Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold286
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: 1428881
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 499 characters in sequence are not A, C, G, or T
File 7 of 9
Found at i:921706 original size:20 final size:20
Alignment explanation
Indices: 921662--921713 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
921652 ACATTTGTTT
*
921662 ATGTATCGATAC-AATCAAC
1 ATGTATCGATACAAAGCAAC
921681 ATGTATCGATACAAAGCATA-
1 ATGTATCGATACAAAGCA-AC
921701 ATGTATCGATACA
1 ATGTATCGATACA
921714 TCTGAAAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.40
20 17 0.57
21 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAC
Found at i:928068 original size:12 final size:12
Alignment explanation
Indices: 928051--928091 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
928041 TGGTTCAACT
928051 AAAAAAAGAAAG
1 AAAAAAAGAAAG
*
928063 AAAAAAAGAAAA
1 AAAAAAAGAAAG
928075 AAAAAAGAGAAAG
1 AAAAAA-AGAAAG
928088 AAAA
1 AAAA
928092 GAGAGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:928102 original size:12 final size:12
Alignment explanation
Indices: 928051--928098 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
928041 TGGTTCAACT
*
928051 AAAAAAAGAAAG
1 AAAAAAAGAGAG
928063 AAAAAAAGA-A-
1 AAAAAAAGAGAG
928073 AAAAAAA-AGAG
1 AAAAAAAGAGAG
928084 AAAGAAAAGAGAG
1 AAA-AAAAGAGAG
928097 AA
1 AA
928099 GAAATAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.03
10 8 0.25
11 4 0.12
12 13 0.41
13 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAG
Found at i:932560 original size:3 final size:3
Alignment explanation
Indices: 932552--932582 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
932542 TTCAAGTCAA
*
932552 CAT CAT CAT CAT CAT CAT CAT CGT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
932583 TTTGAAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.03, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:934299 original size:19 final size:19
Alignment explanation
Indices: 934255--934310 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
934245 CTGCCAGTTT
* **
934255 CATGTATCGATACATTTGTT
1 CATGTATCGATACA-ATGAA
934275 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
934294 CATGTATTGATATAATG
1 CATGTATCGATACAATG
934311 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:936419 original size:13 final size:13
Alignment explanation
Indices: 936401--936426 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
936391 CAATTTTTTG
936401 TGTATCGATACAT
1 TGTATCGATACAT
936414 TGTATCGATACAT
1 TGTATCGATACAT
936427 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:937157 original size:16 final size:16
Alignment explanation
Indices: 937126--937171 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
937116 CTCTCCTTTG
937126 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
937144 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
937160 TCTCCCCCTTAA
1 TCTCCCCCTTAA
937172 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:938995 original size:13 final size:13
Alignment explanation
Indices: 938977--939015 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
938967 ATAATCACCC
*
938977 TGTATCGATACAG
1 TGTATCGATACAA
938990 TGTATCGATACAA
1 TGTATCGATACAA
939003 TGTATCGATACAA
1 TGTATCGATACAA
939016 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:939026 original size:20 final size:20
Alignment explanation
Indices: 939001--939079 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
938991 GTATCGATAC
939001 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
939021 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
939046 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
939065 ACATGTATCGATACA
1 A-ATGTATCGATACA
939080 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:941124 original size:15 final size:15
Alignment explanation
Indices: 941088--941125 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
941078 TACATCAATT
* *
941088 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
941103 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
941118 TCATTTTG
1 TCATTTTG
941126 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:945207 original size:13 final size:13
Alignment explanation
Indices: 945189--945214 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
945179 CAATTTTTTG
945189 TGTATCGATACAT
1 TGTATCGATACAT
945202 TGTATCGATACAT
1 TGTATCGATACAT
945215 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:946422 original size:13 final size:14
Alignment explanation
Indices: 946403--946440 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
946393 CTTGGGTTGA
946403 CTTTTTTTCTCGAT
1 CTTTTTTTCTCGAT
*
946417 -TTTTTTTCTCTAT
1 CTTTTTTTCTCGAT
946430 CTTCTTTTTCT
1 CTT-TTTTTCT
946441 TACTCCACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 2 0.10
15 7 0.33
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.71
Consensus pattern (14 bp):
CTTTTTTTCTCGAT
Found at i:951025 original size:30 final size:30
Alignment explanation
Indices: 950989--951048 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
950979 GATCATTTCT
950989 GGCTAGGCATGATCAGATACCTATTCAAAC
1 GGCTAGGCATGATCAGATACCTATTCAAAC
* *
951019 GGCTAGGCATGATCAGATGCCTATTTAAAC
1 GGCTAGGCATGATCAGATACCTATTCAAAC
951049 CTATGTCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (30 bp):
GGCTAGGCATGATCAGATACCTATTCAAAC
Found at i:956379 original size:94 final size:94
Alignment explanation
Indices: 956260--956482 Score: 263
Period size: 94 Copynumber: 2.4 Consensus size: 94
956250 TGTTTGACTA
* * * *
956260 TATTGGTGTTGGGACCTGGTCAAACCTTTTCATCC-TTCAGTTTGATTGCATTGGTATTAGGG-A
1 TATTGGTGTTGGGACCTGGTCAAACCTTTTCA-CCATTC-CTTTGACTGCATTAGCATTAGGGCA
* **
956323 TGGTCAAACTTTTTCATCC-TCTATTGGATTG
64 TGGTCAAACTTTTTCACCCTTC-ATTGGACCG
* *
956354 TATTGGTGTTGGGACCTGGTCAAACCTTTTCACCATTCCTTTGACTGCATTAGCGTTAGGGCCTG
1 TATTGGTGTTGGGACCTGGTCAAACCTTTTCACCATTCCTTTGACTGCATTAGCATTAGGGCATG
*
956419 GTCAAACTTTTTCACCCTTCATTTGACCG
66 GTCAAACTTTTTCACCCTTCATTGGACCG
* ** *
956448 TATTGGTGTTAGGACCAAGTCAAACTCTTTCCACC
1 TATTGGTGTTGGGACCTGGTCAAAC-CTTTTCACC
956483 CTCATTTAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
93 20 0.18
94 81 0.73
95 10 0.09
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (94 bp):
TATTGGTGTTGGGACCTGGTCAAACCTTTTCACCATTCCTTTGACTGCATTAGCATTAGGGCATG
GTCAAACTTTTTCACCCTTCATTGGACCG
Found at i:956470 original size:47 final size:46
Alignment explanation
Indices: 956252--956739 Score: 223
Period size: 47 Copynumber: 10.4 Consensus size: 46
956242 TCTTTCTTTG
* * * *
956252 TTTGACTATATTGGTGTTGGGACCTGGTCAAACCTTTTCATCCTTCA
1 TTTGACTGTATTGGTGTTAGGACCTGGTCAAACTTTTTCA-CCCTCA
* * * *
956299 GTTTGATTGCATTGGTATTAGGGA--TGGTCAAACTTTTTCATCCTCTA
1 -TTTGACTGTATTGGTGTTA-GGACCTGGTCAAACTTTTTCACCCTC-A
* * * * * *
956346 TTGGATTGTATTGGTGTTGGGACCTGGTCAAACCTTTTCACCATTCC
1 TTTGACTGTATTGGTGTTAGGACCTGGTCAAACTTTTTCACC-CTCA
* * * *
956393 TTTGACTGCATTAGCGTTAGGGCCTGGTCAAACTTTTTCACCCTTCA
1 TTTGACTGTATTGGTGTTAGGACCTGGTCAAACTTTTTCACCC-TCA
* ** *
956440 TTTGACCGTATTGGTGTTAGGACCAAGTCAAACTCTTTCCACCCTCA
1 TTTGACTGTATTGGTGTTAGGACCTGGTCAAACT-TTTTCACCCTCA
* * * ** * * * * * *
956487 TTTAATTGTGTTGGCATTA-AAACTAGTTAAACTCTTTCCACCCTCT
1 TTTGACTGTATTGGTGTTAGGACCTGGTCAAACT-TTTTCACCCTCA
* * * ** ** *
956533 TTTGACTGTATTGGCGTTAAGACCTGGTTAAAATCAAATTT-ACTTTTA
1 TTTGACTGTATTGGTGTTAGGACCTGG-TCAAA-C-TTTTTCACCCTCA
* * * * * * * **
956581 TTTGACTATACTGGTATTAGGACCTAGTCAAACTCTTCCACTCTTG
1 TTTGACTGTATTGGTGTTAGGACCTGGTCAAACTTTTTCACCCTCA
* * ** * * *
956627 TTTAACTGCATTGACGTAAGGACCTGATCAAACTTTCTCCACCCTCA
1 TTTGACTGTATTGGTGTTAGGACCTGGTCAAACTTT-TTCACCCTCA
* * * * * *
956674 TTTGACTGCATTGGTGTT-GGGCCTTAGTCAAACTCTTCTCAACCAT-G
1 TTTGACTGTATTGGTGTTAGGACC-TGGTCAAACT-TTTTC-ACCCTCA
*
956721 TTTGACTGTCTTGGTGTTA
1 TTTGACTGTATTGGTGTTA
956740 TTCCTAGTCA
Statistics
Matches: 324, Mismatches: 99, Indels: 34
0.71 0.22 0.07
Matches are distributed among these distances:
45 5 0.02
46 90 0.28
47 165 0.51
48 58 0.18
49 6 0.02
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (46 bp):
TTTGACTGTATTGGTGTTAGGACCTGGTCAAACTTTTTCACCCTCA
Found at i:957020 original size:42 final size:42
Alignment explanation
Indices: 956973--957091 Score: 100
Period size: 42 Copynumber: 2.8 Consensus size: 42
956963 AGCCCATCAA
956973 CTTAGTCCTCGATCAACCTTTCATCCCTTATTTACCTATTAGT
1 CTTAGTCCTCGATCAACCTTTCATCCCTTATTTACCTA-TAGT
* * * * *
957016 -TTAGT-CTCTGATAAAACCTTT-ATCCCCTCTGTGACCTATCGT
1 CTTAGTCCTC-GAT-CAACCTTTCATCCCTTAT-TTACCTATAGT
* * * *
957058 CTTAGTCCTCGGTCAACCCTTCACCCCTTGTTTA
1 CTTAGTCCTCGATCAACCTTTCATCCCTTATTTA
957092 TATATCGACT
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
41 3 0.05
42 26 0.45
43 26 0.45
44 3 0.05
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (42 bp):
CTTAGTCCTCGATCAACCTTTCATCCCTTATTTACCTATAGT
Found at i:962785 original size:159 final size:159
Alignment explanation
Indices: 962456--962836 Score: 452
Period size: 159 Copynumber: 2.4 Consensus size: 159
962446 CTTAGAATAC
* * * *
962456 AGGGTTGGAGTACCCTCGATAGTAAAAATTTTGATATTTTA-GAAGTAAAAAAGGGTTGGAGTA-
1 AGGGTTGGAGTATCCTCGATGGTGAAAATTTTGATA-TTTAGGAAATAAAAAAGGGTTGGAGTAT
* *
962519 TCCCTCAAAAATAATGGGTTGGAGTATCTCCAATGGTGAAAAATTCGATATTTTTGGAAGTAAAA
65 TCCCTCAAAAATAATGGGTTGGAGTATCTCCAATGGTGAAAAATTCGATATTTTTGAAAATAAAA
*
962584 ATGAGGTTAGAGTATCCCTTCCAAAATAAT
130 ATGAGGTTAGAGTATCCCTTCAAAAATAAT
962614 AGGGTTGGAGTATCCTCGATGGTGAAAATTTTGATATTTAGGAAATAAAAACAGGGTTGGAGTAT
1 AGGGTTGGAGTATCCTCGATGGTGAAAATTTTGATATTTAGGAAATAAAAA-AGGGTTGGAGTAT
* * * *
962679 TTCCTCAAAAGTGATAGGGTTGGAGTATC-CTCAATGGTGAAAAA-TCTATA-TTTTGAAAATAA
65 TCCCTCAAAAATAAT-GGGTTGGAGTATCTC-CAATGGTGAAAAATTCGATATTTTTGAAAATAA
* * *
962741 AAATGGGGTTGGAGTATCTCC-TCAAAAATGAT
128 AAATGAGGTTAGAGTATC-CCTTCAAAAATAAT
* * * * * * * **
962773 GGGGTTGAAGTATCCCCGATGGTGAAAA-ATCGATATTTTGGAAACGAAAATGGGGTTGGAGTAT
1 AGGGTTGGAGTATCCTCGATGGTGAAAATTTTGATATTTAGGAAA-TAAAAAAGGGTTGGAGTAT
962837 CCTCAATGGT
Statistics
Matches: 193, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
157 4 0.02
158 67 0.35
159 76 0.39
160 20 0.10
161 26 0.13
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (159 bp):
AGGGTTGGAGTATCCTCGATGGTGAAAATTTTGATATTTAGGAAATAAAAAAGGGTTGGAGTATT
CCCTCAAAAATAATGGGTTGGAGTATCTCCAATGGTGAAAAATTCGATATTTTTGAAAATAAAAA
TGAGGTTAGAGTATCCCTTCAAAAATAAT
Found at i:962837 original size:79 final size:78
Alignment explanation
Indices: 962488--962842 Score: 392
Period size: 79 Copynumber: 4.5 Consensus size: 78
962478 TAAAAATTTT
* * * *
962488 GATATTTTAGAAGTAAAAA-AGGGTTGGAGTATCCCTCAAAAATAAT-GGGTTGGAGTATCTCCA
1 GATATTTTGGAAATAAAAATGGGGTTGGAGTATCCCTCAAAAATAATAGGGTTGGAGTATCCCCA
962551 ATGGTGAAAAATTC
66 ATGGTGAAAAA-TC
* * * * *
962565 GATATTTTTGGAAGTAAAAATGAGGTTAGAGTATCCCTTCCAAAATAATAGGGTTGGAGTATCCT
1 GATA-TTTTGGAAATAAAAATGGGGTTGGAGTATCCC-TCAAAAATAATAGGGTTGGAGTATCCC
* * *
962630 CGATGGTGAAAATTTT
64 CAATGGTGAAAA-ATC
* ** * * * *
962646 GATATTTAGGAAATAAAAACAGGGTTGGAGTATTTCCTCAAAAGTGATAGGGTTGGAGTATCCTC
1 GATATTTTGGAAATAAAAATGGGGTTGGAGTA-TCCCTCAAAAATAATAGGGTTGGAGTATCCCC
962711 AATGGTGAAAAATC
65 AATGGTGAAAAATC
* * * * *
962725 TATATTTTGAAAATAAAAATGGGGTTGGAGTATCTCCTCAAAAATGATGGGGTTGAAGTATCCCC
1 GATATTTTGGAAATAAAAATGGGGTTGGAGTATC-CCTCAAAAATAATAGGGTTGGAGTATCCCC
*
962790 GATGGTGAAAAATC
65 AATGGTGAAAAATC
**
962804 GATATTTTGGAAACGAAAATGGGGTTGGAGTAT-CCTCAA
1 GATATTTTGGAAATAAAAATGGGGTTGGAGTATCCCTCAA
962843 TGGTGAAAAA
Statistics
Matches: 233, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
77 10 0.04
78 15 0.06
79 109 0.47
80 67 0.29
81 32 0.14
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (78 bp):
GATATTTTGGAAATAAAAATGGGGTTGGAGTATCCCTCAAAAATAATAGGGTTGGAGTATCCCCA
ATGGTGAAAAATC
Found at i:962846 original size:51 final size:51
Alignment explanation
Indices: 962771--962892 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
962761 CTCAAAAATG
* * * *
962771 ATGGGGTTGAAGTATCCCCGATGGTGAAAAATCGATATTTTGGAAACGAAA
1 ATGGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGAAAACAAAA
* * *
962822 ATGGGGTTGGAGTATCCTCAATGGTGAAAAATTGATATTTTGAAAATAAAA
1 ATGGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGAAAACAAAA
*
962873 ACTGGGATTGGAGTATCCCC
1 A-TGGGGTTGGAGTATCCCC
962893 TTAGAAATGA
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 45 0.74
52 16 0.26
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (51 bp):
ATGGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGAAAACAAAA
Found at i:962849 original size:210 final size:210
Alignment explanation
Indices: 962615--963021 Score: 543
Period size: 210 Copynumber: 1.9 Consensus size: 210
962605 CAAAATAATA
* * *
962615 GGGTTGGAGTATCCTCGATGGTGAAAATTTTGATATTTAGGAAATAAAAACAGGG-TTGGAGTAT
1 GGGTTGGAGTATCCTCAATGGTGAAAA-ATTGATATTTAGAAAATAAAAACAGGGATTGGAGTAT
** * * * * **
962679 TTCCTCA-AAAGTGATAGGGTTGGAGTATCCTCAATGGTGAAAAATCTATATTTTGAAAATAAAA
65 CCCCTCAGAAA-TGATAAGGCTGGAGTATCCTCAATAGTGAAAAATCAATATTTCAAAAATAAAA
* ** * *
962743 ATGGGGTTGGAGTATCTCC-TCAAAAATGATGGGGTTGAAGTATCCCCGATGGTGAAAAATCGAT
129 ATGGGGTTAGAGTATC-CCTTCAAAAATGATGGGAATGAAGTAT-CCCAATGGTGAAAAATCAAT
962807 -ATTTTGGAAACGAAAATG
192 AATTTTGGAAACGAAAATG
* *
962825 GGGTTGGAGTATCCTCAATGGTGAAAAATTGATATTTTGAAAATAAAAACTGGGATTGGAGTATC
1 GGGTTGGAGTATCCTCAATGGTGAAAAATTGATATTTAGAAAATAAAAACAGGGATTGGAGTATC
* *
962890 CCCTTAGAAATGATAAGGCTGGAGTATCCTTAATAGTGAAAAATCAATATTTCAAAAATAAAAAT
66 CCCTCAGAAATGATAAGGCTGGAGTATCCTCAATAGTGAAAAATCAATATTTCAAAAATAAAAAT
* * *
962955 GGGTTTAGAGTATCCCTTCAAAAATGATGGGAATGGAGTATCCCAATGGTTAAAAATCAATAATT
131 GGGGTTAGAGTATCCCTTCAAAAATGATGGGAATGAAGTATCCCAATGGTGAAAAATCAATAATT
963020 TT
196 TT
963022 TTTATTAAGA
Statistics
Matches: 170, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
209 42 0.25
210 125 0.74
211 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (210 bp):
GGGTTGGAGTATCCTCAATGGTGAAAAATTGATATTTAGAAAATAAAAACAGGGATTGGAGTATC
CCCTCAGAAATGATAAGGCTGGAGTATCCTCAATAGTGAAAAATCAATATTTCAAAAATAAAAAT
GGGGTTAGAGTATCCCTTCAAAAATGATGGGAATGAAGTATCCCAATGGTGAAAAATCAATAATT
TTGGAAACGAAAATG
Found at i:962959 original size:130 final size:130
Alignment explanation
Indices: 962695--962969 Score: 345
Period size: 131 Copynumber: 2.1 Consensus size: 130
962685 AAAAGTGATA
* *
962695 GGGTTGGAGTATCCTCAATGGTGAAAAATCTATATTTTGAAAATAAAAATGGGGTTGGAGTATCT
1 GGGTTGGAGTATCCTCAATGGTGAAAAATCTATATTTTGAAAATAAAAATGGGATTGGAGTATCC
** * * * * *** *
962760 CCTCAAAAATGATGGGGTTGAAGTATCCCCGATGGTGAAAAATCGATATTTTGGAAACGAAAATG
66 CCTCAAAAATGATAAGGCTGAAGTATCCCCAATAGTGAAAAATCAATATTTCAAAAACAAAAATG
962825 GGGTTGGAGTATCCTCAATGGTGAAAAAT-TGATATTTTGAAAATAAAAACTGGGATTGGAGTAT
1 GGGTTGGAGTATCCTCAATGGTGAAAAATCT-ATATTTTGAAAATAAAAA-TGGGATTGGAGTAT
* * * ** *
962889 CCCCTTAGAAATGATAAGGCTGGAGTATCCTTAATAGTGAAAAATCAATATTTCAAAAATAAAAA
64 CCCCTCAAAAATGATAAGGCTGAAGTATCCCCAATAGTGAAAAATCAATATTTCAAAAACAAAAA
962954 TG
129 TG
* *
962956 GGTTTAGAGTATCC
1 GGGTTGGAGTATCC
962970 CTTCAAAAAT
Statistics
Matches: 123, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
129 1 0.01
130 47 0.38
131 75 0.61
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (130 bp):
GGGTTGGAGTATCCTCAATGGTGAAAAATCTATATTTTGAAAATAAAAATGGGATTGGAGTATCC
CCTCAAAAATGATAAGGCTGAAGTATCCCCAATAGTGAAAAATCAATATTTCAAAAACAAAAATG
Found at i:965381 original size:31 final size:31
Alignment explanation
Indices: 965346--965423 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
965336 AATAGCCTGC
*
965346 ATGTATCAATACATTTAGGCTAAAATCTAGA
1 ATGTATCGATACATTTAGGCTAAAATCTAGA
965377 ATGTATCGATACATTTAGGCTAAAATCTAGA
1 ATGTATCGATACATTTAGGCTAAAATCTAGA
965408 ATGTATCGATACATTT
1 ATGTATCGATACATTT
965424 TGTCTTTCCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (31 bp):
ATGTATCGATACATTTAGGCTAAAATCTAGA
Found at i:966260 original size:155 final size:155
Alignment explanation
Indices: 965924--966248 Score: 354
Period size: 155 Copynumber: 2.1 Consensus size: 155
965914 AAGGTATACC
* * * *
965924 CCAATAACCCTAAAAGACTTGAAAATAGTCCAAAATAATGAACCTATCCCTAATGTGTAACATCA
1 CCAATAACCCTAAAAGACTTAAAAATAGTACAAAATAATGAACATATCCCTAATGTATAACATCA
* * ** * * **
965989 ACATGAAAGTATTCAAGTAATTGCATAAGACTTGGTTTTAATGCCAAATTAACAAAATGCCTTTG
66 ACATGAAAATATCCAAGTAATCACATAAGACTTGATTTTAATGCAAAATTAACAAAATGCCTTAA
*
966054 GAGCATATCTTCGACATGAAAGCAT
131 GAGCATACCTTCGACATGAAAGCAT
* * * * *
966079 CCTAATAATCTTAAAAGACTTAAAAATAGTATAAAATAATGAACATATCGCTAAT-TCAT-ACTT
1 CC-AATAACCCTAAAAGACTTAAAAATAGTACAAAATAATGAACATATCCCTAATGT-ATAACAT
* *
966142 CAACATGAAAATATCCAAGTAATCACATAGGACTTGATTTTAATGTAAAATT-ACTAAAATGCCC
64 CAACATGAAAATATCCAAGTAATCACATAAGACTTGATTTTAATGCAAAATTAAC-AAAATG-CC
* * *
966206 TTAAG-GTATACCTTTGACATCG-AAGTATT
127 TTAAGAGCATACCTTCGACAT-GAAAGCA-T
966235 CCAATAACCCTAAA
1 CCAATAACCCTAAA
966249 GAACTAAAAA
Statistics
Matches: 139, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
154 2 0.01
155 82 0.59
156 55 0.40
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (155 bp):
CCAATAACCCTAAAAGACTTAAAAATAGTACAAAATAATGAACATATCCCTAATGTATAACATCA
ACATGAAAATATCCAAGTAATCACATAAGACTTGATTTTAATGCAAAATTAACAAAATGCCTTAA
GAGCATACCTTCGACATGAAAGCAT
Found at i:969836 original size:28 final size:28
Alignment explanation
Indices: 969792--969845 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
969782 TCGATGATTA
969792 GAAAAAATCGGGATTGGAGTATCCCTTC
1 GAAAAAATCGGGATTGGAGTATCCCTTC
*
969820 GAAAATAA-CGGGGTTGGAGTATCCCT
1 GAAAA-AATCGGGATTGGAGTATCCCT
969846 AATTATGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (28 bp):
GAAAAAATCGGGATTGGAGTATCCCTTC
Found at i:969855 original size:76 final size:78
Alignment explanation
Indices: 969724--969924 Score: 212
Period size: 76 Copynumber: 2.6 Consensus size: 78
969714 GAGATAATAA
* * ** * *
969724 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-
*
969788 A-TT-AGAA-AAAAT
64 ATTTGAGAATAAAAC
* *
969800 CGGGATTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-
* *
969865 TTTGGGAATAAAGC
65 TTTGAGAATAAAAC
* * * *
969879 CGGGGTTGGAGTATCCCCTCGGAAGTAACGAGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
969925 GATGAAATAA
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
75 7 0.07
76 48 0.47
77 2 0.02
78 3 0.03
79 43 0.42
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTGAGAATAAAAC
Found at i:969922 original size:28 final size:28
Alignment explanation
Indices: 969882--969950 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
969872 ATAAAGCCGG
** *
969882 GGTTGGAGTATCCCCTCGGAAGTAACGA
1 GGTTGGAGTATCCCCGAGGAAATAACGA
*
969910 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGAGGAAATAACGA
969938 GGTTGGAGTATCC
1 GGTTGGAGTATCC
969951 TCGATTGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACGA
Found at i:970008 original size:52 final size:50
Alignment explanation
Indices: 969939--970108 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 50
969929 AAATAACGAG
* * *
969939 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTT-GAAATAAAACCGGA
** * *
969991 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTG-AAATAAAACC-GGA
*
970044 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGAA--ATAAAACCGGA
970095 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
970109 TCGAAAATAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.02
51 4 0.04
52 81 0.82
53 12 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAATAAAACCGGA
Found at i:970127 original size:28 final size:28
Alignment explanation
Indices: 970082--970163 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
970072 AGTGTTTTAA
* *
970082 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
970109 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* * *
970136 CGATGATTAACGGGGTTGGGGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
970164 GATTGTGAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 3 0.07
27 23 0.50
28 20 0.43
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:972588 original size:13 final size:13
Alignment explanation
Indices: 972570--972595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
972560 ACAAAGATCC
972570 ATGTATCGATACA
1 ATGTATCGATACA
972583 ATGTATCGATACA
1 ATGTATCGATACA
972596 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:972591 original size:33 final size:33
Alignment explanation
Indices: 972549--972615 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
972539 AAAATTTCCA
***
972549 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
972582 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
972615 A
1 A
972616 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:972659 original size:19 final size:18
Alignment explanation
Indices: 972635--972702 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
972625 CAGTAGCTAA
972635 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
972654 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
972669 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
972686 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
972703 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:972675 original size:13 final size:13
Alignment explanation
Indices: 972657--972681 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
972647 ACAATACTTA
972657 TGTATCGATACAT
1 TGTATCGATACAT
972670 TGTATCGATACA
1 TGTATCGATACA
972682 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:972679 original size:32 final size:32
Alignment explanation
Indices: 972638--972700 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
972628 TAGCTAATTA
*
972638 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
972670 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
972701 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:972804 original size:1 final size:1
Alignment explanation
Indices: 972798--972822 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
972788 TACATTTAAA
972798 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
972823 CAAACACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:976558 original size:13 final size:13
Alignment explanation
Indices: 976540--976565 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
976530 TGCACCAAGT
976540 ATGTATCGATACA
1 ATGTATCGATACA
976553 ATGTATCGATACA
1 ATGTATCGATACA
976566 CAAAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:977992 original size:20 final size:21
Alignment explanation
Indices: 977953--977996 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
977943 TTAAGTACAG
*
977953 ATGTTTTTCAAGCATAAAAATA
1 ATGTCTTTCAAG-ATAAAAATA
977975 ATGTCTTTCAAG-TAAAAATA
1 ATGTCTTTCAAGATAAAAATA
977995 AT
1 AT
977997 TCAAAATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
ATGTCTTTCAAGATAAAAATA
Found at i:978691 original size:36 final size:35
Alignment explanation
Indices: 978646--978717 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
978636 CTAAGTGATT
** *
978646 GAGAGGTTCTATCTTAGCCTTTGAGAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCCATGA-AAAAATAGGGA
978682 GAGAGGTTCTATCTTAGCCCATGAAAAAATAGGGA
1 GAGAGGTTCTATCTTAGCCCATGAAAAAATAGGGA
978717 G
1 G
978718 GTTCTTATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCCATGAAAAAATAGGGA
Found at i:983502 original size:20 final size:21
Alignment explanation
Indices: 983460--983503 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
983450 TTAAGTATAG
983460 ATGTTTTTCAAGCATAAAAATA
1 ATGTTTTTCAAG-ATAAAAATA
*
983482 ATGTTTTTCAAG-TACAAATA
1 ATGTTTTTCAAGATAAAAATA
983502 AT
1 AT
983504 TCAAAGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTTTTTCAAGATAAAAATA
Found at i:983753 original size:20 final size:20
Alignment explanation
Indices: 983701--983755 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
983691 GTATCGATAC
*
983701 ATTGTATCGATAAATGATGA
1 ATTGTATCGATACATGATGA
*
983721 ATTGTATCGATACATGGTGA
1 ATTGTATCGATACATGATGA
983741 ATTGTATCGATACAT
1 ATTGTATCGATACAT
983756 TGAGGCCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:984276 original size:31 final size:30
Alignment explanation
Indices: 984222--984281 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
984212 GTTAGCGAGA
*
984222 GAGGTTCTATCTTAGCCCATGAAAAGATAGG
1 GAGGTTCTATCTTAGACCATG-AAAGATAGG
*
984253 GAGGTTTCTATCTTA-ACCTTGAAAGATAG
1 GAGG-TTCTATCTTAGACCATGAAAGATAG
984282 TGTTGTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 8 0.31
32 10 0.38
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (30 bp):
GAGGTTCTATCTTAGACCATGAAAGATAGG
Found at i:985462 original size:15 final size:17
Alignment explanation
Indices: 985432--985463 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
985422 ATATAGTAAT
985432 ATGACACAAGGAAAATG
1 ATGACACAAGGAAAATG
985449 ATGA-ACAA-GAAAATG
1 ATGACACAAGGAAAATG
985464 GACAACCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.56, C:0.09, G:0.22, T:0.12
Consensus pattern (17 bp):
ATGACACAAGGAAAATG
Found at i:995461 original size:41 final size:41
Alignment explanation
Indices: 995406--995598 Score: 153
Period size: 41 Copynumber: 4.7 Consensus size: 41
995396 ATATGAGAAG
* * *
995406 AGTTAACCATGACAAAACCTACACGTCAACTAAGAGTGAAA
1 AGTTGACCAAGACAAAACCTACAAGTCAACTAAGAGTGAAA
* * *
995447 AGTTGACCAAGACAAAACCAACAAGTTAAGTAAGAGTG-AA
1 AGTTGACCAAGACAAAACCTACAAGTCAACTAAGAGTGAAA
* * * *
995487 AGTTTGACTAGGACGAAACCTACAAGTCAATTAAGAGTGAAA
1 AG-TTGACCAAGACAAAACCTACAAGTCAACTAAGAGTGAAA
* * * * *
995529 GGCTGATCAAGACAAAA-TTGATAAGTCAAC-AA-A-TGAAAAA
1 AGTTGACCAAGACAAAACCT-ACAAGTCAACTAAGAGTG--AAA
* * *
995569 AATTGACCAAGACAAAACCAATAAGTCAAC
1 AGTTGACCAAGACAAAACCTACAAGTCAAC
995599 AAATGAAAAG
Statistics
Matches: 119, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 33 0.28
41 80 0.67
42 3 0.03
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (41 bp):
AGTTGACCAAGACAAAACCTACAAGTCAACTAAGAGTGAAA
Found at i:996879 original size:27 final size:27
Alignment explanation
Indices: 996841--996914 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
996831 TTGAGTGAAA
*
996841 AATGAGGTTGGAGTATCCCCTCGGAGG
1 AATGGGGTTGGAGTATCCCCTCGGAGG
996868 AATGGGGTTGGAGTATCCCCTCGGAGG
1 AATGGGGTTGGAGTATCCCCTCGGAGG
*
996895 AATGGGGTTGGAGTGTCCCC
1 AATGGGGTTGGAGTATCCCC
996915 GATGATGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.23
Consensus pattern (27 bp):
AATGGGGTTGGAGTATCCCCTCGGAGG
Found at i:999892 original size:20 final size:20
Alignment explanation
Indices: 999839--999893 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
999829 AAATTCCCAG
**
999839 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
999859 ATGTATCGATACATTGAGT-A
1 ATGTATCGATACATTGA-TCA
999879 ATGTATCGATACATT
1 ATGTATCGATACATT
999894 TCCTTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:999947 original size:19 final size:19
Alignment explanation
Indices: 999923--1000018 Score: 108
Period size: 19 Copynumber: 5.7 Consensus size: 19
999913 AGCAATACAT
999923 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
999942 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
999955 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
999974 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
999987 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1000006 TGTATCGATACAA
1 TGTATCGATACAA
1000019 ATTGTTGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 18 0.28
14 2 0.03
16 12 0.18
18 2 0.03
19 31 0.48
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:999958 original size:32 final size:32
Alignment explanation
Indices: 999917--1000017 Score: 202
Period size: 32 Copynumber: 3.2 Consensus size: 32
999907 CTTTGTAGCA
999917 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAACACTTATGTATCG
999949 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAACACTTATGTATCG
999981 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAACACTTATGTATCG
1000013 ATACA
1 ATACA
1000018 AATTGTTGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (32 bp):
ATACATTGTATCGATACAACACTTATGTATCG
Found at i:999960 original size:13 final size:13
Alignment explanation
Indices: 999942--999998 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
999932 ACAACACTTA
999942 TGTATCGATACAT
1 TGTATCGATACAT
999955 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
999973 ATGTATCGATACAT
1 -TGTATCGATACAT
999987 TGTATCGATACA
1 TGTATCGATACA
999999 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1000882 original size:49 final size:49
Alignment explanation
Indices: 1000723--1001728 Score: 1062
Period size: 49 Copynumber: 20.6 Consensus size: 49
1000713 GAAGAATGAT
* * * * *
1000723 AATGTGCTGATCCACGGCCAGCGACATTAGACTTGAAGAAGAA--TGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
** * * **
1000770 AATGTGCTGAGACAAGGCCAGCGACATTAGG-CTTAGGAATGTTAAAGACGCC
1 AATGTGCTGATTCAAGGCCAGCGACATT-GGACTTA--AA-GATGAAGGTGCC
* * * * *
1000822 AATATGTTGATTCAGGGCCAACGATATTGGACTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* * *
1000871 AATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGACGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* * ** *
1000920 AATATGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* * *
1000969 AATGTGCTGATTTAAGGCCAGCGACATTTGACTTAAAGATGACGAAAGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT---GAAGGTGCC
* * * * * * *
1001021 AATATGCTGATTCGAGGCCAGTGATACTGGACTTAAAGATAAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* *
1001070 AATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACGAAGGCGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT---GAAGGTGCC
* * *** *
1001122 AATATGCTGATTCAAGGCCAGCGATACCAGACTTAAAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* *
1001171 AATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* * * *
1001220 AATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
*
1001269 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* *
1001318 AATGTGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGCGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT---GAAGGTGCC
* * * * * *
1001370 AATATACTAATTCAAGGCGAGCGATATTGGACTTAAAGATGAAGATGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
1001419 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* *
1001468 AATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGATGGTTGAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G--AAGGTGCC
* * * *
1001520 GATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
** * * *
1001569 AATAAGCTGATTCAAGGCCAGCGATACTGGGC-T-----T----GTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* *
1001608 AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGAT-AAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
* * *
1001656 AATATACTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
*
1001699 AATGTGTTGATTCAAGGCCAGCGACATTGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGG
1001729 TCTTTGAAAG
Statistics
Matches: 797, Mismatches: 134, Indels: 60
0.80 0.14 0.06
Matches are distributed among these distances:
39 31 0.04
40 1 0.00
43 35 0.04
44 1 0.00
45 1 0.00
47 28 0.04
48 36 0.05
49 462 0.58
50 6 0.01
51 3 0.00
52 193 0.24
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (49 bp):
AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCC
Found at i:1000887 original size:101 final size:98
Alignment explanation
Indices: 1000727--1001728 Score: 1036
Period size: 101 Copynumber: 10.3 Consensus size: 98
1000717 AATGATAATG
* * * * * * **
1000727 TGCTGATCCACGGCCAGCGACATTAGACTTGAAGAAG-A-ATGCCAATGTGCTGAGACAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * **
1000790 GCGACATTAGG-CTTAGGAATGTTAAAGACGCCAATA
66 GCGACATT-GGACTTA--AA-GATGAAGGTGCCAATA
* * * *
1000826 TGTTGATTCAGGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
1000891 GCGACATTAGTCTTAAAGATGACGGTGCCAATA
66 GCGACATTGGACTTAAAGATGAAGGTGCCAATA
** *
1000924 TGCTGATTCAAGGCCAGCGATACCGGACTTAAAGATGAAGATGCCAATGTGCTGATTTAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
1000989 GCGACATTTGACTTAAAGATGACGAAAGTGCCAATA
66 GCGACATTGGACTTAAAGAT---GAAGGTGCCAATA
* * * *
1001025 TGCTGATTCGAGGCCAGTGATACTGGACTTAAAGATAAAGATGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
1001090 ACGACATTGGACTTAAAGATGACGAAGGCGCCAATA
66 GCGACATTGGACTTAAAGAT---GAAGGTGCCAATA
*** *
1001126 TGCTGATTCAAGGCCAGCGATACCAGACTTAAAGATGAAGATGCCAATGTGTTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
*
1001191 GCGACATTGGACTTAAAGATGACGGTGCCAATA
66 GCGACATTGGACTTAAAGATGAAGGTGCCAATA
*
1001224 TGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
1001289 GCGACATTGGACTTAAAGATGAAGATGCCAATG
66 GCGACATTGGACTTAAAGATGAAGGTGCCAATA
* * ** * * *
1001322 TGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGCGCCAATATACTAATTCAAGG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGATGCCAATGTGCTGATTCAAGG
* * * *
1001387 CGAGCGATATTGGACTTAAAGATGAAGATGCCAATG
63 CCAGCGACATTGGACTTAAAGATGAAGGTGCCAATA
* *
1001423 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * * *
1001488 GCGACATTGGATTTAAAGATGGTTGAGGTGCCGATG
66 GCGACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* * * * * **
1001524 TGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCCAATAAGCTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * * *
1001589 GCGATACTGGGC-T-----T----GTGCCAATG
66 GCGACATTGGACTTAAAGATGAAGGTGCCAATA
* * * * * *
1001612 TGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGAT-AAGGTGCCAATATACTGATTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
1001676 GCGATATTGGACTT----A--AAGGTGCCAATG
66 GCGACATTGGACTTAAAGATGAAGGTGCCAATA
* *
1001703 TGTTGATTCAAGGCCAGCGACATTGG
1 TGCTGATTCAAGGCCAGCGATATTGG
1001729 TCTTTGAAAG
Statistics
Matches: 792, Mismatches: 94, Indels: 42
0.85 0.10 0.05
Matches are distributed among these distances:
87 36 0.05
88 42 0.05
91 33 0.04
95 1 0.00
98 263 0.33
99 32 0.04
100 3 0.00
101 382 0.48
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (98 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:1001020 original size:150 final size:148
Alignment explanation
Indices: 1000723--1001728 Score: 1033
Period size: 150 Copynumber: 6.9 Consensus size: 148
1000713 GAAGAATGAT
* * * * * * * **
1000723 AATGTGCTGATCCACGGCCAGCGACATTAGACTTGAAGAAGA--ATGCCAATGTGCTGAGACAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAAG
* * * * * * * * *
1000786 GCCAGCGACATTAGG-CTTAGGAATGTTAAAGACGCCAATATGTTGATTCAGGGCCAACGATATT
66 GCCAGCGATATT-GGACTTA--AA-GATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATT
*
1000850 GGACTTAAAGAT-GAAGGTGCC
127 GGACTTAAAGATGGAAAGTGCC
* *
1000871 AATGTGCTGATTCAAGGCCAGCGACATTAGTCTTAAAGATGACGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAAG
** * *
1000936 GCCAGCGATACCGGACTTAAAGATGAAGATGCCAATGTGCTGATTTAAGGCCAGCGACATTTGAC
66 GCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1001001 TTAAAGATGACGAAAGTGCC
131 TTAAAGATG--GAAAGTGCC
* * * * * * * * *
1001021 AATATGCTGATTCGAGGCCAGTGATACTGGACTTAAAGATAAAGATGCCAATGTGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAAG
* * ** * * ***
1001086 GCCAACGACATTGGACTTAAAGATGACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATACCA
66 GCCAGCGATATTGGACTTAAAGAT---GAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
1001151 GACTTAAAGAT-G-AAGATGCC
128 GACTTAAAGATGGAAAG-TGCC
* *
1001171 AATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTTAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAAG
1001236 GCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
66 GCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1001301 TTAAAGAT-G-AAGATGCC
131 TTAAAGATGGAAAG-TGCC
* * * *
1001318 AATGTGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGCGCCAATATACTAATTC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAC---GGTGCCAATATGCTGATTC
*
1001383 AAGGCGAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
63 AAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTG
*
1001448 GACTTAAAGAT-GAAGGTGCC
128 GACTTAAAGATGGAAAGTGCC
* * *
1001468 AATGTGCTGATTCAAGGCCAGCGACATTGGATTTAAAGATGGTTGA-GGTGCCGATGTGCTGATT
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA----TGACGGTGCCAATATGCTGATT
* * * * * **
1001532 CAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGCCAATAAGCTGATTCAAGGCCAGCG--A-T
62 CAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATT
***
1001594 --AC-T---G--GGCTTGTGCC
127 GGACTTAAAGATGGAAAGTGCC
* * * *
1001608 AATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGAT-AAGGTGCCAATATACTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAAG
*
1001672 GCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATGTGTTGATTCAAGGCCAGCGACATTGG
66 GCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGG
1001729 TCTTTGAAAG
Statistics
Matches: 728, Mismatches: 105, Indels: 63
0.81 0.12 0.07
Matches are distributed among these distances:
130 24 0.03
131 1 0.00
132 1 0.00
133 2 0.00
134 1 0.00
135 3 0.00
136 34 0.05
140 42 0.06
141 1 0.00
144 1 0.00
145 2 0.00
147 135 0.19
148 40 0.05
149 5 0.01
150 390 0.54
151 2 0.00
153 41 0.06
154 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (148 bp):
AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAAG
GCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
TTAAAGATGGAAAGTGCC
Found at i:1001679 original size:48 final size:43
Alignment explanation
Indices: 1001513--1001732 Score: 187
Period size: 43 Copynumber: 5.0 Consensus size: 43
1001503 AAGATGGTTG
* * *
1001513 AGGTGCCGATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGA
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT----A--A
** * * *
1001562 AGGTGCCAATAAGCTGATTCAAGGCCAGCGATACTGGGCTT--
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAA
*
1001603 --GTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGATA
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT----A-A
* * * *
1001649 AGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTAA
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAA
*
1001692 AGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTT
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1001733 TGAAAGCTTA
Statistics
Matches: 138, Mismatches: 24, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
39 33 0.24
43 37 0.27
44 1 0.01
48 34 0.25
49 33 0.24
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (43 bp):
AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAA
Found at i:1002499 original size:13 final size:13
Alignment explanation
Indices: 1002481--1002506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1002471 CAATTTTTTG
1002481 TGTATCGATACAT
1 TGTATCGATACAT
1002494 TGTATCGATACAT
1 TGTATCGATACAT
1002507 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1005060 original size:13 final size:13
Alignment explanation
Indices: 1005042--1005073 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1005032 ATAATCACCC
*
1005042 TGTATCGATACAG
1 TGTATCGATACAA
1005055 TGTATCGATACAA
1 TGTATCGATACAA
1005068 TGTATC
1 TGTATC
1005074 TATATAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1005104 original size:20 final size:20
Alignment explanation
Indices: 1005066--1005145 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 20
1005056 GTATCGATAC
* * *
1005066 AATGTATCTATATAAAGAAA
1 AATGTATCGATACATAGAAA
1005086 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACATAGAA-----A
* *
1005111 GATGTATCGATACACAGAAA
1 AATGTATCGATACATAGAAA
*
1005131 CATGTATCGATACAT
1 AATGTATCGATACAT
1005146 TTTGGACATT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATAGAAA
Found at i:1009022 original size:21 final size:21
Alignment explanation
Indices: 1008993--1009037 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1008983 AAGTTTTCAT
*
1008993 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1009013 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1009035 TTT
1 TTT
1009038 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1011270 original size:13 final size:13
Alignment explanation
Indices: 1011252--1011277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1011242 CAATTTTTTG
1011252 TGTATCGATACAT
1 TGTATCGATACAT
1011265 TGTATCGATACAT
1 TGTATCGATACAT
1011278 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1011736 original size:25 final size:26
Alignment explanation
Indices: 1011708--1011767 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
1011698 AACGATATTA
*
1011708 GACTTACA-GGTGCCACAGAGTTGTG
1 GACTTAAAGGGTGCCACAGAGTTGTG
*
1011733 GACTTAAAAGGGTGCCACGGAGTTGTG
1 GACTT-AAAGGGTGCCACAGAGTTGTG
1011760 GACTTAAA
1 GACTTAAA
1011768 AGGAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 5 0.16
26 5 0.16
27 21 0.68
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (26 bp):
GACTTAAAGGGTGCCACAGAGTTGTG
Found at i:1011748 original size:27 final size:27
Alignment explanation
Indices: 1011716--1011770 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1011706 TAGACTTACA
1011716 GGTGCCACAGAGTTGTGGACTTAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAG
*
1011743 GGTGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACAGAGTTGTGGACTTAAAAG
1011770 G
1 G
1011771 AAAAAGAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (27 bp):
GGTGCCACAGAGTTGTGGACTTAAAAG
Found at i:1011790 original size:34 final size:34
Alignment explanation
Indices: 1011738--1011920 Score: 273
Period size: 34 Copynumber: 5.4 Consensus size: 34
1011728 TTGTGGACTT
* *
1011738 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
*
1011772 AAAAGAGTACCACAGAGTTGTCGG-CTTTAAAAGGA
1 AAAAGAGTGCCACAGAGTTGT-GGAC-TTAAAAGGA
1011807 AAAAG-GTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
1011840 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
1011874 AACAGAGTGCCACAGAGTTGTGGGCTTTAAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGAC-TTAAAAGGA
1011909 AAAAGA-TGCCAC
1 AAAAGAGTGCCAC
1011921 TAAGTCATGG
Statistics
Matches: 137, Mismatches: 7, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
33 16 0.12
34 91 0.66
35 30 0.22
ACGTcount: A:0.39, C:0.14, G:0.30, T:0.18
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1011887 original size:102 final size:95
Alignment explanation
Indices: 1011715--1011965 Score: 308
Period size: 102 Copynumber: 2.5 Consensus size: 95
1011705 TTAGACTTAC
*
1011715 AGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGT
1 AGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGT
1011780 ACCACAGAGTTGTCGGCTTTAAAAGGAAAA
66 ACCACAGAGTTGTCGGCTTTAAAAGGAAAA
1011810 AGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGAA
1 AGGTGCCACAGAGTTGTGGACTTAAAA-G-----G-GTGCCACAGAGTTGTGGACTTAAAAGGAA
* * *
1011875 ACAGAGTGCCACAGAGTTGTGGGCTTTAAAAGGAAAA
59 AAAGAGTACCACAGAGTTGTCGGCTTTAAAAGGAAAA
* ** *
1011912 AGATGCCACTA-AGTCATGGACTTAGAAAAGAGGTGCCACTA-AGTCGTGGACTTA
1 AGGTGCCAC-AGAGTTGTGGACTT--AAAAG-GGTGCCAC-AGAGTTGTGGACTTA
1011966 GAAAAGAGAT
Statistics
Matches: 137, Mismatches: 8, Indels: 19
0.84 0.05 0.12
Matches are distributed among these distances:
95 27 0.20
96 1 0.01
98 19 0.14
99 3 0.02
101 1 0.01
102 80 0.58
103 2 0.01
104 4 0.03
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.20
Consensus pattern (95 bp):
AGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGT
ACCACAGAGTTGTCGGCTTTAAAAGGAAAA
Found at i:1011950 original size:30 final size:30
Alignment explanation
Indices: 1011908--1012056 Score: 190
Period size: 30 Copynumber: 4.9 Consensus size: 30
1011898 CTTTAAAAGG
*
1011908 AAAAAGATGCCACTAAGTCATGGACTTAGA
1 AAAAAGATGCCACTAAGTCGTGGACTTAGA
* *
1011938 AAAGAGGTGCCACTAAGTCGTGGACTTAGA
1 AAAAAGATGCCACTAAGTCGTGGACTTAGA
* ** *
1011968 AAAGAGATGCCACTGGGTCGTGGACTTTGA
1 AAAAAGATGCCACTAAGTCGTGGACTTAGA
* *
1011998 AGAAAAGATGCCACTAAGTCGTAGACTTGGA
1 A-AAAAGATGCCACTAAGTCGTGGACTTAGA
*
1012029 AGAAAAGATGCCACTGAGTCGTGGACTT
1 A-AAAAGATGCCACTAAGTCGTGGACTT
1012057 TGAAGGAAAG
Statistics
Matches: 104, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 54 0.52
31 50 0.48
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.21
Consensus pattern (30 bp):
AAAAAGATGCCACTAAGTCGTGGACTTAGA
Found at i:1012010 original size:31 final size:31
Alignment explanation
Indices: 1011807--1012067 Score: 199
Period size: 34 Copynumber: 8.2 Consensus size: 31
1011797 TTTAAAAGGA
* * *
1011807 AAAAGGTGCCAC-AGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCACTA-AGTCGTGGACTTAGAA-G
* *
1011839 AAAAAGAGTGCCAC-AGAGTTGTGGACTTAAAAGG
1 -AAAAGA-TGCCACTA-AGTCGTGGACTTAGAA-G
* * *
1011873 AAACAGAGTGCCAC-AGAGTTGTGGGCTTTAAAAGG
1 AAA-AGA-TGCCACTA-AGTCGTGGAC-TTAGAA-G
*
1011908 AAAAAGATGCCACTAAGTCATGGACTTAGAA-
1 -AAAAGATGCCACTAAGTCGTGGACTTAGAAG
* *
1011939 AAGAGGTGCCACTAAGTCGTGGACTTAGAA-
1 AAAAGATGCCACTAAGTCGTGGACTTAGAAG
* ** *
1011969 AAGAGATGCCACTGGGTCGTGGACTTTGAAG
1 AAAAGATGCCACTAAGTCGTGGACTTAGAAG
* *
1012000 AAAAGATGCCACTAAGTCGTAGACTTGGAAG
1 AAAAGATGCCACTAAGTCGTGGACTTAGAAG
* *
1012031 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTAAGTCGTGGACTTAGAAG
*
1012062 GAAAGA
1 AAAAGA
1012068 GATTTGAAGA
Statistics
Matches: 200, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
30 53 0.26
31 59 0.29
33 13 0.06
34 60 0.30
35 12 0.06
36 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.20
Consensus pattern (31 bp):
AAAAGATGCCACTAAGTCGTGGACTTAGAAG
Found at i:1012053 original size:62 final size:61
Alignment explanation
Indices: 1011908--1012067 Score: 214
Period size: 62 Copynumber: 2.6 Consensus size: 61
1011898 CTTTAAAAGG
* * * * * *
1011908 AAAAAGATGCCACTAAGTCATGGACTTAGAA-AAGAGGTGCCACTAAGTCGTGGACTTAGA
1 AAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTAGACTTAGA
* * *
1011968 AAAGAGATGCCACTGGGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTAGACTTGGA
1 AAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTAGACTTAGA
*
1012029 AGAAAAGATGCCACTGAGTCGTGGACTTTGAAGGAAAGA
1 A-AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGA
1012068 GATTTGAAGA
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 26 0.30
61 26 0.30
62 34 0.40
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (61 bp):
AAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTAGACTTAGA
Found at i:1013278 original size:15 final size:14
Alignment explanation
Indices: 1013258--1013331 Score: 89
Period size: 14 Copynumber: 5.1 Consensus size: 14
1013248 CTTTGCACTC
*
1013258 TTTTTTTTGTGTTG
1 TTTTTTTTGTGTTT
1013272 TTTTTTTTGAT-TTT
1 TTTTTTTTG-TGTTT
1013286 TTGTTTTTTGTGTTT
1 TT-TTTTTTGTGTTT
1013301 TTCTTTTTTGCT-TTT
1 TT-TTTTTTG-TGTTT
1013316 TTTTTTTTGTGTTT
1 TTTTTTTTGTGTTT
1013330 TT
1 TT
1013332 ACTTGTGACT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.02
14 26 0.49
15 25 0.47
16 1 0.02
ACGTcount: A:0.01, C:0.03, G:0.14, T:0.82
Consensus pattern (14 bp):
TTTTTTTTGTGTTT
Found at i:1013287 original size:8 final size:7
Alignment explanation
Indices: 1013260--1013331 Score: 67
Period size: 8 Copynumber: 9.9 Consensus size: 7
1013250 TTGCACTCTT
1013260 TTTTTTG
1 TTTTTTG
*
1013267 TGTTGTT-
1 T-TTTTTG
1013274 TTTTTTG
1 TTTTTTG
1013281 ATTTTTTG
1 -TTTTTTG
1013289 TTTTTTG
1 TTTTTTG
*
1013296 TGTTTTTC
1 T-TTTTTG
1013304 TTTTTTG
1 TTTTTTG
1013311 CTTTTTT-
1 -TTTTTTG
1013318 TTTTTTG
1 TTTTTTG
1013325 TGTTTTT
1 T-TTTTT
1013332 ACTTGTGACT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
6 10 0.19
7 16 0.30
8 28 0.52
ACGTcount: A:0.01, C:0.03, G:0.14, T:0.82
Consensus pattern (7 bp):
TTTTTTG
Found at i:1013329 original size:29 final size:28
Alignment explanation
Indices: 1013258--1013331 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 28
1013248 CTTTGCACTC
*
1013258 TTTTTTTTGTGTTGTTTTTTTTGATTTT
1 TTTTTTTTGTGTTTTTTTTTTTGATTTT
*
1013286 TTGTTTTTTGTGTTTTTCTTTTTTGCTTTT
1 TT-TTTTTTGTGTTTTT-TTTTTTGATTTT
1013316 TTTTTTTTGTGTTTTT
1 TTTTTTTTGTGTTTTT
1013332 ACTTGTGACT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
28 2 0.05
29 27 0.64
30 13 0.31
ACGTcount: A:0.01, C:0.03, G:0.14, T:0.82
Consensus pattern (28 bp):
TTTTTTTTGTGTTTTTTTTTTTGATTTT
Found at i:1013343 original size:29 final size:28
Alignment explanation
Indices: 1013258--1013345 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 28
1013248 CTTTGCACTC
*
1013258 TTTTTTTTGTGTTGTTTTTTTTGA-TTTT
1 TTTTTTTTGTGTT-TTTCTTTTGACTTTT
1013286 TTGTTTTTTGTGTTTTTCTTTTTTG-CTTTT
1 TT-TTTTTTGTGTTTTTC--TTTTGACTTTT
*
1013316 TTTTTTTTGTGTTTTTACTTGTGACTTTT
1 TTTTTTTTGTGTTTTT-CTTTTGACTTTT
1013345 T
1 T
1013346 CATCATTTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
28 9 0.17
29 31 0.60
30 12 0.23
ACGTcount: A:0.03, C:0.05, G:0.14, T:0.78
Consensus pattern (28 bp):
TTTTTTTTGTGTTTTTCTTTTGACTTTT
Found at i:1013777 original size:13 final size:13
Alignment explanation
Indices: 1013759--1013784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1013749 TACAGCAAGT
1013759 ATGTATCGATACA
1 ATGTATCGATACA
1013772 ATGTATCGATACA
1 ATGTATCGATACA
1013785 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1016013 original size:21 final size:21
Alignment explanation
Indices: 1015980--1016024 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1015970 TTGCAAGTTG
*
1015980 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1016002 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1016022 AAA
1 AAA
1016025 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1017848 original size:15 final size:15
Alignment explanation
Indices: 1017828--1017858 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1017818 TAAAAATGTC
*
1017828 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1017843 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1017858 C
1 C
1017859 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1019955 original size:13 final size:13
Alignment explanation
Indices: 1019937--1019975 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1019927 ACATTTTTCT
1019937 TTGTATCGATACA
1 TTGTATCGATACA
1019950 TTGTATCGATACA
1 TTGTATCGATACA
1019963 TTGTATCGATACA
1 TTGTATCGATACA
1019976 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1020139 original size:20 final size:20
Alignment explanation
Indices: 1020096--1020141 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1020086 AAATCTTTTG
1020096 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1020117 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1020137 CAAAA
1 CAAAA
1020142 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1022546 original size:13 final size:13
Alignment explanation
Indices: 1022528--1022553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1022518 TACAGCAAGT
1022528 ATGTATCGATACA
1 ATGTATCGATACA
1022541 ATGTATCGATACA
1 ATGTATCGATACA
1022554 CAAAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1031760 original size:32 final size:33
Alignment explanation
Indices: 1031722--1031870 Score: 115
Period size: 32 Copynumber: 4.8 Consensus size: 33
1031712 TGAAAAGGGT
*
1031722 TGCCACTGACTTGCGTGGGC-TTGAAAAAAAGG
1 TGCCACTGACTTGTGTGGGCTTTGAAAAAAAGG
* * * * *
1031754 TGCCACTAACATATGTGGGCTTTG-AAAAGAGT
1 TGCCACTGACTTGTGTGGGCTTTGAAAAAAAGG
*
1031786 TGCCACTGACTTGTGTGGGCTTTG---AAAGGG
1 TGCCACTGACTTGTGTGGGCTTTGAAAAAAAGG
* * *
1031816 TGCCACTAAC-T-TGTAGGCTTT---TAAAAGG
1 TGCCACTGACTTGTGTGGGCTTTGAAAAAAAGG
1031844 ATGCCACTGAC-T-TGTGGGCTTTGAAAA
1 -TGCCACTGACTTGTGTGGGCTTTGAAAA
1031871 GGATCCCACT
Statistics
Matches: 93, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
28 14 0.15
29 20 0.22
30 12 0.13
32 44 0.47
33 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (33 bp):
TGCCACTGACTTGTGTGGGCTTTGAAAAAAAGG
Found at i:1031856 original size:29 final size:29
Alignment explanation
Indices: 1031710--1032092 Score: 397
Period size: 28 Copynumber: 13.1 Consensus size: 29
1031700 AAAGTGGTGA
*
1031710 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAAA-GGATGCCACTGACTT--GTGGGC
*
1031742 -TTGAAAAAAAGG-TGCCACTAACATATGTGGGC
1 TTTG---AAAAGGATGCCACTGAC-T-TGTGGGC
*
1031774 TTTGAAAAGAGTTGCCACTGACTTGTGTGGGC
1 TTTGAAAAG-GATGCCACTGAC-T-TGTGGGC
* * *
1031806 TTTG-AAAGGGTGCCACTAACTTGTAGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
*
1031834 TTTTAAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
*
1031863 TTTGAAAAGGATCCCACTGACTTGTGGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
*
1031892 TTTTG-AAAGGATGCCGCTGACTTGTGGGC
1 -TTTGAAAAGGATGCCACTGACTTGTGGGC
* * *
1031921 TTTGAAAA-GATGCCAATGTCTTATGGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
*
1031949 TTTGAAAAGG-TGCTACTGACTTGTGGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
* *
1031977 TTTGAAAAGGATGCCACTCACTTATGGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
* * *
1032006 TTTGAAAA-GATGCCATTGTCTTATGGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
* *
1032034 TTTGAAAAAG-TGCCACCGACTTGTGGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
* *
1032062 TTTG-AAAGGGTGCCACTGACTTGTAGGC
1 TTTGAAAAGGATGCCACTGACTTGTGGGC
1032090 TTT
1 TTT
1032093 TGTAGACACT
Statistics
Matches: 300, Mismatches: 36, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
27 4 0.01
28 123 0.41
29 99 0.33
30 19 0.06
31 8 0.03
32 36 0.12
33 6 0.02
34 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
TTTGAAAAGGATGCCACTGACTTGTGGGC
Found at i:1031988 original size:85 final size:85
Alignment explanation
Indices: 1031769--1032092 Score: 418
Period size: 85 Copynumber: 3.8 Consensus size: 85
1031759 CTAACATATG
* * *
1031769 TGGGCTTTGAAAAGAGTTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTTGTAGGC
1 TGGGCTTTGAAAAG-GATGCCACTGAC-T-TGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGC
* * * *
1031834 TTTTAAAAGGATGCCACTGACTTG
63 TTTGAAAA-GATGCCAATGTCTTA
* * *
1031858 TGGGCTTTGAAAAGGATCCCACTGACTTGTGGGCTTTTGAAAGGATGCCGCTGACTTGTGGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGC-TTTGAAAGGATGCCACTGACTTGTAGGCTT
1031923 TGAAAAGATGCCAATGTCTTA
65 TGAAAAGATGCCAATGTCTTA
* * * *
1031944 TGGGCTTTGAAAAGG-TGCTACTGACTTGTGGGCTTTGAAAAGGATGCCACTCACTTATGGGCTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTAGGCTT
*
1032008 TGAAAAGATGCCATTGTCTTA
65 TGAAAAGATGCCAATGTCTTA
* * *
1032029 TGGGCTTTGAAAAAG-TGCCACCGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTAGGCTTT
1 TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTT
1032093 TGTAGACACT
Statistics
Matches: 210, Mismatches: 23, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
84 27 0.13
85 93 0.44
86 34 0.16
87 32 0.15
88 10 0.05
89 14 0.07
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (85 bp):
TGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTAGGCTTT
GAAAAGATGCCAATGTCTTA
Found at i:1032433 original size:33 final size:33
Alignment explanation
Indices: 1032396--1032462 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1032386 TTCAACGATT
1032396 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1032429 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1032462 T
1 T
1032463 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1032434 original size:13 final size:13
Alignment explanation
Indices: 1032416--1032440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1032406 CATAAAATGT
1032416 TGTATCGATACAA
1 TGTATCGATACAA
1032429 TGTATCGATACA
1 TGTATCGATACA
1032441 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1032521 original size:13 final size:13
Alignment explanation
Indices: 1032503--1032527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1032493 ATTACTCAAA
1032503 TGTATCGATACAT
1 TGTATCGATACAT
1032516 TGTATCGATACA
1 TGTATCGATACA
1032528 CTGATCTCTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1035979 original size:13 final size:13
Alignment explanation
Indices: 1035961--1035986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1035951 CAATTTTTTG
1035961 TGTATCGATACAT
1 TGTATCGATACAT
1035974 TGTATCGATACAT
1 TGTATCGATACAT
1035987 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1036051 original size:21 final size:21
Alignment explanation
Indices: 1036025--1036100 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1036015 CTGCCAAGAA
*
1036025 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1036046 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1036066 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1036087 ATGTATCGATACAT
1 ATGTATCGATACAT
1036101 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1036071 original size:20 final size:20
Alignment explanation
Indices: 1036046--1036118 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1036036 CATCTTTTTT
1036046 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1036066 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1036087 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1036107 ATGTATCGATAC
1 ATGTATCGATAC
1036119 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1036082 original size:41 final size:41
Alignment explanation
Indices: 1036025--1036118 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1036015 CTGCCAAGAA
*
1036025 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1036066 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1036107 ATGTATCGATAC
1 ATGTATCGATAC
1036119 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1038595 original size:13 final size:13
Alignment explanation
Indices: 1038577--1038615 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1038567 ATAATCACCC
*
1038577 TGTATCGATACAG
1 TGTATCGATACAA
1038590 TGTATCGATACAA
1 TGTATCGATACAA
1038603 TGTATCGATACAA
1 TGTATCGATACAA
1038616 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1038626 original size:20 final size:20
Alignment explanation
Indices: 1038601--1038679 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1038591 GTATCGATAC
1038601 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1038621 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1038646 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1038666 CATGTATCGATACA
1 AATGTATCGATACA
1038680 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1040714 original size:15 final size:15
Alignment explanation
Indices: 1040694--1040724 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1040684 ATTTCGTTTG
*
1040694 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1040709 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1040724 G
1 G
1040725 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1044804 original size:13 final size:13
Alignment explanation
Indices: 1044786--1044811 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1044776 CAATTTTTTG
1044786 TGTATCGATACAT
1 TGTATCGATACAT
1044799 TGTATCGATACAT
1 TGTATCGATACAT
1044812 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1044876 original size:21 final size:21
Alignment explanation
Indices: 1044850--1044925 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1044840 CTGCCAAGAA
*
1044850 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1044871 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1044891 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1044912 ATGTATCGATACAT
1 ATGTATCGATACAT
1044926 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1044896 original size:20 final size:20
Alignment explanation
Indices: 1044871--1044943 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1044861 CATCTTTTTT
1044871 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1044891 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1044912 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1044932 ATGTATCGATAC
1 ATGTATCGATAC
1044944 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1044907 original size:41 final size:41
Alignment explanation
Indices: 1044850--1044943 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1044840 CTGCCAAGAA
*
1044850 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1044891 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1044932 ATGTATCGATAC
1 ATGTATCGATAC
1044944 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1045869 original size:29 final size:28
Alignment explanation
Indices: 1045835--1046608 Score: 366
Period size: 27 Copynumber: 27.0 Consensus size: 28
1045825 TGAAAAGAGT
* *
1045835 TGCCACTAAATTGTGGGCTTTAAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-AAAAGGG
* *
1045864 TGCCACTAACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* *
1045892 CATGCCAATGACTTGTGGGCTTTGAAAGGG
1 --TGCCACTGACTTGTGGGCTTTAAAAGGG
**
1045922 TGCCACTGACTTGTGGGCTTTGGAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * *
1045950 TGCCACCGATTTGTTGGGCTTTGAAAAGAGT
1 TGCCACTGACTTG-TGGGCTTT-AAAAG-GG
** * * *
1045981 TGCCACCAATTTGTATGGACTTTGAAAAGAGT
1 TGCCACTGACTTG--TGGGCTTT-AAAAG-GG
1046013 TGCCACTGACTTGTGGGCTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-AAAAGGG
** *
1046042 TGCCACTGACTTGT-GAATTTTAAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* **
1046069 TGCCACTGACTTGTCGGCTTTGGAAGGG
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* **
1046097 TGCCACTGATTAGTGTGGGCTTTGAAAAGATT
1 TGCCACTGACT--TGTGGGCTTT-AAAAG-GG
* * ** * *
1046129 TACTA-TCGACTTGTATGGATTTTGAAAAAAGT
1 TGCCACT-GACTTG--TGGGCTTT--AAAAGGG
* * * *
1046161 TGCCACCGACTTGTCTGGACTTTGAAAAAAGT
1 TGCCACTGACTTG--TGGGCTTT--AAAAGGG
* * * *
1046193 TACCACTAACTTGAGGGCTTTGAAAAAGG
1 TGCCACTGACTTGTGGGCTTT-AAAAGGG
* ***
1046222 TGCCACTGACTTGTGGGCTTTGAAATAT
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * *
1046250 TGCCACTGACTTATGGGCATAAAAAGGGG
1 TGCCACTGACTTGTGGGCTTTAAAA-GGG
* *
1046279 TGCCACTGACTTATGGGCTTAAAAAGGGG
1 TGCCACTGACTTGTGGGCTTTAAAA-GGG
** *
1046308 TGCCACTGACTTGTGGGCTTTGGAAGGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * *
1046336 TGCCATTGACTTGTGGGCTTAAAAAGGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
** * * *
1046364 TGCCACAAAGTTGTGGAC-TTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * * * * *
1046391 TGCCACGGAGTTGTAGAC-TTAAAAAGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * * *
1046418 TGCCAC-GAAGTTGTGGAC-TTAAAAAGA
1 TGCCACTG-ACTTGTGGGCTTTAAAAGGG
* *
1046445 TGCCAC-GAAGTTGTGGGC-TTAAAAGGA
1 TGCCACTG-ACTTGTGGGCTTTAAAAGGG
* * * *
1046472 TGCCACGGAGTTGTGGAC-TTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * * *
1046499 TGCCA-TGGAGTTGTGGACTTTAAAACGA
1 TGCCACT-GACTTGTGGGCTTTAAAAGGG
* * * *
1046527 TGCCACAGAGTTGTGGAC-TTAAAAGGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * * * *
1046554 TGCCACTAAATCGTGGACTTT-AAAGGA
1 TGCCACTGACTTGTGGGCTTTAAAAGGG
* * *
1046581 TGCCACTGAATCGTGGACTTTGAAAAGG
1 TGCCACTGACTTGTGGGCTTT-AAAAGG
1046609 TCACAGTTTT
Statistics
Matches: 621, Mismatches: 99, Indels: 50
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.00
27 188 0.30
28 156 0.25
29 121 0.19
30 59 0.10
31 17 0.03
32 75 0.12
33 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTAAAAGGG
Found at i:1045934 original size:28 final size:28
Alignment explanation
Indices: 1045759--1046369 Score: 353
Period size: 28 Copynumber: 20.6 Consensus size: 28
1045749 CGTTACGACA
* *
1045759 GCTTTGAAAGGGTGCCACCGAAATGTGTGG
1 GCTTTGAAAGGGTGCCACTG-ACT-TGTGG
* * *
1045789 GCTTTGAAAAGAGTTACCACCGACTTATGTGG
1 GCTTTG-AAAG-GGTGCCACTGAC-T-TGTGG
** * * *
1045821 ATTTTGAAAAGAGTTGCCACTAAATTGTGG
1 GCTTTG-AAAG-GGTGCCACTGACTTGTGG
* *
1045851 GCTTTAAAAAGGGTGCCACTAACTTGTGG
1 GCTTT-GAAAGGGTGCCACTGACTTGTGG
*
1045880 GCTTTGAAAGGGCATGCCAATGACTTGTGG
1 GCTTTGAAAGGG--TGCCACTGACTTGTGG
1045910 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * *
1045938 GCTTTGGAAGGGTGCCACCGATTTGTTGG
1 GCTTTGAAAGGGTGCCACTGACTTG-TGG
* ** *
1045967 GCTTTGAAAAGAGTTGCCACCAATTTGTATGG
1 GCTTTG-AAAG-GGTGCCACTGACTTG--TGG
* *
1045999 ACTTTGAAAAGAGTTGCCACTGACTTGTGG
1 GCTTTG-AAAG-GGTGCCACTGACTTGTGG
1046029 GCTTTGAAAAGGGTGCCACTGACTTGT-G
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
** * *
1046057 AATTTTAAAGGGTGCCACTGACTTGTCG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
1046085 GCTTTGGAAGGGTGCCACTGATTAGTGTGG
1 GCTTTGAAAGGGTGCCACTGACT--TGTGG
* * **
1046115 GCTTTGAAAAGAT-TTACTATCGACTTGTATGG
1 GCTTTGAAAGGGTGCCAC--T-GACTTG--TGG
** * * *
1046147 ATTTTGAAAAAAGTTGCCACCGACTTGTCTGG
1 GCTTTG--AAAGGGTGCCACTGACTTG--TGG
* * * * * *
1046179 ACTTTGAAAAAAGTTACCACTAACTTGAGG
1 GCTTTG--AAAGGGTGCCACTGACTTGTGG
*
1046209 GCTTTGAAAAAGGTGCCACTGACTTGTGG
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
*** *
1046238 GCTTTGAAATATTGCCACTGACTTATGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* ** *
1046266 GCATAAAAAGGGGTGCCACTGACTTATGG
1 GCTTTGAAA-GGGTGCCACTGACTTGTGG
**
1046295 GCTTAAAAAGGGGTGCCACTGACTTGTGG
1 GCTTTGAAA-GGGTGCCACTGACTTGTGG
* * *
1046324 GCTTTGGAAGGATGCCATTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
** *
1046352 GCTTAAAAAGGATGCCAC
1 GCTTTGAAAGGGTGCCAC
1046370 AAAGTTGTGG
Statistics
Matches: 474, Mismatches: 85, Indels: 46
0.78 0.14 0.08
Matches are distributed among these distances:
27 20 0.04
28 121 0.26
29 121 0.26
30 83 0.18
31 20 0.04
32 101 0.21
34 6 0.01
35 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (28 bp):
GCTTTGAAAGGGTGCCACTGACTTGTGG
Found at i:1046143 original size:148 final size:149
Alignment explanation
Indices: 1045823--1046243 Score: 440
Period size: 148 Copynumber: 2.8 Consensus size: 149
1045813 TTATGTGGAT
* * * * * * *
1045823 TTTGAAAAGAGTTGCCACTAAATTG--TGGGCTTT-AAAAAGGGTGCCACTAACTTGTGGGCTTT
1 TTTGAAAAGAGTTACCACCAACTTGTATGGACTTTGAAAAAAGTTGCCACTGACTTGTGGGCTTT
** *
1045885 G-AAAGGGCATGCCAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGAAGG
66 GAAAAGGG-ATGCCAATGACTTGTGGAATTTGAAAGGGTGCCACTGACTTGTCGGCTTTGGAAGG
*
1045949 GTGCCACCGATTTGTTGGGC
130 GTGCCACCGATTAGTTGGGC
* * *
1045969 TTTGAAAAGAGTTGCCACCAATTTGTATGGACTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTT
1 TTTGAAAAGAGTTACCACCAACTTGTATGGACTTTGAAAAAAGTTGCCACTGACTTGTGGGCTTT
* *
1046034 GAAAAGGG-TGCCACTGACTTGT-GAATTTTAAAGGGTGCCACTGACTTGTCGGCTTTGGAAGGG
66 GAAAAGGGATGCCAATGACTTGTGGAATTTGAAAGGGTGCCACTGACTTGTCGGCTTTGGAAGGG
*
1046097 TGCCACTGATTAGTGTGGGC
131 TGCCACCGATTAGT-TGGGC
* * * * * * *
1046117 TTTGAAAAGATTTACTATCGACTTGTATGGATTTTGAAAAAAGTTGCCACCGACTTGTCTGGACT
1 TTTGAAAAGAGTTACCACCAACTTGTATGGACTTTGAAAAAAGTTGCCACTGACTTG--TGGGCT
** * * * * * ** * *
1046182 TTGAAAAAAGTTACCACTAACTTGAGGGCTTTGAAAAAGGTGCCACTGACTTGTGGGCTTTG
64 TTGAAAAGGGATGCCAATGACTTGTGGAATTTG-AAAGGGTGCCACTGACTTGTCGGCTTTG
1046244 AAATATTGCC
Statistics
Matches: 231, Mismatches: 34, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
146 23 0.10
147 49 0.21
148 73 0.32
149 26 0.11
150 19 0.08
151 11 0.05
152 4 0.02
153 26 0.11
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (149 bp):
TTTGAAAAGAGTTACCACCAACTTGTATGGACTTTGAAAAAAGTTGCCACTGACTTGTGGGCTTT
GAAAAGGGATGCCAATGACTTGTGGAATTTGAAAGGGTGCCACTGACTTGTCGGCTTTGGAAGGG
TGCCACCGATTAGTTGGGC
Found at i:1046171 original size:32 final size:32
Alignment explanation
Indices: 1046116--1046219 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
1046106 TTAGTGTGGG
* * * *
1046116 CTTTGAAAAGATTTACTATCGACTTGTATGGA
1 CTTTGAAAAAAGTTACCACCGACTTGTATGGA
* * *
1046148 TTTTGAAAAAAGTTGCCACCGACTTGTCTGGA
1 CTTTGAAAAAAGTTACCACCGACTTGTATGGA
** *
1046180 CTTTGAAAAAAGTTACCACTAACTTG-A-GGG
1 CTTTGAAAAAAGTTACCACCGACTTGTATGGA
1046210 CTTTGAAAAA
1 CTTTGAAAAA
1046220 GGTGCCACTG
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
30 12 0.20
32 47 0.80
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (32 bp):
CTTTGAAAAAAGTTACCACCGACTTGTATGGA
Found at i:1046213 original size:180 final size:176
Alignment explanation
Indices: 1045759--1046236 Score: 553
Period size: 178 Copynumber: 2.7 Consensus size: 176
1045749 CGTTACGACA
* ** * * * * *
1045759 GCTTTGAAAGGGTGCCACCGAAATGTGTGGGCTTTGAAAAGAGTTACCACCGACTTATGTGGATT
1 GCTTTGAAAGGGTACCACCGACTTGT-TGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGACT
* * * **
1045824 TTGAAAAGAGTTGCCACTAAATTGTGGGCTTTAAAAAGGGTGCCACTAACTTGTGGGCTTTGAAA
65 TTGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGT-GAATTTGAAA
*
1045889 GGGCATGCCAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
129 GGG-ATGCCAATGACTTGTCGGCTTTGAAAGGGTGCCACTGACTTGTGG
* * * * * *
1045938 GCTTTGGAAGGGTGCCACCGATTTGTTGGGCTTTGAAAAGAGTTGCCACCAATTTGTATGGACTT
1 GCTTTGAAAGGGTACCACCGACTTGTTGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGACTT
* *
1046003 TGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGAATTTTAAAGG
66 TGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGAATTTGAAAGG
* * *
1046068 G-TGCCACTGACTTGTCGGCTTTGGAAGGGTGCCACTGATTAGTGTGG
131 GATGCCAATGACTTGTCGGCTTTGAAAGGGTGCCACTGACT--TGTGG
** * * * * *
1046115 GCTTTGAAAAGATTTACTATCGACTTGTATGGATTTTGAAAAAAGTTGCCACCGACTTGTCTGGA
1 GCTTTG-AAAG-GGTACCACCGACTTGT-TGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGA
* * * *
1046180 CTTTGAAAAAAGTTACCACTAACTTGAGGGCTTTGAAAAAGGTGCCACTGACTTGTG
63 CTTTGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTG
1046237 GGCTTTGAAA
Statistics
Matches: 256, Mismatches: 38, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
175 35 0.14
177 21 0.08
178 85 0.33
179 33 0.13
180 82 0.32
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (176 bp):
GCTTTGAAAGGGTACCACCGACTTGTTGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGACTT
TGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGAATTTGAAAGG
GATGCCAATGACTTGTCGGCTTTGAAAGGGTGCCACTGACTTGTGG
Found at i:1046298 original size:180 final size:175
Alignment explanation
Indices: 1045759--1046329 Score: 556
Period size: 180 Copynumber: 3.2 Consensus size: 175
1045749 CGTTACGACA
* ** * * * * *
1045759 GCTTTGAAAGGGTGCCACCGAAATGTGTGGGCTTTGAAAAGAGTTACCACCGACTTATGTGGATT
1 GCTTTGAAAGGGTACCACCGACTTGT-TGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGACT
* *
1045824 TTGAAAAGAGTTGCCACTAAATTGTGGGCTTT-AAAAAGGGTGCCACTAACTTGTGGGCTTTGAA
65 TTGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAA-GGTGCCACTGACTTGTGGGCTTTGAA
* *
1045888 AGGGCATGCCAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
129 A---CATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGG
* * * * * *
1045938 GCTTTGGAAGGGTGCCACCGATTTGTTGGGCTTTGAAAAGAGTTGCCACCAATTTGTATGGACTT
1 GCTTTGAAAGGGTACCACCGACTTGTTGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGACTT
* * ** *
1046003 TGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGT-GAATTTTAAAG
66 TGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAA-
** * *
1046067 GGTGCCACTGACTTGTCGGCTTTGGAAGGGTGCCACTGA-TTAGTGTGG
130 CATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTA---TGG
** * * * * *
1046115 GCTTTGAAAAGATTTACTATCGACTTGTATGGATTTTGAAAAAAGTTGCCACCGACTTGTCTGGA
1 GCTTTG-AAAG-GGTACCACCGACTTGT-TGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGA
* * *
1046180 CTTTGAAAAAAGTTACCACTAACTTGAGGGCTTTGAAAAAGGTGCCACTGACTTGTGGGCTTTGA
63 CTTTGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAAGGTGCCACTGACTTGTGGGCTTTGA
* * * **
1046245 AATATTGCCACTGACTTATGGGCATAAAAAGGGGTGCCACTGACTTATGG
128 AACA-TGCCACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTATGG
** * * *
1046295 GCTTAAAAAGGGGTGCCACTGACTTG-TGGGCTTTG
1 GCTTTGAAA-GGGTACCACCGACTTGTTGGACTTTG
1046330 GAAGGATGCC
Statistics
Matches: 319, Mismatches: 61, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
174 2 0.01
175 35 0.11
177 23 0.07
178 80 0.25
179 49 0.15
180 89 0.28
181 26 0.08
182 12 0.04
183 3 0.01
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (175 bp):
GCTTTGAAAGGGTACCACCGACTTGTTGGACTTTGAAAAGAGTTGCCACCGACTTGTATGGACTT
TGAAAAGAGTTGCCACTAACTTGTGGGCTTTGAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAC
ATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGG
Found at i:1046570 original size:82 final size:82
Alignment explanation
Indices: 1046331--1046607 Score: 337
Period size: 82 Copynumber: 3.4 Consensus size: 82
1046321 TGGGCTTTGG
* * * *
1046331 AAGGATGCCATTGACTTGTGGGC-TTAAAAAGGATGCCACAAAGTTGTGGACTTAAAAGGATGCC
1 AAGGATGCCATGGAGTTGTGGACTTTAAAAA-GATGCCACAGAGTTGTGGACTTAAAAGGATGCC
*
1046395 ACGGAGTTGTAGACTTAA
65 ACGGAGTTGTGGACTTAA
* * * *
1046413 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGATGCCAC-GAAGTTGTGGGCTTAAAAGGATGCC
1 AAGGATGCCATGGAGTTGTGGACTTTAAAAAGATGCCACAG-AGTTGTGGACTTAAAAGGATGCC
1046476 ACGGAGTTGTGGACTTAA
65 ACGGAGTTGTGGACTTAA
*
1046494 AAGGATGCCATGGAGTTGTGGACTTTAAAACGATGCCACAGAGTTGTGGACTTAAAAGGATGCCA
1 AAGGATGCCATGGAGTTGTGGACTTTAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGATGCCA
** * * *
1046559 CTAAATCGTGGACTTTA
66 CGGAGTTGTGGACTTAA
* * *
1046576 AAGGATGCCACT-GAATCGTGGACTTTGAAAAG
1 AAGGATGCCA-TGGAGTTGTGGACTTTAAAAAG
1046608 GTCACAGTTT
Statistics
Matches: 168, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
81 67 0.40
82 99 0.59
83 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (82 bp):
AAGGATGCCATGGAGTTGTGGACTTTAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGATGCCA
CGGAGTTGTGGACTTAA
Found at i:1047946 original size:22 final size:22
Alignment explanation
Indices: 1047900--1047991 Score: 77
Period size: 22 Copynumber: 4.2 Consensus size: 22
1047890 CATGTCCTCG
*
1047900 TTTTTTTATTTT--TTTTGTTCCC
1 TTTTTTTATTTTGCTTTTG--CAC
1047922 TTTTTTTATTTTGCTTTTGCAC
1 TTTTTTTATTTTGCTTTTGCAC
* *
1047944 TTTTTTTGTTTTTCTTTT-CA-
1 TTTTTTTATTTTGCTTTTGCAC
*
1047964 TTTTTTGTGCTTTTGCTTTTG-AC
1 TTTTTT-T-ATTTTGCTTTTGCAC
1047987 TTTTT
1 TTTTT
1047992 CGTCATTTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
20 6 0.10
21 3 0.05
22 40 0.68
23 5 0.08
24 5 0.08
ACGTcount: A:0.05, C:0.12, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTTTTTATTTTGCTTTTGCAC
Found at i:1053860 original size:23 final size:24
Alignment explanation
Indices: 1053811--1053861 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1053801 GCATAAACAC
* *
1053811 TTTTTTTAAAACAAATAAAGATCA
1 TTTTTTTAAAACAAATAAACATAA
1053835 TTTTTTTAAAA-AAA-AAACATAA
1 TTTTTTTAAAACAAATAAACATAA
*
1053857 ATTTT
1 TTTTT
1053862 GAACTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.42
23 3 0.12
24 11 0.46
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTTTTTAAAACAAATAAACATAA
Found at i:1055697 original size:129 final size:127
Alignment explanation
Indices: 1055482--1055820 Score: 477
Period size: 129 Copynumber: 2.7 Consensus size: 127
1055472 GTTAATTATG
** * *
1055482 ATAAATATTAATCGTTTTTAATCTTTTATA-TTCTTAGGGGTATCCGTAGAAGTATAAAAGACTT
1 ATAAATATTAATTATTTTTAATCTTTTATATTTC-TATGGGTATCCGTAGAGGTATAAAAGA-TT
*
1055546 T-AAAAACTTTTCATATCTTTTTGGGTATCCATTAAGGTACAAAATGATTTTTTTCAAACATAA
64 TCAAAAACTTTTCGTATCTTTTTGGGTATCCATTAAGGTACAAAATGATTTTTTTCAAACATAA
* * * *
1055609 ATAAATATTAATTATTTTTCAGTCTTTTATATTTCTATGAGTATTCGTAGGGGTATAAAAGATTT
1 ATAAATATTAATTATTTTT-AATCTTTTATATTTCTATGGGTATCCGTAGAGGTATAAAAGATTT
1055674 CGAAAAACTTTTCGTATCTTTTTGGGTATCCATTAAGGTACAAAATGATTTTTTTCAAACATAA
65 C-AAAAACTTTTCGTATCTTTTTGGGTATCCATTAAGGTACAAAATGATTTTTTTCAAACATAA
* * * *
1055738 ATAAATATTAATTATTTTAAATATTTTATATTCCTATGGGTATCCGTAAAGGTATTAAAAGATTT
1 ATAAATATTAATTATTTTTAATCTTTTATATTTCTATGGGTATCCGTAGAGGTA-TAAAAGATTT
* *
1055803 C-AAAATTTTTTGTATCTT
65 CAAAAACTTTTCGTATCTT
1055821 GACGAATTTC
Statistics
Matches: 188, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
127 35 0.19
128 60 0.32
129 93 0.49
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (127 bp):
ATAAATATTAATTATTTTTAATCTTTTATATTTCTATGGGTATCCGTAGAGGTATAAAAGATTTC
AAAAACTTTTCGTATCTTTTTGGGTATCCATTAAGGTACAAAATGATTTTTTTCAAACATAA
Found at i:1059661 original size:20 final size:20
Alignment explanation
Indices: 1059632--1059689 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
1059622 GTATCCTTAT
1059632 AAAG-TTAATAAAAATATAA
1 AAAGTTTAATAAAAATATAA
*
1059651 AAAGTTTAATAAAAATAAAA
1 AAAGTTTAATAAAAATATAA
*
1059671 AAAGTTTAATAAAATTATA
1 AAAGTTTAATAAAAATATA
1059690 TTTGATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAGTTTAATAAAAATATAA
Found at i:1062683 original size:13 final size:13
Alignment explanation
Indices: 1062667--1062693 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1062657 TTATACATAA
1062667 AAATTTTAAATTT
1 AAATTTTAAATTT
1062680 AAATTTTAAATTT
1 AAATTTTAAATTT
1062693 A
1 A
1062694 GATAAGATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTTTAAATTT
Found at i:1065552 original size:32 final size:31
Alignment explanation
Indices: 1065490--1065561 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
1065480 AAAATACTAC
* * * *
1065490 ATATTTTATTTATTTATTTTTATTTTTAAAT
1 ATATTTTATATATTTAATTTTATGTATAAAT
1065521 ATATTTTATATATTATAATTTTATGTATAAAT
1 ATATTTTATATATT-TAATTTTATGTATAAAT
* *
1065553 TTCTTTTAT
1 ATATTTTAT
1065562 TTCATCTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (31 bp):
ATATTTTATATATTTAATTTTATGTATAAAT
Found at i:1074544 original size:13 final size:13
Alignment explanation
Indices: 1074526--1074578 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1074516 ATTCTTCATA
1074526 TATCGATACATTG
1 TATCGATACATTG
1074539 TATCGATACATTG
1 TATCGATACATTG
*
1074552 --T-G--CCA-TG
1 TATCGATACATTG
1074559 TATCGATACATTG
1 TATCGATACATTG
1074572 TATCGAT
1 TATCGAT
1074579 TCAAAGCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
10 2 0.06
11 1 0.03
12 2 0.06
13 22 0.69
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:1074546 original size:33 final size:33
Alignment explanation
Indices: 1074504--1074602 Score: 110
Period size: 33 Copynumber: 3.0 Consensus size: 33
1074494 TTTGAGGTAA
1074504 TGTATCGATACAATTCTTCATATATCGATACAT
1 TGTATCGATACAATTCTTCATATATCGATACAT
* * *
1074537 TGTATCGATAC-ATTGTGCCATGTATCGATACAT
1 TGTATCGATACAATTCT-TCATATATCGATACAT
* ** * *
1074570 TGTATCGATTCAAAGCATAATATATCGATACAT
1 TGTATCGATACAATTCTTCATATATCGATACAT
1074603 CTAAAAGTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
32 4 0.08
33 48 0.91
34 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAATTCTTCATATATCGATACAT
Found at i:1076297 original size:33 final size:33
Alignment explanation
Indices: 1076254--1076318 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1076244 TTACAAGCAA
*
1076254 TGTATCGATACAAT-TAATCATGTATCGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
*
1076287 TGTATTGATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
1076319 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:1077013 original size:27 final size:22
Alignment explanation
Indices: 1076961--1077005 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1076951 AGATAAATAT
1076961 ATTTCTCCCCCTTTATCAAATC
1 ATTTCTCCCCCTTTATCAAATC
*
1076983 ATTTCTCCCCCTTTGTCAAATC
1 ATTTCTCCCCCTTTATCAAATC
1077005 A
1 A
1077006 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.36, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAATC
Found at i:1078842 original size:13 final size:13
Alignment explanation
Indices: 1078824--1078850 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1078814 ATTGTAACCC
1078824 ATGTATCGATACA
1 ATGTATCGATACA
1078837 ATGTATCGATACA
1 ATGTATCGATACA
1078850 A
1 A
1078851 GGAATGTTGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1085934 original size:9 final size:9
Alignment explanation
Indices: 1085920--1085950 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1085910 CATCAAGGAC
1085920 GATGAAGAT
1 GATGAAGAT
1085929 GATGAAGAT
1 GATGAAGAT
*
1085938 GATGATGAT
1 GATGAAGAT
1085947 GATG
1 GATG
1085951 GTGACTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGAAGAT
Found at i:1090261 original size:13 final size:13
Alignment explanation
Indices: 1090243--1090268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1090233 ACAGCATTCT
1090243 TTGTATCGATACA
1 TTGTATCGATACA
1090256 TTGTATCGATACA
1 TTGTATCGATACA
1090269 GGGGGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1093463 original size:52 final size:52
Alignment explanation
Indices: 1093385--1093513 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1093375 CGAAATATGA
* *
1093385 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
1093437 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1093489 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1093514 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1093526 original size:52 final size:51
Alignment explanation
Indices: 1093385--1093533 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
1093375 CGAAATATGA
*
1093385 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
1093437 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1093489 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1093534 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1093540 original size:13 final size:13
Alignment explanation
Indices: 1093522--1093546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1093512 CAAAGATCAG
1093522 TGTATCGATACAA
1 TGTATCGATACAA
1093535 TGTATCGATACA
1 TGTATCGATACA
1093547 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1093624 original size:33 final size:33
Alignment explanation
Indices: 1093587--1093653 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1093577 AGTAGCTTAA
1093587 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1093620 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1093653 A
1 A
1093654 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1093627 original size:13 final size:13
Alignment explanation
Indices: 1093609--1093633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1093599 CAAAAAAATA
1093609 TGTATCGATACAT
1 TGTATCGATACAT
1093622 TGTATCGATACA
1 TGTATCGATACA
1093634 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1094346 original size:20 final size:21
Alignment explanation
Indices: 1094314--1094365 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
1094304 CCCCTAGGTA
*
1094314 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCGCAACCGG
1094335 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
1094356 GCAGCCCCCA
1 GCA-CCCCCA
1094366 CACTAGCCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.19, C:0.50, G:0.27, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:1096438 original size:19 final size:20
Alignment explanation
Indices: 1096414--1096464 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1096404 TAGCCAAACT
**
1096414 TGTATCGATACA-CACAGTA
1 TGTATCGATACACCACAAAA
*
1096433 TGTATCGATACACCATAAAA
1 TGTATCGATACACCACAAAA
1096453 TGTATCGATACA
1 TGTATCGATACA
1096465 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCACAAAA
Found at i:1096531 original size:20 final size:21
Alignment explanation
Indices: 1096506--1096544 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1096496 TTCAAATGCA
1096506 TGTATCGATACA-TCACAAAT
1 TGTATCGATACATTCACAAAT
1096526 TGTATCGATACATTCACAA
1 TGTATCGATACATTCACAA
1096545 GGGAAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATTCACAAAT
Found at i:1097426 original size:19 final size:18
Alignment explanation
Indices: 1097401--1097468 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1097391 AATTCAACAA
1097401 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1097419 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1097435 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1097451 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
1097469 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1097440 original size:13 final size:13
Alignment explanation
Indices: 1097422--1097446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1097412 ACATAAGTGT
1097422 TGTATCGATACAA
1 TGTATCGATACAA
1097435 TGTATCGATACA
1 TGTATCGATACA
1097447 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.