Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008072.1 Kokia drynarioides strain JFW-HI SEQ_122728, 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: 108838
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:21851 original size:14 final size:14
Alignment explanation
Indices: 21834--21863 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21824 AAAGATTAAG
21834 AATCAAAGTAATCT
1 AATCAAAGTAATCT
21848 AATCAAAGTAATCT
1 AATCAAAGTAATCT
21862 AA
1 AA
21864 CACTGAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (14 bp):
AATCAAAGTAATCT
Found at i:22969 original size:15 final size:15
Alignment explanation
Indices: 22949--22999 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
22939 ATCATAAATT
22949 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
*
22964 TTTTTCTTCTTCTTCC
1 TTTTTCTTCTT-TTTC
*
22980 TTTTT-TTCATTTTC
1 TTTTTCTTCTTTTTC
22994 TTTTTC
1 TTTTTC
23000 AAGTGACTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 8 0.26
15 15 0.48
16 8 0.26
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:23591 original size:19 final size:19
Alignment explanation
Indices: 23567--23619 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
23557 CTAACTTAAC
*
23567 AAAAATGCAATGACAAAAT
1 AAAAATGCAATGAAAAAAT
23586 AAAAATGCAATGAAAAAAT
1 AAAAATGCAATGAAAAAAT
23605 AAAAATGC-ATGAAAA
1 AAAAATGCAATGAAAA
23620 CTATCTACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 7 0.21
19 26 0.79
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.15
Consensus pattern (19 bp):
AAAAATGCAATGAAAAAAT
Found at i:36376 original size:36 final size:37
Alignment explanation
Indices: 36294--36376 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 37
36284 AATTACGCCC
* *
36294 AAACATGTCATTGCATGAGTAATTCTAGATTGCACCCA
1 AAAC-TGTCGTTGCATGAGCAATTCTAGATTGCACCCA
*
36332 AAACTGTCGTTGCATGAGCACTT-TCAGATTGCA-CCA
1 AAACTGTCGTTGCATGAGCAATTCT-AGATTGCACCCA
36368 AAACTGTCG
1 AAACTGTCG
36377 CCGCAGGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
36 13 0.32
37 24 0.59
38 4 0.10
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (37 bp):
AAACTGTCGTTGCATGAGCAATTCTAGATTGCACCCA
Found at i:36519 original size:26 final size:26
Alignment explanation
Indices: 36484--36537 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
36474 CACCCAGGAA
36484 TGTCGCTGCATGAACATGTAC-AGAAT
1 TGTCGCTGCATGAACATGT-CTAGAAT
* *
36510 TGTCGTTGCATGAACGTGTCTAGAAT
1 TGTCGCTGCATGAACATGTCTAGAAT
36536 TG
1 TG
36538 CACCCAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTCTAGAAT
Found at i:37706 original size:21 final size:21
Alignment explanation
Indices: 37682--37729 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
37672 CAATCATATT
37682 GGTAGTACCAATGGAAGTGTC
1 GGTAGTACCAATGGAAGTGTC
37703 GGTAGTACCAATGGAAGTGTC
1 GGTAGTACCAATGGAAGTGTC
37724 GGTAGT
1 GGTAGT
37730 TTTGTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.25
Consensus pattern (21 bp):
GGTAGTACCAATGGAAGTGTC
Found at i:37855 original size:21 final size:21
Alignment explanation
Indices: 37831--37888 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
37821 TAGAAGCACG
*
37831 ACTTGTTTCGGTAGAATTGA-C
1 ACTTGTTTCGGTAGAACT-ATC
* *
37852 ACTTGTATCGATAGAACTATC
1 ACTTGTTTCGGTAGAACTATC
*
37873 ACTTATTTCGGTAGAA
1 ACTTGTTTCGGTAGAA
37889 ATTTGCACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (21 bp):
ACTTGTTTCGGTAGAACTATC
Found at i:38302 original size:11 final size:11
Alignment explanation
Indices: 38286--38328 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
38276 TGCATTTGGT
38286 TTTATTTTTCA
1 TTTATTTTTCA
**
38297 TTTATTTTTGGT
1 TTTATTTTT-CA
*
38309 TTTATATTTCA
1 TTTATTTTTCA
38320 TTTATTTTT
1 TTTATTTTT
38329 GTTTTTTATG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (11 bp):
TTTATTTTTCA
Found at i:38307 original size:23 final size:23
Alignment explanation
Indices: 38280--38334 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
38270 AACTTTTGCA
*
38280 TTTGGTTTTATTTTTCATTTATT
1 TTTGGTTTTATATTTCATTTATT
38303 TTTGGTTTTATATTTCATTTATT
1 TTTGGTTTTATATTTCATTTATT
*
38326 TTTGTTTTT
1 TTTGGTTTT
38335 TATGTGTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.13, C:0.04, G:0.09, T:0.75
Consensus pattern (23 bp):
TTTGGTTTTATATTTCATTTATT
Found at i:41551 original size:44 final size:44
Alignment explanation
Indices: 41489--41576 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
41479 CTAGTACAAT
*
41489 ATAGATAGTCATAATGAAATTATGTAATGCCATATTCATTTATG
1 ATAGATAGTCATAATGAAATTATGTAATACCATATTCATTTATG
41533 ATAGATAGTCATAATGAAATTATGTAATACCATATTCATTTATG
1 ATAGATAGTCATAATGAAATTATGTAATACCATATTCATTTATG
41577 CATGAAGTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (44 bp):
ATAGATAGTCATAATGAAATTATGTAATACCATATTCATTTATG
Found at i:48514 original size:24 final size:23
Alignment explanation
Indices: 48486--48531 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
48476 TTTGGAGAAT
48486 TTTGTGTTTACGTTTTGAGGGTTC
1 TTTGTGTTTACGTTTTG-GGGTTC
* *
48510 TTTGTTTTTAGGTTTTGGGGTT
1 TTTGTGTTTACGTTTTGGGGTT
48532 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.07, C:0.04, G:0.30, T:0.59
Consensus pattern (23 bp):
TTTGTGTTTACGTTTTGGGGTTC
Found at i:49204 original size:39 final size:39
Alignment explanation
Indices: 49160--49234 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
49150 TTAAACACTC
49160 ATATTTCCTCAATTAGGTCAAATTGCATTTCATGCTCTA
1 ATATTTCCTCAATTAGGTCAAATTGCATTTCATGCTCTA
*
49199 ATATTTCCTCAATTGGGTCAAATTGCATTTCATGCT
1 ATATTTCCTCAATTAGGTCAAATTGCATTTCATGCT
49235 TTAACTTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (39 bp):
ATATTTCCTCAATTAGGTCAAATTGCATTTCATGCTCTA
Found at i:56717 original size:22 final size:22
Alignment explanation
Indices: 56692--56761 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
56682 CAGAGATAGG
56692 TTCTTGCTTTGAAAGTAAGGCA
1 TTCTTGCTTTGAAAGTAAGGCA
*
56714 TTCTT-CATTT-ATTA-TGATAGG--
1 TTCTTGC-TTTGA-AAGT-A-AGGCA
56735 TTCTTGCTTTGAAAGTAAGGCA
1 TTCTTGCTTTGAAAGTAAGGCA
56757 TTCTT
1 TTCTT
56762 CATTTGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 18
0.65 0.04 0.32
Matches are distributed among these distances:
20 3 0.08
21 13 0.35
22 18 0.49
23 3 0.08
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (22 bp):
TTCTTGCTTTGAAAGTAAGGCA
Found at i:56747 original size:43 final size:43
Alignment explanation
Indices: 56686--56771 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
56676 CATGGCCAGA
56686 GATAGGTTCTTGCTTTGAAAGTAAGGCATTCTTCATTTATTAT
1 GATAGGTTCTTGCTTTGAAAGTAAGGCATTCTTCATTTATTAT
*
56729 GATAGGTTCTTGCTTTGAAAGTAAGGCATTCTTCATTTGTTAT
1 GATAGGTTCTTGCTTTGAAAGTAAGGCATTCTTCATTTATTAT
56772 AACTTTTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (43 bp):
GATAGGTTCTTGCTTTGAAAGTAAGGCATTCTTCATTTATTAT
Found at i:59780 original size:55 final size:54
Alignment explanation
Indices: 59713--59817 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 54
59703 TATATGTAAA
* * * * *
59713 TTTTTTTTAATTTAGTACTCAAATTTTATA-TTTTTTTCTAATTTGGTACCTTT
1 TTTTTTTTAATTTAGTACTCAAACTTGACACTCTTTTCCTAATTTGGTACCTTT
*
59766 TTTTTTGTCTAATTTGGTACTCAAACTTGACACTCTTTTCCTAATTTGGTAC
1 TTTTTT-T-TAATTTAGTACTCAAACTTGACACTCTTTTCCTAATTTGGTAC
59818 ATAAACTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
53 6 0.14
54 1 0.02
55 19 0.44
56 17 0.40
ACGTcount: A:0.22, C:0.14, G:0.09, T:0.55
Consensus pattern (54 bp):
TTTTTTTTAATTTAGTACTCAAACTTGACACTCTTTTCCTAATTTGGTACCTTT
Found at i:60240 original size:58 final size:60
Alignment explanation
Indices: 60090--60246 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
60080 AACACTTAGG
* * * * * * *
60090 TACCAAATTACGAAAAAATACCGAGTTCAAATACCAAATTGAGTTCAAACAAAGTTTAAG
1 TACCAAATTAAGAAAAAATATCAAGTTCAAGTACCAAATTAAGTTCAAACAAAATTTAAA
* *
60150 TACCGAATTAAGAAAAAATATCAAATTCAAGTACCAAATTAAG-T-AAA-AAAATTTAAA
1 TACCAAATTAAGAAAAAATATCAAGTTCAAGTACCAAATTAAGTTCAAACAAAATTTAAA
* *
60207 TATCAAATTAAAGAAAAAATATCAAGTTGAAGTACCAAAT
1 TACCAAATT-AAGAAAAAATATCAAGTTCAAGTACCAAAT
60247 GTTATATTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 15 0.18
58 31 0.37
59 1 0.01
60 36 0.43
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.24
Consensus pattern (60 bp):
TACCAAATTAAGAAAAAATATCAAGTTCAAGTACCAAATTAAGTTCAAACAAAATTTAAA
Found at i:70493 original size:177 final size:189
Alignment explanation
Indices: 69899--70502 Score: 504
Period size: 200 Copynumber: 3.1 Consensus size: 189
69889 AAAGCATTGT
* * * * *
69899 ATTTACCTATTTAATTTATTTTTACTCATAATTTAAATTACTTTTTTAACTTTTTAGTTTTC-AA
1 ATTTACCTATTTAATTTA-TCTTACTCAAAATTTAAA--A-TATATT--C-TTTTA-TTTTCTGA
* * * **
69963 TATTTAATTTTTTTTATAATTATATTTTTAATAT-T-GAATTTTCCTTTCACTAACATGGTAACT
58 TATTT-ATTATTTTTATAATTAGATTTTTAATATATAGAATTTCCCTTTCAC-AACATAATAA--
** * * * * * * *
70026 TTTTTTTTTGCTATAGAAAAATAACAATACCATGATAAA-AAATCAACATGCATTTATTATTCTT
119 TTTTTTAGTG-TGT--CATAATAACAATACAATGATAAACAATTGAA-GTGCATTTATTATTCTT
* *
70090 AATCTGATGT
180 AATATGATGC
* *
70100 ATTTACCTATTTAATTTCATCTTACTCAAAATTTAAAATATTTTTTTCCTTTTATTTTCTGATCT
1 ATTTACCTATTTAATTT-ATCTTACTCAAAATTTAAAATA---TATT-CTTTTATTTTCTGATAT
* * *
70165 TTATTATTTTTATAATTAGATTTTTAATATTTAGAATTTCCCTTTCACAATATAATAATTTTTTG
61 TTATTATTTTTATAATTAGATTTTTAATATATAGAATTTCCCTTTCACAACATAATAATTTTTTA
* *
70230 GTGTGTCATAGGAAAATAACAATACTATGATAAACAATTGGAGTGCATTTATTTATTCTTAATAT
126 GTGTGTCAT-----AATAACAATACAATGATAAACAATTGAAGTGCATTTA-TTATTCTTAATAT
70295 GATGC
185 GATGC
* * *
70300 ATTTATCTATTTAATTT-T-TTACTCAGAATTTAAACTA-ATT-TTTTATTTT-TGATATTTATT
1 ATTTACCTATTTAATTTATCTTACTCAAAATTTAAAATATATTCTTTTATTTTCTGATATTTATT
* * *
70360 TTTTTTA-AATTAGATTTTTAATA-AT-GTATTT-CCTTTCATCAACATGATAATTTTTTAGTGT
66 ATTTTTATAATTAGATTTTTAATATATAGAATTTCCCTTTCA-CAACATAATAATTTTTTAGTGT
* *
70421 G-C-T-AT-ACAATACAATGATAAATAATTGAAGTGCATTTATTATTCCTAATATGATGC
130 GTCATAATAACAATACAATGATAAACAATTGAAGTGCATTTATTATTCTTAATATGATGC
70477 ATTTACCTATTTAATTTATTCTTACT
1 ATTTACCTATTTAATTTA-TCTTACT
70503 TAGTTCAAAT
Statistics
Matches: 345, Mismatches: 40, Indels: 57
0.78 0.09 0.13
Matches are distributed among these distances:
177 33 0.10
178 30 0.09
179 3 0.01
180 5 0.01
185 1 0.00
186 8 0.02
187 25 0.07
188 1 0.00
189 16 0.05
190 16 0.05
191 9 0.03
193 2 0.01
194 1 0.00
196 2 0.01
197 25 0.07
198 33 0.10
199 46 0.13
200 51 0.15
201 37 0.11
202 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (189 bp):
ATTTACCTATTTAATTTATCTTACTCAAAATTTAAAATATATTCTTTTATTTTCTGATATTTATT
ATTTTTATAATTAGATTTTTAATATATAGAATTTCCCTTTCACAACATAATAATTTTTTAGTGTG
TCATAATAACAATACAATGATAAACAATTGAAGTGCATTTATTATTCTTAATATGATGC
Found at i:70520 original size:177 final size:185
Alignment explanation
Indices: 70149--70493 Score: 440
Period size: 177 Copynumber: 1.9 Consensus size: 185
70139 ATTTTTTTCC
* *
70149 TTTTATTTTCTGATCTTTATTATTTTTATAATTAGATTTTTAATATTTAGAATTTCCCTTTCACA
1 TTTTATTTTCTGATATTTATTATTTTTATAATTAGATTTTTAATATATAGAATTTCCCTTTCACA
* * * *
70214 ATATAATAATTTTTTGGTGTGTCATAGGAAAATAACAATACTATGATAAACAATTGGAGTGCATT
66 ACATAATAATTTTTTAGTGTGTCAT-----AATAACAATACAATGATAAACAATTGAAGTGCATT
* * *
70279 TATTTATTCTTAATATGATGCATTTATCTATTTAATTTTTTACTCAGAATTTAAACTAATT
126 TATTTATTCCTAATATGATGCATTTACCTATTTAATTTTTTACTCAG-ATTCAAACTAATT
* *
70340 TTTTATTTT-TGATATTTATTTTTTTTA-AATTAGATTTTTAATA-AT-GTATTT-CCTTTCATC
1 TTTTATTTTCTGATATTTATTATTTTTATAATTAGATTTTTAATATATAGAATTTCCCTTTCA-C
* *
70400 AACATGATAATTTTTTAGTGTG-C-T-AT-ACAATACAATGATAAATAATTGAAGTGCATTTA-T
65 AACATAATAATTTTTTAGTGTGTCATAATAACAATACAATGATAAACAATTGAAGTGCATTTATT
70460 TATTCCTAATATGATGCATTTACCTATTTAATTT
130 TATTCCTAATATGATGCATTTACCTATTTAATTT
70494 ATTCTTACTT
Statistics
Matches: 141, Mismatches: 12, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
177 33 0.23
178 30 0.21
179 2 0.01
185 1 0.01
186 8 0.06
187 25 0.18
188 1 0.01
189 16 0.11
190 16 0.11
191 9 0.06
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (185 bp):
TTTTATTTTCTGATATTTATTATTTTTATAATTAGATTTTTAATATATAGAATTTCCCTTTCACA
ACATAATAATTTTTTAGTGTGTCATAATAACAATACAATGATAAACAATTGAAGTGCATTTATTT
ATTCCTAATATGATGCATTTACCTATTTAATTTTTTACTCAGATTCAAACTAATT
Found at i:72573 original size:27 final size:27
Alignment explanation
Indices: 72543--72630 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 27
72533 CGTTGACCTG
*
72543 CCATTGACCGTTGATCGTTAACTTTGA
1 CCATTGACCGTTGATCGTTGACTTTGA
* * *
72570 CCATTGATCGTTGACCGTTGACTTGGA
1 CCATTGACCGTTGATCGTTGACTTTGA
** * * *
72597 CTGTTGACCATTGGTTGTTGACTTTGA
1 CCATTGACCGTTGATCGTTGACTTTGA
*
72624 CCGTTGA
1 CCATTGA
72631 TTTGGATCAT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (27 bp):
CCATTGACCGTTGATCGTTGACTTTGA
Found at i:72604 original size:20 final size:20
Alignment explanation
Indices: 72579--72636 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
72569 ACCATTGATC
72579 GTTGACCGTTGACTTGGACT
1 GTTGACCGTTGACTTGGACT
* *
72599 GTTGACCATTG-GTTGTTGACT
1 GTTGACCGTTGACTTG--GACT
*
72620 -TTGACCGTTGATTTGGA
1 GTTGACCGTTGACTTGGA
72637 TCATTGATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
19 5 0.16
20 19 0.61
21 7 0.23
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.40
Consensus pattern (20 bp):
GTTGACCGTTGACTTGGACT
Found at i:84820 original size:13 final size:13
Alignment explanation
Indices: 84802--84834 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
84792 AAATAAGTTC
84802 TGATTTTGATTTT
1 TGATTTTGATTTT
84815 TGATTTTGATTTT
1 TGATTTTGATTTT
84828 T-ATTTTG
1 TGATTTTG
84835 TAGTATCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (13 bp):
TGATTTTGATTTT
Found at i:100075 original size:12 final size:12
Alignment explanation
Indices: 100058--100083 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
100048 TTTTAGGAAG
100058 TTTTCTTTTATT
1 TTTTCTTTTATT
100070 TTTTCTTTTATT
1 TTTTCTTTTATT
100082 TT
1 TT
100084 CTGAACAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTCTTTTATT
Found at i:102481 original size:24 final size:23
Alignment explanation
Indices: 102449--102494 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
102439 CCCGGCCCGG
102449 ATTTATAATAATAATTTTATTTTT
1 ATTTATAATAATAATTTT-TTTTT
* *
102473 ATTTTTAATACTAATTTTTTTT
1 ATTTATAATAATAATTTTTTTT
102495 GCTTGTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTATAATAATAATTTTTTTTT
Found at i:103221 original size:12 final size:12
Alignment explanation
Indices: 103204--103229 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
103194 AATTTGTTTG
103204 TTGTTTTAATAT
1 TTGTTTTAATAT
103216 TTGTTTTAATAT
1 TTGTTTTAATAT
103228 TT
1 TT
103230 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:103964 original size:21 final size:23
Alignment explanation
Indices: 103922--103964 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
103912 AAGTTTTATT
* *
103922 TATTTATATAATAAGTAGTTTTA
1 TATTTATATAACAAGTAATTTTA
103945 TATTTATA-AACAA-TAATTTT
1 TATTTATATAACAAGTAATTTT
103965 TTATAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (23 bp):
TATTTATATAACAAGTAATTTTA
Found at i:104913 original size:3 final size:3
Alignment explanation
Indices: 104905--104953 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
104895 TAATAGCATA
104905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
104953 A
1 A
104954 TGTCTATGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:106273 original size:89 final size:88
Alignment explanation
Indices: 106175--106358 Score: 271
Period size: 89 Copynumber: 2.1 Consensus size: 88
106165 GAATGCCCGT
* * *
106175 GGGTAAAACGGTAATTTTTAGAAGGTTCGGGGTTGAAAATAGAATTTTTAAACATCCGAGGGTAA
1 GGGTAAAACGATAATTTTTAGAAGGTTCGGGGTTAAAAATAGAATTTTTAAACATCCGAGGGCAA
*
106240 AATGGTATTTTTTGGAAAATTTGA
66 AATGGTA-ATTTTGGAAAATTTGA
* * * *
106264 GGGTAAAACGATAATTTTTAGAATGTTTGGGGTTAAAAATAGAATTTTTAGACATTCGAGGGCAA
1 GGGTAAAACGATAATTTTTAGAAGGTTCGGGGTTAAAAATAGAATTTTTAAACATCCGAGGGCAA
*
106329 AATGGTAATTTTGGAAATTTTGA
66 AATGGTAATTTTGGAAAATTTGA
106352 -GGTAAAA
1 GGGTAAAA
106359 AATGGAATTT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 7 0.08
88 14 0.16
89 65 0.76
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (88 bp):
GGGTAAAACGATAATTTTTAGAAGGTTCGGGGTTAAAAATAGAATTTTTAAACATCCGAGGGCAA
AATGGTAATTTTGGAAAATTTGA
Found at i:106338 original size:29 final size:29
Alignment explanation
Indices: 106232--106659 Score: 121
Period size: 29 Copynumber: 14.7 Consensus size: 29
106222 TTAAACATCC
* * *
106232 GAGGGTAAAATGGTATTTTTTGGAAAATTT
1 GAGGGAAAAATGGTAATTTTTAG-AAATTT
* * * *
106262 GAGGGTAAAACGATAATTTTTAGAATGTTT
1 GAGGGAAAAATGGTAATTTTTAGAA-ATTT
* * *
106292 G-GGGTTAAAAATAG-AATTTTTAGACATTC
1 GAGGG--AAAAATGGTAATTTTTAGAAATTT
* *
106321 GAGGGCAAAATGGTAA-TTTTGGAAATTTT
1 GAGGGAAAAATGGTAATTTTTAGAAA-TTT
* *
106350 GAGGTAAAAAATGG-AATTTTTAGATATTT
1 GAGG-GAAAAATGGTAATTTTTAGAAATTT
* * * **
106379 GGGGGTAAAATGGTAA-TTTTGGATGTTT
1 GAGGGAAAAATGGTAATTTTTAGAAATTT
* *
106407 G-GGGTAAAAAT-GTATTTTTTGGAAAATTT
1 GAGGG-AAAAATGGTAATTTTTAG-AAATTT
* *
106436 -AGGGCCAAAATGG-AA-TTTTAGAAAGTCT
1 GAGGG-AAAAATGGTAATTTTTAGAAA-TTT
*
106464 -AGGGGTAAAAAT-GT-ATTTTTGGAAAATTT
1 GA-GGG-AAAAATGGTAATTTTTAG-AAATTT
* * * *
106493 -AGGGTTAAAAT-GAAATTTTAAAAAATTT
1 GAGGG-AAAAATGGTAATTTTTAGAAATTT
* *
106521 -AGGGGTAAAA-GTGTAATTTTTGGAAATTTT
1 GA-GGGAAAAATG-GTAATTTTTAGAAA-TTT
* *
106551 G-GGGTTAAAAAATGG-AA-TTTTGGAAAGTTC
1 GAGGG---AAAAATGGTAATTTTTAGAAA-TTT
* *
106581 GAGGGCAAAAT-GTAATTTTTGGAAAATTT
1 GAGGGAAAAATGGTAATTTTTAG-AAATTT
* * * *
106610 AAGGGTAAAAAT-TTAATTTTTGGAAGTTT
1 GAGGG-AAAAATGGTAATTTTTAGAAATTT
106639 -AGGGTCAAAAAT-GTAATTTTT
1 GAGGG--AAAAATGGTAATTTTT
106660 GTGAAGTTAA
Statistics
Matches: 304, Mismatches: 59, Indels: 71
0.70 0.14 0.16
Matches are distributed among these distances:
27 10 0.03
28 85 0.28
29 107 0.35
30 87 0.29
31 9 0.03
32 5 0.02
33 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
GAGGGAAAAATGGTAATTTTTAGAAATTT
Found at i:106473 original size:28 final size:28
Alignment explanation
Indices: 106357--106709 Score: 167
Period size: 29 Copynumber: 12.2 Consensus size: 28
106347 TTTGAGGTAA
* * *
106357 AAAATGGAATTTTTAG-ATATTTGGGGGT
1 AAAATGTAA-TTTTAGAAAATTTAGGGGT
* **
106385 AAAATGGTAATTTT-GGATGTTT-GGGGT
1 AAAAT-GTAATTTTAGAAAATTTAGGGGT
* * **
106412 AAAAATGTATTTTTTGGAAAATTTAGGGCC
1 -AAAATGTA-ATTTTAGAAAATTTAGGGGT
* * *
106442 AAAATGGAATTTTAGAAAGTCTAGGGGT
1 AAAATGTAATTTTAGAAAATTTAGGGGT
* * *
106470 AAAAATGTATTTTTGGAAAATTTAGGGTT
1 -AAAATGTAATTTTAGAAAATTTAGGGGT
* *
106499 AAAATGAAATTTTAAAAAATTTAGGGGT
1 AAAATGTAATTTTAGAAAATTTAGGGGT
* * *
106527 AAAAGTGTAATTTTTGGAAATTTTGGGGTT
1 AAAA-TGTAATTTTAGAAAATTTAGGGG-T
* * * * *
106557 AAAAAATGGAATTTT-GGAAAGTTCGAGGGC
1 --AAAATGTAATTTTAGAAAATTTAG-GGGT
* *
106587 AAAATGTAATTTTTGGAAAATTTAAGGGT
1 AAAATGTAA-TTTTAGAAAATTTAGGGGT
* * * *
106616 AAAAATTTAATTTTTGGAAGTTTA-GGGT
1 -AAAATGTAATTTTAGAAAATTTAGGGGT
* * * * *
106644 CAAAAATGTAATTTTTGTGAAGTTAAGGGTT
1 --AAAATGTAATTTTAG-AAAATTTAGGGGT
* *
106675 AAAATGTAATTTATGGAAAATTTAAGGGTT
1 AAAATGTAATTT-TAGAAAATTT-AGGGGT
106705 AAAAT
1 AAAAT
106710 ATGATTTTTG
Statistics
Matches: 253, Mismatches: 52, Indels: 38
0.74 0.15 0.11
Matches are distributed among these distances:
27 9 0.04
28 76 0.30
29 104 0.41
30 46 0.18
31 14 0.06
32 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTAGAAAATTTAGGGGT
Found at i:106475 original size:58 final size:58
Alignment explanation
Indices: 106234--106721 Score: 299
Period size: 58 Copynumber: 8.4 Consensus size: 58
106224 AAACATCCGA
* *
106234 GGGT-AAAATGGTATTTTTTGGAAAATTTGAGGGTAAAACGAT--AATTTTTAGAATGTTT-G
1 GGGTAAAAAT-GTAATTTTTGGAAAATTT-AGGGTAAAA--ATGGAA-TTTTAGAAAGTTTAG
* * * * * *
106293 GGGTTAAAAATAG-AATTTTTAG-ACATTCGAGGG-CAAAATGGTAATTTTGGAAA-TTTTG
1 GGG-TAAAAAT-GTAATTTTTGGAAAATT-TAGGGTAAAAATGG-AATTTTAGAAAGTTTAG
* * * * * * *
106351 AGGTAAAAAATGGAATTTTTAG-ATATTTGGGGGT-AAAATGGTAATTTT-GGATGTTT-G
1 GGGT-AAAAATGTAATTTTTGGAAAATTT-AGGGTAAAAATGG-AATTTTAGAAAGTTTAG
* ** *
106408 GGGTAAAAATGTATTTTTTGGAAAATTTAGGGCCAAAATGGAATTTTAGAAAGTCTAG
1 GGGTAAAAATGTAATTTTTGGAAAATTTAGGGTAAAAATGGAATTTTAGAAAGTTTAG
* * * *
106466 GGGTAAAAATGT-ATTTTTGGAAAATTTAGGGTTAAAATGAAATTTTAAAAAATTTAG
1 GGGTAAAAATGTAATTTTTGGAAAATTTAGGGTAAAAATGGAATTTTAGAAAGTTTAG
* * * * *
106523 GGGTAAAAGTGTAATTTTTGGAAATTTTGGGGTTAAAAAATGGAATTTTGGAAAG-TTCG
1 GGGTAAAAATGTAATTTTTGGAAAATTTAGGG-T-AAAAATGGAATTTTAGAAAGTTTAG
* ** * *
106582 AGGG-CAAAATGTAATTTTTGGAAAATTTAAGGGTAAAAATTTAATTTTTGGAAGTTTA-
1 -GGGTAAAAATGTAATTTTTGGAAAATTT-AGGGTAAAAATGGAATTTTAGAAAGTTTAG
* * * * * * *
106640 GGGTCAAAAATGTAATTTTTGTG-AAGTTAAGGGTTAAAATGTAATTTATGGAAAATTTAA
1 GGGT-AAAAATGTAATTTTTG-GAAAATTTAGGGTAAAAATGGAATTT-TAGAAAGTTTAG
* * *
106700 GGGTTAAAATATGATTTTTGGA
1 GGGTAAAAATGTAATTTTTGGA
106722 TTGTTTAGGG
Statistics
Matches: 341, Mismatches: 60, Indels: 56
0.75 0.13 0.12
Matches are distributed among these distances:
56 25 0.07
57 80 0.23
58 115 0.34
59 81 0.24
60 34 0.10
61 6 0.02
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAAATTTAGGGTAAAAATGGAATTTTAGAAAGTTTAG
Found at i:106627 original size:30 final size:30
Alignment explanation
Indices: 106408--106721 Score: 247
Period size: 29 Copynumber: 10.7 Consensus size: 30
106398 TGGATGTTTG
*
106408 GGGTAAAAATGTATTTTTTGGAAAATTT-A
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
** * * * * *
106437 GGGCCAAAATGGAA-TTTTAGAAAGTCTAG
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
106466 GGGTAAAAATGT-ATTTTTGGAAAATTT-A
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
* * ** *
106494 GGGTTAAAATG-AAATTTTAAAAAATTTAG
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
* **
106523 GGGTAAAAGTGTAATTTTTGG-AAATTTTG
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
* * **
106552 GGGTTAAAAAATGGAA-TTTTGGAAAGTTCGA
1 GGG-T-AAAAATGTAATTTTTGGAAAATTTAA
*
106583 GGG-CAAAATGTAATTTTTGGAAAATTTAA
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
* *
106612 GGGTAAAAATTTAATTTTTGG-AAGTTT-A
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
*
106640 GGGTCAAAAATGTAATTTTTGTG--AAGTTAA
1 GGGT-AAAAATGTAATTTTTG-GAAAATTTAA
* *
106670 GGGTTAAAATGTAATTTATGGAAAATTTAA
1 GGGTAAAAATGTAATTTTTGGAAAATTTAA
* * *
106700 GGGTTAAAATATGATTTTTGGA
1 GGGTAAAAATGTAATTTTTGGA
106722 TTGTTTAGGG
Statistics
Matches: 221, Mismatches: 49, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
28 47 0.21
29 100 0.45
30 59 0.27
31 15 0.07
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTTGGAAAATTTAA
Found at i:106660 original size:29 final size:29
Alignment explanation
Indices: 106233--106731 Score: 269
Period size: 30 Copynumber: 17.1 Consensus size: 29
106223 TAAACATCCG
* *
106233 AGGGT-AAAATGGTATTTTTTGGAAAATTT
1 AGGGTAAAAAT-GTAATTTTTGGAAAGTTT
* * *
106262 GAGGGT-AAAACGATAATTTTTAGAATGTTT
1 -AGGGTAAAAATG-TAATTTTTGGAAAGTTT
* * * *
106292 GGGGTTAAAAATAG-AATTTTTAGACA-TTCG
1 AGGG-TAAAAAT-GTAATTTTTGGAAAGTT-T
*
106322 AGGG-CAAAATGGTAA-TTTTGGAAA-TTT
1 AGGGTAAAAAT-GTAATTTTTGGAAAGTTT
* * * *
106349 TGAGGTAAAAAATGGAATTTTTAGATA-TTT
1 AG-GGT-AAAAATGTAATTTTTGGAAAGTTT
* *
106379 GGGGGT-AAAATGGTAA-TTTTGG-ATGTTT
1 -AGGGTAAAAAT-GTAATTTTTGGAAAGTTT
* * *
106407 GGGGTAAAAATGTATTTTTTGGAAAATTT
1 AGGGTAAAAATGTAATTTTTGGAAAGTTT
** * * *
106436 AGGGCCAAAATGGAA-TTTTAGAAAGTCT
1 AGGGTAAAAATGTAATTTTTGGAAAGTTT
*
106464 AGGGGTAAAAATGT-ATTTTTGGAAAATTT
1 A-GGGTAAAAATGTAATTTTTGGAAAGTTT
* * ** *
106493 AGGGTTAAAATG-AAATTTTAAAAAATTT
1 AGGGTAAAAATGTAATTTTTGGAAAGTTT
* *
106521 AGGGGTAAAAGTGTAATTTTTGGAAATTTT
1 A-GGGTAAAAATGTAATTTTTGGAAAGTTT
* * *
106551 GGGGTTAAAAAATGGAA-TTTTGGAAAGTTCG
1 AGGG-T-AAAAATGTAATTTTTGGAAAGTT-T
* *
106582 AGGG-CAAAATGTAATTTTTGGAAAATTT
1 AGGGTAAAAATGTAATTTTTGGAAAGTTT
*
106610 AAGGGTAAAAATTTAATTTTTGG-AAGTTT
1 -AGGGTAAAAATGTAATTTTTGGAAAGTTT
*
106639 AGGGTCAAAAATGTAATTTTTGTG-AAGTTA
1 AGGGT-AAAAATGTAATTTTTG-GAAAGTTT
* * *
106669 AGGGTTAAAATGTAATTTATGGAAAATTT
1 AGGGTAAAAATGTAATTTTTGGAAAGTTT
* * * **
106698 AAGGGTTAAAATATGATTTTTGGATTGTTT
1 -AGGGTAAAAATGTAATTTTTGGAAAGTTT
106728 AGGG
1 AGGG
106732 ACCTTTTGGG
Statistics
Matches: 360, Mismatches: 78, Indels: 63
0.72 0.16 0.13
Matches are distributed among these distances:
27 9 0.03
28 90 0.25
29 117 0.32
30 127 0.35
31 16 0.04
32 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
AGGGTAAAAATGTAATTTTTGGAAAGTTT
Found at i:108094 original size:19 final size:20
Alignment explanation
Indices: 108052--108094 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
108042 AATGAATTTT
***
108052 AATTTATTTTTATTTATTGG
1 AATTTATTTTTATTTATAAA
108072 AATTTA-TTTTATTTATAAA
1 AATTTATTTTTATTTATAAA
108091 AATT
1 AATT
108095 AGGTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
AATTTATTTTTATTTATAAA
Done.