Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013152.1 Kokia drynarioides strain JFW-HI SEQ_128171, 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: 121818
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1079 original size:19 final size:19
Alignment explanation
Indices: 1057--1093 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1047 ATCAAAAGTT
*
1057 GAGAAAAAGAGAAAAATAC
1 GAGAAAAAGAAAAAAATAC
*
1076 GAGAAAAATAAAAAAATA
1 GAGAAAAAGAAAAAAATA
1094 AAAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (19 bp):
GAGAAAAAGAAAAAAATAC
Found at i:6327 original size:10 final size:10
Alignment explanation
Indices: 6312--6342 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
6302 ACAAGCCCAA
6312 ATTTTTATTT
1 ATTTTTATTT
6322 ATTTTTATTT
1 ATTTTTATTT
6332 ATTTATTATTT
1 ATTT-TTATTT
6343 TATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.70
11 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:7045 original size:34 final size:34
Alignment explanation
Indices: 6993--7067 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
6983 TCGGCCATGC
6993 AAAAAGAAAGGAGGATTT-GCTTTGATTTTGAGAGA
1 AAAAAGAAAGGAGGATTTGGCTTTG-TTTTGAGA-A
* *
7028 AAAAAGAAAGGA-TATTTGGTTTTGTTTTGAGAA
1 AAAAAGAAAGGAGGATTTGGCTTTGTTTTGAGAA
7061 AGAAAAG
1 A-AAAAG
7068 GAATGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
33 2 0.06
34 17 0.47
35 17 0.47
ACGTcount: A:0.43, C:0.01, G:0.27, T:0.29
Consensus pattern (34 bp):
AAAAAGAAAGGAGGATTTGGCTTTGTTTTGAGAA
Found at i:7383 original size:29 final size:28
Alignment explanation
Indices: 7343--7556 Score: 119
Period size: 30 Copynumber: 7.2 Consensus size: 28
7333 GCTTTATTTT
*
7343 AAAATT-ATATTTTGACCCAAGCTTTCCA
1 AAAATTCA-ATTTTGACCCAAACTTTCCA
*
7371 AAAATTCCAATTTT-ACCCACGAACATTCCA
1 AAAATT-CAATTTTGACCCA--AACTTTCCA
* *
7401 AAAATTCAAATTTGACCCTTAAATTTTCCA
1 AAAATTCAATTTTGACCC--AAACTTTCCA
* * *
7431 AAAATTAAAATTTGACCCTTAAATTTTCCAA
1 AAAATTCAATTTTGACCC--AAACTTTCC-A
* * *
7462 AAAATTTGAA-TTTAACCCTTAAATTTTCCA
1 AAAA-TTCAATTTTGACCC--AAACTTTCCA
* * *
7492 CAAATTCAATTTTAACCCATAAACTTTCTA
1 AAAATTCAATTTTGACCC--AAACTTTCCA
* * *
7522 AAAATTCAAATTTAACCCTTAAATTTTCCA
1 AAAATTCAATTTTGACCC--AAACTTTCCA
7552 AAAAT
1 AAAAT
7557 ACCAATTTAA
Statistics
Matches: 158, Mismatches: 18, Indels: 18
0.81 0.09 0.09
Matches are distributed among these distances:
28 11 0.07
29 15 0.09
30 104 0.66
31 23 0.15
32 5 0.03
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATTCAATTTTGACCCAAACTTTCCA
Found at i:7430 original size:30 final size:30
Alignment explanation
Indices: 7396--7659 Score: 289
Period size: 30 Copynumber: 8.8 Consensus size: 30
7386 CCCACGAACA
*
7396 TTCCAAAAATTCAAATTTGACCCTTAAATT
1 TTCCAAAAATTCAAATTTAACCCTTAAATT
* *
7426 TTCCAAAAATTAAAATTTGACCCTTAAATT
1 TTCCAAAAATTCAAATTTAACCCTTAAATT
**
7456 TTCCAAAAAATTTGAATTTAACCCTTAAATT
1 TTCC-AAAAATTCAAATTTAACCCTTAAATT
* * * *
7487 TTCCACAAATTCAATTTTAACCCATAAACT
1 TTCCAAAAATTCAAATTTAACCCTTAAATT
*
7517 TTCTAAAAATTCAAATTTAACCCTTAAATT
1 TTCCAAAAATTCAAATTTAACCCTTAAATT
* * *
7547 TTCCAAAAATACCAATTTAACCCTCAAA-T
1 TTCCAAAAATTCAAATTTAACCCTTAAATT
** * *
7576 TTCCAAAAACACCAATTTAACCCCTAAATT
1 TTCCAAAAATTCAAATTTAACCCTTAAATT
** * * *
7606 TTCCAAAAATTTTAATTTGACCCCTGAAGTT
1 TTCCAAAAATTCAAATTT-AACCCTTAAATT
*
7637 TT-CAAAAATTCAAATTTGACCCT
1 TTCCAAAAATTCAAATTTAACCCT
7660 ATTTTAATGT
Statistics
Matches: 197, Mismatches: 34, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
29 30 0.15
30 130 0.66
31 37 0.19
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (30 bp):
TTCCAAAAATTCAAATTTAACCCTTAAATT
Found at i:7443 original size:60 final size:60
Alignment explanation
Indices: 7365--7659 Score: 283
Period size: 60 Copynumber: 4.9 Consensus size: 60
7355 TGACCCAAGC
* * * * *
7365 TTTCCAAAAATTCCAATTTTACCCACGAACATTCCAAAAATTCAAATTTGACCCTTAAAT
1 TTTCCAAAAATTACAATTTGACCCACAAACTTTCCAAAAATTCAAATTTAACCCTTAAAT
* ** * **
7425 TTTCCAAAAATTAAAATTTGACCCTTAAATTTTCCAAAAAATTTGAATTTAACCCTTAAAT
1 TTTCCAAAAATTACAATTTGACCCACAAACTTTCC-AAAAATTCAAATTTAACCCTTAAAT
* * * *
7486 TTTCCACAAATT-CAATTTTAACCCATAAACTTTCTAAAAATTCAAATTTAACCCTTAAAT
1 TTTCCAAAAATTACAA-TTTGACCCACAAACTTTCCAAAAATTCAAATTTAACCCTTAAAT
* * ** * *
7546 TTTCCAAAAA-TACCAATTTAACCCTCAAA-TTTCCAAAAACACCAATTTAACCCCTAAAT
1 TTTCCAAAAATTA-CAATTTGACCCACAAACTTTCCAAAAATTCAAATTTAACCCTTAAAT
** * * * *
7605 TTTCCAAAAATTTTAATTTGACCC-CTGAAGTTTTCAAAAATTCAAATTTGACCCT
1 TTTCCAAAAATTACAATTTGACCCAC-AAACTTTCCAAAAATTCAAATTTAACCCT
7660 ATTTTAATGT
Statistics
Matches: 191, Mismatches: 37, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
58 1 0.01
59 47 0.25
60 92 0.48
61 51 0.27
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (60 bp):
TTTCCAAAAATTACAATTTGACCCACAAACTTTCCAAAAATTCAAATTTAACCCTTAAAT
Found at i:7491 original size:91 final size:89
Alignment explanation
Indices: 7365--7659 Score: 297
Period size: 91 Copynumber: 3.3 Consensus size: 89
7355 TGACCCAAGC
* * * * *
7365 TTTCCAAAAATTCCAATTTTACCCACGAACA-TTCCAAAAATTCAAATTTGACCCTTAAATTTTC
1 TTTCCAAAAATACCAATTTAACCCTC-AA-ATTTCCAAAAATTCAAATTTAACCCATAAATTTTC
7429 CAAAAATTAAAATTTGACCCTTAAAT
64 CAAAAATTAAAATTTGACCCTTAAAT
*** * * * *
7455 TTTCCAAAAAATTTGAATTTAACCCTTAAATTTTCCACAAATTCAATTTTAACCCATAAACTTTC
1 TTTCC-AAAAATACCAATTTAACCCTCAAA-TTTCCAAAAATTCAAATTTAACCCATAAATTTTC
* * *
7520 TAAAAATTCAAATTTAACCCTTAAAT
64 CAAAAATTAAAATTTGACCCTTAAAT
** * *
7546 TTTCCAAAAATACCAATTTAACCCTCAAATTTCCAAAAACACCAATTTAACCCCTAAATTTTCCA
1 TTTCCAAAAATACCAATTTAACCCTCAAATTTCCAAAAATTCAAATTTAACCCATAAATTTTCCA
** * *
7611 AAAATTTTAATTTGACCCCTGAAGT
66 AAAATTAAAATTTGA-CCCTTAAAT
* * *
7636 TTT-CAAAAATTCAAATTTGACCCT
1 TTTCCAAAAATACCAATTTAACCCT
7660 ATTTTAATGT
Statistics
Matches: 168, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
89 59 0.35
90 37 0.22
91 72 0.43
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (89 bp):
TTTCCAAAAATACCAATTTAACCCTCAAATTTCCAAAAATTCAAATTTAACCCATAAATTTTCCA
AAAATTAAAATTTGACCCTTAAAT
Found at i:7497 original size:121 final size:118
Alignment explanation
Indices: 7365--7659 Score: 353
Period size: 121 Copynumber: 2.5 Consensus size: 118
7355 TGACCCAAGC
*
7365 TTTCCAAAAATTCCAATTTTACCCACGAACATTCCAAAAATTCAAATTTGACCCTTAAATTTTCC
1 TTTCCAAAAATT-CAATTTTACCCACGAACTTTCCAAAAATTCAAATTTGACCCTTAAATTTTCC
* * ** *
7430 AAAAATTA-AAATTTGACCCTTAAATTTTCCAAAAA-ATTTGAATTTAACCCTTAAAT
65 AAAAA-TACAAATTTAACCCTCAAA-TTTCCAAAAACA--CCAATTTAACCCCTAAAT
* ** * *
7486 TTTCCACAAATTCAATTTTAACCCATAAACTTTCTAAAAATTCAAATTTAACCCTTAAATTTTCC
1 TTTCCAAAAATTCAATTTT-ACCCACGAACTTTCCAAAAATTCAAATTTGACCCTTAAATTTTCC
*
7551 AAAAATACCAATTTAACCCTCAAATTTCCAAAAACACCAATTTAACCCCTAAAT
65 AAAAATACAAATTTAACCCTCAAATTTCCAAAAACACCAATTTAACCCCTAAAT
* * * *
7605 TTTCCAAAAATTTTAATTTGACCC-CTGAAGTTTTCAAAAATTCAAATTTGACCCT
1 TTTCCAAAAA-TTCAATTTTACCCAC-GAACTTTCCAAAAATTCAAATTTGACCCT
7660 ATTTTAATGT
Statistics
Matches: 148, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
119 52 0.35
120 26 0.18
121 70 0.47
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (118 bp):
TTTCCAAAAATTCAATTTTACCCACGAACTTTCCAAAAATTCAAATTTGACCCTTAAATTTTCCA
AAAATACAAATTTAACCCTCAAATTTCCAAAAACACCAATTTAACCCCTAAAT
Found at i:7693 original size:2 final size:2
Alignment explanation
Indices: 7688--7718 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7678 TATTTTATCC
7688 TA TA TA TA 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 T
7719 TACATGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7813 original size:22 final size:22
Alignment explanation
Indices: 7788--7831 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7778 TATATTATTT
* *
7788 TATTTGTTTTTTTTTATGTATA
1 TATTGGTTTTTTATTATGTATA
*
7810 TATTGGTTTTTTATTATTTATA
1 TATTGGTTTTTTATTATGTATA
7832 CTTGTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (22 bp):
TATTGGTTTTTTATTATGTATA
Found at i:9825 original size:29 final size:29
Alignment explanation
Indices: 9766--10510 Score: 496
Period size: 29 Copynumber: 25.8 Consensus size: 29
9756 GAAAATGAAG
* * **
9766 TTTTGGAGAGTTT-GGGGTTAAAATGCAAT
1 TTTTGGA-AGTTTAGAGGTAAAAATGTGAT
* * *
9795 TTTAGAAAGTTTAAAGGTAAAAATGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * *
9824 TTTTGGAAATTTAGAGGCAAAAATGTAAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * * *
9853 TTTTGGAAGATTGGGGGTAAAAATGTAAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
** * * * *
9882 TTTTTAAAGATCAGGGGTAAAAATGTTAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* *
9911 TTTTGGAAG-TTCGAGGGAAAAATGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
*
9939 TTTTGGAAGTTTAGAGGTAAAAAAGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
9968 TTTTGGAAGTTCGT-G-GGTAAAAATGTGAT
1 TTTTGGAAGTT--TAGAGGTAAAAATGTGAT
* *
9997 TTTTGGAAGTTTAGGGGCAAAAATGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
10026 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
** *
10055 TTTTGGAAGTTCGGAGGTAAAAATGTGAG
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* ** *
10084 TTTTGGAAG-TTCGAGGGCAAAATGTAAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* ** *
10112 TTTTGGAAATTCGGAGGAAAAAATGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * * *
10141 TTTTGGAA-ATTCGAGGGCAAAAATGTAAT
1 TTTTGGAAGTTTAGA-GGTAAAAATGTGAT
* * * *
10170 TTTTAGAAG-TTCGGGAGTAAAAATGTAAT
1 TTTTGGAAGTTTAGAG-GTAAAAATGTGAT
** * * *
10199 TTTTAAAAG-TTCGAGAGTAAAAGTGTAAT
1 TTTTGGAAGTTTAGAG-GTAAAAATGTGAT
* * *
10228 TTTTGTGAAG-TTCGAGGGACAAAATGTAAT
1 TTTTG-GAAGTTTAGAGGTA-AAAATGTGAT
* * * **
10258 TTTTGGAAG-ATCGTGGGCAAAATGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * *
10286 TTTTGGAAG-TTCGAGGGTAAAAATATAAT
1 TTTTGGAAGTTTAGA-GGTAAAAATGTGAT
** *
10315 TTTTGGAAGTTCGGGGGT-AAAATGTGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
** * * * *
10343 TTTTACAAGTTCAGGGGAAAAAATGTTAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * * *
10372 GTTTGGAAGTTCAGAGGAAAAAATATGAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* ** * *
10401 TTTTGGAAG-TTCG-GGGGAAATTGTAAT
1 TTTTGGAAGTTTAGAGGTAAAAATGTGAT
* *
10428 TTTTGGAAGTTTTG-GGATAAAAATGTAAT
1 TTTTGGAAGTTTAGAGG-TAAAAATGTGAT
* * *
10457 TTTTAGAAGTTTA-AGGGAAAAAGTGTAAT
1 TTTTGGAAGTTTAGAGGTAAAAA-TGTGAT
** *
10486 TTTTATAAAGTTTAGAGGTTAAAAT
1 TTTT-GGAAGTTTAGAGGTAAAAAT
10511 ATAATTTTGA
Statistics
Matches: 583, Mismatches: 112, Indels: 41
0.79 0.15 0.06
Matches are distributed among these distances:
27 19 0.03
28 109 0.19
29 413 0.71
30 34 0.06
31 8 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTAGAGGTAAAAATGTGAT
Found at i:9830 original size:58 final size:58
Alignment explanation
Indices: 9766--10589 Score: 549
Period size: 58 Copynumber: 14.2 Consensus size: 58
9756 GAAAATGAAG
* * * * *
9766 TTTTGGAGAGTTT-GGGGTTAAAATGCAATTTTAGAAAGTTTAAAGGTAAAAATGTGAT
1 TTTTGGA-AGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * * * * * *
9824 TTTTGGAAATTTAGAGGCAAAAATGTAATTTTTGGAAGATTGGGGGTAAAAATGTAAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
** * * * * *
9882 TTTTTAAAGATCAGGGGTAAAAATGTTATTTTTGGAAG-TTCGAGGGAAAAATGTGAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * *
9939 TTTTGGAAGTTTAGAGGTAAAAAAGTGATTTTTGGAAGTTCGT-G-GGTAAAAATGTGAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTT--TAGAGGTAAAAATGTGAT
* *
9997 TTTTGGAAGTTTAGGGGCAAAAATGTGATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * * * ** *
10055 TTTTGGAAG-TTCGGAGGTAAAAATGTGAGTTTTGGAAG-TTCGAGGGCAAAATGTAAT
1 TTTTGGAAGTTTAGG-GGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * * * * * * *
10112 TTTTGGAA-ATTCGGAGGAAAAAATGTGATTTTTGGAA-ATTCGAGGGCAAAAATGTAAT
1 TTTTGGAAGTTTAGG-GGTAAAAATGTAATTTTTGGAAGTTTAGA-GGTAAAAATGTGAT
* * ** * * *
10170 TTTTAGAAG-TTCGGGAGTAAAAATGTAATTTTTAAAAG-TTCGAGAGTAAAAGTGTAAT
1 TTTTGGAAGTTTAGGG-GTAAAAATGTAATTTTTGGAAGTTTAGAG-GTAAAAATGTGAT
* * * * **
10228 TTTTGTGAAG-TTCGAGGG-ACAAAATGTAATTTTTGGAAG-ATCGTGGGCAAAATGTGAT
1 TTTTG-GAAGTTTAG-GGGTA-AAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * ** *
10286 TTTTGGAAG-TTCGAGGGTAAAAATATAATTTTTGGAAGTTCGGGGGT-AAAATGTGAT
1 TTTTGGAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
** * * * * * * *
10343 TTTTACAAGTTCAGGGGAAAAAATGTTATGTTTGGAAGTTCAGAGGAAAAAATATGAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
* * * * *
10401 TTTTGGAAG-TTCGGGG-GAAATTGTAATTTTTGGAAGTTTTG-GGATAAAAATGTAAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTAGAGG-TAAAAATGTGAT
* * ** * * *
10457 TTTTAGAAGTTTAAGGG-AAAAAGTGTAATTTTTATAAAGTTTAGAGGTTAAAATAT-AA
1 TTTTGGAAGTTTAGGGGTAAAAA-TGTAATTTTT-GGAAGTTTAGAGGTAAAAATGTGAT
* * * * *
10515 TTTTGAAAAAATTCAAGGGTTAAAATGTAA-TTTTGGAAAAGTTT-GAGGGTAAAAATGTGAT
1 TTTTG--GAAGTTTAGGGGTAAAAATGTAATTTTTGG--AAGTTTAGA-GGTAAAAATGTGAT
*
10576 TTTTGAAAAGTTTA
1 TTTTG-GAAGTTTA
10590 AGGACCTTTT
Statistics
Matches: 617, Mismatches: 116, Indels: 64
0.77 0.15 0.08
Matches are distributed among these distances:
55 2 0.00
56 37 0.06
57 197 0.32
58 279 0.45
59 51 0.08
60 41 0.07
61 10 0.02
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (58 bp):
TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATGTGAT
Found at i:10076 original size:173 final size:172
Alignment explanation
Indices: 9810--10478 Score: 692
Period size: 173 Copynumber: 3.9 Consensus size: 172
9800 AAAGTTTAAA
* * * * * *
9810 GGTAAAAATGTGATTTTTGGAAATTTAGAGGCAAAAATGTAATTTTTGGAAGATTGGGGGTAAAA
1 GGTAAAAATGTGATTTTTAGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAA
** * * *
9875 ATGTAATTTTTTAAAGATCAGGGGTAAAAATGTTATTTTTGGAAGTTCGAGGGAAAAATGTGATT
66 ATGTAATTTTTGGAAGTTC-GGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGAAAAATGTAATT
*
9940 TTTGGAAGTTTAGAGGTAAAAAAGTGATTTTTGGAAGTTCGTG
130 TTTGGAAGTTTAGAGGTAAAAAAGTGATTTTTGGAAGTTCGAG
* *
9983 GGTAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATGTGATTTTTGGAAGTTTAGAGGTAAAA
1 GGTAAAAATGTGATTTTTAGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAA
* * * *
10048 ATGTGATTTTTGGAAGTTCGGAGGTAAAAATGTGAGTTTTGGAAGTTCGAGGGCAAAATGTAATT
66 ATGTAATTTTTGGAAGTTCGG-GGTAAAAATGTAATTTTTGGAAGTTCGAGGGAAAAATGTAATT
* ** *
10113 TTTGGAAATTCGGAGG-AAAAAATGTGATTTTTGGAAATTCGAG
130 TTTGGAAGTTTAGAGGTAAAAAA-GTGATTTTTGGAAGTTCGAG
* * * * ** *
10156 GGCAAAAATGTAATTTTTAGAAG-TTCGGGAGTAAAAATGTAATTTTTAAAAG-TTCGAGAGTAA
1 GGTAAAAATGTGATTTTTAGAAGTTTAGGG-GCAAAAATGTAATTTTTGGAAGTTTAGAG-GTAA
* * * *
10219 AAGTGTAATTTTTGTGAAGTTCGAGGG-ACAAAATGTAATTTTTGGAAGATCGTGGGCAAAATGT
64 AAATGTAATTTTTG-GAAGTTCG-GGGTA-AAAATGTAATTTTTGGAAGTTCGAGGGAAAAATGT
* * * *
10283 GATTTTTGGAAG-TTCGAGGGTAAAAATA-TAATTTTTGGAAGTTCGGG
126 AATTTTTGGAAGTTTAGA-GGTAAAAA-AGTGATTTTTGGAAGTTCGAG
* * * * * * *
10330 GGT-AAAATGTGATTTTTACAAGTTCAGGGGAAAAAATGTTATGTTTGGAAGTTCAGAGGAAAAA
1 GGTAAAAATGTGATTTTTAGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAA
* * * * * *
10394 ATATGATTTTTGGAAGTTCGGGG-GAAATTGTAATTTTTGGAAGTTTTG-GGATAAAAATGTAAT
66 ATGTAATTTTTGGAAGTTCGGGGTAAAAATGTAATTTTTGGAAG-TTCGAGG-GAAAAATGTAAT
* *
10457 TTTTAGAAGTTTA-AGGGAAAAA
129 TTTTGGAAGTTTAGAGGTAAAAA
10479 GTGTAATTTT
Statistics
Matches: 414, Mismatches: 67, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
170 27 0.07
171 23 0.06
172 28 0.07
173 250 0.60
174 79 0.19
175 6 0.01
176 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (172 bp):
GGTAAAAATGTGATTTTTAGAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTTAGAGGTAAAA
ATGTAATTTTTGGAAGTTCGGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGAAAAATGTAATTT
TTGGAAGTTTAGAGGTAAAAAAGTGATTTTTGGAAGTTCGAG
Found at i:10518 original size:29 final size:28
Alignment explanation
Indices: 9785--10592 Score: 303
Period size: 29 Copynumber: 27.9 Consensus size: 28
9775 GTTTGGGGTT
* *
9785 AAAATGCAA-TTTTAGAAAGTTTAAAGGTA
1 AAAATGTAATTTTTAG-AAGTTT-AAGGGA
* * * *
9814 AAAATGTGATTTTTGGAAATTTAGAGGCA
1 AAAATGTAATTTTTAGAAGTTTA-AGGGA
* * **
9843 AAAATGTAATTTTTGGAAGATTGGGGGTA
1 AAAATGTAATTTTTAGAAGTTTAAGGG-A
* * *
9872 AAAATGTAATTTTTTA-AAGATCAGGGGTA
1 AAAATGTAA-TTTTTAGAAGTTTAAGGG-A
* * **
9901 AAAATGTTATTTTTGGAAGTTCGAGGGA
1 AAAATGTAATTTTTAGAAGTTTAAGGGA
* * *
9929 AAAATGTGATTTTTGGAAGTTTAGAGGTA
1 AAAATGTAATTTTTAGAAGTTTA-AGGGA
* * * ***
9958 AAAAAGTGATTTTTGGAAGTTCGTGGGTA
1 AAAATGTAATTTTTAGAAGTTTAAGGG-A
* * *
9987 AAAATGTGATTTTTGGAAGTTTAGGGGCA
1 AAAATGTAATTTTTAGAAGTTTAAGGG-A
* * *
10016 AAAATGTGATTTTTGGAAGTTTAGAGGTA
1 AAAATGTAATTTTTAGAAGTTTA-AGGGA
* * ** *
10045 AAAATGTGATTTTTGGAAGTTCGGAGGTA
1 AAAATGTAATTTTTAGAAGTT-TAAGGGA
* * * ** *
10074 AAAATGTGAGTTTTGGAAGTTCGAGGGC
1 AAAATGTAATTTTTAGAAGTTTAAGGGA
* * ** *
10102 AAAATGTAATTTTTGGAAATTCGGAGGAA
1 AAAATGTAATTTTTAGAAGTT-TAAGGGA
* * * **
10131 AAAATGTGATTTTTGGAAATTCGAGGGCA
1 AAAATGTAATTTTTAGAAGTTTAAGGG-A
**
10160 AAAATGTAATTTTTAGAAG-TTCGGGAGTA
1 AAAATGTAATTTTTAGAAGTTTAAGG-G-A
* ** *
10189 AAAATGTAATTTTTAAAAGTTCGAGAGTA
1 AAAATGTAATTTTTAGAAGTTTAAG-GGA
* * **
10218 AAAGTGTAATTTTTGTGAAGTTCGAGGGA
1 AAAATGTAATTTTT-AGAAGTTTAAGGGA
* * *** *
10247 CAAAATGTAATTTTTGGAAGATCGTGGGC
1 -AAAATGTAATTTTTAGAAGTTTAAGGGA
* * **
10276 AAAATGTGATTTTTGGAAGTTCGAGGGTA
1 AAAATGTAATTTTTAGAAGTTTAAGGG-A
* * *** *
10305 AAAATATAATTTTTGGAAGTTCGGGGGT
1 AAAATGTAATTTTTAGAAGTTTAAGGGA
* * * *
10333 AAAATGTGATTTTTACAAGTTCAGGGGAA
1 AAAATGTAATTTTTAGAAGTTTAAGGG-A
* * * * *
10362 AAAATGTTATGTTTGGAAGTTCAGAGGAA
1 AAAATGTAATTTTTAGAAGTTTA-AGGGA
* * * ** *
10391 AAAATATGATTTTTGGAAG-TTCGGGGG
1 AAAATGTAATTTTTAGAAGTTTAAGGGA
* * *
10418 AAATTGTAATTTTTGGAAGTTT-TGGGATA
1 AAAATGTAATTTTTAGAAGTTTAAGGG--A
10447 AAAATGTAATTTTTAGAAGTTTAAGGGA
1 AAAATGTAATTTTTAGAAGTTTAAGGGA
* **
10475 AAAAGTGTAATTTTTATAAAGTTTAGAGGTT
1 AAAA-TGTAATTTTTA-GAAGTTTA-AGGGA
* * * * * *
10506 AAAATATAATTTTGAAAAAATTCAAGGGTT
1 AAAATGTAATTTT-TAGAAGTTTAAGGG-A
* * *
10536 AAAATGTAATTTTGGAAAAGTTTGAGGGTA
1 AAAATGTAATTTT-TAGAAGTTTAAGGG-A
* *
10566 AAAATGTGATTTTTGAAAAGTTTAAGG
1 AAAATGTAATTTTT-AGAAGTTTAAGG
10593 ACCTTTTGGA
Statistics
Matches: 626, Mismatches: 124, Indels: 57
0.78 0.15 0.07
Matches are distributed among these distances:
27 21 0.03
28 114 0.18
29 372 0.59
30 110 0.18
31 9 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTTAGAAGTTTAAGGGA
Found at i:12170 original size:16 final size:16
Alignment explanation
Indices: 12115--12184 Score: 68
Period size: 17 Copynumber: 4.2 Consensus size: 16
12105 ATTTAATTTA
* *
12115 AAATAAATTTAAACTCA
1 AAATAAATTCAAACT-T
* *
12132 AAATAAGTTCAAATTT
1 AAATAAATTCAAACTT
12148 AAAATAAATTCAAACTT
1 -AAATAAATTCAAACTT
* *
12165 AAATAAATTAAAAATT
1 AAATAAATTCAAACTT
12181 AAAT
1 AAAT
12185 TTGGGTCCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 18 0.41
17 26 0.59
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.31
Consensus pattern (16 bp):
AAATAAATTCAAACTT
Found at i:12180 original size:34 final size:34
Alignment explanation
Indices: 12109--12183 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
12099 TTTTAAATTT
* * *
12109 AATTTAAAATAAATTTAAACTCAAAATAAGTTCA
1 AATTTAAAATAAATTCAAACTCAAAATAAATTAA
*
12143 AATTTAAAATAAATTCAAACT-TAAATAAATTAA
1 AATTTAAAATAAATTCAAACTCAAAATAAATTAA
*
12176 AAATTAAA
1 AATTTAAA
12184 TTTGGGTCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.44
34 20 0.56
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.32
Consensus pattern (34 bp):
AATTTAAAATAAATTCAAACTCAAAATAAATTAA
Found at i:12764 original size:39 final size:39
Alignment explanation
Indices: 12659--13219 Score: 214
Period size: 39 Copynumber: 14.3 Consensus size: 39
12649 CCCCATGATT
* *
12659 GGGGTAAGAGATTGGTTGATGATGATCT-ACCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGACCCAAGCTC
* * *
12697 GGGGTAAGAGATT-G--AATGGCTACAATCTGACCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGG-T--GATCTGACCCAAGCTC
*
12736 GGGGTAAGAGATTGGCTGATGGTGATCTGCCTGCCCTAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTG---ACCC-AAGCTC
** * *
12779 AAGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGACCCAAGCTC
* * * ** * * * * *
12818 AGGGTAAAAGATCGAATGGCT-ATAATCTG-CTTCAGGCTC
1 GGGGTAAGAGATTGGCT-GATGGTGATCTGAC-CCAAGCTC
* * * * *
12857 GGGGTAAGAGATTGGCTGATGATGACCAGCCCCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGACCCAAGCTC
* * ** * * * *
12896 GGGGTAAAAGATCGAATGGCT-ATAATCT-ACCCCAAGCTT
1 GGGGTAAGAGATTGGCT-GATGGTGATCTGA-CCCAAGCTC
* * *
12935 AGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGACCCAAGCTC
* * *
12974 GGGGTAAAAGA-T--C-GAATGGCTGCAATCT-ACCCCAGGCTT
1 GGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGA-CCCAAGCTC
*
13013 GGGGTAAGAGATTGGCTGATGGTGATCTG-CCTCAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGACC-CAAGCTC
* * * *
13052 GAGGTAAGAGA-T--CGGATGGCTACAATCT-ACCCCAAGTTC
1 GGGGTAAGAGATTGGCTGATGG-T--GATCTGA-CCCAAGCTC
* * * * *
13091 AGGGTAAGAGATTGGCTGATGGTGATTTGTCCTAGGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGACCCAAGCTC
* * *
13130 GGGCTAAAAGA-T--C-GAATGGCTGCAATCT-ACCCCAGGCTC
1 GGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGA-CCCAAGCTC
* * *
13169 GAGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTC
1 GGGGTAAGAGATTGGCTGATGGTGATCTGACCCAAGCTC
* *
13208 GAGGTAAAAGAT
1 GGGGTAAGAGAT
13220 CAACTTGTTG
Statistics
Matches: 385, Mismatches: 89, Indels: 97
0.67 0.16 0.17
Matches are distributed among these distances:
35 5 0.01
36 17 0.04
37 6 0.02
38 27 0.07
39 255 0.66
40 14 0.04
41 6 0.02
42 22 0.06
43 33 0.09
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (39 bp):
GGGGTAAGAGATTGGCTGATGGTGATCTGACCCAAGCTC
Found at i:12859 original size:121 final size:120
Alignment explanation
Indices: 12661--12877 Score: 328
Period size: 121 Copynumber: 1.8 Consensus size: 120
12651 CCATGATTGG
* * * *
12661 GGTAAGAGATTGGTTGATGATGATCTACCCAAGCTCGGGGTAAGAGATTGAATGGCTACAATCTG
1 GGTAAGAGATTGGCTGATGATGATCTACCCAAGCTCAGGGTAAAAGATCGAATGGCTACAATCTG
12726 ACCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTGCCCTAAGCTCAA
66 ACCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTGCCCTAAGCTCAA
* * * *
12781 GGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGAATGGCTATAATCT
1 GGTAAGAGATTGGCTGATGATGATCT-ACCCAAGCTCAGGGTAAAAGATCGAATGGCTACAATCT
*
12846 G-CTTCAGGCTCGGGGTAAGAGATTGGCTGATG
65 GAC-CCAGGCTCGGGGTAAGAGATTGGCTGATG
12878 ATGACCAGCC
Statistics
Matches: 86, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
120 24 0.28
121 62 0.72
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (120 bp):
GGTAAGAGATTGGCTGATGATGATCTACCCAAGCTCAGGGTAAAAGATCGAATGGCTACAATCTG
ACCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTGCCCTAAGCTCAA
Found at i:12876 original size:78 final size:77
Alignment explanation
Indices: 12781--13220 Score: 556
Period size: 78 Copynumber: 5.6 Consensus size: 77
12771 CTAAGCTCAA
* *
12781 GGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGAATGGCTATAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC-GGGTAAAAGATCGAATGGCTACAATCT
* **
12846 GCTTCAGGCTCGG
65 ACCCCAGGCTCGG
* * * * *
12859 GGTAAGAGATTGGCTGATGATGACCAGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTATAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC-GGGTAAAAGATCGAATGGCTACAATCT
* **
12924 ACCCCAAGCTTAG
65 ACCCCAGGCTCGG
* *
12937 GGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC-GGGTAAAAGATCGAATGGCTACAATCT
*
13002 ACCCCAGGCTTGG
65 ACCCCAGGCTCGG
* * * *
13015 GGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGAGGTAAGAGATCGGATGGCTACAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG-GGTAAAAGATCGAATGGCTACAATCT
* * *
13080 ACCCCAAGTTCAG
65 ACCCCAGGCTCGG
* * * * *
13093 GGTAAGAGATTGGCTGATGGTGATTTGTCCTAGGCTCGGGCTAAAAGATCGAATGGCTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGG-TAAAAGATCGAATGGCTACAATCT
*
13158 ACCCCAGGCTCGA
65 ACCCCAGGCTCGG
*
13171 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGAGGTAAAAGATC
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG-GGTAAAAGATC
13221 AACTTGTTGC
Statistics
Matches: 312, Mismatches: 47, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
77 3 0.01
78 307 0.98
79 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (77 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGTAAAAGATCGAATGGCTACAATCTA
CCCCAGGCTCGG
Found at i:12961 original size:156 final size:155
Alignment explanation
Indices: 12781--13220 Score: 639
Period size: 156 Copynumber: 2.8 Consensus size: 155
12771 CTAAGCTCAA
* **
12781 GGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGAATGGCTATAATCT
1 GGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTC-GGGTAAAAGATCGAATGGCTGCAATCT
* ** * * *
12846 GCTTCAGGCTCGGGGTAAGAGATTGGCTGATGATGACCAGCCCCAGGCTCGGGGTAAAAGATCGA
65 ACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGAGGTAAAAGATCGA
*
12911 ATGGCTATAATCTACCCCAAGCTT-AG
130 ATGGCTACAATCTACCCCAAG-TTCAG
12937 GGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAATCT
1 GGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTC-GGGTAAAAGATCGAATGGCTGCAATCT
* * * * *
13002 ACCCCAGGCTTGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGGCTCGAGGTAAGAGATCGG
65 ACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGAGGTAAAAGATCGA
13067 ATGGCTACAATCTACCCCAAGTTCAG
130 ATGGCTACAATCTACCCCAAGTTCAG
* * * * *
13093 GGTAAGAGATTGGCTGATGGTGATTTGTCCTAGGCTCGGGCTAAAAGATCGAATGGCTGCAATCT
1 GGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGG-TAAAAGATCGAATGGCTGCAATCT
* *
13158 ACCCCAGGCTCGAGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTCGAGGTAAAAGATC
65 ACCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGAGGTAAAAGATC
13221 AACTTGTTGC
Statistics
Matches: 255, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
155 5 0.02
156 250 0.98
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (155 bp):
GGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGGGTAAAAGATCGAATGGCTGCAATCTA
CCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAGGCTCGAGGTAAAAGATCGAA
TGGCTACAATCTACCCCAAGTTCAG
Found at i:22832 original size:29 final size:28
Alignment explanation
Indices: 22791--23651 Score: 225
Period size: 29 Copynumber: 29.9 Consensus size: 28
22781 AGTTTGAGGT
22791 TAAAATGTAATTTTAAAAAGTTTTAGGGG
1 TAAAATGTAATTTTAAAAAG-TTTAGGGG
* * *
22820 TAAAATGTGATTTTTATAAGTTTAGGGG
1 TAAAATGTAATTTTAAAAAGTTTAGGGG
* *** * *
22848 TAAAAATATAATTTTTGGAAGATTAAGGG
1 T-AAAATGTAATTTTAAAAAGTTTAGGGG
*** **
22877 TAAAAATGTAATTTTTGGAACATTAGGGG
1 T-AAAATGTAATTTTAAAAAGTTTAGGGG
* *** * *
22906 TAAAATTGTGATTTTTGGAAGTTCAAGGGAA
1 TAAAA-TGTAATTTTAAAAAGTT-TAGGG-G
* ***
22937 AAAAATGTAATTTTTGGAAGTTTAGGGG
1 TAAAATGTAATTTTAAAAAGTTTAGGGG
* ** *
22965 TAAAAATGTTATTTTTGAAAGTTCTA-GAG
1 T-AAAATGTAATTTTAAAAAGTT-TAGGGG
* ** *
22994 TAAAATTGTGATTTTTGAAAGTTCAGGGG
1 TAAAA-TGTAATTTTAAAAAGTTTAGGGG
* * *
23023 TAAAAATGTAATTTTTAGAAG-TTCGGGTG
1 T-AAAATGTAATTTTAAAAAGTTTAGGG-G
* *** *
23052 CAAAATTGTAATTTTTGGAAGTTTGAGGGC
1 TAAAA-TGTAATTTTAAAAAGTTT-AGGGG
* * *
23082 T-AAATGTGATTTT-TAAAGTTTAGGGA
1 TAAAATGTAATTTTAAAAAGTTTAGGGG
* *** *
23108 AAAAATGTAATTTTTTGAATTTTAGGGG
1 TAAAATGTAATTTTAAAAAGTTTAGGGG
** * *
23136 TAAAAATGTAATTTTTTAAAGTATAAGGG
1 T-AAAATGTAATTTTAAAAAGTTTAGGGG
** *
23165 TAAAAGTGTAATTTTTATGAAGTTT-GCGG
1 TAAAA-TGTAA-TTTTAAAAAGTTTAGGGG
* * * ** * **
23194 TCAAATGCATTTTTTGAAAGATCGGGGG
1 TAAAATGTAATTTTAAAAAGTTTAGGGG
* * *
23222 TAAATTGT-ATTTTTAAAAG-TTCGAGGG
1 TAAAATGTAATTTTAAAAAGTTTAG-GGG
***
23249 TAAAATTGTAATTTTTGGAAGTTTAGGGG
1 TAAAA-TGTAATTTTAAAAAGTTTAGGGG
* * *
23278 TAAAGATGTAATTTTTAGAAGTTTAAGGG
1 TAAA-ATGTAATTTTAAAAAGTTTAGGGG
* ***
23307 TAAAAATGTGATTTTTGGAAGTTT-GGAGG
1 T-AAAATGTAATTTTAAAAAGTTTAGG-GG
* *** *
23336 TAAAATTGTGATTTTTGGAAGTTTGGGGG
1 TAAAA-TGTAATTTTAAAAAGTTTAGGGG
*** * *
23365 TAAAAATGTAATTTTTGGAAGTTCATGGG
1 T-AAAATGTAATTTTAAAAAGTTTAGGGG
23394 TAAAAATGTAATTTT-AAAAGTTTAGGGG
1 T-AAAATGTAATTTTAAAAAGTTTAGGGG
* * *** * * *
23422 CAAAATGTGATTTTTGGAAGTTCAAGAG
1 TAAAATGTAATTTTAAAAAGTTTAGGGG
* ***
23450 CAAAATGTAATTTTTGTAAGTTT-GAGGG
1 TAAAATGTAATTTTAAAAAGTTTAG-GGG
* * ****
23478 CAAAATGAAATTTTTGGCAGTTTAGGGG
1 TAAAATGTAATTTTAAAAAGTTTAGGGG
* ***
23506 CAAAAGTGTAATTTTTGTGAAGTTTAGGGG
1 TAAAA-TGTAA-TTTTAAAAAGTTTAGGGG
** * *
23536 TCAAAATGTAAATTTGGAAAAG-TTCGATGG
1 T-AAAATGT-AATTTTAAAAAGTTTAG-GGG
* * *
23566 TCAAAATATAATTTTGGAAAAA-TTCAAGGGT
1 T-AAAATGTAATTTT--AAAAAGTT-TAGGGG
* * *
23597 TAAAATATAATATTATAAAAGTTTTAGGGT
1 TAAAATGTAATTTTA-AAAAG-TTTAGGGG
* *
23627 TAAAATGTGATTTTTAGAAAGTTTA
1 TAAAATGT-AATTTTAAAAAGTTTA
23652 AGGACCTTTT
Statistics
Matches: 659, Mismatches: 128, Indels: 90
0.75 0.15 0.10
Matches are distributed among these distances:
26 6 0.01
27 53 0.08
28 135 0.20
29 323 0.49
30 114 0.17
31 27 0.04
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (28 bp):
TAAAATGTAATTTTAAAAAGTTTAGGGG
Found at i:23426 original size:28 final size:29
Alignment explanation
Indices: 22756--23554 Score: 614
Period size: 29 Copynumber: 27.9 Consensus size: 29
22746 AAAAAAAAAA
* *
22756 AGGGATAAAAGATG-AAGTTTTGGAGAGTTT
1 AGGGGTAAAA-ATGTAATTTTTGGA-AGTTT
* * ***
22786 -GAGGTTAAAATGTAATTTTAAAAAGTTTT
1 AGGGGTAAAAATGTAATTTTTGGAAG-TTT
* **
22815 AGGGGT-AAAATGTGATTTTTATAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* *
22843 AGGGGTAAAAATATAATTTTTGGAAGATT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* **
22872 AAGGGTAAAAATGTAATTTTTGGAACATT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * *
22901 AGGGGTAAAATTGTGATTTTTGGAAGTTCA
1 AGGGGTAAAAATGTAATTTTTGGAAGTT-T
**
22931 AGGGAAAAAAATGTAATTTTTGGAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* *
22960 AGGGGTAAAAATGTTATTTTTGAAAGTTCT
1 AGGGGTAAAAATGTAATTTTTGGAAGTT-T
* * * * *
22990 A-GAGTAAAATTGTGATTTTTGAAAGTTC
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
*
23018 AGGGGTAAAAATGTAATTTTTAGAAG-TT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * *
23046 CGGGTGCAAAATTGTAATTTTTGGAAGTTT
1 AGGG-GTAAAAATGTAATTTTTGGAAGTTT
* * *
23076 GAGGGCT--AAATGTGATTTTT-AAAGTTT
1 -AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * *
23103 A-GGGAAAAAATGTAATTTTTTGAATTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
** *
23131 AGGGGTAAAAATGTAATTTTTTAAAGTAT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * *
23160 AAGGGTAAAAGTGTAATTTTTATGAAGTTT
1 AGGGGTAAAAATGTAATTTTT-GGAAGTTT
* * * * * * *
23190 -GCGGT-CAAATGCATTTTTTGAAAGATC
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * **
23217 GGGGGT-AAATTGT-ATTTTTAAAAG-TT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* *
23243 CGAGGGTAAAATTGTAATTTTTGGAAGTTT
1 AG-GGGTAAAAATGTAATTTTTGGAAGTTT
* *
23273 AGGGGTAAAGATGTAATTTTTAGAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* *
23302 AAGGGTAAAAATGTGATTTTTGGAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* *
23331 -GGAGGTAAAATTGTGATTTTTGGAAGTTT
1 AGG-GGTAAAAATGTAATTTTTGGAAGTTT
* *
23360 GGGGGTAAAAATGTAATTTTTGGAAGTTC
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* **
23389 ATGGGTAAAAATGTAA-TTTTAAAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * *
23417 AGGGG-CAAAATGTGATTTTTGGAAGTTC
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * * *
23445 AAGAG-CAAAATGTAATTTTTGTAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAGTTT
* * *
23473 -GAGGG-CAAAATGAAATTTTTGGCAGTTT
1 AG-GGGTAAAAATGTAATTTTTGGAAGTTT
* *
23501 AGGGGCAAAAGTGTAATTTTTGTGAAGTTT
1 AGGGGTAAAAATGTAATTTTTG-GAAGTTT
* *
23531 AGGGGTCAAAATGTAA-ATTTGGAA
1 AGGGGTAAAAATGTAATTTTTGGAA
23555 AAGTTCGATG
Statistics
Matches: 613, Mismatches: 129, Indels: 56
0.77 0.16 0.07
Matches are distributed among these distances:
25 2 0.00
26 3 0.00
27 43 0.07
28 135 0.22
29 365 0.60
30 62 0.10
31 3 0.00
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AGGGGTAAAAATGTAATTTTTGGAAGTTT
Found at i:25224 original size:33 final size:34
Alignment explanation
Indices: 25154--25230 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
25144 ATTTAAATTT
* *
25154 AATTTAAAATAAATTTAAACTCAAAATAAGTTCA
1 AATTTAAAATAAATTCAAACTCAAAATAAGTTAA
* *
25188 AATTTAAAATAAATTCAAACT-TAAATAATTTAA
1 AATTTAAAATAAATTCAAACTCAAAATAAGTTAA
25221 AATTTAAAAT
1 AATTTAAAAT
25231 TTAAAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 19 0.49
34 20 0.51
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (34 bp):
AATTTAAAATAAATTCAAACTCAAAATAAGTTAA
Found at i:25230 original size:17 final size:17
Alignment explanation
Indices: 25154--25230 Score: 77
Period size: 17 Copynumber: 4.6 Consensus size: 17
25144 ATTTAAATTT
25154 AATTTAAAATAAATTT-A
1 AATTTAAAAT-AATTTCA
* * *
25171 AACTCAAAATAAGTTCA
1 AATTTAAAATAATTTCA
*
25188 AATTTAAAATAAATTCA
1 AATTTAAAATAATTTCA
* *
25205 AACTT-AAATAATTTAA
1 AATTTAAAATAATTTCA
25221 AATTTAAAAT
1 AATTTAAAAT
25231 TTAAAATTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
16 17 0.35
17 31 0.65
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAATTTCA
Found at i:25233 original size:14 final size:13
Alignment explanation
Indices: 25132--25244 Score: 64
Period size: 11 Copynumber: 9.2 Consensus size: 13
25122 AATTTGGACG
*
25132 TTTAAAATTCAAA
1 TTTAAAATTAAAA
*
25145 TTT-AAATT-TAA
1 TTTAAAATTAAAA
25156 TTTAAAA-T-AAA
1 TTTAAAATTAAAA
* *
25167 TTTAAACTCAAAA
1 TTTAAAATTAAAA
* *
25180 --T-AAGTTCAAA
1 TTTAAAATTAAAA
25190 TTTAAAA-T-AAA
1 TTTAAAATTAAAA
* *
25201 TTCAAACTTAAATAA
1 TTTAAAATT-AA-AA
25216 TTTAAAATTTAAAA
1 TTTAAAA-TTAAAA
25230 TTTAAAATTAAAA
1 TTTAAAATTAAAA
25243 TT
1 TT
25245 GTGTCCTATT
Statistics
Matches: 77, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
10 6 0.08
11 23 0.30
12 11 0.14
13 16 0.21
14 10 0.13
15 9 0.12
16 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (13 bp):
TTTAAAATTAAAA
Found at i:25242 original size:6 final size:7
Alignment explanation
Indices: 25214--25244 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
25204 AAACTTAAAT
25214 AATTTAA
1 AATTTAA
25221 AATTTAA
1 AATTTAA
25228 AATTTAA
1 AATTTAA
25235 AA-TTAA
1 AATTTAA
25241 AATT
1 AATT
25245 GTGTCCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:27309 original size:6 final size:6
Alignment explanation
Indices: 27300--27324 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27290 AAAAGGAAAA
27300 GAGCAT GAGCAT GAGCAT GAGCAT G
1 GAGCAT GAGCAT GAGCAT GAGCAT G
27325 CAAAGTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GAGCAT
Found at i:32931 original size:3 final size:3
Alignment explanation
Indices: 32923--32955 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
32913 TAACTAAAAC
32923 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
32956 AGCACTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34544 original size:37 final size:36
Alignment explanation
Indices: 34502--34617 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 36
34492 CGTTATAACT
34502 GAAGTAAATTGGCACCCTATGCCTCATTGGAATGTCC
1 GAAGTAAATTGGCA-CCTATGCCTCATTGGAATGTCC
* * * * * **
34539 AAAGT-AATAT-GCATCTA-ACGCTCATCGGTATAACC
1 GAAGTAAAT-TGGCACCTATGC-CTCATTGGAATGTCC
*
34574 GAAGTAAATTGGCACCTAGTGCCTCATTGAAATGTCC
1 GAAGTAAATTGGCACCTA-TGCCTCATTGGAATGTCC
34611 GAAGTAA
1 GAAGTAA
34618 CCAGTACTTG
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
34 1 0.02
35 19 0.33
36 15 0.26
37 22 0.38
38 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (36 bp):
GAAGTAAATTGGCACCTATGCCTCATTGGAATGTCC
Found at i:34578 original size:72 final size:71
Alignment explanation
Indices: 34347--34617 Score: 251
Period size: 72 Copynumber: 3.7 Consensus size: 71
34337 CACTTATCAT
* * * * ** ** * * *
34347 TATAACCGAAATAATTTGGCACCCAATGCCTCATCAGAATGTTTGAAGTAATTTGCGCTCAGTGC
1 TATAACCGAAGTAAATTGGCACCTAGTGCCTCATTGGAATGTCCGAAGTAATATGCTCT-AGCGC
34412 TCATCGC
65 TCATCGC
**
34419 TATAACCGAAGTAAATTGGCA-CTGAGTGCCTCATCACATCGGAACATCCGAAG-AATATGCGTC
1 TATAACCGAAGTAAATTGGCACCT-AGTGCCTCAT----T-GGAATGTCCGAAGTAATATGC-TC
* *
34482 CAGCGCTCATCGT
59 TAGCGCTCATCGC
* * *
34495 TATAACTGAAGTAAATTGGCACCCTA-TGCCTCATTGGAATGTCCAAAGTAATATGCATCTAACG
1 TATAACCGAAGTAAATTGGCA-CCTAGTGCCTCATTGGAATGTCCGAAGTAATATGC-TCTAGCG
*
34559 CTCATCGG
64 CTCATCGC
*
34567 TATAACCGAAGTAAATTGGCACCTAGTGCCTCATTGAAATGTCCGAAGTAA
1 TATAACCGAAGTAAATTGGCACCTAGTGCCTCATTGGAATGTCCGAAGTAA
34618 CCAGTACTTG
Statistics
Matches: 162, Mismatches: 26, Indels: 22
0.77 0.12 0.10
Matches are distributed among these distances:
71 15 0.09
72 91 0.56
76 44 0.27
77 10 0.06
78 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (71 bp):
TATAACCGAAGTAAATTGGCACCTAGTGCCTCATTGGAATGTCCGAAGTAATATGCTCTAGCGCT
CATCGC
Found at i:43648 original size:13 final size:15
Alignment explanation
Indices: 43620--43663 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
43610 ATAACAATTC
43620 AAATATTAATTAAAA
1 AAATATTAATTAAAA
*
43635 AAATA-TAATAAAAA
1 AAATATTAATTAAAA
43649 TAAATTATTAATTAA
1 -AAA-TATTAATTAA
43664 TAAAGTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 8 0.33
16 2 0.08
17 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATTAATTAAAA
Found at i:45891 original size:124 final size:123
Alignment explanation
Indices: 45763--46110 Score: 503
Period size: 123 Copynumber: 2.8 Consensus size: 123
45753 AACATGTATA
*
45763 TTAATATCCTTTTAGAAAGGATATAATGGTTTTAATAAACCTTTCATATATTTCTATAAAAGAAT
1 TTAATATCCTTTTAGAAAGGATATAATGGTTTTAATAAACCTTCCATATATTTCTATAAAAGAAT
* *
45828 AATTCCCTTTTAATATGAGATATTAAATAAACTGG-CATTGAATATTAAAAACATAGAAG
66 AATT-CCTTTTAATATGAGATATTAAATAAA-AGGAAATTGAATATTAAAAACATAGAAG
* *
45887 TTAATATCCTTTTGAGAATA--ATATAAT-GTTTTAATAAACCTTCCATATATTTCTATAGAGGA
1 TTAATATCCTTTT-AGAA-AGGATATAATGGTTTTAATAAACCTTCCATATATTTCTATAAAAGA
*
45949 ATAATT-CTGTATTAATATGAGATATTAAATAAAAGGAAATTGAATATTAAAAACATGGAAG
64 ATAATTCCT-T-TTAATATGAGATATTAAATAAAAGGAAATTGAATATTAAAAACATAGAAG
*
46010 TTAATATCCTTTT-GCAAAGGATATAATGGTTTTAATAAACCTTCCATATATTTCTATAAATGAA
1 TTAATATCCTTTTAG-AAAGGATATAATGGTTTTAATAAACCTTCCATATATTTCTATAAAAGAA
*
46074 TAATT-CTGTTTAACATGAGATATTAAATAAAAGGAAA
65 TAATTCCT-TTTAATATGAGATATTAAATAAAAGGAAA
46111 GGTAGCAGAA
Statistics
Matches: 206, Mismatches: 9, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
121 4 0.02
122 5 0.02
123 129 0.63
124 63 0.31
125 4 0.02
126 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (123 bp):
TTAATATCCTTTTAGAAAGGATATAATGGTTTTAATAAACCTTCCATATATTTCTATAAAAGAAT
AATTCCTTTTAATATGAGATATTAAATAAAAGGAAATTGAATATTAAAAACATAGAAG
Found at i:46008 original size:22 final size:21
Alignment explanation
Indices: 45970--46016 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
45960 TTAATATGAG
45970 ATATTAAATAAAAGGAAATTGA
1 ATATTAAATAAAAGGAAATT-A
* *
45992 ATATTAAA-AACATGGAAGTTA
1 ATATTAAATAA-AAGGAAATTA
46013 ATAT
1 ATAT
46017 CCTTTTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (21 bp):
ATATTAAATAAAAGGAAATTA
Found at i:50193 original size:16 final size:16
Alignment explanation
Indices: 50172--50207 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
50162 GAGCTCAAAC
50172 CCGACCCATTTATGAT
1 CCGACCCATTTATGAT
*
50188 CCGACCCGTTTATGAT
1 CCGACCCATTTATGAT
50204 CCGA
1 CCGA
50208 ACCGAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (16 bp):
CCGACCCATTTATGAT
Found at i:50701 original size:30 final size:30
Alignment explanation
Indices: 50666--50737 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
50656 CCCACTTGAG
*
50666 GTGTGTCTT-TGTCTGTGCTACATATTTGTT
1 GTGTGT-TTCTGTCTGCGCTACATATTTGTT
* *
50696 GTGTGTTTCTGTTTGCGCTACATGTTTGTT
1 GTGTGTTTCTGTCTGCGCTACATATTTGTT
*
50726 GTATGTTTCTGT
1 GTGTGTTTCTGT
50738 TTACACTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.54
Consensus pattern (30 bp):
GTGTGTTTCTGTCTGCGCTACATATTTGTT
Found at i:50738 original size:30 final size:30
Alignment explanation
Indices: 50682--50757 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
50672 CTTTGTCTGT
* * *
50682 GCTACATATTTGTTGTGTGTTTCTGTTTGC
1 GCTACATGTTTGTTGTATGTTTCTGTTTAC
50712 GCTACATGTTTGTTGTATGTTTCTGTTTAC
1 GCTACATGTTTGTTGTATGTTTCTGTTTAC
*
50742 ACT-CAATGTTTGTTGT
1 GCTAC-ATGTTTGTTGT
50758 GTGACGATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 1 0.02
30 40 0.98
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (30 bp):
GCTACATGTTTGTTGTATGTTTCTGTTTAC
Found at i:59448 original size:22 final size:21
Alignment explanation
Indices: 59410--59456 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
59400 TTAATATGAG
59410 ATATTAAATAAAAGAAAATTGA
1 ATATTAAATAAAAGAAAATT-A
* *
59432 ATATTAAA-AACATGAAAGTTA
1 ATATTAAATAA-AAGAAAATTA
59453 ATAT
1 ATAT
59457 CCTTTTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (21 bp):
ATATTAAATAAAAGAAAATTA
Found at i:59513 original size:123 final size:124
Alignment explanation
Indices: 59308--59790 Score: 649
Period size: 122 Copynumber: 3.9 Consensus size: 124
59298 GATTTCATTA
* * * *
59308 AATATT-AAAACATGGATATTAATATCTTTTTGAAAATGATATAATGGTTTTAATCAACTTTCCA
1 AATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAATGGTTTTAATAAACTTTCCA
**
59372 TATATTTCTATAAAGGAATAATTTTGTTTTAATATGAGATATTAAATAAAAGAAAATTG
66 TATATTTCTATAAAGGAATAATTTCATTTTAATATGAGATATTAAATAAAAGAAAATTG
* **
59431 AATATTAAAAACAT-GAAAGTTAATATCCTTTTGGAAATGATATAAT-GTTTGAATAAAAATTCC
1 AATATTAAAAACATGGAAA-TTAATATCCTTTTGGAAATGATATAATGGTTTTAATAAACTTTCC
* *
59494 ATATATTTCTATAAAGGAATAATTTCATTTTAATATGAGATATTAAATAAGAGAAAAATG
65 ATATATTTCTATAAAGGAATAATTTCATTTTAATATGAGATATTAAATAAAAGAAAATTG
* *
59554 AATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAAT--ATTTAATAAACTTTTCA
1 AATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAATGGTTTTAATAAACTTTCCA
* * * * * *
59617 TATATTTTTTTAAAGGAATATTTTCATTTTAATATAAGATATTAAATAAAAGGAAATCG
66 TATATTTCTATAAAGGAATAATTTCATTTTAATATGAGATATTAAATAAAAGAAAATTG
* ** * * *
59676 AATATTAAAAATAT-GAAAGTTAATATTTTTTTGGAAA-G-GATAATGGTTTTAATAATCCTTCC
1 AATATTAAAAACATGGAAA-TTAATATCCTTTTGGAAATGATATAATGGTTTTAATAAACTTTCC
* *
59738 ATATATTTCTATAAAAGAATAATTTCATTTTAACATGAGATATTAAATAAAAG
65 ATATATTTCTATAAAGGAATAATTTCATTTTAATATGAGATATTAAATAAAAG
59791 GAAAGATAGG
Statistics
Matches: 316, Mismatches: 38, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
120 5 0.02
121 5 0.02
122 151 0.48
123 119 0.38
124 36 0.11
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (124 bp):
AATATTAAAAACATGGAAATTAATATCCTTTTGGAAATGATATAATGGTTTTAATAAACTTTCCA
TATATTTCTATAAAGGAATAATTTCATTTTAATATGAGATATTAAATAAAAGAAAATTG
Found at i:61573 original size:24 final size:23
Alignment explanation
Indices: 61524--61567 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
61514 CAAAGAAGTG
*
61524 AAAAAAAATGAAATAAAAAAGAT
1 AAAAAAAATGAAAAAAAAAAGAT
61547 AAAAAAAAT-AAAAAAGAAAAG
1 AAAAAAAATGAAAAAA-AAAAG
61568 CCTAAAGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAAAAAATGAAAAAAAAAAGAT
Found at i:64522 original size:27 final size:25
Alignment explanation
Indices: 64491--64548 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
64481 TTTAAAATAA
64491 AAAAAAATTGTCAACTTTTAAAGAGCCC
1 AAAAAAATT-T-AACTTTTAAAGA-CCC
*
64519 AAAATAAATTTAACTTTTAAGGACCC
1 AAAA-AAATTTAACTTTTAAAGACCC
64545 AAAA
1 AAAA
64549 TTTTTTTACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.25
27 11 0.39
28 5 0.18
29 5 0.18
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.26
Consensus pattern (25 bp):
AAAAAAATTTAACTTTTAAAGACCC
Found at i:65388 original size:24 final size:24
Alignment explanation
Indices: 65360--65405 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
65350 CTAATTTGAT
*
65360 ATTT-GAACTTGATATTTTTTTTTA
1 ATTTGGAACTT-AAATTTTTTTTTA
*
65384 ATTTGGTACTTAAATTTTTTTT
1 ATTTGGAACTTAAATTTTTTTT
65406 GGATTCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.24, C:0.04, G:0.09, T:0.63
Consensus pattern (24 bp):
ATTTGGAACTTAAATTTTTTTTTA
Found at i:65446 original size:60 final size:58
Alignment explanation
Indices: 65308--65485 Score: 171
Period size: 60 Copynumber: 2.9 Consensus size: 58
65298 GTATTTGAAT
* * * * ** *
65308 TTGATATTTTTTCTAAATTTAGTATTTAAACTATTTTTTGA-TCTAATTTGATATTTGAAC
1 TTGATATTTTTTCT-AATTTGGTACTTAAA-TTTTTTTTGATTC-AATTTGGTACCTAAAC
*
65368 TTGATATTTTTTTTTAATTTGGTACTTAAATTTTTTTTGGATTCAATTTGGTACCTAAAC
1 TTGATA-TTTTTTCTAATTTGGTACTTAAATTTTTTTT-GATTCAATTTGGTACCTAAAC
* *
65428 TTGATATTTTTTCCTAATTTGGTAGC-TAAGCTTTTTTTAAGATTCAATTTGGTACCTA
1 TTGATATTTTTT-CTAATTTGGTA-CTTAA-ATTTTTTT-TGATTCAATTTGGTACCTA
65486 TATTTATTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
59 13 0.13
60 52 0.52
61 35 0.35
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.53
Consensus pattern (58 bp):
TTGATATTTTTTCTAATTTGGTACTTAAATTTTTTTTGATTCAATTTGGTACCTAAAC
Found at i:65475 original size:61 final size:60
Alignment explanation
Indices: 65365--65485 Score: 172
Period size: 60 Copynumber: 2.0 Consensus size: 60
65355 TTGATATTTG
** **
65365 AACTTGATATTTTTTTTTAATTTGGTACTTAAATTTTTTTTGGATTCAATTTGGTACCTA
1 AACTTGATATTTTTTCCTAATTTGGTACTTAAATTTTTTTAAGATTCAATTTGGTACCTA
*
65425 AACTTGATATTTTTTCCTAATTTGGTAGC-TAAGCTTTTTTTAAGATTCAATTTGGTACCTA
1 AACTTGATATTTTTTCCTAATTTGGTA-CTTAA-ATTTTTTTAAGATTCAATTTGGTACCTA
65486 TATTTATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
60 28 0.52
61 26 0.48
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (60 bp):
AACTTGATATTTTTTCCTAATTTGGTACTTAAATTTTTTTAAGATTCAATTTGGTACCTA
Found at i:65589 original size:16 final size:18
Alignment explanation
Indices: 65545--65590 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
65535 TTTTTTTGTT
65545 ATGTTACAAAAATATTATC
1 ATGTTA-AAAAATATTATC
*
65564 AGTTTTAAAAAATA-T-TC
1 A-TGTTAAAAAATATTATC
65581 ATGTTAAAAA
1 ATGTTAAAAA
65591 TAGATATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 1 0.04
19 8 0.33
20 4 0.17
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (18 bp):
ATGTTAAAAAATATTATC
Found at i:65724 original size:30 final size:31
Alignment explanation
Indices: 65688--65763 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 31
65678 GGACCTCCAA
* *
65688 AAGTTTAAGTACCAACTTA-AAAAAAATGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAATATC
*
65718 AAGTTTAAGTACCAAATTAGGAAAAAAATATT
1 AAGTTTAAGTACCAAATTA-GAAAAAAATATC
*
65750 AAGTTTGAGTACCA
1 AAGTTTAAGTACCA
65764 TTTAAATATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 18 0.45
32 22 0.55
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAATATC
Found at i:65814 original size:30 final size:30
Alignment explanation
Indices: 65764--65838 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
65754 TTGAGTACCA
*
65764 TTTAAATATCAACTTTAAAAAAAATATCAAG
1 TTTAAATATCAA-ATTAAAAAAAATATCAAG
65795 TTTAAATATCAAATTAAAAAAAATATCAAG
1 TTTAAATATCAAATTAAAAAAAATATCAAG
* *
65825 TTCAAAAATCAAAT
1 TTTAAATATCAAAT
65839 ATTATATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 29 0.71
31 12 0.29
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (30 bp):
TTTAAATATCAAATTAAAAAAAATATCAAG
Found at i:83597 original size:58 final size:58
Alignment explanation
Indices: 83515--83652 Score: 136
Period size: 58 Copynumber: 2.4 Consensus size: 58
83505 TTTTCCTATC
** * * ** * *
83515 CAGAGT-TTGCCACACGGGCTTTTCTTCAACAGAGTTTGCTACAAAGGTGCTTCCTTTA
1 CAGAGTATTGCCACAAAGGCATTTCTTCAACAAAAATCGCTACAAAGGCG-TTCCTTTA
* * * *
83573 CGGAG-ATTGCCACAAAGGCATTTCTTTAACAAAAATCGCTACAAAGGCGTTTCTTTT
1 CAGAGTATTGCCACAAAGGCATTTCTTCAACAAAAATCGCTACAAAGGCGTTCCTTTA
*
83630 CAGAGTTTTGCCACAAAGGCATT
1 CAGAGTATTGCCACAAAGGCATT
83653 CCTTTTCATT
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
57 10 0.16
58 54 0.84
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (58 bp):
CAGAGTATTGCCACAAAGGCATTTCTTCAACAAAAATCGCTACAAAGGCGTTCCTTTA
Found at i:83818 original size:28 final size:28
Alignment explanation
Indices: 83787--83847 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
83777 CGAATAGTTG
*
83787 CCACAAAGGCATTCTTAATAGAGATTTT
1 CCACAAAGACATTCTTAATAGAGATTTT
*
83815 CCACAACGACATTCTTAATAGAGATTTT
1 CCACAAAGACATTCTTAATAGAGATTTT
83843 CCACA
1 CCACA
83848 GAGGTTTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (28 bp):
CCACAAAGACATTCTTAATAGAGATTTT
Found at i:89489 original size:41 final size:41
Alignment explanation
Indices: 89432--89691 Score: 295
Period size: 41 Copynumber: 6.3 Consensus size: 41
89422 CCGAGTCATA
89432 AGTCTTCCTTTAAATATAATCTCATGCTCATCCTGAGTCACG
1 AGTCTTCCTTT-AATATAATCTCATGCTCATCCTGAGTCACG
* * * * *
89474 ATTCTTCCTTTAATATAATCTCATGTTCATCTTGAGACATG
1 AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACG
* * **
89515 AGTCTTCCTTTAATACAATCTCATGCTCATCCCGACACACG
1 AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACG
* * ** * *
89556 AGTCTTCCTTTAATTTAATCTCATGCTTATTTTAAGTCATG
1 AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACG
**
89597 AGTCTTCCTTTAATATAATCTCATGCTCATTTTGAGTCACG
1 AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACG
* * * * * *
89638 AGTCCTCCTTTAATATAATTTCATGCTTATCCTAAGACATG
1 AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACG
89679 AGTCTTCCATTTA
1 AGTCTTCC-TTTA
89692 TACTTAAAGT
Statistics
Matches: 182, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
41 168 0.92
42 14 0.08
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.40
Consensus pattern (41 bp):
AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACG
Found at i:89535 original size:82 final size:82
Alignment explanation
Indices: 89432--89691 Score: 360
Period size: 82 Copynumber: 3.1 Consensus size: 82
89422 CCGAGTCATA
*
89432 AGTCTTCCTTTAAATATAATCTCATGCTCATCCTGAGTCACGATTCTTCCTTTAATATAATCTCA
1 AGTCTTCCTTT-AATATAATCTCATGCTCATCCTGAGTCACGAGTCTTCCTTTAATATAATCTCA
*
89497 TG-TTCATCTTGAGACATG
65 TGCTT-ATCTTAAGACATG
* * ** *
89515 AGTCTTCCTTTAATACAATCTCATGCTCATCCCGACACACGAGTCTTCCTTTAATTTAATCTCAT
1 AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACGAGTCTTCCTTTAATATAATCTCAT
* *
89580 GCTTATTTTAAGTCATG
66 GCTTATCTTAAGACATG
** * *
89597 AGTCTTCCTTTAATATAATCTCATGCTCATTTTGAGTCACGAGTCCTCCTTTAATATAATTTCAT
1 AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACGAGTCTTCCTTTAATATAATCTCAT
*
89662 GCTTATCCTAAGACATG
66 GCTTATCTTAAGACATG
89679 AGTCTTCCATTTA
1 AGTCTTCC-TTTA
89692 TACTTAAAGT
Statistics
Matches: 154, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
82 137 0.89
83 17 0.11
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.40
Consensus pattern (82 bp):
AGTCTTCCTTTAATATAATCTCATGCTCATCCTGAGTCACGAGTCTTCCTTTAATATAATCTCAT
GCTTATCTTAAGACATG
Found at i:89614 original size:123 final size:124
Alignment explanation
Indices: 89432--89669 Score: 334
Period size: 123 Copynumber: 1.9 Consensus size: 124
89422 CCGAGTCATA
* *
89432 AGTCTTCCTTTAAATATAATCTCATGCTCATCCTGAGTCACGATTCTTCCTTTAATATAATCTCA
1 AGTCTTCCTTTAAATATAATCTCATGCTCATCCTAAGTCACGAGTCTTCCTTTAATATAATCTCA
* * *
89497 TGTTCATCTTGAGACATGAGTCTTCCTTTAATACAATCTCATGCTCATCCCGACACACG
66 TGCTCATCTTGAGACACGAGTCCTCCTTTAATACAATCTCATGCTCATCCCGACACACG
* * ** *
89556 AGTCTTCCTTT-AATTTAATCTCATGCTTATTTTAAGTCATGAGTCTTCCTTTAATATAATCTCA
1 AGTCTTCCTTTAAATATAATCTCATGCTCATCCTAAGTCACGAGTCTTCCTTTAATATAATCTCA
* * * * *
89620 TGCTCATTTTGAGTCACGAGTCCTCCTTTAATATAATTTCATGCTTATCC
66 TGCTCATCTTGAGACACGAGTCCTCCTTTAATACAATCTCATGCTCATCC
89670 TAAGACATGA
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
123 88 0.89
124 11 0.11
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (124 bp):
AGTCTTCCTTTAAATATAATCTCATGCTCATCCTAAGTCACGAGTCTTCCTTTAATATAATCTCA
TGCTCATCTTGAGACACGAGTCCTCCTTTAATACAATCTCATGCTCATCCCGACACACG
Found at i:99241 original size:17 final size:17
Alignment explanation
Indices: 99219--99269 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
99209 TCAGTCACTT
*
99219 GAAAAAGAAAAAAATGA
1 GAAAAAGAAAAAAAAGA
99236 GAAAAAGAAAGAGAAAAGA
1 GAAAAAGAAA-A-AAAAGA
99255 -AAAGAAGAAAAAAAA
1 GAAA-AAGAAAAAAAA
99270 TTTATTGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.47
18 5 0.17
19 11 0.37
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
GAAAAAGAAAAAAAAGA
Found at i:99269 original size:12 final size:11
Alignment explanation
Indices: 99220--99269 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
99210 CAGTCACTTG
99220 AAAA-AGAAAA
1 AAAAGAGAAAA
*
99230 AAATGAGAAAA
1 AAAAGAGAAAA
99241 AGAAAGAGAAAA
1 A-AAAGAGAAAA
99253 GAAAAGAAGAAAA
1 -AAAAG-AGAAAA
99266 AAAA
1 AAAA
99270 TTTATTGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 3 0.09
11 7 0.21
12 17 0.50
13 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAGAGAAAA
Found at i:102432 original size:25 final size:23
Alignment explanation
Indices: 102389--102434 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
102379 TTTCTGTTGA
102389 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
102412 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
102435 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:103555 original size:15 final size:15
Alignment explanation
Indices: 103537--103567 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
103527 ATTTTTTTTA
103537 TTTTTCTATTTTAAT
1 TTTTTCTATTTTAAT
*
103552 TTTTTCTCTTTTAAT
1 TTTTTCTATTTTAAT
103567 T
1 T
103568 GCTTTTGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCTATTTTAAT
Found at i:106438 original size:6 final size:6
Alignment explanation
Indices: 106427--106472 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
106417 TAGTACATTT
* * *
106427 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTT
106473 ATTATACACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (6 bp):
ATTTTC
Found at i:106491 original size:6 final size:6
Alignment explanation
Indices: 106424--106477 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
106414 AATTAGTACA
* * * *
106424 TTTATT TTCATT TTCATT TTCATT TTCATT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
106472 TATTAT
1 T-TTAT
106478 ACACTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
6 41 0.91
7 4 0.09
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:107404 original size:14 final size:13
Alignment explanation
Indices: 107375--107408 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
107365 TTAGAAAAAG
107375 AAAAAAAAGTTGA
1 AAAAAAAAGTTGA
107388 AAAGAAAAA-TTGA
1 AAA-AAAAAGTTGA
107401 AAAAAAAA
1 AAAAAAAA
107409 AGAAGAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAAAAAAGTTGA
Found at i:107414 original size:22 final size:23
Alignment explanation
Indices: 107386--107442 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
107376 AAAAAAAGTT
107386 GAAAAGAAAAATTGA-AAAAAAA
1 GAAAAGAAAAATTGAGAAAAAAA
107408 -AAGAAGAGAAAATTGAGAAAAAAA
1 GAA-AAGA-AAAATTGAGAAAAAAA
107432 GAAAAGAAAAA
1 GAAAAGAAAAA
107443 AAAGACAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.06
22 4 0.13
23 12 0.39
24 11 0.35
25 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (23 bp):
GAAAAGAAAAATTGAGAAAAAAA
Found at i:107419 original size:23 final size:22
Alignment explanation
Indices: 107389--107441 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
107379 AAAAGTTGAA
107389 AAGA-AAAATTGAAAAAAAAAAG
1 AAGAGAAAATTG-AAAAAAAAAG
*
107411 AAGAGAAAATTGAGAAAAAAAG
1 AAGAGAAAATTGAAAAAAAAAG
*
107433 AAAAGAAAA
1 AAGAGAAAA
107442 AAAAGACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (22 bp):
AAGAGAAAATTGAAAAAAAAAG
Found at i:107427 original size:33 final size:33
Alignment explanation
Indices: 107390--107452 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
107380 AAAGTTGAAA
** *
107390 AGAAAAATTGAAAA-AAAAAAGAAGAGAAAATTG
1 AGAAAAAAAGAAAAGAAAAAA-AAGACAAAATTG
107423 AGAAAAAAAGAAAAGAAAAAAAAGACAAAA
1 AGAAAAAAAGAAAAGAAAAAAAAGACAAAA
107453 GTGTGTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 20 0.77
34 6 0.23
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (33 bp):
AGAAAAAAAGAAAAGAAAAAAAAGACAAAATTG
Found at i:107443 original size:24 final size:23
Alignment explanation
Indices: 107386--107443 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
107376 AAAAAAAGTT
107386 GAAAAG-AAAAATTGAAAAAAAA
1 GAAAAGAAAAAATTGAAAAAAAA
*
107408 -AAGAAGAGAAAATTGAGAAAAAAA
1 GAA-AAGAAAAAATTGA-AAAAAAA
107432 GAAAAGAAAAAA
1 GAAAAGAAAAAA
107444 AAGACAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 8 0.27
24 15 0.50
25 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (23 bp):
GAAAAGAAAAAATTGAAAAAAAA
Found at i:113676 original size:99 final size:99
Alignment explanation
Indices: 113505--113700 Score: 374
Period size: 99 Copynumber: 2.0 Consensus size: 99
113495 GTGATCAACG
*
113505 AACAAACATTACATTCTTCTATCACCGGAACGTGAGAAAAACCAGAGAGAAATAAAAAGAATTTT
1 AACAAACATTACATTCTTCTATCACCGGAACGTGAGAAAAACCAAAGAGAAATAAAAAGAATTTT
113570 CGAGAGTGAAAATAACAGAATAAAACCGTTGTGT
66 CGAGAGTGAAAATAACAGAATAAAACCGTTGTGT
113604 AACAAACATTACATTCTTCTATCACCGGAACGTGAGAAAAACCAAAGAGAAATAAAAAGAATTTT
1 AACAAACATTACATTCTTCTATCACCGGAACGTGAGAAAAACCAAAGAGAAATAAAAAGAATTTT
*
113669 CGAGAGTGAAAATAACAGAATAAAATCGTTGT
66 CGAGAGTGAAAATAACAGAATAAAACCGTTGT
113701 CTCTAAATAA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.21
Consensus pattern (99 bp):
AACAAACATTACATTCTTCTATCACCGGAACGTGAGAAAAACCAAAGAGAAATAAAAAGAATTTT
CGAGAGTGAAAATAACAGAATAAAACCGTTGTGT
Found at i:120797 original size:28 final size:29
Alignment explanation
Indices: 120755--120945 Score: 124
Period size: 29 Copynumber: 6.6 Consensus size: 29
120745 ACACTTCGAA
*
120755 GTCAAAATAGTAA-TTTTGGAGGTTTAGG
1 GTCAAAATGGTAATTTTTGGAGGTTTAGG
* * * *
120783 GTCAAAATGGGAATTTTTTGATGTTCGAGG
1 GTCAAAATGGTAATTTTTGGAGGTT-TAGG
* ** *
120813 GT-AAAATGGTAATTTTTTGAAGAATTCGAG
1 GTCAAAATGGTAA-TTTTTGGAGGTTTAG-G
* * *
120843 GTCAAAAATGG-GATTTTTGGAAGTTCAGG
1 GTC-AAAATGGTAATTTTTGGAGGTTTAGG
*
120872 CT-AAAATGGTAATTTTTGGAGAGTTTAGG
1 GTCAAAATGGTAATTTTTGGAG-GTTTAGG
* * * **
120901 GTTAAAAT-GAAATTTTTTGAAATTTAGGG
1 GTCAAAATGGTAATTTTTGGAGGTTTA-GG
120930 GT-AAAATGGTAATTTT
1 GTCAAAATGGTAATTTT
120946 GTAGAATTTA
Statistics
Matches: 122, Mismatches: 30, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
27 7 0.06
28 29 0.24
29 49 0.40
30 29 0.24
31 1 0.01
32 7 0.06
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
GTCAAAATGGTAATTTTTGGAGGTTTAGG
Found at i:120909 original size:30 final size:29
Alignment explanation
Indices: 120758--121292 Score: 246
Period size: 30 Copynumber: 18.2 Consensus size: 29
120748 CTTCGAAGTC
* * * *
120758 AAAATAGTAA-TTTTGGAGGTTTAGGGTC
1 AAAATGGTAATTTTTAGAAGTTTAGGGTT
* * * *
120786 AAAATGGGAATTTTTTGATGTTCGAGGG-T
1 AAAATGGTAATTTTTAGAAGTT-TAGGGTT
* * * *
120815 AAAATGGTAATTTTTTGAAGAATTCGAGGTCA
1 AAAATGGTAATTTTTAGAAG-TTTAG-GGT-T
* * * *
120847 AAAATGG-GATTTTTGGAAGTTCA-GGCT
1 AAAATGGTAATTTTTAGAAGTTTAGGGTT
*
120874 AAAATGGTAATTTTTGGAGAGTTTAGGGTT
1 AAAATGGTAATTTTTAGA-AGTTTAGGGTT
* * * *
120904 AAAAT-GAAATTTTTTGAAATTTAGGGGT
1 AAAATGGTAATTTTTAGAAGTTTAGGGTT
*
120932 AAAATGGTAATTTTGTAGAA-TTTAAGGTT
1 AAAATGGTAATTTT-TAGAAGTTTAGGGTT
* * *
120961 AAAAATGG-ATTTTTTAGAGAATTT-GAGGTCA
1 -AAAATGGTAATTTTTAGA-AGTTTAG-GGT-T
* * *
120992 AAAATGG-AATTTTTGGAAATTCGAGGG-T
1 AAAATGGTAATTTTTAGAAGTT-TAGGGTT
* * *
121020 AAAATGATATTTTTTGGAGAA--TTCGAGGTT
1 AAAATGGTAATTTTT--AGAAGTTTAG-GGTT
* * *
121050 AAAAATAG-AATTTTTAGAAATTTAGCGGTA
1 -AAAATGGTAATTTTTAGAAGTTTAG-GGTT
* * *
121080 AAAAT-GTAATTTTTGGAAGTTTAAGGAT
1 AAAATGGTAATTTTTAGAAGTTTAGGGTT
* * * **
121108 AAAATTGTAATTTTTATATTGTTTAGGGGCC
1 AAAATGGTAATTTTTAGA-AGTTTA-GGGTT
121139 AAAAT-GTAATTTTTAGAAAGTTTAAGGGTT
1 AAAATGGTAATTTTTAG-AAGTTT-AGGGTT
* *
121169 AAAAT-GTAATTTTCAAAAAGTTTAAGGGTT
1 AAAATGGTAATTTT-TAGAAGTTT-AGGGTT
* *
121199 AAAAT-GTAATTTTCAAAAAGTTTAAGGGTT
1 AAAATGGTAATTTT-TAGAAGTTT-AGGGTT
*
121229 AAAAT-GTAATTTTTTAAAAGTTTAAGGGTT
1 AAAATGGTAA-TTTTTAGAAGTTT-AGGGTT
* *
121259 -AAAT-GTAATTTTTAGAAAGTTTGGGGTC
1 AAAATGGTAATTTTTAG-AAGTTTAGGGTT
121287 AAAATG
1 AAAATG
121293 CGATTTTTTG
Statistics
Matches: 401, Mismatches: 69, Indels: 72
0.74 0.13 0.13
Matches are distributed among these distances:
27 7 0.02
28 66 0.16
29 123 0.31
30 165 0.41
31 33 0.08
32 7 0.02
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGAAGTTTAGGGTT
Found at i:121181 original size:60 final size:59
Alignment explanation
Indices: 120873--121280 Score: 254
Period size: 59 Copynumber: 6.9 Consensus size: 59
120863 AAGTTCAGGC
** * * * *
120873 TAAAATGGTAATTTTTGGAGAGTTT-AGGGTTAAAATGAAATTTTTTGAAA-TTT-AGGGG
1 TAAAAT-GTAATTTTTATAAAGTTTAAGGG-TAAAATGTAATTTTTAGAAAGTTTAAGGGT
* * * * *
120931 TAAAATGGTAATTTTGTA-GAA-TTTAAGGTTAAAAATGGATTTTTTAGAGAA-TTTGA-GGT
1 TAAAAT-GTAATTTT-TATAAAGTTTAAGGGT-AAAATGTAATTTTTAGA-AAGTTTAAGGGT
* * ** ** * * **
120990 CAAAAATGGAATTTTTGGAAA-TTCGAGGGTAAAATGATATTTTTTGGAGAA-TTCGA-GGT
1 -TAAAATGTAATTTTTATAAAGTTTAAGGGTAAAATG-TAATTTTTAGA-AAGTTTAAGGGT
* * *
121049 TAAAAATAG-AATTTTTAGAAA-TTT-AGCGGTAAAAATGTAATTTTT-GGAAGTTTAA-GGA
1 T-AAAAT-GTAATTTTTATAAAGTTTAAG-GGT-AAAATGTAATTTTTAGAAAGTTTAAGGGT
** * *
121107 TAAAATTGTAATTTTTATATTGTTTAGGGGCCAAAATGTAATTTTTAGAAAGTTTAAGGGT
1 TAAAA-TGTAATTTTTATAAAGTTTAAGGG-TAAAATGTAATTTTTAGAAAGTTTAAGGGT
* * * *
121168 TAAAATGTAATTTTCAAAAAGTTTAAGGGTTAAAATGTAATTTTCAAAAAGTTTAAGGGT
1 TAAAATGTAATTTTTATAAAGTTTAAGGG-TAAAATGTAATTTTTAGAAAGTTTAAGGGT
*
121228 TAAAATGTAATTTTT-TAAAAGTTTAAGGGTTAAATGTAATTTTTAGAAAGTTT
1 TAAAATGTAATTTTTAT-AAAGTTTAAGGGTAAAATGTAATTTTTAGAAAGTTT
121281 GGGGTCAAAA
Statistics
Matches: 282, Mismatches: 47, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
57 11 0.04
58 59 0.21
59 110 0.39
60 95 0.34
61 7 0.02
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (59 bp):
TAAAATGTAATTTTTATAAAGTTTAAGGGTAAAATGTAATTTTTAGAAAGTTTAAGGGT
Found at i:121300 original size:29 final size:30
Alignment explanation
Indices: 121058--121280 Score: 249
Period size: 30 Copynumber: 7.5 Consensus size: 30
121048 TTAAAAATAG
* *
121058 AATTTTTAGAAA-TTT-AGCGGTAAAAATGT
1 AATTTTTAAAAAGTTTAAG-GGTTAAAATGT
** *
121087 AATTTTT-GGAAGTTTAA-GGATAAAATTGT
1 AATTTTTAAAAAGTTTAAGGGTTAAAA-TGT
* ** * **
121116 AATTTTTATATTGTTTAGGGGCCAAAATGT
1 AATTTTTAAAAAGTTTAAGGGTTAAAATGT
*
121146 AATTTTTAGAAAGTTTAAGGGTTAAAATGT
1 AATTTTTAAAAAGTTTAAGGGTTAAAATGT
*
121176 AATTTTCAAAAAGTTTAAGGGTTAAAATGT
1 AATTTTTAAAAAGTTTAAGGGTTAAAATGT
*
121206 AATTTTCAAAAAGTTTAAGGGTTAAAATGT
1 AATTTTTAAAAAGTTTAAGGGTTAAAATGT
*
121236 AATTTTTTAAAAGTTTAAGGGTT-AAATGT
1 AATTTTTAAAAAGTTTAAGGGTTAAAATGT
*
121265 AATTTTTAGAAAGTTT
1 AATTTTTAAAAAGTTT
121281 GGGGTCAAAA
Statistics
Matches: 167, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
28 9 0.05
29 40 0.24
30 112 0.67
31 6 0.04
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (30 bp):
AATTTTTAAAAAGTTTAAGGGTTAAAATGT
Done.