Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015320.1 Kokia drynarioides strain JFW-HI SEQ_130366, 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: 252538
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 242 characters in sequence are not A, C, G, or T
Found at i:5833 original size:24 final size:25
Alignment explanation
Indices: 5796--5842 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5786 ACATGGAAAA
* *
5796 TATTTTTCACAATTTAGTATTATTT
1 TATTTTTCACAATTAAATATTATTT
*
5821 TATTTTTTA-AATTAAATATTAT
1 TATTTTTCACAATTAAATATTAT
5843 AATTTGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTTTCACAATTAAATATTATTT
Found at i:6246 original size:17 final size:17
Alignment explanation
Indices: 6224--6277 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
6214 CATACTCCCT
*
6224 TTAAATTTATTTTAAAA
1 TTAAATTTAGTTTAAAA
6241 TTAAATTT-GTTTAAAA
1 TTAAATTTAGTTTAAAA
*
6257 TTTAAATTAAGTTTAAAA
1 -TTAAATTTAGTTTAAAA
6275 TTA
1 TTA
6278 TTTTCAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 7 0.21
17 18 0.55
18 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTAAATTTAGTTTAAAA
Found at i:6272 original size:18 final size:18
Alignment explanation
Indices: 6223--6298 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 18
6213 CCATACTCCC
* *
6223 TTTAAATTTATTTTAAAA
1 TTTAAATTAAGTTTAAAA
*
6241 -TTAAATT-TGTTTAAAA
1 TTTAAATTAAGTTTAAAA
6257 TTTAAATTAAGTTTAAAA
1 TTTAAATTAAGTTTAAAA
** *
6275 -TTATTTTCAAATTTAAAA
1 TTTAAATT-AAGTTTAAAA
6293 TTTAAA
1 TTTAAA
6299 ATAAATAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
16 7 0.15
17 19 0.41
18 17 0.37
19 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAAATTAAGTTTAAAA
Found at i:6304 original size:18 final size:18
Alignment explanation
Indices: 6223--6304 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 18
6213 CCATACTCCC
* *
6223 TTTAAATTTATTTTAAAA
1 TTTAAATTAAATTTAAAA
**
6241 -TTAAATT-TGTTTAAAA
1 TTTAAATTAAATTTAAAA
*
6257 TTTAAATTAAGTTTAAAA
1 TTTAAATTAAATTTAAAA
**
6275 -TTATTTTCAAATTTAAAA
1 TTTAAATT-AAATTTAAAA
*
6293 TTTAAAATAAAT
1 TTTAAATTAAAT
6305 AAAACCCAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
16 7 0.14
17 19 0.37
18 21 0.41
19 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTAAATTAAATTTAAAA
Found at i:8176 original size:29 final size:29
Alignment explanation
Indices: 8142--8290 Score: 113
Period size: 29 Copynumber: 5.1 Consensus size: 29
8132 GGAAGTTCCT
*
8142 AAACTTCCAAAAATTCCGTTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
8171 GAACTTCAAAAAAAATCCCATTTTTAACCCCA
1 AAACTTC--CAAAAATTCCATTTTT-ACCCCC
* * * *
8203 AAACTACCGAAAATTCTATTTTCACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
8232 AAACTTCCAAAAATCCCA-TTTTACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCC
** *
8260 AATTTTCCCAAAATTACCA-TTTTACCCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCCC
8289 AA
1 AA
8291 GGATCCGAAA
Statistics
Matches: 90, Mismatches: 26, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
28 18 0.20
29 38 0.42
30 11 0.12
31 13 0.14
32 10 0.11
ACGTcount: A:0.36, C:0.32, G:0.03, T:0.29
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:8414 original size:51 final size:51
Alignment explanation
Indices: 8356--8460 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
8346 ACTTTAACCA
*
8356 TTATGCACTCGTATTCTGCATTTTTTATACTTTTCTCTTCATTTCATCTTC
1 TTATGCACTCGTATTCTGCATTTTTTATACTTTTCTCGTCATTTCATCTTC
*
8407 TTATGCACTCGTATTCTGTATTTTTTATACTTTTCTCGTCATTTCATCTTC
1 TTATGCACTCGTATTCTGCATTTTTTATACTTTTCTCGTCATTTCATCTTC
8458 TTA
1 TTA
8461 CTTATCTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.16, C:0.22, G:0.07, T:0.55
Consensus pattern (51 bp):
TTATGCACTCGTATTCTGCATTTTTTATACTTTTCTCGTCATTTCATCTTC
Found at i:11513 original size:5 final size:5
Alignment explanation
Indices: 11503--11536 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
11493 ATATTTATCA
11503 AATTT AATTT AATTT AATTT AATTT AATTT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
11537 CACTCCCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:12478 original size:3 final size:3
Alignment explanation
Indices: 12463--12520 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
12453 AGGTGGGAAT
* * * * *
12463 GAG GAG GAT GAG GAG GAG GGG GAG GAT GAG GAG GAG GAG GAG GAA AAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
*
12511 GAA GAG GAG G
1 GAG GAG GAG G
12521 GTCAAATGAG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.36, C:0.00, G:0.60, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:12486 original size:18 final size:18
Alignment explanation
Indices: 12463--12520 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
12453 AGGTGGGAAT
12463 GAGGAGGATGAGGAGGAG
1 GAGGAGGATGAGGAGGAG
*
12481 GGGGAGGATGAGGAGGAG
1 GAGGAGGATGAGGAGGAG
** *
12499 GAGGAGGAAAAGGAAGAG
1 GAGGAGGATGAGGAGGAG
12517 GAGG
1 GAGG
12521 GTCAAATGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.60, T:0.03
Consensus pattern (18 bp):
GAGGAGGATGAGGAGGAG
Found at i:20273 original size:32 final size:32
Alignment explanation
Indices: 20232--20296 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20222 TCAGTTATAT
20232 ATATAAATACTGTTAATTGAATTGGTGTTTCA
1 ATATAAATACTGTTAATTGAATTGGTGTTTCA
20264 ATATAAATACTGTTAATTGAATTGGTGTTTCA
1 ATATAAATACTGTTAATTGAATTGGTGTTTCA
20296 A
1 A
20297 GTTAATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.43
Consensus pattern (32 bp):
ATATAAATACTGTTAATTGAATTGGTGTTTCA
Found at i:30192 original size:13 final size:13
Alignment explanation
Indices: 30174--30222 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
30164 AATGTGTTTT
30174 TAAAAATAATATA
1 TAAAAATAATATA
30187 TAAAAAT-ATAT-
1 TAAAAATAATATA
30198 TAAAAAATAATATA
1 T-AAAAATAATATA
*
30212 AAATAAATAAT
1 TAA-AAATAAT
30223 GAAACATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 1 0.03
12 10 0.32
13 13 0.42
14 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAATAATATA
Found at i:36628 original size:80 final size:80
Alignment explanation
Indices: 36495--36646 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 80
36485 TGGGCGCAAA
* ** *
36495 TCATTGGTTAATCCAATTAGAATTGGGCTCATTTATTGCGGTGTATCCGCTAGGCACTGGGTGTC
1 TCATTGGTTAATCCAACTAGAAGCGGGCTCATTTATCGCGGTGTATCCGCTAGGCACTGGGTGTC
*
36560 ATGAATTAACGGATT
66 AAGAATTAACGGATT
* *
36575 TCATTGGTTAATCCAACTAG-AGCGAGGCTCATTTATCGCGGTTTATCTGCTAGGCACTGGGTGT
1 TCATTGGTTAATCCAACTAGAAGCG-GGCTCATTTATCGCGGTGTATCCGCTAGGCACTGGGTGT
36639 CAAGAATT
65 CAAGAATT
36647 GATAGAAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
79 2 0.03
80 62 0.97
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (80 bp):
TCATTGGTTAATCCAACTAGAAGCGGGCTCATTTATCGCGGTGTATCCGCTAGGCACTGGGTGTC
AAGAATTAACGGATT
Found at i:38638 original size:17 final size:17
Alignment explanation
Indices: 38605--38657 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
38595 ATTTCAAACC
* *
38605 ATACATTTTATTATTAA
1 ATACATATTATTTTTAA
* *
38622 TTATATATTATTTTTAA
1 ATACATATTATTTTTAA
38639 ATACATA-TA-TTTTAA
1 ATACATATTATTTTTAA
38654 ATAC
1 ATAC
38658 GTGATTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 10 0.33
16 2 0.07
17 18 0.60
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
ATACATATTATTTTTAA
Found at i:45371 original size:30 final size:28
Alignment explanation
Indices: 45312--45619 Score: 294
Period size: 30 Copynumber: 10.5 Consensus size: 28
45302 CCTAAACTAT
* *
45312 CAAAAATCCCATTTTTACCCCTGAACTTC
1 CAAAAATTCCATTTTTACCCC-AAACTTC
* *
45341 CAAAAATACCATTTTTGACTCCAAAACTTC
1 CAAAAATTCCATTTTT-AC-CCCAAACTTC
*
45371 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCC-CAAACTTC
* * *
45400 CGAAAA-TACATTTTTTGACCTCGAAACTTC
1 CAAAAATTCCA-TTTTT-ACC-CCAAACTTC
* *
45430 AAAAAATTCCATTTTTACCCTCAAATTTC
1 CAAAAATTCCATTTTTACCC-CAAACTTC
*
45459 CAAAAATACCATTTTTGACCCCGAAACTTC
1 CAAAAATTCCATTTTT-ACCCC-AAACTTC
* *
45489 CAAAAATTCTATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCC-CAAACTTC
* **
45518 CAAAAATCCCATTTTTTACCTTGAAACTTC
1 CAAAAATTCCA-TTTTTACC-CCAAACTTC
*
45548 CAAAAATTCCATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCC-CAAACTTC
*
45577 CAAAAATTCCATTTTTGACACCGAAACTTC
1 CAAAAATTCCATTTTT-AC-CCCAAACTTC
*
45607 CAAAAATCCCATT
1 CAAAAATTCCATT
45620 ATAGACCTCA
Statistics
Matches: 230, Mismatches: 33, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.03
29 106 0.46
30 110 0.48
31 8 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCCCAAACTTC
Found at i:45397 original size:59 final size:58
Alignment explanation
Indices: 45312--45619 Score: 431
Period size: 59 Copynumber: 5.2 Consensus size: 58
45302 CCTAAACTAT
* *
45312 CAAAAATCCCATTTTTACCC-CTGAACTTCCAAAAATACCATTTTTGACTCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATACCATTTTTGAC-CCGAAACTTC
*
45371 CAAAAATTCCATTTTTACCCTCGAACTTCCGAAAATA-CATTTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATACCA-TTTTTGACC-CGAAACTTC
* * *
45430 AAAAAATTCCATTTTTACCCTCAAATTTCCAAAAATACCATTTTTGACCCCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATACCATTTTTGA-CCCGAAACTTC
* * * *
45489 CAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCTTGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATACCATTTTTGACC-CGAAACTTC
*
45548 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACACCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATACCATTTTTGAC-CCGAAACTTC
*
45607 CAAAAATCCCATT
1 CAAAAATTCCATT
45620 ATAGACCTCA
Statistics
Matches: 223, Mismatches: 19, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
58 5 0.02
59 212 0.95
60 6 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATACCATTTTTGACCCGAAACTTC
Found at i:45634 original size:30 final size:30
Alignment explanation
Indices: 45312--45631 Score: 261
Period size: 29 Copynumber: 10.9 Consensus size: 30
45302 CCTAAACTAT
* ** *
45312 CAAAAATCCCATTTTTACCCCT-GAACTTC
1 CAAAAATTCCATTTTTAGACCTCAAACTTC
*
45341 CAAAAATACCATTTTT-GA-CTCCAAAACTTC
1 CAAAAATTCCATTTTTAGACCT-C-AAACTTC
* *
45371 CAAAAATTCCATTTTTA-CCCTCGAACTTC
1 CAAAAATTCCATTTTTAGACCTCAAACTTC
* * *
45400 CGAAAA-TACATTTTTTGACCTCGAAACTTC
1 CAAAAATTCCATTTTTAGACCTC-AAACTTC
* * *
45430 AAAAAATTCCATTTTTA-CCCTCAAATTTC
1 CAAAAATTCCATTTTTAGACCTCAAACTTC
* *
45459 CAAAAATACCATTTTT-GACCCCGAAACTTC
1 CAAAAATTCCATTTTTAGACCTC-AAACTTC
* * *
45489 CAAAAATTCTATTTTTA-CCCTCGAACTTC
1 CAAAAATTCCATTTTTAGACCTCAAACTTC
* * *
45518 CAAAAATCCCATTTTT-TACCTTGAAACTTC
1 CAAAAATTCCATTTTTAGACC-TCAAACTTC
* *
45548 CAAAAATTCCATTTTTA-CCCTCGAACTTC
1 CAAAAATTCCATTTTTAGACCTCAAACTTC
45577 CAAAAATTCCATTTTT-GACAC-CGAAACTTC
1 CAAAAATTCCATTTTTAGAC-CTC-AAACTTC
* *
45607 CAAAAATCCCA-TTATAGACCTCAAA
1 CAAAAATTCCATTTTTAGACCTCAAA
45632 ACTCTCAAAA
Statistics
Matches: 231, Mismatches: 41, Indels: 38
0.75 0.13 0.12
Matches are distributed among these distances:
27 2 0.01
28 8 0.03
29 107 0.46
30 104 0.45
31 10 0.04
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (30 bp):
CAAAAATTCCATTTTTAGACCTCAAACTTC
Found at i:53639 original size:18 final size:18
Alignment explanation
Indices: 53616--53652 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
53606 ACAATTCATA
53616 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
53634 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
53652 T
1 T
53653 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:56479 original size:195 final size:192
Alignment explanation
Indices: 56076--56516 Score: 510
Period size: 195 Copynumber: 2.3 Consensus size: 192
56066 CTCGATGTTG
* ** * * *
56076 CTCACACGAGCTGTCGAGGATTCGCAACTTATGCGGTACCCCAACAATC-AGTACGGTGTCTATC
1 CTCACACGAGCTGTCGAGGACTCGCAACACATGCAGTACCCCAGCCATCGA-TAC-G-G--TATC
* * * * *
56140 TGTAC-TGTAAATTGTTCCCTAACGATGCTACTTACACGAGCTGTCAAGAGTATGCATAAAGCAT
61 TGTGCATAT-AACTGTTCCCTAACGATGCTACTCACACGAGCTGTCAAGAATATGCATAAAGCAT
* * * * *
56204 AGTCCCAGCCATCGTAGGGCTCGTAATCCATTTAAGATCCATATCTTTTCTTTCGAATCACGATG
125 AATCACAGCCATCGCAGGGCTCGTAATCCATTTAAGATCCATATCTCTTCTTTCCAATCACGATG
*
56269 CTG
190 CTA
* * *
56272 CTCACACGAGCTGTCGAGGACTCGTAACAGATGCAGTACCTCAGCCATCGATACGGTATCTGTGC
1 CTCACACGAGCTGTCGAGGACTCGCAACACATGCAGTACCCCAGCCATCGATACGGTATCTGTGC
* * * * * *
56337 ATATAACTGTTCCCTAACGATGTTGCTCACACGAGCTGTCGATAATATGCACTTATGCATAAATC
66 ATATAACTGTTCCCTAACGATGCTACTCACACGAGCTGTCAAGAATATGCA-TAAAGCAT-AATC
* *
56402 ACAGCCATCGCAGGGCTTGTAATCCATTCTAGGATCCATATCTCTT-TTTCCAACTCACGATGCT
129 ACAGCCATCGCAGGGCTCGTAATCCATT-TAAGATCCATATCTCTTCTTTCCAA-TCACGATGCT
56466 A
192 A
*
56467 CTCACACGAGCTGTCGAGGACTCGCAACACATGCGGTACCCCAGCCATCG
1 CTCACACGAGCTGTCGAGGACTCGCAACACATGCAGTACCCCAGCCATCG
56517 CGTCGGTTTC
Statistics
Matches: 208, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
192 48 0.23
193 8 0.04
194 35 0.17
195 72 0.35
196 44 0.21
197 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (192 bp):
CTCACACGAGCTGTCGAGGACTCGCAACACATGCAGTACCCCAGCCATCGATACGGTATCTGTGC
ATATAACTGTTCCCTAACGATGCTACTCACACGAGCTGTCAAGAATATGCATAAAGCATAATCAC
AGCCATCGCAGGGCTCGTAATCCATTTAAGATCCATATCTCTTCTTTCCAATCACGATGCTA
Found at i:64094 original size:15 final size:14
Alignment explanation
Indices: 64052--64094 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
64042 ATATATAGAA
* * *
64052 CCCAAAATTTGAAT
1 CCCAAACTTTAAAC
64066 CCCAAACTTTAAAC
1 CCCAAACTTTAAAC
64080 CCCAAACTCTTAAAC
1 CCCAAACT-TTAAAC
64095 ATTGAACTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.42, C:0.33, G:0.02, T:0.23
Consensus pattern (14 bp):
CCCAAACTTTAAAC
Found at i:64193 original size:27 final size:27
Alignment explanation
Indices: 64146--64200 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
64136 ACCTAAAAAC
* * * *
64146 CTTAAACCCTAACCCCTAAACCTAAAT
1 CTTAAACCCCAAACCCAAAACCCAAAT
64173 CTTAAACCCCAAACCCAAAACCCAAAT
1 CTTAAACCCCAAACCCAAAACCCAAAT
64200 C
1 C
64201 CGAACCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.40, G:0.00, T:0.16
Consensus pattern (27 bp):
CTTAAACCCCAAACCCAAAACCCAAAT
Found at i:64271 original size:14 final size:13
Alignment explanation
Indices: 64252--64296 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
64242 TGAGATTTGG
64252 GTTTAATGTTTAAA
1 GTTTAA-GTTTAAA
64266 GTTTAAGATTTAAA
1 GTTTAAG-TTTAAA
* *
64280 GTTTGAGTTCAAA
1 GTTTAAGTTTAAA
64293 GTTT
1 GTTT
64297 GAGATTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (13 bp):
GTTTAAGTTTAAA
Found at i:64295 original size:13 final size:14
Alignment explanation
Indices: 64263--64302 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
64253 TTTAATGTTT
* *
64263 AAAGTTTAAGATTT
1 AAAGTTTGAGATTC
64277 AAAGTTTGAG-TTC
1 AAAGTTTGAGATTC
64290 AAAGTTTGAGATT
1 AAAGTTTGAGATT
64303 TGATGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.40
Consensus pattern (14 bp):
AAAGTTTGAGATTC
Found at i:64310 original size:27 final size:28
Alignment explanation
Indices: 64241--64310 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 28
64231 CCCCTAAATC
* *
64241 TTGAGATTTG-GGTTTAATGTTTAAAGT
1 TTGAGATTTGAAGTTTAATGTTCAAAGT
* * *
64268 TTAAGATTTAAAGTTTGA-GTTCAAAGT
1 TTGAGATTTGAAGTTTAATGTTCAAAGT
*
64295 TTGAGATTTGATGTTT
1 TTGAGATTTGAAGTTT
64311 TAAAATTGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.47
Consensus pattern (28 bp):
TTGAGATTTGAAGTTTAATGTTCAAAGT
Found at i:79445 original size:16 final size:16
Alignment explanation
Indices: 79426--79457 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
79416 CTAATAAATC
79426 TATAT-TCAAA-CAAA
1 TATATATCAAATCAAA
79440 TATATATCAAATCAAA
1 TATATATCAAATCAAA
79456 TA
1 TA
79458 CATAACATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (16 bp):
TATATATCAAATCAAA
Found at i:80678 original size:364 final size:365
Alignment explanation
Indices: 79941--80744 Score: 1242
Period size: 364 Copynumber: 2.2 Consensus size: 365
79931 AGAGATCAAC
* * * *
79941 AATGGAAACTTTCAAAAAATTTAACATTTTTACAAATTGGTACATGAGCTAGTTAAATTAAGCTT
1 AATGGAAACTTTCAAAAACTTTAAGAGTTTTACAAATTGGTACATCAGCTAGTTAAATTAAGCTT
*
80006 CCATGACCTCAAATCTATAAAAATTTCAAAGAAATTACTTGAAATTTTACCTTTTATTGATGGTC
66 CCATGACCTCAAATCCATAAAAATTTCAAAGAAATTACTTGAAATTTTACCTTTTATTGATGGTC
*
80071 GAATACTTGAAGCCCTTGGACAAGCATAACTTTCTACCTAAAGCTTCAAATTAAAATTTGATTTC
131 GAATACTTGAAGCCCTTGGACAAGCATAACTTTATACCTAAAGCTTCAAATTAAAATTTGATTTC
80136 ACATATATTCATTAGGGACCTCCTACTTTCTATTACTACCAAAATTTCATAACAATTTTTTGTTT
196 ACATATATTCATTAGGGACCTCCTACTTTCTATTACTACC---A---CA-AACAATTTTTTGTTT
* * * *
80201 TATTCAATTTGATCCTTAATGTACAGAACTAACAATTGAGCTTTACAATCTAGTCATTTTTTAAT
254 TAGTCAATTTGATCCCTAATGTACAGAACTAACAATTAAGCTTAACAATCTAGTCATTTTTTAAT
* *
80266 AATCTAAACTTAATATCTATCAATACTAAATTTGTTCATTTCCCAAT
319 AATCTAAACTTAATATCTATCAACACTAAATTCGTTCATTTCCCAAT
*
80313 AATGGAAACTTTCAAAAACTTTAAGAGTTTTACAAATTGGTACATCATCTAGTTAAATTAAGCTT
1 AATGGAAACTTTCAAAAACTTTAAGAGTTTTACAAATTGGTACATCAGCTAGTTAAATTAAGCTT
*
80378 CCATGACCTCAAATCCATAAAAATTTCAAATAAATTATTTCTTTGAAATTTTACCTTTTATTGAT
66 CCATGACCTCAAATCCATAAAAATTTCAAAGAAATTA---C-TTGAAATTTTACCTTTTATTGAT
80443 GGTCGAATACTTGAAGCCCTTGG-CAAGCATAACTTTATACCTAAAGCTTCAAATTAAAATTTGA
127 GGTCGAATACTTGAAGCCCTTGGACAAGCATAACTTTATACCTAAAGCTTCAAATTAAAATTTGA
*
80507 TTTCACATATATTCATTAGGGACCTCCTACTTTCTATTCCTA-C-C-AA-AATTTTTTGTTTTAG
192 TTTCACATATATTCATTAGGGACCTCCTACTTTCTATTACTACCACAAACAATTTTTTGTTTTAG
*
80568 TCAATTTGATCCCTAATGTACAGAACTAACAATTAAGCTTAACAATTTAGTCATTTTTTAATAAT
257 TCAATTTGATCCCTAATGTACAGAACTAACAATTAAGCTTAACAATCTAGTCATTTTTTAATAAT
* * *
80633 CTAAACTTAATTTC-ATTCAACACTAAATTCGTTTATTTTCCAAT
322 CTAAACTTAATATCTA-TCAACACTAAATTCGTTCATTTCCCAAT
* * * * *
80677 AATGGAAACTTTCAAAAACTTTAAGAGTTTTACAAATTGGTACGTGAGCTAGCTAAATCAAGTTT
1 AATGGAAACTTTCAAAAACTTTAAGAGTTTTACAAATTGGTACATCAGCTAGTTAAATTAAGCTT
80742 CCA
66 CCA
80745 CGATTCAGTT
Statistics
Matches: 402, Mismatches: 25, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
363 1 0.00
364 174 0.43
365 2 0.00
367 1 0.00
372 95 0.24
374 1 0.00
375 82 0.20
376 46 0.11
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (365 bp):
AATGGAAACTTTCAAAAACTTTAAGAGTTTTACAAATTGGTACATCAGCTAGTTAAATTAAGCTT
CCATGACCTCAAATCCATAAAAATTTCAAAGAAATTACTTGAAATTTTACCTTTTATTGATGGTC
GAATACTTGAAGCCCTTGGACAAGCATAACTTTATACCTAAAGCTTCAAATTAAAATTTGATTTC
ACATATATTCATTAGGGACCTCCTACTTTCTATTACTACCACAAACAATTTTTTGTTTTAGTCAA
TTTGATCCCTAATGTACAGAACTAACAATTAAGCTTAACAATCTAGTCATTTTTTAATAATCTAA
ACTTAATATCTATCAACACTAAATTCGTTCATTTCCCAAT
Found at i:93073 original size:113 final size:113
Alignment explanation
Indices: 92936--93166 Score: 390
Period size: 113 Copynumber: 2.0 Consensus size: 113
92926 CCATTAACCT
* * *
92936 AAAAAAAACTTAACGGGAAGAAGATATTGGAACCAAATATATTGAATATTTTGGTTAATAGGTCT
1 AAAAGAAACTTAACGAGAAGAAGATATTAGAACCAAATATATTGAATATTTTGGTTAATAGGTCT
*
93001 TAAATATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTGAAATC
66 TAAAGATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTGAAATC
* * *
93049 AAAAGAAACTTAACGAGAAGAAGATATTAGAACCAAATATATTGAATCTTTTGGTTAATGGGTTT
1 AAAAGAAACTTAACGAGAAGAAGATATTAGAACCAAATATATTGAATATTTTGGTTAATAGGTCT
*
93114 TAAAGATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTGGAATC
66 TAAAGATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTGAAATC
93162 AAAAG
1 AAAAG
93167 GGAAGAATAT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (113 bp):
AAAAGAAACTTAACGAGAAGAAGATATTAGAACCAAATATATTGAATATTTTGGTTAATAGGTCT
TAAAGATTCAAGCTTTGAGACAGATTTGTAACTAAAGATATTGAAATC
Found at i:93269 original size:14 final size:16
Alignment explanation
Indices: 93242--93282 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
93232 TTAGGGTTTA
* *
93242 AAATTTTTAATTAA-T
1 AAATATTTATTTAATT
93257 AAA-ATTTATTTAATT
1 AAATATTTATTTAATT
93272 AAATATTTATT
1 AAATATTTATT
93283 CTCATTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 8 0.36
15 7 0.32
16 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTTATTTAATT
Found at i:97142 original size:16 final size:16
Alignment explanation
Indices: 97118--97166 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
97108 AATTTTATTA
*
97118 TTATTAATTTAAAATT
1 TTATAAATTTAAAATT
*
97134 TTATAAATTATAAAATA
1 TTATAAATT-TAAAATT
*
97151 TT-TAAATTAAAAATT
1 TTATAAATTTAAAATT
97166 T
1 T
97167 ATCATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 6 0.21
16 14 0.50
17 8 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATAAATTTAAAATT
Found at i:122502 original size:24 final size:24
Alignment explanation
Indices: 122475--122521 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
122465 TGACTCAAAT
* *
122475 AAATAAATAGAGTTTAATTGAAAC
1 AAATAAACAGAATTTAATTGAAAC
122499 AAATAAACAGAATTTAATTGAAA
1 AAATAAACAGAATTTAATTGAAA
122522 GATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (24 bp):
AAATAAACAGAATTTAATTGAAAC
Found at i:126201 original size:84 final size:84
Alignment explanation
Indices: 126103--126267 Score: 285
Period size: 84 Copynumber: 2.0 Consensus size: 84
126093 AGAAGATGAA
* *
126103 GATGAAGAAAAGAGACTTGATGAAAAGGATTTAGGGTTTTTTTAATTAAGGCTTAGAGTTTAAAA
1 GATGAAGAAAAGAGACTTGACGAAAAGGATTTAGGGTTTTTTCAATTAAGGCTTAGAGTTTAAAA
126168 ATTTTAATTAATTAAAGAT
66 ATTTTAATTAATTAAAGAT
* * *
126187 GATGAAGAAGAGAGACTTGGCGAAAAGGATTTAGGGTTTTTTCAATTAAGGTTTAGAGTTTAAAA
1 GATGAAGAAAAGAGACTTGACGAAAAGGATTTAGGGTTTTTTCAATTAAGGCTTAGAGTTTAAAA
126252 ATTTTAATTAATTAAA
66 ATTTTAATTAATTAAA
126268 TATTTATTCT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (84 bp):
GATGAAGAAAAGAGACTTGACGAAAAGGATTTAGGGTTTTTTCAATTAAGGCTTAGAGTTTAAAA
ATTTTAATTAATTAAAGAT
Found at i:128737 original size:30 final size:29
Alignment explanation
Indices: 128698--128754 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
128688 GGTTGGATGG
128698 GAGAGGAGTAAAAGTTTTAGGG-GAGAAGT
1 GAGAGGAGTAAAAGTTTT-GGGAGAGAAGT
*
128727 GAGAGAGAGTAAATGTTTTGGGAGAGAA
1 GAGAG-GAGTAAAAGTTTTGGGAGAGAA
128755 TAAAGAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.39, C:0.00, G:0.40, T:0.21
Consensus pattern (29 bp):
GAGAGGAGTAAAAGTTTTGGGAGAGAAGT
Found at i:128761 original size:28 final size:30
Alignment explanation
Indices: 128703--128761 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
128693 GATGGGAGAG
*
128703 GAGTAAAAGTTTTAGGGGAGAAGTGAGAGA
1 GAGTAAAAGTTTTAGGGGAGAAGTGAAAGA
*
128733 GAGTAAATGTTTT-GGGAGAGAA-T-AAAGA
1 GAGTAAAAGTTTTAGGG-GAGAAGTGAAAGA
128761 G
1 G
128762 TTTTGAGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 4 0.15
30 17 0.65
ACGTcount: A:0.41, C:0.00, G:0.37, T:0.22
Consensus pattern (30 bp):
GAGTAAAAGTTTTAGGGGAGAAGTGAAAGA
Found at i:129507 original size:6 final size:6
Alignment explanation
Indices: 129496--129538 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
129486 ATATTATTAA
* * *
129496 ATTTAT ATTTAT ATTTAT ATCTAT ATTTAT ATATAC ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT A
129539 CCATCCATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTAT
Found at i:137087 original size:4 final size:4
Alignment explanation
Indices: 137078--137172 Score: 111
Period size: 4 Copynumber: 23.2 Consensus size: 4
137068 AAATAAACGG
137078 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAAA GAAA GAAAA GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA GAAA
* * * * *
137128 GAAA GGAA GGAA GAAG GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
137173 GTAATGCGTT
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
3 3 0.04
4 66 0.81
5 12 0.15
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:137108 original size:25 final size:25
Alignment explanation
Indices: 137078--137171 Score: 118
Period size: 25 Copynumber: 3.6 Consensus size: 25
137068 AAATAAACGG
137078 GAAAGAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
137103 GAAAGAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
* *
137128 GAAAGGAAGGAAGAAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGAA--A-A-GAAAGAAA
*
137157 G-AAGAAGGAAAGAAA
1 GAAAGAAAGAAAGAAA
137172 GGTAATGCGT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 38 0.63
26 1 0.02
27 1 0.02
28 11 0.18
29 9 0.15
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAGAAAGAAA
Found at i:137173 original size:29 final size:29
Alignment explanation
Indices: 137077--137172 Score: 124
Period size: 29 Copynumber: 3.3 Consensus size: 29
137067 AAAATAAACG
*
137077 GGAAAGAAAGAAAGAAAAGAAAGAAAGAA
1 GGAAAGAAAGAAAGGAAAGAAAGAAAGAA
* *
137106 AGAAAGAAAGAAAAGAAAGAAAGAAAGGAA
1 GGAAAGAAAGAAAGGAAAGAAAGAAA-GAA
* *
137136 GG-AAGAAGGAGAGGAAAGAAAG-AAGAA
1 GGAAAGAAAGAAAGGAAAGAAAGAAAGAA
137163 GGAAAGAAAG
1 GGAAAGAAAG
137173 GTAATGCGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.09
28 8 0.14
29 40 0.70
30 4 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (29 bp):
GGAAAGAAAGAAAGGAAAGAAAGAAAGAA
Found at i:140043 original size:23 final size:23
Alignment explanation
Indices: 140013--140070 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
140003 TGACGTGACA
* *
140013 TCTAGTCAGTAACTTCTAGAAGG
1 TCTAGTCAGTAACTTCCAAAAGG
*
140036 TCTAGTCAGTAGCTTCCAAAAGG
1 TCTAGTCAGTAACTTCCAAAAGG
140059 TCTAGTCAGTAA
1 TCTAGTCAGTAA
140071 TGATGGACGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (23 bp):
TCTAGTCAGTAACTTCCAAAAGG
Found at i:143058 original size:23 final size:23
Alignment explanation
Indices: 143032--143134 Score: 161
Period size: 23 Copynumber: 4.5 Consensus size: 23
143022 AGGAACACTA
*
143032 GTGTGCTTATTGTTTCGCACTTC
1 GTGTGCTTACTGTTTCGCACTTC
143055 GTGTGCTTACTGTTTCGCACTTC
1 GTGTGCTTACTGTTTCGCACTTC
143078 GTGTGCTTACTGTTTCGCACTTC
1 GTGTGCTTACTGTTTCGCACTTC
* * *
143101 GTGTGCTAACTATTTCGCACCTC
1 GTGTGCTTACTGTTTCGCACTTC
*
143124 GTGTGCCTACT
1 GTGTGCTTACT
143135 AATTTGCGCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (23 bp):
GTGTGCTTACTGTTTCGCACTTC
Found at i:143154 original size:23 final size:22
Alignment explanation
Indices: 143128--143179 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
143118 CACCTCGTGT
*
143128 GCCTACTAATTTGCGCTATGTGC
1 GCCTACTAA-TTGCACTATGTGC
* * *
143151 GCCTACTGATTGCACTGTGTGT
1 GCCTACTAATTGCACTATGTGC
143173 GCCTACT
1 GCCTACT
143180 GGATTGCAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (22 bp):
GCCTACTAATTGCACTATGTGC
Found at i:143192 original size:23 final size:22
Alignment explanation
Indices: 143124--143195 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
143114 TTCGCACCTC
* * *
143124 GTGTGCCTACTAATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTGT
*
143147 GTGCGCCTACTGATTGCACTGT
1 GTGTGCCTACTGATTGCACTGT
*
143169 GTGTGCCTACTGGATTGCAGTGT
1 GTGTGCCTACT-GATTGCACTGT
143192 GTGT
1 GTGT
143196 TCTTACTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.40
23 25 0.60
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:148985 original size:11 final size:11
Alignment explanation
Indices: 148969--149002 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
148959 ATTATTTCGG
148969 TTATTTTTATT
1 TTATTTTTATT
*
148980 TTATTTCTA-T
1 TTATTTTTATT
148990 TTATTTTTATT
1 TTATTTTTATT
149001 TT
1 TT
149003 TGGTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:149845 original size:14 final size:13
Alignment explanation
Indices: 149831--149898 Score: 57
Period size: 13 Copynumber: 4.9 Consensus size: 13
149821 GAGTTCGAAT
149831 AAAGAAGAAAAAATA
1 AAAGAAG-AAAAA-A
149846 AAAGAAGGAAAAAA
1 AAAGAA-GAAAAAA
* *
149860 AACGAACAACAAAA
1 AAAGAAGAA-AAAA
149874 AAA-ATAGAAAAAA
1 AAAGA-AGAAAAAA
*
149887 AAAAAAGAAAAA
1 AAAGAAGAAAAA
149899 GGTTCGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 17 0.38
14 16 0.36
15 11 0.24
16 1 0.02
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAGAAGAAAAAA
Found at i:149851 original size:15 final size:14
Alignment explanation
Indices: 149831--149898 Score: 68
Period size: 15 Copynumber: 4.9 Consensus size: 14
149821 GAGTTCGAAT
149831 AAAGAAGAAAAAATA
1 AAAGAAGAAAAAA-A
*
149846 AAAGAAGGAAAAAA
1 AAAGAAGAAAAAAA
* *
149860 AACGAACAACAAAAA
1 AAAGAAGAA-AAAAA
*
149875 AAA-TAGAAAAAAA
1 AAAGAAGAAAAAAA
149888 AAA-AAGAAAAA
1 AAAGAAGAAAAA
149899 GGTTCGAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
13 15 0.34
14 10 0.23
15 19 0.43
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAGAAGAAAAAAA
Found at i:150678 original size:23 final size:23
Alignment explanation
Indices: 150652--150708 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
150642 TGACGTGGCA
* *
150652 TCCAGTCAGGAGCTTCTAGAAGG
1 TCCAGTCAGCAGCTTCTAAAAGG
* *
150675 TCCAATCAACAGCTTCTAAAAGG
1 TCCAGTCAGCAGCTTCTAAAAGG
*
150698 TCTAGTCAGCA
1 TCCAGTCAGCA
150709 ATGATGGATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
TCCAGTCAGCAGCTTCTAAAAGG
Found at i:153273 original size:28 final size:28
Alignment explanation
Indices: 153230--153304 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
153220 CCTTAATTAA
*
153230 TCTACTGTTTACGGTTTAGAGTTTCAAG
1 TCTAGTGTTTACGGTTTAGAGTTTCAAG
* * *
153258 TCTAGTGTTTATGGTTTAGGGTTTTAAG
1 TCTAGTGTTTACGGTTTAGAGTTTCAAG
* * *
153286 TTTAGGGTTTACAGTTTAG
1 TCTAGTGTTTACGGTTTAG
153305 GCTTTAAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (28 bp):
TCTAGTGTTTACGGTTTAGAGTTTCAAG
Found at i:153281 original size:14 final size:14
Alignment explanation
Indices: 153264--153310 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
153254 CAAGTCTAGT
*
153264 GTTTATGGTTTAGG
1 GTTTATAGTTTAGG
153278 GTTT-TAAGTTTAGG
1 GTTTAT-AGTTTAGG
*
153292 GTTTACAGTTTAGG
1 GTTTATAGTTTAGG
*
153306 CTTTA
1 GTTTA
153311 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.04
14 27 0.96
ACGTcount: A:0.19, C:0.04, G:0.28, T:0.49
Consensus pattern (14 bp):
GTTTATAGTTTAGG
Found at i:153554 original size:20 final size:21
Alignment explanation
Indices: 153529--153568 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
153519 GTCCATTTGC
153529 CCCGG-AGGAGTAGAGTATTG
1 CCCGGAAGGAGTAGAGTATTG
153549 CCCGGAAGGAGTAGAGTATT
1 CCCGGAAGGAGTAGAGTATT
153569 ATGGTGGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.20
Consensus pattern (21 bp):
CCCGGAAGGAGTAGAGTATTG
Found at i:155625 original size:16 final size:16
Alignment explanation
Indices: 155604--155652 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
155594 TGATGGGAAT
155604 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
155620 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
155634 A-TATTTTGATAATTA
1 ATTATTTTGATAATTA
155649 ATTA
1 ATTA
155653 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
15 4 0.14
16 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:156321 original size:12 final size:12
Alignment explanation
Indices: 156306--156331 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
156296 AAATTAAAAT
156306 ATTTTAAAATTA
1 ATTTTAAAATTA
156318 ATTTTAAAATTA
1 ATTTTAAAATTA
156330 AT
1 AT
156332 CAAACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:156528 original size:3 final size:3
Alignment explanation
Indices: 156522--156551 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
156512 CTCCTTCCCT
156522 TTC TTC TTC TTC TTC TTC TTCC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TT
156552 TCTTTCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:156530 original size:12 final size:11
Alignment explanation
Indices: 156519--156570 Score: 52
Period size: 12 Copynumber: 4.6 Consensus size: 11
156509 CTTCTCCTTC
156519 CCTTTCTTCTT
1 CCTTTCTTCTT
*
156530 CTTCTTCTTCTT
1 CCT-TTCTTCTT
156542 CC-TTCTTCTT
1 CCTTTCTTCTT
*
156552 TCTTTCTTTCTT
1 CCTTTC-TTCTT
*
156564 TCTTTCT
1 CCTTTCT
156571 CTTTTTTCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 9 0.26
11 6 0.17
12 20 0.57
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
CCTTTCTTCTT
Found at i:156554 original size:4 final size:4
Alignment explanation
Indices: 156547--156585 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
156537 TTCTTCCTTC
*
156547 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TT
156586 TTTACTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:156562 original size:25 final size:26
Alignment explanation
Indices: 156522--156593 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 26
156512 CTCCTTCCCT
156522 TTCTTC-TTC-TTC-TTC-TTCTTCC
1 TTCTTCTTTCTTTCTTTCTTTCTTCC
*
156544 TTCTTCTTTCTTTCTTTCTTTCTTTC
1 TTCTTCTTTCTTTCTTTCTTTCTTCC
*
156570 -TCTTTTTTCTTTCTTT-TTTACTTC
1 TTCTTCTTTCTTTCTTTCTTT-CTTC
156594 AATTTTCGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.14
23 3 0.07
24 6 0.14
25 21 0.50
26 6 0.14
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (26 bp):
TTCTTCTTTCTTTCTTTCTTTCTTCC
Found at i:156566 original size:29 final size:29
Alignment explanation
Indices: 156497--156585 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
156487 AAACACATTA
* *
156497 TCTTT-TTTTTTTCTTC-TCCTTC-CCTT
1 TCTTTCTTTCTTTCTTCTTCCTTCTTCTT
156523 TC-TTC-TTCTTCTTCTTCTTCCTTCTTCTT
1 TCTTTCTTTC-T-TTCTTCTTCCTTCTTCTT
* *
156552 TCTTTCTTTCTTTCTT-TCTCTTTTTTCTT
1 TCTTTCTTTCTTTCTTCT-TCCTTCTTCTT
156581 TCTTT
1 TCTTT
156586 TTTACTTCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
25 4 0.08
26 3 0.06
27 6 0.12
28 7 0.14
29 24 0.47
30 4 0.08
31 3 0.06
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (29 bp):
TCTTTCTTTCTTTCTTCTTCCTTCTTCTT
Found at i:185543 original size:18 final size:18
Alignment explanation
Indices: 185520--185556 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
185510 GAGGAACAGC
185520 AAGCGGA-GATGGCGAAGA
1 AAGCGGACGA-GGCGAAGA
185538 AAGCGGACGAGGCGAAGA
1 AAGCGGACGAGGCGAAGA
185556 A
1 A
185557 GAGACAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.41, C:0.14, G:0.43, T:0.03
Consensus pattern (18 bp):
AAGCGGACGAGGCGAAGA
Found at i:193758 original size:3 final size:3
Alignment explanation
Indices: 193750--193775 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
193740 AATACATAAA
193750 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
193776 ATAGTCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:195801 original size:15 final size:14
Alignment explanation
Indices: 195779--195817 Score: 69
Period size: 15 Copynumber: 2.7 Consensus size: 14
195769 TAAAATTTAT
195779 TTAAAATAAAAAGC
1 TTAAAATAAAAAGC
195793 TTAAAAATAAAAAGC
1 TT-AAAATAAAAAGC
195808 TTAAAATAAA
1 TTAAAATAAA
195818 TAAATAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (14 bp):
TTAAAATAAAAAGC
Found at i:196080 original size:13 final size:13
Alignment explanation
Indices: 196064--196088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
196054 AACAAAAACA
196064 TAAAAAAAAAAAT
1 TAAAAAAAAAAAT
196077 TAAAAAAAAAAA
1 TAAAAAAAAAAA
196089 GCTGATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
TAAAAAAAAAAAT
Found at i:197779 original size:13 final size:13
Alignment explanation
Indices: 197748--197780 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
197738 AAATCAACAA
197748 AAAAAAT-CCTTG
1 AAAAAATCCCTTG
197760 AAAAAATCCCTTG
1 AAAAAATCCCTTG
*
197773 AGAAAATC
1 AAAAAATC
197781 TTATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAAAATCCCTTG
Found at i:200453 original size:23 final size:23
Alignment explanation
Indices: 200425--200468 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
200415 TTGATTTTAG
200425 AAATTTTAAATTAATTCAATTGA
1 AAATTTTAAATTAATTCAATTGA
* * *
200448 AAATTTTGATTTAATTTAATT
1 AAATTTTAAATTAATTCAATT
200469 TTTTAGAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (23 bp):
AAATTTTAAATTAATTCAATTGA
Found at i:203542 original size:15 final size:15
Alignment explanation
Indices: 203522--203551 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
203512 TTGGTCGTGG
203522 CGATGATGATGATGA
1 CGATGATGATGATGA
203537 CGATGATGATGATGA
1 CGATGATGATGATGA
203552 AATGGACGGT
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:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (15 bp):
CGATGATGATGATGA
Found at i:205834 original size:2 final size:2
Alignment explanation
Indices: 205827--205859 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
205817 TGTTTTCTTT
*
205827 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
205860 CTGCTTACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:208561 original size:23 final size:23
Alignment explanation
Indices: 208535--208584 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
208525 ACACTAGCGC
208535 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTTCGTGT
*
208558 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGT
208581 GCTC
1 GCTC
208585 AGTACTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTCGTGT
Found at i:215298 original size:19 final size:17
Alignment explanation
Indices: 215257--215299 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
215247 AATTTTTATT
*
215257 TTAAAAAAATATAAAAT
1 TTAAAAAAATATAAAAG
215274 TCTAAAAAATATATAAAAAG
1 T-TAAAAAA-ATAT-AAAAG
215294 TTAAAA
1 TTAAAA
215300 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 7 0.32
19 9 0.41
20 5 0.23
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
TTAAAAAAATATAAAAG
Found at i:229627 original size:17 final size:16
Alignment explanation
Indices: 229607--229655 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
229597 AAATAAATTT
229607 TAAATATAAATTTATAA
1 TAAAT-TAAATTTATAA
* *
229624 TAAACTTAATTTTAAAA
1 TAAA-TTAAATTTATAA
229641 TAAATTTAAATTTAT
1 TAAA-TTAAATTTAT
229656 TGAGTCCGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAAATTTATAA
Found at i:244474 original size:173 final size:173
Alignment explanation
Indices: 244185--244532 Score: 678
Period size: 173 Copynumber: 2.0 Consensus size: 173
244175 CAATTCTTTT
*
244185 CCTTCCAATGGATGCCATCTTCTGCCAATTTCTTGTCATTCTCATAAGCTTCTTTGAGGTAATCA
1 CCTTCCAATGGATGCCATCTTCTACCAATTTCTTGTCATTCTCATAAGCTTCTTTGAGGTAATCA
*
244250 TTCTGGCTTCCATTTGTGTTGCGGAAGAAAATCTTAGGAAAAAAAGAACACAAAGGAGGTTAATT
66 TTCTGGCTTCCATTTGTGTTGCGGAAGAAAATCTTAGGAAAAAAAGAACACAAAGAAGGTTAATT
244315 TGTATATAATTGCTAGTACTAATCAGGGAAGGTAATAAGTCTG
131 TGTATATAATTGCTAGTACTAATCAGGGAAGGTAATAAGTCTG
244358 CCTTCCAATGGATGCCATCTTCTACCAATTTCTTGTCATTCTCATAAGCTTCTTTGAGGTAATCA
1 CCTTCCAATGGATGCCATCTTCTACCAATTTCTTGTCATTCTCATAAGCTTCTTTGAGGTAATCA
244423 TTCTGGCTTCCATTTGTGTTGCGGAAGAAAATCTTAGGAAAAAAAGAACACAAAGAAGGTTAATT
66 TTCTGGCTTCCATTTGTGTTGCGGAAGAAAATCTTAGGAAAAAAAGAACACAAAGAAGGTTAATT
244488 TGTATATAATTGCTAGTACTAATCAGGGAAGGTAATAAGTCTG
131 TGTATATAATTGCTAGTACTAATCAGGGAAGGTAATAAGTCTG
244531 CC
1 CC
244533 ATTTATACAG
Statistics
Matches: 173, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 173 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (173 bp):
CCTTCCAATGGATGCCATCTTCTACCAATTTCTTGTCATTCTCATAAGCTTCTTTGAGGTAATCA
TTCTGGCTTCCATTTGTGTTGCGGAAGAAAATCTTAGGAAAAAAAGAACACAAAGAAGGTTAATT
TGTATATAATTGCTAGTACTAATCAGGGAAGGTAATAAGTCTG
Found at i:246455 original size:52 final size:53
Alignment explanation
Indices: 246383--246579 Score: 168
Period size: 55 Copynumber: 3.5 Consensus size: 53
246373 GCAATGCAAG
*
246383 GACCGATACTCCCTTTATCAGATAAAAAAA-TTTTTGAGTGTTTGCCAAGCCATT
1 GACCGACAC-CCCTTTATCAGATAAAAAAATTTTTTGAGTGTTTGCCAAGCCA-T
*
246437 G-CCGACACCCCTTTATCAGATAAAAAATATTTTTTTGGGTGTTTGCCAAGCCAT
1 GACCGACACCCCTTTATCAGATAAAAAA-A-TTTTTTGAGTGTTTGCCAAGCCAT
* * *
246491 GATCGACACCCTCTTT-TCTAGATACAAAAAAATATATTTTTTGAGTGTTTGTCAAGCCGT
1 GACCGACACCC-CTTTATC-AGAT----AAAAA-A-ATTTTTTGAGTGTTTGCCAAGCCAT
** * *
246551 GGTCAACACCCTTTTA-CAAGATAAAAAAA
1 GACCGACACCCCTTTATC-AGATAAAAAAA
246580 AATATTTTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
52 19 0.16
53 8 0.07
54 4 0.03
55 36 0.30
56 8 0.07
59 8 0.07
60 35 0.29
61 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (53 bp):
GACCGACACCCCTTTATCAGATAAAAAAATTTTTTGAGTGTTTGCCAAGCCAT
Found at i:246487 original size:55 final size:56
Alignment explanation
Indices: 246347--246618 Score: 220
Period size: 57 Copynumber: 4.8 Consensus size: 56
246337 AAAAATACGT
* * *
246347 ATAAAAAATAATTTTTTTGGGTATTTG-CAATG-CAAGGACCGATACTCCCTTTATC-AG
1 ATAAAAAAT-ATTTTTTTGGGTGTTTGCCAA-GCCATGG-CCGACAC-CCCTTTATCAAG
* *
246404 ATAAAAAA-A--TTTTTGAGTGTTTGCCAAGCCATTGCCGACACCCCTTTATC-AG
1 ATAAAAAATATTTTTTTGGGTGTTTGCCAAGCCATGGCCGACACCCCTTTATCAAG
** *
246456 ATAAAAAATATTTTTTTGGGTGTTTGCCAAGCCATGATCGACACCCTCTTT-TCTAG
1 ATAAAAAATATTTTTTTGGGTGTTTGCCAAGCCATGGCCGACACCC-CTTTATCAAG
* * * * * *
246512 ATACAAAAAAATATATTTTTTGAGTGTTTGTCAAGCCGTGGTCAACACCCTTTTA-CAAG
1 AT---AAAAAATAT-TTTTTTGGGTGTTTGCCAAGCCATGGCCGACACCCCTTTATCAAG
* * * *
246571 ATAAAAAAAAATATTTTTTGGGTGCTTGCCAAGCAATGGCTGACACCC
1 AT-AAAAAATAT-TTTTTTGGGTGTTTGCCAAGCCATGGCCGACACCC
246619 ACGAATAATA
Statistics
Matches: 178, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
52 19 0.11
53 20 0.11
54 6 0.03
55 33 0.19
56 8 0.04
57 45 0.25
59 17 0.10
60 30 0.17
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (56 bp):
ATAAAAAATATTTTTTTGGGTGTTTGCCAAGCCATGGCCGACACCCCTTTATCAAG
Found at i:246604 original size:57 final size:59
Alignment explanation
Indices: 246406--246604 Score: 193
Period size: 60 Copynumber: 3.5 Consensus size: 59
246396 TTTATCAGAT
* * *
246406 AAAAAA-A-TTTTTGAGTGTTTGCCAAGCCATTG-CCGACACCC-CTTTATC-AGAT--AA
1 AAAAAATATTTTTTGGGTGTTTGCCAAGCCA-TGATCAACACCCTCTTTA-CAAGATACAA
* * * *
246460 AAAATAT-TTTTTTGGGTGTTTGCCAAGCCATGATCGACACCCTCTTTTCTAGATACAA
1 AAAAAATATTTTTTGGGTGTTTGCCAAGCCATGATCAACACCCTCTTTACAAGATACAA
* * * *
246518 AAAAATATATTTTTTGAGTGTTTGTCAAGCCGTGGTCAACACCCT-TTTACAAGATA-AA
1 AAAAA-ATATTTTTTGGGTGTTTGCCAAGCCATGATCAACACCCTCTTTACAAGATACAA
*
246576 AAAAAATATTTTTTGGGTGCTTGCCAAGC
1 AAAAAATATTTTTTGGGTGTTTGCCAAGC
246605 AATGGCTGAC
Statistics
Matches: 121, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
54 7 0.06
55 30 0.25
56 8 0.07
57 21 0.17
58 13 0.11
59 11 0.09
60 31 0.26
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (59 bp):
AAAAAATATTTTTTGGGTGTTTGCCAAGCCATGATCAACACCCTCTTTACAAGATACAA
Found at i:246617 original size:57 final size:57
Alignment explanation
Indices: 246406--246618 Score: 208
Period size: 55 Copynumber: 3.8 Consensus size: 57
246396 TTTATCAGAT
* *
246406 AAAAAA-A-TTTTTGAGTGTTTGCCAAGCCATTGC-CGACACCCCTTTATCAGAT-AA
1 AAAAAATATTTTTTGAGTGTTTGCCAAGCCATGGCTCGACACCCTTTTA-CAGATAAA
* * * *
246460 AAAATAT-TTTTTTGGGTGTTTGCCAAGCCAT-GATCGACACCCTCTTTTCTAGATACAA
1 AAAAAATATTTTTTGAGTGTTTGCCAAGCCATGGCTCGACACCCT-TTTAC-AGATA-AA
* * *
246518 AAAAATATATTTTTTGAGTGTTTGTCAAGCCGTGG-TCAACACCCTTTTACAAGATAAA
1 AAAAA-ATATTTTTTGAGTGTTTGCCAAGCCATGGCTCGACACCCTTTTAC-AGATAAA
* * *
246576 AAAAAATATTTTTTGGGTGCTTGCCAAGCAATGGCT-GACACCC
1 AAAAAATATTTTTTGAGTGTTTGCCAAGCCATGGCTCGACACCC
246619 ACGAATAATA
Statistics
Matches: 130, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
54 6 0.05
55 31 0.24
56 7 0.05
57 30 0.23
58 14 0.11
59 11 0.08
60 30 0.23
61 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (57 bp):
AAAAAATATTTTTTGAGTGTTTGCCAAGCCATGGCTCGACACCCTTTTACAGATAAA
Found at i:247757 original size:57 final size:56
Alignment explanation
Indices: 247508--247771 Score: 225
Period size: 56 Copynumber: 4.7 Consensus size: 56
247498 CCCAAAATTT
*
247508 TTTTTTTATCTGAAAAAG-GGGATGTCGGCCATGCCATGG-CAGAC-ACTAAAAAAATA
1 TTTTTTTATCTGAAAAAGAGGG-TGTCGGCCATGGCATGGAC-GACAAC-AAAAAAATA
** * ** * *
247564 TTTCCTTATCTGAAAAAG-GAGATGTCAACCATGGCATAGACGACACCCAAAAAAATA
1 TTTTTTTATCTGAAAAAGAG-GGTGTCGGCCATGGCATGGACGACA-ACAAAAAAATA
* * * *** * * * *
247621 -TTTTTTATTTGAAAACGAAGGTGTCGATAATGACAT-GAGTGACACCCAAAAAATA
1 TTTTTTTATCTGAAAAAGAGGGTGTCGGCCATGGCATGGA-CGACAACAAAAAAATA
* *
247676 TTTTTTTATCTGAAAAAAAAGGTGTCGGCCATGGCATGGACGACAACAAAAAAATA
1 TTTTTTTATCTGAAAAAGAGGGTGTCGGCCATGGCATGGACGACAACAAAAAAATA
* *
247732 TTTTATTTATCTTAAAAAGAGGGTGTTGGCCATGGCATGG
1 TTTT-TTTATCTGAAAAAGAGGGTGTCGGCCATGGCATGG
247772 GCGATACCTA
Statistics
Matches: 165, Mismatches: 34, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
55 12 0.07
56 108 0.65
57 44 0.27
58 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (56 bp):
TTTTTTTATCTGAAAAAGAGGGTGTCGGCCATGGCATGGACGACAACAAAAAAATA
Done.