Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 10 of 163
Found at i:2897964 original size:28 final size:29
Alignment explanation
Indices: 2897902--2897966 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
2897892 TTTCCCATTT
*
2897902 TGGTACCTAAACATTTATTTTTTATTACAAG
1 TGGTACCTAAAC--TTACTTTTTATTACAAG
*
2897933 TGGTACCTAAAC-TACTTTTT-TTCCAAG
1 TGGTACCTAAACTTACTTTTTATTACAAG
2897960 CTGGTAC
1 -TGGTAC
2897967 ATCTACTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 6 0.19
28 13 0.42
31 12 0.39
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (29 bp):
TGGTACCTAAACTTACTTTTTATTACAAG
Found at i:2905427 original size:24 final size:24
Alignment explanation
Indices: 2905400--2905474 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
2905390 AGTTTGACTC
*
2905400 AAACAAATAAACATTGTTTAATTG
1 AAACAAATAAACAGTGTTTAATTG
* *
2905424 AAACAAATAAAGAGAGTTTAATTG
1 AAACAAATAAACAGTGTTTAATTG
* *
2905448 AAACAATTAAACAGTGTTTAACTG
1 AAACAAATAAACAGTGTTTAATTG
2905472 AAA
1 AAA
2905475 GATTATTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAGTGTTTAATTG
Found at i:2907429 original size:24 final size:24
Alignment explanation
Indices: 2907402--2907476 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
2907392 AGTTTGACTT
2907402 AAACAAATAAACATAGTTTAATTG
1 AAACAAATAAACATAGTTTAATTG
* *
2907426 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACATAGTTTAATTG
* *
2907450 AAACAATTAAACAGTA-TTTAACTG
1 AAACAAATAAACA-TAGTTTAATTG
2907474 AAA
1 AAA
2907477 GATATTTCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACATAGTTTAATTG
Found at i:2912362 original size:5 final size:5
Alignment explanation
Indices: 2912352--2912377 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2912342 AAATAATGTT
2912352 AAAGA AAAGA AAAGA AAAGA AAAGA A
1 AAAGA AAAGA AAAGA AAAGA AAAGA A
2912378 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:2917938 original size:111 final size:114
Alignment explanation
Indices: 2917812--2918052 Score: 312
Period size: 117 Copynumber: 2.1 Consensus size: 114
2917802 AATCTATAAA
* * * *
2917812 TAAAATTAAATTAAGAGTGTTGATTTATTTAAACATATTTGAAAAATT-AAC-ATG-T-TCATTG
1 TAAAATTAAACTAAGAGTGTTGACTTATTTAAAAATAATTG-AAAATTCAACTATGATGTCATTG
* *
2917873 GGGCATATAAATAATGCCCAATAGGAAT-ATATAAAGCAGCACTACATTTC
65 GGGCATATAAATAATACCCAATA-AAATAATATAAAGCAGCACTACATTTC
* * *
2917923 TAAAATTAAACTAAGAGTGTTGACTTATTTAAAAATAATTGAGATTTCAACTTTTTGATTGTCAT
1 TAAAATTAAACTAAGAGTGTTGACTTATTTAAAAATAATTGAAAATTCAAC--TATGA-TGTCAT
*
2917988 TTGGGCATATAAATAATACCCAATAAAATAATATAAAGCAGCACTACATTTC
63 TGGGGCATATAAATAATACCCAATAAAATAATATAAAGCAGCACTACATTTC
2918040 TAAAATTAAACTA
1 TAAAATTAAACTA
2918053 CATCCTTTTT
Statistics
Matches: 112, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
110 4 0.04
111 40 0.36
114 2 0.02
116 4 0.04
117 62 0.55
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (114 bp):
TAAAATTAAACTAAGAGTGTTGACTTATTTAAAAATAATTGAAAATTCAACTATGATGTCATTGG
GGCATATAAATAATACCCAATAAAATAATATAAAGCAGCACTACATTTC
Found at i:2920488 original size:19 final size:19
Alignment explanation
Indices: 2920444--2920491 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2920434 AAAAAATTAT
2920444 ACAAATAAAAAGGATGACGA
1 ACAAATAAAAA-GATGACGA
**
2920464 TTAAATGAAAAA-ATGACGA
1 ACAAAT-AAAAAGATGACGA
2920483 ACAAATAAA
1 ACAAATAAA
2920492 TTTCAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 3 0.13
19 11 0.48
20 4 0.17
21 5 0.22
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (19 bp):
ACAAATAAAAAGATGACGA
Found at i:2922606 original size:58 final size:58
Alignment explanation
Indices: 2922516--2922626 Score: 222
Period size: 58 Copynumber: 1.9 Consensus size: 58
2922506 GATGGGCAAA
2922516 GACATTGTTTGTCAAGAATCTAAAAGCATCGGAATGCGTAGTAGGTTATGGGATCCTC
1 GACATTGTTTGTCAAGAATCTAAAAGCATCGGAATGCGTAGTAGGTTATGGGATCCTC
2922574 GACATTGTTTGTCAAGAATCTAAAAGCATCGGAATGCGTAGTAGGTTATGGGA
1 GACATTGTTTGTCAAGAATCTAAAAGCATCGGAATGCGTAGTAGGTTATGGGA
2922627 CCCTGAGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (58 bp):
GACATTGTTTGTCAAGAATCTAAAAGCATCGGAATGCGTAGTAGGTTATGGGATCCTC
Found at i:2925424 original size:73 final size:73
Alignment explanation
Indices: 2925347--2925493 Score: 215
Period size: 73 Copynumber: 2.0 Consensus size: 73
2925337 GAACATCAGT
** * * *
2925347 TTGATGAGATGAGCAATGATGCATCGGATGAAGATCAGATT-GATGAGACGAGCAATGATGTATC
1 TTGATGAGACCAGCAATGATGCATCGGATGAACATCA-ATTAGATGAGACGAGCAATGATGCAGC
2925411 GGATGAAGA
65 GGATGAAGA
* *
2925420 TTGATGAGACCAGCAGTGATGCATCGGATGAACATCAATTAGATGAGACGAGCAGTGATGCAGCG
1 TTGATGAGACCAGCAATGATGCATCGGATGAACATCAATTAGATGAGACGAGCAATGATGCAGCG
2925485 GATGAAGA
66 GATGAAGA
2925493 T
1 T
2925494 CAAGAAATGT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 3 0.05
73 63 0.95
ACGTcount: A:0.35, C:0.12, G:0.31, T:0.22
Consensus pattern (73 bp):
TTGATGAGACCAGCAATGATGCATCGGATGAACATCAATTAGATGAGACGAGCAATGATGCAGCG
GATGAAGA
Found at i:2925496 original size:39 final size:38
Alignment explanation
Indices: 2925347--2925496 Score: 191
Period size: 39 Copynumber: 4.0 Consensus size: 38
2925337 GAACATCAGT
*
2925347 TTGATGAGATGAGCAATGATGCATCGGATGAAGATCAGA
1 TTGATGAGACGAGCAATGATGCATCGGATGAAGATCA-A
*
2925386 TTGATGAGACGAGCAATGATGTATCGGATGAAG----A
1 TTGATGAGACGAGCAATGATGCATCGGATGAAGATCAA
* * *
2925420 TTGATGAGACCAGCAGTGATGCATCGGATGAACATCAA
1 TTGATGAGACGAGCAATGATGCATCGGATGAAGATCAA
* *
2925458 TTAGATGAGACGAGCAGTGATGCAGCGGATGAAGATCAA
1 TT-GATGAGACGAGCAATGATGCATCGGATGAAGATCAA
2925497 GAAATGTGCA
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
34 30 0.31
38 3 0.03
39 64 0.66
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (38 bp):
TTGATGAGACGAGCAATGATGCATCGGATGAAGATCAA
Found at i:2930867 original size:6 final size:6
Alignment explanation
Indices: 2930851--2930881 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
2930841 CTTTCTTTCC
2930851 CTTGTAG CTTGAG CTTGAG CTTGAG CTTGAG
1 CTTG-AG CTTGAG CTTGAG CTTGAG CTTGAG
2930882 TTTTCTCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (6 bp):
CTTGAG
Found at i:2933005 original size:41 final size:41
Alignment explanation
Indices: 2932939--2933157 Score: 307
Period size: 41 Copynumber: 5.3 Consensus size: 41
2932929 AAGGTAAGAG
* *
2932939 AAGCGCCGCT-AAAGATC-AGATCAATAGCGGCGCATATGGAA
1 AAGCGCCGCTAAAAG-TCTA-AGCAATAGCGGCGCTTATGGAA
*
2932980 AAGCGCCGCTAAAAGTCTAAGCAATAGCAGCGCTTATGGAA
1 AAGCGCCGCTAAAAGTCTAAGCAATAGCGGCGCTTATGGAA
* * * *
2933021 AAGCACCGGTAAAAGTCTAAGCAATTGCGGTGCTTATGGAA
1 AAGCGCCGCTAAAAGTCTAAGCAATAGCGGCGCTTATGGAA
* *
2933062 AAGCACCGCGAAAAGTCTAAGCAATAGCGGCGCTTATGGAA
1 AAGCGCCGCTAAAAGTCTAAGCAATAGCGGCGCTTATGGAA
* *
2933103 AAGCGCTGCTAAAAGTCTAAGCAATAGCGGCGCTTATGGCA
1 AAGCGCCGCTAAAAGTCTAAGCAATAGCGGCGCTTATGGAA
2933144 AAGCGCCGCTAAAA
1 AAGCGCCGCTAAAA
2933158 TTTTTACATT
Statistics
Matches: 159, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
41 154 0.97
42 5 0.03
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (41 bp):
AAGCGCCGCTAAAAGTCTAAGCAATAGCGGCGCTTATGGAA
Found at i:2935660 original size:34 final size:34
Alignment explanation
Indices: 2935582--2935672 Score: 101
Period size: 34 Copynumber: 2.7 Consensus size: 34
2935572 ATTTAATTGT
* * *
2935582 TTAATTAAATATTTAATTATTAAAAACAACCCAA
1 TTAATTAATTATTTAATTATTTAAATCAACCCAA
* * * *
2935616 ATACTGAATTATTTAATTATTTAAATCAACTCAA
1 TTAATTAATTATTTAATTATTTAAATCAACCCAA
* *
2935650 TTAATTAATTAATTATTTATTTA
1 TTAATTAATTATTTAATTATTTA
2935673 TTTAAATATT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (34 bp):
TTAATTAATTATTTAATTATTTAAATCAACCCAA
Found at i:2935724 original size:22 final size:20
Alignment explanation
Indices: 2935697--2935760 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 20
2935687 ATAACTCAAA
2935697 TATTTAATTCAAAATATTTAAT
1 TATTTAATT--AAATATTTAAT
2935719 TATTTAATT--ATATTTAAT
1 TATTTAATTAAATATTTAAT
2935737 TATTTAATTAAATATTTAAT
1 TATTTAATTAAATATTTAAT
2935757 TATT
1 TATT
2935761 AAAAACAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 18 0.45
20 13 0.32
22 9 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTAATTAAATATTTAAT
Found at i:2935760 original size:8 final size:8
Alignment explanation
Indices: 2935711--2935746 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
2935701 TAATTCAAAA
2935711 TATTTAAT
1 TATTTAAT
2935719 TATTTAATT
1 TATTTAA-T
2935728 ATATTTAAT
1 -TATTTAAT
2935737 TATTTAAT
1 TATTTAAT
2935745 TA
1 TA
2935747 AATATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 17 0.65
9 2 0.08
10 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTAAT
Found at i:2935792 original size:34 final size:33
Alignment explanation
Indices: 2935741--2935828 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 33
2935731 TTTAATTATT
*
2935741 TAATTAAATATTTAATTATTAAAAACAACCCAAA
1 TAATTAATTATTTAATTATT-AAAACAACCCAAA
* * *
2935775 TACTTAATTATTTAATTAGTTAAATCAACCCAAT
1 TAATTAATTATTTAATTA-TTAAAACAACCCAAA
*
2935809 TAATTAATTAATTAATTATT
1 TAATTAATTATTTAATTATT
2935829 TATTTATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 2 0.04
34 43 0.91
35 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (33 bp):
TAATTAATTATTTAATTATTAAAACAACCCAAA
Found at i:2935907 original size:20 final size:18
Alignment explanation
Indices: 2935873--2935914 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
2935863 TAATTCAAAA
2935873 TATTTAATTATATTTAAT
1 TATTTAATTATATTTAAT
2935891 TATTTAATTAAATATTTAAT
1 TATTTAATT--ATATTTAAT
2935911 TATT
1 TATT
2935915 AAAAACAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTAATTATATTTAAT
Found at i:2935932 original size:154 final size:154
Alignment explanation
Indices: 2935434--2936246 Score: 1271
Period size: 154 Copynumber: 5.2 Consensus size: 154
2935424 TGAATTTTTT
** * * *
2935434 TTAAAT-TTTAAATTAGAAAAAACAGCCCAAATACTTCATTATTTAATTACTTAAATCAACCCAA
1 TTAAATATTT-AATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAA
* *
2935498 TTAATTAATTAGTTAATTATTTATTTATTTAAATATTAAAAATAACCCAAATATTTAATTCAAAA
65 TTAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAA
*
2935563 TATTTAA-T-TATTTAATTGTTTAA
130 TATTTAATTATATTTAATTATTTAA
* *
2935586 TTAAATATTTAATTATTAAAAACAACCCAAATACTGAATTATTTAATTATTTAAATCAA--C--T
1 TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
* * *
2935647 CAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAATAACTCAAATATTTAATTCAAAAT
66 TAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTC---A-
2935712 ATTTAATTATTTAATTATATTTAATTATTTAA
127 A---AA-TATTTAATTATATTTAATTATTTAA
2935744 TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
1 TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
*
2935809 TAATTAATTAATTAATTATTTATTTATATAAATATTAAAAACAACCCAAATATTTAATTCAAAAT
66 TAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAAT
2935874 ATTTAATTATATTTAATTATTTAA
131 ATTTAATTATATTTAATTATTTAA
2935898 TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
1 TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
* *
2935963 TAATTAATTAATTATTTATTTATTTATATAAATATTAAAAACAACCCAAATATTTAATTCAAAAT
66 TAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAAT
2936028 ATTTAATTATATTTAATTATTTAA
131 ATTTAATTATATTTAATTATTTAA
2936052 TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
1 TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
2936117 TAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAAT
66 TAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAAT
2936182 ATTTAATTATTTAATTATATTTACTTATTTAA
131 ATTTAATTA--T-ATT-TA---A-TTATTTAA
*
2936214 TTAAATATTTAATTATTAAAAATAACCCAAATA
1 TTAAATATTTAATTATTAAAAACAACCCAAATA
2936247 ATTTTGATGA
Statistics
Matches: 618, Mismatches: 20, Indels: 36
0.92 0.03 0.05
Matches are distributed among these distances:
148 58 0.09
150 1 0.00
151 1 0.00
152 50 0.08
153 3 0.00
154 315 0.51
155 4 0.01
156 8 0.01
157 4 0.01
158 74 0.12
159 1 0.00
160 1 0.00
161 1 0.00
162 97 0.16
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (154 bp):
TTAAATATTTAATTATTAAAAACAACCCAAATACTTAATTATTTAATTAGTTAAATCAACCCAAT
TAATTAATTAATTAATTATTTATTTATTTAAATATTAAAAACAACCCAAATATTTAATTCAAAAT
ATTTAATTATATTTAATTATTTAA
Found at i:2935946 original size:34 final size:33
Alignment explanation
Indices: 2935895--2935982 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 33
2935885 TTTAATTATT
*
2935895 TAATTAAATATTTAATTATTAAAAACAACCCAAA
1 TAATTAATTATTTAATTATT-AAAACAACCCAAA
* * *
2935929 TACTTAATTATTTAATTAGTTAAATCAACCCAAT
1 TAATTAATTATTTAATTA-TTAAAACAACCCAAA
* *
2935963 TAATTAATTAATTATTTATT
1 TAATTAATTATTTAATTATT
2935983 TATTTATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
33 2 0.04
34 42 0.91
35 2 0.04
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (33 bp):
TAATTAATTATTTAATTATTAAAACAACCCAAA
Found at i:2936061 original size:20 final size:18
Alignment explanation
Indices: 2936027--2936068 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
2936017 TAATTCAAAA
2936027 TATTTAATTATATTTAAT
1 TATTTAATTATATTTAAT
2936045 TATTTAATTAAATATTTAAT
1 TATTTAATT--ATATTTAAT
2936065 TATT
1 TATT
2936069 AAAAACAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTAATTATATTTAAT
Found at i:2936097 original size:34 final size:33
Alignment explanation
Indices: 2936049--2936136 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 33
2936039 TTTAATTATT
*
2936049 TAATTAAATATTTAATTATTAAAAACAACCCAAA
1 TAATTAATTATTTAATTATT-AAAACAACCCAAA
* * *
2936083 TACTTAATTATTTAATTAGTTAAATCAACCCAAT
1 TAATTAATTATTTAATTA-TTAAAACAACCCAAA
*
2936117 TAATTAATTAATTAATTATT
1 TAATTAATTATTTAATTATT
2936137 TATTTATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
33 2 0.04
34 43 0.91
35 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (33 bp):
TAATTAATTATTTAATTATTAAAACAACCCAAA
Found at i:2936192 original size:22 final size:20
Alignment explanation
Indices: 2936167--2936230 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 20
2936157 ACAACCCAAA
2936167 TATTTAATTCAAAATATTTAAT
1 TATTTAATT--AAATATTTAAT
*
2936189 TATTTAATT--ATATTTACT
1 TATTTAATTAAATATTTAAT
2936207 TATTTAATTAAATATTTAAT
1 TATTTAATTAAATATTTAAT
2936227 TATT
1 TATT
2936231 AAAAATAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 17 0.45
20 12 0.32
22 9 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTAATTAAATATTTAAT
Found at i:2939892 original size:43 final size:43
Alignment explanation
Indices: 2939800--2940072 Score: 200
Period size: 43 Copynumber: 6.3 Consensus size: 43
2939790 ATCTGTTAAT
* * * * *
2939800 TTTAGCGGCGTTTGTGGA-AAATACGCCGTTAAAGAACACTATT-
1 TTTAGCGGCGTTTTTGGAGTAA-GCGCCGCTAAAGAACA-TGTTC
* *
2939843 TATAGCGGCGTTTTTGGAGTAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTTTGGAGTAAGCGCCGCTAAAGAACATGTTC
* ** * * *
2939886 TTTAGCGGCGCTTATTCTA-AAAACGCCGCTAAAGAACATGGTC
1 TTTAGCGGCG-TTTTTGGAGTAAGCGCCGCTAAAGAACATGTTC
* * **
2939929 TTTAGCGGCGCTTGTTGAAAAAAGCGCCGCTAAAG-ACTATGTTC
1 TTTAGCGGCG-TTTTTGGAGTAAGCGCCGCTAAAGAAC-ATGTTC
* * * *
2939973 TTTAGAGGCG--TTTGTATCTAAGCGCCGCTAAAGAACATGGTC
1 TTTAGCGGCGTTTTTGGA-GTAAGCGCCGCTAAAGAACATGTTC
* * * *
2940015 TTTAGCGGCGTTTGTAG-GTAAAGCGTCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTTTGGAGT-AAGCGCCGCTAAAGAACATGTTC
*
2940058 TTTTGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
2940073 TTTTTATAAA
Statistics
Matches: 184, Mismatches: 36, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
41 4 0.02
42 32 0.17
43 111 0.60
44 37 0.20
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGGAGTAAGCGCCGCTAAAGAACATGTTC
Found at i:2939935 original size:86 final size:85
Alignment explanation
Indices: 2939845--2940067 Score: 270
Period size: 86 Copynumber: 2.6 Consensus size: 85
2939835 ACACTATTTA
2939845 TAGCGGCGTTTTTGGAGTAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAT-TCTAAAAA
1 TAGCGGCGTTTTTGGAGTAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATATCT--AAA
2939909 CGCCGCTAAAGAACATGGTCTT
64 CGCCGCTAAAGAACATGGTCTT
* * ** * * * * *
2939931 TAGCGGCGCTTGTTGAAAAAAGCGCCGCTAAAGACTATGTTCTTTAGAGGCGTTTGTATCTAAGC
1 TAGCGGCG-TTTTTGGAGTAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATATCTAAAC
2939996 GCCGCTAAAGAACATGGTCTT
65 GCCGCTAAAGAACATGGTCTT
* * * * *
2940017 TAGCGGCGTTTGTAG-GTAAAGCGTCGCTAAAGATCATGTTCTTTTGCGGCG
1 TAGCGGCGTTTTTGGAGT-AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG
2940068 TTTTTTTTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
85 31 0.27
86 40 0.35
87 40 0.35
88 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (85 bp):
TAGCGGCGTTTTTGGAGTAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTATATCTAAACG
CCGCTAAAGAACATGGTCTT
Found at i:2947937 original size:58 final size:58
Alignment explanation
Indices: 2947865--2947984 Score: 172
Period size: 58 Copynumber: 2.1 Consensus size: 58
2947855 ACTTATCAAC
*
2947865 AAACTAAACCCAAATATTTTTGAACCCAAATATAATTTCATTAT-TCAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATT-TCT-AAATAACACTCAT
* * *
2947923 AAACTAAACTCAAATATTTTTAAACCCAACTATAATTTTATTTCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTTCTAAATAACACTCAT
2947981 AAAC
1 AAAC
2947985 AATTATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
57 4 0.07
58 52 0.93
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTTCTAAATAACACTCAT
Found at i:2949565 original size:262 final size:264
Alignment explanation
Indices: 2949094--2949618 Score: 777
Period size: 262 Copynumber: 2.0 Consensus size: 264
2949084 CCCAAAAACT
* * *
2949094 TCCCCGCTCTCACCCCGAAAGCACACTTTTTTGGATTTAACCTCATATTGTAGGCTCGCAAAATA
1 TCCCCGCTCTCACCCCGAAAGCACACTTTTTTGGATTCAACCTCATATTCTAGGCTCACAAAATA
*
2949159 GCAAAAGCTTCAGATAGATCTGCAATATGTCCCTTTAAAGTGCTACTCTTCACCAACATATCGTC
66 GCAAAAGCTTCAGATAGATCTGCAATATGTCCCTTTAAAATGCTACTCTTCACCAACATATCGTC
* * * *
2949224 TACATAAACCTCAATGCTGCGACCAATCTGTTCCTTAAAAATCTTGTTCACCAATCGCTGGTATG
131 CACATAAACCTCAATACTGCGACCAATCTGTTCCTTAAAAATCATGTTCACCAATCGCTGGTACG
* * * *
2949289 TAGTCCCTGCATTTTTTAAATCAAAAGGCATAACCGGATAACAGAATAACCGCTCCTCTGTAACG
196 TAGCCCCCGCATTTTTTAAACCAAAAGGCATAACCGGATAACAGAATAACCCCTCCTCTGTAACG
2949354 AAGG
261 AAGG
*
2949358 TCCCCGCTCTCACCCCGAAAGCACACTTTTTTGGATTCAA-C-CATATTCTTGGCTCACAAAATA
1 TCCCCGCTCTCACCCCGAAAGCACACTTTTTTGGATTCAACCTCATATTCTAGGCTCACAAAATA
* ** *
2949421 GCAAAAGCTTCGGATAGATCTTTAATATGTCCCTTTAAAATGCTACTCTTC-TCAAGCATATCGT
66 GCAAAAGCTTCAGATAGATCTGCAATATGTCCCTTTAAAATGCTACTCTTCACCAA-CATATCGT
** * * * *
2949485 CCACATAAATTTCAATACTGCGACCACTCTGTTCCTTAAAAATCATGTTCACTAATTGCTTGTAC
130 CCACATAAACCTCAATACTGCGACCAATCTGTTCCTTAAAAATCATGTTCACCAATCGCTGGTAC
* * * *
2949550 GTTGCCCCCGCATTTTTTAAACCAAAATGCATAACCGGATAATAGAATAACCCCTCCTCTGTAAT
195 GTAGCCCCCGCATTTTTTAAACCAAAAGGCATAACCGGATAACAGAATAACCCCTCCTCTGTAAC
2949615 GAAG
260 GAAG
2949619 ATGCTCTTAT
Statistics
Matches: 233, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
261 3 0.01
262 190 0.82
263 1 0.00
264 39 0.17
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (264 bp):
TCCCCGCTCTCACCCCGAAAGCACACTTTTTTGGATTCAACCTCATATTCTAGGCTCACAAAATA
GCAAAAGCTTCAGATAGATCTGCAATATGTCCCTTTAAAATGCTACTCTTCACCAACATATCGTC
CACATAAACCTCAATACTGCGACCAATCTGTTCCTTAAAAATCATGTTCACCAATCGCTGGTACG
TAGCCCCCGCATTTTTTAAACCAAAAGGCATAACCGGATAACAGAATAACCCCTCCTCTGTAACG
AAGG
Found at i:2952849 original size:39 final size:39
Alignment explanation
Indices: 2952795--2952873 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
2952785 TCCATTGGCT
2952795 CCATGAAAACCAAAACAGCTATCAACTCAAGCAACATAA
1 CCATGAAAACCAAAACAGCTATCAACTCAAGCAACATAA
*
2952834 CCATGAAAACCAAAACAGCTATCGACTCAAGCAACATAA
1 CCATGAAAACCAAAACAGCTATCAACTCAAGCAACATAA
2952873 C
1 C
2952874 GACGAAAGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.49, C:0.29, G:0.09, T:0.13
Consensus pattern (39 bp):
CCATGAAAACCAAAACAGCTATCAACTCAAGCAACATAA
Found at i:2960341 original size:29 final size:29
Alignment explanation
Indices: 2960299--2960354 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2960289 AAATAATAAC
*
2960299 ATAAGTGACTAAAACGTAACATTTTAAAT
1 ATAAGTGACTAAAACATAACATTTTAAAT
* *
2960328 ATAAGTGATTAAAATATAACATTTTAA
1 ATAAGTGACTAAAACATAACATTTTAA
2960355 TTATTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (29 bp):
ATAAGTGACTAAAACATAACATTTTAAAT
Found at i:2960505 original size:50 final size:51
Alignment explanation
Indices: 2960451--2960550 Score: 159
Period size: 54 Copynumber: 1.9 Consensus size: 51
2960441 ATGACATACT
2960451 TAAAATATG-TT-TTTGGTTTTTACTTAAACGTTTTGATGTAACCTCCTGAC
1 TAAAATATGTTTATTTGGTTTTTACTTAAACGTTTTGATGTAA-CTCCTGAC
2960501 TAAAATATGTTTAAGTTTGGTTTTTACTTAAACGTTTTGATGTAACTCCT
1 TAAAATATGTTT-A-TTTGGTTTTTACTTAAACGTTTTGATGTAACTCCT
2960551 AGGCTGGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
50 9 0.20
51 2 0.04
53 5 0.11
54 30 0.65
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (51 bp):
TAAAATATGTTTATTTGGTTTTTACTTAAACGTTTTGATGTAACTCCTGAC
Found at i:2960878 original size:8 final size:8
Alignment explanation
Indices: 2960865--2960898 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2960855 TTGAGTAAAT
2960865 TATAAAAA
1 TATAAAAA
2960873 TATAAAAA
1 TATAAAAA
2960881 TATTAAAAA
1 TA-TAAAAA
*
2960890 TAAAAAAA
1 TATAAAAA
2960898 T
1 T
2960899 CGATTAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TATAAAAA
Found at i:2966697 original size:25 final size:25
Alignment explanation
Indices: 2966669--2966722 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
2966659 TTTAAAGGGT
2966669 TTATAAGGTTTGGGTTTTAAAAAGG
1 TTATAAGGTTTGGGTTTTAAAAAGG
** *
2966694 TTATTGGGTTTGGTTTTTAAAAAGG
1 TTATAAGGTTTGGGTTTTAAAAAGG
2966719 TTAT
1 TTAT
2966723 TAGATTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (25 bp):
TTATAAGGTTTGGGTTTTAAAAAGG
Found at i:2966723 original size:25 final size:25
Alignment explanation
Indices: 2966675--2966723 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2966665 GGGTTTATAA
2966675 GGTTTGGGTTTTAAAAAGGTTATTG
1 GGTTTGGGTTTTAAAAAGGTTATTG
*
2966700 GGTTTGGTTTTTAAAAAGGTTATT
1 GGTTTGGGTTTTAAAAAGGTTATT
2966724 AGATTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (25 bp):
GGTTTGGGTTTTAAAAAGGTTATTG
Found at i:2966735 original size:25 final size:25
Alignment explanation
Indices: 2966683--2966735 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2966673 AAGGTTTGGG
* * **
2966683 TTTTAAAAAGGTTATTGGGTTTGGT
1 TTTTAAAAAGGTTATTAGATTTAAT
2966708 TTTTAAAAAGGTTATTAGATTTAAT
1 TTTTAAAAAGGTTATTAGATTTAAT
2966733 TTT
1 TTT
2966736 AAAGAATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (25 bp):
TTTTAAAAAGGTTATTAGATTTAAT
Found at i:2969218 original size:13 final size:13
Alignment explanation
Indices: 2969200--2969224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2969190 TTTAGAATTA
2969200 CAGAGAATAGAAG
1 CAGAGAATAGAAG
2969213 CAGAGAATAGAA
1 CAGAGAATAGAA
2969225 TTACAAAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.28, T:0.08
Consensus pattern (13 bp):
CAGAGAATAGAAG
Found at i:2978136 original size:13 final size:13
Alignment explanation
Indices: 2978090--2978137 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
2978080 ACAAGGCAGG
2978090 AAGAAAAAATGAA
1 AAGAAAAAATGAA
2978103 AGAGAAAAAA-GAA
1 A-AGAAAAAATGAA
2978116 CAACGAAAAAATGAA
1 -AA-GAAAAAATGAA
2978131 AAGAAAA
1 AAGAAAA
2978138 CTTCTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.32
14 18 0.58
15 3 0.10
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (13 bp):
AAGAAAAAATGAA
Found at i:2984471 original size:17 final size:17
Alignment explanation
Indices: 2984449--2984496 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
2984439 CCAATTTTAG
*
2984449 ATTTTAAATTTTAATTC
1 ATTTTAAATTTAAATTC
* *
2984466 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTC
2984483 ATTTTAAATTTAAA
1 ATTTTAAATTTAAA
2984497 ATTATTCTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTC
Found at i:2984501 original size:17 final size:17
Alignment explanation
Indices: 2984449--2984502 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
2984439 CCAATTTTAG
*
2984449 ATTTTAAATTT-TAATT
1 ATTTTAAATTTAAAATT
* *
2984465 CATTTTAAGTTTAAATTT
1 -ATTTTAAATTTAAAATT
2984483 ATTTTAAATTTAAAATT
1 ATTTTAAATTTAAAATT
2984500 ATT
1 ATT
2984503 CTGAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 28 0.90
18 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAAATT
Found at i:2985229 original size:15 final size:15
Alignment explanation
Indices: 2985189--2985231 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2985179 AAAAATAAAT
*
2985189 ATATTATTAATAACA
1 ATATTAATAATAACA
*
2985204 ATATTAATAATAATA
1 ATATTAATAATAACA
*
2985219 ATTTTAATAATAA
1 ATATTAATAATAA
2985232 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATTAATAATAACA
Found at i:2986348 original size:29 final size:29
Alignment explanation
Indices: 2986316--2986578 Score: 180
Period size: 30 Copynumber: 8.9 Consensus size: 29
2986306 TTTGACCCCC
*
2986316 AAACTTTCCTAAAATTACATATTAACCC-T
1 AAACTTT-CTAAAATTACATTTTAACCCTT
* *
2986345 AAACTTTTTCAAAAATACATTTTAACCCTT
1 AAACTTTCT-AAAATTACATTTTAACCCTT
*
2986375 AAACTTTCTAAAAATCACATTTTAACCCTT
1 AAACTTTCT-AAAATTACATTTTAACCCTT
* *
2986405 AAATTTTCCAAAAATTACCATTTT-ACCCTT
1 AAACTTT-CTAAAATTA-CATTTTAACCCTT
* * * * *
2986435 AAA-TTTTTGAAATTCCATTTTTACCCTC
1 AAACTTTCTAAAATTACATTTTAACCCTT
* *
2986463 AAATTTTCCAAAAATTACATTTTAACCC-T
1 AAACTTT-CTAAAATTACATTTTAACCCTT
*
2986492 AAACTTTCTAAAAAATTACCATTTT-ACCCTC
1 AAACTTTCT--AAAATTA-CATTTTAACCCTT
* ** * * *
2986523 AGA-TGCCCAAAAATTACATTTTGACCC-C
1 AAACT-TTCTAAAATTACATTTTAACCCTT
* *
2986551 AAATTTTCCAAAATTACCATTTTAACCC
1 AAACTTTCTAAAATTA-CATTTTAACCC
2986579 CAAACATCCA
Statistics
Matches: 186, Mismatches: 33, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
27 6 0.03
28 32 0.17
29 57 0.31
30 75 0.40
31 16 0.09
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
AAACTTTCTAAAATTACATTTTAACCCTT
Found at i:2986386 original size:58 final size:58
Alignment explanation
Indices: 2986316--2986602 Score: 257
Period size: 59 Copynumber: 4.9 Consensus size: 58
2986306 TTTGACCCCC
* *
2986316 AAACTTTCCTAAAATTACATATTAACCCTAAACTTTTTCAAAAA-TACATTTTAACCCTT
1 AAACTTT-CTAAAATTACATTTTAACCCTAAA-TTTTCCAAAAATTACATTTTAACCCTT
*
2986375 AAACTTTCTAAAAATCACATTTTAACCCTTAAATTTTCCAAAAATTACCATTTT-ACCCTT
1 AAACTTTCT-AAAATTACATTTTAACCC-TAAATTTTCCAAAAATTA-CATTTTAACCCTT
* * * *
2986435 AAA-TTTTTGAAATTCCATTTTTACCCTCAAATTTTCCAAAAATTACATTTTAACCC-T
1 AAACTTTCTAAAATTACATTTTAACCCT-AAATTTTCCAAAAATTACATTTTAACCCTT
* ** * *
2986492 AAACTTTCTAAAAAATTACCATTTT-ACCCTCAGA-TGCCCAAAAATTACATTTTGACCC-C
1 AAACTTTCT--AAAATTA-CATTTTAACCCT-AAATTTTCCAAAAATTACATTTTAACCCTT
* * * **
2986551 AAATTTTCCAAAATTACCATTTTAACCCCAAA-CATCCAAAAATTACCATTTT
1 AAACTTTCTAAAATTA-CATTTTAACCCTAAATTTTCCAAAAATTA-CATTTT
2986603 TCCCTCGAGT
Statistics
Matches: 193, Mismatches: 23, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
57 37 0.19
58 51 0.26
59 65 0.34
60 28 0.15
61 12 0.06
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (58 bp):
AAACTTTCTAAAATTACATTTTAACCCTAAATTTTCCAAAAATTACATTTTAACCCTT
Found at i:2986455 original size:88 final size:89
Alignment explanation
Indices: 2986286--2986607 Score: 266
Period size: 88 Copynumber: 3.7 Consensus size: 89
2986276 AAAAGGTCCC
* * * * * * *
2986286 TAAACTATCTAAAAATCATATTTGACCCCCAAACTTTCCTAAAATTA-CATATTAACCC-TAAAC
1 TAAACTTTCTAAAAATCACATTTTAACCCTAAACTTTCCAAAAATTACCAT-TTTACCCTTAAAC
2986349 TTTTTCAAAAATACATTTTAACCCT
65 TTTTTCAAAAATACATTTTAACCCT
*
2986374 TAAACTTTCTAAAAATCACATTTTAACCCTTAAATTTTCCAAAAATTACCATTTTACCCTTAAA-
1 TAAACTTTCTAAAAATCACATTTTAACCC-TAAACTTTCCAAAAATTACCATTTTACCCTTAAAC
* * * *
2986438 TTTTT-GAAATTCCATTTTTACCCT
65 TTTTTCAAAAATACATTTTAACCCT
* * * * * * *
2986462 CAAATTTTCCAAAAATTACATTTTAACCCTAAACTTTCTAAAAAATTACCATTTTACCCTCAGA-
1 TAAACTTTCTAAAAATCACATTTTAACCCTAAACTTTC-CAAAAATTACCATTTTACCCTTAAAC
*** *
2986526 -TGCCCAAAAATTACATTTTGACCC-
65 TTTTTCAAAAA-TACATTTTAACCCT
* * * * * * *
2986550 CAAATTTTC-CAAAATTACCATTTTAACCCCAAAC-ATCCAAAAATTACCATTTTTCCCT
1 TAAACTTTCTAAAAATCA-CATTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCT
2986608 CGAGTGTCCA
Statistics
Matches: 195, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
86 19 0.10
87 18 0.09
88 114 0.58
89 37 0.19
90 7 0.04
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (89 bp):
TAAACTTTCTAAAAATCACATTTTAACCCTAAACTTTCCAAAAATTACCATTTTACCCTTAAACT
TTTTCAAAAATACATTTTAACCCT
Found at i:2986579 original size:29 final size:31
Alignment explanation
Indices: 2986310--2986632 Score: 245
Period size: 29 Copynumber: 11.0 Consensus size: 31
2986300 ATCATATTTG
* * * *
2986310 ACCCCCAAACTTTCCTAAAATTA-CATATTA
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
*
2986340 ACCCT-AAACTTTTTCAAAAA-TA-CATTTTA
1 ACCCTCAAA-TTTTCCAAAAATTACCATTTTA
* * * *
2986369 ACCCTTAAACTTTCTAAAAATCA-CATTTTA
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
*
2986399 ACCCTTAAATTTTCCAAAAATTACCATTTT-
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
* ** *
2986429 ACCCTTAAATTTT--TGAAATT-CCATTTTT
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
2986457 ACCCTCAAATTTTCCAAAAATTA-CATTTTA
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
* *
2986487 ACCCT-AAACTTTCTAAAAAATTACCATTTT-
1 ACCCTCAAATTTTC-CAAAAATTACCATTTTA
* ** *
2986517 ACCCTCAGA-TGCCCAAAAATTA-CATTTTG
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
2986546 ACCC-CAAATTTTCC-AAAATTACCATTTTA
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
**
2986575 ACCC-CAAA-CATCCAAAAATTACCATTTT-
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
* * * * *
2986603 TCCCTC-GAGTGTCCAAAAATTACCGTTTTA
1 ACCCTCAAATTTTCCAAAAATTACCATTTTA
2986633 CTCTCGAATC
Statistics
Matches: 240, Mismatches: 35, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
27 7 0.03
28 40 0.17
29 92 0.38
30 87 0.36
31 14 0.06
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.35
Consensus pattern (31 bp):
ACCCTCAAATTTTCCAAAAATTACCATTTTA
Found at i:2986638 original size:29 final size:29
Alignment explanation
Indices: 2986411--2986667 Score: 140
Period size: 29 Copynumber: 8.9 Consensus size: 29
2986401 CCTTAAATTT
**
2986411 TCCAAAAATTACCATTTTACCCTTAAAT-
1 TCCAAAAATTACCATTTTACCCTCGAATC
**** * *
2986439 TTTTGAAATT-CCATTTTTACCCTCAAATTT
1 TCCAAAAATTACCA-TTTTACCCTCGAA-TC
* *
2986469 TCCAAAAATTA-CATTTTAACCCT-AAACTT
1 TCCAAAAATTACCATTTT-ACCCTCGAA-TC
*
2986498 TCTAAAAAATTACCATTTTACCCTC-AGATGC
1 TC-CAAAAATTACCATTTTACCCTCGA-AT-C
* *
2986529 -CCAAAAATTA-CATTTTGACCC-CAAATTT
1 TCCAAAAATTACCATTTT-ACCCTCGAA-TC
*
2986557 TCC-AAAATTACCATTTTAACCC-C-AAAC
1 TCCAAAAATTACCATTTT-ACCCTCGAATC
* * *
2986584 ATCCAAAAATTACCATTTTTCCCTCGAGTG
1 -TCCAAAAATTACCATTTTACCCTCGAATC
* *
2986614 TCCAAAAATTACCGTTTTACTCTCGAATC
1 TCCAAAAATTACCATTTTACCCTCGAATC
* * *
2986643 TCTAAAAATTACTATCTTACCCTCG
1 TCCAAAAATTACCATTTTACCCTCG
2986668 GGCATCCAAA
Statistics
Matches: 179, Mismatches: 31, Indels: 37
0.72 0.13 0.15
Matches are distributed among these distances:
27 3 0.02
28 41 0.23
29 98 0.55
30 30 0.17
31 7 0.04
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTCGAATC
Found at i:3019012 original size:39 final size:39
Alignment explanation
Indices: 3018969--3019144 Score: 298
Period size: 39 Copynumber: 4.5 Consensus size: 39
3018959 GTTTCCCACA
* * *
3018969 CCAGGGCTCGGACCGGAGTTGGTAAACCTATTTCCCGTT
1 CCAGGGCTTGGACCGGAGTCGGTAAACTTATTTCCCGTT
*
3019008 CCAGGGCTCGGACCGGAGTCGGTAAACTTATTTCCCGTT
1 CCAGGGCTTGGACCGGAGTCGGTAAACTTATTTCCCGTT
*
3019047 CCAGGGCTTGGACCAGAGTCGGTAAACTTATTTCCCGTT
1 CCAGGGCTTGGACCGGAGTCGGTAAACTTATTTCCCGTT
3019086 CCAGGGCTTGGACCGGAGTCGGTAAACTTATTTCCCGTT
1 CCAGGGCTTGGACCGGAGTCGGTAAACTTATTTCCCGTT
*
3019125 CCAGGGCTTGGTCCGGAGTC
1 CCAGGGCTTGGACCGGAGTC
3019145 CTTGATGCCA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 131 1.00
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.26
Consensus pattern (39 bp):
CCAGGGCTTGGACCGGAGTCGGTAAACTTATTTCCCGTT
Found at i:3023545 original size:18 final size:18
Alignment explanation
Indices: 3023516--3023576 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
3023506 GTTCGATCTC
*
3023516 AATTAAATAAAACATTAAA
1 AATTATATAAAA-ATTAAA
3023535 AATT-TATAAAAATATAATA
1 AATTATATAAAAAT-TAA-A
*
3023554 AATTATTTAAAAATTATAA
1 AATTATATAAAAATTA-AA
3023573 AATT
1 AATT
3023577 GGTTTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
17 2 0.06
18 9 0.25
19 16 0.44
20 9 0.25
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTATATAAAAATTAAA
Found at i:3038111 original size:22 final size:23
Alignment explanation
Indices: 3038072--3038123 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
3038062 TCTTTTATTA
* *
3038072 AAGGATATTAATTAAAAAGTTTG
1 AAGGATATAAATTAAAAAGTATG
*
3038095 AAGGAT-TAAATTGAAAAGTATG
1 AAGGATATAAATTAAAAAGTATG
3038117 AGAGGAT
1 A-AGGAT
3038124 CTTTTACCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (23 bp):
AAGGATATAAATTAAAAAGTATG
Found at i:3045536 original size:29 final size:29
Alignment explanation
Indices: 3045499--3045579 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
3045489 ATTTTGGAAT
* *
3045499 AATAAAATTAAATTAATTCTTATAAATAA
1 AATAGAATTAAATTAATGCTTATAAATAA
*
3045528 AATAGAATTAAATTAATGCTTATAAATGA
1 AATAGAATTAAATTAATGCTTATAAATAA
*
3045557 AATAGAATTAAATTAATGATTAT
1 AATAGAATTAAATTAATGCTTAT
3045580 GTATTACTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.37
Consensus pattern (29 bp):
AATAGAATTAAATTAATGCTTATAAATAA
Found at i:3058929 original size:59 final size:59
Alignment explanation
Indices: 3058843--3058967 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 59
3058833 TACTTAAAAC
3058843 TTTTTTTGACCCAATTTAGCACCTGAACTTGACACTTTTTT-TTAATTCGGTACCTAA-A
1 TTTTTTTGACCCAATTTAGCACCTGAACTTGACA-TTTTTTCTTAATTCGGTACCTAAGA
* * * * ** * * *
3058901 TTTTTTTGGATCCAATTTGGTACTTGAACTTGGGATTTTTTCTTATTTTGGTACCTAAGC
1 TTTTTTT-GACCCAATTTAGCACCTGAACTTGACATTTTTTCTTAATTCGGTACCTAAGA
3058961 TTTTTTT
1 TTTTTTT
3058968 TAGATTCAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 13 0.24
59 35 0.64
60 7 0.13
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.50
Consensus pattern (59 bp):
TTTTTTTGACCCAATTTAGCACCTGAACTTGACATTTTTTCTTAATTCGGTACCTAAGA
Found at i:3059230 original size:33 final size:32
Alignment explanation
Indices: 3059193--3059287 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 32
3059183 CGACCCCCAA
3059193 AAATTTAAGTACCAACTTGTAAAAAAAAGTGTC
1 AAATTTAAGTACCAA-TTGTAAAAAAAAGTGTC
* * * **
3059226 AAATTTAGGTATCAAAT-TAGGAAAAAGTGTC
1 AAATTTAAGTACCAATTGTAAAAAAAAGTGTC
* * *
3059257 AAGTTTGAGTACCAAATTGGACAAAAAAAGT
1 AAATTTAAGTACC-AATTGTA-AAAAAAAGT
3059288 TTAGATACCA
Statistics
Matches: 46, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
31 21 0.46
32 4 0.09
33 14 0.30
34 7 0.15
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.26
Consensus pattern (32 bp):
AAATTTAAGTACCAATTGTAAAAAAAAGTGTC
Found at i:3059254 original size:31 final size:31
Alignment explanation
Indices: 3059216--3059331 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
3059206 AACTTGTAAA
*
3059216 AAAAAGTGTCAAATTTAGGTATCAAATTAGG
1 AAAAAGTGTCAAATTTAGGTACCAAATTAGG
*
3059247 AAAAAGTGTCAAGTTT-GAGTACCAAATT-GG
1 AAAAAGTGTCAAATTTAG-GTACCAAATTAGG
* *
3059277 ACAAAA-----AAAGTTTAGATACCAAATTAAG
1 A-AAAAGTGTCAAA-TTTAGGTACCAAATTAGG
* * *
3059305 AAAAAATGTCAAATTCAGGTATCAAAT
1 AAAAAGTGTCAAATTTAGGTACCAAAT
3059332 GTTATATTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
26 2 0.03
27 16 0.24
28 3 0.04
30 4 0.06
31 39 0.58
32 3 0.04
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.26
Consensus pattern (31 bp):
AAAAAGTGTCAAATTTAGGTACCAAATTAGG
Found at i:3059309 original size:27 final size:27
Alignment explanation
Indices: 3059257--3059310 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3059247 AAAAAGTGTC
*
3059257 AAGTTTGAGTACCAAATTGGACAAAAA
1 AAGTTTGAGTACCAAATTAGACAAAAA
*
3059284 AAGTTT-AGATACCAAATTA-AGAAAAA
1 AAGTTTGAG-TACCAAATTAGACAAAAA
3059310 A
1 A
3059311 TGTCAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (27 bp):
AAGTTTGAGTACCAAATTAGACAAAAA
Found at i:3059768 original size:18 final size:19
Alignment explanation
Indices: 3059740--3059776 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
3059730 AAATTCAACC
3059740 ATATGAATTGTACTTATCA
1 ATATGAATTGTACTTATCA
3059759 ATAT-AATTGTACTTATCA
1 ATATGAATTGTACTTATCA
3059777 TTCATGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (19 bp):
ATATGAATTGTACTTATCA
Found at i:3061254 original size:20 final size:19
Alignment explanation
Indices: 3061229--3061278 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
3061219 CGCAGCTCTA
3061229 TAAAAGGATATCTTATATAT
1 TAAAAGGATATCTT-TATAT
3061249 TAAAA-GATA-CATTTATAT
1 TAAAAGGATATC-TTTATAT
*
3061267 GAAAAGG-TATCT
1 TAAAAGGATATCT
3061279 CATAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
18 13 0.50
19 8 0.31
20 5 0.19
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (19 bp):
TAAAAGGATATCTTTATAT
Found at i:3068727 original size:24 final size:24
Alignment explanation
Indices: 3068668--3068728 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3068658 GAGTAATAAG
* *
3068668 AGTTTGACTCAAACAAATAAACAG
1 AGTTTGACTGAAACAAATAAACAA
* *
3068692 AGTTTGATTGAAACAAATACACAA
1 AGTTTGACTGAAACAAATAAACAA
*
3068716 AGTTTAACTGAAA
1 AGTTTGACTGAAA
3068729 GATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (24 bp):
AGTTTGACTGAAACAAATAAACAA
Found at i:3070718 original size:24 final size:24
Alignment explanation
Indices: 3070657--3070719 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
3070647 TAGAGTAATA
* *
3070657 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTGACTGAAACAAATAAAC
*
3070681 AGAGTTTGATTGAAACAAATAAAC
1 AGAGTTTGACTGAAACAAATAAAC
*
3070705 AGAGTTTAACTGAAA
1 AGAGTTTGACTGAAA
3070720 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (24 bp):
AGAGTTTGACTGAAACAAATAAAC
Found at i:3072184 original size:28 final size:28
Alignment explanation
Indices: 3072153--3072244 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
3072143 AAATTCAACT
3072153 CGTCAAAATATTTTTTCAAAACACATCA
1 CGTCAAAATATTTTTTCAAAACACATCA
** * * *
3072181 CGTCAATTTTATTTTTT-AGAACTCATCTT
1 CGTCAA-AATATTTTTTCAAAACACATC-A
*
3072210 C-TCAAAATTATTTTTTTCAAAACACACCA
1 CGTCAAAA-TA-TTTTTTCAAAACACATCA
3072239 CGTCAA
1 CGTCAA
3072245 TTATTTAGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
28 20 0.43
29 16 0.34
30 11 0.23
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (28 bp):
CGTCAAAATATTTTTTCAAAACACATCA
Found at i:3072197 original size:30 final size:29
Alignment explanation
Indices: 3072161--3072246 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
3072151 CTCGTCAAAA
3072161 TATTTTTTCAAAACACATCACGTCAATTT
1 TATTTTTTCAAAACACATCACGTCAATTT
* * * **
3072190 TATTTTTT-AGAACTCATCTTC-TCAAAAT
1 TATTTTTTCAAAACACATC-ACGTCAATTT
*
3072218 TATTTTTTTCAAAACACACCACGTCAATT
1 TA-TTTTTTCAAAACACATCACGTCAATT
3072247 ATTTAGATAT
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
28 15 0.36
29 16 0.38
30 11 0.26
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (29 bp):
TATTTTTTCAAAACACATCACGTCAATTT
Found at i:3072392 original size:30 final size:31
Alignment explanation
Indices: 3072356--3072423 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3072346 CAAAAATGCA
*
3072356 AAATTTAGATATATT-CTTTTGAATTTTTAG
1 AAATTTAGATATATTACTTTTGAAATTTTAG
* *
3072386 AAATTTAGATATGTTAGTTTTGAAATTTTAG
1 AAATTTAGATATATTACTTTTGAAATTTTAG
*
3072417 TAATTTA
1 AAATTTA
3072424 AAAAAAGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.51
Consensus pattern (31 bp):
AAATTTAGATATATTACTTTTGAAATTTTAG
Found at i:3076787 original size:28 final size:28
Alignment explanation
Indices: 3076747--3076808 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
3076737 AAATGAGACT
*
3076747 TTTTGGATACTCGGGGGCAAAATGGTAA
1 TTTTGGATACTCGAGGGCAAAATGGTAA
3076775 TTTTGGACT-CTCGAGGGCAAAATGGTAA
1 TTTTGGA-TACTCGAGGGCAAAATGGTAA
3076803 TTTTGG
1 TTTTGG
3076809 GAAAATTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.32
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATGGTAA
Found at i:3076911 original size:29 final size:29
Alignment explanation
Indices: 3076881--3077079 Score: 160
Period size: 29 Copynumber: 6.8 Consensus size: 29
3076871 AATCGAGATA
* *
3076881 AAAAATGGAATTTTTGGACA-TTCGGGGT
1 AAAAATGGAATTTTTGGAAAGTTTGGGGT
* *
3076909 -AAAATAGTAATTTTT-GAAAGTTTTAGGGTT
1 AAAAAT-GGAATTTTTGGAAAG-TTT-GGGGT
3076939 AAAAATGGAATTTTTGG-AAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAAGTTT-GGGGT
* * *
3076968 AAAAATGTAATTTTTAG-AAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAAG-TTTGGGGT
* *
3076997 TAAAATGGTATTTTTGGAAA-TTTGAGGGT
1 AAAAATGGAATTTTTGGAAAGTTTG-GGGT
* * *
3077026 AAAAATGTAATTTTT-AAAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAAAGTTT-GGGGT
*
3077055 CAAAAATGGAATTTTTGGATAGTTT
1 -AAAAATGGAATTTTTGGAAAGTTT
3077080 AGGGACCTCT
Statistics
Matches: 136, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
27 8 0.06
28 14 0.10
29 67 0.49
30 35 0.26
31 12 0.09
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.39
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAAGTTTGGGGT
Found at i:3076923 original size:58 final size:58
Alignment explanation
Indices: 3076833--3077073 Score: 163
Period size: 58 Copynumber: 4.1 Consensus size: 58
3076823 AAAAATGACA
* *
3076833 TTTTGGACATTCGGGGGTAAAACGATATTTTTTAGAAAAATCGA-GATAAAAAATGGAAT
1 TTTTGGACATTC-GGGGTAAAAAG-TAATTTTTAGAAAAATCGAGGATAAAAAATGGAAT
** ** * *
3076892 TTTTGGACATTCGGGGTAAAATAGTAATTTTT-GAAAGTTTTAGGGTTAAAAATGGAAT
1 TTTTGGACATTCGGGGTAAAA-AGTAATTTTTAGAAAAATCGAGGATAAAAAATGGAAT
* ** ** * * *
3076950 TTTTGGA-AGTTTAGGGGTAAAAATGTAATTTTTAG-AAGTTTTAGGGT-TAAAATGGTAT
1 TTTTGGACA--TTCGGGGTAAAAA-GTAATTTTTAGAAAAATCGAGGATAAAAAATGGAAT
* * ** *
3077008 TTTTGGAAATTTGAGGGTAAAAATGTAATTTTTA-AAAGTTTCGAGG-TCAAAAATGGAAT
1 TTTTGGACATTCG-GGGTAAAAA-GTAATTTTTAGAAA-AATCGAGGATAAAAAATGGAAT
3077067 TTTTGGA
1 TTTTGGA
3077074 TAGTTTAGGG
Statistics
Matches: 154, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
57 10 0.06
58 76 0.49
59 67 0.44
60 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (58 bp):
TTTTGGACATTCGGGGTAAAAAGTAATTTTTAGAAAAATCGAGGATAAAAAATGGAAT
Found at i:3076942 original size:59 final size:56
Alignment explanation
Indices: 3076881--3077073 Score: 230
Period size: 58 Copynumber: 3.3 Consensus size: 56
3076871 AATCGAGATA
*
3076881 AAAAATGGAATTTTTGGACATTCGGGGT-AAAATAGTAATTTTTGAAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGA-ATTAGGGGTAAAAAT-GTAATTTTT-AAAGTTTTAGGGTT
3076939 AAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAGTTTTAGGGTT
1 AAAAATGGAATTTTTGGAA--TTAGGGGTAAAAATGTAATTTTTA-AAGTTTTAGGGTT
* * * *
3076998 -AAAATGGTATTTTTGGAAATTTGAGGGTAAAAATGTAATTTTTAAAAG-TTTCGAGGTC
1 AAAAATGGAATTTTTGG-AATTAG-GGGTAAAAATGTAATTTTT-AAAGTTTTAG-GGTT
3077056 AAAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
3077074 TAGTTTAGGG
Statistics
Matches: 120, Mismatches: 6, Indels: 18
0.83 0.04 0.12
Matches are distributed among these distances:
57 8 0.07
58 60 0.50
59 47 0.39
60 5 0.04
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (56 bp):
AAAAATGGAATTTTTGGAATTAGGGGTAAAAATGTAATTTTTAAAGTTTTAGGGTT
Found at i:3078147 original size:21 final size:21
Alignment explanation
Indices: 3078123--3078211 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 21
3078113 TTTTTTTTAA
3078123 TATTAAATATTTATTTATTGT
1 TATTAAATATTTATTTATTGT
* * *
3078144 TATTAATAAATTCATTATTACTGT
1 TATTAA-ATATTTA-T-TTATTGT
*
3078168 TATT-AATA-TTA-TTATTAT
1 TATTAAATATTTATTTATTGT
*
3078186 TATT-ATTATTT-TTTA-TGT
1 TATTAAATATTTATTTATTGT
3078204 TA-TAAATA
1 TATTAAATA
3078212 ATAAATTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
17 1 0.02
18 19 0.37
19 5 0.10
21 8 0.15
22 7 0.13
23 2 0.04
24 10 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (21 bp):
TATTAAATATTTATTTATTGT
Found at i:3078180 original size:3 final size:3
Alignment explanation
Indices: 3078157--3078195 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
3078147 TAATAAATTC
* * *
3078157 ATT ATT ACT GTT ATT AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3078196 TTTTATGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3078194 original size:24 final size:24
Alignment explanation
Indices: 3078119--3078195 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
3078109 TTTTTTTTTT
*
3078119 TTAATATTAAATATTTATTTATTGTTA
1 TTAATATT-ATTA-TTA-TTATTGTTA
* *
3078146 TTAATA-AATTCATTATTACTGTTA
1 TTAATATTATT-ATTATTATTGTTA
*
3078170 TTAATATTATTATTATTATTATTA
1 TTAATATTATTATTATTATTGTTA
3078194 TT
1 TT
3078196 TTTTATGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
24 27 0.64
25 8 0.19
26 1 0.02
27 6 0.14
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (24 bp):
TTAATATTATTATTATTATTGTTA
Found at i:3078904 original size:17 final size:17
Alignment explanation
Indices: 3078884--3078946 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
3078874 AAATGTATTT
* *
3078884 TAAATTCAAATTTATAA
1 TAAATTTAAATTTAAAA
3078901 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
3078918 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
3078935 TAAACTTAAATT
1 TAAATTTAAATT
3078947 CTGTTGGGTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:3086293 original size:63 final size:64
Alignment explanation
Indices: 3086194--3086340 Score: 188
Period size: 64 Copynumber: 2.3 Consensus size: 64
3086184 CACAAATATG
* * *
3086194 ATTCTCAGTTTTCCAAAATGTGGGCCCAACTAATTTGA-TTTTGCACTAGTTATGCTTAATTTC
1 ATTCTCAATTTTCCAAAATATGGGCCCAACTAATTTGATTTTTGCACTAGTTATGCGTAATTTC
* * * * *
3086257 ATTCTCAATTTTCCAAAATATGGGCCCAGCTAATTTGATTTTTTCTCTAGTTGTGGGTAATTTC
1 ATTCTCAATTTTCCAAAATATGGGCCCAACTAATTTGATTTTTGCACTAGTTATGCGTAATTTC
* * *
3086321 GTTCTCAACTTTCGAAAATA
1 ATTCTCAATTTTCCAAAATA
3086341 ATAGCAGGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
63 35 0.49
64 37 0.51
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (64 bp):
ATTCTCAATTTTCCAAAATATGGGCCCAACTAATTTGATTTTTGCACTAGTTATGCGTAATTTC
Found at i:3091452 original size:18 final size:18
Alignment explanation
Indices: 3091431--3091477 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3091421 TATGATTGCA
3091431 AAATAAATTAAGTGAATT
1 AAATAAATTAAGTGAATT
*
3091449 AAATTAAA-TCAGTGAATT
1 AAA-TAAATTAAGTGAATT
*
3091467 AAATATATTAA
1 AAATAAATTAA
3091478 AGTTTAGCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.12
18 17 0.71
19 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (18 bp):
AAATAAATTAAGTGAATT
Found at i:3092027 original size:20 final size:21
Alignment explanation
Indices: 3091998--3092041 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3091988 TCGTTTGTAC
*
3091998 TTTAGTAAATTT-AGTTGCAT
1 TTTAGGAAATTTCAGTTGCAT
*
3092018 TTTAGGAAATTTCATTTGCAT
1 TTTAGGAAATTTCAGTTGCAT
3092039 TTT
1 TTT
3092042 CTTCAACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTAGGAAATTTCAGTTGCAT
Found at i:3092894 original size:222 final size:225
Alignment explanation
Indices: 3092499--3092912 Score: 599
Period size: 222 Copynumber: 1.8 Consensus size: 225
3092489 TACTATATTC
* * *
3092499 ATTTTTTTTCTTGTTTCAGTCTGTATTATTACTTTTCTAACAATTTGATGGTTGAATAGTTAATA
1 ATTTTTTCTCTTGTTTCAATCTGTATTATTACTTTTCTAACAATTTGATAGTTGAATAGTTAATA
* *
3092564 TCATTTGTATAAGTATTTTTGTTAAAGATCTATGATGTTCCATTTATGTAATCATTGAAAGGGAA
66 TCATTTGTATAAGTATTTTTGATAAAGATCTATGATGTTCCA-TTATGT-ATCATGGAAAGGGAA
3092629 GCATAAATGCTACAATATGTTAAATCTAACTTTATACTATTTGGATGCTGGAAATCA-AAAAGCA
129 GCATAAATGCTACAATATGTTAAATCTAACTTTATACTATTTGGATGCTGGAAATCATAAAAGCA
3092693 GTAATTGAAATTGCATATACTATATTTATTTT
194 GTAATTGAAATTGCATATACTATATTTATTTT
* * *
3092725 ATTTTTTCTCTTGTTTCAATCTTTATTATTTATTTTTCTAACAATTTGATAGTTGAATTGTTAAT
1 ATTTTTTCTCTTGTTTCAATCTGTATTA-TTACTTTTCTAACAATTTGATAGTTGAATAGTT-A-
*
3092790 ATCATCATTTGTATAAGTATTTTTGATAAAGATCTATGATTTTCCA-T-T-T-T-ATGGAAA-GG
63 AT-ATCATTTGTATAAGTATTTTTGATAAAGATCTATGATGTTCCATTATGTATCATGGAAAGGG
** * * *
3092849 AAGCATGCATGCTACAATATGTTAAATTTAACTTTATGCTATTTGGGTGCTGGAAATCATAAAA
127 AAGCATAAATGCTACAATATGTTAAATCTAACTTTATACTATTTGGATGCTGGAAATCATAAAA
3092913 TTACATACTA
Statistics
Matches: 169, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
222 56 0.33
223 10 0.06
224 1 0.01
226 26 0.15
227 31 0.18
228 2 0.01
229 2 0.01
230 41 0.24
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (225 bp):
ATTTTTTCTCTTGTTTCAATCTGTATTATTACTTTTCTAACAATTTGATAGTTGAATAGTTAATA
TCATTTGTATAAGTATTTTTGATAAAGATCTATGATGTTCCATTATGTATCATGGAAAGGGAAGC
ATAAATGCTACAATATGTTAAATCTAACTTTATACTATTTGGATGCTGGAAATCATAAAAGCAGT
AATTGAAATTGCATATACTATATTTATTTT
Found at i:3095899 original size:21 final size:21
Alignment explanation
Indices: 3095874--3095940 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
3095864 CAGCCCACTT
3095874 AAATAATGTGAGTTTAAATTA
1 AAATAATGTGAGTTTAAATTA
* * *
3095895 AAAT-ATAGCT-A-TTGAATTTT
1 AAATAAT-G-TGAGTTTAAATTA
*
3095915 AAATAATGTGGGTTTAAATTA
1 AAATAATGTGAGTTTAAATTA
3095936 AAATA
1 AAATA
3095941 TAGCTATTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
19 1 0.03
20 13 0.38
21 19 0.56
22 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.13, T:0.39
Consensus pattern (21 bp):
AAATAATGTGAGTTTAAATTA
Found at i:3095930 original size:41 final size:41
Alignment explanation
Indices: 3095872--3095957 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
3095862 ATCAGCCCAC
3095872 TTAAATAATGTGAGTTTAAATTAAAATATAGCTATTGAATT
1 TTAAATAATGTGAGTTTAAATTAAAATATAGCTATTGAATT
*
3095913 TTAAATAATGTGGGTTTAAATTAAAATATAGCTATTGAATT
1 TTAAATAATGTGAGTTTAAATTAAAATATAGCTATTGAATT
3095954 TTAA
1 TTAA
3095958 GTTACGACCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (41 bp):
TTAAATAATGTGAGTTTAAATTAAAATATAGCTATTGAATT
Found at i:3095957 original size:21 final size:21
Alignment explanation
Indices: 3095892--3095957 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3095882 TGAGTTTAAA
3095892 TTAAAATATAGCTATTGAATT
1 TTAAAATATAGCTATTGAATT
* * * *
3095913 TTAAATAATGTGGGT-TT-AA-A
1 TT-AA-AATATAGCTATTGAATT
3095933 TTAAAATATAGCTATTGAATT
1 TTAAAATATAGCTATTGAATT
3095954 TTAA
1 TTAA
3095958 GTTACGACCT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 4 0.12
21 8 0.25
22 4 0.12
23 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
TTAAAATATAGCTATTGAATT
Found at i:3100836 original size:18 final size:18
Alignment explanation
Indices: 3100813--3100885 Score: 69
Period size: 18 Copynumber: 3.8 Consensus size: 18
3100803 ATCTAATATA
3100813 AAATAAATAATA-AAAATT
1 AAATAAATAA-ACAAAATT
*
3100831 AAATAAA-AAACAAAATA
1 AAATAAATAAACAAAATT
3100848 AGAATAAATAAAACAAAATT
1 A-AATAAAT-AAACAAAATT
3100868 AAATCTAAATAAAGCAAA
1 AAA--TAAATAAA-CAAA
3100886 TAAATGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.02
17 8 0.17
18 13 0.28
19 2 0.04
20 13 0.28
21 9 0.20
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATAAATAAACAAAATT
Found at i:3102861 original size:35 final size:35
Alignment explanation
Indices: 3102822--3102892 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3102812 AATCATGCTT
3102822 ATGATAAGAAAAACATCAATCACTATTTCAAGTGA
1 ATGATAAGAAAAACATCAATCACTATTTCAAGTGA
3102857 ATGATAAGAAAAACATCAATCACTATTTCAAGTGA
1 ATGATAAGAAAAACATCAATCACTATTTCAAGTGA
3102892 A
1 A
3102893 CATTATTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.25
Consensus pattern (35 bp):
ATGATAAGAAAAACATCAATCACTATTTCAAGTGA
Found at i:3110193 original size:29 final size:29
Alignment explanation
Indices: 3110129--3110187 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
3110119 TTTCACATCA
3110129 CAAAATCAAACCCAAAAAAAAAAACCATT
1 CAAAATCAAACCCAAAAAAAAAAACCATT
3110158 CAAAATCAAACCC-AAAAAAAAAACCATT
1 CAAAATCAAACCCAAAAAAAAAAACCATT
3110186 CA
1 CA
3110188 TTAATCTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.64, C:0.25, G:0.00, T:0.10
Consensus pattern (29 bp):
CAAAATCAAACCCAAAAAAAAAAACCATT
Found at i:3110788 original size:18 final size:18
Alignment explanation
Indices: 3110765--3110807 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3110755 TAATAGATTT
3110765 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
3110783 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
3110801 TTAATTA
1 TTAATTA
3110808 CACTTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:3111071 original size:20 final size:20
Alignment explanation
Indices: 3111046--3111087 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3111036 TTTTCTAATT
* *
3111046 TATTTTTTTAAGAAAAACAA
1 TATTTTATTAAAAAAAACAA
3111066 TATTTTATTAAAAAAAACAA
1 TATTTTATTAAAAAAAACAA
3111086 TA
1 TA
3111088 ATGTAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (20 bp):
TATTTTATTAAAAAAAACAA
Found at i:3112475 original size:21 final size:22
Alignment explanation
Indices: 3112434--3112476 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3112424 ATTAAAATGC
*
3112434 ACTTAATTATTTTTATGAATTT
1 ACTTAATTATTTTTATAAATTT
3112456 ACTTAACTT-TTTTT-TAAATTT
1 ACTTAA-TTATTTTTATAAATTT
3112477 TTTAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 11 0.58
23 2 0.11
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
ACTTAATTATTTTTATAAATTT
Found at i:3113914 original size:8 final size:8
Alignment explanation
Indices: 3113901--3113929 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3113891 ATCCAAGAAA
3113901 AAAAATAT
1 AAAAATAT
3113909 AAAAATAT
1 AAAAATAT
3113917 AAAAATAT
1 AAAAATAT
3113925 AAAAA
1 AAAAA
3113930 AAAATTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:3126771 original size:29 final size:27
Alignment explanation
Indices: 3126738--3126806 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 27
3126728 TAAATCTCAA
*
3126738 AATTATACATGAACTTTGATTTAATGTGC
1 AATTATACATGAACTTTAATTT-A-GTGC
*
3126767 AATTATATACATGAATTTTAATTTAGTGC
1 AA-T-TATACATGAACTTTAATTTAGTGC
*
3126796 AATTATGCATG
1 AATTATACATG
3126807 TGAAACTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 7 0.20
28 1 0.03
29 8 0.23
30 2 0.06
31 17 0.49
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (27 bp):
AATTATACATGAACTTTAATTTAGTGC
Found at i:3126778 original size:31 final size:29
Alignment explanation
Indices: 3126741--3126801 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
3126731 ATCTCAAAAT
*
3126741 TATACATGAACTTTGATTTAATGTGCAATTA
1 TATACATGAACTTTAATTT-A-GTGCAATTA
*
3126772 TATACATGAATTTTAATTTAGTGCAATTA
1 TATACATGAACTTTAATTTAGTGCAATTA
3126801 T
1 T
3126802 GCATGTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.36
30 1 0.04
31 17 0.61
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (29 bp):
TATACATGAACTTTAATTTAGTGCAATTA
Found at i:3127037 original size:29 final size:30
Alignment explanation
Indices: 3126994--3127052 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
3126984 TAATTGGATC
3126994 AAATCAAAATTTCATATATAAAATTCCACA
1 AAATCAAAATTTCATATATAAAATTCCACA
* * *
3127024 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAATTTCATATATAAAATTCCACA
3127053 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTCCACA
Found at i:3127596 original size:20 final size:21
Alignment explanation
Indices: 3127571--3127627 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
3127561 TAGTGATATA
*
3127571 ATATAAATATAAATATAA-AT
1 ATATAATTATAAATATAACAT
* *
3127591 ATATAATTAT-TATTTAACAT
1 ATATAATTATAAATATAACAT
3127611 ATATAATTAATAAATAT
1 ATATAATT-ATAAATAT
3127628 TTTTTATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.17
20 19 0.66
21 2 0.07
22 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATTATAAATATAACAT
Found at i:3130604 original size:5 final size:5
Alignment explanation
Indices: 3130596--3130620 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3130586 TTTTAATACA
3130596 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
3130621 TTTTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:3137097 original size:3 final size:3
Alignment explanation
Indices: 3137084--3137113 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3137074 ATTGTTAGTA
*
3137084 TTC TCC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3137114 CTCCTCCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:3140826 original size:28 final size:26
Alignment explanation
Indices: 3140763--3140826 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
3140753 TATCAAATTT
* * *
3140763 AAAATTAAATTGATATAATTCATAAA
1 AAAAATAAATTGACATAAATCATAAA
*
3140789 AAAAATTAAATTGACATAAATCTTTAAA
1 AAAAA-TAAATTGACATAAATC-ATAAA
3140817 GAAAAATAAA
1 -AAAAATAAA
3140827 ATTTTCCGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 4 0.13
27 14 0.45
28 8 0.26
29 5 0.16
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (26 bp):
AAAAATAAATTGACATAAATCATAAA
Found at i:3155156 original size:136 final size:136
Alignment explanation
Indices: 3154765--3155156 Score: 536
Period size: 136 Copynumber: 2.9 Consensus size: 136
3154755 TTCAACACTA
* * * * *
3154765 AAAATTACTTCATTTCATCCAACTCTATTCATATTAATTAGCTCATGGTTAGAGAACTATTTACG
1 AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
** * ** * * *
3154830 CATTGCTTTACACA-TGGTATCAG-AAATAATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
66 CACAGTTTTACACATTACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
*
3154893 GGGTCT
131 AGGTCT
*
3154899 AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTCACA
1 AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
* * *
3154964 CACAGTTTTACACATTACTAGTAGCAGTTTATCAGTAAACTAAGAGGGACGTCATTCGTTTATTC
66 CACAGTTTTACACATTACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
3155029 AGGTCT
131 AGGTCT
* * *
3155035 AAAATTACTTCATTTCATCCAGTTCTATTCATATTAACTAGCTCATGCTTTGAGAGCCATTTACA
1 AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
* * * * *
3155100 CACGGTTTTACACATTACTATTAGCAGCTTATCAGTAAAGTATGAGGGATGCCATTC
66 CACAGTTTTACACATTACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTC
3155157 ATTCTCATTT
Statistics
Matches: 227, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
134 70 0.31
135 5 0.02
136 152 0.67
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (136 bp):
AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
CACAGTTTTACACATTACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
AGGTCT
Found at i:3158110 original size:20 final size:21
Alignment explanation
Indices: 3158072--3158123 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3158062 GTTTAGAATT
*
3158072 TTTTTTAGATTTTAAATAA-TA
1 TTTTTTAGA-ATTAAATAACTA
*
3158093 TTTTTTAGAATTACATAACTA
1 TTTTTTAGAATTAAATAACTA
*
3158114 TGTTTTAGAA
1 TTTTTTAGAA
3158124 AATTTTCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (21 bp):
TTTTTTAGAATTAAATAACTA
Found at i:3161003 original size:21 final size:21
Alignment explanation
Indices: 3160931--3160999 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 21
3160921 ATATTGTTGC
*
3160931 TTTGGTGCTTTTTTTTACTAT
1 TTTGGTGCTTTTTTTTACTGT
** **
3160952 TTTGGTTGCAATTTTTTGTTGT
1 TTTGG-TGCTTTTTTTTACTGT
*
3160974 TTTAGTG-TTTTTTTTACTGT
1 TTTGGTGCTTTTTTTTACTGT
3160994 TTTGGT
1 TTTGGT
3161000 TGTTGATTTG
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
20 14 0.39
21 7 0.19
22 15 0.42
ACGTcount: A:0.09, C:0.06, G:0.19, T:0.67
Consensus pattern (21 bp):
TTTGGTGCTTTTTTTTACTGT
Found at i:3161082 original size:44 final size:44
Alignment explanation
Indices: 3161033--3161121 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
3161023 ATTGTTTTGA
* * *
3161033 TGCTGCTATTTTAGTTGTTTTTGTTG-TTGTTTTGCTATTATTTT
1 TGCTGCTATTTTAGTTGTTATT-TTGATTGTTTAGATATTATTTT
3161077 TGCTGCTATTTTAGTTGTTATTTTGATTGTTTAGATATTATTTT
1 TGCTGCTATTTTAGTTGTTATTTTGATTGTTTAGATATTATTTT
3161121 T
1 T
3161122 ATGCGTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 3 0.07
44 38 0.93
ACGTcount: A:0.13, C:0.06, G:0.17, T:0.64
Consensus pattern (44 bp):
TGCTGCTATTTTAGTTGTTATTTTGATTGTTTAGATATTATTTT
Found at i:3162474 original size:5 final size:5
Alignment explanation
Indices: 3162464--3162493 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3162454 AAAGTATAAA
*
3162464 TAATT TAATT TAATT TAATC TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT
3162494 ATGCTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:3164288 original size:17 final size:17
Alignment explanation
Indices: 3164266--3164298 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3164256 GTTGGGTCAA
3164266 TAATTTT-CTATTTTTTT
1 TAATTTTGCT-TTTTTTT
3164283 TAATTTTGCTTTTTTT
1 TAATTTTGCTTTTTTT
3164299 AGTAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (17 bp):
TAATTTTGCTTTTTTTT
Found at i:3181664 original size:9 final size:9
Alignment explanation
Indices: 3181646--3181678 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3181636 ACTTTTTTTT
3181646 GGGGGG-GG
1 GGGGGGAGG
3181654 GGGGGGAGG
1 GGGGGGAGG
3181663 GGGGGGAGG
1 GGGGGGAGG
3181672 GGCGGGG
1 GG-GGGG
3181679 GCAGATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.26
9 13 0.57
10 4 0.17
ACGTcount: A:0.06, C:0.03, G:0.91, T:0.00
Consensus pattern (9 bp):
GGGGGGAGG
Found at i:3195131 original size:160 final size:163
Alignment explanation
Indices: 3194965--3195291 Score: 520
Period size: 162 Copynumber: 2.0 Consensus size: 163
3194955 ATAACTTTCA
*
3194965 TTAAATT-AGATTTTATGTTATTTTTTAAATAAAGAAATGATTATGAGACCAATTC-AAA-CTTT
1 TTAAATTCA-ATTTTATGTTATTTTTAAAATAAAGAAATGATTATGAGACCAATTCAAAATCTTT
*
3195027 AGAATAATATCGAAGAACTTTATAATCCTAAATTAAAAGTTGATTA-AGTGTTTATTTGA-CCCC
65 AGAATAATATCGAAGAACTTTATAATCCTAAATTAAAAGCTGATTACA-TGTTTATTTGACCCCC
* * *
3195090 AAATTTTTTATTTTAAAAATTTCTTGTAACTCAAT
129 AAAATTTTTATTTTAAAAATGTCATGTAACTCAAT
3195125 TTAAATTCAATTTTATGTTATTTTTAAAATAAAGAAATGATTATGAGACCAATTCAAAATCTTTA
1 TTAAATTCAATTTTATGTTATTTTTAAAATAAAGAAATGATTATGAGACCAATTCAAAATCTTTA
* * *
3195190 GAATAATATGGAAGAATTTTATAATCCTAGATTAAAAGCTGATTACATGTTTATTTGACCCCCAA
66 GAATAATATCGAAGAACTTTATAATCCTAAATTAAAAGCTGATTACATGTTTATTTGACCCCCAA
*
3195255 AATTTTTATTTTAAAAATGTCATGTAATTCAAT
131 AATTTTTATTTTAAAAATGTCATGTAACTCAAT
3195288 TTAA
1 TTAA
3195292 GTCTAGTGTT
Statistics
Matches: 153, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
160 52 0.34
161 4 0.03
162 57 0.37
163 40 0.26
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (163 bp):
TTAAATTCAATTTTATGTTATTTTTAAAATAAAGAAATGATTATGAGACCAATTCAAAATCTTTA
GAATAATATCGAAGAACTTTATAATCCTAAATTAAAAGCTGATTACATGTTTATTTGACCCCCAA
AATTTTTATTTTAAAAATGTCATGTAACTCAAT
Found at i:3197545 original size:20 final size:20
Alignment explanation
Indices: 3197520--3197557 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3197510 CATCAATCAA
3197520 AATTTTTTCTTCTATAAATC
1 AATTTTTTCTTCTATAAATC
* *
3197540 AATTTTTTTTTTTATAAA
1 AATTTTTTCTTCTATAAA
3197558 ACAACTTTAA
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:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTTTCTTCTATAAATC
Found at i:3197782 original size:31 final size:32
Alignment explanation
Indices: 3197740--3197799 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
3197730 AAAAAAAATT
* *
3197740 AATAGTCCAATGAC-TAAATTAAGAATTTTTG
1 AATAGTCCAATGACTTAAATAAAAAATTTTTG
*
3197771 AATAGTTCAATGACTTAAATAAAAAATTT
1 AATAGTCCAATGACTTAAATAAAAAATTT
3197800 AAATAGTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (32 bp):
AATAGTCCAATGACTTAAATAAAAAATTTTTG
Found at i:3198962 original size:23 final size:22
Alignment explanation
Indices: 3198918--3198963 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3198908 GTCACTCCAC
3198918 TAAAGCTTCATTTAAATATTTT
1 TAAAGCTTCATTTAAATATTTT
* *
3198940 TAAAGCTTCATTTTAATACTTT
1 TAAAGCTTCATTTAAATATTTT
3198962 TA
1 TA
3198964 TATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (22 bp):
TAAAGCTTCATTTAAATATTTT
Found at i:3202989 original size:15 final size:15
Alignment explanation
Indices: 3202971--3203013 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3202961 TATTCATCAG
3202971 TTTTTTATATTTAAT
1 TTTTTTATATTTAAT
*
3202986 TTTTTTA-ATTTTAT
1 TTTTTTATATTTAAT
*
3203000 TTATTTGATATTTA
1 TT-TTTTATATTTA
3203014 TAAATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.35
15 11 0.48
16 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTTTATATTTAAT
Found at i:3205781 original size:2 final size:2
Alignment explanation
Indices: 3205774--3205811 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3205764 TAAATTAAAG
3205774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3205812 TCAATCTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3207182 original size:84 final size:84
Alignment explanation
Indices: 3207094--3207254 Score: 225
Period size: 84 Copynumber: 1.9 Consensus size: 84
3207084 TTTTAAGAAC
* *
3207094 CTAAAGTGTAATTTCACTATAT-ATTAATTTATAATTTATTTATTTATAAAAAGTTTAAATTGAA
1 CTAAAGTGTAATTTCACTAT-TGATTAATTTATAATTTATCTATTTATAAAAAGATTAAATTGAA
3207158 AATTTTTCATTTTGCGAGAG
65 AATTTTTCATTTTGCGAGAG
* * * * * * *
3207178 CTAAAGTTTTATTTCACTATTGATTATTTTATAGTTTCTCTATTTATAAAAGGATTGAATTGAAA
1 CTAAAGTGTAATTTCACTATTGATTAATTTATAATTTATCTATTTATAAAAAGATTAAATTGAAA
3207243 ATTTTTCATTTT
66 ATTTTTCATTTT
3207255 TAAAGAGACA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
83 1 0.01
84 66 0.99
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (84 bp):
CTAAAGTGTAATTTCACTATTGATTAATTTATAATTTATCTATTTATAAAAAGATTAAATTGAAA
ATTTTTCATTTTGCGAGAG
Found at i:3208096 original size:22 final size:23
Alignment explanation
Indices: 3208034--3208097 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
3208024 AAAAAATAAA
3208034 ATAAAATTTATTTAAAT-TTAATG
1 ATAAAA-TTATTTAAATATTAATG
* * *
3208057 ATAAAAATATATACATATTAAT-
1 ATAAAATTATTTAAATATTAATG
*
3208079 ATAAAATTATTTATATATT
1 ATAAAATTATTTAAATATT
3208098 TTCTAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAAATTATTTAAATATTAATG
Found at i:3212903 original size:30 final size:30
Alignment explanation
Indices: 3212863--3212919 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3212853 AGTGGAGCAT
3212863 GTCAAATTGAATTGAATCGAATTTATGAAA
1 GTCAAATTGAATTGAATCGAATTTATGAAA
* *
3212893 GTCAATTTGAATTGAATTGAATTTATG
1 GTCAAATTGAATTGAATCGAATTTATG
3212920 CAAGAAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (30 bp):
GTCAAATTGAATTGAATCGAATTTATGAAA
Found at i:3213106 original size:31 final size:31
Alignment explanation
Indices: 3213041--3213106 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3213031 TTTAGGCACT
* * *
3213041 AAATTGAACATTGAAGTCAAACTTAAGTATC
1 AAATTAAACATTGAAGTCAAACTTAAGAACC
*
3213072 AAATTAAACATTGAAGTTAAA-TTAAGAAACC
1 AAATTAAACATTGAAGTCAAACTTAAG-AACC
3213103 AAAT
1 AAAT
3213107 AGTATATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (31 bp):
AAATTAAACATTGAAGTCAAACTTAAGAACC
Found at i:3213296 original size:16 final size:16
Alignment explanation
Indices: 3213258--3213297 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3213248 GGTTCTTTCG
*
3213258 TTAAAAACTTCATCTG
1 TTAAAAACTTCATCTA
*
3213274 TTAAAAATTTCATCTA
1 TTAAAAACTTCATCTA
3213290 TTTAAAAA
1 -TTAAAAA
3213298 GCAGCGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (16 bp):
TTAAAAACTTCATCTA
Found at i:3213297 original size:17 final size:16
Alignment explanation
Indices: 3213257--3213288 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3213247 CGGTTCTTTC
3213257 GTTAAAAACTTCATCT
1 GTTAAAAACTTCATCT
*
3213273 GTTAAAAATTTCATCT
1 GTTAAAAACTTCATCT
3213289 ATTTAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (16 bp):
GTTAAAAACTTCATCT
Found at i:3218346 original size:15 final size:15
Alignment explanation
Indices: 3218328--3218364 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3218318 TATTTAATAA
3218328 ATTTATATAAATTTT
1 ATTTATATAAATTTT
*
3218343 ATTTAT-TGAATTTT
1 ATTTATATAAATTTT
3218357 -TTTATATA
1 ATTTATATA
3218365 GTCATCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
13 5 0.26
14 8 0.42
15 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTATATAAATTTT
Found at i:3218702 original size:14 final size:13
Alignment explanation
Indices: 3218680--3218710 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3218670 AAATTAAAAC
3218680 ATTACTATTATAT
1 ATTACTATTATAT
3218693 ATTACTTATTATAT
1 ATTAC-TATTATAT
3218707 ATTA
1 ATTA
3218711 TTGTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTACTATTATAT
Found at i:3219110 original size:17 final size:17
Alignment explanation
Indices: 3219059--3219121 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
3219049 TTATGTTATC
3219059 ATTAAATTTTAA-ATTT
1 ATTAAATTTTAATATTT
* *
3219075 A-CAAA-TTTAATAATT
1 ATTAAATTTTAATATTT
3219090 ATT-AATTTTATATATTT
1 ATTAAATTTTA-ATATTT
3219107 ATTAAATTTTAATAT
1 ATTAAATTTTAATAT
3219122 AAATATGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
14 5 0.13
15 9 0.24
16 5 0.13
17 12 0.32
18 7 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTAAATTTTAATATTT
Found at i:3219118 original size:24 final size:24
Alignment explanation
Indices: 3219059--3219119 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
3219049 TTATGTTATC
*
3219059 ATTAAATTTTAAATTTACAAATTT
1 ATTAAATTTTAATTTTACAAATTT
* * *
3219083 AAT-AATTATTAATTTTATATATTT
1 ATTAAATT-TTAATTTTACAAATTT
3219107 ATTAAATTTTAAT
1 ATTAAATTTTAAT
3219120 ATAAATATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 4 0.13
24 22 0.73
25 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTAAATTTTAATTTTACAAATTT
Found at i:3222521 original size:39 final size:39
Alignment explanation
Indices: 3222478--3222556 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3222468 ATGTAATCTC
3222478 AGCTATGTGATTTATAAAGATTTTTTTATTTTCTAAATA
1 AGCTATGTGATTTATAAAGATTTTTTTATTTTCTAAATA
3222517 AGCTATGTGATTTATAAAGATTTTTTTATTTTCTAAATA
1 AGCTATGTGATTTATAAAGATTTTTTTATTTTCTAAATA
3222556 A
1 A
3222557 AATAATTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (39 bp):
AGCTATGTGATTTATAAAGATTTTTTTATTTTCTAAATA
Found at i:3228344 original size:58 final size:59
Alignment explanation
Indices: 3228224--3228476 Score: 250
Period size: 58 Copynumber: 4.3 Consensus size: 59
3228214 TGGATATCTG
* * * *
3228224 GGGGTAAAATGGTAA-TTTTGGTTGAAATTGA-GTCAAAAAGGG-ATTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGG-TAAAATCGAGGTCAAAAAGGGAATTTTGGAAAGTTCA
* * *
3228281 GGGGTAAAACGGTAATTTTTAGTAAAATCGAGGTCAAAAAAGGAA-TTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAAGGGAATTTTGGAAAGTTCA
* * * * * * *
3228339 AGGGTAAAATAGTAATTTTTGGTAAATTTGGGGTTAAAAAGGGAATTTTGGAAAG-TCT
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAAGGGAATTTTGGAAAGTTCA
* * * *
3228397 GGAGGTAAAATGGTAATTTTTGGTGAAATCGAGGGCAAAAATGGAATTTTGGAAAAATT-A
1 GG-GGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAAGGGAATTTTGG-AAAGTTCA
*
3228457 GAGGTAAAAAT-GTAATTTTT
1 GGGGT-AAAATGGTAATTTTT
3228477 AGAAAGTTTT
Statistics
Matches: 159, Mismatches: 29, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
57 21 0.13
58 65 0.41
59 63 0.40
60 9 0.06
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAAGGGAATTTTGGAAAGTTCA
Found at i:3228377 original size:30 final size:30
Alignment explanation
Indices: 3228326--3228657 Score: 171
Period size: 30 Copynumber: 11.2 Consensus size: 30
3228316 AAAAAAGGAA
**
3228326 TTTGGAAAGTTCAAGGG-TAAAATAGTAATT
1 TTTGGAAAGTT-TGGGGTTAAAATAGTAATT
*
3228356 TTTGGTAAA-TTTGGGGTTAAAA-AGGGAA-T
1 TTTGG-AAAGTTTGGGGTTAAAATA-GTAATT
* *
3228385 TTTGGAAAGTCTGGAGG-TAAAATGGTAATT
1 TTTGGAAAGTTTGG-GGTTAAAATAGTAATT
* ** *
3228415 TTTGGTGAAA--TCGAGGGCAAAAAT-GGAA-T
1 TTT-G-GAAAGTTTG-GGGTTAAAATAGTAATT
* * * *
3228444 TTTGGAAAAATTAGAGGTAAAAAT-GTAATT
1 TTTGG-AAAGTTTGGGGTTAAAATAGTAATT
*
3228474 TTTAGAAAGTTTTGGGGTTAAAATA-TAATT
1 TTTGGAAAG-TTTGGGGTTAAAATAGTAATT
*** * *
3228504 TTCAAAAATTTTAGGGTTAAAATA-TAA-T
1 TTTGGAAAGTTTGGGGTTAAAATAGTAATT
*
3228532 TTTGGAGAAGTTTAGAGGTTAAAAT-GTAATT
1 TTTGGA-AAGTTT-GGGGTTAAAATAGTAATT
* *
3228563 TTTAGAAAGTTTTGAGGTTAAAATA-TAA-T
1 TTTGGAAAG-TTTGGGGTTAAAATAGTAATT
*
3228592 TTTGGAGAAGTTTAAGGGTTAAAAT-GTAATT
1 TTTGGA-AAGTTT-GGGGTTAAAATAGTAATT
* *
3228623 TTT-GAAAGTTTTGGGGTCAAAATACT-ATT
1 TTTGGAAAG-TTTGGGGTTAAAATAGTAATT
3228652 TTTGGA
1 TTTGGA
3228658 CTTAACCATT
Statistics
Matches: 236, Mismatches: 36, Indels: 60
0.71 0.11 0.18
Matches are distributed among these distances:
27 1 0.00
28 11 0.05
29 89 0.38
30 108 0.46
31 23 0.10
32 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTGGAAAGTTTGGGGTTAAAATAGTAATT
Found at i:3228404 original size:117 final size:116
Alignment explanation
Indices: 3228225--3228451 Score: 291
Period size: 117 Copynumber: 1.9 Consensus size: 116
3228215 GGATATCTGG
* *
3228225 GGGTAAAATGGTAATTTTGGTTGAAATTGAGTCAAAAAGGGATTTTAGAAAGTTCGGGGGTAAAA
1 GGGTAAAATAGTAATTTTGGTTGAAATTGAGTCAAAAAGGGATTTTAGAAAGTTCGGAGGTAAAA
*
3228290 CGGTAATTTTTAGTAAAATCGAGGTCAAAAAAGGAA-TTTGGAAAGTTCAA
66 CGGTAATTTTTAGTAAAATCGAGGGCAAAAAAGGAATTTTGGAAAGTTCAA
* * *
3228340 GGGTAAAATAGTAATTTTTGG-T-AAATTTGGGGTTAAAAAGGGAATTTTGGAAAG-TCTGGAGG
1 GGGTAAAATAGTAA-TTTTGGTTGAAA-TT-GAGTCAAAAAGGG-ATTTTAGAAAGTTC-GGAGG
* * * *
3228402 TAAAATGGTAATTTTTGGTGAAATCGAGGGCAAAAATGGAATTTTGGAAA
61 TAAAACGGTAATTTTTAGTAAAATCGAGGGCAAAAAAGGAATTTTGGAAA
3228452 AATTAGAGGT
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
114 3 0.03
115 16 0.17
116 19 0.20
117 50 0.52
118 8 0.08
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (116 bp):
GGGTAAAATAGTAATTTTGGTTGAAATTGAGTCAAAAAGGGATTTTAGAAAGTTCGGAGGTAAAA
CGGTAATTTTTAGTAAAATCGAGGGCAAAAAAGGAATTTTGGAAAGTTCAA
Found at i:3228416 original size:59 final size:57
Alignment explanation
Indices: 3228226--3228476 Score: 217
Period size: 59 Copynumber: 4.3 Consensus size: 57
3228216 GATATCTGGG
* * *
3228226 GGTAAAATGGTAA-TTTTGGTTGAAATT-GAGTCAAAAAGGG-ATTTTAGAAAGTTCGGG
1 GGTAAAATGGTAATTTTTGG-T-AAATTGGGGTCAAAAAGGGAATTTTGGAAAGTT-GGA
* * * * * **
3228283 GGTAAAACGGTAATTTTTAGTAAAATCGAGGTCAAAAAAGGAA-TTTGGAAAGTTCAA
1 GGTAAAATGGTAATTTTTGGT-AAATTGGGGTCAAAAAGGGAATTTTGGAAAGTTGGA
* *
3228340 GGGTAAAATAGTAATTTTTGGTAAATTTGGGGTTAAAAAGGGAATTTTGGAAAGTCTGGA
1 -GGTAAAATGGTAATTTTTGGTAAA-TTGGGGTCAAAAAGGGAATTTTGGAAAGT-TGGA
* * * *
3228400 GGTAAAATGGTAATTTTTGGTGAAATCGAGGG-CAAAAATGGAATTTTGGAAAAATTAGA
1 GGTAAAATGGTAATTTTTGGT-AAATTG-GGGTCAAAAAGGGAATTTTGG-AAAGTTGGA
3228459 GGTAAAAAT-GTAATTTTT
1 GGT-AAAATGGTAATTTTT
3228477 AGAAAGTTTT
Statistics
Matches: 157, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
57 20 0.13
58 57 0.36
59 63 0.40
60 17 0.11
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.31
Consensus pattern (57 bp):
GGTAAAATGGTAATTTTTGGTAAATTGGGGTCAAAAAGGGAATTTTGGAAAGTTGGA
Found at i:3228465 original size:29 final size:28
Alignment explanation
Indices: 3228355--3228475 Score: 75
Period size: 29 Copynumber: 4.1 Consensus size: 28
3228345 AAATAGTAAT
* * * *
3228355 TTTTGGTAAATTTGGGGTTAAAAAGGGAA
1 TTTTGGAAAATTAGAGG-TAAAAATGGAA
* *
3228384 TTTTGGAAAGTCTGGAGGT-AAAATGGTAA
1 TTTTGGAAAAT-TAGAGGTAAAAATGG-AA
* * *
3228413 TTTTTGGTGAAA-TCGAGGGCAAAAATGGAA
1 -TTTTGG-AAAATTAGA-GGTAAAAATGGAA
*
3228443 TTTTGGAAAAATTAGAGGTAAAAATGTAA
1 TTTTGG-AAAATTAGAGGTAAAAATGGAA
3228472 TTTT
1 TTTT
3228476 TAGAAAGTTT
Statistics
Matches: 71, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
28 6 0.08
29 39 0.55
30 17 0.24
31 9 0.13
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.33
Consensus pattern (28 bp):
TTTTGGAAAATTAGAGGTAAAAATGGAA
Found at i:3228599 original size:60 final size:60
Alignment explanation
Indices: 3228457--3228657 Score: 232
Period size: 60 Copynumber: 3.4 Consensus size: 60
3228447 GGAAAAATTA
* * * * * * * *
3228457 GAGGTAAAAATGTAATTTT-TAGAAAGTTTTGGGGTTAAAATATAATTTTCA-AAAATTTT
1 GAGGTTAAAATATAATTTTGGAG-AAGTTTAGAGGTTAAAATGTAATTTTTAGAAAGTTTT
3228516 -AGGGTTAAAATATAATTTTGGAGAAGTTTAGAGGTTAAAATGTAATTTTTAGAAAGTTTT
1 GA-GGTTAAAATATAATTTTGGAGAAGTTTAGAGGTTAAAATGTAATTTTTAGAAAGTTTT
3228576 GAGGTTAAAATATAATTTTGGAGAAGTTTA-AGGGTTAAAATGTAATTTTT-GAAAGTTTT
1 GAGGTTAAAATATAATTTTGGAGAAGTTTAGA-GGTTAAAATGTAATTTTTAGAAAGTTTT
* * *
3228635 GGGGTCAAAATACTATTTTTGGA
1 GAGGTTAAAATA-TAATTTTGGA
3228658 CTTAACCATT
Statistics
Matches: 125, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 59 0.47
60 64 0.51
61 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (60 bp):
GAGGTTAAAATATAATTTTGGAGAAGTTTAGAGGTTAAAATGTAATTTTTAGAAAGTTTT
Found at i:3228632 original size:89 final size:88
Alignment explanation
Indices: 3228434--3228633 Score: 283
Period size: 89 Copynumber: 2.2 Consensus size: 88
3228424 ATCGAGGGCA
* ** *
3228434 AAAATGGAATTTTGGAAAAATTAGAGGTAAAAATGTAATTTTTAGAAAGTTTTGGGGTTAAAATA
1 AAAATGTAATTTTGGAAAGTTTAGAGGTAAAAATGTAATTTTTAGAAAGTTTTGAGGTTAAAATA
*
3228499 TAATTTTCAAAAATTTTAGGGTT
66 TAATTTTCAAAAATTTAAGGGTT
* *
3228522 AAAATATAATTTTGGAGAAGTTTAGAGGTTAAAATGTAATTTTTAGAAAGTTTTGAGGTTAAAAT
1 AAAATGTAATTTTGGA-AAGTTTAGAGGTAAAAATGTAATTTTTAGAAAGTTTTGAGGTTAAAAT
* * *
3228587 ATAATTTTGGAGAAGTTTAAGGGTT
65 ATAATTTT-CAAAAATTTAAGGGTT
*
3228612 AAAATGTAATTTTTGAAAGTTT
1 AAAATGTAATTTTGGAAAGTTT
3228634 TGGGGTCAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
88 14 0.14
89 58 0.59
90 26 0.27
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.39
Consensus pattern (88 bp):
AAAATGTAATTTTGGAAAGTTTAGAGGTAAAAATGTAATTTTTAGAAAGTTTTGAGGTTAAAATA
TAATTTTCAAAAATTTAAGGGTT
Found at i:3228652 original size:29 final size:29
Alignment explanation
Indices: 3228463--3228655 Score: 199
Period size: 30 Copynumber: 6.5 Consensus size: 29
3228453 ATTAGAGGTA
*
3228463 AAAATGTAATTTTTAGAAAGTTTTGGGGTT
1 AAAATATAATTTTT-GAAAGTTTTGGGGTT
** * *
3228493 AAAATATAATTTTCAAAAATTTTAGGGTT
1 AAAATATAATTTTTGAAAGTTTTGGGGTT
* * *
3228522 AAAATATAATTTTGGAGAAGTTTAGAGGTT
1 AAAATATAATTTTTGA-AAGTTTTGGGGTT
* *
3228552 AAAATGTAATTTTTAGAAAGTTTTGAGGTT
1 AAAATATAATTTTT-GAAAGTTTTGGGGTT
* **
3228582 AAAATATAATTTTGGAGAAGTTTAAGGGTT
1 AAAATATAATTTTTGA-AAGTTTTGGGGTT
* *
3228612 AAAATGTAATTTTTGAAAGTTTTGGGGTC
1 AAAATATAATTTTTGAAAGTTTTGGGGTT
3228641 AAAATACT-ATTTTTG
1 AAAATA-TAATTTTTG
3228656 GACTTAACCA
Statistics
Matches: 134, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
29 50 0.37
30 82 0.61
31 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.41
Consensus pattern (29 bp):
AAAATATAATTTTTGAAAGTTTTGGGGTT
Found at i:3231150 original size:20 final size:21
Alignment explanation
Indices: 3231111--3231150 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3231101 TTCGGTTCGT
* *
3231111 AAAATGATCAAATTTGGAGAA
1 AAAATGATCAAATATAGAGAA
3231132 AAAATGAT-AAATATAGAGA
1 AAAATGATCAAATATAGAGA
3231151 TAGAACATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.57, C:0.03, G:0.17, T:0.23
Consensus pattern (21 bp):
AAAATGATCAAATATAGAGAA
Found at i:3232606 original size:16 final size:16
Alignment explanation
Indices: 3232585--3232615 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3232575 TGAAAACATT
3232585 ATAAAATGTCAGCATA
1 ATAAAATGTCAGCATA
*
3232601 ATAAAATGTTAGCAT
1 ATAAAATGTCAGCAT
3232616 TAATTAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (16 bp):
ATAAAATGTCAGCATA
Done.