Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007768.1 Hibiscus syriacus cultivar Beakdansim tig00110044_pilon, whole genome shotgun sequence
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: 2539099
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2164632 original size:110 final size:108
Alignment explanation
Indices: 2164360--2164720 Score: 466
Period size: 110 Copynumber: 3.4 Consensus size: 108
2164350 TTGTTGAAGA
* *
2164360 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-GAGTCCTAT
1 TTGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTCGAGTTCTAT
* * *
2164422 ACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGA---
66 ACTCTCTGAAGGAATAGAGAGCGGACACGTT-TTATGAAGATTG
*
2164462 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTA
1 TTGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATT-TTCGAGTTCTA
*
2164527 TACTCTCTGAAGGATTAGAGAGCGGACACGTTTTATGAAGATTG
65 TACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTG
* * ** **
2164571 TTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACTCGTTTATTGAAGATTTTCCGAGTTCT
1 TT-GAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTTT-CGAGTTCT
*
2164636 ATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTG
64 ATACTCTCTGAAGGAATAGAGAGCGGACACGTTTTA-TGAAGATTG
* * *
2164682 TTTGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 -TTGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACA
2164721 CGCTTGCCAA
Statistics
Matches: 228, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
102 51 0.22
105 3 0.01
106 42 0.18
109 4 0.02
110 86 0.38
111 40 0.18
112 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (108 bp):
TTGAGTCCTATACTCCCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTTTCGAGTTCTAT
ACTCTCTGAAGGAATAGAGAGCGGACACGTTTTATGAAGATTG
Found at i:2164742 original size:166 final size:164
Alignment explanation
Indices: 2164413--2164798 Score: 397
Period size: 166 Copynumber: 2.4 Consensus size: 164
2164403 GTTGAAGATT
* * * ** **
2164413 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA--TT-GAGTCCTATAC
1 GAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACTCGTTTATTGAAGATTTTCGAGTCCTATAC
* * *
2164475 TCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGG
66 TCTCTGAAGGAATAGAGAGCGGACAAGTTCATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
* * * * **
2164540 ATTAGAGAGCGGACACGTTTTATGAAGATTGTTC
131 AATAGAGAGCAGACACGCTTGACAAAGATTGTTC
* *
2164574 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACTCGTTTATTGAAGATTTTCCGAGTTCTATA
1 GAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACTCGTTTATTGAAGATTTT-CGAGTCCTATA
** * *
2164639 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTTGAG-TCTTATACTCCCTGA
65 CTCTCTGAAGGAATAGAGAGCGGACAAG-TTCATTGAAGATTGTTCGAGTTC-TATACTCCCTGA
* * *
2164703 ATGAATAGGGAGCAGACACGCTTGCCAAAGATTGTTC
128 AGGAATAGAGAGCAGACACGCTTGACAAAGATTGTTC
* * * ** * *
2164740 GAG-TCTTATACTCCTTAAAAGAATATGGAGCATACTCG-TTATTTGAATATTTTCAAGTC
1 GAGTTC-TATACTCCCTGAAAGAATAGGGAGCGGACTCGTTTA-TTGAAGATTTTCGAGTC
2164799 TCACTTATCC
Statistics
Matches: 184, Mismatches: 33, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
161 42 0.23
163 2 0.01
165 45 0.24
166 95 0.52
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (164 bp):
GAGTTCTATACTCCCTGAAAGAATAGGGAGCGGACTCGTTTATTGAAGATTTTCGAGTCCTATAC
TCTCTGAAGGAATAGAGAGCGGACAAGTTCATTGAAGATTGTTCGAGTTCTATACTCCCTGAAGG
AATAGAGAGCAGACACGCTTGACAAAGATTGTTC
Found at i:2168657 original size:86 final size:86
Alignment explanation
Indices: 2168512--2168685 Score: 285
Period size: 86 Copynumber: 2.0 Consensus size: 86
2168502 GTCATTCAAA
* * *
2168512 CATATATAGTAATAACGATCGGCACCTGTTTAGATTGGTATGAGTATGACACAAGATCAAAGCCT
1 CATATATAGTAATAACGATCAGCACCTGTTTAGATTGGTACGAGTACGACACAAGATCAAAGCCT
2168577 ATAATAGCACAGAAATACATT
66 ATAATAGCACAGAAATACATT
* * *
2168598 CATATATAGTAATAACGATTAGTACCTGTTTAGATTGGTACGAGTGCGACACAAGATCAAAGCCT
1 CATATATAGTAATAACGATCAGCACCTGTTTAGATTGGTACGAGTACGACACAAGATCAAAGCCT
*
2168663 ATAATAGCTCAGAAATACATT
66 ATAATAGCACAGAAATACATT
2168684 CA
1 CA
2168686 ACATTAAAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (86 bp):
CATATATAGTAATAACGATCAGCACCTGTTTAGATTGGTACGAGTACGACACAAGATCAAAGCCT
ATAATAGCACAGAAATACATT
Found at i:2175300 original size:21 final size:21
Alignment explanation
Indices: 2175274--2175349 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
2175264 GCAAATAAGT
2175274 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* * ** *
2175295 AAATCGTAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
2175315 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* *
2175336 AAATTGCAATGCGA
1 AAATCGCAACGCGA
2175350 TACTGACTAT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:2175328 original size:20 final size:20
Alignment explanation
Indices: 2175257--2175330 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
2175247 TTTTCCCAAT
* *
2175257 TCGCAATGCAAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
2175277 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
* *
2175298 TCGTAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
2175318 TCGCAACGCGAAT
1 TCGCAACGCGAAT
2175331 TGGGAAAATT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:2175364 original size:41 final size:41
Alignment explanation
Indices: 2175257--2175349 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
2175247 TTTTCCCAAT
*
2175257 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
2175298 TCGTAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
2175339 TTGCAATGCGA
1 TCGCAATGCGA
2175350 TACTGACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:2175366 original size:20 final size:20
Alignment explanation
Indices: 2175341--2175452 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
2175331 TGGGAAAATT
*
2175341 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* * *
2175361 GCAATGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATC
* * *
2175382 GCAACGAGATACTTACTTTC
1 GCAACGCGATACTGACTATC
*
2175402 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
* *
2175422 GCAACGCGATTCTGACTTTC
1 GCAACGCGATACTGACTATC
2175442 GCAACGCGATA
1 GCAACGCGATA
2175453 ATACATAATC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 61 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:2175380 original size:41 final size:41
Alignment explanation
Indices: 2175335--2175472 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
2175325 GCGAATTGGG
* * * *
2175335 AAAATTGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
2175376 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
2175418 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
2175457 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
2175473 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.40
41 43 0.55
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:2175668 original size:22 final size:22
Alignment explanation
Indices: 2175640--2175683 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2175630 CACTCTCTCA
2175640 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2175662 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2175684 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2176003 original size:20 final size:20
Alignment explanation
Indices: 2175946--2175994 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2175936 GCGATTATCT
**
2175946 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
2175966 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
2175986 TGTTGCGAT
1 CGTTGCGAT
2175995 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:2177346 original size:18 final size:18
Alignment explanation
Indices: 2177325--2177369 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2177315 TCCACTTCGG
*
2177325 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2177343 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
2177361 GAGCCATCA
1 GAGCCATCA
2177370 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2177904 original size:19 final size:20
Alignment explanation
Indices: 2177850--2177916 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2177840 TAGTTTACTT
* *
2177850 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2177870 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2177890 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2177909 TCGCAACG
1 TCGCAACG
2177917 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2177924 original size:14 final size:14
Alignment explanation
Indices: 2177905--2177962 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2177895 ATGCGAAATG
2177905 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2177919 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2177935 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2177951 AAAATCGCAACG
1 AAAATCGCAACG
2177963 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2177947 original size:32 final size:33
Alignment explanation
Indices: 2177889--2177979 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2177879 GGAAATGGCT
*
2177889 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2177922 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2177954 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2177980 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2177973 original size:19 final size:19
Alignment explanation
Indices: 2177850--2177984 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
2177840 TAGTTTACTT
* **
2177850 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
2177870 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2177890 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2177909 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2177923 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
2177941 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2177955 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2177974 TCGCAATGCGA
1 TCGCAACGCGA
2177985 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2178015 original size:14 final size:14
Alignment explanation
Indices: 2177996--2178053 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2177986 TTGTGTTTCG
2177996 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2178010 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2178026 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2178042 CGTTGCGATTTT
1 CGTTGCGATTTT
2178054 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2178030 original size:32 final size:33
Alignment explanation
Indices: 2177991--2178069 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2177981 GCGATTTGTG
2177991 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2178023 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2178056 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2178070 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2178068 original size:19 final size:19
Alignment explanation
Indices: 2178010--2178127 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
2178000 GCGATTTTGT
2178010 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2178028 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
2178042 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
2178061 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
2178081 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2178100 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
2178120 TGTTGCGA
1 CGTTGCGA
2178128 AAGTAAATTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2180127 original size:33 final size:33
Alignment explanation
Indices: 2180082--2180197 Score: 142
Period size: 33 Copynumber: 3.4 Consensus size: 33
2180072 AAAACAGACT
* ***
2180082 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
2180115 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
2180153 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
2180186 ATCACAATGCGA
1 ATCGCAATGCGA
2180198 TTTTCATTTC
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
33 37 0.51
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 30 0.41
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:2180185 original size:19 final size:19
Alignment explanation
Indices: 2180111--2180178 Score: 136
Period size: 19 Copynumber: 3.6 Consensus size: 19
2180101 ATCGCAACGA
2180111 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2180130 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2180149 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2180168 GAAAATCGCAA
1 GAAAATCGCAA
2180179 CGAGAAAATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2180241 original size:20 final size:20
Alignment explanation
Indices: 2180216--2180273 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
2180206 TCGCATTGCG
*
2180216 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2180236 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2180256 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2180274 TCAATGAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2181574 original size:12 final size:12
Alignment explanation
Indices: 2181557--2181581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2181547 ATATAATCCT
2181557 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2181569 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2181581 G
1 G
2181582 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2183894 original size:19 final size:19
Alignment explanation
Indices: 2183872--2184002 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
2183862 GGAAATTACT
2183872 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2183891 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2183905 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2183924 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
2183938 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2183957 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2183971 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2183990 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2184003 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2183914 original size:33 final size:33
Alignment explanation
Indices: 2183872--2183998 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
2183862 GGAAATTACT
2183872 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2183905 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2183937 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2183971 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2183999 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2183979 original size:66 final size:66
Alignment explanation
Indices: 2183873--2184005 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2183863 GAAATTACTA
*
2183873 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2183938 T
66 T
*
2183939 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2184004 T
66 T
2184005 T
1 T
2184006 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2184020 original size:19 final size:20
Alignment explanation
Indices: 2183998--2184040 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2183988 AAATCGCAAC
2183998 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2184017 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2184037 GCGA
1 GCGA
2184041 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2184025 original size:14 final size:14
Alignment explanation
Indices: 2184026--2184059 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2184016 TGCGATTTTC
2184026 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
2184040 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
2184054 ATTTTC
1 ATTTTC
2184060 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:2184200 original size:14 final size:14
Alignment explanation
Indices: 2184181--2184217 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2184171 CATCAATTAA
2184181 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2184195 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2184209 ACAAATCAA
1 ACAAATCAA
2184218 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2185636 original size:21 final size:21
Alignment explanation
Indices: 2185570--2185636 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2185560 GTGAATCGGG
*
2185570 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2185590 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2185612 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2185633 CTCT
1 CTCT
2185637 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2185655 original size:42 final size:41
Alignment explanation
Indices: 2185570--2185692 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
2185560 GTGAATCGGG
* * * *
2185570 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
2185612 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
2185654 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
2185693 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:2186903 original size:20 final size:19
Alignment explanation
Indices: 2186858--2186916 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
2186848 TCTTTTGGTT
2186858 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
2186877 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
2186898 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
2186917 TAGAATCACA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2186976 original size:47 final size:48
Alignment explanation
Indices: 2186883--2186976 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 48
2186873 ACGAGATAAT
* * *
2186883 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCACAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCACAACGA
* *
2186931 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCACAACG
2186977 CGAAATGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 27 0.66
48 14 0.34
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCACAACGA
Found at i:2186989 original size:19 final size:19
Alignment explanation
Indices: 2186967--2187056 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
2186957 GCGACCAGAC
2186967 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2186986 AATCGCAACTGCGAAATAAA
1 AATCGCAAC-GCGAAATGAA
2187006 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2187025 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2187044 AATCGCAATGCGA
1 AATCGCAACGCGA
2187057 TTTTTGTTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2187021 original size:39 final size:38
Alignment explanation
Indices: 2186967--2187056 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
2186957 GCGACCAGAC
2186967 AATCGCAACGCGAAATGAAAATCGCAACTGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAAC-GCGAAATAAA
*
2187006 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
2187044 AATCGCAATGCGA
1 AATCGCAACGCGA
2187057 TTTTTGTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:2187673 original size:20 final size:19
Alignment explanation
Indices: 2187647--2187700 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
2187637 GGCGCTATGT
2187647 AAATCGCGTTGCGAAAGTC
1 AAATCGCGTTGCGAAAGTC
2187666 AGAATCGCGTTGCGAAAGTC
1 A-AATCGCGTTGCGAAAGTC
*
2187686 AATATCTCGTTGCGA
1 AA-ATCGCGTTGCGA
2187701 TTTTGTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (19 bp):
AAATCGCGTTGCGAAAGTC
Found at i:2187734 original size:20 final size:20
Alignment explanation
Indices: 2187709--2187762 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2187699 GATTTTGTAT
2187709 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2187729 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2187749 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2187763 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2187747 original size:61 final size:61
Alignment explanation
Indices: 2187649--2187765 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
2187639 CGCTATGTAA
* * * * *
2187649 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAATATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
* * * *
2187710 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT
2187766 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
Found at i:2187781 original size:61 final size:61
Alignment explanation
Indices: 2187649--2187783 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
2187639 CGCTATGTAA
* * * * * ** *
2187649 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAATATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTCCAAT
* * * *
2187710 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT-CCAAT
2187772 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2187784 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTCCAAT
Found at i:2188772 original size:27 final size:27
Alignment explanation
Indices: 2188741--2188792 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2188731 GGTCCTTATT
* *
2188741 ATTT-ATATATTTTATCATTTTAATTTA
1 ATTTAATAAATTTAATC-TTTTAATTTA
2188768 ATTTAATAAATTTAATCTTTTAATT
1 ATTTAATAAATTTAATCTTTTAATT
2188793 AAATACACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTAATAAATTTAATCTTTTAATTTA
Found at i:2192454 original size:59 final size:59
Alignment explanation
Indices: 2192386--2192679 Score: 507
Period size: 59 Copynumber: 5.0 Consensus size: 59
2192376 TCAAAGAGTC
* *
2192386 CCCCTACTATACGATGTTACTTTTTTAAGTTCATTGACTATTAAAAGTTACAAAATGAT
1 CCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGAT
* *
2192445 CCCCTACTATACGATGTTACTTTTTTAAGTGCCTTGACTATTAAAAGTTACAAAATGGT
1 CCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGAT
* *
2192504 CCCCCTACTATACGATGTTACTTTTTTAAGTCCCTTGACTATTAAAAGTTACAAAATGGT
1 -CCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGAT
2192564 CCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGAT
1 CCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGAT
* *
2192623 CCCCCACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTCACAAAATG
1 CCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATG
2192680 GTCACCCGAC
Statistics
Matches: 226, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
59 168 0.74
60 58 0.26
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (59 bp):
CCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGAT
Found at i:2192545 original size:31 final size:31
Alignment explanation
Indices: 2192510--2192604 Score: 72
Period size: 31 Copynumber: 3.2 Consensus size: 31
2192500 TGGTCCCCCT
2192510 ACTATACGATGTTACTTTTTTAAGTCCCTTG
1 ACTATACGATGTTACTTTTTTAAGTCCCTTG
* * **** * *
2192541 ACTATTA-AAAGTTAC-AAAAT-GGTCCCCT-
1 ACTA-TACGATGTTACTTTTTTAAGTCCCTTG
*
2192569 ACTATACGATGTTACTTTTTTAAGTACCTTG
1 ACTATACGATGTTACTTTTTTAAGTCCCTTG
2192600 ACTAT
1 ACTAT
2192605 TAAAAGTTAC
Statistics
Matches: 42, Mismatches: 17, Indels: 10
0.61 0.25 0.14
Matches are distributed among these distances:
27 2 0.05
28 10 0.24
29 7 0.17
30 6 0.14
31 15 0.36
32 2 0.05
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (31 bp):
ACTATACGATGTTACTTTTTTAAGTCCCTTG
Found at i:2192692 original size:119 final size:119
Alignment explanation
Indices: 2192384--2192692 Score: 530
Period size: 119 Copynumber: 2.6 Consensus size: 119
2192374 AATCAAAGAG
* * *
2192384 TCCCCCTACTATACGATGTTACTTTTTTAAGTTCATTGACTATTAAAAGTTACAAAATGATCCCC
1 TCCCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGGTCCCC
* *
2192449 TACTATACGATGTTACTTTTTTAAGTGCCTTGACTATTAAAAGTTACAAAATGG
66 TACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGA
*
2192503 TCCCCCTACTATACGATGTTACTTTTTTAAGTCCCTTGACTATTAAAAGTTACAAAATGGTCCCC
1 TCCCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGGTCCCC
2192568 TACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGA
66 TACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGA
*
2192622 TCCCCC-ACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTCACAAAATGGTCACC
1 TCCCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGGTC-CC
*
2192686 CGACTAT
65 CTACTAT
2192693 TCTTTGTGTT
Statistics
Matches: 181, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
118 53 0.29
119 128 0.71
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (119 bp):
TCCCCCTACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGGTCCCC
TACTATACGATGTTACTTTTTTAAGTACCTTGACTATTAAAAGTTACAAAATGA
Found at i:2195910 original size:19 final size:19
Alignment explanation
Indices: 2195868--2195911 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2195858 TATGCATTGG
*
2195868 GCTATGAATTTGAAAATAA
1 GCTATGAATATGAAAATAA
* * *
2195887 ACTATGAATATGACAGTAA
1 GCTATGAATATGAAAATAA
2195906 GCTATG
1 GCTATG
2195912 CAAATCTGTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (19 bp):
GCTATGAATATGAAAATAA
Found at i:2198155 original size:18 final size:19
Alignment explanation
Indices: 2198129--2198186 Score: 82
Period size: 18 Copynumber: 3.1 Consensus size: 19
2198119 TTGAGGGATT
2198129 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* *
2198148 AT-AGTGGTTCTTCGGAAC
1 ATCAGTGGTCCTTCGGGAC
2198166 TATCAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCCTTCGGGAC
2198186 A
1 A
2198187 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 14 0.42
19 5 0.15
20 14 0.42
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:2204346 original size:19 final size:19
Alignment explanation
Indices: 2204322--2204373 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
2204312 GAATGCAATT
* *
2204322 AGTGCATCAATGCATAGGG
1 AGTGCATCGATGCATAAGG
2204341 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
2204360 AGTGCATCGATGCA
1 AGTGCATCGATGCA
2204374 CCTGCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:2205035 original size:18 final size:19
Alignment explanation
Indices: 2205009--2205066 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
2204999 TCGAGGGATT
2205009 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* *
2205028 AT-AGTGGTTCTTCGGAAC
1 ATCAGTGGTCCTTCGGGAC
*
2205046 TATCAGTGGTCTTTCGGGAC
1 -ATCAGTGGTCCTTCGGGAC
2205066 A
1 A
2205067 AATATTCAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.44
19 5 0.16
20 13 0.41
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:2206782 original size:19 final size:19
Alignment explanation
Indices: 2206704--2206780 Score: 100
Period size: 19 Copynumber: 4.1 Consensus size: 19
2206694 TATGCATTGG
*
2206704 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
* *
2206723 GCTATGAATCTGACAGTAA
1 GCTATGAATCTGAAAATAA
**
2206742 GCTATGAGCCTGAAAATAA
1 GCTATGAATCTGAAAATAA
*
2206761 GTTATGAATCTGAAAATAA
1 GCTATGAATCTGAAAATAA
2206780 G
1 G
2206781 TTCTGATTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.27
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:2206799 original size:20 final size:19
Alignment explanation
Indices: 2206715--2206795 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 19
2206705 CTATGAATTT
* *
2206715 GAAAATAAGCTATGAATCT
1 GAAAATAAGTTATGAATCA
* * * ** *
2206734 GACAGTAAGCTATGAGCCT
1 GAAAATAAGTTATGAATCA
*
2206753 GAAAATAAGTTATGAATCT
1 GAAAATAAGTTATGAATCA
* *
2206772 GAAAATAAGTTCTGATTCA
1 GAAAATAAGTTATGAATCA
2206791 GAAAA
1 GAAAA
2206796 ATAAATTTTG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (19 bp):
GAAAATAAGTTATGAATCA
Found at i:2206852 original size:12 final size:13
Alignment explanation
Indices: 2206825--2206883 Score: 52
Period size: 12 Copynumber: 4.7 Consensus size: 13
2206815 AATATTTTAT
*
2206825 TATGAACATGGAA
1 TATGAAAATGGAA
2206838 TATGAAAAT-GAA
1 TATGAAAATGGAA
2206850 TAT-ATAAAT-GAA
1 TATGA-AAATGGAA
* *
2206862 TATCAAATTGGAA
1 TATGAAAATGGAA
*
2206875 AATGAAAAT
1 TATGAAAAT
2206884 AAAATAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 1 0.03
12 19 0.50
13 18 0.47
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.27
Consensus pattern (13 bp):
TATGAAAATGGAA
Found at i:2209690 original size:21 final size:21
Alignment explanation
Indices: 2209652--2209691 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2209642 ATGATTAGGA
*
2209652 TTTAAGGTTTATAATTTAGAG
1 TTTAAGGTTTAGAATTTAGAG
* *
2209673 TTTATGGTTTAGAGTTTAG
1 TTTAAGGTTTAGAATTTAG
2209692 GGTCTAGGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTAAGGTTTAGAATTTAGAG
Found at i:2211545 original size:21 final size:22
Alignment explanation
Indices: 2211507--2211549 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2211497 ATTGTCATAG
*
2211507 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
2211529 GGGAACCGA-TACCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
2211550 ATACTGCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTACA
Found at i:2212478 original size:65 final size:65
Alignment explanation
Indices: 2212346--2212553 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 65
2212336 TGCACTAAGA
* * *
2212346 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGTCTGAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGATT
*
2212410 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATTAAA-A-CCTGAGTGCATCGATGCATGGC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA--AAATAGCCTGAGTGCATCGATGCATGG-
2212473 A-T
63 ATT
** * *
2212475 GTGCATCGATGCATAAAATGCATTCGATG--TTCAATTTATTCATTG-GTGCATCGATGCATGGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATA-GC-CTGAGTGCATCGATGCATGGA
2212537 TT
64 TT
*
2212539 GGTGCATCGGTGCAT
1 -GTGCATCGATGCAT
2212554 CCATTTGAAA
Statistics
Matches: 126, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 5 0.04
64 45 0.36
65 69 0.55
66 2 0.02
67 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGATT
Found at i:2212541 original size:20 final size:20
Alignment explanation
Indices: 2212516--2212553 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2212506 CAATTTATTC
2212516 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2212536 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2212554 CCATTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2213952 original size:2 final size:2
Alignment explanation
Indices: 2213947--2213980 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2213937 TGTAAGCGCG
*
2213947 CA CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2213981 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2215223 original size:30 final size:30
Alignment explanation
Indices: 2215183--2215248 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2215173 AGAACCGATA
* * * *
2215183 GAACCGGCTGAGAACCGATAAAACAGGGGT
1 GAACCAGCTGAAAACAGACAAAACAGGGGT
* *
2215213 GAACCAGCTGAAAACAGACAAAACCGGTGT
1 GAACCAGCTGAAAACAGACAAAACAGGGGT
2215243 GAACCA
1 GAACCA
2215249 TCGGTTCTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (30 bp):
GAACCAGCTGAAAACAGACAAAACAGGGGT
Found at i:2215505 original size:24 final size:25
Alignment explanation
Indices: 2215467--2215513 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
2215457 AACTCAAAAA
2215467 AAAATTAGAAGCTCGATTGAAGCCT
1 AAAATTAGAAGCTCGATTGAAGCCT
*
2215492 AAAATTCG-AGCTCGATTGAAGC
1 AAAATTAGAAGCTCGATTGAAGC
2215514 GAAAGAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGCCT
Found at i:2216292 original size:9 final size:9
Alignment explanation
Indices: 2216278--2216307 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2216268 AAAAATGATT
2216278 TTTTTTTCA
1 TTTTTTTCA
2216287 -TTTTTTCA
1 TTTTTTTCA
2216295 TTTTTTTCA
1 TTTTTTTCA
2216304 TTTT
1 TTTT
2216308 ATTTTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:2223756 original size:2 final size:2
Alignment explanation
Indices: 2223749--2223804 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
2223739 TAATCAAACT
2223749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2223791 TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA T
2223805 GAACTATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2225534 original size:11 final size:11
Alignment explanation
Indices: 2225515--2225546 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2225505 GATACACTTT
*
2225515 AAAATTAAAAC
1 AAAAATAAAAC
2225526 AAAAATAAAAC
1 AAAAATAAAAC
2225537 AAAAATAAAA
1 AAAAATAAAA
2225547 TGTATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:2225619 original size:30 final size:29
Alignment explanation
Indices: 2225540--2225640 Score: 81
Period size: 29 Copynumber: 3.7 Consensus size: 29
2225530 ATAAAACAAA
* *
2225540 AATAAAATGTAT-TTT--TTAAAATTAA-
1 AATAAAATATATATTTAATTAAAAATAAG
* *
2225565 AATAATATATATATATTAAATAAAAATAAG
1 AATAAAATATATAT-TTAATTAAAAATAAG
*
2225595 AATAAAATATATATTT-ATGTTAAAATAAG
1 AATAAAATATATATTTAAT-TAAAAATAAG
*
2225624 GAT-AAAT-TATATTTAAT
1 AATAAAATATATATTTAAT
2225641 AATTTAAGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
25 10 0.16
26 1 0.02
27 9 0.15
28 7 0.11
29 21 0.34
30 13 0.21
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
AATAAAATATATATTTAATTAAAAATAAG
Found at i:2225693 original size:30 final size:30
Alignment explanation
Indices: 2225631--2225695 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
2225621 AAGGATAAAT
* *
2225631 TATATTTAATAATTTAAGGTAAGACTAGAA
1 TATATCTAATAATTTAAGGTAAGAATAGAA
** **
2225661 TATATCTAATAATTTAATTTAAGAATCTAA
1 TATATCTAATAATTTAAGGTAAGAATAGAA
2225691 TATAT
1 TATAT
2225696 GTAGTAAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (30 bp):
TATATCTAATAATTTAAGGTAAGAATAGAA
Found at i:2225801 original size:28 final size:28
Alignment explanation
Indices: 2225700--2225812 Score: 127
Period size: 28 Copynumber: 3.9 Consensus size: 28
2225690 ATATATGTAG
2225700 TAAGTTAAAATAAAAATAAGATATATTTTT
1 TAAGTTAAAATAAAAATAA-A-ATATTTTT
* *
2225730 AAACGTTAAGATAAAAAATAAAATATATTTT
1 TAA-GTTAAAAT-AAAAATAAAATAT-TTTT
** * *
2225761 TAAGTTATGATAAGATTAAAATATTTTT
1 TAAGTTAAAATAAAAATAAAATATTTTT
2225789 TAAGTTAAAATAAAAATAAAATAT
1 TAAGTTAAAATAAAAATAAAATAT
2225813 AATTTCAGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 24 0.34
29 11 0.16
30 13 0.19
31 14 0.20
32 8 0.11
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (28 bp):
TAAGTTAAAATAAAAATAAAATATTTTT
Found at i:2225838 original size:57 final size:59
Alignment explanation
Indices: 2225722--2225840 Score: 143
Period size: 57 Copynumber: 2.1 Consensus size: 59
2225712 AAAATAAGAT
* * * * * *
2225722 ATATTTTTAAACGTTAAGATAAAAAATAAAATATATTTTTAAGTTATGATAAGATTAAA
1 ATATTTTTAAACGTTAAAATAAAAAATAAAATATAATTTCAAGTTAAGAAAAGAATAAA
* * *
2225781 ATATTTTTTAA-GTTAAAAT-AAAAATAAAATATAATTTCAGGTTAAGAAAATAATAAA
1 ATATTTTTAAACGTTAAAATAAAAAATAAAATATAATTTCAAGTTAAGAAAAGAATAAA
2225838 ATA
1 ATA
2225841 GATTTAATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
57 34 0.67
58 7 0.14
59 10 0.20
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (59 bp):
ATATTTTTAAACGTTAAAATAAAAAATAAAATATAATTTCAAGTTAAGAAAAGAATAAA
Found at i:2231213 original size:2 final size:2
Alignment explanation
Indices: 2231206--2231236 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2231196 ACCTAATTGA
2231206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2231237 AAAAACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2231289 original size:40 final size:39
Alignment explanation
Indices: 2231228--2231313 Score: 154
Period size: 40 Copynumber: 2.2 Consensus size: 39
2231218 ATATATATAT
2231228 ATATATATAAAAAACATGTAGCATAACCATTATTCTTAA
1 ATATATATAAAAAACATGTAGCATAACCATTATTCTTAA
*
2231267 ATATATATAAAGAAACATGTAGCATAATCATTATTCTTAA
1 ATATATATAAA-AAACATGTAGCATAACCATTATTCTTAA
2231307 ATATATA
1 ATATATA
2231314 AATGTCAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 11 0.24
40 34 0.76
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (39 bp):
ATATATATAAAAAACATGTAGCATAACCATTATTCTTAA
Found at i:2233046 original size:3 final size:3
Alignment explanation
Indices: 2233040--2233102 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
2233030 TTATCCATTT
* * *
2233040 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
2233088 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
2233103 AAAAATAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2234693 original size:23 final size:24
Alignment explanation
Indices: 2234649--2234710 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
2234639 CATTTTGTGA
*
2234649 TATTTCTAAATA-AATAAATATTT
1 TATTTATAAATATAATAAATATTT
*
2234672 TATTTATAAATATAA-AATTATTT
1 TATTTATAAATATAATAAATATTT
*
2234695 T-TTTCATAATTATAAT
1 TATTT-ATAAATATAAT
2234711 TTTGAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 3 0.09
23 28 0.85
24 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTATAAATATAATAAATATTT
Found at i:2236837 original size:14 final size:14
Alignment explanation
Indices: 2236804--2236856 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
2236794 ATTTTAAATA
*
2236804 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
2236818 -TTTACATTTGCCT
1 ATTTACATTTGCAT
2236831 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
2236846 CTTTGCATTTG
1 ATTTACATTTG
2236857 TATTTTTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 11 0.34
14 10 0.31
15 11 0.34
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:2236876 original size:20 final size:20
Alignment explanation
Indices: 2236847--2236885 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2236837 ATTTGGCATC
*
2236847 TTTGCATTTGTATTTTTATG
1 TTTGCATTTGTATTCTTATG
*
2236867 TTTGCTTTTGTATTCTTAT
1 TTTGCATTTGTATTCTTAT
2236886 TATTACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (20 bp):
TTTGCATTTGTATTCTTATG
Found at i:2239837 original size:2 final size:2
Alignment explanation
Indices: 2239830--2239886 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
2239820 CCTTTAATTA
2239830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2239871 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2239887 CATTTGTTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2240234 original size:16 final size:16
Alignment explanation
Indices: 2240215--2240251 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2240205 GGAAACTGAA
2240215 AAAAAGAAAAAAAAGG
1 AAAAAGAAAAAAAAGG
*
2240231 AAAAAGGAAAAAAAGG
1 AAAAAGAAAAAAAAGG
*
2240247 GAAAA
1 AAAAA
2240252 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGG
Found at i:2240234 original size:17 final size:17
Alignment explanation
Indices: 2240214--2240251 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2240204 GGGAAACTGA
2240214 AAAAAAGAAAAAAAAGG
1 AAAAAAGAAAAAAAAGG
* *
2240231 AAAAAGGAAAAAAAGGG
1 AAAAAAGAAAAAAAAGG
2240248 AAAA
1 AAAA
2240252 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGG
Found at i:2240240 original size:25 final size:26
Alignment explanation
Indices: 2240194--2240245 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
2240184 AAAGAAGAAG
* **
2240194 GAAAAAAAAGGGGAAACTGAAAAAAA
1 GAAAAAAAAGGGAAAAAGGAAAAAAA
2240220 GAAAAAAAA-GGAAAAAGGAAAAAAA
1 GAAAAAAAAGGGAAAAAGGAAAAAAA
2240245 G
1 G
2240246 GGAAAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (26 bp):
GAAAAAAAAGGGAAAAAGGAAAAAAA
Found at i:2242749 original size:115 final size:115
Alignment explanation
Indices: 2242498--2242728 Score: 358
Period size: 115 Copynumber: 2.0 Consensus size: 115
2242488 AAGTGTCATG
2242498 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * **
2242563 TGGTTTGGTATGAACCCCAAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGGTTCGGTAGGAACCACAAAAACCAATCATTGGAATTAAAAGATGAAAC
2242613 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
2242678 TGGTTCGGTAGGAACCAC-AGAGCCAATCATTGGAATTAAAAGAT-AAAC
66 TGGTTCGGTAGGAACCACAAAAACCAATCATTGGAATTAAAAGATGAAAC
2242726 TGC
1 TGC
2242729 ATGATCGTCT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 5 0.05
114 21 0.20
115 80 0.75
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTCGGTAGGAACCACAAAAACCAATCATTGGAATTAAAAGATGAAAC
Found at i:2244939 original size:54 final size:54
Alignment explanation
Indices: 2244787--2244952 Score: 242
Period size: 54 Copynumber: 3.1 Consensus size: 54
2244777 CAATGATTGA
* *
2244787 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTAC
* *
2244841 GAACATCTGAGTAGAAACTACAGGAAAAGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTAC
* * ****
2244895 GAACATCTGAGCAGAAGCCACAGGAAATGATGAATGCACAGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTAC
2244949 GAAC
1 GAAC
2244953 CTGCTATTCT
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 100 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTAC
Found at i:2245942 original size:113 final size:113
Alignment explanation
Indices: 2245744--2246415 Score: 819
Period size: 113 Copynumber: 6.0 Consensus size: 113
2245734 TAGCAAAGAT
2245744 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
2245809 AGAAGGAAGAAGAAATTCATAATGAGAA-AATTTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTTTGC
2245857 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
2245922 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * ** *
2245970 TTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA--C-TCATC
* *
2246035 TGAAGAAGGAAGAAGAAATTCATAATCAGAAGAATTTGTTCAACCTTTTGC
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * ****
2246086 TCAAATCTATCACTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
2246151 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * * *
2246199 TCAAATCTATCACTTGATGGATCAGTTTTTCCAG-AGAAGTTCATAATGAGAATAACTCATCT--
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * ** *
2246261 A-AA-GAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
* ** * * * * *
2246308 AT-AATTTTATCA---CA-GCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 -TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* * ** *
2246368 AAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
2246416 AATGACTCTA
Statistics
Matches: 497, Mismatches: 49, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
105 12 0.02
106 26 0.05
108 31 0.06
109 20 0.04
110 40 0.08
112 29 0.06
113 236 0.47
114 3 0.01
115 1 0.00
116 99 0.20
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2246149 original size:229 final size:225
Alignment explanation
Indices: 2245744--2246415 Score: 832
Period size: 229 Copynumber: 3.0 Consensus size: 225
2245734 TAGCAAAGAT
* * *
2245744 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATTTGATGGATCAGCTTTTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGA
* *
2245809 AGAAGGAAGAAGAAATTCATAATGAGAA-AATTTTGTTCAACCTTTTGCTCAAATCCATCATTTG
65 AGAAGGAAGAAGAAATTCATAATGAGAAGAA-TTTGTTCAACCTTTTGCTCAAATCTATCACTTG
2245873 ATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
129 ATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
2245938 TCATAATGAGAAGAATTTGTTCAACCTTTTGT
194 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
2245970 TTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATTCATCATTTGATGGATCAGCTTTTCCAGG-AGAGTTCATAATGAGAAGAA--C-TCATC
*
2246035 TGAAGAAGGAAGAAGAAATTCATAATCAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACT
62 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACT
****
2246100 TGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
127 TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
2246165 GTTCATAATGAGAAGAATTTGTTCAA-CTTTTGGC
192 GTTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * *
2246199 TCAAA-TCTATCACTTGATGGATCAGTTTTTCCA-GAGAAGTTCATAATGAGAATAACTCATCT-
1 TCAAATTC-ATCATTTGATGGATCAGCTTTTCCAGGAG-AGTTCATAATGAGAAGAACTCATCTG
* ** * * *
2246261 -A-AA-GAAGAA-AAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGCAT-AATTTTATCAC
64 AAGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACC-TTTTGC-TCAAATCTATCAC
* * * * * *
2246321 ---A-GCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAGAAGA
126 TTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
** *
2246382 AGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
191 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
2246416 AATGACTCTA
Statistics
Matches: 391, Mismatches: 43, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
218 76 0.19
219 6 0.02
220 3 0.01
221 28 0.07
222 17 0.04
223 2 0.01
225 6 0.02
226 48 0.12
227 2 0.01
228 26 0.07
229 175 0.45
230 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (225 bp):
TCAAATTCATCATTTGATGGATCAGCTTTTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGAT
GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2246630 original size:3 final size:3
Alignment explanation
Indices: 2246624--2246689 Score: 87
Period size: 3 Copynumber: 21.3 Consensus size: 3
2246614 TTTTTTACCC
* * *
2246624 ATT ATT ATT ATT ATT ATT ACT ATA ATT ATT ATT ATT ATA ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
2246673 ATAT ATT ATT ATT ATT A
1 AT-T ATT ATT ATT ATT A
2246690 AAAAATAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 49 0.88
4 7 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:2248296 original size:23 final size:24
Alignment explanation
Indices: 2248264--2248311 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2248254 CATTTTCTGA
*
2248264 TATTTCTAAATAAATAAA-TATTT
1 TATTTATAAATAAATAAATTATTT
*
2248287 TATTTATAAATATATAAATTATTT
1 TATTTATAAATAAATAAATTATTT
2248311 T
1 T
2248312 TTCTCATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTATAAATAAATAAATTATTT
Found at i:2254811 original size:16 final size:16
Alignment explanation
Indices: 2254790--2254825 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2254780 ACAAGCAACA
2254790 AGCATCGATCTTAACG
1 AGCATCGATCTTAACG
2254806 AGCATCGATCTTAACG
1 AGCATCGATCTTAACG
2254822 AGCA
1 AGCA
2254826 ATGAGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (16 bp):
AGCATCGATCTTAACG
Found at i:2254889 original size:22 final size:22
Alignment explanation
Indices: 2254837--2254911 Score: 105
Period size: 22 Copynumber: 3.3 Consensus size: 22
2254827 TGAGGTGAAC
* *
2254837 AACGAGCATCGAGCTTAATGAGT
1 AACGAGCATCGAACTT-ACGAGT
*
2254860 AAACGAGCATCAAACTTACGAGT
1 -AACGAGCATCGAACTTACGAGT
2254883 AACGAGCATCGAACTTACGAGT
1 AACGAGCATCGAACTTACGAGT
2254905 AACGAGC
1 AACGAGC
2254912 TTAACAAGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 28 0.60
23 5 0.11
24 14 0.30
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (22 bp):
AACGAGCATCGAACTTACGAGT
Found at i:2258093 original size:22 final size:22
Alignment explanation
Indices: 2258065--2258110 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2258055 TTTGAATCCC
2258065 TGAACTTGTTTAACAGATCTAT
1 TGAACTTGTTTAACAGATCTAT
2258087 TGAACTTGTTTAACAGATCTAT
1 TGAACTTGTTTAACAGATCTAT
2258109 TG
1 TG
2258111 TCCATCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (22 bp):
TGAACTTGTTTAACAGATCTAT
Found at i:2258729 original size:21 final size:21
Alignment explanation
Indices: 2258705--2258749 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2258695 ATTTTATAAA
*
2258705 AAAATTAA-AATATTAAATATT
1 AAAATTAATAAT-TTAAATACT
2258726 AAAATTAATAATTTAAATACT
1 AAAATTAATAATTTAAATACT
2258747 AAA
1 AAA
2258750 CACGTAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATTAATAATTTAAATACT
Found at i:2259331 original size:22 final size:22
Alignment explanation
Indices: 2259303--2259347 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2259293 TCGTGGCGTT
2259303 TGTTCACAAAAACGCTGCTAAA
1 TGTTCACAAAAACGCTGCTAAA
2259325 TGTTCACAAAAACGCTGCTAAA
1 TGTTCACAAAAACGCTGCTAAA
2259347 T
1 T
2259348 CTTTAGCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (22 bp):
TGTTCACAAAAACGCTGCTAAA
Found at i:2269270 original size:63 final size:62
Alignment explanation
Indices: 2269201--2269721 Score: 462
Period size: 63 Copynumber: 8.3 Consensus size: 62
2269191 TCCCACGATC
* *
2269201 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGTTGCGATAAAATCTCTTAAAA
1 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGG-TGCGACAAAATCTCGTAAAA
* * * ** * ** *
2269264 GAAAGCTCTTGTCGAGC-AGCAACAATGATGATTTCGCACTGTGGG-G-GATGAAATCCCGCGAC
1 GAAAGCTCTTGTCGAGCGA-CGAC-A--ACGATTTCGCACAGTGGGTGCGACAAAATCTCGTAAA
*
2269326 C
62 A
** *
2269327 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGCCACGACAAAATCTCTTAAAA
1 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGG-TGCGACAAAATCTCGTAAAA
* * * * ** * ** **
2269390 GAAAGCTCTTGTCGAGCAGCAACGACGATGATTTCTCACTGTGGG-G-GATGAAATCCCGCGATC
1 GAAAGCTCTTGTCGAGC-G--ACGACAACGATTTCGCACAGTGGGTGCGACAAAATCTCGTAAAA
*
2269453 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAA
1 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGG-TGCGACAAAATCTCGTAAAA
* * * *
2269516 GAACGCTCTTGTCCAGCGACGACGACGATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAA
1 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGG-TGCGACAAAATCTCGTAAAA
* * * ** * ** **
2269579 GAAAGCTCTTGTCGAGCAGCAACGACGATGATTTCGCACTGTGGG-G-GATGAAATCCCGCGATC
1 GAAAGCTCTTGTCGAGC-G--ACGACAACGATTTCGCACAGTGGGTGCGACAAAATCTCGTAAAA
* *
2269642 GAAAGCTTTTGTCGAGCGACGACAACGATTTCGCACAGTGGGATGAGACAAAATCTCGTAAAA
1 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGG-TGCGACAAAATCTCGTAAAA
*
2269705 GAAAGATCTTGTCGAGC
1 GAAAGCTCTTGTCGAGC
2269722 AGCAACGACG
Statistics
Matches: 363, Mismatches: 75, Indels: 40
0.76 0.16 0.08
Matches are distributed among these distances:
60 57 0.16
62 6 0.02
63 236 0.65
64 6 0.02
66 58 0.16
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (62 bp):
GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGTGCGACAAAATCTCGTAAAA
Found at i:2269388 original size:126 final size:126
Alignment explanation
Indices: 2269163--2269528 Score: 633
Period size: 126 Copynumber: 2.9 Consensus size: 126
2269153 AACCACCAGG
*
2269163 TGATGATTTCCCACTGTGGGGGATGAAATCCCACGATCGAAAGCTCTTGTCGAGCGACGACAACG
1 TGATGATTTCCCACTGTGGGGGATGAAATCCCGCGATCGAAAGCTCTTGTCGAGCGACGACAACG
* *
2269228 ATTTCGCACAGTGGGTTGCGATAAAATCTCTTAAAAGAAAGCTCTTGTCGAGCAGCAACAA
66 ATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAAGAAAGCTCTTGTCGAGCAGCAACAA
* *
2269289 TGATGATTTCGCACTGTGGGGGATGAAATCCCGCGACCGAAAGCTCTTGTCGAGCGACGACAACG
1 TGATGATTTCCCACTGTGGGGGATGAAATCCCGCGATCGAAAGCTCTTGTCGAGCGACGACAACG
** *
2269354 ATTTCGCACAGTGGGCCACGACAAAATCTCTTAAAAGAAAGCTCTTGTCGAGCAGCAACGA
66 ATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAAGAAAGCTCTTGTCGAGCAGCAACAA
* *
2269415 CGATGATTTCTCACTGTGGGGGATGAAATCCCGCGATCGAAAGCTCTTGTCGAGCGACGACAACG
1 TGATGATTTCCCACTGTGGGGGATGAAATCCCGCGATCGAAAGCTCTTGTCGAGCGACGACAACG
*
2269480 ATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAAGAACGCTCTTGTC
66 ATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAAGAAAGCTCTTGTC
2269529 CAGCGACGAC
Statistics
Matches: 226, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 226 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (126 bp):
TGATGATTTCCCACTGTGGGGGATGAAATCCCGCGATCGAAAGCTCTTGTCGAGCGACGACAACG
ATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAAGAAAGCTCTTGTCGAGCAGCAACAA
Found at i:2269732 original size:189 final size:189
Alignment explanation
Indices: 2269327--2269739 Score: 691
Period size: 189 Copynumber: 2.2 Consensus size: 189
2269317 TCCCGCGACC
*
2269327 GAAAGCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGCCACGACAAAATCTCTTAAAAGA
1 GAAAGCTCTTGTCGAGCGACGACGACGATTTCGCACAGTGGGCCACGACAAAATCTCTTAAAAGA
*
2269392 AAGCTCTTGTCGAGCAGCAACGACGATGATTTCTCACTGTGGGGGATGAAATCCCGCGATCGAAA
66 AAGCTCTTGTCGAGCAGCAACGACGATGATTTCGCACTGTGGGGGATGAAATCCCGCGATCGAAA
* * *
2269457 GCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAA
131 GCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGATGAGACAAAATCTCGTAAAA
* * **
2269516 GAACGCTCTTGTCCAGCGACGACGACGATTTCGCACAGTGGGCTGCGACAAAATCTCTTAAAAGA
1 GAAAGCTCTTGTCGAGCGACGACGACGATTTCGCACAGTGGGCCACGACAAAATCTCTTAAAAGA
2269581 AAGCTCTTGTCGAGCAGCAACGACGATGATTTCGCACTGTGGGGGATGAAATCCCGCGATCGAAA
66 AAGCTCTTGTCGAGCAGCAACGACGATGATTTCGCACTGTGGGGGATGAAATCCCGCGATCGAAA
*
2269646 GCTTTTGTCGAGCGACGACAACGATTTCGCACAGTGGGATGAGACAAAATCTCGTAAAA
131 GCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGATGAGACAAAATCTCGTAAAA
* *
2269705 GAAAGATCTTGTCGAGCAGCAACGACGATGATTTC
1 GAAAGCTCTTGTCGAGC-G--ACGACGACGATTTC
2269740 CCAACGTGGA
Statistics
Matches: 207, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
189 193 0.93
190 1 0.00
192 13 0.06
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (189 bp):
GAAAGCTCTTGTCGAGCGACGACGACGATTTCGCACAGTGGGCCACGACAAAATCTCTTAAAAGA
AAGCTCTTGTCGAGCAGCAACGACGATGATTTCGCACTGTGGGGGATGAAATCCCGCGATCGAAA
GCTCTTGTCGAGCGACGACAACGATTTCGCACAGTGGGATGAGACAAAATCTCGTAAAA
Found at i:2271623 original size:15 final size:15
Alignment explanation
Indices: 2271603--2271637 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2271593 TGAGAATTTC
*
2271603 TATATTGATGTATGA
1 TATATTGATATATGA
2271618 TATATTGATATATGA
1 TATATTGATATATGA
2271633 TATAT
1 TATAT
2271638 GAGAGTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (15 bp):
TATATTGATATATGA
Found at i:2272517 original size:2 final size:2
Alignment explanation
Indices: 2272512--2272536 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2272502 TTATAATGGG
2272512 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2272537 CACCCAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2272754 original size:2 final size:2
Alignment explanation
Indices: 2272707--2272734 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2272697 TATACTTTTA
2272707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2272735 TTTCTTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2290971 original size:30 final size:28
Alignment explanation
Indices: 2290937--2291303 Score: 231
Period size: 30 Copynumber: 12.6 Consensus size: 28
2290927 ATTTTACATT
*
2290937 TTAACATTAAAAATATATTTTACTTTTATA
1 TTAAC-TTAAAAATATATTTTA-TTTTATC
* *
2290967 TTAACTTATTAAATATATTTTATTTTGTC
1 TTAACTTA-AAAATATATTTTATTTTATC
* *
2290996 TTAACCTAAAAATATATTTTATTCTTATT
1 TTAACTTAAAAATATATTTTATT-TTATC
*
2291025 TTAAATTAAAAATATATTTTAGTCTTTATC
1 TTAACTTAAAAATATATTTTA-T-TTTATC
*
2291055 TTAACTTAAAAATATATTTTATTCTTAAC
1 TTAACTTAAAAATATATTTTATT-TTATC
* * * *
2291084 TTAACTTATTACATAAATTATATTCTTAAT-
1 TTAACTTA-AAAATATATTTTATT-TT-ATC
* ** * * *
2291114 TTAAATTGTTAAACATATTCTATTCTTACC
1 TTAACTT-AAAAATATATTTTATT-TTATC
* * * * *
2291144 TTAAATTATTAAATATAATTAATTCTTATT
1 TTAACTTA-AAAATATATTTTATT-TTATC
* * *
2291174 TTAACTTAAACATATCTTTTATTCCTATC
1 TTAACTTAAAAATATATTTTATT-TTATC
*
2291203 TTAACTTAAAAAATATATTTTTATTTTAGC
1 TTAACTT-AAAAATATA-TTTTATTTTATC
*
2291233 -T-AC--AAAAATATATTTTATTTTTATA
1 TTAACTTAAAAATATATTTTA-TTTTATC
* * *
2291258 TTAACTACAAAAATGTATTATATTTTTATC
1 TTAACT-TAAAAATATATTTTA-TTTTATC
* *
2291288 TTAAATTTAAAATATA
1 TTAACTTAAAAATATA
2291304 GTCATAATAA
Statistics
Matches: 267, Mismatches: 52, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
24 5 0.02
25 14 0.05
26 1 0.00
27 2 0.01
28 17 0.06
29 80 0.30
30 139 0.52
31 9 0.03
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (28 bp):
TTAACTTAAAAATATATTTTATTTTATC
Found at i:2291068 original size:59 final size:59
Alignment explanation
Indices: 2290937--2291303 Score: 261
Period size: 59 Copynumber: 6.3 Consensus size: 59
2290927 ATTTTACATT
* * *
2290937 TTAACATTAAAAATATATTTTACTT-TTATATTAACTTATTAAATATATTTTAT-TTTGTC
1 TTAAC-TTAAAAATATATTTTA-TTCTTATCTTAACTTATAAAATATATTTTATCTTTATC
* * *
2290996 TTAACCTAAAAATATATTTTATTCTTATTTTAAATTA-AAAATATATTTTAGTCTTTATC
1 TTAACTTAAAAATATATTTTATTCTTATCTTAACTTATAAAATATATTTTA-TCTTTATC
* * * * * *
2291055 TTAACTTAAAAATATATTTTATTCTTAACTTAACTTATTACATAAATTATATTCTTAAT-
1 TTAACTTAAAAATATATTTTATTCTTATCTTAACTTATAAAATATATTTTA-TCTTTATC
* ** * * * * * * * *
2291114 TTAAATTGTTAAACATATTCTATTCTTACCTTAAATTATTAAATATAATTAAT-TCTTATT
1 TTAACTT-AAAAATATATTTTATTCTTATCTTAACTTATAAAATATATTTTATCT-TTATC
* * * * *
2291174 TTAACTTAAACATATCTTTTATTCCTATCTTAACTTAAAAAATATATTTTTAT-TTTAGC
1 TTAACTTAAAAATATATTTTATTCTTATCTTAACTTATAAAATATA-TTTTATCTTTATC
* * * * * *
2291233 -T-AC--AAAAATATATTTTATTTTTATATTAAC-TACAAAAATGTATTATATTTTTATC
1 TTAACTTAAAAATATATTTTATTCTTATCTTAACTTA-TAAAATATATTTTATCTTTATC
* *
2291288 TTAAATTTAAAATATA
1 TTAACTTAAAAATATA
2291304 GTCATAATAA
Statistics
Matches: 240, Mismatches: 54, Indels: 28
0.75 0.17 0.09
Matches are distributed among these distances:
54 7 0.03
55 35 0.15
56 1 0.00
57 17 0.07
58 29 0.12
59 92 0.38
60 59 0.25
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (59 bp):
TTAACTTAAAAATATATTTTATTCTTATCTTAACTTATAAAATATATTTTATCTTTATC
Found at i:2291413 original size:29 final size:30
Alignment explanation
Indices: 2291335--2291442 Score: 123
Period size: 30 Copynumber: 3.6 Consensus size: 30
2291325 TTAAGTTGAG
* * * *
2291335 ATAAAAATAAATTATATTTTTTAATTTAAG
1 ATAATAATAAAATATATTTTTTAAATTAAA
*
2291365 ATAATATTAAAATATATTTTTTAAATTAAA
1 ATAATAATAAAATATATTTTTTAAATTAAA
*
2291395 ATAAGAAT-AAA-ATATTTTTTAAAGTTACAA
1 ATAATAATAAAATATATTTTTTAAA-TTA-AA
2291425 A-AATAATAAAATATATTT
1 ATAATAATAAAATATATTT
2291443 AAAAAGTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 12 0.18
29 11 0.17
30 37 0.56
31 6 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAATAATAAAATATATTTTTTAAATTAAA
Found at i:2291443 original size:28 final size:28
Alignment explanation
Indices: 2291378--2291445 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
2291368 ATATTAAAAT
*
2291378 ATATTTTTTAAATTAAAATAAGAATAAA
1 ATATTATTTAAATTAAAATAAGAATAAA
* *
2291406 ATATTTTTTAAAGTTACAAA-AATAATAAA
1 ATATTATTTAAA-TTA-AAATAAGAATAAA
2291435 ATA-TATTTAAA
1 ATATTATTTAAA
2291446 AAGTGAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 19 0.53
29 14 0.39
30 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (28 bp):
ATATTATTTAAATTAAAATAAGAATAAA
Found at i:2293337 original size:18 final size:18
Alignment explanation
Indices: 2293314--2293348 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2293304 AGGGATATAC
*
2293314 AGTGGTCTTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
*
2293332 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
2293349 AATTTCAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:2293988 original size:21 final size:21
Alignment explanation
Indices: 2293962--2294001 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2293952 CGATATTTCT
2293962 ATGCAT-CGATGCACTGTAGTA
1 ATGCATAC-ATGCACTGTAGTA
2293983 ATGCATACATGCACTGTAG
1 ATGCATACATGCACTGTAG
2294002 CACTATTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
ATGCATACATGCACTGTAGTA
Found at i:2299842 original size:23 final size:23
Alignment explanation
Indices: 2299816--2299893 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
2299806 CACCACAACT
2299816 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
2299839 CATATAATTGCACCGGAGTGACG
1 CATATAATTGCACCGAAGTGCCA
* *
2299862 CGTAGAATTGCACC-ATAGTGCCA
1 CATATAATTGCACCGA-AGTGCCA
*
2299885 TATAATAAT
1 CAT-ATAAT
2299894 ATCCATAAGA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
23 38 0.90
24 4 0.10
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:2300085 original size:103 final size:103
Alignment explanation
Indices: 2299904--2300220 Score: 589
Period size: 103 Copynumber: 3.1 Consensus size: 103
2299894 ATCCATAAGA
* * *
2299904 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
*
2299969 TCACACATATTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
*
2300007 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTTACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
2300072 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
2300110 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
2300175 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
2300213 ACCACATA
1 ACCACATA
2300221 GACCCTCGAC
Statistics
Matches: 208, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
Found at i:2301090 original size:64 final size:64
Alignment explanation
Indices: 2300957--2301113 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 64
2300947 TAATGAAGGT
* * * ** *
2300957 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
* *
2301021 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATT-TATT-TTAAA-A
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGT-TTGT-TTATTAAAGA
2301083 G
64 G
* * * *
2301084 AGTGCATCAATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
2301114 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
63 2 0.03
64 72 0.92
65 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
Found at i:2310816 original size:11 final size:11
Alignment explanation
Indices: 2310800--2310828 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2310790 ACAGAAATGG
2310800 AAATGAATATA
1 AAATGAATATA
2310811 AAATGAATATA
1 AAATGAATATA
2310822 AAATGAA
1 AAATGAA
2310829 ATTGAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (11 bp):
AAATGAATATA
Found at i:2318800 original size:23 final size:23
Alignment explanation
Indices: 2318769--2318834 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
2318759 AGATAGAGAA
*
2318769 AAACATGTCATAAAAGCATATAT
1 AAACATGTCATAAAAGCATAGAT
* *
2318792 AAACGTGTCATAAATGCATAGAT
1 AAACATGTCATAAAAGCATAGAT
* *
2318815 AAACATGTCACAAAAACATA
1 AAACATGTCATAAAAGCATA
2318835 ATTATTCTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.23
Consensus pattern (23 bp):
AAACATGTCATAAAAGCATAGAT
Found at i:2318886 original size:15 final size:15
Alignment explanation
Indices: 2318866--2318894 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2318856 AAAAAGACAG
2318866 AGAAAAGACAATCAT
1 AGAAAAGACAATCAT
2318881 AGAAAAGACAATCA
1 AGAAAAGACAATCA
2318895 ACGATTGACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (15 bp):
AGAAAAGACAATCAT
Found at i:2320011 original size:90 final size:88
Alignment explanation
Indices: 2319858--2320021 Score: 238
Period size: 90 Copynumber: 1.8 Consensus size: 88
2319848 TGCAGAGCTA
*
2319858 AATGCACGTTTATGATGTCTACCGCTACGAGTTCAACACAGGCTTAATGACAGAAAACACATAAA
1 AATGCACATTTATGATGTCTACCGCTACGAGTTCAACACAGGCTTAATGACAGAAAACACATAAA
2319923 CACAGAACATAGATACACAACTC
66 CACAGAACATAGATACACAACTC
** ** * * *
2319946 AATGCACATTTATGATGTCTACGACGCTACGAGTTTGACATGGGCTTAATGATAGAAAGCGCATA
1 AATGCACATTTATGATGTCTAC--CGCTACGAGTTCAACACAGGCTTAATGACAGAAAACACATA
2320011 AACACAGAACA
64 AACACAGAACA
2320022 CATGAGTTCG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
88 21 0.32
90 45 0.68
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (88 bp):
AATGCACATTTATGATGTCTACCGCTACGAGTTCAACACAGGCTTAATGACAGAAAACACATAAA
CACAGAACATAGATACACAACTC
Found at i:2327614 original size:27 final size:27
Alignment explanation
Indices: 2327576--2327628 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2327566 TATCTTAATA
*
2327576 AAGTTGCTCGAATCATACCCTGCTATC
1 AAGTTGCTCGAACCATACCCTGCTATC
* *
2327603 AAGTTGTTCGAACCATGCCCTGCTAT
1 AAGTTGCTCGAACCATACCCTGCTAT
2327629 TCTGACACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (27 bp):
AAGTTGCTCGAACCATACCCTGCTATC
Found at i:2327757 original size:27 final size:27
Alignment explanation
Indices: 2327724--2327878 Score: 89
Period size: 27 Copynumber: 6.0 Consensus size: 27
2327714 TTACCTTGAT
*
2327724 CAAGTTG-TTCGAACCATACCTTGTTAC
1 CAAGTTGCTT-GAACCATACCCTGTTAC
*
2327751 CAAGTTGCTTGAACCATGCCCTGTTATC
1 CAAGTTGCTTGAACCATACCCTGTTA-C
** * *
2327779 C---TACCTTG----TTACCCTG--AT
1 CAAGTTGCTTGAACCATACCCTGTTAC
**
2327797 CAAGTTG-TTCGAACCATGTCCTGTTAC
1 CAAGTTGCTT-GAACCATACCCTGTTAC
* * *
2327824 CAAATTGCTTGAACCATGCCCTATTAC
1 CAAGTTGCTTGAACCATACCCTGTTAC
* *
2327851 CAAGTTGTTTGAACCATGCCCTGTTAC
1 CAAGTTGCTTGAACCATACCCTGTTAC
2327878 C
1 C
2327879 CTAACATCTC
Statistics
Matches: 96, Mismatches: 19, Indels: 26
0.68 0.13 0.18
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 2 0.02
21 8 0.08
25 10 0.10
27 68 0.71
28 6 0.06
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (27 bp):
CAAGTTGCTTGAACCATACCCTGTTAC
Found at i:2328125 original size:27 final size:27
Alignment explanation
Indices: 2328057--2328137 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
2328047 GTAGTGTCAG
* *
2328057 AGTAACATGACATGATTTAAGCAACTT
1 AGTAGCATGACATGATTCAAGCAACTT
* ** *
2328084 -GATAGCAGGGTATGATTCGAGCAACTT
1 AG-TAGCATGACATGATTCAAGCAACTT
*
2328111 AGTAGCATGACATGATTCAAACAACTT
1 AGTAGCATGACATGATTCAAGCAACTT
2328138 TATCAGCATA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (27 bp):
AGTAGCATGACATGATTCAAGCAACTT
Found at i:2328454 original size:16 final size:16
Alignment explanation
Indices: 2328433--2328477 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
2328423 TGTATAATTA
2328433 TAAATTAATTAAAAAT
1 TAAATTAATTAAAAAT
*
2328449 TAAATT-ATTTAAAAT
1 TAAATTAATTAAAAAT
*
2328464 AAAATATAATTAAA
1 TAAAT-TAATTAAA
2328478 TTATTTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 12 0.50
16 7 0.29
17 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTAATTAAAAAT
Found at i:2334765 original size:12 final size:12
Alignment explanation
Indices: 2334738--2334771 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2334728 CATCGTCAGG
*
2334738 CACTATTTCACGT
1 CACTA-TTCTCGT
2334751 CACTATTCTCGT
1 CACTATTCTCGT
2334763 CACTATTCT
1 CACTATTCT
2334772 GGTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.21, C:0.32, G:0.06, T:0.41
Consensus pattern (12 bp):
CACTATTCTCGT
Found at i:2335471 original size:3 final size:3
Alignment explanation
Indices: 2335463--2335521 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
2335453 GTAATATTTG
* * **
2335463 TAA TAA TAA TAA TAA TAA TAA TAA T-A TGA -AA TAA TAG TTG TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2335508 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
2335522 TATAGTCTCG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
2 5 0.10
3 43 0.90
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2338705 original size:36 final size:36
Alignment explanation
Indices: 2338665--2338735 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
2338655 TGGTGGCGCT
*
2338665 GGAGGAGGTCTTGGTGGCGGTCTGGGAGGCGGAGCA
1 GGAGGAGGTCTTGGTGGCGGTCTAGGAGGCGGAGCA
* *
2338701 GGAGGAGGTCTTGGTGGCGGTTTAGGAGGTGGAGC
1 GGAGGAGGTCTTGGTGGCGGTCTAGGAGGCGGAGC
2338736 TGGCGGTGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.14, C:0.11, G:0.55, T:0.20
Consensus pattern (36 bp):
GGAGGAGGTCTTGGTGGCGGTCTAGGAGGCGGAGCA
Found at i:2338779 original size:24 final size:24
Alignment explanation
Indices: 2338752--2338828 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
2338742 TGGAGAAGGC
*
2338752 GGAGGTTTCGGAGGTGGTGCTGGT
1 GGAGGTTTCGGAGGCGGTGCTGGT
*** *
2338776 GGAGGAGCCGGAGGCGGTGCAGGT
1 GGAGGTTTCGGAGGCGGTGCTGGT
* * *
2338800 GGTGGTTTCGGAGGCGGCGCTGGC
1 GGAGGTTTCGGAGGCGGTGCTGGT
2338824 GGAGG
1 GGAGG
2338829 AATTGGGGGA
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.10, C:0.14, G:0.57, T:0.18
Consensus pattern (24 bp):
GGAGGTTTCGGAGGCGGTGCTGGT
Found at i:2340314 original size:3 final size:3
Alignment explanation
Indices: 2340306--2340330 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2340296 CATAGGCAAG
2340306 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
2340331 ATTACCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2347240 original size:50 final size:49
Alignment explanation
Indices: 2347131--2347242 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 49
2347121 TCAATTTTAT
* *
2347131 CCTTAAAATTGTTTAATTGCATCATTTATACCCTAACCCTAACTTATAAC
1 CCTT-AAATTATTTAATTGCATCATTTATACCCTAACCCTAACTTATAAA
* * *
2347181 CCTCAAAATTATTTAATTGCATCATTTTATACCTTAATCCTTAACTTA-AAA
1 CCT-TAAATTATTTAATTGCATCA-TTTATACCCTAA-CCCTAACTTATAAA
2347232 CCTTAAATTAT
1 CCTTAAATTAT
2347243 AAATTATAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
50 28 0.53
51 16 0.30
52 9 0.17
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (49 bp):
CCTTAAATTATTTAATTGCATCATTTATACCCTAACCCTAACTTATAAA
Found at i:2347754 original size:22 final size:22
Alignment explanation
Indices: 2347726--2347771 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
2347716 ACACGCACGT
2347726 TCATATATTAGATGACAATAGA
1 TCATATATTAGATGACAATAGA
2347748 TCATATATTAGATGACAATAGA
1 TCATATATTAGATGACAATAGA
2347770 TC
1 TC
2347772 GGATTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATATATTAGATGACAATAGA
Found at i:2348423 original size:28 final size:28
Alignment explanation
Indices: 2348375--2348429 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2348365 TCGTCATTGC
*
2348375 TTTCAAGCAATGACTCGACAACATAATA
1 TTTCAAGCAATGACTAGACAACATAATA
* *
2348403 TTTCAAGCAATGACTATACAATATAAT
1 TTTCAAGCAATGACTAGACAACATAAT
2348430 GTGAACGGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (28 bp):
TTTCAAGCAATGACTAGACAACATAATA
Found at i:2350928 original size:2 final size:2
Alignment explanation
Indices: 2350921--2350961 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2350911 AGTATGAATG
2350921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2350962 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2350966 original size:2 final size:2
Alignment explanation
Indices: 2350961--2350985 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2350951 ATATATATAT
2350961 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2350986 TCTTAAGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2353550 original size:33 final size:33
Alignment explanation
Indices: 2353508--2353570 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
2353498 GGCTACCAAG
2353508 TAATCCCCACGTGAGCTATAACGACAAGTCCAT
1 TAATCCCCACGTGAGCTATAACGACAAGTCCAT
*
2353541 TAATCCCCACGTGAGCTATAACGTCAAGTC
1 TAATCCCCACGTGAGCTATAACGACAAGTC
2353571 TACAACCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (33 bp):
TAATCCCCACGTGAGCTATAACGACAAGTCCAT
Found at i:2356171 original size:42 final size:42
Alignment explanation
Indices: 2356117--2356200 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
2356107 TTTATATTTT
*
2356117 TTTTTTGCTAGTTTCCTGTCCTCCAAGGTATCTTATTTTGCA
1 TTTTTTGCTAGTTTCCTGTCCTCCAAGGTATCCTATTTTGCA
* *
2356159 TTTTTTGCTAGTTTCTTGTCCTCCAAGGTATCCTCTTTTGCA
1 TTTTTTGCTAGTTTCCTGTCCTCCAAGGTATCCTATTTTGCA
2356201 CGTTCTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.13, C:0.23, G:0.14, T:0.50
Consensus pattern (42 bp):
TTTTTTGCTAGTTTCCTGTCCTCCAAGGTATCCTATTTTGCA
Found at i:2363144 original size:45 final size:45
Alignment explanation
Indices: 2363063--2363151 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
2363053 AGTTATAAAA
* * * *
2363063 GAATCCACAGAGACTACCGTCCCGGCCAAGAAGTTTTTCGGTTAG
1 GAATCCACAGAGACCAACGTCCCAGCCAAGAAGTTTTCCGGTTAG
* * *
2363108 GAATCCACAGAGACCAACGTTCCAGCCGAGATGTTTTCCGGTTA
1 GAATCCACAGAGACCAACGTCCCAGCCAAGAAGTTTTCCGGTTA
2363152 CTAATTCTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (45 bp):
GAATCCACAGAGACCAACGTCCCAGCCAAGAAGTTTTCCGGTTAG
Done.