Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 114 of 161
Found at i:36225180 original size:30 final size:30
Alignment explanation
Indices: 36225029--36225340 Score: 138
Period size: 30 Copynumber: 10.5 Consensus size: 30
36225019 ACAGCTGAAG
* * *
36225029 CTATCCTTTTTCATAATTTGATGGTCGTCA
1 CTATCCCTTTTCATTATTCGATGGTCGTCA
* * * * * *
36225059 CCATCCCTCTCCATTGTTCGATGGTCATCC
1 CTATCCCTTTTCATTATTCGATGGTCGTCA
* * * * * * *
36225089 CCATCCATTTTTAATAATTTGATAGTCG-AA
1 CTATCC-CTTTTCATTATTCGATGGTCGTCA
* * *
36225119 GCTATCCCTTTTCA-TAGTTCAATGATAGTCA
1 -CTATCCCTTTTCATTA-TTCGATGGTCGTCA
36225150 CTATCCCTTTTCATTATTCGATGGTCGTCA
1 CTATCCCTTTTCATTATTCGATGGTCGTCA
* * * * * * * *
36225180 CCATCCATTTTAATAATTTGATAGCCG-AA
1 CTATCCCTTTTCATTATTCGATGGTCGTCA
* *
36225209 GTTATCCCTTTTCA-TAGTCGATGGTCGTCA
1 -CTATCCCTTTTCATTATTCGATGGTCGTCA
* * *
36225239 CTATCCCTTTCCATTGTT-GATTGTCGTCA
1 CTATCCCTTTTCATTATTCGATGGTCGTCA
* * * * *
36225268 CCATCCCTTTTCA-TAATCGATAGCCG-AA
1 CTATCCCTTTTCATTATTCGATGGTCGTCA
* * **
36225296 GCTATCCCTTTT--TGTATTCGATAGCCGAAA
1 -CTATCCCTTTTCAT-TATTCGATGGTCGTCA
36225326 CTATCCCTTTTCATT
1 CTATCCCTTTTCATT
36225341 TTTCAATGAC
Statistics
Matches: 202, Mismatches: 65, Indels: 30
0.68 0.22 0.10
Matches are distributed among these distances:
28 3 0.01
29 81 0.40
30 97 0.48
31 21 0.10
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (30 bp):
CTATCCCTTTTCATTATTCGATGGTCGTCA
Found at i:36225264 original size:29 final size:29
Alignment explanation
Indices: 36225211--36225288 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
36225201 TAGCCGAAGT
*
36225211 TATCCCTTTTCATAGTCGATGGTCGTCAC
1 TATCCCTTTCCATAGTCGATGGTCGTCAC
* * *
36225240 TATCCCTTTCCATTGTTGATTGTCGTCAC
1 TATCCCTTTCCATAGTCGATGGTCGTCAC
* * *
36225269 CATCCCTTTTCATAATCGAT
1 TATCCCTTTCCATAGTCGAT
36225289 AGCCGAAGCT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.41
Consensus pattern (29 bp):
TATCCCTTTCCATAGTCGATGGTCGTCAC
Found at i:36225302 original size:29 final size:29
Alignment explanation
Indices: 36225270--36225339 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
36225260 TGTCGTCACC
*
36225270 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAACT
** *
36225299 ATCCCTTTTTGTATTCGATAGCCGAAACT
1 ATCCCTTTTCATAATCGATAGCCGAAACT
36225328 ATCCCTTTTCAT
1 ATCCCTTTTCAT
36225340 TTTTCAATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.37
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCGAAACT
Found at i:36227432 original size:30 final size:30
Alignment explanation
Indices: 36227381--36227734 Score: 183
Period size: 30 Copynumber: 11.9 Consensus size: 30
36227371 TTTTTTGTAA
* **
36227381 TTCGATAACCGAAGTTATCCCTTTTCATAG
1 TTCGATAGCCGAAGCCATCCCTTTTCATAG
* * *
36227411 TTCAATAGCCAAAGCCATCCCTTTTCATAA
1 TTCGATAGCCGAAGCCATCCCTTTTCATAG
* *
36227441 TTTGATAGCCGAAGCTATCCCTTTTCATAG
1 TTCGATAGCCGAAGCCATCCCTTTTCATAG
* * * * *
36227471 TTCAATGGTCGTCA-CCATCCCTTTTCATAA
1 TTCGATAGCCG-AAGCCATCCCTTTTCATAG
* * * *
36227501 TTTGATAGTCGAAGCTATTCCTTTTCATAG
1 TTCGATAGCCGAAGCCATCCCTTTTCATAG
* * *
36227531 TTCGATGGTCGTCA-CCATCCCTTTTCATTA-
1 TTCGATAGCCG-AAGCCATCCCTTTTCA-TAG
* * *
36227561 TTCGATGGTC-ATCA-CCATCCCTTTTCATAA
1 TTCGATAGCCGA--AGCCATCCCTTTTCATAG
* *
36227591 TTGGATAGCCGAAGCTATCCCTTTTCATAG
1 TTCGATAGCCGAAGCCATCCCTTTTCATAG
* * * * *
36227621 -TCGATGGTCGTTA-CCATCCTTTTTCATTG
1 TTCGATAGCCG-AAGCCATCCCTTTTCATAG
* *
36227650 TT-GATGGTC-ATCA-CCATCCCTTTTCATA-
1 TTCGATAGCCGA--AGCCATCCCTTTTCATAG
* * * * * *
36227678 ATCAATAGTCGGAGCTATCCTTTTTCATA-
1 TTCGATAGCCGAAGCCATCCCTTTTCATAG
* * *
36227707 TTCGATAGCCCAAACTATCCCTTTTCAT
1 TTCGATAGCCGAAGCCATCCCTTTTCAT
36227735 TTGTCGATGA
Statistics
Matches: 249, Mismatches: 59, Indels: 33
0.73 0.17 0.10
Matches are distributed among these distances:
28 2 0.01
29 84 0.34
30 158 0.63
31 5 0.02
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (30 bp):
TTCGATAGCCGAAGCCATCCCTTTTCATAG
Found at i:36227442 original size:60 final size:60
Alignment explanation
Indices: 36227378--36227558 Score: 220
Period size: 60 Copynumber: 3.0 Consensus size: 60
36227368 TCCTTTTTTG
* * *
36227378 TAATTCGATAACCGAAGTTATCCCTTTTCATAGTTCAATAG-CCAAAGCCATCCCTTTTCA
1 TAATTTGATAGCCGAAGCTATCCCTTTTCATAGTTCAATAGTCCAAA-CCATCCCTTTTCA
* ***
36227438 TAATTTGATAGCCGAAGCTATCCCTTTTCATAGTTCAATGGTCGTCACCATCCCTTTTCA
1 TAATTTGATAGCCGAAGCTATCCCTTTTCATAGTTCAATAGTCCAAACCATCCCTTTTCA
* * * * ***
36227498 TAATTTGATAGTCGAAGCTATTCCTTTTCATAGTTCGATGGTCGTCACCATCCCTTTTCA
1 TAATTTGATAGCCGAAGCTATCCCTTTTCATAGTTCAATAGTCCAAACCATCCCTTTTCA
36227558 T
1 T
36227559 TATTCGATGG
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 108 0.98
61 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (60 bp):
TAATTTGATAGCCGAAGCTATCCCTTTTCATAGTTCAATAGTCCAAACCATCCCTTTTCA
Found at i:36227524 original size:90 final size:89
Alignment explanation
Indices: 36227397--36227734 Score: 360
Period size: 90 Copynumber: 3.8 Consensus size: 89
36227387 AACCGAAGTT
* * * * *
36227397 ATCCCTTTTCATAGTTCAATAGCCAAAGCCATCCCTTTTCATAATTTGATAGCCG-AAGCTATCC
1 ATCCCTTTTCATAATTCAATAGCCGAAGCTATCCCTTTTCAT-ATTCGATAGCCGTAA-CCATCC
* *
36227461 CTTTTCATAGTTCAATGGTCGTCACC
64 CTTTTCATAGTTCGATGGTCATCACC
** * * * * *
36227487 ATCCCTTTTCATAATTTGATAGTCGAAGCTATTCCTTTTCATAGTTCGATGGTCGTCACCATCCC
1 ATCCCTTTTCATAATTCAATAGCCGAAGCTATCCCTTTTCATA-TTCGATAGCCGTAACCATCCC
36227552 TTTTCATTA-TTCGATGGTCATCACC
65 TTTTCA-TAGTTCGATGGTCATCACC
** * * * * *
36227577 ATCCCTTTTCATAATTGGATAGCCGAAGCTATCCCTTTTCATAGTCGATGGTCGTTACCATCCTT
1 ATCCCTTTTCATAATTCAATAGCCGAAGCTATCCCTTTTCATATTCGATAGCCGTAACCATCCCT
*
36227642 TTTCATTGTT-GATGGTCATCACC
66 TTTCATAGTTCGATGGTCATCACC
* * * ** *
36227665 ATCCCTTTTCATAA-TCAATAGTCGGAGCTATCCTTTTTCATATTCGATAGCCCAAACTATCCCT
1 ATCCCTTTTCATAATTCAATAGCCGAAGCTATCCCTTTTCATATTCGATAGCCGTAACCATCCCT
36227729 TTTCAT
66 TTTCAT
36227735 TTGTCGATGA
Statistics
Matches: 210, Mismatches: 34, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
87 43 0.20
88 28 0.13
89 27 0.13
90 109 0.52
91 3 0.01
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (89 bp):
ATCCCTTTTCATAATTCAATAGCCGAAGCTATCCCTTTTCATATTCGATAGCCGTAACCATCCCT
TTTCATAGTTCGATGGTCATCACC
Found at i:36227655 original size:29 final size:30
Alignment explanation
Indices: 36227457--36227677 Score: 218
Period size: 30 Copynumber: 7.4 Consensus size: 30
36227447 AGCCGAAGCT
*
36227457 ATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * * * *
36227487 ATCCCTTTTCATAATTTGATAGTCG-AAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
*
36227517 ATTCCTTTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
*
36227547 ATCCCTTTTCATTA-TTCGATGGTCATCACC
1 ATCCCTTTTCA-TAGTTCGATGGTCGTCACC
* * * * * *
36227577 ATCCCTTTTCATAATTGGATAGCCG-AAGCT
1 ATCCCTTTTCATAGTTCGATGGTCGTCA-CC
*
36227607 ATCCCTTTTCATAG-TCGATGGTCGTTACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
* * *
36227636 ATCCTTTTTCATTGTT-GATGGTCATCACC
1 ATCCCTTTTCATAGTTCGATGGTCGTCACC
36227665 ATCCCTTTTCATA
1 ATCCCTTTTCATA
36227678 ATCAATAGTC
Statistics
Matches: 152, Mismatches: 32, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
29 46 0.30
30 103 0.68
31 3 0.02
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATGGTCGTCACC
Found at i:36227697 original size:29 final size:29
Alignment explanation
Indices: 36227665--36227734 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
36227655 GGTCATCACC
* ** *
36227665 ATCCCTTTTCATAATCAATAGTCGGAGCT
1 ATCCCTTTTCATAATCAATAGCCCAAACT
* * *
36227694 ATCCTTTTTCATATTCGATAGCCCAAACT
1 ATCCCTTTTCATAATCAATAGCCCAAACT
36227723 ATCCCTTTTCAT
1 ATCCCTTTTCAT
36227735 TTGTCGATGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.26, C:0.27, G:0.09, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAATCAATAGCCCAAACT
Found at i:36235244 original size:30 final size:30
Alignment explanation
Indices: 36235142--36235244 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
36235132 TGGTTGACAC
* * *
36235142 ATCCCTTTTCGTGATTTGATAACCGAAGTT
1 ATCCCTTTTCATAATTTGATAGCCGAAGTT
** * * *
36235172 ATCCCTTTTCATTGTTCGACAGCCGAAGCT
1 ATCCCTTTTCATAATTTGATAGCCGAAGTT
* **
36235202 ATCCATTTTCATAATTTGATAGTTGAAGTT
1 ATCCCTTTTCATAATTTGATAGCCGAAGTT
36235232 ATCCCTTTTCATA
1 ATCCCTTTTCATA
36235245 GTTCGATGGT
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATAGCCGAAGTT
Found at i:36235362 original size:29 final size:29
Alignment explanation
Indices: 36235232--36235391 Score: 153
Period size: 30 Copynumber: 5.4 Consensus size: 29
36235222 AGTTGAAGTT
*
36235232 ATCCCTTTTCATAGTTCGATGGTCGTCACC
1 ATCCCTTTTCATTG-TCGATGGTCGTCACC
* *
36235262 ATCCCTTTTCATTATCTGATGGTCATCACC
1 ATCCCTTTTCATTGTC-GATGGTCGTCACC
* * *** *
36235292 ATCCCTTTTCATAAT-TTGATAG-CCAAAGCT
1 ATCCCTTTTCAT--TGTCGATGGTCGTCA-CC
36235322 ATCCCTTTTCATTGTCGATGGTCGTCACC
1 ATCCCTTTTCATTGTCGATGGTCGTCACC
* * *
36235351 ATCCCTTTTCATTGTTGATGGTTGTCAGC
1 ATCCCTTTTCATTGTCGATGGTCGTCACC
36235380 ATCCCTTTTCAT
1 ATCCCTTTTCAT
36235392 AATCGATAGC
Statistics
Matches: 106, Mismatches: 18, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
28 1 0.01
29 48 0.45
30 55 0.52
31 1 0.01
32 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.14, T:0.40
Consensus pattern (29 bp):
ATCCCTTTTCATTGTCGATGGTCGTCACC
Found at i:36235416 original size:29 final size:29
Alignment explanation
Indices: 36235384--36235449 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
36235374 GTCAGCATCC
* **
36235384 CTTTTCATAATCGATAGCTGAAGGTATCA
1 CTTTTCATAATCGATAGCCGAAACTATCA
* * *
36235413 CTTTTCGTATTCGATAGCCGAAACTATCC
1 CTTTTCATAATCGATAGCCGAAACTATCA
36235442 CTTTTCAT
1 CTTTTCAT
36235450 TTGTCGATGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (29 bp):
CTTTTCATAATCGATAGCCGAAACTATCA
Found at i:36237977 original size:20 final size:20
Alignment explanation
Indices: 36237952--36237989 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
36237942 GGAGAATACC
36237952 AAAAAAATA-ATATATAAAAG
1 AAAAAAATATAT-TATAAAAG
36237972 AAAAAAATATATTATAAA
1 AAAAAAATATATTATAAA
36237990 CTTGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (20 bp):
AAAAAAATATATTATAAAAG
Found at i:36238186 original size:20 final size:21
Alignment explanation
Indices: 36238147--36238186 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
36238137 AATAAACTTG
*
36238147 GAAAGATAAATGAAATTAGAA
1 GAAAGATAAAAGAAATTAGAA
*
36238168 GAAAGA-AAAAGACATTAGA
1 GAAAGATAAAAGAAATTAGA
36238187 TAAGTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.62, C:0.03, G:0.20, T:0.15
Consensus pattern (21 bp):
GAAAGATAAAAGAAATTAGAA
Found at i:36242458 original size:28 final size:29
Alignment explanation
Indices: 36242426--36242481 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
36242416 ATTTGTTCTT
*
36242426 TATTTCTTT-GATTTTATAATTTT-TCCCC
1 TATTT-TTTAGATTTTACAATTTTATCCCC
36242454 TATTTTTTAGATTTTACAATTTTATCCC
1 TATTTTTTAGATTTTACAATTTTATCCC
36242482 TTACTTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 3 0.12
28 18 0.72
29 4 0.16
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.59
Consensus pattern (29 bp):
TATTTTTTAGATTTTACAATTTTATCCCC
Found at i:36243929 original size:139 final size:139
Alignment explanation
Indices: 36243679--36243936 Score: 421
Period size: 139 Copynumber: 1.9 Consensus size: 139
36243669 TTGTTTTGAC
*
36243679 GTTTATTCACCCTTTTTCTAACGAATTTTCATTGTTTCATCCCTCTTTTCTTTTGATTCCTTTTA
1 GTTTATTCACCCTTTTTCTAACAAATTTTCATTGTTTCATCCCTCTTTTCTTTTGATTCCTTTTA
36243744 TGCCTCTATCGTGTTCGACGATTGAACTCGCTCGATTCGGTAAGTATTCGTTTTGCCACTTCTAT
66 TGCCTCTATCGTGTTCGACGATTGAACTCGCTCGATTCGGTAAGTATTCGTTTTGCCACTTCTAT
36243809 CATTCTGAT
131 CATTCTGAT
** * *
36243818 GTTTATTCACCCTTTTTCTGCCAAATTTTCATTGTTTCCTCCCTCTTTTCTTTTGATTTCTTTTA
1 GTTTATTCACCCTTTTTCTAACAAATTTTCATTGTTTCATCCCTCTTTTCTTTTGATTCCTTTTA
* *
36243883 TTCCT-TCATCGTGCTT-GACGGTTGAACTCGCTCGATTCGGTAAGTATTCGTTTT
66 TGCCTCT-ATCGTG-TTCGACGATTGAACTCGCTCGATTCGGTAAGTATTCGTTTT
36243937 TCCATTTTCT
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
138 1 0.01
139 107 0.97
140 2 0.02
ACGTcount: A:0.15, C:0.24, G:0.13, T:0.48
Consensus pattern (139 bp):
GTTTATTCACCCTTTTTCTAACAAATTTTCATTGTTTCATCCCTCTTTTCTTTTGATTCCTTTTA
TGCCTCTATCGTGTTCGACGATTGAACTCGCTCGATTCGGTAAGTATTCGTTTTGCCACTTCTAT
CATTCTGAT
Found at i:36250799 original size:13 final size:14
Alignment explanation
Indices: 36250777--36250806 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
36250767 TTGTTAAGTA
36250777 TTTATCTATTAGAT
1 TTTATCTATTAGAT
36250791 TTTAT-TATTAGAT
1 TTTATCTATTAGAT
36250804 TTT
1 TTT
36250807 TATTTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTATCTATTAGAT
Found at i:36252888 original size:2 final size:2
Alignment explanation
Indices: 36252881--36252934 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
36252871 GCGCCAAATT
36252881 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
36252923 CA CA CA CA CA CA
1 CA CA CA CA CA CA
36252935 TATATAACGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:36253957 original size:20 final size:20
Alignment explanation
Indices: 36253932--36253974 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
36253922 AACTCAATTG
36253932 AAAGAGGAAATAGAAA-AAGA
1 AAAGAGGAAA-AGAAAGAAGA
36253952 AAAGAGGAAAAGAAAGAAGA
1 AAAGAGGAAAAGAAAGAAGA
36253972 AAA
1 AAA
36253975 TAAAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (20 bp):
AAAGAGGAAAAGAAAGAAGA
Found at i:36253980 original size:26 final size:27
Alignment explanation
Indices: 36253943--36253994 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
36253933 AAGAGGAAAT
*
36253943 AGAAAAAGAAAAGAGGAAAA-GAAAGA
1 AGAAAAAGAAAAAAGGAAAAGGAAAGA
*
36253969 AGAAAATA-AAAAAATGAAAAGGAAAG
1 AGAAAA-AGAAAAAAGGAAAAGGAAAG
36253995 GATTTGACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (27 bp):
AGAAAAAGAAAAAAGGAAAAGGAAAGA
Found at i:36255159 original size:19 final size:19
Alignment explanation
Indices: 36255135--36255178 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
36255125 ATAGAAACTT
36255135 ATAAAAGCTACAAAAAA-TC
1 ATAAAA-CTACAAAAAATTC
**
36255154 ATAAAACTTGAAAAAATTC
1 ATAAAACTACAAAAAATTC
36255173 ATAAAA
1 ATAAAA
36255179 ACTTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.64, C:0.11, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAAACTACAAAAAATTC
Found at i:36255235 original size:19 final size:19
Alignment explanation
Indices: 36255192--36255263 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 19
36255182 TTTAAATATT
36255192 ATAA-AAATTATAAAAATA
1 ATAATAAATTATAAAAATA
* *
36255210 CTAATAAATTATAAAAGTA
1 ATAATAAATTATAAAAATA
* **
36255229 ATTATAAAAGATAAAACATA
1 ATAATAAATTATAAAA-ATA
*
36255249 TTAA-AAA-TATAAAAA
1 ATAATAAATTATAAAAA
36255264 CATTCTATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
17 1 0.02
18 9 0.21
19 28 0.67
20 4 0.10
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (19 bp):
ATAATAAATTATAAAAATA
Found at i:36255350 original size:10 final size:10
Alignment explanation
Indices: 36255061--36255354 Score: 66
Period size: 10 Copynumber: 30.1 Consensus size: 10
36255051 TTTTTCTCAT
36255061 AAAAATTAT-
1 AAAAATTATA
*
36255070 AAAAATCATA
1 AAAAATTATA
* *
36255080 AAAGATTATT
1 AAAAATTATA
*
36255090 ACAAATT-T-
1 AAAAATTATA
36255098 -AAAATTATTA
1 AAAAATTA-TA
36255108 AAAAA-TATGA
1 AAAAATTAT-A
* *
36255118 AATATTTATA
1 AAAAATTATA
* *
36255128 GAAACTTAT-
1 AAAAATTATA
** *
36255137 AAAAGCTACA
1 AAAAATTATA
*
36255147 AAAAATCAT-
1 AAAAATTATA
* *
36255156 AAAACTT-GA
1 AAAAATTATA
36255165 AAAAATTCATA
1 AAAAATT-ATA
* *
36255176 AAAACTT-TT
1 AAAAATTATA
*
36255185 AAATATTAT-
1 AAAAATTATA
36255194 AAAAATTAT-
1 AAAAATTATA
36255203 AAAAA-TACTA
1 AAAAATTA-TA
*
36255213 ATAAATTATA
1 AAAAATTATA
36255223 AAAGTAATTAT-
1 AAA--AATTATA
*
36255234 -AAAA-GATA
1 AAAAATTATA
* *
36255242 AAACA-TATT
1 AAAAATTATA
36255251 AAAAA-TATA
1 AAAAATTATA
*
36255260 AAAACATTCTA
1 AAAA-ATTATA
* *
36255271 TAAACTTAT-
1 AAAAATTATA
36255280 AAAAATTATCAAA
1 AAAAATTAT---A
* *
36255293 AAAAATTTTC
1 AAAAATTATA
*
36255303 AAAAGTTATA
1 AAAAATTATA
*
36255313 AAAGATTCATA
1 AAAAATT-ATA
* * *
36255324 ATAAGTTCTA
1 AAAAATTATA
**
36255334 ATGAATTATA
1 AAAAATTATA
36255344 AAAAATTATA
1 AAAAATTATA
36255354 A
1 A
36255355 TTTTTAAGAA
Statistics
Matches: 199, Mismatches: 60, Indels: 51
0.64 0.19 0.16
Matches are distributed among these distances:
7 7 0.04
8 4 0.02
9 70 0.35
10 75 0.38
11 29 0.15
12 6 0.03
13 8 0.04
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:36255379 original size:18 final size:18
Alignment explanation
Indices: 36255345--36255379 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36255335 TGAATTATAA
* *
36255345 AAAATTATAATTTTTAAG
1 AAAATTATAAATATTAAG
36255363 AAAATTATAAATATTAA
1 AAAATTATAAATATTAA
36255380 AAAGCATGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATTATAAATATTAAG
Found at i:36257281 original size:4 final size:4
Alignment explanation
Indices: 36257274--36257302 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
36257264 TTTAGTTGAT
36257274 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
36257303 ATTTATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:36259974 original size:101 final size:102
Alignment explanation
Indices: 36259857--36260041 Score: 347
Period size: 101 Copynumber: 1.8 Consensus size: 102
36259847 AAAGTGATGG
36259857 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGAT-A-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATGATAATGGTCACATGTGTAGT
36259920 ACTATGTGCAGGCTACTATGCATACCAGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCATACCAGATAGTTTCGA
36259958 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGATAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGATAATGGTCACATGTGTAGTA
36260023 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
36260042 TGAACCGAAC
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
100 7 0.09
101 40 0.49
102 35 0.43
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCATACCAGATAGTTTCGA
Found at i:36259987 original size:51 final size:50
Alignment explanation
Indices: 36259857--36260039 Score: 190
Period size: 51 Copynumber: 3.6 Consensus size: 50
36259847 AAAGTGATGG
** * * *
36259857 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCATACCAGAATGATAGA
* * * *
36259907 TCACATGTGTAGTACTATGTGCAGGCTACTATGCATACCAG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCATACCAGAAT-G-ATAGA
** * *
36259958 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATGATAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCATACCAGAATGAT-A-GA
*
36260009 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
36260040 TGTGAACCGA
Statistics
Matches: 110, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
49 3 0.03
50 38 0.35
51 69 0.63
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCATACCAGAATGATAGA
Found at i:36260043 original size:26 final size:26
Alignment explanation
Indices: 36259963--36260043 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
36259953 TTCGATCACG
36259963 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
36259989 CGTGTA-T-CGAATGAT-AATGG-TCAC-A
1 TGTGTAGTAC-TATG-TGCA-GGCT-ACTA
36260014 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
36260040 TGTG
1 TGTG
36260044 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 1 0.03
25 17 0.43
26 21 0.52
27 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:36260136 original size:45 final size:45
Alignment explanation
Indices: 36260045--36260139 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
36260035 TACTATGTGA
* *
36260045 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCC
*
36260090 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGCA-TCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTG-ATTCC
36260135 ACCGA
1 ACCGA
36260140 GTATCTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCC
Found at i:36260209 original size:23 final size:22
Alignment explanation
Indices: 36260183--36260226 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
36260173 AATTGACTAA
36260183 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
36260206 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
36260227 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:36263883 original size:18 final size:18
Alignment explanation
Indices: 36263862--36263926 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
36263852 TTTAAATGAG
36263862 TTTTTTAATAATTTCTA-A
1 TTTTTT-ATAATTTCTATA
* *
36263880 TTTTTCATAATTTTTATA
1 TTTTTTATAATTTCTATA
36263898 TATTTTT-TAATTTCTATAA
1 T-TTTTTATAATTTCTAT-A
*
36263917 ATTTTTATAA
1 TTTTTTATAA
36263927 AATTTTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 9 0.24
18 21 0.55
19 8 0.21
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTTATAATTTCTATA
Found at i:36263908 original size:28 final size:28
Alignment explanation
Indices: 36263863--36263931 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
36263853 TTAAATGAGT
*
36263863 TTTTTA-ATAATTTCTAATTTTTCAT-AA
1 TTTTTATATAATTTCTAATTTCT-ATAAA
* *
36263890 TTTTTATATATTTTTTAATTTCTATAAA
1 TTTTTATATAATTTCTAATTTCTATAAA
*
36263918 TTTTTATAAAATTT
1 TTTTTATATAATTT
36263932 TAAATGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTATATAATTTCTAATTTCTATAAA
Found at i:36263973 original size:10 final size:10
Alignment explanation
Indices: 36263877--36264095 Score: 66
Period size: 10 Copynumber: 23.3 Consensus size: 10
36263867 TAATAATTTC
*
36263877 TAATTTTTCA
1 TAATTTTTTA
36263887 TAA-TTTTTA
1 TAATTTTTTA
36263896 T-ATATTTTT-
1 TAAT-TTTTTA
*
36263905 TAA-TTTCTA
1 TAATTTTTTA
*
36263914 TAAATTTTTA
1 TAATTTTTTA
**
36263924 TAAAATTTTA
1 TAATTTTTTA
*
36263934 -AATGTTTTA
1 TAATTTTTTA
36263943 -AATATGTTTTA
1 TAAT-T-TTTTA
36263954 TTAA--TTTTA
1 -TAATTTTTTA
36263963 TAATTTTTTA
1 TAATTTTTTA
* *
36263973 TAATATATTA
1 TAATTTTTTA
*
36263983 -GATTTTTTA
1 TAATTTTTTA
*
36263992 TGAA-TTTTCA
1 T-AATTTTTTA
* *
36264002 TAA-TATTGA
1 TAATTTTTTA
*
36264011 TAAGTTTTTA
1 TAATTTTTTA
*
36264021 TGATTTTTT-
1 TAATTTTTTA
*
36264030 TAA-TTTTCA
1 TAATTTTTTA
* *
36264039 TAAGTTTATA
1 TAATTTTTTA
36264049 TCAA---TTT-
1 T-AATTTTTTA
36264056 TAATTTTTT-
1 TAATTTTTTA
36264065 TAA-TTTTTA
1 TAATTTTTTA
*
36264074 GTAA-GTTTTA
1 -TAATTTTTTA
36264084 T-ATTTTTTA
1 TAATTTTTTA
36264093 TAA
1 TAA
36264096 ACTTGTTAAT
Statistics
Matches: 158, Mismatches: 27, Indels: 48
0.68 0.12 0.21
Matches are distributed among these distances:
6 2 0.01
7 1 0.01
8 20 0.13
9 58 0.37
10 67 0.42
11 8 0.05
13 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:36263991 original size:49 final size:49
Alignment explanation
Indices: 36263895--36263991 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
36263885 CATAATTTTT
*
36263895 ATATATTTTTTAATTTCTATAAATTTTTATAAAATTTTAAATGTTTTAA
1 ATATATTTTTTAATTTCTATAAATTTTTATAAAATATTAAATGTTTTAA
* * * * *
36263944 ATATGTTTTATTAATTT-TATAATTTTTTATAATATATTAGATTTTTTA
1 ATATATTTT-TTAATTTCTATAAATTTTTATAAAATATTAAATGTTTTA
36263992 TGAATTTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 34 0.83
50 7 0.17
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (49 bp):
ATATATTTTTTAATTTCTATAAATTTTTATAAAATATTAAATGTTTTAA
Found at i:36264026 original size:28 final size:29
Alignment explanation
Indices: 36263986--36264056 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
36263976 TATATTAGAT
*
36263986 TTTTTATGAATTTTCATAATATTGATAAG
1 TTTTTATGAATTTTCATAATATTCATAAG
** *
36264015 TTTTTATG-ATTTTTTTAATTTTCATAAG
1 TTTTTATGAATTTTCATAATATTCATAAG
* *
36264043 TTTATATCAATTTT
1 TTTTTATGAATTTT
36264057 AATTTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 22 0.63
29 13 0.37
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (29 bp):
TTTTTATGAATTTTCATAATATTCATAAG
Found at i:36264092 original size:35 final size:34
Alignment explanation
Indices: 36263949--36264090 Score: 94
Period size: 37 Copynumber: 3.9 Consensus size: 34
36263939 TTTAAATATG
* * *
36263949 TTTTATTAATTTT-ATAATTTTTTATAATATATTAGA
1 TTTTTTTAATTTTCATAAGTTTATATAAT-T-TTA-A
*
36263985 TTTTTTATGAATTTTCATAA-TATTGATA-AGTTTTTATGA
1 TTTTTT-T-AATTTTCATAAGT-TT-ATATA-ATTTTA--A
36264024 TTTTTTTAATTTTCATAAGTTTATATCAATTTTAA
1 TTTTTTTAATTTTCATAAGTTTATAT-AATTTTAA
* *
36264059 TTTTTTTAATTTTTAGTAAGTTT-TATATTTTT
1 TTTTTTTAATTTTCA-TAAGTTTATATAATTTT
36264091 TATAAACTTG
Statistics
Matches: 89, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
34 5 0.06
35 18 0.20
36 15 0.17
37 19 0.21
38 13 0.15
39 16 0.18
40 3 0.03
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (34 bp):
TTTTTTTAATTTTCATAAGTTTATATAATTTTAA
Found at i:36285943 original size:29 final size:29
Alignment explanation
Indices: 36285901--36285961 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
36285891 AGAGATGGGC
* *
36285901 GATGTATCGGACTTCAAGGGTAAAGGAGT
1 GATGCATCGGACTTCAAGGGTAAAGAAGT
36285930 GATGCATCGGACTTCAAGGGTAAAGAAGT
1 GATGCATCGGACTTCAAGGGTAAAGAAGT
36285959 GAT
1 GAT
36285962 ACAAGTTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.23
Consensus pattern (29 bp):
GATGCATCGGACTTCAAGGGTAAAGAAGT
Found at i:36289065 original size:11 final size:11
Alignment explanation
Indices: 36289042--36289103 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
36289032 TTTATTTTTT
*
36289042 TAATTTCAAAA
1 TAATTTTAAAA
*
36289053 TACTTTTAAAA
1 TAATTTTAAAA
* ****
36289064 TACTTTTTTTT
1 TAATTTTAAAA
36289075 TAATTTTAAAA
1 TAATTTTAAAA
*
36289086 TATTTTTAAAA
1 TAATTTTAAAA
36289097 TAATTTT
1 TAATTTT
36289104 TTTAATTTTT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:36289100 original size:22 final size:22
Alignment explanation
Indices: 36289049--36289125 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
36289039 TTTTAATTTC
*
36289049 AAAATACTTTTAAAATACTTTTT
1 AAAATAATTTTAAAATA-TTTTT
***
36289072 -TTTTAATTTTAAAATATTTTT
1 AAAATAATTTTAAAATATTTTT
***
36289093 AAAATAATTTTTTTA-ATTTTT
1 AAAATAATTTTAAAATATTTTT
36289114 AAAATAAATTTT
1 AAAAT-AATTTT
36289126 TGGTATTTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
21 16 0.38
22 26 0.62
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
AAAATAATTTTAAAATATTTTT
Found at i:36289104 original size:12 final size:12
Alignment explanation
Indices: 36289078--36289126 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
36289068 TTTTTTTTAA
36289078 TTTTAAAAT-AT
1 TTTTAAAATAAT
36289089 TTTTAAAATAAT
1 TTTTAAAATAAT
*
36289101 TTTT---TTAAT
1 TTTTAAAATAAT
36289110 TTTTAAAATAAAT
1 TTTTAAAAT-AAT
36289123 TTTT
1 TTTT
36289127 GGTATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 8 0.26
11 9 0.29
12 7 0.23
13 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTAAAATAAT
Found at i:36289104 original size:32 final size:32
Alignment explanation
Indices: 36289035--36289119 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 32
36289025 TATTTTTTTT
*
36289035 ATTTTTTTAATTTCAAAATACTTTTAAAATAC
1 ATTTTTTTAATTTTAAAATACTTTTAAAATAC
* *
36289067 TTTTTTTTTAATTTTAAAATATTTTTAAAATA-
1 -ATTTTTTTAATTTTAAAATACTTTTAAAATAC
36289099 ATTTTTTTAATTTTTAAAATA
1 ATTTTTTTAA-TTTTAAAATA
36289120 AATTTTTGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
31 9 0.19
32 10 0.21
33 28 0.60
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTTTTTAATTTTAAAATACTTTTAAAATAC
Found at i:36289111 original size:21 final size:21
Alignment explanation
Indices: 36289087--36289126 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36289077 ATTTTAAAAT
*
36289087 ATTTTTAAAATAATTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
36289108 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
36289127 GGTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:36289133 original size:22 final size:20
Alignment explanation
Indices: 36289086--36289133 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
36289076 AATTTTAAAA
*
36289086 TATTTTTAAAATAATTTTTT
1 TATTTTTAAAATAATTTTTG
36289106 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
36289129 TATTT
1 TATTT
36289134 ATTTAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 11 0.46
22 11 0.46
23 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:36295814 original size:46 final size:46
Alignment explanation
Indices: 36295747--36295839 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
36295737 AAAATAATCC
* *
36295747 AGAGGTAGAAAATTAAAACGACTTCGACAACCGAACAGTTACTTTA
1 AGAGGTAGAAAAGTAAAACGACTTCAACAACCGAACAGTTACTTTA
*
36295793 AGAGGTAGAAAAGTAAAACGACTTCAACAACCGAGCAGTTACTTTA
1 AGAGGTAGAAAAGTAAAACGACTTCAACAACCGAACAGTTACTTTA
36295839 A
1 A
36295840 CAAGTATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.20
Consensus pattern (46 bp):
AGAGGTAGAAAAGTAAAACGACTTCAACAACCGAACAGTTACTTTA
Found at i:36296282 original size:3 final size:3
Alignment explanation
Indices: 36296274--36296320 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
36296264 AGTTCAACTC
36296274 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
36296321 TGGAAACAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:36302940 original size:61 final size:62
Alignment explanation
Indices: 36302830--36302954 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 62
36302820 TTTTTTTAAC
* * * * *
36302830 TTTTAGTATTAGAATTAAATTGAAAATTTTTGTAAATATTTAGGGCTAAATTTATTGATTTT
1 TTTTAGAATTAGAACTAAATGGAAAATTTTTGTAAATATTGAGGGCTAAATTTATTGAATTT
* *
36302892 TTTTAGAATTAGAACTAGATGGAAAA-TTTTGTAAATATTGAGGGCTAAATTTGTTGAATTT
1 TTTTAGAATTAGAACTAAATGGAAAATTTTTGTAAATATTGAGGGCTAAATTTATTGAATTT
36302953 TT
1 TT
36302955 AGATATAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
61 34 0.61
62 22 0.39
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.46
Consensus pattern (62 bp):
TTTTAGAATTAGAACTAAATGGAAAATTTTTGTAAATATTGAGGGCTAAATTTATTGAATTT
Found at i:36302979 original size:61 final size:60
Alignment explanation
Indices: 36302847--36303007 Score: 166
Period size: 61 Copynumber: 2.6 Consensus size: 60
36302837 ATTAGAATTA
* * * * *
36302847 AATTGAAAATTTTTGTAAATATTTAGGGCTAAATTTATTGATTTTTTTTAGAATTAGAACT
1 AATTGAAAAATTTTGTAAATATTGAGGGCTAAATTTATTGA-TATTTTTAGAATAAGAACG
* * *
36302908 AGA-TGGAAAATTTTGTAAATATTGAGGGCTAAATTTGTTGA-ATTTTTAGATATAAGATCG
1 A-ATTGAAAAATTTTGTAAATATTGAGGGCTAAATTTATTGATATTTTTAGA-ATAAGAACG
* *
36302968 AATTGATAAAA-TATGTAAATATTGGAGGACTAAATTTATT
1 AATTGA-AAAATTTTGTAAATATT-GAGGGCTAAATTTATT
36303008 ATTAGGCCAA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
59 9 0.11
60 20 0.24
61 53 0.64
62 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.42
Consensus pattern (60 bp):
AATTGAAAAATTTTGTAAATATTGAGGGCTAAATTTATTGATATTTTTAGAATAAGAACG
Found at i:36316307 original size:13 final size:14
Alignment explanation
Indices: 36316291--36316331 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
36316281 TCTACAGATA
36316291 CAGATAT-CAGAAT
1 CAGATATACAGAAT
*
36316304 CAGATATGCAGAA-
1 CAGATATACAGAAT
*
36316317 CAAATATACAGAAT
1 CAGATATACAGAAT
36316331 C
1 C
36316332 CTACTCTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (14 bp):
CAGATATACAGAAT
Found at i:36331085 original size:27 final size:26
Alignment explanation
Indices: 36331044--36331138 Score: 91
Period size: 27 Copynumber: 3.5 Consensus size: 26
36331034 TTAGAATACG
*
36331044 CCACGAAGGCATTCCTTTCCATAGATCA
1 CCACAAAGGC-TTCCTTT-CATAGATCA
**
36331072 CCACAAAGGCTTCCATTTCATAGATTG
1 CCACAAAGGCTTCC-TTTCATAGATCA
* * *
36331099 CCAAAAAGGCTTCCATTACATAGATGA
1 CCACAAAGGCTTCC-TTTCATAGATCA
*
36331126 TCACAAAGGCTTC
1 CCACAAAGGCTTC
36331139 TATTTTCTAG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 45 0.79
28 12 0.21
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (26 bp):
CCACAAAGGCTTCCTTTCATAGATCA
Found at i:36337678 original size:17 final size:18
Alignment explanation
Indices: 36337637--36337678 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
36337627 TCTAAGTATT
*
36337637 TTTAATAATTTTTTATAA
1 TTTAATAATTTTTTAGAA
36337655 TAATTAAT-ATTTTTTAGAA
1 T--TTAATAATTTTTTAGAA
36337674 TTTAA
1 TTTAA
36337679 AGTTTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 4 0.19
18 1 0.05
19 11 0.52
20 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTAATAATTTTTTAGAA
Found at i:36347664 original size:21 final size:21
Alignment explanation
Indices: 36347640--36347680 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36347630 AGTGAGTAGG
*
36347640 TTTTACTTT-TAATTTTTTATT
1 TTTTA-TTTCTAAGTTTTTATT
36347661 TTTTATTTCTAAGTTTTTAT
1 TTTTATTTCTAAGTTTTTAT
36347681 CCAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTTCTAAGTTTTTATT
Found at i:36350517 original size:55 final size:55
Alignment explanation
Indices: 36350440--36350568 Score: 170
Period size: 55 Copynumber: 2.3 Consensus size: 55
36350430 GTTTTTTTTC
* * * *
36350440 TTCTGTTCTGTTCTATTCTGCTTTGCTCTATTCTGTTTTTTTATG-TCCTACTCTA
1 TTCTGTTCTGTTCTGTTTTGCTTTGCTCTATTCTATTTTGTTATGTTCC-ACTCTA
* * *
36350495 TTCTGTTATGTTCTGTTTTGCTTTGCTTTGTTCTATTTTGTTATGTTCCACTCTA
1 TTCTGTTCTGTTCTGTTTTGCTTTGCTCTATTCTATTTTGTTATGTTCCACTCTA
*
36350550 TTCTGTTCTGTTATGTTTT
1 TTCTGTTCTGTTCTGTTTT
36350569 TCTCAGTTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 61 0.95
56 3 0.05
ACGTcount: A:0.09, C:0.18, G:0.13, T:0.60
Consensus pattern (55 bp):
TTCTGTTCTGTTCTGTTTTGCTTTGCTCTATTCTATTTTGTTATGTTCCACTCTA
Found at i:36350583 original size:55 final size:55
Alignment explanation
Indices: 36350470--36350583 Score: 124
Period size: 55 Copynumber: 2.1 Consensus size: 55
36350460 CTTTGCTCTA
* * * ** *
36350470 TTCTGTTTTTTTATGTCCTACTCTATTCTGTTATGTTCTGTTTTGCTTTGCTTTG
1 TTCTATTTTGTTATGTCCTACTCTATTCTGTTATGTTATGTTTTGCTCAGCTTAG
* *
36350525 TTCTATTTTGTTATGTTCC-ACTCTATTCTGTTCTGTTATGTTTTTCTCAG-TTCAG
1 TTCTATTTTGTTATG-TCCTACTCTATTCTGTTATGTTATGTTTTGCTCAGCTT-AG
36350580 TTCT
1 TTCT
36350584 GCTATGTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
54 2 0.04
55 44 0.90
56 3 0.06
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.60
Consensus pattern (55 bp):
TTCTATTTTGTTATGTCCTACTCTATTCTGTTATGTTATGTTTTGCTCAGCTTAG
Found at i:36350607 original size:25 final size:25
Alignment explanation
Indices: 36350579--36350701 Score: 70
Period size: 25 Copynumber: 4.7 Consensus size: 25
36350569 TCTCAGTTCA
36350579 GTTCTGCTATGTTATGTTATGTTAT
1 GTTCTGCTATGTTATGTTATGTTAT
* * * *
36350604 GTTCTGCTCTATTCTATTATGCTCTACTTT
1 GTTCTGCTATGTTATGTTATG-T-TA---T
*
36350634 GTTCTGTTCTAT-TT-TGTTATGTTCT
1 GTTCTG--CTATGTTATGTTATGTTAT
* * * *
36350659 GCTCTACTCTGTTATGTTTTGTTAT
1 GTTCTGCTATGTTATGTTATGTTAT
* *
36350684 GTTCTACTATGTTTTGTT
1 GTTCTGCTATGTTATGTT
36350702 TTACTCTTCT
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
23 3 0.04
24 2 0.03
25 46 0.62
26 1 0.01
27 2 0.03
28 1 0.01
29 1 0.01
30 13 0.18
31 2 0.03
32 3 0.04
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (25 bp):
GTTCTGCTATGTTATGTTATGTTAT
Found at i:36350644 original size:15 final size:15
Alignment explanation
Indices: 36350620--36350658 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
36350610 CTCTATTCTA
*
36350620 TTATGCTCTACTTTG
1 TTATGTTCTACTTTG
* *
36350635 TTCTGTTCTATTTTG
1 TTATGTTCTACTTTG
36350650 TTATGTTCT
1 TTATGTTCT
36350659 GCTCTACTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.13, T:0.62
Consensus pattern (15 bp):
TTATGTTCTACTTTG
Found at i:36350654 original size:30 final size:30
Alignment explanation
Indices: 36350523--36350701 Score: 107
Period size: 30 Copynumber: 6.1 Consensus size: 30
36350513 TGCTTTGCTT
* * *
36350523 TGTTCTATTTTGTTATGTTCCACTCTATTC
1 TGTTCTATTTTGTTATGTTCTACTATGTTC
* *
36350553 TGTTCTGTTATGTT-T-TTCT-C-A-GTTC
1 TGTTCTATTTTGTTATGTTCTACTATGTTC
* ** * * **
36350578 AGTTCTGCTATGTTATGTTATGTTATGTTC
1 TGTTCTATTTTGTTATGTTCTACTATGTTC
* * * * *
36350608 TGCTCTATTCTATTATGCTCTACTTTGTTC
1 TGTTCTATTTTGTTATGTTCTACTATGTTC
* * **
36350638 TGTTCTATTTTGTTATGTTCTGCTCTACTC
1 TGTTCTATTTTGTTATGTTCTACTATGTTC
* * *
36350668 TGTTATGTTTTGTTATGTTCTACTATGTTT
1 TGTTCTATTTTGTTATGTTCTACTATGTTC
36350698 TGTT
1 TGTT
36350702 TTACTCTTCT
Statistics
Matches: 109, Mismatches: 35, Indels: 10
0.71 0.23 0.06
Matches are distributed among these distances:
25 15 0.14
26 1 0.01
27 4 0.04
28 3 0.03
29 2 0.02
30 84 0.77
ACGTcount: A:0.12, C:0.16, G:0.15, T:0.58
Consensus pattern (30 bp):
TGTTCTATTTTGTTATGTTCTACTATGTTC
Found at i:36350656 original size:20 final size:20
Alignment explanation
Indices: 36350633--36350681 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
36350623 TGCTCTACTT
* *
36350633 TGTTCTGTTCTATTTTGTTA
1 TGTTCTGTTCTACTCTGTTA
*
36350653 TGTTCTGCTCTACTCTGTTA
1 TGTTCTGTTCTACTCTGTTA
*
36350673 TGTTTTGTT
1 TGTTCTGTT
36350682 ATGTTCTACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.08, C:0.14, G:0.16, T:0.61
Consensus pattern (20 bp):
TGTTCTGTTCTACTCTGTTA
Found at i:36350702 original size:25 final size:25
Alignment explanation
Indices: 36350645--36350703 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
36350635 TTCTGTTCTA
* * *
36350645 TTTTGTTATGTTCTGCTCTACTCTG
1 TTTTGTTTTGTTATGCTCTACTATG
* *
36350670 TTATGTTTTGTTATGTTCTACTATG
1 TTTTGTTTTGTTATGCTCTACTATG
36350695 TTTTGTTTT
1 TTTTGTTTT
36350704 ACTCTTCTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.10, C:0.12, G:0.15, T:0.63
Consensus pattern (25 bp):
TTTTGTTTTGTTATGCTCTACTATG
Found at i:36350714 original size:45 final size:45
Alignment explanation
Indices: 36350631--36350721 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
36350621 TATGCTCTAC
* * * *
36350631 TTTGTTCTGTTCTATTTTGTTATGTTCTGCTCTACTCTGTTATGT
1 TTTGTTATGTTCTACTATGTTATGTTCTACTCTACTCTGTTATGT
* * * *
36350676 TTTGTTATGTTCTACTATGTTTTGTTTTACTCTTCTCTGTTTTGT
1 TTTGTTATGTTCTACTATGTTATGTTCTACTCTACTCTGTTATGT
36350721 T
1 T
36350722 CTGCTTTGTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (45 bp):
TTTGTTATGTTCTACTATGTTATGTTCTACTCTACTCTGTTATGT
Found at i:36360805 original size:11 final size:11
Alignment explanation
Indices: 36360791--36360821 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
36360781 TTATATTTAT
36360791 TTTTTAATGAA
1 TTTTTAATGAA
36360802 TTTTTAATGAA
1 TTTTTAATGAA
36360813 TTATTTAAT
1 TT-TTTAAT
36360822 CAAATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (11 bp):
TTTTTAATGAA
Found at i:36363381 original size:21 final size:22
Alignment explanation
Indices: 36363357--36363398 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
36363347 AGTCAAATTA
36363357 AAGTACAG-AAAATAAATGGAC
1 AAGTACAGCAAAATAAATGGAC
* *
36363378 AAGTACTGCAAAATACATGGA
1 AAGTACAGCAAAATAAATGGA
36363399 TTAATAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (22 bp):
AAGTACAGCAAAATAAATGGAC
Found at i:36364323 original size:13 final size:13
Alignment explanation
Indices: 36364305--36364331 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36364295 CACCCAATTA
36364305 GTCCGCGGAGTTT
1 GTCCGCGGAGTTT
36364318 GTCCGCGGAGTTT
1 GTCCGCGGAGTTT
36364331 G
1 G
36364332 GTTTGGAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.41, T:0.30
Consensus pattern (13 bp):
GTCCGCGGAGTTT
Found at i:36367064 original size:26 final size:26
Alignment explanation
Indices: 36367034--36367137 Score: 109
Period size: 26 Copynumber: 4.0 Consensus size: 26
36367024 ATATACTCAT
* *
36367034 GGTCCTTTGACCAACTCAAACTCAAA
1 GGTCCTCTGACCAACTCAAACTCAAG
* *
36367060 GGTCCTCCGACCAACTCAAACTCAGG
1 GGTCCTCTGACCAACTCAAACTCAAG
* * * *
36367086 GGTCCCCTAACCTACTTAAACTCAAG
1 GGTCCTCTGACCAACTCAAACTCAAG
* * *
36367112 GGTCCTTTGACCCACTTAAACTCAAG
1 GGTCCTCTGACCAACTCAAACTCAAG
36367138 CTTGCTAGGC
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 64 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (26 bp):
GGTCCTCTGACCAACTCAAACTCAAG
Found at i:36371630 original size:10 final size:10
Alignment explanation
Indices: 36371610--36371689 Score: 72
Period size: 10 Copynumber: 7.8 Consensus size: 10
36371600 CTATACTCTT
36371610 TAATATTTTTA
1 TAAT-TTTTTA
36371621 TAATTTTTTA
1 TAATTTTTTA
* *
36371631 TAACTATTTAA
1 TAA-TTTTTTA
* *
36371642 TAAAATTTTAA
1 T-AATTTTTTA
36371653 TAA-TTTTTA
1 TAATTTTTTA
*
36371662 TAACTTTTTA
1 TAATTTTTTA
36371672 TAATTTTTTA
1 TAATTTTTTA
*
36371682 TCATTTTT
1 TAATTTTT
36371690 GTTAAACAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
9 8 0.14
10 33 0.56
11 16 0.27
12 2 0.03
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:36371641 original size:29 final size:29
Alignment explanation
Indices: 36371594--36371689 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 29
36371584 AAAATAATAC
*
36371594 AATTTTCTAT-ACTCTTTAAT-ATTTTTAT
1 AATTTTTTATAACT-TTTAATAATTTTTAT
*
36371622 AATTTTTTATAACTATTTAATAAAATTTTAAT
1 AATTTTTTATAACT-TTTAAT--AATTTTTAT
*
36371654 AA-TTTTTATAACTTTTTATAATTTTTTAT
1 AATTTTTTATAACTTTTAATAA-TTTTTAT
*
36371683 CATTTTT
1 AATTTTT
36371690 GTTAAACAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
28 11 0.20
29 16 0.29
30 9 0.16
31 11 0.20
32 9 0.16
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (29 bp):
AATTTTTTATAACTTTTAATAATTTTTAT
Found at i:36378085 original size:32 final size:32
Alignment explanation
Indices: 36378043--36378108 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
36378033 GAAGAATATT
*
36378043 CCAAAAGAATGA-GGGTTAAAGCTTGAATCTA
1 CCAAAAGAATGAGGGGTTAAAGCTTAAATCTA
36378074 CCAAGAAGAATGAGGGGTTAAAGCTTAAATCTA
1 CCAA-AAGAATGAGGGGTTAAAGCTTAAATCTA
36378107 CC
1 CC
36378109 CCAAATGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 4 0.12
32 8 0.25
33 20 0.62
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (32 bp):
CCAAAAGAATGAGGGGTTAAAGCTTAAATCTA
Found at i:36378219 original size:173 final size:174
Alignment explanation
Indices: 36377924--36378257 Score: 537
Period size: 173 Copynumber: 1.9 Consensus size: 174
36377914 TGGTGTTGCT
***
36377924 CTTAAATCCACCACAAATGAAGATAGTGAATCAACCGAAGAGGTGGATGAAGAAAAAGAGATGTT
1 CTTAAATCCACCACAAATGAAGATAGTGAATCAACCGAAGAGGTGGATGAAGAAAAAGAGATAAC
*
36377989 CATGTTTGCTAGGAGATTCAAGAGATTCATGAAGTTCAATAGAGGAAGAATATTCCAAAAGAATG
66 CATGTTTGCTAGGAGATTCAAGAGATTCATGAAGTTCAATAGAGGAAGAAGATTCCAAAAGAATG
36378054 A-GGGTTAAAGCTTGAATCTACCAAGAAGAATGAGGGGTTAAAG
131 AGGGGTTAAAGCTTGAATCTACCAAGAAGAATGAGGGGTTAAAG
* * * *
36378097 CTTAAATCTACCCCAAATGAAGATAGTGAATCAAGCGAAGAGGTGGATGAAGACAAAGAGATAAC
1 CTTAAATCCACCACAAATGAAGATAGTGAATCAACCGAAGAGGTGGATGAAGAAAAAGAGATAAC
* *
36378162 CATGTTTGCTAGGAGATTGAAGAGATTCCTGAAG-TCTAATAGAGGAAGAAGATTCCAAAAGAAT
66 CATGTTTGCTAGGAGATTCAAGAGATTCATGAAGTTC-AATAGAGGAAGAAGATTCCAAAAGAAT
* *
36378226 GAGGGGTTAAAGCTTGAATCTACTAAGGAGAA
130 GAGGGGTTAAAGCTTGAATCTACCAAGAAGAA
36378258 GGATCTCAAA
Statistics
Matches: 147, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 2 0.01
173 118 0.80
174 27 0.18
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (174 bp):
CTTAAATCCACCACAAATGAAGATAGTGAATCAACCGAAGAGGTGGATGAAGAAAAAGAGATAAC
CATGTTTGCTAGGAGATTCAAGAGATTCATGAAGTTCAATAGAGGAAGAAGATTCCAAAAGAATG
AGGGGTTAAAGCTTGAATCTACCAAGAAGAATGAGGGGTTAAAG
Found at i:36384162 original size:67 final size:67
Alignment explanation
Indices: 36384087--36384231 Score: 161
Period size: 67 Copynumber: 2.2 Consensus size: 67
36384077 ACTAATAATA
* *
36384087 TTTATAATATTCAACCATTTTTAATAATATTTTATAATTTTTCTATG-TTTTTATATATTTCA-A
1 TTTATAATATTCAA-CATTTTCAATAAT-TTTTATAATTTTTCTATGAGTTTTATA-ATTTCATA
36384150 AA-TT
63 AACTT
** * * * *
36384154 TTTATAATATTTTATATTTTCATTAATTTTTATGATTTTTCTATGAGTTTTATAATTTTATAAAC
1 TTTATAATATTCAACATTTTCAATAATTTTTATAATTTTTCTATGAGTTTTATAATTTCATAAAC
36384219 TT
66 TT
*
36384221 GTTATAATATT
1 TTTATAATATT
36384232 ATAGTAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
65 22 0.33
66 20 0.30
67 24 0.36
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (67 bp):
TTTATAATATTCAACATTTTCAATAATTTTTATAATTTTTCTATGAGTTTTATAATTTCATAAAC
TT
Found at i:36384172 original size:18 final size:18
Alignment explanation
Indices: 36384116--36384216 Score: 64
Period size: 18 Copynumber: 5.4 Consensus size: 18
36384106 TTTAATAATA
* *
36384116 TTTTATAATTTTTCTATGT
1 TTTTATAATATTT-TATAT
* *
36384135 TTTTAT-ATATTTCAAAAT
1 TTTTATAATATTT-TATAT
36384153 TTTTATAATATTTTATAT
1 TTTTATAATATTTTATAT
*
36384171 TTTCATTAAT-TTTTATGAT
1 TTTTA-TAATATTTTAT-AT
* *
36384190 TTTTCT-ATGAGTTTTATAA
1 TTTTATAAT-A-TTTTATAT
36384209 TTTTATAA
1 TTTTATAA
36384217 ACTTGTTATA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.03
18 28 0.44
19 27 0.42
20 7 0.11
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTATAATATTTTATAT
Found at i:36384193 original size:9 final size:9
Alignment explanation
Indices: 36384024--36384216 Score: 65
Period size: 10 Copynumber: 20.3 Consensus size: 9
36384014 AGCCTTTAAT
36384024 TAATTTTCTA
1 TAATTTT-TA
* *
36384034 TCATTTCTA
1 TAATTTTTA
36384043 -AATTTTTA
1 TAATTTTTA
36384051 TAATATTTTCA
1 TAAT-TTTT-A
36384062 T-ATTTTTCA
1 TAATTTTT-A
* *
36384071 TAATATACTAA
1 TAAT-T-TTTA
*
36384082 TAATATTTA
1 TAATTTTTA
* *
36384091 TAATATTCA
1 TAATTTTTA
36384100 -ACCATTTTTAA
1 TA--ATTTTT-A
36384111 TAATATTTTA
1 TAAT-TTTTA
*
36384121 TAATTTTTC
1 TAATTTTTA
*
36384130 TATGTTTTTA
1 TA-ATTTTTA
*
36384140 T-ATATTTCA
1 TAAT-TTTTA
*
36384149 AAATTTTTA
1 TAATTTTTA
36384158 TAATATTTTA
1 TAAT-TTTTA
*
36384168 T-ATTTTCA
1 TAATTTTTA
36384176 TTAATTTTTA
1 -TAATTTTTA
*
36384186 TGATTTTTCTA
1 T-AATTTT-TA
* *
36384197 TGAGTTTTA
1 TAATTTTTA
36384206 TAA-TTTTA
1 TAATTTTTA
36384214 TAA
1 TAA
36384217 ACTTGTTATA
Statistics
Matches: 137, Mismatches: 27, Indels: 40
0.67 0.13 0.20
Matches are distributed among these distances:
8 20 0.15
9 47 0.34
10 52 0.38
11 16 0.12
12 2 0.01
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.58
Consensus pattern (9 bp):
TAATTTTTA
Found at i:36384738 original size:18 final size:17
Alignment explanation
Indices: 36384715--36384773 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
36384705 TTTTATAATT
36384715 AAAATCATAAAAATTTA
1 AAAATCATAAAAATTTA
*
36384732 CAAAATCATAGAAATAATTA
1 -AAAATCATA-AAA-ATTTA
* *
36384752 AAAATTATAAAAATATA
1 AAAATCATAAAAATTTA
36384769 AAAAT
1 AAAAT
36384774 GAAAAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.23
18 12 0.34
19 11 0.31
20 4 0.11
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATCATAAAAATTTA
Found at i:36384773 original size:27 final size:28
Alignment explanation
Indices: 36384722--36384849 Score: 88
Period size: 27 Copynumber: 4.6 Consensus size: 28
36384712 ATTAAAATCA
*
36384722 TAAAAATT-TACAAAATCATAGAAATA-AT
1 TAAAAATTATA-AAAAT-ATAAAAATATAT
36384750 TAAAAATTATAAAAATATAAAAATGA-A-
1 TAAAAATTATAAAAATATAAAAAT-ATAT
* *
36384777 AAAAAATTATAACAATATAGAAAA-ATAT
1 TAAAAATTATAAAAATATA-AAAATATAT
* * * **
36384805 TATACATGA-AAAAATATCCAAATATAT
1 TAAAAATTATAAAAATATAAAAATATAT
*
36384832 TAAAATTTATTAAAAATA
1 TAAAAATTA-TAAAAATA
36384850 AAAGTACATG
Statistics
Matches: 78, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
26 4 0.05
27 41 0.53
28 24 0.31
29 9 0.12
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (28 bp):
TAAAAATTATAAAAATATAAAAATATAT
Found at i:36384905 original size:29 final size:30
Alignment explanation
Indices: 36384869--36384925 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
36384859 GTAAATTATA
36384869 TAAATTATG-AAAA-AATATATAAAAATGT
1 TAAATTATGAAAAACAATATATAAAAATGT
*
36384897 TAAAGTTATGAAAAACAATATTTAAAAAT
1 TAAA-TTATGAAAAACAATATATAAAAAT
36384926 ATTATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 4 0.16
31 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (30 bp):
TAAATTATGAAAAACAATATATAAAAATGT
Found at i:36385520 original size:9 final size:9
Alignment explanation
Indices: 36385508--36385630 Score: 52
Period size: 9 Copynumber: 12.7 Consensus size: 9
36385498 TTTTTTGAGC
36385508 TTTTTTATA
1 TTTTTTATA
36385517 TTTTATATATTTA
1 TTTT-T-TA--TA
36385530 TTTTTTATA
1 TTTTTTATA
* **
36385539 CTTCATATA
1 TTTTTTATA
36385548 CTTTTTTAT-
1 -TTTTTTATA
36385557 TTTTTTGAATA
1 TTTTTT--ATA
**
36385568 TTTTGAATA
1 TTTTTTATA
*
36385577 TTTTTCA-A
1 TTTTTTATA
36385585 TTTTTATAATA
1 TTTTT-T-ATA
*
36385596 TTTTTTGTAA
1 TTTTTTAT-A
* *
36385606 TTTATAATA
1 TTTTTTATA
36385615 TTTTTTATAA
1 TTTTTTAT-A
36385625 TTTTTT
1 TTTTTT
36385631 TTTGCACTTT
Statistics
Matches: 84, Mismatches: 17, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
8 12 0.14
9 28 0.33
10 23 0.27
11 14 0.17
12 1 0.01
13 6 0.07
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTTATA
Found at i:36385580 original size:19 final size:19
Alignment explanation
Indices: 36385558--36385600 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
36385548 CTTTTTTATT
*
36385558 TTTTTGAATATTTT-GAATA
1 TTTTTCAAT-TTTTAGAATA
*
36385577 TTTTTCAATTTTTATAATA
1 TTTTTCAATTTTTAGAATA
36385596 TTTTT
1 TTTTT
36385601 TGTAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (19 bp):
TTTTTCAATTTTTAGAATA
Found at i:36385609 original size:19 final size:19
Alignment explanation
Indices: 36385587--36385627 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
36385577 TTTTTCAATT
*
36385587 TTTATAATATTTTTTGTAA
1 TTTATAATATTTTTTATAA
36385606 TTTATAATATTTTTTATAA
1 TTTATAATATTTTTTATAA
36385625 TTT
1 TTT
36385628 TTTTTTGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTATAATATTTTTTATAA
Found at i:36393528 original size:41 final size:39
Alignment explanation
Indices: 36393412--36393535 Score: 128
Period size: 37 Copynumber: 3.2 Consensus size: 39
36393402 CCTAGTGCCA
* * *
36393412 CATCGGATAATTCGAAGTACTAAATTGACACCTAGTGTCT
1 CATCGAATAAATCGAAGTA-TAAATTGACACCCAGTGTCT
* * * *
36393452 CATC-AGTTAAACCGAAG--TAAGTTGGCACCCAGTGTCT
1 CATCGA-ATAAATCGAAGTATAAATTGACACCCAGTGTCT
36393489 CATCGAATAAATCTGAAGTAATAAATTGACACCCAGTGTCT
1 CATCGAATAAATC-GAAGT-ATAAATTGACACCCAGTGTCT
36393530 CATCGA
1 CATCGA
36393536 CTTGAAGTCG
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
37 26 0.39
38 5 0.07
40 12 0.18
41 24 0.36
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (39 bp):
CATCGAATAAATCGAAGTATAAATTGACACCCAGTGTCT
Found at i:36401779 original size:69 final size:69
Alignment explanation
Indices: 36401573--36401844 Score: 332
Period size: 69 Copynumber: 4.0 Consensus size: 69
36401563 ACAACATTCA
* * * * *
36401573 TGTCATATTAAGGCTCGTAGGCGAAGAGCCACAGCCT-CAGTATAGTTAGCGAGAGTAAAGCTCC
1 TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAATACAGTTAGCGAGAGCAAAGCTCC
*
36401637 CACC
66 CAGC
* * * * *
36401641 TGTCATATTAAGGCTCGTAGGCGAAGAG-TGCAGCCTCAAATACAGTTAACGAGAGCAAAGCTCT
1 TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAATACAGTTAGCGAGAGCAAAGCTCC
*
36401705 TAGC
66 CAGC
* * * * * *
36401709 TGTCATATTAAGGCTTGCAAGCGAAAAGCCGCAGCCTCCAACACAGTTAGCGAGAGTAAAACTCC
1 TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAATACAGTTAGCGAGAGCAAAGCTCC
36401774 CAGC
66 CAGC
* * * *
36401778 TGTCATACTAAGGCTCGCAGGCGAAGAGTCGCAGCCTCCAATATAGTTAGCAAGAGCAAAGCTCC
1 TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAATACAGTTAGCGAGAGCAAAGCTCC
36401843 CA
66 CA
36401845 ACTGATTATT
Statistics
Matches: 170, Mismatches: 32, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
67 6 0.04
68 75 0.44
69 89 0.52
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (69 bp):
TGTCATATTAAGGCTCGCAGGCGAAGAGCCGCAGCCTCCAATACAGTTAGCGAGAGCAAAGCTCC
CAGC
Found at i:36402212 original size:21 final size:20
Alignment explanation
Indices: 36402203--36402242 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
36402193 TCCTCCCTCC
36402203 CTTCACCCTCTTCCTCTCCTA
1 CTTCACCCTC-TCCTCTCCTA
36402224 CTTCACCTCTCTCCTCTCC
1 CTTCACC-CTCTCCTCTCC
36402243 CTCAACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.07, C:0.55, G:0.00, T:0.38
Consensus pattern (20 bp):
CTTCACCCTCTCCTCTCCTA
Found at i:36407680 original size:19 final size:20
Alignment explanation
Indices: 36407642--36407681 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
36407632 TTTTGAGTGA
36407642 ATTATGGTTTAGGCATATTTTG
1 ATTATGGTTTA-G-ATATTTTG
36407664 ATTATGGTTTA-ATATTTT
1 ATTATGGTTTAGATATTTT
36407682 ATGGATAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
22 11 0.61
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.55
Consensus pattern (20 bp):
ATTATGGTTTAGATATTTTG
Found at i:36413621 original size:11 final size:11
Alignment explanation
Indices: 36413605--36413662 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
36413595 TTTAATCAAA
36413605 TATATATATTT
1 TATATATATTT
36413616 TATATATA--T
1 TATATATATTT
*
36413625 TA-A-ATATAT
1 TATATATATTT
36413634 TATATATATTT
1 TATATATATTT
*
36413645 TAAATATATATT
1 TATATATAT-TT
36413657 TA-ATAT
1 TATATAT
36413663 GGGTCGGGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 3 0.08
8 1 0.03
9 6 0.15
10 1 0.03
11 25 0.62
12 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATATATTT
Found at i:36413631 original size:20 final size:20
Alignment explanation
Indices: 36413608--36413662 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
36413598 AATCAAATAT
36413608 ATATATTTTATATATATTAA
1 ATATATTTTATATATATTAA
* *
36413628 ATATATTATATATATTTTAA
1 ATATATTTTATATATATTAA
36413648 ATATATATTTA-ATAT
1 ATATAT-TTTATATAT
36413663 GGGTCGGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTTTATATATATTAA
Found at i:36416224 original size:11 final size:11
Alignment explanation
Indices: 36416208--36416232 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36416198 TAGCTATGCC
36416208 ATTACAAGTCT
1 ATTACAAGTCT
36416219 ATTACAAGTCT
1 ATTACAAGTCT
36416230 ATT
1 ATT
36416233 CTACAGGCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTACAAGTCT
Found at i:36418482 original size:13 final size:13
Alignment explanation
Indices: 36418464--36418491 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36418454 ATATTTCTTC
36418464 TTACAAGACTCCA
1 TTACAAGACTCCA
36418477 TTACAAGACTCCA
1 TTACAAGACTCCA
36418490 TT
1 TT
36418492 TAGGAATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (13 bp):
TTACAAGACTCCA
Found at i:36422749 original size:21 final size:21
Alignment explanation
Indices: 36422723--36422771 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
36422713 AGATTATGGC
36422723 TATATATTATT-TT-TCTAATAT
1 TATATATTATTATTGT-TAA-AT
36422744 TATATATTATTATTGTTAAAT
1 TATATATTATTATTGTTAAAT
36422765 TATATAT
1 TATATAT
36422772 AATAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 20 0.77
22 5 0.19
23 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATATATTATTATTGTTAAAT
Found at i:36423037 original size:16 final size:16
Alignment explanation
Indices: 36423013--36423074 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
36423003 TGAATTACTG
*
36423013 ATTATAGCTCTATTCC
1 ATTATAGCTCTATTCA
*
36423029 ATTAGAGCTCTATTCA
1 ATTATAGCTCTATTCA
* *
36423045 ATTACAACTCTATTCA
1 ATTATAGCTCTATTCA
*
36423061 ATTATAGCTTTATT
1 ATTATAGCTCTATT
36423075 TTATTACAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTATAGCTCTATTCA
Found at i:36423081 original size:32 final size:32
Alignment explanation
Indices: 36423020--36423083 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
36423010 CTGATTATAG
*
36423020 CTCTATTCCATTAGAGCTCTATTCAATTACAA
1 CTCTATTCAATTAGAGCTCTATTCAATTACAA
* * **
36423052 CTCTATTCAATTATAGCTTTATTTTATTACAA
1 CTCTATTCAATTAGAGCTCTATTCAATTACAA
36423084 ACGTGTACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (32 bp):
CTCTATTCAATTAGAGCTCTATTCAATTACAA
Found at i:36426112 original size:30 final size:31
Alignment explanation
Indices: 36426055--36426112 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
36426045 CAAAATATTA
*
36426055 TTTTCTAATTTTTAAGGAGTATAAAAAAAGT
1 TTTTCTAATTTTTAAGGAGCATAAAAAAAGT
* *
36426086 TTTTTTAATTTTTAAGG-GCCTAAAAAA
1 TTTTCTAATTTTTAAGGAGCATAAAAAA
36426113 TTTGTATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (31 bp):
TTTTCTAATTTTTAAGGAGCATAAAAAAAGT
Found at i:36427196 original size:14 final size:14
Alignment explanation
Indices: 36427153--36427198 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
36427143 AAAAAGTAAA
36427153 AAAAATTAAATTTAT
1 AAAAATTAAA-TTAT
*
36427168 AAAAA-TAGAAATAT
1 AAAAATTA-AATTAT
36427182 AAAAATTAAATTAT
1 AAAAATTAAATTAT
36427196 AAA
1 AAA
36427199 TTTTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAAATTAAATTAT
Found at i:36428967 original size:51 final size:51
Alignment explanation
Indices: 36428889--36428986 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
36428879 TCTTTGAATG
* * *
36428889 CACTCATTTTCTTCGGAGACTAGATAAATTGAAGTTTCAAGTGGACTGGCC
1 CACTCACTTTCTTCGGAGACTAGATAAAATAAAGTTTCAAGTGGACTGGCC
* *
36428940 CACTCACTTTCTTTGGAGACTATATAAAATAAAGTTTCAAGTGGACT
1 CACTCACTTTCTTCGGAGACTAGATAAAATAAAGTTTCAAGTGGACT
36428987 TAGACATGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CACTCACTTTCTTCGGAGACTAGATAAAATAAAGTTTCAAGTGGACTGGCC
Found at i:36435925 original size:21 final size:22
Alignment explanation
Indices: 36435901--36435948 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
36435891 TCTTTAGAAT
36435901 TTTTTAAAAAAAT-TATA-ATAA
1 TTTTTAAAAAAATATATATA-AA
*
36435922 TTTTTAAAAATATATATATAAA
1 TTTTTAAAAAAATATATATAAA
36435944 TTTTT
1 TTTTT
36435949 GAAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 12 0.50
22 11 0.46
23 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTTAAAAAAATATATATAAA
Found at i:36435984 original size:19 final size:19
Alignment explanation
Indices: 36435941--36435988 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
36435931 ATATATATAT
* *
36435941 AAATT-TTTGAAATTTAAT
1 AAATTATTTTAAATTTAAA
36435959 AAA-TATTTTAAATTTAAA
1 AAATTATTTTAAATTTAAA
36435977 AAATTATTTTAA
1 AAATTATTTTAA
36435989 TTTTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 1 0.04
18 17 0.65
19 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAATTATTTTAAATTTAAA
Found at i:36440639 original size:43 final size:43
Alignment explanation
Indices: 36440578--36440663 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
36440568 GTATTAGAAT
* *
36440578 AGGGAAATAACATTACCAGCGGCAGAGGATTGAGGGTGAGGAG
1 AGGGAAAGAACATTACCAGCAGCAGAGGATTGAGGGTGAGGAG
36440621 AGGGAAAGAACATTACCAGCAGCAGAGGATTGAGGGTGAGGAG
1 AGGGAAAGAACATTACCAGCAGCAGAGGATTGAGGGTGAGGAG
36440664 CATCGAGGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.40, T:0.13
Consensus pattern (43 bp):
AGGGAAAGAACATTACCAGCAGCAGAGGATTGAGGGTGAGGAG
Found at i:36441411 original size:58 final size:59
Alignment explanation
Indices: 36441278--36441419 Score: 164
Period size: 61 Copynumber: 2.4 Consensus size: 59
36441268 TTGTTATTAA
* * * *
36441278 ATTTTAATA-ACATTATTATTAAATATAATTTAATAATAATAAAAATAAATGATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATACAATTTAATAATAAT--AAATAAATAATTTAATAAC
* * *
36441339 ATTTTAACATAATTATAATTAAATACAATTTAATAA-AAT-AATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATACAATTTAATAATAATAAATAAATAATTTAATAAC
36441396 ATTCTTAATATAATTATTATTAAA
1 ATT-TTAATATAATTATTATTAAA
36441420 ATAGTGAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
57 17 0.24
58 18 0.26
60 3 0.04
61 31 0.44
62 1 0.01
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATACAATTTAATAATAATAAATAAATAATTTAATAAC
Found at i:36448731 original size:18 final size:18
Alignment explanation
Indices: 36448705--36448771 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
36448695 GTAGTGATTC
*
36448705 AATTTGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
36448723 AATTCGGTTAATTTGGGT
1 AATTCGGTTAATTCGGGT
*
36448741 AATTCGGTTAATTCGGTT
1 AATTCGGTTAATTCGGGT
*
36448759 AATTTGGTTAATT
1 AATTCGGTTAATT
36448772 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:36448737 original size:27 final size:27
Alignment explanation
Indices: 36448705--36448771 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
36448695 GTAGTGATTC
36448705 AATTTGGTTAATTCGGGTAATTCGGTT
1 AATTTGGTTAATTCGGGTAATTCGGTT
* *
36448732 AATTTGGGTAATTCGGTTAATTCGGTT
1 AATTTGGTTAATTCGGGTAATTCGGTT
36448759 AATTTGGTTAATT
1 AATTTGGTTAATT
36448772 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (27 bp):
AATTTGGTTAATTCGGGTAATTCGGTT
Found at i:36448772 original size:9 final size:9
Alignment explanation
Indices: 36448705--36448771 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
36448695 GTAGTGATTC
*
36448705 AATTTGGTT
1 AATTCGGTT
*
36448714 AATTCGGGT
1 AATTCGGTT
36448723 AATTCGGTT
1 AATTCGGTT
* *
36448732 AATTTGGGT
1 AATTCGGTT
36448741 AATTCGGTT
1 AATTCGGTT
36448750 AATTCGGTT
1 AATTCGGTT
*
36448759 AATTTGGTT
1 AATTCGGTT
36448768 AATT
1 AATT
36448772 TTTAACCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (9 bp):
AATTCGGTT
Found at i:36449177 original size:41 final size:41
Alignment explanation
Indices: 36449107--36449305 Score: 263
Period size: 41 Copynumber: 4.9 Consensus size: 41
36449097 AATATTTTTT
* *
36449107 GCGGCGCTTTTTTAAAAACGCCGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* *
36449148 GCGGTGCTTCTTCAAAAACGCCGCTAAAGACCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* * ** *
36449189 GCGGCGCTTCTTCAGAATCATCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* * *
36449230 GCGGCGCTTCTTCAGAAACGCCGCTAAAGACCCAAGAATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
* **
36449271 GCGGCGCTTCTTCAAAAATGCTACTAAAGACCCGA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGA
36449306 AAACTCAAAA
Statistics
Matches: 137, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 137 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.21
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGACCCGAGCATTA
Found at i:36449417 original size:40 final size:39
Alignment explanation
Indices: 36449356--36449449 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 39
36449346 GAATGCTCAT
36449356 TTTTAGCGGCGTTTTCCTAAAAGCACCGCTAATACTCGA
1 TTTTAGCGGCGTTTTCCTAAAAGCACCGCTAATACTCGA
* * * * *
36449395 TCTTTAGCGGCGTTTTCTTAAAAGCGCCGGTAATGCTTGA
1 T-TTTAGCGGCGTTTTCCTAAAAGCACCGCTAATACTCGA
*
36449435 TTTTAGCGGCATTTT
1 TTTTAGCGGCGTTTT
36449450 TTATCCAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
39 14 0.29
40 34 0.71
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (39 bp):
TTTTAGCGGCGTTTTCCTAAAAGCACCGCTAATACTCGA
Found at i:36449669 original size:89 final size:88
Alignment explanation
Indices: 36449516--36449723 Score: 271
Period size: 89 Copynumber: 2.4 Consensus size: 88
36449506 CCGTTCAACG
* * *
36449516 GATTTTATTCCATTATTTTTA-TTTATTTCCAAACGAGAAATTAAAAGTAAATAAGATCCTTTTC
1 GATTTTATTCTATTATTTTGATTTTATTTCCAAACGAGAAATTAAAAGTAAATAAGATCCATTTC
* **
36449580 GAGATTTATTCCCACTGTAT-AAT
66 GAGATTGATTCCCACCAT-TCAAT
* * *
36449603 AGATTTTATTCTATTATTTTGATTTTATTTCCAAATGAGAAATTAAAGGTAAATAAGATTCATTT
1 -GATTTTATTCTATTATTTTGATTTTATTTCCAAACGAGAAATTAAAAGTAAATAAGATCCATTT
*
36449668 CGAGATTGATTCCCGCCATTCAAT
65 CGAGATTGATTCCCACCATTCAAT
*
36449692 GATTTTATTCTA-AATTTTG-TTTTATTTCCAAA
1 GATTTTATTCTATTATTTTGATTTTATTTCCAAA
36449724 AATGAGTAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
86 13 0.12
87 6 0.06
88 32 0.30
89 56 0.52
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (88 bp):
GATTTTATTCTATTATTTTGATTTTATTTCCAAACGAGAAATTAAAAGTAAATAAGATCCATTTC
GAGATTGATTCCCACCATTCAAT
Found at i:36449736 original size:79 final size:79
Alignment explanation
Indices: 36449653--36449881 Score: 318
Period size: 79 Copynumber: 2.9 Consensus size: 79
36449643 AATTAAAGGT
* * * * *
36449653 AAATAAGATTCATTTCGAGATTGATTCCCGCCATTCAATGATTTTATTCTAAATTTTGTTTTATT
1 AAATAAAATTCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCTAAATTTTGTTTTATT
36449718 TCCAAAAATGAGTA
66 TCCAAAAATGAGTA
*
36449732 AAATAAAATTCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATT-TCAAATTTTATTTTAT
1 AAATAAAATTCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCT-AAATTTTGTTTTAT
36449796 TTCCAAAAATGAGTA
65 TTCCAAAAATGAGTA
* * * * * *
36449811 AAATAAAATCCGTTTCGGGATTGATACCCGTCGCTCAACGATTTTATTC-CAATTTCGATTTTAT
1 AAATAAAATTCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCTAAATTTTG-TTTTAT
36449875 TTCCAAA
65 TTCCAAA
36449882 GCTGAGTATT
Statistics
Matches: 134, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
78 6 0.04
79 128 0.96
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (79 bp):
AAATAAAATTCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCTAAATTTTGTTTTATT
TCCAAAAATGAGTA
Found at i:36450008 original size:87 final size:84
Alignment explanation
Indices: 36449811--36450281 Score: 270
Period size: 84 Copynumber: 5.6 Consensus size: 84
36449801 AAAATGAGTA
** * * * * * *
36449811 AAATAAAATCCGTTTCGGGATTGATACCCGTCGCTC-A-ACGATTTTATTCCAATTTCGATTTTA
1 AAATAAAATATGTTTCGGGATTTATTCCCGTCGTTCAATAAGATTTTATTAC-ATTT-GATTTTG
* ** *
36449874 TTTCCAAAGCTGAGTATTAAAGCT
64 TTTCCAAAAC--AAAATTAAA-TT
* **
36449898 AAATTAAAATATGTTTCGGGATTTATTCCCGTTGTTCAA-CGGA-TTTATTACACTTTGATTTTG
1 AAA-TAAAATATGTTTCGGGATTTATTCCCGTCGTTCAATAAGATTTTATTACA-TTTGATTTTG
36449961 TTTCCAAAAACAAAAAATTAAAATT
64 TTTCC-AAAAC--AAAATT-AAATT
* * * * ** *
36449986 AAATAAAATCTGTTTCAGGATTTATTCTCGTCGTTTAATAAGATTTTATTTGATTTTATTTTGTT
1 AAATAAAATATGTTTCGGGATTTATTCCCGTCGTTCAATAAGATTTTATTACATTTGATTTTGTT
* *
36450051 TCCAAATCAGAATTAAATT
66 TCCAAAACAAAATTAAATT
* * * * *
36450070 AAATAAAATTTGTTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTA-T---TTT-ATTTTGTT
1 AAATAAAATATGTTTCGGGATTTATTCCCGTCGTTCAATAAGATTTTATTACATTTGATTTTGTT
* *
36450130 TCCAAATTC-GAATTAAATT
66 TCCAAA-ACAAAATTAAATT
* * * * * *
36450149 AAATAAAATCTATTTTGGGATTTATTCCTGCCGTTTAATAAGATTTTATT-CGATATTG-TTTTG
1 AAATAAAATATGTTTCGGGATTTATTCCCGTCGTTCAATAAGATTTTATTAC-AT-TTGATTTTG
* * *
36450212 TTTCC-TAACAAAGACGT-AATC
64 TTTCCAAAACAAA-A-TTAAATT
* * * * * * *
36450233 AAAT-AATTCTATTTCGGGATTTATTCTCGTCGTTTAACAAAATTTTATT
1 AAATAAAATATGTTTCGGGATTTATTCCCGTCGTTCAATAAGATTTTATT
36450282 TTGATTTAAT
Statistics
Matches: 317, Mismatches: 50, Indels: 38
0.78 0.12 0.09
Matches are distributed among these distances:
79 66 0.21
80 6 0.02
82 1 0.00
83 42 0.13
84 69 0.22
85 6 0.02
87 49 0.15
88 65 0.21
89 13 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (84 bp):
AAATAAAATATGTTTCGGGATTTATTCCCGTCGTTCAATAAGATTTTATTACATTTGATTTTGTT
TCCAAAACAAAATTAAATT
Found at i:36450084 original size:84 final size:84
Alignment explanation
Indices: 36449976--36450288 Score: 340
Period size: 84 Copynumber: 3.8 Consensus size: 84
36449966 AAAAACAAAA
* * * *
36449976 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTCTCGTCGTTTAATAAGATTTTATTTGATT
1 AATT-AAATTAAATAAAATCTATTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTGATT
36450041 TTATTTTGTTTCCAAATCAG
65 TTATTTTGTTTCCAAATCAG
* *
36450061 AATTAAATTAAATAAAATTTGTTTCGGGATTTATTCTCGCCGTTTAACAAGA---T-TTT-ATTT
1 AATTAAATTAAATAAAATCTATTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTGATTT
36450121 TATTTTGTTTCCAAATTC-G
66 TATTTTGTTTCCAAA-TCAG
* * * *
36450140 AATTAAATTAAATAAAATCTATTTTGGGATTTATTC-CTGCCGTTTAATAAGATTTTATTCGATA
1 AATTAAATTAAATAAAATCTATTTCGGGATTTATTCTC-GCCGTTTAACAAGATTTTATTTGATT
* *
36450204 TTGTTTTGTTTCCTAACA-AAG
65 TTATTTTGTTTCC-AA-ATCAG
** * * * *
36450225 ACGT-AATCAAAT-AATTCTATTTCGGGATTTATTCTCGTCGTTTAACAAAATTTTATTTTGATT
1 AATTAAATTAAATAAAATCTATTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTA-TTTGATT
36450288 T
65 T
36450289 AATGATATAA
Statistics
Matches: 194, Mismatches: 22, Indels: 25
0.80 0.09 0.10
Matches are distributed among these distances:
78 1 0.01
79 66 0.34
80 5 0.03
81 1 0.01
82 1 0.01
83 38 0.20
84 72 0.37
85 9 0.05
86 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (84 bp):
AATTAAATTAAATAAAATCTATTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTGATTT
TATTTTGTTTCCAAATCAG
Found at i:36450136 original size:79 final size:79
Alignment explanation
Indices: 36449976--36450198 Score: 306
Period size: 79 Copynumber: 2.7 Consensus size: 79
36449966 AAAAACAAAA
* *
36449976 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTCTCGTCGTTTAATAAGATTTTATTTGATT
1 AATT-AAATTAAATAAAATCTGTTTCGGGATTTATTCTCGCCGTTTAATAAGA---T-TTT-ATT
36450041 TTATTTTGTTTCCAAA-TCAG
60 TTATTTTGTTTCCAAATTC-G
* *
36450061 AATTAAATTAAATAAAATTTGTTTCGGGATTTATTCTCGCCGTTTAACAAGATTTTATTTTATTT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCTCGCCGTTTAATAAGATTTTATTTTATTT
36450126 TGTTTCCAAATTCG
66 TGTTTCCAAATTCG
* *
36450140 AATTAAATTAAATAAAATCTATTTTGGGATTTATTC-CTGCCGTTTAATAAGATTTTATT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCTC-GCCGTTTAATAAGATTTTATT
36450199 CGATATTGTT
Statistics
Matches: 128, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
78 1 0.01
79 73 0.57
80 5 0.04
81 1 0.01
84 44 0.34
85 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.47
Consensus pattern (79 bp):
AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCTCGCCGTTTAATAAGATTTTATTTTATTT
TGTTTCCAAATTCG
Found at i:36450172 original size:163 final size:164
Alignment explanation
Indices: 36449976--36450288 Score: 413
Period size: 163 Copynumber: 1.9 Consensus size: 164
36449966 AAAAACAAAA
* * *
36449976 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATT-CTCGTCGTTTAATAAGATTTTATTTGAT
1 AATTAAAATTAAATAAAATCTATTTCAGGATTTATTCCT-GCCGTTTAATAAGATTTTATTCGAT
* * * * *
36450040 TTTATTTTGTTTCC-AA-ATCAGAATTAAATTAAATAAAATT-TGTTTCGGGATTTATTCTCGCC
65 ATTATTTTGTTTCCTAACA-AAGAAGT-AATCAAAT--AATTCTATTTCGGGATTTATTCTCGCC
*
36450102 GTTTAACAAGATTTTATTTT-ATTTTGTTTCCAAATTCG
126 GTTTAACAAAATTTTATTTTGATTTTGTTTCCAAATTCG
**
36450140 AATT-AAATTAAATAAAATCTATTTTGGGATTTATTCCTGCCGTTTAATAAGATTTTATTCGATA
1 AATTAAAATTAAATAAAATCTATTTCAGGATTTATTCCTGCCGTTTAATAAGATTTTATTCGATA
* * *
36450204 TTGTTTTGTTTCCTAACAAAGACGTAATCAAATAATTCTATTTCGGGATTTATTCTCGTCGTTTA
66 TTATTTTGTTTCCTAACAAAGAAGTAATCAAATAATTCTATTTCGGGATTTATTCTCGCCGTTTA
36450269 ACAAAATTTTATTTTGATTT
131 ACAAAATTTTATTTTGATTT
36450289 AATGATATAA
Statistics
Matches: 130, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
161 4 0.03
162 39 0.30
163 74 0.57
164 12 0.09
165 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (164 bp):
AATTAAAATTAAATAAAATCTATTTCAGGATTTATTCCTGCCGTTTAATAAGATTTTATTCGATA
TTATTTTGTTTCCTAACAAAGAAGTAATCAAATAATTCTATTTCGGGATTTATTCTCGCCGTTTA
ACAAAATTTTATTTTGATTTTGTTTCCAAATTCG
Found at i:36454573 original size:18 final size:18
Alignment explanation
Indices: 36454550--36454586 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
36454540 ATACAAGGTT
36454550 TGAATTTATACACGTATA
1 TGAATTTATACACGTATA
36454568 TGAATTTATACACGTATA
1 TGAATTTATACACGTATA
36454586 T
1 T
36454587 ACATGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TGAATTTATACACGTATA
Found at i:36454595 original size:18 final size:18
Alignment explanation
Indices: 36454550--36454595 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
36454540 ATACAAGGTT
*
36454550 TGAATTTATACACGTATA
1 TGAATGTATACACGTATA
*
36454568 TGAATTTATACACGTATA
1 TGAATGTATACACGTATA
36454586 T-ACATGTATA
1 TGA-ATGTATA
36454596 AATTATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
TGAATGTATACACGTATA
Found at i:36455789 original size:38 final size:38
Alignment explanation
Indices: 36455747--36455858 Score: 105
Period size: 32 Copynumber: 3.1 Consensus size: 38
36455737 TACATGTACA
*
36455747 CATTTGGTTATAATATTTGTTAAGCATATGTATATATG
1 CATTTGGTTCTAATATTTGTTAAGCATATGTATATATG
* *
36455785 CATTTGG--CTAATATGT-TTAA--A-GTGTATATA--
1 CATTTGGTTCTAATATTTGTTAAGCATATGTATATATG
* *
36455815 CATTTGGTTCTAATATTTGTCATGCATATATGTATATATG
1 CATTTGGTTCTAATATTTGTTAAGC--ATATGTATATATG
36455855 CATT
1 CATT
36455859 CGGCGATTCA
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
30 7 0.12
32 16 0.28
33 3 0.05
35 4 0.07
36 7 0.12
37 1 0.02
38 15 0.26
40 4 0.07
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.46
Consensus pattern (38 bp):
CATTTGGTTCTAATATTTGTTAAGCATATGTATATATG
Found at i:36455829 original size:68 final size:70
Alignment explanation
Indices: 36455746--36455894 Score: 185
Period size: 68 Copynumber: 2.1 Consensus size: 70
36455736 ATACATGTAC
* * * *
36455746 ACATTTGGTTATAATATTTGTTAAGC-ATATGTATATATGCATTTGGCTAAT-ATGTTTAAAGTG
1 ACATTTGGTTATAATATTTGTCAAGCAATATGTATATATGCATTCGGCGAATCATGTTTAAAGAG
36455809 TATAT
66 TATAT
* * * *
36455814 ACATTTGGTTCTAATATTTGTCATGCATATATGTATATATGCATTCGGCGATTCATGTTTATAGA
1 ACATTTGGTTATAATATTTGTCAAGCA-ATATGTATATATGCATTCGGCGAATCATGTTTAAAGA
36455879 GTATAT
65 GTATAT
* *
36455885 GCATTCGGTT
1 ACATTTGGTT
36455895 TTAAATCTTG
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 23 0.34
70 22 0.32
71 23 0.34
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.44
Consensus pattern (70 bp):
ACATTTGGTTATAATATTTGTCAAGCAATATGTATATATGCATTCGGCGAATCATGTTTAAAGAG
TATAT
Found at i:36455920 original size:71 final size:70
Alignment explanation
Indices: 36455746--36455894 Score: 169
Period size: 71 Copynumber: 2.1 Consensus size: 70
36455736 ATACATGTAC
* * * * *
36455746 ACATTTGGTTATAATATTTGTTAA-GC--ATATGTATATATGCATTTGGCTAATATGTTTAAAGT
1 ACATTCGGTTCTAATATTTG-TAATGCATATATGTATATATGCATTCGGCGAATATGTTTAAAGA
36455808 GTATAT
65 GTATAT
* * * *
36455814 ACATTTGGTTCTAATATTTGTCATGCATATATGTATATATGCATTCGGCGATTCATGTTTATAGA
1 ACATTCGGTTCTAATATTTGTAATGCATATATGTATATATGCATTCGGCGAAT-ATGTTTAAAGA
36455879 GTATAT
65 GTATAT
*
36455885 GCATTCGGTT
1 ACATTCGGTT
36455895 TTAAATCTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
67 2 0.03
68 21 0.31
70 22 0.32
71 23 0.34
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.44
Consensus pattern (70 bp):
ACATTCGGTTCTAATATTTGTAATGCATATATGTATATATGCATTCGGCGAATATGTTTAAAGAG
TATAT
Found at i:36456930 original size:20 final size:20
Alignment explanation
Indices: 36456885--36456931 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36456875 ATTTATCCTG
36456885 AATT-ATTTGATTCTAATCA
1 AATTGATTTGATTCTAATCA
** *
36456904 AGGTGATTTGATTTTAATCA
1 AATTGATTTGATTCTAATCA
36456924 AATTGATT
1 AATTGATT
36456932 CAATTGCCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (20 bp):
AATTGATTTGATTCTAATCA
Found at i:36459857 original size:10 final size:10
Alignment explanation
Indices: 36459842--36459895 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
36459832 CATGTGGTTC
36459842 AGCTCATTCG
1 AGCTCATTCG
*
36459852 AGCTCAAGTC-
1 AGCTC-ATTCG
36459862 AGCTCATTCG
1 AGCTCATTCG
36459872 AGCTCAATTC-
1 AGCTC-ATTCG
36459882 AGCTCATT-G
1 AGCTCATTCG
36459891 AGCTC
1 AGCTC
36459896 GTTATTAGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 11 0.29
10 20 0.53
11 7 0.18
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (10 bp):
AGCTCATTCG
Found at i:36459865 original size:20 final size:20
Alignment explanation
Indices: 36459840--36459895 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
36459830 TTCATGTGGT
36459840 TCAGCTCATTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
*
36459860 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCATTCGAGCTCAAG
36459880 TCAGCTCATT-GAGCTC
1 TCAGCTCATTCGAGCTC
36459896 GTTATTAGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 6 0.17
20 29 0.83
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (20 bp):
TCAGCTCATTCGAGCTCAAG
Found at i:36465986 original size:32 final size:33
Alignment explanation
Indices: 36465950--36466022 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
36465940 CAGTTTTTAT
*
36465950 AAAATATTTT-CAGA-ATATTTGCCAAACACTAG
1 AAAATATTTTACAGAGATATAT-CCAAACACTAG
*
36465982 AAAATATTTTACAGAGATCTATCCAAACACTAG
1 AAAATATTTTACAGAGATATATCCAAACACTAG
36466015 AAAATATT
1 AAAATATT
36466023 AACTTTTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 10 0.27
33 23 0.62
34 4 0.11
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (33 bp):
AAAATATTTTACAGAGATATATCCAAACACTAG
Found at i:36467006 original size:29 final size:30
Alignment explanation
Indices: 36466959--36467016 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
36466949 ATAAGTCTTT
* *
36466959 AGAATTTAGTTAATGTACT-TTTATATTTA
1 AGAATTTAGTTAATCTACTCTTGATATTTA
**
36466988 AGAATTTAGTTCCTCTACTCTTGATATTT
1 AGAATTTAGTTAATCTACTCTTGATATTT
36467017 CAAAATTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (30 bp):
AGAATTTAGTTAATCTACTCTTGATATTTA
Found at i:36467165 original size:17 final size:17
Alignment explanation
Indices: 36467143--36467175 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36467133 CTGAAGTAAC
36467143 TAAATTAATTTT-TCAAT
1 TAAATT-ATTTTCTCAAT
36467160 TAAATTATTTTCTCAA
1 TAAATTATTTTCTCAA
36467176 CCAAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAATTATTTTCTCAAT
Found at i:36467323 original size:14 final size:15
Alignment explanation
Indices: 36467300--36467332 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
36467290 ATCAGACTTC
*
36467300 AATTATTTAAAT-AT
1 AATTAATTAAATAAT
36467314 AATTAATTAAATAAT
1 AATTAATTAAATAAT
36467329 AATT
1 AATT
36467333 CAAAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAATTAAATAAT
Found at i:36485432 original size:29 final size:29
Alignment explanation
Indices: 36485356--36485426 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
36485346 CACGATAACG
36485356 TAAGTGACTAAAACGTAACATTTCAAACA
1 TAAGTGACTAAAACGTAACATTTCAAACA
*
36485385 TAAGTGATTAAAACGTAACATTTCAAACA
1 TAAGTGACTAAAACGTAACATTTCAAACA
36485414 TAAGTGACTAAAA
1 TAAGTGACTAAAA
36485427 TATAACTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.25
Consensus pattern (29 bp):
TAAGTGACTAAAACGTAACATTTCAAACA
Found at i:36490829 original size:23 final size:23
Alignment explanation
Indices: 36490803--36490848 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
36490793 CTAAAATGCT
36490803 TATGATTGAATACACCCAACAAG
1 TATGATTGAATACACCCAACAAG
36490826 TATGATTGAATACACCCAACAAG
1 TATGATTGAATACACCCAACAAG
36490849 CACAGATAAT
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:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (23 bp):
TATGATTGAATACACCCAACAAG
Found at i:36497883 original size:23 final size:23
Alignment explanation
Indices: 36497856--36497899 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
36497846 CACCAGTTCA
* *
36497856 TTTAAATCTTTTTTTTTTAATTT
1 TTTAAATATTTATTTTTTAATTT
*
36497879 TTTAATTATTTATTTTTTAAT
1 TTTAAATATTTATTTTTTAAT
36497900 CTAAAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTAAATATTTATTTTTTAATTT
Found at i:36501332 original size:30 final size:30
Alignment explanation
Indices: 36501298--36501386 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 30
36501288 GTGTTCAGAG
* * **
36501298 GTTGGTCCTTTGGTTCGGGCTTTGCCATAT
1 GTTGGTCCTTTGGGTCAGGCTTCACCATAT
**
36501328 GTTGGTCCTCCGGGTCAGGCTTCACCATAT
1 GTTGGTCCTTTGGGTCAGGCTTCACCATAT
* * *
36501358 GTTGATCCTTTGAGTC-GAGCTCCACCATA
1 GTTGGTCCTTTGGGTCAG-GCTTCACCATA
36501387 GGTTTTCCTC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
29 1 0.02
30 46 0.98
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.35
Consensus pattern (30 bp):
GTTGGTCCTTTGGGTCAGGCTTCACCATAT
Done.