Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012901.1 Kokia drynarioides strain JFW-HI SEQ_127915, 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: 77317
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:1266 original size:29 final size:29
Alignment explanation
Indices: 1234--1678 Score: 384
Period size: 29 Copynumber: 15.1 Consensus size: 29
1224 TGGACATCCG
1234 GGGGT-AAAATGGTAATTTTTGGAAGTTTA
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTA
*
1263 GGGGTCAAAAATGGAATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
** * *
1292 GAGGCCAAAAATTGAATTTTTGGAAG-TTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
* *
1321 GAGGGTAAAAATGGGATTTTTTGGAAGTTTG
1 G-GGGTAAAAAT-GGAATTTTTGGAAGTTTA
*** *
1352 GGGGTAAAAACAAAATTTTTGGAAG-TTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * * *
1380 GAGGATAAAAATGAAATTTTTAGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
* * *
1410 GAGGTCAAAAAT-GACATTTTTTGATGTTT-
1 GGGGT-AAAAATGGA-ATTTTTGGAAGTTTA
*
1439 GGGGTTAAAAAT-GAGATTTTTGGAAGTTTG
1 GGGG-TAAAAATGGA-ATTTTTGGAAGTTTA
* *
1469 GGGGTAAAAATGGAATTTTTAGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* *
1498 GGGGTTAAAAATGGGATTTTTGAAAGTTT-
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTA
* *
1527 GAGGGTAAAAATGGGATTTTTAGAAGTTTTA
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTTA
* *
1558 GGGTTAAAAATGGGATTTTTGGAAGTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * *
1587 GGGGTAAAATTGGAATTTTTAGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* ** *
1616 GAGGTTAAAAATGGGTTTTTTGGAAGTTTG
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
*
1646 GGGGTAAAAATGGAATTCTTGGATAGTTTA
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTA
1676 GGG
1 GGG
1679 ACCTCCAGGG
Statistics
Matches: 346, Mismatches: 52, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.01
29 188 0.54
30 144 0.42
31 11 0.03
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:1283 original size:59 final size:58
Alignment explanation
Indices: 1233--1674 Score: 401
Period size: 59 Copynumber: 7.5 Consensus size: 58
1223 TTGGACATCC
* * *
1233 GGGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGAAGTTC
1 GGGGGTAAAATGG-AATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT
*** * *
1292 GAGGCCAAAAATTGAATTTTTGGAAG-TTCGAGGG-TAAAAATGGGATTTTTTGGAAGTTT
1 G-GGGGTAAAATGGAATTTTTGGAAGTTTCG-GGGTTAAAAAT-GGAATTTTTGGAAGTTT
*** * * * *
1351 GGGGGTAAAAACAAAATTTTTGGAAG-TTCGAGGATAAAAATGAAATTTTTAGAAGTTT
1 GGGGGT-AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT
* * * *
1409 CGAGGTCAAAAAT-GACATTTTTTGATGTTT-GGGGTTAAAAAT-GAGATTTTTGGAAGTTT
1 GGGGGT--AAAATGGA-ATTTTTGGAAGTTTCGGGGTTAAAAATGGA-ATTTTTGGAAGTTT
* * * *
1468 GGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGAAAGTTT
1 GGGGGT-AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT
* * * ** *
1527 GAGGGTAAAAATGGGATTTTTAGAAGTTTTAGGGTTAAAAATGGGATTTTTGGAAGTTT
1 GGGGGT-AAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT
* * * **
1586 AGGGGTAAAATTGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGGTTTTTTGGAAGTTT
1 GGGGGTAAAA-TGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT
*
1645 GGGGGTAAAAATGGAATTCTTGGATAGTTT
1 GGGGGT-AAAATGGAATTTTTGGA-AGTTT
1675 AGGGACCTCC
Statistics
Matches: 320, Mismatches: 48, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
58 55 0.17
59 245 0.77
60 20 0.06
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.36
Consensus pattern (58 bp):
GGGGGTAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTT
Found at i:1668 original size:88 final size:87
Alignment explanation
Indices: 1234--1678 Score: 430
Period size: 88 Copynumber: 5.0 Consensus size: 87
1224 TGGACATCCG
* * * * **
1234 GGGGT-AAAATGGTAATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGCC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTT-GGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
1298 AAAAATTGAATTTTTGGAAG-TTC
64 AAAAATGGAATTTTTGGAAGTTTA
* * **** * * *
1321 GAGGGTAAAAATGGGATTTTTTGGAAGTTTGGGGGTAAAAACAAAATTTTTGGAAGTTCGAGGAT
1 G-GGGTAAAAAT-GGAATTTTTGGAAGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGT
* * *
1386 AAAAATGAAATTTTTAGAAGTTTC
64 AAAAATGGAATTTTTGGAAGTTTA
* * * *
1410 GAGGTCAAAAAT-GACATTTTTTGATGTTTGGGGTTAAAAATGAGATTTTTGGAAGTTTGGGGGT
1 GGGGT-AAAAATGGA-ATTTTTGGAAGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGT
* *
1474 AAAAATGGAATTTTTAGAAGTTTT
64 AAAAATGGAATTTTTGGAAGTTTA
* * * * *
1498 GGGGTTAAAAATGGGATTTTTGAAAGTTTGAGGG-TAAAAATGGGATTTTTAGAAGTTTTAGGGT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTG-GGGTTAAAAATGGGATTTTTGGAAG-TTTGGGGG
*
1562 TAAAAATGGGATTTTTGGAAGTTTA
63 TAAAAATGGAATTTTTGGAAGTTTA
* * * *
1587 GGGGTAAAATTGGAATTTTTAGAAGTTTCGAGGTTAAAAATGGGTTTTTTGGAAGTTTGGGGGTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTT-GGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTA
*
1652 AAAATGGAATTCTTGGATAGTTTA
65 AAAATGGAATTTTTGGA-AGTTTA
1676 GGG
1 GGG
1679 ACCTCCAGGG
Statistics
Matches: 298, Mismatches: 47, Indels: 24
0.81 0.13 0.07
Matches are distributed among these distances:
87 3 0.01
88 198 0.66
89 95 0.32
90 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.36
Consensus pattern (87 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAA
AAATGGAATTTTTGGAAGTTTA
Found at i:2718 original size:15 final size:16
Alignment explanation
Indices: 2693--2725 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2683 CCCTTTTTTT
2693 TATTAATTATTAGTAA
1 TATTAATTATTAGTAA
*
2709 TATT-ATTATTATTAA
1 TATTAATTATTAGTAA
2724 TA
1 TA
2726 AAACATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTAATTATTAGTAA
Found at i:3594 original size:6 final size:6
Alignment explanation
Indices: 3551--3633 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
3541 TTTTAATTAA
* * * *
3551 TTAAATT TTAAAT TCAAA- TTAATT TTAAAC TT-AAT TTAAAT TTAAAC
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* **
3598 TTAAAA GAAAAGT TTAAACT TTAAA- TTAAAT TTAAA
1 TTAAAT TTAAA-T TTAAA-T TTAAAT TTAAAT TTAAA
3634 CCCAAAATGA
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
5 12 0.21
6 32 0.55
7 14 0.24
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:3633 original size:18 final size:18
Alignment explanation
Indices: 3549--3634 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 18
3539 TTTTTTAATT
*
3549 AATTAAATTTTAAA-TTCA
1 AATTAAA-TTTAAACTTTA
*
3567 AATTAATTTTAAAC-TTA
1 AATTAAATTTAAACTTTA
* *
3584 ATTTAAATTTAAACTTAA
1 AATTAAATTTAAACTTTA
**
3602 AAGAAAAGTTTAAACTTTA
1 AATTAAA-TTTAAACTTTA
3621 AATTAAATTTAAAC
1 AATTAAATTTAAAC
3635 CCAAAATGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
17 20 0.37
18 19 0.35
19 15 0.28
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTAAATTTAAACTTTA
Found at i:4432 original size:205 final size:204
Alignment explanation
Indices: 4037--4559 Score: 771
Period size: 205 Copynumber: 2.6 Consensus size: 204
4027 ACCATATCAC
* * * * * * ** *
4037 TTGTTTTAATCCACTTCTCTGTGTTTCATCAGGAAGATGATTTTGGTTTACTTCCTC-GTATTTC
1 TTGTTTTAATTCACTTTTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTT-CTCAGTATCTC
* * *
4101 ATCAGGAAGCTAACTGTTTTATTACTTTGACCTGCTTCTCAGTATCTCATCAGGAGGCTAGGGTT
65 ATCAGGAAGCTAACTGTTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTT
4166 AGAAGATTTGTTCATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATG
130 AGAAGATTTGTTCATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATG
4231 ACCGCGTCGT
195 ACCGCGTCGT
*
4241 TTGTTTTAATTCGCTTTTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
1 TTGTTTTAATTCACTTTTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
* * * * * *
4306 TCAGGAAGCTAACCG-TTTGTTGCTTCGACCTGCTTCTCAGTGTCTCATGAGGAAGCTGGGGTTC
66 TCAGGAAGCTAACTGTTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTA
** * *
4370 GAAGATTTGTTCACATCGAGGGTGGGTTTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGAT
131 GAAGATTTGTT--CATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGAT
4435 GACCGCGTCGT
194 GACCGCGTCGT
*
4446 TTGTTTTAATTCACTTTTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
1 TTGTTTTAATTCACTTTTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
* *
4511 TCAAGAAGCTAACTGTTTTATTACTTCGACCTGCTTCTCATTGTCTCAT
66 TCAGGAAGCTAACTGTTTTATTACTTCGACCTGCTTCTCAGTGTCTCAT
4560 TAAGAAGACG
Statistics
Matches: 285, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
203 55 0.19
204 65 0.23
205 135 0.47
206 30 0.11
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (204 bp):
TTGTTTTAATTCACTTTTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCA
TCAGGAAGCTAACTGTTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTA
GAAGATTTGTTCATCGAGCATGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGA
CCGCGTCGT
Found at i:4579 original size:85 final size:85
Alignment explanation
Indices: 4469--4681 Score: 354
Period size: 85 Copynumber: 2.5 Consensus size: 85
4459 CTTTTCTGTA
* **
4469 TCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACTGTTTTATTA
1 TCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAAAAGCTAACCATTTTATTA
*
4534 CTTCGACCTGCTTCTCATTG
66 CTTCGACCTGCTTCTCAGTG
* * *
4554 TCTCATTAAGAAGACGAATTTGGTCCACTTCTTAGTATCTCATTAAAAAGCTAACCATTTTATTA
1 TCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAAAAGCTAACCATTTTATTA
4619 CTTCGACCTGCTTCTCAGTG
66 CTTCGACCTGCTTCTCAGTG
*
4639 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCAT
1 TCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCAT
4682 AAGGAAGATG
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 118 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (85 bp):
TCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAAAAGCTAACCATTTTATTA
CTTCGACCTGCTTCTCAGTG
Found at i:4755 original size:86 final size:87
Alignment explanation
Indices: 4400--4774 Score: 307
Period size: 85 Copynumber: 4.4 Consensus size: 87
4390 GGTGGGTTTG
** * * * *
4400 ATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTTAATTCA-CTTTT
1 ATTTGGTCCACTTCTCAGTATCTCATAAGGAAGATGACCACGTCGTTTGTTTTAATTCAGCTTCT
4464 CTGTATCTCATCAAGAAGACGA
66 CTGTATCTCATCAAGAAGACGA
* * *
4486 ATTTGGTCCACTTCTCAGTATCTCATCAA-GAAGCT-A--AC-T-GTTT-TATTACTTCGACCTG
1 ATTTGGTCCACTTCTCAGTATCTCAT-AAGGAAGATGACCACGTCGTTTGTTTTAATTC-A---G
* *
4544 CTTCTCAT-TGTCTCATTAAGAAGACGA
61 CTTCTC-TGTATCTCATCAAGAAGACGA
* * * * * *
4571 ATTTGGTCCACTTCTTAGTATCTCATTAA-AAAGCT-A--AC--CATTT-TATTACTTCGACCTG
1 ATTTGGTCCACTTCTCAGTATCTCA-TAAGGAAGATGACCACGTCGTTTGTTTTAATTC-A---G
* * *
4629 CTTCTCAGTGTCTCATCAGGAAGACGA
61 CTTCTCTGTATCTCATCAAGAAGACGA
* *
4656 ATTTGGTCCACTTCTCAGTATCTCATAAGGAAGATGACCGCGTCGTTTGTTTTAATT-AGCTTTT
1 ATTTGGTCCACTTCTCAGTATCTCATAAGGAAGATGACCACGTCGTTTGTTTTAATTCAGCTTCT
* *
4720 CTGTATCTTATCAGGAAGACGA
66 CTGTATCTCATCAAGAAGACGA
*
4742 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAG
1 ATTTGGTCCACTTCTCAGTATCTCATAAGGAAG
4775 CTAATCGTTT
Statistics
Matches: 243, Mismatches: 29, Indels: 34
0.79 0.09 0.11
Matches are distributed among these distances:
80 7 0.03
81 5 0.02
82 1 0.00
83 1 0.00
84 3 0.01
85 126 0.52
86 87 0.36
87 1 0.00
88 1 0.00
89 1 0.00
90 4 0.02
91 6 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (87 bp):
ATTTGGTCCACTTCTCAGTATCTCATAAGGAAGATGACCACGTCGTTTGTTTTAATTCAGCTTCT
CTGTATCTCATCAAGAAGACGA
Found at i:5420 original size:27 final size:27
Alignment explanation
Indices: 5390--5449 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
5380 TCAAAAATTC
*
5390 TATTAAAAAGAGGATAAAAGGAAACAA
1 TATTAAAAAGAAGATAAAAGGAAACAA
* * *
5417 TATTAACAAGAAGATCAAAGGAAGCAA
1 TATTAAAAAGAAGATAAAAGGAAACAA
5444 TCATTA
1 T-ATTA
5450 GTTGAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAAGATAAAAGGAAACAA
Found at i:16732 original size:59 final size:58
Alignment explanation
Indices: 16580--16976 Score: 158
Period size: 59 Copynumber: 6.8 Consensus size: 58
16570 GCACGGGGGC
* * * * *
16580 AAAATGGTAATTTTAGGAAAATTTGGGGTTAAAAATAGAATTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTTGG-AAGTTTGGGGTCAAAAATAGAATTTTTAGACATCCGAGGGT
* ** * * * *
16639 AAAAAGGTAA-TTTT-GAGAGTTTTGAAGTCGAAAATAGAGTTTTTTGACATCCTAGGGT
1 AAAATGGTAATTTTTGGA-AG-TTTGGGGTCAAAAATAGAATTTTTAGACATCCGAGGGT
* * * **
16697 CAAATGGTAATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGA-AGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAGTTT-GGGGTCAAAAATAGAATTTTTAGACA-TCCGAGGGT
* * *
16756 AAAAAT-G-AGATTTTGTGGAAGTTTGAGGGT-AAAAACA-AATTTTTTGGA-AGTTCGAGGGT
1 -AAAATGGTA-ATTTT-TGGAAGTTTG-GGGTCAAAAATAGAA-TTTTTAGACA-TCCGAGGGT
* * * * * *
16815 AAAAAAGG-AATTTTTAGAAGTTTCGAGGTTAAAAAT-GAGATTTTTGGA-AGTTCGAGGGT
1 -AAAATGGTAATTTTTGGAAGTTT-GGGGTCAAAAATAGA-ATTTTTAGACA-TCCGAGGGT
** * ** * * * * **
16874 AAAAACGAAATTTTTAAAAGTTTTGAGGTCAAAAATGGGATTTTTTGA-AGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAG-TTTGGGGTCAAAAATAGAATTTTTAGACA-TCCGAGGGT
* *
16933 AAAAATGG-AATTTTTAGAAGTTTTAGGGT-AAAAAT-GAGATTTTT
1 -AAAATGGTAATTTTTGGAAG-TTTGGGGTCAAAAATAGA-ATTTTT
16977 GTATGTTTGG
Statistics
Matches: 274, Mismatches: 43, Indels: 43
0.76 0.12 0.12
Matches are distributed among these distances:
56 1 0.00
57 3 0.01
58 76 0.28
59 163 0.59
60 31 0.11
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAGTTTGGGGTCAAAAATAGAATTTTTAGACATCCGAGGGT
Found at i:16760 original size:29 final size:29
Alignment explanation
Indices: 16698--17191 Score: 427
Period size: 29 Copynumber: 16.9 Consensus size: 29
16688 TCCTAGGGTC
16698 AAATGGTAATTTTTGGAAGTTT-AGGGGTCAA
1 AAATGG-AATTTTTGGAAGTTTGA-GGGT-AA
16729 AAATGGAATTTTTGGAAGTTTGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
16758 AAAT-GAGATTTTGTGGAAGTTTGAGGGTAA
1 AAATGGA-ATTTT-TGGAAGTTTGAGGGTAA
** *
16788 AAA-CAAATTTTTTGGAAGTTCGAGGGTAA
1 AAATGGAA-TTTTTGGAAGTTTGAGGGTAA
* * *
16817 AAAAGGAATTTTTAGAAGTTTCGAGGTTAA
1 AAATGGAATTTTTGGAAGTTT-GAGGGTAA
*
16847 AAAT-GAGATTTTTGGAAGTTCGAGGGTAA
1 AAATGGA-ATTTTTGGAAGTTTGAGGGTAA
* * **
16876 AAACGAAATTTTTAAAAGTTTTGA-GGTCAA
1 AAATGGAATTTTTGGAAG-TTTGAGGGT-AA
* *
16906 AAATGGGATTTTTTGAAGTTTGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* *
16935 AAATGGAATTTTTAGAAGTTTTAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* *
16964 AAAT-GAGATTTTTGTATGTTTG-GGGTCAA
1 AAATGGA-ATTTTTGGAAGTTTGAGGGT-AA
* *
16993 AAATGGGATTTTTAGAAGTTTTG-GGGTCAA
1 AAATGGAATTTTTGGAAG-TTTGAGGGT-AA
* * *
17023 AAATGGGATTGTTGGAAGTTTGGGGGT-A
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* * * *
17051 AAATGAAATTTTTAGAAGTTTTAGGGTCA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* *
17080 AAATGGGATTTTTGTAAGTTTG-GGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* * * *
17108 AAATGAAATTATTAGAAGTTT-AGGGGTCA
1 AAATGGAATTTTTGGAAGTTTGA-GGGTAA
* * * *
17137 AAATGGGATCTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
*
17166 AAATGGAATTCTTGGATAGTTT-AGGG
1 AAATGGAATTTTTGGA-AGTTTGAGGG
17192 ACCTTCAGGG
Statistics
Matches: 376, Mismatches: 65, Indels: 46
0.77 0.13 0.09
Matches are distributed among these distances:
28 51 0.14
29 191 0.51
30 127 0.34
31 7 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTGAGGGTAA
Found at i:25240 original size:59 final size:58
Alignment explanation
Indices: 25088--25484 Score: 158
Period size: 59 Copynumber: 6.8 Consensus size: 58
25078 GCACGGGGGC
* * * * *
25088 AAAATGGTAATTTTAGGAAAATTTGGGGTTAAAAATAGAATTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTTGG-AAGTTTGGGGTCAAAAATAGAATTTTTAGACATCCGAGGGT
* ** * * * *
25147 AAAAAGGTAA-TTTT-GAGAGTTTTGAAGTCGAAAATAGAGTTTTTTGACATCCTAGGGT
1 AAAATGGTAATTTTTGGA-AG-TTTGGGGTCAAAAATAGAATTTTTAGACATCCGAGGGT
* * * **
25205 CAAATGGTAATTTTTGGAAGTTTAGGGGTCAAAAATGGAATTTTTGGA-AGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAGTTT-GGGGTCAAAAATAGAATTTTTAGACA-TCCGAGGGT
* * *
25264 AAAAAT-G-AGATTTTGTGGAAGTTTGAGGGT-AAAAACA-AATTTTTTGGA-AGTTCGAGGGT
1 -AAAATGGTA-ATTTT-TGGAAGTTTG-GGGTCAAAAATAGAA-TTTTTAGACA-TCCGAGGGT
* * * * * *
25323 AAAAAAGG-AATTTTTAGAAGTTTCGAGGTTAAAAAT-GAGATTTTTGGA-AGTTCGAGGGT
1 -AAAATGGTAATTTTTGGAAGTTT-GGGGTCAAAAATAGA-ATTTTTAGACA-TCCGAGGGT
** * ** * * * * **
25382 AAAAACGAAATTTTTAAAAGTTTTGAGGTCAAAAATGGGATTTTTTGA-AGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAG-TTTGGGGTCAAAAATAGAATTTTTAGACA-TCCGAGGGT
* *
25441 AAAAATGG-AATTTTTAGAAGTTTTAGGGT-AAAAAT-GAGATTTTT
1 -AAAATGGTAATTTTTGGAAG-TTTGGGGTCAAAAATAGA-ATTTTT
25485 GTATGTTTGG
Statistics
Matches: 274, Mismatches: 43, Indels: 43
0.76 0.12 0.12
Matches are distributed among these distances:
56 1 0.00
57 3 0.01
58 76 0.28
59 163 0.59
60 31 0.11
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAGTTTGGGGTCAAAAATAGAATTTTTAGACATCCGAGGGT
Found at i:25268 original size:29 final size:29
Alignment explanation
Indices: 25206--25699 Score: 427
Period size: 29 Copynumber: 16.9 Consensus size: 29
25196 TCCTAGGGTC
25206 AAATGGTAATTTTTGGAAGTTT-AGGGGTCAA
1 AAATGG-AATTTTTGGAAGTTTGA-GGGT-AA
25237 AAATGGAATTTTTGGAAGTTTGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
25266 AAAT-GAGATTTTGTGGAAGTTTGAGGGTAA
1 AAATGGA-ATTTT-TGGAAGTTTGAGGGTAA
** *
25296 AAA-CAAATTTTTTGGAAGTTCGAGGGTAA
1 AAATGGAA-TTTTTGGAAGTTTGAGGGTAA
* * *
25325 AAAAGGAATTTTTAGAAGTTTCGAGGTTAA
1 AAATGGAATTTTTGGAAGTTT-GAGGGTAA
*
25355 AAAT-GAGATTTTTGGAAGTTCGAGGGTAA
1 AAATGGA-ATTTTTGGAAGTTTGAGGGTAA
* * **
25384 AAACGAAATTTTTAAAAGTTTTGA-GGTCAA
1 AAATGGAATTTTTGGAAG-TTTGAGGGT-AA
* *
25414 AAATGGGATTTTTTGAAGTTTGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* *
25443 AAATGGAATTTTTAGAAGTTTTAGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* *
25472 AAAT-GAGATTTTTGTATGTTTG-GGGTCAA
1 AAATGGA-ATTTTTGGAAGTTTGAGGGT-AA
* *
25501 AAATGGGATTTTTAGAAGTTTTG-GGGTCAA
1 AAATGGAATTTTTGGAAG-TTTGAGGGT-AA
* * *
25531 AAATGGGATTGTTGGAAGTTTGGGGGT-A
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* * * *
25559 AAATGAAATTTTTAGAAGTTTTAGGGTCA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* *
25588 AAATGGGATTTTTGTAAGTTTG-GGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
* * * *
25616 AAATGAAATTATTAGAAGTTT-AGGGGTCA
1 AAATGGAATTTTTGGAAGTTTGA-GGGTAA
* * * *
25645 AAATGGGATCTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTAA
*
25674 AAATGGAATTCTTGGATAGTTT-AGGG
1 AAATGGAATTTTTGGA-AGTTTGAGGG
25700 ACCTTCAGGG
Statistics
Matches: 376, Mismatches: 65, Indels: 46
0.77 0.13 0.09
Matches are distributed among these distances:
28 51 0.14
29 191 0.51
30 127 0.34
31 7 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTGAGGGTAA
Found at i:26690 original size:15 final size:16
Alignment explanation
Indices: 26665--26697 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
26655 CTTTTTTATT
26665 TATTAATTATTAATAA
1 TATTAATTATTAATAA
*
26681 TATT-ATTATTATTAA
1 TATTAATTATTAATAA
26696 TA
1 TA
26698 AAACATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTATTAATAA
Found at i:26693 original size:18 final size:18
Alignment explanation
Indices: 26664--26748 Score: 63
Period size: 18 Copynumber: 4.8 Consensus size: 18
26654 CCTTTTTTAT
26664 TTATTAATTATTAATAATA
1 TTATT-ATTATTAATAATA
26683 TTATTATTATTAATAA-A
1 TTATTATTATTAATAATA
** **
26700 ACATTTATTATTAATGCCT-
1 TTA-TTATTATTAAT-AATA
*
26719 TTATTAATATTAATAATA
1 TTATTATTATTAATAATA
26737 --ATT-TTATTAATA
1 TTATTATTATTAATA
26749 CCTATTAATG
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 8 0.15
16 3 0.06
17 3 0.06
18 32 0.62
19 6 0.12
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.52
Consensus pattern (18 bp):
TTATTATTATTAATAATA
Found at i:26729 original size:21 final size:21
Alignment explanation
Indices: 26705--26760 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
26695 ATAAAACATT
26705 TATTATTAATGCCTTTATTAA
1 TATTATTAATGCCTTTATTAA
* ***
26726 TATTAATAATAATTTTATTAA
1 TATTATTAATGCCTTTATTAA
*
26747 TACCTATTAATGCC
1 TA-TTATTAATGCC
26761 AATATTTATT
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.48
Consensus pattern (21 bp):
TATTATTAATGCCTTTATTAA
Found at i:27523 original size:17 final size:16
Alignment explanation
Indices: 27489--27542 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
27479 TGGACTTTTT
27489 TTTTAAATTAATTAAA
1 TTTTAAATTAATTAAA
27505 TTTTAAATTCAAATT-AA
1 TTTTAAATT--AATTAAA
27522 TTTTAAACTTAATTTAAA
1 TTTTAAA-TTAA-TTAAA
27540 TTT
1 TTT
27543 AAACTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.33
17 11 0.33
18 11 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAATTAATTAAA
Found at i:27543 original size:6 final size:6
Alignment explanation
Indices: 27500--27582 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
27490 TTTAAATTAA
* * * *
27500 TTAAATT TTAAAT TCAAA- TTAATT TTAAAC TT-AAT TTAAAT TTAAAC
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* **
27547 TTAAAA GAAAAGT TTAAACT TTAAA- TTAAAT TTAAA
1 TTAAAT TTAAA-T TTAAA-T TTAAAT TTAAAT TTAAA
27583 CCCAAAATGG
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
5 12 0.21
6 32 0.55
7 14 0.24
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:27582 original size:18 final size:18
Alignment explanation
Indices: 27498--27583 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 18
27488 TTTTTAAATT
*
27498 AATTAAATTTTAAA-TTCA
1 AATTAAA-TTTAAACTTTA
*
27516 AATTAATTTTAAAC-TTA
1 AATTAAATTTAAACTTTA
* *
27533 ATTTAAATTTAAACTTAA
1 AATTAAATTTAAACTTTA
**
27551 AAGAAAAGTTTAAACTTTA
1 AATTAAA-TTTAAACTTTA
27570 AATTAAATTTAAAC
1 AATTAAATTTAAAC
27584 CCAAAATGGA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
17 20 0.37
18 19 0.35
19 15 0.28
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (18 bp):
AATTAAATTTAAACTTTA
Found at i:28999 original size:29 final size:29
Alignment explanation
Indices: 28967--29236 Score: 256
Period size: 30 Copynumber: 9.2 Consensus size: 29
28957 AAAAATTTTG
* *
28967 TTTTTACCCCCGAACTTCCAAAAATCCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
* *
28996 TTTTTTACCCCTAAACTTCCCAAAATTCCA
1 -TTTTTACCCCCAAACTTCCAAAAATTCCA
* * * *
29026 TTCTTGACCTCGAAACTTCAAAAAATTCCA
1 TT-TTTACCCCCAAACTTCCAAAAATTCCA
* *
29056 TTTTTACCCCTAAACTTCCCAAAATTCCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
*
29085 TTTTTAACCCCAAAACTTCCAAAAATTCCA
1 TTTTT-ACCCCCAAACTTCCAAAAATTCCA
* * * * *
29115 TTCTTACACCCGAACTTCCCAAAATTTCA
1 TTTTTACCCCCAAACTTCCAAAAATTCCA
** *
29144 TTTTTGACCCTAAAATTTCCAAAAATTCCA
1 TTTTT-ACCCCCAAACTTCCAAAAATTCCA
**
29174 TTTTTACCCTAAAACTTCCAAAAATTACCA
1 TTTTTACCCCCAAACTTCCAAAAATT-CCA
* * *
29204 -TTTTGCCCCCGAA-TATCCAAAAATTCAA
1 TTTTTACCCCCAAACT-TCCAAAAATTCCA
29232 TTTTT
1 TTTTT
29237 GATCCCGAAA
Statistics
Matches: 198, Mismatches: 36, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.02
29 95 0.48
30 100 0.51
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
TTTTTACCCCCAAACTTCCAAAAATTCCA
Found at i:29101 original size:89 final size:87
Alignment explanation
Indices: 28967--29236 Score: 296
Period size: 89 Copynumber: 3.1 Consensus size: 87
28957 AAAAATTTTG
** * * *
28967 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCTAAACTTCCCAAAATTCCATTCTTG
1 TTTTTACCCCTAAACTTCCAAAAATTCCA-TTTTTACCCCAAAACTTCCAAAAATTCCATTCTT-
*
29032 AC-CTCGAAACTTCAAAAAATTCCA
64 ACACCCG-AACTTCAAAAAATTCCA
*
29056 TTTTTACCCCTAAACTTCCCAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTCTTA
1 TTTTTACCCCTAAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATTCCATTCTTA
** *
29121 CACCCGAACTTCCCAAAATTTCA
65 CACCCGAACTTCAAAAAATTCCA
* *
29144 TTTTTGA-CCCTAAAATTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTACCATT-T
1 TTTTT-ACCCCT-AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATT-CCATTCT
* * * *
29207 TGCCCCCGAA-TATCCAAAAATTCAA
63 TACACCCGAACT-TCAAAAAATTCCA
29232 TTTTT
1 TTTTT
29237 GATCCCGAAA
Statistics
Matches: 157, Mismatches: 18, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
87 1 0.01
88 74 0.47
89 82 0.52
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (87 bp):
TTTTTACCCCTAAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTCTTAC
ACCCGAACTTCAAAAAATTCCA
Found at i:29208 original size:59 final size:59
Alignment explanation
Indices: 28979--29236 Score: 301
Period size: 59 Copynumber: 4.4 Consensus size: 59
28969 TTTACCCCCG
* * * *
28979 AACTTCCAAAAATCCCATTTTTTACCCCTAAACTTCCCAAAATTCCATTCTTGACCTCGA
1 AACTTCCAAAAATTCCA-TTTTTACCCCTAAACTTCCCAAAATTCCATTTTTGACCCCAA
* *
29039 AACTTCAAAAAATTCCATTTTTACCCCTAAACTTCCCAAAATTCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCCAAAATTCCATTTTTGACCCCAA
* * * *
29098 AACTTCCAAAAATTCCATTCTTACACCC-GAACTTCCCAAAATTTCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTTAC-CCCTAAACTTCCCAAAATTCCATTTTTGACCCCAA
* * **
29157 AATTTCCAAAAATTCCATTTTTA-CCCTAAAACTTCCAAAAATTACCA-TTTTG-CCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCCAAAATT-CCATTTTTGACCCCAA
*
29215 AA-TATCCAAAAATTCAATTTTT
1 AACT-TCCAAAAATTCCATTTTT
29237 GATCCCGAAA
Statistics
Matches: 172, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
57 4 0.02
58 22 0.13
59 126 0.73
60 20 0.12
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCCAAAATTCCATTTTTGACCCCAA
Found at i:29275 original size:58 final size:58
Alignment explanation
Indices: 28968--29295 Score: 160
Period size: 59 Copynumber: 5.6 Consensus size: 58
28958 AAAATTTTGT
* * *
28968 TTTTACCCCCGAACT-TCCAAAAATCCCATTTTTTACCCCT-AAACTTCCCAAAA-TTCCA
1 TTTTACCCCCGAA-TATCCAAAAATTCCA-TTTTTA-CCCTAAAACTTCCAAAAACTACCA
* * * *
29026 TTCTTGA-CCTCGAA-ACTTCAAAAAATTCCATTTTTACCCCT-AAACTTCCCAAAA-TTCCA
1 TT-TT-ACCCCCGAATA--TCCAAAAATTCCATTTTTA-CCCTAAAACTTCCAAAAACTACCA
* * * ** * **
29085 TTTTTAACCCC-AAAACTTCCAAAAATTCCATTCTTACACC-CGAACTTCCCAAAA-TTTCA
1 -TTTTACCCCCGAATA--TCCAAAAATTCCATTTTTAC-CCTAAAACTTCCAAAAACTACCA
*** * *
29144 TTTTTGACCCTAAAATTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTACCA
1 -TTTT-ACCCCCGAATATCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAACTACCA
* * * *
29204 TTTTGCCCCCGAATATCCAAAAATTCAATTTTTGATCCC-GAAAC-TCTC-AAAACTACCC
1 TTTTACCCCCGAATATCCAAAAATTCCATTTTT-A-CCCTAAAACTTC-CAAAAACTACCA
* * * *
29262 TTTTACCCTCGAATGTCTAAAAAGTCCATTTTTA
1 TTTTACCCCCGAATATCCAAAAATTCCATTTTTA
29296 ACTCCAAATT
Statistics
Matches: 219, Mismatches: 34, Indels: 35
0.76 0.12 0.12
Matches are distributed among these distances:
57 1 0.00
58 68 0.31
59 125 0.57
60 23 0.11
61 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (58 bp):
TTTTACCCCCGAATATCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAACTACCA
Found at i:32034 original size:21 final size:21
Alignment explanation
Indices: 32009--32055 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
31999 TAAATCATTA
*
32009 TAATATAA-ACAGATTAAGAAT
1 TAATATAATACAAATT-AGAAT
*
32030 TAATATAATTCAAATTAGAAT
1 TAATATAATACAAATTAGAAT
32051 TAATA
1 TAATA
32056 AATTAGACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (21 bp):
TAATATAATACAAATTAGAAT
Found at i:36571 original size:29 final size:30
Alignment explanation
Indices: 36529--36586 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
36519 TATAGTTTAA
*
36529 TGTGTAATTGTATACATGAA-CTTTGATTG
1 TGTGCAATTGTATACATGAATCTTTGATTG
* *
36558 TGTGCAATTTTATACATGAATTTTTGATT
1 TGTGCAATTGTATACATGAATCTTTGATT
36587 TGATCCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAATCTTTGATTG
Found at i:36596 original size:30 final size:29
Alignment explanation
Indices: 36534--36596 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
36524 TTTAATGTGT
*
36534 AATTGTATACATGAACTTTGATTGTGTGC
1 AATTGTATACATGAACTTTGATTGTGTCC
* *
36563 AATTTTATACATGAATTTTTGATT-TGATCC
1 AATTGTATACATGAA-CTTTGATTGTG-TCC
36593 AATT
1 AATT
36597 CTTGTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (29 bp):
AATTGTATACATGAACTTTGATTGTGTCC
Found at i:39089 original size:16 final size:16
Alignment explanation
Indices: 39064--39094 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39054 TAAAAAAATC
*
39064 AAATACAGTGGAAAAA
1 AAATAAAGTGGAAAAA
39080 AAATAAAGTGGAAAA
1 AAATAAAGTGGAAAA
39095 CGCCGAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.19, T:0.13
Consensus pattern (16 bp):
AAATAAAGTGGAAAAA
Found at i:41268 original size:7 final size:7
Alignment explanation
Indices: 41254--41298 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
41244 GTCGCCACTG
41254 AAGTGTC
1 AAGTGTC
*
41261 AGGTGTC
1 AAGTGTC
41268 AAGTGTC
1 AAGTGTC
41275 AAGTGTC
1 AAGTGTC
41282 AAGTGTC
1 AAGTGTC
41289 AAGTGTC
1 AAGTGTC
41296 AAG
1 AAG
41299 CCAACAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (7 bp):
AAGTGTC
Found at i:42099 original size:18 final size:18
Alignment explanation
Indices: 42076--42118 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42066 GAATATGTTT
42076 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
42094 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
42112 TTAATTA
1 TTAATTA
42119 CATCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:42648 original size:18 final size:17
Alignment explanation
Indices: 42606--42645 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
42596 TCGTAAAAAT
42606 ATAATTTTATATTTTTA
1 ATAATTTTATATTTTTA
42623 ATAA-TTTATATTTTT-
1 ATAATTTTATATTTTTA
42638 ATAATTTT
1 ATAATTTT
42646 TTAAAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATAATTTTATATTTTTA
Found at i:49714 original size:29 final size:29
Alignment explanation
Indices: 49672--49730 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
49662 ACAGGAGATG
49672 ATCGACCTCAATGAATTCAAAGACGACTT
1 ATCGACCTCAATGAATTCAAAGACGACTT
* *
49701 ATCGACCTCAATGAATTCGAAGGCGACTT
1 ATCGACCTCAATGAATTCAAAGACGACTT
49730 A
1 A
49731 CATGGATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (29 bp):
ATCGACCTCAATGAATTCAAAGACGACTT
Found at i:54983 original size:16 final size:16
Alignment explanation
Indices: 54962--55026 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
54952 AATCTATTCA
54962 AAAAAATATATAAAAT
1 AAAAAATATATAAAAT
**
54978 AAAAAATATAT-ATGT
1 AAAAAATATATAAAAT
* *
54993 AAAAACT-TTTAAAATT
1 AAAAAATATATAAAA-T
55009 AAAAAA-A-ATAAAAT
1 AAAAAATATATAAAAT
55023 AAAA
1 AAAA
55027 CCTCAAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
14 7 0.18
15 14 0.37
16 17 0.45
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAAAATATATAAAAT
Found at i:57514 original size:4 final size:4
Alignment explanation
Indices: 57483--57509 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
57473 TGCATGCATG
57483 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
57510 GCATGGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:60413 original size:39 final size:39
Alignment explanation
Indices: 60370--60445 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
60360 CTAACAAATA
* *
60370 TAATAT-TATAAATAGATTAAATTTTCAT-AATAAATAAGT
1 TAATATAT-TAAATAAAGTAAATTTT-ATAAATAAATAAGT
*
60409 TAATATATTAATTAAAGTAAATTTTATAAATAAATAA
1 TAATATATTAAATAAAGTAAATTTTATAAATAAATAA
60446 AATTTAATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.06
39 29 0.91
40 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (39 bp):
TAATATATTAAATAAAGTAAATTTTATAAATAAATAAGT
Found at i:63911 original size:28 final size:26
Alignment explanation
Indices: 63872--63977 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
63862 ACATTACATT
63872 TTTTATAATTTTTTTACGATTTTATAAAA
1 TTTTAT-ATTTTTTTAC-ATTTTAT-AAA
* *
63901 TTTTATATTTTTTTACATTTCTGTATA
1 TTTTATATTTTTTTACATTT-TATAAA
* *
63928 TTTTATAATTTTTTACTATTTTTATGGAA
1 TTTTATATTTTTTTAC-A-TTTTAT-AAA
* * *
63957 TTTTACAATTTTTTATATTTT
1 TTTTATATTTTTTTACATTTT
63978 TATTAAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
27 25 0.38
28 16 0.25
29 24 0.37
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (26 bp):
TTTTATATTTTTTTACATTTTATAAA
Found at i:63912 original size:37 final size:38
Alignment explanation
Indices: 63871--63952 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 38
63861 TACATTACAT
* *
63871 TTTTTATA-ATTTTTTTACGATTTTATAAAATTTTA-TA
1 TTTTTATACATTTCTGTA-GATTTTATAAAATTTTACTA
* * **
63908 TTTTTTTACATTTCTGTATATTTTATAATTTTTTACTA
1 TTTTTATACATTTCTGTAGATTTTATAAAATTTTACTA
63946 TTTTTAT
1 TTTTTAT
63953 GGAATTTTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (38 bp):
TTTTTATACATTTCTGTAGATTTTATAAAATTTTACTA
Found at i:63987 original size:29 final size:29
Alignment explanation
Indices: 63872--63987 Score: 96
Period size: 29 Copynumber: 4.1 Consensus size: 29
63862 ACATTACATT
* *
63872 TTTTATAATTTTTTTACGA-TTTTATAAAA
1 TTTTACAA-TTTTTTACTATTTTTATAAAA
* * * * *
63901 TTTTATATTTTTTTAC-ATTTCTGT-ATA
1 TTTTACAATTTTTTACTATTTTTATAAAA
* **
63928 TTTTATAATTTTTTACTATTTTTATGGAA
1 TTTTACAATTTTTTACTATTTTTATAAAA
63957 TTTTACAATTTTTTA-TATTTTTATTAAAA
1 TTTTACAATTTTTTACTATTTTTA-TAAAA
63986 TT
1 TT
63988 CAATCATTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
27 18 0.25
28 26 0.37
29 27 0.38
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.63
Consensus pattern (29 bp):
TTTTACAATTTTTTACTATTTTTATAAAA
Found at i:72043 original size:18 final size:18
Alignment explanation
Indices: 72006--72040 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
71996 CAAGATGATT
*
72006 TTTTTAAATTATATAAAA
1 TTTTAAAATTATATAAAA
72024 TTTTAAAATTAT-TAAAA
1 TTTTAAAATTATATAAAA
72041 ATTAATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTAAAATTATATAAAA
Found at i:76059 original size:6 final size:6
Alignment explanation
Indices: 76036--76130 Score: 58
Period size: 6 Copynumber: 16.5 Consensus size: 6
76026 ATTTGTTTAA
* * * *
76036 AAATAT AAATTT -ATTTT AAATTT AAATTT -ATTTT GAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * *
76082 -GATTT AAGTTT AAATTT -ATTTT CAAATTT AAAATT --ATTAT AAATTT
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATT-T AAATTT
76128 AAA
1 AAA
76131 ATAAGTAAAG
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
4 2 0.03
5 17 0.25
6 41 0.61
7 7 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:76132 original size:17 final size:17
Alignment explanation
Indices: 76003--76130 Score: 132
Period size: 17 Copynumber: 7.4 Consensus size: 17
75993 CCAAACTCAC
*
76003 TTTAAGTTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
76021 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
*
76039 TATAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
76056 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
*
76073 TTTAAATTTGA-TTTAAG
1 TTTAAATTT-ATTTTAAA
76090 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
76108 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
76125 TTTAAA
1 TTTAAA
76131 ATAAGTAAAG
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
16 1 0.01
17 52 0.57
18 38 0.42
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.