Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008176.1 Hibiscus syriacus cultivar Beakdansim tig00110772_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: 81795
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:20977 original size:12 final size:12
Alignment explanation
Indices: 20948--20981 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20938 CTCCTACGAT
*
20948 ACAACAATCAATC
1 ACAACAAT-AAGC
20961 ACAACAATAAGC
1 ACAACAATAAGC
20973 ACAACAATA
1 ACAACAATA
20982 GTGATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.12
Consensus pattern (12 bp):
ACAACAATAAGC
Found at i:21501 original size:20 final size:20
Alignment explanation
Indices: 21454--21511 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
21444 AAATAACTAA
21454 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* * ***
21474 TAATTTCGCAACACGGTTTC
1 CAAATTCGCAACACGAACTC
* *
21494 CAAATTCGTAACTCGAAC
1 CAAATTCGCAACACGAAC
21512 ATAAATATTT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:23396 original size:24 final size:24
Alignment explanation
Indices: 23369--23503 Score: 103
Period size: 24 Copynumber: 5.6 Consensus size: 24
23359 TATATCAAAA
* * *
23369 ATCAAATCATAATTCACGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
23393 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
23417 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* **
23441 ATCAGATCGGAATCCATA-TC-AGAT
1 ATCAAATCAAAATCCA-AGTCAAG-T
* * *
23465 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
*
23489 ATCAGATCATAAATC
1 ATCAAATCA-AAATC
23504 AAATCGAAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
23 2 0.02
24 86 0.91
25 7 0.07
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAATCAAAATCCAAGTCAAGT
Found at i:23455 original size:48 final size:48
Alignment explanation
Indices: 23386--23503 Score: 157
Period size: 48 Copynumber: 2.4 Consensus size: 48
23376 CATAATTCAC
* *
23386 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAGATCAGA-TATCAGATCAGAATCCAA
** * *
23434 GTCAAGTATCAGATCGGAATCCATATCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAGATCAGATATCAGATCAGAATCCAA
23482 GTCAAGTATCAGATCATAAATC
1 GTCAAGTATCAGATCA-AAATC
23504 AAATCGAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 55 0.92
49 5 0.08
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAGATCAGATATCAGATCAGAATCCAA
Found at i:23517 original size:48 final size:48
Alignment explanation
Indices: 23362--23517 Score: 129
Period size: 48 Copynumber: 3.2 Consensus size: 48
23352 AAACGGATAT
* * * * * * * *
23362 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCGAAATCCAA
* * * *
23410 GTCA-AGTATCAGATCAGAATCCAAGTCAAGTATCAGATCGGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCGAAATCCAA
* * *
23458 ATCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCATAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATC-GAAATCCAA
23506 ATC-GAAAATCAG
1 ATCAG-AAATCAG
23518 GTAAAATATT
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
47 2 0.02
48 82 0.93
49 4 0.05
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.24
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCGAAATCCAA
Found at i:26062 original size:13 final size:13
Alignment explanation
Indices: 26044--26089 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
26034 AACGGGTTAA
26044 CGGGTCAATGGGT
1 CGGGTCAATGGGT
26057 CGGGTCAATGGGT
1 CGGGTCAATGGGT
* **
26070 CGGTTCAACAGGT
1 CGGGTCAATGGGT
26083 CGGGTCA
1 CGGGTCA
26090 GGTCAACGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.17, C:0.20, G:0.41, T:0.22
Consensus pattern (13 bp):
CGGGTCAATGGGT
Found at i:26088 original size:31 final size:31
Alignment explanation
Indices: 26053--26125 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
26043 ACGGGTCAAT
* * *
26053 GGGTCGGGTCAATGGGTCGGTTCAACAGGTC
1 GGGTCGGGTCAACGGGTCGGGTAAACAGGTC
*
26084 GGGTCAGGTCAACGGGTCGGGTAAACAGGTC
1 GGGTCGGGTCAACGGGTCGGGTAAACAGGTC
26115 GGGTCGGGTCA
1 GGGTCGGGTCA
26126 TGACCGGTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.18, C:0.19, G:0.44, T:0.19
Consensus pattern (31 bp):
GGGTCGGGTCAACGGGTCGGGTAAACAGGTC
Found at i:28004 original size:2 final size:2
Alignment explanation
Indices: 27997--28037 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
27987 TTTTTAAAAC
27997 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
28038 CCCCCATTCG
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:28253 original size:24 final size:24
Alignment explanation
Indices: 28238--28355 Score: 139
Period size: 24 Copynumber: 4.9 Consensus size: 24
28228 CATAATTCAC
* * *
28238 GTCAAGTATTATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
28262 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
28286 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
* *
28310 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
28334 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
28356 AAATCGAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 2 0.02
24 77 0.91
25 6 0.07
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:28307 original size:48 final size:48
Alignment explanation
Indices: 28238--28352 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
28228 CATAATTCAC
* * *
28238 GTCAAGTATTATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGGTCAGA-TATCAGATCAGAATCCAA
* *
28286 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAA
28334 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
28353 ATCAAATCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 60 0.98
49 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCAA
Found at i:28369 original size:48 final size:48
Alignment explanation
Indices: 28269--28369 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
28259 CAGGTCAAGT
** *
28269 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
*
28317 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAATCAG-AA
28365 ATCAG
1 ATCAG
28370 GTAAAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
47 1 0.02
48 43 0.91
49 3 0.06
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
Found at i:29102 original size:29 final size:30
Alignment explanation
Indices: 29031--29090 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
29021 CAATTTAAGG
29031 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
29062 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
29091 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:29203 original size:20 final size:20
Alignment explanation
Indices: 29180--29257 Score: 94
Period size: 20 Copynumber: 4.1 Consensus size: 20
29170 TTCAAGATTG
* *
29180 CCCAGGGGGTATAGATTCCC
1 CCCAGGGGGTACAGATACCC
29200 CCCAGGGGGTACAGATA--C
1 CCCAGGGGGTACAGATACCC
29218 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATA-CCC
29236 CCCAGGGGGTACAGATACCC
1 CCCAGGGGGTACAGATACCC
29256 CC
1 CC
29258 TGCAGGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
20 20 0.40
21 11 0.22
ACGTcount: A:0.23, C:0.36, G:0.28, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGTACAGATACCC
Found at i:29226 original size:15 final size:15
Alignment explanation
Indices: 29206--29235 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29196 TCCCCCCAGG
29206 GGGTACAGATACCCC
1 GGGTACAGATACCCC
29221 GGGTACAGATACCCC
1 GGGTACAGATACCCC
29236 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:29263 original size:22 final size:21
Alignment explanation
Indices: 29180--29257 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
29170 TTCAAGATTG
* *
29180 CCCAGGGGGTATAGAT-TCCC
1 CCCAGGGGGTACAGATACCCC
29200 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
29218 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
29236 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
29257 C
1 C
29258 TGCAGGTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
20 15 0.30
21 16 0.32
ACGTcount: A:0.23, C:0.36, G:0.28, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:29332 original size:21 final size:22
Alignment explanation
Indices: 29291--29335 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29281 AACAGAATGT
29291 CCAGGGGGTACCGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCC
29313 CCAGGGGGTACCGATTCCCCCC
1 CCAGGGGGTACCGATTCCCCCC
29335 C
1 C
29336 TGTTCAACAG
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:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (22 bp):
CCAGGGGGTACCGATTCCCCCC
Found at i:29397 original size:21 final size:21
Alignment explanation
Indices: 29371--29413 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29361 ATTTGAATAT
*
29371 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
29392 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
29413 T
1 T
29414 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:29479 original size:20 final size:22
Alignment explanation
Indices: 29441--29480 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
29431 TTTGAGTATA
29441 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
29463 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
29481 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:29736 original size:34 final size:32
Alignment explanation
Indices: 29697--29766 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
29687 TTTTGTAAAG
*
29697 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
29731 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
29763 GGGA
1 GGGA
29767 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:31270 original size:19 final size:20
Alignment explanation
Indices: 31246--31283 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31236 TAAAGATAAT
31246 TTGATTTT-AAAAGCAAAAG
1 TTGATTTTGAAAAGCAAAAG
*
31265 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAAGCAAAA
31284 TAAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGATTTTGAAAAGCAAAAG
Found at i:32619 original size:29 final size:31
Alignment explanation
Indices: 32561--32620 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
32551 CAATTTAAGG
*
32561 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGATTTTGGACTTGAATTGAATTTA
32592 CAAAAT-GATTTTGGACTT-AATTGAATTTA
1 CAAAATGGATTTTGGACTTGAATTGAATTTA
32621 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGATTTTGGACTTGAATTGAATTTA
Found at i:32735 original size:21 final size:21
Alignment explanation
Indices: 32710--32785 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
32700 TTCAAGATTG
* *
32710 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
32731 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
32749 CCCA---GGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
32767 CCCA-GGGGTACAGATACCC
1 CCCAGGGGGTACAGATACCC
32786 TCTGCAGGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
15 10 0.21
18 10 0.21
20 13 0.27
21 15 0.31
ACGTcount: A:0.25, C:0.36, G:0.26, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:32751 original size:20 final size:19
Alignment explanation
Indices: 32728--32785 Score: 70
Period size: 15 Copynumber: 3.2 Consensus size: 19
32718 GTATAGATTC
32728 CCCCCCAGGGGGTACAGATA
1 CCCCCCA-GGGGTACAGATA
32748 --CCCCA--GGTACAGATA
1 CCCCCCAGGGGTACAGATA
32763 CCCCCCCAGGGGTACAGATA
1 -CCCCCCAGGGGTACAGATA
32783 CCC
1 CCC
32786 TCTGCAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
15 10 0.30
18 10 0.30
19 3 0.09
20 10 0.30
ACGTcount: A:0.26, C:0.40, G:0.24, T:0.10
Consensus pattern (19 bp):
CCCCCCAGGGGTACAGATA
Found at i:32768 original size:36 final size:35
Alignment explanation
Indices: 32717--32785 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
32707 TTGCCCAGGG
* *
32717 GGTATAGATTCCCCCCCAGGGGGTACAGATACCCCA
1 GGTACAGATACCCCCCCA-GGGGTACAGATACCCCA
32753 GGTACAGATACCCCCCCAGGGGTACAGATACCC
1 GGTACAGATACCCCCCCAGGGGTACAGATACCC
32786 TCTGCAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 15 0.48
36 16 0.52
ACGTcount: A:0.26, C:0.35, G:0.25, T:0.14
Consensus pattern (35 bp):
GGTACAGATACCCCCCCAGGGGTACAGATACCCCA
Found at i:32861 original size:20 final size:21
Alignment explanation
Indices: 32821--32863 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
32811 AACAGAATGT
32821 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
32842 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
32863 C
1 C
32864 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:32925 original size:21 final size:21
Alignment explanation
Indices: 32899--32941 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
32889 ATTTGAATAT
*
32899 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
32920 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
32941 T
1 T
32942 CTATTTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:33264 original size:34 final size:32
Alignment explanation
Indices: 33225--33294 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
33215 TTTTGTAAAG
*
33225 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
33259 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
33291 GGGA
1 GGGA
33295 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:41379 original size:33 final size:33
Alignment explanation
Indices: 41342--41420 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
41332 AGTTGGCAAG
41342 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
41375 TTGGAAATTTCATCTTGGTTGGTGGCCAATTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
41408 TTGGGAATTTCAT
1 TTGGAAATTTCAT
41421 ATTTGGTGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.42
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:41429 original size:30 final size:32
Alignment explanation
Indices: 41342--41436 Score: 113
Period size: 33 Copynumber: 3.0 Consensus size: 32
41332 AGTTGGCAAG
*
41342 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
41375 TTGGAAATTTCATCTTGGTTGGTGGCCAATTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
41408 TTGGGAATTTCAT-AT-TTGGTGGCTAACTT
1 TTGGAAATTTCATCATGTTGGTGGCCAACTT
41437 GTACACATCG
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
30 12 0.21
32 1 0.02
33 44 0.77
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (32 bp):
TTGGAAATTTCATCATGTTGGTGGCCAACTTA
Found at i:49657 original size:944 final size:944
Alignment explanation
Indices: 47831--49726 Score: 3677
Period size: 944 Copynumber: 2.0 Consensus size: 944
47821 GTCGTCCTCC
*
47831 CTCATCAACAATCCAATGTGAATTCGTTGACAGGGGCAGGGGAATGACGATGGGAAAGAACATGA
1 CTCATCAACAATCCAACGTGAATTCGTTGACAGGGGCAGGGGAATGACGATGGGAAAGAACATGA
47896 AGAGGAGGAGAATAGCCGAGGAAACAAAACTTGCCATGCTGCTTTTGTTTTGACTTTGAAGGAGA
66 AGAGGAGGAGAATAGCCGAGGAAACAAAACTTGCCATGCTGCTTTTGTTTTGACTTTGAAGGAGA
47961 GTAGACGTTGAAGGAGAAGTTACTTGGGACTTTGAAGGAGAAGTTACTTGGGTGGCTTGTTTATA
131 GTAGACGTTGAAGGAGAAGTTACTTGGGACTTTGAAGGAGAAGTTACTTGGGTGGCTTGTTTATA
48026 TAGTGGTGTAAAAGTAGAGACCTATTCTAAATACACTTGTTAATTATTTGTAATTACAAAAGCAC
196 TAGTGGTGTAAAAGTAGAGACCTATTCTAAATACACTTGTTAATTATTTGTAATTACAAAAGCAC
48091 AGCCCTATTCTAATTAAACTCTAACATATTTATTTATTAAGATATATTATCTGTAATCATAAAAT
261 AGCCCTATTCTAATTAAACTCTAACATATTTATTTATTAAGATATATTATCTGTAATCATAAAAT
48156 ATTGATTTGGACATCCCAAAACGGGATAAGTACACAGTTCAACTCCGACCACCTTTGTGATTACT
326 ATTGATTTGGACATCCCAAAACGGGATAAGTACACAGTTCAACTCCGACCACCTTTGTGATTACT
48221 TGGAATAAAATATTAATTTGGTTTTGCACTTTACTTCACTACTGTTTATTGTACATCTATTGTTT
391 TGGAATAAAATATTAATTTGGTTTTGCACTTTACTTCACTACTGTTTATTGTACATCTATTGTTT
48286 GGTTCAATGATAACATCTGCTGTTTAGTCTTTAATTTATGTGCTCTTCAATTCATACTTATTGGT
456 GGTTCAATGATAACATCTGCTGTTTAGTCTTTAATTTATGTGCTCTTCAATTCATACTTATTGGT
48351 TTTTCGCTGGTTAGTGTGTTGGAAAGTGTATTATTCATTTCGTCGTCACCTCTTTTGCAAGATAT
521 TTTTCGCTGGTTAGTGTGTTGGAAAGTGTATTATTCATTTCGTCGTCACCTCTTTTGCAAGATAT
48416 GCTTAAAATTCGATGTTTAATAACCAAGTTATCGTGAAATAAACACCTTTAAAATAAGTTTAACA
586 GCTTAAAATTCGATGTTTAATAACCAAGTTATCGTGAAATAAACACCTTTAAAATAAGTTTAACA
48481 GCCTTGCTCTCTAATAACCGGACAAAAGAGGACGTGTTTTATTTTTTGTTCGACAGGGATTTCAG
651 GCCTTGCTCTCTAATAACCGGACAAAAGAGGACGTGTTTTATTTTTTGTTCGACAGGGATTTCAG
* *
48546 ATCGTACTAGAAAATCCGTAGCTTAATCATCATGCTTCAAACAAAAAACCATTCCAAAATAAACG
716 ATCGTACCAGAAAATCCGTAGCTTAATCATCATGATTCAAACAAAAAACCATTCCAAAATAAACG
*
48611 AGAAGAACAATGCATAAGAAATGATGGCAAAAATTGTAGAATAAGATGACATATATTGTTGTTAA
781 ACAAGAACAATGCATAAGAAATGATGGCAAAAATTGTAGAATAAGATGACATATATTGTTGTTAA
*
48676 TTTCAGTGGAATTTCCGAATCAGTTTCGCTCGTAGGGAGGGGGCCTGGTAATACGTTCTCTTGCT
846 TTTCAGTGGAATTTCCGAATCAGTTTCGCTCGTAGGGAGGGGGCCTGGTAATACGTTCTCTTGAT
*
48741 TACATTGATGGTAGTCGTGGTCTGAGGCATGTGT
911 TACATTGATGGTAGTCGTGGTCTGAGGCATGTGG
48775 CTCATCAACAATCCAACGTGAATTCGTTGACAGGGGCAGGGGAATGACGATGGGAAAGAACATGA
1 CTCATCAACAATCCAACGTGAATTCGTTGACAGGGGCAGGGGAATGACGATGGGAAAGAACATGA
48840 AGAGGAGGAGAATAGCCGAGGAAACAAAACTTGCCATGCTGCTTTTGTTTTGACTTTGAAGGAGA
66 AGAGGAGGAGAATAGCCGAGGAAACAAAACTTGCCATGCTGCTTTTGTTTTGACTTTGAAGGAGA
48905 GTAGACGTTGAAGGAGAAGTTACTTGGGACTTTGAAGGAGAAGTTACTTGGGTGGCTTGTTTATA
131 GTAGACGTTGAAGGAGAAGTTACTTGGGACTTTGAAGGAGAAGTTACTTGGGTGGCTTGTTTATA
*
48970 TAGTGGTGTAAAAGTAGAGACCTATTCTAAATACGCTTGTTAATTATTTGTAATTACAAAAGCAC
196 TAGTGGTGTAAAAGTAGAGACCTATTCTAAATACACTTGTTAATTATTTGTAATTACAAAAGCAC
49035 AGCCCTATTCTAATTAAACTCTAACATATTTATTTATTAAGATATATTATCTGTAATCATAAAAT
261 AGCCCTATTCTAATTAAACTCTAACATATTTATTTATTAAGATATATTATCTGTAATCATAAAAT
*
49100 ATTGATTTGGACATCCCAAAACGGGATAAGTACACAGTTCAACTCCGGCCACCTTTGTGATTACT
326 ATTGATTTGGACATCCCAAAACGGGATAAGTACACAGTTCAACTCCGACCACCTTTGTGATTACT
49165 TGGAATAAAATATTAATTTGGTTTTGCACTTTACTTCACTACTGTTTATTGTACATCTATTGTTT
391 TGGAATAAAATATTAATTTGGTTTTGCACTTTACTTCACTACTGTTTATTGTACATCTATTGTTT
49230 GGTTCAATGATAACATCTGCTGTTTAGTCTTTAATTTATGTGCTCTTCAATTCATACTTATTGGT
456 GGTTCAATGATAACATCTGCTGTTTAGTCTTTAATTTATGTGCTCTTCAATTCATACTTATTGGT
*
49295 TTTTCGCTGGTTAGTGTGTTGGAAAGTGTATTATTCATTTTGTCGTCACCTCTTGTT-CAAGATA
521 TTTTCGCTGGTTAGTGTGTTGGAAAGTGTATTATTCATTTCGTCGTCACCTCTT-TTGCAAGATA
49359 TGCTTAAAATTCGATGTTTAATAACCAAGTTATCGTGAAATAAACACCTTTAAAATAAGTTTAAC
585 TGCTTAAAATTCGATGTTTAATAACCAAGTTATCGTGAAATAAACACCTTTAAAATAAGTTTAAC
* *
49424 AGCCTTGCTCTCTACTAACCGGACAAAAGAGGGCGTGTTTTATTTTTTGTTCGACAGGGATTTCA
650 AGCCTTGCTCTCTAATAACCGGACAAAAGAGGACGTGTTTTATTTTTTGTTCGACAGGGATTTCA
49489 GATCGTACCAGAAAATCCGTAGCTTAATCATCATGATTCAAACAAAAAACCATTCCAAAATAAAC
715 GATCGTACCAGAAAATCCGTAGCTTAATCATCATGATTCAAACAAAAAACCATTCCAAAATAAAC
49554 GACAAGAACAATGCATAAGAAATGATGGCAAAAATTGTAGAATAAGATGACATATATTGTTGTTA
780 GACAAGAACAATGCATAAGAAATGATGGCAAAAATTGTAGAATAAGATGACATATATTGTTGTTA
49619 ATTTCAGTGGAATTTCCGAATCAGTTTCGCTCGTAGGGAGGGGGCCTGGTAATACGTTCTCTTGA
845 ATTTCAGTGGAATTTCCGAATCAGTTTCGCTCGTAGGGAGGGGGCCTGGTAATACGTTCTCTTGA
49684 TTACATTGATGGTAGTCGTGGTCTGAGGCATGTGG
910 TTACATTGATGGTAGTCGTGGTCTGAGGCATGTGG
49719 CTCATCAA
1 CTCATCAA
49727 TTAAGTTTCC
Statistics
Matches: 940, Mismatches: 11, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
944 938 1.00
945 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (944 bp):
CTCATCAACAATCCAACGTGAATTCGTTGACAGGGGCAGGGGAATGACGATGGGAAAGAACATGA
AGAGGAGGAGAATAGCCGAGGAAACAAAACTTGCCATGCTGCTTTTGTTTTGACTTTGAAGGAGA
GTAGACGTTGAAGGAGAAGTTACTTGGGACTTTGAAGGAGAAGTTACTTGGGTGGCTTGTTTATA
TAGTGGTGTAAAAGTAGAGACCTATTCTAAATACACTTGTTAATTATTTGTAATTACAAAAGCAC
AGCCCTATTCTAATTAAACTCTAACATATTTATTTATTAAGATATATTATCTGTAATCATAAAAT
ATTGATTTGGACATCCCAAAACGGGATAAGTACACAGTTCAACTCCGACCACCTTTGTGATTACT
TGGAATAAAATATTAATTTGGTTTTGCACTTTACTTCACTACTGTTTATTGTACATCTATTGTTT
GGTTCAATGATAACATCTGCTGTTTAGTCTTTAATTTATGTGCTCTTCAATTCATACTTATTGGT
TTTTCGCTGGTTAGTGTGTTGGAAAGTGTATTATTCATTTCGTCGTCACCTCTTTTGCAAGATAT
GCTTAAAATTCGATGTTTAATAACCAAGTTATCGTGAAATAAACACCTTTAAAATAAGTTTAACA
GCCTTGCTCTCTAATAACCGGACAAAAGAGGACGTGTTTTATTTTTTGTTCGACAGGGATTTCAG
ATCGTACCAGAAAATCCGTAGCTTAATCATCATGATTCAAACAAAAAACCATTCCAAAATAAACG
ACAAGAACAATGCATAAGAAATGATGGCAAAAATTGTAGAATAAGATGACATATATTGTTGTTAA
TTTCAGTGGAATTTCCGAATCAGTTTCGCTCGTAGGGAGGGGGCCTGGTAATACGTTCTCTTGAT
TACATTGATGGTAGTCGTGGTCTGAGGCATGTGG
Found at i:54808 original size:16 final size:16
Alignment explanation
Indices: 54787--54819 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54777 TACTATTCAT
*
54787 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
54803 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
54819 G
1 G
54820 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:60975 original size:382 final size:382
Alignment explanation
Indices: 60269--61027 Score: 1466
Period size: 382 Copynumber: 2.0 Consensus size: 382
60259 GTAACCAACT
60269 TTCAAAAACCTCACAATAAACGTTATTAACCACACGTGAGAAACCAGCAAAACAGCTCGTTCAAC
1 TTCAAAAACCTCACAATAAACGTTATTAACCACACGTGAGAAACCAGCAAAACAGCTCGTTCAAC
60334 AACAAAGCAGCATGACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTT
66 AACAAAGCAGCATGACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTT
60399 TTTACTAACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACT
131 TTTACTAACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACT
*
60464 CTACACGCTCCTCATCACTTGACTCCAAAGAATTAACTTGAACTTGAGAAACAAGCAACAGTTGC
196 CTACACACTCCTCATCACTTGACTCCAAAGAATTAACTTGAACTTGAGAAACAAGCAACAGTTGC
60529 CTATGTTTAAGAAACATAGGAGCAAACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGGC
261 CTATGTTTAAGAAACATAGGAGCAAACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGGC
60594 AGGAACCTCCTGAACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAAAGCAGCA
326 AGGAACCTCCTGAACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAAAGCAGCA
*
60651 TTCAAAAACCTCACAATAAACGTTATTAACCACACGTGAGAAACCAGCAAAGCAGCTCGTTCAAC
1 TTCAAAAACCTCACAATAAACGTTATTAACCACACGTGAGAAACCAGCAAAACAGCTCGTTCAAC
*
60716 AACAAAGCAGCATGACCCATGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTT
66 AACAAAGCAGCATGACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTT
60781 TTTACTAACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACT
131 TTTACTAACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACT
*
60846 CTACACACTCCTCATCACTTGACTCCAAAGAATTAACTTGAACTTGAGAAACAAGCAACCGTTGC
196 CTACACACTCCTCATCACTTGACTCCAAAGAATTAACTTGAACTTGAGAAACAAGCAACAGTTGC
60911 CTATGTTTAAGAAACATAGGAG-AAGACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGG
261 CTATGTTTAAGAAACATAGGAGCAA-ACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGG
60975 CAGGAACCTCCTGAACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAAAG
325 CAGGAACCTCCTGAACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAAAG
61028 AACAAATCAA
Statistics
Matches: 372, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
381 2 0.01
382 370 0.99
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (382 bp):
TTCAAAAACCTCACAATAAACGTTATTAACCACACGTGAGAAACCAGCAAAACAGCTCGTTCAAC
AACAAAGCAGCATGACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTT
TTTACTAACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACT
CTACACACTCCTCATCACTTGACTCCAAAGAATTAACTTGAACTTGAGAAACAAGCAACAGTTGC
CTATGTTTAAGAAACATAGGAGCAAACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGGC
AGGAACCTCCTGAACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAAAGCAGCA
Found at i:67829 original size:12 final size:12
Alignment explanation
Indices: 67800--67833 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
67790 CTCCTACGAT
*
67800 ACAACAATCAATC
1 ACAACAAT-AAGC
67813 ACAACAATAAGC
1 ACAACAATAAGC
67825 ACAACAATA
1 ACAACAATA
67834 GTGATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.12
Consensus pattern (12 bp):
ACAACAATAAGC
Found at i:68350 original size:20 final size:20
Alignment explanation
Indices: 68303--68360 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
68293 AAATAACTAA
68303 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* * ***
68323 TAATTTCGCAACACGGTTTC
1 CAAATTCGCAACACGAACTC
* *
68343 CAAATTCGTAACTCGAAC
1 CAAATTCGCAACACGAAC
68361 ATAAATATTT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:68547 original size:19 final size:18
Alignment explanation
Indices: 68521--68557 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
68511 ATTCGCCAAT
68521 TTGAAAATTGAGTTGCAA
1 TTGAAAATTGAGTTGCAA
*
68539 TTGACAAATTGTGTTGCAA
1 TTGA-AAATTGAGTTGCAA
68558 AATGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (18 bp):
TTGAAAATTGAGTTGCAA
Found at i:70230 original size:24 final size:24
Alignment explanation
Indices: 70220--70336 Score: 132
Period size: 24 Copynumber: 4.9 Consensus size: 24
70210 CATAATTCAC
* *
70220 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
70244 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
*
70268 GTCAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCAGATCAAAATCCA-A
* *
70293 -TC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
70316 GTC-AGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
70337 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
23 12 0.14
24 71 0.85
25 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:70289 original size:48 final size:48
Alignment explanation
Indices: 70220--70333 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
70210 CATAATTCAC
* * *
70220 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGATCAGA-TATCAGATCAGAATCCAA
* *
70268 GTCAAGTATCAGATCAGAATCCATATCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
70316 GTC-AGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
70334 ATCAAATCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
47 15 0.25
48 44 0.73
49 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
Found at i:70337 original size:12 final size:11
Alignment explanation
Indices: 70251--70333 Score: 62
Period size: 12 Copynumber: 7.1 Consensus size: 11
70241 CAGGTCAAGT
70251 ATCAGATCAGA
1 ATCAGATCAGA
*
70262 ATCCA-AGTCAAGT
1 AT-CAGA-TC-AGA
70275 ATCAGATCAGA
1 ATCAGATCAGA
*
70286 ATCCATATCAGA
1 AT-CAGATCAGA
70298 TATCAGATCAGA
1 -ATCAGATCAGA
*
70310 ATCCATG-TCAGT
1 AT-CA-GATCAGA
70322 ATCAGATCAGA
1 ATCAGATCAGA
70333 A
1 A
70334 ATCAAATCGA
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
10 1 0.02
11 16 0.28
12 32 0.56
13 8 0.14
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (11 bp):
ATCAGATCAGA
Found at i:72832 original size:13 final size:13
Alignment explanation
Indices: 72814--72858 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
72804 CAACGGTTAA
72814 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
72827 CGGGTCAATGGGT
1 CGGGTCAACGGGT
*
72840 CGGGTCAACAGGT
1 CGGGTCAACGGGT
72853 CGGGTC
1 CGGGTC
72859 GGGTAAACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:72845 original size:18 final size:18
Alignment explanation
Indices: 72836--72882 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
72826 TCGGGTCAAT
72836 GGGTCGGGTCAACAGGTC
1 GGGTCGGGTCAACAGGTC
* *
72854 GGGTCGGGTAAACGGGTC
1 GGGTCGGGTCAACAGGTC
72872 GGGTCGGGTCA
1 GGGTCGGGTCA
72883 TGACCGGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (18 bp):
GGGTCGGGTCAACAGGTC
Found at i:72869 original size:13 final size:13
Alignment explanation
Indices: 72814--72875 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 13
72804 CAACGGTTAA
*
72814 CGGGTCAACGGGT
1 CGGGTAAACGGGT
* *
72827 CGGGTCAATGGGT
1 CGGGTAAACGGGT
72840 CGGGTCAACAGGTCGGGT
1 CGGGT-AA-A---CGGGT
72858 CGGGTAAACGGGT
1 CGGGTAAACGGGT
72871 CGGGT
1 CGGGT
72876 CGGGTCATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
13 27 0.66
14 1 0.02
15 1 0.02
16 1 0.02
17 2 0.05
18 9 0.22
ACGTcount: A:0.16, C:0.19, G:0.47, T:0.18
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:74033 original size:35 final size:35
Alignment explanation
Indices: 73985--74051 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
73975 CTTTTTGTAC
*
73985 AAGTAAGGTCCTGAGCACACAGCCGAGGAACCGGT
1 AAGTAAGGCCCTGAGCACACAGCCGAGGAACCGGT
74020 AAGTAAGGCCCTGAGCACACAGCCGAGGAACC
1 AAGTAAGGCCCTGAGCACACAGCCGAGGAACC
74052 TCCAGGTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.33, C:0.28, G:0.30, T:0.09
Consensus pattern (35 bp):
AAGTAAGGCCCTGAGCACACAGCCGAGGAACCGGT
Found at i:74170 original size:24 final size:24
Alignment explanation
Indices: 74138--74227 Score: 137
Period size: 24 Copynumber: 3.8 Consensus size: 24
74128 ATCAATTCAC
*
74138 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
74162 GTAAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
* *
74186 GTCGA-TATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
74209 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
74228 AATCAAATCG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Done.