Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002528.1 Kokia drynarioides strain JFW-HI SEQ_114697, 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: 23556
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Found at i:23 original size:3 final size:3
Alignment explanation
Indices: 15--101 Score: 120
Period size: 3 Copynumber: 28.0 Consensus size: 3
5 AATAACGTTT
* * *
15 TAA TAA TAA TGAA TGA CAT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TGAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA
102 AAAAGTCGAA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
3 66 0.88
4 9 0.12
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1227 original size:30 final size:29
Alignment explanation
Indices: 1193--1255 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1183 AAACTATCCA
*
1193 AAAATCATATTTTCACCCCTAAAATTTTTC
1 AAAATCATATTTTCA-CCCTAAAACTTTTC
* * *
1223 AAAATTATATTTTGACCCTTAAACTTTTC
1 AAAATCATATTTTCACCCTAAAACTTTTC
1252 AAAA
1 AAAA
1256 ATTACATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATCATATTTTCACCCTAAAACTTTTC
Found at i:1257 original size:30 final size:30
Alignment explanation
Indices: 1191--1345 Score: 134
Period size: 30 Copynumber: 5.1 Consensus size: 30
1181 CTAAACTATC
* * * *
1191 CAAAAATCATATTTTCACCCCTAAAATTTTT
1 CAAAAATTATATTTTGA-CCCTCAAACTTTT
*
1222 C-AAAATTATATTTTGACCCTTAAACTTTT
1 CAAAAATTATATTTTGACCCTCAAACTTTT
* *
1251 CAAAAATTACATTTTTGACCCTCAAACTTCT
1 CAAAAATTATA-TTTTGACCCTCAAACTTTT
* * *
1282 CTAATATTATATTTTTAACCC-CAAACTTTT
1 CAAAAATTATA-TTTTGACCCTCAAACTTTT
* * * * *
1312 TAGAAATTACATTTTTACACTCAAACTTTT
1 CAAAAATTATATTTTGACCCTCAAACTTTT
1342 CAAA
1 CAAA
1346 TTTCTATTTT
Statistics
Matches: 100, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
29 19 0.19
30 46 0.46
31 35 0.35
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.41
Consensus pattern (30 bp):
CAAAAATTATATTTTGACCCTCAAACTTTT
Found at i:1270 original size:31 final size:31
Alignment explanation
Indices: 1209--1481 Score: 152
Period size: 30 Copynumber: 9.2 Consensus size: 31
1199 ATATTTTCAC
* * *
1209 CCCTAAAATTTTTC-AAAATTATA-TTTTGA
1 CCCTCAAACTTTTCAAAAATTACATTTTTGA
*
1238 CCCTTAAACTTTTCAAAAATTACATTTTTGA
1 CCCTCAAACTTTTCAAAAATTACATTTTTGA
* * * * *
1269 CCCTCAAACTTCTCTAATATTATATTTTTAA
1 CCCTCAAACTTTTCAAAAATTACATTTTTGA
* *
1300 CCC-CAAACTTTTTAGAAATTACATTTTT-A
1 CCCTCAAACTTTTCAAAAATTACATTTTTGA
* *
1329 CACTCAAACTTTTC--AAATTTCTATTTTTGA
1 CCCTCAAACTTTTCAAAAATTAC-ATTTTTGA
* *
1359 -CATC-GA-TTTTCCAAAAATTACCA-TTTT-A
1 CCCTCAAACTTTT-CAAAAATTA-CATTTTTGA
* ***
1387 CCCTCGAACTTAAAAAAAATTACATTTTT-A
1 CCCTCAAACTTTTCAAAAATTACATTTTTGA
*
1417 CCCT--AA-TTTTCCAAAAATTGCCA-TTTT-A
1 CCCTCAAACTTTT-CAAAAATT-ACATTTTTGA
* * *
1445 CCCTCGAACTTCT-AAAAATTTCATTTTTTGA
1 CCCTCAAACTTTTCAAAAATTACA-TTTTTGA
1476 -CCTCAA
1 CCCTCAA
1482 TGTTTTTGAA
Statistics
Matches: 189, Mismatches: 34, Indels: 41
0.72 0.13 0.16
Matches are distributed among these distances:
27 6 0.03
28 29 0.15
29 41 0.22
30 72 0.38
31 41 0.22
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (31 bp):
CCCTCAAACTTTTCAAAAATTACATTTTTGA
Found at i:1308 original size:61 final size:61
Alignment explanation
Indices: 1221--1356 Score: 163
Period size: 61 Copynumber: 2.3 Consensus size: 61
1211 CTAAAATTTT
* * *
1221 TCAAA-ATTATA-TTTTGACCCTTAAACTTTTCAAAAATTACATTTTTGACCCTCAAACTTC
1 TCAAATATTATATTTTTAACCCTCAAACTTTTCAAAAATTACATTTTT-ACACTCAAACTTC
* * * *
1281 TCTAATATTATATTTTTAACCC-CAAACTTTTTAGAAATTACATTTTTACACTCAAACTTT
1 TCAAATATTATATTTTTAACCCTCAAACTTTTCAAAAATTACATTTTTACACTCAAACTTC
*
1341 TCAAAT-TTCTATTTTT
1 TCAAATATTATATTTTT
1357 GACATCGATT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
59 9 0.14
60 20 0.31
61 28 0.43
62 8 0.12
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (61 bp):
TCAAATATTATATTTTTAACCCTCAAACTTTTCAAAAATTACATTTTTACACTCAAACTTC
Found at i:1503 original size:60 final size:58
Alignment explanation
Indices: 1247--1686 Score: 240
Period size: 58 Copynumber: 7.5 Consensus size: 58
1237 ACCCTTAAAC
*** *
1247 TTTT-CAAAAATTA-CATTTTTGACCCTCAAACTTCTCTAATATT-ATATTTTTAACCCCAAA
1 TTTTCCAAAAATTACCA-TTTT-ACCCTCAAACTTCAAAAAT-TTCAT-TTTTTAACCTC-AA
* * * *** * * *
1307 CTTTT-TAGAAATTA-CATTTTTACACTCAAACTTTTCAAATTTC-TATTTTTGACATCGA
1 -TTTTCCAAAAATTACCA-TTTTACCCTCAAACTTCAAAAATTTCAT-TTTTTAACCTCAA
* * * *
1365 TTTTCCAAAAATTACCATTTTACCCTCGAACTTAAAAAAAATTACA-TTTTTACCCT-AA
1 TTTTCCAAAAATTACCATTTTACCCTCAAACTT--CAAAAATTTCATTTTTTAACCTCAA
* * *
1423 TTTTCCAAAAATTGCCATTTTACCCTCGAACTTCTAAAAATTTCATTTTTTGACCTCAA
1 TTTTCCAAAAATTACCATTTTACCCTCAAACTTC-AAAAATTTCATTTTTTAACCTCAA
*** * * * * *
1482 TGTTTTTGAAAATTACCATTTTGCCC-CTAAACATTCCAAAA-TTCAATTTTTAACCCCGA
1 T-TTTCCAAAAATTACCATTTTACCCTC-AAAC-TTCAAAAATTTCATTTTTTAACCTCAA
* * * *
1541 TTCTTCCCAAAATTACCATTTTACCCCCAAACTTCCAAAAATTTCATTTTTTAATCTCGAT
1 TT-TTCCAAAAATTACCATTTTACCCTCAAACTT-CAAAAATTTCATTTTTTAACCTC-AA
* * * ** * *
1602 TTTTTCAAAAATTACAATTTTACCCCCGGA-TGTCTAAAA-TTC-TGTTTGTAACCTCAAA
1 TTTTCCAAAAATTACCATTTTACCCTCAAACT-TCAAAAATTTCAT-TTTTTAACCTC-AA
* *
1660 TTTTCCCAAAATTACCATTTCACCCTC
1 TTTTCCAAAAATTACCATTTTACCCTC
1687 GAGTGTCCAA
Statistics
Matches: 298, Mismatches: 62, Indels: 41
0.74 0.15 0.10
Matches are distributed among these distances:
57 14 0.05
58 101 0.34
59 74 0.25
60 86 0.29
61 23 0.08
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (58 bp):
TTTTCCAAAAATTACCATTTTACCCTCAAACTTCAAAAATTTCATTTTTTAACCTCAA
Found at i:1562 original size:59 final size:60
Alignment explanation
Indices: 1343--1628 Score: 217
Period size: 60 Copynumber: 4.8 Consensus size: 60
1333 CAAACTTTTC
* * ** * * **
1343 AAATTTCTATTTTTGACATCGATT-TTCCAAAAATTACCATTTTACCCTCGAACTTAAAA
1 AAATTTCAATTTTTAACCCCGATTCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAA
* ** * * * *
1402 AAAATT-ACATTTTT-ACCCTAATT-TTCCAAAAATTGCCATTTTACCCTCGAACTTCTAA
1 AAATTTCA-ATTTTTAACCCCGATTCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAA
* * * * *** * *
1460 AAATTTCATTTTTTGACCTCAATGT-TTTTGAAAATTACCATTTTGCCCCTAAACATTCC-A
1 AAATTTCAATTTTTAACCCCGAT-TCTTCCAAAAATTACCATTTTACCCCCAAAC-TTCCAA
*
1520 AAA-TTCAATTTTTAACCCCGATTCTTCCCAAAATTACCATTTTACCCCCAAACTTCCAA
1 AAATTTCAATTTTTAACCCCGATTCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAA
* * * * * *
1579 AAATTTCATTTTTTAATCTCGATTTTTTCAAAAATTACAATTTTACCCCC
1 AAATTTCAATTTTTAACCCCGATTCTTCCAAAAATTACCATTTTACCCCC
1629 GGATGTCTAA
Statistics
Matches: 181, Mismatches: 38, Indels: 15
0.77 0.16 0.06
Matches are distributed among these distances:
58 52 0.29
59 61 0.34
60 65 0.36
61 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (60 bp):
AAATTTCAATTTTTAACCCCGATTCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAA
Found at i:1581 original size:29 final size:29
Alignment explanation
Indices: 1367--1583 Score: 86
Period size: 29 Copynumber: 7.4 Consensus size: 29
1357 GACATCGATT
* *
1367 TTCCAAAAATTACCATTTTACCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCCCAAAC
** * **
1396 TTAAAAAAAATTA-CATTTTTA-CCCTAATT
1 TT-CCAAAAATTACCA-TTTTACCCCCAAAC
* * *
1425 TTCCAAAAATTGCCATTTTACCCTCGAAC
1 TTCCAAAAATTACCATTTTACCCCCAAAC
* * * **
1454 TTCTAAAAATT-TCATTTTTTGA-CCTCAATGT
1 TTCCAAAAATTACCA--TTTT-ACCCCCAA-AC
*** * *
1485 TTTTGAAAATTACCATTTTGCCCCTAAAC
1 TTCCAAAAATTACCATTTTACCCCCAAAC
* * **
1514 ATTCC-AAAATT-CAATTTTTAACCCCGATTC
1 -TTCCAAAAATTACCA-TTTT-ACCCCCAAAC
*
1544 TTCCCAAAATTACCATTTTACCCCCAAAC
1 TTCCAAAAATTACCATTTTACCCCCAAAC
1573 TTCCAAAAATT
1 TTCCAAAAATT
1584 TCATTTTTTA
Statistics
Matches: 133, Mismatches: 40, Indels: 30
0.66 0.20 0.15
Matches are distributed among these distances:
28 16 0.12
29 55 0.41
30 48 0.36
31 12 0.09
32 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCCCAAAC
Found at i:1698 original size:28 final size:28
Alignment explanation
Indices: 1665--1754 Score: 144
Period size: 28 Copynumber: 3.2 Consensus size: 28
1655 TCAAATTTTC
*
1665 CCAAAATTACCATTTCACCCTCGAGTGT
1 CCAAAATTACCATTTTACCCTCGAGTGT
*
1693 CCAAAATTACAATTTTACCCTCGAGTGT
1 CCAAAATTACCATTTTACCCTCGAGTGT
* *
1721 CCAAAATTACCATTTTACTCTCGGGTGT
1 CCAAAATTACCATTTTACCCTCGAGTGT
1749 CCAAAA
1 CCAAAA
1755 ATCACATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTCGAGTGT
Found at i:13447 original size:49 final size:49
Alignment explanation
Indices: 13318--13638 Score: 180
Period size: 49 Copynumber: 6.3 Consensus size: 49
13308 CAGCACCACG
* * *
13318 AGACATGAAGGGAAAGATCTAAGCCGCAATAGCGGATCTAGTACCACAATAA
1 AGACATGAAGGGAAAGATCTAAGCCGCAATGGCGAACCTAGTACCAC---AA
* * * * * * *
13370 AGACATAAAAGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAC
1 AGACATGAAGGGAAAGATCTAAGCCGCAATGGCGAACCTAGTACCACAA
* * * *
13419 AGACATGAAGGGAAAGATCTAAGCCGCAACGGTGGA-TTCAGTACCACAA
1 AGACATGAAGGGAAAGATCTAAGCCGCAATGGCGAACCT-AGTACCACAA
** * * * * * * ** *
13468 AGACACAAAAGGAAGGGTTTAAGTCGCAATGGCGAACCTTGTACCTTAG
1 AGACATGAAGGGAAAGATCTAAGCCGCAATGGCGAACCTAGTACCACAA
* * * * *
13517 AGGCATGAAGGGAAAGATCTAAGCCTCAATGGCGGATCC-AATACCGCAAGGATACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAATGGC-GAACCTAGTA-C-C------ACAA
* * *
13574 AGACATGAAGGGAAAGATTTAAGCCGCAATGGCAAATCC-AGTACCACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAATGGCGAA-CCTAGTACCACAA
* *
13623 AGGCACGAAGGGAAAG
1 AGACATGAAGGGAAAG
13639 GTTTAGTCGT
Statistics
Matches: 197, Mismatches: 60, Indels: 27
0.69 0.21 0.10
Matches are distributed among these distances:
48 1 0.01
49 113 0.57
50 6 0.03
51 1 0.01
52 38 0.19
55 1 0.01
56 2 0.01
57 35 0.18
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (49 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAATGGCGAACCTAGTACCACAA
Found at i:13506 original size:98 final size:99
Alignment explanation
Indices: 13318--13541 Score: 326
Period size: 98 Copynumber: 2.3 Consensus size: 99
13308 CAGCACCACG
* *
13318 AGACATGAAGGGAAAGATCTAAGCCGCAATAGCGGATCTAGTACCACAATAAAGACATAAAAGGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACAGCGGATCTAGTACCAC-A-AAAGACACAAAAGGA
13383 AAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAC
64 AAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAC
* *
13419 AGACATGAAGGGAAAGATCTAAGCCGCAACGGTGGAT-TCAGTACCAC-AAAGACACAAAAGGAA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACAGCGGATCT-AGTACCACAAAAGACACAAAAGGAA
* * * *
13482 GGGTTTAAGTCGCAATGGCGAACCTTGTACCTTAG
65 AGGTTTAAGTCGCAATGGCGAACCTAGTACCTCAC
*
13517 AGGCATGAAGGGAAAGATCTAAGCC
1 AGACATGAAGGGAAAGATCTAAGCC
13542 TCAATGGCGG
Statistics
Matches: 113, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
98 70 0.62
100 1 0.01
101 42 0.37
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (99 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAACAGCGGATCTAGTACCACAAAAGACACAAAAGGAAA
GGTTTAAGTCGCAATGGCGAACCTAGTACCTCAC
Found at i:13631 original size:57 final size:57
Alignment explanation
Indices: 13520--13632 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 57
13510 ACCTTAGAGG
* ** * *
13520 CATGAAGGGAAAGATCTAAGCCTCAATGGCGGATCCAATACCGCAAGGATACGAAGA
1 CATGAAGGGAAAGATCTAAGCCGCAATGGCAAATCCAATACCACAAGGACACGAAGA
* *
13577 CATGAAGGGAAAGATTTAAGCCGCAATGGCAAATCCAGTACCACGAAGG-CACGAAG
1 CATGAAGGGAAAGATCTAAGCCGCAATGGCAAATCCAATACCAC-AAGGACACGAAG
13633 GGAAAGGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 44 0.92
58 4 0.08
ACGTcount: A:0.39, C:0.21, G:0.27, T:0.13
Consensus pattern (57 bp):
CATGAAGGGAAAGATCTAAGCCGCAATGGCAAATCCAATACCACAAGGACACGAAGA
Found at i:14320 original size:17 final size:17
Alignment explanation
Indices: 14298--14372 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
14288 CAATCTTTAA
14298 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
14315 TTAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
* * * *
14332 TCAAATTTAATTCAAAC
1 TTAAATTTATTTTAAAT
*
14349 TAAAATTTATTTTAAAT
1 TTAAATTTATTTTAAAT
14366 TTAAATT
1 TTAAATT
14373 GAAGATTGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:14971 original size:3 final size:3
Alignment explanation
Indices: 14963--15043 Score: 108
Period size: 3 Copynumber: 26.0 Consensus size: 3
14953 AATAACGTTT
* * *
14963 TAA TAA TAA TGAA TGA CAT TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15009 TAA TAA TAA TAA TAA TAA TAA TAAA TGAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA
15044 AAAGTCGAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
3 60 0.87
4 9 0.13
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:15934 original size:30 final size:30
Alignment explanation
Indices: 15890--16010 Score: 147
Period size: 30 Copynumber: 4.0 Consensus size: 30
15880 CCTTAAACTG
* *
15890 TCCAGAAATCATATTTTGACCCATAAACTTT
1 TCCA-AAATTATATTTTAACCCATAAACTTT
15921 TCCAAAATTATATTTTAA-CCATTAAACTTT
1 TCCAAAATTATATTTTAACCCA-TAAACTTT
* * *
15951 TCCAAAATTACATTTTAACCCCTAAACTTC
1 TCCAAAATTATATTTTAACCCATAAACTTT
*
15981 TCTAAAATTATATTTTTAACCCA-AAACTTT
1 TCCAAAATTATA-TTTTAACCCATAAACTTT
16011 CATAAAATTA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.04
30 60 0.77
31 15 0.19
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (30 bp):
TCCAAAATTATATTTTAACCCATAAACTTT
Found at i:15977 original size:60 final size:60
Alignment explanation
Indices: 15902--16032 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
15892 CAGAAATCAT
* * *
15902 ATTTTGACCCATAAACTTTTCCAAAATTATA-TTTTAA-CCATTAAACTTTTC-CAAAATTAC
1 ATTTTAACCCCTAAACTTCTCCAAAATTATATTTTTAACCCA--AAAC-TTTCACAAAATTAC
* *
15962 ATTTTAACCCCTAAACTTCTCTAAAATTATATTTTTAACCCAAAACTTTCATAAAATTAC
1 ATTTTAACCCCTAAACTTCTCCAAAATTATATTTTTAACCCAAAACTTTCACAAAATTAC
*
16022 ATTTTTACCCC
1 ATTTTAACCCC
16033 CGAACATTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 4 0.06
60 49 0.79
61 6 0.10
62 3 0.05
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (60 bp):
ATTTTAACCCCTAAACTTCTCCAAAATTATATTTTTAACCCAAAACTTTCACAAAATTAC
Found at i:16017 original size:30 final size:28
Alignment explanation
Indices: 15902--16031 Score: 109
Period size: 30 Copynumber: 4.4 Consensus size: 28
15892 CAGAAATCAT
* * *
15902 ATTTTGACCCATAAACTTTTCCAAAATTAT
1 ATTTTAACCCA-AAAC-TTTCTAAAATTAC
*
15932 ATTTTAA-CCATTAAACTTTTCCAAAATTAC
1 ATTTTAACCCA--AAAC-TTTCTAAAATTAC
* *
15962 ATTTTAACCCCTAAACTTCTCTAAAATTAT
1 ATTTTAA-CCCAAAACTT-TCTAAAATTAC
15992 ATTTTTAACCCAAAACTTTCATAAAATTAC
1 A-TTTTAACCCAAAACTTTC-TAAAATTAC
*
16022 ATTTTTACCC
1 ATTTTAACCC
16032 CCGAACATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 13
0.80 0.07 0.12
Matches are distributed among these distances:
29 15 0.17
30 63 0.73
31 6 0.07
32 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.40
Consensus pattern (28 bp):
ATTTTAACCCAAAACTTTCTAAAATTAC
Found at i:16079 original size:59 final size:58
Alignment explanation
Indices: 15948--16408 Score: 321
Period size: 59 Copynumber: 7.8 Consensus size: 58
15938 ACCATTAAAC
** ** * * *
15948 TTTTCC-AAAATTA-CATTTTAACCCCTAAACTTCTCTAAAATTATATTTTTAACCCAAAA
1 TTTTCCAAAAATTACCATTTT-ACCCCCGAACTT-TC-AAAATTCCATTTTTGACCCTAAT
* *
16007 CTTT-CATAAAATTA-CATTTTTACCCCCGAACATTTCAAAATTCCATTTTCGACCCTAAT
1 TTTTCCA-AAAATTACCA-TTTTACCCCCGAAC-TTTCAAAATTCCATTTTTGACCCTAAT
* * *
16066 TTTTCCAAAAATTACGATTTTACCACCGAACTTCTAAAAATTCCA-TTTT-A-CCTCAAT
1 TTTTCCAAAAATTACCATTTTACCCCCGAACTT-TCAAAATTCCATTTTTGACCCT-AAT
* * * *
16123 TTTTCCAAAAATTACCATTTTACCCTCGAACTTTAAAAAATTGCATTTTTGACCCTAAA
1 TTTTCCAAAAATTACCATTTTACCCCCGAACTTT-CAAAATTCCATTTTTGACCCTAAT
* * ** * * * **
16182 TTTTCTAAAAGTTACCATTTTGTCCCCAAACTTTCCAAGATTCCATTTTTAACCCCGAT
1 TTTTCCAAAAATTACCATTTTACCCCCGAACTTT-CAAAATTCCATTTTTGACCCTAAT
* * ** * * * *
16241 TCTTCCCAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTTGATCTCGATT
1 TTTTCCAAAAATTACCATTTTACCCCCGAACTTTC-AAAATTCCA-TTTTTGA-CCCTAAT
* * * **
16302 TTTTCCAAAAATTACCATTTTACCCCCGGA-TGTCTAAAATTCCGTTTTAAACCCTGAA-
1 TTTTCCAAAAATTACCATTTTACCCCCGAACTTTC-AAAATTCCATTTTTGACCCT-AAT
* * * *
16360 CTTTCCCAAAATTACCATTTTACCCCC-AAATATTCAAAAATCACATTTT
1 TTTTCCAAAAATTACCATTTTACCCCCGAACT-TTCAAAATTC-CATTTT
16409 CAAACCCCGA
Statistics
Matches: 316, Mismatches: 67, Indels: 38
0.75 0.16 0.09
Matches are distributed among these distances:
56 4 0.01
57 44 0.14
58 45 0.14
59 148 0.47
60 41 0.13
61 34 0.11
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (58 bp):
TTTTCCAAAAATTACCATTTTACCCCCGAACTTTCAAAATTCCATTTTTGACCCTAAT
Found at i:16164 original size:29 final size:28
Alignment explanation
Indices: 16072--16161 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 28
16062 TAATTTTTCC
*
16072 AAAAATTACGATTTTACCAC-CGAACTTCT
1 AAAAATTACCATTTTACC-CTCGAACTT-T
*
16101 AAAAATT-CCATTTTA-CCTC-AATTTTT
1 AAAAATTACCATTTTACCCTCGAA-CTTT
16127 CCAAAAATTACCATTTTACCCTCGAACTTT
1 --AAAAATTACCATTTTACCCTCGAACTTT
16157 AAAAA
1 AAAAA
16162 ATTGCATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
26 4 0.08
27 4 0.08
28 19 0.37
29 15 0.29
30 7 0.14
31 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAATTACCATTTTACCCTCGAACTTT
Found at i:16169 original size:28 final size:27
Alignment explanation
Indices: 16005--16171 Score: 83
Period size: 29 Copynumber: 5.7 Consensus size: 27
15995 TTTAACCCAA
* *
16005 AACTTTCATAAAATTACATTTTTACCCCCG
1 AACTTT-A-AAAATTCCA-TTTTACCCTCG
*
16035 AACATTTCAAAATTCCATTTTCGACCCT--
1 AAC-TTTAAAAATTCCATTTT--ACCCTCG
* *
16063 AATTTTTCCAAAAATTACGATTTTACCAC-CG
1 AA-CTTT--AAAAATT-CCATTTTACC-CTCG
16094 AACTTCTAAAAATTCCATTTTA-CCTC-
1 AACTT-TAAAAATTCCATTTTACCCTCG
*
16120 AATTTTTCCAAAAATTACCATTTTACCCTCG
1 AA-CTTT--AAAAATT-CCATTTTACCCTCG
*
16151 AACTTTAAAAAATTGCATTTT
1 AACTTT-AAAAATTCCATTTT
16172 TGACCCTAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
26 4 0.04
27 4 0.04
28 29 0.27
29 33 0.31
30 23 0.21
31 14 0.13
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (27 bp):
AACTTTAAAAATTCCATTTTACCCTCG
Found at i:16237 original size:29 final size:29
Alignment explanation
Indices: 15944--16290 Score: 139
Period size: 30 Copynumber: 11.8 Consensus size: 29
15934 TTTAACCATT
* * *
15944 AAACTTTTCCAAAATTACATTTTAACCCCT
1 AAAC-TTTCCAAAATTCCATTTTTACCCCG
* ** * *
15974 AAACTTCTCTAAAATTATATTTTTAACCCA
1 AAACTT-TCCAAAATTCCATTTTTACCCCG
* *
16004 AAACTTTCATAAAATTACATTTTTACCCCCG
1 AAACTTTC-CAAAATTCCATTTTTA-CCCCG
* *
16035 -AACATTT-CAAAATTCCATTTTCGA-CCCT
1 AAAC-TTTCCAAAATTCCATTTT-TACCCCG
** *
16063 AATTTTTCCAAAAATTACGA-TTTTACCACCG
1 AAACTTTCC-AAAATT-CCATTTTTACC-CCG
* *
16094 -AAC-TTCTAAAAATTCCA-TTTTACCTC-
1 AAACTTTC-CAAAATTCCATTTTTACCCCG
**
16120 AATTTTTCCAAAAATTACCA-TTTTACCCTCG
1 AAACTTTCC-AAAATT-CCATTTTTACCC-CG
** * *
16151 -AACTTTAAAAAATTGCATTTTTGA-CCCT
1 AAACTTTCCAAAATTCCATTTTT-ACCCCG
* *
16179 AAATTTTCTAAAAGTTACCATTTTGT-CCCC-
1 AAACTTTCCAAAA-TT-CCATTTT-TACCCCG
*
16209 AAACTTTCCAAGATTCCATTTTTAACCCCG
1 AAACTTTCCAAAATTCCATTTTT-ACCCCG
** * *
16239 ATTCTTCCCAAAATTACCA-TTTTACCCCT
1 AAACTTTCCAAAATT-CCATTTTTACCCCG
16268 AAAC-TTCCAAAAATTCCATTTTT
1 AAACTTTCC-AAAATTCCATTTTT
16291 TGATCTCGAT
Statistics
Matches: 239, Mismatches: 47, Indels: 63
0.68 0.13 0.18
Matches are distributed among these distances:
27 3 0.01
28 40 0.17
29 82 0.34
30 91 0.38
31 22 0.09
32 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTTACCCCG
Found at i:16303 original size:118 final size:119
Alignment explanation
Indices: 16043--16399 Score: 304
Period size: 119 Copynumber: 3.0 Consensus size: 119
16033 CGAACATTTC
* * * * *
16043 AAAATTCCATTTTCGACCCT-AATTTTTCCAAAAATTACGATTTTACCACCGAACT-TCTAAAAA
1 AAAATTCCATTTTTGACCCTAAATTTTTCCAAAAATTACCATTTTACC-CCCAAATGTC-CAAAA
* * * * *
16106 TTCCATTTT--ACCTC-AATTTTTCCAAAAATTACCATTTTA-CCCTCGAACTTTAA
64 TTCCATTTTAAACCCCGAA-CTTTCCCAAAATTACCATTTTACCCCTCAAACTTCAA
* * * ** * *
16159 AAAATTGCATTTTTGACCCTAAA-TTTTCTAAAAGTTACCATTTTGTCCCCAAACTTTCCAAGAT
1 AAAATTCCATTTTTGACCCTAAATTTTTCCAAAAATTACCATTTTACCCCCAAA-TGTCCAAAAT
* * *
16223 TCCATTTTTAACCCCG-ATTCTTCCCAAAATTACCATTTTACCCCT-AAACTTCCA
65 TCCATTTTAAACCCCGAACT-TTCCCAAAATTACCATTTTACCCCTCAAACTTCAA
* * * ** *
16277 AAAATTCCATTTTTTGA-TCTCGATTTTTTCCAAAAATTACCATTTTACCCCCGGATGTCTAAAA
1 AAAATTCCA-TTTTTGACCCT-AAATTTTTCCAAAAATTACCATTTTACCCCCAAATGTCCAAAA
* * *
16341 TTCCGTTTTAAACCCTGAACTTTCCCAAAATTACCATTTTACCCC-CAAATATTCAA
64 TTCCATTTTAAACCCCGAACTTTCCCAAAATTACCATTTTACCCCTCAAA-CTTCAA
16397 AAA
1 AAA
16400 TCACATTTTC
Statistics
Matches: 192, Mismatches: 35, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
115 4 0.02
116 50 0.26
117 6 0.03
118 40 0.21
119 59 0.31
120 33 0.17
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (119 bp):
AAAATTCCATTTTTGACCCTAAATTTTTCCAAAAATTACCATTTTACCCCCAAATGTCCAAAATT
CCATTTTAAACCCCGAACTTTCCCAAAATTACCATTTTACCCCTCAAACTTCAA
Found at i:19718 original size:21 final size:22
Alignment explanation
Indices: 19692--19743 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
19682 TTTTAAAATA
19692 TATTATTTTTAATATATT-ATT
1 TATTATTTTTAATATATTCATT
* *
19713 TATTA-TTTTGATATTTTCATT
1 TATTATTTTTAATATATTCATT
19734 TATTATTTTT
1 TATTATTTTT
19744 TGGTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 13 0.48
22 4 0.15
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTATTTTTAATATATTCATT
Done.