Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011614.1 Kokia drynarioides strain JFW-HI SEQ_126604, 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: 114338
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:34 original size:3 final size:3
Alignment explanation
Indices: 28--96 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
18 ATAACTGTTT
28 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
76 TAA TAA TAA CAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
97 ACGGTAGTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1383 original size:29 final size:29
Alignment explanation
Indices: 1332--1532 Score: 262
Period size: 29 Copynumber: 6.8 Consensus size: 29
1322 TGGAGGTCCT
1332 TAAACTTCCAAAAAATTCCATTTTTACCCC
1 TAAACTTCC-AAAAATTCCATTTTTACCCC
*
1362 TAAACTTCTAAAAATTCCATTTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* * *
1391 GAAGCTTCCAAAAATTCCATTTTTACCCT
1 TAAACTTCCAAAAATTCCATTTTTACCCC
1420 TAAACTTCCAAAAATTCCATTTTTAACCCC
1 TAAACTTCCAAAAATTCCATTTTT-ACCCC
* *
1450 GAAACTTCCAAAAATTCCA-TTTTAGACCC
1 TAAACTTCCAAAAATTCCATTTTTA-CCCC
1479 TAAAACTTCCAAAAATTCCATTTTTA-CCC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
* * *
1508 TCGAACCTCCAAAATTTCCATTTTT
1 T-AAACTTCCAAAAATTCCATTTTT
1533 GACGTTGAAA
Statistics
Matches: 152, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
28 1 0.01
29 98 0.64
30 48 0.32
31 5 0.03
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAACTTCCAAAAATTCCATTTTTACCCC
Found at i:1427 original size:58 final size:57
Alignment explanation
Indices: 1334--1649 Score: 295
Period size: 58 Copynumber: 5.4 Consensus size: 57
1324 GAGGTCCTTA
*
1334 AACTTCCAAAAAATTCCATTTTTACCCCTAAACTTCTAAAAATTCCATTTTTACCCCG
1 AACTTCC-AAAAATTCCATTTTTACCCTTAAACTTCTAAAAATTCCATTTTTACCCCG
*
1392 AAGCTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACCCCG
1 AA-CTTCCAAAAATTCCATTTTTACCCTTAAACTTCTAAAAATTCCATTTTT-ACCCCG
* * *
1451 AAACTTCCAAAAATTCCATTTTAGACCCTAAAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTT-TACCCTTAAACTTCTAAAAATTCCATTTTTACCC-CG
* * * * * **
1511 AACCTCCAAAATTTCCATTTTTGA-CGTTGAAACTT-TCAAAATTATCATTTTGCCCCCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTT-AAACTTCTAAAAATT-CCATTTTTACCCCG
* * * *
1569 AA-TGTCCAAAAACTCCATTTTTGA-CCTCGAAAC-TCTCAAAATTACC-CTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTT-ACCCT-TAAACTTCTAAAAATT-CCATTTTTA-CCCCG
*
1627 AA-TGTCTAAAAATTCCATTTTTA
1 AACT-TCCAAAAATTCCATTTTTA
1650 ACCTCGAATT
Statistics
Matches: 221, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
57 5 0.02
58 115 0.52
59 69 0.31
60 32 0.14
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTTACCCTTAAACTTCTAAAAATTCCATTTTTACCCCG
Found at i:1458 original size:59 final size:58
Alignment explanation
Indices: 1333--1532 Score: 294
Period size: 59 Copynumber: 3.4 Consensus size: 58
1323 GGAGGTCCTT
* *
1333 AAACTTCCAAAAAATTCCATTTTTACCCCTAAACTTCTAAAAATTCCATTTTTACCCCG
1 AAACTTCC-AAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACCCCG
*
1392 AAGCTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
1451 AAACTTCCAAAAATTCCATTTTAGACCCTAAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCTTAAACTTCCAAAAATTCCATTTTTACCC-CG
* *
1511 -AACCTCCAAAATTTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
1533 GACGTTGAAA
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
58 42 0.33
59 57 0.44
60 30 0.23
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:1649 original size:29 final size:28
Alignment explanation
Indices: 1337--1677 Score: 196
Period size: 29 Copynumber: 11.6 Consensus size: 28
1327 GTCCTTAAAC
*
1337 TTCCAAAAAATTCCATTTTTACCC-CTAAA
1 TTCC-AAAAATTCCATTTTTACCCTC-GAA
*
1366 CTTCTAAAAATTCCATTTTTACCC-CGAA
1 -TTCCAAAAATTCCATTTTTACCCTCGAA
**
1394 GCTTCCAAAAATTCCATTTTTACCCTTAAA
1 --TTCCAAAAATTCCATTTTTACCCTCGAA
1424 CTTCCAAAAATTCCATTTTTAACCC-CGAAA
1 -TTCCAAAAATTCCATTTTT-ACCCTCG-AA
* **
1454 CTTCCAAAAATTCCATTTTAGACCCTAAAA
1 -TTCCAAAAATTCCATTTT-TACCCTCGAA
1484 CTTCCAAAAATTCCATTTTTACCCTCGAA
1 -TTCCAAAAATTCCATTTTTACCCTCGAA
* * * *
1513 CCTCCAAAATTTCCATTTTTGA-CGTTGAAA
1 -TTCCAAAAATTCCATTTTT-ACCCTCG-AA
* * * *
1543 CTTTC-AAAATTATCA-TTTTGCCCCCGAA
1 -TTCCAAAAATT-CCATTTTTACCCTCGAA
*
1571 TGTCCAAAAACTCCATTTTTGA-CCTCGAAA
1 T-TCCAAAAATTCCATTTTT-ACCCTCG-AA
* * *
1601 CTCTC-AAAATTACC-CTTTTACCCCCGAA
1 TTC-CAAAAATT-CCATTTTTACCCTCGAA
* *
1629 TGTCTAAAAATTCCATTTTTAACCTCGAA
1 T-TCCAAAAATTCCATTTTTACCCTCGAA
*
1658 TTTTCCCAAAATTACCATTT
1 --TTCCAAAAATT-CCATTT
1678 AGCCCTCAAG
Statistics
Matches: 246, Mismatches: 41, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.00
28 13 0.05
29 149 0.61
30 76 0.31
31 7 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTTACCCTCGAA
Found at i:1696 original size:28 final size:28
Alignment explanation
Indices: 1663--1724 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1653 TCGAATTTTC
1663 CCAAAATTACCA-TTTAGCCCTCAAGAAT
1 CCAAAATTACCATTTTA-CCCTCAAGAAT
* * *
1691 CCAAAATTATCATTTTACCCTCGAGTAT
1 CCAAAATTACCATTTTACCCTCAAGAAT
1719 CCAAAA
1 CCAAAA
1725 GGTCTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTCAAGAAT
Found at i:7783 original size:3 final size:3
Alignment explanation
Indices: 7775--7835 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
7765 NNNNNNNNNN
7775 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
7823 ACA TTA ATA ATA A
1 ATA ATA ATA ATA A
7836 ACGGTAGTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9122 original size:29 final size:29
Alignment explanation
Indices: 9071--9271 Score: 262
Period size: 29 Copynumber: 6.8 Consensus size: 29
9061 TGGAGGTCCT
9071 TAAACTTCCAAAAAATTCCATTTTTACCCC
1 TAAACTTCC-AAAAATTCCATTTTTACCCC
*
9101 TAAACTTCTAAAAATTCCATTTTTACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
* * *
9130 GAAGCTTCCAAAAATTCCATTTTTACCCT
1 TAAACTTCCAAAAATTCCATTTTTACCCC
9159 TAAACTTCCAAAAATTCCATTTTTAACCCC
1 TAAACTTCCAAAAATTCCATTTTT-ACCCC
* *
9189 GAAACTTCCAAAAATTCCA-TTTTAGACCC
1 TAAACTTCCAAAAATTCCATTTTTA-CCCC
9218 TAAAACTTCCAAAAATTCCATTTTTA-CCC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
* * *
9247 TCGAACCTCCAAAATTTCCATTTTT
1 T-AAACTTCCAAAAATTCCATTTTT
9272 GACGTTGAAA
Statistics
Matches: 152, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
28 1 0.01
29 98 0.64
30 48 0.32
31 5 0.03
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAACTTCCAAAAATTCCATTTTTACCCC
Found at i:9166 original size:58 final size:57
Alignment explanation
Indices: 9073--9388 Score: 295
Period size: 58 Copynumber: 5.4 Consensus size: 57
9063 GAGGTCCTTA
*
9073 AACTTCCAAAAAATTCCATTTTTACCCCTAAACTTCTAAAAATTCCATTTTTACCCCG
1 AACTTCC-AAAAATTCCATTTTTACCCTTAAACTTCTAAAAATTCCATTTTTACCCCG
*
9131 AAGCTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACCCCG
1 AA-CTTCCAAAAATTCCATTTTTACCCTTAAACTTCTAAAAATTCCATTTTT-ACCCCG
* * *
9190 AAACTTCCAAAAATTCCATTTTAGACCCTAAAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTT-TACCCTTAAACTTCTAAAAATTCCATTTTTACCC-CG
* * * * * **
9250 AACCTCCAAAATTTCCATTTTTGA-CGTTGAAACTT-TCAAAATTATCATTTTGCCCCCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTT-AAACTTCTAAAAATT-CCATTTTTACCCCG
* * * *
9308 AA-TGTCCAAAAACTCCATTTTTGA-CCTCGAAAC-TCTCAAAATTACC-CTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTT-ACCCT-TAAACTTCTAAAAATT-CCATTTTTA-CCCCG
*
9366 AA-TGTCTAAAAATTCCATTTTTA
1 AACT-TCCAAAAATTCCATTTTTA
9389 ACCTCGAATT
Statistics
Matches: 221, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
57 5 0.02
58 115 0.52
59 69 0.31
60 32 0.14
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTTACCCTTAAACTTCTAAAAATTCCATTTTTACCCCG
Found at i:9197 original size:59 final size:58
Alignment explanation
Indices: 9072--9271 Score: 294
Period size: 59 Copynumber: 3.4 Consensus size: 58
9062 GGAGGTCCTT
* *
9072 AAACTTCCAAAAAATTCCATTTTTACCCCTAAACTTCTAAAAATTCCATTTTTACCCCG
1 AAACTTCC-AAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACCCCG
*
9131 AAGCTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTT-ACCCCG
* *
9190 AAACTTCCAAAAATTCCATTTTAGACCCTAAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCTTAAACTTCCAAAAATTCCATTTTTACCC-CG
* *
9250 -AACCTCCAAAATTTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
9272 GACGTTGAAA
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
58 42 0.33
59 57 0.44
60 30 0.23
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:9388 original size:29 final size:28
Alignment explanation
Indices: 9076--9416 Score: 196
Period size: 29 Copynumber: 11.6 Consensus size: 28
9066 GTCCTTAAAC
*
9076 TTCCAAAAAATTCCATTTTTACCC-CTAAA
1 TTCC-AAAAATTCCATTTTTACCCTC-GAA
*
9105 CTTCTAAAAATTCCATTTTTACCC-CGAA
1 -TTCCAAAAATTCCATTTTTACCCTCGAA
**
9133 GCTTCCAAAAATTCCATTTTTACCCTTAAA
1 --TTCCAAAAATTCCATTTTTACCCTCGAA
9163 CTTCCAAAAATTCCATTTTTAACCC-CGAAA
1 -TTCCAAAAATTCCATTTTT-ACCCTCG-AA
* **
9193 CTTCCAAAAATTCCATTTTAGACCCTAAAA
1 -TTCCAAAAATTCCATTTT-TACCCTCGAA
9223 CTTCCAAAAATTCCATTTTTACCCTCGAA
1 -TTCCAAAAATTCCATTTTTACCCTCGAA
* * * *
9252 CCTCCAAAATTTCCATTTTTGA-CGTTGAAA
1 -TTCCAAAAATTCCATTTTT-ACCCTCG-AA
* * * *
9282 CTTTC-AAAATTATCA-TTTTGCCCCCGAA
1 -TTCCAAAAATT-CCATTTTTACCCTCGAA
*
9310 TGTCCAAAAACTCCATTTTTGA-CCTCGAAA
1 T-TCCAAAAATTCCATTTTT-ACCCTCG-AA
* * *
9340 CTCTC-AAAATTACC-CTTTTACCCCCGAA
1 TTC-CAAAAATT-CCATTTTTACCCTCGAA
* *
9368 TGTCTAAAAATTCCATTTTTAACCTCGAA
1 T-TCCAAAAATTCCATTTTTACCCTCGAA
*
9397 TTTTCCCAAAATTACCATTT
1 --TTCCAAAAATT-CCATTT
9417 AGCCCTCAAG
Statistics
Matches: 246, Mismatches: 41, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.00
28 13 0.05
29 149 0.61
30 76 0.31
31 7 0.03
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (28 bp):
TTCCAAAAATTCCATTTTTACCCTCGAA
Found at i:9435 original size:28 final size:28
Alignment explanation
Indices: 9402--9463 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
9392 TCGAATTTTC
9402 CCAAAATTACCA-TTTAGCCCTCAAGAAT
1 CCAAAATTACCATTTTA-CCCTCAAGAAT
* * *
9430 CCAAAATTATCATTTTACCCTCGAGTAT
1 CCAAAATTACCATTTTACCCTCAAGAAT
9458 CCAAAA
1 CCAAAA
9464 GGTCTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTCAAGAAT
Found at i:15764 original size:66 final size:66
Alignment explanation
Indices: 15649--15774 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
15639 TCAGCTTCTG
* *
15649 CAACGTGCAGCGATTGTCATCTCTTCCTCACTTTATCAGTCTTCTGACACTTACACTTTCGTGGC
1 CAACCTGCAGCGATTGTCATCTCTTCCTCACTTTATCAGTCTTCAGACACTTACACTTTCGTGGC
15714 A
66 A
15715 CAACCTGCAGCGATTGTCATCTCTTCCTCACTTTATCAGTCTTCAGACACTTACACTTTC
1 CAACCTGCAGCGATTGTCATCTCTTCCTCACTTTATCAGTCTTCAGACACTTACACTTTC
15775 ACTAGTGCCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (66 bp):
CAACCTGCAGCGATTGTCATCTCTTCCTCACTTTATCAGTCTTCAGACACTTACACTTTCGTGGC
A
Found at i:16145 original size:2 final size:2
Alignment explanation
Indices: 16138--16171 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
16128 ACATACACTT
* *
16138 TA TA TA TA TA TA TA TA TA TA CA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16172 GATACAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:17547 original size:19 final size:19
Alignment explanation
Indices: 17523--17578 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
17513 AAATACATTC
17523 TAAAATAATAAAAAATCAT
1 TAAAATAATAAAAAATCAT
* *
17542 TAAAAT-TTATAAAAATTAT
1 TAAAATAATA-AAAAATCAT
*
17561 TATAAATTAATTAAAAAT
1 TA-AAA-TAATAAAAAAT
17579 AATAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 2 0.07
19 16 0.55
20 3 0.10
21 7 0.24
22 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATAATAAAAAATCAT
Found at i:17555 original size:20 final size:20
Alignment explanation
Indices: 17513--17578 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
17503 TAGATTGTCC
* *
17513 AAATACATTCTAAAATAATAAA
1 AAAT-CATTATAAATTAAT-AA
*
17535 AAATCATTA-AAATTTATAA
1 AAATCATTATAAATTAATAA
*
17554 AAATTATTATAAATTAATTAA
1 AAATCATTATAAATTAA-TAA
17575 AAAT
1 AAAT
17579 AATAATATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 10 0.27
20 12 0.32
21 11 0.30
22 4 0.11
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATCATTATAAATTAATAA
Found at i:17602 original size:30 final size:31
Alignment explanation
Indices: 17533--17602 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
17523 TAAAATAATA
* * *
17533 AAAAATCATTAAAATTTATAAAAATTATTAT
1 AAAAATAATTAAAAATAATAAAAATTATTAT
* * *
17564 -AAATTAATTAAAAATAAT-AATATTTTTAT
1 AAAAATAATTAAAAATAATAAAAATTATTAT
17593 AAAAATAATT
1 AAAAATAATT
17603 TCGGCCATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAATAATTAAAAATAATAAAAATTATTAT
Found at i:20098 original size:9 final size:9
Alignment explanation
Indices: 20084--20110 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
20074 TCAAGGGAAA
20084 AAAAAAATG
1 AAAAAAATG
20093 AAAAAAATG
1 AAAAAAATG
20102 AAAAAAATG
1 AAAAAAATG
20111 GGGGAAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:21161 original size:17 final size:17
Alignment explanation
Indices: 21139--21174 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21129 TATTACTCGA
* *
21139 ATAATATTTGATGTATT
1 ATAATATTTCAAGTATT
21156 ATAATATTTCAAGTATT
1 ATAATATTTCAAGTATT
21173 AT
1 AT
21175 GATCAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (17 bp):
ATAATATTTCAAGTATT
Found at i:26424 original size:23 final size:23
Alignment explanation
Indices: 26394--26517 Score: 128
Period size: 23 Copynumber: 5.4 Consensus size: 23
26384 GTGCTGGGGT
26394 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
26417 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
26440 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
26463 ATCAGAGAGCACACACAAT--AA
1 AACAGAGAGCACACACAGTGCTA
*
26484 CAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
26508 AACAGAGAGC
1 AACAGAGAGC
26518 GCGCTAGTGT
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.01
22 12 0.14
23 70 0.83
24 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:26450 original size:46 final size:45
Alignment explanation
Indices: 26394--26517 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 45
26384 GTGCTGGGGT
*
26394 AACAGAGAGCACACACAGTGCTAAACAGAGAGTACACA-AAGT-AC
1 AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAA-TAAC
* *
26438 TAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAATAAC
1 -AA-CAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAATAAC
*
26485 AACAGAGAGCACGAGAC-GTGCTAAACAGAGAGC
1 AACAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
26518 GCGCTAGTGT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
45 27 0.39
46 38 0.55
47 4 0.06
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.10
Consensus pattern (45 bp):
AACAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAATAAC
Found at i:32137 original size:18 final size:19
Alignment explanation
Indices: 32114--32193 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 19
32104 AACCTATAAT
32114 GATTAATATTG-GTGGTGA
1 GATTAATATTGAGTGGTGA
* * *
32132 GATTAATTGTTGTAATGGTAA
1 GATTAA-TATTG-AGTGGTGA
*
32153 GATTAATATTGTAGTAGTGA
1 GATTAATATTG-AGTGGTGA
*
32173 GATTAAGATT-AGTGGTGA
1 GATTAATATTGAGTGGTGA
32191 GAT
1 GAT
32194 GTATGTTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
18 16 0.32
19 4 0.08
20 19 0.38
21 11 0.22
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.39
Consensus pattern (19 bp):
GATTAATATTGAGTGGTGA
Found at i:36761 original size:29 final size:30
Alignment explanation
Indices: 36707--36768 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
36697 TACACTTGAG
* **
36707 ATTTAGTCTTTATATTTTAATTTGACA-TA
1 ATTTAGTCTATATATTTTAAAATGACATTA
36736 ATTTAGTC-ATATACTTTTAAAATGACATTA
1 ATTTAGTCTATATA-TTTTAAAATGACATTA
36766 ATT
1 ATT
36769 AATTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 19 0.68
30 5 0.18
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50
Consensus pattern (30 bp):
ATTTAGTCTATATATTTTAAAATGACATTA
Found at i:42816 original size:13 final size:13
Alignment explanation
Indices: 42798--42823 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42788 GAAAAAAAAA
42798 AAAGCTTTCTTTC
1 AAAGCTTTCTTTC
42811 AAAGCTTTCTTTC
1 AAAGCTTTCTTTC
42824 TTTTGCTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
AAAGCTTTCTTTC
Found at i:43578 original size:13 final size:13
Alignment explanation
Indices: 43560--43584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43550 AGAGAGAACA
43560 ATATACATACATC
1 ATATACATACATC
43573 ATATACATACAT
1 ATATACATACAT
43585 ATTTTATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATACATACATC
Found at i:49015 original size:1 final size:1
Alignment explanation
Indices: 49009--49040 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
48999 ATCTAAATTT
49009 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
49041 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:62527 original size:20 final size:20
Alignment explanation
Indices: 62494--62532 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
62484 AAAAAGTTAA
62494 AAAAAAATAAATATTAAAATT
1 AAAAAAATAAATA-TAAAATT
*
62515 AAAAAAAT-TATATAAAAT
1 AAAAAAATAAATATAAAAT
62533 AATTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAATAAATATAAAATT
Found at i:64068 original size:22 final size:22
Alignment explanation
Indices: 64043--64112 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
64033 TAATAATTAA
64043 TAATACAAATTATGTGTAGTTT
1 TAATACAAATTATGTGTAGTTT
* ** * *
64065 TAATACCAAA-CAT-AATAATTAA
1 TAATA-CAAATTATGTGTAGTT-T
64087 TAATACAAATTATGTGTAGTTT
1 TAATACAAATTATGTGTAGTTT
64109 TAAT
1 TAAT
64113 TCGGTTAATT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
21 8 0.24
22 18 0.53
23 8 0.24
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATACAAATTATGTGTAGTTT
Found at i:64075 original size:44 final size:44
Alignment explanation
Indices: 64025--64112 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
64015 AACTGAATTA
64025 ACCAAACATAATAATTAATAATACAAATTATGTGTAGTTTTAAT
1 ACCAAACATAATAATTAATAATACAAATTATGTGTAGTTTTAAT
64069 ACCAAACATAATAATTAATAATACAAATTATGTGTAGTTTTAAT
1 ACCAAACATAATAATTAATAATACAAATTATGTGTAGTTTTAAT
64113 TCGGTTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (44 bp):
ACCAAACATAATAATTAATAATACAAATTATGTGTAGTTTTAAT
Found at i:67867 original size:22 final size:22
Alignment explanation
Indices: 67841--67883 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
67831 GCAACAGTAG
67841 GCACACACAGTACTGAACAGAA
1 GCACACACAGTACTGAACAGAA
*
67863 GCACACACAGTGCTGAACAGA
1 GCACACACAGTACTGAACAGA
67884 GGGCACGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
GCACACACAGTACTGAACAGAA
Found at i:75367 original size:54 final size:54
Alignment explanation
Indices: 75298--75400 Score: 179
Period size: 54 Copynumber: 1.9 Consensus size: 54
75288 ATTAGTCACT
* *
75298 TTCAAGCTCATGGATAAACTCTATCCACTGAATTAACCCCTAATTATTAAGCTA
1 TTCAAGCACATGGATAAACTCTATCAACTGAATTAACCCCTAATTATTAAGCTA
*
75352 TTCAAGCACATGGATAAACTCTATCAATTGAATTAACCCCTAATTATTA
1 TTCAAGCACATGGATAAACTCTATCAACTGAATTAACCCCTAATTATTA
75401 TGCTTATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (54 bp):
TTCAAGCACATGGATAAACTCTATCAACTGAATTAACCCCTAATTATTAAGCTA
Found at i:77543 original size:31 final size:31
Alignment explanation
Indices: 77507--77567 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
77497 AACTTGACCA
*
77507 AAAAAAATATTAATTAAAATG-CTAAAATAAAT
1 AAAAAAA-ATTAAAT-AAATGACTAAAATAAAT
77539 AAAAAAAATTAAATAAATGACTAAAATAA
1 AAAAAAAATTAAATAAATGACTAAAATAA
77568 TTTTTTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 15 0.56
32 7 0.26
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (31 bp):
AAAAAAAATTAAATAAATGACTAAAATAAAT
Found at i:77769 original size:22 final size:21
Alignment explanation
Indices: 77743--77783 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
77733 ATTAATCTAT
77743 TTGGCGGTCAAACATGTTCATA
1 TTGGCGGTCAAACAT-TTCATA
*
77765 TTGGCGGTCAATCATTTCA
1 TTGGCGGTCAAACATTTCA
77784 CATTTAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (21 bp):
TTGGCGGTCAAACATTTCATA
Found at i:81648 original size:18 final size:19
Alignment explanation
Indices: 81625--81668 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
81615 AAACCATATG
81625 TATTTTT-A-CTATTTTTAT
1 TATTTTTAATCTATTTTT-T
*
81643 TATTTTTAATTTATTTTTT
1 TATTTTTAATCTATTTTTT
81662 TATTTTT
1 TATTTTT
81669 GTTATCAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (19 bp):
TATTTTTAATCTATTTTTT
Found at i:81658 original size:11 final size:9
Alignment explanation
Indices: 81625--81673 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
81615 AAACCATATG
*
81625 TATTTTTAC
1 TATTTTTAT
81634 TATTTTTAT
1 TATTTTTAT
81643 TATTTTTAATT
1 TATTTTT-A-T
81654 TATTTTT-T
1 TATTTTTAT
*
81662 TATTTTTGT
1 TATTTTTAT
81671 TAT
1 TAT
81674 CAACAAAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
8 8 0.22
9 19 0.53
10 1 0.03
11 8 0.22
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (9 bp):
TATTTTTAT
Found at i:81818 original size:14 final size:14
Alignment explanation
Indices: 81795--81839 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
81785 TCAAAGTTGG
*
81795 AATATGACCGTTAC
1 AATATAACCGTTAC
*
81809 AATATAACCGTTAG
1 AATATAACCGTTAC
*
81823 AATCTAACCGTTAC
1 AATATAACCGTTAC
81837 AAT
1 AAT
81840 TTCTCGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (14 bp):
AATATAACCGTTAC
Found at i:86216 original size:23 final size:22
Alignment explanation
Indices: 86183--86227 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
86173 TGACTGATTC
86183 ATTTTCTGTTTCA-CAGTCTATT
1 ATTTTCTGTTTCATCAGT-TATT
86205 ATTTTCCTGTTTCATCAGTTATT
1 ATTTT-CTGTTTCATCAGTTATT
86228 TGTGGCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.56
Consensus pattern (22 bp):
ATTTTCTGTTTCATCAGTTATT
Found at i:101233 original size:23 final size:22
Alignment explanation
Indices: 101213--101324 Score: 100
Period size: 23 Copynumber: 4.8 Consensus size: 22
101203 TTATTGTTCA
*
101213 GCACTGTGTGTGCTTACTGTTTC
1 GCACT-TGTGTGCTTACTGATTC
*
101236 GCACTTCGTGTGCTTACTGATTT
1 GCACTT-GTGTGCTTACTGATTC
* * *
101259 GCGCTATGTGCGCCTACTGATT-
1 GCACT-TGTGTGCTTACTGATTC
*
101281 GCACTGTGTGTGCTTACTGTTTC
1 GCACT-TGTGTGCTTACTGATTC
101304 TTAGCACTTGTGTGCTTACTG
1 ---GCACTTGTGTGCTTACTG
101325 TTAAGTACTT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.25
23 36 0.49
24 1 0.01
25 13 0.18
26 5 0.07
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (22 bp):
GCACTTGTGTGCTTACTGATTC
Found at i:111697 original size:24 final size:24
Alignment explanation
Indices: 111652--111703 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
111642 AATTTAGTTG
* *
111652 TTTTTTCTTTTATGTTCTTTTAAC
1 TTTTCTCTTTTATGTTCCTTTAAC
* * *
111676 TTTTCTCTTTTTTTTTCCTTTATC
1 TTTTCTCTTTTATGTTCCTTTAAC
111700 TTTT
1 TTTT
111704 GCTTCTCCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTCTCTTTTATGTTCCTTTAAC
Found at i:113488 original size:4 final size:4
Alignment explanation
Indices: 113479--113564 Score: 86
Period size: 4 Copynumber: 21.2 Consensus size: 4
113469 AAATAAACGG
* * *
113479 GAAA GAAA GAAA CGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* *
113529 G-AA GAAA GAGAG GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
113565 GTAATGTGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
3 6 0.09
4 52 0.75
5 11 0.16
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:113501 original size:17 final size:16
Alignment explanation
Indices: 113479--113564 Score: 86
Period size: 17 Copynumber: 5.3 Consensus size: 16
113469 AAATAAACGG
113479 GAAAGAAAGAAACGAAA
1 GAAAGAAAGAAA-GAAA
*
113496 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGAAA
* *
113512 GAAGGAGAGGAAAGAAA
1 GAAAGA-AAGAAAGAAA
*
113529 G-AAGAAAGAGAGGAAA
1 GAAAGAAAGA-AAGAAA
*
113545 GAAAG-AAGAAGGAAA
1 GAAAGAAAGAAAGAAA
113560 GAAAG
1 GAAAG
113565 GTAATGTGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.24
16 21 0.36
17 24 0.41
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAAGAAA
Found at i:113534 original size:20 final size:20
Alignment explanation
Indices: 113478--113554 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
113468 CAAATAAACG
113478 GGAAAGAAAGAAACGAAAGA-A
1 GGAAAGAAAG-AA-GAAAGAGA
* *
113499 AGAAAGAAAGGAAGAAGGAGA
1 GGAAAGAAA-GAAGAAAGAGA
113520 GGAAAGAAAGAAGAAAGAGA
1 GGAAAGAAAGAAGAAAGAGA
113540 GGAAAGAAAGAAGAA
1 GGAAAGAAAGAAGAA
113555 GGAAAGAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 30 0.60
21 19 0.38
22 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (20 bp):
GGAAAGAAAGAAGAAAGAGA
Done.