Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015256.1 Kokia drynarioides strain JFW-HI SEQ_130301, 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: 145560
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:66 original size:10 final size:10
Alignment explanation
Indices: 51--83 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
41 AATTTTATAA
51 TTTTATATTT
1 TTTTATATTT
61 TTTTATATTT
1 TTTTATATTT
71 TTCTTA-ATTT
1 TT-TTATATTT
81 TTT
1 TTT
84 AATAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.05
10 18 0.82
11 3 0.14
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTATATTT
Found at i:10648 original size:24 final size:24
Alignment explanation
Indices: 10597--10649 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
10587 TCTTTCAGTT
* *
10597 AAATTCTGTTTATTTATTTCAATT
1 AAATTCTGTTTAGTTATTTCAATC
* * *
10621 AAATTCTGTTTAGTTGTTTGAGTC
1 AAATTCTGTTTAGTTATTTCAATC
10645 AAATT
1 AAATT
10650 TTTTGTTAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (24 bp):
AAATTCTGTTTAGTTATTTCAATC
Found at i:13679 original size:23 final size:23
Alignment explanation
Indices: 13649--13796 Score: 95
Period size: 23 Copynumber: 6.3 Consensus size: 23
13639 ATGCAAGCGC
*
13649 GCTTACTGCTTCGCACTTTGTGT
1 GCTTACTGATTCGCACTTTGTGT
* * * *
13672 GCTTACTGTTTCGAACCTTGTAT
1 GCTTACTGATTCGCACTTTGTGT
* * ** * *
13695 GCCTACTGATTTGTGCTATGTGC
1 GCTTACTGATTCGCACTTTGTGT
* *
13718 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGATTCGCACTTTGTGT
*
13740 GCTTACTAGATT-GCACTGTGTGT
1 GCTTACT-GATTCGCACTTTGTGT
*
13763 GCTTACTGTTTTCCTAGCAC-TTGTGT
1 GCTTACTG-ATT-C--GCACTTTGTGT
13789 GCTTACTG
1 GCTTACTG
13797 TTAAGTACTT
Statistics
Matches: 99, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
22 14 0.14
23 68 0.69
26 13 0.13
27 4 0.04
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (23 bp):
GCTTACTGATTCGCACTTTGTGT
Found at i:15050 original size:24 final size:24
Alignment explanation
Indices: 15022--15072 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
15012 AGAAATAATC
* *
15022 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
15046 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
15070 TTT
1 TTT
15073 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:21537 original size:2 final size:2
Alignment explanation
Indices: 21532--21559 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21522 ATTTTGTAAG
21532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21560 ACTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23409 original size:13 final size:13
Alignment explanation
Indices: 23391--23417 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23381 CTTAAATCTC
23391 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
23404 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
23417 T
1 T
23418 CGTTTGATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:25013 original size:28 final size:27
Alignment explanation
Indices: 24961--25014 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
24951 TTTTTTTTAA
* * *
24961 TTTTAAAATATTTTTGAAAATTTATTT
1 TTTTAAAAAATTTTTAAAAAATTATTT
24988 TTTTAAAAAATTTTTAAAAACATTATT
1 TTTTAAAAAATTTTTAAAAA-ATTATT
25015 AAATCATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTAAAAAATTTTTAAAAAATTATTT
Found at i:25247 original size:22 final size:23
Alignment explanation
Indices: 25183--25250 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
25173 GATTTTTAAC
*
25183 TTTTAAATAGTTTTATTAATTTGTA
1 TTTT-AATATTTTTATTAATTT-TA
*
25208 TTTTTAA-CTTTTTA--AATTTTA
1 -TTTTAATATTTTTATTAATTTTA
25229 -TTTAATATTTTTATTAATTTTA
1 TTTTAATATTTTTATTAATTTTA
25251 ATAATGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
19 5 0.14
20 6 0.17
21 2 0.06
22 12 0.33
24 5 0.14
25 2 0.06
26 4 0.11
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (23 bp):
TTTTAATATTTTTATTAATTTTA
Found at i:25314 original size:16 final size:16
Alignment explanation
Indices: 25275--25316 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
25265 AATATATGAA
* *
25275 AATTTAAAAATCATTT
1 AATTTAAAATTAATTT
*
25291 TA-TTAAAATTAATTT
1 AATTTAAAATTAATTT
25306 AATTTAAAATT
1 AATTTAAAATT
25317 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTAAAATTAATTT
Found at i:33536 original size:21 final size:21
Alignment explanation
Indices: 33512--33552 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
33502 TTTTAATATT
*
33512 ATATATAATTCTT-TTTATTTA
1 ATATA-AAATCTTATTTATTTA
33533 ATATAAAATCTTATTTATTT
1 ATATAAAATCTTATTTATTT
33553 TTTATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATAAAATCTTATTTATTTA
Found at i:37168 original size:654 final size:654
Alignment explanation
Indices: 35920--37223 Score: 2320
Period size: 654 Copynumber: 2.0 Consensus size: 654
35910 CAAAAAATTG
*
35920 AAGTGATATTTACCGACCAATCACAACCTTTGCCAAAGAGATCTCAATAATAGCATAAAGTGCAC
1 AAGTGATATTTACCGACCAATCACAACCTTTGCCAAAAAGATCTCAATAATAGCATAAAGTGCAC
* * *
35985 CAAGATCTAGAATACCATTCAATTGGTCATAGTTTATGATTATTATATGTATGTATGCATGTTTC
66 CAAGATCTAGAATACCATCCAATTGGTCATAGTTGATGATTATTACATGTATGTATGCATGTTTC
* * * *
36050 ACTTTTGACTTTTATTATCTCTTGTTTGTACAAAAAACACAAATTCCAACTGTAATAACCTGCGT
131 ACTTTGGACTTTTATTATCTCATGTTTGTACAAAAAACACAAATTCCAACTATAACAACCTGCGT
* *
36115 TATTATTGGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATAATTATCGATAAATGACA
196 TATTATTAGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATAATTATCAATAAATGACA
* *
36180 CCACCTCTTACCAAAGAGGTTTCAATAATAGTGTAACGCCTAACTAGAATCACATAAGCTTTTTT
261 CCACCTCTTACCAAAGAGGTTTCAATAATAGTGTAACACCTAACTAGAATCAAATAAGCTTTTTT
*
36245 TACAAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAGAACAAATAAAGGACATAT
326 TACAAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAAAACAAATAAAGGACATAT
* *
36310 TACTAGCTTCACCAAACTCCATTGGGTGTTGCATCAGTGACAGATGACATCTATAAAAAGTTCGT
391 TACTAGCTTCACCAAACCCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAAAGTTCGT
** *
36375 AATTAATGACGTCCGTAAAAGGTTACAAAATATTGAAGCGATATCTACTAACCAATGGCAACCCT
456 AATTAATGACGTCCACAAAAGGTTACAAAATATTGAAGCGACATCTACTAACCAATGGCAACCCT
*
36440 TGTAAATGAACATAATCTTGTTTTTTGTCCAAACAGAAGAATAACTCACGTGCTTTGTTTGCAGG
521 TGTAAATGAACATAATCTTGTTTTTTGTCCAAACAGAAGAATAACTCACGTGCTTTATTTGCAGG
36505 GACTACGAGAACAAATGAGAAAAAGGCATCATACCAACTTCACCAAACTTCATTGGGTGTCGCAT
586 GACTACGAGAACAAATGAGAAAAAGGCATCATACCAACTTCACCAAACTTCATTGGGTGTCGCAT
36570 ATTA
651 ATTA
* *
36574 AAGTGATATTTACCGACCAATCGCAACGTTTGCCAAAAAGATCTCAATAATAGCATAAAGTGCAC
1 AAGTGATATTTACCGACCAATCACAACCTTTGCCAAAAAGATCTCAATAATAGCATAAAGTGCAC
* * *
36639 CAAGATCTAGAATACCATCCAGTTGGTCATAGTTGATGATTATTCCATGTATTTATGCATGTTTC
66 CAAGATCTAGAATACCATCCAATTGGTCATAGTTGATGATTATTACATGTATGTATGCATGTTTC
*
36704 ACTTTGGACTTTTATTATCTCATGTTTGTACAAAAAACACAAATTCCAACTATAACAACCTGTGT
131 ACTTTGGACTTTTATTATCTCATGTTTGTACAAAAAACACAAATTCCAACTATAACAACCTGCGT
*
36769 TATTATTAGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATGATTATCAATAAATGACA
196 TATTATTAGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATAATTATCAATAAATGACA
36834 CCACCTCTTACCAAAGAGGTTTCAATAATAGTGTAACACCTAACTAGAATCAAATAAGCTTTTTT
261 CCACCTCTTACCAAAGAGGTTTCAATAATAGTGTAACACCTAACTAGAATCAAATAAGCTTTTTT
*
36899 TACCAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAAAACAAATAAAGGACATAT
326 TACAAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAAAACAAATAAAGGACATAT
***
36964 TACTAGCTTCATTGAACCCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAAAGTTCGT
391 TACTAGCTTCACCAAACCCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAAAGTTCGT
37029 AATTAATGACGTCCACAAAAGGTTACAAAATATTGAAGCGACATCTACTAACCAATGGCAACCCT
456 AATTAATGACGTCCACAAAAGGTTACAAAATATTGAAGCGACATCTACTAACCAATGGCAACCCT
*
37094 TGTAAATGAACATAATCTTGTTTTTTGTCCGAACAGAAGAATAACTCACGTGCTTTATTTGCAGG
521 TGTAAATGAACATAATCTTGTTTTTTGTCCAAACAGAAGAATAACTCACGTGCTTTATTTGCAGG
*
37159 GACTACGAGAACAAATGAGAAAAAGGCATCCTACCAACTTCACCAAACTTCATTGGGTGTCGCAT
586 GACTACGAGAACAAATGAGAAAAAGGCATCATACCAACTTCACCAAACTTCATTGGGTGTCGCAT
37224 TAGTGATTTA
Statistics
Matches: 618, Mismatches: 32, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
654 618 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (654 bp):
AAGTGATATTTACCGACCAATCACAACCTTTGCCAAAAAGATCTCAATAATAGCATAAAGTGCAC
CAAGATCTAGAATACCATCCAATTGGTCATAGTTGATGATTATTACATGTATGTATGCATGTTTC
ACTTTGGACTTTTATTATCTCATGTTTGTACAAAAAACACAAATTCCAACTATAACAACCTGCGT
TATTATTAGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATAATTATCAATAAATGACA
CCACCTCTTACCAAAGAGGTTTCAATAATAGTGTAACACCTAACTAGAATCAAATAAGCTTTTTT
TACAAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAAAACAAATAAAGGACATAT
TACTAGCTTCACCAAACCCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAAAGTTCGT
AATTAATGACGTCCACAAAAGGTTACAAAATATTGAAGCGACATCTACTAACCAATGGCAACCCT
TGTAAATGAACATAATCTTGTTTTTTGTCCAAACAGAAGAATAACTCACGTGCTTTATTTGCAGG
GACTACGAGAACAAATGAGAAAAAGGCATCATACCAACTTCACCAAACTTCATTGGGTGTCGCAT
ATTA
Found at i:38043 original size:717 final size:718
Alignment explanation
Indices: 36568--38580 Score: 3105
Period size: 717 Copynumber: 2.8 Consensus size: 718
36558 TGGGTGTCGC
*
36568 ATATTAAAGTGATATTTACCGACCAATCGCAACGTTTGCCAAAAAGATCTCAATAATAGCATAAA
1 ATATTGAAGTGATATTTACCGACCAATCGCAACGTTTGCCAAAAAGATCTCAATAATAGCATAAA
*
36633 GTGCACCAAGATCTAGAATACCATCCAGTTGGTCATAGTTGATGATTATTCCATGTATTTATGCA
66 GTGCACCAAGATCTAGAATACCATCCAGTTGGTCATAGTTGATGATTATTCTATGTATTTATGCA
* * *
36698 TGTTTCACTTTGGACTTTTATTATCTCATGTTTGTACAAAAAACACAAATTCCAACTATAACAAC
131 TGTTTCACTTTGGACTTTTATTATCTCTTGTTCGTACAAAAAACACAAATTCCAACTGTAACAAC
* * * * *
36763 CTGTGTTATTATTAGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATGATTATCAATAA
196 CTGCGTTATTGTTGGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATGATTATCGACAA
** * * *
36828 ATGACACCACCTCTTACCAAAGAGGTTTCAATAATAGTGTAACACCTAACTAGAATCAAATAAGC
261 ATGACACCACCTCTTACCAAAGAGGTTTCAATAATAGCATAACGCCAAACTAGAATCACATAAGC
* *
36893 -TTTTTTTACCAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAAAACAAATAAAG
326 TTTTTTTTGCCAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAGAACAAATAAAG
*** *
36957 GACATATTACTAGCTTCATTGAACCCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAA
391 GACATATTACTAGCTTCACCAAACTCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAA
* * * *
37022 AGTTCGTAATTAATGACGTCCACAAAAGGTTACAAAATATTGAAGCGACATCTACTAACCAATGG
456 AGTTCGTAATTAATGATGTCCGCAAAAGGTTACAAAATATTGAAGTGATATCTACTAACCAATGG
* * * *
37087 CAACCCTTGTAAATGAACATAATCTTGTTTTTTGTCCGAACAGAAGAATAACTCACGTGCTTTAT
521 CAACCCTTGCAAATGAACATAATCTTGTTTTTTGTCCAAACAGAAGAATAACCCACATGCTTTAT
* ** *
37152 TTGCAGGGACTACGAGAACAAATGAGAAAAAGGCATCCTACCAACTTCACCAAACTTCATTGGGT
586 GTGCAGGGACTACGAGAACAAATGAGAAAAAAACATCCTACCAACTTCACCAAACTTCATTAGGT
* *
37217 GTCGCATTAGTGATTTATGACATCCACAAAAAAATCCGTAACTAATGACGCCCACAAAAGGTCAC
651 GTCGCATTAGTGATTTATGACATCCACAAAAAAATCCATAACTAATGACGCCCAAAAAAGGTCAC
37282 AAA
716 AAA
37285 ATATTGAAGTGATATTTACCGACCAATCGCAACGTTTGCCAAAAAGATCTCAATAATAGCATAAA
1 ATATTGAAGTGATATTTACCGACCAATCGCAACGTTTGCCAAAAAGATCTCAATAATAGCATAAA
*
37350 GTGCACCAAGATCTAGAATACCATCCAGTTGGTCATAGTTGATGATTATTCTATGTACTTATGCA
66 GTGCACCAAGATCTAGAATACCATCCAGTTGGTCATAGTTGATGATTATTCTATGTATTTATGCA
37415 TGTTTCACTTTGGACTTTTATTATCTCTTGTTCGTACAAAAAACACAAATTCCAACTGTAACAAC
131 TGTTTCACTTTGGACTTTTATTATCTCTTGTTCGTACAAAAAACACAAATTCCAACTGTAACAAC
* * ** * *
37480 TTACAATATTGTTGGAACTAAAAAAAGATAAATAAATTTAAGGAAGAAAAAATGATTATCGACAA
196 CTGCGTTATTGTTGGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATGATTATCGACAA
*
37545 ATGACACCACCTCTTACCAAAGAGGTTTCAATAATAGCATAGCGCCAAACTAGAATCACATAAGC
261 ATGACACCACCTCTTACCAAAGAGGTTTCAATAATAGCATAACGCCAAACTAGAATCACATAAGC
* **
37610 TTTTTTTTGCCAACGTAAGAATATTTCAAATGCTGTGTGTGCAGAGACTATGAGAACAAATAAAG
326 TTTTTTTTGCCAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAGAACAAATAAAG
*
37675 GACATATTACTAGCTTCACCAAACTCCATTGGGTGTTGCATCAGTGACAGGTGACATCTACAAAA
391 GACATATTACTAGCTTCACCAAACTCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAA
* * * *
37740 AGTTCGTAATTAATTATGTCTGTAAAAGGTTACAAAATATTGAAGTGATATCTACTAACCAATGA
456 AGTTCGTAATTAATGATGTCCGCAAAAGGTTACAAAATATTGAAGTGATATCTACTAACCAATGG
* *
37805 CAACCCTTGCAAATGAACATAATCTTGTTTTTTGTCCAAATAGAAGAATAACCCACATGCTTTGT
521 CAACCCTTGCAAATGAACATAATCTTGTTTTTTGTCCAAACAGAAGAATAACCCACATGCTTTAT
* * *
37870 GTGCAGGGACTACGAGAACAAATGAGAAAAAAACATCCTACTAGCTTCACCGAACTTCATTAGGT
586 GTGCAGGGACTACGAGAACAAATGAGAAAAAAACATCCTACCAACTTCACCAAACTTCATTAGGT
* * * * **
37935 GTTGCATTAGTGATTTGTGACATCCACAAAAAAGTTCATAACTAATGACGTTCAAAAAAGGTCAC
651 GTCGCATTAGTGATTTATGACATCCACAAAAAAATCCATAACTAATGACGCCCAAAAAAGGTCAC
38000 AAA
716 AAA
* * * * *
38003 ATATTGAAGTGATATTTATCGACCAATTGCAAC-ATTGCCAAAGAGATCTCAATAATAACATAAA
1 ATATTGAAGTGATATTTACCGACCAATCGCAACGTTTGCCAAAAAGATCTCAATAATAGCATAAA
* * * **
38067 GTGCACTAAGATCTAG-ATCACCATTCAATTAATCATAGTTGATGATTATTCTATGTATTTATGC
66 GTGCACCAAGATCTAGAAT-ACCATCCAGTTGGTCATAGTTGATGATTATTCTATGTATTTATGC
* *
38131 ATGTTTCGCTTTAGACTTTTATTATCTCTTGTTCGTACAAAAAACACAAATTCCAACTGTAACAA
130 ATGTTTCACTTTGGACTTTTATTATCTCTTGTTCGTACAAAAAACACAAATTCCAACTGTAACAA
*
38196 CCTGCGTTATTGTTGGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATTATTATCGACA
195 CCTGCGTTATTGTTGGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATGATTATCGACA
* * * * *
38261 AATGGCATCACCTCCTACCAAAGAGGTTTCAATAATAGCATAATGCCCAACTAGAATCACATAAG
260 AATGACACCACCTCTTACCAAAGAGGTTTCAATAATAGCATAACGCCAAACTAGAATCACATAAG
* * * *
38326 CTTTTTTCTTTTTTTGCTAATGTAAGAATATCTCACGTGGTGTGTGTGCAGAGATTATGAGAACA
325 C-----T-TTTTTTTGCCAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAGAACA
* * *
38391 AATAAATGACATATTATTAGCTTCACCAAACTCCATTGGGTGTTGCATCAGTGACTGATGACATC
384 AATAAAGGACATATTACTAGCTTCACCAAACTCCATTGGGTGTTGCATCAGTGACAGATGACATC
* * *
38456 TACAAAGAGTTTGTAATTAATGATGTCCGCAAAAGGTTACAAAATATTGAAGTGATATCCACTAA
449 TACAAAAAGTTCGTAATTAATGATGTCCGCAAAAGGTTACAAAATATTGAAGTGATATCTACTAA
* *
38521 CCAATGGCAACCCTTGCAAATGAACATAATTCTTGGTTTTTGTCCAAACAAAAGAATAAC
514 CCAATGGCAACCCTTGCAAATGAACATAA-TCTTGTTTTTTGTCCAAACAGAAGAATAAC
38581 TCATGTGCTT
Statistics
Matches: 1178, Mismatches: 109, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
716 2 0.00
717 566 0.48
718 384 0.33
722 1 0.00
723 198 0.17
724 27 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (718 bp):
ATATTGAAGTGATATTTACCGACCAATCGCAACGTTTGCCAAAAAGATCTCAATAATAGCATAAA
GTGCACCAAGATCTAGAATACCATCCAGTTGGTCATAGTTGATGATTATTCTATGTATTTATGCA
TGTTTCACTTTGGACTTTTATTATCTCTTGTTCGTACAAAAAACACAAATTCCAACTGTAACAAC
CTGCGTTATTGTTGGAACTAGAAAAAGATATATAAATTTAAGGAAGAAAAAATGATTATCGACAA
ATGACACCACCTCTTACCAAAGAGGTTTCAATAATAGCATAACGCCAAACTAGAATCACATAAGC
TTTTTTTTGCCAACGTAAGAATATCTCACGTGCTGTGTGTGCAGAGACTATGAGAACAAATAAAG
GACATATTACTAGCTTCACCAAACTCCATTGGGTGTTGCATCAGTGACAGATGACATCTACAAAA
AGTTCGTAATTAATGATGTCCGCAAAAGGTTACAAAATATTGAAGTGATATCTACTAACCAATGG
CAACCCTTGCAAATGAACATAATCTTGTTTTTTGTCCAAACAGAAGAATAACCCACATGCTTTAT
GTGCAGGGACTACGAGAACAAATGAGAAAAAAACATCCTACCAACTTCACCAAACTTCATTAGGT
GTCGCATTAGTGATTTATGACATCCACAAAAAAATCCATAACTAATGACGCCCAAAAAAGGTCAC
AAA
Found at i:41414 original size:8 final size:8
Alignment explanation
Indices: 41403--41429 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41393 TATTACCGTA
41403 TATGTATT
1 TATGTATT
41411 TATGTATT
1 TATGTATT
41419 TATGTATT
1 TATGTATT
41427 TAT
1 TAT
41430 ACAATTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (8 bp):
TATGTATT
Found at i:45365 original size:46 final size:47
Alignment explanation
Indices: 45251--45365 Score: 108
Period size: 46 Copynumber: 2.4 Consensus size: 47
45241 ACAAAAATAT
*
45251 AATAAATTATTAAAGACAGTCAAAGAGATAGTAAATTATTAAAAACCTCAA
1 AATAAATTATTAAA-A-A-TCAAAGAGAGAGT-AATTATTAAAAACCTCAA
** ** * *
45302 AAT-GTTTCAAGACAAATCAAAGAGAGAGT-ATTATTAAAAACTTCAA
1 AATAAATT-ATTAAAAATCAAAGAGAGAGTAATTATTAAAAACCTCAA
45348 AATAAATTATTAAAAATC
1 AATAAATTATTAAAAATC
45366 TCGTATTATT
Statistics
Matches: 50, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
46 26 0.52
47 2 0.04
48 12 0.24
49 1 0.02
50 3 0.06
51 6 0.12
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (47 bp):
AATAAATTATTAAAAATCAAAGAGAGAGTAATTATTAAAAACCTCAA
Found at i:45589 original size:47 final size:47
Alignment explanation
Indices: 45475--45727 Score: 230
Period size: 47 Copynumber: 5.5 Consensus size: 47
45465 ATATTACAAG
* * * *
45475 AAAACTTCAATATGTTTCAAGACAGACAAAGAA-ATAATAAATTATTT
1 AAAACCTCAAAATGTTTCAAGACAAACAAA-AAGATAATAAATTATTA
45522 AAAACCTCAAAAATGTTTCAAGACAAACAAAAAGATAATAAATTATTA
1 AAAACCTC-AAAATGTTTCAAGACAAACAAAAAGATAATAAATTATTA
* * * *
45570 AAAACCTCAAACTGTTTCAAGATAAAC---AA-ATAGTGAATTA-TA
1 AAAACCTCAAAATGTTTCAAGACAAACAAAAAGATAATAAATTATTA
* * * ** *
45612 AAAACCTCAAAATCTCTCAGGACATCCAAAGAGATAATAAATTATTA
1 AAAACCTCAAAATGTTTCAAGACAAACAAAAAGATAATAAATTATTA
* * * ** * * *
45659 AGAACCTCGAAATGTTTCAAAACTGACAAAGAGATAGTAAATTGTTA
1 AAAACCTCAAAATGTTTCAAGACAAACAAAAAGATAATAAATTATTA
* *
45706 AAAACTTCAAAATATTTCAAGA
1 AAAACCTCAAAATGTTTCAAGA
45728 TAACCTCAAA
Statistics
Matches: 165, Mismatches: 34, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
42 22 0.13
43 9 0.05
44 2 0.01
45 1 0.01
46 9 0.05
47 81 0.49
48 41 0.25
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (47 bp):
AAAACCTCAAAATGTTTCAAGACAAACAAAAAGATAATAAATTATTA
Found at i:45880 original size:47 final size:47
Alignment explanation
Indices: 45829--45989 Score: 166
Period size: 47 Copynumber: 3.5 Consensus size: 47
45819 TCCAAGATAG
* * * *
45829 CCAAAGAGATAGCAAACTATTAAAAACCTCAAAATCTCTCAAGACAA
1 CCAAAGAGATAGTAAATTATTAAAAACCTCAAAATATTTCAAGACAA
* * * *
45876 CCAAAGAGATGGTATATTATTAAAAA-TTCAAAATATTTCAAGATAGA
1 CCAAAGAGATAGTAAATTATTAAAAACCTCAAAATATTTCAAGACA-A
* * * *
45923 -CACAGAGATATTAAATTATTTAAAACCTCAAAATGTTTCAAGACAA
1 CCAAAGAGATAGTAAATTATTAAAAACCTCAAAATATTTCAAGACAA
* *
45969 ACAAAGAGACAGTAAA-TATTA
1 CCAAAGAGATAGTAAATTATTA
45990 TTCAAAAATA
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
46 40 0.44
47 51 0.56
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (47 bp):
CCAAAGAGATAGTAAATTATTAAAAACCTCAAAATATTTCAAGACAA
Found at i:46049 original size:172 final size:171
Alignment explanation
Indices: 45756--46091 Score: 435
Period size: 172 Copynumber: 2.0 Consensus size: 171
45746 AGACAGGTAA
* * * * *
45756 AGAGATAGTATATTACTTAAAATCTCGAAATGTTTCAAGGCAAACAAAGAGAGAGTAAATTATTC
1 AGAGATAGTAAATTACTTAAAACCTCAAAATGTTTCAAGACAAACAAAGAGACAGTAAATTATTC
* * *
45821 CAAGATAGCCAAAGAGATAGCAAACTATTAAAAACCTCAAAATCTCTCAAGACAACCAAAG-AGA
66 AAAAATAGCCAAAGAGATAGCAAACTATTAAAAACCTCAAAATATCTCAAGACAACCAAAGAAG-
** * *
45885 TGGTATATTATTAAAAA-TTCAAAATATTTCAAGATAGACAC
130 TAATAAATTATTAAAAACTTCAAAATACTTCAAGATAGACAC
* *
45926 AGAGATATTAAATTATTTAAAACCTCAAAATGTTTCAAGACAAACAAAGAGACAGTAAATATTAT
1 AGAGATAGTAAATTACTTAAAACCTCAAAATGTTTCAAGACAAACAAAGAGACAGT-AA-ATTAT
** * * *
45991 TCAAAAATAGCCAAAGAGATAGTGAATTATTAAAAACCTCAAAATGAT-TCAGGACAACCAACGA
64 TCAAAAATAGCCAAAGAGATAGCAAACTATTAAAAACCTCAAAAT-ATCTCAAGACAACCAAAGA
*
46055 AGTAATAAATTATTAAAAACTTCAAAATGCTTCAAGA
128 AGTAATAAATTATTAAAAACTTCAAAATACTTCAAGA
46092 AAATCTCAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
170 49 0.35
171 2 0.01
172 72 0.51
173 18 0.13
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.24
Consensus pattern (171 bp):
AGAGATAGTAAATTACTTAAAACCTCAAAATGTTTCAAGACAAACAAAGAGACAGTAAATTATTC
AAAAATAGCCAAAGAGATAGCAAACTATTAAAAACCTCAAAATATCTCAAGACAACCAAAGAAGT
AATAAATTATTAAAAACTTCAAAATACTTCAAGATAGACAC
Found at i:46849 original size:26 final size:25
Alignment explanation
Indices: 46820--46876 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
46810 ATTTTAATCC
*
46820 TTTTATAATTTTTGAAAATTTTATT
1 TTTTATAATTTTTGAAAATTCTATT
* * *
46845 ATTTTTTTATTTTTTAAAATTCTATT
1 -TTTTATAATTTTTGAAAATTCTATT
46871 TTTTAT
1 TTTTAT
46877 TAAATAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (25 bp):
TTTTATAATTTTTGAAAATTCTATT
Found at i:55475 original size:16 final size:17
Alignment explanation
Indices: 55454--55487 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55444 TGGACATTCA
55454 ATTTGA-AATAAGAGGG
1 ATTTGATAATAAGAGGG
*
55470 ATTTGATAATTAGAGGG
1 ATTTGATAATAAGAGGG
55487 A
1 A
55488 ATGTTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (17 bp):
ATTTGATAATAAGAGGG
Found at i:60749 original size:17 final size:16
Alignment explanation
Indices: 60690--60751 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
60680 AAAAAATGTA
* *
60690 AAAAAAATTAAAATCT
1 AAAAAATTTAAAATTT
* *
60706 AAAAAA-GTAAAATTC
1 AAAAAATTTAAAATTT
60721 AAAAAATATTAAAATTT
1 AAAAAAT-TTAAAATTT
60738 ATAAAAATTTAAAA
1 A-AAAAATTTAAAA
60752 GAAATAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
15 12 0.32
16 6 0.16
17 14 0.37
18 6 0.16
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAAATTTAAAATTT
Found at i:60855 original size:14 final size:15
Alignment explanation
Indices: 60835--60873 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
60825 TGCTATTAAT
60835 GAAATTTTCAAAAAA
1 GAAATTTTCAAAAAA
*
60850 -AAA-TTTGAAAAAA
1 GAAATTTTCAAAAAA
60863 GAAATTTTCAA
1 GAAATTTTCAA
60874 TTTTAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (15 bp):
GAAATTTTCAAAAAA
Found at i:61042 original size:15 final size:14
Alignment explanation
Indices: 61012--61058 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
61002 ACATGGTAAC
61012 TTTTAAAAATGA-AT
1 TTTTAAAAAT-ATAT
61026 TTTTAATAAATATAT
1 TTTTAA-AAATATAT
*
61041 TTTTAAAGATATAT
1 TTTTAAAAATATAT
61055 TTTT
1 TTTT
61059 TTTTTGCCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (14 bp):
TTTTAAAAATATAT
Found at i:90757 original size:13 final size:13
Alignment explanation
Indices: 90739--90769 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
90729 TTTGCATATG
90739 AAATTGCATTAAT
1 AAATTGCATTAAT
90752 AAATTGCATTAAT
1 AAATTGCATTAAT
90765 AAATT
1 AAATT
90770 TTTTATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (13 bp):
AAATTGCATTAAT
Found at i:97847 original size:103 final size:101
Alignment explanation
Indices: 97670--97873 Score: 363
Period size: 103 Copynumber: 2.0 Consensus size: 101
97660 TAACAGGCTT
*
97670 CACTGACACGCTGTTAAAGCATGCTGGAGTCCAACCCATGCATGGTGTGTGTATTTCTTGGAAAC
1 CACTGACACGCTGTTAAAGAATGCTGGAGTCCAACCCATGCATGGTGTGTGTATTTCTTGGAAAC
97735 CCTGGACCTATCCAGTCTCTAAGGCTACTATTTAGG
66 CCTGGACCTATCCAGTCTCTAAGGCTACTATTTAGG
*
97771 CACTGACACGCTGTTAAAGAATGCTGGAGTTCATAACCCATGCATGGTGTGTGTATTTCTTGGAA
1 CACTGACACGCTGTTAAAGAATGCTGGAG-TC-CAACCCATGCATGGTGTGTGTATTTCTTGGAA
*
97836 ACCCTGTACCTATCCAGTCTCTAAGGCTACTATTTAGG
64 ACCCTGGACCTATCCAGTCTCTAAGGCTACTATTTAGG
97874 AGCCATTTTT
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 28 0.29
102 2 0.02
103 68 0.69
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (101 bp):
CACTGACACGCTGTTAAAGAATGCTGGAGTCCAACCCATGCATGGTGTGTGTATTTCTTGGAAAC
CCTGGACCTATCCAGTCTCTAAGGCTACTATTTAGG
Found at i:98814 original size:87 final size:87
Alignment explanation
Indices: 98668--98834 Score: 334
Period size: 87 Copynumber: 1.9 Consensus size: 87
98658 TCCATCTTGG
98668 TGTTTGGAATCTGTCAAAAATGCAAGAAATATACCACGGCATAGAATAAATAGCTTTCTTCGAAA
1 TGTTTGGAATCTGTCAAAAATGCAAGAAATATACCACGGCATAGAATAAATAGCTTTCTTCGAAA
98733 ATGTCACTTCTAGAATAAATAT
66 ATGTCACTTCTAGAATAAATAT
98755 TGTTTGGAATCTGTCAAAAATGCAAGAAATATACCACGGCATAGAATAAATAGCTTTCTTCGAAA
1 TGTTTGGAATCTGTCAAAAATGCAAGAAATATACCACGGCATAGAATAAATAGCTTTCTTCGAAA
98820 ATGTCACTTCTAGAA
66 ATGTCACTTCTAGAA
98835 AAGAAAAGGT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (87 bp):
TGTTTGGAATCTGTCAAAAATGCAAGAAATATACCACGGCATAGAATAAATAGCTTTCTTCGAAA
ATGTCACTTCTAGAATAAATAT
Found at i:106963 original size:11 final size:11
Alignment explanation
Indices: 106947--106973 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
106937 ACACTTTTAT
106947 AAAATTTTAAA
1 AAAATTTTAAA
106958 AAAATTTTAAA
1 AAAATTTTAAA
106969 AAAAT
1 AAAAT
106974 AAACCTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATTTTAAA
Found at i:107092 original size:26 final size:27
Alignment explanation
Indices: 107063--107128 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 27
107053 ATGAAACCCC
*
107063 AAAACCTGGAAAAATTTGAG-AACACA
1 AAAACCTGGAAAAACTTGAGAAACACA
* * *
107089 AAAA-CTCGGGAAAACTTGAGAAACTCG
1 AAAACCT-GGAAAAACTTGAGAAACACA
107116 AAAACCTGAGAAA
1 AAAACCTG-GAAA
107129 CCAAAAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 2 0.06
26 15 0.48
27 9 0.29
28 5 0.16
ACGTcount: A:0.52, C:0.17, G:0.18, T:0.14
Consensus pattern (27 bp):
AAAACCTGGAAAAACTTGAGAAACACA
Found at i:107286 original size:28 final size:28
Alignment explanation
Indices: 107255--107309 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
107245 AATTTTGAGT
107255 TCATGGTTTAACGTTTTAGTGTTTATGC
1 TCATGGTTTAACGTTTTAGTGTTTATGC
*
107283 TCATGGTTTAATGTTTTAGTGTTTATG
1 TCATGGTTTAACGTTTTAGTGTTTATG
107310 TTTATAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.07, G:0.22, T:0.53
Consensus pattern (28 bp):
TCATGGTTTAACGTTTTAGTGTTTATGC
Found at i:122956 original size:28 final size:28
Alignment explanation
Indices: 122925--122979 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
122915 AATTCAAGAT
*
122925 ATAAAAAATGTAAAATATTTTTATATTA
1 ATAAAAAATGTAAAATATATTTATATTA
*
122953 ATAAAAAGTGTAAAATATATTTATATT
1 ATAAAAAATGTAAAATATATTTATATT
122980 TTATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (28 bp):
ATAAAAAATGTAAAATATATTTATATTA
Found at i:129513 original size:20 final size:20
Alignment explanation
Indices: 129490--129529 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
129480 GCTGTTTAAA
*
129490 TATATATGTATATATTTATT
1 TATATATGTATATATATATT
* *
129510 TATATGTGTGTATATATATT
1 TATATATGTATATATATATT
129530 CCTTGGGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (20 bp):
TATATATGTATATATATATT
Found at i:145248 original size:20 final size:20
Alignment explanation
Indices: 145215--145263 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
145205 GAAAGAAACA
**
145215 AAAGAAAGGAAGAATTAGAGG
1 AAAGAAA-GAAGAAGGAGAGG
145236 AAAGAAAGAAGAAGGAGAGG
1 AAAGAAAGAAGAAGGAGAGG
*
145256 AAAAAAAG
1 AAAGAAAG
145264 GTAATGTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (20 bp):
AAAGAAAGAAGAAGGAGAGG
Done.