Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003207.1 Hibiscus syriacus cultivar Beakdansim tig00006749_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: 54293
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:54 original size:17 final size:18
Alignment explanation
Indices: 21--54 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11 TCCATTCTGT
*
21 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
39 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
55 GACCTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:3224 original size:2 final size:2
Alignment explanation
Indices: 3217--3257 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3207 ATTTTAAAAC
3217 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
3258 CCCCAATCCG
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:3382 original size:35 final size:35
Alignment explanation
Indices: 3323--3419 Score: 149
Period size: 35 Copynumber: 2.8 Consensus size: 35
3313 CAAGTCCAGT
*
3323 AGGCTCTGAGCACACAGCCGAGGAGCCGGTAAGTA
1 AGGCCCTGAGCACACAGCCGAGGAGCCGGTAAGTA
* * * *
3358 AGGCCCTGAGCACACACCCAAGGAGCTGGTACGTA
1 AGGCCCTGAGCACACAGCCGAGGAGCCGGTAAGTA
3393 AGGCCCTGAGCACACAGCCGAGGAGCC
1 AGGCCCTGAGCACACAGCCGAGGAGCC
3420 TCCAGGTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.28, C:0.31, G:0.32, T:0.09
Consensus pattern (35 bp):
AGGCCCTGAGCACACAGCCGAGGAGCCGGTAAGTA
Found at i:3532 original size:24 final size:24
Alignment explanation
Indices: 3505--3619 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
3495 CATAAATCAA
* * *
3505 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
3529 GTCAAGTGTCAGATCAGAATCCA-
1 GTCAAGTATCAGATCAGAATCCAT
3552 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
3576 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
3600 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
3620 TCAAATCGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 24 0.29
24 56 0.68
25 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:3573 original size:47 final size:47
Alignment explanation
Indices: 3499--3619 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 47
3489 TCAAAACATA
* * * *
3499 AATCAAGTCAAGTATCATATCAAAATCCAGGTCA-AGTGTCAGATCAG
1 AATCCAGTCAAGTATCAGATCAGAATCCAGGTCAGA-TATCAGATCAG
* *
3546 AATCCAGTCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAG
1 AATCCAGTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAG
3593 AATCCATGTCAAGTATCAGATCAGAAT
1 AATCCA-GTCAAGTATCAGATCAGAAT
3620 TCAAATCGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
47 45 0.68
48 21 0.32
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (47 bp):
AATCCAGTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAG
Found at i:5249 original size:18 final size:18
Alignment explanation
Indices: 5227--5267 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5217 CAGCGGTCAA
* *
5227 CGGGTCAACGGGTTGGGT
1 CGGGTAAACGGGTCGGGT
*
5245 TGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
5263 CGGGT
1 CGGGT
5268 TAGAACCGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.51, T:0.22
Consensus pattern (18 bp):
CGGGTAAACGGGTCGGGT
Found at i:6869 original size:12 final size:12
Alignment explanation
Indices: 6854--6946 Score: 59
Period size: 12 Copynumber: 7.8 Consensus size: 12
6844 CAAAACATAA
*
6854 ATCAGGTCAAGT
1 ATCAGATCAAGT
* *
6866 ATCATATCAA-A
1 ATCAGATCAAGT
*
6877 ATCCAGGTCAAGT
1 AT-CAGATCAAGT
*
6890 ATCAGATC-AGA
1 ATCAGATCAAGT
6901 ATCCA-AGTCAAGT
1 AT-CAGA-TCAAGT
*
6914 ATCAGATCAA-A
1 ATCAGATCAAGT
*
6925 ATCCAAATCAAGT
1 AT-CAGATCAAGT
6938 ATCAGATCA
1 ATCAGATCA
6947 GAATCCATGT
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
11 9 0.15
12 42 0.70
13 9 0.15
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (12 bp):
ATCAGATCAAGT
Found at i:6869 original size:24 final size:24
Alignment explanation
Indices: 6842--6989 Score: 102
Period size: 24 Copynumber: 6.2 Consensus size: 24
6832 TATATCAAAA
6842 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
6866 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
6890 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * **
6914 ATCAGATCAAAATCCAAATCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
6938 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
6962 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
6986 ATCA
1 ATCA
6990 TATCAGAATT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
23 6 0.05
24 103 0.93
25 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:6965 original size:72 final size:72
Alignment explanation
Indices: 6860--7021 Score: 220
Period size: 72 Copynumber: 2.3 Consensus size: 72
6850 ATAAATCAGG
*
6860 TCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAAA
1 TCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAAA
6925 ATCCAAA
66 ATCCAAA
* * * * *
6932 TCAAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCATATCAG
1 TCAAGTATCAGATCAAAATCCAGGTCAAG-TATCAGATCAGAATCCAAGTCAAGTATCAGATCAA
*
6996 AATTCAAA
65 AATCCAAA
**
7004 TCAAAAATCAGAT-AAAAT
1 TCAAGTATCAGATCAAAAT
7022 ATTCATGTGA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 6 0.08
72 73 0.92
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.24
Consensus pattern (72 bp):
TCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAAA
ATCCAAA
Found at i:6994 original size:24 final size:24
Alignment explanation
Indices: 6859--7016 Score: 192
Period size: 24 Copynumber: 6.6 Consensus size: 24
6849 CATAAATCAG
* * *
6859 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
6883 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
6907 GTCAAGTATCAGATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
6931 ATCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
6955 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
* *
6979 GTCAAGTATCATATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
7003 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
7017 AAAATATTCA
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
23 2 0.02
24 113 0.97
25 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:8156 original size:17 final size:17
Alignment explanation
Indices: 8123--8174 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
8113 TCCATTTTGT
*
8123 CTTATTATTTAATTCCAG
1 CTTATCATTT-ATTCCAG
*
8141 CTTATCATTTATTCCAA
1 CTTATCATTTATTCCAG
*
8158 CTTATCATTTCTTCCAG
1 CTTATCATTTATTCCAG
8175 ACATTTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.25, C:0.23, G:0.04, T:0.48
Consensus pattern (17 bp):
CTTATCATTTATTCCAG
Found at i:13104 original size:20 final size:21
Alignment explanation
Indices: 13058--13118 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
13048 TCTCCTGTGG
13058 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
13081 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
13101 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
13119 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:21227 original size:24 final size:24
Alignment explanation
Indices: 21200--21275 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
21190 TATATCAAAA
21200 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
21224 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
21248 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
21272 ATCA
1 ATCA
21276 GATCAGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.09
24 42 0.91
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:21276 original size:24 final size:24
Alignment explanation
Indices: 21217--21328 Score: 156
Period size: 24 Copynumber: 4.7 Consensus size: 24
21207 CATAAATCAG
* * *
21217 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
21241 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
21265 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
21289 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
21313 GT-ATAGTATCAGATCA
1 GTCA-AGTATCAGATCA
21329 TAATTCAAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.02
24 77 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:21348 original size:48 final size:48
Alignment explanation
Indices: 21217--21350 Score: 135
Period size: 48 Copynumber: 2.8 Consensus size: 48
21207 CATAAATCAG
* * ** **
21217 GTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAAATCAAAAATCAGATCAGAATCCAA
** * * *
21265 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAAATCAAAAATCAGATCAGAATCCAA
* *
21313 GT-ATAGTATCAGATCATAATTCAAATCAAAAATCAGAT
1 GTCA-AGTATCAGATCAGAATCCAAATCAAAAATCAGAT
21351 AAAATATTCA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
47 1 0.01
48 72 0.99
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAAATCAAAAATCAGATCAGAATCCAA
Found at i:22492 original size:17 final size:17
Alignment explanation
Indices: 22459--22509 Score: 84
Period size: 17 Copynumber: 2.9 Consensus size: 17
22449 TCCATTCTGT
*
22459 CTTATTATTTAATTCCAA
1 CTTATCATTT-ATTCCAA
22477 CTTATCATTTATTCCAA
1 CTTATCATTTATTCCAA
22494 CTTATCATTTATTCCA
1 CTTATCATTTATTCCA
22510 GACATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (17 bp):
CTTATCATTTATTCCAA
Found at i:25314 original size:88 final size:88
Alignment explanation
Indices: 25035--25319 Score: 434
Period size: 87 Copynumber: 3.3 Consensus size: 88
25025 AGTGGAGGTT
* * *
25035 CTAATTATTAA-CCTAACTAATTATGTT-AAATGAATATCTAATTAAAAA-CTAAAAGACTAAAT
1 CTAATTATTAACCCTAATTAATTATGTTAAAAT-AGTATCTAATTAAAAAGCTTAAAGACTAAAT
25097 TGTGAAGAATCTAAAATTGAGGCA
65 TGTGAAGAATCTAAAATTGAGGCA
* *
25121 CTAATTATTAACCCTAATTAATTATGTTAAAAGAGTATCTAATT-AAAAGCTTAAGGACTAAATT
1 CTAATTATTAACCCTAATTAATTATGTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTAAATT
*
25185 GCGAAGAATCTAAAATTGAGGCA
66 GTGAAGAATCTAAAATTGAGGCA
* * *
25208 CTAATTATTAACCCTAATTAATTGTTTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTTAATT
1 CTAATTATTAACCCTAATTAATTATGTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTAAATT
* *
25273 GTGAAGAATCTAAAATTAAGGAA
66 GTGAAGAATCTAAAATTGAGGCA
25296 CTAATTATTAACCCTAATTAATTA
1 CTAATTATTAACCCTAATTAATTA
25320 ACTAATTATG
Statistics
Matches: 180, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
86 15 0.08
87 101 0.56
88 64 0.36
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (88 bp):
CTAATTATTAACCCTAATTAATTATGTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTAAATT
GTGAAGAATCTAAAATTGAGGCA
Found at i:25912 original size:179 final size:177
Alignment explanation
Indices: 25613--25973 Score: 677
Period size: 179 Copynumber: 2.0 Consensus size: 177
25603 AAAAATTTCC
*
25613 AAATAAAATTATTAAAAAAACAAATTTTAGGGCTAATTAATCTAAGGACTAATTAAAACATTCAT
1 AAATAAAATTATTAAAAAAACAAATTTTAGGGCTAATTAATCTAAGGACTAATTAAAACATACAT
25678 AATAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTAG
66 AATAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTAG
25743 TTAAAATCAAACATGCAATCGGAGAATTAAAATCGGGACCCAAGTGGT
131 TTAAAATCAAACATGCAATCGGAGAATTAAAATCGGGACCCAAGT-GT
25791 AAATAAAATTATTAAAAAAAACAAATTTTAGGGCTAATTAATCTAAGGACTAATTAAAACATACA
1 AAATAAAATTATT-AAAAAAACAAATTTTAGGGCTAATTAATCTAAGGACTAATTAAAACATACA
25856 TAATAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTA
65 TAATAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTA
* *
25921 GTTAAAATCAAACATGCAATCTGAGAATTAAAATCGTGACCCAAGTGT
130 GTTAAAATCAAACATGCAATCGGAGAATTAAAATCGGGACCCAAGTGT
25969 AAATA
1 AAATA
25974 GGCGCAAAAA
Statistics
Matches: 179, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
178 20 0.11
179 159 0.89
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (177 bp):
AAATAAAATTATTAAAAAAACAAATTTTAGGGCTAATTAATCTAAGGACTAATTAAAACATACAT
AATAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTAG
TTAAAATCAAACATGCAATCGGAGAATTAAAATCGGGACCCAAGTGT
Found at i:26566 original size:17 final size:16
Alignment explanation
Indices: 26544--26592 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
26534 TATTATTTTT
26544 ATTTAATAAAAATAATA
1 ATTTAATAAAAA-AATA
*
26561 ATTTAATTGAAAAAATA
1 ATTTAA-TAAAAAAATA
*
26578 ATAT-ATAAAAAAATA
1 ATTTAATAAAAAAATA
26593 TTATTATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 9 0.32
16 1 0.04
17 13 0.46
18 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTTAATAAAAAAATA
Found at i:27695 original size:27 final size:27
Alignment explanation
Indices: 27657--27710 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
27647 GTGTATCCTA
*
27657 TACGTGTGATGATCGGTTGTTGCATTT
1 TACGTGTGATGATCGGCTGTTGCATTT
27684 TACGTGTGATGATCGGCTGTTGCATTT
1 TACGTGTGATGATCGGCTGTTGCATTT
27711 CCTAGTTGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.13, G:0.30, T:0.43
Consensus pattern (27 bp):
TACGTGTGATGATCGGCTGTTGCATTT
Found at i:28417 original size:2 final size:2
Alignment explanation
Indices: 28410--28441 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28400 TCAAAACTAC
28410 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
28442 GTTTTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28425 original size:29 final size:30
Alignment explanation
Indices: 28349--28426 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 30
28339 TATCTTCAAA
*
28349 ACTATATATATATACTATATTTTCAAAATT
1 ACTATATATATATACTATATTTTCAAAACT
* * * *
28379 ATTTTTTAAAT-TACTATATTTTCAAAACT
1 ACTATATATATATACTATATTTTCAAAACT
28408 ACTATATATATATA-TATAT
1 ACTATATATATATACTATAT
28427 ATATATATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 29 0.76
30 9 0.24
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (30 bp):
ACTATATATATATACTATATTTTCAAAACT
Found at i:28592 original size:6 final size:5
Alignment explanation
Indices: 28578--28610 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
28568 AGCTATATAT
28578 AATAA AATAAA AATAA AATAA AATAA AATAA AA
1 AATAA AAT-AA AATAA AATAA AATAA AATAA AA
28611 GATGAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:28983 original size:2 final size:2
Alignment explanation
Indices: 28978--29026 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
28968 CCGAAAAAAC
*
28978 AT AT AT TT AT AT AT -T AT AT AT -T AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29017 AT AT -T AT AT A
1 AT AT AT AT AT A
29027 AGTATTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:28996 original size:7 final size:7
Alignment explanation
Indices: 28978--29026 Score: 80
Period size: 7 Copynumber: 6.7 Consensus size: 7
28968 CCGAAAAAAC
28978 ATATATTT
1 ATATA-TT
28986 ATATATT
1 ATATATT
28993 ATATATT
1 ATATATT
29000 ATATATT
1 ATATATT
29007 ATATATAT
1 ATATAT-T
29015 ATATATT
1 ATATATT
29022 ATATA
1 ATATA
29027 AGTATTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 28 0.70
8 12 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATATATT
Found at i:29035 original size:29 final size:29
Alignment explanation
Indices: 28978--29037 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
28968 CCGAAAAAAC
* *
28978 ATATATTTATATATTATATATTATATATT
1 ATATATATATATATTATATAGTATATATT
29007 ATATATATATATATTATATAAGTAT-TATT
1 ATATATATATATATTATAT-AGTATATATT
29036 AT
1 AT
29038 TTTATTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
ATATATATATATATTATATAGTATATATT
Found at i:34375 original size:84 final size:84
Alignment explanation
Indices: 34180--34527 Score: 365
Period size: 84 Copynumber: 4.2 Consensus size: 84
34170 TTTAAAACAA
* * ** *
34180 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
34241 ACACTCAGCTTCGAGGGCAC
66 ACGCTCAGC-TCCAAGGCAC
*
34261 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
34326 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
* * * * * * * *
34345 GTCATTTGCAACACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACT
34410 ACGCTCAGCT-CAACGGCAC
66 ACGCTCAGCTCCAA-GGCAC
* * *
34429 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGATCC-CCGAGTTCGAT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGA-CCTTCGAGTTCGAC
* * *
34489 TCCACTCAGCTCCGAGGGCAC
65 TACGCTCAGCTCC-AAGGCAC
*
34510 ATCATTTACAGCATAACT
1 ATCATTTGCAGCATAACT
34528 CAAGGCTAGA
Statistics
Matches: 225, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
80 23 0.10
81 60 0.27
82 1 0.00
83 3 0.01
84 111 0.49
85 27 0.12
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCAC
Found at i:34634 original size:37 final size:37
Alignment explanation
Indices: 34580--34657 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
34570 GTTTTTCTTA
34580 AAAC-AAATTTCGTCTCCCTTGAGACAGTTTCCCTTG
1 AAACAAAATTTCGTCTCCCTTGAGACAGTTTCCCTTG
* *
34616 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAAATTTCGTCTCCCTTGAGACAGTTTCCCTTG
34653 AAACA
1 AAACA
34658 TAAACATCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.10
37 35 0.90
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.33
Consensus pattern (37 bp):
AAACAAAATTTCGTCTCCCTTGAGACAGTTTCCCTTG
Found at i:34720 original size:36 final size:35
Alignment explanation
Indices: 34673--34757 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
34663 ATCGAAAACA
* ** * *
34673 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAA-CAAAATTGTCTCCCTTGAGACAG
34709 TTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAG
*
34744 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
34758 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 31 0.72
36 12 0.28
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAG
Found at i:34763 original size:100 final size:100
Alignment explanation
Indices: 34585--34849 Score: 449
Period size: 100 Copynumber: 2.6 Consensus size: 100
34575 TCTTAAAACA
* * *
34585 AATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTC
1 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA--TTGTCTCCCTTGAGACAGTTTCTC
34650 TTGAAACATAAACATCGAAAACATTTCCCTTGAAATG
64 TTGAAACATAAACATCGAAAACATTTCCCTTGAAATG
34687 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAGTTTCTCTT
1 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAGTTTCTCTT
*
34752 GAAACATAAACATTGAAAACATTTCCCTTGAAATG
66 GAAACATAAACATCGAAAACATTTCCCTTGAAATG
* *
34787 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAGTTCGTCTCCCTTGAGACAATTTCT
1 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATT-GTCTCCCTTGAGACAGTTTCT
34850 TTTTGAACTA
Statistics
Matches: 156, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
100 100 0.64
101 20 0.13
102 36 0.23
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (100 bp):
AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTGTCTCCCTTGAGACAGTTTCTCTT
GAAACATAAACATCGAAAACATTTCCCTTGAAATG
Found at i:34820 original size:36 final size:36
Alignment explanation
Indices: 34773--34896 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 36
34763 ATTGAAAACA
* *
34773 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
** * * *
34809 TTTCCCTTGAAACAAAGTTCGTCTCCCTTGAGACAA
1 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
** * *
34845 TTTCTTTTTGAACT-AAGTTTTATCTCCCTTGAGACAG
1 TTTC-CCTTGAAATGAA-TTTTGTCTCCCTTGAGACAG
*
34882 TTTCTCTTGAAATGA
1 TTTCCCTTGAAATGA
34897 CACAATTTGC
Statistics
Matches: 68, Mismatches: 17, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
36 42 0.62
37 26 0.38
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
Found at i:35100 original size:106 final size:106
Alignment explanation
Indices: 34910--35878 Score: 1448
Period size: 106 Copynumber: 9.4 Consensus size: 106
34900 AATTTGCTCG
* * *
34910 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
34975 CGAAGGGACCGCTGGTCGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
35016 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
35081 CGAAGGGACCGCTGGTCGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
35122 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACGACGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
35187 CGAAGGGACCGCTGGTCGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * *
35228 AGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
35293 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTT
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
35334 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
35399 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
*
35440 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
35505 TGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
35546 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACTCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
35611 CGAAGGGACCGCTGGTTGT---CAAACAA----ACAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* *
35645 ----CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
35706 CGAAGGGACCGCTGGTTGTCAAC--A-AA-----CAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
* * * *
35739 ----CCAATTTCAATTTCACAACGAATGACATTGGACTCCAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * * *
35800 CGAAGGGACCGCTGGTTGTCAATAAACAA-TTTTCCAGTTCC
66 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCT-CAATTTC
**
35841 AGAGCCAATTTCAACTTCACGGCGGAA-GATATTGGACT
1 AGAGCCAATTTCAACTTCACAAC-GAAGGATATTGGACT
35879 TGGAACAATT
Statistics
Matches: 813, Mismatches: 34, Indels: 32
0.92 0.04 0.04
Matches are distributed among these distances:
94 84 0.10
95 80 0.10
96 2 0.00
97 2 0.00
98 1 0.00
99 7 0.01
102 5 0.01
103 6 0.01
106 623 0.77
107 3 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
Found at i:35616 original size:43 final size:43
Alignment explanation
Indices: 35550--35702 Score: 119
Period size: 43 Copynumber: 3.3 Consensus size: 43
35540 AATTTCAGAG
*
35550 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
1 CCAAGTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
* *** ** *
35593 TCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAAACAAACAATTTC
1 CCAAGTTCAACTTCACAG-CGAA-GGA-TATTGG-ACTC---CAGACAA---C
*
35645 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
1 CCAAGTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
*
35688 GCAAGTTCAACTTCA
1 CCAAGTTCAACTTCA
35703 TGACGAAGGG
Statistics
Matches: 81, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
42 1 0.01
43 32 0.40
44 3 0.04
45 3 0.04
46 8 0.10
49 8 0.10
50 3 0.04
51 3 0.04
52 19 0.23
53 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
CCAAGTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
Found at i:36695 original size:2 final size:2
Alignment explanation
Indices: 36690--36752 Score: 89
Period size: 2 Copynumber: 33.5 Consensus size: 2
36680 CCGAAAAAAC
*
36690 AT AT AT TT AT AT AT -T AT AT AT -T AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36729 AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
36753 AGTATTATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:36724 original size:17 final size:17
Alignment explanation
Indices: 36690--36752 Score: 98
Period size: 17 Copynumber: 3.9 Consensus size: 17
36680 CCGAAAAAAC
36690 ATATATT-TATATAT-T
1 ATATATTATATATATAT
36705 ATATATTATATATATAT
1 ATATATTATATATATAT
36722 ATATATTATATATATAT
1 ATATATTATATATATAT
36739 ATATA-TAT-TATATA
1 ATATATTATATATATA
36753 AGTATTATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.28
16 10 0.22
17 23 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATTATATATATAT
Found at i:36764 original size:17 final size:18
Alignment explanation
Indices: 36690--36753 Score: 91
Period size: 19 Copynumber: 3.7 Consensus size: 18
36680 CCGAAAAAAC
36690 ATATATT-TAT-ATAT-T
1 ATATATTATATAATATAT
36705 ATATATTATAT-ATATAT
1 ATATATTATATAATATAT
36722 ATATATTATATATATATAT
1 ATATATTATATA-ATATAT
36741 ATATATTATATAA
1 ATATATTATATAA
36754 GTATTATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.16
16 7 0.16
17 12 0.27
18 1 0.02
19 18 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATATTATATAATATAT
Found at i:38960 original size:26 final size:26
Alignment explanation
Indices: 38903--38954 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38893 AAGTGCAGTA
38903 GAAATATAGGTTAATATAATAAAGAC
1 GAAATATAGGTTAATATAATAAAGAC
38929 GAAATATAGGTTAATATAATAAAGAC
1 GAAATATAGGTTAATATAATAAAGAC
38955 TTAATAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (26 bp):
GAAATATAGGTTAATATAATAAAGAC
Found at i:39842 original size:19 final size:18
Alignment explanation
Indices: 39818--39860 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
39808 TCTAGACTCG
39818 AGCCCAAGCAAAAAACCCT
1 AGCCCAAG-AAAAAACCCT
*
39837 AGCCC-AGGAAAAACCCT
1 AGCCCAAGAAAAAACCCT
*
39854 AACCCAA
1 AGCCCAA
39861 CTGGAGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 13 0.62
18 3 0.14
19 5 0.24
ACGTcount: A:0.47, C:0.37, G:0.12, T:0.05
Consensus pattern (18 bp):
AGCCCAAGAAAAAACCCT
Found at i:40951 original size:108 final size:107
Alignment explanation
Indices: 40801--41001 Score: 269
Period size: 108 Copynumber: 1.9 Consensus size: 107
40791 CTTAAGCGTG
* * * *
40801 TTTTGCATGTTAGTCACCTATAAGGTCCGAATTTACTATTTACCCATTTTTATGCATGCTATATA
1 TTTTGCATGTTAGTCACCTATAAGGACCGAAGTTACTATTTACACATTTTTATGCATGATATATA
40866 TTTTTTGGGATATTTGCTT-CTTAGTCCCCATAGTTTAGTGTGT
66 -TTTTTGGGATATTTG-TTGCTTAGTCCCCATAGTTTAGTGTGT
* * * ** * *
40909 TTTTGCATGTTGGTCACCTATAGGGACTGAAGTTGTTATTTACACATTTTTATGCATGATGTGTA
1 TTTTGCATGTTAGTCACCTATAAGGACCGAAGTTACTATTTACACATTTTTATGCATGATATATA
*
40974 TTTTTGGGATATTTGTTGTTTAGTCCCC
66 TTTTTGGGATATTTGTTGCTTAGTCCCC
41002 CTTATTTAGG
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
106 2 0.03
107 24 0.30
108 54 0.68
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.46
Consensus pattern (107 bp):
TTTTGCATGTTAGTCACCTATAAGGACCGAAGTTACTATTTACACATTTTTATGCATGATATATA
TTTTTGGGATATTTGTTGCTTAGTCCCCATAGTTTAGTGTGT
Found at i:42109 original size:131 final size:131
Alignment explanation
Indices: 41862--42385 Score: 648
Period size: 131 Copynumber: 4.0 Consensus size: 131
41852 AGTAACACTT
* * * * * *
41862 GAATCAATAATGA-TTTTAGGATGAAATAATAATATCTTTTCATTTCGGTTGGAGTAATATATGA
1 GAATCAATAATGATTTTTAAGACGAAA-AATGATATCTCTTCATTTCGATTGGAGTAATAAATGA
* * * **
41926 CTGCTCTAAGGCATGAGAGGTCATTTATTCTC-TATTGGAAATAATTAGATATTATTGTTTTCTC
65 ATGCTTTAAGGCATGAGAGGTCATTTATTCTCAGATTGGAAATAATTAGATATTATCATTTTCTC
41990 TC
130 TC
* *
41992 GAATCAATATTGATTTTTAAGACGAAAAAGTGATATCTCTTCGTTTCGATTGGAGTAATAAATGA
1 GAATCAATAATGATTTTTAAGACGAAAAA-TGATATCTCTTCATTTCGATTGGAGTAATAAATGA
* *
42057 ATGCTTTAAGGCATGAGAGGTCATTCATTATCAG-TTGGAAATAATTAGATATTATCATTTTCTC
65 ATGCTTTAAGGCATGAGAGGTCATTTATTCTCAGATTGGAAATAATTAGATATTATCATTTTCTC
42121 TC
130 TC
** * * * *
42123 GAATCAATTTTGATTTTTAAGATGAAATAGTGACATCTCTTCATTTCGATTGGAGTAACAAATGA
1 GAATCAATAATGATTTTTAAGACGAAA-AATGATATCTCTTCATTTCGATTGGAGTAATAAATGA
* * * **
42188 ATGCTTTAAGGTATAAGAGGTCATTTATTCT-TGATTGGAAATAATTAGATATTATTGTTTTCTC
65 ATGCTTTAAGGCATGAGAGGTCATTTATTCTCAGATTGGAAATAATTAGATATTATCATTTTCTC
42252 TC
130 TC
* * *
42254 -AGATCGATAATGAATTTTAAGACGAGATAATGATATCTCTTCACTTT-GATTGGAGTAATAAAT
1 GA-ATCAATAATGATTTTTAAGACGA-AAAATGATATCTCTTCA-TTTCGATTGGAGTAATAAAT
* * *
42317 GATTTGCTTTAAGACATGAGATGTCATTTATTCTC-GATTGGAAATAATTAGATATTATCATTTT
63 GA-ATGCTTTAAGGCATGAGAGGTCATTTATTCTCAGATTGGAAATAATTAGATATTATCATTTT
42381 CTCTC
127 CTCTC
42386 TTAAAATCCA
Statistics
Matches: 340, Mismatches: 44, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
130 16 0.05
131 261 0.77
132 63 0.19
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (131 bp):
GAATCAATAATGATTTTTAAGACGAAAAATGATATCTCTTCATTTCGATTGGAGTAATAAATGAA
TGCTTTAAGGCATGAGAGGTCATTTATTCTCAGATTGGAAATAATTAGATATTATCATTTTCTCT
C
Found at i:52890 original size:8 final size:7
Alignment explanation
Indices: 52868--52948 Score: 119
Period size: 7 Copynumber: 11.3 Consensus size: 7
52858 TCGCTTGAAG
52868 AAAGAAA
1 AAAGAAA
52875 AAAGAAA
1 AAAGAAA
52882 AAAGAAA
1 AAAGAAA
52889 AAATGAAA
1 AAA-GAAA
52897 AAATGAAA
1 AAA-GAAA
52905 AAAG-AA
1 AAAGAAA
52911 AAAGAAA
1 AAAGAAA
52918 AAAGAAA
1 AAAGAAA
*
52925 AATGAAA
1 AAAGAAA
52932 AAAGAAAA
1 AAAG-AAA
52940 AAAGAAA
1 AAAGAAA
52947 AA
1 AA
52949 TGGGTTCAAG
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
6 6 0.09
7 41 0.59
8 22 0.32
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Done.