAAGCGCATCCTAGTGC
38746920 AC
1 AC
38746922 GAAGCGTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 4 0.12
18 5 0.16
19 18 0.56
20 1 0.03
21 4 0.12
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.15
Consensus pattern (20 bp):
ACAAAAGCGCATCCTAGTGC
Found at i:38746949 original size:39 final size:38
Alignment explanation
Indices: 38746866--38746953 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
38746856 CTTGCGTACA
38746866 AAAG-GCATCCTAGTGCACAAAGCGCATACTGGCACAC
1 AAAGTGCATCCTAGTGCACAAAGCGCATACTGGCACAC
* * *
38746903 AAAGTGCATCCTAGTGCACGAAGCGTATATTTGGCACAC
1 AAAGTGCATCCTAGTGCACAAAGCGCATA-CTGGCACAC
* *
38746942 GAGGTGCATCCT
1 AAAGTGCATCCT
38746954 GAAAAATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 4 0.09
38 22 0.50
39 18 0.41
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (38 bp):
AAAGTGCATCCTAGTGCACAAAGCGCATACTGGCACAC
Found at i:38748119 original size:25 final size:25
Alignment explanation
Indices: 38748071--38748206 Score: 123
Period size: 25 Copynumber: 5.4 Consensus size: 25
38748061 CCACAAAAGG
** *
38748071 TTTTCCAGATAATACATCATATAGGC
1 TTTT-CAGATAATACGCCACATAGGC
* *
38748097 TTTTCAGATAATATGCAACATAGGC
1 TTTTCAGATAATACGCCACATAGGC
* * *
38748122 -TTTCTAGATAATACACCACATACGT
1 TTTTC-AGATAATACGCCACATAGGC
* * *
38748147 TTTTTAGATAACT-TGCCACAAAGGC
1 TTTTCAGATAA-TACGCCACATAGGC
*
38748172 TTTTCAGATAATACGCCACATAGTC
1 TTTTCAGATAATACGCCACATAGGC
38748197 TTTTCAGATA
1 TTTTCAGATA
38748207 GCTTACCACA
Statistics
Matches: 86, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
24 5 0.06
25 73 0.85
26 8 0.09
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (25 bp):
TTTTCAGATAATACGCCACATAGGC
Found at i:38748156 original size:50 final size:49
Alignment explanation
Indices: 38748050--38748221 Score: 150
Period size: 50 Copynumber: 3.4 Consensus size: 49
38748040 ACAGGCTTTC
* * * * * * *
38748050 CAGATGACTTGCCACAAAAGGTTTTCCAGATAATACATCATATAGGCTTTT
1 CAGATAACTTGCAAC-AAAGGCTTTCTAGATAATACACCACATA-GTTTTT
*
38748101 CAGATAA-TATGCAACATAGGCTTTCTAGATAATACACCACATACGTTTTT
1 CAGATAACT-TGCAACAAAGGCTTTCTAGATAATACACCACATA-GTTTTT
* * *
38748151 TAGATAACTTGCCACAAAGGCTTT-TCAGATAATACGCCACATAGTCTTTT
1 CAGATAACTTGCAACAAAGGCTTTCT-AGATAATACACCACATAGT-TTTT
* * *
38748201 CAGATAGCTTACCACAAAGGC
1 CAGATAACTTGCAACAAAGGC
38748222 ACTGCATAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
49 3 0.03
50 86 0.85
51 12 0.12
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (49 bp):
CAGATAACTTGCAACAAAGGCTTTCTAGATAATACACCACATAGTTTTT
Found at i:38748215 original size:25 final size:24
Alignment explanation
Indices: 38748136--38748216 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 24
38748126 TAGATAATAC
*
38748136 ACCACATACGT-TTTTTAGATAACTT
1 ACCACATA-GTCTTTTCAGAT-ACTT
* * * *
38748161 GCCACAAAGGCTTTTCAGATA-AT
1 ACCACATAGTCTTTTCAGATACTT
38748184 ACGCCACATAGTCTTTTCAGATAGCTT
1 A--CCACATAGTCTTTTCAGATA-CTT
38748211 ACCACA
1 ACCACA
38748217 AAGGCACTGC
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
23 1 0.02
24 2 0.05
25 37 0.88
27 2 0.05
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (24 bp):
ACCACATAGTCTTTTCAGATACTT
Found at i:38756079 original size:27 final size:29
Alignment explanation
Indices: 38756023--38756117 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 29
38756013 TTGCATCACG
* * * *
38756023 AAGGCATTTCTTTT-TCAGATATAGCTACA
1 AAGGC-TTTCTTTTGACAGAGATCGCCACA
* * *
38756052 AAGGCTTT-TTTT-ACGGAGATTGCGACA
1 AAGGCTTTCTTTTGACAGAGATCGCCACA
38756079 AAGGCTTTCTTTTGACAGAGATCGCCACA
1 AAGGCTTTCTTTTGACAGAGATCGCCACA
38756108 AAGGCATTTC
1 AAGGC-TTTC
38756118 ATTTCATAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 22 0.40
28 7 0.13
29 22 0.40
30 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (29 bp):
AAGGCTTTCTTTTGACAGAGATCGCCACA
Found at i:38756224 original size:32 final size:31
Alignment explanation
Indices: 38756188--38756297 Score: 91
Period size: 32 Copynumber: 3.5 Consensus size: 31
38756178 CCAAAGTTTA
38756188 GCCACAAAGGTTGTCCTTTACATCCAGTATTC
1 GCCACAAAGGTT-TCCTTTACATCCAGTATTC
* * ** *
38756220 GCCACAAGGGCTTTCCTGT-C-TAAAGT-TTT
1 GCCACAAAGG-TTTCCTTTACATCCAGTATTC
* * *
38756249 GCCACAAATGCTATCCTTTACATCCAGTACTC
1 GCCACAAA-GGTTTCCTTTACATCCAGTATTC
38756281 GCCACAAAGGCTTTCCT
1 GCCACAAAGG-TTTCCT
38756298 GTCCAAAGAT
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
29 15 0.26
30 6 0.11
31 6 0.11
32 28 0.49
33 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (31 bp):
GCCACAAAGGTTTCCTTTACATCCAGTATTC
Found at i:38756245 original size:61 final size:61
Alignment explanation
Indices: 38756180--38756381 Score: 235
Period size: 61 Copynumber: 3.3 Consensus size: 61
38756170 TTACCTTTCC
* * * *
38756180 AAAGTTTAGCCACAAAGGTTGTCCTTTACATCCAGTATTCGCCACAAGGGCTTTCCTGTCT
1 AAAGTTTAGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
* * *
38756241 AAAGTTTTGCCACAAATGCTATCCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCC
1 AAAGTTTAGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
* * * * * * *
38756302 AAAGATTTA-CCATAAAGACTATGCTTTATATCCATTACTCGCCAAAAAGGCTTTCCTATCT
1 AAAG-TTTAGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
* * *
38756363 AGAGTTTTGCCAAAAAGGC
1 AAAGTTTAGCCACAAAGGC
38756382 GTTCCTTAAC
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
60 3 0.03
61 112 0.95
62 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (61 bp):
AAAGTTTAGCCACAAAGGCTATCCTTTACATCCAGTACTCGCCACAAAGGCTTTCCTGTCT
Found at i:38756617 original size:53 final size:53
Alignment explanation
Indices: 38756504--38756645 Score: 169
Period size: 53 Copynumber: 2.7 Consensus size: 53
38756494 TAAATTTCCC
* * * * *
38756504 CACAAGATGCCATAACTCACTAGTTACAGTCTTACACTATATGGTCTTCTTCC
1 CACATGATGCCATAACTCACCAGTTACGGTCTTACACGATATGGTCTTCTTCA
*
38756557 CACATGATGCCATAAAC-CACCAGTTACGGTCTTACACGATATGGTCTTCTTTA
1 CACATGATGCCAT-AACTCACCAGTTACGGTCTTACACGATATGGTCTTCTTCA
* * ** *
38756610 TATATGATGTTATAACTCACCAATTACGGTCTTACA
1 CACATGATGCCATAACTCACCAGTTACGGTCTTACA
38756646 TGACATGGAC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 3 0.04
53 70 0.92
54 3 0.04
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (53 bp):
CACATGATGCCATAACTCACCAGTTACGGTCTTACACGATATGGTCTTCTTCA
Found at i:38763519 original size:14 final size:14
Alignment explanation
Indices: 38763502--38763528 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38763492 TTATCAGCTC
38763502 TTATTATTTTATTA
1 TTATTATTTTATTA
38763516 TTATTATTTTATT
1 TTATTATTTTATT
38763529 TTGAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:38765043 original size:14 final size:14
Alignment explanation
Indices: 38765026--38765052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38765016 TTATCAGCTC
38765026 TTATTATTTTATTA
1 TTATTATTTTATTA
38765040 TTATTATTTTATT
1 TTATTATTTTATT
38765053 TTGAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:38779269 original size:19 final size:19
Alignment explanation
Indices: 38779247--38779284 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38779237 TCAATCATCC
38779247 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
38779266 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
38779285 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:38791475 original size:43 final size:44
Alignment explanation
Indices: 38791348--38791476 Score: 131
Period size: 44 Copynumber: 3.0 Consensus size: 44
38791338 TTAGGATTCT
**
38791348 ATTATGTG-TTATCGTGTAAGACCACGTCTGGGATGTTGGCATCG
1 ATTATGTGATTA-CGTGTAAGACCACGTCTGGGACATTGGCATCG
* * *
38791392 ACT-TGTGACTTACGTGTAAGACC-CTATCTGGGACAATGGCATCG
1 ATTATGTGA-TTACGTGTAAGACCAC-GTCTGGGACATTGGCATCG
* **
38791436 -TTATGTGATTACATGTAAGACCACGTCTAAGACATTGGCAT
1 ATTATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCAT
38791477 TGTATGAAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
43 32 0.46
44 34 0.49
45 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (44 bp):
ATTATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCATCG
Found at i:38795584 original size:13 final size:14
Alignment explanation
Indices: 38795566--38795594 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38795556 AAAATTGCTT
38795566 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
38795579 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
38795593 AA
1 AA
38795595 GCCACTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:38797899 original size:30 final size:30
Alignment explanation
Indices: 38797863--38797925 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
38797853 AATTATTTTA
38797863 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
38797893 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
38797923 TTG
1 TTG
38797926 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:38802456 original size:51 final size:51
Alignment explanation
Indices: 38802398--38802583 Score: 222
Period size: 51 Copynumber: 3.7 Consensus size: 51
38802388 TGAACATGTT
* *
38802398 TGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATG
1 TGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGTCACGTG
* * *
38802449 TGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGTCACGTG
1 TGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA--TATTGGTCACGTG
*
38802500 TGTAGTACTATGTGAAGGCTACTACGTAG-A-CTG-TAAA-ACTTGATCACGTG
1 TGTAGTACTATGTGAAGGCTACTACGT-GTATC-GATAAATA-TTGGTCACGTG
*
38802550 TGTAGTACTATGTGAAGGCTACTACATGTATCGA
1 TGTAGTACTATGTGAAGGCTACTACGTGTATCGA
38802584 ATGATAATAG
Statistics
Matches: 116, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
49 1 0.01
50 42 0.36
51 71 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (51 bp):
TGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGTCACGTG
Found at i:38804096 original size:54 final size:54
Alignment explanation
Indices: 38803975--38804096 Score: 136
Period size: 54 Copynumber: 2.3 Consensus size: 54
38803965 TCCACCTGTA
* * * * * *
38803975 TAACTCACTGAGTAGGGTCACATGGCCGTGTCACAGGCCGTGTGCCAGACAAAG
1 TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCCAGACAAAG
* * * * * *
38804029 TAACTCTCTGACTTGCGACACACGGCCATGTCGCAGGCCGTGTGCTAGGCCATG
1 TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCCAGACAAAG
38804083 TAACTCACTGACTT
1 TAACTCACTGACTT
38804097 AAAACATTAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (54 bp):
TAACTCACTGACTTGCGACACACGGCCATGTCACAGGCCGTGTGCCAGACAAAG
Found at i:38806158 original size:23 final size:23
Alignment explanation
Indices: 38806113--38806158 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38806103 TGACATATTC
* **
38806113 TTTTATCTTTTATTTACTTAACT
1 TTTTATCTTTTAATTACCAAACT
*
38806136 TTTTTTCTTTTAATTACCAAACT
1 TTTTATCTTTTAATTACCAAACT
38806159 ACTACTTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATCTTTTAATTACCAAACT
Found at i:38810816 original size:18 final size:20
Alignment explanation
Indices: 38810785--38810823 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
38810775 TTAAAAATAA
38810785 ATTTTCTAAAAATATT-TTT
1 ATTTTCTAAAAATATTATTT
38810804 ATTTTCT-AAAATATTATTT
1 ATTTTCTAAAAATATTATTT
38810823 A
1 A
38810824 CCAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTCTAAAAATATTATTT
Found at i:38812647 original size:2 final size:2
Alignment explanation
Indices: 38812640--38812670 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38812630 ACACCACCAT
38812640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38812671 CTTTGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38815808 original size:3 final size:3
Alignment explanation
Indices: 38815802--38815830 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38815792 CCGCCGCCCT
38815802 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
38815831 TGCAAGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:38822368 original size:15 final size:17
Alignment explanation
Indices: 38822330--38822368 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
38822320 AAAAAATATT
38822330 AATTAAATTTCTACAAA
1 AATTAAATTTCTACAAA
38822347 AA-T-AATTT-TA-AAA
1 AATTAAATTTCTACAAA
38822360 AATTAAATT
1 AATTAAATT
38822369 CTAAGAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.25
14 3 0.15
15 9 0.45
16 1 0.05
17 2 0.10
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAATTTCTACAAA
Found at i:38826498 original size:23 final size:23
Alignment explanation
Indices: 38826472--38826517 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
38826462 TTTTAAACTC
38826472 AATCATTATGTTAGCCAAAGTTA
1 AATCATTATGTTAGCCAAAGTTA
38826495 AATCATTATGTTAGCCAAAGTTA
1 AATCATTATGTTAGCCAAAGTTA
38826518 TTTAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
AATCATTATGTTAGCCAAAGTTA
Found at i:38829199 original size:30 final size:30
Alignment explanation
Indices: 38829146--38829202 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
38829136 GGGGTAGGAT
* *
38829146 GGGAGCAAAAGTTATGGGGGGAAAGTGGGA
1 GGGAGCAAAAATTATGGGAGGAAAGTGGGA
* *
38829176 GGGAGTAAAAATTTTGGGAGGAAAGTG
1 GGGAGCAAAAATTATGGGAGGAAAGTG
38829203 AAGAAGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.46, T:0.18
Consensus pattern (30 bp):
GGGAGCAAAAATTATGGGAGGAAAGTGGGA
Found at i:38831136 original size:21 final size:21
Alignment explanation
Indices: 38831110--38831149 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38831100 TTACCATTAT
*
38831110 TGTTG-TAGTTGTTATTATTCA
1 TGTTGTTAGTTATT-TTATTCA
38831131 TGTTGTTAGTTATTTTATT
1 TGTTGTTAGTTATTTTATT
38831150 TATTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.62
Consensus pattern (21 bp):
TGTTGTTAGTTATTTTATTCA
Found at i:38832671 original size:19 final size:18
Alignment explanation
Indices: 38832642--38832678 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
38832632 TTTGTGACCC
38832642 TTCTTTTCTTTTCTTTTT
1 TTCTTTTCTTTTCTTTTT
38832660 TTCTTCTTCTTTTCTTTTT
1 TTCTT-TTCTTTTCTTTTT
38832679 GGGCCTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTCTTTTCTTTTCTTTTT
Found at i:38836224 original size:20 final size:20
Alignment explanation
Indices: 38836199--38836239 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
38836189 TCGGGGAAAA
38836199 GATAAAGTCGTGGACTAAAC
1 GATAAAGTCGTGGACTAAAC
38836219 GATAAAGTCGTGGACTAAAC
1 GATAAAGTCGTGGACTAAAC
38836239 G
1 G
38836240 GTCGTATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (20 bp):
GATAAAGTCGTGGACTAAAC
Found at i:38836538 original size:25 final size:25
Alignment explanation
Indices: 38836482--38836551 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
38836472 GGACTCACCA
* *
38836482 TAGCTCGTATGAGCTTATCGATTTG
1 TAGCTCGTAGGAGCTTACCGATTTG
* *
38836507 CACCTCGTAGGAGCTTACCGATATT-
1 TAGCTCGTAGGAGCTTACCGAT-TTG
*
38836532 TAGCTCGGAGGAGCTTACCG
1 TAGCTCGTAGGAGCTTACCG
38836552 TTTATCGTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (25 bp):
TAGCTCGTAGGAGCTTACCGATTTG
Found at i:38837146 original size:38 final size:38
Alignment explanation
Indices: 38837104--38837180 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
38837094 CATGACTTTG
*
38837104 TTTAAGTTTTGAAATTCCTTATGGTTCTAGAACATAAT
1 TTTAAGTTTTGAAATTCCTTATGATTCTAGAACATAAT
*
38837142 TTTAAGTTTTGAAATTCTTTATGATTCTAGAACATAAT
1 TTTAAGTTTTGAAATTCCTTATGATTCTAGAACATAAT
38837180 T
1 T
38837181 AATGCATTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (38 bp):
TTTAAGTTTTGAAATTCCTTATGATTCTAGAACATAAT
Found at i:38843655 original size:23 final size:23
Alignment explanation
Indices: 38843606--38843660 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
38843596 TTTTTGGAAA
* * *
38843606 ATTCTGCAAAGCCTTTGTGGCGC
1 ATTCTGTAAAGCCTTTGTAGCAC
* *
38843629 ATTCTGTAAAGTCTTTGTAGCAT
1 ATTCTGTAAAGCCTTTGTAGCAC
38843652 ATTCTGTAA
1 ATTCTGTAA
38843661 CACCCTTGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (23 bp):
ATTCTGTAAAGCCTTTGTAGCAC
Found at i:38849110 original size:20 final size:20
Alignment explanation
Indices: 38849085--38849134 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
38849075 TGGCTTTAAA
38849085 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
38849105 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
38849122 GTGGTAGTGGATT
1 TTGGTAGTGGATT
38849135 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:38853749 original size:20 final size:20
Alignment explanation
Indices: 38853724--38853773 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
38853714 TGGCTTTAAA
38853724 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
38853744 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
38853761 GTGGTAGTGGATT
1 TTGGTAGTGGATT
38853774 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:38859616 original size:25 final size:29
Alignment explanation
Indices: 38859584--38859668 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
38859574 ATATTTATAA
38859584 AAAGTCAAAGATATGGGTATC-AA-A-T-
1 AAAGTCAAAGATATGGGTATCAAATATTG
*
38859609 AAAGTCAAAGATATGTGTATCAAATATTGG
1 AAAGTCAAAGATATGGGTATCAAATATT-G
*
38859639 AAAGTCAAAGATATGGGTATCGAGATATTG
1 AAAGTCAAAGATATGGGTATC-AAATATTG
38859669 GCATAAGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 20 0.39
26 2 0.04
27 1 0.02
28 1 0.02
30 21 0.41
31 6 0.12
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (29 bp):
AAAGTCAAAGATATGGGTATCAAATATTG
Found at i:38859645 original size:30 final size:30
Alignment explanation
Indices: 38859584--38859669 Score: 110
Period size: 25 Copynumber: 3.0 Consensus size: 30
38859574 ATATTTATAA
38859584 AAAGTCAAAGATATGGGTATC-AA-A-T--
1 AAAGTCAAAGATATGGGTATCAAATATTGG
*
38859609 AAAGTCAAAGATATGTGTATCAAATATTGG
1 AAAGTCAAAGATATGGGTATCAAATATTGG
*
38859639 AAAGTCAAAGATATGGGTATCGAGATATTGG
1 AAAGTCAAAGATATGGGTATC-AAATATTGG
38859670 CATAAGAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
25 20 0.38
26 2 0.04
27 1 0.02
28 1 0.02
30 20 0.38
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (30 bp):
AAAGTCAAAGATATGGGTATCAAATATTGG
Found at i:38861879 original size:27 final size:27
Alignment explanation
Indices: 38861835--38861956 Score: 118
Period size: 27 Copynumber: 4.5 Consensus size: 27
38861825 ATTTGCCAAT
*
38861835 AAGGTTATTCTCTCAGAGTTCACCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* * **
38861862 AAGTTTATTCTTTTAGAGTTCGTCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* ***
38861889 AAGGTTATTCTTTCAAAGTTTGTCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* * *
38861916 AAGGCTATTCTTTTAGAGCTCACCACA
1 AAGGTTATTCTTTCAGAGTTCACCACA
* *
38861943 AAGGCTGTTCTTTC
1 AAGGTTATTCTTTC
38861957 CTAATGTGTT
Statistics
Matches: 77, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (27 bp):
AAGGTTATTCTTTCAGAGTTCACCACA
Found at i:38861943 original size:54 final size:54
Alignment explanation
Indices: 38861835--38861956 Score: 136
Period size: 54 Copynumber: 2.3 Consensus size: 54
38861825 ATTTGCCAAT
* * ** * **
38861835 AAGGTTATTCTCTCAGAGTTCACCACAAAGTTTATTCTTTTAGAGTTCGTCACA
1 AAGGTTATTCTTTCAAAGTTCACCACAAAGGCTATTCTTTTAGAGCTCACCACA
***
38861889 AAGGTTATTCTTTCAAAGTTTGTCACAAAGGCTATTCTTTTAGAGCTCACCACA
1 AAGGTTATTCTTTCAAAGTTCACCACAAAGGCTATTCTTTTAGAGCTCACCACA
* *
38861943 AAGGCTGTTCTTTC
1 AAGGTTATTCTTTC
38861957 CTAATGTGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (54 bp):
AAGGTTATTCTTTCAAAGTTCACCACAAAGGCTATTCTTTTAGAGCTCACCACA
Found at i:38867499 original size:28 final size:28
Alignment explanation
Indices: 38867440--38867497 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
38867430 TTTCCGAGCC
* *
38867440 TTAGGGTAAAAATGTAATTATGTAAAGT
1 TTAGGGGAAAAATGTAATTATGCAAAGT
* *
38867468 TTAGGGGAAAATTGTAATTTTGACAAAGT
1 TTAGGGGAAAAATGTAATTATG-CAAAGT
38867497 T
1 T
38867498 AGAGTCGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (28 bp):
TTAGGGGAAAAATGTAATTATGCAAAGT
Found at i:38867947 original size:50 final size:50
Alignment explanation
Indices: 38867836--38868084 Score: 300
Period size: 50 Copynumber: 4.8 Consensus size: 50
38867826 ATTTGGGTAA
* * *
38867836 AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC--GAG---ATG
** *
38867892 AGAGGTCCCATGTAAGGTCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
38867942 AGAGGTCCAATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
38867992 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
38868042 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
38868085 TGTTATGATC
Statistics
Matches: 170, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 95 0.56
51 34 0.20
53 3 0.02
55 2 0.01
56 36 0.21
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:38870347 original size:21 final size:21
Alignment explanation
Indices: 38870323--38870380 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
38870313 ATGCTAAACT
38870323 GAAGCCCATAAGGGTTGAACG
1 GAAGCCCATAAGGGTTGAACG
* * *
38870344 GAAGCTCAT-AGGAGCTGAATG
1 GAAGCCCATAAGG-GTTGAACG
*
38870365 GAAACCCATAAGGGTT
1 GAAGCCCATAAGGGTT
38870381 AAACAGAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 3 0.10
21 23 0.79
22 3 0.10
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (21 bp):
GAAGCCCATAAGGGTTGAACG
Found at i:38870389 original size:21 final size:20
Alignment explanation
Indices: 38870365--38870408 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
38870355 GAGCTGAATG
*
38870365 GAAACCCATAAGGGTTAAACA
1 GAAACCCATAAGAGTT-AACA
* *
38870386 GAAACTCATATGAGTTAACA
1 GAAACCCATAAGAGTTAACA
38870406 GAA
1 GAA
38870409 GCTCGTGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (20 bp):
GAAACCCATAAGAGTTAACA
Found at i:38870515 original size:24 final size:24
Alignment explanation
Indices: 38870488--38870575 Score: 158
Period size: 24 Copynumber: 3.7 Consensus size: 24
38870478 TAATTTGTCA
* *
38870488 TCAATTCATCCTTTGTATTTACTG
1 TCAATTCATCCTTTGCATTTACCG
38870512 TCAATTCATCCTTTGCATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
38870536 TCAATTCATCCTTTGCATTTACCG
1 TCAATTCATCCTTTGCATTTACCG
38870560 TCAATTCATCCTTTGC
1 TCAATTCATCCTTTGC
38870576 CATACAACGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.20, C:0.27, G:0.08, T:0.44
Consensus pattern (24 bp):
TCAATTCATCCTTTGCATTTACCG
Found at i:38873305 original size:27 final size:27
Alignment explanation
Indices: 38873254--38873305 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
38873244 TCCTTGTAAG
*
38873254 ATTCGCCACAGAGGCTATCCCTTCATA
1 ATTCGCCACAGAGGCTATCCATTCATA
*
38873281 ATTCGCCACTA-AGGCTATTCATTCA
1 ATTCGCCAC-AGAGGCTATCCATTCA
38873306 GAGTTTGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (27 bp):
ATTCGCCACAGAGGCTATCCATTCATA
Found at i:38875029 original size:26 final size:26
Alignment explanation
Indices: 38874994--38875054 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
38874984 CAATCAACTC
*
38874994 AAACTTAAGGGTCCTCCAACCCATTT
1 AAACTCAAGGGTCCTCCAACCCATTT
* * * *
38875020 AAGCTCAAGGGTCTTTCGACCCATTT
1 AAACTCAAGGGTCCTCCAACCCATTT
38875046 AAACTCAAG
1 AAACTCAAG
38875055 CTCGCTAGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (26 bp):
AAACTCAAGGGTCCTCCAACCCATTT
Found at i:38877711 original size:31 final size:32
Alignment explanation
Indices: 38877647--38877711 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
38877637 ACATAAAAGT
* * *
38877647 ATTAGAATAAATTTTAATATTTTATTAATCTA
1 ATTAGAATAAATTTTAATATCTCATTAACCTA
* *
38877679 ATTAGCATGAATTTTAA-ATCTCATTAACCTA
1 ATTAGAATAAATTTTAATATCTCATTAACCTA
38877710 AT
1 AT
38877712 CATTATTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (32 bp):
ATTAGAATAAATTTTAATATCTCATTAACCTA
Found at i:38882182 original size:17 final size:18
Alignment explanation
Indices: 38882149--38882184 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38882139 TAATGAATAC
*
38882149 ATAAAATAATATTATATA
1 ATAAAAGAATATTATATA
38882167 ATAAAAGAAT-TTATATA
1 ATAAAAGAATATTATATA
38882184 A
1 A
38882185 AAATTAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAGAATATTATATA
Found at i:38884482 original size:21 final size:21
Alignment explanation
Indices: 38884458--38884517 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
38884448 TAGATAAAAA
*
38884458 ATAAATATATATAA-AATTATC
1 ATAAATATAAATAATAA-TATC
*
38884479 ATAAAGATAAATAATAATATC
1 ATAAATATAAATAATAATATC
*
38884500 ATAAATATAAATATTAAT
1 ATAAATATAAATAATAAT
38884518 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATATAAATAATAATATC
Found at i:38888722 original size:17 final size:16
Alignment explanation
Indices: 38888702--38888738 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
38888692 TTGTTTTACA
38888702 TTTTTTCCTTGTTCTGT
1 TTTTTTCCTTGTTCT-T
*
38888719 TTTTTTCCTTTTTCTT
1 TTTTTTCCTTGTTCTT
38888735 TTTT
1 TTTT
38888739 ATTTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTTTCCTTGTTCTT
Found at i:38888777 original size:33 final size:32
Alignment explanation
Indices: 38888726--38888789 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
38888716 TGTTTTTTTC
*
38888726 CTTTTTCTTTTTTATTTGTTTTTCTTTATTTA
1 CTTTTTCTTTTTTATTTGTTTTCCTTTATTTA
38888758 CTTTTTCAGTTTTTT-TTTGTTTTCCTTTATTT
1 CTTTTTC--TTTTTTATTTGTTTTCCTTTATTT
38888790 GTTTATCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.24
33 16 0.55
34 6 0.21
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.77
Consensus pattern (32 bp):
CTTTTTCTTTTTTATTTGTTTTCCTTTATTTA
Found at i:38888781 original size:49 final size:50
Alignment explanation
Indices: 38888684--38888804 Score: 135
Period size: 49 Copynumber: 2.5 Consensus size: 50
38888674 TTTTCTGATT
* * *
38888684 TTTTTTATTTGTTTTACATTT-TTTCCTTGTTCTGTTTTTTTCCTTTTTC
1 TTTTTTATTTGTTTTTCATTTATTTACTTGTTCAGTTTTTTTCCTTTTTC
*
38888733 TTTTTTATTTGTTTTTC-TTTATTTACTTTTTCAGTTTTTTT--TTGTTT-
1 TTTTTTATTTGTTTTTCATTTATTTACTTGTTCAGTTTTTTTCCTT-TTTC
** *
38888780 TCCTTTATTTGTTTATCATTTATTT
1 TTTTTTATTTGTTTTTCATTTATTT
38888805 TATAATATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
47 16 0.26
48 13 0.21
49 33 0.53
ACGTcount: A:0.09, C:0.11, G:0.06, T:0.74
Consensus pattern (50 bp):
TTTTTTATTTGTTTTTCATTTATTTACTTGTTCAGTTTTTTTCCTTTTTC
Found at i:38888833 original size:22 final size:24
Alignment explanation
Indices: 38888800--38888855 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
38888790 GTTTATCATT
*
38888800 TATTTTATAATATTTTA-AATGT-A
1 TATTTTA-AATATTTTATAATATGA
38888823 TATTTTAAATATTTTATAATATGA
1 TATTTTAAATATTTTATAATATGA
38888847 T-TTTTAAAT
1 TATTTTAAAT
38888856 TTTAATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 9 0.30
23 19 0.63
24 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTTTAAATATTTTATAATATGA
Found at i:38888851 original size:23 final size:22
Alignment explanation
Indices: 38888800--38888890 Score: 70
Period size: 23 Copynumber: 4.3 Consensus size: 22
38888790 GTTTATCATT
*
38888800 TATTTTATAATATTTTAAATGTA
1 TATTTTA-AATATTTTAAATATA
38888823 TATTTTAAATATTTTATAATATGA
1 TATTTTAAATATTTTA-AATAT-A
38888847 T-TTTT-AA-ATTTT-AATAT-
1 TATTTTAAATATTTTAAATATA
* *
38888864 TA--TAAAATATTTAAAATATA
1 TATTTTAAATATTTTAAATATA
38888884 TTATTTT
1 -TATTTT
38888891 TAAAGACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
16 1 0.02
17 3 0.06
18 4 0.07
19 10 0.19
21 7 0.13
22 11 0.20
23 16 0.30
24 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTTAAATATTTTAAATATA
Found at i:38889028 original size:20 final size:19
Alignment explanation
Indices: 38888999--38889044 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
38888989 GAATATAATA
38888999 ATTTAAAAAATAATATTGT
1 ATTTAAAAAATAATATTGT
*
38889018 ATTTAATAAAATACTATT-T
1 ATTTAA-AAAATAATATTGT
38889037 -TTTAAAAA
1 ATTTAAAAA
38889045 TTTTAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 5 0.20
19 7 0.28
20 10 0.40
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTAAAAAATAATATTGT
Found at i:38889173 original size:9 final size:10
Alignment explanation
Indices: 38889152--38889199 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
38889142 TAAAATTCAA
38889152 AAAATATTAT
1 AAAATATTAT
38889162 AAAATATT-T
1 AAAATATTAT
*
38889171 AAAATATACATTT
1 AAAATAT---TAT
38889184 AAAATATTAT
1 AAAATATTAT
38889194 AAAATA
1 AAAATA
38889200 AATAATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 8 0.24
10 16 0.48
12 1 0.03
13 8 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATATTAT
Found at i:38889212 original size:10 final size:9
Alignment explanation
Indices: 38889192--38889289 Score: 54
Period size: 10 Copynumber: 10.2 Consensus size: 9
38889182 TTAAAATATT
*
38889192 ATAAAATAA
1 ATAAAAAAA
38889201 ATAATAAAAA
1 ATAA-AAAAA
38889211 ATAAAGAAAA
1 ATAAA-AAAA
*
38889221 ACAAAAAAA
1 ATAAAAAAA
*
38889230 ATCAGAAAAA
1 AT-AAAAAAA
**
38889240 GGACAAAAAA
1 ATA-AAAAAA
* *
38889250 A-ACAGAAA
1 ATAAAAAAA
38889258 ATGAAAAAAA
1 AT-AAAAAAA
*
38889268 ATGAGAAACAA
1 AT-A-AAAAAA
38889279 ATAAAAAAA
1 ATAAAAAAA
38889288 AT
1 AT
38889290 CAGAAAAAGG
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
8 5 0.07
9 19 0.28
10 37 0.54
11 7 0.10
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:38889247 original size:20 final size:19
Alignment explanation
Indices: 38889223--38889300 Score: 86
Period size: 20 Copynumber: 4.1 Consensus size: 19
38889213 AAAGAAAAAC
38889223 AAAAAAAATCAGAAAAAGG
1 AAAAAAAATCAGAAAAAGG
* *
38889242 ACAAAAAAAACAG-AAAATG
1 A-AAAAAAATCAGAAAAAGG
* **
38889261 AAAAAAAATGAGAAACAAAT
1 AAAAAAAATCAGAAA-AAGG
38889281 AAAAAAAATCAGAAAAAGG
1 AAAAAAAATCAGAAAAAGG
38889300 A
1 A
38889301 TAGCAGCAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
18 9 0.19
19 12 0.26
20 26 0.55
ACGTcount: A:0.74, C:0.06, G:0.13, T:0.06
Consensus pattern (19 bp):
AAAAAAAATCAGAAAAAGG
Found at i:38889257 original size:38 final size:37
Alignment explanation
Indices: 38889206--38889297 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 37
38889196 AATAAATAAT
38889206 AAAAAATAA-AGAAAAACAAAAAAAATCAGAAA-AAGGAC
1 AAAAAA-AACAGAAAAACAAAAAAAATCAGAAACAA--AC
** * *
38889244 AAAAAAAACAGAAAATGAAAAAAAATGAGAAACAAAT
1 AAAAAAAACAGAAAAACAAAAAAAATCAGAAACAAAC
38889281 AAAAAAAATCAGAAAAA
1 AAAAAAAA-CAGAAAAA
38889298 GGATAGCAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
37 11 0.24
38 33 0.72
39 2 0.04
ACGTcount: A:0.77, C:0.07, G:0.10, T:0.07
Consensus pattern (37 bp):
AAAAAAAACAGAAAAACAAAAAAAATCAGAAACAAAC
Found at i:38893536 original size:7 final size:6
Alignment explanation
Indices: 38893512--38893554 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
38893502 ATTTTTCATT
*
38893512 TTTTATA TTTTAA TTTTAA TGTTTAA TTTGATA TTTTAA TTTT
1 TTTTA-A TTTTAA TTTTAA T-TTTAA TTTTA-A TTTTAA TTTT
38893555 GTATTCGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 16 0.50
7 16 0.50
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:38893536 original size:13 final size:13
Alignment explanation
Indices: 38893512--38893559 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
38893502 ATTTTTCATT
38893512 TTTTATATTTTAA
1 TTTTATATTTTAA
38893525 TTTTA-ATGTTTAA
1 TTTTATAT-TTTAA
*
38893538 TTTGATATTTTAA
1 TTTTATATTTTAA
*
38893551 TTTTGTATT
1 TTTTATATT
38893560 CGTGGTTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 2 0.07
13 26 0.87
14 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (13 bp):
TTTTATATTTTAA
Found at i:38897034 original size:20 final size:21
Alignment explanation
Indices: 38896986--38897035 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
38896976 GGTAGTAGTT
38896986 TAAATTTTT-ATAACATTTAA
1 TAAATTTTTAATAACATTTAA
*
38897006 TAAA-ATTTAATAAC--TTATA
1 TAAATTTTTAATAACATTTA-A
38897025 TAAATTTTTAA
1 TAAATTTTTAA
38897036 GAAAATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.12
19 8 0.32
20 14 0.56
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATTTTTAATAACATTTAA
Found at i:38897418 original size:18 final size:18
Alignment explanation
Indices: 38897385--38897437 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
38897375 TCAATTAGTT
38897385 TTTTTATATTTTTTTATTAA
1 TTTTTATA--TTTTTATTAA
*
38897405 TTTTTATATTTTTA-TCA
1 TTTTTATATTTTTATTAA
*
38897422 TTTTAATTATTTTTAT
1 TTTTTA-TATTTTTAT
38897438 ATAAGTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 7 0.24
18 14 0.48
20 8 0.28
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATATTTTTATTAA
Found at i:38897521 original size:10 final size:10
Alignment explanation
Indices: 38897506--38897618 Score: 52
Period size: 10 Copynumber: 12.0 Consensus size: 10
38897496 GAACATATTA
38897506 ATAATATTTT
1 ATAATATTTT
38897516 ATAATA--TT
1 ATAATATTTT
38897524 -TAATAGTTTT
1 ATAATA-TTTT
38897534 ATAAT-TTATT
1 ATAATATT-TT
38897544 A-AA-ATTTT
1 ATAATATTTT
* *
38897552 ATGATATTTG
1 ATAATATTTT
*
38897562 ATCAT-TTTT
1 ATAATATTTT
38897571 ATAGAT-TTTCT
1 ATA-ATATTT-T
*
38897582 ATAA-ATTTC
1 ATAATATTTT
*
38897591 A-AA-ATTGT
1 ATAATATTTT
38897599 ATAATATTTT
1 ATAATATTTT
38897609 AATAAT-TTTT
1 -ATAATATTTT
38897619 GGGCTAAAGT
Statistics
Matches: 80, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
7 5 0.06
8 11 0.14
9 15 0.19
10 36 0.45
11 13 0.16
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (10 bp):
ATAATATTTT
Found at i:38897535 original size:18 final size:17
Alignment explanation
Indices: 38897507--38897560 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
38897497 AACATATTAA
38897507 TAATATTTTATAATATT
1 TAATATTTTATAATATT
*
38897524 TAATAGTTTTATAATTTAT
1 TAATA-TTTTATAATAT-T
* *
38897543 TAAAATTTTATGATATT
1 TAATATTTTATAATATT
38897560 T
1 T
38897561 GATCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.23
18 19 0.61
19 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TAATATTTTATAATATT
Found at i:38897682 original size:21 final size:20
Alignment explanation
Indices: 38897637--38897682 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
38897627 GTTTTAGAAT
* *
38897637 AATTTTAATATTTTTATTTT
1 AATTTTAATATTTTTATATA
*
38897657 CATTTTAATTATTTTTATATA
1 AATTTTAA-TATTTTTATATA
38897678 AATTT
1 AATTT
38897683 CTATAATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTTTAATATTTTTATATA
Found at i:38899582 original size:5 final size:5
Alignment explanation
Indices: 38899565--38899608 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
38899555 TAAATTAAAC
*
38899565 CATAT CA-ATT CATAT CATAT CATAT CAGAT CATAT CATAT CATA
1 CATAT CATA-T CATAT CATAT CATAT CATAT CATAT CATAT CATA
38899609 CAAAATCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 1 0.03
5 33 0.94
6 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.36
Consensus pattern (5 bp):
CATAT
Found at i:38900335 original size:30 final size:28
Alignment explanation
Indices: 38900294--38900359 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 28
38900284 TGCATGATTT
* *
38900294 CACATGACCGTGTGCCCCGCACGGCCTAC
1 CACACGACCGTGTGCCCCACA-GGCCTAC
*
38900323 CTACACGACCGTGTGCTCCACAGGCCTAC
1 C-ACACGACCGTGTGCCCCACAGGCCTAC
38900352 CACACGAC
1 CACACGAC
38900360 TATGTGATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.21
29 9 0.27
30 17 0.52
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.14
Consensus pattern (28 bp):
CACACGACCGTGTGCCCCACAGGCCTAC
Found at i:38900380 original size:29 final size:29
Alignment explanation
Indices: 38900313--38900384 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
38900303 GTGTGCCCCG
* *
38900313 CACGGCCTACCTACACGACCGTGTGCTCCA
1 CACGGCCTACC-ACACGACCATGTGATCCA
* *
38900343 CA-GGCCTACCACACGACTATGTGATGCA
1 CACGGCCTACCACACGACCATGTGATCCA
*
38900371 CACGGTCTACCACA
1 CACGGCCTACCACA
38900385 TGGCCTGGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.44
29 18 0.50
30 2 0.06
ACGTcount: A:0.25, C:0.39, G:0.19, T:0.17
Consensus pattern (29 bp):
CACGGCCTACCACACGACCATGTGATCCA
Found at i:38901541 original size:18 final size:18
Alignment explanation
Indices: 38901514--38901550 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38901504 TATAGTTTGA
* *
38901514 TATTCGAGTTATTTGAAT
1 TATTCAAGTTATTCGAAT
38901532 TATTCAAGTTATTCGAAT
1 TATTCAAGTTATTCGAAT
38901550 T
1 T
38901551 CGAAAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (18 bp):
TATTCAAGTTATTCGAAT
Found at i:38905896 original size:51 final size:51
Alignment explanation
Indices: 38905820--38906034 Score: 340
Period size: 51 Copynumber: 4.2 Consensus size: 51
38905810 ACTTCTGATC
* *
38905820 AGTGACAAGTGATAAGTAGTAGCTTCAGCTGCACTTATCTGATCAATGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
38905871 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTATCTGATTAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
38905922 AGTGACAAGTGATAAGTAGTAGCTTTAGCTACCCTTATTTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
38905973 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
38906024 AGTGATAAGTG
1 AGTGACAAGTG
38906035 GTAGCTTTAA
Statistics
Matches: 152, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 152 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:38905921 original size:44 final size:46
Alignment explanation
Indices: 38905813--38906059 Score: 250
Period size: 51 Copynumber: 5.1 Consensus size: 46
38905803 TTTGAGTACT
* *
38905813 TCTGAT-C-AGTGACAAGTGATAAGTAGTAGCTTCAGCTGCACTTA
1 TCTGATACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
* *
38905857 TCTGATCAATGACAAGTGACAAGTGATAAGTAGTAGCTTCAGCTACGCTTA
1 TCTG----AT-ACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
*
38905908 TCTGATTAGTGACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACCCTTA
1 TCTG---A-T-ACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
* *
38905959 TTTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTG---A-T-ACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
* *
38906010 TCTGAT-C-AGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTA
1 TCTGATACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
38906054 TCTGAT
1 TCTGAT
38906060 CAGTGAAGTG
Statistics
Matches: 182, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
44 46 0.25
45 1 0.01
47 1 0.01
48 3 0.02
50 2 0.01
51 129 0.71
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (46 bp):
TCTGATACAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
Found at i:38906060 original size:44 final size:44
Alignment explanation
Indices: 38905973--38906065 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
38905963 ATCAGTGACA
*
38905973 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTATCTGATC
38906017 AGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTATCTGATC
1 AGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTATCTGATC
38906061 AGTGA
1 AGTGA
38906066 AGTGCTATGG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAACTACACTTATCTGATC
Found at i:38909002 original size:27 final size:27
Alignment explanation
Indices: 38908972--38909027 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
38908962 AGAAACTAAA
*
38908972 AACAAA-CATTCAACTAAAAAGAATGAT
1 AACAAATCATTCAACTAAAAA-AATCAT
38908999 AACAAATCATTCAACTAAAAAAATCAT
1 AACAAATCATTCAACTAAAAAAATCAT
38909026 AA
1 AA
38909028 AACGACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.61, C:0.16, G:0.04, T:0.20
Consensus pattern (27 bp):
AACAAATCATTCAACTAAAAAAATCAT
Found at i:38913903 original size:14 final size:15
Alignment explanation
Indices: 38913874--38913926 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
38913864 TATAAACAAT
38913874 ACAAAAATATTAAAA
1 ACAAAAATATTAAAA
38913889 ACAAAAATATTAAAA
1 ACAAAAATATTAAAA
* *
38913904 TAAAAAAATA-AAAAA
1 -ACAAAAATATTAAAA
*
38913919 ATAAAAAT
1 ACAAAAAT
38913927 TACAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.21
15 19 0.56
16 8 0.24
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (15 bp):
ACAAAAATATTAAAA
Found at i:38913908 original size:28 final size:26
Alignment explanation
Indices: 38913884--38913943 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
38913874 ACAAAAATAT
*
38913884 TAAAAACAA-AAATATTAAAATAAAAAAA
1 TAAAAA-AATAAAAATTAAAAT--AAAAA
*
38913912 TAAAAAAATAAAAATTACAATAAAAA
1 TAAAAAAATAAAAATTAAAATAAAAA
38913938 TAAAAA
1 TAAAAA
38913944 TATTGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 11 0.38
27 2 0.07
28 16 0.55
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.18
Consensus pattern (26 bp):
TAAAAAAATAAAAATTAAAATAAAAA
Found at i:38913909 original size:6 final size:6
Alignment explanation
Indices: 38913884--38913945 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
38913874 ACAAAAATAT
* * * *
38913884 TAAAAA CAAAAA TATTAAAA TAAAAA -AATAA -AAAAA TAAAAA TTACAA
1 TAAAAA TAAAAA TA--AAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
38913932 TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TA
38913946 TTGTAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 8 0.18
6 31 0.69
8 6 0.13
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:38913910 original size:16 final size:16
Alignment explanation
Indices: 38913871--38913925 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
38913861 AATTATAAAC
*
38913871 AATACAAAAATATTAA
1 AATAAAAAAATATTAA
*
38913887 AA-ACAAAAATATTAA
1 AATAAAAAAATATTAA
**
38913902 AATAAAAAAATAAAAA
1 AATAAAAAAATATTAA
38913918 AATAAAAA
1 AATAAAAA
38913926 TTACAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
15 15 0.43
16 20 0.57
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (16 bp):
AATAAAAAAATATTAA
Found at i:38913943 original size:7 final size:8
Alignment explanation
Indices: 38913900--38913925 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
38913890 CAAAAATATT
38913900 AAAATAAA
1 AAAATAAA
38913908 AAAATAAA
1 AAAATAAA
38913916 AAAATAAA
1 AAAATAAA
38913924 AA
1 AA
38913926 TTACAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:38913965 original size:19 final size:17
Alignment explanation
Indices: 38913876--38913971 Score: 55
Period size: 18 Copynumber: 5.8 Consensus size: 17
38913866 TAAACAATAC
*
38913876 AAAAATA-TT-AAAAAC
1 AAAAATATTTAAAAAAT
38913891 AAAAATA-TTAAAATAA-
1 AAAAATATTTAAAA-AAT
38913907 AAAAATA---AAAAAAT
1 AAAAATATTTAAAAAAT
**
38913921 AAAAAT-TACAATAAAAAT
1 AAAAATAT-TTA-AAAAAT
38913939 AAAAATATTGTAAAAAAT
1 AAAAATATT-TAAAAAAT
*
38913957 GAAATATATTTAAAA
1 -AAAAATATTTAAAA
38913972 GCTATAGAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 19
0.75 0.03 0.21
Matches are distributed among these distances:
13 2 0.03
14 10 0.15
15 9 0.13
16 10 0.15
17 3 0.04
18 23 0.34
19 10 0.15
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATATTTAAAAAAT
Found at i:38913997 original size:20 final size:18
Alignment explanation
Indices: 38913974--38914047 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
38913964 ATTTAAAAGC
38913974 TATAGAAAATTATTAAAATT
1 TATA-AAAA-TATTAAAATT
*
38913994 TATATAAAATATAAAAATAT
1 TATA-AAAATATTAAAAT-T
38914014 TATAAAAAGTA-TAAAA-T
1 TATAAAAA-TATTAAAATT
*
38914031 TATAAAACAAATTAAAA
1 TATAAAA-ATATTAAAA
38914048 ATATATGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
17 9 0.20
18 6 0.13
19 16 0.35
20 15 0.33
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (18 bp):
TATAAAAATATTAAAATT
Found at i:38914020 original size:29 final size:26
Alignment explanation
Indices: 38913974--38914066 Score: 73
Period size: 29 Copynumber: 3.3 Consensus size: 26
38913964 ATTTAAAAGC
*
38913974 TATAGAAAATTATTAAAATTTATATAAAA
1 TATAAAAAATTA-TAAAA--TATATAAAA
38914003 TATAAAAATATTATAAAA-AGTATAAAA
1 TATAAAAA-ATTATAAAATA-TATAAAA
38914030 TTATAAAACAAATTA-AAAATATATGAAAA
1 -TAT-AAA-AAATTATAAAATATAT-AAAA
38914059 TTATAAAA
1 -TATAAAA
38914067 CTAATATTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
26 1 0.02
27 8 0.14
28 13 0.23
29 28 0.50
30 6 0.11
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (26 bp):
TATAAAAAATTATAAAATATATAAAA
Found at i:38914067 original size:29 final size:28
Alignment explanation
Indices: 38913985--38914067 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 28
38913975 ATAGAAAATT
* *
38913985 ATTAAAATTTATATAAAA-TATAAAA-AT
1 ATTAAAA-ATATATAAAATTATAAAACAA
38914012 ATTATAAAA-AGTATAAAATTATAAAACAA
1 ATTA-AAAATA-TATAAAATTATAAAACAA
38914041 ATTAAAAATATATGAAAATTATAAAAC
1 ATTAAAAATATAT-AAAATTATAAAAC
38914068 TAATATTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
26 1 0.02
27 11 0.23
28 17 0.35
29 19 0.40
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (28 bp):
ATTAAAAATATATAAAATTATAAAACAA
Found at i:38929101 original size:7 final size:7
Alignment explanation
Indices: 38929068--38929126 Score: 59
Period size: 7 Copynumber: 8.1 Consensus size: 7
38929058 ATTAAATAAA
38929068 ATAAAAT
1 ATAAAAT
*
38929075 AAAATAAT
1 ATAA-AAT
38929083 A-AAAACT
1 ATAAAA-T
38929090 ATAAAAT
1 ATAAAAT
38929097 AT-AAAT
1 ATAAAAT
38929103 ATAAAACT
1 ATAAAA-T
38929111 AATAAAAT
1 -ATAAAAT
38929119 ATAAAAT
1 ATAAAAT
38929126 A
1 A
38929127 AAACAAAGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
6 8 0.18
7 21 0.47
8 10 0.22
9 6 0.13
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (7 bp):
ATAAAAT
Found at i:38929121 original size:29 final size:29
Alignment explanation
Indices: 38929068--38929126 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
38929058 ATTAAATAAA
38929068 ATAAAATAAAATAATAAAAACTATAAAAT
1 ATAAAATAAAATAATAAAAACTATAAAAT
38929097 ATAAATATAAAACTAAT-AAAA-TATAAAAT
1 ATAAA-ATAAAA-TAATAAAAACTATAAAAT
38929126 A
1 A
38929127 AAACAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.50
30 10 0.36
31 4 0.14
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (29 bp):
ATAAAATAAAATAATAAAAACTATAAAAT
Found at i:38929138 original size:22 final size:22
Alignment explanation
Indices: 38929066--38929139 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
38929056 TTATTAAATA
38929066 AAATAAAATA-AAATAATAAAA-
1 AAATAAAATATAAAT-ATAAAAC
*
38929087 ACTATAAAATATAAATATAAAAC
1 A-AATAAAATATAAATATAAAAC
*
38929110 TAATAAAATATAAA-ATAAAAC
1 AAATAAAATATAAATATAAAAC
38929131 AAAGTAAAA
1 AAA-TAAAA
38929140 ATAGCTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
21 10 0.22
22 31 0.69
23 4 0.09
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.22
Consensus pattern (22 bp):
AAATAAAATATAAATATAAAAC
Found at i:38930113 original size:22 final size:21
Alignment explanation
Indices: 38930071--38930114 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
38930061 CACCAATATA
*
38930071 TATTTTTATTTTTAATCTCAT
1 TATTTTTATTTTTAATATCAT
* *
38930092 TATTTTTTTTATTTCATATCAT
1 TATTTTTATT-TTTAATATCAT
38930114 T
1 T
38930115 TTAATAGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTTATTTTTAATATCAT
Found at i:38930319 original size:13 final size:13
Alignment explanation
Indices: 38930303--38930353 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
38930293 TCGAACCCCA
*
38930303 AACCTTAACCATG
1 AACCTAAACCATG
38930316 AACCCTAAACC-TG
1 AA-CCTAAACCATG
38930329 AACCTCAAACCATG
1 AACCT-AAACCATG
38930343 AACCTCAAACC
1 AACCT-AAACC
38930354 CAAGGTTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 3 0.09
13 11 0.32
14 20 0.59
ACGTcount: A:0.41, C:0.37, G:0.06, T:0.16
Consensus pattern (13 bp):
AACCTAAACCATG
Found at i:38930320 original size:20 final size:20
Alignment explanation
Indices: 38930295--38930332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38930285 TTTTTACCTC
*
38930295 GAACCCCAAACCTTAACCAT
1 GAACCCCAAACCTGAACCAT
*
38930315 GAACCCTAAACCTGAACC
1 GAACCCCAAACCTGAACC
38930333 TCAAACCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.39, G:0.08, T:0.13
Consensus pattern (20 bp):
GAACCCCAAACCTGAACCAT
Found at i:38930347 original size:14 final size:14
Alignment explanation
Indices: 38930309--38930353 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
38930299 CCCAAACCTT
38930309 AACCATGAACC-CTA
1 AACCATGAACCTC-A
38930323 AACC-TGAACCTCA
1 AACCATGAACCTCA
38930336 AACCATGAACCTCA
1 AACCATGAACCTCA
38930350 AACC
1 AACC
38930354 CAAGGTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.42, C:0.38, G:0.07, T:0.13
Consensus pattern (14 bp):
AACCATGAACCTCA
Done.